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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 984 by gezelter, Mon Jan 26 21:52:56 2004 UTC vs.
Revision 1229 by gezelter, Thu Jun 3 20:02:25 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, globalID;
175	>	int stampID, atomOffset, rbOffset, groupOffset;
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	+	#ifdef IS_MPI
220	+	info[k].globalGroupMembership = new int[mpiSim->getNAtomsGlobal()];
221	+	for (i = 0; i < mpiSim->getNAtomsGlobal(); i++)
222	+	info[k].globalGroupMembership[i] = 0;
223	+	#else
224	+	info[k].globalGroupMembership = new int[info[k].n_atoms];
225	+	for (i = 0; i < info[k].n_atoms; i++)
226	+	info[k].globalGroupMembership[i] = 0;
227	+	#endif
228	+
229		atomOffset = 0;
230	<	excludeOffset = 0;
230	>	groupOffset = 0;
231	>
232		for (i = 0; i < info[k].n_mol; i++){
233		stampID = info[k].molecules[i].getStampID();
234	+	molName = comp_stamps[stampID]->getID();
235
236		molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
237		molInfo.nBonds = comp_stamps[stampID]->getNBonds();
238		molInfo.nBends = comp_stamps[stampID]->getNBends();
239		molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
240	<	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
240	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
241
242	+	nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups();
243	+
244		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];
245
246	+	if (molInfo.nBonds > 0)
247	+	molInfo.myBonds = new Bond*[molInfo.nBonds];
248	+	else
249	+	molInfo.myBonds = NULL;
250	+
251	+	if (molInfo.nBends > 0)
252	+	molInfo.myBends = new Bend*[molInfo.nBends];
253	+	else
254	+	molInfo.myBends = NULL;
255	+
256	+	if (molInfo.nTorsions > 0)
257	+	molInfo.myTorsions = new Torsion *[molInfo.nTorsions];
258	+	else
259	+	molInfo.myTorsions = NULL;
260	+
261		theBonds = new bond_pair[molInfo.nBonds];
262		theBends = new bend_set[molInfo.nBends];
263		theTorsions = new torsion_set[molInfo.nTorsions];
264	<
264	>
265		// make the Atoms
266
267		for (j = 0; j < molInfo.nAtoms; j++){
268		currentAtom = comp_stamps[stampID]->getAtom(j);
269	+
270		if (currentAtom->haveOrientation()){
271		dAtom = new DirectionalAtom((j + atomOffset),
272		info[k].getConfiguration());
#	Line 227 \| Line 280 \| void SimSetup::makeMolecules(void){
280		phi = currentAtom->getEulerPhi() * M_PI / 180.0;
281		theta = currentAtom->getEulerTheta() * M_PI / 180.0;
282		psi = currentAtom->getEulerPsi()* M_PI / 180.0;
230	–
231	–	Axx = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi));
232	–	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);
283
284	<	sux = 0.0;
285	<	suy = 0.0;
245	<	suz = 1.0;
246	<
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);
284	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
285	>
286		}
287		else{
263	–	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
264	–	info[k].getConfiguration());
265	–	}
266	–	molInfo.myAtoms[j]->setType(currentAtom->getType());
288
289	<	#ifdef IS_MPI
289	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
290
291	<	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
291	>	}
292
293	+	molInfo.myAtoms[j]->setType(currentAtom->getType());
294	+	#ifdef IS_MPI
295	+	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
296		#endif // is_mpi
297		}
298
#	Line 278 \| Line 302 \| void SimSetup::makeMolecules(void){
302		theBonds[j].a = currentBond->getA() + atomOffset;
303		theBonds[j].b = currentBond->getB() + atomOffset;
304
305	<	exI = theBonds[j].a;
306	<	exJ = theBonds[j].b;
305	>	tempI = theBonds[j].a;
306	>	tempJ = theBonds[j].b;
307
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	–	}
308		#ifdef IS_MPI
309	<	tempEx = exI;
310	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
311	<	tempEx = exJ;
312	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
309	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
310	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
311	>	#else
312	>	exI = tempI + 1;
313	>	exJ = tempJ + 1;
314	>	#endif
315
316	<	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
316	>	info[k].excludes->addPair(exI, exJ);
317		}
302	–	excludeOffset += molInfo.nBonds;
318
319		//make the bends
320		for (j = 0; j < molInfo.nBends; j++){
#	Line 349 \| Line 364 \| void SimSetup::makeMolecules(void){
364		}
365		}
366
367	<	if (!theBends[j].isGhost){
368	<	exI = theBends[j].a;
369	<	exJ = theBends[j].c;
370	<	}
