[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 1234 by tim, Fri Jun 4 03:15:31 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 809 \| Line 993 \| void SimSetup::gatherInfo(void){
993		}
994
995		//check whether sample time, status time, thermal time and reset time are divisble by dt
996	<	if (!isDivisible(globals->getSampleTime(), globals->getDt())){
996	>	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
997		sprintf(painCave.errMsg,
998		"Sample time is not divisible by dt.\n"
999		"\tThis will result in samples that are not uniformly\n"
#	Line 819 \| Line 1003 \| void SimSetup::gatherInfo(void){
1003		simError();
1004		}
1005
1006	<	if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
1006	>	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
1007		sprintf(painCave.errMsg,
1008		"Status time is not divisible by dt.\n"
1009		"\tThis will result in status reports that are not uniformly\n"
#	Line 855 \| Line 1039 \| void SimSetup::gatherInfo(void){
1039		if (globals->haveSampleTime()){
1040		info[i].sampleTime = globals->getSampleTime();
1041		info[i].statusTime = info[i].sampleTime;
858	–	info[i].thermalTime = info[i].sampleTime;
1042		}
1043		else{
1044		info[i].sampleTime = globals->getRunTime();
1045		info[i].statusTime = info[i].sampleTime;
863	–	info[i].thermalTime = info[i].sampleTime;
1046		}
1047
1048		if (globals->haveStatusTime()){
#	Line 869 \| Line 1051 \| void SimSetup::gatherInfo(void){
1051
1052		if (globals->haveThermalTime()){
1053		info[i].thermalTime = globals->getThermalTime();
1054	+	} else {
1055	+	info[i].thermalTime = globals->getRunTime();
1056		}
1057
1058		info[i].resetIntegrator = 0;
#	Line 886 \| Line 1070 \| void SimSetup::gatherInfo(void){
1070
1071		info[i].useInitXSstate = globals->getUseInitXSstate();
1072		info[i].orthoTolerance = globals->getOrthoBoxTolerance();
1073	<
1073	>
1074	>	// check for thermodynamic integration
1075	>	if (globals->getUseSolidThermInt() && !globals->getUseLiquidThermInt()) {
1076	>	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1077	>	info[i].useSolidThermInt = globals->getUseSolidThermInt();
1078	>	info[i].thermIntLambda = globals->getThermIntLambda();
1079	>	info[i].thermIntK = globals->getThermIntK();
1080	>
1081	>	Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK);
1082	>	info[i].restraint = myRestraint;
1083	>	}
1084	>	else {
1085	>	sprintf(painCave.errMsg,
1086	>	"SimSetup Error:\n"
1087	>	"\tKeyword useSolidThermInt was set to 'true' but\n"
1088	>	"\tthermodynamicIntegrationLambda (and/or\n"
1089	>	"\tthermodynamicIntegrationK) was not specified.\n"
1090	>	"\tPlease provide a lambda value and k value in your .bass file.\n");
1091	>	painCave.isFatal = 1;
1092	>	simError();
1093	>	}
1094	>	}
1095	>	else if(globals->getUseLiquidThermInt()) {
1096	>	if (globals->getUseSolidThermInt()) {
1097	>	sprintf( painCave.errMsg,
1098	>	"SimSetup Warning: It appears that you have both solid and\n"
1099	>	"\tliquid thermodynamic integration activated in your .bass\n"
1100	>	"\tfile. To avoid confusion, specify only one technique in\n"
1101	>	"\tyour .bass file. Liquid-state thermodynamic integration\n"
1102	>	"\twill be assumed for the current simulation. If this is not\n"
1103	>	"\twhat you desire, set useSolidThermInt to 'true' and\n"
1104	>	"\tuseLiquidThermInt to 'false' in your .bass file.\n");
1105	>	painCave.isFatal = 0;
1106	>	simError();
1107	>	}
