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DLPOLY2 USER MANUAL

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1. kgText A v t At V t A1 a At u t At 2 231 Routines rattle R and rattle V apply the bondlength and velocity constraint formulae 2 210 and 2 211 respectively The equations have the same conserved variable Hypr as the LF scheme The integration is performed by the subroutine NVTVV_H1 which calls subroutines RATTLE_R RATTLE_V NPTSCALE_T and NPTSCALE_P Cell size and shape variation The isotropic algorithms may be extended to allowing the cell shape to vary by defining n as a tensor n The LF equations of motion are implemented as ya Tat el At SMB Or 8 Ta A WTr y t Oka Taa Q Q xa z Ai a z nettan n t an VO o Poal XOT nt 5 nt 5 At a t A v t SA v t Ai At E x 1 n 0 un it Lut M Ai sues 340 r t At r t At vt AN n t AN UU AI Rol r t 2A 5 r t r t At 2 232 where 1 is the identity matrix and c the pressure tensor The new cell vectors are calculated from H t At exp K n t z H t 2 233 DL_POLY_2 uses a power series expansion truncated at the quadratic term to approximate the exponential of the tensorial term The new volume is found from V t At V t exp At Tr n 2 234 CCLRC The conserved quantity is 67 1 1 t HNsT U KE PoxV t 5Qx 5WIr n S x 8 kpTox ds 2 235 MNE o T2 This algorithm is implemented in the routine NST_H1 with
2. 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 CCLRC cos 149 cos 162 FINISH SPC Water NUMMOLS 146 ATOMS 3 OW HW HW CONSTRAINTS 1 2 1 3 2 3 FINISH VDW 45 OW OS OS OS CLOSE 4 1 3 1 Format 17 19 161 168 0000 0080 0080 0000 0000 63299 lj 16 10 500 18 10 500 0 8200 0 4100 0 4100 0 12000 0 08485 0 15100 0 15000 180 00 180 00 118 The FIELD file is free formatted though it should be noted that atom names are limited to 8 characters and potential function keys are a maximum of 4 characters The contents of the file are variable and are defined by the use of directives Additional information is associated with the directives The file is not case sensitive 4 1 3 2 Definitions of Variables The file divides into three sections general information molecular descriptions and non bonded interaction descriptions appearing in that order in the file 4 1 3 2 1 General information The first record in the FIELD file is the title It must be followed by the units directive Both of these are mandatory These records may optionally be followed by the neut directive record 1 header record 2 a80 field file header CCLRC 119 units a40 Unit of energy used for
3. Action Standard user response Fix the parameter mxfbp CCLRC 188 Message 90 error system total electric charge nonzero In DL_POLY 2 a check on the total system charge will result in an error if the net charge of the system is nonzero Note In DL_POLY_2 this message has been disabled The program merely prints a warning stating that the system is not electrically neutral but it does not terminate the program watch out for this Action Check the specified atomic charges and their populations Make sure they add up to zero If the system is required to have a net zero charge you can enable the call to this error message in subroutine SYSDEF Message 92 error unidentified atom in tersoff potential list The specification of a Tersoff potential in the FIELD file has referenced an atom type that is unknown Action Locate the erroneous atom type in the Tersoff potential definition in the FIELD file and correct Make sure this atom type is specified by an atoms directive earlier in the file Message 91 error unidentified atom in 4 body potential list The specification of a four body potential in the FIELD file has referenced an atom type that is unknown Action Locate the erroneous atom type in the four body potential definition in the FIELD file and correct Make sure this atom type is specified by an atoms directive earlier in the file Message 93 error cannot use shell model with rigid molecules The dyna
4. Ou ima Da yp an fn g O y Zp 9 ar re p 9 au Nmax h sijL O 2n mXM913 L5 SSD ma Wa B 2 184 n 0 L ij ij L where uj is one of xj yj zj and noting for brevity that x and y derivatives are similar Zp g a 83 OZp g _ a pgjzj exp ig sy 2 185 j and 2n O f on hnGunao _ g iL O hn sijr a Ox iL mF m e l In 1 en Sij L OF Sij L O an hnGiinia y nra hn Sii 0 2 186 Be Zij L Intl N ij I g ml H j Sij L S L CCLRC 51 In DL POLY 2 the partial derivatives of hn sijl 0 sett are calculated by a recursion algorithm Note that when n 0 there is no derivative w r t z The virial and stress tensor terms in real space may be calculated directly from the pair forces and interatomic distances in the usual way and need not be discussed further The calculation of the reciprocal space contributions the terms involving the f g a functions are more difficult Firstly however we note that the reciprocal space contributions to Ozz Oyz and oz may be obtained directly from the force calculations thus aks j oS Da f 2 187 a recip __ Z O yz Zj i recip O xz which renders the calculation of these components trivial The remaining components are calculated from Nmax 2n 2 Cup Urecipduu y a y Ju9v 753 uv recipPuv Leg A n a ujv n 2n t g 4a 2 188 1 fo g a g 2n gt A DPC 2p 9 Za p 9 p 0
5. arising from a tether potential is obtained using the general formula 1 O Orio The contribution to be added to the atomic virial is given by L FT y Ura Tio 2 72 W ro fy 2 73 The contribution to be added to the atomic stress tensor is given by oP rg ff 2 74 where a and 5 indicate the x y z components The atomic stress tensor derived in this way is symmetric In DL POLY 2 bond forces are handled by the routine TETHFRC CCLRC 31 2 2 9 Frozen Atoms DL POLY 2 also allows atoms to be completely immobilised i e frozen at a fixed point in the MD cell This is achieved by setting all forces and velocities associated with that atom to zero during each MD timestep Frozen atoms are signalled by assigning an atom a non zero value for the freeze parameter in the FIELD file DL_POLY_2 does not calculate contributions to the virial or the stress tensor arising from the constraints required to freeze atomic positions In DL_POLY_2 the frozen atom option cannot be used for sites in a rigid body As with the tethering potential the reference position is scaled with the cell vectors in constant pressure simulations In DL POLY 2 the frozen atom option is handled by the subroutine FREEZE 2 3 The Intermolecular Potential Functions In this section we outline the pair body three body and four body potential functions available in DL POLY 2 An important distinction between these and intramolecular bond forces in DL POL
6. nlist_builders pmf_lf pmf_terms pmf_vv strucopt temp_scalers tether_terms utility_pack vv motion 1 vv_rotation_1 vv_rotation_2 dlpoly define_system define_system define_system ensemble_tools ewald_terms ewald_terms_4pt ewald_terms_rsq four_body_terms hkewald_terms nlist_builders spme_terms temp_scalers tersoff_terms 278 CCLRC invert invert invfrc jacobi kinstress kinstress kinstress kinstress kinstress kinstress kinstressf kinstressf kinstressf kinstressf kinstressf kinstressg kinstressg kinstressg kinstressg lf integrate lowcase lowcase lowcase lowcase lowcase lowcase lowcase lowcase lowcase lowcase lowcase lowcase lowcase lowcase lowcase lowcase lowcase lowcase lowcase lowcase lowcase lrcmetal lrcmetal lrcorrect three body terms utility pack dlpoly define system dlpoly ensemble tools lf motion 1 pmf_lf pmf_vv vv_motion_1 ensemble_tools lf rotation 1 lf rotation 2 vv rotation 1 vv_rotation_2 ensemble_tools lf rotation 2 vv rotation 1 vv_rotation_2 dlpoly angle_terms bond_terms define_system define_system dihedral_terms dihedral_terms_4pt dihedral_terms_rsg external field terms four body terms inversion terms metal terms metal terms 4pt metal terms rs pmf terms setup program tersoff terms tether terms three body terms vdw terms vdw terms 4pt vdw terms rs define system dlpoly define system 279 CCLRC machine
7. potential n record 2n 1 potential n record 2n cross term 1 record 2n 1 atmnam 1 a8 first atom type atmnam 2 a8 second atom type variable a real potential parameter see Table 4 16 variable b real potential parameter see Table 4 16 cross term n n 1 2 record 2n n n 1 2 The variables pertaining to each potential are described in Table 4 16 Note that the fifth variable is the range at which the particular Tersoff potential is truncated The distance is in Table 4 16 Tersoff Potential key potential type Variables 1 5 6 11 a b functional form ters Tersoff Ala B b R Potential form single SiB n c d h as shown in Section cross X w 2 3 3 4 1 3 6 External Field The presence of an external field is flagged by the extern directive The next line in the FIELD file should have another directive indicating what type of field is to be applied On the following lines comes the mxf1d parameters five per line that describe the field In the include files supplied with DL_POLY 2 mxf1d is set to 10 The variables pertaining to each potential are described in table 4 17 4 1 3 7 Closing the FIELD File The FIELD file must be closed with the directive close CCLRC 134 Table 4 17 External fields key potential type Variables 1 4 functional formt elec Electric field E Ey E F 4 E oshm Oscillating Shear A n F Acos 2n7 z Lz shrx Cont
8. Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1460 error failed allocation of work arrays in nst_b1 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1470 error failed allocation of density array in nst bl f This is a memory allocation error Probable cause excessive size of simulated system CCLRC 225 Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1480 error failed allocation of work arrays in nst_h1 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1490 error failed allocation of density array in nst_h1 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1500 err
9. Either simulate the system with a periodic boundary or use another ensemble CCLRC 202 Message 391 incorrect number of pimd beads in config file The CONFIG file must specify the position of all the beads in a PIMD simulation not just the positions of the parent atoms otherwise this error results Action The CONFIG file must be reconstructed to provide the required data Message 392 error too many link cells requested The number of link cells required for a given simulation exceeds the number allowed for by the DL_POLY_2 arrays Action Standard user response Fix the parameter mxcell Message 394 error minimum image arrays exceeded The work arrays used in IMAGES have been exceeded Action Standard user response Fix the parameter mxxdf Message 396 error interpolation array exceeded DL POLY 2 has sought to read past the end of an interpolation array This should never happen Action Contact the authors Message 398 error cutoff too small for rprim and delr This error can arise when the multiple timestep option is used It is essential that the primary cutoff rprim is less than the real space cutoff rcut by at least the Verlet shell width delr preferably much larger DL POLY_2 terminates the run if this condition is not satisfied Action Adjust rcut rprim and delr to satisfy the DL_POLY_2 requirement These are defined with the directives cut prim and delr respectively Message 400 er
10. ification of four atomic positions The potential functions available in DL_POLY 2 are as follows 1 Cosine potential cos U dijkn A 1 cos mdijkn 2 31 2 Harmonic harm U ijkn kl ur 0 2 32 3 Harmonic cosine hcos U bitin 5 cos izkn cos o 2 38 4 Triple cosine cos3 U 5 A11 cos 6 5 Aa 1 cos 2 5 As 1 cos 3 2 34 5 Ryckaert Bellemans hydrocarbon potential ryck 5 U ijkn Alao S aicos 6 2 35 i 1 6 Ryckaert Bellemans fluorinated potential rbf 5 U bijen B bo Y gt bicos 2 36 i 1 7 OPLS angle potential U ijkn ao 0 5 a1 1 cos a2 1 cos 20 a3 1 cos 36 2 37 In these formulae ijkn is the dihedral angle defined by Auka COs Blr tan 2 38 with Gn Ejk X Tkn 2 39 GP Lkn Lij x eral x Tin CCLRC 25 With this definition the sign of the dihedral angle is positive if the vector product r j X Tik X Tjk X Tkn is in the same direction as the bond vector rj and negative if in the opposite direction The force on an atom arising from the dihedral potential is given by O fe arg U Pien 2 40 with being one of i j k n and a one of x y z This may be expanded into 1 O U ijkn 4 U dijkn Briss Lik Tkn 2 41 rg igkn Obijkn ijk ara Lig Eik kn ah The derivative of the functi
11. where u v are one or both of the components x y Note that although it is possible to define these contributions to the stress tensor it is not possible to calculate a pressure from them unless a finite arbitrary boundary is imposed on the z direction which is an assumption applied in DL POLY 2 but without implications of periodicity in the z direction The x y components define the surface tension however For bonded molecules as with the standard 3D Ewald sum it is necessary to extract contributions associated with the excluded atom pairs In the DL_POLY_2 HKE imple mentation this amounts to an a posteriori subtraction of the corresponding coulomb terms In DL_POLY_2 the HKE method is handled by several subroutines HKGEN constructs the hn s a convergence functions and their derivatives HKEWALD1 calculates the recipro cal space terms HKEWALD2 and HKEWALD3 calculate the real space terms and the bonded atom corrections respectively HKEWALD4 calculates the primary interactions in the multi ple timestep implementation 2 4 8 Reaction Field In the reaction field method it is assumed that any given molecule is surrounded by a spherical cavity of finite radius within which the electrostatic interactions are calculated explicitly Outside the cavity the system is treated as a dielectric continuum The occurence CCLRC 52 of any net dipole within the cavity induces a polarisation in the dielectric which in turn interacts with the g
12. 184 186 196 hexagonal prism 116 parallelpiped 184 186 196 rhombic dodecahedron 116 slab 196 truncated octahedron 116 CCP5 3 10 11 charge groups 119 151 189 195 constraints bond 4 5 18 57 59 68 69 72 74 83 84 88 89 121 142 150 151 180 185 189 190 205 Gaussian 45 60 150 PMF 59 122 CVS 6 7 direct Coulomb sum 41 42 44 distance dependant dielectric 44 51 107 113 205 distance restraints 20 DLPROTEIN 97 ensemble 6 203 205 Berendsen NoT 6 55 56 108 110 112 Berendsen NPT 6 55 56 110 112 Berendsen NVT 6 55 56 107 108 110 112 canonical 60 Evans NVT 6 55 56 108 110 112 Hoover NoT 6 55 56 110 Hoover NPT 6 55 56 108 110 Hoover NVT 6 55 56 110 microcanonical see ensemble NVE NVE 60 107 110 112 equations of motion Euler 71 rigid body 70 error messages 102 173 242 Ewald Hautman Klein 41 49 100 108 171 optimisation 98 100 SPME 7 41 47 82 98 109 151 summation 41 45 47 77 78 81 99 100 108 110 150 151 194 196 198 206 force field 4 16 18 26 40 98 175 190 AMBER 4 16 DL POLY 4 16 53 286 CCLRC Dreiding 4 16 34 151 152 GROMOS 4 16 OPLS 16 FORTRAN 90 6 8 FTP 10 12 Graphical User Interface 10 96 98 115 GROMOS 4 16 Hautman Klein Ewald see Ewald Hautman Klein Java GUI 5 10 licence 3 long range corrections Sutton Chen 39 van der Waals 33 minimi
13. 2 223 then choosing Yi mi t f t 2 224 Zimio t minimizes the least squares differences between the Newtonian and constrained trajecto ries Following Brown and Clarke 37 the algorithm is implemented in the LF scheme by calculating n 1 1 xAt 2 Text T n u t At 2n 1 v t 1 A yar 2 2 m r t At r t Ato t 5 At 2 225 where 7 is obtained from standard Verlet leapfrog integration Only one iteration is needed two if the system has bond constraints to constrain the instantaneous temperature to ex actly Text however energy is not conserved by this algorithm The algorithm is implemented in the DL POLY routine NVT El for systems with bond constraints The VV implementation of Evan s thermostat is as follows xt Jo mutA mivi t vt w t Swat v t Ai v t Ar fO 1 r t At r t Atv tt 5 At call rattle R 1 At f t At 5A call rattle V Xt rAt mi t At f VT t At v t At vt v t At oU t At At v t At 2 226 Routines rattle R and rattle V apply the bondlength and velocity constraint formulae 2 210 and 2 211 respectively The integration is performed by the subroutine NVTVV_E1 which calls subroutines RATTLE_R and RATTLE_V CCLRC 64 2 5 6 Barostats The size and shape of the simulation cell may be dynamically adjusted by coupling the sys tem to a barostat in order to
14. 3 2 2 22 2 2 2 2 82 267 Metal Potentials 2 24 6 daa ee g k s S 82 2 6 8 Summing the Atomic Forces 2 22 2 2 2 83 2 6 9 The SHAKE RATTLE and Parallel OSHAKE Algorithms 83 3 DL POLY 2 Construction and Execution 85 3 1 Constructing DL POLY 2 an Overview 2 87 3 1 1 Constructing the Standard Version 87 3 1 2 Constructing Nonstandard Versions I 88 3 2 Compiling and Running DL POLY2 2 i u 40 242 63 A RR ER allar ee 91 3 2 1 Compiling the Source Code I uu 91 S22 Running IL POLI 2 i secs ek k a ba eee A 94 Jao Restarting DL POLY 2 2 42 kalu ba d d Ree Rd R h 95 3 3 A Guide to Preparing Input Files 2 2 2 2 2 u 2 2 2 2 22 96 ool Inorganic Materials s sa 4 v 5 265664 buk du k X k s b a 96 3 8 2 Macromolecules 2 V k 4 40 9 RR FR V a kka k v a 97 9 9 43 Adding Solvent toa Structure es ea tes rerep aes 98 3 34 Analysing Results cso cosa I A 4 84 98 3 3 5 Choosing Ewald Sum Variables I 98 3 4 DL POLY 2 Error Processing 2 1 24 ra ma aca a mia Ko e YL 101 3 4 1 The DL_POLY _2 Internal Error Facility 101 4 DL_POLY_2 Data Files 103 4 1 The INPUT Al s Aka ba k ee BS HAGR RD RE PRE ERE UR 4 4 105 4 11 The CONTROL Fil amp 4 234264 84444 2 BSE aR Rea ee 105 412 The CONFIG File one l hls BR ee ee s 114 ala Tie FIELD Eil s v smuk l BA ae k std
15. DL POLY 2 has a fixed limit on the number of unique molecular sites in any given simu lation If this limit is exceeded the program terminates Action Standard user response Fix parameter mxsite Message 21 error duplicate tersoff potential specified The user has defined more than one Tersoff potential for a given pair of atoms types Action Locate the duplication in the FIELD file and correct Message 22 error unsuitable radial increment in TABLE file This arises when the tabulated potentials presented in the TABLE file have an increment that is greater than that used to define the other potentials in the simulation Ideally the increment should be r_cut magrid 4 where r_cut is the potential cutoff for the short range potentials and mxgrid is the parameter defining the length of the interpolation ar rays An increment less than this is permissible however Action The tables must be recalculated with an appropriate increment CCLRC 178 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 poten tials is different When DL_POLY_2 finds a change in the order of specification it assumes that the user has forgotten to enter one Action Check the FIELD and TABLE files Make sure that you correctly specify the pair potentials in
16. Do not confuse this error with that described by message 41 below Action Standard user response Fix the parameter mxtcon Message 41 error too many bond constraints in system DL POLY 2 sets a limit on the number of bond constraints in the simulated system as a whole This number is a combination of the number of molecules and the number of per molecule divided by the number of processing nodes Termination results if this number is exceeded Do not confuse this error with that described by message 40 above Action Standard user response Fix the parameter mxcons Message 42 error transfer buffer too small in mergel The buffer used to transfer data between nodes in the MERGE1 subroutines has been di mensioned too small Action Standard user response Fix the parameter mxbuff Message 45 error too many atoms in CONFIG file DL POLY 2 limits the number of atoms in the system to be simulated and checks for the violation of this condition when it reads the CONFIG file Termination will result if the condition is violated Action Standard user response Fix the parameter mxatms Consider the possibility that the wrong CONFIG file is being used e g similar system but larger size Message 46 ewlbuf array too small in ewald1 The ewlbuf array used to store structure factor data in subroutine EWALD1 has been di mensioned too small CCLRC 181 Action Standard user response Fix the parameter mxebuf
17. N 1 N yn A Upair i j i rj i l j gt i N 2N 1 N 5 Y Us voali j k rif Tr Tp i 1 j gt i k gt j N 1 N F 5 gt Urersoff i j Ti tj RY i l j gt i 3N 2N 1 N 5 XO V Ua body 1 j k n Pay Pps Ty n i l j gt i k gt j n gt k N yp U metal i Ti RN 1 N S gt Uertn i ri vi 2 1 i l where Ubond U angle Udihed Uinv Upair U3_body UTersoff and Ua_body are empirical in teraction functions representing chemical bonds valence angles dihedral angles inversion angles pair body three body Tersoff many body covalent and four body forces respec tively The first four are regarded by DL_POLY_2 as intra molecular interactions and the CCLRC 17 next five as inter molecular interactions The term Umetal is a density dependent and therefore many body metal potential The final term Uecztn represents an external field potential The position vectors r rp T and rq refer to the positions of the atoms specifically involved in a given interaction Almost universally it is the differences in position that determine the interaction A special vector R is used to indicate a many body depen dence The numbers Npond Nangies Nainea and Niny refer to the total numbers of these respective interactions present in the simulated system and the indices tibond tangles tinv and igihed Uniquely specify an individual interaction of each type It is important to note that there is no global specificati
18. all internal accumulators timestep included to zero 3 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_2 force field in chapter 2 is essential reading The various utility routines mentioned in this section are described in greater detail in chapter 6 Many of these have been incorporated into the DL POLY 2 Graphical User Interface 8 and may be convienently used from there 3 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 The utility GENLAT TO constructs the CONFIG file for truncated octahedral boundary conditions Otherwise the input of force field data for crystalline systems is particularly simple if no angular forces are required notable exceptions to this are zeolites and silicate glasses see below Such systems require only the specification of the atomic types and the necessary pair forces The reader is referred to the description of the DL POLY 2 FIELD file for further details section 4 1 3 DL_POLY 2 allows the simulation of zeolites and silicate or other glasses Both these materials requir
19. but also results in a more coarse grain parallelism The consequence of which is that performance with a large number of processors will degrade more quickly than with the atomistic scheme Once the neighbour list has been constructed each node of the parallel computer may proceed independently to calculate the pair force contributions to the atomic forces 2 6 4 Modifications for the Ewald Sum For systems with periodic boundary conditions DL_POLY_2 employs the Ewald Sum to calculate the Coulombic interactions see section 2 4 5 CCLRC 82 Calculation of the real space component in DL_POLY_2 employs the algorithm for the calculation of the nonbonded interactions outlined above The reciprocal space component is calculated using the schemes described in 44 in which the calculation can be paral lelised by distribution of either k vectors or atomic sites Distribution over atomic sites requires the use of a global summation of the q exp ik r terms but is more efficient in memory usage Both strategies are computationally straightforward Subroutine EWALD1 distributes over atomic sites and is often the more efficient of the two approaches Subrou tine EWALD1A distributes over the k vectors and may be more efficient on machines with large communication latencies Other routines required to calculate the ewald sum include EWALD2 EWALD3 and EWALD4 The first of these calculates the real space contribution the second the self int
20. bv1 exp rij p1 Tik P2 bvs2 Truncated Vessal 25 k 6 a p U 0 k 0 0 00 0 bo 27 874 bv2 8 00 T 00 expl r ri p hcos Harmonic Cosine k 00 U 0 amp cos 0 cos 0o hcs cos Cosine Allm U 0 A 1 cos m cos mmsb MM Stretch bend A Oo dab dac U 0 A 0 00 Tab dab Tac dac msb 10 is the a b c angle Note valence angle potentials with a dash as the first character of the keyword do not contribute to the excluded atoms list see section 2 1 In this case DL POLY 2 will calculate the nonbonded pair potentials between the described atoms CCLRC 125 9 10 11 dihedrals n where n is the number of dihedral interactions present in the molecule Each of the following n records contains dihedral key ad potential key See table 4 9 index 1 integer first atomic index index 2 integer second atomic index index 3 integer third atomic index index 4 integer fourth atomic index variable 1 real potential parameter see table 4 9 variable 2 real potential parameter see table 4 9 variable 3 real potential parameter see table 4 9 variable 4 real 1 4 electrostatic interaction scale factor variable 5 real 1 4 Van der Waals interaction scale factor The meaning of the variables 1 3 is given in table 4 9 The variables 4 and 5 specify the scaling factor for the 1 4 electrostatic and Van der Waals nonbonded interactions
21. fldscan gdsum getrec getword lowcase error copystring error getrec error copystring error getrec getword warning error bspcoe bspgen cpy_rtc dcell dcft3 dlpfft3 ele_prd error gdsum invert scl_csum set_block spl_cexp spme_for error images dcell diffsn0 diffsni error gdsum 263 CCLRC system_properties system_properties system_properties system_properties system_properties temp_scalers temp_scalers temp_scalers temp_scalers temp_scalers temp_scalers temp_scalers temp_scalers temp_scalers temp_scalers temp_scalers tersoff_module tersoff_terms tersoff_terms tersoff_terms tersoff_terms tersoff_terms tersoff_terms tersoff_terms tersoff_terms tersoff_terms tersoff_terms tersoff_terms tersoff_terms tether_module tether_terms tether_terms tether_terms tether_terms tether_terms tether_terms tether_terms tether_terms tether_terms three_body_module three_body_terms three_body_terms three_body_terms three_body_terms merge rdf1 revive timchk zden1 error gdsum gstate images invert merge mergel guatgnch shlmerge shmove splice error copystring dcell error gdsum getrec getword gstate invert lowcase tergen terint tersoff3 error copystring error gdsum getrec getword gstate images lowcase strip error copystring dcell error gdsum 264 CCLRC three_body_terms three_body_terms three_body_terms three_body_terms three_body_terms timchk utility_pack uti
22. for the Cray FFT routines e CFFTW for the FFTW public domain FFT routines e CESSL for the IBM scientific library FFT routines e CSGIC for the Silicon Graphics FFT routines The appropriate lines should be uncommented and the references to the DLPFFT3 subroutine should be commented out before compiling 3 Problems with optimization Some subroutines may not compile correctly when using optimization on some com pilers This is not the fault of the DL POLY 2 code but of the compiler concerned This is circumvented by compiling the offending subroutines unoptimised See the entries for various machines in the makefile to see how this is done if you experience problems with other subroutines 4 Adding new functionality To include a new subroutine in the code simply add subroutine o to the list of object names in the makefile The simplest way is to add names to the OBJ_ALL list CCLRC 94 3 2 1 3 Note on Interpolation Schemes In DL POLY 2 the short range Van der Waals contributions to energy and force are evaluated by interpolation of tables constructed at the beginning of execution DL POLY 2 caters for three different interpolation schemes 3 point and 4 point in r space and linear interpolation in r space Tabulation in r avoids the use of the square root function in evaluation of the non bonded interactions and thus typically decreases execution time by 10 15 Note that tabulation in r usually requires more
23. forces and ionic forces also The calculation of the three four body terms is distributed over processors on the basis of the identity of the central atom in the bond A global summation is required to specify the atomic forces fully 2 6 7 Metal Potentials The simulation of metals by DL POLY 2 makes use of density dependent potentials of the Sutton Chen type 3 The dependence on the atomic density presents no difficulty however as this class of potentials can be resolved into pair contributions This permits the use of the distributed Verlet neighbour list outlined above CCLRC 83 2 6 8 Summing the Atomic Forces The final stage in the RD strategy is the global summation of the atomic force arrays This must be done After all the contributions to the atomic forces have been calculated To do this DL POLY 2 employs a global summation algorithm 42 which is generally a system specific utility Similarly the total configuration energy and virial must be obtained as a global sum of the contributing terms calculated on all nodes 2 6 9 The SHAKE RATTLE and Parallel OSHAKE Algorithms The SHAKE and RATTLE algorithms are methods for constraining rigid bonds Parallel adaptations of both are couched in the Replicated Data strategy The essentials of the methods are as follows 1 The bond constraints acting in the simulated system are shared equally between the processing nodes 2 Each node makes a list recording which atoms are bo
24. gdsum gdsum gdsum gdsum gdsum gdsum gdsum gdsum gdsum gdsum gdsum gdsum define_system define_system define_system define_system basic_comms utility_pack dlpoly error dlpoly dlpoly dlpoly setup_program dlpoly dlpoly vdw_terms vdw_terms_4pt vdw_terms_rsg vdw_terms vdw_terms_4pt vdw_terms_rsg dlpoly define_system angle_terms bond_terms core_shell_terms define_system dihedral_terms dihedral_terms_4pt dihedral_terms_rsg dlpoly ensemble_tools ewald_terms ewald_terms_4pt ewald_terms_rsg force_drivers four_body_terms hkewald_terms inversion_terms kinetic_terms 1f_motion_1 lf rotation 2 merge_hcube merge_systol merge_tools 274 CCLRC gdsum gdsum gdsum gdsum gdsum gdsum gdsum gdsum gdsum gdsum gdsum gdsum gdsum gdsum gdsum gdsum gdsum gdsum gdsum getcom getcom getcom getcom getcom getcom getking getking getking getrec getrec getrec getrec getrec getrec getrec getrec getrec getrec getrec getrec getrec getrec getrec getrec metal_terms metal_terms_4pt metal_terms_rsq pmf_lf pmf_vv rigid_body_terms setup_program spme_terms system_properties temp_scalers tersoff_terms tether_terms three_body_terms utility_pack vdw_terms vdw_terms_4pt vdw_terms_rsq vv motion 1 vv rotation 2 lf motion 1 lf rotation 1 lf rotation 2 vv motion 1 vv_rotation_1 vv_rotation_2 ensemble_tools vv_rotation_1 vv_rotation_2 angle_terms bond_terms core_shell_terms
25. gstate gstate gstate gstate gstate gstate gstate gstate gstate gstate gstate gstate gstate gstate gstate gstate gstate gsync gsync gsync gsync gsync gsync gsync hkewaldi vv_rotation_1 vv_rotation_2 basic_comms define_system nlist_builders parse_tools pass_tools dlpoly angle_terms bond_terms define_system dihedral_terms dihedral_terms_4pt dihedral_terms_rsg exclude_terms force_drivers four_body_terms inversion_terms lf integrate lf motion 1 lf rotation 1 lf rotation 2 merge_hcube merge_systol merge_tools nlist_builders parse_tools pass_tools temp_scalers tersoff_terms tether_terms three_body_terms vv_integrate vv_motion_1 vv_rotation_1 vv_rotation_2 dlpoly error merge_hcube merge_systol merge_tools parse_tools pass_tools force_drivers 277 CCLRC hkewald2 hkewald3 hkewald4 hkgen images images images images images images images images images images images images images images images images images images images images images images images images images images initcomms intlist invert invert invert invert invert invert invert invert invert invert invert invert force_drivers force_drivers force_drivers force_drivers angle_terms bond_terms core_shell_terms define_system dihedral_terms dihedral_terms_4pt dihedral_terms_rsq force_drivers inversion_terms 1f_motion_1 lf rotation 1 lf rotation 2 metal terms metal terms 4pt metal terms rs
26. petri alr Ut gg Fat falra gotra x 4 2 gt i sedd 2 105 J O Vij gra ale riz fA Tij wa eln ga Tis I A Tij Palo gg etn x 4 6 Sy a 2 106 and from the third angular term O Jolris Faria ge Yu folrij falrij Xij X 1 ae oe P Tl pm m Tl pm l a z 1 LZ i m gra E gt 2 107 where pp B Wik Jo rik g 0 ijk 2 108 K arg k i j The angular term can have three different contributions depending on the index of the particle participating in the interaction o L Z L Dijk ar ore erw fc rik ara ad wl 2 109 l i XO wik folrik 2 Oijk 2 110 J are a Cik r r ijk CA ij apt wie tate ft y 2 111 CCLRC 37 The derivative of 9 6 is worked out in the following manner Og 1 J tag Tik ag O 2112 ara jk olijk sin Ok Or Tij Tik where Og ijk 2 hi COS Uk sin Vijk 2 113 olijk d hi COS a ME te rik ri 65 by lt ber by Ore TijTik 22 2 Lg ae re ri cos 0jir fos dei Ox ed 2 114 Tij Tik The contribution to be added to the atomic virial can be derived as O Erersoff 3V OU 3V 2 11 a OV 2 gt OV a 1 O weg 3 feront gefn tales Tij 1 a ms oe 5 fot AW Xij 1 Bm B m g Li 1x 2 116 XO wik 9 Oijk k i j 2 falra Tik Orik The contribution to be added to the atomic stress t
27. 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 a4 potential key See table 4 10 index 1 integer first atomic index index 2 integer second atomic index index 3 integer third atomic index index 4 integer fourth atomic index variable 1 real potential parameter see table 4 10 variable 2 real potential parameter see table 4 10 The meaning of the variables 1 2 is given in table 4 10 This directive and associated data records need not be specified if the molecule contains no inversion angle terms See the note on the atomic indices appearing under the shell directive above rigid n where n is the number of rigid units in the molecule It is followed by at least n records each specifying the sites in a rigid unit m integer number of sites in rigid unit site 1 integer first site atomic index CCLRC 126 Table 4 9 Dihedral Angle Potentials key potential type Variables 1 4 functional form cos Cosine A lm U A 1 cos m harm Harmonic k 0o U 6 k do hcos Harmonic cosine k o U 4 E cos cos o cos3 Triple cosine A Ap 43 U LA1 1 cos 6 5 A2 1 cos
28. shrx n TA z gt 20 2 135 4 Gravitational field grav F F mH 2 136 5 Magnetic field magn F Fi qi vi AH 2 137 6 Containing sphere sphr F A Ro r gt gt Reut 2 138 7 Repulsive wall zbnd F A z z A 2 139 It is recommended that the use of an external field should be accompanied by a thermostat this does not apply to examples 6 and 7 since these are conservative fields The user is advised to be careful with units In DL POLY 2 external field forces are handled by the routine EXTNFLD CCLRC 41 2 4 Long Ranged Electrostatic Coulombic Potentials DL POLY 2 incorporates several technigues for dealing with long ranged electrostatic po tentials These are as follows 1 Atomistic and charge group implementation 2 Direct Coulomb sum 3 Truncated and shifted Coulomb sum 4 Coulomb sum with distance dependent dielectric 5 Ewald sum 6 Smoothed Particle Mesh Ewald SPME 7 Hautman Klein Ewald for systems with 2D periodicity 8 Reaction field 9 Dynamical shell model 10 Relaxed shell model Some of these techniques can be combined For example 1 3 and 4 can be used in conjunc tion with 9 The Ewald sum SPME and Hautman Klein Ewald are restricted to periodic or pseudo periodic systems only though DL POLY 2 can handle a broad selection of periodic boundary conditions including cubic orthorhombic parallelepiped truncated octahedral hexagonal prism and
29. un 7 Lut gt AN Vela 740 NO t At lt At v t 5At n t AN r t GAN Rol ret At 5 rt r A 2 229 Like the LF Nos Hoover thermostat several iterations are required to obtain self consis tency DL_POLY_2 uses 4 iterations 5 if bond constraints are present with the standard Verlet leapfrog predictions for the initial estimates of T t P t v t and r t 5 At Note also that the change in box size requires the SHAKE algorithm to be called each iteration with the new cell vectors and volume obtained from V t At V t exp sa n t 5A H t At exp K n t 540 H t 2 230 where H is the cell matrix whose columns are the three cell vectors a b c The isotropic changes to cell volume are implemented in the DL POLY LF routine NPT H1 which allows for systems containing bond constraints The implementation in the VV algorithm follows the scheme xt GAD de SEB Tea SE Wl kui vt a Sheet Janets nor st Se EO mW Ra xn va ai an 1 At f t yth AD w IO 1 r t At r t Atu t 5 At call rattle R V t At V t exp sat n t 340 H t At exp Atn 5 A9 H t At f t At 2 m 1 v t At u t At CCLRC 66 call rattle V Af At KAU mA ntk sa STEN e A Rea x E Atle At At v t A6 V t At n t Atv t At 1 2 AtNrk At xt A x t 5 At 20 SA Te gg Walt At
30. 2 5 A3 1 cos 3 ryck Ryckaert A U 6 A ao aicos azcos a3C0536 Bellemans agcos d ascos ag as pre set rbf Fluorinated B U 6 B bo bicos bacos b b3cos d Ryckaert bacos bscos beexp b7 T Bellemans bo be pre set opls OPLS Ao Ai A2 As U d Ao A1 1 cos 6 A2 1 cos 2 A3 1 cos 3 tb is the a b c d dihedral angle site 2 integer second site atomic index site 3 integer third site atomic index etc site m integer m th site atomic index Up to 15 sites can be specified on the first record Additional records are used if necessary Up to 16 sites are specified per record thereafter This directive and associated data records need not be specified if the molecule contains no rigid units See the note on the atomic indices appearing under the shell directive above 12 teth n where n is the number of tethered atoms in the molecule It is followed by n records specifying the tethered sites in the molecule tether key ad tethering potential key see table 4 11 index integer atomic index CCLRC 127 Table 4 10 Inversion Angle Potentials key potential type Variables 1 2 functional form harm Harmonic k Qo U 6 ikl o hcos Harmonic cosine k oo U E cos cos 60 plan Planar A U A 1 cos t is the inversion angle
31. 2 147 where a 8 are x y z components The atomic stress tensor is symmetric In DL POLY 2 these forces are handled by the routine COUL1 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 The potential is thus gigj 1 Tij 2 U rii 2 148 ij AT EO Z Kai l with the force on atom j given by gig 1 1 2 149 ATE z Tj with the force on atom i the negative of this This removes the heating effects that arise from the discontinuity in the forces at the cutoff in the simple truncated and shifted potential The physics of this potential however are little better It is only recommended for very crude structure optimizations CCLRC 44 The contribution to the atomic virial is which is not the negative of the potential term The contribution to be added to the atomic stress tensor is given by oe ne fe 2 151 where a 8 are x y z components The atomic stress tensor is symmetric In DL POLY 2 these forces are handled by the routine COUL4 2 4 4 Coulomb Sum with Distance Dependent Dielectric This potential attempts to address the difficulties of applying the direct Coulomb sum without the brutal truncation of the previous case It hinges on the assumption that the electrostatic forces are effectively screened in real systems an effect which is approximated by introducin
32. 2 checks all the pair potentials specified in the FIELD file and terminates the program if it can t identify any one of them from the atom types specified earlier in the file Action Correct the erroneous entry in the FIELD file and resubmit Message 82 error calculated pair potential index too large In checking the pair potentials specified in the FIELD file DL POLY 2 calculates a unique integer index that henceforth identifies the potential within the program If this index becomes too large termination of the program results Action Standard user response Fix the parameters mxsvdw and mxvdw Message 83 error too many three body potentials specified DL_POLY 2 has a limit on the number of three body potentials that can be defined in the FIELD file This error results if too many are included Action Standard user response Fix the parameter mxtbp Message 84 error unidentified atom in 3 body potential list DL POLY 2 checks all the 3 body potentials specified in the FIELD file and terminates the program if it can t identify any one of them from the atom types specified earlier in the file CCLRC 187 Action Correct the erroneous entry in the FIELD file and resubmit Message 85 error required velocities not in CONFIG file If the user attempts to start up a DL_POLY 2 simulation with the restart or restart scale directives see description of CONTROL file the program will expect the CONFIG file to contain
33. 3 3cos n rij Rig rig Rig Rs lt Tij lt Sij 2 99 0 Tij gt Sij ig x UHAT LE VE Lig J folrin wir 9 Oij ki j 9 Oij ci d c d hi COS Dijk 2 100 with further mixed parameters defined as aij ai 05 2 bij b b 2 Ag AA Big BiB 2 101 Rij RiR 5 Sij SS Here i j and k label the atoms in the system rj is the length of the ij bond and 0 is the bond angle between bonds ij and ik Single subscripted parameters 11 such as a and ni depend only on the type of atom The chemistry between different atom types is encapsulated in the two sets of bi atomic parameters Xi and wij X 1 Xij Xji Wii 1 4 Wij Wji 5 2 102 which define only one independent parameter for each pair of atom types The x parameter is used to strengthen or weaken the heteropolar bonds relative to the value obtained by simple interpolation The w parameter is used to permit greater flexibility when dealing with more drastically different types of atoms CCLRC 36 The force on an atom derived from this potential is formally calculated with the formula 3 fr F Ptersoff D 2 103 Ors a with atomic label being one of i j k and a indicating the x y z component The derivative in the above formula expands into Oui O O Or org teti alrij W grasou Falris Solna Faria ga Yu 2 104 with the contributions from the first two terms being
34. Case 17 Sodium ion in SPC water A simple simulation of a sodium ion in 140 SPC water molecules 421 sites in all The water molecules are treated as rigid bodies The algorithm is the NVE ensemble and the Ewald sum handles the electrostatic forces The MD box is cubic NVE ensemble 5 1 1 18 Test Case 18 Sodium chloride molecule in SPC water This system resembles test case 17 except that a sodium chloride ion pair is dissolved in 139 SPC water molecules 419 sites in all The MD cell is cubic and the water molecules CCLRC 153 are treated by constraint dynamics in the NVE Evans scheme Ewald s method handles the electrostatics NVT Evans ensemble 5 1 1 19 Test Case 19 Sodium chloride molecule in SPC water This is a repeat of test case 18 except that half of the water molecules are treated using constraint dynamics and the rest by rigid body dynamics The integration algorithm is NPT Hoover NPT Hoover ensemble 5 1 1 20 Test Case 20 Linked benzene ring molecules This test consists of pairs of benzene rings linked via a rigid constraint bond Each molecule has 22 atoms and there are 81 molecules making a total of 1782 sites The benzene rings are treated in a variety of ways in the same system In one third of cases the benzene rings and hydrogens form rigid groups In another third the carbon rings are rigid but the C H bonds are treated via constraints In the final third the C H bonds are fully flexible and the rings are
35. Metal potentials in DL POLY 2 are based on the Finnis Sinclair model 29 The explicit form of potential in DL_POLY_2 is confined to the formulation of Sutton and Chen 3 and Rafii Tabar and Sutton 47 These are also non bonded potentials and are characterised by atom types rather than specific atomic indices The input of metal potential data is signalled by the directive metal n where n is the number of metal potentials to be entered There follows n records each specifying a particular metal potential in the following manner atmnam 1 a8 first atom type atmnam 2 a8 second atom type key a4 potential key See table 4 15 variable 1 real potential parameter see table 4 15 variable 2 real potential parameter see table 4 15 variable 3 real potential parameter see table 4 15 variable 4 real potential parameter see table 4 15 variable 5 real potential parameter see table 4 15 The variables pertaining to each potential are described in table 4 15 Note that any metal potential not specified in the FIELD file will be assumed to be zero CCLRC 132 Table 4 15 Definition of metal potential functions and variables key potential type Variables 1 5 functional form _ fi a stch Sutton Chen e a n m C U r e as Cyril Pi X ji F The Sutton Chen potential will handle alloys but care must be taken to enter the cross terms of the potentials explicitly Note that the rules f
36. SHQNCH performs the temperature scaling The dynamical shell model is used in conjunction with the methods for long range forces described above CCLRC 54 2 4 10 Relaxed Shell Model The relaxed shell model is based on the same electrostatic principles as the dynamical shell model but in this case the shell is assigned a zero mass This means the shell cannot be driven dynamically and instead the procedure is first to relax the shell to a condition of zero or at least negligible force at the start of the integration of the atomic motion and then integrate the motion of the finite mass core by conventional molecular dynamics The relaxation of the shells in DL POLY 2 is accomplished using conjugate gradients Since each timestep of the algorithm entails a minimisation operation the cost per timestep for this algorithm is considerably more than the adiabatic shell model however the integration timestep permitted is much larger as much as a factor 10 so evolution through phase space is not necessarily very different in cost A description of the method is presented in 35 2 5 Integration algorithms 2 5 1 The Verlet Algorithms DL_POLY integration algorithms are based on the Verlet scheme which is both time re versible and simple 11 It generates trajectories in the microcanonical NVE ensemble in which the total energy kinetic plus potential energy is conserved If this property drifts or fluctuates excessively in the course of a s
37. Try reducing the timestep or running a zero kelvin structure optimization for a hundred timesteps or so It is unlikely that simply increasing the iteration number will cure the problem but you can try follow the standard user response to increase the parameter mxquat But the trouble is much more likely to be cured by careful consideration of the physical system being simulated For example is the system stressed in some way Too far from equilibrium Message 330 error mxewld parameter incorrect DL_POLY_2 has two strategies for parallelization of the reciprocal space part of the Ewald sum If EWALD1 is used the parameter mxewld should equal the parameter msatms If EWALDIA is used this parameter should equal mxatms Action Standard user response Set the parameter mxewld to the value appropriate for the version of EWALD1 you are using Recompile the program Message 331 error mxhke parameter incorrect The parameter mxhke which defines the dimension of some arrays used in the Hautman Klein Ewald method should equal the parameter msatms CCLRC 199 Action Standard user response Set the parameter mxhke to the value regquired Recompile the program Message 332 error mxhko parameter too small The parameter mxhko defines the maximum order for the Taylor expansion implicit in the Hautman Klein Ewald method DL POLY 2 has a maximum of mxhko 3 but it can be set to less in some implementations If this error arises when
38. a DL_POLY_2 job 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 CCLRC 106 invoke a particular operation or provide numerical parameters Also associated with each directive may be one or more keywords which may qualify a particular directive by for example adding extra options Directives have the following general form keyword options data The keyword and options are text fields while the data options are numbers integers or reals Directives can appear in any order in the CONTROL file except for the finish directive which marks the end of the file Some of the directives are mandatory for example the timestep directive that defines the timestep others are optional This way of constructing the file is very convenient but it has inherent dangers It is for example quite easy to specify the same directive more than once or specify contradictory directives or invoke algorithms that do not work together By and large DL_POLY_2 tries to sort out these difficulties and print helpful error messages but it does not claim to be foolproof Fortunately in most cases the CONTROL file will be small and easy to check visually It is important to think carefully about a simulation beforehand and ensure that DL POLY 2 is being asked to do something that is physically reasonable It should also be remembered that the present capabilite
39. algorithm These rigid bodies may even be linked to other species including other rigid bodies by extensible bonds However if a rigid body is linked to an atom or another rigid body by a bond constraint the above algorithms are not adequate The reason is that the constraint will introduce an additional force and torque on the body that can only be found after the integration of the unconstrained unit DL POLY 2 has a suite of integration algorithms to cope with this situation in which both the constraint conditions and the quaternion equations are solved similtaneously using an extension of the SHAKE algorithm called QSHAKE 16 It has been cast in both LF and VV forms We will describe here how it works for VV the LF version is decribed in 16 Firstly we assume a rigid body A is connected to another B at timestep t nAt via bonds between atoms at positions Tip and T bp given by Tip Rat day T p B dbp 2 268 where R represents the rigid body COM and d the displacement of the atom from the relevant COM The subscript p indicates that these are the atoms providing the links In the first stage of the VV QSHAKE algorithm the rigid bodies are allowed to move unrestricted Our task is then to find the the constraint force G 4p which would preserve the constraint bondlength i e d4 a dihp Assuming we know this force we can write 1 n 1 At RY R M GB 2 269 in which the tilde X indicates the corresponding variable c
