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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 962 by tim, Mon Jan 19 18:36:21 2004 UTC vs.
Revision 1234 by tim, Fri Jun 4 03:15:31 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	+	#include "ConstraintManager.hpp"
17
18		#ifdef IS_MPI
19		#include "mpiBASS.h"
#	Line 24 | Line 29
29		#define NPTxyz_ENS     4
30
31
32	<	#define FF_DUFF 0
33	<	#define FF_LJ   1
34	<	#define FF_EAM  2
32	>	#define FF_DUFF  0
33	>	#define FF_LJ    1
34	>	#define FF_EAM   2
35	>	#define FF_H2O   3
36
37		using namespace std;
38
#	Line 143 | Line 149 | void SimSetup::createSim(void){
149		// make the output filenames
150
151		makeOutNames();
152	<
147	<	// make the integrator
148	<
149	<	makeIntegrator();
150	<
152	>
153		#ifdef IS_MPI
154		mpiSim->mpiRefresh();
155		#endif
#	Line 155 | Line 157 | void SimSetup::createSim(void){
157		// initialize the Fortran
158
159		initFortran();
160	+
161	+	//creat constraint manager
162	+	for(int i = 0; i < nInfo; i++)
163	+	info[i].consMan = new ConstraintManager(&info[i]);
164	+
165	+	if (globals->haveMinimizer())
166	+	// make minimizer
167	+	makeMinimizer();
168	+	else
169	+	// make the integrator
170	+	makeIntegrator();
171	+
172		}
173
174
175		void SimSetup::makeMolecules(void){
176	<	int k;
177	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
176	>	int i, j, k;
177	>	int exI, exJ, exK, exL, slI, slJ;
178	>	int tempI, tempJ, tempK, tempL;
179	>	int molI, globalID;
180	>	int stampID, atomOffset, rbOffset, groupOffset;
181		molInit molInfo;
182		DirectionalAtom* dAtom;
183	+	RigidBody* myRB;
184	+	StuntDouble* mySD;
185		LinkedAssign* extras;
186		LinkedAssign* current_extra;
187		AtomStamp* currentAtom;
188		BondStamp* currentBond;
189		BendStamp* currentBend;
190		TorsionStamp* currentTorsion;
191	+	RigidBodyStamp* currentRigidBody;
192	+	CutoffGroupStamp* currentCutoffGroup;
193	+	CutoffGroup* myCutoffGroup;
194	+	int nCutoffGroups;// number of cutoff group of a molecule defined in mdl file
195	+	set<int> cutoffAtomSet; //atoms belong to  cutoffgroup defined at mdl file
196
197		bond_pair* theBonds;
198		bend_set* theBends;
199		torsion_set* theTorsions;
200
201	+	set<int> skipList;
202
203	+	double phi, theta, psi;
204	+	char* molName;
205	+	char rbName[100];
206	+
207	+	ConstraintPair* consPair; //constraint pair
208	+	ConstraintElement* consElement1;  //first element of constraint pair
209	+	ConstraintElement* consElement2;  //second element of constraint pair
210	+	int whichRigidBody;
211	+	int consAtomIndex;  //index of constraint atom in rigid body's atom array
212	+	vector<pair<int, int> > jointAtoms;
213	+	double bondLength2;
214		//init the forceField paramters
215
216		the_ff->readParams();
217
182	–
218		// init the atoms
219
220	<	double ux, uy, uz, u, uSqr;
220	>	int nMembers, nNew, rb1, rb2;
221
222		for (k = 0; k < nInfo; k++){
223		the_ff->setSimInfo(&(info[k]));
224
225	+	#ifdef IS_MPI
226	+	info[k].globalGroupMembership = new int[mpiSim->getNAtomsGlobal()];
227	+	for (i = 0; i < mpiSim->getNAtomsGlobal(); i++)
228	+	info[k].globalGroupMembership[i] = 0;
229	+	#else
230	+	info[k].globalGroupMembership = new int[info[k].n_atoms];
231	+	for (i = 0; i < info[k].n_atoms; i++)
232	+	info[k].globalGroupMembership[i] = 0;
233	+	#endif
234	+
235		atomOffset = 0;
236	<	excludeOffset = 0;
236	>	groupOffset = 0;
237	>
238		for (i = 0; i < info[k].n_mol; i++){
239		stampID = info[k].molecules[i].getStampID();
240	+	molName = comp_stamps[stampID]->getID();
241
242		molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
243		molInfo.nBonds = comp_stamps[stampID]->getNBonds();
