# | Line 147 | Line 147 | void SimSetup::createSim(void){ | |
---|---|---|
147 | // make the output filenames | |
148 | ||
149 | makeOutNames(); | |
150 | – | |
151 | – | if (globals->haveMinimizer()) |
152 | – | // make minimizer |
153 | – | makeMinimizer(); |
154 | – | else |
155 | – | // make the integrator |
156 | – | makeIntegrator(); |
150 | ||
151 | #ifdef IS_MPI | |
152 | mpiSim->mpiRefresh(); | |
# | Line 162 | Line 155 | void SimSetup::createSim(void){ | |
155 | // initialize the Fortran | |
156 | ||
157 | initFortran(); | |
158 | + | |
159 | + | if (globals->haveMinimizer()) |
160 | + | // make minimizer |
161 | + | makeMinimizer(); |
162 | + | else |
163 | + | // make the integrator |
164 | + | makeIntegrator(); |
165 | + | |
166 | } | |
167 | ||
168 | ||
# | Line 182 | Line 183 | void SimSetup::makeMolecules(void){ | |
183 | BendStamp* currentBend; | |
184 | TorsionStamp* currentTorsion; | |
185 | RigidBodyStamp* currentRigidBody; | |
186 | + | CutoffGroupStamp* currentCutoffGroup; |
187 | + | CutoffGroup* myCutoffGroup; |
188 | + | int nCutoffGroups;// number of cutoff group of a molecule defined in mdl file |
189 | + | set<int> cutoffAtomSet; //atoms belong to cutoffgroup defined at mdl file |
190 | ||
191 | bond_pair* theBonds; | |
192 | bend_set* theBends; | |
# | Line 215 | Line 220 | void SimSetup::makeMolecules(void){ | |
220 | molInfo.nBends = comp_stamps[stampID]->getNBends(); | |
221 | molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); | |
222 | molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies(); | |
223 | + | |
224 | + | nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups(); |
225 | ||
226 | molInfo.myAtoms = &(info[k].atoms[atomOffset]); | |
227 | ||
228 | if (molInfo.nBonds > 0) | |
229 | < | molInfo.myBonds = new (Bond *) [molInfo.nBonds]; |
229 | > | molInfo.myBonds = new Bond*[molInfo.nBonds]; |
230 | else | |
231 | molInfo.myBonds = NULL; | |
232 | ||
233 | if (molInfo.nBends > 0) | |
234 | < | molInfo.myBends = new (Bend *) [molInfo.nBends]; |
234 | > | molInfo.myBends = new Bend*[molInfo.nBends]; |
235 | else | |
236 | molInfo.myBends = NULL; | |
237 | ||
238 | if (molInfo.nTorsions > 0) | |
239 | < | molInfo.myTorsions = new (Torsion *) [molInfo.nTorsions]; |
239 | > | molInfo.myTorsions = new Torsion *[molInfo.nTorsions]; |
240 | else | |
241 | molInfo.myTorsions = NULL; | |
242 | ||
# | Line 262 | Line 269 | void SimSetup::makeMolecules(void){ | |
269 | else{ | |
270 | ||
271 | molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration()); | |
272 | + | |
273 | } | |
274 | ||
275 | molInfo.myAtoms[j]->setType(currentAtom->getType()); | |
268 | – | |
276 | #ifdef IS_MPI | |
277 | ||
278 | molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]); | |
# | Line 409 | Line 416 | void SimSetup::makeMolecules(void){ | |
416 | info[k].excludes->addPair(exK, exL); | |
417 | } | |
418 | ||
419 | + | |
420 | + | molInfo.myRigidBodies.clear(); |
421 | + | |
422 | for (j = 0; j < molInfo.nRigidBodies; j++){ | |
423 | ||
424 | currentRigidBody = comp_stamps[stampID]->getRigidBody(j); | |
# | Line 418 | Line 428 | void SimSetup::makeMolecules(void){ | |
428 | ||
429 | myRB = new RigidBody(); | |
430 | ||
431 | < | sprintf(rbName,"%s_RB_%s", molName, j); |
