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DLPOLY3 USER MANUAL

1. U rij A exp 52 2 71 P Tij 5 Born Huggins Meyer potential bhm C D U rij A exp Blo rij 5 3 2 72 Ti r 6 Hydrogen bond 12 10 potential hbnd U rij n 2 73 ij ij 7 Shifted force n m potential 31 snm ve a O omy am NGG 0 ga with n m npr 1 m y m 1 y mBr 1 n y n 1 y m 1 _ nm p y 2 75 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 25 CCLRC Section 2 3 8 Morse potential mors U rig Eo 1 exp K rg ro 1 2 76 9 Tabulation tab The potential is defined numerically only The parameters defining these potentials are supplied to DL_POLY 3 at run time see the descrip tion of the FIELD file in Section 5 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 _3 must also be provided with a cutoff radius rydw which sets a range limit on the computation of the interaction Together with the parameters the cutoff is used by the subroutine VDW_GENERATE to construct an interpolation array vvdw for the potential function over the rang
2. CCLRC Section 5 1 a particular RDF pair in the following manner atmnam 1 as first atom type atmnam 2 a8 second atom type By default in DL_POLY_2 and DL _POLY 3 every vdw potential specifies a RDF pair If the control option rdf f is specified in the CONTROL file then all pairs defined in vdw potentials section will also have their RDF calculated For the calculation of RDFs of systems with force fields without vdw potentials some fictitious ones must then be defined The use the rdf n option instead of vdw n provides another way to define RDF pairs not only neater but also memory efficient since DL_POLY 3 will not allocate additional potential arrays that will not be used This option is not available in DL_POLY 2 Note that rdf and vdw are not complementary i e if the former is used none of the pairs defined by the latter will be considered for RDF calculations metal n where n is the number of metal potentials to be entered It is followed by n records each specifying a particular metal potential in the following manner atmnam 1 a8 first atom type atmnam 2 a8 second atom type key ad potential key see Table 5 13 variable 1 real potential parameter see Table 5 13 variable 2 real potential parameter see Table 5 13 variable 3 real potential parameter see Table 5 13 variable 4 real potential parameter see Table 5 13 variable 5 real potential parameter see Table 5 13 The variables pertaining to each potential ar
3. Manner 1 VVI t Las jee O us a iti SETA 2 m 1 r t At x t Atu t 548 3 32 2 RATTLE_VV1 3 FF f t At f t 3 33 4 VV2 1 At f t At u t At ut 5 At Es 3 34 5 RATTLE_VV2 6 Thermostat DU t At f t At e 2 Ekin t At u t At v t At exp x t At At 3 35 The algorithm is self consistent and requires no iterations The LFV implementation the Evans algorithm is iterative as an initial estimate of x t at full step is calculated using an unconstrained estimate of the velocity at full step u t The iterative part is as follows 50 CCLRC Section 3 4 1 FF f t f t At 3 36 2 LFV The iterative part is as follows 1 2 x t At 1 2 S t 4 Af At Ai Ur Ea 1 r t At x t Atu t 340 3 37 3 SHAKE 4 Full step velocity 1 1 1 u t 5 v t SA u t At 3 38 5 Thermostat 2 Ekin t x t lt 3 39 Several iterations are required to obtain self consistency In DL POLY 3 the number of iterations is set to 5 6 if bond constraints are present The conserved quantity by these algorithms is the system kinetic energy The VV and LFV flavours of the Gaussian constraints algorithm are implemented in the DL POLY 3 routines NVT_El_VV and NVT_El_LFV respectively 3 4 3 Berendsen Thermostat In the Berendsen algorithm the instantaneous temperature is pushed towards the desired temper ature Text by scaling the velocities at
4. f t poe a t f t gt 0 ni ci 5 1 is used to help the system relax before each integration of the equations of motion measures taken to conserve the MD cell momentum This must not be thought of as a true energy minimization method Note that this optimisation is applied irrespectively of whether the simulation runs in equilibration or statistical mode 80 CCLRC Section 5 1 The algorithm is developed in the DL POLY _3 routines ZERO_K_OPTIMISE_VV and ZERO_K_OPTIMISE_LFV respectively 8 The pseudo option is intended to be used in highly non equilibrium simulations when users are primarily interested in the structural changes in the core of the simulated system as the the MD cell boundaries of the system are coupled to a Langevin bath stochastic thermostat with temperature the target temperature of the system The stochasticity of the thermostat emulates an infinite environment around the MD cell providing a means for natural heat exchange between the MD system and the heath bath thus aiding possible heat build up in the system In this way the instantaneous temperature of the system is driven naturally towards the target temperature The user is required to specify the width of the pseudo thermostat f in A which must be larger than 2 A and less than or equal to a quarter of minimum width of the MD cell The thermostat is an f A thick buffer layer attached on the inside at the MD cell boundaries Every particle wit
5. Report to authors Message 83 error too many three body potentials specified This should never happen Action Report to authors Message 84 error unidentified atom in three body potential list This shows that DL _POLY 3 has encountered and erroneous entry at tbp definition in FIELD Action Correct FIELD and resubmit Message 85 error required velocities not in CONFIG file If the user attempts to start up a DL POLY 3 simulation with any type of restart directive see description of CONTROL file the program will expect the CONFIG file to contain atomic 167 CCLRC Appendix D velocities as well as positions Termination results if these are not present Action Either replace the CONFIG file with one containing the velocities or if not available remove the restart directive altogether and let DL_POLY_3 create the velocities for itself Message 86 error calculated three body potential index too large This should never happen DL_POLY_3 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 Report to authors Message 87 error too many link cells required in four_body_forces This should not happen The calculation of fo
6. The cutoff for the pair interactions is smaller than twice that for the four body interactions This is a bookkeeping requirement for DL_POLY 3 Action Either use a smaller four body cutoff or a larger pair potential cutoff Message 474 error shell relaxation cycle limit 100 exceeded The conjugate gradient method in the relaxed shell model exceeded the iteration limit 100 Action Corrective action is to increase the limit or decrease the the convergence criterion by hand in CORE_SHELL_RELAX and recompile However it is unlikely that such measures will cure the problem as it is more likely to lay in the physical description of the system being simulated For example are the core shell spring constants well defined Is the system being too far from equilibrium Message 476 error shells MUST all HAVE either zero or non zero masses The polarisation of ions is accounted via a core shell model as the shell dynamics is either relaxed shells have no mass or adiabatic all shells have non zero mass Action Choose which model you would like to use in the simulated system and adapt the shell masses in FIELD to comply with your choice Message 478 error shake algorithms constraints amp pmf failed to converge Your system has both bond and pmf constraints SHAKE RATTLE_VV1 is done by combined application of both bond and pmf constraints SHAKE RATTLE_VV1 in an iterative manner until the pmv constraint virial conve
7. harm Harmonic hcos Harmonic cosine plan Planar k A do do U do U cos cos do U A 1 cos t is the i j k l inversion angle 12 finish This directive is entered to signal to DL _POLY 3 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 5 1 3 2 3 Non bonded Interactions Non bonded interactions are identified by atom types as Opposed to specific atomic indices The following different types of non bonded potentials are available in DL_POLY 3 vdw van der Waals pair metal metal tersoff Tersoff tbp three body and fbp four body Each of these types is specified by a specific keyword as described bellow 1 vdw n where n is the number of pair potentials to be entered It is followed by n records each specifying a particular pair potential in the following manner 95 CCLRC Section 5 1 atmnam 1 atmnam 2 key variable 1 variable 2 variable 3 variable 4 variable 5 as as ad real real real real real first atom type
8. mrs 12 6 12 6 A B U r 4 ij ij 126 rhrm Restraint k To Te U r 3 k rij ro rig ro lt re rhm U r 3kr2 kre lrig rol re rij rol gt re quar Quartic k ro k k U r E rij ro rij ro qur rij ro buck Buckingham A p C U r A exp ru 4 bck l coul Coulomb k U r 2 a cul Note Bond potentials with a dash as the first character of the keyword do not contribute to the excluded atoms list see Section 2 In this case DL_POLY 3 will also calculate the non bonded pair potentials between the described atoms unless these are deactivated by another potential specification 92 CCLRC Section 5 1 Table 5 9 Valence Angle Potentials key potential type Variables 1 4 functional formj harm Harmonic k 00 U 0 5 0 00 hrm quar Quartic k 0o R k U 0 E 0 00 0 00 0 00 qur thrm Truncated harmonic k 00 p U 0 8 00 exp r 15 p thm shrm Screened harmonic k bo pi P2 U 0 k 8 00 exp rij p1 rix p2 shm k 2 272 bvs1 Screened Vessal 25 k 6o pi p2 U 0 pta eo T 0 7 x bvl exp rij p1 rix p2 bvs2 Truncated Vessal 26 k 00 a p U 0 k 0 0 80 0 bo 27 gr bv2 0 80 T 00 expl r ri p hcos Harmonic Cosine k 00 U 9 cos 9 cos 90 hc
9. pseudo_1fv f90 zero_k_optimise_lfv f90 constraints_shake_lfv f90 pmf_shake_lfv f90 nve_1_lfv f90 nvt_11_1fv f90 nvt_el_1fv f90 nvt_b1_lfv f90 nvt_h1_1fv f90 npt_b1_1fv f90 npt_h1_1fv f90 npt_m1_1fv f90 nst_b1_1fv f90 nst_h1_1fv f90 nst_m1_1fv f90 md_1fv f90 Examine targets manually CC rrrrrrrrrrrrrrrrror ecc all echo echo You MUST specify a target machine echo echo Please examine Makefile for permissible targets echo echo If no target suits your system create your own echo using the generic target template provided in echo this Makefile at entry uknown_machine echo Fetch MPI SERIAL subroutines FILES_SERIAL make links_serial 144 CCLRC Appendix C links_serial for file in FILES_SERIAL do echo linking to file rm f file ln s SERIAL file file done Fetch the Velocity Verlet subroutines FILES_VV make links_vv links_vv for file in FILES_VV do echo linking to file rm f file ln s VV file file done Fetch the LeapFrog Verlet subroutines FILES_LFV make links_lfv links_lfv for file in FILES_LFV do echo linking to file rm f file ln s LFV file file done Clean up the source directory clean rm f OBJ_MOD OBJ_ALL FILES_VV FILES_LFV FILES_SERIAL mod Generic target template uknown_machine MAKE LD path to Fortran 90 Linker loaDer
10. Continuous Shear A zo i A z gt zo grav Gravitational Field Gz y 5 F mG magn Magnetic Field Hs Hy Hz F q vx dH sphr Containing Sphere A Ro n Rot E A Ro r r gt Raw zbnd Repulsive Wall A 2 p F A z 2z pz gt pzo 5 1 5 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 i e if the restart directive is not present in the CONTROL file see above The file is unformatted and therefore not human readable DL POLY_3 normally produces the file REVIVE see Section 5 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 3 5 1 5 1 Format The REVOLD file is unformatted All variables appearing are written in native working precision see Section 4 3 5 real representation 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 in terms of parameters from the SETUP_MODULE file see Section 6 2 8 record 1 nstep timestep of final configuration numacc number of configurations used in averages numrdf number of configurations used in rdf averages numzdn number of configurations use
11. E do hcos Harmonic cosine k do U E cos p cos o plan Planar A U A 1 cos p t is the i j k l inversion angle 5 1 3 3 External Field The presence of an external field is flagged by the directive extern The following line in the FIELD file must have another directive indicating what type of field is to be applied The variables pertaining to each potential are described in Table 5 17 Note only one type of field can be applied at a time 5 1 3 4 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 3 will abort 5 1 4 The REFERENCE File The REFERENCE has the same format and structure as CONFIG see Section 5 1 2 file with the exception that imcon MUST BE 0 REFERENCE may contain more or less particles than CONFIG does and may have particles whith identities that are not defined in FIELD see Section 5 1 3 The positions of these particles are used to define the crystalline lattice sites to whitch the particles in CONFIG compare during simulation when the defect detection option defects is used REFERENCE is read by the subroutine DEFECTS_REFERENCE_READ 100 CCLRC Section 5 1 Table 5 17 External Fields key potential type Variables 1 4 functional formt elec Electric Field Ex Ey Ez F qE oshm Oscillating Shear Aln F A cos 2na 2 L shrx
12. core shell unit separation gt rcut This could only happen if FILED and CONFIG do not match each other or CONFIG is damaged Action Regenerate CONFIG and FIELD and resubmit Message 101 error calculated four body potential index too large This should never happen DL_POLY 3 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 Report to authors Message 102 error rcut lt 2 rcter maximum cutoff for tersoff potentials The nature of the Tersoff interaction requires they have at least twice shorter cutoff than the standard pair interctions or the major system cutoff Action Decrease Tersoff cutoffs in FIELD or increase cutoff in CONTROL and resubmit Message 103 error parameter mxlshp exceeded in pass_shared_units Various algorithms constraint and core shell ones require that information about shared atoms be passed between nodes If there are too many such atoms the arrays holding the information will be exceeded and DL_POLY 3 will terminate execution Action Increase the parameter mx1shp in SET_BOUNDS recompile and resubmit Message 104 error arrays listme and Istout exceeded in pass_shared_units This should not happen
13. index integer atomic site index weight real site weighting 89 CCLRC Section 5 1 b pmf unit n2 where n2 is the number of sites in the second unit The subsequent n2 records provide the site indices and weighting Each record contains index integer atomic site index weight real site weighting This directive 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 Note that if a site weighting is not supplied DL_POLY 3 will assume it is zero However DL_POLY 3 detects that all sites in a pmf unit have zero weighting then the pmf unit sites will be assigned the masses of the original atomic sites The pmf bondlength applies to the distance between the centres of the two pmf units The centre R of each unit is given by Dii wj T Ny El 1 Wj where r is a site position and w the site weighting R 5 6 Note that the pmf constraint is intramolecular To define a constraint between two molecules the molecules must be described as part of the same DL_POLY_3 molecule DL_POLY_3 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 in DL POLY 3 pmf constraints are handeled in every available ensemble 7 teth n where n is the number of tethered atoms in the molecule It is followed n records specifying the t
14. second atom type potential key see Table 5 12 potential parameter see Table 5 12 potential parameter see Table 5 12 potential parameter see Table 5 12 potential parameter see Table 5 12 potential parameter see Table 5 12 The variables pertaining to each potential are described in Table 5 12 Note that any pair potential not specified in the FIELD file will be assumed to be zero Table 5 12 Pair Potentials key potential type Variables 1 5 functional form 12 6 12 6 A B U r 4 4 lj Lennard Jones e o U r de 27 27 nm nm Es n ro U r Ca m 22 n 22 buck Buckingham Alp U r A exp 5 amp bhm Born Huggins A B C D U r A exp B o r E R Meyer hbnd 12 10 H bond A B U r 42 4 snm Shifted force E n ro rel Ur ere x nom 81 mera G poner 3 nmaE r 9yro py B Fe UGG GY I mors Morse Eo ro U r Eo 1 exp k r ro 1 tab Tabulation tabulated potential Note in this formula the terms a 8 and y are compound expressions involving the variables Eo n m ro 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 or not specified in the FIELD file 2 rdf n where n is the number of RDF pairs to be entered It is followed by n records each specifying 96
15. 1 2 record 2n n n 1 2 The variables pertaining to each potential are described in Table 5 14 Note that the fifth variable is the range at which the particular tersoff potential is truncated The distance is in Table 5 14 Tersoff Potential key potential type Variables 1 5 6 11 a b functional form ters Tersoff Al a B b R Potential form single S B ln e dlyh as shown in Section cross x w 233 5 tbp n where n is the number of three body potentials to be entered It is followed by n records each specifying a particular metal potential in the following manner atmnam 1 i a8 first atom type 98 CCLRC Section 5 1 atmnam 2 j atmnam 3 k key variable 1 variable 2 variable 3 variable 4 variable 5 a8 a8 ad real real real real real second central atom type third atom type potential key see Table 5 15 potential parameter see Table 5 15 potential parameter see Table 5 15 potential parameter see Table 5 15 potential parameter see Table 5 15 cutoff range for this potential A The variables pertaining to each potential are described in Table 5 15 Note that the fifth variable is the range at which the three body potential is truncated The distance is in measured from the central atom Table 5 15 Three body Potentials key potential type Variables 1 4 functional formt harm Harmonic k 00 U 0 5 0 00 t
16. 186 CCLRC Appendix D Message 1000 error working precision mismatch between FORTRAN 90 and MPI implementation DL_POLY_3 has failed to match the available modes of MPI precision for real numbers to the defined in sc kinds_f90 FORTRAN 90 working precision wp for real numbers wp is a precompile parameter Action This simply mean that wp must have been changed from its original value to something else and the new value is not matched by the mpi_wp variable in COMMS_MODULE It is the user s responsibility to ensure that wp and mpi_wp are compliant Make the necessary corrections to sc kinds_f90 and or COMMS_MODULE Message 1001 error allocation failure in comms_module gt gcheck_vector DL POLY 3 has failed to find available memory to allocate an array or arrays i e there is lack of sufficient memory per node on the execution machine 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 1002 error deallocation failure in comms_module gt gcheck_vector DL POLY 3 has failed to deallocate an array or arrays i e to free memory that is no longer in use Action Talk to your
17. 6 direct Coulomb sum 33 35 77 83 distance dependant dielectric 35 77 83 distance restraints 15 DLPROTEIN 69 Dreiding 12 ensemble 4 176 Berendsen NoT 4 44 77 80 Berendsen NPT 4 44 80 Berendsen NVT 4 44 77 80 canonical 48 Evans NVT 4 44 77 80 Hoover NoT 4 44 77 80 Hoover NPT 4 44 77 80 Hoover NVT 4 44 80 Langevin NVT 4 44 77 80 Martyna Tuckerman Klein NoT 80 Martyna Tuckerman Klein NoT 77 80 Martyna Tuckerman Klein NPT 77 80 microcanonical see ensemble NVE MTK NoT 4 44 MTK NPT 4 44 NVE 4 44 48 77 80 error messages 72 154 Ewald optimisation 70 71 SPME 38 70 77 83 summation 36 37 66 71 79 82 115 118 LIT force field 3 12 13 20 70 117 118 156 171 184 AMBER 3 12 DL_POLY 3 12 Dreiding 3 12 31 GROMOS 3 12 force shifted Coulomb sum 34 78 83 FORTRAN 90 5 6 FTP 9 10 Graphical User Interface 9 69 70 85 GROMOS 3 12 Java GUI 4 9 licence 2 long range corrections Sutton Chen 28 van der Waals 26 parallelisation 4 63 115 Domain Decomposition 4 intramolecular terms 116 117 polarisation 39 40 shell model 3 12 33 39 41 116 117 potential bond 3 69 92 108 116 119 159 178 bonded 118 119 chemical bond 3 12 15 19 20 32 40 116 Lay dihedral 3 12 18 22 94 108 116 117 164 178 198 CCLRC Index electrostatics 3 7 13 15 17 33 77 78 83 108 116 178 extern
18. EX EX BINROOT BINROOT TYPE dirac MAKE LD usr local mpich gm pgroup121 7b bin mpif90 v 0 LDFLAGS 03 L usr local mpich gm pgroup121 7b lib lmpich lfmpich lmpichf90 L usr local gm binary lib lgm L usr local lib FC usr local mpich gm pgroup121 7b bin mpif90 c FCFLAGS fast Knoieee Mdalign 03 EX EX BINROOT BINROOT TYPE Franklin SUNfire cluster setenv HPCF_MPI yes franklin MAKE LD opt SUNWhpc bin mpf90 o LDFLAGS stackvar fsimple 1 x03 xarch v9b DHPCF_MPI lmpi xlic_lib sunperf FC opt SUNWhpc bin mpf90 c FCFLAGS stackvar fsimple 1 x03 xarch v9b xchip ultra xlic_lib sunperf xalias actual fpover ftrap none fnonstd libmil dalign I opt SUNWhpc HPC5 0 include v9 EX EX BINROOT BINROOT TYPE hpcx MAKE LD mpx1f90_r o LDFLAGS 03 q64 qmaxmem 1 FC mpx1f90_r qsuffix f f90 c FCFLAGS 03 q64 qmaxmem 1 qarch pwr5 qtune pwr5 qnosave EX EX BINROOT BINROOT TYPE hpcx debug MAKE LD mpx1f90_r 0 LDFLAGS g C q64 00 lessl lhmd FC mpx1f90_r qsuffix f f90 c FCFLAGS g C q64 00 qarch pwr5 qtune pwr5 qnosave EX EX BINROOT BINROOT TYPE 140 CCLRC Appendix C Default code master message check 0BJ_MOD OBJ_ALL LD EXE OBJ_MOD OBJ_ALL LDFLAGS Check that a machine has been specified
19. Fetch MPI SERIAL subroutines FILES_SERIAL make links_serial 150 CCLRC Appendix C links_serial for file in FILES_SERIAL do echo linking to file rm f file ln s SERIAL file file done Fetch the Velocity Verlet subroutines FILES_VV make links_vv links_vv for file in FILES_VV do echo linking to file rm f file ln s VV file file done Fetch the LeapFrog Verlet subroutines FILES_LFV make links_lfv links_lfv for file in FILES_LFV do echo linking to file rm f file ln s LFV file file done Clean up the source directory clean rm f OBJ_MOD OBJ_ALL FILES_VV FILES_LFV FILES_SERIAL mod Generic target template uknown_machine MAKE LD path to Fortran 90 Linker loaDer LDFLAGS appropriate flags for LD FC path to Fortran 90 compiler FCFLAGS appropriate flags for FC EX EX BINROOT BINROOT TYPE System specific targets follow 151 CCLRC Appendix C sun ultra MAKE LD opt SUNWspro bin f90 v o LDFLAGS 03 xarch v8plusa xchip ultra FC opt SUNWspro bin f90 c FCFLAGS 03 xarch v8plusa xchip ultra EX EX BINROOT BINROOT TYPE MAKE LD f95 o LDFLAGS FC f95 c FCFLAGS 03 EX EX BINROOT BINROOT TYPE Default code master message check 0BJ_MOD OBJ_ALL LD EXE 0BJ_MO
20. H and Sutton A P 1991 Philos Mag Lett 63 217 3 27 116 118 Todd B D and Lynden Bell R M 1993 Surf Science 281 191 3 27 116 118 Tersoff J 1989 Phys Rev B 39 5566 3 28 116 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 3 12 Mayo S Olafson B and Goddard W 1990 J Phys Chem 94 8897 3 12 31 99 Weiner S J Kollman P A Nguyen D T and Case D A 1986 J Comp Chem 7 230 3 12 Smith W 2003 Daresbury Laboratory 4 9 62 69 70 85 132 Allen M P and Tildesley D J 1989 Computer Simulation of Liquids Oxford Clarendon Press 4 36 43 45 48 115 117 Andersen H C 1983 J Comput Phys 52 24 4 45 115 Adelman S A and Doll J 1976 J Chem Phys 64 2375 4 44 48 Evans D J and Morriss G P 1984 Computer Physics Reports 1 297 4 44 48 195 CCLRC Bibliography 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 Berendsen H J C Postma J P M van Gunsteren W DiNola A and Haak J R 1984 J Chem Phys 81 3684 4 44 48 54 Hoover W G 1985 Phys Rev A31 1695 4 44 48 52 54 G M M M E T D J T and M L K 1996 Molec Phys 87 1117 4 44 54 60 Vessal B 1994 J
21. LDFLAGS appropriate flags for LD FC path to Fortran 90 compiler FCFLAGS appropriate flags for FC EX EX BINROOT BINROOT TYPE System specific targets follow 145 CCLRC Appendix C CC rr 2 SUN ULTRA sun ultra MAKE LD opt SUNWspro bin f90 v o LDFLAGS 03 xarch v8plusa xchip ultra FC opt SUNWspro bin f90 c FCFLAGS 03 xarch v8plusa xchip ultra EX EX BINROOT BINROOT TYPE WINDOWS S H win MAKE LD f95 o LDFLAGS FC f95 c FCFLAGS 03 EX EX BINROOT BINROOT TYPE Default code master message check 0BJ_MOD OBJ_ALL LD EXE OBJ_MOD OBJ_ALL LDFLAGS Check that a machine has been specified check if test FC undefined then echo echo Fortran 90 compiler unspecified echo echo Please edit your Makefile entries echo exit 99 fi if test LD undefined then echo echo Fortran 90 Linker loaDer unspecified echo echo Please edit your Makefile entries echo exit 99 fi mkdir p BINROOT message echo DL_POLY_3 compilation in SRL1 mode echo echo Use mpi_module must be uncommented in comms_module f90 echo Declare rules 146 CCLRC Appendix C FC FCFLAGS 90 Declare d
22. Non Cryst Solids 177 103 16 17 31 93 99 Smith W Greaves G N and Gillan M J 1995 J Chem Phys 103 3091 16 17 31 93 99 Allinger N L Y Y H L J H 1998 J Am Chem Soc 111 8551 16 18 Smith W 1993 CCP5 Information Quarterly 39 14 17 20 23 Ryckaert J P and Bellemans A 1975 Chem Phys Lett 30 123 18 94 Schmidt M E S S and A R S Molecular dynamics studies of langmuir monolayers of f cf2 11cooh volume 104 page 2101 1996 18 94 Clarke J H R Smith W and Woodcock L V 1986 J Chem Phys 84 2290 25 96 Finnis M W and Sinclair J E 1984 Philos Mag A 50 45 27 Eastwood J W Hockney R W and Lawrence D N 1980 Comput Phys Commun 19 215 31 32 Neumann M 1985 J Chem Phys 82 5663 35 Fuchs K 1935 Proc R Soc A 151 585 37 39 Essmann U Perera L Berkowitz M L Darden T Lee H and Pedersen L G 1995 J Chem Phys 103 8577 38 118 Fincham D and Mitchell P J 1993 J Phys Condens Matter 5 1031 40 Lindan P J D and Gillan M J 1993 J Phys Condens Matter 5 1019 40 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 40 Ryckaert J P Ciccotti G and Berendsen H J C 1977 J Comput Phys 23 327 45 115 McC
23. Program Library at Daresbury Laboratory in the following manner 1 move to the desired directory on YOUR machine 2 type ftp ftp dl ac uk 3 enter userid anonymous 4 enter passwd use your name and site 5 change to the directory cd ccp5 DL_POLY DOCUMENTS 6 type binary 7 type get LICENCE ps Z or get GROUP LICENCE ps Z 8 type quit The licence file will need to be uncompressed using the unix uncompress command before printing Note that there are two versions of the licence available one for single academic users with perhaps one or two postgraduate students and one for academic groups with perhaps several research staff including postdoctoral and permanent staff Choose the one most suitable for you The licences are package licences which allow you access to all the DL_POLY software Once you have obtained the licence form you should sign it and return it to the following address CCLRC Section 1 6 Dr W Smith DL_POLY Program Library Computational Science and Engineering Department CCLRC Daresbury Laboratory Daresbury Warrington WA4 4AD UK Please return the licence by post please When the signed licence has been received the DL_POLY_3 source code will be transferred by ftp We will need to contact you about this procedure so please supply your e mail address Please note we cannot create accounts on any of our machines for this purpose The DL_POLY_3 User Manual is freely available via Worl
24. are the three cell vectors a b c Like the Nos Hoover thermostat no iterations are required to obtain self consistency If the system contains constrained bonds then DL_POLY 3 uses 2 iterations as in the first P t At and f t are improved for the second Note also that the change in box size requires the RATTLE_VVI algorithm to be called each iteration The LFV flavour of the algorithm is implemented in the DL_POLY 3 routine NPT_H1_LFV in iter ative manner It starts with calculation of initial estimates of x t and n t at full step by using an unconstrained estimate of the velocity at full step u t Also calculated is an unconstrained estimate of the half step position r t 5At ro r t AD 3 81 58 CCLRC Section 3 5 1 FF F f t At 3 82 Ss EO _ x t ult 0 1 1 v t 34t v t At At r t At r t At fat ZAt t At EC sat Ra t BEAD d nt sat At H t vete Di At At 3 83 3 SHAKE 4 Full step velocity and half step position u t 5 ut 3A tolt 3At ret 40 lt z t ut Ta 3 84 5 Thermostat and Barostat 1 2Erin t Pmass ME 20 kp Text 1 x t 5At x t At At dmass x t ae t 5At x t 540 n t ZA fnt t At PE Pas me exp x t At P z he end 540 3 85 Several iterations are required to obtain self consistency In DL POLY 3 the number of iterations is set to 4 5 i
25. echo using the generic target template provided in 138 CCLRC Appendix C echo this Makefile at entry uknown_machine echo Fetch the Velocity Verlet subroutines FILES_VV make links_vv links_vv for file in FILES_VV do echo linking to file rm f file ln s VV file file done Fetch the LeapFrog Verlet subroutines FILES_LFV make links_lfv links_lfv for file in FILES_LFV do echo linking to file rm f file ln s LFV file file done Clean up the source directory clean rm f OBJ_MOD OBJ_ALL FILES_VV FILES_LFV mod Generic target template uknown_machine MAKE LD path to Fortran 90 Linker loaDer LDFLAGS appropriate flags for LD MPI libraries FC path to Fortran 90 compiler FCFLAGS appropriate flags for FC MPI include EX EX BINROOT BINROOT TYPE System specific targets follow 139 CCLRC Appendix C MAKE LD opt intel compiler70 ia32 bin ifc v o LDFLAGS 03 xW prec_div L opt mpich intel lib Impich L opt intel compiler70 ia32 lib 1PEPCF90 FC opt intel compiler70 ia32 bin ifc c FCFLAGS 03 xW prec_div I opt mpich intel include EX EX BINROOT BINROOT TYPE Linux efc SGI ALTIX parallel FFT newton MAKE LD ifort o LDFLAGS tpp2 ip 03 lmpi lguide FC ifort c FCFLAGS 03 tpp2 ip w
26. low values of Raes are likely to lead to slight overestimation of defects If the simulation and reference MD cell have the same number of atoms then the total number of interstitials is always equal to the total number of defects The tolerance for relaxed shell model rlxtol is a last resort option to aid shell relaxation of systems with very energetic and or rough potential surface Users are advised to use it with caution should there really need be as the use of high values may result in physically incorrect dynamics The force selection directives ewald sum ewald precision reaction coul shift dist no elec are handled internally by the integer variable keyfce See Table 5 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 3 uses two different potential cutoffs These are as follows 82 CCLRC Section 5 1 14 15 16 Table 5 4 Electrostatics Key keyfce meaning Electrostatics are evaluated as follows Ignore electrostatic interactions SPME Ewald summation Coulomb sum with distance dependent dielectric Standard truncated Coulomb sum Force shifted Coulomb sum 10 Reaction field electrostatics 0 DD apaEN a reut the universal cutoff se
27. usually because they are too complex e g spline potentials and or a fifth file REFERENCE Section 5 1 4 which is similar to the CONFIG and contains the perfect crystalline structure of the system 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 erecute sub directory A successful run of DL_POLY_3 will generate several data files which appear in the execute sub directory The most obvious one is the file OUTPUT Section 5 2 3 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 5 2 5 and REVCON Section 5 2 4 REVIVE contains the accumulated data for 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 readable 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 5 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 66 CCLRC Section 4 2 Section
28. 5 2 1 provides a time ordered sequence of configurations to facilitate further analysis of the atomic motions By default this file is formatted human readable but with little effort from the user it can be generated unformatted You may move these output files back into the data sub directory using the store macro found in the execute sub directory Lastly DL_POLY_3 may also create the files RDFDAT ZDNDAT and DEFECTS containing the RDF Z density and defects data respectively They are all human readable files 4 2 3 Restarting DL POLY 3 The best approach to running DL_POLY 3 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 3 will usually give diagnostic messages to help you sort out the trouble Running out of job time is common and provided you have correctly specified the job time variables using the close time and job time directives see Section 5 1 1 in the CONTROL file DL_POLY _3 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
29. 7 491549620 2 951142896 2379 766752 0 9720599243E 01 1 787340483 9226 455153 2 503798635 1 021777575 9445 662860 3 732081894 0 5473436377 5365 202509 etc 5 1 2 1 The CONFIG File Format The file is free formatted and not case sensitive Every line is treated as a command sentence record However line records are limited to 72 characters in length Records are read in words as a word must not exceed 40 characters in length Words are recognised as such by separation by one or more space characters The first record in the CONFIG file is a header up to 72 characters long to aid identification of the file Blank and commented lines are not allowed 5 1 2 2 Definitions of Variables in the CONFIG File record 1 header a72 title line record 2 levcfg integer CONFIG file key See Table 5 5 for permitted values imcon integer Periodic boundary key See Table 5 6 for permitted values record 3 omitted if imcon 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 4 omitted if imcon 0 cell 4 real x component of b cell vector 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 84 CCLRC Section 5 1 cell 9 real z component of c cell vector Note that record 2 may contain more informat
30. Dimensions of indicated arrays have been exceeded Action Consider using densvar option in CONTROL for extremely non equilibrium simulations Message 105 error shake algorithm constraints_shake failed to converge The SHAKE algorithm for bond constraints is iterative If the maximum number of permitted iter ations is exceeded the program terminates Possible causes include a bad starting configuration 170 CCLRC Appendix D too large a time step used incorrect force field specification too high a temperature inconsistent constraints over constraint etc Action You may try to increase the limit of iteration cycles in the constraint subroutines by using the direc tive mxshak and or decrease the constraint precision by using the directive shake in CONTROL But the trouble may be 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 link_cell_pairs Construction of the Verlet neighbour list in subroutine LINK_CELL_PAIRS non bonded pair force has exceeded the neighbour list array dimensions Action Consider using densvar option in CONTROL for extremely non equilibrium simulations or increase by hand mxlist in SET_BOUNDS Message 107 error too many pairs for rdf look up specified This should never happen A possible reason is corruption in F
31. Message 515 Message 499 error rattle algorithm pmf rattle failed to converge Action See Message 515 Message 500 error pmf unit of zero length is not permitted PMF unit of zero length is found in FIELD PMF units are either a single atom or a group of atoms usually forming a chemical molecule Action Correct the erroneous entries in FIELD Message 502 error pmf unit member found to be present more than once A PMF unit is a group of unique distingushed atoms sites No repetion of a site is allowed in a PMF unit Action Correct the erroneous entries in FIELD Message 504 error cutoff too large for TABLE file The requested cutoff exceeds the information in the TABLE file Action Reduce the value of the vdw cutoff rvdw in the CONTROL file or reconstruct the TABLE file Message 506 error compress_legend failed to sort a legend array This should never happen Action Report to authors Message 513 error particle assigned to non existent domain in read config This can only happen if particle coordinates do not match the cell parameters in CONFIG Prob ably due to negligence or numerical inaccuracy inaccuracy in generation of big supercell from a small one 183 CCLRC Appendix D Action Make sure lattice parameters and particle coordinates marry each other Increase accuracy when generating a supercell Message 514 error allowed image conventions are 0 1 2 3 and 6 DL_
32. PS AS a Tethering forces Valence angle forces k 1 2 The computed forces are accumulated in atomic force arrays f independently on each pro cessor Dihedral and improper dihedral angle forces Inversion forces 3 The force arrays are used to update the atomic velocities and positions of all the atoms in the domain 4 Any atom which effectively moves from one domain to another is relocated to the neighbour ing processor responsible for that domain 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 3 this is accomplished quite naturally through the DD partitioning of the simulated system Note that this will only work efficiently if the density of the system is reasonably uniform THERE ARE NO LOAD BALANCING ALGORITHMS IN DL_POLY_3 TO COMPENSATE FOR A BAD DENSITY DISTRIBUTION 6 1 2 Distributing the Intramolecular Bonded Terms The intramolecular terms in DL_POLY 3 are managed through bookkeeping arrays which list all atoms sites involved in a particular interaction and point to the appropriate arrays of parameters that define the potential Distribution of the forces calculations is accomplished by the following scheme 1 Every atom site in the simulated system is assigned a unique global index number from 1 to N 2 Every processor maintains a list of the local indices of the the atoms in its domain Thi
33. The data Sub directory LL 8 1 44 The bench Sub directory LL 8 1 4 5 The execute Sub directory LL 8 1 4 6 The build Sub directory e 8 1 4 7 The public Sub directory s s o sci sme sa nca e 8 1 4 8 The java Sub directory ss p e isate aa d ao a a ee 9 1 5 Obtaining the Source Code 2 2 0 eee ee 9 LG Other Tniormatio a RR an re i he BY e O a eee i 10 2 Force Fields 11 2 1 Introduction to DL_POLY 3 Force Field 12 2 2 The Intramolecular Potential Functions o o e e 13 221 Bond Potentials cocinas q eRe A A A 13 22 2 Distance Restraints e cos saa e 2 sek eee ee a a 15 2 2 3 Valence Angle Potentials 020000002220 e 15 22 4 Angular Restraints lt coop a Ree Dee Re Ree ee 17 2 2 5 Dihedral Angle Potentials o sw miec k eas aoa a a e k E 00 0022 E 18 2 2 6 Improper Dihedral Angle Potentials o 20 2 2 7 Inversion Angle Potentials 22 21 228 Tethering Forces i sa co pa sa rieda waaa aa ER SR a 23 220 Fron AIN 6 4 e be e Rui a a E ea a 24 2 3 The Intermolecular Potential Functions o oo e 24 2 3 1 Short Ranged van der Waals Potentials 25 29 2 Metal Potentials i posi gala da aE e a Re ES 27 23 3 Tersoll Potential ocres eda Bak E a 28 23 4 Three Body Potentials oe ou mite seo o a a 31 23 0 Four Body Potentials co s saans e e 32 2 4 Long Ranged Electrostatic coulombic Potentials o oo 33
34. They are primarily included to permit simulation of amorphous materials e g silicate glasses However these have been extended to include the Dreiding 15 hydrogen bond The potential forms available are as follows 1 Harmonic harm k U Ojix 5 Bix 90 2 116 2 Truncated harmonic thrm k U 0 i 5 Ojik 90 expl ri ri 0 2 117 3 Screened Harmonic shrm k U Ojik 3 0 in 80 exp rij p1 rin p2 2 118 4 Screened Vessal 25 bvs1 k 2 U Oji 8 0 mM 00 n jak 1 x ji exp rij p1 fik P2 2 119 5 Truncated Vessal 26 bvs2 U Ojik k 0 x 0 in 00 Ojik 00 27 a ST Oir 90 7 00 expl ri r 09 2 120 6 Dreiding hydrogen bond 15 hbnd U Ojik Dro cos Ojix 5 Rno r n 6 Rao r n 2 121 31 CCLRC Section 2 4 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 valence angle 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 other potentials for example pair potentials may in fact be essential to maintain the st
