[ViewVC] Diff of: group/trunk/OOPSE/libmdtools/SimSetup.cpp

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 1097 by gezelter, Mon Apr 12 20:32:20 2004 UTC vs.
Revision 1212 by chrisfen, Tue Jun 1 17:15:43 2004 UTC

#	Line 10 \| Line 10
10		#include "Integrator.hpp"
11		#include "simError.h"
12		#include "RigidBody.hpp"
13	–	//#include "ConjugateMinimizer.hpp"
13		#include "OOPSEMinimizer.hpp"
14	+	//#include "ConstraintElement.hpp"
15	+	//#include "ConstraintPair.hpp"
16
17		#ifdef IS_MPI
18		#include "mpiBASS.h"
#	Line 147 \| Line 148 \| void SimSetup::createSim(void){
148		// make the output filenames
149
150		makeOutNames();
150	–
151	–	if (globals->haveMinimizer())
152	–	// make minimizer
153	–	makeMinimizer();
154	–	else
155	–	// make the integrator
156	–	makeIntegrator();
151
152		#ifdef IS_MPI
153		mpiSim->mpiRefresh();
#	Line 162 \| Line 156 \| void SimSetup::createSim(void){
156		// initialize the Fortran
157
158		initFortran();
159	+
160	+	if (globals->haveMinimizer())
161	+	// make minimizer
162	+	makeMinimizer();
163	+	else
164	+	// make the integrator
165	+	makeIntegrator();
166	+
167		}
168
169
170		void SimSetup::makeMolecules(void){
171		int i, j, k;
172	<	int exI, exJ, exK, exL, slI;
172	>	int exI, exJ, exK, exL, slI, slJ;
173		int tempI, tempJ, tempK, tempL;
174		int molI;
175		int stampID, atomOffset, rbOffset;
#	Line 182 \| Line 184 \| void SimSetup::makeMolecules(void){
184		BendStamp* currentBend;
185		TorsionStamp* currentTorsion;
186		RigidBodyStamp* currentRigidBody;
187	+	CutoffGroupStamp* currentCutoffGroup;
188	+	CutoffGroup* myCutoffGroup;
189	+	int nCutoffGroups;// number of cutoff group of a molecule defined in mdl file
190	+	set<int> cutoffAtomSet; //atoms belong to cutoffgroup defined at mdl file
191
192		bond_pair* theBonds;
193		bend_set* theBends;
#	Line 190 \| Line 196 \| void SimSetup::makeMolecules(void){
196		set<int> skipList;
197
198		double phi, theta, psi;
199	+	char* molName;
200	+	char rbName[100];
201
202	+	//ConstraintPair* consPair; //constraint pair
203	+	//ConstraintElement* consElement1; //first element of constraint pair
204	+	//ConstraintElement* consElement2; //second element of constraint pair
205	+	//int whichRigidBody;
206	+	//int consAtomIndex; //index of constraint atom in rigid body's atom array
207	+	//vector<pair<int, int> > jointAtoms;
208		//init the forceField paramters
209
210		the_ff->readParams();
#	Line 203 \| Line 217 \| void SimSetup::makeMolecules(void){
217		the_ff->setSimInfo(&(info[k]));
218
219		atomOffset = 0;
220	+	groupOffset = 0;
221
222		for (i = 0; i < info[k].n_mol; i++){
223		stampID = info[k].molecules[i].getStampID();
224	+	molName = comp_stamps[stampID]->getID();
225
226		molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
227		molInfo.nBonds = comp_stamps[stampID]->getNBonds();
228		molInfo.nBends = comp_stamps[stampID]->getNBends();
229		molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
230		molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
231	+
232	+	nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups();
233
234		molInfo.myAtoms = &(info[k].atoms[atomOffset]);
235
236		if (molInfo.nBonds > 0)
237	<	molInfo.myBonds = new (Bond *) [molInfo.nBonds];
237	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
238		else
239		molInfo.myBonds = NULL;
240
241		if (molInfo.nBends > 0)