431 | > | sprintf(rbName,"%s_RB_%d", molName, j); |
432 | myRB->setType(rbName); | |
433 | ||
434 | for (rb1 = 0; rb1 < nMembers; rb1++) { | |
# | Line 460 | Line 470 | void SimSetup::makeMolecules(void){ | |
470 | // used for the exclude list: | |
471 | ||
472 | #ifdef IS_MPI | |
473 | < | exI = info[k].atoms[tempI]->getGlobalIndex() + 1; |
474 | < | exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1; |
473 | > | exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1; |
474 | > | exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1; |
475 | #else | |
476 | < | exI = tempI + 1; |
477 | < | exJ = tempJ + 1; |
476 | > | exI = molInfo.myAtoms[tempI]->getIndex() + 1; |
477 | > | exJ = molInfo.myAtoms[tempJ]->getIndex() + 1; |
478 | #endif | |
479 | ||
480 | info[k].excludes->addPair(exI, exJ); | |
# | Line 477 | Line 487 | void SimSetup::makeMolecules(void){ | |
487 | } | |
488 | ||
489 | ||
490 | + | //create cutoff group for molecule |
491 | + | |
492 | + | cutoffAtomSet.clear(); |
493 | + | molInfo.myCutoffGroups.clear(); |
494 | + | |
495 | + | for (j = 0; j < nCutoffGroups; j++){ |
496 | + | |
497 | + | currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j); |
498 | + | nMembers = currentCutoffGroup->getNMembers(); |
499 | + | |
500 | + | myCutoffGroup = new CutoffGroup(); |
501 | + | |
502 | + | for (int cg = 0; cg < nMembers; cg++) { |
503 | + | |
504 | + | // molI is atom numbering inside this molecule |
505 | + | molI = currentCutoffGroup->getMember(cg); |
506 | + | |
507 | + | // tempI is atom numbering on local processor |
508 | + | tempI = molI + atomOffset; |
509 | + | |
510 | + | myCutoffGroup->addAtom(info[k].atoms[tempI]); |
511 | + | |
512 | + | cutoffAtomSet.insert(tempI); |
513 | + | } |
514 | + | |
515 | + | molInfo.myCutoffGroups.push_back(myCutoffGroup); |
516 | + | }//end for (j = 0; j < molInfo.nCutoffGroups; j++) |
517 | + | |
518 | + | //creat a cutoff group for every atom in current molecule which does not belong to cutoffgroup defined at mdl file |
519 | + | |
520 | + | for(j = 0; j < molInfo.nAtoms; j++){ |
521 | + | |
522 | + | if(cutoffAtomSet.find(molInfo.myAtoms[j]->getIndex()) == cutoffAtomSet.end()){ |
523 | + | myCutoffGroup = new CutoffGroup(); |
524 | + | myCutoffGroup->addAtom(molInfo.myAtoms[j]); |
525 | + | molInfo.myCutoffGroups.push_back(myCutoffGroup); |
526 | + | } |
527 | + | |
528 | + | } |
529 | + | |
530 | + | |
531 | + | |
532 | + | |
533 | // After this is all set up, scan through the atoms to | |
534 | // see if they can be added to the integrableObjects: | |
535 | + | |
536 | + | molInfo.myIntegrableObjects.clear(); |
537 | + | |
538 | ||
539 | for (j = 0; j < molInfo.nAtoms; j++){ | |
540 | ||
# | Line 529 | Line 585 | void SimSetup::makeMolecules(void){ | |
585 | MPIcheckPoint(); | |
586 | #endif // is_mpi | |
587 | ||
532 | – | // clean up the forcefield |
533 | – | |
534 | – | if (!globals->haveLJrcut()){ |
535 | – | |
536 | – | the_ff->calcRcut(); |
537 | – | |
538 | – | } else { |
539 | – | |
540 | – | the_ff->setRcut( globals->getLJrcut() ); |
541 | – | } |
542 | – | |
543 | – | the_ff->cleanMe(); |
588 | } | |
589 | ||
590 | void SimSetup::initFromBass(void){ | |
# | Line 827 | Line 871 | void SimSetup::gatherInfo(void){ | |
871 | } | |
