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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 1035 by tim, Fri Feb 6 21:37:59 2004 UTC vs.
Revision 1211 by tim, Tue Jun 1 15:57:30 2004 UTC

#	Line 9 \| Line 9
9		#include "parse_me.h"
10		#include "Integrator.hpp"
11		#include "simError.h"
12	<	#include "ConjugateMinimizer.hpp"
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 28 \| Line 31
31		#define FF_DUFF 0
32		#define FF_LJ 1
33		#define FF_EAM 2
34	<	#define FF_H2O 3
34	>	#define FF_H2O 3
35
36		using namespace std;
37
#	Line 145 \| Line 148 \| void SimSetup::createSim(void){
148		// make the output filenames
149
150		makeOutNames();
148	–
149	–	if (globals->haveMinimizer())
150	–	// make minimizer
151	–	makeMinimizer();
152	–	else
153	–	// make the integrator
154	–	makeIntegrator();
151
152		#ifdef IS_MPI
153		mpiSim->mpiRefresh();
#	Line 160 \| 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
186	–
212		// init the atoms
213
214	<	double phi, theta, psi;
190	<	double sux, suy, suz;
191	<	double Axx, Axy, Axz, Ayx, Ayy, Ayz, Azx, Azy, Azz;
192	<	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]);
209	–	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
210	–	molInfo.myBonds = new Bond * [molInfo.nBonds];
211	–	molInfo.myBends = new Bend * [molInfo.nBends];
212	–	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 232 \| Line 270 \| void SimSetup::makeMolecules(void){
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));
238	<	Axz = sin(theta) * sin(psi);
239	<
240	<	Ayx = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi));
241	<	Ayy = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi));
242	<	Ayz = sin(theta) * cos(psi);
243	<
244	<	Azx = sin(phi) * sin(theta);
245	<	Azy = -cos(phi) * sin(theta);
246	<	Azz = cos(theta);
276	>	}
277	>	else{
278
279	<	sux = 0.0;
249	<	suy = 0.0;
250	<	suz = 1.0;
279	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
280
281	<	ux = (Axx * sux) + (Ayx * suy) + (Azx * suz);
253	<	uy = (Axy * sux) + (Ayy * suy) + (Azy * suz);
254	<	uz = (Axz * sux) + (Ayz * suy) + (Azz * suz);
255	<
256	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
257	<
258	<	u = sqrt(uSqr);
259	<	ux = ux / u;
260	<	uy = uy / u;
261	<	uz = uz / u;
281	>	}
282
263	–	dAtom->setSUx(ux);
264	–	dAtom->setSUy(uy);
265	–	dAtom->setSUz(uz);
266	–	}
267	–	else{
268	–	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
269	–	info[k].getConfiguration());
270	–	}
283		molInfo.myAtoms[j]->setType(currentAtom->getType());
272	–
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 283 \| 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
289	–	// exclude_I must always be the smaller of the pair
290	–	if (exI > exJ){
291	–	tempEx = exI;
292	–	exI = exJ;
293	–	exJ = tempEx;
294	–	}
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);
302	<	#else // isn't MPI
303	<
304	<	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
305	<	#endif //is_mpi
308	>	info[k].excludes->addPair(exI, exJ);
309		}
307	–	excludeOffset += molInfo.nBonds;
310
311		//make the bends
312		for (j = 0; j < molInfo.nBends; j++){
#	Line 354 \| 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{
362	<	exI = theBends[j].a;
363	<	exJ = theBends[j].b;
364	<	}
365	<
366	<	// exclude_I must always be the smaller of the pair
367	<	if (exI > exJ){
368	<	tempEx = exI;
369	<	exI = exJ;
370	<	exJ = tempEx;
371	<	}
