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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 983 by gezelter, Mon Jan 26 21:45:03 2004 UTC vs.
Revision 1212 by chrisfen, Tue Jun 1 17:15:43 2004 UTC

#	Line 9 \| Line 9
9		#include "parse_me.h"
10		#include "Integrator.hpp"
11		#include "simError.h"
12	+	#include "RigidBody.hpp"
13	+	#include "OOPSEMinimizer.hpp"
14	+	//#include "ConstraintElement.hpp"
15	+	//#include "ConstraintPair.hpp"
16
17		#ifdef IS_MPI
18		#include "mpiBASS.h"
#	Line 24 \| Line 28
28		#define NPTxyz_ENS 4
29
30
31	<	#define FF_DUFF 0
32	<	#define FF_LJ 1
33	<	#define FF_EAM 2
31	>	#define FF_DUFF 0
32	>	#define FF_LJ 1
33	>	#define FF_EAM 2
34	>	#define FF_H2O 3
35
36		using namespace std;
37
#	Line 143 \| Line 148 \| void SimSetup::createSim(void){
148		// make the output filenames
149
150		makeOutNames();
151	<
147	<	// make the integrator
148	<
149	<	makeIntegrator();
150	<
151	>
152		#ifdef IS_MPI
153		mpiSim->mpiRefresh();
154		#endif
#	Line 155 \| 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 k;
172	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
171	>	int i, j, k;
172	>	int exI, exJ, exK, exL, slI, slJ;
173	>	int tempI, tempJ, tempK, tempL;
174	>	int molI;
175	>	int stampID, atomOffset, rbOffset;
176		molInit molInfo;
177		DirectionalAtom* dAtom;
178	+	RigidBody* myRB;
179	+	StuntDouble* mySD;
180		LinkedAssign* extras;
181		LinkedAssign* current_extra;
182		AtomStamp* currentAtom;
183		BondStamp* currentBond;
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;
194		torsion_set* theTorsions;
195
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();
211
181	–
212		// init the atoms
213
214	<	double phi, theta, psi;
185	<	double sux, suy, suz;
186	<	double Axx, Axy, Axz, Ayx, Ayy, Ayz, Azx, Azy, Azz;
187	<	double ux, uy, uz, u, uSqr;
214	>	int nMembers, nNew, rb1, rb2;
215
216		for (k = 0; k < nInfo; k++){
217		the_ff->setSimInfo(&(info[k]));
218
219		atomOffset = 0;
220	<	excludeOffset = 0;
220	>	groupOffset = 0;
221	>
222		for (i = 0; i < info[k].n_mol; i++){
223		stampID = info[k].molecules[i].getStampID();
224	+	molName = comp_stamps[stampID]->getID();
225
226		molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
227		molInfo.nBonds = comp_stamps[stampID]->getNBonds();
228		molInfo.nBends = comp_stamps[stampID]->getNBends();
229		molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
230	<	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
230	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
231
232	+	nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups();
233	+
234		molInfo.myAtoms = &(info[k].atoms[atomOffset]);
204	–	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
205	–	molInfo.myBonds = new Bond * [molInfo.nBonds];
206	–	molInfo.myBends = new Bend * [molInfo.nBends];
207	–	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
235
236	+	if (molInfo.nBonds > 0)
237	+	molInfo.myBonds = new Bond*[molInfo.nBonds];
238	+	else
239	+	molInfo.myBonds = NULL;
240	+
241	+	if (molInfo.nBends > 0)
242	+	molInfo.myBends = new Bend*[molInfo.nBends];
243	+	else
244	+	molInfo.myBends = NULL;
245	+
246	+	if (molInfo.nTorsions > 0)
247	+	molInfo.myTorsions = new Torsion *[molInfo.nTorsions];
248	+	else
249	+	molInfo.myTorsions = NULL;
250	+
251		theBonds = new bond_pair[molInfo.nBonds];
252		theBends = new bend_set[molInfo.nBends];
253		theTorsions = new torsion_set[molInfo.nTorsions];
254	<
254	>
255		// make the Atoms
256
257		for (j = 0; j < molInfo.nAtoms; j++){
258		currentAtom = comp_stamps[stampID]->getAtom(j);
259	+
260		if (currentAtom->haveOrientation()){
261		dAtom = new DirectionalAtom((j + atomOffset),
262		info[k].getConfiguration());
#	Line 224 \| Line 267 \| void SimSetup::makeMolecules(void){
267		// in space using the three Euler angles. We assume the standard
268		// unit vector was originally along the z axis below.