242	<	molInfo.myBends = new (Bend *) [molInfo.nBends];
242	>	molInfo.myBends = new Bend*[molInfo.nBends];
243		else
244		molInfo.myBends = NULL;
245
246		if (molInfo.nTorsions > 0)
247	<	molInfo.myTorsions = new (Torsion *) [molInfo.nTorsions];
247	>	molInfo.myTorsions = new Torsion *[molInfo.nTorsions];
248		else
249		molInfo.myTorsions = NULL;
250
#	Line 259 \| Line 277 \| void SimSetup::makeMolecules(void){
277		else{
278
279		molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
280	+
281		}
282
283		molInfo.myAtoms[j]->setType(currentAtom->getType());
265	–
284		#ifdef IS_MPI
285
286	<	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
286	>	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
287
288		#endif // is_mpi
289		}
#	Line 406 \| Line 424 \| void SimSetup::makeMolecules(void){
424		info[k].excludes->addPair(exK, exL);
425		}
426
427	+
428	+	molInfo.myRigidBodies.clear();
429	+
430		for (j = 0; j < molInfo.nRigidBodies; j++){
431
432		currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
#	Line 414 \| Line 435 \| void SimSetup::makeMolecules(void){
435		// Create the Rigid Body:
436
437		myRB = new RigidBody();
438	+
439	+	sprintf(rbName,"%s_RB_%d", molName, j);
440	+	myRB->setType(rbName);
441
442		for (rb1 = 0; rb1 < nMembers; rb1++) {
443
#	Line 454 \| Line 478 \| void SimSetup::makeMolecules(void){
478		// used for the exclude list:
479
480		#ifdef IS_MPI
481	<	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
482	<	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
481	>	exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
482	>	exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
483		#else
484	<	exI = tempI + 1;
485	<	exJ = tempJ + 1;
484	>	exI = molInfo.myAtoms[tempI]->getIndex() + 1;
485	>	exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
486		#endif
487
488		info[k].excludes->addPair(exI, exJ);
489
490	+	}
491	+	}
492	+
493	+	molInfo.myRigidBodies.push_back(myRB);
494	+	info[k].rigidBodies.push_back(myRB);
495	+	}
496	+
497	+
498	+	//create cutoff group for molecule
499	+
500	+	cutoffAtomSet.clear();
501	+	molInfo.myCutoffGroups.clear();
502	+
503	+	for (j = 0; j < nCutoffGroups; j++){
504	+
505	+	currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j);
506	+	nMembers = currentCutoffGroup->getNMembers();
507	+
508	+	myCutoffGroup = new CutoffGroup();
509	+	myCutoffGroup->setGlobalIndex(globalGroupIndex[j + groupOffset]);
510	+
511	+	for (int cg = 0; cg < nMembers; cg++) {
512	+
513	+	// molI is atom numbering inside this molecule
514	+	molI = currentCutoffGroup->getMember(cg);
515	+
516	+	// tempI is atom numbering on local processor
517	+	tempI = molI + atomOffset;
518	+
519	+	#ifdef IS_MPI
520	+	globalID = info[k].atoms[tempI]->getGlobalIndex()
521	+	#else
522	+	globalID = info[k].atoms[tempI]->getIndex();
523	+	#endif
524	+
525	+	globalGroupMembership[globalID] = globalGroupIndex[j+groupOffset];
526	+
527	+	myCutoffGroup->addAtom(info[k].atoms[tempI]);
528	+
529	+	cutoffAtomSet.insert(tempI);
530	+	}
531	+
532	+	molInfo.myCutoffGroups.push_back(myCutoffGroup);
533	+	groupOffset++;
534	+
535	+	}//end for (j = 0; j < molInfo.nCutoffGroups; j++)
536	+
537	+	//creat a cutoff group for every atom in current molecule which does not belong to cutoffgroup defined at mdl file
538	+
539	+	for(j = 0; j < molInfo.nAtoms; j++){
540	+
