# | Line 88 | Line 88 | void SimSetup::createSim( void ){ | |
---|---|---|
88 | ||
89 | ||
90 | ||
91 | < | if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF(); |
92 | < | else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF(); |
93 | < | else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF(); |
91 | > | if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF(); |
92 | else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); | |
93 | else{ | |
94 | sprintf( painCave.errMsg, | |
# | Line 242 | Line 240 | void SimSetup::createSim( void ){ | |
240 | ||
241 | globalIndex = mpiSim->divideLabor(); | |
242 | ||
245 | – | |
246 | – | |
243 | // set up the local variables | |
244 | ||
245 | int localMol, allMol; | |
246 | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; | |
247 | + | |
248 | + | int* mol2proc = mpiSim->getMolToProcMap(); |
249 | + | int* molCompType = mpiSim->getMolComponentType(); |
250 | ||
251 | allMol = 0; | |
252 | localMol = 0; | |
# | Line 259 | Line 258 | void SimSetup::createSim( void ){ | |
258 | ||
259 | for( j=0; j<components_nmol[i]; j++ ){ | |
260 | ||
261 | < | if( mpiSim->getMyMolStart() <= allMol && |
263 | < | allMol <= mpiSim->getMyMolEnd() ){ |
261 | > | if( mol2proc[j] == worldRank ){ |
262 | ||
263 | local_atoms += comp_stamps[i]->getNAtoms(); | |
264 | local_bonds += comp_stamps[i]->getNBonds(); | |
# | Line 279 | Line 277 | void SimSetup::createSim( void ){ | |
277 | if( local_atoms != simnfo->n_atoms ){ | |
278 | sprintf( painCave.errMsg, | |
279 | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" | |
280 | < | " localAtom (%d) are note equal.\n", |
280 | > | " localAtom (%d) are not equal.\n", |
281 | simnfo->n_atoms, | |
282 | local_atoms ); | |
283 | painCave.isFatal = 1; | |
# | Line 304 | Line 302 | void SimSetup::createSim( void ){ | |
302 | Atom::createArrays(simnfo->n_atoms); | |
303 | the_atoms = new Atom*[simnfo->n_atoms]; | |
304 | the_molecules = new Molecule[simnfo->n_mol]; | |
305 | + | int molIndex; |
306 | ||
307 | + | // initialize the molecule's stampID's |
308 | ||
309 | + | #ifdef IS_MPI |
310 | + | |
311 | + | |
312 | + | molIndex = 0; |
313 | + | for(i=0; i<mpiSim->getTotNmol(); i++){ |
314 | + | |
315 | + | if(mol2proc[i] == worldRank ){ |
316 | + | the_molecules[molIndex].setStampID( molCompType[i] ); |
317 | + | molIndex++; |
318 | + | } |
319 | + | } |
320 | + | |
321 | + | #else // is_mpi |
322 | + | |
323 | + | molIndex = 0; |
324 | + | for(i=0; i<n_components; i++){ |
325 | + | for(j=0; j<components_nmol[i]; j++ ){ |
326 | + | the_molecules[molIndex].setStampID( i ); |
327 | + | molIndex++; |
328 | + | } |
329 | + | } |
330 | + | |
331 | + | |
332 | + | #endif // is_mpi |
333 | + | |
334 | + | |
335 | if( simnfo->n_SRI ){ | |
336 | + | |
337 | + | std::cerr << "n_SRI = " << simnfo->n_SRI << "\n"; |
338 | + | |
339 | Exclude::createArray(simnfo->n_SRI); | |
340 | the_excludes = new Exclude*[simnfo->n_SRI]; | |
341 | + | for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
342 | simnfo->globalExcludes = new int; | |
343 | simnfo->n_exclude = tot_SRI; | |
344 | } | |
