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THE DL-POLY-4 USER MANUAL

1. olijk sin Dijk Or Tij Tik where 5 2 b _ gt 3 Og ijk 2 i cos 0 jk sin dg 2 138 olijk d hi COS Dijk O Tic Tk Tik rij e da da 00 org Tijfik de de Vag Sex de TijTik cos 0 ix fiy 5 4 72 b Sen bu if 2 139 Tij ri The contribution to be added to the atomic virial can be derived as OEtersot 3V OU en e Dia 2 140 1 ju 0 le Wie D folrij fr rij Vi 5 folu falis Tij i ji ll rr on ane oy fo ray falra xi 14 AM LB T gin LEO x 2 141 le S wir 9 0 5k dr Oral ra rsh k i j The contribution to be added to the atomic stress tensor is given by o reff 2 142 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 48 DL_POLY 4 applies no long ranged corrections to the Tersoff potentials In DL_POLY_4 Tersoff forces are handled by the routine TERSOFF_FORCES 39 STFC Section 2 3 2 3 4 Three Body Potentials The thr
2. 4 176 7 1 2 Test Case 3 and 4 DPMC in Water 176 7 1 3 Test Case 5 and 6 KNaSi9O5 LL 176 7 1 4 Test Case 7 and 8 Gramicidin A molecules in Water 177 7 1 5 Test Case 9 and 10 SiC with Tersoff Potentials 177 7 1 6 Test Case 11 and 12 CuzAu alloy with Sutton Chen metal Potentials 177 7 1 7 Test Case 13 and 14 lipid bilayer in water 177 7 1 8 Test Case 15 and 16 relaxed and adiabatic shell model MgO 177 7 1 9 Test Case 17 and 18 Potential of mean force on K in water MgO 177 7 1 10 Test Case 19 and 20 CuzAu alloy with Gupta metal Potentials 177 7 1 11 Test Case 21 and 22 Cu with EAM metal Potentials 177 7 1 12 Test Case 23 and 24 Al with Sutton Chen metal Potentials 178 7 1 13 Test Case 25 and 26 Al with EAM metal Potentials 178 7 1 14 Test Case 27 and 28 NiAl alloy with EAM metal Potentials 178 7 1 15 Test Case 29 and 30 Fe with Finnis Sincair metal Potentials 178 7 1 16 Test Case 31 and 32 Ni with EAM metal Potentials 178 7 1 17 Test Case 33 and 34 SPC IceVII water with constraints 178 7 1 18 Test Case 35 and 36 NaCl molecules in SPC water represented as CBs RBs 178 7 1 19 Test Case 37 and 38 TIP4P water RBs with a massless charged site 178 7 1 20 Test Case 39 and 40 Ionic liquid dimethylimidazolium chloride 179 ix STFC Con
3. 64 STFC Section 3 4 where o kp Tox 3 56 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 of the Berendsen 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 ult 340 v t r t At r t At v iat 3 57 2 RATTLE_VV1 3 FF f t At f t 3 58 4 VV2 NE TEN 1 t u t At ult 544 A 3 59 5 RATTLE_VV2 6 Thermostat At o 1 2 a a E TT at At 1 v t At v t Abt x 3 60 The LFV implementation of 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 f t f t At 3 61 2 LFV The iterative part is as follows 1 1 f t 1 r t At r t Atu t At 3 62 3 SHAKE 4 Full step velocity 1 1 1 u t gt v t 544 u t At 3 63 65 STFC Section 3 4 5 Thermostat xt i yo ae Several iterations are required to obtain self consistency In DL_POLY_4 the number of iterations is set to 3 4 if bond constraints are present Note that t
4. Trin t V t 3 117 and the velocity updates for VV and LFV algorithms as Wi r t At n t r t At v t At LFV rt At n t r t At u t 5At 3 118 This ensemble is optionally extending to constant normal pressure and constant surface area NP AT 56 by semi isotropic constraining of the barostat equation of motion to d E Poe 02 E VB a 2 ganaste md a d a y 3 119 0 a 6 Similarly this ensemble is optionally extending to constant normal pressure and constant surface tesnison NP yT 56 by semi isotropic constraining of the barostat equation of motion to Hol Pext Text V t hz t caa 6 V 0 a d a y d de Pos 1 _ 866 Pon onli VE bed VM 0 a 6 where Yext is the user defined external surface tesnion and h t V t Azy t is the instantenious hight of the MD box or MD box volume over area The VV and LFV flavours of the non isotropic Berendsen barostat and thermostat are im plemented in the DL_POLY 4 routines NST_BO_VV and NST_BO_LFV respectively The routines NST_Bl_vv and NST_B1_LFV implement the same but also incorporate RB dynamics 3 5 4 Nos Hoover Barostat DL_POLY 4 uses the Melchionna modification of the Nos Hoover algorithm 60 in which the equa tions of motion involve a Nos Hoover thermostat and a barostat in the same spirit Additionally as shown in 61 a modification allowing for coupling between the thermostat and barost
5. d qe ult nlt rle d f t R t Tr n0 Spi AAA e qt n x Ltn S 1 20 d a t Pox V t 1 2Exin t 1 Rp nt 4 t 3 98 at Pmass f Pmass Xp Pmass f 3 kg Text Pmass 4 2 3 27 xp d H t H t EHO 1 HO d gO Trin t V t where o is the stress tensor and 1 is the identity matrix The conserved quantity these generate is Pmass Trin nT Hxo Hyve yt Pet V t 3 99 The VV and LFV algorithmic equations are therefore written in the same fashion as in the isotropic case with slight modifications For the VV couched algorithm these are of the following sort nt E a n t As e n t 72 STFC Section 3 5 At o t Pet VEL 2Ejn t 1 Bolt 4 Pmass f Pmass Pmass ny u t exp aa 144 rr nl 140 a u t 1 1 ih a ox nl A At r t At w t 5AM Similarly for the LFV couched algorithms these are 1 n t At exp xp t At Zit Fext Rp t he Sas Pess V t L 2Ekim t 1 4 Pmass f Pmass Pmass 3 At scale 1 x1 145 n t 2 2 scalev 1 3 101 scale At scale f ft RO 1 u t At scale v u t At scale_f 1 1 1 At r t At u t 344 n t 340 c t 340 It is worth noting DL_POLY 4 uses Taylor expansion truncated to the quadratic term to approxi mate exponentials of tensorial terms This ensemble is optionally extending to constant n
6. 277 igPenla lLag X LjrllL jr X Lanl gi WTA legal jlo rielLogtyelo lrg X t 2 54 Ge Arsiltitilo rolrgrjoda lLi x sel h7 Aral Creole e x Teal ha 2 Fenltentenlo T3klEjktknla lEjk X Beal gt The sum of the diagonal elements of the stress tensor is zero since the virial 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_4 and are described in the section on pair potentials below DL_POLY 4 also permits scaling of the 1 4 van der Waals and Coulomb interactions by a numerical factor see Table 5 10 Note that scaling is abandoned when the 1 4 members are also 1 3 members in a valence angle intercation 1 4 checks are performed in DIHEDRALS_14_CHECK routine 1 4 interactions do of course contribute to the atomic virial In DL POLY 4 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_4 makes no distinction between 22 STFC Section 2 2 dihedral and improper dihedral angle functions both are calculated by the same subroutines and all the comments made in the preceding section apply An impo
7. DL_POLY 4 has failed to match the available modes of MPI precision for real numbers to the defined in sc kinds 90 FORTRAN90 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 4 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 4 has failed to deallocate an array or arrays i e to free memory that is no longer in use Action Talk to your systems support people for advice on how to manage this Message 1003 error allocation failure in comms_module gt
8. STFC Section 2 4 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 la b x c 2 179 and u bxe a bxe cxa Jg 2 180 z a bxc w po bxe 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 51 for electrically non neutral MD cells which prevents the build up of a charged background and the introduction of extra pressure 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 k 4z used in the reciprocal space sum These are discussed more fully in Section 4 3 5 DL_POLY 4 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 4 implements the SPME method of Essmann et al 52 Formally this method is capable of treating van der Waals forces also but in DL_POLY 4 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 represen
9. U r Fri 2 68 2 Restrained harmonic rhrm 1 2 92 Ua Lo kre rio re l si a k 2 99 3 Quartic potential quar U rg rio ro E rio 2 70 as in each case rj is the distance between the atom positions at moment t tl and t 0 The force on the atom i arising from a tether potential potential is obtained using the general formula Li s _ Uro Pig 2 71 Tio 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 page f 2 73 where a and 8 indicate the x y z components The atomic stress tensor derived in this way is symmetric In DL POLY 4 tether forces are handled by the routine TETHERS_FORCES 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 4 An important distinction between these and intramolecular bond forces in DL_POLY 4 is that they are specified by atom types rather than atom indices 26 STFC Section 2 3 2 3 1 Short Ranged van der Waals Potentials The short ranged pair forces available in DL_POLY 4 are as follows Ur e 2 74 ij ij 2 Lennard Jones potential lj 12 6 U rij 4e z 2 75 3 n m potential 42 nm Eo To To hi Ute am 2 n 2 2 76 4 Buckingham potential buck 1 12 6 potential 12 6 U rij
10. ___ 2 191 Vcore shell E wml with m the rigid ion 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 49 STFC Section 2 6 net polarisation In practice there is a slow leakage of kinetic energy into the core shell units but this should should not amount to more than a few percent of the total kinetic energy To determine safe shell masses in practice first a rigid ion simulation is performed in order to gather the velocity autocorrelation functions VAC of the ions of interest to polarise Then each VAC is fast fourier tranformed to find their highest frequency of interaction Vrigia ion It is then a safe choice to assign a shell mass x m so that Vcore she11 2 3 Vrigia ion The user must make sure to assign the corect mass 1 x m to the core 2 5 2 Relaxed Massless Shells The relaxed shell model is presented in 54 where shells have no mass and as such their motion is not governed by the us
11. FCFLAGS byteswapio 03 EX EX BINROOT BINROOT TYPE CRAY XT3 6 pathscale compilers DEBUG hector pathscale debug MAKE LD ftn o LDFLAGS byteswapio 00 g ffortran bounds check FC ftn c FCFLAGS byteswapio 00 g ffortran bounds check EX EX BINROOT BINROOT TYPE hector X2 MAKE LD ftn o LDFLAGS 03 Ofp3 Ocache2 rm FC ftn c FCFLAGS 03 Ofp3 Ocache2 rm EX EX BINROOT BINROOT TYPE CRAY X2 DEBUG o cocoon0a hector X2 debug MAKE LD ftn o LDFLAGS GO 00 rm FC ftn c FCFLAGS GO 00 rm EX EX BINROOT BINROOT TYPE Default code master message check 0BJ_MOD OBJ_ALL LD EXE LDFLAGS OBJ_MOD OBJ_ALL Message message echo DL_POLY_4 compilation in MPI mode echo echo Use mpi_module must change to Use mpi in comms_module f90 echo 209 STFC Appendix C Check that a platform has been specified check if test FC undefined then echo echo FORTRAN90 compiler unspecified echo echo Please edit your Makefile entries echo exit 99 fi if test LD undefined then echo echo FORTRAN90 Linker loaDer unspecified echo echo Please edit your Makefile entries echo exit 99 fi mkdir
12. 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 vdw_table_read or metal_table_read Action Standard user response Increase mxbuff in SET_BOUNDS recompile and resubmit Message 49 error frozen shell core shell unit specified The DL_POLY 4 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_4 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 4 limits the number of valence angle 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 Use densvar option in CONTROL to increase mxangl alternatively increase it by hand in SET_BOUNDS and recompile and resubmit 231 STFC Appendix D Message 52 error end of FIELD file encountered This message results
13. and blank lines are not processed and may be 129 STFC Section 5 1 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 al00 field file header record 2 units 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 Kelvin for Kelvin per mol e 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 input and output energies are read in
14. 3 96 Pmass f Pmass nt At t 340 At svie as nt NI re 71 STFC Section 3 5 Several iterations are required to obtain self consistency In DL_POLY_4 the number of iterations is set to 7 8 if bond constraints are present Note also that the change in box size requires the SHAKE algorithm to be called each iteration The VV and LFV flavours of the langevin barostat and Nos Hoover thermostat are implemented in the DL_POLY 4 routines NPT_LO_VV and NPT_LO_LFV respectively Both VV and LFV imple mentations make use of the DL_POLY_4 module LANGEVIN_MODULE The routines NPT_L1_vv and NPT_L1_LFV implement the same but also incorporate RB dynamics Cell size and shape variations The isotropic algorithms VV and LFV may be extended to allowing the cell shape to vary by defining 1 as a tensor n and extending the Langevin pressure variable Rp to a stochastic Langevin tensor Rp k Rp i t Fogle 2 Xp Pmass kpT di d t t j 3 97 which is drawn from Gaussian distribution of zero mean and unit variance Gauss 0 1 scaled by 4 2i A kp is the Boltzmann constant T the target temperature and Pmass the barostat mass Note that Rp has to be symmetric and only 6 independent components must be generated each timestep The equations of motion are written in the same fashion as is in the isotropic algorithm with slight modifications as now the equations with 7 are extended to matrix forms
15. 3 kin t At 1 R t f Pmass Pmass 3 At 3 n t 7 exp x n t 740 3 At u t At exp n t4 At 5 u t At 3 91 3 At 3 n t 1 exp x n t 1 3 At P t At Pex n t At nt qo a ava At 5 ox 2E 32Er t At 1 h R t f Pmass Pmass At nt At exp x E ult AN 70 STFC Section 3 5 11 Thermostat Note Exin t At has changed and changes inside u t At exp x v t At 3 92 The LFV implementation of the Langevin algorithm is iterative until self consistency in the full step velocity u t is obtained Initial estimate of 7 t at full step are calculated 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 At 1 FF f t f t At R t R t At 3 93 Ry t R t At 2 LFV The iterative part is as follows A scale 1 x 1 gt o f 2 2 scale v 1 scale At scale f scale 1 1 t R t u t At scale v v t At scale f FH RO m FAD EA u t LAI N E larl 540 3 94 H t At exp nt At At H t ORD dsp lance 340 At V t 3 SHAKE 4 Full step velocity and half step position To T At Eott tat r t r t At 3 95 1 t A ritto t 5 5 Thermostat and Barostat 1 1 n t 54 exp Xp At nc At At Poe 2Epm t At 1 PUTAN se Me a CEA
16. 4 r f 2 66 i 1 However it is possible to show by thermodynamic arguments cf 39 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 et raS re fh 2 67 25 STFC Section 2 3 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 4 inversion forces are handled by the routine INVERSIONS_FORCES 2 2 8 Tethering Forces DL_POLY 4 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 The tethering potential functions available in DL_POLY 4 are as follows 1 Harmonic harm
17. A exp 2 2 77 5 Born Huggins Meyer potential bhm U rij A exp B o r 2 78 6 Hydrogen bond 12 10 potential hbnd 7 Shifted force n m potential 42 snm iaia Oo DONE OEA aan with E n m ed m y m 1 fy mpr 1 n y n 1 m 1 _ n m p feci 2 81 y a 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 27 STFC Section 2 3 8 Morse potential mors U riz Eo 1 exp k rij ro 1 2 82 9 Shifted Weeks Chandler Anderson WCA potential 43 wea 4 oO 12 o 6 A 25 A U rij 5 2 te TEE 2 83 0 fij gt 250 A The WCA potential is the Lennard Jones potential truncated at the position of the minimum and shifted to eliminate discontinuity includes the effect of excluded volume It is usually used in combination with the FENE 2 10 bond potential This implementation allows for a radius shift of up to half a A lt 0 5 0 with a default of zero Age fault 0 10 Tabulation tab The potential is defined numerically only The parameters defining these potentials are supplied to DL_POLY 4 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
18. For timesteps greater than nstmsd the MSDTMP file is appended at intervals specified by the msdtmp directive in the CONTROL file with the following information for each configuration record i timestep a8 the character string timestep nstep integer the current time step 150 STFC Section 5 2 megatm integer number of atoms in simulation cell again tstep real integration timestep ps time real elapsed simulation time ps This is followed by the configuration for the current timestep i e for each atom in the system the following data are included record a atmnam a8 atomic label iatm integer atom index MSD t real square root of the atomic mean square displacements in A T meam real atomic mean temperature in Kelvin 5 2 3 The DEFECTS File The DEFECTS file is the dump file of atomic coordinates of defects see Section 5 1 4 Its princi pal use is for off line analysis The file is written by the subroutine DEFECTS WRITE The control variables for this file are 1def nsdef isdef and rdef which are created internally based on in formation read from the defects directive in the CONTROL file see Section 5 1 1 The DEFECTS file will be created only if the directive defects 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 Alternative
19. MAKE LD ftn o LDFLAGS 03 fastsse FC ftn c FCFLAGS 03 fastsse EX EX BINROOT BINROOT TYPE hector pgi debug MAKE LD ftn o LDFLAGS 00 W Wall pedantic std f2003 g fbounds check fbacktrace finit real nan finit integer 999999 FC ftn c FCFLAGS 00 W Wall pedantic std f2003 g fbounds check fbacktrace finit real nan finit integer 999999 EX EX BINROOT BINROOT TYPE hector gnu MAKE LD ftn o LDFLAGS 03 Wall pedantic g FC ftn c FCFLAGS 03 Wall pedantic g EX EX BINROOT BINROOT TYPE hector gnu debug MAKE LD ftn o LDFLAGS 03 Wall Wextra pedantic g fbounds check fbacktrace finit integer 9999 finit real nan std f2003 pedantic ffpe trap invalid zero overflow fdump core FC ftn c FCFLAGS 03 Wall Wextra pedantic g fbounds check fbacktrace finit integer 9999 finit real nan std f2003 pedantic ffpe trap invalid zero overflow fdump core EX EX BINROOT BINROOT TYPE hector cray MAKE LD ftn o LDFLAGS 03 en FC ftn c FCFLAGS 03 en EX EX BINROOT BINROOT TYPE hector cray debug MAKE LD ftn o LDFLAGS 03 en G2 208 STFC Appendix C FC ftn c FCFLAGS 03 en G2 EX EX BINROOT BINROOT TYPE hector pathscale MAKE LD ftn o LDFLAGS byteswapio 03 FC ftn c
20. aU Ly Myles rig Org _ y Vry Tj Tki Ork i 1 j i Orij ork j 1 j4k Or Tkj OU2 or Y Opis Tig Orij 2 98 Orr y Opi 2 Orij rk 2 98 a y OF Opix Tix Orik Y OF Oprs Trj Or ia Opi Orie Ork Szyk k Oj OT _ y E di Opng Tg Tki j 1 j k pk Op Or pj Tkj 1 EAM force The same as shown above However it is worth noting that the generation of the force arrays from tabulated data implemented in the METAL TABLE DERIVATIVES routine is done using a five point interpolation precedure 2 Finnis Sinclair force OU 2 2 kj OTR 2 2 rk Co cares cariz rej 0 c1 209153 rh J 1 jG k OU a A rr d Tki 2 Y A ym vr Ara ap E 2 90 Ore j j o 0 3 Extended Finnis Sinclair force aU DL Arrj co terre Cor c3r carey 4 IL 31 STFC Section 2 3 2 2 3 Iki rej c c1 2c2rg 3c3rk Acar Tkj OU2 A Tkj a D g PR vP 21 D 4BP rag 9 Or A 2 Tkj j 1 3 k 4 Sutton Chen force TN ss ne 2 2 Ore j Lj k NR kj OU N me aX Try S Y 5 vet yo 4 2 100 Tk j 1j k BRIJE DER 5 Gupta force N A _ Th a 5 P exp peri mz Th jal jee 0 Par AN OU2 Ban Tkj To Thi A La 24 2 101 e Dt en 101 j l jek With the metal forces thus defined the contribution to be added to the atomic virial from each atom pair is then which equates to OU Y 3V OV v py al ra E E YV1 Y
21. atmnam 1 atmnam 2 a8 a8 first atom type second atom type By default in DL_POLY_2 and DL_POLY 4 every vdw and met potential specifies an RDF pair If the control option rdf fis specified in the CONTROL file then all pairs defined in vdw and or met potentials sections will also have their RDF calculated The user has two choices to enable the calculation of RDFs in systems with force fields that do not have vdw 140 STFC Section 5 1 and or met potentials i to define fictitious potentials with zero contributions or ii to use rdf n option which not only provides a neater way for specification of RDF pairs but also better memory efficiency since DL_POLY 4 will not allocate additional potential arrays for fictitious interactions that will not be used This option is not available in DL_POLY 2 Note that rdf and vdw met are not complementary i e if the former is used none of the pairs defined by the latter will be considered for RDF calculations The selected RDFs are calculated in the RDF_COLLECT by collecting distance information from all two body pairs as encountered in the Verlet neighbour list created in the LINK_CELL_PAIRS routine within the TWO_BODY_FORCES routine In the construction of the Verlet neighbour list pairs of particles part of the exclusion list are excluded The exclusion list contains particles that are part of e core shell units e bond constraints e chemical bonds that are NOT dista
22. lt u t At At r t At r t At u t ZAt n t At EC sat Ra t H t At exp nt iat At H t 3 133 PERAD amp ee Di Lai At V t 3 SHAKE 4 Full step velocity and half step position TE 5 wt At u t At r t r t At 1 a 3 134 r T 9 t lt 3 5 Thermostat and Barostat 1 1 2 Ep p araka i x t At lt x t At At kin t Pmass n t o kp Text 2 2 dmass 79 STFC Section 3 5 x t z X 349 x t 40 2 2 2 n t At exp x t At nc At At 2 PO Pa vo 3 135 nt 5 nlt 5At n 50 Several iterations are required to obtain self consistency In DL_POLY 4 the number of iterations is set to 7 8 if bond constraints are present Note also that the change in box size requires the SHAKE algorithm to be called each iteration The VV and LFV flavours of the Nos Hoover barostat and thermostat are implemented in the DL _POLY 4 routines NPT_HO_vv and NPT_HO_LFV respectively The routines NPT_H1_vv and NPT_H1_LFV implement the same but also incorporate RB dynamics 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 with 7 are extended to matrix forms TO u t n t r t Ro t x
23. x t At x t ua exp xlt 30 v t 3 123 At 2Exkin t Pmass n t 20 kp Text 8 dmass 1 1 x t At x t At 2 Barostat Note Exin t and P t have changed and change inside ni exp x 79 E nl n t TAn e n t i sa dy n t 140 exp x t 140 gt n t 144 y exp ne 340 gt v t 3 124 n t TAn exp x t 140 3 n t 144 nt At e n t l At i 5 mn Peal VO nt 340 exp x t At 3 ne 340 STFC Section 3 5 3 Thermostat Note Exin t has changed and changes inside 3 1 At 2Exin t mass ME At 20 he Tox SACE E N kin t Pmass M t 3At 20 kp Text 8 4 8 mass 3 At v t exp x t At 7 v t 3 125 1 At 2Ekin t mass TE At 20 kg Tox 2 8 8 Imass 4 VVI 1 At f t SAN tn i u t At v 0 3 m H t At exp a t 5At Ar H t VELA cao 1 At At V t 3 126 p a DAI At r t Ro t At ult 548 Bolt 5 RATTLE_VV1 6 FF f t At fit 3 127 Te NVZ ut At v tt 50 qe 3 128 8 RATTLE_VV2 9 Thermostat Note Exjn t At has changed and changes inside At 2Ekin t At Pmass n t 5At 20 kp Text mass ie PAS E exp ree 2 At Z u t At 3 129 5 1 x t At E x t 5At At 2Ekin t At Pmass n t H 1At 20 kp Text 8 mass 3 5 x t At amp x t At 10 Baro
24. 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 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 4 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 447 error only one shells directive per molecule is allowed DL_POLY_4 has found more than one shells entry per molecule in FIELD Action Correct the erroneous part in FIELD and resubmit 250 STFC Appendix D Message 448 error undefined dihedral potential A form of dihedral potential has been requested which DL_POLY_4 does not recognise Action Locate the offending potential in the FIELD file and remove Repla
25. Pij rij These forms recognise that the contribution of a type A atom to the potential of a type B atom may be different from the contribution of a type B atom to the potential of a type A atom In both EAM 47 and FS 14 cases it turns out that wW rg Vs aim though the mixing rules are different in each case beware With regard to density in the EAM case it is required that 47 pig rig pi rij pira pri 2 120 which means that an atom of type A contributes the same density to the environment of an atom of type B as it does to an atom of type A and vice versa 36 STFC Section 2 3 For the FS case 14 a different rule applies Br rig 08 rig BB rig 2 121 so that atoms of type A and B contribute the same densities to each other but not to atoms of the same type Thus when specifying these potentials in the DL_POLY 4 FIELD file for an alloy composed of n different metal atom types both EAM and FS require the specification of n n 1 2 pair functions VB rij However the EAM requires only n density functions pag whereas the FS class requires all the cross functions piP ay or n n 1 2 in total In addition to the n n 1 2 pair functions and n density functions the EAM requires further specification of n functional forms of the density dependence i e the embedding function F p in 2 90 For EAM potentials all the functions are supplied in tabular form via the table file TABEAM
26. 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 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 drt _ a 00 LO D ato 3 22 the kinetic temperature constraint x can be found as follows d d 1 E d i x 7 Ema Dam La 0 E 5 mivilt 4 x t u t p 0 3 23 i Da x t Dult f t X miv t The VV implementation of the Evans algorithm is straight forward The conventional VV1 and VV2 steps are carried out as before the start of VV1 and after the end of VV2 there is an application of thermal constraining This involves the calculation of x t before the VV1 stage and x t At after the VV2 stage with consequtive thermalisation on the unthermostated velocities for half a timestep at each stage in the following manner 59 STFC Section 3 4 1 Thermostat VV1 Di V t f t 2 Ele 0 mew 3 24 2 VVI 1 At f t v t At v t 5 Ea 1 r t At r t At u t 54 3 25 3 RATTLE_VV1 4 FF f t At f t 3 26 5 VV2 fet Ab 1 At t At v t At v t 5 At 3 a 3 27 6 RATTLE_VV2 7 Thermostat VV2 Dult At f t At ERA 2 Epin t At v t 4 At v t At exp axe 3 28 The algorithm is s
27. 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 13 Mayo S Olafson B and Goddard W 1990 J Phys Chem 94 8897 3 13 40 143 Weiner S J Kollman P A Nguyen D T and Case D A 1986 J Comp Chem 7 230 3 13 Smith W 2003 Daresbury Laboratory 4 10 91 100 102 127 183 Allen M P and Tildesley D J 1989 Computer Simulation of Liquids Oxford Clarendon Press 4 46 53 56 59 161 163 276 STFC Bibliography 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 Andersen H C 1983 J Comput Phys 52 24 4 56 161 Fincham D 1992 Molecular Simulation 8 165 4 87 Miller T Eleftheriou M Pattnaik P Ndirango A Newns D and Martyna G 2002 J Chem Phys 116 8649 4 87 Evans D J and Morriss G P 1984 Computer Physics Reports 1 297 4 55 59 Adelman S A and Doll J 1976 J Chem Phys 64 2375 4 55 59 Andersen H C 1979 J Chem Phys T2 2384 4 55 59 Berendsen H J C Postma J P M van Gunsteren W DiNola A and Haak J R 1984 J Chem Phys 81 3684 4 55 59 68 Hoover W G 1985 Phys Rev A31 1695 4 55 59 66 68 Quigley D and Probert M 2004 J Chem Phys 120 11432 4 55 68 Marty
28. core_shell_on_top o comms_module o config_module o core_shell_module o setup_module o core_shell_quench o comms_module o config_module o core_shell_module o kinds_f90 0 setup_module o core_shell_relax o comms_module o config_module o core_shell_module o kinds_f90 0 setup_module o statistics_module o coul_cp_forces o config_module o kinds_f90 0 setup_module o coul_dddp_forces o config_module o kinds_f90 o setup_module o coul_fscp_forces o comms_module o config_module o kinds_f90 0 setup_module o coul_rfp_forces o comms_module o config_module o kinds_f90 0 setup_module o defects1_module o kinds_f90 o setup_module o defects1_write o comms_module o config_module o defectsi_module o io_module o kinds_f90 0 parse_module o setup_module o site_module o defects_link_cells o comms_module o domains_module o kinds_f90 0 setup_module o defects_module o kinds_f90 0 setup_module o defects_reference_export o comms_module o domains_module o kinds_f90 0 setup_module o defects_reference_read o comms_module o config_module o domains_module o io_module o kinds_f90 0 parse_module o setup_module o site_module o defects_reference_read_parallel o comms_module o domains_module o io_module o kinds_f90 0 parse_module o setup_module o defects_reference_set_halo o comms_module o config_module o domains_module o kinds_f90 0 setup_module o defects_reference_write o comms_module o config_module o io_module o kinds_f90 0 setup_module o
29. data 4 real data item 4 force data records number of data records Int ngrid 3 4 146 STFC Section 5 1 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 should not be less than the number of grid points DL_POLY 4 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 4 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 vvdw and gvdw 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 8 or Note this is not the same as the true force During simulation interactions beyond distance Min reu cutpot are discarded 5 1 7 The TABEAM File The TABEAM file contains the tabulated potential functions no explicit analytic form describing the EAM metal interactions in the MD system This file is read by the subroutine METAL_TABLE_READ see Chapter 6 The EAM potential for an n component metal alloy requires the specification of n electron density functions one for each atom type and n embedding functions again one for each atom type and n n 1 2 cross pair potential functions This makes n n 5 2 functions in total
30. 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 restriction Message 350 error too few degrees of freedom This error can arise if a small system is being simulated and the number of constraints applied is too large Action Simulate a larger system or reduce the number of constraints Message 360 error degrees of freedom distribution problem This should not happen Action Report problem to authors immediately Message 380 error simulation temperature not specified or lt 1K DL POLY 4 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 4 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 4 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
31. terms The inclusion of other potentials for example pair potentials may in fact be essential to maintain the structure of the system The four body potentials are very short ranged typically of order 3 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 48 The calculation of the forces virial and stress tensor described in the section on inversion angle potentials above DL_POLY 4 applies no long ranged corrections to the four body potentials The four body forces are calculated by the routine FOUR_BODY_FORCES 2 4 Long Ranged Electrostatic coulombic Potentials DL_POLY 4 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 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 41 STFC Section 2 4 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 condi
32. with the setenv command in a TCSH shell or export in BASH shell 4 2 1 1 Keywords in the 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 specifies the executable name The default name for the executable is DLPOLY Z 3 BINROOT The BINROOT keyword specifies the directory in which the executable is to be stored The default setting is execute 94 STFC Section 4 2 4 2 1 2 Modifying the Makefiles 1 Changing the FORTRANS90 compiler and MPI implementation To specify the FORTRAN90 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 TRAN90 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 2 Adding new functionality To include a new subroutine in the code simply add subroutine o to the list of object names in the mak
33. 0 000000000000000 0 000000000000000 44 028000000000000 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 9720599243E 01 1 787340483 9226 455153 etc 1 484234330 1 872177437 13070 74357 1 972916834 1 577400769 4806 880540 2 125627191 4 336956694 8318 045939 2 503798635 1 021777575 9445 662860 5 1 2 1 The CONFIG File Format 7 274585343 0 7702718106 4432 030587 7 340573742 4 328786484 1255 814536 7 491549620 2 951142896 2379 766752 3 732081894 0 5473436377 5365 202509 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 megatm integer Optinal total number of particles crystalographic entities record 3 omitted if imcon 0 cell 1 real
34. 1 core shell units are dealth with i kinetically by the adiabatic shell model or ii staticly by the dynamic shell model Both contribute to the total system stress pressure but in different manner The former does it via the kinetic stress energy and atomic sterss potential energy due to the core shell spring The latter via atomic sterss potential energy due to the shells move to minimised configuration ol Chapter 3 Integration Algorithms Scope of Chapter This chapter describes the integration algorithms coded into DL_POLY 4 52 STFC Section 3 1 3 1 Introduction As a default the DL _POLY 4 integration algorithms are based on the Velocity Verlet VV scheme which is both simple and time reversible 21 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
35. 165 Nos Hoover 76 82 chemical bond 3 13 14 16 21 22 40 49 162 164 units dihedral 3 13 20 21 23 137 154 162 163 DL_POLY 7 155 233 201 energy 130 EAM 147 pressure 7 77 115 155 electrostatics 3 7 14 16 19 22 41 111 temperature 117 113 116 117 123 154 162 250 user registration 10 external field 3 13 50 51 162 four body 3 13 26 41 138 143 154 162 Verlet neighbour list 93 163 165 240 226 237 238 250 251 WWW iii 2 6 9 10 improper dihedral 3 13 22 23 162 intermolecular 93 intramolecular 26 41 93 inversion 3 13 23 26 41 138 162 163 236 251 metal 3 14 26 29 93 95 138 162 164 238 non bonded 3 14 100 101 115 130 135 136 138 162 164 225 tabulated 146 227 Tersoff 3 13 26 37 39 138 142 162 164 236 tether 3 13 26 154 162 163 234 251 tethered 51 three body 3 13 14 17 26 40 101 138 142 154 162 226 235 237 251 valence angle 3 13 14 17 18 22 23 40 101 134 136 154 162 164 231 van der Waals 14 16 19 22 93 95 124 134 138 248 quaternions 4 87 reaction field 44 45 116 123 rigid body 2 4 54 84 85 163 263 rigid bond see constraints bond stress tensor 16 19 22 25 26 28 29 33 39 45 49 51 58 68 280
36. 6 6 1 2 max number of parameters for bond angle potentials 6 max number of specified dihedral angle potentials in system max number of dihedral angles per node max number of related dihedral angles 1 6 2 6 6 1 2 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 related inversion angles 1 6 6 1 4 max number of parameters for inversion angle potentials 3 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 9 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 5 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 local halo atoms per node m
37. Constant T 0 algorithm Berendsen 28 NST_B1_vv NST_B1_LFV The same as the above but also incorporating RB integration NST_HO_VV NST_HO_LFV Constant T o algorithm Hoover 29 NST_H1_VV NST_H1_LFV The same as the above but also incorporating RB integration NST_MO_VV NST_MO_LFV Constant T o algorithm Martyna Tuckerman Klein 31 NST_MO_VV NST_MO_LFV The same as the above but also incorporating RB integration It is worth noting that the last four ensembles are also optionally available in an extended from to constant normal pressure and constant surface area NP AT or constant surface tesnison NP yT 56 3 2 Bond Constraints The SHAKE algorithm for bond constraints was devised by Ryckaert et al 57 and is widely used in molecular simulation It is a two stage algorithm based on the leapfrog Verlet integration scheme 55 STFC Section 3 2 21 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 2 2 l pij di dij 2A d di Gij x dij 3 15 wh
38. DL_POLY 4 these forces 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 42 STFC Section 2 4 The form of the simple truncated and shifted potential function is U r 22 E 2 156 Amege Tig Teut with qe the charge on an atom labelled Z freut the cutoff radius and r the magnitude of the separation vector Ey Lat 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 ay f1 1 l i i gq 1 Ty _ 2 ris rege Tij ij Pod ra Tout gt ia i 4Areoe Ti i row Teut i i with the force on an atom j given by qiqj 1 1 mo 2 158 j rege E faj with the force on atom 7 the negative of this The force shifted Coulomb potential
39. In this local frame the so called Principal Frame the inertia tensor is therefore constant The orientation of the local body frame with respect to the space fixed frame is described via a four dimensional unit vector the quaternion q q0 1 92 43 3 157 An alternative approach is to define basic and secondary particles The basic particles are the minimun number needed to define a local body axis system The remaining particle positions are expressed in terms of the COM and the basic particles Ordinary bond constraints can then be applied to the basic particles provided the forces and torques arising from the secondary particles are transferred to the basic particles in a physically meaningful way 85 STFC Section 3 6 and the rotational matrix R to transform from the local body frame to the space fixed frame is the unitary matrix R 2 q 9 4 93 amp G 80 G 2 99 49 41 3 158 qg 2 49 909 2 91 9 92 2 2 dii ad a 2 q 93 do 92 a2 43 4 91 9 9 B 9 so that if d is the position of an atom in the local body frame with respect to its COM its position in the universal frame w r t its COM is given by d R d 3 159 Upi With these variables defined we can now consider the equations of motion for the rigid body unit 3 6 2 Integration of the Rigid Body Equations of Motion The equations of translational motion of a rigid body are the same as those describing
40. Note that one needs to specify the three integers kmaxa kmaxb kmaxc referring to the three spatial directions to ensure the reciprocal space sum is equally accurate in all directions The values of kmaxa kmaxb and kmaxc must be commensurate with the cell geometry to ensure the same minimum wavelength 103 STFC Section 4 4 is used in all directions For a cubic cell set kmaxa kmaxb kmaxc However for example in a cell with dimensions 2A 2B C ie a tetragonal cell longer in the c direction than the a and b directions use 2kmaxa 2kmaxb kmaxc If the values for the kmax used are too small the Ewald sum will produce spurious results If values that are too large are used the results will be correct but the calculation will consume unnecessary amounts of cpu time The amount of cpu time increases proportionally to kmaxa x kmaxb x kmaxc It is worth noting that the working values of the k vectors may be larger than their original values depending on the actual processor decomposition This is to satisfy the requirement that the k vector FFT transform down each direction per domain is a multiple of 2 3 and 5 only which is due to the GPFA code single 1D FFT which the DaFT implementation relies on This allowes for greater flexiblity than the power of 2 multiple restriction in DL_POLY 4 predicessor DL POLY 3 As a consequence however execution on different processor decompositions may lead to different working lengths of
41. RBs degrees of freedom 89 Chapter 4 Construction and Execution Scope of Chapter This chapter describes how to compile a working version of DL_POLY 4 and run it 90 STFC Section 4 1 4 1 Constructing DL POLY 4 an Overview 4 1 1 Constructing the Standard Versions DL_POLY_4 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 4 is supplied as a UNIX compressed file tarred and gzipped This must uncom pressed and un tared to create the DL_POLY 4 directory Section 1 4 2 In the build subdirectory you will find the required DL_POLY 4 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 selects
42. 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 104 STFC Section 4 4 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 message number is an integer which used to identify the appropriate message to be printed A full list of the DL_POLY 4 error messages and the appropriate user action can be found in Appendix D of this document 105 Chapter 5 Data Files Scope of Chapter This chapter describes all the input and output files for DL_POLY 4 examples of which are to be found in the data sub directory 106 STFC Section 5 1 5 1 The INPUT Files REVCON OUTPUT HISTORY CONTROL DEFECTS FIE
43. an analytical poten tial in the FS class It has the form Vij rij 4 O 2 94 Tij F p eym Pij iz with parameters a n M C Gupta potential 46 gupt The Gupta potential is another analytical potential in the FS class It has the form ri T Vij rg Aexp pt To TIT Pij rij exp 205 2 2 95 F pi ByYpi with parameters A ro p B qij 30 STFC Section 2 3 All of these metal potentials can be decomposed into pair contributions and thus fit within the general tabulation scheme of DL_POLY_4 where they are treated as pair interactions though note that the metal cutoff rmet has nothing to do with short ranged cutoff ryaw DL _POLY 4 calculates this potential in two stages the first calculates the local density p for each atom and the second calculates the potential energy and forces Interpolation arrays vmet gmet and fmet METAL_GENERATE METAL_TABLE_READ are used in both these stages in the same spirit as in the van der Waals interaction calculations The total force e on an atom k derived from this potential is calculated in the standard way i VkUmetal 2 96 We rewrite the EAM FS potential 2 90 as Umetal i E r U 5 y Vig Tig 2 97 i l jf Us S Flo i 1 where r rj r The force on atom k is the sum of the derivatives of U and U2 with respect to rk which is recognisable as a sum of pair forces
44. as follows 1 Cosine potential cos U ijkn A 1 cos Meijkn 6 2 36 2 Harmonic harm U Pijkn n dijkn do 2 37 3 Harmonic cosine hcos U dijkn 5 cos dijkn cos 0 2 38 4 Triple cosine cos3 U d 5 41 1 cos 6 Ax 1 cos 26 As 1 cos 36 2 39 5 Ryckaert Bellemans 40 with fixed constants a f ryck U A a b cos c cos d cos e cos f cos d 2 40 20 STFC Section 2 2 6 Fluorinated Ryckaert Bellemans 41 with fixed constants a h rbf U A a b cos c cos d cos e cos d f cos g exp h 7 2 41 7 OPLS torsion potential opls U Ao A 1 cos Ag 1 cos 2 Az 1 cos 3 2 42 In these formulae ijkn is the dihedral angle defined by duri cos Bl Es 2 43 with 2 44 Lij X Lik Tjk X Tien B rijs Tjk Tkn i SO 2 z Mes x Call X Ten With this definition the sign of the dihedral angle is positive if the vector product rij X Ljk X Ljk X Len is in the same direction as the bond vector r and negative if in the opposite direction The force on an atom arising from the dihedral potential is given by d fe gra Fist 2 45 with being one of i j k n and a one of x y z This may be expanded into 1 0 TAO iikn F ijkn B Tij Y Lkn 2 4 are U ijkn cot Daga Pik Bra L
45. atmospheres at all times The unit of energy is either DL_POLY units specified above or in other units specified by the user at run time The default is DL_POLY units STFC Section 1 4 1 3 9 Error Messages All errors detected by DL_POLY 4 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_4 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 Directory Structure Vac The entire DL_POLY_4 package is stored in a UNIX directory structure The topmost directory is named dl poly 4 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 contents source primary subroutines for the DL_POLY 4 package utility subroutines programs and example data for all utilities data example input and output files for DL_POLY 4 bench large test cases suitable for benchmarking execute the DL_POLY 4 run time
46. atomic coordinates is the centre of the cell Parallelepiped periodic boundaries imcon 3 LU Figure A 3 The parallelepiped MD cell 181 STFC 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 4 CONFIG file by the vectors La Laz2 La3 Mb Mb2 Mbs Nc1 Nc2 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_P
47. atomic forces the Verlet neighbour list is constructed by LINK_CELL_PAIRS routine using link cell lists Special measures are taken so that the Isit excludes i pairs of atoms that are both in frozen state as well as ii pairs in which one of the atoms has the other in its exclusion list The last is build by BUILD_EXCL_INTRA where the specification of bonded like interactions in the FIELD file are processed Various other subroutines are then called to calculate specific contri butions by different interactions For example VDW_FORCES for the short range van der Waals forces Section 2 3 1 METAL_LRC METAL_LD_COMPUTE and METAL_FORCES for the metal inter actions Section 2 3 2 and EWALD_SPME_FORCES EWALD_REAL_FORCES EWALD_FROZEN_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 and EXTERNAL_FIELD_CORRECT 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 ZERO_K_OPTIMISE and MIN IMISE_RELAX are sometimes required to reduce the magnitude of badly equilibrated forces and to steer the MD system towards
48. bond constraints or and PMF constraints are present in the system the quantity Trig Vv will not converge to the exact value of Pix This is due to iterative nature of the constrained motion in which the constrain and PMF stresses are calculated retrospectively to the forcefield stress 3 5 2 Langevin Barostat DL_POLY 4 implements a Langevin barostat 30 for isotropic and anisotropic cell fluctuations Cell size variations For isotropic fluctuations the equations of motion are dr v t n t r t 68 STFC Section 3 5 _ Ff 3 kg Text Pmass 27 Xp Lua 1080 vit BOVO where x and xp are the user defined constants positive in units of ps specifying the thermostat and barostat friction parameters R t is the Langevin stochastic force see equation 3 34 and Rp is the stochastic Langevin pressure variable Ro Rp t 2 xp Pmass kaT t t 3 82 which is drawn from Gaussian distribution of zero mean and unit variance Gauss 0 1 scaled by a kp is the Boltzmann constant T the target temperature and pmass the barostat mass H is the cell matrix whose columns are the three cell vectors a b c The conserved quantity these generate is ty Hyer Hyve Poss 10 PextV t 3 83 The VV implementation of the Langevin algorithm only requires iterations if bond or PMF con straints are present 4 until satisfactory convergence of the constraint forces is achieved These
