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THE DL-POLY-4 USER MANUAL

1. x t 2 Eat u t u t ep x06 5 3 25 2 VVI v t sat v t He AD c D ATE ZAt 3 26 3 RATTLE_VV1 4 FF f At c F 3 27 5 VV2 u t At ult 340 Et 2 3 28 6 RATTLE VV2 7 Thermostat VV2 Y v At f t At XS s 2 Enlt At P cose xt 057 3 29 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 t f t At 3 30 2 LFV The iterative part is as follows locia S 1 MS scale scale v scale f 2 scale i scale 1 1 f t v t At scale v u t 4 scale f 3 31 m r t At r t Atv E 2At 61 STFC Section 3 4 3 SHAKE 4 Full step velocity u t 4 ult DAI w t 340 3 32 5 Thermostat uo vit f t 3 33 2 Exin t Several iterations are required to obtain self consistency In DL_POLY 4 the number of iterations is set to 8 9 if bond constraints are present The conserved quantity by these algorithms is the system kinetic energy The VV and LFV flavours of the Gaussian constraints algorithm are implemented in the DL POLY 4 routines NVT_EO_VV and NVT_EO_LFV respectively The routines NVT El VV and NVT_El_LFV im plement the same but also inco
2. sin dijkn OPijkn 9 J tay s ng da Sra 2 64 1 Following through the extremely tedious differentiation gives the result 1 f o U diskn 2 65 de xt O ijkn Pisi x CR cos dijkn a 1 aa de dei a fa wa g ri ri Bin Un rij Cin Ben T Em A A ek dei Bm i rj Has Tij Tip Uu JUS kn UknT ik i S zi TNFR Ey k 1a x P ro T 6g dei zu n Ea kn kn Lij Pik are EE d Ukn ik Tik Zij lx A XA Ti t 6mm dei ij z Ps kn kn E rij Lin rij His Lin d Ukn T n Tin Tjj Of A ge Sen dei EU z es j ic Den On Es Lin Ba i Oy r Tin a Ukn T in in This general formula applies to all atoms i j k n It must be remembered however that these formulae apply to just one of the three contributing terms i e one angle of the full inversion potential specifically the inversion angle pertaining to the out of plane vector r The contributions arising from the other vectors r and r are obtained by the cyclic permutation of the indices in the manner described above All these force contributions must be added to the final atomic forces Formally the contribution to be added to the atomic virial is given by W A PIN 2 66 However it is possible to show by thermodynamic arguments cf 40 or simply from the fact that the sum of forces on atoms j k
3. if test LD undefined then echo echo FORTRAN90 Linker loaDer unspecified echo echo Please edit your Makefile entries echo exit 99 fi X mkdir p BINROOT touch dl_poly f90 Declare rules 90 0 FC FCFLAGS f90 Declare dependencies 202 OSTFC Appendix C angles forces o angles module o comms module o config module o kinds f90 0 Setup module o angles module o kinds f90 0 setup module o bonds forces o bonds module o comms module o config module o kinds f90 0 Setup module o bonds module o kinds f90 0 setup module o build book intra o angles module o bonds module o comms module o config module o constraints module o core shell module o dihedrals module o inversions module o pmf module o rigid bodies module o setup module o site module o tethers module o build excl intra o angles module o bonds module o comms module o config module o constraints module o core shell module o dihedrals module o inversions_module o kinds f90 0 rigid bodies module o setup module o check config o comms module o config module o kinds f90 0 setup module o Site module o comms module o kinds f90 0 compress book intra o comms module o config module o kinds f90 0 Setup module o config module o kinds f90 0 setup module o constraints module o kinds f90 0 setup module o constraints pseudo bonds o comms module o config module o constra
4. 184 7 1 11 Test Case 21 and 22 Cu with EAM metal Potentials 184 7 1 12 Test Case 23 and 24 Al with Sutton Chen metal Potentials 185 7 1 13 Test Case 25 and 26 Al with EAM metal Potentials 185 7 1 14 Test Case 27 and 28 NiAl alloy with EAM metal Potentials 185 7 1 15 Test Case 29 and 30 Fe with Finnis Sincair metal Potentials 185 7 1 16 Test Case 31 and 32 Ni with EAM metal Potentials 185 7 1 17 Test Case 33 and 34 SPC IceVII water with constraints 185 ix STFC Contents 7 1 18 Test Case 35 and 36 NaCl molecules in SPC water represented as CBs RBs 7 1 19 Test Case 37 and 38 TIP4P water RBs with a massless charged site 7 1 20 Test Case 39 and 40 Ionic liquid dimethylimidazolium chloride 7 1 21 Test Case 41 and 42 Calcite nano particles in TIP3P water 7 2 Benchmark Cases e esa ie PNE LRL Appendices A DL POLY 4 Periodic Boundary Conditions B DL_POLY_4 Macros C DL POLY 4 Makefiles D DL POLY 4 Error Messages and User Action E DL POLY 4 README Bibliography Index 185 185 186 186 186 186 187 190 194 236 286 291 295 List of Tables o l 5 2 5 3 5 4 5 9 5 6 5 7 5 8 5 9 5 10 5 11 5 12 5 13 5 14 5 15 5 16 5 17 Internal Trajectory Detects File Key 202 304 ries RO RR ae Rw ee 124 Internal Restart Key 30040 a ce eee e a e a ee we E 125 internal Ensemble
5. 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 LFV t VV t VV t 5 5 However the VV algorithms treat CB PMF RB entities in more precise symplectic manner than the LFV ones and thus not only have better numerical stability but also produce more accurate dynamics Makefiles From within the source directory the user may compile the code by Selecting the appropriate Makefile from the build directory cp build Makefile MPI Makefile for parallel execution MPI is needed or cp build Makefile SRLx Makefile for serial execution no MPI needed Note that in comms module f90 it is crucial that line 13 reads as Use mpi module for serial compilation and Use mpi for parallel compilation which is the default If the parallel OS environment you are compiling on is not fully F90 compatible then the Use mpi entry in comms module f90 will be interpreted as erroneous This is easily overcome by commenting out Use mpi and uncommenting Include mpif h just after Implicit None If t
6. ut Lat put 2A 3 92 70 STFC Section 3 5 5 Thermostat Note R t is drown from Gauss 0 1 just once per timestep 1 1 A kp Tex At x t 34t x t 540 exp y 2 NE 1 exp y x1 R t 2 Ein t 2c mass TE e At x t4 At 3 93 At 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 t 2 t JTiNvT Hnve mast A f kp Text f x s ds 3 94 where 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 G vv and NVT_GO_LFV respectively The routines NVT_G1_vv and NVT_G1_LFV implement the same but also incorporate RB dynamics 3 5 Barostats The size and shape of the simulation cell may be dynamically adjusted by coupling the system to a barostat in order to obtain a desired average pressure Pix and or isotropic stress tensor c DL POLY 4 has four such algorithms the Langevin 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 rem
7. 1 4 Directory Structure vac The entire DL POLY 4 package is stored in a UNIX directory structure The topmost directory is named dl poly 4 nn where nn is a generation number Beneath this directory are several sub directories named source utility data bench execute build public and java Briefly the content of each sub directory is as follows sub directory contents source primary subroutines for the DL POLY 4 package utility subroutines programs and example data for all utilities data example input and output files for DL POLY 4 bench large test cases suitable for benchmarking execute the DL POLY 4 run time directory build makefiles to assemble and compile DL POLY 4 programs public directory of routines donated by DL POLY 4 users java directory of Java and FORTRAN routines for the Java GUI A more detailed description of each sub directory follows 1 4 1 The source Sub directory In this sub directory all the essential source code for DL POLY 4 excluding the utility software is stored In keeping with the package concept of DL POLY 4 it does not contain any complete programs these are assembled at compile time using an appropriate makefile The subroutines in this sub directory are documented in Chapter 6 1 4 2 The utility Sub directory This sub directory stores all the utility subroutines functions and programs in DL POLY 4 to gether with examples of data Some of the various routines in this su
8. For molecular systems as opposed to systems comprised simply of point ions additional modifica tions EWALD EXCL FORCES are necessary to correct for the excluded intra molecular coulombic interactions In the real space sum these are simply omitted In reciprocal space however the effects of individual Gaussian charges cannot easily be extracted and the correction is made in real space It amounts to removing terms corresponding to the potential energy of an ion due to the Gaussian charge on a neighbouring charge m or vice versa This correction appears as the final term in the full Ewald formula below The distinction between the error function er f and the more usual complementary error function er fc found in the real space sum should be noted The same considerations and modifications EWALD FROZEN FORCES are taken into account for frozen atoms which mutual coulombic interaction must be excluded The total electrostatic energy is given by the following formula U 1 gt exp MESS D rj Jl 2 Qjdn f ES X T r 2V5eoe io dee vae Taj ie 1 er f or 7 Y 3 nu it nni 2 186 PENE molecules lt m Tim 2 y er arem Es dm f m at rien LE Arrege Vo 3 dj where N is the number of ions in the system and N the same number discounting any excluded intramolecular and frozen interactions M represents the number of excluded atoms in a given molecule F represents the number of frozen atoms in the M
9. PV t 3 115 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 exp x 5 n nt A wn At o t Pexs V t 1 2E 1 Rel 4 3 116 4 Pmass f Pmass Pmass 1 1 1 At u t exp wt At Tr nl 1405 zi u t 1 1 r t At exp nt z At r t At v t 344 Similarly for the LFV couched algorithms these are 1 At nit At exp xp t At nit 3 ne O Pos VEL Brin 1 Rp t Pmass f Pmass i Pmass At scale 1 Ix 1 1 5 o CA 2 scalev 1 3 117 scale At scale f scale l 1 t R t v t At scale v u t 5 4 scale f f t R t a m r t At e r t At fat Lat Fn td zA rt 340 76 STFC Section 3 5 It is worth noting DL POLY 4 uses Taylor expansion truncated to the quadratic term to approxi mate exponentials of tensorial terms This ensemble is optionally extending to constant normal pressure and constant surface area NP AT 60 by semi isotropic constraining of the barostat equation of motion to 2E rin t Rp zz t Ozz t Pext V t m Posti Pmass j Pmass XpNzz t E Pmass a B 3 118 dt 0 Mag 0 0 a b zz Similarly this ensemble is optionally extending to constant normal pressure and constant surface tension NP yT 6
10. The sum of the diagonal elements of the stress tensor is zero since the virial is zero and the matrix is symmetric Lastly it should be noted that the above description does not take into account the possible inclu sion of distance dependent 1 4 interactions as permitted by some force fields Such interactions are permissible in DL POLY 4 and are described in the section on pair potentials below DL_POLY_4 also permits scaling of the 1 4 van der Waals and Coulomb interactions by a numerical factor see Table 5 10 Note that scaling is abandoned when the 1 4 members are also 1 3 members in a valence angle intercation 1 4 checks are performed in DIHEDRALS 14 CHECK routine 1 4 interactions do of course contribute to the atomic virial In DL_POLY 4 dihedral forces are handled by the routine DIHEDRALS FORCES and INTRA_COUL and DIHEDRALS 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 molecules modelled by united atom centres For example a amino acids such as alanine CH3CH NH2 COOH i
11. ll 21 22 7 Inversion Angle Potentials ss 44 4059 a RR EE eee ES 22 2 2 8 The Calcite Four Body Potential 25 2 2 9 Tetheringe Forces 4 22604243 2 Poe ke o9 dn m e hok R33 wx OE Ew 26 2 3 The Intermolecular Potential Functions 27 2 3 1 Short Ranged van der Waals Potentials 27 2 9 2 Metal Potentials so s soes moa mea eai 4 ee p eA Pa em URS hae 4 29 2 9 9 Tersoff Potential s oe si soacre fa 9 domos n Ro Ronc o eh R9 PA eee es 37 2 3 4 Three Body Potentials us Low ex a RR X Roh E Rex Re En Rh Ani 40 2 3 9 JoursBodyPotenuals clean CREER IR xor bos x 41 2 4 Long Ranged Electrostatic coulombic Potentials 42 2 4 1 Direct Coulomb Sum 4 ok e464 224 ox eke RERO o Ru RO A EE ee 42 2 4 2 Force Shifted Coulomb Sum o s saso sadace enoma duces edna 43 2 4 3 Coulomb Sum with Distance Dependent Dielectric 44 DAA Reaction Field 54 due sau apa e a a e A 45 2 4 5 Smoothed Particle Mesh Ewald aoaaa e 46 vi STFC Contents 2 5 Polarisation Shell Models 244 245 04 5604 9 ois we SB a ee a 49 2 5 1 Dynamical Adiabatic Shell gt s e ce e eec ssaa tirerai edea 50 25 2 Relaxed Massless Shells cc c sacrer EG a om OR x Sx EE wd 50 2 0 External Field 024 2 506 wea ee Se ae Ga dodo eed e RO E n 51 2 7 Treatment of Frozen Atoms Rigid Body and Core Shell Units 52 3 Integration Algorithms 53 S
12. 0 0 00005 ae 96 4 1 2 Constructing Non standard Versions 0 00000 eee 97 42 Compiling and Running DLPOLY A isos idas bs ae BR A A 99 4 2 1 Compiling the Source Code gt is es ea aea seboa taitaa a ea eaaa 99 4 2 2 RUDNE uoc dee eo RA ee pa ln a Ses 100 is Paralel T O sis aiya daoen a pedu e soe aa RORIS ee ee eee 101 4 2 4 Restarting coi eee e Pa Sue a e n 102 vii STFC Contents 42 5 Optinising the Starting Structure is nasi ko speck paw ae es 102 4 2 6 Simulation Efficiency and Performance e e 104 4 3 A Guide to Preparing Input Files lt i o cacce uu nadani saaa aa pa 106 4 3 1 Inorganic Materials 2x 9 x x 9e RR oem a 106 4 8 4 Macromolecules 42 seo o m RR EEG REX ES RR 106 4 3 3 Adding Solvent to a Structure Li 107 134 Analyse Results lt span 40494 e en ea 107 4 8 5 Choosing Ewald Sum Variables 2l 107 4 4 Warning and Error Processing 2 2 109 4 4 1 The DL_POLY 4 Internal Warning Facility 109 4 1 2 The DL POLY 4 Internal Error Facility s s se sose t 60 cata 110 5 Data Files 111 ol be INPUT Pileg osa a lr die E Pe A i 112 SLI The CONTROL File iere beaa eee Beh kom o n m PR RR a RR ERE 112 5 1 2 The CONFIG File ood RR 9x e a a a 131 ple The HIELD Pile sc sd ek der E I e e ly ee 134 5 14 The REFERENCE File Lg os pe E a a 150 Slo The REVOLD Ple lt r senei ee REIR A be dee ec Ee Ro I 151 SLO The TABLE PIE 2223
13. Action Delete one of the duplicate entries and resubmit Message 145 error no two body like forces specified This error arises when there are no two body like interactions specified in FIELD and CONTROL Le none of the following interactions exists or if does it has been switched off any coulombic vdw metal tersoff In DL POLY 4 expects that particles will be kept apparat stay separated and never go through each other due to one of the fore specified interactions Action Users must alone take measures to prevent such outcome 257 OSTFC Appendix D Message 150 error unknown van der waals potential selected DL POLY 4 checks when constructing the interpolation tables for the short ranged potentials that the potential function requested is one which is of a form known to the program If the requested potential form is unknown termination of the program results The most probable cause of this is the incorrect choice of the potential keyword in the FIELD file Action Read the DL POLY 4 documentation and find the potential keyword for the potential desired Message 151 error unknown EAM keyword in TABEAM DL_POLY 4 checks when constructing the interpolation tables for the EAM metal potentials that the potential function requested is one which is of a form known to the program If the requested potential form is unknown termination of the program results The most probable cause of this is the incorrect choi
14. 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 intramolecular bookkeeping arrays exceeded in deport atomic data One or more bookkeeping arrays for site related interactions have been exceeded Action Consider using densvar option in CONTROL for extremely non equilibrium simulations Alter natively you will need to print extra diagnostic data from the DEPORT ATOMIC DATA subroutine to find which boded like contribution has exceeded its assumed limit and then correct for it in SET BOUNDS recompile and resubmit Message 114 error legend array exceeded in deport atomic data The array legend has been exceeded Action Try increasing parameter mxfix in SET BOUNDS recompile and resubmit Contact DL POLY 4 authors if the problem persists Message 115 error transfer buffer exceeded
15. JEBE UD gt HF quU ce Praslf gt Geas F J 9099 naf EPR 3 204 nf gt mw F fRBPee0 lf SEPE ili Me MO where f refers to the degrees of freedom in the system see equation 3 11 o is the system target energy see equation 3 57 H is the conserved quantity of the ensemble if there is such defined Exin includes RB COM kinetic energy too and Epot are respectively the kinetic and rotational 93 STFC Section 3 6 energies of the system Pmass is the barostat mass and y and 7 are the barostat friction coefficient or matrix of coefficients respectively 7 There are two slight technicalities with the Evans and Andersen ensembles that are worth men tioning Since both the translational and rotational velocities contribute towards temperature equation 3 24 showing the derivation of the thermostat friction in the Evans ensemble by imposing a Gaussian constraint on the system s instantaneous temperature changes to d d 1 FP A 1 EB j 1 RB x mic oq di 2 meg 2 Mili 30 Lod 0 FP RB RB Eno LOHS VIO BOQ 8 0 o i j j FP RB RB x t E mi 6 M jV3 O 595 6 I e 0 3 205 i j j Xf w f OP VIO Es 0 X P a t 2 x t 2 Exin t Erot t where where 7 is the instantaneous temperature defined in equation 3 10 and Ex n in the final expression contains both the kinetic contribution form the free particles and the RBs COMs In the case of the Andersen ense
16. Message 20 error too many molecule sites specified This should never happen This error most likely arises when the FIELD file or and DL POLY 4 executable are corrupted Action Recompile the program or recreate the FIELD file If neither of these works send the problem to us Message 21 error molecule contains more atoms sites than declared The molecule contains more atom site entries that it declares in the beginning Action Recreate or correct the erroneous entries in the FIELD file and try again Message 22 error unsuitable radial increment in TABLE file This arises when the tabulated potentials presented in the TABLE file have an increment that is greater than that used to define the other potentials in the simulation Ideally the increment should be reut mxgrid 4 where freut is the potential cutoff for the short range potentials and mxgrid is the parameter defining the length of the interpolation arrays An increment less than this is permissible however Action The tables must be recalculated with an appropriate increment Message 23 error incompatible FIELD and TABLE file potentials This error arises when the specification of the short range potentials is different in the FIELD and TABLE files This usually means that the order of specification of the potentials is different When DL POLY 4 finds a change in the order of specification it assumes that the user has forgotten to enter one A
17. TYPE hpcx MAKE LD mpxlf90 r o LDFLAGS 03 q64 qmaxmem 1 FC mpx1f90_r qsuffix f f90 c FCFLAGS 03 q64 qmaxmem 1 qarch pwr5 qtune pwr5 qnosave EX EX BINROOT BINROOT TYPE hpcx debug MAKE LD mpxlf90 r o LDFLAGS g C q64 00 lessl lhmd FC mpx1f90_r qsuffix f f90 c FCFLAGS g C q64 00 qarch pwr5 qtune pwr5 qnosave EX EX BINROOT BINROOT TYPE BGL MAKE LD bgl BlueLight ppcfloor bglsys bin mpixlf95 o LDFLAGS 03 qhot qarch 440d qtune 440 FC bg1 BlueLight ppcfloor bglsys bin mpixlf95 c FCFLAGS 03 qhot qarch 440d qtune 440 EX EX BINROOT BINROOT TYPE 218 OSTFC Appendix C BGP MAKE LD bgsys drivers ppcfloor comm bin mpix1f2003_r 0 LDFLAGS 03 qhot qarch 450d qtune 450 qmaxmem 128000 FC bgsys drivers ppcfloor comm bin mpix1f2003 r c FCFLAGS 03 qhot qarch 450d qtune 450 qmaxmem 128000 EX EX BINROOT BINROOT TYPE hector MAKE LD ftn o LDFLAGS 03 FC ftn c FCFLAGS 03 EX EX BINROOT BINROOT TYPE hector pgi debug MAKE LD ftn o LDFLAGS 00 W Wall pedantic std f2003 g fbounds check fbacktrace finit real nan finit integer 999999 FC ftn c N FCFLAGS 00 W Wall pedantic std f2003 g fbounds check fbacktrace finit real nan finit integer 999999 EX EX BINROOT BINROOT TYPE hector gn
18. m c co Cifig cari car carg pata m d B rij d 2 101 with parameters co c1 C2 C3 C4 C A d B both c and d are cutoffs 4 Sutton Chen potential 14 15 16 stch The Sutton Chen potential is an analytical poten tial in the FS class It has the form Vis rij 2 2 102 Tij F p ceVp pij rij 30 STFC Section 2 3 with parameters a n m c 5 Gupta potential 49 gupt The Gupta potential is another analytical potential in the FS class It has the form Ti TT exp da 2 103 B Api pij rij F pi with parameters A ro p B qij All of these metal potentials can be decomposed into pair contributions and thus fit within the general tabulation scheme of DL POLY 4 where they are treated as pair interactions though note that the metal cutoff rmet has nothing to do with short ranged cutoff rydw 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 f on an atom k derived from this potential is calculated in the standard way i m VkUmetal E 2 104 We rewrite the EAM FS potential 2 98 as Umetal E ui 2 Ui 3
19. 3 6 54 OSTFC Section 3 1 where m is the mass of a site and then the positions are advanced to a full step t At using the new half step velocities r t At r t At v t 340 3 7 Molecular dynamics simulations normally require properties that depend on position and velocity at the same time such as the sum of potential and kinetic energy The velocity at time t is obtained from the average of the velocities half a timestep either side of timestep t u t 5 ott 50 wt 50 3 8 The instantaneous kinetic energy for example can then be obtained from the atomic velocities as Ir a Ekin t gt Nom 3 9 1 and assuming the system has no net momentum the instantaneous temperature is T t 2 Eun t 3 10 where 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 SN frozen 3N shells a M constrains 3 p 3 11 Here N frozen indicates the number of frozen atoms in the system Msrells 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 b
20. 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 6 1 9 The Parallel Rigid Body Implementation The essentials of the DD tailored RB algorithms see Section 3 6 are as follows 1 Every processor works out a list of all local and halo atoms that are qualified as free zero entry or as members of a RB unit entry 2 The rigid body units in the simulated system are allocated between the processors based on the location i e domain of the atoms involved 3 Each processor makes a list of the RB and their constituting atoms that are fully or partially owned by the processors domain 4 Each processor passes a copy of the array to the neighbouring processors which manage the domains in contact with its own The receiving processor compares the incoming list
21. 90 exp rij or rief 2 18 5 Screened Vessal 36 bvs1 Ulin amp i zy fo 9 ia zy x exp rij p1 rix p2 2 19 6 Truncated Vessal 37 bvs2 U Ojik k Ojik 90 05 0 in 00 27 a a 37 6o 7 exp ri ri 09 2 20 7 Harmonic cosine hcos k U Ojik 3 cos 8jix cos 00 2 21 16 STFC Section 2 2 8 Cosine cos U Ojik A 1 cos m Ojik d 2 22 9 MM3 stretch bend 38 mmsb U Ojik A Ojik 00 rij rij ris rik 2 23 10 Compass stretch stretch 39 stst U Ojik A rij r5 Tik rix 2 24 11 Compass stretch bend 39 stbe U Ojik A Ojik 00 rij ri 2 25 12 Compass all terms 39 cmps U Ojik A rij 155 rn Tix Ojik 00 B rij r5 C rik 7 2 26 In these formulae 0 x is the angle between bond vectors Tij and rj T TES T ora ALTER 2 27 Jik rjTik In DL POLY 4 the most general form for the valence angle potentials can be written as U Ojik Tijs Tik Alda Sra Siri S rik 4 2 28 where A 0 is a purely angular function and S r is a screening or truncation function All the function arguments are scalars With this reduction the force on an atom derived from the valence angle potential is given by fe gra O Bis rij Pik Tjk 2 29 T with atomic label being one of i j k and a indicating the x y z component The deriv
22. 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 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 factorisable 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 a quarter of the minimum MD cell width DL POLY 4 has found a check violated while reading CONTROL Action Correct accordingly in CONTROL and resubmit Message 540 error pseudo thermostat MUST only be used in bulk simulations i e imcon MUST be 1 2 or 3 DL POLY 4 has found a check violated while reading CONTROL Action Correct accordingly in CONTROL nve or in CONFIG
23. Schmidt M E Shin S and Rice S A Molecular dynamics studies of langmuir monolayers of f cf3 11cooh volume 104 page 2101 1996 19 143 Rohl A L Wright K and Gale J D 2003 Amer Mineralogist 88 921 25 Raiteri P and Gale J 2010 J Am Chem Soc 132 17623 17634 25 Clarke J H R Smith W and Woodcock L V 1986 J Chem Phys 84 2290 27 145 Weeks J D Chandler D and Anderson H C 1971 J Chem Phys 54 5237 28 J F 1952 Philos Mag 43 153 30 292 OSTFC Bibliography 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 Dai X D Kong Y Li J H and Liu B X 2006 J Phys Condens Matter 18 45274542 30 Cleri F and Rosato F 1993 Phys Rev B 48 22 31 Johnson R A 1989 Phys Rev B 39 12556 37 Eastwood J W Hockney R W and Lawrence D N 1980 Comput Phys Commun 19 215 40 41 42 Fennell C J and Gezelter D J 2006 J Chem Phys 124 234104 44 46 121 122 Neumann M 1985 J Chem Phys 82 5663 45 Fuchs K 1935 Proc R Soc A 151 585 4T 49 Essmann U Perera L Berkowitz M L Darden T Lee H and Pedersen L G 1995 J Chem Phys 103 8577 48 171 Fincham D and Mitchell P J 1993 J Phys Condens Matter 5 1031 50 Lindan P J D and Gillan M J 1993 J Phys Condens
24. Vi Tij 2 105 i 1ljzi N Uz Y F p i 1 r ty j rj The force on atom k is the sum of the derivatives of U and U2 with respect to rg which is recognisable as a sum of pair forces where r QU _ yy ula Vig rag Orig _ DO OWVig 7g Tki Or 1 Orig Ork Piper dr Va QU Ai OF amp Opis rij Orij 2 106 Ore 2 da TA e _ y OF Opix rix Ori e DF Opws rej Ori E Op rik Org Op Orkj Ork i 1 i k j ljzk PE z ar Opry ry Thi juu OPE Op Orkj ru 1 EAM force The same as shown above However it is worth noting that the generation of the force arrays from tabulated data implemented in the METAL TABLE DERIVATIVES routine is done using a five point interpolation precedure 31 OSTFC Section 2 3 2 Finnis Sinclair force j ora 5 20 c co cirk corks rij e e1 2cry T Tk j l jek i U N A fa di Tkj Tk j l jth kj 3 Extended Finnis Sinclair force aU a 5 20 c co cirki cari cari cay ER j l jek Tki ru 0 ei core 3egri Scares 2 108 DU a A 3 Tkj M 5 VP n 205 d 4B ray 9 k j ljzk kj 4 Sutton Chen force QU x a Tkj k j 1 j7k ir KI QU N mee al TR p Da cm 4 EE 2 109 Tk j jek EE 5 Gupta force OU Ap Tkj ro Thi Fr Tk 1 5 70 ro Tkj QU di me Tkj TOY kj er dE SS Vor pj exp 2qk 2 110 Tk j ljzk E With the metal forces thus def
25. before each definition The derivations of the atomic forces virial and stress tensor are also outlined 2 2 1 Bond Potentials Figure 2 1 The interatomic bond vector The bond potentials describe explicit chemical bonds between specified atoms They are all func tions of the interatomic distance Only the coulomb potential makes an exception as it depends on the charges of the specified atoms The potential functions available are as follows 1 Harmonic bond harm 1 U rij jF rij ro 2 2 13 OSTFC Section 2 2 2 Morse potential mors U rij Eo 1 exp K rij ro 1 2 3 Use 5 24 ij ij E 12 5 6 5 Restrained harmonic rhrm 3 12 6 potential bond 12 6 4 Lennard Jones potential lj 1 2 sk rij ro rij Tol lt r U r Puri To ij rel S re 2 6 rij skr2 kre rij Tol rc rij rol gt Te 6 Quartic potential quar k k k U rij 0 ro 3 rig To 7 rig ro 2 7 7 Buckingham potential buck U rij A exp 3 a 2 8 P Tij 8 Coulomb potential coul U r k U E ectrostatics p Y k didj 2 9 7 3 TEJE Tij where qe is the charge on an atom labelled It is worth noting that the Coulomb potential switches to the paricular model of Electrostatics opted in CONTROL 9 Shifted finitely extendible non linear elastic FENE potential 33 34 35 fene E Ute 0
26. 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 OSTFC Section 1 3 1 3 2 Modularisation and Intent DL POLY 4 exploits the full potential of the modularisation concept in FORTRAN90 Variables having in common description of certain feature or method in DL_POLY 4 are grouped in modules This simplifies subroutines calling sequences and decreases error proneness in programming as subroutines
27. e defects module DEFECTS MODULE The defects module defines all defects and configuration related arrays REFERENCE and is dependent on KINDS F90 only However it also develops an allocation method that is dependent on SETUP MODULE e inter molecular interactions modules VDW MODULE METAL MODULE TERSOFF MODULE THREE BODY MODULE FOUR BODY MODULE The intermolecular modules 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 and site related interactions modules CORE SHELL MODULE CONSTRAINTS MODULE PMF MODULE RIGID BODIES MODULE TETHERS MODULE BONDS MODULE ANGLES MODULE DIHEDRALS MODULE INVERSIONS MODULE These modules define all variables and potential arrays needed for the calculation of the particular interaction in the DL POLY 4 scope They depend on KINDS F90 Their allocation methods depend on SETUP MODULE e external field module EXTERNAL FIELD MODULE This module defines all variables and potential arrays needed for the application of an exter nal field in the DL_POLY 4 scope It depends on KINDS_F90 and its allocation method on SETUP MODULE e langevin module LANGEVIN MODULE This module defines all variables and arrays needed for the application of NPT and NoT Langevin routines in the DL POLY 4 scope It depends on KINDS_F90 and its alloc
28. kmaxb kmaxc However for example in a cell with dimensions 2A 2B C ie a tetragonal cell longer in the c direction than the a and b directions use 2kmaxa 2kmaxb kmaxc If the values for the kmax used are too small the Ewald sum will produce spurious results If values that are too large are used the results will be correct but the calculation will consume unnecessary amounts of cpu time The amount of cpu time increases proportionally to kmaxa x kmaxb x kmaxc It is worth noting that the working values of the k vectors may be larger than their original values depending on the actual processor decomposition This is to satisfy the requirement that the k vector FFT transform down each direction per domain is a multiple of 2 3 and 5 only which is due to the GPFA code single 1D FFT which the DaFT implementation relies on This allowes for greater flexiblity than the power of 2 multiple restriction in DL POLY 4 predicessor DL POLY _3 As a consequence however execution on different processor decompositions may lead to different working lengths of the k vectors FFT transforms and therefore slightly different SPME forces energies whithin the same level of SPME Ewald precision accuracy specified Note that although the number of processors along a dimension of the DD grid may be any number numbers that have a large prime as a factor will lead to inefficient performance 4 4 Warning and Error Processing 4 4 1 The DL POLY 4 I
29. 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 275 OSTFC Appendix D Message 634 error rigid body unit MUST have at least one non massless site No RB dynamics is possible if all sites of a body are massless as no rotational inertia can be defined Action Examine FIELD for erroneous directives correct and resubmit Message 638 error coincidence of particles in rigid body unit This indicates a corrupted FIELD file as all members of a RB unit must be destinguishable from one another Action Examine FIELD for erroneous directives correct and resubmit 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
30. where Usnet Utetn Ubond Uangl Udind Uinv Unair Utersoff U3_body and U4 body are empirical interaction functions representing ion core shell polarisation tethered particles chemical bonds valence angles dihedral and improper dihedral angles inversion angles two body Tersoff three body and four body forces respectively The first six are regarded by DL POLY 4 as intra molecular interactions and the next four as inter molecular interactions The final term Uextn represents an external field potential The position vectors r rj r and r4 refer to the positions of the atoms specifically involved in a given interaction Almost universally it is the differences in position 12 STFC Section 2 2 that determine the interaction The numbers Nshel Nei Nvond Nangi Naina and Niny refer to the total numbers of these respective interactions present in the simulated system and the indices ishel tteth bond angl tdihd and iiny uniquely specify an individual interaction of each type It is important to note that there is no global specification of the intramolecular interactions in DL_POLY 4 all core shell units tethered particles chemical bonds valence angles dihedral angles and inversion angles must be individually cited The same applies for bond constraints and PMF constraints The indices j and k n appearing in the intermolecular interactions non bonded terms indicate the atoms involved in the interaction T
31. 264 EAM 153 electrostatics 3 7 13 15 18 21 42 116 118 121 122 128 129 161 169 263 external field 3 12 51 52 169 four body 3 12 27 41 42 144 149 161 169 239 251 252 263 265 improper dihedral 3 12 21 22 169 intermolecular 98 intramolecular 27 41 98 inversion 3 12 22 24 41 42 143 169 170 249 264 metal 3 13 27 29 98 100 144 169 171 252 non bonded 3 13 106 107 121 135 140 142 144 169 171 238 tabulated 152 240 Tersoff 3 12 27 37 40 144 148 169 171 249 tether 3 12 26 161 169 170 247 264 tethered 52 three body 3 12 13 16 27 40 41 106 144 148 161 169 239 248 251 264 valence angle 3 12 13 16 17 21 23 40 41 106 139 142 161 169 171 245 van der Waals 13 15 18 21 98 100 129 141 144 261 quaternions 4 91 reaction field 45 46 121 129 rigid body 2 4 55 89 90 170 276 rigid bond see constraints bond stress tensor 15 18 21 24 26 29 33 40 46 50 52 59 71 sub directory 190 193 bench 8 build 8 data 8 execute 8 java 8 public 8 source 8 utility 8 thermostat 4 52 93 117 118 265 266 Nos Hoover 80 86 units DL POLY 7 162 energy 135 pressure 7 81 121 162 temperature 123 user registration 10 Verlet neighbour list 98 170 172 254 WWW iii 2 9 10 296
32. Action 284 OSTFC Appendix D See Message 1001 Message 1070 error allocation failure in ewald module gt ewald allocate kfrz arrays Action See Message 1001 285 Appendix E DL POLY 4 README DL POLY 4 03 The source is in fully self contained free formatted FORTRAN90 MPI2 code specifically FORTRAN90 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 f95 and FORCHECK f90 standards with exception of the FORTRAN2003 feature TR15581 which is very rarely unavailable in the nowadays FORTRAN95 compilers This version supports ALL features that are available in the standard DL POLY Classic version with the exceptions of 1 RIDGID BODIES linked by constraint bonds CB or potential of mean field PMF constraints 2 Truncated octahedral imcon 4 Rhombic Dodecahedral imcon 5 and Hexagonal Prism imcon 7 periodic boundary conventions 3 Classic Ewald and Hautman Klein Ewald Coulomb evaluations 4 Temperature Accelerated Dynamics Hyper Dynamics and solvation energies No previous DL POLY 3 4 feature is deprecated ALL NEW features 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
33. At e e 4 dmass 6 v t exp x t 10 E 3 69 x t SAR e x t Ad F vu 3 70 2 VVI vet say y A IO r t At r t At v t At 3 71 OSTFC Section 3 4 3 RATTLE VV1 4 FF f t At e f t 3 72 5 VV2 K sia v t At e v t At 5 3 73 6 RATTLE_VV2 7 Thermostat Note Exin t At changes inside 3 1 At 2Exin t At 20 H A t 4 Ce xlt zane q TELA 3 At v t At v t At exp x t 120 7 3 74 ser ha et SA gt Mult At 20 The algorithm is self consistent and requires no iterations The LFV implementation of the Nos Hoover algorithm is iterative as an initial estimate of x t at full step is calculated using an unconstrained estimate of the velocity at full step v t 1 FF f t f t At 3 75 2 LFV The iterative part is as follows 1 ER O wt At u t At At na x t 70 1 ret At r t Atu t At 3 76 3 SHAKE 4 Full step velocity 1 1 1 TORE ol 5At u t4 5 0 3 77 5 Thermostat 1 lac x t 5 x t At At ui 1 1 1 x6 e 5 xa At x t z 3 78 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 5 Hynvr HnNve dass XU f ke Text j
34. Constraint algorithms in DL POLY 4 SHAKE RATTLE see Section 3 2 use default iter ation precision of 107 and limit of iteration cycles of 250 Users may experience that during optimisation of a new built system containing constraints simulation may fail prematurely since a constraint algorithm failed to converge In such cases directives mxshak to increase and shake to decrease may be used to decrease the strain in the system and stablise the simulation numerics until equilibration is achieved DL POLY 4 s DD strategy assumes that the local per domain node or link cell density of various system entities i e atoms bonds angles etc does not vary much during a simula tion and some limits for these are assumed empirically This may not the case in extremely non equilibrium simulations where the assumed limits are prone to be exceeded or in some specific systems where these do not hold from the start A way to tackle such circumstances and avoid simulations crash by controlled termination is to use the densvar f option In the SET BOUNDS subroutine DL POLY 4 makes assumptions at the beginning of the simulation and corrects the lengths of bonded like interaction lists arrays mxshl mxcons mxteth mxbond mxangl mxdihd mxinv as well as the lengths of link cell nxlist and domain 129 OSTFC Section 5 1 23 24 nxatms lists arrays when the option is activated with f gt 0 Greater values of f will cor respond to al
35. DI pig riz 2 99 j ljzi It should be noted that the density is determined by the coordination number of the atom defined by pairs of atoms This makes the metal potential dependent on the local density environmental Vi rij is a pair potential incorporating repulsive electrostatic and overlap interactions N is the number of interacting particles in the MD box The types of metal potentials available in DL POLY 4 are as follows 1 EAM potential eam There are no explicit mathematical expressions for EAM potentials so this potential type is read exclusively in the form of interpolation arrays from the TABEAM table file as implemented in the METAL TABLE READ routine Section 5 1 7 The rules for combining the potentials from different metals to handle alloys are different from the FS class of potentials see below 2 Finnis Sinclair potential 13 fnsc Finnis Sinclair potential is explicitly analytical It has the following form Vis re rij c co cirij C3T7 rT d 3 pi ri ri dpap yu m j F p Aypi with parameters co c1 C2 c A d B both c and d are cutoffs Since first being proposed a number of alternative analysical forms have been proposed some of which are descibed below The rules for combining different metal potentials to model alloys are different from the EAM potentials see below 2 100 3 Extended Finnis Sinclair potential 48 exfs It has the following form Vault
36. DL POLY 4 is also available as a CUDA OpenMP port offered as extra source within the source directory see the README txt for further information The purpose of this development a collaboration with the Irish Centre for High End Computing ICHEC http www ichec ie is to harness the power offered by NVIDIA http www nvidia com GPUs Note that no support is offered for these highly specific developments 1 7 Other Information The DL POLY website http www ccp5 ac uk DL POLY provides additional information in the form of 1 Access to all documentation including licences 2 Frequently asked questions 3 Bug reports 4 Access to the DL POLY online forum Daresbury Laboratory also maintains a DL POLY 4 associated electronic mailing list dl poly 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 A news The DL POLY Forum is a web based centre for all DL POLY users to exchange comments and queries You may access the forum through the DL POLY 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 Fields Scope of Chapter This chapter d
37. Section 5 1 4 which is similar to the CONFIG file and contains the perfect crystalline structure of the system 100 STFC Section 4 2 Examples of input files are found in the data sub directory which can be copied into the execute subdirectory using the select macro found in the execute sub directory A successful run of DL POLY 4 will generate several data files which appear in the execute sub directory The most obvious one is the file OUTPUT Section 5 2 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 5 2 8 and REVCON Section 5 2 7 RE VIVE contains the accumulated data for a number of thermodynamic quantities and RDFs and is intended to be used as the input file for a following run It is not human readable The REVCON file contains the restart configuration i e the final positions velocities and forces of the atoms when the run ended and is human readable The STATIS file Section 5 2 11 contains a catalogue of instantaneous values of thermodynamic and other variables in a form suitable for temporal or statistical analysis Finally the HISTORY file Section 5 2 1 provides a time ordered sequence of co
38. The force arrays are used to update the atomic velocities and positions of all the atoms in the domain 4 Any atom which effectively moves from one domain to another is relocated to the neighbour ing processor responsible for that domain It is important to note that load balancing i e equal and concurrent use of all processors is an essential requirement of the overall algorithm In DL POLY 4 this is accomplished quite naturally 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 6 1 2 Distributing the Intramolecular Bonded Terms The intramolecular terms in DL POLY 4 are managed through bookkeeping arrays which list all atoms sites involved in a particular interaction and point to the appropriate arrays of parameters that define the potential Distribution of the forces calculations is accomplished by the following scheme 1 Every atom site in the simulated system is assigned a unique global index number from 1 to N 2 Every processor maintains a list of the local indices of the atoms in its domain This is the local atom list 169 OSTFC Section 6 1 3 Every processor also maintains a sorted in ascending order local list of global atom indices of the atoms in its domain This is the local sorted atom list 4 Every
39. U d 5 41 1 cos 6 Ao 1 cos 26 As 1 c0s 36 2 39 5 Ryckaert Bellemans 41 with fixed constants a f ryck U A a b cos c cos d cos e cos f cos Q 2 40 6 Fluorinated Ryckaert Bellemans 42 with fixed constants a h rbf U A a b cos c cos p d cos e cos f cos 9 g exp h 2 2 41 7 OPLS torsion potential opls U d Ap A 1 cos Ag 1 cos 29 Az 1 cos 3 2 42 19 OSTFC Section 2 2 In these formulae jkn is the dihedral angle defined by Dijkn COS Br Tijs Ps ELT gt 2 43 with 2 44 Lij X Tjk E B rij jk Can E f Y 7 7 n r Tij X T jk r jk xs With this definition the sign of the dihedral angle is positive if the vector product rij X Ljk X Tjk X Len is in the same direction as the bond vector rj and negative if in the opposite direction The force on an atom arising from the dihedral potential is given by ft gra Pom i 2 45 with being one of i j k n and a one of x y z This may be expanded into lo 1 le O _ ile Ae 2 4 r U ijkn sin ijkn Odijkn U Piin Or rij Pilo Tn 240 The derivative of the function B r rjj kn is o 1 o Bre Pu Tiks Tin E x Tj E Cre peces Iri x Pale X ry Org cos ijkn 1 2 1 2 I x ral are Ir Tjj x Ta Ir Xf 2 are aia x inl
40. ble averages and instantaneous pressure and stress build ups at the thermostat boundary Therefore ensembles lose their meaning as such and so does the conserved quantity for true ensembles f the pseudo thermostat option is specified without any type of temperature con trol in CONTROL then both types will be applied in the order Langevin Direct at each time step during the simulation 127 STFC Section 5 1 12 13 14 15 The algorithms are developed in the DL POLY 4 routines PSEUDO VV and PSEUDO LFV re spectively The defects option will trigger reading of REFERENCE see Section 5 1 4 which defines a reference MD cell with particles positions defining the crystalline lattice sites If REFER ENCE is not found the simulation will either i 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 5 1 5 file has been provided Or ii recover using CONFIG see Section 5 1 2 if it is a new simulation run i e restart option is not used in CONTROL or REVOLD has not been provided The actual defect detection is based on comparison of the simulated MD cell to the reference MD cell based on a user defined site interstitial cutoff Rey Min 0 3 reut 3 A Ra lt Min 1 2 Tcut 2 A 5 5 with a default value of Min 0 75 reut 3 If the supplied value exceeds the limits the simulation execution will halt If
41. in seconds since the beginning of the job system volume in core shell temperature in Kelvin configurational energy due to core shell potentials core shell potential contribution to the virial 161 STFC Section 5 2 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 columns Immediately below these three lines of output the rolling averages of the same variables are also given The maximum number of time steps used to calculate the rolling averages is controlled by the directive stack in file CONTROL see above and listed as parameter mxstak in the SETUP MODULE file see Section 6 2 2 The default value is mxstak 100 Energy Units The energy unit for the energy and
42. is specified with zero frequency it is only applied at timestep zero if equilibration gt steps ie optimise structure at start only This is equvalent to using the optimise directive In this way it can be used as a configuration optimiser at the beginning of the equlibration period or when a dry run steps 0 is performed i e equilibrate without any actual dynamics 5 The variable timestep or also timestep variable option requires the user to specify an initial guess for a reasonable timestep for the system in picoseconds The simulation is unlikely to retain this as the operational timestep however as the latter may change in response to the dynamics of the system The option is used in conjunction with the default values of maxdis 0 10 and mindis 0 03 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 integra
43. nvt gi vv o comms module o config module o domains module o kinds f90 0 kinetic module o langevin module o rigid bodies module o Setup module o site module o nvt hO lfv o comms module o config module o kinds f90 0 kinetic module o Setup module o site module o nvt_h0_scl o config module o kinds f90 0 kinetic module o setup module o nvt hO vv o comms module o config module o kinds f90 0 kinetic module o Setup module o site module o nvt hi lfv o comms module o config module o domains module o kinds f90 0 kinetic module o rigid bodies module o setup module o site module o nvt hi scl o config module o kinds f90 0 kinetic module o rigid bodies module o setup module o nvt hi vv o comms module o config module o domains module o kinds f90 0 kinetic module o rigid bodies module o setup module o site module o nvt 10 lfv o comms module o config module o kinds f90 0 kinetic module o Setup module o site module o 208 OSTFC Appendix C nvt 10 vv o comms module o config module o kinds f90 0 kinetic module o Setup module o site module o nvt l1 lfv o comms module o config module o domains module o kinds f90 0 kinetic module o rigid bodies module o setup module o site module o nvt li vv o comms module o config module o domains module o kinds f90 0 kinetic module o rigid bodies module o setup module o site module o parallel fft o comms module o gpfa module o kinds f90 0 setup module o parse_module o comms m
44. o LDFLAGS 03 L usr local mpich gm pgroupi21 7b lib 1mpich lfmpich lmpichf90 L usr local gm binary lib 1gm L usr local lib FC usr local mpich gm pgroup121 7b bin mpif90 c FCFLAGS fast Knoieee Mdalign 03 EX EX BINROOT BINROOT TYPE Franklin SUNfire cluster setenv HPCF_MPI yes franklin MAKE LD opt SUNWhpc bin mpf90 o LDFLAGS stackvar fsimple 1 x03 xarch v9b DHPCF_MPI lmpi xlic_lib sunperf FC opt SUNWhpc bin mpf90 c FCFLAGS stackvar fsimple 1 x03 xarch v9b xchip ultra xlic lib sunperf xalias actual fpover ftrap none fnonstd libmil dalign I opt SUNWhpc HPC5 0 include v9 EX EX BINROOT BINROOT TYPE hpcx MAKE LD mpxlf90 r o LDFLAGS 03 q64 qmaxmem 1 FC mpx1f90_r qsuffix f f90 c FCFLAGS 03 q64 qmaxmem 1 qarch pwr5 qtune pwr5 qnosave EX EX BINROOT BINROOT TYPE 199 OSTFC Appendix C hpcx debug MAKE LD mpxlf90 r o LDFLAGS g C q64 00 lessl lhmd FC mpx1f90_r qsuffix f f90 c FCFLAGS g C q64 00 qarch pwr5 qtune pwrb qnosave EX EX BINROOT BINROOT TYPE BGL MAKE LD bgl BlueLight ppcfloor bglsys bin mpixlf95 o LDFLAGS 03 qhot qarch 440d qtune 440 FC bg1 BlueLight ppcfloor bglsys bin mpixlf95 c FCFLAGS 03 qhot qarch 440d qtune 440 EX EX BINROOT BINROOT TYPE BG
45. pmass the barostat mass rp a specified time constant for pressure fluctuations P the instantaneous pressure equation 3 95 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 mass t 2 t JiNPT HNve E Di pa ui F Post V t f 1 ks Text J x s ds 3 141 where f is the system s degrees of freedom equation 3 11 The VV implementation of the Nos Hoover algorithm only requires iterations if bond or PMF constraints are present 5 until satisfactory convergence of the constraint forces is achieved These are with respect to the pressure i e n t in the first part VV1 RATTLE VV1 The second part is conventional VV24 RAT TLE V V2 as at the end the velocities are scaled by a factor of x 1 Thermostat Note 2Ex n t changes inside At 2 Exin t Pmass n t 20 kB Text 8 dmass x t At T uy exp x t 340 x TO 3 142 1 1 At 2Ekin t t 2o k Tx x t 2At yx t At 4 kin f Pmass ME 20 kg Text i 8 8 mass 2 Barostat Note Exin t and P t have changed and change inside n ex xtt amp 340 5 no At 3 P t Pex V t 4 Pmass qt Gt n0 n t iat c exp x t4 AD I n t 4 1 At 8 4 RS exp atta Tat 3 v t 3 143 n t Tat c exp x t 4 104 x n t 4 Tat n t At t4
46. see section 5 1 2 but contains only atomic position data and will never contain ei ther velocity or force data i e parameter levcfg is always zero In addition three extra numbers appear on the end of the second line of the file 1 an integer indicating the number of minimisation cycles required to obtain the structure 2 the configuration energy of the minimised configuration expressed in DL POLY 4 units 1 3 7 and 3 the configuration energy of the initial structure expressed in DL POLY 4 units 1 3 7 5 2 6 The OUTPUT File The job output consists of 7 sections Header Simulation control specifications Force field specifi cation System specification Summary of the initial configuration Simulation progress Sample of the final configuration Summary of statistical data and Radial distribution functions and Z density profile These sections are written by different subroutines at various stages of a job Creation of the OUTPUT file always results from running DL POLY 4 It is meant to be a human readable file destined for hardcopy output 5 2 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 5 2 6 2 Simulation Control Specifications Echoes the input from the CONTROL file Some variables may
47. win debug MAKE LD f95 o LDFLAGS 00 C all C undefined FC f95 c N FCFLAGS 00 C all C undefined EX EX BINROOT BINROOT TYPE Default code master message check 0BJ MOD 0BJ ALL LD EXE LDFLAGS 0BJ MOD 0BJ ALL Message message echo DL POLY 4 compilation in SRL1 mode echo echo Use mpi must change to Use mpi_module in comms_module f90 echo Check that a platform has been specified check if test FC undefined then echo echo FORTRAN90 compiler unspecified echo echo Please edit your Makefile entries echo exit 99 fi X if test LD undefined then echo echo FORTRAN90 Linker loaDer unspecified echo echo Please edit your Makefile entries echo exit 99 fi mkdir p BINROOT touch dl_poly f90 Declare rules f90 0 FC FCFLAGS f90 221 OSTFC Appendix C Declare dependencies 0BJ ALL 0BJ MOD 228 OSTFC Appendix C Makefile SRL2 Master makefile for DL POLY 4 03 serial version 2 Author I T Todorov june 2012 Define default settings SHELL bin sh SUFFIXES SUFFIXES f90 o BINROOT execute EX DLPOLY Z EXE BINROOT EX TYPE master FC undefined LD undefined Define object files OBJ_MOD kinds_f90 0 mpi_module o comms_module o setup_module o parse
48. with energy E E gt 0 in kilo eV and direction vector x y z from the Cartesian origin centre of the MD box defaults i 1 j 0 E 0 25 1 y 1 z 1 set the type of Verlet integrator where string can only be leapfrog or velocity as the later is the default 118 OSTFC Section 5 1 io read method j kle io write method rp type j k le job time f maxdis f set the the general I O read interface to method mpiio for MPI I O direct for parallel direct access FORTRAN I O or master for traditional master I O or netcdf for netCDF I O provided DL_POLY 4 is compiled in a netCDF enabled mode default mpiio j reader count 1 lt j lt job size default j gInt Log Min job size 2Vjob size Log 2 is the designated number of processes to carry out I O read operations simultaneously NOTE that k is not applicable for the master method k batch size 1 lt k lt 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 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 Y es default N set the the general I O write interface to method mpiio for MPI I O direct for parallel direct access FORTRAN I
49. 2 real second potential parameter see Table 5 10 variable 3 real third potential parameter see Table 5 10 variable 4 real 1 4 electrostatic interaction scale factor variable 5 real 1 4 van der Waals interaction scale factor variable 6 real fourth potential parameter see Table 5 10 variable 7 real fifth potential parameter see Table 5 10 The meaning of the variables 1 3 6 7 is given in Table 5 10 The variables 4 and 5 specify the scaling factor for the 1 4 electrostatic and van der Waals non bonded interactions respectively This directive and associated data records need not be specified if the molecule contains no dihedral angle terms See the note on the atomic indices appearing under the shell directive above 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 5 11 index 1 i integer first atomic site index central site index 2 7 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 5 11 variable 2 real potential parameter see Table 5 11 variable 3 real potential parameter see Table 5 11 The meaning of the variables 1 2 is given in Table 5 11 This directive and associated data records need not be specified if the molecule contains no inversion angle terms See the note on the atomic ind