# | Line 326 | Line 356 | void SimSetup::createSim( void ){ | |
356 | // set the arrays into the SimInfo object | |
357 | ||
358 | simnfo->atoms = the_atoms; | |
359 | < | simnfo->sr_interactions = the_sris; |
359 | > | simnfo->molecules = the_molecules; |
360 | simnfo->nGlobalExcludes = 0; | |
361 | simnfo->excludes = the_excludes; | |
362 | ||
# | Line 383 | Line 413 | void SimSetup::createSim( void ){ | |
413 | ||
414 | the_ff->setSimInfo( simnfo ); | |
415 | ||
416 | < | makeAtoms(); |
416 | > | makeMolecules(); |
417 | simnfo->identArray = new int[simnfo->n_atoms]; | |
418 | for(i=0; i<simnfo->n_atoms; i++){ | |
419 | simnfo->identArray[i] = the_atoms[i]->getIdent(); | |
420 | } | |
421 | ||
392 | – | if( tot_bonds ){ |
393 | – | makeBonds(); |
394 | – | } |
395 | – | |
396 | – | if( tot_bends ){ |
397 | – | makeBends(); |
398 | – | } |
399 | – | |
400 | – | if( tot_torsions ){ |
401 | – | makeTorsions(); |
402 | – | } |
403 | – | |
404 | – | |
422 | if (the_globals->getUseRF() ) { | |
423 | simnfo->useReactionField = 1; | |
424 | ||
# | Line 638 | Line 655 | void SimSetup::createSim( void ){ | |
655 | ||
656 | // new AllLong( simnfo ); | |
657 | ||
641 | – | if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff ); |
642 | – | if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff ); |
658 | if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff ); | |
659 | if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff ); | |
660 | ||
661 | + | #ifdef IS_MPI |
662 | + | mpiSim->mpiRefresh(); |
663 | + | #endif |
664 | ||
647 | – | |
665 | // initialize the Fortran | |
666 | < | |
666 | > | |
667 | > | |
668 | simnfo->refreshSim(); | |
669 | ||
670 | if( !strcmp( simnfo->mixingRule, "standard") ){ | |
# | Line 683 | Line 701 | void SimSetup::makeMolecules( void ){ | |
701 | BondStamp* currentBond; | |
702 | BendStamp* currentBend; | |
703 | TorsionStamp* currentTorsion; | |
704 | + | |
705 | + | bond_pair* theBonds; |
706 | + | bend_set* theBends; |
707 | + | torsion_set* theTorsions; |
708 | + | |
709 | ||
710 | //init the forceField paramters | |
711 | ||
712 | the_ff->readParams(); | |
713 | ||
714 | ||
715 | < | // init the molecules |
715 | > | // init the atoms |
716 | ||
717 | + | double ux, uy, uz, u, uSqr; |
718 | + | |
719 | atomOffset = 0; | |
720 | excludeOffset = 0; | |
721 | for(i=0; i<simnfo->n_mol; i++){ | |
# | Line 707 | Line 732 | void SimSetup::makeMolecules( void ){ | |
732 | info.myExcludes = &the_excludes[excludeOffset]; | |
733 | info.myBonds = new Bond*[info.nBonds]; | |
734 | info.myBends = new Bend*[info.nBends]; | |
735 | < | info.myTorsions = new Torsions*[info.nTorsions]; |
735 | > | info.myTorsions = new Torsion*[info.nTorsions]; |
736 | ||
737 | theBonds = new bond_pair[info.nBonds]; | |
738 | theBends = new bend_set[info.nBends]; | |
# | Line 717 | Line 742 | void SimSetup::makeMolecules( void ){ | |
742 | ||
743 | for(j=0; j<info.nAtoms; j++){ | |
744 | ||
745 | < | currentAtom = theComponents[stampID]->getAtom( j ); |
745 | > | currentAtom = comp_stamps[stampID]->getAtom( j ); |
746 | if( currentAtom->haveOrientation() ){ | |
747 | ||
748 | dAtom = new DirectionalAtom(j + atomOffset); | |