872 | ||
873 | //check whether sample time, status time, thermal time and reset time are divisble by dt | |
874 | < | if (!isDivisible(globals->getSampleTime(), globals->getDt())){ |
874 | > | if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){ |
875 | sprintf(painCave.errMsg, | |
876 | "Sample time is not divisible by dt.\n" | |
877 | "\tThis will result in samples that are not uniformly\n" | |
# | Line 837 | Line 881 | void SimSetup::gatherInfo(void){ | |
881 | simError(); | |
882 | } | |
883 | ||
884 | < | if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){ |
884 | > | if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){ |
885 | sprintf(painCave.errMsg, | |
886 | "Status time is not divisible by dt.\n" | |
887 | "\tThis will result in status reports that are not uniformly\n" | |
# | Line 873 | Line 917 | void SimSetup::gatherInfo(void){ | |
917 | if (globals->haveSampleTime()){ | |
918 | info[i].sampleTime = globals->getSampleTime(); | |
919 | info[i].statusTime = info[i].sampleTime; | |
876 | – | info[i].thermalTime = info[i].sampleTime; |
920 | } | |
921 | else{ | |
922 | info[i].sampleTime = globals->getRunTime(); | |
923 | info[i].statusTime = info[i].sampleTime; | |
881 | – | info[i].thermalTime = info[i].sampleTime; |
924 | } | |
925 | ||
926 | if (globals->haveStatusTime()){ | |
# | Line 887 | Line 929 | void SimSetup::gatherInfo(void){ | |
929 | ||
930 | if (globals->haveThermalTime()){ | |
931 | info[i].thermalTime = globals->getThermalTime(); | |
932 | + | } else { |
933 | + | info[i].thermalTime = globals->getRunTime(); |
934 | } | |
935 | ||
936 | info[i].resetIntegrator = 0; | |
# | Line 904 | Line 948 | void SimSetup::gatherInfo(void){ | |
948 | ||
949 | info[i].useInitXSstate = globals->getUseInitXSstate(); | |
950 | info[i].orthoTolerance = globals->getOrthoBoxTolerance(); | |
951 | < | |
951 | > | |
952 | > | // check for thermodynamic integration |
953 | > | if (globals->getUseThermInt()) { |
954 | > | if (globals->haveThermIntLambda() && globals->haveThermIntK()) { |
955 | > | info[i].useThermInt = globals->getUseThermInt(); |
956 | > | info[i].thermIntLambda = globals->getThermIntLambda(); |
957 | > | info[i].thermIntK = globals->getThermIntK(); |
958 | > | |
959 | > | Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK); |
960 | > | info[i].restraint = myRestraint; |
961 | > | } |
962 | > | else { |
963 | > | sprintf(painCave.errMsg, |
964 | > | "SimSetup Error:\n" |
965 | > | "\tKeyword useThermInt was set to 'true' but\n" |
966 | > | "\tthermodynamicIntegrationLambda (and/or\n" |
967 | > | "\tthermodynamicIntegrationK) was not specified.\n" |
968 | > | "\tPlease provide a lambda value and k value in your .bass file.\n"); |
969 | > | painCave.isFatal = 1; |
970 | > | simError(); |
971 | > | } |
972 | > | } |
973 | > | else if(globals->haveThermIntLambda() || globals->haveThermIntK()){ |
974 | > | sprintf(painCave.errMsg, |
975 | > | "SimSetup Warning: If you want to use Thermodynamic\n" |
976 | > | "\tIntegration, set useThermInt to 'true' in your .bass file.\n" |
977 | > | "\tThe useThermInt keyword is 'false' by default, so your\n" |
978 | > | "\tlambda and/or k values are being ignored.\n"); |
979 | > | painCave.isFatal = 0; |