244		molInfo.nBends = comp_stamps[stampID]->getNBends();
245		molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
246	<	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
246	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
247
248	+	nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups();
249	+
250		molInfo.myAtoms = &(info[k].atoms[atomOffset]);
202	–	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
203	–	molInfo.myBonds = new Bond * [molInfo.nBonds];
204	–	molInfo.myBends = new Bend * [molInfo.nBends];
205	–	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
251
252	+	if (molInfo.nBonds > 0)
253	+	molInfo.myBonds = new Bond*[molInfo.nBonds];
254	+	else
255	+	molInfo.myBonds = NULL;
256	+
257	+	if (molInfo.nBends > 0)
258	+	molInfo.myBends = new Bend*[molInfo.nBends];
259	+	else
260	+	molInfo.myBends = NULL;
261	+
262	+	if (molInfo.nTorsions > 0)
263	+	molInfo.myTorsions = new Torsion *[molInfo.nTorsions];
264	+	else
265	+	molInfo.myTorsions = NULL;
266	+
267		theBonds = new bond_pair[molInfo.nBonds];
268		theBends = new bend_set[molInfo.nBends];
269		theTorsions = new torsion_set[molInfo.nTorsions];
270	<
270	>
271		// make the Atoms
272
273		for (j = 0; j < molInfo.nAtoms; j++){
274		currentAtom = comp_stamps[stampID]->getAtom(j);
275	+
276		if (currentAtom->haveOrientation()){
277		dAtom = new DirectionalAtom((j + atomOffset),
278		info[k].getConfiguration());
279		info[k].n_oriented++;
280		molInfo.myAtoms[j] = dAtom;
281
282	<	ux = currentAtom->getOrntX();
283	<	uy = currentAtom->getOrntY();
284	<	uz = currentAtom->getOrntZ();
282	>	// Directional Atoms have standard unit vectors which are oriented
283	>	// in space using the three Euler angles.  We assume the standard
284	>	// unit vector was originally along the z axis below.
285
286	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
286	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
287	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
288	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
289
290	<	u = sqrt(uSqr);
291	<	ux = ux / u;
229	<	uy = uy / u;
230	<	uz = uz / u;
231	<
232	<	dAtom->setSUx(ux);
233	<	dAtom->setSUy(uy);
234	<	dAtom->setSUz(uz);
290	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
291	>
292		}
293		else{
237	–	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
238	–	info[k].getConfiguration());
239	–	}
240	–	molInfo.myAtoms[j]->setType(currentAtom->getType());
294
295	<	#ifdef IS_MPI
295	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
296
297	<	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
297	>	}
298
299	+	molInfo.myAtoms[j]->setType(currentAtom->getType());
300	+	#ifdef IS_MPI
301	+	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
302		#endif // is_mpi
303		}
304
#	Line 252 | Line 308 | void SimSetup::makeMolecules(void){
308		theBonds[j].a = currentBond->getA() + atomOffset;
309		theBonds[j].b = currentBond->getB() + atomOffset;
310
311	<	exI = theBonds[j].a;
312	<	exJ = theBonds[j].b;
311	>	tempI = theBonds[j].a;
312	>	tempJ = theBonds[j].b;
313
258	–	// exclude_I must always be the smaller of the pair
259	–	if (exI > exJ){
260	–	tempEx = exI;
261	–	exI = exJ;
262	–	exJ = tempEx;
263	–	}
314		#ifdef IS_MPI
315	<	tempEx = exI;
316	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
317	<	tempEx = exJ;
318	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
315	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
316	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
317	>	#else
318	>	exI = tempI + 1;
319	>	exJ = tempJ + 1;
320	>	#endif
321
322	<	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
271	<	#else  // isn't MPI
272	<
273	<	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