541	+	if(cutoffAtomSet.find(molInfo.myAtoms[j]->getIndex()) == cutoffAtomSet.end()){
542	+	myCutoffGroup = new CutoffGroup();
543	+	myCutoffGroup->addAtom(molInfo.myAtoms[j]);
544	+	myCutoffGroup->setGlobalIndex(globalGroupIndex[j + groupOffset]);
545	+	#ifdef IS_MPI
546	+	globalID = info[k].atoms[atomOffset + j]->getGlobalIndex()
547	+	#else
548	+	globalID = info[k].atoms[atomOffset + j]->getIndex();
549	+	#endif
550	+	globalGroupMembership[globalID] = globalGroupIndex[j+groupOffset];
551	+	molInfo.myCutoffGroups.push_back(myCutoffGroup);
552	+	groupOffset++;
553	+	}
554	+
555	+	}
556	+
557	+	// After this is all set up, scan through the atoms to
558	+	// see if they can be added to the integrableObjects:
559	+
560	+	molInfo.myIntegrableObjects.clear();
561	+
562	+
563	+	for (j = 0; j < molInfo.nAtoms; j++){
564	+
565	+	#ifdef IS_MPI
566	+	slJ = molInfo.myAtoms[j]->getGlobalIndex();
567	+	#else
568	+	slJ = j+atomOffset;
569	+	#endif
570	+
571	+	// if they aren't on the skip list, then they can be integrated
572	+
573	+	if (skipList.find(slJ) == skipList.end()) {
574	+	mySD = (StuntDouble *) molInfo.myAtoms[j];
575	+	info[k].integrableObjects.push_back(mySD);
576	+	molInfo.myIntegrableObjects.push_back(mySD);
577	+	}
578	+	}
579	+
580	+	// all rigid bodies are integrated:
581	+
582	+	for (j = 0; j < molInfo.nRigidBodies; j++) {
583	+	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
584	+	info[k].integrableObjects.push_back(mySD);
585	+	molInfo.myIntegrableObjects.push_back(mySD);
586	+	}
587	+
588	+
589	+	/*
590	+
591	+	//creat ConstraintPair.
592	+	molInfo.myConstraintPair.clear();
593	+
594	+	for (j = 0; j < molInfo.nBonds; j++){
595	+
596	+	//if both atoms are in the same rigid body, just skip it
597	+	currentBond = comp_stamps[stampID]->getBond(j);
598	+	if(!comp_stamps[stampID]->isBondInSameRigidBody(currentBond)){
599	+
600	+	tempI = currentBond->getA() + atomOffset;
601	+	if( comp_stamps[stampID]->isAtomInRigidBody(currentBond->getA(), whichRigidBody, consAtomIndex))
602	+	consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
603	+	else
604	+	consElement1 = new ConstraintAtom(info[k].atoms[tempI]);
605	+
606	+	tempJ = currentBond->getB() + atomOffset;
607	+	if(comp_stamps[stampID]->isAtomInRigidBody(currentBond->getB(), whichRigidBody, consAtomIndex))
608	+	consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
609	+	else
610	+	consElement2 = new ConstraintAtom(info[k].atoms[tempJ]);
611	+
612	+	consPair = new DistanceConstraintPair(consElement1, consElement2);
613	+	molInfo.myConstraintPairs.push_back(consPair);
614	+	}
615	+	}
616	+
617	+	//loop over rigid bodies, if two rigid bodies share same joint, creat a HingeConstraintPair
618	+	for (int rb1 = 0; rb1 < molInfo.nRigidBodies -1 ; rb1++){
619	+	for (int rb2 = rb1 + 1; rb2 < molInfo.nRigidBodies ; rb2++){
620	+
621	+	jointAtoms = comp_stamps[stampID]->getJointAtoms(rb1, rb2);
622	+
623	+	for(size_t m = 0; m < jointAtoms.size(); m++){
624	+	consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[rb1], jointAtoms[m].first);
625	+	consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[rb2], jointAtoms[m].second);
626	+
627	+	consPair = new JointConstraintPair(consElement1, consElement2);
628	+	molInfo.myConstraintPairs.push_back(consPair);
629		}
630	+
631		}
632		}
633
634	+	*/
635		// send the arrays off to the forceField for init.