# | Line 790 | Line 815 | void SimSetup::makeMolecules( void ){ | |
815 | ||
816 | if( currentBend->haveExtras() ){ | |
817 | ||
818 | < | extras = current_bend->getExtras(); |
818 | > | extras = currentBend->getExtras(); |
819 | current_extra = extras; | |
820 | ||
821 | while( current_extra != NULL ){ | |
# | Line 812 | Line 837 | void SimSetup::makeMolecules( void ){ | |
837 | ||
838 | default: | |
839 | sprintf( painCave.errMsg, | |
840 | < | "SimSetup Error: ghostVectorSource was neiter a " |
840 | > | "SimSetup Error: ghostVectorSource was neither a " |
841 | "double nor an int.\n" | |
842 | "-->Bend[%d] in %s\n", | |
843 | j, comp_stamps[stampID]->getID() ); | |
# | Line 907 | Line 932 | void SimSetup::makeMolecules( void ){ | |
932 | ||
933 | the_molecules[i].initialize( info ); | |
934 | atomOffset += info.nAtoms; | |
935 | < | } |
936 | < | |
937 | < | // clean up the forcefield |
913 | < | |
914 | < | the_ff->cleanMe(); |
915 | < | } |
916 | < | |
917 | < | |
918 | < | |
919 | < | void SimSetup::makeAtoms( void ){ |
920 | < | |
921 | < | int i, j, k, index; |
922 | < | double ux, uy, uz, uSqr, u; |
923 | < | AtomStamp* current_atom; |
924 | < | |
925 | < | DirectionalAtom* dAtom; |
926 | < | int molIndex, molStart, molEnd, nMemb, lMolIndex; |
927 | < | |
928 | < | lMolIndex = 0; |
929 | < | molIndex = 0; |
930 | < | index = 0; |
931 | < | for( i=0; i<n_components; i++ ){ |
932 | < | |
933 | < | for( j=0; j<components_nmol[i]; j++ ){ |
934 | < | |
935 | < | #ifdef IS_MPI |
936 | < | if( mpiSim->getMyMolStart() <= molIndex && |
937 | < | molIndex <= mpiSim->getMyMolEnd() ){ |
938 | < | #endif // is_mpi |
939 | < | |
940 | < | molStart = index; |
941 | < | nMemb = comp_stamps[i]->getNAtoms(); |
942 | < | for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){ |
943 | < | |
944 | < | current_atom = comp_stamps[i]->getAtom( k ); |
945 | < | if( current_atom->haveOrientation() ){ |
946 | < | |
947 | < | dAtom = new DirectionalAtom(index); |
948 | < | simnfo->n_oriented++; |
949 | < | the_atoms[index] = dAtom; |
950 | < | |
951 | < | ux = current_atom->getOrntX(); |
952 | < | uy = current_atom->getOrntY(); |
953 | < | uz = current_atom->getOrntZ(); |
954 | < | |
955 | < | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
956 | < | |
957 | < | u = sqrt( uSqr ); |
958 | < | ux = ux / u; |
959 | < | uy = uy / u; |
960 | < | uz = uz / u; |
961 | < | |
962 | < | dAtom->setSUx( ux ); |
963 | < | dAtom->setSUy( uy ); |
964 | < | dAtom->setSUz( uz ); |
965 | < | } |
966 | < | else{ |
967 | < | the_atoms[index] = new GeneralAtom(index); |
968 | < | } |
969 | < | the_atoms[index]->setType( current_atom->getType() ); |
970 | < | the_atoms[index]->setIndex( index ); |
971 | < | |
972 | < | // increment the index and repeat; |
973 | < | index++; |
974 | < | } |
975 | < | |
976 | < | molEnd = index -1; |
977 | < | the_molecules[lMolIndex].setNMembers( nMemb ); |
978 | < | the_molecules[lMolIndex].setStartAtom( molStart ); |
979 | < | the_molecules[lMolIndex].setEndAtom( molEnd ); |
980 | < | the_molecules[lMolIndex].setStampID( i ); |
981 | < | lMolIndex++; |
982 | < | |
983 | < | #ifdef IS_MPI |
984 | < | } |