274	<	#endif  //is_mpi
322	>	info[k].excludes->addPair(exI, exJ);
323		}
276	–	excludeOffset += molInfo.nBonds;
324
325		//make the bends
326		for (j = 0; j < molInfo.nBends; j++){
#	Line 323 | Line 370 | void SimSetup::makeMolecules(void){
370		}
371		}
372
373	<	if (!theBends[j].isGhost){
374	<	exI = theBends[j].a;
375	<	exJ = theBends[j].c;
376	<	}
377	<	else{
331	<	exI = theBends[j].a;
332	<	exJ = theBends[j].b;
333	<	}
334	<
335	<	// exclude_I must always be the smaller of the pair
336	<	if (exI > exJ){
337	<	tempEx = exI;
338	<	exI = exJ;
339	<	exJ = tempEx;
340	<	}
373	>	if (theBends[j].isGhost) {
374	>
375	>	tempI = theBends[j].a;
376	>	tempJ = theBends[j].b;
377	>
378		#ifdef IS_MPI
379	<	tempEx = exI;
380	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
381	<	tempEx = exJ;
382	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
379	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
380	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
381	>	#else
382	>	exI = tempI + 1;
383	>	exJ = tempJ + 1;
384	>	#endif
385	>	info[k].excludes->addPair(exI, exJ);
386
387	<	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
388	<	#else  // isn't MPI
389	<	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
390	<	#endif  //is_mpi
387	>	} else {
388	>
389	>	tempI = theBends[j].a;
390	>	tempJ = theBends[j].b;
391	>	tempK = theBends[j].c;
392	>
393	>	#ifdef IS_MPI
394	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
395	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
396	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
397	>	#else
398	>	exI = tempI + 1;
399	>	exJ = tempJ + 1;
400	>	exK = tempK + 1;
401	>	#endif
402	>
403	>	info[k].excludes->addPair(exI, exK);
404	>	info[k].excludes->addPair(exI, exJ);
405	>	info[k].excludes->addPair(exJ, exK);
406	>	}
407		}
352	–	excludeOffset += molInfo.nBends;
408
409		for (j = 0; j < molInfo.nTorsions; j++){
410		currentTorsion = comp_stamps[stampID]->getTorsion(j);
#	Line 358 | Line 413 | void SimSetup::makeMolecules(void){
413		theTorsions[j].c = currentTorsion->getC() + atomOffset;
414		theTorsions[j].d = currentTorsion->getD() + atomOffset;
415
416	<	exI = theTorsions[j].a;
417	<	exJ = theTorsions[j].d;
416	>	tempI = theTorsions[j].a;
417	>	tempJ = theTorsions[j].b;
418	>	tempK = theTorsions[j].c;
419	>	tempL = theTorsions[j].d;
420
364	–	// exclude_I must always be the smaller of the pair
365	–	if (exI > exJ){
366	–	tempEx = exI;
367	–	exI = exJ;
368	–	exJ = tempEx;
369	–	}
421		#ifdef IS_MPI
422	<	tempEx = exI;
423	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
424	<	tempEx = exJ;
425	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
422	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
423	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
424	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
425	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
426	>	#else
427	>	exI = tempI + 1;
428	>	exJ = tempJ + 1;
429	>	exK = tempK + 1;
430	>	exL = tempL + 1;
431	>	#endif
432
433	<	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
434	<	#else  // isn't MPI
435	<	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
436	<	#endif  //is_mpi
433	>	info[k].excludes->addPair(exI, exJ);
434	>	info[k].excludes->addPair(exI, exK);
435	>	info[k].excludes->addPair(exI, exL);
436	>	info[k].excludes->addPair(exJ, exK);
437	>	info[k].excludes->addPair(exJ, exL);
438	>	info[k].excludes->addPair(exK, exL);
439		}
381	–	excludeOffset += molInfo.nTorsions;
440
441	+
442	+	molInfo.myRigidBodies.clear();
443	+
444	+	for (j = 0; j < molInfo.nRigidBodies; j++){
445
446	<	// send the arrays off to the forceField for init.