50. 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 Ojik 3 Ojik bo 2 152 2 Truncated harmonic thrm k U Ojik 3 ji 00 exp r r3 2 153 3 Screened Harmonic shrm k U Ojik 5 Ojik 69 exp rij p1 rik p2 2 154 4 Screened Vessal 36 bvs1 k 2 Ojik i ji exp rij p1 rix p2 2 155 40 STFC Section 2 3 5 Truncated Vessal 37 bvs2 U Ojik k 05 x 0 ix 00 Ojik 6o 27 a 37 Oir 6o n 69 exp ri ik 0 2 156 6 Dreiding hydrogen bond 19 hbnd U Ojiz Das cost jin 5 Rne T jx 6 Rpo rr 2 187 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 potentia
51. 3 5 SO nt HO CVA Temo VO The changes include one extra dependence to the velocity and barostat equations and removal of the centre of mass variable Ry t dependence in the position equation The modifications in for the VV couched algorithms are of the following sort 1 At P t Pa 2Epin t 1 ol lt T E 1 mit 144 3 165 1 r t At exp Int At At r t At v t 5 At for the isotropic cell fluctuations case and n 00 c aft e RUM 2Erin t 1 4 Pmass ff Pmass v t exp ut Tat zm nl 140 zi u t 3 166 1 1 r t At exp nt 940 At r t At u t 940 for the anisotropic cell fluctuations case Similarly for the LFV couched algorithms these are 1 1 n t z exp x t At t 540 P t Pot 3 Ekin t 1 Pmass Pmass v t 4 2A wt At At E fx 1 gt n o 70 3 167 r t At r t At u t At t At r t Ax At svi for the isotropic cell fluctuations case and n t jM lt exp x t At nit At ie ee Px V t 1 x 2Erin t 1 Pmass f Pmass u t At v t At At ad xo 1 n t uil 1 z 3 168 r t At rt At u t SAO tlt 340 rlt sat for the anisotropic cell fluctuations case This ensemble is optionally extending to constant normal pressure and constant surface area NP AT 60 by semi isotropic constraining of the barostat equation of motion and sligh
52. 5 k R2 In 42 rs Al lt Ro 2 10 ij E oo les Al 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 2 91 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 0 5 Ro with a default of zero Age faut 0 14 OSTFC Section 2 2 In these formulae r is the distance between atoms labelled and j fep S 2 11 where r is the position vector of an atom labelled The force on the atom j arising from a bond potential is obtained using the general formula f xc EE rig 2 12 The force f acting on atom 1 is the negative of this The contribution to be added to the atomic virial is given by with only one such contribution from each bond The contribution to be added to the atomic stress tensor is given by poe 4 2 14 where a and f 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 ro is handled as a special case of bond potentials As a consequence dis tance restr
53. 6 6 8 which is equvalent to spme sum 0 35 12 12 16 would set a 0 35 A kmaxa 12 kmaxb 12 and kmaxc 16 The quickest check on the accuracy of the Ewald sum is to compare the coulombic energy U and virial W in a short simulation Adherence to the relationship U W shows the extent to which the Ewald sum is correctly converged These variables can be found under the columns headed eng_cou and vir cou in the OUTPUT file see Section 5 2 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 damped real space sum and a reciprocal space sum The rate of convergence of both sums is governed by a Evaluation of the real spa
54. Brookhaven database use the utility PROSEQ to generate the file CONFIG This will then function as input for DL POLY 4 Some caution is required here however as the protein structure may not be fully determined and atoms may be missing from the CONFIG file If you have the edit out file produced by AMBER for your molecule use this as the CON NECT_DAT input file for the utility AMBFORCE AMBFORCE will produce the DL POLY 4 FIELD and CONFIG files for your molecule If you do not have the edit out file things are a little more tricky particularly in coming up with appropriate partial charges for atomic sites However there are a series of utilities that will at least produce the CONNECT DAT file for use with AMBFORCE We now outline these utilities and the order in which they should be used 106 OSTFC Section 4 3 If you have a structure from the Cambridge Structural database CSDB then use the utility FRACCON to take fractional coordinate data and produce a CONNECT_DAT and ambforce dat file for use with AMBFORCE Note that you will need to modify FRACCON to get the AMBER names correct for sites in your molecule The version of FRACCON supplied with DL_POLY 4 is specific to the valinomycin molecule If you require an all atom force field and the database file does not contain hydrogen positions then use the utility FRACFILL in place of FRACCON FRACCON produces an output file HFILL which should then be used as input
55. D Message 1025 error allocation failure in config module gt allocate config arrays Action See Message 1001 Message 1026 error allocation failure in site module gt allocate site arrays Action See Message 1001 Message 1027 error allocation failure in tersoff module gt alocate tersoff arrays Action See Message 1001 Message 1028 error deallocation failure in angles module gt deallocate angles arrays Action See Message 1002 Message 1029 error deallocation failure in bonds module gt deallocate bonds arrays Action See Message 1002 Message 1030 error deallocation failure in core shell module gt deallocate core shell arrays Action See Message 1002 Message 1031 error deallocation failure in tethers module gt deallocate tethers arrays Action See Message 1002 Message 1032 error deallocation failure in constraints module gt deallocate constraints arrays Action See Message 1002 281 OSTFC Appendix D Message 1033 error deallocation failure in dihedrals module gt deallocate dihedrals arrays Action See Message 1002 Message 1034 error deallocation failure in inversions module gt deallocate inversions arrays Action See Message 1002 Message 1035 error allocation failure in defects module gt allocate defects arrays Action See Message 1
56. 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 260 OSTFC Appendix D Place a timestep directive in the CONTROL file with the required timestep specified Message 382 error simulation cutoff not specified DL POLY 4 has failed to find a cutoff directive in the CONTROL file Action Place a cutoff directive in the CONTROL file with the required forces cutoff specified Message 387 error system pressure not specified The target system pressure has not been specified in the CONTROL file Applies to NPT simula tions only Action Insert a press directive in the CONTROL file specifying the required system pressure Message 390 error npt nst ensemble requested in non periodic system A non periodic system has no defined volume hence the NPT algorithm cannot be applied Action Either simulate the system with a periodic boundary or use another ensemble Message 392 error too many link cells requested The number of link cells required for a given simulation exceeds the number allowed for by the DL_POLY 4 arrays Probable cause your system has expanded unacceptably much to DL POLY_4 This may not be physically sensible Action Consider using densvar opti
57. Key a sis a A a asda d aa ok x xD exc Aeg e exe dE dodi e ru 126 Electrostalies Bey sta i ina ed p uu Eleg piei g A Ple Ke ERES a 129 CONFIG File Key record d SO2o 24d E OR ded Be Ee a 133 Periodic Boundary Key record 2 o e osse ua 133 Tetherine Potentials 2 asa ag 4x Pee e bee DA Ra a d 139 Chemical Bond Potentials i o s sop karu e m Ro God A e Ro eR la XU d 140 Valence Angle Potentials 22222 142 Dihedral Angle Potentials e 143 Inversion Angle Potentials a 143 Pan Potentials 2k uox oe of ROXURGRUERRECR Rie cm oec EOS DECR Iden REIR COR a 145 Metal Potential s sug ga a i e REDE dee ERO a 146 Tersotl Potential s socs gala ea A AA A 148 Three body Potentials 2 i nasede sa A OR Ew Dea mons d 149 Four body Potentials sr sone a sng kaine ale ROUX a a em So eS E US d 149 External Fieldsi edo sn dk das Soe Rex mex ea A de REOR i e ce e 150 xi List of Figures 2 1 2 2 2 3 2 4 2 5 2 6 3 1 5 1 A l A 2 A 3 The interatomic bond vector s ada gii d mira Wapa ag aaa a i 13 The valence angle and associated vectors ee 16 The dihedral angle and associated vectors 22e 19 The L and D enantiomers and defining vectors o e 22 The inversion angle and associated vectors e 22 The vectors of the calcite potential ee 25 The SHAKE RATTLE_VV1 schematics and associated vectors 57 DL POLY 4 input left and output
58. Message 560 error rdef found to be gt half the shortest interatomic distance in REFERENCE The defect detection option relies on a cutoff rdef to define the vicinity around a site defined in REFERENCES in which a particle can claim to occupy the site Evidently rdef MUST be 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 prop erty recalculation No structural property has been specified for this option to activate itself Action In CONTROL specify properties for recalculation RDFs z density profiles defect detection or alternatively remove the option Message 585 error end of file encountered in HISTORY file This means that the HISTORY file is incomplete in some way Either should you abort the replay HISTORY option or provide a fresh HISTORY file before restart Action In CONTROL specify properties for recalculation RDFs z density profiles defect detection or alternatively remove the option Message 590 error uknown minimisation t e only force ener and dis 9 9 tance are r
59. 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 5 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 F F q E 2 201 2 Oscillating shear oshr E Acos 2n7 z Lz 2 202 3 Continuous shear shrx 1 12 A 2 203 vp GAL gt z 2 203 4 Gravitational field grav F F m G 2 204 5 Magnetic field magn Fi Fit qi vi x H 2 205 6 Containing sphere sphr E A Ro r r gt Ras 2 206 7 Repulsive wall zbnd F A zo 2 ig o S 2 207 51 OSTFC Section 2 7 It is recommended that the use of an external field should be accompanied by a thermostat this does not apply to examples 6 and 7 since these are conservative fields The Oscillating shear field should be used with orthorhombic cell geometry imcon 1 2 and Continuous shear field with slab cell geometry imcon 6 The user is advised to be careful with units In DL_POLY 4 external field forces are handled by the routines EXTERNAL FIELD APPLY and EX TERNAL_FIELD_CORRECT 2 7 Treatment of Frozen Atoms Rigid Body and Co
60. Table 5 16 Four body Potentials key potential type Variables 1 2 functional formi harm Harmonic k Qo U p 5 do hcos Harmonic cosine k do U k cos cos o plan Planar A U A 1 cos t is the i j k l four body angle 149 STFC Section 5 1 5 1 3 3 External Field The presence of an external field is flagged by the directive extern The following line in the FIELD file must contain another directive indicating what type of field is to be applied followed by the field parameters The variables pertaining to each field potential are described in Table 5 17 Note only one type of field can be applied at a time Note that external force parameters are read in terms of the specified energy units and the general DL_POLY units so that the two sides of the equation defining the field are balanced Table 5 17 External Fields key potential type Variables 1 4 functional formi elec Electric Field Ex Ey Ez F qE oshr Oscillating Shear Alon F A cos 2nm z L shrx Continuous Shear A 2 Ale lz gt zo grav Gravitational Field Gz Gy Gz F mG magn Magnetic Field Hs Ay H F q ux dH sphr Containing Sphere A Ro n Rat F A Ro T r gt Rout zbnd Repulsive Wall A z p F A z 2z pz gt pzo 5 1 3 4 Closing the FIELD File The FIELD file must be closed with the directive close
61. Trachenko amp M T Dove J Mater Chem 16 1611 1618 2006 Warnings 1 DL POLY 4 can produce index ordered REVCON HISTORY and MSDTMP files which are restartable by DL POLY Classic Although such 286 OSTFC Appendix E 2 3 4 printed outputs look unscrambled the actual printing process is not Unscrambled printing is slightly more expensive than natural scrambled printing The cost time wise is little lt 1 but HD space wise is approximately 20 This is due to the necessary addition of blanks at the end of data record included to align the ASCII lines of output files human readable to a constant length Printing scrambled outputs is optional Note that these too have blanks aligned records The parallel I 0 ensures i writing speeds of 1075 to 1076 particle per second with optimal number of writers and ii reading speeds of 1074 to 10 5 particles per second per reader For more information on I 0 options consult the user manual REVIVE files produced by different versions are not compatible Furthermore restarting runs across different sub versions may not be possible The DL POLY 4 parallel performance and efficiency are considered very good to excellent as long as i all CPU cores are loaded with no less than 500 particles each and ii the major linked cells algorithm has no dimension less than 4 Although DL POLY 4 can be compiled in a serial mode users are advised to consider DL POLY C
62. Ua mi Ra dit s 5 4 Care must be exercised to prevent introduction of non zero net momentum Users are reminded to use for target temperature the temperature at which the original system was equilibrated in order to avoid simulation instabilities The effect of this algorithm is to relax the buffer region of the system on a local scale and to effectively dissipate the incoming excess kinetic energy 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 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 ensem
63. a word must not exceed 40 characters in length Words are recognised as such by separation by one or more space characters The contents of the file are variable and are defined by the use of directives Additional information is associated with the directives 5 1 3 2 Definitions of Variables in the FIELD File The file divides into three sections general information molecular descriptions and non bonded interaction descriptions appearing in that order in the file 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 135 OSTFC Section 5 1 a eV for electron Volts b kcal mol for k calories per mol 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
64. amended array dimension a direction SPME FFT amended array dimension b direction SPME FFT amended array dimension c direction SPME FFT original array dimension a direction SPME FFT original array dimension b direction SPME FFT original array dimension c direction max number of specified core shell unit types in system max number of core shell units per node max number of related core shell units 1 1 max number of specified bond constraints in system max number of constraint bonds per a node max number of related constraint units 64 1 max number of shared particles per node mxshl mxcons mxlrgd mxrgd Max 2 7 2 n 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 14 1 max number of specified tethered potentials in system max number of tethered atoms per node max number of related tether units 14 1 max number of parameters for tethered potentials 3 180 OSTFC Section 6 2 mxtbnd mxbond mxfbnd mxpbnd mxtang mxangl mxfang mxpang mxtdih mxdihd mxfdih mxpdih mxtinv mxinv mxfinv mxpinv mxgrid mxrdf mxgrdf mxvdw mxpvdw mxmet mxpmet mxter mxpter mxtbp mx2tbp mxptbp mxfbp mx2fbp mxpfbp mxpfld
65. and contributions to the stress tensor are obtained in a manner analagous to that for a bond constraint see previous section The only difference is that the constraint is now applied between the centres of two groups which need not be atoms alone DL_POLY 4 reports the PMF constraint virial Wp y p for each simulation Users can convert this to the PMF constraint force from WPMF dPMF where is dpmr the constraint distance between the two groups used to define the reaction coordi nate GpMF 3 22 The routines PMF SHAKE and PMF RATTLE are called to apply corrections to the atomic positions and respectively the atomic velocities of all particles constituting PMF units In presence of both bond constraints and PMF constraints The constraint procedures i e SHAKE or RATTLE for both types of constraineds are applied iteratively in order bonds PMFs until convergence of Wpyp reached The number of iteration cycles is limited by the same limit as for the 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 six different thermostats Evans Gaussian constrain
66. 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 l i j k n are calculated using the above formulae it is easily seen that the contribution to be added to the atomic stress tensor is given by o r8 prah ere 2 67 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 24 OSTFC Section 2 2 Figure 2 6 The vectors of the calcite potential 2 2 8 The Calcite Four Body Potential This potential 43 44 is designed to help maintain the planar structure of the carbonate anion CO3 7 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 Uabcd U Au E But gt 2 68 where the displacement u is given by u Tab t The x T bd 2 69 Tbe X Toal Vectors Tap ac and raq define bonds between the central atom a and the peripheral atoms b c and d Vectors ry and rpa define the plane and are related to the bond vectors by The Lac Tab Tod Tad Tab 2 70 In what follows it is convenient to define the vector product appearing in both the numerator and
67. be specified once If DL POLY 4 encounters more than one molecules directive it will terminate execution Action Locate the extra molecule directive in the FIELD file and remove and resubmit Message 12 error unknown molecule directive in FIELD file Once DL POLY 4 encounters the molecules directive in the FIELD file it assumes the following records will supply data describing the intramolecular force field It does not then expect to encounter directives not related to these data This error message results if it encounters a unrelated directive The most probable cause is incomplete specification of the data e g when the finish directive has been omitted Action Check the molecular data entries in the FIELD file 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 238 OSTFC Appendix D Message 14 error too many unique atom types specified This should never happen This error most likely arises when the FIELD file or and DL POLY 4 executable are corrupted Action Recompile the program or recreate the FIELD file If neither of these works send the pro
68. by the defects directive in the CONTROL file with the following information for each configuration record i timestep a8 the character string timestep nstep integer the current time step tstep real integration timestep ps time real elapsed simulation time ps imcon integer periodic boundary key see Table 5 6 rdef real site interstitial cutoff A record ii defects aT the character string defects ndefs integer the total number of defects interstitials al3 the character string interstitials ni integer the total number of interstitials vacancies a9 the character string vacancies nv integer the total number of vacancies record iii cell 1 real x component of a cell vector 157 OSTFC Section 5 2 cell 2 real y component of a cell vector cell 3 real z component of a cell vector record iv cell 4 real x component of b cell vector cell 5 real y component of b cell vector cell 6 real z component of b cell vector record v cell 7 real x component of c cell vector cell 8 real y component of c cell vector cell 9 real z component of c cell vector This is followed by the ni interstitials for the current timestep as each interstitial has the following data lines record a atmnam 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
69. changes inside and Ry t drown from Gauss 0 1 is carried over from the previous half timestep x t TAi x t exp I zi E Tex 1 exp y I R t dmass At 2 Exi t 2c 4 4 Imass v t lt v t exp x t 144 x 3 85 1 1 kp Tux At x t 5At x t A0 exp y ley B 1 exp y R t Qmass At 2 Evi t 2c 4 mass 69 OSTFC Section 3 4 2 VVI At fit wt tan e w AE O EX Ay Es HOMES SA 3 86 3 RATTLE_VV1 4 FF fet AD e f 3 87 5 VV2 R T vet At vlt 346 E 2 3 88 6 RATTLE VV2 7 Thermostat Note Exin t At changes inside and R t At is drown anew from Gauss 0 1 and is to be carried over the next half timestep 1 At Tex A x t Ft c x t At exp y 1 E 1 exp y zl Ry t At Imass At 2Ekin t 20 4 Imass ag se exp Xd At x 3 89 At T A XM t JA exp i 1 E 1 exp R t At Qmass At 2 E 2c 4 Qmass 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 e ft At 3 90 2 LFV The iterative part is as follows ult 344 i DAI LA E ch sto r t At e r t At u t 346 3 91 3 SHAKE 4 Full step velocity u t
70. 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 n is the number of tethered atoms in the molecule It is followed n records specifying the tehered sites in the molecule tether key ad potential key see Table 5 7 index 1 i integer atomic site index variable 1 real potential parameter see Table 5 7 variable 2 real potential parameter see Table 5 7 138 OSTFC Section 5 1 The meaning of these variables is given in Table 5 7 This directive and associated data records need not be specified if the molecule contains no flexible chemical bonds See the note on the atomic indices appearing under the shell directive above Table 5 7 Tethering Potentials key potential type Variables 1 3 functional form harm Harmonic k Dre l k ri r 9y rhrm Restraint k fre U r i k ri rt ri rf 9 lt r U r 3 k r2 k re ri 120 ro ri r 9 m quar Quartic k k k U r 5 r ri i ri r9 ri ri 9 bonds n 10 where n is the number of flexible chemical bonds in the molecule Each of the subsequent n records contains bond key index 1 i index 2 7 variable 1 variable 2 variable 3 variable 4 a4 integer integer real real real real potential key see Table 5 8 first atomic site index in bond second atomic
71. debug echo echo Please examine this Makefile s targets for details echo If no target suits your system then create your own echo using the advice in generic target template provided echo in this Makefile under the entry uknown_platform echo Fetch MPI SERIAL subroutines FILES_SERIAL MAKE links_serial links_serial for file in FILES_SERIAL do echo linking to file rm f file 225 OSTFC Appendix C ln s SERIAL file file done Fetch the Velocity Verlet subroutines FILES VV MAKE links vv links vv for file in FILES VV do echo linking to file rm f file 1n s VV file file done Fetch the LeapFrog Verlet subroutines FILES_LFV MAKE links_lfv links_lfv for file in FILES_LFV do echo linking to file rm f file ln s LFV file file done Clean up the source directory clean rm f 0BJ MOD 0BJ ALL FILES VV FILES LFV FILES SERIAL mod Generic target template uknown platform MAKE LD path to FORTRAN90 Linker loaDer LDFLAGS appropriate flags for LD FC path to FORTRAN90 compiler FCFLAGS appropriate flags for FC EX EX BINROOT BINROOT TYPE System specific targets follow 226 OSTFC Appendix C MAKE LD f95 o LDFLAGS 03 FC f95 c FCFLAGS 03 EX EX BINROOT BINROOT TYPE
72. denominator of equation 2 69 as the vector weg vis Wed The X Tha gt 2 71 We also define the quantity y u as y u 2Au 4Bu 2 72 The forces on the individual atoms due to the calcite potential are then given by f IU Wea f Yea X ray Uea y u Wea f Ere X Cab Uda Y U Wed 2 73 Es Si J 25 OSTFC Section 2 3 where weg w 4 and Weg Weq Wea The virial contribution Vatea u is given by Wabea u 2Au 4But 2 74 and the stress tensor contribution oS u by u y u oa TI Woy Wey gt 2 75 Wed In DL POLY 4 the calcite forces are handled by the routine INVERSIONS FORCES which is a con venient intramolecular four body force routine However it is manifestly not an inversion potential as such 2 2 9 Tethering 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 funct
73. elec no index no strict enforces the direct calculation of metal interactions defined by explicit potential forms i e it will not work for metal alloy systems using the EAM TABEAM set minimum distance allowed in variable timestep control to f default f 0 03 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 1075 lt f lt 0 1 default f 0 005 the lowest string CGM minimised configuration during equlibration is saved in a file CFGMIN which has the same format as CONFIG write MSDTMP file containing particles individual V M SD in and Tmean in Kelvin with controls i start timestep for dumping configurations default i 0 j timestep interval between configurations default j 1 act exactly the same as ewald evaluate every n set FIQA iterations limit to n default n 100 set shake rattle iterations limit to n default n 250 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 i j k and FIELD ij_k for a volumetrically expanded versio
74. 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 268 OSTFC Appendix D Consider the physical concept you are trying to imply in the simulation Increase MD cell dimen sions Message 494 error overconstrained PMF units PMF units are oveconstrained Action DL POLY 4 algorithms cannot handle overconstrained PMF units Decrease the number of con straints on the PMFs Message 497 error pmf quench failure Action See Message 515 Message 498 error shake algorithm pmf shake failed to converge Action See Message 515 Message 499 error rattle algorithm pmf rattle failed to converge Action See Message 515 Message 500 error PMF unit of zero length is not permitted PMF unit of zero length is found in FIELD PMF units are either a single atom or a group of atoms usually forming a chemical molecule Action Correct the erroneous entries in FIELD Message 501 error coincidence of particles in PMF unit A PMF unit must be constituted of non repeating particles Acti
75. f90 0 kinetic module o rigid bodies module o setup module o nvt bi vv o comms module o config module o domains module o kinds f90 0 kinetic module o rigid bodies module o setup module o site module o nvt eO lfv o comms module o config module o kinds f90 0 kinetic module o Setup module o site module o nvt eO scl o comms module o config module o kinds f90 0 setup module o nvt eO vv o comms module o config module o kinds f90 0 kinetic module o Setup module o site module o nvt ei lfv o comms module o config module o domains module o kinds f90 0 kinetic module o rigid bodies module o setup module o site module o nvt ei scl o comms module o config module o kinds f90 0 rigid bodies module o setup module o nvt ei vv o comms module o config module o domains module o kinds f90 0 kinetic module o rigid bodies module o setup module o site module o nvt_g0_lfv o comms module o config module o kinds f90 0 kinetic module o langevin_module o setup module o site module o nvt gO0 scl o config module o kinds f90 0 kinetic module o setup module o nvt_g0_vv o comms module o config module o kinds f90 0 kinetic module o langevin_module o setup module o site module o nvt gi lfv o comms module o config module o domains module o kinds f90 0 kinetic module o langevin module o rigid bodies module o Setup module o site module o nvt gi scl o config module o kinds f90 0 kinetic module o rigid bodies module o setup module o
76. 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 Graphical User Interface 21 4 3 5 Choosing Ewald Sum Variables 4 3 5 1 Ewald sum and SPME This section outlines how to optimise the accuracy of the Smoothed Particle Mesh Ewald sum parameters for a given simulation As a guide to beginners DL POLY 4 will calculate reasonable parameters if the ewald precision directive is used in the CONTROL file see Section 5 1 1 A relative error see below of 107 is normally sufficient so the directive 107 OSTFC Section 4 3 ewald precision 1d 6 will make DL POLY 4 evaluate its best guess at the Ewald parameters o 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 four parameters may also be set explicitly by the ewald sum directive in the CONTROL file For example the directive ewald sum 0 35
77. 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 erecute 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 routines are unsupported and come without any guarantee or liability what soever They should be regarded as potentially useful resources to be hacked into shape as needed by the user This directory is available from the CCP5 Program Library by direct FTP see below 1 4 8 The java Sub directory The DL_POLY 4 Java Graphical User Interface GUI is based on the Java language developed by Sun The Java source code for this GUI is to be found in this sub directory The source is complete and sufficient to create a working GUI provided the user has installed the Java Development Kit 1 3 or above which is available free from Sun at http java su
78. 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 256 OSTFC Appendix D 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 CONFIG is ill defined Action Regenerate CONFIG and FIELD and resubmit Message 130 error bond angle unit diameter gt rcut the system cutoff This could only happen if FIELD and CONFIG do not match each other or if CONFIG is ill defined Action Regenerate CONFIG and FIELD and resubmit Message 132 error dihedral angle unit diameter gt rcut the system cutoff This could only happen if FIELD and CONFIG do not match each other or if CONFIG is ill defined Action Regenerate CONFIG and FIELD and resubmit Message 134 error inversion angle unit diameter gt rcut the system cutoff This could only happen if FIELD and CONFIG do not match each other or if CONFIG is ill defined Action Regenerate CONFIG and FIELD and resubmit Message 141 error duplicate metal potential specified During reading of metal potentials pairs of atom types in FIELD DL POLY 4 has found a dupli cate pair of atoms in the list
79. gt re quar Quartic k ro k k Us E rij ro E rij ro qur rij ro buck Buckingham A p C U r A exp 3 bck l coul Coulomb k U r k PE di 24 cul AND fene Shifted FENE k RJ A U r 0 5 k Ro In x sg lt Ro A fne U r e00 ri gt A FA 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 140 STFC Section 5 1 11 12 The meaning of these variables is given in Table 5 9 This directive and associated data records need not be specified if the molecule contains no angular terms See the note on the atomic indices appearing under the shell directive above dihedrals n where n is the number of dihedral interactions present in the molecule Each of the following n records contains dihedral key a4 potential key see Table 5 10 index 1 i integer first atomic site index index 2 7 integer second atomic site index central site index 3 k integer third atomic site index index 4 1 integer fourth atomic site index variable 1 real first potential parameter see Table 5 10 variable
80. has found more than one bonds entry per molecule in FIELD Action Correct the erroneous part in FIELD and resubmit 242 OSTFC Appendix D Message 38 error transfer array exceeded in metal ld export This should never happen Action Consider using densvar option in CONTROL for extremely non equilibrium simulations Alterna tively increase mxbuff in SET BOUNDS recompile and resubmit Send the problem to us if this is persistent Correct the erroneous entry in FIELD and resubmit Message 39 error density array exceeded in metal ld export This should never happen Action You might consider using densvar option in CONTROL Send the problem to us if this is persistent Message 40 error too many bond constraints specified This should never happen Action Recompile the program or recreate the FIELD file If neither of these works send the problem to us Message 41 error too many bond constraints per domain DL_POLY 4 limits the number of bond constraint units in the system to be simulated actually the number to be processed by each node and checks for the violation of this Termination will result if the condition is violated Action Use densvar option in CONTROL to increase mxcons alternatively increase it by hand in SET BOUNDS and recompile and resubmit Message 42 error undefined direction passed to deport atomic data This should never happen Action Send the problem to us M
81. 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 272 OSTFC 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 Action See Message 513 Message 556 error too many atoms in REFERENCE file Action See Message 45 Message 557 error undefined direction passed to defects reference export Action See Message 42 Message 558 error outgoing transfer buffer exceeded in defects reference export Action See Message 54 273 OSTFC Appendix D Message 559 error coordinate array exceeded in defects reference export Action See Message 56
82. 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 system cutoff Le the largest RB type is still within a linked cell volume Action Increase cutoff Message 644 error overconstrained rigid body unit This is a very unlikely message which usually indicates a corrupted FIELD file or unphysically overconstrained system Action Decrease constraint on the system Examine FIELD for erroneous directives if any correct and resubmit Message 646 error overconstrained constraint unit This is a very unlikely message which usually indicates a corrupted FIELD file or unphysically overconstrained system Action Decrease constraint on the system Examine FIELD for erroneous directives if any correct and resubmit 276 OSTFC Appendix D Message 648 error quaternion setup failed This error indicates that the routine RIGID BODIES SETUP has failed in reproducing all the atomic positions in rigid units from the centre of mass and quaternion vectors it has calculated Action Check the contents of the CONFIG file DL_POLY 4 builds its local body description of a rigid unit type from the first occurrence of such a unit in the CONFIG file The error most likely occurs because subsequent occurrences were not sufficientl
83. is as follows 1 1 f t 1 r t At r t Atu t At 3 63 3 SHAKE 4 Full step velocity 1 1 1 v t 3 v t 5AM u t 5 3 64 66 STFC Section 3 4 5 Thermostat x t lt T e yy 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 Hoover algorithm 30 Newton s equations of motion are modified to read dr t do c Ub 20 Lo 3 66 The friction coefficient x is controlled by the first order differential equation dx t _ 2Exin t 20 3 67 dt mass where c is the target thermostat energy equation 3 57 and Qmass 2 0 Ti 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 Ej t changes inside At 2Exin t 20 x t
84. kinds f90 0 Setup module o vdw direct fs generate o kinds f90 0 setup module o vdw module o vdw forces o comms module o config module o kinds f90 0 setup module o vdw module o vdw generate o kinds f90 0 setup module o vdw_module o vdw lrc o comms_module o config module o kinds f90 0 setup module o Site module o vdw module o vdw module o kinds f90 0 setup module o vdw table read o comms module o kinds f90 0 parse module o setup module o Site module o vdw module o warning o comms_module o kinds f90 0 setup module o 211 OSTFC Appendix C write config o comms module o config module o io module o kinds f90 0 Setup module o xscale o comms module o config module o kinds f90 0 kinetic module o rigid bodies module o setup module o statistics module o z density collect o config module o kinds f90 0 setup module o site module o Statistics module o Zz density compute o comms module o config module o kinds f90 0 Setup module o site module o statistics module o zero k optimise o comms module o config module o kinds f90 0 A kinetic module o rigid bodies module o setup module o 212 OSTFC Appendix C Makefile MPI Master makefile for DL POLY 4 03 parallel version Author I T Todorov june 2012 Define default settings SHELL bin sh SUFFIXES SUFFIXES f90 o BINROOT execute EX DLPOLY Z EXE BINROOT EX TYPE master FC undefined LD und
85. kinds f90 0 kinetic module o Setup module o site module o npt mO vv o comms module o config module o kinds f90 0 kinetic module o Setup module o site module o npt mi lfv o comms_module o config module o domains module o kinds f90 0 kinetic module o rigid bodies module o setup module o site module o npt mi vv o comms module o config module o domains module o kinds f90 0 kinetic module o rigid bodies module o setup module o site module o nst bO lfv o comms module o config module o kinds f90 0 kinetic module o Setup module o site module o nst bO vv o comms module o config module o kinds f90 0 kinetic module o Setup module o site module o nst bi lfv o comms module o config module o domains module o kinds f90 0 kinetic module o rigid bodies module o setup module o site module o nst bi vv o comms module o config module o domains module o kinds f90 0 206 OSTFC Appendix C kinetic module o rigid bodies module o setup module o site module o nst hO lfv o comms module o config module o kinds f90 0 kinetic module o Setup module o site module o nst hO scl o config module o kinds f90 0 kinetic module o setup module o nst hO vv o comms module o config module o kinds f90 0 kinetic module o Setup module o site module o nst hi lfv o comms module o config module o domains module o kinds f90 0 kinetic module o rigid bodies module o setup module o site module o nst hi scl o config module o kinds f90 0 kinetic
86. 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 Action Check the FIELD file and make sure the keyword is correctly defined Make sure that subroutine BONDS FORCES contains the code necessary to deal with the requested potential Add the code required if necessary by amending subroutines READ FIELD and BONDS FORCES Message 445 error r 14 gt rcut in dihedrals forces The 1 4 coulombic scaling for a dihedral angle bonding cannot be performed since the 1 4 distance has exceeded the system short range interaction cutoff rcut in subroutine DIHEDRAL FORCES Action To prevent this error occurring again increase 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 rec
87. mode mpiiois the recommended method and for large systems master should be avoided and also THE DIRECT OP TION IS NOT STRICTLY PORTABLE and so may cause problems on some machines rp is an optional specification only applicable to netcdf method for opting the binary precision for real numbers It only takes 32bit or amber for 32 bit float precision other wise 64 bit double precision is defaulted type controls the ordering of the particles on 130 OSTFC Section 5 1 output Possible values are sorted and unsorted sorted ensures that the ordering of the particles the default sequential ascending Whereas unsorted uses the natural internal ordering of DL_POLY 4 which changes during the simulation The recommended and default value is sorted If none is specified DL POLY 4 defaultes to the sorted type of I O It should be noted that the overhead of the sorted otion compared to the unsorted is usually very small Available options depend on which method is to be used and all are optional in each case Where numerical values are to be supplied specifying 0 or a negative numbers indicates that DL POLY 4 will resort to the default value The possible options are e io write mpiio direct netcdf rp sort unsort j k l e j specifies the number of processors that shall access the disk k specifies the maxi mum number of particles that the writing processors shall deal with at any one time Large values give good performance b
88. 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 argu ment is important and the argument is allowed to be changed 1 3 3 Memory Management DL POLY 4 exploits the dynamic array allocation features of FORTRANOO to assign the necessary array dimensions 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 FORTRANO90 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 2 The version number or date of production 3 A brief description of the function of the subroutine 4 A copyright statement Elsewhere FORTRAN90 comment cards are used liberally 1 3 6 FORTRAN090 Parameters and Arithmetic Precision All global parameters defined by
89. number of array elements to follow record ii stpval 1 stpval 5 engcns real total extended system energy i e the conserved quantity temp real system temperature engcfg real configurational energy engsrc real short range potential energy engcpe real electrostatic energy record iii stpval 6 stpval 10 engbnd real chemical bond energy engang real valence angle and 3 body potential energy engdih real dihedral inversion and 4 body potential energy engtet real tethering energy enthal real enthalpy total energy 4 PV record iv stpval 11 stpval 15 tmprot real rotational temperature vir real total virial virsrc real short range virial vircpe real electrostatic virial virbnd real bond virial record v stpval 16 stpval 20 165 OSTFC Section 5 2 virang real valence angle and 3 body virial vircon real constraint bond virial virtet real tethering virial volume real volume tmpshl real core shell temperature record vi stpval 21 stpval 25 engshl real core shell potential energy virshl real core shell virial alpha real MD cell angle a beta real MD cell angle 8 gamma real MD cell angle y record vii stpval 26 stpval 27 virpmf real PMF constraint virial press real pressure the next ntpatm entries amsd 1 real mean squared displacement of first atom types amsd 2 real mean squared displacement of second atom types amsd ntpatm real mean squared displacement of last atom types the next 9 entr
90. o comms_module o config module o kinds f90 0 kinetic module o Setup module o site module o nve 1 lfv o comms module o config module o domains module o kinds f90 0 kinetic module o rigid bodies module o setup module o site module o nve 1 vv o comms_module o config module o domains module o kinds f90 0 kinetic module o rigid bodies module o setup module o site module o nvt a0 lfv o comms module o config module o core shell module o kinds f90 0 kinetic module o setup module o site module o nvt a0 vv o comms module o config module o core shell module o kinds f90 0 kinetic module o setup module o site module o nvt ai lfv o comms module o config module o core shell module o domains module o kinds f90 0 kinetic module o rigid bodies module o Setup module o site module o nvt ai vv o comms module o config module o core shell module o domains module o kinds f90 0 kinetic module o rigid bodies module o 207 OSTFC Appendix C Setup module o site module o nvt bO lfv o comms module o config module o kinds f90 0 kinetic module o Setup module o site module o nvt_b0_scl o config module o kinds f90 0 kinetic module o setup module o nvt_b0_vv o comms module o config module o kinds f90 0 kinetic module o Setup module o site module o nvt bi lfv o comms module o config module o domains module o kinds f90 0 kinetic module o rigid bodies module o setup module o site module o nvt bi scl o config module o kinds
91. o nvt bO scl o nvt bi scl o pseudo_vv o 214 OSTFC Appendix C constraints shake vv o pmf shake vv o constraints rattle o pmf rattle o nvt hO scl o nvt gO scl o npt hO scl o nst_h0_scl o nve O vv o nvt eO vv o nvt 10 vv o nvt aO vv o nvt bO vv o nvt hO vv o nvt_g0_vv o npt 10 vv o npt bO vv o npt hO vv o npt mO vv o nst 10 vv o nst bO vv o nst hO vv o nst mO vv o nvt hi scl o nvt gi scl o npt hi scl o nst hi scl o nve 1 vv o nvt el vv o nvt li vv o nvt_al_vv o nvt bi vv o nvt hi vv o nvt gi vv o npt 11 vv o npt b vv o npt h vv o npt mi vv o nst li vv o nst b vv o nst hi vv o nst mi vv o pseudo_lfv o constraints_shake_lfv o pmf shake lfv o nve O lfv o nvt eO lfv o N nvt 10 lfv o nvt a0 lfv o nvt bO lfv o nvt hO lfv o nvt gO lfv o npt 10 lfv o npt bO lfv o npt hO lfv o npt mO lfv o nst 10 lfv o nst bO lfv o nst hO lfv o nst mO lfv o nve 1 lfv o nvt e lfv o nvt li lfv o nvt ai lfv o nvt bi lfv o nvt hi lfv o nvt gil lfv o npt l1 lfv o npt bi lfv o npt hi lfv o npt mi lfv o nst 11 lfv o nst bi lfv o nst hi lfv o nst mi lfv o xscale o core_shell_kinetic o regauss_temperature o z_density_collect o statistics_collect o system_revive o rdf_compute o z_density_compute o statistics_result o dl poly o Define Velocity Verlet files FILES VV pseudo vv f90 constraints shake vv f90 pmf shake vv f90 constraints rattle f90 pmf rattle
92. of the DL POLY 4 FIELD file for further details Section 5 1 3 DL POLY 4 can simulate zeolites and silicate or other glasses Both these materials require the use of angular forces to describe the local structure correctly In both cases the angular terms are included as three body terms the forms of which are described in Chapter 2 These terms are entered into the FIELD file with the pair potentials An alternative way of handling zeolites is to treat the zeolite framework as a kind of macromolecule see below Specifying all this is tedious and is best done computationally what is required is to determine the nearest image neighbours of all atoms and assign appropriate bond and valence angle potentials What must be avoided at all costs is specifying the angle potentials without specifying 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 4 3 2 Macromolecules Simulations of proteins are best tackled using the package DLPROTEIN 70 which is an adap tation of DL POLY specific to protein modelling However you may simulate proteins and other macromolecules with DL POLY 4 if you wish This is described below If you select a protein structure from a SEQNET file e g from the
93. of this molecule including the constraints pmf rigid teth bonds angles dihedrals and inversions entries described below DL POLY 4 will itself construct the global indices for all atoms in the systems This directive and associated data records need not be specified if the molecule contains no core shell units 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 There follows the definitions of two PMF units a pmf unit n1 where n is the number of sites in the first unit The subsequent n1 records provide the site indices and weighting Each record contains index integer atomic site index weight real site weighting 137 OSTFC Section 5 1 b pmf unit n2 where n2 is the number of sites in the second unit The subsequent n2 records provide the site indices and weighting Each record contains index integer atomic site index weight real site weighting This directive and associated data records need not be specified if no PMF constraints are present See the note on the a
94. potential in the system i e as defined in the FIELD file If there are m distinct types of atom in the system the index can possibly range from 1 to m m 1 2 If the internally calculated index exceeds this number this error report results Action Report to authors Message 87 error too many link cells required in four body forces This should not happen The calculation of four body forces in DL POLY 4 is handled by the link cell algorithm This error arises if the required number of link cells exceeds the permitted array dimension in the code Action Consider using densvar option in CONTROL for extremely non equilibrium simulations Alterna tively increase mxcell in SET BOUNDS recompile and resubmit Message 88 error legend array exceeded in build book intra 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 Message 89 error too many four body potentials specified This should never happen Action Report to authors 251 OSTFC Appendix D Message 91 error unidentified atom in four body potential list The specification of a four body potential in the FIELD file has referenced an atom type that is
95. real failure The semantics in some of the INPUT files is wrong DL POLY 4 has tried to read a number but the has found a word in non number format Action Look into your INPUT files and correct the semantics where appropriate and resubmit DL POLY 4 will have printed out in the OUTPUT file what the found non uniform word is Message 2 error too many atom types in FIELD scan field This error arises when DL POLY 4 scans the FIELD file and discovers that there are too many different types of atoms in the system i e the number of unique atom types exceeds the 1000 Action Increase the number of allowed atom types mmk in SCAN FIELD recompile and resubmit Message 3 error unknown directive found in CONTROL file This error most likely arises when a directive is misspelt in the CONTROL file Action Locate the erroneous directive in the CONTROL file and correct error and resubmit Message 4 error unknown directive found in FIELD file This error most likely arises when a directive is misspelt or is encountered in an incorrect location in the FIELD file which can happen if too few or too many data records are included Action Locate the erroneous directive in the FIELD file and correct error and resubmit Message 5 error unknown energy unit requested The DL POLY 4 FIELD file permits a choice of units for input of energy parameters These may be electron Volts eV k calories per mol kcal mol k Jou
96. 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 erecute directory ready for execution The output file OUTPUT may be compared with the file supplied in the data directory It should be noted that the potentials and the simulation conditions used in the following test cases are chosen to demonstrate functionality only They are not necessarily appropriate for serious simulation of the test systems 7 1 1 Test Case 1 and 2 Sodium Chloride These are a 27 000 and 216 000 ion systems respectively with unit electric charges on sodium and chlorine Simulatio
97. right leg lt 2 secede ewes o ws 112 Whe Gubre MiID Gel senis ok oo deeem Fite Ee RD A SON a 188 The orthorhomie MD c ll s s se woe rosos Re ok noo ee ED ORG ES 188 The parallelepiped MID Gell lt sai 4 as he le ee A da e a 188 xii Chapter 1 Introduction Scope of Chapter This chapter describes the concept design and directory structure of DL POLY 4 and how to obtain a copy of the source code STFC Section 1 2 1 1 The DL POLY Package DL POLY 1 is a package of subroutines programs and data files designed to facilitate molecular dynamics simulations of macromolecules polymers ionic systems and solutions on a distributed memory parallel computer It is available in two forms DL POLY Classic written by Bill Smith amp Tim Forester 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 Data 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 packa
98. rm EX EX BINROOT BINROOT TYPE CRAY X2 DEBUG hector X2 debug MAKE LD ftn o LDFLAGS GO 00 rm FC ftn c N FCFLAGS GO 00 rm N EX EX BINROOT BINROOT TYPE Default code 220 OSTFC Appendix C master message check 0BJ MOD 0BJ ALL LD EXE LDFLAGS 0BJ MOD 0BJ ALL Message message echo DL POLY 4 compilation in MPI mode echo echo Use mpi module must change to Use mpi in comms_module f90 echo Check that a platform has been specified check Qif test FC undefined then echo echo FORTRAN90 compiler unspecified echo echo Please edit your Makefile entries echo exit 99 fir if test LD undefined then echo echo FORTRAN90 Linker loaDer unspecified echo echo Please edit your Makefile entries echo exit 99 fi X mkdir p BINROOT touch dl poly f90 Declare rules 90 0 FC FCFLAGS 90 Declare dependencies OBJ_ALL 0BJ MOD 221 OSTFC Appendix C Makefile SRL1 Master makefile for DL POLY 4 03 serial version 1 Author I T Todorov june 2012 Define default settings SHELL bin sh SUFFIXES SUFFIXES f90 o BINROOT execute EX DLPOLY Z EXE BINROOT EX TYPE master FC undefined LD undefined Def
99. simulation is mxgrid Max mxgrid 1000 Int rcut 0 01 0 5 4 where freut is the main cutoff beyond which the contributions from the short range like interactions are negligible 4 2 2 Running To run the DL_POLY 4 executable DLPOLY Z you will initially require three to six input data files which you must create in the execute sub directory or whichever sub directory you keep the executable program The first of these is the CONTROL file Section 5 1 1 which indicates to DL_POLY 4 what kind of simulation you want to run how much data you want to gather and for how long you want the job to run The second file you need is the CONFIG file Section 5 1 2 This contains the atom positions and depending on how the file was created e g whether this is a configuration created from scratch or the end point of another run the velocities and forces also The third file required is the FIELD file Section 5 1 3 which specifies the nature of the intermolecular interactions the molecular topology and the atomic properties such as charge and mass Sometimes you may require a fourth file TABLE Section 5 1 6 which contains short ranged potential and force arrays for functional forms not available within DL POLY 4 usually because they are too complex e g spline potentials and or a fifth file TABEAM Section 5 1 7 which contains metal potential arrays for non analytic or too complex functional forms and or a sixth file REFERENCE
100. t 4 vo ea 4 4 Pmass 2E 3 bist 1 Rp t f Pmass Pmass 1 At 1 nt At E exp Xp g n t At 1 A dy amp exp nt A x v t 3 101 1 At 1 n t 120 exp Xp g n t 4 1 0 1 1 i At T t Post n t 5A mn t4 140 Fg 3V t ien 2E 3 kin t 1 Rp t f Pmass Pmass 1 At 1 t 54t c exp Xp 3 n t 4 5 3 Thermostat Note Exin t has changed and changes inside v t exp x F eto 3 102 4 VVI At f t R t v t At v t 4 2 a 1 H t At lt exp n z At H t TN RIT In 56 At V t 3 103 1 1 r t At exp nt At At r t At v t At 5 RATTLE_VV1 6 FF f t At f t R t At R t 3 104 R t At E R t 7 VV2 A A t R t vt AD e ate S 5 E 3 105 8 RATTLE_VV2 73 STFC Section 3 5 9 Thermostat Note Exin t At has changed and changes inside TESE exp x u t At 3 106 10 Barostat Note Exin t At and P t At have changed and change inside 1 A 1 n t 544 lt exp Xp n t4 5 At 3 At P t At Port n t 74 lt n t 4 3V ND T ur i AO f Pmass Pmass At 3 ne 340 c exp Xp 8 n t 4 74 MERA exp t At 5 u t At 3 107 nt 340 c Di Xp e n t 4 AA At P t At Pex n t At n t4 3V t Di 4 Pmass a t At 1 R t f Pmass Pmass At n t At exp Xp n t At 11 Thermostat Note Exin t At has changed and changes inside i
101. the FORTRANO0 parameter statements are specified in the mod ule file SETUP_MODULE which is included at compilation time in all subroutines requiring the parameters All parameters specified in SETUP_MODULE are described by one or more comment cards One super global parameter is defined at compilation time in the KINDS_F90 module file specifying the working precision wp by kind for real and complex variables and parameters The default OSTFC Section 1 3 is 64 bit double precision i e Real wp Users wishing to compile the code with quadruple precision must ensure that their architecture and FORTRAN090 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 subroutines and functions assume the use of the following defined molecular units e The unit of time to is 1 x 107 seconds i e picoseconds e The unit of length o is 1 x 10 metres i e Angstroms e The unit of mass mo is 1 6605402 x 107 kilograms i e Daltons atomic mass units e The unit of charge qo is 1 60217733 x 10719 Coulombs i e electrons units of proton charge e The unit of energy E mo l0 t0 is 1 6605402 x 10723 Joules 10 J mol e T