35. allocate_config_arrays Action See Message 1001 Message 1026 error allocation failure in site_ module gt allocate_site_arrays Action See Message 1001 Message 1027 error allocation failure in tersoff_module gt alocate_tersoff_arrays Action See Message 1001 Message 1028 error deallocation failure in angles module gt deallocate_angles_arrays Action See Message 1002 Message 1029 error deallocation failure in bonds_module gt deallocate_bonds_arrays Action See Message 1002 Message 1030 error deallocation failure in core_shell_module gt deallocate_core_shell_arrays Action See Message 1002 Message 1031 error deallocation failure in tethers_module gt deallocate_tethers_arrays Action See Message 1002 Message 1032 error deallocation failure in constraints_module gt deallocate_constraints_arrays Action See Message 1002 190 CCLRC Appendix D Message 1033 error deallocation failure in dihedrals_module gt deallocate_dihedrals_arrays Action See Message 1002 Message 1034 error deallocation failure in inversions_module gt deallocate_inversions_arrays Action See Message 1002 Message 1035 error allocation failure in defects_module gt allocate _defects_arrays Action See Message 1001 Message 1036 error allocation failure in pmf module gt allocate_pmf
36. 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 Note that DL _POLY 3 does not use the basic Ewald method which is an option in DL _POLY 2 on account of it being too slow for large scale systems The SPME method is the standard Ewald method in DL_POLY 3 2 4 1 Direct Coulomb Sum Use of the direct Coulomb sum is sometimes necessary for accurate simulation of isolated non periodic systems It is not recommended for periodic systems The interaction potential for two charged ions is 1 Gidj Line 2149 2 125 rig ATE Tij with qe the charge on an atom labelled and rj the magnitude of the separation vector rj rjr The force on an atom j derived from this force is 1 qiqi ae 2 126 J Are r Tij with the force on atom 7 the negative of this The contribution to the atomic virial is 1 AM Wes 2 127 ATEO Tij 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 5 1 1 33 CCLRC Section 2 4 which is simply the negative of the potential term The contribution to be added to the atomic stress tensor is aa 2 128 where a 8 are x y z components The atomic stress tensor is symmetric In DL_POLY 3 these forc
37. are calculated by METAL_LRC 2 3 3 Tersoff Potential The Tersoff 13 potential has been developed to be used in multi component covalent systems It has 11 atomic and 2 bi atomic parameters The energy is modelled as a sum of pair like interactions 28 CCLRC Section 2 3 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 Fos Lato 2 95 where fr rij Aj exp aij rij falri Bij exp bij rij oo 1 Tij lt Rij folrig 3 3008 7 rij Rij riy Ro Rig lt Tij lt Sy 2 97 0 Tij gt Sij Vig Xig 1 Boa Ly NM Lig Y folra ea Oa kAi j 9 0i x 1 e d c d hi cos 0 x 2 98 with further mixed parameters defined as aij a aj 2 3 bij bi b 2 Apa AA gt Beate By 2 99 Rij BR Sig SiSj Here i j and k label the atoms in the system r is the length of ij bond and 6 is the bond angle between bonds ij and ik Singly subscripted parameters 11 such as a and 7 depend only on the type of atom The chemistry between different atom types is locked in the two sets bi atomic parameters xij and Wij Xi l Xij Xji Wii 1 Wij Wii 5 2 100 which define only one independent parameter each per pair of atom types The x parameter is used to strengthen or w
38. arrays Action See Message 1001 Message 1037 error deallocation failure in pmf module gt deallocate_pmf arrays Action See Message 1002 191 Appendix E DL POLY 3 README DL_POLY_3 06 The code is fully self contained free format FORTRAN90 MPI This version supports ALL features that are in DL_POLY_2 16 with the exceptions of 1 RIDGID BODIES 2 Rhombic Dodecahedral imcon 5 and Hexagonal prism imcon 7 boundary conventions 3 Classic Ewald and Hautman Klein Ewald Coulomb evaluations No previous DL_POLY_3 feature is deprecated All NEW features are documented in the DL_POLY_3 User Manual Warnings 1 DL_POLY_3 now produces index ordered REVCON and HISTORY files which are restartable by DL_POLY_2 Although such printed outputs look unscrambled the actual printing process is not Unscrambled printing is slightly more expensive than natural scrambled printing The cost time wise is little lt 1 but HD space wise is approximately 20 per particle entry This is due to the necessary addition of blanks at the end of data record included to align all textual lines to a constant length of 72 characters n as a new line character 2 REVIVE files produced by version 2 and 3 are not compatible Restarting runs across different sub versions may not be possible 3 Although DL_POLY_3 can be compiled in a serial mode users are strongly advised to consider DL_POLY_2 as a better al
39. arrays CONFIG and is dependent on KINDS_F90 only However it also develops an allocation method that is dependent on SETUP_MODULE e inter molecular interactions modules VDW_MODULE METAL_MODULE TERSOFF_MODULE THREE_BODY_MODULE FOUR_BODY_MODULE The intermolecular modules define all variables and potential arrays needed for the calculation of the particular interaction in the DL_POLY_3 scope They depend on KINDS_F90 Their allocation methods depend on SETUP_MODULE e intra molecular and site related interactions modules CORE_SHELL_MODULE CONSTRAINTS_MODULE PMF_MODULE TETHERS_MODULE BONDS_MODULE ANGLES_MODULE DIHEDRALS_MODULE INVERSIONS_MODULE These modules define all variables and potential arrays needed for the calculation of the particular interaction in the DL_POLY 3 scope They depend on KINDS_F90 Their allocation methods depend on SETUP_MODULE e external field module EXTERNAL_FIELD_MODULE This module defines all variables and potential arrays needed for the application of an exter nal field in the DL_POLY 3 scope It depends on KINDS_F90 and its allocation method on SETUP_MODULE e statistics module STATISTICS_MODULE This module defines all variables and arrays needed for the statistical accountancy of a simula tion in DL_POLY 3 It depends on KINDS_F90 and its allocation method on SETUP_MODULE 6 2 2 DL POLY 3 File Structure Generally the DL_POLY 3 file structure can be divided into four groups as follows e
40. atomic coordinates is the centre of the cell Parallelepiped periodic boundaries imcon 3 LG The parallelepiped MD cell 130 CCLRC Appendix A 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_3 CONFIG file by the vectors La Laz Laz Mb1 Mb2 Mb3 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 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 paral lelogram 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 However it is recommended that it is in the middle of the slab Domain decomposition division across Z axis is limited to 2 If the XY parallelogram is defined by vectors A and B the vectors required in the CONFIG file are A A2 0 B1 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 he
41. available on the same terms see the GUI manual 17 1 2 5 Algorithms 1 2 5 1 Parallel Algorithms DL_POLY 3 exclusively employs the Domain Decomposition parallelisation strategy 8 9 4 5 see Section 6 1 1 1 2 5 2 Molecular Dynamics Algorithms DL_POLY 3 offers a selection of MD integration algorithms couched in both Velocity Verlet VV and Leapfrog Verlet LFV manner 18 These generate NVE NVEgin NVT NPT and NoT ensembles with a selection of thermostats and barostats Parallel versions of the RATTLE 19 and SHAKE 7 algorithms are used for solving bond constraints in the VV and LFV cast integrations respectively The following MD algorithms are available 1 Constant E algorithm 2 Langevin constant T algorithm 20 Evans constant Ex n algorithm 21 gt Ww Berendsen constant T algorithm 22 Hoover constant T algorithm 23 Berendsen constant T P algorithm 22 Hoover constant T P algorithm 23 Martyna Tuckerman and Klein MTK constant T P algorithm 24 O 0 N Q A Berendsen constant T o algorithm 22 10 Hoover constant T algorithm 23 11 Martyna Tuckerman and Klein MTK constant T algorithm 24 1 3 Programming Style The programming style of DL POLY_3 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 CCLRC Section 1 3 1 3 1 Programming Lan
42. can be obtained using the MSD utility program which processes the HISTORY file see DL_POLY_2 User Manual If an NPT NoT simulation is performed the OUTPUT file also provides the mean pressure stress tensor and mean simulation cell vectors 5 2 3 9 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 RDF_COMPUTE First the number of time steps used for the collection of the histograms is stated Then each pre requested 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 atoms 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 5 2 3 10 Z density Profile If both calculation and printing of Z density profiles has been requested by selecting directives zden and print zden in the CONTROL file Z density profiles are printed out as the last part of the OUTPUT file This is written by the subroutine Z_DENSITY_COMPUTE First the number of 109 CCLRC Section 5 2 time steps used for the
43. check if test FC undefined then echo echo Fortran 90 compiler unspecified echo echo Please edit your Makefile entries echo exit 99 fi if test LD undefined then echo echo Fortran 90 Linker loaDer unspecified echo echo Please edit your Makefile entries echo exit 99 fi mkdir p BINROOT message echo DL_POLY_3 compilation in MPI mode echo echo Use mpi_module must be commented out in comms_module f90 and parallel_fft f9 echo Declare rules FC FCFLAGS 90 Declare dependencies OBJ_ALL 0BJ_MOD ewald_spme_forces o parallel_fft o 141 CCLRC Appendix C Makefile SRL1 Master makefile for DL_POLY_3 06 serial version 1 Author I T Todorov February 2006 Define default settings SHELL bin sh SUFFIXES SUFFIXES f90 o BINROOT execute EX DLPOLY Y EXE BINROOT EX TYPE master FC undefined LD undef ined Define object files OBJ_MOD kinds_f90 0 mpi_module o comms_module o setup_module o domains_module o parse_module o site_module o config_module o defects_module o vdw_module o metal_module o tersoff_module o three_body_module o four_body_module o core_shell_module o constraints_module o pmf_module o tethers_module o bonds_module o angles_module o dihedrals_module o inversions_module o external_field_module o statistics_module o O
44. collectively prepare the DL_POLY 3 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 gopoly gopoly is used to submit a DL_POLY 3 job to the HPC which operates a LOAD LEVELER job queuing system It invokes the following script shell usr bin tcsh job_type parallel job_name gopoly cpus 32 node_usage not_shared HO network MPI csss shared US wall_clock_limit 00 30 00 account_no my_account output job_name schedd_host jobid out HQ error job_name schedd_host jobid err notification never bulkxfer yes data_limit 850000000 stack_limit 10000000 queue ENVIRONMENT SETTINGS setenv MP_EAGER_LIMIT 65536 setenv MP_SHARED_MEMORY yes setenv MEMORY_AFFINITY MCM setenv MP_TASK_AFFINITY MCM setenv MP_SINGLE_THREAD yes poe DLPOLY Y Using LOADLEVELLER the job is submitted by the unix command llsubmit gopoly 133 CCLRC Appendix B where Ilsubmit is a local command for submission to the IBM SP4 cluster The number of re quired nodes and the job time are indicated in the above script gui gui is a macro that starts up the DL_POLY_3 Java GUI It invokes the following unix commands java jar java GUI jar In other words the macro invokes the Java Virtual Machine which executes the
45. component along the bond as required by the definition of rigidity In the second stage the deviation from zero of the scalar product d v v is used retrospectively to compute the constraint force needed to keep the bond rigid over the length of the timestep At It is relatively simple to show that the constraint force has the form Dia Hij dij tie v Da dz dij 3 15 The velocity corrections can therefore be written as Bio jedi ee a get At PA de 3 16 i mi mi d 1 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 Either part of the RATTLE algorithm is therefore iterative with the correction cycle being repeated for all bonds until each has converged to the correct length within a given tolerance for RATTLE_VV1 SHAKE and the relative bond velocities are perpendicular to their respective bonds within a given tolerance for RATTLE_VV2 RATTLE The tolerance may be of the order 1074 to 1078 depending on the precision desired The SHAKE procedure may be summarised as follows 1 All atoms in the system are moved using the LFV algorithm as
46. default value 0 75 A if the supplied value exceeds the limits the simulation execution will holt If a particle p is located in the vicinity of a site s defined by a sphere with its centre at this site and a radius Rgef then the particle is a first hand claimee of s and the site is not vacant Otherwise the site is presumed vacant and the particle is presumed a general interstitial If a site s is claimed and another particle p is located within the sphere around it then p becomes an interstitial associated with s After all particles and all sites are considered it is clear which sites are vacancies Finally for every claimed site distances between the site and its first hand claimee and interstitials are compared and the particle with the shortest one becomes the real claimee If a first hand claimee of s is not the real claimee it becomes an interstitial associated with s At this stage it is clear which particles are interstitials The sum of interstitials and vacancies gives the total number of defects in the simulated MD cell Frozen particles and particles detected to be shells of polarisable ions are not considered in the defect detection Note that the algorithm cannot be applied safely if ftaey is larger than half the shortest interatomic distance within the reference MD cell since a particle may i claim more than one site ii be an interstitial associated with more than one site or both i and ii On the other hand
47. 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_3 has failed to find the required record Action 155 CCLRC Appendix D Add units directive to FIELD file and resubmit Message 10 error too many molecule types specified This should never happen This indicates an erroneous FIELD file or corrupted DL_POLY_3 executable Unlike DL_POLY_2 DL_POLY_3 does not have a set limit on the number of kinds of molecules it can handle in any simulation this is not the same as the number of molecules Action Examine FIELD for erroneous directives correct and resubmit 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_3 encounters more than one molecules directive it will terminate execution Action Locate the extra molecule directive in the FIELD file and remove and resubmit Message 12 error unknown molecule directive in FIELD file Once DL_POLY 3 encounters the molecules directive in the FIELD file it assumes the following 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 e
48. file created by the previous job You will also require a new file REVOLD Section 5 1 5 which is an exact copy of the previous REVIVE file If you attempt to restart DL _POLY 3 without this additional file available the job will most probably fail Note that DL_POLY_3 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 regular 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 3 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 start 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 step
49. for many body and tersoff forces in DL_POLY_3 cannot work with less than 27 link cells Depending on the cell size and the chosen cut off DL_POLY_3 may decide that this minimum cannot be achieved and terminate This should never happen Action Decrease many body and tersoff potentials cutoffs or and number of nodes or and increase system size Message 307 error link cell algorithm violation DL_POLY_3 does not like what you are asking it to do Probable cause the cutoff is too large to use link cells in this case Action Rethink the simulation model reduce the cutoff or and number of nodes or and increase system size Message 308 error link cell algorithm in contention with SPME sum precision DL_POLY 3 does not like what you are asking it to do Probable cause you ask for SPME precision that is not achievable by the current settings of the link cell algorithm Action Rethink the simulation model reduce number of nodes or and SPME sum precission or and in crease cutoff 174 CCLRC Appendix D Message 340 error invalid integration option requested DL_POLY _3 has detected an incompatibility in the simulation instructions namely that the re quested integration algorithm is not compatible with the physical model 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 rest
50. hcos U ijin 5 cos iim cos d0 2 51 3 Planar potential plan U dijin A 1 cos dijrn 2 52 In these formulae jkn is the inversion angle defined by Ti a Ww Qijkn cos zn 2 53 TijWkn with and the unit vectors ka fik t Bin ae Cal Deg Cala 2 55 As usual Tij Tz Ty etc and the hat 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 gt n j etc Equivalently the angle d jxn may be written as y2 271 2 Tij Formally the force on an atom arising from the inversion potential is given by fe ZU din 2 57 y Ore ijkn with being one of i j k n and a one of x y z This may be expanded into o 1 o Fra U dijkn U ijkn X Or ijen fr Obijkn ijen ao y2 2 y2 1 2 Ea 6 aa es Opn 2 58 Or ti 22 CCLRC Section 2 2 Following through the extremely tedious differentiation gives the result 1 le fe aes Odijkn ijen 23 al 1 gt dali i fa de da a a g Oe rij Dan Lij Dn Ojo Tij TijWkn Tia Ur A n E ro 6ex bei Tea f rij a a Tik 7 rij kn Tik WEF 2 Tio Ur n m FI n ro 6ex dei narra fes rij kn kn Tij Lik pa Lik DEI Tig Ur ro 6en dei n ri ee
51. instructions in the Java archive file GUI jar which is stored in the java subdirectory of DL_POLY_3 Note Java 1 3 0 or a higher version is required to run the GUI select select is a macro enabling easy selection of one of the test cases It invokes the unix commands cp data TEST 1 CONTROL CONTROL cp data TEST 1 FIELD FIELD cp data TEST 1 CONFIG CONFIG cp data TEST 1 TABLE TABLE cp data TEST 1 REFERENCE REFERENCE select requires one argument an integer to be specified select n where n is test case number which ranges from 1 to 18 This macro sets up the required input files in the execute sub directory to run the n th test case The command to copy the TABLE file will be unnecessary in most cases 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 mkdir data TEST 1 mv OUTPUT data TEST 1 OUTPUT mv REVCON data TEST 1 REVCON mv STATIS data TEST 1 STATIS mv REVIVE data TEST 1 REVIVE mv HISTORY data TEST 1 HISTORY mv DEFECTS data TEST 1 DEFECTS mv RDFDAT data TEST 1 RDFDAT mv ZDNDAT data TEST 1 ZDNDAT chmod 400 data TEST 1 134 CCLRC Appendix B which first creates a new DL_POLY data TEST sub directory and then moves the standard DL_POLY 3 output data files into it store requires one argument store n where n is a unique string or number to l
52. is an approximation only The RATTLE algorithm was devised by Andersen 19 and it fits within the concept of the Velocity Verlet integration scheme It consists of two parts RATTLE_VV1 and RATTLE_VV2 applied respectively in stages one and two of Velocity Verlet algorithm RATTLE_VVI is similar to the SHAKE algorithm as described above and handles the bond length constraint However due to the difference in the velocity update between VV VV1 and LFV schemes the constraint force generated to conserve the bondlength in RATTLE_VVI has the form as in 3 13 but missing the factor of a half 2 12 G x kij dig dis d ij AR d di I 3 14 The constraint force in RATTLE VV2 imposes a new condition of rigidity on constraint bonded atom velocities The SHAKE RATTLE VV1 algorithm calculates the constraint force G G that conserves the bondlength d between atoms i and j following the initial movement to positions and j under the unconstrained forces F and F and velocities v and u 45 CCLRC Section 3 2 The RATTLE VV2 is also a two stage algorithm In the first stage the VV algorithm VV2 calculates the velocities of the atoms in the system assuming a complete absence of the rigid bond forces since forces have just been recalculated afresh after VV1 The relative velocity of atom i to j or vice versa constituting the rigid bond ij is not perpendicular to the bond i e does not have a non zero
53. mandatory a timestep or variable timestep specifying the simulation timestep b temp or zero specifying the system temperature not mutually exclusive c ewald sum or ewald precision or coul or shift or distan or reaction or no elec specifying the required coulombic forces option d cut specifying the short range forces cutoff 2 Some directives are optional If not specified DL_POLY 3 will take default values if necessary The defaults are specified above in the list of directives 3 The variable timestep or also timestep variable option requires the user to specify an initial guess for a reasonable timestep for the system in picoseconds The simulation is unlikely to retain this as the operational timestep however as the latter may change in response to the dynamics of the system The option is used in conjunction with the default values of maxdis 0 03 and mindis 0 10 which can also be optionally altered if used as directives note the rule that maxdis gt 2 5 mindis applies These distances serve as control values in the variable timestep algorithm which calculates the greatest distance a particle has travelled in any timestep during the simulation If the maximum distance is exceeded the timestep variable is halved and the step repeated If the greatest move is less than the minimum allowed the timestep variable is doubled and the step repeated In this way the integration timestep self adjusts in response to
54. nument integer record ii stpval 1 stpval 5 engcns real temp real engcfg real engsrc real engcpe real record iii stpval 6 stpval 10 engbnd real engang real engdih real engtet real enthal real record iv stpval 11 stpval 15 tmprot real vir real virsrc real vircpe real virbnd real record v stpval 16 stpval 20 virang real vircon real virtet real volume real tmpshl real record vi stpval 21 stpval 25 engshl real virshl real alpha real beta real gamma real record vii stpval 26 stpval 27 virpmf real press real the next ntpatm entries amsd 1 real amsd 2 real amsd ntpatm real current MD time step elapsed simulation time number of array elements to follow total extended system energy i e the conserved quantity system temperature configurational energy short range potential energy electrostatic energy chemical bond energy valence angle and 3 body potential energy dihedral inversion and 4 body potential energy tethering energy enthalpy total energy PV rotational temperature total virial short range virial electrostatic virial bond virial valence angle and 3 body virial constraint bond virial tethering virial volume core shell temperature core shell potential energy core shell virial MD cell angle a MD cell angle 8 MD cell angle y pmf constraint virial pressure mean squared displacement of first atom types mean squared displacement of second atom typ
55. of a singular matrix 172 CCLRC Appendix D Action Locate the incorrect matrix and fix it e g are cell vectors correct Message 141 error duplicate metal potential specified During reading of metal potentials pairs of atom types in FIELD DL _POLY 3 has found a dupli cate pair of atoms in the list Action Delete one of the duplicate entries and resubmit Message 145 error no two body like forces specified This error arises when there are no two body like interactions specified in FIELD and CONTROL Le none of the following interactions exists or if does it has been switched off any coulombic vdw metal tersoff In DL_POLY 3 expects that particles will be kept apparat stay separated and never go through each other due to one of the fore specified interactions Action Users must alone take measures to prevent such outcome Message 150 error unknown van der waals potential selected DL_POLY 3 checks when constructing the interpolation tables for the short ranged potentials 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 Action Read the DL_POLY_3 documentation and find the potential keyword for the potential desired Message 150 error unknown van der waals potential selected
56. of licence which we hope will ward off litigation from both sides without denying access to genuine scientific users Further information on the DL_POLY packages may be obtained from the project website http www cse clrc ac uk msi software DL_POLY 1 2 Functionality The following is a list of the features DL_POLY 3 supports 1 2 1 Molecular Systems DL_POLY_3 will simulate the following molecular species Simple atomic systems and mixtures e g Ne Ar Kr etc Simple unpolarisable point ions e g NaCl KCI etc Polarisable point ions and molecules e g MgO H20 etc e Polymers with rigid bonds e g CnHan 2 e Polymers with rigid bonds and point charges e g proteins macromolecules etc Silicate glasses and zeolites CCLRC Section 1 2 e Simple metals and metal alloys e g Al Ni Cu CuzAu etc e Hydro carbons and transition elements e g C Si Ge SiC SiGe ets Note that DL_POLY_3 does not handle molecules containing rigid bodies This is a major distinc tion from DL_POLY_2 1 2 2 Force Field The DL_POLY 3 force field includes the following features 1 All common forms of non bonded atom atom potentials 2 Atom atom site site coulombic potentials Sutton Chen density dependent potentials for metals 10 11 12 Tersoff density dependent potentials for hydro carbons 13 Three body valence angle and hydrogen bond potentials Four body inversion potentials Ion core shell
57. rcut Message 446 error undefined electrostatic key in dihedral_forces The subroutine DIHEDRAL_FORCES has been requested to process a form of electrostatic potential it does not recognise Action The error arises because the integer key keyfrc has an inappropriate value which should not happen in the standard version of DL_POLY _3 Check that the FIELD file correctly specifies the potential Make sure the version of DIHEDRAL_FORCES does contain the potential you are specifying Report the error to the authors if these checks are correct Action To prevent this error occurring again increase rvdw Message 448 error undefined dihedral potential A form of dihedral potential has been requested which DL_POLY_3 does not recognise Action Locate the offending potential in the FIELD file and remove Replace with one acceptable to DL_POLY 3 if this is reasonable Alternatively you may consider defining the required potential in the code yourself Amendments to subroutines READ_FIELD and DIHEDRAL_FORCES and its variants will be required Message 449 error undefined inversion potential A form of inversion potential has been encountered which DL_POLY_3 does not recognise Action 178 CCLRC Appendix D Locate the offending potential in the FIELD file and remove Replace with one acceptable to DL_POLY 3 if this is reasonable Alternatively you may consider defining the required potential in the code yourself Am
58. solvent since evaporation is likely to be a problem Note this boundary condition have to be used with caution DL_POLY 3 is not naturally suited to carry out efficient calculations on systems with great fluctuation of the local density in space as is the case for clusters in vacuum The parallelisation and domain decomposition is therefore limited to eight domains maximum of two in each direction in space This boundary condition should not used with the SPME Ewald summation method 129 CCLRC Appendix A Cubic periodic boundaries imcon 1 The cubic MD cell The cubic MD cell is perhaps the most commonly used in simulation and has the advantage of great simplicity In DL_POLY 3 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 Orthorhombic periodic boundaries imcon 2 LO The orthorhomic MD cell The orthorhombic cell is also a common periodic boundary which closely resembles the cubic cell in use In DL_POLY 3 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
59. systems support people for advice on how to manage this Message 1003 error allocation failure in comms_module gt gisum_vector Action See Message 1001 Message 1004 error deallocation failure in comms_module gt gisum_vector Action See Message 1002 Message 1005 error allocation failure in comms_module gt grsum_vector Action See Message 1001 187 CCLRC Appendix D Message 1006 error Action See Message 1002 Message 1007 error Action See Message 1001 Message 1008 error Action See Message 1002 Message 1009 error Action See Message 1001 Message 1010 error Action See Message 1002 Message 1011 error Action See Message 1001 Message 1012 error Action See Message 1002 Message 1013 error Action See Message 1001 Message 1014 error Action See Message 1001 deallocation failure in comms_module gt grsum_vector allocation failure in comms_module gt gimax_vector deallocation failure in comms_module gt gimax_vector allocation failure in comms_module gt grmax_vector deallocation failure in comms_module gt grmax_vector allocation failure in parse_module gt get_record deallocation failure in parse_module gt get_record allocation failure in angles_module gt allocate_angles_arrays allocation failure in bonds_
60. tedious and is best done computationally what is required is to determine the nearest image neighbours of all atoms and assign appropriate bond and valence angle potentials What must be avoided at all costs is specifying the angle potentials without specifying bond potentials In this case DL_POLY 3 will automatically cancel the non bonded forces between atoms linked via valence angles and the system will collapse The advantage of this method is that the calculation is likely to be faster than using three body forces This method is not recommended for amorphous systems 4 3 2 Macromolecules Simulations of proteins are best tackled using the package DLPROTEIN 45 which is an adap tation of DL_POLY specific to protein modelling However you may simulate proteins and other macromolecules with DL_POLY 3 if you wish This is described below If you select a protein structure from a SEQNET file e g from the Brookhaven database use the utility PROSEQ to generate the file CONFIG This will then function as input for DL_POLY_3 Some caution is required here however as the protein structure may not be fully determined and atoms may be missing from the CONFIG file If you have the edit out file produced by AMBER for your molecule use this as the CON NECT_DAT input file for the utility AMBFORCE AMBFORCE will produce the DL_POLY_3 FIELD and CONFIG files for your molecule If you do not have the edit out file things are a little more
61. to function as the root segment The root segment VV DL_POLY is placed in the source directory and contains the set up and close down calls for a molecular dynamics simula tion It is the routine that first opens the OUTPUT file Section 5 2 which provides the summary of the job The root program calls the molecular dynamics cycle routines LFV MD_LFV or LFV MD_vv implementing the VV and LFV depending on which integrator has been specified for the simulation These routines contain major routines required to perform the simulation con trol the normal molecular dynamics cycle and monitor the cpu and memory usage They also bring about a controlled termination of the program if the cpu usage approaches the allotted job time within a pre set closure time and or if the memory usage approaches the allocated limit for density dependent arrays Users are recommended to study the forementioned root drives as a model for other implementations of the package they may wish to construct The dependencies and calling hierarchies of all the DL_POLY_3 subroutines can be found in the Section 6 2 2 Should additional functionality be added to DL_POLY 3 by the user the SET_BOUNDS routine and its support subroutines may need modifying to allow specification of the dimensions of any new arrays Any molecular dynamics simulation performs five different kinds of operation initialisation forces calculation integration of the equations of motion calcul
62. 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 3 In addition to continue a simulation from a previous job the restart keyword must be included in the CONTROL file The format of the REVIVE file is identical to the REVOLD file described in Section 5 1 5 5 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 a72 configuration name record 2 ntprdf integer number of different RDF pairs tabulated in file mxgrdf integer number of grid points for each RDF pair There follow the data for each individual RDF i e ntprdf times The data supplied are as follows first record atname 1 a8 first atom name atname 2 a8 second atom name following records mzgrdf records radius real interatomic distance A g r real RDF at given radius 110 CCLRC Section 5 2 Note the RDFDAT file is optional and appears when the print rdf option is specified in the CONTROL file 5 2 7 The ZDNDAT File This is a formatted file containing the Z density data Its contents are as follows record 1 cfgname a72 configuration name record 2 ntpatm integer number of unique atom types profiled in file mxgrdf integer number of grid points in the Z density function There follow the
63. zden sampling every f Zero set job time to f seconds set maximum distance allowed in variable timestep control to f A default f 0 10 A set minimum distance allowed in variable timestep control to f A default f 0 03 A set shake rattle iterations limit to f default f 250 ignore electrostatics in simulation ignore short range non bonded interactions in simulation set required system pressure to f katms target pressure for constant pressure ensembles print system data every n timesteps print radial distribution functions print Z density profile enclose the MD cell in a pseudo thermal bath f is the thickness of the thermostat layers attached on the inside at the MD cell boundaries in units of A default f 2 A calculate and collect radial distribution functions every f timesteps default f 1 calculate electrostatic forces using reaction field electrostatics restart job from end point of previous run i e continue current simulation REVOLD required restart job from previous run without scaling system temperature i e begin a new simulation from older run without temperature reset REVOLD is not used restart job from previous run with scaling system temperature i e begin a new simulation from older run with temperature reset REVOLD is not used set tolerance for relaxed shell model to f default f 1 in D ps set required short ranged interactions cutoff to f A rescale atomic velocitie
64. 24 1 Direct Coulomb SUM costra e as a a a 33 2 4 2 Force Shifted Coulomb Sum LL 34 2 4 3 Coulomb Sum with Distance Dependent Dielectric 35 24 4 Reaction Field o s dae foa 68 8h ee he De e ee eS 35 2 4 5 Smoothed Particle Mesh Ewald 2 2 200004 36 2 6 Polarisation Shell Models 20 6 4 sisters bbe wb Ged eee eh Be a 39 vi CCLRC Contents 25 1 Dynamos Adiabatic Shells i e nk eR LG AA 2 5 2 Relaxed Massless Shells 2 2 2 2 2 eee eee ee ee ee 26 Extermal Fields Lia wee RA RR da AA AL EEG Re hee sd 3 Integration Algorithms ol troduction 06d A a e la De A Re Bae bos a2 Bond Constraints e s g i ea k ee ee de oa Hee De eee ee ee ns 3 3 Potential of Mean Force PMF Constraints and the Evaluation of Free Energy od Thermostats AIRE oa Langevin Thermostat i dx pe ep e Roe A ead k E ee i 3 4 2 Evans Thermostat Gaussian Constraints LL 3 4 3 Berendsen Thermostat 00 02 eee ee ee ee ee 3 4 4 Nos Hoover Thermostat LL ooo Bar tats s e s cae ae Oe RA a a A a oe et a E 3 5 1 Instantaneous pressure and stress 2 ee o 3 5 2 Berendsen Barostat ce 44 2p 6 qa EE eA awe A 2039 Whe Hoover Bardstat i pea sene hak eee be pda Se Re Ea 3 5 4 Martyna Tuckerman Klein Barostat 4 Construction and Execution 4 1 Constructing DL_POLY_3 an Overview LL 4 1 1 Constructing the Standard Version ooo 4 1 2 Constructing Non standard
65. 551 sin Dijk Ore Tij Tik where 15 2 b _ DE E Og ijk 2 ci hi cos 0 jk aun Oak 2 111 06 5k d hi cos 6 54 O rita l _ Tik rij are TijTik da re da ra cos 0jik fos TE 72 ae Sex w a 2 112 Tij Tik The contribution to be added to the atomic virial can be derived as o Erersoff 3 V OU i 2 11 w IV a 2 113 i j 1 le le W 2 gr Tela frla Vis gp foi Falrig Tij izj LOTU ij NL i 3 felra falrij Xij 1 Bi a Te a Rene 2 114 lo 5 Wik gl 0 jk dr dra e ra Tik k i j 30 CCLRC Section 2 3 The contribution to be added to the atomic stress tensor is given by o reff 2 115 where a and indicate the x y z components The stress tensor is symmetric Interpolation arrays vter and gter set up in TERSOFF_GENERATE 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 are calculated by the link cell method 33 DL_POLY_3 applies no long range corrections to the Tersoff potentials In DL_POLY_3 Tersoff forces are handled by the routine TERSOFF_FORCES 2 3 4 Three Body Potentials The three body potentials in DL_POLY_3 are mostly valence angle forms
66. BJ_ALL warning o error o numeric_container o kinetic_container o spme_container o scan_field o scan_config o scan_control o set_bound o read_control o vdw_generate o vdw_table_read o metal_generate o tersoff_generate o dihedrals_14_check o read_field o read_config o tag_legend o pass_shared_units o compress_legend o build_book_intra o build_excl_intra o scale_temperature o update_shared_units o core_shell_quench o constraints_tags o constraints_quench o pmf_coms o pmf_tags o pmf_vcoms o pmf_quench o 142 CCLRC Appendix C set_temperature o vdw_lrc o metal_lrc o system_init o export_atomic_data o set_halo_particles o link_cell_pairs o core_shell_on_top o deport_atomic_data o pmf_units_set o compress_book_intra o relocate_particles o metal_1d_collect o metal_ld_export o metal_ld_set_halo o metal_1d_compute o ewald_spme_forc s o metal_forces o vdw_forces o ewald_real_forces o coul_dddp_forces o coul_cp_forces o coul_fscp_forces o coul_rfp_forces o rdf_collect o ewald_excl_forces o ewald_frozen_forces o two_body_forces o tersoff_forces o three_body_forces o four_body_forces o core_shell_forces o tethers_forces o bonds_forces o angles_forces o dihedrals_forces o inversions_forces o core_shell_relax o langevin_forces o nvt_e_scl o nvt_b_scl o external_field_apply_vv o external_field_correct o pseudo_vv o zero_k_optimise_vv o constraints_shake_vv o pmf