40. anisotropy such as a surface These four parameters may also be set explicitly by the ewald sum directive in the CONTROL file For example the directive ewald sum 0 35 6 6 8 CCLRC 99 would set a 0 35 A7 kmax1 6 kmax2 6 and kmax3 8 The quickest check on the accuracy of the Ewald sum is to compare the Coulombic energy U and the coulombic virial W in a short simulation Adherence to the relationship U W shows the extent to which the Ewald sum is correctly converged These variables can be found under the columns headed eng_cou and vir_cou in the OUTPUT file see section 4 2 2 The remainder of this section explains the meanings of these parameters and how they can be chosen The Ewald sum can only be used in a three dimensional periodic system There are three variables that control the accuracy a the Ewald convergence parameter Teut the real space forces cutoff and the kmax1 2 3 integers that effectively define the range of the reciprocal space sum one integer for each of the three axis directions These variables are not independent and it is usual to regard one of them as pre determined and adjust the other two accordingly In this treatment we assume that reut defined by the cutoff directive in the CONTROL file is fixed for the given system The Ewald sum splits the electrostatic sum for the infinite periodic system into a damped real space sum and a reciprocal space sum The rate of convergence of both su
41. as inter molecular Firstly the atoms involved are defined by atom types not specific indices Secondly there are no excluded atoms arising from the four body terms The inclusion of other potentials for example pair potentials may in fact be essential to maintain the structure of the system The four body potentials are very short ranged typically of order 3 A This property plus the fact that four body potentials scale as N4 where N is the number of particles makes it essential that these terms are calculated by the link cell method 28 The calculation of the forces virial and stress tensor described in the section on inversion angle potentials above DL POLY 2 applies no long range corrections to the four body potentials The four body forces are calculated by the routine FBPFRC 2 3 5 Metal Potentials DL_POLY 2 includes density dependent potentials suitable for calculating the properties of metals The basic model is due to Finnis and Sinclair 29 as implemented by Sutton and Chen 3 The form of the potential is stch Use z oyal 2 121 i lt j Vi where the local density p is given by p 2 122 The Sutton Chen potential has the advantage that it is decomposable into pair contributions and thus falls within the general tabulation scheme of DL POLY 2 where it is treated as a short ranged interaction The same form of potential may be used in alloys through the appropriate choice of parameter
42. constant pressure simulations keyword en semble nst in the CONTROL file are only possible if the stress tensor is calculated If isotropic constant pressure simulations are required where the cell volume but not the shape may vary keyword ensemble npt the stress tensor need not be calculated Chapter 5 DL POLY 2 Examples 148 CCLRC 149 Scope of Chapter This chapter describes the standard test cases for DL POLY 2 the input and output files for which are in the data sub directory CCLRC 150 5 1 DL POLY Examples 5 1 1 Test Cases The following example data sets both input and output are stored in the subdirectory data Two versions are provided for the Leapfrog LF and Velocity Verlet VV algorithms respectively so that you may check that your version of DL_POLY is working correctly All the jobs are short and should require no more than a few minutes execution time even on a single processor computer he test cases can be chosen by typing select na from the execute directory where n is the number of the test case and a is either LF or VV The select macro will copy the appropriate CONTROL CONFIG and FIELD files to the execute directory ready for execution The output files OUTPUT REVCON and STATIS may be compared with the files supplied in the data directory The example output files provided in the data directory were obtained on 8 processors of a Cray XD1 parallel system The program was compiled wit
43. directory contents is to be found in the DL POLY 2 Reference Manual 6 1 Miscellaneous Utilities 6 1 1 Useful Macros 6 1 1 1 Macros Macros are simple executable files containing standard unix commands A number of the are supplied with DL_POLY and are found in the execute sub directory The available macros are as follows e cleanup e copy e gopoly e gui e select e store The function of each of these is described below It is worth noting that most of these functions can be performed by the DL POLY 2 java GUI 8 6 1 1 2 cleanup cleanup removes several standard data files from the execute sub directory It contains the unix commands rm OUTPUT REVCON REVOLD STATIS REVIVE gopoly and removes the files OUTPUT REVCON REVOLD STATIS REVIVE and gopoly all variants It is useful for cleaning the sub directory up after a run Useful data should be stored elsewhere however 6 1 1 3 copy copy invokes the unix commands mv CONFIG CONFIG OLD mv REVCON CONFIG mv REVIVE REVOLD CCLRC 157 which collectively prepare the DL_POLY files in the execute sub directory for the continu ation of a simulation It is always a good idea to store these files elsewhere in addition to using this macro 6 1 1 4 gopoly gopoly is used to submit a DL POLY job to the Daresbury IBM SP 2 which operates a LOADLEVELLER job queuing system It invokes the following script min_processors 4 max_processors 4 job_t
44. dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly define_system define_system define_system vv_rotation_2 pmf_vv pmf_lf pmf_lf 282 CCLRC pmf_vectors pmflf pmfvv primlst prneulst grattle_r grattle_v gshake guatbook guatgnch guatgnch guatgnch guench rdf0 rdfOneu rdf1 rdrattle r rdrattle r rdrattle_v rdrattle_v rdrattle_v rdshake_1 rdshake_1 rdshake_1 relax_shells result revive revive rotate_omega scdens scl_csum set_block shellsort shellsort shlfrc shlmerge shlgnch shlgnch shmove shmove shmove shmove shmove simdef pmf_vv lf integrate vv_integrate force_drivers force_drivers vv_rotation_2 vv_rotation_2 lf rotation 2 define system define system dlpoly temp scalers define system force drivers force drivers system properties vv motion 1 vv_rotation_1 pmf_vv vv motion 1 vv_rotation_1 lf motion 1 lf rotation 1 pmf_lf dlpoly dlpoly dlpoly system_properties vv_rotation_2 force_drivers spme_terms spme_terms define_system nlist_builders dlpoly temp_scalers define_system dlpoly lf motion 1 lf rotation 2 temp scalers vv motion 1 vv rotation 2 dlpoly 283 CCLRC spl_cexp splice splice splice splice splice splice splice spme_for srfrce srfrceneu static strip strip strip strip strucopt suttchen sysbook sysdef sysgen sysinit systemp tergen terint tersoff tersoff3 tethfrc thbfrc timchk timchk traject update_guaternions update
45. eee aR S 117 ua The REVOLD File cc kk d A k wi a Be ee eo dU a ee 134 AlS The TABLE Fil ri k is RO ae Goes b la ee k 135 42 The QUTPUT Piles oo Bak tee hvar wn ap eee ie Pe ee A 138 A21 The HISTORY File V 2440 k RaW eR ua 404 ED a 138 CCLRC A22 The OUTPUT Fil amp i aso wa eed Sie TR arr OS a are eos 423 The REVCON File see RY tose tea EU ata ut dia ub 4223 The REVIVE Pile c a am d e REU bo lk OE RO A amp 425 The RDPFDAT File 4 24 9 5 s bk svsk ssda bk k tduhas 4 2 6 The ZDNDAT File u u u k k a k a s k k k k k c AQ The STATIS Piles sator fe poded oein we Y ska v 5 DL_POLY_2 Examples Bil DL PODLY Examples x v ktu 55 k k 4 n ERE bk wn eS Bol Test Case ok eae k eae we be Re ee S k D 12 Benchmark Cases 4 v i ubuvsdss sss sk usi uahu s 6 DL_POLY 2 Utilities 6 1 Miscellaneous Utilities sc p s oo sace ks 6 11 s n Macros ea ce acea Bee p as MU GR A GN Bibliography Appendices The DL_POLY_2 Makefile Periodic Boundary Conditions in DL_POLY DL_POLY Error Messages and User Action Subroutine Locations Called Subroutines H E 9 a w k Calling Subroutines Index 148 150 150 153 155 156 156 159 162 162 167 173 243 252 269 286 List of Tables 4 1 4 2 4 3 4 4 4 9 4 6 4 7 4 8 4 9 4 10 4 11 4 12 4 13 4 14 4 15 4 16 4 17 Internal Restart Key soco coaer i ee k ee a 4 4 112 Internal Ensemble
46. follows 1 3 4 Using the known atomic coordinates r each node calculates a subset of the forces acting between the atoms These are usually comprised of atom atom pair forces e g Lennard Jones Coulombic etc non rigid atom atom bonds c valence angle forces dihedral angle forces improper dihedral angle forces The computed forces are accumulated in incomplete atomic force arrays J inde pendently on each node The atomic force arrays are summed globally over all nodes The complete force arrays are used to update the atomic velocities and positions It is important to note that load balancing i e equal and concurrent use of all processors is an essential requirement of the overall algorithm In DL POLY 2 this is accomplished for the pair forces with an adaptation of the Brode Ahlrichs scheme 22 2 6 2 Distributing the Intramolecular Bonded Terms DL POLY 2 handles the intramolecular in which the atoms involved in any given bond term are explicitly listed Distribution of the forces calculations is accomplished by the following scheme 1 2 Every atom in the simulated system is assigned a unique index number from 1 to N Every intramolecular bonded term Ujype in the system has a unique index number itype from 1 to Niype where type represents a bond angle or dihedral A pointer array Keytype type itype Carries the indices of the specific atoms involved in the potential
47. for imcon gt 0 cell 1 9 a b and c cell vectors real 8 record iii xxx 1 natms atomic x coordinates real 8 record iv yyy 1 natms atomic y coordinates real 8 record v zzz 1 natms atomic z coordinates real 8 record vi only for keytrj gt 0 vxx 1 natms atomic velocities x component real 8 record vii only for keytrj gt 0 vyy 1 natms atomic velocities y component real 8 record viii only for keytrj gt 0 vzz 1 natms atomic velocities z component real 8 record ix only for keytrj gt 1 fxx 1 natms atomic forces x component real 8 record x only for keytrj gt 1 fyy 1 natms atomic forces y component real 8 record xi only for keytrj gt 1 fzz 1 natms atomic forces z component real 8 Note the implied conversion of integer variables to real on record i CCLRC 141 4 2 2 The OUTPUT File The job output consists of 7 sections Header Simulation control specifications Force field specification Summary of the initial configuration Simulation progress Summary of statistical data Sample of the final configuration and Radial distribution functions These sections are written by different subroutines at various stages of a job Creation of the OUTPUT file always results from running DL_POLY 2 It is meant to be a human readable file destined for hardcopy output 4 2 2 1 Header Gives the DL POLY 2 version number the number of processors used and a title for the jo
48. grid points and hence more memory than tabulation in r This is to ensure sufficient accuracy is retained at small r A guide to the minimum number of grid points mxgrid required for interpolation in r to give good energy conservation in a simulation is mxgrid gt 100 rcut rmin where rmin is the smallest position minimum of the non bonded potentials in the sys tem The parameter mxgrid is defined in the DL_PARAMS INC file and must be set before compilation A guide to the minimum number of grid points required for interpolation in r is mxgrid gt 100 rcut rmin where rmin is again the smallest position minimum of the non bonded potentials in the system For users in doubt as whether to use r or r space interpolation we recommend the former This is because tabulation in r is less demanding on memory reguirements and less prone to inaccuracy should too small a value of mxgrid or too large a value of rcut be used Tabulation in r is therefore the default option for DL_POLY r interpolation can be specified at compile time by making the executable with the directive TYPE rsq The other issue of concern to users is the choice of 3 or 4 point schemes in r space in terpolation The relative merits are as follows 4 point interpolation may permit a smaller number of grid points to be used in the interpolation tables thus saving on memory require ments 3 point interpolation is quicker than 4 point interpolation and normally s
49. gt gt gt gt Define default settings P BINROOT execute CC gcc EX DLPOLY X EXE BINROOT EX FC undefined SHELL bin sh STRESS STRESS TYPE 3pt Define object files OBJ_MOD setup_module o angles_module o bonds_module o config_module o core_shell_module o dihed_module o ewald_module o exclude_module o external_field_module o four_body_module o hkewald_module o inversion_module o metal_module o pmf_module o property_module o rigid_body_module o shake_module o site_module o spme_module o tether_module o three_body_module o vdw_module o parse_module o tersoff_module o pair_module o 162 CCLRC 163 OBJ_ALL angle_terms o bond_terms o core_shell_terms o coulomb_terms o define_system o dlpoly o error o exclude_terms o external_field_terms o force_drivers o four_body_terms o hkewald_terms o inversion_terms o neu_coul_terms o neu_ewald_terms o nlist_builders o pmf_terms o rigid_body_terms o setup_program o shake_terms o site_terms o spme_terms o strucopt o system_properties o temp_scalers o tether_terms o three_body_terms o timchk o traject o utility_pack o warning o tersoff_terms o parse_tools o ensemble_tools o kinetic_terms o OBJ_LF lf_integrate o lf_motion_1 o lf_rotation_1 o lf_rotation_2 o pmf_lf o OBJ_VV vv_integrate o vv_motion_1 o vv_rotation_1 o vv rotation 2 0 pmf_vv o OBJ_RRR dihedral_terms o ewald_terms o metal_terms o vdw_terms o OBJ_
50. harmonic and all atoms are explicit The link cell algorithm is in operation NVE ensemble 5 1 1 12 Test Case 12 Hautman Klein test case 2 This is a simple test system consisting of 1024 charged particles in a layer under NVE conditions Lennard Jones forces are used to keep the atoms apart The similation cell is square in the XY plane NVE ensemble 5 1 1 13 Test Case 13 Carbon Nanotube with Tersoff potential This system consists of 800 carbon atoms in a nanotube 41 7 A in length The MD cell is orthorhombic and square in the XY plane The integration algorithm is NPT Berendsen This is a test for the Tersoff potential NPT Berendsen ensemble 5 1 1 14 Test Case 14 Carbon Diamond with Tersoff potential This is another test of the Tersoff potential this time for the carbon diamond structure consisting of 512 atoms A cubic MD cell is used with a NST Hoover integration algorithm NST Hoover ensemble 5 1 1 15 Test Case 15 Silicon Carbide with Tersoff potential This is an alloy system consisting of 2744 atoms of silicon carbide in a diamond structure The potential function used is the Tersoff potential The integration algorithm is NPT Hoover and the initial MD cell is cubic NPT Hoover ensemble 5 1 1 16 Test Case 16 Magnesium Oxide with relaxed shell model Relaxed shell model of magnesium oxide with 324 sites The lattice is cubic and the integration algorithm is NST Berendsen NST Berendsen ensemble 5 1 1 17 Test
51. images merge abort_config_read abort_control_read abort_field_read check_shells check_syschg copystring dcell define_angles define_atoms define_bonds define_constraints define_core_shell define_dihedrals define_external_field define_four_body define_inversions define_metals define_pmf define_rigid_body define_tersoff define_tethers define_three_body define_units define_van_der_waals error exclude exclude_atom exclude_link excludeneu gauss gdsum getrec gimax gisum gstate CCLRC define_system define_system define_system define_system define_system define_system define_system define_system define_system define_system define_system define_system define_system define_system define_system define_system define_system define_system define_system define_system define_system define_system define_system dihed_module dihedral_terms dihedral_terms dihedral_terms dihedral_terms dihedral_terms dihedral_terms dihedral_terms dihedral_terms dihedral_terms_4pt dihedral_terms_4pt dihedral_terms_4pt dihedral_terms_4pt dihedral_terms_4pt dihedral_terms_4pt dihedral_terms_4pt dihedral_terms_4pt dihedral_terms_rsq dihedral_terms_rsq dihedral_terms_rsq dihedral_terms_rsq images intlist invert invert jacobi lowcase lowcase lrcmetal lrcorrect merge merge4 neutbook passcon passpmf passquat quatbook guatgnch guench shellsort shlgnch strip vscaleg warning error copystring error gdsu
52. in the previous sections Thus we need only consider the rotational motion here The rotational equation of motion for a rigid body is T u u Tw 2 250 CCLRC 71 in which J is the angular momentum of the rigid body defined by the expression Nsites j 1 and w is the angular velocity The vector 7 is the torque acting on the body in the universal frame and is given by Nsites r dx f 2 252 j l The rotational equations of motion written in the local frame of the rigid body are given by Euler s equations T A A Ur F yy Tzz WyWz TE T 2 z A AR y set ee Ler Ortiz 2 253 lyy T gt E A oS Wy lee I yy ay Izz The vector w is the angular velocity transformed to the local body frame Integration of w is complicated by the fact that as the rigid body rotates so does the local reference frame So is is necessary to integrate equations 2 253 simultaneously with an integration of the quaternions describing the orientiation of the rigid body The equation describing this is do qo q Q 43 0 1 _ qa 4 4 B Q2 Ur 2 254 q2 212 a qo 4 Wy d3 g 2 q do Wy Rotational motion in DL POLY 2 is handled by two different methods For LF im plementation the Fincham Implicit Quaternion Algorithm FIQA is used 14 The VV implementation uses the NOSQUISH algorithm of Miller et al 15 The LF implementation begins by integrating the angular velocity equation in the
53. input and output record 3 optional neut a40 activate the neutral charge groups option for the electrostatic calculations The energy units on the units directive are described by additional keywords a eV for electron volts b kcal for k calories mol c kJ for k Joules mol d internal for DL POLY 2 internal units 10 J mol If no units keyword is entered DL POLY 2 units are assumed for both input and output The units keyword may appear anywhere on the data record provided it does not exceed column 40 The units directive only affects the input and output interfaces all internal calculations are handled using DL_POLY_2 units 4 1 3 2 2 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 in which they appear in the CONFIG file Failure to adhere to this common sequence will be detected by DL POLY 2 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 be
54. 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 eguilibrium angle of CCLRC 27 35 264 The angle is defined by vectors 712 753 and r34 where the atoms 1 2 3 and 4 are shown in the following figure The figure defines the D and L enantiomers consistent with the international IUPAC convention When defining the dihedral the atom indices are entered in DL POLY 2 in the order 1 2 3 4 L a N C 8 D a C N 8 1234 1234 The L and D enantiomers and defining vectors In DL_POLY_2 improper dihedral forces are handled by the routine DIHFRC 2 2 7 Inversion Angle Potentials The inversion angle and associated vectors The inversion angle potentials describe the interaction arising from a particular ge ometry of three atoms around a central atom The best known example of this is the CCLRC 28 arrangement of hydrogen atoms around nitrogen in ammonia to form a trigonal pyramid The hydrogens can flip like an inverting umbrella to an alternative structure which in this case is identical but in principle causes a change in chirality The force restraining the ammonia to one structure can be described as an inversion potential though it is usually augmented by valence angle potentials also The inversion angle is defined in the figure above note that the inversion angle potential is a sum of
55. merge nlist_builders shellsort pair_module error parse_tools gisum parse_tools gstate parse_tools gsync pass_tools MPI_IRECV pass_tools MPI_SEND pass_tools MPI_WAIT pass_tools error pass_tools gisum pass_tools gstate pass_tools gsync pmf_lf error pmf_lf gdsum pmf_lf images pmf_lf kinstress pmf_lf merge pmf_lf pmf_shake pmf_lf pmf_vectors pmf_lf rdshake_1 pmf_lf splice pmf module error pmf_terms error pmf_terms getrec pmf_terms images pmf_terms lowcase pmf_terms strip pmf vv error pmf vv gdsum pmf vv images pmf vv kinstress pmf vv merge pmf vv pmf rattle v pmf vv pmf_vectors pmf vv rdrattle v pmf vv splice property module error rigid body module error rigid body terms error rigid body terms gdsum CCLRC rigid_body_terms serial setup_program setup_program setup_program setup_program setup_program setup_program setup_program setup_program setup_program setup_program shake_module shake_terms shake_terms shake_terms site_module site_terms site_terms site_terms site_terms site_terms spme_module spme_terms spme_terms spme_terms spme_terms spme_terms spme_terms spme_terms spme_terms spme_terms spme_terms spme_terms spme_terms spme_terms spme_terms strucopt strucopt system_properties system_properties system_properties system_properties system_properties getrec error abortscan cfgscan dcell dcell error
56. more processors or a machine with larger memory per processor CCLRC 228 Message 1625 error failed allocation of work arrays in qrattle_v f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1630 error failed allocation of work arrays in nvtq_b2 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1640 error failed allocation of work arrays in nvtq_h2 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1650 error failed allocation of work arrays in nptq_b2 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1660 error failed allocation of density array in nptq_b2 f This is a memory allocation error Probable caus
57. not confuse this error with that described by message 63 below Action Standard user response Fix the parameter mxteth Message 63 error too many tethered atoms in system The number of tethered atoms in the simulated system is limited by DL_POLY_2 Termi nation results if too many are encountered Do not confuse this error with that described CCLRC 184 by message 62 above Action Standard user response Fix the parameter msteth Message 65 error too many excluded pairs specified This error can arise when DL_POLY_2 is identifying the atom pairs that cannot have a pair potential between them by virtue of being chemically bonded for example see subroutine EXCLUDE Some of the working arrays used in this operation may be exceeded resulting in termination of the program Action Standard user response Fix the parameter mxexcl Message 66 error incorrect boundary condition for HK ewald The Hautman Klein Ewald method can only be used with XY planar periodic boundary conditions i e imcon 6 Action Either the periodic boundary condition or the choice of calculation of the electrostatic forces must be changed Message 67 error incorrect boundary condition in thbfrc Three body forces in DL_POLY 2 are only permissible with cubic orthorhombic and par allelepiped periodic boundaries Use of other boundary conditions results in this error Action If nonperiodic boundaries are required the onl
58. of point ions and gaussian charges becomes the Real Space part of the Ewald sum which is now short ranged and treatable by the methods described above section 2 1 3 The second modification is to superimpose a second set of gaussian charges this time with the same charges as the original point ions and again centred on the point ions so nullifying the effect of the first set of gaussians The potential due to these gaussians is obtained from Poisson s equation and is solved as a Fourier series in Reciprocal Space The complete Ewald sum requires an additional correction known as the self energy correction which arises from a gaussian acting on its own site and is constant Ewald s method therefore replaces a potentially infinite sum in real space by two finite sums one in real space and one in reciprocal space and the self energy correction For molecular systems as opposed to systems comprised simply of point ions additional modifications are necessary to correct for the excluded intra molecular Coulombic inter actions 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 disti
59. of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor CCLRC 218 Message 1060 error failed allocation of dihedral work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1070 error failed allocation of constraint arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1090 error failed allocation of site arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1100 error failed allocation of core_shell arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1110 error failed
60. p nstqscl_p2 nst scl t nstqscl_t2 nstqvv_bl nstqvv_b2 nstgvv h1 nstqvv_h2 nstscale_p nstscale_t nstvv_b1 nstvv_h1 subroutine subroutine function function subroutine subroutine function function subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine force_drivers f force drivers f basic_comms f serial f define system f force drivers f basic comms f serial f vv rotation_l f lf motion l1 f lf motion 1 f lf rotation 1 f lf rotation 2 f If rotation 1 f lf rotation 2 f ensemble tools f ensemble tools f vv_rotation_1 f vv_rotation_2 f vv_rotation_1 f vv_rotation_2 f ensemble_tools f ensemble_tools f vv_motion_1 f vv_motion_1 f lf_motion_1 f lf_motion_1 f lf_rotation_1 f If rotation 2 f lf rotation 1 f If rotation 2 f ensemble tools f ensemble_tools f ensemble_tools f ensemble_tools f ensemble_tools f vv_rotation_1 f vv_rotation_2 f vv_rotation_1 f vv_rotation_2 f ensemble_tools f ensemble_tools f vv_motion_1 f vv_motion_1 f CCLRC numnodes numnodes nve l nveg 1 nveg 2 nvegvv l nvegvv_2 nvevv l nvt bl nvt el nv
61. please supply your e mail address The bench and public subdirectories of DL POLY 2 are not issued in the standard pack age but can be downloaded directly from the FTP site in the ccp5 DL POLY DL POLY 2 directory as described above The DL POLY 2 User Manual is freely available via the website or ftp in the same manner as the licence form 1 6 Other Information The DL POLY website http www cse clrc ac uk msi software DL POLY provides additional information in the form of 1 Access to all documentation including licences 2 Freguently asked guestions 3 Bug reports 4 Access to the DL_POLY online forum Daresbury Laboratory also maintains two DL_POLY_2 associated electronic mailing lists 1 dl poly news to which all registered DL POLY 2 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 2 user but not on this list you may request to be added Contact w smith dl ac uk 2 dl poly mail is a group list which is available to DL POLY 2 users by request Its purpose is to allow DL_POLY_2 users to broadcast information and queries to each other To subscribe to this list send a mail message to majordomo dl ac uk with the one line message subscribe dl _poly mail Subsequent messages may be broadcast by e mailing to the address dl poly mail dl ac uk Note that this is a vetted list so electronic spam is not possible CCLRC 1
62. pmf If f pmf vv f nlist_builders f CCLRC prneulst qrattle_r qrattle_v qshake quatbook quatqnch quench rdfO rdfOneu rdf1 rdrattle T rdrattle v rdshake 1 relax_shells result revive rotate omega scdens scdens scdens scl_csum sdot sdot1 set block shellsort shlfrc shlmerge shlmerge shlmerge shlmerge shlgnch shmove shmove shmove shmove simdef spl_cexp splice splice splice splice spme_for srfrce srfrce subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine function function subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine 250 nlist builders f vv rotation 2 f vv rotation 2 f If rotation 2 f define system f temp scalers f temp scalers f system properties f system properties f system properties f vv_motion_1 f vv_motion_1 f lf motion 1 f core shell terms f system properties f system properties f vv _rotation_l f metal_terms f metal_terms_4pt f metal terms rs f utility pack f utility pack f utility pack f utility pack f utility pack f core shell terms f merge hcube f merge systol f merge
63. quaternion momenta in the order ciCs 01 2 i 2 t 2 gili 01 piCa 6t 2 ciCs 01 2 2 263 which preserves the symplecticness of the operations see reference 17 Note that t is some submultiple of At In DL POLY 2 the default is At 10dt The operators themselves are of the following kind eLO cos Ck t q sin dt Pyg eK cos Cpdt p sin Gr t Pep 2 264 CCLRC 73 where P is a permutation operator with k 0 3 with the following properties Pg 405 92 93 Pig 4 q0 q3 42 Pog 42 93 90 1 Psq 93 92 40 2 265 and the angular velocity Cy is defined as Ck PP 2 266 Eguations 2 263 to 2 265 represent the heart of the NOSOUISH algorithm and are repeatedly applied 10 times in DL POLY 2 The final result is the guaternion updated to the full timestep value i e q t At These equations form part of the first stage of the VV algorithm R In the second stage of the VV algorithm new torgues are used to update the guaternion momenta to a full timestep At At p t At p t 2 gt Ltt At 2 267 The NVE implementation of this algorithm is in the subroutine NVEQVv_1 which calls the NOSQUISH subroutine to perform the rotation operation The subroutine also calls RATTLE_R and RATTLE_V to handle any rigid bonds which may be present Thermostats and Barostats It is straightforward to couple the rigid body equations of motion to a thermostat and or barost
64. replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1550 error failed allocation of work arrays in nptq_h1 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1560 error failed allocation of density array in nptq_h1 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1570 error failed allocation of work arrays in nstq_b1 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1580 error failed allocation of density array in nst bl f This is a memory allocation error Probable cause excessive size of simulated system CCLRC 227 Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1590 error failed allocation of work arrays in
65. rigid The MD cell is orthorhombic nearly cubic and the integration is NPT hoover NPT Hoover ensemble 5 1 2 Benchmark Cases These represent rather larger test cases for DL POLY 2 that are also suitable for bench marking the code on large scale computers They have been selected to show fairly the the capabilities and limitations of the code 5 1 2 1 Benchmark 1 Simulation of metallic aluminium at 300K using a Sutton Chen density dependent potential The system is comprised of 19652 identical atoms The simulation runs on 16 to 512 processors only 5 1 2 2 Benchmark 2 Simulation of a 15 peptide in 1247 water molecules This was designed as an AMBER comparison The system consists of 3993 atoms in all and runs on 8 512 processors It uses neutral group electrostatics and rigid bond constraints and is one of the smallest benchmarks in the set 5 1 2 3 Benchmark 3 Simulation of the enzyme transferrin in 8102 water molecules The simulation makes use of neutral group electrostatics and rigid bond constraints The system is 27539 atoms and runs on 8 512 processors CCLRC 154 5 1 2 4 Benchmark 4 Simulation of a sodium chloride melt with Ewald sum electrostatics and a multiple timestep algorithm to enhance performance The system is comprised of 27000 atoms and runs on 8 512 processors 5 1 2 5 Benchmark 5 Simulation of a sodium potassium disilicate glass Uses Ewald sum electrostatics a mul tiple timestep algorithm and a
66. smaller one the user must consider using more processors or a machine with larger memory per processor Message 1320 error failed allocation of densO array in npt_h0 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1330 error failed allocation of work arrays in npt_h0 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1340 error failed allocation of densO array in nst_b0 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1350 error failed allocation of work arrays in nst_b0 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1360 error failed allocation of densO array in nst_h0 f This is a memory allocation e
67. 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 Message 470 error n lt m in definition of n m potential The specification of a n m potential in the FIELD file implies that the exponent m is larger than exponent n Not all versions of DL_POLY_2 are affected by this Action Locate the n m potential in the FIELD file and reverse the order of the exponents Resubmit the job CCLRC 212 Message 474 error mxxdf too small in parlst subroutine The parameter mxxdf defining working arrays in subroutine PARLST of DL POLY 2 has been found to be too small Action Standard user response Fix the parameter mxxdf Message 475 error mxxdf too small in parlst_nsq subroutine The parameter mxxdf defining working arrays in subroutine PARLST_NSQ DL POLY 2 has been found to be too small Action Standard user response Fix the parameter mxxdf Message 476 error mxxdf too small in parneulst subroutine The parameter mxxdf defining working arrays in subroutine PARNEULST is t
68. subroutine subroutine subroutine function subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine 247 hkewald_terms f hkewald_terms f hkewald_terms f hkewald_terms f hkewald_terms f utility_pack f basic_comms f serial f define system f parse_tools f utility_pack f inversion_terms f utility_pack f utility_pack f kinetic_terms f kinetic_terms f kinetic_terms f If integrate f parse tools f metal terms f metal terms 4pt f metal terms rs f vdw terms f vdw terms 4pt f vdw_terms_rsq f basic_comms f serial f utility pack f merge hcube f merge_systol f merge tools f serial f merge hcube f merge systol f merge tools f serial f merge hcube f merge_systol f merge tools f serial f metal terms f metal terms 4pt f metal_terms_rsq f force_drivers f CCLRC multiple_nsq multipleneu mynode mynode neutbook neutlst nodedim nodedim nosquish npt_b1 npt h1 nptq_bl nptq_b2 nptq_hl nptq_h2 npt scl p npt scl t nptgvv bl nptgvv b2 nptgvv h1 nptgvv h2 nptscale p nptscale_t nptvv bl nptvv hl nst bl nst hl nstq_bl nstq_b2 nstg h1 nstg h2 nstgmtk_p nst scl
69. subroutine subroutine subroutine subroutine subroutine subroutine function function subroutine function subroutine function function subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine 246 exclude_terms f exclude terms f exclude_terms f exclude_terms f basic_comms f serial f external field terms f four body terms f utility pack f parse tools f setup program f force drivers f force drivers f vdw terms f vdw terms 4pt f vdw_terms_rsq f vdw terms f vdw terms 4pt f vdw_terms_rsq f utility_pack f utility_pack f basic_comms f serial f ensemble_tools f kinetic_terms f kinetic_terms f kinetic_terms f kinetic_terms f kinetic_terms f kinetic_terms f ensemble_tools f parse_tools f utility_pack f ensemble_tools f parse_tools f basic_comms f serial f basic comms f serial f utility pack f basic comms f serial f basic comms f serial f CCLRC hkewald1 hkewald2 hkewald3 hkewald4 hkgen images initcomms initcomms intlist intstr invert invfrc jacobi kinstr kinstress kinstressf kinstressg If integrate lowcase Ircmetal Ircmetal Ircmetal Ircorrect Ircorrect Ircorrect machine machine matmul merge merge merge merge mergel mergel mergel mergel merge4 merge4 merge4 merge4 metgen metgen metgen multiple subroutine subroutine subroutine subroutine subroutine subroutine
70. the CONFIG file must be replaced by the REVCON file which is renamed as the CONFIG file The copy macro in the ezecute sub directory of DL POLY 2 does this for you CCLRC Table 4 5 CONFIG file key record 2 levcfg meaning 0 Coordinates included in file 1 Coordinates and velocities included in file 2 Coordinates velocities and forces included in file Table 4 6 Periodic boundary key record 2 imcon meaning ocn NR no periodic boundaries cubic boundary conditions orthorhombic boundary conditions parallelepiped boundary conditions truncated octahedral boundary conditions rhombic dodecahedral boundary conditions x y parallelogram boundary conditions with no periodicity in the z direction hexagonal prism boundary conditions 116 CCLRC 117 4 1 3 The FIELD File The FIELD file contains the force field information defining the nature of the molecular forces It is read by the subroutine SYSDEF Excerpts from a force field file are shown below The example is the antibiotic Valinomycin in a cluster of 146 water molecules Valinomycin Molecule with 146 SPC Waters UNITS kcal MOLECULES 2 Valinomycin NUMMOLS 1 ATOMS 168 0 16 0000 0 4160 1 OS 16 0000 0 4550 1 HC 1 0080 0 0580 1 C 12 0100 0 4770 1 BONDS 78 harn 31 19 674 000 1 44900 harn 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
71. the Z direction They are particularly useful for simulating surfaces The periodic cell in the XY plane can be any parallelogram The origin of the X Y atomic coordinates lies on an axis perpendicular to the centre of the parallelogram The origin of the Z coordinate is where the user specifies it but at or near the surface is recommended If the XY parallelogram is defined by vectors A and B the vectors required in the CONFIG file are A A2 0 Bi B2 0 0 0 D where D is any real number including zero If D is nonzero it will be used by DL_POLY to help determine a working volume for the system This is needed to help calculate RDFs etc The working value of D is in fact taken as one of 3xcutoff or 2xmax abs Z coordinate cutoff or the user specified D whichever is the larger Note that the standard Ewald sum cannot be used with this boundary condition DL_POLY 2 switches automatically to the Hautman Klein Ewald method instead 32 The surface in a system with charges can also be modelled with DL _POLY_2 if period icity is allowed in the Z direction In this case slabs of ions well separated by vacuum zones in the Z direction can be handled with IMCON 2 or 3 Hexagonal prism boundaries IMCON 7 In this case the Z axis lies along a line joining the centres of the hexagonal faces The Y axis is perpendicular to this and passes through the centre of one of the faces The X axis completes the orthonormal set and passes throu
72. the absence of screening terms S r the virial is zero 26 The contribution to be added to the atomic stress tensor is given by ot a ra f 2 30 and the stress tensor is symmetric In DL POLY 2 valence forces are handled by the routine ANGFRC 2 2 4 Angular Restraints In DL_POLY_2 angle restraints in which the angle subtended by a triplet of atoms is maintained around some preset value o is handled as a special case of angle potentials As a consequence angle restraints may be applied only between atoms in the same molecule Unlike with application of the pure angle potentials the electrostatic and van der Waals interactions between the pair of atoms are still evaluated when distance 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 Quartic gur Truncated harmonic thm Screened harmonic shm Screened Vessal 24 bv1 Truncated Vessal 25 bv2 Harmonic cosine hcs Cosine cos oO o No om EB o N MMB stretch bend msb In DL POLY 2 angular restraints are handled by the routine ANGFRC 2 2 5 Dihedral Angle Potentials CCLRC 24 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 spec
73. the reversible integrators of Martyna et al 17 The NVT algorithms in DL_POLY 2 are those of Evans 18 Berendsen 19 and Hoover 20 The NPT algorithms are those of Berendsen 19 and Hoover 20 and the No T algorithms are those of Berendsen 19 and Hoover 20 The full range of MD algorithms available in DL_POLY_2 is described in Section 2 5 1 3 Programming Style The programming style of DL POLY_ 2 is intended to be as uniform as possible The following stylistic rules apply throughout Potential contributors of code are reguested to note the stylistic convention 1 3 1 Programming Language DL_POLY 2 is written exclusively in FORTRAN 90 Use is made of F90 Modules Explicit type declaration is used throughout 1 3 2 Memory Management In DL_POLY_2 the major array dimensions are calculated at the start of execution and the associated arrays created through the dynamic array allocation features of FORTRAN 90 1 3 3 Target Computers DL POLY 2 is intended for distributed memory parallel computers However versions of the program for serial computers are easily produced To facilitate this all machine specific calls are located in dedicated FORTRAN routines to permit substitution by appropriate alternatives DL POLY 2 will run on a wide selection of computers This includes most single pro cessor workstations for which it requires a FORTRAN 90 compiler and preferably a UNIX environment It has also been compiled for a
74. the three possible in version angle terms It resembles a dihedral potential in that it requires the specification of four atomic positions The potential functions available in DL_POLY_2 are as follows 1 Harmonic harm U dijkn DR bin o 2 56 2 Harmonic cosine hcos U din 5 cos ijen cos 6o 2 57 3 Planar potential plan U ijkn A 1 cos ijkn 2 58 In these formulae 6 j4 is the inversion angle defined by T ers w Pijkn cos E j 2 59 TijWkn with and the unit vectors Us fik in l ik Pin te ik lia Pan 2 61 As usual Tij Tj Tq 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 n j etc Equivalently the angle i kn may be written as a y2 5 y2 1 2 Te Ti U jn a rij Un Ti Bkn 2 62 Formally the force on an atom arising from the inversion potential is given by a O I gt aU ijkn 2 63 Ore CCLRC 29 with being one of i j k n and a one of x y z This may be expanded into 1 grg U Pien U ijkn X sin ijkn O ijkn 8 ris An rag ty 2 64 Ore Tij Following through the extremely tedious differentiation gives the result 1 0 a U
75. 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 2 will begin closing down too early How large the close time needs to be to ensure safe close down is system dependent and a matter of experience It generally increases with the job size 3 The starting options for a simulation are governed by the keyword restart If this is not specified in the CONTROL file the simulation will start as new If specifed it will either continue a previous simulation restart or start a new simulation with initial temperature scaling of the previous configuration restart scale or without initial temperature scaling restart noscale Internally these options are handled by the integer variable keyres which is explained in table 4 1 4 The various ensemble options i e nve nvt ber nvt evans nvt hoover npt ber npt hoover nst ber nst hoover are mutually exclusive though none is mandatory the default is the NVE ensemble These options are handled internally by the integer variable keyens The meaning of this variable is explained in table 4 2 5 The force selection directives ewald sum ewald precision reaction coul shift dist no elec and no vdw are handled internally by the integer variable keyfce See table 4 4 fo
76. to N 2 Every intramolecular bonded term Ujypye in the system has a unique index number itype from 1 to Niype where type represents a bond angle or dihedral 3 A pointer array keytype Ntype itype carries the indices of the specific atoms involved in the potential term labelled itype The dimension ngype will be 2 3 or 4 if the term represents a bond valence angle dihedral inversion 4 The array keyype type itype is used to identify the atoms in a bonded term and the appropriate form of interaction and thus to calculate the energy and forces DL POLY 2 calculates the nonbonded pair interactions using a Verlet neighbour list 11 which is reconstructed at intervals during the simulation This list records the indices of all secondary atoms within a certain radius of each primary atom the radius being the cut off radius reut normally applied to the nonbonded potential function plus an additional increment Arc The neighbour list removes the need to scan over all atoms CCLRC 18 in the simulation at every timestep The larger radius reut Arcut means the same list can be used for several timesteps without requiring an update The frequency at which the list must be updated depends on the thickness of the region Arc DL POLY 2 has two methods for constructing the neighbour list the first is based on the Brode Ahlrichs scheme 22 and is used when reut is large in comparison with the simulation cell the second use
77. to it are generated DL POLY 2 comes with three different thermostats Nos Hoover 20 Berendsen 19 and Gaussian constraints 18 Of these only the Nos Hoover algorithm generates trajectories in the canonical NVT ensemble The other methods will produce properties that typically differ from canonical averages by O 1 N 11 2 5 4 1 Nos Hoover Thermostat In the Nos Hoover algorithm 20 Newton s equations of motion are modified to read dr t _ g 20 a gyw 2 212 2 213 The friction coefficient x is controlled by the first order differential equation dy t Nrkp dt Q where Q N phaTextth is the effective mass of the thermoststat rr is a specified time constant normally in the range 0 5 2 ps and Ny is the number of degrees of freedom in the system 7 t is the instantaneous temperature of the system at time t In the LF version of DL_POLY _2 x is stored at half timesteps as it has dimensions of 1 time The integration takes place as T t Text 2 214 x E SAN x 8 Aja AEB T E a wey xa u sat ates 340 u t Ai u t At At m vs at 4 EC as At eee A ie a r AD 2 215 CCLRC 61 Since v t is required to calculate T t and itself the algorithm requires several iterations to obtain self consistency In DL POLY 2 the number of iterations is set to 3 4 if the system has bond constraints The iteration procedure is st
78. to terms in a Taylor expansion of r in s the in plane distance 32 Usually this sum is truncated at Nmaz 1 but in DL POLY 2 can go as high as Tumae 3 In the HKE method the convergence functions are defined as follows hn s a s m l V2 hols a 5 2 177 an 2n The reader is warned that for the purpose of compatibility with other DL POLY 2 Ewald routines we have defined a 0 5 az x where apx is the a parameter defined by Hautman and Klein in 32 CCLRC 50 with ho s a er f as 2 178 and i fa g a n EA 2 179 with fo g er fe g 2a 2 180 In DL POLY 2 the hn s a s functions are derived by a recursion algorithm while the fn g a functions are obtained by direct evaluation The coefficients an are given by an 1 2n 2 n 2 2 181 As pointed out by Hautman and Klein the equation 2 173 allows separation of the ze components via the binomial expansion which greatly simplifies the double sum over atoms in reciprocal space Thus the reciprocal space part of equation 2 173 becomes Nmax Urecip 5 an 5 Ink g a g ent y DC 2 g Z2n p 8 2 182 ZA A 0 g70 with ce a binomial coefficient and N Zp g qz erp ig sj 2 183 j l The force on an ion is obtained by the usual differentiation however in this case the z components have different expressions from the x and y oU Tmaz p 1 1 2 OZ n _ 9 OZp g nJn 9 2 G PS Zon
79. tools f serial f temp scalers f merge hcube f merge systol f merge_tools f serial f define system f spme terms f merge hcube f merge systol f merge tools f serial f spme_terms f vdw_terms f vdw_terms_4pt f CCLRC srfrce srfrceneu srfrceneu srfrceneu static strip striptext strucopt suttchen suttchen suttchen sysbook sysdef sysgen sysinit systemp tergen terint tersoff tersoff3 tethfrc thbfrc timchk traject traject update guaternions vertest vscaleg vv integrate xscale zden0 zdenl subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine 251 vdw_terms_rsq f vdw_terms f vdw_terms_4pt f vdw_terms_rsq f system properties f parse tools f parse_tools f strucopt f metal_terms f metal_terms_4pt f metal terms rs f define system f define system f define system f define_system f define_system f tersoff terms f tersoff terms f tersoff terms f tersoff terms f tether_terms f three_body_terms f timchk f traject f traject_u f If rotation 1 f nlist builders f temp scalers f vv integrate f utility pack f system properties f system properties f Appendix E Called Subro
80. used incorrect force field specification too high a temperature inconsistent constraints involving shared atoms etc Action Corrective action depends on the cause It is unlikely that simply increasing the iteration number will cure the problem but you can try follow the standard user response to increase the control parameter mxshak But the trouble is much more likely to be cured by careful consideration of the physical system being simulated For example is the system stressed in some way Too far from equilibrium CCLRC 191 Message 106 error neighbour list array too small in parlink Construction of the Verlet neighbour list in subroutine parlink nonbonded pair force has exceeded the neighbour list array dimensions Action Standard user response Fix the parameter mxlist Message 107 error neighbour list array too small in parlinkneu Construction of the Verlet neighbour list in subroutine parlinkneu nonbonded pair force has exceeded the neighbour list array dimensions Action Standard user response Fix the parameter mxlist Message 108 error neighbour list array too small in parneulst Construction of the Verlet neighbour list in subroutine parneulst nonbonded pair force has exceeded the neighbour list array dimensions Action Standard user response Fix the parameter mxlist Message 109 error neighbour list array too small in parlst_nsq Construction of the Verlet neighbour list in subrouti