102. unit i e M in equation 3 172 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 90 STFC Section 3 6 The rotational equation of motion for a rigid body is d d J I w 3 182 r giogo ila in which J is the angular momentum of the rigid body defined by the expression Nsites J Y mjdj xw 3 183 j 1 and w is the angular velocity The vector 7 is the torque acting on the body in the universal frame and is given by Nsites T 2 djxf 3 184 j 1 The rotational equations of motion for rigid bodies in a theromostat can be written as Li SJ 3 185 dmass where i 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 i CES Ls Las Oy z Lao x A AEN Oy sot ez lo z Oz 3 186 Ly A T E Pa s ge lyy Or dpi I The vectors and w are the torque and angular velocity acting on the body transformed to the local body frame Integration of is complicated by the fact that as the rigid body rotates so does the local reference frame So it is necessary to integrate equations 3 186 simultaneously with an integration of the quaternions describing the orientation of the rigid body The equation describing thi
103. 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 communication module defines MPI related parameters and develops MPI related func tions and subroutines such as initialisation and exit global synchronisation sum maximum and minimum node ID and number of nodes simulation time It is dependent on KINDS F90 and on MPI MODULE if MPI is emulated for DL POLY 4 compilation in serial mode The MPI MODULE implements all MPI functional calls used in DL POLY 4 e global parameters module SETUP MODULE The global parameters module holds all important global variables and parameters see above It is dependent on KINDS F90 e parse m
104. vector cell 6 real z component of b cell vector record 5 omitted if imcon 0 cell 7 real x component of c cell vector cell 8 real y component of c cell vector cell 9 real z component of c cell vector Note that record 2 may contain more information apart from the mandatory as listed above If the file has been produced by DL POLY 4 then it also contains other items intended to help possible parallel I O reading Subsequent records consists of blocks of between 2 and 4 records depending on the value of the levcfg variable Each block refers to one atom The atoms do not need to be listed sequentially in order of increasing index Within each block the data are as follows record i atmnam a8 atom name index integer atom index 132 OSTFC Section 5 1 record ii XXX real x coordinate yyy real y coordinate ZZZ real z coordinate record iii included only if levcfg gt 0 VXX real x component of velocity vyy real y component of velocity VZZ real x component of velocity record iv included only if levcfg gt 1 fxx real x component of force fyy real y component of force fzz real z component of force Note that on record i only the atom name is strictly mandatory any other items are not read by DL POLY 4 but may be added to aid alternative uses of the file for example the DL POLY 4 Graphical User Interface 21 Table 5 5 CONFIG File Key record 2 levcfg meaning 0 coordinates included in file 1 coordinates and
105. velocities included in file 2 coordinates velocities and forces included in file Table 5 6 Periodic Boundary Key record 2 imcon meaning no periodic boundaries cubic boundary conditions orthorhombic boundary conditions parallelepiped boundary conditions x y parallelogram boundary conditions with no periodicity in the z direction O U uU 5 1 2 3 Further Comments on the CONFIG File The CONFIG file has the same format as the output file REVCON Section 5 2 7 When restarting from a previous run of DL POLY 4 i e using the restart restart noscale or restart scale directives in the CONTROL file above the CONFIG file must be replaced by the REVCON file which is renamed as the CONFIG file The copy macro in the execute sub directory of DL POLY 4 does this for you The CONFIG file has the same format as the optional output file CFGMIN which is only produced when the minimise optimise option has been used during an equilibration simulation or a dry run 133 OSTFC Section 5 1 5 1 3 The FIELD File The FIELD file contains the force field information defining the nature of the molecular forces This information explicitly includes the site topology of the system 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
106. vv f90 constraints rattle f90 pmf rattle f90 nvt hO scl f90 nvt gO scl f90 npt_h0_sc1 f90 nst_h0_scl 90 nve O vv f90 nvt eO vv f90 N nvt 10 vv f90 nvt aO vv f90 nvt bO vv f90 nvt hO vv f90 nvt gO vv f90 npt_10_vv f90 npt_b0_vv f90 npt hO vv f90 npt mO vv f90 N nst 10 vv f90 nst_b0_vv f90 nst hO vv f90 nst mO vv f90 N nvt hi scl f90 nvt gi scl f90 npt_h1_sc1 f90 nst_hi_scl f90 224 OSTFC Appendix C nve 1 vv f90 nvt ei vv f90 nvt 11 vv f90 nvt a1 vv f90 nvt bi vv f90 nvt hi vv f90 nvt gi vv f90 npt 11 vv f90 npt bi vv f90 npt hi vv f90 npt mi vv f90 nst li vv f90 nst bi vv f90 nst hi vv f90 nst mi vv f90 md vv f90 Define LeapFrog Verlet files FILES LFV pseudo lfv f90 constraints shake lfv f90 pmf shake lfv f90 nve O lfv f90 nvt eO lfv f90 nvt 10 1fv f90 nvt aO lfv f90 nvt bO lfv f90 nvt hO lfv f90 nvt gO lfv f90 npt 10 lfv f90 npt bO lfv f90 npt hO lfv f90 npt_m0_lfv 90 nst 10 l1fv f90 nst bO lfv f90 nst hO lfv f90 nst mO lfv f90 nve 1 lfv f90 nvt ei lfv f90 nvt li l1fv f90 nvt ai lfv f90 nvt b lfv f90 nvt h lfv f90 nvt gi lfv f90 npt 11 lfv f90 npt bi lfv f90 npt hi lfv f90 npt mi lfv f90 nst li lfv f90 nst bi lfv f90 nst h lfv f90 nst mi lfv f90 md lfv f90 Examine targets manually all echo echo You MUST specify or choose a permissive target platform echo echo The available permissive targets are displayed below echo echo win win
107. w t nr Su 9 Dae qo ow e f 3 kp Text Pmass 27 Xp CH 10 50 VA Br VO dt 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 95 and R is the stochastic Langevin pressure variable Rp t Rp t 2 xp Pmass kpT 9 t 3 98 which is drawn from Gaussian distribution of zero mean and unit variance Gauss 0 1 scaled by V 2 Xp Pmass kat kp is the Boltzmann constant T the target temperature and pmass the barostat mass H is the cell matrix whose columns are the three cell vectors a b c The conserved quantity these generate is Pian n t Poa V t 3 99 Hyer HnveE The VV implementation of the Langevin algorithm only requires iterations if bond or PMF con straints are present 4 until satisfactory convergence of the constraint forces is achieved These are with respect to the pressure i e n t in the first part VV1 RATTLE_VV1 The second part is conventional VV24 RAT TLE V V2 as at the end the velocities are scaled by a factor of x 1 Thermostat Note 2Ex n t changes inside 0 or x F 20 3 100 72 STFC Section 3 5 2 Barostat Note Exin t and P t have changed and change inside At n exp x Z nl 1 At P t Px n t At qn
108. 0 by semi isotropic constraining of the barostat equation of motion to Taa t Pext Yext h2 t V t 2B nin 4 xo Ree a 8 x y Pmass Pmass Pmass Cms dt mur Fens rw t am ni XpNzz t Poss a B S 0 Magl0 0 04 B x Y 2 3 119 where Yext is the user defined external surface tension and h t V t Az t is the instantaneous hight of the MD box or MD box volume over area The instnatneous surface tension is defined as Yalt hz t eoo t Pe 3 120 The case Yext 0 generates the NPT anisotropic ensemble for the orthorhombic cell imcon 2 in CONFIG see Appendix A 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 d _ eas t 0yy t 2 Poxt Yext he t V t 2 Exi t g si eo 3 121 trato PESTE a 8 The VV and LFV flavours of the non isotropic Langevin barostat and Nos Hoover thermostat are implemented in the DL POLY 4 routines NST LO VV and NST_LO_LFV respectively Both make use of the DL POLY 4 module LANGEVIN MODULE The routines NST L1 VV and NST_L1_LFV implement the same but also incorporate RB dynamics 3 5 3 Berendsen Barostat With the Berendsen barostat the system is made to obey the equation of motio
109. 0 and 256 000 atoms respectively Simulation at 300 K using NVT Evans ensemble with Sutton Chen forces and no electrostatics 7 1 13 Test Case 25 and 26 Al with EAM metal Potentials These systems consist of 32 000 and 256 000 atoms respectively Simulation at 300 K using NVT Evans ensemble with EAM tabulated forces and no electrostatics 7 1 14 Test Case 27 and 28 NiAl alloy with EAM metal Potentials These systems consist of 27 648 and 221 184 atoms respectively Simulation at 300 K using NVT Evans ensemble with EAM tabulated forces and no electrostatics 7 1 15 Test Case 29 and 30 Fe with Finnis Sincair metal Potentials These systems consist of 31 250 and 250 000 atoms respectively Simulation at 300 K using NPT Berendsen ensemble with Finnis Sinclair forces and no electrostatics 7 1 16 Test Case 31 and 32 Ni with EAM metal Potentials These systems consist of 32 000 and 256 000 atoms respectively Simulation at 300 K using NPT Berendsen ensemble with EAM tabulated forces and no electrostatics 7 1 17 Test Case 33 and 34 SPC IceVII water with constraints These systems consist of 11 664 34 992 atoms and 93 312 279 936 atoms water molecules re spectively Simulation at 25 K using NVE ensemble with CGM force minimisation and SPME electrostatics Both constraint bond and rigid body dynamics cases are available 7 1 18 Test Case 35 and 36 NaCl molecules in SPC water represented as CBs RBs These systems consist of 64 512 N
110. 001 Message 1036 error allocation failure in pmf module gt allocate pmf arrays Action See Message 1001 Message 1037 error deallocation failure in pmf module gt deallocate pmf arrays Action See Message 1002 Message 1038 error allocation failure in minimise module gt allocate minimise arrays Action See Message 1001 Message 1039 error deallocation failure in minimise module gt deallocate minimise arrays Action See Message 1002 Message 1040 error allocation failure in ewald module gt ewald allocate kall arrays Action See Message 1001 282 OSTFC Appendix D Message 1041 error allocation failure in langevin module gt langevin allocate arrays Action See Message 1001 Message 1042 error allocation failure in rigid bodies module gt allocate rigid bodies arrays Action See Message 1001 Message 1043 error deallocation failure in rigid bodies module gt deallocate rigid bodies arrays Action See Message 1002 Message 1044 error allocation failure in comms module gt gimin vector Action See Message 1001 Message 1045 error deallocation failure in comms module gt gimin vector Action See Message 1002 Message 1046 error allocation failure in comms module gt grmin vector Action See Message 1001 Message 1047 error deallocation failure in c
111. 1 fxx real x component of force fyy real y component of force fzz real z component of force Thus the data for each atom is a minimum of two records and a maximum of 4 5 2 2 The MSDTMP File The MSDTMP file is the dump file of individual atomic mean square displacements square roots in and mean square temperature square roots in Kelvin Its principal use is for off line analysis The file is written by the subroutine MSD WRITE The control variables for this file are lmsd nstmsd istmsd which are created internally based on information read from the msdtmp directive in the CONTROL file see Section 5 1 1 The MSDTMP file will be created only if the directive msdtmp appears in the CONTROL file The MSDTMP file can become very large especially if it is formatted For serious simulation work it is recommended that the file be written to a scratch disk capable of accommodating a large data file 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 a8 the character string timestep nstep integer the current time step megatm integer number of
112. 10 101 Melchionna S and Cozzini S 1998 University of Rome 106 293 OSTFC Bibliography 71 72 73 74 75 Hockney R W and Eastwood J W 1981 Computer Simulation Using Particles McGraw Hill International 168 170 172 Smith W 1992 Comput Phys Commun 67 392 168 Smith W and Fincham D 1993 Molecular Simulation 10 67 168 Bush I J Todorov I T and Smith W 2006 Computer Physics Communication 175 323 171 Bush I J 2000 Daresbury Laboratory 171 294 Index DL POLY 4 software licence 10 algorithm 4 54 113 FIQA 4 91 NOSQUISH 4 91 92 RATTLE 4 57 58 168 172 271 SHAKE 4 57 59 168 172 254 Verlet 4 29 54 56 59 171 172 Verlet neighbour list 170 AMBER 3 12 106 107 angular momentum 91 angular restraints 18 angular velocity 91 barostat 4 93 117 118 266 Berendsen 77 Nos Hoover 80 86 boundary conditions 3 42 187 cubic 133 CCP5 2 9 constraints bond 2 4 13 57 60 89 137 161 170 172 243 248 254 271 Gaussian 46 47 60 PMF 13 59 60 138 162 170 direct Coulomb sum 42 44 116 129 distance dependant dielectric 44 45 116 129 distance restraints 15 dlpoly2 5 DLPROTEIN 106 Dreiding 12 ensemble 4 262 Andersen NVT 4 56 125 Berendsen NoT 4 56 117 125 126 Berendsen NPT 4 56 117 125 126 Berendsen NVT 4 56 117 125 126 canonical 60 Evans NVT 4 56 117 125 12
113. 2 47 with aa raz X Lju Eje X Len ro rjsrgklo 0n den rsntanlo be 25 Or T rijrjx o 0e dex rjatenla be dei Ten rijrjk o de 025 rjkrjx o bei deg 2r5krijTkn o 0e dex gt 2 48 d a ag X Tjk ENS ari rer jk o 0e dei rijrjk o 0e 9x 2r5i rijri o 0e 025 rijrjx o 0e ej 2 49 0 Q rg Iri X rx 2a rjatjrla Sen See rgktan o 0e Sex 2r sk rs nk o Oe 965 rjktknlo dex den 2 50 Where we have used the the following definition a bla 1 dap a b 2 51 B 20 STFC Section 2 2 Formally the contribution to be added to the atomic virial is given by 4 mus 2 52 i 1 However it is possible to show by tedious algebra using the above formulae or more elegantly by thermodynamic arguments 40 that the dihedral makes no contribution to the atomic virial The contribution to be added to the atomic stress tensor is given by c rap E SD Tis 2 53 cos ijkn A rr rn with P rielt etenla Tkslnjkt la Iri X rjkllrjk X Lin Da rk rita la Tij j rjr rik o lri x snl lt x Tal Dik ri lr T Cxnlac Tinlutela m 2r Pis kn o Wrz x ey P X riy 9 raljera rjkiraroslo lri x vj 2 54 gk 2 rs r ij fala ri igh jlo Ls x ra he 2 r5kCantenla Tgn lLjkLknla lLjk X P ha ArimllimIim a Tik rix amp n o Iro Pel
114. 2A HELLE Fo n t iat exp x t 4 104 x n t 4 2A 3 Thermostat Note Ej t has changed and changes inside 1 At 2E gin t t 1At 20 kg Tex x 3 AL x t At 4 t kinl Pmass n 2 o B lext 8 4 8 dmass 81 STFC Section 3 5 At v t exp x t 4 SA 1 v t 3 144 At 2E t Pmass n t 4At 20 kp Tex Xu CAS a RUE ATA kin t Pmase TIE it 20 ka Ten 8 8 mass 4 VV1 X At f t u t 4 5 v t 4 uer 1 H t At exp nt 540 At H t VIGOR de s ante 56 At V t 3 145 1 1 i et ees nt 340 At EC Rolt At w t 540 Bolt 5 RATTLE VV1 6 FF E At ft 3 146 T VV2 bt At f t v t At w t4 5 os 3 147 8 RATTLE_VV2 9 Thermostat Note Exin t At has changed and changes inside 1 At 2Epin t At Pmass n t At 20 kp Tox XD AN scm lie Aat BuU BU SQ UU feo ior See opio t 8 2 8 mass 5 At URA exp x t A 1 u t At 3 148 At 2Erin t At Pmass Nt At 20 kp Tox ie SAP Hee ne Enron oq i eo dest 4 8 8 dmass 10 Barostat Note Exin t At and P t At have changed and change inside 1 3 At 1 n t At lt exp x t 4 120 nt 54t 3 1 At 3 P t At Pox V t At A t At 4 nt At n t 5At0 TUN 3 3 At 3 wA c exp x t DA x n t At 3 At v At exp nt At 5 u t At 3 149 3 3 At 3 nt At c exp x
115. 4 error allocation failure in bonds module gt allocate bonds arrays Action See Message 1001 Message 1015 error allocation failure in core shell module gt allocate core shell arrays Action See Message 1001 Message 1016 error allocation failure in statistics module gt allocate statitics arrays Action 279 OSTFC Appendix D See Message 1001 Message 1017 error allocation failure in tethers module gt allocate tethers arrays Action See Message 1001 Message 1018 error allocation failure in constraints module gt allocate constraints arrays Action See Message 1001 Message 1019 error allocation failure in external field module gt allocate external field arrays Action See Message 1001 Message 1020 error allocation failure in dihedrals module gt allocate dihedrals arrays Action See Message 1001 Message 1021 error allocation failure in inversions module gt allocate inversion arrays Action See Message 1001 Message 1022 error allocation failure in vdw module gt allocate vdw arrays Action See Message 1001 Message 1023 error allocation failure in metal module gt allocate metal arrays Action See Message 1001 Message 1024 error allocation failure in three body module gt allocate three body arrays Action See Message 1001 280 OSTFC Appendix
116. 6 Gentle Stochastic NVT 56 117 Langevin NoT 4 56 117 125 126 Langevin NPT 4 56 117 125 126 Langevin NVT 4 56 117 125 126 Martyna Tuckerman Klein NoT 125 Martyna Tuckerman Klein NoT 4 56 117 126 Martyna Tuckerman Klein NPT 4 56 117 125 126 microcanonical see ensemble NVE Nos Hoover No T 4 56 117 125 126 Nos Hoover NPT 4 56 117 125 126 Nos Hoover NVT 4 56 117 125 126 NVE 4 56 60 117 125 126 equations of motion Euler 52 91 rigid body 91 error messages 110 236 Ewald optimisation 107 108 SPME 48 107 118 122 128 129 summation 46 47 100 108 124 129 168 171 262 force field 3 12 13 21 107 171 238 254 271 AMBER 3 12 DL POLY 3 12 Dreiding 3 12 40 41 GROMOS 3 12 force shifted Coulomb sum 43 122 129 FORTRANSODQ 5 6 99 100 178 236 FTP 9 Graphical User Interface 9 106 107 133 GROMOS 3 12 Java GUI 4 9 licence 2 long ranged corrections metal 34 van der Waals 29 minimisation 102 conjugate gradients 103 295 OSTFC Index programmed 103 zero temperature 103 parallelisation 4 97 168 Domain Decomposition 4 intramolecular terms 169 170 polarisation 49 50 shell model 3 12 42 50 52 169 170 246 potential bond 3 106 140 161 169 172 242 263 bonded 171 172 calcite 25 26 chemical bond 3 12 13 15 20 21 41 50 169 171 dihedral 3 12 19 23 141 143 161 169 170 247
117. 916834 7 340573742 1 507099154 1 577400769 4 328786484 7455 527553 4806 880540 1255 814536 HW 3 3 258494716 2 125627191 1 491549620 2 413871957 4 336956694 2 951142896 131 OSTFC Section 5 1 7896 278327 8318 045939 2379 766752 OW 4 0 9720599243E 01 2 503798635 3 732081394 1 787340483 1 021777575 0 5473436377 9226 455153 9445 662860 5365 202509 etc 5 1 2 1 The CONFIG File Format The file is free formatted and not case sensitive Every line is treated as a command sentence record However line records are limited to 72 characters in length Records are read in words as a word must not exceed 40 characters in length Words are recognised as such by separation by one or more space characters The first record in the CONFIG file is a header up to 72 characters long to aid identification of the file Blank and commented lines are not allowed 5 1 2 2 Definitions of Variables in the CONFIG File record 1 header a72 title line record 2 levcfg integer CONFIG file key See Table 5 5 for permitted values imcon integer Periodic boundary key See Table 5 6 for permitted values megatm integer Optinal total number of particles crystalographic entities record 3 omitted if imcon 0 cell 1 real x component of a cell vector cell 2 real y component of a cell vector cell 3 real z component of a cell vector record 4 omitted if imcon 0 cell 4 real x component of b cell vector cell 5 real y component of b cell
118. A U r 4e 5 2x beiTg 2504 Chandler Anderson Ur bDiryg 280A 1 Note in this formula the terms a 8 and y are compound expressions involving the variables E n m rg and re See Section 2 3 1 for further details Note re defaults to the general van der Waals cutoff rvdw or rcut if it is set to zero or not specified in the FIELD file Note A defaults to zero if A gt 0 5 or it is not specified in the FIELD file 145 OSTFC Section 5 1 variable 7 real potential parameter see Table 5 13 variable 8 real potential parameter see Table 5 13 variable 9 real potential parameter see Table 5 13 The variables pertaining to each potential are described in Table 5 13 Table 5 13 Metal Potential key potentialtype Variables 1 5 6 9 functional form eam EAM tabulated potential fnsc Finnis Sinclair co c1 c2 c A Ui r rij c co cari car Ay pi jfi pd d B a lea dy pes m ifi exfs Extended co amp c2 c3 ca Ui r 5 A C co cirij cari Car cari Finnis Sinclair c A d B AVE p Y rij d B rij d if stch Sutton Chen ela n m ec U r gt 2 c d jg ue ay pi 2 m gupt Gupta Alro p Bl aj U i r x Aexp p DI we B pi CE Tij TrO n Zew 2 dij Fo 3 rdf n where n is the number of RDF pairs to be entered It is followed by n records each specifying a parti
119. D EXCL INTRA routines Lastly the thermodynamic properties of the system are checked and set intact by the SET TEMPERATURE routine which also generates the initial velocities if required to do so The calculation of the pair like forces is carried out in the TWO BODY FORCES routine and rep resents the main part of any simulation For calculation of the two body contributions to the atomic forces the Verlet neighbour list is constructed by LINK CELL PAIRS routine using link cell lists Special measures are taken so that the lsit excludes i pairs of atoms that are both in frozen state as well as ii pairs in which one of the atoms has the other in its exclusion list The last is build by BUILD EXCL INTRA where the specification of bonded like interactions in the FIELD file are processed Various other subroutines are then called to calculate specific contri butions by different interactions For example VDW FORCES for the short range van der Waals forces Section 2 3 1 METAL LRC METAL LD COMPUTE and METAL FORCES for the metal inter actions Section 2 3 2 and EWALD SPME FORCES EWALD REAL FORCES EWALD FROZEN FORCES and EWALD EXCL FORCES for the Coulombic forces Section 2 4 Higher order intermolecular site related and intramolecular forces require the routines TERSOFF FORCES THREE BODY FORCES FOUR BODY FORCES CORE SHELL FORCES or CORE SHELL RELAX TETHERS FORCES BONDS FORCES ANGLES FORCES DIHEDRALS FORCES and
120. D cell V is the simulation cell volume and k is a reciprocal lattice vector defined by k u mv t nw 2 187 where Z 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 V a b x el 2 188 and b 2r a bxe CXA Jg 2 189 v ii E axb a bxc With these definitions the Ewald formula above is applicable to general periodic systems The last term in the Ewald formula above is the Fuchs correction 54 for electrically non neutral MD cells 47 OSTFC Section 2 4 which prevents the build up of a charged background and the introduction of extra pressure due to it In practice the convergence of the Ewald sum is controlled by three variables the real space cutoff Tcut the convergence parameter a and the largest reciprocal space vector kmar used in the reciprocal space sum These are discussed more fully in Section 4 3 5 DL POLY 4 can provide estimates if requested see CONTROL file description 5 1 1 As its name implies the Smoothed Particle Mesh Ewald SPME method is a modification of the standard Ewald method DL POLY 4 implements the SPME method of Essmann et al 55 Formally this method is capable of treating van der Waals forces also but in DL_POLY 4 it is confined to electrostatic forces only The main difference from the standard Ewald method is in its treatment of the the reciprocal
121. FC f95 c N FCFLAGS 00 C all C undefined EX EX BINROOT BINROOT TYPE Default code master message check 0BJ MOD 0BJ ALL LD EXE LDFLAGS 0BJ MOD 0BJ ALL Message message echo DL POLY 4 compilation in SRL2 mode echo echo Use mpi must change to Use mpi_module in comms_module f90 echo Check that a platform has been specified check if test FC undefined then echo echo FORTRAN90 compiler unspecified echo echo Please edit your Makefile entries echo exit 99 fi X if test LD undefined then echo echo FORTRAN90 Linker loaDer unspecified echo echo Please edit your Makefile entries echo exit 99 fi mkdir p BINROOT touch dl_poly f90 Declare rules f90 0 FC FCFLAGS f90 234 OSTFC Appendix C Declare dependencies 0BJ ALL 0BJ MOD 235 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
122. FDAT data TEST 1 ZDNDAT data TEST 1 which first creates a new DL POLY data TEST sub directory and then moves the standard DL POLY 4 output data files into it Store requires one argument store n where n is a unique string or number to label the output data in the data TESTn sub directory Note that store sets the file access to read only This is to prevent the store macro overwriting existing data without your knowledge 193 Appendix C DL POLY 4 Makefiles Makefile DEV Master makefile for DL POLY 4 03 developer version Author I T Todorov june 2012 Define default settings SHELL bin sh SUFFIXES SUFFIXES f90 o BINROOT execute EX DLPOLY Z EXE BINROOT EX TYPE master FC undefined LD undefined Define object files OBJ_MOD kinds_f90 0 comms_module o setup_module o parse module o development module o netcdf modul o io module o domains module o Site module o config module o defects module o defectsi module o vdw module o metal module o tersoff module o three body module o four body module o core shell module o 194 OSTFC Appendix C constraints module o pmf module o rigid bodies module o tethers module o bonds module o angles module o dihedrals module o inversions module o external_field_module o langevin_module o minimise_module o ewald_module o msd_module o statistics_module o kinetic_module o gpfa
123. FIELD file for missing or incorrect data correct and resubmit Message 53 error end of CONTROL file encountered This message results when DL POLY 4 reaches the end of the CONTROL file without having read all the data it expects Probable cause missing finish directive Action Check CONTROL file correct and resubmit Message 54 error outgoing transfer buffer exceeded in export atomic data This may happen in extremely non equilibrium simulations or usually when the potential in use do not hold the system stable Action Consider using densvar option in CONTROL for extremely non equilibrium simulations Alterna tively increase mxbuff in SET BOUNDS recompile and resubmit Message 55 error end of CONFIG file encountered This error arises when DL POLY 4 attempts to read more data from the CONFIG file than is actually present The probable cause is an incorrect or absent CONFIG file but it may be due to 245 OSTFC Appendix D the FIELD file being incompatible in some way with the CONFIG file Action Check contents of CONFIG file If you are convinced it is correct check the FIELD file for inconsistencies Message 56 error atomic coordinate array exceeded in export atomic data This may happen in extremely non equilibrium simulations or usually when the potential in use do not hold the system stable Action Consider using densvar option in CONTROL for extremely non equilibrium simulations Alterna
124. INVERSIONS FORCES The routines EXTERNAL FIELD APPLY and EXTERNAL FIELD CORRECT are required if the simulated system has an external force field e g electrostatic field operating To help with equilibration simulations routines such as CAP FORCES ZERO_K_OPTIMISE and MIN IMISE_RELAX are sometimes required to reduce the magnitude of badly equilibrated forces and to steer the MD system towards an equlibrium state Integration of the equations of motion is handled by one of the routines listed and described in Chapter 3 As mentioned elsewhere DL POLY_4 does not contain many routines for computing system prop erties during a simulation Radial distributions may be calculated however by using the routines RDF COLLECT RDF EXCL COLLECT and RDF_COMPUTE Similarly Z density distribution may be calculated by using the routines Z DENSITY COLLECT and Z DENSITY COMPUTE Ordinary ther modynamic quantities are calculated by the routine STATISTICS COLLECT which also writes the STATIS file Section 5 2 11 Routine TRAJECTORY WRITE writes the HISTORY Section 5 2 1 file for later postmortem analysis Routine DEFECTS WRITE writes the DEFECTS Section 5 2 3 file for later postmortem analysis Routine MSD WRITE writes the MSDTMP Section 5 2 2 file for later postmortem analysis Routine RSD WRITE writes the RSDDAT Section 5 2 4 file for later postmortem analysis Job termination is handled by the routine STATISTICS RESULT which wri
125. KE algorithm 8 although its implementation in the Domain Decomposition frame work requires no global merging operations and is consequently significantly more efficient The routine CONSTRAINTS SHAKE is called to apply corrections to the atomic positions and the routine CONSTRAINTS RATTLE to apply corrections to the atomic velocities of constrained particles It should be noted that the fully converged constraint forces G make a contribution to the system virial and the stress tensor The contribution to be added to the atomic virial for each constrained bond is W d Gi 3 20 The contribution to be added to the atomic stress tensor for each constrained bond is given by ga ed m a 3 21 where a and f indicate the x y z components The atomic stress tensor derived from the pair forces is symmetric 3 3 Potential of Mean Force PMF Constraints and the Evalua tion of Free Energy A generalization of bond constraints can be made to constrain a system to some point along a reaction coordinate A simple example of such a reaction coordinate would be the distance between two ions in solution If a number of simulations are conducted with the system constrained to different points along the reaction coordinate then the mean constraint force may be plotted as a 59 OSTFC Section 3 4 function of reaction coordinate and the function integrated to obtain the free energy for the overall process 62 The PMF constraint force virial
126. L MODULE CONSTRAINTS MODULE PMF MODULE RIGID BODIES MODULE TETHERS MODULE BONDS MODULE ANGLES MODULE DIHEDRALS MODULE INVERSIONS MODULE EXTERNAL_FIELD_MODULE LANGEVIN MODULE MINIMISE MODULE EWALD MODULE MSD MODULE STATISTICS MODULE KINETIC MODULE GPFA MODULE PARALLEL FFT e general files in the source directory WARNING ERROR SCAN_CONTROL_IO NUMERIC CONTAINER SPME_CONTAINER QUATERNIONS CONTAINER SCAN FIELD READ CONFIG PARALLEL SCAN CONFIG SCAN CONTROL READ CONFIG SET_BOUNDS READ_CONTROL VDW_GENERATE VDW_TABLE_READ VDW_DIRECT_FS_GENERATE METAL_GENERATE METAL TABLE READ METAL TABLE DERIVATIVES TERSOFF_GENERATE DIHEDRALS 14 CHECK READ FIELD CHECK CONFIG SCALE CONFIG WRITE CONFIG TRAJECTORY WRITE SYSTEM_EXPAND RIGID BODIES TAGS RIGID BODIES COMS RIGID BODIES WIDTHS RIGID_BODIES_SETUP TAG_LEGEND REPORT_TOPOLOGY PASS_SHARED_UNITS BUILD_BOOK_INTRA BUILD_EXCL_INTRA 176 OSTFC Section 6 2 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 LRCMETAL LRC SYSTEM INIT EXPORT ATOMIC DATA SET HALO PARTICLES 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 IMPAC
127. Matter 5 1019 50 51 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 51 103 Leimkuhler G Noorizadeh E and Theil F 2009 J Stat Phys 135 261 277 56 60 69 Ikeguchi M 2004 J Comp Chemi 25 529 541 56 77 80 85 87 88 Ryckaert J P Ciccotti G and Berendsen H J C 1977 J Comput Phys 23 327 5T 168 McCammon J A and Harvey S C 1987 Dynamics of Proteins and Nucleic Acids Cam bridge University Press 60 Izaguirre J A Langevin stabilisation of multiscale mollified dynamics In Brandt A Binder K B J editor Multiscale Computational Methods in Chemistry and Physics vol ume 117 of NATO Science Series Series III Computer and System Sciences pages 34 47 IOS Press Amsterdam 2001 60 62 63 Samoletov A Chaplain M and Dettmann C 2007 J Stat Phys 128 13211336 60 69 Melchionna S Ciccotti G and Holian B L 1993 Molec Phys 78 533 80 Martyna G Tobias D and Klein M 1994 J Chem Phys 101 4177 80 88 Todorov I Bush I and Porter A 2009 Parallel Scientific Computing and Optimization Springer Optimization and Its Applications ISSN 1931 6828 27 101 Todorov I Bush I and Smith W 2008 Cray User Group 2008 101 Bush I Todorov I and Smith W 2010 Cray User Group 20
128. N MEMORY vdw direct metal direct i FORCE SHIFT VDW INTERACTIONS S0 THAT ENERGY AND FORCE i CONTRIBUTIONS FALL SMOOTHLY TO ZERO WHEN APPROACHING R CUT vdw shift i RANDOM NUMBER GENERATOR SEEDING seed 100 200 I O READ METHOD READER COUNT BATCH BUFFER SIZES 113 OSTFC Section 5 1 io read mpiio 2 2000000 20000 I O WRITE METHOD TYPE WRITER COUNT BATCH amp BUFFER SIZES io write mpiio sorted 8 2000000 20000 SLAB SIMULATION PARALLEL CONTROL slab RESTART OPTIONS restart noscale dump 1000 steps SYSTEM TARGET TEMPERATURE AND PRESSURE temperature 300 0 Kelvin pressure 0 001 k atmospheres SYSTEM CUTOFFS AND ELECTROSTATICS cutoff 10 0 Angstroms rvdw 8 0 Angstroms exclude epsilon 1 0 ewald precision 1 0e 6 ewald evaluate 4 RELAXED SHELL MODEL TOLERANCE rlxtol 1 0 force CONSTRANTS ITERATION LENGTH and TOLERANCE mxshak 250 cycles shake 1 0e 4 INTEGRATION FLAVOUR ENSEMBLE AND PSEUDO THERMOSTAT integration velocity verlet ensemble nst hoover 0 5 0 5 pseudo langevin 2 0 150 0 INTEGRATION TIMESTEP variable timestep 0 001 pico seconds mindis 0 03 Angstroms 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 114 OSTFC Section 5 1 scale 5 steps regauss 3 steps minimise force 20 1 0 optimise energy 0 001 STATISTICS c
129. O or master for traditional master I O or netcdf for netCDF I O provided DL POLY 4 is compiled in a netCDF enabled mode default mpiio WARRNING direct is not a platfotm portable solution as it fails on LUSTRE but works on GPFS NOTE that rp is only applicable for the netcdf method rp real precision 32bit or amber for 32 bit float otherwise 64 bit double is defaulted if unspecified type sorted or unsorted DD scrambled by global index output default sorted j writer count 1 lt j lt job size default j gInt Log Min job size By 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 u 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 119 OSTFC Section 5 1 metal direct mindis f minimise string n f msdtmp i j multiple timestep n mxquat n mxshak n mxstep f nfold i j k no
130. ORTRANO90 compiler and MPI implementation To specify the FORTRAN90 compiler in a target platform the user must type the full path to the executable in FC and all appropriate options as defined in the relevant FOR TRAN90 manual and the path to the MPI implementation in FCFLAGS The same must be done for the 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 4 2 1 3 Note on the Interpolation Scheme In DL_POLY_4 two body like contributions van der Waals metal and real space Ewald summa tion to energy and force are evaluated by interpolation of tables constructed at the beginning of execution The DL_POLY 4 interpolation scheme is based on a 3 point linear interpolation in r Note that a 5 point linear interpolation in r is ised in DL POLY 4 for interpolation of the EAM metal forces from EAM table data TABEAM The number of grid points mxgrid required for interpolation in r to give good energy conservation in a
131. P MAKE LD bgsys drivers ppcfloor comm bin mpixlf2003_r o LDFLAGS 03 qhot qarch 450d qtune 450 qmaxmem 128000 FC bgsys drivers ppcfloor comm bin mpix1f2003 r c FCFLAGS 03 qhot qarch 450d qtune 450 qmaxmem 128000 EX EX BINROOT BINROOT TYPE hector MAKE LD ftn o LDFLAGS 03 FC ftn c FCFLAGS 03 EX EX BINROOT BINROOT TYPE hector pgi debug MAKE LD ftn o LDFLAGS 00 W Wall pedantic std f2003 g fbounds check fbacktrace finit real nan finit integer 999999 FC ftn c N FCFLAGS 00 W Wall pedantic std f2003 g fbounds check fbacktrace finit real nan finit integer 999999 EX EX BINROOT BINROOT TYPE hector gnu MAKE LD ftn o LDFLAGS 03 Wall pedantic g FC ftn c FCFLAGS 03 Wall pedantic g EX EX BINROOT BINROOT TYPE 200 OSTFC Appendix C hector gnu debug MAKE LD ftn o LDFLAGS 03 Wall Wextra pedantic g fbounds check fbacktrace finit integer 9999 finit real nan std f2003 pedantic ffpe trap invalid zero overflow fdump core FC ftn c N FCFLAGS 03 Wall Wextra pedantic g fbounds check fbacktrace finit integer 9999 finit real nan std f2003 pedantic ffpe trap invalid zero overflow fdump core EX EX BINROOT BINROOT TYPE hector cray MAKE LD ftn o LDFLAGS 03 en FC ftn c N FCFLAGS 03
132. Parallel DD tailored SHAKE and RATTLE Algorithms 172 6 1 9 The Parallel Rigid Body Implementation 173 62 Source diii T 174 6 2 1 Modularisation Principles s s o so tor s socos go RE m RR REDE 174 0 2 2 Due Structure Luo pedina Yee p eA Pa Swe ORIS We hee m 176 6 2 3 Module Files 2 354224 24 484 860425544 6044 04 E REOR EA 178 G24 General Files a 44 4 rade ea i ee A ee ee ee e d 178 zo VV and LFV Specie Eiles ova gs ecg doe ea DE ee we ee s 179 6 2 6 SERIAL Specific Piles cms uoo eR be abe de eR AA eS 179 6 2 7 Comments on MPI Handling i ea dae ceras rra 179 6 2 8 Comments on SETUP_MODULE s ssas e raada enaa ad koe rss 179 7 Examples 182 TA Test Cases co caci 65 e R288 be 8a a a b 30 ee See RO 183 7 1 1 Test Case 1 and 2 Sodium Chloride llle 183 7 1 2 Test Case 3 and 4 DPMC in Water 183 TES Test Case Dand 6t RiNasiabDe vigile Oa ewe eS ee S ROX LEG 183 7 1 4 Test Case 7 and 8 Gramicidin A molecules in Water 184 7 1 5 Test Case 9 and 10 SiC with Tersoff Potentials 184 7 1 6 Test Case 11 and 12 CuzAu alloy with Sutton Chen metal Potentials 184 7 1 7 Test Case 13 and 14 lipid bilayer in water 184 7 1 8 Test Case 15 and 16 relaxed and adiabatic shell model MgO 184 7 1 9 Test Case 17 and 18 Potential of mean force on K in water MgO 184 7 1 10 Test Case 19 and 20 CuzAu alloy with Gupta metal Potentials
133. S 03 FC mpif90 c FCFLAGS 03 EX EX BINROOT BINROOT TYPE lake MAKE LD opt intel compiler70 ia32 bin ifc v 0 LDFLAGS 03 xW prec div L opt mpich intel lib lmpich L opt intel compiler70 ia32 lib 1PEPCF90 FC opt intel compiler70 ia32 bin ifc c FCFLAGS 03 xW prec_div I opt mpich intel include EX EX BINROOT BINROOT TYPE 2I OSTFC Appendix C Linux efc SGI ALTIX parallel FFT newton MAKE LD ifort o LDFLAGS tpp2 ip 03 lmpi lguide FC ifort c FCFLAGS 03 tpp2 ip w EX EX BINROOT BINROOT TYPE dirac MAKE LD usr local mpich gm pgroup121 7b bin mpif90 v o LDFLAGS 03 L usr local mpich gm pgroupi21 7b lib 1mpich lfmpich lmpichf90 L usr local gm binary lib lgm L usr local lib FC usr local mpich gm pgroup121 7b bin mpif90 c FCFLAGS fast Knoieee Mdalign 03 EX EX BINROOT BINROOT TYPE Franklin SUNfire cluster setenv HPCF_MPI yes franklin MAKE LD opt SUNWhpc bin mpf90 o LDFLAGS stackvar fsimple 1 x03 xarch v9b DHPCF_MPI lmpi xlic_lib sunperf FC opt SUNWhpc bin mpf90 c FCFLAGS stackvar fsimple 1 x03 xarch v9b xchip ultra xlic lib sunperf xalias actual fpover ftrap none fnonstd libmil dalign I opt SUNWhpc HPC5 0 include v9 EX EX BINROOT BINROOT
134. T CORE SHELL ON TOP DEPORT_ATOMIC_DATA PMF_UNITS_SET COMPRESS_BOOK_INTRA RELOCATE_PARTICLES LINK_CELL_PAIRS METAL_LD_COLLECT_EAM METAL_LD_COLLECT_FST METAL_LD_EXPORT METAL_LD_SET_HALO METAL_LD_COMPUTE EXCHANGE_GRID EWALD_SPME_FORCES METAL_FORCES VDW_FORCES EWALD_REAL_FORCES COUL_DDDP_FORCES COUL_CP_FORCES COUL_FSCP_FORCES COUL_RFP_FORCES RDF_COLLECT RDF_EXCL_COLLECT EWALD_EXCL_FORCES EWALD_FROZEN_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 CORE_SHELL_RELAX ZERO_K_OPTIMISE NVT_EO_SCL NVT_E1_SCL NVT_BO_SCL NVT_B1_SCL XSCALE CORE SHELL KINETIC REGAUSS_TEMPERATURE Z DENSITY COLLECT STATISTICS COLLECT SYSTEM_REVIVE RDF_COMPUTE Z_DENSITY_COMPUTE STATISTICS_RESULT DL_POLY e VV specific files in the source VV directory PSEUDO VV CONSTRAINTS SHAKE VV PMF_SHAKE_VV CONSTRAINTS RATTLE PMF_RATTLE NVT_HO_SCL NVT_GO_SCL NPT_HO_SCL NST HO SCL 177 OSTFC Section 6 2 NVE_0_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 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_Al_VV NVT Bl VV N
135. 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 03 4 June 2012 STFC Preface ABOUT DL_POLY 4 DL POLY 4 is a general purpose parallel molecular dynamics simulation package developed at Daresbury Laboratory by W Smith and I T Todorov The DL_POLY project was developed under the auspices of the Engineering and Physical Sciences Research Council EPSRC for the EPSRC s Collaborative Computational Project for the Computer Simulation of Condensed Phases CCP5 the Computational Chemistry and Advanced Research Computing Groups CCG amp ARCG at Daresbury Laboratory and the Natural Environment Research Council NERC for the NERC s eScience project Computational Chemistry in the Environment eMinerals directed by M T Dove DL POLY 4 is the property of Daresbury Laboratory and is issued free under licence to academic institutions pursuing scientific research of a non commercial nature Commercial organisations may be permitted a licence to use the package after negotiation with the owners Daresbury Laboratory is the sole centre for distribution of the package Under no account is it to be redistributed to third parties without consent of the owners The purpose of the DL POLY 4 package is to provide software for academic research that is inex pensive accessible and free of commercial considerations Users have direct access
136. The variables pertaining to each potential are described in Table 5 12 Note that any pair potential not specified in the FIELD file will be assumed to be zero 2 metal n where n is the number of metal potentials to be entered It is followed by n records each specifying a particular metal potential in the following manner atmnam 1 a8 first atom type atmnam 2 a8 second atom type key ad potential key see Table 5 13 variable 1 real potential parameter see Table 5 13 variable 2 real potential parameter see Table 5 13 variable 3 real potential parameter see Table 5 13 variable 4 real potential parameter see Table 5 13 variable 5 real potential parameter see Table 5 13 variable 6 real potential parameter see Table 5 13 144 OSTFC Section 5 1 Table 5 12 Pair Potentials key potential type Variables 1 5 functional form tab Tabulation tabulated potential 12 6 12 6 A B U r 4 4 lj Lennard Jones e o U r 4e 2 27 nm nm E n m ro Ute se CE m 2 n 12 buck Buckingham A p C U r A exp 5 bhm Born Huggins A B o C D U r A exp B o r E x Meyer hbnd 12 10 H bond A B U r 4s 4 snm Shifted force Eo n m ro r U r 22 x n m 45 man C9 3 ne C 3 j nma Eo T Yro B de B Hi er CEU 6 mors Morse Eo ro k U r Eo 1 exp k r ro 1 12 6 1 wca Shifted Weeks e o
137. VT_H1_VV NVT Gl VV NPT Ll VV NPT Bl VV NPT Hl VV NPT Ml VV NST Ll VV NST Bl VV NST Hl VV NST Ml VV MD VV e LFV specific files in the source LFV directory PSEUDO LFV CONSTRAINTS SHAKE LFV PMF SHAKE LFV NVE_0_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_Al_LFV NVT Bl LFV NVT Hl LFV NVT Gl LFV NPT_L1_LFV NPT Bl LFV NPT Hl LFV NPT Ml LFV NST_L1_LFV NST_B1_LFV NST Hl LFV NST Ml LFV MD LFV e SERIAL specific files in the source SERIAL directory MPIF H MPI MODULE EWALD SPME FORC S The files in each group are listed in 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 C It is worth noting that the files REPLAY HISTORY F90 MD VV F90 MD LFV MPIF H are in fact inclusion files rather than strict FORTRAN90 type of files Should this prove to be a prob lem and a compiler cannot handle this then they can be incorporated directly in the routines where they are used i e REPLAY HISTORY F90 MD VV F90 MD_LFV in DL POLY F90 and MPIF H in COMMS MODULE F90 and then compilation should be attempted 6 2 3 Module Files The DL POLY 4 module files contain all global variables scalars and arrays and parameters as well as some genera
138. _module o parallel_fft o 0BJ ALL warning o error o scan_control_io o numeric_container o spme_container o quaternions_container o scan_field o read_config_parallel o scan_config o scan_control o read_config o set_bounds o read_control o vdw_generate o vdw_table_read o vdw_direct_fs_generate o metal_generate o metal_table_read o metal_table_derivatives o tersoff_generate o dihedrals 14 check o read field o check config o scale config o write config o trajectory write o system expand o rigid bodies tags o rigid bodies coms o rigid bodies widths o rigid bodies setup o tag legend o report topology o pass shared units o build book intra o build excl intra o Scale temperature o update shared units o core shell quench o constraints tags o constraints quench o pmf coms o pmf tags o pmf vcoms o pmf quench o rigid bodies quench o Set temperature o vdw lrc o metal lrc o system init o export atomic data o set halo particles o rigid bodies stress o read history o defects reference read o defects reference read parallel o defects reference write o defects reference export o defects reference set halo o defects link cells o defectsi write o defects write o msd write o rsd write o impact o core shell on top o deport atomic data o pmf units set o compress book intra o relocate particles o link cell pairs o metal ld collect eam o metal ld collect fst o metal ld
139. a x x v t At 3 108 The LFV implementation of the Langevin algorithm is iterative until self consistency in the full step velocity u t is obtained Initial estimate of n t at full step are calculated using an unconstrained estimate of the velocity at full step u t Also calculated is an unconstrained estimate of the half step position r t At 1 FF JO ee FEA Rt R t At 3 109 R t Ry t At 2 LFV The iterative part is as follows 3 At scale 1 x 1 gt ato f 2 2 Scale v 1 scale At scale f scale 74 STFC Section 3 5 t R t u t At scale v v t At scale f f Alt e AD amp rA Lo At Dad Ant 340 3 110 H t At lt exp nt SA At H t VELA a E ie SA At V t 3 SHAKE 4 Full step velocity and half step position 1 1 1 u t oa 5 F e t 4 At elit lA a ROSE AD 3 111 2 2 5 Thermostat and Barostat 1 1 n t At exp xp At n t At At Pox 2Ekin A 1 At lave ar Plt t pglEbin t At 3 112 Pmass f Pmass pus Ga Aa dp lAS i T MEE GE a Several iterations are required to obtain self consistency In DL_POLY 4 the number of iterations is set to 7 8 if bond constraints are present Note also that the change in box size requires the SHAKE algorithm to be called each iteration The VV and LFV flavours of the langevin barostat and Nos Hoover thermostat are implemented in
140. a particle p is located in the vicinity of a site s defined by a sphere with its centre at this site and a radius Rgef then the particle is a first hand claimee of s and the site is not vacant Otherwise the site is presumed vacant and the particle is presumed a general interstitial If a site s is claimed and another particle p is located within the sphere around it then p becomes an interstitial associated with s After all particles and all sites are considered it is clear which sites are vacancies Finally for every claimed site distances between the site and its first hand claimee and interstitials are compared and the particle with the shortest one becomes the real claimee If a first hand claimee of s is not the real claimee it becomes an interstitial associated with s At this stage it is clear which particles are interstitials The sum of interstitials and vacancies gives the total number of defects in the simulated MD cell Frozen particles and particles detected to be shells of polarisable ions are not considered in the defect detection Note that the algorithm cannot be applied safely if Racy 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 refe
141. a 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 4 152 STFC Section 5 1 data 1 real data item 1 data 2 real data item 2 data 3 real data item 3 data 4 real data item 4 5 1 6 3 Further Comments It should be noted that the number of grid points in the TABLE file should not be less than the number of grid points DL POLY 4 is expecting This number is given by the parameter mxgrid calculated in the SETUP MODULE file see Section 4 2 1 3 and 6 2 8 DL POLY 4 will re interpolate the tables if ngrid gt mxgrid but will abort if ngrid mxgrid The potential and force tables are used to fill the internal arrays vvdw and gvdw respectively see Section 2 3 1 The contents of force arrays are derived from the potential via the formula G r r2 u r 5 8 Note this is not the same as the true force During simulation interactions beyond distance Min reut cutpot are discarded 5 1 7 The TABEAM File The TABEAM file contains the tabulated potential functions no explicit analytic form describing the EAM metal interactions in the MD system This file is read by the subroutine METAL TABLE READ see Chapter 6 The EAM potential for an n component metal alloy requires the specification of n electron density functions one for each atom type and n embedding functions again one for eac
142. aCl ion pairs with 4 480 35 840 water molecules represented by constraint bonds and 4 416 35 328 water molecules represented by ridig bodies Totalling 26 816 214 528 atoms Simulation at 295 K using NPT Berendsen ensemble with CGM energy minimisation and SPME electrostatics 7 1 19 Test Case 37 and 38 TIP4P water RBs with a massless charged site These systems consist of 7 263 and 58 104 TIP4P rigid body water molecules totaling 29 052 and 232 416 particles respectively Simulation at 295 K using NPT Berendsen ensemble with CGM energy minimisation and SPME electrostatics 185 OSTFC Appendix 7 1 20 Test Case 39 and 40 Ionic liquid dimethylimidazolium chloride These systems consist of 44 352 and 354 816 ions respectively Simulation at 400 K using NPT Berendsen ensemble using both particle and rigid body dynamics with SPME electrostatics 7 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 7 2 Benchmark Cases DL POLY 4 benchmark test cases are avaliable to download them from the CCP5 FTP server as follows FTP site ftp dl ac uk Us
143. actions 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 55 74 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 75 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 operations and charge array construction while SPME FORCES calculates the forces Other routines required to calculate the Ewald sum include EWALD MODULE EWALD EXCL FORCES EWALD FROZEN FORCES and SPME CONTAINER 171 OSTFC Section 6 1 6 1 5 Metal Potentials The simulation of metals 2 3 2 by DL POLY 4 makes use of density dependent potentials The dependence on the atomic density presents no difficulty however as this class of potentials can be resolved into pair contributions This permits the use of the distributed Verlet neighbour list as outlined above DL POLY 4 implements these potentials in vario
144. aints 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 i Harmonic potential hrm Morse potential mrs 12 6 potential bond 126 Lennard Jones potential 1j Restrained harmonic rhm Quartic potential qur Buckingham potential bck Coulomb potential cul o 0 No C A W N FENE potential fne In DL POLY 4 distance restraints are handled by the routine BONDS_FORCES and INTRA_COUL called within Note some DL POLY 4 routines may use the convention that ri TiS rj 15 OSTFC Section 2 2 2 2 3 Valence Angle Potentials Figure 2 2 The valence angle and associated vectors The valence angle potentials describe the bond bending terms between the specified atoms They should not be confused with the three body potentials described later which are defined by atom types rather than indices 1 Harmonic harm U Onn OM 6 2 15 2 Quartic quar U Ojik E Oja 09 4 Ojik 09 E 0 1 69 2 16 3 Truncated harmonic thrm U Oyun E Oji 0 exp 0 rfe 2 17 4 Screened harmonic shrm U Orin Ou
145. aints tags o constraints quench o pmf coms o pmf tags o pmf vcoms o pmf quench o rigid bodies quench o set temperature o vdw lrc o metal lrc o system init o export atomic data o set halo particles o rigid bodies stress o read history o defects reference read o defects reference read parallel o defects reference write o defects reference export o defects reference set halo o defects link cells o defectsi write o defects write o msd write o rsd write o impact o core shell on top o deport atomic data o pmf units set o compress book intra o relocate particles o link cell pairs o metal ld collect eam o metal ld collect fst o metal ld export o metal ld set halo o metal ld compute o exchange grid o ewald spme forces o metal forces o vdw forces o ewald real forces o coul dddp forces o coul cp forces o coul fscp forces o coul rfp forces o rdf collect o rdf excl collect o ewald excl forces o ewald frozen forces o two body forces o tersoff forces o three body forces o four body forces o core shell forces o tethers forces o intra coul o bonds forces o angles forces o inversions forces o dihedrals 14 vdw o dihedrals forces o external field apply o external field correct o langevin forces o constraints pseudo bonds o pmf pseudo bonds o rigid bodies split torque o rigid bodies move o minimise relax o core shell relax o zero k optimise o nvt eO scl o nvt ei scl
146. 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 avoided 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 performance of the parallel I O for example putting in CONTROL see Section 5 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 67 68 69 101 OSTFC Section 4 2 4 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 tr
147. ance the positions to a full step t At using the new half step velocities 1 VVI At f t 1 t f t LA n ELL wl u t A c wt E 3 1 where m is the mass of a site and At is the timestep 1 r t At r t At v t 344 3 2 2 FF Between the first and the second stage a recalculation of the force at time t At is required since the positions have changed f t At fit 3 3 3 VV2 In the second stage the half step velocities are advanced to to a full step using the new force 1 At f t At v t At c v t At DE a 3 4 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 psoition The LFV algorithm is one staged It requires values of position r and force f at time t and velocity v at half a timestep behind t 1 2 At Firstly the forces are recalculated afresh at time t from time t At since the positions have changed from the last step 1 FF f lt ft At 3 5 where At is the timestep 2 LFV The velocities are advanced by a timestep to t 1 2 At by integration of the new force 1 1 f t t A At At 3 6 u t 5At vt At ALT
148. and S so chosen that to include the first neighbor shell 1 Tjj lt Rij ij Rij fo rij 5 3 COS x aE Rij lt Tij lt Sij 2 133 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 1 Vig Xij 1 8 LE s Lij 5 fo rik wik 9 0 jk 2 134 kzij b c2 D 1 2 a g 0 jk d d HE hi cos hijr 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 riz and the bond angle 0 x between them with respect to the central atom i The function g 0 has a minimum for h cos 0 x the parameter d determines how sharp the dependence on angle is and c expresses the strength of the angular effect Further mixed parameters are defined as aij a a5 2 dy bi b 2 Aj A A 7 B4 BB 2 135 Rij REA y Sy S S Singly subscripted parameters 11 such as a and n depend only on the type of atom The chemistry between different atom types is locked in the two sets bi atomic parameters x and Wij xi l Xij Xj Wi l Wij wj 2 136 which define only one independent parameter each per pair of atom types The x parameter is used to strengthen or weaken the heteropolar bonds relative to the value obtained by simple inter
