DL_MULTI supplement
Contents
1. 8 CCLRC Qc Qois Qc Q225 Q31c Q315 32 Q325 233c Q335 Qatc Qais Qu2e Q42s Qa3c Qazs 15 D ev aniz i 2 eV 3yizi 2 ei V3 a y She i Y 1 2 3 2 ei 5 3z r7 2 3 gt TE r 2 3 Dean r 2 3 1 net 45 152 17 y7 2 gt e vldriyizi i 5 Leia sen 2 5 gt ei gr y 2 1 4 2 2 gt eig 352 302r 3rf 2 5 3 gt e Fi 32 2 r 2 Ye 5 3 2 ei gizi 3yizir 2 Y EN 2 _ 21 722 ei 5 27 y 72 ri 2 1 2 gt LAN y gt E gt 3x y ey 2 Br y a CCLRC 16 1 Que Y iz V35 a Gay yi i 1 Qus gt GTV 35 2 Yi ziy i DL_MULTI does not use the following directives from DL_POLY bonds con straints pmf angles dihedrals inversions teth For DL_MULTI the records rigid units and mulaxes are described below Note that the atomic site indices referred to below are indices arising from numbering each atom in the molecule from 1 to the number specified in the atoms directive for this molecule This same num bering scheme should be used for all descriptions of this molecule DL_MULTI will itself construct the global indices for all atoms in the systems as for DL_POLY 5 rigid n or rigid units n where n is the number of rigid units in the molecule For DL_MULTT n must be 1 It is followed by one record specifying the sites in a rigid unit m integer number of sites in rigid unit2. 0 igrp integer neutral charge group number This is the same as the standard DL_ POLY Note however that the atomic site charge read here is ignored as it will be read below in the multipole input Also the repeat counter will almost always be 1 as atoms in the molecule with the same atomic number will have different multipoles and will be treated by DL_MULTI as different atomic types ifrz and igrp are not relevant for DL_MULTI use and should be omitted The next record carries the entry without a keyword jpoleo i8 multipole pole order for this atom 0 lt jpoleo lt 4 jpoleo is the pole order for the multipoles for this atom There are then a number of records giving the magnitude of the multipoles depending on jpoleo The real numbers giving the magnitude of the multipoles are f11 0 fixed format In all cases there is a record format f11 0 giving the multipole charge term order 0 If jpoleo gt 1 there is a record format 3f11 0 giving the dipole components If jpoleo gt 2 there is a record format 5f11 0 giving the quadrupole components If poleo gt 3 there is a record format 7f11 0 giving the octopole components If jpoleo gt 4 there are 2 records format 7f11 0 2f11 0 giving the hexadecapole components The order of the multipole components follow the usual order for spherical harmonics 4 Table 1 These are given below Qo e me a i Na 82 r i er wn
3. 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 5 azauracil DL_POLY TEST CASE azauracil units ev molecular types 2 azauracil multipole nummols 96 atoms 11 NI 14 007 0 00 1 4 0 495104 0 001568 0 158410 0 013091 0 459413 0 018431 0 035157 0 425186 0 002068 0 032228 0 664233 0 130477 0 013206 0 245208 2 059576 0 109874 0 287987 0 054286 0 290048 0 887905 0 346797 0 070680 0 105214 0 418582 2 343179 NI 14 007 0 00 1 4 0 608897 0 018043 0 051003 0 098955 0 204276 0 038276 039801 0 041331 0 096621 0 035699 0 202148 109761 0 163215 0 050993 2 800004 0 016288 1 130707 0 159565 055705 0 353922 0 056397 0 058125 0 131937 0 876265 2 423670 ARCE 9 more atoms ooo rigid units 1 11 1 2 3 4 5 6 7 8 9 10 11 mulaxes molaxes 1 3 6 2 3 6 2 3 1 finish azauracil multipole nummols 96 atoms 11 NI 14 007 0 00 1 4 0 495104 0 001568 0 158410 0 013091 0 459413 0 018431 0 035157 0 425186 0 002068 0 032228 0 664233 0 130477 0 013206 0 245208 2 059576 0 109874 CCLRC 12 0 287987 0 054286 0 290048 0 887905 0 346797 0 070680 0 105214 0 418582 2 343179 RER 10 more atons rigid units 1 11 1 2 3 4 5 6 7 8 9 10 11 mulaxes molaxes 1 3 6 2 3 6 2 3 1 finish vdw 15 CA CA buck 3832 1 0 277778 25 287 CA HY buck 689 5 0 272480 5 979 CA HP buck 446 9 0 242131 2 3
4. format 9i5 direction 1 atom la atom 1b direction 2 atom 2a atom 2b atom 2c direction 3 enantiomer flag direction 1 2 and 3 refer to the x y and z directions in the local axis system Use the integer 1 for x 2 for y and 3 for z each of the values must be used once Usually direction 1 will be 1 direction 2 will be 2 and direction 3 will be 3 and this must be the order if the enantiomer flag is 1 The axis in direction 1 normally x axis is defined along the bond from atom la to atom 1b The axis in direction 2 normally y axis is defined in the plane containing atoms 2a 2b and 2c and normal to the axis in direction 1 The axis in direction 3 normally z axis makes a right handed set with 1 and 2 The enantiomer flag can have values 1 or 1 In many crystalline systems the crystal structure contains a mixture of two enantiomers at least experimentally Often this will be the result of a slight departure from planarity in the experimental results which may or may not be physically real To permit the user the option of inputting a pair of enantiomers they are treated by DL_MULTI as two separate molecules However the setting up of the molecular axes using molaxes will set up two right handed axes systems which are not mirror images of each other To allow for this the signs of the appropriate multipole components need to be changed There are two ways the user can do this First the user can change the sign of all the o