81. variable 1 real variable 2 real variable 3 real variable 4 real potential parameter see table 4 11 potential parameter see table 4 11 potential parameter see table 4 11 potential parameter see table 4 11 This directive and associated data records need not be specified if the molecule contains no tethered atoms See the note on the atomic indices appearing under the shell directive above Table 4 11 Tethering potentials key potential type Variables 1 3 functional form harm Harmonic k U r gkr rhrm Restraint k re U r zkr r lt Te U ikr kr r re T gt T guar Ouartic k k k U r kr k 3 Eyd 13 finish This directive is entered to signal to DL POLY 2 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 CCLRC 128 The user is recommended to look at the example FIELD files in the data directory to see how typical FIELD files are constructed 4 1 3 3 Non bonded Interactions Non bonded interactions are identified by atom types as opposed to specific atomic indices The first type of non bonded potentials are the pair potentials The input of pair potential data is signalled by the directive vdw n
82. where n is the number of pair potentials to be entered There follows n records each specifying a particular pair potential in the following manner atmnam 1 a8 first atom type atmnam 2 a8 second atom type key a4 potential key See table 4 12 variable 1 real potential parameter see table 4 12 variable 2 real potential parameter see table 4 12 variable 3 real potential parameter see table 4 12 variable 4 real potential parameter see table 4 12 variable 5 real potential parameter see table 4 12 The variables pertaining to each potential are described in table 4 12 Note that any pair potential not specified in the FIELD file will be assumed to be zero The specification of three body potentials is initiated by the directive tbpn where n is the number of three body potentials to be entered There follows n records each specifying a particular three body potential in the following manner atmnam 1 a8 first atom type atmnam 2 a8 second atom type central site atmnam 3 a8 third atom type key a4 potential key See table 4 13 CCLRC 129 Table 4 12 Definition of pair potential functions and variables key potential type Variables 1 5 functional form 12 6 12 6 A B U r 4 lj Lennard Jones c U r 4e 22 nm n m Eo n m ro U r mm m Z2 n Te buck Buckingham A lp C U r A exp z S bhm Born Huggins A B c C D U r A exp B
83. 2 The DL_POLY_2 LF routines implement this thermostat as follows v t At ue any x t i a ze e 340 alt 740 sr Af a A pdr sat 2 219 As with the Nos Hoover thermostat iteration is required to obtain self consistency of x t v t and T t although it should be noted y has different roles in the two thermostats The Berendsen algorithm conserves total momentum but not energy Here again the pres ence of constraint bonds requires an additional iteration with one application of SHAKE corrections The algorithm is implemented in the DL POLY routine NvT_B1 for systems including bond constraints The VV implementation of Berendsen s algorithm proceeds as folows At f t 1 v t 5At v t 2 rtd AY r t At u t 5 At u t At v t At call rattle V At T 12 FA TT Text v t At yu t At 2 220 call rattle At f t At 2 m R 1 2 Routines rattle R and rattle V apply the bondlength and velocity constraint formulae 2 210 and 2 211 respectively The integration is performed by the subroutine NVTVV_B1 which calls subroutines RATTLE R and RATTLE_V 2 5 5 Gaussian Constraints Kinetic temperature can be made a constant of the equations of motion by imposing an additional constraint on the system If one writes the equations of motions as drt a aut uo ED 2 222 CCLRC 63 with the temperature constraint dT d 2 mii 3 x 2 m v 0
84. 2 pass_tools merge_hcube merge_systol merge_tools pass_tools basic_comms basic_comms basic_comms dlpoly dlpoly dlpoly define_system force_drivers vv_rotation_1 vv_rotation_2 lf integrate lf integrate lf integrate lf integrate lf integrate lf integrate vv rotation 1 vv_rotation_2 vv_rotation_1 vv_rotation_1 vv_rotation_2 vv_integrate vv_integrate vv_integrate vv_integrate vv_motion_1 vv_motion_1 vv_integrate vv_integrate lf integrate lf integrate lf integrate lf integrate lf integrate lf integrate vv rotation 1 vv_rotation_2 vv_rotation_1 vv_rotation_2 281 CCLRC nstgvv b1 nstqvv_b2 nstgvv h1 nstqvv_h2 nstscale_p nstscale_t nstvv_bl nstvv_hi nve_1 nveg_1 nveg_2 nveqvv_1 nveqvv_2 nvevv_1 nvt_b1 nvt_el nvt_hi nvt bl nvt b2 nvt hi nvt h2 nvtqscl nvtqscl nvtgvv b1 nvtqvv_b2 nvtgvv h1 nvtqvv_h2 nvtscale nvtvv_bl nvtvv_el nvtvv_hi parlink parlinkneu parlst parlst_nsq parneulst parset passcon passpmf passquat pivot pmf_rattle_v pmf_shake pmf_vectors vv_integrate vv_integrate vv_integrate vv_integrate vv_motion_1 vv_motion_1 vv_integrate vv_integrate lf integrate lf integrate lf integrate vv_integrate vv_integrate vv_integrate lf integrate lf integrate lf integrate lf integrate lf integrate lf integrate lf integrate vv rotation 1 vv rotation 2 vv_integrate vv_integrate vv_integrate vv_integrate vv_motion_1 vv_integrate vv_integrate vv_integrate
85. 2 The OUTPUT Files DL POLY 2 produces up to seven output files HISTORY OUTPUT REVCON REVIVE RDFDAT ZDNDAT and STATIS These respectively contain a dump file of atomic co ordinates velocities and forces a summary of the simulation the restart configuration statistics accumulators radial distribution data Z density data and a statistical history 4 2 1 The HISTORY File The HISTORY file is the dump file of atomic coordinates velocities and forces Its principal use is for off line analysis The file is written by the subroutines TRAJECT or TRAJECT_U The control variables for this file are ltraj nstraj istraj and keytrj which are cre ated internally based on information read from the traj directive in the CONTROL file see above The HISTORY file will be created only if the directive traj appears in the CONTROL file Note that the HISTORY file can be written in either a formatted or unformatted version We describe each of these separately below The HISTORY file can become very large especially if it is formatted For serious simulation work it is recommended that the file be written to a scratch disk capable of accommodating a large data file Alternatively the file may be written as unformatted below which has the additional advantage of speed However writing an unformatted file has the disadvantage that the file may not be readily readable except by the machine on which it was created This is particularly important if graph
86. 3 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 Chapter 2 DL POLY 2 Force Fields and Algorithms CCLRC 15 Scope of Chapter This chapter describes the interaction potentials and simulation algorithms coded into DL POLY 2 CCLRC 16 2 1 The DL POLY 2 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 2 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 5 Dreiding 6 AMBER 7 and OPLS 21 users have been coded in the package as well as less familiar forms In addition DL_POLY 2 retains the possibility of the user defining additional potentials In DL POLY 2 the total configuration energy of a molecular system may be written as Noond U ri r2 TN 5 Utona ibond Tas T tbond 1 Nangle 5 Uangle iangle Tas Tb Ta iangle l Naihed Ugdihed ldihed Tas rb Le ra idihed 1 Ninv gt Up testy Tb Te Ta tiny 1
87. 4PT dihedral_terms_4pt o ewald_terms_4pt o metal_terms_4pt o vdw_terms_4pt o OBJ_RSQ dihedral_terms_rsq o ewald_terms_rsq o metal_terms_rsq o vdw_terms_rsq o OBJ_PAR basic_comms o merge_tools o pass_tools o Define targets all echo Error please specify a target machine echo Permissible targets for this Makefile are echo echo hpcx parallel echo crayxdi parallel echo macosx xlf g5 mpi parallel echo hitachi sr2201 parallel echo sg8k mpi parallel echo n echo Please examine Makefile for details system specific targets follow CCLRC 164 hpcx MAKE FC mpxlf LD mpxlf o LDFLAGS 03 q64 gmaxmem 1 FFLAGS c 03 qmaxmem 1 garch pwr5 qtune pwr5 gnosave EX EX BINROOT BINROOT TYPE Cray XD1 Portland Group gt crayxdl MAKE LD usr mpich mpich 1 2 6 pgi602 bin mpif90 o LDFLAGS FC usr mpich mpich 1 2 6 pgi602 bin mpif90 N FFLAGS c 00 Mdalign EX EX BINROOT BINROOT TYPE tt Mac0O5X XLF Gb MPl gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt macosx xlf g5 mpi MAKE LD opt ibmcmp xlf 8 1 bin xlf o LDFLAGS L opt mpich mx lib lmpich lpmpich L opt mx lib lmyriexpress L usr lib lSy FC opt ibmcmp xlf 8 1 bin xlf FFLAGS c gstrict 03 garch auto gm
88. 70 error failed allocation of tethering work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1280 error failed allocation of metal arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1290 error failed allocation of work arrays in nvt_h0 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1300 error failed allocation of densO array in npt b0 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor CCLRC 222 Message 1310 error failed allocation of work arrays in npt_b0 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a
89. 84 6 55 56 60 Hoover W G 1985 Phys Rev A31 1695 6 55 56 60 Jorgensen W L Madura J D and Swenson C J 1984 J Amer Chem Soc 106 6638 16 Brode S and Ahlrichs R 1986 Comput Phys Commun 42 41 18 79 80 Hockney R W and Eastwood J W 1981 Computer Simulation Using Particles McGraw Hill International 18 82 Vessal B 1994 J Non Cryst Solids 177 103 21 23 34 124 130 Smith W Greaves G N and Gillan M J 1995 J Chem Phys 103 3091 21 23 34 124 130 Smith W 1993 CCP5 Information Quarterly 39 14 23 26 29 Clarke J H R Smith W and Woodcock L V 1986 J Chem Phys 84 2290 31 32 129 Eastwood J W Hockney R W and Lawrence D N 1980 Comput Phys Com mun 19 215 34 37 38 Finnis M W and Sinclair J E 1984 Philos Mag A 50 45 38 131 Smith W and Fincham D 1993 Molecular Simulation 10 67 46 78 79 84 100 Essmann U Perera L Berkowitz M L Darden T Lee H and Pedersen L G 1995 J Chem Phys 103 8577 47 Hautman J and Klein M L 1992 Molecular Physics 75 379 49 171 Neumann M 1985 J Chem Phys 82 5663 52 Fincham D and Mitchell P J 1993 J Phys Condens Matter 5 1031 53 Lindan P J D and Gillan M J 1993 J Phys Condens Matter 5 1019 54 McCammon J A and Harvey S C 1987 Dynamics of Proteins and Nucleic Acids Cambridge Unive
90. CCLRC 102 In all cases if ERROR is called with a non negative message number the program run terminates If the message number is negative execution continues but even in this case DL POLY_2 will terminate the job at a more appropriate place This feature is used in processing the CONTROL and FIELD file directives A possible modification users may consider is to dump additional data before the call to ERROR is made A full list of the DL POLY 2 error messages and the appropriate user action can be found in Appendix C of this document Chapter 4 DL POLY 2 Data Files 103 CCLRC 104 Scope of Chapter This chapter describes all the input and output files for DL POLY 2 examples of which are to be found in the data sub directory CCLRC 105 4 1 The INPUT files REVCON Figure 4 1 DL POLY_2 input left and output right files Note files marked with an asterisk are non mandatory CONFIG CONTROL TABLE REVOLD DL_POLY 2 requires five input files named CONTROL CONFIG FIELD TABLE and REVOLD The first three files are mandatory while TABLE is used only to input certain kinds of pair potential and is not always required REVOLD is required only if the job represents a continuation of a previous job In the following sections we describe the form and content of these files 4 1 1 The CONTROL File The CONTROL file is read by the subroutine SIMDEF and defines the control variables for running
91. D file Action Correct energy keyword on units directive in FIELD file and resubmit CCLRC 175 Message 6 error energy unit not specified A units directive is mandatory in the FIELD file This error indicates that DL POLY 2 has failed to find the required record Action Add units directive to FIELD file and resubmit Message 7 error energy unit respecified DL POLY 2 expects only one units directive in the FIELD file This error results if it encounters another implying an ambiguity in units Action Locate extra units directive in FIELD file and remove Message 8 error time step not specified DL_POLY_2 requires a timestep directive in the CONTROL file This error results if none is encountered Action Inserttimestep directive in CONTROL file with an appropriate numerical value Message 10 error too many molecule types specified DL POLY 2 has a set limit on the number of kinds of molecules it will handle in any sim ulation this is not the same as the number of molecules If this permitted maximum is exceeded the program terminates The error arises when the molecules directive in the FIELD file specifes too large a number Action Standard user response Fix parameter mxtm1s Message 11 error duplicate molecule directive in FIELD file The number of different types of molecules in a simulation should only be specified once If DL_POLY_2 encounters more than one molecules directive it will ter
92. ILL in place of FRACCON FRACCON produces an output file HFILL which should then be used as input for the utility HFILL The HFILL utility fills out the structure with the missing hydrogens Note that you may need to know what the atomic charges are in some systems for example the AMBER charges from the literature Note with minor modifications the utilities FRACFILL and FRACCON can be used on structures from databases other than the Cambridge structural database CCLRC 98 3 3 3 Adding Solvent to a Structure The utility WATERADD adds water from an equilibrated configuration of 256 SPC water molecules at 300 K to fill out the MD cell The utility SOLVADD fills out the MD box with single site solvent molecules from a f c c 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 2 Remember to delete the bogus entries from the CONFIG file before running DL POLY 2 3 3 4 Analysing Results DL_POLY_2 is not designed to calculate every conceivable property you might wish from a simulation Apart from some obvious thermodynamic quantities and radial distribution functions it does no
93. If the correct form is not available look at the subroutine FORGEN or its variant and define the potential for yourself It is easily done Message 151 error unknown metal potential selected The metal potentials available in DL POLY 2 are confined to density dependent forms of the Sutton Chen type This error results if the user attempts to specify another Action Re specify the potential as Sutton Chen type if possible Check the potential keyword appears in columns 17 20 of the FIELD file CCLRC 194 Message 153 error metals not permitted with multiple timestep The multiple timestep algorithm cannot be used in conjunction with metal potentials in DL POLY 2 Action The simulation must be run without the multiple timestep option Message 160 error unaccounted for atoms in exclude list This error message means that DL_POLY_2 has been unable to find all the atoms described in the exclusion list within the simulation cell This should never occur if it does it means a serious bookkeeping error has occured The probable cause is corruption of the code somehow Action If you feel you can tackle it good luck Otherwise we recommend you get in touch with the program authors Keep all relevant data files to help them find the problem Message 170 error too many variables for statistic array This error means the statistics arrays appearing in subroutine STATIC are too small This can happen if the number of unique a
94. If this is not the case it will be unable to restart the program correctly to continue a run Applies to parallel implementations only Action Standard user response Fix the parameter mxbuff Message 190 error buffer array too small in splice DL POLY 2 uses a workspace array named buffer in several routines Its declared size is a compromise of several r les and may sometimes be too small though in the supplied program this should happen only very rarely The point of failure is in the SPLICE routine which is part of the RD SHAKE algorithm Action Standard user response Fix the parameter mxbuff Message 200 error rdf buffer array too small in revive This error indicates that the buffer array used to globally sum the rdf arrays in subroutine REVIVE is too small Action Standard user response Fix the parameter mxbuff Alternatively mxrdf can be set smaller Message 220 error too many neutral groups in system DL POLY 2 has a fixed limit on the number of charged groups in a simulation This error results if the number is exceeded Action Standard user response Fix the parameter mxneut Message 230 error neutral groups improperly arranged In the DL POLY 2 FIELD file the charged groups must be defined in consecutive order This error results if this convention is not adhered to CCLRC 196 Action The arrangement of the data in the FIELD file must be sorted All atoms in the same group must be arran
95. Key i u 2 u u 2 2 k k k k k k k k 2 112 Internal Trajectory File Key 2 a saos as 112 Non bonded force key Ls 113 CONFIG le key record 211 1 2 24 k ed a ee hoa ala 116 Periodic boundary key record 2 acea sogba lala ee an k EUW li WG 116 Chemical bond potentials FFFF ua 122 Valence Angle potentials FF 2 k k k k k k k A 124 Dihedral Angle Potentials 2 iis s u k 2 k V 2 k 0004 126 Inversion Angle Potentials F k k k k k k k k 2 127 Tethering potentials gt o cs ss k 8 R K ada k ES 127 Definition of pair potential functions and variables 129 Three body potentials 2 acs b seama kov RAG wR REAR RRR Re a 130 Four body Potentials s sss k 44 K RR EG ee h 131 Definition of metal potential functions and variables 132 Tersoff Potential s s ia e uk vk eke ea ee RE e d us 133 External fields 22 8 6625s h Ge bee bee ee Od bb kk kus 134 List of Figures 41 DL POLY 2 input left and output right files Note files marked with an asterisk are non mandatory FFF a Chapter 1 Introduction CCLRC 2 Scope of Chapter This chapter describes the concept design and directory structure of DL POLY 2 and how to obtain a copy of the source code CCLRC 3 1 1 The DL_POLY Package DL POLY 2 1 is a package of subroutines programs and data files designed to facilitate molecular dynamics simulations
96. L POLY 2 CONFIG file are simply D 0 0 0 D 0 0 0 D These are also the cell vectors defining the enscribing cube which posseses twice the volume of the truncated octahedral cell Once again the atomic positions are defined with respect to the cell centre The truncated octahedron can be used with the Ewald summation method Rhombic dodecahedral boundaries IMCON 5 This is another unusual MD cell see figure but which possesses similar advantages to the truncated octahedron but with a slightly greater efficiency in its use of the cell volume the ratio is about 74 to 68 The principal axis in the X direction of the rhombic dodecahedron passes through the centre of the cell and the centre of a rhombic face The Y axis does likewise but is set at 90 degrees to the X axis The Z axis completes the orthonormal set and passes through a vertex where four faces meet If the width D of the cell is defined as the perpendicular distance between two opposite faces the cell vectors required for the DL POLY_2 CONFIG file are D 0 0 0 D 0 0 0 V 2D These also define the enscribing orthorhombic cell which has twice the MD cell volume In DL _POLY_2 the centre of the cell is also the origin of the atomic coordinates The rhombic dodecahedron can be used with the Ewald summation method CCLRC 171 The rhombic dodecahedral MD cell Slab boundary conditions IMCON 6 Slab boundaries are periodic in the X and Y directions but not in
97. Message 47 error transfer buffer too small in merge The buffer used to transfer data between nodes in the MERGE subroutines has been dimen sioned too small Action Standard user response Fix the parameter mxbuff Message 48 error transfer buffer too small in fortab The buffer used to transfer data between nodes in the FORTAB subroutines has been dimen sioned too small Action Standard user response Fix the parameter mxbuff Message 49 error frozen core shell unit specified The DL_POLY 2 option to freeze the location of an atom i e hold it permanently in one position is not permitted for core shell units This includes freezing the core or the shell independently Action Remove the frozen atom option from the FIELD file Consider using a non polarisable atom instead Message 50 error too many bond angles specified DL POLY 2 limits the number of valence angle potentials that can be specified in the FIELD file and checks for the violation of this Termination will result if the condition is violated Do not confuse this error with that described by message 51 below Action Standard user response Fix the parameter mxtang Message 51 error too many bond angles in system DL POLY 2 limits the number of valence angle potentials 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 Do n
98. NC file may render any existing REVOLD file unreadable by the code 4 1 5 The TABLE File The TABLE file provides an alternative way of reading in the short range potentials in tabular form This is particularly useful if an analytical form of the potential does not exist CCLRC 136 or is too complicated to specify in the FORGEN subroutine The table file is read by the subroutine FORTAB F in the VDW_TERMS F file The option of using tabulated potentials is specified in the FIELD file see above The specific potentials that are to be tabulated are indicated by the use of the tab keyword on the record defining the short range potential see table 4 12 The directive vdwtable may be used in place of vdw to indicate that one or more of the short ranged potentials is specified in the form of a table 4 1 5 1 Format The file is fixed formatted with integers as il0 reals as el5 8 Character variables are read as a8 The header record is formatted as 80 alphanumeric characters 4 1 5 2 Definitions of Variables record 1 header a80 file header record 2 delpot real mesh resolution in A cutpot real cutoff used to define tables A ngrid integer number of grid points in tables The subsequent records define each tabulated potential in turn in the order indicated by the specification in the FIELD file Each potential is defined by a header record and a set of data records with the potential and force tables header rec
99. Q Bl Constant T Berendsen 19 with FIQA and SHAKE NVTQ_B2 Constant T Berendsen 19 with OSHAKE NVTG H1 Constant T Hoover 20 with FIOA and SHAKE NVTQ_H2 Constant T Hoover 20 with OSHAKE NPT_Bl Constant T P Berendsen 19 with FIOA and SHAKE NPT H1 Constant T P Hoover 20 with SHAKE NPTG B1 Constant T P Berendsen 19 with FIQA and SHAKE NPTO B2 Constant T P Berendsen 19 with OSHAKE NPTG H1 Constant T P Hoover 20 with FIQA and SHAKE NPTO H2 Constant T P Hoover 20 with OSHAKE NST_Bl Constant T c Berendsen 19 with SHAKE NST H1 Constant Ta Hoover 20 with SHAKE NSTQ_B1 Constant T c Berendsen 19 with FIOA and SHAKE NSTO B2 Constant Ta Berendsen 19 with OSHAKE NN NS NSTQ H1 Constant T c Hoover 20 with FIQA and SHAKE NSTQ_H2 Constant T Hoover 20 with OSHAKE In the above table the FIQA algorithm is Fincham s Implicit Quaternion Algorithm 14 and QSHAKE is the DL POLY 2 algorithm combining rigid bonds and rigid bodies in the same molecule 16 2 5 1 2 Velocity Verlet The VV algorithm assumes that positions velocities and forces are known at each full timestep The algorithm proceeds in two stages as follows In the first stage a half step velocity is calculated v t AN u t sat ao 2 202 and then the full timestep position is obtained r t At r t At v t SAV 2 203 CCLRC 56 In the second stage using the new positions the ne
100. RC 123 of a water molecule DL_POLY_2 allows only one type of pmf constraint per system The value of nummols for this molecule determines the number of pmf constraint in the system Note that the directive ensemble pmf must be specified in the CONTROL file for this option to be implemented correctly 8 angles n where n is the number of valence angle bonds in the molecule Each of the n records following contains angle key ad potential key See table 4 8 index 1 integer first atomic index index 2 integer second atomic index central site index 3 integer third atomic index variable 1 real potential parameter see table 4 8 variable 2 real potential parameter see table 4 8 The meaning of these variables is given in table 4 8 See the note on the atomic indices appearing under the shell directive above This directive and associated data records need not be specified if the molecule contains no angular terms CCLRC 124 Table 4 8 Valence Angle potentials key potential type Variables 1 4 functional formf harm Harmonic k 00 U 0 0 09 hrm quar Quartic k kl K U 6 0 09 E 0 00 EF 0 00 qur thrm Truncated harmonic k 00 p U 0 0 0o exp r r p thm shrm Screened harmonic k pi po U 0 amp 0 00 exp rij pi Tix p2 shm bvs1 Screened Vessal 24 k o pi po U 0 OJ T 0 oT
101. THE DL_POLY_2 USER MANUAL W Smith T R Forester I T Todorov and M Leslie CCLRC Daresbury Laboratory Daresbury Warrington WA4 4AD Cheshire UK Version 2 16 March 2006 CCLRC i ABOUT DL POLY 2 DL POLY 2 is a parallel molecular dynamics simulation package developed at Dares bury Laboratory by W Smith and T R Forester under the auspices of the Engineering and Physical Sciences Research Council EPSRC for the EPSRC s Collaborative Com putational Project for the Computer Simulation of Condensed Phases CCP5 and the Computational Science and Engineering Department at Daresbury Laboratory The pack age is the property of the Council for the Central Laboratory of the Research Councils of the United Kingdom DL POLY 2 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 It should not be redistributed to third parties without consent of the owners The purpose of the DL POLY 2 package is to provide software for academic research that is inexpensive accessible and free of commercial considerations Users have direct access to source code for modification and inspection In the spirit of the enterprise con tributions in the form of working code are welcome provided the code is compatible with DL_POLY
102. Windows PC using the Compaq Visual FOR TRAN compiler The Message Passing Interface MPI software is essential for parallel execution 1 3 4 Version Control System CVS DL POLY 2 was developed with the aid of the CVS version control system We strongly recommend that users of DL POLY_2 adopt this system for local development of the CCLRC 7 DL_POLY_2 code particularly where several users access the same source code For infor mation on CVS please contact info cvs requestQgnu org or visit the website http www cse clrc ac uk msi software DL POLY 1 3 5 Reguired Program Libraries DL POLY 2 is for the most part self contained and does not require access to additional program libraries The exception is the MPI software library reguired for parallel execution Users reguiring the Smoothed Particle Mesh Ewald SPME method may prefer to use a proprietary 3D FFT other than the one sc dlpfft3 supplied with the package for optimal performance There are comments in the source code which provide guidance for applica tions on Cray and IBM computers which use the routines CCFFT3D and DCFTS respectively Similarly users will find comments for the public domain FFT routine FFTWND_FFT 1 3 6 Internal Documentation All subroutines are supplied with a header block of FORTRAN COMMENT records giving 1 The name of the author and or modifying author 2 The version number or date of production A brief description of the f
103. Y 2 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_2 are as follows U ri io a a 2 75 ij ij 5 12 a 6 U ri 4c z lt 2 76 3 n m potential 27 nm E To u To U Ti e m z n z Y 2 77 4 Buckingham potential buck 1 12 6 potential 12 6 2 Lennard Jones 1j ij C U rij A exp i 2 78 P Tij 5 Born Huggins Meyer potential bhm C D U rij A exp Blo rij E 2 79 CCLRC 32 6 Hydrogen bond 12 10 potential hbnd A B ij ij 7 Shifted force n m potential 27 snm aE To 5 1y a To r _ 1 a v Genny mU G peel 67 nmaE Tij Yro BN av ln m Yro MO j 22 with y cut 2 82 To mt m ie amp Vm 2 84 nA 1 m y m 1 ym mr 1 n y n 1 3 This peculiar form has the advantage over the standard shifted n m potential in that both Eo and ro well depth and location of minimum retain their original values after the shifting process 8 Morse potential mors U rij Eol 1 exp k rij ro 1 2 85 9 Tabulation tab The potential is defined numerically only The parameters defining these potentials are supplied to DL POLY_2 at run time see the description of the FIELD file in section 4 1 3 Each atom type in the system is specified by a un
104. Y 2 keeps a record of the specified short range pair potentials as they are read in If it detects that a given pair potential has been specified before no attempt at a resolution of the ambiguity is made and this error message results See specification of FIELD file Action Locate the duplication in the FIELD file and rectify Message 16 error strange exit from FIELD file processing This should never happen However one remote possibility is that there are more than 10 000 directives in the FIELD file It simply means that DL POLY _2 has ceased pro cessing the FIELD data but has not reached the end of the file or encountered a close directive Probable cause corruption of the DL POLY 2 executable or of the FIELD file We would be interested to hear of other reasons CCLRC 177 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 3 body potential specified DL POLY 2 has encountered a repeat specification of a 3 body potential in the FIELD file Action Locate the duplicate entry remove and resubmit job Message 19 error duplicate 4 body potential specified A 4 body potential has been duplicated in the FIELD file Action Locate the duplicated 4 body potential and remove Resubmit job Message 20 error too many molecule sites specified
105. _2 in regard to its interfaces and programming style and it is adequately docu mented CCLRC ii DISCLAIMER Neither the CCLRC EPSRC CCP5 nor any of the authors of the DL POLY _2 package or their derivatives guarantee that the packages are free from error Neither do they accept responsibility for any loss or damage that results from its use CCLRC iii DL POLY 2 ACKNOWLEDGEMENTS DL POLY 2 was developed under the auspices of the Central Laboratory of the Research Councils the Engineering and Physical Sciences Research Council and the former Science and Engineering Research Council under grants from the Computational Science Initiative and the Science and Materials Computing Committee Advice assistance and encouragement in the development of DL POLY 2 has been given by many people We gratefully acknowledge the comments feedback and bug reports from the CCP5 community in the United Kingdom and throughout the world CCLRC iv Manual Notation In the DL_POLY Manual and Reference Manual specific fonts are used to convey specific meanings 1 2 directories itallic font indicate unix file directories ROUTINES small capitals indicate subroutines functions and programs macros sloped text indicates a macro file of unix commands directive bold text indicates directives or keywords variables typewrite text indicates named variables and parameters FILE large capitals indicate filenames Conte
106. _guaternions vertest vscaleg vscaleg vv_integrate warning warning warning warning warning warning spme_terms lf motion 1 lf rotation 2 pmf_lf pmf_vv temp_scalers vv motion 1 vv rotation 2 spme terms force drivers force drivers dlpoly define system external field terms pmf terms tether terms dlpoly force drivers dlpoly dlpoly dlpoly dlpoly dlpoly tersoff terms tersoff terms dlpoly tersoff terms dlpoly dlpoly dlpoly system properties dlpoly lf rotation 1 lf rotation 2 dlpoly define system dlpoly dlpoly define system exclude terms hkewald terms metal terms metal terms 4pt metal terms rs 284 CCLRC warning warning warning warning xscale zden0 zden1 site terms vdw terms vdw terms 4pt vdw terms rs dlpoly dlpoly system properties 285 Index algorithm 5 6 54 106 Brode Ahlrichs 18 79 81 FIGA 5 55 71 multiple timestep 76 78 80 89 109 111 143 150 194 200 202 204 NOSQUISH 5 56 71 72 QSHAKE 6 55 56 74 76 84 RATTLE 5 56 59 83 RD SHAKE 190 195 SHAKE 5 55 79 83 84 206 velocity Verlet 5 54 56 59 Verlet 17 18 33 42 54 57 58 61 63 65 83 Verlet leapfrog 5 54 55 57 AMBER 4 16 97 98 angular momentum 71 angular restraints 23 angular velocity 71 barostat 6 73 108 211 Berendsen 68 76 151 Hoover 64 boundary conditions 5 41 89 97 150 151 167 184 186 cubic 116
107. aals denloc 271 force_drivers force_drivers force_drivers force_drivers spme_terms timchk utility_pack define_system dlpoly ensemble_tools ewald_terms ewald_terms_4pt ewald_terms_rsq four_body_terms hkewald_terms nlist_builders setup_program setup_program spme_terms system_properties tersoff_terms three_body_terms vv_motion_1 vv rotation 1 vv_rotation_2 spme_terms define_system define_system define_system define_system define_system define_system define_system define_system define_system define_system define_system define_system define_system define_system define_system define_system define_system metal_terms CCLRC 272 denloc metal_terms_4pt denloc metal_terms_rsq diffsn0 system_properties diffsni system_properties dihfrc dlpoly dlpfft3 spme terms ele prd spme terms erfcgen force drivers error angle terms error angles module error bond terms error bonds module error config module error core shell module error core shell terms error define system error dihed module error dihedral terms error dihedral terms 4pt error dihedral terms rs error dlpoly error ewald module error ewald terms error ewald terms 4pt error ewald terms rs error exclude module error exclude terms error external field module error external field terms error force drivers error four body module error four body terms error hkewald module er
108. ages numrdf number of configurations used in rdf averages chit relaxation time of thermostat CCLRC chip conint nzden record 2 virtot vircom eta strcns strbod record 3 stpval record 4 sumval record 5 ssgval record 6 zumval record 7 ravval record 8 stkval record 9 xx0 yy0 zzo record 10 XXS yys ZZS record 11 rdf record 12 zdens 4 1 4 2 135 relaxation time of barostat conserved quantity for selected ensemble number of configurations used in z density total system virial rigid body COM virial scaling factors for simulation cell matrix elements 9 constraint stress tensor elements 9 rigid body stress tensor elements 9 instantaneous values of thermodynamic variables mxnstk average values of thermodynamic variables mxnstk fluctuation squared of thermodynamic variables mxnstk running totals of thermodynamic variables mxnstk rolling averages of thermodynamic variables mxnstk stacked values of thermodynamic variables mxstakxmxnstk x component of atomic displacement MSD mxatms y component of atomic displacement MSD mxatms z component of atomic displacement MSD mxatms x coordinates of tether points mxatms y coordinates of tether points mxatms z coordinates of tether points mxatms Optional RDF array mxrdf xmxvdw Optional z density array mxrdf xmxsvdw Further Comments Note that recompiling DL _POLY_2 with a different DL_PARAMS I
109. akefiles may be found in the build sub directory for variants of DLPOLY 2 Users will need to modify the Makefile if they are to add additional functionality to the code or if it requires adaptation for a non specified computer Modifications may also be needed for the Smoothed Particle Mesh Ewald method if a system specific 3D FFT routine is desired see below Modifying the makefile Note the following system requirements for a successful build of DL_POLY_2 1 a FORTRAN 90 compiler 2 the Java SDK from Sun Microsystems if the GUI is required 3 a UNIX operating system or Windows XP if a PC version is required Run the Makefile you copied from the build sub directory in the srcf90 sub directory It will create the executable in the execute sub directory The compilation of the program is initiated by typing the command make target where target is the specification of the required machine e g hpcx For many computer systems this is all that is required to compile a working version of DL_POLY_2 To determine which targets are already defined in the makefile typing the command make without a nominated target will produce a list of known targets The full specification of the make command is as follows make lt TARGET gt lt TYPE gt lt EX gt lt BINROOT gt CCLRC 92 where some or all of the keywords may be omitted The keywords and their uses are described below Note that keywords m
110. akes use of the Verlet neighbour list described above CCLRC 34 2 3 2 Three Body Potentials The three body potentials in DL POLY 2 are mostly valence angle forms They are pri marily included to permit simulation of amorphous materials e g silicate glasses However these have been extended to include the Dreiding 6 hydrogen bond The potential forms available are as follows 1 Truncated harmonic thrm k U Ojik g Ojik 09 exp r r3 P 2 92 2 Screened Harmonic shrm k U Ojik z Ojik bo exp rij pi rix pa 2 93 3 Screened Vessal 24 bvs1 k U Ojik SOx 7 f e T Ojik n J exp rij p1 Tik p2 2 94 4 Truncated Vessal 25 bvs2 U ix Rl0fw jw 00 Oju 8o 2m Sn Ojik 60 7 60 exp ri rix p 2 95 5 Dreiding hydrogen bond 6 hbnd U Ojik Diycos Ojik 5 Rn r jk 6 Rnp r je O 2 96 Note that for the hydrogen bond the hydrogen atom must be the central atom Several of these functions are identical to those appearing in the intra molecular valenceangle de scriptions above There are significant differences in implementation however arising from the fact that the three body potentials are regarded as inter molecular Firstly the atoms involved are defined by atom types not specific indices Secondly there are no excluded atoms arising from the three body terms The inclusion of pair po
111. al virbnd real bond virial record v stpval 16 stpval 20 virang real valence angle 3 body virial vircon real constraint virial virtet real tethering virial volume real volume tmpshl real core shell temperature CCLRC record vi stpval 21 stpval 25 147 core shell potential energy core shell virial MD cell angle a MD cell angle 8 MD cell angle y Potential of Mean Force virial pressure mean sguared displacement of first atom types mean sguared displacement of second atom types mean sguared displacement of last atom types the next 9 entries if the stress tensor is calculated xx component of stress tensor xy component of stress tensor xz component of stress tensor yx component of stress tensor zz component of stress tensor the next 9 entries 4f a NPT simulation is undertaken engshl real virshl real alpha real beta real gamma real record vii stpval 26 stpval 27 virpmf real press real the next ntpatm entries amsd 1 real amsd 2 real amsd ntpatm real stress 1 real stress 2 real stress 3 real stress 4 real real stress 9 real cell 1 real cell 2 real cell 3 real cell 4 real ease real cell 9 real x component of a cell vector y component of a cell vector z component of a cell vector x component of 6 cell vector z component of c cell vector Note The stress tensor is calculated only if the code is compiled with the STRESS option see section 3 2 1 Cell shape varying
112. allocation of core_shell work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1120 error failed allocation of inversion arrays This is a memory allocation error Probable cause excessive size of simulated system CCLRC 219 Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1130 error failed allocation of inversion work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1140 error failed allocation of four body arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1150 error failed allocation of four body work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the use
113. allocation of nptqvv_h2 f densO array This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 2230 error failed allocation of nptqvv_h2 f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 2240 error failed allocation of nstqvv_b1 f dens0 array This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor CCLRC 241 Message 2250 error failed allocation of nstqvv_b1 f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 2260 error failed allocation of nstqvv_b2 f densO array This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a small
114. ameter mxtbnd Message 31 error too many chemical bonds in system DL POLY 2 sets a limit on the number of chemical bond potentials in the simulated system as a whole This number is a combination of the number of molecules and the number CCLRC 179 of bonds per molecule divided by the number of processing nodes Termination results if this number is exceeded Do not confuse this error with that described by message 30 above Action Standard user response Fix the parameter mxbond Message 32 error integer array memory allocation failure DL_POLY_2 has failed to allocate sufficient memory to accommodate one or more of the integer arrays in the code Action This may simply mean that your simulation is too large for the machine you are running on Consider this before wasting time trying a fix Try using more processing nodes if they are available If this is not an option investigate the possibility of increasing the heap size for your application Talk to your systems support people for advice on how to do this Message 33 error real array memory allocation failure DL POLY 2 has failed to allocate sufficient memory to accommodate one or more of the real arrays in the code Action This may simply mean that your simulation is too large for the machine you are running on Consider this before wasting time trying a fix Try using more processing nodes if they are available If this is not an option investigate the poss
115. aries IMCON 3 The parallelepiped MD cell The parallelepiped e g monoclinic or triclinic cell is generally used in simulations of crystalline materials where its shape and dimension is commensurate with the unit cell of the crystal Thus for a unit cell specified by three principal vectors a b c the MD cell is defined in the DL POLY 2 CONFIG file by the vectors La1 La2 La3 Mb1 Mb2 Mbs Nci Mco Nc3 in which L M N are integers reflecting the multiplication of the unit cell in each principal direction Note that the atomic coordinate origin is the centre of the MD cell The parallelepiped boundary condition can be used with the Ewald summation method Truncated octahedral boundaries IMCON 4 CCLRC 170 The truncated octahedral MD cell This is one of the more unusual MD cells available in DL_POLY but it has the advantage of being more nearly spherical than most other MD cells This means it can accommodate a larger spherical cutoff for a given number of atoms which leads to greater efficiency This can be very useful when simulating for example a large molecule in solution where fewer solvent molecules are required for a given simulation cell width The principal axes of the truncated octahedron see figure pass through the centres of the square faces and the width of the cell measured from square face to square face along a principal axis defines the width D of the cell From this the cell vectors required in the D
116. arted with the standard Verlet leapfrog prediction of u t and T t The conserved quantity is derived from the extended Hamiltonian for the system which to within a constant is the Helmholtz free energy 1 t Hyvr U KE 72x0 Sf x s ds 2 216 T o If bond constraints are present an extra iteration is required due to the call to the SHAKE routine The algorithm is implemented in the DL_POLY routine NvT_H1 for systems with bond constraints In the VV version of DL_POLY_2 the Hoover algorithm is split into stages in accordance with the principles of Martyna et al 17 for designing reversible integrators The scheme applied here is sia AN nt T t Taw ve e alia Fan s 1 At f t u t At AS S Hrtan LAFUR TAi call rattle R 1 t At u t At v t At AA 2 2 m call rattle V 1 AtNrk x t At x t 5At 20 2 T t At Text v t At Vv t At at At u t At 2 217 Routines rattle R and rattle V apply the bondlength and velocity constraint formulae 2 210 and 2 211 respectively The equations have the same conserved variable Hnyr as the LF scheme The integration is performed by the subroutine NVTVV_H1 which calls subroutines RATTLE_R RATTLE_V and NVTSCALE 2 5 4 2 Berendsen Thermostat In the Berendsen algorithm the instantaneous temperature is pushed towards the desired temperature by scaling the velocities at each step oy a i 55 2 J 2 218 CCLRC 6
117. at The thermostat is coupled to both the translational and rotational degrees of freedom and so both the translational and rotational velocities are propagated in an analogous manner to the thermostated atomic velocities The barostat however is coupled only to the translational degrees of freedom and not to the rotation DL POLY _2 supports both Hoover and Berendsen thermostats and barostats for systems containing rigid bodies For LF integration the Hoover thermostat is implemented in NVTQ_H1 the Hoover isotropic barostat plus thermostat in NPTQ_H1 and the anisotropic barostat in NSTQ_H1 The analogous routines for the Berendsen algorithms are NVTQ_B1 NPTQ_B1 and NSTQ_B1 These subroutines also call RDSHAKE_1 to handle any rigid bonds which may be present For VV integration the Hoover thermostat is implemented in NVTQVV_H1 NVTQSCL the Hoover isotropic barostat plus thermostat in NPTQVV_H1 NPTOSCL T NPTOSCL P and the anisotropic barostat in NSTQVV_H1 NSTOSCL T NSTOSCL P The analogous routines for the Berendsen algorithms are NVTQVV_B1 NPTQVV_B1 and NSTGVV B1 The subroutines in brackets represent supporting subroutines These subroutines also call RATTLE_R and RATTLE_V to handle any rigid bonds which may be present CCLRC 74 2 5 7 3 Linked Rigid Bodies The above integration algorithms can be used for rigid bodies in systems containing atomic species whose equations of motion are integrated with the standard leapfrog
118. at of SHAKE The only significant difference is that increments to the atomic forces not the atomic positions are passed between processors at the end of each iteration Chapter 3 DL POLY 2 Construction and Execution CCLRC 86 Scope of Chapter This chapter describes how to compile a working version of DL_POLY_2 and how to run it CCLRC 87 3 1 Constructing DL_POLY 2 an Overview 3 1 1 Constructing the Standard Version DL POLY_2 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 simu lation 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 provided the necessary tools to assemble such a version The method of creating the stan dard version is described in detail in this chapter however a brief step by step description follows 1 DL_POLY_2 is supplied as a UNIX compressed tar file This must uncompressed and un tared to create the DL POLY 2 directory section 1 4 2 In the build subdirectory you will find the required DL_POLY_2 makefile see section 3 2 1 and Appendix A where a sample Makefile is listed This must be copied into the subdirectory containing the relevant source code In most cases thi
119. atively FTP may be used to copy the postscript file from the CCP5 Program Library at Daresbury Laboratory in the follow ing manner 1 move to the desired directory on YOUR machine 2 type ftp ftp dl ac uk 3 enter userid anonymous 4 enter passwd your e mail address 5 change to the DL_POLY directory cd ccp5 DL POLY DL POLY 2 6 change to the DOCUMENTS directory cd DOCUMENTS 7 type binary 8 type get LICENCE ps Z or get GROUP LICENCE ps Z 9 type quit The licence file will need to be uncompressed using the unix uncompress command before printing Note that there are two versions of the licence available one for single academic users with perhaps one or two postgraduate students and one for academic groups with perhaps several research staff including postdoctoral and permanent staff Choose the one most suitable for you The licences are package licences which allow you access to all the DL_POLY software Once you have obtained the licence form you should sign it and return it to the following address CCLRC 12 Dr W Smith DL_POLY Program Library Computational Science and Engineering Department CCLRC Daresbury Laboratory Daresbury Warrington WA4 4AD England Alteratively you may Fax the licence to 44 0 1925 603634 or e mail a scanned copy as a PDF file to w smith dl ac uk When the signed licence has been received information on downloading the DL POLY_2 source code will be sent by e mail so
120. 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 2 create the velocities for itself Message 86 error calculated 3 body potential index too large DL POLY 2 has a permitted maximum for the calculated index for any three body poten tial in the system i e as defined in the FIELD file If there are m distinct types of atom in the system the index can possibly range from 1 to m m 1 2 If the internally calculated index exceeds this number this error report results Action Standard user response Fix the parameter mxtbp Message 87 error too many link cells reguired in fbpfrc The FBPFRC subroutine uses link cells to compute the four body forces This message in dicates that the link cell arrays have insufficient size to work properly Action Standard user response Fix the parameter mxcell Message 88 error too many tersoff potentials specified Too many Tersoff potentials have been defined in the FIELD file Certain arrays must be increased in size to accommodate the data Action Standard user response Fix the parameter mxter Message 89 error too many four body potentials specified Too many four body potential have been defined in the FIELD file Certain arrays must be increased in size to accommodate the data
121. axmem 32768 N EX EX BINROOT BINROOT TYPE Hitachi SR2201 hitachi sr2201 MAKE FC xf90 FFLAGS c W0 form fixed opt o 3 langlvl save 0 s TRACE intlist o MAKE LDFLAGS LDLIBS lfmpi lmpi LD xf90 o FC xf90 FFLAGS c WO form fixed opt o 3 langlvl save 0 s TRACE CC xcc EX EX BINROOT BINROOT TYPE sg8k mpi MAKE LD f90 03 64 o FC f90 LDFLAGS 1mpi FFLAGS c 03 64 EX EX BINROOT BINROOT TYPE Interpolation tables options Default code Force tables interpolation in r space 3pt interpolation 3pt check OBJ_MOD OBJ_ALL OBJ_RRR OBJ_PAR OBJ_LF OBJ_VV LD EX 0BJ_MOD OBJ_ALL OBJ_RRR OBJ_PAR M CCLRC 165 OBJ_LF OBJ_VV mv EX EXE Force tables interpolation in r space 4pt interpolation Apt check 0BJ MOD OBJ_ALL OBJ_4PT OBJ_PAR OBJ_LF OBJ_VV LD EX 0OBJ MOD OBJ_ALL 0BJ_4PT 0BJ PAR M OBJ_LF 0BJ VV mv EX EXE Force tables interpolation in r squared rsq check 0BJ MOD OBJ_ALL OBJ_RSQ OBJ_PAR 0BJ_LF OBJ_VV LD EX OBJ_MOD OBJ_ALL OBJ_RSQ OBJ_PAR OBJ_LF OBJ_VV mv EX EXE Check that a machine has been specified check Gif test FC undefined then echo You must specify a target machine Clean up the source directory c
