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THE DL-POLY-4 USER MANUAL

1. REVCON CONFIG CFGMIN REFERENCE OUTPUT E HISTORY HISTORF DEFECTS CONTROL STATIS FIELD OI RSDDAT l a TABLE 1 A O ka VAFDAT_ AG TABEAM fl A H BNDDAT BNDPMF BNDTAB TABBND ANGDAT ANGPMF ANGTAB TABANG DIHDAT DIHPMF DIHTAB TABDIH INVDAT INVPMF INVTAB TABINV RDFDAT VDWPMF VDWTAB REVOLD ZDNDAT REVIVE Figure 6 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 REFER ENCE 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 required only if the job represents a continuation of a previous job In the following sections we describe the form and content of these files 6 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 associate
2. 200 8 1 23 Test Case 45 and 46 Iron Cromium alloy with 2BEAM 200 8 1 24 Test Case 47 and 48 Hexane and methanol melts full atomistic and coarse grained SIMONE kts a te a a Bom ee AR A er wk Gee a ee ee 200 82 Benchmark Cases o sored f 08 46 a Pek es ba E ee a 200 Appendices 200 A DL_POLY_4 Dissipative Particle Dynamics 201 AL Introductorio td ac owe Re ea EO Ok eH Ke ee a a a aaa 201 A2 Ontline af Method lt ssp se madia ee a Re Ee HOR Ke k o ORR p oe EO OS 201 Avo Equation of state and dynamic properties iu e ges en eh eK eR ee we Ek a Oe ew 203 AA Derivation of Equilibrium 0 2444 444 bras OH RR HS GS ew SE Ye CES 204 A 5 Summary of Dissipative Particle Dynamics 0 6 6 sed a Dp ee ees 204 B DL_POLY 4 Periodic Boundary Conditions 205 Biull Titroduciio lt lt ita ee wl See eo Re oe wok a oe Ree ag ee oe ie ee 205 B 2 No periodic boundary incon is chi ac eaee de eet paa r ETa nakok 205 BS Cubie periodic boundaries ames 1 o ese eid e eeoe yee eS PEGE Eee FE GH 205 B 4 Orthorhombic periodic boundaries imcon 2 o eee eee eee 206 B 5 Parallelepiped periodic boundaries imcon 3 co ccoo e 206 BS Slab boundary conditions Gmeon 6 lt es aaa tes ae Rhee ea RS ee a 207 C DL POLY 4 Macros 208 D DL_POLY_4 Error Messages and User Action 212 E DL _POLY_ 4 README wisdom 262 Bal README GZs a 0 62 idad e a id ho de EASY 262 Ez README KIMSE be
3. n 22 buck Buckingham A p C U r A exp 2 bhm Born Huggins A Bi aj C D U r A exp B o r amp 2 Meyer hbnd 12 10 H bond A B U r 42 La snm Shifted force Eo n ro Tet U r one x n m 47 48 meter 1 nam 27 2 nmak r yro py Ba A US G J mors Morse Eo ro k U r Eo 1 exp k r ro 1 12 6 1 wca Shifted 49 Weeks e ot A U r 4e 5 He rij lt 25 y A Chandler Anderson U r Pij S 25 0o A 2 dpd Standard DPD A r U r 5 re i z Pe Groot Warren Ulri ETTE 1 07 1 12 Amoc A MOREE JA ro K om o 2 FF 14 7 pair Note in this formula the terms a 8 and y are compound expressions involving the variables Eo n m ro and re See Section 2 3 1 for further details Note All local potential cutoffs re default to the general van der Waals cutoff rvdw or the general domain decomposition cutoff rcut if unspecified or set to zero in the FIELD file Similarly if the specified value of rvdw and or rcut in CONTROL is found shorter than any of re including the WCA equivalent 26 o A values specified in FIELD then rvdw and or rcut will be reset by DL POLY 4 to the largest of all values Note A defaults to zero if A gt 0 5 or it is not specified in the FIELD file 156 STFC Section 6 1 Table 6 13 Metal Potential
4. 0 000 eee eee ens 184 7 1 4 Modifications for the Ewald Sum o 185 ToL Metal Potentials ae 2244086444 244004 ne awd bode ead eb eh ea ee 185 7 1 6 Tersoff Three Body and Four Body Potentials 0 00008 e 185 7 1 7 Globally Summed Properties s sa s sow as sa ie ia dtre oo ee 185 7 1 8 The Parallel DD tailored SHAKE and RATTLE Algorithms 186 7 1 9 The Parallel Rigid Body Implementation e 186 Ta POCE COJE sosesk as a a a Oe aos ad E a a ee ee 187 T2 Modularisation Principles 2 eee as aiia e a ba ee a aa e a EA 187 22 Wile Structure e s r oc doa e ra a a ee eee a 189 123 Module Files gt o cpat 8854400 aa a aea Ee eee e De a 192 24 General Files sa ao sanea e d piee e a a eR a a EP a EER 192 7 2 5 VV and LFV Specific Files 2 i4 04043545 R A 192 7 2 0 SERIAL Specife Files sos saa e ane 4 8 ba aa a ee Ra Re RS Ee 192 7 2 7 Comments on MPI Handling c oe 2 66544 66 824 a iea bie eee ee ee 192 7 2 8 Comments on SETUP_MODULE s os w esca bee ee eee 193 8 Examples 196 SL est Cases p 2h a ee wes ee ns Boe a ik ee a ee ee ee de e ee 197 8 1 1 Test Case 1 and 2 Sodium Chloride s s se oa ee es 197 S12 West Case 3 and 4 DPMO im Water ac sce oa oe ee ee Eke a 197 6 1 3 Test Case Dand 6 KNadigOs as e p o a wed be Be pia ee ee we Eee Ha d 197 8 1 4 Test Case 7 and 8 Gramicidin A molecules in Water 22 198 8 1 5 Test Case 9 and 10 SiC with Tersoff Potent
5. then which equates to OU Y 3V a OV rij doris 4 ae a 0D eee j gt i 1 ffi y Orij OV 1 35 T Tij 7 V 3 oV rij Wy S555 a 2 Tij i 1 Ai ij Opi _ y E y Opij rij Orig ig Tig me ov r ii o A OF pi 0F pj Opis ri Ya D En Op Ory i 1 Hi Pi y g 1 EAM virial The same as above 2 EEAM virial The same as above 3 2BEAM virial 2 127 2 128 N 1 pig rij z o F OV Ea Orij The same as above but with a second embedding contribution from the extra band complexity Y2 Ys 3 4 2BEEAM virial The same as above but with a second embedding contribution from the extra band complexity Y2 54 yg 5 Finnis Sinclair virial N N 1 Y 5 5 Xo Ari co Crrij Car i rij e c1 2czrij Tij i 1 j i N N 1 Af 1 ri dy Vo A 2 rij d 38 rija 2 129 2 A VPk PG d 6 Extended Finnis Sinclair virial 1 N N Y 3 5 5 Ari e co 4 C1Pij A car cari carij i 1 j i rij o cr 2C2T ij 3c3r Acarizi Tij 2 130 N N i A 1 1 Wa 2 5 rij d 4B rij d Tija eos Lethe 35 STFC Section 2 3 7 Sutton Chen virial n i TA Tij N N m 1 F F pj PS y i i 9 e 2 2 131 2 i jA 2 Opi Op Tij 8 Gupta virial X Ap Tij To Y exp p rij igo 0 N N 1 Bqij 1 Tij 1 Wo exp 2qi Tis 2 132 22 n Fat va or ta ey 9 Many body perturbation compon
6. 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 231 STFC Appendix D 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 po tential 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 152 error undefined direction passed to dpd_v_export This should never happen Action Report to authors Message 154 error outgoing transfer buffer size exceeded in dpd_v_export See notes on message 38 above Action See action notes on message 38 above Message 156 error incoming data transfer size e
7. OSTFC Section 2 2 interactions in DL_POLY_4 all core shell units tethered particles chemical bonds valence angles dihedral angles and inversion angles must be individually cited The same applies for bond constraints and PMF constraints The indices i 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 described 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
8. 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 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 as the character string timestep nstep integer the current time step 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 Treun real atomic mean temperature in Kelvin 6 2 3 The DEFECTS File The DEFECTS file is the dump file of atomic coordinates of defects see Section 6 1 4 Its principal use is for off line analysis The file is written by the subroutine DEFECTS WRITE The control variables for this file are ldef nsdef isdef and rdef which are created internally based on information read from the defects directive in the CONTROL file see Section 6 1 1 The DEFECTS file will be created only if the directive defects appears in the CONTROL file The
9. is performed This includes force generation and system dump REVCON and REVIVE and depending on the rest of the options may include velocity generation force capping application of the CGM minimiser application of the pseudo thermostat and dumps of HIS TORY 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 equilibration period or when a dry run steps 0 is performed i e equilibrate without any actual dynamics Note that the CGM search algorithm stepping uses a step that is proportional to the instantaneous value of the timestep and thus its usage in may lead to algorithm s instability and failure in the cases when optimisation is applied before any dynamics occurs in a model system in an unphysical state i e much away from equilibrium and or with an ill badly defined forcefield for the state Hence special care should be taken when the option is used as optimise or and in a dry run mode with a timestep value too large for the model system state 5 The variable timestep or also timest
10. 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 50 or energy 0 lt f lt 0 01 default f 0 005 or distance maximum absolute displacement in A 10 lt f lt 0 1 default f 0 005 the lowest string CGM minimised configuration during equilibration is saved in a file CFGMIN which has the same format as CONFIG write MSDTMP file containing particles individual y MSD in A and Tmean in Kelvin with controls i start timestep for dumping configurations default i 0 j timestep interval between configurations default 7 1 act exactly the same as ewald evaluate every n option above set FIQA iterations limit to n default n 100 set shake rattle iterations limit to n default n 250 129 OSTFC Section 6 1 mxstep f nfold i j k no elec no index no strict no topology no vafaveraging no vdw no vom optimise string f padding f rpad f pressure f set maximum timestep value in variable timestep control to f ps no default f 0 0 ps but if not opted sets to Huge 1 0 option to create matching CONFIG ij_k and FIELD _ij_k for a volumetr
11. 1 Thermostat Note 2Exin t changes inside u t exp x v t 3 102 2 Barostat Note Exin t and P t have changed and change inside nt exp xp S 10 1 At t Pox n t At e n t 4 hvo t 4 4 Pmass 2Ekin t 1 zeto 3 H f Pmass Pmass 1 At 1 n t 720 exp xo n t 720 1 At ith 4 ee 1 5 n t At 7 v t 3 103 1 At 1 n t 729 exp xo n t 749 78 STFC Section 3 5 At 4 Bve PU Pest y Pmass 2Erinlt 1 Rot f Pmass Pmass n 5 At E exp Xp F n t 4 At 1 1 t A PZA n t at A t 3 Thermostat Note Exin t has changed and changes inside u t exp x v t 3 104 4 VVI 3a e v4 LEE H t At exp at 340 At H i VIAS es exp ante 40 At V t 3 105 ESA Es ees Int At At ER E At 5 RATTLE_VV1 6 FF f t At fit R t At R t 3 106 READ e R t 7 VV2 u t At v t4 i 0 ae 3 107 8 RATTLE_VV2 9 Thermostat Note Exin t At has changed and changes inside u t At lt exp x u t At 3 108 10 Barostat Note Exin t At and P t At have changed and change inside mt 3At exp Xp 5 n t 4 5At At Pex HE AD 2 nt 5 las ie jve PERAD Sit 4 4 Pmass 2E Ent At 1 Rol f Pmass Pmass 3 At 3 nt At E exp Xp n t E At 3 3 At LAE E exp 5 n t TAC x u t At 3 109 79 STFC Section 3 5 3 At 3 n
12. 2 3 4 Three Body Potentials The three 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 19 hydrogen bond The potential forms available are as follows 1 Harmonic harm k U bjir Ojin 90 2 181 2 Truncated harmonic thrm k 2 88178 U 0jix Oir 00 expl ri rin P 2 182 3 Screened Harmonic shrm k 2 U Ojik z Ojik 00 exp rig p1 rik p2 2 183 4 Screened Vessal 37 bvs1 k 2 U Ojik Blan me f e T Ojik my x ju exp rij p1 Tik P2 2 184 5 Truncated Vessal 38 bvs2 U Oji k Orin Ojik 00 Ojik o Qn a a SU Oie 8o T 80 expl ri r e l 2 185 6 Dreiding hydrogen bond 19 hbnd U Ojik Dro cos 9x 5 Rno rjn 6 Rro rjr 2 186 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 po
13. Po d qu 49 0 Lo P j s ga a za Wg l 3 197 P2 2 B do q Ly Wy P3 q3 0Q2 q1 40 Izz Wz and quaternion torques as defined by Yo go 4 2 83 0 Y B 1982 q3 qa Ta 3 198 Y d 23 do q Ty T3 d 2 a 4 Ta 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 E p t T 3 199 OSTFC Section 3 6 Next a sequence of operations is applied to the quaternions and the quaternion momenta in the order cils 5t 2 giLr dt 2 gilr Bt giLa 8t 2 gilo 8t 2 3 200 which preserves the symplecticness of the operations see reference 32 Note that t is some submultiple of At In DL_POLY 4 the default is At 100t The operators themselves are of the following kind eX y cos C dt q sin Cr0t Pr q e t p cos dt p sin Cx0t Pe p 3 201 where Pk is a permutation operator with k 0 3 with the following properties Po q do q1 92 43 Piq do 43 42 3 202 Pq 42 43 do q P q 1 43 42 41 do gt and the angular velocity Cx is defined as l r p P f 3 203 k I kq Equations 3 200 3 202 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 t
14. a reut 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 ceed zero in CONTROL the system temperature not mutually exclusive but if temp has to pro 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 134 STFC Section 6 1 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 may give default values if necessary Some but not all 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 and equilibration directives have a default of zero If not used or used with their de fault values a dry run
15. but will abort if delpot gt dlrvdw The potential and force tables are used to fill the internal arrays vvdw and gvdw respectively see Sec tion 2 3 1 The contents of force arrays are derived from the potential via the formula G r r U r 6 13 or Note this is not the same as the true force During simulation interactions beyond distance cutpot are discarded 6 1 7 The TABEAM File The TABEAM file contains the tabulated potential functions no explicit analytic form describing the EAM or EEAM metal interactions in the MD system This file is read by the subroutine METAL_TABLE_READ see Chapter 7 6 1 7 1 The TABEAM File Format The file is free formatted but blank and commented lines are not allowed 6 1 7 2 Definitions of Variables record 1 header al00 file header record 2 numpot integer number of potential functions in file For an n component alloy numpot is e n n 5 2 for the EAM potential or e 3n n 1 2 for the EEAM potential or 165 STFC Section 6 1 e n n 4 for the 2BEAM potential or e 5n n 1 2 for the 2BEEAM potential The subsequent records for an n component alloy define n n 1 2 cross pair potential functions pairs keyword and e EAM n embedding functions one for each atom type embedding keyword n electron density functions one for each atom type density keyword e EEAM n embedding functions one for each atom type and n for the EEAM potential one
16. c kJ mol for k Joules per mol d Kelvin Boltzmann for Kelvin per Boltzmann 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 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 Molecular details It is important for the user to understand that there is an organisational 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 where n is an integer specifying the number of different types of molecule appearing in t
17. lt exp x t 74 3 n t 74 1 A v t e exp n 7At v t 3 145 1 1 At 1 nt qo exp x t 1 3 n t At 1 1 At 3 P t Poxt V t n t At n t At P e 1 V 2 2 4 4 Pmass 1 1 At 1 nt 54t oa exp x t At 3 nt 54t 3 Thermostat Note Exin t has changed and changes inside At 2Evin t Pmass M t 3At 20 kp Text dmass 3 1 x t At lt x t At 4 86 STFC Section 3 5 v t exp x t SAt A v t 3 146 1 At 2Ekin t Pmass n t At 20 kp Tox E E ee E ae 1 Pmass nE gAt 20 ke Tor 2 8 8 mass 4 VVI 1 At f t u t At tE a m H t At e a t At At H i Viera E cao At At V t 3 147 1 EPA e exp nl t ZAt At x t Bolt At w t 540 Bolt 5 RATTLE_VV1 6 FF f t At f t 3 148 7 VV2 t At E v t4 at 4 a aa 3 149 8 RATTLE_VV2 9 Thermostat Note Exin t At has changed and changes inside At 2Epin t At Pmass n t 4At 20 kg Text 8 mass 5 1 x t At x t 54t f EA E exp wick 2 At A u t At 3 150 At 2E gin t At Pmass n t 5At 20 kp Text 8 dmass 3 5 x t FAt E xt A8 10 Barostat Note Exin t At and P t At have changed and change inside 1 3 At 1 nt 3At exp x t FAL n At 3 1 At 3 P t At Pot V t At nt TAt e ntzat ias pets 3 3 At 3 n 746 exp x
18. re col bei gt H er dei 2 7 2 176 ij Tik The contribution to be added to the atomic virial can be derived as Ww gy Pueri e TAR aus a ee 2 177 i in O 7 Oui OU sn ria fitre fu 5 py 2 Tij Fee ra i j l i Al e ters 19 3 03 folris fatrij Y 5 folris falris rij i jfi Or E folrij falrizj Xij 1 Bj ro Bi ce x 2 178 S wik g Gijk eon fe ra re kAi j e hiks Ww 55 L e eee g e es A i jt Orij 23 19 1J ari ij ij ij 8 E q folrij Farag Xij 1 7 f Ls 2 179 XO wik ra ole y feltru 05 B rij ra Fel ra l kHi j The contribution to be added to the atomic stress tensor is given by oF pe fh 2 180 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 Section 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 N where N is the number of particles makes it essential that these terms are calculated by the link cell method 62 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 44 OSTFC Section 2 3
19. 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 186 STFC Section 7 2 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 sharing 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 circu
20. 2 The version number or date of production 3 A brief description of the function of the subroutine Aa A copyright statement Elsewhere FORTRAN90 comment cards are used liberally 1 3 6 FORTRAN 90 Parameters and Arithmetic Precision All global parameters defined by the FORTRAN90 parameter statements are specified in the module file SETUP_MODULE which is included at compilation time in all subroutines requiring the parameters All parameters specified in SETUP MODULE are described by one or more comment cards One super global parameter is defined at compilation time in the KINDS_F90 module file specifying 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 allow that and then change the default in KINDS_F90 Changing the precision to anything else that is allowed by the FORTRAN90 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 7 Units Internally all DL_POLY_4 subroutines and functions assume the use of the following defined molecular units e The unit of time to is 1 x 1072 seconds i e picoseconds e The unit of length lo is 1 x 107 metres i e Angstroms e The unit of mass
21. 2 gt tmej ma Zrs HR Zone pull out Sel eee k ta Cae Le Nee eae ema Fem Liebe glob AZ Seige SS zrs HR Zone pull in eh re k Sin me ES eis ne H osel Osc Electric Field Ez Ey E wina F q E sin 2rwt Kkcal mol gt DL_POLY 418 4 kkJ mol DL_POLY 100 0 6 11 kx Bolttz gt DL POLY 0 831451115 kpL_POLY DL_POLY 1 0 Obviously for eV units 1 12 x 10 Huno nue e RRN kunit gt DL_POLY kev gt DL POLY 9648 530821 6 12 H eV the FIELD file should be amended to read UNITS eV external magnetic 0 1 1 07564305 162 H MKS 1 07564305 OSTFC Section 6 1 6 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 6 1 4 The REFERENCE File The REFERENCE has the same format and structure as CONFIG see Section 6 1 2 file with the exception that imcon MUST BE 4 0 REFERENCE may contain more or less particles than CONFIG does and may have particles with identities that are not defined in FIELD see Section 6 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 6 1 5 The REVOLD File This file contains statistics arrays from a previous job It is not required if the cur
22. Action See action notes on message 1001 above Message 1022 error allocation failure in vdw_module gt allocate_vdw_arrays See notes on message 1001 above Action See action notes on message 1001 above Message 1023 error allocation failure in metal_module gt allocate_metal_arrays See notes on message 1001 above Action See action notes on message 1001 above 254 STFC Appendix D Message 1024 error allocation failure in three_body_module gt allocate_three_body_arrays See notes on message 1001 above Action See action notes on message 1001 above Message 1025 error allocation failure in config module gt allocate_config_arrays See notes on message 1001 above Action See action notes on message 1001 above Message 1026 error allocation failure in site module gt allocate_site_arrays See notes on message 1001 above Action See action notes on message 1001 above Message 1027 error allocation failure in tersoff_ module gt alocate_tersoff_arrays See notes on message 1001 above Action See action notes on message 1001 above Message 1028 error deallocation failure in angles module gt deallocate_angles_arrays See notes on message 1002 above Action See action notes on message 1002 above Message 1029 error deallocation failure in bonds_module gt deallocate_bonds_arrays See notes on message 100
23. Atom atom and site site coulombic forces c Metal metal local density dependent forces ee Tersoff local density dependent forces for hydro carbons 17 Three body valence angle and hydrogen bond forces O f g Ion core shell polarasation pax ZS Four body inversion forces Do as p Tether forces i Chemical bond forces j k I Valence angle forces oo Dihedral angle and improper dihedral angle forces Inversion angle forces External field forces m The computed forces are accumulated in atomic force arrays f independently on each processor The force arrays are used to update the atomic velocities and positions of all the atoms in the domain Any atom which effectively moves from one domain to another is relocated to the neighbouring 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 through the DD partitioning of the simulated system Note that this will only work efficiently if the density of the system is reasonably uniform THERE ARE NO LOAD BALANCING ALGORITHMS IN DL_POLY_4 TO COMPENSATE FOR A BAD DENSITY DISTRIBUTION 7 1 2 Distributing the Intramolecular Bonded Terms The intramolecular terms in DL_POLY_4 are managed through bookkeeping arrays which list all atoms
24. Compass stretch bend 40 stbe U Ojik A Ojik 00 rig r 2 26 12 Compass all terms 40 cmps U Ojik A rig rij Tik THe Ojik 00 B rig ri C rik 7 2 27 13 AMOEBA force field angle 36 amoe U Ojik k Ojik 00 1 1 4 107 0jix 90 5 6 10 O in 90 7 0 1077 bjir 00 2 2 1075 bjir 90 2 28 14 KKY 41 kky U Ojik fr sin 2 0jix 00 Ku Kir 1 eS exp rij Ta 2 29 15 Tabulated potential tab The potential is defined numerically in TABANG see Section 4 3 and Section 6 1 8 In these formulae 0 is the angle between bond vectors r and rz Fs Pa a Ojik cos zta 2 30 Tijfik In DL POLY 4 the most general form for the valence angle potentials can be written as U Ojik Tijs Trik AO S rij Sr S rik 2 31 where A 0 is a purely angular function and S r is a screening or truncation function All the function arguments are scalars With this reduction the force on an atom derived from the valence angle potential is given by E o ff 7 U Ojik Tij Tik Tjk gt 2 32 with atomic label being one of i j k and a indicating the x y z component The derivative is 0 o grg V Oii Tij Tik Tjk S rij S Tik S rik or A jik ri 19 A Ojik S rik S 15 Se bei S rij Tij Ori ro 0 A Ojik S rig S rin Cex dei S rip Tik OF ik
25. FF f t At Ef f t 3 128 5 VV2 At fl An 1 t t At v t At v t 5 At ae a 3 129 6 RATTLE VV2 7 Thermostat At o 1 2 UTA f E 7 TT at At 1 Ut At vit At x 3 130 83 STFC Section 3 5 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 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 1 FF f t f t At 3 131 2 LFV The iterative part is as follows u t wat u t gt At At za x t r t At e nt r t At o t Tat 3 132 H t At nt Hit V t At n t V t 3 SHAKE 4 Full step velocity O Ec Ah alts o 3 133 a Del 2 2 5 Thermostat i At g 172 KU h y TT Cac 1 eae 6 Barostat R 10 1 Poa PE 3 135 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_BO_vv and NPT_BO_LFV respectively The routines NPT_B1_VV and NPT_B1_LFV implement the sa
26. Internal Ensemble Key keyens meaning 0 Microcanonical ensemble NVE 1 Evans NVT ensemble NVExin 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 NaT ensemble 32 Nos Hoover NoT ensemble 33 Martyna Tuckerman Klein NaT ensemble 9 The zero directive enables a zero temperature optimisation The target temperature of the simu 136 STFC Section 6 1 10 11 lation is reset to 10 Kelvin and a crude energy minimiser 0 iaf a FOF vi f 20 i 5N 4 is used to help the system relax before each integration 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 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 p
27. OSTFC Section 6 2 atmnam al0 atomic label from CONFIG iatm integer atom index from CONFIG ratm real atom displacement from its position att 0 record b XXX real x coordinate yyy real y coordinate ZZZ real z coordinate 6 2 5 The CFGMIN File The CFGMIN file only appears if the user has selected the programmed minimisation option directive minimise or optimise in the CONTROL file Its contents have the same format as the CONFIG file see Section 6 1 2 but contains only atomic position data and will never contain either velocity or force data i e parameter levcfg is always zero In addition 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 minimised configuration expressed in DL_POLY_4 units Section 1 3 7 and 3 the configuration energy of the initial structure expressed in DL POLY_4 units Section 1 3 7 6 2 6 The OUTPUT File The job output consists of 7 sections Header Simulation control specifications Force field specification System specification Summary of the initial configuration Simulation progress Sample of the final configu ration 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 P
28. RATTLE VV2 7 Thermostat VV2 Liult At f t At ia 2 Ekin t At v t At v t At exp xetan 3 29 66 STFC Section 3 4 The algorithm is self 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 e Ft At 3 30 2 LFV The iterative part is as follows At 2 At scale 1 x t scale v W 1 scale f 2 scale scale 1 1 t u t At scale v u t At scale f 0 3 31 m 1 r t At r t At u t At 3 SHAKE 4 Full step velocity u t gt u t At v t 4 5At 3 32 5 Thermostat Vi vilt f t xO to 3 33 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 implement 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 Brownian dynamics such that drj t _ dt
29. See action notes on message 1001 above Message 1073 error allocation failure See notes on message 1001 above Action See action notes on message 1001 above Message 1074 error allocation failure See notes on message 1001 above Action See action notes on message 1001 above Message 1075 error allocation failure See notes on message 1001 above Action See action notes on message 1001 above Message 1076 error allocation failure See notes on message 1001 above Action See action notes on message 1001 above Message 1077 error allocation failure See notes on message 1001 above Action See action notes on message 1001 above Message 1078 error allocation failure See notes on message 1001 above Action See action notes on message 1001 above in bonds_module allocate_bond_pot_arrays in bonds_module allocate_bond_dst_arrays in angles_module allocate_angl pot_arrays in angles_module allocate_angl_dst_arrays in dihedrals_module allocate_dihd_pot_arrays in dihedrals_module allocate_dihd_dst_arrays in inversions_module allocate_invr_pot_arrays 260 STFC Appendix D Message 1079 error allocation failure in inversions_module allocate_invr_dst_arrays See notes on message 1001 above Action See action notes on message 1001 above Message 1080 error allocation failure in greenkubo_module allocate_greenkub
30. The ratio of these two properties the Schmidt number Sc v D is therefore 1 2 412 Si Te A 15 2 70875kpT and for values of the drag coefficient and density frequently used in DPD simulations this value is of the order of unity which is an appropriate magnitude for gases but three orders of magnitude too small for liquids 203 STFC Appendix A This property of standard DPD does not rule it out for simulations of liquid phases except when hydrody namics are important It may also be argued that the self diffusion of DPD particles might not correspond to that of individual molecules and thus a Schmidt number of the order 10 is unnecessary for modelling liq uids 96 Alternative thermostats are available in the DL_MESO 97 http www ccp5 ac uk DL_MESO package which can model systems with higher Schmidt numbers 98 99 A 4 Derivation of Equilibrium The derivation of the DPD algorithm is based on the Fokker Planck equation Op En Lp A 16 where p is the equilibrium distribution function and is the evolution operator which may be split into conservative and stochastic dissipative parts N A 17 with DE Al yee 2o A 18 N 2 Oo 2 O R D _ ao O S Re SPa J3 2 a L 2 8 Op 5 w rij Cij E a yw es 2 f A 19 where a When o y 0 then equation A 16 becomes Op CP _ pc A2 HEP A 20 for which the equilibrium solution is evidently ezo l 3 2 A 21
31. 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 radial distribution function data file Z density distribution data file velocity autocorrelation function data files one file for each species and a statistical history file 6 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 6 1 1 The HISTORY file will be created only if the directive traj appears in the CONTROL file The HISTORY file can become very large especially if it is formatted For serious simulation work it is recommended that the file be written to a scratch disk capable of accommodating a large data file Alternatively the file may be written in netCDF format instead of in ASCIT users must change ensure this functionality is available
32. and Daw M S 1986 Chem Phys Lett 33 7983 4 31 Finnis M W and Sinclair J E 1984 Philos Mag A 50 45 4 31 32 Sutton A P and Chen J 1990 Philos Mag Lett 61 139 4 32 Rafii Tabar H and Sutton A P 1991 Philos Mag Lett 63 217 4 32 40 Todd B D and Lynden Bell R M 1993 Surf Science 281 191 4 32 Tersoff J 1989 Phys Rev B 39 5566 4 41 183 van Gunsteren W F and Berendsen H J C 1987 Groningen Molecular Simulation GROMOS Library Manual BIOMOS Nijenborgh 9747 Ag Groningen The Netherlands Standard GROMOS reference 4 12 Mayo S L Olafson B D and Goddard W A 1990 J Phys Chem 94 8897 4 12 45 160 Weiner S J Kollman P A Nguyen D T and Case D A 1986 J Comp Chem 7 230 4 12 Smith W 2003 Daresbury Laboratory 4 10 106 115 116 117 144 208 Allen M P and Tildesley D J 1989 Computer Simulation of Liquids Oxford Clarendon Press 5 50 60 62 65 182 184 Andersen H C 1983 J Comput Phys 52 24 5 63 182 277 STFC Bibliography 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 5l 52 Fincham D 1992 Molecular Simulation 8 165 5 96 Miller T F Eleftheriou M Pattnaik P Ndirango A Newns D and Martyna G M 2002 J Chem Phys 116 8649 5 96 Evans D J and Morriss G
33. cos Dijk es BARS y 0 GH y E o bi 05 dd Cay Bon O ri TijWkn Tij kn Sa S 2 asap ek dei as fe Tij kn gn Tiz Tik Eg ae WE Ti k hee x he re Sek dei 2 2 f rij Dig One rij Tik 7 rij Do Tik DE VUknTik Tik Tin ty E N a ro Sen dp 2 es A kn Lij Lin LT in iow UknTin Tin Tews Dx F i ro den Sei 2 7 f rij iUn Oen rij Lin ti Oe Ein WEJ UknTin an 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 Tik and rin are obtained by the cyclic permutation of the indices in the manner described above All these force contributions must be added to the final atomic forces Formally the contribution to be added to the atomic virial is given by W D rE 2 69 STFC Section 2 2 However it is possible to show by thermodynamic arguments cf 42 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 co
34. one by imposing that the MD cell change isotropically in the x y plane which leads to the following changes in the equations above raat welt Tuy E j2 L Yext hz t V t x t Naa t a b 2 y 3 164 rin T t Hyp y 0T Hyve 4 a A i E Bnl Pox V t f 2 ke Text J x s ds The VV and LFV flavours of the non isotropic Nos Hoover barostat and thermostat are implemented in the DL_POLY 4 routines 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 90 STFC Section 3 5 3 5 5 Martyna Tuckerman Klein Barostat DL_POLY_4 includes the Martyna Tuckerman Klein MTK interpretation of the VV flavoured Nos Hoover algorithms 32 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 3 142 to Ex NO su fs 143 no ew x t 2 Ewin t Pree EP 20 kB Text mass Lar 3 165 Pmass f 3 kp Text Tp CH 1050 Ev BOVA and the anisotropic cell change case equations 3 157 to d gO ult n r Tr n t fy vo ney O a d 2 Ein t Pmass Tr n t n t 20 a kp Ted ar y or mass 207 3 166 daft Pat VOL 2Egin t 1 qt 7 Pmass 7 Pmass xne Pmass Ves kp
35. 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 2 Every atom site in the simulated system is assigned a unique global index number from 1 to N Every processor maintains a list of the local indices of the atoms in its domain This is the local atom list 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 Every intramolecular bonded term Utype in the system has a unique index number itype 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 On each processor a pointer array keytype Ntype itype Carries the indices of the specific atoms involved in the potential term labelled itype The dimension Ntype 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 NpmF unit o 2 1 for a PMF constraint unit or 1 0 1 NRB unit for a rigid body unit 183 STFC Section 7 1 6 Using the key a
36. v t A LO ai PN where x is the user defined constant positive in units of ps7 specifying the thermostat friction parameter and R t is stochastic force with zero mean that satisfies the fluctuation dissipation theorem REO RL 2 x mi keT y s 11 3 35 where superscripts denote Cartesian indices subscripts particle indices kg is the Boltzmann constant 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 2x mi kgT by y 74 67 STFC Section 3 4 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 76 1 VVI vlt e e v t a 2 T VZ XM EBT 2 0 At 3 36 1 xA V2 kgT RA e E zo At v t Al e exp yx At u t
37. yu Wea fa Tra X Cab Ubea y u Wea i The X Tap Uea Y U Wed 2 76 f SPE gt where Wed W and Weg W q Wed The virial contribution Vatea u is given by Vabcalu 2Au 4Bu 2 77 and the stress tensor contribution oS u by u y u LO 2 78 In DL_POLY_4 the calcite forces are handled by the routine INVERSIONS_FORCES which is a convenient intramolecular four body force routine However it is manifestly not an inversion potential as such 2 2 10 Inversional Restraints In DL_POLY_4 the inversional restraints in which the inversion angle as defined by a quadruplet of atoms is maintained around some preset value Hp is handled as a special case of inversion potential As a consequence angle restraints may be applied only between atoms in the same molecule Unlike with application of the pure dihedral 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 torsional restraints although they have different key words 1 Harmonic hrm 2 Harmonic cosine hcs 3 Planar potential pln 4 Extended planar potential xpl 5 Tabulated potential tab The potential is defined numerically in TABINV see Section 4 3 and Section 6 1 8 In DL_POLY_4 inversional restraints are handled by the routine INVERSIONS_FORCES 2 2 11 Tethering
38. 0 PRINT ANY DEFINED INTER RDF gt VDW INTRA bonded MOLECULAR PDF ANALYSIS print analysis RDF amp Z DENSITY binsize 0 05 Angstroms rdf T steps print rdf zden T steps print zden EXECUTION TIME job time 1000 seconds close time 10 seconds FINISH finish 6 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 124 STFC Section 6 1 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 identification of the file e The last record is a finish directive which marks the end of the input data Between the header and the finish directive a wide choice of control directives may be inserted These are described below 6 1 1 2 The CONTROL File Directives The directives available are as follows directive meaning analyse all sampling every f nbins n rmax r calculate and collect all intra
39. 2 directories indicates UNIX file directories ROUTINES indicates subroutines functions and programs macros indicates a macro file of UNIX commands directive indicates directives or keywords variables indicates named variables and parameters FILE indicates filenames iv Contents THE DL POLY_4 USER MANUAL a About DLPOE A see to i ee Gee Ee 4 ak ee ce Be we BA ee ae BE A i Disclaimer soe 2b ebb edbiaeae eed Geees SEER ESE eS SY Eee Ee eed AER EES ii Acknowledgements s o soono daor toai moe ioe OR ee OEE HA RD eG iii Manual Notation s 24 4 ak ace a ee eG A be Bae ee A A ee ee a ee iv Contents v List of Tables xii List of Figures xiii 0 Quick Word INSTALL amp RUN 1 1 Introduction 2 ii The DL POLY Package 20 34 4 eiaa dende al aa a e a a A 3 12 Functionality oca eoa pa saa ed eno ae ma aa A RS aE a wee ER 3 12 1 Molecular Systeme 00 2 ama o ER a E eh ew E a 3 LoD Forca Field i o a e a cd ee EG a a aae e e d ae aga a A 4 1 23 Boundary Conditions s s saias seios e iaa aaa ee PERG a a a 4 1 24 Jaya Graphical User Interface ss s scsi pu ea ok e dla aok enia ee ee a 4 125 Algorithms s e seose a abep hw ae a eee ee a ae ee oes 5 1 2 6 DL POLY Classic features incompatible or unavalable in DL POLY 4 5 LS Prosramimine SINO i5 a ans shee we Gok RR A SR A a 6 lol Programming Language cap s desgarros ee ke ee G 6 1 3 2 Modularisation and Intent se s ea caa danaa iea Ee ee E
40. 2 241 8 X Piston xpis P 5 P Area L X direction Wh A 2 242 a Mk 9 Harmonic restraint zone in z direction zres A Zeit E Zaz gt Zcom gt maz F 2 243 e A nia E Acom gt Zeom S Zmin 5 where Zcom is the chosen molecule centre of mass 10 Harmonic restraint zone in z direction pull out zrs A z na EZ aa gt a 2 F 2 244 E l A min z BLR S Cae acl Zmin 2 11 Harmonic restraint zone in z direction pull in zrs A z ri ana Z gt max F 2 245 A Coane z gt Z lt Zmin l 12 Oscillating electric field osel F F qi E sin 2rwt 2 246 where t is the simulated time 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 and X piston fields may only be used with orthorhombic cell geometry imcon 1 2 and Continuous shear field with slab cell geometry imcon 6 In the case of the X piston field it is strongly advised that the number of piston particles is chosen to be very small in comparison with the rest of the system lt 5 and that the piston contains its own set of whole molecules i e there are no molecules partially mapped on the piston which do not include any core shell CB PMF or RB units The field releases the system s centre of mass to move unconstrained and gain momentum This makes
41. 217 and bx u ee o v EE 2 218 xb w 2r 7 me 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 65 for electrically non neutral MD cells which prevents the build up of a charged background and the introduction of extra pressure due to it 3Strictly speaking the real space sum ranges over all periodic images of the simulation cell but in the DL POLY_4 imple mentation 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 ol STFC Section 2 4 In practice the convergence of the Ewald sum is controlled by three variables the real space cutoff reut the convergence parameter a and the largest reciprocal space vector kmar used in the reciprocal space sum These are discussed more fully in Section 5 3 5 DL_POLY_4 can provide estimates if requested see CONTROL file description 6 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 66 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 reciprocal space terms By means of an interpolation procedure involving
42. 22 2 Distance Restraints s ss sass pda geba na Bee OE ERE Ee eee Va aS 15 22 3 Valence Angle Potentials lt 0 24 2 oe ed by aaoi eo A A a 15 224A Angular Restraints e s sss 6484446 048 be de edo a ee SED 18 2 2 5 Dihedral Angle Potentials 2 0 2 ee 19 2 2 6 Improper Dihedral Angle Potentials 0200000022 eae 21 22 7 Torsional Restraints 2 2 4 spa Gou 44 245 a eb deeb a ee ba ee 22 2 2 8 Inversion Angle Potentials o oc cecco ee ee 23 22 9 The Calcite Four Body Potential eu see foe adut e dice Pe eee ek a aks 25 2 2 10 Inversional Restraints s lt c a so see ee ee ee 26 220 Tetberino Forces o g ens ER Bk aog E a eee ESE OES 26 2 3 The Intermolecular Potential Pumcetions s os garip sea gow woe a oe ee eS 27 2 3 1 Short Ranged van der Waals Potentials 27 2 3 2 Metal Potentials e o s soc mo aaia bea bed en bee a bee dea Hee LS 31 2 38 Werseir Potentials s r dora e fo OR ee oe ee eek A ee oe 41 234 Three Body Potentials soria ae he EU e e eH Re Res 45 23 0 Four Body Potentials ccoo os a bebe aaa a a RE Ew EE EES 46 2 4 Long Ranged Electrostatic coulombic Potentials o o 46 2 4 1 Direct Coulomb Sumi ss sss abra a ee BE Dae a eS 47 24 2 Force Shifted Coulomb SUM s s a c a sde crios essa a a 05 T SG ee a 47 2 4 3 Coulomb Sum with Distance Dependent Dielectric 48 24A Reaction Field o oaos 06 4 44 2428 ds nee Gee as ORG Ses
43. 6 1 index 3 k integer third atomic site index index 4 1 integer fourth atomic site index variable 1 real first potential parameter see Table 6 10 variable 2 real second potential parameter see Table 6 10 variable 3 real third potential parameter see Table 6 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 6 10 variable 7 real fifth potential parameter see Table 6 10 The meaning of the variables 1 3 6 7 is given in Table 6 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 6 10 Dihedral Angle Potentials key potential type Variables 1 3 6 7 functional formt cos Cosine Al m U p A 1 cos m 6 harm Harmonic k o U k 6 boy hcos Harmonic cosine k do U p k cos cos o cos3 Triple cosine A Ag Az U 6 3 41 1 cos 4 Az 1 cos 2 A3 1 cos 3 ryck Ryckaert Bellemans 43 A U A a b cos c cos p d cos e cos f cos rbf Fluorinated Ryckaert A U A a b cos c cos p Bellemans 44 d cos e cos
44. 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 implementations 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 7 as a tensor 7 and extending the Langevin pressure variable R to a stochastic Langevin tensor Rp Rp Rpt 2 Xp Pmass kgT bij olt E y 3 115 which is drawn from Gaussian distribution of zero mean and unit variance Gauss 0 1 scaled by y kg 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 modifi cations as now the equations with 7 are extended to matrix forms d qe vt nt re df t R t Tr n qt nz TX 1 n t F 1 v t d a t Pex V t 1 2Erin t 1 Rp Tnt o ymt 3 116 al Pmass f Pmass pl Pmass _ f 3 kp Text Pmass 2 3 27 xp d
45. BB AB BA pij Tig Apr Tig Apr Tag F ig ri pt ry pt ray pt ri A rj 2 154 e FS case here a different rule applies 15 ri Hr ri 2 155 so that atoms of type A and B contribute the same densities to each other but not to atoms of the same type 40 OSTFC Section 2 3 The above rules have the following consequences to the specifications of these potentials in the DL_POLY_4 FIELD file for an alloy composed of n different metal atom types both the EAM types and FS types of potentials require the specification of n n 1 2 pair functions Vee rij However the its only the simple EAM type together with all the FS types that require only n density functions Pag ri whereas the EEAM class requires all the cross functions pig rig possible or n in total In addition to the n n 1 2 pair functions and n or n density functions both the EAM and EEAM potentials require further specification of n functional forms of the density dependence i e the embedding function F p in equation 2 110 The matter is further complicated when the 2BEAM type of potential is used with the extra specification of n embedding functions and n n 1 2 density functions for the s band Similarly in the 2BEEAM an extra n embedding functions and n density functions for the s band are required It is worth noting that in the 2BEAM and 2BEEAM the s band contribution is usually only for the alloy component so that local con
46. CONTROL file 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 Probably due to negligence or numerical inaccuracy inaccuracy in generation of big supercell from a small one Action Make sure lattice parameters and particle coordinates marry each other Increase accuracy when generating a supercell Message 514 error allowed image conventions are 0 1 2 3 and 6 DL_POLY_4 has found unsupported boundary condition specified in CONFIG Action Correct your boundary condition or consider using DL_POLY Classic Message 515 error rattle algorithm constraints_rattle failed to converge The RATTLE algorithm for bond constraints is iterative If the maximum number of permitted 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 directive 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 245 STFC Appendix D Message 517 error allowed configuratio
47. 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 to NPT simulations only 235 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 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
48. Chandler Anderson WCA potential 49 wca 4 12 b 6 l N 1 U rij a 5 lara PE 2 AA EA 2 94 0 Tij gt 25 o 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 combi nation with the FENE equation 2 10 bond potential This implementation allows for a radius shift of up to half a A lt 0 5 o with a default of zero Age faut 0 10 Standard DPD potential dpd 2 A O oe aes Ur 2 1 52 S 2 95 i 0 Tij 2 Te It takes the Groot Warren 50 form giving a soft and purely repulsive interaction 28 OSTFC Section 2 3 11 AMOEBA force field 14 7 pair potential 36 amoe 1 07 7 1 12 lc an 2 e 12 Tabulation tab The potential is defined numerically only The parameters defining these potentials are supplied to DL POLY 4 at run time see the description of the FIELD file in Section 6 1 3 Each atom type in the system is specified by a unique eight character label defined by the user The pair potential is then defined internally by the combination of two atom labels As well as the numerical parameters defining the potentials DL POLY_4 should also be provided with a cutoff radius Tydw Which sets a range limit on the computation of the interactions It is worth noting that some interaction come with a hard wired cutoff in their parameter
49. 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 6 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 you want the job to run The second file you need is the CONFIG file Section 6 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 6 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 6 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 6 1 7 which contains metal potential arrays for non analytic or too complex functional forms and or a sixth file REFERENCE Section 6 1 4 which is similar to the CONFIG file and contains the perfect crystalline structure of the system Examples of input files are found in the data sub directory which can be copied into the execute subdirectory using
50. 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 Appendix 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 108 STFC Section 5 2 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 comm
51. E 0 0o exp r 13 p9 thm shrm Screened harmonic k 00 pr pe U 0 0 bo exp rij p1 riz p2 shm bvs1 Screened Vessal 37 k 00 pi pe U 0 T 6o my 0 my x bv1 exp rij p1 ix P2 bvs2 Truncated Vessal 38 k a p U 0 k 0 00 0 0 bo 27 bv2 3m 00 m expl ri Hre hcos Harmonic Cosine k o U 6 E cos 9 cos 9p hcs cos Cosine Alm U 0 A 1 cos m 0 COS mmsb MM3 stretch bend 39 A 00 r 75 U 0 A 0 0o rij r rik TH msb stst Compass 40 AF Tik U 0 A rij r3 rik Tik sts stretch stretch stbe Compass 40 A bo ri U 0 A 0 00 rij r stb stretch bend cmps Compass 40 A B C 0 U 0 A rij r3 rik TH 0 00 x cmp all terms Tip ak B rij r C rik Tip amoe AMOEBA 36 k 0 U 0 k A 1 1 4 1072A 5 6 1075A amo FF angle 7 0 1077A 2 2 10784A4 A 0 bo kky KKY 36 fe Oo Ge To U 0 fk sin 2 0 00 Kij Kik kky Kij 1 exp gr rij ro 10 is the i j k angle Note valence angle potentials with a dash as the first character of the keyword do not contribute to the excluded atoms list see Section 2 In this case DL POLY_4 will calculate the non bonded pair potentials between the described atoms 152 OSTFC Section
52. EEA RoHS EAS 163 6 1 6 The TABLE File socorrista ee eee SEE EES 164 OLI The TABBAM Pile sp aa a ds Pa ek ae TA eee a ds a 165 6 18 The TABBND TABANG TABDIH amp TABINV Files o 167 62 The OUTPUT Files siria rss a a ds aa OS 168 621 The HISTORY Pile ss dore AE A a a dt a aaa 168 6 2 2 The MSDTMP Pile i a s ce b da eee eee hee eh eae ee Pe ee ee 170 6 2 3 The DEFECTS File i ganesa isso 42 45 4 24S Heda Saga hee eS 170 6 2 4 The RSDDAT File 2 0 cee e is aai 172 O25 The CEGMIN File s se 244 4 2 pa ee ee Dee ble eee wD ees Pees 173 6 2 6 The OUTPUT Pile so ba 422 ee Geek Pa ee Ree ea be GS ee EES 173 G27 The REVCON Pile a ah rie beh ho bw RE eB Gh Se eee oe ee eS 176 628 The REVIVE Pile o s 22 4 eck ee hoe ma eS ee A r ek ba ee eG Se a 176 6 2 9 The RDEDAT Files s e684 rs a 4 ena ey Shee aaa aha BES ae Se GH 177 STFC Contents 6 2 10 The ZDNDAT File 4 4 cs 28564 4 244 4 be hed ke a POE Lo eS 177 6 2 11 The VAEDAT Files 4 44 4 94 moare SS ee a Re Be ig 178 6 2 12 The INTDAT INTPMF INTTAB Files o e e e 178 6219 The STATIS Pile 000 saoe is da eR a SR ee 179 7 The DL_POLY_4 Parallelisation and Source Code 181 fol Parallelisation is ls Rs er Es A A we a 182 7 1 1 The Domain Decomposition Strategy o 182 7 1 2 Distributing the Intramolecular Bonded Terms 2 000000 6 183 7 1 3 Distributing the Non bonded Terms
53. Forces DL POLY 4 also allows atomic sites to be tethered to a fixed point in space r 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 26 OSTFC Section 2 3 1 Harmonic harm U rij k rio 2 79 2 Restrained harmonic rhrm 1 2 5k rio e Irala Vig ve lt 0 Me eed 2 80 ri Ler krero re rol gt re coe 3 Quartic potential quar k 2 k 3 k 4 U rij 5 rio rio rio 2 81 2 3 4 as in each case rjg is the distance between the atom positions at moment t tl and t 0 The force on the atom 7 arising from a tether potential potential is obtained using the general formula 1 a Gs E ES Uri Tio 2 82 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 tar 2 84 where a and p indicate the x y z components The atomic stress tensor derived in
54. Geigy VAt pee te x wis 4g eig 2VigkBT wry seig V At 4 Y vj ome 2 ka T wiry Geis At es x vig eige VPiGkBT weai vA as the Shardlow operator where is the random number with zero mean and unit variance unique for every unique pair ij in the system and Wri w rij is the DPD conservative force switching function 3 95 76 STFC Section 3 5 in equation A 4 yij is the drag coefficient between the types of particles 7 and j U vj Y is the inter particle relative velocity and e r rij is the inter particle unit vector kg and T are the Boltzmann constant and the system target temperature If we define the velocity Verlet microcsannonical NVE ensemble sequence as NVE t At then Shardlow s first S1 and second S2 order splittings can be written algorithmically as the following sequential operators applications Sl S At gt NVE t At S2 S At 2 gt NVE t At gt S At 2 3 96 The application of these DPD thermostats are implemented in the DL_POLY_4 routine DPD_THERMOSTAT and which only applies as a perturbation around the NVE integrator incorporating both particle and 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 Pext and or isotropic stress tensor a DL POLY_4 has four such algorithms the Langevi
55. 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 114 STFC Section 5 3 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 Classic User Manual Many of these have been incorporated into the DL_POLY GUI 21 and may be conveniently used from there 5 3 1 Inorganic Materials The utility GENLAT can be used to construct the CONFIG file for relatively simple lattice structures Input is interactive The FIELD file for such systems are normally small and can be constructed by hand Otherwise the input of force field data for crystalline systems is particularly simple if no angular forces are required notable exceptions to this are zeolites and silicate glasses see below Such systems require only the specification of the atomic types and the necessary pair forces The reader is referred to the description of the DL_POLY 4 FIELD file for further details Section 6 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 ar