149. anged corrections apply beyond ret 2 Finnis Sinclair energy correction No long ranged corrections apply beyond cutoffs c and d 3 Extended Finnis Sinclair energy correction No long ranged corrections apply beyond cutoffs c and d 4 Sutton Chen energy correction onND 3 n 3 S ee TN pea a n 3 Fmet 513 n 3 PU i ES 2 122 m 3 Tmet 2 pe 5 Gupta energy correction InN pA 2 U Ud RAD mu 2r met 3 2 3 x p p p Tmet TO exp pt To 27 pr r r gt i PO dora lg 2 123 dij dij dij e 9 ee NB p dij TQ 2 0 a To estimate the virial correction we assume the corrected local densities are constants i e in dependent of distance at least beyond the range rmet This allows the virial correction to be computed by the methods used in the short ranged potentials OVi rij Tij Y I Bis Tij i 1 jf ij N TFij lt Tmet N rij IT met iXX wu ODI E yg W 45 i l jfi i l jf OVi OVi r r3d dr Y 2nNp ru Tmet E x OF Dn Opi riz T y rj 2 124 i Opi jfi Ori N Tij lt Tmet Tij 2Tmet OF pi 7 Opi nd OF pi E Opi rij 0 ee eS DEO SSS 08 0 ed D ig 088 do Ga OF N 2 OF pi Opij r r r3 Wa Arp d dr i 1 Opi Tmet Or Evaluating the integral part of the above equations yields 35 OSTFC Section 2 3 1 EAM virial correction No long ranged corrections apply beyond Yet 2 Finnis Sinclair viria
150. angevin The stochasticity of the Langevin thermostat emulates an infinite environment around the MD cell providing a means for natural heat exchange between the MD system and the heath bath thus aiding possible heat build up in the system In this way the instan taneous temperature of the system is driven naturally towards the bath temperature 126 OSTFC Section 5 1 Every particle within the thermostat buffer layer is coupled to a viscous background and a stochastic heat bath such that dri C x v t u LOTO x t w t 5 2 where x t is the friction parameter from the dynamics in the the MD cell and R t is stochastic force with zero mean that satisfies the fluctuation dissipation theorem Re t R 0 2 x t mi kpT bag t t 5 3 where superscripts denote Cartesian indices subscripts particle indices kg is the Boltz mann constant T the bath temperature and mj 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 Rescale the kinetic energy of the thermostat bath so that particles within have Gaussian distributed kinetic energy with respect to the target temperature and determine the Gaussian constraint friction within the thermostat x t Max o Dilfi
151. ants 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 267 OSTFC Appendix D Message 478 error shake algorithms constraints amp pmf failed to converge Your system has both bond and PMF constraints SHAKE RATTLE_VV1 is done by combined application of both bond and PMF constraints SHAKE RATTLE_VV1 in an iterative manner until the PMF constraint virial converges to a constant No such convergence is achieved Action See Message 515 Message 480 error PMF constraint length gt minimum of all half cell widths The 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
152. apua aoa Reed a ae Ow e aa RR ea 152 51 7 The TABEAM File sc co 65 ao dad 3 3 Bom RR ONUS X EORR o de 153 52 The OUTPUT Piles caso tard 24 BS Rok cR Red es ue eka n Dk ee ari 154 bel The HISTORY File s d cem ea ku RR e ae Gat a eek a 154 5 2 2 The MSDTMP le uuu uer edits alee a E I eG REOR ADR Be Eos XL 156 523 The DEFECTS Pile lt a eor ssaa 24 564 44 64 e Ek 157 524 The BSDDAT File se rc cea 4006845 ko ROTE dae eee ON aw 158 5 2 5 The CRGMIN File o se saa ak ee a a ee PA ue a 160 5 2 0 The OUTPUT File mic rr eo Se A wa ee eae 160 bar The REVCON IE a ga iga bu fee be bee bee oe dea E d 163 5 28 The REVIVE Pile s cs 684 004 e ae ne ee a ee ee ae ai 163 52 9 The RDEDAT Pile o 4 4 4 245 esu 9 kG a eR A na 164 5 2 10 The ZDNIDAT Elle uo ox le re Rep EROR LOS ke UR RR ERR mE 164 Dub Te STATIS Pile s x uuo pe hoe A a 165 6 The DL POLY 4 Parallelisation and Source Code 167 Gad ParsalelBablOl sre sa ec g a uoa yw eo REO E eee e E MONDO i a 168 6 1 1 The Domain Decomposition Strategy 22e 168 vill STFC Contents 6 1 2 Distributing the Intramolecular Bonded Terms 169 6 1 3 Distributing the Non bonded Terms ccr 170 6 1 4 Modifications for the Ewald Sum LL 171 0 L5 Metal Potentials o soos soda oh oo m le GR a ER Roe 4 172 6 1 6 Tersoff Three Body and Four Body Potentials 172 6 1 7 Globally Summed Properties 22 2 om Ro RR REA 172 6 1 8 The
153. are being written for example but they can help a great deal You are advised to keep backup copies of these files noting the times they were written to help you avoid going right back to the start of a simulation You can also extend a simulation beyond its initial allocation of timesteps provided you still have the REVCON and REVIVE files These should be copied to the CONFIG and REVOLD files respectively and the directive timesteps adjusted in the CONTROL file to the new total number of steps required for the simulation For example if you wish to extend a 10000 step simulation by a further 5000 steps use the directive timesteps 15000 in the CONTROL file and include the restart directive Further to the full restart option there is an alternative restart scale directive that will reset the temperature at start or restart noscale that will keep the current kinetics intact bf Note that these two options are not correct restarts but rather modified starts as they make no use of REVOLD file and will reset internal accumulators to zero at start 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 4 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
154. as encountered and erroneous entry for Tersoff potentials in FIELD Action Correct FIELD and resubmit Message 77 error oo 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 78 error too many link cells required in tersoff forces This should not happen The calculation of Tersoff forces in DL POLY 4 is handled by the link cell algorithm This error arises if the required number of link cells exceeds the permitted array 249 OSTFC Appendix D dimension in the code Action Consider using densvar option in CONTROL for extremely non equilibrium simulations Alterna tively increase mxcell in SET BOUNDS recompile and resubmit Message 79 error tersoff potential cutoff undefined This shows that DL_POLY_4 has encountered and erroneous entry for Tersoff potentials in FIELD Action Correct FIELD and resubmit Message 80 error too many pair potentials specified This should never happen Action Report to authors Message 81 error unidentified atom in pair potential list This shows that DL_POLY 4 has encountered and erroneous entry for vdw or metal potentials i
155. ate an array or arrays ie 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 Action See Message 1001 Message 1004 error deallocation failure in comms module gt gisum vector Action See Message 1002 Message 1005 error allocation failure in comms module gt grsum vector Action See Message 1001 Message 1006 error deallocation failure in comms module gt grsum vector Action See Message 1002 Message 1007 error allocation failure in comms module gt gimax vector Action See Message 1001 278 OSTFC Appendix D Message 1008 error deallocation failure in comms module gt gimax vector Action See Message 1002 Message 1009 error allocation failure in comms module gt grmax vector Action See Message 1001 Message 1010 error deallocation failure in comms module gt grmax vector Action See Message 1002 Message 1011 error allocation failure in parse module gt get record Action See Message 1001 Message 1012 error deallocation failure in parse module gt get record Action See Message 1002 Message 1013 error allocation failure in angles module gt allocate angles arrays Action See Message 1001 Message 101
156. ater than nstraj the HISTORY file is appended at intervals specified by the traj directive in the CONTROL file with the following information for each configuration record i timestep a8 the character string timestep nstep integer the current time step megatm integer number of atoms in simulation cell again keytrj integer trajectory key again imcon integer periodic boundary key again tstep real integration timestep ps time real elapsed simulation time ps record ii cell 1 real x component of a cell vector cell 2 real y component of a cell vector cell 3 real z component of a cell vector record iii cell 4 real x component of b cell vector cell 5 real y component of b cell vector cell 6 real z component of b cell vector record iv cell 7 real x component of c cell vector cell 8 real y component of c cell vector cell 9 real z component of c cell vector This is followed by the configuration for the current timestep i e for each atom in the system the following data are included record a atmnam a8 atomic label iatm integer atom index weight real atomic mass a m u charge real atomic charge e 155 OSTFC Section 5 2 rsd real displacement from position at t 0 record b XXX real x coordinate yyy real y coordinate ZZZ real z coordinate record c only for keytrj gt 0 VXX real x component of velocity vyy real y component of velocity VZZ real z component of velocity record d only for keytrj gt
157. ates the atom type represented by the function Then z p z and n z are given in tabular form Output is given from Z L 2 L 2 where L is the length of the MD cell in the Z direction and p z is the mean number density n z is the running integral from L 2 to z of xy cell area x p s ds Note that a readable version of these data is provided by the ZDNDAT file below 5 2 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 6 2 2 The default value is ndump 1000 REVCON is identical in format to the CONFIG input file see Section 5 1 2 REVCON should be renamed CONFIG to continue a simulation from one job to the next This is done for you by the copy macro supplied in the execute directory of DL POLY 4 5 2 8 The REVIVE File This file is unformatted and written by the subroutine SYSTEM_REVIVE It contains the accumu lated statistical data It is updated whenever the file REVCON is updated see previous section REVIVE should be renamed REVOLD to
158. ation method on SETUP MODULE e minimise module MINIMISE MODULE This module defines all variables and arrays needed for the application of a Conjugate Gra dient Method minimisation routine in the DL_POLY 4 scope It depends on KINDS F90 and its allocation method on SETUP MODULE e ewald module EWALD MODULE This module defines all variables and arrays needed for the refreshment of SPME k space driven properties in the DL POLY 4 scope when an infrequent SPME option is opted for in CONTROL It depends on KINDS F90 and its allocation method on SETUP MODULE 175 OSTFC Section 6 2 e msd module MSD MODULE This module globalises a CONTROL variable e statistics module STATISTICS MODULE This module defines all variables and arrays needed for the statistical accountancy of a simula tion in DL POLY 4 It depends on KINDS F90 and its allocation method on SETUP MODULE e kinetic module KINETIC MODULE The kinetic module contains a collection of routines for the calculation of various kinetic properties It is dependent on KINDS F90 6 2 2 File Structure Generally the DL POLY 4 file structure can be divided into four groups as follows e module files in the source directory KINDS F90 COMMS MODULE SETUP MODULE PARSE MODULE DEVELOPMENT MODULE IO MODULE DOMAINS MODULE SITE MODULE CONFIG MODULE DEFECTS MODULE VDW MODULE METAL MODULE TERSOFF MODULE THREE BODY MODULE FOUR BODY MODULE CORE SHEL
159. atistics module o rdf compute o comms module o config module o kinds f90 0 setup module o Site module o statistics module o rdf excl collect o config module o kinds f90 0 setup module o site module o A Statistics module o read config o comms module o config module o domains module o io module o kinds f90 0 parse module o setup module o read config parallel o comms module o config module o domains module o io module o kinds f90 0 parse module o setup module o read control o comms module o config module o defectsi module o development module o kinds f90 0 langevin module o metal module o parse module o setup module o vdw_module o read field o angles module o bonds module o comms module o config module o constraints module o core shell module o dihedrals_module o external field module o four body module o inversions module o 209 OSTFC Appendix C kinds f90 0 metal module o parse module o pmf module o rigid bodies module o setup module o site module o statistics module o tersoff module o tethers_module o three body module o vdw module o read history o comms module o config module o domains module o io module o kinds f90 0 parse module o setup module o site module o regauss temperature o comms module o config module o kinds f90 0 kinetic module o rigid bodies module o setup module o relocate particles o angles module o bonds module o comms module o config module o constraints module o co
160. ative is le arg U Piit Tij Tik Tjk Sri S ik S rie Ss Aix ri A Ojik S rik S rk dej de z riz Tij Orij ro 0 A 85ik S rij S rjk 0a de sS rip Tik Orik P A 05ix S rij S rix Sen de 5 rj 2 30 Tik Tik with 0 1 if a b and 64 0 if a Z b In the absence of screening terms S r this formula reduces to lo lo org ie Tij Tue Tk grg Au 2 31 The derivative of the angular function is le 1 o o J Tij Tik A 0 x A G x s 2 32 ore Ojix OO si 0 Dora TijTik 17 OSTFC Section 2 2 with zs E el ld os Or Tijfik PijTik PijTik cos 0jik de dei gt dex dei 3 2 33 T T ij ik The atomic forces are then completely specified by the derivatives of the particular functions A 0 and S r The contribution to be added to the atomic virial is given by Wa E ds Ef f 2 34 It is worth noting that in the absence of screening terms S r the virial is zero 40 The contribution to be added to the atomic stress tensor is given by g re fe ra fe 2 35 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 07 is handled as a special case of angle potentials As a consequence angle rest
161. atom 6 fbp n where n is the number of four body potentials to be entered It is followed by n records each specifying a particular four body potential in the following manner atmnam 1 i atmnam 2 j atmnam 3 k a8 a8 a8 first central atom type second atom type third atom type 148 OSTFC Section 5 1 Table 5 15 Three body Potentials key potential type Variables 1 4 functional formi harm Harmonic k bo U 0 E 0 69 thrm Truncated harmonic k b p U 0 0 09 exp r2 r5 0 shrm Screened harmonic k 0 pi p2 U 0 E 8 00 exp ri p1 rix pa bvs1 Screened Vessal 36 k 0 pi p2 U 0 Cee T 0 7 x exp rij p1 rik p2 bvs2 Truncated Vessal 37 k 0 a p U 0 k 0 69 6 0 69 0 bo 27 ga 0o x exp r 73 0 hbnd H bond 19 Dna Rab U B Du cos 0 x 5 Fa ri 6 Ras T jx 0 is the 2 j k angle atmnam 4 I a8 fourth atom type key a4 potential key see Table 5 16 variable 1 real potential parameter see Table 5 16 variable 2 real potential parameter see Table 5 16 variable 3 real cutoff range for this potential The variables pertaining to each potential are described in Table 5 16 Note that the third variable is the range at which the four body potential is truncated The distance is in measured from the central atom
162. atoms in simulation cell again tstep real integration timestep ps time real elapsed simulation time ps 156 STFC Section 5 2 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 Trein real atomic mean temperature in Kelvin 5 2 3 The DEFECTS File The DEFECTS file is the dump file of atomic coordinates of defects see Section 5 1 4 Its princi pal use is for off line analysis The file is written by the subroutine DEFECTS WRITE The control variables for this file are 1def nsdef isdef and rdef which are created internally based on in formation read from the defects directive in the CONTROL file see Section 5 1 1 The DEFECTS file will be created only if the directive defects appears in the CONTROL file The DEFECTS file may become very large especially if it is formatted For serious simulation work it is recommended that the file be written to a scratch disk capable of accommodating a large data file The DEFECTS has the following structure record 1 header a72 file header record 2 rdef real site interstitial cutoff 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
163. b 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 OSTFC Section 1 5 1 4 3 The data Sub directory This sub directory contains examples of input and output files for testing the released version of DL POLY 4 The examples of input data are copied into the execute sub directory when a program is being tested The test cases are documented in Chapter 7 Note that these are no longer within the distribution of any DL POLY version but are made available on line at the DL POLY FTP ftp ftp dl ac uk ccp5 DL_POLY 1 4 4 The bench Sub directory This directory contains examples of input and output data for DL_POLY 4 that are suitable for benchmarking DL POLY 4 on large scale computers These are described in Chapter 7 Note that these are no longer within the distribution of any DL_POLY version but are made available on line at the DL POLY FTP ftp ftp dl ac uk ccp5 DL POLY 1 4 5 The execute Sub directory In the supplied version of DL POLY 4 this sub directory contains only a few macros for copying and storing data from and to the data sub directory and for submitting programs for execution see Appendix B However when a DL POLY 4 program is assembled by using the appropriate makefile it will be placed in this sub directory and will subsequently be executed from here The output from the job will also appear here so users will
164. 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 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 only one bonds directive per molecule is allowed DL POLY 4
165. be reset if illegal values were specified in the CONTROL file This part of the file is written from the subroutine READ CONTROL 5 2 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 5 2 6 4 System Specification Echoes system name periodic boundary specification the cell vectors and volume some initial esti mates of long ranged corrections the energy and pressure if appropriate some concise information on topology and degrees of freedom break down list This part of the file is written from the subrou tines SCAN_CONFIG CHECK_CONFIG SYSTEM_INIT REPORT_TOPOLOGY and SET_TEMPERATURE 160 OSTFC Section 5 2 5 2 6 5 Summary of the Initial Configuration This part of the file is written from the main subroutine DL POLY It states the initial configuration of a maximum of 20 atoms in the system The configuration information given is based on the value of levcfg in the CONFIG file If levcfg is 0 or 1 positions and velocities of the 20 atoms are listed If levcfg is 2 forces are also written out 5 2 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
166. ble b variable c real real real potential parameter see Table 5 14 potential parameter see Table 5 14 potential parameter see Table 5 14 cross term n n 1 2 record 2n n n 1 2 The variables pertaining to each potential are described in Table 5 14 Note that the fifth variable is the range at which the particular tersoff potential is truncated The distance is in Table 5 14 Tersoff Potential key potential type Variables 1 5 6 11 a c functional form ters Tersoff single cross A S B b R Potential form nicid h as shown in Section 2 e 5 tbp n where n is the number of three body potentials to be entered It is followed by n records each specifying a particular three body potential in the following manner atmnam 1 i atmnam 2 j atmnam 3 k key variable 1 variable 2 variable 3 variable 4 variable 5 a8 a8 a8 a4 real real real real real first atom type second central atom type third atom type potential key see Table 5 15 potential parameter see Table 5 15 potential parameter see Table 5 15 potential parameter see Table 5 15 potential parameter see Table 5 15 cutoff range for this potential The variables pertaining to each potential are described in Table 5 15 Note that the fifth variable is the range at which the three body potential is truncated The distance is in measured from the central
167. blem to us Message 15 error duplicate vdw potential specified In processing the FIELD file DL_POLY 4 keeps a record of the specified short range pair potentials as they are read in If it detects that a given pair potential has been specified before no attempt at a resolution of the ambiguity is made and this error message results See specification of FIELD file Action Locate the duplication in the FIELD file rectify and resubmit Message 16 error strange exit from FIELD file processing This should never happen It simply means that DL POLY 4 has ceased processing the FIELD data but has not reached the end of the file or encountered a close directive Probable cause corruption of the DL POLY 4 executable or of the FIELD file We would be interested to hear of other reasons Action Recompile the program or recreate the FIELD file If neither of these works send the problem to us Message 17 error strange exit from CONTROL file processing See notes on message 16 above Message 18 error duplicate three body potential specified DL POLY 4 has encountered a repeat specification of a three body potential in the FIELD file Action Locate the duplicate entry remove and resubmit job Message 19 error duplicate four body potential specified A 4 body potential has been duplicated in the FIELD file Action Locate the duplicated four body potential remove and resubmit job 239 OSTFC Appendix D
168. c one by imposing that the MD cell change isotropically in the x y plane which leads to the following changes in the equations above d _ Gas t yy t 2 Pe Yext hz t V t 2 Exi t artes i s Pmass f Pmass X naa t te ex 3 171 2 Mass T ont t HNPy 0T Hyve dass XU E a zi Pa V t f 2 kg Text J 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 66 which is not the case for Nos Hoover NPT and NoT ensembles The NPT and NoT versions of the MTK ensemble are implemented in the DL POLY 4 rou tines NPT M0 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 88 STFC Section 3 6 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 either problematic or impossible Examples in which it is impossible to specify su
169. c module o rigid bodies module o setup module o site module o npt bi vv o comms module o config module o domains module o kinds f90 0 kinetic module o rigid bodies module o setup module o site module o npt hO lfv o comms module o config module o kinds f90 0 kinetic module o Setup module o site module o npt_h0_scl o config module o kinds f90 0 setup module o npt hO vv o comms module o config module o kinds f90 0 kinetic module o Setup module o site module o npt hi lfv o comms module o config module o domains module o kinds f90 0 kinetic module o rigid bodies module o setup module o site module o npt hi scl o config module o kinds f90 0 rigid bodies module o Setup module o npt hi vv o comms module o config module o domains module o kinds f90 0 kinetic module o rigid bodies module o setup module o site module o npt 10 lfv o comms module o config module o kinds f90 0 kinetic module o langevin_module o setup module o site module o npt 10 vv o comms module o config module o kinds f90 0 kinetic module o langevin_module o setup module o site module o npt 11 lfv o comms module o config module o domains module o kinds f90 0 kinetic module o langevin module o rigid bodies module o Setup module o site module o npt li vv o comms module o config module o domains module o kinds f90 0 kinetic module o langevin module o rigid bodies module o Setup module o site module o npt mO lfv o comms module o config module o
170. ce of the potential keyword in the FIELD file Message 170 error too many variables for statistics array This error means the statistics arrays appearing in subroutine STATISTICS COLLECT are too small This should never happen Action Contact DL POLY 4 authors Message 200 error rdf z density buffer array too small in system revive This error indicates that a global summation buffer array in subroutine SYSTEM REVIVE is too small i e mxbuff 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 258 OSTFC Appendix D Message 230 error only one inversions directive per molecule is allowed DL POLY 4 has found more than one inversions entry per molecule in FIELD Action Correct the erroneous part in FIELD and resubmit Message 240 error only one tethers directive per molecule is allowed DL POLY 4 has found more than one tethers entry per molecule in FIELD Action Correct the erroneous part in FIELD and resubmit Message 300 error incorrect boundary condition for l
171. ce sum is truncated at r reut so it is important that a be chosen so that contributions to the real space sum are negligible for terms with r gt reut The relative error e in the real space sum truncated at rey is given approximately by e erfc a reut Teut expl o Teut Teut 4 3 The recommended value for a is 3 2 reut or greater too large a value will make the reciprocal space sum very slowly convergent This gives a relative error in the energy of no greater than 4x 107 in the real space sum When using the directive ewald precision DL POLY 4 makes use of a more sophisticated approximation erfc z 0 56 exp 2 x 4 4 to solve recursively for o using equation 4 3 to give the first guess The relative error in the reciprocal space term is approximately RS exp k2 407 ko us 4 5 lImportant 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 108 OSTFC Section 4 4 where 27 kmax kinaa x L 2 4 6 is largest k vector considered in reciprocal space L is the width of the cell in the specified direction and kmax is an integer For a relative error of 4 x 107 this means using kmar 7 6 2 a kmax is then kmax gt 6 4 L Teut 4 7 In a cubic system freut L 2 implies kmax 14 In practice the above eq
172. cfg eng src eng cou eng bnd eng ang eng dih eng tet time ps eng pv temp rot vir cfg vir src vir cou vir bnd vir ang vir con vir tet cpu s volume temp shl eng shl vir shl alpha beta gamma vir_pmf press The labels refer to line 1 step eng tot temp tot eng cfg eng src eng cou eng bnd eng ang eng dih eng tet line 2 time ps eng pv temp rot vir cfg vir src vir cou vir bnd vir ang vir con vir tet line 3 cpu s volume temp shl eng shl vir shl MD step number total internal energy of the system system temperature in Kelvin configurational energy of the system configurational energy due to short range potential contributions configurational energy due to electrostatic potential configurational energy due to chemical bond potentials configurational energy due to valence angle and three body potentials configurational energy due to dihedral inversion and four body potentials configurational energy due to tethering potentials elapsed simulation time in pico seconds since the beginning of the job enthalpy of system rotational temperature in Kelvin total configurational contribution to the virial short range potential contribution to the virial electrostatic potential contribution to the virial chemical bond contribution to the virial angular and three body potentials contribution to the virial constraint bond contribution to the virial tethering potential contribution to the virial elapsed cpu time
173. cham D 1992 Molecular Simulation 8 165 4 91 Miller T Eleftheriou M Pattnaik P Ndirango A Newns D and Martyna G 2002 J Chem Phys 116 8649 4 91 92 Evans D J and Morriss G P 1984 Computer Physics Reports 1 297 4 56 60 Adelman S A and Doll J 1976 J Chem Phys 64 2375 4 56 60 Andersen H C 1979 J Chem Phys 72 2384 4 56 60 Berendsen H J C Postma J P M van Gunsteren W DiNola A and Haak J R 1984 J Chem Phys 81 3684 4 56 60 71 Hoover W G 1985 Phys Rev A31 1695 4 56 60 67 69 71 Quigley D and Probert M 2004 J Chem Phys 120 11432 4 56 71 72 Martyna G Tuckerman M Tobias D and Klein M 1996 Molec Phys 87 1117 4 56 71 86 92 Warner H R J 1972 ind Eng Chem Fundam 11 379 14 Bird R B e a 1977 Dynamics of Polymeric Liquids volume 1 and 2 Wiley New York 14 Grest G S and Kremer K 1986 Phys Rev A 33 3628 14 Vessal B 1994 J Non Cryst Solids 177 103 16 18 40 142 149 Smith W Greaves G N and Gillan M J 1995 J Chem Phys 103 3091 16 18 41 142 149 Allinger N L Yuh Y H and Lii J H 1998 J Am Chem Soc 111 8551 17 18 142 Sun H 1998 J Phys Chem B 102 38 7338 7364 17 18 142 Smith W 1993 CCP5 Information Quarterly 39 14 18 21 24 Ryckaert J P and Bellemans A 1975 Chem Phys Lett 30 123 19 143
174. cl f90 npt_h0_sc1 f90 nst_h0_scl 90 nve O vv f90 nvt eO vv f90 N nvt 10 vv f90 nvt aO vv f90 nvt bO vv f90 nvt hO vv f90 nvt gO vv f90 npt_10_vv f90 npt_b0_vv f90 npt hO vv f90 npt mO vv f90 N nst 10 vv f90 nst_b0_vv f90 nst hO vv f90 nst mO vv f90 N nvt hi scl f90 nvt gi scl f90 npt hi scl f90 nst hi scl f90 231 OSTFC Appendix C nve 1 vv f90 nvt ei vv f90 nvt 11 vv f90 nvt a1 vv f90 nvt bi vv f90 nvt hi vv f90 nvt gi vv f90 npt 11 vv f90 npt bi vv f90 npt hi vv f90 npt mi vv f90 nst li vv f90 nst bi vv f90 nst hi vv f90 nst mi vv f90 md vv f90 Define LeapFrog Verlet files FILES LFV pseudo lfv f90 constraints shake lfv f90 pmf shake lfv f90 nve O lfv f90 nvt eO lfv f90 nvt 10 1fv f90 nvt aO lfv f90 nvt bO lfv f90 nvt hO lfv f90 nvt gO lfv f90 npt 10 lfv f90 npt bO lfv f90 npt hO lfv f90 npt_m0_lfv 90 nst 10 l1fv f90 nst bO lfv f90 nst hO lfv f90 nst mO lfv f90 nve 1 lfv f90 nvt ei lfv f90 nvt li l1fv f90 nvt ai lfv f90 nvt b lfv f90 nvt h lfv f90 nvt gi lfv f90 npt 11 lfv f90 npt bi lfv f90 npt hi lfv f90 npt mi lfv f90 nst li lfv f90 nst bi lfv f90 nst h lfv f90 nst mi lfv f90 md lfv f90 Examine targets manually all echo echo You MUST specify or choose a permissive target platform echo echo The available permissive targets are displayed below echo echo win win debug echo echo Please examine this Makefile s targets for detail
175. clusive 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 105 OSTFC Section 4 3 4 3 A Guide to Preparing Input Files The CONFIG file and the FIELD file can be quite large and unwieldy particularly if a polymer or biological molecule is involved in the simulation This section outlines the paths to follow when trying to construct files for such systems The description of the DL POLY 4 force field in Chapter 2 is essential reading The various utility routines mentioned in this section are described in greater detail in the DL POLY Classic User Manual Many of these have been incorporated into the DL POLY 4 Graphical User Interface 21 and may be conveniently used from there 4 3 1 Inorganic Materials The utility GENLAT can be used to construct the CONFIG file for relatively simple lattice structures Input is interactive The FIELD file for such systems are normally small and can be constructed by hand Otherwise the input of force field data for crystalline systems is particularly simple if no angular forces are required notable exceptions to this are zeolites and silicate glasses see below Such systems require only the specification of the atomic types and the necessary pair forces The reader is referred to the description
176. code yourself Amendments to subroutines READ FIELD and INVERSIONS FORCES will be required Message 450 error undefined tethering potential A form of tethering potential has been requested which DL POLY 4 does not recognise Action Locate the offending potential in the FIELD file and remove Replace with one acceptable to DL POLY 4 if this is reasonable Alternatively you may consider defining the required potential in the code yourself Amendments to subroutines READ FIELD and TETHERS FORCES will be required Message 451 error three body potential cutoff undefined The cutoff radius for a three body potential has not been defined in the FIELD file 264 OSTFC Appendix D Action Locate the offending three body force potential in the FIELD file and add the required cutoff Resubmit the job Message 452 error undefined vdw potential A form of vdw potential has been requested which DL POLY 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 poten tial in the code yourself Amendments to subroutines READ FIELD VDW_GENERATE and DIHE DRALS 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
177. commended to study the forementioned root drives as a model for other implementations of the package they may wish to construct The dependencies and calling hierarchies of all the DL POLY 4 subroutines can be found in the Section 6 2 2 Should additional functionality be added to DL POLY 4 by the user the SET BOUNDS routine and its support subroutines may need modifying to allow specification of the dimensions of any new arrays Any molecular dynamics simulation performs five different kinds of operation initialisation forces calculation integration of the equations of motion calculation of system properties and job ter mination It is worth considering these operations in turn and to indicate which DL_POLY_4 routines are available to perform them We do not give a detailed description but provide only a guide Readers are recommended to examine the different routines described in the DL POLY 4 User Manual for further details particularly regarding further dependencies i e additional routines that may be called The following outline assumes a system containing flexible molecules held together by rigid bonds Initialisation requires firstly that the program determine what platform resources are made avail able to the specific simulation job This is done by the DL POLY 4 routine MAP DOMAINS in DOMAINS MODULE that attempts to allocate and map the resources nodes in parallel in com pliance with the DD strategy MAP DOMAINS is cal
178. continue a simulation from one job to the next This is done by the copy macro supplied in the execute directory of DL POLY 4 In addition to continue a simulation from a previous job the restart keyword must be included in the CONTROL file The format of the REVIVE file is identical to the REVOLD file described in Section 5 1 5 163 OSTFC Section 5 2 5 2 9 The RDFDAT File This is a formatted file containing em Radial Distribution Function RDF data Its contents are as follows record 1 cfgname a12 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 mxgrdf records radius real interatomic distance g r real RDF at given radius Note the RDFDAT file is optional and appears when the print rdf option is specified in the CONTROL file 5 2 10 The ZDNDAT File This is a formatted file containing the Z density data Its contents are as follows record 1 cfgname a2 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 firs
179. 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 53 In this model the total coulombic potential is given by 1 1 Bor U da d 2 177 e Tra 2 in E 2 177 3 j n 2R 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 ei 1 _ 2 178 0 ed ene with e the dielectric constant outside the cavity The effective pair potential is therefore 1 1 Bor U r ie j 2 179 rij Arepe 90 E 2R3 This expression unfortunately leads to large fluctuations in the system coulombic energy due to the large step in the function at the cavity boundary In DL POLY 4 this is countered by subtracting the value of the potential at the cavity boundary from each pair contribution The term subtracted is 1 2 zl 1 2 180 4meoe Re i 2 45 STFC Section 2 4 The effective pair force on an atom j arising from another atom n within the cavity is given by qiq 1 Bo n Ho 2 181 j Aree 3 x s In DL_POLY 4 the reaction field is optionally extended to emulate long range o
180. 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 l didj U r 2 161 rij 4mege Tij with q the charge on an atom labelled and ri the magnitude of the separation vector r r r ij j Unlike the other elements of the force field the electrostatic forces are NOT specified in the input FIELD file but by setting appropriate directives in the CONTROL file See Section 5 1 1 42 OSTFC Section 2 4 The force on an atom j derived from this force is l q 95 T 2 162 i 4mege r 7 with the force on atom 7 the negative of this The contribution to the atomic virial is 1 Jue wont 2 163 4T7 oe rij which is simply the negative of the potential term The contribution to be added to the atomic stress tensor is pP ep 2 164 where a 8 a
181. ction Check the FIELD and TABLE files Make sure that you correctly specify the pair potentials in the FIELD file indicating which ones are to be presented in the TABLE file Then check the TABLE file to make sure all the tabulated potentials are present in the order the FIELD file indicates Message 24 error end of file encountered in TABLE or TABEAM file This means the TABLE or TABEAM file is incomplete in some way either by having too few potentials included or the number of data points is incorrect Action Examine the TABLE file contents and regenerate it if it appears to be incomplete If it look intact check that the number of data points specified is what DL_POLY 4 is expecting 240 OSTFC Appendix D 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 wit
182. ction 1 4 2 In the build subdirectory you will find the required DL POLY 4 makefiles see Section 4 2 1 and Appendix C where the main Makefiles are listed This must be copied into the subdirec tory containing the relevant source code In most cases this will be the source subdirectory 3 The chosen makefile is executed with an appropriate keyword Section 4 2 1 which selects for specific platforms For DL POLY 4 compilation in parallel mode a FORTRAN90 compiler and an MPI implementation for the specific machine architecture are required in many cases the user sometimes with help from the administrator of their platform will have to create their own keyword entry in the makefile due to the large variety of i software needed for the compilation of DL POLY 4 and ii places where it could be installed PATHS To facilitate the user with the construction of their own keyword entry examples are provided in the makefiles In the case when users use a makefile for DL POLY 4 compilation in serial mode they will have to provide a valid PATH to the FORTRAN90 compiler on their specific platform 4 The makefile produces the executable version of the code which as a default will be named DLPOLY Z and located in the execute subdirectory 5 DL_POLY also has a Java GUI The files for this are stored in the subdirectory java Com pilation of this is simple and requires running the javac compiler and the jar utility Details for these procedures a
183. ctuations in the OUTPUT file to help you with this Message 96 error incorrect atom totals in metal ld set halo This should never happen Action Big trouble Report to authors Message 97 error constraints mixing with rigid bodies not allowed Action Correct FIELD and resubmit 252 OSTFC Appendix D 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 x m 2 6 If the internally calculated index exceeds this number this error report results Action Report to authors Message 102 error rcut 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 resubm
184. cular RDF pair in the following manner a8 a8 first atom type second atom type atmnam 1 atmnam 2 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 de fined 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 po tential arrays for fictitious interactions that will not be used This option is not available in DL POLY Classic 146 OSTFC Section 5 1 Note that rdf and vdw met are not complementary i e if the former is used in FILED none of the pairs defined by the latter will be considered for RDF calculations The selected RDFs are calculated in the RDF COLLECT and RDF EXCL COLLECT by collect ing distance information from all two body pairs as encountered in the Verlet neighbour list created in the LINK CELL PAIRS routine within the TWO BODY FORCES routine In the construction of the Verlet neighbour list pairs of particles part of the exclusion list are excluded The exclusion list contains particles that are pa
185. d then use the make command During cygwin installation make sure that make and gfortran are included in the install A potential problem for Windows based FORTRAN compilers you may encounter is that the compiler may not pick symbolic links To resolve this you will have to use hard linking in the Makefile Compiling with NetCDF functionality The targeted Makefile needs the following substitution within before attempting compilation netcdf modul o gt netcdf module o Note that suitable entry may need to be created within the Makefile So that it matches the particular combination of architecture compiler MPI library amp netCDF library Contacts at STFC Daresbury Laboratory Dr I T Todorov ilian todorov stfc ac uk 289 OSTFC Appendix E 290 Bibliography 10 11 12 13 14 15 16 17 18 19 20 21 Smith W and Forester T 1996 J Molec Graphics 14 136 2 Todorov I and Smith W 2004 Phil Trans R Soc Lond A 362 1835 2 168 Todorov I Smith W Trachenko K and Dove M 2006 J Mater Chem 16 1611 1618 2 168 Smith W 1987 Molecular Graphics 5 71 2 Smith W 1991 Comput Phys Commun 62 229 2 4 168 Smith W 1993 Theoretica Chim Acta 84 385 2 4 168 Smith W and Forester T R 1994 Comput Phys Commun 79 52 2 Smith W and Forester T R 1994 Comput Phys Commun 79 63 2 4 59 Pinches M R S Til
186. d print helpful error messages but it does not claim to be fully foolproof Another common mistake is to specify more than once a directive that has no contradictory disabling altering or antagonistic directives then the one specified last will be used as a control directive for example densvar equil steps press mxshak shake Fortunately in most cases the CONTROL file will be small and easy to check visually It is important to think carefully about a simulation beforehand and ensure that DL POLY 4 is being asked to do something that is physically reasonable It should also be remembered that the present capabilities the package may not allow the simulation required and it may be necessary for you yourself to add new features An example CONTROL file appears below The directives and keywords appearing are described in the following section The exapmle lists all possible and not mutually excluding directives in a particular order Although this order is not mandatory it is highly recommended TITLE RECORD DL POLY 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 4 INDEX AND VERIFICATION BYPASS AND NO TOPOLOGY REPORTING no index no strict no topology INTERACTIONS BYPASS no electostatics no vdw DIRECT CALCULATION OF VDW METAL INTERACTIONS INSTEAD OF EVALUATION BY SPLINING OVER TABULATED VALUES I
187. d the rest are a halo image of link cells forming the surface of the immediate neighbouring domains In this respect if we define performance efficiency as minimising communications with respect to maximising computation minimising the halo volume with respect to the node volume best performance efficiency will require M My 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 M M 2 M 2 M 2 M My M R 4 2 is close to or drops below one In such cases there are three strategies for improving the situation that can be used singly or in combination As obvious from equation 4 2 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 li
188. 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 the FIELD file Once this directive has been encountered DL POLY 4 enters the molecular description envi ronment in which only molecular description keywords and data are valid Immediately following the molecules directive are the records defining individual molecules 1 name of molecule which can be any character string up to 100 characters in length 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 r
189. desley D and Smith W 1991 Molecular Simulation 6 51 2 4 168 Rapaport D C 1991 Comput Phys Commun 62 217 2 4 168 Daw M S and Baskes M L 1984 Phys Rev B 29 6443 3 29 Foiles S M Baskes M I and Daw M S 1986 Chem Phys Lett 33 7983 3 29 Finnis M W and Sinclair J E 1984 Philos Mag A 50 45 3 29 30 Sutton A P and Chen J 1990 Philos Mag Lett 61 139 3 30 Rafii Tabar H and Sutton A P 1991 Philos Mag Lett 63 217 3 30 37 Todd B D and Lynden Bell R M 1993 Surf Science 281 191 3 30 Tersoff J 1989 Phys Rev B 39 5566 3 37 169 van Gunsteren W F and Berendsen H J C 1987 Groningen Molecular Simulation GRO MOS Library Manual BIOMOS Nijenborgh 9747 Ag Groningen The Netherlands Standard GROMOS reference 3 12 Mayo S Olafson B and Goddard W 1990 J Phys Chem 94 8897 3 12 40 41 149 Weiner S J Kollman P A Nguyen D T and Case D A 1986 J Comp Chem 7 230 3 12 Smith W 2003 Daresbury Laboratory 4 9 96 106 107 133 190 291 STFC Bibliography 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 3T 38 39 40 41 42 43 44 45 46 47 Allen M P and Tildesley D J 1989 Computer Simulation of Liquids Oxford Clarendon Press 4 46 54 57 60 168 170 Andersen H C 1983 J Comput Phys 52 24 4 57 168 Fin
190. different kinds Thus two different metals A and B we can distinguish 4 possible variants of each V ra VE ri VG ru Vig rij 36 OSTFC Section 2 3 and AA BB AB BA Dij rij Pij fij Pij rus 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 50 and FS 15 cases it turns out that VE rig VARA reg gt 2 128 though the mixing rules are different in each case beware With regard to density in the EAM case it is required that 50 A Pi ra Pi ra A AA pi ra e a 2 129 which means that an atom of type A contributes the same density to the environment of an atom of type B as it does to an atom of type A and vice versa For the FS case 15 a different rule applies pa rig 0G ra PB rig 2 130 so that atoms of type A and B contribute the same densities to each other but not to atoms of the same type Thus when specifying these potentials in the DL_POLY_4 FIELD file for an alloy composed of n different metal atom types both EAM and FS require the specification of n n 1 2 pair functions We rij However the EAM requires only n density functions jn lri whereas the FS class requires all the cross functions pig rij or n n 1 2 in total In addition to the n n 1 2 pair functions and n density functions t
191. dw table read or metal table read Action Standard user response Increase mxbuff in SET BOUNDS recompile and resubmit Message 49 error frozen shell core shell unit specified The DL POLY 4 option to freeze the location of an atom i e hold it permanently in one position is not permitted for the shells in core shell units Action Remove the frozen atom option from the FIELD file Consider using a non polarisable atom instead 244 OSTFC Appendix D Message 50 error too many bond angles specified This should never happen This error most likely arises when the FIELD file or and DL POLY 4 executable are corrupted Action Recompile the program or recreate the FIELD file If neither of these works send the problem to us Message 51 error too many bond angles per domain DL POLY 4 limits the number of valence angle units in the system to be simulated actually the number to be processed by each node and checks for the violation of this Termination will result if the condition is violated Action Use densvar option in CONTROL to increase mxangl alternatively increase it by hand in SET BOUNDS and recompile and resubmit 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
192. e 57 OSTFC Section 3 2 factor of a half 2 2 2 d2 d2 OQ Pij MT yw Gi a dd dij 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 system assuming a complete absence of the rigid bond forces since forces have just been recalculated afresh after VV1 The relative velocity of atom i with respect to atom j or vice versa constituting the rigid bond ij may not be perpendicular to the bond i e may have a non zero component along the bond However by the stricter definition of rigidity this is is required to be zero as it will otherwise lead to a change in the rigid bond length during the consequent timestepping In the second stage the deviation from zero of the scalar product d vj vj 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 v The velocity corrections can therefore be written as par At Hij Qij Wi vj di mi mi 3 19 ij For a system of simple diatomic molecules computation of the constraint force will in principle allow the correct atomic positions to be calculated in one pass However in the general polyatomic case this correction is
193. e constraints exactly by further optimising the structure using the stiff springs alone without having a significant affect on the overall system energy c Systems with independent constraint bonds and rigid bodies may also be minimised by these methods 3 Of the three minimisation strategies available in DL POLY 4 only the programmed 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 4 2 6 Simulation Efficiency and Performance Although the DL POLY 4 underlining parallelisation strategy DD and link cells see Section 6 1 1 is extremely efficient it cannot always provide linear parallelisation speed gain with increasing pro cessor count for a fixed size system Nevertheless it will always provide speedup of the simulation i e there still is a sufficient speed gain in simulations when the number of nodes used in parallel is increased The simplest explanation why this is is that increasing the processor count for a fixed size system decreases not only the work and memory load per processor but also the ratio size of do
194. e i j k l inversion angle 143 STFC Section 5 1 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 1 vdw n where n is the number of pair potentials to be entered It is followed by m 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 5 12 variable 1 real potential parameter see Table 5 12 variable 2 real potential parameter see Table 5 12 variable 3 real potential parameter see Table 5 12 variable 4 real potential parameter see Table 5 12 variable 5 real potential parameter see Table 5 12
195. e o bonds module o comms module o config module o constraints module o core shell module o dihedrals module o inversions module o io module o kinds f90 0 A parse module o rigid bodies module o setup module o site module o System init o comms module o config module o development module o kinds f90 0 langevin module o metal module o setup module o Site module o statistics module o vdw module o System revive o comms module o config module o development module o kinds f90 0 langevin module o setup module o statistics module o tag legend o setup module o tersoff forces o comms module o config module o domains module o kinds f90 0 Setup module o tersoff module o tersoff generate o kinds f90 0 setup module o tersoff module o tersoff module o kinds f90 0 setup module o tethers forces o comms module o config module o kinds f90 0 setup module o Statistics module o tethers module o tethers module o kinds f90 0 setup module o three body forces o comms module o config module o domains module o kinds f90 0 setup module o three body module o three body module o kinds f90 0 setup module o trajectory write o comms module o config module o io module o kinds f90 0 parse module o setup module o statistics module o two body forces o comms_module o config module o ewald module o kinds f90 0 metal module o setup module o statistics module o vdw module o update shared units o comms module o domains module o
196. ecognised Configuration minimisation can take only these three criteria Action In CONTROL specify the criterion you like followed by the needed arguments 274 OSTFC Appendix D Message 600 error impact option specified more than once in CONTROL Only one instance of the impact option is allowed in CONTROL Action Remove any extra instances of the impact option in CONTROL Message 610 error impact applied on particle that is either frozen or the shell of a core shell unit or part of a RB It is the user s responsibility to ensure that impact is initiated on a valid particle Action In CONTROL remove the impact directive or correct the particle identity in it so that it complies with the requirements 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 responsibility to ensure that no duplicate or mixed up intra molecular entries are specified in FIELD Action Look at the preceding warning message in OUTPUT and find out which entry of what intra molecular like interaction is at fault Correct the bonding description and try running again Message 625 error only one rigid directive per molecule is allowed DL_POLY 4 has found more than one rigids entry per molecule in FIELD Action Correct the erroneous part in FIELD and resubmit Message 630 error
197. ecords 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 0 136 OSTFC Section 5 1 The integer nrept need not be specified if the atom site is not frozen in which case a value of 1 is assumed A number greater than 1 specified here indicates that the next nrept 1 entries in the CONFIG file are ascribed the atomic characteristics given in the current record The sum of the repeat numbers for all atoms in a molecule should equal the number specified by the atoms directive 4 shell n where n is the number of core shell units Each of the subsequent n records contains index 1 i integer site index of core index 2 7 integer site index of shell spring k real force constant of core shell spring The spring potential is 1 with the force constant k entered in units of engunitx where engunit is the energy unit specified in the units directive Note that the atomic site indices referred to above are indices arising from numbering each atom in the molecule from 1 to the number specified in the atoms directive for this molecule This same numbering scheme should be used for all descriptions
198. ed Coulomb sum calculate electrostatic forces using force shifted Coulomb sum with Fennell 52 damping Ewald like convergence parameter o in AI 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 122 OSTFC Section 5 1 stack size n stats every n steps n temperature f trajectory i j k timestep f variable timestep f vdw direct vdw shift zden sampling every f zero a Ewald convergence parameter in kl is twice the maximum k vector index in x direction k2 is twice the maximum k vector index in y direction k3 is twice the maximum k vector index in z direction set rolling average stack to n timesteps accumulate statistics data every n timesteps run simulation for n timesteps default n 0 corresponding to a dry run set required simulation temperature to f Kelvin target temperature for constant temperature ensembles write HISTORY file with controls i start timestep for dumping configurations default i 0 j timestep interval between configurations default j 1 k data level default k 0 see Table 5 1 set timestep to f ps variable timestep start with timestep of f ps enforces the direct calculation of van der Waals interactions defined by explicit potential forms i e it will not work
