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The DL-POLY Classic User Manual

1. 1 EAM force 0U _ 22 OVig rag Orig 5 Veg ng Tki Orr i l j i Orij Ork j 1 j4k Orn Pkj OU5 OF amp Opis Tij Org 2 144 are gt 2 Ori Ori ara 5 OF Opik rik Orik N F Opx raj Oras Op Orin OTK Op Ore Ork i 1 4k j 1 j k N OF OF OP TK kj rI e T jaigee NPR OP Tkj Tkj In DL_POLY Classic the generation of the force arrays from tabulated data implemented in the METAL_DERIV routine is done using a five point interpolation precedure 2 Finnis Sinclair force 9U y 2 2 Tkj r ms Ark co crreg Cary reg O i 2er e Tk rar Vkj j LjAk JU 2 a 1 1 ras d Tj gt 2 En 2 rp d 438 2 145 Ore Le 2 Vee JP j d kj 3 Sutton Chen force U x a Pg On ne A N m 1 1 Tki ee SS E om 2 146 Ork it 2 VPR VPI Nki Thy 36 STFC Section 2 3 4 Gupta force OU YTA TON Tj 14212 P exp pli Ok 1j2k 0 o kj OU No Bar 1 Tkj 2 267 zel 2dkj kj 2 A 2 147 OE gg O APR VR AN With the metal forces thus defined the contribution to be added to the atomic virial from each atom pair is then which equates to OU Y 3V ae y 233 Mil ru B E AB V i 1 A Ori 7 OV na e ss _ ij i OV V OV ri S ek OVS NTS 2 14 Ra m arg TU 2 149 i 1 j i Opi A Opiglrig Org 1 lt pag rag 2 Pijlrij X z gt pa OV a pati jc Hi Ori O
2. 22 2 2 7 Inversion Angle Potentials 2 02000002 eee nee 23 2 2 8 The Calcite Four Body Potential o 25 22 9 Tethering Forces gt sacca s aoada k a a a a 26 2 2 10 Frozen Atoms oo so ee aip a a a a p 27 23 The Intermolecular Potential Pumctiong so os so sacs 4 ecc Ree koe ees 28 23 1 Short Ranged van der Waals Potentials 6 6 46 cocs ere tuts e 28 22 2 Wires Body Potentials 2 ee eae eRe ee Re Ra we ie ee 30 2 3 3 The Tersoff Covalent Potential occ 6 664 cr Bea we ae 31 2 3 4 Four Body Potentials e 34 2 0 0 Metal Potentials 2 2 4 2 24 084 ks 34 20 0 External Pields 2 6 04 2 S ee a 41 2 4 Long Ranged Electrostatic Coulombic Potentials 42 2 4 1 Atomistic and Charge Group Implementation 43 742 Direct Coulomb SMA Se eda ek Re EB AG o SRR eee EO 43 2 4 3 Truncated and Shifted Coulomb Sum 4 44 2 4 4 Damped Shifted Force Coulomb sum 2 00 4 44 2 4 5 Coulomb Sum with Distance Dependent Dielectric 45 ZAG Ewah SU ogo iaa a ke mR ee Re Ree Se ARES RS 46 2 4 7 Smoothed Particle Mesh Ewald 48 248 Hautman Klein Ewald HKE ee a a courses cara a 50 249 Reaction Field us o ir a a ee a se a 52 2 4 10 Dynamical Shell Model a e eee 53 24 11 Relaxed Shell Model o sisp op 64 eA bone BO a Ea 54 2 0 itesration EOS s ee li k ee Ras a a
3. DL_POLY script to run multiple test cases note use of qsub in job submission may need replacing set n 1 set m 2 set TYPE LF VV CB RB while n lt m if e TEST n mkdir TEST n cd TEST n echo TEST n foreach typ TYPE if e data TEST n typ then if e typ mkdir typ cd typ cp data TEST n typ CONTROL cp data TEST n typ CONFIG cp data TEST n typ FIELD if e data TEST n typ TABLE cp data TEST n typ TABLE if e data TEST n typ TABEAM cp data TEST n typ TABEAM qsub gopoly cd endif end dl set n expr n 1 end This macro creates working TEST directories in the execute sub directory one for each test case invoked Appropriate sub directories of these are created for leapfrog LF velocity Verlet VV rigid body minimisation RB and constraint bond minimisation CB Note that supa must be run from the execute sub directory supa requires two arguments supa n m 199 OSTFC Section 9 1 where n and m are integers defining the first and last test case to be run 200 Bibliography 13 14 15 16 17 18 19 20 Smith W and Forester T 1996 J Molec Graphics 14 136 3 Smith W 1987 Molecular Graphics 5 71 3 Finnis M W and Sinclair J E 1984 Philos Mag A 50 45 4 34 35 118 119 Johnson R A 1989 Phys Rev B 39 12
4. 5 system_a i1 i2 identifies the range of atom indices in the CONFIG file that consitute the chromophore in the first state integer i1 i2 6 system_b i3 i4 identifies the range of atom indices in the CONFIG file that consitute the chromophore in the second state integer 13 14 7 endswi closes specification of solvent relaxation option See section 6 4 5 for comments on the specification of atoms in system_a and system_b which are equally valid here Furthermore when system_a and system_b atoms are exchanged under the switch option the former system_a atoms become virtual and system_b become real until they are swapped over again at intervals defined by the period directive The data in the SOLVAT file may be plotted to give a clear representation of the progress of the simulation and the relaxation of specific components of the solvation energy 173 Chapter 7 Metadynamics 174 STFC Section 7 0 Scope of Chapter This chapter describes the facilties within DL_POLY Classic for studying the thermodynamics of phase transitions using the method of metadynamics 175 STFC Section 7 2 7 1 Overview Metadynamics 67 68 is a method for studying the thermodynamics of activated processes for which purpose it accelerates the time scale for structural changes to occur and at the same time accumulates data describing the free energy surface from which the free energy of the the structural transition may be
5. Figure B 3 The parallelepiped MD cell Truncated octahedral boundaries IMCON 4 Figure B 4 The truncated octahedral MD cell This is one of the more unusual MD cells available in DL POLY but it has the advantage of being more nearly spherical than most other MD cells This means it can accommodate a larger spherical cutoff for a given number of atoms which leads to greater efficiency This can be very useful when simulating for example a large molecule in solution where fewer solvent molecules are required for a given simulation cell width The principal axes of the truncated octahedron see figure pass through the centres of the square faces and the width of the cell measured from square face to square face along a principal axis defines the width D of the cell From this the cell vectors required in the DL_POLY Classic CONFIG file are simply D 0 0 0 D 0 0 0 D These are also the cell vectors defining the enscribing cube which posseses twice the volume of the truncated octahedral cell Once again the atomic positions are defined with respect to the cell centre The truncated octahedron can be used with the Ewald summation method Rhombic dodecahedral boundaries IMCON 5 This is another unusual MD cell see figure but which possesses similar advantages to the truncated octahedron but with a slightly greater efficiency in its use of the cell volume the ratio is about 209 STFC Section B 0 74 to 68
6. Hoover Thermostat In the Nos Hoover algorithm 21 Newton s equations of motion are modified to read dr t STFC Section 2 5 du t F i gt x u 2 253 2 254 The friction coefficient x is controlled by the first order differential equation dx t _ Nik T t Tox 2 255 O SEPT Toa 2 255 where Q N Testi is the effective mass of the thermoststat Tr is a specified time constant normally in the range 0 5 2 ps and Np is the number of degrees of freedom in the system T t is the instantaneous temperature of the system at time t In the LF version of DL POLY Classic x is stored at half timesteps as it has dimensions of 1 time The integration takes place as x t Ai x t At Agre T Toxt x 3 xt 540 x 2 340 u AN alt pan a ar fE lio a Ec o At Laila A0 r t At r t 4At u t aN 2 256 Since v t is required to calculate 7 t and itself the algorithm requires several iterations to obtain self consistency In DL_POLY Classic the number of iterations is set to 3 4 if the system has bond constraints The iteration procedure is started with the standard Verlet leapfrog prediction of v t and T t The conserved quantity is derived from the extended Hamiltonian for the system which to within a constant is the Helmholtz free energy 1 t Huvr U KE 50x t 2f x s ds 2 257 T Jo If bond constraints are present an extra iteratio
7. 10 is the a b c angle Note valence angle potentials with a dash as the first character of the keyword do not contribute to the excluded atoms list see section 2 1 In this case DL_POLY Classic will calculate the nonbonded pair potentials between the described atoms 113 STFC Section 4 1 9 dihedrals n where nis the number of dihedral interactions present in the molecule Each of the following n records contains dihedral key index 1 index 2 index 3 index 4 variable 1 variable 2 variable 3 variable 4 variable 5 ad integer integer integer integer real real real real real potential key See table 4 9 first atomic index second atomic index third atomic index fourth atomic index potential parameter see table 4 9 potential parameter see table 4 9 potential parameter see table 4 9 1 4 electrostatic interaction scale factor 1 4 Van der Waals interaction scale factor The meaning of the variables 1 3 is given in table 4 9 The variables 4 and 5 specify the scaling factor for the 1 4 electrostatic and Van der Waals nonbonded interactions respectively This directive and associated data records need not be specified if the molecule contains no dihedral angle terms See the note on the atomic indices appearing under the shell directive above Table 4 9 Dihedral Angle Potentials key potential type Variables 1 4 functional formt cos Cosine A dm U 6 A 1 cos m 0
8. Action Standard user response Fix the parameter mxshl Message 60 error too many dihedral angles specified DL_POLY Classic will accept only a limited number of dihedral angles in the FIELD file and will terminate if too many are present Do not confuse this error with that described by message 61 below Action Standard user response Fix the parameter mxtdih Message 61 error too many dihedral angles in system The number of dihedral angles in the whole simulated system is limited by DL_POLY Classic Ter mination results if too many are encountered Do not confuse this error with that described by message 60 above Action Standard user response Fix the parameter mxdihd Message 62 error too many tethered atoms specified DL_POLY Classic will accept only a limited number of tethered atoms in the FIELD file and will terminate if too many are present Do not confuse this error with that described by message 63 below Action Standard user response Fix the parameter mxteth 221 STFC Section C 0 Message 63 error too many tethered atoms in system The number of tethered atoms in the simulated system is limited by DL POLY Classic Termina tion results if too many are encountered Do not confuse this error with that described by message 62 above Action Standard user response Fix the parameter msteth Message 65 error too many excluded pairs specified This error can arise when DL POLY
9. Close the metadynamics specification endmet 4 Set other CONTROL file directives as follow a Select the restart noscale option if the CONFIG file was pre equilibrated otherwise leave out the restart keyword altogether b Set the length of the simulation required steps and the equilibration period equil both in time steps The equilibration can be short or absent if the system was pre equilibrated c You must select one of the Nos Hoover NVT NPT or NoT ensembles Metadynamics is only available for one of these options The program automatically defaults to velocity Verlet integration if you use shell model electrostatics d If you wish to follow the structural changes set the trajectory option in the CONTROL file This will produce a HISTORY file you can view or analyse later e Set the remaining CONTROL keywords as for a normal molecular dynamics simulation 5 Prepare if required the file STEINHARDT which defines the control variables for the Stein hardt order parameters The file specification is as follows a The file contains data for both Q4 and Qe order parameters b The records describing the Q4 entries appear first There is one information record followed by ng4 data records ng4 is defined in item 3 i above No Q4 entries appear if nq4 is zero After this the records for the Og parameters appear There is one information record followed by nq6 data records ng6 is defined in
10. Message 1250 error failed allocation of excluded atom arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor 255 STFC Section C 0 Message 1260 error failed allocation of tethering arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1270 error failed allocation of tethering work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1280 error failed allocation of metal arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1290 error failed allocation of work arrays in nvt_h0 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated syst
11. e n2 is the identity of the home basin integer e n3 is the identity of the new basin integer TAD Only 5 5 0 3 The CFGBSNnn Files in the BASINS Directory A CFGBSNn file is a text file containing the energy minimised structure of a basin found during the BPD or TAD simulation The number nn rises from 0 to 9999 Internally the format of the file is the same as a CONFIG file see section 4 1 2 though it does not normally contain velocity or force data 156 STFC Section 5 6 5 5 0 4 The CFGTRKnn Files in the TRACKS Directory The CFGTRKnn files have exactly the same format as the CFGBSNnn files The files do not however contain energy minimised structures These files represent consecutive structures written at user defined intervals during the simulation The interval num_track see above is an integer divisor of the number of steps in a BPD or TAD block num_block and the number nn in the file name is modulo max_track where max_track num_block num_track Thus after num_block time steps from the simulation start there are always max_track configurations to search back over to locate the time of a transition nn is an integer ranging from 0 to max_track 5 5 0 5 The PROnn XY Files in the PROFILES Directory The PROnn XY files tabulate the converged configuration energies of the beads in a NEB calcula tion as a function of the reaction coordinate linking the beads nn is an integer ranging from 0 to 9999 The reaction
12. true valence angle energies are present lcomp 3 true dihedral angle energies are present lcomp 4 true inversion angle energies are present lcomp 5 true atomic polarisation energies are present lcomp 6 true coulombic energies are present lcomp 7 true van der Waals energies are present lcomp 8 true 3 body energies are present lcomp 9 true 4 body energies are present record 6 end of file Format 5e14 6 All subsequent records list the calculated data in in dividual blocks for each requested time step Each block record may consist of any or all of the following data records depending on the system being simulated as indicated by record 5 Note that individual data records may require more than one line of the SOLVAT file since only five real numbers are presented on each line In simulations where solvation induced shifts studies are being performed i e where the control variable lexcite is set true see section 6 4 5 each of the data records is duplicated thus providing data for the ground and excited state systems separately see section 6 4 2 In the following mxtmls represents the number of molecule types in the system block record 0 species temperatures mxtmls entries block record 1 bond energies mxtmls entries block record 2 valence angle energies mxtmls entries block record 3 dihedral angle energies mxtmls entries block record 4 inversion angl
13. 8 1 1 14 Test Case 14 Carbon Diamond with Tersoff potential This is another test of the Tersoff potential this time for the carbon diamond structure consisting of 512 atoms A cubic MD cell is used with a NST Hoover integration algorithm NST Hoover ensemble 8 1 1 15 Test Case 15 Silicon Carbide with Tersoff potential This is an alloy system consisting of 2744 atoms of silicon carbide in a diamond structure The potential function used is the Tersoff potential The integration algorithm is NPT Hoover and the initial MD cell is cubic NPT Hoover ensemble 8 1 1 16 Test Case 16 Magnesium Oxide with relaxed shell model Relaxed shell model of magnesium oxide with 324 sites The lattice is cubic and the integration algorithm is NST Berendsen NST Berendsen ensemble 8 1 1 17 Test Case 17 Sodium ion in SPC water A simple simulation of a sodium ion in 140 SPC water molecules 421 sites in all The water molecules are treated as rigid bodies The algorithm is the NVE ensemble and the Ewald sum handles the electrostatic forces The MD box is cubic NVE ensemble 8 1 1 18 Test Case 18 Sodium chloride molecule in SPC water This system resembles test case 17 except that a sodium chloride ion pair is dissolved in 139 SPC water molecules 419 sites in all The MD cell is cubic and the water molecules are treated by constraint dynamics in the NVT Evans scheme Ewald s method handles the electrostatics NVT Evans ensemble 189 ST
14. Action Switch off one of the conflicting options and rerun Message 427 error bond vector work arrays too small in invfrc The work arrays in subroutine INVFRC have been exceeded Action Standard user response Fix the parameter msbad Message 430 error integration routine not available A request for a nonexistent ensemble has been made or a request with conflicting options that DL_POLY Classic cannot deal with e g a Evans thermostat with rigid body equations of motion Action Examine the CONTROL and FIELD files and remove inappropriate specifications Message 432 error intlist failed to assign constraints If the required simulation has constraint bonds DL_POLY Classic attempts to apportion the molecules to processors so that if possible there are no shared atoms between processors If this is not possi ble one or more molecules may be split between processors This message indicates that the code has failed to carry out either of these successfully Action The error may arise from a compiler error Try recompiling INTLIST without the optimization flag turned on If the problem persists it should be reported to the authors after checking the input data for inconsistencies Message 433 error specify rcut before the Ewald sum precision When specifying the desired precision for the Ewald sum in the CONTROL file it is first necessary to specify the real space cutoff rcut Action Place the cut directive
15. Action The user is probably making excessive demands of memory Reconsider the problem size in relation to compute resource Message 2505 Error allocating driven array Unlikely array allocation error which should not occur under normal use Action The user is probably making excessive demands of memory Reconsider the problem size in relation to compute resource Message 2508 Comms error in metadynamics setup This is probably a programming error and should not occur Action Identify and fix the bug if you can Otherwise locate the authors and ask for a fix Message 2509 Cannot bias local and global PE in same run The metadynamics option does not allow the use of both global and local potential energy order parameters at the same time Action Decide which of these options you really need and reset the directives in the CONTROL file Message 2510 Error allocating local force arrays Unlikely array allocation error which should not occur under normal use Action The user is probably making excessive demands of memory Reconsider the problem size in relation to compute resource Message 2511 Error allocating collective variables arrays Unlikely array allocation error which should not occur under normal use Action The user is probably making excessive demands of memory Reconsider the problem size in relation to compute resource Message 2512 Error allocating Wang Landau bins Unlikely array allocation e
16. If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1050 error failed allocation of dihedral arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor 252 STFC Section C 0 Message 1060 error failed allocation of dihedral work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1070 error failed allocation of constraint arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1090 error failed allocation of site arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1100 error failed allocation
17. N p X pylry 2 138 j 1jZi 34 STFC Section 2 3 It should be noted that the density is determined by the coordination number of the atom defined by pairs of atoms This makes the metal potential dependent on the local density environmental Vij rij is a pair potential incorporating repulsive electrostatic and overlap interactions N is the number of interacting particles in the MD box The types of metal potentials available in DL POLY Classic are as follows 1 EAM potential eam There are no explicit mathematical expressions for EAM potentials so this potential type is read exclusively in the form of interpolation arrays from the TABEAM table file as implemented in the METTAB routine Section 4 1 6 The rules for combining the potentials from different metals to handle alloys are different from the FSM class of potentials see below 2 Finnis Sinclair potential 3 fnsc The Finnis Sinclair potential is explicitly analytical It has the following form Vig rig rig O co criz cari Tij d 3 pig tg ryd gui A 2 139 with parameters co C1 C2 C A d 6 both c and d are cutoffs Since first being proposed a number of alternative analytical forms have been proposed some of which are descibed below The rules for combining different metal potentials to model alloys are different from the EAM potentials see below 3 Sutton Chen potential 38 39 40 stch The Sutton Chen potential
18. The contribution to be added to the atomic stress tensor is given by et 2 184 where a 8 are x y z components The atomic stress tensor is symmetric In DL_POLY Classic these forces are handled by the routine COUL1 2 4 4 Damped Shifted Force Coulomb sum A further refinement of the truncated and shifted Coulomb sum is to truncate the 1 r potential at reut and add a linear term to the potential in order to make both the energy and the force zero at the cutoff the shifted force Coulombic potential This is formally equivalent to surrounding each charge with a spherical charge of radius reut which neutralises the charge content of the cutoff sphere The potential is thus iq 1 ij 2 U r B L 2 185 2 Ameo Tig Tout Teut 44 STFC Section 2 4 with the force on atom j given by qua 1 1 Tij 3 2 2 y 2 186 TEO 175 Tout Tij with the force on atom 7 the negative of this This removes the heating effects that arise from the discontinuity in the forces at the cutoff in the simple truncated and shifted potential More recently Wolf et al 42 took the shifted force Coulomb potential a step further by the introduction of an additional damping function to moderate the 1 r dependence This was reported to be a viable alternative to the Ewald summation that was particularly effective for large systems The basic assumption is that in condensed phase systems the electrostatic forces are effectively
19. This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1920 error failed allocation of zero_kelvin f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1925 error failed allocation of strucopt f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1930 error failed allocation of vertest f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1940 error failed allocation of pair arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a ma
20. fldscan force manager subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine function subroutine subroutine subroutine subroutine function subroutine subroutine function subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine function subroutine function subroutine subroutine shake_module f core_shell_module f dihedral_module f external_field_module f four_body_module f inversion_module f metafreeze_module f metal_module f hyper_dynamics_module f pmf_module f rigid_body_module f tersoff_module f tether_module f three_body_module f define_system_module f vdw_module f metafreeze_module f metafreeze_module f property_module f property_module f dihedral_module f spme_module f utility_module f metal_module f utility_module f define_system_module f define_system_module f ewald_module error_module ewald_module ewald_module ewald_module ewald_module define_system_module f spme_module f define_system_module f exclude_module f exclude_module f exclude_module f exclude_module f basic_comms f serial f Hh Hh Hh Fh Fh Ab external_field_module f four_body_module f metafreeze_module f utility_module f p
21. occurs when the parameter mxexcl is exceeded in the EXCLUDENEU routine Action Standard user response Fix parameter mxexcl Message 300 error incorrect boundary condition in parlink The use of link cells in DL_POLY Classic implies the use of appropriate boundary conditions This error results if the user specifies octahedral dodecahedral or slab boundary conditions Action The simulation must be run with cubic orthorhombic or parallelepiped boundary conditions Message 301 error too many rigid body types The maximum number of rigid body types permitted by DL POLY Classic has been exceeded Action Standard user response Fix the parameter mxungp Message 302 error too many sites in rigid body This error arises when DL_POLY Classic finds that the number of sites in a rigid body exceeds the dimensions of the approriate storage arrays Action Standard user response Fix the parameter mxngp 233 STFC Section C 0 Message 303 error too many rigid bodies specified The maximum number of rigid bodies in a simulation has been reached Do not confuse this with message 304 below Action Standard user response Fix the parameter mxgrp Message 304 error too many rigid body sites in system This error occurs when the total number of sites within all rigid bodies exceeds the permitted maximum Do not confuse this with message 303 above Action Standard user response Fix the parameter mxgatms Mes
22. tional properties or viewed as a movie with appropriate software 5 4 Temperature Accelerated Dynamics 5 4 1 Theory of Temperature Accelerated Dynamics Temperature Accelerated Dynamics TAD was devised by Voter et al 63 Like BPD it is also a combination of molecular dynamics and Transition State Theory TST for first order processes TAD works on the principle that while diffusion in the solid state at a low temperature is often too slow to measure at a higher temperature it may be many orders of magnitude faster However it is normally the case that at different temperatures a system will evolve via different diffusion pathways So to exploit the temperature acceleration successfully special care must be taken to preserve the true mechanistic pathway at the required low temperature This is precisely what TAD does An appropriate model for a first order diffusion process supposes a system trapped in a potential basin state A from which it may escape through thermal excitation to a new state state B If the system is created in state A at time zero the probablity of it being found in the same state at a later time t is P t dt kexp kt dt 5 12 147 STFC Section 5 4 where P t is a probability distribution and k is the first order rate constant It follows from this that the mean lifetime 7 of the system in state A is rTr 1 k 5 13 from which we have a universal property of first order systems Tk 1 5 14
23. 0 T gt T2 The parameters r and ra define a range over which the 4 atoms gradually cease to count towards the overall sum Note that the numbers Ne and Mp in the above formulas are formally expected to be the same in a perfect crystal However while N remains fixed Np may fluctuate according to circumstance In fact the switching function replaces the strict cut off in the original definition by Steinhardt et al in which N would be equivalent to wae Je rp rather than a constant Quigley and Rodger also note that order parameter is not scale invariant between systems of different numbers of atoms 68 however this does not matter for simulation where the numbers are fixed The spherical harmonic parameter is confined to the values 4 and 6 in the DL_POLY Classic implementation giving the order parameters Qs and Qe The forces arising from the Steinhardt parameters are given by OV 1 4r 1 Y Tij zij aq QP 20 1 NNo f y fx Din q UAY an Os Ou m 9 R E US Yen Oy oon 7 10 where R and S indicate the Real and Imaginary parts of complex quantities 178 STFC Section 7 4 The stress tensor contributions arising from these forces are given by Dag gt Cop Fri 7 11 7 3 3 Tetrahedral Order Parameters The form of the tetrahedral order parameter in DL_POLY Classic is that of Chau and Hardwick 73 which quantify the degree to which atoms surrounding a chosen atom are arranged tetrahedral
24. 25 27 30 31 33 34 38 44 46 48 53 54 57 58 63 sub directory 195 199 build 8 data 8 execute 8 java 8 source 8 utility 8 Sutton Chen potential see potential Sutton Chen TABEAM file 125 TABLE file 124 temperature accelerated dynamics TAD see hy perdynamics TAD thermostat 5 42 71 74 98 Berendsen 66 67 71 73 Nos Hoover 63 64 71 73 TRACKS directory 157 units DL_POLY 7 131 energy 108 pressure 7 8 63 99 131 Verlet neighbour list 48 74 76 78 102 WWW 3 6 10 ZDNDAT file 133 293
25. 6443 34 118 Foiles S M Baskes M I and Daw M S 1986 Chem Phys Lett 33 7983 34 118 J F 1952 Philos Mag 43 153 34 Sutton A P and Chen J 1990 Philos Mag Lett 61 139 35 78 119 Rafii Tabar H and Sutton A P 1991 Philos Mag Lett 63 217 35 41 119 Todd B and Lynden Bell R 1993 Surf Science 281 191 35 Cleri F and Rosato F 1993 Phys Rev B 48 22 35 119 Wolf D Keblinski P Phillpot S and Eggebrecht J 1999 J Chem Phys 110 8255 45 Fennell C and Gezelter J 2006 J Chem Phys 124 234104 45 Fuchs K 1935 Proc R Soc A 151 585 47 Smith W and Fincham D 1993 Molecular Simulation 10 67 47 74 75 79 90 Essmann U Perera L Berkowitz M L Darden T Lee H and Pedersen L G 1995 J Chem Phys 103 8577 48 Hautman J and Klein M L 1992 Molec Phys 75 379 50 210 202 STFC Section 9 1 48 49 50 5l 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 Neumann M 1985 J Chem Phys 82 5663 52 Fincham D and Mitchell P J 1993 J Phys Condens Matter 5 1031 53 Lindan P J D and Gillan M J 1993 J Phys Condens Matter 5 1019 54 McCammon J A and Harvey S C 1987 Dynamics of Proteins and Nucleic Acids Cam bridge University Press 59 Brown D and Clarke J H R 1984 Molec Phy
26. Aro 3 m 3 Sp SS 2 156 m 3 Tmet 4 Gupta density correction 2 T ie oe 2rmet 2 exp 205 m0 E 2 157 2 a TO The density correction is applied immediately after the local density is calculated The pair term correction is obtained by analogy with the short ranged potentials and is U SN rij 27 pro Opi dij i 1 A N Tij lt Tmet 1 N Tij ZTmet SI gt gt Valu 52 D Vislris U Uy i 1 Hi i 1 A STFC Section 2 3 dU 27Np V r r dr N U gt DN F p 6pi 2 158 4 1 m r ye OF p Us 4r 55 ee r pij r r dr i 1 A i ENO 9 br Note that 9U2 is not required if p has already been corrected Evaluating the integral part of the above equations yields 1 EAM energy correction No long ranged corrections apply beyond met 2 Finnis Sinclair energy correction No long ranged corrections apply beyond cutoffs c and d 3 Sutton Chen energy correction SU a n 3 T met 513 n 3 U E a 5 2 159 m Tmet 2 pe 4 Gupta energy correction 27 N pAr dU SERENO 9 Pok 27 met 2 F 2 2 x Pp P P Tmet TO exp p TO a 2 Tpr SU lt o d ua 2 x 2 160 qij y sa 9 jee NB P qij a 5 7 V 2 To estimate the virial correction we assume the corrected local densities are constants i e in dependent of distance at least beyond the ranged rmet This allows the virial correction t
27. Euler 69 rigid body 69 error messages 92 209 EVENTS file 155 Ewald Hautman Klein 43 50 91 98 207 optimisation 89 90 SPME 6 43 48 78 89 99 summation 43 46 48 74 75 77 89 91 98 100 101 FIELD file 107 Finnis Sinclair potential see potential Finnis Sinclair force field 4 13 15 22 41 42 AMBER 4 13 DL_POLY 4 13 54 Dreiding 4 13 30 31 GROMOS 4 13 OPLS 13 291 STFC Section D 0 FORGE 9 Ewald summation 78 FORTRAN 90 5 7 intramolecular terms 76 free energy Replicated Data 5 thermodynamic integration 163 166 Verlet neighbour list 77 FREENG file 170 potential bond 4 14 17 21 22 27 31 54 76 79 Graphical User Interface 4 9 105 111 130 GROMOS 4 13 Gupta potential see potential Gupta Hautman Klein Ewald see Ewald Hautman Klein HISTORY file 127 formatted 127 unformatted 128 hyperdynamics BPD 138 140 exploring configuration space 147 full path kinetics 143 NEB 139 158 reaction path 139 157 158 TAD 138 147 long ranged corrections metal 38 van der Waals 30 metadynamics 176 collective variables see hyperdynamics or der parameters Gaussian potential 176 METADYNAMICS file 182 order parameter scaling 179 order parameters 177 179 183 potential energy 177 running simulations 179 STEINHARDT file 181 Steinhardt parameters 178 Tetrahedral parameters 179 theory of 176 ZETA file 181 minimisation 87 conjugate g
28. T as T T d p X Gap 2 311 It may be easily shown from this and eguation 2 291 that oh h 1 dip x Gin 2 312 from which it follows that At di das gab x d p 2 313 where we have defined N m m U I dX disp 2 314 and we have used the identity Gp Jape Bp where gp is a scalar quantity Now the true position at timestep tn 1 of the link atom on rigid body A is 1 1 1 rap Ra dap 2 315 and inserting 2 310 and 2 313 leads to n 1 1 AR Kap Ry dp JAB 5 Ya 2 316 where AB 84 e U x di 2 317 Since TAB i TL we can easily obtain sn 1 At Aiko danp 9487 Qa 9B 2 318 Squaring both sides and neglecting terms of order higher than O At gives after rearrangement n ap CB JAB al At dA p Qa Oz 2 319 From which the constraint force may be calculated Iteration is necessary as in SHAKE 72 STFC Section 2 5 In the second stage of QSHAKE we need to calculate another constaint force H E to preserve the orthogonality of the constraint bond vector and the relative velocity of fhe fa atoms in the bond Once again the contraint force implies corrections to the translational and rotational equations of motion which following the methods used above we write directly as n l At yu yo a Va Ya 75 M48 At wath a 5 ha UA 2 320 where ht is a scalar
29. The list frequently changes as more targets are added and redundant ones removed Users are encouraged to extend the Makefile for themselves using existing targets as examples 2 EX The EX keyword specifies the executable name The default name for the executable is DLPOLY X 3 BINROOT The BINROOT keyword specifies the directory in which the executable is to be stored The default setting is execute 3 2 1 2 Modifying the Makefile 1 Changing the TARGET If you do not intend to run DL_POLY Classic on one of the specified machines you must add appropriate lines to the makefile to suit your circumstances The safest way to do this is to modify an existing TARGET option for your purposes The makefile supplied with DL_POLY Classic contains examples for different serial and parallel MPI environments so you should find one close to your requirements You must of course be familiar with the appropriate invocation of the FORTRAN 90 compiler for your local machine and also any alternatives to MPI your local machine may be running If you wish to compile for MPI systems remember to ensure the appropriate library directories are accessible to you If you require a serial version of the code you must remove references to the MPI libraries from the Makefile and add the file serial f to your compilation this will insert replacement dummy routines for the MPI calls 2 Enabling the Smoothed Particle Mesh Ewald The standard
30. Ti dy E k k pa 02 025 k Fa rij ink rij Pik 7 rij kn Tig dn E UknTik r ik Tar Op E nm x ro 02 dei 2 q o ti Lij Dea Olan rij Tik rij Dies Lik Onn E UknT ik Tik Tij Uy a E j ro den 025 u es ii kn kn Cag TN Ein WES n in in Tj Op P k N ro Sen Ovi j 2 os Lij i Din kn a Lij Lin Lij pn Lin dl WES knTin ri This general formula applies to all atoms i j k n It must be remembered however that these formulae apply to just one of the three contributing terms i e one angle of the full inversion potential specifically the inversion angle pertaining to the out of plane vector r The contributions arising from the other vectors r and fin are obtained by the cyclic permutation of the indices in the manner described above All these force contributions must be added to the final atomic forces Formally the contribution to be added to the atomic virial is given by 4 W ene Li i 1 2 71 However it is possible to show by thermodynamic arguments cf 30 or simply from the fact that the sum of forces on atoms j k and n is equal and opposite to the force on atom i that the inversion potential makes no contribution to the atomic virial If the force components f7 for atoms i j k n are calculated using the above formulae it is easily seen that the contribution to be added to the atomic stress tensor is given by
31. Version Control System CVS lt ac o sa ca 40534404 S544 045 pp 1 3 5 Required Program Libraries a s ss sosa a socs a PAE a 29043000040 1 3 6 Internal Documentation es i a sa misa be ae eR ee k YO 1 3 7 Subroutine Function Calling Sequences o o e 138 FORTRAN Parameters s se s isos k RE a k 13 9 Arithmetic Precision i s s s es cesa RA Re E ee EA LIO WAS p oa peco moia GR eke Dee Rew td eae e ade ds 1 3 11 Error Messages comerse a ew ee ee ee ee a 14 The DL POLY Classic Directory 1 4 1 The source Sub directory 1 42 The utility Sub directory 1 43 The data Sub directory 1 44 The bench Sub directory DUCE 34 oe ea Bb k ee 1 45 The execute Sibsdinestory oop c le a eek a ee Re ee ee eS 1 46 The build Sub directory STFC Contents 1 4 7 The java Sub directory 2 ee 9 1 5 Obtaining the Source Code Ls 9 1 6 Other Information e searg ep wep eb Vd a ee Kk ee EES 10 2 Force Fields and Algorithms 11 21 The DL POLY Classic Force Field oa a k se eee 0002000004 13 2 2 The Intramolecular Potential Functions o oo o e e 15 22 1 B nd Potentials s se seges as bee Ree A pna e Re ee Pe 15 2 22 Distance ESTATE o oa ag a eum pa be AY Ee A RR eee eS 17 2 2 0 Valence Angle Potentials 4 se 0 4644 8a dia ERR Ee eR E 17 224 Angular Restraints sos 46 k k Re eee E 19 220 Dihedral Angle Potentials 2 0 44 aa be bee Aw ee ee 20 2 2 6 Improper Dihedral Angle Potentials
32. and associated data records need not be specified if no PMF constraints are present See the note on the atomic indices appearing under the shell directive above The pmf bondlength applies to the distance between the centres of the two pmf units The centre R of each unit is given by La Wala Xa Wa where r is a site position and wa the site weighting Note that the pmf constraint is in tramolecular To define a constraint between two molecules the molecules must be described as part of the same DL POLY molecule This is illustrated in test case 6 where a pmf constraint is imposed between a potassium ion and the centre of mass of a water molecule DL_POLY Classic allows only one type of pmf constraint per system The value of nummols for this molecule determines the number of pmf constraint in the system Note that the directive ensemble pmf must be specified in the CONTROL file for this option to be implemented correctly R 8 angles n where n is the number of valence angle bonds in the molecule Each of the n records following contains angle key a4 potential key See table 4 8 index 1 integer first atomic index index 2 integer second atomic index central site index 3 integer third atomic index variable 1 real potential parameter see table 4 8 variable 2 real potential parameter see table 4 8 variable 2 real potential parameter see table 4 8 variable 3 real potential parameter see table 4 8 variable 4 real potential parame
33. error constraint bond quench failure When a simulation with bond constraints is started DL_POLY Classic attempts to extract the kinetic energy of the constrained atom atom bonds arising from the assignment of initial random 222 STFC Section C 0 velocities If this procedure fails the program will terminate The likely cause is a badly generated initial configuration Action Some help may be gained from increasing the cycle limit by following the standard user response to increase the control parameter mxshak You may also consider reducing the tolerance of the SHAKE iteration the directive shake in the CONTROL file However it is probably better to take a good look at the starting conditions Message 71 error too many metal potentials specified The number of metal potentials that can be specfied in the FIELD file is limited This error results if too many are used Action Standard user response Fix the parameter mxvdw Note that this parameter must be double the number of required metal potentials Recompile the program Message 72 error different metal potential types specified DL_POLY Classic does not permit the user to mix different types of metal potential in the same simulation There are no known rules for making alloys in this way Action Change the FIELD and TABEAM file as required so that only one type of metal potential is used Message 73 error too many inversion potentials specified The
34. f Select which atom type is to be tracked when determining transitions target atom_name where atom_name is the name of the target atom type The default which is selected when this directive does not appear is that all atom types are chosen g Set the size of the simulation BPD block i e the number of time steps between structure optimisations for transition detection e g num_block 500 144 STFC Section 5 3 h Set the number of configurations between each write of a tracking configuration file This should be an integer divisor of the BPD block number e g num track 10 i Set the catch radius i e the minimum distance in Angstroms any atom may be displaced in the minimised structure before it is recorded as a transition e g catch_radius 3 0 j Set the NEB spring constant in specified energy units per AY e g neb spring 1000 0 for DL POLY units This parameter is not required if the noneb flag has been set k Select a minimisation option e g keyword tol Where keyword is one of force energy position and tolis the convergence tolerance The recommended choice is force with a tolerance of 1 0 in DL POLY units 1 Close the BPD definition with the directive endbpd 3 Set other CONTROL file directives as follow a Select the restart noscale option if the CONFIG file was pre equilibrated otherwise leave out the restart keyword altogether b Set the length of the simulation required st
35. functional formt harm hcos plan Planar calc Calcite Harmonic Harmonic cosine k do U 6 ikl do do U 6 5 cos cos o U 6 A 1 cos 6 B U u Au But t is the inversion angle Note that the calcite potential is not dependent on an angle 6 but on a displacement u See section 2 2 8 for details rigid n where n is the number of rigid units in the molecule It is followed by at least n records each specifying the sites in a rigid unit site 1 site 2 site 3 site m integer integer integer integer integer number of sites in rigid unit first site atomic index second site atomic index third site atomic index etc m th site atomic index Up to 15 sites can be specified on the first record Additional records are used if necessary Up to 16 sites are specified per record thereafter This directive and associated data records need not be specified if the molecule contains no rigid units See the note on the atomic indices appearing under the shell directive above 115 STFC Section 4 1 12 teth n where n is the number of tethered atoms in the molecule It is followed by n records specifying the tethered sites in the molecule tether key ad tethering potential key see table 4 11 index integer atomic index variable 1 real potential parameter see table 4 11 variable 2 real potential parameter see table 4 11 variable 3 real potenti
36. incorrect force field specification too high a temperature inconsistent constraints involving shared atoms etc Action Corrective action depends on the cause It is unlikely that simply increasing the iteration number will cure the problem but you can try follow the standard user response to increase the control parameter mxshak But the trouble is much more likely to be cured by careful consideration of the physical system being simulated For example is the system stressed in some way Too far from equilibrium Message 106 error neighbour list array too small in parlink Construction of the Verlet neighbour list in subroutine parlink nonbonded pair force has ex ceeded the neighbour list array dimensions Action Standard user response Fix the parameter mxlist Message 107 error neighbour list array too small in parlinkneu Construction of the Verlet neighbour list in subroutine parlinkneu nonbonded pair force has exceeded the neighbour list array dimensions Action Standard user response Fix the parameter mxlist Message 108 error neighbour list array too small in parneulst Construction of the Verlet neighbour list in subroutine parneulst nonbonded pair force has ex ceeded the neighbour list array dimensions Action Standard user response Fix the parameter mxlist Message 109 error neighbour list array too small in parlst_nsq Construction of the Verlet neighbour list in subroutine parlst_nsq nonbond
37. it apparent that all significant kinds of transition have been observed When this is is anybody s guess but clearly some knowledge of the system gained from other sources it invaluable here With all the information gathered it should now be possible to determine the full diffusion process for the original system at the state point chosen The recommended procedure for running BPD with DL_POLY Classic is as follows 1 Run a normal unbiased simulation of the system at the required state point temperature and volume Make sure the system does not undergo any structural changes that nullify the validity of the BPD approach e g melting Keep the REVCON file to use as the starting CONFIG structure for the BPD simulation Set up the BPD option in the CONTROL file as follows a Set the bpd path directive b Define the energy units for the BPD calculations e g units s where sis one of eV kcal kJ or K signifying electron volts kilo calories per mole kilo joules per mole or Kelvin respectively No units directive means DL POLY internal units apply Forces are given in the chosen energy units per Angstrom c Set the value of the potential bias Epas e g ebias f where fis the bias energy level in Kelvin d Set the value of the bias potential minimum Vmin e g vmin f where fis the energy minimum in Kelvin e If a BPD simulation without NEB calculations is required set the no NEB flag i e noneb
38. process 51 The PMF constraint force virial and contributions to the stress tensor are obtained in a manner analagous to that for a bond constraint see previous section The only difference is that the constraint is now applied between the centres of two groups which need not be atoms alone DL_POLY Classic reports the PMF constraint virial W for each simulation Users can convert this to the PMF constraint force from Gpmr Wpmr dpmr where dpmr is the constraint distance between the two groups used to define the reaction coordinate DL_POLY Classic can calculate the PMF using either LF or VV algorithms Subroutines PM FLF and PMF_SHAKE are used in the LF scheme and subroutines PMFVV PMF_RATTLE_R and PMF_RATTLE_V are used in the VV scheme 2 5 4 Thermostats The system may be coupled to a heat bath to ensure that the average system temperature is maintained close to the requested temperature Text When this is done the equations of motion are modified and the system no longer samples the microcanonical ensemble Instead trajectories in the canonical NVT ensemble or something close to it are generated DL POLY Classic comes with three different thermostats Nos Hoover 21 Berendsen 20 and Gaussian constraints 19 Of these only the Nos Hoover algorithm generates trajectories in the canonical NVT ensemble The other methods will produce properties that typically differ from canonical averages by O 1 N 12 2 5 4 1 Nos
39. symmetric In DL_POLY Classic bond forces are handled by the routine BNDFRC Note some DL POLY Classic routines may use the convention that rij r rj Nobody s perfect 16 STFC Section 2 2 2 2 2 Distance Restraints In DL_POLY Classic distance restraints in which the separation between two atoms is maintained around some preset value ro is handled as a special case of bond potentials As a consequence dis tance restraints may be applied only between atoms in the same molecule Unlike with application of the pure bond potentials the electrostatic and van der Waals interactions between the pair of atoms are still evaluated when distance restraints are applied All the potential forms of the previous section are as avaliable distance restraints although they have different key words Le 2 8 Harmonic potential hrm Morse potential mrs 12 6 potential bond 126 Restrained harmonic rhm Quartic potential qur Buckingham potential bck FENE potential fen Coulombic bond cou In DL_POLY Classic distance restraints are handled by the routine BNDFRC 2 2 3 Valence Angle Potentials Figure 2 2 The valence angle and associated vectors The valence angle potentials describe the bond bending terms between the specified atoms They should not be confused with the three body potentials described later which are defined by atom types rather than indices 1 Har
40. tential in the code yourself Amendments to subroutines SYSDEF and INVFRC will be required Message 450 error undefined tethering potential A form of tethering potential has been requested which DL POLY Classic does not recognise Action Locate the offending potential in the FIELD file and remove Replace with one acceptable to DL_POLY Classic if this is reasonable Alternatively you may consider defining the required po tential in the code yourself Amendments to subroutines SYSDEF and TETHFRC will be required Message 451 error three body potential cutoff undefined The cutoff radius for a three body potential has not been defined in the FIELD file Action Locate the offending three body force potential in the FIELD file and add the required cutoff Resubmit the job Message 452 error undefined pair potential A form of pair potential has been requested which DL_POLY Classic does not recognise Action Locate the offending potential in the FIELD file and remove Replace with one acceptable to DL_POLY Classic if this is reasonable Alternatively you may consider defining the required po tential in the code yourself Amendments to subroutines SYSDEF and FORGEN will be required Message 453 error four body potential cutoff undefined The cutoff radius for a four body potential has not been defined in the FIELD file Action Locate the offending four body force potential in the FIELD file and add the required cutoff Re sub
41. the radius of cutoff in real space which implies the Hautman Klein Ewald method will not be suf ficiently accurate Action The user should respecify the HK control parameters given in the CONTROL file Either the convergence parameter should be increased or the sum expanded to incorporate more images of the central cell Warning increasing the convergence parameter may cause failure in the reciprocal space domain See 4 1 1 Message 487 error HK recip space screening function cutoff violation DL_POLY Classic has detected an unacceptable degree of inaccuracy in the screening function near the radius of cutoff in reciprocal space which implies the Hautman Klein Ewald method will not be sufficiently accurate Action The user should respecify the HK control parameters given in the CONTROL file Either the con vergence parameter should be reduced or more k vectors used Warning reducing the convergence parameter may cause failure in the real space domain See 4 1 1 Message 488 error HK lattice control parameter set too large The Hautman Klein Ewald method in DL_POLY Classic permits the user to perform a real space sum over nearest neighbour and next nearest neighbour cells i e up to nlatt 2 If the user specifies a larger sum than this this error will result Action The user should respecify the HK control parameters given in the CONTROL file and set nlatt to a maximum of 2 See 4 1 1 Message 490 error P
42. wik fc rix Bra Oust 2 126 ares r Fij Aar i Oey 00 folri Fo rie 0 2 127 J r a Wie 9Vije Ore CV i Cie r aJ ijl The derivative of g 0 is worked out in the following manner 0 LE 8 E 2 128 rg OO ijk sin Dijk Or Tij Tik where a 2 h es a e Og ijk _ 2 G hs cos ijk sin Oj 2 129 olijk d hy COS bijk O Tij Tik ro Ta de 00 00 t Or Fi ij rs e ea Sex des a cos 9jik fiy AM 72 Sex bei 7 2 130 Tij ri The contribution to be added to the atomic virial can be derived as OEtersott 3 V Oui 2 131 W V B 3 2 av 2 131 we ST ee 15 folran falra ru 24 E Ori j j j Ori j j j 1 Ni Ni a Ni ni l 75 folrij falris Xij 1 Bi La Bi Lij X 2 132 XO wik 9 Pijk T Ia ra Tik l k i j The contribution to be added to the atomic stress tensor is given by o reff 2 133 where a and 6 indicate the x y z components The stress tensor is symmetric Interpolation arrays vmbp and gmbp set up in subroutine TERGEN similar to those in van der Waals interactions 2 3 1 are used in the calculation of the Tersoff forces virial and stress The Tersoff potentials are very short ranged typically of order 3 A This property plus the fact that Tersoff potentials two and three body contributions scale as N3 where N is the number of particles makes it essential that these terms
43. 0 d0 A zero or negative value for the barostat time constant has been encountered in the CONTROL file Action Locate the ensemble directive in the CONTROL file and assign a positive value to the time constant Message 468 error r0 too large for snm potential with current cutoff The specified location r0 of the potential minimum for a shifted n m potential exceeds the speci fied potential cutoff A potential with the desired minimum cannot be created Action To obtain a potential with the desired minimum it is necessary to increase the van der Waals cutoff Locate the rvdw directive in the CONTROL file and reset to a magnitude greater than r0 Alternatively adjust the value of r0 in the FIELD file Check that the FIELD file is correctly formatted Message 470 error n lt m in definition of n m potential The specification of a n m potential in the FIELD file implies that the exponent m is larger than exponent n Not all versions of DL POLY Classic are affected by this 246 STFC Section C 0 Action Locate the n m potential in the FIELD file and reverse the order of the exponents Resubmit the job Message 474 error mxxdf too small in parlst subroutine The parameter mxxdf defining working arrays in subroutine PARLST of DL_POLY Classic has been found to be too small Action Standard user response Fix the parameter mxxdf Message 475 error mxxdf too small in parlst_nsq subroutine The parameter mxxdf d
44. 0080 0 0580 1 C 12 0100 0 4770 1 BONDS 78 harm 31 19 674 000 1 44900 harm 33 31 620 000 1 52600 harm 168 19 980 000 1 33500 harm 168 162 634 000 1 52200 CONSTRAINTS 90 20 19 1 000017 22 21 1 000032 166 164 1 000087 167 164 0 999968 ANGLES 312 harm 43 2 44 200 00 116 40 harm 69 5 70 200 00 116 40 harm 18 168 162 160 00 120 40 harm 19 168 162 140 00 116 60 DIHEDRALS 371 harm 1 43 2 44 2 3000 180 00 harm 31 43 2 44 2 3000 180 00 cos 149 17 161 16 10 500 180 00 cos 162 19 168 18 10 500 180 00 FINISH SPC Water NUMMOLS 146 107 STFC Section 4 1 ATOMS 3 OW HW HW CONSTRAINTS 1 2 1 3 2 3 FINISH VDW 45 C C C CT OW OS OS OS CLOSE 4 1 3 1 Format 0000 0080 0080 0000 0000 63299 0 8200 0 4100 0 4100 0 12000 3 2963 0 08485 3 2518 0 15100 3 0451 0 15000 2 9400 The FIELD file is free formatted though it should be noted that atom names are limited to 8 characters and potential function keys are a maximum of 4 characters The contents of the file are variable and are defined by the use of directives Additional information is associated with the directives The file is not case sensitive 4 1 3 2 Definitions of Variables The file divides into three sections general information molecular descriptions and non bonded interaction descriptions appearing in that order in the file 4 1 3 2 1 General information The first record in the FIELD file is the title It must be followed by
45. 1 0 rij gt 26 04 A The WCA potential is the Lennard Jones potential truncated at the position of the minimum and shifted to eliminate discontinuity includes the effect of excluded volume It is usually used in combination with the FENE 2 9 bond potential This implementation allows for a radius shift of up to half a A lt 0 5 o with a default of zero Ade faz 0 10 Gaussian potential gaus 3 U ri Y Anezp byr 2 100 n Up to 3 Gaussian terms are permitted unrequired terms have A 0 11 Tabulation tab The potential is defined numerically only The parameters defining these potentials are supplied to DL POLY Classic at run time see the description of the FIELD file in section 4 1 3 Each atom type in the system is specified by a unique eight character label defined by the user The pair potential is then defined internally by the combination of two atom labels As well as the numerical parameters defining the potentials DL POLY Classic must also be provided with a cutoff radius reut which sets a ranged limit on the computation of the interaction Together with the parameters the cutoff is used by the subroutine FORGEN or FORGEN_RSQ to construct an interpolation array vvv for the potential function over the ranged 0 to reut A second array ggg is also calculated which is related to the potential via the formula o G rij Tig U Ci 2 101 ij and is used in the calculation of the forces Both
46. 2009 Molecular Simulation 35 613 176 177 178 179 180 182 183 Laio A Rordiguez Fortea A Gervasio F L Ceccarelli M and Parrinello M 2005 J Phys Chem B 109 6714 177 180 Peters B and Trout B L 2006 J Chem Phys 125 054108 177 Donadio D Raiteri P and Parrinello M 2005 J Phys Chem B 109 5421 177 Steinhardt P J Nelson D R and Ronchetti M 1983 Phys Rev B 28 784 177 178 177 179 184 203 Appendix A The DL POLY Classic Makefile Master makefile for DL_POLY Classic Author W Smith January Dec 2010 gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt tt Define default settings gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt BINROOT execute CC gcc EX DLPOLY X EXE BINROOT EX FC undef ined SHELL bin sh TYPE par Define object files OBJ_MOD parse_module o setup_module o error_module o site_module o config_module o pair_module o utility_module o metafreeze_module o solvation_module o tether_module o vdw
47. 212 8T 0 7 In this formula A is the system area in the XY plane L is a 2D lattice vector representing the 2D periodicity of the system s is the in plane XY component of the interparticle distance rj and g is a reciprocal lattice vector Thus L la bob 2 213 where 4 l2 are integers and vectors a and b are the lattice basis vectors The reciprocal lattice vectors are g MU Nv 2 214 where n1 no are integers u v are reciprocal space vectors defined in terms of the vectors a and b 2r by lt br aby aybx u 2n ay az aeby aybz 2 215 le The functions h s a and f s a are the HKE convergence functions in real and reciprocal space respectively C f the complementary error and gaussian functions of the original Ewald method However they occur to higher orders here as indicated by the sum over subscript n which corresponds to terms in a Taylor expansion of 771 in s the in plane distance 47 Usually this sum is truncated at mar 1 but in DL POLY Classic can go as high as mar 3 In the HKE method the convergence functions are defined as follows hnls a s A 12 ho s a s 2 216 with ho s a er f as 2 217 and n g a anyi a 2 218 with folg a er fe g 2a 2 219 The reader is warned that for the purpose of compatibility with other DL POLY Classic Ewald routines we have defined a 0 5 az x where agx is the a parameter defined by
48. 4 2 Internal Ensemble Key keyens meaning Microcanonical ensemble NVE Evans NVT ensemble Berendsen NVT ensemble Nos Hoover NVT ensemble Berendsen NPT ensemble Nos Hoover NPT ensemble Berendsen NoT ensemble Nos Hoover NoT ensemble Potential of mean force NVE ensemble CONDOBWNHFH Table 4 3 Internal Trajectory File Key keytrj meaning 0 coordinates only in file 1 coordinates and velocities in file 2 coordinates velocities and forces in file Table 4 4 Non bonded force key keyfce meaning odd evaluate short range potentials and electrostatics even evaluate Electrostatic potential only Electrostatics are evaluated as follows Of 11 Ignore Electrostatic interactions 2 3 Ewald summation 4 5 distance dependent dielectric 6 7 standard truncated Coulombic potential 8 9 truncated and shifted Coulombic potential 10 11 Reaction Field electrostatics 12 13 SPME electrostatics 14 15 Hautman Klein Ewald electrostatics keyfce 0 means no non bonded terms are evaluated t keyfce 1 means only short range potentials are evaluated 103 STFC Section 4 1 4 1 2 The CONFIG File The CONFIG file contains the dimensions of the unit cell the key for periodic boundary conditions and the atomic labels coordinates velocities and forces This file is read by the subroutine SYSGEN It is also read by the subroutine S
49. 54 2 5 1 The Verlet Algorithms a s cha a e a Oe RR A 54 25 2 Bond Constraints s s cs da ne a ee A A a 57 2 5 3 Potential of Mean Force PMF Constraints and the Evaluation of Free Energy 59 254 Thermostats 144464 45 a ede k Lb ES as 59 2 5 5 Gaussian Constraints so 22 620 ener a Re i a Re eG ee 62 200 UBAEGSLALS a gos and aa Beg aaae Blass e BOR pae A a a wes 63 2 5 7 Rigid Bodies and Rotational Integration Algorithms 67 2 5 8 The DL POLY Classic Multiple Timestep Algorithm 74 26 DL POLY Parallelisation cores cora eR Re ER RE E OE 74 2 6 1 The Replicated Data Strategy lt e 75 2 6 2 Distributing the Intramolecular Bonded Terms 76 2 6 3 Distributing the Nonbonded Terms 00 000 enue 76 vi STFC Contents 2 6 4 Modifications for the Ewald Sum 2 2 ee ee 77 2 6 5 Modifications for SPME i e sam ss lt lt a p h an a 78 2 6 6 Three and Four Body Forc s o os ssa dir BRR Eee RE EO 78 20 7 Metal Potentials oc sog wo k ecoa aos pr RR ae ik RR a E 78 2 6 8 Summing the Atomic Forces e 78 2 6 9 The SHAKE RATTLE and Parallel QSHAKE Algorithms 79 3 Construction and Execution 81 3 1 Constructing DLPOLY Classie es a racs ala A Re ae me wae 83 Oil QIVORVIOW canaria PE eA ee ED a 83 3 2 Compiling and Running DL_POLY Classic pe s speed o Wirpa 000000 83 ool Compiling the Sotites Code s s e si ceed bee ee GH eRe oS a
50. 83 32 2 R umms DL POLY Classic a s coce ca sione aoe ERAS k oe 86 3 2 3 Restarting DL POLY Classi coso 268s ae Sao b ss 87 3 2 4 Optimising the Starting Structure 0 00 88 3 2 5 Choosing Ewald Sum Variables 2 ee 89 3 3 DL_POLY Classic Error Processing 2 e 92 3 3 1 The DL_POLY Classic Internal Error Facility 92 4 Data Files 93 41 The INPUT files o ssh 22 8s 244 SRS ea a ERE SES ERS SS HS 95 11 1 The CONTROL Fil 441 2 2236 44 24 4064 088455 223 a 95 4 1 2 The CONFIG File 2 0 0 104 41 3 The FIELD File gt o s scap poua kM ea ee na a we RM E a 107 lad Te REVOLD Pile 2 oon Bs Go e ee DA etig k Gee e i 122 Alo The TABLE Fil s mosk ate ges SA ee oe O oe a eS 124 4 126 The TABEAM Fil 2 os ga ied a 2 BR Bie ae Sk eee E x 125 42 The QUTPUT Piles Gus a Se a a eo we a 127 421 The HISTORY File ose a poa aoga da Be Be A k ee Se 127 ly The OUTPUT Fale oca Stee eal aw Bee ea we a A ae 129 423 The REVOON Files osora boa a ss aca Be k ew 132 4 2 4 The CFGMIN File Ls 132 425 Whe REVIVE Pile ose ee bw Re be we EATR a a 133 426 Whe RDFEDAT Pile oscars Pewee Ade k ER Ew we Be 133 Lar Whe 2DNDAT Eil s a iise p amp ee eed pe k Se eee ee 133 a2 The STATIS Ple xo cae Awe ic ee oe Ge Ss BAR oe SS 134 5 Hyperdynamics 136 5 1 Overview of Hyperdynamics lt ee 138 5 2 The Nudged Elastic Band Calculation 2 0 2 002 ee eee eee 139 5 5 Bias Potential DI
51. At 100 The operators themselves are of the following kind eK q cos Cx t q sin C dt Prq Kp cos Cx t p sin Cr t Pep 2 305 where Py is a permutation operator with k 0 3 with the following properties Poq 40 91 92 93 Pia 490 93 42 Poq 42 93 90 0 P3q 93 92 90 2 306 70 STFC Section 2 5 and the angular velocity Ck is defined as as ae Pt 2 307 Equations 2 304 to 2 306 represent the heart of the NOSQUISH algorithm and are repeatedly applied 10 times in DL POLY Classic The final result is the quaternion updated to the full timestep value i e g t At These equations form part of the first stage of the VV algorithm In the second stage of the VV algorithm new torques are used to update the quaternion momenta to a full timestep At At p t At p t Er y Ltt At 2 308 The NVE implementation of this algorithm is in the subroutine NVEQVV_1 which calls the NOSQUISH subroutine to perform the rotation operation The subroutine also calls RATTLE_R and RATTLE_V to handle any rigid bonds which may be present Thermostats and Barostats It is straightforward to couple the rigid body equations of motion to a thermostat and or barostat The thermostat is coupled to both the translational and rotational degrees of freedom and so both the translational and rotational velocities are propagated in an analogous manner to the thermostated atomic velocities The barosta
52. By this procedure after sufficient sampling of states the true low temperature evolution of the system may be determined The stopping time mentioned above is the time at which the high temperature simulation is halted Ideally this is defined with a high probability that no more significant transitions will be found This is determined from the history of the TAD simulation itself Voter et al provided a prescription of this 63 It begins by defining for a supposed undiscovered escape route a very small probability 0 that after the time tstop the system is still in state A This probability must chosen small enough to give confidence that the awaited transition has had sufficient time to occur 6 may be determined from k exp kt dt 5 18 tstop from which it follows that 1 log 5 tstopk 5 19 and hence combining this with 5 15 1 x log 5 tstopVmin exp Emmin KB Thign 5 20 where Vmin and E are the prefactor and activation energy respectively of the supposed undis covered escape route Rearranging this gives log 1 6 mi T mi 42 En kp 5 a The supposed undiscovered escape route is one which may possesses a low temperature occur rence time that is less than the current working minimum The right side of 5 21 may be approximately determined using equation 5 17 if it assumed that the largest observed value of thigh is close to tstop and the lowest possible low temperature time i
53. Classic implements a parallel version of this algorithm 11 see section 2 6 9 The subroutine NVE_1 implements the Verlet leapfrog algorithm with bond constraints for the NVE ensemble The routine RDSHAKE_1 is called to apply the SHAKE corrections to position It should be noted that the fully converged constraint forces G make a contribution to the system virial and the stress tensor 57 STFC Section 2 5 Figure 2 7 The SHAKE algorithm The algorithm calculates the constraint force Gi G that conserves the bondlength d12 between atoms 1 and 2 following the initial movement to positions 1 and 2 under the unconstrained forces F and F3 The contribution to be added to the atomic virial for each constrained bond is The contribution to be added to the atomic stress tensor is given by B ae dae 2 250 where a and 6 indicate the x y z components The atomic stress tensor derived from the pair forces is symmetric 2 5 2 2 RATTLE RATTLE 14 is the VV version of SHAKE It has two parts the first constrains the bondlength and the second adds an additional constaint to the velocities of the atoms in the constrained bond The first of these constraints leads to an expression for the constriant force similar to that for SHAKE Gx pij diy d T a 2 251 Note that this formula differs from eguation 2 248 by a factor of 2 This constraint force is applied during the first stage of the velocity Verlet algorit
54. DL_POLY Classic the HKE method is handled by several subroutines HKGEN constructs the h s a convergence functions and their derivatives HKEWALD1 calculates the reciprocal space terms HKEWALD2 and HKEWALD3 calculate the real space terms and the bonded atom corrections respectively HKEWALD4 calculates the primary interactions in the multiple timestep implementa tion 2 4 9 Reaction Field In the reaction field method it is assumed that any given molecule is surrounded by a spherical cavity of finite radius within which the electrostatic interactions are calculated explicitly Outside the cavity the system is treated as a dielectric continuum The occurence of any net dipole within the cavity induces a polarisation in the dielectric which in turn interacts with the given molecule The model allows the replacement of the infinite Coulomb sum by a finite sum plus the reaction field The reaction field model coded into DL_POLY Classic is the implementation of Neumann based on charge charge interactions 48 In this model the total Coulombic potential is given by 1 Born 2 228 Don i 2 228 j lt n where the second term on the right is the reaction field correction to the explicit sum with Re the radius of the cavity The constant Bo is defined as 2 1 T ak 2 229 261 1 with e the dielectric constant outside the cavity The effective pair potential is therefore 1 1 Bor U rng QiQn A