371	<	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	<	}
367	>	if (theBends[j].isGhost) {
368	>
369	>	tempI = theBends[j].a;
370	>	tempJ = theBends[j].b;
371	>
372		#ifdef IS_MPI
373	<	tempEx = exI;
374	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
375	<	tempEx = exJ;
376	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
373	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
374	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
375	>	#else
376	>	exI = tempI + 1;
377	>	exJ = tempJ + 1;
378	>	#endif
379	>	info[k].excludes->addPair(exI, exJ);
380
381	<	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
382	<	#else // isn't MPI
383	<	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
384	<	#endif //is_mpi
381	>	} else {
382	>
383	>	tempI = theBends[j].a;
384	>	tempJ = theBends[j].b;
385	>	tempK = theBends[j].c;
386	>
387	>	#ifdef IS_MPI
388	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
389	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
390	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
391	>	#else
392	>	exI = tempI + 1;
393	>	exJ = tempJ + 1;
394	>	exK = tempK + 1;
395	>	#endif
396	>
397	>	info[k].excludes->addPair(exI, exK);
398	>	info[k].excludes->addPair(exI, exJ);
399	>	info[k].excludes->addPair(exJ, exK);
400	>	}
401		}
378	–	excludeOffset += molInfo.nBends;
402
403		for (j = 0; j < molInfo.nTorsions; j++){
404		currentTorsion = comp_stamps[stampID]->getTorsion(j);
#	Line 384 \| Line 407 \| void SimSetup::makeMolecules(void){
407		theTorsions[j].c = currentTorsion->getC() + atomOffset;
408		theTorsions[j].d = currentTorsion->getD() + atomOffset;
409
410	<	exI = theTorsions[j].a;
411	<	exJ = theTorsions[j].d;
412	<
413	<	// exclude_I must always be the smaller of the pair
414	<	if (exI > exJ){
415	<	tempEx = exI;
416	<	exI = exJ;
417	<	exJ = tempEx;
418	<	}
419	<	#ifdef IS_MPI
420	<	tempEx = exI;
421	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
422	<	tempEx = exJ;
423	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
424	<
425	<	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
426	<	#else // isn't MPI
427	<	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
428	<	#endif //is_mpi
410	>	tempI = theTorsions[j].a;
411	>	tempJ = theTorsions[j].b;
412	>	tempK = theTorsions[j].c;
413	>	tempL = theTorsions[j].d;
414	>
415	>	#ifdef IS_MPI
416	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
417	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
418	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
419	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
420	>	#else
421	>	exI = tempI + 1;
422	>	exJ = tempJ + 1;
423	>	exK = tempK + 1;
424	>	exL = tempL + 1;
425	>	#endif
426	>
427	>	info[k].excludes->addPair(exI, exJ);
428	>	info[k].excludes->addPair(exI, exK);
429	>	info[k].excludes->addPair(exI, exL);
430	>	info[k].excludes->addPair(exJ, exK);
431	>	info[k].excludes->addPair(exJ, exL);
432	>	info[k].excludes->addPair(exK, exL);
433		}
407	–	excludeOffset += molInfo.nTorsions;
434
435	+
436	+	molInfo.myRigidBodies.clear();
437	+
438	+	for (j = 0; j < molInfo.nRigidBodies; j++){
439
440	<	// send the arrays off to the forceField for init.
440	>	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
441	>	nMembers = currentRigidBody->getNMembers();
442
443	+	// Create the Rigid Body:
444	+
445	+	myRB = new RigidBody();
446	+
447	+	sprintf(rbName,"%s_RB_%d", molName, j);
448	+	myRB->setType(rbName);
449	+
450	+	for (rb1 = 0; rb1 < nMembers; rb1++) {
451	+
452	+	// molI is atom numbering inside this molecule
453	+	molI = currentRigidBody->getMember(rb1);
454	+
455	+	// tempI is atom numbering on local processor
456	+	tempI = molI + atomOffset;
457	+
458	+	// currentAtom is the AtomStamp (which we need for
459	+	// rigid body reference positions)
460	+	currentAtom = comp_stamps[stampID]->getAtom(molI);
461	+
462	+	// When we add to the rigid body, add the atom itself and
463	+	// the stamp info:
464	+
465	+	myRB->addAtom(info[k].atoms[tempI], currentAtom);
466	+
467	+	// Add this atom to the Skip List for the integrators
468	+	#ifdef IS_MPI
469	+	slI = info[k].atoms[tempI]->getGlobalIndex();
470	+	#else
471	+	slI = tempI;
472	+	#endif
473	+	skipList.insert(slI);
474	+
475	+	}
476	+
477	+	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
478	+	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
479	+
480	+	tempI = currentRigidBody->getMember(rb1);
481	+	tempJ = currentRigidBody->getMember(rb2);
482	+
483	+	// Some explanation is required here.