980 | > | simError(); |
981 | > | } |
982 | } | |
983 | ||
984 | //setup seed for random number generator | |
# | Line 957 | Line 1031 | void SimSetup::finalInfoCheck(void){ | |
1031 | void SimSetup::finalInfoCheck(void){ | |
1032 | int index; | |
1033 | int usesDipoles; | |
1034 | + | int usesCharges; |
1035 | int i; | |
1036 | ||
1037 | for (i = 0; i < nInfo; i++){ | |
# | Line 968 | Line 1043 | void SimSetup::finalInfoCheck(void){ | |
1043 | usesDipoles = (info[i].atoms[index])->hasDipole(); | |
1044 | index++; | |
1045 | } | |
1046 | < | |
1046 | > | index = 0; |
1047 | > | usesCharges = 0; |
1048 | > | while ((index < info[i].n_atoms) && !usesCharges){ |
1049 | > | usesCharges= (info[i].atoms[index])->hasCharge(); |
1050 | > | index++; |
1051 | > | } |
1052 | #ifdef IS_MPI | |
1053 | int myUse = usesDipoles; | |
1054 | MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); | |
1055 | #endif //is_mpi | |
1056 | ||
1057 | < | double theEcr, theEst; |
1057 | > | double theRcut, theRsw; |
1058 | ||
1059 | + | if (globals->haveRcut()) { |
1060 | + | theRcut = globals->getRcut(); |
1061 | + | |
1062 | + | if (globals->haveRsw()) |
1063 | + | theRsw = globals->getRsw(); |
1064 | + | else |
1065 | + | theRsw = theRcut; |
1066 | + | |
1067 | + | info[i].setDefaultRcut(theRcut, theRsw); |
1068 | + | |
1069 | + | } else { |
1070 | + | |
1071 | + | the_ff->calcRcut(); |
1072 | + | theRcut = info[i].getRcut(); |
1073 | + | |
1074 | + | if (globals->haveRsw()) |
1075 | + | theRsw = globals->getRsw(); |
1076 | + | else |
1077 | + | theRsw = theRcut; |
1078 | + | |
1079 | + | info[i].setDefaultRcut(theRcut, theRsw); |
1080 | + | } |
1081 | + | |
1082 | if (globals->getUseRF()){ | |
1083 | info[i].useReactionField = 1; | |
1084 | < | |
1085 | < | if (!globals->haveECR()){ |
1084 | > | |
1085 | > | if (!globals->haveRcut()){ |
1086 | sprintf(painCave.errMsg, | |
1087 | < | "SimSetup Warning: No value was set for electrostaticCutoffRadius.\n" |
1087 | > | "SimSetup Warning: No value was set for the cutoffRadius.\n" |
1088 | "\tOOPSE will use a default value of 15.0 angstroms" | |
1089 | < | "\tfor the electrostaticCutoffRadius.\n"); |
1089 | > | "\tfor the cutoffRadius.\n"); |
1090 | painCave.isFatal = 0; | |
1091 | simError(); | |
1092 | < | theEcr = 15.0; |
1092 | > | theRcut = 15.0; |
1093 | } | |
1094 | else{ | |
1095 | < | theEcr = globals->getECR(); |
1095 | > | theRcut = globals->getRcut(); |
1096 | } | |
1097 | ||
1098 | < | if (!globals->haveEST()){ |
1098 | > | if (!globals->haveRsw()){ |
1099 | sprintf(painCave.errMsg, | |
1100 | < | "SimSetup Warning: No value was set for electrostaticSkinThickness.\n" |
1100 | > | "SimSetup Warning: No value was set for switchingRadius.\n" |
1101 | "\tOOPSE will use a default value of\n" | |
1102 | < | "\t0.05 * electrostaticCutoffRadius\n" |
1000 | < | "\tfor the electrostaticSkinThickness\n"); |
1102 | > | "\t0.95 * cutoffRadius for the switchingRadius\n"); |
1103 | painCave.isFatal = 0; | |
1104 | simError(); | |
1105 | < | theEst = 0.05 * theEcr; |
1105 | > | theRsw = 0.95 * theRcut; |
1106 | } | |
1107 | else{ | |
1108 | < | theEst = globals->getEST(); |
1108 | > | theRsw = globals->getRsw(); |
1109 | } | |
1110 | ||
1111 | < | info[i].setDefaultEcr(theEcr, theEst); |