55. DMSO to continue The electrostatic interactions are handled by the reaction field method 8 1 1 37 Test Case 37 Calculation of Solvent Relaxation following Spectral Excita tion This is a Hoover NVT simulation of 512 DMSO molecules in which after a fixed interval 10 DMSO molecules are replaced by DMSO and the subsequent simulation records the energetic response of the solvent to the excitation After another interval the reverse switch is enacted and the DMSO molecules are replaced by DMSO to determine the relaxation after quenching The electrostatic interactions are handled by the reaction field method 8 1 1 38 Test Case 38 Freezing of TIP4P Water This is a metadynamics simulation of the freezing of water at 180K and 1 atmosphere pressure using a 4 centre TIP4P rigid model of the water molecule The system consists of 512 water molecules and the ensemble is Hoover NPT Two order parameters are used to define the structures global potential energy and the Steinhardt Qg parameter Control of the Gaussian convergence is by well tempered dynamics 8 1 1 39 Test Case 39 Calcite Nanoparticle Metadynamics In this case 75 molecules of calcium carbonate in the calcite structure form a nanoparticle which is suspended in 863 water molecules represented by a flexible 3 centre TIP3P model The temperature is 310K and pressure 1 atmosphere maintained in a Hoover NPT ensemble The metadynamics is controlled by 6 order parameters the global pote
56. E 187 ALL West Cages ek ke AR A ER LEE ek Oe OR ee ee PS 187 21 2 Benchmark Cases lt s vos s ecoa gus poe aa te E Ae ee BE e 192 9 Utilities 194 9 1 Mise llaneous Utilities lt p lt io s acs ara soca aa ma eaa a A k a a 195 DLI Tsc MAGOS e poa o e Aa es RE a a LE angie ceeds he RA ee AN 195 Bibliography 201 Appendices 204 viii STFC Contents A The DL_POLY Classic Makefile 204 B Periodic Boundary Conditions in DL_POLY Classic 207 C Error Messages and User Action 212 D Subroutine Locations 282 Index 291 List of Tables 4 1 4 2 4 3 4 4 4 5 4 6 4 7 4 8 4 9 4 10 4 11 4 12 4 13 4 14 4 15 4 16 4 17 Internal Restart Key suda bee da od a a 103 Internal Ensemble Key 2 2 4444 sp Ga eo k ek ee ae we ek ao 103 Internal Trajectory Pile Key oos roa day mis k ae Re ee ee Be ee Ae 103 Non Donded force Rey ep ci moe k te oe eo bee ow ce age eB te we Ge 103 CONFIG file key record 2 cs ed he ed apa eRe AA 106 Periodic boundary key record 2 Lu k SER ERE Eee A ee 106 Chemical bond potentials ss s c sos a 2554 sa oaa k 111 Valence Angle potentials lt as 113 Dihedral Angle Potentials ia 4 soo ia sacs aa bana den ea de ew BR a Ee 114 Diversi n Angle Potentials cos pr orar AR GO a eg A eG 115 Teth ering Potentials coo sa donas a maca p Gb be oe Be Se a ay el d 116 Definition of pair potential functions and variables 2 08 118 Three body potentials xo c ssx m i d eda ee Pe EO RRR ee RE E 119
57. Fourbody Potentials s e caog Ge ke eae he k a Ee 119 Metal Potential ori 84445 ks bo ee eet Peed teed eee ded 120 Tersoff Potential lt sura maie 89 54 a ee Bees BG Ee ae 121 External fields coord a a A a 122 List of Figures A 2 2 2 3 2 4 2 5 2 6 Ll 2 8 2 9 4 1 5 1 5 2 5 3 5 4 BI B 2 Bo B 4 B 5 B 6 The interatomic bond vector 15 The valence angle and associated vectors 2 0 as 17 The dihedral angle and associated vectors oos so ccs aor soemo a nopo e ae 20 The L and D enantiomers and defining vectors a 23 The inversion angle and associated vectors o o sooo o e a a e 23 The vectors of the calcite potential a 26 The SHAKE algorithm 224502 at ara e a a aoi a a ee a 58 The multiple timestep algorithm e 75 The parallel implementation of the Brode Ahlrichs algorithm 77 DL_POLY Classic input and output files lt a 95 Model Potential Energy Surface e 138 Basic NEB Theory gt 206442 ao a EM eee a hoe eR re ey oo RD ew 139 Basie BPD THEORY i tan a bg sl a Se ks as A a a a 141 Basio TAD THEOD 5 ka a a ee as a ee a ee ee ae 149 The cubre MD eel osos a a ee ks Be 208 The orthorhomie MD cell 42 oscura ee a a ae 208 The parallelepiped MD cell i lt s s3 ia cama kacr ap e aa e a a aaa a 209 The truncated octahedral MD cell wk k a a a a cra 209 The rhombic dodecahedral MD cell o a 210 The hexagonal M
58. Functions The following table lists the subroutines and functions in DL_POLY Classic and which source files they can be found in Routine abort_config_read abort_control_read abort_eamtable_read abort_field_read abort_table_read abortscan alloc_ang_arrays alloc_bnd_arrays alloc_config_arrays alloc_csh_arrays alloc_dih_arrays alloc_ewald_arrays alloc_exc_arrays alloc_exi_arrays alloc_fbp_arrays alloc_fld_arrays alloc_free_arrays alloc_hke_arrays alloc_hyper_arrays alloc_inv_arrays alloc_met_arrays alloc_pair_arrays alloc_pmf_arrays alloc_prp_arrays alloc_rgbdy_arrays alloc_shake_arrays alloc_site_arrays alloc_sol_arrays alloc_spme_arrays alloc_tbp_arrays Kind subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine Location define_system_module f define_system_module f metal_module f define_system_module f vdw_module f setup_module f angles_module f bonds module f config module f core shell module f dihedral module f ewald module f exclude module f solvation module f four body module f external field module f solvation module f hkewald module f hyper dynamics module f inversion module f metal module f p
59. Hautman and Klein in 47 50 STFC Section 2 4 In DL_POLY Classic the hy s a s functions are derived by a recursion algorithm while the Fn g a functions are obtained by direct evaluation The coefficients a are given by an 1 25 aly 2 220 As pointed out by Hautman and Klein the eguation 2 212 allows separation of the zi components via the binomial expansion which greatly simplifies the double sum over atoms in e uprocal space Thus the reciprocal space part of equation 2 212 becomes Nmax Unean Goa Do E falo a g PG LCR OZ pla 2221 n 0 940 with ce a binomial coefficient and N Zo 9 5 qjzexp ig sj 2 222 j 1 The force on an ion is obtained by the usual differentiation however in this case the z components have different expressions from the x and y U K grt 2 OZ3n p 9 OZp g n al A j Z n Nmazx h AA Li a HEE ID oie piati 2 223 n 0 L ij ij L where uj is one of j Yj zj and noting for brevity that x and y derivatives are similar 0Zp g 25 AU 9Zp 9 e a paja explig sy 2 224 Zj i and Of am An s YA a aie O hnlsij L a Oz V sri De sin Ox sp 0 2 h n Sij L a 2 ihn Sij L a E a 1 Majo IS 2 225 J Sij L Sij L In DL POLY Classic the partial derivatives of hn s L a s Si 1 are calculated by a recursion algorithm Note that when n 0 there is no derivative w r t z The virial and stre
60. In other words the rate constant is inversely proportional to the lifetime in the initial state According to TST the rate constant exhibits a temperature dependence given by the Arrhenius law k v eE 5 15 where v is the so called the pre exponential factor with the units of frequency and 8 is the Boltzmann factor 1 kgT E is the activation energy of the process which is the energy barrier between the bottom of the potential basin of state A and the saddle point on the energy surface that provides the escape route to state B This equation shows that at different temperatures T and 75 the same escape route from state A has different rate constants k and ka respectively Nevertheless the universal property of equation 5 14 means that Ti ki 79 ko 5 16 which is an important relation underpinning the TAD method showing how the time scale for a barrier crossing event at one temperature is related to the time scale for the same event at another temperature In most practical systems state A is likely to have more than one escape route to distinct states B C D etc each with its own activation energy pre exponential factor and temperature dependent rate constant At any given temperature escape from state A may occur via any one of these routes but is most probable via the route which has the highest rate constant and therefore by equation 5 16 the lowest associated residence time A normal molecular dynamics simulation c
61. LAA te where Wed Weq and Weg Weq Wea The virial contribution qabca u is given by Wabea u 24u 4Bu 2 79 and the stress tensor contribution oF u by uy u bed tt E 4 2 80 Wed In DL_POLY Classic the calcite forces are handled by the routine INVFRC which is a convenient intramolecular four body force routine However it is manifestly not an inversion potential as such 2 2 9 Tethering Forces DL POLY Classic also allows atomic sites to be tethered to a fixed point in space r taken as their position at the beginning of the simulation This is also known as position restraining The 26 STFC Section 2 3 specification which comes as part of the molecular description requires a tether potential type and the associated interaction parameters Note firstly that application of tethering potentials means that momentum will no longer be a conserved quantity of the simulation Secondly in constant pressure simulations where the MD cell changes size or shape the reference position is scaled with the cell vectors The potential functions available in DL_POLY Classic are as follows in each case rjg is the distance of the atom from its position at t 0 1 harmonic potential harm 1 U rio 5h rio 2 81 2 restrained harmonic rhrm 1 2 Ulrio ktrio Tio lt fc 2 82 1 Ulrio He kre rio re Tio gt Te 2 83 3 Quartic potential quar k k k U rio zio
62. PC version is required Run the Makefile you copied from the build sub directory in the source sub directory It will create the executable in the execute sub directory The compilation of the program is initiated by typing the command make target where target is the specification of the required machine e g hpcx For many computer systems this is all that is required to compile a working version of DL_POLY Classic To determine which targets are already defined in the makefile typing the command make without a nominated target will produce a list of known targets The full specification of the make command is as follows make lt TARGET gt lt EX gt lt BINROOT gt where some or all of the keywords may be omitted The keywords and their uses are described below Note that keywords may also be set in the unix environment e g with the setenv command in a C shell For PCs running Windows the makefile assumes the user has installed the Cygwin Unix API available from http sources redhat com cygwin The recommended FORTRAN 90 compiler is GFORTRAN but G95 can also be used see http ftp 995 org 3 2 1 1 Keywords for the Makefile 1 TARGET The TARGET keyword indicates which kind of computer the code is to be compiled for 84 STFC Section 3 2 This must be specifed there is no default value Valid targets can be listed by the make file if the command make is typed without arguments
63. Pile e ccros 2 442846 ka Pee ee Ge Ee ae 164 6 3 Free Energy by Thermodynamic Integration o a e 166 6 3 1 Thermodynamic Integration e 166 6 3 2 Nonlinear NOSE on als a A Re ee we dO a 167 6 3 3 Invoking the DL_POLY Free Energy Option 169 Ged Whe PREBING Pile gig kk eee ei ee k ue BR ee Be 170 6 4 Dolton Spectroscopy s coe ein e ee ee Oe ek ee Re ee e 171 6 4 1 Spectroscopy and Classical Simulations 00002 ee 171 6 4 2 Calculating Solvent Induced Spectral Shifts 171 64 3 Solvent Relaxation 2 46 r Se ke bk a ee 172 6 4 4 Invoking the Solvent Induced Spectral Shift Option ooo aaa 172 6 4 5 Invoking the Solvent Relaxation Option 173 7 Metadynamics 174 Tal o k o OG se te De ee a eh te ee Pe eee 176 7 2 Theory of Metadynamits 4 st 28 k a ee e 176 Tia Order Parameters ooh e ee ee ee ee A ee ae 177 7 3 1 Potential Energy as an Order Parameter 0 00002 e 177 7 3 2 Steinhardt Order Parameters oaa 2 2 0 eee es 178 133 Tetrahedral Order Parameters lt sse spia rss a Re ee eS 179 ied Order Parameter Saling s se ce ek Pee eR RRA Be 179 7 4 Running Metadynamics Simulations s sp sea erresa epi ee 179 741 Additional Considerations oa ss si etneo ega By bee eee eRe 182 7 4 2 Analysing the Metadynamics Results 0 0 00000 ee eee 183 8 Example Simulations 185 Sl DLPOLY Examples s ros s 424 6064 e Se a
64. STFC Section C 0 Message 23 error incompatible FIELD and TABLE file potentials This error arises when the specification of the short range potentials is different in the FIELD and TABLE files This usually means that the order of specification of the potentials is different When DL_POLY Classic finds a change in the order of specification it assumes that the user has forgotten to enter one Action Check the FIELD and TABLE files Make sure that you correctly specify the pair potentials in the FIELD file indicating which ones are to be presented in the TABLE file Then check the TABLE file to make sure all the tabulated potentials are present in the order the FIELD file indicates Message 24 error end of file encountered in TABLE file This means the TABLE file is incomplete in some way either by having too few potentials included or the number of data points is incorrect Action Examine the TABLE file contents and regenerate it if it appears to be incomplete If it look intact check that the number of data points specified is what DL_POLY Classic is expecting Message 25 error wrong atom type found in CONFIG file On reading the input file CONFIG DL_POLY Classic performs a check to ensure that the atoms specified in the configuration provided are compatible with the corresponding FIELD file This message results if they are not Action The possibility exists that one or both of the CONFIG or FIELD files has incorre
65. Specification Echoes the FIELD file A warning line will be printed if the system is not electrically neutral This warning will appear immediately before the non bonded short range potential specifications This part of the file is written from the subroutine SYSDEF 4 2 2 4 Summary of the Initial Configuration This part of the file is written from the subroutine SYSGEN It states the periodic boundary speci fication the cell vectors and volume if appropriate and the initial configuration of a maximum of 20 atoms in the system The configuration information given is based on the value of levcfg in the CONFIG file If levcfg is 0 or 1 positions and velocities of the 20 atoms are listed If levcfg is 2 forces are also written out For periodic systems this is followed by the long range corrections to the energy and pressure 4 2 2 5 Simulation Progress This part of the file is written by the DL_POLY Classic root segment DLPOLY The header line is printed at the top of each page as step eng_tot temp_tot eng_cfg eng_vdw eng_cou eng_bnd eng ang eng_dih eng_tet time eng_pv temp rot vir_cfg vir_vdw vir_cou vir_bnd vir ang vir_con vir_tet cpu time volume temp_shl eng_shl vir_shl alpha beta gamma vir_pmf press The labels refer to line 1 step MD step number eng tot total internal energy of the system temp_tot system temperature eng cfg configurational energy of the system eng vdu configurational energy due to short range potent
66. The principal axis in the X direction of the rhombic dodecahedron passes through the centre of the cell and the centre of a rhombic face The Y axis does likewise but is set at 90 degrees to the X axis The Z axis completes the orthonormal set and passes through a vertex where four faces meet If the width D of the cell is defined as the perpendicular distance between two opposite faces the cell vectors required for the DL_POLY Classic CONFIG file are D 0 0 0 D 0 0 0 2D These also define the enscribing orthorhombic cell which has twice the MD cell volume In DL_POLY Classic the centre of the cell is also the origin of the atomic coordinates The rhombic dodecahedron can be used with the Ewald summation method Figure B 5 The rhombic dodecahedral MD cell Slab boundary conditions IMCON 6 Slab boundaries are periodic in the X and Y directions but not in the Z direction They are particularly useful for simulating surfaces The periodic cell in the XY plane can be any parallel ogram The origin of the X Y atomic coordinates lies on an axis perpendicular to the centre of the parallelogram The origin of the Z coordinate is where the user specifies it but at or near the surface is recommended If the XY parallelogram is defined by vectors A and B the vectors required in the CONFIG file are A1 A2 0 Bi B2 0 0 0 D where D is any real number including zero If D is nonzero it will be used by DL POLY to help determine a w
67. This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 2220 error failed allocation of nptqvv_h2 f densO array This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor 273 STFC Section C 0 Message 2230 error failed allocation of nptqvv_h2 f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 2240 error failed allocation of nstqvv_b1 f densO array This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 2250 error failed allocation of nstqvv_b1 f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user
68. To run a NEB calculation with DL POLY Classic it is first necessary to identify the start and end basins among the CFGBSNnn files in the BASINS directory described in section 5 5 0 3 From the information provided in the EVENTS 5 5 0 2 file it should be possible to decide which files are needed The user then needs to modify the CONTROL file in the following way 1 Remove any directives for the bpd or tad options Directives for the integration algorithm integrator or ensemble ensemble should also be removed The directive for the NEB option should be inserted neb n where n is the number of NEB calculations required On the record following the neb directive a list of n starting basins should be given e g basin 111123 Meaning the 5 reguired NEB calculations start from basin files CFGBSN0001 CFGBSN0001 CFGBSN0001 CFGBSN0002 and CFGBSN0003 Up to 10 NEB calculations are permitted On the second record following the neb directive a list of n final basins should be given e g basin 223434 Meaning the 5 required NEB calculations are between basins 1 2 1 3 1 4 2 3 and 3 4 in this example Define the energy units for the BPD parameters e g units s where s is one of eV kcal kJ or K signifying electron volts kilo cals per mole kilo joules per mole or Kelvin respectively No units directive means DL POLY internal units apply Forces are in chosen energy units per Angstrom Next set the NEB spring
69. a flat surface within the basins of the original potential energy surface In this case BPD is equivalent to a technique known as puddle skimming 66 which is a viable method for Monte Carlo simulation but has a disadvantage for molecular dynamics in that whenever Ebias V RN the atomic forces become discontinuous For dynamics a nonzero value of a is therefore always to be preferred Hamelberg et al provides a workable prescription for obtaining a in reference 64 However for DL POLY Classic a different approach is taken which is outlined below The scheme employed in DL_POLY Classic makes use of the fact that the local potential energy minimum is known at any given instant by virtue of the minimisation operations that occur period ically in the course of the simulations These are necessary to check for any changes in structure This minimum called hereafter Vo is used to define the effective zero point of the configurational energy scale which allows Ebias to be conveniently defined in terms of a temperature Trias such that 3 Etias Vo NkBTbias 5 9 This representation has the advantage that it can be intuitively related to the energetics of the system without prior knowledge of where the system resides on the absolute energy scale One can for example experiment with gradual increases in Tpias until transitions occur at a reasonable rate In a similar way an energy Vmin with an associated temperature Tmin can als
70. a machine with larger memory per processor 251 STFC Section C 0 Message 1014 error failed allocation of vdw arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1015 error failed allocation of Ir correction arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1020 error failed allocation of angle work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1030 error failed allocation of bond arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1040 error failed allocation of bond work arrays This is a memory allocation error Probable cause excessive size of simulated system Action
71. and make sure the keyword is correctly defined Make sure that subroutine 242 STFC Section C 0 FBPFRC contains the code necessary to deal with the requested potential Add the code required if necessary by amending subroutines SYSDEF and FBPFRC Message 444 error undefined bond potential DL_POLY Classic has been requested to process a bond potential it does not recognise Action Check the FIELD file and make sure the keyword is correctly defined Make sure that subroutine BNDFRC contains the code necessary to deal with the requested potential Add the code required if necessary by amending subroutines SYSDEF and BNDFRC Message 445 error undefined many body potential DL_POLY Classic has been requested to process a many body potential it does not recognise Action Check the FIELD file and make sure the keyword is correctly defined Make sure the code version you are using contains the code necessary to deal with the requested potential Add the code required if necessary Message 446 error undefined electrostatic key in dihfrc The subroutine DIHFRC has detected a request for an unknown kind of electrostatic model Action The probable source of the error is an improperly described force field Check the CONTROL file and FIELD files for incompatible requirements Message 447 error 1 4 separation exceeds cutoff range In the subroutine DIHFRC the distance between the 1 4 atoms in the potential is larger than the
72. and or barostat The Hoover and Berendsen thermostated versions are found in NVTQ_H2 and NVTQ B2 respectively The isotropic constant pressure implementations are found in NPTQ_H2 and NPTQ B2 while the anisotropic constant pressure routines are found in NSTQ H2 and NSTQ B2 An outline of the parallel version of QSHAKE is given in section 2 6 9 73 STFC Section 2 6 2 5 8 The DL POLY Classic Multiple Timestep Algorithm For simulations employing a large spherical cutoff reut radius in the calculation of the interactions DL_POLY Classic offers the possibility of using a multiple timestep algorithm to improve the effi ciency The method is based on that described by Streett et al 54 55 with extension to Coulombic systems by Forester et al 56 In the multiple timestep algorithm there are two cutoffs for the pair interactions a relatively large cutoff reut which is used to define the standard Verlet neighbour list and a smaller cutoff Tprim Which is used to define a primary list within the larger cutoff sphere see figure Forces derived from atoms in the primary list are generally much larger than those derived from remaining so called secondary atoms in the neighbour list Good energy conservation is therefore possible if the forces derived from the primary atoms are calculated every timstep while those from the secondary atoms are calculated much less frequently and are merely extrapolated over the interval DL_POLY Classic handle
73. are calculated by the link cell method 34 DL_POLY Classic applies no long ranged corrections to the Tersoff potentials In DL_POLY Classic Tersoff forces are handled by the routines TERSOFF TERINT and TERSOFF3 33 STFC Section 2 3 2 3 4 Four Body Potentials The four body potentials in DL_POLY Classic are entirely inversion angle forms primarily included to permit simulation of amorphous materials particularly borate glasses The potential forms available in DL POLY Classic are as follows 1 Harmonic harm U Oishn 5H ditkn do 2 134 2 Harmonic cosine hcos U dijin 5 eos dijkn cos 6o 2 135 3 Planar potential plan Ulap SA 66 dx 2 136 These functions are identical to those appearing in the intra molecular inversion angle descriptions above There are significant differences in implementation however arising from the fact that the four body potentials are regarded as inter molecular Firstly the atoms involved are defined by atom types not specific indices Secondly there are no excluded atoms arising from the four body terms The inclusion of other potentials for example pair potentials may in fact be essential to maintain the structure of the system The four body potentials are very short ranged typically of order 3 A This property plus the fact that four body potentials scale as N4 where N is the number of particles makes it essential that these terms are calculated by the
74. automatic parameter optimisation 0 lt f lt 1 E 4 Select damped reaction field electrostatics with user chosen damping parameter f A Reset velocities at timestep interval n using Gaussian distribution Restart job from end point of previous run i e continue current simulation Restart job from previous run with no temperature scaling i e begin a new simulation from older run Restart job from previous run with temperature scaling i e begin a new simulation from older run Reset force tolerance for shell relaxation to f DL POLY units 1 0 default Set required vdw forces cutoff to f A Rescale atomic velocities every n steps during equilibration using ad hoc rescaling Set shake tolerance to f default 1078 Calculate electrostatic forces using shifted coulombic potential Select damped shifted coulombic force electrostatics with automatic parameter optimisation 0 lt f lt 1 E 4 Select damped shifted coulombic force electrostatics with user chosen damping parameter f A Select SPME for electrostatics with automatic parameter optimisation 0 lt f lt 5 spme sum a k k2 k3 Select SPME for electrostatics with a Ewald convergence parameter A 99 STFC Section 4 1 k1 maximum k vector index in x direction k2 maximum k vector index in y direction k3 maximum k vector index in z direction stack n Set rolling average stack to n timesteps stats n Accumulate statist
75. be adeguate If your simulation cell is a truncated octahedron or a rhombic dodecahedron then the estimates for the kmax need to be multiplied by 2 3 This arises because twice the normal number of k vectors are required half of which are redundant by symmetry for these boundary contributions 45 If you wish to set the Ewald parameters manually via the ewald sum or spme sum directives the recommended approach is as follows Preselect the value of reut choose a working a value of Important note For the SPME method the values of kmax1 2 3 should be double those obtained in this prescription since they specify the sides of a cube not a radius of convergence 90 STFC Section 3 2 a of about 3 2 rcut and a large value for the kmax say 10 10 10 or more Then do a series of ten or so single step simulations with your initial configuration and with a ranging over the value you have chosen plus and minus 20 Plot the Coulombic energy and W versus a If the Ewald sum is correctly converged you will see a plateau in the plot Divergence from the plateau at small a is due to non convergence in the real space sum Divergence from the plateau at large a is due to non convergence of the reciprocal space sum Redo the series of calculations using smaller kmax values The optimum values for kmax are the smallest values that reproduce the correct Coulombic energy the plateau value and virial at the value of a to be used in the simula
76. closure time to f seconds collect Include equilibration data in overall statistics coul Calculate coulombic forces cut f Set required forces cutoff to f A densvar f Percentage density variation for arrays distan Calculate coulombic forces using distance dependent dielectric delr f Set Verlet neighbour list shell width to f A ensemble nve Select NVE ensemble default ensemble nvt ber f Select NVT ensemble with Berendsen thermostat with relaxation constant f ps ensemble nvt evans Select NVT ensemble with Evans thermostat ensemble nvt hoover f Select NVT ensemble with Hoover Nose thermostat with relaxation constant f ps ensemble npt ber fi f2 97 STFC Section 4 1 Select Berendsen NPT ensemble with fi fo as the thermostat and barostat relaxation times ps ensemble npt hoover fi f2 Select Hoover NPT ensemble with fi f2 as the thermostat and barostat relaxation times ps ensemble nst ber fi f2 Select Berendsen NaT ensemble with fi fo as the thermostat and barostat relaxation times ps ensemble nst hoover f f2 Select Hoover NaT ensemble with fi fo as the thermostat and barostat relaxation times ps ensemble pmf Select NVE potential of mean force ensemble eps f Set relative dielectric constant to f default 1 0 equil n Equilibrate simulation for first n timesteps ewald precision f Select Ewald sum for electrostatics with automatic parameter optimisation 0 lt f lt 1 E 4 ewald sum a k1 k2
77. configurational space This has a number of uses 1 Equilibration at a given temperature is quicker and thermodynamic averages can be obtained with greater reliability 2 It is possible to observe configurations which are difficult to obtain under normal conditions perhaps because they are far from the starting state and the system has slow relaxation times Such configurations may be important from a mechanistic viewpoint 3 The trajectory of the system evolves faster which means that movies of the simulation can show the motions of the system on a reasonable time scale This option is activated in the CONTROL file by using the single line directive bpd dyn fi f2 where f is the value of the required bias Etias f2 is the required value of the operating potential minimum lt Vinin gt both expressed in Kelvin This option runs like a normal DL_POLY Classic simulation except that the system potential is now the biased potential Consequently average system properties are calculated using equation 5 11 The user should note that the zero point of potential energy Vo in this case corresponds to the first energy minimum found in the simulation It does not change when further minima are found This is different from full path dynamics see above It is recommended that the simulation be run with the traject option activated in the CON TROL file so that a HISTORY file is produced This may be further analysed to reveal conforma
78. coordinate is the path distance S between the structure of the reference state and the structure of a converged NEB bead and is defined here as k 1 2 Sn D R RNY 5 23 i 1 where RN is a 3N dimensional vector defining the structure N is the number of atoms and n ranges from 2 to bead number N e in the NEB chain Note that the reaction path does not usually represent a straight line in the 3N dimensional space The file PROnn XY presents two columns of numbers the first is the reaction coordinate and the second is the configuration energy of the bead Both are expressed in DL_POLY Classic units The configuration energy for the first bead at S 0 is the energy of the reference state Normally the PROnn XY file reveals a single maximum in configuration energy as the reaction coordinate increases However in some instances more than one maximum may be obtained The user should note that in these instances DL POLY Classic will take the configuration closest the first minimum and optimise it independently to define the true destination of the transition from the reference state 5 6 Tidying Up the Results of a Hyperdynamics Simulation 5 6 1 Refining the Results A completed BPD or TAD simulation will provide a number of basin files defining the minima of new structures discovered together with the associated profile files describing the energy path between these structures These are the data that are needed to reconstruct the diffusion
79. core or the shell independently Action Remove the frozen atom option from the FIELD file Consider using a non polarisable atom instead 219 STFC Section C 0 Message 50 error too many bond angles specified DL_POLY Classic limits the number of valence angle potentials that can be specified in the FIELD file and checks for the violation of this Termination will result if the condition is violated Do not confuse this error with that described by message 51 below Action Standard user response Fix the parameter mxtang Message 51 error too many bond angles in system DL_POLY Classic limits the number of valence angle potentials in the system to be simulated ac tually the number to be processed by each node and checks for the violation of this Termination will result if the condition is violated Do not confuse this error with that described by message 50 above Action Standard user response Fix the parameter mxangl Consider the possibility that the wrong CONFIG file is being used e g similar system but larger size Message 52 error end of FIELD file encountered This message results when DL POLY Classic reaches the end of the FIELD file without having read all the data it expects Probable causes missing data or incorrect specification of integers on the various directives Action Check FIELD file for missing or incorrect data and correct Message 53 error end of CONTROL file encountered
80. damped real space sum and a reciprocal space sum The rate of convergence of both sums is governed by a Evaluation of the real space sum is truncated at r freut so it is important that a be chosen so that contributions to the real space sum are negligible for terms with r gt reut The relative error e in the real space sum truncated at reut is given approximately by e erfc areut Teut Y exp a reut Teut 3 1 The recommended value for a is 3 2 reyz or greater too large a value will make the reciprocal space sum very slowly convergent This gives a relative error in the energy of no greater than 4 x 107 in the real space sum When using the directive ewald precision DL POLY Classic makes use of a more sophisticated approximation erfc x 0 56 exp 2 x 3 2 to solve recursively for a using equation 3 1 to give the first guess The relative error in the reciprocal space term is approximately Een exp kina 407 kiran 3 3 where 5 knaz kmax 3 4 is the largest k vector considered in reciprocal space L is the width of the cell in the specified direction and kmax is an integer For a relative error of 4 x 107 this means using kmar 6 20 kmax is then kmax gt 3 2 L reut 3 5 In a cubic system freut L 2 implies kmax 7 In practice the above equation slightly over estimates the value of kmax reguired so optimal values need to be found experimentally In the above example kmax 5 or 6 would
81. defined are described in section 2 3 and the Coulombic methods available are described in section 2 4 Note that all the interaction types that are classed as intermolecular above may occur as in tramolecular interactions if the molecule concerned is defined as including them Nevertheless they are counted as intermolecular terms for the purposes of summation by DL_POLY Classic It should also be noted that for technical reasons the program cannot supply the Coulombic decomposition if the SPME option section 2 4 7 is selected but the standard Ewald option is valid for this purpose Furthermore there is no decomposition available for metallic potentials section 2 3 5 or the Tersoff potential section 2 3 3 since these are many body interactions not readily amenable to simple decomposition 6 2 2 Invoking the DL_POLY Energy Decomposition Option The energy decomposition option is activated when the appropriate directive is inserted into the CONTROL file section 4 1 1 The directive may be either decompose or solvate which have the same effect though the user s purpose in invoking each is different Acceptable abbreviations of these directives are decomp or solva The simplest form of invocation is a single line entry decompose n1 n2 or solvate n1 n2 where the number n1 specifies the time step at which DL POLY Classic is to start calculating the required data and n2 is the interval in time steps between calculations of the da
82. displaced by more than a preset distance the catch radius If a transition is detected the program optionally performs a NEB calculation using the two reference structures to find the activation energy E Note that it is not essential calculate an activation energy if one is confident that the bias chosen does not exceed the safe limit described by Voter equation 5 6 3 A determination of the time of the transition is made In DL_POLY Classic the occurrence time of the transition toc is determined by checking back from the detection of the transition through past configurations saved at regular intervals which should be much less than a BPD 143 STFC Section 5 3 block Each saved configuration is energy minimised and compared with the reference state structure until the first occurrence of the new state is found This provides a reasonable accuracy on the transition time somewhat better than using the end time of the BPD block in which the transition occurred The transition time is then corrected for the boost factor in equation 5 5 The new found state becomes the reference state for the next stage of the simulation If no transition was detected the original reference state is left in place In both cases the simulation continues from the end of the block as if uninterrupted Note this is markedly different from the TAD procedure described in section 5 4 The simulation is continued until from inspection
83. each atom type and n embedding functions again one for each atom type and n n 1 2 cross pair potential functions This makes n n 5 2 functions in total Note that the option of using EAM interactions must also be explicitly declared in the FIELD file so that for the n component alloy there are n n 1 2 cross pair potential eam keyword entries in FIELD see above Note that all metal interactions must be of the same type 4 1 6 1 The TABEAM File Format The file is free formatted but blank and commented lines are not allowed 4 1 6 2 Definitions of Variables record 1 header al00 file header record 2 numpot integer number of potential functions in file The subsequent records define the n n 5 2 functions for an n component alloy n electron density functions one for each atom type density keyword n embedding functions again one for each atom type embeding keyword and n n 1 2 cross pair potential functions pairs keyword The functions may appear in any random order in TABEAM as their identification is based on their unique keyword defined first in the function s header record The header record is followed by a predefined number of data records as a maximum of four data per record are read in allowing for incompletion of the very last record header record keyword ad type of EAM function dens embed or pair atom 1 a8 first atom type atom 2 a8 second atom type only specified for pair potential functi
84. energy including system extensions due to thermostats etc It is nominally the conserved variable of the system and is not to be confused with conventional system energy which is a sum of the kinetic and configuration energies The interval for printing out these data is determined by the directive print in the CON TROL file At each time step that printout is requested the instantaneous values of the above statistical variables are given in the appropriate columns Immediately below these three lines of output the rolling averages of the same variables are also given The maximum number of time steps used to calculate the rolling averages is determined by the parameter mxstak defined in the SETUP_MODULE F file The working number of time steps for rolling averages is controlled by the directive stack in file CONTROL see above The default value is mxstak Energy Units The energy unit for the data appearing in the OUTPUT is defined by the units directive appearing in the CONTROL file Pressure units The unit of pressure is k atm irrespective of what energy unit is chosen 4 2 2 6 Summary of Statistical Data This portion of the OUTPUT file is written from the subroutine RESULT The number of time steps used in the collection of statistics is given Then the averages over the production portion of the run are given for the variables described in the previous section The root mean square variation in these variables follow on the next two
85. especially the case when the system contains a strong directional anisotropy such as a surface These four parameters may also be set explicitly by the ewald sum directive in the CONTROL file For example the directive ewald sum 0 35 6 6 8 would set a 0 35 7 kmax1 6 kmax2 6 and kmax3 8 The quickest check on the accuracy of the Ewald sum is to compare the Coulombic energy U and the coulombic virial W 89 STFC Section 3 2 in a short simulation Adherence to the relationship U W shows the extent to which the Ewald sum is correctly converged These variables can be found under the columns headed eng_cou and vir_cou in the OUTPUT file see section 4 2 2 The remainder of this section explains the meanings of these parameters and how they can be chosen The Ewald sum can only be used in a three dimensional periodic system There are three variables that control the accuracy a the Ewald convergence parameter freut the real space forces cutoff and the kmax1 2 3 integers that effectively define the range of the reciprocal space sum one integer for each of the three axis directions These variables are not independent and it is usual to regard one of them as pre determined and adjust the other two accordingly In this treatment we assume that reut defined by the cutoff directive in the CONTROL file is fixed for the given system The Ewald sum splits the electrostatic sum for the infinite periodic system into a
86. gob ai ake ra fe i re fB 2 72 The sum of the diagonal elements of the stress tensor is zero since the virial is zero and the matrix is symmetric In DL_POLY Classic inversion forces are handled by the routine INVFRC 2 2 8 The Calcite Four Body Potential This potential 31 is designed to help maintain the planar structure of the carbonate anion C03 in a similar manner to the planar inversion potential described above However it is not an angular potential It is dependent on the perpendicular displacement u of an atom a from a plane defined by three other atoms b c and d see figure 2 6 and has the form Uabcalu Au But 2 73 Where the displacement u is given by u Tab E The x Tod 2 74 ITbe X Thal 25 STFC Section 2 2 Figure 2 6 The vectors of the calcite potential Vectors Tab ac aud rag define bonds between the central atom a and the peripheral atoms b c and d Vectors rpe and r q define the plane and are related to the bond vectors by Tee Tac Tab Tod gt Yad Tab 2 75 It what follows it is convenient to define the vector product appearing in both the numerator and denominator of equation 2 74 as the vector weg vis Wed The X Tod 2 76 We also define the quantity y u as y u 2Au 4Bu 2 77 The forces on the individual atoms due to the calcite potential are then given by fa V t Wea i eax Tap UWea Y U Wed ig Tap UWca Y U Wea
87. in the FIELD file and resubmit Message 14 error too many unique atom types specified This error arises when DL_POLY Classic scans the FIELD file and discovers that there are too many different types of atoms in the system i e the number of unique atom types exceeds the mxsvdw parameter Action Standard user response Fix parameter mxsvdw Message 15 error duplicate pair potential specified In processing the FIELD file DL POLY Classic keeps a record of the specified short range pair potentials as they are read in If it detects that a given pair potential has been specified before no attempt at a resolution of the ambiguity is made and this error message results See specification of FIELD file Action Locate the duplication in the FIELD file and rectify Message 16 error strange exit from FIELD file processing This should never happen However one remote possibility is that there are more than 10 000 directives in the FIELD file It simply means that DL POLY Classic has ceased processing the 214 STFC Section C 0 FIELD data but has not reached the end of the file or encountered a close directive Probable cause corruption of the DL_POLY Classic executable or of the FIELD file We would be interested to hear of other reasons Action Recompile the program or recreate the FIELD file If neither of these works send the problem to us Message 17 error strange exit from CONTROL file processing See note
88. integration is activated by the directive free in the CONTROL file section 4 1 1 This is followed by additional directives on the following lines terminating with the directive endfre The invocation is therefore made in the following way free start n1 interval n2 lambda r1 mix n3 expo n4 reset mass this is not recommended system a ii i2 system_b i3 i4 endfre The meaning of these directives is as follows 1 free invokes the free energy option and marks the start of the free energy specification in the CONTROL file 2 start n1 specifies the time step at which DL POLY Classic should start producing free energy data integer n1 3 interval n2 specifies the time step interval between free energy data calculations integer n2 4 lambda r1 value of the mixing parameter A in the Hamiltonian equation 6 1 range 0 1 real r1 5 mix n3 key for choice of mixing protocol integer n3 choices are e n3 1 linear mixing equation 6 10 e n3 2 nonlinear mixing equation 6 11 e n3 3 trigonometric mixing equation 6 12 e n3 4 error function mixing equation 6 13 e n3 5 polynomial mixing equation 6 14 e n3 6 spline kernel mixing equation 6 15 6 expo n4 exponent for nonlinear or polynomial mixing as in equations 6 11 and 6 14 respectively required for these options only integer n4 7 reset_mass if this flag is present the Hamiltonian mixing will include the
89. is submitted The close time directive represents the time DL_POLY Classic will require to write and close all the data files at the end of processing This means the effective processing time limit is equal to the job time minus the close time Thus when DL_POLY Classic reaches the effective job time limit it begins the close down procedure with enough time in hand to ensure the files are correctly written In this way you may be sure the restart files etc are complete when the job terminates Note that setting the close time too small will mean the job will crash before the files have been finished If it is set too large DL_POLY Classic will begin closing down too early How large the close time needs to be to ensure safe close down is system dependent and a matter of experience It generally increases with the job size 3 Note that the default time unit for job time is seconds however this may be changed by addition of an extra character after the number on the the directive line Thus m will set it to minutes A to hours and d to days You can even skip the number altogether and put indef which will set the default job time to 1 million years which should be enough for anyone 100 STFC Section 4 1 10 11 12 Note however that you will lose the capability to end the job within the specified close time so you should be sure the job will finish without crashing The starting options for a simulation are governed by the k
90. j n gt k N Y Umeta i ra RV i 1 N V Uertn i ri Vi 2 1 i l where Ubond Uangle Udihed Uinv Upair U3 body UTersoff and Us body are empirical interaction functions representing chemical bonds valence angles dihedral angles inversion angles pair body three body Tersoff many body covalent and four body forces respectively The first four are regarded by DL POLY Classic as intra molecular interactions and the next five as inter molecular interactions The term Umetal is a density dependent and therefore many body metal potential The final term Ueztn represents an external field potential The position vectors ra fp 1 and rq refer to the positions of the atoms specifically involved in a given interaction Almost universally it is the differences in position that determine the interaction A special vector R is used to indicate a many body dependence The numbers Nona Nangies Nainea and Niny refer to the total numbers of these respective interactions present 13 STFC Section 2 1 in the simulated system and the indices bond tangle tinv and igipeg Uniquely specify an individ ual interaction of each type It is important to note that there is no global specification of the intramolecular interactions in DL_POLY Classic all bonds valence angles and dihedrals must be individually cited The indices i j and k n appearing in the pair body and three or four body terms indicate the atoms involved in th
91. k RIA U rij 0 5 k R2 In 142 bck coul Coulombic qi qj CG m cou N ote bond potentials with a dash as the first character of the keyword do not contribute to the excluded atoms list see section 2 1 In this case DL POLY Classic will also calculate the nonbonded pair potentials between the described atoms unless these are deactivated by another potential specification 6 constraints n where n is the number of constraint bonds in the molecule Each of the following n records contains index 1 integer first atomic index index 2 integer second atomic index bondlength real constraint bond length This directive and associated data records need not be specified if the molecule contains no constraint bonds See the note on the atomic indices appearing under the shell directive above 7 pmf b 111 STFC Section 4 1 where b is the potential of mean force bondlength A There follows the definitions of two PMF units a pmf unit n where n is the number of sites in the first unit The subsequent n records provide the site indices and weighting Each record contains index integer atomic site index weight real site weighting b pmf unit nz where na is the number of sites in the second unit The subsequent ng records provide the site indices and weighting Each record contains index integer atomic site index weight real site weighting This directive
92. k3 Select Ewald sum for electrostatics with a Ewald convergence parameter A k1 maximum k vector index in x direction k2 maximum k vector index in y direction k3 maximum k vector index in z direction finish Close the CONTROL file last data record hke precision fij Select HK Ewald sum for electrostatics with automatic parameter optimisation 0 lt f lt 5 reguired order of HKE expansion recommend 1 j required lattice sum order recommend 1 hke sum a k k2 145 Select HK Ewald sum for electrostatics with a Ewald convergence parameter A k1 maximum g vector index in x direction k2 maximum g vector index in y direction nhko required order of HKE expansion recommend 1 nlatt required lattice sum order recommend 1 integrator type Select type of integration algorithm leapfrog leapfrog integration algorithm default velocity velocity Verlet integration algorithm The default is leapfrog if integrator is not specified impact in E ux uy uz Select impact dynamics with identity of impacted atom n time step when impact occurs E the recoil energy of the impacted atom in KeV uz X component of normalised recoil direction vector uy Y component of normalised recoil direction vector uz Z component of normalised recoil direction vector job time f Set job time to f seconds minim energy nf Programmed minimisation based on energy force or position with minim force n f n number of time ste
93. lines The energy and pressure units are as for the preceeding section Also provided in this section is an estimate of the diffusion coefficient for the different species in the simulation which is determined from a single time origin and is therefore very approximate Accurate determinations of the diffusion coefficients can be obtained using the MSD utility program which processes the HISTORY file see chapter 9 If an NPT or NoT simulation is performed the OUTPUT file also provides the mean stress pressure tensor and mean simulation cell vectors 131 STFC Section 4 2 4 2 2 7 Sample of Final Configuration The positions velocities and forces of the 20 atoms used for the sample of the initial configuration see above are given This is written by the subroutine RESULT 4 2 2 8 Radial Distribution Functions If both calculation and printing of radial distribution functions have been requested by selecting directives rdf and print rdf in the CONTROL file radial distribution functions are printed out This is written from the subroutine RDF1 First the number of time steps used for the collection of the histograms is stated Then each function is given in turn For each function a header line states the atom types a and b represented by the function Then r g r and n r are given in tabular form Output is given from 2 entries before the first non zero entry in the g r histogram n r is the average number of atom
94. more than three atoms e g benzene Even when the structure can be defined by bond constraints the network of bonds produced may be problematic Normally they make the iterative SHAKE procedure slow particularly if a ring of constraints is involved as occurs when one defines water as a constrained triangle It is also possible inadvertently to over constrain a molecule e g by defining a methane tetrahedron to have 10 rather than 9 bond constraints in which case the SHAKE procedure will become unstable In addition massless sites e g charge sites cannot be included in a simple constraint approach making modelling with potentials such as TIP4P water impossible All these problems may be circumvented by defining rigid body units the dynamics of which may be described in terms of the translational motion of the center of mass COM and rotation about the COM To do this we need to define the appropriate variables describing the position orientation and inertia of a rigid body and the rigid body equations of motion The mass of a rigid unit M is the sum of the atomic masses in that unit Nsites M Y mj 2 282 j 1 where m is the mass of an atom and the sum includes all sites Nsites in the body The position of the rigid unit is defined as the location of its centre of mass R 1 Nsites Sn 2 Mjrj 2 283 I 5An alternative approach is to define basic and secondary particles The basic particles are the mini
95. mxbuff Alternatively mxrdf can be set smaller Message 220 error too many neutral groups in system DL_POLY Classic has a fixed limit on the number of charged groups in a simulation This error results if the number is exceeded Action Standard user response Fix the parameter mxneut Message 225 error multiple selection of optimisation options The user has specified more than one optimisation directive in the CONTROL file Action Remove redundant optimisation directive s from CONTROL file 232 STFC Section C 0 Message 230 error neutral groups improperly arranged In the DL_POLY Classic FIELD file the charged groups must be defined in consecutive order This error results if this convention is not adhered to Action The arrangement of the data in the FIELD file must be sorted All atoms in the same group must be arranged consecutively Note that reordering the file in this way implies a rearrangement of the CONFIG file also Message 250 error Ewald sum requested with neutral groups DL_POLY Classic will not permit the use of neutral groups with the Ewald sum This error results if the two are used together Action Either remove the neut directive from the FIELD file or use a different method to evaluate the electrostatic interactions Message 260 error parameter mxexcl exceeded in excludeneu routine An error has been detected in the construction of the excluded atoms list for neutral groups This
96. nstqscl_p2 nstqscl_t nstqscl_t2 nstqvv_b1 nstqvv_b2 nstqvv_h1 nstqvv_h2 nstscale_p nstscale_t nstvv_b1 nstvv_h1 numnodes numnodes nve_1 nveq_1 nveq_2 nveqvv_1 nveqvv_2 nvevv_1 nvt_b1 subroutine subroutine function function subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine function function subroutine subroutine subroutine subroutine subroutine subroutine subroutine forces_module f nlist_builders_module basic_comms f serial f vv rotation1 module f lf motion module f lf motion module f lf rotation1 module lf rotation2 module lf rotation1 module lf rotation2 module Fh Fh Fh Fh ensemble_tools_module ensemble_tools_module vv rotation1 module f vv rotation2 module f vv rotation1 module f vv_rotation2_module f ensemble_tools_module ensemble_tools_module vv_motion_module f vv_motion_module f 1f_motion_module f 1f_motion_module f 1f_rotationi_module 1f_rotation2_module 1f_rotation1_module 1f_rotation2_module Fh Fh Fh Fh ensemble_tools_module ensemble_tools_module ensemble_tools_module ensemble_tools_modu
97. one or more atoms are displaced by more than a preset distance the catch radius If a transition is detected a NEB calculation is initiated using the two reference structures to find the activation energy E 148 STFC Section 5 4 log 1 tacc 1 Trigh 1 Tiow Figure 5 4 Basic TAD Theory Plot of log 1 t vs 1 T for the TAD method Simulations at high temperature locate transitions indicated as ti and t2 with t occurring first time increases in a downward direction on this plot Extrapolation to low temperature using equation 5 17 shows that these transitions would have occurred in reverse order If no other transitions occurred t2 would be the observed low temperature transition in an MD simulation The dotted line indicates a possible hypothetical transition that just precedes t2 at low temperature Its high temperature intercept is calculated according to the criterion of Voter et al 63 which gives the estimated stopping time for the simulation 3 Next a determination of the transition time 2 is made As with BPD the occurrence time of the transition t2 is determined by checking back from the detection of the transition through past configurations saved at regular intervals which are saved at intervals much less than a TAD block Each saved configuration is energy minimised and compared with the reference state structure until the first occurrence of the new state is found This provides a reaso
98. or a higher version is required to run the GUL 9 1 1 6 select select is a macro enabling easy selection of one of the test cases It invokes the unix commands bin tcsh DL_POLY utility to gather test data files for program run cp data TEST 1 2 CONTROL CONTROL cp data TEST 1 2 FIELD FIELD cp data TEST 1 2 CONFIG CONFIG if e data TEST 1 2 TABLE then cp data TEST 1 2 TABLE TABLE else if e data TEST 1 2 TABEAM then cp data TEST 1 2 TABEAM TABEAM endif select requires two arguments to be specified select n a where n is the integer test case number which ranges from 1 to 20 and a is the character string LF VV RB or CB according to which algorithm leapfrog LF velocity Verlet VV RB rigid body minimisation or CB constraint bond minimisation is required This macro sets up the required input files in the execute sub directory to run the n th test case 197 OSTFC Section 9 1 9 1 1 7 store The store macro provides a convenient way of moving data back from the execute sub directory to the data sub directory It invokes the unix commands bin tcsh t DL POLY utility to archive I O files to the data directory if e data TEST 1 then mkdir data TEST 1 endif if e data TEST 1 2 then mkdir data TEST 1 2 endif mv CONTROL data TEST 1 2 CONTROL mv FIELD data TEST 1 2 FIELD mv CONFIG data TEST 1 2 CONFIG mv OUTPUT data TEST 1 2 0
99. path in the original system However at this stage there are still some approximations in the results which arise from the chosen tolerances in the energy minimisation of the structures and the NEB calculations To offset these the following refinements are recommended 1 Take each of the basin structures derived from the BPD or TAD simulation and perform a further structural optimisation with DL_POLY using more exacting convergence tolerance For example using a force tolerance of 0 01 DL POLY units in place of the recommended 1 0 used in the BPD and TAD procedures This will provide more accurate reference structures 157 STFC Section 5 7 2 Using the accurately minimised structures in place of the original basins use the NEB option in DL_POLY to recalculate the transition path between the reference states Once again a more exacting tolerance may be used but beware that the NEB calculation may not converge at all if the tolerance is too exacting It is far less stable in this respect than the ordinary structural optimisation Note that the tolerance for the overall NEB minimisation is set internally in DL_POLY Classic to be a factor of 10 larger than that for the minimisation alone The result of these refinements should be a better estimate of the activation energy and low temperature transition time For TAD simulations the activation energy obtained from the refined structures can be used together with the simulated high tem
100. potential 5 is a special example of a density dependent potential which has been designed to reproduce the properties of covalent bonding in systems containing carbon silicon germanium etc and alloys of these elements A special feature of the potential is that it allows bond breaking and associated changes in bond hybridisation The potential has 11 atomic and 2 bi atomic parameters The energy is modelled as a sum of pair like interactions where however the coefficient of the attractive term in the pairlike potential which plays the role of a bond order depends on the local environment giving a many body potential The form of the Tersoff potential is ters Uij folrij Fr rig viz fa rig 2 113 where jay Aij exp aij rij falrij By exp bij rij 2 114 1 Tij lt Rij fo rij 5 5 cos T rij Rij rij Riz Rij lt Tij lt Sij 2 115 0 Tij gt Sij 31 STFC Section 2 3 pax AEB LEA Le X Tera gO Gs k ij g Oijk 1 c d c d hj cos 0ijk 2 116 with further mixed parameters defined as aij a aj 2 bij bi bj 2 Ag APA By BBA 2 117 Rij RRA Sij S S V2 Here i j and k label the atoms in the system r is the length of the ij bond and 6 is the bond angle between bonds ij and ik Single subscripted parameters 11 such as a and 7 depend only on the type of atom The chemistry between different atom types is encapsulated in the two
101. potential type Variables 1 7 functional form eam EAM tabulated potential fnsc Finnis Sinclair co c1 c2 c A d 8 Ui r 5 D ri c co C1fij car Ay pi Al Ti d 3 Pi X ris dy po 1 jAl stch Sutton Chen e a nim c U r E 2 C a Al Pi VI El L gupt Gupta Alro p B ay Uilr 4 5 Aexp p rig we B p JA Y exp jj To JA 2 i Both EAM and FSM potentials can handle alloys but care must be taken to enter the cross terms of the potentials explicitly Note that the rules for defining cross terms of the potential are not the usual rules encountered in Lennard Jones systems see section 2 3 5 4 1 3 5 The Tersoff Potential The Tersoff potential 5 is designed to reproduce the effects of covalency in systems composed of group 4 elements in the periodic table carbon silicon germanium etc and their alloys Like the metal potentials these are also non bonded potentials characterised by atom types rather than specific atomic indices The input of Tersoff potential data is signalled by the directive tersoff n Where n is the number of specified Tersoff potentials It is followed by 2n records specifying n particular Tersoff single atom type parameters and n n 1 2 records specifying cross atom type parameters in the following manner 120 STFC Section 4 1 potential 1 record 1 atmnam as key ad variable 1 real variable 2 real variable 3 real v
102. probe Important The system_b atoms must be the last group of atoms listed in the CONFIG file This is absolutely essential It will be necessary to restructure the FIELD file if changes are made to CONFIG If the chromophore is only part of a molecule instead of being the whole of it it will be found most convenient to let the molecule containing the chromophore be the last one defined in the CONFIG and FIELD files This will make it possible to minimise the the number of virtual atoms it is necessary to define which reduces the file sizes and improves computational efficiency 6 4 5 Invoking the Solvent Relaxation Option This option is activated by inserting the directive switch in the CONTROL file 4 1 1 followed by further directives to enter the control parameters and ending with the endswi directive The specification is as follows switch start n1 inter n2 period n3 system_a ii i2 system_b i3 i4 endswi The meaning of these directives is as follows 1 switch invokes the solvent relaxation option 2 start n1 specifies the time step at which DL_POLY Classic should first switch to the excited state integer n1 3 inter n2 the time step interval sampling interval between spectroscopic data calculations integer n2 4 period n3 the interval in time steps for the system to remain in the excited state before returning to ground state where it will remain for an equal interval to re equilibrate integer n3
103. purpose It is designed to compare start and end configurations in the BASINS subdirectory and list the atoms that have changed location 5 3 4 Things to Be Aware of when Running Full Path Kinetics BPD 1 Choose the catch radius carefully where possible basing it on nearest neighbour distances obtained from the parent crystal A consequence of using too large a catch radius is that transitions that require a short hop in atom positions may be missed during a run Such misses make it difficult to reconstruct the reaction path and in particular cause any NEB calculation to crash since there is no simple path between the reference structures 2 Note that in a BPD simulation the reference state is replaced whenever a new state is found In this respect the reference state follows the diffusion path This is a clear distinction from TAD 1 Assuming just one atom undergoes the transition 146 STFC Section 5 4 3 We repeat again the important message that if any of the transitions reported by PBD has an activation energy that is below the value of the bias term Epas i e Nx E lt Eyjas this represents a violation of the condition in equation 5 6 which means the observed diffusion path is not a valid representation of the original system The simulation should be repeated with a lower value of Epjas 5 3 5 Exploring Configurational Space Running DL_POLY Classic under the BPD option is useful for simply exploring
104. related to the constraint force via AB _ pnt m 1 Hip hip di Bp Now the velocity of the linked atom on molecule A is which on substitution of the above equations gives At aa gfe 1 1 Uap Dap gt hab On 2 322 where aBp nai 1 _ Abp n a 22 DU 2 323 The constraint condition requires that qetl n 1 _ n l 0 2 324 ABp wap UBp j E and substitution of the equation for v and the equivalent for ver leads directly to Ap m 1 n 1 n 1 pret CAB ap T Ep 2 325 Atdip Qa Op which provides the correction for second constraint This again reguires iteration The VV SHAKE algorithm is implemented in DL_POLY Classic in subroutine NVEQVV_2 with the QSHAKE constraint forces calculated in QRATTLE_R and QRATTLE_V Again it is straightfor ward to couple these systems to a Hoover or Berendsen thermostat and or barostat The Hoover and Berendsen thermostated versions are found in NVTQVV_H2 and NVTQVV_B2 respectively The isotropic constant pressure implementations are found in NPTQVV_H2 and NPTQVV_B2 while the anisotropic constant pressure routines are found in NSTQVV_H2 and NSTQVV_B2 The Hoover versions make use of the thermostat and barostat routines NVTQSCL NPTQSCL_T NPTQSCL_P NSTQSCL_T and NSTQSCL_P according to the ensemble The LF QSHAKE algorithm is implemented in NVEQ_2 with the QSHAKE constraint forces applied in QSHAKE This also has different ensemble versions Hoover or Berendsen thermostat
105. result of the transition In general classical simulations are concerned with the interactions between the chromophore and solvent in the ground and excited states DL_POLY Classic offers two capabilities in this area Firstly it can be used to determine the interaction energy between the solvent and the chromophore in the ground and excited states at the instant of the transition information which quantifies the solvent induced spectral shift Secondly it can be used to calculate the relaxation energy resulting from the solvent response to the change in solvent chromophore interaction after the transition 6 4 2 Calculating Solvent Induced Spectral Shifts A chromophore in solution differs from in vacuum by virtue of the solvent chromophore interactions which occur in both the ground and exited states Since the solvation energy usually different for the two states it follows that the spectroscopic transition in solution will be different from the vacuum to an extent determined by the solvation energy difference Spectroscopically the effect of this is to shift the location of the transition in the electromagnetic spectrum Furthermore the solvation energy is not constant but fluctuates in time with a characteristic probability distribution It follows that both the ground and excited states of the chromophore possess a distribution of possible energies which gives rise to a broadening of the spectral line Subject to the assumptions that the tr