1108	>	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1109	>	info[i].useLiquidThermInt = globals->getUseLiquidThermInt();
1110	>	info[i].thermIntLambda = globals->getThermIntLambda();
1111	>	info[i].thermIntK = globals->getThermIntK();
1112	>	}
1113	>	else {
1114	>	sprintf(painCave.errMsg,
1115	>	"SimSetup Error:\n"
1116	>	"\tKeyword useLiquidThermInt was set to 'true' but\n"
1117	>	"\tthermodynamicIntegrationLambda (and/or\n"
1118	>	"\tthermodynamicIntegrationK) was not specified.\n"
1119	>	"\tPlease provide a lambda value and k value in your .bass file.\n");
1120	>	painCave.isFatal = 1;
1121	>	simError();
1122	>	}
1123	>	}
1124	>	else if(globals->haveThermIntLambda() \|\| globals->haveThermIntK()){
1125	>	sprintf(painCave.errMsg,
1126	>	"SimSetup Warning: If you want to use Thermodynamic\n"
1127	>	"\tIntegration, set useSolidThermInt or useLiquidThermInt to\n"
1128	>	"\t'true' in your .bass file. These keywords are set to\n"
1129	>	"\t'false' by default, so your lambda and/or k values are\n"
1130	>	"\tbeing ignored.\n");
1131	>	painCave.isFatal = 0;
1132	>	simError();
1133	>	}
1134		}
1135
1136		//setup seed for random number generator
#	Line 939 \| Line 1183 \| void SimSetup::finalInfoCheck(void){
1183		void SimSetup::finalInfoCheck(void){
1184		int index;
1185		int usesDipoles;
1186	+	int usesCharges;
1187		int i;
1188
1189		for (i = 0; i < nInfo; i++){
#	Line 950 \| Line 1195 \| void SimSetup::finalInfoCheck(void){
1195		usesDipoles = (info[i].atoms[index])->hasDipole();
1196		index++;
1197		}
1198	<
1198	>	index = 0;
1199	>	usesCharges = 0;
1200	>	while ((index < info[i].n_atoms) && !usesCharges){
1201	>	usesCharges= (info[i].atoms[index])->hasCharge();
1202	>	index++;
1203	>	}
1204		#ifdef IS_MPI
1205		int myUse = usesDipoles;
1206		MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1207		#endif //is_mpi
1208
1209	<	double theEcr, theEst;
1209	>	double theRcut, theRsw;
1210
1211	+	if (globals->haveRcut()) {
1212	+	theRcut = globals->getRcut();
1213	+
1214	+	if (globals->haveRsw())
1215	+	theRsw = globals->getRsw();
1216	+	else
1217	+	theRsw = theRcut;
1218	+
1219	+	info[i].setDefaultRcut(theRcut, theRsw);
1220	+
1221	+	} else {
1222	+
1223	+	the_ff->calcRcut();
1224	+	theRcut = info[i].getRcut();
1225	+
1226	+	if (globals->haveRsw())
1227	+	theRsw = globals->getRsw();
1228	+	else
1229	+	theRsw = theRcut;
1230	+
1231	+	info[i].setDefaultRcut(theRcut, theRsw);
1232	+	}
1233	+
1234		if (globals->getUseRF()){
1235		info[i].useReactionField = 1;
1236	<
1237	<	if (!globals->haveECR()){
1236	>
1237	>	if (!globals->haveRcut()){
1238		sprintf(painCave.errMsg,
1239	<	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
1239	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1240		"\tOOPSE will use a default value of 15.0 angstroms"
1241	<	"\tfor the electrostaticCutoffRadius.\n");
1241	>	"\tfor the cutoffRadius.\n");
1242		painCave.isFatal = 0;
1243		simError();
1244	<	theEcr = 15.0;
1244	>	theRcut = 15.0;
1245		}
1246		else{
1247	<	theEcr = globals->getECR();
1247	>	theRcut = globals->getRcut();
1248		}
1249
1250	<	if (!globals->haveEST()){
1250	>	if (!globals->haveRsw()){
1251		sprintf(painCave.errMsg,
1252	<	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1252	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1253		"\tOOPSE will use a default value of\n"
1254	<	"\t0.05 * electrostaticCutoffRadius\n"
982	<	"\tfor the electrostaticSkinThickness\n");