269
270	<	phi = currentAtom->getEulerPhi();
271	<	theta = currentAtom->getEulerTheta();
272	<	psi = currentAtom->getEulerPsi();
270	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
271	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
272	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
273	>
274	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
275
276	<	Axx = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi));
277	<	Axy = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi));
233	<	Axz = sin(theta) * sin(psi);
234	<
235	<	Ayx = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi));
236	<	Ayy = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi));
237	<	Ayz = sin(theta) * cos(psi);
238	<
239	<	Azx = sin(phi) * sin(theta);
240	<	Azy = -cos(phi) * sin(theta);
241	<	Azz = cos(theta);
276	>	}
277	>	else{
278
279	<	sux = 0.0;
244	<	suy = 0.0;
245	<	suz = 1.0;
279	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
280
247	–	ux = (Axx * sux) + (Ayx * suy) + (Azx * suz);
248	–	uy = (Axy * sux) + (Ayy * suy) + (Azy * suz);
249	–	uz = (Axz * sux) + (Ayz * suy) + (Azz * suz);
250	–
251	–	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
252	–
253	–	u = sqrt(uSqr);
254	–	ux = ux / u;
255	–	uy = uy / u;
256	–	uz = uz / u;
257	–
258	–	dAtom->setSUx(ux);
259	–	dAtom->setSUy(uy);
260	–	dAtom->setSUz(uz);
281		}
262	–	else{
263	–	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
264	–	info[k].getConfiguration());
265	–	}
266	–	molInfo.myAtoms[j]->setType(currentAtom->getType());
282
283	+	molInfo.myAtoms[j]->setType(currentAtom->getType());
284		#ifdef IS_MPI
285
286	<	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
286	>	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
287
288		#endif // is_mpi
289		}
#	Line 278 \| Line 294 \| void SimSetup::makeMolecules(void){
294		theBonds[j].a = currentBond->getA() + atomOffset;
295		theBonds[j].b = currentBond->getB() + atomOffset;
296
297	<	exI = theBonds[j].a;
298	<	exJ = theBonds[j].b;
297	>	tempI = theBonds[j].a;
298	>	tempJ = theBonds[j].b;
299
284	–	// exclude_I must always be the smaller of the pair
285	–	if (exI > exJ){
286	–	tempEx = exI;
287	–	exI = exJ;
288	–	exJ = tempEx;
289	–	}
300		#ifdef IS_MPI
301	<	tempEx = exI;
302	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
303	<	tempEx = exJ;
304	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
301	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
302	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
303	>	#else
304	>	exI = tempI + 1;
305	>	exJ = tempJ + 1;
306	>	#endif
307
308	<	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
297	<	#else // isn't MPI
298	<
299	<	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
300	<	#endif //is_mpi
308	>	info[k].excludes->addPair(exI, exJ);
309		}
302	–	excludeOffset += molInfo.nBonds;
310
311		//make the bends
312		for (j = 0; j < molInfo.nBends; j++){
#	Line 349 \| Line 356 \| void SimSetup::makeMolecules(void){
356		}
357		}
358
359	<	if (!theBends[j].isGhost){
360	<	exI = theBends[j].a;
361	<	exJ = theBends[j].c;
362	<	}
363	<	else{
357	<	exI = theBends[j].a;
358	<	exJ = theBends[j].b;
359	<	}
360	<
361	<	// exclude_I must always be the smaller of the pair
362	<	if (exI > exJ){
363	<	tempEx = exI;
364	<	exI = exJ;
365	<	exJ = tempEx;
366	<	}
359	>	if (theBends[j].isGhost) {
360	>
361	>	tempI = theBends[j].a;
362	>	tempJ = theBends[j].b;
363	>
364		#ifdef IS_MPI
365	<	tempEx = exI;
366	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
367	<	tempEx = exJ;
368	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
365	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
366	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
367	>	#else
368	>	exI = tempI + 1;
369	>	exJ = tempJ + 1;
370	>	#endif
371	>	info[k].excludes->addPair(exI, exJ);
372
373	<	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
374	<	#else // isn't MPI
375	<	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
376	<	#endif //is_mpi
373	>	} else {
374	>
375	>	tempI = theBends[j].a;
376	>	tempJ = theBends[j].b;
377	>	tempK = theBends[j].c;
378	>
379	>	#ifdef IS_MPI
380	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
381	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
382	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
383	>	#else
384	>	exI = tempI + 1;
385	>	exJ = tempJ + 1;
386	>	exK = tempK + 1;
387	>	#endif
388	>
389	>	info[k].excludes->addPair(exI, exK);
390	>	info[k].excludes->addPair(exI, exJ);
391	>	info[k].excludes->addPair(exJ, exK);
392	>	}
393		}
378	–	excludeOffset += molInfo.nBends;
394
395		for (j = 0; j < molInfo.nTorsions; j++){
396		currentTorsion = comp_stamps[stampID]->getTorsion(j);
#	Line 384 \| Line 399 \| void SimSetup::makeMolecules(void){
399		theTorsions[j].c = currentTorsion->getC() + atomOffset;
400		theTorsions[j].d = currentTorsion->getD() + atomOffset;
401
402	<	exI = theTorsions[j].a;
403	<	exJ = theTorsions[j].d;
402	>	tempI = theTorsions[j].a;
403	>	tempJ = theTorsions[j].b;
404	>	tempK = theTorsions[j].c;
405	>	tempL = theTorsions[j].d;
406
407	<	// exclude_I must always be the smaller of the pair
408	<	if (exI > exJ){
409	<	tempEx = exI;
410	<	exI = exJ;
411	<	exJ = tempEx;
407	>	#ifdef IS_MPI
408	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
409	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
410	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
411	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
412	>	#else
413	>	exI = tempI + 1;
414	>	exJ = tempJ + 1;
415	>	exK = tempK + 1;
416	>	exL = tempL + 1;
417	>	#endif
418	>
419	>	info[k].excludes->addPair(exI, exJ);
420	>	info[k].excludes->addPair(exI, exK);
421	>	info[k].excludes->addPair(exI, exL);
422	>	info[k].excludes->addPair(exJ, exK);
423	>	info[k].excludes->addPair(exJ, exL);
424	>	info[k].excludes->addPair(exK, exL);
425	>	}
426	>
427	>
428	>	molInfo.myRigidBodies.clear();
429	>
430	>	for (j = 0; j < molInfo.nRigidBodies; j++){
431	>
432	>	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
433	>	nMembers = currentRigidBody->getNMembers();
434	>
435	>	// Create the Rigid Body:
436	>
437	>	myRB = new RigidBody();
438	>
439	>	sprintf(rbName,"%s_RB_%d", molName, j);
440	>	myRB->setType(rbName);
441	>
442	>	for (rb1 = 0; rb1 < nMembers; rb1++) {
443	>
444	>	// molI is atom numbering inside this molecule
445	>	molI = currentRigidBody->getMember(rb1);
446	>
447	>	// tempI is atom numbering on local processor
448	>	tempI = molI + atomOffset;
449	>
450	>	// currentAtom is the AtomStamp (which we need for
451	>	// rigid body reference positions)
452	>	currentAtom = comp_stamps[stampID]->getAtom(molI);
453	>
454	>	// When we add to the rigid body, add the atom itself and
455	>	// the stamp info:
456	>
457	>	myRB->addAtom(info[k].atoms[tempI], currentAtom);
458	>
459	>	// Add this atom to the Skip List for the integrators
460	>	#ifdef IS_MPI
461	>	slI = info[k].atoms[tempI]->getGlobalIndex();
462	>	#else
463	>	slI = tempI;
464	>	#endif
465	>	skipList.insert(slI);
466	>
467		}
468	+
469	+	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
470	+	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
471	+
472	+	tempI = currentRigidBody->getMember(rb1);
473	+	tempJ = currentRigidBody->getMember(rb2);
474	+
475	+	// Some explanation is required here.
