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THE DL-POLY-2 USER MANUAL

1. 53 STFC Section 2 5 NST H1 Constant T c Hoover 21 with SHAKE NSTQ B1 Constant T Berendsen 20 with FIQA and SHAKE NSTQ B2 Constant T o Berendsen 20 with QSHAKE NSTQ H1 Constant T o Hoover 21 with FIQA and SHAKE NSTQ H2 Constant Ta Hoover 21 with QSHAKE In the above table the FIQA algorithm is Fincham s Implicit Quaternion Algorithm 15 and QSHAKE is the DL POLY_2 algorithm combining rigid bonds and rigid bodies in the same molecule 17 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 1 1 f t At t At 222 ult 5 Ja 5 pa 2 225 and then the full timestep position is obtained 1 r t At r t At u t At 2 226 In the second stage using the new positions the next update of the forces f t At is obtained from which the full step velocity is calculated using 1 1 t4 At v t At u t 5A1 5A1 E 2 227 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 NVEQVV_2 Linked rigid units with QSHAKE NVTVV_B1 Constant T Berendsen 20 with RATTLE N
2. 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 9 1 5 Obtaining the Source Code To obtain a copy of DL_POLY 2 it is first necessary to log on to the DL POLY website http www ccp5 ac uk D Follow the links to the registration page where you will firstly be shown the DL_POLY software licence which details the terms and conditions under which the code will be supplied By pro ceeding further with the registration and download process you are signalling your acceptance of the terms of this licence The licence is a package licences which allow you download all current versions of DL_POLY software Click the Registration button to find the registration page where you will be invited to enter your name address and e mail address The code is supplied free of charge to academic users but commercial users will be required to purchase a software licence Once the online registration has been completed information on downloading the DL_POLY_2 source code will be sent automatically by e mail so it is therefore essential to supply a correct e mail address Note that the bench and public subdirectories of DL_POLY_2 are not issued in the standard package but can be downloaded directly from the DL_POLY directory of CCP5 Program Library on the website http www ccp5 ac uk The DL POLY_2 User Manual is
3. 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 simu lated They must be redimensioned Action Standard user response Fix the parameter msgrp 224 STFC Section C 0 Message 508 error rigid bodies not permitted with RESPA algorithm The RESPA algorithm implemented in DL POLY_2 is for atomic systems only Rigid bodies 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 structure opti mizer 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 Messag
4. STFC Section 4 1 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 capabilites 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 de scribed in the following section DL_POLY TEST CASE 1 K Na disilicat
5. A Ojik S rij S rik 2 24 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 0 fr grg V Ori Tis Tit 2 25 with atomic label being one of i j k and a indicating the x y z component The derivative is Ls rij Tik S riz S ri yo alee Ore cee gt us Or Jik A ae A Ojix 5 rin Oj rra ro 0 A 0jix S rij Ser Oi 2 S rix 2 26 Tik Or 18 STFC Section 2 2 with 045 1 if a band bq 0 if a b In the absence of screening terms S r this formula reduces to o o zaU Ojik Tij Tik RGA 2 2 Ore U ik Tijs Tik Ore A Ojik 2 27 The derivative of the angular function is 0 1 o Tij Tik A bjik Aia 3 da 2 28 Or 0 E OO 55h 1 Ore Tiglik with 0 E c Ti 2 80 bes Sex G Or PijTik TijTik PijTik Q Q rij y ik cos Ojik Sp Ori 1 Sex Ovi 2 2 29 Tij Tik The atomic forces are then completely specified by the derivatives of the particular functions A 0 and S r The contribution to be added to the atomic virial is given by W Es FL fy 2 30 It is worth noting that in the absence of screening terms S r the virial is zero 30 The contribution to be added to the atomic stress tensor is given by
6. UB 0 2 306 71 STFC Section 2 5 and substitution of the equation for unt and the equivalent for ups leads directly to hip AB ae a 2 307 CABp 04 2p which provides the correction for second constraint This again reguires 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 NSTQVV_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 applied 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
7. Uij Jolrij Fr riz Vig fali 2 99 where fr rij Aij exp aij rij Jara By exp bij rij 2 100 1 Tij lt Rij felt 4 4cos m ris Rij rij Riy Rij lt Tij lt Sij 2 101 0 i Tij gt Sig Ve p UE LEO Lea Y fet Gx olay k ij 9 9ijk 1 cf d G d hi cos bijr 2 102 with further mixed parameters defined as aij a aj 2 5 bij bi bj 2 AS AA a Bjy BB 2 103 Rij RRA 5 Sij 5 9 3 Here i j and k label the atoms in the system r is the length of the ij bond and ijg is the bond angle between bonds ij and ik Single subscripted parameters 11 such as a and 7 depend only on the type of atom The chemistry between different atom types is encapsulated in the two sets of bi atomic param eters Xij and wij Xi l Xij Xji Wii 1 Wij Wji 5 2 104 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 interpo lation The w parameter is used to permit greater flexibility when dealing with more drastically different types of atoms The force on an atom derived from this potential is formally calculated with the formula o 1 0 ft z Erersott X gt 35Uij 2 105 Or 2 or Aj with atomic label being one of i j k and a indicating the x y z component The derivative in the above formula expa
8. 1 0 U rij Ti 2 89 f rij a r Tijs where Pg r T The force on atom i is the negative of this The contribution to be added to the atomic virial for each pair interaction is The contribution to be added to the atomic stress tensor is given by gt Sef 2 91 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 ranged correction to the system potential energy and virial Explicit formulae are needed for each case and are derived as follows For two atom types a and b the correction for the potential energy is calculated via the integral oo M ana f gav r Uay r r dr 2 92 corr Tout where Na Nj are the numbers of atoms of types a and b V is the system volume and g p r and Uap r are the appropriate pair correlation function and pair potential respectively It is usual to assume gap r 1 for r gt rey DL POLY_2 sometimes makes the additional assumption that the repulsive part of the short ranged potential is negligible beyond reyz The correction for the system virial is Na Na S O Y 2T V gar 5 Uao r r dr 2 93 Tout 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 on
9. 12 13 14 15 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 for an explanation of this variable Note that these options are mutually exclusive The choice of reaction field electrostatics directive reaction requires also the specification of the relative dielectric constant external to the cavity This is specified in the eps directive DL POLY 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 electrostatics 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 lts 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 minimiser to help relax a system before a simulation begins It should not be thought of as a true energy minimisation method The optim directive enables
10. 18 The NVT algorithms in DL POLY 2 are those of Evans 19 Berendsen 20 and Hoover 21 The NPT algorithms are those of Berendsen 20 and Hoover 21 and the NoT algorithms are those of Berendsen 20 and Hoover 21 The full range of MD algorithms available in DL_POLY_2 is described in section 2 5 1 2 5 3 Structure Relaxation Algorithms DL_POLY_2 has a selection of structure relaxation methods available These are useful to improve the starting structure of a molecular dynamics simulation The algorithms available are 1 Zero temperature molecular dynamics sometimes called damped molecular dynamics 2 Conjugate gradients minimisation 3 Programmed energy minimisation involving both molecular dynamics and conjugate gradi ents Starting structure minimisation is described in section 3 2 4 STFC Section 1 3 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 requested 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 Co
11. Ed x t At Tr n t At 3 W A Y E At v t At Sn At u t At 1 AN yk At xli At x t 40 p El At Toxt 30 WT at At 9kpToxt A v t A6 V t At ZA Atju t At 2 259 Routines rattle R and rattle V apply the bondlength and velocity constraint formulae 2 233 and 2 234 respectively The equations have the same conserved variable Hnsr 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 64 STFC Section 2 5 2 5 6 2 Berendsen Barostat With the Berendsen barostat the system is made to obey the equation of motion 2 260 Cell size variations In the isotropic implementation at each step the MD cell volume is scaled by by a factor y and the coordinates and cell vectors by n 3 where At pas 1 P 2 261 and 6 is the isothermal compressibility of the system The Berendesen thermostat is applied at the same time In practice 8 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 Tp Tp 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 v t It calls RDSHAKE_1 to handle constraints The VV version is implemented in subroutine NVTVV_B1 which calls constraint s
12. 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 rj and g is a reciprocal lattice vector Thus L fia bab 2 197 where 41 l2 are integers and vectors a and b are the lattice basis vectors The reciprocal lattice vectors are g nyu nv 2 198 where n1 no are integers u v are reciprocal space vectors defined in terms of the vectors a and b 2n by by axby Ayby u 2r ay az azby aybz 2 199 IS The reader is warned that for the purpose of compatibility with other DL POLY_2 Ewald routines we have defined a 0 5 anK where ayx is the a parameter defined by Hautman and Klein in 45 48 STFC Section 2 4 The functions h s a and f s a are the HKE convergence functions in real and reciprocal 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 to terms in a Taylor expansion of r in s the in plane distance 45 Usually this sum is truncated at Nmaz 1 but in DL POLY_2 can go as high as nmaz 3 In the HKE method the convergence functions are defined as follows hn s 0 s a elsia s 2 200 with ho s a er f as 2 201 and i n g a ens a 2 202 with folg a
13. 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 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 217 STFC Section C 0 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
14. and the rotational matrix R to transform from the local body frame to the space fixed frame is the unitary matrix R 2 q192 4093 d6 ai 45 43 2 q943 q091 2 271 k 4 43 2 q q2 q093 2 q143 q092 2 q143 9092 2 q293 qoq q 13 45 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 2 272 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 Eguations of Motion The eguations 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 2 267 and the mass is the total mass of the rigid body unit i e M in equation 2 264 These equations can be integrated by the standard Verlet LF or VV algorithms described in the previous sections Thus we need only consider the rotational motion here The rotational equation of motion for a rigid body is a dt dt in which J is the angular momentum of the rigid body defined by the expression T Iw l 2 273 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 r Y dxf 2 275 The rotational equations of motion written in the local frame of the rigid body
15. AMBER 4 13 89 DL_POLY 4 13 52 Dreiding 4 13 29 GROMOS 4 13 89 OPLS 13 FORTRAN 90 6 7 FTP 9 Graphical User Interface 5 9 88 90 107 GROMOS 4 13 89 Gupta potential see potential Gupta Hautman Klein Ewald see Ewald Hautman Klein 259 STFC Section D hyperdynamics BPD 140 142 exploring configuration space 148 full path kinetics 144 NEB 141 159 reaction path 141 158 159 TAD 140 148 long ranged corrections metal 36 van der Waals 28 minimisation 87 conjugate gradients 5 52 87 programmed 5 87 zero temperature 5 87 nudged elastic band NEB see hyperdynamics NEB parallelisation 5 73 Ewald summation 75 intramolecular terms 74 Replicated Data 5 Verlet neighbour list 75 potential bond 4 14 17 21 22 26 29 52 74 77 89 113 132 Coulombic see potential electrostatic dihedral 4 13 14 20 23 74 116 132 electrostatic 4 8 14 17 19 40 41 72 73 99 101 105 132 embedded atom EAM 33 122 127 Finnis Sinclair 33 122 four body 4 13 15 26 32 33 77 121 132 Gupta 34 122 improper dihedral 4 22 74 intramolecular 26 32 82 inversion 4 13 23 25 32 33 117 metal 4 13 33 122 nonbonded 4 14 15 75 76 85 89 100 110 113 115 118 Sutton Chen 34 122 tabulated 126 Tersoff 13 14 30 32 123 124 tethered 25 26 117 132 three body 4 13 15 17 26 29 77 89 119 171 152 vale
16. COS ijkn 1 1 2 X ryp Ore alta See E rye X Teal Ore IGER fial with Y Q gra Lig X Lyk Ejk X Lend ij Ijktykla Oak den ejntanla Ser 0e5 rip ILijLjrlal tn Sek TikTknla 02 2i Tin ILL jrlo Lr 603 TRC jr Sei 6 5 2riklLijLrnla 02 Sek 2 44 a Ir X Tik rg llEjkLjrla lde dea rigrznlal r Sex are ij Tija Oak e T T ikla Oti 04j 2 45 Q Ore Irie X Len 2rn rjatjrla Sen See rjxPenla Se Sex arse LenEknla Sex fej ITjkTknla dek Sen 2 46 Where we have used the the following definition a Bla Y 1 bag ad 2 47 B 21 STFC Section 2 2 Formally the contribution to be added to the atomic virial is given by 4 W dor f 2 48 i 1 However it is possible to show by tedious algebra using the above formulae or more elegantly by thermodynamic arguments 30 that the dihedral makes no contribution to the atomic virial The contribution to be added to the atomic stress tensor is given by GP rip raph Tin 2 49 cos dijkn Ie SE with Pi rklEjkEkenla TknlCjkTykla reg X TykllTk X Tknl 2 50 Pao U ltitile Tak ikla rag X LjrllEje X Tan 2 51 Pin T ljkTanlo TenltijTjkla 277 Lijl enla ij X TikllTjk X Lan 2 52 A Atia la ikla Lg El 2 53 9 lyya ray X El oe h Rir ltanfinle TEnlEjktknla l
17. 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 245 STFC Section C 0 Message 2080 error failed allocation of nstvv_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 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 er
18. The atomic stress tensor derived in this way is symmetric In DL POLY 2 bond forces are handled by the routine TETHFRC 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 POLY 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 wo 8 8 a ij ij 12 6 U r de 2 2 2 77 Tij Tij 3 n m potential 31 nm Eo To Po m U rij a In 2 n 2 2 78 2
19. 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 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 55 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 QSHAKE Algorithms The SHAKE and RATTLE algorithms are methods for constraining rigid bonds Parallel adapta tions 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 bonded 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 wi
20. define_system_module f temp_scalers_module f temp_scalers_module f property_module f property_module f property_module f vv_motion_module f vv_motion_module f 1f_motion_module f hyper_dynamics_module f temp_scalers_module f core_shell_module f property_module f property_module f vv_rotationi_module f hyper_dynamics_module f utility_module f hyper_dynamics_module f utility_module f utility_module f utility_module f driver_module f utility_module f core_shell_module f merge_hcube f merge_systol f merge_tools f serial f f f f f temp_scalers_module f 257 STFC Section D 0 shmove shmove shmove shmove simdef spl_cexp splice splice splice splice spme_for sr rce sr rceneu static store_config strip striptext strucopt sysbook sysdef sysgen sysinit systemp tad_option tergen terint tersoff tersoff3 tethfrc thbfrc timchk torgue split traject traject_u transition_properties transition_time turn_rigid_body update_quaternions vertest vertest2 vscaleg vv_integrate warning write_profile write_reference_config xscale zden0 zden1 zero_kelvin 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 subr
21. electrostatic sum for the infinite periodic system into a damped real space sum and a reciprocal space sum The rate of convergence of both sums is governed by a Evaluation of the real space sum is truncated at r freut so it is important that a be chosen so that contributions to the real space sum are negligible for terms with r gt rey The relative error e in the real space sum truncated at reut is given approximately by e erfc areut Teut Y exp 4 Peut 2 Teut 3 1 The recommended value for a is 3 2 reut or greater too large a value will make the reciprocal space sum very slowly convergent This gives a relative error in the energy of no greater than Important note For the SPME method the values of kmax1 2 3 should be double those obtained in this prescription since they specify the sides of a cube not a radius of convergence 90 STFC Section 3 3 e 4 x 107 in the real space sum When using the directive ewald precision DL POLY 2 makes use of a more sophisticated approximation erfe x 0 56exp 27 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 k aq 407 ke ax 3 3 where 9 Era 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 kmaz Z 6
22. hereafter called the reference state against which later structures may be compared to determine any structural transitions 2 The system is simulated at high temperature Trign and halted at regular intervals called a TAD block to energy minimise the structure to construct a reference state This is compared with the existing reference state to determine if a structural transition to state B has occurred A transition is deemed to have occured if one or more atoms are displaced by more than a preset distance the catch radius If a transition is detected a NEB calculation is initiated using the two reference structures to find the activation energy E 149 STFC Section 5 4 log 1 tocc 1 Thigh 1 Tow Figure 5 4 Basic TAD Theory Plot of log 1 t vs 1 T for the TAD method Simulations at high temperature locate transitions indicated as t and t2 with t occurring first time increases in a downward direction on this plot Extrapolation to low temperature using equation 5 16 shows that these transitions would have occurred in reverse order If no other transitions occurred t2 would be the observed low temperature transition in an MD simulation The dotted line indicates a possible hypothetical transition that just precedes to at low temperature Its high temperature intercept is calculated according to the criterion of Voter et al 62 which gives the estimated stopping time for the simulation
23. 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 55 56 Systems containing complex molecules present several difficulties They often contain ionic species which usually require Ewald summation methods 12 57 and intra molecular interactions in addition to nter molecular forces These are handled easily in the RD strategy though the SHAKE algorithm 13 requires significant modification 43 The RD strategy is applied to complex molecular systems as follows 1 Using the known atomic coordinates r each node calculates a subset of the forces acting between the atoms These are usually comprised of a atom atom pair forces e g Lennard Jones Coulombic etc b c d e 2 The computed forces are accumulated in incomplete atomic force arrays J independently on each node non rigid atom atom bonds valence angle forces dihedral
24. subroutine subroutine subroutine subroutine function function subroutine function subroutine function tether_module f three_body_module f define_system_module f vdw_module f property_module f property_module f dihedral_module f spme_module f utility_module f metal_module f utility_module f define_system_module f define_system_module f ewald_module error_module ewald_module ewald_module ewald_module ewald_module define_system_module f spme_module f exclude_module exclude_module exclude_module exclude_module basic_comms f serial f external_field_module f four_body_module f utility_module f parse_module f setup_module f forces_module f forces_module f forces_module f vdw_module f vdw_module f utility_module f metal_module f utility_module f basic_comms f serial f Fh Fh Fh Fh Fh Fh Fh Fh Fh Fh ensemble_tools_module ensemble_tools_module ensemble_tools_module ensemble_tools_module ensemble_tools_module ensemble_tools_module ensemble_tools_module Fh Fh Fh Fh Fh Fh bh 253 STFC Section D O getmass getrec getrotmat getvom getword gimax gimax gisum gisum global_sum_forces gstate gstate gsync gsync hkewald1 hkewald2 hkewald3 hkewald4 hkgen hyper_close hyper_driver hyper_open hyper_start images impact initcomms initcomms intlist intstr intstr3 invert invfrc jacobi kinstr kinstress kinstressf kinstressg 1f_integrate loc8 lowcase lrcmet
25. 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 molecules may be split between processors This message 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 optimization flag turned on If the problem persists it should be reported to the authors after checking the input data for inconsistencies Message 433 e
26. ular units 1 2 The unit of time to is 1 x 10712 seconds i e picoseconds The unit of length 2o is 1 x 10719 metres i e Angstroms The unit of mass mo is 1 6605402 x 10727 kilograms i e atomic mass units The unit of charge qo is 1 60217733 x 107 coulombs i e unit of proton charge The unit of energy E Mo lo to is 1 6605402 x 10723 Joules 10 J mol The unit of pressure P E l is 1 6605402 x 107 Pascal 163 882576 atm Planck s constant A which is 6 350780668 x Est STFC Section 1 4 In addition the following conversion factors are used The coulombic conversion factor yo is 1 4 1380354885 i a ral such that Uuks EoYoU Internal Where U represents the configuration energy The Boltzmann factor kp is 0 831451115 E K such that T Exin kp represents the conversion from kinetic energy in internal units to temperature in Kelvin Note In the DL_POLY_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 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 ev
27. variable 4 variable 5 ad integer integer integer integer real real real real real potential key See table 4 9 first atomic index second atomic index third atomic index fourth atomic index potential parameter see table 4 9 potential parameter see table 4 9 potential parameter see table 4 9 1 4 electrostatic interaction scale factor 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 respectively This directive and associated data records need not be specified if the molecule contains no dihedral angle terms See the note on the atomic indices appearing under the shell directive above Table 4 9 Dihedral Angle Potentials key potential type Variables 1 4 functional formt cos Cosine A dm U 6 A 1 cos m 0 harm Harmonic k do U k bo hcos Harmonic cosine k do U cos cos o cos3 Triple cosine A Ap A3 U 5A1 1 cos 6 542 1 cos 2 34A3 1 cos 3 ryck Ryckaert A U 6 Alag acoso agcos a3cos b Bellemans acost ascos 4 ag as pre set rbf Fluorinated B U B bo bicos bacos b b3cos Ryckaert bacos bscos 6 beexp b7 1 Bellemans bo bg pre set opls OPLS Ao Ay Az Ag U 6 Ao 5 41 1 cos A
28. 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 184 STFC Section B 0 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 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 Figure B 5 The rhombic dodecahedral MD cell Slab boundary conditions IMCON 6 Slab boundaries are periodic in the X and Y directions but not in the Z di
29. 1 4 1 4 2 The utility Sub directory This sub directory stores all the utility subroutines functions and programs in DL POLY 2 to gether with examples of data The various routines in this sub directory are documented in chapter 7 of this manual Users who devise their own utilities are advised to store them in the utility sub directory 1 4 3 The data Sub directory This sub directory contains examples of input and output files for testing the released version of DL POLY 2 The examples of input data are copied into the execute sub directory when a program is being tested The test cases are documented in chapter 6 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 6 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 7 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 POL
30. 1 Mg 2 166 Areo r Tig with the force on atom the negative of this The contribution to the atomic virial is sj 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 te 2 168 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 42 STFC Section 2 4 2 4 4 Damped Shifted Force Coulomb sum A further refinement of the truncated and shifted Coulomb sum 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 shifted force Coulombic potential This is formally equivalent to surrounding each charge with a spherical charge of radius reut which neutralises the charge content of the cutoff sphere The potential is thus qiq 1 Tij 2 4 2 169 i ATE T2 Teut with the force on atom j given by ca GO A 2 170 i 4TEg ri Tom Tiz with the force on atom 7 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 More recently Wolf et al 41 took the shifted force Coulomb potential a step further by the introduction of an additional damping function to moderate the 1 r dependence This was reported to be a viable alternative to the Ewald
31. 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 52 53 with extension to Coulombic systems by Forester et al 54 In the multiple timestep algorithm there are two cutoffs for the pair interactions a relatively large cutoff reut which is used to define the standard Verlet neighbour list and a smaller cutoff Tprim 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 over the interval DL POLY 2 handles this procedure as follows DL_POLY_2 updates the Verlet neighbour list at irregular intervals determined by the move ment 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
32. 5 6 1 Refining the Results A completed BPD or TAD simulation will provide a number of basin files defining the minima of new structures discovered together with the associated profile files describing the energy path between these structures These are the data that are needed to reconstruct the diffusion path in the original system However at this stage there are still some approximations in the results which arise from the chosen tolerances in the energy minimisation of the structures and the NEB calculations To offset these the following refinements are recommended 1 Take each of the basin structures derived from the BPD or TAD simulation and perform a further structural optimisation with DL POLY using more exacting convergence tolerance For example using a force tolerance of 0 01 DL POLY units in place of the recommended 1 0 used in the BPD and TAD procedures This will provide more accurate reference structures 158 STFC Section 5 7 2 Using the accurately minimised structures in place of the original basins use the NEB option in DL_POLY to recalculate the transition path between the reference states Once again a more exacting tolerance may be used but beware that the NEB calculation may not converge at all if the tolerance is too exacting It is far less stable in this respect than the ordinary structural optimisation Note that the tolerance for the overall NEB minimisation is set internally in DL_POLY_2 to be a factor
33. DL_POLY_2 distance restraints are handled by the routine BNDFRC 2 2 3 Valence Angle Potentials Figure 2 2 The valence angle and associated vectors The valence angle potentials describe the bond bending terms between the specified atoms They should not be confused with the three body potentials described later which are defined by atom types rather than indices 1 Ze Harmonic harm k U Ojik 5 Ojik bo 2 14 Quartic quar k E k 3 E 4 U Ojik 5 ji 00 4 3 Ojik 00 q Ori 00 2 15 17 STFC Section 2 2 3 Truncated harmonic thrm U Orin Oji 0 pl BA 2 16 4 Screened harmonic shrm U Oja 5 je 0 expl ras 0n rix pa 2 17 5 Screened Vessal 28 bvs1 U Ojik ay 0 T Ojik gt exp rij p1 rix p2 l 2 18 6 Truncated Vessal 29 bvs2 a a a U Ojik kl ik Ojik 00 O yin 80 27 JT Ojik 00 m 00 expl rh rik 07 2 19 7 Harmonic cosine hcos U Ojix cos 0ja cos 00 2 2 20 8 Cosine cos U Ojik A 1 cos m0jix 2 21 9 MM3 stretch bend potential mmsb U Ojik A Ojik 90 Tig rij rik Tik 2 22 In these formulae 0 is the angle between bond vectors Tij and rig T a T Ojik cos E 2 23 Tijfik In DL POLY 2 the most general form for the valence angle potentials can be written as U Ojik Tij Tik
34. Finnis M W and Sinclair J E 1984 Philos Mag A 50 45 4 33 122 Johnson R A 1989 Phys Rev B 39 12556 4 39 Tersoff J 1989 Phys Rev B 39 5566 4 30 123 124 van Gunsteren W F and Berendsen H J C 1987 Groningen Molecular Simulation GRO MOS Library Manual BIOMOS Nijenborgh 9747 Ag Groningen The Netherlands Standard GROMOS reference 4 13 89 Mayo S Olafson B and Goddard W 1990 J Phys Chem 94 8897 4 13 29 121 Weiner S J Kollman P A Nguyen D T and Case D A 1986 J Comp Chem T 230 4 13 89 Smith W 2003 Daresbury Laboratory 5 10 81 88 90 107 164 171 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 56 57 Allen M P and Tildesley D J 1989 Computer Simulation of Liquids Oxford Clarendon Press 5 14 44 53 55 58 74 75 Ryckaert J P Ciccotti G and Berendsen H J C 1977 J Comput Phys 23 327 5 55 74 Andersen H C 1983 J Comput Phys 52 24 5 57 Fincham D 1992 Molecular Simulation 8 165 5 54 68 Miller T Eleftheriou M Pattnaik P Ndirango A Newns D and Martyna G 2002 J Chem Phys 116 8649 5 55 68 Forester T and Smith W 1998 J Computational Chemistry 19 102 5 54 55 70 Martyna G Tuckerman M Tobias D and Klein M 1996 Molec Phys 87 1117 5 58 69
35. M y TOY Thi 2 a y P exp ip 1 Tkj Tk j Lj k O poe ane OU Baz 1 1 Tkj Tk gd TO Pk Pj o Tkj With the metal forces thus defined the contribution to be added to the atomic virial from each atom pair is then W riy J gt 2 134 which equates to OU Y 3V a Vij ig Orig a OF pi Opi _ v 2353 a OV 122 Dp oy AF i l jfi J i 1 pP rij OV 1 3 Sij SV su Tij 24 OV E 3V OVA Te Mee 22 y 2 135 i 1 j4i ij Tea a y Seg j 1 jAi j L j i Pig j l pHi Mj Y soy OF pi y OF py Opis Tig gt 2 1 j4i Opi Op Orij J 35 STFC Section 2 3 1 EAM virial The same as above 2 Finnis Sinclair virial N N Ari c co C1fij cor rij cr 2c rij Tij NI Me Yi i 1 jAi N N 2 1 Afi 1 Tij d Ya Ds fary ka ma 2 136 i 1 jAi t J 3 Sutton Chen virial i 1 Ai Tij N N m 1 mce OF pi 2 2 Da 2 137 4 Gupta virial N N 1 A Tij r n a i l jzi 0 ro N N Y sD Jon 205 a 2 138 Laja TO Pk Pj ro The contribution to be added to the atomic stress tensor is given by PE A 2 139 where a and 6 indicate the x y z components The atomic stress tensor is symmetric The long ranged correction for the DL POLY 2 metal potential is in two parts Firstly by analogy with the short ranged potentials the correction to the local density is CO pi OS pylri LGA Tij lt Tmet Tij2Tmet pi J opagltag Dd pisl
36. NPT Hoover ensemble 6 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 rigid The MD cell is orthorhombic nearly cubic and the integration is NPT hoover NPT Hoover ensemble 166 STFC Section 6 1 6 1 1 21 Test Case 21 Aluminium metal with EAM potential This case presents an example of the use of the EAM potential for metals in this case aluminium The system is 256 atoms and runs under a berendsen NPT enemble 6 1 1 22 Test Case 22 Copper metal with EAM potential Another example of a metal with an EAM potential 256 copper atoms under a Berendsen NPT ensemble 6 1 1 23 Test Case 23 Copper Gold 3 1 alloy with Gupta potential This is an example of the analytical Gupta potential applied to a copper gold alloy with a 3 1 Cu Au ratio The system consists of 256 atoms in total running under the NVE ensemble 6 1 1 24 Test Case 24 Iron metal with Finnis Sinclair potential In this example the analytical Finnis Sinclair potential is applied to iron The system consi
37. RY and RX remain fixed 5 It is clear that the unconstrained configurations RY would normally relax into the nearest local minimum but that this cannot happen if they are sufficiently constrained by the har monic springs i e knep is strong enough Thus the minimisation of the chain will tend to locate each bead in a position along a path between states A and B like a stretched necklace which approximates the minimum energy path between the two states 6 In practice this simple idea needs refining or nudging Thus care is taken to ensure that the springs forces acting on the beads and the forces optimising bead configurations are approximately orthogonal This means that the atomic forces are zeroed in directions parallel to the path of the chain and the spring forces are zeroed in directions normal to the chain The method of Henkelman and Jonsson 64 is designed to achieve this 7 If the NEB optimisation works correctly the result will be that beads are evenly spaced along the minimum energy path see figure 5 2 Then by fitting the energies of the beads as a function of the distance along the path the maximum energy i e E along the path may be obtained The DL POLY 2 NEB routine does this fit using third order splines 5 3 Bias Potential Dynamics 5 3 1 Theory of Bias Potential Dynamics BPD works on the simple principle that the addition of a suitable potential term to original system potential can have the effect of
38. Ree eon ees 26 231 Short Ranged van der Waals Potentials 6 6 546 660 65604 eee eS 26 22 2 Wires Body Potemials daa ace eRe ee Re RA we ie ee 29 2 3 0 The Tersoff Covalent Potential 4 4 6 064 cs Bee we Oe 30 2 3 4 Four Body Potentials e 32 2 0 0 Metal Potentials se s a co s 24 086 k ks 33 256 External Pields 2 6 0 1 aa Ge S a ee a 40 2 4 Long Ranged Electrostatic Coulombic Potentials 40 2 4 1 Atomistic and Charge Group Implementation 41 742 Direct Coulomb SMA caca ek Re a RA eS 42 2 43 Truncated and Shifted Coulomb Sum a 42 2 4 4 Damped Shifted Force Coulomb sum 00 4 43 2 4 5 Coulomb Sum with Distance Dependent Dielectric 44 ZAG Ewah SU oia ho ke Re BE Ae Re Adee Se ARES RG 44 2 4 7 Smoothed Particle Mesh Ewald o o 46 248 Hautman Klein Ewald HKE ooo 222455 4248 e254 cara as 48 249 Reaction Field us o it ap acs ok a ee a a A a a E a 50 2 4 10 Dynamical Shell Model o E a 51 24 11 Relaxed Shell Model o sist op ree eA bone Pd a Ea 52 20 Ditepraton algorithme s eee soe ll ce A a a a a 53 2 5 1 The Verlet Algorithms os dos poro a e aa o RN A 53 25 2 Bond Constraints cord ne a a a ee EA A 55 2 5 3 Potential of Mean Force PMF Constraints and the Evaluation of Free Energy 57 204 Thermostats 144444 45 ede Sead eae be ER ewe ae a 57 2 5 5 Gaussian Constraints 24 24 6204 444 0 2 Ab Se
39. STFC Section 4 1 Table 4 8 Valence Angle potentials key potential type Variables 1 4 functional formt harm Harmonic k Oo U 0 E 0 bo hrm quar Quartic k o K k U 0 0 00 6 00 0 09 qur thrm Truncated harmonic k 6 p U 0 5 0 0 exp r 15 p thm shrm Screened harmonic k 00 pi po U 0 0 00 exp rij p1 Tik p2 shm bvs1 Screened Vessal 28 k 00 pi po CG OP my 0 my bv1 exp rij p1 Tik P2 bvs2 Truncated Vessal 29 k 0 a p U 0 k 9 9 b0 8 bo 27 gn bv2 0 00 T 00 exp r ri 0 hcos Harmonic Cosine k Oo U 0 E cos 0 cos 0p hcs cos Cosine A 6d m U 0 A 1 cos m0 0 COS mmsb MM Stretch bend A o dab dac U 0 A 0 00 rab 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 115 STFC Section 4 1 9 dihedrals n where nis the number of dihedral interactions present in the molecule Each of the following n records contains dihedral key index 1 index 2 index 3 index 4 variable 1 variable 2 variable 3
40. 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 calculations use 201 STFC Section C 0 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 combine 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 do
41. Tin T ay Vien Lik Vieno 2 i Vik 4 T ii kn kn 22 rij Lim T rij oO Pin Dn 2 in Tij kn den Oi UknTin Ti kos j Xi T den dei j 2 rij Upn Upn e Pin T rij O T Tin rl j 24 STFC Section 2 2 This general formula applies to all atoms 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 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 don f 2 67 i However it is possible to show by thermodynamic arguments cf 30 or simply from the fact that the sum of forces on atoms j k and n is equal and opposite to the force on atom i that the inversion potential makes no contribution to the atomic virial If the force components f7 for atoms i j k n are calculated using the above formulae it is easily seen that the contribution to be added to the atomic stress tensor is given by er FP r FO refe 2 68 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 inversio
42. U dijkn A 1 cos m ijkn 6 2 32 2 Harmonic harm U Pijkn Sh isin 60 2 33 3 Harmonic cosine hcos k UO 3 C05 Eijkn cos 60 2 34 4 Triple cosine cos3 U 6 5 Au 1 cos 6 5 Aa 1 cos 26 5 Aa 1 cos 36 235 5 Ryckaert Bellemans hydrocarbon potential ryck 5 Uldijen Alao gt ascos 6 2 36 i 1 6 Ryckaert Bellemans fluorinated potential rbf 5 U dijkn B bo Y b cos 0 2 37 i 1 7 OPLS angle potential U dijkn ao 0 5 x a1 1 cos a gt 1 cos 26 az 1 cos 3 2 38 20 STFC Section 2 2 In these formulae ijkn is the dihedral angle defined by Pigkn COS Be ij gt Lik Lkn J 2 39 with 2 40 rij X Tjk Tjk X Tkn BOs jk Tkn 2 z gt lta x Ek X Tin With this definition the sign of the dihedral angle is positive if the vector product r j X rjg X Tik X Ten 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 f grg V biien 2 41 with being one of i j k n and a one of x y z This may be expanded into 0 1 0 grg Pigi cot Odijkn Olite gpa P Eig Ejk Lan 2 42 The derivative of the function B rij Tjk kn is 1 BlLij Tj RNS Ge si ore Oni Lkn lrg x TjpllEjk x Tyn 575 Ey x Tik Tik x P i 3
43. Un 1 dp x disp 2 296 70 STFC Section 2 5 and we have used the identity GiB JABLABp where g4p is a scalar quantity Now the true position at timestep tn 1 of the link atom on rigid body A is ray Rat dat 2 297 and inserting 2 292 and 2 295 leads to 1 1 Ar rip EX dep 94 Ya 2 298 where dABp n T 94 Ma UA x d p 2 299 Since d 4 bp f i r Bp we can easily obtain m 1 At dilo danp 9487 Q4 9B 2 300 Squaring both sides and neglecting terms of order higher than O At gives after rearrangement 1 1 OR RN JAB n l 2 301 At dApp OA Op From which the constraint force may be calculated Iteration is necessary as in SHAKE In the second stage of QSHAKE we need to calculate another constaint force HT a to preserve the orthogonality of the constraint bond vector and the relative velocity of 2 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 we write directly as At yu Li A LA 2M4 AB At wy ont gru 2 302 where h is a scalar related to the constraint force via AB 1 _ pn 1 m 1 Hip hap LiBp Now the velocity of the linked atom on molecule A is which on substitution of the above equations gives where dih antl e a 2 305 The constraint condition requires that dihp vat
44. Verlet leapfrog integration Only one iteration is needed two if the system has bond constraints to constrain the instantaneous temperature to exactly 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 60 STFC Section 2 5 x mia fOD mini t ve e v t SAV va SLO 1 r t At r t Ato t At call rattle R At f t At 2 m u t At v t At call rattle V x t At mias t At f t At Y mio t At A ith E dado a At u t At 2 249 Routines rattle R and rattle V apply the bondlength and velocity constraint formulae 2 233 and 2 234 respectively The integration is performed by the subroutine NVTVV_El which calls subroutines RATTLE_R and RATTLE_V 2 5 6 Barostats The size and shape of the simulation cell may be dynamically adjusted by coupling the system to a barostat in order to obtain a desired average pressure Pexi and or isotropic stress tensor 2 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 51 in which the equations of motion couple a Nos Hoover thermostat and a barostat Cell size variation For isotropic fluctuat