56. It is then a safe choice to assign a shell mass x m so that Veore she11 gt 3 Vrigia ion The user must make sure to assign the correct mass 1 x m to the core 2 5 2 Relaxed Massless Shells Model The relaxed shell model is presented in 68 where shells have no mass and as such their motion is not governed by the usual Newtonian equation whereas their cores motion is Because of that shells respond instantaneously to the motion of the cores for any set of core positions the positions of the shells are such that the force on every shell is zero The energy is thus a minimum with respect to the shell positions This represents the physical fact that the system is always in the ground state with respect to the electronic degrees of freedom 54 OSTFC Section 2 6 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 69 in an adaptation as shown in 68 Each time step a few iterations 1030 are needed to achieve convergence to zero net force 2 5 3 Breathing Shell Model Extension While for low symmetry structures the conventional dipolar rigid shell model RSM is sufficient to absorb most of the effects of partial covalency ionic polarisation for some high symmetry systems a breathing shell model BSM 70 is used as a refinement to represent the contrib
57. 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 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 domain topol ogy when bonded like interactions exist by RELOCATE_PARTICLES O N PINYA e Iterative bond and PMF constraint solvers CONSTRAINTS_SHAKE_VV CONSTRAINTS_RATTLE_VV CONSTRAINTS_SHAKE_LFV and PMF_SHAKE_VV PMF_RATTLE_VV PMF_SHAKE_LFV O N PINT where N 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 5 1 5 2 Performance may also affected by the fluctuations in the inter node communication due to unavoidable 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 5 3 A Guide to Preparing
58. 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 244 STFC Appendix D Message 510 error duplicate entry for a density function detected in TABEAM A duplicate density function entry is detected 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 512 error non definable vdw dpd interactions detected in FIELD A VDW corss interaction was uncpecified and recovering it by using a mixing rule proved impossible due to type difference of the single species potentials Action Rethink your FIELD file interactions before restarting the job with a new compatible FIELD and possibly
59. OSTFC Section 5 2 a In the case of rigid bodies atomic forces are resolved into molecular forces and torques The torques are subsequently transformed into an equivalent set of atomic forces which are perpen dicular 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 displace ment 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 minimisa tion This is not normally recommended as a means to incorporate constraints in minimisation procedures as it leads to ill conditioning However if the constraints in the original structure are satisfied we find that provided only small atomic displacements are allowed during relaxation it is possible to converge to a minimum energy structure Furthermore provided the harmonic springs are stiff enough it is possible afterwards to satisfy the constraints exactly by further optimising the structure using the stiff springs alone without having a significant affect on the overall system energy c Systems with independent constraint bonds and rigid bodies may also be minimised by these methods 3 Of the t
60. P 1984 Computer Physics Reports 1 297 5 62 65 Adelman S A and Doll J D 1976 J Chem Phys 64 2375 5 62 65 Andersen H C 1979 J Chem Phys 72 2384 5 62 65 Berendsen H J C Postma J P M van Gunsteren W F DiNola A and Haak J R 1984 J Chem Phys 81 3684 5 62 65 77 Hoover W G 1985 Phys Rev A31 1695 5 62 65 72 74 77 Quigley D and Probert M I J 2004 J Chem Phys 120 11432 5 62 77 Martyna G M Tuckerman M E Tobias D J and Klein M L 1996 Molec Phys 87 1117 5 62 77 91 97 Warner H R J 1972 ind Eng Chem Fundam 11 379 14 151 Bird R B e a 1977 Dynamics of Polymeric Liquids volume 1 and 2 Wiley New York 14 151 Grest G S and Kremer K 1986 Phys Rev A 33 3628 14 151 Ponder J W Wu C Ren P Pande V S Chodera J D Schnieders M J Haque I Mobley D L Lambrecht D S DiStasio Jr R A Head Gordon M Clark G N I Johnson M E and Head Gordon T 2010 J Phys Chem B 114 2549 2564 14 15 17 19 29 151 152 156 Vessal B 1994 J Non Cryst Solids 177 103 16 18 45 152 160 Smith W Greaves G N and Gillan M J 1995 J Chem Phys 103 3091 16 18 45 152 160 Allinger N L Yuh Y H and Lii J H 1998 J Am Chem Soc 111 8551 16 18 152 Sun H 1998 J Phys Chem B 102 38 7338 7364 17 18 19 152 Kumagai N Kawamura K a
61. 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 action notes on message 515 below Message 480 error PMF constraint length gt minimum of all half cell widths The specified PMF length has exceeded the minimum of all half cell widths Action Specify shorter PMF length or increase MD cell dimensions Message 484 error only one potential of mean force permitted Only one potential of mean force is permitted in FIELD Action Correct the erroneous entries in FIELD Message 486 error only one of the PMF units is permitted to have frozen atoms Only one of the PMF units is permitted to have frozen atoms Action Correct the erroneous entries in FIELD Message 488 error too many PMF constraints per domain This should not happen Action Is the use of PMF constraints in your system physically sound Message 490 error local PMF constraint not found locally This should not happen Action Is your system physically sound is your system equilibrated Message 492 error a diameter of a PMF unit gt minimum of all half cell widths The diameter of a PMF unit has exceeded the minimum of all half cell widths Action Consider the physical concept you are trying to imply in the simulation Increase MD cell dimens
62. Software will be used only for Academic Purposes as defined in the Licence Agree ment e you will acknowledge the use of DL_POLY_4 when publishing any data obtained with its assistance by including the following reference I T Todorov W Smith K Trachenko amp M T Dove J Mater Chem 16 1911 1918 2006 e the information given on the Registration Form is true and e you agree to your personal data being used for the purpose of managing your institution s licence of the DL_POLY_4 Software including contacting you to tell you about changes to and error corrections for that software and generally about the software which becomes a contractual agreement between the Licensee and STFC STFC is an executive Non Departmental Public Body established as a Research Council by Royal Charter under the Science and Technology Act 1965 Its address for this agreement is the Daresbury Laboratory Keckwick Lane Warrington WA4 4AD Cheshire United Kingdom and its VAT number is GB 618 3673 25 If you wish to contact STFC about the Licence Agreement or the DL_POLY_4 Software please contact me Dr LT Todorov by emailing to ilian todorov stfc ac uk F 2 The full version LICENCE AGREEMENT PLEASE READ THE LICENCE BELOW COMPLETE THE REGISTRATION INFORMATION 269 STFC Appendix F AND ACCEPT THE TERMS OF THE LICENCE IN ORDER TO DOWNLOAD THE SOFTWARE BY CLICKING ACCEPT AND DOWNLOADING THE SOFTWARE YOU ARE CONFIRMING YOUR INTEN
63. TE ve 7 At bolt Lat At ies Dag qs OEA 3 155 2 2 5 Thermostat and Barostat 2_ 9 x t 5At x t At At 2 Ein t Pmass n t 20 kB Text mass 1 1 t Pox n t 54 exp x t At n t At At aa LV 1 1 1 x e 5 xa SA x t z 3 156 1 1 1 nt gt ht 5 t 540 OSTFC 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 Nos Hoover barostat and thermostat are implemented in the DL_POLY_4 routines NPT_HO_VvV 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 Et w t n t elt Bolt fut EL ko 1000 000 a 2Erin t Pmass Tr n t n t 20 3 kg Text a 7 Giese Umass 207 3 157 zo DATE onto Pmass res kB Text Th TUO nt HO EV TO VO where is the stress tensor equation 3 98 and 1 is the identity ma
64. Text T2 TUO 10 500 EV TO VO The changes include one extra dependence to the velocity and barostat equations and removal of the centre of mass variable R t dependence in the position equation The modifications in for the VV couched algorithms are of the following sort At P t Por QE Kin t 1 n t At nF Bve 3 Pmass 1 At v t exp 14 Z a a S vl f Pmass 3 167 1 1 r t At exp nt Al At r t At v t A 91 STFC Section 3 5 for the isotropic cell fluctuations case and w LO V t 1 2Byin t 1 1 Pmass f Pmass IS v t 3 168 u t exp a t Tat Te nt 40 gt 1 1 r t At exp nt Al At r t At v t 944 for the anisotropic cell fluctuations case Similarly for the LFV couched algorithms these are nt Zt exp x H At nE At PO Pos 2Banlt 1 At av t 3 l Pmass Pmass 1 1 f t 3 wet At E ut ZA At E fx 5 no 70 3 169 r t At r t At u t At n t 4 3At r t 3A8 for the isotropic cell fluctuations case and n t 5At e exp x t At nt F At ee Pext V t t 2Ekin t 1 Pmass f Pmass v t 4 Lat v t Tat At an ko 1 n t eit i 0 3 170 r t At r t At u t sat u t sat r t 50 for the anisotropic cell fluctuations case This ensemble is optionally extending to constant normal pressure and constant surface area NP AT 7
65. Z kgT 3i i l which is of course the Boltzmann distribution function for an equilibrium system Thus it is apparent that for the simulation based on equation A 16 to maintain the same distribution function the terms in the operator LEP of equation A 19 must sum to zero It follows that the conditions given in equations A 7 and A 8 must apply A 5 Summary of Dissipative Particle Dynamics DPD is a simple method that can be viewed as a novel thermostatting method for molecular dynamics All that is required is a system of spherical particles enclosed in a periodic box undergoing time evolution as a result of the above forces It should be noted that all computed interactions are pairwise which means that the principle of the conservation of momentum in the system or Galilean invariance is preserved The conservation of momentum is required for the preservation of hydrodynamic forces Therefore the DPD method is an NVT method that preserves hydrodynamics The presence of hydrodynamics is important in annealing defects in ordered mesophases 100 Thus DPD has an intrinsic advantage over other methods such as traditional molecular dynamics dynamic density functional theory which are purely diffusive or Monte Carlo methods in trying to evolve a system towards an ordered thermodynamic equilibrium state 204 Appendix B DL _POLY 4 Periodic Boundary Conditions B 1 Introduction DL POLY 4 is designed to accommodate a number of differe
66. a fora x ee a sud 2 167 and from the third angular term e ters 0 folris farina a Vis felriy falry xij x 1 i eee es 0 3 1 g Ai 2 gin pm na 2 168 where r ara ij T a Wik fe rik g 0 i ik A 2 169 Ore ro gt j The angular term can have three different contributions depending on the index of the particle par ticipating in the interaction o 0 f be me Wik a 05 r gra oi folrik ga od wl o o L j Ta D wik fo rik Bra Oise 2 170 are kAi j Or Aig oa Wie tan lft uo e kihs o folry fali vi folrij falrij x Ny 1 10 m 1 LH ce oe ali 2 171 where y Ora ij a a y Vik Tij Tik folrik g Oijk 2 172 UL ti It is worth noting that the derivative of wik O te re ra arg T 04 Pi Ti rip 1 Wik Sej Ovi E dex di k 2 173 Or Tij Tik now has three different contributions depending on the index of the particle participating in the interaction Hence the angular term s derivative is more elaborate to express than the one in the ters case 43 STFC Section 2 3 The derivative of g 0 1 is worked out in the following manner o Og 9 5 1 o z Tik a 0 arg ijk olijk sin ijk Or Tij Tik 2 174 where Og ijk e 2 c hj COS Dijk sin Dijk OO ijk 7 de h COS bijk O eer ik rij ora a 505 Oi E Sex 0 2 rg TijTik Tijfik Tijfik 2 175
67. above Action See action notes on message 1001 above Message 1006 error deallocation failure in comms_module gt grsum_vector See notes on message 1002 above Action See action notes on message 1002 above Message 1007 error allocation failure in comms_module gt gimax_vector See notes on message 1001 above Action See action notes on message 1001 above Message 1008 error deallocation failure in comms_module gt gimax_vector See notes on message 1002 above Action See action notes on message 1002 above Message 1009 error allocation failure in comms_module gt grmax_vector See notes on message 1001 above 252 STFC Appendix D Action See action notes on message 1001 above Message 1010 error deallocation failure in comms_module gt grmax_vector See notes on message 1002 above Action See action notes on message 1002 above Message 1011 error allocation failure in parse_module gt get_record See notes on message 1001 above Action See action notes on message 1001 above Message 1012 error deallocation failure in parse_module gt get_record See notes on message 1002 above Action See action notes on message 1002 above Message 1013 error allocation failure in angles_module gt allocate_angles_arrays See notes on message 1001 above Action See action notes on message 1001 above Messa
68. 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 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 140 STFC Section 6 1 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 maximum number of particles that the reading 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 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 th
69. algorithm 5 60 121 FIQA 5 96 NOSQUISH 5 96 RATTLE 5 63 64 182 186 245 SHAKE 5 62 64 182 186 228 Verlet 5 30 60 64 184 186 Verlet neighbour list 184 AMBER 4 12 116 angular momentum 94 angular restraints 19 barostat 5 97 126 127 240 Berendsen 83 Nos Hoover 85 91 boundary conditions 4 46 205 cubic 144 CCP5 3 9 constraints bond 3 5 13 62 64 65 93 94 148 174 183 184 186 218 223 228 245 Gaussian 50 51 65 PMF 13 65 149 175 183 direct Coulomb sum 46 48 125 139 distance dependant dielectric 48 49 126 139 distance restraints 15 dlpoly2 5 DPD 65 Dreiding 12 ensemble 5 236 Andersen NVT 5 62 136 Berendsen NoT 5 62 127 136 Berendsen NPT 5 62 126 136 Berendsen NVT 5 62 126 136 canonical 65 DPD 126 DPD NVT 62 Evans NVT 5 62 126 136 Gentle Stochastic NVT 62 126 Langevin NoT 5 62 127 136 Langevin NPT 5 62 126 136 Langevin NVT 5 62 126 136 Martyna Tuckerman Klein NoT 136 Martyna Tuckerman Klein NoT 5 62 127 136 Martyna Tuckerman Klein NPT 5 62 127 136 microcanonical see ensemble NVE Nos Hoover NoT 5 62 127 136 Nos Hoover NPT 5 62 127 136 Nos Hoover NVT 5 62 126 136 NVE 5 62 65 126 136 equations of motion Euler 57 95 rigid body 95 error messages 119 212 Ewald optimisation 117 118 SPME 52 117 127 128 132 139 summation 50 51 109 117 135 139 182 185 23
70. and rigid bodies In the case of rigid bodies the atomic forces are resolved into molecular forces and torques These matters are discussed in greater 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 functions 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 U rig 5k rig ro 2 2 2 Morse potential mors U rij Eol 1 exp k rig ro 1 2 3 U r 2 4 ij ij 13 3 12 6 potential bond 12 6 STFC Section 2 2 Aya a ij 4 a a ee 2 O e 5 Restrained harmonic rhrm 1 2 Li rig ro e eis U r 2 1 o ij ol Se 2 6 riz skr2 kre riy Tol re ri Tol gt re 2 6 4 Lennard Jones potential 1j 6 Quartic potential quar k U rij zru ro tag ro Horia fo 2 7 7 Buckingham potential buck 8 Coulomb potential coul
71. are no excluded atoms arising from the four body terms The inclusion of other potentials for example pair potentials may in fact be essential to maintain the structure of the system The four body potentials are very short ranged typically of order 3 A This property plus the fact that four body potentials scale as N4 where N is the number of particles makes it essential that these terms are calculated by the link cell method 62 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 All of these can be used in conjunction with the shell model technique used to account for ions polarisation The SPME technique is restricted to periodic systems only Users must exercise care when using pseudo periodic boundary conditions The other techniques can be used with either periodic or non periodic systems safely although in the case of the direct Coulomb sum there are likely to be problems with conver
72. 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 6 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 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 You can also extend a simulation beyond its initia
73. atoms are updated through the usual Verlet algorithm without regard to the bond constraints 5 In the second iterative stage of the algorithms each processor calculates the incremental correction vectors for the bonded atoms in its own list of bond constraints It then sends specific correction vectors to all neighbours that share the same atoms using the information compiled in step 3 6 When all necessary correction vectors have been received and added the positions of the constrained atoms are corrected 7 Steps 5 and 6 are repeated until the bond constraints are converged 8 Finally the change in the atom positions from the previous time step is used to calculate the atomic velocities 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 processor to another In this respect DD SHAKE and DD RATTLE resemble every other intramolecular term Since the allocation of constraints is based purely on geometric considerations it is not practical to arrange for a strict load balancing of the DD SHAKE and DD RATTLE algorithms For many systems however this deficiency has little practical impact on performance 7 1 9 The Parallel Rigid Body Implementation The essentials of the DD tailored RB algorithms see Section 3 6 are as follows
74. by the Licensee as a result STFC will not be liable to the Licensee to the extent that any loss or damage is caused by the Licensee s failure to implement or the Licensee s delay in implementing any correction or advice in in relation to the DL_POLY_4 Software that STFC has made available on the DL_POLY_4 Website or by the Licensee s failure to acquire a licence of and to implement any new release or version of the DL_POLY_4 Software that would have remedied or mitigated the effects of any error defect bug or deficiency in the DL_POLY_4 Software The Licensee acknowledges that proper use of the DL_POLY_4 Software and any Derived Work is dependent on the Licensee its employees and students exercising proper skill and care in inputting data and interpreting the output provided by the DL_POLY_4 Software or that Derived Work STFC will not be liable for the consequences of decisions taken by the Licensee or any other person on the basis of that output STFC does not accept any responsibility for any use which may be made by the Licensee of that output nor for any reliance which may be placed on that output nor for advice or information given in connection with that output Subject to clause 3 7 STFC s liability or any breach of this Licence Agreement any negligence or arising in any other way out of the subject matter of this Licence Agreement or the use of the DL_POLY_4 Software will not extend to any incidental or consequent
75. cell in the specified direction and kmax is an integer For a relative error of 4 x 107 this means using kmar Y 6 2 a kmax is then kmax gt 6 4 L Teut 5 8 In a cubic system reut 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 reut 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 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 Note that one needs to specify the three integers kmaxa kmaxb kmaxc referring to the three spatial directions to en
76. complex B splines the sum in reciprocal space is represented on a three dimensional rectangular grid In this form the Fast Fourier Transform FFT may be used to perform the primary mathematical operation which is a 3D convolution The efficiency of these procedures greatly reduces the cost of the reciprocal space sum when the range of k vectors is large The method briefly is as follows for full details see 66 1 Interpolation of the exp i k r terms Sal here for one dimension exp 27i ujk L b k Mn u exp 2ri k K 2 219 j gt in which k is the integer index of the k vector in a principal direction K is the total number of grid points in the same direction and uj is the fractional coordinate of ion j scaled by a factor K i e uj Ks 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 X Mn 1 exp 2ri ke K 2 220 0 2 Approximation of the structure factor S k S k b1 k1 b2 k2 b3 k3 QU ki ka k3 2 221 where Q1 k1 k2 k3 is the discrete Fourier transform of the charge array Q 1 2 3 defined as N Q 41 L2 3 Soy 5 Mprluij 4 niLa x Mn u2 lo n2La x j 1 n1 n2 n3 M uz 3 n3L3 2 222 in which the sum
77. core shell interaction is described by a harmonic spring potential of the form 1 Uli 5 hors gt 2 228 However sometimes an anharmonic spring is used described by a quartic form l 2 lp 4 Uspring ia zE gei 2 229 Normally in practice k2 is much larger than k4 53 STFC Section 2 5 The effect of an external electric field E is to separate the core and shell by a distance d qsE k2 2 230 giving rise to a polarisation dipole eyed 2 231 The condition of static equilibrium then gives the polarisability as a q kz 2 232 where qs is the shell charge and k is the force constant of the harmonic spring The calculation of the forces virial and stress tensor in this model is based on that for a diatomic molecule with charged atoms The part coming from the spring potential is similar in spirit as for chemical bonds equations 2 13 2 15 while the electrostatics is as described in the above section 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 equation 3 11 2 5 1 Dynamical Adiabatic Shells Shell Model The dynamical shell model is a method of incorporating polarisability into a molecular dynamics simulation The method used in DL_POLY
78. 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 mxbfsh in SET_BOUNDS recompile and resubmit Contact DL_POLY_4 au thors if the problem persists Message 116 error incorrect atom transfer in update_shared_units An atom has become misplaced during transfer between nodes Action 229 STFC Appendix D This happens when the simulation is very numerically unstable Consider carefully the physical grounds of your simulation i e are you using the adiabatic shell model for accounting polarisation with too big a timestep or too large control distances for the variable timestep is the ensemble type NPT or NoT and the system target temperature too close to the melting temperature Message 118 error construction error in pass_shared_units This should not happen Action Report to authors 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
79. current timestep i e for each atom in the system the following data are included record a atmnam a8 iatm integer weight real charge real rsd real record b XXX real yyy real ZZZ real record c only for keytrj gt 0 VXX real vyy real VZZ real record d only for keytrj gt 1 fxx real fyy real fzz real atomic label atom index atomic mass a m u atomic charge e displacement from position at t 0 A x coordinate y coordinate z coordinate x component of velocity y component of velocity z component of velocity x component of force y component of force z component of force Thus the data for each atom is a minimum of two records and a maximum of 4 169 STFC Section 6 2 6 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 1msd nstmsd istmsd which are created internally based on information read from the msdtmp directive in the CONTROL file see Section 6 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
80. defined by a header record and a set of data records with the potential like and force like tables empty record id record info a25 information to follow string atom 1 a8 first atom type atom 2 a8 second atom type atom 3 a8 third atom type only available in ANG files atom 4 a8 forth atom type only available in DIH amp INV files index integer unique index of PDF in file instances integer instances of this unique type of PDF interaction data records 1 bins abscissa real consecutive value over the full cutoff range in A for BNDTAB amp VDWTAB and degrees for ANGTAB DIHTAB amp INVTAB potential real potential at the abscissa grid point in units as specified in FIELD force real complementary force virial for BNDTAB VDWTAB value 6 2 13 The STATIS File The file is formatted with integers as i10 and reals as el4 6 It is written by the subroutine STATIS TICS_COLLECT It consists of two header records followed by many data records of statistical data record 1 cfgname a72 configuration name record 2 string a8 energy units Data records Subsequent lines contain the instantaneous values of statistical variables dumped from the array stpval A specified number of entries of stpval are written in the format 1p 5e14 6 The number of array elements required determined by the parameter mxnstk in the SETUP MODULE file is mxnstk gt 27 ntpatm number of unique atomic sites 9 stress tensor eleme
81. described in Chapter 8 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 45 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 C 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 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 rou
82. distance dependent dielectric Standard truncated Coulomb sum Force shifted Coulomb sum 10 Reaction field electrostatics ant N o ewald evaluate or multiple are not mutually exclusive and it is the first instance of these in CON TROL 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 139 STFC Section 6 1 20 21 22 23 24 25 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 a reut the universal cutoff set by cutoff It applies to the real space part of the electrostatics calculations and to the van der Waals potentials if no other cutoff is applied b Tydw 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 Secti
83. enforce any benefit conferred by this Licence 275 STFC Appendix F 6 8 Agreement unless this Licence Agreement expressly provides otherwise Governing law This Licence Agreement is governed by and is to be construed in accordance with English law The English Courts will have exclusive jurisdiction to deal with any dispute which has arisen or may arise out of or in connection with this Licence Agreement except that STFC may bring proceedings against the Licensee or for an injunction in any jurisdiction 276 Bibliography 10 11 12 13 14 15 16 17 18 19 20 21 22 23 Smith W and Forester T R 1996 J Molec Graphics 14 136 3 Todorov I T and Smith W 2004 Phil Trans R Soc Lond A 362 1835 3 182 Todorov I T Smith W Trachenko K and Dove M T 2006 J Mater Chem 16 1611 1618 3 182 Smith W 1987 Molecular Graphics 5 71 3 Smith W 1991 Comput Phys Commun 62 229 3 5 182 Smith W 1993 Theoretica Chim Acta 84 385 3 5 182 Smith W and Forester T R 1994 Comput Phys Commun 79 52 3 Smith W and Forester T R 1994 Comput Phys Commun 79 63 3 5 64 Pinches M R S Tildesley D and Smith W 1991 Molecular Simulation 6 51 3 5 182 Rapaport D C 1991 Comput Phys Commun 62 217 3 5 182 Daw M S and Baskes M I 1984 Phys Rev B 29 6443 4 31 Foiles S M Baskes M I
84. f cos g exp h 7 opls OPLS torsion Ao Ar Ag U Ao 4 41 1 cos po Az do Ag 1 cos 2 0 Az 1 cos 3 0 to is 12 the i j k l dihedral angle inversions n where n is the number of inversion interactions present in the molecule Each of the following n records contains inversion key ad potential key see Table 6 11 index 1 i integer first atomic site index central site index 2 j integer second atomic site index index 3 k integer third atomic site index index 4 1 integer fourth atomic site index variable 1 real potential parameter see Table 6 11 153 OSTFC Section 6 1 variable 2 real variable 3 real The meaning of the variables 1 2 is given in Table 6 11 potential parameter see Table 6 11 potential parameter see Table 6 11 This directive and associated data records need not be specified if the molecule contains no inversion angle terms See the note on the atomic indices appearing under the shell directive above Table 6 11 Inversion Angle Potentials key potential type Variables 1 3 functional form harm Harmonic hcos Harmonic cosine plan Planar xpln Extended planar calc Calcite k po po Qo U 6 do U cos cos o U A 1 cos U 1 cos m o U u Au But t is th
85. for dumping defects configurations 125 OSTFC Section 6 1 delr f rpad 4f densvar f distance displacements i j f dump n ensemble ensemble ensemble ensemble ensemble ensemble ensemble ensemble ensemble ensemble nve nvt evans nvt langevin f nvt andersen fi fa nvt berendesen f nvt hoover f nvt gst f f2 nvt dpdtype y npt langevin fi f2 npt berendsen fi fa 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 reut 3 lt f lt Min 3 5 rcut 2 A DL_POLY Classic Verlet shell strip cutoff option is iterpreted by DL_POLY 4 as the padding rpad f 4 option so that Tpad gets set to Max rpaa faelr 4 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 forces using Coulomb sum with distance dependent dielectric write displacements trajectory file RSDDAT with controls i start timestep for dumping displacements configurations default i 0 j timestep interval between configurations default 7 1 f displacement qualifying cutoff default f 0 15 A set restart data dump interval to n steps default n 1000 select NVE ensemble default ensemble select NVEkin ensemble type Evans with Gau
86. found in the execute sub directory Lastly DL_POLY_4 may also create the files RDFDAT ZDNDAT MSDTMP RSDDAT and DEFECTS containing the RDF Z density individual means square displacement and temperature RSD and defects data respectively They are all human readable files 5 2 3 Parallel I O Many users that have suffered loss of data in the OUTPUT especially running in parallel and when an error occurs on parallel architectures In such circumstances the OUTPUT may be empty or incomplete despite being clear that the actual simulation has progressed well beyond what has been printed in OUTPUT Ultimately this is due to OS s I O buffers not being flushed as a default by the particular OS when certain kind of errors occurs especially MPI related The safest way to avoid loss of information in such circumstances is to write the OUTPUT data to the default output channel the screen There is an easy 110 OSTFC Section 5 2 way to do this in DL_POLY_4 which is to use the l_scr keyword in the CONTROL file The batch daemon will then place the output in the standard output file which can then be of use to the user or alternatively on many batch systems the output can be redirected into another file allowing an easier following of the job progress over time This latter technique is also useful on interactive systems where simply printing to the screen could lead to large amounts of output However such situations could be easily av
87. 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 6 2 6 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 reut 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 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 da
88. fr and f are the repulsive and attractive pair potential respectively fr rij Aij exp ai rij falrij Bij exp bij rij 2 157 and fc is a smooth cutoff function with parameters R and S so chosen that to include the first neighbor shell e ters 1 Tij lt Rij ij Rij folri 3 5 cos x po 3 Rij lt Trij lt Sij 2 158 0 gt Tij gt Sij e kihs here fc is modified to a have continuous second order differential 1 2 Tij lt Rij ij Rig ij Rij folry gt 2 cos x ae cos 37 A o Rig lt Tij lt Sij 2 159 0 Tij gt Sij Jij expresses a dependence that can accentuate or diminish the attractive force relative to the repulsive force according to the local environment such that 41 STFC Section 2 3 e ters oe Vig Xij 1 Bi LEY m Li Y folrik wik oie 2 160 k i j 2 ce es ee a i a jk ll d de h COS Orito Je e kihs vw 1 L Wik A AN Lig Y folrix g 0 jn exp aitri rin k i j g 05x Cri Go Fijk Ga Fijx 2 161 a Ca hi cos bije go bijr E Cai hi COS Orie Ga Gijk 1 cai exp csi h cos Ga 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 rj rik and the bond angle Oijk between them with respect to the central atom i The function g has a minimum for h cos 0 x
89. gence 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 6 1 1 46 STFC Section 2 4 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_Classic 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 o U ry _ 2 190 ATEDE Tij with ge the charge on an atom labelled and rj the magnitude of the separation vector r r f The force on an atom j derived from this force is 1 Gig a 2 191 j 4rege ri ag with the force on atom 1 the negative of this The contribution to the atomic virial is 1 1 ee 2 192 ATEQE Tij which is simply the negative of the potential term The contribution to be added to the atomic stress tensor is gol rote 2 193 wh
90. gt deallocate_pmf_arrays See notes on message 1002 above Action See action notes on message 1002 above 256 STFC Appendix D Message 1038 error allocation failure in minimise_module gt allocate_minimise_arrays See notes on message 1001 above Action See action notes on message 1001 above Message 1039 error deallocation failure in minimise_module gt deallocate_minimise_arrays See notes on message 1002 above Action See action notes on message 1002 above Message 1040 error allocation failure in ewald_module gt ewald_allocate_kall_arrays See notes on message 1001 above Action See action notes on message 1001 above Message 1041 error allocation failure in langevin_module gt langevin_allocate_arrays See notes on message 1001 above Action See action notes on message 1001 above Message 1042 error allocation failure in rigid_bodies_module gt allocate_rigid_bodies_arrays See notes on message 1001 above Action See action notes on message 1001 above Message 1043 error deallocation failure in rigid_bodies_module gt deallocate_rigid_bodies_arrays See notes on message 1002 above Action See action notes on message 1002 above Message 1044 error allocation failure in comms_module gt gimin_vector See notes on message 1001 above Action See action notes on message 1001 above 257 STFC Append
91. histogram In addition to the PDF s DL_POLY_4 also calculates the respective PMF s and pairwise force dependencies virial for bonds which are stored in the PMF and upon resampling onto a bin edge grid TAB files It is important to note that unlike the PMF files containing the bare In PDF data converted to the requested energy units on the same grid as the PDF histograms the force field data in TAB files are resampled onto max Nmin Ntap grid points located at the bin edges as expected by DL POLY_4 when reading the potential and force tables where Niap is the grid number for the respective intramolecular unit type read in from its TAB file if provided otherwise Niap 0 Thus the TAB files obey the DL POLY_4 format for numerically defined intramolecular force field tables TAB see below and hence can be directly used as such upon renaming BNDTAB gt TABBND ANGTAB gt TABANG DIHTAB gt TABDIH and INVTAB gt TABINV The user is however strongly advised to check the quality of the obtained tabulated force fields before using those as input for a CG simulation Albeit DL_POLY_4 uses a simple smoothing algorithm for noise reduction in PMF s and implements capping of the forces in the regions of zero valued PDF s in undersampled regions the PDF and PMF data are likely to suffer from 102 STFC Section 4 3 inaccuracy and increased noise which most often require extra attention and re fitting manually The ge
92. in a physically meaningful way 94 OSTFC Section 3 6 where d is the displacement vector of the atom j from the COM and is given by di 1y E 3 183 The rigid body angular velocity w is the scalar product of the moment of inertia I inverse and the angular momentum J E 3 184 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 1 is diagonal and the components satisfy Ip gt yy gt Izz In this local frame the so called Principal Frame the inertia tensor is therefore constant The orientation of the local body frame with respect to the space fixed frame is described via a four dimensional unit vector the quaternion q go q1 92 qa 3 185 and the rotational matrix R to transform from the local body frame to the space fixed frame is the unitary matrix R 2 q q2 qo g3 G R E B 2 q2q3 qoq 3 186 2 q 93 40 92 2 9 43 g0090 dG 4 so that if dj is the position of an atom in the local body frame with respect to its COM its position in the universal frame w r t its COM is given by d R d 3 187 PET 2 q q2 qo q3 2 q1 q3
93. interacting via the Coulomb potential The Ewald method 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 50 STFC Section 2 4 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 modifications 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 Gau
94. 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_POLY_4 will begin closing down too early How large the close time needs to 135 STFC Section 6 1 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 specified 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 nosca
95. key potential type Variables 1 5 6 9 functional form eam EAM tabulated potential eeam EEAM tabulated potential 2bea 2BEAM tabulated potential 2bee 2BEEAM tabulated potential fnsc Finnis Sinclair cg ci co c A U r 2 D Cu 0 co 4 C1Tij car AYDi ee ANS d 6 m ry dy 4 puna j i exfs Extended co ci ca c3 c4 Us r 1 2 ra c co errig cari Cari cari Finnis Sinclair c Afd B AE gt p Y ri d B rij d Al stch Sutton Chen eja n m c Ui r e 5 0 e pi 5 p gt 5 iA j i gupt Gupta Alrol p B qij Uilr de O rig ue B P JAA 2 exp 2 a na mbpc MBPC e a mj o to Us r 5 p 3 1 erf a rij ro ph Note that the parameters a and ro must be the same for all defined potentials of this type DL _POLY_4 will set Max 0 ap and ro Max 0 Yo pq for all defined interactions of this type between species p and q If after this any is left undefined i e zero the undefined entities will be set to their defaults a 20 and ro Min 1 5 0 2 reut Note that rdf and vdw met are not complementary i e if the former is used in FIELD none of the pairs defined by the latter will be considered for RDF calculations The selected RDFs are calculated in the RDF_COLLECT RDF_EXCL_COLLECT RDF_FRZN_COLLECT and RDF_COMPUTE by collecting distance information from all two body pairs as encountered i
96. 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 mx1shp alternatively increase it by hand in SET_BOUNDS and recompile and resubmit 227 STFC Appendix D 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 iterations is exceeded the program terminates Possible causes include a bad starting configuration too large
97. number of interstitials is always equal to the total number of defects The displacements option will trigger dump of atom displacements based on a qualifying cutoff in a trajectory like manner Dsiplacemets of atoms from their original position at the end of equilibration the start of statistics 0 is carried out at each timestep 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 6 4 for an explanation of this variable Note that all these options with the exception of the last no elec are mutually exclusive Table 6 4 Electrostatics Key keyfce meaning Electrostatics are evaluated as follows Ignore electrostatic interactions SPM Ewald summation Coulomb sum with
98. number of tethered atoms in the molecule It is followed n records specifying the tehered sites in the molecule tether key a4 potential key see Table 6 7 index 1 i integer atomic site index variable 1 real potential parameter see Table 6 7 variable 2 real potential parameter see Table 6 7 The meaning of these variables is given in Table 6 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 149 STFC Section 6 1 Table 6 7 Tethering Potentials key potential type Variables 1 3 functional form harm Harmonic k U r 4 k ri r1 rhrm Restraint k Te U r k r ri r ri lt re Ur 5 k r2 k rellri ri re ri r gt re quar Quartic mle ee U r r 180 E ri 110 9 10 11 bonds n where n is the number of flexible chemical bonds in the molecule Each of the subsequent n records contains bond key ad potential key see Table 6 8 index 1 i integer first atomic site index in bond index 2 j integer second atomic site index in bond variable 1 real potential parameter see Table 6 8 variable 2 real potential parameter see Table 6 8 variable 3 real potential parameter see Table 6 8 variable 4 real potential parameter see Table 6 8 The meaning of these variables is giv
99. 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_4public library to help with this The utilities available are described in the DL POLY Classic User Manual Users should also be aware that many of these utilities are incorporated into the DL POLY GUI 21 5 3 5 Choosing Ewald Sum Variables 5 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 6 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 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
100. 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 al0 v_atomic label from REFERENCE iatm integer atom index from REFERENCE record b XXX real x coordinate from REFERENCE 171 STFC Section 6 2 yyy real y coordinate from REFERENCE ZZZ real z coordinate from REFERENCE 6 2 4 The RSDDAT File The RSDDAT file is the dump file of atomic coordinates of atoms that are displaced from their original position att 0 farther than a preset cutoff Its principal use is for off line analysis The file is written by the subroutine RSD_WRITE The control variables for this file are lrsd nsrsd isrsd and rrsd which are created internally based on information read from the displacements directive in the CONTROL file see Section 6 1 1 The RSDDAT file will be created only if the directive defects appears in the CONTROL file The RSDDAT file may become very large especially if it is formatted For serious simulation work it is recommended th
101. of the ensemble the centre of mass will not be stationary although the ensemble average warrants its proximity to the its original position i e the COM momentum accumulation ensemble average will tend towards zero By default this accumulation is removed and thus the correct application of stochastic dynamics the user is advised to use in the no vom option in the CONTROL file see Section 6 1 1 If the option is not applied then the dynamics will lead to peculiar thermalisation of different atomic species to mass and system size dependent temperatures 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 3 4 3 Andersen Thermostat This thermostat assumes the idea that the system or some subset of the system has an instantaneous inter action with some fictional particles and exchanges energy Practically this interaction amounts to replacing the momentum of some atoms with a new momentum drawn from the correct 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 Pzollision t 1 e
102. 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 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 238 STFC Appendix D 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 Messag
103. 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 vnl module VNL_MODULE The Verlet neighbour list VNL module defines all VNL related control variables and arrays needed for the VNL conditional update functionality and is dependent on KINDS_F90 only However it is assisted by a VNL_CHECK routine that is dependent on more modules e defects module DEFECTS_MODULE The defects module defines all defects and configuration related arrays REFERENCE and is de pendent on KINDS_F90 only However it also develops an allocation method that is dependent on SETUP_MODULE e inter molecular interactions modules VDW_MODULE METAL_MODULE TERSOFF_MODULE THREE_BODY_MODULE FOUR_BODY_MODULE The intermolecular modules define all variables and potential arrays needed for the calculation of the particular interaction in the DL_ POLY_4 scope They depend on KINDS_F90 Their allocation methods depend on SETUP_MODULE e intra molecular inter
104. 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 outgoing transfer buffer size exceeded in metal_ld_export This should not usually happen Action Consider using densvar option in CONTROL for extremely non equilibrium simulations Alternatively increase mxbfxp parameter in SET_BOUNDS recompile and resubmit Send the problem to us if this is persistent Message 39 error incoming data transfer size exceeds limit in metal_ld_export See notes on message 38 above Action See action notes on message 38 above Message 40 error too many bond constraints specified This should never happen Action See action notes on message 14 above 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 218 STFC Appendix D 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 outgoing transfer buffer size exceeded in dep
105. option requested DL_POLY_4 has detected an incompatibility in the simulation instructions namely that the requested 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 never happen for a dynamically sensical system This error arises if a model system contains one or more free zero mass particles Zero mass mass less particles sites are only allowed for shells in core shell units and as part of rigid bodies mass less but charged RB sites Action Inspect your FIELD to find and correct the erroneous entries and try again Message 380 error simulation temperature not specified or lt 1 K 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
106. 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 5 4 Warning and Error Processing 5 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 5 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 after some additional processing In some case if the cause for error is considered to be mendable it is corrected and
107. 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 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 212 STFC Appendix D Message 2 error too many atom types in FIELD scan_field This error arises when DL_POLY_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
108. qo 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 the motion of a single atom except that the force is the total force acting on the rigid body i e F in equation 3 179 and the mass is the total mass of the rigid body unit i e M in equation 3 174 These equations can be integrated by the standard Verlet LFV 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 relates the torque to the change in angular momentum T ij I w 3 188 In a thermostat it can be written as dmass where is the index of the rigid body x and qmass are the thermostat friction coefficient and mass In the local frame of the rigid body and without the thermostat term these simplify to the Euler s equations ir a A r gt ly Izz Oy Oz Lox z a y 4 ez Log Oz z 3 190 Lyy z 7 gt de a A 02 Irs Ly r Oy 22 95 STFC Section 3 6 The vectors 7 and w are the torque and angular velocity acting on the body transformed to the local body frame Integration of w is complicated by the fact that as the rigid body rotates so does the local reference frame So it is necessary to integrate eq
109. recalculation of the force at time t At is required since the positions have changed FE AlL 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 u t At e v t 4 AN _ At f t At 3 4 2 m DL_POLY 4 also offers integration algorithms based on the leapfrog Verlet LFV scheme 22 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 position The LFV algorithm is one staged It requires values of position r and force f at time t and velocity v at half a timestep behind t 1 2 At Firstly the forces are recalculated afresh at time t from time t At since the positions have changed from the last step 1 FF f e ft AG 3 5 where At is the timestep 2 LFV The velocities are advanced by a timestep to t 1 2 At by integration of the new force 1 1 f At Ath v t 3At v t 5A At 3 6 where m is the mass of a site and then the positions are advanced to a full step t At using the new half step velocities r t At e r t At v t At 3 7 60 OSTFC Section 3 1 Molecular dynamics simulations normally require properties that depend on position and velocity at the sam
110. routine CONSTRAINTS_RATTLE to apply cor rections to the atomic velocities of constrained particles 64 OSTFC Section 3 4 It should be noted that the fully converged constraint forces Gj 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 dij Gy 3 20 The contribution to be added to the atomic stress tensor for each constrained bond is given by g dG 3 21 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 Evaluation of Free Energy A generalization of bond constraints can be made to constrain a system to some point along a reaction coordinate A simple example of such a reaction coordinate would be the distance between two ions in solution If a number of simulations are conducted with the system constrained to different points along the reaction coordinate then the mean constraint force may be plotted as a function of reaction coordinate and the function integrated to obtain the free energy for the overall process 75 The PMF constraint force virial and contributions to the stress tensor are obtained in a manner analogous 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
111. see Table 6 13 variable 7 real potential parameter see Table 6 13 variable 8 real potential parameter see Table 6 13 variable 9 real potential parameter see Table 6 13 The variables pertaining to each potential are described in Table 6 13 4 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 atmnam 1 a8 first atom type atmnam 2 as second atom type By default in DL_POLY_Classic and DL_POLY_4 every vdw and met potential specifies an RDF pair If the control option rdf f is 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 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_Classic 155 STFC Section 6 1 Table 6 12 Pair Potentials key potential type Variables 1 5 functional form tab Tabulation tabulated potential 12 6 126 AIB U r 4 4 lj Lennard Jones e o U r 4e 27 27 nm n m 47 48 Eo n miro U r C m 22
112. select NPT ensemble type Nose Hoover with fi fa as the athermostat and barostat relaxation times in ps select NPT ensemble type Martyna Tuckerman Klein with fi fo as the thermostat and barostat relaxation times in ps select NoT ensemble type Langevin with f f2 as the thermostat and barostat relaxation speed friction constants in ps select NoT ensemble type Berendsen with f f2 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 fo as the thermostat and barostat relaxation times in ps select NP yT ensemble type Q i e lang ber hoover or mtk with f fo as the thermostat and barostat relaxation times in ps and set required simulation target external surface tension to y dyn cm select the same NP yT ensemble as above but with the semi anisotropic constraint so that the MD cell changes isotropically in the x y plane select the NPT anisotropic ensemble for the orthorhombic MD cell orthorhombic constraint equivalent to the NP yT ensemble when y 0 NPny OT select the same NP y OT ensemble as above but with the semi anisotropic constraint so that the MD cell changes isotropically in
