[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 1330 by gezelter, Fri Jul 16 16:29:44 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	+	#include "ConstraintManager.hpp"
17
18		#ifdef IS_MPI
19		#include "mpiBASS.h"
#	Line 147 \| Line 149 \| void SimSetup::createSim(void){
149		// make the output filenames
150
151		makeOutNames();
150	–
151	–	if (globals->haveMinimizer())
152	–	// make minimizer
153	–	makeMinimizer();
154	–	else
155	–	// make the integrator
156	–	makeIntegrator();
152
153		#ifdef IS_MPI
154		mpiSim->mpiRefresh();
#	Line 162 \| Line 157 \| void SimSetup::createSim(void){
157		// initialize the Fortran
158
159		initFortran();
160	+
161	+	//creat constraint manager
162	+	for(int i = 0; i < nInfo; i++)
163	+	info[i].consMan = new ConstraintManager(&info[i]);
164	+
165	+	if (globals->haveMinimizer())
166	+	// make minimizer
167	+	makeMinimizer();
168	+	else
169	+	// make the integrator
170	+	makeIntegrator();
171	+
172		}
173
174
175		void SimSetup::makeMolecules(void){
176		int i, j, k;
177	<	int exI, exJ, exK, exL, slI;
177	>	int exI, exJ, exK, exL, slI, slJ;
178		int tempI, tempJ, tempK, tempL;
179	<	int molI;
180	<	int stampID, atomOffset, rbOffset;
179	>	int molI, globalID;
180	>	int stampID, atomOffset, rbOffset, groupOffset;
181		molInit molInfo;
182		DirectionalAtom* dAtom;
183		RigidBody* myRB;
#	Line 182 \| Line 189 \| void SimSetup::makeMolecules(void){
189		BendStamp* currentBend;
190		TorsionStamp* currentTorsion;
191		RigidBodyStamp* currentRigidBody;
192	+	CutoffGroupStamp* currentCutoffGroup;
193	+	CutoffGroup* myCutoffGroup;
194	+	int nCutoffGroups;// number of cutoff group of a molecule defined in mdl file
195	+	set<int> cutoffAtomSet; //atoms belong to cutoffgroup defined at mdl file
196
197		bond_pair* theBonds;
198		bend_set* theBends;
#	Line 190 \| Line 201 \| void SimSetup::makeMolecules(void){
201		set<int> skipList;
202
203		double phi, theta, psi;
204	+	char* molName;
205	+	char rbName[100];
206
207	+	ConstraintPair* consPair; //constraint pair
208	+	ConstraintElement* consElement1; //first element of constraint pair
209	+	ConstraintElement* consElement2; //second element of constraint pair
210	+	int whichRigidBody;
211	+	int consAtomIndex; //index of constraint atom in rigid body's atom array
212	+	vector<pair<int, int> > jointAtoms;
213	+	double bondLength2;
214		//init the forceField paramters
215
216		the_ff->readParams();
#	Line 202 \| Line 222 \| void SimSetup::makeMolecules(void){
222		for (k = 0; k < nInfo; k++){
223		the_ff->setSimInfo(&(info[k]));
224
225	+	#ifdef IS_MPI
226	+	info[k].globalGroupMembership = new int[mpiSim->getNAtomsGlobal()];
227	+	for (i = 0; i < mpiSim->getNAtomsGlobal(); i++)
228	+	info[k].globalGroupMembership[i] = 0;
229	+	#else
230	+	info[k].globalGroupMembership = new int[info[k].n_atoms];
231	+	for (i = 0; i < info[k].n_atoms; i++)
232	+	info[k].globalGroupMembership[i] = 0;
233	+	#endif
234	+
235		atomOffset = 0;
236	+	groupOffset = 0;
237
238		for (i = 0; i < info[k].n_mol; i++){
239		stampID = info[k].molecules[i].getStampID();
240	+	molName = comp_stamps[stampID]->getID();
241
242		molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
243		molInfo.nBonds = comp_stamps[stampID]->getNBonds();
244		molInfo.nBends = comp_stamps[stampID]->getNBends();
245		molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
246		molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
247	+
248	+	nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups();
249
250		molInfo.myAtoms = &(info[k].atoms[atomOffset]);
251
252		if (molInfo.nBonds > 0)
253	<	molInfo.myBonds = new (Bond *) [molInfo.nBonds];
253	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
254		else
255		molInfo.myBonds = NULL;
256
257		if (molInfo.nBends > 0)
258	<	molInfo.myBends = new (Bend *) [molInfo.nBends];
258	>	molInfo.myBends = new Bend*[molInfo.nBends];
259		else
260		molInfo.myBends = NULL;
261
262		if (molInfo.nTorsions > 0)
263	<	molInfo.myTorsions = new (Torsion *) [molInfo.nTorsions];
263	>	molInfo.myTorsions = new Torsion *[molInfo.nTorsions];
264		else
265		molInfo.myTorsions = NULL;
266
#	Line 259 \| Line 293 \| void SimSetup::makeMolecules(void){
293		else{
294
295		molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
296	+
297		}
298
299		molInfo.myAtoms[j]->setType(currentAtom->getType());
265	–
300		#ifdef IS_MPI
301	<
268	<	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
269	<
301	>	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