476	+	// Fortran indexing starts at 1, while c indexing starts at 0
477	+	// Also, in parallel computations, the GlobalIndex is
478	+	// used for the exclude list:
479	+
480		#ifdef IS_MPI
481	<	tempEx = exI;
482	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
483	<	tempEx = exJ;
484	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
481	>	exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
482	>	exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
483	>	#else
484	>	exI = molInfo.myAtoms[tempI]->getIndex() + 1;
485	>	exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
486	>	#endif
487	>
488	>	info[k].excludes->addPair(exI, exJ);
489	>
490	>	}
491	>	}
492
493	<	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
494	<	#else // isn't MPI
404	<	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
405	<	#endif //is_mpi
493	>	molInfo.myRigidBodies.push_back(myRB);
494	>	info[k].rigidBodies.push_back(myRB);
495		}
496	<	excludeOffset += molInfo.nTorsions;
496	>
497
498	+	//create cutoff group for molecule
499
500	<	// send the arrays off to the forceField for init.
500	>	cutoffAtomSet.clear();
501	>	molInfo.myCutoffGroups.clear();
502	>
503	>	for (j = 0; j < nCutoffGroups; j++){
504
505	+	currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j);
506	+	nMembers = currentCutoffGroup->getNMembers();
507	+
508	+	myCutoffGroup = new CutoffGroup();
509	+	myCutoffGroup->setGlobalIndex(globalGroupIndex[j + groupOffset]);
510	+
511	+	for (int cg = 0; cg < nMembers; cg++) {
512	+
513	+	// molI is atom numbering inside this molecule
514	+	molI = currentCutoffGroup->getMember(cg);
515	+
516	+	// tempI is atom numbering on local processor
517	+	tempI = molI + atomOffset;
518	+
519	+	#ifdef IS_MPI
520	+	globalID = info[k].atoms[tempI]->getGlobalIndex()
521	+	#else
522	+	globalID = info[k].atoms[tempI]->getIndex();
523	+	#endif
524	+
525	+	globalGroupMembership[globalID] = globalGroupIndex[j+groupOffset];
526	+
527	+	myCutoffGroup->addAtom(info[k].atoms[tempI]);
528	+
529	+	cutoffAtomSet.insert(tempI);
530	+	}
531	+
532	+	molInfo.myCutoffGroups.push_back(myCutoffGroup);
533	+	groupOffset++;
534	+
535	+	}//end for (j = 0; j < molInfo.nCutoffGroups; j++)
536	+
537	+	//creat a cutoff group for every atom in current molecule which does not belong to cutoffgroup defined at mdl file
538	+
539	+	for(j = 0; j < molInfo.nAtoms; j++){
540	+
541	+	if(cutoffAtomSet.find(molInfo.myAtoms[j]->getIndex()) == cutoffAtomSet.end()){
542	+	myCutoffGroup = new CutoffGroup();
543	+	myCutoffGroup->addAtom(molInfo.myAtoms[j]);
544	+	myCutoffGroup->setGlobalIndex(globalGroupIndex[j + groupOffset]);
545	+	#ifdef IS_MPI
546	+	globalID = info[k].atoms[atomOffset + j]->getGlobalIndex()
547	+	#else
548	+	globalID = info[k].atoms[atomOffset + j]->getIndex();
549	+	#endif
550	+	globalGroupMembership[globalID] = globalGroupIndex[j+groupOffset];
551	+	molInfo.myCutoffGroups.push_back(myCutoffGroup);
552	+	groupOffset++;
553	+	}
554	+
555	+	}
556	+
557	+	// After this is all set up, scan through the atoms to
558	+	// see if they can be added to the integrableObjects:
559	+
560	+	molInfo.myIntegrableObjects.clear();
561	+
562	+
563	+	for (j = 0; j < molInfo.nAtoms; j++){
564	+
565	+	#ifdef IS_MPI
566	+	slJ = molInfo.myAtoms[j]->getGlobalIndex();
567	+	#else
568	+	slJ = j+atomOffset;
569	+	#endif
570	+
571	+	// if they aren't on the skip list, then they can be integrated
572	+
573	+	if (skipList.find(slJ) == skipList.end()) {
574	+	mySD = (StuntDouble *) molInfo.myAtoms[j];
575	+	info[k].integrableObjects.push_back(mySD);
576	+	molInfo.myIntegrableObjects.push_back(mySD);
577	+	}
578	+	}
579	+
580	+	// all rigid bodies are integrated:
581	+
582	+	for (j = 0; j < molInfo.nRigidBodies; j++) {
583	+	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
584	+	info[k].integrableObjects.push_back(mySD);
585	+	molInfo.myIntegrableObjects.push_back(mySD);
586	+	}
587	+
588	+
589	+	/*
590	+
591	+	//creat ConstraintPair.