113. 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 apply the mixing rule to all specified analytical single species van der Waals potential interactions to generate cross species interactions when i the latter has not already been specified ii single species potentials are available specified and of the same type and iii their type is allowed to mix i e of 12 6 or LJ or DPD or AMOE or WCA type The available mixing rules are as follows lorentz for the Lorentz Berthelot type of mixing fender for the Fender Halsey type of mixing hogervorst for the Hogervorst good hope type of mixing halgren for the Halgren HHG type of mixing tang for the Tang Toennies type of mixing functional for the Functional type of mixing The mixing formulae can be found in Section 2 3 1 apply a force shifting procedure to all van der Waals potentials except the shifted force n m potential so that the VDW interactions energy and force contributions fall to zero smoothly for distances approaching recut calculate and collect the Z density profile every f timesteps default f 1 perform zero temperature MD run reset target system 133 OSTFC Section 6 1 SPECIAL OPTIONS 1 dis 1_fast Lhis lorgz y zn l rin l rout l_scr ltor
114. sets Thus any provided cutoff radius Tydw Will be reset if it is not equal or larger that the largest of these all 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 rydw A second array gvdw is also calculated which is related to the potential via the formula o G riz Trigg U rig 5 2 97 1 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 6 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 f 2 eve z 2 98 ij where r rj r The force on atom 7 is the negative of this The contribution to be added to the atomic virial for each pair interaction is W ryj f 2 99 The contribution to be added to the atomic stress tensor is given by a Sa a 2 100 where a and indicate the x y z components The a
115. sum without the brutal truncation of the previous case It hinges on the assumption that the electrostatic forces are effectively screened in real systems an effect which is approximated by introducing a dielectric term that increases with distance 48 STFC Section 2 4 The interatomic potential for two charged ions is 1 dj U r didi 2 201 ri Arege Tij Tij j with qe the charge on an atom labelled and rj the magnitude of the separation vector r rj rT elr is the distance dependent dielectric function In DL POLY 4 it is assumed that this function has the form e r er 2 202 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 Gig ae 2 203 j 2rege ri ll with the force on atom i the negative of this The contribution to the atomic virial is W ryh 2 204 which is 2 times the potential term The contribution to be added to the atomic stress tensor is given by gol reg 2 205 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 c
116. temperature 10 Kelvin SPECIAL OPTIONS check and report on the minimum separation distance abandon global safety checks which gives more speed to simulations run at too few link cells per domain regimes by abandoning global safety checks however in case of parallel failures no controlled manner termination will happen OS s feedback dependence generate a one frame HISTORY from CONFIG and terminate straight after translate CONFIG along a vector x y z default 0 0 0 into CFGORG with configuration level n default 0 after reading input amp terminate read REVOLD in ASCII default is binary write REVIVE in ASCII default is binary redirect OUTPUT file s contents to the OS s default output channel screen interactive abandon the production of REVIVE and REVCON between all Verlet neighbour list pairs at re start 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 6 1 Internal Trajectory Defects File Key keytrj meaning 1 0 coordinates only in file 2 coordinates velocities and forces in file coordinates and velocities in file 6 1 1 3 Further Comments on the CONTROL File 1 A number of the directives or their mutually exclusive alternatives are mandatory
117. tensor yx component of stress tensor zz component of stress tensor the next 9 entries if a NPT or NoT simulation is undertaken x component of a cell vector y component of a cell vector z component of a cell vector x component of b cell vector temp real engcfg real engsrc real engcpe real record iii stpval 6 stpval 10 engbnd real engang real engdih real engtet real enthal real record iv stpval 11 stpval 15 tmprot real vir real virsrc real vircpe real virbnd real record v stpval 16 stpval 20 virang real vircon real virtet real volume real tmpshl real record vi stpval 21 stpval 25 engshl real virshl real alpha real beta real gamma real record vii stpval 26 stpval 27 virpmf real press real the next ntpatm entries amsd 1 real amsd 2 real amsd ntpatm real the next 9 entries for the stress tensor stress 1 real stress 2 real stress 3 real stress 4 real Set real stress 9 real cell 1 real cell 2 real cell 3 real cell 4 real sts real cell 9 real z component of c cell vector 180 Chapter 7 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 181 STFC Section 7 1 7 1 Parallelisation DL_POLY 4 is a distributed parallel mol
118. the x y plane semi orthorhombic constraint equivalent to the NP y OT semi ensemble 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 1 or undefined defaults ton 1 n gt 10 defaults to n 4 calculate electrostatic forces using Ewald sum with automatic parameter optimisation for precission f 107 lt f lt 0 5 default f 105 127 OSTFC Section 6 1 ewald sum a ky ka k3 exclude finish impactij E xyz integrator string io read method j k le io write method rp type j kle 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 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 1 0 E 00 14 1 2 1 set the type of Verlet integrator w
119. the DL_POLY_4 Software and any Derived Work whether obtained from STFC or from the Licensee only if it has completed the registration process on the DL_POLY_4 Website and agreed to the terms and conditions of the Licence Agreement for the use of the DL_POLY_4 Software for Academic Purposes that then appear on the DL_POLY_4 Website This Licence Agreement allows the Licensee to use only the release or version of the DL_POLY_4 Software downloaded by the Licensee from the DL_POLY_4 Website immediately after the Licensee agrees to the terms and conditions of this Licence Agreement the Licensee must acquire a new licence for any future release or version of the DL_POLY_4 Software that it wishes to use The Licensee will not tamper with or remove any copyright or other proprietary notice or any disclaimer that appears on or in any part of the DL_POLY_4 Software and will reproduce the same in all copies of any of the DL_POLY_4 Software and in all Derived Works The Licensee may not itself distribute any Derived Work If the Licensee would like any Derived Work made by or for the Licensee or by any of its employees or students based on any of the DL_POLY_4 Software to be considered for wider distribution it should notify STFC of such Derived Work and provide STFC with a copy of that Derived Work in source code a Contribution In providing STFC with such a Contribution the Licensee grants STFC an irrevocable indefinite licence to make tha
120. the PMF constraint virial Wpmpr for each simulation Users can convert this to the PMF constraint force from WPMF GpmF aoe 3 22 where is dpyr the constraint distance between the two groups used to define the reaction coordinate 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 constraints are applied iteratively in order bonds PMFs until convergence of Wemr reached The number of iteration cycles is limited by the same limit as for the bond constraints procedures SHAKE RATTLE 3 4 Thermostats The system may be coupled to a heat bath to ensure that the average system temperature is maintained close to the requested temperature Text When this is done the equations of motion are modified and the system no longer samples the microcanonical ensemble Instead trajectories in the canonical NVT ensemble or something close to it are generated DL POLY_4 comes with seven different thermostats Evans Gaussian constraints 26 Langevin 27 76 Andersen 28 Berendsen 29 Nos Hoover N H 30 and the gentle stochastic thermostat GST 72 77 as well as Dissipative Particle Dynamics DPD method 78 79 50 71 Of these only the Langevin N H GST and DPD algorithms generate true
121. 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 6 2 6 which provides an effective summary of the job run the input information starting configuration instantaneous 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 6 2 8 and REVCON Section 6 2 7 REVIVE contains the accumulated data for a number of thermodynamic quantities and RDFs and is intended to be used as the input file for a following run It is not human readable The REVCON file contains the restart configuration i e the final positions velocities and forces of the atoms when the run ended and is human readable The STATIS file Section 6 2 13 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 6 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
122. ther mostat mass Tr a specified time constant for temperature fluctuations the target thermostat energy equation 3 57 Pmass the barostat mass Tp a specified time constant for pressure fluctuations P the instantaneous pressure equation 3 97 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 2 mass t 2 g Hnpr Hnve 4 E a mi an Pot V t f 1 kp Text J x s ds 3 143 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 re spect 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 2Exin t changes inside At 2Ekin t Pmass n t 20 kp Toxt x t ZA e xlt 8 dmass 1 A v t lt exp x t gt 2 v t 3 144 At 2Ekin t Pmass n t 20 kg Text 1 1 t At x t ZA x t 74t x t At ce 2 Barostat Note Exin t and P t have changed and change inside nt exp x t Gat E 160 1 At 3 t Pext V t n t At e n t 4 eee 4 4 Pmass 1 1 At 1 n t qo
123. thermostat 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 temperature 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 63 damping Ewald like convergence parameter a in A calculate electrostatic forces using reaction field electrostatics with Fennell 63 damping Ewald like convergence derived by automatic parameter optimisation for precision f as for Ewald summation 107 lt f lt 0 5 default f 10720 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 RDFs z density profiles defects and displacements trajectories execution halts if no property is specified abort simulation and replay the HISTORF file a HISTORY copy with full force evaluation driven by FIELD different from the one used for the HISTORF generation restart job from end point of previous run ie continue current simulation REVOLD required 131 OSTFC Section 6 1 restart noscale restart s
124. 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 minimum for a shifted n m potential exceeds the specified potential cutoff A potential with the desired minimum cannot be created Action 240 STFC Appendix D 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 rcu
125. virial vir_src short range potential contribution to the virial vir_cou electrostatic potential contribution to the virial vir_bnd chemical bond contribution to the virial vir_ang angular and three body potentials contribution to the virial vir_con constraint bond contribution to the virial vir_tet tethering potential contribution to the virial line 3 cpu s elapsed cpu time in seconds since the beginning of the job 174 OSTFC Section 6 2 volume system volume in A3 temp_shl core shell temperature in Kelvin eng_shl configurational energy due to core shell potentials vir_shl core shell potential contribution to the virial alpha angle between b and c cell vectors in degrees beta angle between c and a cell vectors in degrees gamma angle between a and b cell vectors in degrees vir_pmf PMF constraint contribution to the virial 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 column
126. which has the additional advantage of speed The HISTORY has the following structure record 1 header a72 file header 168 OSTFC Section 6 2 record 2 keytrj integer trajectory key see Table 6 1 in last frame imcon integer periodic boundary key see Table 6 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 For timesteps greater than nstraj the HISTORY file is appended at intervals specified by the traj directive in the CONTROL file with the following information for each configuration record i timestep nstep megatm keytrj imcon tstep time record ii cell 1 cell 2 cell 3 record iii cell 4 cell 5 cell 6 record iv cell 7 cell 8 cell 9 a8 integer integer integer integer real real real real real real real real real real real the character string timestep the current time step number of atoms in simulation cell again trajectory key again periodic boundary key again integration timestep ps elapsed simulation time ps x component of a cell vector y component of a cell vector z component of a cell vector x component of b cell vector y component of b cell vector z component of b cell vector x component of c cell vector y component of c cell vector z component of c cell vector This is followed by the configuration for the
127. with an appropriate keyword Section 5 2 1 which is selected 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 4 also has a Java GUI The files for this are stored in the subdirectory java Compilation of this is simple and requires running the javac compiler and the jar utility Details for these procedures are provided in the GUI manual 21 6 To run 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 d
128. with fixed constants a f ryck U A a b cos c cos p d cos e cos f cos Fluorinated Ryckaert Bellemans 44 with fixed constants a h rbf U A a b cos c cos d cos e cos f cos g exp h d 7 y 19 2 39 2 40 2 41 2 42 2 43 2 44 STFC Section 2 2 7 OPLS torsion potential opls U Ao A 1 cos Ag 1 cos 2 Az 1 cos 3 2 45 8 Tabulated potential tab The potential is defined numerically in TABDIH see Section 4 3 and Section 6 1 8 In these formulae ijkn is the dihedral angle defined by Pijkn cos 7HB rij tie Tin 2 46 with 2 47 fij x Tip Tap x a lites x Tito lyk X T kn With this definition the sign of the dihedral angle is positive if the vector product Ca a X Tjk X Tkn is in the same direction as the bond vector r and negative if in the opposite irection B rij Tiks Lkn The force on an atom arising from the dihedral potential is given by o a ainia 2 48 Fi 5 0 isin 2 48 with being one of i j k n and a one of x y z This may be expanded into o 1 o o UlQijkn 4 ijkn lt B Tij Lik Lkn 2 49 areal jkn ot rr jk o Cig Lito Pen 12449 The derivative of the function B r j tjk kn is o 1 o grg Co Tiks Tkn E x Tik Tjk X Tkn tij X Ljrl Ejk X Lyn Ore cos Qij
129. 00000000 0 000000000000000 0 000000000000000 44 028000000000000 OW 1 2 505228382 1 484234330 7 274585343 0 5446573999 1 872177437 0 7702718106 3515 939287 13070 74357 4432 030587 HW 2 1 622622646 1 972916834 7 340573742 1 507099154 1 577400769 4 328786484 7455 527553 4806 880540 1255 814536 Te I O effects are excluded from comparison with a default simualtion and comparisons are carried over a few hundreds of timesteps This is usually accounting for over 90 of the time tosolution 142 OSTFC Section 6 1 HW 3 3 258494716 2 125627191 7 491549620 2 413871957 4 336956694 2 951142896 7896 278327 8318 045939 2379 766752 OW 4 0 9720599243E 01 2 503798635 3 732081894 1 787340483 1 021777575 0 5473436377 9226 455153 9445 662860 5365 202509 etc 6 1 2 1 The CONFIG File Format The file is free formatted and not case sensitive Every line is treated as a command sentence record However line records are limited to 72 characters in length Records are read in words as a word must not exceed 40 characters in length Words are recognised as such by separation by one or more space characters The first record in the CONFIG file is a header up to 72 characters long to aid identification of the file Blank and commented lines are not allowed 6 1 2 2 Definitions of Variables in the CONFIG File record 1 header a12 title line record 2 levcfg integer CONFIG file key See Table 6 5 for permitte
130. 08 5 2 1 Compiling the Source Code c sa 26542 c iard aa u trada a eee 108 e RUUMID to 3g aa ee E e a ae ek aoe a a a SE a ee oe Bs 110 A AA A 110 O24 Restarting eu 4 0 s a a ee ee ea A be oS 111 5 2 5 Optimising the Starting Structure s adorer oa hi aae a ee we 112 5 2 6 Simulation Efficiency and Performance s c 2 402464 44 8e 6 ee bate a be eG 113 5 3 A Guideto Preparing Input Files 2 224044 0 4 e484 be eb eee eee hee de eed 114 6 3 1 Inorganic Materials s s 2 4 44 cee oe ee ek ee aD ERE ER REE ES 115 0 3 2 Macromolecules ai s soss nce fe eee Sk ae Gk eek OR eae be ee an 115 5 3 0 Adding Solvent to Structure 24 25 446004 haw e kG SS oe oe be Re 116 5 34 Analysing Results o soe a ese aoe ida a wa ae EERE a 117 5 3 5 Choosing Ewald Sum Variables sc s sanac o o o ig ee 117 DA Warming and Error Processing 442 64 ee eee eR a a Pee es 119 5 4 1 The DL POLY_4 Internal Warning Facility o 119 5 4 2 The DL POLY 4 Internal Error Facility o e 119 6 Data Files 120 Gal The INPUT Piles corra ar Re ok ek EE AG ek a D e ee we BS 121 Gla The CONTROL Pile ua A bo ee ewe EG ao be Bae Oe A ed 121 61 2 The CONFIG Fil se sa nonr pa toen 44 2460 8 bse 2d aa 142 Gell be FIELD Eile ss p ee ark ee Sha ie ea a oh ees Boe we 2 eee aoe BR 145 GLA The REFERENCE File 5406 e402 68 pe A ee Pe eh ke Th aa 163 61 5 The REVOLD File 4 224444 280546865684 oe RAG
131. 1 C2 C3 C4 C A d B both c and d are cutoffs 7 Sutton Chen potential 14 15 16 stch The Sutton Chen potential is an analytical potential in the FS class It has the form n Vis rij 2 pijlTij 2 2 116 Tij F p cm with parameters a n m c Note that the parameter c for the mixed potential in multi component allys is irrelevant as outlined in 15 8 Gupta potential 59 gupt The Gupta potential is another analytical potential in the FS class It has the form Vij rij 2A exp p To Tij 7 pis Tij exp 20 e 2 2 117 F pi B P with parameters A ro p B qij 32 OSTFC Section 2 3 9 Many body perturbation component potential 54 mbpc This component is another analytical potential in the FS class which two body part may be defined by a matching van der Waals potential in the vdw section of the FIELD file It has the form Vij riz 0 Pilrij 5 1 erf a rij ro 2 118 ij F pi EV Pi with parameters e a m and To Note that the parameters a and ro must be the same for all defined potentials of this type DL_POLY_4 will set a Max 0 apq and ro Max 0 ro_pq for all defined interactions of this type between species p and q If after this any is left undefined i e zero the undefined entities will be set to their defaults a 20 and ro Min 1 5 0 2 reut All of these metal potentials can be decomposed into p
132. 1 Ninv Ne Uinv inis Ea Th Tes ra linv 1 4 y y Ss vdw electostatics TG Ir r sl 2 1 i 1 g gt i N N N Y YY Utersos tj kr Ti rt Th i 1 Ai Aj N 2N 1 N 5 Y Y sea j k r Perper Th i 1 j gt i k gt j N 3N 2N 1 N D iD iD de U4 body i j k n Li Lj Ek En i 1 j gt i k gt j n gt k N gt D Vestn i Ti vi gt i 1 metal where Ushel Uteth Ubond Uangl Udind Uinv Us body gt Utersoff U3 body and U4 body Are empirical inter action 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 Uextn represents an external field potential The po sition vectors r 1 7 and rg refer to the positions of the atoms specifically involved in a given interac tion Almost universally it is the differences in position that determine the interaction The numbers Nshels Nteths Noonds Nangi Naina and Niny refer to the total numbers of these respective interactions present in the simulated system and the indices shel tteths tbonds tangl 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 12
133. 2 above Action See action notes on message 1002 above Message 1030 error deallocation failure in core_shell_module gt deallocate_core_shell_arrays See notes on message 1002 above Action See action notes on message 1002 above 255 STFC Appendix D Message 1031 error deallocation failure in tethers_module gt deallocate_tethers_arrays See notes on message 1002 above Action See action notes on message 1002 above Message 1032 error deallocation failure in constraints_module gt deallocate_constraints_arrays See notes on message 1002 above Action See action notes on message 1002 above Message 1033 error deallocation failure in dihedrals module gt deallocate_dihedrals_arrays See notes on message 1002 above Action See action notes on message 1002 above Message 1034 error deallocation failure in inversions module gt deallocate_inversions_arrays See notes on message 1002 above Action See action notes on message 1002 above Message 1035 error allocation failure in defects_module gt allocate_defects_arrays See notes on message 1001 above Action See action notes on message 1001 above Message 1036 error allocation failure in pmf_module gt allocate_pmf_arrays See notes on message 1001 above Action See action notes on message 1001 above Message 1037 error deallocation failure in pmf_module
134. 2010 111 Hockney R W and Eastwood J W 1981 Computer Simulation Using Particles McGraw Hill International 182 184 185 Smith W 1992 Comput Phys Commun 67 392 182 Smith W and Fincham D 1993 Molecular Simulation 10 67 182 Bush I J Todorov I T and Smith W 2006 Computer Physics Communication 175 323 185 Bush I J 2000 Daresbury Laboratory 185 Reith D P tz M and M ller Plathe F 2003 J Comp Chem 24 1624 200 R hle V Junghans C Lukyanov A Kremer K and Andrienko D 2009 J Chem Theory Comput 5 3211 200 Pagonabarraga I and Frenkel D 2001 Journal of Chemical Physics 115 11 5015 5026 203 Trofimov S Y Nies E L F and Michels M A J 2002 Journal of Chemical Physics 117 20 9383 9394 203 Koelman J M V A and Hoogerbrugge P J 1993 EPL Europhysics Letters 21 3 363 368 203 Mar C A Backx G and Ernst M H 1997 Physical Review E 56 2 1676 1691 203 Peters E A J F 2004 EPL Europhysics Letters 66 3 311 317 204 Seaton M Anderson R Metz S and Smith W 2013 Molecular Simulation 39 10 796 821 204 Lowe C P 1999 EPL Europhysics Letters 47 2 145 151 204 Stoyanov S D and Groot R D 2005 Journal of Chemical Physics 122 11 114112 204 Gonella G orlandini E and Yeomans J M 1997 Phys Rev Lett 78 1695 204 280 Index DL_POLY_4 software licence 10
135. 3 by semi isotropic constraining of the barostat equation of motion and slight amending the thermostat equation of motion and the conserved quantity to Le p pan X t Nez t a b e dt 0 Magl 0 0 a B 2 d 2 Fin E Pmass Tr n t n t 20 kp Text ow x 3 171 aX mass mass t Pmass Tr n 1 t Hyp at Hyve q a 5 S PoxV t f 1 ke Text x s ds Similarly this ensemble is optionally extending to constant normal pressure and constant surface tension NP 7T 73 by semi isotropic constraining of the barostat equation of motion and slight amending the thermostat equation of motion and the conserved quantity to Taa t Pext Yext hz t V t 2Erin t 1 x Oma t a 8 x y d Pmass f Pmass nag t E l de alt z t Fes vO Fen x t M22 t a 6 2 0 Mag 0 0 a B 2 y z 92 STFC Section 3 6 2Exin t Pmass TrIn t n t T 20 3 kg Tex 00 ares 3 172 dt mass mass t Pmass Trin n t Har Fee 2 Ki y H Post V t f 3 ke Toxt i dds where Yext is the user defined external surface tension and h t V t Azy t is the instantaneous hight of the MD box or MD box volume over area One defines the instantaneous surface tension as given in equation 3 122 The case yYext 0 generates the NPT anisotropic ensemble for the orthorhombic cell imcon 2 in CONFIG see Appendix B This can be considered as an orthorhom
136. 35 4835 electrostatics conversion factor to internal units i e Ge 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 nconf 11 configuration file input channel nfield 12 force field input channel ntable 13 tabulated potentials file input channel nrefdt 14 reference configuration input channel nrite 6 main output channel nstats 21 statistical data file output channel nrest 22 output channel accumulators restart dump file nhist 23 trajectory history file channel ndefdt 24 output channel for defects data file nrdfdt 25 output channel for RDF data nzdfdt 26 output channel for Z density data file nrsddt 27 output channel for displacements data files npdfdt 28 output channel for raw PDF files ngdfdt 29 output channel for normalised RDF data files seed 1 3 variable pair of seeds for the random number generator lseed variable logical swich on off indicator for seeding mxsite variable max number of molecular sites mxatyp variable max number of unique atomic types mxtmls variable max number of unique molecule types mxexcl variable max number of excluded interactions per atom mxspl variable SPME FFT B spline order mxspl1 variable SPME FFT B spline possible extension when pag gt 0 kmaxa variable SPME FFT amended array dimension a direction kmaxb variable SPME FFT amended array dimension b direction kmaxc variable SPME FFT am
137. 37 13 iJ 9 Many body perturbation component density correction Amp a joes 2 138 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 Ui DAA rij i 1 Ai N Tij lt Tmet 1 N Tij2Tmet U gt yE Vil Tij Has 5 Vij riz U U i 1 Jri i 1 jf dU 27Np Vij r r dr Tmet N Uz _ F p 6p 2 139 i 1 N N OF pi U gt y F a U 6U2 i 1 i 1 U inp a ne pislr jr 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 ret 2 EEAM energy correction No long ranged corrections apply beyond rmet 3 2BEAM energy correction No long ranged corrections apply beyond ret 4 2BEEAM energy correction No long ranged corrections apply beyond ryet 5 Finnis Sinclair energy correction No long ranged corrections apply beyond cutoffs c and d 37 STFC Section 2 3 6 Extended Finnis Sinclair energy correction No long ranged corrections apply beyond cutoffs c and d 7 Sutton Chen energy correction on ND 3 n 3 Sie amp TN pea a 03 Net Aroa m 3 N 6U ss a 2 140 z met 2 Pi 8 Gupta energy correction TN pAr r ro 2 OU eel rea 2r met 2 x Pp Pp P Tmet 2 ex
138. 4 is that devised by Fincham et al 67 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 Vcore she11 of the harmonic spring which depends on the reduced mass i e 1 k 1 2 Veore shell on Eres 2 233 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 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 VAF of the ions of interest to polarise Each VAF is then Fast Fourier transformed to find their highest frequency of interaction Vrigid ion
139. 49 2 4 5 Smoothed Particle Mesh Ewald 0 o e ee eee 50 vi vil STFC Contents 2 5 Polarisation Shell Models gt scata ouaaa rekbaar iao Rae REE da LS 53 2 5 1 Dynamical Adiabatic Shells Shell Model o oo 54 2 5 2 Relaxed Massless Shells Model coco 2244 ra e A 54 2 5 3 Breathing Shell Model Extension e 55 204 E rther Notes s s e iaa o Rs A a a aw 55 2 6 External Fields 4 225444 46488444 68 8G re a a Hee 55 2 7 Treatment of Frozen Atoms Rigid Body and Core Shell Units 57 2 8 Tabulation and interpolation in the treatment of intermolecular interactions 57 2 9 Open Knowledgebase of Interatomic Models openKIM 00000004 58 3 Integration Algorithms 59 3 1 Imtroditction 24 44 h 464 a a das 60 32 Bond Constraints a lt ss ma eed ee eae ERS a ee RE SG a ee Be Yee 62 3 3 Potential of Mean Force PMF Constraints and the Evaluation of Free Energy 65 dl Thermostats 4 5 44202304 be ye eee we ee Po ee ae ea SS 65 3 4 1 Evans Thermostat Gaussian Constraints e 0000000048 66 34 2 Langevin Thermostat a oc twa sasoina i bee a ee ee Re e e 67 3 4 8 Andersen Thermostat gt lt ce ooe ciapa Re ke e Ba ee 69 3AA Berendsen Thermostat sa a aded dieo a ana ta ee e A A 71 3 4 5 Nose Hoover Thermostat lt o st 64 5 2 he RR RA AE ss da a 72 3 4 6 Gentle Stochastic Thermostat s soi pian
140. 5 529 541 62 82 85 90 92 Ryckaert J P Ciccotti G and Berendsen H J C 1977 J Comput Phys 23 327 62 182 McCammon J A and Harvey S C 1987 Dynamics of Proteins and Nucleic Acids Cambridge University Press 65 Izaguirre J A Langevin stabilisation of multiscale mollified dynamics In Brandt A Binder K B J editor Multiscale Computational Methods in Chemistry and Physics volume 117 of NATO Science Series Series III Computer and System Sciences pages 34 47 IOS Press Amsterdam 2001 65 68 77 Samoletov A Chaplain M A J and Dettmann C P 2007 J Stat Phys 128 1321 1336 65 74 78 Hoogerbrugge P J and Koelman J M V A 1992 EPL Europhysics Letters 19 3 155 160 65 279 STFC Bibliography 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 Espa ol P and Warren P 1995 EPL Europhysics Letters 30 4 191 196 65 201 Melchionna S Ciccotti G and Holian B L 1993 Molec Phys 78 533 85 Martyna G M Tobias D J and Klein M L 1994 J Chem Phys 101 4177 85 93 Todorov I T Bush I J and Porter A R 2009 Parallel Scientific Computing and Optimization Springer Optimization and Its Applications ISSN 1931 6828 27 111 Todorov I T Bush I J and Smith W 2008 Cray User Group 2008 111 Bush I J Todorov I T and Smith W 2010 Cray User Group
141. 6 NVT_El_VV NVT_El_LFV The same as the above but also incorporating RB integration NVT_LO_Vv NVT_LO_LFV Constant T algorithm Langevin 27 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 28 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 29 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 30 NVT_H1_vv NVT_H1_LFV The same as the above but also incorporating RB integration NVT_GO_VV NVT_GO_LFV Constant T algorithm GST 72 NVT_G1_VV NVT_G1_LFV The same as the above but also incorporating RB integration NPT_LO_VV NPT_LO_LFV Constant T P algorithm Langevin 31 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 29 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 30 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 32 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 31 NPT_L1_VV NPT_L1_LFV The same as the above but also incor
142. 6 0000 0 8200 HW 1 0080 0 4100 HW 1 0080 0 4100 CONSTRAINTS 3 1 2 1 0000 1 3 1 0000 2 3 1 63299 FINISH VDW 45 C C lj 0 12000 3 2963 C CT 1j 0 08485 3 2518 OW OS 1j 0 15100 3 0451 OS OS 1j 0 15000 2 9400 CLOSE 6 1 3 1 The FIELD File Format The file is free formatted and not case sensitive Every line is treated as a command sentence record Commented records beginning with a and blank lines are not processed and may be added to aid legibility see example above Records must be limited in length to 100 characters Records are read in words as a word must not exceed 40 characters in length Words are recognised as such by separation by one or more space characters The contents of the file are variable and are defined by the use of directives Additional information is associated with the directives 6 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 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 146 STFC Section 6 1 a eV for electron Volts b kcal mol for k calories per mol
143. 7 force field 4 12 13 21 116 184 214 228 245 AMBER 4 12 DL_POLY 4 12 Dreiding 4 12 45 GROMOS 4 12 force shifted Coulomb sum 47 132 139 FORTRANDO 6 7 108 109 212 FTP 9 GROMOS 4 12 GUI 10 115 117 144 inversional restraints 26 Java GUI 4 10 licence 3 long ranged corrections metal 36 van der Waals 29 minimisation 112 conjugate gradients 112 programmed 112 zero temperature 112 parallelisation 5 107 182 Domain Decomposition 5 281 OSTFC Index intramolecular terms 183 polarisation 53 54 shell model 4 12 46 53 55 57 183 221 shell models 53 potential 2BEAM 32 bond 4 115 151 174 183 186 217 237 bonded 184 185 calcite 25 26 chemical bond 4 12 15 20 21 45 54 183 184 dihedral 4 12 19 21 23 153 174 183 222 238 EAM 31 165 EEAM 31 165 electrostatics 4 8 13 15 18 21 22 26 46 125 127 128 131 132 139 174 183 238 external field 4 12 55 57 183 four body 4 12 27 46 154 160 161 174 183 215 226 237 239 improper dihedral 4 12 21 183 intermolecular 108 intramolecular 27 46 108 inversion 4 12 23 25 46 154 183 224 238 metal 4 13 27 31 108 109 154 183 185 226 non bonded 4 13 115 116 130 146 151 152 154 183 185 214 tabulated 164 216 Tersoff 4 12 27 41 44 154 159 183 185 tether 4 12 26 27 174 183 222 239 tethered 57 three b
144. ALO 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 RDF_EXCL_COLLECT RDF_FRZN_COLLECT EWALD_EXCL_FORCES EWALD_FRZN_FORCES TWO_BODY_FORCES TERSOFF_FORCES THREE_BODY_FORCES FOUR_BODY_FORCES CORE_ SHELL_FORCES TETHERS_FORCES INTRA_COUL BONDS_FORCES ANGLES_FORCES INVERSIONS_FORCES DIHEDRALS_14_VDW DIHEDRALS_FORCES EXTERNAL_FIELD_APPLY EXTERNAL_FIELD_CORRECT LANGEVIN_FORCES CONSTRAINTS_PSEUDO_BONDS PMF_PSEUDO_BONDS RIGID_BODIES_SPLIT_TORQUE RIGID_BODIES_MOVE MINIMISE_RELAX 190 STFC Section 7 2 CORE_SHELL_RELAX ZERO_K_OPTIMISE VAF_COLLECT NVT_EO_SCL NVT_E1_SCL NVT_BO_SCL NVT_B1_SCL XSCALE CORE_SHELL_KINETIC REGAUSS_TEMPERATURE Z_DENSITY_COLLECT STATISTICS_COLLECT STATISTICS_CONNECT_SET STATISTICS CONNECT_SPREAD STATISTICS CONNECT_FRAMES SYSTEM_REVIVE RDF_COMPUTE Z_DENSITY_COMPUTE VAF_COMPUTE BONDS_COMPUTE ANGLES_COMPUTE DIHEDRALS_COMPUTE INVERSIONS_COMPUTE STATISTICS_RESULT W_IMPACT_OPTION W_WRITE_OPTIONS W_CALCULATE_FORCES W_REFRESH_MAPPINGS W_KINETIC_OPTIONS W_STATISTICS_REPORT W_REFRESH_OUTPUT W_REPLAY_HISTORY W_REPLAY_HISTORF 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 NVT_GO_SCL NPT_HO_SCL NST_HO_SCL NVE_O_VV NVT_EO_VV NVT_LO_VV NVT_AO_VV NVT_BO_VV NVT_HO_VV NVT_GO_VV NPT_LO_VV NPT_BO_VV
145. D file with fictitious records for all the interactions to be tabulated with the interaction keywords and parameters chosen arbitrarily in accord with Table 6 8 Table 6 9 Table 6 10 and Table 6 11 Note that DL CGMAP as well as VOTCA creates FIELD_CG files that already contain interaction descriptors with the tab keyword s in place so if the route ii is chosen the user needs to replace those records with the fictitious ones it is advisory to store the initial FIELD_CG for the future use when the actual TAB files are ready e Run DL_POLY 4 with the replay history rdf and or analysis options invoked in the CONTROL file which will result in creation of the targeted inter and intra molecular PDF data files RDFDAT BNDDAT ANGDAT DIHDAT INVDAT and the respective PMF files as described above Note that only and only when the rdf and analysis options are both active then the VDWPMF and VDWTAB files derived from RDF s will be produced along with RDFDAT They are structured in the same manner and format as their intramolecular counterparts The user can then convert the VDWTAB file into a correctly formatted TABLE file by using the utility called pmf2tab f subject to compilation found in DL_POLY_4 directory utility as follows userChost pmf2tab exe lt VDWTAB e Check the data for accuracy and amend the tabulated force fields Redo the analysis on coarser finer grid s if necessary e When satisfied with the created TAB files
146. 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 The DEFECTS has the following structure record 1 header a72 file header 170 OSTFC Section 6 2 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 6 6 rdef real site interstitial cutoff record ii defects aT the character string defects ndefs integer the total number of defects interstitials al3 the character string interstitials ni integer the total number of interstitials vacancies a9 the character string vacancies nv integer the total number of vacancies record iii cell 1 real x component of a cell vector cell 2 real y component of a cell vector cell 3 real z component of a cell vector record iv cell 4 real x component of b cell vector cell 5 real y component of b cell vector cell 6 real z component
147. EAD EEA Ra REL 161 External Fields o 244444 42 o 844 Deh ede ERAS Adee Hee eee ee ge eee SE 162 xii List of Figures 2 1 2 2 2 3 2 4 2 5 2 6 3 1 6 1 B 1 B 2 B 3 The interatomic bond Vector s m sa eae a eR a a AA a EO 13 The valence angle and associated vectors e a e 16 The dihedral angle and associated vectors e 19 The L and D enantiomers and defining vectors soosoo ea a ee 22 The inversion angle and associated vectors e 23 The vectors of the calcite potential e 25 The SHAKE RATTLE VV1 schematics and associated vectors 63 DL POLY 4 input left and output right les ooo coins ar oe wx 121 The cubice MDcell o 2 sice p G4 oom Bae a e aa da a e a we Ble bes 206 The orthorhomie MID Gell 6 corria a Be eae So ER A e e Sea ee BS 206 The parallelepiped MD cell ee 206 xiii STFC Contents XIV Chapter 0 Quick Word INSTALL RUN For the experienced and quick minded this is a very brief resume of how to INSTALL amp RUN DL_POLY 4 which is no excuse for skipping the Introduction Chapter 1 For the rest of us it sketches out how to start running DL_POLY_4 jobs and where one should look to obtain more detailed information if need be If you have followed the procedure for obtaining and downloading the DL POLY_4 package see Obtain ing the Source Code Section 7 have successfully unpacked it and are ready to compile the source co
148. EVIVE 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 233 STFC Appendix D 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 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 re sults if the user specifies octahedral or dodecahedral boundary conditions which are only available in DL_POLY_Classic Action Correct your boundary condition or consider using DL POLY Classic Message 305 error too few link cells per dimension for many body and tersoff forces sub routines
149. G file by the vectors Lay La2 La3 Mb1 Mb2 Mb3 Nc1 Nc2 Ncz3 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 B 6 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 parallelogram The origin of the X Y atomic coordinates lies on an axis perpendicular to the centre of the parallelogram The origin of the Z coordinate is where the user specifies it However it is recommended that it is in the middle of the slab Domain decomposition division across Z axis is limited to 2 If the XY parallelogram is defined by vectors A and B the vectors required in the CONFIG file are A A2 0 B1 B2 0 0 0 D where D is any real number including zero If D is nonzero it will be used by DL_POLY to 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
150. H t t H t CH ne HU d av Trin t Ve where is the stress tensor equation 3 98 and 1 is the identity matrix The conserved quantity these generate is Pmass Tr n nT Hnot Hyve 4 PV t 3 117 2 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 ex x F 20 At 0 t Po VEL 2Ejn t 1 Ret 4 Pmass f Pmass Pmass Gale u t lt exp ut At ait nt 749 5 u t 1 r t At exp nt sat At r t At v t 544 81 STFC Section 3 5 Similarly for the LFV couched algorithms these are nit sat exp xp t At nit y a t Pax V t 1 P 2Ekin t 1 Rp t At A Pmass f Pmass Pmass 3 At scale 1 x1 ty n t a 2 scale v 1 3 119 m scale At scale f 1 1 t R t v t At scale v u t At scale f FO RU WE m CLD do AA u t i AL n t At ee 50 It is worth noting DL POLY_4 uses Taylor expansion truncated to the quadratic term to approximate exponentials of tensorial terms This ensemble is optionally extending to constant normal pressure and constant surface area NP AT 73 by semi isotropic constraining of the barostat equation of motion to Salt es t Foxt VO 4 2Bhinl yn t Pell a f z Ga dt 0 Mag 0 0 CAI Similarl
151. MODULE GPFA_MODULE PARALLEL_FFT 189 STFC Section 7 2 e general files in the source directory WARNING ERROR SCAN_CONTROL_IO NUMERIC_CONTAINER SPME_CONTAINER QUATERNIONS_CONTAINER SCAN_FIELD SCAN_CONTROL_PRE READ_CONFIG_PARALLEL SCAN_CONFIG SCAN_CONTROL READ_CONFIG SET_BOUNDS READ_CONTROL VDW_GENERATE VDW_TABLE_READ VDW_DIRECT_FS_GENERATE METAL_GENERATE_ERF METAL_GENERATE METAL_TABLE_READ METAL_TABLE_DERIVATIVES TERSOFF_GENERATE DIHEDRALS_14_CHECK READ_FIELD CHECK_CONFIG ORIGIN_CONFIG SCALE_CONFIG WRITE_CONFIG TRAJECTORY_WRITE SYSTEM_EXPAND RIGID_BODIES_TAGS RIGID_BODIES_COMS RIGID_BODIES_WIDTHS RIGID_BODIES_SETUP INIT_INTRA TAG_LEGEND REPORT_TOPOLOGY PASS_SHARED_UNITS BUILD_BOOK_INTRA BUILD_EXCL_INTRA SCALE_TEMPERATURE UPDATE_SHARED_UNITS CORE_SHELL_QUENCH CONSTRAINTS_TAGS CONSTRAINTS_QUENCH PMF_COMS PMF_TAGS PMF_VCOMS PMF_QUENCH RIGID_BODIES_QUENCH SET_TEMPERATURE VDW_LRC METAL_LRC SYSTEM_INIT VNL_CHECK EXPORT_ATOMIC_DATA SET_HALO_PARTICLES EXPORT_ATOMIC_POSITIONS REFRESH_ HALO_POSITIONS RIGID_BODIES_STRESS READ_HISTORY 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 RSD_WRITE VAF_WRITE 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_H
152. NPT_HO_VV NPT_MO_VV NST_LO_VV NST_BO_VV NST_HO_VV NST_MO_VV NVT_H1_SCL NVT_G1_SCL NPT_H1_SCL NST_H1_SCL NVE_1_VV NVT_El_Vv NVT_L1_VV NVT_A1_VV NVT_B1_VV NVT_H1_VV NVT_G1_VV NPT_L1_VV NPT_B1_VV NPT_H1_VV NPT_M1_VV NST_L1_VV NST_B1_VV NST_H1_VV NST_M1_VvV W_AT_START_VV W_INTEGRATE_VV W_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 NVT_GO_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 NVT_G1_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 W_AT_START_LFV W_INTEGRATE_LFV W_MD_LFV e SERIAL specific files in the source SERIAL directory MPIF H MPI_LMODULE EWALD_SPME_FORC S The files in each group are listed in hierarchal 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 hierarchal order is followed in the makefiles see Appendix 191 STFC Section 7 2 It is worth noting that the all w_ F90 files in source and source V are in fact inclusion files that are wrapped as routines within DL POLY This wrapping up of functional calls is done to shorten the length of the code by reusing general functional sequences where possible 7 2 3 Module Files The DL_POLY_4 module files contain al
153. OL 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 223 STFC Appendix D 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 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 recompile and resubmit Message 79 error tersoff potential cutoff undefined This show
154. OLY_4 It is meant to be a human readable file destined for hardcopy output 6 2 6 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 6 2 6 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 6 2 6 3 Force Field Specification Echoes the FIELD file A warning line will be printed if the system is not electrically neutral This warning will appear immediately before the non bonded short range potential specifications This part of the file is written from the subroutine READ_FIELD 173 STFC Section 6 2 6 2 6 4 System Specification Echoes system name periodic boundary specification the cell vectors and volume some initial estimates 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 subroutines SCAN_CONFIG CHECK_CONFIG SYSTEM_INIT REPORT_TOPOLOGY and SET_TEMPERATURE 6 2 6 5 Summary of the Initial Configuration This part of the file is written from the main subroutine DL_POLY _ It states the initi
155. S_F90 and its allocation method on SETUP_MODULE 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 methods on SETUP_MODULE and COMMS_MODULE e greenkubo module GREENKUBO_MODULE This module defines all variables and arrays needed for calculation of Green Kubo relations during a simulation in DL_POLY_4 It depends on KINDS_F90 and its allocation methods 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 7 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 VNL_MODULE DEFECTS_MODULE DEFECTS1_MODULE VDW_MODULE METAL_MODULE TERSOFF_MODULE THREE_BODY_MODULE FOUR_BODY_MODULE RDF_MODULE Z_DENSITY_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 GREENKUBO_MODULE KINETIC_
156. T 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 a limited set of relevant functionality over a limited extent of molecular systems complexity only They are not necessarily appropriate for serious simulation of the test systems In other words the tests are not warranted to have well defined force field in terms of applicability transferability and fullness as well as to have a well defined state point thus initial configurations may be away from equilibrium if physical at all 8 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 8 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 8 1 3 Test Case 5 and 6 KNaSi O Potassium Sodium disilicate glass NaKSi2O5 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
157. T21 tar gz 2 Move DL_POLY input files to the DL_POLY_4 ZZ execute directory cd execute cp data TEST21 CONFIG cp data TEST21 CONTROL cp data TEST21 FIELD 3 Edit FIELD and change metal 1 table Cu Cu eam close to vdw 1 Cu Cu mors 3 42900e 01 2 86600e 00 1 35880e 00 close 4 Edit CONTROL and remove restart scale 267 OSTFC Appendix E change steps 6000 steps equilibration 5000 steps to steps 100 steps equilibration 10 steps and cutoff 5 0 Angstroms to cutoff 6 76342e 00 Angstroms 5 Run and save the native simulation DLPOLY Z mv OUTPUT OUTPUT native 6 Edit FILED and change vdw 1 Cu Cu mors 3 42900e 01 2 86600e 00 1 35880e 00 close to kim Pair_Morse_GirifalcoWeizer_LowCutoff_Cu__MO 7 Run and save the kim simulation DLPOLY Z mv OUTPUT OUTPUT kim 8 Compare simulation outputs form the native and KIM interaction models diff OUTPUT native OUTPUT kim Good luck January 2015 Ryan Elliott Ilian Todorov and Henry Boateng 268 Appendix F DL POLY 4 Academic Licence Agreement F 1 The short story By registering for any version of DL_POLY_4 you confirm that e the institution whose name appears as the Licensee in the Registration Form agrees to the terms of the Licence Agreement e you have authority to agree to the terms of the Licence Agreement and to enter into a contract with STFC on behalf of that institution e the DL_POLY_4
158. THE DL POLY 4 USER MANUAL I T Todorov amp W Smith STFC Daresbury Laboratory Daresbury Warrington WA4 4AD Cheshire England United Kingdom Version 4 07 January 2015 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 Compu tational 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 institu tions 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 inexpensive accessible and free of commercial considerations Users have direct
159. TION TO ENTER INTO A LEGALLY BINDING AGREEMENT GOVERNED BY THE TERMS AND CONDITIONS SET OUT BELOW THE AGREEMENT IN THE FOLLOWING TERMS AND CONDITIONS YOU ARE REFERRED TO AS THE LICENSEE 1 DEFINITIONS AND INTERPRETATION 1 1 In this Licence Agreement the following expressions have the meanings set opposite Academic Purposes fundamental or basic research or academic teaching including any fundamental research that is funded by any public or charitable body but not any purpose that generates revenue as opposed to grant income for the Licensee or any third party Any research that is wholly or partially sponsored by any profit making organisation or that is carried out for the benefit of any profit making organisation is not an Academic Purpose a Derived Work any modification of or enhancement or improvement to any of the DL_POLY_4 Software and any software or other work developed or derived from any of the DL_POLY_4 Software the DL_POLY_4 Software the release and version of the DL_POLY_4 Software downloaded by the Licensee from the DL_POLY_4 Website immediately after the Licensee agrees to the terms and conditions of this Licence Agreement the DL_POLY_4 Website the website with the URL http www ccp5 ac uk DL_POLY and any website that from time to time replaces that website a Harmful Element any virus worm time bomb time lock drop dead device trap and access code or anything else that might disrupt disable
160. The link cells algorithms for many body and tersoff forces in DL_POLY_4 cannot work with less than 3 secondary link cells per dimension This depends on the cell size widths as supplied in CONFIG and the largest system cut off as specified in CONTROL although it may be drawn or overridden by cutoffs specified as part of some potentials parameter sets in FIELD 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 precision or and increase cutoff Message 321 error LFV quaternion integrator failed This indicates unstable integration but may be due to many reasons Action 234 STFC Appendix D Rethink the simulation model Increase mxquat in CONTROL and resubmit or use VV integration to check system stability Message 340 error invalid integration
161. U riz k y Electrostatics rij gt aa 2 9 TEQE Tij where qe is the charge on an atom labelled It is worth noting that the Coulomb potential switches to the particular model of Electrostatics opted in CONTROL 9 Shifted finitely extendible non linear elastic FENE potential 33 34 35 fene AN iA 0 5 k R In i 542 r A lt Ro 2 10 ij OO rij A gt Ro 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 equation 2 94 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 Ages ante 0 10 AMOEBA force field bond potential 36 amoe U rig k rig ro 1 2 55 rig ro 7 12 2 55 rij 70 2 11 11 Tabulated potential tab The potential is defined numerically in TABBND see Section 4 3 and Section 6 1 8 In these formulae r is the distance between atoms labelled and j Tij Ir Sah 2 12 where ry is the position vector of an atom labelled The force on the atom j arising from a bond potential is obtained using the general formula 0 i re Tij gt 2 13 Tij Note some DL_POLY_4 routines may use the convention that Tij T rj 14 STFC Secti
162. Wallenius J Domain C Nordlund K and Malerba L 2005 Phys Rev B 72 2141191 2141196 31 Dai X D Kong Y Li J H and Liu B X 2006 J Phys Condens Matter 18 4527 4542 32 Cleri F and Rosato F 1993 Phys Rev B 48 22 32 Johnson R A 1989 Phys Rev B 39 12556 40 Kumagai T Izumi S Hara S and Sakai S 2007 Comput Mat Sci 39 457 41 Eastwood J W Hockney R W and Lawrence D N 1980 Comput Phys Commun 19 215 44 45 46 Fennell C J and Gezelter D J 2006 J Chem Phys 124 234104 48 50 131 132 Neumann M 1985 J Chem Phys 82 5663 49 Fuchs K 1935 Proc R Soc A 151 585 51 53 Essmann U Perera L Berkowitz M L Darden T Lee H and Pedersen L G 1995 J Chem Phys 103 8577 52 185 Fincham D and Mitchell P J 1993 J Phys Condens Matter 5 1031 54 Lindan P J D and Gillan M J 1993 J Phys Condens Matter 5 1019 54 55 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 55 112 Schroder U 1966 Solid State Commun 4 347 349 55 Shardlow T 2003 SIAM Journal on Scientific Computing 24 4 1267 1282 62 65 76 Leimkuhler B Noorizadeh E and Theil F 2009 J Stat Phys 135 261 277 62 65 74 Ikeguchi M 2004 J Comp Chemi 2
