[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 1214 by gezelter, Tue Jun 1 18:42:58 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;
174	>	int molI, globalID;
175	>	int stampID, atomOffset, rbOffset, groupOffset;
176		molInit molInfo;
177		DirectionalAtom* dAtom;
178		RigidBody* myRB;
#	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 201 \| Line 215 \| void SimSetup::makeMolecules(void){
215
216		for (k = 0; k < nInfo; k++){
217		the_ff->setSimInfo(&(info[k]));
218	+
219	+	#ifdef IS_MPI
220	+	info[k].globalGroupMembership = new int[mpiSim->getNAtomsGlobal()];
221	+	for (i = 0; i < mpiSim->getNAtomsGlobal(); i++)
222	+	info[k].globalGroupMembership[i] = 0;
223	+	#else
224	+	info[k].globalGroupMembership = new int[info[k].n_atoms];
225	+	for (i = 0; i < info[k].n_atoms; i++)
226	+	info[k].globalGroupMembership[i] = 0;
227	+	#endif
228
229		atomOffset = 0;
230	+	groupOffset = 0;
231
232		for (i = 0; i < info[k].n_mol; i++){
233		stampID = info[k].molecules[i].getStampID();
234	+	molName = comp_stamps[stampID]->getID();
235
236		molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
237		molInfo.nBonds = comp_stamps[stampID]->getNBonds();
238		molInfo.nBends = comp_stamps[stampID]->getNBends();
239		molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
240		molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
241	+
242	+	nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups();
243
244		molInfo.myAtoms = &(info[k].atoms[atomOffset]);
245
246		if (molInfo.nBonds > 0)
247	<	molInfo.myBonds = new (Bond *) [molInfo.nBonds];
247	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
248		else
249		molInfo.myBonds = NULL;
250
251		if (molInfo.nBends > 0)
252	<	molInfo.myBends = new (Bend *) [molInfo.nBends];
252	>	molInfo.myBends = new Bend*[molInfo.nBends];
253		else
254		molInfo.myBends = NULL;
255
256		if (molInfo.nTorsions > 0)
257	<	molInfo.myTorsions = new (Torsion *) [molInfo.nTorsions];
257	>	molInfo.myTorsions = new Torsion *[molInfo.nTorsions];
258		else
259		molInfo.myTorsions = NULL;
260
#	Line 259 \| Line 287 \| void SimSetup::makeMolecules(void){
287		else{
288
289		molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
290	+
291		}
292
293		molInfo.myAtoms[j]->setType(currentAtom->getType());
265	–
294		#ifdef IS_MPI
295	<
268	<	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
269	<
295	>	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
296		#endif // is_mpi
297		}
298
#	Line 406 \| Line 432 \| void SimSetup::makeMolecules(void){
432		info[k].excludes->addPair(exK, exL);
433		}
434
435	+
436	+	molInfo.myRigidBodies.clear();
437	+
438		for (j = 0; j < molInfo.nRigidBodies; j++){
439
440		currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
#	Line 414 \| Line 443 \| void SimSetup::makeMolecules(void){
443		// Create the Rigid Body:
444
445		myRB = new RigidBody();
446	+
447	+	sprintf(rbName,"%s_RB_%d", molName, j);
448	+	myRB->setType(rbName);
449
450		for (rb1 = 0; rb1 < nMembers; rb1++) {
451
#	Line 454 \| Line 486 \| void SimSetup::makeMolecules(void){
486		// used for the exclude list:
487
488		#ifdef IS_MPI
489	<	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
490	<	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
489	>	exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
490	>	exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
491		#else
492	<	exI = tempI + 1;
493	<	exJ = tempJ + 1;
492	>	exI = molInfo.myAtoms[tempI]->getIndex() + 1;
