| 248 |
|
|
| 249 |
|
int localMol, allMol; |
| 250 |
|
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
| 251 |
+ |
|
| 252 |
+ |
int* mol2proc = mpiSim->getMolToProcMap(); |
| 253 |
+ |
int* molCompType = mpiSim->getMolComponentType(); |
| 254 |
|
|
| 255 |
|
allMol = 0; |
| 256 |
|
localMol = 0; |
| 262 |
|
|
| 263 |
|
for( j=0; j<components_nmol[i]; j++ ){ |
| 264 |
|
|
| 265 |
< |
if( mpiSim->getMyMolStart() <= allMol && |
| 263 |
< |
allMol <= mpiSim->getMyMolEnd() ){ |
| 265 |
> |
if( mol2proc[j] == worldRank ){ |
| 266 |
|
|
| 267 |
|
local_atoms += comp_stamps[i]->getNAtoms(); |
| 268 |
|
local_bonds += comp_stamps[i]->getNBonds(); |
| 281 |
|
if( local_atoms != simnfo->n_atoms ){ |
| 282 |
|
sprintf( painCave.errMsg, |
| 283 |
|
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
| 284 |
< |
" localAtom (%d) are note equal.\n", |
| 284 |
> |
" localAtom (%d) are not equal.\n", |
| 285 |
|
simnfo->n_atoms, |
| 286 |
|
local_atoms ); |
| 287 |
|
painCave.isFatal = 1; |
| 306 |
|
Atom::createArrays(simnfo->n_atoms); |
| 307 |
|
the_atoms = new Atom*[simnfo->n_atoms]; |
| 308 |
|
the_molecules = new Molecule[simnfo->n_mol]; |
| 309 |
+ |
int molIndex; |
| 310 |
+ |
|
| 311 |
+ |
// initialize the molecule's stampID's |
| 312 |
+ |
|
| 313 |
+ |
#ifdef IS_MPI |
| 314 |
+ |
|
| 315 |
+ |
|
| 316 |
+ |
molIndex = 0; |
| 317 |
+ |
for(i=0; i<mpiSim->getTotNmol(); i++){ |
| 318 |
+ |
|
| 319 |
+ |
if(mol2proc[i] == worldRank ){ |
| 320 |
+ |
the_molecules[molIndex].setStampID( molCompType[i] ); |
| 321 |
+ |
molIndex++; |
| 322 |
+ |
} |
| 323 |
+ |
} |
| 324 |
+ |
|
| 325 |
+ |
#else // is_mpi |
| 326 |
+ |
|
| 327 |
+ |
molIndex = 0; |
| 328 |
+ |
for(i=0; i<n_components; i++){ |
| 329 |
+ |
for(j=0; j<components_nmol[i]; j++ ){ |
| 330 |
+ |
the_molecules[molIndex].setStampID( i ); |
| 331 |
+ |
molIndex++; |
| 332 |
+ |
} |
| 333 |
+ |
} |
| 334 |
+ |
|
| 335 |
|
|
| 336 |
+ |
#endif // is_mpi |
| 337 |
|
|
| 338 |
+ |
|
| 339 |
|
if( simnfo->n_SRI ){ |
| 340 |
|
Exclude::createArray(simnfo->n_SRI); |
| 341 |
|
the_excludes = new Exclude*[simnfo->n_SRI]; |
| 356 |
|
// set the arrays into the SimInfo object |
| 357 |
|
|
| 358 |
|
simnfo->atoms = the_atoms; |
| 329 |
– |
simnfo->sr_interactions = the_sris; |
| 359 |
|
simnfo->nGlobalExcludes = 0; |
| 360 |
|
simnfo->excludes = the_excludes; |
| 361 |
|
|
| 412 |
|
|
| 413 |
|
the_ff->setSimInfo( simnfo ); |
| 414 |
|
|
| 415 |
< |
makeAtoms(); |
| 415 |
> |
makeMolecules(); |
| 416 |
|
simnfo->identArray = new int[simnfo->n_atoms]; |
| 417 |
|
for(i=0; i<simnfo->n_atoms; i++){ |
| 418 |
|