484	+	// Fortran indexing starts at 1, while c indexing starts at 0
485	+	// Also, in parallel computations, the GlobalIndex is
486	+	// used for the exclude list:
487	+
488	+	#ifdef IS_MPI
489	+	exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
490	+	exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
491	+	#else
492	+	exI = molInfo.myAtoms[tempI]->getIndex() + 1;
493	+	exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
494	+	#endif
495	+
496	+	info[k].excludes->addPair(exI, exJ);
497	+
498	+	}
499	+	}
500	+
501	+	molInfo.myRigidBodies.push_back(myRB);
502	+	info[k].rigidBodies.push_back(myRB);
503	+	}
504	+
505	+
506	+	//create cutoff group for molecule
507	+
508	+	cutoffAtomSet.clear();
509	+	molInfo.myCutoffGroups.clear();
510	+
511	+	for (j = 0; j < nCutoffGroups; j++){
512	+
513	+	currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j);
514	+	nMembers = currentCutoffGroup->getNMembers();
515	+
516	+	myCutoffGroup = new CutoffGroup();
517	+
518	+	#ifdef IS_MPI
519	+	myCutoffGroup->setGlobalIndex(globalGroupIndex[groupOffset]);
520	+	#else
521	+	myCutoffGroup->setGlobalIndex(groupOffset);
522	+	#endif
523	+
524	+	for (int cg = 0; cg < nMembers; cg++) {
525	+
526	+	// molI is atom numbering inside this molecule
527	+	molI = currentCutoffGroup->getMember(cg);
528	+
529	+	// tempI is atom numbering on local processor
530	+	tempI = molI + atomOffset;
531	+
532	+	#ifdef IS_MPI
533	+	globalID = info[k].atoms[tempI]->getGlobalIndex();
534	+	info[k].globalGroupMembership[globalID] = globalGroupIndex[groupOffset];
535	+	#else
536	+	globalID = info[k].atoms[tempI]->getIndex();
537	+	info[k].globalGroupMembership[globalID] = groupOffset;
538	+	#endif
539	+	myCutoffGroup->addAtom(info[k].atoms[tempI]);
540	+	cutoffAtomSet.insert(tempI);
541	+	}
542	+
543	+	molInfo.myCutoffGroups.push_back(myCutoffGroup);
544	+	groupOffset++;
545	+
546	+	}//end for (j = 0; j < molInfo.nCutoffGroups; j++)
547	+
548	+
549	+	// create a cutoff group for every atom in current molecule which
550	+	// does not belong to cutoffgroup defined at mdl file
551	+
552	+	for(j = 0; j < molInfo.nAtoms; j++){
553	+
554	+	if(cutoffAtomSet.find(molInfo.myAtoms[j]->getIndex()) == cutoffAtomSet.end()){
555	+	myCutoffGroup = new CutoffGroup();
556	+	myCutoffGroup->addAtom(molInfo.myAtoms[j]);
557	+
558	+	#ifdef IS_MPI
559	+	myCutoffGroup->setGlobalIndex(globalGroupIndex[groupOffset]);
560	+	globalID = info[k].atoms[atomOffset + j]->getGlobalIndex();
561	+	info[k].globalGroupMembership[globalID] = globalGroupIndex[groupOffset];
562	+	#else
563	+	myCutoffGroup->setGlobalIndex(groupOffset);
564	+	globalID = info[k].atoms[atomOffset + j]->getIndex();
565	+	info[k].globalGroupMembership[globalID] = groupOffset;
566	+	#endif
567	+	molInfo.myCutoffGroups.push_back(myCutoffGroup);
568	+	groupOffset++;
569	+	}
570	+	}
571	+
572	+	// After this is all set up, scan through the atoms to
573	+	// see if they can be added to the integrableObjects:
574	+
575	+	molInfo.myIntegrableObjects.clear();
576	+
577	+
578	+	for (j = 0; j < molInfo.nAtoms; j++){
579	+
580	+	#ifdef IS_MPI
581	+	slJ = molInfo.myAtoms[j]->getGlobalIndex();
582	+	#else
583	+	slJ = j+atomOffset;
584	+	#endif
585	+
586	+	// if they aren't on the skip list, then they can be integrated
587	+
588	+	if (skipList.find(slJ) == skipList.end()) {
589	+	mySD = (StuntDouble *) molInfo.myAtoms[j];
590	+	info[k].integrableObjects.push_back(mySD);
591	+	molInfo.myIntegrableObjects.push_back(mySD);
592	+	}
593	+	}
594	+
595	+	// all rigid bodies are integrated:
596	+
597	+	for (j = 0; j < molInfo.nRigidBodies; j++) {
598	+	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
599	+	info[k].integrableObjects.push_back(mySD);
600	+	molInfo.myIntegrableObjects.push_back(mySD);
601	+	}
602	+
603	+
604	+	/*
605	+
606	+	//creat ConstraintPair.
607	+	molInfo.myConstraintPair.clear();
608	+
609	+	for (j = 0; j < molInfo.nBonds; j++){
610	+
611	+	//if both atoms are in the same rigid body, just skip it
612	+	currentBond = comp_stamps[stampID]->getBond(j);
613	+	if(!comp_stamps[stampID]->isBondInSameRigidBody(currentBond)){
614	+
615	+	tempI = currentBond->getA() + atomOffset;
616	+	if( comp_stamps[stampID]->isAtomInRigidBody(currentBond->getA(), whichRigidBody, consAtomIndex))
617	+	consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
618	+	else
619	+	consElement1 = new ConstraintAtom(info[k].atoms[tempI]);
620	+
621	+	tempJ = currentBond->getB() + atomOffset;
622	+	if(comp_stamps[stampID]->isAtomInRigidBody(currentBond->getB(), whichRigidBody, consAtomIndex))
623	+	consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
624	+	else
625	+	consElement2 = new ConstraintAtom(info[k].atoms[tempJ]);
626	+
627	+	consPair = new DistanceConstraintPair(consElement1, consElement2);
628	+	molInfo.myConstraintPairs.push_back(consPair);
629	+	}
630	+	}
631	+
632	+	//loop over rigid bodies, if two rigid bodies share same joint, creat a HingeConstraintPair
633	+	for (int rb1 = 0; rb1 < molInfo.nRigidBodies -1 ; rb1++){
634	+	for (int rb2 = rb1 + 1; rb2 < molInfo.nRigidBodies ; rb2++){
635	+
636	+	jointAtoms = comp_stamps[stampID]->getJointAtoms(rb1, rb2);
637	+
638	+	for(size_t m = 0; m < jointAtoms.size(); m++){
639	+	consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[rb1], jointAtoms[m].first);
640	+	consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[rb2], jointAtoms[m].second);
641	+
642	+	consPair = new JointConstraintPair(consElement1, consElement2);
643	+	molInfo.myConstraintPairs.push_back(consPair);
644	+	}
645	+
646	+	}
647	+	}
648	+
649	+	*/
650	+	// send the arrays off to the forceField for init.