49. can be elegantly extended to emulate long range ordering by including distance depending damping function er fc a rij identical to that seen in the real space portion of the Ewald sum and thus mirror the effective charge screening 49 as shown below U r GQ raat Lee Teut j 2a exp a iw r _ Amege Tij Chi vi out er fela Teut n Le Teut 2a exp a Tout Tout 2 159 Teut Teit VT Teut with the force on an atom j given by Ud er fela rij 2a exp a ri Arege a vi Tij vo S Teut 2a exp o rta Lig 2 160 er fc Teut yT Tout with the force on atom 7 the negative of this Tij It is worth noting that as discussed in 49 and references therein this is only an approximation of the Ewald sum and its accuracy and effectiveness become better when the cutoff is large gt 10 preferably 12 The contribution to the atomic virial is W tys i 2 161 which is not the negative of the potential term in this case The contribution to be added to the atomic stress tensor is given by een 2 162 where a 8 are x y z components The atomic stress tensor is symmetric In DL_POLY 4 these forces are handled by the routine COUL_FSCP_FORCES 43 STFC 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
50. config_module o pmf_module o setup_module o pmf_vcoms o comms_module o config_module o kinds_f90 0 pmf_module o setup_module o quaternions_container o comms_module o config_module o kinds_f90 0 rigid_bodies_module o setup_module o rdf_collect o config_module o kinds_f90 0 setup_module o site_module o statistics_module o rdf_compute o comms_module o config_module o kinds_f90 0 setup_module o site_module o statistics_module o read_config o comms_module o config_module o domains_module o io_module o kinds_f90 0 parse_module o setup_module o read_config_parallel o comms_module o config_module o domains_module o io_module o kinds_f90 0 parse_module o setup_module o read_control o comms_module o config_module o defects1_module o development_module o kinds_f90 0 langevin_module o metal_module o parse_module o setup_module o vdw_module o read_field o angles_module o bonds_module o comms_module o config_module o constraints_module o core_shell_module o dihedrals_module o external_field_module o four_body_module o inversions_module o kinds_f90 0 metal_module o parse_module o pmf_module o rigid_bodies_module o setup_module o site_module o statistics_module o tersoff_module o tethers_module o three_body_module o vdw_module o read_history o comms_module o config_module o domains_module o io_module o kinds_f90 0 parse_module o setup_module o site_module o regauss_temperature o comms_module o config_module o kinds_f
51. consistency in the full step velocity u t is obtained Initial estimates of x t and n t at full step are calculated using an unconstrained estimate of the velocity at full step v t 1 FF f t f t At 3 111 2 LFV The iterative part is as follows v t tat lt u t At At De x t r t At nu r t At v t sat 3 112 H t At nt H t V t At n t V t 3 SHAKE 4 Full step velocity Fore ol 2 At bla 540 3 113 5 Thermostat n vo t oO OR i Bow 1 3 114 6 Barostat At n t 1 a Pat P t 3 115 Several iterations are required to obtain self consistency In DL_POLY 4 the number of iterations is set to 7 8 if bond constraints are present Note also that the change in box size requires the SHAKE algorithm to be called each iteration The Berendsen algorithms conserve total momentum but not energy The VV and LFV flavours of the Berendsen barostat and thermostat are implemented in the DL_POLY_4 routines NPT_B0_vv and NPT_BO_LFV respectively The routines NPT_B1_vv and NPT_B1_LFV implement the same but also incorporate RB dynamics Cell size and shape variations The extension of the isotropic algorithm to anisotropic cell variations is straightforward A tensor n is defined as O L Pos 1 2 0 V 0 3 116 Is 75 STFC Section 3 5 where 1 is the identity matrix Then new cell vectors and volume are given by H t At n t H V t At
52. cos e cos f cos g exp h 7 opls OPLS torsion Ao At Ao U Ao 41 1 cos po A3 do Ag 1 cos 2 do Az 1 cos 3 do t is the i j k l dihedral angle 12 inversions n where n is the number of inversion interactions present in the molecule Each of the following n records contains inversion key ad index 1 i integer index 2 j integer index 3 k integer index 4 1 integer variable 1 real variable 2 real variable 3 real potential key see Table 5 11 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 potential parameter see Table 5 11 The meaning of the variables 1 2 is given in Table 5 11 137 STFC Section 5 1 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 3 functional formt harm Harmonic k do U 5 do hcos Harmonic cosine k do U k cos cos o plan Planar A U A 1 cos xpln Extended planar k m Po Ulo E 1 cos m o t is the i j k l inve
53. 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 517 error allowed configuration information levels are 0 1 and 2 DL_POLY 4 has found an erroneous configuration information level 0 le l le 2 i for the tra jectory option in CONTROL or ii in the header of CONFIG Action Correct the error in CONFIG and rerun Message 518 error control distances for variable timestep not intact DL_POLY 4 has found the control distances for the variable 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 is incompatible or does not exist Either REVOLD does not exist or its formatting is incompatible Action Change the restart option in CONTROL and rerun Message 520 error domain decomposition failed A DL_POLY 4 check during the domain decomposition mapping has been violated The number of nodes allowed for imcon 0 is only 1 2 4 and 8 The number of nodes allowed for imcon 6 258 STFC Appendix D is restricted to 2 along the z direction The number of nodes should not be a prime number since these are not factorisable decomposable Action You must ensure DL_POLY 4 execution on a number of
54. 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 MSDTMP File The MSDTMP file is the dump file of individual atomic mean square displacements square roots in A and mean square temperature square roots in Kelvin Its principal use is for off line analysis The file is written by the subroutine MSD_WRITE The control variables for this file are lmsd nstmsd istmsd which are created internally based on information read from the msdtmp directive in the CONTROL file see Section 5 1 1 The MSDTMP file will be created only if the directive msdtmp appears in the CONTROL file The MSDTMP 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 MSDTMP has the following structure record 1 header a52 file header record 2 megatm integer number of atoms in simulation cell in last frame frame integer number configuration frames in file records integer number of records in file
55. integration algorithms couched in both Velocity Verlet VV and Leapfrog Verlet LFV manner 21 These generate NVE NVEgin NVT NPT and NoT ensembles with a selection of thermostats and barostats Parallel versions of the RATTLE 22 and SHAKE 7 algorithms are used for solving bond constraints in the VV and LFV cast integrations respectively The rotational motion of rigid bodies RBs is handled with Fincham s implicit quaternion algorithm FIQA 23 under the LF scheme or with the NOSQUISH algorithm of Miller et al 24 under the VV integration The following MD algorithms are available 1 Constant E algorithm 2 Evans constant Ex n algorithm 25 Langevin constant T algorithm 26 Ae Ww Andersen constant T algorithm 27 Berendsen constant T algorithm 28 Nos Hoover constant T algorithm 29 Langevin constant T P algorithm 30 Berendsen constant T P algorithm 28 O 0 N Q A Nos Hoover constant T P algorithm 29 10 Martyna Tuckerman and Klein MTK constant T P algorithm 31 11 Langevin constant T o algorithm 30 12 Berendsen constant T algorithm 28 13 Nos Hoover constant T algorithm 29 14 Martyna Tuckerman and Klein MTK constant T algorithm 31 STFC Section 1 3 1 2 6 DL POLY 2 features incompatible or unavalable in DL POLY 4 e Force field Rigid bodies connected with constraint links are not available Shell models specification is solely
56. is exercised to prevent introduction of non zero net momentum when scaling velocities Users are reminded to use for target temperature the temperature at which the original system was equilibrated in order to avoid simulation instabilities Due to the unphysical nature of this temperature control the thermostat width does not matter to the same extent as in the case of the Langevin thermostat 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 Therefore ensembles lose their meaning as such and so does the conserved quantity for true ensembles If the pseudo thermostat option is specified without any type of temperature con trol in CONTROL then both types will be applied in the order Langevin Direct at each time step during the simulation The algorithms are developed in the DL_POLY_4 routines PSEUDO_VV and PSEUDO_LFV re spectively 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 simulat
57. minimised configuration expressed in DL_POLY 4 units 1 3 8 and 3 the configuration energy of the initial structure expressed in DL_POLY 4 units 1 3 8 5 2 5 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 from running DL_POLY 4 It is meant to be a human readable file destined for hardcopy output 5 2 5 1 Header Gives the DL_POLY 4 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 5 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 5 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 par
58. name 157 STFC Section 5 2 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 2x maxatdm if msdtmp option is used 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 current MD time step time real elapsed simulation time nument integer number of array elements to follow record ii stpval 1 stpval 5 engcns real total extended system energy i e the conserved quantity temp real system temperature engcfg real configurational energy engsrc real short range potential energy engcpe real electrostatic energy record iii stpval 6 stpval 10 engbnd real chemical bond energy engang real valence angle and 3 body potential energy engdih real dihedral inversion and 4 body potential energy engtet real tethering energy enthal real enthalpy total energy PV
59. normal pressure and constant surface tesnison NP yT 56 by semi isotropic constraining of the barostat equation of motion and slight amending the thermostat equation of motion and the conserved quantity to gaa Paa gea OL VO 4 REO 1 inant A 2 9 Napglt n gol des zia VO 4 Pill 1 lt ez a f z 0 aA B 2 y 2 d i 2Ekin t Pmass Tr n t i no 20 3 kp Ton 3 150 q a 3 150 mass t 2 Pmass Trin n t HynpPayr Hnvet E Pi z Pot V t f 3 kp Text J x s ds where Yext is the user defined external surface tesnion and h t V t Axy t is the instantenious hight of the MD box or MD box volume over area The Martyna Tuckerman Klein equations of motion have same conserved quantities as the Nos Hoover s ones but are proven 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 61 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 4 rou tines NPT_MO_VV and NST_MO_vv in VV flavour and NPT_MO_LFV and NST_MO_LFV LFV flavour respectively The corresponding routines incorporating RB dynamics are NPT_M1_VV and NPT_M1_LFV and NST_M1_vv and NST_M1_LFV 3 6 Rigid Bodies and Rotational Integration Algorithms 3 6 1 Description of Rigid Body Units A rigid body unit is a collection of poin
60. npt_10_1fv f90 npt_b0_1fv f90 npt_hO_lfv f90 npt_m0_ nst_10_1fv f90 nst_b0_1fv f90 nst_hO_lfv f90 nst_m0_ nve_i_lfv f90 nvt_e1_lfv f90 nvt_11_1fv f90 nvt_al_lfv f90 nvt_bi_lfv f90 nvt_hi_ npt_11_1fv f90 npt_b1_1fv f90 npt_hi_lfv f90 npt_m1_ nst_11_1fv f90 nst_b1_1fv f90 nst_hi_lfv f90 nst_mi_ md_1fv f90 Examine targets manually all echo echo You MUST specify a target platform echo echo Please examine Makefile for permissible targets echo 90 90 90 90 90 90 lfv 90 90 lfv lfv lfv lfv lfv echo If no target suits your system create your own echo using the generic target template provided in echo this Makefile at entry uknown_platform echo Fetch the Velocity Verlet subroutines FILES_VV MAKE links_vv 190 90 90 90 90 A A STFC Appendix C 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_platform MAKE LD path to FORTRAN90 Linker loaDer LDFLAGS appropriate flags for LD MPI libr
61. o rigid_bodies_move o minimise_relax o core_shell_relax o zero_k_optimise o nvt_e0_scl o nvt_el_scl o nvt_b0_scl o nvt_bi_scl o pseudo_vv o constraints_shake_vv o pmf_shake_vv o constraints_rattle o pmf_rattle o nvt_h0_scl o npt_h0_scl o nst_h0_scl o nve_O_vv o nvt_e0_vv o nvt_10_vv o nvt_a0_vv o nvt_b0_vv o nvt_h0_vv o A npt_10_vv o npt_b0_vv o npt_h0_vv o npt_m0_vv o 212 STFC Appendix C nst_10_vv o nst_b0_vv o nst_h0_vv o nst_m0_vv o nvt_hi_scl o npt_h1_scl o nst_hi_scl o nve_1_vv o nvt_el_vv o nvt_li_vv o nvt_al_vv o nvt_b1_vv o nvt_hi_vv o npt_li_vv o npt_bi_vv o npt_hi_vv o npt_mi_vv o nst_11_vv o nst_b1_vv o nst_hi_vv o nst_ml_vv o pseudo_lfv o constraints_shake_lfv o pmf_shake_lfv o nve_0_lfv o nvt_e0_lfv o nvt_10_lfv o nvt_a0_lfv o nvt_b0_lfv o nvt_h0_lfv o npt_10_lfv o npt_b0_lfv o npt_h0_lfv o npt_m0_lfv o nst_10_lfv o nst_b0_lfv o nst_h0_lfv o nst_m0_lfv o nve_1_lfv o nvt_el_lfv o nvt_11_1lfv o nvt_al_lfv o nvt_b1_lfv o nvt_hi_lfv o npt_11_1fv o npt_b1_lfv o npt_h1_lfv o npt_mi_lfv o nst_11_1fv o nst_b1_lfv o nst_h1_1lfv o nst_m1_lfv o xscale o core_shell_kinetic o regauss_temperature o defects_reference_read o defects_reference_read_parallel o defects_reference_write o defects_reference_export o defects_reference_set_halo o defects_link_cells o defects1_write o defects_write o msd_write o z_density_collect o statistics_collec
62. of 6 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 al0 i_atomic label from CONFIG iatm integer atom index from CONFIG record b XXX real x coordinate yyy real y coordinate ZZZ real z coordinate This is followed by the nv vacancies for the current timestep as each vacancy has the following data lines record a atmnam a10 v_atomic label from REFERENCE iatm integer atom index from REFERENCE record b XXX real x coordinate from REFERENCE yyy real y coordinate from REFERENCE ZZZ real z coordinate from REFERENCE 5 2 4 The CFGMIN File The CFGMIN file only appears if the user has selected the programmed minimisation option di rective minimise or optimise in the CONTROL file Its contents have the same format as the 152 STFC Section 5 2 CONFIG file see section 5 1 2 but contains only atomic position data and will never contain ei ther velocity or force data i e parameter levcfg is always zero In addition three extra numbers appear on the end of the second line of the file 1 an integer indicating the number of minimisation cycles required to obtain the structure 2 the configuration energy of the
63. pair potential is then defined internally by the combination of two atom labels As well as the numerical parameters defining the potentials DL POLY 4 must also be provided with a cutoff radius ryaw 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 range 0 to ryqw A second array gvdw is also calculated which is related to the potential via the formula G rij ry Uri 2 84 Tij 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 4 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 E reo Pij 2 85 where r r ri The force on atom is the negative of this j The contribution to be added to the atomic virial for each pair interaction is The con
64. 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 which 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 260 STFC Appendix D Message 570 error unsupported image convention 0 for system expansion option nfold System expansion is possible only for system with periodicity on their boundaries Action Change the image convention in CONFIG to any other suitable periodic boundary condition Message 580 error replay HISTORY option can only be used for structural prop erty recalculation No structural property has been specified for this option to activate itself Action In CONTROL specify properties for recalculation RDFs z density profi
65. processing This should never happen It simply means that DL_POLY 4 has ceased processing the FIELD data but has not reached the end of the file or encountered a close directive Probable cause corruption of the DL_POLY 4 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 4 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 226 STFC Appendix D 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_4 executable are corrupted Action Recompile the program or recreate the FIELD file If neither of these works send the problem to us 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 potenti
66. see section 5 1 7 to which DL_POLY 4 is redirected by the FIELD file data The FS potentials are defined via the necessary parameters in the FIELD file 2 3 3 Tersoff Potential The Tersoff 16 potential has been developed to be used in multi component covalent systems by an effective coupling of two body and higher many body correlations into one model The central idea is that in real systems the strength of each bond depends on the local environment i e an atom with many neighbors forms weaker bonds than an atom with few neighbors Effectively it is a pair potential the strength of which depends on the environment It has 11 atomic and 2 bi atomic parameters The energy is modelled as a sum of pair like interactions where however the coefficient of the attractive term in the pair like 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 U fclrij fr ra tij fari gt 2 122 where fr and fa are the repulsive and attractive pair potential respectively fr ri Aig amp xp a riz fari Bij exp bij rig 2 123 and fc is a smooth cutoff function with parameters R and S so chosen that to include the first neighbor shell 1 Tij lt Rij 1 1 ig Rij S folri 5 5 COS x p Rij lt Tij lt Sij x 2 124 0 Tij gt Sig Jij expresses a dependence that can accentuate or diminish the attractive force relative
67. 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 which is equvalent to spme sum 0 35 12 12 16 would set a 0 35 A kmaxa 12 kmaxb 12 and kmaxc 16 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 Section 5 2 5 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 variables that control the accuracy a the Ewald convergence parameter freut the real space force cutoff and the kmaxa kmaxb and kmaxc integers that specify the dimensions of the SPME charge array as well as FFT arrays The three integers effectively define the range of the reciprocal Important note As the SPME method substitues the standard Ewald the values of kmaxa kmaxb and kmaxc are the double of those in the prescription of the stan
68. site atomic index Up to 15 sites can be specified on the first record Additional records can be used if necessary Up to 16 sites are specified per record thereafter This directive and associated data records need not be specified if the molecule contains no rigid units See the note on the atomic indices appearing under the shell directive above teth n where n is the number of tethered atoms in the molecule It is followed n records specifying the tehered 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 Table 5 7 Tethering Potentials key potential type Variables 1 3 functional form harm Harmonic k U r 5 k ri pe 0 rhrm Restraint k Te U r gt k ri pro Iri rt 0 lt r Cr 5 kr k rellri rt re rr gt r quar Quartic k k k U r k ri iy k ri nimos 7 ri i 9 bonds n where n is the number of flexible chemical bonds in the molecule Each of the subsequent n records contains 133 STFC Section 5 1 10 11 bond key ad p
69. 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 didj Uri 2 163 ri 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 4 it is assumed that this function has the form e r er 2 164 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 ES e 2 165 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 2 166 which is 2 times the potential term The contribution to be added to the atomic stress tensor is given by 2E E 2 167 where a 8 are x y z components The atomic stress tensor is symmetric In DL POLY 4 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 induce
70. the following UNIX commands java jar java GUI jar 1 Qu In other words the macro invokes the Java Virtual Machine which executes the instructions in the Java archive file GUI jar which is stored in the java subdirectory of DL_POLY_4 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 TABEAM TABEAM 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 last three copy commands may not be necessary 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 cp CONTROL data TEST 1 CONTROL cp FIELD data TEST 1 FIELD cp CONFIG data TEST 1 CONFIG cp TABLE data TEST 1 TABLE cp TABEAM data TEST 1 TABEAM cp REFERENCE data TEST 1 REFERENCE mv OUTPUT data TEST 1 0UTPUT mv STATIS data TEST 1 STATIS mv REVCON data TEST 1 REVCON 185 STFC Appendix B mv REVIVE mv HISTORY mv D
71. the k vectors FFT transforms and therefore slightly different SPME forces energies whithin the same level of SPME Ewald precision accuracy specified Note that although the number of processors along a dimension of the DD grid may be any number numbers that have a large prime as a factor will lead to inefficient performance 4 4 Warning and Error Processing 4 4 1 The DL_POLY 4 Internal Warning Facility DL_POLY 4 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 4 supplying a default value or DL_POLY 4 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 notifying the user of the nature of the problem 4 4 2 The DL_POLY 4 Internal Error Facility DL_POLY 4 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
72. the motion of a single atom except that the force is the total force acting on the rigid body i e F in equation 3 154 and the mass is the total mass of the rigid body unit i e M in equation 3 151 These equations can be integrated by the standard Verlet LF or VV algorithms described in the previous sections Thus we need only consider the rotational motion here The rotational equation of motion for a rigid body is r gan dt dt in which J is the angular momentum of the rigid body defined by the expression I w 3 160 Nsites j l and w is the angular velocity The vector 7 is the torque acting on the body in the universal frame and is given by des 3 162 The rotational equations of motion written in the local frame of the rigid body are given by Euler s equations di a ou da Wy z Lox wy ia La Wy We 3 163 ly x Ty A gt ch a Izz The vectors and w are the torque and angular velocity acting on the body transformed to the local body frame Integration of is complicated by the fact that as the rigid body rotates so does the local reference frame So it is necessary to integrate equations 3 163 simultaneously 86 STFC Section 3 6 with an integration of the quaternions describing the orientiation of the rigid body The equation describing this is qo do q G 43 0 i 1 n A q A 4 B 2 Wa 3 164 q2 q2 43 do TA Wy d3 ga 2 q Wy Rotational motion in DL
73. to NPT simula tions only 247 STFC Appendix D 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 Action Either simulate the system with a periodic boundary or use another ensemble 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 4 arrays Probable cause your system has expanded unacceptably much to DL_POLY_4 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 4 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_4 has found more than one ensemble directive in the CONTROL file Action Lo
74. to a temperature of 10 Kelvin The subroutine that performs this procedure is ZERO_K_OPTIMISE 2 Conjugate Gradients Metod CGM minimisation This is nominally a simple minimisation of the system configuration energy using the conjugate gradients method 55 The algorithm coded into DL_POLY 4 is an adaptation that allows for rotation and translation of rigid bodies Rigid contraint bonds however are treated as stiff harmonic springs a strategy which we find does allow the bonds to converge within the accuracy required by SHAKE The subroutine that performs this procedure is MINIMISE_ RELAX which makes use of MIN IMISE_MODULE 3 Programmed energy minimisation involving both MD and CGM This method combines the two as minimisation is invoked by user defined intervals of usually low temperature dynamics in a cycle of minimisation dynamics minimisation etc which is intended to help the structure relax from overstrained conditions see Section 5 1 1 When using the programmed minimisation DL_POLY 4 writes and rewrites the file CFGMIN 5 2 4 which represents the lowest energy structure found during the programmed minimisation CFGMIN is written in CONFIG file format see section 5 1 2 and can be used in place of the original CONFIG file 97 STFC Section 4 2 It should be noted that none of these algorithms permit the simulation cell to change shape It is only the atomic structure that is relaxed After which it is as
75. to incorporate constraints in minimisation procedures as it leads to ill conditioning However if the constraints in the original structure are satisfied we find that provided only small atomic displacements are allowed during relaxation it is possible to converge to a minimum energy structure Furthermore provided the harmonic springs are stiff enough it is possible afterwards to satisfy the constraints exactly by further optimising the structure using the stiff springs alone without having a significant affect on the overall system energy c Systems with independent constraint bonds and rigid bodies may also be minimised by these methods 3 Of the three minimisation strategies available in DL_POLY_4 only the programmed min imiser is capable of finding more than one minimum without the user intervening 4 Finally we emphasise once again that the purpose of the minimisers in DL_POLY 4 is to help improve the quality of the starting structure and we believe they are adequate for that purpose We do not recommend them as general molecular structure optimisers They may however prove useful for relaxing crystal structures to 0 Kelvin for the purpose of identifying a true crystal structure 4 2 5 Simulation Efficiency and Performance Although the DL_POLY 4 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 cesso
76. to the repulsive force according to the local environment such that a al se N Ni MN Vig Xij 1 Bi Li TA Lij 5 fo rik wik 9 0 jk 2 125 kZi j ce ce Qi 1 E a 1 51 d d hi COS Og 37 STFC Section 2 3 where the term defines the effective coordination number of atom i i e the number of nearest neighbors taking into account the relative distance of the two neighbors i and k rij ri and the bond angle 0 x between them with respect to the central atom i The function g has a minimum for h cos 0 x the parameter d determines how sharp the dependence on angle is and c expresses the strength of the angular effect Further mixed parameters are defined as aij ai aj 2 bij bi bj 2 Aj AAJ y By BB 2 126 Ri RRA E Sij SiS Singly subscripted parameters 11 such as a and n 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 2 127 which define only one independent parameter each per pair of atom types The x parameter is used to strengthen or weaken 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 In DL_POLY 4 a third additional parameter A is also available It only takes the
77. under which the code will be supplied By proceeding further with the registration and download process you are signalling your acceptance of the terms of this licence Click the Registration button to find the registration page where you will be invited to enter your name address and e mail address The code is supplied free of charge to academic users but commercial users will be required to purchase a software licence Once the online registration has been completed information on downloading the DL_POLY 4 source code will be sent by e mail so it is therefore essential to supply a correct e mail address The data and bench subdirectories of DL_POLY 4 are not issued in the standard package but can be downloaded directly from the FTP site in the ccp5 DL_POLY DL_POLY 4 0 directory Note Daresbury Laboratory is the sole centre for the distribution of DL POLY 4 and copies obtained from elsewhere will be regarded as illegal and will not be supported 1 6 OS and Hardware Specific Ports DL_POLY 4 is available as a Microsoft port offered with Microsoft http www microsoft com self installers MSI for 32 and 64 bit Windows OS s to build an OS native executable which can utilise the parallelism of modern multi core multi processor personal computers DL_POLY 4 is also available as a CUDA OpenMP port offered as extra source within the source directory see the README txt for further information The purpose of this developm
78. user may compile the code by selecting the appropriate Makefile from the build directory cp build Makefile_MPI Makefile for parallel execution MPI is needed or cp build Makefile_SRLx Makefile for serial execution no MPI needed Note that in comms_module f90 it is crucial that line 13 reads as Use mpi_module for serial compilation and Use mpi for parallel compilation which is the default If the parallel OS environment you are compiling on is not fully F90 compatible then the Use mpi entry in comms_module f90 will be interpreted as erroneous This is easly overcome by commenting out Use mpi and insering Include mpif h after Implicit None If there is an entry in the Makefile for the particular combination of architecture compiler amp MPI library then the user may instantiate the compilation by make entry If there is not a suitable entry the user should advise with a computer scientist or the administrator of the particular machine The necessary components for the sourse compilation are 1 a FORTRAN90 compliant compiler if the full PATH to it is not passed to the DEFAULT ENVIRONMENT PATH then it MUST be explicitly supplied in the Makefile 2 MPI2 or MPI1 MPI I 0 libraries COMPILED for the architecture and the tageted compiler if the full PATH to these is not passed to the DEFAULT ENVIRONMENT PATH then it MUST be explicitly suppli
79. virial correction rE naana a ee n 3 Tmet Aro 3 n 3 N Uy m ee 2 116 m 3 Fmet 2 00 35 STFC Section 2 3 5 Gupta virial correction p 2nNpAro To roy roy OW ro Tag ria Br et p Or met p 6 Dp x Tmet no exp p ro dal 2 3 jj LNT OL Tr T Tr Uy LAS at lt oe 01 To qij dij dij dij Ja mes no NB P dij di 2 8 i 2 In the energy and virial corrections we have used the approximation N 1 2 N NA a 2 118 i lt p gt where lt 0 23 is regarded as a constant of the system In DL_POLY 4 the metal forces are handled by the routine METAL_FORCES The local density is cal culated by the routines METAL _LD_COLLECT_EAM METAL _LD_COLLECT_FST METAL _LD_COMPUTE METAL_LD_SET_HALO and METAL_LD_EXPORT The long ranged corrections are calculated by METAL_LRC Reading and generation of EAM table data from TABEAM is handled by METAL_TABLE_READ and METAL_TABLE_DERIVATIVES Notes on the Treatment of Alloys The distinction to be made between EAM and FS potentials with regard to alloys concerns the mixing rules for unlike interactions Starting with equations 2 90 and 2 91 it is clear that we require mixing rules for terms Vij r j and p j r j when atoms and j are of different kinds Thus two different metals A and B we can distinguish 4 possible variants of each ra Ve ru and AA BB AB BA Pij rij Pij rah Pij rij
80. when DL_POLY 4 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 4 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 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 4 attempts to read more data from the CONFIG file than is actually present The probable cause is an incorrect or absent CONFIG file but it may be due to the FIELD file being incompatible in some way with the CONFIG file 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 simulati
81. wider range of densities 256 STFC Appendix D Message 507 error metal density embedding out of range In the case of EAM type of metal interactions this indicates that the electron density of a particle in the system has exceeded the limits for which the embedding function for this particle s type is defined as supplied in TABEAM In the case of Finnis Sinclair type of metal interactions this indicates that the density has become negative Action Reconsider the physical sanity and validity of the metal interactions in your system and this type of simulation You MUST change the interactions parameters and or the way the physical base of your investigation is handled in MD terms Message 508 error EAM metal interaction entry in TABEAM unspecified in FIELD The specified EAM metal interaction entry found in TABEAM is not specified in FIELD Action For N metal atom types there are 5N N 2 EAM functions in the TABEAM file One density N and one embedding N function for each atom type and N N 2 cross interaction functions Fix the table entries and resubmit Message 509 error duplicate entry for a pair interaction detected in TABEAM A duplicate cross interaction function entry is detected in the TABEAM file Action Remove all duplicate entries in the TABEAM file and resubmit Message 510 error duplicate entry for a density function detected in TABEAM A duplicate density function entry is detect
82. 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 may require a fourth file TABLE Section 5 1 6 which contains short ranged potential and force arrays for functional forms not available within DL_POLY_4 usually because they are too complex e g spline potentials and or a fifth file TABEAM Section 5 1 7 which contains metal potential arrays for non analytic or too complex functional forms and or a sixth file REFERENCE Section 5 1 4 which is similar to the CONFIG file and contains the perfect crystalline structure of the system 95 STFC Section 4 2 Examples of input files are found in the data sub directory which can be copied into the execute subdirectory using the select macro found in the execute sub directory A successful run of DL_POLY_4 will generate several data files which appear in the execute sub directory The most obvious one is the file OUTPUT Section 5 2 5 which provides an effective summary of the job run the input information starting configuration instanta
83. 0_vv f90 nst_10_vv f90 nst_b0_vv f90 nst_h0_vv f90 nst_m0_vv f90 nvt_h1_sc1 f90 npt_h1_sc1 f90 nst_hi_scl f90 nve_1_vv f90 nvt_el_vv f90 219 STFC Appendix C nvt_li_vv f90 nvt_ai_vv f90 nvt_bi_vv f90 nvt_hi_vv f90 npt_11_vv f90 npt_b1_vv f90 npt_h1_vv f90 npt_mi_vv 90 nst_11_vv f90 nst_b1_vv f90 nst_h1_vv f90 nst_m1_vv f90 md_vv f90 Define LeapFrog Verlet files FILES_LFV pseudo_lfv f90 constraints_shake_lfv f90 pmf_shake_lfv f90 nve_0_lfv f90 nvt_e0_lfv f90 nvt_10_1fv f90 nvt_a0_lfv f90 nvt_bO_lfv f90 nvt_h0_1fv f90 npt_10_1fv f90 npt_b0_1fv f90 npt_hO_lfv f90 npt_m0_lfv 90 nst_10_1fv f90 nst_b0_1fv f90 nst_hO_lfv f90 nst_m0_lfv 90 nve_1_1fv f90 nvt_ei_lfv f90 nvt_11_1fv f90 nvt_ai_lfv f90 nvt_b1_1fv f90 nvt_hi_lfv f90 npt_11_1fv f90 npt_b1_1fv f90 npt_hi_lfv f90 npt_m1_1fv f90 nst_11_1fv f90 nst_b1_1fv f90 nst_h1_1fv f90 nst_mi_lfv f90 md_1fv f90 A A Examine targets manually all echo echo You MUST specify a target platform 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_platform echo Fetch MPI SERIAL subroutines FILES_SERIAL MAKE links_serial links_serial for file in FILES_SERIAL do echo linking to file rm f file ln s SERIAL file fi
84. 1 62 63 64 65 66 67 Eastwood J W Hockney R W and Lawrence D N 1980 Comput Phys Commun 19 215 39 40 41 Fennell C J and Gezelter D J 2006 J Chem Phys 124 234104 43 45 116 117 Neumann M 1985 J Chem Phys 82 5663 44 Fuchs K 1935 Proc R Soc A 151 585 47 49 Essmann U Perera L Berkowitz M L Darden T Lee H and Pedersen L G 1995 J Chem Phys 103 8577 47 164 Fincham D and Mitchell P J 1993 J Phys Condens Matter 5 1031 49 Lindan P J D and Gillan M J 1993 J Phys Condens Matter 5 1019 50 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 50 97 Ikeguchi M 2004 J Comp Chemi 25 529 541 55 73 76 81 83 84 Ryckaert J P Ciccotti G and Berendsen H J C 1977 J Comput Phys 23 327 55 161 McCammon J A and Harvey S C 1987 Dynamics of Proteins and Nucleic Acids Cam bridge University Press 58 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 59 61 Melchionna S Ciccotti G and Holian
85. 1 VVI a ERAD ee AA v t 344 3 47 2 RATTLE_VV1 3 FF f t At f t 3 48 4 VV2 A v t At t At O 2 3 49 5 RATTLE VV2 63 STFC Section 3 4 6 Thermostat Note that the MD cell centre of mass momentum must not change a At If mi0 lt 1 exp Then TT kgT mi u t At au t Ab 11 02 v t At End Tf Batt At Gauss 0 1 3 50 The algorithm is self consistent and requires no iterations The LFV implementation of the Andersen algorithm is as follows 1 FF f t f t At 3 51 2 LFV 1 1 f t t At t At At u t 5 ul 5 At 1 r t At rt Atut At 3 52 3 Full step velocity 1 1 1 v t lt 5 ol JAM a t 7 0 3 53 4 Thermostat Note that the MD cell centre of mass momentum must not change At If uni lt 1 exp Then TT ien 1 kpT un t At al mi Gauss 0 1 1 1 1 1 u t ul t 54 End If 5 SHAKE The algorithm is self consistent and requires no iterations The VV and LFV flavours of the Andersen thermostat are implemented in the DL_POLY_4 routines NVT_AO_Vv and NvT_AO_LFV respectively The routines NVT_A1_vv and NVT_A1_LFV implement the same but also incorporate RB dynamics 3 4 4 Berendsen Thermostat In the Berendsen algorithm the instantaneous temperature is pushed towards the desired temper ature Text by scaling the velocities at each step by x i E Cac i yo CH
86. 196 STFC Appendix C defects_write o comms_module o config_module o defects1_module o defects_module o io_module o kinds_f90 0 parse_module o setup_module o site_module o deport_atomic_data o angles_module o bonds_module o comms_module o config_module o constraints_module o core_shell_module o dihedrals_module o domains_module o ewald_module o inversions_module o kinds_f90 0 langevin_module o minimise_module o msd_module o pmf_module o rigid_bodies_module o setup_module o statistics_module o tethers_module o development_module o comms_module o kinds_f90 0 parse_module o setup_module o dihedrals_14_check o kinds_f90 0 setup_module o dihedrals_forces o comms_module o config_module o dihedrals_module o kinds_f90 0 setup_module o vdw_module o dihedrals_module o kinds_f90 0 setup_module o dl_poly o angles_module o bonds_module o comms_module o config_module o constraints_module o core_shell_module o development_module o dihedrals_module o external_field_module o four_body_module o inversions_module o io_module o kinds_f90 0 kinetic_module o metal_module o msd_module o parse_module o pmf_module o rigid_bodies_module o setup_module o site_module o statistics_module o tersoff_module o tethers_module o three_body_module o vdw_module o md_1fv f90 md_vv f90 replay_history f90 domains_module o comms_module o kinds_f90 o error o comms_module o setup_module o ewald_excl_forces o config_module o ewal
87. 2 i 1 Al Tij Ori _ OV 1 35 VB fij ue OV 2 3V OVi ri Wo L Vig rij ij ri 2 103 i DIRE dr 9 2 103 i 1 j i Opi Oph Oto dl del 2 pis riz gt 7 Da vani OV w E iti Ori OV 3V Fip Org OF pi y OF 05 Opis rij y gt Tij pms Opi Op Orij 1 EAM virial The same as above 2 Finnis Sinclair virial 1 NN Y aL c co cit or rig c1 2earig rig i 1 j i OREA rij dy Wee SGD Were va f2 ry 4 30ST ma 2 104 i 1 jAt STFC Section 2 3 3 Extended Finnis Sinclair virial Y LSS al Tij c co cirij cari cari car as i 1 j i rij e ci 2c2Fi 30377 Acgrigi Tij 2 105 ESA Wo 222 3 Vet vri 2 rij d 4B rij d rija 4 Sutton Chen virial N N a tie En re Pre n Paen 2 106 Ip Tij 5 Gupta virial ey e i I Sas Tij ro 3 Di gt VPk vpj exp i Lera Tij 2 107 i lj i The contribution to be added to the atomic stress tensor is given by pesa 2 108 where a and indicate the x y z components The atomic stress tensor is symmetric The long ranged correction for the DL_POLY 4 metal potential is in two parts Firstly by analogy with the short ranged potentials the correction to the local density is 00 pi X pylri j 1 j i Tij lt Tmet Tij2Tmet pi DI puly DI pig riz pi 60 2 109 j l j t j 1 jzi 00 pi Amp pisirjar Tmet where p i
88. 2 QN Q Ta 87 STFC Section 3 6 It should be noted that vectors p and Y are 4 component vectors The quaternion momenta are first updated a half step using the formula p t p t SO i 3 172 Next a sequence of operations is applied to the quaternions and the quaternion momenta in the order il3 61 2 giLr 6t 2 gilr Bt giLr 6t 2 gilo 8t 2 3 173 which preserves the symplecticness of the operations see reference 31 Note that t is some submultiple of At In DL_POLY 4 the default is At 106t The operators themselves are of the following kind ge q cos C t q sin Cr t Pk q ef 5t p cos Gk t p sin Ck t Pep 3 174 where P is a permutation operator with k 0 3 with the following properties Po q do 41 42 43 Pa 4q1 do 93 92 3 175 Pza 4q 43 do 1 Ps q ia 42 41 qo gt and the angular velocity is defined as l r p R 3 176 nerd Equations 3 173 to 3 175 represent the heart of the NOSQUISH algorithm and are repeatedly applied 10 times in DL POLY 4 The final result is the quaternion updated to the full timestep value i e q t At These equations form part of the first stage of the VV algorithm VV1 In the second stage of the VV algorithm VV2 new torques are used to update the quaternion momenta to a full timestep At At p t At p t CR I At 3 177 3 6 3 Thermostats and Barostats coupling to the Rigid Bod
89. 38 A 0o r U 0 A 0 rij r msb stretch bend mmsb Compass 38 A BC amp U 0 A rij r3 rik TH 0 00 x msb_ all terms i Tk B rij ri C rik rig 10 is the 7 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 4 will calculate the non bonded pair potentials between the described atoms 136 STFC Section 5 1 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 Al m U A 1 cos m harm Harmonic k do U E 9 do hcos Harmonic cosine k Uo k cos cos o cos3 Triple cosine Ay Ao Az U 5 4 1 cos Ag 1 cos 2 Az 1 cos 3 ryck Ryckaert Bellemans 40 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 41 d
90. 4 2 2 The valence angle and associated vectors 1 2 eee ee 17 2 3 The dihedral angle and associated vectors ee 20 2 4 The L and D enantiomers and defining vectors 0002 000 23 2 9 The inversion angle and associated vectors o lt lt o lt 24 3 1 The SHAKE RATTLE_VV1 schematics and associated vectors 56 5 1 DL POLY 4 input left and output right files 2 2 505054 25024 aes 107 Ai The cube MID Gelli i ect A a a ee AE ee ee ae ta 181 AS The orthornomie MD cell i gio fa eae he e be ae eee Oe pi di 181 A 3 The parallelepiped MD cell 181 xii Chapter 1 Introduction Scope of Chapter This chapter describes the concept design and directory structure of DL_POLY_4 and how to obtain a copy of the source code STFC 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 amp Tim Forester and DL_POLY 4 written by Ilian Todorov amp Bill Smith 2 Both versions were originally written on behalf of CCP5 the UK s Collaborative Computational Project on Molecular Simulation which has been in existence since 1980 3 http www ccp5 ac uk DL_POLY The two forms of DL_POLY differ primarily in
91. 4 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 4 FIELD file permits a choice of units for input of energy parameters These may be electron volts eV k calories kcal k joules kJ Kelvin Kelvin or the DL_POLY 4 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 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 ind
92. 43 Andersen Thermostat e 63 3 4 4 Berendsen Thermostat 0002 eee ee ee ee ee 64 3 4 5 Nos Hoover Thermostat e 66 moo Barfoshate ono Gea a Pore hae oe we Se eo be he OR De Ae De 68 3 5 1 Instantaneous pressure and Stress 68 3 0 2 Langevin Barostat s s 66 552 i ee es 68 3 5 3 Berendsen Barostat lt cc 64 RE ee ee 74 3 0 4 Nos Hooyer Barostat e c eae sene ta oea e Shwe we ee ee 76 3 5 5 Martyna Tuckerman Klein Barostat LL 82 3 6 Rigid Bodies and Rotational Integration Algorithms 84 3 6 1 Description of Rigid Body Units 84 3 6 2 Integration of the Rigid Body Equations of Motion 86 3 6 3 Thermostats and Barostats coupling to the Rigid Body Equations of Motion 88 4 Construction and Execution 90 4 1 Constructing DL_POLY 4 an Overview 02 0 0 0200005 91 4 1 1 Constructing the Standard Versions oaoa 91 4 1 2 Constructing Non standard Versions 00 050202 ae 92 42 Compiling and Running DLPOLYA saos sor bee ee a Re eee eS 94 4 2 1 Compiling the Source Code gt ea o sero citoar adora euna ria 94 de UNE o na eh a gs e eee Gets 95 a ek pl em at Eo eo Rk eh ee eal bts A le eh ae 96 4 2 4 Optimising the Starting Structure e e 97 4 2 5 Simulation Efficiency and Performance LL 98 vii STFC Contents 4 3 A Guide to Preparing Input Files 100 4 3 1 Inorganic Materials osoa acs aa oe ao