45. 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 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 235 STFC Section C 0 Message 1590 error failed allocation of work arrays in 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
46. alloc_csh_arrays alloc_dih_arrays alloc_ewald_arrays alloc_exc_arrays alloc_fbp_arrays alloc_fld_arrays alloc_hke_arrays alloc_hyper_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 Kind 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 Location define_system_module f define_system_module f metal_module f define_system_module f vdw_module f setup_module f angles_module f bonds_module f config_module f core_shell_module f dihedral_module f ewald_module f exclude_module f four_body_module f external_field_module f hkewald_module f hyper_dynamics_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 spme_module f three_body_module f tersoff_module f tether_module f vdw_module f 251 STFC Section D 0 angfrc bndfrc bodystress bomb bpd forces bpd option bspcoe bspgen cell propagate cell update cerfr cfgscan check_bas
47. 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 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 237 STFC Section C 0 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 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 cons
48. associated with it a rotational inertia matrix I whose components are given by Nsites Top Y my d s d r 2 268 j where d is the displacement vector of the atom j from the COM and is given by d 1j R 2 269 It is common practice in the treatment of rigid body motion to define the position R of the body in a universal frame of reference the so called laboratory or inertial frame but to describe the moment of inertia tensor in a frame of reference that is localised in the rigid body and changes as the rigid body rotates Thus the local body frame is taken to be that in which the rotational inertia tensor I is diagonal and the components satisfy Ly gt Luy gt Izz In this local frame the so called Principal Frame the inertia tensor is therefore constant 5An 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 66 STFC Section 2 5 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 do q1 q2 93 2 270
49. be necessary to improve the accuracy of the cal culated activation energy or to determine the activation energy in transitions not fully evaluated when they occurred in a BPD or TAD simulation due to the occurrence of a multiple maximum on the reaction path 159 STFC Section 5 7 To run a NEB calculation with DL POLY 2 it is first necessary to identify the start and end basins among the CFGBSNnn files in the BASINS directory described in section 5 5 0 3 From the information provided in the EVENTS 5 5 0 2 file it should be possible to decide which files are needed The user then needs to modify the CONTROL file in the following way 1 Remove any directives for the bpd or tad options Directives for the integration algorithm integrator or ensemble ensemble should also be removed The directive for the NEB option should be inserted neb n where n is the number of NEB calculations required On the record following the neb directive a list of n starting basins should be given e g basin 111123 Meaning the 5 reguired NEB calculations start from basin files CFGBSN0001 CFGBSN0001 CFGBSN0001 CFGBSN0002 and CFGBSN0003 Up to 10 NEB calculations are permitted On the second record following the neb directive a list of n final basins should be given e g basin 2 23434 Meaning the 5 required NEB calculations are between basins 1 2 1 3 1 4 2 3 and 3 4 in this example Define the energy units for the BP
50. 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 srcmod directory of DL_POLY_2 Changing ndump necessitates recompiling DL POLY 2 REVCON is identical in format to the CONFIG input file see section 4 1 2 except that two extra numbers appear on the end of the second line of the file 1 an integer indicating the current time step number format I10 2 the current value of the simulation time in picoseconds format F20 REVCON should be renamed CONFIG to continue a simulation from one job to the next This is done for you by the copy macro supplied in the execute directory of DL_POLY_2 4 2 4 The CFGMIN File The CFGMIN file only appears if the user has selected the programmed minimisation option di rective minim in the CONTROL file Its contents have the same format as the CONFIG file see section 4 1 2 but contains only atomic position data and will never contain either velocity or force data i e parameter levcfg is always zero In addition two extra numbers appear on the end of the second line of the file 1 an integer indicating the number of minimisation cycles required to obtain the structure format 110 2 the configuration energy of the final structure expressed in DL POLY units 1 3 10 format F20 134 STFC Section 4 2 4 2 5 The REVIVE File This file is unfor
51. but their role in DL_POLY_2 is not to provide users with true structural optimisation procedures capable of finding the ground state structure They are simply intended to help users improve the quality of the starting structure prior to a dynamical simulation The available algorithms are 1 Zero temperature molecular dynamics This is equivalent to a dynamical simulation at low temperature At each time step the molecules move in the direction of the computed forces and torques but are not allowed to acquire a velocity larger than that corresponding to a temperature of 1 Kelvin The subroutine that performs this procedure is ZERO_KELVIN which is found in the file OPTIMISER_MODULE F 2 Conjugate Gradients CG minimisation This is nominally a simple minimisation of the system configuration energy using the conjugate gradients method 59 The algorithm coded into DL POLY_2 allows is an adaptation that allows for rotation and translation of rigid bodies Rigid contraint bonds however are treated as stiff harmonic springs a strategy which we find does allow the bonds to converge within the accuracy required by SHAKE The subroutine that performs this procedure is STRUCOPT which is found in the file OPTI MISER_MODULE F 3 Programmed energy minimisation involving both molecular dynamics and conjugate gra dients This method combines conjugate gradient minimisation with molecular dynamics Minimisation is followed by user d
52. dt u t als _ OO 2 235 2 236 The friction coefficient x is controlled by the first order differential equation dx t _ Nik dt Q where Q N skpTextTh is the effective mass of the thermoststat Tr is a specified time constant normally in the range 0 5 2 ps and Np is the number of degrees of freedom in the system T t is the instantaneous temperature of the system at time t In the LF version of DL POLY_2 y is stored at half timesteps as it has dimensions of 1 time The integration takes place as Z t Text 2 237 cee At xii At Pay ah a T t Toa m S Ix At LA 540 vit 5A ot AN AI ES r vos Ome Ec a sat Kalti 340 r t At rA sat 2 238 Since v t is required to calculate 7 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 started with the standard Verlet leapfrog prediction of v 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 Hnvr U KE 50x t Sf x s ds 2 239 TE 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 algorith
53. empty directories e BASINS to receive any new structures found e TRACKS to store the tracking configurations e PROFILES to store any transition pathways found by NEB calculations If the directories BASINS TRACKS and PROFILES already exist then carefully archive the data before deleting the contents These directories should not be emptied if the simulation is continuing restarting and a full history of the kinetics is required More about these directories and the files they contain can be found in section 5 5 5 Run the BPD simulation This will perform a simulation at the state point requested checking for structural transitions at the BPD block intervals specified Each time it finds a structural transition it will record the new state determine the activation energy by the NEB method and the unbiased transition time using the boost factor in equation 5 5 and then continue the simulation 146 STFC Section 5 3 6 When the simulation ends proceed as follows a Check the EVENTS file to see if any structural transitions have been obtained Each NS NS NS event is represented by a single record and transitions are flagged with the keyword TRA at the start of the record Use unix grep to locate these entries No observed transitions indicates that either a longer simulation is necessary or running with a higher bias Epias should be considered Important If any of the reported tr
54. equilibration data in overall statistics coul calculate coulombic forces cut f set required forces cutoff to f A densvar f percentage density variation for arrays 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 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 f2 select Berendsen NPT ensemble with fi fa as the thermostat and barostat relaxation times ps ensemble npt hoover f f2 select Hoover NPT ensemble with fi f2 as the thermostat and barostat relaxation times ps ensemble nst ber fi fo select Berendsen NoT ensemble with fi f2 as the thermostat and barostat relaxation times ps 99 STFC Section 4 1 ensemble nst hoover fi f2 select Hoover Na T ensemble with fi f2 as the thermostat and barostat relaxation times ps ensemble pmf select NVE potential of mean force ensemble eps f set relative dielectric constant to f default 1 0 equil n equilibrate simulation for first n timesteps ewald precision f select Ewald sum for electrostatics with automatic parameter optimisation 0 lt f lt 1 5 4 ewald sum a k k2 k3 select Ewald sum for electrostatic
55. equilibrium angle of 35 264 The angle is defined by vectors rj9 ro3 and T34 Where the atoms 1 2 3 and 4 are shown in the following figure The figure defines the D and L enantiomers consistent with the international IUPAC convention When defining the dihedral the atom indices are entered in DL_POLY_2 in the order 1 2 3 4 In DL_POLY_2 improper dihedral forces are handled by the routine DIHFRC 22 STFC Section 2 2 L aa N C 8 D a C N 8 123 4 123 4 Figure 2 4 The L and D enantiomers and defining vectors Figure 2 5 The inversion angle and associated vectors 2 2 7 Inversion Angle Potentials The inversion angle potentials describe the interaction arising from a particular geometry of three atoms around a central atom The best known example of this is the arrangement of hydrogen atoms around nitrogen in ammonia to form a trigonal pyramid The hydrogens can flip like an inverting umbrella to an alternative structure which in this case is identical but in principle causes a change in chirality The force restraining the ammonia to one structure can be described as an inversion potential though it is usually augmented by valence angle potentials also The inversion angle is defined in the figure above note that the inversion angle potential is a sum of the three possible inversion angle terms It resembles a dihedral potential in that it requires the specification of four atomic positions The potential functions
56. 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 virial virbnd real bond virial record v stpval 16 stpval 20 virang real valence angle 3 body virial 136 STFC Section 4 2 vircon real constraint virial virtet real tethering virial volume real volume tmpshl real core shell temperature record vi stpval 21 stpval 25 engshl real core shell potential energy virshl real core shell virial alpha real MD cell angle a beta real MD cell angle 8 gamma real MD cell angle y record vii stpval 26 stpval 27 virpmf real Potential of Mean Force virial press real pressure the next ntpatm entries amsd 1 real mean squared displacement of first atom types amsd 2 real mean squared displacement of second atom types amsd ntpatm real mean squared displacement of last atom types the next 9 entries if the stress tensor is calculated stress 1 real xx component
57. 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 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 also require a TABLE file 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 Sometimes you will also require a TABEAM file section 4 1 6 if your simulation includes embedded atom potentials for metallic systems Examples of input files are found in the data sub directory which can be copied into the execute subdirectory using the select macro found in the execute sub directory A successful run of DL_POLY 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 configuration instantaneous and rolling averaged thermodynamic data final configurations radial distribution functions RDFs and job timing data The OUTPUT file is human readable Also present will be the
58. forces option not specified DL POLY 2 has failed to find any directive specifying the electrostatic interactions options in the CONTROL file 211 STFC Section C 0 Action Ensure the CONTROL file contains at least one directive specifying the electrostatic potentials 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 Message 386 error primary cutoff larger than rcut The primary cutoff specified by the prim directive in the CONTROL file exceeds the value speci fied 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 NP
59. if illegal values were specified in the CONTROL file This part of the file is written from the subroutine SIMDEF 131 STFC Section 4 2 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 speci fication 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 ps 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 The labels refer to line 1 step MD step number eng t
60. 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 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 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 6 Calculation of the real space component in DL POLY_2 employs the algorithm for the calcula tion of the nonbonded interactions outlined above The reciprocal space component is calculated using the schemes described in 57 in which the calculation can be parallelised by distribution of either k vectors or atomic sites Distribution over atomic sites requires the use of a global sum mation of the g exp ik rj terms but is more efficient in memory usage Both strategies are computationally straightf
61. in this chapter users of the hyperdynamics features of DL_POLY_2 should see Chapter 5 where additional files specific to that purpose are described 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 created 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 graphical 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
62. 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 220 STFC Section C 0 Message 462 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 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 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 t
63. is a density dependent and therefore many body metal potential The final term Uertn represents an external field potential The position vectors ra Tp 1 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 dependence The numbers Nona Nangies Nainea and Niny refer to the total numbers of these respective interactions present 13 STFC Section 2 1 in the simulated system and the indices bond tangles tiny aNd idiheq uniquely specify an indi vidual interaction of each type It is important to note that there is no global specification of the intramolecular interactions in DL POLY 2 all bonds valence angles and dihedrals must be individually cited The indices i j 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 electrostatic Coulombic forces The former are regarded as short ranged interactions and the latter as long ranged Long ranged 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
64. is confined to electrostatic forces only The main difference from the standard Ewald method is in its treatment of the the reciprocal space terms By means of an interpolation procedure involving complex B splines the sum in reciprocal space is represented on a three dimensional rectangular grid In this form the Fast Fourier Transform FFT may be used to perform the 46 STFC Section 2 4 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 44 1 Interpolation of the exp ik rj terms given here for one dimension exp 2riu k L b k Mn Vezp 2nikl K 2 188 j R in which k is the integer index of the amp vector in a principal direction K is the total number of grid points in the same direction and uj is the fractional coordinate of ion j scaled by a factor K i e uj K 85 Note that the definition of the B splines implies a dependence on the integer K which limits the formally infinite sum over The coefficients M u are B splines of order n and the factor b k is a constant computable from the formula n 2 1 b k exp 2ri n 1 k K 5 Mn l ljexp 2rikl K 2 189 0 2 Approximation of the structure factor S k S k bi k1 bo k2 b3 k3 Q ka k2 ks 2 190 where Ol k ka k3 is the discrete Fourier trans
65. must consider using more processors or a machine with larger memory per processor 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 248 STFC Section C 0 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 smaller 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 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 2290 error failed allocation of nstqvv_h1 f work arrays This is a memo
66. 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 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 93 STFC Section 3 4 MACHINE FORGEN SYSDEF INTLIST L PASSCON SYSGEN GAUSS AAA SHMOVE QUENCH L SPLICE VERTEST VSCALE PARLST LRCORRECT MULTIPLE EWALD1 BNDFRC PRIMLST ANGFRC SRFRCE DLPOLY DIHFRC EWALD2 4 EXTNFLD COULO 1 or 2 GDSUM FORCES EWALD3 FCAP RDFO SHMOVE VSCALE RDSHAKE_1 SPLICE STATIC MERGE REVIVE DIFFSNO 1 TRAJECT REVIVE RESULT RDF1 Figure 3 1 A sample DL_POLY structure 94 Chapter 4 DL POLY 2 Data Files STFC Section 4 0 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 96 STF
67. not recom mended 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 Cubic periodic boundaries IMCON 1 The cubic MD cell is perhaps the most commonly used in simulation and has the advantage of great simplicity In DL_POLY_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 182 STFC Section B 0 Figure B 1 The cubic MD cell 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 Figure B 2 The orthorhomic MD cell Parallelepiped periodic boundaries IMCON 3 The parallelepiped e g monoclinic or triclinic cell is ge
68. of 10 larger than that for the minimisation alone The result of these refinements should be a better estimate of the activation energy and low temperature transition time For TAD simulations the activation energy obtained from the refined structures can be used together with the simulated high temperature transition time to recalculate the low temperature transition time from equation 5 16 Note this may alter the original low temperature diffusion path so be alert to this possibility and change the starting basin for any subsequent simulation These refinements have no impact on the BPD simulations other than to improve the quality of the calculated kinetic properties 5 6 2 Treatment of Multiple Maxima in the Reaction Path The NEB calculations that occur while the BPD or TAD simulations are running may sometimes report a multiple maximum on the reaction path see the TRA entry for the EVENTS file in section 5 5 0 2 More than two maxima is probably indicative of problems with the NEB convergence and should be regarded with suspicion but obtaining two maxima is a real possibility In such cases DL POLY 2 stores both the end structure of the NEB chain and the structure corresponding to the first minimum in the energy profile along the reaction path but it does not record the activation energies beyond the first peak A BPD simulation requires a complete description of the potential energy surface kinetics so determination of the second activa
69. 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 185 STFC Section B 0 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 4 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 Figure B 6 The hexagonal MD cell This MD cell is particularly suitable for simulating strands or fibres i e systems with a pro nounced anisotropy in the Z direction such as DNA strands in solution or stretched polymer chains 186 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 recommended 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 v
70. of stress tensor stress 2 real xy component of stress tensor stress 3 real xz component of stress tensor stress 4 real yx component of stress tensor T real y stress 9 real zz component of stress tensor the next 9 entries if a NPT simulation is undertaken cell 1 real x component of a cell vector cell 2 real y component of a cell vector cell 3 real z component of a cell vector cell 4 real x component of 6 cell vector ea real x cell 9 real z component of c cell vector 137 Chapter 5 DL POLY 2 and Hyperdynamics 138 STFC Section 5 0 Scope of Chapter This chapter describes the facilties within DL POLY 2 for performing accelerated dynamics or hy perdynamics using the Bias Potential Dynamics and Temperature Accelerated Dynamics methods 139 STFC Section 5 1 5 1 Overview of Hyperdynamics The first thing to note about the hyperdynamics methods in DL_POLY_2 is that they were designed for studies of kinetic processes in the solid state which mostly means diffusion In solids diffusion is characterised by infrequent atomic hops occurring on a time scale of order 100 ps to 1000 ps per hop which is too infrequent to give a measurable diffusion in a normal molecular dynamics simulation Hyperdynamics methods are designed to overcome this problem by accelerating the hopping frequency The hyperdynamics methods built into DL POLY 2 are Bias Potential Dynamics BPD 61 and Temperature Accelerated Dynami
71. phigh 3 Next a determination of the transition time t 9 is made As with BPD the occurrence time of the transition t 9 is determined by checking back from the detection of the transition through past configurations saved at regular intervals which are saved at intervals much less than a TAD block Each saved configuration is energy minimised and compared with the reference state structure until the first occurrence of the new state is found This provides a reasonable accuracy on the transition time somewhat better than using the end time of the TAD block in which the transition occurred 4 The time t 9 is extropolated to the corresponding time of occurrence t 2 at Toy This is done by combining equations 5 14 and 5 15 and taking the logarithm plow high E 1 1 lo occ lo 5 16 a jhigh pow kp on Dias om See figure 5 4 for an indication of how the extrapolation works 5 The system is returned to state A and the simulation recommenced Returning the system to its original state means resetting the atomic coordinates to a structure in the starting basin and resetting the velocities according to a Boltzmann distribution while retaining the total system energy of the original state The simulation is continued to obtain information on other transitions to states C D E etc that may occur from state A This is a key difference from the BPD method 6 A determination of the simulation stopping tim
72. potential 3 fnsc The Finnis Sinclair potential is explicitly analytical It has the following form Varis rij CJ co crrij cariz rij d Pij rij ry ap BCID 2 F p AvVPi with parameters co C1 Co C A d 0 both c and d are cutoffs Since first being proposed a number of alternative analytical forms have been proposed some of which are descibed below The rules for combining different metal potentials to model alloys are different from the EAM potentials see below 2 125 33 STFC Section 2 3 3 Sutton Chen potential 37 38 39 stch The Sutton Chen potential is an analytical po tential in the FSM class It has the form a n Vij rij 2 pijlTij a 2 126 Tij Flpi ceypi with parameters a n M C 4 Gupta potential 40 gupt The Gupta potential is another analytical potential in the FSM class It has the form Tis T Vi rij Aexp p 7 2 ro J mT pislrij exp 2qij 2 2 2 127 with parameters A ro p B qij All of these metal potentials can be decomposed into pair contributions and thus fit within the general tabulation scheme of DL POLY 2 where they are treated as pair interactions though note that the metal cutoff me has nothing to do with short ranged cutoff ryqw DL POLY_2 calculates this potential in two stages the first calculates the local density p for each atom and the second calculates the
73. potential energy and forces Interpolation arrays vmet gmet and fmet METGEN METTAB are used in both these stages in the same spirit as in the van der Waals interaction calculations The total force 1 on an atom k derived from this potential is calculated in the standard way F VkUmetal 2 128 We rewrite the EAM FSM potential 2 123 as Umetal Ur o Ut LS iai rij 2 129 i l Ai N U2 J F 4 1 where r rj 7 The force on atom k is the sum of the derivatives of U and U2 with respect to rg which is recognisable as a sum of pair forces 1 EAM force OU 22 OVig rig Orig L Vig Mug THI Ork iA Dr Or jdt Org Tj OU N aF Dona Orij 2 130 ry 25 2 Bry Ork 20 34 STFC Section 2 3 E E OF Opik rik Orik N F Opxj rej Oras E Tiar OPi Orik Ore jalg ek OPE Ore Ore OF OF Oprs rij Tki p IL JAK i Z Of bi Tki In DL POLY 2 the generation of the force arrays from tabulated data implemented in the METAL DERIV routine is done using a five point interpolation precedure 2 Finnis Sinclair force U 2 2 kj 5 Ari cMe0 ar c2rkj rrj c c1 2er 43 Tk ar Tkj E J 1 j k OU N AYA 1 d fki A S 4 2 rk d ggr ag EAS 2 131 15 E Pk Pi A kj 3 Sutton Chen force U y ie a Tkj rk Higa NOS Thy VONE i mce iS as a J Tkj 2 132 Ori jan 2 VPk VDI Neij Yh 4 Gupta force OU
74. 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 227 STFC Section C 0 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 1115 error failed allocation of hyperdynamics 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 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 1120 error failed allocation of inversion arrays This is a memory allocation error Probable cause excessive size of simulated system Action If the simulated syste
75. reducing the depth of the potential basin see figure 5 3 so assisting escape to neighbouring states The biased system potential Viias R is thus given by Vias RY V R Wbias RN 5 4 where V RN is the original system potential and Woias RN is the bias potential Voter 61 has shown that using a bias potential accelerates the diffusion rate constant k797 as defined by Transition State Theory by a boost factor peer ay KEST 5 5 bias bias where 3 1 kgT and the ensemble average which is calculated in the biased system represents the boost factor However this simple accelerative factor alone is not sufficient if a faithful description of the dif fusion path in the original system is required Voter 61 showed that to recover the true diffusional path it is important that the bias potential does not affect the structure of the transition state i e the saddle points for the system potential energy surface If this is the case then the relative rate constants for escape from a given structure or state to any other neighbouring state remains constant i e for transitions from state A to state B or state C TST TST ka B kap 5 6 LIST _ LEST Ap gt C A C 142 STFC Section 5 3 Emin Figure 5 3 Basic BPD Theory The normal potential energy surface continuous line is characterised by deep basins such as Emin from which escape is improbable The biased potential Vias dashed line re
76. 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 component of the dihedral force and not necessarily a vanishing 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 218 STFC Section C 0 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 th
77. restart files REVIVE section 4 2 5 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 velocities and forces of the atoms when the run ended and is human readable The STATIS file section 4 2 8 contains a catalogue of instantaneous values of thermodynamic and other variables in a form suitable for temporal or statistical analysis Finally the HISTORY file section 4 2 1 provides a time ordered sequence of configurations to facilitate further analysis 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 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 simulation you wish to perform and create the input files specific to this requirement The program will then perform the requested simulation but may terminate prematurely through error inadequate time
78. 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 file 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 performed concurrently on all nodes and that in circumstances where a different result may obtain on different nodes a call to the global status routine 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 requires 92 STFC Section 3 4 the user to state the identity of the calling node
79. simulation cell volume and k is a reciprocal lattice vector defined by k lu mu nw 2 181 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 V a bx c 2 182 and u mn u am 2 183 axb 277 E With these definitions the Ewald formula above is applicable to general periodic systems A small additional modification is necessary for rhombic dodecahedral and truncated octahedral simulation cells 43 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 45 STFC Section 2 4 In practice the convergence of the Ewald sum is controlled by three variables the real space cutoff reut the convergence parameter a and the largest reciprocal space vector kmar used in the reciprocal space sum These are discussed more fully in section 3 3 5 DL POLY 2 can provide estimates if requested see CONTROL file description 4 1 1 The force on an atom j is obtained by differentiation and is i dj V ikexplik r PORAD 5 exp ik r k Voo po oo i qj da dn 2ATnj d Zi 2 iy gt e exp a ra tng 2 184 T 2 erflare aw patri re The electrostatic contribution t
80. start and end points are too far apart so that one or more intermedate states have been missed This leads to multiple maxima on the reaction path which may be the problem In which case examine the operational choices made in running the TAD or BPD simulation and see if changing them will reduce the danger of this happening Message 2330 error too many basin files found increase mxbsn A TAD or BPD run has generated more than 100 basin files which is the internal operational limit Action Reset the mxbsn parameter which is defined at the top of the hyper dynamics module f file to a larger number and recompile Message 2340 error hyperdynamics diffs arrays exceeded increase mxdiffs A TAD or BPD run has generated more than 300 recorded differences between the reference struc ture and all subsequent new basins found Effectively this means it has recorded more than 300 atomic jumps which is the internal operational limit Action Reset the madiffs parameter which is defined at the top of the hyper_dynamics_module f file to a larger number and recompile 250 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 Routine abort_config_read abort_control_read abort_eamtable_read abort_field_read abort_table_read abortscan alloc_ang_arrays alloc_bnd_arrays alloc_config_arrays
81. 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 230 STFC Section C 0 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 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 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 proces
82. t 5At v t 3At At 2 222 where m is the mass of a site and At is the timestep The positions are then advanced using the new velocities 1 r t At r t At v t At 2 223 Molecular dynamics simulations normally require properties that depend on position and ve locity 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 u t 5 ul 1 5 ule ZA v t At 2 224 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 QSHAKE NVT_Bl Constant T Berendsen 20 with SHAKE NVT_El Constant T Evans 19 with SHAKE NVT H1 Constant T Hoover 21 with SHAKE NVTQ B1 Constant T Berendsen 20 with FIQA and SHAKE NVTQ B2 Constant T Berendsen 20 with QSHAKE NVTG H1 Constant T Hoover 21 with FIQA and SHAKE NVTG H2 Constant T Hoover 21 with QSHAKE NPT_B1 Constant T P Berendsen 20 with FIQA and SHAKE NPT_H1 Constant T P Hoover 21 with SHAKE NPTG B1 Constant T P Berendsen 20 with FIQA and SHAKE NPTQ B2 Constant T P Berendsen 20 with QSHAKE NPTQ H1 Constant T P Hoover 21 with FIQA and SHAKE NPTQ H2 Constant T P Hoover 21 with QSHAKE NST B1 Constant T Berendsen 20 with SHAKE
83. the DL_POLY_2 Graphical User Interface 9 4 1 2 3 Further Comments The CONFIG file has the same format as the output files REVCON section 4 2 3 and CFGMIN section 3 2 4 When restarting from a previous run of DL POLY 2 i e using the restart or restart scale directives in the CONTROL file above the CONFIG file must be replaced by the REVCON file which is renamed as the CONFIG file The copy macro in the ezecute sub directory of DL_POLY_2 does this for you 107 STFC Section 4 1 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 aowbrWNFH 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 108 STFC Section 4 1 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 Valinomyc
84. thermostat is implemented in NVTQ_H1 the Hoover isotropic barostat plus thermostat in NPTG 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 69 STFC Section 2 5 For VV integration the Hoover thermostat is implemented in NVTQVV_H1 NVTQSCL the Hoover isotropic barostat plus thermostat in NPTQVV_H1 NPTQSCL_T NPTQSCL_P and the anisotropic barostat in NSTQVV_H1 NSTQSCL_T NSTQSCL_P The analogous routines for the Berendsen algorithms are NVTQVV_B1 NPTQVV_B1 and NSTQVV_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 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 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
85. 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 reproduce all the atomic positions in rigid units from the centre of mass and quaternion vectors it has calculated Action Check the contents of the CONFIG file DL POLY 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 structure If the problem persists increase the value of the variable tol in QUA
86. to desired temperature 3 start new simulation from CONFIG file without rescaling the velocities Table 4 2 Internal Ensemble Key keyens meaning 0 Microcanonical ensemble NVE 1 Evans NVT ensemble 2 Berendsen NVT ensemble 3 Nos Hoover NVT ensemble 4 Berendsen NPT ensemble 5 Nos Hoover NPT ensemble 6 Berendsen No T ensemble 7 Nos Hoover NaT ensemble 8 Potential of mean force NVE ensemble 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 directory to see how different files are constructed 104 STFC Section 4 1 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 01 1t Ignore Electrostatic interactions 2 3 Ewald summation 4 5 distance dependent dielectric 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 105 STFC Section 4 1 4 1 2 The CONFIG File The CONFIG file contains the dimensions of the unit cel
87. to evaluate electrostatic interactions e g by usinf the coul directive in the CONTROL file 206 STFC Section C 0 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 termi nates if more than this is requested 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 parameters mxnstk mxstak If this is not the case it will be unable to restart the program correctly to con tinue 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 com promise 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 ar
88. 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 directions to ensure the reciprocal space sum is equally 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 91 STFC Section 3 4 which specifies the required accuracy of the HKE convergence functions plus two additional in tegers 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 ra
89. 0 passcon passpmf passpmf passquat passquat pivot pmf_rattle_r pmf_rattle_v pmf_shake pmf_vectors pmf1f pm vv primlst print_optim prneulst pseudo_shake put_shells_on_cores qrattle_r qrattle_v qshake quatbook guatgnch guench rdf0 rdfOneu rdf1 rdrattle r rdrattle_v rdshake_1 read_reference_config regauss relax_shells result revive rotate_omega scan_profile scl_csum scramble_velocities sdot0 sdot1 set block shell relaxation shellsort shlfrc shlmerge shlmerge shlmerge shlmerge shlgnch 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 function function subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine serial f pass_tools f serial f pass_tools f serial f vv_rotation2_module f pmf_module f pmf_module pmf_module pmf_module pmf_module pmf_module f nlist_builders_module f define_system_module f nlist_builders_module f optimiser_module f core_shell_module f vv_rotation2_module f vv_rotation2_module f 1f_rotation2_module f
90. 20 error failed allocation of work arrays 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 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 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 replace
91. 20 kmax is then kmax gt 3 2 L Teut 3 5 In a cubic system freut L 2 implies kmax 7 In practice the above equation slightly over estimates the value of kmax required so optimal values need to be found experimentally In the above example kmax 5 or 6 would be adequate If your simulation cell is a truncated octahedron or a rhombic dodecahedron then the estimates for the kmax need to be multiplied by 2 3 This arises because twice the normal number of k vectors are required half of which are redundant by symmetry for these boundary contributions 43 If you wish to set the Ewald parameters manually via the ewald sum or spme sum directives the recommended approach is as follows Preselect the value of reut choose a working a value of a of about 3 2 rcut and a large value for the kmax say 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 20 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 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
