# | 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 190 | Line 195 | void SimSetup::makeMolecules(void){ | |
195 | set<int> skipList; | |
196 | ||
197 | double phi, theta, psi; | |
198 | + | char* molName; |
199 | + | char rbName[100]; |
200 | ||
201 | //init the forceField paramters | |
202 | ||
# | Line 206 | Line 213 | void SimSetup::makeMolecules(void){ | |
213 | ||
214 | for (i = 0; i < info[k].n_mol; i++){ | |
215 | stampID = info[k].molecules[i].getStampID(); | |
216 | + | molName = comp_stamps[stampID]->getID(); |
217 | ||
218 | molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); | |
219 | molInfo.nBonds = comp_stamps[stampID]->getNBonds(); | |
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 259 | 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()); | |
265 | – | |
276 | #ifdef IS_MPI | |
277 | ||
278 | < | molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]); |
278 | > | molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]); |
279 | ||
280 | #endif // is_mpi | |
281 | } | |
# | Line 406 | 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 414 | Line 427 | void SimSetup::makeMolecules(void){ | |
427 | // Create the Rigid Body: | |
428 | ||
429 | myRB = new RigidBody(); | |
430 | + | |
431 | + | sprintf(rbName,"%s_RB_%d", molName, j); |
432 | + | myRB->setType(rbName); |
433 | ||
434 | for (rb1 = 0; rb1 < nMembers; rb1++) { | |
435 | ||
# | Line 454 | 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 470 | Line 486 | void SimSetup::makeMolecules(void){ | |
486 | info[k].rigidBodies.push_back(myRB); | |
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 | ||
541 | #ifdef IS_MPI | |
# | Line 522 | Line 584 | void SimSetup::makeMolecules(void){ | |
584 | sprintf(checkPointMsg, "all molecules initialized succesfully"); | |
585 | MPIcheckPoint(); | |
586 | #endif // is_mpi | |
525 | – | |
526 | – | // clean up the forcefield |
527 | – | |
528 | – | if (!globals->haveLJrcut()){ |
529 | – | |
530 | – | the_ff->calcRcut(); |
531 | – | |
532 | – | } else { |
533 | – | |
534 | – | the_ff->setRcut( globals->getLJrcut() ); |
535 | – | } |
587 | ||
537 | – | the_ff->cleanMe(); |
588 | } | |
589 | ||
590 | void SimSetup::initFromBass(void){ | |
# | Line 821 | 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 831 | 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 867 | Line 917 | void SimSetup::gatherInfo(void){ | |
917 | if (globals->haveSampleTime()){ | |
918 | info[i].sampleTime = globals->getSampleTime(); | |
919 | info[i].statusTime = info[i].sampleTime; | |
870 | – | info[i].thermalTime = info[i].sampleTime; |
920 | } | |
921 | else{ | |
922 | info[i].sampleTime = globals->getRunTime(); | |
923 | info[i].statusTime = info[i].sampleTime; | |
875 | – | info[i].thermalTime = info[i].sampleTime; |
924 | } | |
925 | ||
926 | if (globals->haveStatusTime()){ | |
# | Line 881 | 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 951 | Line 1001 | void SimSetup::finalInfoCheck(void){ | |
1001 | void SimSetup::finalInfoCheck(void){ | |
1002 | int index; | |
1003 | int usesDipoles; | |
1004 | + | int usesCharges; |
1005 | int i; | |
1006 | ||
1007 | for (i = 0; i < nInfo; i++){ | |
# | Line 962 | Line 1013 | void SimSetup::finalInfoCheck(void){ | |
1013 | usesDipoles = (info[i].atoms[index])->hasDipole(); | |
1014 | index++; | |
1015 | } | |
1016 | < | |
1016 | > | index = 0; |
1017 | > | usesCharges = 0; |
1018 | > | while ((index < info[i].n_atoms) && !usesCharges){ |
1019 | > | usesCharges= (info[i].atoms[index])->hasCharge(); |
1020 | > | index++; |
1021 | > | } |
1022 | #ifdef IS_MPI | |
1023 | int myUse = usesDipoles; | |
1024 | MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); | |
1025 | #endif //is_mpi | |
1026 | ||
1027 | < | double theEcr, theEst; |
1027 | > | double theRcut, theRsw; |
1028 | ||
1029 | < | if (globals->getUseRF()){ |
1030 | < | info[i].useReactionField = 1; |
1029 | > | if (globals->haveRcut()) { |
1030 | > | theRcut = globals->getRcut(); |
1031 | ||
1032 | < | if (!globals->haveECR()){ |