5. site 1 integer first site atomic index site 2 integer second site atomic index site 3 integer third site atomic index e etc site m integer m th site atomic index Up to 15 sites can be specified on the first record Additional records are used if necessary Up to 16 sites are specified per record thereafter The format is 1615 6 mulaxes mulaxes a40 Define the axis system used to define the multipoles There is a second keyword on the mulaxes directive rotint the multipole components are described with respect to the principle mo ments of inertia axis system As for DL_POLY the principal axes are assigned to molecular types with the components of the rotational inertia tensor L obey ing Lua gt yy gt Izz to insure all processors converge on the same axes system There is an addition in DL_MULTI from the standard DL_POLY which ensures that the principal axes are always in the same direction with respect to multi plication by 1 This ensures that the multipole components can be defined with respect to this axis system unambiguously CCLRC 17 molaxes the multipole components are described with respect to an axis system defined by atoms in the molecule This will be the normal input method for DL_MULTI although internally the program will carry out a conversion using Wigner matrices to the rotint convention before carrying out any calculation The mulaxes record must be followed by one record with 9 integer values
6. 2 1 Molecular Systems 7 1 2 2 Force Field 22 0 2 ay a RA BO sel 7 1 2 3 Boundary Conditions 8 1 2 4 Target Computers 0 202000 eee ee ee 8 1 3 Obtaining the Source Code 8 2 DL MULTI Data Files 9 21 Phe INPUT Fles ose ge tek Be Bo re en un a ANR as A 10 2 1 1 The CONTROL File 10 212 The CONFIG File 2 22 us 2 4 dons Zus aan ann are Ba 10 ZLS The FIBED File 220 fog a Bae 2a Sera 11 2 2 The OUTPUT Biles sip pra a ar oe a ERG ie A 19 224 The OUTPUT File rat A he nes 19 Chapter 1 Introduction Scope of Chapter This chapter describes the concept design and directory structure of DL_POLY and how to obtain a copy of the source code CCLRC 1 1 DL_MULTI is an extension of DL_POLY It is designed to carry out simulations on rigid molecules whose electrostatics are described using the distributed multipole analysis of The DL_MULTI Package Stone et al 1 In the next section we outline the differences of DL_MULTI compared with DL_ POLY as briefly as possible 1 2 The current version of DL_MULTI is based on DL_POLY 2 13 We describe below the Extensions in DL_MULTI compared with DL_POLY extensions in DL_MULTI compared with DL_POLY and also the limitations 1 2 1 Molecular Systems DL_MULTI will simulate the following molecular species 1 2 3 Simple rigid mole
7. 74 CA NI buck 3179 5 0 271003 19 007 CA OX buck 3022 8 0 264550 17 160 HY HY buck 124 1 0 267380 1 414 HY HP buck 80 4 0 238095 0 561 HY NI buck 572 1 0 265957 4 494 HY OX buck 543 9 0 259740 4 057 HP HP buck 52 1 0 214592 0 223 HP NI buck 370 8 0 236967 1 784 OX HP buck 352 6 0 232019 1 611 NI NI buck 2638 0 0 264550 14 286 NI OX buck 2508 0 0 258398 12 898 OX OX buck 2384 5 0 252525 11 645 close 2 1 3 1 Format The FIELD file is fixed formatted Integers are formatted as i5 reals are normally f12 0 although the multipole moments are f11 0 and characters are a4 a8 a40 or a80 depending on context 2 1 3 2 Definitions of Variables The file divides into three sections general information molecular descriptions and non bonded interaction descriptions appearing in that order in the file 2 1 3 2 1 General information There are no changes from DL_POLY record 4 optional mpdist a40 Distance units used to define the multipoles The distance units on the mpdist directive are described by additional keywords angstrom for CCLRC 13 au for atomic units The default if the mpdist directive is omitted is au 2 1 3 2 2 Molecular details As is the case for standard DL_POLY the FIELD file must give the molecular details for the molecule types in the same order as they appear in the CONFIG file The entry of the molecular details begins with the mandatory directive molecule
8. Forester T R 1994 Comput Phys Commun 79 52 3 Smith W and Forester T R 1994 Comput Phys Commun 79 63 4 Stone A In Maksi Z B editor Theoretical Models of Chemical Bonding Part 4 Springer Verlag 1991 20