636
637		the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
#	Line 482 \| Line 647 \| void SimSetup::makeMolecules(void){
647		delete[] theBonds;
648		delete[] theBends;
649		delete[] theTorsions;
650	<	}
486	<
487	<	// build up the integrableObjects vector:
488	<
489	<	for (i = 0; i < info[k].n_atoms; i++) {
490	<
491	<	#ifdef IS_MPI
492	<	slI = info[k].atoms[i]->getGlobalIndex();
493	<	#else
494	<	slI = i;
495	<	#endif
496	<
497	<	if (skipList.find(slI) == skipList.end()) {
498	<	mySD = (StuntDouble *) info[k].atoms[i];
499	<	info[k].integrableObjects.push_back(mySD);
500	<	}
501	<	}
502	<	for (i = 0; i < info[k].rigidBodies.size(); i++) {
503	<	mySD = (StuntDouble *) info[k].rigidBodies[i];
504	<	info[k].integrableObjects.push_back(mySD);
505	<	}
506	<
650	>	}
651		}
652
653		#ifdef IS_MPI
#	Line 511 \| Line 655 \| void SimSetup::makeMolecules(void){
655		MPIcheckPoint();
656		#endif // is_mpi
657
514	–	// clean up the forcefield
515	–
516	–	if (!globals->haveLJrcut()){
517	–
518	–	the_ff->calcRcut();
519	–
520	–	} else {
521	–
522	–	the_ff->setRcut( globals->getLJrcut() );
523	–	}
524	–
525	–	the_ff->cleanMe();
658		}
659
660		void SimSetup::initFromBass(void){
#	Line 809 \| Line 941 \| void SimSetup::gatherInfo(void){
941		}
942
943		//check whether sample time, status time, thermal time and reset time are divisble by dt
944	<	if (!isDivisible(globals->getSampleTime(), globals->getDt())){
944	>	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
945		sprintf(painCave.errMsg,
946		"Sample time is not divisible by dt.\n"
947		"\tThis will result in samples that are not uniformly\n"
#	Line 819 \| Line 951 \| void SimSetup::gatherInfo(void){
951		simError();
952		}
953
954	<	if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
954	>	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
955		sprintf(painCave.errMsg,
956		"Status time is not divisible by dt.\n"
957		"\tThis will result in status reports that are not uniformly\n"
#	Line 855 \| Line 987 \| void SimSetup::gatherInfo(void){
987		if (globals->haveSampleTime()){
988		info[i].sampleTime = globals->getSampleTime();
989		info[i].statusTime = info[i].sampleTime;
858	–	info[i].thermalTime = info[i].sampleTime;
990		}
991		else{
992		info[i].sampleTime = globals->getRunTime();
993		info[i].statusTime = info[i].sampleTime;
863	–	info[i].thermalTime = info[i].sampleTime;
994		}
995
996		if (globals->haveStatusTime()){
#	Line 869 \| Line 999 \| void SimSetup::gatherInfo(void){
999
1000		if (globals->haveThermalTime()){
1001		info[i].thermalTime = globals->getThermalTime();
1002	+	} else {
1003	+	info[i].thermalTime = globals->getRunTime();
1004		}
1005
1006		info[i].resetIntegrator = 0;
#	Line 886 \| Line 1018 \| void SimSetup::gatherInfo(void){
1018
1019		info[i].useInitXSstate = globals->getUseInitXSstate();
1020		info[i].orthoTolerance = globals->getOrthoBoxTolerance();
1021	<
1021	>
1022	>	// check for thermodynamic integration
1023	>	if (globals->getUseSolidThermInt() && !globals->getUseLiquidThermInt()) {
1024	>	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1025	>	info[i].useSolidThermInt = globals->getUseSolidThermInt();
1026	>	info[i].thermIntLambda = globals->getThermIntLambda();
1027	>	info[i].thermIntK = globals->getThermIntK();
1028	>
1029	>	Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK);
1030	>	info[i].restraint = myRestraint;
1031	>	}
1032	>	else {
1033	>	sprintf(painCave.errMsg,
1034	>	"SimSetup Error:\n"
1035	>	"\tKeyword useSolidThermInt was set to 'true' but\n"
1036	>	"\tthermodynamicIntegrationLambda (and/or\n"
1037	>	"\tthermodynamicIntegrationK) was not specified.\n"
1038	>	"\tPlease provide a lambda value and k value in your .bass file.\n");
1039	>	painCave.isFatal = 1;
1040	>	simError();
1041	>	}
1042	>	}