93. 59 Chapter 6 The DL POLY 4 Parallelisation and Source Code Scope of Chapter This chapter we discuss the DL_POLY 4 parallelisation strategy describe the principles used in the DL_POLY 4 modularisation of the source code and list the file structure found in the source subdirectory 160 STFC Section 6 1 6 1 Parallelisation DL_POLY 4 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 4 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 strategy 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 Le 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_4 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 thi
94. 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 Nos Hoover ensemble with Tersoff forces and no electrostatics 7 1 6 Test Case 11 and 12 CuzAu alloy with Sutton Chen metal Potentials These systems consist of 32 000 and 256 000 atoms respectively Simulation at 300 K using NVT Nos Hoover ensemble with Sutton Chen 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 CONTROL 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 SHAK
95. 9 Evans NVT 4 55 111 119 120 Langevin NoT 112 120 Langevin NoT 4 55 119 Langevin NPT 4 55 112 119 120 Langevin NVT 4 55 111 119 120 Martyna Tuckerman Klein NoT 119 Martyna Tuckerman Klein NoT 4 55 112 120 Martyna Tuckerman Klein NPT 4 55 112 119 120 microcanonical see ensemble NVE Nos Hoover NoT 4 55 112 119 120 Nos Hoover NPT 4 55 112 119 120 Nos Hoover NVT 4 55 112 119 120 NVE 4 55 59 111 119 120 equations of motion Euler 51 86 rigid body 86 error messages 105 223 Ewald optimisation 102 103 SPME 47 102 112 113 117 123 summation 46 95 102 118 123 161 164 249 force field 3 13 14 22 101 164 225 240 258 AMBER 3 13 DL_POLY 3 13 Dreiding 3 13 40 GROMOS 3 13 force shifted Coulomb sum 42 117 123 FORTRAN90 5 7 94 95 171 223 FTP 9 Graphical User Interface 9 100 102 127 GROMOS 3 13 Java GUI 4 9 licence 2 long ranged corrections metal 33 van der Waals 29 minimisation 97 279 STFC Index conjugate gradients 97 sub directory 183 186 programmed 97 bench 8 zero temperature 97 build 8 Se data 8 parallelisation 4 92 161 execute 8 Domain Decomposition 4 java 8 intramolecular terms 162 163 public 8 polarisation 49 50 source 8 shell model 3 13 42 49 51 162 163 233 utility 8 potential bond 3 100 135 154 162 165 228 250 thermostat 4 51 88 111 112 252 bonded 164
96. 90 0 kinetic_module o rigid_bodies_module o setup_module o relocate_particles o angles_module o bonds_module o comms_module o config_module o constraints_module o core_shell_module o dihedrals_module o domains_module o inversions_module o kinds_f90 0 pmf_module o rigid_bodies_module o setup_module o site_module o tethers_module o report_topology o angles_module o bonds_module o comms_module o constraints_module o core_shell_module o dihedrals_module o inversions_module o pmf_module o rigid_bodies_module o setup_module o site_module o tethers_module o rigid_bodies_coms o comms_module o config_module o kinds_f90 0 199 STFC Appendix C rigid_bodies_module o setup_module o rigid_bodies_module o kinds_f90 0 setup_module o rigid_bodies_move o config_module o kinds_f90 0 rigid_bodies_module o setup_module o rigid_bodies_quench o comms_module o config_module o kinds_f90 0 rigid_bodies_module o setup_module o rigid_bodies_setup o comms_module o config_module o kinds_f90 0 rigid_bodies_module o setup_module o site_module o rigid_bodies_split_torque o comms_module o config_module o kinds_f90 0 rigid_bodies_module o setup_module o rigid_bodies_stress o comms_module o config_module o kinds_f90 0 rigid_bodies_module o setup_module o rigid_bodies_tags o comms_module o config_module o rigid_bodies_module o setup_module o rigid_bodies_widths o comms_module o config_module o kinds_f90 0 rigid_bodies_mod
97. B L 1993 Molec Phys 78 533 76 Martyna G Tobias D and Klein M 1994 J Chem Phys 101 4177 76 84 Melchionna S and Cozzini S 1998 University of Rome 101 Hockney R W and Eastwood J W 1981 Computer Simulation Using Particles McGraw Hill International 161 163 165 Smith W 1992 Comput Phys Commun 67 392 161 Smith W and Fincham D 1993 Molecular Simulation 10 67 161 Bush I J Todorov I T and Smith W 2006 Computer Physics Communication 175 323 164 Bush I J 2000 Daresbury Laboratory 164 278 Index DL_POLY 4 software licence 10 algorithm 4 53 108 FIQA 4 87 NOSQUISH 4 87 RATTLE 4 56 57 161 165 258 SHAKE 4 55 58 161 165 240 Verlet 4 29 53 58 164 165 Verlet neighbour list 163 AMBER 3 13 101 angular momentum 86 angular restraints 20 angular velocity 86 barostat 4 88 112 252 253 Berendsen 74 Nos Hoover 76 82 boundary conditions 3 42 180 cubic 128 CCP5 2 9 constraints bond 2 4 14 56 59 84 85 132 154 163 165 230 235 240 258 Gaussian 46 59 PMF 14 58 59 132 154 163 CVS 6 direct Coulomb sum 42 44 111 123 distance dependant dielectric 44 111 123 distance restraints 16 dlpoly2 5 DLPROTEIN 101 Dreiding 13 ensemble 4 249 Andersen NVT 4 55 119 Berendsen NoT 4 55 112 119 120 Berendsen NPT 4 55 112 119 120 Berendsen NVT 4 55 111 119 120 canonical 5
98. DL_POLY 4 is compiled in a netCDF enabled mode mpiio is the recommended method and for large systems master should be avoided Available options depend on which method is to be used and all are optional in each case Where numerical values are to be supplied specifying 0 or a negative numbers indicates that DL_POLY 4 will resort to the default value The possible options are e io read mpiio direct netcdf j k l e j specifies the number of processors that shall access the disk k specifies the maxi mum number of particles that the reading processors shall deal with at any one time 124 STFC Section 5 1 Large values give good performance but may results in an unacceptable memory overhead specifies the maximum number of particles that the reading processors shall read from the disk in one I O transaction Large values give good performance but may results in an unacceptable memory overhead e accepts Yes only to switch global error checking performed by the I O subsystem the default is No e io read master I l specifies the maximum number of particles that the reading process shall read from the disk in one I O transaction Large values give good performance but may results in an unacceptable memory overhead b io write method rp type options With action set to write the io command controls how the writing of large files is per formed method controls how the disk is accessed Possible values are mpiio in whi
99. Documentation e 6 1 3 7 FORTRAN090 Parameters and Arithmetic Precision 7 Lace Witte siena pe RR Bek as BYP ee ee ee AO Eee A 7 STFC Contents LSI Error Mossa oo a a hed ek a ewe py Boe e Gn 8 LA Directory Structtit o o ss La a A Ri e ae ee e a E a 8 114 1 The source Sub directory lt a saaa 24400 4 a i i 8 1 4 2 The utility Sub directory osca sed aoa naa ee 8 1 4 8 The data Sub directory o o ma a 9 1 44 The bench Sub directory o ee 9 14 5 The grecute Sib divestory os i a ra A RO me ee ee 9 1 4 6 The build Sub directory LL 9 1 4 7 The public Sub ditectory lt s o ias e e RR ee a d 9 1 4 8 The java Sub directory os a seac osscar ee 9 1 5 Obtaining the Source Code 10 1 6 OS and Hardware Specific Ports LL 10 L7 Cierra i iaia Dani ala Sane a da a a 10 2 Force Fields 12 2 1 Introduction to the DL_POLY 4 Force Field 13 2 2 The Intramolecular Potential Functions LL 14 221 Bend Potentials i sa doa era ea RE A ae oe a a 14 2 2 2 Distance Restraints LL 16 2 2 3 Valence Angle Potentials 22 17 224 Anpular Restraints 6 a4 a Beeb Oa Ow ee a 19 2 2 5 Dihedral Angle Potentials e 20 2 2 6 Improper Dihedral Angle Potentials o 22 2 2 7 Inversion Angle Potentials oroe soa eas aoea w e 20000 0002 e a 23 22 8 Tetlerine Forc s 2 2 i ec e ceca e Dasan a a a 26 2 3 The Interm
100. E RATTLE algorithm for the constrained motion 7 1 10 Test Case 19 and 20 CuzAu alloy with Gupta metal Potentials These systems consist of 32 000 and 256 000 atoms respectively Simulation at 300 K using NVT Nos Hoover ensemble with Gupta forces and no electrostatics 7 1 11 Test Case 21 and 22 Cu with EAM metal Potentials These systems consist of 32 000 and 256 000 atoms respectively Simulation at 300 K using NPT Berendsen ensemble with EAM tabulated forces and no electrostatics 177 STFC Section 7 1 7 1 12 Test Case 23 and 24 Al with Sutton Chen metal Potentials These systems consist of 32 000 and 256 000 atoms respectively Simulation at 300 K using NVT Evans ensemble with Sutton Chen forces and no electrostatics 7 1 13 Test Case 25 and 26 Al with EAM metal Potentials These systems consist of 32 000 and 256 000 atoms respectively Simulation at 300 K using NVT Evans ensemble with EAM tabulated forces and no electrostatics 7 1 14 Test Case 27 and 28 NiAl alloy with EAM metal Potentials These systems consist of 27 648 and 221 184 atoms respectively Simulation at 300 K using NVT Evans ensemble with EAM tabulated forces and no electrostatics 7 1 15 Test Case 29 and 30 Fe with Finnis Sincair metal Potentials These systems consist of 31 250 and 250 000 atoms respectively Simulation at 300 K using NPT Berendsen ensemble with Finnis Sinclair forces and no electrostatics 7 1 16 Test Case 31 and 32
101. EFECTS mv RDFDAT mv ZDNDAT chmod R a w data TEST 1 REVIVE data TEST 1 HISTORY data TEST 1 DEFECTS data TEST 1 RDFDAT data TEST 1 ZDNDAT data TEST 1 which first creates a new DL_POLY data TEST sub directory and then moves the standard DL_POLY 4 output data files into it store requires one argument store n where n is a unique string or number to label 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 186 Appendix C DL POLY 4 Makefiles Makefile DEV Master makefile for DL_POLY_4 01 developer version Author I J Bush october 2010 Define default settings SHELL bin sh SUFFIXES SUFFIXES 90 o BINROOT execute EX DLPOLY Z EXE BINROOT EX TYPE master FC undefined LD undef ined Define object files OBJ_MOD kinds_f90 0 comms_module o setup_module o parse_module o development_module o netcdf_modul o io_module o domains_module o site_module o config_module o defects_module o defectsi_module o vdw_module o metal_module o tersoff_module o three_body_module o four_body_module o core_shell_module o 187 STFC Appendix C constraints_module o pmf_module o rigid_bodies_module o tethers_module o bonds_module o angles_module o dihedrals_module o inversions_module o
102. ERENCE 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 144 STFC Section 5 1 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_4 normally produces the file REVIVE see Section 5 2 7 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 4 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 vari
103. FC Appendix C EX EX BINROOT BINROOT TYPE win debug MAKE LD f95 o LDFLAGS 00 C all C undefined FC 95 c FCFLAGS 00 C all C undefined EX EX BINROOT BINROOT TYPE Default code master message check 0BJ_MOD OBJ_ALL LD EXE LDFLAGS OBJ_MOD OBJ_ALL Message message echo DL_POLY_4 compilation in SRL1 mode echo echo Use mpi must change to Use mpi_module in comms_module f90 echo Check that a platform has been specified check if test FC undefined then echo echo FORTRAN90 compiler unspecified echo echo Please edit your Makefile entries echo exit 99 fi if test LD undefined then echo echo FORTRAN90 Linker loaDer unspecified echo echo Please edit your Makefile entries echo exit 99 fis mkdir p BINROOT touch dl_poly f90 Declare rules 90 0 FC FCFLAGS 90 Declare dependencies OBJ_ALL OBJ_MOD 216 STFC Appendix C Makefile SRL2 Master makefile for DL_POLY_4 01 serial version 2 Author I T Todorov october 2010 Define default settings SHELL bin sh SUFFIXES SUFFIXES f90 o BINROOT execute EX DLPOLY Z EXE BINROOT EX TYPE master FC undefined LD undef ined Define object files OBJ_MOD kinds_f90 0 mpi_module o comms_modul
104. IELD and CONFIG do not match each other or if CONFIG is ill defined Action Regenerate CONFIG and FIELD and resubmit Message 130 error bond angle unit diameter gt rcut the system cutoff This could only happen if FIELD and CONFIG do not match each other or if CONFIG is ill defined Action Regenerate CONFIG and FIELD and resubmit 243 STFC Appendix D Message 132 error dihedral angle unit diameter gt rcut the system cutoff This could only happen if FIELD and CONFIG do not match each other or if CONFIG is ill defined Action Regenerate CONFIG and FIELD and resubmit Message 134 error inversion angle unit diameter gt rcut the system cutoff This could only happen if FIELD and CONFIG do not match each other or if CONFIG is ill defined Action Regenerate CONFIG and FIELD and resubmit Message 141 error duplicate metal potential specified During reading of metal potentials pairs of atom types in FIELD DL_POLY 4 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 4 expects that particles will be kept apparat stay separated and never go t
105. J_ALL FILES_VV FILES_LFV mod Generic target template uknown_platform MAKE LD path to FORTRAN90 Linker loaDer LDFLAGS appropriate flags for LD MPI libraries FC path to FORTRAN90 compiler FCFLAGS appropriate flags for FC MPI include EX EX BINROOT BINROOT TYPE System specific targets follow Cambridge HPC darwin Woodcrest hpc MAKE LD mpif90 o LDFLAGS 03 FC mpif90 c FCFLAGS 03 EX EX BINROOT BINROOT TYPE lake MAKE LD opt intel compiler70 ia32 bin ifc v 0 LDFLAGS 03 xW prec_div L opt mpich intel lib lmpich 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 SCI ALTIX parallel FFT newton MAKE LD ifort o LDFLAGS tpp2 ip 03 lmpi lguide FC ifort c FCFLAGS 03 tpp2 ip w EX EX BINROOT BINROOT TYPE dirac MAKE LD usr local mpich gm pgroup121 7b bin mpif90 v o 206 STFC Appendix C 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 F
106. LAX CORE_SHELL_RELAX ZERO_K_OPTIMISE NVT_EO_SCL NVT_E1_SCL NVT_BO_SCL NVT_B1_SCL XSCALE CORE_SHELL_KINETIC REGAUSS_TEMPERATURE DEFECTS_REFERENCE_READ DEFECTS_REFERENCE_READ_PARALLEL DEFECTS_REFERENCE_WRITE DEFECTS_REFERENCE_EXPORT DEFECTS_REFERENCE_SET_HALO DEFECTS_LINK_CELLS DEFECTS1_WRITE DEFECTS_WRITE MSD_WRITE Z_DENSITY_COLLECT STATISTICS_COLLECT SYSTEM_REVIVE RDF_COMPUTE Z_DENSITY_COMPUTE STATISTICS_RESULT DL_POLY e VV specific files in the source VV directory PSEUDO_VV CONSTRAINTS_SHAKE_VV PMF_SHAKE_VV CONSTRAINTS_RATTLE PMF_RATTLE NVT_HO_SCL NPT_HO_SCL NST_HO_SCL NVE_O_VV NVT_EO_VV 170 STFC Section 6 2 NVT_LO_VV NVT_AO_VV NVT_BO_VV NVT_HO_VV NPT_LO_VV NPT_BO_VV NPT_HO_VV NPT_MO_VV NST_LO_VV NST_BO_VV NST_HO_VV NST_MO_VV NVE_1_VV NVT_E1_VV NVT_L1_VV NVT_Al_VV NVT_B1_VV NVT_H1_VV NPT_L1_VV NPT_B1_VV NPT_H1_VV NPT_M1_vv NST_L1_VV NST_B1_VV NST_H1_VV NST_M1_VV MD_VV e LFV specific files in the source LFV directory PSEUDO_LFV CONSTRAINTS_SHAKE_LFV PMF_SHAKE_LFV NVE_O_LFV NVT_EO_LFV NVT_LO_LFV NVT_AO_LFV NVT_BO_LFV NVT_HO_LFV NPT_LO_LFV NPT_BO_LFV NPT_HO_LFV NPT_MO_LFV NST_LO_LFV NST_BO_LFV NST_HO_LFV NST_MO_LFV NVT_L1_LFV NVT_A1_LFV NVT_B1_LFV NVT_H1_LFV NPT_L1_LFV NPT_B1_LFV NPT_H1_LFV NPT_M1_LFV NST_L1_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 EWALD_SPME_FORC S The files in each group are listed in hierarchial
107. LD MSDTMP TABLE STATIS TABEAM CFGMIN REFERENCE RDFDAT ZDNDAT REVOLD REVIVE Figure 5 1 DL_POLY 4 input left and output right files Note files marked with an asterisk are non mandatory DL_POLY 4 requires seven input files named CONTROL CONFIG FIELD TABLE TABEAM REFERENCE and REVOLD The first three files are mandatory whereas TABLE and TABEAM are only used to input certain kinds of pair or metal potentials and may not always be required REFERENCE is required only if defect detection is switched on in CONTROL REVOLD is re quired 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 4 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 may qualify a particular directive by for example adding extra options Directives can 107 STFC Section 5 1 appear in any order in the CONTROL file except for the finish directive which marks the end of the file Some of the dir
108. LY 4 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 7 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 When specifed it will continue a previous simulation restart provided all needed restart files are in place and not corrupted If they are not in place or are found corrupted it will start a new simulation without initial 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 8 The various ensemble options i e nve nvt evans nvt andersen nvt langevin nvt berendsen nvt hoover npt langevin npt berendsen npt hoover npt mtk nst langevin nst berendsen 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 The nst keyword is also used in the NoT ensembles extension to NP AT and NP yT ones Note that 119 STFC Section 5 1 9 10 Table 5 2 Internal Restart Key keyres meaning O start new simulation from CONFIG file and assign velocities from Gaussian dis
109. L_POLY 4 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_4 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 4 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 original CONTROL file augment it to include the restart directive and or extend the length and duration of the new targeted MD run the FIELD and TABLE and or TABEAM file and a CONFIG file which is the exact copy of the REVCON file created by the previous job You will also require a new file REVOLD Section 5 1 5 which is an exact copy of the previous REVIVE file If you attempt to restart DL_POLY_4 without this additional file available the job will most probably fail Note that DL_POLY 4 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
110. La 01 03 03 At ota Ry 61 r t At r t XAT STFC Section 3 4 with i ah exp t o PERA pets 3 37 k x and R vectors of independent standard Gaussian random numbers of zero mean and unit variance Gauss 0 1 easily related to the Langevin random forces as defined in equation 3 34 2 RATTLE_VV1 3 FF f t At f t 3 38 4 VV2 At f t At 1 t A A 3 39 u t At u t 3At 3 39 5 RATTLE_VV2 The algorithm is self consistent and requires no iterations The LFV implementation of the Langevin algorithm is straightforward 1 FF ft ft A40 R t R t At 3 40 3 41 2 LFV and Thermostat At 2 At scale 1 x scalev 1 scale_f 2 scale scale 1 1 t R t v t 2At scale v v t At scale_f FO RO 3 42 2 2 m 1 r t At e r 0 Ato t 5 At where R t are the Langevin random forces as defined in equation 3 34 3 SHAKE 4 Full step velocity 1 1 1 v t a u t At u t At 3 43 The VV and LFV flavours of the Langevin thermostat are implemented in the DL_POLY 4 routines NVT_LO_vv and NVT_LO_LFV respectively The routines NVT_L1_vv and NVT_L1_LFV implement the same but also incorporate RB dynamics 62 STFC Section 3 4 3 4 3 Andersen Thermostat This thermostat assumes the idea that the system or some subset of the system has an instanta neous interaction with some fictional particles and exchang
111. NIX file directories 2 ROUTINES indicates subroutines functions and programs 3 macros 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 THE DL POLY_4 USER MANUAL a About DL POLYA i cagA ewe La e EA dea be euaes i Distlaimer pu sai gos og oe ee BG EO a a es a ee ee aa ii Acknowledgements 2 225 456 84548 42 Dee Ree Ae ee a ee a as 111 Manual Notation sis a eos oa a por apai i a ae eG BE ee wR ew Da ee ES iv Contents v List of Tables xi List of Figures xii 1 Introduction 1 1 1 The DL POLY Package 00 sse pa kik a a E RPS 2 12 Functionally 10 cs pe li ae ke Bae ee a ee E Ga D li 2 1 2 1 Molecular Syst ms o lt s s s ss a emacs acura yor e a F 2 L22 Porce Field ora monk di a ad E ee RE eek Be ak i eS 3 12 0 Boundary Conditions ss s a ioa s som i p pee ee TRE e OS 3 1 24 Java Graphical User Interiane a oo ee e le Be bw ei 4 LED BIST 2 42 6 rr a a a E AR Re E i 4 1 2 6 DL_POLY_2 features incompatible or unavalable in DL_ POLY4 5 18 Programming Style ego coran feri OR AR A ee BRS 5 El Programming Language 3 La e E Sek A i 5 13 2 Modularisationand Intent 4 646 Ta 6 Las Memory Managerment Se ioe 505 aoe folk ee Be ek Sie EOE Be eo at eS 6 1 3 4 Target Computers o esgos bene RT RE ee BS 6 Loo Version Control System CVS 64 4 ace he e ew ob A i 6 1 3 6 Internal
112. Ni with EAM metal Potentials These systems consist of 32 000 and 256 000 atoms respectively Simulation at 300 K using NPT Berendsen ensemble with EAM tabulated forces and no electrostatics 7 1 17 Test Case 33 and 34 SPC IceVII water with constraints These systems consist of 11 664 34 992 atoms and 93 312 279 936 atoms water molecules re spectively Simulation at 25 K using NVE ensemble with CGM force minimisation and SPME electrostatics Both constraint bond and rigid body dynamics cases are available 7 1 18 Test Case 35 and 36 NaCl molecules in SPC water represented as CBs RBs These systems consist of 64 512 NaCl ion pairs with 4 480 35 840 water molecules represented by constraint bonds and 4 416 35 328 water molecules represented by ridig bodies Totalling 26 816 214 528 atoms Simulation at 295 K using NPT Berendsen ensemble with CGM energy minimisation and SPME electrostatics 7 1 19 Test Case 37 and 38 TIP4P water RBs with a massless charged site These systems consist of 7 263 and 58 104 TIP4P rigid body water molecules totaling 29 052 and 232 416 particles respectively Simulation at 295 K using NPT Berendsen ensemble with CGM energy minimisation and SPME electrostatics 178 STFC Section 7 2 7 1 20 Test Case 39 and 40 Ionic liquid dimethylimidazolium chloride These systems consist of 44 352 and 354 816 ions respectively Simulation at 400 K using NPT Berendsen ensemble using both particle and rigid
113. Note that the option of using EAM interactions must also be explicitly declared in the FIELD file so that for the n component alloy there are n n 1 2 cross pair potential eam keyword entries in FIELD see above Note that all metal interactions must be of the same type 5 1 7 1 The TABEAM File Format The file is free formatted but blank and commented lines are not allowed 5 1 7 2 Definitions of Variables record 1 header al00 file header record 2 numpot integer number of potential functions in file The subsequent records define the n n 5 2 functions for an n component alloy n electron density functions one for each atom type density keyword n embedding functions again one for each atom type embeding keyword and n n 1 2 cross pair potential functions pairs 147 STFC Section 5 2 keyword The functions may appear in any random order in TABEAM as their identification is based on their unique keyword defined first in the function s header record The header record is followed by predefined number of data records as a maximum of four data per record are read in allowing for incompletion of the very last record header record keyword ad type of EAM function dens embed or pair atom 1 a8 first atom type atom 2 a8 second atom type only specified for pair potential functions ngrid integer number of function data points to read in limit 1 real lower interpolation limit in for dens and pair or in de
114. O BREET BN RECON ara 3 13 Here FP stands for a free particle i e a particle not participating in the constitution of a rigid body and RB for a rigid body In general a rigid body has 3 translational tra degrees of freedom corresponding to its centre of mass being allowed to move in the 3 general direction of space and 3 rotational rot corresponding to the RB being allowed to rotate around the 3 general axis in space It is not far removed to see that for a not fully frozen rigid body one must assign 0 translational degrees of freedom but depending on the frozenness of the RB one may assign 1 rotational degrees of freedom when all the frozen sites are in line i e rotation around one axis only or 3 when just one site is frozen The routines NVE_0_vv and NVE_O_LFV implement the Verlet algorithm in velocity and leapfrog flavours respectively for free particles and calculate the instantaneous temperature Whereas the 54 STFC Section 3 2 routines NVE_1_vv and NVE_1_LFV implement the same for systems also containing rigid bodies The conserved quantity is the total energy of the system Hyve U Ekin gt 3 14 where U is the potential energy of the system and Erin the kinetic energy at time t The full selection of integration algorithms indicating both VV and LFV cast integration within DL_POLY 4 is as follows NVE_O_VV NVE_O_LFV Constant E algorithm NVE_1_VV NVE_1_LFV The same as the above b
115. OLY to help 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 4 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 3 182 Appendix B DL POLY 4 Macros Introduction Macros are simple executable files containing standard UNIX commands A number of the are supplied with DL_POLY 4 and are found in the execute sub directory These are not guaranteed to be immaculate but with little adaptation they can become a useful tool to a researcher 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 20 cleanup cleanup removes several standard data files from the execute sub directory It contains the UNIX commands rm OUTPUT STATIS REVCON REVOLD REVIVE RDFDAT ZDNDAT 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 c
116. R t is stochastic force with zero mean that satisfies the fluctuation dissipation theorem RO R 2 x mi kBT dij dog lt t 3 34 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 Stokes Einstein relation for the diffusion coefficient can then be used to show that the average value of R t over a time step in thermal equilibrium should be a random deviate drawn from a Gaussian distribution of zero mean and unit variance Gauss 0 1 scaled by 2x mi ET The effect of this algorithm is thermostat 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 of the algorithm is tailored in a Langevin Impulse LI manner 59 1 VV1 v it e v t 5 JO m 1 V2 kgT gt v t Ate exp x At u t te E A x At 3 35 1 y A 2 T exp x At leds V2 x m kg Z X Xm where Z x At and Za x At are joint Gaussian random variables of zero mean sampling from a bivariate Gaussian distribution 59 Mile ox e Ey 3 36
117. RACCON to get the AMBER names correct for sites in your molecule The version of FRACCON supplied with DL _POLY 4 is specific 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 utility 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_4 Remember to delete the bogus entries from
118. Rot A fne U r r gt Ro A Note A defaults to zero if A gt 0 5 Ro or if it is not specified in the FIELD file 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 4 will also calculate the non bonded pair potentials between the described atoms unless these are deactivated by another potential specification 135 STFC Section 5 1 Table 5 9 Valence Angle Potentials key potential type Variables 1 4 functional formi harm Harmonic k 00 U 0 E 0 90 hrm quar Quartic k 00 k k U 0 E 0 0o E 0 bo E o o qur thrm Truncated harmonic k Oo p U 0 E 0 00 exp ri r p thm shrm Screened harmonic k 00 pi pe U 0 0 00 exp rij p1 rik p2 shm bvs1 Screened Vessal 35 k o pi P2 U O eo T 0 my a bv1 exp rij p1 ri p2 bvs2 Truncated Vessal 36 kl a p U 0 k 0 00 0 0 0 27 bv2 97 71 00 my expl tri Hri 0 hcos Harmonic Cosine k 00 U 0 k cos cos 00 hcs cos Cosine A 6 m U 0 A 1 cos m 0 COS mmsb MMB stretch bend 37 A 00 Tir oe U 0 A 0 00 rij rg rik Tip msb mmsb Compass 38 A Pee Tor U 0 A rij ri Tik Tik msb stretch stretch mmsb Compass
119. S byteswapio 00 g ffortran bounds check FC ftn c FCFLAGS byteswapio 00 g ffortran bounds check EX EX BINROOT BINROOT TYPE hector X2 MAKE LD ftn o LDFLAGS 03 Ofp3 Ocache2 rm FC ftn c FCFLAGS 03 Ofp3 Ocache2 rm EX EX BINROOT BINROOT TYPE hector X2 debug MAKE LD ftn o LDFLAGS GO 00 rm FC ftn c FCFLAGS GO 00 rm 194 STFC Appendix C EX EX BINROOT BINROOT TYPE Default code master message check 0BJ_MOD OBJ_ALL LD EXE LDFLAGS OBJ_MOD OBJ_ALL Message message echo DL_POLY_4 compilation in MPI mode echo echo Use mpi_module must change to Use mpi in comms_module f90 echo Check that a platform has been specified check if test FC undefined then echo echo FORTRAN90 compiler unspecified echo echo Please edit your Makefile entries echo exit 99 fip if test LD undefined then echo echo FORTRAN90 Linker loaDer unspecified echo echo Please edit your Makefile entries echo exit 99 fi mkdir p BINROOT touch dl_poly f90 Declare rules 90 0 FC FCFLAGS 90 Declare dependencies angles_forces o angles_module o comms_module o config_module o kinds_f90 0 setup_module o angles_module o kinds_f90 0 setup_module o bonds_forces o bon
120. SYSTEM_REVIVE is too small i e mxbuff lt mxgrdf This should never happen Action Contact DL_POLY 4 authors Message 210 error only one angles directive per molecule is allowed DL_POLY 4 has found more than one angles entry per molecule in FIELD Action Correct the erroneous part in FIELD and resubmit Message 220 error only one dihedrals directive per molecule is allowed DL_POLY 4 has found more than one dihedrals entry per molecule in FIELD Action Correct the erroneous part in FIELD and resubmit Message 230 error only one inversions directive per molecule is allowed DL_POLY 4 has found more than one inversions entry per molecule in FIELD Action Correct the erroneous part in FIELD and resubmit Message 240 error only one tethers directive per molecule is allowed DL_POLY 4 has found more than one tethers entry per molecule in FIELD Action Correct the erroneous part in FIELD and resubmit 245 STFC Appendix D Message 300 error incorrect boundary condition for link cell algorithms The use of link cells in DL_POLY 4 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
121. TFC Section 5 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 magrdf records radius real interatomic distance A g r real RDF at given radius Note the RDFDAT file is optional and appears when the print rdf option is specified in the CONTROL file 5 2 9 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 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 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 10 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
122. THE DL POLY 4 USER MANUAL I T Todorov amp W Smith STFC Daresbury Laboratory Daresbury Warrington WA4 4AD Cheshire UK Version 4 01 0 October 2010 STFC Preface ABOUT DL_POLY 4 DL_POLY 4 is a general purpose parallel molecular dynamics simulation package developed at Daresbury Laboratory by W Smith and I T Todorov The DL_POLY project was developed under the auspices of the Engineering and Physical Sciences Research Council EPSRC for the EPSRC s Collaborative Computational Project for the Computer Simulation of Condensed Phases CCP5 the Computational Chemistry and Advanced Research Computing Groups CCG amp ARCG at Daresbury Laboratory and the Natural Environment Research Council NERC for the NERC s eScience project Computational Chemistry in the Environment eMinerals directed by M T Dove DL_POLY 4 is the property of Daresbury Laboratory and is issued free under licence to academic institutions pursuing scientific research of a non commercial nature 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 _4 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 f
123. TICLES routine Systems containing complex molecules present several difficulties They often contain ionic species which usually require Ewald summation methods 21 64 and intra molecular interactions in ad dition 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 intramolecular 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 57 22 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 processor to inform its neighbours whenever it updates the position of a shared atom during every SHAKE RATTLE_VV1 cycle RATTLE_VV2 updates the velocities so that all relevant 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 65 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 161 STFC Section 6 1 The DD strategy is applied to complex molecular systems as follow
124. TRAINTS_SHAKE_LFV and PMF_SHAKE_VV PMF_RATTLE_VV PMF_SHAKE_LFV O N P N 3 where M is the number of particles P P Py P the total number of domains in the MD cell and the rest of the quantities are as defined in equations 4 2 4 2 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 computing 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 description of the DL_POLY 4 force field in Chapter 2 is essential reading The various utility routines mentioned in this section are described in greater detail in the DL_POLY_2 User Manual Many of these have been incorporated into the DL_POLY_4 Graphical User Interface 20 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 normall
125. _PARALLEL SCAN_CONFIG SCAN_CONTROL READ_CONFIG SET_BOUNDS READ_CONTROL VDW_GENERATE VDW_TABLE_READ METAL_GENERATE METAL_TABLE_READ METAL_TABLE_DERIVATIVES TERSOFF_GENERATE DIHEDRALS_14_CHECK READ FIELD CHECK_CONFIG SCALE_CONFIG WRITE_CONFIG TRAJECTORY_WRITE SYSTEM_EXPAND RIGID_BODIES_TAGS RIGID_BODIES_COMS RIGID_BODIES_WIDTHS RIGID_BODIES_SETUP TAG_LEGEND REPORT_TOPOLOGY PASS_SHARED_UNITS BUILD_BOOK_INTRA BUILD_EXCL_INTRA 169 STFC Section 6 2 SCALE_TEMPERATURE UPDATE_SHARED_UNITS CORE_SHELL_QUENCH CONSTRAINTS_TAGS CONSTRAINTS_QUENCH PMF_COMSPMF_TAGS PMF_VCOMS PMF_QUENCH RIGID_BODIES_QUENCH SET_TEMPERATURE VDW_LRCMETAL_LRC SYSTEM_INIT EXPORT_ATOMIC_DATA SET_HALO_PARTICLES RIGID_BODIES_STRESS READ_HISTORY IMPACT CORE_SHELL_ON_TOP DEPORT_ATOMIC_DATA PMF_UNITS_SET COMPRESS_BOOK_INTRA RELOCATE_PARTICLES LINK_CELL_PAIRS METAL_LD_COLLECT_EAM METAL _LD_COLLECT_FST METAL_LD_EXPORT METAL_LD_SET_HALO METAL_LD_COMPUTE 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_FORCES CORE_SHELL_FORCES TETHERS_FORCES BONDS_FORCES ANGLES_FORCES DIHEDRALS_FORCES INVERSIONS_FORCES EXTERNAL_FIELD_APPLY EXTERNAL_FIELD_CORRECT LANGEVIN_FORCES CONSTRAINTS_PSEUDO_BONDS PMF_PSEUDO_BONDS RIGID_BODIES_SPLIT_TORQUE RIGID_BODIES_MOVE MINIMISE_RE
126. _POLY 4 is handled by two different methods For LF implementation the Fincham Implicit Quaternion Algorithm FIQA is used 23 The VV implementation uses the NOSQUISH algorithm of Miller et al 24 The implementation of FIQA is coded in Q_UPDATE and NOSQUSH in NO_SQUISH both contained within QUATERNION_CONTAINER The LF implementation begins by integrating the angular velocity equation in the local frame At At Oet gt 0 t gt At d t 3 165 The new quaternions are found using the FIQA algorithm In this algorithm the new quaternions are found by solving the implicit equation At g t At a t gt Q la 1 WH Q a t At alt At 3 166 where 0 Y and Q g is do 4 42 43 1 z Q Z 5 qi qo q3 q2 3 167 q2 43 qdo TA q 79 q1 qo The above equation is solved iteratively with q t At q t At Qla t w t 3 168 as the first guess Typically no more than 3 or 4 iterations are needed for convergence At each step the normalisation constraint lat At 1 3 169 is imposed While all the above is enough to build LFV implementations the VV implementations based on the NOSQUISH algorithm of Miller et al 24 also require treatment of the quaternion momenta as defined by Po do q G 4 0 l Pij s P 8 4 sel 3 170 p2 q 4B do 7 yy Wy P3 da 2 qdo Izz Wz Yo do NM 9 43 0 Y Di 1 co d da qa Ta i 3 171 Ta d da do I Ty T3 d
127. _book_intra o relocate_particles o link_cell_pairs o metal_ld_collect_eam o metal_ld_collect_fst o metal_ld_export o metal_ld_set_halo o metal_ld_compute 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 external_field_apply o external_field_correct o langevin_forces o constraints_pseudo_bonds o pmf_pseudo_bonds o rigid_bodies_split_torque o rigid_bodies_move o minimise_relax o core_shell_relax o zero_k_optimise o nvt_e0_scl o nvt_el_scl o nvt_b0_scl o nvt_bi_scl o pseudo_vv o constraints_shake_vv o pmf_shake_vv o constraints_rattle o pmf_rattle o nvt_h0_scl o npt_h0_scl o nst_h0_scl o nve_O_vv o nvt_e0_vv o nvt_10_vv o nvt_a0_vv o nvt_b0_vv o nvt_h0_vv o A npt_10_vv o npt_b0_vv o npt_h0_vv o npt_m0_vv o 203 STFC Appendix C nst_10_vv o nst_b0_vv o nst_h0_vv o nst_m0_vv o nvt_hi_scl o npt_h1_scl o nst_hi_scl o nve_1_vv o nvt_el_vv o nvt_li_vv o nvt_al_vv o nvt_b1_vv o nvt_hi_vv o npt_li_vv o npt_bi_vv o npt_hi_vv o npt_mi_vv o nst_11_vv o nst_b1_vv o nst_hi_vv o nst_ml_vv o pseudo_lfv o constraints_sha
128. _m1_vv f90 md_vv f90 204 STFC Appendix C Define LeapFrog Verlet files FILES_LFV pseudo_lfv f90 constraints_shake_lfv f90 pmf_shake_lfv f90 nve_0_lfv f90 nvt_e0_lfv 90 nvt_10_1fv f90 nvt_a0_1fv f90 nvt_bO_lfv f90 nvt_h0_1fv f90 npt_10_1fv f90 npt_b0_1fv f90 npt_h0_1fv f90 npt_m0_1fv f90 nst_10_1fv f90 nst_b0_1fv f90 nst_hO_lfv f90 nst_m0_1fv f90 nve_1_1fv f90 nvt_ei_lfv f90 nvt_11_1fv f90 nvt_ai_lfv f90 nvt_b1_1fv f90 nvt_hi_lfv f90 npt_11_1fv f90 npt_b1_1fv f90 npt_hi_lfv f90 npt_m1_1fv f90 nst_11_1fv f90 nst_b1_1fv f90 nst_h1_1fv f90 nst_m1_1fv f90 md_lfv f 90 aA as Examine targets manually all echo echo You MUST specify a target platform 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_platform 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 A done Fetch the LeapFrog Verlet subroutines FILES_LFV MAKE links_lfv 205 STFC Appendix C 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 OB
129. a node max number of related PMF units 1 1 max number of types RB units max number of RB units per node max number of constituent particles of an RB unit max number of related RB units 1 1 max number of specified tethered potentials in system max number of tethered atoms per node max number of related tether units 1 1 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 related chemical bonds 1 6 6 1 2 173 STFC Section 6 2 mxpbnd mxtang mxangl mxfang mxpang mxtdih mxdihd mxfdih mxpdih mxtinv mxinv mxfinv mxpinv mxgrid mxrdf mxgrdf mxvdw mxpvdw mxmet mxpmet mxter mxpter mxtbp mx2tbp mxptbp mxfbp mx2fbp mxpfbp mxpfld mxstak mxnstk mxlist mxcell mxatms mxatms mxbuff zero_plus half_minus engunit 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 variable 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 related bond angles 1
130. able variable variable configuration file input channel force field input channel tabulated potentials file input channel reference configuration input channel main output channel statistical data file output channel output channel accumulators restart dump file trajectory history file channel output channel for defects data file output channel for RDF data output channel for Z density data file pair of seeds for the random number generator logical swich on off indicator for seeding max number of molecular sites max number of unique atomic types max number of unique molecule types max number of excluded interactions per atom SPME FFT B spline order SPME FFT amended array dimension a direction SPME FFT amended array dimension b direction SPME FFT amended array dimension c direction SPME FFT original array dimension a direction SPME FFT original array dimension b direction SPME FFT original array dimension c direction max number of specified core shell unit types in system max number of core shell units per node max number of related core shell units 1 1 max number of specified bond constraints in system max number of constraint bonds per a node max number of related constraint units 6 1 max number of shared particles per node mxshl mxcons mxrgd Max 2 SS 2 mons number of A ode in DD hypercube 26 max number of specified particles in a PMF unit 1 2 max number of PMF constraints per
131. ables 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 used 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 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 145 STFC Section 5 1 record 13 Optional zdens Z density array mxgrdf xmxatyp 5 1 5 2 Further Comments Note that different versions of DL_POLY_4 may have a different order of the above parameters or include more or less such Theref
132. accumulators to zero at start Note that all these options are mutually exlusive 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 Optimising the Starting Structure The preparation of the initial structure of a system for a molecular dynamics simulation can be difficult It is quite likely that the structure created does not correspond to one typical of the equilibrium state for the required state point for the given force field employed This can make the simulation unstable in the initial stages and can even prevent it from proceeding For this reason DL_POLY 4 has available a selection of structure relaxation methods Broadly speaking these are energy minimisation algorithms but their role in DL_POLY 4 is not to provide users with true structural optimisation procedures capable of finding the ground state structure They are simply intended to help users improve the quality of the starting structure prior to a statistical dynamical simulation which implies useage during the equlibration period only The available algorithms are 1 Zero temperature molecular dynamics This is equivalent to a dynamical simulation at low temperature At each time step the molecules move in the direction of the computed forces and torques but are not allowed to acquire a velocity larger than that corresponding
133. ach node and checks for the violation of this Termination will result if the condition is violated Action Use densvar option in CONTROL to increase mxdihd alternatively increase it by hand in SET_BOUNDS and 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 233 STFC Appendix D Message 63 error too many tethered atoms per domain DL_POLY 4 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 Use densvar option in CONTROL to increase mxteth alternatively increase it by hand in SET_BOUNDS and 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 4 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 working arrays used in this operation may be exceeded resulting in termination of the program Action Contact authors Message 66 error coincid
134. adient mimimiser cycle limit exceeded The conjugate gradient minimiser exceeded the iteration limit 100 for the relaxed shell model 1000 for the configuration minimiser Action Decrease the respective convergence criterion Alternatively you may try to increase the limit by hand in CORE_SHELL_RELAX or in MINIMISE_RELAX respectively 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 PMF constraint virial converges to a constant No such convergence is achieved Action See Message 515 Message 480 error PMF constraint length gt minimum of all half cell widths The spec
135. al_table_derivatives o tersoff_generate o dihedrals_14_check o read_field o check_config o scale_config o write_config o trajectory_write o system_expand o rigid_bodies_tags o rigid_bodies_coms o rigid_bodies_widths o rigid_bodies_setup o tag_legend o report_topology o pass_shared_units 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 rigid_bodies_quench o set_temperature o vdw_lrc o metal_lrc o system_init o export_atomic_data o set_halo_particles o rigid_bodies_stress o read_history o impact o core_shell_on_top o deport_atomic_data o pmf_units_set o compress_book_intra o relocate_particles o link_cell_pairs o metal_ld_collect_eam o metal_ld_collect_fst o metal_ld_export o metal_ld_set_halo o metal_ld_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 external_field_apply o external_field_correct o langevin_forces o constraints_pseudo_bonds o pmf_pseudo_bonds o rigid_bodies_split_torque
136. als in the simulation Ideally the increment should be reut mxgrid 4 where rcut 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 4 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 or TABEAM file This means the TABLE or TABEAM 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 4 is expecting Message 25 error wrong atom typ
137. ams 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 5 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 time steps used for the collection of the histograms is stated Then each function is given in turn For each function a header line states the atom type represented by the function Then z p z and n z are given in tabular form Output is given from Z L 2 L 2 where L is the length of the MD cell in the Z direction and p z is the mean number density n z is the running integral from L 2 to z of xy cell area x p s ds Note that a readable version of these data is provided by the ZDNDAT file below 5 2 6 The REVCON File This file is formatted and written by the subroutine REVIVE REVCON is the restart configuration file The file is wri
138. an equlibrium state Integration of the equations of motion is handled by one of the routines listed and described in Chapter 3 As mentioned elsewhere DL_POLY 4 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 also writes the STATIS file Section 5 2 10 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 3 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 7 and 5 2 6 respectively 93 STFC Section 4 2 4 2 Compiling and Running DL POLY 4 4 2 1 Compiling the Source Code When you have obtained DL_POLY 4 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 4 and Makefile SRL1 and Makefile SRL2 for compiling a serial versions see Appendi