92. 243 60 Melchionna S Ciccotti G and Holian B L 1993 Molec Phys 78 533 61 Tildesley D J Streett W B and Saville G 1978 Molec Phys 35 639 72 Tildesley D J and Streett W B Multiple time step methods and an improved poten tial function for molecular dynamics simulations of molecular liquids In Lykos P editor Computer Modelling of Matter ACS Symposium Series No 86 1978 72 Forester T and Smith W 1994 Molecular Simulation 13 195 72 73 Smith W 1991 Comput Phys Commun 62 229 73 74 77 Smith W 1993 Theoretica Chim Acta 84 385 73 74 75 Smith W 1992 Comput Phys Commun 67 392 74 75 Vessal B Amini M Leslie M and Catlow C R A 1990 Molecular Simulation 5 1 76 Shewchuk J R August 4 1994 An Introduction to the Conjugate Gradient Method Without the Agonizing Pain Edition 1 1 4 School of Computer Science Carnegie Mellon University Pittsburgh PA 15213 87 Melchionna S and Cozzini S 1998 University of Rome 89 Voter A 1997 J Chem Phys 106 4665 140 142 Sorensen M and Voter A 2000 J Chem Phys 112 9599 140 148 150 151 Hamelberg D Mongan J and McCammon J A 2004 J Chem Phys 120 11919 140 143 144 Henkelman G and Jonsson H 2000 J Chem Phys 113 9978 141 142 Rahman J A and Tully J C 2002 J Chem Phys 116 8750 144 178 Appendix A The DL POLY 2 Makefile Master
93. 3 4 Analysing Results DL POLY 2 is not designed to calculate every conceivable property you might wish from a sim ulation Apart from some obvious thermodynamic quantities and radial distribution functions it does not calculate anything beyond the atomic trajectories on line You must therefore be prepared 89 STFC Section 3 3 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 Users are invited to submit code to the DL_POLY 2 public library to help with this Users should be aware that many of these utilities are incorporated into the DL_POLY Graphical User Interface 9 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 simu lation 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 preci sion 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 e
94. 3 n 3 N A kai ES 2 145 m 3 Tmet 2 p 4 Gupta energy correction 27N pAro 2 p ha ine 2 2 22 Tmet TO exp p 37 U STFC Section 2 3 2 an 27 met 2 2 2 x 2 146 ij ij E 9 je NB p dij ro 24 9 2 To estimate the virial correction we assume the corrected local densities are constants i e in dependent of distance at least beyond the ranged rmet This allows the virial correction to be computed by the methods used in the short ranged potentials 27 pro qij U a ES OVij OVi rij Yi y Tij i 1 Hi ary N Tij lt Tmet ms ri N Tij2Tmet OVij r nel y 6 is 5 AG i 1 ji 1 i l jfi Tij Uo OV OW 27Np Mt Sap Tmet Tij OF Opis r a 3 5 LS pul Dr 2 147 1 OPE aziu Sri OF pi Tij lt Tmet Api p as Op ri A y _ i ij i ig Tag f pe Opi 2 Org V y on 2 Ori V i 1 j t i 1 J i meno OF pi did Op r OW 4rp A S Dy Opi Tmet Or Evaluating the integral part of the above equations yields 1 EAM virial correction No long ranged corrections apply beyond Tmet 2 Finnis Sinclair virial correction No long ranged corrections apply beyond cutoffs c and d 3 Sutton Chen virial correction sv nre a n 3 Tmet Arpa a NT Ne e m 25 2 148 4 Gupta virial correction p 2xNpAro 3 2 o an 3 6 6 r p Tmet T WT met P O met 2 ag F x Tmet TO ex
95. 5 29 32 Daw M S and Baskes M I 1984 Phys Rev B 29 6443 33 122 Foiles S M Baskes M I and Daw M S 1986 Chem Phys Lett 33 7983 33 122 J F 1952 Philos Mag 43 153 33 Sutton A P and Chen J 1990 Philos Mag Lett 61 139 34 77 122 Rafii Tabar H and Sutton A P 1991 Philos Mag Lett 63 217 34 39 122 Todd B and Lynden Bell R 1993 Surf Science 281 191 34 Cleri F and Rosato F 1993 Phys Rev B 48 22 34 122 Wolf D Keblinski P Phillpot S and Eggebrecht J 1999 J Chem Phys 110 8255 43 Fennell C and Gezelter J 2006 J Chem Phys 124 234104 43 Smith W and Fincham D 1993 Molecular Simulation 10 67 45 73 74 78 91 Essmann U Perera L Berkowitz M L Darden T Lee H and Pedersen L G 1995 J Chem Phys 103 8577 46 47 Hautman J and Klein M L 1992 Molec Phys 75 379 48 49 185 Neumann M 1985 J Chem Phys 82 5663 51 Fincham D and Mitchell P J 1993 J Phys Condens Matter 5 1031 51 177 STFC Section 7 1 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 Lindan P J D and Gillan M J 1993 J Phys Condens Matter 5 1019 52 McCammon J A and Harvey S C 1987 Dynamics of Proteins and Nucleic Acids Cam bridge University Press 57 Brown D and Clarke J H R 1984 Molec Phys 51 1
96. 6 1 12 6 potential 12 6 2 Lennard Jones lj STFC Section 2 3 4 Buckingham potential buck ij C U rij A exp g 2 79 P Tij 5 Born Huggins Meyer potential bhm C D U rij A exp B o r 2 2 80 Ti Ti 6 Hydrogen bond 12 10 potential hbnd U rij Zn 2 81 ij ij 7 Shifted force n m potential 31 snm no E lr E O Er ON p with E a 2 83 E ET 2 84 0 n m 2 85 ngr 1 m y m 1 y7 MBNA n y n 1 y This peculiar form has the advantage over the standard shifted n m potential in that both E and ro well depth and location of minimum retain their original values after the shifting process 8 Morse potential mors U rij Eol l exp k rig 0 1 2 86 9 Shifted Weeks Chandler Anderson WCA potential 32 wea 4 5 12 gt 6 a A U rij x 53 me LOak 2 87 0 4 Tij gt 95 A The WCA potential is the Lennard Jones potential truncated at the position of the minimum and shifted to eliminate discontinuity includes the effect of excluded volume It is usually used in combination with the FENE 2 9 bond potential This implementation allows for a radius shift of up to half a A lt 0 5 0 with a default of zero Ade fault 0 10 Tabulation tab The potential is defined numerically only 27 STFC Section 2 3 The parameters defining t
97. 80 STFC Section 3 1 3 1 Constructing DL POLY 2 an Overview 3 1 1 Constructing the Standard Version DL POLY 2 was originally designed as a package of useful subroutines rather than a single program which means that users were meant to be able to construct a working simulation program of their own design from the subroutines available which is capable of performing a specific simulation However we recognise that many perhaps most users will be content with creating a standard version that covers all of the possible applications and for this reason we have provided the necessary tools to assemble such a version The method of creating the standard version is described in detail in this chapter however a brief step by step description follows 1 DL_POLY_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 this will be the srcmod subdirectory 3 The makefile is executed with the appropriate keywords section 3 2 1 which selects for spe cific computers including serail and parallel machines and the appropriate communication software 4 The makefile produces the executable version of the code which as a default will b
98. 9 STFC Section C 0 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 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 more 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 sim
99. B calculation is unlikely to converge as there 160 STFC Section 5 7 will be no simple path with preferably a single energy maximum between the start and end states 4 When running an NEB calculation to improve the accuracy of the activation energy a more stringent tolerance must be set For example the recommended value for the force tolerance is normally 1 0 in DL_POLY units but values one or two orders of magnitude less may be tried It should be noted however that before the NEB calculation is run the configurations representing the start and end configurations must first be minimised to the accuracy required by the new tolerance by using the DL_POLY_2 optim option These optimised structures must be returned to the BASINS directory with the same file numbers as the original CFGBSN files 161 Chapter 6 DL POLY 2 Examples 162 STFC Section 6 0 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 163 STFC Section 6 1 6 1 DL POLY Examples 6 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 ev
100. C Section 4 1 4 1 The INPUT files REVCON OUTPUT HISTORY STATIS CONFIG CONTROL TAB EAM REVOLD ZDNDAT REVIVE Figure 4 1 DL POLY 2 input and output files Input files appear on the left and output files on the right Files marked with an asterisk are non mandatory File CFGMIN not shown appears as an output file if the user selects the programmed minimisation option see 3 2 4 In normal use DL_POLY_2 requires six input files named CONTROL CONFIG FIELD TA BLE TABEAM and REVOLD The first three files are mandatory while files TABLE and TABEAM TAB EAM in the figure are used only to input certain kinds of pair potential and are 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 Note In addition to the files described in this chapter users of the hyperdynamics features of DL POLY 2 should see Chapter 5 where additional files specific to that purpose are described 4 1 1 The CONTROL File The CONTROL file is read by the subroutine SIMDEF and defines the control variables for running 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 invoke a particular operation or provide numerical parameters Also associated with each directive may be one or 97
101. C subroutine uses link cells to compute the four body forces This message indicates 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 in creased in size to accommodate the data Action Standard user response Fix the parameter mxfbp 200 STFC Section C 0 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 91 error unidentified atom in 4 body potential list The specification of a four body potential in the FIEL
102. D 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 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 un known 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 93 error cannot use shell model with rigid molecules The dynamical 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 the perpendicular width of the simulation cell
103. D parameters e g units s where s is one of eV kcal kJ or K signifying electron volts kilo cals per mole kilo joules per mole or Kelvin respectively No units directive means DL POLY internal units apply Forces are in chosen energy units per Angstrom Next set the NEB spring constant in specified energy units per A e g neb spring 1000 0 in DL_POLY units Select a minimisation option e g force key tol Where key is one of force energy position and tol is the convergence tolerance Close the NEB definition with the directive endneb 5 7 1 Things to Aware of when Running a NEB Calculation 1 Note that the NEB calculation assumes that the basin files for the start and end states are in the BASINS directory and that DL_POLY_2 is being run from the execute directory where the DLPOLY X executable is located Needless to say if these files are placed anywhere else the calculation will fail Note also that the NEB calculation places the reaction path profile for a given pair of states in the PROFILES direction with the file name PRXnn XY where nn is a negative number that is compounded from the identities of the start n and end states n2 thus nn 100 xn na It is important to be sure that the start and end states represent real observed transitions in the BPD or TAD simulation The danger here is using two structures that are not mech anistically close If this is not the case the NE
104. Ejk X Lan 2 55 hy ArknltanTknlo TkljkTknla Tjk x Beal 2 56 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 inter actions 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 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
105. Evans D J and Morriss G P 1984 Computer Physics Reports 1 297 5 53 54 58 Berendsen H J C Postma J P M van Gunsteren W DiNola A and Haak J R 1984 J Chem Phys 81 3684 5 53 54 55 58 176 STFC Section 7 1 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 Hoover W G 1985 Phys Rev A31 1695 5 53 54 55 58 Jorgensen W L Madura J D and Swenson C J 1984 J Amer Chem Soc 106 6638 13 Brode S and Ahlrichs R 1986 Comput Phys Commun 42 41 14 74 75 Hockney R W and Eastwood J W 1981 Computer Simulation Using Particles McGraw Hill International 14 15 76 Warner H R J 1972 ind Eng Chem Fundam 11 379 16 Bird R B e a 1977 Dynamics of Polymeric Liguids volume 1 and 2 Wiley New York 16 Grest G S and Kremer K 1986 Phys Rev A 33 3628 16 Vessal B 1994 J Non Cryst Solids 177 103 18 19 29 115 121 Smith W Greaves G N and Gillan M J 1995 J Chem Phys 103 3091 18 19 29 115 121 Smith W 1993 CCP5 Information Quarterly 39 14 19 22 25 Clarke J H R Smith W and Woodcock L V 1986 J Chem Phys 84 2290 26 27 119 Weeks J D Chandler D and Anderson H C 1971 J Chem Phys 54 5237 27 Eastwood J W Hockney R W and Lawrence D N 1980 Comput Phys Commun 19 21
106. GBSNnn file as CONFIG Once again an initial equilibration of the system to high temperature is recommended This is not strictly a restart of an unfinished simulation but the start of a new one which is part of a TAD series The previous simulation ended but did not record any transitions In this case it is advised to start the simulation afresh using a higher operating temperature than before The previous simulation ended without crashing and recorded some transitions but did not reach the required stop time In this case simply restart the program as for a normal DL_POLY continuation run using the REVCON REVIVE and HYPRES files renamed CONFIG REVOLD and HYPOLD and using the unqualified restart directive in the CONTROL file Remember to increase the number of required time steps if necessary The previous simulation crashed If this means a crash for unknown reasons then the situation may be unrecoverable as with any unexpected DL_POLY crash Try to locate the problem and fix it If however the simulation arrived at this end point due to a time out error then there is hope It may be possible to restart from the last REVCON REVIVE HYPRES files presuming they are uncorrupted and have the same time stamp Be aware that such a restart may cause data duplication in other files such as STATIS EVENTS BASINS PROFILES and HISTORY and the user should remove such a possibility by editing or sometimes even removing the files before restar
107. OE which calculates B spline coefficients SPL_CEXP which calculates the FFT and B spline complex exponentials EWALD_SPME which calculates the re ciprocal space contributions SPME_FOR which calculates the reciprocal space forces and DLPFFT3 which calculates the 3D complex fast Fourier transform default code only Cray SGI IBM SP ma chines 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 performed 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 usually zero 2 4 8 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 45 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 Nmax Ue 7 2 on Sanya zie XO Jalg a exp ig sij eA E ij g 0 wd se Le ij L qidj H Anz 2n 1 8TE0 Dies L Tij L ij S 10 a ha Na En mr 2 2 196
108. Re eR Re ea ee 60 200 UBAEGSLALS za a Gee a ek Gigs ee LER a eee Be bee wes 61 2 5 7 Rigid Bodies and Rotational Integration Algorithms 65 2 5 8 The DL POLY 2 Multiple Timestep Algorithm 72 26 DE POLY Parallelisation coses cenar Pe aA ee A PS 73 2 6 1 The Replicated Data Strategy lt 202000200200 0004 73 2 6 2 Distributing the Intramolecular Bonded Terms 74 2 6 3 Distributing the Nonbonded Terms 00000 enue 75 vi STFC Contents 2 6 4 Modifications for the Ewald Sum ee ee 75 2 6 5 Modifications for SPME i a sam ss ee ap 75 2 6 6 Three and Four Body Forc s o ore s sosa toaa erg ppa ke tgk EO 76 20 7 Metal Potentials coses k ecas si RR ee we g Kk 77 2 6 8 Summing the Atomic Forces 2 is 77 2 6 9 The SHAKE RATTLE and Parallel QSHAKE Algorithms 77 3 DL POLY 2 Construction and Execution 79 3 1 Constructing DL_POLY_2 an Overview 2 0 000 a eee ees 81 3 1 1 Constructing the Standard Version a 81 3 1 2 Constructing Nonstandard Versions 0000 ee eee nee 81 3 2 Compiling and Running DL POLY 2 2 1 2 6 086s be ee Oe ee a a 83 32 1 Compiling the Soutce Code s lt ates a piagas daa a eee a 83 322 Ruming DL POLY 2 e re e Ge is sia eee Eee ee ea be 86 32 3 Restarting DL POLY 2 oe ea koks ok kok k ae ee 86 3 2 4 Optimising the Starting Structure a 87 3 3 A Guide to Preparing Input Files o m
109. T simula tions 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 212 STFC Section C 0 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 Either simulate the system with a periodic boundary or use another ensemble Message 391 error 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
110. TBOOK and recompile If problems still persist double the value of dettest in QUATBOOK and recompile If you still encounter problems contact the authors 209 STFC Section C 0 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 guaternion integrator failed The guaternion 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 temperature inconsistent constraints involving shared atoms etc Action Corrective action depends on the cause 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 mxguat 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 eguilibrium Mes
111. TFC Section C 0 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 between 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 config uration 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 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 Message 106 error neighbour list array too small in parlink Construction of the Verlet neighbour list in subroutine parlink nonbonded pair force has ex ceeded the neighbour list array dimensions Action Standard user respo
112. THE DL POLY 2 USER MANUAL W Smith T R Forester and I T Todorov STFC Daresbury Laboratory Daresbury Warrington WA4 4AD Cheshire UK Version 2 19 April 2008 STFC Preface ABOUT DL_POLY_2 DL_POLY_2 is a parallel molecular dynamics simulation package developed at Daresbury Labo ratory by W Smith and T R Forester under the auspices of the Engineering and Physical Sciences Research Council EPSRC for the EPSRC s Collaborative Computational Project for the Com puter Simulation of Condensed Phases CCP5 and the Computational Science and Engineering Department at Daresbury Laboratory The package is the property of the Science Facilities Re search Council STFC 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 Daresbury Laboratory 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 contributions in the form of working code are welcome provided the code is compatible with DL_POLY_2 in regar
113. VTVV_El Constant T Evans 19 with RATTLE NVTVV_H1 Constant T Hoover 21 with RATTLE NVTQVV_B1 Constant T Berendsen 20 with NOSQUISH and RATTLE NVTQVV_B2 Constant T Berendsen 20 with QSHAKE NVTQVV_H1 Constant T Hoover 21 with NOSQUISH and RATTLE NVTQVV_H2 Constant T Hoover 21 with QSHAKE NPTVV_B1 Constant T P Berendsen 20 with NOSQUISH and RATTLE NPTVV_H1 Constant T P Hoover 21 with RATTLE NPTQVV_Bl Constant T P Berendsen 20 with NOSQUISH and RATTLE NPTQVV_B2 Constant T P Berendsen 20 with QSHAKE NPTQVV_H1 Constant T P Hoover 21 with NOSQUISH and RATTLE NPTQVV_H2 Constant T P Hoover 21 with QSHAKE NSTVV_B1 Constant T Berendsen 20 with RATTLE 54 STFC Section 2 5 NSTVV_H1 Constant T z Hoover 21 with RATTLE NSTQVV_B1 Constant T a Berendsen 20 with NOSQUISH and RATTLE NSTQVV B2 Constant T a Berendsen 20 with QSHAKE NSTQVV_H1 Constant T a Hoover 21 with NOSQUISH and RATTLE NSTQVV H2 Constant T a Hoover 21 with QSHAKE In the above table the NOSQUISH algorithm is the rotational algorithm of Miller et al 16 and QSHAKE is the DL_POLY_2 algorithm combining rigid bonds and rigid bodies in the same molecule 17 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 q Vem t kpf where i labels particles
114. Y 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 appropriate subroutines from the srcmod sub directory and deposit the executable program in the execute directory The user is advised to copy the appropriate makefile into the srcmod directory in case any modifications are required The copy in the build sub directory will then serve as a backup 1 4 7 The public Sub directory This sub directory contains assorted routines donated by DL_POLY users Potential users should note that these routines are unsupported and come without any guarantee or liability what soever They should be regarded as potentially useful resources to be hacked into shape as needed by the user This directory is available from the CCP5 Program Library by direct FTP see below 1 4 8 The java Sub directory The DL POLY_2 Java Graphical User Interface GUI is based on the Java language developed by Sun The Java source code for this GUI is to be found in this sub directory along with a few FORTRAN sub sub directories which contain some additional capabilities accessible from the GUI These sources are complete and sufficient to create a working GUI provided the user has installed the Java Development Kit 1 4 or above which is available free from Sun at http java sun com STFC Section 1 6
115. a tensor 7 The LF equations of motion are implemented as 1 1 AtNrkp x t At x t At Q At x t 340 T t Text SWT 9kpText 1 x zp i 1 2 ne an ne an VO o Poat DT alt nt nt At n t 540 9 2 e At a ADEA IL n 7 at 4 Lut 5At ult 540 r t At r t At vt wat t At ke At Ro r t At r t r t At 2 255 63 STFC Section 2 5 where 1 is the identity matrix and the pressure tensor The new cell vectors are calculated from 1 H t At exp E n t A0 H t 2 256 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 2 257 The conserved quantity is 1 1 Unsr U KE Pext t 50x t 5WTr n t 6 72 x s s 9kBText ds 2 258 This algorithm is implemented in the routine NST H1 with bond constraints The VV version of this algorithm is implemented as x t At E o oe 39 0WT rial Ok pTexa w t w t xa Auto n An yo US Poo XT rato wt ve Ene 50040 22 1 A te At e IU 1 r t At r t t Atou t At call rattle R V t At V t exp sat n t 540 H t At lt exp at n t 40 H t v t At vlt i 1 2 m call rattle V 1 MEAN lt lt n t 5At S qu E n t At
116. a bond potential is obtained using the general formula 110 f EA Tijs 2 11 Tij The force f acting on atom i is the negative of this The contribution to be added to the atomic virial is given by W Lij Ls 2 12 with only one such contribution from each bond The contribution to be added to the atomic stress tensor is given by ani 2 13 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 1Note some DL_POLY_2 routines may use the convention that ri Tor 16 STFC Section 2 2 2 2 2 Distance Restraints In DL POLY 2 distance restraints in which the separation between two atoms is maintained around some preset value ro is handled as a special case of bond potentials As a consequence dis tance restraints may be applied only between atoms in the same molecule Unlike with application of the pure bond potentials the electrostatic and van der Waals interactions between the pair of atoms are still evaluated when distance restraints are applied All the potential forms of the previous section are avaliable as distance restraints although they have different key words 1 2 T Harmonic potential hrm Morse potential mrs 12 6 potential bond 126 Restrained harmonic rhm Quartic potential gur Buckingham potential bck FENE potential fen In
117. a conjugate gradient energy minimisation of the configuration There are three additional options energy force and position which decide convergence on the basis of energy force or position The recommended option is force which is suitable for most cases Note that the additional parameter the user must supply is the tolerance for the convergence This must be appropriate for the chosen option All are expressed in DL_POLY internal units For the force option a value of about 1 0 is appropriate for many cases The minim directive enables a programmed minimisation which combines conjugate gradient minimisation with a molecular dynamics search The three additional options energy force and position refer to the CG minimisation as described for the optim directive above The user must also supply an integer number of time steps for the interval between successive CG minimisations and the convergence tolerance for each minimisation The tolerance is expressed in the appropriate internal units 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 number 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 mu1tt gt 2 then statistics for radial distribution functions are collected only at updates of the secondary nei
118. ad aip i e aa 88 Brack Tnoresmie Materials oc mip ose k a a ee ae 89 Due Macromolecules s ar do aa dis ir e 89 330 Adding Solvent tom SUCUS sia e ia e ee Be da eS 89 334 Analysing Results imss s acras e a A A a a 89 3 3 5 Choosing Ewald Sum Variables oaoa a 90 34 DL POLY 2 Error Processiig ce s oa k eae a ORS ee ae 92 3 4 1 The DL_POLY_2 Internal Error Facility o s sa sadi anaa o 92 4 DL_POLY_2 Data Files 95 Al The INPUT les 0 ad a r a A S a A 97 ALI The CONTROL Eil s s r tira OR Se ee le ee a 97 412 The CONFIG File 2 0 ks da a Bo Bo a S Se 106 41 3 The FIELD Ple sorsra iioi m a el We a we a ee ae 109 414 The REVOLD File osea ss aca BO aes AO a a Be 125 AL5 The TABLE Eil e s ecg a ee eR ee e RR e ee OR Se 126 41 6 The TABEAM File orcos crees k a a eS 127 42 The OUTPUT Biles ico rr rasa aa K a 129 421 The HISTORY File s a sie amp 2054 4 pea a ss RR Rae oe 129 422 The OUTPUT File rie a pk Sd eee a oes eA Re SOR 131 420 The REVYCON File scce ea dav tin Boa Rew eRe CARR ees 134 424 The CFGMIN Pile coo secas retrasada ae Se Pw ox 134 42 5 The REVIVE File 26 56 k 0444 68 4 vs 608446 a 135 4 2 6 The RDFDAT File is 135 4 2 7 The ZDNDAT File e 135 4 2 8 The STATIS File is 136 5 DL_POLY_2 and Hyperdynamics 138 5 1 Overview of Hyperdynamics ooo es 140 5 2 The Nudged Elastic Band Calculation 2 0 0 0 eee eee 141 5 3 Bias Potential Dynamics lt a 142 5 3 1 Theory of B
119. 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 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 36 error failed fmet array allocation in mettab DL POLY 2 is unable to allocate the fmet array in the definition of an EAM potential Action Most probable cause is working too near the memory limit for the machine Try using more processors to free up some memory Check the TABEAM file in case the data are incorrectly specifie
120. aint 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 6 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 6 1 1 9 Test Case 9 A surfactant at the air water interface The system 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 6 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 water molecules The DNA is aligned in the Z direction and hexagonal prism periodic boundary 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 distributi
121. al lrcorrect machine machine matmul merge merge merge merge 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 function function subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine function subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine ensemble_tools_module parse_module f utility_module f ensemble_tools_module parse_module f basic_comms f serial f basic_comms f serial f utility_module f basic_comms f serial f basic_comms f serial f hkewald module f hkewald module f hkewald module f hkewald module f hkewald module f hyper dynamics module hyper dynamics module hyper dynamics module hyper dynamics module utility module f temp scalers module f basic comms f serial f define system module f parse_module f utility_module f utility_module f inversion_module f utility_module f ensemble_tools_module ensemble_tools_module ensemble_tools_module ensemble_tools_module integrator_module f utility_module f parse_module f metal_module f vdw_module f basic_comms f serial f utility_module f merge_hcube f m
122. al force field Examples of field available include 1 Electric field elec Fi Fi qu H 2 154 2 Oscillating shear oshm F Acos 2nr z Lz 2 155 3 Continuous shear shrx 1l v pa z gt 20 2 156 4 Gravitational field grav F m H 2 157 5 Magnetic field magn F Fi qi vi A H 2 158 6 Containing sphere sphr 7 Repulsive wall zbnd E A zo 2 Z gt Zo 2 160 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 2 4 Long Ranged Electrostatic Coulombic Potentials DL_POLY_2 incorporates several techniques for dealing with long ranged electrostatic potentials 2 These are as follows 1 Atomistic and charge group implementation 2 Direct Coulomb sum 2Unlike the other elements of the force field the electrostatic forces are NOT specified in the input FIELD file but by setting appropriate directives in the CONTROL file See section 4 1 1 40 STFC Section 2 4 3 Truncated and shifted Coulomb sum 4 Damped shifted force Coulomb sum 5 Coulomb sum with distance dependent dielectric 6 Ewald sum 7 Smoothed Particle Mesh Ewald SPME 8 Hautman Klein Ewald for systems with 2D periodicity 9 Reaction field 10 Dynamical s
123. al systems state A is likely to have more than one escape route to distinct states B C D etc each with its own activation energy pre exponential factor and temperature dependent rate constant At any given temperature escape from state A may occur via any one of these routes but is most probable via the route which has the highest rate constant and therefore by equation 5 15 the lowest associated residence time A normal molecular dynamics simulation commencing from state A will undergo a transition to a neighbouring state via the first encountered route and never sample the alternatives Since the different routes have different temperature dependent rates it follows that at different temperatures the system may evolve along completely different paths The TAD method avoids this possibility at high temperature by returning the system to state after every transition so that practically all of the escape routes at this temperature may be discovered From the calculated properties of these escape routes the true low temperature escape route may be determined by extrapolation Thus TAD provides a high temperature method for identifying the transitions that mark out the low temperature diffusion pathway The characteristics of the method are as follows in which it is assumed that the kinetic prop erties of a system at the temperature Tlow are required 1 Thestarting structure state A is energy minimised to provide a reference structure
124. 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 17 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 17 Firstly we assume a rigid body A is connected to another B at timestep tn nAt via bonds between atoms at positions Ap and TBp given by rap RA dip rap RB dbp 2 291 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 unre stricted Our task is then to find the the constraint force G which would preserve the constraint bondlength i e dy Bp dihp Assuming we know this force we can write 2 At Bean 4 Op 2 292 2MA in which the tilde indicates the corresponding variable computed 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 ie T as T T day X Cap 2 293 It may be easily shown from this and eguation 2 273 that 1 wh Wa 17 da x Gan 2 294 from which it follows that ar JAP dart dap T z SaBUA x d p 2 295 where we have defined
125. allocation or computer failure Errors in input data are your responsibility 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 CONTROL 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 section 4 1 4 which is an exact copy of the previous REVIVE file If you attempt to restart DL_POLY_2 without this additional file available the job will fail Note that DL POLY 2 will append new data to the existing STATIS 86 STFC Section 3 2 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 jo
126. als 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 Ulrij shri E 2 2 2 Morse potential mors U rij Eo 1 exp k rig ro 1 2 3 3 12 6 potential bond 12 6 4 Restrained harmonic rhrm Ulrij shri To ri rol lt re 2 5 Un Skr krellrij rol re rij ro gt rc 2 6 15 STFC Section 2 2 5 Quartic potential quar k A k E 4 U rig 5 rig ro rij ro ri To 2 7 2 3 4 6 Buckingham potential buck Tij C U rij A exp 52 B 2 8 aj 7 Shifted finitely extendible non linear elastic FENE potential 25 26 27 fene 2 may 5 U ry 05 Ro In 1 42 gt tig lt RotA 26 co Tij gt R A The FENE potential is used to maintain the distance between connected beads and to prevent chains from crossing each other It is used in combination with the WCA 2 87 potential to create a potential well for the flexible bonds of a molecule that maintains the topology of the molecule This implementation allows for a radius shift of up to half a R A lt 0 5 Ro with a default of zero Agefault O In these formulae rij is the distance between atoms labelled i and j rij e ril 2 10 where r is the position vector of an atom labelled The force on the atom j arising from
127. ample Retrieve the REVCON file and rename it as CONFIG for the TAD run In principle this equilibration can be skipped and a TAD simulation started right away with a suitable equilibration period at the start but it is probably wiser to do this stage beforehand and make sure the system behaves properly at this temperature 2 Set up the TAD simulation using the directives in the CONTROL file as follows a b Q Nr Set the tad directive followed by records defining the operating conditions Define the energy units for the TAD parameters e g units s where s is one of eV kcal kJ or K signifying electron volts kilo cals per mole kilo joules per mole or Kelvin respectively No units directive means DL POLY internal units apply Forces are in chosen energy units per Angstrom Set the size of the simulation TAD block i e the number of time steps between structure optimisations e g num_block 500 Set the number of configurations between each write of a tracking configuration file This should be an integer divisor of the TAD block number e g num_track 10 Set the blackout period in time steps following a transition detection e g blackout 200 A blackout period is intended to stop the program recording transitions that are corre lated with a previous one These are classified as ignored transitions Set the catch radius i e the minimum distance in Angstroms any atom may be displaced in the minimis
128. an 3 or 4 iterations are needed for convergence At each step the constraint lat At I 1 2 282 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 16 In addition to the quaternions it requires quaternion momenta defined by Po qo q q G3 0 _ Le P gt 4 da q pen 2 283 p2 d 43 wm q LyyyWy P3 qa qa q go 1 20 and guaternion torgues defined by Yo do q q2 G3 0 T B gt 1 _ 9 q1 qo 43 Q2 Tx 2 284 T 03 qo q Ty T3 d 2 a 4 z STFC Section 2 5 It should be noted that vectors p and Y are 4 component vectors The quaternion momenta are first updated a half step using the formula p t p t At rcs 2 285 Next a sequence of operations is applied to the quaternions and the quaternion momenta in the order e s 6t 2 e La 6t 2 ef St e Lz 6t 2 ets 6t 2 2 286 which preserves the symplecticness of the operations see reference 18 Note that t is some submultiple of At In DL_POLY_2 the default is At 109t The operators themselves are of the following kind ciL 6t q cos Gg tj sin dt Pr q ey cos Cx t p sin Cx t Psp 2 287 where Py is a permutation operator with k 0 3 with the following propert
129. and the job time are indicated in the above script 7 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 instructions in the Java archive file GUL 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 7 1 1 6 select select is a macro enabling easy selection of one of the test cases It invokes the unix commands cp data TEST 1 2 CONTROL CONTROL cp data TEST 1 2 FIELD FIELD cp data TEST 1 2 CONFIG CONFIG 172 STFC Section 7 1 if e data TEST 1 2 TABLE then cp data TEST 1 2 TABLE TABLE else if e data TEST 1 2 TABEAM then cp data TEST 1 2 TABEAM TABEAM endif 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 character string LF VV RB or CB according to which algorithm leapfrog LF velocity Verlet VV RB rigid body minimisation or CB constraint bond minimisation is required This macro sets up the required input files in the execute sub directory to run the n th test case 7 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 if e data TEST 1 then mkdi
130. angle forces improper dihedral angle forces 3 The atomic force arrays are summed globally over all nodes 4 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 23 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 Every atom in the simulated system is assigned a unique index number from 1 to N 2 Every intramolecular bonded term U ype 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 keypype Ntypes itype carries the indices of the specific atoms involved in the potential term labelled itype The dimension type will be 2 3 or 4 if the term represents a bond angle or dihedral 4 The array keytype Ntypes itype is used to identify the atoms in a bonded term and the ap propriate form of interaction and thus to calculate the energy and forces Each processor is assigned the independent task of evaluating a block of Int Niotar Nnodes interactions The same scheme works for a
131. ansitions has a system activation energy that is below Ebias i e N E lt Ebias Vmin where N is the number of atoms in the system this represents a violation of the condition in equation 5 6 which means the observed diffusion path is not a valid representation of the original system The simulation should be repeated with a lower value of Epjas If the required number of time steps has not been reached the simulation can be restarted from the REVCON REVIVE and HYPRES files renaming them as CONFIG REVOLD and HYPOLD for the purpose and setting the directive restart with no qualifier in the CONTROL file Use the DL_POLY Java GUI to plot the system energy and temperature for the whole of the simulation Apart from the equilibration period these should hold their values within normal thermodynamic fluctuation even if transitions have occured If they do not the system has probably not been equilibrated adequately to begin with in which case the simulation should be started again Check that all the new states the program found are present in the BASINS directory Examine them using the DL_POLY Java GUI There may be signs of imperfect minimi sation atoms not quite on lattice sites etc but this is not a problem in this instance More accurate NEB calculations can be performed later see section 5 6 Check that the profiles for all the reported transitions have been written in the PRO FILES directory These record the chang
132. are given by Euler s equations T de aaa Wr A Lyy 1z2 y z TE T a gt AA iy Ta Ine ele 2 276 Ly E T 2 2 A A Wy T lee Ly Oxy The vector 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 67 STFC Section 2 5 is necessary to integrate equations 2 276 simultaneously with an integration of the quaternions describing the orientiation of the rigid body The equation describing this is do do q Q 43 0 aj_1ja w B q r 2 277 q2 qd 43 do q Wy d3 da 2 q Q We Rotational motion in DL_POLY_2 is handled by two different methods For LF implementation the Fincham Implicit Quaternion Algorithm FIQA is used 15 The VV implementation uses the NOSQUISH algorithm of Miller et al 16 The LF implementation begins by integrating the angular velocity equation in the local frame At 2 The new quaternions are found using the FIQA algorithm In this algorithm the new quaternions 1 O t 3 o t Atl 7 2 2 278 are found by solving the implicit equation g t At alt S QO QuE ADAE At 2 279 where 0 0 and Ola is qo TU 702 43 Q Liam qd 83 42 2 280 q2 43 qo g 43 Q2 q1 qdo The above equation is solved iteratively with alt At q t At Qla t Ji t 2 281 as the first guess Typically no more th
133. array in 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 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 more processors or a machine with larger memory per processor 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 co