1043	>	else if(globals->getUseLiquidThermInt()) {
1044	>	if (globals->getUseSolidThermInt()) {
1045	>	sprintf( painCave.errMsg,
1046	>	"SimSetup Warning: It appears that you have both solid and\n"
1047	>	"\tliquid thermodynamic integration activated in your .bass\n"
1048	>	"\tfile. To avoid confusion, specify only one technique in\n"
1049	>	"\tyour .bass file. Liquid-state thermodynamic integration\n"
1050	>	"\twill be assumed for the current simulation. If this is not\n"
1051	>	"\twhat you desire, set useSolidThermInt to 'true' and\n"
1052	>	"\tuseLiquidThermInt to 'false' in your .bass file.\n");
1053	>	painCave.isFatal = 0;
1054	>	simError();
1055	>	}
1056	>	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1057	>	info[i].useLiquidThermInt = globals->getUseLiquidThermInt();
1058	>	info[i].thermIntLambda = globals->getThermIntLambda();
1059	>	info[i].thermIntK = globals->getThermIntK();
1060	>	}
1061	>	else {
1062	>	sprintf(painCave.errMsg,
1063	>	"SimSetup Error:\n"
1064	>	"\tKeyword useLiquidThermInt was set to 'true' but\n"
1065	>	"\tthermodynamicIntegrationLambda (and/or\n"
1066	>	"\tthermodynamicIntegrationK) was not specified.\n"
1067	>	"\tPlease provide a lambda value and k value in your .bass file.\n");
1068	>	painCave.isFatal = 1;
1069	>	simError();
1070	>	}
1071	>	}
1072	>	else if(globals->haveThermIntLambda() \|\| globals->haveThermIntK()){
1073	>	sprintf(painCave.errMsg,
1074	>	"SimSetup Warning: If you want to use Thermodynamic\n"
1075	>	"\tIntegration, set useSolidThermInt or useLiquidThermInt to\n"
1076	>	"\t'true' in your .bass file. These keywords are set to\n"
1077	>	"\t'false' by default, so your lambda and/or k values are\n"
1078	>	"\tbeing ignored.\n");
1079	>	painCave.isFatal = 0;
1080	>	simError();
1081	>	}
1082		}
1083
1084		//setup seed for random number generator
#	Line 939 \| Line 1131 \| void SimSetup::finalInfoCheck(void){
1131		void SimSetup::finalInfoCheck(void){
1132		int index;
1133		int usesDipoles;
1134	+	int usesCharges;
1135		int i;
1136
1137		for (i = 0; i < nInfo; i++){
#	Line 950 \| Line 1143 \| void SimSetup::finalInfoCheck(void){
1143		usesDipoles = (info[i].atoms[index])->hasDipole();
1144		index++;
1145		}
1146	<
1146	>	index = 0;
1147	>	usesCharges = 0;
1148	>	while ((index < info[i].n_atoms) && !usesCharges){
1149	>	usesCharges= (info[i].atoms[index])->hasCharge();
1150	>	index++;
1151	>	}
1152		#ifdef IS_MPI
1153		int myUse = usesDipoles;
1154		MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1155		#endif //is_mpi
1156
1157	<	double theEcr, theEst;
1157	>	double theRcut, theRsw;
1158
1159	+	if (globals->haveRcut()) {
1160	+	theRcut = globals->getRcut();
1161	+
1162	+	if (globals->haveRsw())
1163	+	theRsw = globals->getRsw();
1164	+	else
1165	+	theRsw = theRcut;
1166	+
1167	+	info[i].setDefaultRcut(theRcut, theRsw);
1168	+
1169	+	} else {
1170	+
1171	+	the_ff->calcRcut();
1172	+	theRcut = info[i].getRcut();
1173	+
1174	+	if (globals->haveRsw())
1175	+	theRsw = globals->getRsw();
1176	+	else
1177	+	theRsw = theRcut;
1178	+
1179	+	info[i].setDefaultRcut(theRcut, theRsw);
1180	+	}
1181	+
1182		if (globals->getUseRF()){
1183		info[i].useReactionField = 1;
1184	<
1185	<	if (!globals->haveECR()){
1184	>
1185	>	if (!globals->haveRcut()){
1186		sprintf(painCave.errMsg,
1187	<	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
1187	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1188		"\tOOPSE will use a default value of 15.0 angstroms"
1189	<	"\tfor the electrostaticCutoffRadius.\n");
1189	>	"\tfor the cutoffRadius.\n");
1190		painCave.isFatal = 0;
1191		simError();
1192	<	theEcr = 15.0;
1192	>	theRcut = 15.0;
1193		}
1194		else{
1195	<	theEcr = globals->getECR();
1195	>	theRcut = globals->getRcut();
1196		}
1197
1198	<	if (!globals->haveEST()){
1198	>	if (!globals->haveRsw()){
