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, |
246 |
|
|
247 |
|
int localMol, allMol; |
248 |
|
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
249 |
+ |
|
250 |
+ |
int* mol2proc = mpiSim->getMolToProcMap(); |
251 |
+ |
int* molCompType = mpiSim->getMolComponentType(); |
252 |
|
|
253 |
|
allMol = 0; |
254 |
|
localMol = 0; |
260 |
|
|
261 |
|
for( j=0; j<components_nmol[i]; j++ ){ |
262 |
|
|
263 |
< |
if( mpiSim->getMyMolStart() <= allMol && |
263 |
< |
allMol <= mpiSim->getMyMolEnd() ){ |
263 |
> |
if( mol2proc[j] == worldRank ){ |
264 |
|
|
265 |
|
local_atoms += comp_stamps[i]->getNAtoms(); |
266 |
|
local_bonds += comp_stamps[i]->getNBonds(); |
279 |
|
if( local_atoms != simnfo->n_atoms ){ |
280 |
|
sprintf( painCave.errMsg, |
281 |
|
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
282 |
< |
" localAtom (%d) are note equal.\n", |
282 |
> |
" localAtom (%d) are not equal.\n", |
283 |
|
simnfo->n_atoms, |
284 |
|
local_atoms ); |
285 |
|
painCave.isFatal = 1; |
304 |
|
Atom::createArrays(simnfo->n_atoms); |
305 |
|
the_atoms = new Atom*[simnfo->n_atoms]; |
306 |
|
the_molecules = new Molecule[simnfo->n_mol]; |
307 |
+ |
int molIndex; |
308 |
+ |
|
309 |
+ |
// initialize the molecule's stampID's |
310 |
+ |
|
311 |
+ |
#ifdef IS_MPI |
312 |
+ |
|
313 |
+ |
|
314 |
+ |
molIndex = 0; |
315 |
+ |
for(i=0; i<mpiSim->getTotNmol(); i++){ |
316 |
+ |
|
317 |
+ |
if(mol2proc[i] == worldRank ){ |
318 |
+ |
the_molecules[molIndex].setStampID( molCompType[i] ); |
319 |
+ |
molIndex++; |
320 |
+ |
} |
321 |
+ |
} |
322 |
|
|
323 |
+ |
#else // is_mpi |
324 |
+ |
|
325 |
+ |
molIndex = 0; |
326 |
+ |
for(i=0; i<n_components; i++){ |
327 |
+ |
for(j=0; j<components_nmol[i]; j++ ){ |
328 |
+ |
the_molecules[molIndex].setStampID( i ); |
329 |
+ |
molIndex++; |
330 |
+ |
} |
331 |
+ |
} |
332 |
+ |
|
333 |
|
|
334 |
+ |
#endif // is_mpi |
335 |
+ |
|
336 |
+ |
|
337 |
|
if( simnfo->n_SRI ){ |
338 |
|
Exclude::createArray(simnfo->n_SRI); |
339 |
|
the_excludes = new Exclude*[simnfo->n_SRI]; |
354 |
|
// set the arrays into the SimInfo object |
355 |
|
|
356 |
|
simnfo->atoms = the_atoms; |
329 |
– |
simnfo->sr_interactions = the_sris; |
357 |
|
simnfo->nGlobalExcludes = 0; |
358 |
|
simnfo->excludes = the_excludes; |
359 |
|
|
410 |
|
|
411 |
|
the_ff->setSimInfo( simnfo ); |
412 |
|
|
413 |
< |
makeAtoms(); |
413 |
> |
makeMolecules(); |
414 |
|
simnfo->identArray = new int[simnfo->n_atoms]; |
415 |
|
for(i=0; i<simnfo->n_atoms; i++){ |
416 |
|
simnfo->identArray[i] = the_atoms[i]->getIdent(); |
417 |
|
} |
418 |
|
|
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 |
– |
|
419 |
|
if (the_globals->getUseRF() ) { |
420 |
|
simnfo->useReactionField = 1; |
421 |
|
|
652 |
|
|
653 |
|
// new AllLong( simnfo ); |
654 |
|
|
641 |
– |
if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff ); |
642 |
– |
if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff ); |
655 |
|
if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff ); |
656 |
|
if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff ); |
657 |
|
|
922 |
|
} |
923 |
|
|
924 |
|
// clean up the forcefield |
925 |
< |
|
925 |
> |
the_ff->calcRcut(); |
926 |
|
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 ); |
927 |
|
} |
928 |
|
|
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 |
– |
} |
1191 |
– |
} |
1192 |
– |
|
1193 |
– |
#ifdef IS_MPI |
1194 |
– |
sprintf( checkPointMsg, |
1195 |
– |
"Successfully created the bends list.\n" ); |
1196 |
– |
MPIcheckPoint(); |
1197 |
– |
#endif // is_mpi |
1198 |
– |
|
1199 |
– |
|
1200 |
– |
the_ff->initializeBends( the_bends ); |
1201 |
– |
} |
1202 |
– |
|
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 ); |
1271 |
– |
} |
1272 |
– |
|
929 |
|
void SimSetup::initFromBass( void ){ |
930 |
|
|
931 |
|
int i, j, k; |