199. ed to DL_POLY 4 at run time see the descrip tion of the FIELD file in Section 5 1 3 Each atom type in the system is specified by a unique eight character label defined by the user The pair potential is then defined internally by the combination of two atom labels As well as the numerical parameters defining the potentials DLL POLY 4 must also be provided with a cutoff radius ryaw which sets a range limit on the computation of the interaction Together with the parameters the cutoff is used by the subroutine VDW GENERATE to construct an interpolation array vvdw for the potential function over the range 0 to rvaw A second array gvdw is also calculated which is related to the potential via the formula lo G rij ri 3r Orig 2 92 ij and is used in the calculation of the forces Both arrays are tabulated in units of energy The use of interpolation arrays rather than the explicit formulae makes the routines for calculating the potential energy and atomic forces very general and enables the use of user defined pair potential functions DL POLY 4 also allows the user to read in the interpolation arrays directly from a file implemented in the VDW_TABLE_READ routine and the TABLE file Section 5 1 6 This is particularly useful if the pair potential function has no simple analytical description e g spline potentials 28 OSTFC Section 2 3 The force on an atom j derived from one of these potentials is formally calcula
200. ee 3 127 2 2 m 6 RATTLE_VV2 7 Thermostat At lol 1 2 14 1 sl 77 Er FAY v t At v t At y 3 128 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 v t 1 FF f t f t At 3 129 78 STFC Section 3 5 2 LFV The iterative part is as follows ult 340 lat Lam at SO x Ese AD dct eto Auk SA 3 130 H t At nt H t V t At nlt V t 3 SHAKE 4 Full step velocity v t Lut At u t 4 z 3 131 5 Thermostat UE x t lt E 5 0 1 om 6 Barostat n t 21 Pext P t 3 133 Several iterations are required to obtain self consistency In DL POLY 4 the number of iterations is set to 7 8 if bond constraints are present Note also that the change in box size requires the SHAKE algorithm to be called each iteration The Berendsen algorithms conserve total momentum but not energy The VV and LFV flavours of the Berendsen barostat and thermostat are implemented in the DL_POLY 4 routines NPT_B0_vv and NPT_BO_LFV respectively The routines NPT_B1_vv and NPT Bl LFV implement the same but also incorporate RB dynamics Cell size and shape variations The extens
201. ee A E a ES RUE a 6 1 9 9 Internal Documentation cnt dc wee oe eee ee 6 1 3 6 FORTRAN9O Parameters and Arithmetic Precision 6 Dif Unita casual ee PA eC es didus imos ee Be A 7 1 3 8 Error Messages ii i ee ea ee RE ee eee 8 STFC Contents 2 1 4 Directory SLEUCUUEB oc ecl Oeo wh a Roe eee i eo ERE 8 1 4 1 The source Sub directory ee ee 8 143 The utility Sub directory 3 245024 x 428 ee 80e Ro 9 A 8 LAS The data Subsdirectory soles coke eR Geor i ACRES RR RR a 9 1 4 4 The benchSub directory s LL 9 14 5 The egecute Sub directory Lon lo copo ala RE o REESE 9 1 4 6 The build Sub directory e aacr enma a wa llle 9 14 7 The public Sub directory lt s o s 503 a soma sao gk RR LI EG 9 1A The java Subsdirectory uo nuoc ke ea eoe m G ek Re Rm RR A A 9 1 5 Obtaining the Source Code 2 4545 46 58 6224 ee om f RO eee oPoegli 10 L6 OS and Hardware Specitic Ports s e a a wea a e e Ge a RO ege e LE s 10 l7 Other Information sid koe fa e bbe A Eom doe ROS BR RE was 10 Force Fields 11 2 1 Introduction to the DL POLY 4 Force Field 12 2 2 The Intramolecular Potential Functions a 13 22 1 Bond Potente uulgus mox sede pe RR EUER a a 13 2 2 2 Distance Restraints ola a 15 2 23 Valence Angle Potentials 22222 16 22 4 Angular Restraints 30233 9o X be xo X eae bee ROG woe ON UE G 18 2 2 5 Dihedral Angle Potentials 22e 19 2 2 6 Improper Dihedral Angle Potentials
202. efined Define object files OBJ_MOD kinds_f90 0 comms_module o setup_module o parse module o development module o netcdf modul o io module o domains module o Site module o config module o defects module o defects1_module o vdw module o metal module o tersoff module o three body module o four body module o core shell module o constraints module o pmf module o rigid bodies module o tethers module o bonds module o angles module o dihedrals module o inversions module o external_field_module o langevin_module o minimise_module o ewald_module o msd_module o statistics_module o kinetic_module o gpfa_module o parallel_fft o 0BJ ALL warning o error o scan_control_io o numeric_container o spme_container o quaternions_container o scan_field o read config parallel o scan config o scan control o read config o 213 OSTFC Appendix C set bounds o read control o vdw generate o vdw table read o vdw direct fs generate o metal generate o metal table read o metal table derivatives o tersoff generate o dihedrals 14 check o read field o check config o scale config o write config o trajectory write o system expand o rigid bodies tags o rigid bodies coms o rigid bodies widths o rigid bodies setup o tag legend o report topology o pass shared units o build book intra o build excl intra o Scale temperature o update shared units o core shell quench o constr
203. egligence 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 permit ted iterations is exceeded the program terminates Possible causes include incorrect force field specification too high a temperature inconsistent constraints over constraint etc Action You may try to increase the limit of iteration cycles in the constraint subroutines by using the direc tive mxshak and or decrease the constraint precision by using the directive shake in CONTROL But the trouble may be much more likely to be cured by careful consideration of the physical system being simulated For example is the system stressed in some way Too far from equilibrium Message 517 error allowed configuration information levels are 0 1 and 2 DL POLY 4 has found an erroneous configuration information level l 0 le l le 2 i for the tra jectory option in CONTROL or ii in the header of CONFIG 271 OSTFC Appendix D
204. elepiped e g monoclinic or triclinic cell is generally used in simulations of crystalline materials where its shape and dimension is commensurate with the unit cell of the crystal Thus for a unit cell specified by three principal vectors a b c the MD cell is defined in the DL POLY 4 CONFIG file by the vectors La Laz2 La3 Mb Mb2 Mbs Nc1 Nc2 Nc3 in which L M N are integers reflecting the multiplication of the unit cell in each principal direction Note that the atomic coordinate origin is the centre of the MD cell Slab boundary conditions imcon 6 Slab boundaries are periodic in the X and Y directions but not in the Z direction They are particularly useful for simulating surfaces The periodic cell in the XY plane can be any paral lelogram The origin of the X Y atomic coordinates lies on an axis perpendicular to the centre of the parallelogram The origin of the Z coordinate is where the user specifies it However it is recommended that it is in the middle of the slab Domain decomposition division across Z axis is limited to 2 If the XY parallelogram is defined by vectors A and B the vectors required in the CONFIG file are A1 A5 0 B1 B5 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 coo
205. ely 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 Langevin constant T algorithm 27 Ae Andersen constant T algorithm 28 Berendsen constant T algorithm 29 Nos Hoover constant T algorithm 30 Langevin constant T P algorithm 31 Berendsen constant T P algorithm 29 O 00 N Q C Nos Hoover constant T P algorithm 30 10 Martyna Tuckerman and Klein MTK constant T P algorithm 32 11 Langevin constant T c algorithm 31 12 Berendsen constant T c algorithm 29 13 Nos Hoover constant T o algorithm 30 14 Martyna Tuckerman and Klein MTK constant T c algorithm 32 OSTFC Section 1 3 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 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
206. ely The routines NVT L1 vv and NVT_L1_LFV implement the same but also incorporate RB dynamics 63 OSTFC Section 3 4 3 4 3 Andersen Thermostat This thermostat assumes the idea that the system or some subset of the system has an instanta neous interaction with some fictional particles and exchanges energy Practically this interaction amounts to replacing the momentum of some atoms with a new momentum drawn from the cor rect Boltzmann distribution at the desired temperature The strength of the thermostat can be adjusted by setting the average time interval over which the interactions occur and by setting the magnitude of the interaction The collisions are best described as a random Poisson process so that the probability that a collision occurs in a time step At is At Porisionlh exp gt 3 45 TT where 7r is the thermostat relaxation time The hardest collision is to completely reset the mo mentum of the Poisson selected atoms in the system with a new one selected from the Boltzmann distribution 3 2 mi mi Vi kpTexc F v exp Gauss 0 1 3 46 2 a 7 xu 2m ur EA 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 up drawn from F v with the old momentum v0 9 vaa icai 347 where a 0 a lt 1 is the softness of the thermosta
207. en EX EX BINROOT BINROOT TYPE hector cray debug MAKE LD ftn o LDFLAGS 03 en G2 FC ftn c N FCFLAGS 03 en G2 EX EX BINROOT BINROOT TYPE hector pathscale MAKE LD ftn o LDFLAGS byteswapio 03 FC ftn c N FCFLAGS byteswapio 03 EX EX BINROOT BINROOT TYPE CRAY XT3 6 pathscale compilers DEBUG hector pathscale debug MAKE LD ftn o LDFLAGS byteswapio 00 g ffortran bounds check FC ftn c FCFLAGS byteswapio 00 g ffortran bounds check EX EX BINROOT BINROOT TYPE hector X2 MAKE LD ftn o LDFLAGS 03 0fp3 Ocache2 rm 201 OSTFC Appendix C FC ftn c N FCFLAGS 03 Ofp3 Ocache2 rm EX EX BINROOT BINROOT TYPE hector X2 debug MAKE LD ftn o LDFLAGS GO 00 rm FC ftn c N FCFLAGS GO 00 rm N EX EX BINROOT BINROOT TYPE Default code master message check 0BJ MOD 0BJ ALL LD EXE LDFLAGS 0BJ MOD 0BJ ALL Message message echo DL POLY 4 compilation in MPI mode echo echo Use mpi module must change to Use mpi in comms_module f90 echo Check that a platform has been specified check Qif test FC undefined then echo echo FORTRAN90 compiler unspecified echo echo Please edit your Makefile entries echo exit 99 fi
208. ent qualifying cutoff default f 0 15 A set restart data dump interval to n steps default n 1000 116 OSTFC Section 5 1 ensemble ensemble ensemble ensemble ensemble ensemble ensemble ensemble ensemble ensemble ensemble ensemble ensemble ensemble ensemble ensemble ensemble nve nvt evans nvt langevin f nvt andersen f fa nvt berendesen f nvt hoover f nvt gst fi fo npt langevin fi f2 npt berendsen fi fa npt hoover fi fa npt mtk f f nst langevin fi fa nst berendsen fi fo nst hoover f f2 nst mtk fi fo nst Q fifo area nst Q fife tension y select NVE ensemble default ensemble select NVExin ensemble type Evans with Gaussian constraints thermostat select NVT ensemble type Langevin with thermostat relaxation speed friction constant f in ps select NVT ensemble type Andersen with fi fo as the thermostat relaxation time in ps and softness 0 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 fi in ps 1 select NPT ensemble type Langevin with fi fo as the thermostat and barostat relaxation speed friction constants in ps select NPT ensemble type Berendsen wit
209. eometrical 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 P is the number of processors and allocated to specific processors In DL POLY 4 the domain allocation is handled by the routine DOMAINS MODULE and the decision of approximate sizes of various bookkeeping arrays in SET BOUNDS The division of the configuration data in 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 the forces computation and integration of the equations of motion are shared reasonably equally between processors and to a large extent can be computed independently on each processor The method is conceptually simple though tricky to program and is particularly suited to large scale simulations where efficiency is highest The DD strategy underpinning DL POLY 4 is based on the link cell algorithm of Hockney and Eastwood 71 as implemented by various authors e g Pinches et al 9 and Rapaport 10 This requir
210. ep 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 6 2 8 record 1 nstep timestep of final configuration numacc number of configurations used in averages numrdf number of configurations used in RDF averages numzdn number of configurations used in Z density averages time elapsed simulation time tmst elapsed simulation before averages were switched on chit thermostat related quantity first chip barostat related quantity cint thermostat related quantity second record 2 eta scaling factors for simulation cell matrix elements 9 record 3 stpval instantaneous values of thermodynamic variables nxnstk record 4 sumval average values of thermodynamic variables nxnstk record 5 ssqval fluctuation squared of thermodynamic variables mxnstk record 6 zumval running totals of thermodynamic variables nxnstk 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 151 OSTFC Section 5 1 record 13 Optional zdens Z density array mxgrdf xmxatyp 5 1 5 2 Further Comments Note that different vers
211. ername 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 186 Appendix A DL POLY 4 Periodic Boundary Conditions Introduction DL POLY 4 is designed to accommodate a number of different periodic boundary conditions which are defined by the shape and size of the simulation cell Briefly these are as follows which also indicates the IMCON flag defining the simulation cell type in the CONFIG file see 5 1 2 1 None e g isolated polymer in space imcon 0 2 Cubic periodic boundaries imcon 1 3 Orthorhombic periodic boundaries imcon 2 4 Parallelepiped periodic boundaries imcon 3 5 Slab X Y periodic Z non periodic imcon 6 We shall now look at each of these in more detail Note that in all cases the cell vectors and the positions of the atoms in the cell are to be specified in Angstroms A No periodic boundary imcon 0 Simulations requiring no periodic boundaries are best suited to in vacuuo simulations such as the conformational study of an isolated polymer molecule This boundary condition is not recom mended for studies in a solvent since evaporation is 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
212. ertial frame but to describe the moment of inertia tensor in a frame of reference that is localised in the rigid body and changes as the rigid body rotates Thus the local body frame is taken to be that in which the rotational inertia tensor I is diagonal and the components satisfy yx 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 je q d0 q1 92 93 gt 3 179 and the rotational matrix R to transform from the local body frame to the space fixed frame is the unitary matrix R 2 qiq2 qo 9 d 9 9 9 2 d245 404 3 180 q q2 q 2 q1d2 4043 2 qi 93 40 92 DA _ 2 2 2 2 2 q 43 qo 92 a2 q3 qo d1 46 di 45 9 so that if d is the position of an atom in the local body frame with respect to its COM its position in the universal frame w r t its COM is given by d R d 3 181 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 3 175 and the mass is the total mass of the rigid body
213. es indicates UNIX file directories 2 ROUTINES indicates subroutines functions and programs 3 macros indicates a macro file of UNIX commands 4 directive indicates directives or keywords 5 variables indicates named variables and parameters 6 FILE indicates filenames iv Contents THE DL POLY 4 USER MANUAL a About DLPOLY A i su ae hoe da debe bed Shed RO ea dhe eas i Disclaimer zuo eaa ia E FUR Gc 9e x 9o RR 4 X x ho RO Poem E FU Red R8 OE a ii Acknowledgements 2222 ess s Soros iii Marital Notation pupi xencexoR osx E u e ae DA Hexe ons iv Contents v List of Tables xi List of Figures xii 1 Introduction 1 11 The DL POLY Package sust 9G bom ko Ro ok zo oe 244 a EO S 2 1 2 Functionality ss aos e ox be Bie Exec be x de Uu deccm Re pne m Rem pd 2 1 2 1 Molecular Systems s sco m RR Roe Rog Ro ch Rm GE a 2 L2 2 Foree Field sosse ss Gaga ARE Xa xv Uu dee ERE SR ER RU did 3 L2 Boundary Conditions esa ecGeRx ia ORG RIP SR PORE RUE S 3 1 24 Java Graphical User Interface i 4 45 Abrams 024a 4 oS A eaim a a 4 1 2 6 DL POLY Classic features incompatible or unavalable in DL POLY 4 5 1 3 Programming Style 2 i Ro y dele ae be ee gee OE RO Xe ea ee Rd 5 1 3 1 Programming Language e 5 1 39 2 Modularisation and Intent o s sace fe A e bo RS RR eee a 6 1 9 9 Memory Management 2 2 sosia sk heh ee sd ER RURSUS Sh we 6 134 Target Platforms a mnm Res gos gem F
214. es that the cutoff applied to the interatomic potentials is relatively short ranged In DL POLY 4 the link cell list is build by the routine LINK CELL PAIRS As with all DD algorithms there is a need for the processors to exchange halo data which in the context of link cells means sending the contents of the link cells at the boundaries of each domain to the neighbouring pro cessors so that each may have all necessary information to compute the pair forces acting on the atoms belonging to its allotted domain This in DL_POLY 4 is handled by the SET_HALO_PARTICLES routine Systems containing complex molecules present several difficulties They often contain ionic species which usually require Ewald summation methods 22 72 and intra molecular interactions in ad dition 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 intramolecular bonds to deal with The allocation in this case is based on the atoms present in the processor s domain The SHAKE and RATTLE algorithms 61 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 VVI1 cycle RATTLE VV2 updates the veloc
215. escribes the variety of interaction potentials available in DL POLY 4 11 OSTFC Section 2 1 2 1 Introduction to the DL POLY 4 Force Field The force field is the set of functions needed to define the interactions in a molecular system These may have a wide variety of analytical forms with some basis in chemical physics which must be parameterised to give the correct energy and forces A huge variety of forms is possible and for this reason the DL POLY 4 force field is designed to be adaptable While it is not supplied with its own force field parameters many of the functions familiar to GROMOS 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 ri T2 TN 5 Ushel ishet T Peores Tshell ishel l Nteth DI Uretn iter ri O t U 0 iteth 1 Nbond P 5 Ubona ibond Tas Ty tbond 1 Nangl JE 5 Uangi angl Tarlo fe iangl 1 Naihd do U hndlidihd futi faf tdiha 1 Ninv 5 Uinv iin Tas Lb Tor Ta pue eX XU Gs nj 2 1 i l j i N N N d NN Urersoff li j k rif Ej E Tk i ljzikzj N 2N 1 N x Y Us voali j ht Ti Tn Th i 1 j gt i k gt j N 3N 2N 1 N y 5 y 5 U4 body i j k N Ti Tj Fk Tn i l j i k j n gt k N Y 5 Uesin i Tij Vi i 1
216. essage 43 error deport atomic data outgoing transfer buffer exceeded This may happen in extremely non equilibrium simulations or usually when the potential in use do not hold the system stable Action 243 OSTFC Appendix D Consider using densvar option in CONTROL for extremely non equilibrium simulations Alterna tively increase mxbuff in SET BOUNDS recompile and resubmit Message 44 error deport atomic data incoming transfer buffer exceeded Action See Message 43 Message 45 error too many atoms in CONFIG file 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 Message 48 error transfer buffer too small in v
217. estep or variable timestep specifying the simulation timestep Use only one instance of these in CONTROL If a dry run is performed see below and a timestep length is not supplied a default one of 0 001 ps is provided d ewald spme sum precision or coul or shift or distan or reaction or no elec specifying the required coulombic forces option Apart from no elec the rest of the directives are mutually exclusive from one another If none is specified then none is applied 2 Some directives are optional If not specified DL POLY 4 will take default values if necessary The defaults are specified above in the list of directives However fail safe DL POLY 4 is not always will it assume a default value for certain parameters To enable DL POLY 4 to be even more liberal in the fail safe features users are recommended to use no strict option 3 The steps and equilibration directives have a default of zero If not used or used with their default values a dry run is performed This includes force generation and system dump REVCON and REVIVE and depending on the rest of the options may include veloc ity generation force capping application of the CGM minimiser application of the pseudo thermostat and dumps of HISTORY DEFECTS RDFDAT ZDNDAT and MSDTMP Note that since no actual dynamics is to be performed the temperature and pressure directives do not play any role and are therefore not necessary 4 If the CGM minimiser minimise
218. ex 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 prevent any drifts The user must take care to have the impact initiated after any possible equlibration Otherwise the system will be thermostated and the impact energy disipated during the equlibration The pseudo option is intended to be used in highly non equilibrium simulations when users are primarily interested in the structural changes in the core of the simulated system as the the MD cell boundaries of the system are coupled to a thermal bath The thermal bath can be used with two types of temperature scaling algorithms i Langevin stochastic thermostat and ii Direct direct thermostat If no type is specified then the Langevin temperature control algorithm is applied first followed the Direct one The user is also required to specify the width of the pseudo thermostat fi in which must be larger than 2 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 l
219. execute sub directory for the continuation of a simulation It is always a good idea to store these files elsewhere in addition to using this macro gopoly gopoly is used to submit a DL POLY 4 job to the HPCz which operates a LOAD LEVELER job queuing system It invokes the following script 0 shell usr bin tcsh job_type parallel job name gopoly 40 cpus 32 node usage not shared HO network MPI csss shared US 40 wall clock limit 00 30 00 account no my account 40 output job name schedd host jobid out 40 error job name schedd host jobid err 40 notification never 40 bulkxfer yes 40 data limit 850000000 40 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 llsubmit gopoly 191 OSTFC Appendix B where llsubmit is a local command for submission to the IBM SP4 cluster The number of re quired nodes and the job time are indicated in the above script gui gui is a macro that starts up the DL POLY 4 Java GUI It invokes the following UNIX commands java jar java GUI jar 1 amp In other words the macro invokes the Java Virtual Machine which executes the instructions in the Java archive file GUI ja
220. export o metal ld set halo o metal ld compute o exchange grid o ewald spme forces o metal forces o vdw forces o ewald real forces o coul dddp forces o coul cp forces o coul fscp forces o 195 OSTFC Appendix C coul rfp forces o rdf collect o rdf excl collect o ewald excl forces o ewald frozen forces o two body forces o tersoff forces o three body forces o four body forces o core shell forces o tethers forces o intra coul o bonds forces o angles forces o inversions forces o dihedrals 14 vdw o dihedrals forces o external field apply o external field correct o langevin forces o constraints pseudo bonds o pmf pseudo bonds o rigid bodies split torque o rigid bodies move o minimise relax o core shell relax o zero k optimise o nvt eO scl o nvt ei scl o nvt bO scl o nvt bi scl o pseudo_vv o constraints_shake_vv o pmf_shake_vv o constraints_rattle o pmf_rattle o nvt_h0_scl o nvt_g0_scl o npt_h0_scl o nst_h0_scl o nve O vv o nvt_e0_vv o nvt 10 vv o nvt aO vv o nvt bO vv o nvt hO vv o nvt_g0_vv o npt 10 vv o npt bO vv o npt hO vv o npt mO vv o nst 10 vv o nst bO vv o nst hO vv o nst mO vv o nvt hi scl o nvt gi scl o npt hi scl o nst hi scl o nve 1 vv o nvt el vv o nvt li vv o nvt_al_vv o nvt bi vv o nvt hi vv o nvt gi vv o npt 11 vv o npt b vv o npt h vv o npt mi vv o nst li vv o nst b vv o nst hi vv o nst mi vv o A pseudo_lfv o constraints shake l
221. eyfce meaning Electrostatics are evaluated as follows Ignore electrostatic interactions SPM Ewald summation Coulomb sum with distance dependent dielectric Standard truncated Coulomb sum Force shifted Coulomb sum 10 Reaction field electrostatics 0 daN ewald evaluate or multiple are not mutually exclusive and it is the first instance of these in CONTROL that is read and applied in the following simulation The choice of reaction field electrostatics directive reaction relies on the specification of the relative dielectric constant external to the cavity This is specified by the eps directive The directive ewald spme evaluate is only triggered when ewald spme sum precision is present It sets an infrequent evaluation of the k space contributions to the Ewald summation Although this option decreases the simulation cost it also inherently decreases the accuracy of the dynamics Note that the usage of this feature may lead to inacuarte or even wrong and unphysical dynamics as the less frequent the evaluation the greater the inacuarcy DL_POLY 4 uses two different potential cutoffs These are as follows a Treut the universal cutoff set by cutoff It applies to the real space part of the electro statics calculations and to the van der Waals potentials if no other cutoff is applied b rvaw the user specified cutoff for the van der Waals potentials set by rvdw If not specified its value defaults to rc
222. eyond the cutoff In DL POLY 4 the short ranged forces are calculated by the subroutine VDW FORCES The long ranged corrections are calculated by routine VDW LRC The calculation makes use of the Verlet neighbour list see above 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 terms of the local electronic density They are suitable for calculating the properties of metals and metal alloys For single component metals the two approaches are the same However they are subtly dif ferent in the way they are extended to handle alloys see below It follows that EAM and FS class potentials cannot be mixed in a single simulation Furthermore even for FS class potentials 29 OSTFC Section 2 3 possessing different analytical forms there is no agreed procedure for mixing the parameters The user is therefore strongly advised to be consistent in the choice of potential when modelling alloys The general form of the EAM and FS potentials is 47 1 N N N Umetal 2 5 5 Vig rig gt F pi 2 98 i l jzi i 1 where F p is a functional describing the energy of embedding an atom in the bulk density pj which is defined as N pi
223. f nfield ntable nrefdt nrite nstats nrest nhist ndefdt nrdfdt nzdfdt seed 1 2 lseed mxsite mxatyp mxtmls mxexcl mxspl kmaxa kmaxb kmaxc kmaxal kmaxb1 kmaxci mxtshl mxshl mxfshl mxtcon mxcons mxfcon mxlshp mxproc mxtpmf 1 2 mxpmf mxfpmf mxtrgd mxrgd mxlrgd mxfrgd mxtteth mxteth mxftet mxpteth 0 163882576 5 11 12 13 14 6 21 22 23 24 25 26 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 conversion factor for pressure from internal units to katms main input channel configuration file input channel force field input channel tabulated potentials file input channel reference configuration input channel main output channel statistical data file output channel output channel accumulators restart dump file trajectory history file channel output channel for defects data file output channel for RDF data output channel for Z density data file pair of seeds for the random number generator logical swich on off indicator for seeding max number of molecular sites max number of unique atomic types max number of unique molecule types max number of excluded interactions per atom SPME FFT B spline order SPME FFT
224. f90 nvt hO scl f90 nvt gO scl f90 npt_h0_sc1 f90 nst_h0_scl 90 nve O vv f90 nvt eO vv f90 N nvt 10 vv f90 nvt aO vv f90 nvt bO vv f90 nvt hO vv f90 nvt gO vv f90 npt 10 vv f90 npt_b0_vv f90 npt hO vv f90 npt mO vv f90 nst 10 vv f90 nst_b0_vv f90 nst hO vv f90 nst mO vv f90 nvt hi scl f90 nvt gi scl f90 npt hi scl f90 nst_hi_scl f90 nve 1 vv f90 nvt ei vv f90 nvt 11 vv f90 nvt a1 vv f90 nvt bli vv f90 nvt hi vv f90 nvt gi vv f90 npt 11 vv f90 npt bi vv f90 npt hi vv f90 npt mi vv f90 nst li vv f90 nst bi vv f90 nst hi vv f90 nst mi vv f90 md vv f90 215 OSTFC Appendix C Define LeapFrog Verlet files FILES LFV pseudo lfv f90 constraints shake lfv f90 pmf shake lfv f90 nve O lfv f90 nvt eO lfv f90 nvt 10 l1fv f90 nvt aO lfv f90 nvt bO lfv f90 nvt hO lfv f90 nvt gO lfv f90 npt 10 lfv f90 npt bO lfv f90 npt hO lfv f90 npt_m0_1fv f90 nst 10 l1fv f90 nst bO lfv f90 nst hO lfv f90 nst mO lfv f90 nve 1 lfv f90 nvt el lfv f90 nvt li l1fv f90 nvt ai lfv f90 nvt b lfv f90 nvt h lfv f90 nvt gi lfv f90 npt 11 lfv f90 npt bi lfv f90 npt hi lfv f90 npt mi lfv f90 nst li lfv f90 nst bi lfv f90 nst h lfv f90 nst mi lfv f90 md lfv f90 Examine targets manually all echo echo You MUST specify or choose a permissive target platform echo echo The available permissive targets are displayed below echo echo hpc lake newton dirac franklin echo
225. fficient bond constraints are 1 linear molecules with more than 2 atoms e g CO2 2 planar molecules with more than three atoms e g benzene Even when the structure can be defined by bond constraints the network of bonds produced may be problematic Normally they make the iterative SHAKE in the LFV integration or RATTLE in the VV integration procedure slow particularly if a ring of constraints is involved as occurs when one defines water as a constrained triangle It is also possible inadvertently to over constrain a molecule e g by defining a methane tetrahedron to have 10 rather than 9 bond constraints in which case the SHAKE RATTLE procedure will become unstable In addition massless sites e g charge sites cannot be included in a simple constraint approach making modelling with potentials such as TIPAP 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 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 X mj 3 172 j 1 where m is the mass of an atom and the sum includes all sites Nsites in the body The position of the rigid unit is defined as the location of i
226. for systems using tabulated potentials TABLE applies a force shifting procedure to all van der Waals potentials except the shifted force n m potential so that the VDW interactions s energy and force contributions fall to zero smoothly for distances aproaching recu calculate and collect the Z density profile every f timesteps default f 1 perform zero temperature MD run reset target system temperature 10 Kelvin Note that in some cases additional keywords shown in brackets may also be supplied in the directives or directives may be used in a long form However it is strongly recommended that the user uses only the bold part of these directives 5 1 1 3 Further Comments on the CONTROL File 1 A number of the directives or their mutually exclusive alternatives are mandatory a cut specifying the short range forces cutoff It is compulsory in all circumstances as all DL_POLY 4 algorithms are directly or indirectly dependent on it 123 OSTFC Section 5 1 Table 5 1 Internal Trajectory Defects File Key keytrj meaning 0 coordinates only in file 1 coordinates and velocities in file 2 coordinates velocities and forces in file b temp or zero specifying the system temperature not mutually exclusive but if temp has to preceed zero in CONTROL if zero is needed Use only one instance of these in CONTROL If a dry run is performed see below these can be omitted c tim
227. for the utility HFILL The HFILL utility fills out the structure with the missing hydrogens Note that you may need to know what the atomic charges are in some systems for example the AMBER charges from the literature Note with minor modifications the utilities FRACFILL and FRACCON can be used on structures from databases other than the Cambridge structural database 4 3 8 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 4 3 4 Analysing Results DL POLY 4 is not designed to calculate every conceivable property you might wish from a sim ulation Apart from some obvious thermodynamic quantities and radial distribution functions it does not calculate anything beyond the atomic trajectories You must therefore be prepared to post process the HISTORY
228. fv o pmf shake lfv o nve O lfv o nvt eO lfv o nvt 10 lfv o nvt a0 lfv o nvt bO lfv o nvt hO lfv o nvt gO lfv o npt 10 lfv o npt bO lfv o npt hO lfv o npt mO lfv o nst 10 lfv o nst bO lfv o nst hO lfv o nst mO lfv o nve 1 lfv o nvt e lfv o nvt li lfv o nvt ai lfv o nvt bi lfv o nvt hi lfv o nvt gi lfv o npt li lfv o npt bi lfv o npt hi lfv o npt mi lfv o nst l1 lfv o nst bi lfv o nst hi lfv o nst mi lfv o xscale o core_shell_kinetic o regauss_temperature o z_density_collect o statistics_collect o system_revive o rdf_compute o z_density_compute o statistics_result o dl_poly o Define Velocity Verlet files FILES_VV 196 OSTFC Appendix C pseudo vv f90 constraints shake vv f90 pmf shake vv f90 constraints rattle f90 pmf rattle f90 nvt hO scl f90 nvt gO scl f90 npt_h0_sc1 f90 nst_hO_scl f90 nve O vv f90 nvt eO vv f90 N nvt 10 vv f90 nvt aO vv f90 nvt bO vv f90 nvt hO vv f90 nvt gO vv f90 npt 10 vv f90 npt_b0_vv f90 npt hO vv f90 npt mO vv f90 nst 10 vv f90 nst bO vv f90 nst hO vv f90 nst mO vv f90 nvt hi scl f90 nvt gi scl f90 npt hi scl f90 nst_hi_scl f90 nve 1 vv f90 nvt ei vv f90 nvt 11 vv f90 nvt a1 vv f90 nvt bi vv f90 nvt hi vv f90 nvt gi vv f90 npt 11 vv f90 npt bi vv f90 npt hi vv f90 npt mi vv f90 nst li vv f90 nst bi vv f90 nst hi vv f90 nst mi vv f90 md vv f90 Define LeapFrog Verlet files FILES LFV pseudo lfv f90 constraints s
229. g KNOs NH4 280 etc e Polymers with rigid bonds e g CnHan 2 e Polymers with flexible and rigid bonds and point charges e g proteins macromolecules etc e Silicate glasses and zeolites e Simple metals and metal alloys e g Al Ni Cu CuzAu etc OSTFC Section 1 2 e Covalent systems as hydro carbons and transition elements e g C Si Ge SiC SiGe ets 1 2 2 Force Field The DL POLY 4 force field includes the following features 10 11 12 13 All common forms of non bonded atom atom van der Waals potentials Atom atom and site site coulombic potentials Metal metal local density dependent potentials 11 12 13 14 15 16 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 Chemical bond potentials Valence angle potentials Dihedral angle and improper dihedral angle potentials Inversion angle potentials External field potentials The parameters describing these potentials may be obtained for example from the GROMOS 18 Dreiding 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 8 Boundary Conditions DL POLY 4 will accommodate the following boundary conditions 1 None e g isolated molecules n vacuo Cubic periodic boundar
230. gative of this The force shifted Coulomb potential can be elegantly extended to emulate long range ordering by including distance depending damping function er fc a rjj identical to that seen in the real space 43 OSTFC Section 2 4 portion of the Ewald sum and thus mirror the effective charge screening 52 as shown below U rij dij er fc a rij sre Tout x 2a exp o 2 ATrege rij Lm vm out er f c a reut x erfc a rex 20 exp o riu r 2 168 T cut la Vili Tout i with the force on an atom 7 given by didj Es rij 20 exp o 2 2 j ATege 7 vm lij 24g Tout 2a exp o rta ij 2 169 2 T x Tout Vm Tcut Tij with the force on atom 7 the negative of this It is worth noting that as discussed in 52 and references therein this is only an approximation of the Ewald sum and its accuracy and effectiveness become better when the cutoff is large gt 10 preferably 12 The contribution to the atomic virial is 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 p eq p 2 171 where a B 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 sum without the br
231. ges 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 incor porated We obviously have ideas of our own and CCP5 strongly influences developments but other input would be welcome nevertheless We also request that our users respect the integrity of DL POLY 4 source and not pass it on to third parties We require that all users of the package register with us not least because we need to keep everyone abreast of new developments and discovered bugs We have developed various forms of licence which we hope will ward off litigation from both sides without denying access to genuine scientific users Further information on the DL POLY packages may be obtained from the DL POLY project website http www ccp5 ac uk DL POLY 1 2 Functionality The following is a list of the features DL POLY 4 supports 1 2 4 Molecular Systems DL POLY 4 will simulate the following molecular species e Simple atomic systems and mixtures e g Ne Ar Kr etc e Simple unpolarisable point ions e g NaCl KCl etc e Polarisable point ions and molecules e g MgO H20 etc e Simple rigid molecules e g CCl4 SFe Benzene etc e Rigid molecular ions with point charges e
232. h atom type and n n 4 1 2 cross pair potential functions This makes n n 5 2 functions in total Note that the option of using EAM interactions must also be ezplicitly declared in the FIELD file so that for the n component alloy there are n n 4 1 2 cross pair potential eam keyword entries in FIELD see above Note that all metal interactions must be of the same type 5 1 7 1 The TABEAM File Format The file is free formatted but blank and commented lines are not allowed 5 1 7 2 Definitions of Variables record 1 header al00 file header record 2 numpot integer number of potential functions in file The subsequent records define the n n 5 2 functions for an n component alloy n electron density functions one for each atom type density keyword n embedding functions again one for each atom type embeding keyword and n n 1 2 cross pair potential functions pairs 153 OSTFC Section 5 2 keyword The functions may appear in any random order in TABEAM as their identification is based on their unique keyword defined first in the function s header record The header record is followed by predefined number of data records as a maximum of four data per record are read in allowing for incompletion of the very last record header record keyword ad type of EAM function dens embed or pair atom 1 a8 first atom type atom 2 a8 second atom type only specified for pair potential functions ngrid integer number of fu
233. h fi fo as the thermostat and barostat relaxation times in ps select NPT ensemble type Nose Hoover with fi fo 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 fi fo as the thermostat and barostat relaxation speed friction constants in ps select NoT ensemble type Berendsen with fi f2 as the thermostat and barostat relaxation times in ps select NaT ensemble type Nose Hoover with fi 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 fi fo as the thermostat and barostat relaxation times in ps select NP yT ensemble type Q i e lang ber 117 1 1 OSTFC Section 5 1 hoover or mtk with fi fo as the thermostat and barostat relaxation times in ps and set required simulation target external surface tension to y dyn cm ensemble nst Q fi f2 tens y semi 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 ensemble nst Q f f2 orthorhombic select the NPT anisotropic ensemble for the orthorhombic ensemble nst Q ff orth semi epsilon constant f eq
234. h it Message 26 error neutral group option now redundant DL POLY 4 does not have the neutral group option Action Use the Ewald sum option It s better anyway Message 27 error rigid body option now redundant DL POLY 4 does not have a rigid body option Action Consider using DL POLY Classic instead Message 28 error wrongly indexed atom entries found in CONFIG file DL_POLY 4 has detected that the atom indices in the CONFIG file do not form a contnual and or non repeating group of indices Action Make sure the CONFIG file is complies with the DL POLY 4 standards You may use the no index option in the CONTROL file to override the crystalographic sites reading from the CONFIG file from reading by index 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 Recompile the program or recreate the FIELD file If neither of these works send the problem to us 241 OSTFC Appendix D Message 31 error too many chemical bonds per domain DL_POLY 4 limits the number of chemical bond units in the system to be simulated actually the number to
235. hake lfv f90 pmf shake lfv f90 nve O lfv f90 nvt eO lfv f90 nvt 10 l1fv f90 nvt aO lfv f90 nvt bO lfv f90 nvt hO lfv f90 nvt gO lfv f90 npt 10 lfv f90 npt bO lfv f90 npt hO lfv f90 npt_m0_lfv f90 nst 10 l1fv f90 nst bO lfv f90 nst hO lfv f90 nst mO lfv f90 nve 1 lfv f90 nvt el lfv f90 nvt li l1fv f90 nvt ai lfv f90 nvt b lfv f90 nvt h lfv f90 nvt gi lfv f90 npt 11 lfv f90 npt bi lfv f90 npt hi lfv f90 npt mi lfv f90 nst li lfv f90 nst bi lfv f90 nst h lfv f90 nst mi lfv f90 md lfv f90 Examine targets manually echo You MUST specify or choose a permissive target platform echo The available permissive targets are displayed below echo hpc lake newton dirac franklin echo hpcx hpcx debug BGL BGP echo hector hector pgi debug echo hector gnu hector gnu debug echo hector cray hector cray debug echo hector pathscale hector pathscale debug echo hector X2 hector X2 debug echo Please examine this Makefile s targets for details 197 OSTFC Appendix C echo If no target suits your system then create your own echo using the advice in generic target template provided echo in this Makefile under the entry uknown_platform echo Fetch the Velocity Verlet subroutines FILES_VV MAKE links_vv links_vv for file in FILES_VV do echo linking to file rm f file 1n s VV f
236. 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 yyy real y coordinate from REFERENCE ZZZ real z coordinate from REFERENCE 5 2 4 The RSDDAT File The RSDDAT file is the dump file of atomic coordinates of atoms that are displaced from their original position at t 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 1rsd nsrsd isrsd and rrsd which are created internally based on information read from the displacements directive in the CONTROL file see Section 5 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 that the file be written to a scratch disk capable of accommodating a large data file The RSDDAT has the following structure 158 OSTFC Section 5 2 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 dis placements directive in the CONTROL file with the following information for each configuration
237. 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 50 OSTFC Section 2 6 of the shells are such that the force on every shell is zero The energy is thus a minimum with respect to the shell positions This represents the physical fact that the system is always in the ground state with respect to the electronic degrees of freedom Relaxation of the shells is carried out at each time step and involves a search in the multidimensional space of shell configurations The search in DL POLY 4 is based on the powerful conjugate gradients technique 58 in an adaptation as shown in 57 Each time step a few iterations 10 30 are needed to achieve convergence to zero net force In DL POLY 4 the shell forces are handled by the routine CORE SHELL FORCES In case of the adiabatic shell model the kinetic energy is calculated by CORE SHELL KINETIC and temperature scaling applied by routine CORE SHELL QUENCH In case of the relaxed shell model shell are relaxed to zero force by CORE SHELL RELAXED Either shell model can be used in conjunction with the methods for long ranged forces described above Note that DL POLY 4 determines which shell model to use by scanning shell weights provided the FIELD file see Section 5 1 3 If all shells have zero weight the DL
238. he EAM requires further specification of n functional forms of the density dependence i e the embedding function F p in 2 98 For EAM potentials all the functions are supplied in tabular form via the table file TABEAM see section 5 1 7 to which DL POLY 4 is redirected by the FIELD file data The FS potentials are defined via the necessary parameters in the FIELD file 2 3 3 Tersoff Potential The Tersoff 17 potential has been developed to be used in multi component covalent systems by an effective coupling of two body and higher many body correlations into one model The central idea is that in real systems the strength of each bond depends on the local environment i e an atom with many neighbors forms weaker bonds than an atom with few neighbors Effectively it is a pair potential the strength of which depends on the environment It has 11 atomic and 2 bi atomic parameters The energy is modelled as a sum of pair like interactions where however the coefficient of the attractive term in the pair like potential which plays the role of a bond order depends on the local environment giving a many body potential The form of the Tersoff potential is ters Uij folrij Fr rig va falrig 2 131 where fr and fa are the repulsive and attractive pair potential respectively fr rij Aj exp aij rig fa ri Bij exp bij rij 2 132 37 OSTFC Section 2 3 and fc is a smooth cutoff function with parameters R
239. he inclusion of other potentials for example pair potentials may in fact be essential to maintain the structure of the system 41 OSTFC Section 2 4 The four body potentials are very short ranged typically of order 3 This property plus the fact that four 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 51 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 convergence DL POLY 4 will
240. he unit of pressure P E07 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 e The coulombic conversion factor yo is 1l _ 1389354835 TS Eo 4t olo B i such that Uwgs EoYoUinternal where U represents the configuration energy e The Boltzmann factor kg is 0 831451115 E K such that T Exin kp 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 The default is DL POLY units OSTFC Section 1 4 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
241. here is an entry in the Makefile for the particular combination of architecture compiler amp MPI library then the user may instantiate the compilation by make entry If there is not a suitable entry the user should advise with a computer scientist or the administrator of the particular machine The necessary components for the source compilation are 1 a FORTRAN90 compliant compiler if the full PATH to it is not passed to the DEFAULT ENVIRONMENT PATH then it MUST be explicitly supplied in the Makefile 2 MPI2 or MPI1 MPI I 0 libraries COMPILED for the architecture and the targeted compiler if the full PATH to these is not passed to the DEFAULT ENVIRONMENT PATH then it MUST be 288 OSTFC Appendix E explicitly supplied in the Makefile 3 a MAKE command Makefile interpreter in the system SHELL Note that 2 is not necessary for compilation in SERIAL mode By default if compilation is successful an executable build will be placed in execute directory at the same level as the directory where the code is compiled Should it not exist one will be created automatically The build can then be moved renamed etc and used as the user wishes However when executed the program will look for input files in the directory of execution Serial Compilation on Windows The best way to get around it is to install cygwin on the system http www cygwin com to emulate a UNIX Linux like environment an
242. here is normally a very large number of these and they are therefore specified globally according to the atom types involved rather than indices In DL POLY 4 it is assumed that the pure two body terms arise from van der Waals interactions regarded as short ranged and electrostatic interactions coulombic also regarded as long ranged Long ranged forces require special techniques to evaluate accurately see Section 2 4 The metal terms are many body interactions which are functionally presented in an expansion of many two body contributions augmented by a function of the local density which again is derived from the two body spatial distribution and these are therefore evaluated in the two body routines In DL POLY 4 the three body terms are restricted to valence angle and H bond forms Throughout this chapter the description of the force field assumes the simulated system is de scribed as an assembly of atoms This is for convenience only and readers should understand that DL_POLY 4 does recognize molecular entities defined through constraint bonds and rigid bodies In the case of rigid bodies the atomic forces are resolved into molecular forces and torques These matters are discussed in 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
243. hould 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 247 OSTFC Appendix D 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 Correct the erroneous entry in FIELD and resubmit Message 67 error coincidence of particles in dihedral unit DL POLY 4 has found a fault in the definition of a dihedral unit in the FIELD file Action Correct the erroneous entry in FIELD and resubmit Message 68 error coincidence of particles in inversion unit DL POLY 4 has found a fault in the definition of a inversion unit in the FIELD file Action Correct the erroneous entry in FIELD and resubmit Message 69 error too many link cells required in three body forces This should not happen The calculation of three body forces in DL_POLY 4 is handled by the link cell algorithm This error arises if the required number of link cells exceeds the permitted array dimension in the code Action Consider using densvar opti
244. hpcx hpcx debug BGL BGP echo hector hector pgi debug echo hector gnu hector gnu debug echo hector cray hector cray debug echo hector pathscale hector pathscale debug echo hector X2 hector X2 debug echo echo Please examine this Makefile s targets for details echo If no target suits your system then create your own echo using the advice in generic target template provided echo in this Makefile under the entry uknown_platform echo Fetch the Velocity Verlet subroutines FILES VV MAKE links vv links vv for file in FILES VV do echo linking to file 216 OSTFC Appendix C rm f file ln s VV file file done Fetch the LeapFrog Verlet subroutines FILES_LFV MAKE links_lfv links_lfv for file in FILES_LFV do echo linking to file rm f file 1n s LFV file file done Clean up the source directory clean rm f 0BJ MOD 0BJ ALL FILES VV FILES LFV mod Generic target template uknown platform MAKE LD path to FORTRAN90 Linker loaDer LDFLAGS appropriate flags for LD MPI libraries FC path to FORTRAN90 compiler FCFLAGS appropriate flags for FC MPI include EX EX BINROOT BINROOT TYPE System specific targets follow D8 sea Cambridge HPC darwin Woodcrest hpc MAKE LD mpif90 o LDFLAG
245. ices appearing under the shell directive above Note that the calcite potential is not dependent on an angle but on a displacement u See section 2 2 8 for details 141 OSTFC Section 5 1 Table 5 9 Valence Angle Potentials key potential type Variables 1 4 functional formt harm Harmonic k do U 0 k 0 69 hrm quar Quartic k 069 k k U 0 5 0 0o 4 K 0 09 E o 09 qur thrm Truncated harmonic k 609 p U 0 E 0 00 exp ri 78 8 thm shrm Screened harmonic k 00 pr po U d E 9 69 exp rij p1 ri p2 shm bvs1 Screened Vessal 36 k 09 pr pa U 0 SEEM a 0 7 x bv1 exp rij p1 rix p2 bvs2 Truncated Vessal 37 kl a p U 0 k 0 09 0 0 bo 21 bv2 t 09 m exp r r 9 hcos Harmonic Cosine k 00 U 9 cos 0 cos 69 hcs cos Cosine Alim U 0 A 1 cos m 0 6 cos mmsb MM3 stretch bend 38 A 6o rg rji U 0 A 0 69 rij rj rik TH msb mmsb Compass 39 Alta ae U 0 A rij r2 ris r msb stretch stretch mmsb Compass 39 A do ro U 0 A 0 69 rij r msb stretch bend mmsb Compass 39 A BC 69 U 0 A rij r3 ris r 0 00 x msb all terms r Tok B rij 73 C ris ri 10 is the i j k angle Note valence ang
246. id 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 Gs l pij d di de M 2 At d di oo 3 16 where uij 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 Figure 3 1 The SHAKE RATTLE_VV1 schematics and associated vectors The algorithm cal culates the constraint force G G that conserves the bondlength d between atoms i and j following the initial movement to positions 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_VVI has the form as in 3 16 but missing th
247. ies Orthorhombic periodic boundaries Parallelepiped periodic boundaries Slab x y periodic z non periodic These are described in detail in Appendix A Note that periodic boundary conditions PBC 1 and 9 above require careful consideration to enable efficient load balancing on a parallel computer OSTFC Section 1 2 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 B and also its porta bility across platforms The compiled GUI may be run without recompiling on any Java supported machine The GUI is an integral component of the DL POLY suites and is available on the same terms see the GUI manual 21 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 Section 6 1 1 1 2 5 2 Molecular Dynamics Algorithms DL POLY 4 offers a selection of MD integration algorithms couched in both Velocity Verlet VV and Leapfrog Verlet LFV manner 22 These generate NVE NVExin NVT NPT and NoT 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 respectiv
248. ies for the stress tensor stress 1 real xx component of stress tensor stress 2 real xy component of stress tensor stress 3 real xz component of stress tensor stress 4 real yx component of stress tensor Du real de stress 9 real zz component of stress tensor the next 9 entries ifa NPT or NcT simulation is undertaken 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 cell 4 real x component of b cell vector ss real Hs cell 9 real z component of c cell vector 166 Chapter 6 The DL POLY 4 Parallelisation and Source Code Scope of Chapter This chapter we discuss the DL_POLY 4 parallelisation strategy describe the principles used in the DL POLY 4 modularisation of the source code and list the file structure found in the source subdirectory 167 STFC Section 6 1 6 1 Parallelisation DL_POLY 4 is a distributed parallel molecular dynamics package based on the Domain Decom position 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 6 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 g