67. D OBJ_ALL LDFLAGS Check that a machine has been specified check if test FC undefined then echo echo echo fi echo Fortran 90 compiler unspecified echo Please edit your Makefile entries exit 99 if test LD undefined then echo echo echo fi echo Fortran 90 Linker loaDer unspecified echo Please edit your Makefile entries exit 99 mkdir p BINROOT message echo echo echo echo Declare DL_POLY_3 compilation in SRL2 mode Use mpi_module must be uncommented in comms_module f90 and parallel_fft f90 rules FCFLAGS f90 152 CCLRC Appendix C Declare dependencies OBJ_ALL OBJ_MOD ewald_spme_forces o parallel_fft o 153 Appendix D DL POLY 3 Error Messages and User Action Introduction In this appendix we document the error messages encoded in DL_POLY_3 and the recommended user action The correct response is described as the standard user response in the appropriate 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 public version of DL_POLY 3 Note that the wording of some of the messages may have changed over time usually to provide more specific information The most recent wording appears below The Standa
68. DL_POLY_3 checks when constructing the interpolation tables for the metal potentials 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 Action Read the DL_POLY 3 documentation and find the potential keyword for the potential desired Message 170 error too many variables for statistic array This error means the statistics arrays appearing in subroutine STATISTICS_COLLECT are too small This should never happen Action Contact DL_POLY 3 authors 173 CCLRC Appendix D Message 200 error rdf z density buffer array too small in system revive This error indicates that a global summation buffer array in subroutine SYSTEM_REVIVE is too small i e mxbuff lt mxgrdf This should never happen Action Contact DL POLY_3 authors Message 300 error incorrect boundary condition for link cell algorithms The use of link cells in DL POLY 3 implies the use of appropriate boundary conditions This error results if the user specifies octahedral or dodecahedral boundary conditions which are only available in DL_POLY 2 Action Correct your boundary condition or consider using DL_POLY_2 Message 305 error too few link cells per dimension for many body and tersoff forces subroutines The link cells algorithms
69. DO _body i j k Ej Ej E rp i 1 j gt i k gt j N 3N 2N 1 N gt DE D VU body i Jk N Fi taa i l j gt i k gt j n gt k N extn i ti vi gt i l where Ushei Utetn Ubond Uangl Udihd Uinv Ubair Utersof f U3_body and Ua_body are empirical interaction functions representing ion core shell polarisation tethered particles chemical bonds valence angles dihedral and improper dihedral angles inversion angles two body Tersoff three body and four body forces respectively The first six are regarded by DL_POLY 3 as intra molecular interactions and the next four as inter molecular interactions The final term Uezin represents an external field potential The position vectors r r r and rq refer to the positions of the atoms specifically involved in a given interaction Almost universally it is the differences in position 12 CCLRC Section 2 2 that determine the interaction The numbers Nsnet Neeth Nbond Nangi Naina and Niny refer to the total numbers of these respective interactions present in the simulated system and the indices ishel tteths bonds tangl gt tdihd and iiny uniquely specify an individual interaction of each type It is important to note that there is no global specification of the intramolecular interactions in DL_POLY 3 all core shell units tethered particles chemical bonds valence angles dihedral angles and inversion angles must be individually cited The same applies for bond constraints a
70. EDRALS 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 ATOMS 3 OW 16 0000 0 8200 HW 1 0080 0 4100 HW 1 0080 0 4100 CONSTRAINTS 3 1 2 1 0000 1 3 1 0000 2 3 1 63299 FINISH VDW 45 C C lj 0 12000 3 2963 C CT lj 0 08485 3 2518 OW OS 1j 0 15100 3 0451 OS OS lj 0 15000 2 9400 CLOSE 5 1 3 1 The FIELD File Format The file is free formatted and not case sensitive Every line is treated as a command sentence record Commented records beginning with a and blank lines are not processed and may be added to aid legibility see example above Records must be limited in length to 100 characters Records are read in words as a word must not exceed 40 characters in length Words are recognised as such by separation by one or more space characters The contents of the file are variable and are defined by the use of directives Additional information is associated with the directives 5 1 3 2 Definitions of Variables in the FIELD File The file divides into three sections general information molecular descriptions and non bonded interaction descriptions appearing in that order in the file 5 1 3 2 1 General information The first viable record in the FIELD file is the title The second is the units directive Both of these are mandatory record 1 header a100 field file header 87 CCLRC Section 5 1 record 2 u
71. FV and NST_M1_LFV LFV flavour 60 Chapter 4 Construction and Execution Scope of Chapter This chapter describes how to compile a working version of DL POLY_3 and run it 61 CCLRC Section 4 1 4 1 Constructing DL POLY 3 an Overview 4 1 1 Constructing the Standard Version DL POLY 3 was designed as a package of useful subroutines rather than a single program which means that users are to be able to construct a working simulation program of their own design from the subroutines available which is capable of performing a specific simulation However we recognise that many perhaps most users will be content with creating a standard version that covers all of the possible applications and for this reason we have only provided the necessary tools to assemble such a version The method of creating the standard version is described in detail in this chapter however a brief step by step description follows 1 DL_POLY 3 is supplied as a UNIX compressed file tarred and gzipped This must uncom pressed and un tared to create the DL_POLY _3 directory Section 1 4 2 In the build subdirectory you will find the required DL_POLY 3 makefiles see Section 4 2 1 and Appendix C where the main Makefiles are listed This must be copied into the subdirec tory containing the relevant source code In most cases this will be the source subdirectory 3 The chosen makefile is executed with an appropriate keyword Section 4 2 1 which se
72. IELD or and DL_POLY_3 exe cutable Action Reconstruct FIELD recompile afresh DL_POLY_3 and resubmit If the problem persists get in touch with DL_POLY 3 authors Message 108 error unidentified atom in rdf look up list During reading of rdf look up pairs in FIELD DL_POLY 3 has found an unlisted previously atom type Action Correct FIELD by either defining the new atom type or changing it to an already defined one in the erroneous line Resubmit Message 109 error calculated pair rdf index too large This should never happen In checking the rdf pairs specified in the FIELD file DL_POLY_3 calculates a unique integer index that henceforth identify every rdf pair within the program If this index becomes too large termination of the program results Action Report to authors Message 108 error duplicate rdf look up pair specified During reading of rdf look up pairs in FIELD DL_POLY 3 has found a duplicate entry in the list Action 171 CCLRC Appendix D Delete the duplicate line and resubmit Message 111 error incomplete bond constraint found in constraints_tags This should never happen DL _POLY 3 has not been able to find an atom in a processor domain or its bordering neighbours Action Probable cause link cells too small Use larger potential cutoff Contact DL_POLY_3 authors Message 113 error intramolecular bookkeeping arrays exceeded in deport_atomic data One or more bookkeeping
73. LE algorithms see Section 3 2 are as follows 1 The bond constraints acting in the simulated system are allocated between the processors based on the location i e domain of the atoms involved 2 Each processor makes a list of the atoms bonded by constraints it must process Entries are zero if the atom is not bonded 3 Each processor passes a copy of the array to the neighbouring processors which manage the domains in contact with its own The receiving processor compares the incoming list with its own and keeps a record of the shared atoms and the processors which share them 4 In the first stage of the the algorithms the atoms are updated through the usual Verlet algorithm without regard to the bond constraints 5 In the second iterative stage of the algorithms each processor 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 6 When all necessary correction vectors have been received and added the positions of the constrained atoms are corrected 7 Steps 5 and 6 are repeated until the bond constraints are converged 8 Finally the change in the atom positions from the previous time step is used to calculate the atomic velocities 119 CCLRC Section 6 2 The compilation of the list of constrained atoms on each processor and the cir
74. OLY_3 also allows atomic sites to be tethered to a fixed point in space ro taken as their position at the beginning of the simulation t 0 This is also known as position restraining The 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 the 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 tethers reference positions are scaled with the cell vectors 23 CCLRC Section 2 3 The tethering potential functions available in DL_POLY 3 are as follows 1 Harmonic harm 1 U rij 5h rio 2 62 2 Restrained harmonic rhrm 1 2 xk rio rio lt re Ulss 2 63 ri l kr kre rio re Iriol gt re 3 Quartic potential quar k k k U rij rio gt rio rio 2 64 2 3 4 as in each case rio is the distance between the atom positions at moment t tl and t 0 The force on the atom 7 arising from a tether potential potential is obtained using the general formula 5 Ura Park 2 65 rio The contribution to be added to the atomic virial is given by The contribution to be added to the atomic stress tensor is given by o raf 2 67 where a and 8 indicate the x y z components The atomic stress tensor derive
75. ORCES CORE_SHELL_FORCES TETHERS_FORCES BONDS_FORCES ANGLES_FORCES DIHEDRALS_FORCES INVERSIONS_FORCES CORE_SHELL_RELAX LANGEVIN_FORCES NVT_E_SCL NVT_B_SCL XSCALE CORE_SHELL_KINETIC TRAJECTORY_WRITE DEFECTS_REFERENCE_READ DEFECTS_REFERENCE_EXPORT DEFECTS_REFERENCE_SET_HALO DEFECTS_LINK_CELLS DEFECTS_WRITE STATISTICS_COLLECT Z_DENSITY_COLLECT SYSTEM_REVIVE RDF_COMPUTE Z_DENSITY_COMPUTE STATISTICS_RESULT DL_POLY e VV specific files in the source VV directory EXTERNAL_FIELD_APPLY_VV EXTERNAL_FIELD_CORRECT PSEUDO_VV ZERO_K_OPTIMISE_VV CONSTRAINTS_SHAKE_VV PMF_SHAKE_VV CONSTRAINTS_RATTLE PMF_RATTLE NVT_H_SCL NPT_H_SCL NST_H_SCL NVE_1_VV NVT_L1_VV NVT_El_VV NVT_Bl_vv NVT_H1l_vv NPT_B1_VV NPT_H1_VV NPT_M1_vv NST_B1_VV NST_H1_VV NST_M1_Vv MD_VV e LFV specific files in the source LFV directory EXTERNAL_FIELD_APPLY_LFV PSEUDO_LFV ZERO_K_OPTIMISE_LFV 122 CCLRC Section 6 2 CONSTRAINTS_SHAKE_LFV PMF_SHAKE_LFV NVE_1_LFV NVT_L1_LFV NVT_El_LFV NVT_B1_LFV NVT_H1_LFV NPT_B1_LFV NPT_H1_LFV NPT_M1_LFV NST_B1_LFV NST H1_LFV NST_M1_LFV MD_LFV e SERIAL specific files in the source SERIAL directory MPIF H MPI_MODULE SET_BOUND EWALD_SPME_FORC S The files in each group are listed in hierarchial order as closely as possible The further down the list the file the more dependent it is on the files listed before it 6 2 3 Module Files The DL_POLY_3 module files contain all global variables scalars and arrays and param
76. POLY 3 routines NVT_H1_vv and NVT_H1_LFV respectively 3 5 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 Pext and or isotropic stress tensor 0 DL_POLY 3 has three such algorithms the Berendsen barostat 22 the Hoover type barostat 23 and the Martyna Tuckerman Klein MTK barsotat 24 Only the last two have a well defined conserved quantities 54 CCLRC Section 3 5 3 5 1 Instantaneous pressure and stress The instantaneous pressure in a system 2Ekin t Watomic t Weonstrain t At Woeme t At 3V t i P t 3 64 is a function of the system volume kinetic energy and virial W Note that when bond constraints or and PMF constraints are present in the system P will not converge to the exact value of P xt This is due to iterative nature of the constrained motion in which the virials Weonstrain and Wpwmr are calculated retrospectively to the forcefield virial Watomic The instantaneous stress tensor in a system a t Spin t stomicl Coal E At pur E At 2 3 65 is a sum of the forcefield o constrain o and PMF a Stresses atomic constrains PMF Note that when bond constraints or and PMF constraints are present in the system the quantity Tr o i will not converge to the exact value of Pext This is due to iterative nature of the constrained motio
77. POLY _3 has found unsupported boundary condition specified in CONFIG Action Correct your boundary condition or consider using DL_POLY 2 Message 515 error rattle algorithm constraints rattle failed to converge The RATTLE algorithm for bond constraints is iterative If the maximum number of permit ted iterations is exceeded the program terminates Possible causes include incorrect force field specification too high a temperature inconsistent constraints over constraint etc Action You may try to increase the limit of iteration cycles in the constraint subroutines by using the direc tive mxshak and or decrease the constraint precision by using the directive shake in CONTROL But the trouble may be 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 516 error the number nodes MUST be a power of 2 series number The SPME development in DL_POLY 3 supports only 2 x 2 x 2 type of domain decomposition Action You must ensure DL_POLY 3 execution on number of processors represented as 2 x 2 x 2 Message 517 error allowed configuration levels are 0 1 and 2 DL_POLY 3 has found erroneous configuration level in CONFIG Action Correct the error in CONFIG and rerun Message 518 error control distances for variable timestep not intact DL POLY 3 has found the control distances for the var
78. READ_CONFIG routine which reads the CONFIG file The SYSTEM_INIT routine is called next to initialise various simulation arrays and variables intact with the data so far and detects if the job is a restart of previous simulation run If so it reads the REVOLD Section 5 1 5 to supply some arrays and variables with the necessary values as saved from the previous job The domain halo is constructed strait after by the routine SET_HALO_PARTICLES After gathering all these data bookkeeping 63 CCLRC Section 4 2 and exclusion arrays are created for the intramolecular and site related interactions core shell constraint and tether units by BUILD_BOOK_INTRA and BUILD_EXCL_INTRA routines Following is the building of the link cell lists by LINK_CELL_PAIRS which takes into account the frozen state of atoms and the occurrence of atoms in the excluded atoms list when building the link cell lists Lastly the thermodynamic properties of the system are checked and set intact by the SET_TEMPERATURE routine which also generates the initial velocities if required to do so The calculation of the pair forces represents the main part of any simulation A Verlet neighbour list is used by DL_POLY 3 in calculating the atomic forces The routine that constructs this this from the link cell lists and calculates all pair forces is called TWO_BODY_FORCES Variety of subroutines are called within this one to calculate specific contributions by different interaction
79. THE DL POLY 3 USER MANUAL I T Todorov and W Smith CCLRC Daresbury Laboratory Daresbury Warrington WA4 4AD Cheshire UK Version 3 06 March 2006 CCLRC Preface ABOUT DL _POLY 3 DL_POLY 3 is a parallel molecular dynamics simulation package developed at Daresbury Labo ratory by W Smith and I T Todorov The package was developed under the auspices of the Engineering and Physical Sciences Research Council EPSRC for the EPSRC s Collaborative Com putational Project for the Computer Simulation of Condensed Phases CCP5 the Computational Chemistry Group at Daresbury Laboratory and the NERC e Science Project Computational Chem istry in the Environment directed by M Dove DL_POLY 3 is the property of Daresbury Laboratory and is issued free under licence to academic institutions pursuing scientific research of a non commercial nature A handling fee is charged for new DL_POLY 3 licence for NON UK users Commercial organisations may be permitted a licence to use the package after negotiation with the owners Daresbury Laboratory is the sole centre for distribution of the package Under no account is it to be redistributed to third parties without consent of the owners The purpose of the DL POLY_3 package is to provide software for academic research that is inex pensive accessible and free of commercial considerations Users have direct access to source code for modification and inspection In the spirit of the enterprise contri
80. TROL files for each shell model are provided separately 7 1 9 Test Case 17 and 18 Potential of mean force on K in water MgO These systems consist of 13 500 500 PMFs and 53 248 2 048 PMFs atoms respectively Simu lation at 300 K using NPT Berendsen ensemble with SPME and SHAKE RATTLE algorithm for the constrained motion 7 2 Benchmark Cases DL_POLY_3 benchmark test cases are distributed only with the authors permission 128 Appendix A DL POLY 3 Periodic Boundary Conditions Introduction DL_POLY 3 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 simulation cell type in the CONFIG file see 5 1 2 1 None e g isolated polymer in space imcon 0 2 Cubic periodic boundaries imcon 1 3 Orthorhombic periodic boundaries imcon 2 4 Parallelepiped periodic boundaries imcon 3 5 Slab X Y periodic Z non periodic imcon 6 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
81. ULE eee eee eee 124 CCLRC Contents 7 Examples 126 Fal Test Gabes ca ath com ais a Aa a 127 7 1 1 Test Case 1 and 2 Sodium Chloride 127 7 1 2 Test Case 3 and 4 DPMC in Water 127 7 1 3 Test Case 5 and 6 KNaSigO5 naaa a 127 7 1 4 Test Case 7 and 8 Gramicidin A molecules in Water 127 7 1 5 Test Case 9 and 10 SiC with Tersoff Potentials 127 7 1 6 Test Case 11 and 12 CugAu with Metal Potentials 128 7 1 7 Test Case 13 and 14 lipid bilayer in water 128 7 1 8 Test Case 15 and 16 relaxed and adiabatic shell model MgO 128 7 1 9 Test Case 17 and 18 Potential of mean force on K in water MgO 128 T2 Benchmark Cases ou aaa a ee p a A a A 128 Appendices 129 A DL_POLY 3 Periodic Boundary Conditions 129 B DL_POLY_3 Macros 132 C DL POLY 3 Makefiles 136 D DL_POLY 3 Error Messages and User Action 154 E DL POLY 3 README 192 Bibliography 195 Index 198 ix List of Tables 5 1 5 2 5 3 5 4 5 0 5 6 5 7 5 8 5 9 5 10 5 11 5 12 5 13 5 14 5 15 5 16 5 17 Internal Trajectory Defects File Key o o ee eee 79 Internal Restart Key o o ss a Se PR Sek ee ee a Se 80 Internal Ensemble Key e 80 Electrostaties Key ooo s e ek pa ia a A Bs 83 CONFIG File Key record 2 subi ew ade a 85 Periodic Boundary Key record io sia dna Dd Se A i 85 Tethering Potentia
82. Versions 2 20 42 Compiling and Running DL POLY 3 ia de Se Re ee eee 4 2 1 Compiling the DL_POLY_3 Source Code o o e 422 Running DL POLY 8 24 544 a SR e a a E 42 3 Restarting DL POLY 3 e cs isme didas ko dwana de ae 4 2 4 Notes on the DL_POLY 3 Simulation Efficiency and Performance 4 3 A Guide to Preparing Input Files 4 3 1 Tworganic Materiale i s 34 ios FEE E aa a Ea A RR 4 3 2 Macromolecules fece a a 4a a i A a a 43 3 Adding Solvent toa Structure 645 i e a 4 34 Analysing Results 2 4 445 8 3 2 lt lt A a es 4 3 5 Choosing Ewald Sum Variables 2 2 a 4 4 DL_POLY_3 Warning and Error Processing o o o e 4 4 1 The DL POLY_3 Internal Warning Facility 0 4 42 The DL POLY_3 Internal Error Facility 0 vii 42 43 45 47 48 48 50 51 52 54 595 55 56 60 CCLRC Contents 5 Data Files 73 Dl The INPUT Files odios a RR a a 74 SLI The CONTROL File ig Da o a hae Lera a bee eS 74 91 2 Whe CONFIG File 2 ig a seca ad a bh EE eli bo 83 dla The FIELD PS Liga i Goa ERA E a e Ratt 86 5 1 4 The REFERENCE File 100 Silio Whe REVOLD File 22 ga raca 0 E AE ET hk we a a 101 ola The TABLE Pile s tao ba a enb a a p a E a a 102 de THe OUTE UT Filep il e asriga LA E a no ea 103 92 1 The HISTORY Fil curs i aa A A ati doaa gia Pe ee a i 104 Oe The DEFECIS File ss posunie pacu y p hio ra EE E a 105 Dae The QUTPUT File
83. _shake_vv o constraints_rattle o pmf_rattle o nvt_h_scl o npt_h_scl o nst_h_scl o nvt_li_vv o nve_1_vv o nvt_el_vv o nvt_b1_vv o nvt_hi_vv o npt_bi_vv o npt_h1_vv o npt_ml_vv o nst_b1_vv o nst_hi_vv o nst_mi_vv o external_field_apply_lfv o pseudo_lfv o zero_k_optimise_lfv o constraints_shake_lfv o pmf_shake_lfv o nvt_11_1fv o nve_i_lfv o nvt_ei_lfv o nvt_b1_lfv o nvt_hi_lfv o A npt_bi_lfv o npt_hi_lfv o npt_mi_lfv o nst_bi_lfv o nst_hi_lfv o nst_mi_lfv o A xscale o core_shell_kinetic o trajectory_write o defects_reference_read o defects_reference_export o defects_reference_set_halo o defects_link_cells o defects_write o statistics_collect o z_density_collect o system_revive o rdf_compute o z_density_compute o statistics_result o dl_poly o Define MPI SERIAL files FILES_SERIAL mpi_module f90 mpif h set_bound f90 ewald_spme_forc s f90 143 CCLRC Appendix C Define Velocity Verlet files FILES_VV external_field_apply_vv f90 external_field_correct f90 pseudo_vv f90 zero_k_optimise_vv f90 constraints_shake_vv f90 pmf_shake_vv f90 constraints_rattle f90 pmf_rattle f90 nvt_h_sc1 f90 npt_h_scl f90 nst_h_scl f90 nve_1_vv f90 nvt_li_vv f90 nvt_el_vv f90 nvt_b1_vv f90 nvt_h1_vv f90 npt_b1_vv f90 npt_h1_vv f90 npt_m1_vv f90 nst_b1_vv f90 nst_h1_vv f90 nst_m1_vv f90 md_vv f90 Define LeapFrog Verlet files FILES_LFV external_field_apply_lfv f90
84. a k ka k3 exclude finish integrator string include equilibration data in overall statistics calculate electrostatic forces using direct Coulomb sum set required long ranged interactions cutoff to f A write DEFECTS file with controls i start timestep for dumping defects configurations default 0 j timestep interval between configurations default j 1 f site interstitial cutoff default f 0 75 A see Table 5 1 allow for local variation in system particle density of f useful for extremely non equilibrium simulations default f 0 calculate electrostatic forces using Coulomb sum with distance dependent dielectric set restart data dump interval to n steps select NVE ensemble default ensemble select NVT ensemble with Berendsen thermostat with relaxation constant f in ps select NVE ensemble with Evans thermostat Gaussian constraints select NVT ensemble with Hoover Nose thermostat with with relaxation constant f in ps select NVT ensemble with Langevin thermostat with relaxation speed friction constant f in ps 1 select Berendsen NPT ensemble with fi f2 as the thermostat and barostat relaxation times in ps select Hoover NPT ensemble with fi fa as the thermostat and barostat relaxation times in ps select Martyna Tuckerman Klein NPT ensemble with fi fo as the thermostat and barostat relaxation times in ps select Berendsen NoT ensemble with fi f2 as the thermostat and barostat relaxa
85. a program is being tested The test cases are documented in Chapter 7 1 4 4 The bench Sub directory This directory contains examples of input and output data for DL_POLY 3 that are suitable for benchmarking DL_POLY_3 on large scale computers These are described in Chapter 7 1 4 5 The execute Sub directory In the supplied version of DL _POLY 3 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 see Appendix B However when a DL_POLY 3 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 3 as intended The experienced user is not absolutely required to use DL_POLY 3 this way however 1 4 6 The build Sub directory This sub directory contains the standard makefiles for the creation i e compilation and linking of the DL_POLY 3 simulation program The makefiles supplied select the appropriate subroutines from the source sub directory and deposit the executable program in the execute directory 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 public Sub directory This sub directory contains
86. abel the output data in the data TESTn sub directory Note that store sets the file access to read only This is to prevent the store macro overwriting existing data without your knowledge 135 Appendix C DL POLY 3 Makefiles Makefile MPI Master makefile for DL_POLY_3 06 parallel version Author I T Todorov February 2006 Define default settings SHELL bin sh SUFFIXES SUFFIXES f90 o BINROOT execute EX DLPOLY Y EXE BINROOT EX TYPE master FC undefined LD undef ined Define object files OBJ_MOD kinds_f90 0 comms_module o setup_module o domains_module o parse_module o site_module o config_module o defects_module o vdw_module o metal_module o tersoff_module o three_body_module o four_body_module o core_shell_module o constraints_module o pmf_module o tethers_module o bonds_module o angles_module o dihedrals_module o inversions_module o 136 CCLRC Appendix C external_field_module o statistics_module o OBJ_ALL warning o error o numeric_container o kinetic_container o spme_container o scan_field o scan_config o scan_control o set_bounds o read_control o vdw_generate o vdw_table_read o metal_generate o tersoff_generate o dihedrals_14_check o read_field o read_config o tag_legend o pass_shared_units o compress_legend o build_book_intra o build_excl_intra o scale_temperature o update_shared_units o core_shell_quench o constrain
87. age 454 error undefined external field A form of external field potential has been requested which DL_POLY_3 does not recognise Action Locate the offending potential in the FIELD file and remove Replace with one acceptable to DL POLY 3 if this is reasonable Alternatively you may consider defining the required potential in the code yourself Amendments to subroutines READ_FIELD and EXTERNAL_FIELD_APPLY will be required 179 CCLRC Appendix D Message 452 error undefined metal potential A form of metal potential has been requested which DL_POLY 3 does not recognise Action Locate the offending potential in the FIELD file and remove Replace with one acceptable to DL POLY 3 if this is reasonable Message 462 error thermostat friction constant must be gt 0 A zero or negative value for the thermostat friction 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 464 error thermostat relaxation time constant must be gt 0 A zero or negative value for the thermostat relaxation 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 relaxation time constant must be gt 0 A zero or negative value for the barostat relaxation time constant has been encou
88. age the half step velocities are advanced to to a full step using the new force 1 At f t At u t At v t At gt a 3 4 DL_POLY 3 also offers integration algorithms based on the leapfrog Verlet LFV scheme 18 Although LFV scheme is somewhat simpler and numerically faster than the VV scheme it is not time reversible and does not offer the numerical stability the VV scheme does Furthermore properties estimators are approximate The LFV algorithm is one staged It requires values of position r and force f at time t and velocity v at half a timestep behind t 1 2 At Firstly the forces are recalculated afresh at time t from time t At since the positions have changed from the last step 1 FF f f t At 3 5 where At is the timestep 2 LFV The velocities are advanced by a timestep to t 1 2 At by integration of the new force 1 1 f t t A At At 3 6 u t At ult GAM At 3 6 43 CCLRC Section 3 2 where m is the mass of a site and then the positions are advanced to a full step t At using the new half step velocities r t At r t At u t 340 3 7 Molecular dynamics simulations normally require properties that depend on position and velocity at the same time such as the sum of potential and kinetic energy The velocity at time t is obtained from the average of the velocities half a timestep either side of timestep t u t 5 et a olt 3A8 3 8 The in
89. al field 12 41 four body 3 12 24 32 95 100 108 115 116 157 168 169 177 179 improper dihedral 3 12 20 21 116 intermolecular 64 intramolecular 24 32 64 inversion 3 12 21 23 32 95 100 116 117 166 178 metal 3 13 24 27 95 116 118 non bonded 3 13 69 70 78 87 92 93 95 116 118 156 nonbonded 156 Sutton Chen see potential metal see poten tial metal see potential metal tabulated 102 158 Tersoff 3 12 24 28 31 95 98 166 tersoff 116 118 tether 3 12 23 24 108 116 117 164 179 three body 3 12 13 15 24 31 32 69 95 99 108 115 116 157 165 168 179 valence angle 3 12 13 15 16 22 31 32 69 91 93 108 116 118 162 van der Waals 13 15 17 64 66 83 94 95 176 reaction field 35 36 78 83 rigid body 45 rigid bond see constraints bond shell model 33 stress tensor 14 17 20 23 24 26 28 31 32 34 36 40 47 54 sub directory 132 135 bench 7 build 7 data 7 execute 7 java 7 public 7 source 7 utility 7 thermostat 4 41 77 180 Nos Hoover 56 58 60 units DL_POLY 6 109 energy 88 pressure 6 7 56 78 109 temperature 78 Verlet neighbour list 64 117 119 171 WWW 2 5 9 10 199
90. also writes the STATIS file Section 5 2 8 Routine TRAJECTORY_WRITE writes the HISTORY Section 5 2 1 file for later postmortem anal ysis Routine DEFECTS_WRITE writes the DEFECTS Section 5 2 2 file for later postmortem analysis Job termination is handled by the routine STATISTICS_RESULT which writes the final summaries in the OUTPUT file and dumps the restart files REVIVE and REVCON Sections 5 2 5 and 5 2 4 respectively 4 2 Compiling and Running DL POLY 3 4 2 1 Compiling the DL _POLY 3 Source Code When you have obtained DL_POLY_3 from Daresbury Laboratory and unpacked it your next task will be to compile it To aid compilation three general makefiles have been provided in the sub directory build These are Makefile MPI for compiling a parallel version of DL_POLY_3 and Makefile SRL1 and Makefile SRL2 for compiling a serial versions see Appendix C After choosing what the default compilation is to be the appropriate makefile is to be copied as 64 CCLRC Section 4 2 Makefile in the sub directory source The general DL _POLY_3 makefile will build an executable with the full range of functionality sufficient for the test cases and for most users requirements In most cases the user will have to modify few entries in the specification part of their makefile to match the location of certain software on their system architecture Note that only FORTRAN 90 compiler is required for successful b
91. ammon J A and Harvey S C 1987 Dynamics of Proteins and Nucleic Acids Cam bridge University Press 47 Izaguirre J A Langevin stabilisation of multiscale mollified dynamics In Brandt A Binder K B J editor Multiscale Computational Methods in Chemistry and Physics vol ume 117 of NATO Science Series Series III Computer and System Sciences pages 34 47 IOS Press Amsterdam 2001 48 49 43 Melchionna S Ciccotti G and Holian B L 1993 Molec Phys 78 533 56 44 G M M D J T and M L K 1994 J Chem Phys 101 4177 56 60 196 CCLRC Bibliography 45 46 47 48 49 Melchionna S and Cozzini S 1998 University of Rome 69 Hockney R W and Eastwood J W 1981 Computer Simulation Using Particles McGraw Hill International 115 117 119 Smith W 1992 Comput Phys Commun 67 392 115 Smith W and Fincham D 1993 Molecular Simulation 10 67 115 Bush I T 2000 Daresbury Laboratory 118 197 Index algorithm 4 43 75 RATTLE 4 45 46 115 119 184 SHAKE 4 45 47 115 119 170 Verlet 4 27 43 47 117 119 Verlet neighbour list 117 AMBER 3 12 69 70 angular restraints 18 barostat 4 77 180 Berendsen 55 Hoover 56 60 boundary conditions 3 33 129 cubic 85 CCP5 2 9 constraints bond 2 4 13 45 48 89 108 117 119 160 165 169 170 184 Gaussian 36 37 48 pmf 13 47 48 90 108 117 tether 169 CVS 5
92. 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 avaliable as angular restraints although they have different key words 1 Harmonic hrm 2 Quartic qur 3 Truncated harmonic thm 4 Screened harmonic shm 5 Screened Vessal 25 bv1 6 Truncated Vessal 26 bv2 17 CCLRC Section 2 2 7 Harmonic cosine hcs 8 Cosine cos 9 MM3 stretch bend 27 msb In DL_POLY 3 angular restraints are handled by the routine ANGLES_FORCES 2 2 5 Dihedral Angle Potentials Vix 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 DL_POLY 3 are as follows 1 Cosine potential cos U Pijn A 1 cos m ijen 9 2 31 2 Harmonic harm U Pijkn n dijkn do 2 32 3 Harmonic cosine hcos U Pijkn a cos ijkn cos do 2 33 4 Triple cosine cos3 U d 5 41 1 cos Az 1 cos 26 As 1 cos 36 2 34 5 Ryckaert Belle
93. arrays for site related interactions have been exceeded Action You will need to print extra diagnostic data from the DEPORT_ATOMIC_DATA subroutine to find where it has gone wrong Message 114 error legend array exceeded in deport_atomic_data The array legend has been exceeded Action Try increasing parameter mxfix in SET_BOUNDS recompile and resubmit Contact DL _POLY 3 authors if the problem persists Message 115 error transfer buffer exceeded in update_shared_units The transfer buffer has been exceeded Action Consider increasing parameter mxbuff in SET_BOUNDS recompile and resubmit Contact DL_POLY_3 authors if the problem persists Message 116 error incorrect atom transfer in update_shared_units An atom has become misplaced during transfer between nodes Action This happens when the simulation is very numerically unstable Consider carefully the physical grounds of your simulation i e are you using the adiabatic shell model for accounting polarisation with too big a timestep or too large control distances for the variable timestep is the ensemble type NPT or NoT and the system target temperature too close to the melting temperature Message 120 error invalid determinant in matrix inversion DL_POLY_3 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
94. as been in existence since 1980 3 http www ccp5 ac uk Further develop ments of DL POLY_3 were fostered by the NERC eScience Project on Computational Chemistry in the Environment headed by Martin Dove at Cambridge The two forms of DL_POLY differ primarily in their method of exploiting parallelism DL_POLY_2 uses a Replicated Data RD strategy 4 5 6 7 which works well for computing systems of order 100 processors and molecular simulations up to order 30 000 atoms DL_POLY 3 is based on the Domain Decomposition DD strategy 2 8 9 4 5 and is best suited to large computer systems to any number of processors presentable as 2 and molecular simulations from 103 to 10 atoms The two packages are reasonably compatible so that it is possible to scale up from a DL_POLY_2 to a DL POLY 3 simulation with very little effort It should be apparent from these comments that DL_POLY 3 is not intended as a replacement for DL_POLY 2 Users are reminded that we are interested in hearing what other features could be usefully incor porated We obviously have ideas of our own and CCP5 strongly influences developments but other input would be welcome nevertheless We also request that our users respect the integrity of DL_POLY_3 source and not pass it on to third parties We require that all users of the package register with us not least because we need to keep everyone abreast of new developments and discovered bugs We have developed various forms
95. assorted routines donated by DL _POLY users Potential users should note that these routines are unsupported and come without any guarantee or liability what CCLRC Section 1 5 soever They should be regarded as potentially useful resources to be hacked into shape as needed by the user This directory is available from the CCP5 Program Library by direct FTP see below 1 4 8 The java Sub directory The DL POLY 3 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 3 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 17 1 5 Obtaining the Source Code To obtain a copy of DL_POLY 3 it is first necessary to obtain a licence from Daresbury Laboratory A copy of the licence form may be obtained in two ways either by selecting the licence button on the World Wide Web site http www cse clrc ac uk msi software DL_POLY and downloading and printing the file or by using FTP to copy the postscript file from the CCP5
96. at the beginning of execution The DL_POLY_3 interpolation scheme is based on a 3 point linear interpolation in r The number of grid points mxgrid required for interpolation in r to give good energy conservation in a simulation is mxgrid Max 1000 Int rcut 0 01 0 5 4 where rey is the main cutoff beyond which the contributions from the short range like interactions are negligible 4 2 2 Running DL _POLY 3 To run the DL POLY 3 executable DLPOLY Y 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 5 1 1 which indicates to DL_POLY_3 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 5 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 velocities and forces also The third file required is the FIELD file Section 5 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 require a fourth file TABLE Section 5 1 6 which contains the potential and force arrays for functional forms not available within DL_POLY _3
97. ation of system properties and job ter mination It is worth considering these operations in turn and to indicate which DL_POLY_3 routines are available to perform them We do not give a detailed description but provide only a guide Readers are recommended to examine the different routines described in the DL_POLY_3 User Manual for further details particularly regarding further dependencies i e additional routines that may be called Initialisation requires firstly that the program determine what platform resources are made available to the the specific simulation job This is done by the DL_POLY_3 routine MAP_DOMAINS in DOMAINS_MODULE that attempts to allocate and map the resources nodes in parallel in compliance with the DD strategy Next the routine SET_BOUNDS sets the limits for simulation array sizes and variables to convenient values based on rough scan through the CONFIG CONTROL FIELD and optionally TABLE Section 5 1 files After allocation of all necessary simulation arrays and variables compulsory initialisation to zero value the job control information is required this is obtained by the routine READ_CONTROL which reads the CONTROL file The description of the system to be simulated the types of atoms and molecules present and the intermolecular forces are obtained by the READ_FIELD routine which reads the FIELD file Lastly the atomic positions and optionally velocities and forces must be provided These are obtained by the
98. bles that control the accuracy a the Ewald convergence parameter rey the real space force cutoff and the kmax1 2 3 integers that specify the dimensions of the SPME charge and FFT array The kmax1 2 3 integers 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 others 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 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 reut so it is important that a be chosen so that contributions to the real space sum are negligible for terms with r gt rey The relative error e in the real space sum truncated at freut is given approximately by e erfe a reut Teut exp a Teut Teut 4 2 The recommended value for a is 3 2 rcut 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 e 4 x 107 in the real space sum When using the directive ewald precision DL_POLY_3 makes use of a more sophisticated approximation erfc x 0 56 exp a x 4 3 to solve recursive
