# | Line 183 | 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 216 | 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 481 | 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 | ||
# | Line 536 | Line 585 | void SimSetup::makeMolecules(void){ | |
585 | MPIcheckPoint(); | |
586 | #endif // is_mpi | |
587 | ||
539 | – | // clean up the forcefield |
540 | – | |
541 | – | if (!globals->haveLJrcut()){ |
542 | – | |
543 | – | the_ff->calcRcut(); |
544 | – | |
545 | – | } else { |
546 | – | |
547 | – | the_ff->setRcut( globals->getLJrcut() ); |
548 | – | } |
549 | – | |
550 | – | the_ff->cleanMe(); |
588 | } | |
589 | ||
590 | void SimSetup::initFromBass(void){ | |
# | Line 834 | 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 844 | 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 880 | Line 917 | void SimSetup::gatherInfo(void){ | |
917 | if (globals->haveSampleTime()){ | |
918 | info[i].sampleTime = globals->getSampleTime(); | |
919 | info[i].statusTime = info[i].sampleTime; | |
883 | – | info[i].thermalTime = info[i].sampleTime; |
920 | } | |
921 | else{ | |
922 | info[i].sampleTime = globals->getRunTime(); | |
923 | info[i].statusTime = info[i].sampleTime; | |
888 | – | info[i].thermalTime = info[i].sampleTime; |
924 | } | |
925 | ||
926 | if (globals->haveStatusTime()){ | |
# | Line 894 | 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 911 | 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 987 | Line 1054 | void SimSetup::finalInfoCheck(void){ | |
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->getUseRF()){ |
1060 | < | info[i].useReactionField = 1; |
1059 | > | if (globals->haveRcut()) { |
1060 | > | theRcut = globals->getRcut(); |
1061 | ||
1062 | < | if (!globals->haveECR()){ |
1063 | < | sprintf(painCave.errMsg, |
1064 | < | "SimSetup Warning: No value was set for electrostaticCutoffRadius.\n" |
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->haveRcut()){ |
1086 | > | sprintf(painCave.errMsg, |
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" |
1013 | < | "\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 1033 | Line 1122 | void SimSetup::finalInfoCheck(void){ | |
1122 | } | |
1123 | else{ | |
1124 | if (usesDipoles || usesCharges){ | |
1125 | < | if (!globals->haveECR()){ |
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" |
1054 | < | "\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 | ||
1063 | – | info[i].setDefaultEcr(theEcr, theEst); |
1154 | } | |
1155 | } | |
1156 | } | |
# | Line 1068 | 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 1195 | 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 1282 | 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 1317 | 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 1365 | Line 1489 | void SimSetup::mpiMolDivide(void){ | |
1489 | int localMol, allMol; | |
1490 | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; | |
1491 | int local_rigid; | |
1368 | – | vector<int> globalAtomIndex; |
1492 | vector<int> globalMolIndex; | |
1493 | ||
1494 | mpiSim = new mpiSimulation(info); | |
1495 | ||
1496 | mpiSim->divideLabor(); | |
1497 | globalAtomIndex = mpiSim->getGlobalAtomIndex(); | |
1498 | < | globalMolIndex = mpiSim->getGlobalMolIndex(); |
1498 | > | //globalMolIndex = mpiSim->getGlobalMolIndex(); |
1499 | ||
1500 | // set up the local variables | |
1501 | ||
# | Line 1408 | Line 1531 | void SimSetup::mpiMolDivide(void){ | |
1531 | } | |
1532 | local_SRI = local_bonds + local_bends + local_torsions; | |
1533 | ||
1534 | < | info[0].n_atoms = mpiSim->getMyNlocal(); |
1534 | > | info[0].n_atoms = mpiSim->getLocalNatoms(); |
1535 | ||
1536 | ||
1537 | if (local_atoms != info[0].n_atoms){ | |
# | Line 1493 | Line 1616 | void SimSetup::makeSysArrays(void){ | |
1616 | info[l].atoms = the_atoms; | |
1617 | info[l].molecules = the_molecules; | |
1618 | info[l].nGlobalExcludes = 0; | |
1619 | < | |
1619 | > | |
1620 | the_ff->setSimInfo(info); | |
1621 | } | |
1622 | } |
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