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		}
383	–	excludeOffset += molInfo.nBends;
394
395		for (j = 0; j < molInfo.nTorsions; j++){
396		currentTorsion = comp_stamps[stampID]->getTorsion(j);
#	Line 389 \| 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;
404	<
405	<	// exclude_I must always be the smaller of the pair
406	<	if (exI > exJ){
407	<	tempEx = exI;
408	<	exI = exJ;
409	<	exJ = tempEx;
402	>	tempI = theTorsions[j].a;
403	>	tempJ = theTorsions[j].b;
404	>	tempK = theTorsions[j].c;
405	>	tempL = theTorsions[j].d;
406	>
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
409	<	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
410	<	#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
423	–
643		info[k].molecules[i].initialize(molInfo);
644
645
#	Line 428 \| Line 647 \| void SimSetup::makeMolecules(void){
647		delete[] theBonds;
648		delete[] theBends;
649		delete[] theTorsions;
650	<	}
650	>	}
651		}
652
653		#ifdef IS_MPI
#	Line 436 \| Line 655 \| void SimSetup::makeMolecules(void){
655		MPIcheckPoint();
656		#endif // is_mpi
657
439	–	// clean up the forcefield
440	–
441	–	the_ff->calcRcut();
442	–	the_ff->cleanMe();
658		}
659
660		void SimSetup::initFromBass(void){
#	Line 726 \| 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 736 \| 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 772 \| Line 987 \| void SimSetup::gatherInfo(void){
987		if (globals->haveSampleTime()){
988		info[i].sampleTime = globals->getSampleTime();
989		info[i].statusTime = info[i].sampleTime;
775	–	info[i].thermalTime = info[i].sampleTime;
990		}
991		else{
992		info[i].sampleTime = globals->getRunTime();
993		info[i].statusTime = info[i].sampleTime;
780	–	info[i].thermalTime = info[i].sampleTime;
994		}
995
996		if (globals->haveStatusTime()){
#	Line 786 \| 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 803 \| 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->getUseThermInt()) {
1024	>	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1025	>	info[i].useThermInt = globals->getUseThermInt();
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 useThermInt 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->haveThermIntLambda() \|\| globals->haveThermIntK()){
1044	>	sprintf(painCave.errMsg,
1045	>	"SimSetup Warning: If you want to use Thermodynamic\n"
1046	>	"\tIntegration, set useThermInt to 'true' in your .bass file.\n"
1047	>	"\tThe useThermInt keyword is 'false' by default, so your\n"
1048	>	"\tlambda and/or k values are being ignored.\n");
1049	>	painCave.isFatal = 0;
1050	>	simError();
1051	>	}
1052		}
1053
1054		//setup seed for random number generator
#	Line 856 \| Line 1101 \| void SimSetup::finalInfoCheck(void){
1101		void SimSetup::finalInfoCheck(void){
1102		int index;
1103		int usesDipoles;
1104	+	int usesCharges;
1105		int i;
1106
1107		for (i = 0; i < nInfo; i++){
#	Line 867 \| Line 1113 \| void SimSetup::finalInfoCheck(void){
1113		usesDipoles = (info[i].atoms[index])->hasDipole();
1114		index++;
1115		}
1116	<
1116	>	index = 0;
1117	>	usesCharges = 0;
1118	>	while ((index < info[i].n_atoms) && !usesCharges){
1119	>	usesCharges= (info[i].atoms[index])->hasCharge();
1120	>	index++;
1121	>	}
1122		#ifdef IS_MPI
1123		int myUse = usesDipoles;
1124		MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1125		#endif //is_mpi
1126
1127	<	double theEcr, theEst;
1127	>	double theRcut, theRsw;
1128
1129	+	if (globals->haveRcut()) {