493	>	exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
494		#endif
495
496		info[k].excludes->addPair(exI, exJ);
497
498	+	}
499	+	}
500	+
501	+	molInfo.myRigidBodies.push_back(myRB);
502	+	info[k].rigidBodies.push_back(myRB);
503	+	}
504	+
505	+
506	+	//create cutoff group for molecule
507	+
508	+	cutoffAtomSet.clear();
509	+	molInfo.myCutoffGroups.clear();
510	+
511	+	for (j = 0; j < nCutoffGroups; j++){
512	+
513	+	currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j);
514	+	nMembers = currentCutoffGroup->getNMembers();
515	+
516	+	myCutoffGroup = new CutoffGroup();
517	+
518	+	#ifdef IS_MPI
519	+	myCutoffGroup->setGlobalIndex(globalGroupIndex[j + groupOffset]);
520	+	#else
521	+	myCutoffGroup->setGlobalIndex(j + groupOffset);
522	+	#endif
523	+
524	+	for (int cg = 0; cg < nMembers; cg++) {
525	+
526	+	// molI is atom numbering inside this molecule
527	+	molI = currentCutoffGroup->getMember(cg);
528	+
529	+	// tempI is atom numbering on local processor
530	+	tempI = molI + atomOffset;
531	+
532	+	#ifdef IS_MPI
533	+	globalID = info[k].atoms[tempI]->getGlobalIndex();
534	+	info[k].globalGroupMembership[globalID] = globalGroupIndex[j+groupOffset];
535	+	#else
536	+	globalID = info[k].atoms[tempI]->getIndex();
537	+	info[k].globalGroupMembership[globalID] = j + groupOffset;
538	+	#endif
539	+
540	+
541	+
542	+	myCutoffGroup->addAtom(info[k].atoms[tempI]);
543	+
544	+	cutoffAtomSet.insert(tempI);
545	+	}
546	+
547	+	molInfo.myCutoffGroups.push_back(myCutoffGroup);
548	+	groupOffset++;
549	+
550	+	}//end for (j = 0; j < molInfo.nCutoffGroups; j++)
551	+
552	+	//creat a cutoff group for every atom in current molecule which does not belong to cutoffgroup defined at mdl file
553	+
554	+	for(j = 0; j < molInfo.nAtoms; j++){
555	+
556	+	if(cutoffAtomSet.find(molInfo.myAtoms[j]->getIndex()) == cutoffAtomSet.end()){
557	+	myCutoffGroup = new CutoffGroup();
558	+	myCutoffGroup->addAtom(molInfo.myAtoms[j]);
559	+
560	+	#ifdef IS_MPI
561	+	myCutoffGroup->setGlobalIndex(globalGroupIndex[j + groupOffset]);
562	+	globalID = info[k].atoms[atomOffset + j]->getGlobalIndex();
563	+	info[k].globalGroupMembership[globalID] = globalGroupIndex[j+groupOffset];
564	+	#else
565	+	myCutoffGroup->setGlobalIndex(j + groupOffset);
566	+	globalID = info[k].atoms[atomOffset + j]->getIndex();
567	+	info[k].globalGroupMembership[globalID] = j+groupOffset;
568	+	#endif
569	+	molInfo.myCutoffGroups.push_back(myCutoffGroup);
570	+	groupOffset++;
571	+	}
572	+
573	+	}
574	+
575	+	// After this is all set up, scan through the atoms to
576	+	// see if they can be added to the integrableObjects:
577	+
578	+	molInfo.myIntegrableObjects.clear();
579	+
580	+
581	+	for (j = 0; j < molInfo.nAtoms; j++){
582	+
583	+	#ifdef IS_MPI
584	+	slJ = molInfo.myAtoms[j]->getGlobalIndex();
585	+	#else
586	+	slJ = j+atomOffset;
587	+	#endif
588	+
589	+	// if they aren't on the skip list, then they can be integrated
590	+
591	+	if (skipList.find(slJ) == skipList.end()) {
592	+	mySD = (StuntDouble *) molInfo.myAtoms[j];
593	+	info[k].integrableObjects.push_back(mySD);
594	+	molInfo.myIntegrableObjects.push_back(mySD);
595	+	}
596	+	}
597	+
598	+	// all rigid bodies are integrated:
599	+
600	+	for (j = 0; j < molInfo.nRigidBodies; j++) {
601	+	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
602	+	info[k].integrableObjects.push_back(mySD);
603	+	molInfo.myIntegrableObjects.push_back(mySD);
604	+	}
605	+
606	+
607	+	/*
608	+
609	+	//creat ConstraintPair.