simnfo->identArray[i] = the_atoms[i]->getIdent(); |
| 419 |
|
} |
| 420 |
|
|
| 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 |
– |
|
| 421 |
|
if (the_globals->getUseRF() ) { |
| 422 |
|
simnfo->useReactionField = 1; |
| 423 |
|
|
| 913 |
|
excludeOffset += info.nTorsions; |
| 914 |
|
|
| 915 |
|
|
| 916 |
< |
|
| 901 |
< |
|
| 902 |
< |
|
| 903 |
< |
|
| 904 |
< |
|
| 905 |
< |
|
| 906 |
< |
void SimSetup::makeAtoms( void ){ |
| 907 |
< |
|
| 908 |
< |
int i, j, k, index; |
| 909 |
< |
double ux, uy, uz, uSqr, u; |
| 910 |
< |
AtomStamp* current_atom; |
| 911 |
< |
|
| 912 |
< |
DirectionalAtom* dAtom; |
| 913 |
< |
int molIndex, molStart, molEnd, nMemb, lMolIndex; |
| 914 |
< |
|
| 915 |
< |
lMolIndex = 0; |
| 916 |
< |
molIndex = 0; |
| 917 |
< |
index = 0; |
| 918 |
< |
for( i=0; i<n_components; i++ ){ |
| 919 |
< |
|
| 920 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
| 921 |
< |
|
| 922 |
< |
#ifdef IS_MPI |
| 923 |
< |
if( mpiSim->getMyMolStart() <= molIndex && |
| 924 |
< |
molIndex <= mpiSim->getMyMolEnd() ){ |
| 925 |
< |
#endif // is_mpi |
| 926 |
< |
|
| 927 |
< |
molStart = index; |
| 928 |
< |
nMemb = comp_stamps[i]->getNAtoms(); |
| 929 |
< |
for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){ |
| 930 |
< |
|
| 931 |
< |
current_atom = comp_stamps[i]->getAtom( k ); |
| 932 |
< |
if( current_atom->haveOrientation() ){ |
| 933 |
< |
|
| 934 |
< |
dAtom = new DirectionalAtom(index); |
| 935 |
< |
simnfo->n_oriented++; |
| 936 |
< |
the_atoms[index] = dAtom; |
| 937 |
< |
|
| 938 |
< |
ux = current_atom->getOrntX(); |
| 939 |
< |
uy = current_atom->getOrntY(); |
| 940 |
< |
uz = current_atom->getOrntZ(); |
| 941 |
< |
|
| 942 |
< |
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
| 943 |
< |
|
| 944 |
< |
u = sqrt( uSqr ); |
| 945 |
< |
ux = ux / u; |
| 946 |
< |
uy = uy / u; |
| 947 |
< |
uz = uz / u; |
| 948 |
< |
|
| 949 |
< |
dAtom->setSUx( ux ); |
| 950 |
< |
dAtom->setSUy( uy ); |
| 951 |
< |
dAtom->setSUz( uz ); |
| 952 |
< |
} |
| 953 |
< |
else{ |
| 954 |
< |
the_atoms[index] = new GeneralAtom(index); |
| 955 |
< |
} |
| 956 |
< |
the_atoms[index]->setType( current_atom->getType() ); |
| 957 |
< |
the_atoms[index]->setIndex( index ); |
| 958 |
< |
|
| 959 |
< |
// increment the index and repeat; |
| 960 |
< |
index++; |
| 961 |
< |
} |
| 962 |
< |
|
| 963 |
< |
molEnd = index -1; |
| 964 |
< |
the_molecules[lMolIndex].setNMembers( nMemb ); |
| 965 |
< |
the_molecules[lMolIndex].setStartAtom( molStart ); |
| 966 |
< |
the_molecules[lMolIndex].setEndAtom( molEnd ); |
| 967 |
< |
the_molecules[lMolIndex].setStampID( i ); |