139. anks aligned records The parallel I 0 ensures i writing speeds of 1075 to 1076 particle per second with optimal number of writers and ii reading speeds of 10 4 to 10 5 particles per second per reader For more information on I 0 options consult the user manual REVIVE files produced by version 2 and 3 are not compatible Furthermore restarting runs across different sub versions may not be possible The DL_POLY_4 parallel performace and efficiency are considered very good to excellent as long as i all CPU cores are loaded with no less than 500 particles each and ii the major linked cells algorithm has no dimension less than 4 Although DL_POLY_4 can be compiled in a serial mode users are advised to consider DL_POLY_2 as a suitable alternative to DL_POLY_4 when simulations are likely to be serial jobs for systems containing lt 500 particles per processor In such circumstances with both codes compiled in serial mode the difference in performance measured by the time per timestep ratio DL_POLY_2 t DL_POLY_4 t DL_POLY_2 t varies in the range 5 5 This variation depends strongly on the system force field complexity and very weakly on the system size 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 2 3 Integration can be developed
140. are with respect to the pressure i e n t in the first part VV1 RATTLE_VV1 The second part is conventional VV2 RATTLE_VV2 as at the end the velocities are scaled by a factor of x 1 Thermostat Note 2Ex n t changes inside u t exp x v t 3 84 2 Barostat Note Exjin t and P t have changed and change inside nt exp x 100 1 At P t Pex nt At n t via 4 4 Pmass 2Ex 3 kin t 1 dl Rp t f Pmass Pmass 1 At 1 n t At exp x n t At 4 8 4 ii a gt dep jia 104 S u t 3 85 1 At 1 n t 14 exp x n t 1 1 1 At P t Pex 2E Kin t 1 Rp t f Pmass Pmass 1 At 1 n t 340 exp x n t 54 W STFC Section 3 5 3 Thermostat Note Exin t has changed and changes inside A u t exp x F 0 3 86 4 VVI 1 o t ere f t R t H t At exp n t ZAt ad H t VEAD eS nl t At At V t 3 87 1 r t At exp t At arl r t At v t At 5 RATTLE_VV1 6 FF f t At f t R t At R t 3 88 R At R t 7 VV2 At At f t R t t At vw t4 BRE 3 89 8 RATTLE_VV2 9 Thermostat Note Exin t At has changed and changes inside At v t At exp x gt u t At 3 90 10 Barostat Note Exin t At and P t At have changed and change inside 1 At 1 n t 544 exp xo n t Al 3 1 At Pit At Pext A ne das ner zan E sve y i QE
141. ariables 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 tab Tabulation tabulated potential 12 6 12 6 A B U r 4 2 lj Lennard Jones e o U r 4e 5 27 nm n m Ez n m ro U r C m 22 n 42 buck Buckingham A p C U r A exp 5 amp bhm Born Huggins A B o C D U r A exp B o r G E Meyer hbnd 12 10 H bond A B U r 4x 4 snm Shifted force Es n m rol re U r a x vm 12 ON nmaEo T 7To B B m es C 1G 6 mors Morse Eo ro k U r Eo 1 exp k r r9 1 12 6 1 wea Shifted Weeks e oO A U r 4e x te rig lt 260 t 4 Chandler Anderson Un 0 rg 250 A Note in this formula the terms a 3 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 rvaw or rcut if it is set to zero or not specified in the FIELD file Note A defaults to zero if A gt 0 5 o or it is not specified in the FIELD file 2 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 atmnam 2 k
142. aries FC path to FORTRAN90 compiler FCFLAGS appropriate flags for FC MPI include EX EX BINROOT BINROOT TYPE System specific targets follow s Cambridge HPC darwin Woodcrest hpc MAKE LD mpif90 o LDFLAGS 03 FC mpif90 c FCFLAGS 03 EX EX BINROOT BINROOT TYPE lake MAKE LD opt intel compiler70 ia32 bin ifc v o LDFLAGS 03 xW prec_div L opt mpich intel lib lmpich 191 STFC Appendix C 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 EX EX BINROOT BINROOT TYPE dirac MAKE LD usr local mpich gm pgroup121 7b bin mpif90 v o 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 A xlic_l
143. as been specified check if test FC undefined then echo echo FORTRAN90 compiler unspecified echo echo Please edit your Makefile entries echo exit 99 fi if test LD undefined then echo echo FORTRAN90 Linker loaDer unspecified echo echo Please edit your Makefile entries echo exit 99 fis mkdir p BINROOT touch dl_poly f90 Declare rules 90 0 FC FCFLAGS 90 Declare dependencies OBJ_ALL OBJ_MOD 222 Appendix D DL POLY 4 Error Messages and User Action Introduction In this appendix we document the error messages encoded in DL_POLY_4 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 4 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 Standard User Response DL_POLY_4 uses FORTRAN90 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 requ
144. as developed with the aid of the CVS version control system We strongly recommend that users of DL _POLY 4 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 cvs request gnu org or visit the web site http www cyclic com 1 3 6 Internal Documentation All subroutines are supplied with a header block of FORTRAN90 comment records giving 1 A CVS revision number and associated data 2 The name of the author and or modifying author The version number or date of production A brief description of the function of the subroutine a A 0 A copyright statement Elsewhere FORTRAN90 comment cards are used liberally STFC Section 1 3 1 3 7 FORTRAN9O Parameters and Arithmetic Precision All global parameters defined by the FORTRAN90 parameter statements are specified in the mod ule 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 the 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 FORTRAN90 compiler can all
145. 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 the dynamics of the system 6 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 4 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 4 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 _PO
146. at Note Exin t At changes inside 3 1 At 2Exin t At 20 t A t A xt FAs x t za 7 tto 3 At RA exp x t Ft gt 3 73 At 2Epin t At 20 3 A x E At x t FA 5 ron The algorithm is self consistent and requires no iterations The LFV implementation of 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 1 FF f t f t At 2 LFV The iterative part is as follows 1 1 u t At u t At At 2000 1 r t At r t Atu t At 3 SHAKE 4 Full step velocity 1 1 1 oe EC A u t 340 5 Thermostat 1 1 2Ekin t 2 x t At lt x t 1 At At Ent 20 dmass 1 x 5 x 1 1 t 540 x t 340 3 74 3 75 3 76 3 77 Several iterations are required to obtain self consistency In DL_POLY_4 the number of iterations is set to 2 3 if bond constraints are present The conserved quantity is derived from the extended Hamiltonian for the system which to within a constant is the Helmholtz free energy Mass t 2 A Hxvr HyNvE mass XY f kp Text f x s ds 67 3 78 STFC Section 3 5 where f is the system s degrees of freedom equation 3 11 The VV and LFV flavours of the Nos Hoover thermostat are implemented in the DL _POLY 4 routines NVT_HO_vv and NVT_HO_LFV respectively Th
147. at is also introduced Cell size variation For isotropic fluctuations the equations of motion are Lo ult 70 00 Balt v t AOL x t n t v t 2 o ext dx Bel Pane TA 2 kp T 76 STFC Section 3 5 mass 20 TF 3 121 Sift MOLL onl f 3 kp Text TA Pmass CHO 1050 Ev BOVO where y is the barostat friction coefficient Ry t the system centre of mass at time t Qmass the thermostat mass Tr a specified time constant for temperature fluctuations pmass the barostat mass Tp a specified time constant for pressure fluctuations P the instantaneous pressure and V the system volume H is the cell matrix whose columns are the three cell vectors a b c The conserved quantity is to within a constant the Gibbs free energy of the system Mass t gt Mass t t Hynpr Hnve E 7 i ui Pot V t f 1 ks Text I x s ds 3 122 where f is the system s degrees of freedom equation 3 11 The VV implementation of the Nos Hoover algorithm only requires iterations if bond or PMF constraints are present 5 until satisfactory convergence of the constraint forces is achieved These are with respect to the pressure i e n t in the first part VV1 RATTLE_VV1 The second part is conventional VV2 RATTLE_VV2 as at the end the velocities are scaled by a factor of x 1 Thermostat Note 2Ex n t changes inside At 2Exkin t Pmass n t 20 kB Text 8 dmass
148. ation of the equations of motion measures are 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 The algorithm is developed in the DL_POLY_4 routine ZERO_K_OPTIMISE The impact i j E x y z directive will not be activated if the particle index is beyond the one of the last particle The option will fail in a controlled manner at application time if the 120 STFC Section 5 1 11 particle is found to be in a frozen state or the shell of an ion or part of a rigid body During application the center of mass momentum is re zeroed to prevent any drifts The user must take care to have the impact initiated after any possible equlibration Otherwise the system will be thermostated and the impact energy disipated during the equlibration 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 thermal bath The thermal bath can be used with two types of temperature scaling algorithms i Langevin stochastic thermostat and ii Direct direct thermostat If no type is specified then the Langevin temperature control algorithm is applied first followed the Direct one The user is also re
149. ax number of local atoms per node max dimension of the principle transfer buffer the machime representation of 0 at working precision the machime representation of 0 5 at working precision the system energy unit 174 Chapter 7 Examples Scope of Chapter This chapter describes the standard test cases for DL_POLY_4 the input and output files for which are in the data sub directory 175 STFC Section 7 1 7 1 Test Cases Because of the size of the data files for the DL_POLY_4 standard test cases they are not shipped in the standard download of the DL_POLY 4 source Instead users are requested to download them from the CCP5 FTP server as follows FTP site ftp dl ac uk Username anonymous Password your email address Directory ccp5 DL_POLY DL_POLY_4 0 DATA Files test_X tar gz where _X stands for the test case number Remember to use the BINARY data option when transferring these files Unpack the files in the data subdirectory using firstly gunzip to uncompress them and then tar xf to create the TEST_X directory These are provided so that you may check that your version of DL_POLY 4 is working correctly All the jobs are of a size suitable to test the code in parallel execution They not not be 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 num
150. be obtained for example from the GROMOS 17 Dreiding 18 or AMBER 19 forcefield which share functional forms It is relatively easy to adapt DL POLY 4 to user specific force fields 1 2 3 Boundary Conditions DL_ POLY_4 will accommodate the following boundary conditions 1 2 3 4 5 None e g isolated molecules in vacuo Cubic periodic boundaries Orthorhombic periodic boundaries Parallelepiped periodic boundaries 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 STFC Section 1 2 1 2 4 Java Graphical User Interface The DL_POLY 4 Graphical User Interface GUI is the one that comes with 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 available on the same terms see the GUI manual 20 1 2 5 Algorithms 1 2 5 1 Parallel Algorithms DL_POLY 4 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 4 offers a selection of MD
151. 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 463 error barostat friction constant must be gt 0 A zero or negative value for the barostat 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 252 STFC Appendix D Message 466 error barostat relaxation time constant must be gt 0 A zero or negative value for the barostat 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 467 error rho must not be zero in valid buckingham potential User specified vdw type buckingham potential has a non zero force and zero rho constants Only both zero or both non zero are allowed Action Inspect the FIELD file and change the values in question appropriately Message 468 error r0 too large for snm potential with current cutoff The specified location r0 of the potential m
152. ber of the test case The select macro will copy the appropriate CONTROL CONFIG and FIELD files to the execute directory ready for execution The output file OUTPUT may be compared with the file supplied in the data directory 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 KNaSiz05 Potassium Sodium disilicate glass NaKSi205 using two and three body potentials Some of the two body potentials are read from the TABLE file Simulation at 1000 K using NVT Nos Hoover ensemble with SPME Cubic periodic boundaries are in use System size is 69120 and 552960 ions respectively 176 STFC Section 7 1 7 1 4 Test Case 7 and 8 Gramicidin A molecules in Water These systems consist of
153. between configurations default j 1 act exactly the same as ewald evaluate every n set FIQA iterations limit to n default n 100 114 STFC Section 5 1 mxshak n nfold i j k no elec no index no strict no vdw optimise string f pressure f print every n print rdf print zden pseudo string fi fo set shake rattle iterations limit to n default n 250 option to create matching CONFIG i _j_k and FIELD ijk for a volumetrically expanded version of the current system CONFIG and FIELD by replicating CONFIG s contents i j k times along the MD cell lattice vectors while preserving FIELD s topology template intact ignore electrostatics in simulation ignore particles indices as read from the CONFIG file and set particles indexing by order of reading this option assumes that the FIELD topology description matches the crystalographic sites from the CONFIG file by their order of reading rather than by their actual indexing i abort strict checks such as on existance of well defined system cutoff on contiguity of particles indices when connecting CONFIG crystallographic listing to FIELD topology on IO when io mpiio direct sorted is selected etc ii abort display of warnings non leading to error messages and of iteration cycles in minimisation relaxation routines iii assume safe defaults for the general simulation cutoff temperature pressure and job times ignore s
154. ble type Martyna Tuckerman Klein with fi fo as the thermostat and barostat relaxation times in ps select NoT ensemble type Langevin with fi f2 as the thermostat and barostat relaxation speed friction constants in ps select NoT ensemble type Berendsen with fi fo as the thermostat and barostat relaxation times in ps select NoT ensemble type Nose Hoover with f f2 as the thermostat and barostat relaxation times in ps select NoT ensemble type Martyna Tuckerman Klein with fi fo as the thermostat and barostat relaxation times in ps select NP AT ensemble type Q i e lang ber hoover or mtk with f f2 as the thermostat and barostat relaxation times in ps select NP yT ensemble type Q i e lang ber hoover or mtk with f f2 as the thermostat and barostat relaxation times in ps and set required simulation target external surface tension to y dyn cm set relative dielectric constant to f default f 1 0 equilibrate system for the first n timesteps default n 0 evaluate the k space contributions to the Ewald sum once every n timesteps 1 lt n lt 10 activated when n gt 2 n lt lor undefined defaults to n 1 n gt 10 defaults to n 4 calculate electrostatic forces using Ewald sum with automatic parameter optimisation 10720 lt f lt 0 5 default f 10729 112 STFC Section 5 1 ewald sum a k ka kg exclude finish impactij E xyz integrator string io read me
155. body dynamics with SPME electrostatics 7 2 Benchmark Cases DL_POLY 4 benchmark test cases are avaliable to download them from the CCP5 FTP server as follows FTP site ftp dl ac uk Username anonymous Password your email address Directory ccp5 DL_POLY DL_POLY_4 0 BENCH The DL _POLY 4 authors provide these on an AS IS terms For more information refer to the README txt file within 179 Appendix A DL POLY 4 Periodic Boundary Conditions Introduction DL_POLY 4 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 solvent since evaporation is li
156. body unit This indicates a corrupted FIELD file as all members of a RB unit must be destinguishable from one another Action Examine FIELD for erroneous directives correct and resubmit 262 STFC Appendix D Message 640 error too many rigid body units per domain DL_POLY 4 limits the number of rigid body 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 Use densvar option in CONTROL to increase mxrgd alternatively increase it by hand in SET_BOUNDS and recompile and resubmit Message 642 error rigid body unit diameter gt rcut the system cutoff DL_POLY_4 domain decomposition limits the size of a RB to a largest diagonal lt system cutoff Le the largest RB type is still within a linked cell volume Action Increase cutoff Message 644 error overconstrained rigid body unit This is a very unlikely message which usually indicates a corrupted FIELD file or unphysically overconstrained system Action Decrease constraint on the system Examine FIELD for erroneous directives if any correct and resubmit Message 646 error overconstrained constraint unit This is a very unlikely message which usually indicates a corrupted FIELD file or unphysically overconstrained system Action Decrease constraint on the system Examine FIELD for erroneous directives i
157. bove 2 3 2 Metal Potentials The metal potentials in DL_POLY 4 follow two similar but distinct formalisms The first of these is the embedded atom model EAM 10 11 and the second is the Finnis Sinclair model FS 12 Both are density dependent potentials derived from density functional theory DFT and describe the bonding of a metal atom ultimately in terms of the local electronic density They are suitable for calculating the properties of metals and metal alloys For single component metals the two approaches are the same However they are subtly dif ferent in the way they are extended to handle alloys see below It follows that EAM and FS class potentials cannot be mixed in a single simulation Furthermore even for FS class potentials possessing different analytical forms there is no agreed procedure for mixing the parameters The user is therefore strongly advised to be consistent in the choice of potential when modelling alloys The general form of the EAM and FS potentials is 44 N N N Umetat 5 DD Vis ri Flo 2 90 i l j i i l where F p is a functional describing the energy of embedding an atom in the bulk density p which is defined as N pi DI pyly 2 91 j Ljri It should be noted that the density is determined by the coordination number of the atom defined by pairs of atoms This makes the metal potential dependent on the local density environmental 29 STFC Section 2 3 Vij rij i
158. by the routine ANGLES_FORCES 2 2 4 Angular Restraints In DL_POLY 4 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 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 35 bv1 6 Truncated Vessal 36 bv2 7 Harmonic cosine hes 8 Cosine cos 9 MM3 stretch bend 37 msb 19 STFC Section 2 2 10 Compass stretch stretch 38 sts 11 Compass stretch bend 38 stb 12 Compass all terms 38 cmp In DL_POLY 4 angular restraints are handled by the routine ANGLES_FORCES 2 2 5 Dihedral Angle Potentials Figure 2 3 The dihedral angle and associated vectors The dihedral angle potentials describe the interaction arising from torsional forces in molecules They are sometimes referred to as torsion potentials They require the specification of four atomic positions The potential functions available in DL_POLY 4 are
159. cate extra ensemble directives in CONTROL file and remove Message 416 error conflicting force options in CONTROL file DL_POLY_4 has found incompatible directives in the CONTROL file specifying the electrostatic interactions options Action 248 STFC Appendix D Locate the conflicting directives in the CONTROL file and correct Message 430 error integration routine not available A request for a non existent ensemble has been made or a request with conflicting options that DL_POLY 4 cannot deal with Action Examine the CONTROL and FIELD files and remove inappropriate specifications Message 432 error undefined tersoff potential This shows that DL_POLY 4 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 4 does not recognise Action Locate the
160. ce 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 erf and the more usual 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 00 1 exp l SEO U Si 2Vo 0 2 1 gt di pios Li Tnj er fe arnj 1 er f are Arene Y y sf i n 2 177 TEDE molecules lt m lm 2 y flare ae 2 edm l em rp fem La Atrege Vo 3 dj f 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 mut nw 2 178 3Strictly speaking the real space sum ranges over all periodic images of the simulation cell but in the DL_POLY_4 implementation the parameters are chosen to restrict the sum to the simulation cell and its nearest neighbours i e the minimum images of the cell contents 46
161. ce Restraints In DL POLY 4 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 available as distance restraints although they have different key words 1 Harmonic potential hrm 2 Morse potential mrs 3 12 6 potential bond 126 4 Lennard Jones potential 1j 5 Restrained harmonic rhm 6 Quartic potential qur 7 Buckingham potential bck 8 Coulomb potential cul 9 FENE potential fne In DL_POLY 4 distance restraints are handled by the routine BONDS_FORCES 16 STFC Section 2 2 Figure 2 2 The valence angle and associated vectors 2 2 3 Valence Angle Potentials The valence angle potentials describe the bond bending terms between the specified atoms They should not be confused with the three body potentials described later which are defined by atom types rather than indices 1 Harmonic harm k U Ojik 5 sir b0 2 15 2 Quartic quar k r k 4 k 4 U 0 ik z jik 00 3 Ojik 00 q Ori 00 2 16 3 Truncated harmo
162. ce with one acceptable to DL_POLY 4 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 4 does not recognise Action Locate the offending potential in the FIELD file and remove Replace with one acceptable to DL_POLY 4 if this is reasonable Alternatively you may consider defining the required potential in the code yourself Amendments 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_4 does not recognise Action Locate the offending potential in the FIELD file and remove Replace with one acceptable to DL_POLY 4 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
163. cells algorithms for many body and tersoff forces in DL_POLY 4 cannot work with less than 27 link cells Depending on the cell size and the chosen cut off DL_POLY_4 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 4 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 4 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 Message 321 error LFV quaternion integrator failed This indicates unstable integration but may be due to many reasons Action Rethink the simulation model Increase mxquat in CONTROL and resubmit or use VV integration to check system stability 246 STFC Appendix D Message 340 error invalid integration option requested DL_POLY 4 has detected an incompatibility in the simulation instructions namely that the re
164. ch case MPI I O is used direct which uses parallel FORTRAN direct access files and master which performs all I O through a master processor or netcdf for netCDF I O provided DL_POLY 4 is compiled in a netCDF enabled mode mptio is the recommended method and for large systems master should be avoided and also THE DIRECT OP TION IS NOT STRICTLY PORTABLE and so may cause problems on some machines rp is an optional specification only applicable to netcdf method for opting the binary precision for real numbers It only takes 32bit or amber for 32 bit float precision other wise 64 bit double precision is defaulted type controls the ordering of the particles on output Possible values are sorted and unsorted sorted ensures that the ordering of the particles the default sequential ascending Whereas unsorted uses the natural internal ordering of DL_POLY_4 which changes during the simulation The recommended and default value is sorted If none is specified DL POLY_4 defaultes to the sorted type of I O It should be noted that the overhead of the sorted otion compared to the unsorted is usually very small Available options depend on which method is to be used and all are optional in each case Where numerical values are to be supplied specifying 0 or a negative numbers indicates that DL_POLY_4 will resort to the default value The possible options are e io write mpiio direct netcdf rp sort unsort j k I e j specifies the number of p
165. ction 1 3 1 3 2 Modularisation and Intent DL_POLY 4 exploits the full potential of the modularisation concept in FORTRAN90 Variables having in common description of certain feature or method in DL_POLY 4 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 4 exploits the dynamic array allocation features of FORTRAN90 to assign the necessary array dimensions 1 3 4 Target Computers DL_POLY 4 is intended for distributed memory parallel computers It was developed on Cray T3E and IBM SP4 architectures Compilation of DL _POLY 4 in parallel mode requires only a FORTRAN90 compiler and Message Passing Interface MPI to handle communications Compilation of DL_POLY 4 in serial mode is also possible and requires only a FORTRAN090 compiler 1 3 5 Version Control System CVS DL_POLY_4 w
166. ctively dynamic chang ing in response to local changes 6 1 3 Distributing the Non bonded Terms DL_POLY 4 calculates the non bonded pair interactions using the link cell algorithm due to Hock ney and Eastwood 63 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 21 The Verlet list records the indices 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 and frozen atoms see below In DL_POLY 4 the neighbour list is constructed simulta
167. d users are refered to the README_CUDA txt within the CUDA folder for further information Contacts at STFC Daresbury Laboratory Dr I T Todorov ilian todorov stfc ac uk Prof W Smith bill smith stfc ac uk 275 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 2 161 Smith W 1987 Molecular Graphics 5 71 2 Smith W 1991 Comput Phys Commun 62 229 2 4 161 Smith W 1993 Theoretica Chim Acta 84 385 2 4 161 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 58 Pinches M R S Tildesley D and Smith W 1991 Molecular Simulation 6 51 2 4 161 Rapaport D C 1991 Comput Phys Commun 62 217 2 4 161 Daw M S and Baskes M I 1984 Phys Rev B 29 6443 3 29 Foiles S M Baskes M I and Daw M S 1986 Chem Phys Lett 33 7983 3 29 Finnis M W and Sinclair J E 1984 Philos Mag A 50 45 3 29 30 Sutton A P and Chen J 1990 Philos Mag Lett 61 139 3 30 Rafii Tabar H and Sutton A P 1991 Philos Mag Lett 63 217 3 30 36 37 Todd B D and Lynden Bell R M 1993 Surf Science 281 191 3 30 Tersoff J 1989 Phys Rev B 39 5566 3 37 162 van Gunsteren
168. d_module o kinds_f90 0 setup_module o ewald_frozen_forces o comms_module o config_module o domains_module o ewald_module o kinds_f90 o setup_module o ewald_module o config_module o kinds_f90 o setup_module o ewald_real_forces o comms_module o config_module o kinds_f90 0 setup_module o ewald_spme_forces o comms_module o config_module o domains_module o ewald_module o kinds_f90 0 parallel_fft o setup_module o ewald_spme_force o comms_module o config_module o domains_module o ewald_module o kinds_f90 0 setup_module o exchange_grid o comms_module o domains_module o kinds_f90 0 setup_module o export_atomic_data o comms_module o config_module o domains_module o kinds_f90 0 setup_module o external_field_apply o comms_module o config_module o core_shell_module o external_field_module o kinds_f90 0 rigid_bodies_module o A setup_module o external_field_correct o config_module o external_field_module o kinds_f90 0 rigid_bodies_module o external_field_module o kinds_f90 0 setup_module o four_body_forces o comms_module o config_module o domains_module o four_body_module o kinds_f90 0 setup_module o four_body_module o kinds_f90 0 setup_module o 197 STFC Appendix C gpfa_module o kinds_f90 0 impact o comms_module o config_module o core_shell_module o kinds_f90 0 kinetic_module o rigid_bodies_module o inversions_forces o comms_module o config_module o inversions_module o kinds_f90 0 setup_module o inver
169. dard Ewald since they specify the sides of a cube not a radius of convergence 102 STFC Section 4 3 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 reut The relative error e in the real space sum truncated at freut is given approximately by e erfc reut Teut expl a Tont rcut 4 3 The recommended value for a is 3 2 reut 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 1075 in the real space sum When using the directive ewald precision DL_POLY 4 makes use of a more sophisticated approximation erfc x 0 56 exp x x 4 4 to solve recursively for a using equation 4 3 to give the first guess The relative error in the reciprocal space term is approximately e exp k7ax 40 Kira
170. ded to aid alternative uses of the file for example the DL_POLY_4 Graphical User Interface 20 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 127 STFC Section 5 1 Table 5 6 Periodic Boundary Key record 2 imcon meaning no periodic boundaries cubic boundary conditions orthorhombic boundary conditions parallelepiped boundary conditions x y parallelogram boundary conditions with no periodicity in the z direction awnr 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 6 When restarting from a previous run of DL POLY 4 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 4 does this for you The CONFIG file has the same format as the optional output file CFGMIN which is only produced when the minimise optimise option has been used during an equilibration simulation or a dry run 5 1 3 The FIELD File The FIELD file contains the force field information defining the nature of the molecular forces This information explicitly includes the site topology of the system wh
171. determined by the presence of mass on the shells Dihedral potentials with more than three original parameters see OPLS have two artificially added parameters defining the 1 4 electrostatic and van der Waals scaling factors which must be placed at fourth and fifth position respectively extending the original parameter list split by them e Boundary conditions Truncated octahedral periodic boundaries imcon 4 are not available Rhombic dodecahedral periodic boundaries imcon 5 are not available Hexagonal prism periodic boundaries imcon 7 are not available e Electrostatics Standard Ewald Summation is not available but is substituted by Smoothed Particle Mesh Ewald SPME summation Hautman Klein Ewald Summation for 3D non periodic but 2D periodic systems is not available e Non standard functionality Temperature Accelerated Dynamics Hyperdynamics Solvation Energies 1 3 Programming Style The programming style of DL_POLY 4 is intended to be as uniform as possible The following stylistic rules apply throughout Potential contributors of code are requested to note the stylistic convention 1 3 1 Programming Language DL_POLY 4 is written in free format FORTRAN90 In DL_POLY 4 we have adopted the convention 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 Kind wp etc STFC Se
172. ding interactions It is the user s responsibility to ensure that no duplicate or mixed up intra molecular entries are specified in FIELD Action Look at the preceding warning message in OUTPUT and find out which entry of what intra molecular like interaction is at fault Correct the bonding description and try running again Message 625 error only one rigid directive per molecule is allowed DL_POLY 4 has found more than one rigids entry per molecule in FIELD Action Correct the erroneous part in FIELD and resubmit Message 630 error too many rigid body units specified This should never happen This indicates an erroneous FIELD file or corrupted DL_POLY_4 executable Unlike DL_POLY_2 DL_POLY 4 does not have a set limit on the number of rigid body types it can handle in any simulation this is not the same as the total number of RBs in the system or per domain Action Examine FIELD for erroneous directives correct and resubmit Message 632 error rigid body unit MUST have at least 2 sites This is likely to be a corrupted FIELD file Action Examine FIELD for erroneous directives correct and resubmit Message 634 error rigid body unit MUST have at least one non massless site No RB dynamics is possible if all sites of a body are massless as no rotational inertia can be defined Action Examine FIELD for erroneous directives correct and resubmit Message 638 error coincidence of particles in rigid
173. directory build makefiles to assemble and compile DL_POLY 4 programs public directory of routines donated by DL_POLY 4 users java directory of Java and FORTRAN routines for the Java GUI A more detailed description of each sub directory follows 1 4 1 The source Sub directory In this sub directory all the essential source code for DL_POLY _4 excluding the utility software is stored In keeping with the package concept of DL _POLY 4 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 4 to gether with examples of data Some of the various routines in this sub directory are documented in the DL_POLY _2 User Manual Users who devise their own utilities are advised to store them in the utility sub directory STFC Section 1 4 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 4 The examples of input data are copied into the execute sub directory when a program is being tested The test cases are documented in Chapter 7 Note that these are no longer within the distribution of any DL_POLY version but are made available on line at the DL_POLY FTP ftp ftp dl ac uk ccp5 DL_POLY 1 4 4 The bench S
174. ds_module o comms_module o config_module o kinds_f90 0 setup_module o bonds_module o kinds_f90 0 setup_module o build_book_intra o angles_module o bonds_module o comms_module o config_module o constraints_module o core_shell_module o dihedrals_module o inversions_module o pmf_module o 195 STFC Appendix C rigid_bodies_module o setup_module o site_module o tethers_module o build_excl_intra o angles_module o bonds_module o comms_module o config_module o constraints_module o core_shell_module o dihedrals_module o inversions_module o kinds_f90 0 rigid_bodies_module o setup_module o check_config o comms_module o config_module o kinds_f90 0 setup_module o site_module o comms_module o kinds_f90 0 compress_book_intra o comms_module o config_module o kinds_f90 0 setup_module o config_module o kinds_f90 0 setup_module o constraints_module o kinds_f90 0 setup_module o constraints_pseudo_bonds o comms_module o config_module o constraints_module o kinds_f90 o setup_module o constraints_quench o comms_module o config_module o constraints_module o kinds_f90 0 setup_module o constraints_tags o comms_module o config _module o constraints_module o kinds_f90 0 setup_module o core_shell_forces o comms_module o config_module o core_shell_module o kinds_f90 0 setup_module o core_shell_kinetic o comms_module o config_module o core_shell_module o kinds_f90 0 core_shell_module o kinds_f90 o setup_module o
175. duction the force on an atom derived from the valence angle potential is given by lo f gra U Ojik Pigs Tiks Tjk 2 29 Tg with atomic label being one of i j k and a indicating the x y z component The derivative is lo lo _ pre U Piik Tij Tik Tjk ri S ri S rje Fra As ri A Ojik S Tik S rin Sey 905 S rij Tij Orij r 0 A O5ix S rig 5 rjr Ook da E Sr Tik OT ik ta A O jir S rij 5 rite Oe dei SC 2 30 Tik Tik with dai 1 if a b and 64 0 if a b In the absence of screening terms S r this formula reduces to 9 org A Oi 2 31 lo n gra O Ojik Tig Pik Tjk 18 STFC Section 2 2 The derivative of the angular function is 9 1 O Tij Ck Beg bn E DO ara fumi 222 with o Tij Ti ra Ta a e da E er sei Ore Tora Tal TijfTik rij r cos 0 ik Sp dei gt dex de gt 2 33 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 rij f Lik La 2 34 It is worth noting that in the absence of screening terms S r the virial is zero 39 The contribution to be added to the atomic stress tensor is given by o r af r fe 2 35 and the stress tensor is symmetric In DL_POLY 4 valence forces are handled
176. dule o config_module o kinds_f90 0 setup_module o site_module o vdw_module o vdw_module o kinds_f90 0 setup_module o vdw_table_read o comms_module o kinds_f90 0 parse_module o setup_module o site_module o vdw_module o warning o comms_module o kinds_f90 0 setup_module o write_config o comms_module o config_module o io_module o kinds_f90 0 setup_module o xscale o comms_module o config_module o kinds_f90 0 kinetic_module o rigid_bodies_module o setup_module o statistics_module o z_density_collect o config_module o kinds_f90 0 setup_module o site_module o statistics_module o z_density_compute o comms_module o config_module o kinds_f90 0 setup_module o site_module o statistics_module o zero_k_optimise o comms_module o config_module o kinds_f90 0 kinetic_module o rigid_bodies_module o setup_module o 201 STFC Appendix C Makefile MPI Master makefile for DL_POLY_4 01 parallel version Author I T Todorov october 2010 Define default settings SHELL bin sh SUFFIXES SUFFIXES f90 o BINROOT execute EX DLPOLY Z EXE BINROOT EX TYPE master FC undefined LD undef ined Define object files OBJ_MOD kinds_f90 0 comms_module o setup_module o parse_module o development_module o netcdf_modul o io_module o domains_module o site_module o config_module o defects_module o defectsi_module o vdw_module o metal_module o tersoff_module o three_body_mod
177. e 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 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 real force constant of core shell spring The spring potential is 1 with the force constant k entered in units of engunitxA where engunit is the energy unit specified in the units directive Note that the atomic site indices referred to above are indices arising fr
178. e all variables and potential arrays needed for the calculation of the particular interaction in the DL_POLY 4 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 RIGID_BODIES_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 4 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 4 scope It depends on KINDS_F90 and its allocation method on SETUP_MODULE e langevin module LANGEVIN_MODULE This module defines all variables and arrays needed for the application of NPT and NoT Langevin routines in the DL POLY_4 scope It depends on KINDS_F90 and its allocation method on SETUP_MODULE e minimise module MINIMISE_MODULE This module defines all variables and arrays needed for the application of a Conjugate Gra dient Method minimisation routine in the DL_POLY 4 scope It depends on KINDS_F90 and its allocation method on SETUP_MODULE e ewald module EWALD_MODULE This module defines all variables and arrays needed for the refreshment of SPME k space dr
179. e b real potential parameter see Table 5 14 variable c real potential parameter see Table 5 14 cross term n n 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 c functional form ters Tersoff A a B b R Potential form single S B n c dlhkh as shown in Section cross x w d 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 three body potential in the following manner atmnam 1 i a8 first atom type atmnam 2 j a8 second central atom type atmnam 3 k a8 third atom type key ad potential key see Table 5 15 variable 1 real potential parameter see Table 5 15 variable 2 real potential parameter see Table 5 15 variable 3 real potential parameter see Table 5 15 variable 4 real potential parameter see Table 5 15 variable 5 real 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 A measured from the central atom 6 fbp n where n is the number of four body potentials to be entered It is follow
180. e eA er TE 156 5 29 Whe ZDNDAT Pile see 6 4 oboe the bee Bed Oe Bow phoebe 157 52 10 The STATIS Files s die e a RAS a Se ee a 157 6 The DL_POLY 4 Parallelisation and Source Code 160 6 1 Parallelisation o o cis e raid eee hee Re a SEES a es 161 6 1 1 The Domain Decomposition Strategy o o 161 6 1 2 Distributing the Intramolecular Bonded Terms 162 6 1 3 Distributing the Non bonded Terms 00 000048 163 6 1 4 Modifications for the Ewald Sumo 164 viii STFC Contents 615 Metal Potentials li saca s srada ee Re ee A O 165 6 1 6 Tersoff Three Body and Four Body Potentials 165 6 1 7 Globally Summed Properties 165 6 1 8 The Parallel DD tailored SHAKE and RATTLE Algorithms 165 6 1 9 The Parallel Rigid Body Implementation 166 6 2 SOUTO Code La aes a dae dead we ah ee EP ake eck ea ete De ee eo 167 6 2 1 Modularisation Principles corro sis BY A eee ee pe 167 622 Pile GHUE ee vu ave ea ade a a SA 169 Ga Module Piles asa a a ae A E A A eee ee 171 6 2 4 General Files occiso A i e ee 171 6 2 5 VV and LFV Specific Files sii sassa ha Sa a a 172 6 2 6 SERIAL Specific Files 172 6 2 7 Comments on MPI Handling osa s ss aa e 172 6 2 8 Comments on SETUP_MODULE 0000 eee ee ee ee 172 7 Examples 175 fil TES PASES ia ko ee PE ee be ae be he be Be PR Ae Ee 176 7 1 1 Test Case 1 and 2 Sodium Chloride
181. e 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 23 qe k 2 190 where qs and qe 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 kinetic energy and the temperature is different however as the core shell unit is permitted only three translational degrees of freedom and the degrees of freedom corresponding to rotation and vibration of the unit are discounted 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 4 is that devised by Fincham et al 53 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 x is chosen to ensure that the natural frequency of vibration Ucore she11 Of the harmonic spring which depends on the reduced mass i e 1 k 1 2 2
182. e found in CONFIG file On reading the input file CONFIG DL_POLY 4 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 or the parallel reading wrongly assumed that CONFIG complies with the DL_POLY 3 4 style Action 227 STFC Appendix D 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 If the reason is in the parallel reading then produce a new CONFIG using a serial reading and continue working with it Message 26 error neutral group option now redundant DL_POLY 4 does not have the neutral group option Action Use the Ewald sum option It s better anyway Message 27 error rigid body option now redundant DL_POLY 4 does not have a rigid body option Action Consider using DL_POLY 2 instead Message 28 error wrongly indexed atom entries found in CONFIG file DL_POLY 4 has detected that the atom indices in the CONFIG file do not form a contnual and or non repeating group of indices Action Make sure the CONFIG file is complies with the DL_POLY 4 standards You may use the no index option in the CONTROL file to override the crystalographic sites reading from the CONFIG file from reading by index t
183. e insight on the DL_POLY 4 source code structure 4 1 2 Constructing Non standard Versions In constructing a non standard DL_POLY 4 simulation program the first requirement is for the user to write a program 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 4 subroutines can be found in the Section 6 2 2 Should additional functionality be added to DL_POLY 4 by the user the SET_BOUNDS routine and its support subroutines may need modifying to allow s
184. e o setup_module o parse_module o development_module o netcdf_modul o io_module o domains_module o site_module o config_module o defects_module o defectsi_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 rigid_bodies_module o tethers_module o bonds_module o angles_module o dihedrals_module o inversions_module o external_field_module o langevin_module o minimise_module o ewald_module o msd_module o statistics_module o kinetic_module o gpfa_module o parallel_fft o OBJ_ALL warning o error o scan_control_io o numeric_container o spme_container o quaternions_container o scan_field o read_config_parallel o scan_config o scan_control o read_config o 217 STFC Appendix C set_bounds o read_control o vdw_generate o vdw_table_read o metal_generate o metal_table_read o metal_table_derivatives o tersoff_generate o dihedrals_14_check o read_field o check_config o scale_config o write_config o trajectory_write o system_expand o rigid_bodies_tags o rigid_bodies_coms o rigid_bodies_widths o rigid_bodies_setup o tag_legend o report_topology o pass_shared_units 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 rigid_bodies_qu
185. e permitted array dimension in the code Action 237 STFC Appendix D 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 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 92 error specified metal potentials have different types The specified metal interactions in the FIELD file are referencing more than one generic type of metal potentials Only one such type is allowed in the system Action Locate the errant metal type in the metal potential definition in the FIELD file and correct Make sure only one meta