1130	+	theRcut = globals->getRcut();
1131	+
1132	+	if (globals->haveRsw())
1133	+	theRsw = globals->getRsw();
1134	+	else
1135	+	theRsw = theRcut;
1136	+
1137	+	info[i].setDefaultRcut(theRcut, theRsw);
1138	+
1139	+	} else {
1140	+
1141	+	the_ff->calcRcut();
1142	+	theRcut = info[i].getRcut();
1143	+
1144	+	if (globals->haveRsw())
1145	+	theRsw = globals->getRsw();
1146	+	else
1147	+	theRsw = theRcut;
1148	+
1149	+	info[i].setDefaultRcut(theRcut, theRsw);
1150	+	}
1151	+
1152		if (globals->getUseRF()){
1153		info[i].useReactionField = 1;
1154	<
1155	<	if (!globals->haveECR()){
1154	>
1155	>	if (!globals->haveRcut()){
1156		sprintf(painCave.errMsg,
1157	<	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
1157	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1158		"\tOOPSE will use a default value of 15.0 angstroms"
1159	<	"\tfor the electrostaticCutoffRadius.\n");
1159	>	"\tfor the cutoffRadius.\n");
1160		painCave.isFatal = 0;
1161		simError();
1162	<	theEcr = 15.0;
1162	>	theRcut = 15.0;
1163		}
1164		else{
1165	<	theEcr = globals->getECR();
1165	>	theRcut = globals->getRcut();
1166		}
1167
1168	<	if (!globals->haveEST()){
1168	>	if (!globals->haveRsw()){
1169		sprintf(painCave.errMsg,
1170	<	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1170	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1171		"\tOOPSE will use a default value of\n"
1172	<	"\t0.05 * electrostaticCutoffRadius\n"
899	<	"\tfor the electrostaticSkinThickness\n");
1172	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1173		painCave.isFatal = 0;
1174		simError();
1175	<	theEst = 0.05 * theEcr;
1175	>	theRsw = 0.95 * theRcut;
1176		}
1177		else{
1178	<	theEst = globals->getEST();
1178	>	theRsw = globals->getRsw();
1179		}
1180
1181	<	info[i].setDefaultEcr(theEcr, theEst);
1181	>	info[i].setDefaultRcut(theRcut, theRsw);
1182
1183		if (!globals->haveDielectric()){
1184		sprintf(painCave.errMsg,
#	Line 918 \| Line 1191 \| void SimSetup::finalInfoCheck(void){
1191		info[i].dielectric = globals->getDielectric();
1192		}
1193		else{
1194	<	if (usesDipoles){
1195	<	if (!globals->haveECR()){
1194	>	if (usesDipoles \|\| usesCharges){
1195	>
1196	>	if (!globals->haveRcut()){
1197		sprintf(painCave.errMsg,
1198	<	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
1198	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1199		"\tOOPSE will use a default value of 15.0 angstroms"
1200	<	"\tfor the electrostaticCutoffRadius.\n");
1201	<	painCave.isFatal = 0;
1202	<	simError();
1203	<	theEcr = 15.0;
1204	<	}
1200	>	"\tfor the cutoffRadius.\n");
1201	>	painCave.isFatal = 0;
1202	>	simError();
1203	>	theRcut = 15.0;
1204	>	}
1205		else{
1206	<	theEcr = globals->getECR();
1206	>	theRcut = globals->getRcut();
1207		}
1208	<
1209	<	if (!globals->haveEST()){
1210	<	sprintf(painCave.errMsg,
1211	<	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1208	>
1209	>	if (!globals->haveRsw()){
1210	>	sprintf(painCave.errMsg,
1211	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1212		"\tOOPSE will use a default value of\n"
1213	<	"\t0.05 * electrostaticCutoffRadius\n"
940	<	"\tfor the electrostaticSkinThickness\n");
1213	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1214		painCave.isFatal = 0;
1215		simError();
1216	<	theEst = 0.05 * theEcr;
1216	>	theRsw = 0.95 * theRcut;
1217		}
1218		else{
1219	<	theEst = globals->getEST();
1219	>	theRsw = globals->getRsw();
1220		}
1221	+