1254	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1255		painCave.isFatal = 0;
1256		simError();
1257	<	theEst = 0.05 * theEcr;
1257	>	theRsw = 0.95 * theRcut;
1258		}
1259		else{
1260	<	theEst = globals->getEST();
1260	>	theRsw = globals->getRsw();
1261		}
1262
1263	<	info[i].setDefaultEcr(theEcr, theEst);
1263	>	info[i].setDefaultRcut(theRcut, theRsw);
1264
1265		if (!globals->haveDielectric()){
1266		sprintf(painCave.errMsg,
#	Line 1001 \| Line 1273 \| void SimSetup::finalInfoCheck(void){
1273		info[i].dielectric = globals->getDielectric();
1274		}
1275		else{
1276	<	if (usesDipoles){
1277	<	if (!globals->haveECR()){
1276	>	if (usesDipoles \|\| usesCharges){
1277	>
1278	>	if (!globals->haveRcut()){
1279		sprintf(painCave.errMsg,
1280	<	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
1280	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1281		"\tOOPSE will use a default value of 15.0 angstroms"
1282	<	"\tfor the electrostaticCutoffRadius.\n");
1283	<	painCave.isFatal = 0;
1284	<	simError();
1285	<	theEcr = 15.0;
1286	<	}
1282	>	"\tfor the cutoffRadius.\n");
1283	>	painCave.isFatal = 0;
1284	>	simError();
1285	>	theRcut = 15.0;
1286	>	}
1287		else{
1288	<	theEcr = globals->getECR();
1288	>	theRcut = globals->getRcut();
1289		}
1290	<
1291	<	if (!globals->haveEST()){
1290	>
1291	>	if (!globals->haveRsw()){
1292		sprintf(painCave.errMsg,
1293	<	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1293	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1294		"\tOOPSE will use a default value of\n"
1295	<	"\t0.05 * electrostaticCutoffRadius\n"
1023	<	"\tfor the electrostaticSkinThickness\n");
1295	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1296		painCave.isFatal = 0;
1297		simError();
1298	<	theEst = 0.05 * theEcr;
1298	>	theRsw = 0.95 * theRcut;
1299		}
1300		else{
1301	<	theEst = globals->getEST();
1301	>	theRsw = globals->getRsw();
1302		}
1303	+
1304	+	info[i].setDefaultRcut(theRcut, theRsw);
1305
1032	–	info[i].setDefaultEcr(theEcr, theEst);
1306		}
1307		}
1308		}
#	Line 1037 \| Line 1310 \| void SimSetup::finalInfoCheck(void){
1310		strcpy(checkPointMsg, "post processing checks out");
1311		MPIcheckPoint();
1312		#endif // is_mpi
1313	+
1314	+	// clean up the forcefield
1315	+	the_ff->cleanMe();
1316		}
1317
1318		void SimSetup::initSystemCoords(void){
#	Line 1167 \| Line 1443 \| void SimSetup::makeOutNames(void){
1443		}
1444		}
1445
1446	+	strcpy(info[k].rawPotName, inFileName);
1447	+	nameLength = strlen(info[k].rawPotName);
1448	+	endTest = &(info[k].rawPotName[nameLength - 5]);
1449	+	if (!strcmp(endTest, ".bass")){
1450	+	strcpy(endTest, ".raw");
1451	+	}
1452	+	else if (!strcmp(endTest, ".BASS")){
1453	+	strcpy(endTest, ".raw");
1454	+	}
1455	+	else{
1456	+	endTest = &(info[k].rawPotName[nameLength - 4]);
1457	+	if (!strcmp(endTest, ".bss")){
1458	+	strcpy(endTest, ".raw");
1459	+	}
1460	+	else if (!strcmp(endTest, ".mdl")){
1461	+	strcpy(endTest, ".raw");
1462	+	}
1463	+	else{
1464	+	strcat(info[k].rawPotName, ".raw");
1465	+	}
1466	+	}
1467	+
1468		#ifdef IS_MPI
1469
1470		}
#	Line 1251 \| Line 1549 \| void SimSetup::compList(void){
1549		LinkedMolStamp* headStamp = new LinkedMolStamp();
1550		LinkedMolStamp* currentStamp = NULL;
1551		comp_stamps = new MoleculeStamp * [n_components];
1552	+	bool haveCutoffGroups;
1553
1554	+	haveCutoffGroups = false;
1555	+
1556		// make an array of molecule stamps that match the components used.