610	+	molInfo.myConstraintPair.clear();
611	+
612	+	for (j = 0; j < molInfo.nBonds; j++){
613	+
614	+	//if both atoms are in the same rigid body, just skip it
615	+	currentBond = comp_stamps[stampID]->getBond(j);
616	+	if(!comp_stamps[stampID]->isBondInSameRigidBody(currentBond)){
617	+
618	+	tempI = currentBond->getA() + atomOffset;
619	+	if( comp_stamps[stampID]->isAtomInRigidBody(currentBond->getA(), whichRigidBody, consAtomIndex))
620	+	consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
621	+	else
622	+	consElement1 = new ConstraintAtom(info[k].atoms[tempI]);
623	+
624	+	tempJ = currentBond->getB() + atomOffset;
625	+	if(comp_stamps[stampID]->isAtomInRigidBody(currentBond->getB(), whichRigidBody, consAtomIndex))
626	+	consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
627	+	else
628	+	consElement2 = new ConstraintAtom(info[k].atoms[tempJ]);
629	+
630	+	consPair = new DistanceConstraintPair(consElement1, consElement2);
631	+	molInfo.myConstraintPairs.push_back(consPair);
632	+	}
633	+	}
634	+
635	+	//loop over rigid bodies, if two rigid bodies share same joint, creat a HingeConstraintPair
636	+	for (int rb1 = 0; rb1 < molInfo.nRigidBodies -1 ; rb1++){
637	+	for (int rb2 = rb1 + 1; rb2 < molInfo.nRigidBodies ; rb2++){
638	+
639	+	jointAtoms = comp_stamps[stampID]->getJointAtoms(rb1, rb2);
640	+
641	+	for(size_t m = 0; m < jointAtoms.size(); m++){
642	+	consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[rb1], jointAtoms[m].first);
643	+	consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[rb2], jointAtoms[m].second);
644	+
645	+	consPair = new JointConstraintPair(consElement1, consElement2);
646	+	molInfo.myConstraintPairs.push_back(consPair);
647		}
648	+
649		}
650		}
651
652	+	*/
653		// send the arrays off to the forceField for init.
654
655		the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
#	Line 476 \| Line 659 \| void SimSetup::makeMolecules(void){
659		theTorsions);
660
661		info[k].molecules[i].initialize(molInfo);
662	<
663	<
662	>
663	>
664		atomOffset += molInfo.nAtoms;
665		delete[] theBonds;
666		delete[] theBends;
667		delete[] theTorsions;
668		}
669
487	–	// build up the integrableObjects vector:
670
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
671
672	<	if (skipList.find(slI) == skipList.end()) {
673	<	mySD = (StuntDouble *) info[k].atoms[i];
674	<	info[k].integrableObjects.push_back(mySD);
675	<	}
676	<	}
677	<	for (i = 0; i < info[k].rigidBodies.size(); i++) {
678	<	mySD = (StuntDouble *) info[k].rigidBodies[i];
679	<	info[k].integrableObjects.push_back(mySD);
680	<	}
672	>	#ifdef IS_MPI
673	>	// Since the globalGroupMembership has been zero filled and we've only
674	>	// poked values into the atoms we know, we can do an Allreduce
675	>	// to get the full globalGroupMembership array (We think).
676	>	// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
677	>	// docs said we could.