446	>	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
447	>	nMembers = currentRigidBody->getNMembers();
448	>
449	>	// Create the Rigid Body:
450	>
451	>	myRB = new RigidBody();
452	>
453	>	sprintf(rbName,"%s_RB_%d", molName, j);
454	>	myRB->setType(rbName);
455	>
456	>	for (rb1 = 0; rb1 < nMembers; rb1++) {
457	>
458	>	// molI is atom numbering inside this molecule
459	>	molI = currentRigidBody->getMember(rb1);
460	>
461	>	// tempI is atom numbering on local processor
462	>	tempI = molI + atomOffset;
463	>
464	>	// currentAtom is the AtomStamp (which we need for
465	>	// rigid body reference positions)
466	>	currentAtom = comp_stamps[stampID]->getAtom(molI);
467	>
468	>	// When we add to the rigid body, add the atom itself and
469	>	// the stamp info:
470	>
471	>	myRB->addAtom(info[k].atoms[tempI], currentAtom);
472	>
473	>	// Add this atom to the Skip List for the integrators
474	>	#ifdef IS_MPI
475	>	slI = info[k].atoms[tempI]->getGlobalIndex();
476	>	#else
477	>	slI = tempI;
478	>	#endif
479	>	skipList.insert(slI);
480	>
481	>	}
482	>
483	>	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
484	>	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
485	>
486	>	tempI = currentRigidBody->getMember(rb1);
487	>	tempJ = currentRigidBody->getMember(rb2);
488	>
489	>	// Some explanation is required here.
490	>	// Fortran indexing starts at 1, while c indexing starts at 0
491	>	// Also, in parallel computations, the GlobalIndex is
492	>	// used for the exclude list:
493	>
494	>	#ifdef IS_MPI
495	>	exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
496	>	exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
497	>	#else
498	>	exI = molInfo.myAtoms[tempI]->getIndex() + 1;
499	>	exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
500	>	#endif
501	>
502	>	info[k].excludes->addPair(exI, exJ);
503	>
504	>	}
505	>	}
506	>
507	>	molInfo.myRigidBodies.push_back(myRB);
508	>	info[k].rigidBodies.push_back(myRB);
509	>	}
510	>
511	>
512	>	//create cutoff group for molecule
513	>
514	>	cutoffAtomSet.clear();
515	>	molInfo.myCutoffGroups.clear();
516	>
517	>	for (j = 0; j < nCutoffGroups; j++){
518	>
519	>	currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j);
520	>	nMembers = currentCutoffGroup->getNMembers();
521	>
522	>	myCutoffGroup = new CutoffGroup();
523	>
524	>	#ifdef IS_MPI
525	>	myCutoffGroup->setGlobalIndex(globalGroupIndex[groupOffset]);
526	>	#else
527	>	myCutoffGroup->setGlobalIndex(groupOffset);
528	>	#endif
529	>
530	>	for (int cg = 0; cg < nMembers; cg++) {
531	>
532	>	// molI is atom numbering inside this molecule
533	>	molI = currentCutoffGroup->getMember(cg);
534	>
535	>	// tempI is atom numbering on local processor
536	>	tempI = molI + atomOffset;
537	>
538	>	#ifdef IS_MPI
539	>	globalID = info[k].atoms[tempI]->getGlobalIndex();
540	>	info[k].globalGroupMembership[globalID] = globalGroupIndex[groupOffset];
541	>	#else
542	>	globalID = info[k].atoms[tempI]->getIndex();
543	>	info[k].globalGroupMembership[globalID] = groupOffset;
544	>	#endif
545	>	myCutoffGroup->addAtom(info[k].atoms[tempI]);
546	>	cutoffAtomSet.insert(tempI);
547	>	}
548	>
549	>	molInfo.myCutoffGroups.push_back(myCutoffGroup);
550	>	groupOffset++;
551	>
552	>	}//end for (j = 0; j < molInfo.nCutoffGroups; j++)
553	>
554	>
555	>	// create a cutoff group for every atom in current molecule which
556	>	// does not belong to cutoffgroup defined at mdl file
557	>
558	>	for(j = 0; j < molInfo.nAtoms; j++){
559	>
560	>	if(cutoffAtomSet.find(molInfo.myAtoms[j]->getIndex()) == cutoffAtomSet.end()){
561	>	myCutoffGroup = new CutoffGroup();
562	>	myCutoffGroup->addAtom(molInfo.myAtoms[j]);
563	>
564	>	#ifdef IS_MPI
565	>	myCutoffGroup->setGlobalIndex(globalGroupIndex[groupOffset]);
566	>	globalID = info[k].atoms[atomOffset + j]->getGlobalIndex();
567	>	info[k].globalGroupMembership[globalID] = globalGroupIndex[groupOffset];
568	>	#else
569	>	myCutoffGroup->setGlobalIndex(groupOffset);
570	>	globalID = info[k].atoms[atomOffset + j]->getIndex();