1557		// also extract the used stamps out into a separate linked list
1558
#	Line 1286 \| Line 1587 \| void SimSetup::compList(void){
1587		headStamp->add(currentStamp);
1588		comp_stamps[i] = headStamp->match(id);
1589		}
1590	+
1591	+	if(comp_stamps[i]->getNCutoffGroups() > 0)
1592	+	haveCutoffGroups = true;
1593		}
1594	+
1595	+	for (i = 0; i < nInfo; i++)
1596	+	info[i].haveCutoffGroups = haveCutoffGroups;
1597
1598		#ifdef IS_MPI
1599		strcpy(checkPointMsg, "Component stamps successfully extracted\n");
#	Line 1295 \| Line 1602 \| void SimSetup::calcSysValues(void){
1602		}
1603
1604		void SimSetup::calcSysValues(void){
1605	<	int i;
1605	>	int i, j;
1606	>	int ncutgroups, atomsingroups, ngroupsinstamp;
1607
1608		int* molMembershipArray;
1609	+	CutoffGroupStamp* cg;
1610
1611		tot_atoms = 0;
1612		tot_bonds = 0;
1613		tot_bends = 0;
1614		tot_torsions = 0;
1615		tot_rigid = 0;
1616	+	tot_groups = 0;
1617		for (i = 0; i < n_components; i++){
1618		tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1619		tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1620		tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1621		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1622		tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1623	+
1624	+	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1625	+	atomsingroups = 0;
1626	+	for (j=0; j < ncutgroups; j++) {
1627	+	cg = comp_stamps[i]->getCutoffGroup(j);
1628	+	atomsingroups += cg->getNMembers();
1629	+	}
1630	+	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups + ncutgroups;
1631	+	tot_groups += components_nmol[i] * ngroupsinstamp;
1632		}
1633
1634		tot_SRI = tot_bonds + tot_bends + tot_torsions;
#	Line 1322 \| Line 1641 \| void SimSetup::calcSysValues(void){
1641		info[i].n_torsions = tot_torsions;
1642		info[i].n_SRI = tot_SRI;
1643		info[i].n_mol = tot_nmol;
1644	<
1644	>	info[i].ngroup = tot_groups;
1645		info[i].molMembershipArray = molMembershipArray;
1646		}
1647		}
#	Line 1333 \| Line 1652 \| void SimSetup::mpiMolDivide(void){
1652		int i, j, k;
1653		int localMol, allMol;
1654		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1655	<	int local_rigid;
1655	>	int local_rigid, local_groups;
1656	>	vector<int> globalMolIndex;
1657	>	int ncutgroups, atomsingroups, ngroupsinstamp;
1658	>	CutoffGroupStamp* cg;
1659
1660		mpiSim = new mpiSimulation(info);
1661
1662	<	globalIndex = mpiSim->divideLabor();
1662	>	mpiSim->divideLabor();
1663	>	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1664	>	globalGroupIndex = mpiSim->getGlobalGroupIndex();
1665	>	//globalMolIndex = mpiSim->getGlobalMolIndex();
1666
1667		// set up the local variables
1668
#	Line 1351 \| Line 1676 \| void SimSetup::mpiMolDivide(void){
1676		local_bends = 0;
1677		local_torsions = 0;
1678		local_rigid = 0;
1679	<	globalAtomIndex = 0;
1679	>	local_groups = 0;
1680	>	globalAtomCounter = 0;
1681
1682		for (i = 0; i < n_components; i++){
1683		for (j = 0; j < components_nmol[i]; j++){
#	Line 1361 \| Line 1687 \| void SimSetup::mpiMolDivide(void){
1687		local_bends += comp_stamps[i]->getNBends();
1688		local_torsions += comp_stamps[i]->getNTorsions();