592	+	molInfo.myConstraintPair.clear();
593	+
594	+	for (j = 0; j < molInfo.nBonds; j++){
595	+
596	+	//if both atoms are in the same rigid body, just skip it
597	+	currentBond = comp_stamps[stampID]->getBond(j);
598	+	if(!comp_stamps[stampID]->isBondInSameRigidBody(currentBond)){
599	+
600	+	tempI = currentBond->getA() + atomOffset;
601	+	if( comp_stamps[stampID]->isAtomInRigidBody(currentBond->getA(), whichRigidBody, consAtomIndex))
602	+	consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
603	+	else
604	+	consElement1 = new ConstraintAtom(info[k].atoms[tempI]);
605	+
606	+	tempJ = currentBond->getB() + atomOffset;
607	+	if(comp_stamps[stampID]->isAtomInRigidBody(currentBond->getB(), whichRigidBody, consAtomIndex))
608	+	consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
609	+	else
610	+	consElement2 = new ConstraintAtom(info[k].atoms[tempJ]);
611	+
612	+	consPair = new DistanceConstraintPair(consElement1, consElement2);
613	+	molInfo.myConstraintPairs.push_back(consPair);
614	+	}
615	+	}
616	+
617	+	//loop over rigid bodies, if two rigid bodies share same joint, creat a HingeConstraintPair
618	+	for (int rb1 = 0; rb1 < molInfo.nRigidBodies -1 ; rb1++){
619	+	for (int rb2 = rb1 + 1; rb2 < molInfo.nRigidBodies ; rb2++){
620	+
621	+	jointAtoms = comp_stamps[stampID]->getJointAtoms(rb1, rb2);
622	+
623	+	for(size_t m = 0; m < jointAtoms.size(); m++){
624	+	consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[rb1], jointAtoms[m].first);
625	+	consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[rb2], jointAtoms[m].second);
626	+
627	+	consPair = new JointConstraintPair(consElement1, consElement2);
628	+	molInfo.myConstraintPairs.push_back(consPair);
629	+	}
630	+
631	+	}
632	+	}
633	+
634	+	*/
635	+	// send the arrays off to the forceField for init.
636	+
637		the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
638		the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
639		the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
640		the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
641		theTorsions);
642
418	–
643		info[k].molecules[i].initialize(molInfo);
644
645
#	Line 423 \| Line 647 \| void SimSetup::makeMolecules(void){
647		delete[] theBonds;
648		delete[] theBends;
649		delete[] theTorsions;
650	<	}
650	>	}
651		}
652
653		#ifdef IS_MPI
#	Line 431 \| Line 655 \| void SimSetup::makeMolecules(void){
655		MPIcheckPoint();
656		#endif // is_mpi
657
434	–	// clean up the forcefield
435	–
436	–	the_ff->calcRcut();
437	–	the_ff->cleanMe();
658		}
659
660		void SimSetup::initFromBass(void){
#	Line 635 \| Line 855 \| void SimSetup::gatherInfo(void){
855		else if (!strcasecmp(force_field, "EAM")){
856		ffCase = FF_EAM;
857		}
858	+	else if (!strcasecmp(force_field, "WATER")){
859	+	ffCase = FF_H2O;
860	+	}
861		else{
862		sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
863		force_field);
#	Line 718 \| Line 941 \| void SimSetup::gatherInfo(void){
941		}
942
943		//check whether sample time, status time, thermal time and reset time are divisble by dt
944	<	if (!isDivisible(globals->getSampleTime(), globals->getDt())){
944	>	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
945		sprintf(painCave.errMsg,
946		"Sample time is not divisible by dt.\n"
947		"\tThis will result in samples that are not uniformly\n"
#	Line 728 \| Line 951 \| void SimSetup::gatherInfo(void){
951		simError();
952		}
953
954	<	if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
954	>	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
955		sprintf(painCave.errMsg,
956		"Status time is not divisible by dt.\n"
957		"\tThis will result in status reports that are not uniformly\n"
#	Line 764 \| Line 987 \| void SimSetup::gatherInfo(void){
987		if (globals->haveSampleTime()){
988		info[i].sampleTime = globals->getSampleTime();
989		info[i].statusTime = info[i].sampleTime;
767	–	info[i].thermalTime = info[i].sampleTime;
990		}
991		else{
992		info[i].sampleTime = globals->getRunTime();
993		info[i].statusTime = info[i].sampleTime;
772	–	info[i].thermalTime = info[i].sampleTime;
994		}
995
996		if (globals->haveStatusTime()){
#	Line 778 \| Line 999 \| void SimSetup::gatherInfo(void){
999
1000		if (globals->haveThermalTime()){
1001		info[i].thermalTime = globals->getThermalTime();
1002	+	} else {
1003	+	info[i].thermalTime = globals->getRunTime();
1004		}
1005
1006		info[i].resetIntegrator = 0;
#	Line 795 \| Line 1018 \| void SimSetup::gatherInfo(void){
1018
1019		info[i].useInitXSstate = globals->getUseInitXSstate();
1020		info[i].orthoTolerance = globals->getOrthoBoxTolerance();
1021	<
1021	>
1022	>	// check for thermodynamic integration
1023	>	if (globals->getUseSolidThermInt() && !globals->getUseLiquidThermInt()) {
1024	>	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1025	>	info[i].useSolidThermInt = globals->getUseSolidThermInt();
1026	>	info[i].thermIntLambda = globals->getThermIntLambda();
1027	>	info[i].thermIntK = globals->getThermIntK();
1028	>
1029	>	Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK);