678	>
679	>	int* ggMjunk = new int[mpiSim->getNAtomsGlobal()];
680	>
681	>	MPI_Allreduce(info[k].globalGroupMembership,
682	>	ggMjunk,
683	>	mpiSim->getNAtomsGlobal(),
684	>	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
685	>
686	>	for (i = 0; i < mpiSim->getNAtomsGlobal(); i++)
687	>	info[k].globalGroupMembership[i] = ggMjunk[i];
688	>
689	>	delete[] ggMjunk;
690
691	+	#endif
692	+
693	+
694	+
695		}
696
697		#ifdef IS_MPI
698		sprintf(checkPointMsg, "all molecules initialized succesfully");
699		MPIcheckPoint();
700		#endif // is_mpi
513	–
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	–	}
701
525	–	the_ff->cleanMe();
702		}
703
704		void SimSetup::initFromBass(void){
#	Line 809 \| Line 985 \| void SimSetup::gatherInfo(void){
985		}
986
987		//check whether sample time, status time, thermal time and reset time are divisble by dt
988	<	if (!isDivisible(globals->getSampleTime(), globals->getDt())){
988	>	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
989		sprintf(painCave.errMsg,
990		"Sample time is not divisible by dt.\n"
991		"\tThis will result in samples that are not uniformly\n"
#	Line 819 \| Line 995 \| void SimSetup::gatherInfo(void){
995		simError();
996		}
997
998	<	if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
998	>	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
999		sprintf(painCave.errMsg,
1000		"Status time is not divisible by dt.\n"
1001		"\tThis will result in status reports that are not uniformly\n"
#	Line 855 \| Line 1031 \| void SimSetup::gatherInfo(void){
1031		if (globals->haveSampleTime()){
1032		info[i].sampleTime = globals->getSampleTime();
1033		info[i].statusTime = info[i].sampleTime;
858	–	info[i].thermalTime = info[i].sampleTime;
1034		}
1035		else{
1036		info[i].sampleTime = globals->getRunTime();
1037		info[i].statusTime = info[i].sampleTime;
863	–	info[i].thermalTime = info[i].sampleTime;
1038		}
1039
1040		if (globals->haveStatusTime()){
#	Line 869 \| Line 1043 \| void SimSetup::gatherInfo(void){
1043
1044		if (globals->haveThermalTime()){
1045		info[i].thermalTime = globals->getThermalTime();
1046	+	} else {
1047	+	info[i].thermalTime = globals->getRunTime();
1048		}
1049
1050		info[i].resetIntegrator = 0;
#	Line 886 \| Line 1062 \| void SimSetup::gatherInfo(void){
1062
1063		info[i].useInitXSstate = globals->getUseInitXSstate();
1064		info[i].orthoTolerance = globals->getOrthoBoxTolerance();
1065	<
1065	>
1066	>	// check for thermodynamic integration
1067	>	if (globals->getUseSolidThermInt() && !globals->getUseLiquidThermInt()) {
1068	>	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1069	>	info[i].useSolidThermInt = globals->getUseSolidThermInt();
1070	>	info[i].thermIntLambda = globals->getThermIntLambda();
1071	>	info[i].thermIntK = globals->getThermIntK();
1072	>
1073	>	Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK);
1074	>	info[i].restraint = myRestraint;
1075	>	}
1076	>	else {
1077	>	sprintf(painCave.errMsg,
1078	>	"SimSetup Error:\n"
1079	>	"\tKeyword useSolidThermInt was set to 'true' but\n"
1080	>	"\tthermodynamicIntegrationLambda (and/or\n"
1081	>	"\tthermodynamicIntegrationK) was not specified.\n"
1082	>	"\tPlease provide a lambda value and k value in your .bass file.\n");
1083	>	painCave.isFatal = 1;
1084	>	simError();
1085	>	}
1086	>	}
1087	>	else if(globals->getUseLiquidThermInt()) {
1088	>	if (globals->getUseSolidThermInt()) {
1089	>	sprintf( painCave.errMsg,
1090	>	"SimSetup Warning: It appears that you have both solid and\n"
1091	>	"\tliquid thermodynamic integration activated in your .bass\n"
1092	>	"\tfile. To avoid confusion, specify only one technique in\n"