249. ig module o development module o kinds f90 0 Scale temperature o comms module o config module o kinds f90 0 kinetic module o rigid bodies module o setup module o Scan config o comms module o io module o kinds f90 0 parse module o A Setup module o scan control o comms_module o kinds f90 0 msd module o parse module o Setup module o Scan control io o comms module o config module o io module o kinds f90 0 parse module o setup module o Scan field o comms module o kinds f90 0 metal module o parse module o Setup module o vdw module o set bounds o comms module o config module o domains module o kinds f90 0 msd module o setup module o 210 OSTFC Appendix C set halo particles o comms module o config module o domains module o kinds f90 0 rigid bodies module o setup module o site module o Set temperature o comms module o config module o core shell module o kinds f90 0 kinetic module o rigid bodies module o setup module o site module o Setup module o kinds f90 o Site module o kinds f90 0 setup module o Spme container o comms module o kinds f90 0 setup module o statistics collect o comms module o config module o kinds f90 0 msd module o Setup module o site module o statistics module o Statistics module o kinds f90 0 setup module o statistics result o comms module o config module o kinds f90 0 msd module o Setup module o site module o statistics module o System expand o angles modul
250. ile file done Fetch the LeapFrog Verlet subroutines FILES_LFV MAKE links_lfv links_lfv for file in FILES_LFV do echo linking to file rm f file ln s LFV file file done Clean up the source directory clean rm f 0BJ MOD 0BJ ALL FILES VV FILES LFV mod Generic target template uknown platform MAKE LD path to FORTRAN90 Linker loaDer LDFLAGS appropriate flags for LD MPI libraries FC path to FORTRAN90 compiler FCFLAGS appropriate flags for FC MPI include EX EX BINROOT BINROOT TYPE System specific targets follow 198 OSTFC Appendix C Cambridge HPC darwin Woodcrest hpc MAKE LD mpif90 o LDFLAGS 03 FC mpif90 c FCFLAGS 03 EX EX BINROOT BINROOT TYPE lake MAKE LD opt intel compiler70 ia32 bin ifc v 0 LDFLAGS 03 xW prec div L opt mpich intel lib lmpich L opt intel compiler70 ia32 lib 1PEPCF90 FC opt intel compiler70 ia32 bin ifc c FCFLAGS 03 xW prec_div I opt mpich intel include EX EX BINROOT BINROOT TYPE Linux efc SGI ALTIX parallel FFT newton MAKE LD ifort o LDFLAGS tpp2 ip 03 lmpi lguide FC ifort c FCFLAGS 03 tpp2 ip w EX EX BINROOT BINROOT TYPE dirac MAKE LD usr local mpich gm pgroup121 7b bin mpif90 v
251. imulated For example is the system stressed in some way Too far from equilibrium Message 106 error neighbour list array too small in link cell pairs Construction of the Verlet neighbour list in subroutine LINK CELL PAIRS non bonded pair force has exceeded the neighbour list array dimensions Action Consider using densvar option in CONTROL for extremely non equilibrium simulations or increase by hand mxlist in SET BOUNDS Message 107 error too many pairs for rdf look up specified This should never happen A possible reason is corruption in FIELD or and DL POLY 4 exe cutable Action Reconstruct FIELD recompile afresh DL_POLY_4 and resubmit If the problem persists get in touch with DL POLY 4 authors Message 108 error unidentified atom in rdf look up list During reading of RDF look up pairs in FIELD DL POLY 4 has found an unlisted previously atom type Action Correct FIELD by either defining the new atom type or changing it to an already defined one in the erroneous line Resubmit Message 109 error calculated pair rdf index too large This should never happen In checking the RDF pairs specified in the FIELD file DL POLY 4 calculates a unique integer index that henceforth identify every RDF pair within the program If this index becomes too large termination of the program results Action Report to authors 254 OSTFC Appendix D Message 108 error duplicate rdf look up pair specified
252. in update shared units The transfer buffer has been exceeded Action Consider increasing parameter mxbuff in SET BOUNDS recompile and resubmit Contact DL POLY 4 authors if the problem persists 255 OSTFC Appendix D Message 116 error incorrect atom transfer in update shared units An atom has become misplaced during transfer between nodes Action This happens when the simulation is very numerically unstable Consider carefully the physical grounds of your simulation i e are you using the adiabatic shell model for accounting polarisation with too big a timestep or too large control distances for the variable timestep is the ensemble type NPT or NoT and the system target temperature too close to the melting temperature Message 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 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
253. ine object files OBJ_MOD kinds_f90 0 mpi_module o comms_module o setup_module o parse module o development module o netcdf modul o io module o domains module o Site module o config module o defects module o defects1_module o vdw module o metal module o tersoff module o three body module o four body module o core shell module o constraints module o pmf module o rigid bodies module o tethers module o bonds module o angles module o dihedrals module o inversions module o external_field_module o langevin_module o minimise_module o ewald_module o msd_module o statistics_module o kinetic_module o 0BJ ALL warning o error o scan_control_io o numeric_container o spme_container o quaternions_container o scan_field o read config parallel o scan_config o scan control o read config o 222 OSTFC Appendix C set bounds o read control o vdw generate o vdw table read o vdw direct fs generate o metal generate o metal table read o metal table derivatives o tersoff generate o dihedrals 14 check o read field o check config o scale config o write config o trajectory write o system expand o rigid bodies tags o rigid bodies coms o rigid bodies widths o rigid bodies setup o tag legend o report topology o pass shared units o build book intra o build excl intra o Scale temperature o update shared units o core shell quench o constraints tags o constraints quench
254. ined the contribution to be added to the atomic virial from each atom pairis then which equates to OU y 3V dd OV r Or dpi y y ig ig 3p 3 t P V XY Ole x OV Ori OV 1 3 Sij SV su Tij L OV I SV OVi ri y Di Em ci Pij 2 112 i ljzi ij 32 OSTFC Section 2 3 Opi Opig rig Orig 1 M pyly 3 Pij rij X i ES gt gt 4j os 7 Ljzi juga Uu cH HS Ong OF pi DE pi Opig rig y ij El Opi Op Orij e 1 EAM virial The same as above 2 Finnis Sinclair virial Ts Vi 2 rij c co T Cirij 4 car rij cr ER 2c rij Tij i ljzi p AA rij dy Wo DXX LE eu d espe 2 113 i l j 3 Extended Finnis Sinclair virial vu A LS a rij c co erij cor cari cari i l jzi rig c e 2eri 3car7 T Acriji Taj 2 114 I NN me 5 DI Vex vP 2 rij d 4B rig ay rija i l Mu d 4 Sutton Chen virial TL Vi En i 1ljzi Tij N N i aM ds diu 522 2e l 2 115 Op rij 5 Gupta virial eda dem i PA 1 Bqij Tjj ro by TO Vek Pj exp RE ER fij 2 116 i 1 jzi The contribution to be added to the atomic stress tensor is given by efe 2 117 Kr jo 2 117 where a and 6 indicate the x y z components The atomic stress tensor is symmetric 33 OSTFC Section 2 3 The long ranged correction for the DL POLY 4 metal potential is in t
255. ink cell algorithms The use of link cells in DL POLY 4 implies the use of appropriate boundary conditions This error results if the user specifies octahedral or dodecahedral boundary conditions which are only available in DL POLY 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 subroutines The link cells algorithms for many body and tersoff forces in DL POLY 4 cannot work with less than 27 link cells Depending on the cell size and the chosen cut off DL POLY 4 may decide that this minimum cannot be achieved and terminate This should never happen Action Decrease many body and tersoff potentials cutoffs or and number of nodes or and increase system size Message 307 error link cell algorithm violation DL POLY 4 does not like what you are asking it to do Probable cause the cutoff is too large to use link cells in this case Action Rethink the simulation model reduce the cutoff or and number of nodes or and increase system size Message 308 error link cell algorithm in contention with SPME sum precision DL POLY 4 does not like what you are asking it to do Probable cause you ask for SPME precision that is not achievable by the current settings of the link cell algorithm Action 259 OSTFC Appendix D Rethink the simulation model reduce number of nodes or and SPME sum precis
256. intramolecular bonded term Utype in the system has a unique index number type from 1 to Nyype where type represents a bond angle dihedral or inversion Also attached there with unique index numbers are core shell units bond constraint units PMF constraint units rigid body units and tethered atoms their definition by site rather than by chemical type 5 On each processor a pointer array keytype Ntype itype carries the indices of the specific atoms involved in the potential term labelled itype The dimension nyype will be 1 if the term represents a tether 1 2 for a core shell unit or a bond constraint unit or a bond 1 2 3 for a valence angle and 1 2 3 4 for a dihedral or an inversion 1 pur unit o 2 1 for a PMF constraint unit or 1 0 1 NRB unit for a rigid body unit 6 Using the key array each processor can identify the global indices of the atoms in the bond term and can use this in conjunction with the local sorted atoms list and a binary search algorithm to find the atoms in local atom list 7 Using the local atom identity the potential energy and force can be calculated It is worth mentioning that although rigid body units are not bearing any potential parameters their definition requires that their topology is distributed in the same manner as the rest of the intra molecular like interactions Note that at the start of a simulation DL POLY 4 allocates individual bonded interactions to spe cific proces
257. ints module o kinds f90 0 setup module o constraints quench o comms module o config module o constraints module o kinds f90 0 setup module o constraints rattle o comms module o config module o constraints module o kinds f90 0 setup module o constraints shake lfv o comms module o config module o constraints module o kinds f90 0 setup module o constraints shake vv o comms module o config module o constraints module o kinds f90 0 setup module o constraints tags o comms module o config module o constraints module o kinds f90 0 setup module o core shell forces o comms module o config module o core shell module o kinds f90 0 setup module o core shell kinetic o comms module o config module o core shell module o kinds f90 0 core shell module o kinds f90 0 setup module o core shell on top o comms module o config module o core shell module o Setup module o core shell quench o comms module o config module o core shell module o kinds f90 0 setup module o core shell relax o comms module o config module o core shell module o kinds f90 0 kinetic module o setup module o statistics module o coul cp forces o config module o kinds f90 0 setup module o coul dddp forces o config module o kinds f90 0 setup module o coul fscp forces o comms module o config module o kinds f90 0 setup module o coul rfp forces o comms_module o config module o kinds f90 0 setup module o 203 OSTFC Appendix C defects1_
258. ion of the isotropic algorithm to anisotropic cell variations is straightforward A tensor n is defined as Mer Pes 1 o 0 V 0 3 134 I3 where where is the stress tensor equation 3 96 and 1 is the identity matrix Then new cell vectors and volume are given by H t At n t H t V t At Trin t VO 3 135 and the velocity updates for VV and LFV algorithms as Wi r tL Af e nE r t At w t 340 LFV r t At e NE r At w t 5 At 3 136 STFC Section 3 5 This ensemble is optionally extending to constant normal pressure and constant surface area NP AT 60 by semi isotropic constraining of the barostat equation of motion to Pu 022 t V t a 6 2 Mas t 4 1 a d a y 3 137 0 a 0 Similarly this ensemble is optionally extending to constant normal pressure and constant surface tension NP yT 60 by semi isotropic constraining of the barostat equation of motion to FA Ps Text V t Ae t aalt VO a 0 w y e BAL Pra oz V las ons 0 t REO where Yext is the user defined external surface tension and h t V t Az 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 3 120 The case yx 0 generates the NPT anisotropic ensemble for the orthorhombic cell imcon 2 in CONFIG see Appendix A This can be considered as an orthorhombic const
259. ion or and increase cutoff Message 321 error LFV quaternion integrator failed This indicates unstable integration but may be due to many reasons Action Rethink the simulation model Increase mxquat in CONTROL and resubmit or use VV integration to check system stability Message 340 error invalid integration option requested DL_POLY_4 has detected an incompatibility in the simulation instructions namely that the re quested integration algorithm is not compatible with the physical model It may be possible to override this error trap but it is up to the user to establish if this is sensible Action This is a non recoverable error unless the user chooses to override the 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
260. ions available in DL POLY 4 are as follows 1 Harmonic harm 1 U rij 5 ro 2 76 2 Restrained harmonic rhrm lk rig rio r U r 24 2 9 i 2 77 ij f skr2 kre rio Te riol gt Te 3 Quartic potential quar k k k U rij z rio rio rio 2 78 2 3 4 as in each case rio is the distance between the atom positions at moment t tl and t 0 The force on the atom i arising from a tether potential potential is obtained using the general formula Li 1 le i i0 oc 22 rio l2 ii o 2R The contribution to be added to the atomic virial is given by The contribution to be added to the atomic stress tensor is given by o rff 2 81 where a and f indicate the x y z components The atomic stress tensor derived in this way is symmetric In DL POLY 4 tether forces are handled by the routine TETHERS FORCES 26 OSTFC Section 2 3 2 3 The Intermolecular Potential Functions In this section we outline the two body metal Tersoff three body and four body potential func tions 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 Dc 5 z 3 2 82 ij ij 2 Lennard Jones potential 1j 12 6 U rij de 2 2 83 3 n m poten
261. ions of DL_POLY_4 may have a different order of the above parameters or include more or less such Therefore a different versions of DL_POLY 4 may render any existing REVOLD file unreadable by the code 5 1 6 The TABLE File The TABLE file provides an alternative way of reading in the short range potentials in tabular form This is particularly useful if an analytical form of the potential does not exist or is too complicated to specify in the VDW_GENERATE subroutine The table file is read by the subroutine VDW_TABLE_READ see Chapter 6 The option of using tabulated potentials is specified in the FIELD file see above The specific potentials that are to be tabulated are indicated by the use of the tab keyword on the record defining the short range potential see Table 5 12 5 1 6 1 The TABLE File Format The file is free formatted but blank and commented lines are not allowed 5 1 6 2 Definitions of Variables record 1 header a100 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 header record atom 1 a8 first atom type atom 2 a8 second atom type potential data records number of dat
262. it Message 103 error parameter mxlshp exceeded in pass shared units Various algorithms constraint and core shell ones require that information about shared atoms be passed between nodes If there are too many such atoms the arrays holding the information will be exceeded and DL POLY 4 will terminate execution Action Use densvar option in CONTROL to increase mxlshp alternatively increase it by hand in SET_BOUNDS and recompile and resubmit Message 104 error arrays listme and lstout 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 253 OSTFC Appendix D Message 105 error shake algorithm constraints shake failed to converge The SHAKE algorithm for bond constraints is iterative If the maximum number of permitted iter ations is exceeded the program terminates Possible causes include a bad starting configuration too large a time step used incorrect force field specification too high a temperature inconsistent constraints over constraint etc Action You may try to increase the limit of iteration cycles in the constraint subroutines by using the direc tive mxshak and or decrease the constraint precision by using the directive shake in CONTROL But the trouble may be much more likely to be cured by careful consideration of the physical system being s
263. ities 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 73 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 168 OSTFC Section 6 1 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 a All common forms of non bonded atom atom van der Waals forces Atom atom and site site coulombic forces Metal metal local density dependent forces Tersoff local density dependent forces for hydro carbons 17 Three body valence angle and hydrogen bond forces Four body inversion forces Ion core shell polarasation Tether forces Chemical bond forces Valence angle forces Dihedral angle and improper dihedral angle forces Inversion angle forces External field forces 2 The computed forces are accumulated in atomic force arrays f independently on each pro cessor 3
264. ive 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 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 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 266 OSTFC Appendix D Message 470 error n m in definition of n m potential The specification of a
265. ives The directives available are as follows directive binsize f cap forces f close time f collect coulomb cutoff f defects i j f densvar f distance displacements i j f dump n meaning set the bin size for radial and z density distribution functions to fA i 107 lt f lt reu 40or undefined f defaults to 0 05 A cap forces during equilibration period f is maximum cap in units of kg T default f 1000 kg T set job closure time to f seconds include equilibration data in overall statistics calculate electrostatic forces using direct Coulomb sum set required long ranged interactions cutoff reut to f A write defects trajectory file DEFECTS with controls i start timestep for dumping defects configurations default i 0 j timestep interval between configurations default j 1 f site interstitial cutoff default f Min 0 75 rey 3 A Min 0 3 reut 3 lt f lt Min 1 2 rcut 2 A allow for local variation of f 96 in the system density of 1 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 j 1 f displacem
266. ke vv o pmf shake vv o constraints rattle o pmf rattle o nvt hO scl o nvt gO scl o npt hO scl o nst_h0_scl o nve O vv o nvt eO vv o nvt 10 vv o nvt aO vv o nvt bO vv o nvt hO vv o nvt_g0_vv o npt 10 vv o npt bO vv o npt hO vv o npt mO vv o nst 10 vv o nst bO vv o nst hO vv o nst mO vv o nvt hi scl o nvt gi scl o npt hi scl o nst hi scl o nve 1 vv o nvt el vv o nvt li vv o nvt_al_vv o nvt bi vv o nvt hi vv o nvt gi vv o npt 11 vv o npt b vv o npt h vv o npt mi vv o nst li vv o nst b vv o nst hi vv o nst mi vv o pseudo_lfv o constraints_shake_lfv o pmf shake lfv o nve O lfv o nvt eO lfv o N nvt 10 lfv o nvt a0 lfv o nvt bO lfv o nvt hO lfv o nvt gO lfv o npt 10 lfv o npt bO lfv o npt hO lfv o npt mO lfv o nst 10 lfv o nst bO lfv o nst hO lfv o nst mO lfv o nve 1 lfv o nvt e lfv o nvt li lfv o nvt ai lfv o nvt bi lfv o nvt hi lfv o nvt gil lfv o npt l1 lfv o npt bi lfv o npt hi lfv o npt mi lfv o nst 11 lfv o nst bi lfv o nst hi lfv o nst mi lfv o xscale o core_shell_kinetic o regauss_temperature o z_density_collect o statistics_collect o system_revive o rdf_compute o z_density_compute o statistics_result o dl poly o Define MPI SERIAL files FILES SERIAL mpi_module f90 mpif h Define Velocity Verlet files FILES VV N pseudo vv f90 constraints shake vv f90 pmf shake vv f90 constraints rattle f90 pmf rattle f90 nvt hO scl f90 nvt gO s
267. l Introduction ese beeen a RA dup or Re E v Bud SE ne eus 54 s Bond Gousteaib iu a Rege A qx ARIS XS RR EOS e hU eee RE dh x 57 3 3 Potential of Mean Force PMF Constraints and the Evaluation of Free Energy 59 9 4 LhermostatS c ea sa m x Ro do e a eee Gate RE ALA 60 3 4 1 Evans Thermostat Gaussian Constraints o 60 342 Langevin Thermostat s s ma mien ea BR bos ee dou aa 62 3 4 3 Andersen Thermostat les 64 3 4 4 Berendsen Thermostat e 65 3 4 5 Nos Hoover Thermostat e 67 3 4 6 Gentle Stochastic Thermostat lt se as o o 02000000 ee eee 69 doo Barostals 2242 4824 04 pad be AG o a id e doe T1 3 5 1 Instantaneous pressure and stress LL 71 3 9 2 Langer Barostabi cia ao one as RODA ee Ee up E 72 3 5 3 Berendsen Barostat aaa a hA a e a Ba aa E Ea a aa TT 39 4 JNos Hoover Barostat o s sos 230 244 2 ke bog ee RE ORR EUER d 80 3 5 5 Martyna Tuckerman Klein Barostat 86 3 6 Rigid Bodies and Rotational Integration Algorithms 89 3 6 1 Description of Rigid Body Units e 89 3 6 2 Integration of the Rigid Body Equations of Motion 90 3 6 3 Thermostats and Barostats coupling to the Rigid Body Equations of Motion 93 4 Construction and Execution 95 4 1 Constructing DL_POLY 4 an Overview 2 2 2 2 0 00000 eee eee 96 4 1 1 Constructing the Standard Versions
268. l correction No long ranged corrections apply beyond cutoffs c and d 3 Extended Finnis Sinclair virial correction No long ranged corrections apply beyond cutoffs c and d 4 Sutton Chen virial correction No 3 n 3 sv noe pea a n 3 Fmet zd n 3 N ST more 3 2 125 m 3 Tmet 2 00 5 Gupta virial correction p 2x N pAro To roy roy V E ES NE riu 3rt et pP 6T met P 6 P Xx m exp p ro 255 2 3 ji 2mpr r r r dv WAP 8 Bra Grimes 6 2 x 2126 To dij dij dij dij PE 9 je NB p Qij e 2 2 2 In the energy and virial corrections we have used the approximation N 1 2 N i lt P gt where lt pl 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 cal culated by the routines METAL LD COLLECT EAM METAL_LD_COLLECT_FST METAL_LD_COMPUTE METAL LD SET HALO and METAL _LD_EXPORT The long ranged corrections are calculated by METAL LRC Reading and generation of EAM table data from TABEAM is handled by METAL TABLE READ and METAL TABLE DERIVATIVES Notes on the Treatment of Alloys The distinction to be made between EAM and FS potentials with regard to alloys concerns the mixing rules for unlike interactions Starting with equations 2 98 and 2 99 it is clear that we require mixing rules for terms Vj rij and pi rij when atoms and j are of
269. l methods and generic functions intrinsically related to the purpose or and contents of the specific module The file names and the methods or and functions developed in them have self explanatory names More information of their purpose can be found in their headers The rest of files in DL POLY 4 are dependent on the module files in various ways The dependency relation to a module file is explicitly stated in the declaration part of the code 6 2 4 General Files The DL POLY 4 general files are common to both MPI and SERIAL version of the code In most cases they have self explanatory names as their order is matched as closely as possible to 178 OSTFC Section 6 2 that occurring in the main segment of the code DL POLYv 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 6 2 5 VV and LFV Specific Files These implement the specific integration scheme as file names are finished with the flavour they develop if they have a counterpart implementing the same algorithm but in the alternative flavour Names are self explanatory 6 2 6 SERIAL Specific Files These implement an emulation of some general MPI calls used in DL POLY 4 source code when compiling in serial mode as well as some
270. lassic 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 Integration Defaults The default ensemble is NVE The default integration scheme is Trotter derived Velocity Verlet VV although Leapfrog Verlet LFV is also available VV is considered superior to LFV since 1 2 3 Integration can be developed in symplectic manner for certain ensembles such as NVE NVEk NVT Evans as well as all Nose Hoover ensembles NVT amp NPT amp NsT when there is no external field applied on the system otherwise they do not conserve the phase space volume and MTK ensembles NPT amp NsT All ensemble variables are updated synchronously and thermodynamic quantities and estimators are exact at the every step whereas in LFV particle velocities and thermostat and barostat friction velocities are half an integration time step behind the rest of the ensemble variables and due to this certain estimators are approximated at full timestep It offers better numerical stability and faster convergence 287 OSTFC Appendix E
271. lates the FFT and B spline complex exponentials 2 PARALLEL_FFT and GPFA MODULE native DL POLY 4 subroutines that respect the domain decomposition concept which calculate the 3D complex fast Fourier transforms 3 EWALD SPME FORCES which calculates the reciprocal space contributions uncorrected 4 EWALD REAL FORCES which calculates the real space contributions corrected 5 EWALD EXCL FORCES which calculates the reciprocal space corrections due to the coulombic exclusions in intramolecular interactions 6 EWALD FROZEN FORCES which calculates the reciprocal space corrections due to the exclu sion interactions between frozen atoms 7 TWO_BODY_FORCES in which all of the above subroutines are called sequentially and also the Fuchs correction 54 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 2 198 where jz is the induced dipole and E is the electric field The constant a is the polarisability 49 OSTFC Section 2 5 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 se
272. le o dihedrals 14 check o kinds f90 0 setup module o dihedrals 14 vdw o kinds f90 0 setup module o vdw_module o dihedrals forces o comms module o config module o dihedrals module o kinds f90 0 setup module o vdw module o dihedrals module o kinds f90 0 setup module o dl poly o angles module o bonds module o comms module o config module o constraints module o core shell module o development module o dihedrals module o external field module o four body module o inversions_module o io module o kinds f90 0 kinetic module o langevin module o metal module o msd module o parse module o pmf module o rigid bodies module o setup module o site module o statistics module o tersoff module o tethers_module o three body module o vdw module o md lfv f90 md vv f90 replay history f90 domains_module o comms module o kinds f90 0 error o comms module o setup module o ewald excl forces o config module o ewald module o kinds f90 0 Setup module o ewald frozen forces o comms module o config module o ewald module o kinds f90 0 setup module o ewald module o config module o kinds f90 0 setup module o ewald real forces o comms module o config module o kinds f90 0 204 OSTFC Appendix C Setup module o ewald spme forces o comms module o config module o domains module o ewald module o kinds f90 0 parallel fft o setup module o exchange grid o comms_module o domains module o kinds f90 0 setup mod
273. le potentials with a dash as the first character of the keyword do not contribute to the ezcluded atoms list see Section 2 In this case DL POLY 4 will calculate the non bonded pair potentials between the described atoms 142 OSTFC Section 5 1 Table 5 10 Dihedral Angle Potentials key potential type Variables 1 3 6 7 functional formi cos Cosine Al m U A 1 cos m 6 harm Harmonic k do U s do hcos Harmonic cosine k Po U E cos d cos o cos3 Triple cosine Aj A2 Aa U 5 4 1 cos 9 Ag 1 cos 2 As 1 cos 3 ryck Ryckaert Bellemans 41 A U A a b cos c cos d cos e cos f cos rbf Fluorinated Ryckaert A U A a b cos c cos Bellemans 42 d cos e cos f cos d g exp h 7 opls OPLS torsion Ao Ay A U Ao 3 A1 1 cos o Aa do Az 1 cos 2 do Az 1 cos 3 do td is the i j k l dihedral angle Table 5 11 Inversion Angle Potentials key potential type Variables 1 3 functional formi harm Harmonic k do U 9 6 do hcos Harmonic cosine k do U E cos cos o plan Planar A U A 1 cos xpln Extended planar k m do U 1 cos m 9 do calc Calcite AIB U u Au But Eo is th
274. led within the routine SET BOUNDS which also sets the necessary limits for various simulation array sizes and all global variables as de clared in SETUP MODULE to convenient values based on rough scan through the CONFIG CON TROL FIELD and optionally TABLE and TABEAM Section 5 1 files The routine also calls the READ CONFIG routine to obtain atomic positions and optionally velocities and forces the CONFIG file After allocation of all necessary simulation arrays and variables with compulsory initiali sation to zero value the job control information is required this is obtained by the routine READ CONTROL which reads the CONTROL file The description of the system to be simu 97 OSTFC Section 4 2 lated the types of atoms and molecules present and the intermolecular forces are obtained by the READ FIELD routine which reads the FIELD file The SYSTEM INIT routine is called next to initialise various simulation arrays and variables intact with the data so far and detects if the job is a restart of previous simulation run If so it reads the REVOLD Section 5 1 5 to supply some arrays and variables with the necessary values as saved from the previous job The domain halo is constructed strait after by the routine SET HALO PARTICLES After gathering all these data bookkeeping and exclusion arrays are created for the intramolecular and site related inter actions core shell constraint and tether units by BUILD BOOK INTRA and BUIL
275. les 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 237 OSTFC Appendix D Action Add units directive to FIELD file and resubmit Message 8 error ewald precision must be a POSITIVE real number Ewald precision must be a positive non zero real number For example 10e 5 is accepted as a standard Action Put a correct number at the ewald precision directive in the CONTROL file and resubmit Message 10 error too many molecule types specified This should never happen This indicates an erroneous FIELD file or corrupted DL POLY 4 executable Unlike DL POLY 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
276. lf interaction between the core and shell of the same atom Non coulombic interactions arise from the shell alone The effect of an electric field is to separate the core and shell giving rise to a polarisation dipole The condition of static equilibrium gives the polarisability as a 293 a2 k 2 199 where gs and ge are the shell and core charges and k is the force constant of the harmonic spring The calculation of the virial and stress tensor in this model is based on that for a diatomic molecule with charged atoms The electrostatic and short ranged forces are calculated as described above The forces of the harmonic springs are calculated as described for intramolecular harmonic bonds The relationship between the kinetic energy and the temperature is different however as the core shell unit is permitted only three translational degrees of freedom and the degrees of freedom corresponding to rotation and vibration of the unit are discounted as if the kinetic energy of these is regarded as zero 3 11 2 5 1 Dynamical Adiabatic Shells The dynamical shell model is a method of incorporating polarisability into a molecular dynamics simulation The method used in DL POLY 4 is that devised by Fincham et al 56 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 fre
277. local density in space as is the case for clusters in vacuum The parallelisation and domain decomposition is therefore limited to eight domains maximum of two in each direction in space This boundary condition should not used with the SPM Ewald summation method Cubic periodic boundaries imcon 1 The cubic MD cell is perhaps the most commonly used in simulation and has the advantage of great simplicity In DL_POLY 4 the cell is defined with the principle axes passing through the centres of the faces Thus for a cube with sidelength D the cell vectors appearing in the CONFIG file should be D 0 0 0 D 0 0 0 D Note the origin of the atomic coordinates is the centre of the cell 187 OSTFC Appendix A Z Y X Figure A 1 The cubic MD cell Orthorhombic periodic boundaries imcon 2 gt X Figure A 2 The orthorhomic MD cell The orthorhombic cell is also a common periodic boundary which closely resembles the cubic cell in use In DL_POLY 4 the cell is defined with principle axes passing through the centres of the faces For an orthorhombic cell with sidelengths D in X direction E in Y direction and F in Z direction the cell vectors appearing in the CONFIG file should be D 0 0 0 E 0 0 0 F Note the origin of the atomic coordinates is the centre of the cell Parallelepiped periodic boundaries imcon 3 LU Figure A 3 The parallelepiped MD cell 188 OSTFC Appendix A The parall
278. location bigger global arrays and larger memory consumption by DL POLY 4 during the simulation Note that this option may demand more memory than available on the computer architecture In such cases DL_POLY_4 will terminate with an array allocation failure message As a default DL POLY 4 does not store statistical data during the equilibration period If the directive collect is used equilibration data will be incorporated into the overall statistics io action options controls how I O is performed by DL POLY 4 The options can help the performance of I O operations within DL POLY 4 for potentially large files during the run The form of the command depends on the value of action which may take the value either read or write In general this command should only be used for tuning the I O subsystem in DL_POLY 4 for large runs For small to average sized systems the built in defaults usually suffice a io read method options With action set to read the io command controls how the reading of large files is performed method controls how the disk is accessed Possible values are mpiio in which case MPLI 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 mpiiois the recommended method and for large systems master should be avoided Available options depend on which method is to be
279. lri gras Oie 2 145 The derivative of 9 6 is worked out in the following manner N 21 er 90 51 ix d E 2 146 are O0 sin ijk Org rij Tik where Og ijk _ 2cj hi cos Bij sin Oija 2 147 055k d h cos 0 5 a cU dei i er bu Ea cos 0 ik foy D E en dai e 2 148 Tij ri 39 OSTFC Section 2 3 The contribution to be added to the atomic virial can be derived as OEtersott 3V QUi We VS a 22 3v 2 149 0 le W Y PACS CO Tij ij ij i jAi 1 i p aa mol 3 fo ri fa rig Xij 1 bi DD BEL X 2 150 o Y wir 9 0 k ac Solri Tik kzi j is The contribution to be added to the atomic stress tensor is given by o ref 2 151 where a and indicate the x y z components The stress tensor is symmetric Interpolation arrays vter and gter set up in TERSOFF GENERATE similar to those in van der Waals interactions 2 3 1 are used in the calculation of the Tersoff forces virial and stress The Tersoff potentials are very short ranged typically of order 3 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 51 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 2
280. ls 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 51 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 2 3 5 Four Body Potentials The four body potentials in DL POLY 4 are entirely inversion angle forms primarily included to permit simulation of amorphous materials particularly borate glasses The potential forms available in DL POLY 4 are as follows 1 Harmonic harm U sin 5 Gi do 2 158 2 Harmonic cosine hcos U sio 5 cos dijim cos d0 2 159 3 Planar potential plan U deus lud 2 160 These functions are identical to those appearing in the intra molecular inversion angle descriptions above There are significant differences in implementation however arising from the fact that the four body potentials are regarded as inter molecular Firstly the atoms involved are defined by atom types not specific indices Secondly there are no excluded atoms arising from the four body terms T
281. lse LI manner 63 1 VVI t ed e ayi 2 m 1 V2 kpT gt u t At e exp yx At v t 4 A Z1 x At 3 36 rt At c rl 4 APEX a e XE BPE Ze At 62 OSTFC Section 3 4 where Zx At and Zo x At are joint Gaussian random variables of zero mean sampling from a bivariate Gaussian distribution 63 1 2 Zi LM fy 3 37 La 01 02 05 Ai ale yr Ro with 1 A on au z X55 12 3 38 and AH 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 VVI 3 FF f t At f t 3 39 4 VV2 f At 1 At t t A A 4 u t At ult 5 t e 3 a 3 40 5 RATTLE_VV2 The algorithm is self consistent and requires no iterations The LFV implementation of the Langevin thermostat is straightforward 1 FF f f t At R R t At 3 41 3 42 2 LFV and Thermostat At 2 At scale 1 x scalev 1 scale f 2 scale scale 1 1 t R t v t At scale v v t At scale f fO 80 3 43 m 1 r t At rit tAtult At 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 ut At u t 340 3 44 The VV and LFV flavours of the Langevin thermostat are implemented in the DL_POLY 4 routines NVT_LO vv and NVT LO LFV respectiv
282. main to size of halo both in counts of link cells When this ratio falls down to values close to one and below the time DL_POLY 4 spends on inevitable communication MPI messages across neighbouring domains to refresh the halo data increases with respect to and eventually becomes prevalent to the time DL POLY 4 spends on numeric calculations integration and forces In such regimes the overall DL POLY 4 efficiency falls down since processors spend more time on staying idle while communicating than on computing It is important that the user recognises when DL POLY 4 becomes vulnerable to decreased effi ciency and what possible measures could be taken to avoid this DL POLY 4 calculates and reports the major and secondary link cell algorithms M M M employed in the simulations immedi ately after execution M 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 E z cutoff W MD box width L plane y 2 4 1 P nodes z direction gt where x y and z represent the directions along the MD cell lattice vectors Every domain node of the MD cell is loaded with M 2 M 2 M 4 2 link cells of which M My M belong to that 104 STFC Section 4 3 domain an
283. mandatory whereas TABLE and TABEAM are only used to input certain kinds of pair or metal potentials and may not always be required REFERENCE is required only if defect detection is switched on in CONTROL REVOLD is re quired only if the job represents a continuation of a previous job In the following sections we describe the form and content of these files 5 1 1 The CONTROL File The CONTROL file is read by the subroutine READ_CONTROL and defines the control variables for running a DL POLY 4 job It is also read by the subroutine SCAN_CONTROL in the SET_BOUNDS routine It makes extensive use of directives and keywords Directives are character strings that appear as the first entry on a data record or line and which invoke a particular operation or provide numerical parameters Also associated with each directive may be one or more keywords which may qualify a particular directive by for example adding extra options Directives can 112 STFC Section 5 1 appear in any order in the CONTROL file except for the finish directive which marks the end of the file Some of the 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 tries to sort out these difficulties an
284. mble if a Poisson selected particle constitutes a RB then the 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 94 Chapter 4 Construction and Execution Scope of Chapter This chapter describes how to compile a working version of DL POLY 4 and run it 95 OSTFC Section 4 1 4 1 Constructing DL POLY 4 an Overview 4 1 1 Constructing the Standard Versions DL POLY 4 was designed as a package of useful subroutines rather than a single program which means that users are to be able to construct a working simulation program of their own design from the subroutines available which is capable of performing a specific simulation However we recognise that many perhaps most users will be content with creating a standard version that covers all of the possible applications and for this reason we have only provided the necessary tools to assemble such a version The method of creating the standard version is described in detail in this chapter however a brief step by step description follows 1 DL POLY 4 is supplied as a UNIX compressed file tarred and gzipped This must uncom pressed and un tared to create the DL POLY 4 directory Se
285. merely an interim adjustment not only because the above formula is ap proximate but the successive correction of other bonds in a molecule has the effect of perturbing previously corrected bonds Either part of the RATTLE algorithm is therefore iterative with the correction cycle being repeated for all bonds until each has converged to the correct length within a given tolerance for RATTLE VV1 SHAKE and the relative bond velocities are perpendicular to their respective bonds within a given tolerance for RATTLE_VV2 RATTLE The tolerance may be of the order 1074 A to 1078 A depending on the precision desired The SHAKE procedure may be summarised as follows 1 All atoms in the system are moved using the LFV algorithm assuming an absence of rigid bonds constraint forces This is stage 1 of the SHAKE algorithm 2 The deviation in each bondlength is used to calculate the corresponding constraint force 3 16 that retrospectively corrects the bond length 3 After the correction 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 constitutes stage 2 of the SHAKE algorithm The RATTLE procedures may be summarised as follows 1 RATTLE stage 1 a All atoms in the system are moved using the VV algorithm assu
286. ming an absence of rigid bonds constraint forces This is stage 1 of the RATTLE_VVI algorithm 58 STFC Section 3 3 b The deviation in each bondlength is used to calculate the corresponding constraint force 3 17 that retrospectively corrects the bond length c After the correction 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 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 SHA
287. modified counterparts of the general files changed to allow for faster and or better memory optimised serial execution Names are self explanatory 6 2 7 Comments on MPI Handling Only a few files make explicit calls to MPI routines COMMS MODULE IO MODULE READ CONFIG PARALLEL READ CONFIG WRITE CONFIG 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 DEFECTS 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 6 2 8 Comments on SETUP MODULE The most important module by far is SETUP MODULE which holds the most important global parameters and variables some of which serve as parameters for global array bounds set in SET BOUNDS A brief account of these is given below parameter value function pi 3 1415926535897932 7 constant sqrpi 1 7724538509055160 YT constant rt2 1 4142135662373095 2 constant rt3 1 7320508075688772 4 3 constant r4pie0 138935 4835 electrostatics conversion factor to internal units i e Ge boltz 0 831451115 Boltzmann constant in internal units 179 OSTFC Section 6 2 prsunt nread ncon
288. module o rigid bodies module o setup module o nst hi vv o comms module o config module o domains module o kinds f90 0 kinetic module o rigid bodies module o setup module o site module o nst 10 lfv o comms module o config module o kinds f90 0 kinetic module o langevin_module o setup module o site module o nst l0 vv o comms module o config module o kinds f90 0 kinetic module o langevin_module o setup module o site module o nst l1 lfv o comms module o config module o domains module o kinds f90 0 kinetic module o langevin module o rigid bodies module o Setup module o site module o nst li vv o comms module o config module o domains module o kinds f90 0 kinetic module o langevin module o rigid bodies module o Setup module o site module o nst mO lfv o comms module o config module o kinds f90 0 kinetic module o Setup module o site module o nst mO vv o comms module o config module o kinds f90 0 kinetic module o Setup module o site module o nst mi lfv o comms module o config module o domains module o kinds f90 0 kinetic module o rigid bodies module o setup module o site module o nst mi vv o comms module o config module o domains module o kinds f90 0 kinetic module o rigid bodies module o setup module o site module o numeric container o comms module o config module o kinds f90 0 Setup module o nve O lfv o comms module o config module o kinds f90 0 kinetic module o Setup module o site module o nve O vv
289. module o kinds f90 0 setup module o defectsi write o comms module o config module o defects1_module o io module o kinds f90 0 parse module o setup module o site module o defects link cells o comms module o domains module o kinds f90 0 Setup module o defects module o kinds f90 0 setup module o defects reference export o comms module o domains module o kinds f90 0 Setup module o defects reference read o comms module o config module o domains module o io module o kinds f90 0 parse module o setup module o site module o defects reference read parallel o comms module o domains module o io module o kinds f90 0 parse module o setup module o defects reference set halo o comms module o config module o domains module o kinds f90 0 setup module o defects reference write o comms module o config module o io module o kinds f90 0 setup module o defects write o comms module o config module o defects1_module o defects module o io module o kinds f90 0 parse module o Setup module o site module o deport atomic data o angles module o bonds module o comms module o config module o constraints module o core shell module o dihedrals module o domains module o ewald module o inversions_module o kinds f90 0 langevin module o minimise module o msd module o pmf module o rigid bodies module o setup module o Statistics module o tethers module o development module o comms module o kinds f90 0 parse module o Setup modu
290. module o development module o netcdf modul o io module o domains module o Site module o config module o defects module o defects1_module o vdw module o metal module o tersoff module o three body module o four body module o core shell module o constraints module o pmf module o rigid bodies module o tethers module o bonds module o angles module o dihedrals module o inversions module o external_field_module o langevin_module o minimise_module o ewald_module o msd_module o statistics_module o kinetic_module o gpfa_module o parallel_fft o 0BJ ALL warning o error o scan_control_io o numeric_container o spme_container o quaternions_container o scan field o read config parallel o scan config o scan control o read config o 229 OSTFC Appendix C set bounds o read control o vdw generate o vdw table read o vdw direct fs generate o metal generate o metal table read o metal table derivatives o tersoff generate o dihedrals 14 check o read field o check config o scale config o write config o trajectory write o system expand o rigid bodies tags o rigid bodies coms o rigid bodies widths o rigid bodies setup o tag legend o report topology o pass shared units o build book intra o build excl intra o Scale temperature o update shared units o core shell quench o constraints tags o constraints quench o pmf coms o pmf tags o pmf vcoms o pmf quench o rigid bodies
291. mulation a restart final configuration file a restart final statistics accumulators file a radial distribution data file Z density data file and a statistical history file 5 2 1 The HISTORY File The HISTORY file is the dump file of atomic coordinates velocities and forces Its principal use is for off line analysis The file is written by the subroutine TRAJECTORY_WRITE The control variables for this file are ltraj nstraj istraj and keytrj which are created internally based on information read from the traj directive in the CONTROL file see Section 5 1 1 The HISTORY file will be created only if the directive traj appears in the CONTROL file 154 STFC Section 5 2 The HISTORY file can become very large especially if it is formatted For serious simulation work it is recommended that the file be written to a scratch disk capable of accommodating a large data file Alternatively the file may be written in netCDF format instead of in ASCII users must change ensure this functionality is available which has the additional advantage of speed The HISTORY has the following structure record 1 header a72 file header record 2 keytrj integer trajectory key see Table 5 1 in last frame imcon integer periodic boundary key see Table 5 6 in last frame megatm integer number of atoms in simulation cell in last frame frame integer number configuration frames in file records integer number of records in file For timesteps gre
292. mulation at 300 K using NVT Nos Hoover ensemble with Sutton Chen forces and no electrostatics 7 1 7 Test Case 13 and 14 lipid bilayer in water These systems consist of 12 428 and 111 852 atoms respectively Simulation at 300 K using NVT Berendsen ensemble with SPME and SHAKE RATTLE algorithm for the constrained motion 7 1 8 Test Case 15 and 16 relaxed and adiabatic shell model MgO These systems consist of 8 000 4 000 shells and 64 000 32 000 shells atoms respectively Simula tion at 3000 K using NPT Berendsen ensemble with SPME FIELD and CONTROL files for each shell model are provided separately 7 1 9 Test Case 17 and 18 Potential of mean force on K in water MgO These systems consist of 13 500 500 PMFs and 53 248 2 048 PMFs atoms respectively Simu lation at 300 K using NPT Berendsen ensemble with SPME and SHAKE RATTLE algorithm for the constrained motion 7 1 10 Test Case 19 and 20 CuzAu alloy with Gupta metal Potentials These systems consist of 32 000 and 256 000 atoms respectively Simulation at 300 K using NVT Nos Hoover ensemble with Gupta forces and no electrostatics 7 1 11 Test Case 21 and 22 Cu with EAM metal Potentials These systems consist of 32 000 and 256 000 atoms respectively Simulation at 300 K using NPT Berendsen ensemble with EAM tabulated forces and no electrostatics 184 OSTFC Section 7 1 7 1 12 Test Case 23 and 24 Al with Sutton Chen metal Potentials These systems consist of 32 00
293. mxstak mxnstk mxlist mxcell mxatms mxatms mxbuff zero plus half minus engunit variable variable variable variable variable variable variable variable variable variable variable variable variable variable variable variable variable variable variable variable variable variable variable variable variable variable variable variable variable variable variable variable variable variable variable variable variable variable variable variable variable variable 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 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 specified dihedral angle potentials in system max number of dihedral angles per node max number of related dihedral angles 1 6 2 6 6 1 2 max number of parameters for dihedral angle potentials 7 max number of specified inversion angle potentials in system max number of inversion angles per node max number of related inversion angles 1 6 6 1 4 max number of parameters for inversion angle potentials 3 max number of grid points in potential arrays max number of pairwise RDF in system number of grid points for RDF a
294. n FIELD Action Correct FIELD and resubmit Message 82 error calculated pair potential index too large This should never happen In checking the vdw and metal potentials specified in the FIELD file DL POLY 4 calculates a unique integer indices that henceforth identify every specific potential within the program If this index becomes too large termination of the program results Action Report to authors Message 83 error too many three body potentials specified This should never happen Action Report to authors Message 84 error unidentified atom in three body potential list This shows that DL_POLY_4 has encountered and erroneous entry at tbp definition in FIELD Action Correct FIELD and resubmit 250 OSTFC Appendix D Message 85 error required velocities not in CONFIG file If the user attempts to start up a DL_POLY_4 simulation with any type of restart directive see description of CONTROL file the program will expect the CONFIG file to contain atomic velocities as well as positions Termination results if these are not present Action Either replace the CONFIG file with one containing the velocities or if not available remove the restart directive altogether and let DL POLY 4 create the velocities for itself Message 86 error calculated three body potential index too large This should never happen DL POLY 4 has a permitted maximum for the calculated index for any three body
295. n at 500 K with a NVT Berendsen ensemble The SPME method is used to calculate the Coulombic interactions 7 1 2 Test Case 3 and 4 DPMC in Water These systems consist of 200 and 1 600 DMPC molecules in 9379 and 75032 water molecules respectively Simulation at 300 K using NVE ensemble with SPME and RATTLE algorithm for the constrained motion Total system size is 51737 and 413896 atoms respectively 7 1 3 Test Case 5 and 6 KNaS1505 Potassium Sodium disilicate glass NaKSi205 using two and three body potentials Some of the two body potentials are read from the TABLE file Simulation at 1000 K using NVT Nos Hoover ensemble with SPME Cubic periodic boundaries are in use System size is 69120 and 552960 ions respectively 183 OSTFC Section 7 1 7 1 4 Test Case 7 and 8 Gramicidin A molecules in Water These systems consist of 8 and 16 gramicidin A molecules in aqueous solution 32 096 and 256 768 water molecules with total number of atoms 99 120 and 792 960 respectively Simulation at 300 K using NPT Berendsen ensemble with SPME and SHAKE RATTLE algorithm for the constrained motion 7 1 5 Test Case 9 and 10 SiC with Tersoff Potentials These systems consist of 74 088 and 343 000 atoms respectively Simulation at 300 K using NPT Nos Hoover ensemble with Tersoff forces and no electrostatics 7 1 6 Test Case 11 and 12 CuzAu alloy with Sutton Chen metal Potentials These systems consist of 32 000 and 256 000 atoms respectively Si
296. n at the beginning of each step dt TP i where P is the instantaneous pressure equation 3 95 and Tp is the barostat relaxation time constant Cell size variations TT STFC Section 3 5 In the isotropic implementation at each step the MD cell volume is scaled by a factor 7 and the coordinates and cell vectors by 7 3 _ Bat n t 1 E Pera P t 3 123 where 6 is the isothermal compressibility of the system In practice 6 is a specified constant which DL POLY 4 takes to be the isothermal compressibility of liquid water The exact value is not critical to the algorithm as it relies on the ratio 7p P Tp is a specified time constant for pressure fluctuations supplied by the user It is worth noting that the barostat and the thermostat are independent and fully separable The VV implementation of the Berendsen algorithm only requires iterations if bond or PMF con straints are present 7 until satisfactory convergence of the constraint forces is achieved These are with respect to the pressure i e n t in the first part VVI RATTLE VV1 The second part is conventional VV2 RATTLE_VV2 as at the end the velocities are scaled by a factor of x 1 VVI 1 _ At f t u t At w 5 FAD e 0 r t At v t 344 3 124 H t At t HE V t A n t V t 2 RATTLE VVI 3 Barostat BAt n t 1 Pat P t 3 125 4 FF f t At f t 3 126 5 VV2 RE v t At u t A