106. screened by charge ordering so that at long ranged any given charge looks like a neutral object Meanwhile the force shifting is formally equivalent to surrounding each charge with a spherical charge that neutralises the charge content of the cutoff sphere thus resembling the natural screening on a predetermined distance scale reut The method thus assumes that these two effects are the same The Wolf et al method 42 was cast into a form suitable for molecular dynamics by Fennell and Gezelter 43 which is the form implemented in DL POLY Classic In this form damping function is the same complementary error function as appears in the Ewald sum see section 2 4 6 qiq erfelarij erfclare er fc arcut 2a exp a r U ij 2 ri Ate Tij Tout T fy qi 2 Teut rij Teut a SS EEEE SS da rij lt Pout 2 187 The corresponding force is given by f dias erfclary 2a exp o r er fc 0 cut 2a exp a r Tij Are re qi 2 Ti i qr1 2 Teut Tij S ias ia Gi An ii a setae de a e o niai ania ied Das rij lt Teut 2 188 Note these formulae reduce to the basic shifted force Coulombic potential forms when the conver gence parameter a is zero The contribution to the atomic virial is which is not the negative of the potential term The contribution to be added to the atomic stress tensor is given by 2 190 where a 8 are x y z components The atomic stress tensor is symmetric In DL_POLY
107. sets of bi atomic param eters Xij and wij Xi l Xij Xji w 1 Wij Wji 2 118 which define only one independent parameter for each pair of atom types The x parameter is used to strengthen or weaken the heteropolar bonds relative to the value obtained by simple interpo lation The w parameter is used to permit greater flexibility when dealing with more drastically different types of atoms The force on an atom derived from this potential is bind calculated with the formula o f z Etersoff D gt 2 119 Or ET aa with atomic label being one of i j k and a indicating the x y z component The derivative in the above formula expands into OU 0 0 Ore are Joris fr rig Vig Brg eCa Faris fotra Faria Ya 2 120 with the contributions from the first two terms being 0 Brg eras Faris 24 4 frlria groa x 5 1 je di wi 2 121 O Vij gra ale riz fA Tij ij fel iia fa riz falta Solri x i e 2 122 0 foltra Faria o Ya folrij falrij Xij X and from the third angular term 1 y 1 0 Ni fpi 29 Mi mol 5 ERE e en OF A BEI 32 STFC Section 2 3 where Dp Ore qe a7 5 Wik fe rik g 0 ijk 2 124 k i j The angular term can have three different contributions depending on the index of the particle participating in the interaction 0 L i af E Wik fo 0554 Br gra oli Jolrik ara ad sy 2 125 0 j ae X
108. specified earlier in the file Action Correct the erroneous entry in the FIELD file and resubmit Message 82 error calculated pair potential index too large In checking the pair potentials specified in the FIELD file DL POLY Classic calculates a unique integer index that henceforth identifies the potential within the program If this index becomes too large termination of the program results Action Standard user response Fix the parameters mxsvdw and mxvdw Message 83 error too many three body potentials specified DL_POLY Classic has a limit on the number of three body potentials that can be defined in the FIELD file This error results if too many are included Action Standard user response Fix the parameter mxtbp Message 84 error unidentified atom in 3 body potential list DL_POLY Classic checks all the 3 body potentials specified in the FIELD file and terminates the program if it can t identify any one of them from the atom types specified earlier in the file Action Correct the erroneous entry in the FIELD file and resubmit 224 STFC Section C 0 Message 85 error required velocities not in CONFIG file If the user attempts to start up a DL_POLY Classic simulation with the restart or restart scale directives see description of CONTROL file the program will expect the CONFIG file to contain atomic velocities as well as positions Termination results if these are not present Action Either r
109. t is the inversion angle The EAM potentials are tabulated and are supplied to DL POLY Classic in the input file TABEAM see 4 1 6 The FSM potentials are analytical and DL_POLY Classic supports the explicit forms due to Finnis and Sinclair 3 Sutton and Chen 38 39 and Gupta 41 Metal potentials like van der Waals potentials are also non bonded potentials and are char acterised by atom types rather than specific atomic indices The input of metal potential data is signalled by the directive metal n where nis the number of metal potentials to be entered There follows n records each specifying a particular metal potential in the following manner atmnam 1 atmnam 2 key variable 1 a8 a8 a4 real first atom type second atom type potential key See table 4 15 potential parameter see table 4 15 119 STFC Section 4 1 variable 2 real variable 3 real variable 4 real variable 5 real variable 6 real variable 7 real potential parameter see table 4 15 potential parameter see table 4 15 potential parameter see table 4 15 potential parameter see table 4 15 potential parameter see table 4 15 potential parameter see table 4 15 The variables pertaining to each potential are described in table 4 15 Note that any metal potential not specified in the FIELD file will be assumed to be zero This includes cross terms for alloys Table 4 15 Metal Potential key
110. the angular momentum of the rigid body defined by the expression Nsites j 1 and w is the angular velocity The vector 7 is the torque acting on the body in the universal frame and is given by d X f 2 293 The rotational eguations of motion written in the local frame of the rigid body are given by Euler s eguations se Ge ty Lisos Lex x T La Tne Ine Wels 2 294 Lyy x T A aa y x t Le Tuy aig Izz The vector w is the angular velocity transformed to the local body frame Integration of w is complicated by the fact that as the rigid body rotates so does the local reference frame So it is necessary to integrate equations 2 294 simultaneously with an integration of the quaternions describing the orientiation of the rigid body The equation describing this is do do Q 43 0 1 B h q a 4 B q Wa 2 295 q2 qd 93 qo 41 Wy d3 d 2 QU 4 Wy Rotational motion in DL_POLY Classic is handled by two different methods For LF implemen tation the Fincham Implicit Quaternion Algorithm FIQA is used 15 The VV implementation uses the NOSQUISH algorithm of Miller et al 16 The LF implementation begins by integrating the angular velocity equation in the local frame a 2 a E The new quaternions are found using the FIQA algorithm In this algorithm the new quaternions are found by solving the implicit equation At H t 2 296 a t At q t a Qull Q
111. the code a generous close time in the CONTROL file so that these optimisation tasks have a chance to complete before the axe falls 153 STFC Section 5 5 5 4 4 Things to Be Aware of when Running TAD 1 Choose the catch radius carefully where possible basing it on nearest neighbour distances obtained form the parent crystal A consequence of using too large a catch radius is that transitions that require a short hop in atom positions may be missed during a run Such misses make it difficult to reconstruct the reaction path and in particular cause the NEB calculation to crash since there is no simple path between the reference structures 2 The user may sometimes observe successive transitions into the same state If a transition to an already visited state occurs it is indicated with the flag TRR repeat transition in the EVENTS file Such repeated transitions are normal but if they occur in succession it implies that there is some correlation creeping into the resetting of the system back into the starting state This however is harmless as the accumulated simulation time is reset back to the restart state after each transition and so does not affect the time of the later transition to a new state 3 Note that in a TAD simulation the reference state is always the same The reference state does not follow the diffusion path as it does in BPD 4 It is useful to determine which atoms have relocated during a transit
112. the processing nodes Each node makes a list recording which atoms are bonded by constraints it is to process Entries are zero if the atom is not bonded A copy of the array is passed to each other node in turn The receiving node compares the incoming list with its own and keeps a record of the shared atoms and the nodes which share them In the first stage of the SHAKE algorithm the atoms are updated through the usual Verlet algorithm without regard to the bond constraints In the second iterative stage of SHAKE each node calculates the incremental correction vectors for the bonded atoms in its own list of bond constraints It then sends specific correction vectors to all neighbours that share the same atoms using the information compiled in step 3 When all necessary correction vectors have been received and added the positions of the constrained atoms are corrected Steps 5 and 6 are repeated until the bond constraints are converged After convergence the coordinate arrays on each node are passed to all the other nodes The coordinates of atoms that are not in the constraint list of a given node are taken from the incoming arrays an operation we term splicing Finally the change in the atom positions is used to calculate the atomic velocities The above scheme is complete for a implementation based on the leapfrog integration algorithm However a velocity Verlet VV scheme requires additional s
113. the subdirectory java Com pilation of this is simple and requires running the javac compiler and the jar utility Details for these procedures are provided in the GUI manual 9 6 To run the executable for the first time you require the files CONTROL FIELD and CONFIG and possibly TABLE or TABEAM if you have tabulated potentials These must be present in the directory from which the program is executed See section 4 1 for the description of the input files 7 Executing the program will produce the files OUTPUT REVCON and REVIVE and option ally STATIS HISTORY RDFDAT and ZDNDAT in the executing directory See section 4 2 for the description of the output files This simple procedure is enough to create a standard version to run most DL_POLY Classic applications However it sometimes happens that additional modifications may be necessary On starting DL_POLY Classic scans the input data and makes an estimate of the sizes of the arrays it requires to do the simulation Sometimes the estimates are not good enough The most common occurrences of this are NPT and NST simulations or simulations where the local density on the MD cell may significantly exceed the mean density of the cell systems with a vacuum gap for example Under these circumstances arrays initally allocated may be insufficent In which case DL_POLY Classic may report a memory problem and request that you recompile the code with hand adjusted array dimensions This topi
114. the subroutines TRAJECT or TRAJECT_U The control variables for this file are ltraj nstraj istraj and keytrj which are created internally based on information read from the traj directive in the CONTROL file see above The HISTORY file will be created only if the directive traj appears in the CONTROL file Note that the HISTORY file can be written in either a formatted or unformatted version We describe each of these separately below If you want your HISTORY data to have maximum numerical precision you should use the unformatted version The HISTORY file can become very large especially if it is formatted For serious simulation work it is recommended that the file be written to a scratch disk capable of accommodating a large data file Alternatively the file may be written as unformatted below which has the additional advantage of speed However writing an unformatted file has the disadvantage that the file may not be readily readable except by the machine on which it was created This is particularly important if graphical processing of the data is required 4 2 1 1 The Formatted HISTORY File The formatted HISTORY file is written by the subroutine TRAJECT and has the following structure record 1 a80 header a80 file header record 2 3i10 keytrj integer trajectory key see table 4 3 imcon integer periodic boundary key see table 4 6 natms integer number of atoms in simulation cell For timesteps greater than nstraj the HISTOR
115. therefore different on each node DL_POLY Classic uses a method based on the Brode Ahlrichs scheme 23 see figure 2 9 to construct the neighbour list Additional modifications are necessary to handle the excluded atoms 58 A distributed excluded atoms list is constructed by DL POLY Classic at the start of the simulation The list is constructed so that the excluded atoms are referenced in the same order as they would appear in the Verlet neighbour list if the bonded interactions were ignored allowing for the distributed structure of the neighbour list 76 STFC Section 2 6 Brode Ahlrichs Algorithm 12 Atoms 4 processors Processor 0 10 11 10 12 10 1 10 2 10 3 11 12 11 1 11 2 11 3 11 4 12 1 12 2 12 3 12 4 12 5 Figure 2 9 The parallel implementation of the Brode Ahlrichs algorithm This diagram illustrates the reordering of the upper triangular matrix of n n 1 2 pair interactions so that the rows of the matrix are of approximately equally length Each entry in the table consists of a primary atom index constant within a row and a neighbouring atom index Rows are assigned sequentially to nodes In the diagram node 0 deals with rows 1 5 and 9 node 1 to rows 2 6 and 10 etc When a charge group scheme as opposed to an atomistic scheme is used for the non bonded terms the group group interactions are distributed using the Brode Ahlrichs approach This makes the Verlet list considerably smaller thus saving mem
116. time steps Fortunately it is possible in many cases to set up the Hamiltonians H and H so that the mixed Hamiltonian does not require scaling of the kinetic energy In these cases there is no problem with the equations of motion For the awkward cases where the kinetic energy really must be scaled DL POLY Classic has the option reset_mass which scales the masses as required Ideally however this circumstance should be avoided if at all possible 2 Secondly it is well known that when A approaches 0 or 1 the average H gt H in equation 6 3 is subject to large statistical error This arises because the modified dynamics of the mixed Hamiltonian permits unnaturally close approaches between atoms and the configura tion energy terms arising from this are inevitably extremely large Fortunately this problem can be mitigated by the use of a suitable weighting function examples of which are described in the following section As an example of how this approach maybe used we present the calculation of the free energy of a solution of a solute A in a solvent S An appropriate choice of Hamiltonians for this is H Ks KaA Vss Vaa Vas Hy Ks KA Vss Vaas 6 4 in which Kg and Ka are the kinetic energies of the solvent and solute respectively Vss VAa and Vag are the interaction energies between solvent solvent solute solute and solute solvent molecules respectively Hamiltonian A contains a term Vas that causes the solvent
117. to transfer data between nodes in the MERGE1 subroutines has been dimensioned too small Action Standard user response Fix the parameter mxbuff Message 45 error too many atoms in CONFIG file DL_POLY Classic limits the number of atoms in the system to be simulated and checks for the violation of this condition when it reads the CONFIG file Termination will result if the condition is violated Action Standard user response Fix the parameter mxatms Consider the possibility that the wrong CONFIG file is being used e g similar system but larger size Message 46 error ewlbuf array too small in ewald1 The ewlbuf array used to store structure factor data in subroutine EWALD1 has been dimensioned too small Action Standard user response Fix the parameter mxebuf Message 47 error transfer buffer too small in merge The buffer used to transfer data between nodes in the MERGE subroutines has been dimensioned too small Action Standard user response Fix the parameter mxbuff Message 48 error transfer buffer too small in fortab The buffer used to transfer data between nodes in the FORTAB subroutines has been dimensioned too small Action Standard user response Fix the parameter mxbuff Message 49 error frozen core shell unit specified The DL_POLY Classic option to freeze the location of an atom i e hold it permanently in one posi tion is not permitted for core shell units This includes freezing the
118. two steps of a multi step and by extrapolation afterwards 2 6 1 The Replicated Data Strategy The Replicated Data RD strategy 57 is one of several ways to achieve parallelisation in MD Its name derives from the replication of the configuration data on each node of a parallel computer i e the arrays defining the atomic coordinates r velocities v and forces f for all N atoms i i 1 N in the simulated system are reproduced on every processing node In this strategy most of the forces computation and integration of the equations of motion can be shared easily and equally between nodes and to a large extent be processed independently on each node The method is relatively simple to program and is reasonably efficient Moreover it can be collapsed to run on a single processor very easily However the strategy can be expensive in memory and have high communication overheads but overall it has proven to be successful over a wide range of applications These issues are explored in more detail in 57 58 Systems containing complex molecules present several difficulties They often contain ionic species which usually require Ewald summation methods 12 59 and intra molecular interactions in addition to inter molecular forces These are handled easily in the RD strategy though the SHAKE algorithm 13 requires significant modification 45 The RD strategy is applied to complex molecular systems as follows 1 Using the known
119. with larger memory per processor Message 1640 error failed allocation of work arrays in nvtq_h2 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1650 error failed allocation of work arrays in nptq_b2 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor 262 STFC Section C 0 Message 1660 error failed allocation of density array in nptq_b2 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1670 error failed allocation of work arrays in nptq_h2 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1680 error failed allocation of density array in nptq_h2 f This is a memory allocation error Probable cause exce
120. work with rigid molecules This error results if these two options are simultaneously selected Action In some circumstances you may consider overriding this error message and continuing with your simulation For example if your simulation does not require the polarisability to be a feature of the rigid species but is confined to free atoms or flexible molecules in the same system The appropriate error trap is found in subroutine SYSDEF Message 95 error potential cutoff exceeds half cell width In order for the minimum image convention to work correctly within DL_POLY Classic it is neces sary to ensure that the cutoff applied to the pair potentials does not exceed half the perpendicular width of the simulation cell The perpendicular width is the shortest distance between opposing cell faces Termination results if this is detected In NVE simulations this can only happen at the start of a simulation but in NPT it may occur at any time Action Supply a cutoff that is less than half the cell width If running constant pressure calculations use a cutoff that will accommodate the fluctuations in the simulation cell Study the fluctuations in the OUTPUT file to help you with this Message 97 error cannot use shell model with neutral groups The dynamical shell model was not designed to work with neutral groups This error results if an attempt is made to combine both 226 STFC Section C 0 Action There is no genera
121. workstations for which it requires a FORTRAN 90 compiler and preferably a UNIX environment It has also been compiled for a Windows PC using both the GFORTRAN and G95 FORTRAN compiler augmented by the CygWin UNIX shell The Message Passing Interface MPI software is essential for parallel execution 1 3 4 Version Control System CVS DL_POLY Classic was developed with the aid of the CVS version control system We strongly rec ommend that users of DL POLY Classic adopt this system for local development of the DL_POLY Classic code particularly where several users access the same source code For information on CVS please contact info cvs requestQ gnu org or visit the website http www ccp5 ac uk DL_POLY _CLASSIC 1 3 5 Required Program Libraries DL_POLY Classic is for the most part self contained and does not require access to additional program libraries The exception is the MPI software library required for parallel execution Users requiring the Smoothed Particle Mesh Ewald SPME method may prefer to use a propri etary 3D FFT other than the one DLPFFT3 supplied with the package for optimal performance There are comments in the source code which provide guidance for applications on Cray and IBM computers which use the routines CCFFT3D and DCFT3 respectively Similarly users will find comments for the public domain FFT routine FFTWND_FFT 1 3 6 Internal Documentation All subroutines are supplied with a header blo
122. xAt 2 2 265 Text a 7 1 1 t u t 54t 2n 1 v t Lan pare rb At Eli Atu t AI 2 266 where 7 is obtained from standard Verlet leapfrog integration Only one iteration is needed two if the system has bond constraints to constrain the instantaneous temperature to exactly Text however energy is not conserved by this algorithm The algorithm is implemented in the DL_POLY routine NVT_El for systems with bond constraints The VV implementation of Evan s thermostat is as follows x t mito 0 mite e O e ult 5 At yy EE r t At r 1 A4tou t At call rattle R At f t At 2 m 1 At call ee x E At gt muvi t At f t At Y mu t At v tt At o t A vet At vet At S x i AWE At 2 267 62 STFC Section 2 5 Routines rattle R and rattle V apply the bondlength and velocity constraint formulae 2 251 and 2 252 respectively The integration is performed by the subroutine NVTVV_El which calls subroutines RATTLE_R and RATTLE_V 2 5 6 Barostats The size and shape of the simulation cell may be dynamically adjusted by coupling the system to a barostat in order to obtain a desired average pressure P xt and or isotropic stress tensor DL_POLY Classic has two such algorithms a Hoover barostat and the Berendsen barostat Only the former has a well defined conserved quantity 2 5 6 1 The Hoover Barostat DL_POLY Clas
123. 0 Nneb such that i 0 indicates state A and i Nnep indicates state B and RN RY i Nneb BN Eo 5 1 For convenience these configurations are called the beads of the NEB chain Each bead has a configuration energy which may be written as Ve RN This is the usual configuration energy for a system with an atomic structure RY 159 STFC Section 5 3 3 Each bead in the NEB chain is then connected to its two nearest neighbours by a harmonic spring except for the end beads which have only one neighbour each so that the beads make a chain strung from state A to state B The spring energy of the whole chain is then defined as Nneb KN Ha Y AV RP y 5 2 where kneb is the spring force constant 4 With the chain thus defined the objective is now to minimise the energy function E RX where Nneb 1 Y VEN 5 3 i 1 E BN 2 Z Vs BN nes in which the adjustable variables are the configurations RN i e the atomic coordinates in each structure while the chain end beads at RY and RN remain fixed 5 It is clear that the unconstrained configurations RV would normally relax into the nearest local minimum but that this cannot happen if they are sufficiently constrained by the har monic springs i e kneb is strong enough Thus the minimisation of the chain will tend to locate each bead in a position along a path between states A and B like a stretched necklace which approxima
124. 1 6605402 x 10723 Joules 10 J mol The unit of pressure P Eol3 is 1 6605402 x 107 Pascal 163 882576 atm Planck s constant A which is 6 350780719 x Est In addition the following conversion factors are used The coulombic conversion factor yo is 1 2 L do 138935 4835 E 4TE Lo such that Uuks EoYo U internal STFC Section 1 4 Where U represents the configuration energy The Boltzmann factor kg is 0 831451115 E K such that T Erin kb represents the conversion from kinetic energy in internal units to temperature in Kelvin Note In the DL_POLY Classic CONTROL and OUTPUT files the pressure is given in units of kilo atmospheres k atm at all times The unit of energy is either DL_POLY Classic units specified above or in other units specified by the user at run time The default is DL POLY units 1 3 11 Error Messages All errors detected by DL_POLY Classic during run time initiate a call to the subroutine ERROR which prints an error message in the standard output file and terminates the program All termi nations of the program are global i e every node of the parallel computer will be informed of the termination condition and stop executing In addition to terminal error messages DL_POLY Classic will sometimes print warning mes sages These indicate that the code has detected something that is unusual or inconsistent The detection is non fatal but the user shou
125. 177 i Fee 2 177 with gy the charge on an atom labelled and rj the magnitude of the separation vector r 7 1 The force on an atom 7 derived from this force is _ 1 aa rae Tij 2 178 1 43 STFC Section 2 4 with the force on atom 7 the negative of this The contribution to the atomic virial is 1 e r 2 179 47 EG Tij which is simply the negative of the potential term The contribution to be added to the atomic stress tensor is si 2 180 where a 8 are x y z components The atomic stress tensor is symmetric In DL_POLY Classic these forces are handled by the routines COULO and COULONEU 2 4 3 Truncated and Shifted Coulomb Sum This form of the Coulomb sum has the advantage that it drastically reduces the ranged of electro static interactions without giving rise to a violent step in the potential energy at the cutoff Its main use is for preliminary preparation of systems and it is not recommended for realistic models The form of the potential function is U r EY 2 2 181 A4meg Tij Teut with qe the charge on an atom labelled reut the cutoff radius and r the magnitude of the separation vector Ts its The force on an atom j derived from this potential within the radius reyz is 1 qiqi m 2 182 i Ane rg rij l with the force on atom 7 the negative of this The contribution to the atomic virial is which is not the negative of the potential term in this case
126. 3 rio q ra 2 84 The force on the atom arising from a tether potential is obtained using the general formula ae i 22 raat Trio Uro za 2 85 The contribution to be added to the atomic virial is given by W Tio fi 2 86 The contribution to be added to the atomic stress tensor is given by o r9 ff 2 87 where a and 8 indicate the x y z components The atomic stress tensor derived in this way is symmetric In DL_POLY Classic bond forces are handled by the routine TETHFRC 2 2 10 Frozen Atoms DL POLY Classic also allows atoms to be completely immobilised i e frozen at a fixed point in the MD cell This is achieved by setting all forces and velocities associated with that atom to zero during each MD timestep Frozen atoms are signalled by assigning an atom a non zero value for the freeze parameter in the FIELD file DL POLY Classic does not calculate contributions to the virial or the stress tensor arising from the constraints required to freeze atomic positions In DL_POLY Classic the frozen atom option cannot be used for sites in a rigid body As with the tethering potential the reference position is scaled with the cell vectors in constant pressure simulations In DL_POLY Classic the frozen atom option is handled by the subroutine FREEZE 27 STFC Section 2 3 2 3 The Intermolecular Potential Functions In this section we outline the pair body three body and four body potential functi
127. 3 5 Erin Figure 5 1 Model Potential Energy Surface The potential energy surface of a solid is characterised by deep energy basins such as Emin representing the various structural states Escape to other states i e diffusion must go via saddle points on the surface indicated by points E and Ey The energy differences Fy Emin or E2 Emin represent the activation energies E required to enable escape via the respective saddle points Thermal excitation alone is insufficient to achieve escape in a reasonable time The basic problem in simulating diffusion in solids is that each possible structure of the system is trapped in a deep basin in the potential energy surface see figure 5 1 representing a particular state For diffusion to occur the system must become sufficiently thermally excited to achieve the activation energy E necessary to escape In dimensions higher than 1 E represents a saddle point on the potenial energy surface Special techniques are required to accelerate the escape and achieve a measurable diffusion in a reasonable time These however must be devised so that the kinetic processes of the original system may be faithfully reconstructed Both the BPD and TAD methods in DL POLY Classic which are respectively described in sections 5 3 and 5 4 below satisfy this requirement 138 STFC Section 5 2 It is apparent from the discussion above that an important requirement in hyperd
128. 556 4 41 Tersoff J 1989 Phys Rev B 39 5566 4 31 120 121 van Gunsteren W F and Berendsen H J C 1987 Groningen Molecular Simulation GRO MOS Library Manual BIOMOS Nijenborgh 9747 Ag Groningen The Netherlands Standard GROMOS reference 4 13 Mayo S Olafson B and Goddard W 1990 J Phys Chem 94 8897 4 13 30 31 119 Weiner S J Kollman P A Nguyen D T and Case D A 1986 J Comp Chem 7 230 4 13 Smith W 2003 Daresbury Laboratory 4 9 83 105 187 195 Smith W and Forester T R 1994 Comput Phys Commun 79 52 5 Smith W and Forester T R 1994 Comput Phys Commun 79 63 5 57 59 Allen M P and Tildesley D J 1989 Computer Simulation of Liquids Oxford Clarendon Press 5 14 46 54 57 59 75 76 Ryckaert J P Ciccotti G and Berendsen H J C 1977 J Comput Phys 23 327 5 57 75 Andersen H C 1983 J Comput Phys 52 24 5 58 Fincham D 1992 Molecular Simulation 8 165 5 55 69 Miller T Eleftheriou M Pattnaik P Ndirango A Newns D and Martyna G 2002 J Chem Phys 116 8649 5 56 69 70 Forester T and Smith W 1998 J Computational Chemistry 19 102 5 55 56 71 Martyna G Tuckerman M Tobias D and Klein M 1996 Molec Phys 87 1117 5 60 70 Evans D J and Morriss G P 1984 Computer Physics Reports 1 297 5 55 56 59 Berendsen H J C Postma J P M va
129. AGS OBJ_MOD OBJ_PAR OBJ_SRC mv EX EXE gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt Check that a machine has been specified check Cif test FC undefined N then echo You must specify a target machine exit 99 fi gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt Clean up the source directory clean 205 STFC Section A rm f OBJ_MOD OBJ_PAR OBJ_SRC mod gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt tt Declare dependencies f o FC FFLAGS f c o CC c c 22 Declare dependency on module files OBJ_SRC 0BJ_MOD 206 Appendix B Periodic Boundary Conditions in DL_POLY Classic Introduction DL_POLY Classic is designed to accommodate a number of different periodic boundary conditions which are defined by the shape and size of the simulation cell Briefly these are as follows which also indicates the IMCON flag defining the
130. ATBOOK and recompile If you still encounter problems contact the authors 234 STFC Section C 0 Message 320 error site in multiple rigid bodies DL_POLY Classic has detected that a site is shared by two or more rigid bodies There is no integration algorithm available in this version of the package to deal with this type of model Action The only course is to redefine the molecular model e g introducing flexible bonds and angles in suitable places to allow DL POLY Classic to proceed Message 321 error quaternion integrator failed The quaternion algorithm has failed to converge If the maximum number of permitted iterations is exceeded the program terminates Possible causes include a bad starting configuration too large a time step used incorrect force field specification too high a temperature inconsistent constraints involving shared atoms etc Action Corrective action depends on the cause Try reducing the timestep or running a zero kelvin structure optimization for a hundred timesteps or so It is unlikely that simply increasing the iteration number will cure the problem but you can try follow the standard user response to increase the parameter mxquat But the trouble is much more likely to be cured by careful consideration of the physical system being simulated For example is the system stressed in some way Too far from equilibrium Message 330 error mxewld parameter incorrect DL_POLY Classic has t
131. B 2 230 Taj Anco 454n E 2R3 This expression unfortunately leads to large fluctuations in the system Coulombic energy due to the large step in the function at the cavity boundary In DL_POLY Classic this is countered by 52 STFC Section 2 4 subtracting the value of the potential at the cavity boundary from each pair contribution The term subtracted is T gt i 3 2 231 The effective pair force on an atom j arising from another atom n within the cavity is given by i He a Fl 233 The contribution of each effective pair interaction to the atomic virial is W Taj f 2 233 and the contribution to the atomic stress tensor is p 2 234 In DL POLY Classic the reaction field is handled by the routines COUL3 and COUL3NEU 2 4 10 Dynamical Shell Model An atom or ion is polarisable if it develops a dipole moment when placed in an electric field It is commonly expressed by the eguation L AE 2 235 where yp is the induced dipole and E is the electric field The constant a is the polarisability The dynamical shell model is a method of incorporating polarisability into a molecular dynamics simulation The method used in DL_POLY Classic is that devised by Fincham et al 49 and is known as the adiabatic shell model In the static shell model a polarisable atom is represented by a massive core and massless shell connected by a harmonic spring hereafter called the core shell unit The core and shell carry dif
132. CONTROL file format The file is free formatted integers reals and additional keywords are entered following the keyword on each record Real and integer numbers must be separated by a non numeric character preferably a space or comma to be correctly interpreted No logical variables appear in the control file Comment records beginning with a and blank lines may be added to aid legibility see example above The CONTROL file is not case sensitive e The first record in the CONTROL file is a header 80 characters long to aid identification of the file e The last record is a finish directive which marks the end of the input data Between the header and the finish directive a wide choice of control directives may be inserted These are described below 4 1 1 2 The CONTROL File Directives Users of the hyperdynamics features of DL_POLY Classic including nudged elastic band calcula tions should also consult Chapter5 where additional CONTROL directives specific to this function are described Similarly users of the solvation features energy decomposition free energy and sol vation induced spectral shifts should consult Chapter 6 The directives available for other functions are as follows directive meaning all pairs Use all pairs for calculating electrostatic interactions with multiple time step method cap f Cap forces during equilibration period fis maximum cap in units of kT A default f 1000 close time f Set job
133. Classic is identifying the atom pairs that cannot have a pair po tential between them by virtue of being chemically bonded for example see subroutine EXCLUDE Some of the working arrays used in this operation may be exceeded resulting in termination of the program Action Standard user response Fix the parameter mxexcl Message 66 error incorrect boundary condition for HK ewald The Hautman Klein Ewald method can only be used with XY planar periodic boundary conditions i e imcon 6 Action Either the periodic boundary condition or the choice of calculation of the electrostatic forces must be changed Message 67 error incorrect boundary condition in thbfre Three body forces in DL POLY Classic are only permissible with cubic orthorhombic and paral lelepiped periodic boundaries Use of other boundary conditions results in this error Action If nonperiodic boundaries are required the only option is to use a very large simulation cell with the required system at the centre surrounded by a vacuum This is not very efficient however and use of a realistic periodic system is the best option Message 69 error too many link cells required in thbfre The calculation of three body forces in DL_POLY Classic is handled by the link cell algorithm This error arises if the required number of link cells exceeds the permitted array dimension in the code Action Standard user response Fix the parameter mxcel1 Message 70
134. Classic these forces are handled by the routine COUL4 2 4 5 Coulomb Sum with Distance Dependent Dielectric As with the previous case this potential attempts to soften the impact of truncating the direct Coulomb sum It also assumes that the electrostatic forces are effectively screened in real systems an effect which is approximated by introducing a dielectic term that increases with distance 45 STFC Section 2 4 The interatomic potential for two charged ions is e 1 UO Arege Ti Tij with gy the charge on an atom labelled and rj the magnitude of the separation vector r 7 1 e r is the distance dependent dielectric function In DL POLY Classic it is assumed that this function has the form e r er 2 192 where e is a constant Inclusion of this term effectively accelerates the rate of convergence of the Coulomb sum The force on an atom 7 derived from this potential is 1 gq 155 2 193 i 2mEYE ri Taj with the force on atom 7 the negative of this The contribution to the atomic virial is which is 2 times the potential term The contribution to be added to the atomic stress tensor is given by gr Sie 2 195 where a 8 are x y z components The atomic stress tensor is symmetric In DL_POLY Classic these forces are handled by the routines COUL2 and COUL2NEU One last point to note is that the reaction field method can also be implemented with the damped shifted force Coulombic poten
135. D celli sa oox s Ko cra RR ee EE 211 xi Chapter 1 Introduction STFC Section 1 0 Scope of Chapter This chapter describes the concept design and directory structure of DL_POLY Classic and how to obtain a copy of the source code STFC Section 1 2 1 1 The DL POLY Classic Package DL_POLY Classic 1 is a molecular simulation package designed to facilitate molecular dynamics simulations of macromolecules polymers ionic systems solutions and other molecular systems on a distributed memory parallel computer The package was written to support the UK project CCP5 by Bill Smith and Tim Forester 2 under grants from the Engineering and Physical Sciences Research Council and is the copyright of the Science and Technology Facilities Council STFC DL_POLY Classic is based on a replicated data parallelism It is suitable for simulations of up to 30 000 atoms on up to 100 processors Though it is designed for distributed memory parallel machines we have taken care to ensure that it can with minimum modification be run on the popular workstations Scaling up a simulation from a small workstation to a massively parallel machine is therefore a useful feature of the package We request that our users respect the copyright of the DL POLY Classic source and not alter any authorship or copyright notices within Further information about the DL POLY Classic package can be obtained from our website http www ccp5 ac uk DL_POLY CLAS
136. FC Section 8 1 8 1 1 19 Test Case 19 Sodium chloride molecule in SPC water This is a repeat of test case 18 except that half of the water molecules are treated using constraint dynamics and the rest by rigid body dynamics The integration algorithm is NPT Hoover NPT Hoover ensemble 8 1 1 20 Test Case 20 Linked benzene ring molecules This test consists of pairs of benzene rings linked via a rigid constraint bond Each molecule has 22 atoms and there are 81 molecules making a total of 1782 sites The benzene rings are treated in a variety of ways in the same system In one third of cases the benzene rings and hydrogens form rigid groups In another third the carbon rings are rigid but the C H bonds are treated via constraints In the final third the C H bonds are fully flexible and the rings are rigid The MD cell is orthorhombic nearly cubic and the integration is NPT hoover NPT Hoover ensemble 8 1 1 21 Test Case 21 Aluminium metal with EAM potential This case presents an example of the use of the EAM potential for metals in this case aluminium The system is 256 atoms and runs under a berendsen NPT enemble 8 1 1 22 Test Case 22 Copper metal with EAM potential Another example of a metal with an EAM potential 256 copper atoms under a Berendsen NPT ensemble 8 1 1 23 Test Case 23 Copper Gold 3 1 alloy with Gupta potential This is an example of the analytical Gupta potential applied to a copper gold alloy with a 3 1 Cu Au ra
137. FUSOS e s oe pa Gd ee HR we RO ee ee ee eee a ee RO 140 5 3 1 Theory of Bias Potential Dynamics e tepu asi trp 140 Bae R nmine a BPD Similan s erw ei epon eee e eee Ge eRe SOs 143 Dao Full Path Wines se fhe RAE eee Re EERE REESE AREER 143 5 3 4 Things to Be Aware of when Running Full Path Kinetics BPD 146 5 3 5 Exploring Configurational Space ee 147 5 4 Temperature Accelerated Dynamics e e 147 5 4 1 Theory of Temperature Accelerated Dynamics 147 54 2 Tinie a TAD Simulatior ee ee oe as ee ed ee Re ee ee 150 bao Restertine a TAD Simulation aces ook ee Soe oe ek ewe S Be 153 vii STFC Contents 5 4 4 Things to Be Aware of when Running TAD 154 5 5 DL_POLY Classic Hyperdynamics Files 02005204 e 154 5 6 Tidying Up the Results of a Hyperdynamics Simulation 157 5 0 1 Refining the Results xo hee ee k ee 157 5 6 2 Treatment of Multiple Maxima in the Reaction Path 158 5 7 Running a Nudged Elastic Band Calculation osoa oa a a 158 5 7 1 Things to be Aware of when Running a NEB Calculation 159 6 Solvation 161 6 1 Overview and Background ss soa dogh Re RR a OE Ps 163 6 2 DL_POLY Energy Decomposition s sess esans resc rp dua mkr 163 A 2 4 So aene fee RA ee Be Ae Re Ge Ge e S 163 6 2 2 Invoking the DL_POLY Energy Decomposition Option 164 62 3 The SOLVAT
138. For this reason DL POLY Classic has available a selection of structure relaxation methods Broadly speaking these are energy minimisation algorithms but their role in DL POLY Classic is not to provide users with true structural optimisation procedures capable of finding the ground state structure They are simply intended to help users improve the quality of the starting structure prior to a dynamical simulation The available algorithms are 1 Zero temperature molecular dynamics This is equivalent to a dynamical simulation at low temperature At each time step the molecules move in the direction of the computed forces and torques but are not allowed to acquire a velocity larger than that corresponding to a temperature of 1 Kelvin The subroutine that performs this procedure is ZERO_KELVIN which is found in the file OPTIMISER_MODULE F 2 Conjugate Gradients CG minimisation This is nominally a simple minimisation of the system configuration energy using the conjugate gradients method 61 The algorithm coded into DL_POLY Classic allows is an adaptation that allows for rotation and translation of rigid bodies Rigid contraint bonds however are treated as stiff harmonic springs a strategy which we find does allow the bonds to converge within the accuracy required by SHAKE The subroutine that performs this procedure is STRUCOPT which is found in the file OPTI MISER_MODULE F 3 Programmed energy minimisation involving both m
139. IMDEF if the ewald precision directive is used The first few records of a typical CONFIG file are shown below Lennard Jones Argon 2 3 255 176595 066855 21 023998260000 0 000000000000 O 000000000000 Ar 1 7 798997031 2 12339759919 417 940093856 Ar 2 2 821617729 1 07786776343 188 920889755 Ar 3 8 113009749 0 388066563418 O 000000000000 21 023998260000 0 000000000000 2 409934763 1 85576903413 292 432569373 0 7180021261 2 773816641 1 37628108908 0 000000000000 0 000000000000 21 023998260000 5 506441637 0 125163024806 472 434039806 7 417288159 0 168433841280E 01 0 269392807911 413 545510271 294 149380530 5 199345225 1 24723236452 608 168259627 422 414753563 250 737138386 Ar 4 10 31216635 1 76536230573 66 0234000384 2 857971798 1 58904200978 47 6492437764 8 090920140 2 48066272817 90 0074615387 etc 4 1 2 1 Format The file is fixed formatted integers as i10 reals as f20 0 The header record is formatted as 80 alphanumeric characters 4 1 2 2 Definitions of Variables record 1 header a80 title line record 2 levcfg integer COMFIG file key See table 4 5 for permitted values imcon integer Periodic boundary key See table 4 6 for permitted values natms integer Number of atoms in file engcfg real Configuration energy in DL_POLY units record 3 omitted if imcon 0 cell 1 real x component of a cell vector cell 2 re
140. If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 2080 error failed allocation of nstvv_h1 f densO array This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 2090 error failed allocation of nstvv_b1 f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 2100 error failed allocation of nveqvv_1 f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor 271 STFC Section C 0 Message 2110 error failed allocation of nveqvv_2 f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 2120 erro
141. It may be possible to override this error trap but it is up to the user to establish if this is sensible Action This is a non recoverable error unless the user chooses to override the restriction Message 350 error too few degrees of freedom This error can arise if a small system is being simulated and the number of constraints applied is too large Action Simulate a larger system or reduce the number of constraints Message 360 error frozen atom found in rigid body DL_POLY Classic does not permit a site in a rigid body to be frozen i e fixed in one location in space Action Remove the freeze condition from the site concerned Consider using a very high site mass to achieve a similar effect Message 380 error simulation temperature not specified DL_POLY Classic has failed to find a temp directive in the CONTROL file Action Place a temp directive in the CONTROL file with the required temperature specified Message 381 error simulation timestep not specified DL_POLY Classic has failed to find a timestep directive in the CONTROL file Action Place a timestep directive in the CONTROL file with the required timestep specified Message 382 error simulation cutoff not specified DL POLY Classic has failed to find a cutoff directive in the CONTROL file Action Place a cutoff directive in the CONTROL file with the required forces cutoff specified 236 STFC Section C 0 Message 383
142. LES already exist then carefully archive the data before deleting the contents Do not empty these directories if continuing restarting the simulation in the original starting basin The information in these directories is still live in this case Further information on these files can be found in section 5 5 5 Run the TAD simulation This will perform a simulation at the high temperature requested checking for structural transitions at the intervals specified Each time it finds a structural transition it will record the new state determine the activation energy transition pathway and stopping time then revert back to the starting basin and continue 6 When the simulation ends proceed as follows a Check the EVENTS file to see if any structural transitions have been obtained Each event is represented by a single record and transitions are flagged with the keyword TRA at the start of the record Use unix grep to locate these entries No observed transitions indicates either a longer simulation is necessary or a higher temperature simulation should be considered b Check that the simulation was sufficiently long to guarantee all high temperature tran sitions have been found that are compliant with the specified reliability deltad The estimated stop time derived from this factor appears as the last entry of the TRA record in the EVENTS file c If the simulation stop time has not been reached the job must be resta
143. L_POLY Classic are as follows 1 Cosine potential cos U Pijkn A 1 cos Mdijkn 9 2 36 2 Harmonic harm U ijkn klijen boy 2 37 3 Harmonic cosine hcos Ul Gin gt c0s bijkn cos 60 2 38 20 STFC Section 2 2 4 Triple cosine cos3 U d 5Au 1 cos 5 Aa 1 cos 26 5As 1 c0s 36 239 5 Ryckaert Bellemans hydrocarbon potential ryck 5 U dijkn Alao Z acorta 2 40 6 Ryckaert Bellemans fluorinated potential rbf U dijkn B bo Yoo 2 41 7 OPLS angle potential U dijkn ao 0 5 a1 1 cos 6 aa 1 cos 26 az 1 cos 3 2 42 In these formulae 6 j4 is the dihedral angle defined by Pigkn cos BC ri Tito Tin 2 43 with Lij x Tik Lik X Thn 2 44 Tij x Tikl Tjk rey With this definition the sign of the dihedral angle is positive if the vector product r j X rjg X Lik X Ten is in the same direction as the bond vector rj and negative if in the opposite direction The force on an atom arising from the dihedral potential is given by B rij Tiks Tkn o f Tarp V Piden 2 45 with being one of i j k n and a one of x y z This may be expanded into o 1 o o gra V Piika Ei Toat U Dijen gpa B Eig Ejk Ek 2 46 The derivative of the function B rij Tik kn iS 0 1 o a O Eo ee Bal OPH A Tan 2 47 cos dijkn 1 0 P 1 0 2 rij x Cl are rij rep Iri
144. ME routines have not been compiled in The inclusion of the SPME algorithm in DL_POLY Classic is optional at the compile stage If the executable does not contain the SPME routines but the method is requested by the user this error results Action DL_POLY Classic must be recompiled with the SPME flags set Beware that your system has the necessary fast Fourier transform routines to permit this Message 516 error repeat of impact option specified More than one impact option has been specified in the CONTROL file Only one is allowed Action Remove the offending impact directive from the CONTROL file and rerun Message 601 error Ewald SPME incompatible with solvation The options in DL_POLY Classic that use the energy decomposition solvation facility do not per mit the use of the SPME option It is possible however to use the standard Ewald method Action Change the SPME directive in the CONTROL file to ewald and rerun 250 STFC Section C 0 Message 602 error Ewald HK incompatible with solvation The options in DL_POLY Classic that use the energy decomposition solvation facility do not per mit the use of the Hautman Klein Ewald option It is possible however to use the standard Ewald method Action Change the HKE directive in the CONTROL file to ewald Make sure the system model includes a large vacuum gap between material slabs to offset the effects of the periodic boundary Message 1000 error failed allocati
145. MF parameter mxpmf too small in passpmf The bookkeeping arrays have been exceeded in PASSPMF Action Standard user response Fix the parameter mxpmf Set equal to mxatms Message 492 error parameter mxcons lt number of PMF constraints The parameter mxcons is too small for the number of PMF constraints in the system 248 STFC Section C 0 Action Standard user response Fix the value of mxcons Message 494 error in csend pvmfinitsend The PVM routine PVMFINITSEND has returned an error It is invoked by the routine CSEND Action Check your system implementation of PVM Message 496 error in csend pvmfpack The PVM routine PVMFPACK has returned an error It is invoked by the routine CSEND Action Check your system implementation of PVM Message 498 error in csend pvmfsend The PVM routine PVMFSEND has returned an error It is invoked by the routine CSEND Action Check your system implementation of PVM Message 500 error in crecv pvmfrecv The PVM routine PVMFRECV has returned an error It is invoked by the routine CRECV Action Check your system implementation of PVM Message 502 error in crecv pymfunpack The PVM routine PVMFUNPACK has returned an error It is invoked by the routine CRECV Action Check your system implementation of PVM Message 504 error cutoff too large for TABLE file The requested cutoff exceeds the information in the TABLE file Action Reduce the value of t
146. REVOLD The first three files are mandatory while files TABLE and TABEAM TAB EAM in the figure are used only to input certain kinds of pair potential and are not always required REVOLD is required only if the job represents a continuation of a previous job In the following sections we describe the form and content of these files Note In addition to the files described in this chapter users of the hyperdynamics features of DL_POLY Classic should see Chapter 5 where additional files specific to that purpose are described Users are strongly advised to study the example input files appearing in the data sub directory to see how different files are constructed 4 1 1 The CONTROL File The CONTROL file is read by the subroutine SIMDEF and defines the control variables for running a DL POLY Classic job It makes extensive use of directives and keywords Directives are 95 STFC Section 4 1 character strings that appear as the first entry on a data record or line and which invoke a particular operation or provide numerical parameters Also associated with each directive may be one or more keywords which may qualify a particular directive by for example adding extra options Directives have the following general form keyword options data The keyword and options are text fields while the data options are numbers integers or reals Directives can appear in any order in the CONTROL file except for the finish directive which
147. ROR i e node 0 will print the error message The variable message_number is an integer used to identify the appropriate message to be printed In all cases if ERROR is called with a non negative message number the program run terminates If the message number is negative execution continues but even in this case DL_POLY Classic will terminate the job at a more appropriate place This feature is used in processing the CONTROL and FIELD file directives A possible modification users may consider is to dump additional data before the call to ERROR is made A full list of the DL_POLY Classic error messages and the appropriate user action can be found in Appendix C of this document 92 Chapter 4 Data Files 93 STFC Section 4 0 Scope of Chapter This chapter describes all the input and output files for DL_POLY Classic examples of which are to be found in the data sub directory 94 STFC Section 4 1 4 1 The INPUT files REVCON OUTPUT HISTORY STATIS CONFIG CONTROL TAB EAM REVOLD ZDNDAT REVIVE Figure 4 1 DL POLY Classic input and output files Input files appear on the left and output files on the right Files marked with an asterisk are non mandatory File CFGMIN not shown appears as an output file if the user selects the programmed minimisation option see 3 2 4 In normal use DL_POLY Classic requires six input files named CONTROL CONFIG FIELD TABLE TABEAM and
148. SIC 1 2 Functionality The following is a list of the features DL_POLY Classic 1 2 1 Molecular Systems DL_POLY Classic will simulate the following molecular species 1 Simple atomic systems and mixtures e g Ne Ar Kr etc 2 Simple unpolarisable point ions e g NaCl KCl etc 3 Polarisable point ions and molecules e g MgO H20 etc D 4 Simple rigid molecules e g CCl4 SFe Benzene etc 5 Rigid molecular ions with point charges e g KNO3 NH1 2SOu etc 6 Polymers with rigid bonds e g C Han 2 7 Polymers with rigid bonds and point charges e g proteins 8 Macromolecules and biological systems 9 Molecules with flexible bonds 10 Silicate glasses and zeolites 11 Simple metals and alloys e g Al Ni Cu etc 12 Covalent systems e g C Si Ge SiC SiGe etc STFC Section 1 2 1 2 2 The DL POLY Classic Force Field The DL_POLY Classic force field includes the following features 1 All common forms of non bonded atom atom potential 2 Atom atom site site Coulombic potentials Valence angle potentials Dihedral angle potentials Inversion potentials Improper dihedral angle potentials 3 body valence angle and hydrogen bond potentials 4 body inversion potentials Finnis Sinclair and embedded atom type density dependent potentials for metals 3 4 10 The Tersoff density dependent potential for covalent systems 5 The parameters describing many of these these potentials may be obtained
149. T Halo 65 STFC Section 2 5 wi LO Salts fan ult 5AM EL 1 r t4 At r t At u t At call rattle R 1 V t At V t exp sat n t 540 H t At exp at n t 5A1 H t ui E At o At De S a0 call rattle V net At nerian Aas n t At Pog xlt ADT r n t At At v t At nte At u t At x t At x t At E At Text UE rt At Ok p Text v t At V t A1 xt At v t At 2 277 Routines rattle R and rattle V apply the bondlength and velocity constraint formulae 2 251 and 2 252 respectively The equations have the same conserved variable HysT as the LF scheme The integration is performed by the subroutine NVTVV H1 which calls subroutines RATTLE_R RATTLE_V NSTSCALE_T and NSTSCALE_P 2 5 6 2 Berendsen Barostat With the Berendsen barostat the system is made to obey the equation of motion Pax P tp 2 278 Cell size variations In the isotropic implementation at each step the MD cell volume is scaled by by a factor 7 and the coordinates and cell vectors by 7 3 where At y 1 Bea P 2 279 and is the isothermal compressibility of the system The Berendesen thermostat is applied at the same time In practice 6 is a specified constant which DL POLY Classic takes to be the isothermal compressibility of liquid water The exact value is not critical to the algorithm as it relies on the ratio Tp G Tp is spe
150. The DL POLY Classic User Manual W Smith T R Forester and I T Todorov STFC Daresbury Laboratory Daresbury Warrington WA4 4AD Cheshire UK Version 1 9 April 2012 STFC Preface About DL_POLY Classic DL_POLY Classic is a parallel molecular dynamics simulation package developed at Daresbury Laboratory by W Smith T R Forester and I T Todorov under the auspices of the Engineering and Physical Sciences Research Council EPSRC for the EPSRC s Collaborative Computational Project for the Computer Simulation of Condensed Phases CCP5 and the Computational Science and Engineering Department at Daresbury Laboratory The package is the copyright of the Science Facilities Research Council STFC of the United Kingdom DL_POLY Classic is derived from the DL POLY 2 package written by W Smith and T R Forester DL_POLY Classic is issued free under a BSD licence under the terms of which the source code may be freely modified and distributed as long as the copyright statements in the code are retained and proper acknowledgement is made of the authors and Daresbury Laboratory as the place of origin The purpose of the DL_POLY Classic package is to provide software for scientific research that is free accessible and documented STFC Preface Disclaimer None of the authors nor any of the organisations STFC EPSRC CCP5 nor any contributor to the DL_POLY Classic package or its derivatives guarantee that the software and associated
151. This message results when DL POLY Classic reaches the end of the CONTROL file without hav ing read all the data it expects Probable cause missing finish directive Action Check CONTROL file and correct Message 54 error problem reading CONFIG file This message results when DL POLY Classic encounters a problem reading the CONFIG file Pos sible cause corrupt data Action Check CONFIG file and correct Message 55 error end of CONFIG file encountered This error arises when DL_POLY Classic attempts to read more data from the CONFIG file than is actually present The probable cause is an incorrect or absent CONFIG file but it may be due to the FIELD file being incompatible in some way with the CONFIG file 220 STFC Section C 0 Action Check contents of CONFIG file If you are convinced it is correct check the FIELD file for inconsistencies Message 57 error too many core shell units specified DL_POLY Classic has a restriction of the number of types of core shell unit in the FIELD file and will terminate if too many are present Do not confuse this error with that described by message 59 below Action Standard user response Fix the parameter mxtshl Message 59 error too many core shell units in system DL_POLY Classic limits the number of core shell units in the simulated system Termination re sults if too many are encountered Do not confuse this error with that described by message 57 above
152. UTPUT mv REVIVE data TEST 1 2 REVIVE mv REVCON data TEST 1 2 REVCON if e TABLE then mv TABLE data TEST 1 2 TABLE endif if e TABEAM then mv TABEAM data TEST 1 2 TABEAM endif if e STATIS then mv STATIS data TEST 1 2 STATIS endif if e RDFDAT then mv RDFDAT data TEST 1 2 RDFDAT endif if e ZDNDAT then mv ZDNDAT data TEST 1 2 ZDNDAT endif if e CFGMIN then mv CFGMIN data TEST 1 2 CFGMIN endif which first creates a new DL_POLY data TEST if necessary sub directory and then moves the standard DL_POLY output data files into it store requires two arguments storen a where n is a unique string or number to label the output data in the data TESTn sub directory and a is the character string LF VV RB or CB according to which algorithm leapfrog LF ve locity Verlet VV RB rigid body minimisation or CB constraint bond minimisation has been performed 198 STFC Section 9 1 9 1 1 8 supa The supa macro provides a convenient way of running the DL POLY test cases in batch mode It is currently structured to submit batch jobs to the Daresbury Xeon cluster but can easily be adapted for other machines where batch queuing is possible The key statement in this context in the qsub commmand which submits the gopoly script described above This statement may be replaced by the equivalent batch queuing command for your machine The text of supa is given below bin tcsh
153. V 3V di Or T gt e pi Ba Opis Tis 2 Tij i 1 j i Opi Op Orij 1 EAM virial The same as above 2 Finnis Sinclair virial 1 N v 5 gt Ari c co criz car rij O er 2earij Tij i 1 j i TENA i 1 rij d Y 2222 2 rij d 38 p rija 2 150 2 i l Ai VPi VP d 3 Sutton Chen virial Y DO i 1 jf Tij DA E 5 e l 2 151 2 2 2 2 VP yo Nro 37 STFC Section 2 3 4 Gupta virial a Ap Tij PO Y 23 exp p a Tij N Ba gt 1 1 2 Tij 2 exp 2qi rij 2 152 i 1 j i 0 VPi VP ro The contribution to be added to the atomic stress tensor is given by Wa Va ot Ser 2 153 where a and 6 indicate the x y z components The atomic stress tensor is symmetric The long ranged correction for the DL_POLY Classic metal potential is in two parts Firstly by analogy with the short ranged potentials the correction to the local density is CO pi X A j Lj i Tij lt Tmet Tij Tmet pi J pulru Dd puly pi 6p 2 154 j 1 j i j LjiAi Co dp 4rp pij r dr 5 2 155 Tmet where p is the uncorrected local density and pis the mean particle density Evaluating the integral part of the above equation yields 1 EAM density correction No long ranged corrections apply beyond ret 2 Finnis Sinclair density correction No long ranged corrections apply beyond cutoffs c and d 3 Sutton Chen density correction
154. Y file is appended at intervals specified by the traj directive in the CONTROL file with the following information for each configuration record i a8 4i10 f12 6 timestep as the character string timestep nstep integer the current time step natms integer number of atoms in configuration keytrj integer trajectory key again imcon integer periodic boundary key again 127 STFC Section 4 2 tstep real integration timestep record ii 3g12 4 for imcon gt 0 cell 1 real x component of a cell vector cell 2 real y component of a cell vector cell 3 real z component of a cell vector record iii 3g12 4 for imcon gt 0 cell 4 real x component of 6 cell vector cell 5 real y component of b cell vector cell 6 real z component of b cell vector record iv 3g12 4 for imcon gt 0 cell 7 real x component of c cell vector cell 8 real y component of c cell vector cell 9 real z component of c cell vector This is followed by the configuration for the current timestep i e for each atom in the system the following data are included record a a8 i10 2f 12 6 atmnam a8 iatm i10 weight f12 6 charge f12 6 record b 3e12 4 XXX real yyy real ZZZ real record c 3e12 4 only for keytrj gt 0 VXX real vyy real VZZ real record d 3e12 4 only for keytrj gt 1 xx real fyy real fzz real atomic label atom index atomic mass a m u atomic charge e x coordinate y coordinate z coordinate x comp
155. _module o property_module o rigid_body_module o angles_module o bonds_module o shake_module o inversion_module o dihedral_module o core_shell_module o exclude module o ewald module o coulomb module oN external field module o four body module o N hkewald module o metal module o ensemble tools module o N temp scalers module o three body module o spme_module o N tersoff module o neu_coul_module o N nlist builders module o forces module o N lf motion module o 1f_rotation1_module o lf rotation2 module o vv motion module o vv rotation1 module o vv_rotation2_module o pmf module o integrator module o optimiser module o N hyper dynamics module o driver module o define system module o 204 STFC Section A 0 OBJ_SRC dlpoly o OBJ_PAR basic_comms o merge_tools o pass_tools o Define targets all echo Error please specify a target machine echo Permissible targets for this Makefile are echo pe echo gfortran parallel echo woodcrest parallel echo i echo Please examine Makefile for details system specific targets follow gfortran MAKE FC mpif90 LD mpif90 o LDFLAGS 02 ffast math FFLAGS c 02 ffast math EX EX BINROOT BINROOT TYPE woodcrest MAKE LD mpif90 o LDFLAGS FC mpif90 FFLAGS c 03 EX EX BINROOT BINROOT TYPE Default code for parallel MPI execution par check 0BJ_MOD OBJ_PAR OBJ_SRC LD EX LDFL
156. a 4 real data item 4 4 1 5 3 Further Comments It should be noted that the number of grid points in the TABLE file should not be less than the num ber of grid points DL POLY Classic is expecting This number is given by the parameter mxgrid 124 STFC Section 4 1 which is defined in the PARSET F subroutine in the SETUP_PROGRAM F file DL POLY Classic will re interpolate the tables if ngrid gt mxgrid but will abort if ngrid lt mxgrid The potential and force tables are used to fill the internal arrays vvv and ggg respectively see section 2 3 1 The contents of force arrays are derived from the potential via the formula G r U 1 r 5 U r Note this is a virial expression and not the same as the true force Important The potential and force arrays in the TABLE file are written in the same units as the FIELD file So if you specified a particular unit using the UNITS directive in the FIELD file the same units are expected here It is useful to note that the definition of the force arrays given above means that the units are the same as for the potential i e are handled using the same conversion factors 4 1 6 The TABEAM File The TABEAM file contains the tabulated potential functions no explicit analytic form describing the metal interactions in the MD system This file is read by the subroutine METTAB The EAM potential for an n component metal alloy requires the specification of n electron density functions one for
157. a grant from the Franco British Alliance fund 4 The metadynamics features were developed by David Quigley and Mark Rodger at the Uni versity of Warwick ili STFC Preface Manual Notation In the DL_POLY Classic User Manual specific fonts are used to convey specific meanings 1 2 directories itallic font indicate unix file directories ROUTINES small capitals indicate subroutines functions and programs macros sloped text indicates a macro file of unix commands directive bold text indicates directives or keywords variables typewriter text indicates named variables and parameters FILE large capitals indicate filenames Contents The DL_POLY Classic User Manual About DL_POLY Classic Disclaimer occ Acknowledgements Manual Notation Contents List of Tables List of Figures 1 Introduction 1 1 The DL_POLY Classic Package 1 2 Fu unchionalty lt lt cage da 48a 4 be ke bE ek we ee Bee Se ha SSS 1 2 1 Molecular Systems o c so ose 4 200445 eee ee es 1 2 2 The DL_POLY Classic Force Field o 1 2 3 Boundary Conditions ls oc sursa ma aa a a GO 1 2 4 The Java Graphical User Interface ooo Lap E ie Programming Style ou a bow a A ee Pg ee Bs ee a Le Programm Language ercer Bo bone A a oe ES 1 3 2 Memory Management 0020 ee eee ee eee 1 3 3 Target Computers o s atat d p eee we be eae a ba ee 134