302		#endif // is_mpi
303		}
304
#	Line 406 \| Line 438 \| void SimSetup::makeMolecules(void){
438		info[k].excludes->addPair(exK, exL);
439		}
440
441	+
442	+	molInfo.myRigidBodies.clear();
443	+
444		for (j = 0; j < molInfo.nRigidBodies; j++){
445
446		currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
#	Line 414 \| Line 449 \| void SimSetup::makeMolecules(void){
449		// Create the Rigid Body:
450
451		myRB = new RigidBody();
452	+
453	+	sprintf(rbName,"%s_RB_%d", molName, j);
454	+	myRB->setType(rbName);
455
456		for (rb1 = 0; rb1 < nMembers; rb1++) {
457
#	Line 454 \| Line 492 \| void SimSetup::makeMolecules(void){
492		// used for the exclude list:
493
494		#ifdef IS_MPI
495	<	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
496	<	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
495	>	exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
496	>	exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
497		#else
498	<	exI = tempI + 1;
499	<	exJ = tempJ + 1;
498	>	exI = molInfo.myAtoms[tempI]->getIndex() + 1;
499	>	exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
500		#endif
501
502		info[k].excludes->addPair(exI, exJ);
503
504		}
505		}
506	+
507	+	molInfo.myRigidBodies.push_back(myRB);
508	+	info[k].rigidBodies.push_back(myRB);
509		}
510	+
511	+
512	+	//create cutoff group for molecule
513	+
514	+	cutoffAtomSet.clear();
515	+	molInfo.myCutoffGroups.clear();
516	+
517	+	for (j = 0; j < nCutoffGroups; j++){
518	+
519	+	currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j);
520	+	nMembers = currentCutoffGroup->getNMembers();
521	+
522	+	myCutoffGroup = new CutoffGroup();
523	+
524	+	#ifdef IS_MPI
525	+	myCutoffGroup->setGlobalIndex(globalGroupIndex[groupOffset]);
526	+	#else
527	+	myCutoffGroup->setGlobalIndex(groupOffset);
528	+	#endif
529	+
530	+	for (int cg = 0; cg < nMembers; cg++) {
531	+
532	+	// molI is atom numbering inside this molecule
533	+	molI = currentCutoffGroup->getMember(cg);
534	+
535	+	// tempI is atom numbering on local processor
536	+	tempI = molI + atomOffset;
537	+
538	+	#ifdef IS_MPI
539	+	globalID = info[k].atoms[tempI]->getGlobalIndex();
540	+	info[k].globalGroupMembership[globalID] = globalGroupIndex[groupOffset];
541	+	#else
542	+	globalID = info[k].atoms[tempI]->getIndex();
543	+	info[k].globalGroupMembership[globalID] = groupOffset;
544	+	#endif
545	+	myCutoffGroup->addAtom(info[k].atoms[tempI]);
546	+	cutoffAtomSet.insert(tempI);
547	+	}
548	+
549	+	molInfo.myCutoffGroups.push_back(myCutoffGroup);
550	+	groupOffset++;
551	+
552	+	}//end for (j = 0; j < molInfo.nCutoffGroups; j++)
553	+
554	+
555	+	// create a cutoff group for every atom in current molecule which
556	+	// does not belong to cutoffgroup defined at mdl file
557	+
558	+	for(j = 0; j < molInfo.nAtoms; j++){
559	+
560	+	if(cutoffAtomSet.find(molInfo.myAtoms[j]->getIndex()) == cutoffAtomSet.end()){
561	+	myCutoffGroup = new CutoffGroup();
562	+	myCutoffGroup->addAtom(molInfo.myAtoms[j]);
563	+
564	+	#ifdef IS_MPI
565	+	myCutoffGroup->setGlobalIndex(globalGroupIndex[groupOffset]);
566	+	globalID = info[k].atoms[atomOffset + j]->getGlobalIndex();
567	+	info[k].globalGroupMembership[globalID] = globalGroupIndex[groupOffset];
568	+	#else
569	+	myCutoffGroup->setGlobalIndex(groupOffset);
570	+	globalID = info[k].atoms[atomOffset + j]->getIndex();
571	+	info[k].globalGroupMembership[globalID] = groupOffset;
572	+	#endif
573	+	molInfo.myCutoffGroups.push_back(myCutoffGroup);
574	+	groupOffset++;
575	+	}
576	+	}
577	+
578	+	// After this is all set up, scan through the atoms to
579	+	// see if they can be added to the integrableObjects:
580	+
581	+	molInfo.myIntegrableObjects.clear();
582
583	+
584	+	for (j = 0; j < molInfo.nAtoms; j++){
585	+
586	+	#ifdef IS_MPI
587	+	slJ = molInfo.myAtoms[j]->getGlobalIndex();
588	+	#else
589	+	slJ = j+atomOffset;
590	+	#endif
591	+
592	+	// if they aren't on the skip list, then they can be integrated
593	+
594	+	if (skipList.find(slJ) == skipList.end()) {
595	+	mySD = (StuntDouble *) molInfo.myAtoms[j];
596	+	info[k].integrableObjects.push_back(mySD);
597	+	molInfo.myIntegrableObjects.push_back(mySD);
598	+	}
599	+	}
600	+
601	+	// all rigid bodies are integrated:
602	+
603	+	for (j = 0; j < molInfo.nRigidBodies; j++) {
604	+	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
605	+	info[k].integrableObjects.push_back(mySD);
606	+	molInfo.myIntegrableObjects.push_back(mySD);
607	+	}
608	+
609		// send the arrays off to the forceField for init.