985 | < | #endif //is_mpi |
986 | < | |
987 | < | molIndex++; |
988 | < | } |
989 | < | } |
990 | < | |
991 | < | #ifdef IS_MPI |
992 | < | for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] ); |
993 | < | |
994 | < | delete[] globalIndex; |
995 | < | |
996 | < | mpiSim->mpiRefresh(); |
997 | < | #endif //IS_MPI |
998 | < | |
999 | < | the_ff->initializeAtoms(); |
1000 | < | } |
1001 | < | |
1002 | < | void SimSetup::makeBonds( void ){ |
1003 | < | |
1004 | < | int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
1005 | < | bond_pair* the_bonds; |
1006 | < | BondStamp* current_bond; |
1007 | < | |
1008 | < | the_bonds = new bond_pair[tot_bonds]; |
1009 | < | index = 0; |
1010 | < | offset = 0; |
1011 | < | molIndex = 0; |
1012 | < | |
1013 | < | for( i=0; i<n_components; i++ ){ |
1014 | < | |
1015 | < | for( j=0; j<components_nmol[i]; j++ ){ |
1016 | < | |
1017 | < | #ifdef IS_MPI |
1018 | < | if( mpiSim->getMyMolStart() <= molIndex && |
1019 | < | molIndex <= mpiSim->getMyMolEnd() ){ |
1020 | < | #endif // is_mpi |
1021 | < | |
1022 | < | for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){ |
1023 | < | |
1024 | < | current_bond = comp_stamps[i]->getBond( k ); |
1025 | < | the_bonds[index].a = current_bond->getA() + offset; |
1026 | < | the_bonds[index].b = current_bond->getB() + offset; |
1027 | < | |
1028 | < | exI = the_bonds[index].a; |
1029 | < | exJ = the_bonds[index].b; |
1030 | < | |
1031 | < | // exclude_I must always be the smaller of the pair |
1032 | < | if( exI > exJ ){ |
1033 | < | tempEx = exI; |
1034 | < | exI = exJ; |
1035 | < | exJ = tempEx; |
1036 | < | } |
1037 | < | |
1038 | < | |
1039 | < | #ifdef IS_MPI |
1040 | < | |
1041 | < | the_excludes[index*2] = |
1042 | < | the_atoms[exI]->getGlobalIndex() + 1; |
1043 | < | the_excludes[index*2 + 1] = |
1044 | < | the_atoms[exJ]->getGlobalIndex() + 1; |
1045 | < | |
1046 | < | #else // isn't MPI |
1047 | < | |
1048 | < | the_excludes[index*2] = exI + 1; |
1049 | < | the_excludes[index*2 + 1] = exJ + 1; |
1050 | < | // fortran index from 1 (hence the +1 in the indexing) |
1051 | < | #endif //is_mpi |
1052 | < | |
1053 | < | // increment the index and repeat; |
1054 | < | index++; |
1055 | < | } |
1056 | < | offset += comp_stamps[i]->getNAtoms(); |
1057 | < | |
1058 | < | #ifdef IS_MPI |
1059 | < | } |
1060 | < | #endif //is_mpi |
1061 | < | |
1062 | < | molIndex++; |
1063 | < | } |
1064 | < | } |
1065 | < | |
1066 | < | the_ff->initializeBonds( the_bonds ); |
1067 | < | } |
1068 | < | |
1069 | < | void SimSetup::makeBends( void ){ |
1070 | < | |
1071 | < | int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
1072 | < | bend_set* the_bends; |
1073 | < | BendStamp* current_bend; |
1074 | < | LinkedAssign* extras; |
1075 | < | LinkedAssign* current_extra; |
1076 | < | |
1077 | < | |
1078 | < | the_bends = new bend_set[tot_bends]; |
1079 | < | index = 0; |
1080 | < | offset = 0; |
1081 | < | molIndex = 0; |
1082 | < | for( i=0; i<n_components; i++ ){ |
1083 | < | |
1084 | < | for( j=0; j<components_nmol[i]; j++ ){ |
1085 | < | |
1086 | < | #ifdef IS_MPI |
1087 | < | if( mpiSim->getMyMolStart() <= molIndex && |