651	+
652		the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
653		the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
654		the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
655		the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
656		theTorsions);
657
418	–
658		info[k].molecules[i].initialize(molInfo);
659	<
660	<
659	>
660	>
661		atomOffset += molInfo.nAtoms;
662		delete[] theBonds;
663		delete[] theBends;
664		delete[] theTorsions;
665		}
666	+
667	+
668	+
669	+	#ifdef IS_MPI
670	+	// Since the globalGroupMembership has been zero filled and we've only
671	+	// poked values into the atoms we know, we can do an Allreduce
672	+	// to get the full globalGroupMembership array (We think).
673	+	// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
674	+	// docs said we could.
675	+
676	+	int* ggMjunk = new int[mpiSim->getNAtomsGlobal()];
677	+
678	+	MPI_Allreduce(info[k].globalGroupMembership,
679	+	ggMjunk,
680	+	mpiSim->getNAtomsGlobal(),
681	+	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
682	+
683	+	for (i = 0; i < mpiSim->getNAtomsGlobal(); i++)
684	+	info[k].globalGroupMembership[i] = ggMjunk[i];
685	+
686	+	delete[] ggMjunk;
687	+
688	+	#endif
689	+
690	+
691	+
692		}
693
694		#ifdef IS_MPI
695		sprintf(checkPointMsg, "all molecules initialized succesfully");
696		MPIcheckPoint();
697		#endif // is_mpi
433	–
434	–	// clean up the forcefield
698
436	–	the_ff->calcRcut();
437	–	the_ff->cleanMe();
699		}
700
701		void SimSetup::initFromBass(void){
#	Line 634 \| Line 895 \| void SimSetup::gatherInfo(void){
895		}
896		else if (!strcasecmp(force_field, "EAM")){
897		ffCase = FF_EAM;
898	+	}
899	+	else if (!strcasecmp(force_field, "WATER")){
900	+	ffCase = FF_H2O;
901		}
902		else{
903		sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
#	Line 718 \| Line 982 \| void SimSetup::gatherInfo(void){
982		}
983
984		//check whether sample time, status time, thermal time and reset time are divisble by dt
985	<	if (!isDivisible(globals->getSampleTime(), globals->getDt())){
985	>	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
986		sprintf(painCave.errMsg,
987		"Sample time is not divisible by dt.\n"
988		"\tThis will result in samples that are not uniformly\n"
#	Line 728 \| Line 992 \| void SimSetup::gatherInfo(void){
992		simError();
993		}
994
995	<	if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
995	>	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
996		sprintf(painCave.errMsg,
997		"Status time is not divisible by dt.\n"
998		"\tThis will result in status reports that are not uniformly\n"
#	Line 764 \| Line 1028 \| void SimSetup::gatherInfo(void){
1028		if (globals->haveSampleTime()){
1029		info[i].sampleTime = globals->getSampleTime();
1030		info[i].statusTime = info[i].sampleTime;
767	–	info[i].thermalTime = info[i].sampleTime;
1031		}
1032		else{
1033		info[i].sampleTime = globals->getRunTime();
1034		info[i].statusTime = info[i].sampleTime;
772	–	info[i].thermalTime = info[i].sampleTime;
1035		}
1036
1037		if (globals->haveStatusTime()){
#	Line 778 \| Line 1040 \| void SimSetup::gatherInfo(void){
1040
1041		if (globals->haveThermalTime()){
1042		info[i].thermalTime = globals->getThermalTime();
1043	+	} else {
1044	+	info[i].thermalTime = globals->getRunTime();
1045		}
1046
1047		info[i].resetIntegrator = 0;
#	Line 795 \| Line 1059 \| void SimSetup::gatherInfo(void){
1059
1060		info[i].useInitXSstate = globals->getUseInitXSstate();
1061		info[i].orthoTolerance = globals->getOrthoBoxTolerance();
1062	<
1062	>
1063	>	// check for thermodynamic integration
1064	>	if (globals->getUseSolidThermInt() && !globals->getUseLiquidThermInt()) {
1065	>	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1066	>	info[i].useSolidThermInt = globals->getUseSolidThermInt();
1067	>	info[i].thermIntLambda = globals->getThermIntLambda();
1068	>	info[i].thermIntK = globals->getThermIntK();
1069	>
1070	>	Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK);
1071	>	info[i].restraint = myRestraint;
1072	>	}
1073	>	else {
1074	>	sprintf(painCave.errMsg,
1075	>	"SimSetup Error:\n"
1076	>	"\tKeyword useSolidThermInt was set to 'true' but\n"
1077	>	"\tthermodynamicIntegrationLambda (and/or\n"
1078	>	"\tthermodynamicIntegrationK) was not specified.\n"
1079	>	"\tPlease provide a lambda value and k value in your .bass file.\n");
1080	>	painCave.isFatal = 1;
1081	>	simError();
1082	>	}
1083	>	}
1084	>	else if(globals->getUseLiquidThermInt()) {
1085	>	if (globals->getUseSolidThermInt()) {
1086	>	sprintf( painCave.errMsg,
1087	>	"SimSetup Warning: It appears that you have both solid and\n"