1199		sprintf(painCave.errMsg,
1200	<	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1200	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1201		"\tOOPSE will use a default value of\n"
1202	<	"\t0.05 * electrostaticCutoffRadius\n"
982	<	"\tfor the electrostaticSkinThickness\n");
1202	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1203		painCave.isFatal = 0;
1204		simError();
1205	<	theEst = 0.05 * theEcr;
1205	>	theRsw = 0.95 * theRcut;
1206		}
1207		else{
1208	<	theEst = globals->getEST();
1208	>	theRsw = globals->getRsw();
1209		}
1210
1211	<	info[i].setDefaultEcr(theEcr, theEst);
1211	>	info[i].setDefaultRcut(theRcut, theRsw);
1212
1213		if (!globals->haveDielectric()){
1214		sprintf(painCave.errMsg,
#	Line 1001 \| Line 1221 \| void SimSetup::finalInfoCheck(void){
1221		info[i].dielectric = globals->getDielectric();
1222		}
1223		else{
1224	<	if (usesDipoles){
1225	<	if (!globals->haveECR()){
1224	>	if (usesDipoles \|\| usesCharges){
1225	>
1226	>	if (!globals->haveRcut()){
1227		sprintf(painCave.errMsg,
1228	<	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
1228	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1229		"\tOOPSE will use a default value of 15.0 angstroms"
1230	<	"\tfor the electrostaticCutoffRadius.\n");
1231	<	painCave.isFatal = 0;
1232	<	simError();
1233	<	theEcr = 15.0;
1234	<	}
1230	>	"\tfor the cutoffRadius.\n");
1231	>	painCave.isFatal = 0;
1232	>	simError();
1233	>	theRcut = 15.0;
1234	>	}
1235		else{
1236	<	theEcr = globals->getECR();
1236	>	theRcut = globals->getRcut();
1237		}
1238	<
1239	<	if (!globals->haveEST()){
1238	>
1239	>	if (!globals->haveRsw()){
1240		sprintf(painCave.errMsg,
1241	<	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1241	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1242		"\tOOPSE will use a default value of\n"
1243	<	"\t0.05 * electrostaticCutoffRadius\n"
1023	<	"\tfor the electrostaticSkinThickness\n");
1243	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1244		painCave.isFatal = 0;
1245		simError();
1246	<	theEst = 0.05 * theEcr;
1246	>	theRsw = 0.95 * theRcut;
1247		}
1248		else{
1249	<	theEst = globals->getEST();
1249	>	theRsw = globals->getRsw();
1250		}
1251	+
1252	+	info[i].setDefaultRcut(theRcut, theRsw);
1253
1032	–	info[i].setDefaultEcr(theEcr, theEst);
1254		}
1255		}
1256		}
#	Line 1037 \| Line 1258 \| void SimSetup::finalInfoCheck(void){
1258		strcpy(checkPointMsg, "post processing checks out");
1259		MPIcheckPoint();
1260		#endif // is_mpi
1261	+
1262	+	// clean up the forcefield
1263	+	the_ff->cleanMe();
1264		}
1265
1266		void SimSetup::initSystemCoords(void){
#	Line 1164 \| Line 1388 \| void SimSetup::makeOutNames(void){
1388		}
1389		else{
1390		strcat(info[k].statusName, ".stat");
1391	+	}
1392	+	}
1393	+
1394	+	strcpy(info[k].rawPotName, inFileName);
1395	+	nameLength = strlen(info[k].rawPotName);
1396	+	endTest = &(info[k].rawPotName[nameLength - 5]);
1397	+	if (!strcmp(endTest, ".bass")){
1398	+	strcpy(endTest, ".raw");
1399	+	}
1400	+	else if (!strcmp(endTest, ".BASS")){
1401	+	strcpy(endTest, ".raw");
1402	+	}
1403	+	else{
1404	+	endTest = &(info[k].rawPotName[nameLength - 4]);
1405	+	if (!strcmp(endTest, ".bss")){
1406	+	strcpy(endTest, ".raw");
1407		}
1408	+	else if (!strcmp(endTest, ".mdl")){
1409	+	strcpy(endTest, ".raw");
1410	+	}
1411	+	else{
1412	+	strcat(info[k].rawPotName, ".raw");
1413	+	}
1414		}
1415
1416		#ifdef IS_MPI
#	Line 1251 \| Line 1497 \| void SimSetup::compList(void){
1497		LinkedMolStamp* headStamp = new LinkedMolStamp();
1498		LinkedMolStamp* currentStamp = NULL;
1499		comp_stamps = new MoleculeStamp * [n_components];
1500	+	bool haveCutoffGroups;
1501
1502	+	haveCutoffGroups = false;
1503	+
1504		// make an array of molecule stamps that match the components used.