| 968 |
< |
lMolIndex++; |
| 916 |
> |
// send the arrays off to the forceField for init. |
| 917 |
|
|
| 918 |
< |
#ifdef IS_MPI |
| 919 |
< |
} |
| 920 |
< |
#endif //is_mpi |
| 921 |
< |
|
| 974 |
< |
molIndex++; |
| 975 |
< |
} |
| 976 |
< |
} |
| 977 |
< |
|
| 978 |
< |
#ifdef IS_MPI |
| 979 |
< |
for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] ); |
| 980 |
< |
|
| 981 |
< |
delete[] globalIndex; |
| 982 |
< |
|
| 983 |
< |
mpiSim->mpiRefresh(); |
| 984 |
< |
#endif //IS_MPI |
| 985 |
< |
|
| 986 |
< |
the_ff->initializeAtoms(); |
| 987 |
< |
} |
| 988 |
< |
|
| 989 |
< |
void SimSetup::makeBonds( void ){ |
| 990 |
< |
|
| 991 |
< |
int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
| 992 |
< |
bond_pair* the_bonds; |
| 993 |
< |
BondStamp* current_bond; |
| 994 |
< |
|
| 995 |
< |
the_bonds = new bond_pair[tot_bonds]; |
| 996 |
< |
index = 0; |
| 997 |
< |
offset = 0; |
| 998 |
< |
molIndex = 0; |
| 999 |
< |
|
| 1000 |
< |
for( i=0; i<n_components; i++ ){ |
| 1001 |
< |
|
| 1002 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
| 1003 |
< |
|
| 1004 |
< |
#ifdef IS_MPI |
| 1005 |
< |
if( mpiSim->getMyMolStart() <= molIndex && |
| 1006 |
< |
molIndex <= mpiSim->getMyMolEnd() ){ |
| 1007 |
< |
#endif // is_mpi |
| 1008 |
< |
|
| 1009 |
< |
for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){ |
| 1010 |
< |
|
| 1011 |
< |
current_bond = comp_stamps[i]->getBond( k ); |
| 1012 |
< |
the_bonds[index].a = current_bond->getA() + offset; |
| 1013 |
< |
the_bonds[index].b = current_bond->getB() + offset; |
| 1014 |
< |
|
| 1015 |
< |
exI = the_bonds[index].a; |
| 1016 |
< |
exJ = the_bonds[index].b; |
| 1017 |
< |
|
| 1018 |
< |
// exclude_I must always be the smaller of the pair |
| 1019 |
< |
if( exI > exJ ){ |
| 1020 |
< |
tempEx = exI; |
| 1021 |
< |
exI = exJ; |
| 1022 |
< |
exJ = tempEx; |
| 1023 |
< |
} |
| 1024 |
< |
|
| 1025 |
< |
|
| 1026 |
< |
#ifdef IS_MPI |
| 1027 |
< |
|
| 1028 |
< |
the_excludes[index*2] = |
| 1029 |
< |
the_atoms[exI]->getGlobalIndex() + 1; |
| 1030 |
< |
the_excludes[index*2 + 1] = |
| 1031 |
< |
the_atoms[exJ]->getGlobalIndex() + 1; |
| 1032 |
< |
|
| 1033 |
< |
#else // isn't MPI |
| 1034 |
< |
|
| 1035 |
< |
the_excludes[index*2] = exI + 1; |
| 1036 |
< |
the_excludes[index*2 + 1] = exJ + 1; |
| 1037 |
< |
// fortran index from 1 (hence the +1 in the indexing) |
| 1038 |
< |
#endif //is_mpi |
| 1039 |
< |
|
| 1040 |
< |
// increment the index and repeat; |
| 1041 |
< |
index++; |
| 1042 |
< |
} |
| 1043 |
< |
offset += comp_stamps[i]->getNAtoms(); |
| 1044 |
< |
|
| 1045 |
< |