9. THE DL_MULTI USER MANUAL M Leslie CCLRC Daresbury Laboratory Daresbury Warrington WA4 4AD England Version 2 00 Jan 2003 CCLRC 1 ABOUT DL_MULTI DL MULTI is an extension to the standard DL_POLY package developed at Daresbury Laboratory by M Leslie for the EPSRC s Collaborative Computational Project for the Computer Simulation of Condensed Phases CCP5 The package is the property of The Council for the Central Laboratory of the Research Councils CCLRC DL MULTI is issued free under licence to academic institutions pursuing scientific research of a non commercial nature Commercial organisations may be permitted a licence to use the package after negotiation with the owners Daresbury Laboratory is the sole centre for distribution of the package Under no account is it to be redistributed to third parties without consent of the owners The purpose of the DL MULTI 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 MULTI in regard to its interfaces and programming style and it is adequately documented CCLRC 2 DISCLAIMER Neither the CCLRC EPSRC CCP5 nor any of the authors of the DL MULTI package or its derivatives guarantee that the package is free f
10. control variables for running a DL_POLY or DL_MULTI job The only difference in the CONTROL file between DL_MULTI and DL_POLY is in the definition of the Ewald sum precision DL_POLY uses the record ewald precision f whereas DL MULTI uses the following records mulp precision fdo fd1 fd2 fds fd4 fro fri fr2 fr3 fre fd0 is the Ewald precision in direct space for pole order 0 fd1 for pole order 1 and so on fr0 fri are the corresponding terms for reciprocal space It is recommended that the user sets a high precision smaller value of the f parameter for pole orders greater than 0 in direct space If this is not done there will be an energy drift due to energy changes when the higher order poles cross the cutoff boundary Values of 0 001 can be used for pole order 0 and for all the reciprocal space terms although smaller values will give better energy stability Values not less than 0 000001 should be used for the higher order terms in direct space 2 1 2 The CONFIG File The format of the CONFIG file for DL_MULTI is exactly the same as for DL_POLY Remember that all molecules of a particular molecule type must come together in the file and all atoms of a molecule must come together in the same order for all molecules If the molecule has enantiomers these are treated as two different molecules and all configurations of the first enantiomer must come before any of the second CCLRC 11 2 1 3 The FIELD File The FIELD
11. cules e g CCl4 SFe Benzene etc Rigid molecular ions with point charges e g KNO3 NH4 2SOu etc Systems which consist of mixtures of different types of molecule However the following systems cannot be treated 1 Molecules with flexible bonds 1 2 2 Force Field The DL_POLY force field is used and includes the following features 1 Ze 3 All common forms of non bonded atom atom potential Atom atom site site Coulombic potentials Atom atom site site distributed multipole potentials The following DL_POLY force field features should not be used in DL MULTI 1 2 3 4 5 6 7 Valence angle potentials Dihedral angle potentials Inversion potentials Improper dihedral angle potentials 3 body valence angle and hydrogen bond potentials 4 body inversion potentials Sutton Chen density dependent potentials for metals CCLRC 8 1 2 3 Boundary Conditions DL_MULTI has only been tested in parallelepiped periodic boundary conditions The author of DL_MULTI cannot guarantee that the other boundary conditions in DL_POLY will work 1 2 3 1 Parallel Algorithms DL_MULTI exclusively employs the Replicated Data parallelisation strategy 2 3 1 2 4 Target Computers DL_MULTI is targeted towards 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 rou
12. dd z components in the multipole description of the second molecule Secondly the user can use the enantiomer flag 1 and leave the components as they are DL_MULTI will then change the sign of the odd z components Note that if a non standard order of the axes in molaxes is used then the first method must be used The user will need to change the sign of the odd x or odd y components for the second molecule according to which axis is defined third in the description 7 finish This directive is entered to signal to DL_POLY that the entry of the details of a CCLRC 18 molecule has been completed The entries for a second molecule may now be entered beginning with the name of molecule record and ending with the finish directive The cycle is repeated until all the types of molecules indicated by the molecules directive have been entered The user is recommended to look at the example FIELD files in the data directory to see how typical FIELD files are constructed 2 1 3 3 Non bonded Interactions Non bonded interactions are identified by atom types as opposed to specific atomic indices The description in DL_MULTI is the same as in DL_POLY CCLRC 19 2 2 The OUTPUT Files DL_MULTI writes the same output files as DL_POLY The only differences are in the OUTPUT file 2 2 1 The OUTPUT File The job output consists of 7 sections Header Simulation control specifications Force field specification Summary of the initial c