297. n com The GUI once compiled may be executed on any machine where Java is installed 21 9 OSTFC Section 1 7 1 5 Obtaining the Source Code To obtain a copy of DL POLY 4 it is necessary to have internet connection Log on to the DL POLY website http www ccp5 ac uk DL POLY and follow the links to the DL POLY 4 registration page where you will firstly be shown the DL POLY 4 software licence which details the terms and conditions under which the code will be supplied By proceeding further with the registration and download process you are signalling your acceptance of the terms of this licence Click the Registration button to find the registration page where you will be invited to enter your name address and e mail address The code is supplied free of charge to academic users but commercial users will be required to purchase a software licence Once the online registration has been completed information on downloading the DL POLY 4 source code will be sent by e mail so it is therefore essential to supply a correct e mail address The data and bench subdirectories of DL POLY 4 are not issued in the standard package but can be downloaded directly from the FTP site in the ccp5 DL_POLY DL_POLY 4 0 directory Note Daresbury Laboratory is the sole centre for the distribution of DL_POLY_4 and copies obtained from elsewhere will be regarded as illegal and will not be supported 1 6 OS and Hardware Specific Ports
298. 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 2 rctbp maximum cutoff for three body potentials The cutoff for the pair interactions is smaller than twice that for the three body interactions This is a bookkeeping requirement for DL POLY 4 Action Either use a smaller three body cutoff or a larger pair potential cutoff Message 472 error rcut 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 const
299. n of integration algorithms indicating both VV and LFV cast integration within DL POLY 4 is as follows NVE_O_VV NVE_O_LFV Constant E algorithm NVE_1_VV NVE_1_LFV The same as the above but also incorporating RB integration NVT_EO_VV NVT_EO_LFV Constant Ekin algorithm Evans 26 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 A1 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 Bl VV NVT Bl 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 GO0 VV NVT_GO_LFV Constant T algorithm GST 59 NVT Gl 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 Hl VV NPT_H1_LFV The same as the above but also incorp
300. n of motion and slight amending the thermostat equation of motion and the conserved quantity to in i nO P VO _ Aalt a 8 z a 0 5 Nap 0 9 a B 2 d 2Exin t Pmass Tr n t n t 20 kp Text qM ae 3 160 at Amass mass t Pmass Tr n n t Hnp aAT Hnve 4 q AI 2 PeaV t f 1 kg Text J x s ds Similarly this ensemble is optionally extending to constant normal pressure and constant surface tension NP yT 60 by semi isotropic constraining of the barostat equation of motion and slight amending the thermostat equation of motion and the conserved quantity to Taa O Poe en RATO y naa f a 8 2 y d Pmass qe msi is VO _ x t maz t a p 2 0 mag 0 0 af P 2 y 2 d 2 Ekin t F Pmass Tr n t j nt 20 3 kp Text 4X0 pom 3 161 T Hean Hyg Eee XU Pre 707 ives e Tow f xe where Yext is the user defined external surface tension and h t V t Az 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 3 120 The case yext 0 generates the NPT anisotropic ensemble for the orthorhombic cell imcon 2 in CONFIG see Appendix A This can be considered as an orthorhombic constraint on the NoT ensemble The constraint can be strengthened further to 85 STFC Section 3 5 a semi orthorhombic one by imposing that the MD cell change isotropically in the x
301. n 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 120 OSTFC Section 5 1 no topology no vdw optimise string f pressure f print every n print rdf print zden pseudo string fi fo quaternion tolerance f rdf sampling every f reaction field reaction field damp a system cutoff on contiguity of particles indices when connecting CONFIG crystallographic listing to FIELD topology on IO when io mpiio direct sorted is selected etc ii abort display of warnings non leading to error messages and of iteration cycles in minimisation relaxation routines iii assume safe defaults for the general simulation cutoff temperature pressure and job times skip detailed topology reporting during read of FIELD in OUTPUT no FIELD replication useful for large bio chemcal simulations ignore short range non bonded interactions in simulation minimise the system configuration at start during equilib
302. n 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 r45 r4 and T34 where the atoms 1 2 3 and 4 are shown in the following figure The figure defines the D and 21 OSTFC Section 2 2 L a N C f D a C N f 1 2 3 4 12 3 4 Figure 2 4 The L and D enantiomers and defining vectors L enantiomers consistent with the international IUPAC convention When defining the dihedral the atom indices are entered in DL POLY 4 in the order 1 2 3 4 In DL POLY 4 improper dihedral forces are handled by the routine DIHEDRALS FORCES 2 2 7 Inversion Angle Potentials Figure 2 5 The inversion angle and associated vectors The inversion angle potentials describe the interaction arising from a particular geometry of three atoms around a central atom The best known example of this is the arrangement of hydrogen 22 OSTFC Section 2 2 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 defi
303. n your system and this type of simulation You MUST change the interactions parameters and or the way the physical base of your investigation is handled in MD terms Message 508 error EAM metal interaction entry in TABEAM unspecified in FIELD The specified EAM metal interaction entry found in TABEAM is not specified in FIELD Action For N metal atom types there are 5N N 2 EAM functions in the TABEAM file One density N and one embedding N function for each atom type and N 4 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 270 OSTFC Appendix D Remove all duplicate entries in the TABEAM file and resubmit Message 510 error duplicate entry for a density function detected in TABEAM A duplicate density function entry is 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 513 error particle assigned to non existent domain in read config This can only happen if particle coordinates do not match the cell parameters in CONFIG Prob ably due to n
304. n2 n3 Mn usj l3 n3L3 2 193 in which the sums over n1 2 3 etc are required to capture contributions from all relevant periodic cell images which in practice means the nearest images 3 Approximating the reciprocal space energy Urecip 1 recip Sir G ky ko k ki ko k 2 194 gU Ww do Ki k2 k3 Q k1 k2 k3 48 OSTFC Section 2 5 where G is the discrete Fourier transform of the function _ 2 2 G k1 ka k3 n ta in which Q k1 ko k3 is the complex conjugate of Q ki ka k3 and B Ki ko k3 Q k ka k3 2 195 B Ki ka Ka b1 1 1 b2 k2 b3 3 1 2 196 The function G k1 ka k3 is thus a relatively simple product of the Gaussian screening term appearing in the conventional Ewald sum the function B k1 k2 k3 and the discrete Fourier transform of Q k1 ka k3 4 Calculating the atomic forces which are given formally by OUrecip 1 o p k k k f or nl Fs En ks 1 42 3 OQ ki ka k3 dr 2 197 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 calcu
305. nction data points to read in limit 1 real lower interpolation limit in A for dens and pair or in density units for embed limit 2 real upper interpolation limit in A for dens and pair or in density units for embed function data records number of data records Int ngrid 3 4 data 1 real data item 1 data 2 real data item 2 data 3 real data item 3 data 4 real data item 4 5 1 7 3 Further Comments The tabled data are used to fill the internal arrays gmet fmet and vmet respectively see Sec tion 2 3 2 The force arrays are generated from these by the METAL TABLE DERIVATIVES rou tine using a five point interpolation precedure During simulation interactions beyond distance Min reut Limit2 are discarded whereas interactions at distances shorter than limit 1 will cause the simulation to abort The simulation will also abort if any local density exceeds the limits for the embedding function 5 2 The OUTPUT Files DL_POLY 4 produces up to ten output files HISTORY DEFECTS MSDTMP CFGMIN OUT PUT REVCON REVIVE RDFDAT ZDNDAT and STATIS These respectively contain an incremental dump file of all atomic coordinates velocities and forces an incremental dump file of atomic coordinates of defected particles interstitials and sites vacancies an incremental dump file of of individual atomic mean square displacement and temperature a dump file of all atomic coordinates of a minimised structure an incremental summary file of the si
306. nd Z density max number of van der Waals potentials in system max number of van der Waals potential parameters 5 max number of metal potentials in system max number of metal potential parameters 9 max number of Tersoff potentials in system max number of Tersoff potential parameters 11 max number of three body potentials in system array dimension of three body potential parameters max number of three body potential parameters 5 max number of four body potentials in system array dimension of four body potential parameters max number of four body potential parameters 3 max number of external field parameters 5 dimension of stack arrays for rolling averages max number of stacked variables max number of atoms in the verlet list on a node max number of link cells per node max number of local halo atoms per node max number of local atoms per node max dimension of the principle transfer buffer the machime representation of 0 at working precision the machime representation of 0 5 at working precision the system energy unit 181 Chapter 7 Examples Scope of Chapter This chapter describes the standard test cases for DL POLY 4 the input and output files for which are in the data sub directory 182 OSTFC Section 7 1 7 1 Test Cases Because of the size of the data files for the DL POLY 4 standard test cases they are not shipped in the standard download of the DL_POLY 4 source Instead users are
307. nd was broken Action Examine FIELD for erroneous directives if any correct and resubmit Message 1000 error working precision mismatch between FORTRAN90 and MPI implementation 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 ensure that wp and mpi wp are compliant Make the necessary corrections to sc kinds f90 and or COMMS MODULE 277 OSTFC Appendix D Message 1001 error allocation failure in comms module gt gcheck vector DL_POLY 4 has failed to find available memory to allocate an array or arrays i e there is lack of sufficient memory per node on the execution machine Action This may simply mean that your simulation is too large for the machine you are running on Consider this before wasting time trying a fix Try using more processing nodes if they are available If this is not an option investigate the possibility of increasing the heap size for your application Talk to your systems support people for advice on how to do this Message 1002 error deallocation failure in comms module gt gcheck vector DL POLY 4 has failed to dealloc
308. ndersen thermostat are implemented in the DL POLY 4 routines NVT_A0_VV and NVT_AO_LFV respectively The routines NVT_A1_vv and NVT_A1_LFV implement the same but also incorporate RB dynamics 3 4 4 Berendsen Thermostat In the Berendsen algorithm the instantaneous temperature is pushed towards the desired temper ature Text by scaling the velocities at each step by x i 5 6 pu 65 STFC Section 3 4 where p ka Ta 3 57 is the target thermostat energy depending on the external temperature and the system total degrees of freedom f equation 3 11 and Tr a specified time constant for temperature fluctuations normally in the range 0 5 2 ps The VV implementation of the Berendsen algorithm is straight forward A conventional VV1 and VV2 thermally unconstrained steps are carried out At the end of VV2 velocities are scaled by a factor of x in the following manner 1 VV1 wi At f t v t4 5 At v t ar 1 r t At e r t At u t 540 3 58 2 RATTLE VV1 3 FF f t At f t 3 59 4 VV2 f At 1 t u t At v t 34 Dur dc e 3 60 5 RATTLE_VV2 6 Thermostat At Oo 1 2 Nep A a i i 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 v t 1 FF f t f t At 3 62 2 LFV The iterative part
309. ned 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 as follows 1 Harmonic harm k U ijkn 3 hijen do 2 55 2 Harmonic cosine hcos k U Pijkn 2 cos ijkn cos o 2 56 3 Planar potential plan U igkn A 1 cos dijkn 2 57 4 Extended planar potential xpln k U dijkn 5 1 cos m dijkn o 2 58 In these formulae jkn is the inversion angle defined by T Coy WwW dijkn cos Sie a 2 59 TijWkn with and the unit vectors tie fik in l ik fa Dum Ufer ts 2 61 As usual Tij Ej rj etc and the hat f 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 k gt n gt j etc Equivalently the angle j may be written as EV 21 2 T Ti U Pijkn cass f rij Un rij kn 2 62 Tij Formally the force on an atom arising from the inversion potential is given by as 2 0 U oi 2 63 f dr dijkn 23 OSTFC Section 2 2 with being one of i j k n and a one of x y z This may be expanded into 10 1 grg Pun U dijin X
310. nfigurations to facilitate further analysis of the atomic motions By default this file is formatted human readable but with little effort from the user it can be generated unformatted You may move these output files back into the data sub directory using the store macro found in the execute sub directory Lastly DL POLY 4 may also create the files RDFDAT ZDNDAT MSDTMP 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 4 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 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
311. nk cell algorithm can work with 1 1 1 corresponding to ratio R 1 26 It is worth outlining in terms of the O computation communication function what the rough scaling performance is like of the most computation and communication intensive parts of DL POLY 4 in an MD timestep a Domain hallo re construction in SET HALO PARTICLES METAL_LD_SET_HALO and DEFECTS REFERENCE SET HALO O N P N R b Verlet neighbourlist construction by link cells in LINK CELL PAIRS O W P 0 may take up to 4096 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 4096 of the time per timestep d Particle exchange between domains involving construction and connection of new out of do main topology when bonded like interactions exist by RELOCATE_PARTICLES O N P N d 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 i P N where N is the number of particles P P P P the total number of domains in the MD cell and the rest of the quantities are as defined in equations 4 2 4 2 Performance may also affected by the fluctuations in the inter node communication due to un avoidable communication traffic when a simulation job does not have ex
312. nstituting it These contribute towards the total system stress and pressure As seen in Section 2 5 1 core shell units are dealth with i kinetically by the adiabatic shell model or ii staticly by the dynamic shell model Both contribute to the total system stress pressure but in different manner The former does it via the kinetic stress energy and atomic sterss potential energy due to the core shell spring The latter via atomic sterss potential energy due to the shells move to minimised configuration 52 Chapter 3 Integration Algorithms Scope of Chapter This chapter describes the integration algorithms coded into DL POLY 4 53 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 10 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 adv
313. nsvar option in CONTROL to increase mxsh1 alternatively increase it by hand in SET BOUNDS and recompile and resubmit 246 OSTFC Appendix D Message 60 error too many dihedral angles specified This should never happen Action Recompile the program or recreate the FIELD file If neither of these works send the problem to us Message 61 error too many dihedral angles per domain DL_POLY 4 limits the number of dihedral angle units in the system to be simulated actually the number to be processed by 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 mxdihd alternatively increase it by hand in SET BOUNDS and recompile and resubmit Message 62 error too many tethered atoms specified This should never happen Action Recompile the program or recreate the FIELD file If neither of these works send the problem to us 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 s
314. nternal 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 109 OSTFC Section 4 4 WARNING is called resulting in an appropriate message that identifies the inconsistency In some cases an inconsistency is resolved by DL POLY 4 supplying a default value or DL POLY 4 assuming a priority of one directive over the another in clash of mutually exclusive directives However in other cases this cannot be done and controlled termination of the program execution is called by the subroutine ERROR In any case appropriate diagnostic message is displayed notifying the user of the nature of the problem 4 4 2 The DL POLY 4 Internal Error Facility DL POLY 4 contains a number of in built error checks scattered throughout the package which detect a wide range of possible errors In all cases when an error is detected the subroutine ERROR is called resulting in an appropriate message and termination of the program execution either immediately or after some additional processing In some case if the cause for error is considered to be mendable it is corrected and the subroutine WARNING results in an appropriate message Users intending to insert new error checks should ensure that all error checks are performed con currently on all nodes and that in circumstances where a different resul
315. o 223 OSTFC Appendix C constraints shake vv o pmf shake vv o constraints rattle o pmf rattle o nvt hO scl o nvt gO scl o npt hO scl o nst_h0_scl o nve O vv o nvt eO vv o nvt 10 vv o nvt aO vv o nvt bO vv o nvt hO vv o nvt_g0_vv o npt 10 vv o npt bO vv o npt hO vv o npt mO vv o nst 10 vv o nst bO vv o nst hO vv o nst mO vv o nvt hi scl o nvt gi scl o npt hi scl o nst hi scl o nve 1 vv o nvt el vv o nvt li vv o nvt_al_vv o nvt bi vv o nvt hi vv o nvt gi vv o npt 11 vv o npt b vv o npt h vv o npt mi vv o nst li vv o nst b vv o nst hi vv o nst mi vv o pseudo_lfv o constraints_shake_lfv o pmf shake lfv o nve O lfv o nvt eO lfv o N nvt 10 lfv o nvt a0 lfv o nvt bO lfv o nvt hO lfv o nvt gO lfv o npt 10 lfv o npt bO lfv o npt hO lfv o npt mO lfv o nst 10 lfv o nst bO lfv o nst hO lfv o nst mO lfv o nve 1 lfv o nvt e lfv o nvt li lfv o nvt ai lfv o nvt bi lfv o nvt hi lfv o nvt gil lfv o npt l1 lfv o npt bi lfv o npt hi lfv o npt mi lfv o nst 11 lfv o nst bi lfv o nst hi lfv o nst mi lfv o xscale o core_shell_kinetic o regauss_temperature o z_density_collect o statistics_collect o system_revive o rdf_compute o z_density_compute o statistics_result o dl poly o Define MPI SERIAL files FILES SERIAL mpi module f90 mpif h ewald_spme_forc s f90 Define Velocity Verlet files FILES VV N pseudo vv f90 constraints shake vv f90 pmf shake
316. o pmf coms o pmf tags o pmf vcoms o pmf quench o rigid bodies quench o set temperature o vdw lrc o metal lrc o system init o export atomic data o set halo particles o rigid bodies stress o read history o defects reference read o defects reference read parallel o defects reference write o defects reference export o defects reference set halo o defects link cells o defectsi write o defects write o msd write o rsd write o impact o core shell on top o deport atomic data o pmf units set o compress book intra o relocate particles o link cell pairs o metal ld collect eam o metal ld collect fst o metal ld export o metal ld set halo o metal ld compute o ewald spme forc s o metal forces o vdw forces o ewald real forces o coul dddp forces o coul cp forces o coul fscp forces o coul rfp forces o rdf collect o rdf excl collect o ewald excl forces o ewald frozen forces o two body forces o tersoff forces o three body forces o four body forces o core shell forces o tethers forces o intra coul o bonds forces o angles forces o inversions forces o dihedrals 14 vdw o dihedrals forces o external field apply o external field correct o langevin forces o constraints pseudo bonds o pmf pseudo bonds o rigid bodies split torque o rigid bodies move o minimise relax o core shell relax o zero k optimise o nvt eO scl o nvt ei scl o nvt bO scl o nvt bi scl o pseudo_vv
317. odies see Section 3 6 the first part of equation 3 11 f 3N 3N frozen 3 12 splits into rozen rozen rozen f 3NFP 3NEP BN PBC ai gy RB 3 72079 3 13 Or fi FP y felt y PRP eet f 3 14 Here FP stands for a free particle i e a particle not participating in the constitution of a rigid body and RB for a rigid body In general a rigid body has 3 translational tra degrees of freedom corresponding to its centre of mass being allowed to move in the 3 general direction of space and 3 rotational rot corresponding to the RB being allowed to rotate around the 3 general axis in space It is not far removed to see that for a not fully frozen rigid body one must assign 0 translational degrees of freedom but depending on the frozenness of the RB one may assign 1 rotational degrees of freedom when all the frozen sites are in line i e rotation around one axis only or 3 when just one site is frozen 55 STFC Section 3 2 The routines NVE_O_VV and NVE_O_LFV implement the Verlet algorithm in velocity and leapfrog flavours respectively for free particles and calculate the instantaneous temperature Whereas the 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 3 15 where U is the potential energy of the system and Erin the kinetic energy at time t The full selectio
318. odule PARSE MODULE The parse module develops several methods used to deal with textual input get line strip blanks lower case get word word 2 real Depending on the method dependencies on KINDS_F90 COMMS MODULE SETUP MODULE DOMAINS MODULE are found e development module DEVELOPMENT MODULE The development module contains several methods used to help with testing and debug ging DL POLY 4 Depending on the method dependencies on KINDS F90 COMMS MODULE SETUP MODULE DOMAINS MODULE are found e I O module IO 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 174 OSTFC Section 6 2 e domains module DOMAINS MODULE The domains module defines DD parameters and maps the available computer resources on a DD grid The module does not depend on previous modules but its mapping subroutine is dependent on KINDS F90 and COMMS MODULE e site module SITE MODULE The site module defines all site related arrays FIELD and is dependent on KINDS F90 only However it also develops an allocation method that is dependent on SETUP MODULE e configuration module CONFIG MODULE The configuration module defines all configuration related arrays CONFIG and is dependent on KINDS_F90 only However it also develops an allocation method that is dependent on SETUP MODULE
319. odule o kinds f90 0 setup module o pass shared units o comms module o config module o domains module o kinds f90 0 rigid bodies module o setup module o pmf coms o comms module o config module o kinds f90 0 pmf module o Setup module o pmf module o kinds f90 0 setup module o pmf pseudo bonds o comms module o config module o kinds f90 0 pmf module o Setup module o pmf quench o comms module o config module o kinds f90 0 pmf module o Setup module o pmf rattle o comms module o config module o kinds f90 0 pmf module o Setup module o pmf shake lfv o comms module o config module o kinds f90 0 pmf module o Setup module o pmf shake vv o comms module o config module o kinds f90 0 pmf module o Setup module o pmf tags o config module o kinds f90 0 pmf module o setup module o pmf units set o comms module o config module o pmf module o setup module o pmf vcoms o comms module o config module o kinds f90 0 pmf module o Setup module o pseudo lfv o comms module o config module o core shell module o kinds f90 0 kinetic module o rigid bodies module o setup module o site module o pseudo vv o comms module o config module o core shell module o kinds f90 0 kinetic module o rigid bodies module o setup module o site module o quaternions container o comms module o config module o kinds f90 0 rigid bodies module o setup module o rdf collect o config module o kinds f90 0 setup module o site module o St
320. ognise 263 OSTFC Appendix D 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 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
321. ollect 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 RDF amp Z DENSITY binsize 0 05 Angstroms rdf 7T steps print rdf zden 7 steps print zden EXECUTION TIME job time 1000 seconds close time 10 seconds FINISH finish 5 1 1 1 The CONTROL File Format The file is free formatted and not case sensitive Every line is treated as a command sentence record Commented records beginning with a and blank lines are not processed and may be added to aid legibility see example above Records must be limited in length to 100 characters Records are read in words directives and additional keywords and numbers as a word must not exceed 40 characters in length Words are recognised as such by separation by one or more space characters Additional annotation is not recommended but may be added onto a directive line after the last control word in it 115 OSTFC Section 5 1 e The first record in the CONTROL file is a header up to 100 characters long to aid identifi cation of the file e The last record is a finish directive which marks the end of the input data Between the header and the finish directive a wide choice of control directives may be inserted These are described below 5 1 1 2 The CONTROL File Direct
322. omms module gt grmin vector Action See Message 1002 Message 1048 error error allocation failure in comms module gt grsum matrix Action See Message 1001 283 OSTFC Appendix D Message 1049 error deallocation failure in comms module gt grsum matrix Action See Message 1002 Message 1050 error sorted I O base communicator not set Possible corruption if 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 Message 1056 error unkown write option given to sorted I O This should 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 1061 error allocation failure in vdw_module gt allocate_vdw_table_arrays Action See Message 1001 Message 1063 error allocation failure in vdw_module gt allocate_vdw_direct_fs_arrays Action See Message 1001 Message 1069 error allocation failure in metal_module gt allocate_metal_table_arrays
323. oms 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 pro ceed independently to calculate the pair force contributions to the atomic forces see routine TWO_BODY_FORCES The potential energy and forces arising from the non bonded interactions as well as metal and Ter soff interactions are calculated using interpolation tables These are generated in the following rou tines VDW_GENERATE METAL GENERATE METAL TABLE DERIVATIVES and TERSOFF GENERATE 6 1 4 Modifications for the Ewald Sum For systems with periodic boundary conditions DL POLY 4 employs the Ewald Sum to calculate the coulombic interactions see Section 2 4 5 It should be noted that DL POLY 4 uses only the Smoothed Particle Mesh SPME form of the Ewald sum Calculation of the real space component in DL POLY 4 employs the algorithm for the calculation of the non bonded inter
324. on 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 269 OSTFC Appendix D Correct the erroneous entries in FIELD Message 504 error cutoff too large for TABLE file The requested cutoff exceeds the information in the TABLE file Action Reduce the value of the vdw cutoff rvdw in the CONTROL file or reconstruct the TABLE file Message 505 error EAM metal densities or pair crossfunctions out of range The resulting densities or pair crossfunctions are not defined in the TABEAM file Action Recreate a TABEAM file with wider interval of defined densities and pair cross functions Message 506 error EAM metal densities out of range The resulting densities are not defined in the TABEAM file Action Recreate a TABEAM file with 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 i
325. on in CONTROL for extremely non equilibrium simulations Alterna tively increase mxcell in SET BOUNDS recompile and resubmit 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 261 OSTFC Appendix D Locate the variable imcon in the CONFIG file and correct to suit the cell vectors Message 414 error conflicting ensemble options in CONTROL file DL POLY 4 has found more than one ensemble directive in the CONTROL file Action 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 inapprop
326. on in CONTROL for extremely non equilibrium simulations Alterna tively increase mxcell in SET_BOUNDS recompile and resubmit Message 70 error constraint quench failure When a simulation with bond constraints is started DL POLY 4 attempts to extract the kinetic energy of the constrained atom atom bonds arising from the assignment of initial random velocities If this procedure fails the program will terminate The likely cause is a badly generated initial configuration Action Some help may be gained from increasing the cycle limit by using the directive mxshak in the CONTROL file You may also consider reducing the tolerance of the SHAKE iteration using the directive shake in the CONTROL file However it is probably better to take a good look at the starting conditions 248 OSTFC Appendix D Message 71 error too many metal potentials specified This should never happen Action Report to authors Message 72 error too many tersoff potentials specified This should never happen Action Report to authors Message 73 error too many inversion potentials specified This should never happen Action Report to authors Message 74 error unidentified atom in tersoff potential list This shows that DL POLY 4 has encountered and erroneous entry for Tersoff potentials in FIELD Action Correct FIELD and resubmit Message 76 error duplicate tersoff potential specified This shows that DL_POLY_4 h
327. orating 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 c algorithm Langevin 31 NPT L1 VV NPT_L1_LFV The same as the above but also incorporating RB integration NST_BO_VV NST_BO_LFV Constant T c algorithm Berendsen 29 NST Bl VV NST B1 LFV The same as the above but also incorporating RB integration NST_HO_VV NST_HO_LFV Constant T c algorithm Hoover 30 NST Hl VV NST_H1_LFV The same as the above but also incorporating RB integration NST_MO_VV NST_MO_LFV Constant T c algorithm Martyna Tuckerman Klein 32 NST M0 VV NST M0 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 7yT 60 56 OSTFC Section 3 2 3 2 Bond Constraints The SHAKE algorithm for bond constraints was devised by Ryckaert et al 61 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 rig
328. ouble Running out of job time is common and provided you have correctly specified the job time variables using the close time and job time directives see Section 5 1 1 in the CONTROL file DL POLY 4 will stop in a controlled manner allowing you to restart the job as if it had not been interrupted To restart a simulation after normal termination you will again require the original CONTROL file augment it to include the restart directive and or extend the length and duration of the new targeted MD run the FIELD and TABLE and or TABEAM file and a CONFIG file which is the exact copy of the REVCON file created by the previous job You will also require a new file REVOLD Section 5 1 5 which is an exact copy of the previous REVIVE file If you attempt to restart DL POLY 4 without this additional file available the job will most probably fail Note that DL_POLY 4 will append new data to the existing STATIS and HISTORY files if the run is restarted other output files will be overwritten In the event of machine failure you should be able 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
329. oved at the end of the integration algorithms with barostats 3 5 1 Instantaneous pressure and stress The instantaneous pressure in a system Ekin t Watomic t Weonstrain t At Wpwmr t At 3V t P t 3 95 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 P4 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 E pin Lt atomic O train t v At purl E At 3 96 71 STFC Section 3 5 is a sum of the forcefield o constrain g and PMF c stresses atomic constrains PMF Note that when bond constraints or and PMF constraints are present in the system the quantity e will not converge to the exact value of Pox 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 retrospectively 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 For isotropic fluctuations the equations of motion are Cr
330. polation The w parameter is used to permit greater flexibility when dealing with more drastically different types of atoms In DL POLY 4 a third additional parameter A is also available It only takes the values of 0 as if not specified and 1 any other value apart from 0 and can be used to remove the pure two body part of a specific tersoff cross interaction from the system and so leave out only the pure angular one The force on an atom derived from this potential is formally calculated with the formula lo 1 o fe a Etrersott RT Sy UM 2 137 Or 2 eda OFS i jzi 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 QU le le le are are 0 CM n Gra Va grato Cuala fem Faria goma i 2 138 38 OSTFC Section 2 3 with the contributions from the first in the forms o a 3 E arg Ie fnr retro ge fate fringe etra x fay rie ZI 2 139 ua e 2 140 and from the third angular term feltroa s folrij falrij Xi X 3 1 t ce P gm ce gesta 2 141 where Fett Fe Ore x wik fo rik I 0ijk 2 142 The angular term can have three different contributions depending on the index of the particle participating in the interaction o L i dal fi Wik a Dijk 5r ag fein detras 2 143 oe lo Wik fc rik Bra Pak 2 144 are 2 Or Fi j ta o lo ia E org Wig IOs ra fe Gru fo
331. potential in the FIELD file and add the required cutoff Resubmit the job Message 454 error unknown external field A form of external field potential has been requested which DL POLY 4 does not recognise Action Locate the offending potential in the FIELD file and remove Replace with one acceptable to DL_POLY 4 if this is reasonable Alternatively you may consider defining the required potential in the code yourself Amendments to subroutines READ FIELD and EXTERNAL FIELD APPLY will be required Message 461 error undefined metal potential A form of metal potential has been requested which DL_POLY_4 does not recognise Action Locate erroneous entry in the FIELD file and correct the potental interaction to one of the allowed ones for metals in DL POLY 4 Message 462 error thermostat friction constant must be gt 0 A zero or negative value for the thermostat friction constant has been encountered in the CONTROL file Action Locate the ensemble directive in the CONTROL file and assign a positive value to the time constant 265 OSTFC Appendix D 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 negat
332. provided all needed restart files are in place and not corrupted If they are not in place or are found corrupted it will start a new simulation without initial temperature scaling of the previous configuration restart noscale Internally these options are handled by the integer variable keyres which is explained in Table 5 2 Table 5 2 Internal Restart Key keyres meaning 0 start new simulation from CONFIG file and assign velocities from Gaussian distribution 1 continue current simulation start new simulation from CONFIG file and rescale velocities to desired temperature 3 start new simulation from CONFIG file and do not rescale velocities 8 The various ensemble options i e nve nvt evans nvt andersen nvt langevin nvt berendsen nvt hoover npt langevin npt berendsen npt hoover npt mtk nst langevin nst berendsen nst hoover nst mtk are mutually exclusive though none is mandatory the default is the NVE ensemble These options are handled internally by the integer variable keyens The meaning of this variable is explained in Table 5 3 The nst keyword is also used in the No T ensembles extension to NP AT and NP yT ones Note that these semi isotropic ensembles are only correct for infinite interfaces placed perpendicularly to the z axis This means that the interface is homogenious unbroken and continuous in the x y plane of the MD cell which assumes that that two of the cell vecto
333. q 8 qo 7 Tyy Wy P3 q3 qd2 q1 do I Wy and quaternion torques as defined by To do lt Q Q G 0 Y B s 1 _ 9 q qo q3 q2 Ta 3 194 Y d d3 do q Ty Ts da d2 q 4 Tz It should be noted that vectors p and Y are 4 component vectors The quaternion momenta are first updated a half step using the formula pet Z e pt YO 3 195 t gt 3 195 Next a sequence of operations is applied to the quaternions and the quaternion momenta in the order cis t 2 ci c2 0 2 eif t gi 2 0 2 eis t 2 3 196 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 106t The operators themselves are of the following kind eic 50 q cos ot q sin dt Pk q gy p cos Cx0t p sin dt Pk p 3 197 where Pj is a permutation operator with k 0 3 with the following properties Po q do 41 42 43 Pi q i a q0 93 q2 3 198 P q 93 go q1 P3 q 1 3 q2 01 do gt 92 STFC Section 3 6 and the angular velocity Cj is defined as 1 gt Pe 3 199 Equations 3 196 to 3 198 represent the heart of the NOSQUISH algorithm and are repeatedly applied 10 times in DL_POLY 4 The final result is the quaternion updated to the full timestep value i e q t At These equations form part of the first stage of the VV algorithm VV1 In the second stage of the VV algorithm VV2 new torques are u
334. quench o set temperature o vdw lrc o metal lrc o system init o export atomic data o set halo particles o rigid bodies stress o read history o defects reference read o defects reference read parallel o defects reference write o defects reference export o defects reference set halo o defects link cells o defectsi write o defects write o msd write o rsd write o impact o core shell on top o deport atomic data o pmf units set o compress book intra o relocate particles o link cell pairs o metal ld collect eam o metal ld collect fst o metal ld export o metal ld set halo o metal ld compute o exchange grid o ewald spme forces o metal forces o vdw forces o ewald real forces o coul dddp forces o coul cp forces o coul fscp forces o coul rfp forces o rdf collect o rdf excl collect o ewald excl forces o ewald frozen forces o two body forces o tersoff forces o three body forces o four body forces o core shell forces o tethers forces o intra coul o bonds forces o angles forces o inversions forces o dihedrals 14 vdw o dihedrals forces o external field apply o external field correct o langevin forces o constraints pseudo bonds o pmf pseudo bonds o rigid bodies split torque o rigid bodies move o minimise relax o core shell relax o zero k optimise o nvt eO scl o nvt ei scl o nvt bO scl o nvt bi scl o pseudo_vv o 230 OSTFC Appendix C constraints sha
335. quency of vibration Ucore she11 Of the harmonic spring which depends on the reduced mass i e 1 k 1 2 Vcore shell de Ix gt 2 200 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 VAC of the ions of interest to polarise Then each VAC is fast fourier tranformed to find their highest frequency of interaction Vrigia ion It is then a safe choice to assign a shell mass x m so that Vcore she11 2 3 Vrigia ion The user must make sure to assign the corect mass 1 x m to the core 2 5 2 Relaxed Massless Shells The relaxed shell model is presented in 57 where shells
336. r which is stored in the java subdirectory of DL POLY _4 Note Java 1 3 0 or a higher version is required to run the GUI select select is a macro enabling easy selection of one of the test cases It invokes the UNIX commands cp data TEST 1 CONTROL CONTROL cp data TEST 1 FIELD FIELD cp data TEST 1 CONFIG CONFIG cp data TEST 1 TABLE TABLE cp data TEST 1 TABEAM TABEAM cp data TEST 1 REFERENCE REFERENCE select requires one argument an integer to be specified select n where n is test case number which ranges from 1 to 18 This macro sets up the required input files in the execute sub directory to run the n th test case The last three copy commands may not be necessary in most cases store The store macro provides a convenient way of moving data back from the execute sub directory to the data sub directory It invokes the UNIX commands mkdir data TEST 1 cp CONTROL data TEST 1 CONTROL cp FIELD data TEST 1 FIELD cp CONFIG data TEST 1 CONFIG cp TABLE data TEST 1 TABLE cp TABEAM data TEST 1 TABEAM cp REFERENCE data TEST 1 REFERENCE mv OUTPUT data TEST 1 0UTPUT mv STATIS data TEST 1 STATIS mv REVCON data TEST 1 REVCON 192 OSTFC Appendix B mv mv mv mv mv mv chmod R a w REVIVE HISTORY DEFECTS RSDDAT RDFDAT ZDNDAT data TEST 1 REVIVE data TEST 1 HISTORY data TEST 1 DEFECTS data TEST 1 RSDDAT data TEST 1 RD
337. raint 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 Mao t 1 Pa V t Gua t oy t fext halt 2V0 a 0 3 139 The VV and LFV flavours of the non isotropic Berendsen barostat and thermostat are im plemented in the DL_POLY 4 routines NST B 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 65 in which the equa tions of motion involve a Nos Hoover thermostat and a barostat in the same spirit Additionally as shown in 66 a modification allowing for coupling between the thermostat and barostat is also introduced Cell size variation For isotropic fluctuations the equations of motion are Saf v t n e Rolo Lo no ato d 2Ekin t Pmass M t 20 kp Text ax lla Gina Lar 3 140 d P t Poxt 470 3V x t n t Pmass 80 STFC Section 3 5 Pmass f 3 kp Text Ti SA 1080 dv BOVO where 7 is the barostat friction coefficient Ry t the system centre of mass at time t Qmass the thermostat mass Tr a specified time constant for temperature fluctuations o the target thermo stat energy equation 3 57
338. raints may be applied only between atoms in the same molecule Unlike with application of the pure angle potentials the electrostatic and van der Waals interactions between the pair of atoms are still evaluated when distance restraints are applied All the potential forms of the previous section are avaliable as angular restraints although they have different key words 1 Harmonic hrm 2 Quartic qur Truncated harmonic thm Screened harmonic shm Screened Vessal 36 bv1 Truncated Vessal 37 bv2 Harmonic cosine hcs Cosine cos c 0 1 C dl A C2 MMB stretch bend 38 msb 10 Compass stretch stretch 39 sts 11 Compass stretch bend 39 stb 12 Compass all terms 39 cmp In DL_POLY 4 angular restraints are handled by the routine ANGLES FORCES 18 OSTFC Section 2 2 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 ijkn A 1 cos m ijkn 2 36 2 Harmonic harm U ijkn a hijen do 2 37 3 Harmonic cosine hcos U ign 7 cos dijkn cos do 2 38 4 Triple cosine cos3
339. ration 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 107 lt f lt 0 1 default f 0 005 the CGM minimised configuration is saved in a file CFGMIN which has the same format as CONFIG set required system pressure to f katms target pressure for constant pressure ensembles print system data every n timesteps print radial distribution functions print Z density profile attach a pseudo thermal bath with a thermostat of type string where string can only be langevin or direct if neither is specified both are applied in order langevin direct f is the thickness of the thermostat layers attached on the inside of the MD cell boundaries in units of A default f1 2 A fo 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 52 damping Ewald like convergence 121 OSTFC Section 5 1 regauss every n replay restart restart noscale restar
340. rdering in a force shifted manner by countering the reaction term and using a distance depending damping function er fc a rij identical to that seen in the real space portion of the Ewald sum and thus mirror the effective charge screening 52 Uc qidj erfela rij 24g Fent 2a exp a 2 ro H 2 ATEOE ns fs Vn Teut er fela Teut erfc a ret 2a exp a r Bo r7 ria Tout EE AU DENS 2 T Fu vm Tout 2r3 cut with the force on an atom 7 given by didj Es Tu Za exp a 3 2 i 4mepoe Tout 2 182 T i vm rij erfe a rot 20 exp a r24 Borij Ty Tua vm Tout m cut with the force on atom 7 the negative of this Q 2 183 gt 2 188 It is worth noting that as discussed in 52 and references therein this is only an approximation of the Ewald sum and its accuracy and effectiveness become better when the cutoff is large gt 10 preferably 12 The contribution of each effective pair interaction to the atomic virial is and the contribution to the atomic stress tensor is gi ey 2 185 where a B 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 sy
341. rdinate cutoff or the user specified D whichever is the larger The surface in a system with charges can also be modelled with DL POLY 4 if periodicity is allowed in the Z direction In this case slabs of ions well separated by vacuum zones in the Z direction can be handled with imcon 1 2 or 3 189 Appendix B DL POLY 4 Macros Introduction Macros are simple executable files containing standard UNIX commands A number of the are supplied with DL POLY 4 and are found in the execute sub directory These are not guaranteed to be immaculate but with little adaptation they can become a useful tool to a researcher The available macros are as follows e cleanup e copy e gopoly e gui e select e store 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 CODy copy invokes the UNIX commands 190 OSTFC Appendix B mv CONFIG CONFIG OLD mv REVCON CONFIG mv REVIVE REVOLD which collectively prepare the DL_POLY 4 files in the
342. re 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 of frozen rigid bodies their centre of mass is scaled with the cell vectors in constant pressure simulations and the positions of their constituent sites are thenmoved accordingly In DL POLY 4 the frozen atom option is handled by the subroutine FREEZE ATOMS The rigid body dynamics see Section 3 6 is resolved by solving the Eulerian equations of rotational motion However their statics includes calculation of the individual contributions of each RB s centre of mass stress and virial due to the action of the resolved forces on sites atoms co
343. re provided in the GUI manual 21 6 Torun the executable for the first time you require the files CONTROL FIELD and CONFIG and possibly TABLE if you have tabulated van der Walls potentials TABEAM if you have tabulated metal potentials and REFERENCE if defect detection is opted for These must be present in the directory from which the program is executed See Section 5 1 for the description of the input files 7 Executing the program will produce the files OUTPUT STATIS REVCON and REVIVE and optionally HISTORY RDFDAT ZDNDAT MSDTMP REFERENCE DEFECTS in the executing directory See Section 5 2 for the description of the output files This simple procedure is enough to create a standard version to run most simulations There may however be some difficulty with array sizes DL POLY 4 contains features which allocate arrays after scanning the input files for a simulation Sometimes these initial estimates are insufficient for a long simulation when for example the system volume changes markedly during the simulation or 96 STFC Section 4 1 when a system is artificially constructed to have a non uniform density Usually simply restarting the program will cure the problem but sometimes especially when the local atom density is a way higher than the global one or there is a sort of clustering in the system undergoes and the distribution of bonded like interactions is far from uniform it may be necessary to amend the a
344. re shell module o dihedrals module o domains module o inversions module o kinds f90 0 pmf module o rigid bodies module o setup module o site module o tethers module o report topology o angles module o bonds module o comms module o constraints module o core shell module o dihedrals_module o inversions module o pmf module o rigid bodies module o setup module o Site module o tethers_module o rigid bodies coms o comms module o config module o kinds f90 0 rigid bodies module o setup module o rigid bodies module o kinds f90 0 setup module o rigid bodies move o config module o kinds f90 0 rigid bodies module o Setup module o rigid bodies quench o comms module o config module o kinds f90 0 rigid bodies module o setup module o rigid bodies setup o comms module o config module o kinds f90 0 rigid bodies module o setup module o site module o rigid bodies split torque o comms module o config module o kinds f90 0 rigid bodies module o setup module o rigid bodies stress o comms module o config module o kinds f90 0 rigid bodies module o setup module o rigid bodies tags o comms module o config module o rigid bodies module o Setup module o rigid bodies widths o comms module o config module o kinds f90 0 rigid bodies module o setup module o rsd write o comms module o config module o io module o kinds f90 0 parse module o setup module o site module o statistics module o Scale config o conf
345. re 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 ri 29 E 2 165 4m o Tij Tout with qe the charge on an atom labelled Z reut the cutoff radius and r the magnitude of the separation vector p eg e A further refinement of this approach is to truncate the 1 r potential at reut and add a linear term to the potential in order to make both the energy and the force zero at the cutoff This removes the heating effects that arise from the discontinuity in the forces at the cutoff in the simple truncated and shifted potential the formula above The physics of this potential however is little better It is only recommended for very crude structure optimizations The force shifted potential is thus aq f1 1 di gig 1 ty _ 2 ry Areoe rij tm d Tout Tua 5d 4reoe rij Tout l J cut cut J cut with the force on an atom j given by ig 1 1 mi E 2 167 ij 2 ATrEgE rj fato with the force on atom 7 the ne
346. record i timestep nstep tstep time imcon rrsd record ii displacements nrsd record iii cell 1 cell 2 cell 3 record iv cell 4 cell 5 cell 6 record v cell 7 cell 8 cell 9 as integer real real integer real al3 integer real real real real real real real real real the character string timestep the current time step integration timestep ps elapsed simulation time ps periodic boundary key see Table 5 6 displacement qualifying cutoff A the character string displacements the total number of displacements 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 nrsd displacements for the current timestep as each atom has the following data lines record a atmnam iatm ratm record b XXX yyy ZZZ al0 integer real real real real atomic label from CONFIG atom index from CONFIG atom displacement from its position at t 0 x coordinate y coordinate z coordinate 159 OSTFC Section 5 2 5 2 5 The CFGMIN File The CFGMIN file only appears if the user has selected the programmed minimisation option di rective minimise or optimise in the CONTROL file Its contents have the same format as the CONFIG file
347. rence MD cell have the same number of atoms then the total 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 equlibration the start of statistics t 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 128 OSTFC Section 5 1 16 17 18 19 20 21 22 The force selection directives ewald spme sum precision reaction coul shift dist no elec are handled internally by the integer variable keyfce See Table 5 4 for an explanation of this variable Note that all these options with the exception of the last no elec are mutually exclusive Table 5 4 Electrostatics Key k
348. rget is the specification of the required machine For many computer systems this is all that is required to compile a working version of DL POLY 4 To determine which targets are already defined in the makefile examine it or type the command make without a nominated target it will produce a list of known targets The full specification of the make command is as follows make lt TARGET gt lt EX gt lt BINROOT gt where some or all of the keywords may be omitted The keywords and their uses are described below Note that keywords may also be set in the UNIX environment e g with the setenv command in a TCSH shell or export in BASH shell 4 2 1 1 Keywords in the Makefiles 1 TARGET The TARGET keyword indicates which kind of computer the code is to be compiled for This must be specified there is no default value Valid targets can be listed by the makefile if the command make is typed without arguments The list frequently changes as more targets are added and redundant ones removed Users are encouraged to extend the makefile for themselves using existing targets as examples 2 EX The EX keyword specifies the executable name The default name for the executable is DLPOLY Z 3 BINROOT The BINROOT keyword specifies the directory in which the executable is to be stored The default setting is execute 99 OSTFC Section 4 2 4 2 1 2 Modifying the Makefiles 1 Changing the F
349. riate specifications Message 432 error undefined tersoff potential This shows that DL_POLY 4 has encountered an unfamiliar entry for Tersoff potentials in FIELD Action Correct FIELD and resubmit Message 433 error rcut must be specified for the Ewald sum precision When specifying the desired precision for the Ewald sum in the CONTROL file it is also necessary to specify the real space cutoff rcut Action Place the cut directive before the ewald precision directive in the CONTROL file and rerun Message 436 error unrecognised ensemble An unknown ensemble option has been specified in the CONTROL file Action Locate ensemble directive in the CONTROL file and amend appropriately 262 OSTFC Appendix D Message 440 error undefined angular potential A form of angular 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