#ifdef IS_MPI |
| 1046 |
< |
} |
| 1047 |
< |
#endif //is_mpi |
| 1048 |
< |
|
| 1049 |
< |
molIndex++; |
| 1050 |
< |
} |
| 1051 |
< |
} |
| 1052 |
< |
|
| 1053 |
< |
the_ff->initializeBonds( the_bonds ); |
| 1054 |
< |
} |
| 1055 |
< |
|
| 1056 |
< |
void SimSetup::makeBends( void ){ |
| 1057 |
< |
|
| 1058 |
< |
int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
| 1059 |
< |
bend_set* the_bends; |
| 1060 |
< |
BendStamp* current_bend; |
| 1061 |
< |
LinkedAssign* extras; |
| 1062 |
< |
LinkedAssign* current_extra; |
| 1063 |
< |
|
| 1064 |
< |
|
| 1065 |
< |
the_bends = new bend_set[tot_bends]; |
| 1066 |
< |
index = 0; |
| 1067 |
< |
offset = 0; |
| 1068 |
< |
molIndex = 0; |
| 1069 |
< |
for( i=0; i<n_components; i++ ){ |
| 1070 |
< |
|
| 1071 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
| 1072 |
< |
|
| 1073 |
< |
#ifdef IS_MPI |
| 1074 |
< |
if( mpiSim->getMyMolStart() <= molIndex && |
| 1075 |
< |
molIndex <= mpiSim->getMyMolEnd() ){ |
| 1076 |
< |
#endif // is_mpi |
| 1077 |
< |
|
| 1078 |
< |
for( k=0; k<comp_stamps[i]->getNBends(); k++ ){ |
| 1079 |
< |
|
| 1080 |
< |
current_bend = comp_stamps[i]->getBend( k ); |
| 1081 |
< |
the_bends[index].a = current_bend->getA() + offset; |
| 1082 |
< |
the_bends[index].b = current_bend->getB() + offset; |
| 1083 |
< |
the_bends[index].c = current_bend->getC() + offset; |
| 1084 |
< |
|
| 1085 |
< |
if( current_bend->haveExtras() ){ |
| 1086 |
< |
|
| 1087 |
< |
extras = current_bend->getExtras(); |
| 1088 |
< |
current_extra = extras; |
| 1089 |
< |
|
| 1090 |
< |
while( current_extra != NULL ){ |
| 1091 |
< |
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
| 1092 |
< |
|
| 1093 |
< |
switch( current_extra->getType() ){ |
| 1094 |
< |
|
| 1095 |
< |
case 0: |
| 1096 |
< |
the_bends[index].ghost = |
| 1097 |
< |
current_extra->getInt() + offset; |
| 1098 |
< |
the_bends[index].isGhost = 1; |
| 1099 |
< |
break; |
| 1100 |
< |
|
| 1101 |
< |
case 1: |
| 1102 |
< |
the_bends[index].ghost = |
| 1103 |
< |
(int)current_extra->getDouble() + offset; |
| 1104 |
< |
the_bends[index].isGhost = 1; |
| 1105 |
< |
break; |
| 1106 |
< |
|
| 1107 |
< |
default: |
| 1108 |
< |
sprintf( painCave.errMsg, |
| 1109 |
< |
"SimSetup Error: ghostVectorSource was neiter a " |
| 1110 |
< |
"double nor an int.\n" |
| 1111 |
< |
"-->Bend[%d] in %s\n", |
| 1112 |
< |
k, comp_stamps[i]->getID() ); |
| 1113 |
< |
painCave.isFatal = 1; |
| 1114 |
< |
simError(); |
| 1115 |
< |
} |
| 1116 |
< |
} |
| 1117 |
< |
|
| 1118 |
< |
else{ |
| 1119 |
< |
|
| 1120 |
< |
sprintf( painCave.errMsg, |
| 1121 |
< |