610
611		the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
#	Line 475 \| Line 614 \| void SimSetup::makeMolecules(void){
614		the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
615		theTorsions);
616
478	–	info[k].molecules[i].initialize(molInfo);
617
618	+	//creat ConstraintPair.
619	+	molInfo.myConstraintPairs.clear();
620	+
621	+	for (j = 0; j < molInfo.nBonds; j++){
622
623	+	//if bond is constrained bond, add it into constraint pair
624	+	if(molInfo.myBonds[j]->is_constrained()){
625	+
626	+	//if both atoms are in the same rigid body, just skip it
627	+	currentBond = comp_stamps[stampID]->getBond(j);
628	+
629	+	if(!comp_stamps[stampID]->isBondInSameRigidBody(currentBond)){
630	+
631	+	tempI = currentBond->getA() + atomOffset;
632	+	if( comp_stamps[stampID]->isAtomInRigidBody(currentBond->getA(), whichRigidBody, consAtomIndex))
633	+	consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
634	+	else
635	+	consElement1 = new ConstraintAtom(info[k].atoms[tempI]);
636	+
637	+	tempJ = currentBond->getB() + atomOffset;
638	+	if(comp_stamps[stampID]->isAtomInRigidBody(currentBond->getB(), whichRigidBody, consAtomIndex))
639	+	consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
640	+	else
641	+	consElement2 = new ConstraintAtom(info[k].atoms[tempJ]);
642	+
643	+	bondLength2 = molInfo.myBonds[j]->get_constraint()->get_dsqr();
644	+	consPair = new DistanceConstraintPair(consElement1, consElement2, bondLength2);
645	+
646	+	molInfo.myConstraintPairs.push_back(consPair);
647	+	}
648	+	}//end if(molInfo.myBonds[j]->is_constrained())
649	+	}
650	+
651	+	//loop over rigid bodies, if two rigid bodies share same joint, creat a JointConstraintPair
652	+	for (int rb1 = 0; rb1 < molInfo.nRigidBodies -1 ; rb1++){
653	+	for (int rb2 = rb1 + 1; rb2 < molInfo.nRigidBodies ; rb2++){
654	+
655	+	jointAtoms = comp_stamps[stampID]->getJointAtoms(rb1, rb2);
656	+
657	+	for(size_t m = 0; m < jointAtoms.size(); m++){
658	+	consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[rb1], jointAtoms[m].first);
659	+	consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[rb2], jointAtoms[m].second);
660	+
661	+	consPair = new JointConstraintPair(consElement1, consElement2);
662	+	molInfo.myConstraintPairs.push_back(consPair);
663	+	}
664	+
665	+	}
666	+	}
667	+
668	+
669	+	info[k].molecules[i].initialize(molInfo);
670	+
671	+
672		atomOffset += molInfo.nAtoms;
673		delete[] theBonds;
674		delete[] theBends;
675		delete[] theTorsions;
676		}
677
487	–	// build up the integrableObjects vector:
678
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
679
680	<	if (skipList.find(slI) == skipList.end()) {
681	<	mySD = (StuntDouble *) info[k].atoms[i];
682	<	info[k].integrableObjects.push_back(mySD);
683	<	}
684	<	}
685	<	for (i = 0; i < info[k].rigidBodies.size(); i++) {
686	<	mySD = (StuntDouble *) info[k].rigidBodies[i];
687	<	info[k].integrableObjects.push_back(mySD);
688	<	}
680	>	#ifdef IS_MPI
681	>	// Since the globalGroupMembership has been zero filled and we've only
682	>	// poked values into the atoms we know, we can do an Allreduce
683	>	// to get the full globalGroupMembership array (We think).