163. YPES analyse all sample every 100 nbins 1000 rmax 5 0 DIRECTIVES TO INVOKE PRINTING FOR ANY DEFINED INTER RDF gt VDW amp INTRA bonded MOLECULAR PDF ANALYSIS print analysis The analyse directive acts in a similar manner to that of the rdf directive outlining i the frequency of sampling in steps frames and ii the number of bins over the cutoff interval of the specified interaction It is only for bonded pairs that this cutoff needs specifying whereas for angles the possible ranges are known a priory by definition If no cutoff is supplied for bonds then it defaults to 2 A It is worth noting that for Poe cutofl max the sake of accuracy the number of bins per PDF must be larger than or equal to Nmin nint where the max bin size Ajax is defined internally for each type of PDF see setup module f90 Otherwise it will default to max Nmin Niap where Niap is the number of bins on the grid defined in the corresponding tabulated force field data file TAB if it is provided otherwise Niap 0 In particular for bonds Amax is 0 01 A and for angles it is 0 27 180 i e 0 2 degree If analyse all option is used in conjunction with any specific directive then it triggers the analysis on all PDFs while enforcing on the individually targeted PDF s the following parameters i its sampling interval frames only if it is smaller than and ii its grid number only if it is larger than those specified for the target
164. _POLY 4 has found more than one ensemble directive in the CONTROL file Action Locate extra ensemble directives in CONTROL file and remove Message 416 error conflicting force options in CONTROL file DL_POLY_4 has found incompatible directives in the CONTROL file specifying the electrostatic interactions options Action Locate the conflicting directives in the CONTROL file and correct Message 430 error integration routine not available A request for a non existent 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 236 STFC Appendix D 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 angula
165. a RD strategy 5 6 7 8 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 3 9 10 5 6 and is best suited for large molecular simulations from 10 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_Classic 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 Classic Users are reminded that we are interested in hearing what other features could be usefully incorporated 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 Systems DL_ POLY_4 will simulate the following molecular
166. 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 directive 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 ex ceeded the neighbour list array dimensions Action Consider using densvar option in CONTROL for extremely non equilibrium simulations or increase by hand mxlist in SET_BOUNDS Message 107 error too many pairs for rdf look up specified This should never happen A possible reason is corruption in FIELD or and DL_POLY 4 executable Action See action notes on message 14 above 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 h
167. 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 jo Wj Tj R S 6 7 2 j 1 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 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 i s etc site m integer m th 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 8 teth n where nis the
168. 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_O_VV and NVE_0_LFV implement the Verlet algorithm in velocity and leapfrog flavours respectively for free particles and calculate the instantaneous temperature Whereas the 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 15 where U is the potential energy of the system and Ekin 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 61 STFC Section 3 2 NVE_0_vvV NVE_0_LFV Constant E algorithm NVE_1_VV NVE_1_LFV The same as the above but also incorporating RB integration DPD_THERMOSTAN A Constant T algorithm DPD 71 NVT_EO_vV NVT_EO_LFV Constant Egin algorithm Evans 2
169. able to provide See Section 7 2 2 for more insight on the DL POLY_4 source code structure 5 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 simulation It is the routine that first opens the OUTPUT file Section 6 2 which provides the summary of the job The root program calls the molecular dynamics cycle routines LEV mMD_LFV or LEV 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 control 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 aforementioned root directories 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 Section 7 2 2 Should additional functionality be added to DL_POLY_4 by the user the SET_BOUNDS routine and its support s
170. access to source code for 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 STFC Preface ACKNOWLEDGEMENTS DL_POLY_4 was developed at Daresbury Laboratory DL http www dl ac uk the Science and Tech nology 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 Re search Council NERC http www nerc ac uk Advice assistance and encouragement in the development of DL_POLY_4 has been given by many peo ple 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
171. acteristic paramteres for energy e and distance or ro terms The available types of mixing within DL POLY 4 are borrowed from 51 The rules names and formulae are as follows 1 Lorentz Berthelot Oi 0 Eij y Ej Dij 9 2 103 2 Fender Halsey 2 104 3 Hogervorst good hope j JG 5 Vij Oi Oj 2 105 4 Halgren HHG EP ej o 0 5 Waldman Hagler rd 5 oy FFE 2 107 6 Tang Toennies 13 137 13 cijah feo ejos jo a eH 2 108 7 Functional 3 7 3 3 2 5727 3 6 Ej 0 Oj 1 o 03 Eij a UA Do 4 o o l 2 109 2 k o L 0 i Oi 0 4 0 ci It is woth noting that the and j symbols in the equations for mixing denote atom types species and the indices for the same species interaction parameters are contracted to a single species index for simplicity 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 above 30 OSTFC Section 2 3 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 11 12 and the second is the Finnis Sinclair model FS 13 Both are density dependent potentials derived from density functional theory DFT and describe the bonding of a metal atom ultimately in te
172. actions and site related modules RDF_MODULE Z_DENSITY_MODULE 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 or statistical grid arrays needed for the calculation of the particular interaction or distribution function in the DL _POLY_4 scope They all depend on KINDS_F90 with allocation methods depending on SETUP_MODULE e external field module EXTERNAL_FIELD_MODULE This module defines all variables and potential arrays needed for the application of an external field in the DL_POLY_4 scope It depends on KINDS_F90 and its allocation method on SETUP_MODULE 188 STFC Section 7 2 e langevin module LANGEVIN_MODULE This module defines all variables and arrays needed for the application of NPT and Na T Langevin rou tines 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 Gradient 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 driven properties in the DL_POLY_4 scope when an infrequent SPME option is opted for in CONTROL It depends on KIND
173. ain 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 reports results Action Report to authors Message 88 error legend array exceeded in build_book_intra The second dimension of a legend array has been exceeded Action If you have an intra molecular like interaction present in abundance in your model that you suspect is driving this out of bound error increase its legend bound value mxfinteraction at the end of SCAN_FIELD recompile and resubmit If the error persists contact authors 225 STFC Appendix D Message 89 error too many four body dihedrals inversions potentials specified This should never happen Action Report to authors Message 90 error specified tersoff potentials have different types This is not allowed Only one general type of tersoff potential is al
174. air 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 ryqw 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 a on an atom k derived from this potential is calculated in the standard way i NV U metal 2 119 We rewrite the EAM FS potential equation 2 110 as Umetal de U D rij 2 120 i 1 jAi N Us Y F pi i 1 where r F A i The force on atom k is the sum of the derivatives of U and U2 with respect to rx which is a ale as a sum of pair forces OU _ Ln Ue ovaa Orig _ y Ves Tj Tki Org AA Orij Ork Err Or Tkj oUz A ar Opi riz Orij 2 121 ork 2 Op Pr Ori Org _ E OF pik rik Orik X F Ors rej Ok Op Orik Ork Op Orkj Ork i 1 4k j l JAk a z ar Opry Taj Tki jek OPR 005 Orkj Trj 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 proce
175. al configuration of a maximum of 20 atoms in the system The configuration information given is based on the value of levcfg in the CONFIG file If levcfg is 0 or 1 positions and velocities of the 20 atoms are listed If levcfg is 2 forces are also written out 6 2 6 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 MD step number eng tot total internal energy of the system temp_tot system temperature in Kelvin eng cfg configurational energy of the system eng src configurational energy due to short range potential contributions eng_cou configurational energy due to electrostatic potential eng bnd configurational energy due to chemical bond potentials eng_ang configurational energy due to valence angle and three body potentials eng dih configurational energy due to dihedral inversion and four body potentials eng tet configurational energy due to tethering potentials line 2 time ps elapsed simulation time in pico seconds since the beginning of the job eng pv enthalpy of system temp_rot rotational temperature in Kelvin vir_cfg total configurational contribution to the
176. al 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 InOut the coming in value of the argument 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 STFC Section 1 3 1 3 4 Target Platforms DL_POLY_4 is intended for distributed memory parallel computers 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 FORTRAN9O compiler 1 3 5 Internal Documentation All subroutines are supplied with a header block of FORTRAN90 comment records giving 1 The name of the author and or modifying author
177. al parameter see Table 6 14 variable 8 real potential parameter see Table 6 14 variable 9 real potential parameter see Table 6 14 variable 10 real potential parameter see Table 6 14 variable 11 real potential parameter see Table 6 14 potential n record 2n 1 potential n record 2n cross term 1 record 2n 1 atmnam 1 a8 first atom type atmnam 2 a8 second atom type variable a real potential parameter see Table 6 14 variable b real potential parameter see Table 6 14 variable c real potential parameter see Table 6 14 cross term n n 1 2 record 2n n n 1 2 e kihs atomkey expects 3n records specifying n particular Tersoff single atom type parameter sets in the following manner potential 1 record 1 atmnam a8 atom type key a4 potential key see Table 6 14 variable 1 real potential parameter see Table 6 14 variable 2 real potential parameter see Table 6 14 variable 3 real potential parameter see Table 6 14 variable 4 real potential parameter see Table 6 14 variable 5 real cutoff range for this potential 158 STFC Section 6 1 potential 1 variable 6 variable 7 variable 8 variable 9 variable 10 variable 11 potential 1 variable 12 variable 13 variable 14 variable 15 variable 16 potential n potential n record 2 real real real real real real record 3 real real real real real record 2n record 2n 1 potential parameter potential parameter pote
178. and make without a nominated target it will produce a list of known targets The full specification of the make command is as follows make lt TARGET gt lt EX gt lt BINROOT gt where some or all of the keywords may be omitted The keywords and their uses are described below Note that keywords may also be set in the UNIX environment e g with the setenv command in a TCSH shell or export in BASH shell 5 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 5 2 1 2 Modifying the Makefiles 1 Changing the FORTRAN9O 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 FORTRAN90 man ual and the path to the MPI implem
179. and printing of Z density profiles have 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 6 2 6 11 Velocity Autocorrelation Functions If both calculation and printing of velocity autocorrelation functions have been requested by selecting directives vaf and print vaf in the CONTROL file the velocity autocorrelation function for the system either time averaged or the last complete sample is printed out as the last part of the OUTPUT file This is written by the subroutine VAF_COMPUTE First the details of the calculations are stated either the number of samples used to give a time averaged profile or the number of the last completed sample with its starting time The absolute value of the velocity autocorrelation function for the system at t 0 C 0 is then stated The
180. any temperature control options control the full kinetic energy of the system 56 OSTFC Section 2 9 and thus the only ensemble valid under this conditions and possible within DL_POLY_4 at the present is the micro canonical NVE The user is advised to be careful with the parameters units For more insight do examine Table 6 17 and the example at equation 6 9 in Section 6 1 3 In DL_POLY_4 external field forces are handled by the routines EXTERNAL_FIELD_APPLY and EXTERNAL_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 to 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
181. appen 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 228 STFC Appendix D 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 Contact 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 Action Correct the erroneous part in FIELD and resubmit Message 113 error intra molecular 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 Alternatively 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
182. ariable variable variable variable variable variable variable variable variable variable variable variable max number of grid points in potential arrays gt 1004 max number of PDFs per type max number of grid points for PDFs arrays max number of grid points for chemical bonds PDFs max number of grid points for bond angles PDFs max number of grid points for dihedral angles PDFs max number of grid points for inversion angles PDFs 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 max number of local atoms per node max dimension of the transfer buffer for deport functions max dimension of the transfer buffer for statistics functions max dimension of the transfer buffer for export functions max dimension of the transfer buffer for shared units functions max dimension of the principle transfer buffer the machine representation of 0 at working precision the machine representation of 0 5 at working precision the machine representation
183. as follows 1 Harmonic harm U dijen 5 isan 0 2 58 2 Harmonic cosine hcos U itkn c08 dizkn coslo 2 59 3 Planar potential plan U dijkn A 1 cos ijkn 2 60 4 Extended planar potential xpln U bijtn 5 1 cos m dijin do 2 61 5 Tabulated potential tab The potential is defined numerically in TABINV see Section 4 3 and Section 6 1 8 In these formulae ijkn is the inversion angle defined by T gt 8 W Pijkn cos E 2 62 TijWkn with 23 STFC Section 2 2 and the unit vectors le MERA ERE ca Dj ME Ll 2 64 As usual Tij rj T etc and the hat indicates a unit vector in the direction of r The total inversion potential requires the calculation of three such angles the formula being derived from the above using the cyclic permutation of the indices j gt k gt n gt j etc Equivalently the angle ijen may be written as 9 21 2 Te Ti U dijkn cos Eiz fin A en 2 65 ij Formally the force on an atom arising from the inversion potential is given by A f fe gra O Pien 2 66 with being one of i j k n and a one of x y z This may be expanded into O 1 f Pd By eet a Uld are dijkn ort Odbijkn dijkn x o eg tpn a Lij TA 2 67 Ore Tij Following through the extremely tedious differentiation gives the result 1 o a U biin X 2 68
184. at the file be written to a scratch disk capable of accommodating a large data file The RSDDAT has the following structure record 1 header a72 file header record 2 rdef real displacement qualifying cutoff A in last frame frame integer number configuration frames in file records integer number of records in file For timesteps greater than nsrsd the RSDDAT file is appended at intervals specified by the displacements 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 6 6 rrsd real displacement qualifying cutoff A record ii displacements al3 the character string displacements nrsd integer the total number of displacements record iii cel1 1 real x component of a cell vector cel1 2 real y component of a cell vector cel1 3 real z component of a cell vector record iv cell 4 real x component of b cell vector cell 5 real y component of b cell vector cel1 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 nrsd displacements for the current timestep as each atom has the following data lines record a 172
185. ate of the velocity at full step v t 1 FF f t f t At 3 75 2 LFV The iterative part is as follows 1 1 f t u t At ult At At xl 70 HEE AD r t At u t 5 At 3 76 3 SHAKE 4 Full step velocity 1 1 1 At u t A u t 3 e 48 u t 5A 3 77 5 Thermostat 1 1 PA E eee x t At e x t 3At At kin t 20 2 2 dmass 1 1 1 TE zp At 4 x 340 3 78 STFC Section 3 4 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 A e HuvtT Hyve mass AU f kp Text J x s ds 3 79 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 The routines NVT H1 VV and NVT_H1_LFV implement the same but also incorporate RB dynamics 3 4 6 Gentle Stochastic Thermostat The Gentle Stochastic Thermostat 72 77 is an extension of the Nos Hoover algorithm 30 dr t a a 20 9 _ vu 3 80 in which the thermostat friction x has its own Brownian dynamics NN 2 k Tex mass t dx t _ 2Epin t 20 aati V2 7 kB Text q dw t 3 81 dt mass mass dt governed b
186. atom models supplied in PDB file format into input files that are recognisable and ready to run with DL_POLY Classic and DL_POLY_4 programs with minimum users intervention This basically involves the conversion of the users atomic configuration in simple xyz coordinates into identifiable atom types base on a particular user selectable potential schemes and then automatically generate the DL_POLY configuration file CONFIG the force field file FIELD and a generic control file CONTROL 2 Force field editor DL_FIELD allows the user to edit or modify parameters of a particular force field scheme in order to produce a customised scheme that is specific to a particular simulation model In addition the standard force field model framework can also be easily modified For instance introduction of pseudo points and rigid body implementation to an otherwise standard potential scheme such as CHARMM or AMBER etc 3 Force field library repertoire DL_FIELD contains a range of popular potential schemes see below all described in a single DL_FIELD format that are also easily recognisable by the user for maintenance purposes Users can easily expand the existing library to include other new molecules 115 STFC Section 5 3 Force Field Schemes The available force field schemes are as follows CHARMM proteins ethers some lipids and carbohydrates AMBER proteins and Glycam for carbohydrates OPLSAA proteins DREIDING General for
187. avity the system is treated as a dielectric continuum The occurrence of any net dipole within the cavity induces a polarisation in the dielectric which in turn interacts with the given molecule The model allows the replacement of the infinite Coulomb sum by a finite sum plus the reaction field The reaction field model coded into DL POLY 4 is the implementation of Neumann based on charge charge interactions 64 In this model the total coulombic potential is given by 1 Born 5 2 206 a Gj In Taj 2R3 where the second term on the right is the reaction field correction to the explicit sum with Re the radius of the cavity The constant Bo is defined as 2 1 1 2 207 aan 2 207 with e the dielectric constant outside the cavity The effective pair potential is therefore 1 Bor U rij dj a 2 208 rij grege oY F 2R3 49 STFC Section 2 4 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 44 2 209 Arege Re 2 The effective pair force on an atom j arising from another atom n within the cavity is given by E A ims 2 210 4reoe r ie In DL_POLY_4 the reaction field is optionally extended to emulate long range orderin
188. bic constraint on the NoT ensemble The constraint can be strengthened further to a semi orthorhombic one by imposing that the MD cell change isotropically in the x y plane which leads to the following changes in the equations above raat _ orx t Tyy t 2 Pext ZZ Yext hz t V t 2 Exin t X t Nao t f Pmass f Pmass a 8 zx y 3 173 2 mass T a t Hyp y 0T Hnvet dass 0 aL wl Pot V t f 2 kp Text 7 x s ds Although the Martyna Tuckerman Klein equations of motion have same conserved quantities as the Nos Hoover s ones they 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 81 which is not the case for Nos Hoover NPT and NaT ensembles The NPT and NoT versions of the MTK ensemble are implemented in the DL_POLY_4 routines 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 point 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 eit
189. c uk DL_POLY and examine the useful links within FAQ User Forum etc If you are looking to gain more in depth experience then regular training workshops are available To find about upcoming workshops subscribe to our mail list by following instructions in Section 1 7 If you need one to one training wish to collaborate scientifically and or would like to become a contribu tor developer then get in touch with me Dr I T Todorov by emailing to ilian todorovUstfc ac uk Best of luck 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 OSTFC 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 dy namics simulations of macromolecules polymers ionic systems and solutions on a distributed memory parallel computer It is available in two forms DL _POLY Classic written by Bill Smith Tim Forester http www ccp5 ac uk DL_POLY_CLASSIC and DL POLY_4 written by Ilian Todorov amp Bill Smith 2 3 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 4 http www ccp5 ac uk DL_POLY The two forms of DL_POLY differ primarily in their method of exploiting parallelism DL POLY Classic uses a Replicated Dat
190. ca da A a aa 2 we IA we SR Be 266 F DL POLY 4 Academic Licence Agreement 269 El Whe Snort Story sia 2 we ee A a a a ee es 269 STFC Contents F2 The full version s o sana on 6 do aa 6 a BERR A A ESS DSS BE 269 Bibliography 277 Index 281 Xl List of Tables 6 1 6 2 6 3 6 4 6 5 6 6 6 7 6 8 6 9 6 10 6 11 6 12 6 13 6 14 6 15 6 16 6 17 Internal Tragectory Defects Pile Key 224424 e644 6545 36 6564 852 oe es 134 Internal Restart Key ooo Bas eed ea Pew de eae ee be hee ede ke 136 Interital Ensemble Key eo 24 8 we Se ee OE ae Rs Ee ee oe Ga a 136 Blectrostatics Key cams ye kee A ae ewe ee ae ee a Ee 139 CONFIG File Key record 2 lt c bs ge ee Bee REA AAA A 144 Periodic Boundary Key record 2 i465 424588 4 he DER RG eed a kaded 144 Tethering Potentials coords a d ale ataa ic RE REAR EEE EE Ree YS 150 Chemical Bond Potentials s s s cos s a poa 68844 5 eb 5G 2 bebe RES PERE eG a 151 Valence Angle Potentials o a sore i sos pud a ae kh eae a A Ra ea a e a p 152 Dihedral Angle Potentials a eaa ee 153 Inversion Angle Potentials s 206 eg poe deui goin a aa G SR RE a a 154 Pair Potentials s ccecce 444 50 4 kbs Bade bee beds e ae eae a AS 156 Metal Potential cios raros ede a ede FAAS RE Eee As a 157 Tersott Potential cocos e cin eb AG eee ee ade be ae ek ee 159 Three body Potentials 2 4 5404 54 fs ee he oe a aaa a EEE a ES 160 Four body Potentials lt o se sa asara 28 445684 3b RE H
191. cale rcut f cutoff f rlxtol f rpad f padding f rvdw cutoff f scale temperature every n seed nj Na n3 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 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 act exactly the same as the cutoff f option above set tolerance for relaxed shell model to f default f lin DA ps act exactly the same as padding f option above set required short ranged interactions cutoff to f A rescale system temperature every n steps during equilibration with respect to the last equilibration step atomic velocities are scaled collectively seed control to the random number generator used in the generation of gaussian distributions and stochastic processes set shake rattle tolerance to f default f 1079 calculate electrostatic forces using force shifted Coulomb sum calculate electrostatic forces using force shifted Coulomb sum with Fennell 63 damping Ewald like convergence parameter a in Ao calculate electrostatic forces using force shifted Coulomb sum with Fennell 63 damping Ewald like convergence d
192. case or ii sdensity functions in the 2BEAM potential case or iii sden and dden functions in the 2BEEAM potential case ngrid integer number of function data points to read in limit 1 real lower interpolation limit in A for dens sden dden and pair or in density units for embe semb demb limit 2 real upper interpolation limit in A for dens sden dden and pair or in density units for embe semb demb function data records number of data records Int ngrid 3 4 data 1 real data item 1 data 2 real data item 2 data 3 real data item 3 data 4 real data item 4 6 1 7 3 Further Comments The tabled data are used to fill the internal arrays vmet dmet and fmet and optionally dmes and fmes for the 2B extensions of EAM and EEAM see Section 2 3 2 The force arrays are generated from these by the METAL_TABLE_DERIVATIVES routine using a five point interpolation procedure During simulation 166 OSTFC Section 6 1 interactions beyond distance Min reut Limit 2 are discarded whereas interactions at distances shorter than limit 1 will cause the simulation to abort For the purpose of extrapolating the embedding functions F p beyond its limit 2 specified in the tabulated array it is assumed that F p gt limit 2 F p limit 2 6 14 The simulation will however abort if any local density is less than the limit 1 for its corresponding embed ding function It is worth noting that in the 2BEAM and 2BEEAM the s band contribution
193. ce field for covalent molecules PCFF Polyorganics and other covalent molecules Model Construction DL_FIELD does not have feature to construct molecular models This can be achieved by either using DL_POLY GUI 21 or any other standard molecular building packages The output files must be converted into the PDB format In the case of proteins these structures are usually obtained from data banks such as PDB These raw PBD files must first be preprocessed by the user before they are in a readable format for DL_FIELD To ensure this it is advisable that users take into consideration the following steps 1 Decide on inclusion exclusion of and if necessary manually delete molecular residues that involve multiple occupancies in crystalline structures 2 Usually hydrogen atoms are not assigned in the raw PDB file The molecules must therefore be pre filled with hydrogen atoms protonated by using any standard packages available The user must ensure that proper care is taken of terminal residues which must also be appropriately terminated 3 Decide on the various charge states of some amino acids such as histidine HIS lysine LYS glu tamic acid GLU etc by adding or deleting the appropriate hydrogen atoms Force field schemes such as CHARMM will have different three letter notations for amino acids of different charge states DL_FIELD will automatically identify these differences and assign the appropriate potential parame ters ac
194. centrations of a single element revert to the standard EAM or EEAM In such case the densities functions must be zeroed in the DL_POLY_4 TABEAM file For EAM EEAM 2BEAM and 2BEEAM potentials all the functions are supplied in tabular form via the table file TABEAM see section 6 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 Potentials The Tersoff 17 potential is is a bond order potential 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 At the present there are two versions of this potential available in DL_POLY_4 ters and kihs In these particular implementations ters has 11 atomic and 2 bi atomic parameters whereas kihs 61 has 16 atomic parameters The energy is modelled as a sum of pair like interactions where 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 Uij folriz frlrij vag falrig 2 156 where
195. cle 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 138 STFC Section 6 1 13 14 15 16 17 18 19 a site s is claimed and another particle p is located within the sphere around it then p becomes an interstitial associated with s After all particles and all sites are considered it is clear which sites are vacancies Finally for every claimed site distances between the site and its first hand claimee and interstitials are compared and the particle with the shortest one becomes the real claimee If a first hand claimee of s is not the real claimee it becomes an interstitial associated with s At this stage it is clear which particles are interstitials The sum of interstitials and vacancies gives the total number of defects in the simulated MD cell Frozen particles and particles detected to be shells of polarisable ions are not considered in the defect detection Note that the algorithm cannot be applied safely if Rgef 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 Raef 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
196. consist of 44 352 and 354 816 ions respectively Simulation at 400 K using NPT Berendsen ensemble using both particle and rigid body dynamics with SPME electrostatics 8 1 21 Test Case 41 and 42 Calcite nano particles in TIP3P water In this case 600 and 4 800 molecules of calcium carbonate in the calcite structure form 8 and 64 nano particles which are suspended in 6 904 and 55 232 water molecules represented by a flexible 3 centre TIP3P model Simulation with SPME electrostatics at 310 K and 1 atmosphere maintained in a Hoover NPT ensemble These systems consist of 23 712 and 189 696 ions respectively 199 STFC Appendix 8 1 22 Test Case 43 and 44 Iron Carbon alloy with EEAM In this case a steel alloy of iron and carbon in ratio 35132 to 1651 is modelled using an EEAM potential forcefield Simulation at 1000 K and O atmosphere is maintained in a Berendsen NPT ensemble These systems consist of 36 803 and 294 424 particles respectively 8 1 23 Test Case 45 and 46 Iron Cromium alloy with 2BEAM In this case a steel alloy of iron and chromium in ratio 27635 to 4365 is modelled using an 2BEAM potential forcefield Simulation at 300 K and 0 atmosphere is maintained in an Evans NVT isokinetic ensemble These systems consist of 32 000 and 256 000 particles respectively 8 1 24 Test Case 47 and 48 Hexane and methanol melts full atomistic and coarse grained simulations TEST47 and TEST48 contain a Hexane and a Methanol melts respective
197. cordingly 4 For cysteine CYS molecules with disulphide bonds thiolate hydrogen atoms must be removed DL FIELD will automatically define disulphide bonds between the molecules provided the S S dis tance is within a sensible value 5 DL_FIELD does not solvate the molecules and it is the user s responsibility to add water by using any standard package available for example the DL_POLY GUI 21 Fore more details or further information please consult the DL_FIELD manual and website http www ccp5 ac uk DL_FIELD 5 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 the CONFIG file before running DL_POLY_4 116 STFC Section 5 3 5 3 4 Analysing Results DL_POLY_4 is not designed to calculate every conceivable property you might wish from a simulation Apart from some
198. 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 per mol kcal mol k Joules per mol kJ mol Kelvin per Boltzmann Kelvin Boltzmann or the DL POLY 4 internal units 10 Joules per mol internal There is no default value Failure to specify any of these correctly or reference to other energy units will result in this error message See documentation of the FIELD file Action Correct energy keyword on units directive in FIELD file and resubmit Message 6 error energy unit not specified A units directive is mandatory in the FIELD file This error indicates that DL POLY_4 has failed to find the required record Action Add units directive to FIELD file and resubmit Message 7 error selected external field incompatible with selected ensemble NVE only Action Change the external field directive in FIELD file and or the type of ensemble in CONTROL and resubmit Message 8 error ewald precision must be a POSITIVE real number Ewald
199. cp vpLH data TEST 1 HISTORY cp vpLH data TEST 1 FIELD cp vpLH data TEST 1 TAB cp vpLH data TEST 1 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 pv data TEST 1 cp vpLH CONTROL data TEST 1 cp vpLH CONFIG data TEST 1 cp vpLH FIELD data TEST 1 cp vpLH TAB data TEST 1 cp vpLH REFERENCE data TEST 1 cp vpLH HISTORY data TEST 1 mv v REVCON data TEST 1 mv v CFGMIN data TEST 1 mv v OUTPUT data TEST 1 mv v HISTORF data TEST 1 mv v DEFECTS data TEST 1 mv v STATIS data TEST 1 mv v DAT data TEST 1 mv v PMF data TEST 1 mv v TAB data TEST 1 mv v REVIVE data TEST 1 chmod R a w 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 210 STFC Appendix C 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
200. d FS classes see below 31 STFC Section 2 3 3 2BEAM potential 2beam Similar to EEAM for the s density terms and to EAM for the d ones It is and given in the form of interpolation arrays from the TABEAM file but the rules for combining the potentials from different metals are different from both EAM EEAM and FS classes see below 4 2BEEAM potential 2beeam Similar to EEAM for both s and d density terms It is and given in the form of interpolation arrays from the TABEAM file but the rules for combining the potentials from different metals are different from both EAM EEAM 2BEAM and FS classes see below 5 Finnis Sinclair potential 13 fnsc Finnis Sinclair potential is explicitly analytical It has the fol lowing form AE rij cy co Cir ij car gt Py SC gt 2 rig d eae ptr q Ta a B 7 rd 2 114 0 rj gt d F p Aypi with parameters co C1 C2 C A d 8 both c and d are cutoffs Since first being proposed a number of alternative analytical forms have been proposed some of which are described below The rules for combining different metal potentials to model alloys are different from the EAM potentials see below 6 Extended Finnis Sinclair potential 58 exfs It has the following form Vis rij rij c co CIT ij cari cari F cary 1 i Se JME UY 0 2 Tij gt C rij d B Uri dd riz lt d pyra Le ii 2 115 F p Ay with parameters co C
201. d centre for all DL_POLY users to exchange comments and queries You may access 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 10 Chapter 2 Force Field Interactions Scope of Chapter This chapter describes the variety of interaction potentials available in DL_POLY 4 11 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 agnostic and adaptable While it is not supplied with its own force field parameters many of the functions familiar to GROMOS 18 Dreiding 19 and AMBER 20 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 U r Toye N 5 Ushet tshels Peores Tshell ishel l Neeth So Uteth iteth T T gt tteth 1 Noond 5 Ural ends Pas Tp lbond 1 Nangl 5 Uangl iangl Tab fe tangl 1 Ndiha 5 aia tata Tas Tb Te Ta tdiha
202. d 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 1 e j specifies the number of processors that shall access the disk k specifies the maximum 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 26 The no vom option will trigger a default bypass of the GETVOM routine which will return zero and thus no COM removal will happen Note that this will lead to COM momentum accumulation for many though not all ensembles Such accumulation will propagate to the generation of flow in the MD cell and ultimately suppress the thermal motion of the particles in the system lea
203. d the sum includes all sites Nsites in the body The position of the rigid unit is defined as the location of its centre of mass R 1 Nsites R u 5 Mil gt 3 175 j l where r is the position vector of atom j The rigid body translational velocity V is defined by 1 Nsites V gt 3 m9 3 176 j 1 and its angular momentum J can then be defined by the expression Nsites J 5 Mj 4 x e v 3 177 j 1 where v is the velocity of atom j and d is the displacement vector of the atom j from the COM is given by r R 3 178 The net translational force F acting on the rigid body unit is the vector sum of the forces acting on the atoms of the body He Xd 3 179 T d xf 3 180 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 1 Y m dfbap ary 3 181 j l and COM stress and virial respectively written down as Nsites B ap _ Q oP X df j l Nsites W Y Gt 3 182 j 1 1 An alternative approach is to define basic and secondary particles The basic particles are the minimum 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
204. d values imcon integer Periodic boundary key See Table 6 6 for permitted values megatm integer Optinal total number of particles crystalographic entities record 3 omitted if imcon 0 cell 1 real x component of the a cell vector in cel1 2 real y component of the a cell vector in A cell 3 real z component of the a cell vector in A record 4 omitted if imcon 0 cell 4 real x component of the 6 cell vector in A cel1 5 real y component of the 6 cell vector in A cel1 6 real z component of the b cell vector in A record 5 omitted if imcon 0 cell 7 real x component of the c cell vector in A cell 8 real y component of the c cell vector in A cell 9 real z component of the c cell vector in A 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 Also it is worth mentioning that the periodic boundary conditions PBC as specified in Table 6 6 and described in detail in Appendix B refer generally to a triclinic type of super cell for which there are no symmetry assumptions Records 3 4 and 5 contain the Cartesian components of the super cell s lattice vectors in A DL_ POLY 4 can only tract triclinic type of super cells as the only types of super cell shapes that are commensurate with the domain decomposition DD parallelisation strategy of it However this is not a restrictio
205. d with each directive may be one or more keywords which may qualify a particular directive by for example adding extra options Directives can appear in any order in the CONTROL file except for the finish directive which marks the end of the file Some of the directives are mandatory for example the timestep directive that defines 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_4 121 STFC Section 6 1 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 keyw
206. de then jump to the Makefiles section of the DL POLY_4 README Appendix E or alternatively view the README TXT in source and follow the instructions within If you have compiled successfully then a freshly date stamped file named DLPOLY Z should appear in the listing of the execute subdirectory the 1s haltr command issued on a Linux Unix like shell within execute will place the executable in the last row of the list If unsuccessful then you should read the Compiling and Running DL POLY_4 Section 5 2 1 To run the code you first need to place the necessary input files within execute TEST cases containing suitable input files as well as examples of output files can be obtained at the DL POLY 4 FTP site ftp ftp dl ac uk cep5 DL_POLY Examine the contents of data README txt and bench README txt for more information To run the serial version you simply issue the command DLPOLY Z or DLPOLY Z cu within the execute subdirectory If you have compiled a parallel version and are running it on a parallel machine then naturally you will need to familiarise yourself with the local procedures of how to run jobs on that machine In general though running a parallel job will usually require that you issue a necessary run command e g mpirun n 8 DLPOLY Z or submit a job script from within execute If you need to know more then search the manual and examine sections of interests You may also wish to visit DL_POLY project web page http www ccp5 a
207. demic 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 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 3 Bug reports 4 Access to the DL_POLY online forum Daresbury Laboratory also maintains a DL_POLY_4 associated electronic mailing list dipoly_4_news to which all registered DL_POLY_4 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_4 user but not on this list you may request to be added by sending a mail message to majordomo dl ac uk with the one line message subscribe dl_poly 4_news The DL POLY Forum is a web base
208. der to use openKIM functionality within DL_POLY_4 one must further ensure that DL_POLY_4 is cross compiled with openKIM For guidance on this together with testing please refer to README_KIM TXT in source and follow instructions within 58 Chapter 3 Integration Algorithms Scope of Chapter This chapter describes the integration algorithms coded into DL_POLY_4 99 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 22 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 VV1 o 1 At f t t A 1 vtt 3At olet gt E 3 1 where m is the mass of a site and At is the timestep 1 r t At e r t At v t At 3 2 2 FF Between the first and the second stage a
209. ding to the so called frozen ice cube effect It is worth nothing that this option must be turned on for the correct application of stochastic dynamics via the langevin temperature control NVT Langevin If 141 STFC Section 6 1 27 28 the option is not applied then the dynamics will lead to peculiar thermalisation of different atomic species to mass and system size dependent temperatures The replay force option will attempt to open a renamed HISTORY as HISTORF and instead fol lowing any integration scheme specified in CONTROL read the positions as integration outcomes and proceed with the usual MD cycle There are a couple of restrictions that may lead to failures of this feature s application e The CONFIG file at re start must be the same as the frame in HISTORF that CONTROL REVOLD attempts to re start from e If any two HISTROF consecutive frames are too far apart in time from each other then domain information reallocation follow up may break when the feature is used in parallel The rpad pad option will add extra distance pad if larger than f gt Min 0 05 0 5 reut A to the major cutoff rout to construct a larger link cell width rink Teut Tpad Which will trigger a construction of a larger Verlet neighbour list VNL while at the same time facilitate its conditional update rather at every timestpe The VNL conditaional update is check at the end of each tiemstep and triggered only when the m
210. distinguish 4 possible variants of each A Vers Vee Vie rag VPA rig and AA BB AB BA Pij rij Pij rij Pij rij Pij rij These forms recognise that the contribution of a type A atom to the potential of a type B atom may be different from the contribution of a type B atom to the potential of a type A atom In both EAM 60 and FS 15 cases it turns out that Yi ra Vee a a 2 148 though the mixing rules are different in each case beware This has the following implications to densities of mixtures for different potential frameworks e EAM case it is required that 60 pig rig pi rig pig rig pig rig gt 2 149 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 e EEAM case all densities can be different 52 53 po rig amp 0B rig A O44 raz A PEA Tag 2 150 e 2BEAM case similarly to the EAM case it is required that q AB q BB pij ry pij rij BA AA py rig Py Cy 2 151 for the d band densities whereas for the s band ones A A pip rig Pig Tis 2 152 which means that an atom of type A contributes the same s density to the environment of an atom of type B as an atom of type B to an environment of an atom of type A However in general Ar F 087 rag AA ri 2 153 e 2BEEAM case similarly to the EEAM case all s and d densities can be different AA
211. dure 33 STFC Section 2 3 2 EEAM force Information the same as that for EAM 3 2BEAM force Information the same as that for EAM However as there is a second embedding contribution from the extra band complexity Uz U U 4 2BEEAM force Information the same as that for EAM However as there is a second embedding contribution from the extra band complexity Uz U Ug 5 Finnis Sinclair force au N A 3 Tkj a 2 7uj Co cara carkj raj er 2c2r45 ky E j 1 Ak N d 2 Tki U D s i pal fate 4 4 3g rks d pu 2 122 Org jalgee 2 VPk PG f g 6 Extended Finnis Sinclair force U al e 5 Ari c co cir KR 4 Cor Car Cari j 1G h The rki c1 2c2rkj 3Cr Acyri 2 123 U N 1 1 y 3 Tki 2 rkj d 4B rk d 2 Ort La SS pe i lee 7 Sutton Chen force UM 8 Y tH Org j Lj k kI kj 9U mece 1 1 a rg e e Df is a j Lj k vPk Pij MTP Tk 8 Gupta force _0U1 wane 2AP x 1420 Tkj ork 7 TO E p ro Tki j l j k OU Bar 1 1 Tki Tro kj E de dj oo 20 12 2 125 Tk ER ro VPRO Pij TO Tkj 9 Many body perturbation component potential force e A Org OU2 N amet A 1 a Tkj a 2 126 Tk j Lj k vPk PG Tki Tki STFC Section 2 3 With the metal forces thus defined the contribution to be added to the atomic virial from each atom pair is i Y
212. e 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 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 DL POLY_4 is compiled in a netCDF enabled mode mpiio is the recommended method and for large systems master should be avoided and also THE DIRECT OPTION 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 otherwise 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 depen
213. e in fact it is and then failing at the current point It is quite possible despite considered as wrong practice that the user defined system of linear RBs is in fact generated from a system of CBs 3 per RB which has not been run in a high enough SHAKE RATTLE tolerance accuracy 10 8 and higher may be needed Check the definition of the rigid unit in the CONFIG file if sensible report the error to the authors Message 655 error FENE bond breaking failure A FENE type bond was broken Action Examine FIELD for erroneous directives if any correct and resubmit Message 660 error TABBND or PDF bond breaking failure A bond with potential defined in TABBND or for which intra molecular potential distribution is collected has exceeded its bondleghth limit Action If there is a TABBND present reconstruct TABBND with potentials defined over larger cutoff and try again If bonds PDF are collected increase their cutoff value in CONTROL Message 1000 error working precision mismatch between FORTRAN90 and MPI imple mentation DL_POLY_4 has failed to match the available modes of MPI precision for real numbers to the defined in sc kinds_f90 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 e
214. e y r t At r t where Z x At and Za x At are joint Gaussian random variables of zero mean sampling from a bivariate Gaussian distribution 76 Zi _ 07 0 Ry 3 37 La a gao At of0 4 Ry with ga PA LAN yeis 3 38 x and Ry 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 35 2 RATTLE_VV1 3 FF f t At e f t 3 39 4 VV2 1 u t At v t 4 At y 3 40 5 RATTLE VV2 The algorithm is self consistent and requires no iterations It is worth noting that the integration is condi tional upon the Cholesky factorisation which is impossible when At lt 02 07 That is why a safety check is put in place which when failed iteratively increases the integration timestep to a safe value with respect to the above condition The LFV implementation of the Langevin thermostat is straightforward 1 FF t e f t At E R t At 3 41 0 IS Ga a OSTFC Section 3 4 2 LFV and Thermostat At 2 At scale l y scalev 1 scale_f 2 scale scale 1 1 t R t v t At scale v u t At scale_f E RO 3 43 2 2 m 1 r t At r t At u t 54 where R t are the Langevin random forces as defined in equation 3 35 3 SHAKE 4 Full step velocity 1 1 1 u t 5 v t At u t At 3 44 Note that by the nature
215. e 452 error undefined vdw potential A form of vdw 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 VDW_GENERATE and DIHEDRALS_14_VDW will be required Message 453 error four body potential cutoff undefined The cutoff radius for a four body potential has not been defined in the FIELD file Action Locate the offending four body force potential in the FIELD file and add the required cutoff Resubmit the job 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 456 error external field xpis ton is applied to a layer with at least one frozen particle For a layer to emulate a piston no particle constituting it must be frozen Action Locate the offending site s in the FIELD file and unfreeze the particles 239 STFC Appendix D Message 461 error undefined metal pot
216. e 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 Message 69 error too many link cells required in three_body_forces The number of link cells required for the build up of the Verlet neighbour list as in link_cell_pairs or the calculation of three amp four body as well tersoff forces as in three_body forces four_body_forces ter soft body forces in the given model 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 Consider using densvar option in CONTROL for extremely non equilibrium simulations 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 help may be gained from increasing the cycle limit by using the directive mxshak in the CONTR
217. e d Pe eee be ee ee Pee 74 3 4 7 Dissipative Particle Dynamics Thermostat 76 Sw DArOStaiS 2 2 gc ae Ge Eo ARS E Rote ead See A ees 77 3 5 1 Instantaneous pressure and stress oo a e a 77 g2 Lanto vin Barostat uu sd case do Roe e a ee ae ea ae Be a 77 Sono Berendsen Barostal ueno foe a dad a ihe a ee oe ee fhe ee 83 3504 Nos Hoover Barostat i sa 6 420006 boo dee ee ee e ee 85 3 5 5 Martyna Tuckerman Klein Barostat es 91 3 6 Rigid Bodies and Rotational Integration Algorithms 93 3 01 Dese ption ot Rigid Body Unit lt i s acu a p ioe sd aa ale a ae 93 3 6 2 Integration of the Rigid Body Equations of Motion 95 3 6 3 Thermostats and Barostats coupling to the Rigid Body Equations of Motion 97 4 Coarse Graining Functionality 99 4 1 User Defined Coarse Grain Models with Tabulated Force FieldS 100 4 2 Intramolecular Probability Distribution Function PDF Analysis 100 4 3 Setting up Tabulated Intramolecular Force Field Files 103 5 Construction and Execution 105 5 1 Constructing DL_POLY_4 an Overview s sc ec pa bor i a e ee 106 STFC Contents 5 1 1 Constructing the Standard Versions 2 e 106 5 1 2 Constructing Non standard Versions ss sacs i r ea i aoa oa aee i eie a a ee eee 107 5 27 Compiling and Running DL POLY A s seos arhe i a fea eee a a ee e e Ye oe a 1
218. e 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 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 forces This method is not recommended for amorphous systems 5 3 2 Macromolecules To set up force fields for macromolecules or indeed any covalent molecules it is best to use DL_FIELD http www ccp5 ac uk DL_FIELD It is a program application tool developed to facilitate the construc tion of force field models for biological molecules and other molecules with complex geometries For instance proteins carbohydrates polymers and networked molecules such as graphenes and organic cages Although created to assist DL_POLY_4 DL_FIELD is a separate program suite that requires separate registration The primary functions of DL_FIELD are as follows 1 Force field model converter DL_FIELD converts the users