1030	>	info[i].restraint = myRestraint;
1031	>	}
1032	>	else {
1033	>	sprintf(painCave.errMsg,
1034	>	"SimSetup Error:\n"
1035	>	"\tKeyword useSolidThermInt was set to 'true' but\n"
1036	>	"\tthermodynamicIntegrationLambda (and/or\n"
1037	>	"\tthermodynamicIntegrationK) was not specified.\n"
1038	>	"\tPlease provide a lambda value and k value in your .bass file.\n");
1039	>	painCave.isFatal = 1;
1040	>	simError();
1041	>	}
1042	>	}
1043	>	else if(globals->getUseLiquidThermInt()) {
1044	>	if (globals->getUseSolidThermInt()) {
1045	>	sprintf( painCave.errMsg,
1046	>	"SimSetup Warning: It appears that you have both solid and\n"
1047	>	"\tliquid thermodynamic integration activated in your .bass\n"
1048	>	"\tfile. To avoid confusion, specify only one technique in\n"
1049	>	"\tyour .bass file. Liquid-state thermodynamic integration\n"
1050	>	"\twill be assumed for the current simulation. If this is not\n"
1051	>	"\twhat you desire, set useSolidThermInt to 'true' and\n"
1052	>	"\tuseLiquidThermInt to 'false' in your .bass file.\n");
1053	>	painCave.isFatal = 0;
1054	>	simError();
1055	>	}
1056	>	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1057	>	info[i].useLiquidThermInt = globals->getUseLiquidThermInt();
1058	>	info[i].thermIntLambda = globals->getThermIntLambda();
1059	>	info[i].thermIntK = globals->getThermIntK();
1060	>	}
1061	>	else {
1062	>	sprintf(painCave.errMsg,
1063	>	"SimSetup Error:\n"
1064	>	"\tKeyword useLiquidThermInt was set to 'true' but\n"
1065	>	"\tthermodynamicIntegrationLambda (and/or\n"
1066	>	"\tthermodynamicIntegrationK) was not specified.\n"
1067	>	"\tPlease provide a lambda value and k value in your .bass file.\n");
1068	>	painCave.isFatal = 1;
1069	>	simError();
1070	>	}
1071	>	}
1072	>	else if(globals->haveThermIntLambda() \|\| globals->haveThermIntK()){
1073	>	sprintf(painCave.errMsg,
1074	>	"SimSetup Warning: If you want to use Thermodynamic\n"
1075	>	"\tIntegration, set useSolidThermInt or useLiquidThermInt to\n"
1076	>	"\t'true' in your .bass file. These keywords are set to\n"
1077	>	"\t'false' by default, so your lambda and/or k values are\n"
1078	>	"\tbeing ignored.\n");
1079	>	painCave.isFatal = 0;
1080	>	simError();
1081	>	}
1082		}
1083
1084		//setup seed for random number generator
#	Line 837 \| Line 1120 \| void SimSetup::gatherInfo(void){
1120		for (int i = 0; i < nInfo; i++){
1121		info[i].setSeed(seedValue);
1122		}
1123	<
1123	>
1124		#ifdef IS_MPI
1125	<	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
1125	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
1126		MPIcheckPoint();
1127		#endif // is_mpi
1128		}
#	Line 848 \| Line 1131 \| void SimSetup::finalInfoCheck(void){
1131		void SimSetup::finalInfoCheck(void){
1132		int index;
1133		int usesDipoles;
1134	+	int usesCharges;
1135		int i;
1136
1137		for (i = 0; i < nInfo; i++){
#	Line 859 \| Line 1143 \| void SimSetup::finalInfoCheck(void){
1143		usesDipoles = (info[i].atoms[index])->hasDipole();
1144		index++;
1145		}
1146	<
1146	>	index = 0;
1147	>	usesCharges = 0;
1148	>	while ((index < info[i].n_atoms) && !usesCharges){
1149	>	usesCharges= (info[i].atoms[index])->hasCharge();
1150	>	index++;
1151	>	}
1152		#ifdef IS_MPI
1153		int myUse = usesDipoles;
1154		MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1155		#endif //is_mpi
1156
1157	<	double theEcr, theEst;
1157	>	double theRcut, theRsw;
1158
1159	<	if (globals->getUseRF()){
1160	<	info[i].useReactionField = 1;
1159	>	if (globals->haveRcut()) {
1160	>	theRcut = globals->getRcut();
1161
1162	<	if (!globals->haveECR()){
1163	<	sprintf(painCave.errMsg,
1164	<	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
1162	>	if (globals->haveRsw())
1163	>	theRsw = globals->getRsw();
1164	>	else
1165	>	theRsw = theRcut;
1166	>
1167	>	info[i].setDefaultRcut(theRcut, theRsw);
1168	>
1169	>	} else {
1170	>
1171	>	the_ff->calcRcut();
1172	>	theRcut = info[i].getRcut();
1173	>
1174	>	if (globals->haveRsw())
1175	>	theRsw = globals->getRsw();
1176	>	else
1177	>	theRsw = theRcut;
1178	>
1179	>	info[i].setDefaultRcut(theRcut, theRsw);
1180	>	}
1181	>
1182	>	if (globals->getUseRF()){
1183	>	info[i].useReactionField = 1;
1184	>
1185	>	if (!globals->haveRcut()){
1186	>	sprintf(painCave.errMsg,
1187	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1188		"\tOOPSE will use a default value of 15.0 angstroms"
1189	<	"\tfor the electrostaticCutoffRadius.\n");
1189	>	"\tfor the cutoffRadius.\n");
1190		painCave.isFatal = 0;
1191		simError();
1192	<	theEcr = 15.0;
1192	>	theRcut = 15.0;
1193		}
1194		else{
1195	<	theEcr = globals->getECR();
1195	>	theRcut = globals->getRcut();
1196		}
1197
1198	<	if (!globals->haveEST()){
1198	>	if (!globals->haveRsw()){
1199		sprintf(painCave.errMsg,
1200	<	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1200	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1201		"\tOOPSE will use a default value of\n"
1202	<	"\t0.05 * electrostaticCutoffRadius\n"
891	<	"\tfor the electrostaticSkinThickness\n");
1202	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1203		painCave.isFatal = 0;