1222	+	info[i].setDefaultRcut(theRcut, theRsw);
1223
949	–	info[i].setDefaultEcr(theEcr, theEst);
1224		}
1225		}
1226		}
#	Line 954 \| Line 1228 \| void SimSetup::finalInfoCheck(void){
1228		strcpy(checkPointMsg, "post processing checks out");
1229		MPIcheckPoint();
1230		#endif // is_mpi
1231	+
1232	+	// clean up the forcefield
1233	+	the_ff->cleanMe();
1234		}
1235
1236		void SimSetup::initSystemCoords(void){
#	Line 1084 \| Line 1361 \| void SimSetup::makeOutNames(void){
1361		}
1362		}
1363
1364	+	strcpy(info[k].rawPotName, inFileName);
1365	+	nameLength = strlen(info[k].rawPotName);
1366	+	endTest = &(info[k].rawPotName[nameLength - 5]);
1367	+	if (!strcmp(endTest, ".bass")){
1368	+	strcpy(endTest, ".raw");
1369	+	}
1370	+	else if (!strcmp(endTest, ".BASS")){
1371	+	strcpy(endTest, ".raw");
1372	+	}
1373	+	else{
1374	+	endTest = &(info[k].rawPotName[nameLength - 4]);
1375	+	if (!strcmp(endTest, ".bss")){
1376	+	strcpy(endTest, ".raw");
1377	+	}
1378	+	else if (!strcmp(endTest, ".mdl")){
1379	+	strcpy(endTest, ".raw");
1380	+	}
1381	+	else{
1382	+	strcat(info[k].rawPotName, ".raw");
1383	+	}
1384	+	}
1385	+
1386		#ifdef IS_MPI
1387
1388		}
#	Line 1168 \| Line 1467 \| void SimSetup::compList(void){
1467		LinkedMolStamp* headStamp = new LinkedMolStamp();
1468		LinkedMolStamp* currentStamp = NULL;
1469		comp_stamps = new MoleculeStamp * [n_components];
1470	+	bool haveCutoffGroups;
1471
1472	+	haveCutoffGroups = false;
1473	+
1474		// make an array of molecule stamps that match the components used.
1475		// also extract the used stamps out into a separate linked list
1476
#	Line 1203 \| Line 1505 \| void SimSetup::compList(void){
1505		headStamp->add(currentStamp);
1506		comp_stamps[i] = headStamp->match(id);
1507		}
1508	+
1509	+	if(comp_stamps[i]->getNCutoffGroups() > 0)
1510	+	haveCutoffGroups = true;
1511		}
1512	+
1513	+	for (i = 0; i < nInfo; i++)
1514	+	info[i].haveCutoffGroups = haveCutoffGroups;
1515
1516		#ifdef IS_MPI
1517		strcpy(checkPointMsg, "Component stamps successfully extracted\n");
#	Line 1212 \| Line 1520 \| void SimSetup::calcSysValues(void){
1520		}
1521
1522		void SimSetup::calcSysValues(void){
1523	<	int i;
1523	>	int i, j;
1524	>	int ncutgroups, atomsingroups, ngroupsinstamp;
1525
1526		int* molMembershipArray;
1527	+	CutoffGroupStamp* cg;
1528
1529		tot_atoms = 0;
1530		tot_bonds = 0;
1531		tot_bends = 0;
1532		tot_torsions = 0;
1533	+	tot_rigid = 0;
1534	+	tot_groups = 0;
1535		for (i = 0; i < n_components; i++){
1536		tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1537		tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1538		tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1539		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1540	<	}
1540	>	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1541
1542	+	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1543	+	atomsingroups = 0;
1544	+	for (j=0; j < ncutgroups; j++) {
1545	+	cg = comp_stamps[i]->getCutoffGroup(j);
1546	+	atomsingroups += cg->getNMembers();
1547	+	}
1548	+	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups + ncutgroups;
1549	+	tot_groups += components_nmol[i] * ngroupsinstamp;
1550	+	}
1551	+
1552		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1553		molMembershipArray = new int[tot_atoms];
1554
#	Line 1237 \| Line 1559 \| void SimSetup::calcSysValues(void){
1559		info[i].n_torsions = tot_torsions;
1560		info[i].n_SRI = tot_SRI;