219. e force on atom 7 the negative of this The force shifted Coulomb potential can be elegantly extended to emulate long range ordering by including distance depending damping function erfc a rij identical to that seen in the real space portion of the Ewald sum and thus mirror the effective charge screening 63 as shown below idj f ij f cu 2 a r UG UD e ra elo t 2a exp a rat wb 2 T rege Tij tai yT Teut fase Fout ES Toit M 2a exp a 2w tas 2 197 2 Tout Tout yT Tout with the force on an atom 7 given by ag ferfc ariy 2a exp a r3 J Areoe r VT Tij 49 Si erfc a reut 2a exp a r u Tij 2 198 ee Vr Tout Tij with the force on atom 7 the negative of this It is worth noting that as discussed in 63 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 i The contribution to the atomic virial is W rij f 2 199 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 gare 3 2 200 where a 6 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 2 4 3 Coulomb Sum with Distance Dependent Dielectric This potential attempts to address the difficulties of applying the direct Coulomb
220. e i j k l inversion angle Note that the calcite potential is not dependent on an angle but on a displacement u See Sec tion 2 2 9 for details 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 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 When DL_POLY _4 is cross compiled with an openKIM functionality see Section 2 9 it is possible to specify a complete model of inter molecular interactions kim by calling the openKIM model name provided it available in your local KIM library 1 kim model_name where model_name is the openKIM model identifier 154 OSTFC Section 6 1 Note that although a KIM model fully describes a model system it is stil
221. e middle of MD cell Also as both the cell vectors and the particles positions are specified in A there is a fine connection between them This would not be the case if the particles positions were kept in reduced space with fractional coordinates Last but not least it is worth pointing out that composite entities such as velocities and forces have their units expressed as composites of the DL_POLY units as shown in Section 1 3 7 Table 6 5 CONFIG File Key record 2 levcfg meaning 0 coordinates included in file 1 coordinates and velocities included in file 2 coordinates velocities and forces included in file Table 6 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 r 0W0N Ra Oo 6 1 2 3 Further Comments on the CONFIG File The CONFIG file has the same format as the output file REVCON Section 6 2 7 When restarting from a previous run of DL_POLY_4 i e using the restart restart noscale or restart scale directives in the 144 STFC Section 6 1 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 o
222. e potential is defined numerically in TABBND see Section 4 3 and Section 6 1 8 In DL POLY 4 distance restraints are handled by the routine BONDS_FORCES and INTRA_COUL called within 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 15 STFC Section 2 2 i Figure 2 2 The valence angle and associated vectors 1 Harmonic harm k U Ojik z sin 00 2 16 2 Quartic quar k 2 k 3 k 4 U 0jix 5 jik 00 Ojik 00 q Ojik 00 2 17 3 Truncated harmonic thrm k 2 81 831 8 U Ojik 5 Ojik 00 expl ri rir P 2 18 4 Screened harmonic shrm k 2 U Ojik 5 Ojik 90 exp rij P1 rir p2 2 19 5 Screened Vessal 37 bvs1 k 5 212 U Ojik 8 Oj T 0 Tr Ojik Tr x exp rij pi rik P2 2 20 6 Truncated Vessal 38 bvs2 U Ojik k Ojik 90 OF n Ojir O0 2m MO peri 2 21 7 Harmonic cosine hcos k U Ojik z cos 0jir cos 00 2 22 8 Cosine cos U Ojik A 1 cos m Ojik 2 23 9 MM3 stretch bend 39 mmsb U Ojik A Ojik 00 rij rij Tik THe 2 24 16 OSTFC Section 2 2 10 Compass stretch stretch 40 stst U Ojik A rig rij rik Tip 2 25 11
223. e 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 1 1 u t lt Lut At u t 4 z 3 8 The instantaneous kinetic energy for example can then be obtained from the atomic velocities as E Exin t 5 X matt 3 9 1 and assuming the system has no net momentum the instantaneous temperature is T t Z Erant 3 10 where i labels particles that can be free atoms or rigid bodies M 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 3N Frozen 3N shells E N constants 3 P 3 11 Here NFrozen indicates the number of frozen atoms in the system Nsheis 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 fl 3N 3N Frozen 3 12 splits into fr 3NF 3N f been GAPPED BEET BN RBGOH gy aea 3 13 or fra fEP q fPB tra y pRB rot 3 14 Here FP stands for a free particle i e a particle not participating in the constitution of
224. e whole RB is Poisson selected Poisson selected RBs translational 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 RBs degrees of freedom 98 Chapter 4 Coarse Graining Functionality Scope of Chapter This chapter describes the coarse graining functionality available in DL_POLY_4 99 STFC Section 4 2 4 1 User Defined Coarse Grain Models with Tabulated Force Fields One can use DL_POLY 4 for preparing and running simulations of numerically coarse grained CG models by using tabulated effective force fields FF derived from either i potentials of mean force PMF or ii iteratively optimised CG models In outline systematic coarse graining SCG of an atomistic system implies the application of a geometrical projection or mapping of the original system onto a considerably reduced set of degrees of freedom DoF whence referred to as a coarse grained model The procedure is to recover the average configurational often termed physical and topological often termed chemical force field related properties of the original full atom FA model Integrating out degrees of freedom ultimately leads to loss of information However if this is done selectively and consistently the intrinsic i
225. eads A B A BONDS Probability Density Functions PDF histogram bin hist_sum bins dr_bin bins cutoff frames types 250 5 000 2285 1 r Angstroms PDF_norm r PDF_norm r dVol r dr_bin 0 02000 type index instances A B 1 2000 0 01000 0 000000E 00 0 000000E 00 0 03000 0 000000E 00 0 000000E 00 0 05000 0 000000E 00 0 000000E 00 4 95000 0 000000E 00 0 000000E 00 4 97000 0 000000E 00 0 000000E 00 101 STFC Section 4 2 4 99000 0 000000E 00 0 000000E 00 userChost more ANGDAT TITLE Hexane FA OPLSAA gt CG mapped with 3 beads A B A ANGLES Probability Density Functions PDF histogram bin hist_sum bins dTheta_bin bins cutoff frames types 360 180 2285 1 Theta degrees PDF_norm Theta PDF_norm Theta sin Theta dTheta_bin 0 50000 type index instances A B A 1 1000 0 25000 0 000000E 00 0 000000E 00 0 75000 0 000000E 00 0 000000E 00 1 25000 0 000000E 00 0 000000E 00 178 75000 1 380569E 02 6 328564E 01 179 25000 8 368490E 03 393238E 01 179 75000 2 901532E 03 6 649842E 01 O One can see that all the header lines are commented out due to starting with the hash symbol Nonethe less the header contains some useful information The title is as usual placed in the first line which is followed by an explanatory line with the definition of a normalised PDF The third line provides the four most important descriptors the number of bins on the histogram grid
226. eatures are documented in the DL_POLY_4 User Manual Reference 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 20 1911 1918 2006 Warnings 1 DL_POLY_4 can produce index ordered REVCON HISTORY and MSDTMP 262 STFC Appendix E files which are restartable by DL_POLY_Classic Although such printed outputs look unscrambled the actual printing process is not Unscrambled printing is slightly more expensive than natural scrambled printing The cost time wise is little lt 1 but HD space wise is approximately 20 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 blanks aligned records The parallel I O 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 2 REVIVE files produced by different versions are not compatible Furthermore restarting runs across different sub versions may not be possible 3 The DL_POLY_4 parallel performance and efficiency are considered ve
227. ecomes 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 efficiency and what possible measures could be taken to avoid this DL POLY_4 calculates and reports the major and secondary link cell algorithms MM My Mz employed in the simulations immediately 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 body and or Tersoff interactions short range cutoffs specified for the system W P M nint 2 z cutoff W MD box width L plane y z 5 1 i nodes o 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 My 2 M 2 link cells of which Mg My M belong to that domain 113 STFC Section 5 3 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 vo
228. ecular dynamics package based on the Domain Decomposition parallelisation strategy 2 3 9 10 5 6 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 techniques as they are described in the above references 7 1 1 The Domain Decomposition Strategy The Domain Decomposition DD strategy 2 3 5 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 I e the arrays defining the atomic coordinates r velocities v and forces f for all N atoms in the simulated system are divided in to sub arrays of approximate size N P where Pi 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 this way is based on the location of the atoms in the simulation cell such a geometric allocation of system data is the hallmark of DD algorithms Note that in order for this strategy to work efficiently the simulated system must possess a reasonably uniform density so that each processor is allocated almost an equal portion of atom data as much as possible Through this approach t
229. ed PDFs In the case of bonds it will also enforce the grid range rmax only if it is larger than that specified in the analyse bonds directive Hence the analyse all directive allows to quickly override and or unify the sampling frequencies and max grid numbers for all PDFs provided its parameters improve on the accuracy of the collected data compared to the specifications for the individually targeted PDF s While the statistics are always collected and stored for the future use in the binary REVIVE file for all targeted PDF s see Section 6 2 8 using the print analysis directive will instruct DL_POLY_4 to addition ally print the data in the OUTPUT and DAT files the latter containing each type of PDF s separately the asterisk stands for one of the following BND ANG DIH or INV As a result apart from OUTPUT three data files will be created for each of the targeted distribution types BNDDAT BNDPMF amp BNDTAB for bonds ANGDAT ANGPMF amp ANGTAB for angles DIHDAT DIHPMF amp DIHTAB for dihedrals and INVDAT INVPMF amp INVTAB for inversions the PMF and TAB files containing tabulated data for the respective potential of mean force and force virial TAB files bearing the data from PMF files but resampled onto a finer grid see the last paragraph in this section Partial examples of the DAT files for bonds and angles are given below user host more BNDDAT TITLE Hexane FA OPLSAA gt CG mapped with 3 b
230. ed 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 All shell models 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 6 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 the 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 6 2 6 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 Fi kFi qi i E 2 235 STFC Section 2 6 2 Oscillating shear oshr E Acos 2nz z Lz 2 236 3 Continuous shear shrx 1 1 v 347 z gt zo 2 237 4 Gravitational field grav F Fit m G 2 238 5 Magnetic field magn F Fi qi vi x H 2 239 6 Containing sphere sphr F A Ro r FS Reut 2 240 7 Repulsive wall zbnd F A zo z Pp Z gt P Zo
231. ed to defects_reference_export See notes on message 42 above Action See action notes on message 42 above Message 558 error outgoing transfer buffer exceeded in defects_reference_export See notes on message 38 above Action See action notes on message 38 above 247 STFC Appendix D Message 559 error incoming data transfer size exceeds limit in defects_reference_export See notes on message 38 above Action See action notes on message 38 above 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 REF ERENCES 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 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 property recalculation No structural property has been specified for this option to activate itself Action In CONTROL specify properties for recalculation RDFs z density profiles defect detection or alternati
232. ee 6 13 3 Memory Management 20 ic eo GA ee A GO ee a ee a 6 L34 Target Plattorme s L s soga ee eae ee ee OH a Pa eae ee eee 7 133 5 Internal Documentation io hs soea 44204 eae ok dhe de Oe ee ee a 7 1 3 6 FORTRAN9SO Parameters and Arithmetic Precision 2 7 A NE 7 13 8 Error Messages cora e aoet a o a A Ok Sa ee 8 STFC Contents 2 LA Directory Structure 2 2 34 2 44448 246 48 845 ebe be RSE PERSE EELS 8 LAL Thesource Su b directory ps lt pard aa a Ae we a OE Be ee SS 9 1 4 2 The utility Sul directory 2 4 ae a be eA En ee A ee ed 9 1 43 The data Sub directory lt so sp as duie ai eade RoR eGR ee RE Ea hee 9 LAA Thesbeneh Sub drectory sc sea da aea a aope a a k ia a ai a aa BA ae E a 9 L amp S The exerute Sub direetory secs eee Se ioe p kut e Eae A RA ba ee ES 9 146 The build Sub directory conr a d aa e ee dp da e eee we a i 9 LAT Thepubhe Sulbsdirectory ssc kis ea io aa e D e R 9 I amp S The java Sub directOry ns s nie wl soak ds a A ae da 10 1 5 Obtaining the Source Code sa a s s a det ai moa a aaa ee 10 1 6 OS and Hardware Specific Ports 2 4 4 4 sa soco ea ag ar a 10 LT Other Information s sims isg a eo ee AR be ee 10 Force Field Interactions 11 2 1 Introduction to the DL POLY 4 Force Field 2 ca e agera a Eip eara 12 2 2 The Intramolecular Potential Functions o e s aa e sa aa aoea daa ace aeoe a a a ee 13 221 Bond Potentials ie T a i ose aa a OR em E ws g a a BSS 13
233. em 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 v v is used retrospectively to compute the constraint force needed to keep the bond rigid over the length of the timestep At It is relatively simple to show that the constraint force has the form Hij dij vj v d Bij x At d2 Qij 3 18 The velocity corrections can therefore be written as uf At By _ bij dis vj 04 dij 3 19 2 Mi mi d j 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 63 STFC Section 3 2 correction is merely an interim adjustment not only because the above formula is approximate 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 r
234. en in Table 6 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 6 9 index 1 i integer first atomic site index index 2 7 integer second atomic site index central site index 3 k integer third atomic site index variable 1 real potential parameter see Table 6 9 variable 2 real potential parameter see Table 6 9 variable 3 real potential parameter see Table 6 9 variable 4 real potential parameter see Table 6 9 The meaning of these variables is given in Table 6 9 This directive and associated data records need not be specified if the molecule contains no angular terms See the note on the atomic indices appearing under the shell directive above dihedrals n where n is the number of dihedral interactions present in the molecule Each of the following n records contains dihedral key ad potential key see Table 6 10 index 1 i integer first atomic site index index 2 j integer second atomic site index central site 150 STFC Section 6 1 Table 6 8 Chemical Bond Potentials key potential type Variables 1 4 functional form harm Harmonic k ro U r gt k rij ro h
235. ended array dimension c direction kmaxal variable SPME FFT original array dimension a direction kmaxb1 variable SPME FFT original array dimension b direction kmaxc1 variable SPME FFT original array dimension c direction mxtshl variable max number of specified core shell unit types in system mxshl variable max number of core shell units per node 193 OSTFC Section 7 2 mxfshl mxtcon mxcons mxfcon mx1shp mxproc mxtpmf 1 2 mxpmf mxfpmf mxtrgd mxrgd mxlrgd mxfrgd mxtteth mxteth mxftet mxpteth mxtbnd mxbond mxfbnd mxpbnd mxgbnd mxtang mxangl mxfang mxpang mxgang mxtdih mxdihd mxfdih mxpdih mxgdih mxtinv mxinv mxfinv mxpinv mxginv mxrdf mxgrdf mxgele mxvdw mxpvdw mxgvdw mxmet mxmed mxmds mxpmet mxgmet mxter mxpter mxgter 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 variable variable variable variable variable variable variable variable variable variable variable variable 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 un
236. ensemble nvt dpdINT line and if it is non zero a global override will occur Otherwise when the requirements for a DPD thermostat are not satisfied everything else will result in a controlled termination A 3 Equation of state and dynamic properties The form of the conservative force determines the equation of state for a DPD fluid which can be derived using the virial theorem to express system pressure as follows 1 P pkpT 3 Ea rj 15 A 10 j gt i pkgT p A 1 2 rg r dr A 11 0 Te where g r is a radial distribution function for the soft sphere model 50 and p is the DPD particle density For sufficiently large densities p gt 2 g r takes the same form and the equation of state can be well approximated by P pkgT 04p A 12 where the parameter a 0 101 0 001 has units equivalent to r4 This expression permits the use of fluid compressibilities to obtain conservative force parameters for bulk fluids e g for water A 75kgT p Alternative equations of state may be obtained by modifying the functional form of conservative interactions to include localized densities i e many body DPD 92 93 Transport coefficients for a DPD fluid can be derived using the expressions for the drag and stochastic forces 50 94 95 The kinematic viscosity can be found to be 45kpT 2mypr ues z A 13 Ary pre 1575 while the self diffusion coefficient is given as 45kgT Dx d A 14 2rypr3
237. ent virial Y 0 N N 1 LL me AF pi ao a Vo 2 133 2 2 2 2 Op Op re The contribution to be added to the atomic stress tensor is given by Era 2 134 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 CO a J pylri Jal jt Tij lt Tmet Tij 2Tmet pi Y pylty t Y pislrij 0 40 j LjA I 1 5 Ai CO dpi 4Tp pi r dr Tmet 2 135 where p is 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 Yet 2 EEAM density correction No long ranged corrections apply beyond ret 3 2BEAM density correction No long ranged corrections apply beyond ret 4 2BEAM density correction No long ranged corrections apply beyond ret 5 Finnis Sinclair density correction No long ranged corrections apply beyond cutoffs c and d 36 STFC Section 2 3 6 Extended Finnis Sinclair density correction No long ranged corrections apply beyond cutoffs c and d 7 Sutton Chen density correction Aro 3 m 3 5p ll 2 l 2 136 m 3 Tmet 8 Gupta density correction 2T Pro pi 2 qij 2 r r Tmet T Pat 2P met 2 2 2 exp 205 2 2 1
238. entation in FCFLAGS The same must be done for 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 makefile OBJ_ALL Note that there is a hierarchal 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 5 2 1 3 Note on the Interpolation Scheme In DL_POLY_4 two body like contributions van der Waals metal and real space Ewald summation 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 109 STFC Section 5 2 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 reus 0 01 0 5 4 where reut is the main cutoff beyond which the contributions from the short range like interactions are negligible 5 2 2 Running To run the DL POLY 4 executable
239. ential 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 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 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
240. ep 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 10 A and mindis 0 03 A which can also be optionally altered if used as directives note the rule that maxdis gt 2 5 mindis applies Also an additional mxstep in ps control can be applied These 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 provided it does not exceed the user specified mxstep If it does then it scales to mxstep and the step is repeated In this way the integration timestep self adjusts in response to the dynamics of the system Note that this option is abandoned when used in conjunction with DPD thermostats ensemble nvt dpdtype y since it cannot be applied efficiently and furthermore it is not well defined in a DPD sense either 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
241. epeated for all bonds until each has converged to the correct length within a given tolerance for RATTLE_VV1 SHAKE and the relative bond velocities are perpendicular to their respective bonds within a given tolerance for RATTLE_VV2 RATTLE The tolerance may be of the order 1074 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 equa tion 3 16 that retrospectively corrects the bond length 3 After the correction equation 3 16 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 con stitutes 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_VV1 algorithm b The deviation in each bondlength is used to calculate the corresponding constraint force equa tion 3 17 that retrospectively corrects the bond lengt
242. er MgO These systems consist of 13 500 500 PMFs and 53 248 2 048 PMFs atoms respectively Simulation at 300 K using NPT Berendsen ensemble with SPME and SHAKE RATTLE algorithm for the constrained motion 8 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 8 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 8 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 198 STFC Section 8 1 8 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 8 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 8 1 15 Test Case 29 and 30 Fe with Finnis Sincair metal Potentials These systems consist of 31 250 a
243. er algorithm 30 Newton s equations of motion are modified to read dr t _ e UY 20 200 5 66 The friction coefficient x is controlled by the first order differential equation dx t _ 2Epin t 20 3 67 dt mass where is the target thermostat energy equation 3 57 and qmass 2 0 Th 3 68 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 Exin t changes inside At 2Exin t 20 x t At x t 4 mass 1 At a E wD exp x t At 2 3 69 1 1 At 2Epin t 20 x t 4 At x t4 A 4 ome 3 70 72 STFC Section 3 4 2 VVI 1 At f t otta e Ut ae a ret At r t At olt A 3 71 3 RATTLE_VV1 4 FF f t At f t 3 72 5 VV2 A u t At u t 5 At a ae 2 3 73 6 RATTLE VV2 7 Thermostat Note Exin t At changes inside At 2E pin t At 20 4 dmass ebay E ETA exp ee At gt 3 74 3 1 x t 1 x t At At 2E pin t At 20 4 mass 3 x t At x t 740 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 estim
244. er specifications in the FIELD files This directive and associated data records need not be specified if the molecule contains no core shell units 5 constraints n where n is the number of constraint bonds in the molecule Each of the following n records contains index 1 integer first atomic site index index 2 integer second atomic site index bondlength real constraint bond length This directive and associated data records need not be specified if the molecule contains no constraint bonds See the note on the atomic indices appearing under the shell directive above 6 pmf b where b is the potential of mean force bondlength A There follows the definitions of two PMF units a pmf unit n1 where ni is the number of sites in the first unit The subsequent ni records provide the site indices and weighting Each record contains index integer atomic site index weight real site weighting 148 OSTFC Section 6 1 b pmf unit n2 where n2 is the number of sites in the second unit The subsequent n2 records provide the site indices and weighting Each record contains index integer atomic site index weight real site weighting This directive and associated data records need not be specified if no PMF constraints are present See the note on the atomic indices appearing under the shell directive Note that if a site weighting is not supplied DL_POLY_4 will assume it is zero However DL_POLY_4 detects that all sites in
245. ere a 8 are x y z components The atomic stress tensor is symmetric In 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 The form of the simple truncated and shifted potential function is U rig HU E 2 194 rrep Tij Teut with qe the charge on an atom labelled reut the cutoff radius and r the magnitude of the separation vector Ej Ep A further refinement of this approach is to truncate the 1 r potential at rey 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 47 STFC Section 2 4 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 qiqi 1 1 1 1 Ud 1 Tij 2 U r Pis r A 2 195 ri TEp i eo J E az Amege Tig T Teut with the force on an atom j given by Gq 1 1 Teas 2 196 I 4Teoe 3 u with th
246. ere f is the system s degrees of freedom equation 3 11 The VV and LFV flavours of the Gentle Stochastic Thermostat are implemented in the DL_POLY_4 routines NVT G0_VV and NVT_GO_LFV respectively The routines NVT_G1_vv and NvT_G1_LFV implement the same but also incorporate RB dynamics 3 4 7 Dissipative Particle Dynamics Thermostat An elegant way to integrate the DPD equations of motions as shown in Appendix A is introduced by Shardlow 71 By applying ideas commonly used in solving differential equations to the case of integrating the equations of motion in DPD the integration process is factorised by splitting the conservative forces calculation from that of the dissipative and random terms In this way the conservative part can be solved using traditional molecular dynamics methods while the fluctuation dissipation part is solved separately as a stochastic differential Langevin equation There are two Shardlow integrators called S1 dpds1 and S2 dpds2 based on splitting the equations of motion up to first and second order respectively using Suzuki Trotter Strang expansion of the Lioville evolution operator and thus warranting the integrators symplectic To describe the two integrators we define the algorithmic sequence For all pairs of particles for which rj lt re D a E ti a 10n Win Meg At HipkaT wei VAt 2 uy v Ta frw y iy eij At V2 7 kB TW Cijes VAt S At 3 u amp ut oa Pgh aT wr
247. erived by automatic parameter optimisation for precision f as for Ewald summation 107 lt f lt 0 5 default f 1072 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 AW 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 ot set rolling average stack to n timesteps 132 OSTFC Section 6 1 stats every n accumulate statistics data every n timesteps steps n run simulation for n timesteps default n 0 corresponding to a dry run temperature f set required simulation temperature to f Kelvin target temperature for constant temperature ensembles trajectory i j k write HISTORY file with controls i start timestep for dumping configurations default 0 j timestep interval between configurations default j 1 k data level default k 0 see Table 6 1 vaf sampling every i bin size n calculate and collect velocity autocorrelation function profiles timestep f variable timestep f vdw direct vdw mix rule vdw shift zden sampling every f Zero every i timesteps default 50 with a bin size set to n timesteps default n 2i if i ge 100 or n 100 otherwise
248. es 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 r12 793 and r34 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 TUPAC convention When defining the dihedral the atom indices are entered in DL_POLY_4 in the order 1 2 3 4 In DL_POLY_4 improper dihedral forces are handled by the routine DIHEDRALS_FORCES 21 STFC Section 2 2 L a N C f D a C N f 1 2 3 4 1 2 3 4 Figure 2 4 The L and D enantiomers and defining vectors 2 2 7 Torsional Restraints In DL_POLY_4 the torsional restraints in which the dihedral angle as defined by a quadruplet of atoms is maintained around some preset value dp is handled as a special case of dihedral potential As a consequence angle restraints may be applied only between atoms in the same molecule Unlike with application of the pure dihedral 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 torsional restraints although they have different key word
249. ess 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 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 22 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 simultaneously on each node using the DD adaptation of the link cell algorithm to share the total burden of the work reasonably equally between nodes Each node is thus responsible for a unique set of non bonded interactions and the neighbour list is therefore different on each node A feature in the construction of the Verlet neighbour list for macromolecules is the concept of excluded atoms which a
250. essage 128 above Action See action notes on message 128 above Message 132 error dihedral angle unit diameter gt rcut the system cutoff See notes on message 128 above Action See action notes on message 128 above Message 134 error inversion angle unit diameter gt rcut the system cutoff See notes on message 128 above Action See action notes on message 128 above Message 138 error incorrect atom totals assignments in refresh_halo_positions This should never happen although sometimes it could due to ill defined force field and or and or starting form a configuration which is too much away from equilibrium Action Try using the variable timestep option and or running in serial to determine if particles gain too much speed and leave domains Message 141 error duplicate metal potential specified During reading of metal potentials pairs of atom types in FIELD DL_ POLY_4 has found a duplicate pair of atoms in the list Action Delete one of the duplicate entries and resubmit Message 145 error no two body like interactions 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 through each other due to one of the fore specified interactions
251. essage 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 size exceeded in export_atomic_data See notes on message 38 above Action 220 STFC Appendix D See naction otes on message 38 above 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 incoming data transfer size exceeds limit in export_atomic_data See notes on message 38 above Action See action notes on message 38 above Message 57 error too many core shell units specified This should never happen Action See action notes on message 14 above Message 58 error number of atoms in system not conserved Either and an atom has been lost in transfer between nodes domains or your FIELD is ill defined with respect to what is supplied in CONFIG HISTORY Action If this error is issued at start before timestep zero in a simulation then it is either your FIELD file is ill defi
252. etrospectively to the forcefield stress 3 5 2 Langevin Barostat DL_POLY_4 implements a Langevin barostat 31 for isotropic and anisotropic cell fluctuations Cell size variations 77 STFC Section 3 5 For isotropic fluctuations the equations of motion are Cr ADAN Sut EPIRO 4 143 m0 f 3 kg Text Pmass 27 Xp Lue 1050 EV BOVA 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 35 P the instantaneous pressure equation 3 97 and R is the stochastic Langevin pressure variable Rp t R t 2 Xp Pmass kgT t t 3 100 which is drawn from Gaussian distribution of zero mean and unit variance Gauss 0 1 scaled by ae kpg 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 Pmass Ca Hyper HNveE PextV t 3 101 The VV implementation of the Langevin algorithm only requires iterations if bond or PMF constraints are present 4 until satisfactory convergence of the constraint forces is achieved These are with re spect 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
253. f 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 inversion angle pot arrays gt 1004 max number of pairwise RDF in system number of grid points for RDF and Z density arrays gt 1004 max number of grid points for ewald exclusion potential arrays max number of van der Waals potentials in system max number of van der Waals potential parameters 5 max number of grid points in vdw potential arrays gt 1004 max number of metal potentials in system max number of metal density potentials in system max number of metal extra density potentials in system max number of metal potential parameters 9 max number of grid points in metal potential arrays gt 1004 max number of Tersoff potentials in system max number of Tersoff potential parameters 11 max number of grid points in tersoff potential arrays gt 1004 194 STFC Section 7 2 mxgrid mxtana mxgana mxgbnd mxgang mxgdih mxginv mxtbp mx2tbp mxptbp mxfbp mx2fbp mxpfbp mxpfld mxstak mxnstk mxlist mxcell mxatms mxatdm mxbfdp mxbfss mxbfxp mxbfsh mxbuff zero_plus half_plus half minus engunit variable variable variable variable variable variable variable variable variable variable variable variable variable variable variable variable variable v
254. for each non commuting pair of atoms types e 2BEAM n s band embedding functions one for each atom type sembedding keyword n n 1 2 s band density functions one for each cross pair of atoms types sdensity keyword n d band embedding functions one for each atom type dembedding or embeedding keyword and n d band density functions one for each atom types ddensity or density keyword e 2BEEAM n s band embedding functions one for each atom type sembedding keyword n s band density functions one for each non commuting pair of atoms types sdensity keyword n d band embedding functions one for each atom type dembedding or embeedding keyword and n d band density functions one for each non commuting pair of atoms types ddensity or density 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 pair embed or density with 2B extension alternatives for the s band sembed and sdensity and d band dembed embed and ddensity density atom 1 a8 first atom type atom 2 as second atom type only specified for pair potential functions and for the i density functions in the EEAM potential
255. g in a force shifted manner by countering the reaction term and using a distance depending damping function erfc a riz identical to that seen in the real space portion of the Ewald sum and thus mirror the effective charge screening 63 GG erfc a rij erfc a rat 2a exp a r U rij 3 Tij TENE Tij Tout VT Tout ene Put Es Te 2a exp a rai Bol r2 Tout eg 2 f 3 Teut yT Pout a Tout 2 211 with the force on an atom 7 given by Ud erfc a Tij 2a exp a ry 5 I Amege rij yT Tij Teut E 2a exp a aw a Tij 2 212 aad vr Tout re am cut Tij with the force on atom 7 the negative of this It is worth noting that as discussed in 63 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 oP 70 68 2 214 where a 6 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 2 4 5 Smoothed Particle Mesh Ewald The Ewald sum 22 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
256. g to each potential are described in Table 6 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 6 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 in the following manner field key ad external field key see Table 6 17 160 STFC Section 6 1 Table 6 16 Four body Potentials key potential type Variables 1 2 functional form harm Harmonic k do U p 5 boy hcos Harmonic cosine k do U E cos cos g plan Planar A U A 1 cos to is the 7 7 k l four body angle variable 1 real potential parameter see Table 6 17 variable 2 real potential parameter see Table 6 17 variable 3 real potential parameter see Table 6 17 variable 4 real potential parameter see Table 6 17 variable 5 real potential parameter see Table 6 17 The variables pertaining to each field potential are described in Table 6 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 For example the magnetic field units H H
257. ge 1014 error allocation failure in bonds_module gt allocate_bonds_arrays See notes on message 1001 above Action See action notes on message 1001 above Message 1015 error allocation failure in core_shell module gt allocate_core_shell_arrays See notes on message 1001 above Action See action notes on message 1001 above Message 1016 error allocation failure in statistics_module gt allocate_statitics_arrays See notes on message 1001 above Action See action notes on message 1001 above 253 STFC Appendix D Message 1017 error allocation failure in tethers_module gt allocate_tethers_arrays See notes on message 1001 above Action See action notes on message 1001 above Message 1018 error allocation failure in constraints_module gt allocate_constraints_arrays See notes on message 1001 above Action See action notes on message 1001 above Message 1019 error allocation failure in external field_ module gt allocate_external_field_arrays See notes on message 1001 above Action See action notes on message 1001 above Message 1020 error allocation failure in dihedrals_module gt allocate_dihedrals_arrays See notes on message 1001 above Action See action notes on message 1001 above Message 1021 error allocation failure in inversions_module gt allocate_inversion_arrays See notes on message 1001 above
258. ge 648 error quaternion setup failed This error indicates that the routine Q_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 Q_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 250 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 remote 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 Another more likely possibility in case of linear molecules is that the precision of the coordinates of these linear molecules constituentsi as produced by the user is not good enough which leads DL_POLY_4 to accepting it as non linear whil
259. 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 the cygwin installation please make sure that the make and gfortran components are specifically opted for components as they may not be included as default ones in the install A potential problem for Windows based FORTRAN compilers one may encounter is that the compiler may not pick symbolic links This can be resolved by substituting the soft links with hard in the Makefile For parallel compilation all openMPI components must also be opted for during the cygwin install Compiling with NetCDF functionality The targeted Makefile needs the following substitution within before 265 STFC Appendix E 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 OS compiler MPI library amp netCDF library Contacts at STFC Daresbury Laboratory Dr I T Todorov ilian todorov stfc ac uk E 2 README KIM txt KIM API Installation Instructions 0 Presumptions Linux OS for wget downloads internet starting in the DL_POLY_4 XX main directory 1 Download the kim api v1 6 X tgz wget http s3 openkim org kim api kim api v1 6 X tgz 2 Unpack the tarball in the DL_POLY_4 ZZ source directory mv kim api v1 6 X tgz DL_POLY_4 ZZ s
260. h c After the correction equation 3 17 has been applied to all bonds every bondlength is checked If the largest deviation found exceeds the desired tolerance the correction calculation is repeated d Steps b and c are repeated until all bondlengths satisfy the convergence criterion this iteration constitutes stage 2 of the RATTLE_VV1 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 v d in each bond is used to calculate the corresponding constraint force that retrospectively corrects the bond velocities c After the correction equation 3 18 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 8 although its implementation in the Domain Decomposition framework 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
261. harm or impede the operation of any information system or that might corrupt damage destroy or render inaccessible any software data or file on or that may allow any unauthorised person to gain access to any information system or any software data or file on it Intellectual Property patents trade marks service marks registered designs copyrights database rights design rights know how confidential information 270 STFC Appendix F the applications for any of the above and any similar right recognised from time to time in any jurisdiction together with all rights of action in relation to the infringement of any of the above Licence Period the period beginning when the Licensee agrees to the terms and conditions of this Licence Agreement and downloads the DL_POLY_4 Software from the DL_POLY_4 Website and ending on the termination of this Licence Agreement under clause 5 2 2 LICENCE 2 1 2 3 STFC grants the Licensee an indefinite non exclusive non transferable royalty free licence to use copy modify and enhance the DL_POLY_4 Software during the Licence Period on the terms and conditions of this Licence Agreement provided that 2 1 1 the Licensee may not distribute any of the DL_POLY_4 Software or any Derived Work to any third party or share their use with any third party whether free of charge or otherwise and the Licensee may not sub license the use of any of the DL_POLY_4 Software to an
262. he FIELD file Once this directive has been encountered DL_POLY_4 enters the molecular description environment 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 Note this is not a directive just a simple character string 2 nummols n where n is the number of times a molecule of this type appears in the simulated system The molecular data then follow in subsequent records 3 atoms n where n indicates the number of atoms in this type of molecule A number of records follow each giving details of the atoms in the molecule i e site names masses and charges Each record carries the entries sitnam a8 atomic site name weight real atomic site mass chge real atomic site charge nrept integer repeat counter ifrz integer frozen atom if ifrz gt 0 147 STFC Section 6 1 The integer nrept need not be specified if the atom site is not frozen in which case a value of 1 is assumed A number greater than 1 specified here indicates that the next nrept 1 entries in the CONFIG file are ascribed the atomic characteristics given in the current record The sum of the repeat numbers for all atoms in a molecule should equal the number specified by the atoms directive 4 shell n where n is the number of core shell units Each of the
263. he VV algorithm VV2 new torques are used to update the quaternion momenta to a full timestep A At t p t At plt 5 t A 3 204 3 6 3 Thermostats and Barostats coupling to the Rigid Body Equations of Motion In the presence of rigid bodies in the atomic system the system s instantaneous pressure equation 3 97 2E bin t Watomic t Wcom t Weonstrain t At a Wome t At O 3 205 P t and stress equation 3 98 a t Erin t Z atomic t 2com t E Oe E At ZPMF t E At 3 206 are augmented to include the RBs COM virial and stress contributions Note that the kinetic energy and stress in the above also include the contributions of the RB s COM kinetic energy and stress 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 transla tional 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 Therefore if we notion the change of the system s degrees of freedom as f gt F f4 PRA O eal 3 207 then all equations of motion defining the ensembles as described in this chapter are subject to the following notional changes in order to include the RB contrib
264. he 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 85 as implemented by various authors e g Pinches et al 9 and Rapaport 10 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 processors 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_PARTICLES routine Systems containing complex molecules present several difficulties They often contain ionic species which usually require Ewald summation methods 22 86 and intra molecular interactions in addition to inter molecular forces Intramolecular interactions are handled in the same way as in DL_POLY _Classic where each processor is allocated a subset of intramolecula
265. heck 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 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 and or recreate the FIELD file afresh If no combination 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 214 STFC Appendix D Action Locate the duplication in the FIELD file rectify and resubmit Message 16 error strange exit from FIELD file 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 directi
266. hell usr bin tcsh job_type parallel job_name gopoly cpus 32 node_usage not_shared network MPI csss shared US wall_clock_limit 00 30 00 account_no my_account HQ 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 where Ilsubmit is a local command for submission to the IBM SP4 cluster The number of required 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 the following UNIX commands java jar java GUI jar 1 amp 209 STFC Appendix C In other words the macro invokes the Java Virtual Machine which executes the instructions in the Java archive file GUL jar which is stored in the java subdirectory of DL POLY_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 vpLH data TEST 1 CONTROL cp vpLH data TEST 1 CONFIG
267. her 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 problem atic 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 con strained 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 the COM 93 STFC Section 3 6 To do this we need to define the appropriate variables describing the position orientation and inertia of a rigid body and the rigid body equations of motion The mass of a rigid unit M is the sum of the atomic masses in that unit Nsites M Y m 3 174 j l where m is the mass of an atom an
268. here string can only be leapfrog or velocity as the later is the default set 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 9Int Log Min job size 2 job size beg 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 10 000 000 default 2 000 000 is the maximum number of particle entities in a batch i e multiples of species indez r u f etc transmitted between I O groups I O readers for domain distribution purposes l buffer size 100 lt 1 lt 100 000 default 20 000 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 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 fl
269. hree minimisation strategies available in DL_POLY_4 only the programmed minimiser is capable of finding more than one minimum without the user intervening 4 Finally we emphasise once again that the purpose of the minimisers in DL_POLY_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 5 2 6 Simulation Efficiency and Performance Although the DL POLY 4 underlining parallelisation strategy DD and link cells see Section 7 1 1 is ex tremely efficient it cannot always provide linear parallelisation speed gain with increasing processor count for a fixed size system Nevertheless it will always provide speedup of the simulation i e there still is a sufficient speed gain in simulations when the number of nodes used in parallel is increased The simplest explanation why this is is that increasing the processor count for a fixed size system decreases not only the work and memory load per processor but also the ratio size of domain to size of halo both in counts of link cells When this ratio falls down to values close to one and below the time DL_POLY_4 spends on inevitable communication MPI messages across neighbouring domains to refresh the halo data increases with respect to and eventually b
270. ial damages or losses or any loss of profits loss of revenue loss of data loss of contracts or opportunity whether direct or indirect even if the Licensee has advised STFC of the possibility of those losses arising or if they were or are within STFC s contemplation Subject to clause 3 7 the aggregate liability of STFC for any and all breaches of this Licence Agreement any negligence or arising in any other way out of the subject matter of this Licence Agreement or the use of the DL_POLY_4 Software will not exceed in total 5 000 Nothing in this Licence Agreement limits or excludes STFC s liability for death or personal injury caused by its negligence or for any fraud or for any sort of liability that by law cannot be limited or excluded The express undertakings and given by STFC in this Licence Agreement and the terms of this Licence Agreement are in lieu of all warranties conditions terms undertakings and obligations on the part of STFC whether express or implied by statute common law custom trade usage course of dealing or in any other way 273 STFC Appendix F All of these are excluded to the fullest extent permitted by law 4 INTELLECTUAL PROPERTY RIGHTS AND ACKNOWLEDGEMENTS 4 1 5 2 5 3 Nothing in this Licence Agreement assigns or transfers any Intellectual Property Rights in any of the DL_POLY_4 Software Those rights are reserved to STFC The Licensee will ensure that if any of its emplo
271. ials 198 8 1 6 Test Case 11 and 12 CuzAu alloy with Sutton Chen metal Potentials 198 8 1 7 Test Case 13 and 14 lipid bilayer in water 2000 198 8 1 8 Test Case 15 and 16 relaxed and adiabatic shell model MgO 198 8 1 9 Test Case 17 and 18 Potential of mean force on K in water MgO 198 8 1 10 Test Case 19 and 20 CuzAu alloy with Gupta metal Potentials 198 8 1 11 Test Case 21 and 22 Cu with EAM metal Potentials 198 8 1 12 Test Case 23 and 24 Al with Sutton Chen metal Potentials 198 STFC Contents 8 1 13 Test Case 25 and 26 Al with EAM metal Potentials 199 8 1 14 Test Case 27 and 28 NiAl alloy with EAM metal Potentials 199 8 1 15 Test Case 29 and 30 Fe with Finnis Sincair metal Potentials 199 8 1 16 Test Case 31 and 32 Ni with EAM metal Potentials 199 8 1 17 Test Case 33 and 34 SPC IceVI water with constraints 0 199 8 1 18 Test Case 35 and 36 NaCl molecules in SPC water represented as CBs RBs 199 8 1 19 Test Case 37 and 38 TIP4P water RBs with a massless charged site 199 8 1 20 Test Case 39 and 40 Ionic liquid dimethylimidazolium chloride 199 8 1 21 Test Case 41 and 42 Calcite nano particles in TIP3P water 199 8 1 22 Test Case 43 and 44 Iron Carbon alloy with EEAM
272. ically 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 crystallographic sites from the CONFIG file by their order of reading rather than by their actual indexing i abort strict checks such as on existence 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 and its padding temperature pressure and job times skip detailed topology reporting during read of FIELD in OUTPUT no FIELD replication useful for large bio chemcal simulations ignore time averaging of velocity autocorrelation functions VAFs report all calculated VAF profiles for individual species to VAFDAT files and final profile for all species in OUTPUT ignore short range non bonded interactions in simulation ignore Centre of Mass momentum removal during the simulation minimise the system conf