99. butions in the form of working code are welcome provided the code is compatible with DL_POLY 3 in regard to its interfaces and programming style and it is adequately documented CCLRC Preface DISCLAIMER Neither the CCLRC EPSRC NERC CCP5 nor any of the authors of the DL_POLY 3 package or its derivatives guarantee that the package is free from error Neither do they accept responsibility for any loss or damage that results from its use il CCLRC Preface ACKNOWLEDGEMENTS DL_POLY_3 was developed at the Central Laboratory of the Research Councils Daresbury Labo ratory with support from the Engineering and Physical Sciences Research Council and the Natural Environment Research Council The package is the property of the Council for the Central Labo ratory of the Research Councils of the United Kingdom Advice assistance and encouragement in the development of DL_POLY_3 has been given by many people We gratefully acknowledge the following T R Forester lan Bush M F Guest M Leslie R J Allan D Tildesley M Pinches D Ra paport the UK s Materials Consortium under C R A Catlow and the NERC e Science project Computational Chemistry in the Environment under M Dove iii CCLRC Preface Manual Notation In the DL_POLY manuals specific fonts are used to convey specific meanings 1 directories indicates unix file directories 2 ROUTINES indicates subroutines functions and programs 3 ma
100. by 0 ibi 2 24 with atomic label being one of i j k and a indicating the x y z component The derivative is 2 2 Pi T S ri S ri at grg O sita aj Ti ISA 5p AO ae A Ojik S rik Oe be prg C ra 0 A Ojik S rij 0 de Sa 2 25 Tik Orik 16 CCLRC Section 2 2 with 0 1 if a b and 64 0 if a b In the absence of screening terms S r this formula reduces to tg POE he 2 26 Ore jik igs lik ore jik Pg The derivative of the angular function is 9 1 7 O Vig Tik a Bre Ari bjir Alin a l rijTik gt 2 27 with O rag Ti ri ri uote 60 a E Sen 602 Ore rijrir Tijfik Tijfik ri Tik cos 0 ik de dei z Sex de a 2 28 Tij ik 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 Ep tg Ti 2 29 It is worth noting that in the absence of screening terms S r the virial is zero 28 The contribution to be added to the atomic stress tensor is given by 0 raf 12 10 2 30 and the stress tensor is symmetric In DL_POLY_3 valence forces are handled by the routine ANGLES_FORCES 2 2 4 Angular Restraints In DL POLY 3 angle restraints in which the angle subtended by a triplet of atoms is maintained around some preset value is handled as a special case of
101. cate the x y z components The atomic stress tensor derived from the pair forces is symmetric 3 3 Potential of Mean Force PMF Constraints and the Evalua tion 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 process 41 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 3 reports the PMF constraint virial Wp y p for each simulation Users can convert this to the PMF constraint force from W GPMF a 3 3 19 47 CCLRC Section 3 4 where is dpyp the constraint distance between the two groups used to define the reaction coordi nate The routines PMF_SHAKE and PMF_RATTLE are called to apply corrections to the atomic positions and respectively the atomic velocities of all particles constituting pmf units In presence of both bond constraints and pmf co
102. 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 5 2 4 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 3 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 controlled by the directive dump in file CONTROL see above and listed as parameter ndump in the SETUP_MODULE file see Section 6 2 2 The default value is ndump 1000 REVCON is identical in format to the CONFIG input file see Section 5 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 3 5 2 5 The REVIVE File This file is unformatted and written by the subroutine SYSTEM_REVIVE It contains the accumu lated statistical data It is
103. complementary error function er fc found in the real space sum should be noted The same considerations and modifications EWALD_FROZEN_FORCES are taken into account for frozen atoms which mutual coulombic interaction must be excluded The total electrostatic energy is given by the following formula 1 exp exp k 4a 9 gs djQn U a 5 73 Ea exp r FA i er fc arnj 00 ky veko EO eg O 1 M er f afrim Tm um btm n 2 146 NED molecules lt m Tim form 1 1 f amp Y ETJ ATem qedm de dj Tr o De where N is the number of ions in the system and N the same number discounting any excluded intramolecular and frozen interactions M represents the number of excluded atoms in a given molecule F represents the number of frozen atoms in the MD cell V is the simulation cell volume and k is a reciprocal lattice vector defined by k fu mu nuw 2 147 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 2 148 and b u 2r Ixe a bxc cxa Jp 2 149 v aa do on 2 2 a bxc With these definitions the Ewald formula above is applicable to general periodic systems The last term in the Ewald formula above is the Fuchs correction 35 for electrically non neutral MD cells which prevents the build up of a charged background and the introduction of extra p
104. cos cos o cos3 Triple cosine A Ag A3 U 3 Ai 1 cos d Az 1 cos 2 A3 1 cos 39 ryck Ryckaert Bellemans 29 A U A a b cos c cos d cos e cos f cos rbf Fluorinated Ryckaert A U A a b cos c cos Bellemans 30 d cos e cos f cos g exp h m opls OPLS torsion Ao Ay Ag U Ap 5 A 1 cos do A3 do Ag 1 cos 2 do Az 1 cos 4 0 t is the i j k l dihedral angle 11 inversions n where nis the number of inversion interactions present in the molecule Each of the following n records contains inversion key ad potential key see Table 5 11 94 CCLRC Section 5 1 index 1 i index 2 j index 3 k index 4 1 variable 1 variable 2 integer integer integer integer real real first atomic site index central site second atomic site index third atomic site index fourth atomic site index potential parameter see Table 5 11 potential parameter see Table 5 11 The meaning of the variables 1 2 is given in Table 5 11 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 5 11 Inversion Angle Potentials key potential type Variables 1 2 functional formi
105. cros indicates a macro file of unix commands 4 directive indicates directives or keywords 5 variables indicates named variables and parameters 6 FILE indicates filenames Contents Title Page About DLPOLY3 Disclaimer Acknowledgements Manual Notation Contents List of Tables List of Figures 1 Introduction 1 1 The DL_POLY Package 1 2 Functionality 10 aoe doe li ae k Be I ee ee Ga ke we ee ee G 1 2 1 Molecular SYStems o lt s s s ss a ecmain ee ee DR ee Es Laz Porce Field jora menk i a i e e RE en Be ak E ee A eS 1 23 Boundary Conditions ss s es ic e som a E e OS 1 24 Java Graphical User interface a coros mice a Rei Lo ALSO AAN lp Programming Style os eot aie Geach a e e i 1 241 Programming Language ccce s seca A Ee RR ES Lis Modulsrisstian and intent o cues e E Se ee ee i 1 30 Memory Management s s ss 608 e Te ER e ee Ee Lod Target Computers ego oe ech ATR e RE eek Bg ae ee ek A 1 3 5 Version Control System CVS os sek eve bebe eee ee ee aG tek 136 Internal Documentation ecos eck i ane Po ee ne Be a oe ee es 1 3 7 FORTRAN 90 Parameters and Arithmetic Precision Li UMOS ia ee le Set ete i MR ete ee eee RA et BS 1 3 9 Error Messages xi CCLRC Contents 1 4 The DL POLY 3 Directory Structure o 7 1 4 1 The source Sub directory so o sos eos akon mUa p e a aa a E a Oa E 8 14 2 The wuy SUITE a ca aae ae A k ey AR a 8 1 43
106. ction Supply a properly formatted REFERENCE configuartion Message 553 error REFERENCE is inconsistent An atom has been lost in transfer between nodes This should never happen Action Big trouble Report problem to authors immediately 185 CCLRC Appendix D Message 554 error REFERENCE s format different from CONFIG s REFERENCE complies to the same rulls as CONFIG with the exception that image convention MUST be imcon 1 2 3 or 6 Action Supply a properly formatted REFERENCE configuartion Message 555 error particle assigned to non existent domain in defects_read_reference Action See Message 513 Message 556 error too many atoms in REFERENCE file Action See Message 45 Message 557 error undefined direction passed to defects_reference_export Action See Message 42 Message 558 error outgoing transfer buffer exceeded in defects_reference_export Action See Message 54 Message 559 error coordinate array exceeded in defects_reference_export Action See Message 56 Message 560 error rdef found to be gt half the shortest interatomic distance in REFERENCE The defect detection option relies on a cutoff rdef to define the vicinity around a site defined in REFERENCES in whitch a particle can claim to occupy the site Evidently rdef MUST be lt half the shortest interatomic distance in REFERENCE Action Decrease the value of rdef at directive defect in CONTROL
107. ctuations pmass the barostat mass Tp a specified time constant for pressure fluctuations P the instantaneous pressure and V the system volume The conserved quantity is to within a constant the Gibbs free energy of the system Mass t gt mass t 2 i Her Hyve PS XO 4 Powe ET PAVE S1 ke Tes f x 6 ds 8 71 where f is the system s degrees of freedom equation 3 11 The VV flavour of the algorithm is implemented in the DL_POLY_3 routine NPT_H1_vv in the following manner 56 CCLRC Section 3 5 1 Thermostat Note 2Ex n t changes inside At 2Exkin t Pmass n t 20 kB Text 8 mass 1 At e sie x t 346 E 3 72 At 2Ekin t Pmass n ty 20 kB Text 8 mass x t 340 x t 1 1 x t At x t At 2 Barostat Note Ekin t and P t have changed and change inside MO 10 exp xet zan E nlt TA nfl ALI Fa n 30 oo 140 exp x t 4 EAn ina ep nt 720 3 3 73 n AD 3 n 20 exp x t 144 n t 4 324 nlt At 4 SPO Pow V t 3 Thermostat Note Exin t has changed and changes inside 1 At 2Exin t t HAt 20 kp Tox xlt SA x t4 zat kin t Pmass N 3 o B text 8 dmass 3 At v t v t exp x t At 1 3 74 1 3 At 2Ekin t Pmass n t HAt 20 kg Tox EE ae E T kin t Pmass N t 34t B Text 2 8 8 mass 4 VVI 1 At f t H t At exp nt sat At H
108. culated using Fast Fourier Transform FFT scheme of the SMPE method 36 Section 2 4 5 The parallelisation of this scheme is entirely handled within the DL POLY 3 by the 3D FFT routine PARALLEL _FFT which is known as the Daresbury Advanced Fourier Transform due to I J Bush 49 This FFT distributes the SPME charge array over the processors in a manner that is completely commensurate with the distribution of the configuration data under the DD strategy As a consequence the FFT handles all the necessary communication implicit in a distributed SPME application The DL_POLY _3 subroutine EWALD_SPME_FORCES perfoms the bulk of the FFT operations and charge array construction while SPME_FORCES calcu lates the forces Other routines required to calculate the Ewald sum include EWALD_EXCL_FORCES and EWALD_FROZEN_FORCES 6 1 5 Metal Potentials The simulation of metals 2 3 2 by DL _POLY 3 makes use of density dependent potentials of the Sutton Chen type 10 11 12 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 as outlined above DL_POLY_3 implements these potentials in various subroutines with names beginning with METAL 118 CCLRC Section 6 1 6 1 6 Tersoff Three Body and Four Body Potentials DL_POLY 3 can calculate Tersoff three body and four body interactions Although some of the
109. culation of the list items 1 3 above is done at the start of the simulation but thereafter needs only to be done every time a constraint bond atom is relocated from one processor to another In this respect DD SHAKE and DD RATTLE resemble every other intramolecular term Since the allocation of constraints is based purely on geometric considerations it is not practical to arrange for a strict load balancing of the DD SHAKE algorithm For many systems however this deficiency has little practical impact on performance 6 2 DL POLY 3 Source Code 6 2 1 DL_POLY_ 3 Modularisation Principles Modules in DL_POLY 3 are constructed to define parameters and variables scalars and arrays and or develop methods that share much in common The division is far from arbitrary and module interdependence is reduced to minimum However some dependencies exist which leads to the following division by groups in hierarchical order e precision module KINDS_F90 The precision module defines the working precision tt wp of all real variables and parameters in DL_POLY _3 By default it is set to 64 bit double precision If the precision is changed the user must check whether the specific platform supports it and make sure it is allowed for in the MPI implementation If all is OK then the code must be recompiled e MPI module MPI_MODULE The MPI module implements all MPI functional calls used in DL_POLY_3 It is only used when DL_POLY 3 is to be compiled i
110. d Wide Web or ftp in the same manner as the licence form The much larger DL_POLY_2 Reference Manual is also available The bench and public subdirectories of DL POLY_3 are not issued in the standard package but can be downloaded directly by FTP from FTP site in the ccp5 DL_POLY DL_POLY_3 directory as described above Note Daresbury Laboratory is the sole centre for the distribution of DL_POLY_3 and copies obtained from elsewhere will be regarded as illegal and will not be supported 1 6 Other Information The DL_POLY 3 web site http www cse clrc ac uk msi software DL_POLY provides additional information in the form of 1 Access to all documentation including licences 2 Frequently asked questions 3 Bug reports Daresbury Laboratory also maintains two DL_POLY associated electronic mailing lists 1 dl_poly_news to which all registered DL_POLY 3 users are automatically subscribed It is via this list that error reports and announcements of new versions are made If you are a DL_POLY 3 user but not on this list you may request to be added Contact w smith dl ac uk 2 dl poly mail is a group list which is available to DL_POLY 3 users by request Its purpose is to allow DL_POLY 3 users to broadcast information and queries to each other To subscribe to this list send a mail message to majordomo dl ac uk with the one line message subscribe dl_poly_mail Subsequent messages may be broadcast by e mailing to dl_poly_mail d
111. d in Z density averages time elapsed simulation time tmst elapsed simulation before averages were switched on chit thermostat related quantity first chip barostat related quantity cint thermostat related quantity second record 2 eta scaling factors for simulation cell matrix elements 9 101 CCLRC Section 5 1 record 3 stpval instantaneous values of thermodynamic variables mxnstk record 4 sumval average values of thermodynamic variables mxnstk record 5 ssqval fluctuation squared of thermodynamic variables mxnstk record 6 zumval running totals of thermodynamic variables mxnstk record 7 ravval rolling averages of thermodynamic variables mxnstk record 8 stkval stacked values of thermodynamic variables mxstak xmxnstk record 9 strcon constraint bond stress 9 record 10 strpmf pmf constraint stress 9 record 11 stress atomic stress 9 record 12 Optional rdf RDF array mxgrdf xmxrdf record 13 Optional zdens Z density array mxgrdf xmxatyp 5 1 5 2 Further Comments Note that different versions of DL_POLY_3 may have a different order of the above parameters or include more or less such Therefore a different versions of DL_POLY_3 may render any existing REVOLD file unreadable by the code 5 1 6 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 no
112. d in this way is symmetric In DL_POLY 3 tether forces are handled by the routine TETHERS_FORCES 2 2 9 Frozen Atoms DL_POLY 3 also allows atoms to be completely immobilized 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 3 does not calculate contributions to the virial or the stress tensor arising from the constraints required to freeze atomic positions Neither does it calculate contributions from intramolecular interactions between frozen atoms In DL_POLY 3 the frozen atom option is handled by the subroutine FREEZE_ATOMS 2 3 The Intermolecular Potential Functions In this section we outline the two body metal Tersoff three body and four body potential functions in DL POLY 3 An important distinction between these and intramolecular bond forces in DL_POLY_3 is that they are specified by atom types rather than atom indices 24 CCLRC Section 2 3 2 3 1 Short Ranged van der Waals Potentials The short ranged pair forces available in DL_POLY 3 are as follows co 4 x ij ij 12 6 U rij de 2 2 69 Tij Tij 3 n m potential 31 nm Eo To l To k U rij 2 n 2 2 70 4 Buckingham potential buck 1 12 6 potential 12 6 2 Lennard Jones 1j
113. data for each individual Z density function i e ntpatm times The data supplied are as follows first record atname a8 unique atom name following records magrdf records Z real distance in z direction A p z real 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 5 2 8 The STATIS File The file is formatted with integers as 10 and reals as el4 6 It is written by the subroutine STATISTICS_COLLECT It consists of two header records followed by many data records of statistical data record 1 cfgname a72 configuration name record 2 string a8 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 SETUP_MODULE file is mxnstk gt 27 ntpatm number of unique atomic sites 9 stress tensor elements 9 if constant pressure simulation requested 111 CCLRC Section 5 2 The STATIS file is appended at intervals determined by the stats directive in the CONTROL file The energy unit is as specified in the FIELD file with 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 time real
114. ded atoms are as follows A distributed excluded atoms list is constructed by the DL_POLY 3 routine BUILD_EXCL_INTRA at the start of the simu lation and is then used in conjunction with the Verlet neighbour list builder LINK_CELL_PAIRS to ensure that excluded interactions are left out of the pair force calculations The excluded atoms list is also updated during the atom relocation process described above DL_POLY 3 routine EX CHANGE_PARTICLES Once the neighbour list has been constructed each node of the parallel computer may pro ceed independently to calculate the pair force contributions to the atomic forces see routine TWO_BODY_FORCES The potential energy and forces arising from the non bonded interactions as well as metal and Tersoff interactions are calculated using interpolation tables These are generated in the following routines VDW_GENERATE METAL_GENERATE and TERSOFF_GENERATE 6 1 4 Modifications for the Ewald Sum For systems with periodic boundary conditions DL_POLY_3 employs the Ewald Sum to calculate the coulombic interactions see Section 2 4 5 It should be noted that DL_POLY 3 uses only the Smoothed Particle Mesh SPME form of the Ewald sum Calculation of the real space component in DL _POLY_3 employs the algorithm for the calculation of the non bonded interactions outlined above since the real space interactions are now short ranged implemented in EWALD_REAL_FORCES routine The reciprocal space component is cal
115. description of the DL POLY_3 force field in 68 CCLRC Section 4 3 Chapter 2 is essential reading The various utility routines mentioned in this section are described in greater detail in the DL_POLY_2 Reference Manual Many of these have been incorporated into the DL POLY 3 Graphical User Interface 17 and may be conveniently used from there 4 3 1 Inorganic Materials The utility GENLAT can be used to construct the CONFIG file for relatively simple lattice structures Input is interactive The FIELD file for such systems are normally small and can be constructed by hand Otherwise the input of force field data for crystalline systems is particularly simple if no angular forces are required notable exceptions to this are zeolites and silicate glasses see below Such systems require only the specification of the atomic types and the necessary pair forces The reader is referred to the description of the DL POLY 3 FIELD file for further details Section 5 1 3 DL_POLY 3 can simulate zeolites and silicate or other glasses Both these materials require the use of angular forces to describe the local structure correctly In both cases the angular terms are included as three body terms the forms of which are described in Chapter 2 These terms are entered into the FIELD file with the pair potentials An alternative way of handling zeolites is to treat the zeolite framework as a kind of macromolecule see below Specifying all this is
116. dom 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 using the directive mxshak in the CONTROL file You may also consider reducing the tolerance of the SHAKE iteration using 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 This should never happen Action Report to authors 165 CCLRC Appendix D Message 72 error too many tersoff potentials specified This should never happen Action Report to authors Message 72 error too many inversion potentials specified This should never happen Action Report to authors Message 74 error unidentified atom in tersoff potential list This shows that DL_POLY 3 has encountered and erroneous entry for Tersoff potentials in FIELD Action Correct FIELD and resubmit Message 76 error duplicate tersoff potential specified This shows that DL_POLY 3 has encountered and erroneous entry for Tersoff potentials in FIELD Action Correct FIELD and resubmit Message 77 error too many inversion angles per domain DL_POLY 3 limits the number of inversion potentials in the system to be simulated actually the number to be processed by each node and checks for the violation of this Termination wil
117. e 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 3 arrays Probable cause your system has expanded unacceptably much to DL_POLY_3 This may not be physically sensible Action Increase the parameter mxcel1 Message 402 error van der waals not specified The user has not set any cutoff in CONTROL rvdw the van der Waals potentials cutoff is needed in order for DL_POLY 3 to proceed 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 cell 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 414 error conflicting ensemble options in CONTROL file DL_POLY_3 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 3 has found incompatible directives in the CONTROL file specifying the electrostatic interactions options Action Locate the conflicting directives in the CONTROL file and correct Message 430 error integration routine not available A request for a non existent
118. e variable variable variable variable variable variable variable variable variable variable variable variable variable variable variable variable variable variable variable variable variable variable variable variable variable variable variable variable variable variable variable variable variable variable variable variable variable variable max number of constraint bonds per a node max number of specified particles in pmf units 1 2 max number of pmf constraints per a node max number of shared particles per node Max 1 2 mxsh1 2 mxcons number of neighbour nodes in DD hypercube 26 max number of specified tethered potentials in system max number of tethered atoms per node max number of parameters for tethered potentials 3 max number of specified chemical bond potentials in system max number of chemical bonds per node max number of parameters for chemical bond potentials 4 max number of specified bond angle potentials in system max number of bond angles per node max number of parameters for bond angle potentials 4 max number of specified dihedral angle potentials in system max number of dihedral angles per node max number of parameters for dihedral angle potentials 7 max number of specified inversion angle potentials in system max number of inversion angles per node max number of parameters for inversion angle potentials 2 max number of excluded interactions per atom max number of bonds link
119. e 0 to Tudw A second array gvdw is also calculated which is related to the potential via the formula lo G rij rig U rig 2 77 ij and is used in the calculation of the forces Both 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 _3 also allows the user to read in the interpolation arrays directly from a file implemented in the VDW TABLE READ routine and the TABLE file Section 5 1 6 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 lo where t fy Ts The force on atom i is the negative of this 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 eten 2 80 where a and 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 rydw it is necessary to apply a long range 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 a
120. e described in Table 5 13 Table 5 13 Metal Potential potential type Variables 1 5 functional form stch Sutton Chen e a n m C U r e Djs E Cyril Pi X jzi F Tij 4 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 potential 1 record 1 atmnam key a8 a4 atom type potential key see Table 5 14 97 CCLRC Section 5 1 variable 1 real potential parameter see Table 5 14 variable 2 real potential parameter see Table 5 14 variable 3 real potential parameter see Table 5 14 variable 4 real potential parameter see Table 5 14 variable 5 real cutoff range for this potential A 5 14 potential 1 record 2 variable 6 real potential parameter see Table 5 14 variable 7 real potential parameter see Table 5 14 variable 8 real potential parameter see Table 5 14 variable 9 real potential parameter see Table 5 14 variable 10 real potential parameter see Table 5 14 variable 11 real potential parameter see Table 5 14 potential n record 2n 1 potential n record 2n cross term 1 record 2n 1 atmnam 1 a8 first atom type atmnam 2 a8 second atom type variable a real potential parameter see Table 5 14 variable b real potential parameter see Table 5 14 cross term n n
121. e halo data increases with respect to and eventually becomes prevalent to the time DL_POLY 3 spends on numeric calculations integration and forces In such regimes the overall DL_POLY_3 efficiency falls down since processors stay idle and no power is harnessed while communications are not finished It is important that the user recognises when DL _POLY 3 becomes vulnerable to decreased eff ciency and what possible measures could be taken to avoid this DL_POLY 3 calculates and reports the link cell algorithms My My Mz employed in the simulations immediately after execution M analogously for My and M is the integer number of the ratio of the width of the system domains in x direction to the maximal short range cutoff specified for the system Max Tij nodes x direction Max cutoff M Nin 4 1 Every domain node of the MD cell is loaded with M 2 My 2 Mz 2 link cells of which Mz My M belong to that domain and the rest are a halo image of link cells from neighbouring domains In this respect the more linked cells per domain the less halo data to keep the more efficient the load distribution per node and the less the communications between nodes and therefore the better the parallelisation DL_POLY 3 issues a built in warning when a link cell algorithms has a dimension less than four i e less than four link cells per domain in given direction A useful rule of thumb is that parallelisation sp
122. e k vector in a principal direction K is the total number of grid points in the same direction and wu is the fractional coordinate of ion j scaled by a factor K i e u K 87 Note that the definition of the B splines implies a dependence on the integer K which limits the formally infinite sum over 0 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 X M 1 exp 2ri k0 K 2 151 0 2 Approximation of the structure factor S k S k b1 k1 ba ka b3 k3 QUka ka k3 2 152 where Q k1 ka k3 is the discrete Fourier transform of the charge array Q 1 2 3 defined as N Qll lab Sig Y Mnluij Li niL1 x Malus lo noLo x n1 n2 N3 Mn usj l3 n3L3 2 153 in which the sums over 71 23 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 1 Vo R gt G k ka k3 Q k1 k2 ks 2 154 ka k3 Urecip where GT is the discrete Fourier transform of the function exp k 4a G k1 ka k3 2 B ky ka k3 Q k1 ka k3 gt 2 155 38 CCLRC Section 2 5 in which Q k1 ka k3 is the complex conjugate of Q k1 k2 k3 and B k1 k2 k3 b1 1 1 b2 k2 b3 k3 2 156 The function G k1 ka k3 is thus a re
123. e working precision wp by kind for real and complex variables and parameters The default is 64 bit double precision i e Real wp Users wishing to compile the code with quadruple precision must ensure that their architecture and FORTRAN 90 compiler can allow that and then change the default in KINDS_F90 Changing the precision to anything else that is allowed by the FORTRAN 90 compiler and the machine architecture must also be compliant with the MPI working precision mpi_wp as defined in COMMS_MODULE in such cases users must correct for that in there 1 3 8 Units Internally all DL_POLY_3 subroutines and functions assume the use of the following defined molec ular units e The unit of time to is 1 x 1071 seconds i e picoseconds e The unit of length o is 1 x 107 metres i e Angstroms e The unit of mass mo is 1 6605402 x 107 kilograms i e Daltons atomic mass units e The unit of charge qo is 1 60217733 x 107 coulombs i e electrons units of proton charge e The unit of energy E mo l0 t0 is 1 6605402 x 10723 Joules 10 J mol e The unit of pressure Po E073 is 1 6605402 x 10 Pascals 163 882576 atmospheres e Planck s constant A which is 6 350780668 x Eto In addition the following conversion factors are used CCLRC Section 1 4 e The coulombic conversion factor Yo is 1 _ _ 139935 4935 w E Ateolo K j such that Uuks EoyoU Internal where U represents the co
124. each step by At oO 1 2 aa 340 where o kg Test 3 41 is the target thermostat energy depending on the external temperature and the system total degrees of freedom f equation 3 11 and Tr a specified time constant for temperature fluctuations normally in the range 0 5 2 ps The VV implementation the algorithm is straight forward A conventional VV1 and VV2 thermally unconstrained steps are carried out At the end of VV2 velocities are scaled by a factor of x in the following manner 1 VVI v t At v t a a r t At rl Ato t sat 3 42 2 RATTLE_VV1 5l CCLRC Section 3 4 3 FF f t At f t 3 43 4 VV2 At FAS 1 t ft At u t At ult 54 i ae 3 44 5 RATTLE_VV2 6 Thermostat At o 1 2 t At 1 1 cas il TT Fas ut At v t Aty 3 45 The LFV implementation the Berendsen algorithm is iterative as an initial estimate of x t at full step is calculated using an unconstrained estimate of the velocity at full step v t 1 FF fi f t At 3 46 2 LFV The iterative part is as follows 3 SHAKE 4 Full step velocity 5 Thermostat ult 340 he TA At o x t HEAD amp a ale sat 3 47 Ore EC At E z 3 48 At o 1 2 x t lt i T e 1 3 49 Several iterations are required to obtain self consistency In DL _POLY 3 the number of iterations is set to 2 3 if bond constraints are present The Berendsen algorithms co
125. eaken the heteropolar bonds relative to the value obtained by simple inter polation 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 formally calculated with the formula 1 fe Sog etti 2 2 Tagli gt 2 101 with atomic label being one of j k and a indicating the x y z component The derivative after the summation is worked out as OU O O O are are folrij fr vig Yiz gra eCa fali fotra Faria o Ya a 2 102 with the contributions from the first in the forms O O O org o CuS foltra gr RC frla gp Solr x fon La ai 2 103 ri re 29 CCLRC Section 2 3 o lo o Vi grg tou Faris Vij COA farag Seles x ro ro fet ALA 2 104 Hry Zit and from the third angular term 0 Felis fali Y folrij fAlrij Xij X 1 vespri d pra M pm 2 n pil z 1 6 C7 Bim LE rali 2 105 where 9 apa tii DE Wik fc rik g 0 ijk 2 106 ro a A The angular term can have three different contributions depending on the index of the particle participating in the interaction SI ms dis LEI fola goa 2 107 A i dg Y wr folri z i I 0 jk 2 108 are ii a Or af a a la tn ett ta Lar 2 109 f Ore i 4 org i Or ie The derivative of g 6 is worked out in the following manner KAO _ 9g Gijx za 2 110 e 00
126. ecognise Action Locate the offending potential in the FIELD file and remove Replace with one acceptable to DL_POLY 3 if this is reasonable Alternatively you may consider defining the required potential in the code yourself Amendments to subroutines READ_FIELD and THREE_BODY_FORCES will be required Message 443 error undefined four body potential DL_POLY 3 has been requested to process a four body potential it does not recognise Action 177 CCLRC Appendix D Check the FIELD file and make sure the keyword is correctly defined Make sure that subroutine THREE_BODY_FORCES contains the code necessary to deal with the requested potential Add the code required if necessary by amending subroutines READ_FIELD and THREE_BODY_FORCES Message 444 error undefined bond potential DL POLY 3 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 BONDS_FORCES contains the code necessary to deal with the requested potential Add the code required if necessary by amending subroutines READ_FIELD and BONDS_FORCES Message 445 error r_14 gt rcut in dihedrals_forces The 1 4 coulombic scaling for a dihedral angle bonding cannot be performed since the 1 4 distance has exceeded the system short range interaction cutoff rcut in subroutine DIHEDRAL_FORCES Action To prevent this error occurring again increase
127. eedup inefficiency is expected when the ratio My My M R Mz 2 My 2 M 2 Mz My M is close to or drops below one In such cases there are three strategies for improving the situation that can be used singly or in combination As obvious from equation 4 1 these are i decrease the number of nodes used in parallel ii decrease the cutoff and iii increase system size It is crucial to note that increased parallelisation efficiency remains even when the link cell algorithm is used inefficiently However DL_POLY 3 will issue an error message and cease execution if detects it cannot fit a link cell per domain as this is the minimum the DL_POLY 3 link cell algorithm can work with 1 1 1 corresponding to ratio R 1 26 Performance may also affected by the fluctuations in the inter node communication due to un avoidable communication traffic when a simulation job does not have exclusive use of all machine resources Such effects may worsen the performance much especially when the average calculation time is of the same magnitude as or less than the average communication time i e nodes spend more time communicating rather than calculating 4 3 A Guide to Preparing Input Files The CONFIG file and the FIELD file can be quite large and unwieldy particularly if a polymer or biological molecule is involved in the simulation This section outlines the paths to follow when trying to construct files for such systems The
128. ehered sites in the molecule tether key ad potential key see Table 5 7 index 1 i integer atomic site index variable 1 real potential parameter see Table 5 7 variable 2 real potential parameter see Table 5 7 The meaning of these variables is given in Table 5 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 8 bonds n where n is the number of flexible chemical bonds in the molecule Each of the subsequent n records contains bond key ad potential key see Table 5 8 index 1 i integer first atomic site index in bond index 2 7 integer second atomic site index in bond variable 1 real potential parameter see Table 5 8 variable 2 real potential parameter see Table 5 8 90 CCLRC Section 5 1 Table 5 7 Tethering Potentials key potential type Variables 1 3 functional form harm Harmonic k U r 35 k r 7 rhrm Restraint k re U r k rr lr r1 lt re U r gt k r24 k re lri r r ri ri20 gt r quar Quartic k k k U r r rf K r ri 8 aan 10 variable 3 real potential parameter see Table 5 8 variable 4 real potential parameter see Table 5 8 The meaning of these variables is given in Table 5 8 This directive and associated data records need not be specified if the m
129. emory than available on the computer architecture In such cases DL_POLY 3 will terminate with an array allocation failure message As a default DL POLY 3 does not store statistical data during the equilibration period If the directive collect is used equilibration data will be incorporated into the overall statistics Users are advised to study the example CONTROL files appearing in the data sub directory to see how different files are constructed 5 1 2 The CONFIG File The CONFIG file contains the dimensions of the unit cell the key for periodic boundary condi tions and the atomic labels coordinates velocities and forces This file is read by the subroutine READ_CONFIG It is also read by the subroutine SCAN_CONFIG in the SET_BOUNDS routine The first few records of a typical CONFIG file are shown below Icel structure 6x6x6 unit cells with proton disorder 83 CCLRC Section 5 1 2 3 26 988000000000000 0 000000000000000 13 494000000000000 23 372293600000000 O 000000000000000 OW 1 2 505228382 0 5446573999 3515 939287 HW 2 1 622622646 1 507099154 7455 527553 HW 3 3 258494716 2 413871957 7896 278327 OW 4 0 000000000000000 O 000000000000000 0 000000000000000 44 028000000000000 1 484234330 1 872177437 13070 74357 7 274585343 0 7702718106 4432 030587 1 972916834 1 577400769 4806 880540 7 340573742 4 328786484 1255 814536 2 125627191 4 336956694 8318 045939
130. en de TirTrnla 2 04 Ten ILijLjnlaldex dej Ljntjrla dei 25 2riklLijLrnlal L Sek gt 2 43 setto x r gl 2ripllrintjnla Or dei rijtjrlo bg dex 2r5 Ir ij rijla Sek de rijPjrla Sei E de gt 2 44 2 Q Ore Ejk X tanl 2rfn lc at rlo en Sek tjrtenla 0gj dek 2r5k centanlo 0ek e rjatanla dex den 2 45 19 CCLRC Section 2 2 Where we have used the the following definition a bla Y_ 1 Fag a b 2 46 B Formally the contribution to be added to the atomic virial is given by 4 W dor f 2 47 i 1 However it is possible to show by tedious algebra using the above formulae or more elegantly by thermodynamic arguments 28 that the dihedral makes no contribution to the atomic virial The contribution to be added to the atomic stress tensor is given by oP repf rapi TED 2 48 COS ij e reg ra gh rane ren hf with Pr rialietenlo rinlesatiela Lig X LjkllEje Lanl Pr 13k Lijra ri eget gkla ra x Peale X teal Dik ri lr etenlo Tin LijLjrlo ar Fie ig kmla Li x cala X Trl 9 2 rijlr tirle rielLatalo lrig X ml 2 49 gd Arjellilijlo rh Lijljrla Li X F g hy 2 Teen Ceale Tenltjnlenla ik x Pell ha 2 renltentanla TjklLjhTrnla jr X tana The sum of the diagonal elements of the stress tensor is zero since the virial
131. en 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 Harmonic harm k U Ojik 5 sir 00 2 13 2 Quartic quar k o k k 4 U Ojik z jik 00 3 jik 00 q ii 00 2 14 15 CCLRC Section 2 2 3 Truncated harmonic thrm k U O5ix 5 Ojik 90 expl r ri 03 2 15 4 Screened harmonic shrm U Orin Oji 60 expl rii p1 a p 2 16 5 Screened Vessal 25 bvs1 e 00 T jin n x exp rij p1 rik p2 2 17 U Ojik 6 Truncated Vessal 26 bvs2 U 9jin kl Oik Ojik 90 Ojik 09 27 a a at Oie bo T 80 expl ri r 0 1 2 18 7 Harmonic cosine hcos k U Ojik 3 cos 0j x cos 89 2 19 8 Cosine cos U 0 ix A 1 cos m0 ik 0 2 20 9 MM3 stretch bend 27 mmsb U Ojik A Ojik 00 rig rij Tik THe 2 21 In these formulae 0 x is the angle between bond vectors r and r y Ojik cos E 2 22 In DL_POLY_3 the most general form for the valence angle potentials can be written as U Ojik Tij rik ACA S rij S rik 2 23 where A 0 is a purely angular function 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