684	>	// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
685	>	// docs said we could.
686	>
687	>	int* ggMjunk = new int[mpiSim->getNAtomsGlobal()];
688	>
689	>	MPI_Allreduce(info[k].globalGroupMembership,
690	>	ggMjunk,
691	>	mpiSim->getNAtomsGlobal(),
692	>	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
693	>
694	>	for (i = 0; i < mpiSim->getNAtomsGlobal(); i++)
695	>	info[k].globalGroupMembership[i] = ggMjunk[i];
696	>
697	>	delete[] ggMjunk;
698
699	+	#endif
700	+
701	+
702	+
703		}
704
705		#ifdef IS_MPI
706		sprintf(checkPointMsg, "all molecules initialized succesfully");
707		MPIcheckPoint();
708		#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	–	}
709
525	–	the_ff->cleanMe();
710		}
711
712		void SimSetup::initFromBass(void){
#	Line 732 \| Line 916 \| void SimSetup::gatherInfo(void){
916		painCave.isFatal = 1;
917		simError();
918		}
919	+	if (globals->haveForceFieldVariant()) {
920	+	strcpy(forcefield_variant, globals->getForceFieldVariant());
921	+	has_forcefield_variant = 1;
922	+	}
923	+
924	+	// get the ensemble
925
736	–	// get the ensemble
737	–
926		strcpy(ensemble, globals->getEnsemble());
927
928		if (!strcasecmp(ensemble, "NVE")){
#	Line 809 \| Line 997 \| void SimSetup::gatherInfo(void){
997		}
998
999		//check whether sample time, status time, thermal time and reset time are divisble by dt
1000	<	if (!isDivisible(globals->getSampleTime(), globals->getDt())){
1000	>	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
1001		sprintf(painCave.errMsg,
1002		"Sample time is not divisible by dt.\n"
1003		"\tThis will result in samples that are not uniformly\n"
#	Line 819 \| Line 1007 \| void SimSetup::gatherInfo(void){
1007		simError();
1008		}
1009
1010	<	if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
1010	>	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
1011		sprintf(painCave.errMsg,
1012		"Status time is not divisible by dt.\n"
1013		"\tThis will result in status reports that are not uniformly\n"
#	Line 855 \| Line 1043 \| void SimSetup::gatherInfo(void){
1043		if (globals->haveSampleTime()){
1044		info[i].sampleTime = globals->getSampleTime();
1045		info[i].statusTime = info[i].sampleTime;
858	–	info[i].thermalTime = info[i].sampleTime;
1046		}
1047		else{
1048		info[i].sampleTime = globals->getRunTime();
1049		info[i].statusTime = info[i].sampleTime;
863	–	info[i].thermalTime = info[i].sampleTime;
1050		}
1051
1052		if (globals->haveStatusTime()){
#	Line 869 \| Line 1055 \| void SimSetup::gatherInfo(void){
1055
1056		if (globals->haveThermalTime()){
1057		info[i].thermalTime = globals->getThermalTime();
1058	+	} else {
1059	+	info[i].thermalTime = globals->getRunTime();
1060		}
1061
1062		info[i].resetIntegrator = 0;
#	Line 886 \| Line 1074 \| void SimSetup::gatherInfo(void){
1074
1075		info[i].useInitXSstate = globals->getUseInitXSstate();
1076		info[i].orthoTolerance = globals->getOrthoBoxTolerance();
1077	<
1077	>
1078	>	// check for thermodynamic integration
1079	>	if (globals->getUseSolidThermInt() && !globals->getUseLiquidThermInt()) {
1080	>	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1081	>	info[i].useSolidThermInt = globals->getUseSolidThermInt();
1082	>	info[i].thermIntLambda = globals->getThermIntLambda();
1083	>	info[i].thermIntK = globals->getThermIntK();
1084	>
1085	>	Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK);
1086	>	info[i].restraint = myRestraint;
1087	>	}
1088	>	else {
1089	>	sprintf(painCave.errMsg,
1090	>	"SimSetup Error:\n"
1091	>	"\tKeyword useSolidThermInt was set to 'true' but\n"
1092	>	"\tthermodynamicIntegrationLambda (and/or\n"
1093	>	"\tthermodynamicIntegrationK) was not specified.\n"
1094	>	"\tPlease provide a lambda value and k value in your .bass file.\n");
1095	>	painCave.isFatal = 1;
1096	>	simError();
1097	>	}
1098	>	}
1099	>	else if(globals->getUseLiquidThermInt()) {
1100	>	if (globals->getUseSolidThermInt()) {
1101	>	sprintf( painCave.errMsg,
1102	>	"SimSetup Warning: It appears that you have both solid and\n"
1103	>	"\tliquid thermodynamic integration activated in your .bass\n"