1033 | < | sprintf(painCave.errMsg, |
1034 | < | "SimSetup Warning: No value was set for electrostaticCutoffRadius.\n" |
1032 | > | if (globals->haveRsw()) |
1033 | > | theRsw = globals->getRsw(); |
1034 | > | else |
1035 | > | theRsw = theRcut; |
1036 | > | |
1037 | > | info[i].setDefaultRcut(theRcut, theRsw); |
1038 | > | |
1039 | > | } else { |
1040 | > | |
1041 | > | the_ff->calcRcut(); |
1042 | > | theRcut = info[i].getRcut(); |
1043 | > | |
1044 | > | if (globals->haveRsw()) |
1045 | > | theRsw = globals->getRsw(); |
1046 | > | else |
1047 | > | theRsw = theRcut; |
1048 | > | |
1049 | > | info[i].setDefaultRcut(theRcut, theRsw); |
1050 | > | } |
1051 | > | |
1052 | > | if (globals->getUseRF()){ |
1053 | > | info[i].useReactionField = 1; |
1054 | > | |
1055 | > | if (!globals->haveRcut()){ |
1056 | > | sprintf(painCave.errMsg, |
1057 | > | "SimSetup Warning: No value was set for the cutoffRadius.\n" |
1058 | "\tOOPSE will use a default value of 15.0 angstroms" | |
1059 | < | "\tfor the electrostaticCutoffRadius.\n"); |
1059 | > | "\tfor the cutoffRadius.\n"); |
1060 | painCave.isFatal = 0; | |
1061 | simError(); | |
1062 | < | theEcr = 15.0; |
1062 | > | theRcut = 15.0; |
1063 | } | |
1064 | else{ | |
1065 | < | theEcr = globals->getECR(); |
1065 | > | theRcut = globals->getRcut(); |
1066 | } | |
1067 | ||
1068 | < | if (!globals->haveEST()){ |
1068 | > | if (!globals->haveRsw()){ |
1069 | sprintf(painCave.errMsg, | |
1070 | < | "SimSetup Warning: No value was set for electrostaticSkinThickness.\n" |
1070 | > | "SimSetup Warning: No value was set for switchingRadius.\n" |
1071 | "\tOOPSE will use a default value of\n" | |
1072 | < | "\t0.05 * electrostaticCutoffRadius\n" |
994 | < | "\tfor the electrostaticSkinThickness\n"); |
1072 | > | "\t0.95 * cutoffRadius for the switchingRadius\n"); |
1073 | painCave.isFatal = 0; | |
1074 | simError(); | |
1075 | < | theEst = 0.05 * theEcr; |
1075 | > | theRsw = 0.95 * theRcut; |
1076 | } | |
1077 | else{ | |
1078 | < | theEst = globals->getEST(); |
1078 | > | theRsw = globals->getRsw(); |
1079 | } | |
1080 | ||
1081 | < | info[i].setDefaultEcr(theEcr, theEst); |
1081 | > | info[i].setDefaultRcut(theRcut, theRsw); |
1082 | ||
1083 | if (!globals->haveDielectric()){ | |
1084 | sprintf(painCave.errMsg, | |
# | Line 1013 | Line 1091 | void SimSetup::finalInfoCheck(void){ | |
1091 | info[i].dielectric = globals->getDielectric(); | |
1092 | } | |
1093 | else{ | |
1094 | < | if (usesDipoles){ |
1095 | < | if (!globals->haveECR()){ |
1094 | > | if (usesDipoles || usesCharges){ |
1095 | > | |
1096 | > | if (!globals->haveRcut()){ |
1097 | sprintf(painCave.errMsg, | |
1098 | < | "SimSetup Warning: No value was set for electrostaticCutoffRadius.\n" |
1098 | > | "SimSetup Warning: No value was set for the cutoffRadius.\n" |
1099 | "\tOOPSE will use a default value of 15.0 angstroms" | |
1100 | < | "\tfor the electrostaticCutoffRadius.\n"); |
1101 | < | painCave.isFatal = 0; |
1102 | < | simError(); |
1103 | < | theEcr = 15.0; |
1104 | < | } |
1100 | > | "\tfor the cutoffRadius.\n"); |
1101 | > | painCave.isFatal = 0; |
1102 | > | simError(); |
1103 | > | theRcut = 15.0; |
1104 | > | } |
1105 | else{ | |
1106 | < | theEcr = globals->getECR(); |
1106 | > | theRcut = globals->getRcut(); |
1107 | } | |
1108 | < | |
1109 | < | if (!globals->haveEST()){ |
1108 | > | |
1109 | > | if (!globals->haveRsw()){ |
1110 | sprintf(painCave.errMsg, | |
1111 | < | "SimSetup Warning: No value was set for electrostaticSkinThickness.\n" |
1111 | > | "SimSetup Warning: No value was set for switchingRadius.\n" |
1112 | "\tOOPSE will use a default value of\n" | |
1113 | < | "\t0.05 * electrostaticCutoffRadius\n" |
1035 | < | "\tfor the electrostaticSkinThickness\n"); |
1113 | > | "\t0.95 * cutoffRadius for the switchingRadius\n"); |
1114 | painCave.isFatal = 0; | |
1115 | simError(); | |
1116 | < | theEst = 0.05 * theEcr; |
1116 | > | theRsw = 0.95 * theRcut; |
1117 | } | |
1118 | else{ | |
1119 | < | theEst = globals->getEST(); |