1111 | > | info[i].setDefaultRcut(theRcut, theRsw); |
1112 | ||
1113 | if (!globals->haveDielectric()){ | |
1114 | sprintf(painCave.errMsg, | |
# | Line 1019 | Line 1121 | void SimSetup::finalInfoCheck(void){ | |
1121 | info[i].dielectric = globals->getDielectric(); | |
1122 | } | |
1123 | else{ | |
1124 | < | if (usesDipoles){ |
1125 | < | if (!globals->haveECR()){ |
1124 | > | if (usesDipoles || usesCharges){ |
1125 | > | |
1126 | > | if (!globals->haveRcut()){ |
1127 | sprintf(painCave.errMsg, | |
1128 | < | "SimSetup Warning: No value was set for electrostaticCutoffRadius.\n" |
1128 | > | "SimSetup Warning: No value was set for the cutoffRadius.\n" |
1129 | "\tOOPSE will use a default value of 15.0 angstroms" | |
1130 | < | "\tfor the electrostaticCutoffRadius.\n"); |
1131 | < | painCave.isFatal = 0; |
1132 | < | simError(); |
1133 | < | theEcr = 15.0; |
1134 | < | } |
1130 | > | "\tfor the cutoffRadius.\n"); |
1131 | > | painCave.isFatal = 0; |
1132 | > | simError(); |
1133 | > | theRcut = 15.0; |
1134 | > | } |
1135 | else{ | |
1136 | < | theEcr = globals->getECR(); |
1136 | > | theRcut = globals->getRcut(); |
1137 | } | |
1138 | < | |
1139 | < | if (!globals->haveEST()){ |
1138 | > | |
1139 | > | if (!globals->haveRsw()){ |
1140 | sprintf(painCave.errMsg, | |
1141 | < | "SimSetup Warning: No value was set for electrostaticSkinThickness.\n" |
1141 | > | "SimSetup Warning: No value was set for switchingRadius.\n" |
1142 | "\tOOPSE will use a default value of\n" | |
1143 | < | "\t0.05 * electrostaticCutoffRadius\n" |
1041 | < | "\tfor the electrostaticSkinThickness\n"); |
1143 | > | "\t0.95 * cutoffRadius for the switchingRadius\n"); |
1144 | painCave.isFatal = 0; | |
1145 | simError(); | |
1146 | < | theEst = 0.05 * theEcr; |
1146 | > | theRsw = 0.95 * theRcut; |
1147 | } | |
1148 | else{ | |
1149 | < | theEst = globals->getEST(); |
1149 | > | theRsw = globals->getRsw(); |
1150 | } | |
1151 | + | |
1152 | + | info[i].setDefaultRcut(theRcut, theRsw); |
1153 | ||
1050 | – | info[i].setDefaultEcr(theEcr, theEst); |
1154 | } | |
1155 | } | |
1156 | } | |
# | Line 1055 | Line 1158 | void SimSetup::finalInfoCheck(void){ | |
1158 | strcpy(checkPointMsg, "post processing checks out"); | |
1159 | MPIcheckPoint(); | |
1160 | #endif // is_mpi | |
1161 | + | |
1162 | + | // clean up the forcefield |
1163 | + | the_ff->cleanMe(); |
1164 | } | |
1165 | ||
1166 | void SimSetup::initSystemCoords(void){ | |
# | Line 1182 | Line 1288 | void SimSetup::makeOutNames(void){ | |
1288 | } | |
1289 | else{ | |
1290 | strcat(info[k].statusName, ".stat"); | |
1291 | + | } |
1292 | + | } |
1293 | + | |
1294 | + | strcpy(info[k].rawPotName, inFileName); |
1295 | + | nameLength = strlen(info[k].rawPotName); |
1296 | + | endTest = &(info[k].rawPotName[nameLength - 5]); |
1297 | + | if (!strcmp(endTest, ".bass")){ |
1298 | + | strcpy(endTest, ".raw"); |
1299 | + | } |
1300 | + | else if (!strcmp(endTest, ".BASS")){ |
1301 | + | strcpy(endTest, ".raw"); |
1302 | + | } |
1303 | + | else{ |
1304 | + | endTest = &(info[k].rawPotName[nameLength - 4]); |
1305 | + | if (!strcmp(endTest, ".bss")){ |
1306 | + | strcpy(endTest, ".raw"); |
1307 | } | |
1308 | + | else if (!strcmp(endTest, ".mdl")){ |
1309 | + | strcpy(endTest, ".raw"); |