122. ay also be set in the unix environment e g with the setenv command in a C shell For PCs running Windows the makefile assumes the user has installed the Cygwin Unix API available from http sources redhat com cygwin The recommended FORTRAN 90 compiler is Compaq Visual Fortran see http www compaq com fortran visual Both of these are copyrighted products 3 2 1 1 Keywords for the Makefile 1 TARGET The TARGET keyword indicates which kind of computer the code is to be com piled for This must be specifed 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 TYPE The TYPE keyword creates variants of the DL_POLY_2 code which determine which scheme is to be used for the interpolation of the short range potential and force arrays The arguments are e 3pt compile with 3 point interpolation default e pt compile with 4 point interpolation e rsq compile with r interpolation A discussion of the merits of the different interpolation methods is given below section IZLI 3 EX The EX keyword specifies the executable name The default name for the executable is DLPOLY X 4 BINROOT The BINROOT keyword specifies the directory in which the executable is to be st
123. b as given in the header line of the input file CONTROL This part of the file is written from the subroutines DLPOLY and SIMDEF 4 2 2 2 Simulation Control Specifications Echoes the input from the CONTROL file Some variables may be reset if illegal values were specified in the CONTROL file This part of the file is written from the subroutine SIMDEF 4 2 2 3 Force Field Specification Echoes the FIELD file A warning line will be printed if the system is not electrically neutral This warning will appear immediately before the non bonded short range potential specifications This part of the file is written from the subroutine SYSDEF 4 2 2 4 Summary of the Initial Configuration This part of the file is written from the subroutine SYSGEN It states the periodic boundary specification the cell vectors and volume if appropriate and the initial configuration of a maximum of 20 atoms in the system The configuration information given is based on the value of levcfg in the CONFIG file If levcfg is 0 or 1 positions and velocities of the 20 atoms are listed If levcfg is 2 forces are also written out For periodic systems this is followed by the long range corrections to the energy and pressure 4 2 2 5 Simulation Progress This part of the file is written by the DL_POLY_2 root segment DLPOLY The header line is printed at the top of each page as step eng_tot temp tot eng_cfg eng vdw eng cou eng bnd eng ang eng_dih eng tet time p
124. bine both Action There is no general remedy for this error if you wish to combine both these capabilities However if your simulation does not require the polarisability to be a feature of rigid species comprising the charged groups but is confined to free atoms or flexible molecules in the same system you may consider overriding this error message and continuing with your simulation The appropriate error trap is found in subroutine SYSDEF Message 99 error cannot use shell model with constraints The dynamical shell model was not designed to work in conjunction with constraint bonds This error results if both are used in the same simulation Action There is no general remedy if you wish to combine both these capabilities However if your simulation does not require the polarisability to be a feature of the constrained species but is confined to free atoms or flexible molecules you may consider overriding this error message and continuing with your simulation The appropriate error trap is in subroutine SYSDEF Message 100 error forces working arrays too small There are a number of arrays in DL POLY 2 that function as workspace for the forces cal culations Their dimension is equal to the number of atoms in the simulation cell divided by the number of nodes If these arrays are likely to be exceeded DL POLY 2 will terminate execution Action Standard user response Fix the parameter msatms CCLRC 190 Message 101
125. body_module f external_field_module f hkewald_module f inversion_module f metal_module f pair_module f pmf_module f property_module f rigid_body_module f shake_module f site_module f CCLRC alloc_spme_arrays alloc_tbp_arrays alloc_ter_arrays alloc_tet_arrays alloc_vdw_arrays angfre bndfre bodystress bomb bspcoe bspgen cell_propagate cell_update cerfr cfgscan check shells check syschg conscan copystring corshl coul0 coul0neu coull coul2 coul2neu coul3 coul3neu coul4 cpy rtc crecv crecv csend csend dblstr dcell define_angles define_atoms define_bonds define_constraints define_core_shell define_dihedrals define_dihedrals define_dihedrals define_external_field subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine function subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine function subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine 244 spme_module f three_body_module f tersoff module f tether_module f vdw_module f angle_terms f bond_terms f rigid body terms f utility pack f spme terms f spme_terms f ensemble_tools f ensemble_tools f hke
126. bond constraints The VV version of this algorithm is implemented as x t wat x t T t Text s WTO 9kpText vt wf Txb A U ne za n Pete Ra x0OTr 6 wit AA ne zara w t 5 At ion r t At r t Atu tt 5 At call rattle R 1 V t At V t exp 31 n t z H t At exp K an 740 H i At f t At 2 m 1 v t Ath u t At 1 At V t At EFA netia a n t At Pool x t At Tr n t A At t At V t At ult At u t At 1 AtNskBp X t At YXY t zAt 2Q A v t At V t A1 xt At t At 20 THM S A WwTr n t At 9kpText 2 236 Routines rattle R and rattle V apply the bondlength and velocity constraint formulae 2 210 and 2 211 respectively The equations have the same conserved variable Hngr as the LF scheme The integration is performed by the subroutine NVTVV_H1 which calls subroutines RATTLE_R RATTLE_V NSTSCALE_T and NSTSCALE_P CCLRC 68 2 5 6 2 Berendsen Barostat With the Berendsen barostat the system is made to obey the equation of motion dP _ ap Pext P TP 2 237 Cell size variations In the isotropic implementation at each step the MD cell volume is scaled by by a factor n and the coordinates and cell vectors by n1 3 where At Sie Pau P 2 238 TP and f is the isothermal compressibility of the system The Berendesen thermostat is applie
127. cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1760 error failed allocation of ewald_spme f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1770 error failed allocation of quench f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1780 error failed allocation of quatqnch f work arrays This is a memory allocation error Probable cause excessive size of simulated system CCLRC 231 Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1790 error failed allocation of quatbook f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1800 error failed allocation of intlist f work arra
128. ciprocal space terms EWALD2 EWALD2_2PT EWALD2_RSQ and EWALD4 EWALD4 2PT handle the real space terms with the same Verlet neighbour list routines that are used to calculate the short range forces and EWALD3 calculates the self interac tion corrections It should be noted that the Ewald potential and force interpolation arrays in DL POLY 2 are erc and fer respectively 2 4 6 Smoothed Particle Mesh Ewald As its name implies the Smoothed Particle Mesh Ewald SPME method is a modification of the standard Ewald method DL POLY_2 implements the SPME method of Essmann et al 31 Formally this method is capable of treating van der Waals forces also but in DL_POLY_2 it is confined to electrostatic forces only The main difference from the standard Ewald method is in its treatment of the the reciprocal space terms By means of an interpolation procedure involving complex B splines the sum in reciprocal space is represented on a three dimensional rectangular grid In this form the Fast Fourier Trans form 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 31 1 Interpolation of the exp ik rj terms given here for one dimension ezp 2Tiu k L b k M u Oezp 2mikt K 2 165 j in which k is the intege
129. constant h which is 6 350780668 x Eoto In addition the following conversion factors are used The coulombic conversion factor yo is _ 1 6 _ 139935 4935 T E anet such that UMKS Eo YoU Internal Where U represents the configuration energy The Boltzmann factor kg is 0 831451115 E K such that T Ekin kB represents the conversion from kinetic energy in internal units to temperature in Kelvin Note In the DL_POLY_2 CONTROL and OUTPUT files the pressure is given in units of kilo atmospheres katm at all times The unit of energy is either DL POLY 2 units specified above or in other units specified by the user at run time The default is DL_POLY units CCLRC 9 1 3 11 Error Messages All errors detected by DL_POLY_2 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 2 will sometimes print warning mes sages These indicate that the code has detected something that is unusual or inconsistent The detection is non fatal but the user should make sure that the warning does represent a harmless condition 1 4 The DL POLY 2 Directory Structure The entire DL POLY 2 package is stored in a Unix directory structure The
130. cular connectivity data and establish the communication procedure between nodes and the QUENCH routine is required to set the starting velocities correctly Also needed in the initialisation is the routine FOR GEN which constructs the interpolation arrays for the short range forces calculations and the routine EXCLUDE which identifies atoms that are explictly chemically bonded through bonds constraints or valence angles The resulting list is known as the excluded atoms list The calculation of the pair forces represents the bulk of any simulation A Verlet neighbour list is used by DL_POLY 2 in calculating the atomic forces The routine that CCLRC 89 constructs this this is called PARLST This routine builds the neighbour list taking into account the occurrence of atoms in the excluded atoms list The routine SRFRCE calculates the short range van der Waals forces making use of the IMAGES routine to handle any periodic boundary conditions Coulombic forces are handled by a varity of routines COULO COUL1 and COUL2 handle Coulombic forces without periodic boundaries EWALD1 EWALD2 and EWALD3 are used for systems with periodic boundaries an additional routine EWALD4 is necessary for the multiple timestep algorithm Intramolecular forces require the routines ANGFRC BNDFRC and DIHFRC If the multiple timestep algorithm is required the routine MULTIPLE must be used to call the various forces routines It also calls the PRIMLST routine to sp
131. d at the same time In practice is a specified constant which DL _POLY_2 takes to be the isothermal compressibility of liquid water The exact value is not critical to the algorithm as it relies on the ratio 7Tp 5 rp is specified by the user The LF version of this algorithm is implemented in NPT_B1 with 4 or 5 iterations used to obtain self consistency in the u t It calls RDSHAKE_1 to handle constraints The VV version is implemented in subroutine NVTVV B1 which calls constraint subroutines RATTLE_R and RATTLE_V Cell size and shape variations The extension of the isotropic algorithm to anisotropic cell variations is straightforward The tensor 77 is defined by At 1 P godd g 2 239 Lo Is and the new cell vectors given by H t At nH t 2 240 As in the isotropic case the Berendsen thermostat is applied simultaneously and 4 or 5 iterations are used to obtain convergence The LF version of the algorithm is implemented in subroutine NST B1 and the VV version in NSTVV B1 The former calls RDSHAKE 1 to handle constraints and the latter calls subroutines RATTLE_R and RATTLE_V 2 5 7 Rigid Bodies and Rotational Integration Algorithms 2 5 7 1 Description of Rigid Body Units A rigid body unit is a collection of point atoms whose local geometry is time invariant One way to enforce this in a simulation is to impose a sufficient number of bond constraints between the atoms in the unit However in many cases this is ma
132. d on neutral groups of atoms then at worst at long distance the interaction will be a dipole dipole interaction and vary as 1 r The truncation effects at the cutoff are therefore much less severe than if an atomistic scheme is used In DL_POLY_2 the interaction is evaluated between all atoms of both groups if any site of the first group is within the cutoff distance of any site of the second group The groups are known interchangeably as charge groups or neutral groups in the documentation which serves as a reminder that the advantages of using such a scheme are lost if the groups carry an overall charge There is no formal requirement in DL_POLY_2 that the groups actually be electrically neutral The charge group scheme is more cpu intensive than a simple atomistic cutoff scheme as more computation is required to determine whether or not to include a set of interactions However the size of the Verlet neighbourhood list easily the largest array in DL POLY 2 is considerably smaller with a charge group scheme than an atomistic scheme as only a list of interacting groups need be stored as opposed to a list of interacting atoms 2 4 2 Direct Coulomb Sum Use of the direct Coulomb sum is sometimes necessary for accurate simulation of isolated nonperiodic systems It is not recommended for periodic systems The interaction potential for two charged ions is 1 gigj Fe 2 140 rij Ame Tij with g the charge on an atom label
133. d vectors r and Tip brig cos Y 4 Uh 2 22 VijVik In DL_POLY_2 the most general form for the valence angle potentials can be written as U Ojik Tij Tik A Pjik S rij S Tik 2 23 where A 0 is a purely angular function and S r is a screening or truncation function All the function arguments are scalars With this reduction the force on an atom derived from the valence angle potential is given by A O r gra Ojik Pigs Tik 2 24 with atomic label being one of i j k and a indicating the x y z component The derivative is O org U ins Tij Tik lri S ri Fg A Cain ae 0 A 0 ji S rik ej de rg dry TO r o A jix S ris See Ii S rik 2 25 Tik Orik with 64 1 if a band d 0 if a Z b In the absence of screening terms S r this formula reduces to O O org U Piit Tij Tik grg Ai 2 26 The derivative of the angular function is O 1 O o Tij Tik A 0 ik A 0jix 2 2 2 Ore 0 k P OO ii 0 k Or TijTik 3 0 with O J riz T Tik T e 62 bei E n n Org TiTik ijTik TijTik re ro cos Ojik fos bei a ek wE 2 28 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 W ley f tir fa 2 29 CCLRC 23 It is worth noting that in
134. d with the flag DPVM set but the number of PVM nodes was not stated Action Delete the module INITCOMMS O from the srcf90 directory and re make the executable this time including the directive PVM_NODES n where n is the number of nodes you require with the make command Message 2 error machine not a hypercube The number of nodes on the parallel machine is not a power of 2 Action Specify an appropriate number of processors for job execution If you are using PVM see Action for error message 1 Message 3 error unknown directive found in CONTROL file This error most likely arises when a directive is misspelt Action Locate incorrect directive in CONTROL file and replace Message 4 error unknown directive found in FIELD file This error most likely arises when a directive is misspelt or is encountered in an incorrect lo cation 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 Message 5 error unknown energy unit requested The DL POLY 2 FIELD file permits a choice of units for input of energy parameters These may be electron volts ev kilocalories kcal kilojoules kj or the DL POLY 2 internal units 10 J mol internal There is no default value Failure to specify any of these correctly or reference to other energy units will result in this error message See documen tation of the FIEL
135. data are copied into the execute sub directory when a program is being tested The test cases are documented in chapter 5 1 4 4 The bench Sub directory This directory contains examples of input and output data for DL POLY 2 that are suitable for benchmarking DL POLY 2 on large scale computers These are described in chapter 5 1 4 5 The execute Sub directory In the supplied version of DL POLY 2 this sub directory contains only a few macros for copying and storing data from and to the data sub directory and for submitting programs for execution These are decribed in section 6 1 1 However when a DL POLY 2 program is assembled using its makefile it will be placed in this sub directory and will subsequently be executed from here The output from the job will also appear here so users will find it convenient to use this sub directory if they wish to use DL POLY 2 as intended The experienced user is not absolutely required to use DL POLY 2 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 2 simulation programs The makefiles supplied select the ap propriate subroutines from the srcf90 sub directory and deposit the executable program in the execute directory The user is advised to copy the appropriate makefile into the srcf90 directory in case any modifications are required The copy in the build sub directory will then ser
136. define_system dihedral_terms dihedral_terms_4pt dihedral_terms_rsq external_field_terms four_body_terms inversion_terms metal_terms metal_terms_4pt metal_terms_rsq pmf_terms rigid_body_terms setup_program 275 CCLRC 276 getrec shake_terms getrec site_terms getrec tersoff_terms getrec tether_terms getrec three_body_terms getrec vdw_terms getrec vdw_terms_4pt getrec vdw_terms_rsq getrotmat 1f_rotation_1 getrotmat 1f_rotation_2 getrotmat vv_rotation_1 getrotmat vv_rotation_2 getvom 1f motion 1 getvom If rotation 1 getvom If rotation 2 getvom vv motion 1 getvom vv rotation 1 getvom vv_rotation_2 getword angle terms getword bond terms getword dihedral terms getword dihedral terms 4pt getword dihedral terms rs getword external field terms getword four body terms getword inversion terms getword metal terms getword metal terms 4pt getword metal terms rs getword setup_program getword site_terms getword tersoff_terms getword tether_terms getword three_body_terms getword vdw_terms getword vdw_terms_4pt getword vdw_terms_rsq gimax define_system gimax exclude_terms gimax force_drivers gimax If rotation_1 gimax 1f_rotation_2 gimax merge_hcube gimax nlist_builders CCLRC gimax gimax gisum gisum gisum gisum gisum global_sum_forces gstate gstate gstate gstate gstate gstate gstate gstate gstate gstate gstate
137. ders should understand that DL POLY 2 does recognise molecular entities defined either through con straint bonds or 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 later in sections 2 5 2 1 and 2 5 7 2 2 The Intramolecular Potential Functions In this section we catalogue and describe the forms of potential function available in DL_POLY_2 The key words required to select potential forms are given in brackets before each definition The derivations of the atomic forces virial and stress tensor are also outlined 2 2 1 Bond Potentials CCLRC 19 The interatomic bond vector The bond potentials describe explicit bonds between specified atoms They are functions of the interatomic distance only The potential functions available are as follows 1 Harmonic bond harm 1 U rig 5klrij ro 2 2 2 Morse potential mors U rij Eo 1 exp k rij ro 1 23 U rii 5 y 2 4 ij ij 4 Restrained harmonic rhrm 3 12 6 potential bond 12 6 1 U rij gh rig 19 ra to Sre 2 5 1 U rij 5hre kre fg Fal Ta r rol gt Te 2 6 5 Guartic potential guar k 5 k kl 4 U ris 5 Tij To 3 rij To F ij To 2 7 2 3 4 6 Buckingham potential buck Tij C ij A 2 8 Uey A ew T 5 2 8 In these for
138. diikn X 2 65 Ji g Obijkn Pisin 22 COS Gi jk 1 ao ON dej dei an Ma IC de Unig teen Un Lij Ben Ofna T Tij Ukn Tis Uy N j M ro ek ti o Z r Lij Upn kn rig Tik rig kn Tik WEF UknTik Tik Tis k Pi N M ro n J w r Tae kn kn Lij Tik Lij kn Tik ann UknTik Vik Tipo tp N 1 2 A a en Sei R r rij pn kn rij Tin 7 ri rn Tin a UknTin in 3 a den bw a tig Oyna Opn lag Tin l g rn Ein DES UknTin Tin 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 6 of the full inversion potential specifically the inversion angle pertaining to the out of plane vector r j 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 4 W rn 2 66 i l However it is possible to show by thermodynamic arguments cf 26 or simply from the fact that the sum of forces on atoms j k and n is egual and opposite to the force on atom i that the inversion potential makes no contribution to the atomic virial If the force componen
139. directions to ensure the reciprocal space sum is egually accurate in all directions The values of kmax1 kmax2 and kmax3 must be commensurate with the cell geometry to ensure the same minimum wavelength is used in all directions For a cubic cell set kmax1 kmax2 kmax3 However for example in a cell with dimensions 2A 2B C ie a tetragonal cell longer in the c direction than the a and b directions use 2kmaxl 2kmax2 kmax3 If the values for the kmax used are too small the Ewald sum will produce spurious results If values that are too large are used the results will be correct but the calculation will consume unnecessary amounts of cpu time The amount of cpu time increases with kmax1 x kmax2 x kmax3 3 3 5 2 Hautman Klein Ewald Optimisation Setting the HKE parameters can also be achieved rather simply by the use of a hke precision directive in the CONTROL file e g hke precision 1d 6 1 1 which specifies the required accuracy of the HKE convergence functions plus two additional integers the first specifying the order of the HKE expansion nhko and the second the maximum lattice parameter nlatt DL POLY 2 will permit values of nhko from 1 3 meaning the HKE Taylor series expansion may range from zeroth to third order Also nlatt may range from 1 2 meaning that 1 the nearest neighbour and 2 and next nearest neighbour cells are explicitly treated in the real space part of the Ewald sum Increasing either of these
140. e excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1670 error failed allocation of work arrays in nptq_h2 f This is a memory allocation error Probable cause excessive size of simulated system CCLRC 229 Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1680 error failed allocation of density array in nptq_h2 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1690 error failed allocation of work arrays in nstq_b2 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1700 error failed allocation of density array in nstq_b2 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger
141. e lf integrate lf integrate lf integrate lf integrate lf integrate lf integrate lf integrate lf motion 1 lf motion 1 lf motion 1 lf motion 1 lf motion 1 lf motion 1 lf motion 1 lf motion 1 lf motion 1 lf motion 1 lf motion 1 lf motion 1 lf motion 1 lf motion 1 lf rotation 1 lf rotation 1 lf rotation 1 lf rotation 1 gdsum error gstate npt_bi npt_hi nptq_bi nptq_b2 nptq_hi nptq_h2 nst bl nst_hi nst bl nst b2 nst hi nstq_h2 nve_1 nveg_1 nveg_2 nvt bl nvt el nvt_hi nvt bl nvt b2 nvt hi nvt h2 pmflf cell_propagate error error gdsum getcom getvom gstate images kinstress matmul merge rdshake 1 shmove splice bodystress cell propagate error getcom 259 CCLRC lf rotation 1 lf rotation 1 lf rotation 1 lf rotation 1 lf rotation 1 lf rotation 1 lf rotation 1 lf rotation 1 lf rotation 1 lf rotation 1 lf rotation 1 lf rotation 2 lf rotation 2 lf rotation 2 lf rotation 2 lf rotation 2 lf rotation 2 lf rotation 2 lf rotation 2 lf rotation 2 lf rotation 2 lf rotation 2 lf rotation 2 lf rotation 2 lf rotation 2 lf rotation 2 lf rotation 2 lf rotation 2 lf rotation 2 lf rotation 2 lf rotation 2 merge_hcube merge_hcube merge_hcube merge_hcube merge_hcube merge_hcube merge_hcube merge_hcube merge_systol merge_systol merge_systol merge_systol merge_systol getrotmat getvom gimax gstate images kinstressf matmul merge mergel rdsha
142. e 4 13 potential parameter see table 4 13 potential parameter see table 4 13 cutoff range for this potential A The variables pertaining to each potential are described in table 4 13 Note that the fifth variable is the range at which the three body potential is truncated The distance is in A measured from the central atom The specification of four body potentials is initiated by the directive fbp n where n is the number of four body potentials to be entered There follows n records each specifying a particular four body potential in the following manner atmnam 1 a8 atmnam 2 a8 atmnam 3 a atmnam 4 a key a4 variable 1 real variable 2 real variable 3 real first atom type central site second atom type third atom type fourth atom type potential key See table 4 14 potential parameter see table 4 14 potential parameter see table 4 14 cutoff range for this potential CCLRC 131 The variables pertaining to each potential are described in table 4 14 Note that the third variable is the range at which the four body potential is truncated The distance is in A measured from the central atom Table 4 14 Four body Potentials key potential type Variables 1 2 functional formi harm Harmonic k do U 5k b 0 hcos Harmonic cosine k Qo U 6 E cos cos o plan Planar A U A 1 cos to is the inversion angle 4 1 3 4 Metal Potentials
143. e Ewald SPME see Ewald SPME stress tensor 58 stress tensor 23 26 29 31 33 34 37 39 42 44 46 52 53 58 64 206 sub directory 156 158 bench 9 build 9 data 9 execute 9 174 java 9 public 9 source 9 utility 9 thermostat 6 40 73 77 108 205 211 Berendsen 68 73 76 150 151 Nos Hoover 64 65 73 76 89 150 CCLRC units DL_POLY 8 143 energy 119 pressure 8 64 109 143 Verlet neighbour list 47 76 77 80 82 88 89 111 191 WWW 3 11 12 288
144. e normal VV scheme CCLRC 84 2 When the velocity is updated iteration of the constraint force takes place The incre mental changes to the velocity are communicated between nodes sharing constrained atoms as for the bondlength constraints 3 Iteration is repeated until the bond constraints are converged 4 After convergence the velocity arrays on each node are passed to all the other nodes by splicing This scheme contains a number of non trivial operations which are described in detail in 30 However some general comments are worth making The compilation of the list of constrained atoms on each node and the circulation of the list items 1 3 above need only be done once in any given simulation It also transpires that in sharing bond contraints between nodes there is an advantage to keeping as many of the constraints pertaining to a particular molecule together on one node as is possible within the requirement for load balancing This reduces the data that need to be transferred between nodes during the iteration cycle It is also advantageous if the molecules are small to adjust the load balancing between processors to prevent shared atoms The loss of balance is compensated by the elimination of communications during the SHAKE cycle These techniques are exploited by DL_POLY_2 The QSHAKE algorithm is an extension of the SHAKE algorithm for constraint bonds between rigid bodies The parallel strategy is very similar to th
145. e processors or a machine with larger memory per processor Message 1850 error failed allocation of multipleneu f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1860 error failed allocation of multiple_nsq f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1870 error failed allocation of parlst_nsq f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1880 error failed allocation of parlst f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1890 error failed allocation of parlink f work arrays This is a memory allocation error Probable cause excessive size of simula
146. e subroutine REVIVE REVCON is the restart con figuration 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 2 will always produce a REVCON file but a failed job may not produce the file if an insufficient number of timesteps have elapsed ndump is a parameter defined in the PARSET F subroutine of the SETUP_PROGRAM F file found in the srcf90 directory of DL_POLY_2 Changing ndump ne cessitates recompiling DL_POLY_2 REVCON is identical in format to the CONFIG input file see section 4 1 2 REVCON should be renamed CONFIG to continue a simulation from one job to the next This is done for you by the copy macro supplied in the execute directory of DLPOLY 2 4 2 4 The REVIVE File This file is unformatted and written by the subroutine REVIVE It contains the accumulated statistical data It is updated whenever the file REVCON is updated see previous section REVIVE should be renamed REVOLD to continue a simulation from one job to the next This is done by the copy macro supplied in the execute directory of DL_POLY_2 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 4 1 4 4 2 5 The RDFDAT File This is a formatted file containing em Radial Distribution Function RDF data Its con tents are a
147. e 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 Note CCLRC 97 that you cannot use truncated octahedral or rhombic dodecahedral boundary conditions in conjunction with three body forces due to the use of the link cell algorithm for evaluating the forces 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 This may require the definition of new bond forces in subroutine BNDFRC but this is easy What must be avoided at all costs is specifying the angle potentials without specifying bond potentials In this case DL POLY 2 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 using three body forces This method is not recommended for amorphous systems 3 3 2 Macromolecules Simulations of proteins are best tackled using the package DLPROTEIN 46 which is an adaptation of DL_POLY specific to protein modelling However you may simulate proteins and othe
148. e write directly as 2 278 ca VA M nl A WH k C 2 279 where hn is a scalar related to the constraint force via eg n 1 jn 1 Hi dL Now the velocity of the linked atom on molecule A is V l twy x ad 2 280 which on substitution of the above equations gives A i ct St 2 281 CCLRC 76 where dap gn Q ua I 2 282 A Ma A The constraint condition requires that dihp Uap VBb 2 283 and substitution of the equation for vib and the equivalent for ur leads directly to tl ml _ antl n 1 _ 2dABp Gap _ OB Aid s Q4 Op which provides the correction for second constraint This again requires iteration The VV QSHAKE algorithm is implemented in DL_POLY_2 in subroutine NVEQVV_2 with the QSHAKE constraint forces calculated in QRATTLE_R and QRATTLE_V Again it is straightforward to couple these systems to a Hoover or Berendsen thermostat and or barostat The Hoover and Berendsen thermostated versions are found in NVTQVV_H2 and NVTQVV_B2 respectively The isotropic constant pressure implementations are found in NPTQVV_H2 and NPTQVV_B2 while the anisotropic constant pressure routines are found in NSTOVV H2 and NSTQVV_B2 The Hoover versions make use of the thermostat and barostat routines NVTQSCL NPTQSCL_T NPTQSCL_P NSTQSCL_T and NSTQSCL_P according to the ensemble The LF QSHAKE algorithm is implemented in NVEQ_2 with the QSHAKE constraint forces appl
149. eal potential parameter see table 4 7 variable 3 real potential parameter see table 4 7 variable 4 real potential parameter see table 4 7 The meaning of these variables is given in table 4 7 This directive and associated data records need not be specified if the molecule contains no flexible chemical bonds See the note on the atomic indices appearing under the shell directive above 6 constraints n where n is the number of constraint bonds in the molecule Each of the following n records contains index 1 integer first atomic index index 2 integer second atomic index bondlength real constraint bond length This directive and associated data records need not be specified if the molecule contains no constraint bonds See the note on the atomic indices appearing under the shell directive above 7 pmf b where b is the potential of mean force bondlength There follows the definitions of two PMF units a pmf unit n where n is the number of sites in the first unit The subsequent n records provide the site indices and weighting Each record contains index integer atomic site index weight real site weighting b pmf unit n where no is the number of sites in the second unit The subsequent ng records provide the site indices and weighting Each record contains CCLRC 122 Table 4 7 Chemical bond potentials key potential type Variables 1 4 functional form harm Harmonic k ro U r k r ro hrm m
150. ectangular or triclinic MD cells only It is not suitable for any other shape of MD cell Action The user must reconstruct the system according to one of the permitted periodic boundaries Message 1976 error too many link cells required in tersoff f The number of link cells required by the Tersoff routines exceeds the amount allowed for by DL POLY 2 This can happen if the system is simulated under NPT or NST conditions and the system volume increases dramatically Action The problem may cure itself on restart provided the restart configuration has already ex pande significantly Otherwise the user must locate and adjust the mxcel1 according to the standard response procedure Message 1978 error undefined potential in tersoff f A form of Tersoff potential has been requested which DL POLY 2 does not recognise Action Locate the offending potential in the FIELD file and remove Replace with one acceptable to DL_POLY_2 if this is reasonable Alternatively you may consider defining the required CCLRC 236 potential in the code yourself Amendments to subroutines SYSDEF and TERSOFF will be required Message 1980 error failed allocation of nvevv_1 f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1990 e
151. electric constant to f default 1 0 equilibrate simulation for first n timesteps select Ewald sum for electrostatics with automatic parameter optimisation 0 lt f lt 5 ewald sum a k1 k2 k3 finish hke precision f j hke sum a k1 k2ij integrator type job time f select Ewald sum for electrostatics with a Ewald convergence parameter k1 maximum k vector index in x direction k2 maximum k vector index in y direction k3 maximum k vector index in z direction close the CONTROL file last data record select HK Ewald sum for electrostatics with automatic parameter optimisation 0 lt f lt 5 i required order of HKE expansion recommend 1 j required lattice sum order recommend 1 select HK Ewald sum for electrostatics with a Ewald convergence parameter k1 maximum g vector index in x direction k2 maximum g vector index in y direction nhko required order of HKE expansion recommend 1 nlatt required lattice sum order recommend 1 select type of integration algorithm leapfrog leapfrog integration algorithm default velocity velocity Verlet integration algorithm set job time to f seconds CCLRC mult n no elec no vdw pres f prim f print n print rdf quaternion f rdf f reaction restart restart scale rvdw f scale n shake f shift spme precision f 109 set multiple timestep multi step interval activated when n gt 2 ignore coulombic int
152. ell 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 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 cal culated as described above The forces of the harmonic springs are calculated as described for intramolecular harmonic bonds The relationship between the kinetic energy and the temperature is different however as the core shell unit is permitted only three translational degrees of freedom and the degrees of freedom corresponding to rotation and vibration of the unit are discounted the kinetic energy of these is regarded as zero In DL POLY 2 the shell forces are handled by the routine SHLFRC The kinetic en ergy is calculated by CORSHL and the routine
153. em are moved using the Verlet algorithm assuming an absence of rigid bonds constraint forces This is stage 1 of the SHAKE algorithm 2 The deviation in each bondlength is used to calculate the corresponding constraint force 2 207 that retrospectively corrects the bond length 3 After the correction 2 207 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 DL_POLY_2 implements a parallel version of this algorithm 10 see section 2 6 9 The subroutine NVE_1 implements the Verlet leapfrog algorithm with bond constraints for the NVE ensemble The routine RDSHAKE 1 is called to apply the SHAKE corrections to position It should be noted that the fully converged constraint forces G make a contribution to the system virial and the stress tensor The contribution to be added to the atomic virial for each constrained bond is The contribution to be added to the atomic stress tensor is given by gob doy Gf 2 209 where a and indicate the x y z components The atomic stress tensor derived from the pair forces is symmetric CCLRC 59 2 5 2 2 RATTLE RATTLE 13 is the VV version of SHAKE It has two parts the first constrains the bondlength and the second adds a
154. en encountered DL POLY 2 enters the molecular description environment in which only molecular decription keywords and data are valid Immediately following the molecules directive are the records defining individual molecules 1 name of molecule which can be any character string up to 80 characters in length Note this is not a directive just a simple character string 2 nummols n where n is the number of times a molecule of this type appears in the simulated system The molecular data then follow in subsequent records CCLRC 120 3 atoms n where n indicates the number of atoms in this type of molecule A number of records follow each giving details of the atoms in the molecule i e site names masses and charges Each record carries the entries sitnam a8 atomic site name weight real atomic site mass chge real atomic site charge nrept integer repeat counter ifrz integer frozen atom if ifrz gt 0 igrp integer neutral charge group number Note that these entries are order sensitive Do not leave blank entries unless all parameters appearing after the last specified are void The integer nrept need not be specified in which case a value 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 t
155. ensor is given by ob ref 2 117 where a and 5 indicate the z y z components The stress tensor is symmetric Interpolation arrays vmbp and gmbp set up in subroutine TERGEN similar to those in van der Waals interactions 2 3 1 are used in the calculation of the Tersoff forces virial and stress The Tersoff potentials are very short ranged typically of order 3 A This property plus the fact that Tersoff potentials two and three body contributions scale as N where N is the number of particles makes it essential that these terms are calculated by the link cell method 28 DL POLY 2 applies no long range corrections to the Tersoff potentials In DL POLY 2 Tersoff forces are handled by the routines TERSOFF TERINT and TERSOFF3 2 3 4 Four Body Potentials The four body potentials in DL _POLY_ 2 are entirely inversion angle forms primarily in cluded to permit simulation of amorphous materials particularly borate glasses The potential forms available in DL POLY 2 are as follows CCLRC 38 1 Harmonic harm U ijkn Shirin o 2 118 2 Harmonic cosine hcos U dijkn tos 6ijnn cos 60 2 119 3 Planar potential plan U iim A L cos ijkn 2 120 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
156. equested which DL_POLY_2 does not recognise Action Locate the offending potential in the FIELD file and remove Replace with one acceptable CCLRC 209 to DL POLY 2 if this is reasonable Alternatively you may consider defining the required potential in the code yourself Amendments to subroutines SYSDEF and TETHFRC will be required Message 451 error three body potential cutoff undefined The cutoff radius for a three body potential has not been defined in the FIELD file Action Locate the offending three body force potential in the FIELD file and add the required cutoff Resubmit the job Message 452 error undefined pair potential A form of pair potential has been requested which DL POLY 2 does not recognise Action Locate the offending potential in the FIELD file and remove Replace with one acceptable to DL_POLY_2 if this is reasonable Alternatively you may consider defining the required potential in the code yourself Amendments to subroutines SYSDEF and FORGEN will be required Message 453 error four body potential cutoff undefined The cutoff radius for a four body potential has not been defined in the FIELD file Action Locate the offending four body force potential in the FIELD file and add the required cut off Resubmit the job Message 454 error undefined external field A form of external field potential has been requested which DL_POLY_2 does not recognise Action Locate the offending poten
157. er one the user must consider using more processors or a machine with larger memory per processor Message 2270 error failed allocation of nstqvv_b2 f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 2280 error failed allocation of nstqvv_h1 f dens0 array This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 2290 error failed allocation of nstqvv_h1 f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 2300 error failed allocation of nstqvv_h2 f dens0 array This is a memory allocation error Probable cause excessive size of simulated system CCLRC 242 Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 2310 error failed allocation of nstqvv_h2 f work arrays This is a memory al
158. er the interval DL POLY 2 handles this procedure as follows CCLRC TT DL POLY 2 updates the Verlet neighbour list at irregular intervals determined by the movement of atoms in the neighbour list see section 2 1 The interval between updates is usually of the order of 20 timesteps Partitioning the Verlet list into primary and secondary atoms always occurs when the Verlet list is updated and thereafter at intervals of multt timesteps i e the multi step interval specified by the user see section 4 1 1 Immediately after the partitioning the force contributions from both the primary and secondary atoms are calculated The forces are again calculated in total in the subsequent timestep Thereafter for multt 2 timesteps the forces derived from the primary atoms are calculated explicitly while those derived from the secondary atoms are calculated by linear extrapolation of the exact forces obtained in the first two timesteps of the multi step interval It is readily apparent how this scheme can lead to a significant saving in execution time Extension of this basic idea to simulations using the Ewald sum reguires the following 1 the reciprocal space terms are calculated only for the first two timesteps of the multi step 2 the contribution to the reciprocal space terms arising from primary interactions are immediately subtracted leaving only the long range components This is done in real space by subtracting erf terms 3 t
159. eraction corrections and the third is required for the multiple timestep option 2 6 5 Modifications for SPME The SPME method requires relatively little modification for parallel computing The real space terms are calculated exactly as they are for the normal Ewald sum as described above The reciprocal space sum requires a 3D Fast Fourier Transform FFT which in principle should be distributed over the processors but in DL POLY 2 the decision was made to implement a complete 3D FFT on every processor This is expensive in memory and potentially expensive in computer time However a multi processor FFT requires communication between processors and this has significant impact on the famed efficiency of the FFT It transpires that a single processor FFT is so efficient that the adopted strategy is still effective The charge array that is central to the SPME method see section 2 4 6 is however built in a distributed manner and then globally summed prior to the FFT operation 2 6 6 Three and Four Body Forces DL POLY 2 can calculate three four body interactions of the valence angle type 45 These are not dealt with in the same way as the normal nonbonded interactions They are generally very short ranged and are most effectively calculated using a link cell scheme 23 No reference is made to the Verlet neighbour list nor the excluded atoms list It follows that atoms involved in the same three four body term can interact via nonbonded pair
160. eractions ignore short range non bonded interactions set required system pressure to f katm target pressure for constant pressure ensembles set primary cutoff to f A for multiple timestep algorithm only print system data every n timesteps print radial distribution functions set quaternion tolerance to f default 1078 calculate radial distribution functions at intervals of f timesteps select reaction field electrostatics restart job from end point of previous run i e continue current simulation restart job from previous run with temperature scaling i e begin a new simulation from older run set reguired vdw forces cutoff to f A rescale atomic velocities every n steps during eguilibration set shake tolerance to f default 1078 calculate electrostatic forces using shifted coulombic potential select Ewald sum for electrostatics with automatic parameter optimisation 0 lt f lt 5 spme sum a k k2 k3 stack n stats n steps n temp f trajijk timestep f zden Zero select Ewald sum for electrostatics with a Ewald convergence parameter A k1 maximum k vector index in x direction k2 maximum k vector index in y direction k3 maximum k vector index in z direction set rolling average stack to n timesteps accumulate statistics data every n timesteps run simulation for n timesteps set required simulation temperature to f K write HISTORY file with controls i start timestep for dumping c
161. error PMF UNIT record expected A pmf unit directive was expected as the next record in the FIELD file but was not found Action Locate the pmf directive in the FIELD file and examine the following entries Insert the missing pmf unit directive and resubmit Message 463 error unidentified atom in metal potential list DL POLY 2 checks all the metal potentials specified in the FIELD file and terminates the program if it can t identify any one of them from the atom types specified earlier in the file Action Correct the erroneous entry in the FIELD file and resubmit CCLRC 211 Message 465 error calculated pair potential index too large A zero or negative value for the thermostat time constant has been encountered in the CONTROL file Action Locate the ensemble directive in the CONTROL file and assign a positive value to the time constant Message 464 error thermostat time constant must be gt 0 d0 A zero or negative value for the thermostat time constant has been encountered in the CONTROL file Action Locate the ensemble directive in the CONTROL file and assign a positive value to the time constant Message 466 error barostat time constant must be gt 0 d0 A zero or negative value for the barostat time constant has been encountered in the CON TROL file Action Locate the ensemble directive in the CONTROL file and assign a positive value to the time constant Message 468 error r0 too large for
162. error calculated 4 body potential index too large DL_POLY_2 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 x m 1 m 2 6 If the internally calculated index exceeds this number this error report results Action Standard user response Fix the parameter mxfbp Message 102 error parameter mxproc exceeded in shake arrays The RD SHAKE algorithm distributes data over all nodes of a parallel computer Certain arrays in RD SHAKE have a minimum dimension equal to the maximum number of nodes DL POLY 2 is likely to encounter If the actual number of nodes exceeds this the program terminates Action Standard user response Fix the parameter mxproc Message 103 error parameter mxlshp exceeded in shake arrays The RD SHAKE algorithm requires that information about shared atoms be passed be tween nodes If there are too many atoms the arrays holding the information will be exceeded and DL_POLY_2 will terminate execution Action Standard user response Fix the parameter mxlshp Message 105 error shake algorithm failed to converge The RD SHAKE algorithm for bond constraints is iterative If the maximum number of permitted iterations is exceeded the program terminates Possible causes include a bad starting configuration too large a time step
163. error failed allocation of pair arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor CCLRC 234 Message 1945 error failed allocation of tersoff arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1950 error shell relaxation cycle limit exceeded There has been a convergence failure during the execution of relaxed shell polarisation model Probable cause the system is unstable e g in an abnormally high energy configu ration Action Increasing the maximum number of cycles permitted in the shell relaxation set by variable mxpass in the dlpoly f root program may help but it is unlikely A better option is to relax the structure somehow first e g using the zero option in the CONTROL file Message 1953 error tersoff radius of cutoff not defined The Tersoff potential requires the user to specify a short ranged cutoff as part of the po tential description This is distinct from the normal cutoff used by the Van der Waals interactions Action Check the Tersoff potential description in the FIELD file Make sure it i
164. essage 508 error rigid bodies not permitted with RESPA algorithm The RESPA algorithm implemented in DL POLY 2 is for atomic systems only Rigid bod ies or constraints cannot be treated Action There is no cure for this The code simply does not have this capability Consider writing it for yourself Message 510 error structure optimiser not permitted with RESPA The RESPA algorithm in DL POLY 2 has not been implemented to work with the struc ture optimizer You have asked for a forbidden operation Action There is no fix for this In any case it does not make sense to use the RESPA algorithm for this purpose Message 513 error SPME not available for given boundary conditions The SPME algorithm in DL POLY 2 does not work for aperiodic IMCON 0 or slab IMCON 6 boundary conditions Action If the system must have aperiodic or slab boundaries nothing can be done In the latter case however it may be acceptable to represent the same system with slabs replicated in the z direction thus permitting a periodic simulation CCLRC 216 Message 514 error SPME routines have not been compiled in The inclusion of the SPME algorithm in DL POLY 2 is optional at the compile stage If the executable does not contain the SPME routines but the method is requested by the user this error results Action DL POLY 2 must be recompiled with the SPME flags set Beware that your system has the necessary fast Fourier transform rou
165. excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1230 error failed allocation of pmf_shake work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1240 error failed allocation of ewald arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1250 error failed allocation of excluded atom arrays This is a memory allocation error Probable cause excessive size of simulated system CCLRC 221 Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1260 error failed allocation of tethering arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 12
166. ference 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 is diagonal and the components satisfy Iss gt Iyy gt Izz In this local frame the so called Principal Frame the inertia tensor is therefore constant The orientation of the local body frame with respect to the space fixed frame is described via a four dimensional unit vector the quaternion q 20 41 42 4 2 247 and the rotational matrix R to transform from the local body frame to the space fixed frame is the unitary matrix e qG 8 2 qq 043 2 q193 gog2 R 22 ma 93 q a 42 43 2 4293 qoa 2 248 2 q193 9042 2 q293 g001 d4 d 3 rd 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 2 249 With these variables defined we can now consider the eguations of motion for the rigid body unit 2 5 7 2 Integration of the Rigid Body Equations of Motion The equations of translational motion of a rigid body are the same as those describing the motion of a single atom except that the force is the total force acting on the rigid body i e F in equation 2 244 and the mass is the total mass of the rigid body unit i e M in equation 2 241 These equations can be integrated by the standard Verlet LF or VV algorithms described
167. g matmul merge mergel nosquish nptqscl_p nptqscl_t nstqscl_p2 nstqscl_t2 267 CCLRC vv_rotation_2 vv_rotation_2 vv_rotation_2 vv_rotation_2 vv_rotation_2 vv_rotation_2 vv_rotation_2 nvtqscl pivot qrattle_r qrattle_v rotate_omega shmove splice 268 Appendix F Calling Subroutines Calling Subroutines The following table lists the subroutines in DL_POLY_2 and where they are called from Called routine abort_config_read abort_control_read abort_field_read abort_table_read abort_table_read abort_table_read Calling routine define_system define_system define_system vdw_terms vdw_terms_4pt vdw_terms_rsq abortscan setup_program alloc_ang_arrays dlpoly alloc_bnd_arrays dlpoly alloc_config_arrays dlpoly alloc_csh_arrays dlpoly alloc_dih_arrays dlpoly alloc_ewald_arrays dlpoly alloc_exc_arrays dlpoly alloc_fbp_arrays dlpoly alloc_fld_arrays dlpoly alloc_hke_arrays dlpoly alloc_inv_arrays dlpoly alloc_met_arrays dlpoly alloc_pair_arrays dlpoly alloc_pmf_arrays dlpoly alloc_prp_arrays dlpoly alloc_rgbdy_arrays dlpoly alloc_shake_arrays dlpoly alloc_site_arrays dlpoly alloc_spme_arrays dlpoly 269 CCLRC alloc_tbp_arrays alloc_ter_arrays alloc_tet_arrays alloc_vdw_arrays angfrc bndfrc bodystress bodystress bodystress bodystress bomb bspcoe bspgen cell_propagate cell_propagate cell_propagate cell_u
168. g a dielectic term that increases with distance The interatomic potential for two charged ions is 1 gidj Anegelrij Tij UG 2 152 with g the charge on an atom labelled and r the magnitude of the separation vector Tij Tj Ti r is the distance dependent dielectric function In DL POLY 2 it is assumed that this function has the form e r er 2 153 where is a constant Inclusion of this term effectively accelerates the rate of convergence of the Coulomb sum The force on an atom j derived from this potential is 1 dgigj L 2 154 i 2rege T tg with the force on atom i 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 EI 2 156 where a are x y z components The atomic stress tensor is symmetric In DL POLY 2 these forces are handled by the routines COUL2 and COUL2NEU CCLRC 45 2 4 5 Ewald Sum The Ewald sum 11 is the best technique for calculating electrostatic interactions in a periodic or pseudo periodic system The basic model for a neutral periodic system is a system of charged point ions mutually interacting via the Coulomb potential The Ewald method makes two amendments to this simple model Firstly each ion is effectively neutralised at long range by the superposition of a spherical gaussian cloud of opposite charge centred on the ion The combined assembly
169. gaussian screening term appearing in the conventional Ewald sum the function B k1 ko k3 and the discrete Fourier transform of Q k1 ko k 4 Calculating the atomic forces which are given formally by OQ ki k2 k3 Ort 2 172 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 2 subroutines required to calculate the SPME contributions are BSPGEN which calculates the B splines BSPCOE which calculates B spline coefficients SPL_CEXP which calculates the FFT and B spline complex exponentials EWALD_SPME which calculates the reciprocal space contributions SPME_FOR which calculates the recip rocal space forces and DLPFFT3 which calculates the 3D complex fast Fourier transform default code only Cray SGI IBM SP machines have their own FFT routines selected at compile time and the FFTW public FFT is also an option These subroutines calculate the reciprocal space components of the Ewald sum only the real space calculations are per formed by EWALD2 EWALD3 and EWALD 4 as for the normal Ewald sum In addition there are a few minor utility routines CPY_RTC copies a real array to a complex array ELE PRD is an element for element product of two arrays SCL_CSUM is a scalar sum of elements of a complex array and SET_BLOCK initialises an array to a preset value us
170. ge 381 error simulation timestep not specified DL_POLY_2 has failed to find a timestep directive in the CONTROL file Action Place a timestep directive in the CONTROL file with the required timestep specified Message 382 error simulation cutoff not specified DL POLY 2 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 383 error simulation forces option not specified DL POLY 2 has failed to find any directive specifying the electrostatic interactions options in the CONTROL file Action Ensure the CONTROL file contains at least one directive specifying the electrostatic po tentials e g ewald coul no electrostatics etc Message 384 error verlet strip width not specified DL POLY 2 has failed to find the delr directive in the CONTROL file Action Insert a delr directive in the CONTROL file specifying the width of the verlet strip augmenting the forces cutoff Message 385 error primary cutoff not specified DL POLY 2 has failed to find the prim directive in the CONTROL file Necessary only if multiple timestep option required Action Insert a prim directive in the CONTROL file specifying the primary cutoff radius in the multiple timestep algorithm CCLRC 201 Message 386 error primary cutoff larger than rcut The primary cutoff specified by the prim directive in the CONTROL file exceeds
171. ged consecutively Note that reordering the file in this way implies a rearrangement of the CONFIG file also Message 250 error Ewald sum requested with neutral groups DL_POLY_2 will not permit the use of neutral groups with the Ewald sum This error results if the two are used together Action Either remove the neut directive from the FIELD file or use a different method to evaluate the electrostatic interactions Message 260 error parameter mxexcl exceeded in excludeneu routine An error has been detected in the construction of the excluded atoms list for neutral groups This occurs when the parameter mxexcl is exceeded in the EXCLUDENEU routine Action Standard user response Fix parameter mxexcl Message 300 error incorrect boundary condition in parlink The use of link cells in DL POLY 2 implies the use of appropriate boundary conditions This error results if the user specifies octahedral dodecahedral or slab boundary conditions Action The simulation must be run with cubic orthorhombic or parallelepiped boundary condi tions Message 301 error too many rigid body types The maximum number of rigid body types permitted by DL POLY 2 has been exceeded Action Standard user response Fix the parameter mxungp Message 302 error too many sites in rigid body This error arises when DL_POLY_2 finds that the number of sites in a rigid body exceeds the dimensions of the approriate storage arrays Action S
172. gh the centre of an edge that is parallel to the Z axis Note It is important to get this convention right The origin of the atomic coordinates is the centre of the cell If the length of one of the hexagon edges is D the cell vectors required in the CONFIG file are 3D 0 0 0 3D 0 0 0 H where H is the prism height the distance between hexagonal faces The orthorhombic cell also defined by these vectors enscribes the hexagonal prism and possesses twice the volume but the height and the centre are the same The Ewald summation method may be used with this periodic boundary condition CCLRC 172 The hexagonal MD cell This MD cell is particularly suitable for simulating strands or fibres i e systems with a pronounced anisotropy in the Z direction such as DNA strands in solution or stretched polymer chains Appendix C DL_POLY Error Messages and User Action Introduction In this appendix we document the error messages encoded in DL POLY 2 and the recom mended user action The correct response is described as the standard user response in the approriate sections below to which the user should refer before acting on the error encountered The reader should also be aware that some of the error messages listed below may be either disabled in or absent from the installed version of DL POLY 2 Disabled messages generally apply to older releases of the code while absent messages apply to newer versions of the code and wi
173. h larger memory per processor Message 1410 error failed allocation of work arrays in nvt hl f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor CCLRC 224 Message 1420 error failed allocation of work arrays in npt_bl f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1430 error failed allocation of density array in npt_b1 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1440 error failed allocation of work arrays in npt_h1 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1450 error failed allocation of density array in npt_h1 f This is a memory allocation error Probable cause excessive size of simulated system
174. h the three point interpolation option 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 ap propriate for serious simulation of the test systems Note also that the DL POLY 2 Graphical User Interface 8 provides a convenient means for running and viewing these test cases 5 1 1 1 Test Case 1 KNaSi50 Potassium Sodium disilicate glass NaKSi2O5 using two and three body potentials Some of the two body potentials are read from the TABLE file Electrostatics are handled by a multiple timestep Ewald sum method Cubic periodic boundaries are in use NVE ensemble 5 1 1 2 Test Case 2 Metal simulation with Sutton Chen potentials FCC Aluminium using Sutton Chen potentials Temperature is controlled by the method of Gaussian constraints NVT Evans ensemble 5 1 1 3 Test Case 3 An antibiotic in water Valinomycin in 1223 spc water molecules The temperature is controlled by a Nos Hoover thermostat while electrostatics are handled by a shifted Coulombic potential The water is defined as a rigid body while bond constraints are applied to all chemical bonds in the valinomycin Truncated octahedral boundary conditions are used NVT Hoover ensemble 5 1 1 4 Test Case 4 Shell model of water 256 molecules of water with a polarizable oxygen atom using adiabatic dynamics Tem perature is controlled by the Berendsen thermostat
175. he atoms directive 4 shell n m where n is the number of core shell units and m is an integer specifying which shell model is required e m 1 for adiabatic shell model e m 2 for relaxed shell model Each of the subsequent n records contains index 1 integer site index of core index 2 integer site index of shell spring real force constant of core shell spring The spring force constant is entered in units of engunit A where engunit is the energy unit specified in the units directive The adiabatic and relaxed shell models are mutually exclusive options in the same simulation Note that the atomic site indices referred to in this table are indices arising from 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 de scriptions of this molecule including the bonds constraints angles and dihe drals entries described below DL POLY 2 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 CCLRC 121 5 bonds n where n is the number of flexible chemical bonds in the molecule Each of the subse quent n records contains bond key ad see table 4 7 index 1 integer first atomic site in bond index 2 integer second atomic site in bond variable 1 real potential parameter see table 4 7 variable 2 r
176. he directives available are as follows directive meaning all pairs use all pairs for electrostatic calculations cap f cap forces during eguilibration period fis maximum cap in units of kT A default f 1000 close time f set job closure time to f seconds collect include eguilibration data in overall statistics coul calculate coulombic forces cut f set required forces cutoff to f A distan calculate coulombic forces using distance dependent dielectric delr f set Verlet neighbour list shell width to f A ensemble nve select NVE ensemble default ensemble nvt ber f select NVT ensemble with Berendsen thermostat with relaxation constant f ps ensemble nvt evans CCLRC 108 select NVT ensemble with Evans thermostat ensemble nvt hoover f select NVT ensemble with Hoover Nose thermostat with relaxation constant f ps ensemble npt ber fi fo select Berendsen NPT ensemble with fi fo as the thermostat and barostat relaxation times ps ensemble npt hoover fi f2 select Hoover NPT ensemble with fi fo as the thermostat and barostat relaxation times ps ensemble nst ber f f2 select Berendsen NaT ensemble with fi f2 as the thermostat and barostat relaxation times ps ensemble nst hoover f f gt ensemble pmf eps f equil n ewald precision f select Hoover NaT ensemble with fi f2 as the thermostat and barostat relaxation times ps select NVE potential of mean force ensemble set relative di
177. he enscribing tetragonal simulation cell CCLRC 193 Action Check the specified simulation cell vectors and correct accordingly Message 141 error duplicate metal potential specified The user has specified a particular metal potential more than once in the FIELD file Action Locate the metal potential specification in the FIELD file and remove or correct the po tential concerned Message 145 error no van der waals potentials defined This error arises when there are no VDW potentials specified in the FIELD file but the user has not specified no vdw in the CONTROL file In other words DL_POLY_2 expects the FIELD file to contain VDW potential specifications Action Edit the FIELD file to insert the required potentials or specify no vdw in the CONTROL file Message 150 error unknown van der waals potential selected DL POLY 2 checks when constructing the interpolation tables for the short ranged poten tials that the potential function requested is one which is of a form known to the program If the requested potential form is unknown termination of the program results The most probable cause of this is the incorrect choice of the potential keyword in the FIELD file or one in the wrong columns input is formatted Action Read the DL POLY 2 documentation and find the potential keyword for the potential desired Insert the correct index in the FIELD file definition and ensure it occurs in the correct columns 17 20
178. he real space Coulombic forces arising from the secondary atoms are calculated in the first two timesteps of the multi step using the normal Ewald expressions i e the erfc terms 4 the Coulombic forces arising from primary atoms are calculated at every timestep in real space assuming the full Coulombic force In this way the Coulombic forces can be handled by the same multiple timestep scheme as the van der Waals forces The algorithm is described in detail in 41 Note that the accuracy of the algorithm is a function of the multi step interval multt and decreases as multt increases Also the algorithm is not time reversible and is therefore susceptible to energy drift Its use with a thermostat is therefore advised CCLRC 78 The multiple timestep algorithm The atoms surrounding the central atom open circle are classified as primary if they occur within a radius Tprim and secondary if outside this radius but within reut Interactions arising from primary atoms are evaluated every timestep Interactions from secondary atoms are calculated exactly for the first two steps of a multi step and by extrapolation afterwards 2 6 DL POLY Parallelisation DL POLY 2 is a distributed parallel molecular dynamics package based on the Replicated Data parallelisation strategy 42 43 In this section we briefly outline the basic method ology Users wishing to add new features DL POLY 2 will need to be familiar with the underlying tech
179. he unit of pressure is k atm irrespective of what energy unit is chosen 4 2 2 6 Summary of Statistical Data This portion of the OUTPUT file is written from the subroutine RESULT The number of time steps used in the collection of statistics is given Then the averages over the production portion of the run are given for the variables described in the previous section The root mean square variation in these variables follow on the next two lines The energy and pressure units are as for the preceeding section Also provided in this section is an estimate of the diffusion coefficient for the different species in the simulation which is determined from a single time origin and is therefore very approximate Accurate determinations of the diffusion coefficients can be obtained using the MSD utility program which processes the HISTORY file see chapter 6 If an NPT or NoT simulation is performed the OUTPUT file also provides the mean stress pressure tensor and mean simulation cell vectors 4 2 2 7 Sample of Final Configuration The positions velocities and forces of the 20 atoms used for the sample of the initial configuration see above are given This is written by the subroutine RESULT 4 2 2 8 Radial Distribution Functions If both calculation and printing of radial distribution functions have been requested by selecting directives rdf and print rdf in the CONTROL file radial distribution functions are printed out This is written fro
180. hell temperature configurational energy due to core shell potentials core shell potential contribution to the virial angle between b and c cell vectors angle between c and a cell vectors angle between a and b cell vectors Potential of mean force constraint contribution to the virial pressure Note The total internal energy of the system variable tot_energy includes all contri butions 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 CCLRC 143 the above statistical variables are given in the appropriate columns Immediately below these three lines of output the rolling averages of the same variables are also given The maximum number of time steps used to calculate the rolling averages is determined by the parameter mxstak defined in the PARSET F subroutine of the SETUP_PROGRAM F file The working number of time steps for rolling averages is controlled by the directive stack in file CONTROL see above The default value is mxstak Energy Units The energy unit for the data appearing in the OUTPUT is defined by the units directive appearing in the CONTROL file Pressure units T
181. herlands Standard GROMOS reference 4 16 Mayo S Olafson B and Goddard W 1990 J Phys Chem 94 8897 4 16 34 130 Weiner S J Kollman P A Nguyen D T and Case D A 1986 J Comp Chem 7 230 4 16 Smith W 2003 Daresbury Laboratory 5 11 87 96 98 115 150 156 Smith W and Forester T R 1994 Comput Phys Commun 79 52 5 Smith W and Forester T R 1994 Comput Phys Commun 79 63 5 58 59 Allen M P and Tildesley D J 1989 Computer Simulation of Liquids Oxford Clarendon Press 5 17 45 54 57 60 78 80 Ryckaert J P Ciccotti G and Berendsen H J C 1977 J Comput Phys 23 327 5 57 79 Andersen H C 1983 J Comput Phys 52 24 5 59 Fincham D 1992 Molecular Simulation 8 165 5 55 71 Miller T Eleftheriou M Pattnaik P Ndirango A Newns D and Martyna G 2002 J Chem Phys 116 8649 5 56 71 72 Forester T and Smith W 1998 J Computational Chemistry 19 102 6 55 56 74 159 CCLRC 160 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 Martyna G Tuckerman M Tobias D and Klein M 1996 Molecular Physics 87 1117 6 61 72 Evans D J and Morriss G P 1984 Computer Physics Reports 1 297 6 55 56 60 Berendsen H J C Postma J P M van Gunsteren W DiNola A and Haak J R 1984 J Chem Phys 81 36
182. his additional file available the job will fail Note that DL POLY_2 will append new data to the existing STATIS and HISTORY files if the run is restarted other output files will be overwritten In the event of machine failure you should be able to restart the job in the same way from the surviving REVCON and REVIVE files which are dumped at intervals to meet just such an emergency In this case check carefully that the input files are intact and use the HISTORY and STATIS files with caution there may be duplicated or missing records The reprieve processing capabilities of DL POLY 2 are not foolproof the job may crash while these files are being written for example but they can help a great deal You are advised to keep backup copies of these files noting the times they were written to help you avoid going right back to the start of a simulation You can also extend a simulation beyond its initial allocation of timesteps provided you still have the REVCON and REVIVE files These should be copied to the CONFIG and REVOLD files respectively and the directive timesteps adjusted in the CONTROL file to the new total number of steps required for the simulation For example if you wish to extend a 10000 step simulation by a further 5000 steps use the directive timesteps 15000 in the CONTROL file and include the restart directive You can use the restart scale directive if you want to reset the temperature at the restart but note that this also resets
183. ibility of increasing the heap size for your application Talk to your systems support people for advice on how to do this Message 34 error character array memory allocation failure DL POLY_2 has failed to allocate sufficient memory to accommodate one or more of the character arrays in the code Action This may simply mean that your simulation is too large for the machine you are running on Consider this before wasting time trying a fix Try using more processing nodes if they are available If this is not an option investigate the possibility of increasing the heap size for your application Talk to your systems support people for advice on how to do this Message 35 error logical array memory allocation failure DL POLY 2 has failed to allocate sufficient memory to accommodate one or more of the logical arrays in the code CCLRC 180 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 40 error too many bond constraints specified DL POLY 2 sets a limit on the number of bond constraints that can be specified in the FIELD file Termination results if this number is exceeded See FIELD file documentation
184. ical processing of the data is required 4 2 1 1 The Formatted HISTORY File The formatted HISTORY file is written by the subroutine TRAJECT and has the following structure record 1 a80 header a80 file header record 2 3i10 keytrj integer trajectory key see table 4 3 imcon integer periodic boundary key see table 4 6 natms integer number of atoms in simulation cell For timesteps greater than nstraj the HISTORY file is appended at intervals speci fied by the traj directive in the CONTROL file with the following information for each configuration record i a8 4i10 f12 6 timestep a8 the character string timestep nstep integer the current time step natms integer number of atoms in configuration keytrj integer trajectory key again CCLRC imcon integer tstep real record ii 3g12 4 for imcon gt 0 cell 1 real cell 2 real cell 3 real record iii 3g12 4 for imcon gt 0 cell 4 real cell 5 real cell 6 real record iv 3g12 4 for imcon gt 0 cell 7 real cell 8 real cell 9 real 139 periodic boundary key again integration timestep 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 6 cell vector z component of 6 cell vector x component of c cell vector y component of c cell vector z component of c cell vector This is followed by the configuration for the current timestep i e for each atom in the s
185. id unit is defined as the location of its centre of mass R Nsites X Mjrj 2 242 j l es 1 M where r is the position vector of atom j The rigid body translational velocity V is defined by Nsites Y Mjvj 2 243 j l IS 1 M where v is the velocity of atom j The net translational force acting on the rigid body unit is the vector sum of the forces acting on the atoms of the body Nsites F J 2 244 j 1 where J is the force on a rigid unit site 5 An alternative approach is to define basic and secondary particles The basic particles are the minimun number needed to define a local body axis system The remaining particle positions are expressed in terms of the COM and the basic particles Ordinary bond constraints can then be applied to the basic particles provided the forces and torques arising from the secondary particles are transferred to the basic particles in a physically meaningful way CCLRC 70 A rigid body also has associated with it a rotational inertia matrix I whose components are given by Nsites Tog X mj dj ng d r 2 245 j where d is the displacement vector of the atom j from the COM and is given by d r A 2 246 It is common practice in the treatment of rigid body motion to define the position R of the body in a universal frame of reference the so called laboratory or inertial frame but to describe the moment of inertia tensor in a frame of re
186. ied in QSHAKE This also has different ensemble versions Hoover or Berendsen thermostat and or barostat The Hoover and Berendsen thermostated versions are found in NVTQ_H2 and NVTQ_B2 respectively The isotropic constant pressure implementations are found in NPTQ_H2 and NPTQ_B2 while the anisotropic constant pressure routines are found in NSTQ_H2 and NSTQ_B2 An outline of the parallel version of QSHAKE is given in section 2 6 9 2 5 8 The DL POLY 2 Multiple Timestep Algorithm For simulations employing a large spherical cutoff reut in the calculation of the interactions DL POLY 2 offers the possibility of using a multiple timestep algorithm to improve the efficiency The method is based on that described by Streett et al 39 40 with extension to Coulombic systems by Forester et al 41 In the multiple timestep algorithm there are two cutoffs for the pair interactions a relatively large cutoff rcut which is used to define the standard Verlet neighbour list and a smaller cutoff rppim which is used to define a primary list within the larger cutoff sphere see figure Forces derived from atoms in the primary list are generally much larger than those derived from remaining so called secondary atoms in the neighbour list Good energy conservation is therefore possible if the forces derived from the primary atoms are calculated every timstep while those from the secondary atoms are calculated much less frequently and are merely extrapolated ov
187. igue eight character label defined by the user The pair potential is then defined internally by the combination of two atom labels As well as the numerical parameters defining the potentials DL POLY 2 must also be provided with a cutoff radius reut which sets a range limit on the computation of the interaction Together with the parameters the cutoff is used by the subroutine FORGEN or FORGEN_RSQ to construct an interpolation array vvv for the potential function over the range 0 to freut A second array ggg is also calculated which is related to the potential via the formula O G rij rij z U Cu 2 86 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 CCLRC 33 calculating the potential energy and atomic forces very general and enables the use of user defined pair potential functions DL POLY 2 also allows the user to read in the interpolation arrays directly from a file see the description of the TABLE file section 4 1 5 This is particularly useful if the pair potential function has no simple analytical description e g spline potentials The force on an atom j derived from one of these potentials is formally calculated with the standard formula f ae vum Tijs 2 87 1 Jj Tij where Tj Tj Ti The force on atom i is the negative of this The contribution to be added t
188. ik Tina Tauta lw 2 ida bis X Ljkl Ejk X enl 2 51 OF Urh jela r klrgrirla Iry X nk l 2 52 Ge ArGelragtagla T5 Eijtykla Itis X Lyx 2 53 hf Urin inla Tkali enla l X Caml 2 54 ha rk ltetinla Tyleetele ls Xtal 2 55 The sum of the diagonal elements of the stress tensor is zero since the virial is zero and the matrix is symmetric Lastly it should be noted that the above description does not take into account the possible inclusion of distance dependent 1 4 interactions as permitted by some force fields Such interactions are permissible in DL POLY 2 and are described in the section on pair potentials below DL POLY 2 also permits scaling of the 1 4 interactions by a numerical factor 1 4 interactions do of course contribute to the atomic virial In DL_POLY_2 dihedral forces are handled by the routine DIHFRC 2 2 6 Improper Dihedral Angle Potentials Improper dihedrals are used to restrict the geometry of molecules and as such need not have a simple relation to conventional chemical bonding DL POLY 2 makes no distinction between dihedral angle functions and improper dihedrals both are calculated by the same subroutines and all the comments made in the preceeding section apply An important example of the use of the improper dihedral is to conserve the structure of chiral centres in molecules modelled by united atom centres For example a amino acids such as alanine CH3CH NH2 COOH in which
189. ile and indicate whether it is the real or reciprocal space sums that is questionable 3 4 DL POLY 2 Error Processing 3 4 1 The DL POLY 2 Internal Error Facility DL POLY 2 contains a number of in built error checks scattered throughout the package which detect a wide range of possible errors In all cases when an error is detected the subroutine ERROR is called resulting in an appropriate message and termination of the program execution either immediately or after additional processing Users intending to insert new error checks should ensure that all error checks are per formed concurrently on all nodes and that in circumstances where a different result may obtain on different nodes a call to the global status routine GSTATE is made to set the appropriate global error flag on all nodes Only after this is done a call to subroutine ERROR may be made An example of such a procedure might be logical safe safe test_condition call gstate safe if not safe call error node id message number In this example it is assumed that the logical operation test_condition will result in the answer true if it is safe for the program to proceed and false otherwise The call to ERROR reguires the user to state the identity of the calling node node id so that only the nominated node in ERROR i e node 0 will print the error message The variable message number is an integer used to identify the appropriate message to be printed
190. ile specifying the elec trostatic interactions options Action Locate the conflicting directives in the CONTROL file and correct CCLRC 204 Message 418 error bond vector work arrays too small in bndfrc The work arrays in BNDFRC have been exceeded Action Standard user response Fix the parameter msbad Message 419 error bond vector work arrays too small in angfrc The work arrays in ANGFRC have been exceeded Action Standard user response Fix the parameter msbad Message 420 error bond vector work arrays too small in tethfrc The work arrays in TETHFRC have been exceeded Action Standard user response Fix the parameter msbad Message 421 error bond vector work arrays too small in dihfrc The work arrays in DIHFRC have been exceeded Action Standard user response Fix the parameter msbad Message 422 error all pairs must use multiple timestep In DL_POLY_2 the all pairs option must be used in conjunction with the multiple timestep Action Activate the multiple timestep option in the CONTROL file and resubmit Message 423 error bond vector work arrays too small in shlfrc The dimensions of the interatomic distance vectors have been exceeded in subroutine SHL FRC Action Standard user response Fix the parameter msbad Set equal to the value of the parameter mxshl CCLRC 205 Message 424 error electrostatics incorrect for all pairs When using the all pairs option in conjunction w
191. imulation it indicates that the timestep is too large or the potential cutoffs too small relative r m s fluctuations in the total energy of 107 are typical with this algorithm DL POLY 2 contains two versions of the Verlet algorithm The first is the Verlet leapfrog LF algorithm and the second is the velocity Verlet VV 2 5 1 1 Verlet Leapfrog The LF algorithm requires values of position r and force f at time t while the velocities v are half a timestep behind The first step is to advance the velocities to t 1 2 At by integration of the force ult 5AM i I At At E 2 199 where m is the mass of a site and At is the timestep The positions are then advanced using the new velocities r t At r t At ut 3 At 2 200 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 In the LF algorithm the velocity at time t is obtained from the average of the velocities half a timestep either side of time t 1 1 v t 5At v t 5 At 2 201 NI v t CCLRC 55 The full selection of LF integration algorithms within DL_POLY_2 is as follows NVE 1 Verlet leaprog with SHAKE NVEQ 1 Rigid units with FIQA and SHAKE NVEQ_2 Linked rigid units with OSHAKE NVT B1 Constant T Berendsen 19 with SHAKE NVT_El Constant T Evans 18 with SHAKE NVT H1 Constant T Hoover 20 with SHAKE NVT
192. inuous Shear A 20 z gt 20 vx 1 2 A z 72 grav Gravitational Field Gz Gy G F m G magn Magnetic Field He Hy H F q vx H sphr Containing Sphere A Ro n Rew r gt Rew F A Ro r zbnd Repulsive wall A Zo f 1 zf gt Zof F A z Zo harmonic which signals the end of the force field data Without this directive DL POLY 2 will abort 4 1 4 The REVOLD File This file contains statistics arrays from a previous job It is not required if the current job is not a continuation of a previous run ie if the restart directive is not present in the CONTROL file see above The file is unformatted and therefore not readable by normal people DL POLY 2 normally produces the file REVIVE see section 4 2 4 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 2 4 1 4 1 Format The REVOLD file is unformatted All variables appearing are written in native real 8 representation Nominally integer quantities e g the timestep number nstep are repre sented by the the nearest real number The contents are as follows the dimensions of array variables are given in brackets and are defined in the appropriate Fortran modules record 1 nstep timestep of final configuration numacc number of configurations used in aver
193. ith NOSQUISH and RATTLE NSTQVV_H2 Constant T Hoover 20 with OSHAKE In the above table the NOSQUISH algorithm is the rotational algorithm of Miller et al 15 and QSHAKE is the DL POLY 2 algorithm combining rigid bonds and rigid bodies in the same molecule 16 2 5 1 3 Temperature and Energy Conservation For both VV and LF the instantaneous temperature can be obtained from the atomic velocities assuming the system has no net momentum TH mv t 2 205 CCLRC 57 where i labels particles which can be atoms or rigid molecules N the number of particles in the system kg Boltzmanns constant and f the number of degrees of freedom in the system 3M 3 if the system is periodic and without constraints The total energy of the system is a conserved quantity Hnve U KE 2 206 where U is the potential energy of the system and KE the kinetic energy at time t 2 5 2 Bond Constraints 2 5 2 1 SHAKE The SHAKE algorithm for bond constraints was devised by Ryckaert et al 12 and is based on the Verlet leapfrog integration scheme 11 It is a two stage scheme In the first stage the leapfrog algorithm calculates the motion of the atoms in the system assuming a complete absence of the rigid bond forces The positions of the atoms at the end of this stage do not conserve the distance constraint required by the rigid bond and a correction is necessary In the second stage the deviation in the length of a given rigid bond i
194. ith electrostatic forces the electrostatics must be handled with either the standard Coulomb sum or with the distance dependent dielectric Action Rerun the simulation with the appropriate electrostatic option Message 425 error transfer buffer array too small in shlmerge The buffer used to transfer data between nodes in the subroutine SHLMERGE has been di mensioned too small Action Standard user response Fix the parameter mxbuff Message 426 error neutral groups not permitted with all pairs DL POLY 2 will not permit simulations using both the neutral group and all pairs options together Action Switch off one of the conflicting options and rerun Message 427 error bond vector work arrays too small in invfrc The work arrays in subroutine INVFRC have been exceeded Action Standard user response Fix the parameter msbad Message 430 error integration routine not available A request for a nonexistent ensemble has been made or a request with conflicting options that DL POLY 2 cannot deal with e g a Evans thermostat with rigid body equations of motion Action Examine the CONTROL and FIELD files and remove inappropriate specifications Message 432 error intlist failed to assign constraints If the required simulation has constraint bonds DL POLY 2 attempts to apportion the molecules to processors so that if possible there are no shared atoms between processors If this is not possible one or more m
195. iven 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 2 is the implementation of Neumann based on charge charge interactions 33 In this model the total Coulombic potential is given by 1 U AT EO 1 Born i 2 1 Eon 1 2 189 where the second term on the right is the reaction field correction to the explicit sum with R the radius of the cavity The constant Bo is defined as 2 e1 1 i 2 190 with e the dielectric constant outside the cavity The effective pair potential is therefore Tnj 2R3 U rnj 2 191 ATE din 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 2 this is countered by subtracting the value of the potential at the cavity boundary from each pair contribution The term subtracted is 1 l 2 1 a 2 192 Are Re L 2 The effective pair force on an atom j arising from another atom n within the cavity is given by djAn 1 Bo z 2 1 f ATE z Taj The contribution of each effective pair interaction to the atomic virial is W Lnj Ji 2 194 and the contribution to the atomic stress tensor is g yfo 2 195 In DL POLY 2 the reaction field is handled by the routines COUL3 and COUL3NEU 2 4 9 Dynamical Shell Model An atom or i
196. k k k LO ther Information s soseo a Oi jal a a ee ep ee Tal DL POLY 2 Force Fields and Algorithms 21 The DL POLY 2 Force Field 14 44 cosa ha L ee ees 2 2 The Intramolecular Potential Functions 2 21 Bond Potentials ao u 8256 6 2 EU See een ae ee 22 2 Distance Restraints k 4 3 en oe hea es ldi aoe a elo 2 al s 2 2 3 Valence Angle Potentials k k 2 2 2 424 Ang l r Restraints 1 so aaas k k ila sla DR a wR ee 22 0 Dihedral Angle Potentials sos soci soe Bl w ulu uu b e k UU a k 2 2 6 Improper Dihedral Angle Potentials 2 2 7 Inversion Angle Potentials i u 2 2 k k 2 2 2 22 8 Tethenne Forces sa 5 ik eek AV sla EO BA a ewe A Wn 2 29 Frozen ATSMS parenka ek AD he a we ER WU BH ee Ba a 2 3 The Intermolecular Potential Functions 2 2 3 1 Short Ranged van der Waals Potentials 2 9 2 Three Body Potentials x X saa sag RR RD ioa eae 2 3 3 The Tersoff Covalent Potential 2544 Four Body Potentials s sa se emadus kok kh AR ks 2 3 0 Metal Potentials a s sae ue pa ay eek oo Bk ete eS 23 6 External Fields o o c ss 446228484 ee eR thee hoe te a 2 4 Long Ranged Electrostatic Coulombic Potentials 2 41 Atomistic and Charge Group Implementation 24 2 Direct Coulomb Sum 2 4 6483 k ee ee ee a 2 4 3 Truncated and Shifted Coulomb Sum 2 4 4 Coulomb Su
197. ke 1 update guaternions bodystress cell propagate error gdsum getcom getrotmat getvom gimax gstate images kinstressf kinstressg matmul merge mergel merge4 gshake shmove splice update_guaternions MPI_IRECV MPI_SEND MPI_WAIT error gdsum gimax gstate gsync MPI_IRECV MPI_SEND MPI_WAIT error gdsum 260 CCLRC merge_systol merge_systol merge_tools merge_tools merge_tools merge_tools merge_tools merge_tools merge_tools metal_module metal_terms metal_terms metal_terms metal_terms metal_terms metal_terms metal_terms metal_terms metal_terms metal_terms metal_terms_4pt metal_terms_4pt metal_terms_4pt metal_terms_4pt metal_terms_4pt metal_terms_4pt metal_terms_4pt metal_terms_4pt metal_terms_4pt metal_terms_4pt metal_terms_rsq metal_terms_rsq metal_terms_rsq metal_terms_rsq metal_terms_rsq metal_terms_rsq metal_terms_rsq metal_terms_rsq metal_terms_rsq metal_terms_rsq nlist_builders nlist_builders nlist_builders nlist_builders gstate gsync MPI_IRECV MPI_SEND MPI_WAIT error gdsum gstate gsync error copystring denloc error gdsum getrec getword images lowcase metgen warning copystring denloc error gdsum getrec getword images lowcase metgen warning copystring denloc error gdsum getrec getword images lowcase metgen warning dcell error gimax gisum 261 CCLRC 262 nlist_builders gstate nlist_builders images nlist_builders invert nlist_builders
198. l The most prob able cause is the incorrect definition of the simulation cell vectors present in the input file CONFIG these must equal the vectors of the enscribing cubic cell Action Check the specified simulation cell vectors and correct accordingly Message 135 error incorrect hexagonal prism boundary condition When calculating minimum images DL_POLY_2 checks that the periodic boundary of the simulation cell is compatible with the specifed minimum image algorithm Program termi nation results if an inconsistency is found In this case the error refers to the hexagonal prism minimum image which is inconsistent with the simulation cell The most probable cause is the incorrect definition of the simulation cell vectors present in the input file CON FIG these must equal the vectors of the enscribing orthorhombic cell Action Check the specified simulation cell vectors and correct accordingly Message 140 error incorrect dodecahedral boundary condition When calculating minimum images DL POLY 2 checks that the periodic boundary of the simulation cell is compatible with the specifed minimum image algorithm Program ter mination results if an inconsistency is found In this case the error refers to the rhombic dodecahedral minimum image which is inconsistent with the simulation cell The most probable cause is the incorrect definition of the simulation cell vectors present in the input file CONFIG these must equal the vectors of t
199. l cell Warning increasing the convergence parameter may cause failure in the reciprocal space domain See 4 1 1 Message 487 error HK recip space screening function cutoff violation DL_POLY_2 has detected an unacceptable degree of inaccuracy in the screening function near the radius of cutoff in reciprocal space which implies the Hautman Klein Ewald method will not be sufficiently accurate Action The user should respecify the HK control parameters given in the CONTROL file Either the convergence parameter should be reduced or more k vectors used Warning reducing the convergence parameter may cause failure in the real space domain See 4 1 1 Message 488 error HK lattice control parameter set too large The Hautman Klein Ewald method in DL_POLY_2 permits the user to perform a real space sum over nearest neighbour and next nearest neighbour cells i e up to nlatt 2 If the user specifies a larger sum than this this error will result Action The user should respecify the HK control parameters given in the CONTROL file and set nlatt to a maximum of 2 See 4 1 1 Message 490 error PMF parameter mxpmf too small in passpmf The bookkeeping arrays have been exceeded in PASSPMF CCLRC 214 Action Standard user response Fix the parameter mxpmf Set equal to mxatms Message 492 error parameter mxcons lt number of PMF constraints The parameter mxcons is too small for the number of PMF constraints in the s
200. le Key keyens meaning Microcanonical ensemble NVE Evans NVT ensemble Berendsen NVT ensemble Nos Hoover NVT ensemble Berendsen NPT ensemble Nos Hoover NPT ensemble Berendsen NoT ensemble Nos Hoover NoT ensemble Potential of mean force NVE ensemble OSJIOQOUVURW NHO Table 4 3 Internal Trajectory File Key keytrj meaning 0 coordinates only in file 1 coordinates and velocities in file 2 coordinates velocities and forces in file 112 CCLRC Table 4 4 Non bonded force key keyfce meaning odd evaluate short range potentials and electrostatics even evaluate Electrostatic potential only Electrostatics are evaluated as follows 07 1 Ignore Electrostatic interactions 2 3 Ewald summation 4 5 distance dependent dielectric constant 6 7 standard truncated Coulombic potential 8 9 truncated and shifted Coulombic potential 10 11 Reaction Field electrostatics 12 13 SPME electrostatics 14 15 Hautman Klein Ewald electrostatics keyfce 0 means no non bonded terms are evaluated t keyfce 1 means only short range potentials are evaluated 113 CCLRC 4 1 2 The CONFIG File The CONFIG file contains the dimensions of the unit cell the key for periodic boundary conditions and the atomic labels coordinates velocities and forces This file is read by the subroutine SYSGEN It is also read by the subroutine SIMDEF if
201. le those obtained in this prescription since they specify the sides of a cube not a radius of convergence CCLRC 100 If your simulation cell is a truncated octahedron or a rhombic dodecahedron then the estimates for the kmax need to be multiplied by 21 3 This arises because twice the normal number of k vectors are required half of which are redundant by symmetry for these boundary contributions 30 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 rcu and a large value for the kmax say 10 10 10 or more Then do a series of ten or so single step simulations with your initial configuration and with a ranging over the value you have chosen plus and minus 2096 Plot the Coulombic energy and W versus a If the Ewald sum is correctly converged you will see a plateau in the plot Divergence from the plateau at small a is due to non convergence in the real space sum Divergence from the plateau at large a is due to non convergence of the reciprocal space sum Redo the series of calculations using smaller kmax values The optimum values for kmax are the smallest values that reproduce the correct Coulombic energy the plateau value and virial at the value of a to be used in the simulation Note that one needs to specify the three integers kmax1 kmax2 kmax3 referring to the three spatial
202. lean rm f OBJ_MOD OBJ_ALL OBJ_RRR OBJ_PAR OBJ_LF OBJ_VV OBJ_RSQ OBJ_4PT mod Declare dependencies c preprocess all f files f 0 FC FFLAGS f C O CC c c Declare dependency on module files OBJ_ALL 0BJ_MOD OBJ_LF 0BJ_MOD CCLRC OBJ_VV OBJ_MOD OBJ_RRR OBJ_MOD OBJ_RSQ 0BJ MOD 0BJ 4PT O0BJ MOD 166 Appendix B Periodic Boundary Conditions in DL POLY Introduction DL POLY 2 is designed to accommodate a number of different periodic boundary condi tions 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 4 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 Truncated octahedral periodic boundaries IMCON 4 6 Rhombic dodecahedral periodic boundaries IMCON 5 7 Slab X Y periodic Z nonperiodic IMCON 6 8 Hexagonal prism periodic boundaries IMCON 7 We shall now look at each of these in more detail Note that in all cases the cell vectors and the positions of the atoms in the cell are to be specified in Angstroms A No periodic boundary IMCON 0 Simulations requiring no periodic boundaries are best suited to in vacuuo simulati
203. led and r the magnitude of the separation vector T Tj i The force on an atom j derived from this force is f r 2 141 with the force on atom i the negative of this The contribution to the atomic virial is 1 WM Was 8 2 142 ATE Tij which is simply the negative of the potential term The contribution to be added to the atomic stress tensor is o 2 143 where a 8 are x y z components The atomic stress tensor is symmetric In DL_POLY_2 these forces are handled by the routines COULO and COULONEU CCLRC 43 2 4 3 Truncated and 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 potential function is U r FU SR 2 144 Are Tij Tcut with g the charge on an atom labelled reut the cutoff radius and r the magnitude of the separation vector Tij LY tp The force on an atom j derived from this potential within the radius reut is 1 aq T 2 145 ATE T with the force on atom i the negative of this 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 gd fo