"SimSetup Error: unhandled bend assignment:\n" |
| 1122 |
< |
" -->%s in Bend[%d] in %s\n", |
| 1123 |
< |
current_extra->getlhs(), |
| 1124 |
< |
k, comp_stamps[i]->getID() ); |
| 1125 |
< |
painCave.isFatal = 1; |
| 1126 |
< |
simError(); |
| 1127 |
< |
} |
| 1128 |
< |
|
| 1129 |
< |
current_extra = current_extra->getNext(); |
| 1130 |
< |
} |
| 1131 |
< |
} |
| 1132 |
< |
|
| 1133 |
< |
if( !the_bends[index].isGhost ){ |
| 1134 |
< |
|
| 1135 |
< |
exI = the_bends[index].a; |
| 1136 |
< |
exJ = the_bends[index].c; |
| 1137 |
< |
} |
| 1138 |
< |
else{ |
| 1139 |
< |
|
| 1140 |
< |
exI = the_bends[index].a; |
| 1141 |
< |
exJ = the_bends[index].b; |
| 1142 |
< |
} |
| 1143 |
< |
|
| 1144 |
< |
// exclude_I must always be the smaller of the pair |
| 1145 |
< |
if( exI > exJ ){ |
| 1146 |
< |
tempEx = exI; |
| 1147 |
< |
exI = exJ; |
| 1148 |
< |
exJ = tempEx; |
| 1149 |
< |
} |
| 1150 |
< |
|
| 1151 |
< |
|
| 1152 |
< |
#ifdef IS_MPI |
| 1153 |
< |
|
| 1154 |
< |
the_excludes[(index + tot_bonds)*2] = |
| 1155 |
< |
the_atoms[exI]->getGlobalIndex() + 1; |
| 1156 |
< |
the_excludes[(index + tot_bonds)*2 + 1] = |
| 1157 |
< |
the_atoms[exJ]->getGlobalIndex() + 1; |
| 1158 |
< |
|
| 1159 |
< |
#else // isn't MPI |
| 1160 |
< |
|
| 1161 |
< |
the_excludes[(index + tot_bonds)*2] = exI + 1; |
| 1162 |
< |
the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1; |
| 1163 |
< |
// fortran index from 1 (hence the +1 in the indexing) |
| 1164 |
< |
#endif //is_mpi |
| 1165 |
< |
|
| 1166 |
< |
|
| 1167 |
< |
// increment the index and repeat; |
| 1168 |
< |
index++; |
| 1169 |
< |
} |
| 1170 |
< |
offset += comp_stamps[i]->getNAtoms(); |
| 1171 |
< |
|
| 1172 |
< |
#ifdef IS_MPI |
| 1173 |
< |
} |
| 1174 |
< |
#endif //is_mpi |
| 918 |
> |
the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
| 919 |
> |
the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
| 920 |
> |
the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
| 921 |
> |
the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
| 922 |
|
|
| 1176 |
– |
molIndex++; |
| 1177 |
– |
} |
| 1178 |
– |
} |
| 923 |
|
|
| 924 |
< |
#ifdef IS_MPI |
| 925 |
< |
sprintf( checkPointMsg, |
| 1182 |
< |
"Successfully created the bends list.\n" ); |
| 1183 |
< |
MPIcheckPoint(); |
| 1184 |
< |
#endif // is_mpi |
| 1185 |
< |
|
| 1186 |
< |
|
| 1187 |
< |
the_ff->initializeBends( the_bends ); |
| 1188 |
< |
} |
| 1189 |
< |
|
| 1190 |
< |
void SimSetup::makeTorsions( void ){ |
| 1191 |
< |
|
| 1192 |
< |
int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
| 1193 |
< |
torsion_set* the_torsions; |
| 1194 |
< |