134. as not been defined in the FIELD file Action Locate the offending four body force potential in the FIELD file and add the required cutoff Re submit 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 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 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 molecular unit Consequently DL_POLY_2 will abandon the job if this is found to be the case 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 ap propriate 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
135. asin and any new basins found TAD only and the atomic coordinates of the current basin taken at the last check point such as the end of the last BPD orTAD block 5 5 0 2 The EVENTS File The EVENTS file is a text file that reports the results of actions taken by the hyperdynamics routines Each record in the file specifies a particular kind of event The possible events described are as follows Note that the real variables specified in this file are in units specified by the user 1 Blackout period reset BLK n1 n2 where e nl is the time step at which a blackout period was initiated e n2 is time step at which the new blackout period will end TAD only 2 Equilibration period reset EQL n1 n2 where e nl is the time step at which the equilibration period was reset e n2 is time step at which the new equilibration period will end 3 Minimisation completed MIN n1 n2 n3 n4 rl r2 r3 where e nl is the time step at which the minimisation commenced integer e n2 is number of cycles required by the minimiser to converge integer e n3 is the BPD TAD block for which the minimisation took place integer e n4is the optimisation convergence criterion key O for forces 1 for energy 2 for position integer e rl is the convergence tolerance used by the minimiser real e 12 is the energy of the minimised configuration real e 13 is the the convergence actually achieved by the minimiser real Users should note that a final conv
136. at you correctly specify the pair potentials in the FIELD file indicating which ones are to be presented in the TABLE file Then check the TABLE file to make sure all the tabulated potentials are present in the order the FIELD file indicates Message 24 error end of file encountered in TABLE file This means the TABLE file is incomplete in some way either by having too few potentials included or the number of data points is incorrect Action Examine the TABLE file contents and regenerate it if it appears to be incomplete If it look intact check that the number of data points specified is what DL_POLY_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 speci fied 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 191 STFC Section C 0 Message 26 error cutoff smaller than EAM potential range DL POLY 2 has detected an inconsistency in the definition of the EAM potential namely that the user is not using the correct potential range Action Look up the correct range for this potential and adjust t
137. ate is replaced whenever a new state is found In this respect the reference state follows the diffusion path This is a clear distinction from TAD 3 We repeat again the important message that if any of the transitions reported by PBD has an activation energy that is below the value of the bias term Epjas i e N E lt Epvias Vmin this represents a violation of the condition in equation 5 6 which means the observed diffusion path is not a valid representation of the original system The simulation should be repeated with a lower value of Epjas 5 3 5 Exploring Configurational Space Running DL POLY 2 under the BPD option is useful for simply exploring configurational space This has a number of uses 1 Equilibration at a given temperature is quicker and thermodynamic averages can be obtained with greater reliability 2 It is possible to observe configurations which are difficult to obtain under normal conditions perhaps because they are far from the starting state and the system has slow relaxation times Such configurations may be important from a mechanistic viewpoint 3 The trajectory of the system evolves faster which means that movies of the simulation can show the motions of the system on a reasonable time scale This option is activated in the CONTROL file by using the single line directive bpd dyn fi f2 s where f is the value of the required bias Epias f2 is the required value of the operating potential min
138. atomic index etc 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 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 117 STFC Section 4 1 tether key ad tethering potential key see table 4 11 index integer atomic index variable 1 real potential parameter see table 4 11 variable 2 real potential parameter see table 4 11 variable 3 real potential parameter see table 4 11 variable 4 real 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 kr rhrm Restraint k re U r kr CLT U skr2 kre r re T gt To quar Quartic k k k U r r k r k rt 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 molecul
139. available in DL_POLY_2 are as follows 1 Harmonic harm U 6ijkn sh isin boy 2 57 23 STFC Section 2 2 2 Harmonic cosine hcos k U dijkn 5 cos bijkn cos 60 2 58 3 Planar potential plan U dijkn A 1 cos Qijtn 2 59 In these formulae ijkn is the inversion angle defined by T e Y WwW Pijkn cos 22a 2 60 Tij Ukn with and the unit vectors tig fir E Cet Gal rn E Bint 2 62 As usual Tij Tj T etc and the hat 7 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 j n may be written as a y2 A 5211 2 Tij Formally the force on an atom arising from the inversion potential is given by o A E 2 64 with being one of i j k n and a one of x y z This may be expanded into o 1 0 Sl ijkn G U ijkn X ar 6 jk ERI OPijkn 6 jk a y2 a 3211 2 A rn rij rn 2 65 Or te Following through the extremely tedious differentiation gives the result 1 o cos Pijkn a 1 de CALA nm NRO Op des ish dpe y s ri Lij han in Caz Bin On Tij TijWkn i A e 945 b E a j Lij Ben Wen Ea Tik r Tij l r Tik kn 2 nli a Tik re rij Up ry
140. b 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 all internal accumulators timestep included to zero 3 2 4 Optimising the Starting Structure The preparation of the initial structure of a system for a molecular dynamics simulation can be difficult It is quite likely that the structure created does not correspond to one typical of the equilibrium state for the required state point for the given force field employed This can make the simulation unstable in the initial stages and can even prevent it from proceeding For this reason DL_POLY_2 has available a selection of structure relaxation methods Broadly speaking these are energy minimisation algorithms
141. b_module f coulomb_module f neu_coul_module f coulomb_module f neu_coul_module f coulomb_module f utility_module f basic_comms f serial f basic_comms f serial f parse_module f setup_module f angles_module f site_module f bonds_module f shake_module f core_shell_module f dihedral_module f external_field_module f four_body_module f inversion_module f metal_module f hyper_dynamics_module f pmf_module f rigid_body_module f tersoff_module f 252 STFC Section D O define_tethers define_three_body define_units define_van_der_waals diffsno0 diffsn1 dihfrc dlpfft3 duni eamden ele prd energy unit ensemble selection erfcgen error ewaldi ewald2 ewald3 ewald4 ewald_selection ewald_spme exclude exclude_atom exclude_link excludeneu exitcomms exitcomms extnfld fbpfre fcap findstring fldscan force manager forces forcesneu forgen fortab freeze fsden gauss gdsum gdsum getcom getkin getkinf getking getkinr getkins getkint subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine function subroutine subroutine function 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
142. cannot be replaced by a smaller one the user must consider using more processors or a machine with larger memory per processor Message 1940 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 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 configuration 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 1951 error no shell dynamics algorithm specified The user has failed to specify which of the available shell dynamics algorithm is to be used in the simulation Options include adiabtic shells and
143. cation of nptqvv_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 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 allocation of nptqvv_h2 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 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 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
144. ccession it implies that there is some correlation creeping into the resetting of the system back into the starting state This however is harmless as the accumulated simulation time is reset back to the restart state after each transition and so does not affect the time of the later transition to a new state 3 Note that in a TAD simulation the reference state is always the same The reference state does not follow the diffusion path as it does in BPD 4 It is useful to determine which atoms have relocated during a transition The program bsncmp f in the utility directory may be used for this purpose It is designed to compare start and end configurations in the BASINS subdirectory and list the atoms that have changed location 5 5 DL POLY 2 Hyperdynamics Files The DL_POLY_2 BPD and TAD options generate a potentially large number of files in addition to those normally produced and described in Chapter 4 Some are sufficient in number to warrant creation of additional sub directories of the DL_POLY execute sub directory These files are as follows 1 HYPRES the hyperdynamics restart file which stores unformatted data to permit contin uation of an unfinished BPD or TAD simulation It is created in the execute sub directory This file becomes the HYPOLD file which is used in restarting a BPD or TAD simulation 2 EVENTS a summary of events that have occurred in the course of a hyperdynamics simu lation one record per eve
145. ce There are comments in the source code which provide guidance for applications on Cray and IBM computers which use the routines CCFFT3D and DCFT3 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 STFC Section 1 3 2 The version number or date of production 3 A brief description of the function of the subroutine 4 A copyright statement 5 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 m 6 logical and logical arrays Character and character arrays Integer real and complex Integer arrays real and complex arrays This is admittedly arbitrary but it really does help with error detection 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 molec
146. ce The user is at liberty to chose any value Epias gt Vmin which is useful for configurational sampling but for hyperdynamics satisfying the Voter condition 5 6 Etias must not exceed the system configuration energy at any saddle point representing an escape route from a potential basin Finally it should be noted that simulations performed under the influence of a bias potential naturally do not return system averages corresponding to the thermodynamic state of the original system at the specified temperature and pressure The calculation of the true thermodynamic averages requires a correction in the form of a weighted average 63 The true thermodynamic average lt A gt of a property A is thus given by N A Ae Wvias E gt bias N lt e6Wiias It gt bias lt A gt 5 10 Where the ensemble averages are obtained in the biased system When running the BPD options DL POLY 2 calculates all system averages in this way 5 3 2 Running a BPD Simulation Two ways of running bias potential dynamics are available in DL POLY 2 The first is referred to as Full Path Kinetics since it attempts to reproduce a full description of the diffusion path with the associated activation energies This is described in section 5 3 3 The second is configurational sampling which exploits BPD to explore the range of structural states available to a system which need not necessarily be in the solid state It may also be used to impro
147. cessor 244 STFC Section C 0 Message 2020 error failed allocation of nptvv_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 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 by 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
148. chemical bond potentials in the simulated system as a whole This number is a combination of the number of molecules and the number 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 192 STFC Section C 0 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 possibility of increasing the heap size for your application Talk to your systems support people for
149. cros 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 Contents THE DL POLY 2 USER MANUAL About DL POLY 2 Disclaimer c es Acknowledgements Manual Notation Contents List of Tables List of Figures 1 Introduction 1 1 The DL POLY Packape o caco saaie daei he whee k des 1 2 Fu nchionalty es 6a 3 Pe eh be deo a hee Bee Se ha SSS 1 2 1 Molecular Systems c soo se et s omo moade a daaa ee ee es 1 22 The DL POLY 2 Force Field 4 cocos o ocat phe ee eR a 1 2 3 Boundary Conditions 2 6 40 a4 4 a a eR a a h 1 2 4 The Java Graphical User Interface is L amp p E is Programming Style conecta Re e bow a e a Pg ee E a da a Ll Progamming Language sio e toros Bobo A eai i aoe A eiaa 1 3 2 Memory Management 1 3 3 Target Computers os s atat d p ee ek ew be eae a ba ee 134 Version Control System CVS lt ac o sa ca 40534404 S544 045 pp 1 3 5 Required Program Libraries a s ss sosa a socs a PAE a 29043000040 1 3 6 Internal Documentation es i a sa misa be ae eR ee k YO 1 3 7 Subroutine Function Calling Sequences o o e 138 FORTRAN Parameters s ses iao 42 s ee ae Da ke RE a k 1 3 9 Arithmetic Precision lt s s s es cesar Re Re E ee ES L310 UNAS k EEG RE Re Dee Rew td Bae e ade bas 1 3 11 Er
150. cs TAD 62 both of which were conceived by Voter et al though the implementation of BPD in the program uses the bias potential devised by Hamelberg Mongan and McCammon 63 which is simpler to use In passing it is useful to note that BPD can be used to improve configurational sampling in systems other than solids and this facility has been retained in the DL_POLY_2 implementation see section 5 3 5 E Erin Figure 5 1 Model Potential Energy Surface The potential energy surface of a solid is characterised by deep energy basins such as Emin representing the various structural states Escape to other states i e diffusion must go via saddle points on the surface indicated by points E and Ey The energy differences Ei Emin or E2 Emin represent the activation energies E required to enable escape via the respective saddle points Thermal excitation alone is insufficient to achieve escape in a reasonable time The basic problem in simulating diffusion in solids is that each possible structure of the system is trapped in a deep basin in the potential energy surface see figure 5 1 representing a particular state For diffusion to occur the system must become sufficiently thermally excited to achieve the activation energy E necessary to escape In dimensions higher than 1 E represents a saddle point on the potenial energy surface Special techniques are required to accelerate the escape and achieve a
151. cules 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 Science and Technology Facilities Council STFC 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 workstations 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 usefully 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 new developments and discove
152. d 193 STFC Section C 0 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 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 dimensioned 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
153. d 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 GUl is an integral component of the DL_POLY_2 package and is available on exactly the same terms See 9 1 2 5 Algorithms 1 2 5 1 Parallel Algorithms DL_POLY_2 exclusively employs the Replicated Data parallelisation strategy 10 11 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 12 In the leapfrog scheme a parallel version of the SHAKE algorithm 13 11 is used for bond constraints and a similar adaptation of the RATTLE algorithm 14 is implmented in the velocity Verlet scheme Rigid body rotational motion is handled under the leapfrog scheme with Fincham s implicit quaternion algorithm FIQA 15 For velocity Verlet integration of rigid bodies DL POLY_2 uses the NOSQUISH algorithm of Miller et al 16 Rigid molecular species linked by rigid bonds are handled with an algorithm of our own devising called the QSHAKE algorithm 17 which has been adapted for both leapfrog and velocity Verlet schemes NVE NVT NPT and NoT ensembles are available with a selection of thermostats and barostats The velocity Verlet versions are based on the reversible integrators of Martyna et al
154. d by a smaller one the user must consider using more processors or a machine with larger memory per processor 233 STFC Section C 0 Message 1470 error failed allocation of density array 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 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 error 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 arra
155. d 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 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 split 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 i
156. d to its interfaces and programming style and it is adequately documented STFC Preface DISCLAIMER Neither the STFC 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 i STFC Preface DL POLY 2 ACKNOWLEDGEMENTS DL POLY 2 was developed under the auspices of the Science and Technology Facilities Council 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 Maurice Leslie contributed the NOSQUISH rotational algorithm at the heart of many of the rigid body routines The hyperdy namics algorithms in DL_POLY_2 were developed in a collaboration with Duncan Harris and John Harding iii STFC Preface Manual Notation In the DL_POLY Manual and Reference Manual specific fonts are used to convey specific mean ings 1 Ze directories itallic font indicate unix file directories ROUTINES small capitals indicate subroutines functions and programs ma
157. d values natms integer Number of atoms in file engcfg real Configuration energy in DL_POLY units record 3 omitted if imcon 0 cell 1 real x component of a cell vector cell 2 real y component of a cell vector cell 3 real z component of a cell vector record 4 omitted if imcon 0 cell 4 real x component of b cell vector 106 STFC Section 4 1 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 a8 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 xx 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
158. ded 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 Finnis Sinclair and embedded atom type density dependent potentials for metals 3 4 The Tersoff density dependent potential for covalent systems 5 The parameters describing many of these these potentials may be obtained for example from the GROMOS 6 Dreiding 7 or AMBER 8 forcefield which share functional forms It is rela tively easy to adapt DL_POLY_2 to user specific force fields Note that DL POLY 2 does not have its own official force field 1 2 3 Boundary Conditions DL POLY 2 will accommodate the following boundary conditions 1 None e g isolated polymer in space Cubic periodic boundaries Orthorhombic periodic boundaries Parallelepiped periodic boundaries Truncated octahedral periodic boundaries Rhombic dodecahedral periodic boundaries Slab x y periodic z nonperiodic Hexagonal prism periodic boundaries These are describe in detail in Appendix B STFC Section 1 3 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 programming environment is free an
159. duces the basin depth making transitions more likely To preserve the kinetic pathway of the original system the bias potential must be less than the saddle points Ej and Es and for molecular dynamics purposes ideally should join continuously to the normal system potential see text where A represents state A simulated with the bias potential present With this condition satisfied for all possible transitions a simulation will reproduce the diffusional path obtained in the original system but at an accelerated rate An early difficulty with BPD was defining the bias potential However a particularly convenient form has been devised by Hamelberg et al 63 which has the form Ebias VA a Ebias gt V RY Wbias RN H Etias V RM 5 7 where a is a constant that controls the curvature of the bias potential see below Ebias is a fixed potential energy level above which the bias potential Woias RY becomes zero and the unbiased potential is restored This is controlled by H x a Heaviside function which is zero if the argument x lt 0 and 1 if x gt 0 Thus setting Ebias correctly provides a means to preserve the structure of the saddle points of the original surface Note however that the user must determine a safe value for this A value of Erias set above the value of the activation energy E anywhere on the surface invalidates Voter s condition 5 6 Using the definition of the bias potential 5 7 it is
160. dw record 12 zdens Optional z density array mxrdf xmxsvdw 4 1 4 2 Further Comments Note that recompiling DL_POLY_2 with a different DL_PARAMS INC 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 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 i10 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 126 STFC Section 4 1 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 orde
161. e tstop is made see below When the simulation reaches the calculated stopping time it is terminated 150 STFC Section 5 4 When the simulation has ended the transition with the shortest determined occurence time 0 at Tiow indicates the state to which the system would have transformed in a molecular dynamics simulation at that temperature This new state becomes the starting point for a new high temperature simulation of the system exploring transitions from this state to futher new states By this procedure after sufficient sampling of states the true low temperature evolution of the system may be determined The stopping time mentioned above is the time at which the high temperature simulation is halted Ideally this is defined with a high probability that no more significant transitions will be found This is determined from the history of the TAD simulation itself Voter et al provided a prescription of this 62 It begins by defining for a supposed undiscovered escape route a very small probability 6 that after the time tstop the system is still in state A This probability must chosen small enough to give confidence that the awaited transition has had sufficient time to occur 6 may be determined from s k exp kt dt 5 17 tstop from which it follows that 1 log 5 tstopk 5 18 and hence combining this with 5 14 1 x log gt tstopVmin exp Ein kB high 5 19 where Vmin and E in are th
162. e It is also possible inadvertently to over constrain a molecule e g by defining a methane tetrahedron to 65 STFC Section 2 5 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 YX mj 2 264 j 1 where m is the mass of an atom and the sum includes all sites Nsites in the body The position of the rigid unit is defined as the location of its centre of mass R 1 Nsites R r Y mjr 2 265 j 1 where r is the position vector of atom j The rigid body translational velocity V is defined by 1 Nsites V T 2 7 2 266 j 1 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 R Y i 2 267 j l where f is the force on a rigid unit site A rigid body also has
163. e The key statement in this context in the qsub commmand which submits the gopoly script described above This statement may be replaced by the equivalent batch queuing command for your machine The text of supa is given below bin csh set n 1 set m 2 set TYPE LF VV CB RB while n lt m if e TEST n mkdir TEST n cd TEST n echo TEST n foreach typ TYPE if e data TEST n typ then if e typ mkdir typ cd typ cp data TEST n typ CONTROL cp data TEST n typ CONFIG cp data TEST n typ FIELD if e data TEST n typ TABLE cp data TEST n typ TABLE if e data TEST n typ TABEAM cp data TEST n typ TABEAM qsub gopoly cd endif end Ed sf set n expr n 1 end This macro creates working TEST directories in the execute sub directory one for each test case invoked Appropriate sub directories of these are created for leapfrog LF velocity Verlet VV 174 STFC Section 7 1 rigid body minimisation RB and constraint bond minimisation CB Note that supa must be run from the execute sub directory supa requires two arguments supa n m where n and m are integers defining the first and last test case to be run 175 Bibliography 13 14 15 16 17 18 19 20 Smith W and Forester T 1996 J Molec Graphics 14 136 3 Smith W 1987 Molecular Graphics 5 71 3
164. 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 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 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 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 23
165. 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 requires the following 1 the reciprocal space terms are calculated only for the first two timesteps of the multi step 72 STFC Section 2 6 2 the contribution to the reciprocal space terms arising from primary interactions are imme diately subtracted leaving only the long range components This is done in real space by subtracting erf terms 3 the 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 Waal
166. e 4 1 1 Message 490 error PMF parameter mxpmf too small in passpmf The bookkeeping arrays have been exceeded in PASSPMF 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 system 223 STFC Section C 0 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 pymfunpack The PVM routine PVMFUNPACK has returned an error It is invoked by the routine CRECV Action Check your system implementation of PVM Message 504 error cutoff too large for TABLE file The requested cutoff exceeds the information in the TABLE file
167. e 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 re sult if the condition is violated Do not confuse this error with that 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 195 STFC Section C 0 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 f
168. e 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 exe cutable 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 routines to permit this Message 516 error repeat of impact option specified More than one impact option has been specified in the CONTROL file Only one is allowed Action Remove the offending impact directive from the CONTROL file and rerun 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 225 STFC Section C 0 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 syste
169. e 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 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 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 219 STFC Section C 0 Message 453 error four body potential cutoff undefined The cutoff radius for a four body potential h
170. e Tersoff potential 5 is designed to reproduce the effects of covalency in systems composed 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 a8 key a4 variable 1 real variable 2 real variable 3 real variable 4 real variable 5 real potential 1 record 2 variable 6 real variable 7 real variable 8 real variable 9 real variable 10 real variable 11 real atom type potential key see Table 4 16 potential parameter potential parameter potential parameter potential parameter see Table 4 16 see Table 4 16 see Table 4 16 see Table 4 16 cutoff range for this potential A 4 16 potential parameter potential parameter potential parameter potential parameter potential parameter potential parameter 123 see Table 4 16 see Table 4 16 see Table 4 16 see Table 4 16 see Table 4 16 see Table 4 16 STFC Section 4 1 potential n record 2n 1 potential n record 2n cross term 1 record 2n 1 at
171. e and conjugate gradient optimisation proceeds to zero force convergence 167 STFC Section 6 1 6 1 1 30 Test Case 30 Zero Kelvin structure optimisation of DNA The DNA structure of Test Case 10 1260 atoms is here placed in a vacuum and a zero Kelvin optimisation is applied to reduce the overall system energy The smoothed particle mesh method is used to handle the electrostatics 6 1 1 31 Test Case 31 Linear molecule fluid NPT Hoover simulation of a fluid consisting of 675 linear molecules parameters approximate a polyacetylene chain A 6 site rigid body is used to represent the molecules 4050 atoms NPT ensemble 6 1 1 32 Test Case 32 TAD Simulation of Diffusion in Solid Argon The TAD method is applied to Lennard Jones argon A crystal of 255 argon atoms FCC lattice plus one vacancy is simulated in the NVE ensemble 6 1 1 33 Test Case 33 BPD Simulation of Diffusion in Solid Sodium Chloride Bias potential dynamics is applied to a crystal of sodium chloride with the rocksalt structure NVE ensemble 998 ions are present and two vacancies in a neutral structure BPD is used to investigate the diffusional hops and determine the activation energies 6 1 2 Benchmark Cases These represent rather larger test cases for DL POLY 2 that are also suitable for benchmarking the code on large scale computers They have been selected to show fairly the the capabilities and limitations of the code 6 1 2 1 Benchmark 1 Simulation of m
172. e direct Coulomb sum is sometimes necessary for accurate simulation of isolated nonpe riodic systems It is not recommended for periodic systems The interaction potential for two charged ions is 1 1 U rij 14 2 161 ATEO Tij with g the charge on an atom labelled and r j the magnitude of the separation vector T Tj r The force on an atom j derived from this force is 1 ig Tj 2 162 i Areo rg S with the force on atom 7 the negative of this The contribution to the atomic virial is 1 1 Wea 2 163 dr Tij which is simply the negative of the potential term The contribution to be added to the atomic stress tensor is tz 2 164 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 2 4 3 Truncated and Shifted Coulomb Sum This form of the Coulomb sum has the advantage that it drastically reduces the ranged of electro static 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 Ur e L 2 165 4166 Tig Teut with qe the charge on an atom labelled reut the cutoff radius and rj the magnitude of the separation vector Tij Cy io The force on an atom j derived from this potential within the radius reyz is
173. e glass temperature 1000 0 pressure 0 0000 ensemble nve integrator leapfrog steps 500 equilibration 200 multiple 5 scale 10 print 10 stack 100 stats 10 rdf 10 timestep 0 0010 primary 9 0000 cutoff 12 030 delr 1 0000 rvdw 7 6000 ewald precision 1 0E 5 print rdf job time 1200 0 close time 100 00 finish 98 OSTFC Section 4 1 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 identification of the file e The last record is a finish directive which marks the end of the input data Between the header and the finish directive a wide choice of control directives may be inserted These are described below 4 1 1 2 The CONTROL File Directives The directives available are as follows directive meaning all pairs use all pairs for electrostatic calculations cap f cap forces during equilibration period fis maximum cap in units of kT A default f 1000 close time f set job closure time to f seconds collect include
174. e in configuration energy as a function of reaction coordinate or diffusion path Plot these using the DL_POLY Java GUI Use the GUI spline option to get a better idea of what the profiles look like Take special note of any double or multiple maxima The transition is considered to end at the first minimum in these cases It follows that the activation energy for the second peak is not available in this case but it can be obtained later by running the NEB facility independently for the states concerned see section 5 6 It is useful to determine which atoms have relocated during a transition The program bsncmp f in the utility directory may be used for this purpose It is designed to compare start and end configurations in the BASINS subdirectory and list the atoms that have changed location 5 3 4 Things to Be Aware of when Running Full Path Kinetics BPD 1 Choose the catch radius carefully where possible basing it on nearest neighbour distances obtained from the parent crystal A consequence of using too large a catch radius is that transitions that require a short hop in atom positions may be missed during a run Such misses make it difficult to reconstruct the reaction path and in particular cause the NEB calculation to crash since there is no simple path between the reference structures 1 Assuming just one atom unergoes the transition 147 STFC Section 5 4 2 Note that in a BPD simulation the reference st
175. e may now be entered beginning with the name of molecule record and ending with the finish directive The cycle is repeated until all the types of molecules indicated by the molecules directive have been entered The user is recommended to look at the example FIELD files in the data directory to see how typical FIELD files are constructed 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 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 ad potential key See table 4 12 118 STFC Section 4 1 variable 1 real variable 2 real variable 3 real variable 4 real variable 5 real potential parameter see table 4 12 potential parameter see table 4 12 potential parameter see table 4 12 potential parameter see table 4 12 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 Table 4 12 Definition of pair potential functions and variables key potential type Variables 1 5 functio
176. e 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 Com pilation of this is simple and requires running the javac compiler and the jar utility Details for these procedures are provided in the GUI manual 9 6 To run the executable for the first time you require the files CONTROL FIELD and CON FIG and possibly TABLE if you have tabulated potentials 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 option ally 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 appli cations However it sometimes happens that additional modifications may be necessary 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 occurrences of this are NPT and NST simulations or simulations where the local density on the MD cell may significantly exceed the mean density of the cell systems with a vacuum gap for example Under these circumstances arrays initally allocated may be insufficent In which case DL_POLY_2 may report a
177. e of the routines SRFRCE SR FRCE_RSQ and SRFRCENEU The long ranged corrections are calculated by routine LRCORRECT The calculation makes use of the Verlet neighbour list described above 28 STFC Section 2 3 2 3 2 Three Body Potentials The three body potentials in DL_POLY_2 are mostly valence angle forms They are primarily included to permit simulation of amorphous materials e g silicate glasses However these have been extended to include the Dreiding 7 hydrogen bond The potential forms available are as follows 1 Truncated harmonic thrm U oji Oji 80 exp 78 0 2 94 2 Screened Harmonic shrm Oj 5 Oji 00 expl rig p1 ri pa 2 95 3 Screened Vessal 28 bvs1 U Ojix Sa ap Ul a gt exp rij p1 Tik p2 2 96 4 Truncated Vessal 29 bvs2 jik Ojik 00 T 00 exp ri rix p7 2 97 a U Ojik k 0 5 0 jik 00 Ojik 00 270 gan 5 Dreiding hydrogen bond 7 hbnd U Ojik Drycos 0jix 5 Rro rin 6 Ras T 5 2 98 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 descriptions above There are significant differences in implementation however arising from the fact that the three body potentials are regarded as inter molecular Firstly the atoms involved are defined by ato
178. e prefactor and activation energy respectively of the supposed undis covered escape route Rearranging this gives log 1 0 mi Tanl min ee En kp 5 2 The supposed undiscovered escape route is one which may possesses a low temperature occur rence time that is less than the current working minimum 777 The right side of 5 20 may be approximately determined using equation 5 16 if it assumed that the largest observed value of thigh is close to tstop and the lowest possible low temperature time is close to Mi see figure 5 4 OCC Combining the two equations and rearranging gives too ELO i laja Tiow Thigh on PA Vmin log 1 0 l Voter 62 argues that Vmin is commonly of the order 1012 101 s or 1 10 in DL POLY units and suggests 0 001 as a working value These represent practical working values for approximating tstop 5 4 2 Running a TAD Simulation This section describes the procedure for running a TAD simulation The reader will notice some resemblance to the BPD procedure described in section 5 3 This is intentional for operational reasons but the reader should always be alert to the key differences between the two We recommend the following procedure 1 Run a normal simulation of the system at the high temperature Thigh needed to perform the TAD simulation Make sure the system behaves itself before moving to the next stage 151 STFC Section 5 4 and doesn t melt for ex
179. e the cavity The effective pair potential is therefore 1 y Bora 2 214 Tni qiqn 192 Arg din Tnj 2R 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 qjdn TA 1 2 2 215 The effective pair force on an atom j arising from another atom n within the cavity is given by B The contribution of each effective pair interaction to the atomic virial is W frj J 2 217 and the contribution to the atomic stress tensor is er ar ie 2 218 In DL_POLY_2 the reaction field is handled by the routines COUL3 and COUL3NEU 2 4 10 Dynamical Shell Model An atom or ion is polarisable if it develops a dipole moment when placed in an electric field It is commonly expressed by the equation AE 2 219 where y 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 47 and is known as the adiabatic shell model 51 STFC Section 2 5 In the static shell model a polarisable atom is represented by a massive core and massless shell connected by a harmonic spring her
180. e with n the time step interval between configurations w the z density bin width 4 z the range of z coordinate required 2 2 z 2 A zero perform zero temperature MD run 4 1 1 3 Further Comments on the CONTROL File 1 Users of the hyperdynamics features of DL_POLY_2 should also consult Chapter 5 where additional CONTROL directives specific to this function are described 2 A number of the directives or their mutually exclusive alternatives are mandatory 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 required coulombic forces option d e prim specifying primary forces cutoff if mult gt 2 only cut and delr specifying the short range forces cutoff and Verlet strip 3 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 j