1689		local_rigid += comp_stamps[i]->getNRigidBodies();
1690	+
1691	+	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1692	+	atomsingroups = 0;
1693	+	for (k=0; k < ncutgroups; k++) {
1694	+	cg = comp_stamps[i]->getCutoffGroup(k);
1695	+	atomsingroups += cg->getNMembers();
1696	+	}
1697	+	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups +
1698	+	ncutgroups;
1699	+	local_groups += ngroupsinstamp;
1700	+
1701		localMol++;
1702		}
1703		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1704	<	info[0].molMembershipArray[globalAtomIndex] = allMol;
1705	<	globalAtomIndex++;
1704	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1705	>	globalAtomCounter++;
1706		}
1707
1708		allMol++;
#	Line 1373 \| Line 1710 \| void SimSetup::mpiMolDivide(void){
1710		}
1711		local_SRI = local_bonds + local_bends + local_torsions;
1712
1713	<	info[0].n_atoms = mpiSim->getMyNlocal();
1713	>	info[0].n_atoms = mpiSim->getNAtomsLocal();
1714
1378	–
1715		if (local_atoms != info[0].n_atoms){
1716		sprintf(painCave.errMsg,
1717		"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
#	Line 1385 \| Line 1721 \| void SimSetup::mpiMolDivide(void){
1721		simError();
1722		}
1723
1724	+	info[0].ngroup = mpiSim->getNGroupsLocal();
1725	+	if (local_groups != info[0].ngroup){
1726	+	sprintf(painCave.errMsg,
1727	+	"SimSetup error: mpiSim's localGroups (%d) and SimSetup's\n"
1728	+	"\tlocalGroups (%d) are not equal.\n",
1729	+	info[0].ngroup, local_groups);
1730	+	painCave.isFatal = 1;
1731	+	simError();
1732	+	}
1733	+
1734		info[0].n_bonds = local_bonds;
1735		info[0].n_bends = local_bends;
1736		info[0].n_torsions = local_torsions;
#	Line 1421 \| Line 1767 \| void SimSetup::makeSysArrays(void){
1767
1768
1769		molIndex = 0;
1770	<	for (i = 0; i < mpiSim->getTotNmol(); i++){
1770	>	for (i = 0; i < mpiSim->getNMolGlobal(); i++){
1771		if (mol2proc[i] == worldRank){
1772		the_molecules[molIndex].setStampID(molCompType[i]);
1773		the_molecules[molIndex].setMyIndex(molIndex);
#	Line 1433 \| Line 1779 \| void SimSetup::makeSysArrays(void){
1779		#else // is_mpi
1780
1781		molIndex = 0;
1782	<	globalAtomIndex = 0;
1782	>	globalAtomCounter = 0;
1783		for (i = 0; i < n_components; i++){
1784		for (j = 0; j < components_nmol[i]; j++){
1785		the_molecules[molIndex].setStampID(i);
1786		the_molecules[molIndex].setMyIndex(molIndex);
1787		the_molecules[molIndex].setGlobalIndex(molIndex);
1788		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1789	<	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1790	<	globalAtomIndex++;
1789	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1790	>	globalAtomCounter++;
1791		}
1792		molIndex++;
1793		}
#	Line 1458 \| Line 1804 \| void SimSetup::makeSysArrays(void){
1804		info[l].atoms = the_atoms;
1805		info[l].molecules = the_molecules;
1806		info[l].nGlobalExcludes = 0;
1807	<
1807	>
1808		the_ff->setSimInfo(info);
1809		}
1810		}

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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 1234 by tim, Fri Jun 4 03:15:31 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 1234 by tim, Fri Jun 4 03:15:31 2004 UTC