158. a simulation will reproduce the diffusional path obtained in the original system but at an accelerated rate An early difficulty with BPD was defining the bias potential However a particularly convenient form has been devised by Hamelberg et al 64 which has the form Ebias E V RY E Py S X Wrias R A Evias Vii a Erias z vB 5 7 where a is a constant that controls the curvature of the bias potential see below Ebias is a fixed potential energy level above which the bias potential Woias RY becomes zero and the unbiased potential is restored This is controlled by H x a Heaviside function which is zero if the argument x lt 0 and 1 ifx gt 0 Thus setting Ebias correctly provides a means to preserve the structure of the saddle points of the original surface Note however that the user must determine a safe value 141 STFC Section 5 3 for this A value of Epias set above the value of the activation energy E anywhere on the surface invalidates Voter s condition 5 6 Using the definition of the bias potential 5 7 it is easy to show that the atomic forces in the biased system are given by Pe f 2 g N j Ebias gt V R 5 8 t Frias aa i l When Ebias lt V RN the atomic forces are the same as for the unbiased system The constant a in equation 5 7 plays an important role If it is set to zero then Vpias RY Ebias 1 e the biased system potential 5 4 becomes
159. abelled itype The dimension niypye will be 2 3 or 4 if the term represents a bond angle or dihedral 4 The array keytype Ntypes itype is used to identify the atoms in a bonded term and the ap propriate form of interaction and thus to calculate the energy and forces Each processor is assigned the independent task of evaluating a block of Int Niotar Nnodes interactions The same scheme works for all types of bonded interactions The global summation of the force arrays does not occur until all the force contributions including nonbonded forces has been completed 2 6 3 Distributing the Nonbonded Terms In DL_POLY Classic the nonbonded interactions are handled with a Verlet neighbour list 12 which is reconstructed at intervals during the simulation This list records the indices of all secondary atoms within a certain radius of each primary atom the radius being the cut off radius reut normally applied to the nonbonded potential function plus an additional increment Ars The larger radius reut Arcuz permits the same list to be used for several timesteps without requiring an update The frequency at which the list must be updated clearly depends on the thickness of the region Ar In RD the neighbour list is constructed simultaneously on each node and in such a way as to share the total burden of the work equally between nodes Each node is responsible for a unique set of nonbonded interactions and the neighbour list is
160. aced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1390 error failed allocation of work arrays in nvt_el f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1400 error failed allocation of work arrays in nvt_b1 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1410 error failed allocation of work arrays in nvt_h1 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1420 error failed allocation of work arrays in npt_b1 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1430 error failed allocation of density array in npt_b1 f This is a memor
161. ailable If this is not an option investigate the possibility of increasing the heap size for your application Talk to your systems support people for advice on how to do this Message 36 error failed fmet array allocation in mettab DL_POLY Classic is unable to allocate the fmet array in the definition of an EAM potential Action Most probable cause is working too near the memory limit for the machine Try using more processors to free up some memory Check the TABEAM file in case the data are incorrectly specified Message 40 error too many bond constraints specified DL_POLY Classic sets a limit on the number of bond constraints that can be specified in the FIELD file Termination results if this number is exceeded See FIELD file documentation Do not confuse this error with that described by message 41 below Action Standard user response Fix the parameter mxtcon Message 41 error too many bond constraints in system DL_POLY Classic sets a limit on the number of bond constraints in the simulated system as a whole This number is a combination of the number of molecules and the number of per molecule divided by the number of processing nodes Termination results if this number is exceeded Do not confuse this error with that described by message 40 above Action Standard user response Fix the parameter mxcons 218 STFC Section C 0 Message 42 error transfer buffer too small in mergel The buffer used
162. air module f pmf_module f property_module f rigid_body_module f shake_module f site_module f solvation_module f spme_module f three_body_module f 282 STFC Section D O alloc_ter_arrays alloc_tet_arrays alloc_vdw_arrays angfrc bndfrc bodystress bomb bpd forces bpd option bspcoe bspgen cell propagate cell update cerfr cfgscan check_basins check_for_transition check_shells check_syschg compute_bias_potential comput_steinhardt compute_steinhardt_forces compute_tet_nlist compute_tetrahedral compute_tetrahedral_forces config write conscan copy_force copystring corshl could coulOneu coull coul2 coul2neu coul3 coul3neu coul4 coul_nsq cpy_rtc crecv crecv csend csend dblstr dcell define_angles define_atoms define_bonds subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine function subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine function subroutine subroutine subroutine subroutine tersoff_module f tether_module f vdw_module f angles_module f bonds_module f rigid_
163. al parameter see table 4 11 variable 4 real potential parameter see table 4 11 This directive and associated data records need not be specified if the molecule contains no tethered atoms See the note on the atomic indices appearing under the shell directive above Table 4 11 Tethering potentials key potential type Variables 1 3 functional form harm Harmonic k U r 5kr rhrm Restraint k lr U r ikr r lt Te U 5kr2 kro r re ro quar Quartic k k k U r Er K r3 E rt 13 finish This directive is entered to signal to DL POLY Classic that the entry of the details of a molecule has been completed The entries for a second molecule may now be entered beginning with the name of molecule record and ending with the finish directive The cycle is repeated until all the types of molecules indicated by the molecules directive have been entered The user is recommended to look at the example FIELD files in the data directory to see how typical FIELD files are constructed 4 1 3 3 Non bonded Interactions Non bonded interactions are identified by atom types as opposed to specific atomic indices The first type of non bonded potentials are the pair potentials The input of pair potential data is signalled by the directive vdw n 116 STFC Section 4 1 where n is the number of pair potentials to be entered There follows n records each specifying a particular pair pote
164. al y component of a cell vector cell 3 real z component of a cell vector record 4 omitted if imcon 0 cell 4 real x component of b cell vector 104 STFC Section 4 1 cell 5 real y component of b cell vector cell 6 real z component of b cell vector record 5 omitted if imcon 0 cell 7 real x component of c cell vector cell 8 real y component of c cell vector cell 9 real z component of c cell vector Subsequent records consists of blocks of between 2 and 4 records depending on the value of the levcfg variable Each block refers to one atom The atoms must be listed sequentially in order of increasing index Within each block the data are as follows record i atmnam a8 atom name index integer atom index atmnum integer atomic number record ii XXX real x coordinate yyy real y coordinate ZZZ real z coordinate record iii included only if levcfg gt 0 VXX real x component of velocity vyy real y component of velocity VZZ real x component of velocity record iv included only if levcfg gt 1 xx real x component of force fyy real y component of force fzz real z component of force Note that on record i only the atom name is mandatory any other items are not read by DL_POLY Classic but may be added to aid alternative uses of the file for example the DL_POLY Classic Graphical User Interface 9 4 1 2 3 Further Comments The CONFIG file has the same format as the output files REVCON section 4 2 3 and CFGMIN sect
165. an expensive operation if M gt 3 Once the free energy is mapped onto fewer dimensions the free energy barrier heights and free energy differences can be read off directly 2 Following the system trajectory It is often useful to track the trajectory of the system in the space of the order parameters to see how well the simulation is exploring that space For this purpose is is possible to plot the contents of the METADYNAMICS file graphically in a selection of 2D sections Simple graphics are generally sufficient for this purpose Alternatively the HISTORY file may be viewed as a movie using packages such as VMD 74 to show the transformations that occur 184 Chapter 8 Example Simulations 185 STFC Section 8 0 Scope of Chapter This chapter describes the standard test cases for DL_POLY Classic the input and output files for which are in the data sub directory 186 STFC Section 8 1 8 1 DL POLY Examples 8 1 1 Test Cases The following example data sets both input and output are stored in the subdirectory data Two versions are provided for the Leapfrog LF and Velocity Verlet VV algorithms respectively so that you may check that your version of DL_POLY is working correctly All the jobs are short and should require no more than a few minutes execution time even on a single processor computer The test cases can be chosen by typing select na from the execute directory where n is the number of the test c
166. and fix the error Message 30 error too many chemical bonds specified DL_POLY Classic sets a limit on the number of chemical bond potentials that can be specified in the FIELD file Termination results if this number is exceeded See FIELD file documentation Do not confuse this error with that described by message 31 below Action Standard user response Fix parameter mxtbnd Message 31 error too many chemical bonds in system DL_POLY Classic sets a limit on the number of chemical bond potentials in the simulated system as a whole This number is a combination of the number of molecules and the number of bonds per molecule divided by the number of processing nodes Termination results if this number is exceeded Do not confuse this error with that described by message 30 above Action Standard user response Fix the parameter mxbond Message 32 error integer array memory allocation failure DL_POLY Classic has failed to allocate sufficient memory to accommodate one or more of the in teger arrays in the code Action This may simply mean that your simulation is too large for the machine you are running on Consider this before wasting time trying a fix Try using more processing nodes if they are available If this is not an option investigate the possibility of increasing the heap size for your application Talk to your systems support people for advice on how to do this Message 33 error real array memory alloca
167. and solute to interact while H has no such interaction The mixed Hamiltonian in this case is Ay Ks Ka Vss Vaa 1 A Vas 6 5 It will be appreciated that when A is 0 this Hamiltonian represents the solution of A in S and when A is 1 it represents complete independence of the solute and solvent from each other The Hamiltonian thus encapsulates the process of solvation It should also be noted that there is no scaling of the kinetic energy in this case so instabilities are not expected in the dynamics when A is near 0 or 1 Following the above prescription we see that in this case dF T Vas 6 6 and A Argas f Vas d 6 7 This equation represents the free energy difference between the free solvent and solute and the solution The quantity A F32 is thus the free energy of solution 6 3 2 Nonlinear Mixing As mentioned above the linear mixing of Hamiltonians represented by equations 6 1 and 6 5 gives rise to poor statistical convergence of the required averages when A approaches either 0 or 1 167 STFC Section 6 3 One way to reduce the effect this has on the quality of the free energy calculation is to introduce weighting into the averaging process so that poor convergence of the averages at the extremes of A is of less importance This is done by defining a more general form for the mixing as follows Ay 1 f A H f A Ha 6 8 in which f A is an appropriately designed funct
168. aneous Utilities 9 1 1 Useful Macros 9 1 1 1 Macros Macros are simple executable files containing standard unix commands A number of the are supplied with DL_POLY and are found in the execute sub directory The available macros are as follows e cleanup e copy e gopoly e gui e select e store e supa The function of each of these is described below It is worth noting that most of these functions can be performed by the DL POLY Classic java GUI 9 9 1 1 2 cleanup cleanup removes several standard data files from the execute sub directory It contains the unix commands bin tcsh DL_POLY utility to clean up after a program run if e CFGMIN rm CFGMIN if e OUTPUT rm OUTPUT if e RDFDAT rm RDFDAT if e REVCON rm REVCON if e REVIVE rm REVIVE if e REVOLD rm REVOLD if e STATIS rm STATIS if e ZDNDAT rm ZDNDAT and removes the files if present CFGMIN OUTPUT REVCON REVOLD STATIS REVIVE RDFDAT and ZDNDAT Useful data should be stored elsewhere beforehand 195 STFC Section 9 1 9 1 1 3 copy copy invokes the unix commands bin tcsh utility to set up data for DL_POLY continuation run mv CONFIG CONFIG OLD mv REVCON CONFIG mv REVIVE REVOLD which collectively prepare the DL_POLY files in the execute sub directory for the continuation of a simulation It is always a good idea to store these files elsewhere in addition to using this macro 9 1 1 4 gopoly g
169. ansition is instantaneous and that the chromophore retains the same geometric structure DL_POLY Classic can calculate both of these effects The technique is to simulate the chromophore in solution in the ground state at equilibrium and at regular intervals after obtaining the solvation energy of the ground state molecule replace it with its excited state changing its interaction potential with the solvent but not its molecular structure and obtain the interaction energy of the excited state The replacement is not permanent the excited state is used only to probe the solvation energy and has no influence on the system dynamics It is a ghost molecule The average of the difference in the solvation energies determines the spectral shift and the distribution of the energy differences determines the line broadening The same procedure may be used to study the emission process In this case the simulation is based on an equilibrated solution of the chromophore in the excited state with replacement by the ground state chromophore at intervals The data produced by this option are written in the SOLVAT file see section 6 2 3 The utility programs solsta f and soldis f are useful for analysing these results 171 STFC Section 6 4 6 4 3 Solvent Relaxation Following the absorption of a photon a chromophore may persist in an excited state for an extended period This period may be long enough for the solvent to relax around the excite
170. aracterise the structure of the system Hr Y gt M V s r t 7 1 i 1 4 In this equation U r is the usual potential energy function describing the interactions between and within the molecules p is the momentum of the th atom and m its mass The novel term V s r t is the time dependent bias potential which is a function of a vector sM that is an ordered set of M order parameters each of which is defined by the instantaneous positions r of the atoms in system The bias potential is time dependent in the sense that it can be grown by adding at periodic intervals of time TG a Gaussian term of weight w and width dh kta s t 20h Vis AN VY p 7 2 where k runs over all previously deposited Gaussians and Ng int t 7G The force on each atom f derived from the Hamiltonian 7 1 is given by X U r z Visj r 7 3 If the deposition rate w tTg is slow enough the motion of the order parameters s is adiabatically separated from the motion of the atomic system After a sufficiently long simulation the bias potential cancels out or fills the free energy landscape of the potential U r and permits an The term collective variable may be used as an alternative to order parameter 176 STFC Section 7 3 accelerated dynamics Meanwhile the bias potential becomes a measure of the free energy surface ie lim Fa s Vis E 1 7 4 t 00 Th
171. ariable 4 real variable 5 real potential 1 record 2 variable 6 real variable 7 real variable 8 real variable 9 real variable 10 real variable 11 real potential n record 2n 1 potential n record 2n cross term 1 record 2n 1 atmnam 1 atmnam 2 variable a variable b a8 a8 real real atom type potential key see Table 4 16 potential parameter see Table 4 16 potential parameter see Table 4 16 potential parameter see Table 4 16 potential parameter see Table 4 16 cutoff range for this potential A 4 16 potential parameter see Table 4 16 potential parameter see Table 4 16 potential parameter see Table 4 16 potential parameter see Table 4 16 potential parameter see Table 4 16 potential parameter see Table 4 16 first atom type second atom type potential parameter see Table 4 16 potential parameter see Table 4 16 cross term n n 1 2 record 2n n n 1 2 The variables pertaining to each potential are described in Table 4 16 Note that the 11 parameters A to h required for the cross interactions between dissimilar elements are calculated internally by DL_POLY Classic using the prescription given by Tersoff 5 There is no prescription for the x and w cross parameters so these must be given explicitly Note also that the fifth variable is the range at which the particular Tersoff potential is truncated The distance is in Table 4 16 Tersoff Potential
172. arrays are tabulated in units of energy The use of interpolation arrays rather than the explicit formulae makes the routines for calculating the potential energy and atomic forces very general and enables the use of user defined pair potential functions DL POLY Classic also allows the user to read in the interpolation arrays directly from a file see the description of the TABLE file section 4 1 5 This is particularly useful if the pair potential function has no simple analytical description e g spline potentials The force on an atom j derived from one of these potentials is formally calculated with the standard formula 1 0 where Tij Ly Ep The force on atom i is the negative of this 29 STFC Section 2 3 The contribution to be added to the atomic virial for each pair interaction is The contribution to be added to the atomic stress tensor is given by er 2 104 where a and 6 indicate the x y z components The atomic stress tensor derived from the pair forces is symmetric Since the calculation of pair potentials assumes a spherical cutoff reut it is necessary to apply a long ranged correction to the system potential energy and virial Explicit formulae are needed for each case and are derived as follows For two atom types a and b the correction for the potential energy is calculated via the integral NaN ye corr co 27 gav r Uas r r dr 2 105 Tout where Na Np are the numbers of atoms of
173. arse_module f setup_module f forces_module f 284 STFC Section D O forces forces_neu forgen fortab free_energy_option free_energy_write free_kinetic freegen freeze fsden gauss gdsum gdsum get_prntime get_simtime getcom getcom_mol getkin getkinf getking getkinr getkins getkint getmass getrec getrotmat getvom getword gimax gimax gisum gisum global_sum_forces gstate gstate gsync gsync hkewald1 hkewald2 hkewald3 hkewald4 hkgen hyper_close hyper_driver hyper_open hyper_start images impact initcomms subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine function function subroutine function subroutine function function subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine forces_module f forces_module f vdw_module f vdw_module f define_system_module f solvation_module f solvation_module f solvation_module f utility_module f metal_module f utility_module f basic_comms f serial f utility_module f utility_module f ensemble_tools_module f utility_module f ensemble_tools_module ensemble_to
174. art of a simulation You can also extend a simulation beyond its initial allocation of timesteps provided you still have the REVCON and REVIVE files These should be copied to the CONFIG and REVOLD files respectively and the directive timesteps adjusted in the CONTROL file to the new total number of steps required for the simulation For example if you wish to extend a 10000 step simulation by a further 5000 steps use the directive timesteps 15000 in the CONTROL file and include the restart directive Note that you can use the restart scale directive if you want to reset the temperature at the restart but note also that this also resets all internal accumulators timestep included to zero Alternatively you can use the restart noscale directive if you want to leave the atomic velocities unchanged at restart but wish to start a fresh simulation This will also reset internal accumulators and timestep number to zero Both the restart scale and restart noscale options will therefore ignore the REVOLD file 87 STFC Section 3 2 3 2 4 Optimising the Starting Structure The preparation of the initial structure of a system for a molecular dynamics simulation can be difficult It is quite likely that the structure created does not correspond to one typical of the equilibrium state for the required state point for the given force field employed This can make the simulation unstable in the initial stages and can even prevent it from proceeding
175. ase and a is either LF VV CB or RB The select macro will copy the appropriate CONTROL CONFIG FIELD and if necessary the TABLE or TABEAM files to the execute directory ready for execution The output files OUTPUT REVCON and STATIS may be compared with the files supplied in the data directory The example output files provided in the data directory were obtained on 8 processors of an Intel Xeon Woodcrest cluster with the following characteristics e Intel Xeon Dual core processor 3GHz 32 compute nodes 2x2 cores each master node 2 NFS file servers e 8 GB memory per node e SUSE LINUX 10 1 with kernel 2 6 16 21 0 25 smp e Intel Compilers version 10 1 Intel Cluster Tool kit including Intel MPI 3 0 MKL 9 1 and VTune e InfiniPath interconnect software stack 2 1 It should be noted that the potentials and the simulation conditions used in the following test cases are chosen to demonstrate functionality only They are not necessarily appropriate for serious simulation of the test systems Note also that the DL_POLY Classic Graphical User Interface 9 provides a convenient means for running and viewing these test cases 8 1 1 1 Test Case 1 KNaSiz05 Potassium Sodium disilicate glass NaKSi205 using two and three body potentials Some of the two body potentials are read from the TABLE file Electrostatics are handled by a multiple timestep Ewald sum method Cubic periodic boundaries are in use NVE ensemble 8 1 1 2 Test Ca
176. ategy 10 11 see section 2 6 1 1 2 5 2 Molecular Dynamics Algorithms The DL POLY Classic MD algorithms are optionally available in the form of the Verlet Leapfrog or the Velocity Verlet integration algorithms 12 In the leapfrog scheme a parallel version of the SHAKE algorithm 13 11 is used for bond constraints and a similar adaptation of the RATTLE algorithm 14 is implmented in the velocity Verlet scheme Rigid body rotational motion is handled under the leapfrog scheme with Fincham s implicit quaternion algorithm FIQA 15 For velocity Verlet integration of rigid bodies DL_POLY Classic uses the NOSQUISH algorithm of Miller et al 16 Rigid molecular species linked by rigid bonds are handled with an algorithm of our own devising called the QSHAKE algorithm 17 which has been adapted for both leapfrog and velocity Verlet schemes NVE NVT NPT and NoT ensembles are available with a selection of thermostats and barostats The velocity Verlet versions are based on the reversible integrators of Martyna et al 18 The NVT algorithms in DL_POLY Classic are those of Evans 19 Berendsen 20 and Hoover 21 The NPT algorithms are those of Berendsen 20 and Hoover 21 and the NoT algorithms are those of Berendsen 20 and Hoover 21 The full range of MD algorithms available in DL_POLY Classic is described in section 2 5 1 2 5 3 Structure Relaxation Algorithms DL_POLY Classic has a selection of structure relaxatio
177. atomic coordinates r each node calculates a subset of the forces acting between the atoms These are usually comprised of atom atom pair forces e g Lennard Jones Coulombic etc non rigid atom atom bonds c valence angle forces dihedral angle forces improper dihedral angle forces 75 STFC Section 2 6 2 The computed forces are accumulated in incomplete atomic force arrays J independently on each node 3 The atomic force arrays are summed globally over all nodes 4 The complete force arrays are used to update the atomic velocities and positions It is important to note that load balancing i e equal and concurrent use of all processors is an essential requirement of the overall algorithm In DL_POLY Classic this is accomplished for the pair forces with an adaptation of the Brode Ahlrichs scheme 23 2 6 2 Distributing the Intramolecular Bonded Terms DL_POLY Classic handles the intramolecular in which the atoms involved in any given bond term are explicitly listed Distribution of the forces calculations is accomplished by the following scheme 1 Every atom in the simulated system is assigned a unique index number from 1 to N 2 Every intramolecular bonded term Utype in the system has a unique index number itype from 1 to Niype where type represents a bond angle or dihedral 3 A pointer array keypype Ntype itype carries the indices of the specific atoms involved in the potential term l
178. averages thermostat momentum barostat momentum conserved quantity for selected ensemble number of configurations used in z density total system virial rigid body COM virial scaling factors for simulation cell matrix elements 9 constraint stress tensor elements 9 rigid body stress tensor elements 9 instantaneous values of thermodynamic variables mxnstk average values of thermodynamic variables mxnstk fluctuation squared of thermodynamic variables mxnstk running totals of thermodynamic variables mxnstk rolling averages of thermodynamic variables mxnstk stacked values of thermodynamic variables mxstakxmxnstk x component of atomic displacement MSD mxatms y component of atomic displacement MSD mxatms z component of atomic displacement MSD mxatms x coordinates of tether points mxatms y coordinates of tether points mxatms z coordinates of tether points mxatms Optional RDF array mxrdf xmxvdw Optional z density array mxrdf xmxsvdw Further Comments Note that recompiling DL_POLY Classic with a different DL PARAMS INC file may render any existing REVOLD file unreadable by the code 123 STFC Section 4 1 4 1 5 The TABLE File The TABLE file provides an alternative way of reading in the short range potentials in tabular form This is particularly useful if an analytical form of the potential does not exist or is too complicated to specify in the FORGEN subroutine The table file
179. before the ewald precision directive in the CONTROL file and rerun Message 434 error illegal entry into STRESS related routine The calculation of the stress tensor in DL_POLY Classic requires additional code that must be included at compile time through the use of the STRESS keyword If this is not done and DL_POLY Classic is later required to calculate the stress tensor this error will result Action The program must be recompiled with the STRESS keyword activated This will ensure all the relevant code is in place See section 3 2 1 241 STFC Section C 0 Message 435 error specify rcut before the coulomb precision When specifying the desired precision for the coulomb sum in the CONTROL file it is first neces sary to specify the real space cutoff rcut Action Place the cut directive before the coulomb precision directive in the CONTROL file and rerun Message 436 error unrecognised ensemble An unknown ensemble option has been specified in the CONTROL file Action Locate ensemble directive in the CONTROL file and amend appropriately Message 438 error PMF constraints failed to converge The constraints in the potential of mean force algorithm have not converged in the permitted num ber of cycles The SHAKE algorithm for PMF constraints is iterative Possible causes include a bad starting configuration too large a time step used incorrect force field specification too high a temperature inconsisten
180. ble The REVCON file contains the restart configuration i e the final positions velocities and forces of the atoms when the run ended and is human readable The STATIS file section 4 2 8 contains a catalogue of instantaneous values of thermodynamic and other variables in a form suitable for temporal or statistical analysis Finally the HISTORY file section 4 2 1 provides a time ordered sequence of configurations to facilitate further analysis of the atomic motions Depending on which version of the TRAJECT subroutine you compiled in the code this file may be either formatted human readable or unformatted You may move these output files back into the data sub directory using the store macro found in the execute sub directory Note that versions of DL POLY Classic after 2 10 may also create the files RDFDAT and ZDNDAT containing the RDF and Z density data respectively They are both human readable files 3 2 3 Restarting DL POLY Classic The best approach to running DL_POLY Classic is to define from the outset precisely the simulation you wish to perform and create the input files specific to this requirement The program will then perform the requested simulation but may terminate prematurely through error inadequate time allocation or computer failure Errors in input data are your responsibility but DL POLY Classic will usually give diagnostic messages to help you sort out the trouble Running out of job time is common and provided you ha
181. body_module f utility_module f hyper_dynamics_module f define_system_module f spme_module f spme_module f ensemble_tools_module f ensemble_tools_module f hkewald_module f setup_module f hyper_dynamics_module f hyper_dynamics_module f core_shell_module f site_module f metafreeze_module metafreeze_module metafreeze_module metafreeze_module metafreeze_module metafreeze_module utility_module f setup_module f solvation_module f parse_module f core_shell_module f coulomb_module f neu_coul_module f coulomb_module f coulomb_module f neu_coul_module f coulomb_module f neu_coul_module f coulomb_module f coulomb_module f utility_module f basic_comms f serial f Fh Fh Fh Fh Fh FH basic comms f serial f parse module f setup_module f angles_module f site_module f bonds_module f 283 STFC Section D O define_constraints define_core_shell define_dihedrals define_external_field define_four_body define_inversions define_metadynamics define_metals define_minimum_state define_pmf define_rigid_body define_tersoff define_tethers define_three_body define_units define_van_der_waals deposit_gaussian dfc diffsno0 diffsn1 dihfrc dlpfft3 duni eamden ele prd energy unit ensemble selection erfcgen error ewaldi ewald2 ewald3 ewald4 ewald_selection ewald_spme excitation_option exclude exclude_atom exclude_link excludeneu exitcomms exitcomms extnfld fbpfre fc fcap findstring
182. broutine STATIC It consists of two header records followed by many data records of statistical data record 1 cfgname character configuration name record 2 string character energy units Data records Subsequent lines contain the instantaneous values of statistical variables dumped from the array stpval A specified number of entries of stpval are written in the format 1p 5e14 6 The number of array elements required determined by the parameter mxnstk in the DL_PARAMS INC file is mxnstk gt 27 ntpatm number of unique atomic sites 9 if stress tensor calculated 9 if constant pressure simulation requested The STATIS file is appended at intervals determined by the stats directive in the CONTROL file The energy unit is as specified in the CONTROL file with the the units directive and are compatible with the data appearing in the OUTPUT file The contents of the appended information is record i nstep integer current MD time step time real elapsed simulation time nstepx At nument integer number of array elements to follow record ii stpval 1 stpval 5 engcns real total extended system energy i e the conserved guantity temp real system temperature engcfg real configurational energy engsrp real VdW metal Tersoff energy engcpe real electrostatic energy record iii stpval 6 stpval 10 engbnd real chemical bond energy engang real valence angle 3 body potential energy engdih real dihedral inversion four body en
183. broutine subroutine subroutine subroutine subroutine 1f_motion_module f 1f_motion_module f lf rotation1 module lf rotation2 module lf rotation1 module lf rotation2 module Fh Fh Fh Fh ensemble_tools_module vv rotation1 module f vv_rotation2_module f vv rotation1 module f vv rotation2 module f ensemble tools module vv motion module f vv motion module f vv motion module f optimiser_module f nlist_builders_module nlist_builders_module nlist_builders_module nlist_builders_module nlist_builders_module setup_module f pass_tools f serial f pass_tools f serial f pass_tools f serial f vv_rotation2_module f pmf_module f pmf_module pmf_module pmf_module pmf_module pmf_module pmf_module f Fh Fh Fh Fh Fh nlist_builders_module define_system_module f nlist_builders_module optimiser_module f core_shell_module f vv_rotation2_module f vv_rotation2_module f 1f_rotation2_module f define system module f temp scalers module f temp scalers module f property module f property module f 288 Hh Fh Fh Fh Fh f f STFC Section D O rdf1 rdrattle_r rdrattle_v rdshake_1 read_reference_config regauss relax_shells result revive rotate_omega scan_profile scl_csum scramble_velocities sdot0 sdot1 set_block shell_relaxation shellsort shlfrc shlmerge shlmerge shlqnch shmove shmove simdef solva_temp solvation_option solvation_write spl_cexp splic
184. bution to the system virial can be obtained as the negative of the Coulombic energy However in DL_POLY Classic this formal equality can be used as a check on the convergence of the Ewald sum The actual electrostatic virial is obtained during the calculation of the diagonal of the stress tensor The electrostatic contribution to the stress tensor is given by 00 1 T 1 1 exp pl 3 AA f i r K a exp ik r k 0 el fo arn Orei esp a R 2 201 ET J CLArn exp Q Tr a i Ate Fee af nI vr nj nj 1 M 1 2ar 5 E ferflary t exp a 2r Ra Ra Areo a h yT where matrices K and Ry are defined as follows K Ip 2 202 tr 2 203 In DL_POLY Classic the full Ewald sum is handled by several routines EWALD1 and EWALD1A handle the reciprocal space terms EWALD2 EWALD2_2PT EWALD2_RSQ and EWALD4 EWALD4_2PT handle the real space terms with the same Verlet neighbour list routines that are used to calcu late the short ranged forces and EWALD3 calculates the self interaction corrections It should be noted that the Ewald potential and force interpolation arrays in DL_POLY Classic are erc and fer respectively 2 4 7 Smoothed Particle Mesh Ewald As its name implies the Smoothed Particle Mesh Ewald SPME method is a modification of the standard Ewald method DL POLY Classic implements the SPME method of Essmann et al 46 Formally this method is capable of treating van der Waa
185. c is dealt with more fully in Appendix C 3 2 Compiling and Running DL POLY Classic 3 2 1 Compiling the Source Code When you have obtained DL_POLY Classic from Daresbury Laboratory and unpacked it your next task will be to compile it To aid compilation a set of makefiles has been provided in the sub directory build see example in Appendix A of this document The versions go by the names of 83 STFC Section 3 2 e MakePAR to build a parallel MPI version on a unix platform e MakeSEQ to build a sequential one processor unix version e MakeWIN to build a Windows one processor XP version Select the one you need and copy it into the source directory In what follows we assume the makefile in the source directory is called Makefile The Makefile will build an executable with a wide range of functionality sufficient for the test cases and for most users requirements Users will need to modify the Makefile if they are to add additional functionality to the code or if it requires adaptation for a non specified computer Modifications may also be needed for the Smoothed Particle Mesh Ewald method if a system specific 3D FFT routine is desired see below Modifying the makefile Note the following system requirements for a successful build of DL_POLY Classic 1 A FORTRAN 90 compiler 2 The Java SDK from Sun Microsystems if the GUI is required 3 A UNIX operating system or Windows XP with CygWin if a
186. c restraint zone in z direction zres F A Zmaz Zom gt Zcom gt 2max 2 175 F A Zmin Zoom gt Zcom lt Zmin 2 176 where Zcom is the chosen molecule centre of mass It is recommended that the use of an external field should be accompanied by a thermostat this does not apply to examples 6 and 7 since these are conservative fields The user is advised to be careful with units In DL_POLY Classic external field forces are handled by the routine EXTNFLD 2 4 Long Ranged Electrostatic Coulombic Potentials DL_POLY Classic incorporates several techniques for dealing with long ranged electrostatic poten tials These are as follows 1 Atomistic and charge group implementation 2 Direct Coulomb sum 3 Truncated and shifted Coulomb sum 4 Damped shifted force Coulomb sum 5 Coulomb sum with distance dependent dielectric 6 Ewald sum 7 Smoothed Particle Mesh Ewald SPME 8 Hautman Klein Ewald for systems with 2D periodicity 9 Reaction field 2Unlike the other elements of the force field the electrostatic forces are NOT specified in the input FIELD file but by setting appropriate directives in the CONTROL file See section 4 1 1 42 STFC Section 2 4 10 Dynamical shell model 11 Relaxed shell model Some of these techniques can be combined For example 1 3 and 4 can be used in conjunction with 9 The Ewald sum SPME and Hautman Klein Ewald are restricted to periodic or pseudo perio
187. c valence forces are handled by the routine ANGFRC 2 2 4 Angular Restraints In DL_POLY Classic angle restraints in which the angle subtended by a triplet of atoms is main tained around some preset value 69 is handled as a special case of angle potentials As a consequence angle restraints may be applied only between atoms in the same molecule Unlike with application of the pure angle potentials the electrostatic and van der Waals interactions between the pair of atoms are still evaluated when distance restraints are applied All the potential forms of the previous section are available as angular restraints although they have different key words 19 STFC Section 2 2 1 Harmonic hrm 2 Quartic qur 3 Truncated harmonic thm 4 Screened harmonic shm 5 Screened Vessal 28 bv1 6 Truncated Vessal 29 bv2 7 Harmonic cosine hcs 8 Cosine cos 9 MM3 stretch bend msb 10 Compass stretch stretch sts 11 Compass stretch bend stb 12 Compass all terms cmp In DL_POLY Classic angular restraints are handled by the routine ANGFRC 2 2 5 Dihedral Angle Potentials Figure 2 3 The dihedral angle and associated vectors The dihedral angle potentials describe the interaction arising from torsional forces in molecules They are sometimes referred to as torsion potentials They require the specification of four atomic positions The potential functions available in D
188. ceeded the program terminates The error arises when the molecules directive in the FIELD file specifes too large a number Action Standard user response Fix parameter mxtmls 213 STFC Section C 0 Message 11 error duplicate molecule directive in FIELD file The number of different types of molecules in a simulation should only be specified once If DL_POLY Classic encounters more than one molecules directive it will terminate execution Action Locate the extra molecule directive in the FIELD file and remove Message 12 error unknown molecule directive in FIELD file Once DL_POLY Classic encounters the molecules directive in the FIELD file it assumes the fol lowing records will supply data describing the intramolecular force field It does not then expect to encounter directives not related to these data This error message results if it encounters a unrelated directive The most probable cause is incomplete specification of the data e g when the finish directive has been omitted Action Check the molecular data entries in the FIELD file and correct Message 13 error molecule species not yet specified This error arises when DL_POLY Classic encounters non bonded force data in the FIELD file be fore the molecular species have been specified Under these circumstances it cannot assign the data correctly and therefore terminates Action Make sure the molecular data appears before the non bonded forces data
189. chine with larger memory per processor 267 STFC Section C 0 Message 1945 error failed allocation of tersoff arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1950 error shell relaxation cycle limit exceeded There has been a convergence failure during the execution of relaxed shell polarisation model Probable cause the system is unstable e g in an abnormally high energy configuration Action Increasing the maximum number of cycles permitted in the shell relaxation set by variable mxpass in the dlpoly f root program may help but it is unlikely A better option is to relax the structure somehow first e g using the zero option in the CONTROL file Message 1951 error no shell dynamics algorithm specified The user has failed to specify which of the available shell dynamics algorithm is to be used in the simulation Options include adiabtic shells and relaxed shells Action Locate the definition of the core shell units in the FIELD file and check that all necessary integer keys have been supplied Consult the user manual if in doubt Message 1953 error tersoff radius of cutoff not defined The Tersoff potential requires the user to specify a short ranged cutoff as part of the potential description Thi
190. cified by the user The LF version of this algorithm is implemented in NPT_B1 with 4 or 5 iterations used to obtain self consistency in the u t It calls RDSHAKE_1 to handle constraints The VV version is implemented in subroutine NVTVV_B1 which calls constraint subroutines RATTLE_R and RATTLE_V Cell size and shape variations 66 STFC Section 2 5 The extension of the isotropic algorithm to anisotropic cell variations is straightforward The tensor n is defined by 1 Pext1 2 2 280 2 72 3 and the new cell vectors given by H t At nH i 2 281 As in the isotropic case the Berendsen thermostat is applied simultaneously and 4 or 5 iterations are used to obtain convergence The LF version of the algorithm is implemented in subroutine NST_B1 and the VV version in NSTVV_B1 The former calls RDSHAKE_1 to handle constraints and the latter calls subroutines RATTLE_R and RATTLE_V 2 5 7 Rigid Bodies and Rotational Integration Algorithms 2 5 7 1 Description of Rigid Body Units A rigid body unit is a collection of point atoms whose local geometry is time invariant One way to enforce this in a simulation is to impose a sufficient number of bond constraints between the atoms in the unit However in many cases this is may be either problematic or impossible Examples in which it is impossible to specify sufficient bond constraints are 1 linear molecules with more than 2 atoms e g CO2 2 planar molecules with
191. ck of FORTRAN COMMENT records giving 1 The name of the author and or modifying author 2 The version number or date of production 3 A brief description of the function of the subroutine 4 A copyright statement Elsewhere FORTRAN COMMENT cards are used liberally STFC Section 1 3 1 3 7 Subroutine Function Calling Sequences The variables in the subroutine arguments are specified in the order 1 6 logical and logical arrays character and character arrays integer real and complex integer arrays real and complex arrays This is admittedly arbitrary but it really does help with error detection 1 3 8 FORTRAN Parameters All global parameters defined by the FORTRAN parameter statements are specified in the module SETUP_MODULE All parameters specified in SETUP_MODULE are described by one or more comment cards 1 3 9 Arithmetic Precision All real variables and parameters are specified in 64 bit precision i e real 8 1 3 10 Units Internally all DL_POLY Classic subroutines and functions assume the use of the following defined molecular units 1 2 6 E The unit of time to is 1 x 10712 seconds i e picoseconds The unit of length is 1 x 10719 metres i e Angstroms The unit of mass mo is 1 6605402 x 10727 kilograms i e atomic mass units The unit of charge qo is 1 60217733 x 10719 coulombs i e unit of proton charge The unit of energy E Mo lo to is
192. compilation of DL_POLY Classic will incorporate a basic 3D Fast Fourier Trans form FFT routine to enable the SPME functionality Users may wish to try alternative FFT routines which may offer faster performance Some hooks for these appear in the code as comment lines in the FORTRAN source The user should search for the following keys in the code e CCRAY for the Cray FFT routines e CFFTW for the FFTW public domain FFT routines CESSL for the IBM scientific library FFT routines CSGIC for the Silicon Graphics FFT routines The appropriate lines should be uncommented and the references to the DLPFFTS3 subrou tine should be commented out before compiling 3 Problems with optimization 85 STFC Section 3 2 Some subroutines may not compile correctly when using optimization on some compilers This is not necessarily the fault of the DL_POLY Classic code some compilers are just flakey This can be circumvented by compiling the offending subroutines separately with optimisation flags turned off 4 Adding new functionality To include a new subroutine in the code simply add subroutine o to the list of object names in the makefile The simplest way is to add names to the OBJ_SRC list However for more substantial modifications it is advisable to construct a proper F90 module containing several related subroutines and add this to the OBJ_MOD list 3 2 1 3 Note on Interpolation In DL POLY Classic the s
193. constant in specified energy units per A e g neb spring 1000 0 in DL_POLY units Select a minimisation option e g keyword tol Where keyword is one of force energy position and tol is the convergence tolerance Close the NEB definition with the directive endneb 5 7 1 Things to be Aware of when Running a NEB Calculation 1 Note that the NEB calculation assumes that the basin files for the start and end states are in the BASINS directory and that DL_POLY Classic is being run from the execute directory where the DLPOLY X executable is located Needless to say if these files are placed anywhere else the calculation will fail Note also that the NEB calculation places the reaction path profile for a given pair of states in the PROFILES direction with the file name PRXnn XY where nn is a negative number that is compounded from the identities of the start n and end states n2 thus nn 100 xn na It is important to be sure that the start and end states represent real observed transitions in the BPD or TAD simulation The danger here is using two structures that are not mech anistically close If this is not the case the NEB calculation is unlikely to converge as there 159 STFC Section 5 7 will be no simple path with preferably a single energy maximum between the start and end states 4 When running an NEB calculation to improve the accuracy of the activation energy a more string
194. ction 3 3 that if any of these parameters prove to be insufficiently accurate DL_POLY Classic will issue an error in the OUTPUT file and indicate whether it is the real or reciprocal space sums that is questionable 3 3 DL POLY Classic Error Processing 3 3 1 The DL_POLY Classic Internal Error Facility DL_POLY Classic contains a number of in built error checks scattered throughout the package which detect a wide range of possible errors In all cases when an error is detected the subroutine ERROR is called resulting in an appropriate message and termination of the program execution either immediately or after additional processing Users intending to insert new error checks should ensure that all error checks are performed concurrently on all nodes and that in circumstances where a different result may obtain on different nodes a call to the global status routine GSTATE is made to set the appropriate global error flag on all nodes Only after this is done a call to subroutine ERROR may be made An example of such a procedure might be logical safe safe test_condition call gstate safe if not safe call error node_id message_number In this example it is assumed that the logical operation test_condition will result in the answer true if it is safe for the program to proceed and false otherwise The call to ERROR requires the user to state the identity of the calling node node_id so that only the nominated node in ER
195. ctly specified the atoms in the system The user must locate the ambiguity using the data printed in the OUTPUT file as a guide and make the appropriate alteration Message 26 error cutoff smaller than EAM potential range DL_POLY Classic has detected an inconsistency in the definition of the EAM potential namely that the user is not using the correct potential range Action Look up the correct range for this potential and adjust the DL POLY cutoff accordingly Message 27 error incompatible FIELD and TABEAM file potentials The user has or has not specified a set of EAM potentials in the FIELD file which are not or are available in the TABEAM file Action Examine the FIELD file Make sure you have correctly specified the EAM potentials Check that these appear in the TABEAM file if required Message 28 error transfer buffer too small in mettab The number of points specifying an EAM potential in the TABEAM file exceeds the default buffer size in METTAB F 216 STFC Section C 0 Action Reset the mxbuff parameter in PARSET F subroutine to accommodate the required array length and recompile Message 29 error end of file encountered in TABEAM file DL_POLY Classic has reached the end of the TABEAM file without finding all the data it expects Action Either the TABEAM file is incomplete or it is improperly defined Check the structure and content of the file with the TABEAM file specification in the manual
196. cute PROFILES sub directory and are plotable XY files 5 CFGTRAnn a configuration file used to interpolate when a transition has occured nn is an integer rising from 0 to 9999 All such files are generated in the execute TRACKS sub directory These files are described in further detail below 154 STFC Section 5 5 5 5 0 1 The HYPRES and HYPOLD Files The HYPRES and HYPOLD files are unformatted i e not human readable and are restart files for BPD or TAD runs of DL_POLY Classic The HYPRES file is produced by the program at regular intervals during the program run and also at the end of a run It must subeguently be renamed HYPOLD to be read by DL POLY Classic when the simulation is recommenced The user does not need to know the contents of these files but for the curious it can be said that they contain current file numbers for the BASINS TRACKS and PROFILES directories the structural differences between the current reference basin and any new basins found TAD only and the atomic coordinates of the current basin taken at the last check point such as the end of the last BPD orTAD block 5 5 0 2 The EVENTS File The EVENTS file is a text file that reports the results of actions taken by the hyperdynamics routines Each record in the file specifies a particular kind of event The possible events described are as follows Note that the real variables specified in this file are in units specified by the user 1 Blackout pe
197. cutoff that is applied to the 1 4 potential meaning the potential will not be computed though it may be an essential component of the dihedral force and not necessarily a vanishing force Action The probable source of the error is an improperly described force field Effectively the 1 4 distance is not being restrained sufficently Check the 1 4 potential parameters and the valence angles that help define the dihedral geometry If these are correct then you may have to comment out this error condition in the DIHFRC F subroutine but beware that when the 1 4 atoms are too widely separated the dihedral angle can become indeterminable Message 448 error undefined dihedral potential A form of dihedral potential has been requested which DL_POLY Classic does not recognise Action Locate the offending potential in the FIELD file and remove Replace with one acceptable to 243 STFC Section C 0 DL_POLY Classic if this is reasonable Alternatively you may consider defining the required po tential in the code yourself Amendments to subroutines SYSDEF and DIHFRC and its variants will be required Message 449 error undefined inversion potential A form of inversion potential has been encountered which DL POLY Classic does not recognise Action Locate the offending potential in the FIELD file and remove Replace with one acceptable to DL_POLY Classic if this is reasonable Alternatively you may consider defining the required po
198. d Message 1974 error incorrect period boundary in tersoff f The implementation of the Tersoff potential in DL_POLY Classic is based on the link cell algorithm which is suitable for rectangular or triclinic MD cells only It is not suitable for any other shape of MD cell Action The user must reconstruct the system according to one of the permitted periodic boundaries Message 1976 error too many link cells required in tersoff f The number of link cells required by the Tersoff routines exceeds the amount allowed for by DL_POLY Classic This can happen if the system is simulated under NPT or NST conditions and the system volume increases dramatically Action The problem may cure itself on restart provided the restart configuration has already expande significantly Otherwise the user must locate and adjust the mxcell according to the standard response procedure Message 1978 error undefined potential in tersoff f A form of Tersoff potential has been requested which DL POLY Classic does not recognise Action Locate the offending potential in the FIELD file and remove Replace with one acceptable to DL_POLY Classic if this is reasonable Alternatively you may consider defining the required po tential in the code yourself Amendments to subroutines SYSDEF and TERSOFF will be required Message 1980 error failed allocation of nvevv_1 f work arrays This is a memory allocation error Probable cause excessive size of simu
199. d Action Standard user response Fix the parameter mxxdf Message 396 error interpolation array exceeded DL_POLY Classic has sought to read past the end of an interpolation array This should never happen Action Contact the authors Message 398 error cutoff too small for rprim and delr This error can arise when the multiple timestep option is used It is essential that the primary cutoff rprim is less than the real space cutoff rcut by at least the Verlet shell width delr preferably much larger DL POLY Classic terminates the run if this condition is not satisfied Action Adjust rcut rprim and delr to satisfy the DL POLY Classic requirement These are defined with the directives cut prim and delr respectively Message 400 error rvdw greater than cutoff DL POLY Classic requires the real space cutoff rcut to be larger than or equal to the van der Waals cutoff rvdw and terminates the run if this condition is not satisfied 238 STFC Section C 0 Action Adjust rvdw and rcut to satisfy the DL POLY Classic requirement Message 402 error van der waals cutoff unset The user has not set a cutoff rvdw for the van der Waals potentials The simulation cannot proceed without this being specified Action Supply a cutoff value for the van der Waals terms in the CONTROL file using the directive rvdw and resubmit job Message 410 error cell not consistent with image convention The simulation ce
200. d intramolecular interactions M represents the number of excluded atoms in a given molecule and includes the atomic self correction The final term on the right is the Fuchs correction for charged systems 44 V is the simulation cell volume and k is a reciprocal lattice vector defined by k lu mu nw 2 197 where m n are integers and u v w are the reciprocal space basis vectors Both V and u v w are derived from the vectors a b c defining the simulation cell Thus Vo a b x c 2 198 and bx n a Ei v i 2 199 axb E E With these definitions the Ewald formula above is applicable to general periodic systems A small additional modification is necessary for rhombic dodecahedral and truncated octahedral simulation cells 45 In practice the convergence of the Ewald sum is controlled by three variables the real space cutoff reut the convergence parameter a and the largest reciprocal space vector kmag used in the reciprocal space sum These are discussed more fully in section 3 2 5 DL POLY Classic can provide estimates if requested see CONTROL file description 4 1 1 The force on an atom j is obtained by differentiation and is CO 2 2 N Sy p SPL Ma i Wa S ikexp ik r 73 S dn exp ik rn k 0 n qi y In 20F nj 2 2 2 200 reo r3 AIS T EPT raj Tap n nj M j 2aryj iE Jer flary epa ry 4Teo E Te T 47 STFC Section 2 4 The electrostatic contri
201. d by the Ewald sum The water is treated as a constrained triangle PMF ensemble 8 1 1 7 Test Case 7 Linked rigid bodies 8 biphenyl molecules in cubic boundary conditions Each phenyl ring is treated as a rigid body with a constraint bond to the other ring of the molecule In the centre of each ring are three massless charge sites which imparts a quadrupole moment to the ring NVE ensemble 8 1 1 8 Test Case 8 An osmosis experiment with a semi permeable membrane The membrane is a collection of tethered sites interconnected by harmonic springs There are no electrostatic forces in the system The simulation is run with the Hoover anisotropic constant presure algorithm NST Hoover ensemble 8 1 1 9 Test Case 9 A surfactant at the air water interface The system is comprised of 32 surfactant molecules trimethylaminododecane bromide or TAB C12 arranged either side of a slab of 342 water molecules approximately 30 A thick The surfactant chains are treated with rigid bonds and the water molecules are treated as rigid bodies The TAB headgroup has fractional charges summing to 1 the bromide ion has charge 1 The Ewald sum handles the electrostatic calculations The short range forces are taken from the Dreiding force field NVE ensemble 8 1 1 10 Test Case 10 DNA strand in water This system consists of a strand of DNA 1260 atoms in length in a solution of 706 SPC water molecules The DNA is aligned in the Z direction and hexago
202. d chromophore and lower the configuration energy to some degree Subject to the assumption that the chro mophore structure does not change during the relaxation period the relaxation energy may be calculated by simulation A the same time the relaxation time of the solvent may be estimated In DL_POLY Classic this is accomplished by switching from the ground to the excited state molecule at intervals during the simulation leaving sufficient time for the solvent to relax to equilibrium around the excited state At the end of the chosen relaxation interval the system may be switched back to the ground state to afford the determination of the relaxation around the ground state The relaxation energy may be extracted from the energy difference between the equilibrated ground and excited state systems and the relaxation time from fitting to the average of many energy relaxation time plots The data from these simulations are written to the SOLVAT file see section 6 2 3 at the user defined intervals 6 4 4 Invoking the Solvent Induced Spectral Shift Option This option is activated by inserting the directive excite in the CONTROL file 4 1 1 followed by further directives to enter the control parameters and ending with the endexc directive The specification is as follows excite start n1 inter n2 system a ii i2 system_b i3 i4 endexc The meaning of these directives is as follows 1 excite invokes the solvent induced shift option 2 s
203. d units with NOSQUISH and RATTLE NVEQVV_2 Linked rigid units with QSHAKE NVTVV_B1 Constant T Berendsen 20 with RATTLE NVTVV_El Constant T Evans 19 with RATTLE NVTVV_H1 Constant T Hoover 21 with RATTLE NVTQVV_B1 Constant T Berendsen 20 with NOSQUISH and RATTLE NVTQVV_B2 Constant T Berendsen 20 with QSHAKE NVTQVV_H1 Constant T Hoover 21 with NOSQUISH and RATTLE NVTQVV_H2 Constant T Hoover 21 with QSHAKE NPTVV_B1 Constant T P Berendsen 20 with NOSQUISH and RATTLE NPTVV_H1 Constant T P Hoover 21 with RATTLE NPTQVV_Bl Constant T P Berendsen 20 with NOSQUISH and RATTLE NPTQVV_B2 Constant T P Berendsen 20 with QSHAKE NPTQVV_H1 Constant T P Hoover 21 with NOSQUISH and RATTLE NPTQVV_H2 Constant T P Hoover 21 with QSHAKE NSTVV_B1 Constant T z Berendsen 20 with RATTLE NSTVV_H1 Constant T a Hoover 21 with RATTLE NSTQVV_B1 Constant T c Berendsen 20 with NOSQUISH and RATTLE NSTQVV_B2 Constant T g Berendsen 20 with QSHAKE NSTQVV_H1 Constant T c Hoover 21 with NOSQUISH and RATTLE NST VV H2 Constant Tr Hoover 21 with QSHAKE In the above table the NOSQUISH algorithm is the rotational algorithm of Miller et al 16 and QSHAKE is the DL_POLY Classic algorithm combining rigid bonds and rigid bodies in the same molecule 17 2 5 1 3 Temperature and Energy Conservation For both VV and LF the instantaneous temperature can be obtained from the atomic velocities assuming th
204. dic systems only though DL POLY Classic can handle a broad selection of periodic boundary conditions including cubic orthorhombic parallelepiped truncated octahedral hexagonal prism and rhombic dodecahedral The Ewald sum is the method of choice for periodic systems The other techniques can be used with either periodic or non periodic systems though in the case of the direct Coulomb sum there are likely to be problems with convergence DL_POLY Classic will correctly handle the electrostatics of both molecular and atomic species However it is assumed that the system is electrically neutral A warning message is printed if the system is found to be charged but otherwise the simulation proceeds as normal No correction for non neutrality is applied except in the case of the Ewald based methods 2 4 1 Atomistic and Charge Group Implementation The Ewald sum is an accurate method for summing long ranged Coulomb potentials in periodic systems This can be a very cpu intensive calculation and the use of more efficient but less accurate methods is common Invariably this involves truncation of the potential at some finite distance Teute If an atomistic scheme is used for the truncation criterion there is no guarantee that the interaction sphere will be neutral and spurious charging effects will almost certainly be seen in a simulation This arises because the potential being truncated is long ranged 1 r for charge charge interactions Howev
205. ding the nominated line of the ZETA file Action Probably a missing or corrupted data line Locate and fix Message 2531 Comms error on reading METADYNAMICS This is probably a programming error and should not occur Action Identify and fix the bug if you can Otherwise locate the authors and ask for a fix Message 2532 Error in fc function out of range The switching function has been incorrectly defined in a hyperdynamics simulation Action Check the value reported and make the necessary correction in the STEINHARDT or ZETA file concerned Message 2533 Error allocating solvation arrays for metadynamics Unlikely array allocation error which should not occur under normal use Action The user is probably making excessive demands of memory Reconsider the problem size in relation to compute resource 279 STFC Section C 0 Message 2534 Error allocating comms buffer arrays Unlikely array allocation error which should not occur under normal use Action The user is probably making excessive demands of memory Reconsider the problem size in relation to compute resource Message 2535 Solvation list overrun The arrays tabulating the coordination list for either Steinhardt or tetrahedral order parameters have been exceeded Action Locate the specification of the variable mazneigh in the metafreeze_module f file there are 3 oc currences and reset to a larger number Message 2536 Error deallocating solva
206. documentation is free from error Neither do they accept responsibility for any loss or damage that results from its use The responsibility for ensuring that the software is fit for purpose lies entirely with the user i STFC Preface DL_POLY Classic Acknowledgements DL_POLY Classic was developed under the auspices of the Science and Technology Facilities Council the Engineering and Physical Sciences Research Council and the former Science and Engineering Research Council under grants from the Computational Science Initiative and the Science and Materials Computing Committee Advice assistance and encouragement in the development of DL POLY Classic has been given by many people We gratefully acknowledge the comments feedback and bug reports from the CCP5 community in the United Kingdom and throughout the world In addition we thank the following people for contributing code to the package 1 Maurice Leslie contributed the NOSQUISH rotational algorithm at the heart of many of the rigid body routines 2 The hyperdynamics algorithms in DL POLY Classic were developed in a collaboration with Duncan Harris and John Harding at the University of Sheffield and formerly the University of London 3 The solvation free energy and solvent induced spectral shift features were developed in collab oration with P A Cazade P Bordat and R Brown at the University of Pau Travel between Pau and Daresbury by the collaborators was enabled by
207. e splice spme_for sr rce sr rceneu static store_config strip striptext strucopt switch switch_atm switching_option sysbook sysdef sysgen sysinit systemp tad_option tergen subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine function function subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine property_module f vv_motion_module f vv_motion_module f 1f_motion_module f hyper_dynamics_module f temp_scalers_module f core_shell_module f property_module f property_module f vv rotation1 module f hyper dynamics module f utility module f hyper dynamics module f utility module f utility module f utility module f driver_module f utility_module f core_shell_module f merge_tools f serial f temp_scalers_module f merge_tools f serial f define system module f solvation_module f define system module f solvation_module f spme_module f merge_tools f serial f spme_module f vdw_module f vdw_module f property_module f hyper_dynamics_module f parse_module f pars
208. e Make sure the simulation behaved sensibly and terminated cleanly If the required number of time steps has not been reached the simulation can be restarted from the REVCON and REVIVE files renaming them as CONFIG and REVOLD for the purpose and setting the directive restart with no qualifier in the CONTROL file Use the DL_POLY Java GUI to plot the system energy and temperature for the whole of the simulation and make sure no key variables misbehave The HISTORY file if requested contains the trajectory of the system This may be viewed or otherwise investigated by appropriate viewing or analysis software The METADYNAMICS file produced by the run contains the data describing the evo lution of the time dependent bias potential equation 7 1 This file consists of a series of records the content of each is The meta step current time step number divided by the Gaussian deposition interval meta_step_int Format i8 All ncolvar order parameters selected Format ncolvar e15 6 The height of the deposited Gaussian divided by kT Format e15 6 7 4 1 Additional Considerations 1 Choosing the Gaussian convergence scheme DL POLY Classic offers three different schemes for handling the addition of the Gaussians to the bias potential Further details on these schemes can be obtained from Quigley and Rodger 68 a Simple addition Gaussians with fixed height and width parameters are simply added b NS to th