204. lit the interaction list into primary and secondary neighbours The decision to update the neighbour list is handled by the routine VERTEST The routine EXTNFLD is required if the simulated system has an external force field e g electrostatic field operating To help with equilibration simulations the routine FCAP is sometimes required to reduce the magnitude of badly equilibrated forces Since DL POLY 2 is based on the replicated data strategy a global sum routine GDSUM is required to sum the atomic forces on all nodes Integration of the equations of motion is handled by one of the routines listed and described in section 2 5 For example routines NVE_O NVT_EO NVT_HO NVT_BO etc are used if no constraint forces are present These routines treat the NVE Evans NVT Hoover Nos NVT and NVT Berendsen ensembles respectively The corresponding versions of these routines which handle constraint forces are NVE_1 NVT_El NVT H1 or NVT B1 These versions call the routine RDSHAKE 1 to handle the constraints RDSHAKE l itself calls a number of additional routines MERGE SHMOVE and SPLICE For ad hoc temperature scaling the routine VSCALEG is required As mentioned elsewhere DL POLY 2 does not contain many routines for computing system properties during a simulation Radial distributions may be calculated however using the routines RDFO and RDF1 Similarly DIFFSNO and DIFFSN1 calculate approximate mean square displacements Ordinary thermodynamic qua
205. lity_pack utility_pack utility_pack utility_pack utility_pack utility_pack vdw_module vdw_terms vdw_terms vdw_terms vdw_terms vdw_terms vdw_terms vdw_terms vdw_terms vdw_terms vdw_terms vdw_terms_4pt vdw_terms_4pt vdw_terms_4pt vdw_terms_4pt vdw_terms_4pt vdw_terms_4pt vdw_terms_4pt vdw_terms_4pt vdw_terms_4pt vdw_terms_4pt vdw_terms_rsq vdw_terms_rsq vdw_terms_rsq vdw_terms_rsq vdw_terms_rsq vdw_terms_rsq vdw_terms_rsq vdw_terms_rsq vdw_terms_rsq vdw_terms_rsq getrec getword gstate invert lowcase date_and_time date_and_time error exit gdsum images invert merge error abort_table_read copystring error forgen fortab gdsum getrec getword lowcase warning abort_table_read copystring error forgen fortab gdsum getrec getword lowcase warning abort_table_read copystring error forgen fortab gdsum getrec getword lowcase warning 265 CCLRC vv_integrate vv_integrate vv_integrate vv_integrate vv_integrate vv_integrate vv_integrate vv_integrate vv_integrate vv_integrate vv_integrate vv_integrate vv_integrate vv_integrate vv_integrate vv_integrate vv_integrate vv_integrate vv_integrate vv_integrate vv_integrate vv_integrate vv_integrate vv_integrate vv_integrate vv_motion_1 vv_motion_1 vv_motion_1 vv_motion_1 vv_motion_1 vv_motion_1 vv_motion_1 vv_motion_1 vv_motion_1 vv_motion_1 vv_motion_1 vv_motion_1 vv_motion_1 vv_motion_1 vv_motion_1 vv_m
206. ll not usually apply to previous releases They are all included for completeness Note that the wording of some of the messages may also have changed over time usually to provide more specific information The most recent wording appears below DL_POLY 2 incorporates FORTRAN 90 dynamic array allocation to set the array sizes at run time It is not foolproof however Sometimes an estimate of the required array sizes is difficult to obtain and the calculated value may be too small For this reason DL POLY_2 retains a number of array dimension checks and will terminate when an array bound error occurs When a dimension error occurs the standard user response is to edit the DL_POLY_2 subroutine PARSET F Locate where the variable defining the array dimension is fixed and increase accordingly To do this you should make use of the dimension information that DL POLY 2 prints in the OUTPUT file prior to termination If no information is supplied simply doubling the size of the variable will usually do the trick If the variable concerned is defined in one of the support subroutines CFGSCAN F FLDSCAN F CONSCAN F you will need to insert a new line in PARSET F to redefine it after the relevant subroutine has been called Finally the code must be recompiled but in this case it will be necessary only to recompile PARSET F and not the whole code 173 CCLRC 174 The DL_POLY_2 Error Messages Message 1 error PVM_NODES unset The code was C preprocesse
207. local frame wt ao t Atl z t 2 255 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 Qoae Qla t At t At 2 256 CCLRC 72 where 0 2 and Q q is g q 42 43 lia go q3 g ae 2 257 Q 2 a qdo 4 q3 4q2 q1 do The above equation is solved iteratively with q t At q t At GO g t t 2 258 as the first guess Typically no more than 3 or 4 iterations are needed for convergence At each step the constraint lar At 1 2 259 is imposed The NVE LF algorithm is implemented in NVEQ_1 which allows for a system containing a mixture of rigid bodies and atomistic species provided the rigid bodies are not linked to other species by constraint bonds The VV implementation is based on the NOSQUISH algorithm of Miller et al 15 In addition to the quaternions it requires quaternion momenta defined by Do go q4 03 0 _ Lent Pi j u do 03 2 yrr 2 260 p2 go G3 qo q lyy amp y pg g3 2 q do 120 z and quaternion torques defined by To qo q91 q G3 0 Tro o o 9o B Ta 2 261 T2 g 23 q 4 Ty T3 g 2 q Q Tz It should be noted that vectors p and T are 4 component vectors The quaternion mo menta are first updated a half step using the formula plt 3 p ri 2 262 Next a sequence of operations is applied to the quaternions and the
208. location error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Appendix D Subroutine Locations The Locations of Subroutines and Functions The following table lists the subroutines and functions in DL_POLY_2 and which source files they can be found in Subroutine Name abort_config_read abort_control_read abort_field_read abort_table_read abort_table_read abort_table_read abortscan alloc_ang_arrays alloc_bnd_arrays alloc_config_arrays alloc_csh_arrays alloc_dih_arrays alloc_ewald_arrays alloc_exc_arrays alloc_fbp_arrays alloc_fid_arrays alloc_hke_arrays alloc_inv_arrays alloc_met_arrays alloc_pair_arrays alloc_pmf_arrays alloc_prp_arrays alloc_rgbdy_arrays alloc_shake_arrays alloc_site_arrays Type subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine 243 Located in Source File define_system f define_system f define system f vdw terms f vdw terms 4pt f vdw_terms_rsq f setup_program f angles_module f bonds_module f config module f core_shell_module f dihed_module f ewald_module f exclude_module f four_
209. lowcase strip could coulOneu coul2 coul2neu coul3 coul3neu coul4 erfcgen error ewaldi ewald2 ewald3 ewald4 257 CCLRC force_drivers force_drivers force_drivers force_drivers force_drivers force_drivers force_drivers force_drivers force_drivers force_drivers force_drivers force_drivers force_drivers force_drivers force_drivers force_drivers force_drivers force_drivers force_drivers four_body_module four_body_terms four_body_terms four_body_terms four_body_terms four_body_terms four_body_terms four_body_terms four_body_terms four_body_terms hkewald_module hkewald_terms hkewald_terms hkewald_terms hkewald_terms hkewald_terms inversion_module inversion_terms inversion_terms inversion_terms inversion_terms inversion_terms inversion_terms inversion_terms inversion_terms ewald_spme gdsum gimax gstate hkewald1 hkewald2 hkewald3 hkewald4 hkgen images neutlst primlst prneulst rdf0 rdfOneu scdens srfrce srfrceneu suttchen error copystring dcell error gdsum getrec getword gstate invert lowcase error dcell error gdsum invert warning error copystring error gdsum getrec getword gstate images lowcase 258 CCLRC kinetic_terms lf integrate lf integrate lf integrate lf integrate lf integrate lf integrate lf integrate lf integrate lf integrate lf integrate lf integrate lf integrate lf integrate lf integrate lf integrate lf integrate lf integrate lf integrat
210. m getrec getword gstate images lowcase copystring error gdsum getrec getword gstate images lowcase copystring error gdsum getrec 254 CCLRC dihedral_terms_rsq dihedral_terms_rsq dihedral_terms_rsq dihedral_terms_rsq dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly 255 getword gstate images lowcase alloc ang arrays alloc_bnd_arrays alloc_config_arrays alloc_csh_arrays alloc_dih_arrays alloc_ewald_arrays alloc_exc_arrays alloc_fbp_arrays alloc_fld_arrays alloc_hke_arrays alloc_inv_arrays alloc_met_arrays alloc_pair_arrays alloc_pmf_arrays alloc_prp_arrays alloc_rgbdy_arrays alloc_shake_arrays alloc_site_arrays alloc_spme_arrays alloc_tbp_arrays alloc_ter_arrays alloc_tet_arrays alloc_vdw_arrays angfrc bndfrc bomb corshl dcell dihfrc error exitcomms extnfld fbpfrc fcap forces forcesneu freeze gdsum global_sum_ forces gsync CCLRC dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly dl
211. m is comprised of 32 surfactant molecules trimethylaminododecane bromide or TAB C12 arranged either side of a slab of 342 water molecules approximately 30 A thick The surfactant chains are treated with rigid bonds and the water molecules are treated as rigid bodies The TAB headgroup has fractional charges summing to 1 the bromide ion has charge 1 The Ewald sum handles the electrostatic calculations The short range forces are taken from the Dreiding force field NVE ensemble 5 1 1 10 Test Case 10 DNA strand in water This system consists of a strand of DNA 1260 atoms in length in a solution of 706 SPC wa ter molecules The DNA is aligned in the Z direction and hexagonal prism periodic bound ary conditions applied The electrostatic interactions are calculated using the Smoothed Particle Mesh Ewald method Note that the system has a strong overall negative charge which is strongly anisotropic in distribution The short range forces are taken from the Dreiding force field and constraints are used for all covalent bonds For simplicity H bonds are treated as harmonic bonds with an equilibrium bondlength of 1 724 A NVE ensemble CCLRC 152 5 1 1 11 Test Case 11 Hautman Klein test case 1 The system consists of 100 short chain surfactant molecules in a layer simulated under NVE conditions The total system size is 2300 atoms and the XY periodicity is a square The Dreiding force field describes the molecular interactions All bonds are
212. m the subroutine RDF1 First the number of time steps used for the collection of the histograms is stated Then each function is given in turn For each function a header line states the atom types a and b represented by the function Then r g r and n r are given in tabular form Output is given from 2 entries before the first non zero entry in the g r histogram n r is the average number of 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 CCLRC 144 4 2 2 9 Z Density Profile If both calculation and printing of Z density profiles has been requested by selecting direc tives zden and print rdf in the CONTROL file Z density profiles are printed out as the last part of the OUTPUT file This is written by the subroutine ZDEN1 First the number of time steps used for the collection of the histograms is stated Then each function is given in turn For each function a header line states the atom type represented by the function Then z p z and n z are given in tabular form Output is given from Z L 2 L 2 where L is the length of the MD cell in the Z direction and p z is the mean number density n z is the running integral from L 2 to z of xy cell area p s ds Note that a readable version of these data is provided by the ZDNDAT file below 4 2 3 The REVCON File This file is formatted and written by th
213. m with Distance Dependent Dielectric JAn Evald DaN e ea he eee oR K eo ee Se Be ee ee le Se RS 24 6 Smoothed Particle Mesh Ewald a 0 0 06 S 24 7 Hautman Klein Ewald HERE ss 22 Peak we bee Eas 2408 Reaction Field 12 x 4 sca ae we Bale WED GA ae we Y En 2 4 9 Dynamical Shell Model 22 454 ka acr soadh a aaa ee ED 2 4 10 Relaxed Shell Model lt lt a 2 a Intepration algorithms s sons 4 lt 6 scra a 2 be woe ee kua UR A a aes 251 The Verlet Algorithms ak ba ata a aula 4 b u m a 20 2 Bond Conese sk aoa kal eR Rae a eee vi 10 10 10 10 10 10 11 12 CCLRC vii 2 5 3 Potential of Mean Force PMF Constraints and the Evaluation of Free Pmerey 22 xb a Ed u ark a Ka a amp k 59 254 Thermostats sesa 66 mm a eee Ba ddesg BE a ad UE 60 20 0 Gaussian Constrainl8 s k 4 e Toe sa eg eek bP ee ea we eS 62 2 5 0 Bl a kaos Ba ww be Rows RE k ew 64 2 5 7 Rigid Bodies and Rotational Integration Algorithms 68 2 5 8 The DL POLY 2 Multiple Timestep Algorithm 76 25 DL POLY Parallelisation o 2 548 2 ee Se a RR Dn la 78 2 6 1 The Replicated Data Strategy a 78 2 6 2 Distributing the Intramolecular Bonded Terms 79 2 6 3 Distributing the Nonbonded Terms 80 264 Modifications for the Ewald Sumi oos eo scce ee ee He RR ee 81 26 0 Modifications tor SPME 4 1 1 2 h 80 Peak ee eee we 82 2 6 6 Three and Four Body Forces
214. matmul matmul matmul matmul matmul matmul matmul merge merge merge merge merge merge merge merge merge merge merge merge merge merge mergel mergel mergel mergel mergel merge4 merge4 metgen metgen metgen MPI_BARRIER MPI_COMM_RANK MPI_COMM_SIZE MPI_FINALIZE MPI_IRECV MPI_IRECV MPI_IRECV MPI_IRECV MPI_RECV MPI_SEND MPI_SEND MPI_SEND 280 dlpoly ensemble_tools lf motion 1 lf rotation 1 lf rotation 2 vv motion 1 vv_rotation_1 vv_rotation_2 core_shell_terms define_system 1f_motion_1 lf rotation 1 lf rotation 2 nlist builders pmf_lf pmf vv system_properties temp_scalers utility_pack vv_motion_1 vv_rotation_1 vv_rotation_2 lf rotation 1 lf rotation 2 temp scalers vv_rotation_1 vv_rotation_2 define_system lf rotation 2 metal terms metal terms 4pt metal terms rs basic comms basic comms basic comms basic comms merge_hcube merge_systol merge_tools pass_tools basic_comms merge_hcube merge_systol merge_tools CCLRC MPI_SEND MPI_WAIT MPI_WAIT MPI_WAIT MPI_WAIT MPI allreduce MPI init MPI send multiple multiple ns multipleneu neutbook neutlst nosguish nosguish npt_bi npt_hi npt bl npt b2 npt hi npt h2 npt scl p npt scl p npt scl t nptqscl_t nptqscl_t nptgvv b1 nptqvv_b2 nptgvv h1 nptqvv_h2 nptscale_p nptscale_t nptvv_bl nptvv_hi nst_bl nst_hi nst bl nst b2 nst hi nst h2 nst scl p nstgscl_p2 nstgscl_t nstgscl_t
215. memory per processor Message 1710 error failed allocation of work arrays in nstq_h2 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1720 error failed allocation of density array in nstq_h2 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor CCLRC 230 Message 1730 error failed allocation of HK Ewald arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1740 error failed allocation of property arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1750 error failed allocation of spme arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system
216. mical shell model implemented in DL POLY 2 is not designed to work with rigid molecules This error results if these two options are simultaneously selected Action In some circumstances you may consider overriding this error message and continuing with your simulation For example if your simulation does not require the polarisability to be a feature of the rigid species but is confined to free atoms or flexible molecules in the same system The appropriate error trap is found in subroutine SYSDEF Message 95 error potential cutoff exceeds half cell width In order for the minimum image convention to work correctly within DL POLY 2 it is necessary to ensure that the cutoff applied to the pair potentials does not exceed half CCLRC 189 the perpendicular width of the simulation cell The perpendicular width is the shortest distance between opposing cell faces Termination results if this is detected In NVE simulations this can only happen at the start of a simulation but in NPT it may occur at any time Action Supply a cutoff that is less than half the cell width If running constant pressure calcula tions use a cutoff that will accommodate the fluctuations in the simulation cell Study the fluctuations in the OUTPUT file to help you with this Message 97 error cannot use shell model with neutral groups The dynamical shell model was not designed to work with neutral groups This error results if an attempt is made to com
217. minate execution Action Locate the extra molecule directive in the FIELD file and remove Message 12 error unknown molecule directive in FIELD file Once DL POLY 2 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 CCLRC 176 expect to encounter directives not related to these data This error message results if it encounters a unrelated directive The most probable cause is incomplete specification of the data e g when the finish directive has been omitted Action Check the molecular data entries in the FIELD file and correct Message 13 error molecule species not specified This error arises when DL POLY _2 encounters non bonded force data in the FIELD file before the molecular species have been specified Under these circumstances it cannot as sign the data correctly and therefore terminates Action Make sure the molecular data appears before the non bonded forces data in the FIELD file and resubmit Message 14 error too many unique atom types specified This error arises when DL POLY 2 scans the FIELD file and discovers that there are too many different types of atoms in the system i e the number of unique atom types exceeds the mxsvdw parameter Action Standard user response Fix parameter mxsvdw Message 15 error duplicate pair potential specified In processing the FIELD file DL POL
218. ms is governed by a Evaluation of the real space sum is truncated at r Tcut SO it is important that a be chosen so that contributions to the real space sum are negligible for terms with r gt reut The relative error e in the real space sum truncated at freut is given approximately by erfc areut Teut exp a Teut Teut 3 1 The recommended value for a is 3 2 rcu 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 2 makes use of a more sophisticated approximation erfc z 0 56 exp 2 x 3 2 to solve recursively for a using equation 3 1 to give the first guess The relative error in the reciprocal space term is approximately Een exp kmax 4a7 kmag 3 3 where 5 kmar kmax 3 4 is the largest k vector considered in reciprocal space L is the width of the cell in the specified direction and kmax is an integer For a relative error of 4 x 107 this means using kmas 6 20 kmax is then kmax gt 3 2 L reut 3 5 In a cubic system reut L 2 implies kmax 7 In practice the above equation slightly over estimates the value of kmax reguired so optimal values need to be found experimentally In the above example kmax 5 or 6 would be adeguate Important note For the SPME method the values of kmax1 2 3 should be doub
219. mulae r j is the distance between atoms labelled i and j rij r ril 2 9 where ry is the position vector of an atom labelled The force on the atom j arising from a bond potential is obtained using the general formula Jj Tij p pede z 2 10 ij The force f acting on atom i is the negative of this Note some DL POLY 2 routines may use the convention that rij r Tj CCLRC 20 The contribution to be added to the atomic virial is given by W frij Fy 2 11 with only one such contribution from each bond The contribution to be added to the atomic stress tensor is given by GPS 2 12 where a and 5 indicate the x y z components The atomic stress tensor derived in this way is symmetric In DL POLY 2 bond forces are handled by the routine BNDFRC 2 2 2 Distance Restraints In DL POLY 2 distance restraints in which the separation between two atoms is main tained around some preset value ro is handled as a special case of bond potentials As a consequence distance restraints may be applied only between atoms in the same molecule Unlike with application of the pure bond potentials the electrostatic and van der Waals interactions between the pair of atoms are still evaluated when distance restraints are ap plied All the potential forms of the previous section are avaliable as distance restraints although they have different key words 1 Harmonic potential hrm 2 Morse potential mr
220. mxvdw Note that this parameter must be double the number of required metal potentials Recompile the program Message 73 error too many inversion potentials specified The number of inversion potentials specified in the FIELD file exceeds the permitted max imum Action Standard user response Fix the parameter mxtinv Message 75 error too many atoms in specified system DL POLY 2 places a limit on the number of atoms that can be simulated Termination results if too many are specified Action Standard user response Fix the parameter mxatms Message 77 error too many inversion potentials in system The simulation contains too many inversion potentials overall causing termination of run Action Standard user response Fix the parameter mxinv CCLRC 186 Message 79 error incorrect boundary condition in fbpfrc The 4 body force routine assumes a cubic or parallelepiped periodic boundary condition is in operation The job will terminate if this is not adhered to Action You must reconfigure your simulation to an appropriate boundary condition Message 80 error too many pair potentials specified DL POLY 2 places a limit on the number of pair potentials that can be specified in the FIELD file Exceeding this number results in termination of the program execution Action Standard user response Fix the parameters mxsvdw and mxvdw Message 81 error unidentified atom in pair potential list DL POLY
221. n If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 2180 error failed allocation of nptqvv_b2 f densO array This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 2190 error failed allocation of nptqvv_b2 f work arrays This is a memory allocation error Probable cause excessive size of simulated system CCLRC 240 Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 2200 error failed allocation of nptqvv_h1 f densO array This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 2210 error failed allocation of nptqvv_h1 f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 2220 error failed
222. n additional constaint to the velocities of the atoms in the constrained bond The first of these constraints leads to an expression for the constriant force similar to that for SHAKE 2 2 G x Hij di di y L 2 210 Note that this formula differs from eguation 2 207 by a factor of 2 This constraint force is applied during the first stage of the velocity Verlet algorithm The second constraint condition attempts to maintain the relative velocities of the atoms sharing a bond to a direction perpendicular to the bond vector This provides another constraint force H x 2 hij dij vj u ij At a Zij 2 211 This constraint force is applied during the second stage of the velocity Verlet algorithm Both constraint force calculations are iterative and are brought to convergence before pro ceeding to the next stage of the velocity Verlet scheme DL POLY 2 implements a parallel version of RATTLE that is based on the same ap proach as SHAKE 10 see section 2 6 9 The subroutine NVEVV_1 implements the velocity Verlet algorithm with bond constraints in the NVE ensemble The subroutine RDRATTLE_R is called to apply the corrections to atom positions and the subroutine RDRATTLE V is called to correct the atom velocities 2 5 3 Potential of Mean Force PMF Constraints and the Evaluation of Free Energy A generalization of bond constraints can be made to constrain a system to some point along a reaction coordinate A simple exam
223. nction between the error function er f and the more usual complementary error function er fc found in the real space sum should be noted The total electrostatic energy is given by the following formula 1 oo exp k 4a N 1 N djdn Us 22 2 y gj exp ik Tj er fc arnj 2Voeo k ATE Tnj k 0 J n lt J 1 a erf arem gt gt um om R u 2 157 m molecules lt m AT 0 where N is the number of ions in the system and N the same number discounting any excluded intramolecular interactions M represents the number of excluded atoms in a given molecule and includes the atomic self correction V is the simulation cell volume and k is a reciprocal lattice vector defined by k lu mu nw 2 158 3Strictly speaking the real space sum ranges over all periodic images of the simulation cell but in the DL_POLY_2 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 CCLRC 46 where m n are integers and u v w are the reciprocal space basis vectors Both V and u v w are derived from the vectors a b c defining the simulation cell Thus Vo a b x c 2 159 and bxc 2 m 2 Ta bxc cxa 2 160 v ETF axb 2 i a bxc With these definitions the Ewald formula above is applicable to general periodic systems A small additional modification is
224. nded by constraints it is to process Entries are zero if the atom is not bonded 3 A copy of the array is passed to each other node in turn The receiving node compares the incoming list with its own and keeps a record of the shared atoms and the nodes which share them 4 In the first stage of the SHAKE algorithm the atoms are updated through the usual Verlet algorithm without regard to the bond constraints 5 In the second iterative stage of SHAKE each node calculates the incremental cor rection vectors for the bonded atoms in its own list of bond constraints It then sends specific correction vectors to all neighbours that share the same atoms using the information compiled in step 3 6 When all necessary correction vectors have been received and added the positions of the constrained atoms are corrected 7 Steps 5 and 6 are repeated until the bond constraints are converged 8 After convergence the coordinate arrays on each node are passed to all the other nodes The coordinates of atoms that are not in the constraint list of a given node are taken from the incoming arrays an operation we term splicing 9 Finally the change in the atom positions is used to calculate the atomic velocities The above scheme is complete for a implementation based on the leapfrog integration algorithm However a velocity Verlet VV scheme requires additional steps 1 Step 9 above does not apply for VV The velocity is integrated under th
225. ne subroutine subroutine subroutine subroutine subroutine subroutine subroutine 245 four_body_terms f inversion_terms f metal_terms f metal_terms_4pt f metal_terms_rsq f pmf_terms f rigid body terms f tersoff terms f tether terms f three body terms f define system f vdw terms f vdw terms 4pt f vdw_terms_rsq f metal_terms f metal_terms_4pt f metal_terms_rsq f system_properties f system_properties f dihedral_terms f dihedral_terms_4pt f dihedral_terms_rsq f spme_terms f utility_pack f utility_pack f ewald_terms f ewald_terms_4pt f ewald_terms_rsq f error f ewald_terms f ewald terms 4pt f ewald_terms_rsq f ewald_terms f ewald_terms_4pt f ewald_terms_rsq f neu_ewald_terms f ewald_terms f ewald_terms_4pt f ewald_terms_rsq f neu_ewald_terms f ewald_terms f ewald_terms_4pt f ewald_terms_rsq f spme_terms f CCLRC exclude exclude_atom exclude_link excludeneu exitcomms exitcomms extnfld fbpfre fcap findstring fldscan forces forcesneu forgen forgen forgen fortab fortab fortab freeze gauss gdsum gdsum getcom getkin getkinf getking getkinr getkins getkint getmass getrec getrotmat getvom getword gimax gimax gisum gisum global sum forces gstate gstate gsync gsync subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine function subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine
226. ne parlst_nsq nonbonded pair force has exceeded the neighbour list array dimensions Action Standard user response Fix the parameter mxlist Message 110 error neighbour list array too small in parlst Construction of the Verlet neighbour list in subroutine parlst nonbonded pair force has exceeded the neighbour list array dimensions Action Standard user response Fix the parameter mxlist Message 112 error vertest array too small This error results when the dimension of the DL_POLY_2 VERTEST arrays which are used in checking if the Verlet list needs updating have been exceeded CCLRC 192 Action Standard user response Fix the parameter mslst Message 120 error invalid determinant in matrix inversion DL_POLY_2 occasionally needs to calculate matrix inverses usually the inverse of the ma trix of cell vectors which is of size 3 x 3 For safety s sake a check on the determinant is made to prevent inadvertent use of a singular matrix Action Locate the incorrect matrix and fix it e g are cell vectors correct Message 130 error incorrect octahedral boundary condition When calculating minimum images DL POLY 2 checks that the periodic boundary of the simulation cell is compatible with the specifed minimum image algorithm Program termi nation results if an inconsistency is found In this case the error refers to the truncated octahedral minimum image which is inconsistent with the simulation cel
227. necessary for rhombic dodecahedral and truncated oc tahedral simulation cells 30 In practice the convergence of the Ewald sum is controlled by three variables the real space cutoff reut the convergence parameter a and the largest reciprocal space vector kmar used in the reciprocal space sum These are discussed more fully in section 3 3 5 DL_POLY 2 can provide estimates if requested see CONTROL file description 4 1 1 The force on an atom 7 is obtained by differentiation and is qj x lt a exp k 4o fr 5 koole o EAE yg o ik Tn J Voeg k kz0 a a Ameo Tai i VT n bai qj qe 20Tgj 2 2 a erf aru exp a r ra The electrostatic contribution to the system virial can be obtained as the negative of the Coulombic energy However in DL POLY 2 this formal equality can be used as a check on the convergence of the Ewald sum The actual electrostatic virial is obtained during the calculation of the diagonal of the stress tensor The electrostatic contribution to the stress tensor is given by oo ie 1 1 exp ee y 1 2 gt gt K or 1 N 1 qjq 2arnj 5 3 ferfearn A a Ran 2 162 j lt n mj 1 uk 20rgj er f arg exp a rjj Ry Ameg y T VT AT EO CCLRC AT where matrices K and Ry are defined as follows KL geg 2 163 ip opt 2 164 In DL POLY 2 the full Ewald sum is handled by several routines EWALD1 and EWALD1A handle the re
228. neighbour list is therefore different on each node DL POLY 2 uses a method based on the Brode Ahlrichs scheme 22 see figure below to construct the neighbour list Additional modifications are necessary to handle the excluded atoms 43 A distributed excluded atoms list is constructed by DL POLY 2 at the start of the simulation The list is constructed so that the excluded atoms are referenced in the same order as they would appear in the Verlet neighbour list if the bonded interactions were ignored allowing for the distributed structure of the neighbour list CCLRC 81 Brode Ahlrichs Algorithm 12 Atoms 4 processors Processor 0 10 11 10 12 10 1 10 2 10 3 11 12 11 1 11 2 11 3 11 4 12 1 12 2 12 3 12 4 12 5 Schematic diagram of the parallel implementation of the Brode Ahlrichs algorithm The diagram illustrates the reordering of the upper triangular matrix of n n 1 2 pair interactions so that the rows of the matrix are of approximately equally length Each entry in the table consists of a primary atom index constant within a row and a neighbouring atom index Rows are assigned sequentially to nodes In the diagram node 0 deals with rows 1 5 and 9 node 1 to rows 2 6 and 10 etc When a charge group scheme as opposed to an atomistic scheme is used for the non bonded terms the group group interactions are distributed using the Brode Ahlrichs approach This makes the Verlet list considerably smaller thus saving memory
229. ng features 1 2 3 9 10 All common forms of non bonded atom atom potential Atom atom site site Coulombic potentials Valence angle potentials Dihedral angle potentials Inversion potentials Improper dihedral angle potentials 3 body valence angle and hydrogen bond potentials 4 body inversion potentials Sutton Chen density dependent potentials for metals 3 The Tersoff density dependent potential for covalent systems 4 The parameters describing many of these these potentials may be obtained for example from the GROMOS 5 Dreiding 6 or AMBER 7 forcefield which share functional forms It is relatively easy to adapt DL _POLY 2 to user specific force fields Note that DL POLY_2 does not have its own official force field CCLRC 5 1 2 3 Boundary Conditions DL_POLY_2 will accommodate the following boundary conditions 1 None e g isolated polymer in space 2 Cubic periodic boundaries 3 Orthorhombic periodic boundaries 4 Parallelepiped periodic boundaries 5 Truncated octahedral periodic boundaries 6 Rhombic dodecahedral periodic boundaries 7 Slab x y periodic z nonperiodic 8 Hexagonal prism periodic boundaries These are describe in detail in Appendix B 1 2 4 The Java Graphical User Interface DL_POLY 2 has a Graphical User Interface GUI written specifically for the package in the Java programming language from Sun microsystems The Java prog
230. nigues as they are described in greater detail in references 30 43 2 6 1 The Replicated Data Strategy The Replicated Data RD strategy 42 is one of several ways to achieve parallelisation in MD Its name derives from the replication of the configuration data on each node of a parallel computer i e the arrays defining the atomic coordinates r velocities v and forces f for all N atoms i i 1 N in the simulated system are reproduced on every processing node In this strategy most of the forces computation and integration of the equations of motion can be shared easily and equally between nodes and to a large extent be processed independently on each node The method is relatively simple to program and is reasonably efficient Moreover it can be collapsed to run on a single processor very easily However the strategy can be expensive in memory and have high communication overheads but overall it has proven to be successful over a wide range of applications These issues are explored in more detail in 42 43 Systems containing complex molecules present several difficulties They often contain ionic species which usually require Ewald summation methods 11 44 and intra molecular CCLRC 79 interactions in addition to intermolecular forces These are handled easily in the RD strategy though the SHAKE algorithm 12 requires significant modification 30 The RD strategy is applied to complex molecular systems as
231. nstq_h1 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1600 error failed allocation of density array in nst hl f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1610 error failed allocation of work arrays in qshake f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1615 error failed allocation of work arrays in qrattle_q f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1620 error failed allocation of work arrays in nveq_2 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using
232. ntities are calculated by the routine STATIC which also writes the STATIS file section 4 2 7 Routine TRAJECT writes the HISTORY section 4 2 1 file for later analysis Job termination is handled by the routine RESULT which writes the final summaries in the OUTPUT file and dumps the restart files REVIVE and REVCON sections 4 2 4 and 4 2 3 respectively An idea of the construction of a DL POLY 2 program can be obtained from the following flowchart The example represents a DL POLY 2 program which uses the multiple timestep algorithm with bond constraints and the Nos Hoover thermostat CCLRC 90 CCLRC 91 3 2 Compiling and Running DL_POLY_2 3 2 1 Compiling the Source Code When you have obtained DL_POLY_2 from Daresbury Laboratory and unpacked it your next task will be to compile it To aid compilation a set of makefiles has been provided in the sub directory build see example in Appendix A of this document The versions go by the names of e MakePAR to build a parallel MPI version on a unix platform e MakeSEQ to build a sequential one processor unix version e MakeWIN to build a Windows one processor XP version Select the one you need and copy it into the srcf90 directory In what follows we as sume the makefile in the srcf90 directory is called Makefile The Makefile will build an executable with a wide range of functionality sufficient for the test cases and for most users requirements Other m
233. nts Title Page About DL_POLY 2 Disclaimer Acknowledgements Manual Notation Contents List of Tables List of Figures 1 Introduction 11 The DL POLY Package 1 2 Functionality Molecular Systems TheDL POLY 2 Force Field Boundary Conditions The Java Graphical User Interface Fad un aei oi 12 34 2 k 0 ee Gow e y 1 1 3 Programming Style Ll 1 2 2 1 2 3 1 2 4 1 2 5 1 3 1 Programming Language 1 3 2 Memory Management 1 3 3 Target Computers 1 3 4 Version Control System CVS 1 3 5 Required Program Libraries 1 3 6 Internal Documentation 1 3 7 Subroutine Function Calling Sequences 1 3 8 FORTRAN Parameters 1 3 9 Arithmetic Precision 1 3 10 Units soe a rr k s f de ka 1 3 11 Error Messages 1 4 The DL_POLY 2 Directory Structure 1 4 1 The srcf90 Sub directory ix lt OOLOLOOOSVSISIJVJVAOO0GOACTClUJURWO I 0 CCLRC 142 The nutikt Sibsdlirectory nu ya kava a ala ee A K 4 Rm eee 143 The data Sub direetory b s kkk i d Kasa REED 144 The bench Sub directory ss sk k k RE A8 1 4 5 The execute Sub directory oe e rae sapene tiandat as 1 4 6 The build Sub directory I kpaa 1 4 7 The public Sub directory 1 4 aaor ie ea p a a 1 4 8 The java Sub directory o 4 642544 452808 454048444 64 1 5 Obtaining the Source Code GI k s k k k
234. o r S 5 Meyer hbnd 12 10 H bond A B U r ain snm Shifted force Eo n m ro rc U r c x n To y 1 m m To ym 1 a vm r om cay By cwr e 7 nmaEo T Yro wen 0 2 mors Morse Eo ro k U r Eo 1 exp k r r9 1 tab Tabulation tabulated potential T Note in this formula the terms a 8 and y are compound expressions involving the variables o m m rg and rc See section 2 3 1 for further details Note rc defaults to the general van der Waals cutoff rvdw or rcut if it is set to zero or not specified or not specified in the FIELD file CCLRC 130 Table 4 13 Three body potentials key potential type Variables 1 4 functional formf thrm Truncated harmonic shrm Screened harmonic bvs1 Screened Vessal 24 bvs2 Truncated Vessal 25 hbnd H bond 6 k Oo k 00 k A e los Drob Rho p p p p2 p2 U 0 0 0o exp r ri P NIS U 0 5 0 b0 exp rij p1 rik p2 U 9 sgip 00 m 0 n exp rij p1 Tik p2 U 6 k 9 00 0 8 27 87781 9 8o m 6 exp r ri 0 U 9 Dnocos 9 5 Rno T 5x 6 Rib rjk 9 10 is the a b c angle variable 1 real variable 2 real variable 3 real variable 4 real variable 5 real potential parameter see table 4 13 potential parameter see tabl
235. o the atomic virial for each pair interaction is The contribution to be added to the atomic stress tensor is given by f 2 89 where a and 6 indicate the x y z components The atomic stress tensor derived from the pair forces is symmetric Since the calculation of pair potentials assumes a spherical cutoff reut it is necessary to apply a long range correction to the system potential energy and virial Explicit formulae are needed for each case and are derived as follows For two atom types a and b the correction for the potential energy is calculated via the integral Uw N N corr 27 oo L gav r Uas r r dr 2 90 Tout where Na Np are the numbers of atoms of types a and b V is the system volume and ggp r and U p r are the appropriate pair correlation function and pair potential respectively It is usual to assume gap r 1 for r gt freute DL POLY_2 sometimes makes the additional assumption that the repulsive part of the short ranged potential is negligible beyond Teut The correction for the system virial is we MM corr V Jab r 5 Uanlr r dr 2 91 where the same approximations are applied Note that these formulae are based on the assumption that the system is reasonably isotropic beyond the cutoff In DL POLY 2 the short ranged forces are calculated by one of the routines SRFRCE SRFRCE_RSQ and SRFRCENEU The long range corrections are calculated by routine LR CORRECT The calculation m
236. obtain a desired average pressure P x and or isotropic stress tensor a DL POLY 2 has two such algorithms a Hoover barostat and the Berendsen barostat Only the former has a well defined conserved quantity 2 5 6 1 The Hoover Barostat DL_POLY 2 uses the Melchionna modification of the Hoover algorithm 38 in which the equations of motion couple a Nos Hoover thermostat and a barostat Cell size variation For isotropic fluctuations the equations of motion are ED alb n r t Bo EO _ byt n ult My TO Ta 5 Wale kpText at n t P t Pe x t n t TO Bovo F where Q NykaluaT is the effective mass of the thermostat and W NekpTextT is the effective mass of the barostat Ny is the number of degrees of freedom n is the barostat friction coefficient Ro the system centre of mass 77 and Tp are specified time constants for temperature and pressure fluctuations respectively P t is the instantaneous pressure and V the system volume The conserved quantity is to within a constant the Gibbs free energy of the system 1 1 t Hnupr U KE Pas V t 50x t W t 8 X 5 kpText ds 2 228 o TT The algorithm is readily implemented in the LF scheme as x t At x t At a AIN rj ag eT Q Q x t u xe sat x t 540 ner gAn gAn Ar T my Paa x onto 1 1 nt 5 ne 5 5 At n t A CCLRC 65 Ix n
237. occurrences of this are NPT and NST simulations or simulations where the CCLRC 88 local density on the MD cell may significantly exceed the mean density of the cell systems with a vaccum gap for example Under these circmstances arrays initally allocated may be insufficent In which case DL_POLY_2 may report a memory problem and request that you recompile the code with hand adjusted array dimensions This topic is dealt with more fully in Appendix C 3 1 2 Constructing Nonstandard Versions In constructing a nonstandard DL POLY 2 simulation program the first requirement is for the user to write a program to function as the root segment The srcf90 directory contains an example of such a root program DLPOLY This root program calls the major routines required to perform the simulation and also controls the normal molecular dynamics cy cle which consists of forces calculation followed by integration of the equation of motion DLPOLY also monitors the cpu usage and brings about a controlled termination of the pro gram if the usage approaches the allotted job time within a pre set closure time Lastly DLPOLY is the routine that first opens the OUTPUT file section 4 2 2 which provides the summary of the job Users are recommended to study the DLPOLY root as a model for other implementations of the package they may wish to construct If additional functionality is added to DL_POLY_2 by the user the PARSET F subroutine and its support
238. of macromolecules polymers ionic systems solutions and other molecular systems on a distributed memory parallel computer The package was written to support the UK project CCP5 by Bill Smith and Tim Forester 2 under grants from the Engineering and Physical Sciences Research Council and is the property of the Council for the Central Laboratory of the Research Councils Two forms of DL POLY exist DL POLY 2 is the earlier version and is based on a replicated data parallelism It is suitable for simulations of up to 30 000 atoms on up to 100 processors DL POLY 3 is a domain decomposition version written by I T Todorov and W Smith and is designed for systems beyond the range of DL_POLY_2 up to 10 000 000 atoms and beyond and 1000 processors This document is entirely concerned with DL_POLY_2 Though DL POLY 2 is designed for distributed memory parallel machines but we have taken care to ensure that it can with minimum modification be run on the popular work stations Scaling up a simulation from a small workstation to a massively parallel machine is therefore a useful feature of the package Users are reminded that we are interested in hearing what other features could be use fully incorporated We also request that our users respect the copyright of the DL_POLY 2 source and not alter any authorship or copyright notices within We require that all users of the package register with us not least because we need to keep everyone abreast of ne
239. olecules may be split between processors This message CCLRC 206 indicates that the code has failed to carry out either of these successfully Action The error may arise from a compiler error Try recompiling INTLIST without the optimiza tion flag turned on If the problem persists it should be reported to the authors after checking the input data for inconsistencies Message 433 error specify rcut before the Ewald sum precision When specifying the desired precision for the Ewald sum in the CONTROL file it is first necessary to specify the real space cutoff rcut Action Place the cut directive before the ewald precision directive in the CONTROL file and rerun Message 434 error illegal entry into STRESS related routine The calculation of the stress tensor in DL POLY 2 requires additional code that must be included at compile time through the use of the STRESS keyword If this is not done and DL_POLY_2 is later required to calculate the stress tensor this error will result Action The program must be recompiled with the STRESS keyword activated This will ensure all the relevant code is in place See section 3 2 1 Message 436 error unrecognised ensemble An unknown ensemble option has been specified in the CONTROL file Action Locate ensemble directive in the CONTROL file and amend appropriately Message 438 error PMF constraints failed to converge The constraints in the potential of mean force alg
240. omputed in the absence of the constraint force For brevity in this and subsequent equations we leave out corresponding equations for body B We can also write the true torque at timestep tn i e T as T F 4 dh xG p 2 270 It may be easily shown from this and equation 2 250 that a in NL m wy bat 1 dip x Gis 2 271 from which it follows that n m 1 A h n j dap dap z JABU A x dap 2 272 where we have defined F U E dip x disp 2 273 CCLRC 75 and we have used the identity GAR JABJABp where gp is a scalar quantity Now the true position at timestep tn 1 of the link atom on rigid body A is i FD 2 274 and inserting 2 269 and 2 272 leads to 1 1 At r Ry dag dis Oa 2 275 where TL 84 aer UN x iy 2 276 Since dihp ret we can easily obtain n l At Aiko daBp 9AB BA Op 2 277 Squaring both sides and neglecting terms of order higher than O At gives after rearrange ment a EE Gy 9 AP ate Qa Op From which the constraint force may be calculated Iteration is necessary as in SHAKE In the second stage of OSHAKE we need to calculate another constaint force H to preserve the orthogonality of the constraint bond vector and the relative velocity of the two atoms in the bond Once again the contraint force implies corrections to the translational and rotational equations of motion which following the methods used above w
241. on B r rjk T4n IS 1 B r r x FA 2 42 are Lijs jk ae r x Pell jk x T kn are Eu x Tip Tn x Tkn cos ijkn 1 1 5 2 ri x rik Ore i iy r 7 Tra are Eik Tl with 2 a Bret tis x Tjk Gi x Tkn ris LjkT jk la Oe den rjxTxn e n _ gj Tk UrijT klo en Sek TikTanla 025 dei Tin Cis Tikla Ok e Trig ti j 2rikltijTanla 02 Sex 2 43 O 5 Ora s X Tik 2r T jkTikla das ci SH rijTjkla ej Ovk 2r Uni Ti lo a gj r Tjk oe ei E 603 s 2 44 O 5 a ara rjg X Een 2r amp n Urjxtjkla tn ek ik Tknla 9 m ar Fe TknThnlo Ok 025 TjnTxn e k tn 2 45 Where we have used the the following definition a bla X 1 ag afb 2 46 B CCLRC 26 Formally the contribution to be added to the atomic virial is given by 4 Yr 2 47 i 1 However it is possible to show by tedious algebra using the above formulae or more elegantly by thermodynamic arguments 26 that the dihedral makes no contribution to the atomic virial The contribution to be added to the atomic stress tensor is given by oe r p F rap TY 2 48 COS isk _608 Pijkn 7 n re rag riage r eh ae with Pr r klTgkTkn u TinlTxTjn e ri X Lyell ge X Tan 2 49 Pa U kliatiela r jlrjktjela ri X Calle Dn 2 50 P
242. on is polarisable if it develops a dipole moment when placed in an electric field It is commonly expressed by the equation u ak 2 196 CCLRC 53 where u is the induced dipole and E is the electric field The constant a is the polarisability The dynamical shell model is a method of incorporating polarisability into a molecular dynamics simulation The method used in DL_POLY_2 is that devised by Fincham et al 34 and is known as the adiabatic shell model In the static shell model a polarisable atom is represented by a massive core and massless shell connected by a harmonic spring hereafter called the core shell unit The core and shell carry different electric charges the sum of which equals the charge on the original atom There is no electrostatic interaction i e self interaction between the core and shell of the same atom Non Coulombic interactions arise from the shell alone The 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 qQ k 2 197 where q is the shell charge and k is the force constant of the harmonic spring In the adiabatic method a fraction of the atomic mass is assigned to the shell to permit a dynamical description The fraction of mass is chosen to ensure that the natural frequency of vibration v of the harmonic spring i e 1 k 1 2 v Een wal 2 198 with m the atomic mass is w
243. on of the intramolecular interactions in DL_POLY_2 all bonds valence angles and dihedrals must be individually cited The indices i 7 and k n appearing in the pair body and three or four body terms indicate the atoms involved in the interaction There is normally a very large number of these and they are therefore specified according to atom types rather than indices In DL_POLY 2 it is assumed that the pair body terms arise from van der Waals and or elec trostatic Coulombic forces The former are regarded as short ranged interactions and the latter as long ranged Long range forces require special techniques to evaluate accurately see section 2 4 In DL POLY 2 the three body terms are restricted to valence angle and H bond forms The nonbonded three body four body and Tersoff interactions are glob ally specified according to the types of atoms involved DL POLY 2 also has the ability to handle metals via density dependent functions see below Though essentially many body potentials their particular form means they are handled in a manner very similar to pair potentials In DL POLY 2 the intramolecular bonded terms are handled using bookkeeping arrays which specify the atoms involved in a particular interaction and point to the appropriate arrays of parameters that define the potential The calculation of bonded forces therefore follows the simple scheme 1 Every atom in the simulated system is assigned a unique index number from 1