1088	>	"\tliquid thermodynamic integration activated in your .bass\n"
1089	>	"\tfile. To avoid confusion, specify only one technique in\n"
1090	>	"\tyour .bass file. Liquid-state thermodynamic integration\n"
1091	>	"\twill be assumed for the current simulation. If this is not\n"
1092	>	"\twhat you desire, set useSolidThermInt to 'true' and\n"
1093	>	"\tuseLiquidThermInt to 'false' in your .bass file.\n");
1094	>	painCave.isFatal = 0;
1095	>	simError();
1096	>	}
1097	>	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1098	>	info[i].useLiquidThermInt = globals->getUseLiquidThermInt();
1099	>	info[i].thermIntLambda = globals->getThermIntLambda();
1100	>	info[i].thermIntK = globals->getThermIntK();
1101	>	}
1102	>	else {
1103	>	sprintf(painCave.errMsg,
1104	>	"SimSetup Error:\n"
1105	>	"\tKeyword useLiquidThermInt was set to 'true' but\n"
1106	>	"\tthermodynamicIntegrationLambda (and/or\n"
1107	>	"\tthermodynamicIntegrationK) was not specified.\n"
1108	>	"\tPlease provide a lambda value and k value in your .bass file.\n");
1109	>	painCave.isFatal = 1;
1110	>	simError();
1111	>	}
1112	>	}
1113	>	else if(globals->haveThermIntLambda() \|\| globals->haveThermIntK()){
1114	>	sprintf(painCave.errMsg,
1115	>	"SimSetup Warning: If you want to use Thermodynamic\n"
1116	>	"\tIntegration, set useSolidThermInt or useLiquidThermInt to\n"
1117	>	"\t'true' in your .bass file. These keywords are set to\n"
1118	>	"\t'false' by default, so your lambda and/or k values are\n"
1119	>	"\tbeing ignored.\n");
1120	>	painCave.isFatal = 0;
1121	>	simError();
1122	>	}
1123		}
1124
1125		//setup seed for random number generator
#	Line 837 \| Line 1161 \| void SimSetup::gatherInfo(void){
1161		for (int i = 0; i < nInfo; i++){
1162		info[i].setSeed(seedValue);
1163		}
1164	<
1164	>
1165		#ifdef IS_MPI
1166	<	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
1166	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
1167		MPIcheckPoint();
1168		#endif // is_mpi
1169		}
#	Line 848 \| Line 1172 \| void SimSetup::finalInfoCheck(void){
1172		void SimSetup::finalInfoCheck(void){
1173		int index;
1174		int usesDipoles;
1175	+	int usesCharges;
1176		int i;
1177
1178		for (i = 0; i < nInfo; i++){
#	Line 859 \| Line 1184 \| void SimSetup::finalInfoCheck(void){
1184		usesDipoles = (info[i].atoms[index])->hasDipole();
1185		index++;
1186		}
1187	<
1187	>	index = 0;
1188	>	usesCharges = 0;
1189	>	while ((index < info[i].n_atoms) && !usesCharges){
1190	>	usesCharges= (info[i].atoms[index])->hasCharge();
1191	>	index++;
1192	>	}
1193		#ifdef IS_MPI
1194		int myUse = usesDipoles;
1195		MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1196		#endif //is_mpi
1197
1198	<	double theEcr, theEst;
1198	>	double theRcut, theRsw;
1199
1200	<	if (globals->getUseRF()){
1201	<	info[i].useReactionField = 1;
1200	>	if (globals->haveRcut()) {
1201	>	theRcut = globals->getRcut();
1202
1203	<	if (!globals->haveECR()){
1203	>	if (globals->haveRsw())
1204	>	theRsw = globals->getRsw();
1205	>	else
1206	>	theRsw = theRcut;
1207	>
1208	>	info[i].setDefaultRcut(theRcut, theRsw);
1209	>
1210	>	} else {
1211	>
1212	>	the_ff->calcRcut();
1213	>	theRcut = info[i].getRcut();
1214	>
1215	>	if (globals->haveRsw())
1216	>	theRsw = globals->getRsw();
1217	>	else
1218	>	theRsw = theRcut;
1219	>
1220	>	info[i].setDefaultRcut(theRcut, theRsw);
1221	>	}
1222	>
1223	>	if (globals->getUseRF()){
1224	>	info[i].useReactionField = 1;
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");
1230	>	"\tfor the cutoffRadius.\n");
1231		painCave.isFatal = 0;
1232		simError();
1233	<	theEcr = 15.0;
1233	>	theRcut = 15.0;
1234		}
1235		else{
1236	<	theEcr = globals->getECR();
1236	>	theRcut = globals->getRcut();
1237		}
1238
1239	<	if (!globals->haveEST()){
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"
891	<	"\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].setDefaultEcr(theEcr, theEst);
1252	>	info[i].setDefaultRcut(theRcut, theRsw);
1253
1254		if (!globals->haveDielectric()){
1255		sprintf(painCave.errMsg,
#	Line 910 \| Line 1262 \| void SimSetup::finalInfoCheck(void){
1262		info[i].dielectric = globals->getDielectric();
1263		}
1264		else{
1265	<	if (usesDipoles){
1266	<	if (!globals->haveECR()){
1265	>	if (usesDipoles \|\| usesCharges){
1266	>
1267	>	if (!globals->haveRcut()){
1268		sprintf(painCave.errMsg,
1269	<	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
1269	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1270		"\tOOPSE will use a default value of 15.0 angstroms"
1271	<	"\tfor the electrostaticCutoffRadius.\n");
1272	<	painCave.isFatal = 0;
1273	<	simError();
1274	<	theEcr = 15.0;