1561		info[i].n_mol = tot_nmol;
1562	<
1562	>	info[i].ngroup = tot_groups;
1563		info[i].molMembershipArray = molMembershipArray;
1564		}
1565		}
#	Line 1248 \| Line 1570 \| void SimSetup::mpiMolDivide(void){
1570		int i, j, k;
1571		int localMol, allMol;
1572		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1573	+	int local_rigid, local_groups;
1574	+	vector<int> globalMolIndex;
1575	+	int ncutgroups, atomsingroups, ngroupsinstamp;
1576	+	CutoffGroupStamp* cg;
1577
1578		mpiSim = new mpiSimulation(info);
1579
1580	<	globalIndex = mpiSim->divideLabor();
1580	>	mpiSim->divideLabor();
1581	>	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1582	>	//globalMolIndex = mpiSim->getGlobalMolIndex();
1583
1584		// set up the local variables
1585
#	Line 1264 \| Line 1592 \| void SimSetup::mpiMolDivide(void){
1592		local_bonds = 0;
1593		local_bends = 0;
1594		local_torsions = 0;
1595	<	globalAtomIndex = 0;
1595	>	local_rigid = 0;
1596	>	local_groups = 0;
1597	>	globalAtomCounter = 0;
1598
1269	–
1599		for (i = 0; i < n_components; i++){
1600		for (j = 0; j < components_nmol[i]; j++){
1601		if (mol2proc[allMol] == worldRank){
#	Line 1274 \| Line 1603 \| void SimSetup::mpiMolDivide(void){
1603		local_bonds += comp_stamps[i]->getNBonds();
1604		local_bends += comp_stamps[i]->getNBends();
1605		local_torsions += comp_stamps[i]->getNTorsions();
1606	+	local_rigid += comp_stamps[i]->getNRigidBodies();
1607	+
1608	+	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1609	+	atomsingroups = 0;
1610	+	for (k=0; k < ncutgroups; k++) {
1611	+	cg = comp_stamps[i]->getCutoffGroup(k);
1612	+	atomsingroups += cg->getNMembers();
1613	+	}
1614	+	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups +
1615	+	ncutgroups;
1616	+	local_groups += ngroupsinstamp;
1617	+
1618		localMol++;
1619		}
1620		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1621	<	info[0].molMembershipArray[globalAtomIndex] = allMol;
1622	<	globalAtomIndex++;
1621	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1622	>	globalAtomCounter++;
1623		}
1624
1625		allMol++;
#	Line 1286 \| Line 1627 \| void SimSetup::mpiMolDivide(void){
1627		}
1628		local_SRI = local_bonds + local_bends + local_torsions;
1629
1630	<	info[0].n_atoms = mpiSim->getMyNlocal();
1631	<
1630	>	info[0].n_atoms = mpiSim->getNAtomsLocal();
1631	>
1632		if (local_atoms != info[0].n_atoms){
1633		sprintf(painCave.errMsg,
1634		"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
#	Line 1297 \| Line 1638 \| void SimSetup::mpiMolDivide(void){
1638		simError();
1639		}
1640
1641	+	info[0].ngroup = mpiSim->getNGroupsLocal();
1642	+	if (local_groups != info[0].ngroup){
1643	+	sprintf(painCave.errMsg,
1644	+	"SimSetup error: mpiSim's localGroups (%d) and SimSetup's\n"
1645	+	"\tlocalGroups (%d) are not equal.\n",
1646	+	info[0].ngroup, local_groups);
1647	+	painCave.isFatal = 1;
1648	+	simError();
1649	+	}
1650	+
1651		info[0].n_bonds = local_bonds;
1652		info[0].n_bends = local_bends;
1653		info[0].n_torsions = local_torsions;
#	Line 1319 \| Line 1670 \| void SimSetup::makeSysArrays(void){
1670
1671		Atom** the_atoms;
1672		Molecule* the_molecules;
1322	–	Exclude** the_excludes;
1673
1324	–
1674		for (l = 0; l < nInfo; l++){
1675		// create the atom and short range interaction arrays
1676
#	Line 1335 \| Line 1684 \| void SimSetup::makeSysArrays(void){
1684
1685
1686		molIndex = 0;
1687	<	for (i = 0; i < mpiSim->getTotNmol(); i++){