209. e specification of four atomic positions The potential functions available in DL_POLY Classic are as follows 1 Harmonic harm 1 U Pijkn Aiken 60 2 61 2 Harmonic cosine hcos k U dijkn 3 C05 Eijkn cos 60 2 62 3 Planar potential plan U 6ijkn A 1 cos 6ijkn 2 63 In these formulae ijkn is the inversion angle defined by T WwW Pijkn cos E o 2 64 Tij Wkn with and the unit vectors kn fik Pin ta inl Dig tip o Lil 2 66 As usual Tiy i fy ete and the hat 7 indicates a unit vector in the direction of r The total inversion potential requires the calculation of three such angles the formula being derived from the above using the cyclic permutation of the indices j gt k n j etc Equivalently the angle 6 j may be written as a y2 gt 521 2 ij Ukn ij Ukn Tij Formally the force on an atom arising from the inversion potential is given by fE LU Gijn 2 68 t Ore ijkn gt with being one of i j k n and a one of x y z This may be expanded into o 1 0 zaU Pijem U ijkn X Or Dijen Obijkn Dijen a y2 a 3211 2 EE 6 rn Lij Oia 2 69 Ore Tij 24 STFC Section 2 2 Following through the extremely tedious differentiation gives the result p 9 i a ort Odijkn U dijen X 2 70 cos Pijkn a 1 Se ea lt Aaa us 66 G5 L AA ij ij Wkn
210. e 2 Tin are IT ik Tin 2 with arla X Tik Tik X Cen ri lEjktjkla en Sen Lik knla Sex 25 rix ILijLjrlal tn Oek Cjktknlal ej 2i Then TisTikla ek 005 TikTikla Oti 5 Zil tis Tknlo 025 Sex 2 48 21 STFC Section 2 2 sl X Piel 2ripllLjrLinlal2 Dai tis Tikla 025 dex 2ri lag Pagla Sex 025 lijLjrlal ei 5 5 2 49 0 2 a gra Lik X Tel 2rin ltiktjkla den Sek Tik Tknlo 02 Sex 275 kn Tinla tk 025 Tik Tunla Ok On 2 50 Where we have used the the following definition a Bla Y 1 bag ad 2 51 B Formally the contribution to be added to the atomic virial is given by 4 ef 2 52 i 1 However it is possible to show by tedious algebra using the above formulae or more elegantly by thermodynamic arguments 30 that the dihedral makes no contribution to the atomic virial The contribution to be added to the atomic stress tensor is given by are rope T ro Dh ie 2 53 cos dj jkn sn ne reg rag rah IS with pe r TiklLjrLrnla T Tin TikTiklo tis x Tikl Tjk X Lin 2 54 Pao rielliljrlo Tik ikla tag X EgrllL jr X Lin 2 55 Die Blt pePenle Pin lagh pele rikis Tinlo ITis X TikllTik X Peni 2 56 a roleta TF elragtjala ij X El 2 57 Ik rile ij Tijla Tij ligt gale tag as snl 2 58 hi Arillint
211. e Theory by a boost factor bias Rist e Wvias i kTST 5 5 bias where 3 1 kgT and the ensemble average which is calculated in the biased system represents the boost factor 140 STFC Section 5 3 Emin Figure 5 3 Basic BPD Theory The normal potential energy surface continuous line is characterised by deep basins such as Emin from which escape is improbable The biased potential Vias dashed line reduces the basin depth making transitions more likely To preserve the kinetic pathway of the original system the bias potential must be less than the saddle points Ej and Es and for molecular dynamics purposes ideally should join continuously to the normal system potential see text However this simple accelerative factor alone is not sufficient if a faithful description of the dif fusion path in the original system is required Voter 62 showed that to recover the true diffusional path it is important that the bias potential does not affect the structure of the transition state i e the saddle points for the system potential energy surface If this is the case then the relative rate constants for escape from a given structure or state to any other neighbouring state remains constant i e for transitions from state A to state B or state C TST REST REST g Ap C A C where A represents state A simulated with the bias potential present With this condition satisfied for all possible transitions
212. e accuracy of this estimation of the free energy surface is dependent on the deposition rate and the effective diffusion constant of the order parameters Typically the error is of order w the Gaussian weight A discussion of these issues is given by Laio et al 69 and Quigley and Rodger 68 The importance of using order parameters in the Hamiltonian 7 1 is that they are a direct measure of the structure of a particular phase Increasing the bias potential therefore has the effect of destabilising phases that are characterised by these parameters forcing the simulation to move to alternative structures with lower free energy In general several different order parameters can be used at the same time to improve the control of the selectivity of the various phases and the pathways between them However this must be weighed against the additional computational cost which grows exponentially with the number of order parameters Quigley and Rodger have described a protocol for deciding which order parameters to use in 68 Firstly a set of simulations of the disordered state and any accessible crystalline polymorph are performed and the equilibrium distributions for the candidate order parameters obtained see section 7 4 1 Any sets of parameters for which the distributions overlap are discarded until the sets remaining describe the known states with minimum ambiguity This ensures that the realisable structures are distinct in the collective space
213. e bias potential This option is selected by setting hkey 0 in the metadynamics section of the CONTROL file Wang Landau recursion Starting from a given Gaussian height a histogram is ac cumulated with each Gaussian addition recording the visits to each square of the order parameter space Once this histogram is approximately say 80 flat the Gaussian height is halved the histogram is reset to zero and then the process continues until a higher degree of flatness has been achieved and so on The procedure is meant to en sure that the added Gaussians make progressively finer contributions as convergence is approached Set hkey 1 for this option Note this option has been implemented only for the case where ncolvar 1 Well tempered dynamics The well tempered scheme uses a maximum energy crite rion A threshold energy Vinaz is set above the largest expected energy barrier and at 182 STFC Section 7 4 each step the Gaussian deposition height is given by M U woexp VauglsS WV peal where Vaug is the current value of the bias energy The parameters wo and Vinar are defined by the input directives ref_W_aug and wt_Dt in the CONTROL file see above Set hkey 2 for this option 2 Defining the switching function fe r The switching function is determined by the parameters r and ra in formula 7 9 These must be chosen so that 79 absolutely excludes near neighbouring atoms that are not intended to be considered part of the su
214. e energies mxtmls entries block record 5 atomic polarisation energies mxtmls entries block record 6 coulombic energies mxtmls mxtmls 1 2 entries 165 STFC Section 6 3 block record 7 van der Waals energies mxtmls mxtmls 1 2 entries block record 8 3 body energies mxtmls 2 mxtmls 3 mxtmls 6 entries block record 9 4 body energies mxtmls 6 mxtmls 11 mxtmls 6 mxtmls 24 entries It should be noted that writing the 2 3 and 4 body energies as a linear stream implies a certain ordering of molecule pairs indices i j triplets indices i j k and quartets indices i j k m The appropriate sequence order can be reconstructed from simple nested loops for pair triple or quadruple indices subject to the conditions i gt j for pairs i gt j gt k for triplets and i gt j gt k gt m for quartets with 7 as the outermost loop index For example the following code generates the correct sequence for a quartet as variable index index 0 do i 1 mxtmls do j 1 i do k 1 j do m 1 k index index 1 enddo enddo enddo enddo To assist users with analysis of the SOLVAT file two utility programs are available in the utility directory The program solsta f will calculate the averages and RMS deviations for all the variables in the file and the program soldis f will construct the distribution functions of all the variables in a form suitable for plotting 6 3 Free Energy by Thermodynamic Integration 6 3 1 Thermodyna
215. e in other scientific areas In particular the energy decomposition can be employed in any system of mixed species and the free energy feature can be used for other systems where a free energy difference is required A DL_POLY Classic module SOLVATION_MODULE F has been devised for these purposes It was developed in a collaboration between Daresbury Laboratory and the Institut Pluridisciplinaire de Recherche sur Environment et les Materiaux IPREM at the University of Pau The collaborators included Ross Brown Patrice Bordat and Pierre Andre Cazade at Pau and Bill Smith at Daresbury The bulk of the software development was done by Pierre Andre Cazade and was extended and adaptated for general DL_POLY distribution by Bill Smith 6 2 DL POLY Energy Decomposition 6 2 1 Overview In DL_POLY Classic the energy decomposition capability breaks down the system configuration energy into its contributions from the constituent molecular types What consitutes a molecule in this context is what is defined as such in the DL_POLY Classic FIELD file see section 4 1 3 It is not essential that all the atoms in the molecular definition be linked together by chemical bonds Nor is it essential for all identical molecules to be declared as one molecular type Groups of like molecules or individual molecules can be separated out if there is a compelling reason to do so It is not however possible to split molecules that are linked by chemical bonds into sub molecule
216. e interaction There is normally a very large number of these and they are therefore specified according to atom types rather than indices In DL POLY Classic it is assumed that the pair body terms arise from van der Waals and or electrostatic Coulombic forces The former are regarded as short ranged interactions and the latter as long ranged Long ranged forces require special techniques to evaluate accurately see section 2 4 In DL POLY Classic the three body terms are restricted to valence angle and H bond forms The nonbonded three body four body and Tersoff interactions are globally specified according to the types of atoms involved DL_POLY Classic also has the ability to handle metals via density dependent functions see below Though essentially many body potentials their particular form means they are handled in a manner very similar to pair potentials In DL_POLY Classic the intramolecular bonded terms are handled using bookkeeping arrays which specify the atoms involved in a particular interaction and point to the appropriate arrays of parameters that define the potential The calculation of bonded forces therefore follows the simple scheme 1 Every atom in the simulated system is assigned a unique index number from 1 to N 2 Every intramolecular bonded term Uiype in the system has a unique index number itype from 1 to Niype where type represents a bond angle or dihedral 3 A pointer array keyrype Ntype itype carries the ind
217. e same type Thus when specifying these potentials in the DL_POLY Classic FIELD file for an alloy composed of n different metal atom types both EAM and FSM require the specification of n n 1 2 pair functions v rij However the EAM requires only n density functions E lri whereas the FSM class reguires all the cross functions pi rij or n n 1 2 in total In addition to the n n 1 2 pair functions and n density functions the EAM requires further specification of n functional forms of the density dependence i e the embedding function F p in 2 137 For EAM potentials all the functions are supplied in tabular form via the table file TABEAM see section 4 1 6 to which DL POLY Classic is redirected by the FIELD file data The FSM potentials are defined via the necessary parameters in the FIELD file 2 3 6 External Fields In addition to the molecular force field DL_POLY Classic allows the use of an external force field Examples of field available include 1 Electric field elec Fi Fi qi H 2 168 2 Oscillating shear oshm EF Acos 2n7 z Lz 2 169 Al STFC Section 2 4 3 Continuous shear shrx 1 12 z4 gt z gt Zo 2 170 4 Gravitational field grav Fi Fi mi H 2 171 5 Magnetic field magn F F qu v AH 2 172 6 Containing sphere sphr F A Ro r ir gt Reut 2 173 7 Harmonic repulsive wall in z direction zbnd E A z 2 12 25 2 174 8 Harmoni
218. e system has no net momentum Ni mivilt 7 2 246 56 STFC Section 2 5 where i labels particles which can be atoms or rigid molecules M the number of particles in the system kg Boltzmanns constant and f the number of degrees of freedom in the system 3M 3 if the system is periodic and without constraints The total energy of the system is a conserved quantity HUnve U KE 2 247 where U is the potential energy of the system and KE the kinetic energy at time t 2 5 2 Bond Constraints 2 5 2 1 SHAKE The SHAKE algorithm for bond constraints was devised by Ryckaert et al 13 and is based on the Verlet leapfrog integration scheme 12 It is a two stage scheme In the first stage the leapfrog algorithm calculates the motion of the atoms in the system assuming a complete absence of the rigid bond forces The positions of the atoms at the end of this stage do not conserve the distance constraint required by the rigid bond and a correction is necessary In the second stage the deviation in the length of a given rigid bond is used retrospectively to compute the constraint force needed to conserve the bondlength It is relatively simple to show that the constraint force has the form 5 i biz dj dj o wid BAe dy dy 2 248 where pij is the reduced mass of the two atoms connected by the bond d and dij are the original and intermediate bond vectors dj is the constrained bondlength and At is the Verlet integra
219. e user must consider using more processors or a machine with larger memory per processor Message 1140 error failed allocation of four body arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1150 error failed allocation of four body work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1170 error failed allocation of three body arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1180 error failed allocation of three body work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor 254 STFC Section C 0 Message 1200 error failed allocation of external field arrays This is a memory allocatio
220. e velocities v are half a timestep behind The first step is to advance the velocities to t 1 2 At by integration of the force 1 f t 1 54 STFC Section 2 5 where m is the mass of a site and At is the timestep The positions are then advanced using the new velocities r t At r t At v t sat 2 241 Molecular dynamics simulations normally require properties that depend on position and ve locity at the same time such as the sum of potential and kinetic energy In the LF algorithm the velocity at time t is obtained from the average of the velocities half a timestep either side of time t 1 1 u t 7 vl 1 5 ult At ult 5At 2 242 The full selection of LF integration algorithms within DL_POLY Classic is as follows NVE 1 Verlet leaprog with SHAKE NVEQ 1 Rigid units with FIQA and SHAKE NVEQ 2 Linked rigid units with QSHAKE NVT_Bl Constant T Berendsen 20 with SHAKE NVT_El Constant T Evans 19 with SHAKE NVT H1 Constant T Hoover 21 with SHAKE NVTQ B1 Constant T Berendsen 20 with FIQA and SHAKE NVTQ B2 Constant T Berendsen 20 with QSHAKE NVTQ_H1 Constant T Hoover 21 with FIQA and SHAKE NVTG H2 Constant T Hoover 21 with QSHAKE NPT_B1 Constant T P Berendsen 20 with FIQA and SHAKE NPT_H1 Constant T P Hoover 21 with SHAKE NPTG B1 Constant T P Berendsen 20 with FIQA and SHAKE NPTQ B2 Constant T P Berendsen 20 with QSHAKE NPTQ H1 Constant T P Hoover 21
221. e with larger memory per processor Message 1730 error failed allocation of HK Ewald arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1740 error failed allocation of property arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1750 error failed allocation of spme arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1760 error failed allocation of ewald_spme f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1770 error failed allocation of quench f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system can
222. e_module f optimiser_module f solvation_module f solvation_module f define_system_module define_system_module define_system_module define_system_module define_system_module define_system_module define_system_module tersoff_module f Hh Hh Hh Hh Hh hh hh 289 STFC Section D 0 terint tersoff tersoff3 tethfrc thbfrc timchk torgue split traject traject_u transition_properties transition_time turn_rigid_body update_ghost update_quaternions vertest vertest2 vscaleg vv_integrate warning write_profile write_reference_confi xscale zden0 zden1 zero_kelvin subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine tersoff_module f tersoff_module f tersoff_module f tether_module f three_body_module f utility_module f optimiser_module f utility_module f utility_module f hyper_dynamics_module f hyper_dynamics_module f optimiser_module f solvation_module f lf rotation1 module f nlist_builders_module f nlist_builders_module f temp_scalers_module f integrator_module f error_module f hyper_dynamics_module f hyper_dynamics_module f tether_module f property_module f property_module f optimiser_module f 290 Index algorithm 5 54 96 Brode Ahlrich
223. eal variable 3 real potential key See table 4 14 potential parameter see table 4 14 potential parameter see table 4 14 cutoff range for this potential A The variables pertaining to each potential are described in table 4 14 Note that the third variable is the range at which the four body potential is truncated The distance is in A measured from the central atom 4 1 3 4 Metal Potentials Metal potentials in DL_POLY Classic are based on the Finnis Sinclair model FSM 3 118 the embedded atom model EAM 35 36 and STFC Section 4 1 Table 4 13 Three body potentials key potential type Variables 1 4 functional form thrm Truncated harmonic k 00 p U 0 6 bo exp r ri 07 shrm Screened harmonic k b pi p2 U 0 E 9 00 exp ri p1 Tik p2 bvs1 Screened Vessal 28 k 00 Pi Po U 0 CE my 0 m7 exp rij p1 Tik p2 bvs2 Truncated Vessal 29 k 00 a p U 0 k 0 0 b0 8 bo 27 gn 9 00 2 00 expl ri ri 0 hbnd H bond 7 Dro Rib U 0 Dnpcos 9 5 Rno T 5x 6 Rro rir 9 10 is the a b c angle Table 4 14 Four body Potentials key potential type Variables 1 2 functional formt harm Harmonic k Qo U k do hcos Harmonic cosine k Qo U E cos d cos 60 2 plan Planar A U 6 A 1 cos
224. ed pair force has exceeded the neighbour list array dimensions Action Standard user response Fix the parameter mxlist 228 STFC Section C 0 Message 110 error neighbour list array too small in parlst Construction of the Verlet neighbour list in subroutine parlst nonbonded pair force has exceeded the neighbour list array dimensions Action Standard user response Fix the parameter mxlist Message 112 error vertest array too small This error results when the dimension of the DL_POLY Classic VERTEST arrays which are used in checking if the Verlet list needs updating have been exceeded Action Standard user response Fix the parameter mslst Message 120 error invalid determinant in matrix inversion DL_POLY Classic occasionally needs to calculate matrix inverses usually the inverse of the matrix of cell vectors which is of size 3 x 3 For safety s sake a check on the determinant is made to prevent inadvertent use of a singular matrix Action Locate the incorrect matrix and fix it e g are cell vectors correct Message 130 error incorrect octahedral boundary condition When calculating minimum images DL_POLY Classic checks that the periodic boundary of the simulation cell is compatible with the specifed minimum image algorithm Program termination results if an inconsistency is found In this case the error refers to the truncated octahedral mini mum image which is inconsistent with the simulat
225. efining working arrays in subroutine PARLST_NSQ DL_POLY Classic has been found to be too small Action Standard user response Fix the parameter mxxdf Message 476 error mxxdf too small in parneulst subroutine The parameter mxxdf defining working arrays in subroutine PARNEULST is too small Action Standard user response Fix the parameter mxxdf Message 477 error mxxdf too small in prneulst subroutine The parameter mxxdf defining working arrays in subroutine PRNEULST is too small Action Standard user response Fix the parameter mxxdf Message 478 error mxxdf too small in forcesneu subroutine The parameter mxxdf defining working arrays in subroutine FORCESNEU is too small Action Standard user response Fix the parameter mxxdf Message 479 error mxxdf too small in multipleneu subroutine The parameter mxxdf defining working arrays in subroutine MULTIPLENEU is too small Action Standard user response Fix the parameter mxxdf 247 STFC Section C 0 Message 484 error only one potential of mean force permitted It is not permitted to define more than one potential of mean force in the FIELD file Action Check that the FIELD file contains only one PMF specification If more than one is needed DL_POLY Classic cannot handle it Message 486 error HK real space screening function cutoff violation DL_POLY Classic has detected an unacceptable degree of inaccuracy in the screening function near
226. electric charge nonzero In DL_POLY Classic a check on the total system charge will result in an error if the net charge of the system is nonzero Note In DL_POLY Classic this message has been disabled The program merely prints a warning stating that the system is not electrically neutral but it does not terminate the program watch out for this 225 STFC Section C 0 Action Check the specified atomic charges and their populations Make sure they add up to zero If the system is required to have a net zero charge you can enable the call to this error message in subroutine SYSDEF Message 91 error unidentified atom in 4 body potential list The specification of a four body potential in the FIELD file has referenced an atom type that is unknown Action Locate the erroneous atom type in the four body potential definition in the FIELD file and correct Make sure this atom type is specified by an atoms directive earlier in the file Message 92 error unidentified atom in tersoff potential list The specification of a Tersoff potential in the FIELD file has referenced an atom type that is un known Action Locate the erroneous atom type in the Tersoff potential definition in the FIELD file and correct Make sure this atom type is specified by an atoms directive earlier in the file Message 93 error cannot use shell model with rigid molecules The dynamical shell model implemented in DL_POLY Classic is not designed to
227. em cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1300 error failed allocation of densO array in npt_b0 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1310 error failed allocation of work arrays in npt_b0 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor 256 STFC Section C 0 Message 1320 error failed allocation of densO array in npt_h0 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1330 error failed allocation of work arrays in npt_h0 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1340 error failed alloca
228. ent tolerance must be set For example the recommended value for the force tolerance is normally 1 0 in DL_POLY units but values one or two orders of magnitude less may be tried It should be noted however that before the NEB calculation is run the configurations representing the start and end configurations must first be minimised to the accuracy required by the new tolerance by using the DL_POLY Classic optim option These optimised struc tures must be returned to the BASINS directory with the same file numbers as the original CFGBSN files 160 Chapter 6 Solvation 161 STFC Section 6 0 Scope of Chapter This chapter describes the features within DL_POLY Classic relevant to the subject of solvation The main features are decomposing the system configuration energy into its molecular components free energy calculations by thermodynamic integration and the calculation of solvent induced spectral shifts Some of these features are sufficently general to have applications in other areas besides solutions 162 STFC Section 6 2 6 1 Overview and Background This chapter is about the features within DL_POLY Classic for studying solutions These include decomposing the system configuration energy into various molecular components calculating free energies by the method of thermodynamic integration and calculating solvent induced spectral shifts Despite the focus on solutions however some of these features are applicabl
229. eplace the CONFIG file with one containing the velocities or if not available remove the restart directive altogether and let DL_POLY Classic create the velocities for itself Message 86 error calculated 3 body potential index too large DL_POLY Classic has a permitted maximum for the calculated index for any three body potential in the system i e as defined in the FIELD file If there are m distinct types of atom in the system the index can possibly range from 1 to m m 1 2 If the internally calculated index exceeds this number this error report results Action Standard user response Fix the parameter mxtbp Message 87 error too many link cells required in fbpfrc The FBPFRC subroutine uses link cells to compute the four body forces This message indicates that the link cell arrays have insufficient size to work properly Action Standard user response Fix the parameter mxcel1 Message 88 error too many tersoff potentials specified Too many Tersoff potentials have been defined in the FIELD file Certain arrays must be increased in size to accommodate the data Action Standard user response Fix the parameter mxter Message 89 error too many four body potentials specified Too many four body potential have been defined in the FIELD file Certain arrays must be in creased in size to accommodate the data Action Standard user response Fix the parameter mxfbp Message 90 error system total
230. eps and the equilibration period equil both in time steps The equilibration can be short or absent if the system was pre equilibrated In which case a useful alternative is to choose one of the NVT algorithms c In setting the job close time it is recommended to set the number to at least 500 times the clock time it takes to do one normal MD time step This is to prevent the program running out of time during a structural minimisation The timing information for this may be taken from the previous equilibration run d Set the remaining CONTROL keywords as were defined for the initial equilibration simulations 4 Before starting the BPD simulation use the UNIX mkdir command to make the following empty directories e BASINS to receive any new structures found e TRACKS to store the tracking configurations e PROFILES to store any transition pathways found by NEB calculations If the directories BASINS TRACKS and PROFILES already exist then carefully archive the data before deleting the contents These directories should not be emptied if the simulation is continuing restarting and a full history of the kinetics is required More about these directories and the files they contain can be found in section 5 5 5 Runthe BPD simulation This will perform a simulation at the state point requested checking for structural transitions at the BPD block intervals specified Each time it finds a structural transition it will reco
231. er if the cutoff scheme is based on neutral groups of atoms then at worst at long distance the interaction will be a dipole dipole interaction and vary as 1 r The truncation effects at the cutoff are therefore much less severe than if an atomistic scheme is used In DL POLY Classic the interaction is evaluated between all atoms of both groups if any site of the first group is within the cutoff distance of any site of the second group The groups are known interchangeably as charge groups or neutral groups in the documentation which serves as a reminder that the advantages of using such a scheme are lost if the groups carry an overall charge There is no formal requirement in DL_POLY Classic that the groups actually be electrically neutral The charge group scheme is more cpu intensive than a simple atomistic cutoff scheme as more computation is required to determine whether or not to include a set of interactions However the size of the Verlet neighbourhood list easily the largest array in DL POLY Classic is considerably smaller with a charge group scheme than an atomistic scheme as only a list of interacting groups need be stored as opposed to a list of interacting atoms 2 4 2 Direct Coulomb Sum Use of the direct Coulomb sum is sometimes necessary for accurate simulation of isolated nonpe riodic systems It is not recommended for periodic systems The interaction potential for two charged ions is 1 ga Ulr 2
232. er one the user must consider using more processors or a machine with larger memory per processor 272 STFC Section C 0 Message 2170 error failed allocation of nptqvv_b1 f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 2180 error failed allocation of nptqvv_b2 f dens0 array This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 2190 error failed allocation of nptqvv_b2 f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 2200 error failed allocation of nptqvv_h1 f dens0 array This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 2210 error failed allocation of nptqvv_h1 f work arrays
233. ergy engtet real tethering energy enthal real enthalpy total energy PV record iv stpval 11 stpval 15 tmprot real rotational temperature vir real total virial virsrp real VdW metal Tersoff virial vircpe real electrostatic virial virbnd real bond virial record v stpval 16 stpval 20 virang real valence angle 3 body virial 134 STFC Section 4 2 vircon real constraint virial virtet real tethering virial volume real volume tmpshl real core shell temperature record vi stpval 21 stpval 25 engshl real core shell potential energy virshl real core shell virial alpha real MD cell angle a beta real MD cell angle 8 gamma real MD cell angle y record vii stpval 26 stpval 27 virpmf real Potential of Mean Force virial press real pressure the next ntpatm entries amsd 1 real mean squared displacement of first atom types amsd 2 real mean squared displacement of second atom types amsd ntpatm real mean squared displacement of last atom types the next 9 entries if the stress tensor is calculated stress 1 real xx component of stress tensor stress 2 real xy component of stress tensor stress 3 real xz component of stress tensor stress 4 real yx component of stress tensor T real y stress 9 real zz component of stress tensor the next 9 entries if a NPT simulation is undertaken cell 1 real x component of a cell vector cell 2 real y component of a cell vector cell 3 real z component of a cell vector cell 4 real x comp
234. error simulation forces option not specified DL_POLY Classic has failed to find any directive specifying the electrostatic interactions options in the CONTROL file Action Ensure the CONTROL file contains at least one directive specifying the electrostatic potentials e g ewald coul no electrostatics etc Message 384 error verlet strip width not specified DL_POLY Classic has failed to find the delr directive in the CONTROL file Action Insert a delr directive in the CONTROL file specifying the width of the verlet strip augmenting the forces cutoff Message 385 error primary cutoff not specified DL_POLY Classic has failed to find the prim directive in the CONTROL file Necessary only if multiple timestep option required Action Insert a prim directive in the CONTROL file specifying the primary cutoff radius in the multiple timestep algorithm Message 386 error primary cutoff larger than rcut The primary cutoff specified by the prim directive in the CONTROL file exceeds the value speci fied for the forces cutoff directive cut Applies only if the multiple timestep option is required Action Locate the prim directive in the CONTROL file and alter the chosen cutoff Alternatively increase the real space cutoff specified with the cut directive Take care to avoid error number 398 Message 387 error system pressure not specified The target system pressure has not been specified in the CONTROL file Applies t
235. es also The third file required is the FIELD file section 4 1 3 which specifies the nature of the intermolecular interactions the molecular topology and the atomic properties such as charge and mass Sometimes you will also require a TABLE file section 4 1 5 which contains the potential and force arrays for functional forms not available within DL POLY Classic usually because they are too complex e g spline potentials Sometimes you will also require a TABEAM file section 4 1 6 if your simulation includes embedded atom potentials for metallic systems Examples of input files are found in the data sub directory which can be copied into the execute subdirectory using the select macro found in the execute sub directory A successful run of DL_POLY Classic will generate several data files which appear in the execute sub directory The most obvious one is the file OUTPUT section 4 2 2 which provides an effective summary of the job run the input information starting configuration instantaneous and rolling averaged thermodynamic data final configurations radial distribution functions RDFs and job timing data The OUTPUT file is human readable Also present will be the restart files REVIVE section 4 2 5 and REVCON section 4 2 3 REVIVE contains the accumulated data for 86 STFC Section 3 2 a number of thermodynamic quantities and RDFs and is intended to be used as the input file for a following run It is not human reada
236. etadynamics simulation has been long enough is a matter of judging whether the system is diffusing like a random walk in the space of the order parameters i e that it is sampling all the available parameter space This is somewhat easier in the cases of Wang Landau recursion and well tempered dynamics as it is indicated by the parameter w the Gaussian height becoming relatively small In general a degree of experience in the technique is required to make a good judgement 6 Contra indications A useful point to note is that if a simulation does not reach a state where transitions between minima occur rapidly without residual hysteresis then by implication the original choice of order parameters was poor 7 4 2 Analysing the Metadynamics Results Analysis of the results of a metadynamics simulation can take a number of forms some of which are outlined here 1 Determination of free energy The information in the METADYNAMCS file is sufficient to define the system free energy 183 STFC Section 7 4 surface through equation 7 4 The free energy is a function of the M order parameters in the vector sM rN This information can be used to determine the free energy of activation and free energy differences between states in the following manner Firstly the free energy is projected down to a smaller subset of order parameters usually about 2 by integrating exp F kgT over the other order parameters and then Boltzman inverting This is
237. etails For TAD objective is to find the escape route for a transition from the starting state and halting the analysis of the reaction path at the first minimum is sufficient to define the escape The intermediate state provides a valid possible basin for further study of the kinetics of the system This is sensible if the two peaks on the reaction path are of similar magnitude However it is quite possible that the second peak is much higher or much lower than the first The first of these possibilities means that choosing the first minimum as the starting basin for a new simulation will most likely consistently return the system to the original starting state The second possibility suggests that the second state on the reaction path is a better option for the next phase of the study To decide between these possibilities it is necessary to determine the activation energy of the second peak Thus in both BPD and TAD when a multiple maximum is found on the reaction path a NEB calculation is needed to complete the path analysis See the following section 5 7 for details 5 7 Running a Nudged Elastic Band Calculation Running an independent NEB calculation may be necessary to improve the accuracy of the cal culated activation energy or to determine the activation energy in transitions not fully evaluated when they occurred in a BPD or TAD simulation due to the occurrence of a multiple maximum on the reaction path 158 STFC Section 5 7
238. eters e g k units s where s is one of eV kcal kJ or K signifying electron volts kilo cals per mole kilo joules per mole or Kelvin respectively No units directive means DL_POLY internal units apply Forces are in chosen energy units per Angstrom Set the size of the simulation TAD block i e the number of time steps between structure optimisations e g num_block 500 Set the number of configurations between each write of a tracking configuration file This should be an integer divisor of the TAD block number e g num_track 10 Set the blackout period in time steps following a transition detection e g blackout 200 A blackout period is intended to stop the program recording transitions that are corre lated with a previous one These are classified as ignored transitions Set the catch radius i e the minimum distance in Angstroms any atom may be displaced in the minimised structure before it is recorded as a transition e g catch_radius 3 0 Set the NEB spring constant in specified energy units per A e g neb spring 1000 0 in DL POLY units Set the reliability factor for the high temperature simulation For input purposes this is defined as the ratio log 1 9 Vinin see above e g deltad 0 001 Set the low temperature To for the TAD method i e the temperature for which the results are needed in Kelvin e g low_temp 30 0 Select a minimisation option e g keyword tol Where key
239. eyword restart If this is not specified in the CONTROL file the simulation will start as new If specifed it will either continue a previous simulation restart or start anew simulation with initial temperature scaling of the previous configuration restart scale or without initial temperature scaling restart noscale Internally these options are handled by the integer variable keyres which is explained in table 4 1 The various ensemble options i e nve nvt ber nvt evans nvt hoover npt ber npt hoover nst ber nst hoover are mutually exclusive though none is mandatory the default is the NVE ensemble These options are handled internally by the integer variable keyens The meaning of this variable is explained in table 4 2 The force selection directives ewald sum ewald precision reaction coul shift dist no elec and no vdw are handled internally by the integer variable keyfce See table 4 4 for an explanation of this variable Note that these options are mutually exclusive The choice of reaction field electrostatics directive reaction requires also the specification of the relative dielectric constant external to the cavity This is specified in the eps directive DL_POLY Classic uses as many as three different potential cutoffs These are as follows a cut this is the universal cutoff It applies to the real space part of the electrostatics calculations and to the van der Waals potentials if no other c
240. f 1 is assumed A number greater than 1 specified here indicates that the next 109 STFC Section 4 1 nrept 1 entries in the CONFIG file are ascribed the atomic characteristics given in the current record The sum of the repeat numbers for all atoms in a molecule should equal the number specified by the atoms directive 4 shell n m where n is the number of core shell units and m is an integer specifying which shell model is required e m 1 for adiabatic shell model e m 2 for relaxed shell model Each of the subsequent n records contains index 1 integer site index of core index 2 integer site index of shell k real force constant of core shell spring k4 real quartic anharmonic force constant of spring The spring force constant k is entered in units of engunit A or engunit A for ky where engunit is the energy unit specified in the units directive The general spring potential has the form 1 L 4 Vora 0 Sri F g kari where usually k gt gt k The adiabatic and relaxed shell models are mutually exclusive options in the same simulation Note that the atomic site indices referred to in this table are indices arising from num bering each atom in the molecule from 1 to the number specified in the atoms directive for this molecule This same numbering scheme should be used for all descriptions of this molecule including the bonds constraints angles and dihedrals entries described below DL_POLY Class
241. f DL_POLY Classic Changing ndump necessitates recompiling DL_POLY Classic REVCON is identical in format to the CONFIG input file see section 4 1 2 REVCON should be renamed CONFIG to continue a simulation from one job to the next This is done for you by the copy macro supplied in the execute directory of DL POLY Classic 4 2 4 The CFGMIN File The CFGMIN file only appears if the user has selected the programmed minimisation option di rective minim in the CONTROL file Its contents have the same format as the CONFIG file see section 4 1 2 but contains only atomic position data and will never contain either velocity or force data i e parameter levcfg is always zero In addition two extra numbers appear on the end of the second line of the file 1 an integer indicating the number of minimisation cycles required to obtain the structure format 110 132 STFC Section 4 2 2 the configuration energy of the final structure expressed in DL POLY units 1 3 10 format F20 4 2 5 The REVIVE File This file is unformatted and written by the subroutine REVIVE It contains the accumulated statis tical data It is updated whenever the file REVCON is updated see previous section REVIVE should be renamed REVOLD to continue a simulation from one job to the next This is done by the copy macro supplied in the execute directory of DL POLY Classic In addition to continue a simulation from a previous job the restart keyword must be i
242. f the SHAKE algorithm for constraint bonds between rigid bodies The parallel strategy is very similar to that of SHAKE The only significant difference is that increments to the atomic forces not the atomic positions are passed between processors at the end of each iteration 80 Chapter 3 Construction and Execution 81 STFC Section 3 0 Scope of Chapter This chapter describes how to compile a working version of DL_POLY Classic and how to run it 82 STFC Section 3 2 3 1 Constructing DL POLY Classic 3 1 1 Overview The DL_POLY Classic executable program is constructed as follows 1 DL POLY Classic is supplied as a UNIX compressed tar file This must uncompressed and un tared to create the DL_POLY Classic directory section 1 4 2 In the build subdirectory you will find the required DL_POLY Classic makefile see section 3 2 1 and Appendix A where a sample Makefile is listed This must be copied into the subdirectory containing the relevant source code In most cases this will be the source sub directory 3 The makefile is executed with the appropriate keywords section 3 2 1 which selects for spe cific computers including serail and parallel machines and the appropriate communication software 4 The makefile produces the executable version of the code which as a default will be named DLPOLY X and located in the execute subdirectory 5 DL_POLY also has a Java GUI The files for this are stored in
243. ferent electric charges the sum of which equals the charge on the original atom There is no electrostatic interaction i e self interaction between the core and shell of the same atom Non Coulombic interactions arise from the shell alone The harmonic spring has a potential of the form 1 Veringa Ti a hrs 2 236 Sometimes an anharmonic spring is used which is quartic in form l2 lia Vspringlrij kr kario a Normally k is much larger than k The effect of an electric field is to separate the core and shell giving rise to a polarisation dipole The condition of static equilibrium gives the polarisability as a q k 2 238 where qs is the shell charge and k is the force constant of the harmonic spring In the adiabatic method a fraction of the atomic mass is assigned to the shell to permit a dynamical description The fraction of mass is chosen to ensure that the natural frequency of vibration v of the harmonic spring i e bea Ee L 2 239 STFC Section 2 5 with m the atomic mass is well above the frequency of vibration of the whole atom in the bulk system Dynamically the core shell unit resembles a diatomic molecule with a harmonic bond however the high vibrational frequency of the bond prevents effective exchange of kinetic energy between the core shell unit and the remaining system Therefore from an initial condition in which the core shell units have negligible internal vibrational energy the units will
244. for example from the GROMOS 6 Dreiding 7 or AMBER 8 forcefield which share functional forms It is rel atively easy to adapt DL_POLY Classic to user specific force fields Note that DL POLY Classic does not have its own force field It is designed to be used with existing force fields 1 2 3 Boundary Conditions DL_POLY Classic will accommodate the following boundary conditions 1 None e g isolated polymer in space 2 Cubic periodic boundaries Orthorhombic periodic boundaries Parallelepiped periodic boundaries Truncated octahedral periodic boundaries Rhombic dodecahedral periodic boundaries Slab x y periodic z nonperiodic o ND oO B OQ Hexagonal prism periodic boundaries These are describe in detail in Appendix B 1 2 4 The Java Graphical User Interface DL_POLY Classic has a Graphical User Interface GUI written specifically for the package in the Java programming language from Sun microsystems The Java programming environment is free and it is particularly suitable for building graphical user interfaces An attractive aspect of java is the portability of the compiled GUI which may be run without recompiling on any Java supported machine The GUI is an integral component of the DL_POLY Classic package and is available under the same terms See 9 STFC Section 1 3 1 2 5 Algorithms 1 2 5 1 Parallel Algorithms DL_POLY Classic exclusively employs the Replicated Data parallelisation str
245. for investigation by TAD or BPD Message 2355 error cannot run both TAD and BPD together The TAD and BPD options are not meant to run concurrently Choose one or the other Action Remove either the TAD or BPD option from the CONTROL file Message 2500 error in number of collective variables ncolvar too small The number of order parameters in a metadynamics simulation has not been properly specified Action Check input data in CONTROL file and correct accordingly Message 2501 Wang Landau style recursion not yet implemented for ncolvar gt 1 The Wang Landau recursion option in metadynamics is currently limted to one order parameter only Action Select another Gaussian convergence option in the CONTROL file Message 2502 Unrecognised Gaussian height scheme An invalid option has been selected for the metadynamics Gaussian convergence scheme which is rstricted to values 0 1 and 2 Action Reset the hkey option to an acceptable value in the CONTROL file Message 2503 Error maxhis exceeded in metadynamics The internal storage of Gaussian data in metadynamics has been exceeded Action This can be recovered if a greater number of processing nodes is used at restart but ideally a less ambitious Gaussian deposition rate should be considered 276 STFC Section C 0 Message 2504 Error allocating comms buffer in compute_bias_potential Unlikely array allocation error which should not occur under normal use
246. harm Harmonic k do U k bo hcos Harmonic cosine k 60 U cos cos o cos3 Triple cosine A Ap A3 U 5A1 1 cos 6 542 1 cos 2 34A3 1 cos 3 ryck Ryckaert A U 6 Alag acoso agcos a3cos b Bellemans acost ascos 4 ag as pre set rbf Fluorinated B U B bo bicos bacos b b3cos Ryckaert bacos bscos 6 beexp b7 1 Bellemans bo bg pre set opls OPLS Ao Ay Az Ag U 6 Ao 5 41 1 cos Ax 1 cos 2 A3 1 cos 3 t is the a b c d dihedral angle 10 inversions n where nis the number of inversion interactions present in the molecule Each of the following 114 STFC Section 4 1 11 n records contains inversion key index 1 index 2 index 3 index 4 variable 1 variable 2 ad integer integer integer integer real real potential key See table 4 10 first atomic index second atomic index third atomic index fourth atomic index potential parameter see table 4 10 potential parameter see table 4 10 The meaning of the variables 1 2 is given in table 4 10 This directive and associated data records need not be specified if the molecule contains no inversion angle terms See the note on the atomic indices appearing under the shell directive above Table 4 10 Inversion Angle Potentials key potential type Variables 1 2
247. he test cases are documented in chapter 8 1 4 4 The bench Sub directory This directory contains examples of input and output data for DL_POLY Classic that are suitable for benchmarking DL POLY Classic on large scale computers These are described in chapter 8 1 4 5 The execute Sub directory In the supplied version of DL POLY Classic this sub directory contains only a few macros for copying and storing data from and to the data sub directory and for submitting programs for execution These are decribed in section 9 1 1 However when a DL POLY Classic program is assembled using its makefile it will be placed in this sub directory and will subsequently be executed from here The output from the job will also appear here so users will find it convenient to use this sub directory if they wish to use DL_POLY Classic as intended The experienced user is not absolutely required to use DL_POLY Classic this way however 1 4 6 The build Sub directory This sub directory contains the standard makefiles for the creation i e compilation and link ing of the DL POLY Classic simulation programs The makefiles supplied select the appropriate subroutines from the source sub directory and deposit the executable program in the execute di rectory The user is advised to copy the appropriate makefile into the source directory in case any modifications are required The copy in the build sub directory will then serve as a backup 1 4 7 The java Sub direc
248. he vdw cutoff rvdw in the CONTROL file or reconstruct the TABLE file Message 506 error work arrays too small for quaternion integration The working arrays associated with quaternions are too small for the size of system being simu lated They must be redimensioned Action Standard user response Fix the parameter msgrp 249 STFC Section C 0 Message 508 error rigid bodies not permitted with RESPA algorithm The RESPA algorithm implemented in DL POLY Classic is for atomic systems only Rigid bodies or constraints cannot be treated Action There is no cure for this The code simply does not have this capability Consider writing it for yourself Message 510 error structure optimiser not permitted with RESPA The RESPA algorithm in DL POLY Classic has not been implemented to work with the structure optimizer You have asked for a forbidden operation Action There is no fix for this In any case it does not make sense to use the RESPA algorithm for this purpose Message 513 error SPME not available for given boundary conditions The SPME algorithm in DL POLY Classic does not work for aperiodic IMCON 0 or slab IM CON 6 boundary conditions Action If the system must have aperiodic or slab boundaries nothing can be done In the latter case however it may be acceptable to represent the same system with slabs replicated in the z direction thus permitting a periodic simulation Message 514 error SP
249. hermostat several iterations are required to obtain self consistency DL_POLY Classic uses 4 iterations 5 if bond constraints are present with the standard Verlet leapfrog predictions for the initial estimates of T t P t u t and r t At Note also that the change in box size requires the SHAKE algorithm to be called each iteration with the new cell vectors and volume obtained from V t At V t exp bat n t 340 Hee Ad E ks fatne 5A1 H t 2 271 where H is the cell matrix whose columns are the three cell vectors a b c The isotropic changes to cell volume are implemented in the DL POLY LF routine NPT_H1 which allows for systems containing bond constraints The implementation in the VV algorithm follows the scheme AN yk At xt A 0 SLB TE Toa y Wol ke Taa Ye ae Fixe Zanele nes 5a nf Y OPO Pea xn wl alis Aae ut say w O 1 r t At r t Atutt At call rattle R 1 V t At lt V t exp sat nt 5an HG AI eh E n t 40 H t JEVA E WCE ANA At f t At 2 2 m call rattle V nt At nt At mere P t At Ps x t At n t At At v t At Sn At v t At y tt At xlt Ai E FEL At Toxt S Wal At kpToxt v t At V t A1 Ata Atju t At 2 272 64 STFC Section 2 5 Routines rattle R and rattle V apply the bondlength and velocity constraint formulae 2 251 and 2 252 re
250. hm The second constraint condition attempts to maintain the relative velocities of the atoms sharing a bond to a direction perpendicular to the bond vector This provides another constraint force 58 STFC Section 2 5 2hij dij gt vj vi y At de 0 Hya 2 252 This constraint force is applied during the second stage of the velocity Verlet algorithm Both constraint force calculations are iterative and are brought to convergence before proceeding to the next stage of the velocity Verlet scheme DL_POLY Classic implements a parallel version of RATTLE that is based on the same ap proach as SHAKE 11 see section 2 6 9 The subroutine NVEVV_1 implements the velocity Verlet algorithm with bond constraints in the NVE ensemble The subroutine RDRATTLE_R is called to apply the corrections to atom positions and the subroutine RDRATTLE_V is called to correct the atom velocities 2 5 3 Potential of Mean Force PMF Constraints and the Evaluation of Free Energy A generalization of bond constraints can be made to constrain a system to some point along a reaction coordinate A simple example of such a reaction coordinate would be the distance between two ions in solution If a number of simulations are conducted with the system constrained to different points along the reaction coordinate then the mean constraint force may be plotted as a function of reaction coordinate and the function integrated to obtain the free energy for the overall
251. hort range Van der Waals contributions to energy and force are eval uated by interpolation of tables constructed at the beginning of execution DL_POLY Classic employs a 3 point interpolation scheme A guide to the minimum number of grid points mxgrid required for interpolation in r to give good energy conservation in a simulation is mxgrid gt 100 rcut rmin where rmin is the smallest position minimum of the non bonded potentials in the system The parameter mxgrid is defined in the DL_PARAMS INC file and must be set before compilation A utility program TABCHK is provided in the DL_POLY utility sub directory to help users choose a sufficiently accurate interpolation scheme including array sizes for their needs 3 2 2 Running DL_POLY Classic To run the DL POLY Classic executable DLPOLY X for most applications you will initially require three possibly four input data files which you must create in the execute sub directory or whichever sub directory you keep the executable program The first of these is the CONTROL file section 4 1 1 which indicates to DL_POLY Classic what kind of simulation you want to run how much data you want to gather and for how long you want the job to run The second file you need is the CONFIG file section 4 1 2 This contains the atom positions and depending on how the file was created e g whether this is a configuration created from scratch or the end point of another run the velociti
252. ials eng_cou configurational energy due to electrostatic potential eng bnd configurational energy due to chemical bond potentials eng_ang configurational energy due to valence angle and three body potentials eng dih configurational energy due to dihedral inversion and four body potentials eng tet configurational energy due to tethering potentials line 2 time elapsed simulation time fs ps ns since the beginning of the job eng _pv enthalpy of system temp_rot rotational temperature vir_cfg total configurational contribution to the virial vir_vdw short range potential contribution to the virial vir_cou electrostatic potential contribution to the virial 130 STFC Section 4 2 vir_bnd chemical bond contribution to the virial vir_ang angular and three body potentials contribution to the virial vir_con constraint bond contribution to the virial vir_tet tethering potential contribution to the virial line 3 cpu time elapsed cpu time s m h d since the beginning of the job volume system volume temp_shl core shell temperature eng _shl configurational energy due to core shell potentials vir_shl core shell potential contribution to the virial alpha angle between b and c cell vectors beta angle between c and a cell vectors gamma angle between a and b cell vectors vir_pmf Potential of mean force constraint contribution to the virial press pressure Note The total internal energy of the system variable tot_energy includes all contributions to the
253. ic boundary condition can be used with the Ewald summation method 207 STFC Section B 0 Figure B 1 The cubic MD cell Orthorhombic periodic boundaries IMCON 2 The orthorhombic cell is also a common periodic boundary which closely resembles the cubic cell in use In DL_POLY Classic the cell is defined with principle axes passing through the centres of the faces For an orthorhombic cell with sidelengths D in X direction E in Y direction and F in Z direction the cell vectors appearing in the CONFIG file should be D 0 0 0 E 0 0 0 F Note the origin of the atomic coordinates is the centre of the cell The orthorhombic boundary condition can be used with the Ewald summation method Figure B 2 The orthorhomic MD cell Parallelepiped periodic boundaries IMCON 3 The parallelepiped e g monoclinic or triclinic cell is generally used in simulations of crystalline materials where its shape and dimension is commensurate with the unit cell of the crystal Thus for a unit cell specified by three principal vectors a b c the MD cell is defined in the DL_POLY Classic CONFIG file by the vectors La Laz Laz Mb1 Mb2 Mbs Nc Mc2 Nc3 in which L M N are integers reflecting the multiplication of the unit cell in each principal direction Note that the atomic coordinate origin is the centre of the MD cell The parallelepiped boundary condition can be used with the Ewald summation method 208 STFC Section B 0
254. ic will itself construct the global indices for all atoms in the systems This directive and associated data records need not be specified if the molecule contains no core shell units 5 bonds n where n is the number of flexible chemical bonds in the molecule Each of the subsequent n records contains bond key ad see table 4 7 index 1 integer first atomic site in bond index 2 integer second atomic site in bond variable 1 real potential parameter see table 4 7 variable 2 real potential parameter see table 4 7 variable 3 real potential parameter see table 4 7 variable 4 real potential parameter see table 4 7 The meaning of these variables is given in table 4 7 This directive and associated data records need not be specified if the molecule contains no flexible chemical bonds See the note on the atomic indices appearing under the shell directive above 110 STFC Section 4 1 Table 4 7 Chemical bond potentials key potential type Variables 1 4 functional form harm Harmonic k ro U r 5k r ro hrm mors Morse Eo ro k U r Eo 1 exp k r r0 1 mrs 12 6 12 6 A B U r 4 126 rhrm Restraint k ro Te U r k r ro lr rol lt re Ur kr kre r rol re r rol gt Te rhm quar Quartic k ro ko RY U r r ro Kr ro 4 E r ro gur buck Buckingham Alp C U r Aexp r p C r bck A 2 fene FENE
255. ices of the specific atoms involved in the potential term labelled itype The dimension type will be 2 3 or 4 if the term represents a bond valence angle dihedral inversion 4 The array keytype Ntypes itype is used to identify the atoms in a bonded term and the appro priate form of interaction and thus to calculate the energy and forces DL_POLY Classic calculates the nonbonded pair interactions using a Verlet neighbour list 12 which is reconstructed at intervals during the simulation This list records the indices of all sec ondary atoms within a certain radius of each primary atom the radius being the cut off radius reut normally applied to the nonbonded potential function plus an additional increment Ar yz The neighbour list removes the need to scan over all atoms in the simulation at every timestep The larger radius reut Areut means the same list can be used for several timesteps without requiring an update The frequency at which the list must be updated depends on the thickness of the region Afreut DL POLY Classic has two methods for constructing the neighbour list the first is based on the Brode Ahlrichs scheme 23 and is used when reut is large in comparison with the simulation cell the second uses the link cell algorithm 24 when reut is relatively small The potential energy and forces arising from the nonbonded interactions are calculated using interpolation tables A complication in the construction of
256. ics data every n timesteps steps n Run simulation for n timesteps temp f Set required simulation temperature to f K trajijk Write HISTORY file with controls start timestep for dumping configurations j timestep interval between configurations k data level i e variable keytrj see table 4 3 timestep f Set timestep to f ps zden n wz Calculate the z density profile with n the time step interval between configurations w the z density bin width 4 z the range of z coordinate required 2 2 z 2 A zero Perform zero temperature MD run 4 1 1 3 Further Comments on the CONTROL File 1 A number of the directives or their mutually exclusive alternatives are mandatory a timestep specifying the simulation timestep b temp or zero specifying the system temperature not mutually exclusive c ewald sum or ewald precision or spme sum or spme precision or hke sum or hke precision or coul or shift or distan or reaction or no elec specifying the required coulombic forces option d cut and delr specifying the short range forces cutoff and Verlet strip e prim specifying primary forces cutoff if mult gt 2 only 2 The job time and close time directives are required to ensure a controlled close down procedure when a job runs out of time The time specified by the job time directive indicates the total time allowed for the job This must obviously be set equal to the time specified to the operating system when the job
257. igid bodies linked by constraints may also be minimised by these methods 3 Of the three minimisation methods available in DL POLY Classic only the programmed minimiser is capable of finding more than one minimum without the user intervening 4 Finally we emphasise once again that the purpose of the minimisers in DL POLY Classic is to help improve the quality of the starting structure and we believe they are adequate for that purpose We do not recommend them as general molecular structure optimisers They may however prove useful for relaxing crystal structures to 0 Kelvin for the purpose of identifying a true crystal structure 3 2 5 Choosing Ewald Sum Variables 3 2 5 1 Ewald sum and SPME This section outlines how to optimise the accuracy of the Ewald sum parameters for a given simu lation In what follows the directive spme may be used anywhere in place of the directive ewald if the user wishes to use the Smoothed Particle Mesh Ewald method As a guide to beginners DL_POLY Classic will calculate reasonable parameters if the ewald precision directive is used in the CONTROL file see section 4 1 1 A relative error see below of 109 is normally sufficient so the directive ewald precision 1d 6 will cause DL_POLY Classic to evaluate its best guess at the Ewald parameters a kmax1 kmax2 and kmax3 The user should note that this represents an estimate and there are sometimes circumstances where the estimate can be improved upon This is
258. ind all the atoms described in the exclusion list within the simulation cell This should never occur if it does it means a serious bookkeeping error has occured The probable cause is corruption of the code somehow Action If you feel you can tackle it good luck Otherwise we recommend you get in touch with the program authors Keep all relevant data files to help them find the problem Message 170 error too many variables for statistic array This error means the statistics arrays appearing in subroutine STATIC are too small This can happen if the number of unique atom types is too large Action Standard user response Fix the parameter mxnstk mxnstk should be at least 45 number of unique atom types Message 180 error Ewald sum requested in non periodic system DL_POLY Classic can use either the Ewald method or direct summation to calculate the electro static potentials and forces in periodic or pseudo periodic systems For non periodic systems only direct summation is possible If the Ewald summation is requested with the ewald sum or ewald precision directives in the CONTROL file without periodic boundary conditions termination of the program results Action Select periodic boundaries by setting the variable imcon gt 0 in the CONFIG file if possible or use a different method to evaluate electrostatic interactions e g by usinf the coul directive in the CONTROL file 231 STFC Section C 0 Message 185 e
259. inlo TEnlEjkLinla lLjx X El 2 59 he Uralita lenta A tal 2 60 The sum of the diagonal elements of the stress tensor is zero since the virial is zero and the matrix 1s symmetric Lastly it should be noted that the above description does not take into account the possible inclusion of distance dependent 1 4 interactions as permitted by some force fields Such interactions are permissible in DL_POLY Classic and are described in the section on pair potentials below DL_POLY Classic also permits scaling of the 1 4 interactions by a numerical factor 1 4 interactions do of course contribute to the atomic virial In DL_POLY Classic dihedral forces are handled by the routine DIHFRC 2 2 6 Improper Dihedral Angle Potentials Improper dihedrals are used to restrict the geometry of molecules and as such need not have a simple relation to conventional chemical bonding DL POLY Classic makes no distinction between 22 STFC Section 2 2 dihedral angle functions and improper dihedrals both are calculated by the same subroutines and all the comments made in the preceeding section apply An important example of the use of the improper dihedral is to conserve the structure of chiral centres in molecules modelled by united atom centres For example a amino acids such as alanine CH3CH NH2 COOH in which it is common to represent the CH3 and CH groups as single centres Conservation of the chirality of the a carbon is achieved by defini
260. ion The program bsncmp f in the utility directory may be used for this purpose It is designed to compare start and end configurations in the BASINS subdirectory and list the atoms that have changed location 5 5 DL POLY Classic Hyperdynamics Files The DL_POLY Classic BPD and TAD options generate a potentially large number of files in addition to those normally produced and described in Chapter 4 Some are sufficient in number to warrant creation of additional sub directories of the DL_POLY execute sub directory These files are as follows 1 HYPRES the hyperdynamics restart file which stores unformatted data to permit contin uation of an unfinished BPD or TAD simulation It is created in the execute sub directory This file becomes the HYPOLD file which is used in restarting a BPD or TAD simulation 2 EVENTS a summary of events that have occurred in the course of a hyperdynamics simu lation one record per event It is generated in the execute sub directory 3 CFGBSNnn a basin file which contains the coordinates of each distinct state DL POLY Classic has found during the BPD or TAD run nn is an integer rising from 0 to 9999 All such files are generated in the erecute BASINS sub directory 4 PROnn XY a profile file which is a list of the reaction coordinate and configuration energy of each bead in the converged NEB calculation nn is an integer rising from 0 to 9999 All such files are generated in the ere