1104	>	"\tfile. To avoid confusion, specify only one technique in\n"
1105	>	"\tyour .bass file. Liquid-state thermodynamic integration\n"
1106	>	"\twill be assumed for the current simulation. If this is not\n"
1107	>	"\twhat you desire, set useSolidThermInt to 'true' and\n"
1108	>	"\tuseLiquidThermInt to 'false' in your .bass file.\n");
1109	>	painCave.isFatal = 0;
1110	>	simError();
1111	>	}
1112	>	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1113	>	info[i].useLiquidThermInt = globals->getUseLiquidThermInt();
1114	>	info[i].thermIntLambda = globals->getThermIntLambda();
1115	>	info[i].thermIntK = globals->getThermIntK();
1116	>	}
1117	>	else {
1118	>	sprintf(painCave.errMsg,
1119	>	"SimSetup Error:\n"
1120	>	"\tKeyword useLiquidThermInt was set to 'true' but\n"
1121	>	"\tthermodynamicIntegrationLambda (and/or\n"
1122	>	"\tthermodynamicIntegrationK) was not specified.\n"
1123	>	"\tPlease provide a lambda value and k value in your .bass file.\n");
1124	>	painCave.isFatal = 1;
1125	>	simError();
1126	>	}
1127	>	}
1128	>	else if(globals->haveThermIntLambda() \|\| globals->haveThermIntK()){
1129	>	sprintf(painCave.errMsg,
1130	>	"SimSetup Warning: If you want to use Thermodynamic\n"
1131	>	"\tIntegration, set useSolidThermInt or useLiquidThermInt to\n"
1132	>	"\t'true' in your .bass file. These keywords are set to\n"
1133	>	"\t'false' by default, so your lambda and/or k values are\n"
1134	>	"\tbeing ignored.\n");
1135	>	painCave.isFatal = 0;
1136	>	simError();
1137	>	}
1138		}
1139
1140		//setup seed for random number generator
#	Line 939 \| Line 1187 \| void SimSetup::finalInfoCheck(void){
1187		void SimSetup::finalInfoCheck(void){
1188		int index;
1189		int usesDipoles;
1190	+	int usesCharges;
1191		int i;
1192
1193		for (i = 0; i < nInfo; i++){
#	Line 950 \| Line 1199 \| void SimSetup::finalInfoCheck(void){
1199		usesDipoles = (info[i].atoms[index])->hasDipole();
1200		index++;
1201		}
1202	<
1202	>	index = 0;
1203	>	usesCharges = 0;
1204	>	while ((index < info[i].n_atoms) && !usesCharges){
1205	>	usesCharges= (info[i].atoms[index])->hasCharge();
1206	>	index++;
1207	>	}
1208		#ifdef IS_MPI
1209		int myUse = usesDipoles;
1210		MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1211		#endif //is_mpi
1212
1213	<	double theEcr, theEst;
1213	>	double theRcut, theRsw;
1214
1215	+	if (globals->haveRcut()) {
1216	+	theRcut = globals->getRcut();
1217	+
1218	+	if (globals->haveRsw())
1219	+	theRsw = globals->getRsw();
1220	+	else
1221	+	theRsw = theRcut;
1222	+
1223	+	info[i].setDefaultRcut(theRcut, theRsw);
1224	+
1225	+	} else {
1226	+
1227	+	the_ff->calcRcut();
1228	+	theRcut = info[i].getRcut();
1229	+
1230	+	if (globals->haveRsw())
1231	+	theRsw = globals->getRsw();
1232	+	else
1233	+	theRsw = theRcut;
1234	+
1235	+	info[i].setDefaultRcut(theRcut, theRsw);
1236	+	}
1237	+
1238		if (globals->getUseRF()){
1239		info[i].useReactionField = 1;
1240	<
1241	<	if (!globals->haveECR()){
1240	>
1241	>	if (!globals->haveRcut()){
1242		sprintf(painCave.errMsg,
1243	<	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
1243	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1244		"\tOOPSE will use a default value of 15.0 angstroms"
1245	<	"\tfor the electrostaticCutoffRadius.\n");
1245	>	"\tfor the cutoffRadius.\n");
1246		painCave.isFatal = 0;
1247		simError();
1248	<	theEcr = 15.0;
1248	>	theRcut = 15.0;
1249		}
1250		else{
1251	<	theEcr = globals->getECR();
1251	>	theRcut = globals->getRcut();
1252		}
1253
1254	<	if (!globals->haveEST()){
1254	>	if (!globals->haveRsw()){
1255		sprintf(painCave.errMsg,
1256	<	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1256	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1257		"\tOOPSE will use a default value of\n"
1258	<	"\t0.05 * electrostaticCutoffRadius\n"
982	<	"\tfor the electrostaticSkinThickness\n");
1258	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1259		painCave.isFatal = 0;
1260		simError();
1261	<	theEst = 0.05 * theEcr;
1261	>	theRsw = 0.95 * theRcut;
1262		}