244. onfigurations j timestep interval between configurations k data level i e variable keytrj see table 4 3 set timestep to f ps calculate the z density profile perform zero temperature MD run CCLRC 110 4 1 1 3 Further Comments on the CONTROL File 1 A number of the directives or their mutually exclusive alternatives are manda tory a timestep specifying the simulation timestep b temp or zero specifying the system temperature not mutually exclusive c ewald sum or ewald precision or spme sum or spme precision or hke sum or hke precision or coul or shift or distan or reaction or no elec specifying the reguired coulombic forces option d cut and delr specifying the short range forces cutoff and Verlet strip e prim specifying primary forces cutoff if mult gt 2 only 2 The job time and close time directives are reguired 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 egual to the time specified to the operating system when the job is submitted The close time directive represents the time DL POLY 2 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 2 reaches the effective Job time limit it begins the close down procedure with enough
245. ons such as the conformational study of an isolated polymer molecule This boundary condition is not recommended for studies in a solvent since evaporation is likely to be a problem Note this boundary condition cannot be used with the Ewald summation method 167 CCLRC 168 Cubic periodic boundaries IMCON 1 The cubic MD cell The cubic MD cell is perhaps the most commonly used in simulation and has the advantage of great simplicity In DL_ POLY 2 the cell is defined with the principle axes passing through the centres of the faces Thus for a cube with sidelength D the cell vectors appearing in the CONFIG file should be D 0 0 0 D 0 0 0 D Note the origin of the atomic coordinates is the centre of the cell The cubic boundary condition can be used with the Ewald summation method Orthorhombic periodic boundaries IMCON 2 The orthorhombic cell is also a common periodic boundary which closely resembles the cubic cell in use In DL_POLY_2 the cell is defined with principle axes passing through the centres of the faces For an orthorhombic cell with sidelengths D in X direction E in Y direction and F in Z direction the cell vectors appearing in the CONFIG file should be D 0 0 0 E 0 0 0 F Note the origin of the atomic coordinates is the centre of the cell The orthorhombic boundary condition can be used with the Ewald summation method CCLRC 169 The orthorhomic MD cell Parallelepiped periodic bound
246. oo small Action Standard user response Fix the parameter mxxdf Message 477 error mxxdf too small in prneulst subroutine The parameter mxxdf defining working arrays in subroutine PRNEULST is too small Action Standard user response Fix the parameter mxxdf Message 478 error mxxdf too small in forcesneu subroutine The parameter mxxdf defining working arrays in subroutine FORCESNEU is too small Action Standard user response Fix the parameter mxxdf Message 479 error mxxdf too small in multipleneu subroutine The parameter mxxdf defining working arrays in subroutine MULTIPLENEU is too small Action Standard user response Fix the parameter mxxdf CCLRC 213 Message 484 error only one potential of mean force permitted It is not permitted to define more than one potential of mean force in the FIELD file Action Check that the FIELD file contains only one PMF specification If more than one is needed DL POLY 2 cannot handle it Message 486 error HK real space screening function cutoff violation DL POLY 2 has detected an unacceptable degree of inaccuracy in the screening function near the radius of cutoff in real space which implies the Hautman Klein Ewald method will not be sufficiently accurate Action The user should respecify the HK control parameters given in the CONTROL file Either the convergence parameter should be increased or the sum expanded to incorporate more images of the centra
247. or failed allocation of work arrays in nveq_1 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1510 error failed allocation of work arrays in nvtg bl f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1520 error failed allocation of work arrays in nvt h1 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor CCLRC 226 Message 1530 error failed allocation of work arrays in nptg bl f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1540 error failed allocation of density array in npt bl f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be
248. or Probable cause excessive size of simulated system CCLRC 238 Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 2090 error failed allocation of nstvv_b1 f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 2100 error failed allocation of nveqvv_1 f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 2110 error failed allocation of nveqvv_2 f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 2120 error failed allocation of nvtqvv_b1 f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with la
249. or defining cross terms of the potential are not the usual rules encountered in Lennard Jones systems 47 4 1 3 5 The Tersoff Potential The Tersoff potential 4 is designed to reproduce the effects of covalency in systems com posed of group 4 elements in the periodic table carbon silicon germanium etc and their alloys Like the metal potentials these are also non bonded potentials characterised by atom types rather than specific atomic indices The input of Tersoff potential data is signalled by the directive tersoff n Where n is the number of specified Tersoff potentials It is followed by 2n records specifying n particular Tersoff single atom type parameters and n n 1 2 records specifying cross atom type parameters in the following manner potential 1 record 1 atmnam a atom type key a4 potential key see Table 4 16 variable 1 real potential parameter see Table 4 16 variable 2 real potential parameter see Table 4 16 variable 3 real potential parameter see Table 4 16 variable 4 real potential parameter see Table 4 16 variable 5 real cutoff range for this potential 4 16 potential 1 record 2 variable 6 real potential parameter see Table 4 16 variable 7 real potential parameter see Table 4 16 variable 8 real potential parameter see Table 4 16 variable 9 real potential parameter see Table 4 16 variable 10 real potential parameter see Table 4 16 variable 11 real potential parameter see Table 4 16 CCLRC 133
250. ord atom 1 a8 first atom type atom 2 a8 second atom type potential data records number of data records Int ngrid 3 4 data 1 real data item 1 data 2 real data item 2 data 3 real data item 3 data 4 real data item 4 force data records number of data records Int ngrid 3 4 data 1 real data item 1 data 2 real data item 2 data 3 real data item 3 data 4 real data item 4 4 1 5 3 Further Comments It should be noted that the number of grid points in the TABLE file should not be less than the number of grid points DL POLY 2 is expecting This number is given by the param CCLRC 137 eter mxgrid which is defined in the PARSET F subroutine in the SETUP_PROGRAM F file DL_POLY_2 will re interpolate the tables ifngrid gt mxgrid but will abort if ngrid lt mxgrid The potential and force tables are used to fill the internal arrays vvv and ggg respectively see section 2 3 1 The contents of force arrays are derived from the potential via the formula G r 2 U r Note this is not the same as the true force Important The potential and force arrays in the TABLE file are written in the same units as the FIELD file So if you specified a particular unit using the UNITS directive in the FIELD file the same units are expected here It is useful to note that the definition of the force arrays given above means that the units are the same as for the potential i e are handled using the same conversion factors CCLRC 138 4
251. ored The default setting is execute 3 2 1 2 Modifying the Makefile 1 Changing the TARGET If you do not intend to run DL POLY 2 on one of the specified machines you must CCLRC 93 add appropriate lines to the makefile to suit your circumstances The safest way to do this is to modify an existing TARGET option for your purposes The makefile supplied with DL_POLY_2 contains examples for serial and MPI environments as well as for different parallel machines so you should find one close to your requirements You must of course be familiar with the appropriate invocation of the FORTRAN compiler for your local machine and also any alternatives to MPI your local machine may be running If you wish to compile for MPI systems remember to ensure the appropriate library directories are accessible to you If you require a serial version of the code you must remove references to the MPI libraries from the Makefile and add the file serial f to your compilation this will insert replacement dummy routiens for the MPI calls 2 Enabling the Smoothed Particle Mesh Ewald The standard compilation of DL_POLY_2 will incorporate a basic 3D Fast Fourier Transform FFT routine to enable the SPME functionality Users may wish to try alternative FFT routines which may offer faster performance Some hooks for these appear in the code as comment lines in the FORTRAN source The user should search for the following keys in the code e CCRAY
252. orithm have not converged in the permit ted number of cycles The SHAKE algorithm for PMF constraints is iterative Possible causes include a bad starting configuration too large a time step used incorrect force field specification too high a temperature inconsistent constraints involving shared atoms etc Action Corrective action depends on the cause It is unlikely that simply increasing the iteration number will cure the problem but you can try follow standard user response to increase the parameter mxshak But the trouble is much more likely to be cured by careful consideration CCLRC 207 of the physical system being simulated For example is the system stressed in some way Too far from equilibrium Message 440 error undefined angular potential A form of angular potential has been requested which DL POLY 2 does not recognise Action Locate the offending potential in the FIELD file and remove Replace with one acceptable to DL POLY 2 if this is possible Alternatively you may consider defining the required potential in the code yourself Amendments to subroutines SYSDEF and ANGFRC will be required Message 442 error undefined three body potential A form of three body potential has been requested which DL POLY 2 does not recognise Action Locate the offending potential in the FIELD file and remove Replace with one acceptable to DL_POLY_2 if this is reasonable Alternatively you may consider defining the required
253. ors Morse Eo ro k U r Eo 1 exp k r ro 1 mrs 12 6 12 6 A B U r 4 126 rhrm Restraint k ro Te U r k r ro r ro lt re U r ikr kre r rol re r r gt r rhm quar Quartic k ro k Re U r 8 r ro k r ro E r To gur buck Buckingham Alp C U r Aexp r p C r bck Note bond potentials with a dash as the first character of the keyword do not con tribute to the excluded atoms list see section 2 1 In this case DL POLY 2 will also calculate the nonbonded pair potentials between the described atoms unless these are deactivated by another potential specification atomic site index site weighting integer real index weight This directive and associated data records need not be specified if no PMF con straints are present See the note on the atomic indices appearing under the shell directive above The pmf bondlength applies to the distance between the centres of the two pmf units The centre R of each unit is given by L X Wala Ya Wa where r is a site position and Wa 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 molecule This is illustrated in test case 6 where a pmf constraint is imposed between a potassium ion and the centre of mass R CCL
254. ot confuse this error with that CCLRC 182 described by message 50 above Action Standard user response Fix the parameter mxangl Consider the possibility that the wrong CONFIG file is being used e g similar system but larger size Message 52 error end of FIELD file encountered This message results when DL POLY 2 reaches the end of the FIELD file without having read all the data it expects Probable causes missing data or incorrect specification of integers on the various directives Action Check FIELD file for missing or incorrect data and correct Message 53 error end of CONTROL file encountered This message results when DL POLY 2 reaches the end of the CONTROL file without having read all the data it expects Probable cause missing finish directive Action Check CONTROL file and correct Message 54 error problem reading CONFIG file This message results when DL _POLY_2 encounters a problem reading the CONFIG file Possible cause corrupt data Action Check CONFIG file and correct Message 55 error end of CONFIG file encountered This error arises when DL_POLY_2 attempts to read more data from the CONFIG file than is actually present The probable cause is an incorrect or absent CONFIG file but it may be due to the FIELD file being incompatible in some way with the CONFIG file Action Check contents of CONFIG file If you are convinced it is correct check the FIELD file for inconsistencie
255. otion_1 vv_motion_1 vv_motion_1 vv_motion_1 error gstate nptgvv b1 nptqvv_b2 nptgvv h1 nptqvv_h2 nptvv_bl nptvv h1 nstgvv b1 nstqvv_b2 nstqvv_hi nstqvv_h2 nstvv_bl nstvv h1 nvegvv 1 nvegvv 2 nvevv 1 nvtgvv b1 nvtqvv_b2 nvtgvv h1 nvtqvv_h2 nvtvv_bl nvtvv_el nvtvv h1 pmfvv dcell error gdsum getcom getvom gstate images kinstress matmul merge nptscale_p nptscale_t nstscale_p nstscale_t nvtscale rdrattle_r rdrattle_v shmove splice 266 CCLRC vv_rotation_1 vv_rotation_1 vv_rotation_1 vv_rotation_1 vv_rotation_1 vv_rotation_1 vv_rotation_1 vv_rotation_1 vv_rotation_1 vv_rotation_1 vv_rotation_1 vv_rotation_1 vv_rotation_1 vv_rotation_1 vv_rotation_1 vv_rotation_1 vv_rotation_1 vv_rotation_1 vv_rotation_1 vv_rotation_1 vv_rotation_1 vv_rotation_1 vv_rotation_1 vv_rotation_1 vv_rotation_2 vv_rotation_2 vv_rotation_2 vv_rotation_2 vv_rotation_2 vv_rotation_2 vv_rotation_2 vv_rotation_2 vv_rotation_2 vv_rotation_2 vv_rotation_2 vv_rotation_2 vv_rotation_2 vv_rotation_2 vv_rotation_2 vv_rotation_2 vv_rotation_2 vv_rotation_2 vv_rotation_2 vv_rotation_2 bodystress dcell error getcom getking getrotmat getvom gimax gstate images kinstressf kinstressg matmul merge mergel nosguish nptgscl_p nptgscl_t nptgscl_t nstgscl_p nstgscl_t nvtgscl rdrattle_r rdrattle_v bodystress dcell gdsum getcom getking getrotmat getvom gimax gstate images kinstressf kinstress
256. parameters will increase the accuracy but also substantially increase the cpu time of a simulation The recommended value for both these parameters is 1 and if both these integers are left out the default values will be adopted As with the standard Ewald and SPME methods the user may set alternative control CCLRC 101 parameters with the CONTROL file hke sum directive e g hke sum 0 056611 which would set a 0 05 7 kmax1 6 kmax2 6 Once again one may check the accuracy by comparing the Coulombic energy with the virial as described above The last two integers specify once again the values of nhko and nlatt respectively Note it is possible to set either of these to zero in this case Estimating the parameters required for a given simulation follows a similar procedure as for the standard Ewald method above but is complicated by the occurrence of higher orders of the convergence functions Firstly a suitable value for a may be obtained when nlatt 0 from the rule a 3 reuz where reut is the largest real space cutoff compatible with a single MD cell and G 3 46 4 37 5 01 5 55 when nhko 0 1 2 3 respectively Thus in the usual case where nhko 1 G 4 37 When nlatt0 this 8 value is multiplied by a factor 1 2 x nlatt 1 The estimation of kmax1 2 is the same as that for the standard Ewald method above Note that if any of these parameters prove to be insufficiently accurate DL_POLY 2 will issue an error in the OUTPUT f
257. pdate cfgscan check_shells check_syschg copystring copystring copystring copystring copystring copystring copystring copystring copystring copystring copystring copystring copystring copystring copystring copystring copystring copystring copystring copystring corshl could coulOneu coul2 dlpoly dlpoly dlpoly dlpoly dlpoly dlpoly lf rotation 1 lf rotation 2 vv_rotation_1 vv_rotation_2 dlpoly spme_terms spme_terms lf motion 1 lf rotation 1 lf rotation 2 ensemble tools setup program define system define system angle terms bond terms define system dihedral terms dihedral terms 4pt dihedral terms rs external field terms four body terms inversion terms metal terms metal terms 4pt metal terms rs shake terms site terms tersoff terms tether terms three body terms vdw terms vdw terms 4pt vdw terms rs dlpoly force drivers force drivers force drivers 270 CCLRC coul2neu coul3 coul3neu coul4 cpy_rtc date_and_time date_and_time dcell dcell dcell dcell dcell dcell dcell dcell dcell dcell dcell dcell dcell dcell dcell dcell dcell dcell dcft3 define_angles define_atoms define_bonds define_constraints define_core_shell define_dihedrals define_external_field define_four_body define_inversions define_metals define_pmf define_rigid_body define_tersoff define_tethers define_three_body define_units define_van_der_w
258. placed by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1014 error failed allocation of vdw arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1020 error failed allocation of angle work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1030 error failed allocation of bond arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1040 error failed allocation of bond work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1050 error failed allocation of dihedral arrays This is a memory allocation error Probable cause excessive size
259. ple of such a reaction coordinate would be the distance between two ions in solution If a number of simulations are conducted with the system constrained to different points along the reaction coordinate then the mean constraint force may be plotted as a function of reaction coordinate and the function integrated to obtain the free energy for the overall process 36 The PMF constraint force virial and contributions to the stress tensor are obtained in a manner analagous to that for a bond constraint see previous section The only difference is that the constraint is now applied between the centres of two groups which need not be atoms alone DL POLY 2 reports the PMF constraint virial W for each simulation Users can convert this to the PMF constraint force from GPMF Wemr dpmr where dpmr is the constraint distance between the two groups used to define the reaction coordinate CCLRC 60 DL POLY 2 can calculate the PMF using either LF or VV algorithms Subroutines PMFLF and PMF_SHAKE are used in the LF scheme and subroutines PMFVV PMF_RATTLE_R and PMF_RATTLE_V are used in the VV scheme 2 5 4 Thermostats The system may be coupled to a heat bath to ensure that the average system temperature is maintained close to the requested temperature Text When this is done the equations of motion are modified and the system no longer samples the microcanonical ensemble Instead trajectories in the canonical NVT ensemble or something close
260. ples 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 2 will generate several data files which appear in the execute sub directory The most obvious one is the file OUTPUT section 4 2 2 which provides an effective summary of the job run the input information starting configura tion instantaneous and rolling averaged thermodynamic data final configurations radial distribution functions RDFs and job timing data The OUTPUT file is human readable Also present will be the restart files REVIVE section 4 2 4 and REVCON section 4 2 3 REVIVE contains the accumulated data for a number of thermodynamic quantities and RDFs and is intended to be used as the input file for a following run It is not human readable The REVCON file contains the restart configuration i e the final positions ve locities and forces of the atoms when the run ended and is human readable The STATIS file section 4 2 7 contains a catalogue of instantaneous values of thermodynamic and other variables in a form suitable for temporal or statistical analysis Finally the HISTORY file section 4 2 1 provides a time ordered sequence of configurations to facilitate further anal ysis of the atomic motions Depending on which version of the TRAJECT subroutine you compiled in the code this file may be either formatted human readable or
261. poly dlpoly dlpoly dlpoly ensemble_tools ensemble_tools ensemble_tools ensemble_tools ensemble_tools initcomms invfrc kinstress lf integrate lrcmetal machine multiple multiple_nsg multipleneu parlink parlinkneu parlst parlst_nsg parneulst parset guatgnch relax shells result revive shlfrc shlgnch simdef static strucopt sysbook sysdef sysgen sysinit systemp tersoff tethfrc thbfrc timchk traject vertest vscaleg vv_integrate xscale zden0 cell_update dcell gdsum getking invert 256 CCLRC ensemble_tools ensemble_tools ensemble_tools ensemble_tools error error ewald_module ewald_terms ewald_terms ewald_terms ewald_terms ewald_terms_4pt ewald_terms_4pt ewald_terms_4pt ewald_terms_4pt ewald_terms_rsq ewald_terms_rsq ewald_terms_rsq ewald_terms_rsq exclude_module exclude_terms exclude_terms exclude_terms exclude_terms external_field_module external_field_terms external_field_terms external_field_terms external_field_terms external_field_terms external_field_terms force_drivers force_drivers force_drivers force_drivers force_drivers force_drivers force_drivers force_drivers force_drivers force_drivers force_drivers force_drivers force_drivers kinstress kinstressf kinstressg matmul exitcomms gsync error dcell error gdsum invert dcell error gdsum invert dcell error gdsum invert error error gimax gstate warning error copystring error getrec getword
262. potential in the code yourself Amendments to subroutines SYSDEF and THBFRC will be required Message 443 error undefined four body potential DL POLY 2 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 FBPFRC contains the code necessary to deal with the requested potential Add the code required if necessary by amending subroutines SYSDEF and FBPFRC Message 444 error undefined bond potential DL POLY 2 has been requested to process a bond potential it does not recognise Action Check the FIELD file and make sure the keyword is correctly defined Make sure that subroutine BNDFRC contains the code necessary to deal with the requested potential Add the code required if necessary by amending subroutines SYSDEF and BNDFRC Message 446 error undefined electrostatic key in dihfrc The subroutine DIHFRC has detected a request for an unknown kind of electrostatic model CCLRC 208 Action The probable source of the error is an improperly described force field Check the CON TROL file and FIELD files for incompatible requirements Message 447 error 1 4 separation exceeds cutoff range In the subroutine DIHFRC the distance between the 1 4 atoms in the potential is larger than the cutoff that is applied to the 1 4 potential meaning the potential will not be computed though it may be an essential componen
263. r an explanation of this variable Note that these options are mutually exclusive CCLRC 111 6 10 11 12 13 The choice of reaction field electrostatics directive reaction reguires also the spec ification of the relative dielectric constant external to the cavity This is specified in the eps directive DL POLY 2 uses as many as three different potential cutoffs These are as follows a cut this is the universal cutoff It applies to the real space part of the elec trostatics calculations and to the van der Waals potentials if no other cutoff is applied b rvdw this is the user specified cutoff for the van der Waals potentials If not specified its value defaults to rcut It cannot exceed cut c rprim this is used in the multiple timestep algorithm to specify the primary atom region see section 2 5 8 It has no meaning if the multiple timestep option is not used Some directives are optional If not specified DL POLY 2 will take default values if necessary The defaults appear in the above table The zero directive enables a zero temperature simulation This is intended as a crude energy minimizer to help relax a system before a simulation begins It should not be thought of as a true energy minimization method The DL POLY 2 multiple timestep option is invoked if the number appearing with the mult directive is greater than 2 This number stored in the variable multt specifies the numbe
264. r 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 Ks Note that the definition of the B splines implies a dependence on the integer K which limits the formally infinite sum over C The coefficients M u are B splines of order n and the factor b k is a constant computable from the formula m 2 1 b k exp 2ri n 1 k K gt Mn l ljexp 2rikl K 2 166 0 2 Approximation of the structure factor S k S k b1 k1 bo k2 b3 k3 Q ki ko ka 2 167 CCLRC 48 where Q k1 ko k3 is the discrete Fourier transform of the charge array Q 1 2 b3 defined as N Qhi 2 03 Soa S Mn usy t1 miL1 Mn u2j 02 ngL2 Mn ugj l3 n3Ls jl n1 1nN2 N3 2 168 in which the sums over n123 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 Was p G ki ko k3 Q ki ko ks 2 169 k2 k3 Urecip in which G is the discrete Fourier transform of the function exp k 4a 1 G ki ko ks R Bb ka k3 OT ki ko k3 2 170 and where B ka ko k3 bi ki ba ka F b3 ka 2 171 and Q E1 ko k3 is the complex conjgate of Q k1 ko k3 The function G ki ko ks is thus a relatively simple product of the
265. r macromolecules with DL_POLY_2 if you wish This is described below If you select a protein structure from a SEQNET file e g from the Brookhaven database use the utility PROSEQ to generate the file CONFIG This will then function as input for DL_POLY_2 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 CONNECT_DAT input file for the utility AMBFORCE AMBFORCE will produce the DL_POLY_2 FIELD and CONFIG files for your molecule If you do not have the edit out file things are a little more tricky particularly in coming up with appropriate partial charges for atomic sites However there are a series of utilities that will at least produce the CONNECT_DAT file for use with AMBFORCE We now outline these utilities and the order in which they should be used If you have a structure from the Cambridge Structural database CSDB then use the utility FRACCON to take fractional coordinate data and produce a CONNECT_DAT and ambforce dat file for use with AMBFORCE Note that you will need to modify FRACCON to get the AMBER names correct for sites in your molecule The version of FRACCON supplied with DL POLY 2 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 FRACF
266. r must consider using more processors or a machine with larger memory per processor Message 1170 error failed allocation of three body arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1180 error failed allocation of three body work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor CCLRC 220 Message 1200 error failed allocation of external field arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1210 error failed allocation of pmf arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1220 error failed allocation of pmf_lf or pmf_vv work arrays This is a memory allocation error Probable cause
267. r of timesteps the multi step that elapse between partitions of the full Verlet neighbour list into primary and secondary atoms If a multiple time step is used i e multt gt 2 then statistics for radial distribution functions are collected only at updates of the secondary neighbour list The num ber specified on the rdf directive the variable nstbgr means that RDF data are accumulated at intervals of nstbgr xmultt timesteps As a default DL_POLY_2 does not store statistical data during the equilibration period If the directive collect is used equilibration data will be incorporated into the overall statistics The directive delr specifies the width of the border to be used in the Verlet neighbour list construction The width is stored in the variable delr The list is updated whenever two or more atoms have moved a distance of more then delr 2 from their positions at the last update of the Verlet list Users are advised to study the example CONTROL files appearing in the data sub directory to see how different files are constructed CCLRC Table 4 1 Internal Restart Key keyres meaning 0 start new simulation from CONFIG file 1 continue current simulation 2 start new simulation from CONFIG file and rescale velocities to desired temperature 3 start new simulation from CONFIG file without rescaling the velocities and assign velocities from Gaussian distribution Table 4 2 Internal Ensemb
268. ramming environment is free and it is particularly suitable for building graphical user interfaces An atractive aspect of java is the portability of the compiled GUI which may be run without recompiling on any Java supported machine The GUI is an integral component of the DL POLY 2 package and is available on exactly the same terms See 8 1 2 5 Algorithms 1 2 5 1 Parallel Algorithms DL POLY 2 exclusively employs the Replicated Data parallelisation strategy 9 10 see section 2 6 1 1 2 5 2 Molecular Dynamics Algorithms The DL POLY 2 MD algorithms are optionally available in the form of the Verlet Leapfrog or the Velocity Verlet integration algorithms 11 In the leapfrog scheme a parallel version of the SHAKE algorithm 12 10 is used for bond constraints and a similar adaptation of the RATTLE algorithm 13 is implmented in the velocity Verlet scheme Rigid body rotational motion is handled under the leapfrog scheme with Fincham s implicit quaternion algorithm FIQA 14 For velocity Verlet integration of rigid bodies DL POLY 2 uses the NOSOUISH algorithm of Miller et al 15 CCLRC 6 Rigid molecular species linked by rigid bonds are handled with an algorithm of our own devising called the OSHAKE algorithm 16 which has been adapted for both leapfrog and velocity Verlet schemes NVE NVT NPT and NaT ensembles are available with a selection of thermostats and barostats The velocity Verlet versions are based on
269. rger memory per processor Message 2130 error failed allocation of nvtqvv_b2 f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor CCLRC 239 Message 2140 error failed allocation of nvtqvv_h1 f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 2150 error failed allocation of nvtqvv_h2 f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 2160 error failed allocation of nptqvv_b1 f densO array This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 2170 error failed allocation of nptgvv_bl f work arrays This is a memory allocation error Probable cause excessive size of simulated system Actio
270. rhombic dodecahedral The Ewald sum is the method of choice for periodic systems The other techniques can be used with either periodic or non periodic systems though in the case of the direct Coulomb sum there are likely to be problems with convergence DL POLY 2 will correctly handle the electrostatics of both molecular and atomic species However it is assumed that the system is electrically neutral A warning message is printed if the system is found to be charged but otherwise the simulation proceeds as normal No correction for non neutrality is applied 2 4 1 Atomistic and Charge Group Implementation The Ewald sum is an accurate method for summing long ranged Coulomb potentials in periodic systems This can be a very cpu intensive calculation and the use of more efficient but less accurate methods is common Invariably this involves truncation of the potential at some finite distance reut If an atomistic scheme is used for the truncation criterion there is no guarantee that the interaction sphere will be neutral and spurious charging effects will almost certainly be seen in a simulation This arises because the potential being truncated 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 4 1 1 CCLRC 42 is long ranged 1 r for charge charge interactions However if the cutoff scheme is base
271. roduce all the atomic po sitions in rigid units from the centre of mass and quaternion vectors it has calculated Action Check the contents of the CONFIG file DL POLY 2 builds its local body description of a rigid unit type from the first occurrence of such a unit in the CONFIG file The error most likely occurs because subsequent occurrences were not sufficiently similar to this reference CCLRC 198 structure If the problem persists increase the value of the variable tol in QUATBOOK and recompile If problems still persist double the value of dettest in QUATBOOK and recompile If you still encounter problems contact the authors Message 320 error site in multiple rigid bodies DL POLY 2 has detected that a site is shared by two or more rigid bodies There is no integration algorithm available in this version of the package to deal with this type of model Action The only course is to redefine the molecular model e g introducing flexible bonds and angles in suitable places to allow DL POLY 2 to proceed Message 321 error quaternion integrator failed The quaternion algorithm has failed to converge If the maximum number of permitted iterations is exceeded the program terminates Possible causes include a bad starting configuration too large a time step used incorrect force field specification too high a tem perature inconsistent constraints involving shared atoms etc Action Corrective action depends on the cause
272. ror hkewald terms error inversion module error inversion terms error 1f_integrate error 1f motion 1 error 1f motion 1 error 1f rotation 1 error lf rotation 2 error merge_hcube error merge_systol error merge tools CCLRC error error error error error error error error error error error error error error error error error error error error error error error error error error error error error error error error error error error error error error error ewald1 ewald2 ewald3 ewald4 ewald spme metal module metal terms metal terms 4pt metal terms rs nlist builders pair module pass tools pmf_lf pmf module pmf terms pmf_vv property_module rigid_body_module rigid_body_terms serial setup_program shake_module shake_terms site_module site_terms spme_module spme_terms strucopt system_properties temp_scalers tersoff_module tersoff_terms tether_module tether_terms three_body_module three_body_terms utility_pack vdw_module vdw_terms vdw_terms_4pt vdw_terms_rsq vv_integrate vv motion 1 vv rotation 1 force drivers force drivers force drivers force drivers force drivers 273 CCLRC exclude exclude_atom exclude_link excludeneu exit exit exitcomms exitcomms extnfld fbpfrc fcap fldscan forces forcesneu forgen forgen forgen fortab fortab fortab freeze gauss gdsum gdsum gdsum gdsum gdsum gdsum gdsum gdsum gdsum gdsum
273. ror rvdw greater than cutoff DL POLY 2 requires the real space cutoff rcut to be larger than or equal to the van der Waals cutoff rvdw and terminates the run if this condition is not satisfied CCLRC 203 Action Adjust rvdw and rcut to satisfy the DL POLY 2 requirement Message 402 error van der waals cutoff unset The user has not set a cutoff rvdw for the van der Waals potentials The simulation cannot proceed without this being specified Action Supply a cutoff value for the van der Waals terms in the CONTROL file using the directive rvdw and resubmit job Message 410 error cell not consistent with image convention The simulation cell vectors appearing in the CONFIG file are not consistent with the spec ified image convention Action Locate the variable imcon in the CONFIG file and correct to suit the cell vectors Message 412 error mxxdf parameter too small for shake routine In DL_POLY_2 the parameter mxxdf must be greater than or equal to the parameter mxcons If it is not this error is a possible result Action Standard user response Fix the parameter mxxdf Message 414 error conflicting ensemble options in CONTROL file DL POLY_2 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 2 has found incompatible directives in the CONTROL f
274. rror failed allocation of nvtvv_b1 f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 2000 error failed allocation of nvtvv_el f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 2010 error failed allocation of nvtvv h1 f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 2020 error failed allocation of nptvv_b1 f dens0 array This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor CCLRC 237 Message 2030 error failed allocation of nptvv_b1 f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced b
275. rror Probable cause excessive size of simulated system CCLRC 223 Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1370 error failed allocation of work arrays in nst_h0 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1380 error failed allocation of work arrays in nve_1 f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1390 error failed allocation of work arrays in nvt_el f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1400 error failed allocation of work arrays in nvt bl f This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine wit
276. rsity Press 59 Brown D and Clarke J H R 1984 Molecular Physics 51 1243 63 CCLRC 161 38 Melchionna S Ciccotti G and Holian B L 1993 Molecular Physics 78 533 64 39 Tildesley D J Streett W B and Saville G 1978 Molec Phys 35 639 76 40 Tildesley D J and Streett W B Multiple time step methods and an improved Al 42 43 44 45 46 47 potential function for molecular dynamics simulations of molecular liquids In Lykos P editor Computer Modelling of Matter ACS Symposium Series No 86 1978 76 Forester T and Smith W 1994 Molecular Simulation 13 195 76 77 Smith W 1991 Comput Phys Commun 62 229 78 83 Smith W 1993 Theoretica Chim Acta 84 385 78 80 Smith W 1992 Comput Phys Commun 67 392 78 82 Vessal B Amini M Leslie M and Catlow C R A 1990 Molecular Simulation 5 1 82 Melchionna S and Cozzini S 1998 University of Rome 97 Rafii Tabar H and Sutton A P 1991 Philos Mag Lett 63 217 131 132 Appendix A The DL POLY 2 Makefile Master makefile for DL POLY 2 0 Author W Smith February 2005 wl 2001 08 31 11 11 20 1 15 Exp J gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt
277. s 12 6 potential bond 126 Restrained harmonic rhm Ouartic potential gur o cu EB WwW Buckingham potential bck In DL POLY 2 distance restraints are handled by the routine BNDFRC 2 2 3 Valence Angle Potentials CCLRC 21 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 k U Ojik g Ojik bo 2 13 2 Quartic quar k 2 k 3 k U 8 jin 5 Ojik Oo y Bin 90 y Ojik 80 5 2 14 3 Truncated harmonic thrm k U Oi 5 Ojik 09 exp ri r P 2 15 4 Screened harmonic shrm k U Ojik 5 0jix 80 exp rij pi rin p2 2 16 5 Screened Vessal 24 bvsl k 2 2 U Ojik Bll 7 f ce T Ojik T exp rij p1 Tik 2 2 17 6 Truncated Vessal 25 bvs2 a U Ojik klPjik Ojik 60 Ojik 00 27 R Ojik 00 7 80 expl rh ri 0 2 18 7 Harmonic cosine hcos U Ojik eos Djir cos 00 2 2 19 8 Cosine cos U Ojik All cos mBjix 2 20 9 MM3 stretch bend potential mmsb U Ojik A 0 ik o rig ri rin Tik 2 21 CCLRC 22 In these formulae 60 is the angle between bon
278. s Message 57 error too many core shell units specified DL POLY 2 has a restriction of the number of types of core shell unit in the FIELD file and will terminate if too many are present Do not confuse this error with that described CCLRC 183 by message 59 below Action Standard user response Fix the parameter mxtshl Message 59 error too many core shell units in system DL POLY 2 limits the number of core shell units in the simulated system Termination results if too many are encountered Do not confuse this error with that described by mes sage 57 above Action Standard user response Fix the parameter mxshl Message 60 error too many dihedral angles specified DL_POLY_2 will accept only a limited number of dihedral angles in the FIELD file and will terminate if too many are present Do not confuse this error with that described by message 61 below Action Standard user response Fix the parameter mxtdih Message 61 error too many dihedral angles in system The number of dihedral angles in the whole simulated system is limited by DL POLY 2 Termination results if too many are encountered Do not confuse this error with that described by message 60 above Action Standard user response Fix the parameter mxdihd Message 62 error too many tethered atoms specified DL POLY 2 will accept only a limited number of tethered atoms in the FIELD file and will terminate if too many are present Do
279. s and a The parameters n and m however must be the same for all component elements DL POLY 2 calculates this potential in two stages the CCLRC 39 first calculates the local density p for each atom and the second calculates the potential energy and forces Interpolation arrays are used in both these stages The total force i on an atom j derived from this potential is calculated in the standard way I VjUsc 2 123 which gives n 7 M m 1 jtor e n a ce 1 2 Pi 1 2 Ea a Tij 2 124 i Tij 2 Tij Tij A which is recognisable as a sum of pair forces for example the force on atom j due to the atom 2 a P Cm 1 2 1 2 a o 1 c n 4 rij 2 125 where Tij ES Tj Ti The force on atom 4 is the negative of this With the pair forces thus defined the contribution to be added to the atomic virial from each atom pair is then The contribution to be added to the atomic stress tensor is given by PE 2 127 where a and 5 indicate the z y z components The atomic stress tensor is symmetric The long range correction for the system potential is in two parts Firstly by analogy with the short ranged potentials the correction to the local density is obtained by co a m Pi P AD 2 r dr 2 128 Tout r where p is the uncorrected local density and J is the mean particle density Evaluating the integral yields 243 m 3 pa a 6p 4 T 2 129 f 4 m 3 which is the local densit
280. s eng pv temp rot vir_cfg vir vdw 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 CCLRC 142 The labels refer to line 1 step eng tot temp_tot eng_cfg eng_vdw eng_cou eng bnd eng_ang eng dih eng_tet line 2 time ps eng pv temp rot vir_cfg vir_vdw vir_cou vir_bnd vir_ang vir_con vir_tet line 3 cpu s volume temp_shl eng_shl vir_shl alpha beta gamma vir_pmf press MD step number total internal energy of the system system temperature configurational energy of the system configurational energy due to short range potentials configurational energy due to electrostatic potential configurational energy due to chemical bond potentials configurational energy due to valence angle and three body potentials configurational energy due to dihedral inversion and four body potentials configurational energy due to tethering potentials elapsed simulation time ps since the beginning of the job enthalpy of system rotational temperature total configurational contribution to the virial short range potential contribution to the virial electrostatic potential contribution to the virial chemical bond contribution to the virial angular and three body potentials contribution to the virial constraint bond contribution to the virial tethering potential contribution to the virial elapsed cpu time since the beginning of the job system volume core s
281. s the link cell algorithm 23 when feut is relatively small The potential energy and forces arising from the nonbonded interactions are calculated using interpolation tables A complication 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 candi dates The assumption behind this requirement is that atoms that are formally bonded in a chemical sense should not participate in nonbonded interactions However this is not a universal requirement of all force fields The same considerations are needed in dealing with charged excluded atoms DL_POLY_2 has several subroutines available for construct ing the Verlet neighbour list while taking care of the excluded atoms see chapter 3 for further information Three and four body nonbonded forces are assumed to be short ranged and therefore calculated using the link cell algorithm 23 They ignore the possibility of there being any excluded interactions involving the atoms concerned Throughout this section the description of the force field assumes the simulated system is described as an assembly of atoms This is for convenience only and rea
282. s follows record 1 cfgname character A80 configuration name record 2 ntpvdw integer il0 number of RDFs in file CCLRC 145 mxrdf integer i10 number of data points in each RDF There follow the data for each individual RDF i e ntpvdw times The data supplied are as follows first record atname 1 character A8 first atom name atname 2 character A8 second atom name following records mzrdf records radius real el4 interatomic distance A g r real el4 RDF at given radius Note the RDFDAT file is optional and appears when the print rdf option is specified in the CONTROL file 4 2 6 The ZDNDAT File This is a formatted file containing the Z density data Its contents are as follows record 1 cfgname character A80 configuration name record 2 mxrdf integer i10 number of data points in the Z density function following records mzrdf records z real e14 distance in z direction A p z real e14 Z density at given height z Note the ZDNDAT file is optional and appears when the print rdf option is specified in the CONTROL file 4 2 7 The STATIS File The file is formatted with integers as 110 and reals as el4 6 It is written by the subroutine STATIC It consists of two header records followed by many data records of statistical data record 1 cfgname character configuration name record 2 string character energy units CCLRC 146 Data records Subsequent lines contain the ins
283. s fully complete Message 1955 error failed allocation of tersoff work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1960 error conflicting shell option in FIELD file The relaxed shell and adiabatic shell polarisation options in DL_POLY 2 are mutually ex clusive The user has request both options in the same simulation Action Locate the occurrences of the shell directives in the FIELD file and ensure they specify the same shell model CCLRC 235 Message 1970 error failed allocation of shell_relax work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1972 error unknown tersoff potential defined in FIELD file DL_POLY_2 has failed to recognise the Tersoff potentials specified by the user in the FIELD file Action Locate the Tersoff potential specification in the FIELD fiel and ensure it is correctly defined Message 1974 error incorrect period boundary in tersoff f The implementation of the Tersoff potential in DL_POLY_2 is based on the link cell algo rithm which is suitable for r
284. s 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 DL_POLY TEST CASE 1 K Na disilicate glass temperature 1000 0 pressure 0 0000 ensemble nve integrator leapfrog steps 500 equilibration 200 multiple step 5 scale 10 print 10 stack 100 stats 10 rdf 10 timestep 0 0010 primary cutoff 9 0000 cutoff 12 030 delr width 1 0000 rvdw cutoff 7 6000 CCLRC 107 ewald precision 1 0E 5 print rdf job time 1200 0 close time 100 00 finish 4 1 1 1 The CONTROL file format The file is free formatted integers reals and additional keywords are entered following the keyword on each record Real and integer numbers must be separated by a non numeric character preferably a space or comma to be correctly interpreted No logical variables appear in the control file Comment records beginning with a and blank lines may be added to aid legibility see example above The CONTROL file is not case sensitive e The first record in the CONTROL file is a header 80 characters long to aid 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 4 1 1 2 The CONTROL File Directives T
285. s 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 Mild di o Gij Dew d d 2 207 where 1 is the reduced mass of the two atoms connected by the bond d and di are the original and intermediate bond vectors dij is the constrained bondlength and At is the Verlet integration timestep It should be noted that this formula is an approximation only V P Gy CCLRC 58 The SHAKE algorithm calculates the constraint force Gi G that conserves the bondlength di between atoms 1 and 2 following the initial movement to positions 1 and 2 under the unconstrained forces F and Fy For a system of simple diatomic molecules computation of the constraint force will in principle allow the correct atomic positions to be calculated in one pass However in the general polyatomic case this correction is merely an interim adjustment not only because the above formula is approximate but the successive correction of other bonds in a molecule has the effect of perturbing previously corrected bonds The SHAKE algorithm is therfore iterative with the correction cycle being repeated for all bonds until each has converged to the correct length within a given tolerance The tolerance may be of the order 1074 A to 1078 A depending on the precision desired The procedure may be summarised as follows 1 All atoms in the syst
286. s will be the srcf90 subdirectory 3 The makefile is executed with the appropriate keywords section 3 2 1 which select for specific computers and if a parallel machine is used the appropriate communication software 4 The makefile produces the executable version of the code which as a default will be named DLPOLY X and located in the execute subdirectory 5 DL_POLY also has a Java GUI The files for this are stored in the subdirectory java Compilation of this is simple and requires running the javac compiler and the jar utility Details for these procedures are provided in the GUI manual 8 6 To run the executable for the first time you require the files CONTROL FIELD and CONFIG and possibly TABLE if you have tabulated potentials These must be present in the directory from which the program is executed See section 4 1 for the description of the input files 7 Executing the program will produce the files OUTPUT REVCON and REVIVE and optionally STATIS HISTORY RDFDAT and ZDNDAT in the executing directory See section 4 2 for the description of the output files This simple procedure is enough to create a standard version to run most DL_POLY_2 applications However it sometimes happens that additional modifications may be neces sary On starting DL_POLY 2 scans the input data and makes an estimate of the sizes of the arrays it requires to do the simulation Sometimes the estimates are not good enough The most common