1088 | < | molIndex <= mpiSim->getMyMolEnd() ){ |
1089 | < | #endif // is_mpi |
1090 | < | |
1091 | < | for( k=0; k<comp_stamps[i]->getNBends(); k++ ){ |
1092 | < | |
1093 | < | current_bend = comp_stamps[i]->getBend( k ); |
1094 | < | the_bends[index].a = current_bend->getA() + offset; |
1095 | < | the_bends[index].b = current_bend->getB() + offset; |
1096 | < | the_bends[index].c = current_bend->getC() + offset; |
1097 | < | |
1098 | < | if( current_bend->haveExtras() ){ |
1099 | < | |
1100 | < | extras = current_bend->getExtras(); |
1101 | < | current_extra = extras; |
1102 | < | |
1103 | < | while( current_extra != NULL ){ |
1104 | < | if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
1105 | < | |
1106 | < | switch( current_extra->getType() ){ |
1107 | < | |
1108 | < | case 0: |
1109 | < | the_bends[index].ghost = |
1110 | < | current_extra->getInt() + offset; |
1111 | < | the_bends[index].isGhost = 1; |
1112 | < | break; |
1113 | < | |
1114 | < | case 1: |
1115 | < | the_bends[index].ghost = |
1116 | < | (int)current_extra->getDouble() + offset; |
1117 | < | the_bends[index].isGhost = 1; |
1118 | < | break; |
1119 | < | |
1120 | < | default: |
1121 | < | sprintf( painCave.errMsg, |
1122 | < | "SimSetup Error: ghostVectorSource was neiter a " |
1123 | < | "double nor an int.\n" |
1124 | < | "-->Bend[%d] in %s\n", |
1125 | < | k, comp_stamps[i]->getID() ); |
1126 | < | painCave.isFatal = 1; |
1127 | < | simError(); |
1128 | < | } |
1129 | < | } |
1130 | < | |
1131 | < | else{ |
1132 | < | |
1133 | < | sprintf( painCave.errMsg, |
1134 | < | "SimSetup Error: unhandled bend assignment:\n" |
1135 | < | " -->%s in Bend[%d] in %s\n", |
1136 | < | current_extra->getlhs(), |
1137 | < | k, comp_stamps[i]->getID() ); |
1138 | < | painCave.isFatal = 1; |
1139 | < | simError(); |
1140 | < | } |
1141 | < | |
1142 | < | current_extra = current_extra->getNext(); |
1143 | < | } |
1144 | < | } |
1145 | < | |
1146 | < | if( !the_bends[index].isGhost ){ |
1147 | < | |
1148 | < | exI = the_bends[index].a; |
1149 | < | exJ = the_bends[index].c; |
1150 | < | } |
1151 | < | else{ |
1152 | < | |
1153 | < | exI = the_bends[index].a; |
1154 | < | exJ = the_bends[index].b; |
1155 | < | } |
1156 | < | |
1157 | < | // exclude_I must always be the smaller of the pair |
1158 | < | if( exI > exJ ){ |
1159 | < | tempEx = exI; |
1160 | < | exI = exJ; |
1161 | < | exJ = tempEx; |
1162 | < | } |
1163 | < | |
1164 | < | |
1165 | < | #ifdef IS_MPI |
1166 | < | |
1167 | < | the_excludes[(index + tot_bonds)*2] = |
1168 | < | the_atoms[exI]->getGlobalIndex() + 1; |
1169 | < | the_excludes[(index + tot_bonds)*2 + 1] = |
1170 | < | the_atoms[exJ]->getGlobalIndex() + 1; |
1171 | < | |
1172 | < | #else // isn't MPI |
1173 | < | |
1174 | < | the_excludes[(index + tot_bonds)*2] = exI + 1; |
1175 | < | the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1; |
1176 | < | // fortran index from 1 (hence the +1 in the indexing) |
1177 | < | #endif //is_mpi |
1178 | < | |
1179 | < | |
1180 | < | // increment the index and repeat; |
1181 | < | index++; |
1182 | < | } |
1183 | < | offset += comp_stamps[i]->getNAtoms(); |
1184 | < | |
1185 | < | #ifdef IS_MPI |