1310 | + | } |
1311 | + | else{ |
1312 | + | strcat(info[k].rawPotName, ".raw"); |
1313 | + | } |
1314 | } | |
1315 | ||
1316 | #ifdef IS_MPI | |
# | Line 1269 | Line 1397 | void SimSetup::compList(void){ | |
1397 | LinkedMolStamp* headStamp = new LinkedMolStamp(); | |
1398 | LinkedMolStamp* currentStamp = NULL; | |
1399 | comp_stamps = new MoleculeStamp * [n_components]; | |
1400 | + | bool haveCutoffGroups; |
1401 | ||
1402 | + | haveCutoffGroups = false; |
1403 | + | |
1404 | // make an array of molecule stamps that match the components used. | |
1405 | // also extract the used stamps out into a separate linked list | |
1406 | ||
# | Line 1304 | Line 1435 | void SimSetup::compList(void){ | |
1435 | headStamp->add(currentStamp); | |
1436 | comp_stamps[i] = headStamp->match(id); | |
1437 | } | |
1438 | + | |
1439 | + | if(comp_stamps[i]->getNCutoffGroups() > 0) |
1440 | + | haveCutoffGroups = true; |
1441 | } | |
1442 | + | |
1443 | + | for (i = 0; i < nInfo; i++) |
1444 | + | info[i].haveCutoffGroups = haveCutoffGroups; |
1445 | ||
1446 | #ifdef IS_MPI | |
1447 | strcpy(checkPointMsg, "Component stamps successfully extracted\n"); | |
# | Line 1313 | Line 1450 | void SimSetup::calcSysValues(void){ | |
1450 | } | |
1451 | ||
1452 | void SimSetup::calcSysValues(void){ | |
1453 | < | int i; |
1453 | > | int i, j; |
1454 | > | int ncutgroups, atomsingroups, ngroupsinstamp; |
1455 | ||
1456 | int* molMembershipArray; | |
1457 | + | CutoffGroupStamp* cg; |
1458 | ||
1459 | tot_atoms = 0; | |
1460 | tot_bonds = 0; | |
1461 | tot_bends = 0; | |
1462 | tot_torsions = 0; | |
1463 | tot_rigid = 0; | |
1464 | + | tot_groups = 0; |
1465 | for (i = 0; i < n_components; i++){ | |
1466 | tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); | |
1467 | tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); | |
1468 | tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); | |
1469 | tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); | |
1470 | tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies(); | |
1471 | + | |
1472 | + | ncutgroups = comp_stamps[i]->getNCutoffGroups(); |
1473 | + | atomsingroups = 0; |
1474 | + | for (j=0; j < ncutgroups; j++) { |
1475 | + | cg = comp_stamps[i]->getCutoffGroup(j); |
1476 | + | atomsingroups += cg->getNMembers(); |
1477 | + | } |
1478 | + | ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups + ncutgroups; |
1479 | + | tot_groups += components_nmol[i] * ngroupsinstamp; |
1480 | } | |
1481 | ||
1482 | tot_SRI = tot_bonds + tot_bends + tot_torsions; | |
# | Line 1340 | Line 1489 | void SimSetup::calcSysValues(void){ | |
1489 | info[i].n_torsions = tot_torsions; | |
1490 | info[i].n_SRI = tot_SRI; | |
1491 | info[i].n_mol = tot_nmol; | |
1492 | < | |
1492 | > | info[i].ngroup = tot_groups; |
1493 | info[i].molMembershipArray = molMembershipArray; | |
1494 | } | |
1495 | } | |
# | Line 1351 | Line 1500 | void SimSetup::mpiMolDivide(void){ | |
1500 | int i, j, k; | |
1501 | int localMol, allMol; | |
1502 | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; | |
1503 | < | int local_rigid; |
1355 | < | vector<int> globalAtomIndex; |
1503 | > | int local_rigid, local_groups; |
1504 | vector<int> globalMolIndex; | |
1505 | + | int ncutgroups, atomsingroups, ngroupsinstamp; |