186. e routines NVT_H1_vv and NVT_H1_LFV implement the same but also incorporate RB dynamics 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 Poxi and or isotropic stress tensor 0 DL_POLY 4 has three such algorithms with the Langevin type barostat 30 the Berendsen baro stat 28 the Nos Hoover type barostat 29 and the Martyna Tuckerman Klein MTK barsotat 31 Only the Berendsen barostat does not have defined conserved quantity Note that the MD cell s centre of mass momentum is removed at the end of the integration algorithms with barostats 3 5 1 Instantaneous pressure and stress The instantaneous pressure in a system 2 Ekin t Watomic t Woonstrain t At vi Wpwmr t At de 3V 1 3 79 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 g t 2 2 atomic t constrain t At apur AL 3 80 is a sum of the forcefield 7 constrain o and PMF a stresses atomic constrains PMF Note that when
187. e 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 PMF unit o 2 1 for a PMF constraint unit or 1 0 1 NRB unit for a rigid body 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 It is worth mentioning that although rigid body units are not bearing any potential parameters their definition requires that their topology is distributed in the same manner as the rest of the intra molecular like interactions Note that at the start of a simulation DL _POLY 4 allocates individual bonded interactions to spe cific processors based on the domains of the relevant atoms DL_POLY 4 routine 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 4 routine RELOCATE_PARTICLES Thus the allocation of bonded terms is effe
188. ea o a a a a D a a aa a ai 100 aoe DMasromolentles si ia e spa a ee a a eee Aia hee a 101 4 3 3 Adding Solvent to a Structure saosaoa a 101 484 Analysing Results Li s iosas aa d a AA ee ee N 102 4 3 5 Choosing Ewald Sum Variables a noaoo a a 102 4A Warming and Error Processing s so ia sacas amaca a toai doa aw a h e em na 104 4 4 1 The DL POLY 4 Internal Warning Facility 0 104 4 4 2 The DL_POLY 4 Internal Error Facility aoaaa 104 5 Data Files 106 Del The INPUT Piles cca ra ahot Boe ra e SO Ee a Se ae E 107 SLI The CONTROL Files 24 a4 4 6 ke 4 be hee bed Oe Owe ee A 107 Bi Whe CONFIG Fil iu 466 bea e Ae A e 126 Bla Whe FIELD File sce ta saaie dagarna ew Ree eR SERRE Re Ee 128 BA The REFERENCE Fil ess 2 0444 46844 E eae 144 5 Lb The REVOUD File sce 44 s saa ob hah hee be ea we Ae a 145 51 6 The TABLE File ca a is Pew oe PO A A ae oe Pe ee 146 Bll Whe TABEAM File coacciones 448044 bee eb Shwe Re ES 147 5 2 The OUTPUT Piles ee 04 50 eh By E Be eS ee oe A a 148 bal The HISTORY File cx 6 saoe tha dee Bed OA Oe phe be 148 52 2 The MBDTMP Elle asas bea be Ke A ee a 150 be The DEFECTS File 2 24 co 208860444865 bee PEER ERE Re ES 151 poe The CFGMIN Pile c a te a s toe e 1 152 boo Whe OUTPUT File oce oo eke She A e Gla Se Ae ES 153 526 The REVOON File iaa 4 we Pew ee Se ER e oe Pe a 156 Bt The REVIVE File ga a e a e eee hee ES 156 B28 Whe RDEDAT File sc ao eae 4k eh Bae he
189. ease 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 FIELD or and DL_POLY 4 exe cutable Action Reconstruct FIELD recompile afresh DL _POLY 4 and resubmit If the problem persists get in touch with DL_POLY 4 authors Message 108 error unidentified atom in rdf look up list During reading of RDF look up pairs in FIELD DL_POLY_4 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_4 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 4 has found a duplicate entry in the list Action Delete the duplicate line and resubmit Message 111 error bond constraint unit separation gt rcut the system cutoff This should never happen DL _POLY 4 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 Co
190. eater detail in Sections 3 2 and 3 6 2 2 The Intramolecular Potential Functions In this section we catalogue and describe the forms of potential function available in DL_POLY_4 The keywords required to select potential forms are given in brackets before each definition The derivations of the atomic forces virial and stress tensor are also outlined 2 2 1 Bond Potentials Figure 2 1 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 Uri ZEC ro 22 14 STFC Section 2 2 2 Morse potential mors U rij Eol l exp k rig ro 1 2 3 A B U rij 5 ce ij ij 4 Lennard Jones potential 1j n 12 5 6 ij ij 5 Restrained harmonic rhrm 3 12 6 potential bond 12 6 1 2 sk rij ro lrg Tol lt r U r QV 8 o 1 Led 2 6 ri skr2 krellrij rol re f rij to gt Te ee 6 Quartic potential quar k 9 k 3 k 4 U rij 5 tig Po rij Po rig To 2 7 2 3 4 7 Buckingham potential buck Tij C ij A ng 2 Uey A ew 7 q 2 8 8 Coulomb potential coul U r k dii _ k G5 2 9 3 ATEOE Tij where qe is the charge on an a
191. ections 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 19 The contribution to be added to the atomic stress tensor for each constrained bond is given by ode 3 20 where a and indicate 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 58 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 4 reports the PMF constraint virial Wp y p for each simulation Users can convert t
192. ectives are mandatory for example the timestep directive that defines the timestep others are optional This way of constructing the file is very convenient but it has inherent dangers It is for example quite easy to specify contradictory directives or invoke algorithms that do not work together By large DL_POLY 4 tries to sort out these difficulties and print helpful error messages but it does not claim to be fully 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 shake 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 4 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 The exapmle lists all possible and not mutually excluding directives in a particular order Although this order is not mandatory it is highly recommended TITLE RECORD DL_POLY_3 SAFE ORDER OF CONTROL DIRECTIVES SYSTEM REPLICATION am
193. ed by n records each specifying a particular four body potential in the following manner 142 STFC Section 5 1 Table 5 15 Three body Potentials key potential type Variables 1 4 functional formj harm Harmonic k bo U 0 E 0 b0 thrm Truncated harmonic k 00 p U 0 k 0 00 exp r r p3 shrm Screened harmonic k 0 pi p2 U 0 E 0 00 exp ri p1 rix p2 bvs1 Screened Vessal 35 k 00 pr p2 U 0 Oy 0 my 0 my x exp rij p1 rix p2 bvs2 Truncated Vessal 36 k 0 a p U 0 k 0 00 0 0 00 0 00 27 37 00 my exp r r 0 hbnd H bond 18 Dhp Rn U 0 Du cos 0 x Rno rjg 6 Rno rjn 9 10 is the 7 j k angle atmnam 1 i atmnam 2 j atmnam 3 k atmnam 4 1 key variable 1 variable 2 variable 3 a8 a8 a8 a8 a4 real real real first central atom type second atom type third atom type fourth 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 A 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 formi
194. ed in the Makefile 274 STFC Appendix E 3 a MAKE command Makefile interpreter in the system SHELL Note that 2 is not necessary for compilation in SERIAL mode By default if compilation is successful an executable build will be placed in execute directory at the same level as the directory where the code is compiled Should it not exist one will be created automatically The build can then be moved renamed etc and used as the user wishes However when executed the program will look for input files in the directory of execution 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 Linux like environment and then use the make command During cygwin installation make sure that make and gfortran are included in the install A potential problem for Windows based FORTRAN compilers you may encounter is that the compiler may not pick symbolic links To resolve this you will have to use hard linking in the Makefile Compiling with NetCDF functionality The targeted Makefile needs the following substitution within before attempting compilation netcdf_modul o gt netcdf_module o Note that suitable entry may need to be created within the Makefile so that it matches the particular combination of architecture compiler MPI library amp netCDF library Compiling the CUDA OpenMP Port This is not a supported feature an
195. ed in the TABEAM file Action Remove all duplicate entries in the TABEAM file and resubmit Message 511 error duplicate entry for an embedding function detected in TABEAM A duplicate embedding function entry is detected in the TABEAM file Action Remove all duplicate entries in the TABEAM file and resubmit 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 Action 257 STFC Appendix D 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_POLY 4 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
196. edantic std f2003 g fbounds check fbacktrace finit real nan finit integer 999999 FC ftn c FCFLAGS 00 W Wall pedantic std f2003 g fbounds check fbacktrace finit real nan finit integer 999999 EX EX BINROOT BINROOT TYPE hector gnu MAKE LD ftn o LDFLAGS 03 Wall pedantic g FC ftn c FCFLAGS 03 Wall pedantic g EX EX BINROOT BINROOT TYPE hector gnu debug MAKE LD ftn o LDFLAGS 03 Wall Wextra pedantic g fbounds check fbacktrace finit integer 9999 finit real nan std f2003 pedantic ffpe trap invalid zero overflow fdump core FC ftn c FCFLAGS 03 Wall Wextra pedantic g fbounds check fbacktrace finit integer 9999 finit real nan std f2003 pedantic ffpe trap invalid zero overflow fdump core 193 STFC Appendix C EX EX BINROOT BINROOT TYPE hector cray MAKE LD ftn o LDFLAGS 03 en FC ftn c FCFLAGS 03 en EX EX BINROOT BINROOT TYPE hector cray debug MAKE LD ftn o LDFLAGS 03 en G2 FC ftn c FCFLAGS 03 en G2 EX EX BINROOT BINROOT TYPE hector pathscale MAKE LD ftn o LDFLAGS byteswapio 03 FC ftn c FCFLAGS byteswapio 03 EX EX BINROOT BINROOT TYPE CRAY XT3 6 pathscale compilers DEBUG hector pathscale debug MAKE LD ftn o LDFLAG
197. ee body potentials in DL_POLY_4 are mostly valence angle forms They are primarily included to permit simulation of amorphous materials e g silicate glasses However these have been extended to include the Dreiding 18 hydrogen bond The potential forms available are as follows 1 Harmonic harm k U Ojik 5 Ojik bo 2 143 2 Truncated harmonic thrm k U Ojik z Ojik 09 exp r r3 07 2 144 3 Screened Harmonic shrm k U Oji 5 Ojik 80 expl rij P1 rir p2 2 145 4 Screened Vessal 35 bvs1 k 2 U Ojik 80 mM 00 T Ojik n x ji exp rij p1 Tik P2 2 146 5 Truncated Vessal 36 bvs2 U 0 ip Fin jim 90 Ojiz 09 27 Oj 90 m 00 exp r r8 0 2 147 6 Dreiding hydrogen bond 18 hbnd U Ojik Dp cos 0 iy 5 Rro rjx 6 Rnp rjx Y 2 148 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
198. efile 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 Interpolation Scheme In DL_POLY 4 two body like contributions van der Waals metal and real space Ewald summa tion to energy and force are evaluated by interpolation of tables constructed at the beginning of execution The DL_POLY 4 interpolation scheme is based on a 3 point linear interpolation in r Note that a 5 point linear interpolation in r is ised in DL_POLY 4 for interpolation of the EAM metal forces from EAM table data TABEAM The number of grid points mxgrid required for interpolation in r to give good energy conservation in a simulation is mxgrid Max mxgrid 1000 Int rcut 0 01 0 5 4 where reut is the main cutoff beyond which the contributions from the short range like interactions are negligible 4 2 2 Running To run the DL POLY 4 executable DLPOLY Z you will initially require three to six 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 _ 4 what kind of simulation you want to run how much data you want to gather and for how long
199. efully 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 118 error construction error in pass_shared_units This should not happen Action Report to authors 242 STFC Appendix D Message 120 error invalid determinant in matrix inversion DL_POLY 4 occasionally needs to calculate matrix inverses usually the inverse of the matrix of cell vectors which is of size 3 x 3 For safety s sake a check on the determinant is made to prevent inadvertent use of a singular matrix Action Locate the incorrect matrix and fix it e g are cell vectors correct Message 122 error FIELD file not found DL_POLY 4 failed to find a FIELD file in your directory Action Supply a valid FIELD file before you start a simulation Message 124 error CONFIG file not found DL_POLY 4 failed to find a CONFIG file in your directory Action Supply a valid CONFIG file before you start a simulation Message 126 error CONTROL file not found DL_POLY 4 failed to find a CONTROL file in your directory Action Supply a valid CONTROL file before you start a simulation Message 128 error chemical bond unit separation gt rcut the system cutoff This could only happen if F
200. elf consistent and requires no iterations The LFV implementation of 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 v t The iterative part is as follows 1 FF f t f t At 3 29 2 LFV The iterative part is as follows le 1 x t Al 1 1 le_f v scale f coe s EE PRESA e egale i scale 1 1 t v t At scale_v v t At scale_f 0 3 30 2 2 m 1 r t At rt Atu t 5 At 3 SHAKE 4 Full step velocity 1 1 1 v t gt v t At u t At 3 31 60 STFC Section 3 4 5 Thermostat 2 Ekin t x t lt 3 32 Several iterations are required to obtain self consistency In DL_POLY_4 the number of iterations is set to 8 9 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 4 routines NVT_EO_VV and NVT_EO_LFV respectively The routines NVT_El_vv and NVT_El_LFV im plement the same but also incorporate RB dynamics 3 4 2 Langevin Thermostat The Langevin thermostat works by coupling every particle to a viscous background and a stochastic heath bath such that dri t _ dt v t a _ LO FEO a 3 33 where x is the user defined constant positive in units of ps specifying the thermostat friction parameter and
201. ence of particles in bond angle unit DL_POLY 4 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 4 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 4 has found a fault in the definition of a inversion unit in the FIELD file Action Correct the erroneous entry in FIELD and resubmit 234 STFC Appendix D 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 4 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 4 attempts to extract the kinetic energy of the constrained atom atom bonds arising from the assignment of initial random velocities If this procedure fails the program will terminate The likely cause is a badly generated initial configuration Action Some hel
202. ench o set_temperature o vdw_lrc o metal_lrc o system_init o export_atomic_data o set_halo_particles o rigid_bodies_stress o read_history o impact o core_shell_on_top o deport_atomic_data o pmf_units_set o compress_book_intra o relocate_particles o link_cell_pairs o metal_ld_collect_eam o metal_ld_collect_fst o metal_ld_export o metal_ld_set_halo o metal_ld_compute 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 external_field_apply o external_field_correct o langevin_forces o constraints_pseudo_bonds o pmf_pseudo_bonds o rigid_bodies_split_torque o rigid_bodies_move o minimise_relax o core_shell_relax o zero_k_optimise o nvt_e0_scl o nvt_el_scl o nvt_b0_scl o nvt_bi_scl o pseudo_vv o constraints_shake_vv o pmf_shake_vv o constraints_rattle o pmf_rattle o nvt_h0_scl o npt_h0_scl o nst_h0_scl o nve_O_vv o nvt_e0_vv o nvt_10_vv o nvt_a0_vv o nvt_b0_vv o nvt_h0_vv o A npt_10_vv o npt_b0_vv o npt_h0_vv o npt_m0_vv o 218 STFC Appendix C nst_10_vv o nst_b0_vv o nst_h0_vv o nst_m0_vv o nvt_hi_scl o
203. ent a collaboration with the Irish Centre for High End Computing ICHEC http www ichec ie is to harness the power offered by NVIDIA http www nvidia com GPUs Note that no support is offered for these highly specific developments 1 7 Other Information The DL_POLY website http www ccp5 ac uk DL_POLY provides additional information in the form of 1 Access to all documentation including licences 2 Frequently asked questions W Bug reports 4 Access to the DL_POLY online forum Daresbury Laboratory also maintains two DL_POLY associated electronic mailing lists 10 STFC Section 1 7 1 dl_poly_news to which all registered DL POLY 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 user but not on this list you may request to be added Contact ilian todorov stfc ac uk 2 dl_poly mail is a group list which is available to DL _POLY users by request Its pur pose is to allow DL_POLY 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 mes sage subscribe dl_poly_mail Subsequent messages may be broadcast by e mailing to dl_poly_mail dl ac uk Note that this is a vetted list so electronic spam is not possible The DL_POLY Forum is a web based centre for all DL_POLY users to exchange comments and queries You may access
204. ere pij is the reduced mass of the two atoms connected by the bond d 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 is an approximation only Figure 3 1 The SHAKE RATTLE_VV1 schematics and associated vectors The algorithm cal culates the constraint force G G that conserves the bondlength d between atoms 1 and j following the initial movement to positions 7 and j under the unconstrained forces F and F and velocities v and vj The RATTLE algorithm was devised by Andersen 22 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 15 but missing the factor of a half 2 12 Cm Li di diz i O Zij Ate a di ij 3 16 The constraint force in RATTLE VV2 imposes a new condition of rigidity on constraint bonded atom velocities RATTLE VV2 is also a two stage algorithm In the first stage the VV2 algorithm 56 STFC Section 3 2 calculates the velocities of
205. erge Action See Message 515 255 STFC Appendix D 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 501 error coincidence of particles in PMF unit A PMF unit must be constituted of non repeating particles 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 repetition 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 505 error EAM metal densities or pair crossfunctions out of range The resulting densities or pair crossfunctions are not defined in the TABEAM file Action Recreate a TABEAM file with wider interval of defined densities and pair cross functions Message 506 error EAM metal densities out of range The resulting densities are not defined in the TABEAM file Action Recreate a TABEAM file with
206. es Action Correct the erroneous entry in FIELD and resubmit Message 34 error length of constraint bond unit gt real space cutoff rcut DL_POLY 4 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 4 has found a faulty chemical bond in FIELD defined between the same particle Action Correct the erroneous entry in FIELD and resubmit Message 36 error only one bonds directive per molecule is allowed DL_POLY_4 has found more than one bonds entry per molecule in FIELD Action Correct the erroneous part 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 extremely 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 229 STFC Appendix D 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 speci
207. es 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 mandatory a cut specifying the short range forces cutoff It is compulsory in all circumstances as all DL_POLY 4 algorithms are directly or indirectly dependent on it b temp or zero specifying the system temperature not mutually exclusive but if temp has to preceed zero in CONTROL if zero is needed Use only one instance of these in CONTROL If a dry run is performed see below these can be omitted c timestep or variable timestep specifying the simulation timestep Use only one instance of these in CONTROL If a dry run is performed see below and a timestep length is not supplied a default one of 0 001 ps is provided d ewald spme sum precision or coul or shift or distan or reaction or no elec specifying the required coulombic forces option Apart from no elec the rest of the directives are mutually exclusive from one another If none is specified then none is applied 2 Some directives are optional If not specified DL_POLY 4 will take default values if necessary The defaults are specified above in the list of directives However fail safe DL_POLY 4 is not always will it assume a default value for certain parameters To enable DL_POLY_4 to be even more liberal in the fail safe features users are recommended to use no strict option 3 The steps a
208. es NST_HO_vv and NST_HO_LFV respectively The routines NST_H1_VV and NST_H1_LFV implement the same but also incorporate RB dynamics 3 5 5 Martyna Tuckerman Klein Barostat DL_POLY 4 includes the Martyna Tuckerman Klein MTK interpretation of the VV flavoured Nos Hoover algorithms 31 for isotropic and anisotropic cell fluctuations in which the equations of motion are only slightly augmented with respect to those for the coupled Nos Hoover thermostat and barostat Compare the isotropic cell changes case equations 3 121 to d qe ult n t r d t 3 Sut E uo 143 no oe d 2Exin t Pmass n ty 20 kB Text ax mass mass 20 Ti 3 143 d Lex E in Pmass f F 3 kg Text Ti d CH n HM d pl Bal VE and the anisotropic cell change case equations 3 136 to d dl ult n t erl d t Tr n t fy ito Lil d 2Exin t Pmass Tr n t non d0 3 kp Text Qmass 20 Ti 3 144 dl o Pmass li f Pmass A Pmass res kB Text TP d SHO n H d qv Trin t VO The changes include one extra dependence to the velocity and barostat equations and removal of the centre of mass variable Ry t dependence in the position equation 82 STFC Section 3 5 The modifications in for the VV couched algorithms are of the following sort 1 At P t Pat 2Erin t 1 i Bes 1 de gt T TAn a 3 145 1 1 r t At exp nt zA At r t At v t 5 At for
209. es and forces the CONFIG file After allocation of all necessary simulation arrays and variables with compulsory initiali sation 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 simu 92 STFC Section 4 2 lated the types of atoms and molecules present and the intermolecular forces are obtained by the READ_FIELD routine which reads the FIELD 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 and exclusion arrays are created for the intramolecular and site related inter actions core shell constraint and tether units by BUILD_BOOK_INTRA and BUILD_EXCL_INTRA routines 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 like forces is carried out in the TWO_BODY_FORCES routine and rep resents the main part of any simulation For calculation of the two body contributions to the
210. es energy Practically this interaction amounts to replacing the momentum of some atoms with a new momentum drawn from the cor rect Boltzmann distribution at the desired temperature The strength of the thermostat can be adjusted by setting the average time interval over which the interactions occur and by setting the magnitude of the interaction The collisions are best described as a random Poisson process so that the probability that a collision occurs in a time step At is At Pesitieten tb 1 exp gt 3 44 TT where Tr is the thermostat relaxsation time The hardest collision is to completely reset the momentum of the Poisson selected atoms in the system with a new one selected from the Boltzmann distribution 3 2 mi mi U5 kgT ext F v ESSE A G 0 1 3 45 i a o set 2mi o a where subscripts denote particle indeces kg is the Boltzmann constant Text the target temperature and m the particle s mass The thermostat can be made softer by mixing the new momentum v7 drawn from F v with the old momentum v 4 v av t V a uy 3 46 where a 0 lt a lt 1 is the softness of the thermostat In practice a uniform distribution random number uni i is generated for each particle in the system which is compared to the collision A probability If uni i lt 1 exp 42 the particle momentum is changed as described above The VV implementation of the Andersen algorithm is as follows
211. es 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 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 gt lfi t Ri t 0 t mi v t 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 x t Maz o 5 4 121 STFC Section 5 1 12 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 from the rest of the system thus emulating 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 e pseudo direct The Direct thermostat is the simplest possible model allowing for heat exchange between the MD system and the heath bath All mass non frozen particles within the bath have their kinetic energy scaled to 1 5 kgT at the end of each time step during the simulation Care
212. ethod makes two amendments to this simple model Firstly each ion is effectively neutralised at long ranged 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 Gaussians The potential due to these Gaussians is obtained from Poisson s equation and is solved as a Fourier series in Reciprocal Space The complete Ewald sum requires an additional correction known as the self energy correction which arises from a Gaussian acting on its own site and is constant Ewald s method therefore replaces a potentially infinite sum in real space by two finite sums one in real space and one in 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 spa
213. external_field_module o langevin_module o minimise_module o ewald_module o msd_module o statistics_module o kinetic_module o gpfa_module o parallel_fft o OBJ_ALL warning o error o scan_control_io o numeric_container o spme_container o quaternions_container o scan_field o read_config_parallel o scan_config o scan_control o read_config o set_bounds o read_control o vdw_generate o vdw_table_read o metal_generate o metal_table_read o metal_table_derivatives o tersoff_generate o dihedrals_14_check o read_field o check_config o scale_config o write_config o trajectory_write o system_expand o rigid_bodies_tags o rigid_bodies_coms o rigid_bodies_widths o rigid_bodies_setup o tag_legend o report_topology o pass_shared_units 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 rigid_bodies_quench o set_temperature o vdw_lrc o metal_lrc o system_init o export_atomic_data o set_halo_particles o rigid_bodies_stress o read_history o impact o core_shell_on_top o deport_atomic_data o pmf_units_set o compress_book_intra o relocate_particles o link_cell_pairs o metal_ld_collect_eam o metal_ld_collect_fst o metal_ld_export o metal_ld_set_halo o metal_ld_compute o exchange_grid o ewald_spme_forces o metal_forces o vdw_forces o ewa
214. ey variable 1 a8 a8 a4 real first atom type second atom type potential key see Table 5 13 potential parameter see Table 5 13 139 STFC Section 5 1 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 variable 6 real potential parameter see Table 5 13 variable 7 real potential parameter see Table 5 13 variable 8 real potential parameter see Table 5 13 variable 9 real potential parameter see Table 5 13 The variables pertaining to each potential are described in Table 5 13 Table 5 13 Metal Potential key potential type Variables 1 5 6 9 functional form eam EAM tabulated potential fnsc Finnis Sinclair co cr co c A U r 5 2 ri a co cing car Api A o 3 dp pi E 1 7 00 2 ifi exfs Extended co c1 c2 c3 ca Ui r 3 2 Pi c eo citij cari cari cary IF Finnis Sinclair c A d B AJP P X rig d B rij d IA h Sutton Ch Ulr e lin 21 stc utton Chen e pan mc ir Se gt 4 CVPi a ym a re gupt Gupta Alro p B ay U r IE pro BVPi __Tig T0 Pi 2 exp 2 a 3 rdf n where n is the number of RDF pairs to be entered It is followed by n records each specifying a particular RDF pair in the following manner
215. f any correct and resubmit Message 648 error quaternion setup failed This error indicates that the routine RIGID_BODIES_SETUP has failed in reproducing all the atomic positions in rigid units from the centre of mass and quaternion vectors it has calculated Action Check the contents of the CONFIG file DL_POLY 4 builds its local body description of a rigid unit type from the first occurrence of such a unit in the CONFIG file The error most likely occurs because subsequent occurrences were not sufficiently similar to this reference structure If the problem persists increase the value of tol in RIGID_BODIES_SETUP and recompile If problems still persist double the value of dettest in RIGID_BODIES_SETUP and recompile If you still encounter problems contact the authors 263 STFC Appendix D Message 650 error failed to find principal axis system This error indicates that the routine RIGID_BODIES_SETUP has failed to find the principal axis for a rigid unit Action This is an unlikely error DL_POLY 4 should correctly handle linear planar and 3 dimensional rigid units There is the possibility that the unit has all of its mass bearing particles frozen while some of the massless are not or the unit has just one mass bearing particle Check the definition of the rigid unit in the CONFIG file if sensible report the error to the authors Message 1000 error working precision mismatch between FORTRAN90 and MPI implementation
216. f 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 165 STFC Section 6 1 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 The compilation of the list of constrained atoms on each processor and the circulation of the list items 1 3 above is done at the start of the simulation but thereafter it needs only to be done every time a constraint bond atom is relocated from one pr
217. fact be essential to maintain the structure of the system The three body potentials are very short ranged typically of order 3 A This property plus the fact that three body potentials scale as N4 where N is the number of particles makes it essential that these terms are calculated by the link cell method 48 The calculation of the forces virial and stress tensor as described in the section valence angle potentials above DL_POLY 4 applies no long ranged corrections to the three body potentials The three body forces are calculated by the routine THREE_BODY_FORCES 40 STFC Section 2 4 2 3 5 Four Body Potentials The four body potentials in DL_POLY 4 are entirely inversion angle forms primarily included to permit simulation of amorphous materials particularly borate glasses The potential forms available in DL_POLY 4 are as follows 1 Harmonic harm U Pijkn a dijkn do 2 149 2 Harmonic cosine hcos k U Gijkn 5 COS dijkn cos do 2 150 3 Planar potential plan U dijkn A 1 cos dijkn 2 151 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
218. fied 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 4 limits the number of bond constraint 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 Use densvar option in CONTROL to increase mxcons alternatively increase it by hand in SET_BOUNDS and recompile and resubmit 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 increase 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 230 STFC Appendix D 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
219. for specific platforms For DL POLY 4 compilation in parallel mode a FORTRAN90 compiler and an MPI implementation for the specific machine architecture are required in many cases the user sometimes with help from the administrator of their platform will have to create their own keyword entry in the makefile due to the large variety of i software needed for the compilation of DL_POLY 4 and ii places where it could be installed PATHS 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_4 compilation in serial mode they will have to provide a valid PATH to the FORTRAN90 compiler on their specific platform 4 The makefile produces the executable version of the code which as a default will be named DLPOLY Z 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 20 6 Torun the executable for the first time you require the files CONTROL FIELD and CONFIG and possibly TABLE if you have tabulated van der Walls potentials TABEAM if you have tabulated metal potentials and REFERENCE if defect detection is opted for These must be present in the directory from which the program is executed See Section 5 1 f
220. g ging DL_POLY 4 Depending on the method dependencies on KINDS_F90 COMMS_MODULE SETUP_MODULE DOMAINS_MODULE are found e I O module 10_MODULE The I O module contains all important global variables that define the I O methods and types used in the package and contains basic routines essential for the I O in DL_POLY 4 It is dependent on KINDS_F90 167 STFC Section 6 2 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 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 arrays CONFIG and is dependent on KINDS_F90 only However it also develops an allocation method that is dependent on SETUP_MODULE e defects module DEFECTS_MODULE The defects module defines all defects and configuration related arrays REFERENCE 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 defin
221. ge 1001 Message 1049 error deallocation failure in comms_module gt grsum_matrix Action See Message 1002 Message 1050 error sorted I O base communicator not set Possible corruption if 10_MODULE This should never happen Action Make sure you have a clean copy of DL_POLY_4 compiled without any suspicious warning mes sages Contact authors if the problem persists Message 1053 error sorted I O allocation error Your I O buffer and possibly batch size is too big Action Decrease the value of the I O buffer and possibly batch size in CONTROL and restart your job Message 1056 error unkown write option given to sorted I O This should never happen Action Contact authors if the problem persists 270 STFC Appendix D Message 1059 error unknown write level given to sorted I O This should never happen Action Contact authors if the problem persists 271 Appendix E DL_POLY 4 README DL_POLY_4 01 The source is in fully self contained free formatted FORTRAN90 MPI2 code specifically FORTRAN90 TR15581 MPI1 MPI I 0 only The available NetCDF functionality makes the extended code dependent upon it The non extended code complies with the NAGWare 95 and FORCHECK 90 standards with exception of the FORTRAN2003 feature TR15581 which is very rarely unavailable in the nowadays FORTRAN95 compilers This version supports ALL features that are available in the
222. gisum_vector Action See Message 1001 264 STFC Appendix D Message 1004 error Action See Message 1002 Message 1005 error Action See Message 1001 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 deallocation failure in comms_module gt gisum_vector allocation failure in comms_module gt grsum_vector 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 265 STFC Appendix D Message 1013 error allocation failure in angles_ module gt allocate_angles_arrays Action See Message 1001 Message 1014 error allocation failure in bonds_module gt allocate_bonds_arrays Action See Message 1001 Message 1015 error allocation failure in core_shell
223. h 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_4 TO COMPENSATE FOR A BAD DENSITY DISTRIBUTION 6 1 2 Distributing the Intramolecular Bonded Terms The intramolecular terms in DL_POLY_4 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 This is the local atom list 162 STFC Section 6 1 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 4 Every intramolecular bonded term Ujype in the system has a unique index number sqpe from 1 to Niype 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 rigid body 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 th
224. harm Harmonic k Qo U k d do hcos Harmonic cosine k do U E cos cos o plan Planar A U A 1 cos t is the i j k l four body angle 143 STFC Section 5 1 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 contain another directive indicating what type of field is to be applied followed by the field parameters The variables pertaining to each field potential are described in Table 5 17 Note only one type of field can be applied at a time Note that external force parameters are read in terms of the specified energy units and the general DL_POLY units so that the two sides of the equation defining the field are balanced Table 5 17 External Fields key potential type Variables 1 4 functional formt elec Electric Field Ey Ey Ez F qE oshr Oscillating Shear A ln F A cos 2na z Lz shrx Continuous Shear A zo v ak z gt zo grav Gravitational Field Gz y 5 F mG magn Magnetic Field Hy Hy H F q ux H sphr Containing Sphere A Ro n Rae E A Ro r r gt Rout zbnd Repulsive Wall A 2 p F A z 2z pz gt pzo 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 4 will abort 5 1 4 The REF
225. he MD cell s centre of mass momentum is removed at the end of the integration algorithms The Berendsen algorithms conserve total momentum but not energy The VV and LFV flavours of the Berendsen thermostat are implemented in the DL_POLY 4 routines NVT_BO_VV and NVT_BO_LFV respectively The routines NVT_B1_VV and NVT_B1_LFV implement the same but also incorporate RB dynamics 3 4 5 Nos Hoover Thermostat In the Nos Hoover algorithm 29 Newton s equations of motion are modified to read dr t _ ae du t _ f t a Sa t u t 3 65 The friction coefficient x is controlled by the first order differential equation dx t z 2Ekin t 20 3 66 dt mass where is the target thermostat energy equation 3 56 and mass 20 T 3 67 is the thermostat mass which depends on a specified time constant Tr for temperature fluctuations normally in the range 0 5 2 ps The VV implementation of the Nos Hoover algorithm takes place in a symplectic manner as follows 1 Thermostat Note Ex n t changes inside At 2Ekin t 20 x t 144 x t 4 Amass iO a exp dit 144 gt 3 68 1 1 At 2Epin t 20 x t 300 x t GAN EL 3 69 2 VVI 1 At f t v t 544 oft Ca mil mada At 3 70 66 STFC Section 3 4 3 RATTLE_VV1 4 FF f t At f t 3 71 5 VV2 At f t At 1 t F LA At 4 u t t lt atts 5 2 3 72 6 RATTLE_VV2 7 Thermost
226. he dynamical one In case when some shells are massless and some are not DL_POLY_4 will terminate execution controllably and provide information about the error and possible possible choices of action in the OUTPUT file see Section 5 2 5 2 6 External Fields In addition to the molecular force field DL POLY 4 allows the use of an external force field Examples of fields available include 1 Electric field elec F F q E 2 192 2 Oscillating shear oshr EF Acos 2n7 2 L 2 193 3 Continuous shear shrx Up To sal gt 20 2 194 50 STFC Section 2 7 4 Gravitational field grav F F m G 2 195 5 Magnetic field magn F Fi qi vi x H 2 196 6 Containing sphere sphr F A Ro r in Rout 2 197 7 Repulsive wall zbnd F A z 2 12 gt Zo s 2 198 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 4 external field forces are handled by the routines EXTERNAL_FIELD_APPLY and EX TERNAL_FIELD_CORRECT 2 7 Treatment of Frozen Atoms Rigid Body and Core Shell Units Frozen atoms core shell units and rigid body units are treated in a manner similar t
227. his to the PMF constraint force from W GPMF a 3 21 58 STFC 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 constraints The constraint procedures i e SHAKE or RATTLE for both types of constraineds are applied iteratively in order bonds PMFs until convergence of Wpyp 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 Toxt 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_4 comes with five different thermostats Evans Gaussian constraints 25 Langevin 26 59 Andersen 27 Berendsen 28 and Nos Hoover 29 Of these only the Nos Hoover algorithm generates trajectories in the canonical NVT ensemble The rest will produce properties that typically differ from canonical averages by O 1 N 21 as the Evans algorithm generates trajectories in the NVE gin ensemble
228. hort range non bonded interactions in simulation minimise the system configuration at start during equilibration using conjugate gradient method CGM with respect to the criterion string and tolerance f where the criterion can only be force 1 lt f lt 1000 default f 100 or energy 0 lt f lt 0 01 default f 0 005 or distance maximum absolute displacement in A 107 lt f lt 0 1 default f 0 005 the CGM minimised configuration is saved in a file CFGMIN which has the same format as CONFIG 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 attach a pseudo thermal bath with a thermostat of type string where string can only be langevin or direct if neither is specified both are applied in order langevin direct f is the thickness of the thermostat 115 STFC Section 5 1 quaternion tolerance f rdf sampling every f reaction field reaction field damp a reaction field precision f regauss every n replay restart restart noscale restart scale rlxtol f rvdw cutoff f scale temperature every n seed n Na layers attached on the inside of the MD cell boundaries in units of A default f1 2 A fa is the thermostat temperature in Kelvin f2 gt 1 which when unspecified defaults to the system target tempe
229. hrough 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 4 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_4 documentation and find the potential keyword for the potential desired Message 151 error unknown EAM keyword in TABEAM DL_POLY 4 checks when constructing the interpolation tables for the EAM metal potentials that the potential function requested is one which is of a form known to the program If the requested 244 STFC Appendix D 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 Message 170 error too many variables for statistics array This error means the statistics arrays appearing in subroutine STATISTICS_COLLECT are too small This should never happen Action Contact DL_POLY 4 authors Message 200 error rdf z density buffer array too small in system_revive This error indicates that a global summation buffer array in subroutine
230. 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 IDO _body t 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 Usnei 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 4 as intra molecular interactions and the next four as inter molecular interactions The final term Uertn 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 13 STFC 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 tbond angl 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 4 all core shell units tethered particles chemical bonds valence angles dihedral angles and i
231. ial configuration see above are given This is written by the main subroutine DL_POLY 5 2 5 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 atomic species in the simulation These are determined from a single time origin and are therefore approximate Accurate determinations of the diffusion coefficients 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 5 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 155 STFC Section 5 2 collection of the histogr
232. ial distribution data file Z density data file and a statistical history file 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 information 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 148 STFC Section 5 2 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 in last frame imcon integer periodic boundary key see Table 5 6 in last frame megatm integer number of atoms in simulation cell in last frame frame integer number configuration frames in file records integer number of records in file Fo
233. ib 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 0 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 BGL MAKE LD bg1 BlueLight ppcfloor bglsys bin mpixlf95 o 192 STFC Appendix C LDFLAGS 03 qhot qarch 440d qtune 440 FC bg1 BlueLight ppcfloor bglsys bin mpixlf95 c FCFLAGS 03 qhot qarch 440d qtune 440 EX EX BINROOT BINROOT TYPE BGP MAKE LD bgsys drivers ppcfloor comm bin mpix1f2003_r o LDFLAGS 03 qhot qarch 450d qtune 450 qmaxmem 128000 FC bgsys drivers ppcfloor comm bin mpixlf2003_r c FCFLAGS 03 qhot qarch 450d qtune 450 qmaxmem 128000 EX EX BINROOT BINROOT TYPE hector MAKE LD ftn o LDFLAGS 03 fastsse FC ftn c FCFLAGS 03 fastsse EX EX BINROOT BINROOT TYPE hector pgi debug MAKE LD ftn o LDFLAGS 00 W Wall p
234. icates that DL_POLY 4 has failed to find the required record 224 STFC Appendix D Action Add units directive to FIELD file and resubmit Message 8 error ewald precision must be a POSITIVE real number Ewald precision must be a positive non zero real number For example 10e 5 is accepted as a standard Action Put a correct number at the ewald precision directive in the CONTROL 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_4 executable Unlike DL_POLY_2 DL _POLY 4 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 4 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 4 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 Th
235. ich sequence must be matched implicitly in the crystallographic description of the system in the CONFIG file The FIELD file 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 128 STFC Section 5 1 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 harm 69 5 70 200 00 116 harm 18 168 162 160 00 120 harm 19 168 162 140 00 116 DIHEDRALS 371 harm 1 43 2 44 2 3000 harm 31 43 2 44 2 3000 cos 149 17 161 16 10 500 cos 162 19 168 18 10 500 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 C CT lj 0 08485 OW OS lj 0 15100 OS OS lj 0 15000 CLOSE 5 1 3 1 The FIELD File Format 40 40 00 00 00 00 The file is free formatted and not case sensitive Every line is treated as a command sentence record Commented records beginning with a