1687	>	for (i = 0; i < mpiSim->getNMolGlobal(); i++){
1688		if (mol2proc[i] == worldRank){
1689		the_molecules[molIndex].setStampID(molCompType[i]);
1690		the_molecules[molIndex].setMyIndex(molIndex);
#	Line 1347 \| Line 1696 \| void SimSetup::makeSysArrays(void){
1696		#else // is_mpi
1697
1698		molIndex = 0;
1699	<	globalAtomIndex = 0;
1699	>	globalAtomCounter = 0;
1700		for (i = 0; i < n_components; i++){
1701		for (j = 0; j < components_nmol[i]; j++){
1702		the_molecules[molIndex].setStampID(i);
1703		the_molecules[molIndex].setMyIndex(molIndex);
1704		the_molecules[molIndex].setGlobalIndex(molIndex);
1705		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1706	<	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1707	<	globalAtomIndex++;
1706	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1707	>	globalAtomCounter++;
1708		}
1709		molIndex++;
1710		}
#	Line 1364 \| Line 1713 \| void SimSetup::makeSysArrays(void){
1713
1714		#endif // is_mpi
1715
1716	<
1717	<	if (info[l].n_SRI){
1718	<	Exclude::createArray(info[l].n_SRI);
1370	<	the_excludes = new Exclude * [info[l].n_SRI];
1371	<	for (int ex = 0; ex < info[l].n_SRI; ex++){
1372	<	the_excludes[ex] = new Exclude(ex);
1373	<	}
1374	<	info[l].globalExcludes = new int;
1375	<	info[l].n_exclude = info[l].n_SRI;
1376	<	}
1377	<	else{
1378	<	Exclude::createArray(1);
1379	<	the_excludes = new Exclude * ;
1380	<	the_excludes[0] = new Exclude(0);
1381	<	the_excludes[0]->setPair(0, 0);
1382	<	info[l].globalExcludes = new int;
1383	<	info[l].globalExcludes[0] = 0;
1384	<	info[l].n_exclude = 0;
1385	<	}
1386	<
1716	>	info[l].globalExcludes = new int;
1717	>	info[l].globalExcludes[0] = 0;
1718	>
1719		// set the arrays into the SimInfo object
1720
1721		info[l].atoms = the_atoms;
1722		info[l].molecules = the_molecules;
1723		info[l].nGlobalExcludes = 0;
1724	<	info[l].excludes = the_excludes;
1393	<
1724	>
1725		the_ff->setSimInfo(info);
1726		}
1727		}
#	Line 1662 \| Line 1993 \| void SimSetup::setupZConstraint(SimInfo& theInfo){
1993		}
1994
1995		theInfo.addProperty(zconsForcePolicy);
1996	+
1997	+	//set zcons gap
1998	+	DoubleData* zconsGap = new DoubleData();
1999	+	zconsGap->setID(ZCONSGAP_ID);
2000	+
2001	+	if (globals->haveZConsGap()){
2002	+	zconsGap->setData(globals->getZconsGap());
2003	+	theInfo.addProperty(zconsGap);
2004	+	}
2005
2006	+	//set zcons fixtime
2007	+	DoubleData* zconsFixtime = new DoubleData();
2008	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
2009	+
2010	+	if (globals->haveZConsFixTime()){
2011	+	zconsFixtime->setData(globals->getZconsFixtime());
2012	+	theInfo.addProperty(zconsFixtime);
2013	+	}
2014	+
2015	+	//set zconsUsingSMD
2016	+	IntData* zconsUsingSMD = new IntData();
2017	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
2018	+
2019	+	if (globals->haveZConsUsingSMD()){
2020	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
2021	+	theInfo.addProperty(zconsUsingSMD);
2022	+	}
2023	+
2024		//Determine the name of ouput file and add it into SimInfo's property list
2025		//Be careful, do not use inFileName, since it is a pointer which
2026		//point to a string at master node, and slave nodes do not contain that string
#	Line 1692 \| Line 2050 \| void SimSetup::setupZConstraint(SimInfo& theInfo){
2050		tempParaItem.zPos = zconStamp[i]->getZpos();
2051		tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
2052		tempParaItem.kRatio = zconStamp[i]->getKratio();