350. rlet 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 adap tation of the link cell algorithm to share the total burden of the work reasonably equally between 170 STFC Section 6 1 nodes Each node is thus responsible for a unique set of non bonded interactions and the neighbour list is therefore different on each node A feature in the construction of the Verlet neighbour list for macromolecules is the concept of excluded atoms which arises from the need to exclude certain atom pairs from the overall list Which atom pairs need to be excluded is dependent on the precise nature of the force field model but as a minimum atom pairs linked via extensible bonds or constraints and atoms grouped in pairs linked via valence angles are probable candidates The assumption behind this requirement is that atoms that are formally bonded in a chemical sense should not participate in non bonded interactions However this is not a universal requirement of all force fields The same considerations are needed in dealing with charged excluded at
351. rporate 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 dr t E u t E LOTO uq 3 34 where x is the user defined constant positive in units of ps specifying the thermostat friction parameter and R t is stochastic force with zero mean that satisfies the fluctuation dissipation theorem REO RI 2 x mi kg dij bas t t 3 35 where superscripts denote Cartesian indices subscripts particle indices kg is the Boltzmann con stant T the target temperature and m the particle s mass The Stokes Einstein relation for the diffusion coefficient can then be used to show that the average value of R t over a time step in thermal equilibrium should be a random deviate drawn from a Gaussian distribution of zero mean and unit variance Gauss 0 1 scaled by 4 2 xmi Ear 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 Impu
352. rray sizes in accordance with the error message obtained A way to trigger lengthening of the density dependent global arrays the user may use the densvar option in the CONTROL Section 5 1 1 file However lengthening these array will require a larger amount of memory resources from the execution machine for the simulation which it may not be able to provide See Section 6 2 2 for more insight on the DL POLY 4 source code structure 4 1 2 Constructing Non standard Versions In constructing a non standard DL_POLY 4 simulation program the first requirement is for the user to write a program to function as the root segment The root segment V V DL POLY is placed in the source directory and contains the set up and close down calls for a molecular dynamics simula tion It is the routine that first opens the OUTPUT file Section 5 2 which provides the summary of the job The root program calls the molecular dynamics cycle routines LFV MD_LFV or LFV MD vv implementing the VV and LFV depending on which integrator has been specified for the simulation These routines contain major routines required to perform the simulation con trol the normal molecular dynamics cycle and monitor the cpu and memory usage They also bring about a controlled termination of the program if the cpu usage approaches the allotted job time within a pre set closure time and or if the memory usage approaches the allocated limit for density dependent arrays Users are re
353. rs 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 9 The zero directive enables a zero temperature optimisation The target temperature of the simulation is reset to 10 Kelvin and a crude energy minimiser 0 vi f lt 0 ll A v f 20 ia e 5 1 es 2 Ss SS 125 OSTFC Section 5 1 10 11 Table 5 3 Internal Ensemble Key keyens meaning 0 Microcanonical ensemble NVE 1 Evans NVT ensemble NVE n 10 Langevin NVT ensemble 11 Berendsen NVT ensemble 12 Nos Hoover NVT ensemble 20 Langevin NPT ensemble 21 Berendsen NPT ensemble 22 Nos Hoover NPT ensemble 23 Martyna Tuckerman Klein NPT ensemble 30 Langevin NoT ensemble 31 Berendsen NoT ensemble 32 Nos Hoover NoT ensemble 33 Martyna Tuckerman Klein NoT ensemble 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 ind
354. rt of e core shell units e bond constraints e chemical bonds that are NOT distance restraints e valence angles that are NOT distance restraints e dihedrals e inversions e frozen particles RDF pairs containing type s of particles that fall in this list will be polluted However there are many ways to overcome such effects 4 tersoff n where n is the number of specified Tersoff potentials It is followed by 2n records specifying n particular Tersoff single atom type parameters and n n 4 1 2 records specifying cross atom type parameters in the following manner potential 1 record 1 atmnam a8 atom type key ad potential key see Table 5 14 variable 1 real potential parameter see Table 5 14 variable 2 real potential parameter see Table 5 14 variable 3 real potential parameter see Table 5 14 variable 4 real potential parameter see Table 5 14 variable 5 real cutoff range for this potential A 5 14 potential 1 record 2 variable 6 real potential parameter see Table 5 14 variable 7 real potential parameter see Table 5 14 variable 8 real potential parameter see Table 5 14 variable 9 real potential parameter see Table 5 14 variable 10 real potential parameter see Table 5 14 variable 11 real potential parameter see Table 5 14 potential n record 2n 1 potential n record 2n cross term 1 record 2n 1 atmnam 1 a8 first atom type atmnam 2 a8 second atom type 147 OSTFC Section 5 1 variable a varia
355. s echo If no target suits your system then create your own echo using the advice in generic target template provided echo in this Makefile under the entry uknown_platform echo Fetch MPI SERIAL subroutines FILES_SERIAL MAKE links_serial links_serial for file in FILES_SERIAL do echo linking to file rm f file 232 OSTFC Appendix C ln s SERIAL file file done Fetch the Velocity Verlet subroutines FILES VV MAKE links vv links vv for file in FILES VV do echo linking to file rm f file 1n s VV file file done Fetch the LeapFrog Verlet subroutines FILES_LFV MAKE links_lfv links_lfv for file in FILES_LFV do echo linking to file rm f file ln s LFV file file done Clean up the source directory clean rm f 0BJ MOD 0BJ ALL FILES VV FILES LFV FILES SERIAL mod Generic target template uknown platform MAKE LD path to FORTRAN90 Linker loaDer LDFLAGS appropriate flags for LD FC path to FORTRAN90 compiler FCFLAGS appropriate flags for FC EX EX BINROOT BINROOT TYPE System specific targets follow 233 OSTFC Appendix C MAKE LD f95 o LDFLAGS 03 FC f95 c FCFLAGS 03 EX EX BINROOT BINROOT TYPE win debug MAKE LD f95 o LDFLAGS 00 C all C undefined
356. s is do d Up Q 0 i 1 B q A 4 B Q2 Wa 3 187 q2 2 43 qo q Wy d3 d3 2 QU qo Gs Rotational motion in DL POLY 4 is handled by two different methods For 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 G t a t AtI a t 3 188 The new quaternions are found using the FIQA algorithm In this algorithm the new quaternions are found by solving the implicit equation q t At q t Q la t W t Q a t 0 t AD 3 189 91 STFC Section 3 6 where y 0 2 and Qg is d 1 79 ija do 43 G82 L 3 190 Q 2 92 9 do q a 2 I do The above equation is solved iteratively with a t At q t At Qla t 0 3 191 as the first guess Typically no more than 3 or 4 iterations are needed for convergence At each step the normalisation constraint is imposed lat At 1 3 192 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 Po do q 43 _ 0 _ Lot P s 4 3B a gom Wg 3 193 p2
357. scend 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 a In the case of rigid bodies atomic forces are resolved into molecular forces and torques The torques are subsequently transformed into an equivalent set of atomic forces which are perpendicular both to the instantaneous axis of rotation defined by the torque vector and to the cylindrical radial displacement vector of the atom from the axis These modified forces are then used in place of the original atomic forces in the conjugate gradient scheme The atomic displacement induced in the conjugate gradient algorithm is corrected to maintain the magnitude of the radial position vector as required for circular motion 103 OSTFC Section 4 2 b With regard to constraint bonds these are replaced by stiff harmonic bonds to permit minimisation This is not normally recommended as a means to incorporate constraints in minimisation procedures as it leads to ill conditioning However if the constraints in the original structure are satisfied we find that provided only small atomic displacements are allowed during relaxation it is possible to converge to a minimum energy structure Furthermore provided the harmonic springs are stiff enough it is possible afterwards to satisfy th
358. se when extended NoT ensembles are used then 162 OSTFC Section 5 2 further mean x y plain area and mean surface tension are also displayed in the OUTPUT file 5 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 5 2 6 10 Z density Profile If both calculation and printing of Z density profiles has been requested by selecting directives zden and print zden in the CONTROL file Z density profiles are printed out as the last part of the OUTPUT file This is written by the subroutine Z_DENSITY_COMPUTE First the number of time steps used for the collection of the histograms is stated Then each function is given in turn For each function a header line st
359. sed to update the quaternion momenta to a full timestep Ab A p t At p t4 5 TE At 3 200 3 6 3 Thermostats and Barostats coupling to the Rigid Body Equations of Mo tion In the presence of rigid bodies in the atomic system the system s instantaneous pressure equation 3 95 2 Ekin t E Watomic t Weom t Weonstrain t At WPMF t m At 201 P t n 3 201 and stress equation 3 96 a t Dip t T T atomic t T 2com t C constrain t At Cour t v At 3 202 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 translational and rotational velocities are thermostated in the same manner as the purely atomic velocities The barostat however is coupled only to the translational degrees of freedom and does not contribute to the rotational motion Therefore if we notion the change of the system s degrees of freedom as f gt F f greca geet 3 203 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 contributions o f o F _ o f fEB tra
360. site index in bond potential parameter see Table 5 8 potential parameter see Table 5 8 potential parameter see Table 5 8 potential parameter see Table 5 8 The meaning of these variables is given in Table 5 8 This directive and associated data records need not be specified if the molecule contains no flexible chemical bonds See the note on the atomic indices appearing under the shell directive above angles n where n is the number of valence angle bonds in the molecule Each of the n records following contains angle key index 1 i index 2 7 index 3 k variable 1 variable 2 variable 3 variable 4 a4 integer integer integer real real real real potential key see Table 5 9 first atomic site index second atomic site index central site third atomic site index potential parameter see Table 5 9 potential parameter see Table 5 9 potential parameter see Table 5 9 potential parameter see Table 5 9 139 OSTFC Section 5 1 Table 5 8 Chemical Bond Potentials key potential type Variables 1 4 functional form harm Harmonic k ro U r 3 k rij ro hrm mors Morse Eo ro k U r Eo 1 exp k rij ro 1 mrs 12 6 12 6 A B U r 4 126 o I2 m lj Lennard Jones e o U r 4e E 2 lj rhrm Restraint k ro fe U r 2 i k ri ro rij rol re rhm U r 2 3 kr2 k re rij ro re rij rol
361. sors 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 chang ing in response to local changes 6 1 3 Distributing the Non bonded Terms DL POLY 4 calculates the non bonded pair interactions using the link cell algorithm due to Hock ney and Eastwood 71 In this algorithm a relatively short ranged potential cutoff reut is assumed The simulation cell is logically divided into so called link cells which have a width not less than or equal to the cutoff distance It is easy to determine the identities of the atoms in each link cell When the pair interactions are calculated it is already known that atom pairs can only interact if they are in the same link cell or are in link cells that share a common face Thus using the link cell address of each atom interacting pairs are located easily and efficiently via the link list that identifies the atoms in each link cell So efficient is this process that the link list can be recreated every time step at negligible cost For reasons partly historical the link list is used to construct a Ve
362. space terms By means of an interpolation procedure involving complex B splines the sum in reciprocal space is represented on a three dimensional rectangular grid In this form the Fast Fourier Transform FFT may be used to perform the primary mathematical operation which is a 3D convolution The efficiency of these procedures greatly reduces the cost of the reciprocal space sum when the range of k vectors is large The method briefly is as follows for full details see 55 1 Interpolation of the erp i k r terms given here for one dimension exp 2ri u k L b k Y Mn u exp 2ri kt K 2 190 oo 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 u is the fractional coordinate of ion j scaled by a factor K i e uj K sj 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 5 Mn l 1 exp 2ri ke K 2 191 0 2 Approximation of the structure factor S k S k b1 k1 ba ko b3 k3 Q k1 ko k3 2 192 where Q k1 ka k3 is the discrete Fourier transform of the charge array Q L1 l2 l3 defined as N QUito ls Sig M Ma uj 4 mlLi x My uoj j nL x j l n1
363. stem of charged point ions mutually interacting via the Coulomb potential The Ewald method makes two amendments to this simple model Firstly each ion is effectively neutralised at long ranged by the superposition of a spherical Gaussian cloud of opposite charge centred on the ion The combined assembly of point ions and Gaussian charges becomes the Real Space part of the Ewald sum which is now short ranged and treatable by the methods described above Section 2 The second modification is to superimpose a second set of Strictly speaking the real space sum ranges over all periodic images of the simulation cell but in the DL POLY 4 implementation the parameters are chosen to restrict the sum to the simulation cell and its nearest neighbours i e the minimum images of the cell contents 46 OSTFC Section 2 4 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
364. t 340 At bin t P io o kp Text 1 1 Px t n t At exp x t At nt 3At At Ll VO 1 1 1 x6 3 t SAt x t z 3 154 1 1 1 n t lt 5 nl 5 n t 4 z STFC Section 3 5 Several iterations are required to obtain self consistency In DL POLY 4 the number of iterations is set to 7 8 if bond constraints are present Note also that the change in box size requires the SHAKE algorithm to be called each iteration The VV and LFV flavours of the Nos Hoover barostat and thermostat are implemented in the DL_POLY_4 routines NPT HO vV and NPT_HO_LFV respectively The routines NPT_H1_vv and NPT_H1_LFV implement the same but also incorporate RB dynamics Cell size and shape variation The isotropic algorithms VV and LFV may be extended to allowing the cell shape to vary by defining n 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 SO v t n elt Bolt quo m b 6 1 n 0 v t d z 2Ekin t Pmass Tr n t non 20 32 kp Text a E dmass Qmass 20 TA 3 155 axo E po Pmass E i 3 kp Text TZ H 10 50 d g Trim V where is the stress tensor equation 3 96 and 1 is the identity matrix The VV and LFV algorithmic equations are therefore written in the same fashion as above with slight modifications in i
365. t In practice a uniform distribution random number uni i is generated for each particle in the system which is compared to the collision A probability If uni i 1 exp 4 the particle momentum is changed as described above TT The VV implementation of the Andersen algorithm is as follows 1 VV1 1 At f t lt V t 2 2 m 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 3 50 u t At ult 344 Gen a 2 m 5 RATTLE_VV2 64 OSTFC Section 3 4 6 Thermostat Note that the MD cell centre of mass momentum must not change s At If mi0 lt 1 exp Then TT kpT i up t At Gauss 0 1 3 51 v t At av t At Vv1 a v t At End If The algorithm is self consistent and requires no iterations The LFV implementation of the Andersen algorithm is as follows 1 FF f t f t At 3 52 2 LFV TE jM id DAI At du r t At r t At u t 344 3 53 3 Full step velocity Oe 5 vt At v t4 z 3 54 4 Thermostat Note that the MD cell centre of mass momentum must not change cm At If mi0 lt 1 exp Then TT aam it kpT un t 5 At lt Dm Gauss 0 1 1 1 iL vi t 3At ayi tt At 11 02 xi tc At 3 55 1 u t ult At End If 5 SHAKE The algorithm is self consistent and requires no iterations The VV and LFV flavours of the A
366. t 4 74 x nt 746 At t At Pal V t At n t At n t4 3 At SPESO SAGRE 4 4 Pmass At PERNES exp x t Ft x n t At OSTFC Section 3 5 11 Thermostat Note Exin t At has changed and changes inside At 2Epin t At mass Nt At 20 kg Tox Me AD A A kia E AO Poia N EA a gait 8 4 8 Imass 7 At olt At e exp x t EAs 1 u t At 3 150 At 2Exin t At mass Nt At 20 kpg Tox v t At v t At Vo t At where V 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 estimate of the half step position r t 5At Also calculated is an unconstrained 1 FF FO e ft At 3 151 2 LFV The iterative part is as follows 1 1 t vet tat vlt LA At E x t E v t 2 2 m 1 1 r t At r t At u t 5 At n t At Irt 50 Ro e 1 H t At exp n At At H t 3 152 VLAD cdit ntt 56 At V t 3 SHAKE 4 Full step velocity and half step position 1 1 1 v t 3 Ec 5 At Hult 4 5 0 relay e TOFEE A 3 153 2 2 5 Thermostat and Barostat 1 1 2E in Mass t 2_ 20 Tex x E 5At x
367. t amending 87 STFC Section 3 6 the thermostat equation of motion and the conserved quantity to d had fusi E Jua x ms t a B 2 di Ma cow ra d i 2Ekin t Pmass Tr n t ty 20 kp Text 3 169 ad i Qmass mass t Pmass Tr n i 1 t HNP AT HNVE d A 2 PV t sp f 1 kg Text x s ds Similarly this ensemble is optionally extending to constant normal pressure and constant surface tension NP yT 60 by semi isotropic constraining of the barostat equation of motion and slight amending the thermostat equation of motion and the conserved quantity to Coo t Pext Yext hz t V t 2Exin t 1 x t na t a B x y d Pmass Pmass nag t 7 aem eset VO na x 0 es t i a 0 Nog 0 a 0 2z y 2 d 2Exin t Pmass Tr n t nos 20 3 kp Text ae ES 3 170 aX mass mass t Pmass Tr n n t Hype Hav mmm MT mem AO Pow t 3 ks Toa f x 9 ds where Yext is the user defined external surface tension and h t V t Az 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 3 120 The case e amp 0 generates the NPT anisotropic ensemble for the orthorhombic cell imcon 2 in CONFIG see Appendix A This can be considered as an orthorhombic constraint on the NoT ensemble The constraint can be strengthened further to a semi orthorhombi
368. t 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 iest condition Call gcheck safe If not safe Call error message number In this example it is assumed that the logical operation fest 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 110 Chapter 5 Data Files Scope of Chapter This chapter describes all the input and output files for DL POLY 4 examples of which are to be found in the data sub directory 111 OSTFC Section 5 1 5 1 The INPUT Files REVCON OUTPUT CONFIG HISTORY CONTROL DEFECTS FIELD RSDDAT MSDTMP TABLE STATIS TABEAM CFGMIN REFERENCE RDFDAT REVOLD ZDNDAT REVIVE Figure 5 1 DL POLY 4 input left and output right files Note files marked with an asterisk are non mandatory DL POLY 4 requires seven input files named CONTROL CONFIG FIELD TABLE TABEAM REFERENCE and REVOLD The first three files are
369. t record atname a8 unique atom name following records mxgrdf records z real distance in z direction p z real Z density at given height z Note the ZDNDAT file is optional and appears when the print rdf option is specified in the CONTROL file 164 OSTFC Section 5 2 5 2 11 The STATIS File The file is formatted with integers as i10 and reals as e14 6 It is written by the subroutine STATISTICS_COLLECT It consists of two header records followed by many data records of statistical data record 1 cfgname a72 configuration name record 2 string a8 energy units Data records Subsequent lines contain the instantaneous values of statistical variables dumped from the array stpval A specified number of entries of stpval are written in the format 1p 5e14 6 The number of array elements required determined by the parameter mxnstk in the SETUP_MODULE file is mxnstk gt 27 ntpatm number of unique atomic sites 9 stress tensor elements 9 if constant pressure simulation requested 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
370. t scale rlxtol f rvdw cutoff f scale temperature every n seed n Na shake tolerance f shift shift damp a slab spme evaluate every n spme precision f spme sum a k ka k3 parameter o in AI 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 restart job from end point of previous run i e continue current simulation REVOLD required restart job from previous run without scaling system temperature i e begin a new simulation from older run without temperature reset REVOLD is not used restart job from previous run with scaling system temperature i e begin a new simulation from older run with temperature reset REVOLD is not used set tolerance for relaxed shell model to f default f linD ps 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 107 calculate electrostatic forces using force shift
371. ted with the standard formula f Ung 2 93 U rij rj Fd Tij Orij sai ii ae where r rj r The force on atom is the negative of this j The contribution to be added to the atomic virial for each pair interaction is The contribution to be added to the atomic stress tensor is given by toa 2 95 where a and f indicate the x y z components The atomic stress tensor derived from the pair forces is symmetric Since the calculation of pair potentials assumes a spherical cutoff 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 6 the correction for the potential energy is calculated via the integral ya MEA i corr V Kag gav r Uas r r dr 2 96 where Na M are the numbers of atoms of types a and b in the system V is the system volume and gay r and U r are the appropriate pair correlation function and pair potential respectively It is usual to assume gap r 1 for r gt ryay DL POLY 4 sometimes makes the additional assumption that the repulsive part of the short ranged potential is negligible beyond fyaw The correction for the system virial is NaN 99 o wo 2 V di Jal 3 Uan r r dr 2 97 vdw where the same approximations are applied Note that these formulae are based on the assumption that the system is reasonably isotropic b
372. tes the final summaries in the OUTPUT file and dumps the restart files REVIVE and REVCON Sections 5 2 8 and 5 2 7 respectively 98 OSTFC Section 4 2 4 2 Compiling and Running DL POLY 4 4 2 1 Compiling the Source Code When you have obtained DL_POLY 4 from Daresbury Laboratory and unpacked it your next task will be to compile it To aid compilation three general makefiles have been provided in the sub directory build These are Makefile MPI for compiling a parallel version of DL_POLY_4 and Makefile SRL1 and Makefile SRL2 for compiling a serial versions see Appendix C After choosing what the default compilation is to be the appropriate makefile is to be copied as Makefile in the sub directory source The general DL POLY 4 makefile will build an executable with the full range of functionality sufficient for the test cases and for most users requirements In most cases the user will have to modify few entries in the specification part of their makefile to match the location of certain software on their system architecture Note that only FORTRANO90 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 ta
373. that the structure created does not correspond to one typical of the equilibrium state for the required state point for the given force field employed This can make the simulation unstable in the initial stages and can even prevent it from proceeding For this reason DL POLY 4 has available a selection of structure relaxation methods Broadly 102 OSTFC Section 4 2 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 temperature At each time step the molecules move in the direction of the computed forces and torques but are not allowed to acquire a velocity larger than that corresponding to a temperature of 10 Kelvin The subroutine that performs this procedure is ZERO K OPTIMISE 2 Conjugate Gradients Method CGM minimisation This is nominally a simple minimisa tion of the system configuration energy using the conjugate gradients method 58 The algorithm coded into DL POLY 4 is an adaptation that allows for rotation and translation of rigid bodies Rigid constraint bonds ho
374. that the wording of some of the messages may have changed over time usually to provide more specific information The most recent wording appears below The Standard User Response DL POLY 4 uses FORTRAN90 dynamic array allocation to set the array sizes at run time This means that a single executable may be compiled to over all the likely uses of the code It is not foolproof however Sometimes an estimate of the 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 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 236 OSTFC Appendix D The DL POLY 4 Error Messages Message 1 error word 2
375. the DL POLY 4 routines NPT L0 VV and NPT LO LFV respectively Both VV and LFV imple mentations make use of the DL POLY 4 module LANGEVIN_MODULE The routines NPT L1 VV and NPT Ll LFV implement the same but also incorporate RB dynamics Cell size and shape variations The isotropic algorithms VV and LFV may be extended to allowing the cell shape to vary by defining 1 as a tensor n and extending the Langevin pressure variable Rp to a stochastic Langevin tensor Rp E io it Ros 2 Xp Das hal Oy 0 t 3 113 which is drawn from Gaussian distribution of zero mean and unit variance Gauss 0 1 scaled by 2 Xp Pmass EnT kp is the Boltzmann constant T the target temperature and pmass the barostat mass Note that Rp has to be symmetric and only 6 independent components must be generated each timestep The equations of motion are written in the same fashion as is in the isotropic algorithm with slight modifications as now the equations with 7 are extended to matrix forms TO v t n t r t 79 STFC Section 3 5 a f RW Lom Z bO q KAFU 37 1 01 d c t Pets V t 1 2Exin t 1 Rp ant s t 3 114 act Pmass f Pmass Xp Pmass f 3 kp Text Pmass 3 2n xp d H t t H t SH a t HC d all Tin V where o is the stress tensor equation 3 96 and 1 is the identity matrix The conserved quantity these generate is Pmass Trin i n7 HNoT Hyve
376. 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 08 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 cos 149 17 161 16 10 500 180 00 OSTFC Section 5 1 cos 162 19 168 18 10 500 180 00 FINISH SPC Water NUMMOLS 146 ATOMS 3 OW 16 0000 0 8200 HW 1 0080 0 4100 HW 1 0080 0 4100 CONSTRAINTS 3 1 2 1 0000 1 3 1 0000 2 3 1 63299 FINISH VDW 45 C C 1j 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 5 1 3 1 The FIELD File Format The file is free formatted and not case sensitive Every line is treated as a command sentence record Commented records beginning with a and blank lines are not processed and may be added to aid legibility see example above Records must be limited in length to 100 characters Records are read in words as
377. 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 2E nt Pmass Tr n t n t 20 3 kp Text 8 dmass x t At x t 1 At v t lt exp n t At 3 u t 3 156 1 At t Pea V t 1 qtia e ng St eo Pee VOL 4 Sl 4 Pmass whereas for the LFV couched algorithm they are 2Exin t Pmass Tr n t n t 20 bg Ta BECAS x xlt Ai A mass 9 _ Go 1 100 t 3 157 m v t At ult Nip N 1 2 A At 2 STFC Section 3 5 t Pess V t 1 Pmass 1 1 n t 541 exp x DAt nt 3At At Z The modifications in ii are the same for both the VV and LFV couched algorithms H t At exp a t 50 At H t VEAJ Sp n e 546 At V t 3 158 It is worth noting DL_POLY_4 uses Taylor expansion truncated to the quadratic term to approxi mate exponentials of tensorial terms The conserved quantity is to within a constant the Gibbs free energy of the system amass x t n Pmass Tr n a 11 t y HPV t F 3 kg Toxt 1 x s ds 3 159 Hnot Hxve 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 60 by semi isotropic constraining of the barostat equatio
378. tial 45 nm E To To di U rij 2 n 2 2 84 4 Buckingham potential buck 1 12 6 potential 12 6 Ugg A exp 5 2 85 To 5 Born Huggins Meyer potential bhm U ri A exp B o 5 ss 2 86 6 Hydrogen bond 12 10 potential hbnd veo 4 8 29 7 Shifted force n m potential 45 snm oo pn UU O 0 SAO eam 27 OSTFC Section 2 3 with u n m n8 1 m y m 1 y mB 1 n y n 1 m l _ n m B y i 2 89 y This peculiar form has the advantage over the standard shifted n m potential in that both E and ro well depth and location of minimum retain their original values after the shifting process 8 Morse potential mors U rij Eo 1 exp k rij ro 1 2 90 9 Shifted Weeks Chandler Anderson WCA potential 46 wca 12 a 6 oi U rij 3a xta TE i Tis Pr 2 91 0 gt Tij 2 26 C A The WCA potential is the Lennard Jones potential truncated at the position of the minimum and shifted to eliminate discontinuity includes the effect of excluded volume It is usually used in combination with the FENE 2 10 bond potential This implementation allows for a radius shift of up to half a o A lt 0 5 o with a default of zero Ade fault 0 10 Tabulation tab The potential is defined numerically only The parameters defining these potentials are suppli
379. tion timestep self adjusts in response to the dynamics of the system 124 OSTFC Section 5 1 6 The job time and close time directives are required to ensure a controlled close down procedure when a job runs out of time The time specified by the job time directive indicates the total time allowed for the job This must obviously be set equal to the time specified to the operating system when the job is submitted The close time directive represents the time DL POLY 4 will require to write and close all the data files at the end of processing This means the effective processing time limit is equal to the job time minus the close time Thus when DL POLY 4 reaches the effective job time limit it begins the close down procedure with enough time in hand to ensure the files are correctly written In this way you may be sure the restart files etc are complete when the job terminates Note that setting the close time too small will mean the job will crash before the files have been finished If it is set too large DL_POLY_4 will begin closing down too early How large the close time needs to be to ensure safe close down is system dependent and a matter of experience It generally increases with increasing simulation system size 7 The starting options for a simulation are governed by the keyword restart If this is not specified in the control file the simulation will start as new When specifed it will continue a previous simulation restart
380. tively increase mxatms in SET BOUNDS recompile and resubmit Message 57 error too many core shell units specified This should never happen Action Recompile the program or recreate the FIELD file If neither of these works send the problem to us Message 58 error number of atoms in system not conserved 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 defined 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 de
381. 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 ii STFC Preface ACKNOWLEDGEMENTS DL POLY 4 was developed at Daresbury Laboratory DL http www dl ac uk the Science and Technology Facilities Council STFC http www stfc ac uk UK with support from the Engineering and Physical Sciences Research Council EPSRC http www epsrc ac uk and the Natural Environment Research Council NERC http www nerc ac uk Advice assistance and encouragement in the development of DL_POLY 4 has been given by many people We gratefully acknowledge the following T R Forester I J Bush M Leslie M F Guest R J Allan D Tildesley M Pinches D Rapaport the UK s Materials Chemistry Consortium under C R A Catlow and the eMinerals project under M T Dove This document is produced with BIFX amp hdvipdfm ii STFC Preface Manual Notation In the DL_POLY manuals specific fonts are used to convey specific meanings 1 directori
382. tomic indices appearing under the shell directive Note that if a site weighting is not supplied DL POLY 4 will assume it is zero However DL POLY 4 detects that all sites in a PMF unit have zero weighting then the PMF unit sites will be assigned the masses of the original atomic sites The PMF bondlength applies to the distance between the centres of the two PMF units The centre R of each unit is given by ttis T de Dar i Ti 5 7 Di 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 T 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 is 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
383. ts 26 Langevin 27 63 Andersen 28 Berendsen 29 Nos Hoover 30 and the gentle stochastic thermostat 59 64 Of these only the gentle stochastic thermostat Nos Hoover and Langevin algorithms generate trajectories in the canonical NVT ensemble The rest will produce properties that typically differ from canonical averages by 0 1 N 22 where N is the number of particles in the system as the Evans algorithm generates trajectories in the NVE gin ensemble 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 qz o5 3 wW PO ea 3 23 the kinetic temperature constraint x can be found as follows d d 1 d P e 7 Ema dammi Gui 0 2 mult E x t x 0 3 24 x t 2420 FW gt mio t 60 OSTFC Section 3 4 where 7 is the instantaneous temperature defined in equation 3 10 The VV implementation of the Evans algorithm is straight forward The conventional VV1 and V V2 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 alt 0
384. ts centre of mass R 1 Nsites R M 2 TT gt 3 173 j where r is the position vector of atom j The rigid body translational velocity V is defined by 1 Nsites V M 2 MjUz 3 174 where v is the velocity of atom j The net translational force acting on the rigid body unit is the vector sum of the forces acting on the atoms of the body Nsites Bes des 3 175 j 1 1An alternative approach is to define basic and secondary particles The basic particles are the minimun number needed to define a local body axis system The remaining particle positions are expressed in terms of the COM and the basic particles Ordinary bond constraints can then be applied to the basic particles provided the forces and torques arising from the secondary particles are transferred to the basic particles in a physically meaningful way 89 STFC Section 3 6 where is the force on a rigid unit site A rigid body also has associated with it a rotational inertia matrix L whose components are given by Nsites 2 Tog Y mj a drf 3 176 j l and COM stress and virial respectively written down as Nsites 8 o Y df j 1 Nsites W gt def 3 177 j 1 where d is the displacement vector of the atom j from the COM and is given by d r HR 3 178 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 in
385. ts communication overheads and provides smooth parallelisation to large processor counts 6 1 8 The Parallel DD tailored SHAKE and RATTLE Algorithms The essentials of the DD tailored SHAKE and RATTLE algorithms see Section 3 2 are as follows 1 The bond constraints acting in the simulated system are allocated between the processors based on the location i e domain 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 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 172 STFC Section 6 1 specific correction vectors to all neighbours that share the same atoms using the information compiled in step 3 6 When all necessary correction vectors have been received and added the positions of the constrained atoms are corrected 7 Steps 5 and 6 are repeated until the bond constraints are converged
386. u MAKE LD ftn o LDFLAGS 03 Wall pedantic g FC ftn c N FCFLAGS 03 Wall pedantic g EX EX BINROOT BINROOT TYPE hector gnu debug MAKE LD ftn o LDFLAGS 03 Wall Wextra pedantic g fbounds check fbacktrace finit integer 9999 finit real nan std f2003 pedantic ffpe trap invalid zero overflow fdump core FC ftn c N FCFLAGS 03 Wall Wextra pedantic g fbounds check fbacktrace finit integer 9999 finit real nan std f2003 pedantic ffpe trap invalid zero overflow fdump core EX EX BINROOT BINROOT TYPE hector cray 219 OSTFC Appendix C MAKE LD ftn o LDFLAGS 03 en FC ftn c N FCFLAGS 03 en EX EX BINROOT BINROOT TYPE hector cray debug MAKE LD ftn o LDFLAGS 03 en G2 FC ftn c FCFLAGS 03 en G2 EX EX BINROOT BINROOT TYPE hector pathscale MAKE LD ftn o LDFLAGS byteswapio 03 FC ftn c FCFLAGS byteswapio 03 EX EX BINROOT BINROOT TYPE CRAY XT3 6 pathscale compilers DEBUG hector pathscale debug MAKE LD ftn o LDFLAGS byteswapio 00 g ffortran bounds check FC ftn c N FCFLAGS byteswapio 00 g ffortran bounds check EX EX BINROOT BINROOT TYPE hector X2 MAKE LD ftn o LDFLAGS 03 0fp3 Ocache2 rm FC ftn c FCFLAGS 03 Ofp3 Ocache2
387. uation 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 r 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 o ranging over the value you have chosen plus and minus 2096 Plot the Coulombic energy W versus a If the Ewald sum is correctly converged you will see a plateau in the plot Divergence from the plateau at small a is due to non convergence in the real space sum Divergence from the plateau at large a is due to non convergence of the reciprocal space sum Redo the series of calculations using smaller kmax values The optimum values for kmax are the smallest values that reproduce the correct Coulombic energy the plateau value and virial at the value of a to be used in the simulation Note that one needs to specify the three integers kmaxa kmaxb kmaxc referring to the three spatial directions to ensure the reciprocal space sum is equally accurate in all directions The values of kmaxa kmaxb and kmaxc must be commensurate with the cell geometry to ensure the same minimum wavelength is used in all directions For a cubic cell set kmaxa
388. uilibration steps n ewald evaluate every n ewald precision f ewald sum a k ka ks exclude finish impactij E xyz integrator string MD cell orthorhombic constraint equivalent to the NPnyT ensemble when y 0 NP y OT select the same NP y OT ensemble as above but with the semi anisotropic constraint so that the MD cell changes isotropically in the x y plane semi orthorhombic constraint equivalent to the NP 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 lor undefined defaults ton 1 n gt 10 defaults ton 4 calculate electrostatic forces using Ewald sum with automatic parameter optimisation 1072 lt f lt 0 5 default f 10720 calculate electrostatic forces using Ewald sum with a Ewald convergence parameter in 7 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
389. ule o export atomic data o comms module o config module o domains module o kinds f90 0 setup module o external field apply o comms module o config module o core shell module o external field module o kinds f90 0 rigid bodies module o Setup module o external field correct o config module o external field module o kinds f90 0 rigid bodies module o external field module o kinds f90 0 setup module o four body forces o comms module o config module o domains module o four body module o kinds f90 0 setup module o four body module o kinds f90 0 setup module o gpfa module o kinds f90 o impact o comms module o config module o core shell module o kinds f90 0 kinetic module o rigid bodies module o intra coul o kinds f90 0 setup module o inversions forces o comms module o config module o inversions module o kinds f90 0 setup module o inversions module o kinds f90 0 setup module o io module o comms module o kinds f90 0 netcdf modul o kinetic module o comms module o config module o kinds f90 0 rigid bodies module o setup module o langevin forces o comms module o config module o kinds f90 0 setup module o site module o langevin module o kinds f90 0 setup module o link cell pairs o comms module o config module o development module o domains module o kinds f90 0 setup module o metal forces o config module o kinds f90 0 metal module o setup module o metal generate o kinds f90 0 metal mod
390. ule o setup module o site module o metal ld collect eam o config module o kinds f90 0 metal module o Setup module o metal ld collect fst o config module o kinds f90 0 metal module o Setup module o metal ld compute o comms module o config module o kinds f90 0 metal module o Setup module o metal ld export o comms module o config module o domains module o kinds f90 0 setup module o metal ld set halo o comms module o config module o kinds f90 0 Setup module o metal lrc o comms module o config module o kinds f90 0 metal module o Setup module o site module o metal module o kinds f90 0 setup module o metal table derivatives o kinds f90 0 setup module o metal table read o comms module o kinds f90 0 metal module o parse module o Setup module o site module o minimise module o kinds f90 0 setup module o 205 OSTFC Appendix C minimise relax o comms module o config module o kinds f90 0 minimise module o rigid bodies module o setup module o msd write o comms module o config module o io module o kinds f90 0 parse module o setup module o site module o statistics module o netcdf modul o kinds f90 o npt bO lfv o comms_module o config module o kinds f90 0 kinetic module o Setup module o site module o npt bO vv o comms module o config module o kinds f90 0 kinetic module o Setup module o site module o npt bi lfv o comms module o config module o domains module o kinds f90 0 kineti
391. unknown Action Locate the errant atom type in the four body potential definition in the FIELD file and correct Make sure this atom type is specified by an atoms directive earlier in the file Message 92 error specified metal potentials have different types The specified metal interactions in the FIELD file are referencing more than one generic type of metal potentials Only one such type is allowed in the system Action Locate the errant metal type in the metal potential definition in the FIELD file and correct Make sure only one 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 gt minimum of all half cell widths In order for the minimum image convention to work correctly within DL POLY 4 it is necessary to ensure that the major cutoff applied to the pair interactions does not exceed half the perpendicular width of the simulation cell The perpendicular width is the shortest distance between opposing cell faces Termination results if this is detected In NVE and NVT simulations this can only happen at the start of a simulation but in NPT and NoT it may occur at any time Action Supply a cutoff that is less than half the cell width If running constant pressure calculations use a cutoff that will accommodate the fluctuations in the simulation cell Study the flu
392. us subroutines with names beginning with METAL 6 1 6 Tersoff Three Body and Four Body Potentials DL POLY 4 can calculate Tersoff three body and four body interactions Although some of these interactions have similar terms to some intramolecular ones three body to the bond angle and four body to inversion angle these are not dealt with in the same way as the normal bonded interactions They are generally very short ranged and are most effectively calculated using a link cell scheme 71 No reference is made to the Verlet neighbour list nor the excluded atoms list It follows that atoms involved these interactions can interact via non bonded pair forces and ionic forces also Note that contributions from frozen pairs of atoms to these potentials are excluded The calculation of the Tersoff three body and four body terms is distributed over processors on the basis of the domain of the central atom in them DL_POLY_4 implements these potentials in the following routines TERSOFF_FORCES TERSOFF GENERATE THREE BODY FORCES and FOUR BODY FORCES 6 1 7 Globally Summed Properties The final stage in the DD strategy is the global summation of different by terms of potentials contributions to energy virial and sterss which must be obtained as a global sum of the contributing terms calculated on all nodes The DD strategy does not require a global summation of the forces unlike the Replicated Data method used in DL POLY Classic which limi
393. used and all are optional in each case Where numerical values are to be supplied specifying 0 or a negative numbers indicates that DL POLY 4 will resort to the default value The possible options are e io read mpiio direct netcdf j k 1 e j specifies the number of processors that shall access the disk k specifies the maxi mum number of particles that the reading processors shall deal with at any one time 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 Y es only to switch global error checking performed by the I O subsystem the default is No e io read master i l specifies the maximum number of particles that the reading process shall read from the disk in one I O transaction Large values give good performance but may results in an unacceptable memory overhead b io write method rp type options With action set to write the io command controls how the writing of large files is per formed method controls how the disk is accessed Possible values are mpiio in 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
394. ut 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 Y es only to switch global error checking performed by the I O subsystem the default is No io write master sort unsort I l specifies the maximum number of particles that the writing process shall write to the disk in one I O transaction Large values give good performance but may results in an unacceptable memory overhead Users are advised to study the example CONTROL files appearing in the data sub directory to see how different files are constructed 5 1 2 The CONFIG File The CONFIG file contains the dimensions of the unit cell the key for periodic boundary condi tions and the atomic labels coordinates velocities and forces This file is read by the subroutine READ CONFIG optionally by SCAN_CONFIG in the SET_BOUNDS routine The first few records of a typical CONFIG file are shown below Icel structure 6x6x6 unit cells with proton disorder 3 276 26 988000000000000 0 000000000000000 0 000000000000000 13 494000000000000 23 372293600000000 0 000000000000000 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 1 972
395. utal truncation of the previous case It hinges on the assumption that the electrostatic forces are effectively screened in real systems an effect which is approximated by introducing a dielectric term that increases with distance The interatomic potential for two charged ions is l dig PT 2 172 Arege Ti Tij i U rij with q the charge on an atom labelled and r the magnitude of the separation vector r rj fr e r is the distance dependent dielectric function In DL POLY 4 it is assumed that this function has the form er er 2 173 where e is a constant Inclusion of this term effectively accelerates the rate of convergence of the Coulomb sum 44 STFC Section 2 4 The force on an atom j derived from this potential is l qa ay 2 174 j 2mnepe rj Lij with the force on atom 7 the negative of this The contribution to the atomic virial is which is 2 times the potential term The contribution to be added to the atomic stress tensor is given by gib ege 2 176 where a B are x y z components The atomic stress tensor is symmetric In DL POLY 4 these forces are handled by the routine COUL DDDP FORCES 2 4 4 Reaction Field In the reaction field method it is assumed that any given molecule is surrounded by a spherical cavity of finite radius within which the electrostatic interactions are calculated explicitly Outside the cavity the system is treated as a dielectric
396. virial data appearing in the OUTPUT is defined by the units directive appearing in the FIELD file System energies are therefore read in units per MD cell Pressure Units The unit of pressure is katms irrespective of what energy unit is chosen 5 2 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 5 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 displace ment for the different atomic species in the simulation These are determined from a single time origin and are therefore approximate Accurate determinations of the diffusion coefficients can be obtained using the MSD utility program which processes the HISTORY file see DL POLY Classic User Manual If an NPT Nc T simulation is performed the OUTPUT file also provides the mean pressure stress tensor and mean simulation cell vectors In ca
397. wever 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 minimisation involving both MD and CGM This method combines the two as minimisation is invoked by user defined intervals of usually low temperature dynamics in a cycle of minimisation dynamics minimisation etc which is intended to help the structure relax from overstrained conditions see Section 5 1 1 When using the programmed minimisation DL POLY 4 writes and rewrites the file CFGMIN 5 2 5 which represents the lowest energy structure found during the programmed minimisation CFGMIN is written in CONFIG file format see section 5 1 2 and can be used in place of the original CONFIG file 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 de
398. which signals the end of the force field data Without this directive DL POLY 4 will abort 5 1 4 The REFERENCE File The REFERENCE has the same format and structure as CONFIG see Section 5 1 2 file with the exception that incon MUST BE 0 REFERENCE may contain more or less particles than CONFIG does and may have particles whith identities that are not defined in FIELD see Section 5 1 3 The positions of these particles are used to define the crystalline lattice sites to whitch the particles in CONFIG compare during simulation when the defect detection option defects is used REFERENCE is read by the subroutine DEFECTS REFERENCE READ 150 OSTFC Section 5 1 5 1 5 The REVOLD File This file contains statistics arrays from a previous job It is not required if the current job is not a continuation of a previous run i e if the restart directive is not present in the CONTROL file see above The file is unformatted and therefore not human readable DL POLY 4 normally produces the file REVIVE see Section 5 2 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 5 1 5 1 Format The REVOLD file is unformatted All variables appearing are written in native working precision see Section 4 3 5 real representation Nominally integer quantities e g the timestep number nst
399. 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 circulation of the list is done at the start of the simulation but thereafter these need updating on a local level every time a RB site atom is relocated from one processor to another In this respect RBs topology transfer resembles every other intramolecular term 173 OSTFC Section 6 2 Since the allocation of RBs is based purely on geometric considerations it is not practical to arrange for a strict load balancing For many systems however this deficiency has little practical impact on performance 6 2 Source Code 6 2 1 Modularisation Principles Modules in DL_POLY 4 are constructed to define parameters and
400. wo parts Firstly by analogy with the short ranged potentials the correction to the local density is CO pi OSS pu j 1 j i Tij lt Tmet Tij IT met pi DI pig DI pig ig 07 6p 2 118 j Ljzi j Ljzi oo p Amp pia Tmet where p is the uncorrected local density and p is the mean particle density Evaluating the integral part of the above equation yields 1 EAM density correction No long ranged corrections apply beyond ret 2 Finnis Sinclair density correction No long ranged corrections apply beyond cutoffs c and d 3 Extended Finnis Sinclair density correction No long ranged corrections apply beyond cutoffs c and d 4 Sutton Chen density correction 47 pa a es 2 119 Pp m T 3 Pa 5 Gupta density correction 2 Tmet T 1j 1j The density correction is applied immediately after the local density is calculated The pair term correction is obtained by Ed with the short ranged potentials and is Ur SS Tij 27 pro Opi Qij i 1 A N Tig lt Tmet N rij 2Tmet Uy 2 5 Vizi Tij d D y Vi Tij U U i 1 i 1 A dU 27Np Vij r r2dr Tmet N Ur YF p 2 121 i 1 gt or eS OF pi o 0 Us SUCEDE U i i 1 4 U 4m ps 2E P n pij ryr dr i 1 Tmet Note that 9U2 is not required if p has already been corrected Evaluating the integral part of the above equations yields 34 OSTFC Section 2 3 1 EAM energy correction No long r
401. x s ds 3 79 68 OSTFC Section 3 4 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 Hl VV and NVT_H1_LFV implement the same but also incorporate RB dynamics 3 4 6 Gentle Stochastic Thermostat The Gentle Stochastic Thermostat 59 64 is an extension of the Nos Hoover algorithm 30 dr t x 20 E O 3 80 in which the thermostat friction x has its own Brownian dynamics dx t 2Ekin t 2 2 y kp Text Imass dw t x t kin t o aa tq em dt mass mass dt 3 81 governed by the Langevin friction y positive in units of ps where w t is the standard Brownian motion Wiener process Gauss 0 1 o is the target thermostat energy as in equation 3 57 Qmass 2 0 Ti 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 ac dw 3 83 dt 2 T7g 3 Ra which for a given realization of the Wiener process w t has exact solution e2 1 Xn 1 Xn 0 oa Aw 3 84 where e a6 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 Ex n t
402. y plane which leads to the following changes in the equations above ils oss o4 0 2 Pes cese D V t Onde e 3 162 mass Trin si t HNPay 0T ip ERE B n un Pa V t f 2 kg Text n x s ds The VV and LFV flavours of the non isotropic Nos Hoover barostat and thermostat are im plemented 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 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 3 140 to d e ult n re d t 3 Sut 2 kos 149 ne 20 d 2E nin t Pmass n t 20 kpg Text ax H mass mass 20 Ti 3 163 ELO H PAN 2 T vm E vu x t n t Pmass f 3 kp Text TP d SHO nlt HO d gO BOVO and the anisotropic cell change case equations 3 155 to d GIO Ult n re t Tr n t w t I x t 1 n t z 1 v t d 2E in t Pmass Tr n t no 20 3 kp Text mass 20 TA 3 164 d o AP V 1 25g t 1 ac i Pmass m f Dmass one Pmass res kp Text Tp 86 STFC Section
403. y similar to this reference structure If the problem persists increase the value of tol in RIGID BODIES SETUP and recompile If problems still persist double the value of dettest in RIGID BODIES SETUP and recompile If you still encounter problems contact the authors 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 while 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 1078 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 bo

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