261. ion 3 2 4 When restarting from a previous run of DL_POLY Classic i e using the restart restart scale or restart noscale directives in the CONTROL file above the CONFIG file must be replaced by the REVCON file which is renamed as the CONFIG file The copy macro in the execute sub directory of DL_POLY Classic does this for you 105 STFC Section 4 1 Table 4 5 CONFIG file key record 2 levcfg meaning 0 Coordinates included in file 1 Coordinates and velocities included in file 2 Coordinates velocities and forces included in file Table 4 6 Periodic boundary key record 2 imcon meaning aowbrWNFH no periodic boundaries cubic boundary conditions orthorhombic boundary conditions parallelepiped boundary conditions truncated octahedral boundary conditions rhombic dodecahedral boundary conditions x y parallelogram boundary conditions with no periodicity in the z direction hexagonal prism boundary conditions 106 STFC Section 4 1 4 1 3 The FIELD File The FIELD file contains the force field information defining the nature of the molecular forces It is read by the subroutine SYSDEF Excerpts from a force field file are shown below The example is the antibiotic Valinomycin in a cluster of 146 water molecules Valinomycin Molecule with 146 SPC Waters UNITS kcal MOLECULES 2 Valinomycin NUMMOLS 1 ATOMS 168 0 16 0000 0 4160 1 OS 16 0000 0 4550 1 HC 1
262. ion cell The most probable cause is the incorrect definition of the simulation cell vectors present in the input file CONFIG these must equal the vectors of the enscribing cubic cell Action Check the specified simulation cell vectors and correct accordingly Message 135 error incorrect hexagonal prism boundary condition When calculating minimum images DL_POLY Classic checks that the periodic boundary of the simulation cell is compatible with the specifed minimum image algorithm Program termination results if an inconsistency is found In this case the error refers to the hexagonal prism minimum image which is inconsistent with the simulation cell The most probable cause is the incorrect definition of the simulation cell vectors present in the input file CONFIG these must equal the vectors of the enscribing orthorhombic cell Action Check the specified simulation cell vectors and correct accordingly 229 STFC Section C 0 Message 140 error incorrect dodecahedral boundary condition When calculating minimum images DL_POLY Classic checks that the periodic boundary of the simulation cell is compatible with the specifed minimum image algorithm Program termination results if an inconsistency is found In this case the error refers to the rhombic dodecahedral mini mum image which is inconsistent with the simulation cell The most probable cause is the incorrect definition of the simulation cell vectors present in the input fi
263. ion of the mixing parameter A In this case the derivative of the free energy with respect to A is a un a wy 6 9 As before this equation may be integrated to give the free energy difference as in equation 6 3 It should now be apparent what desirable properties f A needs to have Firstly it should be zero when A 0 and unity when A 1 Secondly the derivative of the function should approach zero when A approaches either 0 or 1 where it will diminish the contribution of the extremes of the integral to the overall result With these requirements in mind DL POLY Classic has a number of options for the function f A 1 Standard linear mixing fA 6 10 2 Nonlinear mixing erat 6 11 where k is an integer exponent 3 Trigonometric mixing 1 1 f zQ sin a A 2 6 12 4 Error function mixing j E exp o a Yas 6 13 exp a gi where a is a parameter of order 10 11 5 Polynomial mixing FO 13 ae 6 14 where k is an integer exponent 6 Spline kernel mixing f A 2A 8 A 1 2 1 abs A 1 2 1 2 6 15 All these functions except 6 10 and 6 11 have the required properties though not all are equally effective Function 6 11 is suitable for mixed Hamiltonians which have only one problematic end point such as 6 5 when A 1 168 STFC Section 6 3 6 3 3 Invoking the DL POLY Free Energy Option The free energy option using thermodynamic
264. irective fbp n where n is the number of four body potentials to be entered There follows n records each specifying a particular four body potential in the following manner atmnam 1 a8 first atom type central site atmnam 2 a8 second atom type atmnam 3 a8 third atom type atmnam 4 a8 fourth atom type 117 STFC Section 4 1 Table 4 12 Definition of pair potential functions and variables key potential type Variables 1 5 functional form 12 6 12 6 A B U r 4 lj Lennard Jones o U r 4e 2 27 nm n m Eo n m ro Ur c m 2e n 22 buck Buckingham Aaa U r A exp 5 amp bhm Born Huggins A B 0 C D U r A exp B o r amp R Meyer hbnd 12 10 H bond A B U r 4 snm Shifted force E n m ro ret U r aie x BA mart G fone ica 5 nmabBo T YTo By Bare nm Yro yi 5 mors Morse Eo ro k U r Eo 1 exp k r ro 1 ay12_ ay6 1 6 wea WCA elo U r 4e 2 2 r lt ox2t 6 tab Tabulation tabulated potential see section 4 1 5 T Note in this formula the terms a 3 and y are compound expressions involving the variables Eo n m 7ro and re See section 2 3 1 for further details Note re defaults to the general van der Waals cutoff rvdw or rcut if it is set to zero or not specified in the FIELD file key ad variable 1 real variable 2 r
265. is an analytical po tential in the FSM class It has the form a n Vis riz 2 m a pij rij a 2 140 F pi cey pi with parameters a n m C 4 Gupta potential 41 gupt The Gupta potential is another analytical potential in the FSM class It has the form Tis r Vijlrij Aexp 19 2 TO Ti r Pijlrij exp 205 S 2 2 141 with parameters A ro p B qij All of these metal potentials can be decomposed into pair contributions and thus fit within the general tabulation scheme of DL POLY Classic where they are treated as pair interactions though note that the metal cutoff rmet has nothing to do with short ranged cutoff rvaw DL POLY Classic calculates this potential in two stages the first calculates the local density p for each atom and the second calculates the potential energy and forces Interpolation arrays vmet gmet and fmet 35 STFC Section 2 3 METGEN METTAB are used in both these stages in the same spirit as in the van der Waals interaction calculations The total force o on an atom k derived from this potential is calculated in the standard way F VkUmetal 2 142 We rewrite the EAM FSM potential 2 137 as U metal Ur a UL EE val rij 2 143 N U Y Flo 4 1 Tij rj Tri The force on atom k is the sum of the derivatives of U and U2 with respect to rg which is recognisable as a sum of pair forces where r
266. is read by the subroutine FORTAB F in the VDW_TERMS F file The option of using tabulated potentials is specified in the FIELD file see above The specific potentials that are to be tabulated are indicated by the use of the tab keyword on the record defining the short range potential see table 4 12 The directive vdwtable may be used in place of vdw to indicate that one or more of the short ranged potentials is specified in the form of a table 4 1 5 1 Format The file is fixed formatted with integers as i10 reals as el5 8 Character variables are read as a8 The header record is formatted as 80 alphanumeric characters 4 1 5 2 Definitions of Variables record 1 header a80 file header record 2 delpot real mesh resolution in A cutpot real cutoff used to define tables A ngrid integer number of grid points in tables The subsequent records define each tabulated potential in turn in the order indicated by the specification in the FIELD file Each potential is defined by a header record and a set of data records with the potential and force tables header record atom 1 a8 first atom type atom 2 a8 second atom type potential data records number of data records Int ngrid 3 4 data 1 real data item 1 data 2 real data item 2 data 3 real data item 3 data 4 real data item 4 force data records number of data records Int ngrid 3 4 data 1 real data item 1 data 2 real data item 2 data 3 real data item 3 dat
267. item 3 j above The records are free format and the content of the information records is ignored by the program c Each data record for both Q4 and Og consists of in order The name of the atom type a max 8 characters The name of the atom type 8 max 8 characters The control parameter r for the function f r in equation 7 9 real The control parameter r2 for the function f r in equation 7 9 real The scale factor for the order parameter real The number Ne of expected atoms of type 8 around the a atom integer gt 6 Prepare if required the file ZETA which defines the control variables for the tetrahedral order parameters The file specification is as follows 181 STFC Section 7 4 a The file consists of 1 information record followed by ntet data records The data records are free format and the content of the information record is ignored by the program b Each data record consists of in order The name of the atom type a max 8 characters The cutoff parameter r for the function f r real The cutoff parameter ra for the function f r real The scale factor for the order parameter real The number Ne of expected atoms of type a around each a atom integer 7 Run the metadynamics simulation This will perform a simulation at the temperature and pressure requested When the simulation ends proceed as follows a Check the OUTPUT fil
268. j y exp rij P1 Tik p2 2 110 U Ojik 5 Truncated Vessal 29 bvs2 a U Ojik kl Ojik 00 Ojik 00 27 gt Oji 00 1 009 expl ri ra 0 2 111 6 Dreiding hydrogen bond 7 hbnd U Ojik Dnycos Ojix 5 Rno rjn 6 Rro rin 2 112 Note that for the hydrogen bond the hydrogen atom must be the central atom Several of these functions are identical to those appearing in the intra molecular valenceangle descriptions above There are significant differences in implementation however arising from the fact that the three body potentials are regarded as inter molecular Firstly the atoms involved are defined by atom types not specific indices Secondly there are no excluded atoms arising from the three body terms The inclusion of pair potentials may in fact be essential to maintain the structure of the system The three body potentials are very short ranged typically of order 3 A This property plus the fact that three body potentials scale as N where N is the number of particles makes it essential that these terms are calculated by the link cell method 34 The calculation of the forces virial and stress tensor as described in the section valence angle potentials above DL_POLY Classic applies no long ranged corrections to the three body potentials The three body forces are calculated by the routine THBFRC 2 3 3 The Tersoff Covalent Potential The Tersoff
269. key potential type Variables 1 5 6 11 a b functional form ters Tersoff A b R Potential form single S c d h as shown in Section cross X 23 24 121 STFC Section 4 1 4 1 3 6 External Field The presence of an external field is flagged by the extern directive The next line in the FIELD file should have another directive indicating what type of field is to be applied On the following lines comes the mxf1d parameters five per line that describe the field In the include files supplied with DL POLY Classic mxfld is set to 10 The variables pertaining to each potential are described in table 4 17 Table 4 17 External fields key potential type Variables 1 5 functional form elec Electric field E Ey E F qEB oshm Oscillating Shear Aln EF Acos 2nr z Lz shrx Continuous Shear A 2 z gt zo va 1 2 A z z grav Gravitational Field Gz Gy Gz E m G magn Magnetic Field Hz Hy H P qux H sphr Containing Sphere A Ro n Reut r gt Ret F A Ro r zbnd Repulsive wall A Z f l zf gt Zof F A z Zo harmonic zres Restraint zone ni na A Zmin Bm HA ma Zom Zom gt inias harmonic F A Zmin Zeom gt Zeom lt Zmin Zcom an Mizi M M X 2 Mi 4 1 3 7 Closing the FIELD File The FIELD file must be closed with the directive close which signals the end of the force field data Without this directive DL_POLY C
270. kinetic energy The default obtained by removing this flag is that there is no mixing of the kinetic energy 8 system_a i1 i2 identifies the range of atom indices that consitute the species A in the CONFIG file integer 11 12 9 system_b i3 i4 identifies the range of atom indices that consitute the species B in the CONFIG file integer 13 14 10 endfre closes specification of free energy 169 STFC Section 6 4 The invocation of the free energy option means that DL POLY Classic will produce an output file named FREENG the contents of which are described in section 6 3 4 below Some further comments are in order Firstly it should be noted that the solute species A and B which are specified using directives system a and system_b are identified by specifying the range of atom indices these components have in the CONFIG file see section 4 1 2 It is apparent that this allows the user to specify atoms in the categories of A and B which are not related to underlying molecular structures This is a simple way of identifying the distinct components of the combined system However there is a clear need for the user to be cautious in defining the system if strange simulations are to be avoided Also it is apparent that atoms that do not fall under the categories of A or B will be deemed to be solvent atoms It is not really sensible to specify all atoms as either A or B with no solvent atoms in category S at all In some circ
271. l is used to maintain the distance between connected beads and to prevent chains from crossing each other It is used in combination with the WCA 2 99 potential to create a potential well for the flexible bonds of a molecule that maintains the topology of the molecule This implementation allows for a radius shift of up to half a R A lt 0 5 Ro with a default of zero Age fault O 8 Coulomb potential coul 1 ij ATE Tij U rij 2 10 Note that the Coulombic bond potential is not normally required as generally the electro static interactions are handled as nonbonded terms elsewhere in the program However it is sometimes explicit in the description of the chemical bond in a way that is different from the default electrostatic treatment and needs to be introduced as an extra feature In these formulae rj is the distance between atoms labelled i and j rig lr ril 2 11 where r is the position vector of an atom labelled The force on the atom j arising from a bond potential is obtained using the general formula 1 0 i E ut Tij 2 12 The force f acting on atom is the negative of this The contribution to be added to the atomic virial is given by W Lij fp 2 13 with only one such contribution from each bond The contribution to be added to the atomic stress tensor is given by ja 2 14 Weg where a and 5 indicate the x y z components The atomic stress tensor derived in this way is
272. l remedy for this error if you wish to combine both these capabilities However if your simulation does not require the polarisability to be a feature of rigid species comprising the charged groups but is confined to free atoms or flexible molecules in the same system you may consider overriding this error message and continuing with your simulation The appropriate error trap is found in subroutine SYSDEF Message 99 error cannot use shell model with constraints The dynamical shell model was not designed to work in conjunction with constraint bonds This error results if both are used in the same simulation Action There is no general remedy if you wish to combine both these capabilities However if your simulation does not require the polarisability to be a feature of the constrained species but is confined to free atoms or flexible molecules you may consider overriding this error message and continuing with your simulation The appropriate error trap is in subroutine SYSDEF Message 100 error forces working arrays too small There are a number of arrays in DL_POLY Classic that function as workspace for the forces cal culations Their dimension is equal to the number of atoms in the simulation cell divided by the number of nodes If these arrays are likely to be exceeded DL POLY Classic will terminate exe cution Action Standard user response Fix the parameter msatms Message 101 error calculated 4 body potential index too
273. l space and the self energy correction 3Strictly speaking the real space sum ranges over all periodic images of the simulation cell but in the DL_POLY Classic implementation the parameters are chosen to restrict the sum to the simulation cell and its nearest neighbours i e the minimum images of the cell contents 46 STFC Section 2 4 For molecular systems as opposed to systems comprised simply of point ions additional mod ifications are necessary to correct for the excluded intra molecular Coulombic interactions In the real space sum these are simply omitted In reciprocal space however the effects of individual gaussian charges cannot easily be extracted and the correction is made in real space It amounts to removing terms corresponding to the potential energy of an ion due to the gaussian charge on a neighbouring charge m or vice versa This correction appears as the final term in the full Ewald formula below The distinction between the error function er f and the more usual complementary error function er fc found in the real space sum should be noted The total electrostatic energy is given by the following formula 1 S ol 4a 2 1 S Gm Si 2V 2 2 qj exp ik Ty r er fc arng ag k40 0 n lt j nj 2 1 er f arem 11 X J 5 i 4 54 dca 2 196 reo molecules lt m yT Tom Em 41e Va j where N is the number of ions in the system and N the same number discounting any exclude
274. la t Adal At 2 297 69 STFC Section 2 5 where y 0 6 7 and Qlg is qo q 02 49 lla q 8 2 E 2 2 298 2 q 43 do q 8B 2 G qo The above equation is solved iteratively with q t At q t At Rla t w t 2 299 as the first guess Typically no more than 3 or 4 iterations are needed for convergence At each step the constraint lat Az 1 2 300 is imposed The NVE LF algorithm is implemented in NVEQ_1 which allows for a system containing a mixture of rigid bodies and atomistic species provided the rigid bodies are not linked to other species by constraint bonds The VV implementation is based on the NOSQUISH algorithm of Miller et al 16 In addition to the quaternions it requires quaternion momenta defined by Po do q 43 0 m s B R Irr r 2 301 p2 q 9 Go a yd P3 da 2 q 4 Izz z and quaternion torques defined by To qo 4 0 T E gt 1 9 qi qo d3 q Ta 2 302 T2 d 4d do q1 Ty Ts Bg 2 u Q Tz It should be noted that vectors p and Y are 4 component vectors The quaternion momenta are first updated a half step using the formula At p t 3 p t 2 303 Next a sequence of operations is applied to the quaternions and the quaternion momenta in the order pila 5t 2 jiLa 8t 2 gili St piCa 0t 2 pila 61 2 2 304 which preserves the symplecticness of the operations see reference 18 Note that t is some submultiple of At In DL_POLY Classic the default is
275. large DL_POLY Classic has a permitted maximum for the calculated index for any four body potential in the system i e as defined in the FIELD file If there are m distinct types of atom in the system the index can possibly range from 1 to m m 1 m 2 6 If the internally calculated index exceeds this number this error report results Action Standard user response Fix the parameter mxfbp Message 102 error parameter mxproc exceeded in shake arrays The RD SHAKE algorithm distributes data over all nodes of a parallel computer Certain arrays in RD SHAKE have a minimum dimension equal to the maximum number of nodes DL_POLY Classic is likely to encounter If the actual number of nodes exceeds this the program terminates Action Standard user response Fix the parameter mxproc Message 103 error parameter mxlshp exceeded in shake arrays The RD SHAKE algorithm requires that information about shared atoms be passed between nodes If there are too many atoms the arrays holding the information will be exceeded and 227 STFC Section C 0 DL_POLY Classic will terminate execution Action Standard user response Fix the parameter mxlshp Message 105 error shake algorithm failed to converge The RD SHAKE algorithm for bond constraints is iterative If the maximum number of permitted iterations is exceeded the program terminates Possible causes include a bad starting config uration too large a time step used
276. lassic will abort 4 1 4 The REVOLD File This file contains statistics arrays from a previous job It is not required if the current job is not a continuation of a previous run ie if the restart directive is not present in the CONTROL file see above The file is unformatted and therefore not readable by normal people DL POLY Classic normally produces the file REVIVE see section 4 2 5 at the end of a job which contains the statistics data REVIVE should be copied to REVOLD before a continuation run commences This may be done by the copy macro supplied in the execute sub directory of DL POLY Classic 122 STFC Section 4 1 4 1 4 1 Format The REVOLD file is unformatted All variables appearing are written in native real 8 represen tation Nominally integer quantities e g the timestep number nstep are represented by the the nearest real number The contents are as follows the dimensions of array variables are given in brackets and are defined in the appropriate Fortran modules record 1 nstep numacc numrdf chit chip conint nzden record 2 virtot vircom eta strcns strbod record 3 stpval record 4 sumval record 5 ssqval record 6 zumval record 7 ravval record 8 stkval record 9 xx0 yy0 zz0 record 10 XXS yys ZZS record 11 rdf record 12 zdens 4 1 4 2 timestep of final configuration number of configurations used in averages number of configurations used in rdf
277. lated system 269 STFC Section C 0 Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1990 error failed allocation of nvtvv_b1 f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 2000 error failed allocation of nvtvv_el f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 2010 error failed allocation of nvtvv_h1 f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 2020 error failed allocation of nptvv_b1 f densO array This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per proces
278. ld make sure that the warning does represent a harmless condition More on error handling can be found in section 3 3 1 4 The DL_POLY Classic Directory Structure The entire DL_POLY Classic package is stored in a Unix directory structure The topmost directory is named dl poly class Beneath this directory are several sub directories sub directory contents source primary subroutines for the DL_POLY Classic package utility subroutines programs and example data for all utilities data example input and output files for DL_POLY Classic execute the DL_POLY Classic run time directory build makefiles to assemble and compile DL_POLY Classic programs java directory of Java and FORTRAN routines for the Java GUI A more detailed description of each sub directory follows 1 4 1 The source Sub directory In this sub directory all the essential source code for DL_POLY Classic excluding the utility soft ware The modules are assembled at compile time using an appropriate makefile 1 4 2 The utility Sub directory This sub directory stores all the utility programs in DL POLY Classic Users who devise their own utilities are advised to store them in the utility sub directory STFC Section 1 6 1 4 3 The data Sub directory This sub directory contains examples of input and output files for testing the released version of DL_POLY Classic The examples of input data are copied into the execute sub directory when a program is being tested T
279. le ensemble_tools_module vv rotation1 module f vv_rotation2_module f vv rotation1 module f vv_rotation2_module f ensemble_tools_module ensemble_tools_module vv_motion_module f vv_motion_module f basic_comms f serial f 1f_motion_module f 1f_rotation1_module 1f_rotation2_module vv rotation1 module vv rotation2 module vv motion module f lf motion module f Fh Fh Fh Fh 287 Hh Fh Fh Fh hh STFC Section D O nvt_el nvt_h1 nvtq_b1 nvtq_b2 nvtq_hi nvtq_h2 nvtqscl nvtqvv_b1 nvtqvv_b2 nvtqvv_h1 nvtqvv_h2 nvtscale nvtvv_b1 nvtvv_el nvtvv_h1 optimisation_selector parlink parlinkneu parlst parlst_nsq parneulst parset passcon passcon passpmf passpmf passquat passquat pivot pmf_rattle_r pmf_rattle_v pmf_shake pmf_vectors pmf1f pmflfq_1 pm vv primlst print_optim prneulst pseudo_shake put_shells_on_cores qrattle_r qrattle_v qshake quatbook guatgnch guench rdf0 rdfOneu subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine su
280. le CONFIG these must equal the vectors of the enscribing tetragonal simulation cell Action Check the specified simulation cell vectors and correct accordingly Message 141 error duplicate metal potential specified The user has specified a particular metal potential more than once in the FIELD file Action Locate the metal potential specification in the FIELD file and remove or correct the potential concerned Message 142 error interpolation outside range of metal potential attempted The program has found that an interatomic distance in a simulated metallic system is such that it requires a potential value outside range for which the potential is defined Action The probable cause of this is that the density of the system is unrealistic or the potential is being used in unsuitable circumstances The attempted simulation should be examined and if considered reasonable a new potential must be found Message 145 error no van der waals potentials defined This error arises when there are no VDW potentials specified in the FIELD file but the user has not specified no vdw in the CONTROL file In other words DL_POLY Classic expects the FIELD file to contain VDW potential specifications Action Edit the FIELD file to insert the required potentials or specify no vdw in the CONTROL file Message 150 error unknown van der waals potential selected DL_POLY Classic checks when constructing the interpolation tables for the sho
281. le when constructing the FIELD file It is not as difficult as it sounds The entry of the molecular details begins with the mandatory directive molecules n where n is an integer specifying the number of different types of molecule appearing in the FIELD file Once this directive has been encountered DL_POLY Classic enters the molecular description environment in which only molecular decription keywords and data are valid Immediately following the molecules directive are the records defining individual molecules 1 name of molecule which can be any character string up to 80 characters in length Note this is not a directive just a simple character string 2 nummols n where n is the number of times a molecule of this type appears in the simulated system The molecular data then follow in subsequent records 3 atoms n where n indicates the number of atoms in this type of molecule A number of records follow each giving details of the atoms in the molecule i e site names masses and charges Each record carries the entries sitnam a8 atomic site name weight real atomic site mass chge real atomic site charge nrept integer repeat counter ifrz integer frozen atom if ifrz gt 0 igrp integer neutral charge group number Note that these entries are order sensitive Do not leave blank entries unless all parameters appearing after the last specified are void The integer nrept need not be specified in which case a value o
282. link cell method 34 The calculation of the forces virial and stress tensor described in the section on inversion angle potentials above DL_POLY Classic applies no long ranged corrections to the four body potentials The four body forces are calculated by the routine FBPFRC 2 3 5 Metal Potentials The metal potentials in DL POLY Classic follow two similar but distinct formalisms The first of these is the embedded atom model EAM 35 36 and the second is the Finnis Sinclair model FSM 3 Both are density dependent potentials derived from density functional theory DFT and describe the bonding of a metal atom ultimately in terms of the local electronic density They are suitable for calculating the properties of metals and metal alloys For single component metals the two approaches are the same However they are subtly different in the way they are extended to handle alloys see below It follows that EAM and FSM potentials cannot be mixed in a single simulation Furthermore even for FSM potentials possessing different analytical forms there is no agreed procedure for mixing the parameters The user is therefore strongly advised to be consistent in the choice of potential when modelling alloys The general form of the EAM and FSM potentials is 37 1 N N N Umetal 2 5 5 Vij riz 5 F pi gt 2 137 i l j4i i l where F p is a functional describing the energy of embedding an atom in the bulk density pi which is defined as
283. ll vectors appearing in the CONFIG file are not consistent with the specified image convention Action Locate the variable imcon in the CONFIG file and correct to suit the cell vectors Message 412 error mxxdf parameter too small for shake routine In DL_POLY Classic the parameter mxxdf must be greater than or equal to the parameter mxcons If it is not this error is a possible result Action Standard user response Fix the parameter mxxdf Message 414 error conflicting ensemble options in CONTROL file DL_POLY Classic has found more than one ensemble directive in the CONTROL file Action Locate extra ensemble directives in CONTROL file and remove Message 416 error conflicting force options in CONTROL file DL_POLY Classic has found incompatible directives in the CONTROL file specifying the electro static interactions options Action Locate the conflicting directives in the CONTROL file and correct Message 418 error bond vector work arrays too small in bndfrc The work arrays in BNDFRC have been exceeded Action Standard user response Fix the parameter msbad 239 STFC Section C 0 Message 419 error bond vector work arrays too small in angfrc The work arrays in ANGFRC have been exceeded Action Standard user response Fix the parameter msbad Message 420 error bond vector work arrays too small in tethfrc The work arrays in TETHFRC have been exceeded Action Standard user respon
284. ls forces also but in DL POLY Classic it is confined to electrostatic forces only The main difference from the standard Ewald method is in its treatment of the the reciprocal space terms By means of an interpolation procedure involving complex B splines the sum in reciprocal space is represented on a three dimensional rectangular grid In this form the Fast Fourier Transform FFT may be used to perform the primary mathematical operation which is a 3D convolution The efficiency of these procedures greatly reduces the cost of the reciprocal space sum when the range of k vectors is large The method briefly is as follows for full details see 46 1 Interpolation of the exp ik rj terms given here for one dimension ezp 2Tiu k L b k Mn u 2exp 2rike K 2 204 j ee in which amp is the integer index of the amp vector in a principal direction K is the total number of grid points in the same direction and uj is the fractional coordinate of ion j scaled by a factor K i e uj K 85 Note that the definition of the B splines implies a dependence 48 STFC Section 2 4 on the integer K which limits the formally infinite sum over The coefficients M u are B splines of order n and the factor b k is a constant computable from the formula n 2 1 b k exp 2ri n 1 k K y Ma Dexp 2rikl K 2 205 0 2 Approximation of the structure factor S k S k b1 k1 b2 k2 b3 k3 OT ki ko k3 2 206
285. ly When the chosen atom and its surrounding neighbours are of the same type a the parameter is defined by formula Na Na Na La 7 poe gt del felris felrix cosOjix 1 3 7 12 i 1 jZi k gt j where indices 7 j and k run up to Na atoms of type a Integer Ne and function fe r are as for the Steinhardt parameters i e fe once again replaces a fixed cut off and Ne is a fixed constant This order parameter is maximal for tetrahedral atomic arrangements The atomic forces that arise from this order parameter can be expressed in terms of pair forces between atoms i and j and between i and k which are given by Ls gt 2 feliz feliz Cos jax 1 3 fik FijcosO jin cos jin ya Kr ik fi i 7 13 Lax x felrij fel rik COSA ji 1 3 Pij FikcoSO jik L Aly d e 1 A c050jik ay enw frita 7 14 The stress tensor contributions can be described in terms of these forces CaB Cag T f r i ij 7 15 7 3 4 Order Parameter Scaling The order parameter vector a consists of an ordered set of different order parameters and it is not generally the case that all of them return numbers of the same order of magnitude This is partic ularly true for the potential energy It is therefore sensible that when using the order parameters collectively to define the state of a system that they should be scaled to give numbers of simular magnitudes So when specifying order parameters to define the metad
286. ly restart the program as for a normal DL_POLY continuation run using the REVCON REVIVE and HYPRES files renamed CONFIG REVOLD and HYPOLD and using the unqualified restart directive in the CONTROL file Remember to increase the number of required time steps if necessary The previous simulation crashed If this means a crash for unknown reasons then the situation may be unrecoverable as with any unexpected DL_POLY crash Try to locate the problem and fix it If however the simulation arrived at this end point due to a time out error then there is hope It may be possible to restart from the last REVCON REVIVE HYPRES files presuming they are uncorrupted and have the same time stamp Be aware that such a restart may cause data duplication in other files such as STATIS EVENTS BASINS PROFILES and HISTORY and the user should remove such a possibility by editing or sometimes even removing the files before restart The objective is to remove any entries in these files that occured after the restart files were written It is therefore important to determine what was going on when the program crashed With TAD it may be found that the time out error is most likely to happen during a NEB calculation or a structure optimisation In which case it will be hard work deciding what needs to be patched up before continuing though the time stamp of the restart files is still the crucial factor This situation is best avoided in the first place by giving
287. m in equation 7 7 or 7 12 r should not be so short that is sometimes does not include atoms that should be fully counted The range r ra should be set to correspond to the minimum in the appropriate pair correlation functions in the relevant system states This choice minimises spurious forces that can arise from order parameters that have different ranges 68 3 Using DL_POLY Classic to help select appropriate order parameters Section 7 2 outlined a protocol for deciding suitable order parameters for a particular meta dynamics study which required the construction of distribution functions for candidate order parameters These may be obtained from DL_POLY Classic by perform simulations of the relevant system states with the metadynamics directive set in the CONTROL file but with the Gaussian accumulation disabled by setting the Gaussian height parameter ref_W_aug to zero The resultant dynamics will be time independent and the METADYNAMICS file will tabulate values of the order parameters at regular intervals It remains then to construct histograms of these parameters to determine the degree of overlap between them as required 4 Choosing order parameter scaling factors The widths of the histograms for the order parameter distributions described in the previous paragraph should also be used to set the appropriate order parameter scaling factors referred to in section 7 3 4 5 Deciding the simulation length Deciding that the m
288. mall in compute_tet_nlist The internal estimate of the array allocation variable nnn is too small for the purpose Action Locate where variable is defined in metafreeze_module f and reset to a larger number Message 2544 mxflist too small in metafreeze_module The internal estimate of the array allocation variable maflist is too small for the purpose Action Locate where variable is defined in metafreeze_module f and reset to a larger number Message 2545 Memory deallocation error in compute_tet_nlist Unlikely array deallocation error which should not occur under normal use Action Probable system error Raise issue with system manager Message 2546 Memory allocation error in compute_tet_nlist Unlikely array allocation error which should not occur under normal use Action The user is probably making excessive demands of memory Reconsider the problem size in relation to compute resource Message 2547 Memory deallocation error in compute_tet_nlist Unlikely array deallocation error which should not occur under normal use Action Probable system error Raise issue with system manager Message 2548 Memory allocation error in compute_tet_nlist Unlikely array allocation error which should not occur under normal use Action The user is probably making excessive demands of memory Reconsider the problem size in relation to compute resource 281 Appendix D Subroutine Locations The Locations of Subroutines and
289. maller one the user must consider using more processors or a machine with larger memory per processor Message 1870 error failed allocation of parlst_nsq f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1880 error failed allocation of parlst f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1890 error failed allocation of parlink f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor 266 STFC Section C 0 Message 1900 error failed allocation of parlinkneu f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1910 error failed allocation of parneulst f work arrays
290. marks the end of the file Some of the directives are mandatory for example the timestep directive that defines the timestep others are optional This way of constructing the file is very convenient but it has inherent dangers It is for example quite easy to specify the same directive more than once or specify contradictory directives or invoke algorithms that do not work together By and large DL_POLY Classic tries to sort out these difficulties and print helpful error messages but it does not claim to be foolproof Fortunately in most cases the CONTROL file will be small and easy to check visually It is important to think carefully about a simulation beforehand and ensure that DL_POLY Classic is being asked to do something that is physically reasonable It should also be remembered that the present capabilites the package may not allow the simulation required and it may be necessary for you yourself to add new features An example CONTROL file appears below The directives and keywords appearing are de scribed in the following section DL_POLY TEST CASE 1 K Na disilicate glass temperature 1000 0 pressure 0 0000 ensemble nve integrator leapfrog steps 500 equilibration 200 multiple 5 scale 10 print 10 stack 100 stats 10 rdf 10 timestep 0 0010 primary 9 0000 cutoff 12 030 delr 1 0000 rvdw 7 6000 ewald precision 1 0E 5 print rdf job time 1200 0 close time 100 00 96 STFC Section 4 1 finish 4 1 1 1 The
291. method may be used with this periodic boundary condition Figure B 6 The hexagonal MD cell This MD cell is particularly suitable for simulating strands or fibres i e systems with a pro nounced anisotropy in the Z direction such as DNA strands in solution or stretched polymer chains 211 Appendix C Error Messages and User Action Introduction In this appendix we document the error messages encoded in DL_POLY Classic and the recom mended user action The correct response is described as the standard user response in the approriate sections below to which the user should refer before acting on the error encountered The reader should also be aware that some of the error messages listed below may be either disabled in or absent from the installed version of DL_POLY Classic Disabled messages generally apply to older releases of the code while absent messages apply to newer versions of the code and will not usually apply to previous releases They are all included for completeness Note that the wording of some of the messages may also have changed over time usually to provide more specific information The most recent wording appears below DL_POLY Classic incorporates FORTRAN 90 dynamic array allocation to set the array sizes at run time It is not foolproof however Sometimes an estimate of the required array sizes is difficult to obtain and the calculated value may be too small For this reason DL POLY Classic retains a numbe
292. mic Integration Thermodynamic Integration TI is a well established method for calculating the free energy dif ference between two systems defined by distinct Hamiltonians H and H A mixed Hamiltonian is defined with the aid of a mixing parameter A where 0 lt A lt 1 as follows Ay 1 A Ay Ao 6 1 so that when A 0 the Hamiltonian corresponds to system 1 and when A 1 it corresponds to system 2 Intermediate values A mix the two systems in different proportions From such a Hamiltonian and the relationship between the free energy F and the system partition function it is easy to show that dF i From this it follows that if the average of the difference Hz H is calculated from a series of simulations over a range of A values between 0 and 1 it is possible to integrate this equation numerically and obtain the free energy difference between systems 1 and 2 i e H Hr 6 2 1 Alis Ho ih ad 6 3 166 STFC Section 6 3 Though simple in principle there are two problems with the basic technique 1 Firstly if the mixed Hamiltonian requires the kinetic energy components to be scaled by either A or 1 A the the equations of motion become unstable when A approaches either 0 or 1 This is because scaling the kinetic energy components amounts to a rescaling of the atomic masses which can thus approach zero at the extremes of A Near zero mass dynamics is not stable for normal
293. mit the job 244 STFC Section C 0 Message 454 error undefined external field A form of external field potential has been requested which DL_POLY Classic does not recognise Action Locate the offending potential in the FIELD file and remove Replace with one acceptable to DL_POLY Classic if this is reasonable Alternatively you may consider defining the required po tential in the code yourself Amendments to subroutines SYSDEF and EXTNFLD will be required Message 456 error core and shell in same rigid unit It is not sensible to fix both the core and the shell of a polarisable atom in the same molecular unit Consequently DL_POLY Classic will abandon the job if this is found to be the case Action Locate the offending core shell unit there may be more than one in your FIELD file and release the shell preferably from the rigid body specification Message 458 error too many PMF constraints param mspmf too small The number of constraints in the potential of mean force is too large The dimensions of the ap propriate arrays in DL_POLY Classic must be increased Action Standard user response Fix the parameter mspmf Message 460 error too many PMF sites parameter mxspmf too small The number of sites defined in the potential of mean force is too large The dimensions of the appropriate arrays in DL_POLY Classic must be increased Action Standard user response Fix the parameter mxspmf Message 461 e
294. monic harm 2 k U Ojik z Ojik bo 2 15 Quartic quar k 5 k 3 E 4 U Ojik 5 iit 09 4 J Ojik 00 g Ojik 80 2 16 17 STFC Section 2 2 3 Truncated harmonic thrm U Ojas jir 90 expl A A 2 17 4 Screened harmonic shrm U Ojik E ji 0 exp rig pi rix p2 2 18 5 Screened Vessal 28 bvs1 U Oji Sa ap Ul my jak gt exp rij p1 Ti p2 l 2 19 6 Truncated Vessal 29 bvs2 a aq U Ojik KP Ojik 00 Ojik 00 27 Sao Ojiz 00 T 00 expl ri ri 0 2 20 7 Harmonic cosine hcos U Oji cos 0jix cos 00 2 21 8 Cosine cos U juz All cos mBjix 8 2 22 9 MM3 stretch bend mmsb U jir A Ojix 90 rig r3 rik Tik 2 23 10 Compass stretch stretch stst U jik Alry rej Tik Tip 2 24 11 Compass stretch bend stbe U Ojik A Ojik 90 Tig Tip 2 25 12 Compass all terms cmps U Ojik Alrij ri rik Tik Ojik 90 B rig 733 Cik 7 2 26 In these formulae 0 4 is the angle between bond vectors r j and r g Ti Te Ojik cos ie 2 27 VijVik In DL POLY Classic the most general form for the valence angle potentials can be written as U Ojik fij Tik A 0jik S ri5 S rik 2 28 18 STFC Section 2 2 where A 0 is a purely angular f
295. mory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 2310 error failed allocation of nstqvv_h2 f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 2320 error NEB convergence failure The nudged elastic band calculation in the temperature accelerated dynamics or bias potential dynamics has failed to converge Action The best approach is to halt the TAD or BPD simulation and focus on the NEB calculation in isolation First try to reproduce the error by a straightforward NEB calculation using the same start and end points for the chain Adjusting the convergence criteria may offer a way forward Try minimising the start and end points independently to a higher precision It is possible that the start and end points are too far apart so that one or more intermedate states have been missed This leads to multiple maxima on the reaction path which may be the problem In which case examine the operational choices made in running the TAD or BPD simulation and see if changing them will reduce the danger of this happening Message 2330 er
296. mponent real 8 record viii only for keytrj gt 0 vzz 1 natms atomic velocities z component real 8 record ix only for keytrj gt 1 fxx 1 natms atomic forces x component real 8 record x only for keytrj gt 1 fyy 1 natms atomic forces y component real 8 record xi only for keytrj gt 1 fzz 1 natms atomic forces z component real 8 Note the implied conversion of integer variables to real on record i 4 2 2 The OUTPUT File The job output consists of 7 sections Header Simulation control specifications Force field spec ification Summary of the initial configuration Simulation progress Summary of statistical data Sample of the final configuration and Radial distribution functions These sections are written by different subroutines at various stages of a job Creation of the OUTPUT file always results from running DL_POLY Classic It is meant to be a human readable file destined for hardcopy output 4 2 2 1 Header Gives the DL POLY Classic version number the number of processors used and a title for the job as given in the header line of the input file CONTROL This part of the file is written from the subroutines DLPOLY and SIMDEF 129 STFC Section 4 2 4 2 2 2 Simulation Control Specifications Echoes the input from the CONTROL file Some variables may be reset if illegal values were specified in the CONTROL file This part of the file is written from the subroutine SIMDEF 4 2 2 3 Force Field
297. mun number needed to define a local body axis system The remaining particle positions are expressed in terms of the COM and the basic particles Ordinary bond constraints can then be applied to the basic particles provided the forces and torques arising from the secondary particles are transferred to the basic particles in a physically meaningful way 67 STFC Section 2 5 where r is the position vector of atom j The rigid body translational velocity V is defined by 1 Nsites V gt 3 2 mu 2 284 j 1 where v is the velocity of atom j The net translational force acting on the rigid body unit is the vector sum of the forces acting on the atoms of the body Nsites y f 2 285 j 1 where f is the force on a rigid unit site A rigid body also has associated with it a rotational inertia matrix I whose components are given by Nsites Tap Y mi di8ag d r 2 286 J where d is the displacement vector of the atom j from the COM and is given by d 7 R 2 287 It is common practice in the treatment of rigid body motion to define the position R of the body in a universal frame of reference the so called laboratory or inertial frame but to describe the moment of inertia tensor in a frame of reference that is localised in the rigid body and changes as the rigid body rotates Thus the local body frame is taken to be that in which the rotational inertia tensor I is diagonal and the components satisfy Ip gt
298. must consider using more processors or a machine with larger memory per processor Message 2260 error failed allocation of nstqvv_b2 f densO array This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 2270 error failed allocation of nstqvv_b2 f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 2280 error failed allocation of nstqvv_h1 f densO array This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor 274 STFC Section C 0 Message 2290 error failed allocation of nstqvv_h1 f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 2300 error failed allocation of nstqvv_h2 f densO array This is a me
299. n Gunsteren W DiNola A and Haak J R 1984 J Chem Phys 81 3684 5 55 56 59 201 STFC Section 9 1 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 Hoover W G 1985 Phys Rev A31 1695 5 55 56 59 Jorgensen W L Madura J D and Swenson C J 1984 J Amer Chem Soc 106 6638 13 Brode S and Ahlrichs R 1986 Comput Phys Commun 42 41 14 76 Hockney R W and Eastwood J W 1981 Computer Simulation Using Particles McGraw Hill International 14 15 78 Warner H R J 1972 ind Eng Chem Fundam 11 379 16 Bird R B e a 1977 Dynamics of Polymeric Liguids volume 1 and 2 Wiley New York 16 Grest G S and Kremer K 1986 Phys Rev A 33 3628 16 Vessal B 1994 J Non Cryst Solids 177 103 18 20 31 113 119 Smith W Greaves G N and Gillan M J 1995 J Chem Phys 103 3091 18 20 31 113 119 Smith W 1993 CCP5 Information Quarterly 39 14 19 22 25 Rohl A L Wright K and Gale J D 2003 Amer Mineralogist 88 921 25 Clarke J H R Smith W and Woodcock L V 1986 J Chem Phys 84 2290 28 118 Weeks J D Chandler D and Anderson H C 1971 J Chem Phys 54 5237 29 Eastwood J W Hockney R W and Lawrence D N 1980 Comput Phys Commun 19 215 31 33 34 Daw M S and Baskes M I 1984 Phys Rev B 29
300. n error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1210 error failed allocation of pmf arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1220 error failed allocation of pmf_lf or pmf_vv work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1230 error failed allocation of pmf_shake work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1240 error failed allocation of ewald arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor
301. n is required due to the call to the SHAKE routine The algorithm is implemented in the DL_POLY routine NVT_Hl for systems with bond constraints In the VV version of DL_POLY Classic the Hoover algorithm is split into stages in accordance with the principles of Martyna et al 18 for designing reversible integrators The scheme applied here is x t wat x t a EE 7G vl ae Shel ado u t sat vi t t si 1 r t A1 e r t Atu t Al call rattle R 60 STFC Section 2 5 i 1 At f t At v t4 At u t At 5 call rattle V 1 AtNyk XERAL x t 0 SO T t At Tai v t At v t At At u t At 2 258 Routines rattle R and rattle V apply the bondlength and velocity constraint formulae 2 251 and 2 252 respectively The equations have the same conserved variable Hyxyr as the LF scheme The integration is performed by the subroutine NVTVV_H1 which calls subroutines RATTLE_R RATTLE_V and NVTSCALE 2 5 4 2 Berendsen Thermostat In the Berendsen algorithm the instantaneous temperature is pushed towards the desired temper ature by scaling the velocities at each step we E i _ 1 2 259 The DL_POLY Classic LF routines implement this thermostat as follows v t 7At E Ai a x t u t vt At v t 540 r t At r t Atu t At 2 260 As with the Nos Hoover thermostat iteration is required to obtain self consistency of y t u
302. n methods available These are useful to improve the starting structure of a molecular dynamics simulation The algorithms available are 1 Zero temperature molecular dynamics sometimes called damped molecular dynamics 2 Conjugate gradients minimisation 3 Programmed energy minimisation involving both molecular dynamics and conjugate gradi ents Starting structure minimisation is described in section 3 2 4 1 3 Programming Style The programming style of DL_POLY Classic is intended to be as uniform as possible The following stylistic rules apply throughout Potential contributors of code are requested to note the stylistic convention 1 3 1 Programming Language DL_POLY Classic is written exclusively in FORTRAN 90 Use is made of F90 Modules Explicit type declaration is used throughout STFC Section 1 3 1 3 2 Memory Management In DL_POLY Classic the major array dimensions are calculated at the start of execution and the associated arrays created through the dynamic array allocation features of FORTRAN 90 1 3 3 Target Computers DL_POLY Classic is intended for distributed memory parallel computers However versions of the program for serial computers are easily produced To facilitate this all machine specific calls are located in dedicated FORTRAN routines to permit substitution by appropriate alternatives DL_POLY Classic will run on a wide selection of computers This includes most single processor
303. n period these should hold their values within normal thermodynamic fluctuation even if transitions have occured If they do not the system has probably not been equilibrated adequately to begin with in which case the simulation should be started again O gt Check that all the new states the program found are present in the BASINS directory Examine them using the DL POLY Java GUI There may be signs of imperfect minimi sation atoms not quite on lattice sites etc but this is not a problem in this instance More accurate NEB calculations can be performed later see section 5 6 Check that the profiles for all the reported transitions have been written in the PRO FILES directory These record the change in configuration energy as a function of reaction coordinate or diffusion path Do not do this if the option noneb was taken Plot these using the DL_POLY Java GUI Use the GUI spline option to get a better idea of what the profiles look like Take special note of any double or multiple maxima The transition is considered to end at the first minimum in these cases It follows that the activation energy for the second peak is not available in this case but it can be obtained later by running the NEB facility independently for the states concerned see section 5 6 eH g It is useful to determine which atoms have relocated during a transition The program bsncmp f in the utility directory may be used for this
304. nable accuracy on the transition time somewhat better than using the end time of the TAD block in which the transition occurred 4 The time ttigh is extropolated to the corresponding time of occurrence tY at Tlow This is done by combining equations 5 15 and 5 16 and taking the logarithm plow krigh E 1 1 log 4 2 4 See figure 5 4 for an indication of how the extrapolation works 5 The system is returned to state A and the simulation recommenced Returning the system to its original state means resetting the atomic coordinates to a structure in the starting basin and resetting the velocities according to a Boltzmann distribution while retaining the total system energy of the original state The simulation is continued to obtain information on other transitions to states C D E etc that may occur from state A This is a key difference from the BPD method 149 STFC Section 5 4 6 A determination of the simulation stopping time tstop is made see below When the simulation reaches the calculated stopping time it is terminated When the simulation has ended the transition with the shortest determined occurence time t at Tiow indicates the state to which the system would have transformed in a molecular dynamics simulation at that temperature This new state becomes the starting point for a new high temperature simulation of the system exploring transitions from this state to futher new states
305. nal prism periodic boundary conditions applied The electrostatic interactions are calculated using the Smoothed Particle Mesh Ewald method Note that the system has a strong overall negative charge which is strongly anisotropic in distribution The short range forces are taken from the Dreiding force field and constraints are used for all covalent bonds For simplicity H bonds are treated as harmonic bonds with an equilibrium bondlength of 1 724 A NVE ensemble 188 STFC Section 8 1 8 1 1 11 Test Case 11 Hautman Klein test case 1 The system consists of 100 short chain surfactant molecules in a layer simulated under NVE con ditions The total system size is 2300 atoms and the XY periodicity is a square The Dreiding force field describes the molecular interactions All bonds are harmonic and all atoms are explicit The link cell algorithm is in operation NVE ensemble 8 1 1 12 Test Case 12 Hautman Klein test case 2 This is a simple test system consisting of 1024 charged particles in a layer under NVE conditions Lennard Jones forces are used to keep the atoms apart The similation cell is square in the XY plane NVE ensemble 8 1 1 13 Test Case 13 Carbon Nanotube with Tersoff potential This system consists of 800 carbon atoms in a nanotube 41 7 A in length The MD cell is or thorhombic and square in the XY plane The integration algorithm is NPT Berendsen This is a test for the Tersoff potential NPT Berendsen ensemble
306. ncluded in the CONTROL file The format of the REVIVE file is identical to the REVOLD file described in section 4 1 4 4 2 6 The RDFDAT File This is a formatted file containing em Radial Distribution Function RDF data Its contents are as follows record 1 cfgname character A80 configuration name record 2 ntpvdw integer i10 number of RDFs in file mxrdf integer i10 number of data points in each RDF There follow the data for each individual RDF i e ntpvdw times The data supplied are as follows first record atname 1 character A8 first atom name atname 2 character A8 second atom name following records mzrdf records radius real e14 interatomic distance A g r real e14 RDF at given radius Note the RDFDAT file is optional and appears when the print rdf option is specified in the CONTROL file 4 2 7 The ZDNDAT File This is a formatted file containing the Z density data Its contents are as follows record 1 cfgname character A80 configuration name record 2 mxrdf integer i10 number of data points in the Z density function following records mzrdf records z real e14 distance in z direction A p z real e14 Z density at given height z Note the ZDNDAT file is optional and appears when the print rdf option is specified in the CONTROL file 133 STFC Section 4 2 4 2 8 The STATIS File The file is formatted with integers as i10 and reals as el4 6 It is written by the su
307. neu f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1830 error failed allocation of neutlst f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor 265 STFC Section C 0 Message 1840 error failed allocation of multiple f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1850 error failed allocation of multipleneu f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1860 error failed allocation of multiple_nsq f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a s
308. ng a harmonic improper dihedral angle potential with an equilibrium angle of 35 264 The angle is defined by vectors r19 ro3 and T34 where the atoms 1 2 3 and 4 are shown in the following figure The figure defines the D and L enantiomers consistent with the international IUPAC convention When defining the dihedral the atom indices are entered in DL POLY Classic in the order 1 2 3 4 L 0a N C B D a C N 8 1234 123 4 Figure 2 4 The L and D enantiomers and defining vectors In DL_POLY Classic improper dihedral forces are handled by the routine DIHFRC 2 2 7 Inversion Angle Potentials Figure 2 5 The inversion angle and associated vectors 23 STFC Section 2 2 The inversion angle potentials describe the interaction arising from a particular geometry of three atoms around a central atom The best known example of this is the arrangement of hydrogen atoms around nitrogen in ammonia to form a trigonal pyramid The hydrogens can flip like an inverting umbrella to an alternative structure which in this case is identical but in principle causes a change in chirality The force restraining the ammonia to one structure can be described as an inversion potential though it is usually augmented by valence angle potentials also The inversion angle is defined in the figure above note that the inversion angle potential is a sum of the three possible inversion angle terms It resembles a dihedral potential in that it requires th
309. nged corrections are calculated by LRCMETAL Reading and generation of EAM table data from TABEAM is handled by METTAB and METAL_DERIV 40 STFC Section 2 3 Notes on the Treatment of Alloys The distinction to be made between EAM and FSM potentials with regard to alloys concerns the mixing rules for unlike interactions Starting with equations 2 137 and 2 138 it is clear that we require mixing rules for terms Vj rj and pi rij when atoms i and j are of different kinds Thus two different metals A and B we can distinguish 4 possible variants of each Vip ria VE ria Vig ria V rio and AA BB AB BA Pij rij Pij rij Pij rij Pij rij These forms recognise that the contribution of a type A atom to the potential of a type B atom may be different from the contribution of a type B atom to the potential of a type A atom In both EAM 4 and FSM 39 cases it turns out that Vee ra V re 4 216 though the mixing rules are different in each case beware With regard to density in the EAM case it is required that 4 AB BB Pij Tig pij Tag pig rig pig Pia 2 166 which means that an atom of type A contributes the same density to the environment of an atom of type B as it does to an atom of type A and vice versa For the FSM case 39 a different rule applies PEP rag OG ria a 2 167 so that atoms of type A and B contribute the same densities to each other but not to atoms of th
310. nhardt or tetrahedral order parameters discussed in the following sections This allows the use of potential energy in association with these order parameters This approach has the advantage that it allows the user to drive structural changes in parts of the system that are of greatest interest and not say the solvent or substrate In implementing this a corresponding calculation of the local potential energy and stress tensor needs to be added to each DL_POLY force routine It turns out that it is not practical to do this in all of DL_POLY s force routines in particular those that determine many body forces e g Tersoff and metal potentials do not have this capability A similar omission occurs with the reciprocal space term of the Ewald sum 7 3 2 Steinhardt Order Parameters The parameters of Steinhardt Nelson and Ronchetti 72 employ spherical harmonics to describe the local order of atoms of type surrounding an atom of type a thus An 1 2 ds dl E par NNa en 20 where 288 V Fels Yem Ob o 7 8 b 1 The summation in equation 7 8 runs over all N atoms of type 8 within a prescribed cutoff surrounding an atom of type a and r represents the scalar distance between the a and atoms The function fe r is a switching function that sets the cutoff range at the required separation in a continuous and therefore differentiable manner It has the form 1 r lt r flr 4 cos Fee 1 Ti lt T ST 7 9
311. not be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor 264 STFC Section C 0 Message 1780 error failed allocation of quatqnch f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1790 error failed allocation of quatbook f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1800 error failed allocation of intlist f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1810 error failed allocation of forces f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1820 error failed allocation of forces
312. ntial energy and 5 Steinhardt Q4 parameters Gaussian convergence is controlled by well tempered dynamics 8 1 2 Benchmark Cases These represent rather larger test cases for DL_POLY Classic that are also suitable for benchmark ing the code on large scale computers They have been selected to show fairly the the capabilities and limitations of the code 8 1 2 1 Benchmark 1 Simulation of metallic aluminium at 300K using a Sutton Chen density dependent potential The system is comprised of 19652 identical atoms The simulation runs on 16 to 512 processors only 192 STFC Section 8 1 8 1 2 2 Benchmark 2 Simulation of a 15 peptide in 1247 water molecules This was designed as an AMBER comparison The system consists of 3993 atoms in all and runs on 8 512 processors It uses neutral group electrostatics and rigid bond constraints and is one of the smallest benchmarks in the set 8 1 2 3 Benchmark 3 Simulation of the enzyme transferrin in 8102 water molecules The simulation makes use of neutral group electrostatics and rigid bond constraints The system is 27539 atoms and runs on 8 512 processors 8 1 2 4 Benchmark 4 Simulation of a sodium chloride melt with Ewald sum electrostatics and a multiple timestep al gorithm to enhance performance The system is comprised of 27000 atoms and runs on 8 512 processors 8 1 2 5 Benchmark 5 Simulation of a sodium potassium disilicate glass Uses Ewald sum electrostatics a multiple time
313. ntial in the following manner atmnam 1 a8 first atom type atmnam 2 a8 second atom type key a4 potential key See table 4 12 variable 1 real potential parameter see table 4 12 variable 2 real potential parameter see table 4 12 variable 3 real potential parameter see table 4 12 variable 4 real potential parameter see table 4 12 variable 5 real potential parameter see table 4 12 The variables pertaining to each potential are described in table 4 12 Note that any pair potential not specified in the FIELD file will be assumed to be zero The specification of three body potentials is initiated by the directive tbp n where n is the number of three body potentials to be entered There follows n records each specifying a particular three body potential in the following manner atmnam 1 a8 first atom type atmnam 2 a8 second atom type central site atmnam 3 a8 third atom type key a4 potential key See table 4 13 variable 1 real potential parameter see table 4 13 variable 2 real potential parameter see table 4 13 variable 3 real potential parameter see table 4 13 variable 4 real potential parameter see table 4 13 variable 5 real cutoff range for this potential A The variables pertaining to each potential are described in table 4 13 Note that the fifth variable is the range at which the three body potential is truncated The distance is in A measured from the central atom The specification of four body potentials is initiated by the d
314. number of inversion potentials specified in the FIELD file exceeds the permitted maximum Action Standard user response Fix the parameter mxtinv Message 75 error too many atoms in specified system DL_POLY Classic places a limit on the number of atoms that can be simulated Termination re sults if too many are specified Action Standard user response Fix the parameter mxatms Message 77 error too many inversion potentials in system The simulation contains too many inversion potentials overall causing termination of run Action Standard user response Fix the parameter mxinv 223 STFC Section C 0 Message 79 error incorrect boundary condition in fbpfre The 4 body force routine assumes a cubic or parallelepiped periodic boundary condition is in op eration The job will terminate if this is not adhered to Action You must reconfigure your simulation to an appropriate boundary condition Message 80 error too many pair potentials specified DL_POLY Classic places a limit on the number of pair potentials that can be specified in the FIELD file Exceeding this number results in termination of the program execution Action Standard user response Fix the parameters mxsvdw and mxvdw Message 81 error unidentified atom in pair potential list DL_POLY Classic checks all the pair potentials specified in the FIELD file and terminates the program if it can t identify any one of them from the atom types