236. ified 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 254 STFC Appendix D 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 494 error overconstrained PMF units PMF units are oveconstrained Action DL POLY 4 algorithms cannot handle overconstrained PMF units Decrease the number of con straints on the PMFs Message 497 error pmf_quench failure Action See Message 515 Message 498 error shake algorithm pmf_shake failed to conv
237. ig Lito Thn ven The derivative of the function B r j jk pn iS 0 1 lo grg Liss Lito Len Iris x jnlp X Ton are Eu x Tjk i jk X Tkn cos Pijkn 1 Da 1 0 2 l x Tip are alla x eel Ir Log 2 are alla x Tele 2 47 with ore his X Tjk Cie X Len rij rsetirlo 0 den rjatinla bex de rie igh jkla Oen de rjatenla de 2i Tkn lrijtirlo de dej rjntjrla dei de5 2rik Lil imlo OL dek gt 2 48 a a rig X Lje WE lCjktjklal egj de riLrlal e See 2r5k rijtizla de n de H rijtjrlo dei de 2 49 21 STFC Section 2 2 0 a org Eik ce 2rEn rjatsrlo 6en Sek rjrtanla dj 2x 2r5k rentknlo 0 fej rjatenla dex den 2 50 Where we have used the the following definition a Bla 1 ap 2 51 8 Formally the contribution to be added to the atomic virial is given by W Son f 2 52 However it is possible to show by tedious algebra using the above formulae or more elegantly by thermodynamic arguments 39 that the dihedral makes no contribution to the atomic virial The contribution to be added to the atomic stress tensor is given by o ra pi PD TED 2 53 cos dijkn a ro rogi 7h ren hf with P rieltintenlo Thal pel jela tag X Teall jx X Cenl Pr renltaPeele ni tollartynla a x Piel Pe X Peal Pik rilc ntenla rinlCigtigla
238. imise_module o kinds_f90 0 setup_module o minimise_relax o comms_module o config_module o kinds_f90 0 minimise_module o rigid_bodies_module o setup_module o msd_write o comms_module o config_module o io_module o kinds_f90 0 parse_module o setup_module o site_module o statistics_module o netcdf_module o kinds_f90 0 netcdf_modul o kinds_f90 0 numeric_container o comms_module o config_module o kinds_f90 0 setup_module o nvt_bO_scl o config_module o kinds_f90 0 kinetic_module o setup_module o nvt_bi_scl o config_module o kinds_f90 0 kinetic_module o rigid_bodies_module o setup_module o nvt_e0_scl o comms_module o config_module o kinds_f90 0 setup_module o nvt_el_scl o comms_module o config_module o kinds_f90 0 A rigid_bodies_module o setup_module o 198 STFC Appendix C parallel_fft o comms_module o gpfa_module o kinds_f90 0 setup_module o parse_module o comms_module o kinds_f90 0 setup_module o pass_shared_units o comms_module o config_module o domains_module o kinds_f90 0 rigid_bodies_module o setup_module o pmf_coms o comms_module o config_module o kinds_f90 0 pmf_module o setup_module o pmf_module o kinds_f90 0 setup_module o pmf_pseudo_bonds o comms_module o config_module o kinds_f90 0 pmf_module o setup_module o pmf_quench o comms_module o config_module o kinds_f90 0 pmf_module o setup_module o pmf_tags o config_module o kinds_f90 0 pmf_module o setup_module o pmf_units_set o comms_module o
239. 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 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 It offers better numerical stability and faster convergence when i constraint solvers CB PMF RATTLE VV versus SHAKE LFV 273 STFC Appendix E are involved and or ii RB dynamics is integrated The LFV integration may take less cpu time than the VV one for the certain ensembles type of system CB PMF RB and type of ensemble dependent Usually LFV is slightly faster than VV when CB PMF RB are present in the system The relative performance between the LVF and VV integration per timestep is observed to vary in the limits LFV t VV t VV t 5 5 However the VV algorithms treat CB PMF RB entities in more precise symplectic manner than the LFV ones and thus not only have better numerical strability but also produce more accurate dynamics Makefiles From within the source directory the
240. increase it by hand in SET_BOUNDS and recompile and resubmit Message 104 error arrays listme and Istout exceeded in pass_shared_units This should not happen 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 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 240 STFC Appendix D Consider using densvar option in CONTROL for extremely non equilibrium simulations or incr
241. inimum 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 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 4 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 4 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 The cutoff for the pair interactions is smaller than twice that for the four body interactions This is a bookkeeping requirement for DL_POLY 4 253 STFC Appendix D Action Either use a smaller four body cutoff or a larger pair potential cutoff Message 474 error conjugate gr
242. ion 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 Rae f Min 0 3 reut 3 A lt Rag lt Min 1 2 Tcut 2 A 5 5 with a default value of Min 0 75 reut 3 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 122 STFC Section 5 1 13 14 15 16 17 18 19 F
243. ired array sizes is difficult to obtain and the calculated value may be too small For this reason DL_POLY 4 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 4 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 4 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 223 STFC Appendix D The DL_POLY 4 Error Messages Message 1 error word_2_real failure The semantics in some of the INPUT files is wrong DL_POLY 4 has tried to read a number but the has found a word in non number format Action Look into your INPUT files and correct the semantics where appropriate and resubmit DL_POLY_4 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_
244. is 0 10 Angstroms SUMULATION amp EQUILIBRATION LENGTH steps 10000 steps equilibration 1000 steps EQUILIBRATION DIRECTIVES Zero cap 2000 kT Angstrom scale 5 steps regauss 3 steps 109 STFC Section 5 1 minimise force 20 1 0 optimise energy 0 001 STATISTICS collect stack 50 deep stats 10 steps OUTPUT print 2 steps HISTORY replay trajectory 20 30 0 DEFECTS defects 40 15 0 75 MSDTMP msdtmp 1000 100 RDF amp Z DENSITY binsize 0 05 Angstroms rdf 7 steps print rdf zden 7 steps print zden EXECUTION TIME job time 1000 seconds close time 10 seconds FINISH 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 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 i
245. is error message results if it encounters a unrelated directive The most probable cause is incomplete specification of the data e g when the finish directive has been omitted Action Check the molecular data entries in the FIELD file correct and resubmit Message 13 error molecule species not specified This error arises when DL_POLY 4 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 225 STFC Appendix D 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_4 executable are corrupted Action Recompile the program or recreate the FIELD file If neither of these works send the problem to us Message 15 error duplicate vdw potential specified In processing the FIELD file DL_POLY 4 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
246. iven properties in the DL_POLY_4 scope when an infrequent SPME option is opted for in CONTROL It depends on KINDS_F90 and its allocation method on SETUP_MODULE 168 STFC Section 6 2 e msd module MSD_MODULE This module globalises a CONTROL variable e statistics module STATISTICS_MODULE This module defines all variables and arrays needed for the statistical accountancy of a simula tion in DL_POLY 4 It depends on KINDS_F90 and its allocation method on SETUP_MODULE e kinetic module KINETIC_MODULE The kinetic module contains a collection of routines for the calculation of various kinetic properties It is dependent on KINDS_F90 6 2 2 File Structure Generally the DL_POLY 4 file structure can be divided into four groups as follows e module files in the source directory KINDS_F90 COMMS_MODULE SETUP_MODULE PARSE_MODULE DEVELOPMENT_MODULE IO_MODULE DOMAINS_MODULE SITE_MODULE CONFIG_MODULE DEFECTS_MODULE VDW_MODULE METAL_MODULE TERSOFF_MODULE THREE_BODY_MODULE FOUR_BODY_MODULE CORE_SHELL_MODULE CONSTRAINTS_MODULE PMF_MODULE RIGID_BODIES_MODULE TETHERS_MODULE BONDS_MODULE ANGLES_MODULE DIHEDRALS_MODULE INVERSIONS_MODULE EXTERNAL_FIELD_MODULE LANGEVIN_MODULE MINIMISE_MODULE EWALD_MODULE MSD_MODULE STATISTICS_MODULE KINETIC_MODULE GPFA_MODULE PARALLEL_FFT e general files in the source directory WARNING ERROR SCAN _CONTROL_IO NUMERIC_CONTAINER SPME_CONTAINER QUATERNIONS_CONTAINER SCAN_FIELD READ_CONFIG
247. ke_lfv o pmf_shake_lfv o nve_0_lfv o nvt_e0_lfv o nvt_10_lfv o nvt_a0_lfv o nvt_b0_lfv o nvt_h0_lfv o npt_10_lfv o npt_b0_lfv o npt_h0_lfv o npt_m0_lfv o nst_10_lfv o nst_b0_lfv o nst_h0_lfv o nst_m0_lfv o nve_1_lfv o nvt_el_lfv o nvt_11_1lfv o nvt_al_lfv o nvt_b1_lfv o nvt_hi_lfv o npt_11_1fv o npt_b1_lfv o npt_h1_lfv o npt_mi_lfv o nst_11_1fv o nst_b1_lfv o nst_h1_1lfv o nst_m1_lfv o xscale o core_shell_kinetic o regauss_temperature o defects_reference_read o defects_reference_read_parallel o defects_reference_write o defects_reference_export o defects_reference_set_halo o defects_link_cells o defects1_write o defects_write o msd_write o z_density_collect o statistics_collect o system_revive o rdf_compute o z_density_compute o statistics_result o dl_poly o Define Velocity Verlet files FILES_VV pseudo_vv f90 constraints_shake_vv f90 pmf_shake_vv f90 constraints_rattle f90 pmf_rattle f90 nvt_h0_scl f90 npt_h0_sc1 f90 nst_h0_sc1 f90 nve_0_vv f90 nvt_e0_vv f90 nvt_10_vv f90 nvt_a0_vv f90 nvt_b0_vv f90 nvt_hO_vv f90 npt_10_vv f90 npt_b0_vv f90 npt_h0_vv f90 npt_m0_vv f90 nst_10_vv f90 nst_b0_vv f90 nst_h0_vv f90 nst_m0_vv f90 nvt_h1_sc1 f90 npt_h1_sc1 f90 nst_hi_scl f90 nve_1_vv f90 nvt_el_vv f90 nvt_11_vv f90 nvt_al_vv f90 nvt_b1_vv f90 nvt_h1_vv f90 npt_11_vv f90 npt_b1_vv f90 npt_h1_vv f90 npt_mi_vv f90 nst_11_vv f90 nst_b1_vv f90 nst_h1_vv f90 nst
248. kely to be a problem Note this boundary condition have to be used with caution DL_POLY 4 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 SPM Ewald summation method Cubic periodic boundaries imcon 1 The cubic MD cell is perhaps the most commonly used in simulation and has the advantage of great simplicity In DL_POLY 4 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 180 STFC Appendix A Z Y X Figure A 1 The cubic MD cell Orthorhombic periodic boundaries imcon 2 gt X Figure A 2 The orthorhomic MD cell The orthorhombic cell is also a common periodic boundary which closely resembles the cubic cell in use In DL_POLY 4 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
249. l type is specified for all relevan atom interactions in the file Message 93 error PMFs mixing with rigid bodies not allowed Action Correct FIELD and resubmit 238 STFC Appendix D 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 4 it is necessary to ensure that the major cutoff applied to the pair interactions 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 constraints mixing with rigid bodies not allowed 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 shells as part of a constraint rigid body or tether Action Co
250. l_lfv o nvt_li_lfv o nvt_al_lfv o nvt_b1_lfv o nvt_hi_lfv o npt_11_1fv o npt_b1_lfv o npt_h1_lfv o npt_mi_lfv o nst_li_lfv o nst_b1_lfv o nst_h1_lfv o nst_m1_lfv o xscale o core_shell_kinetic o regauss_temperature o defects_reference_read o defects_reference_read_parallel o a defects_reference_write o defects_reference_export o defects_reference_set_halo o defects_link_cells o defectsi_write o defects_write o msd_write o z_density_collect o statistics_collect o system_revive o rdf_compute o z_density_compute o statistics_result o dl_poly o Define Velocity Verlet files FILES_VV pseudo_vv f90 189 STFC Appendix C constraints_shake_vv f90 pmf_shake_vv f90 constraints_rattle f90 pmf_rattle f90 nvt_h0_sc1 f90 npt_h0_sc1 f90 nst_h0_sc1 f90 nve_0_vv f90 nvt_e0_vv f90 nvt_10_vv f90 nvt_a0_vv f90 nvt_b0_vv f90 nvt_h0_vv npt_10_vv f90 npt_b0_vv f90 npt_h0_vv f90 npt_m0_vv nst_10_vv f90 nst_b0_vv f90 nst_h0_vv f90 nst_m0_vv nvt_h1_sc1 f90 npt_h1_sc1 f90 nst_hi_scl f90 nve_1_vv f90 nvt_el_vv f90 nvt_11_vv f90 nvt_al_vv f90 nvt_b1_vv f90 nvt_hi_vv npt_li_vv f90 npt_b1_vv f90 npt_h1_vv f90 npt_m1_vv nst_11_vv f90 nst_b1_vv f90 nst_hi_vv f90 nst_m1_vv md_vv f90 Define LeapFrog Verlet files FILES_LFV pseudo_lfv f90 constraints_shake_lfv f90 pmf_shake_lfv f90 nve_0_lfv f90 nvt_e0_1fv f90 nvt_10_1fv f90 nvt_a0_1fv f90 nvt_bO_lfv f90 nvt_h0_
251. ld_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 188 STFC Appendix C external_field_apply o external_field_correct o langevin_forces o constraints_pseudo_bonds o pmf_pseudo_bonds o rigid_bodies_split_torque o rigid_bodies_move o minimise_relax o core_shell_relax o zero_k_optimise o nvt_e0_scl o nvt_el_scl o nvt_b0_scl o nvt_bi_scl o pseudo_vv o constraints_shake_vv o pmf_shake_vv o constraints_rattle o pmf_rattle o nvt_h0_scl o npt_h0_scl o nst_h0_scl o nve_0_vv o nvt_e0_vv o nvt_10_vv o nvt_a0_vv o nvt_b0_vv o nvt_h0_vv o Ps npt_10_vv o npt_b0_vv o npt_h0_vv o npt_m0_vv o nst_10_vv o nst_b0_vv o nst_h0_vv o nst_m0_vv o nvt_hi_scl o npt_h1_scl o nst_h1_scl o nve_1_vv o nvt_el_vv o nvt_li_vv o nvt_al_vv o nvt_b1_vv o nvt_hi_vv o Pd npt_li_vv o npt_bi_vv o npt_hi_vv o npt_mi_vv o nst_li_vv o nst_b1_vv o nst_h1_vv o nst_ml_vv o pseudo_lfv o constraints_shake_lfv o pmf_shake_lfv o nve_0_lfv o nvt_e0_lfv o nvt_10_lfv o nvt_a0_lfv o nvt_b0_lfv o nvt_h0_lfv o npt_10_lfv o npt_bO_lfv o npt_h0_lfv o npt_m0_lfv o nst_10_lfv o nst_b0_lfv o nst_h0_lfv o nst_m0_lfv o nve_1_lfv o nvt_e
252. le done Fetch the Velocity Verlet subroutines 220 STFC Appendix C 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_platform MAKE LD path to FORTRAN90 Linker loaDer LDFLAGS appropriate flags for LD FC path to FORTRAN90 compiler FCFLAGS appropriate flags for FC EX EX BINROOT BINROOT TYPE System specific targets follow win MAKE LD f95 o LDFLAGS 03 FC f95 c FCFLAGS 03 221 STFC Appendix C EX EX BINROOT BINROOT TYPE win debug MAKE LD f95 o LDFLAGS 00 C all C undefined FC 95 c FCFLAGS 00 C all C undefined EX EX BINROOT BINROOT TYPE Default code master message check 0BJ_MOD OBJ_ALL LD EXE LDFLAGS OBJ_MOD OBJ_ALL Message message echo DL_POLY_4 compilation in SRL2 mode echo echo Use mpi must change to Use mpi_module in comms_module f90 echo Check that a platform h
253. les defect detection or alternatively remove the option Message 585 error end of file encountered in HISTORY file This means that the HISTORY file is incomplete in some way Either should you abort the replay HISTORY option or provide a fresh HISTORY file before restart Action In CONTROL specify properties for recalculation RDFs z density profiles defect detection or alternatively remove the option Message 590 error uknown minimisation type only force energy and dis tance are recognised Configuration minimisation can take only these three criteria Action In CONTROL specify the criterion you like followed by the needed arguments Message 600 error impact option specified more than once in CONTROL Only one instance of the impact option is allowed in CONTROL Action Remove any extra instances of the impact option in CONTROL Message 610 error impact applied on particle that is either frozen or the shell of a core shell unit or part of a RB It is the user s responsibility to ensure that impact is initiated on a valid particle Action In CONTROL remove the impact directive or correct the particle identity in it so that it complies with the requirements 261 STFC Appendix D Message 620 error duplicate or mixed intra molecular entries specified in FIELD The FIELD parser has detected an inconsistency in the description of bon
254. les and parameters in DL POLY 4 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 4 It is only used when DL_POLY 4 is to be compiled in 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 as initialisation and exit global synchronisation sum maximum and minimum node ID and number of nodes simulation time It is dependent on KINDS_F90 and on MPI_MODULE if MPI is emulated for DL_POLY 4 compilation in serial mode The MPI_MODULE implements all MPI functional calls used in DL_POLY 4 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 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 e development module DEVELOPMENT_MODULE The development module contains several methods used to help with testing and debu
255. locate_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 267 STFC Appendix D 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 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_arrays Action See Message 1001 268 STFC Appendix D Message 1037 error deallocation failure in
256. ls 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 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 172 STFC Section 6 2 nconf nfield ntable nrefdt nrite nstats nrest nhist ndefdt nrdfdt nzdfdt seed 1 2 lseed mxsite mxatyp mxtmls mxexcl mxspl kmaxa kmaxb kmaxc kmaxal kmaxb1 kmaxc1 mxtshl mxshl mxfshl mxtcon mxcons mxfcon mx1shp mxproc mxtpmf 1 2 mxpmf mxfpmf mxtrgd mxrgd mxlrgd mxfrgd mxtteth mxteth mxftet mxpteth mxtbnd mxbond mxfbnd 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 vari
257. ly 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 record 2 rdef real site interstitial cutoff A in last frame frame integer number configuration frames in file records integer number of records in file For timesteps greater than nsdef the DEFECTS file is appended at intervals specified by the defects directive in the CONTROL file with the following information for each configuration record i timestep a8 the character string timestep nstep integer the current time step tstep real integration timestep ps time real elapsed simulation time ps imcon integer periodic boundary key see Table 5 6 rdef real site interstitial cutoff record ii 151 STFC Section 5 2 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 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
258. mal bonded interactions They are generally very short ranged and are most effectively calculated using a link cell scheme 63 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_4 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 RATTLE 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 o
259. 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 266 STFC Appendix D 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 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 allocate_config_arrays Action See Message 1001 Message 1026 error allocation failure in site_module gt al
260. n the same manner The excluded atoms list is updated during the atom relocation process described above DL_POLY 4 routine EXCHANGE_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 Ter soff interactions are calculated using interpolation tables These are generated in the following rou tines VDW_GENERATE METAL_GENERATE METAL_TABLE_DERIVATIVES and TERSOFF_GENERATE 6 1 4 Modifications for the Ewald Sum For systems with periodic boundary conditions DL_POLY_4 employs the Ewald Sum to calculate the coulombic interactions see Section 2 4 5 It should be noted that DL _POLY 4 uses only the Smoothed Particle Mesh SPME form of the Ewald sum Calculation of the real space component in DL_POLY_4 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 calculated using Fast Fourier Transform FFT scheme of the SMPE method 52 66 Section 2 4 5 The parallelisation of this scheme is entirely handled within the DL_POLY 4 by the 3D FFT routine PARALLEL_FFT using GPFA_MODULE which is known as the Daresbury advanced Fourier Tran
261. na G Tuckerman M Tobias D and Klein M 1996 Molec Phys 87 1117 4 55 68 82 88 Warner H R J 1972 ind Eng Chem Fundam 11 379 15 Bird R B e a 1977 Dynamics of Polymeric Liquids volume 1 and 2 Wiley New York 15 Grest G S and Kremer K 1986 Phys Rev A 33 3628 15 Vessal B 1994 J Non Cryst Solids 177 103 17 19 40 136 143 Smith W Greaves G N and Gillan M J 1995 J Chem Phys 103 3091 17 19 40 136 143 Allinger N L Yuh Y H and Lii J H 1998 J Am Chem Soc 111 8551 18 19 136 Sun H 1998 J Phys Chem B 102 38 7338 7364 18 20 136 Smith W 1993 CCP5 Information Quarterly 39 14 19 22 25 Ryckaert J P and Bellemans A 1975 Chem Phys Lett 30 123 20 137 Schmidt M E Shin S and Rice S A Molecular dynamics studies of langmuir monolayers of f cf2 11cooh volume 104 page 2101 1996 21 137 Clarke J H R Smith W and Woodcock L V 1986 J Chem Phys 84 2290 27 139 Weeks J D Chandler D and Anderson H C 1971 J Chem Phys 54 5237 28 J F 1952 Philos Mag 43 153 29 Dai X D Kong Y Li J H and Liu B X 2006 J Phys Condens Matter 18 45274542 30 Cleri F and Rosato F 1993 Phys Rev B 48 22 30 Johnson R A 1989 Phys Rev B 39 12556 36 277 STFC Bibliography 48 49 50 51 52 53 54 55 56 57 58 59 60 6
262. nates and cell vectors by 71 3 10 1 22 Poe PO 3 105 where 3 is the isothermal compressibility of the system In practice is a specified constant which DL_POLY 4 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 It is worth noting that the barostat and the thermostat are independent and fully separable The VV implementation of the Berendsen algorithm only requires iterations if bond or PMF con straints are present 7 until satisfactory convergence of the constraint forces is achieved These are with respect to the pressure i e n t in the first part VV1 RATTLE_VV1 The second part is conventional VV2 RATTLE_VV2 as at the end the velocities are scaled by a factor of x 1 VVI 1 At f t ut 5At Uli r tt At n t 3 r 1 At w t 344 3 106 H t At ne H t V t At n V t 2 RATTLE_VV1 3 Barostat Ai n t 1 ces Post P t 3 107 Tp 4 FF f t At f t 3 108 5 VV2 eae v t At v t 4 At n i 3 109 6 RATTLE_VV2 74 STFC Section 3 5 7 Thermostat At o 1 2 SO de h g TT Gai At i v t At ult At x 3 110 where H is the cell matrix whose columns are the three cell vectors a b c The LFV implementation of the Berendsen algorithm is iterative until self
263. nce restraints e valence angles that are NOT distance restraints e dihedrals e inversions e frozen particles RDF pairs containing type s of particles that fall in this list will be polluted However there are many ways to overcome such effects 4 tersoff n where nis 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 a8 key a4 variable 1 real variable 2 real variable 3 real variable 4 real variable 5 real potential 1 record 2 variable 6 real variable 7 real variable 8 real variable 9 real variable 10 real variable 11 real potential n record 2n 1 potential n record 2n atom type potential key see Table 5 14 potential parameter potential parameter potential parameter potential parameter cutoff range for this potential A 5 14 potential parameter potential parameter potential parameter potential parameter potential parameter potential parameter 141 see Table 5 14 see Table 5 14 see Table 5 14 see Table 5 14 see Table 5 14 see Table 5 14 see Table 5 14 see Table 5 14 see Table 5 14 see Table 5 14 STFC Section 5 1 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 variabl
264. nd equilibration directives have a default of zero If not used or used with their default values a dry run is performed This includes force generation and system dump 118 STFC Section 5 1 REVCON and REVIVE and depending on the rest of the options may include veloc ity generation force capping application of the CGM minimiser application of the pseudo thermostat and dumps of HISTORY DEFECTS RDFDAT ZDNDAT and MSDTMP Note that since no actual dynamics is to be performed the temperature and pressure directives do not play any role and are therefore not necessary 4 If the CGM minimiser minimise is specified with zero frequency it is only applied at timestep zero if equilibration gt steps i e optimise structure at start only This is equvalent to using the optimise directive In this way it can be used as a configuration optimiser at the beginning of the equlibration period or when a dry run steps 0 is performed i e equilibrate without any actual dynamics 5 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 A and mindis 0 10 A which can also be optionally altered if used
265. nd inertia of a rigid body and the rigid body equations of motion The mass of a rigid unit M is the sum of the atomic masses in that unit Nsites M Se 3 151 where m is the mass of an atom and the sum includes all sites sites in the body The position of the rigid unit is defined as the location of its centre of mass R 1 Nsites R SO mr 3 152 Ma where r is the position vector of atom j The rigid body translational velocity V is defined by 1 Nsites o 2 MjUj 3 153 where v is the velocity of atom j The net translational force acting on the rigid body unit is the vector sum of the forces acting on the atoms of the body Nsites F gt de 3 154 j 1 where f is the force on a rigid unit site A rigid body also has associated with it a rotational inertia matrix I whose components are given by Nsites Top Y mjas derf 3 155 j l where d is the displacement vector of the atom j from the COM and is given by dj r R 3 156 It is common practice in the treatment of rigid body motion to define the position R of the body in a universal frame of reference the so called laboratory or inertial frame but to describe the moment of inertia tensor in a frame of reference that is localised in the rigid body and changes as the rigid body rotates Thus the local body frame is taken to be that in which the rotational inertia tensor I is diagonal and the components satisfy Iss gt yy gt Izz
266. neous and rolling averaged thermodynamic data minimisation information final configurations radial distribution functions RDFs Z density profiles and job timing data The OUTPUT file is human readable Also present will be the restart files REVIVE Section 5 2 7 and REVCON Section 5 2 6 RE VIVE 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 10 contains a catalogue of instantaneous values of thermodynamic and other variables in a form suitable for temporal or statistical analysis Finally the HISTORY file Section 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_4 may also create the files RDFDAT ZDNDAT MSDTMP and DEFECTS containing the RDF Z density individual means square displacement and temperature and defects data respectively They are all human readable files 4 2 3 Restarting The best approach to running D
267. neously on each node using the DD adaptation of the link cell algorithm to share the total burden of the work reasonably equally 163 STFC Section 6 1 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 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 excluded and frozen atoms are as follows A distributed excluded atoms list is constructed by the DL_POLY_4 routine BUILD_EXCL_INTRA at the start of the simulation 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 Note that completely frozen pairs of atoms are excluded i
268. never happen Action Report to authors Message 84 error unidentified atom in three body potential list This shows that DL_POLY 4 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 4 simulation with any type of restart directive see description of CONTROL file the program will expect the CONFIG file to contain atomic velocities as well as positions Termination results if these are not present Action Either replace the CONFIG file with one containing the velocities or if not available remove the restart directive altogether and let DL_POLY 4 create the velocities for itself Message 86 error calculated three body potential index too large This should never happen DL_POLY 4 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 four body forces in DL_POLY 4 is handled by the link cell algorithm This error arises if the required number of link cells exceeds th
269. ng 6 Strict bookkeeping is necessary to avoid multiple counting of kinetic properties r v v updates are necessary for halo parts particles of partially shared RBs For all domains the kinetic contributions from each fully or partially present RB are evaluated in full and then waited with the ratio number of RB s sites local to the domain to total RB s sites and then globally summed The compilation of the lists in items 1 3 above and their circulation of the list is done at the start of the simulation but thereafter these need updating on a local level every time a RB site atom is relocated from one processor to another In this respect RBs topology transfer resembles every other intramolecular term 166 STFC Section 6 2 Since the allocation of RBs is based purely on geometric considerations it is not practical to arrange for a strict load balancing For many systems however this deficiency has little practical impact on performance 6 2 Source Code 6 2 1 Modularisation Principles Modules in DL_POLY 4 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 wp of all real variab
270. nic thrm k U 0 ik 5 Ojik 00 expl ri ri 0 2 17 4 Screened harmonic shrm k U Ojik 5 Ojik 00 exp rij p1 rin p2 2 18 5 Screened Vessal 35 bvs1 k a 212 U Ojik 8 4 ik T 00 Tr Ojik Tr x expl ri p1 Tik Pa 2 19 6 Truncated Vessal 36 bvs2 U Ojix k Ojik 90 OF Osan 00 27 a a gT o r expl ri rik 0 2 20 Note some DL_POLY_4 routines may use the convention that rij TiS rj 17 STFC Section 2 2 7 Harmonic cosine hcos U Ojik cos 0j cos 89 2 21 8 Cosine cos U Ojik A 1 cos m Ojik 9 2 22 9 MMB stretch bend 37 mmsb U Ojik A Ojik 00 rig r3 Tik Fix 2 23 10 Compass stretch stretch 38 stst U Ojik A rig riz Tik Tik 2 24 11 Compass stretch bend 38 stbe U Ojik A Pik 90 rig ri 2 25 12 Compass all terms 38 emps U Ojik A rig 155 Tik Tik Ojik 90 B rig r C rik ri 2 26 In these formulae 0 x is the angle between bond vectors r and r g Tr o T Burn a1 Zij ik i 2 27 jik COS i a 2 27 In DL_POLY_4 the most general form for the valence angle potentials can be written as U Ojik Tijs Tik A 0 ik S rij S ra S rik 2 28 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 re
271. npt_h1_scl o nst_hi_scl o nve_1_vv o nvt_el_vv o nvt_li_vv o nvt_al_vv o nvt_b1_vv o nvt_hi_vv o npt_li_vv o npt_bi_vv o npt_hi_vv o npt_mi_vv o nst_11_vv o nst_b1_vv o nst_hi_vv o nst_ml_vv o pseudo_lfv o constraints_shake_lfv o pmf_shake_lfv o nve_0_lfv o nvt_e0_lfv o nvt_10_lfv o nvt_a0_lfv o nvt_b0_lfv o nvt_h0_lfv o npt_10_lfv o npt_b0_lfv o npt_h0_lfv o npt_m0_lfv o nst_10_lfv o nst_b0_lfv o nst_h0_lfv o nst_m0_lfv o nve_1_lfv o nvt_el_lfv o nvt_11_1lfv o nvt_al_lfv o nvt_b1_lfv o nvt_hi_lfv o npt_11_1fv o npt_b1_lfv o npt_h1_lfv o npt_mi_lfv o nst_11_1fv o nst_b1_lfv o nst_h1_1lfv o nst_m1_lfv o xscale o core_shell_kinetic o regauss_temperature o defects_reference_read o defects_reference_read_parallel o defects_reference_write o defects_reference_export o defects_reference_set_halo o defects_link_cells o defects1_write o defects_write o msd_write o z_density_collect o statistics_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 Define Velocity Verlet files FILES_VV pseudo_vv f90 constraints_shake_vv f90 pmf_shake_vv f90 constraints_rattle f90 pmf_rattle f90 nvt_h0_scl f90 npt_h0_sc1 f90 nst_h0_sc1 f90 nve_0_vv f90 nvt_e0_vv f90 nvt_10_vv f90 nvt_a0_vv f90 nvt_b0_vv f90 nvt_h0_vv f90 npt_10_vv f90 npt_b0_vv f90 npt_h0_vv f90 npt_m
272. nput data 110 STFC Section 5 1 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 binsize f cap forces f close time f collect coulomb cutoff f defects i j f densvar f distance dump n ensemble nve ensemble nvt evans ensemble nvt langevin f ensemble nvt andersen f f2 ensemble nvt berendesen f meaning set the bin size for radial and z density distribution functions to fA 105 lt f lt reu 4 or undefined f defaults to 0 05 A cap forces during equilibration period f is maximum cap in units of kgT A default f 1000 kgT set job closure time to f seconds include equilibration data in overall statistics calculate electrostatic forces using direct Coulomb sum set required long ranged interactions cutoff reut to f A write DEFECTS file with controls i start timestep for dumping defects configurations default i 0 j timestep interval between configurations default j 1 f site interstitial cutoff default f Min 0 75 reut 3 A Min 0 3 Tcut 3 lt f lt Min 1 2 reut 2 A allow for local variation of f in the system density of i particles and ii any present bonded like entities very useful for extremely non equilibrium simulations default f 0 calculate electrostatic fo
273. nsity units for embed limit 2 real upper interpolation limit in for dens and pair or in density units for embed funtion 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 7 3 Further Comments The tabled data are used to fill the internal arrays gmet fmet and vmet respectively see Sec tion 2 3 2 The force arrays are generated from these by the METAL_TABLE_DERIVATIVES rou tine using a five point interpolation precedure During simulation interactions beyond distance Min reut Limit2 are discarded whereas interactions at distances shorter than limit 1 will cause the simulation to abort The simulation will also abort if any local density exceeds the limits for the embedding function 5 2 The OUTPUT Files DL_POLY 4 produces up to ten output files HISTORY DEFECTS MSDTMP CFGMIN OUT PUT REVCON REVIVE 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 defected particles interstitials and sites vacancies an incremental dump file of of individual atomic mean square displacement and temperature a dump file of all atomic coordinates of a minimised structure an incremental summary file of the simulation a restart final configuration file a restart final statistics accumulators file a rad
274. ntact DL_POLY_4 authors Message 112 error only one constraints directive per molecule is allowed DL_POLY 4 has found more than one constraints entry per molecule in FIELD 241 STFC Appendix D Action Correct the erroneous part in FIELD and resubmit Message 113 error intramolecular bookkeeping arrays exceeded in deport_atomic_data One or more bookkeeping arrays for site related interactions have been exceeded Action Consider using densvar option in CONTROL for extremely non equilibrium simulations Alter natively you will need to print extra diagnostic data from the DEPORT_ATOMIC_DATA subroutine to find which boded like contribution has exceeded its assumed limit and then correct for it in SET_BOUNDS recompile and resubmit 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_4 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 4 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 car
275. nversion angles must be individually cited The same applies for bond constraints and 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_4 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 terms are many body interactions which are functionally presented in an expansion of many two body contributions augmented by a function of the local density which again is derived from the two body spatial distribution and these are therefore evaluated in the two body routines In DL_POLY_4 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_4 does recognize molecular entities defined through constraint bonds and rigid bodies In the case of rigid bodies the atomic forces are resolved into molecular forces and torques These matters are discussed in gr
276. o reading by order of the atom entries with consecutive incremental indexing Using this option assumes that the FIELD topology description matches the crystalographic sites atoms entries in the CONFIG file by order consecutively 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_4 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 4 limits the number of chemical bond 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 Use densvar option in CONTROL to increase mxbond alternatively increase it by hand in SET_BOUNDS and recompile and resubmit 228 STFC Appendix D Message 32 error coincidence of particles in core shell unit DL_POLY 4 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 4 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 sit
277. o that of the intra molecular interactions due to their by site definition DL_POLY 4 allows for 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 4 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 intra and inter molecular interactions between frozen atoms As with the tethering potential the reference position of a frozen site is scaled with the cell vectors in constant pressure simulations In the case of frozen rigid bodies their centre of mass is scaled with the cell vectors in constant pressure simulations and the positions of their constituent sites are thenmoved accordingly In DL_POLY 4 the frozen atom option is handled by the subroutine FREEZE_ATOMS The rigid body dynamics see Section 3 6 is resolved by solving the Eulerian equations of rotational motion However their statics includes calculation of the individual contributions of each RB s centre of mass stress and virial due to the action of the resolved forces on sites atoms constituting it These contribute towards the total system stress and pressure As seen in Section 2 5
278. ocessor 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 and DD RATTLE algorithms For many systems however this deficiency has little practical impact on performance 6 1 9 The Parallel Rigid Body Implementation The essentials of the DD tailored RB algorithms see Section 3 6 are as follows 1 Every processor works out a list of all local and halo atoms that are qualified as free zero entry or as members of a RB unit entry 2 The rigid body units in the simulated system are allocated between the processors based on the location i e domain of the atoms involved 3 Each processor makes a list of the RB and their constituting atoms that are fully or partially owned by the processors domain 4 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 RBs and RBs constituent atoms and the processors which share them Note that a RB can be shared between up to eight domains 5 The dynamics of each RB is calculated in full on each domain but domains only update r v f of RB atoms which they own Note that a site atom belongs to one and only one domain at a time no shari
279. ody and or Tersoff interactions short range cutoffs specified for the system W P M Nint el z cutoff W MD box width L plane y z 4 1 Pp no0des z direction gt where x y and z represent the directions along the MD cell lattice vectors Every domain node of the MD cell is loaded with Mz 2 M 2 M 2 link cells of which M My M belong to that domain and the rest are a halo image of link cells forming the surface of the immediate neighbouring domains In this respect if we define performance efficiency as minimising communications with respect to maximising computation minimising the halo volume with respect to the node volume best performance efficiency will require M My Mz M and M gt 1 The former expression is a necessary condition and only guarantees good communication distribution ballancing Whereas the latter is a sufficent condition and guarantees prevalance of computation over communications DL_POLY 4 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 speed up inefficiency is expected when the ratio Mz My M R M 2 M 2 M 2 M Ma M 4 2 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 2 the
280. offending potential in the FIELD file and remove Replace with one acceptable to DL_POLY 4 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 4 does not recognise Action Locate the offending potential in the FIELD file and remove Replace with one acceptable to DL_POLY 4 if this is reasonable Alternatively you may consider defining the required potential 249 STFC Appendix D 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 4 has been requested to process a four body potential it does not recognise Action 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 4 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
281. olecular Potential Functions 26 2 3 1 Short Ranged van der Waals Potentials 27 23 2 Metal Potentials cda Ton waira eA a an Bak ie ee eA we ea A 29 Zoo Torso Potential 2 2 2 e a erano the bee Bed A Ow phe bo 37 2 3 4 Three Body Potentials 20002 eee eee 40 2 0 0 Four Body Potentials e c a waaa s emagi e EE ea 41 2 4 Long Ranged Electrostatic coulombic Potentials LL 41 ZA Direct Coulomb SUM ie 4 66804 Toa aiok ee Oe Gla e Ae Re 42 2 4 2 Force Shifted Coulomb Sum LL 42 2 4 3 Coulomb Sum with Distance Dependent Dielectric 44 244 Reaction Field s Lu eee EE we a Ee DSA ee ee 44 2 4 5 Smoothed Particle Mesh Ewald o e 46 vi STFC Contents 2 0 Polarisation Shell Models 224344445 25 4 rx ee ee RA a 49 2 5 1 Dynamical Adiabatic Shells 002 0000 2 eee 49 2 5 2 Relaxed Massless Shells o orcos trar 50 26 External Fielde c cio Gan ga aiu oaoa a n pa e ee eG i 50 2 7 Treatment of Frozen Atoms Rigid Body and Core Shell Units 51 3 Integration Algorithms 52 adi POMO cu ra a a ta ad e 53 a2 Bond Constraints o macs sa edi ER K RR BRA ee PO 55 3 3 Potential of Mean Force PMF Constraints and the Evaluation of Free Energy 58 34A lit to sos tae ea da e dean ag dew e Hw ok a n la 59 3 4 1 Evans Thermostat Gaussian Constraints 59 342 Langevin Thermostat 2 4 ee a Beek Swe Re oe 61 3
282. om 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 rigid teth bonds angles dihedrals and inversions entries described below DL_POLY_4 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 131 STFC Section 5 1 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 index integer atomic site index weight real site weighting 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 a
283. ompile 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 4 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 79 error tersoff potential cutoff undefined This shows that DL_POLY_4 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 4 has encountered and erroneous entry for vdw or metal potentials in FIELD Action Correct FIELD and resubmit 236 STFC Appendix D 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 4 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 Report to authors Message 83 error too many three body potentials specified This should
284. onds every bondlength is checked If the largest deviation found exceeds the desired tolerance the correction calculation is repeated 57 STFC 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 step assuming an absence of rigid bonds This is stage 1 of the RATTLE_VV2 algorithm b The deviation of d vj d in each bond is used to calculate the corresponding constraint force that retrospectively corrects the bond velocities c After the correction 3 17 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 _ 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 4 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 corr
285. ons 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 232 STFC Appendix D 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 4 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 Use densvar option in CONTROL to increase mxsh1 alternatively increase it by hand in SET_BOUNDS and recompile and resubmit Message 60 error too many dihedral angles 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 61 error too many dihedral angles per domain DL_POLY 4 limits the number of dihedral angle units in the system to be simulated actually the number to be processed by e
286. ontains dihedral key ad potential key see Table 5 10 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 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 10 134 STFC Section 5 1 Table 5 8 Chemical Bond Potentials key potential type Variables 1 4 functional form harm Harmonic k ro U r k rij ro hrm mors Morse Eo ro k U r Ep 1 exp k rij ro 1 mrs 12 6 12 6 A B U r 4 4 126 XII oy lj Lennard Jones o U r 4e lj rhrm Restraint k ro te U r 3 k rij ro rij ro lt re rhm U r 3kr2 kre rig ro re rig ro gt re quar Quartic k ro k k U r E rij ro 7 rij ro qur rig ro buck Buckingham A p C U r A exp 52 lt bck l coul Coulomb k U r kU Pletrostaties m Tex 10 cul 2 fene Shifted FENE k Ro A U r 0 5 k Ro In 142 ri lt
287. opy copy invokes the UNIX commands 183 STFC Appendix B mv CONFIG CONFIG OLD mv REVCON CONFIG mv REVIVE REVOLD which collectively prepare the DL_POLY 4 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 4 job to the HPCx 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 Z Using LOADLEVELLER the job is submitted by the UNIX command submit gopoly 184 STFC 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_4 Java GUI It invokes
288. or the description of the input files 7 Executing the program will produce the files OUTPUT STATIS REVCON and REVIVE and optionally HISTORY RDFDAT ZDNDAT MSDTMP REFERENCE 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 4 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 91 STFC Section 4 1 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 higher than the global one or there is a sort of clustering in the system undergoes and the distribution of bonded like interactions is far from uniform 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 mor