181. eafter 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 45 k 2 220 where qs 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 E gt Laa 12 2 221 with m the atomic mass is well above the frequency of vibration of the whole atom in the bulk system Dynamically the core shell unit resembles a diatomic molecule with a harmonic bond however the high vibrational frequency of the bond prevents effective exchange of kinetic energy between the core shell unit and the remaining system Therefore from an initial condition in which the core shell units have negligible internal vibrational energy the units will remain close to this condition throughout the simulation This is essential if the core shell unit is to maintain a net polarisation In practice there is a slow leakage of kinetic en
182. easy to show that the atomic forces in the biased system are given by 2 L J Epi aE Ebias gt V RN 5 8 When Ebias lt V RN the atomic forces are the same as for the unbiased system The constant a in equation 5 7 plays an important role If it is set to zero then Vpias RY Ebias 1 e the biased system potential 5 4 becomes a flat surface within the basins of the original potential energy surface In this case BPD is equivalent to a technique known as puddle skimming 143 STFC Section 5 3 65 which is a viable method for Monte Carlo simulation but has a disadvantage for molecular dynamics in that whenever Epia V R the atomic forces become discontinuous For dynamics a nonzero value of a is therefore always to be preferred Hamelberg et al 63 give the following prescription for obtaining a Firstly the system is simulated under normal conditions at the required state point and the mean value for the system configuration energy is determined This average value is referred to as Vmin and is used to represent the minimum configuration energy Then a value of Epjgs is chosen that is able to to provide a suitable boost factor as in equation 5 5 a is then defined to be a Ebias Vmin 5 9 This prescription gives a system bias potential 5 4 which is everywhere differentiable with con tinuous forces and usefully retains some semblance of the shape of the original potential energy surfa
183. ection 2 4 The contribution to be added to the atomic stress tensor is given by ot sf 2 174 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 5 Coulomb Sum with Distance Dependent Dielectric As with the previous case this potential attempts to soften the impact of truncating the direct Coulomb sum It also assumes that the electrostatic forces are effectively screened in real systems an effect which is approximated by introducing a dielectic term that increases with distance The interatomic potential for two charged ions is 1 Ud Cia A 2 175 ij Anegelrij Tij with qe the charge on an atom labelled and r the magnitude of the separation vector Lij SS at e r is the distance dependent dielectric function In DL POLY_2 it is assumed that this function has the form e r er 2 176 where e is a constant Inclusion of this term effectively accelerates the rate of convergence of the Coulomb sum The force on an atom 7 derived from this potential is 1 gid Ti 2 177 I 2T p ri e with the force on atom 7 the negative of this The contribution to the atomic virial is which is 2 times the potential term The contribution to be added to the atomic stress tensor is given by Pra 2 179 where a 8 are x y z components The atomic stress tensor is symmetric In DL_POLY_2 these forces are handled b
184. ectors present in the input file CONFIG 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 simula tion cell is compatible with the specifed minimum image algorithm Program termination 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 the enscribing tetragonal simulation cell 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 potential 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 o
185. ed 4 Steps 2 and 3 are repeated until all bondlengths satisfy the convergence criterion This iter ation constitutes stage 2 of the SHAKE algorithm DL POLY 2 implements a parallel version of this algorithm 11 see section 2 6 9 The subrou tine 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 pb db 2 232 where a and 6 indicate the x y z components The atomic stress tensor derived from the pair forces is symmetric 56 STFC Section 2 5 2 5 2 2 RATTLE RATTLE 14 is the VV version of SHAKE It has two parts the first constrains the bondlength and the second adds an 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 a a Pada HH y n A dl 2 233 Note that this formula differs from equation 2 230 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 a
186. ed 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 4 2 2 9 Z Density Profile If both calculation and printing of Z density profiles has been requested by selecting directives 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 the subroutine REVIVE REVCON is the restart configuration file The file is written every ndump time steps in case of a system crash during execution and at the termination of the job A successful run of DL_POLY 2 will always produce a REVCON file
187. ed 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 7 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 58 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 24 No reference is made to the Verlet neighbour list nor the excluded atoms list It follows that atoms involved in the 76 STFC Section 2 6 same three four body term can interact via nonbonded pair 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 37
188. ed structure before it is recorded as a transition e g catch_radius 3 0 Set the NEB spring constant in specified energy units per A2 e g neb_spring 1000 0 in DL POLY units Set the reliability factor for the high temperature simulation For input purposes this is defined as the ratio log 1 9 Vimin see above e g deltad 0 001 Set the low temperature To for the TAD method i e the temperature for which the results are needed in Kelvin e g low_temp 30 0 Select a minimisation option e g force key tol Where key is one of force energy position and tol is the convergence tolerance The recommended tolerance for force option is 1 0 in DL POLY units Close the TAD definition with the directive endtad 3 Set other CONTROL file keywords as follow a The simulation temperature i e the high temperature Thign for the TAD method using the temp directive b Select the restart noscale option if the CONFIG file was pre equilibrated otherwise leave out the restart keyword altogether 152 STFC Section 5 4 c Set the length of the simulation required steps and the equilibration period equil both in time steps The equilibration can be short if the system was pre equilibrated d In setting the job close time it is recommended to set the number to at least 500 times the clock time it takes to do one normal MD time step This is to prevent the program running out of time during a structu
189. ee documentation of the FIELD file Action Correct energy keyword on units directive in FIELD file and resubmit Message 6 error energy unit not specified A units directive is mandatory in the FIELD file This error indicates that DL POLY 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 188 STFC Section C 0 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 simulation 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
190. ee of inaccuracy in the screening function near the radius of cutoff in real space which implies the Hautman Klein Ewald method will not be suffi ciently 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 central 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 con vergence 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 Se
191. efined intervals of usually low temperature dynamics in a cycle of minimisation dynamics minimisation etc which is intended to help the structure relax from overstrained conditions When using the programmed minimisation DL_POLY_2 writes and rewrites the file CFGMIN 4 2 4 which represents the lowest energy structure found during the programmed minimisation CFGMIN is written in CONFIG file format see section 4 1 2 and can be used in place of the original CONFIG file 87 STFC Section 3 3 It should be noted that none of these algorithms permit the simulation cell to change shape It is only the atomic structure that is relaxed After which it is assumed that normal molecular dynamics will commence from the final structure Comments on the Minimisation Procedures 1 The zero temperature dynamics is really dynamics conducted at 1 Kelvin However the dynamics has been modified so that the velocities of the atoms are always directed along the force vectors Thus the dynamics follows the steepest descent to the local minimum From any given configuration it will always descend to the same minimum 2 The conjugate gradient procedure has been adapted to take account of the possibilites of constraint bonds and rigid bodies being present in the system If neither of these is present the conventional unadapted procedure is followed a In the case of rigid bodies atomic forces are resolved into molecular forces and torques The t
192. en 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 VV CB or RB The select macro will copy the appropriate CONTROL CONFIG FIELD and if necessary the TABLE or TABEAM 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 It should be noted that the potentials and the simulation conditions used in the following test cases are chosen to demonstrate functionality only They are not necessarily appropriate for serious simulation of the test systems Note also that the DL_POLY_2 Graphical User Interface 9 provides a convenient means for running and viewing these test cases 6 1 1 1 Test Case 1 KNaSi205 Potassium Sodium disilicate glass NaKSi205 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 6 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 Gaus sian constraints NVT Evans ensemble 6 1 1 3 Test Case 3 An antibiotic in water Valinomycin
193. eneu 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 conditions 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 Standard user response Fix the parameter mxngp 208 STFC Section C 0 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 permitted maximum Do not confuse
194. ep at which a transition was detected but ignored because it was during an equilibration or blackout period integer TAD Only 7 Transition repeated TRR n1 n2 n3 where e nl is the time step at which a transition was detected but it was identified as a repeat and no further analysis was underatken integer e n2 is the identity of the home basin integer e n3 is the identity of the new basin integer TAD Only 5 5 0 3 The CFGBSNnn Files in the BASINS Directory A CFGBSNn file is a text file containing the energy minimised structure of a basin found during the BPD or TAD simulation The number nn rises from 0 to 9999 Internally the format of the file is the same as a CONFIG file see section 4 1 2 though it does not normally contain velocity or force data 157 STFC Section 5 6 5 5 0 4 The CFGTRKnn Files in the TRACKS Directory The CFGTRKnn files have exactly the same format as the CFGBSNnn files The files do not however contain energy minimised structures These files represent consecutive structures written at user defined intervals during the simulation The interval num_track see above is an integer divisor of the number of steps in a BPD or TAD block num_block and the number nn in the file name is modulo max_track where max_track num_block num_track Thus after num_block time steps from the simulation start there are always max_track configurations to search back over to locate the time of a transition
195. er fe g 2a 2 203 In DL POLY 2 the hn s a s functions are derived by a recursion algorithm while the f g 0 functions are obtained by direct evaluation The coefficients a are given by an 1 2n 2 n 2 204 As pointed out by Hautman and Klein the equation 2 196 allows separation of the zi components via the binomial expansion which greatly simplifies the double sum over atoms in te ptal space Thus the reciprocal space part of equation 2 196 becomes Nmax Urecip 5 an 5 Fal g po 1 Ye POZA 9 23n p 9 2 205 a deg A n 0 gx with ce a binomial coefficient and N Zy 9 X ajzhexp ig sy 2 206 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 E Nmaz 1 2n 023 p 9 OZp 9 duj a 2 2 diia Ye Cp 79 du Enel du Nmaz 2 s s Y D andi a 2 2 ij nee 2 207 n 0 L ij ij L where uj is one of j Yj zj and noting for brevity that x and y derivatives are similar OZ 9 TA iggy zh explig sj 0Zp g E 2 Paz erplig si 2 208 J 49 STFC Section 2 4 and 0 2 ratte 2 Za 0 Gee Zij L ij L 2 J 2n4 1 Y Fa an 1 Oz SL Sij L OX Sij L Of an hin Sit L o 2n 1hnlSij15 0 2 209 Oz IL mH ij L antl l j GE Sij L In DL POLY 2 the partial derivatives of hn sij L 0 sit are calculated by a recursion algorith
196. er 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 algorithm which is suitable for rectangular 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 243 STFC Section C 0 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 expande significantly Otherwise the user must locate and adjust the mxcell 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 Re
197. eractions However this is not a universal requirement of all force fields The same consid erations are needed in dealing with charged excluded atoms DL POLY_2 has several subroutines 14 STFC Section 2 2 available for constructing 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 calcu lated using the link cell algorithm 24 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 readers should understand that DL_POLY_2 does recognise molecular entities defined either through constraint 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 rs Ij Figure 2 1 The interatomic bond vector The bond potenti
198. erge_systol f merge_tools f serial f 254 f f f f f f Fh Fh Fh Fh STFC Section D 0 mergel mergel mergel mergel merge4 merge4 merge4 merge4 metal_deriv metdens met rc metgen mettab minimiser mkwd8 molecular_dynamics multiple multiple_nsq multipleneu mynode mynode neb_driver neb_option neb_spring_forces neb_system_forces neutbook neutlst nlist_driver nodedim nodedim nosquish npt_b1 npt_h1 nptq_b1 nptq_b2 nptq_hi nptq_h2 nptqscl_p nptqscl_t nptqvv_b1 nptqvv_b2 nptqvv_h1 nptqvv_h2 nptscale_p nptscale_t nptvv_b1 nptvv_h1 nst_b1 nst_h1 subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine function subroutine subroutine subroutine subroutine function function 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 merge_hcube f merge_systol f merge_tools f serial f merge_hcube f merge_systol f merge_tools f serial f metal_module metal_module metal_module metal_module metal_module driver_module f parse_module f driver_module forces_module forces_module forces_module basic_c
199. ergence value r3 greater than the convergence criterion r1 indicates incomplete convergence 4 Nudged Elastic Band completed NEB n1 n2 n3 n4 rl r2 where e nl is the time step at which the NEB calculation commenced integer e n2 is number of cycles required by the NEB calculation to converge integer 156 STFC Section 5 5 e n3 is the maximum allowed number of cycles integer e n4 is the number of beads in the NEB chain integer e rl is the energy of the home basin starting state configuration real e r2 is the energy of the end basin new state configuration real Users should note that when n2 and n3 are equal this implies that convergence of the NEB chain has not been achieved Note also that the characteristics of the reaction path are given by the subsequent TRA event below 5 Transition detected TRA n1 n2 n3 n4 rl r2 r3 r4 where e nl is the time step at which the transition was first detected integer e n2 is the home basin starting state of the transition integer e n3 is the new basin ending state of the transition integer e n4 is the number or turning points in the transition profile integer e rl is the activation energy obtained from the NEB calculation real e r2 is the observed transition time real e r3 is the calculated extrapolated transition time real e r4 is the calculated stopping time real TAD only 6 Transition ignored TRI n1 where e nl is the time st
200. ergy 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 calculated as described above The forces of the harmonic springs are calculated as described for intramolecular harmonic bonds The relationship between the kinetic energy and the temperature is different however as the core shell unit is permitted only three translational degrees of freedom and the degrees of freedom corresponding to rotation and vibration of the unit are discounted the kinetic energy of these is regarded as zero In DL_POLY_2 the shell forces are handled by the routine SHLFRC The kinetic energy is calculated by CORSHL and the routine SHQNCH performs the temperature scaling The dynamical shell model is used in conjunction with the methods for long ranged forces described above 2 4 11 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 dyna
201. ersions of the code and will 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 The DL_POLY_2 Error Messages Message 1 error PVM NODES unset The code was C preproce
202. ery 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 messages These indicate that the code has detected something that is unusual or inconsistent The detection is non fatal but the user should make sure that the warning does represent a harmless condition 1 4 The DL POLY 2 Directory Structure The entire DL_POLY_2 package is stored in a Unix directory structure The topmost directory is named dl _poly 2 nn where nn is a generation number Beneath this directory are several sub directories sub directory contents srcmod 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 sremod 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 STFC Section
203. es in the makefile The simplest way is to add names to the OBJ_SRC list However for more substantial modifications it is advisable to construct a proper F90 module containing several related subroutines and add this to the OBJ_MOD list 3 2 1 3 Note on Interpolation 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 employs a 3 point interpolation scheme 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 system The parameter mxgrid is defined in the DL_PARAMS INC file and must be set before compilation 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 85 STFC Section 3 2 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
204. es 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 calculations 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 Message 101 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 202 S
205. et 5 53 54 57 Verlet 14 15 28 41 53 55 56 58 60 62 77 Verlet leapfrog 5 53 55 AMBER 4 18 89 angular momentum 67 angular restraints 19 angular velocity 67 barostat 5 69 70 99 Berendsen 65 72 Hoover 61 bias potential dynamics BPD see hyperdynam ics BPD boundary conditions 4 41 82 89 179 cubic 108 hexagonal prism 108 rhombic dodecahedron 108 truncated octahedron 108 CCP5 3 9 charge groups 110 constraints bond 3 5 14 15 55 57 65 66 68 70 77 78 82 83 113 132 Gaussian 44 45 58 PMF 57 114 CVS 6 7 direct Coulomb sum 41 42 distance dependent dielectric 44 51 99 105 Fennel and Gezelter method 43 truncated and shifted 42 Wolf method 43 distance restraints 17 DLPROTEIN 89 embedded atom potential see potential embedded atom EAM ensemble 5 Berendsen NoT 5 53 55 99 102 104 Berendsen NPT 5 53 54 102 104 Berendsen NVT 5 53 54 99 102 104 canonical 58 Evans NVT 5 53 54 99 102 104 Hoover NoT 5 54 55 102 Hoover NPT 5 53 54 99 102 Hoover NVT 5 53 54 102 microcanonical see ensemble NVE NVE 57 99 102 104 equations of motion Euler 67 rigid body 67 error messages 93 184 Ewald Hautman Klein 41 48 91 100 182 optimisation 90 91 SPME 6 41 46 75 90 101 summation 41 44 46 72 74 75 90 91 100 102 103 Finnis Sinclair potential see potential Finnis Sinclair force field 4 13 15 22 40
206. etallic 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 6 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 6 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 6 1 2 4 Benchmark 4 Simulation of a sodium chloride melt with Ewald sum electrostatics and a multiple timestep al gorithm to enhance performance The system is comprised of 27000 atoms and runs on 8 512 processors 168 STFC Section 6 1 6 1 2 5 Benchmark 5 Simulation of a sodium potassium disilicate glass Uses Ewald sum electrostatics a multiple timestep algorithm and a 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 6 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 c
207. etected 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 been 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 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 param
208. eters 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 111 STFC Section 4 1 nrept 1 entries in the CONFIG file are ascribed the atomic characteristics given in the current record The sum of the repeat numbers for all atoms in a molecule should equal the number specified by the atoms directive 4 shell n 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 num bering each atom in the molecule from 1 to the number specified in the atoms directive for this molecule This same numbering scheme should be used for all descriptions of this molecule including the bonds constraints angles and dihedrals entries described below DL_POLY_2 will itself construct the global indices for all atoms in the systems Thi
209. form of the charge array Q 1 l2 3 defined as N Q 1 La 15 u 5 Mn ur 1 ni L1 My luz 2 n2L2 M usj 3 nga L3 j 1 n1 n2 n3 2 191 in which the sums over ni 23 etc are required to capture contributions from all relevant periodic cell images which in practice means the nearest images 3 Approximating the reciprocal space energy Urecip 1 2Voc0 a gt G ki ka ks Qs ka ka 2 192 ko k3 Urecip in which GT is the discrete Fourier transform of the function exp k 4a G ki ko k3 B k1 ko k3 Q k ko ks 2 193 k2 and where B k1 ko k3 b ki 7 b2 k2 bs ka 2 194 and Q k1 ka k3 is the complex conjgate of Q ki ko k3 The function G k1 ko ks is thus a relatively simple product of the gaussian screening term appearing in the conventional Ewald sum the function B k k2 k3 and the discrete Fourier transform of Q k ka k3 4 Calculating the atomic forces which are given formally by OU recip 1 a kk fj Ore Voco 8 5 G k 2 k3 1 oQ k ka ks ore 2 195 STFC Section 2 4 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 BSPC
210. forms The nonbonded three body four body and Tersoff interactions are globally 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 pa rameters 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 to N 2 Every intramolecular bonded term Uiype 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 keyrype Ntype itype carries the indices of the specific atoms involved in the potential term labelled itype The dimension type will be 2 3 or 4 if the term represents a bond valence angle dihedral inversion 4 The array keytype Ntypes itype is used to identify the atoms in a bonded term and the appro priate form of interaction and thus to calculate the energy and forces DL_POLY_2 calculates the nonbonded pair interactions using a Verlet neighbour list 12 which is reconstructed at intervals during the simulation This list records the indices
211. freely available via the DL_POLY website 1 6 Other Information The DL_POLY website http www ccp5 ac uk DL_POLY provides additional information in the form of 1 Access to all documentation 2 Frequently asked questions 3 Bug reports 4 Access to the DL_POLY online forum Daresbury Laboratory also maintains an associated DL POLY 2 electronic mailing list 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 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 It is a good place to contact other users and discuss applications 10 Chapter 2 DL POLY 2 Force Fields and Algorithms STFC Section 2 0 Scope of Chapter This chapter describes the interaction potentials and simulation algorithms coded into DL_POLY_2 12 STFC Section 2 1 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
212. 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 mod ifications are necessary to correct for the excluded intra molecular Coulombic interactions In the real space sum these are simply omitted In reciprocal space however the effects of individual gaussian charges cannot easily be extracted and the correction is made in real space It amounts to removing terms corresponding to the potential energy of an ion due to the gaussian charge on a neighbouring charge m or vice versa This correction appears as the final term in the full Ewald formula below The distinction between the error function er f and the more usual complementary error function er fc found in the real space sum should be noted The total electrostatic energy is given by the following formula y dada er earn n lt j Unj CO 1 ex k 4a U 5 pl e 2 qj exp ik r 2Vo 0 ka a 1 M gt gt o Uam hos dnt heres 2 180 molecules lt m Tom Arey 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
213. g i e begin a new simulation from older run restart job from previous run with temperature scaling i e begin a new simulation from older run reset force tolerance for shell relaxation to f DL POLY units 1 0 default set required vdw forces cutoff to f rescale atomic velocities every n steps during equilibration set shake tolerance to f default 1078 calculate electrostatic forces using shifted coulombic potential damped shifted coulombic force electrostatics with automatic parameter optimisation 0 lt f lt 1 E 4 damped shifted coulombic force electrostatics with user chosen damping parameter f A select Ewald sum for electrostatics with automatic parameter optimisation 0 lt f lt 5 spme sum a k1 k2 k3 stack n stats n steps n temp f trajijk select Ewald sum for electrostatics with a Ewald convergence parameter A 1 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 configurations 101 STFC Section 4 1 j timestep interval between configurations k data level i e variable keytrj see table 4 3 timestep f set timestep to f ps zden n wz calculate the z density profil
214. g from the fact that the four body potentials are regarded as inter molecular Firstly the atoms involved are defined by atom types not specific indices Secondly there are no excluded atoms arising from the four body terms The inclusion of other potentials for example pair 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 33 32 STFC Section 2 3 The calculation of the forces virial and stress tensor described in the section on inversion angle potentials above DL POLY 2 applies no long ranged corrections to the four body potentials The four body forces are calculated by the routine FBPFRC 2 3 5 Metal Potentials The metal potentials in DL_POLY_2 follow two similar but distinct formalisms The first of these is the embedded atom model EAM 34 35 and the second is the Finnis Sinclair model FSM 3 Both are density dependent potentials derived from density functional theory DFT and describe the bonding of a metal atom ultimately in terms of the local electronic density They are suitable for calculating the properties of metals and metal alloys For single component metals the two approaches are the same However they are subtly different in the
215. ghbour list The number 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 103 STFC 16 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 17 Users are strongly advised to study the example CONTROL files appearing in the data sub update of the Verlet list The directive impact is intended to simulate the effects of a high energy atomsic impact such as occurs in radiation damage The user must supply the integer identity of the impacted atom the time step when the impact takes place usually after equilibration the recoil energy of the impacted atom in kilo electron volts and the direction of the recoil i e three components of a unit vector specifying the direction Table 4 1 Internal Restart Key keyres meaning 0 start new simulation from CONFIG file and assign velocities from Gaussian distribution 1 continue current simulation 2 start new simulation from CONFIG file and rescale velocities
216. gorithm 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 Action Place a temp directive in the CONTROL file with the required temperature specified Message 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
217. 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 Declare dependency on module files 180 STFC Section A 0 OBJ_SRC 0BJ MOD 181 Appendix B Periodic Boundary Conditions in DL POLY Introduction DL POLY 2 is designed to accommodate a number of different periodic boundary conditions which are defined by the shape and size of the simulation cell Briefly these are as follows which also indicates the IMCON flag defining the simulation cell type in the CONFIG File see 4 1 2 1 None e g isolated polymer in space IMCON 0 2 Cubic periodic boundaries IMCON 1 Orthorhombic periodic boundaries IMCON 2 0 Parallelepiped periodic boundaries IMCON 3 Truncated octahedral periodic boundaries IMCON 4 Rhombic dodecahedral periodic boundaries IMCON 5 Slab X Y periodic Z nonperiodic IMCON 6 o N Q gl 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 No periodic boundary IMCON 0 Simulations requiring no periodic boundaries are best suited to in vacuuo simulations such as the conformational study of an isolated polymer molecule This boundary condition is
218. he DL POLY cutoff accordingly Message 27 error incompatible FIELD and TABEAM file potentials The user has or has not specified a set of EAM potentials in the FIELD file which are not or are available in the TABEAM file Action Examine the FIELD file Make sure you have correctly specified the EAM potentials Check that these appear in the TABEAM file if required Message 28 error transfer buffer too small in mettab The number of points specifying an EAM potential in the TABEAM file exceeds the default buffer size in METTAB F Action Reset the mxbuff parameter in PARSET F subroutine to accommodate the required array length and recompile Message 29 error end of file encountered in TABEAM file DL_POLY_2 has reached the end of the TABEAM file without finding all the data it expects Action Either the TABEAM file is incomplete or it is improperly defined Check the structure and content of the file with the TABEAM file specification in the manual and fix the error 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 documentation Do not confuse this error with that described by message 31 below Action Standard user response Fix parameter mxtbnd Message 31 error too many chemical bonds in system DL POLY 2 sets a limit on the number of
219. he 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 averages numrdf number of configurations used in rdf averages chit thermostat momentum chip barostat momentum conint conserved quantity for selected ensemble nzden number of configurations used in z density record 2 virtot total system virial vircom rigid body COM virial eta scaling factors for simulation cell matrix elements 9 strcns constraint stress tensor elements 9 strbod rigid body stress tensor elements 9 record 3 125 STFC Section 4 1 stpval instantaneous values of thermodynamic variables mxnstk record 4 sumval average values of thermodynamic variables mxnstk record 5 ssqval fluctuation squared of thermodynamic variables mxnstk record 6 zumval running totals of thermodynamic variables mxnstk record 7 ravval rolling averages of thermodynamic variables mxnstk record 8 stkval stacked values of thermodynamic variables mxstak xmxnstk record 9 xx0 x component of atomic displacement MSD mxatms yy0 y component of atomic displacement MSD mxatms zz0 z component of atomic displacement MSD mxatms record 10 XXS x coordinates of tether points mxatms yys y coordinates of tether points mxatms ZZS z coordinates of tether points mxatms record 11 rdf Optional RDF array mxrdf xmxv
220. he end of the force field data Without this directive DL POLY 2 will abort 124 STFC Section 4 1 Table 4 17 External fields key potential type Variables 1 4 functional formt elec Electric field E Ey E F qEB oshm Oscillating Shear Aln F Acos 2n7 z Lz shrx Continuous Shear A 20 z gt o vg 1 2 A z 2 grav Gravitational Field Gz Gy Gz E m G magn Magnetic Field Hy Hy H F q ux H sphr Containing Sphere A Ro n Rout r gt Reus E A Ro r zbnd Repulsive wall A Zo f zwl zf gt Zof F A z Zo harmonic 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 5 at the end of a job which contains the statistics data REVIVE should be copied to REVOLD before a continuation run commences This may be done by the copy macro supplied in the execute sub directory of DL_POLY_2 4 1 4 1 Format The REVOLD file is unformatted All variables appearing are written in native real 8 represen tation Nominally integer quantities e g the timestep number nstep are represented by the the nearest real number The contents are as follows t
221. he 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 CONTROL file Action Locate the ensemble directive in the CONTROL file and assign a positive value to the time constant Message 468 error r0 too large for snm potential with current cutoff The specified location r0 of the potential minimum for a shifted n m potential exceeds the speci fied 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 221 STFC Section C 0 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 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
222. 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 specified 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 imcon integer periodic boundary key again tstep real integration timestep record ii 3g12 4 for imcon gt 0 cell 1 real x component of a cell vector 129 STFC Section 4 2 cell 2 real y component of a cell vector cell 3 real z component of a cell vector record iii 3g12 4 for imcon gt 0 cell 4 real x component of 6 cell vector cell 5 real y component of b cell vector cell 6 real z component of b cell vector record iv 3g12 4 for imcon gt 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 This is followed by the configuration for the current timestep i e for each atom in the system the following data are included record a a8 il0 2f12 6 atmnam a8 atomic label iatm 110 atom index weight 112 6 atomic mass a m u charge 12 6 atomic charge e record b 3e12 4 XXX real x co
223. hell model 11 Relaxed shell model Some of these techniques can be combined For example 1 3 and 4 can be used in conjunction 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 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 How ever 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 except in the case of the Ewald based methods 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 Tcut If an atomistic scheme is used for the truncation criterion there is no guarantee that the interacti
224. hese 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 unique eight character label defined by the user The pair potential is then defined internally by the combination of two atom labels As well as the numerical parameters defining the potentials DL_POLY_2 must also be provided with a cutoff radius reut which sets a ranged 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 ranged 0 to reut A second array ggg is also calculated which is related to the potential via the formula o G rij Ti g U ris 2 88 ij and is used in the calculation of the forces Both arrays are tabulated in units of energy The use of interpolation arrays rather than the explicit formulae makes the routines for calculating the potential energy and atomic forces very general and enables the use of user defined pair potential functions DL_POLY_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
225. i 162 TT 164 TT 164 T 168 170 bak ee Ble 171 m wh eee 171 176 179 179 182 187 251 259 List of Tables 4 1 4 2 4 3 4 4 4 5 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 2 beta a a bee da od ba So 104 Internal Ensemble Key 2 4444 sp Goa oe Rk a we ek a ow 104 Internal Trajectory Pile Key oos roa De mis k eR ee ee Be ee He 104 Non Donded force Key nck moe k S te oe eo bee owe ce age eB te we Ge 105 CONFIG file key record in ce RR eRe AA 108 Periodic boundary key record 2 Lu ee ee k Eee ee 108 Chemical bond potentials s ss s c sos a 2554 4 need k a a 113 Valence Angle potentials a a a ee 115 Dihedral Angle Potentials ia 4 55 ia sacs aa bana dea A a Da a 116 Diversi n Angle Potentials cos pr aa GO a eg A eG 117 Teth ering potentials 4 5 sa donas a macip poka RA RA k al G 118 Definition of pair potential functions and variables lt a 119 Three body potentials xo c sx m i i eda ee Pe AR ee RE 121 Fourbody Potentials iia mann ae eae he k Be 122 Metal Potential orion dr bo ee eet Pee teed ae A 123 Tersoff Potential 22 44 46 80 54 a ee Bee BG Ee ae 124 External fields oscurecer ma ee Ae SE ee 125 List of Figures A 2 2 2 3 2 4 2 5 2 6 Ll 2 8 3 1 4 1 5 1 5 2 5 3 5 4 Bul B 2 B 3 B 4 B 5 B 6 The interatomic bond vector sec a sa s rasa aoaaa aaa a e e 15 The valence angle and associated vectors sos
226. i step interval activated when n gt 2 no elec ignore coulombic interactions no link do not use link cells for vdw or metal forces no vdw ignore short range non bonded interactions optim energy f optim force f 100 STFC Section 4 1 optim position f pres f prim f print n print rdf quaternion f rdf n w reaction relax structure based on energy force or position f permitted variation tolerance DL POLY units 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 with n the time step interval between configurations w the RDF bin width A Note range Teut select reaction field electrostatics reaction precision fdamped reaction field electrostatics reaction damped f regauss n restart restart noscale restart scale rixtol f rvdw f scale n shake f shift shift precision f shift damped f spme precision f with automatic parameter optimisation 0 lt f lt 1 E 4 damped reaction field electrostatics with user chosen damping parameter f A reset velocities at timestep interval n restart job from end point of previous run i e continue current simulation restart job from previous run with no temperature scalin
227. ias Potential Dynamics o oa 0 0000 eee 142 Doe Runnine a BPO irnulali ii o so s mos so k eon Pe eek ee A ee See a p 144 Dio Full Path Kinetics r be 2 i Shh eee See ee ee S ee BE 144 vii OSTFC Contents 5 3 4 Things to Be Aware of when Running Full Path Kinetics BPD 5 3 5 Exploring Configurational Space o o 5 4 Temperature Accelerated Dynamics o e 5 4 1 Theory of Temperature Accelerated Dynamics 542 Running a TAD Simulation sa ceta k Oe eee oes 5 4 3 Restarting a TAD Simulation lt s sss siara aos da ipa 5 4 4 Things to Be Aware of when Running TAD 5 5 DL POLY 2 Hyperdynamics Files as 5 6 Tidying Up the Results of a Hyperdynamics Simulation 5 6 1 Refining the Results oaoa As 5 6 2 Treatment of Multiple Maxima in the Reaction Path 5 7 Running a Nudged Elastic Band Calculation 5 71 Things to Aware of when Running a NEB Calculation 6 DL_POLY_2 Examples Kal DLPOLY Examples sos sa t aria k a AE oe dia a OLI Test Casts a a a ta bob a 6 1 2 Benchmark Cases c sos zoe k ua a eek ee Re S 7 DL POLY 2 Utilities Tl WMiseellaneous Utilities lt c os scesa p 4 oS S a ae a A k TLL Useful Macros ii a n RE de G ck haa wk Bibliography Appendices A The DL_POLY_2 Makefile B Periodic Boundary Conditions in DL POLY C DL POLY Error Messages and User Action D Subroutine Locations Index vil