1263		else{
1264	<	theEst = globals->getEST();
1264	>	theRsw = globals->getRsw();
1265		}
1266
1267	<	info[i].setDefaultEcr(theEcr, theEst);
1267	>	info[i].setDefaultRcut(theRcut, theRsw);
1268
1269		if (!globals->haveDielectric()){
1270		sprintf(painCave.errMsg,
#	Line 1001 \| Line 1277 \| void SimSetup::finalInfoCheck(void){
1277		info[i].dielectric = globals->getDielectric();
1278		}
1279		else{
1280	<	if (usesDipoles){
1281	<	if (!globals->haveECR()){
1280	>	if (usesDipoles \|\| usesCharges){
1281	>
1282	>	if (!globals->haveRcut()){
1283		sprintf(painCave.errMsg,
1284	<	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
1284	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1285		"\tOOPSE will use a default value of 15.0 angstroms"
1286	<	"\tfor the electrostaticCutoffRadius.\n");
1287	<	painCave.isFatal = 0;
1288	<	simError();
1289	<	theEcr = 15.0;
1290	<	}
1286	>	"\tfor the cutoffRadius.\n");
1287	>	painCave.isFatal = 0;
1288	>	simError();
1289	>	theRcut = 15.0;
1290	>	}
1291		else{
1292	<	theEcr = globals->getECR();
1292	>	theRcut = globals->getRcut();
1293		}
1294	<
1295	<	if (!globals->haveEST()){
1294	>
1295	>	if (!globals->haveRsw()){
1296		sprintf(painCave.errMsg,
1297	<	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1297	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1298		"\tOOPSE will use a default value of\n"
1299	<	"\t0.05 * electrostaticCutoffRadius\n"
1023	<	"\tfor the electrostaticSkinThickness\n");
1299	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1300		painCave.isFatal = 0;
1301		simError();
1302	<	theEst = 0.05 * theEcr;
1302	>	theRsw = 0.95 * theRcut;
1303		}
1304		else{
1305	<	theEst = globals->getEST();
1305	>	theRsw = globals->getRsw();
1306		}
1307	+
1308	+	info[i].setDefaultRcut(theRcut, theRsw);
1309
1032	–	info[i].setDefaultEcr(theEcr, theEst);
1310		}
1311		}
1312		}
#	Line 1037 \| Line 1314 \| void SimSetup::finalInfoCheck(void){
1314		strcpy(checkPointMsg, "post processing checks out");
1315		MPIcheckPoint();
1316		#endif // is_mpi
1317	+
1318	+	// clean up the forcefield
1319	+	the_ff->cleanMe();
1320		}
1321
1322		void SimSetup::initSystemCoords(void){
#	Line 1164 \| Line 1444 \| void SimSetup::makeOutNames(void){
1444		}
1445		else{
1446		strcat(info[k].statusName, ".stat");
1447	+	}
1448	+	}
1449	+
1450	+	strcpy(info[k].rawPotName, inFileName);
1451	+	nameLength = strlen(info[k].rawPotName);
1452	+	endTest = &(info[k].rawPotName[nameLength - 5]);
1453	+	if (!strcmp(endTest, ".bass")){
1454	+	strcpy(endTest, ".raw");
1455	+	}
1456	+	else if (!strcmp(endTest, ".BASS")){
1457	+	strcpy(endTest, ".raw");
1458	+	}
1459	+	else{
1460	+	endTest = &(info[k].rawPotName[nameLength - 4]);
1461	+	if (!strcmp(endTest, ".bss")){
1462	+	strcpy(endTest, ".raw");
1463	+	}
1464	+	else if (!strcmp(endTest, ".mdl")){
1465	+	strcpy(endTest, ".raw");
1466		}
1467	+	else{
1468	+	strcat(info[k].rawPotName, ".raw");
1469	+	}
1470		}
1471
1472		#ifdef IS_MPI
#	Line 1216 \| Line 1518 \| void SimSetup::createFF(void){
1518		void SimSetup::createFF(void){
1519		switch (ffCase){
1520		case FF_DUFF:
1521	<	the_ff = new DUFF();
1521	>	the_ff = new DUFF();
1522		break;
1523
1524		case FF_LJ:
#	Line 1224 \| Line 1526 \| void SimSetup::createFF(void){
1526		break;
1527
1528		case FF_EAM:
1529	<	the_ff = new EAM_FF();
1529	>	if (has_forcefield_variant)
1530	>	the_ff = new EAM_FF(forcefield_variant);
1531	>	else
1532	>	the_ff = new EAM_FF();
1533		break;
1534
1535		case FF_H2O:
#	Line 1238 \| Line 1543 \| void SimSetup::createFF(void){
1543		simError();
1544		}
1545
1546	+
1547		#ifdef IS_MPI
1548		strcpy(checkPointMsg, "ForceField creation successful");
1549		MPIcheckPoint();
#	Line 1251 \| Line 1557 \| void SimSetup::compList(void){
1557		LinkedMolStamp* headStamp = new LinkedMolStamp();
1558		LinkedMolStamp* currentStamp = NULL;
1559		comp_stamps = new MoleculeStamp * [n_components];
1560	+	bool haveCutoffGroups;
1561
1562	+	haveCutoffGroups = false;
1563	+
1564		// make an array of molecule stamps that match the components used.