1275	<	}
1271	>	"\tfor the cutoffRadius.\n");
1272	>	painCave.isFatal = 0;
1273	>	simError();
1274	>	theRcut = 15.0;
1275	>	}
1276		else{
1277	<	theEcr = globals->getECR();
1277	>	theRcut = globals->getRcut();
1278		}
1279	<
1280	<	if (!globals->haveEST()){
1279	>
1280	>	if (!globals->haveRsw()){
1281		sprintf(painCave.errMsg,
1282	<	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1282	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1283		"\tOOPSE will use a default value of\n"
1284	<	"\t0.05 * electrostaticCutoffRadius\n"
932	<	"\tfor the electrostaticSkinThickness\n");
1284	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1285		painCave.isFatal = 0;
1286		simError();
1287	<	theEst = 0.05 * theEcr;
1287	>	theRsw = 0.95 * theRcut;
1288		}
1289		else{
1290	<	theEst = globals->getEST();
1290	>	theRsw = globals->getRsw();
1291		}
1292	+
1293	+	info[i].setDefaultRcut(theRcut, theRsw);
1294
941	–	info[i].setDefaultEcr(theEcr, theEst);
1295		}
1296		}
1297		}
#	Line 946 \| Line 1299 \| void SimSetup::finalInfoCheck(void){
1299		strcpy(checkPointMsg, "post processing checks out");
1300		MPIcheckPoint();
1301		#endif // is_mpi
1302	+
1303	+	// clean up the forcefield
1304	+	the_ff->cleanMe();
1305		}
1306
1307		void SimSetup::initSystemCoords(void){
#	Line 1073 \| Line 1429 \| void SimSetup::makeOutNames(void){
1429		}
1430		else{
1431		strcat(info[k].statusName, ".stat");
1432	+	}
1433	+	}
1434	+
1435	+	strcpy(info[k].rawPotName, inFileName);
1436	+	nameLength = strlen(info[k].rawPotName);
1437	+	endTest = &(info[k].rawPotName[nameLength - 5]);
1438	+	if (!strcmp(endTest, ".bass")){
1439	+	strcpy(endTest, ".raw");
1440	+	}
1441	+	else if (!strcmp(endTest, ".BASS")){
1442	+	strcpy(endTest, ".raw");
1443	+	}
1444	+	else{
1445	+	endTest = &(info[k].rawPotName[nameLength - 4]);
1446	+	if (!strcmp(endTest, ".bss")){
1447	+	strcpy(endTest, ".raw");
1448		}
1449	+	else if (!strcmp(endTest, ".mdl")){
1450	+	strcpy(endTest, ".raw");
1451	+	}
1452	+	else{
1453	+	strcat(info[k].rawPotName, ".raw");
1454	+	}
1455		}
1456
1457		#ifdef IS_MPI
#	Line 1136 \| Line 1514 \| void SimSetup::createFF(void){
1514		the_ff = new EAM_FF();
1515		break;
1516
1517	+	case FF_H2O:
1518	+	the_ff = new WATER();
1519	+	break;
1520	+
1521		default:
1522		sprintf(painCave.errMsg,
1523		"SimSetup Error. Unrecognized force field in case statement.\n");
#	Line 1156 \| Line 1538 \| void SimSetup::compList(void){
1538		LinkedMolStamp* headStamp = new LinkedMolStamp();
1539		LinkedMolStamp* currentStamp = NULL;
1540		comp_stamps = new MoleculeStamp * [n_components];
1541	+	bool haveCutoffGroups;
1542
1543	+	haveCutoffGroups = false;
1544	+
1545		// make an array of molecule stamps that match the components used.
1546		// also extract the used stamps out into a separate linked list
1547
#	Line 1191 \| Line 1576 \| void SimSetup::compList(void){
1576		headStamp->add(currentStamp);
1577		comp_stamps[i] = headStamp->match(id);
1578		}
1579	+
1580	+	if(comp_stamps[i]->getNCutoffGroups() > 0)
1581	+	haveCutoffGroups = true;
1582		}
1583	+
1584	+	for (i = 0; i < nInfo; i++)
1585	+	info[i].haveCutoffGroups = haveCutoffGroups;
1586
1587		#ifdef IS_MPI
1588		strcpy(checkPointMsg, "Component stamps successfully extracted\n");
#	Line 1200 \| Line 1591 \| void SimSetup::calcSysValues(void){
1591		}
1592
1593		void SimSetup::calcSysValues(void){
1594	<	int i;
1594	>	int i, j;
1595	>	int ncutgroups, atomsingroups, ngroupsinstamp;
1596
1597		int* molMembershipArray;
1598	+	CutoffGroupStamp* cg;
1599
1600		tot_atoms = 0;
1601		tot_bonds = 0;
1602		tot_bends = 0;
1603		tot_torsions = 0;
1604	+	tot_rigid = 0;
1605	+	tot_groups = 0;
1606		for (i = 0; i < n_components; i++){
1607		tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1608		tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1609		tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1610		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1611	<	}
1611	>	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1612
1613	+	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1614	+	atomsingroups = 0;
1615	+	for (j=0; j < ncutgroups; j++) {
1616	+	cg = comp_stamps[i]->getCutoffGroup(j);
1617	+	atomsingroups += cg->getNMembers();
1618	+	}
1619	+	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups + ncutgroups;
1620	+	tot_groups += components_nmol[i] * ngroupsinstamp;
1621	+	}
1622	+
1623		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1624		molMembershipArray = new int[tot_atoms];
1625
#	Line 1225 \| Line 1630 \| void SimSetup::calcSysValues(void){
1630		info[i].n_torsions = tot_torsions;
1631		info[i].n_SRI = tot_SRI;