1186 | < | } |
1187 | < | #endif //is_mpi |
1188 | < | |
1189 | < | molIndex++; |
1190 | < | } |
935 | > | delete[] theBonds; |
936 | > | delete[] theBends; |
937 | > | delete[] theTorsions; |
938 | } | |
939 | ||
940 | #ifdef IS_MPI | |
941 | < | sprintf( checkPointMsg, |
1195 | < | "Successfully created the bends list.\n" ); |
941 | > | sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
942 | MPIcheckPoint(); | |
943 | #endif // is_mpi | |
1198 | – | |
944 | ||
945 | < | the_ff->initializeBends( the_bends ); |
946 | < | } |
945 | > | // clean up the forcefield |
946 | > | the_ff->calcRcut(); |
947 | > | the_ff->cleanMe(); |
948 | ||
1203 | – | void SimSetup::makeTorsions( void ){ |
1204 | – | |
1205 | – | int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
1206 | – | torsion_set* the_torsions; |
1207 | – | TorsionStamp* current_torsion; |
1208 | – | |
1209 | – | the_torsions = new torsion_set[tot_torsions]; |
1210 | – | index = 0; |
1211 | – | offset = 0; |
1212 | – | molIndex = 0; |
1213 | – | for( i=0; i<n_components; i++ ){ |
1214 | – | |
1215 | – | for( j=0; j<components_nmol[i]; j++ ){ |
1216 | – | |
1217 | – | #ifdef IS_MPI |
1218 | – | if( mpiSim->getMyMolStart() <= molIndex && |
1219 | – | molIndex <= mpiSim->getMyMolEnd() ){ |
1220 | – | #endif // is_mpi |
1221 | – | |
1222 | – | for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){ |
1223 | – | |
1224 | – | current_torsion = comp_stamps[i]->getTorsion( k ); |
1225 | – | the_torsions[index].a = current_torsion->getA() + offset; |
1226 | – | the_torsions[index].b = current_torsion->getB() + offset; |
1227 | – | the_torsions[index].c = current_torsion->getC() + offset; |
1228 | – | the_torsions[index].d = current_torsion->getD() + offset; |
1229 | – | |
1230 | – | exI = the_torsions[index].a; |
1231 | – | exJ = the_torsions[index].d; |
1232 | – | |
1233 | – | |
1234 | – | // exclude_I must always be the smaller of the pair |
1235 | – | if( exI > exJ ){ |
1236 | – | tempEx = exI; |
1237 | – | exI = exJ; |
1238 | – | exJ = tempEx; |
1239 | – | } |
1240 | – | |
1241 | – | |
1242 | – | #ifdef IS_MPI |
1243 | – | |
1244 | – | the_excludes[(index + tot_bonds + tot_bends)*2] = |
1245 | – | the_atoms[exI]->getGlobalIndex() + 1; |
1246 | – | the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = |
1247 | – | the_atoms[exJ]->getGlobalIndex() + 1; |
1248 | – | |
1249 | – | #else // isn't MPI |
1250 | – | |
1251 | – | the_excludes[(index + tot_bonds + tot_bends)*2] = exI + 1; |
1252 | – | the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1; |
1253 | – | // fortran indexes from 1 (hence the +1 in the indexing) |
1254 | – | #endif //is_mpi |
1255 | – | |
1256 | – | |
1257 | – | // increment the index and repeat; |
1258 | – | index++; |
1259 | – | } |
1260 | – | offset += comp_stamps[i]->getNAtoms(); |
1261 | – | |
1262 | – | #ifdef IS_MPI |
1263 | – | } |
1264 | – | #endif //is_mpi |
1265 | – | |
1266 | – | molIndex++; |
1267 | – | } |
1268 | – | } |
1269 | – | |
1270 | – | the_ff->initializeTorsions( the_torsions ); |
949 | } | |
950 | ||
951 | void SimSetup::initFromBass( void ){ |
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