1505		// also extract the used stamps out into a separate linked list
1506
#	Line 1286 \| Line 1535 \| void SimSetup::compList(void){
1535		headStamp->add(currentStamp);
1536		comp_stamps[i] = headStamp->match(id);
1537		}
1538	+
1539	+	if(comp_stamps[i]->getNCutoffGroups() > 0)
1540	+	haveCutoffGroups = true;
1541		}
1542	+
1543	+	for (i = 0; i < nInfo; i++)
1544	+	info[i].haveCutoffGroups = haveCutoffGroups;
1545
1546		#ifdef IS_MPI
1547		strcpy(checkPointMsg, "Component stamps successfully extracted\n");
#	Line 1295 \| Line 1550 \| void SimSetup::calcSysValues(void){
1550		}
1551
1552		void SimSetup::calcSysValues(void){
1553	<	int i;
1553	>	int i, j;
1554	>	int ncutgroups, atomsingroups, ngroupsinstamp;
1555
1556		int* molMembershipArray;
1557	+	CutoffGroupStamp* cg;
1558
1559		tot_atoms = 0;
1560		tot_bonds = 0;
1561		tot_bends = 0;
1562		tot_torsions = 0;
1563		tot_rigid = 0;
1564	+	tot_groups = 0;
1565		for (i = 0; i < n_components; i++){
1566		tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1567		tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1568		tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1569		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1570		tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1571	+
1572	+	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1573	+	atomsingroups = 0;
1574	+	for (j=0; j < ncutgroups; j++) {
1575	+	cg = comp_stamps[i]->getCutoffGroup(j);
1576	+	atomsingroups += cg->getNMembers();
1577	+	}
1578	+	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups + ncutgroups;
1579	+	tot_groups += components_nmol[i] * ngroupsinstamp;
1580		}
1581
1582		tot_SRI = tot_bonds + tot_bends + tot_torsions;
#	Line 1322 \| Line 1589 \| void SimSetup::calcSysValues(void){
1589		info[i].n_torsions = tot_torsions;
1590		info[i].n_SRI = tot_SRI;
1591		info[i].n_mol = tot_nmol;
1592	<
1592	>	info[i].ngroup = tot_groups;
1593		info[i].molMembershipArray = molMembershipArray;
1594		}
1595		}
#	Line 1333 \| Line 1600 \| void SimSetup::mpiMolDivide(void){
1600		int i, j, k;
1601		int localMol, allMol;
1602		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1603	<	int local_rigid;
1603	>	int local_rigid, local_groups;
1604	>	vector<int> globalMolIndex;
1605	>	int ncutgroups, atomsingroups, ngroupsinstamp;
1606	>	CutoffGroupStamp* cg;
1607
1608		mpiSim = new mpiSimulation(info);
1609
1610	<	globalIndex = mpiSim->divideLabor();
1610	>	mpiSim->divideLabor();
1611	>	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1612	>	//globalMolIndex = mpiSim->getGlobalMolIndex();
1613
1614		// set up the local variables
1615
#	Line 1351 \| Line 1623 \| void SimSetup::mpiMolDivide(void){
1623		local_bends = 0;
1624		local_torsions = 0;
1625		local_rigid = 0;
1626	<	globalAtomIndex = 0;
1626	>	local_groups = 0;
1627	>	globalAtomCounter = 0;
1628
1629		for (i = 0; i < n_components; i++){
1630		for (j = 0; j < components_nmol[i]; j++){
#	Line 1361 \| Line 1634 \| void SimSetup::mpiMolDivide(void){
1634		local_bends += comp_stamps[i]->getNBends();
1635		local_torsions += comp_stamps[i]->getNTorsions();
1636		local_rigid += comp_stamps[i]->getNRigidBodies();
1637	+
1638	+	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1639	+	atomsingroups = 0;