571	>	info[k].globalGroupMembership[globalID] = groupOffset;
572	>	#endif
573	>	molInfo.myCutoffGroups.push_back(myCutoffGroup);
574	>	groupOffset++;
575	>	}
576	>	}
577
578	+	// After this is all set up, scan through the atoms to
579	+	// see if they can be added to the integrableObjects:
580	+
581	+	molInfo.myIntegrableObjects.clear();
582	+
583	+
584	+	for (j = 0; j < molInfo.nAtoms; j++){
585	+
586	+	#ifdef IS_MPI
587	+	slJ = molInfo.myAtoms[j]->getGlobalIndex();
588	+	#else
589	+	slJ = j+atomOffset;
590	+	#endif
591	+
592	+	// if they aren't on the skip list, then they can be integrated
593	+
594	+	if (skipList.find(slJ) == skipList.end()) {
595	+	mySD = (StuntDouble *) molInfo.myAtoms[j];
596	+	info[k].integrableObjects.push_back(mySD);
597	+	molInfo.myIntegrableObjects.push_back(mySD);
598	+	}
599	+	}
600	+
601	+	// all rigid bodies are integrated:
602	+
603	+	for (j = 0; j < molInfo.nRigidBodies; j++) {
604	+	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
605	+	info[k].integrableObjects.push_back(mySD);
606	+	molInfo.myIntegrableObjects.push_back(mySD);
607	+	}
608	+
609	+	// send the arrays off to the forceField for init.
610	+
611		the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
612		the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
613		the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
#	Line 390 | Line 615 | void SimSetup::makeMolecules(void){
615		theTorsions);
616
617
618	<	info[k].molecules[i].initialize(molInfo);
618	>	//creat ConstraintPair.
619	>	molInfo.myConstraintPairs.clear();
620	>
621	>	for (j = 0; j < molInfo.nBonds; j++){
622	>
623	>	//if bond is constrained bond, add it into constraint pair
624	>	if(molInfo.myBonds[j]->is_constrained()){
625	>
626	>	//if both atoms are in the same rigid body, just skip it
627	>	currentBond = comp_stamps[stampID]->getBond(j);
628	>
629	>	if(!comp_stamps[stampID]->isBondInSameRigidBody(currentBond)){
630	>
631	>	tempI = currentBond->getA() + atomOffset;
632	>	if( comp_stamps[stampID]->isAtomInRigidBody(currentBond->getA(), whichRigidBody, consAtomIndex))
633	>	consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
634	>	else
635	>	consElement1 = new ConstraintAtom(info[k].atoms[tempI]);
636	>
637	>	tempJ =  currentBond->getB() + atomOffset;
638	>	if(comp_stamps[stampID]->isAtomInRigidBody(currentBond->getB(), whichRigidBody, consAtomIndex))
639	>	consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
640	>	else
641	>	consElement2 = new ConstraintAtom(info[k].atoms[tempJ]);
642	>
643	>	bondLength2 = molInfo.myBonds[j]->get_constraint()->get_dsqr();
644	>	consPair = new DistanceConstraintPair(consElement1, consElement2, bondLength2);
645
646	+	molInfo.myConstraintPairs.push_back(consPair);
647	+	}
648	+	}//end if(molInfo.myBonds[j]->is_constrained())
649	+	}
650	+
651	+	//loop over rigid bodies, if two rigid bodies share same joint, creat a JointConstraintPair
652	+	for (int rb1 = 0; rb1 < molInfo.nRigidBodies -1 ; rb1++){
653	+	for (int rb2 = rb1 + 1; rb2 < molInfo.nRigidBodies ; rb2++){
654	+
655	+	jointAtoms = comp_stamps[stampID]->getJointAtoms(rb1, rb2);
656
657	+	for(size_t m = 0; m < jointAtoms.size(); m++){
658	+	consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[rb1], jointAtoms[m].first);
659	+	consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[rb2], jointAtoms[m].second);
660	+
661	+	consPair = new JointConstraintPair(consElement1, consElement2);
662	+	molInfo.myConstraintPairs.push_back(consPair);
663	+	}
664	+
665	+	}
666	+	}
667	+
668	+
669	+	info[k].molecules[i].initialize(molInfo);
670	+
671	+
672		atomOffset += molInfo.nAtoms;
673		delete[] theBonds;
674		delete[] theBends;
675		delete[] theTorsions;
676		}
677	+
678	+
679	+
680	+	#ifdef IS_MPI
681	+	// Since the globalGroupMembership has been zero filled and we've only
682	+	// poked values into the atoms we know, we can do an Allreduce
683	+	// to get the full globalGroupMembership array (We think).