228. ider 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 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 238 STFC Section C 0 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 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 caus
229. ies Poq 90 41 92 93 Pia 4 q0 43 42 Pog 42 4q3 q0 q1 Psq q3 q2 q1 90 2 288 and the angular velocity Ck is defined as l T p Pq 2 289 Ck gp Pra Equations 2 286 to 2 288 represent the heart of the NOSQUISH algorithm and are repeatedly applied 10 times in DL POLY 2 The final result is the quaternion updated to the full timestep value i e g t At These equations form part of the first stage of the VV algorithm In the second stage of the VV algorithm new torques are used to update the quaternion momenta to a full timestep At p t At p t 2 At g At 2 290 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 barostat 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
230. ile 1 TARGET The TARGET keyword indicates which kind of computer the code is to be compiled for This must be specifed there is no default value Valid targets can be listed by the make file if the command make is typed without arguments The list frequently changes as more targets are added and redundant ones removed Users are encouraged to extend the Makefile for themselves using existing targets as examples 2 EX The EX keyword specifies the executable name The default name for the executable is DLPOLY X 3 BINROOT The BINROOT keyword specifies the directory in which the executable is to be stored 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 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 different serial and parallel MPI environments so you should find one close to your requirements You must of course be familiar with the appropri ate invocation of the FORTRAN 90 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 remem ber to ensure the appropriate library directories are accessible to you If you require a serial version of the code you m
231. ile than is actually present The probable cause is an incorrect or absent CONFIG file but it may be due to the FIELD file being incompatible in some way with the CONFIG file Action Check contents of CONFIG file If you are convinced it is correct check the FIELD file for inconsistencies Message 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 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 message 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 ter minate 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 Termina tion results if too many are encountered Do not confuse this error with that de
232. imum Vmin and s is one of eV kcal kJ or K signifying the energy unit of the values entered This option runs like a normal DL_POLY_2 simulation except that the system potential is now the biased potential Consequently average system properties are calculated using equation 5 10 It is recommended that the simulation be run with the traject option activated in the CON TROL file so that a HISTORY file is produced This may be further analysed to reveal conforma tional properties or viewed as a movie with appropriate software 5 4 Temperature Accelerated Dynamics 5 4 1 Theory of Temperature Accelerated Dynamics Temperature Accelerated Dynamics TAD was devised by Voter et al 62 Like BPD it is also a combination of molecular dynamics and Transition State Theory TST for first order processes TAD works on the principle that while diffusion in the solid state at a low temperature is often too slow to measure at a higher temperature it may be many orders of magnitude faster However it is normally the case that at different temperatures a system will evolve via different diffusion pathways So to exploit the temperature acceleration successfully special care must be taken to preserve the true mechanistic pathway at the required low temperature This is precisely what TAD does An appropriate model for a first order diffusion process supposes a system trapped in a potential basin state A from which it may escape through thermal excitat
233. in 1223 spc water molecules The temperature is controlled by a Nos Hoover thermo stat while electrostatics are handled by a screened reaction field 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 6 1 1 4 Test Case 4 Shell model of water 256 molecules of water with a polarizable oxygen atom using adiabatic dynamics Temperature is controlled by the Berendsen thermostat while electrostatics are handled by the reaction field method with a charge group cutoff scheme Slab period boundary conditions are used The water molecule apart from the shell is treated as a rigid body NVT Berendsen ensemble 6 1 1 5 Test Case 5 Shell model of MgCl at constant pressure Adiabatic shell model simulation of MgClz Temperature and pressure are controlled by a Berend sen thermostat and barostat An Ewald sum is used with cubic periodic boundary conditions NPT Berendsen ensemble 164 STFC Section 6 1 6 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 6 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 constr
234. in Molecule with 146 SPC Waters UNITS kcal MOLECULES 2 Valinomycin NUMMOLS 1 ATOMS 168 0 16 0000 0 4160 1 OS 16 0000 0 4550 1 HC 1 0080 0 0580 1 C 12 0100 0 4770 1 BONDS 78 harm 31 19 674 000 1 44900 harm 33 31 620 000 1 52600 harm 168 19 980 000 1 33500 harm 168 162 634 000 1 52200 CONSTRAINTS 90 20 19 1 000017 22 21 1 000032 166 164 1 000087 167 164 0 999968 ANGLES 312 harm 43 2 44 200 00 116 40 harm 69 5 70 200 00 116 40 harm 18 168 162 160 00 120 40 harm 19 168 162 140 00 116 60 DIHEDRALS 371 harm 1 43 2 44 2 3000 180 00 harm 31 43 2 44 2 3000 180 00 cos 149 17 161 16 10 500 180 00 cos 162 19 168 18 10 500 180 00 FINISH SPC Water NUMMOLS 146 109 STFC Section 4 1 ATOMS 3 OW HW HW CONSTRAINTS 1 2 1 3 2 3 FINISH VDW 45 C C C CT OW OS OS OS CLOSE 4 1 3 1 Format 0000 0080 0080 0000 0000 63299 0 8200 0 4100 0 4100 0 12000 3 2963 0 08485 3 2518 0 15100 3 0451 0 15000 2 9400 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 a
235. in any random order in TABEAM as their identification is based on their unique keyword defined first in the function s header record The header record is followed by a predefined number of data records as a maximum of four data per record are read in allowing for incompletion of the very last record header record keyword ad type of EAM function dens embed or pair atom 1 a8 first atom type atom 2 a8 second atom type only specified for pair potential functions ngrid integer number of function data points to read in limit 1 real lower interpolation limit in for dens and pair or in density units for embed limit 2 real upper interpolation limit in for dens and pair or in density units for embed function data records number of data records Int ngrid 3 4 data 1 real data item 1 data 2 real data item 2 data 3 real data item 3 data 4 real data item 4 128 STFC Section 4 2 4 2 The OUTPUT Files DL POLY 2 produces up to eight output files HISTORY OUTPUT REVCON REVIVE RDF DAT ZDNDAT STATIS and CFGMIN These respectively contain a dump file of atomic coor dinates velocities and forces a summary of the simulation the restart configuration statistics accumulators radial distribution data Z density data a statistical history and the configuration with the lowest configurational energy Some of these files are optional and appear only when certain options are used Note In addition to the files described
236. ination It is worth considering these operations in turn and to indicate 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 constraint bonds the routine PASSCON is required to process molecular 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 FORGEN which constructs the interpolation arrays for the short range forces calculations an
237. ins check_for_transition check_shells check_syschg config write conscan copystring corshl could coulOneu coul1 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_external_field define_four_body define_inversions define_metals define_minimum_state define_pmf define_rigid_body define_tersoff 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 subroutine subroutine subroutine function subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine angles_module f bonds_module f rigid_body_module f utility_module f hyper_dynamics_module f define_system_module f spme_module f spme_module f ensemble_tools_module f ensemble_tools_module f hkewald_module f setup_module f hyper_dynamics_module f hyper_dynamics_module f core_shell_module f site_module f utility_module f setup_module f parse_module f core_shell_module f coulomb_module f neu_coul_module f coulom
238. ion to a new state state B If the system is created in state A at time zero the probablity of it being found in the same state at a later time t is P t dt kexp kt dt 5 11 148 STFC Section 5 4 where P t is a probability distribution and k is the first order rate constant It follows from this that the mean lifetime 7 of the system in state A is r 1 k 5 12 from which we have a universal property of first order systems riel 5 13 In other words the rate constant is inversely proportional to the lifetime in the initial state According to TST the rate constant exhibits a temperature dependence given by the Arrhenius law k v eE 5 14 where v is the so called the pre exponential factor with the units of frequency and 8 is the Boltzmann factor 1 kgT E is the activation energy of the process which is the energy barrier between the bottom of the potential basin of state A and the saddle point on the energy surface that provides the escape route to state B This equation shows that at different temperatures T and 75 the same escape route from state A has different rate constants k and ka respectively Nevertheless the universal property of equation 5 13 means that Ti ki 79 ko 5 15 which is an important relation underpinning the TAD method showing how the time scale for a barrier crossing event at one temperature is related to the time scale for the same event at another temperature In most practic
239. ions the equations of motion are E v t nro Ro A OOO ext a T t e away kpText att 2 VIP Pess x t n t VO Bravo 12290 where Q N skBTextTh is the effective mass of the thermostat and W N tkpTextTh is the effective mass of the barostat Ny is the number of degrees of freedom 7 is the barostat friction 61 STFC Section 2 5 coefficient Ry 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 k Hypr U KE PoV t 50x Wn 6 l Sx s kpText ds 2 251 o ET The algorithm is readily implemented in the LF scheme as A O A rs Toa Wat k Ti E 5 xe At x t 4 z niet 5a nt 500 AtS SLP Poa xn n t lt 5 ne Ai n t 4 z 1 1 ut At lt u t At At EN i i E AD olt 7 9 HIM E E ut i At n t At ke 5At z Bo r t sat de r t r t At 2 252 Like the LF Nos Hoover thermostat several iterations are required to obtain self consistency 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 u t and r t At Note also that the change in box size requires the SHAKE algori
240. iori 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 reciprocal space terms HKEWALD2 and HKEWALD3 calculate the real space terms and the bonded atom corrections respectively HKEWALD4 calculates the primary interactions in the multiple timestep implementa tion 2 4 9 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 50 STFC Section 2 4 the cavity the system is treated as a dielectric continuum The occurence of any net dipole within the cavity induces a polarisation in the dielectric which in turn interacts with the given molecule The model allows the replacement of the infinite Coulomb sum by a finite sum plus the reaction field The reaction field model coded into DL_POLY _2 is the implementation of Neumann based on charge charge interactions 46 In this model the total Coulombic potential is given by o 1l ATEO 1 Bgr U X djan 7 2 212 c qin 2R3 IKN where the second term on the right is the reaction field correction to the explicit sum with Re the radius of the cavity The constant Bo is defined as 2 e1 1 _ 2 213 Ba 1 28 with e the dielectric constant outsid
241. k number e g num_track 10 g Set the catch radius i e the minimum distance in Angstroms any atom may be displaced in the minimised structure before it is recorded as a transition e g catch_radius 3 0 h Set the NEB spring constant in specified energy units per A e g neb_spring 1000 0 for DL POLY units i Select a minimisation option e g force key tol Where key is one of force energy position and tol is the convergence tolerance The recommended choice is force with a tolerance of 1 0 in DL POLY units j Close the BPD definition with the directive endbpd 3 Set other CONTROL file directives as follow a Select the restart noscale option if the CONFIG file was pre equilibrated otherwise leave out the restart keyword altogether b Set the length of the simulation required steps and the equilibration period equil both in time steps The equilibration can be short if the system was pre equilibrated c In setting the job close time it is recommended to set the number to at least 500 times the clock time it takes to do one normal MD time step This is to prevent the program running out of time during a structural minimisation The timing information for this may be taken from the previous equilibration run d Set the remaining CONTROL keywords as were defined for the initial equilibration simulations 4 Before starting the BPD simulation use the UNIX mkdir command to make the following
242. kefile 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 with CygWin if a PC version is required Run the Makefile you copied from the build sub directory in the srcmod 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 83 STFC Section 3 2 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 EX gt lt BINROOT gt where some or all of the keywords may be omitted The keywords and their uses are described below Note that keywords may also be set in the unix environment e g with the setenv command in a C shell 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 G95 http ftp g95 org Both of these are copyrighted products 3 2 1 1 Keywords for the Makef
243. l 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 the ewald precision directive is used The first few records of a typical CONFIG file are shown below Lennard Jones Argon 2 3 255 176595 066855 21 023998260000 0 000000000000 O 000000000000 Ar 1 7 798997031 2 12339759919 417 940093856 Ar 2 2 821617729 1 07786776343 188 920889755 Ar 3 8 113009749 0 388066563418 O 000000000000 21 023998260000 0 000000000000 2 409934763 1 85576903413 292 432569373 0 7180021261 2 773816641 1 37628108908 0 000000000000 0 000000000000 21 023998260000 5 506441637 0 125163024806 472 434039806 7 417288159 0 168433841280E 01 0 269392807911 413 545510271 294 149380530 5 199345225 1 24723236452 608 168259627 422 414753563 250 737138386 Ar 4 10 31216635 1 76536230573 66 0234000384 2 857971798 1 58904200978 47 6492437764 8 090920140 2 48066272817 90 0074615387 etc 4 1 2 1 Format The file is fixed formatted integers as i10 reals as f20 0 The header record is formatted as 80 alphanumeric characters 4 1 2 2 Definitions of Variables record 1 header a80 title line record 2 levcfg integer COMFIG file key See table 4 5 for permitted values imcon integer Periodic boundary key See table 4 6 for permitte
244. lease specify a target machine echo Permissible targets for this Makefile are echo l echo crayxd1 parallel echo echo Please examine Makefile for details system specific targets follow crayxd1 MAKE LD mpif90 o LDFLAGS FC mpif90 FFLAGS c 0 Mdalign EX EX BINROOT BINROOT TYPE Default code for Windows execution par check 0BJ_MOD OBJ_PAR OBJ_SRC LD EX LDFLAGS OBJ_MOD OBJ_PAR OBJ_SRC mv EX EXE 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 Check that a machine has been specified check Cif test FC undefined then echo You must specify a target machine exit 99 fi 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 Clean up the source directory clean rm f 0BJ MOD OBJ_PAR OBJ_SRC mod 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 tt Declare dependencies f o FC FFLAGS f gt gt
245. led 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 zero_kelvin 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 241 STFC Section C 0 Message 1925 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
246. les computation of the constraint force will in principle allow the correct atomic positions to be calculated in one pass However in the general polyatomic case this correction is merely an interim adjustment not only because the above formula is ap proximate but the successive correction of other bonds in a molecule has the effect of perturbing previously corrected bonds 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 55 STFC Section 2 5 Figure 2 6 The SHAKE algorithm The algorithm calculates the constraint force Gi G that conserves the bondlength d12 between atoms 1 and 2 following the initial movement to positions 1 and 2 under the unconstrained forces F and F3 1 All atoms in the system 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 2 230 that retrospectively corrects the bond length 3 After the correction 2 230 has been applied to all bonds every bondlength is checked If the largest deviation found exceeds the desired tolerance the correction calculation is repeat
247. ll 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 74 STFC Section 2 6 2 6 3 Distributing the Nonbonded Terms In DL POLY_2 the nonbonded interactions are handled with a Verlet neighbour list 12 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 Arcut The larger radius freut ATcus 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 Ar 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 neighbour list is therefore different on each node DL_POLY 2 uses a method based on the Brode Ahlrichs scheme 23 see figure 2 8 to construct the neighbour list Additional modifications are necessary to handle the excluded atoms 56 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
248. ltiple 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 atom 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 electrostatic potentials and forces in periodic or pseudo periodic systems For non periodic systems only di rect 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
249. m 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 fn g a functions are more difficult Firstly however we note that the reciprocal space contributions to Ozz 055 and oz may be obtained directly from the force calculations thus recip __ ft Ortz Yzf J ed Nu 2 210 J recip __ pz Ozz Yzf j which renders the calculation of these components trivial The remaining components are calculated from 1 Nmax g a Urecipduw T 5 an 5 JuJv 75731 uv 4egA n 0 g70 an 2n 2n 1 fo g a 1 2 42 4 2 211 z7 40 2 211 2n Y DC 2p 9 Za p 9 p 0 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 z y components define the surface tension however For bonded molecules as with the standard 3D Ewald sum it is necessary to extract contri butions associated with the excluded atom pairs In the DL_POLY_2 HKE implementation this amounts to an a poster
250. m NST Hoover ensemble 6 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 6 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 6 1 1 17 Test 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 6 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 are treated by constraint dynamics in the NVT Evans scheme Ewald s method handles the electrostatics NVT Evans ensemble 6 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
251. m types not specific indices Secondly there are no excluded atoms arising from the three body terms The inclusion of pair potentials may in fact be essential to maintain the structure of the system The three body potentials are very short ranged typically of order 3 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 33 The calculation of the forces virial and stress tensor as described in the section valence angle potentials above DL_POLY_2 applies no long ranged corrections to the three body potentials The three body forces are calculated by the routine THBFRC 29 STFC Section 2 3 2 3 3 The Tersoff Covalent Potential The Tersoff potential 5 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
252. m Alp C U r Aexp r p C r bck 2 r p A32 fene FENE k RIA U rij 0 5 k R2 In 1 142 bck Note bond 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 also calculate the nonbonded pair potentials between the described atoms unless these are deactivated by another potential specification index 1 index 2 bondlength integer integer real first atomic index second atomic index 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 A 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 113 STFC Section 4 1 weight real site weighting b pmf unit no where na is the number of sites in the second unit The subsequent ng records provide the site indices and weighting Each record contains index integer atomic site index weight real site weighting This directive and associated data records need not be specified if no PMF constraints are present See the note on the atomic i
253. m 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 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 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 226 STFC Section C 0 Message 1030 error failed allocation of bond arrays This is a mem
254. m 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 228 STFC Section C 0 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 user 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 b
255. m is split into stages in accordance with the principles of Martyna et al 18 for designing reversible integrators The scheme applied here is 58 STFC Section 2 5 x t wat lt x t EN TGQ Tia vl wt Shee au u t sat lt vi t t Sa 1 r At rt Atou t 54M call rattle R 1 At f t At v t At vu t J At E 2 call e AtN yk x t At x t 5At 20 F T t At Text At v t At v t At y Xx Atju t At 2 240 Routines rattle R and rattle V apply the bondlength and velocity constraint formulae 2 233 and 2 234 respectively The equations have the same conserved variable Hyxyr 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 temper ature by scaling the velocities at each step x t h Ga yr 2 241 The DL POLY 2 LF routines implement this thermostat as follows Us wat EE ji ansat x t u t 5 e t At o t 540 r t At r t Atv t At 2 242 As with the Nos Hoover thermostat iteration is required to obtain self consistency of y t v t and T t although it should be noted x has different roles in the two thermostats The Berendsen algorithm conserves total momentum but not energy Here again the presence of constrai
256. makefile for DL_POLY_2 0 Author W Smith March 2008 N gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt tt Define default settings PaaS SSeS a a ee Se ea a ee a ee gt gt gt SS eS BINROOT execute EX DLPOLY X EXE BINROOT EX FC undef ined SHELL bin sh TYPE par Define object files OBJ_MOD parse_module o setup_module o error_module o site_module o config_module o pair_module o utility_module o tether_module o vdw_module o property_module o rigid_body_module o angles_module o bonds_module o shake_module o inversion_module o dihedral_module o core_shell_module o exclude_module o ewald_module o coulomb_module o external_field_module o four_body_module o hkewald_module o metal_module o ensemble_tools_module o temp_scalers_module o N three_body_module o spme_module o tersoff_module o neu_coul_module o nlist_builders_module o forces_module o 1f_motion_module o 1f_rotation1_module o 1f_rotation2_module o vv_motion_module o vv rotation1 module o N vv_rotation2_module o pmf_module o integrator module o define_system_module o optimiser_module o hyper_dynamics_module o driver_module o 179 OSTFC Section A 0 OBJ_SRC dlpoly o OBJ_PAR basic_comms o merge_tools o pass_tools o Define targets all echo Error p
257. matted and written by the subroutine REVIVE It contains the accumulated statis tical 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 6 The RDFDAT File This is a formatted file containing em Radial Distribution Function RDF data Its contents are as follows record 1 cfgname character A80 configuration name record 2 ntpvdw integer i10 number of RDFs in file 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 e14 interatomic distance A g r real e14 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 7 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 poin
258. measurable diffusion in a reasonable time These however must be devised so that the kinetic processes of the original system may be faithfully reconstructed Both the BPD and TAD methods in DL POLY_2 which are respectively described in sections 5 3 and 5 4 below satisfy this requirement It is apparent from the discussion above that an important requirement in hyperdynamics is the calculation of the activation energy which is equivalent to determining the saddle point between two states This is accomplished in DL POLY_2 by a technique known as the Nudged Elastic 140 STFC Section 5 2 Band NEB method Understanding the NEB method is a prerequisite for using the DL POLY 2 hyperdynamics methods correctly so a description of it is given in the following section 5 2 The Nudged Elastic Band Calculation 2 094 Fe wo L s 2 096 al 2 09 J Figure 5 2 Basic NEB Theory Plot of bead configuration energy vs reaction path for a NEB calculation of a structural transition in a Lennard Jones solid The Nudged Elastic Band NEB method is a standard method for determining the energy optimised pathway between two known structures In DL_POLY_2 it is used to find the escape pathway also called the reaction path between structural basins yielding the activation energy in the process The implementation is based on the method described by Henkelman and Jonsson 64 though it has been adapted to
259. 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 srcmod directory contains an example 81 STFC Section 3 1 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 cycle 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 program 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 subroutines will need modifying to allow specification of the dimensions of any new arrays Any molecular dynamics simulation performs five different kinds of operation initialisation forces calculation integration of the equations of motion calculation of system properties and job term
260. mics 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 48 52 STFC Section 2 5 2 5 Integration algorithms 2 5 1 The Verlet Algorithms DL_POLY integration algorithms are based on the Verlet scheme which is both time reversible and simple 12 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 simulation it indicates that the timestep is too large or the potential cutoffs too small relative r m s fluctuations in the total energy of 107 are typical with this algorithm 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 1 1 F t A At At 2 222 v
261. mixing rules are different in each case beware With regard to density in the EAM case it is required that 4 AB BB Pij Tig pij Tig BA AA pij ris pij Tag gt 2 152 which means that an atom of type A contributes the same density to the environment of an atom of type B as it does to an atom of type A and vice versa For the FSM case 38 a different rule applies PEP rag OG ria rag 2 153 so that atoms of type A and B contribute the same densities to each other but not to atoms of the same type Thus when specifying these potentials in the DL_POLY_2 FIELD file for an alloy composed of n different metal atom types both EAM and FSM require the specification of n n 1 2 pair functions 39 STFC Section 2 4 VA ri However the EAM requires only n density functions a te whereas the FSM class requires all the cross functions pig rig or n n 1 2 in total In addition to the n n 1 2 pair functions and n density functions the EAM requires further specification of n functional forms of the density dependence i e the embedding function F p in 2 123 For EAM potentials all the functions are supplied in tabular form via the table file TABEAM see section 4 1 6 to which DL POLY_2 is redirected by the FIELD file data The FSM potentials are defined via the necessary parameters in the FIELD file 2 3 6 External Fields In addition to the molecular force field DL POLY_2 allows the use of an extern
262. mnam 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 11 parameters A to h required for the cross interactions between dissimilar elements are calculated internally by DL_POLY_2 using the prescription given by Tersoff 5 There is no prescription for the x and w cross parameters so these must be given explicitly Note also 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 S Blrnjeld A as shown in Section cross X Ww 23 24 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 mxfld 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 which signals t
263. mputers 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 processor workstations for which it requires a FORTRAN 90 compiler and preferably a UNIX environment It has also been compiled for a Windows PC using the G95 FORTRAN compiler augmented by the CygWin UNIX shell 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 rec ommend that users of DL POLY 2 adopt this system for local development of the DL POLY 2 code particularly where several users access the same source code For information on CVS please contact info cus request gnu org or visit the website http www ccp5 ac uk DL POLY 1 3 5 Required 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 required for parallel execution Users requiring the Smoothed Particle Mesh Ewald SPME method may prefer to use a propri etary 3D FFT other than the one DLPFFT3 supplied with the package for optimal performan
264. 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 too 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 222 STFC Section C 0 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 degr
265. 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 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_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 232 STFC Section C 0 Message 1410 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 Message 14
266. n above means that the units are the same as for the potential i e are handled using the same conversion factors 4 1 6 The TABEAM File The TABEAM file contains the tabulated potential functions no explicit analytic form describing the metal interactions in the MD system This file is read by the subroutine METTAB The EAM potential for an n component metal alloy requires the specification of n electron density functions one for each atom type and n embedding functions again one for each atom type and n n 1 2 cross pair potential functions This makes n n 5 2 functions in total 127 STFC Section 4 1 Note that the option of using EAM interactions must also be explicitly declared in the FIELD file so that for the n component alloy there are n n 1 2 cross pair potential eam keyword entries in FIELD see above Note that all metal interactions must be of the same type 4 1 6 1 The TABEAM File Format The file is free formatted but blank and commented lines are not allowed 4 1 6 2 Definitions of Variables record 1 header al00 file header record 2 numpot integer number of potential functions in file The subsequent records define the n n 5 2 functions for an n component alloy n electron density functions one for each atom type density keyword n embedding functions again one for each atom type embeding keyword and n n 1 2 cross pair potential functions pairs keyword The functions may appear
267. n force constraint contribution to the virial press pressure Note The total internal energy of the system variable tot_energy includes all contributions to the energy including system extensions due to thermostats etc It is nominally the conserved variable of the system and is not to be confused with conventional system energy which is a sum of the kinetic and configuration energies The interval for printing out these data is determined by the directive print in the CONTROL file At each time step that printout is requested the instantaneous values of the above statistical variables are given in the appropriate columns Immediately below these three lines of output the 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 The 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 The
268. n forces are handled by the routine INVFRC 2 2 8 Tethering Forces DL POLY 2 also allows atomic sites to be tethered to a fixed point in space rp 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 rio is the distance of the atom from its position at t O 1 harmonic potential harm 1 U rio zk rio 2 69 2 restrained harmonic rhrm 1 2 Ulrio 5k rio Tio lt fc 2 70 1 U r Hr krelrio Te Tio gt Te 2 71 3 Quartic potential quar E af Ej 2 72 k U rio rio 3 ii 2 25 STFC Section 2 3 The force on the atom arising from a tether potential is obtained using the general formula E Tio 1 0 A Urio Tio 2 73 The contribution to be added to the atomic virial is given by W a La 2 74 The contribution to be added to the atomic stress tensor is given by go ie 2 75 where a and 5 indicate the x y z components
269. n 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 7 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 133 STFC Section 4 2 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 from 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 represent
270. nal form 12 6 12 6 A B U r 5 lj Lennard Jones e 0 U r 4e E 27 nm n m E n ro U r c m Z2 n 22 buck Buckingham A p U r A exp 5 S bhm Born Huggins A B CID U r A exp B o r E 2 Meyer hbnd 12 10 H bond A B U r A 4 snm Shifted force E n ro Tet Ur c x nan 31 mar 2 5 yoner 1a G nmabBo T YTo B nm B m H E E mors Morse Eo ro U r Eo 1 exp k r ro 1 ay12_ a 6 1 6 wea WCA e o U r 4e 2 DA e r lt ax 2 tab Tabulation tabulated potential T Note in this formula the terms a 3 and y are compound expressions involving the variables Eo n mM ro and re See section 2 3 1 for further details Note re defaults to the general van der Waals cutoff rvdw or rcut if it is set to zero or not specified or not specified in the FIELD file The specification of three body potentials is initiated by the directive tbp n 119 STFC Section 4 1 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 atmnam 2 atmnam 3 key a8 as a8 a4 first atom type second atom type central site third atom type potential key See table 4 13 120 STFC Section 4 1 Table 4 13 Three body potentials key potential type Variables 1 4 f
271. nce angle 4 13 14 17 18 23 29 74 76 82 89 114 115 132 van der Waals 14 17 19 73 82 85 103 116 quaternions 5 54 68 101 reaction field 50 51 101 rigid body 3 5 26 54 55 66 68 70 78 82 rigid bond see constraints bond shell model polarisation 51 52 dynamical shell model 51 52 relaxed shell model 52 software licence DL_POLY 3 10 SPME see Ewald SPME stress tensor 19 22 25 26 28 29 32 33 36 42 44 46 51 52 56 61 sub directory 171 174 bench 8 build 8 data 8 execute 8 java 8 public 8 source 8 utility 8 Sutton Chen potential see potential Sutton Chen temperature accelerated dynamics TAD see hy perdynamics TAD thermostat 5 40 69 70 73 99 Berendsen 65 69 72 Nos Hoover 61 62 69 70 72 83 units DL_POLY 7 133 energy 110 pressure 7 8 62 101 133 user registration 10 Verlet neighbour list 46 72 75 77 82 103 104 WWW 3 10 260
272. ndices 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 La Wala La Wa where r is a site position and wa the site weighting Note that the pmf constraint is in tramolecular 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 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 R 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 114
273. nds into oUi o 0 0 one arg TV Faria W Gea Fong Falta fol falta pra Tu 2 106 30 STFC Section 2 3 with the contributions from the first two terms being 0 0 o Brg era Faris 22 raat Jabra ge let X ar E ai 2 107 o Vij gra ale riz FAC Tij ij Cor Tij falrij faradas feto x ij hetat i 2 108 and from the third angular term 0 fotrij falrij avs Jolrij falrij Xij X 1 i pi i ml 0 where 2 Brg ti X Wik fe rik g 0 ijk 2 110 k i j The angular term can have three different contributions depending on the index of the particle participating in the interaction 0 0 i 2 s D oot Dijk 57 gra eC T 2 111 o 0 L J ore Lij Wik Jo rik a raO Oaar 2 112 Tj k i j de o 0 KEGI 5 5 arg Wi 90ije grato lie folre Fag ise 2 113 The derivative of g 0 1 is worked out in the following manner ati Ll A A Bit l 2 114 rg olijk sin ijk Org Tij Tik where Og 0 _ 2 c h cos Ojjk sin Oi 7 2 115 olijk d hi cos 0 j4 2 2 l o nyt r E ara ut Sp bei k H ok t 4 ro Tijk Tijfik TijVik cos 9jik fos Te 2 i Sex bu 7 2 116 Tij ri 31 STFC Section 2 3 The contribution to be added to the atomic virial can be derived as WwW oe ay DU 2 117 Aj WO 23 clrij falrij pl Tij I J J 1 Ori J J J SB is ais A RAR 2 118 o S wir 9 Gijk Or Or O
274. nerally 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 La Laz Laz Mb Mb2 Mbs Nc Mc2 Nc3 in which L M N are integers reflecting the multiplication of the unit cell in each principal direction Note that the atomic coordinate origin is the centre of the MD cell The parallelepiped boundary condition can be used with the Ewald summation method 183 STFC Section B 0 Figure B 3 The parallelepiped MD cell Truncated octahedral boundaries IMCON 4 Figure B 4 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 DL_POLY_2 CONFIG file are simply D 0
275. nge 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 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 param eters with the CONTROL file hke sum directive e g hke sum 0 056611 which would set a 0 05 A 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 B reut Where Tes is the largest real space cutoff compatible with a single MD cell and 8 3 46 4 37 5 01 5 55 when nhko 0 1 2 3 respectively Thus in the usual case where nhko 1 8 4 37 When nlatt0 this P value is multiplied by a factor 1 2 x nlatt 1 The estimation of kmax1 2 is the
276. nimiser is capable of finding more than one minimum without the user intervening 4 Finally we emphasise once again that the purpose of the minimisers in DL_POLY_2 is to help improve the quality of the starting structure and we believe they are adequate for that purpose We do not recommend them as general molecular structure optimisers They may however prove useful for relaxing crystal structures to 0 Kelvin for the purpose of identifying a true crystal structure 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 7 Many of these have been incorporated into the DL_POLY_2 Graphical User Interface 9 and may be convienently used from there 88 STFC Section 3 3 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 sy