273. iguration 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 50 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 optional padding to the major cutoff Tout to f A f gt Min 0 05 0 5 rcut default f 0 set required system pressure to f katms target pressure for constant pressure ensembles 130 STFC Section 6 1 print every n print analysis print rdf print vaf print zden pseudo string f f2 quaternion tolerance f rdf sampling every f reaction field reaction field damp a reaction field precision f regauss every n replay history replay history force restart print system data every n timesteps print any opted for analysis inter amp and intra molecular PDFs in OUTPUT as well as their corresponding files FDAT PMF TAB print radial distribution functions print velocity autocorrelation functions print Z density profile attach a pseudo thermal bath with a thermostat of type string where string can only be langevin gauss or direct if none is specified then langevin direct are applied successively f is the thickness of the
274. imisation 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 6 1 1 When using the programmed minimisation DL POLY_4 writes and rewrites the file CFGMIN 6 2 5 which represents the lowest energy structure found during the programmed minimisation CFGMIN is written in CONFIG file format see section 6 1 2 and can be used in place of the original CONFIG file It should be noted that none of these algorithms permit the simulation cell to change shape It is only the atomic structure that is relaxed After which it is assumed that normal molecular dynamics will commence from the final structure 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 possibilities of constraint bonds and rigid bodies being present in the system If neither of these is present the conventional unadapted procedure is followed 112
275. imulation 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_ Classic User Manual If an NPT NaT simulation is performed the OUTPUT file also provides the mean pressure stress tensor and mean simulation cell vectors In case when extended NaT ensembles are used then further mean x y plain area and mean surface tension are also displayed in the OUTPUT file 175 STFC Section 6 2 6 2 6 9 Radial Distribution Functions If both calculation and printing of radial distribution functions have been requested by selecting directives rdf and print rdf in the CONTROL file radial distribution functions are printed out This is written from the subroutine RDF_COMPUTE First the number of time steps used for the collection of the histograms is stated Then each pre requested function is given in turn For each function a header line states the atom types a and b represented by the function Then r g r and n r are given in tabular form Output is given from 2 entries before the first non zero entry in the g r histogram n r is the average number of atoms of type b within a sphere of radius r around an atom of type a Note that a readable version of these data is provided by the RDFDAT file below 6 2 6 10 Z density Profile If both calculation
276. in both Velocity Verlet VV and Leapfrog Verlet LFV manner 22 These generate NVE NVE NVT NPT and NaT ensembles with a selection of thermostats and barostats Parallel versions of the RATTLE 23 and SHAKE 8 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 24 under the LFV scheme or with the NOSQUISH algorithm of Miller et al 25 under the VV integration The following MD algorithms are available 1 Constant E algorithm 2 Evans constant Egin algorithm 26 3 Langevin constant T algorithm 27 4 Andersen constant T algorithm 28 5 Berendsen constant T algorithm 29 6 Nos Hoover constant T algorithm 30 7 Langevin constant T P algorithm 31 8 Berendsen constant T P algorithm 29 9 Nos Hoover constant T P algorithm 30 10 Martyna Tuckerman and Klein MTK constant T P algorithm 32 11 Langevin constant T algorithm 31 12 Berendsen constant T algorithm 29 13 Nos Hoover constant T a algorithm 30 14 Martyna Tuckerman and Klein MTK constant T algorithm 32 1 2 6 DL POLY Classic 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 determined by the presence of mass on the shells Dihedral potentials with
277. ing up a PMF based force field for example in the case of initial coarse graining of an atomistic system In particular one can convert the VDWTAB file into a correctly formatted TABLE file Section 6 1 6 by using the utility called pmf2tab f subject to compilation found in DL_POLY_4 directory utility as follows userChost pmf2tab exe lt VDWTAB see Section 4 1 for completeness 6 2 10 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 177 STFC Section 6 2 first record atname a8 unique atom name following records mxgrdf records Zz real distance in z direction A p z real Z density at given height z Note the ZDNDAT file is optional and appears when the print rdf option is specified in the CONTROL file 6 2 11 The VAFDAT Files These are formatted files containing Velocity Autocorrelation Function VAF data An individual file is created for each atomic species i e VAFDAT_atname Their contents are as follows record cfgname a12 configuration name There follow the data for the VAF either a single time averaged profile or successive profiles separated by two blank
278. ints are applied All the potential forms of the previous section are available 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 37 bv1 6 Truncated Vessal 38 bv2 7 Harmonic cosine hcs 8 Cosine cos 9 MM3 stretch bend 39 msb 10 Compass stretch stretch 40 sts 11 Compass stretch bend 40 stb 18 OSTFC Section 2 2 12 Compass all terms 40 cmp 13 AMOEBA force field angle 36 amo 14 KKY 41 kky 15 Tabulated potential tab The potential is defined numerically in TABANG see Section 4 3 and Section 6 1 8 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 as follows 1 Cosine potential cos U dijkn A 1 cos Mpijkn 9 Harmonic harm k Uae 5 dijkn 90 Harmonic cosine hcos cos Pijen cos dp Triple cosine cos3 U d 5 41 1 cos Az 1 cos 26 As 1 cos 39 Ryckaert Bellemans 43
279. ion 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 l where P is the instantaneous pressure equation 3 97 and Tp is the barostat relaxation time constant Cell size variations In the isotropic implementation at each step the MD cell volume is scaled by a factor 7 and the coordinates and cell vectors by nl E ao 1 2 Poa P E 3 125 where P is the isothermal compressibility of the system In practice P 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 constraints are present 13 until satisfactory convergence of the constraint forces is achieved These are with re spect to the pressure i e 7 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 VV1 1 At f t utti e q ret At E nle r t At olt ZA 3 126 H t At n Hit VE A x t Vit 2 RATTLE_VV1 3 Barostat BAt n t 1 Pet P E 3 127 TP 4
280. ions 242 STFC Appendix D Message 494 error overconstrained PMF units PMF units are oveconstrained Action DL_POLY_4 algorithms cannot handle overconstrained PMF units Decrease the number of constraints on the PMFs Message 497 error pmf_quench failure Action See notes on message 515 below Message 498 error shake algorithm pmf_shake failed to converge Action See action notes on message 515 below Message 499 error rattle algorithm pmf_rattle failed to converge See notes on message 515 below Action See action notes on message 515 below 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 243 STFC Appendix D Message 504 error cutoff too large for TABLE TABBND file The requested cutoff exceeds the information in the TABLE file or the TABBND cutoff is larger than half the sy
281. irectory from which the program is executed See Section 6 1 for the description of the input files 7 Executing the program will produce the files OUTPUT STATIS REVCON and REVIVE and op tionally HISTORY RDFDAT ZDNDAT MSDTMP REFERENCE DEFECTS in the executing directory See Section 6 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 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 somewhat higher than the global one or the system undergoes some form of clustering 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 To trigger lengthening of the density dependent global arrays the user may use the densvar option in the CONTROL Section 6 1 1 file However lengthening these arrays will require a larger amount of memory from the 106 OSTFC Section 5 1 execution machine for the simulation which it may not be
282. is regarded as a type of thermostat on its own it is an off lattice discrete particle method for modelling mesoscopic systems in a fluid state It has little in common with Lattice Gas Automata and Lattice Boltzmann dynamics methods except in its application to systems of similar length and time scales and last but not least that it captures hydrodynamics behaviour The DPD method inherits its methodology from Brownian Langevin Dynamics BD However it differs from BD in an important way it is Galilean invariant and for this reason conserves hydrodynamic behaviour while the BD method does not its microscopic behaviour is only diffusive Many systems in their fluid state are crucially dependent on hydrodynamic interactions and it is essential to retain this feature in their models DPD is particularly useful for simulating coarse grained systems on the near molecular scale such as polymers biopolymers lipids emulsions and surfactants systems in which large scale structure evolves on a time scale that is too long to be modelled effectively by traditional MD The particles in DPD 79 are not regarded as molecules in a fluid but as lumps of molecules grouped to form a fluid particle in much the same spirit as the renormalisation group has been applied in polymer physics where lumps of monomers are grouped to form a bead Hence the beads are regarded as carriers of momentum It is worth noting that DPD may also be used when such systems ex
283. is usually only for the alloy component so that local concentrations of a single element revert to the standard EAM or EEAM In such case the densities functions must be zeroed in the DL_POLY_4 TABEAM file A convenient way to do this for example will be data record of the type SDEN Atom1 Atomi 1 O 1 0 6 1 8 The TABBND TABANG TABDIH TABINV Files DL_POLY 4 allows the specification of tabulated data for intramolecular interactions e TABBND for chemical bonds potentials distance dependent e TABANG for bond angles potentials angle dependent e TABDIH for dihedrals torsional potentials angle dependent e TABINV for inversions potentials angle dependent The files have the same formatting rules with examples shown in Section 4 3 Refer to Section 4 1 for their derivation and usage in coarse grained model systems 6 1 8 1 Definitions of Variables record 1 header al00 file header record 2 al a hash symbol cutpot real cutoff in A only expected in TABBND as the cutoff ranges are known for TABANG TABDIH amp TABINV ngrid integer number of grid points in table for all potentials record 3 al a hash symbol 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 empty record id record al a hash symbol atom 1 a8 fir
284. it 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 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 I e 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 overcon strained 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 overcon strained system Action Decrease constraint on the system Examine FIELD for erroneous directives if any correct and resubmit Messa
285. ite expensive to evaluate if run unoptimised The memory tabulation could be overridden for non tabulated interactions upon user specified options such as metal direct for metal interactions and vdw direct for van der Waals interactions When energy and force are calculated for tabulated interactions a 3 point interpolation scheme of our own is used to interpolate the value for the requested distance A 5 point interpolation is used for finding the numerical derivatives of 2B E EAM type potentials which are supplied in TABEAM by the user For this a Lagrange formula is used which can be found in any textbook on numerical methods 57 STFC Section 2 9 2 9 Open Knowledgebase of Interatomic Models openKIM DL_POLY_4 force field allows for full model interactions specification by using an openKIM model http OpenKIM org A KIM model contains all necessary interactions bonded and non bonded of any kind and their parameters for a specific model within a designated container Thus a KIM model can be used as a force field container when made available to DL_POLY_4 at run time see the description of the FIELD file in Section 6 1 3 upon a specification within FIELD together with a matching molecular description for the model system also specified in FIELD Due to the history of the openKIM initiative and the constraints of the logic of the DL_POLY_4 FIELD file the designated place for a KIM model specification is in the VDW section In or
286. ities 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 Gauss Rescale the kinetic energy of the thermostat bath so that particles within have Gaussian distributed kinetic energy with respect to the target temperature 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 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 ensemble averages and instantaneous pressure and stress build ups at the
287. its 6 1 max number of shared particles per node mxshl mxcons mxlrgd mxrgd Max 2 2 3 number of neighbour nodes in DD hypercube 26 max number of specified particles in a PMF unit 1 2 max number of PMF constraints per 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 max number of parameters for chemical bond potentials 4 max number of grid points in chemical bond pot arrays gt 1004 max number of specified bond angle potentials in system max number of bond angles per node max number of related bond angles 1 6 6 1 2 max number of parameters for bond angle potentials 6 max number of grid points in bond angle pot arrays gt 1004 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 grid points in dihedral angle pot arrays gt 1004 max number o
288. ix D Message 1045 error deallocation failure in comms_module gt gimin_vector See notes on message 1002 above Action See action notes on message 1002 above Message 1046 error allocation failure in comms_module gt grmin_vector See notes on message 1001 above Action See action notes on message 1001 above Message 1047 error deallocation failure in comms_module gt grmin_vector See notes on message 1002 above Action See action notes on message 1002 above Message 1048 error error allocation failure in comms_module gt grsum_matrix See notes on message 1001 above Action See action notes on message 1001 above Message 1049 error deallocation failure in comms_module gt grsum_matrix See notes on message 1002 above Action See action notes on message 1002 above Message 1050 error sorted I O base communicator not set Possible corruption if IO_MODULE This should never happen Action Make sure you have a clean copy of DL POLY_4 compiled without any suspicious warning messages 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 258 STFC Appendix D Message 1056 error unkown write option given to sorted I O This shou
289. j H2 H3 in the DL POLY FIELD scope will follow from the interaction definition as seen in Table 6 17 F qluxH therefore _ F _ im la 2 qa de _ Dalton A ps Dalton a proton A ps proton ps 8 H 1 037837512 x 10 Tesla 6 9 H DL_POLY H MKS 1 037837512 x 101 Thus to apply a magnetic field of 1 Tesla along the y axis one could specify in FIELD the following UNITS internal external magnetic O 1 1 037837512e04 0 when working in DL_POLY internal units If we worked in unit units then H x Energy Energy DL_POLY Energy unit kunit gt DL_POLY H DL_POLY H MKS 1 037837512 x 10 6 10 1 037837512 x 104 H unit H MKS Kunit DL_POLY with the following conversion factors values kev DL_POLY 9648 530821 161 STFC Section 6 1 Table 6 17 External Fields key potential type Variables 1 5 functional form elec Electric Field Ex Ey E F qE oshr Oscillating Shear A n E A cos 2nr z Lz shrx Continuous Shear A zo yaz Arl lzl gt 20 grav Gravitational Field Gy Y G F mG magn Magnetic Field H Hy H F q wx H sphr Containing Sphere A Ro n Reut F A RBRo r r gt Reut zbnd Repulsive Wall A 20 P F A z 2z p z gt p 2 xpis X Piston Cats joie Pee E E ACA de Vk 9 k i mp me zres Molecule in HR Zone 9 glob k z 2 P A Zem Zma Zem gt 2ma ind ind mn mI z A Zmn Zem ELA Zn alob glob A 2 2ma
290. kn 1 1 9 GE Pik XT 2 50 2 rig X Likl are Tjkl je X Tink are tak Tn 2 50 with 0 Q apa tay X Pie Ejk XLim r Tijlllsmtiulal t den Cjktknl al ek 005 2 ree llLijLjrlal tn Sek EjrLanla 2 Sei Ten Cig Tjkla Oew 025 njrLjrla lO 025 2rik Pi enla lg Sen gt 2 51 ralla X taal rth Lx purse Sey du rigrjulal r Sex 2rie lragPigla Sen dej rag Pjrla Ses 405 gt 2 52 2 Q E XTenl Zrin IEjiP jrla lO Sek rikt imlal n 2x 25 ULT imla OL Sej rik Pkenla Sexr 2n 2 53 20 OSTFC Section 2 2 Where we have used the following definition a dla Y 1 Sap afb 2 54 B Formally the contribution to be added to the atomic virial is given by 4 i l However it is possible to show by tedious algebra using the above formulae or more elegantly by thermo dynamic arguments 42 that the dihedral makes no contribution to the atomic virial The contribution to be added to the atomic stress tensor is given by F ripe TS TED 2 56 cos Pijkn ros ok rane rent l 2 with pe ik Likt knla Play E x all X Trl Pr ik LijLjrla a ri selec ray x Poll Eje X kn Pik ee Likt knla Erin rit jka z 25h rigPenla rag x Tall jk X Tr a Arey laljele 17 lLijLirla lLij X riel 2 57 Ik 2 rjelPagPigle ri lijt jk
291. l 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 tem perature 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 accumulators to zero at start 111 STFC Section 5 2 Note that all these options are mutually exclusive 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 5 2 5 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 f
292. l 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 7 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 the first five files are exception of that rule WARNING and ERROR are important reporting subroutines that have call points at various places in the code and NUMERIC_CONTAINER and SPME_CONTAINER are containers of simple functions and subroutines related in some way to their purpose in the code 7 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 7 2 6 SERIAL Specific Files These implement an emulation of some general MPI calls used in DL_POLY_4 source code when co
293. l possible to specify further complementing intra and inter molecular interactions in the FIELD This is a viable option only when the model system is extended beyond what the specific KIM model is intended to describes 2 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 a8 first atom type atmnam 2 a8 second atom type key a4 potential key see Table 6 12 variable 1 real potential parameter see Table 6 12 variable 2 real potential parameter see Table 6 12 variable 3 real potential parameter see Table 6 12 variable 4 real potential parameter see Table 6 12 variable 5 real potential parameter see Table 6 12 The variables pertaining to each potential are described in Table 6 12 Note that any pair potential not specified in the FIELD file will be assumed to be zero 3 metal n where n is the number of metal potentials to be entered It is followed by n records each specifying a particular metal potential in the following manner atmnam 1 a8 first atom type atmnam 2 a8 second atom type key a4 potential key see Table 6 13 variable 1 real potential parameter see Table 6 13 variable 2 real potential parameter see Table 6 13 variable 3 real potential parameter see Table 6 13 variable 4 real potential parameter see Table 6 13 variable 5 real potential parameter see Table 6 13 variable 6 real potential parameter
294. la lCiz x rial h Ur renCenla RnlLjrL enla lEjr X Lan h A 7 tla te teal 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 inclusion 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 6 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 and INTRA_COUL and DIHE DRALS_14_VDW called within 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 dihedral and improper dihedral angle functions both are calculated by the same subroutines and all the comments made in the preceding section apply An important example of the use of the improper dihedral is to conserve the structure of chiral centres in molecul
295. lation 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 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 7 2 Source Code 7 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 variables 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 com
296. ld never happen Action Contact authors if the problem persists Message 1059 error unknown write level given to sorted I O This should never happen Action Contact authors if the problem persists Message 1060 error allocation failure See notes on message 1001 above Action See action notes on message 1001 above Message 1061 error allocation failure See notes on message 1001 above Action See action notes on message 1001 above Message 1063 error allocation failure i See notes on message 1001 above Action See action notes on message 1001 above Message 1066 error allocation failure i See notes on message 1001 above Action See action notes on message 1001 above Message 1069 error allocation failure See notes on message 1001 above Action See action notes on message 1001 above Message 1070 error allocation failure See notes on message 1001 above in in in in statistics_module allocate_statitics_connect statistics_module deallocate_statitics_connect vdw module gt allocate _vdw_table_arrays vdw_module gt allocate_vdw_direct_fs_arrays metal_module gt allocate_metal_table_arrays ewald_module gt ewald_allocate_kfrz_arrays 259 OSTFC Appendix D Action See action notes on message 1001 above Message 1072 error allocation failure See notes on message 1001 above Action
297. le Internally these options are handled by the integer variable keyres which is explained in Table 6 2 Table 6 2 Internal Restart Key keyres meaning O start new simulation from CONFIG file and assign velocities from Gaussian distribution 1 continue current simulation 2 start new simulation from CONFIG file and rescale velocities to desired temperature 3 start new simulation from CONFIG file and do not rescale velocities 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 6 3 The nst keyword is also used in the NoT ensembles extension to NP AT and NP yT ones Note that these semi isotropic ensembles are only correct for infinite inter faces 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 6 3
298. le VV is considered superior to LFV since 1 Integration can be developed in symplectic manner for certain ensembles such as NVE NVEk NVT Evans as well as all Nose Hoover ensembles NVT amp NPT amp NsT when there is no external field applied on the system otherwise they do not conserve the phase space volume and MTK ensembles NPT amp NsT 263 STFC Appendix E 2 All ensemble variables are updated synchronously and thermodynamic quantities and estimators are exact at the every step whereas in LFV particle velocities and thermostat and barostat friction velocities are half an integration time step behind the rest of the ensemble variables and due to this certain estimators are approximated at full timestep 3 It offers better numerical stability and faster convergence when i constraint solvers CB PMF RATTLE VV versus SHAKE LFV 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 xxx LFV t VV t VV t 5 5 However the VV algorithms treat CB PMF RB entities in a more precise symplectic manner than the LFV ones and thus not only have better numerical stability but als
299. lines The data supplied are as follows first record atname a8 atom name binvaf integer number of data points in VAF profile excluding t 0 vaforigin real absolute value of VAF at t 0 C 0 3kgT m vaftime0 real simulation time ps at beginning of last VAF profile t 0 following records binvaf 1 records t real time ps Z t real scaled velocity autocorrelation function C t C 0 at given time t Note the VAFDAT files are optional and appear when the print vaf option is specified in the CONTROL file 6 2 12 The INTDAT INTPMF amp INTTAB Files These files where INT is referring to INTra molecular interactions and VDW RDF derived inter molecular have very similar formatting rules with some examples shown in Section 4 2 Refer to Section 4 2 for their meaning and usage in coarse grained model systems record 1 title a100 file header title record 2 header a100 file information header record 3 info a30 information to follow string bins integer number of bins for all PDFs cutoff real cutoff in for bonds and RDFs or degrees for angular intramolecular interactions types integer number of unique types of these interactions record 4 al a hash symbol record 5 178 STFC Section 6 2 info 1 al00 information to follow string record 6 al a hash symbol The subsequent records define each PDF potential in turn in the order indicated by the specification in the FIELD file Each potential is
300. lowed in FIELD as there are no mixing rules between different tersoff potentials Action Correct your model representation in FIELD and try again Message 91 error unidentified atom in four body dihedrals inversions potential list The specification of a four body or dihedrals or inversions potential in the FIELD file has referenced an atom type that is unknown Action Locate the errant atom type in the four body dihedrals inversions 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 metal 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 Message 95 error error rcut or rcut rpad 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 plus its possible padding distance applied to the pair interactions does not exceed half the perpendicular width of the simulation cell The
301. ls 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 TABBND TABANG TABDIH TABINV file This means the TABLE TABBND TABANG TABDIH TABINV 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 type 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 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
302. lume best performance efficiency will require Mz My M M and M gt 1 The former expression is a necessary condition and only guarantees good communication distribution balancing Whereas the latter is a sufficient condition and guarantees prevalence 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 Mz Mz 2 My 2 M 2 Mz My M R 5 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 5 1 these are i decrease the number of nodes used in parallel ii decrease the cutoff and iii increase system size It is crucial to note that increased parallelisation efficiency remains even when the link cell algorithm is used inefficiently However DL_POLY_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
303. ly 1000 molecules each modelled by the OPLSAA force field FF Each system is also supplied in a CG mapped representation as converted by VOTCA http www votca org or DL_ CGMAP http www ccp5 ac uk projects ccp5_cg shtml These test cases are to exemplify the Coarse Graining CG procedure see Chapter 4 including FA to CG mapping and obtaining the PMF data by means of Boltzmann Inversion 90 As a result DL_POLY_4 could be used for simulating a CG system with numerically defined tabulated FFs see TABBND TABANG TABDIH and TABINV files for intra molecular potentials and TABLE for inter molecular short range VDW potentials Both tests are also available as parts of the tutorial cases from the VOTCA package 91 Therefore the CONFIG CONTROL and FIELD input files are fully consistent with the corresponding setup files found in the VOTCA tutorial directories csg tutorials hexane and csg tutorials methanol 8 2 Benchmark Cases DL_POLY 4 benchmark test cases are available 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 200 Appendix A DL_POLY 4 Dissipative Particle Dynamics A 1 Introduction Although in a Molecular Dynamics sense Dissipative Particle Dynamics DPD
304. ly in order to instruct DL POLY _4 to use tabulated intramolecular force fields read from the TAB files the user has to specify in the FIELD file the keyword tab or tab for each intramolecular interaction thereby chosen for tabulation similarly to how it is described in Section 6 1 3 The dash symbol in front of the keyword tab is only valid for bonds and angles and is interpreted in the same manner as in Table 6 8 and Table 6 9 Note that VOTCA package is also capable of collecting both intra and inter molecular stats and producing correct TAB files provided the FIELD and HISTORY files exist albeit VOTCA saves the distributions in a format different from DAT files Below we summarise the sequence of operations the user has to follow in order to perform the CG distribution analysis and prepare the TAB files for a newly coarse grained system e Perform CG mapping of the original FA system with the aid of DL_CGMAP or VOTCA in the case of using VOTCA follow its manual the remainder of the list describes using DL_POLY_4 only e Move the data files for the newly CG mapped system FIELD_CG CONFIG_CG HISTORY_CG into a separate directory under the standard names FIELD CONFIG HISTORY and create the corresponding CONTROL file containing the analysis and replay history directives e As no TAB files are yet available for the CG system at this stage one can either i create the initial TAB files padded with zeros or ii use a FIEL
305. ly the particles are subject to a drag force which depends on the relative velocity between interacting pairs of particles Ti e ij rij rij vii 2 gt A 6 ij where w r j is once again a switching function and Uj vj Y is the inter particle relative veloc ity The constant yj is the drag coefficient It follows from the fluctuation dissipation theorem that for thermodynamic equilibrium to result from this method the following relations must hold of 2 yijkgT A 7 w ry wr A 8 202 OSTFC Appendix A In practice the switching functions are defined through 2 R C wa le e a A 9 which ensures that all interactions are switched off at the range rij re In many DPD simulations the stochastic and drag coefficients are often constant for all interactions i e oj o and yj y although this assumption does not have to apply In DL POLY_4 the qij coefficients may be supplied at the end of each specified vdw interaction potential as a parameter further to the last one for the particular vdw potential form For a DPD thermostat to work correctly all possible two body interactions must be defined and all y 4 0 What DL_POLY 4 will attempt first if a two body interaction is missing is to derive it using mixing rules default may be overridden by user specification However if any of yij 0 then DL POLY 4 will check for the existence of a global y that may be optionally supplied by the user on the
306. me but also incorporate RB dynamics Cell size and shape variations The extension of the isotropic algorithm to anisotropic cell variations is straightforward A tensor y is defined as a 10 1 Poa 1 a V O 3 136 where where is the stress tensor equation 3 98 and 1 is the identity matrix Then new cell vectors and volume are given by H At nt H V t At Trin t V 3 137 84 STFC Section 3 5 and the velocity updates for VV and LFV algorithms as wi r t At n t r t Atut sat IS LFV r t At e n t r t Atu t sat 3 138 IS This ensemble is optionally extending to constant normal pressure and constant surface area NP AT 73 by semi isotropic constraining of the barostat equation of motion to 1 E Pot o22 t V H a 6 2 Mas t 4 1 a d a y 3 139 0 fees Similarly this ensemble is optionally extending to constant normal pressure and constant surface tension NP yT 73 by semi isotropic constraining of the barostat equation of motion to 1 ES Posa Yext V t hz t Caalt VO a 9 x y mast 4 y _ BA Pext 022 t V t eos oe 0 afd where Yext is the user defined external surface tension and h t V t Azy t is the instantaneous hight of the MD box or MD box volume over area One defines the instantaneous surface tension as given in equation 3 122 The case yYext 0 generates the NPT anisotropic ensemble fo
307. mo is 1 6605402 x 1072 kilograms i e Daltons atomic mass units e The unit of charge qo is 1 60217733 x 107 Coulombs i e electrons units of proton charge e The unit of energy E mo lo to is 1 6605402 x 1072 Joules 10 J mol e The unit of pressure P Elz is 1 6605402 x 107 Pascals 163 882576 atmospheres e Planck s constant A which is 6 350780668 x Eoto In addition the following conversion factors are used 7 STFC Section 1 4 e The coulombic conversion factor yo is 1 _ _ _ 1389354885 P T rra i such that Uukxs EoYoUlnternal gt where U represents the configuration energy e The Boltzmann factor kg is 0 831451115 E K such that T Exin kb 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 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 see Section 6 1 3 The default is the DL POLY unit Externally DL_POLY_4 accepts information in its own specific formatting as described in Section 6 1 Irrespective of formatting rules all values provided to define input entities are read in DL POLY units except otherwise specified as in the case of energy units or their composite mixture representing the corresponding entity physically i e velocities com
308. molecular PDFs every f timesteps default f 1 using a grid with n bins and bonds cutoff of r A default r 2 A analyse bonds sampling every f nbins n rmax r calculate and collect bonds PDFs every f timesteps default f 1 using a grid with n bins in the range 0 7 default r 2 A analyse angles sampling every f nbins n calculate and collect angles PDFs every f timesteps default f 1 using a grid with n bins in the range 0 180 degrees analyse dihedrals sampling every f nbins n calculate and collect dihedrals PDF s every f timesteps default f 1 using a grid with n bins in the range 180 180 degrees analyse inversions sampling every f nbins n calculate and collect inversions PDFs binsize f cap forces f close time f collect coulomb cutoff f rcut f defects i j f every f timesteps default f 1 using a grid with n bins in the range 0 180 degrees set the bin size for radial and z density distribution functions to f if105 lt f lt reu 4or 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 A 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 write defects trajectory file DEFECTS with controls i start timestep
309. 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 STFC Section 1 3 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 1 3 2 Modularisation and Intent DL_POLY_4 exploits the full potenti
310. mped 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 be chosen so that contributions to the real space 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 standard Ewald since they specify the sides of a cube not a radius of convergence 117 STFC Section 5 3 sum are negligible for terms with r gt freut The relative error e in the real space sum truncated at Tout is given approximately by e erfe Tot Te exp a Teut 7 Teut 5 3 which reciprocally gives an estimate for a for a given e ln e Teut a _ _ _ 5 4 Tout The recommended value for is 3 2 T 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 erfe x 0 56 exp 2 x 5 5 to solve recursively for a using equation 5 3 to give the first guess The relative error in the reciprocal space term is approximately ex exp k 9 407 Kira 5 6 where EN T ax max gt 5 7 k 7 5 5 7 is largest k vector considered in reciprocal space L is the width of the
311. mpiling 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 7 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 VDW_TABLE_READ CHECK_CONFIG SYSTEM_EXPAND SYSTEM_INIT 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 RSD_WRITE SYSTEM_REVIVE The rest of the files that use MPI functionality in any way make implicit calls via generic functions developed in COMMS_MODULE 192 STFC Section 7 2 7 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 14159265358979312 m constant twopi 6 28318530717958623 27 constant fourpi 12 56637061435917246 47 constant sqrpi 1 772453850905588 YT constant rtwopi 0 15915494309189535 z constant rt2 1 41421356237309515 Y 2 constant rt3 1 73205080756887719 Y 3 constant r4pie0 1389
312. munication module defines MPI related parameters and develops MPI related functions 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 187 STFC Section 7 2 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 debugging 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 e domains module DOMAINS_MODULE The domains module defines DD parameters and maps the available computer resources
313. n Chen virial correction Us AA Ae ar a m 3 l nt ae l 2 144 m 3 Tmet 2 7 00 Gupta virial correction p 4t NpAro ro roy ro 3 t r3 a Br xe 72 Grin e 2 x TO Pp P P Pp Tmet 2 exp p ro r ro V EN e DO lx 2 145 qij qij qij 7 NB exp Qij aa 24 p 9 Many body perturbation component virial correction 2 SV dij 2T pro TO dij Vi 0 Arp N j Som e A 2 146 m 3 rin rie 2 p In the energy and virial corrections we have used the approximation N 1 2 N D Sioa 2 147 i lt p gt where lt p 2 gt 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 calculated 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 39 STFC Section 2 3 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 2 110 and 2 111 it is clear that we require mixing rules for terms Vj rij and p rij when atoms i and j are of different kinds Thus two different metals A and B we can
314. n for the replicated data RD parallelisation that DL_POLY_Classic adopts and thus it can also accept truncated octahedral and rhombic dodecahedral periodic boundaries 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 143 STFC Section 6 1 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 in A yyy real y coordinate in A ZZZ real z coordinate in 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 Classic but may be added to aid alternative uses of the file for example alike DL POLY GUI 21 DL_POLY_Classic assume that the atoms indices are in a sequentially ascending order starting form 1 However DL POLY_4 needs the index or the no index option needs to be specified in the CONTROL file It is worth mentioning that DL_POLY_4 as well as DL_POLY_Classic assumes that the origin of Cartesian system with respect to which the particle positions are specified is th
315. n force interactions based on the calculation of the corresponding intramolecular distributions e Preparation and use of the tabulated intramolecular potentials Note Although these steps are also applicable to atomistic systems which can be useful for benchmarking purposes below we shall assume that the CG mapping has been done and the following data files have been generated for the CG mapped model system CONTROL FIELD CONFIG andi alternatively HISTORY 4 2 Intramolecular Probability Distribution Function PDF Analysis Albeit the distribution analysis can be performed on the fly in the course of a simulation run for CG purposes it has to be done on an existing CG mapped trajectory by invoking the replay history and analysis directives see Section 6 1 1 To trigger the PDF collection and subsequent output of PMF s for any of the following intarmolecular interactions bonds angles dihedrals and or inversions the CONTROL file must contain any combination of the options demonstrated in the example below TITLE EXAMPLE OF DL_POLY_4 PDF ANALYSIS DIRECTIVES SNIPPET DIRECTIVES TO INVOKE INTRAMOLECULAR PDF ANALYSIS BY TYPE analyse bonds sample every 100 nbins 250 rmax 5 0 analyse angles sample every 100 nbins 360 0 pi analyse dihedrals sample every 100 nbins 720 pi pil 100 OSTFC Section 4 2 analyse inversions sample every 100 nbins 360 O pil DIRECTIVES TO INVOKE INTRAMOLECULAR PDF ANALYSIS FOR ALL T
316. n 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 trajectory 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 is restricted to 2 along the z direction The number of nodes should not be a prime number since these are not factoris able decomposable Action You must ensure DL_POLY_4 execution on a number of 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 the
317. n t and Z t are given in tabular form Z t C t C 0 is the value of the velocity autocorrelation function C t u 0 u t scaled by C 0 3kgT m Note that a readable version of these data for individual species is provided by the VAFDAT files below 6 2 7 The REVCON File This file is formatted and written by the subroutine REVIVE REVCON is the restart configuration file The file is written every ndump time steps in case of a system crash during execution and at the termination of the job A successful run of DL_POLY_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 7 2 2 The default value is ndump 1000 REVCON is identical in format to the CONFIG input file see Section 6 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 6 2 8 The REVIVE File This file is unformatted and written by the subroutine SYSTEM_REVIVE It contains the accumulated sta tistical 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 176 OSTFC Section 6 2 supplied in
318. n the Makefile issue make press lt Enter gt and then examine the Makefile entries corresponding to the keywords reported If there is not a suitable entry then you should seek advice from a computer scientist or the support staff of the particular machine HPC service The necessary components for the source compilation are 1 a FORTRAN9O TR15581 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 an MPI2 or MPI1 MPI I 0 implementation COMPILED for the architecture 0S and the targeted compiler if the full PATH to these is not passed to the DEFAULT ENVIRONMENT PATH then it MUST be explicitly supplied in the Makefile 3 a MAKE command Makefile interpreter in the system SHELL where 2 is not necessary for compilation in SERIAL mode Note that for the TR15581 compliance gfortran requires a gcc version 4 2 0 or above By default if the compilation process is successful then an executable build will be placed in execute directory at the same level as the source directory where the code is compiled Should the execute directory not exist then it will be created automatically by the Makefile script The build may 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 Compilation on Windows The best way to
319. n 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 chemical bonds that are NOT distance restraints valence angles that are NOT distance restraints dihedrals inversions 157 STFC Section 6 1 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 5 tersoff n where n is the number of specified Tersoff potentials There are two types of Tersoff potential forms that cannot be mixed used simultaneously They are shorthanded as ters and kihs atomkeys e ters atomkey expects 2n records specifying n particular Tersoff single atom type parameter sets and n n 1 2 records specifying cross atom type parameter sets in the following manner potential 1 record 1 atmnam a8 atom type key ad potential key see Table 6 14 variable 1 real potential parameter see Table 6 14 variable 2 real potential parameter see Table 6 14 variable 3 real potential parameter see Table 6 14 variable 4 real potential parameter see Table 6 14 variable 5 real cutoff range for this potential A potential 1 record 2 variable 6 real potential parameter see Table 6 14 variable 7 real potenti
320. n type barostat 31 the Berendsen barostat 29 the Nos Hoover type barostat 30 and the Martyna Tuckerman Klein MTK barsotat 32 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 LE rin t E Watomic t _ Weonstrain t At WPMF t At 3V t P t 3 97 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 during equilibration in NPT and NoT simulations This is due to iterative nature of the constrained motion in which the virials Weonstrain and Wpmr are calculated retrospectively to the forcefield virial Watomic The instantaneous stress tensor in a system a t Cin t O torie t 0 constrain t At t At 3 98 Toy is a sum of the forcefield 7 _ constrain a __ and PMF a stresses atomic constrains PMF ic Tr O Note that when bond constraints or and PMF constraints are present in the system the quantity v will not converge to the exact value of Pax during equilibration in NPT and NoT simulations This is due to iterative nature of the constrained motion in which the constraint and PMF stresses are calculated r
321. nd 250 000 atoms respectively Simulation at 300 K using NPT Berendsen ensemble with Finnis Sinclair forces and no electrostatics 8 1 16 Test Case 31 and 32 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 8 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 respectively Simulation at 25 K using NVE ensemble with CGM force minimisation and SPME electrostatics Both constraint bond and rigid body dynamics cases are available 8 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 8 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 8 1 20 Test Case 39 and 40 Ionic liquid dimethylimidazolium chloride These systems
322. nd Yokokawa T 1994 Mol Simul 12 3 9 177 17 19 Smith W 1993 CCP5 Information Quarterly 39 14 18 21 25 Ryckaert J P and Bellemans A 1975 Chem Phys Lett 30 123 19 22 153 Schmidt M E Shin S and Rice S A 1996 J Chem Phys 104 2101 19 22 153 Rohl A L Wright K and Gale J D 2003 Amer Mineralogist 88 921 25 Raiteri P and Gale J D 2010 J Am Chem Soc 132 17623 17634 25 Mie G 1903 Annalen der Physik 11 657 697 27 28 156 Clarke J H R Smith W and Woodcock L V 1986 J Chem Phys 84 2290 27 28 156 Weeks J D Chandler D and Anderson H C 1971 J Chem Phys 54 5237 28 156 Groot R D and Warren P B 1997 J Chem Phys 107 11 4423 4435 28 65 201 203 Al Matar A K and Rockstraw D A 2004 J Comput Chem 25 660 668 30 Hepburn D J and Ackland G J 2008 Phys Rev B 78 16 165115 31 40 278 OSTFC Bibliography 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 Lau T T F rst C J Lin X Gale J D Yip S and Vliet K J V 2007 Phys Rev Lett 98 21 215501 31 40 Cooper M W D Rushton M J D and Grimes R W 2014 J Phys Condens Matter 26 105401 31 33 J F 1952 Philos Mag 43 153 31 Ackland G J and Reed S K 2003 Phys Rev B 67 1741081 1741089 31 Olsson P
323. ned or that your CONFIG file or the first frame of your HISTRORY being replayed Check out for mistyped number or identities of molecules atoms etc in FIELD and for mangled blank lines in CONFIG HISTORY or a blank line s at the end of CONFIG or missing FOF End Of File character in CONFIG If this error is issued after timestep zero in a simulation that is not replaying HISTORY then it is big trouble and you should report that to the authors If it is during replaying HISTORY then your HISTORY file has corrupted frames and you must correct it before trying again 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 221 STFC Appendix D Action See action notes on message 14 above 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 each node and checks for the violation of this Termination will result if the condition is violated Action Use densvar op
324. neral format of the above discussed files is shown in Section 6 2 12 4 3 Setting up Tabulated Intramolecular Force Field Files For a user defined e g coarse grained model system the effective potentials must be provided in a tabulated form For non bonded short range VdW interactions the TABLE file must be prepared as described in Section 6 1 6 However the tabulated data format for intramolecular interactions bonds bending angles dihedral and inversion angles in a polymer differs from that of the TABLE file and assumes three columns abscissa distance in A or angle in degrees and two ordinates potential and force data virial for distance dependent interactions e g bonds and force for angle dependent interactions e g angles Shown below are examples of TABBND and TABANG files corresponding to the above PDF examples Note that the PMF and force data have been resampled onto a finer grid with points located at bin edges userChost more TABBND TITLE Hexane FA OPLSAA gt CG mapped with 3 beads A B A 5 0 500 FAB 1 00000e 02 9 0906600e 02 1 3954000e 00 2 00000e 02 9 1046200e 02 2 7908000e 00 3 00000e 02 9 1185700e 02 4 1862000e 00 userChost more TABANG TITLE Hexane FA OPLSAA gt CG mapped with 3 beads A B A 1000 ABA 1 80000e 01 8 8720627e 01 6 9119576e 01 3 60000e 01 8 8596227e 01 6 9119227e 01 5 40000e 01 8 8471827e 01 6 9118704e 01 The input tables for bonds angles dihedrals and inve
325. nformation pertaining to the dominating interactions within the FA system that govern its behaviour towards phenomena of interest and the most important thermodynamic properties are retained Then the greatly reduced phase space of the CG model system allows for efficient access to much longer length and time scales for investigating microscopic phenomena using of the well established classical MD machinery The reduced DoF mapping leads to the generation of an effective CG FF in terms of the effective interaction potentials and forces between the CG particles which are often tabulated numerically The initial coarse grain mapping of the original FA trajectory can be done with the aid of DL CGMAP tool http www ccp5 ac uk software After the CG mapped trajectory has been obtained the relevant distribution analysis and the Boltzmann Inversion procedure producing tabulated PMF s can be performed by using DL POLY_4 in replay history mode with the corresponding directives in CONTROL file For further iterative optimisation of the CG model the user is advised to use DL_POLY_4 as simulation engine within the framework of VOTCA package http www votca org which provides a handful of various systematic coarse graining methodologies For more details the user should refer to the manuals of these tools This section describes how to use DL_POLY_4 for two SCG tasks e Post simulation analysis of the intramolecular bonded and angular mea
326. ng Action Recreate or correct the erroneous entries in the FIELD file and try again 215 STFC Appendix D Message 22 error unsuitable radial increment in TABLE TABBND TABANG TABDIH TABIN file This arises when the tabulated van der Waals potentials presented in the TABLE file have an increment that is greater than that used to define the other potentials in the simulation Ideally the increment should be Teut mxgrid 4 where reut is the largest potential cutoff of all supplied for the short range potentials and the domain decomposition link cell size and mxgrid is the parameter defining the length of the interpolation arrays An increment less than this is permissible however The same argument holds for the tabulated intra molecular interactions that are possibly supplied via the TABBND TABANG TABDIH and TABINV files All should have grids sized less than the generic mxgrid 4 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 potentia
327. not have the neutral group option Action Use the Ewald sum option It s better anyway 216 STFC Appendix D Message 27 error unit s member indexed outside molecule s site range An intra molecular or intra molecular alike interaction topological unit has member site which is given a number outside the scope of the molecule it is part of Action Find the erroneous entry in FIELD correct it and try running DL_POLY_4 again 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 to 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 See action notes on message 14 above Message 31 error too many chemical bonds per domain DL_POLY 4 limits the number of chemical bond units in the system to be