1204		simError();
1205	<	theEst = 0.05 * theEcr;
1205	>	theRsw = 0.95 * theRcut;
1206		}
1207		else{
1208	<	theEst = globals->getEST();
1208	>	theRsw = globals->getRsw();
1209		}
1210
1211	<	info[i].setDefaultEcr(theEcr, theEst);
1211	>	info[i].setDefaultRcut(theRcut, theRsw);
1212
1213		if (!globals->haveDielectric()){
1214		sprintf(painCave.errMsg,
#	Line 910 \| Line 1221 \| void SimSetup::finalInfoCheck(void){
1221		info[i].dielectric = globals->getDielectric();
1222		}
1223		else{
1224	<	if (usesDipoles){
1225	<	if (!globals->haveECR()){
1224	>	if (usesDipoles \|\| usesCharges){
1225	>
1226	>	if (!globals->haveRcut()){
1227		sprintf(painCave.errMsg,
1228	<	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
1228	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1229		"\tOOPSE will use a default value of 15.0 angstroms"
1230	<	"\tfor the electrostaticCutoffRadius.\n");
1231	<	painCave.isFatal = 0;
1232	<	simError();
1233	<	theEcr = 15.0;
1234	<	}
1230	>	"\tfor the cutoffRadius.\n");
1231	>	painCave.isFatal = 0;
1232	>	simError();
1233	>	theRcut = 15.0;
1234	>	}
1235		else{
1236	<	theEcr = globals->getECR();
1236	>	theRcut = globals->getRcut();
1237		}
1238	<
1239	<	if (!globals->haveEST()){
1238	>
1239	>	if (!globals->haveRsw()){
1240		sprintf(painCave.errMsg,
1241	<	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1241	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1242		"\tOOPSE will use a default value of\n"
1243	<	"\t0.05 * electrostaticCutoffRadius\n"
932	<	"\tfor the electrostaticSkinThickness\n");
1243	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1244		painCave.isFatal = 0;
1245		simError();
1246	<	theEst = 0.05 * theEcr;
1246	>	theRsw = 0.95 * theRcut;
1247		}
1248		else{
1249	<	theEst = globals->getEST();
1249	>	theRsw = globals->getRsw();
1250		}
1251	+
1252	+	info[i].setDefaultRcut(theRcut, theRsw);
1253
941	–	info[i].setDefaultEcr(theEcr, theEst);
1254		}
1255		}
1256		}
#	Line 946 \| Line 1258 \| void SimSetup::finalInfoCheck(void){
1258		strcpy(checkPointMsg, "post processing checks out");
1259		MPIcheckPoint();
1260		#endif // is_mpi
1261	+
1262	+	// clean up the forcefield
1263	+	the_ff->cleanMe();
1264		}
1265
1266		void SimSetup::initSystemCoords(void){
#	Line 1076 \| Line 1391 \| void SimSetup::makeOutNames(void){
1391		}
1392		}
1393
1394	+	strcpy(info[k].rawPotName, inFileName);
1395	+	nameLength = strlen(info[k].rawPotName);
1396	+	endTest = &(info[k].rawPotName[nameLength - 5]);
1397	+	if (!strcmp(endTest, ".bass")){
1398	+	strcpy(endTest, ".raw");
1399	+	}
1400	+	else if (!strcmp(endTest, ".BASS")){
1401	+	strcpy(endTest, ".raw");
1402	+	}
1403	+	else{
1404	+	endTest = &(info[k].rawPotName[nameLength - 4]);
1405	+	if (!strcmp(endTest, ".bss")){
1406	+	strcpy(endTest, ".raw");
1407	+	}
1408	+	else if (!strcmp(endTest, ".mdl")){
1409	+	strcpy(endTest, ".raw");
1410	+	}
1411	+	else{
1412	+	strcat(info[k].rawPotName, ".raw");
1413	+	}
1414	+	}
1415	+
1416		#ifdef IS_MPI
1417
1418		}
#	Line 1136 \| Line 1473 \| void SimSetup::createFF(void){
1473		the_ff = new EAM_FF();
1474		break;
1475
1476	+	case FF_H2O:
1477	+	the_ff = new WATER();
1478	+	break;
1479	+
1480		default:
1481		sprintf(painCave.errMsg,
1482		"SimSetup Error. Unrecognized force field in case statement.\n");
#	Line 1156 \| Line 1497 \| void SimSetup::compList(void){
1497		LinkedMolStamp* headStamp = new LinkedMolStamp();
1498		LinkedMolStamp* currentStamp = NULL;
1499		comp_stamps = new MoleculeStamp * [n_components];
1500	+	bool haveCutoffGroups;
1501
1502	+	haveCutoffGroups = false;
1503	+
1504		// make an array of molecule stamps that match the components used.
1505		// also extract the used stamps out into a separate linked list
1506
#	Line 1191 \| Line 1535 \| void SimSetup::compList(void){
1535		headStamp->add(currentStamp);
1536		comp_stamps[i] = headStamp->match(id);
1537		}
1538	+
1539	+	if(comp_stamps[i]->getNCutoffGroups() > 0)
1540	+	haveCutoffGroups = true;
1541		}
1542	+
1543	+	for (i = 0; i < nInfo; i++)
1544	+	info[i].haveCutoffGroups = haveCutoffGroups;
1545
1546		#ifdef IS_MPI
1547		strcpy(checkPointMsg, "Component stamps successfully extracted\n");
#	Line 1200 \| Line 1550 \| void SimSetup::calcSysValues(void){
1550		}
1551
1552		void SimSetup::calcSysValues(void){
1553	<	int i;
1553	>	int i, j;
1554	>	int ncutgroups, atomsingroups, ngroupsinstamp;
1555
1556		int* molMembershipArray;
1557	+	CutoffGroupStamp* cg;
1558
1559		tot_atoms = 0;
1560		tot_bonds = 0;
1561		tot_bends = 0;
1562		tot_torsions = 0;
1563	+	tot_rigid = 0;
1564	+	tot_groups = 0;
1565		for (i = 0; i < n_components; i++){
1566		tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1567		tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1568		tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1569		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1570	<	}
1570	>	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1571
1572	+	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1573	+	atomsingroups = 0;
1574	+	for (j=0; j < ncutgroups; j++) {