287. sation conjugate gradients 54 parallelisation 5 78 Ewald summation 82 intramolecular terms 79 Replicated Data 5 Verlet neighbour list 81 polarisation 52 53 151 152 dynamical shell model 53 54 188 189 relaxed shell model 54 potential bond 4 17 20 25 26 30 34 53 79 83 97 122 142 178 207 Coulombic see potential electrostatic dihedral 4 16 17 24 28 79 125 142 183 208 electrostatic 4 8 17 20 23 41 76 77 107 109 113 142 150 151 200 205 Finnis Sinclair see potential metal four body 4 16 18 31 37 38 82 130 131 142 177 186 188 190 207 209 improper dihedral 4 26 79 intramolecular 31 38 89 287 inversion 4 16 27 29 37 38 127 185 208 metal 4 17 38 131 185 193 nonbonded 4 17 18 80 82 94 97 98 109 118 122 124 128 176 Sutton Chen see potential metal see po tential metal tabulated 136 177 178 Tersoff 16 17 35 37 132 133 152 187 188 235 tethered 30 31 126 142 151 183 208 three body 4 16 18 21 31 34 82 97 128 130 142 177 184 186 187 209 valence angle 4 16 18 21 22 28 34 79 82 88 97 123 124 142 181 van der Waals 17 20 23 77 89 94 111 125 202 203 quaternions 5 55 71 109 reaction field 51 52 109 rigid body 3 6 31 55 57 69 70 72 74 84 88 150 151 188 196 199 205 210 215 rigid bond see constraints bond rigid molecule see rigid body SPME se
288. subroutines will need modifying to allow specification of the dimensions of any new arrays Any molecular dynamics simulation performs five different kinds of operation initial isation forces calculation integration of the equations of motion calculation of system properties and job termination It is worth considering these operations in turn and to in dicate which DL_POLY_2 routines are available to perform them We do not give a detailed description but provide only a guide The following outline assumes a system containing flexible molecules held together by rigid bonds but without rigid bodies Initialisation requires firstly that the program determine what kind of parallel machine it is running on The routine MACHINE determines how many processing nodes are being used and also returns the node identity to each process Next the job control information is required this is obtained by the routine SIMDEF which reads the CONTROL file section 4 1 1 The description of the system to be simulated the types of atoms and molecules present and the intermolecular forces are obtained by the SYSDEF routine which reads the FIELD file section 4 1 3 Lastly the atomic positions and velocities must be provided These are obtained by the SYSGEN routine which reads the CONFIG file section 4 1 2 and also generates the initial velocities if required to do so If the system contains con straint bonds the routine PASSCON is required to process mole
289. t calculate anything beyond the atomic trajectories on line You must therefore be prepared to post process the HISTORY file if you want other information There are some utilities in the DL_POLY_2 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 2 public library to help with this The utilities available are described in the DL POLY 2 Reference Manual Chapter 6 Users should also be aware that many of these utilities are incorporated into the DL_POLY Graphical User Interface 8 3 3 5 Choosing Ewald Sum Variables 3 3 5 1 Ewald sum and SPME This section outlines how to optimise the accuracy of the Ewald sum parameters for a given simulation In what follows the directive spme may be used anywhere in place of the directive ewald if the user wishes to use the Smoothed Particle Mesh Ewald method As a guide to beginners DL_POLY_2 will calculate reasonable parameters if the ewald precision directive is used in the CONTROL file see section 4 1 1 A relative error see below of 1079 is normally sufficient so the directive ewald precision 1d 6 will cause DL_POLY 2 to evaluate its best guess at the Ewald parameters a kmax1 kmax2 and kmax3 The user should note that this represents an estimate and there are some times circumstances where the estimate can be improved upon This is especially the case when the system contains a strong directional
290. t of the dihedral force and not necessarily a van ishing force Action The probable source of the error is an improperly described force field Effectively the 1 4 distance is not being restrained sufficently Check the 1 4 potential parameters and the valence angles that help define the dihedral geometry If these are correct then you may have to comment out this error condition in the DIHFRC F subroutine but beware that when the 1 4 atoms are too widely separated the dihedral angle can become indeterminable Message 448 error undefined dihedral potential A form of dihedral potential has been requested which DL POLY 2 does not recognise Action Locate the offending potential in the FIELD file and remove Replace with one acceptable to DL_POLY_2 if this is reasonable Alternatively you may consider defining the required potential in the code yourself Amendments to subroutines SYSDEF and DIHFRC and its variants will be required Message 449 error undefined inversion potential A form of inversion potential has been encountered which DL_POLY 2 does not recognise Action Locate the offending potential in the FIELD file and remove Replace with one acceptable to DL_POLY_2 if this is reasonable Alternatively you may consider defining the required potential in the code yourself Amendments to subroutines SYSDEF and INVFRC will be required Message 450 error undefined tethering potential A form of tethering potential has been r
291. t_hl nvt bl nvtq_b2 nvtq_hl nvtq_h2 nvtqscl nvtgvv_b1 nvtqvv_b2 nvtgvv h1 nvtqvv_h2 nvtscale nvtvv_bl nvtvv_el nvtvv_hl parlink parlinkneu parlst parlst_nsq parneulst parset passcon passcon passpmf passpmf passquat passquat pivot pmf_rattle_r pmf_rattle_v pmf_shake pmf_vectors pmflf pmfvv primlst function function subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine 249 basic_comms f serial f lf motion 1 f lf rotation 1 f lf rotation 2 f vv_rotation_1 f vv_rotation_2 f vv_motion_1 f lf motion_1 f If motion 1 f lf motion 1 f If rotation 1 f If rotation 2 f lf rotation 1 f lf_rotation_2 f ensemble_tools f vv_rotation_1 f vv_rotation_2 f vv_rotation_1 f vv_rotation_2 f ensemble_tools f vv_motion_1 f vv_motion_1 f vv_motion_1 f nlist_builders f nlist_builders f nlist_builders f nlist_builders f nlist_builders f setup_program f pass_tools f serial f pass tools f serial f pass tools f serial f vv_rotation_2 f pmf_vv f pmf_vv f pmf If f pmf_terms f
292. tandard user response Fix the parameter mxngp CCLRC 197 Message 303 error too many rigid bodies specified The maximum number of rigid bodies in a simulation has been reached Do not confuse this with message 304 below Action Standard user response Fix the parameter mxgrp Message 304 error too many rigid body sites in system This error occurs when the total number of sites within all rigid bodies exceeds the permit ted maximum Do not confuse this with message 303 above Action Standard user response Fix the parameter mxgatms Message 305 error box size too small for link cells The link cells algorithm in DL_POLY_2 cannot work with less than 27 link cells Depending on the cell size and the chosen cut off DL POLY 2 may decide that this minimum cannot be achieved and terminate Action If a smaller cut off is acceptable use it Otherwise do not use link cells Consider running a larger system where link cells will work Message 306 error failed to find principal axis system This error indicates that the routine QUATBOOK has failed to find the principal axis for a rigid unit Action This is an unlikely error The code should correctly handle linear planar and 3 dimensional rigid units Check the definition of the rigid unit in the CONFIG file if sensible report the error to the authors Message 310 error quaternion setup failed This error indicates that the routine QUATBOOK has failed to rep
293. tantaneous values of statistical variables dumped from the array stpval A specified number of entries of stpval are written in the format 1p 5e14 6 The number of array elements required determined by the parameter mxnstk in the DL PARAMS INC file is mxnstk gt 27 ntpatm number of unique atomic sites 9 if stress tensor calculated 9 if constant pressure simulation requested The STATIS file is appended at intervals determined by the stats directive in the CON TROL file The energy unit is as specified in the CONTROL file with the the units directive and are compatible with the data appearing in the OUTPUT file The contents of the appended information is record i nstep integer current MD time step time real elapsed simulation time nstepx At nument integer number of array elements to follow record ii stpval 1 stpval 5 engcns real total extended system energy i e the conserved guantity temp real system temperature engcfg real configurational energy engsrp real VdW metal Tersoff energy engcpe real electrostatic energy record iii stpval 6 stpval 10 engbnd real chemical bond energy engang real valence angle 3 body potential energy engdih real dihedral inversion four body energy engtet real tethering energy enthal real enthalpy total energy PV record iv stpval 11 stpval 15 tmprot real rotational temperature vir real total virial virsrp real VdW metal Tersoff virial vircpe real electrostatic viri
294. ted system CCLRC 233 Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1900 error failed allocation of parlinkneu f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1910 error failed allocation of parneulst f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1920 error failed allocation of strucopt f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1930 error failed allocation of vertest f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1940
295. tentials may in fact be essential to maintain the structure of the system The three body potentials are very short ranged typically of order 3 A This property plus the fact that three body potentials scale as N where N is the number of particles makes it essential that these terms are calculated by the link cell method 28 The calculation of the forces virial and stress tensor as described in the section valence angle potentials above DL POLY 2 applies no long range corrections to the three body potentials The three body forces are calculated by the routine THBFRC CCLRC 35 2 3 3 The Tersoff Covalent Potential The Tersoff potential 4 is a special example of a density dependent potential which has been designed to reproduce the properties of covalent bonding in systems containing carbon silicon germanium etc and alloys of these elements A special feature of the potential is that it allows bond breaking and associated changes in bond hybridisation The potential has 11 atomic and 2 bi atomic parameters The energy is modelled as a sum of pair like interactions where however the coefficient of the attractive term in the pairlike potential which plays the role of a bond order depends on the local environment giving a many body potential The form of the Tersoff potential is ters Ui folrij fr riz Yy fari 2 97 where Tr rij Ay exp aiy rij fAUTij By expl bij rij 2 98 1 Tij lt Rij folrg
296. term labelled itype The dimension ntype will be 2 3 or 4 if the term represents a bond angle or dihedral The array keytype Ntype itype is used to identify the atoms in a bonded term and the appropriate form of interaction and thus to calculate the energy and forces Each processor is assigned the independent task of evaluating a block of Int Niotat Nnodes interactions The same scheme works for all types of bonded interactions The global summation of the force arrays does not occur until all the force contributions including nonbonded forces has been completed CCLRC 80 2 6 3 Distributing the Nonbonded Terms In DL_POLY_2 the nonbonded interactions are handled with a Verlet neighbour list 11 which is reconstructed at intervals during the simulation This list records the indices of all secondary atoms within a certain radius of each primary atom the radius being the cut off radius reut normally applied to the nonbonded potential function plus an additional increment Arey The larger radius reut Arcus permits the same list to be used for several timesteps without requiring an update The frequency at which the list must be updated clearly depends on the thickness of the region Arcu In RD the neighbour list is constructed simultaneously on each node and in such a way as to share the total burden of the work equally between nodes Each node is responsible for a unique set of nonbonded interactions and the
297. the FIELD file indicating which ones are to be presented in the TABLE file Then check the TABLE file to make sure all the tabulated potentials are present in the order the FIELD file indicates Message 24 error end of file encountered in TABLE file This means the TABLE file is incomplete in some way either by having too few potentials included or the number of data points is incorrect Action Examine the TABLE file contents and regenerate it if it appears to be incomplete If it look intact check that the number of data points specified is what DL POLY 2 is expecting Message 25 error wrong atom type found in CONFIG file On reading the input file CONFIG DL POLY 2 performs a check to ensure that the atoms specified in the configuration provided are compatible with the corresponding FIELD file This message results if they are not Action The possibility exists that one or both of the CONFIG or FIELD files has incorrectly specified the atoms in the system The user must locate the ambiguity using the data printed in the OUTPUT file as a guide and make the appropriate alteration Message 30 error too many chemical bonds specified DL POLY 2 sets a limit on the number of chemical bond potentials that can be specified in the FIELD file Termination results if this number is exceeded See FIELD file docu mentation Do not confuse this error with that described by message 31 below Action Standard user response Fix par
298. the ewald precision directive is used The first few records of a typical CONFIG file are shown below IceI structure 6x6x6 unit cells with proton disorder 26 988000000000000 13 494000000000000 0 000000000000000 2 OW 2 505228382 0 5446573999 3515 939287 HW 1 622622646 1 507099154 7455 527553 HW 3 258494716 2 413871957 7896 278327 OW 0 9720599243E 01 1 787340483 9226 455153 etc 4 1 2 1 Format The file is fixed formatted integers as il0 reals as f20 0 The header record is format 1 4 0 000000000000000 23 372293600000000 1 484234330 1 872177437 13070 74357 1 972916834 1 577400769 4806 880540 2 125627191 4 336956694 8318 045939 2 503798635 1 021777575 9445 662860 ted as 80 alphanumeric characters 4 1 2 2 Definitions of Variables record 1 header a80 record 2 levcfg integer imcon integer record 3 cell 1 real title line CONFIG file key See table 4 5 for permitted values Periodic boundary key See table 4 6 for permitted values omitted if imcon 0 O 000000000000000 O 000000000000000 0 000000000000000 44 028000000000000 7 274585343 0 7702718106 4432 030587 7 340573742 4 328786484 1255 814536 7 491549620 2 951142896 2379 766752 3 732081894 0 5473436377 5365 202509 x component of a cell vector CCLRC 115 cell 2 real y component of a cell vector cell 3 real z component of a cell
299. the user requestes an order in excess of this parameter Action Standard user response Set the parameter mxhko to a higher value if it is lt 3 and recompile the program Alternatively request a lower order in the CONTROL file through the nhko variable see 4 1 1 Message 340 error invalid integration option requested DL POLY 2 has detected an incompatibility in the simulation instructions namely that the requested integration algorithm is not compatible with the physical model It may be possible to override this error trap but it is up to the user to establish if this is sensible Action This is a non recoverable error unless the user chooses to override the restriction Message 350 error too few degrees of freedom This error can arise if a small system is being simulated and the number of constraints applied is too large Action Simulate a larger system or reduce the number of constraints Message 360 error frozen atom found in rigid body DL POLY 2 does not permit a site in a rigid body to be frozen i e fixed in one location in space Action Remove the freeze condition from the site concerned Consider using a very high site mass to achieve a similar effect Message 380 error simulation temperature not specified DL POLY 2 has failed to find a temp directive in the CONTROL file CCLRC 200 Action Place a temp directive in the CONTROL file with the required temperature specified Messa
300. the value specified for the forces cutoff directive cut Applies only if the multiple timestep option is required Action Locate the prim directive in the CONTROL file and alter the chosen cutoff Alternatively increase the real space cutoff specified with the cut directive Take care to avoid error number 398 Message 387 error system pressure not specified The target system pressure has not been specified in the CONTROL file Applies to NPT simulations only Action Insert a press directive in the CONTROL file specifying the required system pressure Message 388 error npt incompatible with multiple timestep The use of NPT constant pressure and temperature is not compatible with the multiple timestep option Action Simulation must be run at fixed volume in this case But note it may be possible to use NPT without the multiple timestep in ourder to estimate the required system volume then switch back to multiple timestep and NVT dynamics at the required volume Message 389 number of pimd beads not specified in field file The user has failed to specify how many quantum beads is required in a Path Integral Molecular Dyamics simulation Applies to PIMD version of DL_POLY_2 only Action The required numer of beads must be specified in the FIELD file Message 390 error npt ensemble requested in non periodic system A non periodic system has no defined volume hence the NPT algorithm cannot be applied Action
301. three body valence angle potentials to support the silicate structure It also using tabluated two body potentials stored in the file TABLE The system is comprised of 8640 atoms and runs on 16 512 processors 5 1 2 6 Benchmark 6 Simulation of a potassium valinomycin complex in 1223 water molecules using an adapted AMBER forcefield and truncated octahedral periodic boundary conditions The system size is 3838 atoms and runs on 16 512 processors 5 1 2 7 Benchmark 7 Simulation of gramicidin A molecule in 4012 water molecules using neutral group elec trostatics The system is comprised of 12390 atoms and runs on 8 512 processors This example was provided by Lewis Whitehead at the University of Southampton 5 1 2 8 Benchmark 8 Simulation of an isolated magnesium oxide microcrystal comprised of 5416 atoms originally in the shape of a truncated octahedron Uses full coulombic potential Runs on 16 512 processors 5 1 2 9 Benchmark 9 Simulation of a model membrane with 196 41 unit membrane chains 8 valinomycin molecules and 3144 water molecules using an adapted AMBER potential multiple timestep algorithm and Ewald sum electrostatics The system is comprised of 18866 atoms and runs on 8 512 processors Chapter 6 DL POLY 2 Utilities 155 CCLRC 156 Scope of Chapter This chapter describes the more important utility programs and subroutines of DL_POLY 2 found in the sub directory utility A more complete description of the sub
302. tial in the FIELD file and remove Replace with one acceptable to DL POLY 2 if this is reasonable Alternatively you may consider defining the required potential in the code yourself Amendments to subroutines SYSDEF and EXTNFLD will be required Message 456 error core and shell in same rigid unit It is not sensible to fix both the core and the shell of a polarisable atom in the same molec ular unit Consequently DL POLY 2 will abandon the job if this is found to be the case CCLRC 210 Action Locate the offending core shell unit there may be more than one in your FIELD file and release the shell preferably from the rigid body specification Message 458 error too many PMF constraints param mspmf too small The number of constraints in the potential of mean force is too large The dimensions of the appropriate arrays in DL POLY 2 must be increased Action Standard user response Fix the parameter mspmf Message 460 error too many PMF sites parameter mxspmf too small The number of sites defined in the potential of mean force is too large The dimensions of the appropriate arrays in DL_POLY _2 must be increased Action Standard user response Fix the parameter mxspmf Message 461 error undefined metal potential The user has requested a metal potential DL_POLY 2 does not recognise Action Locate the metal potential specification in the FIELD file and replace with a recognised potential Message 462
303. tines to permit this Message 1000 error failed allocation of configuration arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1010 error failed allocation of angle arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1011 error failed allocation of dihedral arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1012 error failed allocation of exclude arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1013 error failed allocation of rigid body arrays This is a memory allocation error Probable cause excessive size of simulated system CCLRC 217 Action If the simulated system cannot be re
304. to run the n th test case 6 1 1 7 store The store macro provides a convenient way of moving data back from the execute sub directory to the data sub directory It invokes the unix commands mkdir data TEST 1 mkdir data TEST 1 2 mv OUTPUT data TEST 1 2 0UTPUT mv REVCON data TEST 1 2 REVCON mv STATIS data TEST 1 2 STATIS mv REVIVE data TEST 1 2 REVIVE mv RDFDAT data TEST 1 2 RDFDAT mv ZDNDAT data TEST 1 2 ZDNDAT chmod 400 data TEST 1 2 which first creates a new DL POLY data TEST sub directory and then moves the stan dard DL_POLY output data files into it store requires two arguments storena where n is a unique string or number to label the output data in the data TESTn sub directory and a is a string LF or VV according to the integration algorithm leafrog LF or velocity Verlet VV Note that store sets the file access to read only This is to prevent the store macro overwriting existing data without your knowledge Bibliography 10 11 12 13 14 15 16 Smith W and Forester T 1996 J Molec Graphics 14 136 3 Smith W 1987 Molecular Graphics 5 71 3 Sutton A P and Chen J 1990 Philos Mag Lett 61 139 4 38 82 131 Tersoff J 1989 Phys Rev B 39 5566 4 35 132 van Gunsteren W F and Berendsen H J C 1987 Groningen Molecular Simu lation GROMOS Library Manual BIOMOS Nijenborgh 9747 Ag Groningen The Net
305. tom types is too large Action Standard user response Fix the parameter mxnstk mxnstk should be at least 45 number of unique atom types Message 180 error Ewald sum requested in non periodic system DL_POLY_2 can use either the Ewald method or direct summation to calculate the elec trostatic potentials and forces in periodic or pseudo periodic systems For non periodic systems only direct summation is possible If the Ewald summation is requested with the ewald sum or ewald precision directives in the CONTROL file without periodic boundary conditions termination of the program results Action Select periodic boundaries by setting the variable imcon gt 0 in the CONFIG file if possible or use a different method to evaluate electrostatic interactions e g by usinf the coul directive in the CONTROL file Message 185 error too many reciprocal space vectors DL POLY 2 places hard limit on the number of k vectors to be used in the Ewald sum and terminates if more than this is requested CCLRC 195 Action Either consider using fewer k vectors in the Ewald sum and a larger cutoff in real space or follow standard user response to reset the parameters kmaxb kmaxc Message 186 error transfer buffer array too small in sysgen In the subroutine SYSGEN F DL POLY 2 requires dimension of the array buffer defined by the parameter mxbuff to be no less than the parameter mxatms or the product of pa rameters mxnstk mxstak
306. topmost directory is named dl_poly_2 nn where nn is a generation number Beneath this directory are several sub directories sub directory contents srcf90 primary subroutines for the DL_POLY_2 package utility subroutines programs and example data for all utilities data example input and output files for DL_POLY_2 bench large test cases suitable for benchmarking execute the DL_POLY_2 run time directory build makefiles to assemble and compile DL_POLY 2 programs public directory of routines donated by DL_POLY_2 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 srcf90 Sub directory In this sub directory all the essential source code for DL_POLY 2 excluding the utility software In keeping with the package concept of DL POLY 2 it does not contain any complete programs these are assembled at compile time using an appropriate makefile 1 4 2 The utility Sub directory This sub directory stores all the utility subroutines functions and programs in DL POLY_2 together with examples of data The various routines in this sub directory are documented in chapter 6 of this manual Users who devise their own utilities are advised to store them in the utility sub directory CCLRC 10 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_2 The examples of input
307. ts f for atoms i j k n are calculated using the above formu lae it is easily seen that the contribution to be added to the atomic stress tensor is given by oP f E r2 f 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 2 inversion forces are handled by the routine INVFRC CCLRC 30 2 2 8 Tethering Forces DL POLY 2 also allows atomic sites to be tethered to a fixed point in space rg taken as their position at the beginning of the simulation 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 momentum will no longer be a conserved quantity of the simulation Secondly in constant pressure simulations where the MD cell changes size or shape the reference position is scaled with the cell vectors The potential functions available in DL_POLY 2 are as follows in each case r o is the distance of the atom from its position at t 0 1 harmonic potential harm 1 U rio sri 2 68 2 restrained harmonic rhrm 1 2 U r y F rio rio lt Te 2 69 1 Ulrio gt Ero krelrio Te Ti gt Te 2 70 3 Guartic potential guar k k k U rio 5 rio 3 rio yA Ti 2 71 The force on the atom
308. ually zero CCLRC 49 2 4 7 Hautman Klein Ewald HKE The method of Hautman and Klein is an adaptation of the Ewald method for systems which are periodic in two dimensions only 32 DL POLY 2 assumes this periodicity is in the XY plane The HKE method gives the following formula for the electrostatic energy of a system of N nonbonded ions that is overall charge neutral max Uc 4 gt ane ij 2 Jal ga 2n exp ig 8ij o 0 i g70 1 Nmax h 817 13 A y y aey ld O ij Yij L mn Sij L Q Q N S Di L grbe 2 173 8TE0 In this formula A is the system area in the XY plane L is a 2D lattice vector representing the 2D periodicity of the system s is the in plane XY component of the interparticle distance r and g is a reciprocal lattice vector Thus L ha 90 2 174 where 1 5 are integers and vectors a and b are the lattice basis vectors The reciprocal lattice vectors are g Nyu nau 2 175 where n n2 are integers u v are reciprocal space vectors defined in terms of the vectors a and b I 2 by b asby aybz v 2M ay ax axby Gyr 2 176 The functions h s a and fr s are the HKE convergence functions in real and recipro cal space respectively C f the complementary error and gaussian functions of the original Ewald method However they occur to higher orders here as indicated by the sum over subscript n which corresponds
309. ufficiently accurate The choice involves decisions about speed accuracy and memory requirements 3 point interpolation is the default option A utility program TABCHK is provided in the DL_POLY utility sub directory to help users choose a sufficiently accurate interpolation scheme including array sizes for their needs 3 2 2 Running DL POLY 2 To run the DL POLY 2 executable DLPOLY X you will initially require three possibly four input data files which you must create in the execute sub directory or whichever sub directory you keep the executable program The first of these is the CONTROL file section 4 1 1 which indicates to DL POLY_2 what kind of simulation you want to run how much data you want to gather and for how long you want the job to run The second file you need is the CONFIG file section 4 1 2 This contains the atom positions and CCLRC 95 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 also The third file required is the FIELD file section 4 1 3 which specifies the nature of the intermolecular interactions the molecular topology and the atomic properties such as charge and mass Sometimes you will require a fourth file TABLE section 4 1 5 which contains the potential and force arrays for functional forms not available within DL_POLY 2 usually because they are too complex e g spline potentials Exam
310. unction of the subroutine A copyright statement cu E o A CVS revision number and associated data Elsewhere FORTRAN COMMENT cards are used liberally 1 3 7 Subroutine Function Calling Sequences The variables in the subroutine arguments are specified in the order 1 logical and logical arrays 2 character and character arrays integer real and complex integer arrays o cu EB o real and complex arrays This is admittedly arbitrary but it really does help with error detection CCLRC 8 1 3 8 FORTRAN Parameters All global parameters defined by the FORTRAN parameter statements are specified in the module SETUP_MODULE All parameters specified in SETUP_MODULE are described by one or more comment cards 1 3 9 Arithmetic Precision All real variables and parameters are specified in 64 bit precision i e real 8 1 3 10 Units Internally all DL_POLY_2 subroutines and functions assume the use of the following defined molecular units 1 The unit of time to is 1 x 10712 seconds i e picoseconds 2 The unit of length lo is 1 x 10719 metres i e Angstroms 3 The unit of mass mo is 1 6605402 x 10727 kilograms i e atomic mass units 4 The unit of charge go is 1 60217733 x 10719 coulombs i e unit of proton charge 5 The unit of energy E Mo lo to is 1 6605402 x 1072 Joules 10 J mol 6 The unit of pressure P E 7 is 1 6605402 x 107 Pascal 163 882576 atm 7 Planck s
311. unformatted You may move these output files back into the data sub directory using the store macro found in the execute sub directory Note that versions of DL_POLY 2 after 2 10 may also create the files RDFDAT and ZDNDAT containing the RDF and Z density data respectively They are both human readable files 3 2 3 Restarting DL POLY 2 The best approach to running DL_POLY 2 is to define from the outset precisely the simula tion 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 responsibil ity but DL POLY 2 will usually give diagnostic messages to help you sort out the trouble Running out of job time is common and provided you have correctly specified the job time variables using the close time and job time directives see section 4 1 1 in the CON TROL file DL_POLY 2 will stop in a controlled manner allowing you to restart the job as if it had not been interrupted To restart a simulation after normal termination you will again require the CONTROL file the FIELD and TABLE file and a CONFIG file which is the exact copy of the REVCON file created by the previous job You will also require a new file REVOLD CCLRC 96 section 4 1 4 which is an exact copy of the previous REVIVE file If you attempt to restart DL POLY 2 without t
312. utines Subroutines Called The following table lists the subroutines in DL_POLY_2 and which subroutines they call Calling routine Called routine angle_terms copystring angle_terms error angle_terms gdsum angle_terms getrec angle_terms getword angle_terms gstate angle_terms images angle_terms lowcase angles_module error basic_comms basic_comms basic_comms basic_comms MPI BARRIER MPI COMM RANK MPI_COMM_SIZE MPI FINALIZE basic comms MPI RECV basic comms MPI allreduce basic comms MPI init basic comms MPI send basic comms exit basic comms gisum bond terms copystring bond_terms error bond_terms gdsum bond_terms getrec bond_terms getword bond_terms gstate bond_terms images 252 CCLRC bond_terms bonds_module config_module core_shell_module core_shell_terms core_shell_terms core_shell_terms core_shell_terms core_shell_terms define_system define_system define_system define_system define_system define_system define_system define_system define_system define_system define_system define_system define_system define_system define_system define_system define_system define_system define_system define_system define_system define_system define_system define_system define_system define_system define_system define_system define_system define_system define_system define_system define_system define_system define_system 253 lowcase error error error error gdsum getrec
313. ve 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 whatsoever They should be regarded as potentially useful resources to be hacked into shape as needed by the user This directory is available from the CCP5 Program Library by direct FTP see below 1 4 8 The java Sub directory The DL POLY 2 Java Graphical User Interface GUI is based on the Java language de veloped by Sun The Java source code for this GUI is to be found in this sub directory along with a few FORTRAN sub sub directories which contain some additional capabilities accessible from the GUI These sources are complete and sufficient to create a working GUI CCLRC 11 provided the user has installed the Java Development Kit 1 4 or above which is available free from Sun at http java sun com The GUI once compiled may be executed on any machine where Java is installed though note the FORTRAN components will need to be recompiled if the machine is changed See 8 1 5 Obtaining the Source Code To obtain a copy of DL_POLY_2 it is first necessary to obtain a licence from Daresbury Laboratory A copy of the licence form may be obtained by selecting the licence link on the DL_POLY website http www cse clrc ac uk msi software DL POLY and downloading and printing the file Altern
314. vector record 4 omitted if imcon 0 cell 4 real x component of b cell vector cell 5 real y component of b cell vector cell 6 real z component of b cell vector record 5 omitted if imcon 0 cell 7 real x component of c cell vector cell 8 real y component of c cell vector cell 9 real z component of c cell vector Subsequent records consists of blocks of between 2 and 4 records depending on the value of the levcfg variable Each block refers to one atom The atoms must be listed sequentially in order of increasing index Within each block the data are as follows record i atmnam as atom name index integer atom index atmnum integer atomic number record ii XXX real x coordinate yyy real y coordinate ZZZ real z coordinate record iii included only if levcfg gt 0 VXX real x component of velocity vyy real y component of velocity VZZ real x component of velocity record iv included only if levcfg gt 1 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 mandatory any other items are not read by DL POLY 2 but may be added to aid alternative uses of the file for example the DL_POLY 2 Graphical User Interface 8 4 1 2 3 Further Comments The CONFIG file has the same format as the output file REVCON section 4 2 3 When restarting from a previous run of DL_POLY_2 i e using the restart or restart scale di rectives in the CONTROL file above
315. w developments and discovered bugs We have developed a licence for this purpose which we hope will ward off litigation from both sides without denying access to genuine scientific users Further information about the DL_POLY package can be obtained from our website http www cse clrc ac uk msi software DL POLY 1 2 Functionality The following is a list of the features DLPOLY 2 It is worth reminding users that DL POLY_2 represents a package rather than a single program so users may consider piecing together their own program with the desired functionality We will however supply a consolidated program in the distributed source 1 2 1 Molecular Systems DL_POLY_2 will simulate the following molecular species 1 Simple atomic systems and mixtures e g Ne Ar Kr etc 2 Simple unpolarisable point ions e g NaCl KCl etc 3 Polarisable point ions and molecules e g MgO H2O etc D Simple rigid molecules e g CCl4 SFe Benzene etc CCLRC 5 6 7 8 9 10 11 12 Rigid molecular ions with point charges e g KNOg NH4 9S04 etc Polymers with rigid bonds e g CaHon42 Polymers with rigid bonds and point charges e g proteins Macromolecules and biological systems Molecules with flexible bonds Silicate glasses and zeolites Simple metals and alloyse g Al Ni Cu etc Covalent systems e g C Si Ge SiC SiGe etc 1 2 2 The DL POLY 2 Force Field The DL_POLY 2 force field includes the followi
316. wald_terms f setup_program f core_shell_terms f site_terms f setup_program f parse_tools f core_shell_terms f coulomb_terms f neu_coul_terms f coulomb_terms f coulomb_terms f neu_coul_terms f coulomb_terms f neu_coul_terms f coulomb_terms f utility_pack f basic_comms f serial f basic_comms f serial f parse tools f utility pack f angle terms f site terms f bond terms f shake terms f core shell terms f dihedral_terms f dihedral_terms_4pt f dihedral_terms_rsq f external_field_terms f CCLRC define_four_body define_inversions define_metals define_metals define_metals define_pmf define rigid body define_tersoff define_tethers define_three_body define_units define_van_der_waals define_van_der_waals define_van_der_waals denloc denloc denloc diffsn0 diffsn1 dihfre dihfre dihfre dlpfft3 duni ele prd erfcgen erfcgen erfcgen error ewald1 ewald1 ewald1 ewald2 ewald2 ewald2 ewald2neu ewald3 ewald3 ewald3 ewald3_neu ewald4 ewald4 ewald4 ewald_spme subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine function subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subrouti
317. while electrostatics are handled by the CCLRC 151 reaction field method with a charge group cutoff scheme Slab period boundary condi tions are used The water molecule apart from the shell is treated as a rigid body NVT Berendsen ensemble 5 1 1 5 Test Case 5 Shell model of MgCl at constant pressure Adiabatic shell model simulation of MgCl9 Temperature and pressure are controlled by a Berendsen thermostat and barostat An Ewald sum is used with cubic periodic boundary conditions NPT Berendsen ensemble 5 1 1 6 Test Case 6 PMF calculation Potential of mean force calculation of a potassium ion in SPC water Electrostatics are handled by the Ewald sum The water is treated as a constrained triangle PMF ensemble 5 1 1 7 Test Case 7 Linked rigid bodies 8 biphenyl molecules in cubic boundary conditions Each phenyl ring is treated as a rigid body with a constraint bond to the other ring of the molecule In the centre of each ring are three massless charge sites which imparts a quadrupole moment to the ring NVE ensemble 5 1 1 8 Test Case 8 An osmosis experiment with a semi permeable membrane The membrane is a collection of tethered sites interconnected by harmonic springs There are no electrostatic forces in the system The simulation is run with the Hoover anisotropic constant presure algorithm NST Hoover ensemble 5 1 1 9 Test Case 9 A surfactant at the air water interface The syste
318. xt update of the forces f t At is obtained from which the full step velocity is calculated using f t At 1 1 u t At u t 5 At At 2 204 Thus at the end of the two stages full synchronisation of the positions forces and velocities is obtained The full selection of VV integration algorithms within DL_POLY 2 is as follows NVEVV 1 Velocity Verlet with RATTLE NVEGVV 1 Rigid units with NOSQUISH and RATTLE NVEGVV 2 Linked rigid units with GSHAKE NVTVV B1 Constant T Berendsen 19 with RATTLE NVTVV El Constant T Evans 18 with RATTLE NVTVV H1 Constant T Hoover 20 with RATTLE NVTOVV Bl Constant T Berendsen 19 with NOSQUISH and RATTLE NVTOVV B2 Constant T Berendsen 19 with QSHAKE NVTQVV_H1 Constant T Hoover 20 with NOSQUISH and RATTLE NVTOVV H2 Constant T Hoover 20 with GSHAKE NPTVV B1 Constant T P Berendsen 19 with NOSQUISH and RATTLE NPTVV Hl Constant T P Hoover 20 with RATTLE NPTQVV_Bl Constant T P Berendsen 19 with NOSQUISH and RATTLE NPTOVV B2 Constant T P Berendsen 19 with OSHAKE NPTGVV H1 Constant T P Hoover 20 with NOSOUISH and RATTLE NPTOVV H2 Constant T P Hoover 20 with OSHAKE NSTVV B1 Constant T c Berendsen 19 with RATTLE NSTVV_H1 Constant T c Hoover 20 with RATTLE NSTGVV B1 Constant Tio Berendsen 19 with NOSQUISH and RATTLE NSTQVV_B2 Constant T c Berendsen 19 with OSHAKE NSTQVV_H1 Constant Tio Hoover 20 w
319. y a smaller one the user must consider using more processors or a machine with larger memory per processor Message 2040 error failed allocation of nptvv_h1 f densO array This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 2050 error failed allocation of nptvv_h1 f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 2060 error failed allocation of nstvv_b1 f densO array This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 2070 error failed allocation of nstvv_b1 f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 2080 error failed allocation of nstvv_h1 f densO array This is a memory allocation err
320. y be either problematic or impossible Examples in which it is impossible to specify sufficient bond constraints are CCLRC 69 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 procedure slow particu larly if a ring of constraints is involved as occurs when one defines water as a constrained triangle It is also possible inadvertently to over constrain a molecule e g by defining a methane tetrahedron to have 10 rather than 9 bond constraints in which case the SHAKE procedure will become unstable In addition massless sites e g charge sites cannot be included in a simple constraint approach making modelling with potentials such as TIP4P water impossible All these problems may be circumvented by defining rigid body units the dynamics of which may be described in terms of the translational motion of the center of mass COM and rotation about the COM To do this we need to define the appropriate variables describing the position orientation and inertia of a rigid body and the rigid body equations of motion The mass of a rigid unit M is the sum of the atomic masses in that unit Nsites M Y mj 2 241 j l where m is the mass of an atom and the sum includes all sites sites in the body The position of the rig
321. y correction and is identical for all atoms The correction is applied immediately after the local density is calculated The density term of the Sutton Chen potential needs no further correction The pair term correction is obtained by analogy with the short ranged potentials and is N epa a U 2 2 130 corr T n 3 _ The correction to the local density having already been applied To estimate the virial correction we assume the corrected local densities are constants i e independent of distance at least beyond the range reut This allows the virial CCLRC 40 correction to be computed by the methods used in the short ranged potentials The result is n 3 272 m 3 N Ware zapa nNe a me C a Sa 2 131 n 3 Veut m 3 eut 2 This correction may be used as it stands or with the further approximation N 1 2 N Y BT 2 132 i lt Pi gt where lt p 2 gt is regarded as a constant of the system In DL POLY 2 the metal forces are handled by the routine SUTTCHEN The local density is calculated by routines SCDENS and DENLOC The long range corrections are calculated by LRCMETAL 2 3 6 External Fields In addition to the molecular force field DL_POLY 2 allows the use of an external force field Examples of field available include 1 Electric field elec Fi Fi qi H 2 133 2 Oscillating shear oshm F Acos 2n7 z L z 2 134 3 Continuous shear
322. y option is to use a very large simulation cell with the required system at the centre surrounded by a vacuum This is not very efficient however and use of a realistic periodic system is the best option Message 69 error too many link cells required in thbfrc The calculation of three body forces in DL POLY 2 is handled by the link cell algorithm This error arises if the required number of link cells exceeds the permitted array dimension in the code Action Standard user response Fix the parameter mxcell CCLRC 185 Message 70 error constraint bond quench failure When a simulation with bond constraints is started DL_POLY_2 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 following the standard user response to increase the control parameter mxshak You may also consider reducing the tolerance of the SHAKE iteration the directive shake in the CONTROL file However it is probably better to take a good look at the starting conditions Message 71 error too many metal potentials specified The number of metal potentials that can be specfied in the FIELD file is limited This error results if too many are used Action Standard user response Fix the parameter
323. ype parallel 80 requirements Adapter hps_ip amp amp Pool 2 executable usr bin poe cpu_limit 00 10 00 80 arguments dl_poly_2 10 execute DLPOLY X euilib ip output gopoly o error gopoly e class dev queue Using LOADLEVELLER the job is submitted by the unix command submit gopoly where Ilsubmit is a local command for submission to the SP 2 The number of required nodes and the job time are indicated in the above script 6 1 1 5 gui gui is a macro that starts up the DL_POLY_2 Java GUI It invokes the following unix commands java jar java GUI jar In other words the macro invokes the Java Virtual Machine which executes the instruc tions in the Java archive file GUI jar which is stored in the java subdirectory of DL_POLY_2 Note Java 1 3 0 or a higher version is required to run the GUL 6 1 1 6 select select is a macro enabling easy selection of one of the test cases It invokes the unix commands CCLRC 158 cp data TEST 1 2 CONTROL CONTROL cp data TEST 1 2 FIELD FIELD cp data TEST 1 2 CONFIG CONFIG cp data TEST 1 2 TABLE TABLE select requires two arguments to be specified select n a where n is the integer test case number which ranges from 1 to 20 and a is the charac ter string LF or VV according to which algorithm leapfrog LF or velcioty Verlet VV is required This macro sets up the required input files in the execute sub directory
324. ys This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1810 error failed allocation of forces f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1820 error failed allocation of forcesneu f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1830 error failed allocation of neutlst f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor CCLRC 232 Message 1840 error failed allocation of multiple f work arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated system cannot be replaced by a smaller one the user must consider using mor
325. ystem Action Standard user response Fix the value of mxcons Message 494 error in csend pvmfinitsend The PVM routine PVMFINITSEND has returned an error It is invoked by the routine CSEND Action Check your system implementation of PVM Message 496 error in csend pvmfpack The PVM routine PVMFPACK has returned an error It is invoked by the routine CSEND Action Check your system implementation of PVM Message 498 error in csend pvmfsend The PVM routine PVMFSEND has returned an error It is invoked by the routine CSEND Action Check your system implementation of PVM Message 500 error in crecv pvmfrecv The PVM routine PVMFRECV has returned an error It is invoked by the routine CRECV Action Check your system implementation of PVM Message 502 error in crecv pvmfunpack The PVM routine PVMFUNPACK has returned an error It is invoked by the routine CRECV Action Check your system implementation of PVM CCLRC 215 Message 504 error cutoff too large for TABLE file The requested cutoff exceeds the information in the TABLE file Action Reduce the value of the vdw cutoff rvdw in the CONTROL file or reconstruct the TABLE file Message 506 error work arrays too small for quaternion integration The working arrays associated with quaternions are too small for the size of system being simulated They must be redimensioned Action Standard user response Fix the parameter msgrp M
326. ystem the following data are included record a a8 il0 2f12 6 atmnam a8 iatm 110 weight 12 6 charge 12 6 record b 3e12 4 XXX real yyy real ZZZ real record c 3e12 4 only for keytrj gt 0 VXX real vyy real VZZ real record d 3e12 4 only for keytrj gt 1 fxx real fyy real fzz real atomic label atom index atomic mass a m u atomic charge e x coordinate y coordinate Z coordinate x component of velocity y component of velocity z component of velocity x component of force y component of force z component of force Thus the data for each atom is a minimum of two records and a maximum of 4 4 2 1 2 The Unformatted HISTORY File The unformatted HISTORY file is written by the subroutine TRAJECT_U and has the fol lowing structure CCLRC 140 record 1 header configuration name character 80 record 2 natms number of atoms in the configuration real 8 record 3 atname 1 natms atom names or symbols character 8 record 4 weight 1 natms atomic masses real 8 record 5 charge 1 natms atomic charges real 8 For time steps greater than nstraj the HISTORY file is appended at intervals specified by the traj directive in the CONTROL file with the following information record i nstep the current time step real 8 natms number of atoms in configuration real 8 keytrj trajectory key real 8 imcon image convention key real 8 tstep integration timestep real 8 record ii

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