315. o NPT simula tions only Action Insert a press directive in the CONTROL file specifying the required system pressure Message 388 error npt incompatible with multiple timestep The use of NPT constant pressure and temperature is not compatible with the multiple timestep option Action Simulation must be run at fixed volume in this case But note it may be possible to use NPT without the multiple timestep in ourder to estimate the required system volume then switch back to multiple timestep and NVT dynamics at the required volume 237 STFC Section C 0 Message 390 error npt ensemble requested in non periodic system A non periodic system has no defined volume hence the NPT algorithm cannot be applied Action Either simulate the system with a periodic boundary or use another ensemble Message 391 error incorrect number of pimd beads in config file The CONFIG file must specify the position of all the beads in a PIMD simulation not just the positions of the parent atoms otherwise this error results Action The CONFIG file must be reconstructed to provide the required data Message 392 error too many link cells requested The number of link cells required for a given simulation exceeds the number allowed for by the DL_POLY Classic arrays Action Standard user response Fix the parameter mxcel1 Message 394 error minimum image arrays exceeded The work arrays used in IMAGES have been exceede
316. o a condition of zero or at least negligible force at the start of the integration of the atomic motion and then integrate the motion of the finite mass core by conventional molecular dynamics The relaxation of the shells in DL_POLY Classic is accomplished using conjugate gradients Since each timestep of the algorithm entails a minimisation operation the cost per timestep for this algorithm is considerably more than the adiabatic shell model however the integration timestep permitted is much larger as much as a factor 10 so evolution through phase space is not necessarily very different in cost A description of the method is presented in 50 2 5 Integration algorithms 2 5 1 The Verlet Algorithms DL_POLY integration algorithms are based on the Verlet scheme which is both time reversible and simple 12 It generates trajectories in the microcanonical NVE ensemble in which the total energy kinetic plus potential energy is conserved If this property drifts or fluctuates excessively in the course of a simulation it indicates that the timestep is too large or the potential cutoffs too small relative r m s fluctuations in the total energy of 107 are typical with this algorithm DL_POLY Classic contains two versions of the Verlet algorithm The first is the Verlet leapfrog LF algorithm and the second is the velocity Verlet VV 2 5 1 1 Verlet Leapfrog The LF algorithm requires values of position r and force f at time t while th
317. o be computed by the methods used in the short ranged potentials 2 OVij OVi rij Wy ep Tij i 1 AH N Tij lt Tmet OVij r N Tij ZT met OV ri Bane oe a oe i 1 j i i 1 j i ER Uo dy 39 STFC Section 2 3 Vl Tmet Tij N _ OF pi Opis Tis f Y 2 J 2 Bry T 2 161 1 Ai OW 27Np dr a J 2 Tmet N es lt Tmet N OF p Opis Ti OF p Opis riz Y 2 r A i l p ji Orij i 1 do Ai Orij W dW N OF i Opij T r r3 UW 4 OW L 25 T or dr Evaluating the integral part of the above equations yields 1 EAM virial correction No long ranged corrections apply beyond met 2 Finnis Sinclair virial correction No long ranged corrections apply beyond cutoffs c and d 3 Sutton Chen virial correction Ane n 3 Su y TN pea a n 3 Tmet Aro 3 n 3 N dis Ly 2 2 162 m 3 Tmet 2 0 4 Gupta virial correction 27 N pAr r ro 2 ro Rey fattia p rome 5 G Tmet TO ep p 2 3 qij 2T Pro ro ro ro U ara L Gree E E lx 2 163 To qij f m 2 z 2 2 eee EEE 2 no 24 p In the energy and virial corrections we have used the approximation VW N i lt P gt where lt pi 2 gt is regarded as a constant of the system In DL_POLY Classic the metal forces are handled by the routine METFRC The local density is calculated by the routines METDENS EAMDEN and FSDEN The long ra
318. o be defined with respect to Vo such that Vmin represents the actual minimum of the biased potential Vin RY equation 5 7 It can easily be shown that the minima of both Vbias RN and V RN occur at the same position R and this gives rise to the following expression for the constant a Evias Vo Evias T Vmin 3NKkBTbias Thies Triin Vmin Vo 2Tmin 5 10 Under this scheme the user has easy control of the depth of the biased potential Vbias RA to any depth between Ebias and Vo Note that it does not matter if the system moves to a different potential basin and hence adopts a different value of Vo Thias and Tmin will be at the same heights above the minimum of the new basin In this sense the the scheme outlined is adaptive with respect to the true energy surface As with the original scheme of Hamelberg et al 64 this prescription gives a system bias potential 5 4 which is everywhere differentiable with continuous forces and usefully retains some semblance of the topology of the original potential energy surface The user is at liberty to chose any value Ebvias gt Vo which is useful for configurational sampling but for hyperdynamics satisfying the Voter condition 5 6 Epas must not exceed the system configuration energy at any saddle point representing an escape route from a potential basin Finally it should be noted that simulations performed under the influence of a bias potential naturally do not return sy
319. obtained The specific implementation within DL_POLY Classic uses this method in the context of transitions to from crystalline phases Phase transitions for example from the liquid to the solid state frequently exhibit hysteresis such that one state persists after it has become thermodynamically unstable This is due to the existence of a free energy barrier between the states which inhibits the transition Metadynamics provides a means to overcome the free energy barrier and facilitate the phase transition on a timescale accessible by molecular dynamics simulation Metadynamics was originally devised by Laio and Parrinello 67 and the implementation in DL POLY Classic is based on the methodology described by Quigley and Rodger 68 The meta dynamics routines in DL_POLY Classic were originally written by David Quigley and Mark Rodger at the University of Warwick and incorporated into the package by W Smith Note that it is intended that this facility be used to study phase transitions and there is an accompanying expectation that such studies will be undertaken using either an NVT NPT or NoT ensemble Note also that when used together with shell model electrostatics the metadynamics routines revert to velocity Verlet integration 7 2 Theory of Metadynamics In metadynamics the Hamiltonian that defines the dynamics of an N particle system is augmented by a time dependent bias potential which is a function of appropriate order parameters that ch
320. of core_shell arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1115 error failed allocation of hyperdynamics work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1010 error failed allocation of angle arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor 253 STFC Section C 0 Message 1120 error failed allocation of inversion arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1130 error failed allocation of inversion work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one th
321. of the order parameters However this approach does not guarantee that pathways between states will match those that occur in the unbiased system though it does set an upper bound for the corresponding free energy barrier An alternative method devised by Peters and Trout offers a better description of pathways 70 7 3 Order Parameters The order parameters available in DL_POLY Classic are as follows 1 Potential energy 71 2 The Q4 and Q6 parameters of Steinhardt et al 72 3 The tetrahedral parameter of Chau and Hardwick 73 These order parameters are described below 7 3 1 Potential Energy as an Order Parameter The use of potential energy as an order parameter was pioneered by Donadio et al 71 It is self evident that the configuration energy is a well behaved function that takes on distinct values for different structures It has the additional advantage that it requires no additional computation time since it is normally calculated automatically during any molecular dynamics simulation It is also straightforward to calculate the associated biasing forces and stress tensor contributions OV LA 57 7 5 OV a gt tag 7 6 In addition to using potential energy as a global parameter Quigley and Rodger advocate its use as a local parameter 68 which pertains to a specific subset of atoms in the system namely those 177 STFC Section 7 3 that form the central atoms in the definitions of the Stei
322. olecular dynamics and conjugate gra dients This method combines conjugate gradient minimisation with molecular dynamics Minimisation is followed by user defined intervals of usually low temperature dynamics in a cycle of minimisation dynamics minimisation etc which is intended to help the structure relax from overstrained conditions When using the programmed minimisation DL POLY Classic writes and rewrites the file CFGMIN 4 2 4 which represents the low est energy structure found during the programmed minimisation CFGMIN is written in CONFIG file format see section 4 1 2 and can be used in place of the original CONFIG file It should be noted that none of these algorithms permit the simulation cell to change shape It is only the atomic structure that is relaxed After which it is assumed that normal molecular dynamics will commence from the final structure Comments on the Minimisation Procedures 1 The zero temperature dynamics is really dynamics conducted at 1 Kelvin However the dynamics has been modified so that the velocities of the atoms are always directed along the force vectors Thus the dynamics follows the steepest descent to the local minimum From any given configuration it will always descend to the same minimum 2 The conjugate gradient procedure has been adapted to take account of the possibilites of constraint bonds and rigid bodies being present in the system If neither of these is present the conventional
323. ols_module ensemble_tools_module ensemble_tools_module ensemble_tools_module ensemble_tools_module ensemble_tools_module parse_module f utility_module f ensemble_tools_module f parse_module f basic_comms f serial f basic_comms f serial f utility_module f basic_comms f serial f Hh Hh Hh FH Hh Fh hh basic_comms f serial f hkewald module f hkewald module f hkewald module f hkewald module f hkewald module f hyper dynamics module hyper dynamics module hyper dynamics module hyper dynamics module utility module f temp scalers module f basic comms f Hh Fh Fh hh 285 STFC Section D 0 initcomms intlist intstr intstr3 invert invfrc jacobi kinstr kinstress kinstressf kinstressg lf integrate loc2 loc3 loc4 lowcase lrcmetal lrcorrect lrcorrect_fre lrcorrect sol machine machine mat mul merge merge mergel mergel merge4 merge4 metafreeze_driver metal_deriv metdens metfrc metgen mettab mfrz error minimiser mkwd8 molecular_dynamics multiple multiple_neu multiple_nsq mynode mynode neb_driver neb_option neb_spring_forces neb_system_forces neutbook subroutine subroutine function function subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine function function function subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subr
324. ommencing from state A will undergo a transition to a neighbouring state via the first encountered route and never sample the alternatives Since the different routes have different temperature dependent rates it follows that at different temperatures the system may evolve along completely different paths The TAD method avoids this possibility at high temperature by returning the system to state A after every transition so that practically all of the escape routes at this temperature may be discovered From the calculated properties of these escape routes the true low temperature escape route may be determined by extrapolation Thus TAD provides a high temperature method for identifying the transitions that mark out the low temperature diffusion pathway The characteristics of the method are as follows in which it is assumed that the kinetic prop erties of a system at the temperature Tlow are required 1 The starting structure state A is energy minimised to provide a reference structure hereafter called the reference state against which later structures may be compared to determine any structural transitions 2 The system is simulated at high temperature Trign and halted at regular intervals called a TAD block to energy minimise the structure to construct a reference state This is compared with the existing reference state to determine if a structural transition to state B has occurred A transition is deemed to have occured if
325. on of configuration arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1010 error failed allocation of angle arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1011 error failed allocation of dihedral arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1012 error failed allocation of exclude arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1013 error failed allocation of rigid body arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or
326. onent of 6 cell vector ea real x cell 9 real z component of c cell vector 135 Chapter 5 Hyperdynamics 136 STFC Section 5 0 Scope of Chapter This chapter describes the facilties within DL_POLY Classic for performing accelerated dynamics or hyperdynamics using the Bias Potential Dynamics and Temperature Accelerated Dynamics methods 137 STFC Section 5 1 5 1 Overview of Hyperdynamics The first thing to note about the hyperdynamics methods in DL_POLY Classic is that they were designed for studies of kinetic processes in the solid state which mostly means diffusion In solids diffusion is characterised by infrequent atomic hops occurring on a time scale of order 100 ps to 1000 ps per hop which is too infrequent to give a measurable diffusion in a normal molecular dy namics simulation Hyperdynamics methods are designed to overcome this problem by accelerating the hopping frequency The hyperdynamics methods built into DL POLY Classic are Bias Potential Dynamics BPD 62 and Temperature Accelerated Dynamics TAD 63 both of which were conceived by Voter et al though the implementation of BPD in the program uses the bias potential devised by Hamelberg Mongan and McCammon 64 which is simpler to use In passing it is useful to note that BPD can be used to improve configurational sampling in systems other than solids and this facility has been retained in the DL_POLY Classic implementation see section 5
327. onent of velocity y component of velocity z component of velocity x component of force y component of force z component of force Thus the data for each atom is a minimum of two records and a maximum of 4 4 2 1 2 The Unformatted HISTORY File The unformatted HISTORY file is written by the subroutine TRAJECT_U and has the following structure record 1 header record 2 natms record 3 atname 1 record 4 natms configuration name character 80 number of atoms in the configuration real 8 atom names or symbols character 8 128 STFC Section 4 2 weight 1 natms atomic masses real 8 record 5 charge 1 natms atomic charges real 8 For time steps greater than nstraj the HISTORY file is appended at intervals specified by the traj directive in the CONTROL file with the following information record i nstep the current time step real 8 natms number of atoms in configuration real 8 keytrj trajectory key real 8 imcon image convention key real 8 tstep integration timestep real 8 record ii for imcon gt 0 cell 1 9 a band c cell vectors real 8 record iii xxx 1 natms atomic x coordinates real 8 record iv yyy 1 natms atomic y coordinates real 8 record v zzz 1 natms atomic z coordinates real 8 record vi only for keytrj gt 0 vxx 1 natms atomic velocities x component real 8 record vii only for keytrj gt 0 vyy 1 natms atomic velocities y co
328. ons ngrid integer number of function data points to read in limit 1 real lower interpolation limit in for dens and pair 125 STFC Section 4 1 or in density units for embed limit 2 real upper interpolation limit in Afor dens and pair or in density units for embed function data records number of data records Int ngrid 3 4 data 1 real data item 1 data 2 real data item 2 data 3 real data item 3 data 4 real data item 4 126 STFC Section 4 2 4 2 The OUTPUT Files DL_POLY Classic produces up to eight output files HISTORY OUTPUT REVCON REVIVE RDFDAT ZDNDAT STATIS and CFGMIN These respectively contain a dump file of atomic coordinates velocities and forces a summary of the simulation the restart configuration statistics accumulators radial distribution data Z density data a statistical history and the configuration with the lowest configurational energy Some of these files are optional and appear only when certain options are used Note In addition to the files described in this chapter users of the hyperdynamics features of DL_POLY Classic should see Chapter 5 where additional files specific to that purpose are described Similarly the output files specific to the solvation features of DL POLY Classic are descrived in Chapter 6 4 2 1 The HISTORY File The HISTORY file is the dump file of atomic coordinates velocities and forces Its principal use is for off line analysis The file is written by
329. ons available in DL_POLY Classic An important distinction between these and intramolecular bond forces in DL_POLY Classic is that they are specified by atom types rather than atom indices 2 3 1 Short Ranged van der Waals Potentials The short ranged pair forces available in DL POLY Classic are as follows 1 12 6 potential 12 6 2 Lennard Jones 1j 3 n m potential 32 U ry e a ij ij A 12 5 6 vew al s nm co a re e 4 Buckingham potential buck U rij A exp 52 S p Tij 5 Born Huggins Meyer potential bhm C D U rij A explBlo ri 5 35 1 1 6 Hydrogen bond 12 10 potential hbnd 7 Shifted force n m Ulrij with U rij e n ij ij potential 32 snm lA AA em ld Tout To oil 1 E Y yal n m ner m y m 1 y MBNA n y n 1 y 28 2 88 2 89 2 90 2 91 2 92 2 93 2 94 2 95 2 96 2 97 STFC Section 2 3 This peculiar form has the advantage over the standard shifted n m potential in that both E and ro well depth and location of minimum retain their original values after the shifting process 8 Morse potential mors U rij Eo 1 exp k rig ro 1 2 98 9 Shifted Weeks Chandler Anderson WCA potential 33 wea 4 5 12 m 6 o A Uris 55 513 wE i L 444 2 99
330. opoly is used to submit a DL POLY job to the Daresbury Intel Xeon cluster and takes a form similar for batch processing on many parallel machines The following is for an 8 processor job bin bash The parallel environment to run in and the number of nodes pe mpich 2 Run from the directory the job was submitted from cwd Export all environment variables from submission shell to the job V Merge stderr and stdout streams j yes What to name the output o GOPOLY JOB_ID How many processors per node PPN 4 The location of the binary to run binary home user dl_poly_2 20 execute DLPOLY X Create the machinefile sed s 4 HOME mpich mpich_hosts JOB_ID gt HOME mpich ndfile JOB_ID Do it mpirun np NSLOTS PPN M 196 STFC Section 9 1 machinefile HOME mpich ndfile JOB_ID binary Normally the job is submitted by the unix command qsub gopoly where qsub is a local command for submission to the Xeon cluster The number of required nodes and the job time are indicated in the above script 9 1 1 5 gui gui is a macro that starts up the DL_POLY Classic Java GUI It invokes the following unix com mands java jar java GUI jar In other words the macro invokes the Java Virtual Machine which executes the instructions in the Java archive file GUL jar which is stored in the java subdirectory of DL POLY Classic Note Java 1 3 0
331. orking volume for the system This is needed to help calculate RDFs etc The working value of D is in fact taken as one of 3xcutoff or 2xmax abs Z coordinate cutoff or the user specified D whichever is the larger Note that the standard Ewald sum cannot be used with this boundary condition DL_POLY Classic switches automatically to the Hautman Klein Ewald method instead 47 The surface in a system with charges can also be modelled with DL_POLY Classic if periodicity is allowed in the Z direction In this case slabs of ions well separated by vacuum zones in the Z direction can be handled with IMCON 2 or 3 Hexagonal prism boundaries IMCON 7 In this case the Z axis lies along a line joining the centres of the hexagonal faces The Y axis is perpendicular to this and passes through the centre of one of the faces The X axis completes the orthonormal set and passes through the centre of an edge that is parallel to the Z axis Note It is important to get this convention right The origin of the atomic coordinates is the centre of the 210 STFC Section B 0 cell If the length of one of the hexagon edges is D the cell vectors required in the CONFIG file are 3D 0 0 0 4 3D 0 0 0 H where H is the prism height the distance between hexagonal faces The orthorhombic cell also defined by these vectors enscribes the hexagonal prism and possesses twice the volume but the height and the centre are the same The Ewald summation
332. ory but also results in a more coarse grain parallelism The consequence of which is that performance with a large number of processors will degrade more quickly than with the atomistic scheme Once the neighbour list has been constructed each node of the parallel computer may proceed independently to calculate the pair force contributions to the atomic forces 2 6 4 Modifications for the Ewald Sum For systems with periodic boundary conditions DL POLY Classic employs the Ewald Sum to cal culate the Coulombic interactions see section 2 4 6 Calculation of the real space component in DL POLY Classic employs the algorithm for the calculation of the nonbonded interactions outlined above The reciprocal space component is cal 77 STFC Section 2 6 culated using the schemes described in 59 in which the calculation can be parallelised by distri bution of either k vectors or atomic sites Distribution over atomic sites requires the use of a global summation of the q exp ik r terms but is more efficient in memory usage Both strategies are computationally straightforward Subroutine EWALD1 distributes over atomic sites and is often the more efficient of the two approaches Subroutine EWALD1A distributes over the k vectors and may be more efficient on machines with large communication latencies Other routines required to calculate the ewald sum include EWALD2 EWALD3 and EWALD4 The first of these calculates the real space cont
333. outine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine function subroutine subroutine subroutine subroutine function function subroutine subroutine subroutine subroutine subroutine serial f define_system_module f parse_module f utility_module f utility_module f inversion_module f utility_module f ensemble_tools_module ensemble_tools_module ensemble_tools_module ensemble_tools_module Hh Hh Fh hh integrator_module f utility_module f utility_module f utility_module f parse_module f metal_module f vdw_module f solvation_module f solvation_module f basic_comms f serial f utility_module f merge_tools f serial f merge_tools f serial f merge_tools f serial f metafreeze_module f metal_module f metal_module f metal_module f metal_module f metal_module f metafreeze_module f driver_module f parse_module f driver_module forces_module forces_module Hh Hh Fh hh forces_module basic_comms f serial f hyper_dynamics_module f define_system_module f hyper_dynamics_module f hyper_dynamics_module f define_system_module f 286 STFC Section D O neutlst nlist_driver nodedim nodedim nosquish npt_b1 npt_h1 nptq_b1 nptq_b2 nptq_hi nptq_h2 nptqscl_p nptqscl_t nptqvv_b1 nptqvv_b2 nptqvv_h1 nptqvv_h2 nptscale_p nptscale_t nptvv_b1 nptvv_h1 nst_b1 nst_h1 nstq_b1 nstq_b2 nstq_hi nstq_h2 nstqmtk_p nstqscl_p
334. perature transition time to recalculate the low temperature transition time from equation 5 17 Note this may alter the original low temperature diffusion path so be alert to this possibility and change the starting basin for any subsequent simulation These refinements have no impact on the BPD simulations other than to improve the quality of the calculated kinetic properties 5 6 2 Treatment of Multiple Maxima in the Reaction Path The NEB calculations that occur while the BPD or TAD simulations are running may sometimes report a multiple maximum on the reaction path see the TRA entry for the EVENTS file in section 5 5 0 2 More than two maxima is probably indicative of problems with the NEB convergence and should be regarded with suspicion but obtaining two maxima is a real possibility In such cases DL_POLY Classic stores both the end structure of the NEB chain and the structure corresponding to the first minimum in the energy profile along the reaction path but it does not record the activation energies beyond the first peak A BPD simulation requires a complete description of the potential energy surface kinetics so determination of the second activation energy and the corresponding transition time is essential After recording the transition the subsequent dynamics correctly starts for BPD from the final state of the double transition but the loss of information is ignored A NEB calculation is therefore necessary to determine the lost d
335. ps between minimisations and 98 STFC Section 4 1 minim position n f mult n no elec no fic no link no vdw optim energy f optim force f optim position f pres f prim f print n print rdf put shells on cores quaternion f rdf n w reaction f permitted variation tolerance DL POLY units Set multiple timestep multi step interval activated when n gt 2 Ignore all coulombic interactions Activate flying ice cube prevention for Berendsen NVT NPT etc Do not use link cells for vdw or metal forces Ignore all short range non bonded interactions Relax structure based on energy force or position with f permitted variation tolerance DL POLY units Set required system pressure to f k atm target pressure for constant pressure ensembles Set primary cutoff to f A for multiple timestep algorithm only Print system data every n timesteps Print radial distribution functions Superimpose electrostatic shells and cores at start Set quaternion tolerance to f default 1078 Calculate radial distribution functions with n the time step interval between configurations w the RDF bin width A Note range reut Select reaction field electrostatics reaction precision fSelect damped reaction field electrostatics reaction damped f regauss n restart restart noscale restart scale rlxtol f rvdw f scale n shake f shift shift precision f shift damped f spme precision f with
336. pter 2 Force Fields and Algorithms STFC Section 2 0 Scope of Chapter This chapter describes the interaction potentials and simulation algorithms coded into DL_POLY Classic 12 STFC Section 2 1 2 1 The DL POLY Classic Force Field The force field is the set of functions needed to define the interactions in a molecular system These may have a wide variety of analytical forms with some basis in chemical physics which must be parameterised to give the correct energy and forces A huge variety of forms is possible and for this reason the DL POLY Classic force field is designed to be adaptable While it is not supplied with its own force field parameters many of the functions familiar to GROMOS 6 Dreiding 7 AMBER 8 and OPLS 22 users have been coded in the package as well as less familiar forms In addition DL POLY Classic retains the possibility of the user defining additional potentials In DL_POLY Classic the total configuration energy of a molecular system may be written as Noond U r ro as TN 5 Ubona ibond Za b toond 1 Nangle 5 Uangleliangle Tas Tb Te langle 1 Naihed 5 Uginea Udineds Tas Tb Ves Ta tdihed 1 Ninv 5 Uinv linv Las Tb Tos a ling 1 N 1 N 5 Y Upairl i A r l i 1 j gt i 2N 1 N T S Y Us bodyli j K Ti j h i 1 a k gt j y Y Urersop il i uu i 1 j gt i 3N 2N 1 N 5 5 gt Das body t J K N Li Lj Lies En j gt i k gt
337. r failed allocation of nvtqvv_b1 f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 2130 error failed allocation of nvtqvv_b2 f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 2140 error failed allocation of nvtqvv_h1 f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 2150 error failed allocation of nvtqvv_h2 f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 2160 error failed allocation of nptqvv_b1 f densO array This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a small
338. r body term can interact via nonbonded pair forces and ionic forces also The calculation of the three four body terms is distributed over processors on the basis of the identity of the central atom in the bond A global summation is required to specify the atomic forces fully 2 6 7 Metal Potentials The simulation of metals by DL POLY Classic makes use of density dependent potentials of the Sutton Chen type 38 The dependence on the atomic density presents no difficulty however as this class of potentials can be resolved into pair contributions This permits the use of the distributed Verlet neighbour list outlined above 2 6 8 Summing the Atomic Forces The final stage in the RD strategy is the global summation of the atomic force arrays This must be done After all the contributions to the atomic forces have been calculated To do this DL_POLY Classic employs a global summation algorithm 57 which is generally a system specific utility Similarly the total configuration energy and virial must be obtained as a global sum of the contributing terms calculated on all nodes 78 STFC Section 2 6 2 6 9 The SHAKE RATTLE and Parallel QSHAKE Algorithms The SHAKE and RATTLE algorithms are methods for constraining rigid bonds Parallel adapta tions of both are couched in the Replicated Data strategy The essentials of the methods are as follows 9 The bond constraints acting in the simulated system are shared equally between
339. r of array dimension checks and will terminate when an array bound error occurs When a dimension error occurs the standard user response is to edit the DL_POLY Classic subroutine PARSET F Locate where the variable defining the array dimension is fixed and increase accordingly To do this you should make use of the dimension information that DL POLY Classic prints in the OUTPUT file prior to termination If no information is supplied simply doubling the size of the variable will usually do the trick If the variable concerned is defined in one of the support subroutines CFGSCAN F FLDSCAN F CONSCAN F you will need to insert a new line in PARSET F to redefine it after the relevant subroutine has been called Finally the code must be recompiled but in this case it will be necessary only to recompile PARSET F and not the whole code The DL POLY Classic Error Messages Message 3 error unknown directive found in CONTROL file This error most likely arises when a directive is misspelt Action Locate incorrect directive in CONTROL file and replace Message 4 error unknown directive found in FIELD file This error most likely arises when a directive is misspelt or is encountered in an incorrect location in the FIELD file which can happen if too few or too many data records are included 212 STFC Section C 0 Action Locate the erroneous directive in the FIELD file and correct error Message 5 error unknown energy unit reques
340. r using more processors or a machine with larger memory per processor Message 1480 error failed allocation of work arrays in nst_h1 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1490 error failed allocation of density array in nst_h1 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor 259 STFC Section C 0 Message 1500 error failed allocation of work arrays in nveq_1 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1510 error failed allocation of work arrays in nvtq_b1 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1520 error failed allocation of work arrays in nvtq_h1 f This is a memory alloca
341. radients 5 54 88 programmed 5 88 zero temperature 5 88 nudged elastic band NEB see hyperdynamics NEB OUTPUT file 129 parallelisation 5 75 calcite 25 26 Coulombic see potential electrostatic dihedral 4 13 14 20 24 75 76 114 130 electrostatic 4 7 14 17 19 42 43 74 97 99 103 130 embedded atom EAM 34 35 118 125 Finnis Sinclair 34 35 118 119 four body 4 13 15 28 34 78 117 118 130 Gupta 35 119 improper dihedral 4 23 75 intramolecular 28 34 inversion 4 13 24 25 34 115 metal 4 13 34 118 nonbonded 4 14 15 76 78 86 99 108 111 113 116 Sutton Chen 35 119 tabulated 124 Tersoff 13 14 31 33 120 121 tethered 26 27 116 130 131 three body 4 13 15 17 28 30 31 78 117 130 131 valence angle 4 13 14 17 19 24 30 31 To 78 112 113 130 van der Waals 14 17 19 74 86 101 114 PROFILES directory 157 PROnn XY file 157 quaternions 5 55 69 99 RDFDAT file 133 reaction field 52 53 99 REVCON file 132 REVIVE file 133 REVOLD file 122 rigid body 3 5 27 55 57 67 68 70 71 80 rigid bond see constraints bond shell model polarisation 53 54 dynamical shell model 53 54 relaxed shell model 54 SOLVAT file 164 solvation energy 163 see energy decomposition spectroscopic excitation 163 171 292 STFC Section D SPME see Ewald SPME STATIS file 134 stress tensor 19 22
342. rd the new state determine the activation energy by the NEB method if requested and the unbiased transition time using the boost factor in equation 5 5 and then continue the simulation 6 When the simulation ends proceed as follows 145 STFC Section 5 3 a Check the EVENTS file to see if any structural transitions have been obtained Each event is represented by a single record and transitions are flagged with the keyword TRA at the start of the record Use unix grep to locate these entries No observed transitions indicates that either a longer simulation is necessary or running with a higher bias Ebias should be considered b Important If any of the reported transitions has a system activation energy that is below Ebias ie N x E lt Epias where N is the number of atoms in the system this represents a violation of the condition in equation 5 6 which means the observed diffusion path is not a valid representation of the original system The simulation should be repeated with a lower value of Epias io Y If the required number of time steps has not been reached the simulation can be restarted from the REVCON REVIVE and HYPRES files renaming them as CONFIG REVOLD and HYPOLD for the purpose and setting the directive restart with no qualifier in the CONTROL file d Use the DL_POLY Java GUI to plot the system energy and temperature for the whole of the simulation Apart from the equilibratio
343. remain close to this condition throughout the simulation This is essential if the core shell unit is to maintain a net polarisation In practice there is a slow leakage of kinetic energy into the core shell units but this should should not amount to more than a few percent of the total kinetic energy The calculation of the virial and stress tensor in this model is based on that for a diatomic molecule with charged atoms The electrostatic and short ranged forces are calculated as described above The forces of the harmonic springs are calculated as described for intramolecular harmonic bonds The relationship between the kinetic energy and the temperature is different however as the core shell unit is permitted only three translational degrees of freedom and the degrees of freedom corresponding to rotation and vibration of the unit are discounted the kinetic energy of these is regarded as zero In DL_POLY Classic the shell forces are handled by the routine SHLFRC The kinetic energy is calculated by CORSHL and the routine SHQNCH performs the temperature scaling The dynamical shell model is used in conjunction with the methods for long ranged forces described above 2 4 11 Relaxed Shell Model The relaxed shell model is based on the same electrostatic principles as the dynamical shell model but in this case the shell is assigned a zero mass This means the shell cannot be driven dynamically and instead the procedure is first to relax the shell t
344. rest neighbour cells are explicitly treated in the real space part of the Ewald sum Increasing either of these parameters will increase the accuracy but also substantially increase the cpu time of a simulation The recommended value for both these parameters is 1 and if both these integers are left out the default values will be adopted As with the standard Ewald and SPME methods the user may set alternative control param eters with the CONTROL file hke sum directive e g hke sum 0 056611 which would set a 0 05 A kmax1 6 kmax2 6 Once again one may check the accuracy by comparing the Coulombic energy with the virial as described above The last two integers specify once again the values of nhko and nlatt respectively Note it is possible to set either of these to zero in this case Estimating the parameters required for a given simulation follows a similar procedure as for the standard Ewald method above but is complicated by the occurrence of higher orders of the convergence functions Firstly a suitable value for may be obtained when nlatt 0 from the rule a B reut Where Tes is the largest real space cutoff compatible with a single MD cell and 8 3 46 4 37 5 01 5 55 when nhko 0 1 2 3 respectively Thus in the usual case where nhko 1 8 4 37 When nlatt0 this P value is multiplied by a factor 1 2 x nlatt 1 The estimation of kmax1 2 is the same as that for the standard Ewald method above Note 91 STFC Se
345. ribution the second the self interaction corrections and the third is required for the multiple timestep option 2 6 5 Modifications for SPME The SPME method requires relatively little modification for parallel computing The real space terms are calculated exactly as they are for the normal Ewald sum as described above The reciprocal space sum requires a 3D Fast Fourier Transform FFT which in principle should be distributed over the processors but in DL_POLY Classic the decision was made to implement a complete 3D FFT on every processor This is expensive in memory and potentially expensive in computer time However a multi processor FFT requires communication between processors and this has significant impact on the famed efficiency of the FFT It transpires that a single processor FFT is so efficient that the adopted strategy is still effective The charge array that is central to the SPME method see section 2 4 7 is however built in a distributed manner and then globally summed prior to the FFT operation 2 6 6 Three and Four Body Forces DL_POLY Classic can calculate three four body interactions of the valence angle type 60 These are not dealt with in the same way as the normal nonbonded interactions They are generally very short ranged and are most effectively calculated using a link cell scheme 24 No reference is made to the Verlet neighbour list nor the excluded atoms list It follows that atoms involved in the same three fou
346. riod reset BLK n1 n2 where e nl is the time step at which a blackout period was initiated e n2 is time step at which the new blackout period will end TAD only 2 Equilibration period reset EQL n1 n2 where e nl is the time step at which the equilibration period was reset e n2 is time step at which the new equilibration period will end 3 Minimisation completed MIN nl n2 n3 n4 rl r2 r3 where e nl is the time step at which the minimisation commenced integer e n2 is number of cycles required by the minimiser to converge integer e n3 is the BPD TAD block for which the minimisation took place integer e n4is the optimisation convergence criterion key 0 for forces 1 for energy 2 for position integer e rl is the convergence tolerance used by the minimiser real e 12 is the energy of the minimised configuration real e 13 is the the convergence actually achieved by the minimiser real Users should note that a final convergence value r3 greater than the convergence criterion r1 indicates incomplete convergence 4 Nudged Elastic Band completed NEB n1 n2 n3 n4 rl r2 where e nl is the time step at which the NEB calculation commenced integer 155 STFC Section 5 5 e n2 is number of cycles required by the NEB calculation to converge integer e n3 is the maximum allowed number of cycles integer e n4 is the number of beads in the NEB chain integer e rl is the energy of the home basin starting s
347. ror too many basin files found increase mxbsn A TAD or BPD run has generated more than 100 basin files which is the internal operational limit Action Reset the mxbsn parameter which is defined at the top of the hyper_dynamics_module f file to a larger number and recompile Message 2340 error TAD diffs arrays exceeded increase mxdiffs A TAD or BPD run has generated more than 300 recorded differences between the reference struc ture and all subsequent new basins found Effectively this means it has recorded more than 300 275 STFC Section C 0 atomic jumps which is the internal operational limit Action Reset the madiffs parameter which is defined at the top of the hyper_dynamics_module f file to a larger number and recompile Message 2350 error kinks found in NEB chain during optimisation During a TAD or BPD run the nudged elastic band calculation is unable to converge because kink ing of the chain has occurred Action Tricky This implies there is something extreme about the system potential energy surface such as it having an excessive number of undulations or perhaps the simulation has start and end states are too far apart This may be fixed by trying different operational parameters such as using a different number of beads in the NEB chain or perhaps the simulation is being run at too high a temperature Some experimentation is required but it may be possible that the system just isn t suitable
348. rror too many reciprocal space vectors DL_POLY Classic places hard limit on the number of k vectors to be used in the Ewald sum and terminates if more than this is requested Action Either consider using fewer k vectors in the Ewald sum and a larger cutoff in real space or follow standard user response to reset the parameters kmaxb kmaxc Message 186 error transfer buffer array too small in sysgen In the subroutine SYSGEN F DL POLY Classic requires dimension of the array buffer defined by the parameter mxbuff to be no less than the parameter mxatms or the product of parameters mxnstk mxstak If this is not the case it will be unable to restart the program correctly to continue a run Applies to parallel implementations only Action Standard user response Fix the parameter mxbuff Message 190 error buffer array too small in splice DL_POLY Classic uses a workspace array named buffer in several routines Its declared size is a compromise of several r les and may sometimes be too small though in the supplied program this should happen only very rarely The point of failure is in the SPLICE routine which is part of the RD SHAKE algorithm Action Standard user response Fix the parameter mxbuff Message 200 error rdf buffer array too small in revive This error indicates that the buffer array used to globally sum the rdf arrays in subroutine REVIVE is too small Action Standard user response Fix the parameter
349. rror undefined metal potential The user has requested a metal potential DL_POLY Classic does not recognise Action Locate the metal potential specification in the FIELD file and replace with a recognised potential Message 462 error PMF UNIT record expected A pmf unit directive was expected as the next record in the FIELD file but was not found Action Locate the pmf directive in the FIELD file and examine the following entries Insert the missing pmf unit directive and resubmit 245 STFC Section C 0 Message 463 error unidentified atom in metal potential list DL_POLY Classic checks all the metal potentials specified in the FIELD file and terminates the program if it can t identify any one of them from the atom types specified earlier in the file Action Correct the erroneous entry in the FIELD file and resubmit Message 464 error thermostat time constant must be gt 0 d0 A zero or negative value for the thermostat time constant has been encountered in the CONTROL file Action Locate the ensemble directive in the CONTROL file and assign a positive value to the time constant Message 465 error calculated pair potential index too large A zero or negative value for the thermostat time constant has been encountered in the CONTROL file Action Locate the ensemble directive in the CONTROL file and assign a positive value to the time constant Message 466 error barostat time constant must be gt
350. rror which should not occur under normal use Action The user is probably making excessive demands of memory Reconsider the problem size in relation to compute resource 277 STFC Section C 0 Message 2515 Error allocating Steinhardt parameter arrays Unlikely array allocation error which should not occur under normal use Action The user is probably making excessive demands of memory Reconsider the problem size in relation to compute resource Message 2516 Could not open STEINHARDT The STEINHARDT data input file cannot be opened Action The file is probably not available or is unreadable Restore the file as required and rerun Message 2517 Error allocating q4site Unlikely array allocation error which should not occur under normal use Action The user is probably making excessive demands of memory Reconsider the problem size in relation to compute resource Message 2518 Error allocating q6site Unlikely array allocation error which should not occur under normal use Action The user is probably making excessive demands of memory Reconsider the problem size in relation to compute resource Message 2519 Error deallocating buff Unlikely array deallocation error which should not occur under normal use Action Possible system error Raise issue with system manager Message 2521 Error reading line _ of STEINHARDT The nominated line of the STEINHARDT file cannot be read Action Probably mis
351. rt ranged poten tials that the potential function requested is one which is of a form known to the program If the requested potential form is unknown termination of the program results The most probable cause of this is the incorrect choice of the potential keyword in the FIELD file or one in the wrong columns input is formatted Action Read the DL_POLY Classic documentation and find the potential keyword for the potential desired 230 STFC Section C 0 Insert the correct index in the FIELD file definition and ensure it occurs in the correct columns 17 20 If the correct form is not available look at the subroutine FORGEN or its variant and define the potential for yourself It is easily done Message 151 error unknown metal potential selected The metal potentials available in DL POLY Classic are confined to density dependent forms of the Sutton Chen type This error results if the user attempts to specify another Action Re specify the potential as Sutton Chen type if possible Check the potential keyword appears in columns 17 20 of the FIELD file Message 153 error metals not permitted with multiple timestep The multiple timestep algorithm cannot be used in conjunction with metal potentials in DL_POLY Classic Action The simulation must be run without the multiple timestep option Message 160 error unaccounted for atoms in exclude list This error message means that DL POLY Classic has been unable to f
352. rted from the REVCON REVIVE and HYPRES files renaming them as CONFIG REVOLD and HYPOLD for the purpose and continued until the stop time has been reached After the simulation finally stops a new simulation can be started from the basin file obtained from the earliest shortest extrapolated time low temperature transition See section 5 4 3 for more information on restarting a TAD simulation d Use the DL_POLY Java GUI to plot the system energy and temperature for the whole of the simulation Apart from the equilibration period these should hold their values within normal thermodynamic fluctuation even if transitions have occured If they do not the system probably has not been equilibrated adequately to begin with in which case start the simulation again See sction 5 4 3 152 STFC Section 5 4 e Check that all the new states the program found are in the BASINS directory Note that there may be fewer new states than the number of transitions observed because some transitions may end in the same basin more than once so a new state is not stored in this case Examine them using the DL_POLY Java GUI There may be signs of imperfect minimisation atoms not quite on lattice sites etc but this is normal at this stage Corrective action can be taken later see section 5 6 Check that the profiles for all the reported transitions have been written in the PRO FILES directory These record the change in configuration energy a
353. s 51 1243 62 Melchionna S Ciccotti G and Holian B L 1993 Molec Phys 78 533 63 Tildesley D J Streett W B and Saville G 1978 Molec Phys 35 639 74 Tildesley D J and Streett W B Multiple time step methods and an improved poten tial function for molecular dynamics simulations of molecular liquids In Lykos P editor Computer Modelling of Matter ACS Symposium Series No 86 1978 74 Forester T and Smith W 1994 Molecular Simulation 13 195 74 Smith W 1991 Comput Phys Commun 62 229 74 75 78 Smith W 1993 Theoretica Chim Acta 84 385 74 75 76 Smith W 1992 Comput Phys Commun 67 392 75 78 Vessal B Amini M Leslie M and Catlow C R A 1990 Molecular Simulation 5 1 78 Shewchuk J R August 4 1994 An Introduction to the Conjugate Gradient Method Without the Agonizing Pain Edition 1 1 4 School of Computer Science Carnegie Mellon University Pittsburgh PA 15213 88 Voter A 1997 J Chem Phys 106 4665 138 140 141 Sorensen M and Voter A 2000 J Chem Phys 112 9599 138 147 149 150 Hamelberg D Mongan J and McCammon J A 2004 J Chem Phys 120 11919 138 141 142 143 Henkelman G and Jonsson H 2000 J Chem Phys 113 9978 139 140 Rahman J A and Tully J C 2002 J Chem Phys 116 8750 142 Laio A and Parrinello M 2002 Proc Natl Acad Sci 99 12562 176 Quigley D and Rodger P
354. s 14 76 77 FIQA 5 55 69 multiple timestep 74 76 99 101 102 131 NOSQUISH 5 56 69 70 QSHAKE 5 55 56 71 73 80 RATTLE 5 56 58 79 SHAKE 5 55 75 79 80 velocity Verlet 5 54 56 59 Verlet 14 15 30 43 54 57 60 62 64 79 Verlet leapfrog 5 54 55 57 AMBER 4 13 angular momentum 69 angular restraints 20 angular velocity 69 barostat 5 71 98 Berendsen 66 73 Hoover 63 BASINS directory 156 bias potential dynamics BPD see hyperdynam ics BPD boundary conditions 4 43 204 cubic 106 hexagonal prism 106 rhombic dodecahedron 106 truncated octahedron 106 CCP5 3 CFGBSNnn file 156 CFGMIN file 132 CFGTRKmnn file 157 charge groups 108 CONFIG file 104 constraints bond 3 5 14 15 57 59 67 70 71 79 80 111 131 Gaussian 46 47 59 PMF 59 112 CONTROL file 96 CVS 6 direct Coulomb sum 43 distance dependent dielectric 45 46 52 97 103 Fennel and Gezelter method 45 truncated and shifted 44 Wolf method 45 distance restraints 17 embedded atom potential see potential embedded atom EAM energy decomposition 163 ensemble 5 Berendsen NoT 5 55 56 98 101 103 Berendsen NPT 5 55 56 101 103 Berendsen NVT 5 55 56 97 98 101 103 canonical 59 Evans NVT 5 55 56 97 101 103 Hoover NoT 5 55 56 101 Hoover NPT 5 55 56 98 101 Hoover NVT 5 55 56 101 microcanonical see ensemble N VE NVE 59 97 101 103 equations of motion
355. s a function of reaction coordinate Plot these using the DL_POLY Java GUI Use the GUI spline option to get a better idea of what the profiles look like Take special note of any double or multiple maxima The transition is considered to end at the first minimum in these cases A basin file for the first intermediate state is written to the BASINS directory 5 4 3 Restarting a TAD Simulation It may be necessary to restart a TAD simulation for a number of reasons a The earliest low temperature transition from the current basin has been found and the user now wants to investigate transitions from the new basin This basin corresponds to that which a molecular dynamics simulation would have reached first at the low tem perature In which case users should save their data from the first study and commence the simulation from the new basin exactly as in the previous study i e renaming the appropriate basin CFGBSNnn file as CONFIG Once again an initial equilibration of the system to high temperature is recommended This is not strictly a restart of an unfinished simulation but the start of a new one which is part of a TAD series The previous simulation ended but did not record any transitions In this case it is advised to start the simulation afresh using a higher operating temperature than before The previous simulation ended without crashing and recorded some transitions but did not reach the required stop time In this case simp
356. s close to Mi see figure 5 4 Combining the two equations and rearranging gives ty EUD Fiol Thon cm L Ge log 1 6 Voter 63 argues that Vmin is commonly of the order 1012 101 s or 1 10 in DL POLY units and suggests 0 001 as a working value These represent practical working values for approximating tstop 5 4 2 Running a TAD Simulation This section describes the procedure for running a TAD simulation The reader will notice some resemblance to the BPD procedure described in section 5 3 This is intentional for operational reasons but the reader should always be alert to the key differences between the two We recommend the following procedure 150 STFC Section 5 4 1 Run a normal simulation of the system at the high temperature Thigh needed to perform the TAD simulation Make sure the system behaves itself before moving to the next stage and doesn t melt for example Retrieve the REVCON file and rename it as CONFIG for the TAD run In principle this equilibration can be skipped and a TAD simulation started right away with a suitable equilibration period at the start but it is probably wiser to do this stage beforehand and make sure the system behaves properly at this temperature 2 Set up the TAD simulation using the directives in the CONTROL file as follows a Set the tad directive followed by records defining the operating conditions b Define the energy units for the TAD param
357. s for this purpose The configuration energy decomposition available in DL POLY Classic can be summarised as follows 1 For each unique molecular type in the system A B C etc the program will calculate e the net bond energy e the net valence angle energy e the net dihedral angle energy e the net inversion angle energy and e the net atomic polarisation energy These are the so called intramolecular interactions while those below are considered to be intermolecular 2 For each unique pair of molecular types in the system AA AB AC BB BC CC etc the program will calculate e the net coulombic energy and e the net Van der Waals energy 3 For each unique triplet of molecular types in the system AAA AAB AAC ABB ABC ACC etc the program will calculate 163 STFC Section 6 2 e the net three body angle energy 4 For each unique quartet of molecular types in the system AAAA AAAB AAAC AABB AABC AACC etc the program will calculate e the net four body angle energy These are calculated at user specified intervals in the simulation from a chosen starting point and written to a data file called SOLVAT which is decribed in section 6 2 3 below It is not required that all the above different kinds of interaction are present in the same system The types of intramolecular interaction that may be defined in DL_POLY Classic are described in section 2 2 The types of intermolecular terms that can be
358. s is distinct from the normal cutoff used by the Van der Waals interactions Action Check the Tersoff potential description in the FIELD file Make sure it is fully complete Message 1955 error failed allocation of tersoff work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1960 error conflicting shell option in FIELD file The relaxed shell and adiabatic shell polarisation options in DL_POLY Classic are mutually exclu sive The user has request both options in the same simulation Action Locate the occurrences of the shell directives in the FIELD file and ensure they specify the same shell model 268 STFC Section C 0 Message 1970 error failed allocation of shell_relax work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1972 error unknown tersoff potential defined in FIELD file DL_POLY Classic has failed to recognise the Tersoff potentials specified by the user in the FIELD file Action Locate the Tersoff potential specification in the FIELD fiel and ensure it is correctly define
359. s of type b within a sphere of radius r around an atom of type a Note that a readable version of these data is provided by the RDFDAT file below 4 2 2 9 Z Density Profile If both calculation and printing of Z density profiles has been requested by selecting directives zden and print rdf in the CONTROL file Z density profiles are printed out as the last part of the OUTPUT file This is written by the subroutine ZDEN1 First the number of time steps used for the collection of the histograms is stated Then each function is given in turn For each function a header line states the atom type represented by the function Then z p z and n z are given in tabular form Output is given from Z L 2 L 2 where L is the length of the MD cell in the Z direction and p z is the mean number density n z is the running integral from L 2 to z of xy cell area p s ds Note that a readable version of these data is provided by the ZDNDAT file below 4 2 3 The REVCON File This file is formatted and written by the subroutine REVIVE REVCON is the restart configuration file The file is written every ndump time steps in case of a system crash during execution and at the termination of the job A successful run of DL_POLY Classic will always produce a REVCON file but a failed job may not produce the file if an insufficient number of timesteps have elapsed ndump is a parameter defined in the SETUP_MODULE F file found in the source directory o
360. s on message 16 above Message 18 error duplicate 3 body potential specified DL_POLY Classic has encountered a repeat specification of a 3 body potential in the FIELD file Action Locate the duplicate entry remove and resubmit job Message 19 error duplicate 4 body potential specified A 4 body potential has been duplicated in the FIELD file Action Locate the duplicated 4 body potential and remove Resubmit job Message 20 error too many molecule sites specified DL_POLY Classic has a fixed limit on the number of unique molecular sites in any given simulation If this limit is exceeded the program terminates Action Standard user response Fix parameter mxsite Message 21 error duplicate tersoff potential specified The user has defined more than one Tersoff potential for a given pair of atoms types Action Locate the duplication in the FIELD file and correct Message 22 error unsuitable radial increment in TABLE file This arises when the tabulated potentials presented in the TABLE file have an increment that is greater than that used to define the other potentials in the simulation Ideally the increment should be r_cut magrid 4 where r_cut is the potential cutoff for the short range potentials and mxgrid is the parameter defining the length of the interpolation arrays An increment less than this is permissible however Action The tables must be recalculated with an appropriate increment 215
361. s this procedure as follows DL_POLY Classic updates the Verlet neighbour list at irregular intervals determined by the movement of atoms in the neighbour list see section 2 1 The interval between updates is usually of the order of 20 timesteps Partitioning the Verlet list into primary and secondary atoms always occurs when the Verlet list is updated and thereafter at intervals of multt timesteps i e the multi step interval specified by the user see section 4 1 1 Immediately after the partitioning the force contributions from both the primary and secondary atoms are calculated The forces are again calculated in total in the subsequent timestep Thereafter for multt 2 timesteps the forces derived from the primary atoms are calculated explicitly while those derived from the secondary atoms are calculated by linear extrapolation of the exact forces obtained in the first two timesteps of the multi step interval It is readily apparent how this scheme can lead to a significant saving in execution time Extension of this basic idea to simulations using the Ewald sum requires the following 1 the reciprocal space terms are calculated only for the first two timesteps of the multi step 2 the contribution to the reciprocal space terms arising from primary interactions are imme diately subtracted leaving only the long range components This is done in real space by subtracting erf terms 3 the real space Coulombic forces arising from
362. sage 305 error box size too small for link cells The link cells algorithm in DL_POLY Classic cannot work with less than 27 link cells Depending on the cell size and the chosen cut off DL_POLY Classic may decide that this minimum cannot be achieved and terminate Action If a smaller cut off is acceptable use it Otherwise do not use link cells Consider running a larger system where link cells will work Message 306 error failed to find principal axis system This error indicates that the routine QUATBOOK has failed to find the principal axis for a rigid unit Action This is an unlikely error The code should correctly handle linear planar and 3 dimensional rigid units Check the definition of the rigid unit in the CONFIG file if sensible report the error to the authors Message 310 error quaternion setup failed This error indicates that the routine QUATBOOK has failed to reproduce all the atomic positions in rigid units from the centre of mass and quaternion vectors it has calculated Action Check the contents of the CONFIG file DL POLY Classic builds its local body description of a rigid unit type from the first occurrence of such a unit in the CONFIG file The error most likely occurs because subsequent occurrences were not sufficiently similar to this reference structure If the problem persists increase the value of the variable tol in QUATBOOK and recompile If problems still persist double the value of dettest in QU
363. sation as described for the optim directive above The user must also supply an integer number of time steps for the interval between successive CG minimisations and the convergence tolerance for each minimisation The tolerance is expressed in the appropriate internal units 101 STFC Section 4 1 13 14 15 16 17 18 19 The DL_POLY Classic multiple timestep option is invoked if the number appearing with the mult directive is greater than 2 This number stored in the variable multt specifies the number of timesteps the multi step that elapse between partitions of the full Verlet neighbour list into primary and secondary atoms If a multiple time step is used i e multt gt 2 then statistics for radial distribution functions are collected only at updates of the secondary neighbour list The number specified on the rdf directive the variable nstbgr means that RDF data are accumulated at intervals of nstbgrxmultt timesteps As a default DL_POLY Classic does not store statistical data during the equilibration pe riod If the directive collect is used equilibration data will be incorporated into the overall statistics The directive delr specifies the width of the border to be used in the Verlet neighbour list construction The width is stored in the variable delr The list is updated whenever two or more atoms have moved a distance of more then delr 2 from their positions at the last update of the Verlet li
364. se Fix the parameter msbad Message 421 error bond vector work arrays too small in dihfrc The work arrays in DIHFRC have been exceeded Action Standard user response Fix the parameter msbad Message 422 error all pairs must use multiple timestep In DL_POLY Classic the all pairs option must be used in conjunction with the multiple timestep Action Activate the multiple timestep option in the CONTROL file and resubmit Message 423 error bond vector work arrays too small in shlfrc The dimensions of the interatomic distance vectors have been exceeded in subroutine SHLFRC Action Standard user response Fix the parameter msbad Set equal to the value of the parameter mxshl Message 424 error electrostatics incorrect for all pairs When using the all pairs option in conjunction with electrostatic forces the electrostatics must be handled with either the standard Coulomb sum or with the distance dependent dielectric Action Rerun the simulation with the appropriate electrostatic option Message 425 error transfer buffer array too small in shlmerge The buffer used to transfer data between nodes in the subroutine SHLMERGE has been dimensioned too small Action Standard user response Fix the parameter mxbuff 240 STFC Section C 0 Message 426 error neutral groups not permitted with all pairs DL_POLY Classic will not permit simulations using both the neutral group and all pairs options together
365. se 2 Metal simulation with Sutton Chen potentials FCC Aluminium using Sutton Chen potentials Temperature is controlled by the method of Gaus sian constraints NVT Evans ensemble 8 1 1 3 Test Case 3 An antibiotic in water Valinomycin in 1223 spc water molecules The temperature is controlled by a Nos Hoover thermo stat while electrostatics are handled by a screened reaction field Coulombic potential The water is defined as a rigid body while bond constraints are applied to all chemical bonds in the valinomycin Truncated octahedral boundary conditions are used NVT Hoover ensemble 187 STFC Section 8 1 8 1 1 4 Test Case 4 Shell model of water 256 molecules of water with a polarizable oxygen atom using adiabatic dynamics Temperature is controlled by the Berendsen thermostat while electrostatics are handled by the reaction field method with a charge group cutoff scheme Slab period boundary conditions are used The water molecule apart from the shell is treated as a rigid body NVT Berendsen ensemble 8 1 1 5 Test Case 5 Shell model of MgCl at constant pressure Adiabatic shell model simulation of MgClz Temperature and pressure are controlled by a Berend sen thermostat and barostat An Ewald sum is used with cubic periodic boundary conditions NPT Berendsen ensemble 8 1 1 6 Test Case 6 PMF calculation Potential of mean force calculation of a potassium ion in SPC water Electrostatics are handle
366. sic uses the Melchionna modification of the Hoover algorithm 53 in which the equations of motion couple a Nos Hoover thermostat and a barostat Cell size variation For isotropic fluctuations the equations of motion are att v t n r t Ro WO Pomo a a T t Text away kpText amo V t P t Pese xN VO novo ee where Q N fhe ltt is the effective mass of the thermostat and W N pha LATE is the effective mass of the barostat Ny is the number of degrees of freedom 77 is the barostat friction coefficient Ry the system centre of mass 77 and Tp are specified time constants for temperature and pressure fluctuations respectively P t is the instantaneous pressure and V the system volume The conserved quantity is to within a constant the Gibbs free energy of the system 1 1 Hnpr U KE PetV t 50x t 5Wn t NO kpText ds 2 269 o TT The algorithm is readily implemented in the LF scheme as 1 AtNrkp At x t At x t 5 At O T t Text G Walt keText x t 5 MU 3A x t 3A8 nlt 5At nt 540 a A Pext xno nt 5 nt 540 Alt 3At 1 v t 5 At u t At At f t T K n 7 63 STFC Section 2 5 u t Ec At u t A0 r t4 At r t At vt At n t sat ka At Eo 1 1 r t At Si r t r t At 2 270 Like the LF Nos Hoover t
367. simulation cell type in the CONFIG File see 4 1 2 1 None e g isolated polymer in space IMCON 0 Cubic periodic boundaries IMCON 1 Orthorhombic periodic boundaries IMCON 2 Parallelepiped periodic boundaries IMCON 3 Truncated octahedral periodic boundaries IMCON 4 Rhombic dodecahedral periodic boundaries IMCON 5 Slab X Y periodic Z nonperiodic IMCON 6 o nnn E WO N Hexagonal prism periodic boundaries IMCON 7 We shall now look at each of these in more detail Note that in all cases the cell vectors and the positions of the atoms in the cell are to be specified in Angstroms A No periodic boundary IMCON 0 Simulations requiring no periodic boundaries are best suited to in vacuuo simulations such as the conformational study of an isolated polymer molecule This boundary condition is not recom mended for studies in a solvent since evaporation is likely to be a problem Note this boundary condition cannot be used with the Ewald summation method Cubic periodic boundaries IMCON 1 The cubic MD cell is perhaps the most commonly used in simulation and has the advantage of great simplicity In DL POLY Classic the cell is defined with the principle axes passing through the centres of the faces Thus for a cube with sidelength D the cell vectors appearing in the CONFIG file should be D 0 0 0 D 0 0 0 D Note the origin of the atomic coordinates is the centre of the cell The cub