1575	+	cg = comp_stamps[i]->getCutoffGroup(j);
1576	+	atomsingroups += cg->getNMembers();
1577	+	}
1578	+	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups + ncutgroups;
1579	+	tot_groups += components_nmol[i] * ngroupsinstamp;
1580	+	}
1581	+
1582		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1583		molMembershipArray = new int[tot_atoms];
1584
#	Line 1225 \| Line 1589 \| void SimSetup::calcSysValues(void){
1589		info[i].n_torsions = tot_torsions;
1590		info[i].n_SRI = tot_SRI;
1591		info[i].n_mol = tot_nmol;
1592	<
1592	>	info[i].ngroup = tot_groups;
1593		info[i].molMembershipArray = molMembershipArray;
1594		}
1595		}
#	Line 1236 \| Line 1600 \| void SimSetup::mpiMolDivide(void){
1600		int i, j, k;
1601		int localMol, allMol;
1602		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1603	+	int local_rigid, local_groups;
1604	+	vector<int> globalMolIndex;
1605	+	int ncutgroups, atomsingroups, ngroupsinstamp;
1606	+	CutoffGroupStamp* cg;
1607
1608		mpiSim = new mpiSimulation(info);
1609
1610	<	globalIndex = mpiSim->divideLabor();
1610	>	mpiSim->divideLabor();
1611	>	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1612	>	//globalMolIndex = mpiSim->getGlobalMolIndex();
1613
1614		// set up the local variables
1615
#	Line 1252 \| Line 1622 \| void SimSetup::mpiMolDivide(void){
1622		local_bonds = 0;
1623		local_bends = 0;
1624		local_torsions = 0;
1625	<	globalAtomIndex = 0;
1625	>	local_rigid = 0;
1626	>	local_groups = 0;
1627	>	globalAtomCounter = 0;
1628
1257	–
1629		for (i = 0; i < n_components; i++){
1630		for (j = 0; j < components_nmol[i]; j++){
1631		if (mol2proc[allMol] == worldRank){
#	Line 1262 \| Line 1633 \| void SimSetup::mpiMolDivide(void){
1633		local_bonds += comp_stamps[i]->getNBonds();
1634		local_bends += comp_stamps[i]->getNBends();
1635		local_torsions += comp_stamps[i]->getNTorsions();
1636	+	local_rigid += comp_stamps[i]->getNRigidBodies();
1637	+
1638	+	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1639	+	atomsingroups = 0;
1640	+	for (k=0; k < ncutgroups; k++) {
1641	+	cg = comp_stamps[i]->getCutoffGroup(k);
1642	+	atomsingroups += cg->getNMembers();
1643	+	}
1644	+	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups +
1645	+	ncutgroups;
1646	+	local_groups += ngroupsinstamp;
1647	+
1648		localMol++;
1649		}
1650		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1651	<	info[0].molMembershipArray[globalAtomIndex] = allMol;
1652	<	globalAtomIndex++;
1651	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1652	>	globalAtomCounter++;
1653		}
1654
1655		allMol++;
#	Line 1274 \| Line 1657 \| void SimSetup::mpiMolDivide(void){
1657		}
1658		local_SRI = local_bonds + local_bends + local_torsions;
1659
1660	<	info[0].n_atoms = mpiSim->getMyNlocal();
1661	<
1660	>	info[0].n_atoms = mpiSim->getNAtomsLocal();
1661	>
1662		if (local_atoms != info[0].n_atoms){
1663		sprintf(painCave.errMsg,
1664		"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
#	Line 1285 \| Line 1668 \| void SimSetup::mpiMolDivide(void){
1668		simError();
1669		}
1670
1671	+	info[0].ngroup = mpiSim->getNGroupsLocal();
1672	+	if (local_groups != info[0].ngroup){
1673	+	sprintf(painCave.errMsg,
1674	+	"SimSetup error: mpiSim's localGroups (%d) and SimSetup's\n"
1675	+	"\tlocalGroups (%d) are not equal.\n",
1676	+	info[0].ngroup, local_groups);
1677	+	painCave.isFatal = 1;
1678	+	simError();
1679	+	}
1680	+
1681		info[0].n_bonds = local_bonds;
1682		info[0].n_bends = local_bends;
1683		info[0].n_torsions = local_torsions;
#	Line 1307 \| Line 1700 \| void SimSetup::makeSysArrays(void){
1700
1701		Atom** the_atoms;
1702		Molecule* the_molecules;
1310	–	Exclude** the_excludes;
1703
1312	–
1704		for (l = 0; l < nInfo; l++){
1705		// create the atom and short range interaction arrays
1706
#	Line 1323 \| Line 1714 \| void SimSetup::makeSysArrays(void){
1714
1715
1716		molIndex = 0;
1717	<	for (i = 0; i < mpiSim->getTotNmol(); i++){
1717	>	for (i = 0; i < mpiSim->getNMolGlobal(); i++){
1718		if (mol2proc[i] == worldRank){
1719		the_molecules[molIndex].setStampID(molCompType[i]);
1720		the_molecules[molIndex].setMyIndex(molIndex);
#	Line 1335 \| Line 1726 \| void SimSetup::makeSysArrays(void){
1726		#else // is_mpi
1727
1728		molIndex = 0;
1729	<	globalAtomIndex = 0;
1729	>	globalAtomCounter = 0;
1730		for (i = 0; i < n_components; i++){
1731		for (j = 0; j < components_nmol[i]; j++){
1732		the_molecules[molIndex].setStampID(i);
1733		the_molecules[molIndex].setMyIndex(molIndex);
1734		the_molecules[molIndex].setGlobalIndex(molIndex);
1735		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1736	<	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1737	<	globalAtomIndex++;
1736	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1737	>	globalAtomCounter++;
1738		}
1739		molIndex++;
1740		}
#	Line 1352 \| Line 1743 \| void SimSetup::makeSysArrays(void){
1743
1744		#endif // is_mpi
1745
1746	<
1747	<	if (info[l].n_SRI){
1748	<	Exclude::createArray(info[l].n_SRI);
1358	<	the_excludes = new Exclude * [info[l].n_SRI];