1632		info[i].n_mol = tot_nmol;
1633	<
1633	>	info[i].ngroup = tot_groups;
1634		info[i].molMembershipArray = molMembershipArray;
1635		}
1636		}
#	Line 1236 \| Line 1641 \| void SimSetup::mpiMolDivide(void){
1641		int i, j, k;
1642		int localMol, allMol;
1643		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1644	+	int local_rigid, local_groups;
1645	+	vector<int> globalMolIndex;
1646	+	int ncutgroups, atomsingroups, ngroupsinstamp;
1647	+	CutoffGroupStamp* cg;
1648
1649		mpiSim = new mpiSimulation(info);
1650
1651	<	globalIndex = mpiSim->divideLabor();
1651	>	mpiSim->divideLabor();
1652	>	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1653	>	globalGroupIndex = mpiSim->getGlobalGroupIndex();
1654	>	//globalMolIndex = mpiSim->getGlobalMolIndex();
1655
1656		// set up the local variables
1657
#	Line 1252 \| Line 1664 \| void SimSetup::mpiMolDivide(void){
1664		local_bonds = 0;
1665		local_bends = 0;
1666		local_torsions = 0;
1667	<	globalAtomIndex = 0;
1667	>	local_rigid = 0;
1668	>	local_groups = 0;
1669	>	globalAtomCounter = 0;
1670
1257	–
1671		for (i = 0; i < n_components; i++){
1672		for (j = 0; j < components_nmol[i]; j++){
1673		if (mol2proc[allMol] == worldRank){
#	Line 1262 \| Line 1675 \| void SimSetup::mpiMolDivide(void){
1675		local_bonds += comp_stamps[i]->getNBonds();
1676		local_bends += comp_stamps[i]->getNBends();
1677		local_torsions += comp_stamps[i]->getNTorsions();
1678	+	local_rigid += comp_stamps[i]->getNRigidBodies();
1679	+
1680	+	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1681	+	atomsingroups = 0;
1682	+	for (k=0; k < ncutgroups; k++) {
1683	+	cg = comp_stamps[i]->getCutoffGroup(k);
1684	+	atomsingroups += cg->getNMembers();
1685	+	}
1686	+	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups +
1687	+	ncutgroups;
1688	+	local_groups += ngroupsinstamp;
1689	+
1690		localMol++;
1691		}
1692		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1693	<	info[0].molMembershipArray[globalAtomIndex] = allMol;
1694	<	globalAtomIndex++;
1693	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1694	>	globalAtomCounter++;
1695		}
1696
1697		allMol++;
#	Line 1274 \| Line 1699 \| void SimSetup::mpiMolDivide(void){
1699		}
1700		local_SRI = local_bonds + local_bends + local_torsions;
1701
1702	<	info[0].n_atoms = mpiSim->getMyNlocal();
1703	<
1702	>	info[0].n_atoms = mpiSim->getNAtomsLocal();
1703	>
1704		if (local_atoms != info[0].n_atoms){
1705		sprintf(painCave.errMsg,
1706		"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
#	Line 1285 \| Line 1710 \| void SimSetup::mpiMolDivide(void){
1710		simError();
1711		}
1712
1713	+	info[0].ngroup = mpiSim->getNGroupsLocal();
1714	+	if (local_groups != info[0].ngroup){
1715	+	sprintf(painCave.errMsg,
1716	+	"SimSetup error: mpiSim's localGroups (%d) and SimSetup's\n"
1717	+	"\tlocalGroups (%d) are not equal.\n",
1718	+	info[0].ngroup, local_groups);
1719	+	painCave.isFatal = 1;
1720	+	simError();
1721	+	}
1722	+
1723		info[0].n_bonds = local_bonds;
1724		info[0].n_bends = local_bends;
1725		info[0].n_torsions = local_torsions;
#	Line 1307 \| Line 1742 \| void SimSetup::makeSysArrays(void){
1742
1743		Atom** the_atoms;
1744		Molecule* the_molecules;
1310	–	Exclude** the_excludes;
1745
1312	–
1746		for (l = 0; l < nInfo; l++){
1747		// create the atom and short range interaction arrays
1748
#	Line 1323 \| Line 1756 \| void SimSetup::makeSysArrays(void){
1756
1757
1758		molIndex = 0;
1759	<	for (i = 0; i < mpiSim->getTotNmol(); i++){
1759	>	for (i = 0; i < mpiSim->getNMolGlobal(); i++){
1760		if (mol2proc[i] == worldRank){
1761		the_molecules[molIndex].setStampID(molCompType[i]);
1762		the_molecules[molIndex].setMyIndex(molIndex);
#	Line 1335 \| Line 1768 \| void SimSetup::makeSysArrays(void){
1768		#else // is_mpi
1769
1770		molIndex = 0;
1771	<	globalAtomIndex = 0;
1771	>	globalAtomCounter = 0;
1772		for (i = 0; i < n_components; i++){
1773		for (j = 0; j < components_nmol[i]; j++){
1774		the_molecules[molIndex].setStampID(i);
1775		the_molecules[molIndex].setMyIndex(molIndex);
1776		the_molecules[molIndex].setGlobalIndex(molIndex);
1777		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1778	<	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1779	<	globalAtomIndex++;
1778	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1779	>	globalAtomCounter++;
1780		}
1781		molIndex++;
1782		}
#	Line 1352 \| Line 1785 \| void SimSetup::makeSysArrays(void){
1785
1786		#endif // is_mpi
1787
1788	<
1789	<	if (info[l].n_SRI){
1790	<	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	<
1788	>	info[l].globalExcludes = new int;