1565		// also extract the used stamps out into a separate linked list
1566
#	Line 1286 \| Line 1595 \| void SimSetup::compList(void){
1595		headStamp->add(currentStamp);
1596		comp_stamps[i] = headStamp->match(id);
1597		}
1598	+
1599	+	if(comp_stamps[i]->getNCutoffGroups() > 0)
1600	+	haveCutoffGroups = true;
1601		}
1602	+
1603	+	for (i = 0; i < nInfo; i++)
1604	+	info[i].haveCutoffGroups = haveCutoffGroups;
1605
1606		#ifdef IS_MPI
1607		strcpy(checkPointMsg, "Component stamps successfully extracted\n");
#	Line 1295 \| Line 1610 \| void SimSetup::calcSysValues(void){
1610		}
1611
1612		void SimSetup::calcSysValues(void){
1613	<	int i;
1613	>	int i, j;
1614	>	int ncutgroups, atomsingroups, ngroupsinstamp;
1615
1616		int* molMembershipArray;
1617	+	CutoffGroupStamp* cg;
1618
1619		tot_atoms = 0;
1620		tot_bonds = 0;
1621		tot_bends = 0;
1622		tot_torsions = 0;
1623		tot_rigid = 0;
1624	+	tot_groups = 0;
1625		for (i = 0; i < n_components; i++){
1626		tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1627		tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1628		tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1629		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1630		tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1631	+
1632	+	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1633	+	atomsingroups = 0;
1634	+	for (j=0; j < ncutgroups; j++) {
1635	+	cg = comp_stamps[i]->getCutoffGroup(j);
1636	+	atomsingroups += cg->getNMembers();
1637	+	}
1638	+	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups + ncutgroups;
1639	+	tot_groups += components_nmol[i] * ngroupsinstamp;
1640		}
1641
1642		tot_SRI = tot_bonds + tot_bends + tot_torsions;
#	Line 1322 \| Line 1649 \| void SimSetup::calcSysValues(void){
1649		info[i].n_torsions = tot_torsions;
1650		info[i].n_SRI = tot_SRI;
1651		info[i].n_mol = tot_nmol;
1652	<
1652	>	info[i].ngroup = tot_groups;
1653		info[i].molMembershipArray = molMembershipArray;
1654		}
1655		}
#	Line 1333 \| Line 1660 \| void SimSetup::mpiMolDivide(void){
1660		int i, j, k;
1661		int localMol, allMol;
1662		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1663	<	int local_rigid;
1663	>	int local_rigid, local_groups;
1664	>	vector<int> globalMolIndex;
1665	>	int ncutgroups, atomsingroups, ngroupsinstamp;
1666	>	CutoffGroupStamp* cg;
1667
1668		mpiSim = new mpiSimulation(info);
1669
1670	<	globalIndex = mpiSim->divideLabor();
1670	>	mpiSim->divideLabor();
1671	>	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1672	>	globalGroupIndex = mpiSim->getGlobalGroupIndex();
1673	>	//globalMolIndex = mpiSim->getGlobalMolIndex();
1674
1675		// set up the local variables
1676
#	Line 1351 \| Line 1684 \| void SimSetup::mpiMolDivide(void){
1684		local_bends = 0;
1685		local_torsions = 0;
1686		local_rigid = 0;
1687	<	globalAtomIndex = 0;
1687	>	local_groups = 0;
1688	>	globalAtomCounter = 0;
1689
1690		for (i = 0; i < n_components; i++){
1691		for (j = 0; j < components_nmol[i]; j++){
#	Line 1361 \| Line 1695 \| void SimSetup::mpiMolDivide(void){
1695		local_bends += comp_stamps[i]->getNBends();
1696		local_torsions += comp_stamps[i]->getNTorsions();
1697		local_rigid += comp_stamps[i]->getNRigidBodies();
1698	+
1699	+	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1700	+	atomsingroups = 0;
1701	+	for (k=0; k < ncutgroups; k++) {
1702	+	cg = comp_stamps[i]->getCutoffGroup(k);
1703	+	atomsingroups += cg->getNMembers();
1704	+	}
1705	+	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups +
1706	+	ncutgroups;
1707	+	local_groups += ngroupsinstamp;
1708	+
1709		localMol++;
1710		}