1359	<	for (int ex = 0; ex < info[l].n_SRI; ex++){
1360	<	the_excludes[ex] = new Exclude(ex);
1361	<	}
1362	<	info[l].globalExcludes = new int;
1363	<	info[l].n_exclude = info[l].n_SRI;
1364	<	}
1365	<	else{
1366	<	Exclude::createArray(1);
1367	<	the_excludes = new Exclude * ;
1368	<	the_excludes[0] = new Exclude(0);
1369	<	the_excludes[0]->setPair(0, 0);
1370	<	info[l].globalExcludes = new int;
1371	<	info[l].globalExcludes[0] = 0;
1372	<	info[l].n_exclude = 0;
1373	<	}
1374	<
1746	>	info[l].globalExcludes = new int;
1747	>	info[l].globalExcludes[0] = 0;
1748	>
1749		// set the arrays into the SimInfo object
1750
1751		info[l].atoms = the_atoms;
1752		info[l].molecules = the_molecules;
1753		info[l].nGlobalExcludes = 0;
1754	<	info[l].excludes = the_excludes;
1381	<
1754	>
1755		the_ff->setSimInfo(info);
1756		}
1757		}
#	Line 1650 \| Line 2023 \| void SimSetup::setupZConstraint(SimInfo& theInfo){
2023		}
2024
2025		theInfo.addProperty(zconsForcePolicy);
2026	+
2027	+	//set zcons gap
2028	+	DoubleData* zconsGap = new DoubleData();
2029	+	zconsGap->setID(ZCONSGAP_ID);
2030	+
2031	+	if (globals->haveZConsGap()){
2032	+	zconsGap->setData(globals->getZconsGap());
2033	+	theInfo.addProperty(zconsGap);
2034	+	}
2035	+
2036	+	//set zcons fixtime
2037	+	DoubleData* zconsFixtime = new DoubleData();
2038	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
2039	+
2040	+	if (globals->haveZConsFixTime()){
2041	+	zconsFixtime->setData(globals->getZconsFixtime());
2042	+	theInfo.addProperty(zconsFixtime);
2043	+	}
2044	+
2045	+	//set zconsUsingSMD
2046	+	IntData* zconsUsingSMD = new IntData();
2047	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
2048	+
2049	+	if (globals->haveZConsUsingSMD()){
2050	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
2051	+	theInfo.addProperty(zconsUsingSMD);
2052	+	}
2053
2054		//Determine the name of ouput file and add it into SimInfo's property list
2055		//Be careful, do not use inFileName, since it is a pointer which
#	Line 1680 \| Line 2080 \| void SimSetup::setupZConstraint(SimInfo& theInfo){
2080		tempParaItem.zPos = zconStamp[i]->getZpos();
2081		tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
2082		tempParaItem.kRatio = zconStamp[i]->getKratio();
2083	<
2083	>	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
2084	>	tempParaItem.cantVel = zconStamp[i]->getCantVel();
2085		zconsParaData->addItem(tempParaItem);
2086		}
2087
#	Line 1697 \| Line 2098 \| void SimSetup::setupZConstraint(SimInfo& theInfo){
2098
2099		//push data into siminfo, therefore, we can retrieve later
2100		theInfo.addProperty(zconsParaData);
2101	+	}
2102	+
2103	+	void SimSetup::makeMinimizer(){
2104	+
2105	+	OOPSEMinimizer* myOOPSEMinimizer;
2106	+	MinimizerParameterSet* param;
2107	+	char minimizerName[100];
2108	+
2109	+	for (int i = 0; i < nInfo; i++){
2110	+
2111	+	//prepare parameter set for minimizer
2112	+	param = new MinimizerParameterSet();
2113	+	param->setDefaultParameter();
2114	+
2115	+	if (globals->haveMinimizer()){
2116	+	param->setFTol(globals->getMinFTol());
2117	+	}
2118	+
2119	+	if (globals->haveMinGTol()){
2120	+	param->setGTol(globals->getMinGTol());
2121	+	}
2122	+
2123	+	if (globals->haveMinMaxIter()){
2124	+	param->setMaxIteration(globals->getMinMaxIter());
2125	+	}
2126	+
2127	+	if (globals->haveMinWriteFrq()){
2128	+	param->setMaxIteration(globals->getMinMaxIter());
2129	+	}
2130	+
2131	+	if (globals->haveMinWriteFrq()){
2132	+	param->setWriteFrq(globals->getMinWriteFrq());
2133	+	}
2134	+
2135	+	if (globals->haveMinStepSize()){
2136	+	param->setStepSize(globals->getMinStepSize());
2137	+	}
2138	+
2139	+	if (globals->haveMinLSMaxIter()){
2140	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
2141	+	}
2142	+
2143	+	if (globals->haveMinLSTol()){
2144	+	param->setLineSearchTol(globals->getMinLSTol());
2145	+	}
2146	+
2147	+	strcpy(minimizerName, globals->getMinimizer());
2148	+
2149	+	if (!strcasecmp(minimizerName, "CG")){
2150	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2151	+	}
2152	+	else if (!strcasecmp(minimizerName, "SD")){
2153	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
2154	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
2155	+	}
2156	+	else{
2157	+	sprintf(painCave.errMsg,
2158	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
2159	+	painCave.isFatal = 0;
2160	+	simError();
2161	+
2162	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2163	+	}
2164	+	info[i].the_integrator = myOOPSEMinimizer;
2165	+
2166	+	//store the minimizer into simInfo
2167	+	info[i].the_minimizer = myOOPSEMinimizer;
2168	+	info[i].has_minimizer = true;
2169	+	}
2170	+
2171		}

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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents): Revision 983 by gezelter, Mon Jan 26 21:45:03 2004 UTC vs. Revision 1212 by chrisfen, Tue Jun 1 17:15:43 2004 UTC

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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 983 by gezelter, Mon Jan 26 21:45:03 2004 UTC vs.
Revision 1212 by chrisfen, Tue Jun 1 17:15:43 2004 UTC