684	+	// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
685	+	// docs said we could.
686	+
687	+	int* ggMjunk = new int[mpiSim->getNAtomsGlobal()];
688	+
689	+	MPI_Allreduce(info[k].globalGroupMembership,
690	+	ggMjunk,
691	+	mpiSim->getNAtomsGlobal(),
692	+	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
693	+
694	+	for (i = 0; i < mpiSim->getNAtomsGlobal(); i++)
695	+	info[k].globalGroupMembership[i] = ggMjunk[i];
696	+
697	+	delete[] ggMjunk;
698	+
699	+	#endif
700	+
701	+
702	+
703		}
704
705		#ifdef IS_MPI
#	Line 405 | Line 707 | void SimSetup::makeMolecules(void){
707		MPIcheckPoint();
708		#endif // is_mpi
709
408	–	// clean up the forcefield
409	–
410	–	the_ff->calcRcut();
411	–	the_ff->cleanMe();
710		}
711
712		void SimSetup::initFromBass(void){
#	Line 609 | Line 907 | void SimSetup::gatherInfo(void){
907		else if (!strcasecmp(force_field, "EAM")){
908		ffCase = FF_EAM;
909		}
910	+	else if (!strcasecmp(force_field, "WATER")){
911	+	ffCase = FF_H2O;
912	+	}
913		else{
914		sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
915		force_field);
#	Line 637 | Line 938 | void SimSetup::gatherInfo(void){
938		}
939		else{
940		sprintf(painCave.errMsg,
941	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
942	<	"reverting to NVE for this simulation.\n",
941	>	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
942	>	"\treverting to NVE for this simulation.\n",
943		ensemble);
944		painCave.isFatal = 0;
945		simError();
#	Line 670 | Line 971 | void SimSetup::gatherInfo(void){
971		if (!the_components[i]->haveNMol()){
972		// we have a problem
973		sprintf(painCave.errMsg,
974	<	"SimSetup Error. No global NMol or component NMol"
975	<	" given. Cannot calculate the number of atoms.\n");
974	>	"SimSetup Error. No global NMol or component NMol given.\n"
975	>	"\tCannot calculate the number of atoms.\n");
976		painCave.isFatal = 1;
977		simError();
978		}
#	Line 692 | Line 993 | void SimSetup::gatherInfo(void){
993		}
994
995		//check whether sample time, status time, thermal time and reset time are divisble by dt
996	<	if (!isDivisible(globals->getSampleTime(), globals->getDt())){
996	>	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
997		sprintf(painCave.errMsg,
998	<	"Sample time is not divisible by dt \n");
998	>	"Sample time is not divisible by dt.\n"
999	>	"\tThis will result in samples that are not uniformly\n"
1000	>	"\tdistributed in time.  If this is a problem, change\n"
1001	>	"\tyour sampleTime variable.\n");
1002		painCave.isFatal = 0;
1003		simError();
1004		}
1005
1006	<	if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
1006	>	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
1007		sprintf(painCave.errMsg,
1008	<	"Status time is not divisible by dt\n");
1008	>	"Status time is not divisible by dt.\n"
1009	>	"\tThis will result in status reports that are not uniformly\n"
1010	>	"\tdistributed in time.  If this is a problem, change \n"
1011	>	"\tyour statusTime variable.\n");
1012		painCave.isFatal = 0;
1013		simError();
1014		}
1015
1016		if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