1093	>	"\tyour .bass file. Liquid-state thermodynamic integration\n"
1094	>	"\twill be assumed for the current simulation. If this is not\n"
1095	>	"\twhat you desire, set useSolidThermInt to 'true' and\n"
1096	>	"\tuseLiquidThermInt to 'false' in your .bass file.\n");
1097	>	painCave.isFatal = 0;
1098	>	simError();
1099	>	}
1100	>	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1101	>	info[i].useLiquidThermInt = globals->getUseLiquidThermInt();
1102	>	info[i].thermIntLambda = globals->getThermIntLambda();
1103	>	info[i].thermIntK = globals->getThermIntK();
1104	>	}
1105	>	else {
1106	>	sprintf(painCave.errMsg,
1107	>	"SimSetup Error:\n"
1108	>	"\tKeyword useLiquidThermInt was set to 'true' but\n"
1109	>	"\tthermodynamicIntegrationLambda (and/or\n"
1110	>	"\tthermodynamicIntegrationK) was not specified.\n"
1111	>	"\tPlease provide a lambda value and k value in your .bass file.\n");
1112	>	painCave.isFatal = 1;
1113	>	simError();
1114	>	}
1115	>	}
1116	>	else if(globals->haveThermIntLambda() \|\| globals->haveThermIntK()){
1117	>	sprintf(painCave.errMsg,
1118	>	"SimSetup Warning: If you want to use Thermodynamic\n"
1119	>	"\tIntegration, set useSolidThermInt or useLiquidThermInt to\n"
1120	>	"\t'true' in your .bass file. These keywords are set to\n"
1121	>	"\t'false' by default, so your lambda and/or k values are\n"
1122	>	"\tbeing ignored.\n");
1123	>	painCave.isFatal = 0;
1124	>	simError();
1125	>	}
1126		}
1127
1128		//setup seed for random number generator
#	Line 939 \| Line 1175 \| void SimSetup::finalInfoCheck(void){
1175		void SimSetup::finalInfoCheck(void){
1176		int index;
1177		int usesDipoles;
1178	+	int usesCharges;
1179		int i;
1180
1181		for (i = 0; i < nInfo; i++){
#	Line 950 \| Line 1187 \| void SimSetup::finalInfoCheck(void){
1187		usesDipoles = (info[i].atoms[index])->hasDipole();
1188		index++;
1189		}
1190	<
1190	>	index = 0;
1191	>	usesCharges = 0;
1192	>	while ((index < info[i].n_atoms) && !usesCharges){
1193	>	usesCharges= (info[i].atoms[index])->hasCharge();
1194	>	index++;
1195	>	}
1196		#ifdef IS_MPI
1197		int myUse = usesDipoles;
1198		MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1199		#endif //is_mpi
1200
1201	<	double theEcr, theEst;
1201	>	double theRcut, theRsw;
1202
1203	+	if (globals->haveRcut()) {
1204	+	theRcut = globals->getRcut();
1205	+
1206	+	if (globals->haveRsw())
1207	+	theRsw = globals->getRsw();
1208	+	else
1209	+	theRsw = theRcut;
1210	+
1211	+	info[i].setDefaultRcut(theRcut, theRsw);
1212	+
1213	+	} else {
1214	+
1215	+	the_ff->calcRcut();
1216	+	theRcut = info[i].getRcut();
1217	+
1218	+	if (globals->haveRsw())
1219	+	theRsw = globals->getRsw();
1220	+	else
1221	+	theRsw = theRcut;
1222	+
1223	+	info[i].setDefaultRcut(theRcut, theRsw);
1224	+	}
1225	+
1226		if (globals->getUseRF()){
1227		info[i].useReactionField = 1;
1228	<
1229	<	if (!globals->haveECR()){
1228	>
1229	>	if (!globals->haveRcut()){
1230		sprintf(painCave.errMsg,
1231	<	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
1231	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1232		"\tOOPSE will use a default value of 15.0 angstroms"
1233	<	"\tfor the electrostaticCutoffRadius.\n");
1233	>	"\tfor the cutoffRadius.\n");
1234		painCave.isFatal = 0;
1235		simError();
1236	<	theEcr = 15.0;
1236	>	theRcut = 15.0;
1237		}
1238		else{
1239	<	theEcr = globals->getECR();
1239	>	theRcut = globals->getRcut();
1240		}
1241
1242	<	if (!globals->haveEST()){
1242	>	if (!globals->haveRsw()){
1243		sprintf(painCave.errMsg,
1244	<	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1244	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1245		"\tOOPSE will use a default value of\n"