13. onfiguration 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_MULTI It is meant to be a human readable file destined for hardcopy output 2 2 1 1 Header DL_MULTI output is the same as DL_POLY 2 2 1 2 Simulation Control Specifications DL_MULTI writes out the Ewald convergence parameter that DL_POLY would use and the reciprocal space cutoffs These values are not used by DL_MULTI The correct values are printed when the force field and initial configuration have been read in 2 2 1 3 Force Field Specification In addition to the normal DL_POLY output DL_MULTI writes out the input distributed multipoles 2 2 1 4 Summary of the Initial Configuration In addition to the normal DL_POLY output the cutoffs for the Ewald sum for each pole order are written out These are also recalculated every 100 time steps and written to the OUTPUT file since for simulations in which the cell volume changes the cutoffs may need to be changed to obtain the same accuracy 2 2 1 5 Simulation Progress This is the same as DL_POLY apart from the cutoff recalculation 2 2 1 6 Remaining subsections These are all the same as for DL_POLY Bibliography 1 Price S L Stone A J and Alderton M 1984 Mol Phys 52 987 1001 2 Smith W and
14. rom error Neither do they accept responsibility for any loss or damage that results from its use Use of the DL MULTI package without charge is confined to academic research only Commercial use is only permissible following negotiation with Daresbury Laboratory Users are not entitled to redistribute the program to third parties CCLRC 3 ACKNOWLEDGEMENTS DL_MULTI was developed under the auspices of the Council for the Central Laboratory of the Research Councils and the Engineering and Physical Sciences Research Council The package is the property of the Council for the Central Laboratory of the Research Councils of the United Kingdom Advice assistance and encouragement in the development of DL_MULTI has been given by many people We gratefully acknowledge the following W Smith D Willock S L Price A Stone CCLRC Manual Notation In the DL_MULTI manual the same notation is used as in the DL_POLY Manual Specific fonts are used to convey specific meanings T 2 directories indicates unix file directories ROUTINES indicates subroutines functions and programs macros indicates a macro file of unix commands directive indicates directives or keywords variables indicates named variables and parameters FILE indicates filenames Contents 1 Introduction 6 1 1 The DE MUETE Package 4 2 2 22 zn 2 ee Paule ica ee 7 1 2 Extensions in DL_LMULTI compared with DL POLY 7 1
15. s n or molecular types n where nis an integer specifying the number of different types of molecule appearing in the FIELD file Note that enantiomers are counted as two different types of molecule Once this directive has been encountered DL_MULTI enters the molecular description environment in which only molecular decription keywords and data are valid Immediately following the molecular types directive are the records defining individ ual molecules The first directive is the same as in DL POLY 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 The next directive tells DL_MULTI that there are multipoles in the FIELD file 2 multipole The next directive is the same as DL_POLY 3 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 4 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 multipole order and multipole components Unlike the standard DL POLY there are several records for each atom The first record carries the entries sitnam a8 atomic site name weight real atomic site mass chge real atomic site charge nrept integer repeat counter P g P CCLRC 14 ifrz integer frozen atom if ifrz gt
16. tines to permit substitution by ap propriate alternatives or even deletion Note that some of the communication routines in DL_MULTI which have routines in DL_POLY with the same name have been modified and have only been tested using MPI If you are planning to use a different parallelisation method you should test these routines yourself DL_MULTI has been tested on on the the following computers 1 IBM SP 2 2 SUN SPARC and ULTRA SPARC 3 Beowulf systems Porting of DL_MULTI to these and other machines requires MPI message passing tools 1 3 Obtaining the Source Code Holders of a licence for DL_POLY can obtain a copy of DL MULTI as a separate stand alone program Chapter 2 DL MULTI Data Files Scope of Chapter This chapter describes all the input and output files for DL_POLY examples of which are to be found in the data sub directory CCLRC 10 2 1 The INPUT files DL_MULTI requires five input files named CONTROL CONFIG FIELD TABLE and REVOLD The first three files are mandatory while TABLE is used only to input certain kinds of pair potential and is not always required REVOLD is required only if the job rep resents a continuation of a previous job TABLE and REVOLD are the same in DL_MULTI as in DL_POLY and are not described further here In the following sections we describe the changes to the standard DL_POLY files 2 1 1 The CONTROL File The CONTROL file is read by the subroutine SIMDEF and defines the
Download Pdf Manuals
Related Search