289. or modification and inspection In the spirit of the enterprise contributions in the form of working code are welcome provided the code is compatible with DL_POLY_4 in regard to its interfaces and programming style and it is adequately documented STFC Preface DISCLAIMER Neither the STFC EPSRC NERC CCP5 nor any of the authors of the DL_POLY 4 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 STFC Preface ACKNOWLEDGEMENTS DL_POLY 4 was developed at Daresbury Laboratory DL http www dl ac uk the Science and Technology Facilities Council STFC http www stfc ac uk UK with support from the Engineering and Physical Sciences Research Council EPSRC http www epsrc ac uk and the Natural Environment Research Council NERC http www nerc ac uk Advice assistance and encouragement in the development of DL_POLY 4 has been given by many people We gratefully acknowledge the following T R Forester I J Bush M Leslie M F Guest R J Allan D Tildesley M Pinches D Rapaport the UK s Materials Chemistry Consortium under C R A Catlow and the eMinerals project under M T Dove This document is produced with BIFX amp hdvipdfm iii STFC Preface Manual Notation In the DL_POLY manuals specific fonts are used to convey specific meanings 1 directories indicates U
290. order as closely as possible The further down the list the file the more dependent it is on the files listed above it The same hierarchial order is followed in the makefiles see Appendix C It is worth noting that the files REPLAY_HISTORY F90 MD_vv F90 MD_LFV MPIF H are in fact inclusion files rather than strict FORTRAN90 type of files Should this prove to be a prob lem and a compiler cannot handle this then they can be incorporated directly in the routines where they are used i e REPLAY_HISTORY F90 MD_VV F90 MD_LFV in DL_POLY F90 and MPIF H in COMMS_MODULE F90 and then compilation should be attempted 6 2 3 Module Files The DL_POLY 4 module files contain all global variables scalars and arrays and parameters 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_4 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 4 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
291. ore a different versions of DL_POLY_4 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 not exist or is too complicated to specify in the VDW_GENERATE subroutine The table file is read by the subroutine VDW_TABLE_READ 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 header al00 file header record 2 delpot real mesh resolution in delport cal cutpot real cutoff used to define tables in 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
292. ormal pressure and constant surface area NP AT 56 by semi isotropic constraining of the barostat equation of motion to Pmass Pmass Pmass 0 a b z ozz t Pext V t i 2Ekin t A Rp zz t a Similarly this ensemble is optionally extending to constant normal pressure and constant surface tesnison NP yT 56 by semi isotropic constraining of the barostat equation of motion to Oaa O Pos et Me t V t E 2Ekin t __ XpNaa t de Del f a 8 x y d gns ozz t Poxt V t 2Erin t 1 Ros t l ee mi Fa OE aes i des fl z i af P 2 y 2 3 103 where Yext is the user defined external surface tesnion and h t V t Axy t is the instantenious hight of the MD box or MD box volume over area The VV and LFV flavours of the non isotropic Langevin barostat and Nos Hoover thermostat are implemented in the DL_POLY 4 routines NST_LO_VV and NST_LO_LFV respectively Both make use of the DL_POLY_4 module LANGEVIN_MODULE The routines NST_L1_VV and NST_L1_LFV implement the same but also incorporate RB dynamics 73 STFC Section 3 5 3 5 3 Berendsen Barostat With the Berendsen barostat the system is made to obey the equation of motion at the beginning of each step dt Tp i 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 n and the coordi
293. otential 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 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 molecule 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 ad 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 c
294. ow that and then change the default in KINDS_F90 Changing the precision to anything else that is allowed by the FORTRAN090 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 subroutines and functions assume the use of the following defined molecular units e The unit of time to is 1 x 10712 seconds i e picoseconds e The unit of length o is 1 x 1071 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 10719 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 P Elz 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 e The coulombic conversion factor yo is 1 2 aes ai do 138935 4835 Eo 4reolo such that Ungs EoYoUtnternal gt where U represents the configuration energy e The Boltzmann factor kg is 0 831451115 E K7 such that T Erin k represents the conversion from kinetic energy in internal units to temperature in Kelvin Note In the DL_POLY_4 OUTPUT file the print out of pressure is in units of katms kilo
295. p BINROOT touch dl_poly f90 Declare rules 90 0 FC FCFLAGS f90 Declare dependencies OBJ_ALL OBJ_MOD 210 STFC Appendix C Makefile SRL1 Master makefile for DL_POLY_4 01 serial version 1 Author I T Todorov october 2010 Define default settings SHELL bin sh SUFFIXES SUFFIXES f90 o BINROOT execute EX DLPOLY Z 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 parse_module o development_module o netcdf_modul o io_module o domains_module o site_module o config_module o defects_module o defectsi_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 rigid_bodies_module o tethers_module o bonds_module o angles_module o dihedrals_module o inversions_module o external_field_module o langevin_module o minimise_module o ewald_module o msd_module o statistics_module o kinetic_module o OBJ_ALL warning o error o scan_control_io o numeric_container o spme_container o quaternions_container o scan_field o read_config_parallel o scan_config o scan_control o read_config o 211 STFC Appendix C set_bounds o read_control o vdw_generate o vdw_table_read o metal_generate o metal_table_read o met
296. p IMPACT OPTION nfold 10 10 10 impact 1 2000 7 5 1 0 2 0 3 0 DENSITY VARIATION ARRAY BOOST densvar 10 INDEX AND VERIFICATION BYPASS no index no strict INTERACTIONS BYPASS no electostatics no vdw DIRECT CALCULATION OF VDW METAL INTERACTIONS INSTEAD OF EVALUATION BY SPLINING OVER TABULATED VALUES IN MEMORY vdw direct metal direct FORCE SHIFT VDW INTERACTIONS SO THAT ENERGY AND FORCE CONTRIBUTIONS FALL SMOOTHLY TO ZERO WHEN APPROACHING R_CUT vdw shift RANDOM NUMBER GENERATOR SEEDING seed 100 200 I O READ METHOD READER COUNT BATCH amp BUFFER SIZES io read mpiio 2 50000 5000 108 STFC Section 5 1 I O WRITE METHOD TYPE WRITER COUNT BATCH amp BUFFER SIZES io write mpiio sorted 8 50000 5000 SLAB SIMULATION PARALLEL CONTROL slab RESTART OPTIONS restart noscale dump 1000 steps SYSTEM TARGET TEMPERATURE AND PRESSURE temperature 300 0 Kelvin pressure 0 001 k atmospheres SYSTEM CUTOFFS AND ELECTROSTATICS cutoff 10 0 Angstroms rvdw 8 0 Angstroms exclude epsilon 1 0 ewald precision 1 0e 6 ewald evaluate 4 RELAXED SHELL MODEL TOLERANCE rlxtol 1 0 force CONSTRANTS ITERATION LENGTH and TOLERANCE mxshak 250 cycles shake 1 0e 4 INTEGRATION FLAVOUR ENSEMBLE AND PSEUDO THERMOSTAT integration velocity verlet ensemble nst hoover 0 5 0 5 pseudo langevin 2 0 150 0 INTEGRATION TIMESTEP variable timestep 0 001 pico seconds mindis 0 03 Angstroms maxd
297. p 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 Message 72 error too many tersoff potentials specified This should never happen Action Report to authors Message 73 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 4 has encountered and erroneous entry for Tersoff potentials in FIELD Action Correct FIELD and resubmit 235 STFC Appendix D Message 76 error duplicate tersoff potential specified This shows that DL_POLY_4 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 4 limits the number of inversion 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 Use densvar option in CONTROL to increase mxinv alternatively increase it by hand in SET_BOUNDS and rec
298. pecification 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 calculation of system properties and job ter mination It is worth considering these operations in turn and to indicate which DL_POLY_4 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 4 User Manual for further details particularly regarding further dependencies i e additional routines that may be called The following outline assumes a system containing flexible molecules held together by rigid bonds Initialisation requires firstly that the program determine what platform resources are made avail able to the the specific simulation job This is done by the DL_POLY 4 routine MAP_DOMAINS in DOMAINS_MODULE that attempts to allocate and map the resources nodes in parallel in com pliance with the DD strategy MAP_DOMAINS is called within the routine SET_BOUNDS which also sets the necessary limits for various simulation array sizes and all global variables as de clared in SETUP_MODULE to convenient values based on rough scan through the CONFIG CON TROL FIELD and optionally TABLE and TABEAM Section 5 1 files The routine also calls the READ_CONFIG routine to obtain atomic positions and optionally velociti
299. planation of this variable Note that all these options with the exception of the last no elec are mutually exclusive Table 5 4 Electrostatics Key keyfce meaning Electrostatics are evaluated as follows Ignore electrostatic interactions SPM Ewald summation Coulomb sum with distance dependent dielectric Standard truncated Coulomb sum Force shifted Coulomb sum 10 Reaction field electrostatics 0 DaINO ewald evaluate or multiple are not mutually exclusive and it is the first instance of these in CONTROL that is read and applied in the following simulation The choice of reaction field electrostatics directive reaction relies on the specification of the relative dielectric constant external to the cavity This is specified by the eps directive The directive ewald spme evaluate is only triggered when ewald spme sum precision is present It sets an infrequent evaluation of the k space contributions to the Ewald summation Although this option decreases the simulation cost it also inherently decreases the accuracy of the dynamics Note that the usage of this feature may lead to inacuarte or even wrong and unphysical dynamics as the less frequent the evaluation the greater the inacuarcy DL POLY 4 uses two different potential cutoffs These are as follows 123 STFC Section 5 1 20 21 22 23 a Teut the universal cutoff set by cutoff It applies to the real space part of the elec
300. pmf_module gt deallocate_pmf_arrays Action See Message 1002 Message 1038 error allocation failure in minimise_module gt allocate_minimise_arrays Action See Message 1001 Message 1039 error deallocation failure in minimise module gt deallocate_minimise_arrays Action See Message 1002 Message 1040 error allocation failure in ewald_module gt ewald_allocate_arrays Action See Message 1001 Message 1041 error allocation failure in langevin_module gt langevin_allocate_arrays Action See Message 1001 Message 1042 error allocation failure in rigid bodies_ module gt allocate_rigid_bodies_arrays Action See Message 1001 Message 1043 error deallocation failure in rigid_bodies_module gt deallocate_rigid_bodies_arrays Action See Message 1002 Message 1044 error allocation failure in comms_module gt gimin_vector Action See Message 1001 269 STFC Appendix D Message 1045 error deallocation failure in comms_module gt gimin_vector Action See Message 1002 Message 1046 error allocation failure in comms_module gt grmin_vector Action See Message 1001 Message 1047 error deallocation failure in comms_module gt grmin_vector Action See Message 1002 Message 1048 error error allocation failure in comms_module gt grsum_matrix Action See Messa
301. processors that complies with the advise above 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 4 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 4 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 configuration 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 Action Supply a properly formatted REFERENCE configuration 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 259 STFC Appendix D Message 554 error REFERENCE s format different from CONFIG s REFERENCE complies to the same rules 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
302. quired 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 The temperature of the bath is specified by the user T f in Kelvin which must be larger than 1 Kelvin If none is supplied by the user T defaults to the system target temperature e pseudo langevin The stochasticity of the Langevin 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 instan taneous temperature of the system is driven naturally towards the bath temperature Every particle within the thermostat buffer layer is coupled to a viscous background and a stochastic heat bath such that dri t _ ar v t De AOE 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 REO R 4 2 x t mi kgT dij Jag lt t 5 3 where superscripts denote Cartesian indices subscripts particle indices kg is the Boltz mann constant T the bath temperature and m the particle s mass The algorithm is implemented in routine PSEUDO and has two stages Generate random forc
303. r 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 98 STFC Section 4 2 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 4 spends on inevitable communication MPI messages across neighbouring domains to refresh the halo data increases with respect to and eventually becomes prevalent to the time DL_POLY 4 spends on numeric calculations integration and forces In such regimes the overall DL_POLY 4 efficiency falls down since processors spend more time on staying idle while communicating than on computing It is important that the user recognises when DL_POLY_4 becomes vulnerable to decreased effi ciency and what possible measures could be taken to avoid this DL_POLY_4 calculates and reports the major and secondary link cell algorithms My My Mz employed in the simulations immedi ately after execution My analogously for My and Mz is the integer number of the ratio of the width of the system domains in x direction i e perpendicular to the y z plane to the major and secondary coming from three and or four b
304. r 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 a8 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 component 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 cel1 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 record a atmnam a8 atomic label iatm integer atom index 149 STFC Section 5 2 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
305. r_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 MD step number total internal energy of the system system temperature in Kelvin 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 in pico seconds since the beginning of the job enthalpy of system rotational temperature in Kelvin 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 in seconds since the beginning of the job system volume in A core shell temperature in Kelvin configurational energy due to core shell potentials core shell potential contribution to the virial angle between b and c cell vectors in degrees angle between c and a cell vectors in degrees angle between a and b cell vectors in deg
306. ranklin SUNfire cluster setenv HPCF_MPI yes franklin MAKE LD opt SUNWhpc bin mpf90 o LDFLAGS stackvar fsimple 1 x03 xarch v9b DHPCF_MPI lmpi A 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 0 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 BGL MAKE LD bg1 BlueLight ppcfloor bglsys bin mpix1f95 o LDFLAGS 03 qhot qarch 440d qtune 440 FC bg1 BlueLight ppcfloor bglsys bin mpixlf95 c FCFLAGS 03 qhot qarch 440d qtune 440 EX EX BINROOT BINROOT TYPE BGP MAKE LD bgsys drivers ppcfloor comm bin mpix1f2003_r o LDFLAGS 03 qhot qarch 450d qtune 450 qmaxmem 128000 FC bgsys drivers ppcfloor comm bin mpixlf2003_r c FCFLAGS 03 qhot qarch 450d qtune 450 qmaxmem 128000 EX EX BINROOT BINROOT TYPE 207 STFC Appendix C hector
307. ration step atomic velocities are scaled collectively seed control to the random number generator used in the 116 STFC Section 5 1 shake tolerance f shift shift damp a shift precision f slab spme evaluate every n spme precision f spme sum a k ka kg stack size n stats every n steps n temperature f trajectory i j k timestep f variable timestep f vdw direct generation of gaussian distributions and stochastic processes set shake rattle tolerance to f default f 1076 calculate electrostatic forces using force shifted Coulomb sum calculate electrostatic forces using force shifted Coulomb sum with Fennell 49 damping Ewald like convergence parameter a in AT calculate electrostatic forces using force shifted Coulomb sum with Fennell 49 damping Ewald like automatic parameter optimisation 107 lt f lt 0 5 default f 10729 limits the number of processors in z direction to 2 for slab simulations act exactly the same as ewald evaluate every n act exactly the same as ewald precision f calculate electrostatic forces using Ewald sum with a Ewald convergence parameter in 7 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 set rolling average stack to n timesteps accumulate statistics data every n timesteps run simulation for n timestep
308. rature set quaternion tolerance to f default 1078 calculate and collect radial distribution functions every f timesteps default f 1 calculate electrostatic forces using reaction field electrostatics calculate electrostatic forces using reaction field electrostatics with Fennell 49 damping Ewald like convergence parameter a in A calculate electrostatic forces using reaction field electrostatics with Fennell 49 damping Ewald like automatic parameter optimisation 107 lt f lt 0 5 default f 10729 resample the instantaneous system momenta distribution every n steps during equilibration with respect to the last equilibration step abort simulation and replay HISTORY to recalculate structural properties such as RDF z density profiles defects detection execution holts if no property is specified 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 1in D ps set required short ranged interactions cutoff to f rescale system temperature every n steps during equilibration with respect to the last equilib
309. rces This method is not recommended for amorphous systems 4 3 2 Macromolecules Simulations of proteins are best tackled using the package DLPROTEIN 62 which is an adap tation of DL_POLY specific to protein modelling However you may simulate proteins and other macromolecules with DL_POLY_4 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 4 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_4 FIELD and CONFIG files for your molecule If you do not have the edit out file things are a little more 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 F
310. rces using Coulomb sum with distance dependent dielectric set restart data dump interval to n steps default n 1000 select NVE ensemble default ensemble select NVE kin ensemble type Evans with Gaussian constraints thermostat select NVT ensemble type Langevin with thermostat relaxation speed friction constant f in ps select NVT ensemble type Andersen with fi f2 as the thermostat relaxation time in ps and softness 0 lt f2 lt 1 select NVT ensemble type Berendsen with thermostat 111 STFC Section 5 1 ensemble ensemble ensemble ensemble ensemble ensemble ensemble ensemble ensemble ensemble ensemble nvt hoover f npt langevin fi f2 npt berendsen fi fa npt hoover fi f2 npt mtk fi f2 nst langevin fi fe nst berendsen f f2 nst hoover fi fo nst mtk fi f nst Q fifo area nst Q f f2 tension y epsilon constant f equilibration steps n ewald evaluate every n ewald precision f relaxation constant f in ps select NVT ensemble type Nose Hoover with thermostat relaxation constant f in ps select NPT ensemble type Langevin with fi f2 as the thermostat and barostat relaxation speed friction constants in ps select NPT ensemble type Berendsen with f1 fo as the thermostat and barostat relaxation times in ps select NPT ensemble type Nose Hoover with f1 fa as the athermostat and barostat relaxation times in ps select NPT ensem
311. record iv stpval 11 stpval 15 tmprot real rotational temperature vir real total virial virsrc real short range virial vircpe real electrostatic virial virbnd real bond virial record v stpval 16 stpval 20 virang real valence angle and 3 body virial vircon real constraint bond virial virtet real tethering virial volume real volume tmpshl real core shell temperature record vi stpval 21 stpval 25 engshl real core shell potential energy virshl real core shell virial 158 STFC Section 5 2 alpha real MD cell angle a beta real MD cell angle 8 gamma real MD cell angle y record vii stpval 26 stpval 27 virpmf real PMF constraint virial press real pressure the next ntpatm entries amsd 1 real mean squared displacement of first atom types amsd 2 real mean squared displacement of second atom types amsd ntpatm real mean squared displacement of last atom types the next 9 entries for the stress tensor stress 1 real xx component of stress tensor stress 2 real xy component of stress tensor stress 3 real xz component of stress tensor stress 4 real yx component of stress tensor sigs real ee stress 9 real zz component of stress tensor the next 9 entries if a NPT or NoT simulation is undertaken cell 1 real x component of a cell vector cell 2 real y component of a cell vector cell 3 real z component of a cell vector cell 4 real x component of 6 cell vector Li real e cell 9 real z component of c cell vector 1
312. rees PMF constraint contribution to the virial 154 STFC Section 5 2 press pressure in kilo atmospheres 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 rolling averages of the same variables are also given The maximum 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 energy and virial 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 5 7 Sample of Final Configuration The positions velocities and forces of the 20 atoms used for the sample of the init
313. 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 su Y Gi ki ko k3 Q ki ko k3 2 185 2V 0 k1 k2 k3 Urecip where GT is the discrete Fourier transform of the function exp k 4a cara in which Q k1 ka k3 is the complex conjugate of Q k1 ko k3 and G k1 ko kg Blk1 k2 k3 Q k ko k3 2 186 B ky k2 k3 bi k1 b2 k2 b3 3 1 2 187 The function G k1 ka k3 is thus a relatively simple product of the Gaussian screening term appearing in the conventional Ewald sum the function B k1 k2 k3 and the discrete Fourier transform of Q k1 ka k3 4 Calculating the atomic forces which are given formally by DU es 1 a TEC Gt k k k fi ore at kr Ra ks 1 2 3 OQ k1 ka k3 Or 2 188 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 4 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_MODULE native DL_POLY 4 subroutines tha
314. rgy correction No long ranged corrections apply beyond cutoffs c and d 4 Sutton Chen energy correction a a a Tmet SU Arpa n 3 N 6U 3 75 2 113 i met 2 Pi 34 STFC Section 2 3 5 Gupta energy correction 27 N pAr a JU SIE T et 2rmet 2 2 2 x Pp p p Tmet TO exp pe To 27 pr io SETA A 2 x 2 114 dij E a T 9 je NB SN Na a 2 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 V riz tS 39 na fij i 1 Ai N Tij lt Tmet V ri N Tij fmet y a Y S Y 7 id ny 3 gt a rij Y V i 1 J i i l jf OV ow mee di A Tmet Orij OF pala v gt La Bil i 2 115 i 1 Op or ig OF Tij lt Tmet 0 Tij IT met 0 YU SdF pi y Pij bali S pi y pij rij rij y 6V3 ni Op 54 Orij 5 ET Ori N OF Opij r r3 Ya np i Ndr 1 Opi Tmet Or Evaluating the integral part of the above equations yields 1 EAM virial correction No long ranged corrections apply beyond rmet 2 Finnis Sinclair virial correction No long ranged corrections apply beyond cutoffs c and d 3 Extended Finnis Sinclair virial correction No long ranged corrections apply beyond cutoffs c and d 4 Sutton Chen
315. rocessors that shall access the disk k specifies the maxi mum number of particles that the writing processors shall deal with at any one time Large values give good performance but may results in an unacceptable memory overhead l specifies the maximum number of particles that the writing processors shall write to the disk in one I O transaction Large values give good performance but may results in an unacceptable memory overhead e accepts Yes only to switch global error checking performed by the I O subsystem the default is No e io write master sort unsort I l specifies the maximum number of particles that the writing process shall write to the disk in one I O transaction Large values give good performance but may results in an unacceptable memory overhead Users are advised to study the example CONTROL files appearing in the data sub directory to see how different files are constructed 125 STFC Section 5 1 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 optionally by 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 2 3 276 26 988000000000000 0 000000000000000 0 000000000000000 13 494000000000000 23 372293600000000 0 000000000000000
316. rozen 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 Rae 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 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 difference between the directives ewald and spme is only in the ewald spme sum directive in which the ewald sum specifies the indices of the maximum k vector whereas the spme sum the dimensions of the 3D charge array which are exactly twice the maximum k vector indices Note that in either case DL_POLY 4 will carry out the SPME coulombic evaluation The force selection directives ewald spme sum precision reaction coul shift dist no elec are handled internally by the integer variable keyfce See Table 5 4 for an ex
317. rrect FIELD and resubmit Message 100 error core shell unit separation gt rcut the system cutoff This could only happen if FIELD 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_4 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 239 STFC Appendix D 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 4 will terminate execution Action Use densvar option in CONTROL to increase mxlshp alternatively
318. rse_module o setup_module o site_module o system_init o comms_module o config_module o development_module o kinds_f90 0 langevin_module o metal_module o setup_module o site_module o statistics_module o vdw_module o system_revive o comms_module o config_module o development_module o kinds_f90 0 langevin_module o setup_module o statistics_module o tag_legend o setup_module o 200 STFC Appendix C tersoff_forces o comms_module o config_module o domains_module o kinds_f90 0 setup_module o tersoff_module o tersoff_generate o kinds_f90 0 setup_module o tersoff_module o tersoff_module o kinds_f90 0 setup_module o tethers_forces o comms_module o config_module o kinds_f90 0 setup_module o statistics_module o tethers_module o tethers_module o kinds_f90 0 setup_module o three_body_forces o comms_module o config_module o domains_module o kinds_f90 0 setup_module o three_body_module o three_body_module o kinds_f90 0 setup_module o trajectory_write o comms_module o config_module o io_module o kinds_f90 0 parse_module o setup_module o statistics_module o two_body_forces o comms_module o config_module o ewald_module o kinds_f90 0 metal_module o setup_module o statistics_module o vdw_module o update_shared_units o comms_module o domains_module o kinds_f90 0 setup_module o vdw_forces o config_module o kinds_f90 0 setup_module o vdw_module o vdw_generate o kinds_f90 0 setup_module o vdw_module o vdw_lrc o comms_mo
319. rsion angle 13 finish This directive is entered to signal to DL_POLY_4 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 4 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 atmnam 1 as first atom type atmnam 2 a8 second atom type key ad potential key see Table 5 12 variable 1 real potential parameter see Table 5 12 variable 2 real potential parameter see Table 5 12 variable 3 real potential parameter see Table 5 12 variable 4 real potential parameter see Table 5 12 variable 5 real potential parameter see Table 5 12 138 STFC Section 5 1 The v
320. rtant example of the use of the improper dihedral is to conserve the structure of chiral centres in molecules modelled by united atom centres For example a amino acids such as alanine CH3CH NH2 COOH in which it is common to represent the CH3 and CH groups as single centres Conservation of the chirality of the a carbon is achieved by defining a harmonic improper dihedral angle potential with an equilibrium angle of 35 264 The angle is defined by vectors rs r93 and T34 where the atoms 1 2 3 and 4 are shown in the following figure The figure defines the D and L enantiomers consistent with the international IUPAC convention When defining the dihedral the atom indices are entered in DL_POLY 4 in the order 1 2 3 4 L a N C D a 0N 1 2 3 4 1 2 3 4 Figure 2 4 The L and D enantiomers and defining vectors In DL_POLY_4 improper dihedral forces are handled by the routine DIHEDRALS_FORCES 2 2 7 Inversion Angle Potentials The inversion angle potentials describe the interaction arising from a particular geometry of three atoms around a central atom The best known example of this is the arrangement of hydrogen atoms around nitrogen in ammonia to form a trigonal pyramid The hydrogens can flip like an inverting umbrella to an alternative structure which in this case is identical but in principle causes a change in chirality The force restraining the ammonia to one structure can be described as an inversion potential though it is u
321. s 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 van der Waals forces b Cc x Atom atom and site site coulombic forces Metal metal local density dependent forces ae Tersoff local density dependent forces for hydro carbons 16 Three body valence angle and hydrogen bond forces O a Sy f g Four body inversion forces lon core shell polarasation TD us py Tether forces i Chemical bond forces j k 1 Valence angle forces Dihedral angle and improper dihedral angle forces ro Inversion angle forces External field forces m 2 The computed forces are accumulated in atomic force arrays independently on each pro cessor 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 4 this is accomplished quite naturally throug
322. s default n 0 corresponding to a dry run 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 enforces the direct calculation of van der Waals interactions defined by explicit potential forms i e it will not work for systems using tabulated potentials TABLE 117 STFC Section 5 1 vdw shift applies a force shifting procedure to all van der Waals potentials except the shifted force n m potential so that the VDW interactions s energy and force contributions fall to zero smoothly for distances aproaching reut zden sampling every f calculate and collect the Z density profile every f timesteps default f 1 zero perform zero temperature MD run reset target system temperature 10 Kelvin 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 coordinat
323. s a pair potential incorporating repulsive electrostatic and overlap interactions N is the number of interacting particles in the MD box The types of metal potentials available in DL_POLY 4 are as follows 1 EAM potential eam There are no explicit mathematical expressions for EAM potentials so this potential type is read exclusively in the form of interpolation arrays from the TABEAM table file as implemented in the METAL_TABLE_READ routine Section 5 1 7 The rules for combining the potentials from different metals to handle alloys are different from the FS class of potentials see below Finnis Sinclair potential 12 fnsc Finnis Sinclair potential is explicitly analytical It has the following form Vii rg ry 0 Co crrij car y Tij d 3 pislrij rg D pei Y with parameters co C1 C2 C A d B both c and d are cutoffs Since first being proposed a number of alternative analysical forms have been proposed some of which are descibed below The rules for combining different metal potentials to model alloys are different from the EAM potentials see below 2 92 Extended Finnis Sinclair potential 45 exfs It has the following form Vislrij tig e co C1fij cari car carg pij rij rig d B rij d 2 93 with parameters co C1 C2 C3 C4 C A d B both c and d are cutoffs Sutton Chen potential 13 14 15 stch The Sutton Chen potential is
324. s 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 4 is the implementation of Neumann based on charge charge interactions 50 In this model the total coulombic potential is given by 1 Bora 2 aan 2R3 2 168 44 STFC 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 e1 1 _ 2 169 dal 2209 with e the dielectric constant outside the cavity The effective pair potential is therefore 1 1 Bor U rg dj J a 2 170 ri Arepe Y E l 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 4 this is countered by subtracting the value of the potential at the cavity boundary from each pair contribution The term subtracted is 1 su S 1 2 171 4reoe Re e 2 The effective pair force on an atom j arising from another atom n within the cavity is given by qidj 1 Bo id 2 172 i A4reoe 3 A SI In DL POLY 4 the reaction field is optionally extended to emulate long range ordering in a force shifted manner by countering the reaction term and using a distance depending damping func
325. s the uncorrected local density and J is the mean particle density Evaluating the integral part of the above equation yields 1 EAM density correction No long ranged corrections apply beyond rmet 2 Finnis Sinclair density correction No long ranged corrections apply beyond cutoffs c and d 33 STFC Section 2 3 3 Extended Finnis Sinclair density correction No long ranged corrections apply beyond cutoffs c and d 4 Sutton Chen density correction 3 19 m 3 TRA A 2 110 m 3 rmet 5 Gupta density correction 2 Ti Tri Tmet Y rit 2rmet 2 F2 2 exp 20 mento 2 111 ij ij The density correction is applied immediately after the local density is calculated The pair term correction is obtained by analogy with the short ranged potentials and is 1 N Ce 32 Valy 27 pro dpi 2 dij i 1 j i 1 N Tij lt Tmet 1 N Tij 2Tmet Ui 39 2 Vilra t t53 2o Vislris Uf Ui i 1 ji i 1 ji dU 2aNp Vij r r2dr Tmet N U SF o 6p 2 112 i 1 N N OF pi Ur YP Yop 03 dt i 1 i 1 E N F pi o U 4rp ek pij r r dr Note that 9U2 is not required if p has already been corrected Evaluating the integral part of the above equations yields 1 EAM energy correction No long ranged corrections apply beyond rmet 2 Finnis Sinclair energy correction No long ranged corrections apply beyond cutoffs c and d 3 Extended Finnis Sinclair ene
326. s 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 almost an equal portion of atom data as much 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 4 is based on the link cell algorithm of Hockney and Eastwood 63 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 4 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 pro cessors 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 4 is handled by the SET_HALO_PAR
327. se 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 4 will issue an error message and cease execution if it detects it cannot fit a link cell per domain as this is the minimum the DL_POLY 4 link cell algorithm can work with 1 1 1 corresponding to ratio R 1 26 It is worth outlining in terms of the O computation communication function what the rough scaling performance is like of the most computation and communication intensive parts of DL_POLY_4 in an MD timestep a Domain hallo re construction in SET_HALO_PARTICLES METAL_LD_SET_HALO and DEFECTS_REFERENCE_SET_HALO O N P N R 99 STFC Section 4 3 b Verlet neighbourlist construction by link cells in LINK_CELL_PAIRS O N P 0 may take up to 40 of the time per timestep c Calculation of k space contributions to energy and forces from SMPE by EWALD_SPME_FORCES depends on PARALLEL_FFT which depends on GPFA_MODULE O N log N N log P P may take up to 40 of the time per timestep d Particle exchange between domains involving construction and connection of new out of do main topology when bonded like interactions exist by RELOCATE_PARTICLES O N PIN 2 e Iterative bond and PMF constraint solvers CONSTRAINTS_SHAKE_VV CONSTRAINTS_RATTLE_VV CONS
328. serve as a backup 1 4 7 The public Sub directory This sub directory contains assorted routines donated by DL_POLY users Potential users should note that these routines are unsupported and come without any guarantee or liability what 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 4 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 STFC Section 1 7 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 20 1 5 Obtaining the Source Code To obtain a copy of DL_POLY 4 it is necessary to have internet connection Log on to the DL_POLY website http www ccp5 ac uk DL_POLY and follow the links to the DL_POLY 4 registration page where you will firstly be shown the DL_POLY 4 software licence which details the terms and conditions
329. sform due to I J Bush 67 This routine 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 However the FFT communications are only patterned in a power of two series manner The DL_POLY_4 subroutine EWALD_SPME_FORCES perfoms the bulk of the FFT operations and charge array construction while SPME_FORCES calculates the forces Other routines required to calculate the Ewald sum include EWALD_MODULE EWALD_EXCL_FORCES EWALD_FROZEN_FORCES and SPME_CONTAINER 164 STFC Section 6 1 6 1 5 Metal Potentials The simulation of metals 2 3 2 by DL POLY_4 makes use of density dependent potentials 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 4 implements these potentials in various subroutines with names beginning with METAL 6 1 6 Tersoff Three Body and Four Body Potentials DL_POLY 4 can calculate Tersoff three body and four body interactions Although some of these 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 nor
330. sing the new half step velocities r t At r t At u t At 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 1 u t 5 et 34M 5A 3 8 The instantaneous kinetic energy for example can then be obtained from the atomic velocities as LG Exin t 5 N miu t 3 9 1 and assuming the system has no net momentum the instantaneous temperature is T t 2 Ekin 0 3 10 where labels particles that can be free atoms or rigid bodies N the number of particles free atoms and rigid bodies in the system kg the Boltzmann s constant and f the number of degrees of freedom in the system f 3N a BN Frozen 3N shells A Ngonstraints 3 p 3 11 Here N frozen indicates the number of frozen atoms in the system Mshells 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 which we impose and p is zero for periodic or three for non periodic systems where it accounts for fixing angular momentum about origin which we impose In the case of rigid bodies see Section 3 6 the first part of equation 3 11 fr 3N BN Frozen 3 12 splits into f1 8NFP IN Frozen BN BB
331. sions_module o kinds_f90 0 setup_module o io_module o comms_module o kinds_f90 0 netcdf_modul o kinetic_module o comms_module o config_module o kinds_f90 0 rigid_bodies_module o setup_module o langevin_forces o comms_module o config_module o core_shell_module o kinds_f90 0 setup_module o langevin_module o kinds_f90 0 setup_module o link_cell_pairs o comms_module o config_module o domains_module o kinds_f90 0 setup_module o link_cell_pair o comms_module o config_module o domains_module o kinds_f90 0 setup_module o metal_forces o config_module o kinds_f90 0 metal_module o setup_module o metal_generate o kinds_f90 0 metal_module o setup_module o site_module o metal_ld_collect_eam o config_module o kinds_f90 0 metal_module o setup_module o metal_ld_collect_fst o config_module o kinds_f90 0 metal_module o setup_module o metal_ld_compute o comms_module o config_module o kinds_f90 0 metal_module o setup_module o metal_ld_export o comms_module o config_module o domains_module o kinds_f90 0 setup_module o metal_ld_set_halo o comms_module o config_module o domains_module o kinds_f90 0 setup_module o metal_lrc o comms_module o config_module o kinds_f90 0 metal_module o setup_module o site_module o metal_module o kinds_f90 0 setup_module o metal_table_derivatives o kinds_f90 0 setup_module o metal_table_read o comms_module o kinds_f90 0 metal_module o parse_module o setup_module o site_module o min
332. standard DL_POLY_2 20 version with the exceptions of 1 RIDGID BODIES linked by constraint bonds CB or potential of mean field PMF constraints 2 Truncated octahedral imcon 4 Rhombic Dodecahedral imcon 5 and Hexagonal Prism imcon 7 periodic boundary conventions 3 Classic Ewald and Hautman Klein Ewald Coulomb evaluations 4 Temperature Accelerated Dynamics Hyperdynamics and solvation energies No previous DL_POLY_3 4 feature is deprecated ALL NEW features are documented in the DL_POLY_4 User Manual Refernce Thank you for using the DL_POLY_4 package in your work Please acknowledge our efforts by including the following reference when publishing data obtained using DL_POLY_4 I T Todorov W Smith K Trachenko amp M T Dove J Mater Chem 16 1611 1618 2006 Warnings 1 DL_POLY_4 can produce index ordered REVCON HISTORY and MSDTMP files which are restartable by DL_POLY_2 Although such 272 STFC Appendix E 2 3 4 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 This is due to the necessary addition of blanks at the end of data record included to align the ASCII lines of output files human readable to a constant length Printing scrambled outputs is optional Note that these too have bl
333. stat Note Exin t At and P t At have changed and change inside 1 3 At 1 n t At exp x t qh 3 n t At 3 1 _ At 3 P t At Poat V t At n 74t 7 t4 At ha nu 3 dadi 3 n t 74 exp x t 74 3 n t 729 3 At ER ee exp n t At x u t At 3 130 STFC Section 3 5 3 3 At 3 nt 766 exp x t At n t At A t At Poel V t At 4 4 Pmass 3 At n t At exp x t At n t At 11 Thermostat Note Exin t At has changed and changes inside At 2 Erin t F At Pmass n t F At 20 kg Text 7 3 x t At x t At 8 Imass 7 At v t At exp x t 4 gat 1 u t At 3 131 7 At 2Ekin t At mass Nt At 20 bp Tex x E At xlt 004 to x PAU en a u t At v t At Vo t At where Vo t At is the c o m velocity at timestep At and H is the cell matrix whose columns are the three cell vectors a b c The LFV implementation of the Nos Hoover algorithm is iterative until self consistency in the full step velocity u t is obtained Initial estimates of x t and n t at full step are calculated 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 1 FF f t f t At 3 132 2 LFV The iterative part is as follows Ss IO L x t ult wl 1 1 u t At
334. stems DL_POLY 4 will simulate the following molecular species e Simple atomic systems and mixtures e g Ne Ar Kr etc e Simple unpolarisable point ions e g NaCl KCl etc e Polarisable point ions and molecules e g MgO H30 etc e Simple rigid molecules e g CCl4 SFe Benzene etc e Rigid molecular ions with point charges e g KNOs NH4 2SOu etc e Polymers with rigid bonds e g CnHan 2 e Polymers with flexible and rigid bonds and point charges e g proteins macromolecules etc e Silicate glasses and zeolites e Simple metals and metal alloys e g Al Ni Cu CugAu etc STFC Section 1 2 e Covalent systems as hydro carbons and transition elements e g C Si Ge SiC SiGe ets 1 2 2 Force Field The DL_POLY 4 force field includes the following features di 10 11 12 13 All common forms of non bonded atom atom van der Waals potentials Atom atom and site site coulombic potentials Metal metal local density dependent potentials 10 11 12 13 14 15 Tersoff local density dependent potentials for hydro carbons 16 Three body valence angle and hydrogen bond potentials Four body inversion potentials Ion core shell polarasation Tether potentials Chemical bond potentials Valence angle potentials Dihedral angle and improper dihedral angle potentials Inversion angle potentials External field potentials The parameters describing these potentials may
335. sually 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 23 STFC Section 2 2 Figure 2 5 The inversion angle and associated vectors The potential functions available in DL_POLY_4 are as follows 1 Harmonic harm k U Qijin 2 Qijkn i do 2 55 2 Harmonic cosine hcos k 2 U dijkn 5 cOS Gijkn cos o 2 56 3 Planar potential plan U Pijkin A 1 cos dijkn 2 57 4 Extended planar potential xpln k U ijkn 5 1 cos m Pijkn do l 2 58 In these formulae jkn is the inversion angle defined by Tz der WwW Qijkn cos Et 2 59 TijWkn with and the unit vectors Un Pix in ik Pin Din E Lin Taal 2 61 As usual Tij Tj E ete and the hat indicates a unit vector in the direction of r The total J 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 24 STFC Section 2 2 Equivalently the angle may be written as Un o 21 2 Pijkn dos l ess Den rij kn 2 62 Tij Formally the force on an atom arising from the inversion potential is gi