1246	<	"\t0.05 * electrostaticCutoffRadius\n"
982	<	"\tfor the electrostaticSkinThickness\n");
1246	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1247		painCave.isFatal = 0;
1248		simError();
1249	<	theEst = 0.05 * theEcr;
1249	>	theRsw = 0.95 * theRcut;
1250		}
1251		else{
1252	<	theEst = globals->getEST();
1252	>	theRsw = globals->getRsw();
1253		}
1254
1255	<	info[i].setDefaultEcr(theEcr, theEst);
1255	>	info[i].setDefaultRcut(theRcut, theRsw);
1256
1257		if (!globals->haveDielectric()){
1258		sprintf(painCave.errMsg,
#	Line 1001 \| Line 1265 \| void SimSetup::finalInfoCheck(void){
1265		info[i].dielectric = globals->getDielectric();
1266		}
1267		else{
1268	<	if (usesDipoles){
1269	<	if (!globals->haveECR()){
1268	>	if (usesDipoles \|\| usesCharges){
1269	>
1270	>	if (!globals->haveRcut()){
1271		sprintf(painCave.errMsg,
1272	<	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
1273	<	"\tOOPSE will use a default value of 15.0 angstroms"
1274	<	"\tfor the electrostaticCutoffRadius.\n");
1275	<	painCave.isFatal = 0;
1276	<	simError();
1277	<	theEcr = 15.0;
1278	<	}
1279	<	else{
1280	<	theEcr = globals->getECR();
1272	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1273	>	"\tOOPSE will use a default value of 15.0 angstroms"
1274	>	"\tfor the cutoffRadius.\n");
1275	>	painCave.isFatal = 0;
1276	>	simError();
1277	>	theRcut = 15.0;
1278	>	}
1279	>	else{
1280	>	theRcut = globals->getRcut();
1281		}
1282	<
1283	<	if (!globals->haveEST()){
1282	>
1283	>	if (!globals->haveRsw()){
1284		sprintf(painCave.errMsg,
1285	<	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1285	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1286		"\tOOPSE will use a default value of\n"
1287	<	"\t0.05 * electrostaticCutoffRadius\n"
1023	<	"\tfor the electrostaticSkinThickness\n");
1287	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1288		painCave.isFatal = 0;
1289		simError();
1290	<	theEst = 0.05 * theEcr;
1290	>	theRsw = 0.95 * theRcut;
1291		}
1292		else{
1293	<	theEst = globals->getEST();
1293	>	theRsw = globals->getRsw();
1294		}
1295	+
1296	+	info[i].setDefaultRcut(theRcut, theRsw);
1297
1032	–	info[i].setDefaultEcr(theEcr, theEst);
1298		}
1299		}
1300		}
#	Line 1037 \| Line 1302 \| void SimSetup::finalInfoCheck(void){
1302		strcpy(checkPointMsg, "post processing checks out");
1303		MPIcheckPoint();
1304		#endif // is_mpi
1305	+
1306	+	// clean up the forcefield
1307	+	the_ff->cleanMe();
1308		}
1309
1310		void SimSetup::initSystemCoords(void){
#	Line 1167 \| Line 1435 \| void SimSetup::makeOutNames(void){
1435		}
1436		}
1437
1438	+	strcpy(info[k].rawPotName, inFileName);
1439	+	nameLength = strlen(info[k].rawPotName);
1440	+	endTest = &(info[k].rawPotName[nameLength - 5]);
1441	+	if (!strcmp(endTest, ".bass")){
1442	+	strcpy(endTest, ".raw");
1443	+	}
1444	+	else if (!strcmp(endTest, ".BASS")){
1445	+	strcpy(endTest, ".raw");
1446	+	}
1447	+	else{
1448	+	endTest = &(info[k].rawPotName[nameLength - 4]);
1449	+	if (!strcmp(endTest, ".bss")){
1450	+	strcpy(endTest, ".raw");
1451	+	}
1452	+	else if (!strcmp(endTest, ".mdl")){
1453	+	strcpy(endTest, ".raw");
1454	+	}
1455	+	else{
1456	+	strcat(info[k].rawPotName, ".raw");
1457	+	}
1458	+	}
1459	+
1460		#ifdef IS_MPI
1461
1462		}
#	Line 1251 \| Line 1541 \| void SimSetup::compList(void){
1541		LinkedMolStamp* headStamp = new LinkedMolStamp();
1542		LinkedMolStamp* currentStamp = NULL;
1543		comp_stamps = new MoleculeStamp * [n_components];
1544	+	bool haveCutoffGroups;
1545
1546	+	haveCutoffGroups = false;
1547	+
1548		// make an array of molecule stamps that match the components used.