1789	>	info[l].globalExcludes[0] = 0;
1790	>
1791		// set the arrays into the SimInfo object
1792
1793		info[l].atoms = the_atoms;
1794		info[l].molecules = the_molecules;
1795		info[l].nGlobalExcludes = 0;
1796	<	info[l].excludes = the_excludes;
1381	<
1796	>
1797		the_ff->setSimInfo(info);
1798		}
1799		}
#	Line 1650 \| Line 2065 \| void SimSetup::setupZConstraint(SimInfo& theInfo){
2065		}
2066
2067		theInfo.addProperty(zconsForcePolicy);
2068	+
2069	+	//set zcons gap
2070	+	DoubleData* zconsGap = new DoubleData();
2071	+	zconsGap->setID(ZCONSGAP_ID);
2072	+
2073	+	if (globals->haveZConsGap()){
2074	+	zconsGap->setData(globals->getZconsGap());
2075	+	theInfo.addProperty(zconsGap);
2076	+	}
2077	+
2078	+	//set zcons fixtime
2079	+	DoubleData* zconsFixtime = new DoubleData();
2080	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
2081	+
2082	+	if (globals->haveZConsFixTime()){
2083	+	zconsFixtime->setData(globals->getZconsFixtime());
2084	+	theInfo.addProperty(zconsFixtime);
2085	+	}
2086	+
2087	+	//set zconsUsingSMD
2088	+	IntData* zconsUsingSMD = new IntData();
2089	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
2090
2091	+	if (globals->haveZConsUsingSMD()){
2092	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
2093	+	theInfo.addProperty(zconsUsingSMD);
2094	+	}
2095	+
2096		//Determine the name of ouput file and add it into SimInfo's property list
2097		//Be careful, do not use inFileName, since it is a pointer which
2098		//point to a string at master node, and slave nodes do not contain that string
#	Line 1680 \| Line 2122 \| void SimSetup::setupZConstraint(SimInfo& theInfo){
2122		tempParaItem.zPos = zconStamp[i]->getZpos();
2123		tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
2124		tempParaItem.kRatio = zconStamp[i]->getKratio();
2125	<
2125	>	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
2126	>	tempParaItem.cantVel = zconStamp[i]->getCantVel();
2127		zconsParaData->addItem(tempParaItem);
2128		}
2129
#	Line 1698 \| Line 2141 \| void SimSetup::setupZConstraint(SimInfo& theInfo){
2141		//push data into siminfo, therefore, we can retrieve later
2142		theInfo.addProperty(zconsParaData);
2143		}
2144	+
2145	+	void SimSetup::makeMinimizer(){
2146	+
2147	+	OOPSEMinimizer* myOOPSEMinimizer;
2148	+	MinimizerParameterSet* param;
2149	+	char minimizerName[100];
2150	+
2151	+	for (int i = 0; i < nInfo; i++){
2152	+
2153	+	//prepare parameter set for minimizer
2154	+	param = new MinimizerParameterSet();
2155	+	param->setDefaultParameter();
2156	+
2157	+	if (globals->haveMinimizer()){
2158	+	param->setFTol(globals->getMinFTol());
2159	+	}
2160	+
2161	+	if (globals->haveMinGTol()){
2162	+	param->setGTol(globals->getMinGTol());
2163	+	}
2164	+
2165	+	if (globals->haveMinMaxIter()){
2166	+	param->setMaxIteration(globals->getMinMaxIter());
2167	+	}
2168	+
2169	+	if (globals->haveMinWriteFrq()){
2170	+	param->setMaxIteration(globals->getMinMaxIter());
2171	+	}
2172	+
2173	+	if (globals->haveMinWriteFrq()){
2174	+	param->setWriteFrq(globals->getMinWriteFrq());
2175	+	}
2176	+
2177	+	if (globals->haveMinStepSize()){
2178	+	param->setStepSize(globals->getMinStepSize());
2179	+	}
2180	+
2181	+	if (globals->haveMinLSMaxIter()){
2182	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
2183	+	}
2184	+
2185	+	if (globals->haveMinLSTol()){
2186	+	param->setLineSearchTol(globals->getMinLSTol());
2187	+	}
2188	+
2189	+	strcpy(minimizerName, globals->getMinimizer());
2190	+
2191	+	if (!strcasecmp(minimizerName, "CG")){
2192	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2193	+	}
2194	+	else if (!strcasecmp(minimizerName, "SD")){
2195	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
2196	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
2197	+	}
2198	+	else{
2199	+	sprintf(painCave.errMsg,
2200	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
2201	+	painCave.isFatal = 0;
2202	+	simError();
2203	+
2204	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2205	+	}
2206	+	info[i].the_integrator = myOOPSEMinimizer;
2207	+
2208	+	//store the minimizer into simInfo
2209	+	info[i].the_minimizer = myOOPSEMinimizer;
2210	+	info[i].has_minimizer = true;
2211	+	}
2212	+
2213	+	}

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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents): Revision 984 by gezelter, Mon Jan 26 21:52:56 2004 UTC vs. Revision 1229 by gezelter, Thu Jun 3 20:02:25 2004 UTC

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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 984 by gezelter, Mon Jan 26 21:52:56 2004 UTC vs.
Revision 1229 by gezelter, Thu Jun 3 20:02:25 2004 UTC