1119 | > | theRsw = globals->getRsw(); |
1120 | } | |
1121 | + | |
1122 | + | info[i].setDefaultRcut(theRcut, theRsw); |
1123 | ||
1044 | – | info[i].setDefaultEcr(theEcr, theEst); |
1124 | } | |
1125 | } | |
1126 | } | |
# | Line 1049 | Line 1128 | void SimSetup::finalInfoCheck(void){ | |
1128 | strcpy(checkPointMsg, "post processing checks out"); | |
1129 | MPIcheckPoint(); | |
1130 | #endif // is_mpi | |
1131 | + | |
1132 | + | // clean up the forcefield |
1133 | + | the_ff->cleanMe(); |
1134 | } | |
1135 | ||
1136 | void SimSetup::initSystemCoords(void){ | |
# | Line 1263 | Line 1345 | void SimSetup::compList(void){ | |
1345 | LinkedMolStamp* headStamp = new LinkedMolStamp(); | |
1346 | LinkedMolStamp* currentStamp = NULL; | |
1347 | comp_stamps = new MoleculeStamp * [n_components]; | |
1348 | + | bool haveCutoffGroups; |
1349 | ||
1350 | + | haveCutoffGroups = false; |
1351 | + | |
1352 | // make an array of molecule stamps that match the components used. | |
1353 | // also extract the used stamps out into a separate linked list | |
1354 | ||
# | Line 1298 | Line 1383 | void SimSetup::compList(void){ | |
1383 | headStamp->add(currentStamp); | |
1384 | comp_stamps[i] = headStamp->match(id); | |
1385 | } | |
1386 | + | |
1387 | + | if(comp_stamps[i]->getNCutoffGroups() > 0) |
1388 | + | haveCutoffGroups = true; |
1389 | } | |
1390 | + | |
1391 | + | for (i = 0; i < nInfo; i++) |
1392 | + | info[i].haveCutoffGroups = haveCutoffGroups; |
1393 | ||
1394 | #ifdef IS_MPI | |
1395 | strcpy(checkPointMsg, "Component stamps successfully extracted\n"); | |
# | Line 1346 | Line 1437 | void SimSetup::mpiMolDivide(void){ | |
1437 | int localMol, allMol; | |
1438 | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; | |
1439 | int local_rigid; | |
1440 | + | vector<int> globalMolIndex; |
1441 | ||
1442 | mpiSim = new mpiSimulation(info); | |
1443 | ||
1444 | < | globalIndex = mpiSim->divideLabor(); |
1444 | > | mpiSim->divideLabor(); |
1445 | > | globalAtomIndex = mpiSim->getGlobalAtomIndex(); |
1446 | > | //globalMolIndex = mpiSim->getGlobalMolIndex(); |
1447 | ||
1448 | // set up the local variables | |
1449 | ||
# | Line 1363 | Line 1457 | void SimSetup::mpiMolDivide(void){ | |
1457 | local_bends = 0; | |
1458 | local_torsions = 0; | |
1459 | local_rigid = 0; | |
1460 | < | globalAtomIndex = 0; |
1460 | > | globalAtomCounter = 0; |
1461 | ||
1462 | for (i = 0; i < n_components; i++){ | |
1463 | for (j = 0; j < components_nmol[i]; j++){ | |
# | Line 1376 | Line 1470 | void SimSetup::mpiMolDivide(void){ | |
1470 | localMol++; | |
1471 | } | |
1472 | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){ | |
1473 | < | info[0].molMembershipArray[globalAtomIndex] = allMol; |
1474 | < | globalAtomIndex++; |
1473 | > | info[0].molMembershipArray[globalAtomCounter] = allMol; |
1474 | > | globalAtomCounter++; |
1475 | } | |
1476 | ||
1477 | allMol++; | |
# | Line 1445 | Line 1539 | void SimSetup::makeSysArrays(void){ | |
1539 | #else // is_mpi | |
1540 | ||
1541 | molIndex = 0; | |
1542 | < | globalAtomIndex = 0; |
1542 | > | globalAtomCounter = 0; |
1543 | for (i = 0; i < n_components; i++){ | |
1544 | for (j = 0; j < components_nmol[i]; j++){ | |
1545 | the_molecules[molIndex].setStampID(i); | |
1546 | the_molecules[molIndex].setMyIndex(molIndex); | |
1547 | the_molecules[molIndex].setGlobalIndex(molIndex); | |
1548 | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){ | |
1549 | < | info[l].molMembershipArray[globalAtomIndex] = molIndex; |
1550 | < | globalAtomIndex++; |
1549 | > | info[l].molMembershipArray[globalAtomCounter] = molIndex; |
1550 | > | globalAtomCounter++; |
1551 | } | |
1552 | molIndex++; | |
1553 | } | |
# | Line 1470 | Line 1564 | void SimSetup::makeSysArrays(void){ | |
1564 | info[l].atoms = the_atoms; | |
1565 | info[l].molecules = the_molecules; | |
1566 | info[l].nGlobalExcludes = 0; | |
1567 | < | |
1567 | > | |
1568 | the_ff->setSimInfo(info); | |
1569 | } | |
1570 | } |
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