1549		// also extract the used stamps out into a separate linked list
1550
#	Line 1286 \| Line 1579 \| void SimSetup::compList(void){
1579		headStamp->add(currentStamp);
1580		comp_stamps[i] = headStamp->match(id);
1581		}
1582	+
1583	+	if(comp_stamps[i]->getNCutoffGroups() > 0)
1584	+	haveCutoffGroups = true;
1585		}
1586	+
1587	+	for (i = 0; i < nInfo; i++)
1588	+	info[i].haveCutoffGroups = haveCutoffGroups;
1589
1590		#ifdef IS_MPI
1591		strcpy(checkPointMsg, "Component stamps successfully extracted\n");
#	Line 1295 \| Line 1594 \| void SimSetup::calcSysValues(void){
1594		}
1595
1596		void SimSetup::calcSysValues(void){
1597	<	int i;
1597	>	int i, j;
1598	>	int ncutgroups, atomsingroups, ngroupsinstamp;
1599
1600		int* molMembershipArray;
1601	+	CutoffGroupStamp* cg;
1602
1603		tot_atoms = 0;
1604		tot_bonds = 0;
1605		tot_bends = 0;
1606		tot_torsions = 0;
1607		tot_rigid = 0;
1608	+	tot_groups = 0;
1609		for (i = 0; i < n_components; i++){
1610		tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1611		tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1612		tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1613		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1614		tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1615	+
1616	+	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1617	+	atomsingroups = 0;
1618	+	for (j=0; j < ncutgroups; j++) {
1619	+	cg = comp_stamps[i]->getCutoffGroup(j);
1620	+	atomsingroups += cg->getNMembers();
1621	+	}
1622	+	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups + ncutgroups;
1623	+	tot_groups += components_nmol[i] * ngroupsinstamp;
1624		}
1625
1626		tot_SRI = tot_bonds + tot_bends + tot_torsions;
#	Line 1322 \| Line 1633 \| void SimSetup::calcSysValues(void){
1633		info[i].n_torsions = tot_torsions;
1634		info[i].n_SRI = tot_SRI;
1635		info[i].n_mol = tot_nmol;
1636	<
1636	>	info[i].ngroup = tot_groups;
1637		info[i].molMembershipArray = molMembershipArray;
1638		}
1639		}
#	Line 1333 \| Line 1644 \| void SimSetup::mpiMolDivide(void){
1644		int i, j, k;
1645		int localMol, allMol;
1646		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1647	<	int local_rigid;
1647	>	int local_rigid, local_groups;
1648	>	vector<int> globalMolIndex;
1649	>	int ncutgroups, atomsingroups, ngroupsinstamp;
1650	>	CutoffGroupStamp* cg;
1651
1652		mpiSim = new mpiSimulation(info);
1653
1654	<	globalIndex = mpiSim->divideLabor();
1654	>	mpiSim->divideLabor();
1655	>	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1656	>	globalGroupIndex = mpiSim->getGlobalGroupIndex();
1657	>	//globalMolIndex = mpiSim->getGlobalMolIndex();
1658
1659		// set up the local variables
1660
#	Line 1351 \| Line 1668 \| void SimSetup::mpiMolDivide(void){
1668		local_bends = 0;
1669		local_torsions = 0;
1670		local_rigid = 0;
1671	<	globalAtomIndex = 0;
1671	>	local_groups = 0;
1672	>	globalAtomCounter = 0;
1673
1674		for (i = 0; i < n_components; i++){
1675		for (j = 0; j < components_nmol[i]; j++){
#	Line 1361 \| Line 1679 \| void SimSetup::mpiMolDivide(void){
1679		local_bends += comp_stamps[i]->getNBends();
1680		local_torsions += comp_stamps[i]->getNTorsions();