368. sing or corrupted data line in file Locate and correct Message 2522 Error allocating Steinhardt parameter arrays Unlikely array allocation error which should not occur under normal use Action The user is probably making excessive demands of memory Reconsider the problem size in relation to compute resource Message 2523 Could not open ZETA The ZETA data input file cannot be opened Action The file is probably not available or is unreadable Restore the file as required and rerun 278 STFC Section C 0 Message 2524 Error allocating zetasite Unlikely array allocation error which should not occur under normal use Action The user is probably making excessive demands of memory Reconsider the problem size in relation to compute resource Message 2525 Error allocating full neighbour list Unlikely array allocation error which should not occur under normal use Action The user is probably making excessive demands of memory Reconsider the problem size in relation to compute resource Message 2527 Number of collective variables incorrect for specified order parameters The internal check of the requested number of order parameters in a metadynamics simulation has found an inconsistency Action Check the total number of collective variables ncolvar matches total number specified by nq4 nq6 ntet and potential energy parameters Message 2529 Error reading line of ZETA There has been an error rea
369. sor Message 2030 error failed allocation of nptvv_b1 f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 2040 error failed allocation of nptvv_h1 f densO array This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor 270 STFC Section C 0 Message 2050 error failed allocation of nptvv_h1 f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 2060 error failed allocation of nstvv_b1 f densO array This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 2070 error failed allocation of nstvv_b1 f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action
370. spectively The equations have the same conserved variable Hnpr as the LF scheme The integration is performed by the subroutine NVTVV H1 which calls subroutines RATTLE_R RATTLE_V NPTSCALE_T and NPTSCALE_P Cell size and shape variation The isotropic algorithms may be extended to allowing the cell shape to vary by defining 7 as a tensor 7 The LF equations of motion are implemented as 1 1 AtN yk x E 5At x t 340 T t Text WT r n t Oko Text Q Q Ee x t Tat ree 340 nit At lt nit At O a t Poet Atx t n t nt 5 nt At n t 540 t At v t At At a x 0 1 n 0 7 i e Lut Ah aed 2 r t At r t At vt At n t At EC At Ro Hoe sat L r t r t A8 2 273 where 1 is the identity matrix and the pressure tensor The new cell vectors are calculated from 1 H t At exp lat n t At H t 2 274 DL_POLY Classic uses a power series expansion truncated at the quadratic term to approximate the exponential of the tensorial term The new volume is found from V t At V t exp At Tr n 2 275 The conserved quantity is 1 1 Hyer U KE PaaV t Qx 0 WTr n t xe at OkpTea ds 2 276 This algorithm is implemented in the routine NST_H1 with bond constraints The VV version of this algorithm is implemented as xlt At at age Tat SWT Ska Text v alt i ano n au yo US Pood O
371. ss tensor terms in real space may be calculated directly from the pair forces and interatomic distances in the usual way and need not be discussed further The calculation of the reciprocal space contributions the terms involving the fn g a functions are more difficult Firstly however we note that the reciprocal space contributions to Ozz 055 and oz may be obtained directly from the force calculations thus recip __ ft ore Daf j Pii gt zf 2 226 J on Dai J 0 51 STFC Section 2 4 which renders the calculation of these components trivial The remaining components are calculated from Nmax eo opis Urecip UV Ei an 5 Suo T 0 B 970 2n 1 1 n Nios a eop 9 4a 2 227 g ay T 2n V PC Zo Zn p 9 p 0 where u v are one or both of the components x y Note that although it is possible to define these contributions to the stress tensor it is not possible to calculate a pressure from them unless a finite arbitrary boundary is imposed on the z direction which is an assumption applied in DL POLY Classic but without implications of periodicity in the z direction The x y components define the surface tension however For bonded molecules as with the standard 3D Ewald sum it is necessary to extract contribu tions associated with the excluded atom pairs In the DL POLY Classic HKE implementation this amounts to an a posteriori subtraction of the corresponding coulomb terms In
372. ssive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor 261 STFC Section C 0 Message 1615 error failed allocation of work arrays in qrattle_q f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1620 error failed allocation of work arrays in nveq_2 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1625 error failed allocation of work arrays in qrattle_v f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1630 error failed allocation of work arrays in nvtq_b2 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine
373. ssive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1690 error failed allocation of work arrays in nstq_b2 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1700 error failed allocation of density array in nstq_b2 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1710 error failed allocation of work arrays in nstq_h2 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor 263 STFC Section C 0 Message 1720 error failed allocation of density array in nstq_h2 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machin
374. st The directive impact is intended to simulate the effects of a high energy atomsic impact such as occurs in radiation damage The user must supply the integer identity of the impacted atom the time step when the impact takes place usually after equilibration the recoil energy of the impacted atom in kilo electron volts and the direction of the recoil i e three components of a unit vector specifying the direction The directive no fic activates and option that tries to prevent the occurrence of the flying ice cubethat sometimes arises in long time simulations using the Berendsen method for ther mostating This arises through accumulated numerical round off which gradually transfers momentum from the system kinetic energy to the centre of mass momentum resulting in a zero Kelvin structure with a net linear momentum This option removes the COM momentum at user selected intervals The put shells on cores directive ensures that associated cores and shells start the simula tion at exactly the same place It is not usual to do this however 102 STFC Section 4 1 Table 4 1 Internal Restart Key keyres meaning 0 start new simulation from CONFIG file continue current simulation start new simulation from CONFIG file and rescale velocities to desired temperature start new simulation from CONFIG file without rescaling the velocities and assign velocities from Gaussian distribution Table
375. stem averages corresponding to the thermodynamic state of the original system at the specified temperature and pressure The calculation of the true thermodynamic 142 STFC Section 5 3 averages requires a correction in the form of a weighted average 64 The true thermodynamic average lt A gt of a property A is thus given by N lt Ac Wosas E gt bias N lt e Wrias R gt bias lt gt 5 11 Where the ensemble averages are obtained in the biased system In practice if the system visits many basins in the course of the simulation i e passes through many states it is not always sensible to compute such averages over the run DL POLY Classic only does this when using BPD to explore configuration space see below section 5 3 5 in which case Vo is defined to be the first minimum visted in the simulation 5 3 2 Running a BPD Simulation Two ways of running bias potential dynamics are available in DL POLY Classic The first is referred to as Full Path Kinetics since it attempts to reproduce a full description of the diffusion path with the associated activation energies This is described in section 5 3 3 A variation of Full Path Kinetics allows the user to bypass the Nudged Elatic Band calculations which is useful in circumstances where the NEB has problems The second is configurational sampling which exploits BPD to explore the range of structural states available to a system which need no
376. step algorithm and a three body valence angle potentials to support the silicate structure It also using tabluated two body potentials stored in the file TABLE The system is comprised of 8640 atoms and runs on 16 512 processors 8 1 2 6 Benchmark 6 Simulation of a potassium valinomycin complex in 1223 water molecules using an adapted AMBER forcefield and truncated octahedral periodic boundary conditions The system size is 3838 atoms and runs on 16 512 processors 8 1 2 7 Benchmark 7 Simulation of gramicidin A molecule in 4012 water molecules using neutral group electrostatics The system is comprised of 12390 atoms and runs on 8 512 processors This example was provided by Lewis Whitehead at the University of Southampton 8 1 2 8 Benchmark 8 Simulation of an isolated magnesium oxide microcrystal comprised of 5416 atoms originally in the shape of a truncated octahedron Uses full coulombic potential Runs on 16 512 processors 8 1 2 9 Benchmark 9 Simulation of a model membrane with 196 41 unit membrane chains 8 valinomycin molecules and 3144 water molecules using an adapted AMBER potential multiple timestep algorithm and Ewald sum electrostatics The system is comprised of 18866 atoms and runs on 8 512 processors 193 Chapter 9 Utilities 194 STFC Section 9 1 Scope of Chapter This chapter describes the more important utility programs and subroutines of DL_POLY Classic found in the sub directory utility 9 1 Miscell
377. t and T t although it should be noted x has different roles in the two thermostats The Berendsen algorithm conserves total momentum but not energy Here again the presence of constraint bonds requires an additional iteration with one application of SHAKE corrections The algorithm is implemented in the DL_POLY routine NVT B1 for systems including bond constraints The VV implementation of Berendsen s algorithm proceeds as folows seian oy ZEO 1 r t At r t Ato t 5At call rattle R TN Wes Ae v t At u t At gt call rattle V bey Xx 1 4 1 Tr Text v t At yu t At 2 261 Routines rattle R and rattle V apply the bondlength and velocity constraint formulae 2 251 and 2 252 respectively The integration is performed by the subroutine NVTVV B1 which calls subroutines RATTLE_R and RATTLE_V 61 STFC Section 2 5 2 5 5 Gaussian Constraints Kinetic temperature can be made a constant of the equations of motion by imposing an additional constraint on the system If one writes the equations of motions as dr t a 20 sio EO _ oun 2 262 2 263 with the temperature constraint dT d Ge ae E Mvi x 2 mi vil 0 2 264 then choosing Ls mid t f t di mv t minimises the least squares differences between the Newtonian and constrained trajectories Following Brown and Clarke 52 the algorithm is implemented in the LF scheme by calculating n 1 1
378. t however is coupled only to the translational degrees of freedom and not to the rotation DL_POLY Classic supports both Hoover and Berendsen thermostats and barostats for systems containing rigid bodies For LF integration the Hoover thermostat is implemented in NVTQ_H1 the Hoover isotropic barostat plus thermostat in NPTQ_H1 and the anisotropic barostat in NSTQ_H1 The analogous routines for the Berendsen algorithms are NVTQ B1 NPTQ_B1 and NSTQ B1 These subroutines also call RDSHAKE_1 to handle any rigid bonds which may be present For VV integration the Hoover thermostat is implemented in NVTQVV_H1 NVTQSCL the Hoover isotropic barostat plus thermostat in NPTQVV_H1 NPTQSCL_T NPTQSCL_P and the anisotropic barostat in NSTQVV_H1 NSTQSCL_T NSTQSCL_P The analogous routines for the Berendsen algorithms are NVTQVV_B1 NPTQVV_B1 and NSTQVV_B1 The subroutines in brackets represent supporting subroutines These subroutines also call RATTLE_R and RATTLE_V to handle any rigid bonds which may be present 2 5 7 3 Linked Rigid Bodies The above integration algorithms can be used for rigid bodies in systems containing atomic species whose equations of motion are integrated with the standard leapfrog algorithm These rigid bodies may even be linked to other species including other rigid bodies by extensible bonds However if a rigid body is linked to an atom or another rigid body by a bond constraint the above algorithms are not adequa
379. t necessarily be in the solid state It may also be used to improve thermodynamic averaging of a system at a given temperature where equilibration is problematical due to long time scales This is described in section 5 3 5 5 3 3 Full Path Kinetics This option is intended to determine the true diffusional path that a solid state system follows at a given temperature but at an accelerated rate Each time the system transforms from one structure to another i e from one state to another the program records the states it encounters and optionally calculates the activation energy E associated with the transition and extrapolates to the time at which the transition would have occured in the unbiased system This information may subsequently be used to determine the full kinetics of the system The method in outline is as follows 1 The first operation of the program is to construct a reference state for the structure by energy minimisation The simulation then proceeds with the biased potential option in much the same manner as a normal simulation but during which a running estimate of the boost factor in equation 5 5 is computed 2 At user defined intervals called here a BPD block the simulation is halted and the structure energy minimised to create new reference structure which is compared with the original reference state to determine if a transition has occurred A transition is deemed to have occured if one or more atoms are
380. t constraints involving shared atoms etc Action Corrective action depends on the cause It is unlikely that simply increasing the iteration number will cure the problem but you can try follow standard user response to increase the parameter mxshak But the trouble is much more likely to be cured by careful consideration of the physical system being simulated For example is the system stressed in some way Too far from equilibrium Message 440 error undefined angular potential A form of angular potential has been requested which DL_POLY Classic does not recognise Action Locate the offending potential in the FIELD file and remove Replace with one acceptable to DL_POLY Classic if this is possible Alternatively you may consider defining the required potential in the code yourself Amendments to subroutines SYSDEF and ANGFRC will be required Message 442 error undefined three body potential A form of three body potential has been requested which DL_POLY Classic does not recognise Action Locate the offending potential in the FIELD file and remove Replace with one acceptable to DL_POLY Classic if this is reasonable Alternatively you may consider defining the required po tential in the code yourself Amendments to subroutines SYSDEF and THBFRC will be required Message 443 error undefined four body potential DL_POLY Classic has been requested to process a four body potential it does not recognise Action Check the FIELD file
381. t is not needed for Helmholtz NVT free energies Note that the configuration energy and virial differences include the factor df A dA that appears in equation 6 9 To facilitate the averaging operation the DL_POLY Classic utility directory contains a program fresta f which calculates the averages of the potential and kinetic energies and their RMS deviations 170 STFC Section 6 4 6 4 Solution Spectroscopy 6 4 1 Spectroscopy and Classical Simulations Spectroscopy is the study of the absorption of photons by an atomic or molecular species the chromophore to create an excited state and the subsequent de excitation of the excited state by photon emission or quenching Absorption M hv gt M Emission M gt M hv 6 16 Quenching M gt M Clearly these are quantum mechanical processes with limited scope for modelling by classical molec ular dynamics However if certain simplifying assumptions are made classical simulation can yield useful information An example of this is the calculation of solvent induced spectral shifts in which a solvent affects a spectroscopic transition absorption or emission through broadening the spec tral line and shifting its location in the energy spectrum In this case the simplifying assumptions are that the spectroscopic transition occurs instantaneously without a change in the structural conformation of the chromophore though its interaction with the solvent is expected to change as a
382. t the structural optimisation proceeds via a programmed minimisation involving alternating periods of molecular dynamics and conjugate gra dient minimisation Once again both rigid body RB and constraint bond CB models are used to define the water molecule structure and conjugate gradient optimisation proceeds to zero force convergence 8 1 1 30 Test Case 30 Zero Kelvin structure optimisation of DNA The DNA structure of Test Case 10 1260 atoms is here placed in a vacuum and a zero Kelvin optimisation is applied to reduce the overall system energy The smoothed particle mesh method is used to handle the electrostatics 8 1 1 31 Test Case 31 Linear molecule fluid NPT Hoover simulation of a fluid consisting of 675 linear molecules parameters approximate a polyacetylene chain A 6 site rigid body is used to represent the molecules 4050 atoms NPT ensemble 8 1 1 32 Test Case 32 TAD Simulation of Diffusion in Solid Argon The TAD method is applied to Lennard Jones argon A crystal of 255 argon atoms FCC lattice plus one vacancy is simulated in the NVE ensemble 8 1 1 33 Test Case 33 BPD Simulation of Diffusion in Solid Sodium Chloride Bias potential dynamics is applied to a crystal of sodium chloride with the rocksalt structure NVE ensemble 998 ions are present and two vacancies in a neutral structure BPD is used to investigate the diffusional hops and determine the activation energies 8 1 1 34 Test Case 34 Energy Decomposi
383. ta The invocation may also be made in a more informative way decompose or solvate start n1 interval n2 enddec or endsol in which start and interval specify the start time step n1 and time step interval n2 respectively Directives enddec or endsol close the data specification 6 2 3 The SOLVAT File The SOLVAT file is a file in which DL POLY Classic writes all the energy decomposition solvation data It is an appendable file and is written to at intervals defined by the user during the 164 STFC Section 6 2 simulation Restarts of DL POLY Classic will continue to append data to an existing SOLVAT file so the user must be careful to ensure that this is what is actually wanted Its contents are as follows record 1 Format 80a1 The job title as defined at the top of the CONTROL file record 2 Format 40a1 Energy units as defined in the FIELD file header record 3 Format 2110 natms mxtmls the numbers of atoms and molecule types in system record 4 Format 1x 11a4 Information record labels contents of record 5 lex Isw bnd ang dih inv shl cou vdw 3bd 4bd record 5 Format 11L4 lexcite lswitch lcomp 1 9 Logical control variables where each indicates the following lexcite true spectroscopic excited state calculation see section 6 4 2 Iswitch true switching between states for solvent relaxation study see section 6 4 3 lcomp 1 true bond energies are present lcomp 2
384. tart n1 specifies the time step of the first calculation of the solvation energy of the excited state integer n1 3 inter n2 the time step interval sampling interval between excited state solvation calcula tions integer n2 4 system_a i1 i2 identifies the range of atom indices in the CONFIG file that consitute the chromophore in the first state integer i1 i2 5 system_b i3 i4 identifies the range of atom indices in the CONFIG file that consitute the chromophore in the second state integer i3 i4 6 endexc closes specification of solvent induced shift option The following additional comments should be noted Atoms in the CONFIG file that are not included in the ranges defined by either directive system_a or system_b are categorised as solvent atoms This categorisation has no effect on their physical properties Both system_a and system_b directives specify the atoms of the chro mophore though they represent different states of the chromophore This of course means the 172 STFC Section 6 4 chromophore appears twice in the CONFIG file The atoms specified by system_a are consid ered to be real atoms and participate fully in the molecular dynamics of the system The atoms specified by system_b are considered to be virtual and do not affect the dynamics or contribute to the energy of the system They are however used to determine the interaction energy of the chromophore with the solvent in the manner of a virtual
385. tate configuration real e r2 is the energy of the end basin new state configuration real Users should note that when n2 and n3 are equal this implies that convergence of the NEB chain has not been achieved Note also that the characteristics of the reaction path are given by the subsequent TRA event below 5 Transition detected TRA n1 n2 n3 n4 r1 r2 r3 r4 where e nl is the time step at which the transition was first detected integer e n2 is the home basin starting state of the transition integer e n3 is the new basin ending state of the transition integer e n4 is the number or turning points in the transition profile integer e rl is the activation energy obtained from the NEB calculation real e 12 is the observed transition time real e 13 is the calculated extrapolated transition time real e r4 is the calculated stopping time real TAD only Note that iof the user has set the noneb directive in a BPD simulation the entry for the activation energy is replaced by the bias potential which sets a lower bound for the activation energy 6 Transition ignored TRI n1 where e nl is the time step at which a transition was detected but ignored because it was during an equilibration or blackout period integer TAD Only 7 Transition repeated TRR n1 n2 n3 where e nl is the time step at which a transition was detected but it was identified as a repeat and no further analysis was underatken integer
386. te The reason is that the constraint will introduce an additional force and torque on the body that can only be found after the integration of the unconstrained unit DL_POLY Classic has a suite of integration algorithms to cope with this situation in which both the constraint conditions and the quaternion equations are solved similtaneously using an extension of the SHAKE algorithm called QSHAKE 17 It has been cast in both LF and VV forms We will describe here how it works for VV the LF version is decribed in 17 Firstly we assume a rigid body A is connected to another B at timestep t nAt via bonds between atoms at positions Tip and B given by Tip Rat day rep Ret dpp 2 309 71 STFC Section 2 5 where R represents the rigid body COM and d the displacement of the atom from the relevant COM The subscript p indicates that these are the atoms providing the links In the first stage of the VV QSHAKE algorithm the rigid bodies are allowed to move unre stricted Our task is then to find the the constraint force G g which would preserve the constraint bondlength ie dip dihp Assuming we know this force we can write n 1 At n 1 R T Ry 2M B 2 310 in which the tilde indicates the corresponding variable computed in the absence of the constraint force For brevity in this and subsequent equations we leave out corresponding equations for body B We can also write the true torque at timestep tn ie
387. ted The DL_POLY Classic FIELD file permits a choice of units for input of energy parameters These may be electron volts ev kilocalories kcal kilojoules kj or the DL_POLY Classic internal units 10 J mol internal There is no default value Failure to specify any of these correctly or reference to other energy units will result in this error message See documentation of the FIELD file Action Correct energy keyword on units directive in FIELD file and resubmit Message 6 error energy unit not specified A units directive is mandatory in the FIELD file This error indicates that DL_POLY Classic has failed to find the required record Action Add units directive to FIELD file and resubmit Message 7 error energy unit respecified DL_POLY Classic expects only one units directive in the FIELD file This error results if it en counters another implying an ambiguity in units Action Locate extra units directive in FIELD file and remove Message 8 error time step not specified DL_POLY Classic requires a timestep directive in the CONTROL file This error results if none is encountered Action Inserttimestep directive in CONTROL file with an appropriate numerical value Message 10 error too many molecule types specified DL_POLY Classic has a set limit on the number of kinds of molecules it will handle in any simu lation this is not the same as the number of molecules If this permitted maximum is ex
388. teps 1 2 Step 9 above does not apply for VV The velocity is integrated under the normal VV scheme When the velocity is updated iteration of the constraint force takes place The incremental changes to the velocity are communicated between nodes sharing constrained atoms as for the bondlength constraints Iteration is repeated until the bond constraints are converged After convergence the velocity arrays on each node are passed to all the other nodes by splicing This scheme contains a number of non trivial operations which are described in detail in 45 However some general comments are worth making The compilation of the list of constrained atoms on each node and the circulation of the list items 1 3 above need only be done once in any given simulation It also transpires that in sharing bond contraints between nodes there is an advantage to keeping as many of the constraints 79 STFC Section 2 6 pertaining to a particular molecule together on one node as is possible within the requirement for load balancing This reduces the data that need to be transferred between nodes during the iteration cycle It is also advantageous if the molecules are small to adjust the load balancing between processors to prevent shared atoms The loss of balance is compensated by the elimination of communications during the SHAKE cycle These techniques are exploited by DL_POLY Classic The QSHAKE algorithm is an extension o
389. ter see table 4 8 The meaning of these variables is given in table 4 8 See the note on the atomic indices appearing under the shell directive above This directive and associated data records need not be specified if the molecule contains no angular terms 112 STFC Section 4 1 Table 4 8 Valence Angle potentials key potential type Parameters p1 74 functional form harm Harmonic k 0 U 0 E 9 6 hrm quar Quartic k Oo K k U 0 0 00 0 90 6 00 gur thrm Truncated harmonic k 00 p U 0 ko 0o exp r 15 p thm shrm Screened harmonic k O pi po U 80 E 9 00 expl ri p1 Tik p2 shm bvs1 Screened Vessal 28 k 00 pi po C CE my 0 my bv1 exp rij p1 Tik p2 bvs2 Truncated Vessal 29 k 4 a p U 0 k 9 9 b0 0 bo 27 gn bv2 9 6 a 00 expl rf rip 0 hcos Harmonic Cosine k o U 0 E cos 0 cos 0p hcs cos Cosine A 6 m U 0 A 1 cos m 0 COS mmsb MM Stretch bend Al bo dab dac U 0 A 0 90 Tav dab Tac dac msb stst Compass A dap dac Ubac AlTab dab Tac dac sts stretch stretch stbe Compass A 9 dab U as A 0 00 Tab dab stb stretch bend cmps Compass A B C 60 Ubac AlTab dab Tac dac 0 90 cmp all terms P5 dab P6 dac Bla dab C Tac dac
390. tes the minimum energy path between the two states 6 In practice this simple idea needs refining or nudging Thus care is taken to ensure that the springs forces acting on the beads and the forces optimising bead configurations are approximately orthogonal This means that the atomic forces are zeroed in directions parallel to the path of the chain and the spring forces are zeroed in directions normal to the chain The method of Henkelman and Jonsson 65 is designed to achieve this 7 If the NEB optimisation works correctly the result will be that beads are evenly spaced along the minimum energy path see figure 5 2 Then by fitting the energies of the beads as a function of the distance along the path the maximum energy i e E along the path may be obtained The DL POLY Classic NEB routine does this fit using third order splines 5 3 Bias Potential Dynamics 5 3 1 Theory of Bias Potential Dynamics BPD works on the simple principle that the addition of a suitable potential term to original system potential can have the effect of reducing the depth of the potential basin see figure 5 3 so assisting escape to neighbouring states The biased system potential Vpias RY is thus given by Voias RN V R Woias RN 5 4 where V RY is the original system potential and Wpias R is the bias potential Voter 62 has shown that using a bias potential accelerates the diffusion rate constant k 97 as defined by Transition Stat
391. tetrahedral order parameters are required activate the option with the directive ltet If the global potential energy order parameter is required activate the the option with the directive lglobpe If local potential energy order parameters are required activate the option with the directive note that global and local potential energy are mutually exclusive options llocpe Set the scale factor for the global potential energy order parameter globpe scale f where f is a real number Set the scale factor for the local potential energy order parameter locpe scale f where f is a real number Set the number of Steinhardt Q4 parameters required nq4 n where n is an integer Set the number of Steinhardt Og parameters required nq6 n where n is an integer Set the number of tetrahedral parameters required ntet n where n is an integer Set the Gaussian potential deposition interval in units of time steps meta_step_int n where n is an integer Set the height w of the Gaussian potentials in units of kgT where T is the simulation temperature 180 STFC Section 7 4 q ref_W_aug f where f is a real number Set the Gaussian potential width parameter h_aug f where f is a real number Set the Gaussian control key hkey n where n is an integer See section 7 4 1 for guidance Set the control parameter for well tempered dynamics required when hkey is 2 wt_Dt f where f is a real number
392. the Verlet neighbour list for macromolecules is the concept of excluded atoms which arises from the need to exclude certain atom pairs from the overall list Which atom pairs need to be excluded is dependent on the precise nature of the force field model but as a minimum atom pairs linked via extensible bonds or constraints and atoms grouped in pairs linked via valence angles are probable candidates The assumption behind this requirement is that atoms that are formally bonded in a chemical sense should not participate in nonbonded interactions with each other However this is not a universal requirement of all force fields The same considerations are needed in dealing with charged excluded atoms DL POLY Classic has 14 STFC Section 2 2 several subroutines available for constructing the Verlet neighbour list while taking care of the excluded atoms see chapter 3 for further information Three and four body nonbonded forces are assumed to be short ranged and therefore calcu lated using the link cell algorithm 24 They ignore the possibility of there being any excluded interactions involving the atoms concerned Throughout this section the description of the force field assumes the simulated system is described as an assembly of atoms This is for convenience only and readers should understand that DL POLY Classic does recognise molecular entities defined either through constraint bonds or rigid bodies In the case of rigid bodies
393. the atomic forces are resolved into molecular forces and torques These matters are discussed in greater detail later in sections 2 5 2 1 and 2 5 7 2 2 The Intramolecular Potential Functions In this section we catalogue and describe the forms of potential function available in DL_POLY Classic The key words required to select potential forms are given in brackets before each definition The derivations of the atomic forces virial and stress tensor are also outlined 2 2 1 Bond Potentials rs Ij Figure 2 1 The interatomic bond vector The bond potentials describe explicit bonds between specified atoms They are functions of the interatomic distance only The potential functions available are as follows 1 Harmonic bond harm Ulrij shri E 2 2 2 Morse potential mors U rij Eo 1 exp k rig ro 1 2 3 3 12 6 potential bond 12 6 4 Restrained harmonic rhrm Ulrij shri To ri rol lt re 2 5 Un Skr krellrij rol re rij ro gt rc 2 6 15 STFC Section 2 2 5 Quartic potential quar k 3 k 4 k 4 U rig 5 rig Po a y To Pig To 2 7 2 3 4 6 Buckingham potential buck fij C Mod we a 2 U r A exp 52 5 23 7 Shifted finitely extendible non linear elastic FENE potential 25 26 27 fene D 2 U r 0 5 k RE ln 1 24729 o Ty lt Ro tA 29 ij gt 00 rij gt Ro A The FENE potentia
394. the secondary atoms are calculated in the first two timesteps of the multi step using the normal Ewald expressions i e the erfc terms 4 the Coulombic forces arising from primary atoms are calculated at every timestep in real space assuming the full Coulombic force In this way the Coulombic forces can be handled by the same multiple timestep scheme as the van der Waals forces The algorithm is described in detail in 56 Note that the accuracy of the algorithm is a function of the multi step interval multt and decreases as multt increases Also the algorithm is not time reversible and is therefore susceptible to energy drift Its use with a thermostat is therefore advised 2 6 DL_POLY Parallelisation DL_POLY Classic is a distributed parallel molecular dynamics package based on the Replicated Data parallelisation strategy 57 58 In this section we briefly outline the basic methodology Users wishing to add new features DL_POLY Classic will need to be familiar with the underlying techniques as they are described in greater detail in references 45 58 74 STFC Section 2 6 Figure 2 8 The multiple timestep algorithm The atoms surrounding the central atom open circle are classified as primary if they occur within a radius rprim and secondary if outside this radius but within reut Interactions arising from primary atoms are evaluated every timestep Interactions from secondary atoms are calculated exactly for the first
395. the units directive Both of these are mandatory These records may optionally be followed by the neut directive record 1 header record 2 units a80 a40 record 3 optional neut The energy units on the units directive are described by additional keywords a40 a eV for electron volts field file header Unit of energy used for input and output activate the neutral charge groups option for the electrostatic calculations b kcal for k calories mol c kJ for k Joules mol 108 STFC Section 4 1 d K for Kelvin e internal for DL POLY Classic internal units 10 J mol If no units keyword is entered DL _POLY Classic units are assumed for both input and output The units keyword may appear anywhere on the data record provided it does not exceed column 40 The units directive only affects the input and output interfaces all internal calculations are handled using DL_POLY Classic units 4 1 3 2 2 Molecular details It is important for the user to understand that there is an structural correspondence between the FIELD file and the CONFIG file described above It is required that the order of specification of molecular types and their atomic constituents in the FIELD file follows the order in which they appear in the CONFIG file Failure to adhere to this common sequence will be detected by DL_POLY Classic and result in premature termination of the job It is therefore essential to work from the CONFIG fi
396. tial described above section 2 4 4 so that polarisation of the long ranged medium by the dipole of the cutoff sphere may be accounted for 2 4 6 Ewald Sum The Ewald sum 12 is the best technique for calculating electrostatic interactions in a periodic or pseudo periodic system The basic model for a neutral periodic system is a system of charged point ions mutually inter acting via the Coulomb potential The Ewald method makes two amendments to this simple model Firstly each ion is effectively neutralised at long range by the superposition of a spherical gaussian cloud of opposite charge centred on the ion The combined assembly of point ions and gaussian charges becomes the Real Space part of the Ewald sum which is now short ranged and treatable by the methods described above section 2 1 gt The second modification is to superimpose a second set of gaussian charges this time with the same charges as the original point ions and again centred on the point ions so nullifying the effect of the first set of gaussians The potential due to these gaussians is obtained from Poisson s equation and is solved as a Fourier series in Reciprocal Space The complete Ewald sum requires an additional correction known as the self energy correction which arises from a gaussian acting on its own site and is constant Ewald s method therefore replaces a potentially infinite sum in real space by two finite sums one in real space and one in reciproca
397. tio The system consists of 256 atoms in total running under the NVE ensemble 8 1 1 24 Test Case 24 Iron metal with Finnis Sinclair potential In this example the analytical Finnis Sinclair potential is applied to iron The system consists of 250 iron atoms and runs under a Berendsen NPT ensemble 8 1 1 25 Test Case 25 Nickel Aluminium 1 1 alloy with EAM potential Another example of an alloy using the EAM potential This is a Nickel Aluminium alloy in the 1 1 ratio The NVE ensemble is used and the system has 432 atoms 8 1 1 26 Test Case 26 Nickel metal with EAM potential Another EAM simulation of a metal 256 Nickel atoms under the Berendsen NPT ensemble 8 1 1 27 Test Case 27 Calcite NVE simulation of 420 molecules 2100 atoms of calcium carbonate in the calcite crystal structure The carbonate anion is handled as a flexible unit with Morse potential bonds and harmonic bond angles NVE ensemble 190 STFC Section 8 1 8 1 1 28 Test Case 28 Optimisation of Ice VII structure 432 SPC water molecules are arranged in a thermally excited Ice VII structure and the congugate gradient method is used to optimise the structure to recover the perfect crystal form Both rigid body RB and constraint bond CB models are used to define the water molecule structure The optimisation proceeds to zero force convergence 8 1 1 29 Test Case 29 Programmed minimisation of Ice VII structure This test is a repeat of Test Case 28 except tha
398. tion Note that one needs to specify the three integers kmax1 kmax2 kmax3 referring to the three spatial directions to ensure the reciprocal space sum is equally accurate in all directions The values of kmax1 kmax2 and kmax3 must be commensurate with the cell geometry to ensure the same minimum wavelength is used in all directions For a cubic cell set kmax1 kmax2 kmax3 However for example in a cell with dimensions 2A 2B C ie a tetragonal cell longer in the c direction than the a and b directions use 2kmaxl 2kmax2 kmax3 If the values for the kmax used are too small the Ewald sum will produce spurious results If values that are too large are used the results will be correct but the calculation will consume unnecessary amounts of cpu time The amount of cpu time increases with kmax1 x kmax2 x kmax3 3 2 5 2 Hautman Klein Ewald Optimisation Setting the HKE parameters can also be achieved rather simply by the use of a hke precision directive in the CONTROL file e g hke precision 1d 6 1 1 which specifies the required accuracy of the HKE convergence functions plus two additional in tegers the first specifying the order of the HKE expansion nhko and the second the maximum lattice parameter nlatt DL_POLY Classic will permit values of nhko from 1 3 meaning the HKE Taylor series expansion may range from zeroth to third order Also nlatt may range from 1 2 meaning that 1 the nearest neighbour and 2 and next nea
399. tion timestep It should be noted that this formula is an approximation only For a system of simple diatomic molecules computation of the constraint force will in principle allow the correct atomic positions to be calculated in one pass However in the general polyatomic case this correction is merely an interim adjustment not only because the above formula is ap proximate but the successive correction of other bonds in a molecule has the effect of perturbing previously corrected bonds The SHAKE algorithm is therfore iterative with the correction cycle being repeated for all bonds until each has converged to the correct length within a given tolerance The tolerance may be of the order 1074 A to 1078 A depending on the precision desired The procedure may be summarised as follows 1 All atoms in the system are moved using the Verlet algorithm assuming an absence of rigid bonds constraint forces This is stage 1 of the SHAKE algorithm 2 The deviation in each bondlength is used to calculate the corresponding constraint force 2 248 that retrospectively corrects the bond length 3 After the correction 2 248 has been applied to all bonds every bondlength is checked If the largest deviation found exceeds the desired tolerance the correction calculation is repeated 4 Steps 2 and 3 are repeated until all bondlengths satisfy the convergence criterion This iter ation constitutes stage 2 of the SHAKE algorithm DL_POLY
400. tion arrays for metadynamics Unlikely array deallocation error which should not occur under normal use Action Possible system error Raise issue with system manager Message 2537 Error deallocating comms buffer arrays Unlikely array deallocation error which should not occur under normal use Action Possible system error Raise issue with system manager Message 2538 Error allocating solvation arrays for metadynamics Unlikely array allocation error which should not occur under normal use Action The user is probably making excessive demands of memory Reconsider the problem size in relation to compute resource Message 2540 Error allocating force prefactor arrays Unlikely array allocation error which should not occur under normal use Action The user is probably making excessive demands of memory Reconsider the problem size in relation to compute resource Message 2541 Memory allocation error in compute_tet_nlist Unlikely array allocation error which should not occur under normal use Action The user is probably making excessive demands of memory Reconsider the problem size in relation to compute resource Message 2542 Error in metafreeze_module f90 mxninc too small The internal estimate of the array allocation variable mzninc is too small for the purpose Action Locate where variable is defined in metafreeze_module f and reset to a larger number 280 STFC Section C 0 Message 2543 nnn too s
401. tion error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1530 error failed allocation of work arrays in npt bl f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1540 error failed allocation of density array in npt bl f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1550 error failed allocation of work arrays in nptq_h1 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor 260 STFC Section C 0 Message 1560 error failed allocation of density array in nptq_h1 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider
402. tion failure DL_POLY Classic has failed to allocate sufficient memory to accommodate one or more of the real arrays in the code Action This may simply mean that your simulation is too large for the machine you are running on Consider this before wasting time trying a fix Try using more processing nodes if they are available If this is not an option investigate the possibility of increasing the heap size for your application Talk to your systems support people for advice on how to do this 217 STFC Section C 0 Message 34 error character array memory allocation failure DL_POLY Classic has failed to allocate sufficient memory to accommodate one or more of the character arrays in the code Action This may simply mean that your simulation is too large for the machine you are running on Consider this before wasting time trying a fix Try using more processing nodes if they are available If this is not an option investigate the possibility of increasing the heap size for your application Talk to your systems support people for advice on how to do this Message 35 error logical array memory allocation failure DL_POLY Classic has failed to allocate sufficient memory to accommodate one or more of the log ical arrays in the code Action This may simply mean that your simulation is too large for the machine you are running on Consider this before wasting time trying a fix Try using more processing nodes if they are av
403. tion in Liquid DMSO The energy decomposition or solvation energy facility is used to provide a breakdown of the molecular configuration energy terms occuring in liquid dimethyl sulfoxide DMSO The basic ensemble is obtained from Berendsen s NVT algorithm The DMSO molecule has flexible angles but rigid constraint bonds 512 molecules are present in the system Reaction field electrostatics are used 8 1 1 35 Test Case 35 Free Energy Difference of DMSO DMSO in DMSO Solvent This simulation represents a single point in a thermodynamic integration procedure to determine the free energy difference between an excited DMSO molecule labelled DMSO and the ground state DMSO molecule The simulation corresponds to a mixed Hamiltonian system of 512 DMSO molecules 502 representing the solvent 10 representing the ground state and 10 DMSO excited 191 STFC Section 8 1 molecules The mixing uses the error function method with A 0 25 The basic ensemble is pro vided by the Hoover NVT algorithm The electrostatic interactions are handled by the reaction field method 8 1 1 36 Test Case 36 Calculation of Solvent Induced Spectral Shift In this simulation 512 DMSO molecules are simulated in the Hoover NVT ensemble and at intervals 10 DMSO molecules are substituted by DMSO molecules in the same configuration in order to determine the instantaneous solvation energy of the DMSO The simulation immediately reverts back to the groundstate
404. tion of densO array in nst_b0 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1350 error failed allocation of work arrays in nst_b0 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1360 error failed allocation of densO array in nst_h0 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1370 error failed allocation of work arrays in nst_h0 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor 257 STFC Section C 0 Message 1380 error failed allocation of work arrays in nve_1 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be repl
405. tory The DL_POLY Classic Java Graphical User Interface GUI is based on the Java language developed by Sun The Java source code for this GUI is to be found in this sub directory along with a few FORTRAN sub sub directories which contain some additional capabilities accessible from the GUI These sources are complete and sufficient to create a working GUI provided the user has installed the Java Development Kit 1 4 or above which is available free from Sun at http java sun com The GUI once compiled may be executed on any machine where Java is installed though note the FORTRAN components will need to be recompiled if the machine is changed See 9 1 5 Obtaining the Source Code DL_POLY Classic source code and the associated test data is available from CCPForge at http ccpforge cse rl ac uk STFC Section 1 6 1 6 Other Information The DL_POLY Classic website http www ccp5 ac uk DL_POLY CLASSIC provides additional information in the form of 1 Access to all documentation 2 Frequently asked questions 3 Bug reports 4 Access to the DL_POLY online forum The DL_POLY Forum is a web based centre for all DL_POLY users to exchange comments and queries You may access the forum through the DL_POLY Classic website A registration and vetting process is required before you can use the forum but it is open in principle to everyone It is a good place to contact other users and discuss applications 10 Cha
406. types a and b V is the system volume and gay r and Uap r are the appropriate pair correlation function and pair potential respectively It is usual to assume gap r 1 for r gt rey DL POLY Classic sometimes makes the additional assumption that the repulsive part of the short ranged potential is negligible beyond rey The correction for the system virial is Ww AL a mo O E 2 106 V Jret Or where the same approximations are applied Note that these formulae are based on the assumption that the system is reasonably isotropic beyond the cutoff In DL_POLY Classic the short ranged forces are calculated by one of the routines SRFRCE SRFRCE_RSQ and SRFRCENEU The long ranged corrections are calculated by routine LRCORRECT The calculation makes use of the Verlet neighbour list described above 2 3 2 Three Body Potentials The three body potentials in DL_POLY Classic are mostly valence angle forms They are primarily included to permit simulation of amorphous materials e g silicate glasses However these have been extended to include the Dreiding 7 hydrogen bond The potential forms available are as follows 1 Harmonic harm k U Ojik 5 sir 00 2 107 2 Truncated harmonic thrm k U Ojik ziik 09 exp rf r3 0 2 108 3 Screened Harmonic shrm k 2 U Ojik 5 jik 8o exp rij p1 rir p2 2 109 30 STFC Section 2 3 4 Screened Vessal 28 bvs1 TT T 00 T O
407. umstances A and B may have atoms in common in which case these can be be treated as part of the solvent without affecting their physical properties It is permissible to have no atoms in category A or category B if that is required 6 3 4 The FREENG File The FREENG file is a formatted in which DL_POLY Classic writes all the free energy data re quested It is an appendable file and program restarts will continue to add data to it if it already exists The data are written at user defined intervals during the simulation The contents of the file are as follows record 1 Format 80a1 The job title as defined at the top of the CONTROL file record 2 Format 40a1 Energy units as defined in the FIELD file header record 3 Format 4e16 8 lambda lambdal lambda2 dlambda with e lambda Hamiltonian mixing parameter A real e lambdal mixing factor 1 f A real e lambda2 mixing factor f A real e dlambda derivative of lambdal w r t A record 4 end of file Format i10 2e16 8 nstep engcfg vircfg where e nstep time step of data integer e engcfg configuration energy difference V2 Vj real e vircfg virial difference V2 Y real The configuration energy presented in the FREENG file may be averaged over the entire run to obtain the configuration energy contribution to the average on the right of equation 6 1 The virial presented there may be used in the calculation of the Gibbs free energy but i
408. unadapted procedure is followed 88 STFC Section 3 2 a In the case of rigid bodies atomic forces are resolved into molecular forces and torques The torques are subsequently transformed into an equivalent set of atomic forces which are perpendicular both to the instantaneous axis of rotation defined by the torque vector and to the cylindrical radial displacement vector of the atom from the axis These modified forces are then used in place of the original atomic forces in the conjugate gradient scheme The atomic displacement induced in the conjugate gradient algorithm is corrected to maintain the magnitude of the radial position vector as required for circular motion b With regard to constraint bonds these are replaced by stiff harmonic bonds to permit minimisation This is not normally recommended as a means to incorporate constraints in minimisation procedures as it leads to ill conditioning However if the constraints in the original structure are satisfied we find that provided only small atomic displacements are allowed during relaxation it is possible to converge to a minimum energy structure Furthermore provided the harmonic springs are stiff enough it is possible afterwards to satisfy the constraints exactly by further optimising the structure using the stiff springs alone without having a significant affect on the overall system energy c Systems with independent constraint bonds and rigid bodies and systems with r
409. unction and S r is a screening or truncation function All the function arguments are scalars With this reduction the force on an atom derived from the valence angle potential is given by 0 f grg V Oie Tig Tin 2 29 with atomic label being one of i j k and a indicating the x y z component The derivative is o 0 grg U Piik Tig rir S r Sia gpa A Orit T A Ojik S rir e tl Ong DU rg 0 A Ojik S rij ber ei S rik 2 30 Tik Orik with 045 1 if a b and 64 0 if a b In the absence of screening terms S r this formula reduces to 0 o jik Tijs Tik 3 AO5 2 31 Or U 0 k Tij T k dro 0 k 3 The derivative of the angular function is 0 1 o Tij Tik A 0jik Albi l 2 L 22 2 32 Ore 0 k E 00 55h J k org l Tijfik with ry ri ra r e 00 Oi Sex 04 Ore Tijfik TijTik TijTik Q a ij Tik cos jin fos 00 2 Ser 004 2 33 Tij Tik The atomic forces are then completely specified by the derivatives of the particular functions A 0 and S r The contribution to be added to the atomic virial is given by W rij J Tik Fe 2 34 It is worth noting that in the absence of screening terms S r the virial is zero 30 The contribution to be added to the atomic stress tensor is given by 038 r2 8 12 10 2 35 and the stress tensor is symmetric In DL_POLY Classi
410. using more processors or a machine with larger memory per processor Message 1570 error failed allocation of work arrays in nstq_b1 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1580 error failed allocation of density array in nstq_bl f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1590 error failed allocation of work arrays in nstq_h1 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1600 error failed allocation of density array in nstq_h1 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1610 error failed allocation of work arrays in qshake f This is a memory allocation error Probable cause exce
411. utoff is applied b rvdw this is the user specified cutoff for the van der Waals potentials If not specified its value defaults to rcut It cannot exceed cut c rprim this is used in the multiple timestep algorithm to specify the primary atom region see section 2 5 8 It is ignored if the multiple timestep option is not used Some directives are optional If not specified DL POLY Classic will take default values if necessary The defaults appear in the above table The zero directive enables a zero temperature simulation This is intended as a crude energy minimiser to help relax a system before a simulation begins It should not be thought of as a true energy minimisation method The optim directive enables a conjugate gradient energy minimisation of the configuration There are three additional options energy force and position which decide convergence on the basis of energy force or position The recommended option is force which is suitable for most cases Note that the additional parameter the user must supply is the tolerance for the convergence This must be appropriate for the chosen option All are expressed in DL_POLY internal units For the force option a value of about 1 0 is appropriate for many cases The minim directive enables a programmed minimisation which combines conjugate gradient minimisation with a molecular dynamics search The three additional options energy force and position refer to the CG minimi
412. ve correctly specified the job time variables using the close time and job time directives see section 4 1 1 in the CONTROL file DL_POLY Classic will stop in a controlled manner allowing you to restart the job as if it had not been interrupted To restart a simulation after normal termination you will again require the CONTROL file the FIELD and TABLE file and a CONFIG file which is the exact copy of the REVCON file created by the previous job You will also require a new file REVOLD section 4 1 4 which is an exact copy of the previous REVIVE file If you attempt to restart DL_POLY Classic without this additional file available the job will fail Note that DL POLY Classic will append new data to the existing STATIS and HISTORY files if the run is restarted other output files will be overwritten In the event of machine failure you should be able to restart the job in the same way from the surviving REVCON and REVIVE files which are dumped at intervals to meet just such an emergency In this case check carefully that the input files are intact and use the HISTORY and STATIS files with caution there may be duplicated or missing records The reprieve processing capabilities of DL_POLY Classic are not foolproof the job may crash while these files are being written for example but they can help a great deal You are advised to keep backup copies of these files noting the times they were written to help you avoid going right back to the st
413. where Q k1 ko k3 is the discrete Fourier transform of the charge array Q 1 b2 l3 defined as N Qt 2 63 Y qj Y Mnluij L1 ni L1 Mn ua la n2Lo Mp us 3 m3Lg3 j l ni no n3 2 207 in which the sums over n1 2 3 etc are required to capture contributions from all relevant periodic cell images which in practice means the nearest images 3 Approximating the reciprocal space energy Urecip Y G ba ko ks Q kr ka ka 2 208 U AS RA recip 2V 0 1 in which GT is the discrete Fourier transform of the function 2 Gi kas by CMO o ks O kr ka ka 2 209 and where B k1 ka ks b1 1 1 b2 2 1 b3 3 1 2 210 and Q k1 ko k3 is the complex conjgate of Qt k1 ko k3 The function G k1 ko ks is thus a relatively simple product of the gaussian screening term appearing in the conventional Ewald sum the function B k1 k2 k3 and the discrete Fourier transform of Q k1 ko k3 4 Calculating the atomic forces which are given formally by OU pecip 1 fF wit 5 G ki ko k3 2 Or Vol k ko kg OQ 1 ka k3 or 2 211 Fortunately due to the recursive properties of the B splines these formulae are easily evaluated The virial and the stress tensor are calculated in the same manner as for the conventional Ewald sum The DL_POLY Classic subroutines required to calculate the SPME contributions are BSPGEN which calculates the B splines BSPCOE
414. which calculates B spline coefficients SPL_CEXP which calculates the FFT and B spline complex exponentials EWALD_SPME which calculates the re ciprocal space contributions SPME_FOR which calculates the reciprocal space forces and DLPFFT3 which calculates the 3D complex fast Fourier transform default code only Cray SGI IBM SP ma chines have their own FFT routines selected at compile time and the FFTW public FFT is also an option These subroutines calculate the reciprocal space components of the Ewald sum only the real space calculations are performed by EWALD2 EWALD3 and EWALD 4 as for the normal Ewald sum In addition there are a few minor utility routines CPY_RTC copies a real array to a complex array ELE_PRD is an element for element product of two arrays SCL_CSUM is a scalar sum of elements of a complex array and SET_BLOCK initialises an array to a preset value usually zero 49 STFC Section 2 4 2 4 8 Hautman Klein Ewald HKE The method of Hautman and Klein is an adaptation of the Ewald method for systems which are periodic in two dimensions only 47 DL POLY Classic assumes this periodicity is in the XY plane The HKE method gives the following formula for the electrostatic energy of a system of N nonbonded ions that is overall charge neutral Nmax Ue i A 2 naaa Zij ny Falg o 97 explig siz ij g 0 Nmax hn 955730 DY e 24 anzi mF 0 izj L VG Sij L L Na xs elt a De qi 2
415. with FIQA and SHAKE NPTQ H2 Constant T P Hoover 21 with QSHAKE NST_B1 Constant T a Berendsen 20 with SHAKE NST H1 Constant Ta Hoover 21 with SHAKE NSTQ B1 Constant T Berendsen 20 with FIQA and SHAKE a a a a NSTQ B2 Constant T Berendsen 20 with QSHAKE NSTQ H1 Constant T Hoover 21 with FIQA and SHAKE NSTQ H2 Constant T Hoover 21 with QSHAKE In the above table the FIQA algorithm is Fincham s Implicit Quaternion Algorithm 15 and QSHAKE is the DL_POLY Classic algorithm combining rigid bonds and rigid bodies in the same molecule 17 2 5 1 2 Velocity Verlet The VV algorithm assumes that positions velocities and forces are known at each full timestep The algorithm proceeds in two stages as follows In the first stage a half step velocity is calculated oes sat ue ZA O 2 243 55 STFC Section 2 5 and then the full timestep position is obtained 1 r t At r t At v t At 2 244 In the second stage using the new positions the next update of the forces f t At is obtained from which the full step velocity is calculated using 1 1 t 4At u t At lt u t 5At At 2 245 Thus at the end of the two stages full synchronisation of the positions forces and velocities is obtained The full selection of VV integration algorithms within DL POLY Classic is as follows NVEVV 1 Velocity Verlet with RATTLE NVEGVV 1 Rigi
416. wo strategies for parallelization of the reciprocal space part of the Ewald sum If EWALD1 is used the parameter mxewld should equal the parameter msatms If EWALD1A is used this parameter should equal mxatms Action Standard user response Set the parameter mxewld to the value appropriate for the version of EWALD1 you are using Recompile the program Message 331 error mxhke parameter incorrect The parameter mxhke which defines the dimension of some arrays used in the Hautman Klein Ewald method should equal the parameter msatms Action Standard user response Set the parameter mxhke to the value regquired Recompile the program Message 332 error mxhko parameter too small The parameter mxhko defines the maximum order for the Taylor expansion implicit in the Hautman Klein Ewald method DL POLY Classic has a maximum of mxhko 3 but it can be set to less in some implementations If this error arises when the user requestes an order in excess of this parameter Action Standard user response Set the parameter mxhko to a higher value if it is lt 3 and recompile the 235 STFC Section C 0 program Alternatively request a lower order in the CONTROL file through the nhko variable see 4 1 1 Message 340 error invalid integration option requested DL_POLY Classic has detected an incompatibility in the simulation instructions namely that the requested integration algorithm is not compatible with the physical model
417. word is one of force energy position and tol is the convergence tolerance The recommended tolerance for force option is 1 0 in DL POLY units e g force 1 0 Close the TAD definition with the directive endtad 3 Set other CONTROL file keywords as follow a The simulation temperature i e the high temperature Thigh for the TAD method using the temp directive 151 STFC Section 5 4 b Select the restart noscale option if the CONFIG file was pre equilibrated otherwise leave out the restart keyword altogether c Set the length of the simulation required steps and the equilibration period equil both in time steps The equilibration can be short if the system was pre equilibrated d In setting the job close time it is recommended to set the number to at least 500 times the clock time it takes to do one normal MD time step This is to prevent the program running out of time during a structural minimisation The timing information for this may be taken from the previous equilibration run e Set the remaining CONTROL keywords as were defined for the initial equilibration simulations 4 Before starting the TAD simulation use the UNIX mkdir command to make the following empty directories e BASINS to receive any new structures found e TRACKS to store the tracking configurations e PROFILES to store any transition pathways found by NEB calculation If the directories BASINS TRACKS and PROFI
418. y allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor 258 STFC Section C 0 Message 1440 error failed allocation of work arrays in npt_h1 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1450 error failed allocation of density array in npt_h1 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1460 error failed allocation of work arrays in nst_b1 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1470 error failed allocation of density array in nst_b1 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must conside
419. ynamics is the calculation of the activation energy which is equivalent to determining the saddle point between two states This is accomplished in DL_POLY Classic by a technique known as the Nudged Elastic Band NEB method Understanding the NEB method is a prerequisite for using the DL_POLY Classic hyperdynamics methods correctly so a description of it is given in the following section 5 2 The Nudged Elastic Band Calculation 2 094 F pi N a ab Figure 5 2 Basic NEB Theory Plot of bead configuration energy vs reaction path for a NEB calculation of a structural transition in a Lennard Jones solid The Nudged Elastic Band NEB method is a standard method for determining the energy optimised pathway between two known structures In DL_POLY Classic it is used to find the escape pathway also called the reaction path between structural basins yielding the activation energy in the process The implementation is based on the method described by Henkelman and Jonsson 65 though it has been adapted to work in parallel The method is as follows 1 The start and end points of the NEB construction are the energy minimised structures for states A and B A structure RY is defined as the set of 3N coordinates locating all N atoms in the system 2 A series of states is constructed by linear interpolation between the structures of states A and B i e a series of configurations RY is generated with i
420. ynamics DL_POLY Classic allows the user to include a scale factor in the definition This appears in the STEINHARDT and ZETA data files described in the following section 7 4 Running Metadynamics Simulations The recommended procedure for running metadynamics with DL POLY Classic is as follows 1 Scope out the appropriate choices of order parameters for your system following the method of Quigley and Rodger outlined above in section 7 2 and in 68 You should use one of the equilibrated REVCON files as the starting configuration for your metadynamics study 179 STFC Section 7 4 2 Decide a suitable interval tg for depositing the Gaussians 7 2 and an appropriate Gaussian height w and width dh to ensure accuracy for the free energy calculation See 69 and 68 for details Along with this the user must also choose a Gaussian deposition convergence scheme see section 7 4 1 3 Set up the metadynamics option in the CONTROL file as follows a Set the metadynamics directive metadynamics or use the eguivalent directive metafreeze Then enter the metadynamics control variables one per record as indicated below Com ment records may be inserted if the first character is the hash symbol or the am persand amp Set the number of order parameters to be used ncolvar ncolvar n where n is an integer If Steinhardt order parameters are required activate the option with the directive Istein If
421. yy gt Izz In this local frame the so called Principal Frame the inertia tensor is therefore constant The orientation of the local body frame with respect to the space fixed frame is described via a four dimensional unit vector the quaternion q go q1 q2 q3 2 288 and the rotational matrix R to transform from the local body frame to the space fixed frame is the unitary matrix 2 q192 4093 4 4 2 q943 q091 2 289 q 4 42 45 2 q1q2 093 2 q143 q092 R 2 q143 q092 2 g gt 93 qoq q 13 45 so that if dj is the position of an atom in the local body frame with respect to its COM its position in the universal frame w r t its COM is given by R d 2 290 aa With these variables defined we can now consider the equations of motion for the rigid body unit 2 5 7 2 Integration of the Rigid Body Equations of Motion The equations of translational motion of a rigid body are the same as those describing the motion of a single atom except that the force is the total force acting on the rigid body i e F in equation 2 285 and the mass is the total mass of the rigid body unit i e M in equation 2 282 These 68 STFC Section 2 5 equations can be integrated by the standard Verlet LF or VV algorithms described in the previous sections Thus we need only consider the rotational motion here The rotational equation of motion for a rigid body is r 51 5 1 2 291 in which J is

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