336. sumed that normal molecular dynamics will commence from the final structure Notes on the Minimisation Procedures 1 The zero temperature dynamics is really dynamics conducted at 10 Kelvin However the dynamics has been modified so that the velocities of the atoms are always directed along the force vectors Thus the dynamics follows the steepest descent to the local minimum From any given configuration it will always descend to the same minimum 2 The conjugate gradient procedure has been adapted to take account of the possibilites of constraint bonds and rigid bodies being present in the system If neither of these is present the conventional unadapted procedure is followed a In the case of rigid bodies atomic forces are resolved into molecular forces and torques The torques are subsequently transformed into an equivalent set of atomic forces which are perpendicular both to the instantaneous axis of rotation defined by the torque vector and to the cylindrical radial displacement vector of the atom from the axis These modified forces are then used in place of the original atomic forces in the conjugate gradient scheme The atomic displacement induced in the conjugate gradient algorithm is corrected to maintain the magnitude of the radial position vector as required for circular motion b With regard to constraint bonds these are replaced by stiff harmonic bonds to permit minimisation This is not normally recommended as a means
337. t se RO 1 n t u t d _ 2Ein t Pmass Trin t n 6 7 20 3 kg Text gi E dmass mass 20 T 3 136 du E O Pmass res kp Text Tp CH 10 50 d YO TRAVO where o 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 are of the following sort At 2Ekin t Pmass Tr n t ne 20 3 kB Text 8 dmass x t sat x t 1 At u t exp n t4 74 5 u t 3 137 1 At a t Poxt V t 1 nt Gat nf 5 alt VOL 80 STFC Section 3 5 whereas for the LFV couched algorithm they are 2Exkin t Pmass Tr n t n t 20 3 kg Toxt x t 340 x t At At a u t 4 At v t 3At At 10 Dat 1 n t 0 3 138 n t ZAt exp x t At he At At a t ll The modifications in ii are the same for both the VV and LFV couched algorithms 1 H t At exp ut At At H t 1 V t At exp rr nl 540 At V t 3 139 It is worth noting DL_POLY_4 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 s
338. 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 At f t 3 3 3 VV2 In the second stage 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 e 3 4 DL_POLY 4 also offers integration algorithms based on the leapfrog Verlet LFV scheme 21 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 all kinetic related properties have approximate estimators due to the half a step out of phase between velocity and psoition 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 TO 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 t v t At v t At At 0 i 3 6 2 2 m 53 STFC Section 3 1 where m is the mass of a site and then the positions are advanced to a full step t At u
339. t entities whose local geometry is time invariant One way to enforce this in a simulation is to impose a sufficient number of bond constraints between the atoms in the unit However in many cases this may be either problematic or impossible Examples in which it is impossible to specify sufficient bond constraints are 1 linear molecules with more than 2 atoms e g CO2 2 planar molecules with more than three atoms e g benzene Even when the structure can be defined by bond constraints the network of bonds produced may be problematic Normally they make the iterative SHAKE in the LFV integration or RATTLE in the VV integration procedure slow particularly if a ring of constraints is involved as occurs when one defines water as a constrained triangle It is also possible inadvertently to over constrain a molecule e g by defining a methane tetrahedron to have 10 rather than 9 bond constraints in which case the SHAKE RATTLE procedure will become unstable In addition massless sites e g charge sites cannot be included in a simple constraint approach making modelling with potentials such as TIP4P water impossible All these problems may be circumvented by defining rigid body units the dynamics of which may be described in terms of the translational motion of the centre of mass COM and rotation about 84 STFC Section 3 6 the COM To do this we need to define the appropriate variables describing the position orientation a
340. t 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 ewald_spme_forc s f90 Define Velocity Verlet files FILES_VV pseudo_vv f90 constraints_shake_vv f90 pmf_shake_vv f90 constraints_rattle f90 pmf_rattle f90 nvt_h0_scl f90 npt_h0_sc1 f90 nst_h0_sc1 f90 nve_0_vv f90 nvt_e0_vv f90 nvt_10_vv f90 nvt_a0_vv f90 nvt_b0_vv f90 nvt_h0_vv f90 npt_10_vv f90 npt_b0_vv f90 npt_h0_vv f90 npt_m0_vv f90 nst_10_vv f90 nst_b0_vv f90 nst_h0_vv f90 nst_m0_vv f90 nvt_h1_sc1 f90 npt_h1_sc1 f90 nst_hi_scl f90 nve_1_vv f90 nvt_el_vv f90 213 STFC Appendix C nvt_li_vv f90 nvt_ai_vv f90 nvt_bi_vv f90 nvt_hi_vv f90 npt_11_vv f90 npt_b1_vv f90 npt_h1_vv f90 npt_mi_vv 90 nst_11_vv f90 nst_b1_vv f90 nst_h1_vv f90 nst_m1_vv f90 md_vv f90 Define LeapFrog Verlet files FILES_LFV pseudo_lfv f90 constraints_shake_lfv f90 pmf_shake_lfv f90 nve_0_lfv f90 nvt_e0_lfv f90 nvt_10_1fv f90 nvt_a0_lfv f90 nvt_bO_lfv f90 nvt_h0_1fv f90 npt_10_1fv f90 npt_b0_1fv f90 npt_hO_lfv f90 npt_m0_lfv 90 nst_10_1fv f90 nst_b0_1fv f90 nst_hO_lfv f90 nst_m0_lfv 90 nve_1_1fv f90 nvt_ei_lfv f90 nvt_11_1fv f90 nvt_ai_lfv f90 nvt_b1_1fv f90 nvt_hi_lfv f90 npt_11_1fv f90 npt_b1_1fv f90 npt_hi_lfv f90 npt_m1_1fv f90 nst_11_1fv f90 nst_b1_1fv f90 nst_h1_1fv f90 nst_mi_lfv f90 md_1fv f90 A A Examine
341. t of the file is written from the subroutine READ_FIELD 5 2 5 4 System Specification Echoes system name periodic boundary specification the cell vectors and volume some initial esti mates of long ranged corrections the energy and pressure if appropriate some concise information on topology and degrees of freedom break down list This part of the file is written from the subrou tines SCAN_CONFIG CHECK_CONFIG SYSTEM_INIT REPORT_TOPOLOGY and SET_TEMPERATURE 5 2 5 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 information given is based on the 153 STFC Section 5 2 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 5 6 Simulation Progress This part of the file is written by the DL_POLY 4 root segment DL_POLY_ The header line is printed at the top of each page as 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 vi
342. t 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 48 STFC Section 2 5 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 also the Fuchs correction 51 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 abE 2 189 where yz is the induced dipole and 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 electrostatic interaction i e self interaction between the core and shell of the same atom Non coulombic interactions arise from the shell alone Th
343. targets manually all echo echo You MUST specify a target platform 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_platform echo Fetch MPI SERIAL subroutines FILES_SERIAL MAKE links_serial 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 214 STFC Appendix C 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_platform MAKE LD path to FORTRAN90 Linker loaDer LDFLAGS appropriate flags for LD FC path to FORTRAN90 compiler FCFLAGS appropriate flags for FC EX EX BINROOT BINROOT TYPE System specific targets follow win MAKE LD f95 o LDFLAGS 03 FC f95 c FCFLAGS 03 215 ST
344. ted 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 52 1 Interpolation of the exp i k r terms given here for one dimension exp 2ri u k L b k Y Mn us exp 2ri kl K 2 181 00 in which amp is the integer index of the amp vector in a principal direction K is the total number of grid points in the same direction and uj is the fractional coordinate of ion j scaled by a factor K i e u K 85 Note that the definition of the B splines implies a dependence on the integer K which limits the formally infinite sum over The coefficients M u are B splines of order n and the factor b k is a constant computable from the formula n 2 1 b k exp 2ri n 1 k K Y Mp 1 exp 2ri kt K 2 182 0 2 Approximation of the structure factor S k S k b1 k1 ba ka b3 k3 Q1 k1 k2 kg 2 183 AT STFC Section 2 4 where Q k1 ka k3 is the discrete Fourier transform of the charge array Q 1 2 l3 defined as N QUito ts Sig YU Mnluij L1i niL1 x Malus lo noLo x jal 21 N2 N3 Mn uz 3 n3Lg3 2 184 in which the sums over n1 2 3 etc are
345. tents 2 Benchmark CASES og La kk a do e A Re we E e a a 179 Appendices 180 A DL POLY 4 Periodic Boundary Conditions 180 B DL_POLY 4 Macros 183 C DL POLY 4 Makefiles 187 D DL_POLY 4 Error Messages and User Action 223 E DL POLY 4 README 272 Bibliography 276 Index 279 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 a 118 Internal Restart Key 00 02 4254 a Si SE Be a a a 120 Internal Ensemble Key 120 Electrostaties Key ooo ce sa ia EEE E A A So 123 CONFIG File Key record 2 cocos ew ae e 127 Periodic Boundary Key record 2 co ia ee SE aa E eG 128 Tethering Potentials ios 444 244 64 o bee be pee eG eee ae 133 Chemical Bond Potentials 0 2 42 4 05505 48 e RD eR a a 135 Valence Angle Potentials 0 2 0 0 0 eee ee 136 Dihedral Angle Potentials o i osa m moai ti ari Sek Be a ee ee Be 137 Inversion Angle Potentials 0 0 02 eee ee ee 138 Pair Potentials s cso ea eA a EEE ee OE a Se Ee Se 139 Metal Potential o o sai 5664245460 220444 0854 22 OOS be eee ee 140 Tersott Potential i 2228495468 bee0 Kee Yee ee ER Ea ee eG 142 Three body Potentials sos e sosoo m 446 854842 bow bee Be pk EG ed a 143 Four body Potentials ses 4 24 2 adn dn GS Re we OR ae a ae 143 Extertial Fields o o e scia fog 8 8 a E 3S be dG ee e ee be a es 144 xi List of Figures 2 1 The interatomic bond vector LL 1
346. the CONFIG file before running DL_POLY 4 101 STFC Section 4 3 4 3 4 Analysing Results DL_POLY 4 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 4 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 4 public library to help with this The utilities available are described in the DL_POLY_2 User Manual Users should also be aware that many of these utilities are incorporated into the DL_POLY Graphical User Interface 20 4 3 5 Choosing Ewald Sum Variables 4 3 5 1 Ewald sum and SPME This section outlines how to optimise the accuracy of the Smoothed Particle Mesh Ewald sum parameters for a given simulation As a guide to beginners DL_POLY 4 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 will make DL_POLY 4 evaluate its best guess at the Ewald parameters a kmaxa kmaxb and kmaxc or their doubles if ewald rather than spme is specified The user
347. 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 with respect to atom j or vice versa constituting the rigid bond ij may not be perpendicular to the bond i e may have a non zero component along the bond However by the stricter definition of rigidity this is is required to be zero as it will otherwise lead to a change in the rigid bond length during the consequent timestepping In the second stage the deviation from zero of the scalar product d uj 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 Hij dij vj vi The velocity corrections can therefore be written as v 3 18 corr _ x Bij _ Mij dij o UG Vi AN 2 dij Mi mi d 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
348. the first five files are exception of that rule WARNING and ERROR are important reporting subroutines that have call points at 171 STFC Section 6 2 various places in the code and NUMERIC_CONTAINER and SPME_CONTAINER are containers of simple functions and subroutines related in some way to their purpose in the code 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 These implement an emulation of some general MPI calls used in DL_POLY 4 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 6 2 7 Comments on MPI Handling Only a few files make explicit calls to MPI routines COMMS_MODULE IO_MODULE READ_CONFIG_PARALLEL READ_CONFIG WRITE_CONFIG CHECK_CONFIG SYSTEM_EXPAND PASS_SHARED_UNITS UPDATE_SHARED_UNITS EXPORT_ATOMIC_DATA READ_HISTORY DEPORT_ATOMIC_DATA METAL_LD_EXPORT PARALLEL_FFT EXCHANGE_GRID DEFECTS_REFERENCE_WRITE DEFECTS_REFERENCE_READ_PARALLEL DEFECTS_REFERENCE_READ DEFECTS_REFERENCE_EXPORT DEFECTS_WRITE DEFECTS1_WRITE TRAJECTORY_WRITE MSD_WRITE SYSTEM_REVIVE The rest of the files that use MPI functionality in any way make implicit cal
349. the forum through the DL_POLY website A registration and vetting process is required before you can use the forum but it is open in principle to everyone 11 Chapter 2 Force Fields Scope of Chapter This chapter describes the variety of interaction potentials available in DL_POLY 4 12 STFC Section 2 1 2 1 Introduction to the DL POLY 4 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_4 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 17 Dreiding 18 and AMBER 19 users have been coded in the package as well as less familiar forms In addition DL_POLY 4 retains the possibility of the user defining additional potentials In DL_POLY 4 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 gt Uangi Canals Tab Te tangl 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
350. the isotropic cell fluctuations case and At ore V t 1 2Exin t 1 1 1 t 4 At t 21 4 2 Pmass f Pmass i ti ut At ai nl 145 S sat 3 146 1 r t At exp nl At At r t At v t At for the anisotropic cell fluctuations case Similarly for the LFV couched algorithms these are mt 3At e spl 1 P t Pat 2Evin t 1 nt E 300 Do sve Pmass ae f utes At E li A0 At E x t i 1 gt n o o 3 147 1 1 1 ALA e e bl u t 300 nlt 5At r t 50 for the isotropic cell fluctuations case and 1 1 n t At exp x st At At a t Poxt V t 1 2E pin t 1 he E 3 ae mt Pmass f Pmass mee At at at At an n x t L nlt Sul 1 l 0 3 148 ret At x t tat fult 340 a t 346 olt 340 for the anisotropic cell fluctuations case This ensemble is optionally extending to constant normal pressure and constant surface area NP AT 56 by semi isotropic constraining of the barostat equation of motion and slight amending the thermostat equation of motion and the conserved quantity to Le o _ o Fs V t Eri t ae x t nz2 t a B z m a a8 2 d 2Ekin t Pmass Tr n t s nt 20 kg Text ae ram 3 149 di qmass mass t Pmass Tr n n t Hyp ar Hyve q x FA z Pat V t f 1 ke Text J x s ds 83 STFC Section 3 6 Similarly this ensemble is optionally extending to constant
351. their method of exploiting parallelism DL_POLY_2 uses a Replicated Data RD strategy 4 5 6 7 which works well simulations of up to 30 000 atoms on up to 100 processors DL_POLY 4 is based on the Domain Decomposition DD strategy 2 8 9 4 5 and is best suited for large molecular simulations from 103 to 10 atoms on large processor counts The two packages are reasonably compatible so that it is possible to scale up from a DL_POLY 2 to a DL_POLY 4 simulation with little effort It should be apparent from these comments that DL POLY 4 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 4 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 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 DL_POLY project website http www ccp5 ac uk DL_POLY 1 2 Functionality The following is a list of the features DL_POLY 4 supports 1 2 1 Molecular Sy
352. thod j k le io write method rp type j k le calculate electrostatic forces using Ewald sum with a Ewald convergence parameter in A kl is the maximum k vector index in x direction k2 is the maximum k vector index in y direction k3 is the maximum k vector index in z direction switch 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 initiate impact on the particle with index i gt 1 at timestep j i gt 0 with energy E E gt 0 in kilo eV and direction vector x y z from the Cartesian origin centre of the MD box defaults i 1 j 0 E 0 xz 1 y 1 z 1 set the type of Verlet integrator where string can only be leapfrog or velocity as the later is the default set the the general I O read interface to method mpiio for MPI I O direct for parallel direct access FORTRAN I O or master for traditional master I O or netcdf for netCDF I O provided DL POLY 4 is compiled in a netCDF enabled mode default mpiio j reader count 1 lt j lt job size default j gInt Log Min job size 2 job size Log 2 is the designated number of processes to carry out I O read operations simultaneously NOTE that k is not applicable for the master method k batch size 1 lt k lt 1 000 000 default 50 000 is the maximum number of particle enti
353. ties in a batch i e multiples of species index r v f etc transmitted between I O groups I O readers for domain distribution purposes l buffer size 100 lt 1 lt 100 000 default 5 000 is the maximum number of ASCII line records read in a batch NOTE that e is not applicable for the master method e parallel error check Yes default N set the the general I O write interface to method mpiio for MPI I O direct for parallel direct access FORTRAN I O or master for traditional master I O or netcdf for netCDF I O provided DL _POLY 4 is compiled in a netCDF enabled mode default mpiio WARRNING direct is not a platfotm portable solution as it fails on LUSTRE but works on GPFS NOTE that rp is only applicable for the netcdf method rp real precision 32bit or amber for 32 bit float 113 STFC Section 5 1 job time f maxdis f metal direct mindis f minimise string n f msdtmp i j multiple timestep n mxquat n otherwise 64 bit double is defaulted if unspecified type sorted or unsorted DD scrambled by global index output default sorted j writer count 1 lt j lt job size default j gInt Log Min job size 8y job size Log 2 is the designated number of processes to carry out I O write operations simultaneously NOTE that k is not applicable for the master method k batch size 1 lt k lt 1 000 000 default 50 000 is the maximum number of particle entities in a batch i e m
354. tion erfc a rij identical to that seen in the real space portion of the Ewald sum and thus mirror the effective charge screening 49 Uj er fc a rij erfc a ret 2a exp a r Ul r e ae rig 4TEO E 7 To T VT Teut rig ar Tout 2 Lee Tout x 2a exp a rat ros x Bo r 12 4 Tij 2 3 Teut yT Tout 2r cut with the force on an atom j given by qa erfela rg 2a exp a r2 j Are 2 n 0 Tij yT Tij erfc a Teut 2a exp a r2 Borij ti r2 or yT r 3 cut cut r cut with the force on atom 7 the negative of this Tout 2 173 2 174 Tij It is worth noting that as discussed in 49 and references therein this is only an approximation of the Ewald sum and its accuracy and effectiveness become better when the cutoff is large gt 10 preferably 12 A The contribution of each effective pair interaction to the atomic virial is and the contribution to the atomic stress tensor is e 2 176 where a 8 are x y z components The atomic stress tensor is symmetric In DL_POLY 4 the reaction field is handled by the subroutine COUL_RFP_FORCES 45 STFC Section 2 4 2 4 5 Smoothed Particle Mesh Ewald The Ewald sum 21 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 m
355. tions 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 4 will correctly handle the electrostatics of both molecular and atomic species However it is assumed that the system is electrically neutral A warning message is printed if the system is found to be charged but otherwise the simulation proceeds as normal Note that DL_POLY 4 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 4 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 gg AT ENE Tij with q the charge on an atom labelled and r the magnitude of the separation vector r rj fr The force on an atom j derived from this force is 1 dj ji 2 153 j A4reoe ri Tij with the force on atom the negative of this The contribution to the atomic virial is 1 1 Wa ee 2 154 ATEQE Tij which is simply the negative of the potential term The contribution to be added to the atomic stress tensor is av ane fs 2 155 where a 8 are x y z components The atomic stress tensor is symmetric In
356. 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 4 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 96 STFC Section 4 2 You can also extend a simulation beyond its initial allocation of timesteps provided you still have the REVCON and REVIVE files These should be copied to the CONFIG and REVOLD files respectively and the directive timesteps adjusted in the CONTROL file to the new total number of steps required for the simulation For example if you wish to extend a 10000 step simulation by a further 5000 steps use the directive timesteps 15000 in the CONTROL file and include the restart directive Further to the full restart option there is an alternative restart scale directive that will reset the temperature at start or restart noscale that will keep the current kinetics intact bf Note that these two options are not correct restarts but rather modified starts as they make no use of REVOLD file and will reset internal
357. tom labelled It is worth noting that the Coulomb potential switches to the paricular model of Electrostatics opted in CONTROL 9 Shifted finitely extendible non linear elastic FENE potential 32 33 34 fene AN U r 705 k R3 In i 42 ry lt Ro A 2 10 13 7 00 Tij gt Ro A The FENE potential is used to maintain the distance between connected beads and to prevent chains from crossing each other It is used in combination with the WCA 2 83 potential to create a potential well for the flexible bonds of a molecule that maintains the topology of the molecule This implementation allows for a radius shift of up to half a Ro A lt 0 5 Ro with a default of zero Age fault 0 15 STFC Section 2 2 In these formulae r is the distance between atoms labelled and j rg tl 2 11 where r is the position vector of an atom labelled The force on the atom j arising from a bond potential is obtained using the general formula 110 gt utr Tij a 2 12 The force f acting on atom is the negative of this The contribution to be added to the atomic virial is given by with only one such contribution from each bond The contribution to be added to the atomic stress tensor is given by emi 2 14 where a and indicate the x y z components The atomic stress tensor derived in this way is symmetric In DL_POLY 4 bond forces are handled by the routine BONDS_FORCES 2 2 2 Distan
358. tomic 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 4 will assume it is zero However DL_POLY 4 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 Ri of each unit is given by jar Wj Ej Ry ar 5 7 jai Wj where r is a site position and w the site weighting 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 4 molecule DL_POLY 4 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 4 PMF constraints are handeled in every available ensemble 132 STFC Section 5 1 7 rigid n where n is the number of basic rigid units in the molecule It is followed by at least n records each specifying the sites in a rigid unit m integer number of sites in rigid unit site 1 integer first site atomic index site 2 integer second site atomic index site 3 integer third site atomic index si etc site m integer m th
359. tribution 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 these semi isotropic ensembles are only correct for infinite interfaces placed perpendicularly to the z axis This means that the interface is homogenious unbroken and continuous in the x y plane of the MD cell which assumes that that two of the cell vectors have a cross product only in the z direction For example if the MD box is defined by its lattice vectors a b c then a x b 0 0 1 It is the users responsibility to ensure this holds for their model system Table 5 3 Internal Ensemble Key keyens meaning 0 Microcanonical ensemble NVE 1 Evans NVT ensemble NVE gin 10 Langevin NVT ensemble 11 Berendsen NVT ensemble 12 Nos Hoover NVT ensemble 20 Langevin NPT ensemble 21 Berendsen NPT ensemble 22 Nos Hoover NPT ensemble 23 Martyna Tuckerman Klein NPT ensemble 30 Langevin NoT ensemble 31 Berendsen NoT ensemble 32 Nos Hoover NoT ensemble 33 Martyna Tuckerman Klein NoT ensemble 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 i vi f lt 0 tu 1 vi Gli v f 20 5 2 Ss SS is used to help the system relax before each integr
360. tribution to be added to the atomic stress tensor is given by o re fe 2 87 28 STFC Section 2 3 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 ryqw it is necessary to apply a long ranged correction to the system potential energy and virial Explicit formulae are needed for each case and are derived as follows For two atom types a and b the correction for the potential energy is calculated via the integral qe ap Nado j corr V PER Jablr Ua r r dr 2 88 where Na N are the numbers of atoms of types a and b in the system V is the system volume and Jablr and Uap r are the appropriate pair correlation function and pair potential respectively It is usual to assume g p r 1 for r gt rvaw DL POLY_4 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 w2 a f ge Tara gt 2 89 corr Tvdw 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 4 the short ranged forces are calculated by the subroutine VDW_FORCES The long ranged corrections are calculated by routine VDW_LRC The calculation makes use of the Verlet neighbour list see a
361. tro 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 reut Constraint algorithms in DL_POLY 4 SHAKE RATTLE see Section 3 2 use default iter ation precision of 107 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 4 s DD strategy assumes that the local per domain node or link cell density of various system entities i e atoms bonds angles etc does not vary much during a simula tion and some limits for these are assumed empirically This may not the case in extremely non equilibrium simulations where the assumed limits are prone to be exceeded or in some specific systems where these do not hold from the start A way to tackle such circumstances and avoid simulations crash by controlled termination is to use the densvar f option In the SET_BOUNDS subroutine DL_POLY_4 makes assumptions at the beginning of the simulation and corrects the lengths of bonded like interaction lists arrays mxshl mxcons mxteth mxbond mxangl m
362. tten 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 4 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 4 5 2 7 The REVIVE File This file is unformatted and written by the subroutine SYSTEM_REVIVE It contains the accumu lated statistical data It is updated whenever the file REVCON is updated see previous section REVIVE should be renamed REVOLD to continue a simulation from one job to the next This is done by the copy macro supplied in the execute directory of DL_POLY 4 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 8 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 2 156 S
363. ual 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 4 is based on the powerful conjugate gradients technique 55 in an adaptation as shown in 54 Each time step a few iterations 10 30 are needed to achieve convergence to zero net force In DL_POLY 4 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 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 ranged forces described above Note that DL_POLY_4 determines which shell model to use by scanning shell weights provided the FIELD file see Section 5 1 3 If all shells have zero weight the DL_POLY 4 will choose the relaxed shell model If no shell has zero weight then DL POLY_4 will choose t
364. ub directory This directory contains examples of input and output data for DL_POLY 4 that are suitable for benchmarking DL_POLY 4 on large scale computers These are described in Chapter 7 Note that these are no longer within the distribution of any DL_POLY version but are made available on line at the DL_POLY FTP ftp ftp dl ac uk ccp5 DL_POLY 1 4 5 The execute Sub directory In the supplied version of DL_POLY 4 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 4 program is assembled by using the appropriate 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 4 as intended The experienced user is not at all required to use DL_POLY 4 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 4 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
365. ule o four_body_module o core_shell_module o constraints_module o pmf_module o rigid_bodies_module o tethers_module o bonds_module o angles_module o dihedrals_module o inversions_module o external_field_module o langevin_module o minimise_module o ewald_module o msd_module o statistics_module o kinetic_module o gpfa_module o parallel_fft o OBJ_ALL warning o error o scan_control_io o numeric_container o spme_container o quaternions_container o scan_field o read_config_parallel o scan_config o scan_control o read_config o 202 STFC Appendix C set_bounds o read_control o vdw_generate o vdw_table_read o metal_generate o metal_table_read o metal_table_derivatives o tersoff_generate o dihedrals_14_check o read_field o check_config o scale_config o write_config o trajectory_write o system_expand o rigid_bodies_tags o rigid_bodies_coms o rigid_bodies_widths o rigid_bodies_setup o tag_legend o report_topology o pass_shared_units 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 rigid_bodies_quench o set_temperature o vdw_lrc o metal_lrc o system_init o export_atomic_data o set_halo_particles o rigid_bodies_stress o read_history o impact o core_shell_on_top o deport_atomic_data o pmf_units_set o compress
366. ule o setup_module o scale_config o config_module o development_module o kinds_f90 0 scale_temperature o comms_module o config_module o kinds_f90 0 kinetic_module o rigid_bodies_module o setup_module o scan_config o comms_module o io_module o kinds_f90 0 parse_module o setup_module o scan_control o comms_module o kinds_f90 0 msd_module o parse_module o setup_module o scan_control_io o comms_module o config_module o io_module o kinds_f90 0 parse_module o setup_module o scan_field o comms_module o kinds_f90 o parse_module o setup_module o set_bounds o comms_module o config_module o domains_module o kinds_f90 0 msd_module o setup_module o set_halo_particles o comms_module o config_module o domains_module o kinds_f90 0 rigid_bodies_module o setup_module o site_module o set_temperature o comms_module o config_module o core_shell_module o kinds_f90 0 kinetic_module o rigid_bodies_module o setup_module o site_module o setup_module o kinds_f90 0 site_module o kinds_f90 0 setup_module o spme_container o comms_module o kinds_f90 o setup_module o statistics_collect o comms_module o config_module o kinds_f90 0 msd_module o setup_module o site_module o statistics_module o statistics_module o kinds_f90 0 setup_module o statistics_result o comms_module o config_module o kinds_f90 0 msd_module o setup_module o site_module o statistics_module o system_expand o comms_module o config_module o io_module o kinds_f90 0 pa
367. ultiples of species indez r v f etc transmitted between I O groups I O writers for global sorting purposes l buffer size 100 lt 1 lt 100 000 default 5 000 is the maximum number of ASCII line records written in a batch NOTE that e is not applicable for the master method e parallel error check Yes default N set job time to f seconds set maximum distance allowed in variable timestep control to f A default f 0 10 A enforces the direct calculation of metal interactions defined by explicit potential forms i e it will not work for metal alloy systems using the EAM TABEAM set minimum distance allowed in variable timestep control to f A default f 0 03 A minimise the instantaneous system configuration every n steps during equilibration with respect to the last equilibration step using conjugate gradient method CGM with respect to the criterion string and tolerance f where this criterion can only be force 1 lt f lt 1000 default f 100 or energy 0 lt f lt 0 01 default f 0 005 or distance maximum absolute displacement in 1076 lt f lt 0 1 default f 0 005 the lowest string CGM minimised configuration during equlibration is saved in a file CFGMIN which has the same format as CONFIG write MSDTMP file containing particles individual V M SD in and Tmean in Kelvin with controls i start timestep for dumping configurations default i 0 j timestep interval
368. units per MD cell Note that all energy bearing potential parameters are read in terms of the specified energy units If such a parameter depends on an angle then the dependence is read in terms of radians although the following angle in the parameter sequence is read in terms of degrees 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_4 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 130 STFC Section 5 1 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 4 enters the molecular description envi ronment in which only 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 Not
369. 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 A to 1078 A 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 assuming an absence of rigid bonds constraint forces This is stage 1 of the SHAKE algorithm 2 The deviation in each bondlength is used to calculate the corresponding constraint force 3 15 that retrospectively corrects the bond length 3 After the correction 3 15 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 All 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 16 that retrospectively corrects the bond length c After the correction 3 16 has been applied to all b
370. ut also incorporating RB integration NVT_EO_VV NVT_EO_LFV Constant Ekin algorithm Evans 25 NVT_El_VV NVT_E1_LFV The same as the above but also incorporating RB integration NVT_LO_VV NVT_LO_LFV Constant T algorithm Langevin 26 NVT_L1_vv NVT_L1_LFV The same as the above but also incorporating RB integration NVT_AO_VV NVT_AO_LFV Constant T algorithm Andersen 27 NVT_Al_vv NVT_A1_LFV The same as the above but also incorporating RB integration NVT_BO_VV NVT_BO_LFV Constant T algorithm Berendsen 28 NVT_B1_Vv NVT_B1_LFV The same as the above but also incorporating RB integration NVT_HO_VV NVT_HO_LFV Constant T algorithm Hoover 29 NVT_H1_VV NVT_H1_LFV The same as the above but also incorporating RB integration NPT_LO_VV NPT_LO_LFV Constant T P algorithm Langevin 30 NPT_L1_VV NPT_L1_LFV The same as the above but also incorporating RB integration NPT_BO_VV NPT_BO_LFV Constant T P algorithm Berendsen 28 NPT_Bl_vv NPT_B1_LFV The same as the above but also incorporating RB integration NPT_HO_VV NPT_HO_LFV Constant T P algorithm Hoover 29 NPT_H1_VV NPT_H1_LFV The same as the above but also incorporating RB integration NPT_MO_VV NPT_MO_LFV Constant T P algorithm Martyna Tuckerman Klein 31 NPT_M1_vv NPT_M1_LFV The same as the above but also incorporating RB integration NPT_LO_VV NPT_LO_LFV Constant T o algorithm Langevin 30 NPT_L1_VV NPT_L1_LFV The same as the above but also incorporating RB integration NST_BO_VV NST_BO_LFV
371. values of 0 as if not specified and 1 any other value apart from 0 and can be used to remove the pure two body part of a specific tersoff cross interaction from the system and so leave out only the pure angular one The force on an atom derived from this ae is eee calculated with the formula o fr va Etersott sD g Ui 2 128 Or ie i JA with atomic label being one of i j and a indicating the x y z component The derivative after the summation is worked out as OU are 95a fo rig fr rig Vig org tora fala folris Fala gpa Vs 2 129 with the contributions from the first in the forms Brg o a Faris prat F falra ge Seles x ar i ta 2 130 Vij gra ale riz FAC Tij fc ria Falris F falra Sr fe ri x fat a 1 2 131 and from the third angular term folry falis Za Vis folrij fAlrij Xij X L 1 i Ni Sai li mol 0 3 1 6 CR gir LD pali a a 38 STFC Section 2 3 where 9 pra cis da XO wi folrik 9 9ijn 2 133 g rg k i j The angular term can have three different contributions depending on the index of the particle participating in the interaction d lo i it cal Dijk Ar ora oC Sorin gra aI so 2 134 pe ava 2 135 are Wik JCTik Jr aro ijk Fi j o para e a ft ae 050 2 136 OFF Or The derivative of g 0 jx is worked out in the following manner gti 20 LI E 2 137 e
372. ven by lo Ve pg 2 63 with being one of i j k n and a one of x y z This may be expanded into o 1 o U ijkn n U ijkn X Or od jk E OPijkn od jk gt y2 2 2 1 2 O then Pa a 2 64 Or Tij Following through the extremely tedious differentiation gives the result 1 lo cos di kn a 1 a a f o a tu dye s 0 Uli Ln Ukn Lij Dam ofr Fa TijWkn Tij Uy R A x A dex dei 2 Tis Lij kn kn rij Tik T rij thin Lik kn UknTik VknTik 4 4 n a amp AQ a den dl E fi fg rij Un rij Lin rij Hora Lin en E Li SE Tij k x A A z ek dei rs Pg Dr pa te Tik Gy kn Lik Dien hgh S Uknlin 2 3 a This general formula applies to all atoms i j k n It must be remembered however that these formulae apply to just one of the three contributing terms i e one angle of the full inversion potential specifically the inversion angle pertaining to the out of plane vector r The contributions arising from the other vectors r and r 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 sb Ti Op a den dei E n n fr rij FB Og Eiz Pin rij kn Tin kn n an Formally the contribution to be added to the atomic virial is given by
373. which DL_POLY 4 does not recognise Action Locate the offending potential in the FIELD file and remove Replace with one acceptable to DL_POLY 4 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 251 STFC Appendix D Action Locate the offending four body force potential in the FIELD file and add the required cutoff Resubmit the job Message 454 error unknown external field A form of external field potential has been requested which DL_POLY 4 does not recognise Action Locate the offending potential in the FIELD file and remove Replace with one acceptable to DL POLY 4 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 Message 461 error undefined metal potential A form of metal potential has been requested which DL_POLY 4 does not recognise Action Locate erroneous entry in the FIELD file and correct the potental interaction to one of the allowed ones for metals in DL_POLY_4 Message 462 error thermostat friction constant must be gt 0 A zero or negative value for the thermostat friction constant has
374. x 4 5 where da tee T ax A 4 L3 4 6 is largest k vector considered in reciprocal space L is the width of the cell in the specified direction and kmax is an integer For a relative error of 4 x 107 this means using kmar 6 2 a kmax is then kmax gt 6 4 L Teut 4 7 In a cubic system freut 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 If you wish to set the Ewald parameters manually via the ewald sum or spme sum directives the recommended approach is as follows Preselect the value of reut choose a working a value of a of about 3 2 rcut and a large value for the kmax say 20 20 20 or more Then do a series of ten or so single step simulations with your initial configuration and with a ranging over the value you have chosen plus and minus 20 Plot the Coulombic energy W versus a If the Ewald sum is correctly converged you will see a plateau in the plot Divergence from the plateau at small a is due to non convergence in the real space sum Divergence from the plateau at large a is due to non convergence of the reciprocal space sum Redo the series of calculations using smaller kmax values The optimum values for kmax are the smallest values that reproduce the correct Coulombic energy the plateau value and virial at the value of a to be used in the simulation
375. x C After choosing what the default compilation is to be the appropriate makefile is to be copied as Makefile in the sub directory source The general DL_POLY_4 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 FORTRAN90 compiler is required for successful build of DL_POLY 4 in serial mode and only FORTRAN90 and MPI implementation for DL_POLY_ 4 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_4 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
376. x component of a cell vector 126 STFC Section 5 1 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 cell 9 real z component of c cell vector Note that record 2 may contain more information apart from the mandatory as listed above If the file has been produced by DL_POLY 4 then it also contains other items intended to help possible parallel I O reading 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 4 but may be ad
377. xdihd mxinv as well as 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 cor respond to allocation bigger global arrays and larger memory consumption by DL_POLY 4 during the simulation Note that this option may demand more memory than available on the computer architecture In such cases DL_POLY 4 will terminate with an array allocation failure message As a default DL_POLY 4 does not store statistical data during the equilibration period If the directive collect is used equilibration data will be incorporated into the overall statistics io action options controls how I O is performed by DL_POLY 4 The options can help the performance of I O operations within DL_POLY 4 for potentially large files during the run The form of the command depends on the value of action which may take the value either read or write In general this command should only be used for tuning the I O subsystem in DL_POLY 4 for large runs For small to average sized systems the built in defaults usually suffice a io read method options With action set to read the io command controls how the reading of large files is performed method controls how the disk is accessed Possible values are mpiio in which case MPI I O is used direct which uses parallel FORTRAN direct access files and master which performs all I O through a master processor or netcdf for netCDF I O provided
378. y Equations of Mo tion It is straightforward to couple the rigid body equations of motion to a thermostat and or barostat The thermostat is coupled to both the translational and rotational degrees of freedom and so both the translational and rotational velocities are thermostated in the same manner as the purely atomic velocities The barostat however is coupled only to the translational degrees of freedom and does not contribute to the rotational motion There are two slight technicalities with the Evans and Andersen ensembles that are worth men tioning Since both the translational and rotational velocities contribute towards temperature equation 3 24 showing the derivation of the the thermostat friction in the Evans ensemble by imposing a 88 STFC Section 3 6 Gaussian cosntraint on the system s instantenious temperature changes to d d 1 Z 1 EB 3 elogia g x di 3 Dmitri 3 Milj 3 0 8 Y FP RB RB Eno Sieg V t BOT S lt 20 3 178 i j j FP RB RB si x t E ma MAE 070 i sol J j In the case of the Andersen ensemble if a Poisson slected particle constitues a RB then the whole RB is Poisson selected Poisson slected RBs tarnslational and angular velocities together with Poisson selected FPs velocities sample the same Gaussian distribution isokinetically Boltzmann distribution where the isokineticity to target temperature is dependent upon the total of the Poisson selected FPs and
379. y 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 4 FIELD file for further details Section 5 1 3 DL_POLY 4 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 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 100 STFC Section 4 3 bond potentials In this case DL _POLY 4 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 fo
380. ystem mass x t Pmass Tr n a n t y PoaV 1 32 ks Toxt ni x s ds 3 140 Hnor Hnvet where f is the system s degrees of freedom equation 3 11 This ensemble is optionally extending to constant normal pressure and constant surface area NP AT 56 by semi isotropic constraining of the barostat equation of motion and slight amending the thermostat equation of motion and the conserved quantity to dy E O n a A 2 a 0 a8 2 d 2Exin t Pmass Tr n t nt 20 kg Text ae ra 141 aX Amass 3 mass t a Pmass Tr n n t Hyp ar Hyve q x 2 PoxtV t f 1 kp Text f x s ds Similarly this ensemble is optionally extending to constant normal pressure and constant surface tesnison NP yT 56 by semi isotropic constraining of the barostat equation of motion and slight amending the thermostat equation of motion and the conserved quantity to Tania O x t mral E a A ay d i dio S MENO a f gt 0 a rB 2 y 2 d 2Exin t Pmass Tr n t m 6 7 20 3 kg Text Bx Em 3 142 F Hyp yr Hyve a po o pe PoaV t f 3 ka Text J E STFC Section 3 5 where Yext is the user defined external surface tesnion and h t V t Azy t is the instantenious hight of the MD box or MD box volume over area The VV and LFV flavours of the non isotropic Nos Hoover barostat and thermostat are im plemented in the DL POLY 4 routin

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