1711		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1712	<	info[0].molMembershipArray[globalAtomIndex] = allMol;
1713	<	globalAtomIndex++;
1712	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1713	>	globalAtomCounter++;
1714		}
1715
1716		allMol++;
#	Line 1373 \| Line 1718 \| void SimSetup::mpiMolDivide(void){
1718		}
1719		local_SRI = local_bonds + local_bends + local_torsions;
1720
1721	<	info[0].n_atoms = mpiSim->getMyNlocal();
1721	>	info[0].n_atoms = mpiSim->getNAtomsLocal();
1722
1378	–
1723		if (local_atoms != info[0].n_atoms){
1724		sprintf(painCave.errMsg,
1725		"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
#	Line 1385 \| Line 1729 \| void SimSetup::mpiMolDivide(void){
1729		simError();
1730		}
1731
1732	+	info[0].ngroup = mpiSim->getNGroupsLocal();
1733	+	if (local_groups != info[0].ngroup){
1734	+	sprintf(painCave.errMsg,
1735	+	"SimSetup error: mpiSim's localGroups (%d) and SimSetup's\n"
1736	+	"\tlocalGroups (%d) are not equal.\n",
1737	+	info[0].ngroup, local_groups);
1738	+	painCave.isFatal = 1;
1739	+	simError();
1740	+	}
1741	+
1742		info[0].n_bonds = local_bonds;
1743		info[0].n_bends = local_bends;
1744		info[0].n_torsions = local_torsions;
#	Line 1421 \| Line 1775 \| void SimSetup::makeSysArrays(void){
1775
1776
1777		molIndex = 0;
1778	<	for (i = 0; i < mpiSim->getTotNmol(); i++){
1778	>	for (i = 0; i < mpiSim->getNMolGlobal(); i++){
1779		if (mol2proc[i] == worldRank){
1780		the_molecules[molIndex].setStampID(molCompType[i]);
1781		the_molecules[molIndex].setMyIndex(molIndex);
#	Line 1433 \| Line 1787 \| void SimSetup::makeSysArrays(void){
1787		#else // is_mpi
1788
1789		molIndex = 0;
1790	<	globalAtomIndex = 0;
1790	>	globalAtomCounter = 0;
1791		for (i = 0; i < n_components; i++){
1792		for (j = 0; j < components_nmol[i]; j++){
1793		the_molecules[molIndex].setStampID(i);
1794		the_molecules[molIndex].setMyIndex(molIndex);
1795		the_molecules[molIndex].setGlobalIndex(molIndex);
1796		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1797	<	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1798	<	globalAtomIndex++;
1797	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1798	>	globalAtomCounter++;
1799		}
1800		molIndex++;
1801		}
#	Line 1458 \| Line 1812 \| void SimSetup::makeSysArrays(void){
1812		info[l].atoms = the_atoms;
1813		info[l].molecules = the_molecules;
1814		info[l].nGlobalExcludes = 0;
1815	<
1815	>
1816		the_ff->setSimInfo(info);
1817		}
1818		}
#	Line 1466 \| Line 1820 \| void SimSetup::makeIntegrator(void){
1820		void SimSetup::makeIntegrator(void){
1821		int k;
1822
1823	<	NVE<RealIntegrator>* myNVE = NULL;
1824	<	NVT<RealIntegrator>* myNVT = NULL;
1825	<	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1826	<	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1827	<	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1823	>	NVE<Integrator<BaseIntegrator> >* myNVE = NULL;
1824	>	NVT<Integrator<BaseIntegrator> >* myNVT = NULL;
1825	>	NPTi<NPT<Integrator<BaseIntegrator> > >* myNPTi = NULL;
1826	>	NPTf<NPT<Integrator<BaseIntegrator> > >* myNPTf = NULL;
1827	>	NPTxyz<NPT<Integrator<BaseIntegrator> > >* myNPTxyz = NULL;
1828
1829		for (k = 0; k < nInfo; k++){
1830		switch (ensembleCase){

Diff Legend

-–
+Removed lines
-+
+Added lines
-<
+Changed lines
->
+Changed lines

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents): Revision 1097 by gezelter, Mon Apr 12 20:32:20 2004 UTC vs. Revision 1330 by gezelter, Fri Jul 16 16:29:44 2004 UTC

Diff Legend

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 1097 by gezelter, Mon Apr 12 20:32:20 2004 UTC vs.
Revision 1330 by gezelter, Fri Jul 16 16:29:44 2004 UTC