277. nn is an integer ranging from 0 to max_track 5 5 0 5 The PROnn XY Files in the PROFILES Directory The PROnn XY files tabulate the converged configuration energies of the beads in a NEB calcula tion as a function of the reaction coordinate linking the beads nn is an integer ranging from 0 to 9999 The reaction coordinate is the path distance S between the structure of the reference state and the structure of a converged NEB bead and is defined here as k 1 2 Sn D R RNY 5 22 i 1 where RN is a 3N dimensional vector defining the structure N is the number of atoms and n ranges from 2 to bead number Npneb in the NEB chain Note that the reaction path does not usually represent a straight line in the 3N dimensional space The file PROnn XY presents two columns of numbers the first is the reaction coordinate and the second is the configuration energy of the bead Both are expressed in DL POLY_2 units The configuration energy for the first bead at Sn 0 is the energy of the reference state Normally the PROnn XY file reveals a single maximum in configuration energy as the reaction coordinate increases However in some instances more than one maximum may be obtained The user should note that in these instances DL POLY 2 will take the configuration closest the first minimum and optimise it independently to define the true destination of the transition from the reference state 5 6 Tidying Up the Results of a Hyperdynamics Simulation
278. nner atmnam 1 a8 first atom type atmnam 2 a8 second atom type key ad 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 variable 6 real potential parameter see table 4 15 variable 7 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 This includes cross terms for alloys Both EAM and FSM potentials can handle alloys but care must be taken to enter the cross terms of the potentials explicitly Note that the rules for defining cross terms of the potential are not the usual rules encountered in Lennard Jones systems see section 2 3 5 122 STFC Section 4 1 Table 4 15 Metal Potential key potential type Variables 1 7 functional form eam EAM tabulated potential fnsc Finnis Sinclair co c1 c2 c A d B U r 5 ry c co Cita car Ay Pi IA AN p M ris dy pease IA tch Sutton Ch Ui r e LR 2 stc utton Chen e a n m c n 22 Pi m a a Pi 2 E gupt Gupta A ro Pp B aj Ue 22269 p 2 By pi S O GTO Pi exo 2413 4 1 3 5 The Tersoff Potential Th
279. nse 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 ex ceeded the neighbour list array dimensions Action Standard user response Fix the parameter mxlist 203 STFC Section C 0 Message 109 error neighbour list array too small in parlst_nsq Construction of the Verlet neighbour list in subroutine 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 check ing if the Verlet list needs updating have been exceeded Action Standard user response Fix the parameter mslst Message 120 error invalid determinant in matrix inversion DL POLY 2
280. nsider using more processors or a machine with larger memory per processor 236 STFC Section C 0 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 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 1670 error failed allocation of work arrays in nptq_h2 f This is a memory
281. nstraint 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 Gpmr Wpemr dpmr where dpmr is the constraint distance between the two groups used to define the reaction coordinate 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 57 STFC Section 2 5 are modified and the system no longer samples the microcanonical ensemble Instead trajectories in the canonical NVT ensemble or something close to it are generated DL_POLY_2 comes with three different thermostats Nos Hoover 21 Berendsen 20 and Gaussian constraints 19 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 12 2 5 4 1 Nos Hoover Thermostat In the Nos Hoover algorithm 21 Newton s equations of motion are modified to read dr t _
282. nt It is generated in the execute sub directory 3 CFGBSNnn a basin file which contains the coordinates of each distinct state DL_POLY_2 has found during the BPD or TAD run nn is an integer rising from 0 to 9999 All such files are generated in the erecute BASINS sub directory 4 PROnn XY a profile file which is a list of the reaction coordinate and configuration energy of each bead in the converged NEB calculation nn is an integer rising from 0 to 9999 All such files are generated in the erecute PROFILES sub directory and are plotable XY files 5 CFGTRAnn a configuration file used to interpolate when a transition has occured nn is an integer rising from 0 to 9999 All such files are generated in the execute TRACKS sub directory These files are described in further detail below 155 STFC Section 5 5 5 5 0 1 The HYPRES and HYPOLD Files The HYPRES and HYPOLD files are unformatted i e not human readable and are restart files for BPD or TAD runs of DL POLY_2 The HYPRES file is produced by the program at regular intervals during the program run and also at the end of a run It must subequently be renamed HYPOLD to be read by DL POLY 2 when the simulation is recommenced The user does not need to know the contents of these files but for the curious it can be said that they contain current file numbers for the BASINS TRACKS and PROFILES directories the structural differences between the current reference b
283. nt 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 ALE 2 m v t At v t 59 STFC Section 2 5 1 r t At lt r t Atu t 5 Mt call rattle R t At v t At u e Zas LEA call rattle V AN x 1 1 Tr Text v it At xvu t At 2 243 2 m Routines rattle R and rattle V apply the bondlength and velocity constraint formulae 2 233 and 2 234 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 dr t gt 200 sio O 2 244 2 245 with the temperature constraint Z x e Stn x mult f t 0 2 246 then choosing 2 mio t f t Dy mee t minimises the least squares differences between the Newtonian and constrained trajectories Following Brown and Clarke 50 the algorithm is implemented in the LF scheme by calculating n 1 1 xAt 2 2 247 E Text T 1 1 t u t 5 At 2n Do t At parto 1 r t At r t Atu t At 2 248 where 7 is obtained from standard
284. o 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 1 1 exp ia a F a K a exp ik r CO 1 ae a gt f T 1 TE N 5 2 ferfelarn E exp ar3 Roj 2 185 j lt n nj T l 2 dile 2are 9 T 3er flare 2 exp a7 rf Ray j lt l Tej VT Ane where matrices K and Ry are defined as follows Ke Kek 2 186 Re tT 2 187 In DL POLY_2 the full Ewald sum is handled by several routines EWALD1 and EWALD1A han dle the reciprocal 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 ranged forces and EWALD3 calculates the self interaction corrections It should be noted that the Ewald potential and force interpolation arrays in DL_POLY_2 are erc and fer respectively 2 4 7 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 44 Formally this method is capable of treating van der Waals forces also but in DL_POLY_2 it
285. ob ar ref 2 31 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 04 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 qur Truncated harmonic thm Screened harmonic shm Screened Vessal 28 bv1 Truncated Vessal 29 bv2 Harmonic cosine hes Cosine cos MM3 stretch bend msb In DL POLY_2 angular restraints are handled by the routine ANGFRC 19 STFC Section 2 2 2 2 5 Dihedral Angle Potentials Figure 2 3 The dihedral angle and associated vectors The dihedral angle potentials describe the interaction arising from torsional forces in molecules They are sometimes referred to as torsion potentials They require the specification of four atomic positions The potential functions available in DL POLY 2 are as follows 1 Cosine potential cos
286. ob time minus the close time Thus when DL_POLY_2 reaches the effective job time limit it begins the close down procedure with enough time in hand to ensure the files are correctly written In this way you may be sure the restart files etc are complete when the job terminates Note that setting the close time too small will mean the job will crash before the files have been finished If it is set too large DL POLY_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 4 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 5 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 2 102 STFC Section 4 1 6 10 11
287. occasionally needs to calculate matrix inverses usually the inverse of the matrix of cell vectors which is of size 3 x 3 For safety s sake a check on the determinant is made to prevent inadvertent use of a singular matrix Action Locate the incorrect matrix and fix it e g are cell vectors correct Message 130 error incorrect octahedral boundary condition When calculating minimum images DL POLY 2 checks that the periodic boundary of the simula tion cell is compatible with the specifed minimum image algorithm Program termination results if an inconsistency is found In this case the error refers to the truncated octahedral 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 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 simula tion cell is compatible with the specifed minimum image algorithm Program termination 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 204 STFC Section C 0 of the simulation cell v
288. ode are passed to all the other nodes by splicing This scheme contains a number of non trivial operations which are described in detail in 43 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 that 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 78 Chapter 3 DL POLY 2 Construction and Execution 79 STFC Section 3 0 Scope of Chapter This chapter describes how to compile a working version of DL_POLY_2 and how to run it
289. ody 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 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 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 229 STFC Section C 0 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
290. of all secondary atoms within a certain radius of each primary atom the radius being the cut off radius recut normally applied to the nonbonded potential function plus an additional increment Ars The neighbour list removes the need to scan over all atoms in the simulation at every timestep The larger radius reut Areut 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 Areut DL POLY 2 has two methods for constructing the neighbour list the first is based on the Brode Ahlrichs scheme 23 and is used when reut is large in comparison with the simulation cell the second uses the link cell algorithm 24 when reut 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 candidates The assumption behind this requirement is that atoms that are formally bonded in a chemical sense should not participate in nonbonded int
291. omms f serial f hyper_dynamics_module f define_system_module f hyper_dynamics_module f hyper_dynamics_module f define_system_module f forces_module f nlist_builders_module f basic_comms f serial f vv_rotationi_module f 1f_motion_module f 1f_motion_module f lf rotation1 module lf rotation2 module lf rotation1 module lf rotation2 module ensemble tools module f ensemble tools module f vv_rotationi_module f vv_rotation2_module f vv_rotationi_module f vv_rotation2_module f ensemble_tools_module f ensemble_tools_module f vv_motion_module f vv_motion_module f 1f_motion_module f 1f_motion_module f Hh Fh Fh Fh Fh Fh Fh Fh Fh Hh Hh Hh hh 255 STFC Section D 0 nstq_b1 nstq_b2 nstq_hi nstq_h2 nstqmtk_p nstqscl_p nstqscl_p2 nstqscl_t nstqscl_t2 nstqvv_b1 nstqvv_b2 nstqvv_h1 nstqvv_h2 nstscale_p nstscale_t nstvv_b1 nstvv_h1 numnodes numnodes nve_1 nveq_1 nveq_2 nveqvv_1 nveqvv_2 nvevv_1 nvt_b1 nvt_el nvt_h1 nvtq_b1 nvtq_b2 nvtq_hi nvtq_h2 nvtqscl nvtqvv_b1 nvtqvv_b2 nvtqvv_h1 nvtqvv_h2 nvtscale nvtvv_b1 nvtvv_el nvtvv_h1 optimisation_selector parlink parlinkneu parlst parlst_nsq parneulst parset passcon subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine function function subroutine subroutine subroutine subroutine subro
292. on 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 6 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 con ditions 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 harmonic and all atoms are explicit The link cell algorithm is in operation NVE ensemble 6 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 165 OSTFC Section 6 1 6 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 or thorhombic and square in the XY plane The integration algorithm is NPT Berendsen This is a test for the Tersoff potential NPT Berendsen ensemble 6 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 algorith
293. on aooe as 17 The dihedral angle and associated vectors oos so ccs aor soemo a opo e ae 20 The L and D enantiomers and defining vectors sooo a 23 The inversion angle and associated vectors e 23 The SHAKE algorit ss soe gaoi poe ee Re ee e a e a 56 The multiple timestep algorithm 0 e 73 The parallel implementation of the Brode Ahlrichs algorithm 76 A sample DL POLY stricture s s ss coe A eR ee ER a RES 94 DL POLY 2 input and output Al s e s a sacs aek aoa a ede Ree ee a es 97 Model Potential Energy Surfac oc ce o supa b Re a ae 140 Basie NEB Theoiy nacos da a Bie Be be ee ee owe ee Bee He 141 Basie BPD Thegiy st a eA i ee A A ee A 143 Basie TAD Theory 2 447 4h ida Pe ee SA ae Se e 150 The cubre MID celle cos ek ag SOR a poe es A A a AS a tes ee 183 The ortborhamme MD cell sa wos da o a RA ee 183 The parallelepiped MD cell os ssa cee ee ea k ERR ee RO 184 The truncated octahedral MD cell a 184 The rhombic dodecahedral MD cell o e e 185 The hexagonal MD cell so pei cee eee ee ae e 186 Chapter 1 Introduction STFC Section 1 0 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 STFC Section 1 2 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 of macromole
294. on sphere will be neutral and spurious charging effects will almost certainly be seen in a simulation This arises because the potential being truncated is long ranged 1 r for charge charge interactions However if the cutoff scheme is based 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 Al STFC Section 2 4 2 4 2 Direct Coulomb Sum Use of th
295. onditions The system size is 3838 atoms and runs on 16 512 processors 6 1 2 7 Benchmark 7 Simulation of gramicidin A molecule in 4012 water molecules using neutral group electrostatics 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 6 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 6 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 169 Chapter 7 DL POLY 2 Utilities 170 STFC Section 7 1 Scope of Chapter This chapter describes the more important utility programs and subroutines of DL_POLY_2 found in the sub directory utility 7 1 Miscellaneous Utilities 7 1 1 Useful Macros 7 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 e supa The function of each of these is described below It is worth noting that mo
296. ordinate yyy real y coordinate ZZZ real z coordinate record c 3e12 4 only for keytrj gt 0 VXX real x component of velocity vyy real y component of velocity VZZ real z component of velocity record d 3e12 4 only for keytrj gt 1 xx real x component of force fyy real y component of force fzz real z component of force Thus the data for each atom is a minimum of two records and a maximum of 4 4 2 1 2 The Unformatted HISTORY File The unformatted HISTORY file is written by the subroutine TRAJECT_U and has the following structure 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 8 130 STFC Section 4 2 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 for imcon gt 0 cell 1 9 a band 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 coo
297. orques are subsequently transformed into an equivalent set of atomic forces which are perpendicular both to the instantaneous axis of rotation defined by the torque vector and to the cylindrical radial displacement vector of the atom from the axis These modified forces are then used in place of the original atomic forces in the conjugate gradient scheme The atomic displacement induced in the conjugate gradient algorithm is corrected to maintain the magnitude of the radial position vector as required for circular motion 2 With regard to constraint bonds these are replaced by stiff harmonic bonds to permit minimisation This is not normally recommended as a means to incorporate constraints in minimisation procedures as it leads to ill conditioning However if the constraints in the original structure are satisfied we find that provided only small atomic displacements are allowed during relaxation it is possible to converge to a minimum energy structure Furthermore provided the harmonic springs are stiff enough it is possible afterwards to satisfy the constraints exactly by further optimising the structure using the stiff springs alone without having a significant affect on the overall system energy c Systems with independent constraint bonds and rigid bodies and systems with rigid bodies linked by constraints may also be minimised by these methods 3 Of the three minimisation methods available in DL_POLY_2 only the programmed mi
298. orward Subroutine EWALD1 distributes over atomic sites and is often the more efficient of the two approaches Subroutine 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 interaction 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 75 STFC Section 2 6 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 Figure 2 8 The parallel implementation of the Brode Ahlrichs algorithm This 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 distribut
299. ory 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 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 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
300. ot total internal energy of the system temp_tot system temperature eng cfg configurational energy of the system eng vdu configurational energy due to short range potentials eng_cou configurational energy due to electrostatic potential eng bnd configurational energy due to chemical bond potentials eng ang configurational energy due to valence angle and three body potentials eng dih configurational energy due to dihedral inversion and four body potentials eng tet configurational energy due to tethering potentials line 2 time ps elapsed simulation time ps since the beginning of the job eng pv enthalpy of system temp rot rotational temperature vir_cfg total configurational contribution to the virial vir_vdw short range potential contribution to the virial vir_cou electrostatic potential contribution to the virial vir_bnd chemical bond contribution to the virial vir_ang angular and three body potentials contribution to the virial vir_con constraint bond contribution to the virial vir_tet tethering potential contribution to the virial line 3 132 STFC Section 4 2 cpu s elapsed cpu time since the beginning of the job volume system volume temp_shl core shell temperature eng _shl configurational energy due to core shell potentials vir_shl core shell potential contribution to the virial alpha angle between b and c cell vectors beta angle between c and a cell vectors gamma angle between a and b cell vectors vir_pmf Potential of mea
301. outine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine subroutine merge_hcube f merge_systol f merge_tools f serial f define_system_module f spme_module f merge_hcube f merge_systol f merge_tools f serial f spme_module f vdw_module f vdw_module f property_module f hyper_dynamics_module f parse_module f parse_module f optimiser_module f define_system_module define_system_module define_system_module define_system_module define_system_module define_system_module tersoff_module f tersoff_module f tersoff_module f tersoff_module f tether_module f three_body_module f utility_module f optimiser_module f utility_module f utility_module f hyper_dynamics_module f hyper_dynamics_module f optimiser_module f 1f_rotation1_module f nlist_builders_module f nlist_builders_module f temp_scalers_module f integrator_module f error_module f hyper_dynamics_module f hyper_dynamics_module f tether_module f property_module f property_module f optimiser_module f Fh Fh Fh Fh Fh Fh 258 Index algorithm 5 53 98 Brode Ahlrichs 14 74 75 FIQA 5 53 54 68 multiple timestep 72 73 75 82 83 100 101 103 133 NOSQUISH 5 54 55 68 QSHAKE 5 53 55 70 72 78 RATTLE 5 54 55 57 77 SHAKE 5 53 54 74 77 78 velocity Verl
302. p to locate these entries No observed transitions indicates either a longer simulation is necessary or a higher temperature simulation should be considered b Check that the simulation was sufficiently long to guarantee all high temperature tran sitions have been found that are compliant with the specified reliability deltad The estimated stop time derived from this factor appears as the last entry of the TRA record in the EVENTS file c If the simulation stop time has not been reached the job must be restarted from the REVCON REVIVE and HYPRES files renaming them as CONFIG REVOLD and HYPOLD for the purpose and continued until the stop time has been reached After the simulation finally stops a new simulation can be started from the basin file obtained from the earliest shortest extrapolated time low temperature transition See section 5 4 3 for more information on restarting a TAD simulation Use the DL_POLY Java GUI to plot the system energy and temperature for the whole of the simulation Apart from the equilibration period these should hold their values within normal thermodynamic fluctuation even if transitions have occured If they do not the system probably has not been equilibrated adequately to begin with in which case start the simulation again See sction 5 4 3 amp 153 STFC Section 5 4 e Check that all the new states the program found are in the BASINS directory Note that there ma
303. p p Vi 38 STFC Section 2 3 2 3 Ti T T roe Oe es 2 6 met 2 6 2 x 2 149 17 a ij m 9 jee NB P dij 0 2 8 1 In the energy and virial corrections we have used the approximation Gig 27 Pro To qij Wa N 1 2 N Lat a 2 2 150 i lt p gt where lt 0 gt is regarded as a constant of the system In DL POLY 2 the metal forces are handled by the routine METFRC The local density is cal culated by the routines METDENS EAMDEN and FSDEN The long ranged corrections are calculated by LRCMETAL Reading and generation of EAM table data from TABEAM is handled by METTAB and METAL_DERIV Notes on the Treatment of Alloys The distinction to be made between EAM and FSM potentials with regard to alloys concerns the mixing rules for unlike interactions Starting with equations 2 123 and 2 124 it is clear that we require mixing rules for terms Vij r j and p rj when atoms i and j are of different kinds Thus two different metals A and B we can distinguish 4 possible variants of each AA BB AB BA Vis ris Vig tig Vij ris Vig ri and AA BB AB BA Pij rij Pij rij Pij rij Pij rij These forms recognise that the contribution of a type A atom to the potential of a type B atom may be different from the contribution of a type B atom to the potential of a type A atom In both EAM 4 and FSM 38 cases it turns out that Vig A rig Vga ri gt 2 151 though the
304. place 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 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 error 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 pro
305. potential specified In processing the FIELD file DL_POLY_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 direc tives in the FIELD file It simply means that DL POLY_2 has ceased processing the FIELD data but has not reached the end of the file or encountered a close directive Probable cause corruption of the DL POLY 2 executable or of the FIELD file We would be interested to hear of other reasons Action Recompile the program or recreate the FIELD file If neither of these works send the problem to us Message 17 error strange exit from CONTROL file processing See notes on message 16 above Message 18 error duplicate 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 er
306. ppearing 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 units a80 a40 record 3 optional neut The energy units on the units directive are described by additional keywords a40 a eV for electron volts field file header Unit of energy used for input and output activate the neutral charge groups option for the electrostatic calculations b kcal for k calories mol c kJ for k Joules mol 110 STFC Section 4 1 d K for Kelvin e 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 structural 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 d
307. r data TEST 1 endif if e data TEST 1 2 then mkdir data TEST 1 2 endif mv CONTROL data TEST 1 2 CONTROL mv FIELD data TEST 1 2 FIELD mv CONFIG data TEST 1 2 CONFIG mv OUTPUT data TEST 1 2 0UTPUT mv REVIVE data TEST 1 2 REVIVE mv REVCON data TEST 1 2 REVCON if e TABLE then mv TABLE data TEST 1 2 TABLE endif if e TABEAM then mv TABEAM data TEST 1 2 TABEAM endif if e STATIS then mv STATIS data TEST 1 2 STATIS endif if e RDFDAT then mv RDFDAT data TEST 1 2 RDFDAT endif if e ZDNDAT then mv ZDNDAT data TEST 1 2 ZDNDAT endif if e CFGMIN then mv CFGMIN data TEST 1 2 CFGMIN 173 STFC Section 7 1 endif chmod 400 data TEST 1 2 which first creates a new DL POLY data TEST if necessary sub directory and then moves the standard 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 the character string LF VV RB or CB according to which algorithm leapfrog LF ve locity Verlet VV RB rigid body minimisation or CB constraint bond minimisation has been performed 7 1 1 8 supa The supa macro provides a convenient way of running the DL POLY test cases in batch mode It is currently structured to submit batch jobs to the Daresbury Cray XD1 but can easily be adapted for other machines where batch queuing is possibl
308. r indicated by the specification in the FIELD file Each potential is defined by a header record and a set of data records with the potential and force tables header record atom 1 a8 first atom type atom 2 a8 second atom type potential data records number of data records Int ngrid 3 4 data 1 real data item 1 data 2 real data item 2 data 3 real data item 3 data 4 real data item 4 force data records number of data records Int ngrid 3 4 data 1 real data item 1 data 2 real data item 2 data 3 real data item 3 data 4 real data item 4 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 parameter mxgrid which is defined in the PARSET F subroutine in the SETUP_PROGRAM F file DL POLY 2 will re interpolate the tables if ngrid gt mxgrid but will abort if ngrid lt mxgrid The potential and force tables are used to fill the internal arrays vvv and ggg respectively see section 2 3 1 The contents of force arrays are derived from the potential via the formula 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 give
309. r 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 potentials that the potential function requested is one which is of a form known to the program If the requested potential form is unknown termination of the program results The most probable cause of this is the incorrect choice of the potential keyword in the FIELD file 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 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 205 STFC Section C 0 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 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 mu
310. ra ru k i j The contribution to be added to the atomic stress tensor is given by o reff 2 119 where a and 6 indicate the x 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 This property plus the fact that Tersoff potentials two and three body contributions scale as N3 where N is the number of particles makes it essential that these terms are calculated by the link cell method 33 DL POLY 2 applies no long ranged 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 included to permit simulation of amorphous materials particularly borate glasses The potential forms available in DL POLY 2 are as follows 1 Harmonic harm 1 U Pijkn Aiken 60 2 120 2 Harmonic cosine hcos k U 6ijkn 5 co8 ijn cos 60 2 121 3 Planar potential plan U bijzkn A 1 cos 6ijkn 2 122 These functions are identical to those appearing in the intra molecular inversion angle descriptions above There are significant differences in implementation however arisin
311. ral minimisation The timing information for this may be taken from the previous equilibration run e Set the remaining CONTROL keywords as were defined for the initial equilibration simulations 4 Before starting the TAD simulation use the UNIX mkdir command to make the following empty directories e BASINS to receive any new structures found e TRACKS to store the tracking configurations e PROFILES to store any transition pathways found by NEB calculation If the directories BASINS TRACKS and PROFILES already exist then carefully archive the data before deleting the contents Do not empty these directories if continuing restarting the simulation in the original starting basin The information in these directories is still live in this case Further information on these files can be found in section 5 5 5 Run the TAD simulation This will perform a simulation at the high temperature requested checking for structural transitions at the intervals specified Each time it finds a structural transition it will record the new state determine the activation energy transition pathway and stopping time then revert back to the starting basin and continue 6 When the simulation ends proceed as follows a Check the EVENTS file to see if any structural transitions have been obtained Each event is represented by a single record and transitions are flagged with the keyword TRA at the start of the record Use unix gre
312. ray 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 225 error multiple selection of optimisation options The user has specified more than one optimisation directive in the CONTROL file Action Remove redundant optimisation directive s from CONTROL file 207 STFC Section C 0 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 Action The arrangement of the data in the FIELD file must be sorted All atoms in the same group must be arranged 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 exclud
313. rdinates 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 4 2 2 The OUTPUT File The job output consists of 7 sections Header Simulation control specifications Force field spec ification 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 job 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
314. rection They are particularly useful for simulating surfaces The periodic cell in the XY plane can be any parallel ogram 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 A1 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 45 The surface in a system with charges can also be modelled with DL_POLY_2 if periodicity is allowed in the Z direction In this case slabs of ions well separated by vacuum zones in the Z direction can be handled with IMCON 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 through the centre
315. red 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 ccp5 ac uk 1 2 Functionality The following is a list of the features DL POLY_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 do 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 H20 etc D 4 Simple rigid molecules e g CCl4 SFe Benzene etc 5 Rigid molecular ions with point charges e g KNOs NH4 9S04 etc 6 Polymers with rigid bonds e g C Han 2 7 Polymers with rigid bonds and point charges e g proteins 8 Macromolecules and biological systems 9 Molecules with flexible bonds STFC Section 1 2 10 11 12 Silicate glasses and zeolites Simple metals and alloys e 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 following features il 10 All common forms of non bon
316. relaxed shells Action Locate the definition of the core shell units in the FIELD file and check that all necessary integer keys have been supplied Consult the user manual if in doubt 242 STFC Section C 0 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 potential 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 is 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 exclusive 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 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 consid
317. 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 mxcel1 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 213 STFC Section C 0 Message 400 error 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 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 simula
318. rij pi 09pi 2 140 j Lj i JA OO pi Amp pylr dr 2 141 Tmet where p is the uncorrected local density and Jis the mean particle density Evaluating the integral part of the above equation yields 1 EAM density correction No long ranged corrections apply beyond ret 2 Finnis Sinclair density correction No long ranged corrections apply beyond cutoffs c and d 36 STFC Section 2 3 3 Sutton Chen density correction An pa a yes i 2 142 3p m 3 4 Gupta density correction 2 Tmet T Thet 2rmet 2 2 2 exp 205 2 143 ij ij The density correction is applied immediately after the local density is calculated The pair term correction is obtained by analogy with the short ranged potentials and is U Sl rij 27 Pro Opi dij i 1 AH N Tij lt Tmet N TijZT met U 53 Y Vislrij 5 D SO Vis rij UY U i 1 m i 1 Ai dU 21Np Var Tmet N Us S F pe 5pi 2 144 i 1 N U Flo ei JO 55 U2 80 N F p oo dUs 4r pS tn Ya pij r r dr i l met Note that 9U2 is not required if p has already been corrected Evaluating the integral part of the above eguations yields 1 EAM energy correction No long ranged corrections apply beyond ret 2 Finnis Sinclair energy correction No long ranged corrections apply beyond cutoffs c and d 3 Sutton Chen energy correction O n 3 A 27 N pea a n 3 met 24
319. ror 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 larger 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 246 STFC Section C 0 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 sy
320. ror too many molecule sites specified DL POLY 2 has a fixed limit on the number of unique molecular sites in any given simulation If this limit is exceeded the program terminates Action Standard user response Fix parameter mxsite 190 STFC Section C 0 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 arrays An increment less than this is permissible however Action The tables must be recalculated with an appropriate increment Message 23 error incompatible FIELD and TABLE file potentials This error arises when the specification of the short range potentials is different in the FIELD and TABLE files This usually means that the order of specification of the potentials is different When DL POLY 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 th
321. ror Messages 2 2 cee coe emaa eee ewe e e a 14 The DL POLY 2 Directory Stractite k a ee es 1 4 1 The sremod Sub directory o ee 1 4 2 The utility Sub directory lt o a 4 4 4 1 43 The data Sub directory ses o is 1 44 The bench Sub directory ss s o a s s d ioar ae a a k a aa a a h L45 The execute Sab diregtory oop c le soa we e a Re Rn ee ee ae 1 4 6 The build Sub directory STFC Contents 14 7 The public Sub directory surco Sk Ge ee we ee a a 9 1 48 The java Sub directory 4 i a 266 a em ee 9 1 5 Obtaining the Source Code oe esa edor t a a REE RE BS 10 1 6 Other IntoraaloR e score aa ke ed ee ee RE HE K Fee He 10 2 DL_POLY_2 Force Fields and Algorithms 11 21 The DL POLY 2 Force Field sa sa da 4 45 o RE Re ee a em ee 13 2 2 The Intramolecular Potential Functions 2 02520004 15 221 Bond Potentials sa se aes os woo we be Oe RE k ee 15 222 Distance Restraints s esa 6b ee Pe hye PRR Ew RE REE 17 2 238 Valence Angle Potentials oc 24 545 eee Bd hee eee 17 224 Angular Restrald s cascos Pee eee ee Gwe oe Re OS 19 2 2 5 Dihedral Angle Potentials o 202220004 20 2 2 6 Improper Dihedral Angle Potentials o o 22 2 2 7 Inversion Angle Potentials 23 228 Tethering Fortes gt conos k hrs aa a 25 2 2 9 Frozen Atoms sanaaa is 26 23 The Intermolecular Potential Functions so os so sacs 4 ee kee
322. rrays 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 SHLFRC Action Standard user response Fix the parameter msbad Set equal to the value of the parameter mxshl Message 424 error electrostatics incorrect for all pairs When using the all pairs option in conjunction with 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 215 STFC Section C 0 Message 425 error transfer buffer array too small in shlmerge The buffer used to transfer data between nodes in the subroutine SHLMERGE has been dimensioned
323. rror 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 216 STFC Section C 0 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 435 error specify rcut before the coulomb precision When specifying the desired precision for the coulomb sum in the CONTROL file it is first neces sary to specify the real space cutoff rcut Action Place the cut directive before the coulomb precision directive in the CONTROL file and rerun Message 436 error unrecognised ensemble An unknown ensemble option has been specified in the CONTROL file Action Locate ensemble directive in the CONTROL file and amend appropriately Message 438 error PMF constraints failed to converge The constraints in the potential of mean force algorithm have not converged in the permitted num ber of cycles
324. ry 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 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 2310 error failed allocation of nstqvv_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 249 STFC Section C 0 Message 2320 error NEB convergence failure The nudged elastic band calculation in the temperature accelerated dynamics or bias potential dynamics has failed to converge Action The best approach is to halt the TAD or BPD simulation and focus on the NEB calculation in isolation First try to reproduce the error by a straightforward NEB calculation using the same start and end points for the chain Adjusting the convergence criteria may offer a way forward Try minimising the start and end points independently to a higher precision It is possible that the
325. s with a Ewald convergence parameter A 1 k1 maximum k vector index in x direction k2 maximum k vector index in y direction k3 maximum k vector index in z direction finish close the CONTROL file last data record hke precision fij 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 hke sum a k k2 15 select HK Ewald sum for electrostatics with a Ewald convergence parameter A 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 integrator type select type of integration algorithm leapfrog leapfrog integration algorithm default velocity velocity Verlet integration algorithm impact in E ux uy uz identity of impacted atom n time step when impact occurs E the recoil energy of the impacted atom in KeV ux X component of normalised recoil direction vector uy Y component of normalised recoil direction vector uz Z component of normalised recoil direction vector job time f set job time to f seconds minim energy n f minim force n f minim distance n f programmed minimisation based on energy force or position n number of time steps between minimisations f permitted variation tolerance DL_POLY units mult n set multiple timestep mult