1640	+	for (k=0; k < ncutgroups; k++) {
1641	+	cg = comp_stamps[i]->getCutoffGroup(k);
1642	+	atomsingroups += cg->getNMembers();
1643	+	}
1644	+	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups +
1645	+	ncutgroups;
1646	+	local_groups += ngroupsinstamp;
1647	+
1648		localMol++;
1649		}
1650		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1651	<	info[0].molMembershipArray[globalAtomIndex] = allMol;
1652	<	globalAtomIndex++;
1651	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1652	>	globalAtomCounter++;
1653		}
1654
1655		allMol++;
#	Line 1373 \| Line 1657 \| void SimSetup::mpiMolDivide(void){
1657		}
1658		local_SRI = local_bonds + local_bends + local_torsions;
1659
1660	<	info[0].n_atoms = mpiSim->getMyNlocal();
1660	>	info[0].n_atoms = mpiSim->getNAtomsLocal();
1661
1378	–
1662		if (local_atoms != info[0].n_atoms){
1663		sprintf(painCave.errMsg,
1664		"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
#	Line 1385 \| Line 1668 \| void SimSetup::mpiMolDivide(void){
1668		simError();
1669		}
1670
1671	+	info[0].ngroup = mpiSim->getNGroupsLocal();
1672	+	if (local_groups != info[0].ngroup){
1673	+	sprintf(painCave.errMsg,
1674	+	"SimSetup error: mpiSim's localGroups (%d) and SimSetup's\n"
1675	+	"\tlocalGroups (%d) are not equal.\n",
1676	+	info[0].ngroup, local_groups);
1677	+	painCave.isFatal = 1;
1678	+	simError();
1679	+	}
1680	+
1681		info[0].n_bonds = local_bonds;
1682		info[0].n_bends = local_bends;
1683		info[0].n_torsions = local_torsions;
#	Line 1421 \| Line 1714 \| void SimSetup::makeSysArrays(void){
1714
1715
1716		molIndex = 0;
1717	<	for (i = 0; i < mpiSim->getTotNmol(); i++){
1717	>	for (i = 0; i < mpiSim->getNMolGlobal(); i++){
1718		if (mol2proc[i] == worldRank){
1719		the_molecules[molIndex].setStampID(molCompType[i]);
1720		the_molecules[molIndex].setMyIndex(molIndex);
#	Line 1433 \| Line 1726 \| void SimSetup::makeSysArrays(void){
1726		#else // is_mpi
1727
1728		molIndex = 0;
1729	<	globalAtomIndex = 0;
1729	>	globalAtomCounter = 0;
1730		for (i = 0; i < n_components; i++){
1731		for (j = 0; j < components_nmol[i]; j++){
1732		the_molecules[molIndex].setStampID(i);
1733		the_molecules[molIndex].setMyIndex(molIndex);
1734		the_molecules[molIndex].setGlobalIndex(molIndex);
1735		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1736	<	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1737	<	globalAtomIndex++;
1736	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1737	>	globalAtomCounter++;
1738		}
1739		molIndex++;
1740		}
#	Line 1458 \| Line 1751 \| void SimSetup::makeSysArrays(void){
1751		info[l].atoms = the_atoms;
1752		info[l].molecules = the_molecules;
1753		info[l].nGlobalExcludes = 0;
1754	<
1754	>
1755		the_ff->setSimInfo(info);
1756		}
1757		}

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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents): Revision 1097 by gezelter, Mon Apr 12 20:32:20 2004 UTC vs. Revision 1212 by chrisfen, Tue Jun 1 17:15:43 2004 UTC

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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 1097 by gezelter, Mon Apr 12 20:32:20 2004 UTC vs.
Revision 1212 by chrisfen, Tue Jun 1 17:15:43 2004 UTC