328. nsure 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 251 STFC Appendix D 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 gisum_vector See notes on message 1001 above Action See action notes on message 1001 above Message 1004 error deallocation failure in comms_module gt gisum_vector See notes on message 1002 above Action See action notes on message 1002 above Message 1005 error allocation failure in comms_module gt grsum_vector See notes on message 1001
329. nt 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 Section 6 1 2 II None e g isolated polymer in space imcon Cubic periodic boundaries Orthorhombic periodic boundaries imcon I E imcon II w Parallelepiped periodic boundaries imcon Slab X Y periodic Z non periodic HS A O I N o A ae SES II a imcon 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 B 2 No periodic boundary imcon 0 Simulations requiring no periodic boundaries are best suited to in vacuuo simulations such as the confor mational study of an isolated polymer molecule This boundary condition is not recommended for studies in a solvent since evaporation is likely 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 B 3 Cubic periodic bounda
330. ntial parameter potential parameter potential parameter potential parameter potential parameter potential parameter potential parameter potential parameter potential parameter see Table 6 14 see Table 6 14 see Table 6 14 see Table 6 14 see Table 6 14 see Table 6 14 see Table 6 14 see Table 6 14 see Table 6 14 see Table 6 14 see Table 6 14 The variables pertaining to each potential are described in Table 6 14 Note that the fifth variable is the range at which the particular tersoff potential is truncated The distance is in Table 6 14 Tersoff Potential key potential type Variables 1 5 6 11 a c 12 16 functional form ters Tersoff Ala B R Potential forms single S B8 n d h cross x w lo as shown in kihs KIHS Aja B b R S 6 a e C3 Section 2 3 3 ca cs hl al p 6 tbp n where n is the number of three body potentials to be entered specifying a particular three body potential in the following manner atmnam 1 i atmnam 2 j atmnam 3 k key variable 1 variable 2 variable 3 variable 4 variable 5 as as as ad real real real real real It is followed by n records each first atom type second central atom type third atom type potential key see Table 6 15 potential parameter see Table 6 15 potential parameter see Table 6 15 potential parameter see Table 6 15 potential parameter see Table 6 15 cutoff range for this poten
331. ntribution to be added to the atomic stress tensor is given by oF raff tra fe tree 2 70 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 9 The Calcite Four Body Potential Figure 2 6 The vectors of the calcite potential This potential 45 46 is designed to help maintain the planar structure of the carbonate anion CO3 in a similar manner to the planar inversion potential described above However it is not an angular potential It is dependent on the perpendicular displacement u of an atom a from a plane defined by three other atoms b c and d see Figure 2 6 and has the form Uabea u Au F Bu 2 71 where the displacement u is given by Tab Tbe X Tod 2 72 The X Toal Vectors Tabac and rag define bonds between the central atom a and the peripheral atoms b c and d Vectors Tp and rpa define the plane and are related to the bond vectors by Tbe Fac Tab Tod Yad Tad 2 73 In what follows it is convenient to define the vector product appearing in both the numerator and denomi nator of equation 2 72 as the vector Weg vis Wed The X Tod 2 74 25 STFC Section 2 2 We also define the quantity y u as y u 2Au 4Bu 2 75 The forces on the individual atoms due to the calcite potential are then given by fa
332. nts 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 179 OSTFC Section 6 2 i e the conserved quantity system temperature configurational energy short range potential energy electrostatic energy chemical bond energy valence angle and 3 body potential energy dihedral inversion and 4 body potential energy tethering energy enthalpy total energy PV rotational temperature total virial short range virial electrostatic virial bond virial valence angle and 3 body virial constraint bond virial tethering virial volume core shell temperature core shell potential energy core shell virial MD cell angle a MD cell angle 8 MD cell angle y PMF constraint virial pressure mean squared displacement of first atom types mean squared displacement of second atom types mean squared displacement of last atom types xx component of stress tensor xy component of stress tensor xz component of stress
333. o produce more accurate dynamics Makefiles amp compilation From within the source directory the user may compile the code by selecting the appropriate Makefile from the build directory and copying it across by typing at the command line cp build Makefile_MPI Makefile intended for parallel execution on multi processor platforms an MPI implementation is needed or cp build Makefile_SRLx Makefile intended for serial execution no MPI required followed by lt Enter gt Note that in comms_module f90 it is crucial that line 13 reads as Use mpi_module for serial compilation or as Use mpi for parallel compilation which is the default If the parallel OS environment one is compiling on is not fully F90 compatible then the Use mpi entry in the comms_module f90 file may be interpreted as erroneous This is easily overcome by commenting out the Use mpi line and uncommenting the Include mpif h one situated immediately after the Implicit None line If there is an entry in the Makefile for the particular combination of architecture compiler amp MPI implementation then the user may instantiate the compilation by issuing at the command line make entry 264 STFC Appendix E and then pressing lt Enter gt Usually the one named hpc is suitable for the majority of platforms To find out the keywords for all available entries withi
334. o_arrays See notes on message 1001 above Action See action notes on message 1001 above Message 1081 error allocation failure in dpd_module allocate_dpd_arrays See notes on message 1001 above Action See action notes on message 1001 above 261 Appendix E DL POLY 4 README wisdom E 1 README txt DL_POLY_4 07 The source is in fully self contained free formatted FORTRAN90 MPI2 code specifically FORTRAN9O TR15581 MPI1 MPI 1 0 only The available NetCDF functionality makes the extended code dependent upon it The non extended code complies with the NAGWare and FORCHECK F90 standards with exception of the FORTRAN2003 feature TR15581 which is very rarely unavailable in the nowadays FORTRAN90 95 compilers This version supports ALL features that are available in the standard DL_POLY_Classic version with the exceptions of 1 Rigid bodies RBs linked via i constraint bonds CBs or ii potential of mean field constraints PMFs 2 Truncated octahedral imcon 4 Rhombic Dodecahedral imcon 5 and Hexagonal Prism imcon 7 periodic boundary MD cell conventions PBC Note that the last one is easily convertible to orthorhombic imcon 2 see utility nfold f90 3 Classic Ewald and Hautman Klein Ewald Coulomb evaluations 4 Hyper Dynamics Temperature Accelerated Dynamics Biased Potential Dynamics Meta Dynamics and solvation features No previous DL_POLY_3 4 feature is deprecated ALL NEW f
335. oat otherwise 64 bit double is defaulted if unspecified type sorted or unsorted DD scrambled by global index output default sorted 128 STFC Section 6 1 job time f maxdis f metal direct metal sqrtrho mindis f minimise string n f msdtmp i j multiple timestep n mxquat n mxshak n j writer count 1 lt j lt job size default j 9Int Log Min job size 8 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 10 000 000 default 2 000 000 is the maximum number of particle entities in a batch i e multiples 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 20 000 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 enforce the direct calculation of metal interactions defined by explicit potential forms i e it will not work for metal alloy systems using the EAM EEAM 2BEAM or 2BEEAM TABEAM swich the TABEAM default of reading embedding functions F p as interpolated over densities p to as interpolated over p i e F F yp
336. ody 4 12 13 15 27 45 115 154 174 183 215 225 239 valence angle 4 12 13 15 17 21 23 45 150 152 174 183 184 220 van der Waals 13 15 18 21 22 26 108 140 153 154 236 160 115 109 quaternions 5 96 reaction field 49 50 131 139 rigid body 3 5 61 93 94 183 184 250 rigid bond see constraints bond stress tensor 15 18 21 25 27 29 36 44 50 54 57 65 77 sub directory 208 210 bench 8 build 8 data 8 execute 8 java 8 public 8 source 8 utility 8 thermostat 5 56 97 126 127 240 Nos Hoover 85 91 torsional restraints 22 units DL_POLY 7 175 energy 146 pressure 7 8 86 130 175 temperature 133 user registration 10 Verlet neighbour list 107 184 185 228 WWW iii 3 10 58 100 115 116 200 204 282
337. of 0 5 at working precision the system energy unit 195 Chapter 8 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 196 STFC Section 8 1 8 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 number 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 OUTPU
338. 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 then moved 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 core shell units are dealt with i kinetically by the adiabatic shell model or ii statically 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 stress potential energy due to the core shell spring The latter via atomic stress potential energy due to the shells move to minimised configuration 2 8 Tabulation and interpolation in the treatment of intermolecular in teractions By default DL_POLY_4 tabulates in memory most of the intermolecular interactions keeping values of the potential and the negative of its first derivative times the distance or virial over an equidistant grid This is done for reasons of speed as due to the large variety of potential forms some could be qu
339. oided by redirecting the output using the gt symbol for instance mpirun n 4 DLPOLY Z gt OUTPUT It is also worth noting that the use of large batch and buffer numbers can speed up enormously the perfor mance of the parallel I O for example putting in CONTROL see Section 6 1 1 io read mpiio 128 10000000 1000000 io write mpiio 512 10000000 1000000 at large processor count jobs over 1000 However this help comes at a price as larger batches and buffers also requires more memory So at smaller processor counts the job will abort at the point of trying to use some of the allocated arrays responsible for these More information about DL_POLY 4 parallel I O can be found in the following references 82 83 84 5 2 4 Restarting The best approach to running DL_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 6 1 1 in the CONTROL file DL_POLY_4 will stop in a controlled manner allowing you to restart the job
340. ok A Ojik S rij S rin Sex 05 S rik 5 2 33 Tjk OF ik with 64 1 if a b and dq 0 if a b In the absence of screening terms S r this formula reduces to o o 17 STFC Section 2 2 The derivative of the angular function is E 5 9 3 0 Tio Lik gra Aris E D0 ik A a Tirik gt 2 35 with NR ri rij a enta 60 ni er 60 Ore Tijfik TijTik TijTik col di J ek 004 2 36 T Tij Tik The atomic forces are then completely specified by the derivatives of the particular functions A 0 and S r The contribution to be added to the atomic virial is given by W Ari f np 2 37 It is worth noting that in the absence of screening terms S r the virial is zero 42 The contribution to be added to the atomic stress tensor is given by ae nh 8 ra 8 2 38 and the stress tensor is symmetric In DL_POLY_4 valence forces are handled 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 o 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 restra
341. on Standard user response Increase mxgrid parameter 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 See action notes on message 14 above 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 Message 52 error end of FIELD file encountered This message results 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 m
342. on 2 2 The force f acting on atom 7 is the negative of this The contribution to be added to the atomic virial is given by W Pij T gt 2 14 with only one such contribution from each bond The contribution to be added to the atomic stress tensor is given by gr a a 2 15 where a and p 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 and INTRA_COUL called within 2 2 2 Distance Restraints In DL_POLY 4 distance restraints in which the separation between two atoms is maintained around some preset value rp is handled as a special case of bond potentials As a consequence distance 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 13 5 Restrained harmonic rhm 6 Quartic potential qur 7 Buckingham potential bck 8 Coulomb potential cul 9 FENE potential fne 10 AMOEBA force field bond potential 36 amo 11 Tabulated potential tab Th
343. on 3 2 use default iteration pre cision 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 simulation 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 mxrgd mxteth mxbond mxangl mxdihd mxinv as well as the lengths of link cell mxlist and domain mxatms mxatdm lists arrays when the option is activated with f gt 0 Greater values of f will correspond to allocation bigger global arrays and larger memory consumption by DL_POLY_4 during the simulation No
344. 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 7 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 stress which must be obtained as a global sum of the contributing terms calculated on all nodes 185 STFC Section 7 1 The DD strategy does not require a global summation of the forces unlike the Replicated Data method used in DL_POLY_Classic which limits communication overheads and provides smooth parallelisation to large processor counts 7 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 of the atoms involved 2 Each processor makes a list of the atoms bonded by constraints it must process Entries are zero if the atom is not bonded 3 Each processor passes a copy of the array to the neighbouring processors which manage the domains in contact with its own The receiving processor compares the incoming list with its own and keeps a record of the shared atoms and the processors which share them 4 In the first stage of the algorithms the
345. onded interactions as well as metal and Ter soff interactions are calculated using interpolation tables These are generated in the following routines VDW_GENERATE METAL_GENERATE METAL_TABLE_DERIVATIVES and TERSOFF_GENERATE 7 1 4 Modifications for the Ewald Sum For systems with periodic boundary conditions DL POLY_4 employs the Ewald Sum to calculate the coulom bic 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 66 88 as discussed in 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 Transform due to I J Bush 89 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 The DL_POLY_4 subroutine EWALD_SPME_FORCES perfoms the bulk of the FFT o
346. ons and optionally velocities and forces from the CONFIG file After allocation of all necessary simulation arrays and variables with compulsory initialisation to zero value the job control information is required this is obtained by the routine READ_CONTROL which reads the CONTROL file The description of the system to be simulated the types of atoms and molecules present and the intermolecular forces are obtained by the READ_FIELD routine which reads the FIELD file The SYSTEM_INIT routine is called next to initialise various simu lation arrays and variables with the data available so far and detects if the job is a restart of previous simulation run If so it reads the REVOLD Section 6 1 5 to supply some arrays and variables with the necessary values as saved from the previous job The domain halo is constructed immediately afterwards by the routine SET_HALO_PARTICLES After gathering all these data bookkeeping and exclusion arrays are created for the intramolecular and site related interactions core shell constraint and tether units by the BUILD_BOOK_INTRA and BUILD_EXCL_INTRA routines Lastly the thermodynamic properties of the system are checked and set 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 represents the main part of any simulation For calculation of the two body contribution
347. or 3 207 Appendix C 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 The function of each of these is described below It is worth noting that most of these functions could be performed by the DL POLY Java GUI 21 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 copy copy invokes the UNIX commands mv v CONFIG CONFIG OLD mv v REVCON CONFIG mv v REVIVE REVOLD which collectively prepare the DL_POLY 4 files in the execute sub directory for the continuation of a simu lation It is always a good idea to store these files elsewhere in addition to using this macro 208 STFC Appendix C gopoly gopoly is used to submit a DL_POLY_4 job to the HPCz which operates a LOAD LEVELER job queuing system It invokes the following script s
348. ords appearing are described in the following section The example 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_4 SAFE ORDER OF CONTROL DIRECTIVES SYSTEM REPLICATION amp 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 AND NO TOPOLOGY REPORTING no index no strict no topology INTERACTIONS BYPASS no electostatics no vdw APPLY MIXING TO ALLOWED amp AVAILABLE VDW CROSS INTERACTIONS LorentzBerthelot Fender Halsey Hogervorst good hope Halgren HHG Tang Toennies vdw mixing Lorentz 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 100 200 300 I O READ METHOD READER COUNT BATCH BUFFER SIZES io read mpiio 2 2000000 20000 1 0 WRITE METHOD TYPE WRITER COUNT BATCH BUFFER SIZES io write mpiio sorted 8 2000000 20000 122 STFC Section 6 1 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 atmo
349. ort_atomic_data This may happen in extremely non equilibrium simulations or usually when the potentials in use do not hold the system stable Action Consider using densvar option in CONTROL for extremely non equilibrium simulations Alternatively increase mxbfdp parameter in SET_BOUNDS recompile and resubmit Message 44 error incoming data transfer size exceeds limit in deport_atomic_data Action See action notes on message 43 above Message 45 error too many atoms in CONFIG file or per domain This can happen in circumstances when indeed the CONFIG file has more atoms listed than defined in FIELD or when one of the domains managed by an MPI process has higher particle density than the system average and contains more particles than allowed by the default based on the system Action Check if CONFIG and FIELD numbers of particles match Try executing on various number of processors Try using the densvar option in CONTROL to increase mxatms alternatively increase it by hand in SET_BOUNDS and recompile and resubmit Send the problem to us if this is persistent Message 46 error undefined direction passed to export_atomic_data This should never happen Action Send the problem to us Message 47 error undefined direction passed to metal_ld_export This should never happen Action Send the problem to us 219 STFC Appendix D Message 48 error transfer buffer too small in _table_read Acti
350. ost travelled particle has moved a distance larger than rpaq 2 It is worth noting that padding is at expense of extra memory but if used wisely it could improve time to solution from 10 to 100 depending on force field complexity If it is too large or too small that is why the f gt Min 0 05 0 5 recut A limit it will lead to performace degradation It is recomended that pad is set up at a value of 1 5 of the cutoff reut as long as the major link cell algorithm uses a link cell decomposition that not worse than 4 amp 4 8 4 per domain For such setups in practice one may expect average compute speedups of the order of 10 30 for force fields involving the Ewald summation methodology and 60 100 for force fields without electrostatics evaluations involving the Ewald summation methodology Users are advised to study the example CONTROL files appearing in the data sub directory to see how different files are constructed 6 1 2 The CONFIG File The CONFIG file contains the dimensions of the unit cell the key for periodic boundary conditions and the atomic labels coordinates velocities and forces This file is read by the subroutine 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 0000000
351. ource cd DL_POLY_4 ZZ source tar xzvf kim api v1 6 X 3 Download and unpack the testing Model and its Model Driver of cd kim api v1 6 X src model_drivers wget http www aem umn edu elliott Pair_Morse__MD tgz tar xzvf Pair_Morse__MD tgz cd models wget http www aem umn edu elliott Pair_Morse_GirifalcoWeizer_LowCutoff_Cu__MO tgz tar xzvf Pair_Morse_GirifalcoWeizer_LowCutoff_Cu__MO tgz cd 4 Configure the openkim api package according to the instructions in INSTALL cp Makefile KIM_Config example Makefile KIM_Config vi Makefile KIM_Config Edit file as appropriate In particular change the KIM_DIR variable make 266 STFC Appendix E 5 Copy the DL_POLY_4 ZZ makefile and compile cd cp build Makefile_SRL2_KIM Makefile vi Makefile Edit the KIM_API_DIR variable as appropriate make gnu cd execute ls haltr The last listed file should be DLPOLY Z and have the current date stamp Similarly one may build DL_POLY_4 in parallel by copying build Makefile_MPI_KIM and compiling accordingly Test Verify KIM 1 Obtain DL_POLY_4 TEST21 following the README txt advice from the DL_POLY_4 ZZ data directory cd data ftp ftp dl ac uk ftp username anonymous ftp password email google com enter your email ftp gt cd ccp5 DL_POLY DL_POLY_4 0 DATA ftp gt binary transfer mode ftp gt get TEST21 tar gz ftp gt quit tar xzvf TES
352. p p TO 2 re 2rmet 2 2 x 2 141 ij ij z 2 a NB P Qij ro 2 0 a 9 Many body perturbation component energy correction 27 Pro qij U U 0 i gee E 2 142 m 3 ra pes 2 pe To estimate the virial correction we assume the corrected local densities are constants i e independent of distance at least beyond the range ret This allows the virial correction to be computed by the methods used in the short ranged potentials n A i 1 jAti Orij N Tij lt Tmet V ri N Tij2Tmet Vj ri Y D y ij 3Y Y eee ij rij Y t i 1 a i 1 jf OV OW ANP is Tmet Tij Y OF pi Y Opis vig we gt Do Ap Tis 2 143 i 1 Pi ja Mi N T j lt Tmet Tij2YTmet OF f Opis ri X OF pi Oper i 1 Pi GA Tij i 1 Pi Ai Tij F A 00 ij Da my a f ih 2 Tmet Evaluating the integral part of the above equations yields 1 EAM virial correction No long ranged corrections apply beyond ret 38 STFC Section 2 3 2 EEAM virial correction No long ranged corrections apply beyond ret 3 2BEAM virial correction No long ranged corrections apply beyond rymet 4 2BEEAM virial correction No long ranged corrections apply beyond ret 5 Finnis Sinclair virial correction No long ranged corrections apply beyond cutoffs c and d 6 Extended Finnis Sinclair virial correction No long ranged corrections apply beyond cutoffs c and d 7 Sutto
353. perations 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_FRZN_FORCES and SPME_CONTAINER 7 1 5 Metal Potentials The simulation of metals Section 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 7 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 inter actions have similar terms to some intramolecular ones three body to the bond angle and four body to inversion angle these are not dealt with in the same way as the normal bonded interactions They are gen erally very short ranged and are most effectively calculated using a link cell scheme 85 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
354. perience shear and flow gradients A 2 Outline of Method Following 50 the DPD algorithm can be summarised by the following e A condensed phase system may be modelled as a system of free particles interacting directly through soft forces Note that DL_POLY_4 allows for the application of the DPD thermostat beyond systems of free particles only Thus it will be valid on systems with any inratamolecular like interactions e The system is coupled to a heat bath via stochastic forces which act on the particles in a pairwise manner The particles also experience a damping or drag force which also acts in a pairwise manner Thermodynamic equilibrium is maintained through the balance of the stochastic and drag forces i e the method satisfies the fluctuation dissipation theorem 201 STFC Appendix A e At equilibrium or steady state the properties of the system are calculated as averages over the individual particles as in traditional Molecular Dynamics Therefore the equation of motion are the same as these for the microcanonical ensemble NVE but force fi on particle is now a sum of pair forces N i 2 464 42 28 A 1 IA in which i i and i are the conservative drag and random or stochastic pair forces respectively Each represents the force exerted on particle due to the presence of particle j The conservative interactions are usually soft i e weakly interacting so that the particles can pass b
355. 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 NaT 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 226 STFC Appendix D Message 96 error incorrect atom totals assignments 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 99 error cannot have shells as part of a constraint rigid body or tether Action Correct 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 of atom in the system the index can possibly range from 1 to m m 1
356. ponents are in Angsroms picosecond 1 3 8 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 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 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 rou
357. ponsibility 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_Classic 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 249 STFC Appendix D Message 638 error coincidence of particles in rigid body un
358. porating RB integration NST_BO_VV NST_BO_LFV Constant T a algorithm Berendsen 29 NST_B1_vv NST_B1_LFV The same as the above but also incorporating RB integration NST_HO_VV NST_HO_LFV Constant T algorithm Hoover 30 NST_H1_VV NST_H1_LFV The same as the above but also incorporating RB integration NST_MO_VV NST_MO_LFV Constant T algorithm Martyna Tuckerman Klein 32 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 tension NP yT 73 3 2 Bond Constraints The SHAKE algorithm for bond constraints was devised by Ryckaert et al 74 and is widely used in molecular simulation It is a two stage algorithm based on the leapfrog Verlet integration scheme 22 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 Gun l Mij di di de ES o 1 O 2AP dd dis whe
359. precision must be a positive non zero real number For example 10e 5 is accepted as a standard Action 213 STFC Appendix D Put a correct number at the ewald precision directive in the CONTROL file and resubmit Message 10 error too many molecular types specified This should never happen This indicates an erroneous FIELD file or corrupted DL_POLY_4 executable Unlike DL_POLY _Classic 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 intra molecular force field It does not then expect to encounter directives not related to these data This error message results if it encounters a unrelated directive The most probable cause is incomplete specification of the data e g when the finish directive has been omitted Action C
360. 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 FIELD and CONFIG do not match each other or if the instantaneous configuration is ill defined because of generation of large forces on bonded particles This may be due to having a badly defined force field and or starting form a configuration which is too much away from equilibrium Action Regenerate CONFIG and FIELD and resubmit Try topology verification by using nfold 1 1 1 in CON TROL Try using options as scale cap zero and optimise Try using smaller SHAKE tolerance if constraints are present in the system You may as well try using the variable timestep option 230 STFC Appendix D Message 130 error bond angle unit diameter gt rcut the system cutoff See action notes on m
361. ptional output file CFGMIN which is only produced when the minimise optimise option has been used during an equilibration simulation or a dry run 6 1 3 The FIELD File The FIELD file contains the force field information defining the nature of the molecular forces This infor mation explicitly includes the site topology of the system which 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 harm 168 19 980 000 1 33500 harm 168 162 634 000 1 52200 CONSTRAINTS 90 20 19 1 000017 22 21 1 000032 166 164 1 000087 167 164 0 999968 ANGLES 312 harm 43 2 44 200 00 116 40 harm 69 5 70 200 00 116 40 harm 18 168 162 160 00 120 40 harm 19 168 162 140 00 116 60 DIHEDRALS 371 harm 1 43 2 44 2 3000 180 00 harm 31 43 2 44 2 3000 180 00 145 STFC Section 6 1 cos 149 17 161 16 10 500 180 00 cos 162 19 168 18 10 500 180 00 FINISH SPC Water NUMMOLS 146 ATOMS 3 OW 1
362. r 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 74 23 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_Classic where global updates of the atom positions merging and splicing are required 87 The absence of the merge requirement means that the DD tailored SHAKE and RATTLE are less communications dependent and thus more efficient particularly with large processor counts The DD strategy is applied to complex molecular systems as follows 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 182 OSTFC Section 7 1 a All common forms of non bonded atom atom van der Waals forces b ro
363. r 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 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 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 237 STFC Appendix D Action Check the FIELD file and make sure the keyword is correctly defined Make sure that s
364. r the orthorhombic cell imcon 2 in CONFIG see Appendix B This can be considered as an orthorhombic constraint on the NoT ensemble The constraint can be strengthened further to a semi orthorhombic one by imposing that the MD cell change isotropically in the x y plane which leads to the following change in the equations above BAt V t _ Oxa t Fyy t aa t 1 Pex ex Maat TP eae ES 2 Vit G 0 D e 3 141 The VV and LFV flavours of the non isotropic Berendsen barostat and thermostat are implemented in the DL_POLY_4 routines NST_BO_VV and NST_BO_LFV respectively The routines NST_B1_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 80 in which the equations of motion involve a Nos Hoover thermostat and a barostat in the same spirit Additionally as shown in 81 a modification allowing for coupling between the thermostat and barostat is also introduced Cell size variation For isotropic fluctuations the equations of motion are Er u t n t r t Ro t d t qo 9 _ he nwt d 2Ekin t Pmass n t 20 kg Text aX p qmass mass 20 TA 3 142 85 STFC Section 3 5 gto OPI _ on Pmass f 3 kp Text Tp SH 1050 EV But Ve where 7 is the barostat friction coefficient Ro t the system centre of mass at time t Qmass the
365. rations The LFV implementation of the Andersen algorithm is as follows 1 FF f t f t At 3 52 2 LFV 1 1 t v t At SEO At At 40 2 2 m 1 r t At r t At vu t At 3 53 3 Full step velocity 1 1 1 v t Ec At u t A 3 54 2 2 2 4 Thermostat Note that the MD cell centre of mass momentum must not change e At If uni i lt 1 exp Then TT is 1 kgT ot At lt gt Gauss 0 1 1 1 1 us t At autt At 11 02 t At 3 55 1 u t u t At End Tf 70 OSTFC Section 3 4 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_Al_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 temperature Text by scaling the velocities at each step by At o 1 2 w b Slay 359 where o kp Text 3 57 is the target thermostat energy depending on the external temperature and the system total degrees of freedom f equation 3 11 and 77 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 ou
366. rces and to steer the MD system towards an equilibrium 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 properties dur ing a simulation Radial distributions may be calculated however by using the routines RDF_COLLECT RDF_EXCL_COLLECT RDF_FRZN_COLLECT a and RDF_COMPUTE Similarly Z density distributions may be calculated by using the routines Z DENSITY_COLLECT and Z DENSITY_COMPUTE while velocity autocorre lation functions may be calculated using the routines VAF_COLLECT and VAF_COMPUTE Ordinary ther modynamic quantities are calculated by the routine STATISTICS_COLLECT which also writes the STATIS file Section 6 2 13 Routine TRAJECTORY_WRITE writes the HISTORY Section 6 2 1 file for later post mortem analysis Routine DEFECTS_WRITE writes the DEFECTS Section 6 2 3 file for later postmortem analysis Routine MSD_WRITE writes the MSDTMP Section 6 2 2 file for later postmortem analysis Rou tine RSD_WRITE writes the RSDDAT Section 6 2 4 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 6 2 8 and 6 2 7 respectively 5 2 Compiling and Running DL POLY 4 5 2 1 Compiling the Source Code When you have obtained DL_POLY_4 from
367. re ij is the reduced mass of the two atoms connected by the bond di and di are the original and intermediate bond vectors d is the constrained bondlength and At is the Verlet integration time step It should be noted that this formula is an approximation only 62 STFC Section 3 2 Figure 3 1 The SHAKE RATTLE_VV1 schematics and associated vectors The algorithm calculates the constraint force G G that conserves the bondlength dj 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 v The RATTLE algorithm was devised by Andersen 23 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_VV1 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_VV1 has the form as in 3 16 but missing the factor of a half ng Hij di F dj de hy At2 di di 4 3 17 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 calculates the velocities of the atoms in the syst
368. reiding 19 or AMBER 20 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 None e g isolated molecules in vacuo 2 Cubic periodic boundaries 3 Orthorhombic periodic boundaries 4 Parallelepiped periodic boundaries 5 Slab x y periodic z non periodic These are described in detail in Appendix B Note that periodic boundary conditions PBC 1 and 5 above require careful consideration to enable efficient load balancing on a parallel computer 1 2 4 Java Graphical User Interface The DL POLY 4 Graphical User Interface GUI is the same one that also comes with DL POLY Classic 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 B supported machine The GUI is an integral component of the DL_POLY suites and is available on the same terms see the GUI manual 21 OSTFC Section 1 2 1 2 5 Algorithms 1 2 5 1 Parallel Algorithms DL_POLY_4 exclusively employs the Domain Decomposition parallelisation strategy 9 10 5 6 see Sec tion 7 1 1 1 2 5 2 Molecular Dynamics Algorithms DL_POLY_4 offers a selection of MD integration algorithms couched
369. rent job is not a con tinuation 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 6 2 8 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 6 1 5 1 Format The REVOLD file is unformatted All variables appearing are written in native working precision see Section 5 3 5 real representation Nominally integer quantities e g the timestep number nstep are represented by the nearest real number The contents are as follows the dimensions of array variables are given in brackets in terms of parameters from the SETUP_MODULE file see Section 7 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 a
370. revent any drifts The user must take care to have the impact initiated after any possible equilibration Otherwise the system will be thermostatted and the impact energy dissipated during the equilibration 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 stochas tic thermostat ii Gauss and iii 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 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
371. ries 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 205 STFC Appendix B Z Y X Figure B 1 The cubic MD cell B 4 Orthorhombic periodic boundaries imcon 2 LO Figure B 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 atomic coordinates is the centre of the cell B 5 Parallelepiped periodic boundaries imcon 3 LU Figure B 3 The parallelepiped MD cell 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 206 STFC Appendix B by three principal vectors a b c the MD cell is defined in the DL_POLY_4 CONFI
372. rises 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 in 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 proceed independently to calculate the pair force contributions to the atomic forces see routine TWO_BODY_FORCES 184 OSTFC Section 7 1 The potential energy and forces arising from the non b
373. rm mors Morse Eo ro k U r Eo H1 exp k rij ro 1 mrs 12 6 12 6 AIB e 4 _ 3 126 a o o lj Lennard Jones o U r 4e 5 lj rhrm Restraint k ro Te U r 4 k rij ro ra rol Sr rhm U r kr k rellrij rol Te rij rol gt re quar Quartic k ro k k U r E rij ro E rij ro qur E rij ro buck Buckingham Alp C U r A exp amp bck l coul Coulomb k U r k UBlectrostatics p E_9 cul AN2 fene Shifted FENE k Ro A U r 0 5 k Ro In 1 5 ry lt RotA fne 33 34 35 U r 00 rij gt Ro A amoe AMOEBA 36 k ro U r k 6 1 2 55 6 7 12 2 55 0 6 r ro amo FF bond 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 151 STFC Section 6 1 Table 6 9 Valence Angle Potentials key potential type Variables 1 4 functional formt harm Harmonic k o U 0 E 9 00 hrm quar Quartic k 0 k k U 0 9 0 0 00 6 6 4 qur thrm Truncated harmonic k 00 p U 6
374. rmostat 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 246 STFC Appendix D 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 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 particle assigned to non existent domain in defects_read_reference See notes on message 513 above Action See action notes on message 513 above Message 556 error too many atoms in REFERENCE file See notes on message 45 above Action See action notes on message 45 above Message 557 error undefined direction pass
375. rms of the local electronic density They are suitable for calculating the properties of metals and metal alloys The extended EAM EEAM 52 53 is a generalisation of the EAM formalism which can include both EAM and FS type of mixing rules see below It is worth noting that the same formalism applies to the many body perturbation component of the actinide oxide potentials as in 54 Thus their many body component description is included in this Section For single component metals the two main approaches FS and EAM are the same However they are subtly different 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 Mixing EAM and EEAM potentials is only possible if the EAM ones are generalised to EEAM form see below 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 types of potentials is 55 1 N N N U metal 3 y 5 Vij rij 5 F pi 2 110 i l Ai i 1 where F p is a functional describing the energy of embedding an atom in the bulk density p which is defined as N pi Dd pig riz 2 111 j l 5H It should be noted that the density is determined by the coordination number of the atom defined by pairs of atom
376. rom 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 usage during the equilibration period only The available algorithms are 1 Zero temperature molecular dynamics This is equivalent to a dynamical simulation at low tempera ture At each time step the molecules move in the direction of the computed forces and torques but are not allowed to acquire a velocity larger than that corresponding to a temperature of 10 Kelvin The subroutine that performs this procedure is ZERO_K_OPTIMISE 2 Conjugate Gradients Method CGM minimisation This is nominally a simple minimisation of the system configuration energy using the conjugate gradients method 69 The algorithm coded into DL_POLY 4 is an adaptation that allows for rotation and translation of rigid bodies Rigid constraint 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 MINIMISE_MODULE 3 Programmed energy min
377. rray 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 specific 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 effectively dynamic changing in response to local changes 7 1 3 Distributing the Non bonded Terms DL_POLY_4 calculates the non bonded pair interactions using the link cell algorithm due to Hockney and Eastwood 85 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 l
378. rsions are named TABBND TABANG TABDIH and TABINV correspondingly The format of these files is fixed in terms of the line or record order In particular the initial two header lines must contain a title and a record with the grid specification and each of the following blocks of tabulated data must be preceded by an empty line and a one line descriptor record containing the white space delimited names of the atoms making up the given intermolecular interaction unit same as a unit type in DAT files These descriptor lines can be commented out or not i e having as the first symbol would not affect the reading operation but it would ease importing of the data for plotting and manipulating in Xm Grace software In all TAB files the number of grid points bins must be specified on the second line commented out or not For angles TABANG TABDIH TABINV no other information needs to be provided as their ranges are pre determined 0 lt O in TABANG amp TABINV lt 180 and 180 lt in TABDIH lt 180 In the TABBND file however the bond cutoff rmax A must be precede the grid number Note that all potential and force data are to be provided in the same energy units as specified by the user in the FIELD file see Section 6 1 3 with distances in and angles in degrees All the data related to angles are internally transformed and handled by DL_POLY_4 with angles measured in radians 103 STFC Section 4 3 Final
379. run a DL_POLY 4 simulation for the prepared CG or simply user defined model system 104 Chapter 5 Construction and Execution Scope of Chapter This chapter describes how to compile a working version of DL_POLY_4 and run it 105 STFC Section 5 1 5 1 Constructing DL_POLY_4 an Overview 5 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 uncompressed 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 5 2 1 and Ap pendix where the main Makefiles are listed This must be copied into the subdirectory containing the relevant source code In most cases this will be the source subdirectory 3 The chosen makefile is executed
380. ry 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 4 Although DL_POLY_4 can be compiled in a serial mode users are advised to consider DL_POLY_Classic 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_Classic t DL_POLY_4 t DL_POLY_Classic t varies in the range 5 5 This variation depends strongly on the system force field complexity and very weakly on the system size 5 The rpad no strict CONTROL options should be used with care especially in conjunction with the variable timestep option when iterative algorithms are present in the simulation Such may be driven by a combination of options such as minimise ensemble npt ensemble nst in the presence of constraints associated with the tolerance and mxshake options and or core shells units dealt by the relaxed shell model and associated with the rlxtol option in the model system as defined in the FIELD file Integration Defaults The default ensemble is NVE The default integration scheme is Trotter derived Velocity Verlet VV although Leapfrog Verlet LFV is also availab
381. s 1 Cosine potential cos 2 Harmonic hrm 3 Harmonic cosine hcs 4 Triple cosine cs3 5 Ryckaert Bellemans 43 with fixed constants a f rck 6 Fluorinated Ryckaert Bellemans 44 with fixed constants a h rbf 7 OPLS torsion potential opl 8 Tabulated potential tab The potential is defined numerically in TABDIH see Section 4 3 and Section 6 1 8 In DL_POLY_4 torsional restraints are handled by the routine DIHEDRALS_FORCES 22 STFC Section 2 2 Figure 2 5 The inversion angle and associated vectors 2 2 8 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 usually augmented by valence angle potentials also The inversion angle is defined in the figure above note that the inversion angle potential is a sum of the three possible inversion angle terms It resembles a dihedral potential in that it requires the specification of four atomic positions The potential functions available in DL_POLY_4 are
382. s 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 7 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 6 2 6 7 Sample of Final Configuration The positions velocities and forces of the 20 atoms used for the sample of the initial configuration see above are given This is written by the main subroutine DL_POLY 6 2 6 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 displacement for the different atomic species in the s
383. s This makes the metal potential dependent on the local density environmental Vj rij is a pair potential incorporating repulsive electrostatic and overlap interactions N is the number of interacting particles in the MD box In DL_POLY_4 EAM and thus EEAM can be further generalised to include two band 2B densities 56 57 for s and d bands F pi F FU 2 112 where N p D2 Cu 458d ee j Lj i instead of just the one s as in equations 2 110 and 2 111 These will be referred in the following text as 2BEAM and 2BEEAM Mixing 2BEAM and EAM and alternatively 2BEEAM and EEAM potentials is only possible if the single band ones are generalised to 2B forms The user is again reminded to be consistent in the choice of potential when modelling alloys 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 6 1 7 The rules for combining the potentials from different metals to handle alloys are different from the FS class of potentials see below 2 EEAM potential eeam Similar to EAM above it is given in the form of interpolation arrays from the TABEAM file but the rules for combining the potentials from different metals are different from both EAM an
384. s of the DL_POLY_4 Software that it or any of its employees or students then holds 5 4 Clauses 1 2 2 3 4 5 3 5 4 5 5 and 6 will survive the expiry of the Licence Period and the termination of this Licence Agreement and will continue indefinitely 274 STFC Appendix F 5 5 STFC may stop providing any assistance or advice in relation to or any corrections new releases or versions of the DL_POLY_4 and may stop updating or publishing the DL_POLY_4 Website at any time 6 GENERAL 6 1 6 2 6 3 6 4 6 5 6 6 6 7 Headings The headings in this Licence Agreement are for ease of reference only they do not affect its construction or interpretation Assignment etc The Licensee may not assign or transfer this Licence Agreement as a whole or any of its rights or obligations under it without first obtaining the written consent of STFC Illegal unenforceable provisions If the whole or any part of any provision of this Licence Agreement is void or unenforceable in any jurisdiction the other provisions of this Licence Agreement and the rest of the void or unenforceable provision will continue in force in that jurisdiction and the validity and enforceability of that provision in any other jurisdiction will not be affected Waiver of rights If STFC fails to enforce or delays in enforcing an obligation of the Licensee or fails to exercise or delays in exercising a right under this Licence Agreement
385. s over n1 23 etc are required to capture contributions from all relevant periodic cell images which in practice means the nearest images 3 Approximating the reciprocal space energy Urecip 1 a t 2 22 Vo XO G k1 k2 k3 Q k1 k2 k3 2 223 k1 k2 k3 Urecip where Gt is the discrete Fourier transform of the function exp k 4a G k1 ko k3 E B k k2 k3 Q k ka k3 2 224 in which Q k1 ka k3 is the complex conjugate of Q k1 k2 k3 and B k1 ka ka b1 1 1 b2 k2 b3 3 1 2 225 The function G k1 ka k3 is thus a relatively simple product of the Gaussian screening term appear ing in the conventional Ewald sum the function B k k2 k3 and the discrete Fourier transform of Q k1 ka k3 52 OSTFC Section 2 5 4 Calculating the atomic forces which are given formally by OU res 1 i c 5 G ky ka k3 J Or V epe a ds OQ ki k2 k3 or 2 226 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 na
386. s 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 or cited TABle file Action Correct FIELD and or cited TABle file 224 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 angles potentials specified This should never happen Action Report to authors Message 84 error unidentified atom in three body angles potential list This shows that DL POLY_4 has encountered and erroneous entry at three body or angles definitions 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 cont
387. s to the atomic forces the Verlet neighbour list is constructed by the LINK_CELL_PAIRS routine using link cell lists Special measures are taken so that the list excludes i pairs of atoms that are both in a frozen state as well as ii pairs in 107 STFC Section 5 2 which one of the atoms has the other in its exclusion list The last is built by BUILD EXCL_INTRA where the specifications of bond like interactions in the FIELD file are processed Various other subroutines are then called to calculate specific contributions 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 interactions Section 2 3 2 and EWALD_SPME_FORCES EWALD_REAL_FORCES EWALD_FRZN_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 ex ternal force field e g electrostatic field operating To help with equilibration simulations routines such as CAP_FORCES ZERO_K_OPTIMISE and MINIMISE_RELAX are sometimes required to reduce the magnitude of badly equilibrated fo
388. semi isotropic constraining of the barostat equation of motion and slight amending the thermostat equation of motion and the conserved quantity to 4 a t l sat VO eel a A z di 0 ma 0 0 a8 2 d 2Ekpin t pmass Tr n t n 07 20 kg Text y t 3 162 ga mass mass t Pa Tring t Hnr aar Hyve d t H 2 Poa V t 0 e Text l x s ds Similarly this ensemble is optionally extending to constant normal pressure and constant surface tension NP 7yT 73 by semi isotropic constraining of the barostat equation of motion and slight amending the thermostat equation of motion and the conserved quantity to Lal Pest MMIVO mar lt a 8 2 Y Emap t at azalt Pes VO _ tiza lt a A z 0 Mag 0 0 a AB 2 y 2 d 2E kin t Pmass Tr n t n t 7 20 3 kg Text 3 163 ar dmass l mass t 2 Pmass Tr n 1 y Hnp yt Hyve a Al a a PoV t f 3 kp Text f x s ds where Yext is the user defined external surface tension and h t V t Azy t is the instantaneous hight of the MD box or MD box volume over area One defines the instantaneous surface tension as given in equation 3 122 The case Yext 0 generates the NPT anisotropic ensemble for the orthorhombic cell imcon 2 in CONFIG see Appendix B This can be considered as an orthorhombic constraint on the NoT ensemble The constraint can be strengthened further to a semi orthorhombic