132. endments to subroutines READ_FIELD and INVERSIONS_FORCES will be required Message 450 error undefined tethering potential A form of tethering potential has been requested which DL_POLY_3 does not recognise Action Locate the offending potential in the FIELD file and remove Replace with one acceptable to DL_POLY 3 if this is reasonable Alternatively you may consider defining the required potential in the code yourself Amendments to subroutines READ_FIELD and TETHERS_FORCES 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 vdw potential A form of vdw potential has been requested which DL_POLY 3 does not recognise Action Locate the offending potential in the FIELD file and remove Replace with one acceptable to DL_POLY 3 if this is reasonable Alternatively you may consider defining the required potential in the code yourself Amendments to subroutines READ_FIELD and VDW_GENERATE 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 Resubmit the job Mess
133. ensemble has been made or a request with conflicting options that DL_POLY_3 cannot deal with 176 CCLRC Appendix D Action Examine the CONTROL and FIELD files and remove inappropriate specifications Message 432 error undefined tersoff potential This shows that DL _POLY 3 has encountered an unfamiliar entry for Tersoff potentials in FIELD Action Correct FIELD and resubmit Message 433 error rcut must be specified for the Ewald sum precision When specifying the desired precision for the Ewald sum in the CONTROL file it is also necessary to specify the real space cutoff rcut Action Place the cut directive before the ewald 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 440 error undefined angular potential A form of angular potential has been requested which DL_POLY 3 does not recognise Action Locate the offending potential in the FIELD file and remove Replace with one acceptable to DL_POLY 3 if this is possible Alternatively you may consider defining the required potential in the code yourself Amendments to subroutines READ_FIELD and ANGLES_FORCES will be required Message 442 error undefined three body potential A form of three body potential has been requested which DL_POLY_3 does not r
134. ependencies OBJ_ALL OBJ_MOD 147 CCLRC Appendix C Makefile SRL2 Master makefile for DL_POLY_3 06 serial version 2 Author I T Todorov February 2006 Define default settings SHELL bin sh SUFFIXES SUFFIXES f90 o BINROOT execute EX DLPOLY Y EXE BINROOT EX TYPE master FC undefined LD undef ined Define object files OBJ_MOD kinds_f90 0 mpi_module o comms_module o setup_module o domains_module o parse_module o site_module o config_module o defects_module o vdw_module o metal_module o tersoff_module o three_body_module o four_body_module o core_shell_module o constraints_module o pmf_module o tethers_module o bonds_module o angles_module o dihedrals_module o inversions_module o external_field_module o statistics_module o OBJ_ALL warning o error o numeric_container o kinetic_container o spme_container o scan_field o scan_config o scan_control o set_bounds o read_control o vdw_generate o vdw_table_read o metal_generate o tersoff_generate o dihedrals_14_check o read_field o read_config o tag_legend o pass_shared_units o compress_legend o build_book_intra o build_excl_intra o scale_temperature o update_shared_units o core_shell_quench o constraints_tags o constraints_quench o pmf_coms o pmf_tags o pmf_vcoms o pmf_quench o 148 CCLRC Appendix C set_temperature o vdw_lrc o metal_lrc o system_init o export_a
135. es mean squared displacement of last atom types the next 9 entries for the stress tensor stress 1 real xx component of stress tensor 112 CCLRC Section 5 2 stress 2 real xy component of stress tensor stress 3 real xz component of stress tensor stress 4 real yx component of stress tensor d real stress 9 real zz component of stress tensor the next 9 entries if a NPT or NoT simulation is undertaken cell 1 real ox component of a cell vector cell 2 real y component of a cell vector cel1 3 real z component of a cell vector cell 4 real x component of b cell vector TT real La cell 9 real z component of c cell vector 113 Chapter 6 DL POLY 3 Parallelisation Source Code Modularisation and Structure Scope of Chapter This chapter we discuss the DL_POLY 3 parallelisation strategy describe the he principles used in the DL_POLY_3 modularisation of the source code and list the file structure found in the source subdirectory 114 CCLRC Section 6 1 6 1 DL POLY 3 Parallelisation DL_POLY 3 is a distributed parallel molecular dynamics package based on the Domain Decompo sition parallelisation strategy 2 8 9 4 5 In this section we briefly outline the basic methodology Users wishing to add new features DL _POLY 3 will need to be familiar with the underlying tech niques as they are described in the above references 6 1 1 The Domain Decomposition Strategy The Domain Decomposition DD st
136. es are handled by the subroutine COUL_CP_FORCES 2 4 2 Force Shifted Coulomb Sum This form of the Coulomb sum has the advantage that it drastically reduces the range of electrostatic 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 simple truncated and shifted potential function is U r 4 a 2 129 ATE Tij Tout with ge the charge on an atom labelled freut the cutoff radius and r the magnitude of the separation vector ri r T ij j A further refinement of this approach 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 This removes the heating effects that arise from the discontinuity in the forces at the cutoff in the simple truncated and shifted potential the formula above The physics of this potential however is little better It is only recommended for very crude structure optimizations The Force Shifted potential is thus id 1 ij 2 U r EL ee 2 130 2 Ameo Tij Tout Tout with the force on an atom 7 given by didj 1 1 Ba 2 131 j A4reo 3 dh 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 The contribu
137. ese implement an emulation of some general MPI calls used in DL_POLY_3 source code when compiling in serial mode as well as some modified counterparts of the general files changed to allow for faster and or better memory optimised serial execution Names are self explanatory 123 CCLRC Section 6 2 6 2 7 Comments on MPI Handling Only a few files make explicit calls to MPI routines COMMS_MODULE READ_CONFIG PASS_SHARED_UNITS UPDATE_SHARED_UNITS EXPORT_ATOMIC_DATA DEPORT_ATOMIC_DATA METAL_LD_EXPORT PARALLEL_FFT EXCHANGE_GRID DEFECTS_REFERENCE_READ DEFECTS_REFERENCE_EXPORT DEFECTS_WRITE TRAJECTORY_WRITE SYSTEM_REVIVE The rest of the files that use MPI functionality in any way make implicit calls via generic functions developed in COMMS_MODULE 6 2 8 Comments on SETUP_MODULE The most important module by far is SETUP_MODULE which holds the most important global parameters and variables some of which serve as parameters for global array bounds set in SET_BOUNDS A brief account of these is given below parameter value function pi 3 1415926535897932 m constant sqrpi 1 7724538509055160 YT constant rt2 1 4142135662373095 2 constant rt3 1 7320508075688772 Y 3 constant r4pie0 138935 4835 electrostatics conversion factor to internal units i e ma boltz 0 831451115 Boltzmann constant in internal units prsunt 0 163882576 conversion factor for pressure from internal units to katms nread 5 main input channel nrite 6 mai
138. ess tensor are also outlined 2 2 1 Bond Potentials Fi The interatomic bond vector The bond potentials describe explicit chemical bonds between specified atoms They are all func tions of the interatomic distance Only the coulomb potential makes an exception as it depends on the charges of the specified atoms The potential functions available are as follows 1 Harmonic bond harm 1 U rij Ari roy 2 2 2 Morse potential mors U rij EoK 1 exp k rig ro 1 2 3 13 CCLRC Section 2 2 U r D 24 ij ij 1 2 sk rij To rij Tol lt r U r QV 8 o 1 vcd 2 5 ri 3kr krellrij rol re x rij to gt Te 2 5 3 12 6 potential bond 12 6 4 Restrained harmonic rhrm 5 Quartic potential quar k 2 k 3 k 4 Ulrij z uo 3 To g ia 2 6 6 Buckingham potential buck z C U 35 A exp 52 6 2 7 P Tij 7 Coulomb potential coul k qiq U rij 2 8 ri ATEQE Tij 28 where q is the charge on an atom labelled In these formulae rij is the distance between atoms labelled and j rij g ril 2 9 where ry 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 o f E utr rij 2 10 The force acting on atom is the negative of this The contribution to be added to the atomic virial is given by W fij f g
139. eters as well as some general methods and generic functions intrinsically related to the purpose or and contents of the specific module The file names and the methods or and functions developed in them have self explanatory names More information of their purpose can be found in their headers The rest of files in DL_POLY_3 are dependent on the module files in various ways The dependency relation to a module file is explicitly stated in the declaration part of the code 6 2 4 General Files The DL_POLY 3 general files are common to both MPI and SERIAL version of the code In most cases they have self explanatory names as their order is matched as closely as possible to that occurring in the main segment of the code DL POLY Only the first five files are exception of that rule WARNING and ERROR are important reporting subroutines that have call points at various places in the code and NUMERIC_CONTAINER KINETIC_CONTAINER and SPME_CONTAINER are containers of simple functions and subroutines related in some way to their purpose in the code Only one explicit internal dependence between files in this group exists EWALD_SPME_FORCES depends on PARALLEL_FFT 6 2 5 VV and LFV Specific Files These implement the specific integration scheme as file names are finished with the flavour they develop if they have a counterpart implementing the same algorithm but in the alternative flavour Names are self explanatory 6 2 6 SERIAL Specific Files Th
140. f bond constraints are present Note also that the change in box size requires the SHAKE algorithm to be called each iteration Cell size and shape variation The isotropic algorithms VV and LFV may be extended to allowing the cell shape to vary by defining 7 as a tensor 7 The equations of motion are written in the same fashion as is in the isotropic algorithm with slight modifications as now the equations for y and V are extended to matrix forms for y and H 2Ekin t 20 3 kg Tex dmass gut SPS ents Pmass ei kg Text Tp 3 86 59 CCLRC Section 3 5 d H t da d YO TOVE l 3 x Ja x where is the stress tensor and 1 is the identity matrix The VV and LFV algorithmic equations are therefore written in the same fashion as above with slight modifications in i the equations for the thermostat and barostat frictions and ii the equations for the system volume and cell parameters The modifications in i for the VV couched algorithm read as At ZE Pmass Tr n t i non 20 3 kB Text x t SAM x t 8 Imass 1 At alt Pox Vit 1 nt Ab nu a t AVE 3 87 2 2 Pmass whereas for the LFV couched algorithm as 1 1 2Ekin t Pmass Tr n t f nt 20 3 kp Text x t At x t At At 2 2 mass 1 1 t Pxa V t 1 n t 3At n t 340 At alt n VO exp y t At 3 88 The modifications in ii are the sa
141. guage DL_POLY 3 is written in free format FORTRAN 90 In DL_POLY 3 we have adopted the conven tion of explicit type declaration i e we have used Implicit None in all subroutines Thus all variables must be given an explicit type Integer Real wp etc 1 3 2 Modularisation and Intent DL_POLY 3 exploits the full potential of the modularisation concept in FORTRAN 90 Variables having in common description of certain feature or method in DL_POLY 3 are grouped in modules This simplifies subroutines calling sequences and decreases error proneness in programming as subroutines must define what they use and from which module To decrease error proneness further arguments that are passed in calling sequences of functions or subroutines have defined intent i e whether they are to be e passed in only Intent In the argument is not allowed to be changed by the routine e passed out only Intent Out the coming in value of the argument is unimportant e passed in both directions in and out Intent In0ut the coming in value of the argu ment is important and the argument is allowed to be changed 1 3 3 Memory Management DL_POLY 3 exploits the dynamic array allocation features of FORTRAN 90 to assign the necessary array dimensions 1 3 4 Target Computers DL_POLY 3 is intended for distributed memory parallel computers It was developed on Cray T3E and IBM SP4 architectures Compilation of DL_POLY 3 in parallel m
142. he DEFAULT ENVIRONMENT PATH then it MUST be supplied in Makefile 3 a MAKE command Makefile interpreter in the system SHELL Serial Compilation on Windows The best way to get around it is to install cygwin on the system http www cygwin com to emulate a unix like environment and then use the make command A potential problem you may encounter is that a FORTRAN90 compiler may not pick symbolic links To resolve this you will have to use hard linking in the Makefile Contacts Dr I T Todorov at CCLRC Daresbury Laboratory e mail I T Todorov dl ac uk Dr W Smith at CCLRC Daresbury Laboratory e mail W SmithCdl ac uk 194 Bibliography 10 11 12 13 14 15 16 17 18 19 20 21 Smith W and Forester T 1996 J Molec Graphics 14 136 2 Todorov I and Smith W 2004 Phil Trans R Soc Lond A 362 1835 2 115 Smith W 1987 Molecular Graphics 5 71 2 Smith W 1991 Comput Phys Commun 62 229 2 4 115 Smith W 1993 Theoretica Chim Acta 84 385 2 4 115 Smith W and Forester T R 1994 Comput Phys Commun 79 52 2 Smith W and Forester T R 1994 Comput Phys Commun 79 63 2 4 47 Pinches M R S Tildesley D and Smith W 1991 Molecular Simulation 6 51 2 4 115 Rapaport D C 1991 Comput Phys Commun 62 217 2 4 115 Sutton A P and Chen J 1990 Philos Mag Lett 61 139 3 27 116 118 Rafii Tabar
143. he system potential is in two parts Firstly by analogy with the short ranged potentials the correction to the local density is obtained by co a Pi P 4p 5 r dr 2 90 Tout r where p is the uncorrected local density and J is the mean particle density Evaluating the integral part of the above equation yields p tn CO i 2 91 Teut which is the local density correction and is identical for all atoms The correction is applied immediately after the local density is calculated The density term of the Sutton Chen potential needs no further correction The pair term correction is obtained by analogy with the short ranged potentials and is Nepa a y U 2 2 92 corr T n 3 ia The correction to the local density having already been applied To estimate the virial correction we assume the corrected local densities are constants i e in dependent of distance at least beyond the range rmet This allows the virial correction to be computed by the methods used in the short ranged potentials The result is i an FT YES LYS it ew Tout Tout This correction may be used as it stands or with the further approximation N 1 2 N 5 Pi 1 2 gt 2 94 i lt p gt where lt p P gt is regarded as a constant of the system In DL POLY_3 the metal forces are handled by the routine METAL_FORCES The local density is cal culated by routine METAL_LD_COMPUTE The long range corrections
144. hin the buffer is coupled to a viscous background and a stochastic heat bath such that drt _ nore x t u t 5 2 where x t is the friction parameter from the dynamics in the the MD cell and R t is stochastic force with zero mean that satisfies the fluctuation dissipation theorem RO R O 2 x t mi kBT dij bap lt t 5 3 where superscripts denote Cartesian indices subscripts particle indices kg is the Boltzmann constant T the target temperature and m the particle s mass The algorithm is implemented in routine PSEUDO and has two stages e Generate random forces on all particles within the thermostat Here care must be exercised to prevent introduction of non zero net force when the random forces are added to the system force field e Rescale the kinetic energy of the thermostat bath so that particles within have Gaussian distributed kinetic energy with respect to the target temperature and determine the Gaussian constraint friction within the thermostat x t Max 0 sumifrac f t R t dotvecv t m vecu t i 5 4 Care must be exercised to prevent introduction of non zero net momentum Users are reminded to use for target temperature the temperature at which the original system was equilibrated in order to avoid simulation instabilities The effect of this algorithm is to relax the buffer region of the system on a local scale and to effectively dissipate the incoming excess kinetic energy f
145. hrm Truncated harmonic k O p U 0 0 00 exp r3 r p3 shrm Screened harmonic k 0 pi p2 U 0 g 8 00 exp rij p1 rix p2 n _ k 0 2_ 0 2 2 bvs1 Screened Vessal 25 k 00 pr p2 U 0 80 00 fK o 0 m x exp rij p1 rik p2 bvs2 Truncated Vessal 26 k o a p U 0 k 0 0 00 0 00 27 Gre 8 0 7 00 exp ri r 01 hbnd H bond 15 Dn Ru U 0 Du cos 0 x 5SCRro rjx 2 6 Raw r 5x 10 is the 7 j k angle 6 fbp n where n is the number of four body potentials to be entered It is followed by n records each specifying a particular metal potential in the following manner atmnam 1 i atmnam 2 j atmnam 3 k atmnam 3 1 key variable 1 variable 2 variable 3 a8 a8 a8 a8 al real real real first central atom type second atom type third atom type forth atom type potential key see Table 5 16 potential parameter see Table 5 16 potential parameter see Table 5 16 cutoff range for this potential 99 CCLRC Section 5 1 The variables pertaining to each potential are described in Table 5 16 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 Table 5 16 Four body Potentials key potential type Variables 1 2 functional formt harm Harmonic k do U
146. i ga a ere i ei n p i i a 107 5 24 The REVGON Fl o fe Gog ka a E a poe hk Barats 110 5 2 5 The REVIVE File coso di i a A i e i we ee 110 26 The RDEDAT PE s 2 8 ggg kw a a gee E AE ET hw ere eS 110 pag The ZDNDAT File 2 aoe aud BM bm e a ook a ak ade bo 111 Ores We STASIS Pile ee doe keg E Ba dy eed E pee I Rae 111 6 DL POLY 3 Parallelisation Source Code Modularisation and Structure 114 6 1 DL POLY 3 Parallelisation 2 o soe 05 aa m ee ee Be ee ae ee a 115 6 1 1 The Domain Decomposition Strategy lt a 115 6 1 2 Distributing the Intramolecular Bonded Terms 116 6 1 3 Distributing the Non bonded Terms 00 00004 117 6 1 4 Modifications for the Ewald Sum e o 118 6 1 5 Metal Potentials ocio as bs the Pg ea be e a 118 6 1 6 Tersoff Three Body and Four Body Potentials 119 6 1 7 Globally Summed Properties 119 6 1 8 The Parallel DD tailored SHAKE and RATTLE Algorithms 119 6 2 DL POLY 3 Saune Code osas Be eA eee a ee GS 120 6 2 1 DL POLY 3 Modularisation Principles 120 62 2 DE POLY 3 Eile Siructite s s o fe eee ioe A a 121 6023 Module Piles es se u oe o ee e EE ed aw eae E a 123 0 24 General Fils Be Re Bae e ea we eRe a 123 6 2 5 VV and LFV Specific Files 123 6 2 6 SERIAL Specific Files se s sa e aiae a saon a e si a a a a e 123 6 2 7 Comments on MPI Handling s rones ea aoa a Sh eA wee eee a a 124 6 2 8 Comments on SETUP MOD
147. iable timestep algorithm to be in contention with each other Action mxdis MUST BE gt 2 5x mndis Correct in CONTROL and rerun Message 519 error REVOLD not readable If REVOLD exists it is either corrupted or generated by an older version of DL_POLY 3 184 CCLRC Appendix D Action Change the restart option in CONTROL and rerun Message 520 error number of nodes MUST be presentable as a product of three integers A DL_POLY 3 check during the domain decomposition mapping has been violated Action You have not provided number of processors represented as 2 x 2y X 2z Message 530 error pseudo thermostat thickness MUST comply with 2 Angs lt thick ness lt a quarter of the minimum MD cell width DL _POLY 3 has found a check violated while reading CONTROL Action Correct accordingly in CONTROL and resubmit Message 540 error pseudo thermostat MUST only be used in bulk simulations i e imcon MUST be 1 2 or 3 DL_POLY_3 has found a check violated while reading CONTROL Action Correct accordingly in CONTROL nve or in CONFIG imcon and resubmit Message 551 error REFERENCE not found The defect detection option is used in conjunction with restart but no REFERENCE file is found Action Supply a REFERENCE configuartion Message 552 error REFERENCE must contain cell parameters REFERENCE MUST contain cell parameters i e image convention MUST be imcon 1 2 3 or 6 A
148. ians 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 3Strictly speaking the real space sum ranges over all periodic images of the simulation cell but in the DL_POLY_3 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 36 CCLRC Section 2 4 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 reciprocal space and the self energy correction For molecular systems as opposed to systems comprised simply of point ions additional modifica tions EWALD_EXCL_FORCES 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
149. ices of all atoms within the cutoff radius reut of a given atom The use of a neighbour list is not strictly necessary in the context of link cells but it has the advantage here of allowing a neat solution to the problem of excluded pair interactions arising from the intramolecular terms see below or frozen atoms In DL_POLY 3 the neighbour list is constructed simultaneously on each node using the DD adaptation of the link cell algorithm to share the total burden of the work reasonably equally between nodes Each node is thus responsible for a unique set of non bonded interactions and the neighbour list is therefore different on each node A feature in the construction of 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 117 CCLRC Section 6 1 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 non bonded interactions However this is not a universal requirement of all force fields The same considerations are needed in dealing with charged excluded atoms The modifications necessary to handle the exclu
150. ility SOLVADD fills out the MD box with single site solvent molecules from a fcc lattice The FIELD files will then need to be edited to account for the solvent molecules added to the file Hint to save yourself some work in entering the non bonded interactions variables involving solvent sites to the FIELD file put two bogus atoms of each solvent type at the end of the CONNECT _DAT file for AMBER force fields the utility AMBFORCE will then evaluate all the non bonded variables required by DL_POLY_3 Remember to delete the bogus entries from the CONFIG file before running DL_POLY 3 4 3 4 Analysing Results DL_POLY 3 is not designed to calculate every conceivable property you might wish from a sim ulation Apart from some obvious thermodynamic quantities and radial distribution functions it does not calculate anything beyond the atomic trajectories You must therefore be prepared to post process the HISTORY file if you want other information There are some utilities in the DL_POLY_3 package to help with this but the list is far from exhaustive In time we hope to have many more Our users are invited to submit code to the DL_POLY 3 public library to help with this The utilities available are described in the DL_POLY_2 Reference Manual Users should also be aware that many of these utilities are incorporated into the DL POLY Graphical User Interface 17 4 3 5 Choosing Ewald Sum Variables 4 3 5 1 Ewald sum and SPME This section outli
151. ill produce the files OUTPUT STATIS REVCON and REVIVE and optionally HISTORY RDFDAT ZDNDAT DEFECTS in the executing directory See Section 5 2 for the description of the output files This simple procedure is enough to create a standard version to run most simulations There may however be some difficulty with array sizes DL_POLY_3 contains features which allocate arrays after scanning the input files for a simulation Sometimes these initial estimates are insufficient for a long simulation when for example the system volume changes markedly during the simulation or when a system is artificially constructed to have a non uniform density Usually simply restarting the program will cure the problem but sometimes especially when the local atom density is a way 62 CCLRC Section 4 1 higher than the global one it may be necessary to amend the array sizes in accordance with the error message obtained A way to trigger lengthening of the density dependent global arrays the user may use the densvar option in the CONTROL Section 5 1 1 file However lengthening these array will require a larger amount of memory resources from the execution machine for the simulation which it may not be able to provide See Section 6 2 2 for more insight on the DL_POLY 3 source code structure 4 1 2 Constructing Non standard Versions In constructing a non standard DL_POLY 3 simulation program the first requirement is for the user to write a program
152. ined in equation 3 21 2 RATTLE_VV1 3 FF FEF At f t 3 25 4 VV2 A t t u t At u t 5At gt PRA 3 26 m 5 RATTLE_VV2 The algorithm is self consistent and requires no iterations The LFV implementation the Langevin algorithm is straightforward 1 FF f t f t At 3 27 2 LFV and Thermostat 1 2 xAt 1 2 f t R t t At Uta e Tye a oa m 1 r t At rt At u t At 3 28 where R t are Langevin random forces 3 SHAKE 4 Full step velocity 1 1 v t 5 fut JAM ut At 3 29 The VV and LFV flavours of the Langevin algorithm are implemented in the DL_POLY 3 routines NVT_L1_VV and NVT_L1_LFV respectively 49 CCLRC Section 3 4 3 4 2 Evans Thermostat 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 motion as dr t _ a 0 dat 7 10 x t v t 3 30 the kinetic temperature constraint x can be found as follows d d 1 d pred xX H Da miti qu 0 f S milt Era x t v t 0 3 31 DaO AA i Di miw t The VV implementation the algorithm is straight forward A conventional VV1 and VV2 thermally unconstrained steps are carried out At the end of VV2 x t At is calculated exactly and then the thermal constraint applied on the unthermostated velocities at full step t At in the following
153. ing arrays used in this operation may be exceeded resulting in termination of the program Action Contact authors 164 CCLRC Appendix D Message 66 error coincidence of particles in bond angle unit DL_POLY 3 has found a fault in the definition of a bond angle in the FIELD file Action Correct the erroneous entry in FIELD and resubmit Message 67 error coincidence of particles in dihedral unit DL_POLY 3 has found a fault in the definition of a dihedral unit in the FIELD file Action Correct the erroneous entry in FIELD and resubmit Message 68 error coincidence of particles in inversion unit DL_POLY 3 has found a fault in the definition of a inversion unit in the FIELD file Action Correct the erroneous entry in FIELD and resubmit Message 69 error too many link cells required in three_body_forces This should not happen The calculation of three body forces in DL_POLY 3 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 Consider using densvar option in CONTROL for extremely non equilibrium simulations Alterna tively increase mxcell in SET_BOUNDS recompile and resubmit Message 70 error constraint_quench failure When a simulation with bond constraints is started DL POLY_3 attempts to extract the kinetic energy of the constrained atom atom bonds arising from the assignment of initial ran
154. ion apart from the mandatory as listed in it any other items are not read by DL_POLY 3 but may be added to aid alternative uses of the file 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 do not need to 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 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 fxx 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 strictly mandatory any other items are not read by DL_POLY_3 but may be added to aid alternative uses of the file for example the DL_POLY_3 Graphical User Interface 17 Table 5 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 5 6 Periodic Boundary Key record2 imcon meaning no periodic boundaries cubic boundary conditions orthorhombic boundary conditions parallelepiped boundary conditions x y parallelogram boundary condit
155. ions with no periodicity in the z direction awnr 85 CCLRC Section 5 1 5 1 2 3 Further Comments on the CONFIG File The CONFIG file has the same format as the output file REVCON Section 5 2 4 When restarting from a previous run of DL_POLY 3 i e using the restart restart noscale or restart scale 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_3 does this for you 5 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 READ_FIELD It is also read by the subroutine SCAN_FIELD in the SET_BOUNDS routine 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 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 86 CCLRC Section 5 1 DIH
156. is zero and the matrix is symmetric Lastly it should be noted that the above description does not take into account the possible inclu sion of distance dependent 1 4 interactions as permitted by some force fields Such interactions are permissible in DL_POLY_3 and are described in the section on pair potentials below DL_POLY_3 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 3 dihedral forces are handled by the routine DIHEDRALS_FORCES 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_3 makes no distinction between dihedral and improper dihedral angle functions both are calculated by the same subroutines and all the comments made in the preceding 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 COOH8 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 defining a harmonic improper dihedral 20 CCLRC Section 2 2 angle potential with an equilibrium angle of 35 264 The angle is defined by vectors rj9 ro3 and T34 where the atoms 1 2 3 and 4 a
157. job enthalpy of system rotational temperature total configurational contribution to the virial short range potential contribution to the virial electrostatic potential contribution to the virial chemical bond contribution to the virial angular and three body potentials contribution to the virial constraint bond contribution to the virial tethering potential contribution to the virial elapsed cpu time since the beginning of the job system volume core shell temperature configurational energy due to core shell potentials core shell potential contribution to the virial angle between b and c cell vectors angle between c and a cell vectors angle between a and b cell vectors pmf constraint contribution to the virial pressure Note The total internal energy of the system variable tot_energy includes all contributions to the 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 CONTROL 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 108 CCLRC Section 5 2 rolling averages of the same variables are also given The maxim
158. k into your INPUT files and correct the semantics where appropriate and resubmit DL_POLY_3 will have printed out in the OUTPUT file what the found non uniform word is Message 2 error too many atom types in FIELD scan_field This error arises when DL_POLY_3 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 1000 Action Increase the number of allowed atom types mmk in SCAN_FIELD recompile and resubmit Message 3 error unknown directive found in CONTROL file This error most likely arises when a directive is misspelt in the CONTROL file Action Locate the erroneous directive in the CONTROL file and correct error and resubmit 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 Action Locate the erroneous directive in the FIELD file and correct error and resubmit Message 5 error unknown energy unit requested The DL POLY_3 FIELD file permits a choice of units for input of energy parameters These may be electron volts ev k calories kcal k joules kj or the DL_POLY 3 internal units 10 J internal There is no default value Failure to specify any of these correctly or reference to other energy units will result in this
159. kn kn rij Lin rij vien Lin tien a UknTin in Pig k fu di A ro Sen dei rs Wi Dig a Lij Lo Lij Una a WEJ VknTin Tin This general formula applies to all atoms 2 7 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 y 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 Wee Ef 2 60 i 1 However it is possible to show by thermodynamic arguments cf 28 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 f 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 o are Pt re fe tre fe 2 61 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 3 inversion forces are handled by the routine INVERSIONS_FORCES 2 2 8 Tethering Forces DL_P
160. l ac uk Note that this is a vetted list so electronic spam is not possible 10 Chapter 2 Force Fields Scope of Chapter This chapter describes the variety of interaction potentials available in DL_POLY 3 11 CCLRC Section 2 1 2 1 Introduction to DL POLY 3 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 3 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 14 Dreiding 15 and AMBER 16 users have been coded in the package as well as less familiar forms In addition DL_POLY _3 retains the possibility of the user defining additional potentials In DL_POLY 3 the total configuration energy of a molecular system may be written as Nshel Udi 12 rn gt Usnel ishel Pcore gt E shell ishet 1 Nieth 5 Uteth itetn ri U t r U 0 tteth 1 Noond 5 Ubonalibond Tas Tp ibond 1 Nangi y Uangi Canals Tab Te tangi 1 Naina F y Udind tdihds Tas Tb Ve Ta tdind 1 Ninv Y Umali Pastistata 2 tal gt Sufre i j lr rl 2 1 i l j gt i N N N DD Utersofs i J k Ti T Tj E p i 1 j7i Aj N 2N 1 N I
161. l result if the condition is violated Action Increase the parameter mxinv in SET_BOUNDS recompile and resubmit Message 78 error too many link cells required in tersoff_forces This should not happen The calculation of Tersoff forces in DL_POLY_3 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 Consider using densvar option in CONTROL for extremely non equilibrium simulations Alterna tively increase mxcell in SET_BOUNDS recompile and resubmit 166 CCLRC Appendix D Message 79 error tersoff potential cutoff undefined This shows that DL_POLY_3 has encountered and erroneous entry for Tersoff potentials in FIELD Action Correct FIELD and resubmit Message 80 error too many pair potentials specified This should never happen Action Report to authors Message 81 error unidentified atom in pair potential list This shows that DL_POLY_3 has encountered and erroneous entry for vdw or metal potentials in FIELD Action Correct FIELD and resubmit Message 82 error calculated pair potential index too large This should never happen In checking the vdw and metal potentials specified in the FIELD file DL_POLY _3 calculates a unique integer indices that henceforth identify every specific potential within the program If this index becomes too large termination of the program results Action
162. l temperature scaling of the previous configuration restart noscale Internally these options are handled by the integer variable keyres which is explained in Table 5 2 Table 5 2 Internal Restart Key keyres meaning 0 start new simulation from CONFIG file and assign velocities from Gaussian distribution 1 continue current simulation start new simulation from CONFIG file and rescale velocities to desired temperature 3 start new simulation from CONFIG file and do not rescale velocities 6 The various ensemble options i e nve nvt lang nvt evans nvt ber nvt hoover npt ber npt hoover npt mtk nst ber nst hoover nst mtk 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 5 3 Table 5 3 Internal Ensemble Key keyens meaning Microcanonical ensemble NVE Langevin NVT ensemble Evans NVT ensemble Berendsen NVT ensemble Nos Hoover NVT ensemble Berendsen NPT ensemble Nos Hoover NPT ensemble Martyna Tuckerman Klein NPT ensemble Berendsen NaT ensemble Nos Hoover NoT ensemble Martyna Tuckerman Klein NoT ensemble o DN D UU WHO E j 7 The zero directive enables a zero temperature optimisation The target temperature of the simulation is reset to 10 Kelvin and a crude energy minimiser 0 u t FO lt 0 v t
163. latively simple product of the gaussian screening term appearing in the conventional Ewald sum the function B k1 ka k3 and the discrete Fourier transform of Q k1 ka k3 4 Calculating the atomic forces which are given formally by pel Boa Cuba OO 2 157 or VOEO pikak or 1 2 3 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 3 subroutines required to calculate the SPME contributions are 1 SPME_CONTAINER containing a BSPGEN which calculates the B splines b BSPCOE which calculates B spline coefficients c SPL_CEXP which calculates the FFT and B spline complex exponentials 2 PARALLEL_FFT and GPFA_WRAP native DL_POLY_3 subroutines that respect the domain decomposition concept which calculate the 3D complex fast Fourier transforms 3 EWALD_SPME_FORCES which calculates the reciprocal space contributions uncorrected 4 EWALD_REAL_FORCES which calculates the real space contributions corrected 5 EWALD_EXCL_FORCES which calculates the reciprocal space corrections due to the coulombic exclusions in intramolecular interactions 6 EWALD_FROZEN_FORCES which calculates the reciprocal space corrections due to the exclu sion interactions between frozen atoms 7 TWO_BODY_FORCES in which all of the above subroutines are called sequentially and al
164. le CONFIG DL_POLY_3 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 incorrectly 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 neutral group option now redundant DL_POLY_3 does not have the neutral group option Action Use the Ewald sum option It s better anyway 158 CCLRC Appendix D Message 27 error rigid body option now redundant DL_POLY 3 does not have a rigid body option Action Consider using DL_POLY 2 instead Message 28 error PMF option now redundant DL_POLY_3 does not have the potential of mean force option yet Action Consider using DL_POLY 2 instead Message 30 error too many chemical bonds specified This should never happen This error most likely arises when the FIELD file or and DL POLY_3 executable are corrupted Action Recompile the program or recreate the FIELD file If neither of these works send the problem to us Message 31 error too many chemical bonds per domain DL_POLY 3 sets a limit on the number of chemical bond potentials in the simulated system as a whole This number is a function of the total number of chemical bonds in the
165. le Record Example CONTROL file for DL_POLY_3 state parameters target temperature temperature 300 0 Kelvin target pressure pressure 10 0 katms integration options ensemble and options ensemble npt hoover 0 1 1 0 ps integration timestep timestep 0 0005 ps simulation options full length of simulation steps 2000 length of equilibration equilibration 1000 steps temperature scaling interval during equilibration scale 5 steps force capping option during equilibration cap 2000 KT A cutoffs long ranged interactions cutoff cut 7 6 A short ranged interactions cutoff rvdw 4 6 A ewald summation parameters ewald sum 0 48 32 32 32 statistics controls 75 CCLRC Section 5 1 print controller for OUTPUT print 100 steps statistics averaging interval stack 100 deep statistics collection interval for STATIS stats 2000 steps rdf sampling option rdf 10 steps rdf print controller for OUTPUT and RDFDAT print rdf trajectory sampling controls for HISTORY start step step interval level of information trajectory 1 50 0 job time and permitted wind up time job time 36000 s close time 20 s finish 5 1 1 1 The CONTROL File Format The file is free formatted and not case sensitive Every line is treated as a command sentence record Commented records beginning with a and blank lines are not processed and may be added