1681		local_rigid += comp_stamps[i]->getNRigidBodies();
1682	+
1683	+	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1684	+	atomsingroups = 0;
1685	+	for (k=0; k < ncutgroups; k++) {
1686	+	cg = comp_stamps[i]->getCutoffGroup(k);
1687	+	atomsingroups += cg->getNMembers();
1688	+	}
1689	+	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups +
1690	+	ncutgroups;
1691	+	local_groups += ngroupsinstamp;
1692	+
1693		localMol++;
1694		}
1695		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1696	<	info[0].molMembershipArray[globalAtomIndex] = allMol;
1697	<	globalAtomIndex++;
1696	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1697	>	globalAtomCounter++;
1698		}
1699
1700		allMol++;
#	Line 1373 \| Line 1702 \| void SimSetup::mpiMolDivide(void){
1702		}
1703		local_SRI = local_bonds + local_bends + local_torsions;
1704
1705	<	info[0].n_atoms = mpiSim->getMyNlocal();
1705	>	info[0].n_atoms = mpiSim->getNAtomsLocal();
1706
1378	–
1707		if (local_atoms != info[0].n_atoms){
1708		sprintf(painCave.errMsg,
1709		"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
#	Line 1385 \| Line 1713 \| void SimSetup::mpiMolDivide(void){
1713		simError();
1714		}
1715
1716	+	info[0].ngroup = mpiSim->getNGroupsLocal();
1717	+	if (local_groups != info[0].ngroup){
1718	+	sprintf(painCave.errMsg,
1719	+	"SimSetup error: mpiSim's localGroups (%d) and SimSetup's\n"
1720	+	"\tlocalGroups (%d) are not equal.\n",
1721	+	info[0].ngroup, local_groups);
1722	+	painCave.isFatal = 1;
1723	+	simError();
1724	+	}
1725	+
1726		info[0].n_bonds = local_bonds;
1727		info[0].n_bends = local_bends;
1728		info[0].n_torsions = local_torsions;
#	Line 1421 \| Line 1759 \| void SimSetup::makeSysArrays(void){
1759
1760
1761		molIndex = 0;
1762	<	for (i = 0; i < mpiSim->getTotNmol(); i++){
1762	>	for (i = 0; i < mpiSim->getNMolGlobal(); i++){
1763		if (mol2proc[i] == worldRank){
1764		the_molecules[molIndex].setStampID(molCompType[i]);
1765		the_molecules[molIndex].setMyIndex(molIndex);
#	Line 1433 \| Line 1771 \| void SimSetup::makeSysArrays(void){
1771		#else // is_mpi
1772
1773		molIndex = 0;
1774	<	globalAtomIndex = 0;
1774	>	globalAtomCounter = 0;
1775		for (i = 0; i < n_components; i++){
1776		for (j = 0; j < components_nmol[i]; j++){
1777		the_molecules[molIndex].setStampID(i);
1778		the_molecules[molIndex].setMyIndex(molIndex);
1779		the_molecules[molIndex].setGlobalIndex(molIndex);
1780		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1781	<	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1782	<	globalAtomIndex++;
1781	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1782	>	globalAtomCounter++;
1783		}
1784		molIndex++;
1785		}
#	Line 1458 \| Line 1796 \| void SimSetup::makeSysArrays(void){
1796		info[l].atoms = the_atoms;
1797		info[l].molecules = the_molecules;
1798		info[l].nGlobalExcludes = 0;
1799	<
1799	>
1800		the_ff->setSimInfo(info);
1801		}
1802		}

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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 1214 by gezelter, Tue Jun 1 18:42:58 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 1214 by gezelter, Tue Jun 1 18:42:58 2004 UTC