TorsionStamp* current_torsion; |
| 1195 |
< |
|
| 1196 |
< |
the_torsions = new torsion_set[tot_torsions]; |
| 1197 |
< |
index = 0; |
| 1198 |
< |
offset = 0; |
| 1199 |
< |
molIndex = 0; |
| 1200 |
< |
for( i=0; i<n_components; i++ ){ |
| 1201 |
< |
|
| 1202 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
| 1203 |
< |
|
| 1204 |
< |
#ifdef IS_MPI |
| 1205 |
< |
if( mpiSim->getMyMolStart() <= molIndex && |
| 1206 |
< |
molIndex <= mpiSim->getMyMolEnd() ){ |
| 1207 |
< |
#endif // is_mpi |
| 1208 |
< |
|
| 1209 |
< |
for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){ |
| 1210 |
< |
|
| 1211 |
< |
current_torsion = comp_stamps[i]->getTorsion( k ); |
| 1212 |
< |
the_torsions[index].a = current_torsion->getA() + offset; |
| 1213 |
< |
the_torsions[index].b = current_torsion->getB() + offset; |
| 1214 |
< |
the_torsions[index].c = current_torsion->getC() + offset; |
| 1215 |
< |
the_torsions[index].d = current_torsion->getD() + offset; |
| 1216 |
< |
|
| 1217 |
< |
exI = the_torsions[index].a; |
| 1218 |
< |
exJ = the_torsions[index].d; |
| 1219 |
< |
|
| 1220 |
< |
|
| 1221 |
< |
// exclude_I must always be the smaller of the pair |
| 1222 |
< |
if( exI > exJ ){ |
| 1223 |
< |
tempEx = exI; |
| 1224 |
< |
exI = exJ; |
| 1225 |
< |
exJ = tempEx; |
| 1226 |
< |
} |
| 1227 |
< |
|
| 1228 |
< |
|
| 1229 |
< |
#ifdef IS_MPI |
| 1230 |
< |
|
| 1231 |
< |
the_excludes[(index + tot_bonds + tot_bends)*2] = |
| 1232 |
< |
the_atoms[exI]->getGlobalIndex() + 1; |
| 1233 |
< |
the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = |
| 1234 |
< |
the_atoms[exJ]->getGlobalIndex() + 1; |
| 1235 |
< |
|
| 1236 |
< |
#else // isn't MPI |
| 1237 |
< |
|
| 1238 |
< |
the_excludes[(index + tot_bonds + tot_bends)*2] = exI + 1; |
| 1239 |
< |
the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1; |
| 1240 |
< |
// fortran indexes from 1 (hence the +1 in the indexing) |
| 1241 |
< |
#endif //is_mpi |
| 1242 |
< |
|
| 1243 |
< |
|
| 1244 |
< |
// increment the index and repeat; |
| 1245 |
< |
index++; |
| 1246 |
< |
} |
| 1247 |
< |
offset += comp_stamps[i]->getNAtoms(); |
| 1248 |
< |
|
| 1249 |
< |
#ifdef IS_MPI |
| 1250 |
< |
} |
| 1251 |
< |
#endif //is_mpi |
| 1252 |
< |
|
| 1253 |
< |
molIndex++; |
| 1254 |
< |
} |
| 924 |
> |
the_molecules[i].initialize( info ); |
| 925 |
> |
atomOffset += info.nAtoms; |
| 926 |
|
} |
| 927 |
|
|
| 928 |
< |
the_ff->initializeTorsions( the_torsions ); |
| 928 |
> |
// clean up the forcefield |
| 929 |
> |
the_ff->calcRcut(); |
| 930 |
> |
the_ff->cleanMe(); |
| 931 |
|
} |
| 932 |
|
|
| 933 |
|
void SimSetup::initFromBass( void ){ |