166. lects for specific parallel platforms For DL_POLY 3 compilation in parallel mode Fortran 90 compiler and MPI implementation for the specific machine architecture are required in many if not most cases users or the administrators of these platforms will have to create their own keyword entry in the makefile due to the large variety of i software needed for compilation of DL_POLY 3 and ii installation paths on different platforms To facilitate the user with the construction of their own keyword entry examples are provided in the makefiles In the case when users use a makefile for DL_POLY_3 compilation in serial mode they will have to provide valid path to the Fortran 90 compiler on the specific platform 4 The makefile produces the executable version of the code which as a default will be named DLPOLY Y and located in the execute subdirectory 5 DL_POLY also has a Java GUI The files for this are stored in 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 17 6 To run the executable for the first time you require the files CONTROL FIELD and CON FIG and possibly TABLE if you have tabulated potentials and REFERENCE if defect detection is opted in These must be present in the directory from which the program is executed See Section 5 1 for the description of the input files 7 Executing the program w
167. led by the routines EXTERNAL_FIELD_APPLY_VV EX TERNAL_FIELD_APPLY_VV and EXTERNAL_FIELD_CORRECT Al Chapter 3 Integration Algorithms Scope of Chapter This chapter describes the integration algorithms coded into DL_POLY 3 42 CCLRC Section 3 1 3 1 Introduction As a default the DL _POLY 3 integration algorithms are based on the Velocity Verlet VV scheme which is both simple and time reversible 18 It generates trajectories in the microcanonical NVE ensemble in which the total energy kinetic plus potential 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 The VV algorithm has two stages VV1 and VV2 At the first stage it requires values of position r velocity v and force f at time t The first stage is to advance the velocities to t 1 2 At by integration of the force and then to advance the positions to a full step t At using the new half step velocities 1 VVI F t 1 A t v t At u t EE 3 1 2 2 m where m is the mass of a site and At is the timestep 1 r t At r t At v t 5M 3 2 2 FF Between the first and the second stage a recalculation of the force at time t At is required since the positions have changed f t f At 3 3 3 VV2 In the second st
168. lgorithm of Hockney and Eastwood 46 as implemented by various authors e g Pinches et al 8 and Rapaport 9 This requires that the cutoff applied to the interatomic potentials is relatively short ranged In DL_POLY_3 the link cell list is build by the routine LINK_CELL_PAIRS As with all DD algorithms there is a need for the processors to exchange halo data which in the context of link cells means sending the contents of the link cells at the boundaries of each domain to the neighbouring proces sors so that each may have all necessary information to compute the pair forces acting on the atoms belonging to its allotted domain This in DL_POLY 3 is handled by the SET_HALO_PARTICLES rou tine three body and four body Systems containing complex molecules present several difficulties They often contain ionic species which usually require Ewald summation methods 18 47 and intra molecular interactions in addition to inter molecular forces Intramolecular interactions are handled in the same way as in DL_POLY_2 where each processor is allocated a subset of in tramolecular bonds to deal with The allocation in this case is based on the atoms present in the processor s domain The SHAKE and RATTLE algorithms 40 19 require significant modification Each processor must deal with the constraint bonds present in its own domain but it must also deal with bonds it effectively shares with its neighbouring processors This requires each processo
169. lp determine a working 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 The surface in a system with charges can also be modelled with DL_POLY 3 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 1 2 or 3 131 Appendix B DL POLY 3 Macros Introduction Macros are simple executable files containing standard unix commands A number of the are supplied with DL_POLY_3 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 noindent 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 Java GUI 17 cleanup cleanup removes several standard data files from the execute sub directory It contains the unix commands rm OUTPUT REVCON REVOLD STATIS REVIVE DEFECTS gopoly and removes the files OUTPUT REVCON REVOLD STATIS REVIVE DEFECTS and gopoly all variants It is useful for cleaning the sub directory up after a run Useful data should be stored elsewhere however copy copy invokes the unix commands 132 CCLRC Appendix B mv CONFIG CONFIG OLD mv REVCON CONFIG mv REVIVE REVOLD which
170. ls ic 444 244 e642 a pee kG bes a 91 Chemical Bond Potentials 0 2 4 4 05545 48 e Re ee ES 92 Valence Angle Potentials 0 2 0 0 0 ee ee 93 Dihedral Angle Potentials 22 u wati avi s Sek po a a ee i aa 94 Inversion Angle Potentials LL 95 Pair Potentials 02 0s 645 a a Bae a EEE e a a Ea a E A 96 Metal Potential o o sai p d eidoh aeaii 220444 0844 O aai B a a 97 Tersott Potential s sacs pugni i ea u arat e aa ara a a Yee a ER aa ee a 98 Three body Potentials sos e sosoo moa 446 85464 k dd a A 99 Four body Potentials 04 ii EEA a A AA AA 100 Extertial Fields Li es ea dad ne e ee ee Ds aes 101 List of Figures 5 1 DL_POLY 3 input left and output right files Note files marked with an asterisk are DONADAS xi Chapter 1 Introduction Scope of Chapter This chapter describes the concept design and directory structure of DL_POLY_3 and how to obtain a copy of the source code CCLRC Section 1 2 1 1 The DL POLY Package DL_POLY 1 is a package of subroutines programs and data files designed to facilitate molecular dynamics simulations of macromolecules polymers ionic systems and solutions on a distributed memory parallel computer It is available in two forms DL _POLY 2 written by Bill Smith and Tim Forester and DL_POLY_3 written by Bill Smith and Ilian Todorov 2 Both versions were originally written on behalf of CCP5 the UK s Collaborative Computational Project on Molecular Simulation which h
171. ly for a using equation 4 2 to give the first guess The relative error in the reciprocal space term is approximately es exPl Kirar 400 Kina 4 4 where ds T ax koar 4 5 AE 4 5 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 1075 this means using kmar 6 2 a kmax is then kmax gt 6 4 L Teut 4 6 71 CCLRC Section 4 4 In a cubic system rent L 2 implies kmax 14 In practice the above equation slightly over estimates the value of kmax required so optimal values need to be found experimentally In the above example kmax 10 or 12 would be adequate 4 4 DL_POLY_3 Warning and Error Processing 4 4 1 The DL_POLY 3 Internal Warning Facility DL_POLY_3 contains a number of various in built checks scattered throughout the package which detect a range of possible inconsistencies or errors In all cases such a check fails the subroutine WARNING is called resulting in an appropriate message that identifies the inconsistency In some cases an inconsistency is resolved by DL_POLY 3 supplying a default value or DL_POLY 3 assuming a priority of one directive over the another in clash of mutually exclusive directives However in other cases this cannot be done and controlled termination of the program execution is called by the subroutine ERROR In any case appropriate diagnostic message is displayed
172. ly non equilibrium simulations Alterna tively increase mxbuff in SET_BOUNDS recompile and resubmit Send the problem to us if this is persistent Correct the erroneous entry in FIELD and resubmit Message 39 error density array exceeded in metal ld export This should never happen Action You might consider using densvar option in CONTROL Send the problem to us if this is persistent Message 40 error too many bond constraints specified This should never happen Action Recompile the program or recreate the FIELD file If neither of these works send the problem to us Message 41 error too many bond constraints per domain DL POLY 3 sets a limit on the number of bond constraints in the simulated system as a whole This number is a function of the total number of constraint bonds in the system and by the number of processing nodes Termination results if this number is exceeded Action Increase mxcons in SET_BOUNDS recompile and resubmit 160 CCLRC Appendix D Message 42 error undefined direction passed to deport_atomic_data This should never happen Action Send the problem to us Message 43 error deport_atomic data outgoing transfer buffer exceeded This may happen in extremely non equilibrium simulations or usually when the potential in use do not hold the system stable Action Consider using densvar option in CONTROL for extremely non equilibrium simulations Alterna tively inc
173. mans 29 with fixed constants a f ryck U A a b cos cos d cos e cos f cos 2 35 6 Fluorinated Ryckaert Bellemans 30 with fixed constants a h rbf U A a b cos c cos d cos e cos f cos g exp h 7 2 36 18 CCLRC Section 2 2 7 OPLS torsion potential opls U d Ao A 1 cos Ag 1 cos 2 Az 1 cos 4 2 37 In these formulae ijkn is the dihedral angle defined by Pijkn COS Br ij Eta gt 2 38 with 2 39 Lij X Lik Tjk X Tkn B rijs Tjk Tkn i dd 2 z rij x tal X l knl With this definition the sign of the dihedral angle is positive if the vector product rij x Tip x Dir X rn 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 o f o Qijkn gt 2 40 with being one of i j k n and a one of x y z This may be expanded into le 1 O O Brg U Piakn U Pijkn gpa P Cig Eje Pan 2 41 sin ijkn OPijken The derivative of the function B rij x kn is o 1 o gra P E Tiks Tkn Lug x Tjk a Wie Lij X Eje lLjr X tan Org cos Pijkn 1 le 9 1 le 2 42 2 ig Ea rg H Ter Pang eri jo 04 with org Ci X Ti Ca XL gm rij irsetizlo Sex den Cir Trnlal L de5 rip rigtirlo S
174. mation read from the traj directive in the CONTROL file see Section 5 1 1 The HISTORY file will be created only if the directive traj appears in the CONTROL file 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 users must change that themselfs and recompile 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 The HISTORY has the following structure record 1 header a72 file header record 2 keytrj integer trajectory key see Table 5 1 imcon integer periodic boundary key see Table 5 6 megatm integer number of atoms in simulation cell For timesteps greater than nstraj the HISTORY file is appended at intervals specified by the traj directive in the CONTROL file with the following information for each configuration record i timestep as the character string timestep nstep integer the current time step megatm integer number of atoms in simulation cell again keytrj integer trajectory key again imcon integer periodic boundary key again tstep real integration timestep ps time real elapsed simulation time ps record ii cell 1 real x component of a cell vector cell 2 real y componen
175. may qualify a particular directive by for example adding extra options Directives can appear in any order in the CONTROL file except for the finish directive which marks the end of the file Some of the directives are mandatory for example the timestep directive that defines 74 CCLRC Section 5 1 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 contradictory directives or invoke algorithms that do not work together By large DL_POLY 3 tries to sort out these difficulties and print helpful error messages but it does not claim to be foolproof Another common mistake is to specify more than once a directive that has no contradictory disabling altering or antagonistic directives then the one specified last will be used as a control directive for example densvar equil steps press mxshak tolnce 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 3 is being asked to do something that is physically reasonable It should also be remembered that the present capabilities 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 described in the following section Tit
176. me for both the VV and LFV couched algorithms 1 H t A exp ut 34 At H t 1 VELAS VO rr nl A0 At 3 89 It is worth noting DL _POLY 3 uses Taylor expansion truncated to the quadratic term to approxi mate exponentials of tensorial terms The conserved quantity is to within a constant the Gibbs free energy of the system Imass x t Pmass Trin n t z Post V t F 3 ko Text x s ds 3 90 Hnor Hyve where f is the system s degrees of freedom equation 3 11 The VV and LFV flavours of the non isotropic Nos Hoover barostat and thermostat are imple mented in the DL_POLY 3 routines NST_H1_vv and NST_H1_LFV respectively 3 5 4 Martyna Tuckerman Klein Barostat DL POLY 3 includes the Martyna Tuckerman Klein MTK interpretation of the VV flavoured Hoover algorithms 24 for isotropic and anisotropic cell fluctuations in which the equations of motion are slightly modified to those for the coupled Nos Hoover thermostat and barostat so that to exclude the use of Ry in the position scaling due to the barostat In this way they are proved to generate ensembles that conserve the phase space volume and thus have well defined conserved quantities even in presence of forces external to the system 44 which is not the case for Nos Hoover NPT and NoT ensembles The NPT and NoT versions of the MTK ensemble are implemented in the DL_POLY_3 routines NPT_M1_vv and NST_M1_vv VV flavour and NPT_M1_L
177. me of the two body potentials are read from the TABLE file Simulation at 1000 K using NVT Hoover ensemble with SPME Cubic periodic boundaries are in use System size is 69120 and 552960 ions respectively 7 1 4 Test Case 7 and 8 Gramicidin A molecules in Water These systems consist of 8 and 16 gramicidin A molecules in aqueous solution 32 096 and 256 768 water molecules with total number of atoms 99 120 and 792 960 respectively Simulation at 300 K using NPT Berendsen ensemble with SPME and SHAKE RATTLE algorithm for the constrained motion 7 1 5 Test Case 9 and 10 SiC with Tersoff Potentials These systems consist of 74 088 and 343 000 atoms respectively Simulation at 300 K using NPT Hoover ensemble with Tersoff forces and no electrostatics 127 CCLRC Section 7 2 7 1 6 Test Case 11 and 12 CuzAu with Metal Potentials These systems consist of 32 000 and 256 000 atoms respectively Simulation at 300 K using NVT Hoover ensemble with metal forces and no electrostatics 7 1 7 Test Case 13 and 14 lipid bilayer in water These systems consist of 12 428 and 111 852 atoms respectively Simulation at 300 K using NVT Berendsen ensemble with SPME and SHAKE RATTLE algorithm for the constrained motion 7 1 8 Test Case 15 and 16 relaxed and adiabatic shell model MgO These systems consist of 8 000 4 000 shells and 64 000 32 000 shells atoms respectively Simula tion at 3000 K using NPT Berendsen ensemble with SPME FIELD and CON
178. me than the VV one for the certain ensembles type of system constraints and ensemble dependent Usually LFV is faster than VV when bonds constraints are present in the system The relative performance between the LVF and VV integration per timestep is observed to vary in the limits LET t VV t VV t 7 15 However the VV algorithms treat bond constraints in more precise symplectic manner than the LFV ones and thus produce more accurate constraint dynamics Makefiles The user may compile the code selecting the appropriate Makefile cp Makefile_MPI Makefile for parallel execution MPI needed or cp Makefile_SRLx Makefile for serial execution no MPI needed Note that for serial compilation Use mpi_module has to be uncommented in comms_module f90 as well as in parallel_fft f90 if Makefile_SRL2 is used Makefile_SRL1 compiles the code with a memory bound SPME algorithm whereas Makefile_SRL2 with a speed bound one 193 CCLRC Appendix E If there is not an entry for the architecture the user wishes to compile the code for the user should advise with the administrator of the machine Needed for compilation are 1 a FORTRAN90 compliant compiler if the PATH to it is not passed to the DEFAULT ENVIRONMENT PATH then it MUST be supplied in Makefile 2 MPI libraries COMPILED for the architecture and the compiler to be used if the PATH to them is not passed to t
179. module gt allocate_bonds_arrays 188 CCLRC Appendix D Message 1015 error allocation failure in core_shell_ module gt allocate_core_shell_arrays Action See Message 1001 Message 1016 error allocation failure in statistics_module gt allocate_statitics_arrays Action See Message 1001 Message 1017 error allocation failure in tethers_module gt allocate_tethers_arrays Action See Message 1001 Message 1018 error allocation failure in constraints_module gt allocate_constraints_arrays Action See Message 1001 Message 1019 error allocation failure in external field module gt allocate_external_field_arrays Action See Message 1001 Message 1020 error allocation failure in dihedrals_module gt allocate_dihedrals_arrays Action See Message 1001 Message 1021 error allocation failure in inversions_module gt allocate_inversion_arrays Action See Message 1001 Message 1022 error allocation failure in vdw_module gt allocate_vdw_arrays Action See Message 1001 Message 1023 error allocation failure in metal_ module gt allocate_metal_arrays Action See Message 1001 189 CCLRC Appendix D Message 1024 error allocation failure in three_body_module gt allocate _three_body_arrays Action See Message 1001 Message 1025 error allocation failure in config_module gt
180. module files in the source directory KINDS_F90 COMMS_MODULE SETUP_MODULE DOMAINS_MODULE PARSE_MODULE SITE_MODULE CONFIG_MODULE VDW_MODULE METAL MODULE METAL MODULE TERSOFF_MODULE THREE_BODY_MODULE FOUR_BODY_MODULE CORE_SHELL_MODULE CONSTRAINTS_MODULE PMF_MODULE TETHERS_MODULE BONDS_MODULE ANGLES_MODULE DIHEDRALS_MODULE INVERSIONS_MODULE EXTERNAL_FIELD_MODULE STATISTICS_MODULE DEFECTS_MODULE e general files in the source directory WARNING ERROR NUMERIC_CONTAINER KINETIC_CONTAINER SPME_CONTAINER SCAN_FIELD SCAN_CONFIG SCAN _CONTROL SET_BOUNDS 121 CCLRC Section 6 2 READ_CONTROL VDW_GENERATE VDW_TABLE_READ METAL _GENERATE TERSOFF_GENERATE DIHEDRALS_14_CHECK READ FIELD READ_CONFIG TAG_LEGEND PASS_SHARED_UNITS COMPRESS_LEGEND BUILD_BOOK_INTRA BUILD_EXCL_INTRA SCALE_TEMPERATURE UPDATE_SHARED_UNITS CORE_SHELL_QUENCH CONSTRAINTS_TAGS CONSTRAINTS_QUENCH PMF_COMS PMF_TAGS PMF_VCOMS PMF_QUENCH SET_TEMPERATURE VDW_LRC METAL_LRC SYSTEM_INIT EXPORT_ATOMIC_DATA SET_HALO_PARTICLES LINK_CELL_PAIRS CORE_SHELL_ON_TOP O DEPORT_ATOMIC_DATA PMF_UNITS_SET COMPRESS_BOOK_INTRA RELOCATE_PARTICLES METAL_LD_COLLECT METAL _LD_EXPORT METAL_LD_SET_HALO METAL_LD_COMPUTE GPFA_WRAP PARALLEL_FFT EXCHANGE_GRID EWALD_SPME_FORCES METAL_FORCES VDW_FORCES EWALD_REAL_FORCES COUL_DDDP_FORCES COUL_CP_FORCES COUL_FSCP_FORCES COUL_RFP_FORCES RDF_COLLECT EWALD_EXCL_FORCES EWALD_FROZEN_FORCES TWO_BODY_FORCES TERSOFF_FORCES THREE_BODY_FORCES FOUR_BODY_F
181. mponents The atomic stress tensor is symmetric In DL _POLY 3 these forces are handled by the routine COUL_DDDP_FORCES 2 4 4 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 occurrence 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 3 is the implementation of Neumann based on charge charge interactions 34 In this model the total coulombic potential is given by 1 1 Bol U sala 2 139 e Trey 2 ans 23 35 CCLRC Section 2 4 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 1 _ 2 140 a 1 ane with e the dielectric constant outside the cavity The effective pair potential is therefore 1 1 Bor U ri dj J 2 141 rij Are ud ri 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 3 this is countered by subtracting the val
182. n in which the constrain and PMF stresses are calculated retrospectively to the forcefield stress 3 5 2 Berendsen Barostat With the Berendsen barostat the system is made to obey the equation of motion at the beginning of each step dP t Pex P t gt 3 66 where P is the instantaneous pressure and Tp is the barostat relaxation time constant Cell size variations In the isotropic implementation at each step the MD cell volume is scaled by a factor 7 and the coordinates and cell vectors by n 3 where n t 1 44 Foa P t 3 67 and is the isothermal compressibility of the system In practice 8 is a specified constant which DL_POLY_3 takes to be the isothermal compressibility of liquid water The exact value is not critical to the algorithm as it relies on the ratio 7p P Tp is a specified time constant for pressure fluctuations supplied by the user In the VV implementation equation 3 67 imposes an uniform scaling of all cell parameters and particle positions during VV1 No iterations are needed for the VV implementation of this algo rithm However when bond constraints are present in the system 3 iterations are needed in VV1 until satisfactory convergence of the constraint forces to conserve bond length is achieved Note also that the change in box size requires the RATTLE_VV1 algorithm to be called each iteration with the new cell vectors This algorithm is implemented in NPT_B1_vv In the LFV impleme
183. n output channel nfield 7 force field input channel nconf 10 configuration file input channel nstats 20 statistical data file output channel nhist 21 trajectory history file channel nrest 22 output channel accumulators restart dump file ntable 23 tabulated potentials file input channel nrdfdt 24 output channel for RDF data nzdfdt 25 output channel for Z density data file nrefdt 26 reference configuration input channel ndefdt 27 output channel for defects data file mxsite variable max number of molecular sites mxatyp variable max number of unique atomic types mxtmls variable max number of unique molecule types mxspl variable SPME FFT B spline order kmaxa variable SPME FFT array dimension a direction kmaxb variable SPME FFT array dimension b direction kmaxc variable SPME FFT array dimension c direction mxtshl variable max number of specified core shell unit types in system mxshl variable max number of core shell units per node mxtcon variable max number of specified bond constraints in system 124 CCLRC Section 6 2 mxcons mxtpmf 1 2 mxpmf mx1shp mxproc mxtteth mxteth mxpteth mxtbnd mxbond mxpbnd mxtang mxangl mxpang mxtdih mxdihd mxpdih mxtinv mxinv mxpinv mxexcl mxfix mxgrid mxrdf mxgrdf mxvdw mxpvdw mxmet mxpmet mxter mxpter mxtbp mx2tbp mxptbp mxfbp mx2fbp mxpfbp mxpfld mxstak mxnstk mxlist mxcell mxatms mxbuff variable variable variable variable variable variabl
184. n serial mode e communication module COMMS_MODULE MPI_MODULE The communication module defines MPI related parameters and develops MPI related func tions and subroutines such us initialisation and exit global sum maximum and minimum node ID and number of nodes It is dependent on KINDS_F90 and on MPI_MODULE if MPI is emulated for DL_POLY_3 compilation in serial mode The MPI_MODULE implements all MPI functional calls used in DL_POLY 3 e global parameters module SETUP_MODULE The global parameters module holds all important global variables and parameters see above It is dependent on KINDS_F90 e domains module DOMAINS_MODULE The domains module defines DD parameters and maps the available computer resources on a DD grid The module does not depend on previous modules but its mapping subroutine is dependent on KINDS_F90 and COMMS_MODULE e parse module PARSE_MODULE The parse module develops several methods used to deal with textual input get_line strip blanks lower_case get_word word_2 real Depending on the method dependencies on KINDS_F90 COMMS_MODULE SETUP_MODULE DOMAINS_MODULE are found 120 CCLRC Section 6 2 e site module SITE_MODULE The site module defines all site related arrays FIELD and is dependent on KINDS_F90 only However it also develops an allocation method that is dependent on SETUP_MODULE e configuration module CONFIG_MODULE The configuration module defines all configuration related
185. nce_export o defects_reference_set_halo o defects_link_cells o defects_write o statistics_collect o z_density_collect o system_revive o rdf_compute o z_density_compute o statistics_result o dl_poly o Define MPI SERIAL files FILES_SERIAL mpi_module f90 mpif h 149 CCLRC Appendix C Define Velocity Verlet files FILES_VV external_field_apply_vv f90 external_field_correct f90 pseudo_vv f90 zero_k_optimise_vv f90 constraints_shake_vv f90 pmf_shake_vv f90 constraints_rattle f90 pmf_rattle f90 nvt_h_sc1 f90 npt_h_scl f90 nst_h_scl f90 nve_1_vv f90 nvt_li_vv f90 nvt_el_vv f90 nvt_b1_vv f90 nvt_h1_vv f90 npt_b1_vv f90 npt_h1_vv f90 npt_m1_vv f90 nst_b1_vv f90 nst_h1_vv f90 nst_m1_vv f90 md_vv f90 Define LeapFrog Verlet files FILES_LFV external_field_apply_lfv f90 pseudo_1fv f90 zero_k_optimise_lfv f90 constraints_shake_lfv f90 pmf_shake_lfv f90 nve_1_lfv f90 nvt_11_1fv f90 nvt_el_1fv f90 nvt_b1_lfv f90 nvt_h1_1fv f90 npt_b1_1fv f90 npt_h1_1fv f90 npt_m1_1fv f90 nst_b1_1fv f90 nst_h1_1fv f90 nst_m1_1fv f90 md_1fv f90 Examine targets manually CC rrrrrrrrrrrrrrrrror ecc all echo echo You MUST specify a target machine echo echo Please examine Makefile for permissible targets echo echo If no target suits your system create your own echo using the generic target template provided in echo this Makefile at entry uknown_machine echo
186. ncounters 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 correct and resubmit Message 13 error molecule species not specified This error arises when DL_POLY_3 encounters non bonded force data in the FIELD file before 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 in the FIELD file and resubmit Message 14 error too many unique atom types specified This should never happen This error most likely arises when the FIELD file or and DL_POLY_3 executable are corrupted Action Recompile the program or recreate the FIELD file If neither of these works send the problem to us 156 CCLRC Appendix D Message 15 error duplicate vdw potential specified In processing the FIELD file DL_POLY 3 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 rectify and resubmit Message 16 error strange exit from FIELD file processing This should neve
187. nd pmf constraints The indices j and k n appearing in the intermolecular interactions non bonded terms indicate the atoms involved in the interaction There is normally a very large number of these and they are therefore specified globally according to the atom types involved rather than indices In DL_POLY_3 it is assumed that the pure two body terms arise from van der Waals interactions regarded as short ranged and electrostatic interactions coulombic also regarded as long ranged Long ranged forces require special techniques to evaluate accurately see Section 2 4 The metal forces are many body forces which are functionally presented in an expansion of many two body contributions and so evaluated in the two body routines In DL POLY 3 the three body terms are restricted to valence angle and H bond forms Throughout this chapter the description of the force field assumes the simulated system is de scribed as an assembly of atoms This is for convenience only and readers should understand that DL_POLY_3 does recognize molecular entities defined through constraint bonds These matters are discussed in greater detail in Section 3 2 2 2 The Intramolecular Potential Functions In this section we catalogue and describe the forms of potential function available in DL_POLY_3 The keywords required to select potential forms are given in brackets before each definition The derivations of the atomic forces virial and str
188. nd R t is stochastic force with zero mean that satisfies the fluctuation dissipation theorem R E R E 2 x mi kBT dij Sag lt t 3 21 where superscripts denote Cartesian indices subscripts particle indices kg is the Boltzmann con stant T the target temperature and m the particle s mass The effect of this algorithm is thermo stat the system on a local scale Particles that are too cold are given more energy by the noise term and particles that are too hot are slowed down by the friction Numerical instabilities which usually arise from inaccurate calculation of a local collision like process are thus efficiently kept under control and cannot propagate The generation of random forces is implemented in the routine LANGEVIN_FORCES The VV implementation the algorithm is tailored in a Langevin Impulse LI manner 42 1 VVI v t e v t 5 1 s 48 CCLRC Section 3 4 1 STATUE v t 3At e exp xAt u t 6 ES Zi A 3 22 1 exp yA Ar r t At r t xAt ut 6 AE Zy Ar where Z1 x At and Za At are joint Gaussian random variables of zero mean sampling from a bivariate Gaussian distribution 42 1 2 oa i dr Ey 3 23 Z 01 02 03 At o 931 Ro with 1 A 0 e XA geis 3 24 and R vectors of independent standard Gaussian random numbers of zero mean and unit variance easily related to the langevin random forces as def
189. nd b the correction for the potential energy is calculated via the integral Deo oq Nae s corr V on gas r U a r r dr 2 81 where Na N are the numbers of atoms of types a and b in the system V is the system volume and gav r and Uap r are the appropriate pair correlation function and pair potential respectively It is 26 CCLRC Section 2 3 usual to assume gap 7 1 for r gt rydw DL_POLY 3 sometimes makes the additional assumption that the repulsive part of the short ranged potential is negligible beyond fyaw The correction for the system virial is NaMy fe Wi 21 V i i dla 2 82 Tudw 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 3 the short ranged forces are calculated by the subroutine VDW_FORCES The long range corrections are calculated by routine VDW_LRC The calculation makes use of the Verlet neighbour list see above 2 3 2 Metal Potentials DL_POLY 3 includes density dependent potentials suitable for calculating the properties of metals The basic model is due to Finnis and Sinclair 32 as implemented by Sutton and Chen 10 11 12 The form of the potential is stch Ug E gt cgn 2 83 i lt j Tij where the local density pi is given by m a p 2 84 The Sutton Chen potential has the advantage that it is decomposable into pair contrib
190. nd requires no iterations The LFV implementation the Nos Hoover algorithm is iterative as an initial estimate of x t at full step is calculated using an unconstrained estimate of the velocity at full step v t 53 CCLRC Section 3 5 1 FF TO ft At 3 59 2 LFV The iterative part is as follows 1 1 i u t At u t At At mn O 7 1 r t At r Atu t 54 3 60 3 SHAKE 4 Full step velocity 1 1 1 v t lt 5 ol 5At ult 540 3 61 5 Thermostat dela e ne Apa e a 2 2 dmass 1 1 1 x 3 xe At x t 7 0 3 62 Several iterations are required to obtain self consistency In DL POLY 3 the number of iterations is set to 3 if no bond constraints are present If bond constraints are present an extra iteration is required due to the call to the SHAKE routine Note that the SHAKE corrections need only be applied during the first iteration as subsequent to this the velocities relative to the bond c o m velocity will be orthogonal to the bond vectors The velocity scaling imposed by the thermostat is isotropic so does not destroy this orthogonality The conserved quantity is derived from the extended Hamiltonian for the system which to within a constant is the Helmholtz free energy 2 2 t Hynvr Hyve oo f kp Text x s ds 3 63 where f is the system s degrees of freedom equation 3 11 The VV and LFV flavours of the Nos Hoover algorithm are implemented in the DL
191. nes how to optimise the accuracy of the Smoothed Particle Mesh Ewald sum parameters for a given simulation As a guide to beginners DL_POLY 3 will calculate reasonable parameters if the ewald precision directive is used in the CONTROL file see Section 5 1 1 A relative error see below of 107 is normally sufficient so the directive ewald precision 1d 6 70 CCLRC Section 4 3 will make DL_POLY 3 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 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 A 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 virial W 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 Section5 2 3 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 five varia
192. nfiguration energy e The Boltzmann factor kg is 0 831451115 E Kt such that T Exin kb represents the conversion from kinetic energy in internal units to temperature in Kelvin Note In the DL_POLY_3 OUTPUT file the print out of pressure is in units of kilo atmospheres at all times The unit of energy is either DL_POLY 3 units specified above or in other units specified by the user at run time The default is DL_POLY units 1 3 9 Error Messages All errors detected by DL_POLY 3 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 terminations 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_3 will sometimes print warning messages These indicate that the code has detected something that is unusual or inconsistent The detection is non fatal but the user should make sure that the warning does represent a harmless condition 1 4 The DL_POLY 3 Directory Structure The entire DL_POLY _3 package is stored in a Unix directory structure The topmost directory is named dl _poly_3 nn where nn is a generation number Beneath this directory are several sub directories named source utility data bench execute build public and java Briefly the content of each sub directory is as follows sub directory conte
193. nits a40 Unit of energy used for input and output The energy units on the units directive are described by additional keywords a eV for electron volts per mol b kcal for k calories per mol c kJ for k Joules per mol d internal for DL_POLY internal units 10 Joules per mol If no units keyword is entered DL_POLY internal units are assumed for both input and output The units directive only affects the input and output interfaces all internal calculations are handled using DL_POLY units System output energies are read in units per MD cell 5 1 3 2 2 Molecular details It is important for the user to understand that there is an or ganisational 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 of indices in which they appear in the CONFIG file Failure to adhere to this common sequence will be detected by DL_POLY_3 and result in premature termination of the job It is therefore essential to work from the CONFIG file 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 3 enters the molecular description envi ronment in which onl
194. notifying the user of the nature of the problem 4 4 2 The DL_POLY 3 Internal Error Facility DL_POLY_3 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 some additional processing In some case if the cause for error is considered to be mendable it is corrected and the subroutine WARNING results in an appropriate message Users intending to insert new error checks should ensure that all error checks are performed con currently on all nodes and that in circumstances where a different result may obtain on different nodes a call to the global status routine GCHECK 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 gcheck safe If not safe Call error 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 nessage_number is an integer which used to identify the appropriate message to be printed A full list of the DL_POLY 3 error messages and the appropria
195. npt_hi_lfv o npt_mi_lfv o nst_bi_lfv o nst_hi_lfv o nst_mi_lfv o A xscale o core_shell_kinetic o trajectory_write o defects_reference_read o defects_reference_export o defects_reference_set_halo o defects_link_cells o defects_write o statistics_collect o z_density_collect o system_revive o rdf_compute o z_density_compute o statistics_result o dl_poly o Define Velocity Verlet files FILES_VV external_field_apply_vv f90 external_field_correct f90 pseudo_vv f90 zero_k_optimise_vv f90 constraints_shake_vv f90 pmf_shake_vv f90 constraints_rattle f90 pmf_rattle f90 nvt_h_sc1 f90 npt_h_scl f90 nst_h_scl f90 nve_1_vv f90 nvt_li_vv f90 nvt_el_vv f90 nvt_b1_vv f90 nvt_h1_vv f90 npt_b1_vv f90 npt_hi_vv f90 npt_m1_vv f90 nst_b1_vv f90 nst_hi_vv f90 nst_m1_vv f90 md_vv f90 Define LeapFrog Verlet files FILES_LFV external_field_apply_lfv f90 pseudo_1fv f90 zero_k_optimise_lfv f90 constraints_shake_lfv f90 pmf_shake_lfv f90 nve_1_lfv f90 nvt_11_1fv f90 nvt_el_lfv f90 nvt_b1_lfv f90 nvt_h1_1fv f90 npt_b1_1fv f90 npt_h1_1fv f90 npt_m1_1fv f90 nst_b1_1fv f90 nst_h1_1fv f90 nst_m1_1fv f90 md_1fv f90 Examine targets manually f o o oooooooooooeeososoos oo o o o o all echo echo You MUST specify a target machine echo echo Please examine Makefile for permissible targets echo echo If no target suits your system create your own
196. ns 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 and NVT simulations this can only happen at the start of a simulation but in NPT and NoT 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 96 error incorrect atom totals in metal_ld_set_halo This should never happen Action Big trouble Report to authors Message 97 error cannot have tethered shells Shells in core shell units cannot be tethered The dynamical shell model was not designed to work in conjunction with tethered shells This error results if both are used in the same simulation Action Correct FIELD and resubmit Message 98 error incorrect atom assignments metal_ld_set_halo This should never happen Action Big trouble Report to authors Message 99 error cannot have constrained shells Shells in core shell units cannot be constrained 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 169 CCLRC Appendix D Action Correct FIELD and resubmit Message 100 error
197. nserve total momentum but not energy The VV and LFV flavours of the Berendsen algorithm are implemented in the DL_POLY 3 routines NVT_B1_VV and NVT_B1_LFV respectively 3 4 4 Nos Hoover Thermostat In the Nos Hoover algorithm 23 Newton s equations of motion are modified to read dr t a E ee 20 9 0 3 50 CCLRC Section 3 4 The friction coefficient x is controlled by the first order differential equation x t _ 2Exin t 20 3 51 dt mass where is the target thermostat energy equation 3 41 and mass 20 T 3 52 is the thermostat mass which depends on a specified time constant Ty for temperature fluctuations normally in the range 0 5 2 ps The VV implementation the algorithm takes place in symplectic manner as follows 1 Thermostat Note Exin t changes inside At 2Ekin t 20 x t 144 x t 4 mass 1 At e exp x t 40 E 3 53 1 1 At 2Egin t 20 x t At x t At 7 Tui 3 54 2 VVI 1 At f t u t At u t 5 E 1 r t At r t Ato t 54t 3 55 3 RATTLE_VV1 4 FF Ft At f t 3 56 5 VV2 i At f t At t u t At v t z ta a 3 57 6 RATTLE_VV2 7 Thermostat Note Exin t At changes inside 3 1 At 2Ekin t At 20 x t 74 x t 5AM n E 3 At v t At v t As exp x t At gt 3 58 3 At 2Ejin t At 2 KEAN e zas Ge ttan The algorithm is self consistent a
198. nstraints The constraint procedures i e SHAKE or RATTLE for both types of constraineds are applied iteratively in order bonds pmfs until con vergence of Wpmr reached The number of iteration cycles is limited by the same limit as for the constraint procedures 3 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 3 comes with four different thermostats Langevin 20 42 Evans Gaussian constraints 21 Berendsen 22 and Nos Hoover 23 Of these only the Nos Hoover algorithm generates trajectories in the canonical NVT ensemble Evans and Berendsen algorithms will produce properties that typically differ from canonical averages by O 1 N 18 as the Evans algorithm generates trajectories in the NVEgin ensemble The Langevin method does not generate any proper enesemble at all as it impose Brownian Dynamics or Stochastic Dynamics on the system 3 4 1 Langevin Thermostat The Langevin thermostat works by coupling every particle to a viscous background and a stochastic heath bath such that dr t dt v t w LOR pais cd where x is a constant user defined in units of ps friction parameter positive a