2053	<
2053	>	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
2054	>	tempParaItem.cantVel = zconStamp[i]->getCantVel();
2055		zconsParaData->addItem(tempParaItem);
2056		}
2057
#	Line 1713 \| Line 2072 \| void SimSetup::makeMinimizer(){
2072
2073		void SimSetup::makeMinimizer(){
2074
2075	<	OOPSEMinimizerBase* myOOPSEMinimizerBase;
1717	<	ObjFunctor1 * objFunc;
1718	<	OutputFunctor* outputFunc;
1719	<	ConcreteNLModel1* nlp;
2075	>	OOPSEMinimizer* myOOPSEMinimizer;
2076		MinimizerParameterSet* param;
2077	<	ConjugateMinimizerBase* minimizer;
1722	<	int dim;
2077	>	char minimizerName[100];
2078
2079		for (int i = 0; i < nInfo; i++){
2080	<	//creat
1726	<	myOOPSEMinimizerBase = new OOPSEMinimizerBase(&(info[i]), the_ff);
1727	<
1728	<	info[i].the_integrator = myOOPSEMinimizerBase;
1729	<	//creat the object functor;
1730	<	objFunc = (ObjFunctor1*) new ClassMemObjFunctor1<OOPSEMinimizerBase>
1731	<	(myOOPSEMinimizerBase, &OOPSEMinimizerBase::calcGradient);
1732	<
1733	<	//creat output functor;
1734	<	outputFunc = new ClassMemOutputFunctor<OOPSEMinimizerBase>
1735	<	(myOOPSEMinimizerBase, &OOPSEMinimizerBase::output);
1736	<
1737	<	//creat nonlinear model
1738	<	dim = myOOPSEMinimizerBase->getDim();
1739	<	nlp = new ConcreteNLModel1(dim, objFunc);
1740	<
1741	<	nlp->setX(myOOPSEMinimizerBase->getCoor());
1742	<
2080	>
2081		//prepare parameter set for minimizer
2082		param = new MinimizerParameterSet();
2083		param->setDefaultParameter();
#	Line 1764 \| Line 2102 \| void SimSetup::makeMinimizer(){
2102		param->setWriteFrq(globals->getMinWriteFrq());
2103		}
2104
2105	<	if (globals->haveMinResetFrq()){
2106	<	param->setResetFrq(globals->getMinResetFrq());
2105	>	if (globals->haveMinStepSize()){
2106	>	param->setStepSize(globals->getMinStepSize());
2107		}
2108
2109		if (globals->haveMinLSMaxIter()){
#	Line 1775 \| Line 2113 \| void SimSetup::makeMinimizer(){
2113		if (globals->haveMinLSTol()){
2114		param->setLineSearchTol(globals->getMinLSTol());
2115		}
1778	–
1779	–	//creat the minimizer
1780	–	minimizer = new PRCGMinimizer(nlp, param);
1781	–	minimizer->setLineSearchStrategy(nlp, GoldenSection);
1782	–	minimizer->setOutputFunctor(outputFunc);
2116
2117	+	strcpy(minimizerName, globals->getMinimizer());
2118	+
2119	+	if (!strcasecmp(minimizerName, "CG")){
2120	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2121	+	}
2122	+	else if (!strcasecmp(minimizerName, "SD")){
2123	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
2124	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
2125	+	}
2126	+	else{
2127	+	sprintf(painCave.errMsg,
2128	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
2129	+	painCave.isFatal = 0;
2130	+	simError();
2131	+
2132	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2133	+	}
2134	+	info[i].the_integrator = myOOPSEMinimizer;
2135	+
2136		//store the minimizer into simInfo
2137	<	info[i].the_minimizer = minimizer;
2137	>	info[i].the_minimizer = myOOPSEMinimizer;
2138		info[i].has_minimizer = true;
2139		}
2140

Diff Legend

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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents): Revision 1035 by tim, Fri Feb 6 21:37:59 2004 UTC vs. Revision 1211 by tim, Tue Jun 1 15:57:30 2004 UTC

Diff Legend

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 1035 by tim, Fri Feb 6 21:37:59 2004 UTC vs.
Revision 1211 by tim, Tue Jun 1 15:57:30 2004 UTC