1506 | + | CutoffGroupStamp* cg; |
1507 | ||
1508 | mpiSim = new mpiSimulation(info); | |
1509 | ||
1510 | mpiSim->divideLabor(); | |
1511 | globalAtomIndex = mpiSim->getGlobalAtomIndex(); | |
1512 | < | globalMolIndex = mpiSim->getGlobalMolIndex(); |
1512 | > | //globalMolIndex = mpiSim->getGlobalMolIndex(); |
1513 | ||
1514 | // set up the local variables | |
1515 | ||
# | Line 1373 | Line 1523 | void SimSetup::mpiMolDivide(void){ | |
1523 | local_bends = 0; | |
1524 | local_torsions = 0; | |
1525 | local_rigid = 0; | |
1526 | + | local_groups = 0; |
1527 | globalAtomCounter = 0; | |
1528 | ||
1529 | for (i = 0; i < n_components; i++){ | |
# | Line 1383 | Line 1534 | void SimSetup::mpiMolDivide(void){ | |
1534 | local_bends += comp_stamps[i]->getNBends(); | |
1535 | local_torsions += comp_stamps[i]->getNTorsions(); | |
1536 | local_rigid += comp_stamps[i]->getNRigidBodies(); | |
1537 | + | |
1538 | + | ncutgroups = comp_stamps[i]->getNCutoffGroups(); |
1539 | + | atomsingroups = 0; |
1540 | + | for (k=0; k < ncutgroups; k++) { |
1541 | + | cg = comp_stamps[i]->getCutoffGroup(k); |
1542 | + | atomsingroups += cg->getNMembers(); |
1543 | + | } |
1544 | + | ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups + |
1545 | + | ncutgroups; |
1546 | + | local_groups += ngroupsinstamp; |
1547 | + | |
1548 | localMol++; | |
1549 | } | |
1550 | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){ | |
# | Line 1395 | Line 1557 | void SimSetup::mpiMolDivide(void){ | |
1557 | } | |
1558 | local_SRI = local_bonds + local_bends + local_torsions; | |
1559 | ||
1560 | < | info[0].n_atoms = mpiSim->getMyNlocal(); |
1560 | > | info[0].n_atoms = mpiSim->getNAtomsLocal(); |
1561 | ||
1400 | – | |
1562 | if (local_atoms != info[0].n_atoms){ | |
1563 | sprintf(painCave.errMsg, | |
1564 | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n" | |
# | Line 1407 | Line 1568 | void SimSetup::mpiMolDivide(void){ | |
1568 | simError(); | |
1569 | } | |
1570 | ||
1571 | + | info[0].ngroup = mpiSim->getNGroupsLocal(); |
1572 | + | if (local_groups != info[0].ngroup){ |
1573 | + | sprintf(painCave.errMsg, |
1574 | + | "SimSetup error: mpiSim's localGroups (%d) and SimSetup's\n" |
1575 | + | "\tlocalGroups (%d) are not equal.\n", |
1576 | + | info[0].ngroup, local_groups); |
1577 | + | painCave.isFatal = 1; |
1578 | + | simError(); |
1579 | + | } |
1580 | + | |
1581 | info[0].n_bonds = local_bonds; | |
1582 | info[0].n_bends = local_bends; | |
1583 | info[0].n_torsions = local_torsions; | |
# | Line 1443 | Line 1614 | void SimSetup::makeSysArrays(void){ | |
1614 | ||
1615 | ||
1616 | molIndex = 0; | |
1617 | < | for (i = 0; i < mpiSim->getTotNmol(); i++){ |
1617 | > | for (i = 0; i < mpiSim->getNMolGlobal(); i++){ |
1618 | if (mol2proc[i] == worldRank){ | |
1619 | the_molecules[molIndex].setStampID(molCompType[i]); | |
1620 | the_molecules[molIndex].setMyIndex(molIndex); | |
# | Line 1480 | Line 1651 | void SimSetup::makeSysArrays(void){ | |
1651 | info[l].atoms = the_atoms; | |
1652 | info[l].molecules = the_molecules; | |
1653 | info[l].nGlobalExcludes = 0; | |
1654 | < | |
1654 | > | |
1655 | the_ff->setSimInfo(info); | |
1656 | } | |
1657 | } |
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