199. nt T algorithm Hoover 23 NPT_Bl_vv NPT_B1_LFV Constant T P algorithm Berendsen 22 NPT_H1_vv NPT_H1_LFV Constant T P algorithm Hoover 23 NPT_M1_VV NPT_M1_LFV Constant T P algorithm MTK 24 NST_B1_Vv NST_B1_LFV Constant T 0 algorithm Berendsen 22 NST_H1_vv NST_H1_LFV Constant To algorithm Hoover 23 NST_M1_vv NST_M1_LFV Constant T 0 algorithm MTK 24 44 CCLRC Section 3 2 3 2 Bond Constraints The SHAKE algorithm for bond constraints was devised by Ryckaert et al 40 and is widely used in molecular simulation It is a two stage algorithm based on the leapfrog Verlet integration scheme 18 In the first stage the LFV 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 a vu Gia l pij di a dij d O Zij Y 9 AP de di ij gt 3 13 where pij is the reduced mass of the two atoms connected by the bond dj and di are the original and intermediate bond vectors dj is the constrained bondlength and At is the Verlet integration time step It should be noted that this formula
200. ntation the inclusion of equation 3 67 is by an iterative schema with 4 3 if bond constraints are present iterations used to obtain self consistency in the v t This algorithm is implemented in NPT_B1_LFV 55 CCLRC Section 3 5 Cell size and shape variations The extension of the isotropic algorithm to anisotropic cell variations is straightforward A tensor 7 is defined by bAt Pext V t 1 a t t 1 3 68 10 1 E 3 68 where 1 is the identity matrix Then new cell vectors are given by H t At n t H t 3 69 The VV and LFV flavours of the non isotropic Berendsen barostat and thermostat are imple mented in the DL _POLY 3 routines NST_B1_vv and NST_B1_LFV respectively 3 5 3 The Hoover Barostat DL POLY 3 uses the Melchionna modification of the Hoover algorithm 43 in which the equations of motion involve a Nos Hoover thermostat and a barostat in the same spirit Additionally as shown in 44 a modification allowing for coupling between the thermostat and barostat is also introduced Cell size variation For isotropic fluctuations the equations of motion are dr u t n t r t Ro 6 0 ento d 2Eginlt 20 kg Text q 7 dmass mass 2 oT ey dat avo ZO O Pmass f A 3 kg Text Tp CVA BOVO where n is the barostat friction coefficient Ro t the system centre of mass at time t Qmass the thermostat mass Tr a specified time constant for temperature flu
201. ntered 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 specified 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 180 CCLRC Appendix D 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 3 are affected by this Action Locate the n m potential in the FIELD file and reverse the order of the exponents Resubmit the job Message 471 error rcut lt 2 rctbp maximum cutoff for three body potentials The cutoff for the pair interactions is smaller than twice that for the three body interactions This is a bookkeeping requirement for DL_POLY 3 Action Either use a smaller three body cutoff or a larger pair potential cutoff Message 472 error rcut lt 2 rcfbp maximum cutoff for four body potentials
202. nts source primary subroutines for the DL_POLY 8 package utility subroutines programs and example data for all utilities data example input and output files for DL_POLY_3 bench large test cases suitable for benchmarking execute the DL _POLY 3 run time directory build makefiles to assemble and compile DL_POLY 3 programs public directory of routines donated by DL_POLY 3 users java directory of Java and FORTRAN routines for the Java GUI A more detailed description of each sub directory follows CCLRC Section 1 4 1 4 1 The source Sub directory In this sub directory all the essential source code for DL_POLY 3 excluding the utility software is stored In keeping with the package concept of DL_POLY 3 it does not contain any complete programs these are assembled at compile time using an appropriate makefile The subroutines in this sub directory are documented in Chapter 6 1 4 2 The utility Sub directory This sub directory stores all the utility subroutines functions and programs in DL_POLY 3 to gether with examples of data The various routines in this sub directory are documented in the DL_POLY_2 Reference Manual Users who devise their own utilities are advised to store them in the utility sub directory 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 3 The examples of input data are copied into the execute sub directory when
203. o test the code in parallel execution They are not suitable for a single processor computer The files are stored in compressed format The test cases can be run by typing select n from the execute directory where n is the number of the test case The select macro will copy the appropriate CONTROL CONFIG and FIELD files to the erecute directory ready for execution The output file OUTPUT may be compared with the file supplied in the data directory The example output provided in the data directory were obtained on an IBM SP4 parallel system 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 7 1 1 Test Case 1 and 2 Sodium Chloride These are a 27 000 and 216 000 ion systems respectively with unit electric charges on sodium and chlorine Simulation at 500 K with a NVT Berendsen ensemble The SPME method is used to calculate the Coulombic interactions 7 1 2 Test Case 3 and 4 DPMC in Water These systems consist of 200 and 1 600 DMPC molecules in 9379 and 75032 water molecules respectively Simulation at 300 K using NVE ensemble with SPME and RATTLE algorithm for the constrained motion Total system size is 51737 and 413896 atoms respectively 7 1 3 Test Case 5 and 6 KNaSiz0O5 Potassium Sodium disilicate glass NaKSi205 using two and three body potentials So
204. ode requires only a FORTRAN 90 compiler and Message Passing Interface MPI to handle communications Compilation of DL_POLY 3 in serial mode is also possible requires only a FORTRAN 90 compiler 1 3 5 Version Control System CVS DL_POLY_3 was developed with the aid of the CVS version control system We strongly recommend that users of DL_POLY_3 adopt this system for local development of the code particularly where several users access the same source code For information on CVS please contact info cus request gnu org or visit the web site http www cyclic com CCLRC Section 1 3 1 3 6 Internal Documentation All subroutines are supplied with a header block of FORTRAN 90 comment records giving 1 A CVS revision number and associated data 2 The name of the author and or modifying author 3 The version number or date of production 4 A brief description of the function of the subroutine 5 A copyright statement Elsewhere FORTRAN 90 comment cards are used liberally 1 3 7 FORTRAN 90 Parameters and Arithmetic Precision All global parameters defined by the FORTRAN 90 parameter statements are specified in the module file SETUP_MODULE which is included at compilation time in all subroutines requiring the parameters All parameters specified in SETUP_MODULE are described by one or more comment cards One super global parameter is defined at compilation time in the KINDS_F90 module file specifying th
205. olecule contains no flexible chemical bonds See the note on the atomic indices appearing under the shell directive above angles n where n is the number of valence angle bonds in the molecule Each of the n records following contains angle key al potential key see Table 5 9 index 1 i integer first atomic site index index 2 j integer second atomic site index central site index 3 k integer third atomic site index variable 1 real potential parameter see Table 5 9 variable 2 real potential parameter see Table 5 9 variable 3 real potential parameter see Table 5 9 variable 4 real potential parameter see Table 5 9 The meaning of these variables is given in Table 5 9 This directive and associated data records need not be specified if the molecule contains no angular terms See the note on the atomic indices appearing under the shell directive above dihedrals n where n is the number of dihedral interactions present in the molecule Each of the following n records contains dihedral key al potential key see Table 5 10 index 1 i integer first atomic site index index 2 7 integer second atomic site index central site index 3 k integer third atomic site index 91 CCLRC Section 5 1 Table 5 8 Chemical Bond Potentials key potential type Variables 1 4 functional form harm Harmonic k ro U r 3 k rij ro hrm mors Morse Eo ro k U r Eo 1 exp k rij ro 1
206. om running DL_POLY 3 It is meant to be a human readable file destined for hardcopy output 5 2 3 1 Header Gives the DL_POLY _3 version number the number of processors in use the link cell algorithm in use 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 DL_POLY_ SET_BOUNDS and READ_CONTROL 5 2 3 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 READ_CONTROL 5 2 3 3 Force Field 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 READ_FIELD 5 2 3 4 System Specification Echoes system name periodic boundary specification the cell vectors and volume some initial estimates of long range corrections the energy and pressure if appropriate and degrees of freedom break down list This part of the file is written from the subroutines READ_CONFIG SYSTEM_INIT and SET_TEMPERATURE 5 2 3 5 Summary of the Initial Configuration This part of the file is written from the main subroutine DL_POLY_ It states the initial configuration of a maximum of 20 atoms in the system The configuration info
207. on 5 1 1 The DEFECTS file will be created only if the directive defe appears in the CONTROL file The DEFECTS file may 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 users must change that themselfs and recompile 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 The DEFECTS has the following structure record 1 header a72 file header For timesteps greater than nsdef the DEFECTS file is appended at intervals specified by the defe directive in the CONTROL file with the following information for each configuration record i timestep as the character string timestep nstep integer the current time step tstep real integration timestep ps time real elapsed simulation time ps 105 CCLRC Section 5 2 imcon integer periodic boundary key see Table 5 6 rdef real site interstitial cutoff A record ii defects aT the character string defects ndefs integer the total number of defects interstitials al3 the character string interstitials ni integer the total number of interstitials vacancies a9 the character string vacancies nv integer the total number of vacancies record iii cell 1
208. otentials 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 link cell method 33 The calculation of the forces virial and stress tensor described in the section on inversion angle potentials above DL_POLY_3 applies no long range corrections to the four body potentials The four body forces are calculated by the routine FOUR_BODY_FORCES 32 CCLRC Section 2 4 2 4 Long Ranged Electrostatic coulombic Potentials DL_POLY 3 incorporates several techniques for dealing with long ranged electrostatic potentials These are as follows 1 Direct Coulomb sum 2 Force shifted Coulomb sum 3 Coulomb sum with distance dependent dielectric 4 Reaction field 5 Smoothed Particle Mesh Ewald SPME All of these can be used in conjunction with the shell model technique used to account for ions polarisation The SPME technique is restricted to periodic systems only Users must exercise care when using pseudo periodic boundary conditions The other techniques can be used with either periodic or non periodic systems safely although in the case of the direct Coulomb sum there are likely to be problems with convergence DL POLY 3 will correctly handle the electrostatics of both molecular
209. outine BUILD_BOOK_INTRA This means that each processor does not have to handle every possible bond term to find those relevant to its domain Also this allocation is updated as atoms move from domain to domain i e during the relocation process that follows the integration of the equations of motion DL_POLY_3 routine RELOCATE_PARTICLES Thus the allocation of bonded terms is effectively dynamic chang ing in response to local changes 6 1 3 Distributing the Non bonded Terms DL_POLY 3 calculates the non bonded pair interactions using the link cell algorithm due to Hock ney and Eastwood 46 In this algorithm a relatively short ranged potential cutoff reut is assumed The simulation cell is logically divided into so called link cells which have a width not less than or equal to the cutoff distance It is easy to determine the identities of the atoms in each link cell When the pair interactions are calculated it is already known that atom pairs can only interact if they are in the same link cell or are in link cells that share a common face Thus using the link cell address of each atom interacting pairs are located easily and efficiently via the link list that identifies the atoms in each link cell So efficient is this process that the the link list can be recreated every time step at negligible cost For reasons partly historical the link list is used to construct a Verlet neighbour list 18 The Verlet list records the ind
210. p assuming an absence of rigid bonds This is stage 1 of the RATTLE_VV2 algorithm b The deviation of d uv d in each bond is used to calculate the corresponding constraint force that retrospectively corrects the bond velocities c After the correction 3 15 has been applied to all bonds every bond velocity is checked against the above condition If the largest deviation found exceeds the desired tolerance the correction calculation is repeated d NS Steps b and c are repeated until all bonds satisfy the convergence criterion this iteration constitutes stage 2 of the RATTLE _VV2 algorithm The parallel version of the RATTLE algorithm as implemented in DL_POLY 3 is derived from the RD SHAKE algorithm 7 although its implementation in the Domain Decomposition frame work requires no global merging operations and is consequently significantly more efficient The routine CONSTRAINTS_SHAKE is called to apply corrections to the atomic positions and the routine CONSTRAINTS_RATTLE to apply corrections to the atomic velocities of constrained particles It should be noted that the fully converged constraint forces G j make a contribution to the system virial and the stress tensor The contribution to be added to the atomic virial for each constrained bond is W d Gi 3 17 The contribution to be added to the atomic stress tensor for each constrained bond is given by ode 3 18 where a and indi
211. pecifies the executable name The default name for the executable is DLPOLY Y 3 BINROOT The BINROOT keyword specifies the directory in which the executable is to be stored The 199 default setting is execute 4 2 1 2 Modifying the DL_POLY_3 Makefiles 1 Changing the FORTRAN 90 compiler and MPI implementation To specify the FORTRAN 90 compiler in a target platform the user must type the full path to the executable in FC and all appropriate options as defined in the relevant FOR TRAN 90 manual and the path to the MPI implementation in FCFLAGS The same must be done for the the linker the path to the executable in LD and the appropriate options and the path to the MPI implementation in LDFLAGS 65 CCLRC Section 4 2 2 Adding new functionality To include a new subroutine in the code simply add subroutine o to the list of object names in the makefile OBJ ALL Note that there is a hierarchial order of adding file names in the OBJ_MOD list whereas such order does not exist in the OBJ_ALL list Therefore should dependence exist between routines listed in the OBJ_ALL list it must be explicitly declared in the makefile 4 2 1 3 Note on the DL POLY 3 Interpolation Scheme In DL_POLY _3 the some short range like contributions Van der Waals Sutton Chen real space Ewald summation to energy and force are evaluated by interpolation of tables constructed
212. polarasation Tether potentials o CON a dl A WwW Chemical bond potentials 10 Valence angle potentials 11 Dihedral angle and improper dihedral angle potentials 12 Inversion angle potentials 13 External fieldpotentiallexternal field potentials The parameters describing these potentials may be obtained for example from the GROMOS 14 Dreiding 15 or AMBER 16 forcefield which share functional forms It is relatively easy to adapt DL_POLY 3 to user specific force fields 1 2 3 Boundary Conditions DL_POLY_3 will accommodate the following boundary conditions 1 None e g isolated molecules in vacuo 2 Cubic periodic boundaries 3 Orthorhombic periodic boundaries 4 Parallelepiped periodic boundaries 5 Slab x y periodic z non periodic These are describe in detail in Appendix A Note that periodic boundary conditions PBC 1 and 5 above require careful consideration to enable efficient load balancing on a parallel computer CCLRC Section 1 3 1 2 4 Java Graphical User Interface The DL_POLY_3 Graphical User Interface GUI is the same as that for DL_POLY_2 which is written in the Java programming language from Sun Microsystems A major advantage of this is the free availability of the Java programming environment from Sun and also its portability across platforms The compiled GUI may be run without recompiling on any Java supported machine The GUI is an integral component of the DL_POLY suite and is
213. r to inform its neighbours whenever it updates the position of a shared atom during every SHAKE RATTLE_VV1 cycle for RATTLE_VV2 it is velocity that needs to be updated so that all rele vant processors may incorporate this update into its own iterations In the case of the DD strategy the SHAKE RATTLE algorithm is simpler than for the Replicated Data method of DL_POLY 2 where global updates of the atom positions merging and splicing are required 48 The absence of the merge requirement means that the DD tailored SHAKE and RATTLE are less communications dependent and thus more efficient particularly with large processor counts The DD strategy is applied to complex molecular systems as follows 115 CCLRC Section 6 1 1 Using the atomic coordinates r each processor calculates the forces acting between the atoms in its domain this requires additional information in the form of the halo data which must be passed from the neighbouring processors beforehand The forces are usually comprised of a All common forms of non bonded atom atom forces b Cc ro Atom atom site site coulombic forces Sutton Chen density dependent forces for metals 10 11 12 E Tersoff density dependent forces for hydro carbons 13 f 4 body inversion forces g i Chemical bond forces i 3 body valence angle and hydrogen bond forces O _ Aa lon core shell model polarisation forces
214. r happen It simply means that DL POLY_3 has ceased processing the FIELD data but has not reached the end of the file or encountered a close directive P robable cause corruption of the DL_POLY 3 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 notes on message 16 above Message 18 error duplicate three body potential specified DL_POLY 3 has encountered a repeat specification of a three body potential in the FIELD file Action Locate the duplicate entry remove and resubmit job Message 19 error duplicate four body potential specified A 4 body potential has been duplicated in the FIELD file Action Locate the duplicated four body potential remove and resubmit job Message 20 error too many molecule sites specified This should never happen This error most likely arises when the FIELD file or and DL POLY_3 executable are corrupted Action Recompile the program or recreate the FIELD file If neither of these works send the problem to us 157 CCLRC Appendix D 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 Ideall
215. range forces described above Note that DL_POLY_3 determines which shell model to use by the supplied shell weights If all shells have no mass the DL_POLY_3 will choose the relaxed If all shells have masses then DL POLY 3 will choose the dynamical Otherwise if some shells have masses and some do not DL_POLY_3 will terminate execution At any case DL_POLY 3 prints information about the choice and possible errors in OUTPUT see Section 5 2 3 2 6 External Fields In addition to the molecular force field DL_POLY 3 allows the use of an external force fieldpoten tiallexternal field Examples of fields available include 1 Electric field elec Fi Fi q E 2 161 2 Oscillating shear oshm F Acos 2n7 z L 2 162 3 Continuous shear shrx 1 12 A E 2 163 7 il gt 2 163 4 Gravitational field grav F F m H 2 164 5 Magnetic field magn F Fi qi vi x H 2 165 6 Containing sphere sphr F A Ro r r gt Reut 2 166 7 Repulsive wall zbnd F A z 2 12 gt Zo 2 167 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 Oscillating shear field should be used with orthorhombic cell geometry imcon 1 2 and Continuous shear field with slab cell geometry imcon 6 The user is advised to be careful with units In DL_POLY 3 external field forces are hand
216. rategy 2 4 is one of several ways to achieve parallelisation in MD Its name derives from the division of the simulated system into equi geometrical spatial blocks or domains each of which is allocated to a specific processor of a parallel computer l e the arrays defining the atomic coordinates r velocities v and forces f for all N atoms in the simulated system are divided in to sub arrays of approximate size N P where P is the number of processors and allocated to specific processors In DL_POLY_3 the domain allocation is handled by the routine DOMAINS_MODULE and the decision of approximate sizes of various bookkeeping arrays in SET_BOUNDS The division of the configuration data in this way is based on the location of the atoms in the simulation cell such a geometric allocation of system data is the hallmark of DD algorithms Note that in order for this strategy to work efficiently the simulated system must possess a reasonably uniform density so that each processor is allocated an equal portion of atom data as far as possible Through this approach the forces computation and integration of the equations of motion are shared reasonably equally between processors and to a large extent can be computed independently on each processor The method is conceptually simple though tricky to program and is particularly suited to large scale simulations where efficiency is highest The DD strategy underpinning DL_POLY 3 is based on the link cell a
217. rd User Response DL POLY 3 uses FORTRAN 90 dynamic array allocation to set the array sizes at run time This means that a single executable may be compiled to over all the likely uses of the code 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 3 retains 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 3 subroutine SET_BOUNDS 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_3 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 SCAN_CONFIG SCAN_FIELD SCAN_CONTROL you will need to insert a new line in SET_BOUNDS to redefine it after the relevant subroutine has been called Finally the code must be recompiled as in this case it will only be necessary to recompile SET_BOUNDS and not the whole code 154 CCLRC Appendix D The DL POLY 3 Error Messages Message 1 error word_2_real failure The semantics in some of the INPUT files is wrong DL POLY_3 has tried to read a number but the has found a word in non number format Action Loo
218. re shell units but this should should not amount to more than a few percent of the total kinetic energy 2 5 2 Relaxed Massless Shells The relaxed shell model is presented in 38 where shells have no mass and as such their motion is not governed by the usual Newtonian equation whereas their cores motion is Because of that shells respond instantaneously to the motion of the cores for any set of core positions the positions of the shells are such that the force on every shell is zero The energy is thus a minimum with respect to the shell positions This represents the physical fact that the system is always in the ground state with respect to the electronic degrees of freedom Relaxation of the shells is carried out at each time step and involves a search in the multidimensional space of shell configurations The search in DL_POLY 3 is based on the powerful conjugate gradients technique 39 in an adaptation as shown in 38 Each time step a few iterations 10 30 are needed to achieve convergence to zero net force In DL_POLY 3 the shell forces are handled by the routine CORE_SHELL_FORCES In case of the adiabatic shell model the kinetic energy is calculated by CORE_SHELL_KINETIC and temperature 40 CCLRC Section 2 6 scaling applied by routine CORE_SHELL_QUENCH In case of the relaxed shell model shell are relaxed to zero force by CORE_SHELL_RELAXED Either shell model can be used in conjunction with the methods for long
219. re 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 3 in the order 1 2 3 4 L a N C f D a C N f 1 2 3 4 1 2 3 4 The L and D enantiomers and defining vectors In DL_POLY_3 improper dihedral forces are handled by the routine DIHEDRALS_FORCES 2 2 7 Inversion Angle Potentials The inversion angle and associated vectors 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 21 CCLRC Section 2 2 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 the specification of four atomic positions The potential functions available in DL_POLY 3 are as follows 1 Harmonic harm U Gist 5 Gin do 2 50 2 Harmonic cosine
220. real force constant of core shell spring The spring potential is 1 with the force constant k entered in units of engunit A where engunit is the energy unit specified in the units directive Note that the atomic site indices referred to above are indices arising from numbering 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 constraints pmf bonds angles dihedrals inversions and teth entries described below DL_POLY _3 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 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 site index index 2 integer second atomic site 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 6 pmf b where b is the potential of mean force bondlength A There follows the definitions of two PMF units a pmf unit n1 where ni is the number of sites in the first unit The subsequent n1 records provide the site indices and weighting Each record contains
221. 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 iv cell 4 real x component of b cell vector cell 5 real y component of b cell vector cell 6 real z component of b cell vector record v 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 ni interstitials for the current timestep as each interstitial has the following data lines record a atmnam iatm record b XXX yyy ZZZ i atomic label from CONFIG atom index from CONFIG x coordinate y coordinate z coordinate This is followed by the nv vacancies for the current timestep as each vacancy has the following data lines record a atmnam iatm record b XXX yyy ZZZ v atomic label from REFERENCE atom index from REFERENCE x coordinate from REFERENCE y coordinate from REFERENCE z coordinate from REFERENCE 106 CCLRC Section 5 2 5 2 3 The OUTPUT File The job output consists of 7 sections Header Simulation control specifications Force field specifi cation System specification Summary of the initial configuration Simulation progress Sample of the final configuration Summary of statistical data and Radial distribution functions and Z density profile These sections are written by different subroutines at various stages of a job Creation of the OUTPUT file always results fr
222. rease mxbuff in SET_BOUNDS recompile and resubmit Message 44 error deport_atomic_data incoming transfer buffer exceeded Action See Message 43 Message 45 error too many atoms in CONFIG file This should never happen Action Recompile and resubmit Send the problem to us if this is persistent Message 46 error undefined direction passed to export_atomic data This should never happen Action Send the problem to us Message 47 error undefined direction passed to metal_ld_export This should never happen Action Send the problem to us Message 48 error transfer buffer too small in read_table Action Standard user response Increase mxbuff in SET_BOUNDS recompile and resubmit 161 CCLRC Appendix D Message 49 error frozen shell core shell unit specified The DL_POLY 3 option to freeze the location of an atom i e hold it permanently in one position is not permitted for the shells in core shell units Action Remove the frozen atom option from the FIELD file Consider using a non polarisable atom instead Message 50 error too many bond angles specified This should never happen This error most likely arises when the FIELD file or and DL_POLY 3 executable are corrupted Action Recompile the program or recreate the FIELD file If neither of these works send the problem to us Message 51 error too many bond angles per domain DL POLY 3 limits the number of valence angle poten
223. ressure due to it In practice the convergence of the Ewald sum is controlled by three variables the real space cutoff Tcut the convergence parameter a and the largest reciprocal space vector kmar used in the reciprocal 37 CCLRC Section 2 4 space sum These are discussed more fully in Section 4 3 5 DL_POLY _3 can provide estimates if requested see CONTROL file description 5 1 1 As its name implies the Smoothed Particle Mesh Ewald SPME method is a modification of the standard Ewald method DL_POLY_3 implements the SPME method of Essmann et al 36 Formally this method is capable of treating van der Waals forces also but in DL_POLY_3 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 36 1 Interpolation of the exp i k r terms given here for one dimension exp 2ri u k L b k M u exp 2ri k K 2 150 j de in which k is the integer index of th
224. rges to a constant No such convergence is achieved 181 CCLRC Appendix D Action See Message 515 Message 480 error pmf length gt minimum of all half cell widths The specified PMF length has exceeded the minimum of all half cell widths Action Specify shorter PMF length or increase MD cell dimensions Message 484 error only one potential of mean force permitted Only one potential of mean force is permitted in FIELD Action Correct the erroneous entries in FIELD Message 486 error only one of the pmf units is permitted to have frozen atoms Only one of the PMF units is permitted to have frozen atoms Action Correct the erroneous entries in FIELD Message 488 error too many pmf constraints per domain This should not happen Action Is the use of PMF constraints in your system physically sound Message 490 error local pmf constraint not found locally This should not happen Action Is your system physically sound is your system equilibrated Message 492 error a diameter of a pmf unit gt minimum of all half cell widths The diameter of a PMF unit has exceeded the minimum of all half cell widths Action Consider the physical concept you are trying to imply in the simulation Increase MD cell dimen sions Message 497 error pmf_quench failure Action 182 CCLRC Appendix D See Message 515 Message 498 error shake algorithm pmf shake failed to converge Action See
225. riction 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 380 error simulation temperature not specified or lt 1 K DL_POLY 3 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 3 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 3 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 Message 387 error system pressure not specified The target system pressure has not been specified in the CONTROL file Applies to NPT simula tions only Action Insert a press directive in the CONTROL file specifying the required system pressure Message 390 error npt nst ensemble requested in non periodic system A non periodic system has no defined volume hence the NPT algorithm cannot be applied 175 CCLRC Appendix D Action Either simulate the system with a periodic boundary or use another ensembl
226. rmation 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 5 2 3 6 Simulation Progress This part of the file is written by the DL_POLY 3 root segment DL_POLY_ The header line is printed at the top of each page as 107 CCLRC Section 5 2 step eng_tot temp_tot eng_cfg eng_src eng_cou eng_bnd eng_ang eng_dih eng_tet time ps eng_pv temp_rot vir_cfg vir_src vir_cou vir_bnd vir_ang vir_con vir_tet cpu s volume temp_shl eng_shl vir_shl alpha beta gamma vir_pmf press The labels refer to line 1 step eng_tot temp_tot eng_cfg eng_src eng_cou eng_bnd eng_ang eng_dih eng_tet line 2 time ps eng_pv temp_rot vir_cfg vir_src vir_cou vir_bnd vir_ang vir_con vir_tet line 3 cpu s volume temp_shl eng_shl vir_shl alpha beta gamma vir_pmf press MD step number total internal energy of the system system temperature configurational energy of the system configurational energy due to short range potential contributions configurational energy due to electrostatic potential configurational energy due to chemical bond potentials configurational energy due to valence angle and three body potentials configurational energy due to dihedral inversion and four body potentials configurational energy due to tethering potentials elapsed simulation time ps since the beginning of the
227. rom the rest of the system thus em ulating an infinite like environment surrounding the MD cell The thermostat width matters as the more violent the events on the inside of the MD cell the bigger width may be needed in order to ensure safe dissipation of the excess kinetic energy Note that embedding a thermostat in the MD cell walls is bound to produce wrong ensem ble averages and instantaneous pressure and stress build ups at the thermostat boundary 81 CCLRC Section 5 1 10 11 12 13 Therefore ensembles lose their meaning as such and so does the conserved quantity for true ensembles The algorithm is developed in the DL_POLY 3 routines PSEUDO_VV and PSEUDO_LFV respec tively The defects option will trigger reading of REFERENCE see Section 5 1 4 which defines a reference MD cell with particles positions defining the crystalline lattice sites If REFER ENCE is not found the simulation will either i holt if the simulation has been restarted i e is a continuation of an old one the restart option is used in CONTROL and the REVOLD see Section 5 1 5 file has been provided or ii recover using CONFIG see Section 5 1 2 if it is a new simulation run i e restart option is not used in CONTROL or REVOLD has not been provided The actual defect detection is based on comparison of the simulated MD cell to the reference MD cell based on a user defined site interstitial cutoff 0 3 A lt Rae f 12 A
228. ructure 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 N4 where N is the number of particles makes it essential that these terms are calculated by the link cell method 33 The calculation of the forces virial and stress tensor as described in the section valence angle potentials above DL POLY 3 applies no long range corrections to the three body potentials The three body forces are calculated by the routine THREE_BODY_FORCES 2 3 5 Four Body Potentials The four body potentials in DL_POLY_3 are entirely inversion angle forms primarily included to permit simulation of amorphous materials particularly borate glasses The potential forms available in DL_POLY 3 are as follows 1 Harmonic harm k U ijkn 3 dijkn do 2 122 2 Harmonic cosine hcos k U Gijkn 5 COS Gijkn cos o 2 123 3 Planar potential plan U dijkn A 1 cos dizkn 2 124 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 p
229. s For example VDW_FORCES for the short range van der Waals forces Section 2 3 1 METAL_LD_COMPUTE and METAL_FORCES for the Sutton Chen metal interactions Section 2 3 2 and EWALD_SPME_FORCES EWALD_REAL_FORCES and EWALD_EXCL_FORCES for the Coulombic forces Section 2 4 Higher order intermolecular site related and intramolecular forces require the routines TERSOFF_FORCES THREE_BODY_FORCES FOUR_BODY_FORCES CORE_SHELL_FORCES or CORE_SHELL_RELAX TETHERS_FORCES BONDS_FORCES ANGLES_FORCES DIHEDRALS_FORCES and INVERSIONS_FORCES The routines EXTERNAL_FIELD_APPLY_VV and EXTERNAL_FIELD_CORRECT and EXTERNAL_FIELD_APPLY_LFV are required if the simulated system has an external force field e g electrostatic field operating To help with equilibration simulations routines such as CAP_FORCES and ZERO_K_OPTIMISE_VV and ZERO_K_OPTIMISE_LFV are sometimes required to reduce the magnitude of badly equilibrated forces Integration of the equations of motion is handled by one of the routines listed and described in Chapter 3 As mentioned elsewhere DL_POLY_3 does not contain many routines for computing system prop erties during a simulation Radial distributions may be calculated however by using the routines RDF_COLLECT and RDF_COMPUTE Similarly Z density distribution may be calculated by using the routines Z_DENSITY_COLLECT and Z_DENSITY_COMPUTE Ordinary thermodynamic quantities are calculated by the routine STATISTICS_COLLECT which
230. s cos Cosine Al m U 0 A 1 cos m 9 COS 10 is the i j k 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 In this case DL_POLY_3 will calculate the non bonded pair potentials between the described atoms 93 CCLRC Section 5 1 index 4 1 integer fourth atomic site index variable 1 real first potential parameter see Table 5 10 variable 2 real second potential parameter see Table 5 10 variable 3 real third potential parameter see Table 5 10 variable 4 real 1 4 electrostatic interaction scale factor variable 5 real 1 4 Van der Waals interaction scale factor variable 6 real fourth potential parameter see Table 5 10 variable 7 real fifth potential parameter see Table 5 10 The meaning of the variables 1 3 6 7 is given in Table 5 10 The variables 4 and 5 specify the scaling factor for the 1 4 electrostatic and Van der Waals non bonded 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 5 10 Dihedral Angle Potentials key potential type Variables 1 3 6 7 functional formi cos Cosine A m U A 1 cos m harm Harmonic k do U 6 do hcos Harmonic cosine k do U
231. s every n steps during equilibration with respect to the last equilibration step set shake rattle tolerance to f default f 1079 calculate electrostatic forces using force shifted Coulomb sum set rolling average stack to n timesteps accumulate statistics data every n timesteps run simulation for n timesteps set required simulation temperature to f Kelvin target temperature for constant temperature ensembles write HISTORY file with controls i start timestep for dumping configurations default i 0 j timestep interval between configurations default j 1 k data level default k 0 see Table 5 1 set timestep to f ps variable timestep start with timestep of f ps calculate and collect the Z density profile every f timesteps default f 1 perform zero temperature MD run reset required system temperature 10 Kelvin 78 CCLRC Section 5 1 Note that in some cases additional keywords shown in brackets may also be supplied in the directives or directives may be used in a long form However it is strongly recommended that the user uses only the bold part of these directives Table 5 1 Internal Trajectory Defects File Key keytrj meaning 0 coordinates only in file 1 coordinates and velocities in file 2 coordinates velocities and forces in file 5 1 1 3 Further Comments on the CONTROL File 1 A number of the directives or their mutually exclusive alternatives are