389. 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 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 sites Action Correct the erroneous entry in FIELD and resubmit 217 STFC Appendix D 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_Classic 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
390. 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 H20 etc e Simple rigid molecules e g CCl4 SFe Benzene etc e Rigid molecular ions with point charges e g KNO3 NH4 2SOu etc e Polymers with rigid bonds e g C Han 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 CuzAu etc e Covalent systems as hydro carbons and transition elements e g C Si Ge SiC SiGe ets STFC Section 1 2 1 2 2 Force Field The DL POLY_4 force field includes the following features 1 All common forms of non bonded atom atom van der Waals potentials 2 Atom atom and site site coulombic potentials Metal metal local density dependent potentials 11 12 13 14 15 16 Ae Ww Tersoff local density dependent potentials for hydro carbons 17 Three body valence angle and hydrogen bond potentials Four body inversion potentials Ion core shell polarasation Tether potentials O 0 N Q OH Chemical bond potentials 10 Valence angle potentials 11 Dihedral angle and improper dihedral angle potentials 12 Inversion angle potentials 13 External field potentials The parameters describing these potentials may be obtained for example from the GROMOS 18 D
391. spheres SYSTEM CUTOFFS AND ELECTROSTATICS recut 10 0 Angstroms rpad 0 35 Angstroms rvdw 8 0 Angstroms exclude epsilon 1 0 ewald precision 1 0e 5 ewald evaluate RELAXED SHELL MODEL TOLERANCE rlxtol 1 0 force CONSTRANTS ITERATION LENGTH and TOLERANCE mxshak 250 cycles shake 1 0e 5 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 maxdis 0 10 Angstroms mxstep 0 005 pico seconds SUMULATION amp EQUILIBRATION LENGTH steps 10000 steps equilibration 1000 steps EQUILIBRATION DIRECTIVES zero cap 2000 kT Angstrom scale 5 steps regauss 3 steps minimise force 20 1 0 optimise energy 0 001 STATISTICS collect 123 STFC Section 6 1 stack 50 deep stats 10 steps OUTPUT print 2 steps HISTORY replay trajectory 20 30 0 DEFECTS TRAJECTORY DEFECTS defects 40 15 0 75 DISPLACEMENTS TRAJECTORY RSDDAT displacements 70 10 0 25 MSDTMP msdtmp 1000 100 INTRAMOLECULAR PDF ANALYSIS BY TYPE IF PRESENT analyse bonds sample every 100 nbins 250 rmax 5 0 analyse angles sample every 100 nbins 360 0 pi analyse dihedrals sample every 100 nbins 720 pi pil analyse inversions sample every 100 nbins 360 0 pil INTRAMOLECULAR PDF ANALYSIS FOR ALL TYPES PRESENT analyse all sample every 100 nbins 1000 rmax 5
392. ssian charges cannot easily be extracted and the correction is made in real space It amounts to removing terms corresponding to the potential energy of an ion due to the Gaussian charge on a neighbouring charge m or vice versa This correction appears as the final term in the full Ewald formula below The distinction between the error function erf and the more usual complementary error function erfc found in the real space sum should be noted The same considerations and modifications EWALD_FRZN_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 L i exp k 4a qjq U exp ik IP erfe arn IE 2 ha O E en 1 erf ar a Py iin a eran 2 215 MEOE molecules lt m Tim F aTr em 1 0 erf arim T j y A 2 acam i m ro tm Areye 2V 02 gt dj where N is the number of ions in the system and N the same number discounting any excluded in tramolecular and frozen interactions M represents the number of excluded atoms in a given molecule F represents the number of frozen atoms in the MD cell V is the simulation cell volume and k is a reciprocal lattice vector defined by k fu mu nw 2 216 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 bx c 2
393. ssian 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 fa lt 1 select NVT ensemble type Berendsen with thermostat relaxation constant f in ps select NVT ensemble type Nose Hoover with thermostat relaxation constant f in ps select NVT ensemble type Gentle Stochastic with thermostat relaxation constant f in ps and Langevin friction f in ps select NVT ensemble with a DPD thermostat of type s1 or s2 for Shardlow s splitting of first or second order respectively with an optional system global drag coefficient y in Dalton 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 126 STFC Section 6 1 ensemble ensemble ensemble ensemble ensemble ensemble ensemble ensemble ensemble ensemble ensemble npt hoover f f2 npt mtk fi fo nst langevin fi fa nst berendsen f f2 nst hoover fi f2 nst mtk fi fe nst Q fifo area nst Q fife tension y nst Q ff tens y semi nst Q f f2 orthorhombic nst Q fife orth semi epsilon constant f equilibration steps n ewald evaluate every n ewald precision f
394. st atom type atom 2 a8 second atom type 167 STFC Section 6 2 atom 3 a8 third atom type only required for TABANG atom 4 a8 forth atom type only required for TABDIH amp TABINV interaction data records 0 1 ngrid abscissa real consecutive value over the full cutoff range in for TABBND and degrees for TABANG TABDIH amp TABINV potential real potential at the abscissa grid point in units as specified in FIELD force real complementary force virial for TABBND value 6 1 8 2 Further Comments It should be noted that the number of grid points in the table files should not be less than the number of grid points DL_POLY_4 is expecting For more information the reader is advised to examine SETUP MODULE and inspect the mxgint variables where int refers to bnd for bonds ang for angles dih for dihedrals and inv for inversions The potential and force tables are used to fill the internal arrays vint and gint for the respective intrmolecular potential see Chapter 2 The contents of force arrays for TABBND are derived from the potential via the formula U r 6 15 Note this is not the same as the true force During simulation interactions beyond distance cutpot will bring the run to a controlled termination 6 2 The OUTPUT Files DL_POLY_4 produces up to 20 kinds of output files Some of these are HISTORY DEFECTS MSDTMP CFGMIN OUTPUT REVCON REVIVE RDFDAT ZDNDAT VDFDAT_ and STATIS These respec tively contain
395. stem cutoff rcut Action In the case when this is received while reading TABLE reduce the value of the vdw cutoff rvdw in the CONTROL file or reconstruct the TABLE file In the case when this is received while reading TABBND then specify a larger rcut in CONTROL 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 or MBPC metal densities out of range The resulting densities are not defined in the TABEAM file if EAM is used or ill defined due to atoms nearly overlapping when MBPC metal potential is in use Action Recreate a TABEAM file with wider range of densities 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 simula tion You MUST change the interactions parameters and or the way the physical base of your investigation is handled in
396. subsequent n records contains index 1 i integer site index of core index 2 7 integer site index of shell ka real force constant of core shell spring k4 real quartic anharmonic force constant of spring The spring potential is 1 1 U r 5hariz giri o 6 6 with the force constant ka entered in units of engunitxA and ky in engunit 7 where usually ka gt gt k4 The engunit is the energy unit specified in the units directive Note that the atomic site indices referred to above are indices arising from numbering each atom in the molecule from 1 to the number specified in the atoms directive for this molecule This same numbering scheme should be used for all descriptions of this molecule including the constraints pmf 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 Note that DL_POLY_4 determines which shell model to use by scanning shells weights provided the FIELD file see Section 2 5 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 the 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 6 2 6 Shell models extensions are dealt according to the us
397. sure 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 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 de pending 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 118 OSTFC Section 5 4 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 the k vectors FFT transforms and therefore slightly different SPME forces energies whithin the same level of SPME Ewald
398. t At n t 4 74 A AEN ee exp nt At u t At 3 151 3 3 At 3 n TA exp x t FAL t At At 3 P t At Pax V t At 4 Pmass 3 n t At nt At n t At exp x t At n t At 87 STFC Section 3 5 11 Thermostat Note Exin t At has changed and changes inside 7 3 At 2Ekin t At pmass MEP At 20 kg Tox xe lA e yx t At kin Pmass n ES 8 4 8 mass 7 At v t At expl x t gt a u t At 3 152 7 At 2Epin t At Pmass n t At 20 kg Text t At At xtA xtA i v t At v t At Vo t At where Vo t At is the c o m velocity at timestep t 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 v t Also calculated is an unconstrained estimate of the half step position r t At 1 FF f t f t At 3 153 2 LFV The iterative part is as follows f t m x t n t v t r t At r t At u t At n t 4 gt At r e 544 Role H t At exp n 40 At H t 3 154 VELADO e em sult 50 At V t 3 SHAKE 4 Full step velocity and half step position
399. t qo exp xo n t 720 3 At t At Pe n t At E netia ave apa 5 a 3 chk t At 1 di R t f Pmass Pmass At n t At exp xo n t At 11 Thermostat Note Exin t At has changed and changes inside At u t At lt exp XZ u t At 3 110 The LFV implementation of the Langevin algorithm is iterative until self consistency in the full step velocity v 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 5 At 1 FF f t f t At Rit R t At 3 111 R t R t At 2 LFV The iterative part is as follows 3 At sale See me f 2 2 scalev ll scale At scale f scale t R t u t At scale_v u t At scale_f f t RE r t At r t At u t At nft A0r t 540 3 112 H t At exp ntt 5 At At H i VRAD 42 ne 40 At V t 3 SHAKE 4 Full step velocity and half step position ee z BE 340 u t 340 r t4 5At 4 HO EEE AY 3 113 5 Thermostat and Barostat 1 1 n t At lt exp Xp At n t 54 t At Px 2Exrin t At 1 At aves an se e l ht ds sat n t ZAt 3 114 nt N 80 OSTFC Section 3 5 Several iterations are required to obtain self consistency In DL_POLY_4 the number of iterations is set to
400. t At the end of VV2 velocities are scaled by a factor of x in the following manner 1 VVl 1 At f t u t 4 At v t 3 n fA O At 3 58 2 RATTLE_VV1 3 FF fGen F t 3 59 4 VV2 At f t At 1 t v t At v t At FS m 3 60 5 RATTLE VV2 6 Thermostat At o 1 2 t At 1 1 x Fay ATT v t At v t At y 3 61 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 u t 1 FF f t f t At 3 62 71 STFC Section 3 4 2 LFV The iterative part is as follows v t 5AM z he At At 0 x t r t At e r t At w t 5AM 3 63 3 SHAKE 4 Full step velocity u t 4 5 ute At 4 u t 50 3 64 5 Thermostat A ii t o whe 14 Gan 1 3 65 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 the 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 Hoov
401. t 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 Action Either use a smaller four body cutoff or a larger pair potential cutoff Message 474 error conjugate gradient 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 241 STFC Appendix D Message 478 error shake algorithms constraints amp pmf failed to converge Your system has both bond and
402. t Contribution available to any third party on such terms and conditions as STFC may from time to time decide The Licensee warrants that it owns or has the necessary rights to such Contribution to give effect to this clause 3 WARRANTIES AND LIABILITY 3 1 The DL_ POLY Software is provided for Academic Purposes free of charge Therefore STFC gives no warranty and makes no representation in relation to the DL_POLY_4 Software or any assistance or advice that STFC may give in connection with the DL_POLY_4 Software The Licensee will indemnify STFC against any and all claims arising as a result of the Licensee having made any of the DL_POLY_4 Software or any Derived Work available to any third party Before using any of the DL_POLY_4 Software the Licensee will check that the DL_POLY_4 Software does not contain any Harmful Element STFC does not warrant that the DL_POLY_4 Software will run without interruption or be error free or be free from any Harmful Element STFC is not obliged to provide any support or error correction service assistance or advice in relation to the DL_POLY_4 Software but the Licensee may access any error corrections and on line assistance that STFC chooses to make available on the 272 STFC Appendix F 3 3 3 4 3 6 3 8 DL_POLY_4 Website from time to time If STFC does provide that sort of service assistance or advice subject to clause 3 7 STFC will not be liable for any loss or damage suffered
403. t half timestep 1 At x t 4 74 x t4 At exp y l At 2 E xin t 20 4 mass A UEFA e v t At exp x t Ft x kB Text mass exp y R t At 3 89 A kg Tox At xt At x t At exp F y Bees 1 exp 1 R t At dmass l At 2Ekin t 20 4 mass The algorithm is self consistent and requires no iterations The LFV implementation of the Gentle Stochastic Thermostat 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 lt f t At 3 90 2 LFV The iterative part is as follows EO _ 40 sto 1 1 u t 4 At v t At At HELADO E ds sat 3 91 3 SHAKE 75 STFC Section 3 4 4 Full step velocity u t 3 eE 340 ult 3A 3 92 5 Thermostat Note R t is drown from Gauss 0 1 just once per timestep 1 ex x t At x t AD exp kB Text 1 exp y FI R t 2 2 4 mass 4 t 2Ekin t 20 dmass IE GAS x t Al 3 93 A N xt 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 The conserved quantity is derived from the extended Hamiltonian for the system which to within a constant is the Helmholtz free energy mass t A e Huvt Hyve L XA f kp Text J x s ds 3 94 wh
404. te 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 The vaf directive switches on velocity autocorrelation function VAF calculations for individual atomic species in DL_POLY_4 after equilibration or immediately at start if the directive collect is used It controls how often VAF profiles are started what the size of each profile in timesteps Overlapping profiles are possible and require more memory to store them and initial velocities while they are being calculated By default DL_POLY_4 will report time averaged VAF profiles This can be overridden using the no vafaveraging directive which will instead report individual instantaneous VAF profiles io action options controls how I O is performed by DL_POLY_4 The options can help the perfor mance 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
405. tentials for example pair potentials may in fact be essential to maintain the structure of the system The three body potentials are very short ranged typically of order 3 This property plus the fact that three body potentials scale as N where N is the number of particles makes it essential that these terms are calculated by the link cell method 62 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 45 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 sim ulation of amorphous materials particularly borate glasses The potential forms available in DL_POLY_4 are as follows 1 Harmonic harm U ditin 5 isin do 2 187 2 Harmonic cosine hcos U disk 5 C08 dizkn coslo 2 188 3 Planar potential plan U dijkn A 1 cos ijkn 2 189 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 po tentials are regarded as inter molecular Firstly the atoms involved are defined by atom types not specific indices Secondly there
406. that failure or delay will not affect its right to enforce that obligation or constitute a waiver of that right Any waiver by STFC of any provision of this Licence Agreement will not unless expressly stated to the contrary constitute a waiver of that provision on a future occasion Entire agreement This Licence Agreement constitutes the entire agreement between the parties relating to its subject matter The Licensee acknowledges that it has not entered into this Licence Agreement on the basis of any warranty representation statement agreement or undertaking except those expressly set out in this Licence Agreement The Licensee waives any claim for breach of or any right to rescind this Licence Agreement in respect of any representation which is not an express provision of this Licence Agreement However this clause does not exclude any liability which STFC may have to the Licensee or any right which the Licensee may have to rescind this Licence Agreement in respect of any fraudulent misrepresentation or fraudulent concealment before the signing of this Licence Agreement Amendments No variation of or amendment to this Licence Agreement will be effective unless it is made in writing and signed by each party s representative Third parties No one who is not a party to this Licence Agreement has any right to prevent the amendment of this Licence Agreement or its termination and no one except a party to this Licence Agreement may
407. the parameter d in ters and cz in kihs determines how sharp the dependence on angle is whereas the rest express the strength of the angular effect Further mixed parameters are defined as aij ai aj 2 bij bi b5 2 AgS MAA a B Be 2 162 Rij RRA 5 Sig S 1 Singly subscripted parameters such as a and n depend only on the type of atom For ters 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 Wji 2 163 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 interpolation The w parameter is used to permit greater flexibility when dealing with more drastically different types of atoms The force on an atom derived from this potential is formally calculated with the formula o 1 o fe pq Erersoff a D gt gt zUij gt 2 164 Or 25 Zi Or with atomic label being one of i j k and a indicating the x y z component The derivative after the summation is worked out as OU o are gra e Curl mia Fela falra Joli Faria Fa Va 2 165 42 STFC Section 2 3 with the contributions from the first two terms being fo rij fr rij COA F Jabra go tetra x Or CE i 2 166 Tej o o o Vii grg to in Falria Vj fotra a Aa falta
408. the cutoff interval absolute value of the span over which the distributions are sampled the number of frames samples used and the number of unique unit types analysed where unit is one of the following bonds angles dihedrals or inversions The last explanatory line in the header found in between two empty commented out lines defines the meaning of the columns and at the end the grid bin size The PDF histograms within a DAT file are separated by uncommented empty lines which makes it possible to directly import and plot all the data as separate lines in Xm Grace 2D plotter For clarity the data of each histogram are preceded by a commented out line specifying the type index and number of instances of the analysed interaction unit the latter being counted over the entire system In all DAT files the first column bears the bin centered abscissa values distance or angle the second column is the distribution histogram normalized to unity i e its integral equals 1 whereas the third column if any contains the PDF data corrected for the volumetric entropic degeneracy of the grid points Thus it is the data of the last column found that are used for calculating PMF ln PDF The OUTPUT file will contain copies of the first and second columns of all collected PDF s but normalised so that the figures in the second column sum up to 1 which can be checked by examining the third column as it bears the running sum of a PDF
409. 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 6 1 5 6 2 9 The RDFDAT File This is a formatted file containing Radial Distribution Function RDF data Its contents are as follows record 1 cfgname a72 configuration name record 2 ntprdf integer number of different RDF pairs tabulated in file mxgrdf integer number of grid points for each RDF pair There follow the data for each individual RDF i e ntprdf times The data supplied are as follows first record atname 1 a8 first atom name atname 2 a8 second atom name following records mzgrdf records radius real interatomic distance A g r real RDF at given radius Note 1 The RDFDAT file is optional and appears when the print rdf option is specified in the CONTROL file Note 2 Along with the RDFDAT file two other files will be created whenever the print analysis direc tive is invoked VDWPMF amp VDWTAB both containing the data for potentials of mean force and the corresponding virials calculated based on the obtained RDF s i e PMF In RDF in the energy units specified in the FIELD file These files have a simple three column format the same as that used for PMF files in the case of bonded units see Section 4 2 The purpose of these files is to provide the user with means of sett
410. the subroutine WARNING results in an appropriate message Users intending to insert new error checks should ensure that all error checks are performed concurrently on all nodes and that in circumstances where a different result may obtain on different nodes a call to the global status routine GCHECK is made to set the appropriate global error flag on all nodes Only after this is done a call to subroutine ERROR may be made An example of such a procedure might be Logical safe safe test_condition Call gcheck safe If not safe Call error message number In this example it is assumed that the logical operation test_condition will result in the answer true if it is safe for the program to proceed and false otherwise The call to ERROR requires the user to state the 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 119 Chapter 6 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 120 STFC Section 6 1 6 1 The INPUT Files
411. the tab keyword on the record defining the short range potential see Table 6 12 6 1 6 1 The TABLE File Format The file is free formatted but blank and commented lines are not allowed 6 1 6 2 Definitions of Variables record 1 header al00 file header record 2 delpot real mesh resolution in delpot a 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 164 STFC Section 6 1 header record atom 1 a8 first atom type atom 2 a8 second atom type potential data records number of data records Int ngrid 3 4 data 1 real data item 1 data 2 real data item 2 data 3 real data item 3 data 4 real data item 4 force data records number of data records Int ngrid 3 4 data 1 real data item 1 data 2 real data item 2 data 3 real data item 3 data 4 real data item 4 6 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 mxgvdw calculated in the SETUP_MODULE file see Section 5 2 1 3 and 7 2 8 DL POLY_4 will re interpolate the tables if delpot a lt dlrvdw T 3 usually when ngrid gt mxgvdw
412. 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 control 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 respectively The defects option will trigger reading of REFERENCE see Section 6 1 4 which defines a reference MD cell with particles positions defining the crystalline lattice sites If REFERENCE is not found the simulation will either i halt 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 6 1 5 file has been provided or ii recover using CONFIG see Section 6 1 2 if it is a new simulation run i e restart option is not used in CONTROL or REVOLD has not been provided The actual defect detection is based on comparison of the simulated MD cell to the reference MD cell based on a user defined site interstitial cutoff Rae Min 0 3 reut 3 A lt Raef lt Min 1 2 rcut 2 A 6 5 with a default value of Min 0 75 rcut 3 A If the supplied value exceeds the limits the simulation execution will halt 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 parti
413. 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 2 3 1 Short Ranged van der Waals Potentials The short ranged pair forces available in DL_POLY_4 are as follows U r 5 E 2 85 ij ij pa 12 pa 6 Eo To k To a U rij em gt n 2 87 1 12 6 potential 12 6 2 Lennard Jones potential 13 3 n m potential 47 48 nm STFC Section 2 3 4 Buckingham potential buck ij C U rij A exp E 2 88 P Tij 5 Born Huggins Meyer potential bhm U rij A exp B o ri l 2 89 6 Hydrogen bond 12 10 potential hbnd wore 4 8 m 7 Shifted force n m potential 47 48 snm ws SO a T eon with es n m ner m y m 1 y7 m6r 1 n y n 1 y m l _ nm p 4 Z 2 92 y This peculiar form has the advantage over the standard shifted n m potential in that both Eo and ro well depth and location of minimum retain their original values after the shifting process 8 Morse potential mors U rij Eo H1 exp k rij 70 1 2 93 9 Shifted Weeks
414. this way the instantaneous 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 drit dt v t aO LOFRO ni o 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 REE R O 2 x t mi kBT di bap lt t 6 3 where superscripts denote Cartesian indices subscripts particle indices kg is the Boltzmann constant T the bath temperature and m the particle s mass The algorithm is implemented in routine PSEUDO and has two stages Generate random forces on all particles within the thermostat Here care must be exercised to prevent introduction of non zero net force when the random forces are added to the system force field 137 STFC Section 6 1 12 Rescale the kinetic energy of the thermostat bath so that particles within have Gaussian dis tributed kinetic energy with respect to the target temperature and determine the Gaussian constraint friction within the thermostat Dal fi t Ri t 0 mi TF t x t Maz o 6 4 Care must be exercised to prevent introduction of non zero net momentum Users are reminded to use for target temperature the temperature at which the original system was equilibrated in order to avoid simulation instabil
415. tial A The variables pertaining to each potential are described in Table 6 15 159 STFC Section 6 1 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 Table 6 15 Three body Potentials key potential type Variables 1 4 functional form harm Harmonic k 0 U 0 E 0 0 thrm Truncated harmonic k Op U 0 9 00 exp rs r p8 shrm Screened harmonic k 0 a p2 U 0 E 0 00 exp ri p1 riz p2 bvs1 Screened Vessal 37 k 0 pi p2 U 0 TENE 1 0 aT es exp rij p1 ri p2 bvs2 Truncated Vessal 38 k bo a p U 0 k 0 00 lay 00 0 0o 27 37 0 m expl ri ri 0 hbnd H bond 19 Dr Rap U 0 Dhp cos 0 x 5 Rno r5x 6 Rno r5x 10 is the 7 j k angle 7 fbp n where nis the number of four body potentials to be entered It is followed by n records each specifying a particular four body potential in the following manner atmnam 1 i a8 first central atom type atmnam 2 j a8 second atom type atmnam 3 k a8 third atom type atmnam 4 1 a8 fourth atom type key ad potential key see Table 6 16 variable 1 real potential parameter see Table 6 16 variable 2 real potential parameter see Table 6 16 variable 3 real cutoff range for this potential A The variables pertainin
416. tines are unsupported and come without any guarantee or liability whatsoever 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 STFC Section 1 7 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 The source is complete and sufficient to create a working GUI provided the user has installed the Java Development Kit 1 4 or above which is available free from Sun at http java sun com The GUI once compiled may be executed on any machine where Java is installed 21 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 academic software licence see Appendix F which details the terms and conditions 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 aca
417. tines for the Java GUI A more detailed description of each sub directory follows OSTFC Section 1 4 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 7 1 4 2 The utility Sub directory This sub directory stores all the utility subroutines functions and programs in DL_POLY_4 together with examples of data Some of the various routines in this sub directory are documented in the DL_POLY_Classic User Manual Users who devise their own utilities are advised to store them in the utility sub directory 1 4 3 The data Sub directory This sub directory contains examples of input and output files for testing the released version of DL_POLY_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 8 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 Sub directory This directory contains examples of input and output data for DL_POLY_4 that are suitable for benchmark ing DL_POLY_4 on large scale computers These are
418. tion 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 See action notes on message 14 above 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 coincidence 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 222 STFC Appendix D Correct the erroneous entry in FIELD and resubmit Messag
419. tive DL POLY_4 subroutines that respect the domain decom position concept which calculate the 3D complex fast Fourier transforms 3 EWALD_SPME_FORCES which calculates the reciprocal space contributions uncorrected 4 EWALD_REAL_FORCES which calculates the real space contributions corrected 5 EWALD_EXCL_FORCES which calculates the reciprocal space corrections due to the coulombic exclusions in intramolecular interactions 6 EWALD_FRZN_FORCES which calculates the reciprocal space corrections due to the exclusion interac tions between frozen atoms 7 TWO_BODY_FORCES in which all of the above subroutines are called sequentially and also the Fuchs correction 65 for electrically non neutral MD cells is applied if needed 2 5 Polarisation Shell Models An atom or ion is polarisable if it develops a dipole moment when placed in an electric field It is commonly expressed by the equation p aE 2 227 where pu is the induced dipole and E is the electric field The constant a is the polarisability In the static shell model a polarisable atom is represented by a massive core and massless shell connected by a harmonic spring hereafter called the core shell unit The core and shell carry different electric charges the sum of which equals the charge on the original atom There is no electrostatic interaction i e self interaction between the core and shell of the same atom Non coulombic interactions arise from the shell alone The
420. to prevent the store macro overwriting existing data without your knowledge 211 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 FORTRAN9O dynamic array allocation to set the array sizes at run time This means that a single executable may be compiled to over all the likely uses of the code It is not foolproof however Sometimes an estimate of the required array sizes is difficult to obtain and the calculated value may be too small For this reason DL_POLY_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
421. tomic stress tensor derived from the pair forces is symmetric Since the calculation of pair potentials assumes a spherical cutoff ryaw 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 yo NaNo corr 27 D gar T Uay r r dr 2 101 Tydw where Na Mp are the numbers of atoms of types a and b in the system V is the system volume and gab r and U p r are the appropriate pair correlation function and pair potential respectively It is usual to assume Jablr 1 for r gt ryaw DL POLY_4 sometimes makes the additional assumption that the repulsive part of the short ranged potential is negligible beyond fyaw 29 STFC Section 2 3 The correction for the system virial is corr NaNp yo 2r y f galr Uas r r dr 2 102 vdw where the same approximations are applied Note that these formulae are based on the assumption that the system is reasonably isotropic beyond the cutoff DL_POLY_4 allows a short cut for mixing some of the explicitly specified pair interactions for single species of the same type so that cross species interactions are generated if unspecified This is only possible for the 12 6 lj dpd amoeba amp wea types The mixing is derived from the Lennard Jones style char
422. trajectories in the canonical NVT ensemble The rest will produce properties that typically differ from canonical averages by O 1 N 22 where N is the number of particles in the system as the Evans algorithm generates trajectories in the NVE in ensemble 65 STFC Section 3 4 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 dr t a E 20 L 9 _ eu pan the kinetic temperature constraint x can be found as follows d d 1 y do ae x 7 Ema Emos Su 0 Y miuilt E x t to 0 3 24 Di walt f t Dima t 7 where T is the instantaneous temperature defined in equation 3 10 x 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 consecutive thermalisation on the unthermostated velocities for half a timestep at each stage in the following manner 1 Thermostat VV1 Di vilt f t x t lt 2 End A u t aah 3 25 2 VVI v t ZAt e e z ga LA AO A At 3 26 3 RATTLE_VV1 4 FF f t At EL 3 27 5 VV2 v t At e u t LAS 4 gt 3 28 6
423. trix 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 2 Exin Pmass Tr n t nt 20 3 kB Text 8 dmass 1 1A v t E exp a t 748 n u t 3 158 1 At t Pxt V t 1 n t zat 0 3 a A A whereas for the LFV couched algorithm they are 7 7 T E ext aE A0 x t At y py PLE Prass T ar n t 20 3 kp T v t 5At lt v t gt At At x t 1 2 t 0 EN t Poe V t 1 Pmass 1 1 nt 3At e exp x A0 nt 3At At Z The modifications in ii are the same for both the VV and LFV couched algorithms H t At exp ut sat At H t 89 STFC Section 3 5 VOLT amp 68 1 hae 5A2 At v amp 3 160 It is worth noting DL_POLY_4 uses Taylor expansion truncated to the quadratic term to approximate exponentials of tensorial terms The conserved quantity is to within a constant the Gibbs free energy of the system mass X t Pmass Trin n t Hxor Hyve 2 xO PVD De J x s ds 3 161 2 2 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 73 by
424. uations 3 190 simultaneously with an integration of the quaternions describing the orientation of the rigid body The equation describing this is do do 9 4 03 0 1 O R q Ia 4 q3 q Wa 3 191 q2 q2 43 do q Wy d3 da 2 q 4 We Rotational motion in DL_POLY 4 is handled by two different methods For the LFV implementation the Fincham Implicit Quaternion Algorithm FIQA is used 24 The VV implementation uses the NOSQUISH algorithm of Miller et al 25 The implementation of FIQA is coded in Q UPDATE and NOSQUSH in NO_SQUISH both contained within QUATERNION_CONTAINER The LFV implementation begins by integrating the angular velocity equation in the local frame t 0 t F At a t 3 192 The new quaternions are found using the FIQA algorithm In this algorithm the new quaternions are found by solving the implicit equation g t At g t Q a at Q alt At E AD 3 193 where 0 and Qlg is 1 Q 5 q 90 da a 3 194 The above equation is solved iteratively with q t At g t At Qla t t 3 195 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 3 196 is imposed While all the above is enough to build LFV implementations the VV implementations based on the NOSQUISH algorithm of Miller et al 25 also require treatment of the quaternion momenta as defined by
425. ubroutine BONDS_FORCES contains the code necessary to deal with the requested potential Add the code required if necessary by amending subroutines READ_FIELD and BONDS_FORCES Message 445 error r_14 gt rcut in dihedrals_forces The 1 4 coulombic scaling for a dihedral angle bonding cannot be performed since the 1 4 distance has exceeded the system short range interaction cutoff rcut in subroutine DIHEDRAL_FORCES Action To prevent this error occurring again increase 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 Message 448 error undefined dihedral potential A form of dihedral potential has been requested which DL_POLY 4 does not recognise Action Locate the
426. ubroutines may need modifying to allow specification of the dimensions of any new arrays Any molecular dynamics simulation performs five different kinds of operation initialisation forces calcu lation integration of the equations of motion calculation of system properties and job termination 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 available to 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 compliance 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 declared in SETUP_MODULE to convenient values based on a rough scan through the CONFIG CONTROL FIELD and optionally TABLE and TABEAM Section 6 1 files The routine also calls the READ_CONFIG routine to obtain atomic positi
427. use System size is 69120 and 552960 ions respectively 197 STFC Section 8 1 8 1 4 Test Case 7 and 8 Gramicidin A molecules in Water These systems consist of 8 and 16 gramicidin A molecules in aqueous solution 32 096 and 256 768 water molecules with total number of atoms 99 120 and 792 960 respectively Simulation at 300 K using NPT Berendsen ensemble with SPME and SHAKE RATTLE algorithm for the constrained motion 8 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 8 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 8 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 8 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 Simulation at 3000 K using NPT Berendsen ensemble with SPME FIELD and CONTROL files for each shell model are provided separately 8 1 9 Test Case 17 and 18 Potential of mean force on K in wat
428. ution of higher order charge deformations of oxide species This is done by the inclusion of non central ion interaction to account for a finite ion shell radius r which is allowed to deform isotropically under its environment However all short range repulsion potentials i e vdw a BSM ion interacts by with its environment must act upon the radius of the ion U U r r rather than the nuclear position U U r A further constraining potential is then added to represent the self energy of the ion s breathing shell This most commonly uses the same shape as the one of the harmonic bond see Section 2 2 1 U r EM 98 2 234 where 7 and j are the intramolecular index of the ion s core and shell respectively Hence to employ the BSM the user needs to specify an extra bonded interaction for each BSM ed core shell pair in the relevant bonds sections in the FIELD file for all molecules that contain BSM ions It is worth noting that the BSM energy and virial are thus part of the bonds energy and virial and their calculation as part of the bonds forces routine BONDS_FORCES The most significant consequence of the introduction of the BSM is that by coupling the repulsive interac tions via common shell radii it creates a many body effect that is able to reproduce the Cauchy violation C44 4 C12 for rock salt structured materials 2 5 4 Further Notes In DL_POLY_4 the core shell forces of the rigid shell model are handl
429. utions olf gt o F o f fRB tra fPBEot UD gt HUF Meee ag Prat gt pr trea Hf 3 208 nf gt E gf FPP A RSP GEA 97 STFC Section 3 6 where f refers to the degrees of freedom in the system see equation 3 11 is the system target energy see equation 3 57 H is the conserved quantity of the ensemble if there is such defined Ekin tincludes RB COM kinetic energy too and Epot are respectively the kinetic and rotational energies of the system Dmass is the barostat mass and 7 and 7 are the barostat friction coefficient or matrix of coefficients respectively There are two slight technicalities with the Evans and Andersen ensembles that are worth mentioning Since both the translational and rotational velocities contribute towards temperature equation 3 24 show ing the derivation of the thermostat friction in the Evans ensemble by imposing a Gaussian constraint on the system s instantaneous temperature changes to a7 0 aS 5 MY 1 ay 1 0 0 q A 32 i a FP Saos 0 LUO Lae io i colmo roy Vit nett on 3 209 j J EE u LO DF O EA DF ale 20 x t a Exin t Eror t where where 7 is the instantaneous temperature defined in equation 3 10 and Ekin in the final expression contains both the kinetic contribution form the free particles and the RBs COMs In the case of the Andersen ensemble if a Poisson selected particle constitutes a RB then th
430. ve Probable cause corruption of the DL_POLY_4 executable or of the FIELD file We would be interested to hear of other reasons Action See action notes on message 14 above Message 17 error strange exit from CONTROL file processing This should never happen It simply means that DL POLY 4 has ceased processing the CONTROL 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 and or recreate the CONTROL file afresh If no combination of these works send the problem to us 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 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 See action notes on message 14 above Message 21 error molecule contains more atoms sites than declared The molecule contains more atom site entries that it declares in the beginni
431. vely 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 HIS TORY 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 distance 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 248 STFC Appendix D 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 Message 620 error duplicate or mixed intra molecular entries specified in FIELD The FIELD parser has detected an inconsistency in the description of bonding interactions It is the user s res
432. verage values of thermodynamic variables mxnstk record 5 ssqval fluctuation squared of thermodynamic variables mxnstk record 6 163 STFC Section 6 1 zumval running totals of thermodynamic variables mxnstk record 7 ravval rolling averages of thermodynamic variables mxnstk record 8 stkval stacked values of thermodynamic variables mxstakxmxnstk record 9 strcon constraint bond stress 9 record 10 strpmf PMF constraint stress 9 record 11 stress atomic stress 9 record 12 Optional rdf RDF array mxgrdf xmxrdf record 13 Optional zdens Z density array mxgrdf xmxatyp record 14 Optional vaf VAF arrays sizes dependent on sampling frequency and VAF bin size 6 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 Therefore different versions of DL POLY 4 may render any existing REVOLD file unreadable by the code 6 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 7 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
433. xceeds limit in dpd_v_export See notes on message 38 above Action See action notes on message 38 above Message 158 error incorrect atom totals assignments in dpd_v_set_halo This should never happen Action Big trouble Report to authors Message 160 error undefined direction passed to statistics _connect_spread This should never happen Message 163 error outgoing transfer buffer size exceeded in statistics_connect_spread The transfer buffer has been exceeded 232 STFC Appendix D Action Consider using densvar option in CONTROL for extremely non equilibrium simulations Alternatively increase mxbfss parameters in SET_BOUNDS recompile and resubmit Message 164 error incoming data transfer size exceeds limit in statistics_connect_spread See notes on message 163 above Action See action notes on message 163 above 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 172 error duplicate intra molecular entries specified in TABBND TABANG TABDIH TA A duplicate entry has been encountered in the intra molecular table file 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 SYSTEM_R
434. xp gt 3 45 TT where Tr is the thermostat relaxation 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 Vi kpT ext F v 1 G 0 1 3 46 vs mae exp ee Y 2m paren 3 46 where subscripts denote particle indices 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 vy apt Vina a 3 47 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 probability If uni i lt 1 exp 4 the particle momentum is changed as described above The VV implementation of the Andersen algorithm is as follows 69 STFC Section 3 4 1 VV1 1 At f t wet Zar e w St 1 r t At r t Atu t At 3 48 2 RATTLE_VV1 3 FF f t At f t 3 49 4 VV2 CEAN 1 At ft At t At At 4 3 50 t At cols Sat SE 3 50 5 RATTLE_VV2 6 Thermostat Note that the MD cell centre of mass momentum must not change At If gt lt 1 exp Then TT e sa 0 1 3 51 se vu t 4 At E au t At V1 a u t At End If The algorithm is self consistent and requires no ite
435. y this ensemble is optionally extending to constant normal pressure and constant surface tension NP yT 73 by semi isotropic constraining of the barostat equation of motion to Don fel V t Pent XpNaa t sde Emol r a B 2 y d Naglt 5 3 121 ap gar Pot VO 4 Era _ yon t eB 2 a P x2 di 0 nag 0 0 a B 2 y z where Yext is the user defined external surface tension and h t V t Azy t is the instantaneous hight of the MD box or MD box volume over area The instnatneous surface tension is defined as Yalt h t led Poxt 3 122 The case Yext 0 generates the NPT anisotropic ensemble for the orthorhombic cell imcon 2 in CONFIG see Appendix B This can be considered as an orthorhombic constraint on the NoT ensemble The constraint can be strengthened further to a semi orthorhombic one by imposing that the MD cell change isotropically in the x y plane which leads to the following modification in the NP yT set of equatons e Cra Tyy t 2 _ LP ext hz t V t 4 2 Exin t pe Pmass f Pmass AS 3 123 Xplaa t The VV and LFV flavours of the non isotropic Langevin barostat and Nos Hoover thermostat are im plemented 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 82 STFC Sect
436. y each other or even through each other relatively easily so that equilibrium is achieved quickly A common form of interaction potential is an inverse parabola part of VDW types of potentials see Section 2 3 1 Aij SN a V rij 5 k E A 2 gt Ty 2 Te where rij Ir rj Tc is a cutoff radius and Aj is the interaction strength that may be the same for all particle pairs or may be different for different particle types Equation A 1 gives rise to a repulsive force of the form Tij Tij Lij fE Aij we rig Aij 2 a A 3 9 ij Te Tij This is the deterministic or conservative force L exerted on particle by particle j Note the switching function 1 rs E Pos w rij G T A 4 0 gt Tij Te and the force are zero when rij gt re and thus the particles have an effective diameter of 1 in units of the cutoff radius re In the DL_POLY_4 context all inter and intra molecular forces will fall into this category of force The stochastic forces experienced by the particles is again pairwise in nature and takes the form pe 1 Ti oi riz Cig At 2 a j A 5 Tij in which At is the time step and w r j is a switching function which imposes a finite limit on the range of the stochastic force ij is a random number with zero mean and unit variance The constant o0 is related to the temperature as is understood from the role of the stochastic force in representing a heat bath Final
437. y the Langevin friction y positive in units of ps where w t is the standard Brownian motion Wiener process Gauss 0 1 is the target thermostat energy as in equation 3 57 mass 20 ip 3 82 is the thermostat mass which depends on a specified time constant Tr for temperature fluctuations normally in the range 0 5 2 ps It is worth noting that equation 3 81 similar to the Ornstein Uhlenbeck equation dx ao dw 3 83 dt 2 dt oo which for a given realization of the Wiener process w t has an exact solution e e2 et 1 Xn 1 e Xa t Aw 3 84 where e ag 2 and Aw N 0 1 The VV implementation of the Gentle Stochastic Thermostat algorithm takes place in a symplectic manner as follows 1 Thermostat Note Exin t changes inside and R t drown from Gauss 0 1 is carried over from the previous half timestep x t TAi x t exp y i E Toxt 1 exp y R t mass i At 2Exin t 20 4 mass 74 STFC Section 3 4 OO exp x t FAL 2 3 85 A Bi A x t 5 At x t TAi exp y y e 1 exp y zl R t i At 2Ekin t 20 4 mass 2 VVI TES ai a za HEAD 0 ult 5 At 3 86 3 RATTLE_VV1 4 FF f t At f t 3 87 5 VV2 nee u t At ult 5AM gt E i 3 88 6 RATTLE_VV2 7 Thermostat Note Exin t At changes inside and Ry t At is drown anew from Gauss 0 1 and is to be carried over the nex
438. y third party unless in each case that third party has complied with clause 2 3 below 2 1 2 the Licensee may not use the DL_POLY_4 Software on behalf of or for the benefit of any third party including without limitation using it to provide bureau outsourcing or application services or facilities management services party unless that third party has complied with clause 2 3 below and 2 1 3 the DL_POLY_4 Software and any Derived Work may be used by the Licensee and its employees and registered students for Academic Purposes only If the Licensee wishes to use the DL_POLY_4 Software or any Derived Work in any way except for Academic Purposes or wishes to distribute or make the DL_POLY_4 Software or any Derived Work available to any third party for non Academic Purposes it must obtain a commercial licence from STFC STFC may refuse to grant the Licensee a commercial licence If STFC agrees to grant a commercial licence that licence will be on such terms and conditions as STFC sees fit If the Licensee wishes to carry out any collaboration for Academic Purposes with any third party and that third party needs to use the DL_POLY_4 Software in connection with that collaboration or if the Licensee wishes to make the DL_POLY_4 Software available on line to any third party for Academic Purposes the Licensee must direct 271 STFC Appendix F 2 4 2 5 2 6 that third party to the DL_POLY_4 Website That third party may use
439. yees or students publishes any article or other material resulting from or relating to a project or work undertaken with the assistance of any part of the DL_POLY_4 Software that publication will contain the following acknowledgement DL_POLY_4 is a molecular dynamics simulation package written by I T Todorov and W Smith and has been obtained from STFC s Daresbury Laboratory via the website http www ccp5 ac uk DL_POLY and cite the following reference I T Todorov W Smith K Trachenko amp M T Dove J Mater Chem 16 1911 1918 2006 TERMINATION This Licence Agreement will take effect and the Licence Period will start when the Licensee has agreed to the terms and conditions of this Licence Agreement and downloaded the DL_POLY_4 Software from the DL_POLY_4 Website This Licence Agreement will terminate immediately and automatically if 5 2 1 the Licensee is in breach of this Licence Agreement or 5 2 2 the Licensee becomes insolvent or if an order is made or a resolution is passed for its winding up except voluntarily for the purpose of solvent amalgamation or reconstruction or if an administrator administrative receiver or receiver is appointed over the whole or any part of its assets or if it makes any arrangement with its creditors The Licensee s right to use the DL_POLY_4 Software will cease immediately on the termination of this Licence Agreement and the Licensee will destroy all copie

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