326. s 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 60 which is an adap tation of DL_POLY specific to protein modelling However you may simulate proteins and other 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 CONFIG file 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 There are further somewhat limited tools for processing proteins in the MACROMOL subdi rectory of the DL POLY 2 utility directory These utilities will allow you build a biological system and create the necessary FIELD file from the GROMOS 6 or AMBER 8 force fields 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 3
327. s directive and associated data records need not be specified if the molecule contains no core shell units 5 bonds n where n is the number of flexible chemical bonds in the molecule Each of the subsequent 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 real 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 112 STFC Section 4 1 Table 4 7 Chemical bond potentials key potential type Variables 1 4 functional form harm Harmonic k ro U r 5k r ro hrm mors Morse Eo ro k U r Eo 1 exp k r r0 1 mrs 12 6 12 6 A B U r 4 126 rhrm Restraint k ro re U r 3k r ro lr ro lt re Ur kr kre r rol re r rol gt Te rhm quar Quartic k ro ko RY U r r ro Kr ro 4 E r ro gur buck Buckingha
328. s forces The algorithm is described in detail in 54 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 Figure 2 7 The multiple timestep algorithm The atoms surrounding the central atom open circle are classified as primary if they occur within a radius rprim 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 55 56 In this section we briefly outline the basic methodology Users wishing to add new features DL_POLY_2 will need to be familiar with the underlying techniques as they are described in greater detail in references 43 56 2 6 1 The Replicated Data Strategy The Replicated Data RD strategy 55 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 73 STFC Section 2 6 ie the arrays defining the atomic coordinates r velocities v and forces fp for all N atoms
329. s 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 mxvdw Note that this parameter must be double the number of required metal potentials Recompile the program Message 72 error different metal potential types specified DL_POLY_2 does not permit the user to mix different types of metal potential in the same simu lation There are no known rules for making alloys in this way Action Change the FIELD and TABEAM file as required so that only one type of metal potential is used Message 73 error too many inversion potentials specified The number of inversion potentials specified in the FIELD file exceeds the permitted maximum 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 198 STFC Section C 0 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 Message 79 error incorrect bo
330. s 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 0 NVT_EO NVT_HO NVT_BO etc are used if no con straint forces are present These routines treat the NVE Evans NVT Hoover Nos NVT and 82 STFC Section 3 2 NVT Berendsen ensembles respectively The corresponding versions of these routines which han dle constraint forces are NVE_1 NVT_El NVT_H1 or NVT B1 These versions call the routine RDSHAKE_1 to handle the constraints RDSHAKE_1 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 quantities are calculated by the routine STATIC which also writes the STATIS file section 4 2 8 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 OUT PUT file and dump
331. s the restart files REVIVE and REVCON sections 4 2 5 and 4 2 3 respectively An idea of the construction of a DL POLY_2 program can be obtained from the following flowchart Figure 3 1 2 The example represents a DL_POLY_2 program which uses the multiple timestep algorithm with bond constraints and the Nos Hoover thermostat 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 sremod directory In what follows we assume the makefile in the srcmod 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 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 ma
332. sage 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 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 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 210 STFC Section C 0 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 re quested integration al
333. sage 67 error incorrect boundary condition in thbfre Three body forces in DL_POLY_2 are only permissible with cubic orthorhombic and parallelepiped periodic boundaries Use of other boundary conditions results in this error Action If nonperiodic boundaries are required the only 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 thbfre 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 197 STFC Section C 0 Action Standard user response Fix the parameter mxcel1 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 i
334. scribed by message 60 above Action Standard user response Fix the parameter mxdihd 196 STFC Section C 0 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 ter minate if too many are present Do 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 Termination results if too many are encountered Do not confuse this error with that described 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 poten tial 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 ie imcon 6 Action Either the periodic boundary condition or the choice of calculation of the electrostatic forces must be changed Mes
335. sor 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 231 STFC Section C 0 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 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 1370 error failed allocation of work arrays in nst_h0 f This is a memory allocation error Probable cause excessive size of simulated system Actio
336. ssed with the flag DPVM set but the number of PVM nodes was not stated Action Delete the module INITCOMMS O from the sremod 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 187 STFC Section C 0 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 location in the FIELD file which can happen if too few or too many data records are included Action Locate the erroneous directive in the FIELD file and correct error 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 ref erence to other energy units will result in this error message S
337. st of these functions can be performed by the DL POLY_2 java GUI 9 7 1 1 2 cleanup cleanup removes several standard data files from the execute sub directory It contains the unix commands if e CFGMIN rm CFGMIN if e OUTPUT rm OUTPUT if e RDFDAT rm RDFDAT if e REVCON rm REVCON if e REVIVE rm REVIVE if e REVOLD rm REVOLD if e STATIS rm STATIS if e ZDNDAT rm ZDNDAT and removes the files if present CFGMIN OUTPUT REVCON REVOLD STATIS REVIVE RDFDAT and ZDNDAT Useful data should be stored elsewhere beforehand 171 STFC Section 7 1 7 1 1 3 copy copy invokes the unix commands mv CONFIG CONFIG OLD mv REVCON CONFIG mv REVIVE REVOLD which collectively prepare the DL_POLY files in the execute sub directory for the continuation of a simulation It is always a good idea to store these files elsewhere in addition to using this macro 7 1 1 4 gopoly gopoly is used to submit a DL_POLY job to the Daresbury Cray XD1 and takes a form similar for batch processing on many parallel machines The following is for an 8 processor job bin sh S bin bash 1 pn compute 1 h_rt 01 00 00 pe am mpi 8 N GOPOLY cwd j y mpirun np NSLOTS hostfile TMPDIR machines home w1 d1_poly_2 18 execute DLPOLY X Normally the job is submitted by the unix command gsub gopoly where qsub is a local command for submission to the Cray XD1 The number of required nodes
338. stem 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 nptqvv_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 2180 error failed allocation of nptqvv_b2 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 2190 error failed allocation of nptqvv_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 247 STFC Section C 0 Message 2200 error failed allo
339. stems 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 require the use of angular forces to describe the local structure correctly In both cases the angular terms are included as three body terms the forms of which are described in chapter 2 These terms are entered into the FIELD file with the pair potentials Note 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 macro molecule 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 with out specifying bond potentials In this case DL_POLY_2 will automatically cancel the non bonded force
340. stimate and there are sometimes circum stances where the estimate can be improved upon This is especially the case when the system contains a strong directional anisotropy such as a surface These four parameters may also be set explicitly by the ewald sum directive in the CONTROL file For example the directive ewald sum 0 35668 would set a 0 35 Tl 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 freut 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
341. sts of 250 iron atoms and runs under a Berendsen NPT ensemble 6 1 1 25 Test Case 25 Nickel Aluminium 1 1 alloy with EAM potential Another example of an alloy using the EAM potential This is a Nickel Aluminium alloy in the 1 1 ratio The NVE ensemble is used and the system has 432 atoms 6 1 1 26 Test Case 26 Nickel metal with EAM potential Another EAM simulation of a metal 256 Nickel atoms under the Berendsen NPT ensemble 6 1 1 27 Test Case 27 Calcite NVE simulation of 420 molecules 2100 atoms of calcium carbonate in the calcite crystal structure The carbonate anion is handled as a flexible unit with Morse potential bonds and harmonic bond angles NVE ensemble 6 1 1 28 Test Case 28 Optimisation of Ice VII structure 432 SPC water molecules are arranged in a thermally excited Ice VII structure and the congugate gradient method is used to optimise the structure to recover the perfect crystal form Both rigid body RB and constraint bond CB models are used to define the water molecule structure The optimisation proceeds to zero force convergence 6 1 1 29 Test Case 29 Programmed minimisation of Ice VII structure This test is a repeat of Test Case 28 except that the structural optimisation proceeds via a programmed minimisation involving alternating periods of molecular dynamics and conjugate gra dient minimisation Once again both rigid body RB and constraint bond CB models are used to define the water molecule structur
342. 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 445 error undefined many body potential DL_POLY_2 has been requested to process a many body potential it does not recognise Action Check the FIELD file and make sure the keyword is correctly defined Make sure the code version you are using contains the code necessary to deal with the requested potential Add the code required if necessary Message 446 error undefined electrostatic key in dihfre The subroutine DIHFRC has detected a request for an unknown kind of electrostatic model Action The probable source of the error is an improperly described force field Check the CONTROL file and FIELD files for incompatible
343. summation that was particularly effective for large systems The basic assumption is that in condensed phase systems the electrostatic forces are effectively screened by charge ordering so that at long ranged any given charge looks like a neutral object Meanwhile the force shifting is formally equivalent to surrounding each charge with a spherical charge that neutralises the charge content of the cutoff sphere thus resembling the natural screening on a predetermined distance scale reut The method thus assumes that these two effects are the same The Wolf et al method 41 was cast into a form suitable for molecular dynamics by Fennell and Gezelter 42 which is the form implemented in DL POLY 2 In this form damping function is the same complementary error function as appears in the Ewald sum see section 2 4 6 qiq erfclary erfcloras er fc arcut 2a exp a r U ij oo eee riz Areo rij TZ 1 2 a rij Teut A E EE eran ducers a E rij lt Tout 2 171 The corresponding force is given by qua erfe arij 2a exp a r er fC QT cut 2a exp a r2 4 ee f 3 j 1 2 2 2 1 2 se S J dre Ki T rij Tout T Tout Tij a O E he eee rij lt Tout 2 172 Note these formulae reduce to the basic shifted force Coulombic potential forms when the conver gence parameter a is zero The contribution to the atomic virial is oie f 2 173 which is not the negative of the potential term 43 STFC S
344. system but larger size Message 46 error ewlbuf array too small in ewald1 The ewlbuf array used to store structure factor data in subroutine EWALD1 has been dimensioned too small Action Standard user response Fix the parameter mxebuf Message 47 error transfer buffer too small in merge The buffer used to transfer data between nodes in the MERGE subroutines has been dimensioned too small Action Standard user response Fix the parameter mxbuff 194 STFC Section C 0 Message 48 error transfer buffer too small in fortab The buffer used to transfer data between nodes in the FORTAB subroutines has been dimensioned 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 posi tion 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 Messag
345. t The objective is to remove any entries in these files that occured after the restart files were written It is therefore important to determine what was going on when the program crashed With TAD it may be found that the time out error is most likely to happen during a NEB calculation or a structure optimisation In which case it will be hard work deciding what needs to be patched up before continuing though the time stamp of the restart files is still the crucial factor This situation is best avoided in the first place by giving the code a generous close time in the CONTROL file so that these optimisation tasks have a chance to complete before the axe falls 154 STFC Section 5 5 5 4 4 Things to Be Aware of when Running TAD 1 Choose the catch radius carefully where possible basing it on nearest neighbour distances obtained form the parent crystal A consequence of using too large a catch radius is that transitions that require a short hop in atom positions may be missed during a run Such misses make it difficult to reconstruct the reaction path and in particular cause the NEB calculation to crash since there is no simple path between the reference structures 2 The user may sometimes observe successive transitions into the same state If a transition to an already visited state occurs it is indicated with the flag TRR repeat transition in the EVENTS file Such repeated transitions are normal but if they occur in su
346. than one molecules directive it will terminate 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 expect to en counter 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 yet 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 assign the data correctly and therefore terminates Action Make sure the molecular data appears before the non bonded forces data in the FIELD file and resubmit Message 14 error too many unique atom types specified This 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 189 STFC Section C 0 parameter Action Standard user response Fix parameter mxsvdw Message 15 error duplicate pair
347. the catch radius If a transition is detected a NEB calculation is initiated using the two reference structures to find the activation energy E A determination of the time of the transition is made In DL POLY _2 the occurrence time of the transition toce is determined by checking back from the detection of the transition through past configurations saved at regular intervals which should be much less than a BPD block Each saved configuration is energy minimised and compared with the reference state structure until the first occurrence of the new state is found This provides a reasonable accuracy on the transition time somewhat better than using the end time of the BPD block in which the transition occurred The transition time is then corrected for the boost factor in equation 5 5 The new found state becomes the reference state for the next stage of the simulation If no transition was detected the original reference state is left in place In both cases the simulation continues from the end of the block as if uninterrupted Note this is markedly different from the TAD procedure described in section 5 4 The simulation is continued until from inspection it apparent that all significant kinds of transition have been observed When this is is anybody s guess but clearly some knowledge of the system gained from other sources it invaluable here With all the information gathered it should now be possible
348. 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 6 Dreiding 7 AMBER 8 and OPLS 22 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 ra ro os TN 5 Ubona ibond Za b toond 1 Nangle 5 Uangleliangle Tas Tb Te langle 1 Naihed 5 Uginea Udineds Tas Tb Ves Ta tdihed 1 Ninv 5 Uinv linv Las Tb Tos a ling 1 N 1 N 5 Y Upairl i A r l i 1 j gt i 2N 1 N T S Y Us bodyli j K Ti j h i 1 a k gt j y Y Urersop il i uu i 1 j gt i 3N 2N 1 N 5 5 gt Das body t J K N Li Lj Lies En j gt i k gt j n gt k N Y Umeta i ra RV i 1 N V Uertn i ri Vi 2 1 i l where Ubond Uangle Udined Uinv Upair U3 body UTersoff and U4 body are empirical interaction functions representing chemical bonds valence angles dihedral angles inversion angles pair body three body Tersoff many body covalent and four body forces respectively The first four are regarded by DL POLY 2 as intra molecular interactions and the next five as inter molecular inter actions The term Umeta
349. thm to be called each iteration with the new cell vectors and volume obtained from V t At V t exp sat n t 5A HA ante 5A1 H t 2 253 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 AN kg At x t 5A SLB TO Toa y Wale koTos Y ae Fixe 40000 ner 5d LP Pa xO wl vt Sales Aae 62 STFC Section 2 5 At sO 1 u t At V t Em r t At lt r t Ato t At call rattle R VELO Ve jat ne 7 0 HEA exp Atnt 3A HO v t At lt v t S At iG call rattle V nt At nft 5At EE P t At Poa xlt Ad n t An W t A6 v t At Ent Atju t At AD a llas At 2 T t At Toa Wat At kpToxt v t At v t At t l Atju t At 2 254 Routines rattle R and rattle V apply the bondlength and velocity constraint formulae 2 233 and 2 234 respectively The equations have the same conserved variable Hynpr 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 7 as
350. thout regard to the bond constraints 5 In the second iterative stage of SHAKE each node calculates the incremental correction vectors for the bonded atoms in its own list of bond constraints It then sends specific correction vectors to all neighbours that share the same atoms using the information compiled in step 3 6 When all necessary correction vectors have been received and added the positions of the constrained atoms are corrected 7 Steps 5 and 6 are repeated until the bond constraints are converged 8 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 77 STFC Section 2 6 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 the normal VV scheme 2 When the velocity is updated iteration of the constraint force takes place The incremental 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 n
351. tion Standard user response Fix the parameter mxtbp 199 STFC Section C 0 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 pro gram 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 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 di rectives see description of CONTROL file the program will expect the CONFIG file to contain atomic velocities as well as positions Termination results if these are not present Action Either replace the CONFIG file with one containing the velocities or if not available remove the restart directive altogether and let DL_POLY_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 potential in the system i e as defined in the FIELD file If there are m distinct types of atom in the system the index can possibly range from 1 to m m 1 2 If the internally calculated index exceeds this number this error report results Action Standard user response Fix the parameter mxtbp Message 87 error too many link cells required in fbpfrc The FBPFR
352. tion 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 specified 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 file specifying the electrostatic interactions options Action Locate the conflicting directives in the CONTROL file and correct 214 STFC Section C 0 Message 418 error bond vector work arrays too small in bndfre 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 a
353. tion energy and the corresponding transition time is essential After recording the transition the subsequent dynamics correctly starts for BPD from the final state of the double transition but the loss of information is ignored A NEB calculation is therefore necessary to determine the lost details For TAD objective is to find the escape route for a transition from the starting state and halting the analysis of the reaction path at the first minimum is sufficient to define the escape The intermediate state provides a valid possible basin for further study of the kinetics of the system This is sensible if the two peaks on the reaction path are of similar magnitude However it is quite possible that the second peak is much higher or much lower than the first The first of these possibilities means that choosing the first minimum as the starting basin for a new simulation will most likely consistently return the system to the original starting state The second possibility suggests that the second state on the reaction path is a better option for the next phase of the study To decide between these possibilities it is necessary to determine the activation energy of the second peak Thus in both BPD and TAD when a multiple maximum is found on the reaction path a NEB calculation is needed to complete the path analysis See the following section 5 7 for details 5 7 Running a Nudged Elastic Band Calculation Running an independent NEB calculation may
354. to determine the full diffusion process for the original system at the state point chosen The recommended procedure for running BPD with DL_POLY_2 is as follows 1 Run a normal unbiased simulation of the system at the required state point temperature and volume Make sure the system does not undergo any structural changes that nullify the validity of the BPD approach e g melting Record the average configuration energy Vmin of the system Keep the REVCON file to use as the starting CONFIG structure for the BPD simulation Set up the BPD option in the CONTROL file as follows a Set the bpd path directive b Define the energy units for the BPD parameters e g units s where s is one of eV kcal kJ or K signifying electron volts kilo cals per mole kilo joules per mole or Kelvin respectively No units directive means DL POLY internal units apply Forces are given in chosen energy units per Angstrom c Set the value of the average potential Vmin g vmin f where fis the known average potential d Set the value of the potential bias Epias e g ebias f where fis the bias energy level 145 STFC Section 5 3 e Set the size of the simulation BPD block i e the number of time steps between structure optimisations for transition detection e g num_block 500 f Set the number of configurations between each write of a tracking configuration file This should be an integer divisor of the BPD bloc
355. tom type potential key See table 4 14 potential parameter see table 4 14 potential parameter see table 4 14 cutoff range for this potential A 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 121 STFC Section 4 1 Table 4 14 Four body Potentials key potential type Variables 1 2 functional formt harm Harmonic k do U 5k o bo hcos Harmonic cosine k Qo U E cos d cos o plan Planar A U 6 A 1 cos t is the inversion angle 4 1 3 4 Metal Potentials Metal potentials in DL POLY 2 are based on the embedded atom model EAM 34 35 and the Finnis Sinclair model FSM 3 The EAM potentials are tabulated and are supplied to DL_POLY_2 in the input file TABEAM see 4 1 6 The FSM potentials are analytical and DL_POLY_2 supports the explicit forms due to Finnis and Sinclair 3 Sutton and Chen 37 38 and Gupta 40 Metal potentials like van der Waals potentials are also non bonded potentials and are char acterised by atom types rather than specific atomic indices The input of metal potential data is signalled by the directive metal n where nis the number of metal potentials to be entered There follows n records each specifying a particular metal potential in the following ma
356. toms sharing a bond to a direction perpendicular to the bond vector This provides another constraint force Hra Quiz dij gt vj m 2 234 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 proceeding to the next stage of the velocity Verlet scheme DL POLY 2 implements a parallel version of RATTLE that is based on the same approach as SHAKE 11 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 example of such a reaction coordinate would be the distance between two ions in solution If a number of simulations are conducted with the system constrained to different points along the reaction coordinate then the mean constraint force may be plotted as a function of reaction coordinate and the function integrated to obtain the free energy for the overall process 49 The PMF constraint force virial and contributions to the stress tensor are obtained in a manner analagous to that for a bond co
357. ts 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 135 STFC Section 4 2 4 2 8 The STATIS File The file is formatted with integers as i10 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 Data records Subsequent lines contain the instantaneous values of statistical variables dumped from the array stpval A specified number of entries of stpval are written in the format 1p 5e14 6 The number of array elements required determined by the parameter mxnstk in the 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 CONTROL 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
358. ubroutines RATTLE_R and RATTLE_V Cell size and shape variations The extension of the isotropic algorithm to anisotropic cell variations is straightforward The tensor n is defined by At 1i CS ai a 2 262 and the new cell vectors given by H t At nH t 2 263 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 may be either problematic or impossible Examples in which it is impossible to specify sufficient bond constraints are 1 linear molecules with more than 2 atoms e g CO2 2 planar molecules with more than three atoms e g benzene Even when the structure can be defined by bond constraints the network of bonds produced may be problematic Normally they make the iterative SHAKE procedure slow particularly if a ring of constraints is involved as occurs when one defines water as a constrained triangl
359. ulated 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 240 STFC Section C 0 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 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 1900 error fai
360. unctional form thrm Truncated harmonic k 00 p U 0 6 bo exp r ri 07 shrm Screened harmonic k b pi p2 U 0 E 9 00 exp ri p1 Tik p2 bvs1 Screened Vessal 28 k 00 Pi Po U 0 OR 1600 my 0 m7 exp rij p1 Tik p2 bvs2 Truncated Vessal 29 k 00 a p U 0 k 0 0 b0 8 bo 27 gn 9 00 T 00 expl ri ri 0 hbnd H bond 7 Dro Rio U 0 Dpycos 9 5 Rnw T jx 6Rro ri 10 is the a b c angle variable 1 variable 2 variable 3 variable 4 variable 5 real real real real real potential parameter see table 4 13 potential parameter see table 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 atmnam 2 atmnam 3 atmnam 4 key variable 1 variable 2 variable 3 as a8 a8 a8 a4 real real real first atom type central site second atom type third atom type fourth a
361. undary condition in fbpfre The 4 body force routine assumes a cubic or parallelepiped periodic boundary condition is in op eration 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 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 Ac
362. 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 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 1270 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
363. ust remove references to the MPI libraries from the Makefile and 84 STFC Section 3 2 add the file serial f to your compilation this will insert replacement dummy routines 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 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 DLPFFTS3 subrou tine should be commented out before compiling 3 Problems with optimization Some subroutines may not compile correctly when using optimization on some compilers This is not the fault of the DL_POLY_2 code but of the compiler concerned This is cir cumvented 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 sub routines 4 Adding new functionality To include a new subroutine in the code simply add subroutine o to the list of object nam
364. utine 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 1f_rotationi_module 1f_rotation2_module lf rotation1 module lf rotation2 module Hh Hh Hh hh ensemble_tools_module ensemble_tools_module ensemble_tools_module ensemble_tools_module ensemble_tools_module vv_rotationi_module f vv_rotation2_module f vv_rotationi_module f vv_rotation2_module f ensemble_tools_module ensemble_tools_module vv_motion_module f vv_motion_module f basic_comms f serial f lf motion module f lf rotation1 module lf rotation2 module vv rotation1 module vv rotation2 module vv motion module f lf motion module f lf motion module f lf motion module f lf rotation1 module lf rotation2 module lf rotation1 module lf rotation2 module Hh Hh Hh hh Hh Fh Hh hh ensemble_tools_module vv_rotationi_module f vv_rotation2_module f vv_rotationi_module f vv_rotation2_module f ensemble_tools_module vv_motion_module f vv_motion_module f vv_motion_module f optimiser_module f nlist_builders_module nlist_builders_module nlist_builders_module nlist_builders_module nlist_builders_module setup_module f pass_tools f 256 Hh Fh Fh Fh Fh Fh Fh Fh Fh Fh STFC Section D
365. ve thermodynamic averaging of a system at a given temperature where equilibration is problematical due to long time scales This is described in section 5 3 5 5 3 3 Full Path Kinetics This option is intended to determine the true diffusional path that a solid state system follows at a given temperature but at an accelerated rate Each time the system transforms from one structure to another i e from one state to another the program records the states it encounters and calculates both the activation energy E associated with the transition and extrpolates the time at which the transition would have occured in the unbiased system This information may subsequently be used to determine the full kinetics of the system The method in outline is as follows 1 The first operation of the program is to construct a reference state for the structure by energy minimisation The simulation then proceeds with the biased potential option in much the 144 STFC Section 5 3 same manner as a normal simulation but during which a running estimate of the boost factor in equation 5 5 is computed At user defined intervals called here a BPD block the simulation is halted and the structure energy minimised to create new reference structure which is compared with the original reference state to determine if a transition has occurred A transition is deemed to have occured if one or more atoms are displaced by more than a preset distance
366. way they are extended to handle alloys see below It follows that EAM and FSM potentials cannot be mixed in a single simulation Furthermore even for FSM potentials possessing different analytical forms there is no agreed procedure for mixing the parameters The user is therefore strongly advised to be consistent in the choice of potential when modelling alloys The general form of the EAM and FSM potentials is 36 1 N N N Umetat 5 gt 2 Vis ris FC gt 2 123 i 1 jAi i 1 where F p is a functional describing the energy of embedding an atom in the bulk density pi which is defined as N pi Dd pislrij 2 124 j lj i It should be noted that the density is determined by the coordination number of the atom defined by pairs of atoms This makes the metal potential dependent on the local density environmental Vij rij is a pair potential incorporating repulsive electrostatic and overlap interactions N is the number of interacting particles in the MD box The types of metal potentials available in DL POLY 2 are as follows 1 EAM potential eam There are no explicit mathematical expressions for EAM potentials so this potential type is read exclusively in the form of interpolation arrays from the TABEAM table file as implemented in the METTAB routine Section 4 1 6 The rules for combining the potentials from different metals to handle alloys are different from the FSM class of potentials see below 2 Finnis Sinclair
367. which can be atoms or rigid molecules M 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 2 229 2 228 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 13 and is based on the Verlet leapfrog integration scheme 12 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 is used retrospectively to compute the constraint force needed to conserve the bondlength It is relatively simple to show that the constraint force has the form Baldy des p 2 230 297 DNE d i where pij is the reduced mass of the two atoms connected by the bond d and dij are the original and intermediate bond vectors d j is the constrained bondlength and Ati is the valei integration timestep It should be noted that this formula is an approximation only For a system of simple diatomic molecu
368. work in parallel The method is as follows 1 The start and end points of the NEB construction are the energy minimised structures for states A and B A structure RV is defined as the set of 3N coordinates locating all N atoms in the system 2 A series of states is constructed by linear interpolation between the structures of states A and B i e a series of configurations RN is generated with i 0 Nnep such that i 0 indicates state A and i Ne indicates state B and RN RY i Nueo BN Eo 5 1 For convenience these configurations are called the beads of the NEB chain Each bead has a configuration energy which may be written as VA RN This is the usual configuration energy for a system with an atomic structure RY i 3 Each bead in the NEB chain is then connected to its two nearest neighbours by a harmonic spring except for the end beads which have only one neighbour each so that the beads make a chain strung from state A to state B The spring energy of the whole chain is then defined as Nneb Va RNnes 5 Eneb gt RN RM 5 2 where kneb is the spring force constant 141 STFC Section 5 3 4 With the chain thus defined the objective is now to minimise the energy function E RN where Nueb 1 VRA a Y VRY 5 3 7 1 E RN es in which the adjustable variables are the configurations RN i e the atomic coordinates in each structure while the chain end beads at
369. x 1 cos 2 A3 1 cos 3 t is the a b c d dihedral angle 10 inversions n where nis the number of inversion interactions present in the molecule Each of the following 116 STFC Section 4 1 11 12 n records contains inversion key ad index 1 integer index 2 integer index 3 integer index 4 integer variable 1 real variable 2 real potential key See table 4 10 first atomic index second atomic index third atomic index fourth atomic index potential parameter see table 4 10 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 Table 4 10 Inversion Angle Potentials key potential type Variables 1 2 functional formt harm Harmonic k hcos Harmonic cosine k plan Planar A do U 6 ikl do do U 6 5 cos cos 60 U 6 A 1 cos 6 t is the inversion angle 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 site 1 integer site 2 integer site 3 integer site m integer number of sites in rigid unit first site atomic index second site atomic index third site
370. y be fewer new states than the number of transitions observed because some transitions may end in the same basin more than once so a new state is not stored in this case Examine them using the DL_POLY Java GUI There may be signs of imperfect minimisation atoms not quite on lattice sites etc but this is normal at this stage Corrective action can be taken later see section 5 6 Check that the profiles for all the reported transitions have been written in the PRO FILES directory These record the change in configuration energy as a function of reaction coordinate Plot these using the DL_POLY Java GUI Use the GUI spline option to get a better idea of what the profiles look like Take special note of any double or multiple maxima The transition is considered to end at the first minimum in these cases A basin file for the first intermediate state is written to the BASINS directory 5 4 3 Restarting a TAD Simulation It may be necessary to restart a TAD simulation for a number of reasons a The earliest low temperature transition from the current basin has been found and the user now wants to investigate transitions from the new basin This basin corresponds to that which a molecular dynamics simulation would have reached first at the low tem perature In which case users should save their data from the first study and commence the simulation from the new basin exactly as in the previous study i e renaming the appropriate basin CF
371. y the routines COUL2 and COUL2NEU One last point to note is that the reaction field method can also be implemented with the damped shifted force Coulombic potential described above section 2 4 4 so that polarisation of the long ranged medium by the dipole of the cutoff sphere may be accounted for 2 4 6 Ewald Sum The Ewald sum 12 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 inter acting via the Coulomb potential The Ewald method makes two amendments to this simple model Firstly each ion is effectively neutralised at long range by the superposition of a spherical gaussian cloud of opposite charge centred on the ion The combined assembly of point ions and gaussian 44 STFC Section 2 4 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 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
372. ys in nvtq_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 1520 error failed allocation of work arrays in nvtq_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 234 STFC Section C 0 Message 1530 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 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 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

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