232. s is the local atom list 3 Every processor also maintains a sorted in ascending order local list of global atom indices of the atoms in its domain This is the local sorted atom list 116 CCLRC Section 6 1 4 Every intramolecular bonded term Ujype in the system has a unique index number sqpe from 1 to Nyype where type represents a bond angle dihedral or inversion Also attached there with unique index numbers are core shell units bond constraint units pmf constraint units and tethered atoms their definition by site rather than by chemical type 5 On each processor a pointer array keytype Ntype itype carries the indices of the specific atoms involved in the potential term labelled itype The dimension nyype will be 1 if the term represents a tether 1 2 for a core shell unit or a bond constraint unit or a bond 1 2 3 for a valence angle and 1 2 3 4 for a dihedral or an inversion 1 pm funitio 2 1 for a pmf constraint unit 6 Using the key array each processor can identify the global indices of the atoms in the bond term and can use this in conjunction with the local sorted atoms list and a binary search algorithm to find the atoms in local atom list 7 Using the local atom identity the potential energy and force can be calculated Note that at the start of a simulation DL_POLY 3 allocates individual bonded interactions to spe cific processors based on the domains of the relevant atoms DL_POLY 3 r
233. s to an atom max number of grid points in potential arrays max number of pairwise RDF in system number of grid points for RDF and Z density max number of van der Waals potentials in system max number of van der Waals potential parameters 5 max number of metal potentials in system max number of metal potential parameters 5 max number of Tersoff potentials in system max number of Tersoff potential parameters 11 max number of three body potentials in system array dimension of three body potential parameters max number of three body potential parameters 4 max number of four body potentials in system array dimension of four body potential parameters max number of four body potential parameters 3 max number of external field parameters 5 dimension of stack arrays for rolling averages max number of stacked variables max number of atoms in the verlet list on a node max number of link cells per node max number of atoms per node max dimension of the principle transfer buffer 125 Chapter 7 Examples Scope of Chapter This chapter describes the standard test cases for DL_POLY 3 the input and output files for which are in the data sub directory 126 CCLRC Section 7 1 7 1 Test Cases The following example data sets both input and output are stored in the subdirectory data These are provided so that you may check that your version of DL_POLY_3 is working correctly All the jobs are of a size suitable t
234. s use the directive timesteps 15000 in the CONTROL file and include the restart directive You can use the restart scale directive if you want to reset the temperature at the restart or restart noscale directive if you want to keep the current kinetics intact but note that the latter makes no use of REVOLD and all internal accumulators are reset to zero If none of the restart options is specified velocities are generated anew with Gaussian distribution of the target kinetic energy based on the provided temperature in the CONTROL file 4 2 4 Notes on the DL_POLY 3 Simulation Efficiency and Performance Although the DL POLY 3 underlining parallelisation strategy DD and link cells see Section 6 1 1 is extremely efficient it cannot always provide linear parallelisation speed gain with increasing pro 67 CCLRC Section 4 3 cessor count for a fixed size system Nevertheless it will always provide speedup of the simulation i e there still is a sufficient speed gain in simulations when the number of nodes used in parallel is increased The simplest explanation why this is is that increasing the processor count for a fixed size system decreases not only the work and memory load per processor but also the ratio size of domain to size of halo both in counts of link cells When this ratio falls down to values close to one and below the time DL_POLY_3 spends on inevitable communication MPI messages across neighbouring domains to refresh th
235. se interactions have similar terms to some intramolecular ones three body to the bond angle and four body to inversion angle these are not dealt with in the same way as the normal bonded interactions They are generally very short ranged and are most effectively calculated using a link cell scheme 46 No reference is made to the Verlet neighbour list nor the excluded atoms list It follows that atoms involved these interactions can interact via non bonded pair forces and ionic forces also Note that contributions from frozen pairs of atoms to these potentials are excluded The calculation of the Tersoff three body and four body terms is distributed over processors on the basis of the domain of the central atom in them DL _POLY 3 implements these potentials in the following routines TERSOFF_FORCES TERSOFF_GENERATE THREE_BODY_FORCES and FOUR_BODY_FORCES 6 1 7 Globally Summed Properties The final stage in the DD strategy is the global summation of different by terms of potentials contributions to energy virial and sterss which must be obtained as a global sum of the contributing terms calculated on all nodes The DD strategy does not require a global summation of the forces unlike the Replicated Data method used in DL_POLY_2 which limits communication overheads and provides smooth paral lelisation to large processor counts 6 1 8 The Parallel DD tailored SHAKE and RATTLE Algorithms The essentials of the DD tailored SHAKE and RATT
236. so the Fuchs correction 35 for electrically non neutral MD cells is applied if needed 2 5 Polarisation Shell Models An atom or ion is polarisable if it develops a dipole moment when placed in an electric field It is commonly expressed by the equation p aE 2 158 where y is the induced dipole and E is the electric field The constant a is the polarisability 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 different electric charges the sum of which equals the charge on the original atom There is no 39 CCLRC Section 2 5 electrostatic interaction i e self interaction between the core and shell of the same atom Non coulombic interactions arise from the shell alone 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 293 92 k 2 159 where gs and q are the shell and core charges and k is the force constant of the harmonic spring 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 kine
237. stantaneous kinetic energy for example can then be obtained from the atomic velocities as N 1 Erin t 53 _mivi t 3 9 1 and assuming the system has no net momentum the instantaneous temperature is 2 T t Exin t 3 10 kgf where i labels particles N the number of particles in the system kg the Boltzmann s constant and f the number of degrees of freedom in the system f 3N 3 3N Frozen 3Nshells sa N constraints p 3 11 Here N frozen indicates the number of frozen atoms in the system Nshelts number of core shell units and Neonstraints number of bond and pmf constraints Three degrees of freedom are subtracted for the centre of mass zero net momentum we impose and p is zero for periodic or three for non periodic systems The routines NVE_1_vv and NVE_1_LFV implement the Verlet algorithm in velocity and leapfrog flavours respectively and calculate the instantaneous temperature The conserved quantity is the total energy of the system Hyve U Ekin where U is the potential energy of the system and Ekin the kinetic energy at time t 3 12 The full selection of integration algorithms indicating both VV and LFV cast integration within DL_POLY 3 is as follows NVE_1_VV NVE_1_LFV Constant E algorithm NVT_L1_VV NVT_L1_LFV Constant T algorithm Langevin 20 NVT_El_vv NVT_El_LFV Constant Ekin algorithm Evans 21 NVT_B1_VV NVT_B1_LFV Constant T algorithm Berendsen 22 NVT_H1_VV NVT_H1_LFV Consta
238. suming 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 3 13 that retrospectively corrects the bond length 3 After the correction 3 13 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 iteration constitutes stage 2 of the SHAKE algorithm The RATTLE procedures may be summarised as follows 1 RATTLE stage 1 a AIl atoms in the system are moved using the VV algorithm assuming an absence of rigid bonds constraint forces This is stage 1 of the RATTLE_VVI algorithm b The deviation in each bondlength is used to calculate the corresponding constraint force 3 14 that retrospectively corrects the bond length c After the correction 3 14 has been applied to all bonds every bondlength is checked If the largest deviation found exceeds the desired tolerance the correction calculation is repeated 46 CCLRC Section 3 3 d Steps b and c are repeated until all bondlengths satisfy the convergence criterion this iteration constitutes stage 2 of the RATTLE_VVI algorithm 2 Forces calculated afresh 3 RATTLE stage 2 a All atom velocities are updated to a full ste
239. system and by the number of processing nodes Termination results if this number is exceeded Action Increase mxbond in SET_BOUNDS recompile and resubmit Message 32 error coincidence of particles in core shell unit DL_POLY_3 has found a fault in the definition of a core shell unit in the FIELD file The same particle has been assigned to the core and shell sites Action Correct the erroneous entry in FIELD and resubmit Message 33 error coincidence of particles in constraint bond unit DL_POLY_3 has found a fault in the definition of a constraint bond unit in the FIELD file The same particle has been assigned to the both sites Action Correct the erroneous entry in FIELD and resubmit 159 CCLRC Appendix D Message 34 error length of constraint bond unit gt real space cutoff rcut DL_POLY 3 has found a constraint bond unit length FIELD larger than the real space cutoff rcut CONTROL Action Increase cutoff in CONTROL or decrease the constraint bondlength in FIELD and resubmit For small system consider using DL_POLY 2 Message 35 error coincidence of particles in chemical bond unit DL_POLY 3 has found a faulty chemical bond in FIELD defined between the same particle Action Correct the erroneous entry in FIELD and resubmit Message 38 error transfer array exceeded in metal ld export This should never happen Action Consider using densvar option in CONTROL for extreme
240. t vikan VE ane 40 At 3 75 V t At V t us 1 a le Rolt At ult At Bolt 5 RATTLE_VV1 6 FF f t At f t 3 76 57 CCLRC Section 3 5 7 VV2 v t At v t 3 77 At f t 2 m 8 RATTLE_VV2 9 Thermostat Note 2E n t changes inside At 2Ekin t At Pmass n t 5 At 20 kp Text 8 dmass 5 1 x t At x t At u t At At exp x t 4 At 3 78 At 2Ekin t At Pmass M t 3A8 20 kg Text 8 dmass 3 5 x At x t At 10 Barostat Note Exin t At and P t At have changed and change inside 1 3 At n t 4 5 At nt 5 At exp x t 4 JA AOL A HO ADA At 3 P t At Pext V t At i 2 4 Pmass 3 3a At n t 74 qe 74 exp x t 4 At _ 3 At u At ott A exp n TAN 5 3 79 2 3 3 At n t 1 t 1 exp x t 4 TONO i n t At n t4 7 At 4 n 3 P t At Pea V t At Pmass 11 Thermostat Note Exin t At has changed and changes inside At 2Ekin t At Pmass n t At 20 kB Text 7 3 x t At x t At 8 Imass 7 At RAD CO exp x t 346 T 3 80 7 At 2Exin t At mass Nt At 20 kg Tox x t At x t 74 3 kint At p Ni aD o de DE u t At v t4 At Vo t At whereVo t At is the c o m velocity at timestep t At and H is the cell matrix whose columns
241. t 2 11 with only one such contribution from each bond The contribution to be added to the atomic stress tensor is given by Pref 2 12 where a and 8 indicate the x y z components The atomic stress tensor derived in this way is symmetric In DL_POLY_3 bond forces are handled by the routine BONDS_FORCES Note some DL_POLY_3 routines may use the convention that Tij r f 14 CCLRC Section 2 2 2 2 2 Distance Restraints In DL_POLY_3 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 avaliable as distance restraints although they have different key words 1 Harmonic potential hrm 2 Morse potential mrs 3 12 6 potential bond 126 4 Restrained harmonic rhm 5 Quartic potential qur 6 Buckingham potential bck 7 Coulomb potential cul In DL_POLY 3 distance restraints are handled by the routine BONDS_FORCES 2 2 3 Valence Angle Potentials The valence angle and associated vectors The valence angle potentials describe the bond bending terms betwe
242. t by cutoff It applies to the real space part of the electro statics calculations and to the van der Waals potentials if no other cutoff is applied b rvaw the user specified cutoff for the van der Waals potentials set by rvdw If not specified its value defaults to freut Constraint algorithms in DL_POLY 3 SHAKE RATTLE see Section 3 2 use default iter ation precision of 1078 and limit of iteration cycles of 250 Users may experience that during optimisation of a new built system containing constraints simulation may fail prematurely since a constraint algorithm failed to converge In such cases directives mxshak to increase and shake to decrease may be used to decrease the strain in the system and stablise the simulation numerics until equilibration is achieved DL_POLY 3 s DD strategy assumes that the global density of a system does not vary much during a simulation which is not the case in extremely non equilibrium simulations or some specific systems A way to tackle such circumstances and avoid simulations crash is to use the densvar f option In the SET_BOUNDS subroutine DL_POLY 3 makes assumptions at the beginning of the simulation and corrects the lengths of link cell mxlist and domain mxatms lists arrays when the option is activated with f gt 0 Greater values of f will correspond to allocation bigger global arrays and larger memory consumption by DL_POLY 3 during the simulation Note that this option may demand more m
243. t exist or is too complicated to specify in the VDW_GENERATE subroutine The table file is read by the subroutine READ_TABLE see Chapter 6 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 5 12 5 1 6 1 The TABLE File Format The file is free formatted but blank and commented lines are not allowed 5 1 6 2 Definitions of Variables record 1 102 CCLRC Section 5 2 header al00 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 data 4 real data item 4 5 1 6 3 Further Comments It should be noted that the number of grid points in the TABLE file sho
244. t of a cell vector cell 3 real z component of a cell vector record iii cell 4 real x component of b cell vector cell 5 real y component of b cell vector cell 6 real z component of b cell vector record iv 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 104 CCLRC Section 5 2 record a atmnam a8 atomic label iatm integer atom index weight real atomic mass a m u charge real atomic charge e rsd real displacement from position at t 0 A record b XXX real x coordinate yyy real y coordinate ZZZ real z coordinate record c only for keytrj gt 0 VXX real x component of velocity vyy real y component of velocity VZZ real z component of velocity record d only for keytrj gt 1 fxx real x component of force fyy real y component of force fzz real z component of force Thus the data for each atom is a minimum of two records and a maximum of 4 5 2 2 The DEFECTS File The DEFECTS file is the dump file of atomic coordinates of defects see Section 5 1 4 Its principal use is for off line analysis The file is written by the subroutine DEFECTS_WRITE The control variables for this file are ldef nsdef isdef and rdef which are created internally based on information read from the defe directive in the CONTROL file see Secti
245. t or absent CONFIG file but it may be due to the FIELD file being incompatible in some way with the CONFIG file Action Check contents of CONFIG file If you are convinced it is correct check the FIELD file for inconsistencies Message 56 error atomic coordinate array exceeded in export_atomic_data This may happen in extremely non equilibrium simulations or usually when the potential in use do not hold the system stable Action Consider using densvar option in CONTROL for extremely non equilibrium simulations Alterna tively increase mxatms in SET_BOUNDS recompile and resubmit Message 57 error too many core shell units specified This should never happen Action Recompile the program or recreate the FIELD file If neither of these works send the problem to us Message 58 error number of atoms in system not conserved An atom has been lost in transfer between nodes This should never happen Action Big trouble Report problem to authors immediately Message 59 error too many core shell units per domain DL_POLY 3 limits the number of core shell units in the system to be simulated actually the number to be processed by each node and checks for the violation of this Termination will result if the condition is violated Action Increase the parameter mxshl in SET_BOUNDS recompile and resubmit Message 60 error too many dihedral angles specified This should never happen 163 CCLRC Appendi
246. te user action can be found in Appendix D of this document 72 Chapter 5 Data Files Scope of Chapter This chapter describes all the input and output files for DL_POLY 3 examples of which are to be found in the data sub directory 73 CCLRC Section 5 1 5 1 The INPUT Files REVCON OUTPUT HISTORY DEFECTS STATIS RDFDAT ZDNDAT REVIVE Figure 5 1 DL_POLY 3 input left and output right files Note files marked with an asterisk are non mandatory DL_POLY 3 requires six input files named CONTROL CONFIG FIELD TABLE REFERENCE and REVOLD The first three files are mandatory whereas TABLE is used only to input certain kinds of pair potentials and is not always required REFERENCE is required only if defect detec tion is switched on in CONTROL 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 5 1 1 The CONTROL File The CONTROL file is read by the subroutine READ_CONTROL and defines the control variables for running a DL POLY 3 job It is also read by the subroutine SCAN CONTROL in the SET_BOUNDS routine It makes extensive use of directives and keywords Directives are 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
247. ternative to DL_POLY_3 when simulations are likely to be serial jobs or and for systems containing lt 5000 particles For such systems with both codes compiled in serial modes DL_POLY_2 WILL outperform DL_POLY_3 by a factor of X Where X depends 192 CCLRC Appendix E strongly on the system size from 3 1 for a 1000 atom system to 1 4 for 5000 atom system and weakly on the system force field complexity in favour of DL_POLY_3 Integration Defaults The default ensemble is NVE The default integration scheme is Trotter derived Velocity Verlet VV although Leapfrog Verlet LFV is also available VV is considered superior to LFV since 1 integration can be developed in symplectic manner for certain ensembles such as NVE NVEk NVT Evans as well as all Nose Hoover ensembles NVT amp NPT amp NsT when there is no external field applied on the system otherwise they do not conserve the phase space volume and MTK ensembles NPT amp NsT 2 all ensemble variables are updated synchronously and thermodynamic quantities and estimators are exact at the every step whereas in LFV particle velocities and thermostat and barostat friction velocities are half an integration time step behind the rest of the ensemble variables and due to this certain estimators are approximated at full timestep 3 it offers better numerical stability and faster convergence in iteration algorithms The LFV integration may take less cpu ti
248. the dynamics of the system 4 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 is submitted The close time directive represents the time DL_POLY 3 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 3 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 3 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 increasing simulation system size 79 CCLRC Section 5 1 5 The starting options for a simulation are governed by the keyword 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 a new simulation without initia
249. tials in the system to be simulated actually the number to be processed by each node and checks for the violation of this Termination will result if the condition is violated Action Increase the parameter mxangl in SET_BOUNDS recompile and resubmit Message 52 error end of FIELD file encountered This message results when DL_POLY_3 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 correct and resubmit Message 53 error end of CONTROL file encountered This message results when DL_POLY 3 reaches the end of the CONTROL file without having read all the data it expects Probable cause missing finish directive Action Check CONTROL file correct and resubmit Message 54 error outgoing transfer buffer exceeded in export_atomic data This may happen in extremely non equilibrium simulations or usually when the potential in use do not hold the system stable Action 162 CCLRC Appendix D Consider using densvar option in CONTROL for extremely non equilibrium simulations Alterna tively increase mxbuff in SET_BOUNDS recompile and resubmit Message 55 error end of CONFIG file encountered This error arises when DL_POLY_3 attempts to read more data from the CONFIG file than is actually present The probable cause is an incorrec
250. tic 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 as if the kinetic energy of these is regarded as zero 3 11 2 5 1 Dynamical Adiabatic Shells The dynamical shell model is a method of incorporating polarisability into a molecular dynamics simulation The method used in DL _POLY 3 is that devised by Fincham et al 37 and is known as the adiabatic shell model 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 1 k 1 2 US ee pres wal 2 160 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 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 co
251. tion times in ps select Hoover NoT ensemble with fi f2 as the thermostat and barostat relaxation times in ps select Martyna Tuckerman Klein NoT ensemble with fi fa as the thermostat and barostat relaxation times in ps set relative dielectric constant to f default f 1 0 equilibrate simulation for first n timesteps calculate electrostatic forces using Ewald sum with automatic parameter optimisation 0 lt f lt 0 5 calculate electrostatic forces using Ewald sum with a Ewald convergence parameter in A kl is twice the maximum k vector index in x direction k2 is twice the maximum k vector index in y direction k3 is twice the maximum k vector index in z direction switches on extended coulombic exclusion affecting intra molecular interactions such as chemical bonds and bond angles as well as bond constraints between ions that have shells and cores close the CONTROL file last data record set the type of Verlet integrator where string can only be leapfrog or velocity the later being the default 77 CCLRC Section 5 1 job time f maxdis f mindis f mxshak f no elec no vdw pressure f print every n print rdf print zden pseudo f rdf sampling every f reaction restart restart noscale restart scale rlxtol f rvdw cutoff f scale n shake tolerance f shift stack size n stats every n steps n temperature f trajectory i j k timestep f variable timestep f
252. tion to be added to the atomic stress tensor is given by uE 2 133 where a 8 are x y z components The atomic stress tensor is symmetric In DL_POLY 3 these forces are handled by the routine COUL_FSCP_FORCES 34 CCLRC Section 2 4 2 4 3 Coulomb Sum with Distance Dependent Dielectric This potential attempts to address the difficulties of applying the direct Coulomb sum without the brutal truncation of the previous case It hinges on the assumption that the electrostatic forces are effectively screened in real systems an effect which is approximated by introducing a dielectric term that increases with distance The interatomic potential for two charged ions is 1 0105 U r 2 134 ris Arege Ti Tij i with ge the charge on an atom labelled and rj the magnitude of the separation vector rj TP e r is the distance dependent dielectric function In DL_POLY 3 it is assumed that this function has the form e r er 2 135 where e is a constant Inclusion of this term effectively accelerates the rate of convergence of the Coulomb sum The force on an atom j derived from this potential is 1 gid 2 e 2 136 j Wee ri Tij with the force on atom 7 the negative of this The contribution to the atomic virial is W rij f gt 2 137 which is 2 times the potential term The contribution to be added to the atomic stress tensor is given by 2E E 2 138 where a 8 are x y z co
253. to aid legibility see example above Records must be limited in length to 100 characters Records are read in words directives and additional keywords and numbers as a word must not exceed 40 characters in length Words are recognised as such by separation by one or more space characters Additional annotation is not recommended but may be added onto a directive line after the last control word in it e The first record in the CONTROL file is a header up to 100 characters long to aid identifi cation 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 5 1 1 2 The CONTROL File Directives The directives available are as follows directive meaning cap forces f cap forces during equilibration period f is maximum cap in units of kgT A default f 1000 kgT close time f set job closure time to f seconds 76 CCLRC Section 5 1 collect coulomb cutoff f defects i j f densvar f distance dump n ensemble ensemble ensemble ensemble ensemble ensemble ensemble ensemble ensemble ensemble ensemble nve nvt ber f nvt evans nvt hoover f nvt lang f npt ber f f2 npt hoover fi f2 npt mtk fi f2 nst ber fi fo nst hoover fi fa nst mtk fi fo epsilon constant f equilibration steps n ewald precision f ewald sum
254. tomic_data o set_halo_particles o link_cell_pairs o core_shell_on_top o deport_atomic_data o pmf_units_set o compress_book_intra o relocate_particles o metal_1d_collect o metal_ld_export o metal_ld_set_halo o metal_1d_compute o gpfa_wrap o parallel_fft o exchange_grid o ewald_spme_forces o metal_forces o vdw_forces o ewald_real_forces o coul_dddp_forces o coul_cp_forces o coul_fscp_forces o coul_rfp_forces o rdf_collect o ewald_excl_forces o ewald_frozen_forces o two_body_forces o tersoff_forces o three_body_forces o four_body_forces o core_shell_forces o tethers_forces o bonds_forces o angles_forces o dihedrals_forces o inversions_forces o core_shell_relax o langevin_forces o nvt_e_scl o nvt_b_scl o external_field_apply_vv o external_field_correct o pseudo_vv o zero_k_optimise_vv o constraints_shake_vv o pmf_shake_vv o constraints_rattle o pmf_rattle o nvt_h_scl o npt_h_scl o nst_h_scl o nvt_li_vv o nve_1_vv o nvt_el_vv o nvt_b1_vv o nvt_hi_vv o npt_bi_vv o npt_h1_vv o npt_ml_vv o nst_b1_vv o nst_hi_vv o nst_mi_vv o external_field_apply_lfv o pseudo_lfv o zero_k_optimise_lfv o constraints_shake_lfv o pmf_shake_lfv o nvt_11_1fv o nve_i_lfv o nvt_ei_lfv o nvt_b1_lfv o nvt_hi_lfv o A npt_bi_lfv o npt_hi_lfv o npt_mi_lfv o nst_bi_lfv o nst_hi_lfv o nst_mi_lfv o A xscale o core_shell_kinetic o trajectory_write o defects_reference_read o defects_refere
255. tricky particularly in coming up with appropriate partial charges for atomic sites However there are a series of utilities that will at least produce the CONNECT_DAT file for use with AMBFORCE We now outline these utilities and the order in which they should be used If you have a structure from the Cambridge Structural database CSDB then use the utility FRACCON to take fractional coordinate data and produce a CONNECT_DAT and ambforce dat file for use with AMBFORCE Note that you will need to modify FRACCON to get the AMBER names correct for sites in your molecule The version of FRACCON supplied with DL_POLY 3 is specific 69 CCLRC Section 4 3 to the valinomycin molecule If you require an all atom force field and the database file does not contain hydrogen positions then use the utility FRACFILL in place of FRACCON FRACCON produces an output file HFILL which should then be used as input for the utility HFILL The HFILL utility fills out the structure with the missing hydrogens Note that you may need to know what the atomic charges are in some systems for example the AMBER charges from the literature Note with minor modifications the utilities FRACFILL and FRACCON can be used on structures from databases other than the Cambridge structural database 4 3 3 Adding Solvent to a Structure The utility WATERADD adds water from an equilibrated configuration of 256 SPC water molecules at 300 K to fill out the MD cell The ut
256. ts_tags o constraints_quench o pmf_coms o pmf_tags o pmf_vcoms o pmf_quench o set_temperature o vdw_lrc o metal_lrc o system_init o export_atomic_data o set_halo_particles o link_cell_pairs o core_shell_on_top o deport_atomic_data o pmf_units_set o compress_book_intra o relocate_particles o metal_1d_collect o metal_ld_export o metal_ld_set_halo o metal_1d_compute o gpfa_wrap o parallel_fft o exchange_grid o ewald_spme_forces o metal_forces o vdw_forces o ewald_real_forces o coul_dddp_forces o coul_cp_forces o coul_fscp_forces o coul_rfp_forces o rdf_collect o ewald_excl_forces o ewald_frozen_forces o two_body_forces o tersoff_forces o three_body_forces o four_body_forces o core_shell_forces o tethers_forces o bonds_forces o angles_forces o dihedrals_forces o inversions_forces o core_shell_relax o langevin_forces o nvt_e_scl o nvt_b_scl o external_field_apply_vv o external_field_correct o pseudo_vv o zero_k_optimise_vv o constraints_shake_vv o pmf_shake_vv o constraints_rattle o pmf_rattle o nvt_h_scl o npt_h_scl o nst_h_scl o nvt_11_vv o nve_1_vv o nvt_el_vv o nvt_b1_vv o nvt_hi_vv o npt_b1_vv o npt_hi_vv o npt_m1_vv o nst_b1_vv o nst_hi_vv o nst_mi_vv o external_field_apply_lfv o pseudo_lfv o zero_k_optimise_lfv o constraints_shake_lfv o pmf_shake_lfv o nvt_11_1fv o nve_1_lfv o nvt_ei_lfv o nvt_b1_lfv o nvt_hi_lfv o A 137 CCLRC Appendix C npt_b1_lfv o
257. ue of the potential at the cavity boundary from each pair contribution The term subtracted 1S Z 2 1 qiqi ATE Re 1 2 142 The effective pair force on an atom j arising from another atom n within the cavity is given by j Are ri RB The contribution of each effective pair interaction to the atomic virial is and the contribution to the atomic stress tensor is JB sari 2 145 where a 8 are x y z components The atomic stress tensor is symmetric In DL_POLY 3 the reaction field is handled by the subroutine COUL_RFP_FORCES 2 4 5 Smoothed Particle Mesh Ewald The Ewald sum 18 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 interacting 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 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 gauss
258. uild of DL_POLY 3 in serial mode and only FORTRAN 90 and MPI implementation for DL_POLY_3 in parallel mode Should the user add additional functionality to the code major changes of the makefile may be required In UNIX environment the compilation of the program is initiated by typing the command make target where target is the specification of the required machine For many computer systems this is all that is required to compile a working version of DL_POLY_3 To determine which targets are already defined in the makefile examine it or type the command make without a nominated target it 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 4 2 1 1 Keywords for the DL_POLY _3 Makefiles 1 TARGET The TARGET keyword indicates which kind of computer the code is to be compiled for This must be specified there is no default value Valid targets can be listed by the makefile if the command make is typed without arguments 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 s
259. uld not be less than the number of grid points DL POLY_3 is expecting This number is given by the parameter mxgrid calculated in the SETUP_MODULE file see Section 4 2 1 3 and 6 2 8 DL_POLY 3 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 r U r 5 7 ar Note this is not the same as the true force 5 2 The OUTPUT Files DL_POLY_3 produces up to eight output files HISTORY DEFECTS OUTPUT REVCON RE VIVE RDFDAT ZDNDAT and STATIS These respectively contain an incremental dump file of all atomic coordinates velocities and forces an incremental dump file of atomic coordinates of de fected particles interstitials and sites vacancies an incremental summary file of the simulation a restart final configuration file a restart final statistics accumulators file a radial distribution data file Z density data file and a statistical history file 103 CCLRC Section 5 2 5 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 the subroutine TRAJECTORY_WRITE The control variables for this file are ltraj nstraj istraj and keytrj which are created internally based on infor
260. um number of time steps used to calculate the rolling averages is controlled by the directive stack in file CONTROL see above and listed as parameter mxstak in the SETUP_MODULE file see Section 6 2 2 The default value is mxstak 100 Energy Units The energy unit for the data appearing in the OUTPUT is defined by the units directive appearing in the FIELD file System energies are therefore read in units per MD cell Pressure units The unit of pressure is katms irrespective of what energy unit is chosen 5 2 3 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 main subroutine DL_POLY_ 5 2 3 8 Summary of Statistical Data This portion of the OUTPUT file is written from the subroutine STATISTICS_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 lines The energy and pressure units are as for the preceding section Also provided in this section are estimates of the diffusion coefficient and the mean square displace ment for the different species in the simulation These are determined from a single time origin and are therefore approximate Accurate determinations of the diffusion coefficients
261. ur body forces in DL_POLY 3 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 Consider using densvar option in CONTROL for extremely non equilibrium simulations Alterna tively increase mxcell in SET_BOUNDS recompile and resubmit Message 88 error legend array exceeded in build book intra This should never happen Dimension of legend array exceeded Action Increase parameter mxfix in SET_BOUNDS recompile and resubmit If the error persists contact authors Message 89 error too many four body potentials specified This should never happen Action Report to authors Message 90 error fluctuations in the total number of frozen particles This should never happen Action Big trouble Report to authors 168 CCLRC Appendix D Message 91 error unidentified atom in four 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 errant 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 95 error error rcut gt minimum of all half cell widths In order for the minimum image convention to work correctly within DL_POLY 3 it is necessary to ensure that the major cutoff applied to the pair interactio
262. utions and thus falls within the general tabulation scheme of DL_POLY_3 where it is treated as a pair interaction although the metal cutoff rmez has nothing to do with short ranged one rvaw The same form of potential may be used in alloys through the appropriate choice of parameters e and a The parameters n and m however must be the same for all component elements of the alloy DL_POLY_3 calculates this potential in two stages the first calculates the local density pi for each atom and the second calculates the potential energy and forces Interpolation arrays vmet and gmet METAL_GENERATE similar to those in van der Waals interactions 2 3 1 are used in both these stages The total force ie on an atom j derived from this potential is calculated in the standard way ee V Uso gt 2 85 a Cm _ a 1 pp Parana a eas 14 2 which is recognizable as a sum of pair forces For example the force on atom j due to the atom a ii Cm 1 2 1 2 a m 1 LE fr 2 9 P e 3 Vij 2 87 27 which gives CCLRC Section 2 3 where ta E The force on atom i is the negative of this With the pair forces thus defined the contribution to be added to the atomic virial from each atom pair is then The contribution to be added to the atomic stress tensor is given by Gene 2 89 where a and indicate the x y z components The atomic stress tensor is symmetric The long range correction for t
263. x D Action Recompile the program or recreate the FIELD file If neither of these works send the problem to us Message 61 error too many dihedral angles per domain DL_POLY 3 limits the number of dihedral angles in the system to be simulated actually the number to be processed by each node and checks for the violation of this Termination will result if the condition is violated Action Increase the parameter mxdihd in SET_BOUNDS recompile and resubmit Message 62 error too many tethered atoms specified This should never happen Action Recompile the program or recreate the FIELD file If neither of these works send the problem to us Message 63 error too many tethered atoms per domain DL POLY 3 limits the number of tethered atoms in the system to be simulated actually the number to be processed by each node and checks for the violation of this Termination will result if the condition is violated Action Increase the parameter mxteth in SET_BOUNDS recompile and resubmit Message 64 error incomplete core shell unit found in build_book_intra This should never happen Action Report problem to authors Message 65 error too many excluded pairs specified This should never happen This error arises when DL POLY 3 is identifying the atom pairs that cannot have a pair potential between them by virtue of being chemically bonded for example see subroutine BUILD_EXCL_INTRA Some of the work
264. y molecular description 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 100 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 88 CCLRC Section 5 1 The integer nrept need not be specified if the atom site is not frozen in which case a value of 1 is assumed A number greater than 1 specified here indicates that the next 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 where n is the number of core shell units Each of the subsequent n records contains index 1 i integer site index of core index 2 7 integer site index of shell spring k
265. y the increment should be reut magrid 4 where reut 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 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 3 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 3 is expecting Message 25 error wrong atom type found in CONFIG file On reading the input fi

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