1017		sprintf(painCave.errMsg,
1018	<	"Thermal time is not divisible by dt\n");
1018	>	"Thermal time is not divisible by dt.\n"
1019	>	"\tThis will result in thermalizations that are not uniformly\n"
1020	>	"\tdistributed in time.  If this is a problem, change \n"
1021	>	"\tyour thermalTime variable.\n");
1022		painCave.isFatal = 0;
1023		simError();
1024		}
1025
1026		if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
1027		sprintf(painCave.errMsg,
1028	<	"Reset time is not divisible by dt\n");
1028	>	"Reset time is not divisible by dt.\n"
1029	>	"\tThis will result in integrator resets that are not uniformly\n"
1030	>	"\tdistributed in time.  If this is a problem, change\n"
1031	>	"\tyour resetTime variable.\n");
1032		painCave.isFatal = 0;
1033		simError();
1034		}
#	Line 726 | Line 1039 | void SimSetup::gatherInfo(void){
1039		if (globals->haveSampleTime()){
1040		info[i].sampleTime = globals->getSampleTime();
1041		info[i].statusTime = info[i].sampleTime;
729	–	info[i].thermalTime = info[i].sampleTime;
1042		}
1043		else{
1044		info[i].sampleTime = globals->getRunTime();
1045		info[i].statusTime = info[i].sampleTime;
734	–	info[i].thermalTime = info[i].sampleTime;
1046		}
1047
1048		if (globals->haveStatusTime()){
#	Line 740 | Line 1051 | void SimSetup::gatherInfo(void){
1051
1052		if (globals->haveThermalTime()){
1053		info[i].thermalTime = globals->getThermalTime();
1054	+	} else {
1055	+	info[i].thermalTime = globals->getRunTime();
1056		}
1057
1058		info[i].resetIntegrator = 0;
#	Line 757 | Line 1070 | void SimSetup::gatherInfo(void){
1070
1071		info[i].useInitXSstate = globals->getUseInitXSstate();
1072		info[i].orthoTolerance = globals->getOrthoBoxTolerance();
1073	<
1073	>
1074	>	// check for thermodynamic integration
1075	>	if (globals->getUseSolidThermInt() && !globals->getUseLiquidThermInt()) {
1076	>	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1077	>	info[i].useSolidThermInt = globals->getUseSolidThermInt();
1078	>	info[i].thermIntLambda = globals->getThermIntLambda();
1079	>	info[i].thermIntK = globals->getThermIntK();
1080	>
1081	>	Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK);
1082	>	info[i].restraint = myRestraint;
1083	>	}
1084	>	else {
1085	>	sprintf(painCave.errMsg,
1086	>	"SimSetup Error:\n"
1087	>	"\tKeyword useSolidThermInt was set to 'true' but\n"
1088	>	"\tthermodynamicIntegrationLambda (and/or\n"
1089	>	"\tthermodynamicIntegrationK) was not specified.\n"
1090	>	"\tPlease provide a lambda value and k value in your .bass file.\n");
1091	>	painCave.isFatal = 1;
1092	>	simError();
1093	>	}
1094	>	}
1095	>	else if(globals->getUseLiquidThermInt()) {
1096	>	if (globals->getUseSolidThermInt()) {
1097	>	sprintf( painCave.errMsg,
1098	>	"SimSetup Warning: It appears that you have both solid and\n"
1099	>	"\tliquid thermodynamic integration activated in your .bass\n"
1100	>	"\tfile. To avoid confusion, specify only one technique in\n"
1101	>	"\tyour .bass file. Liquid-state thermodynamic integration\n"
1102	>	"\twill be assumed for the current simulation. If this is not\n"
1103	>	"\twhat you desire, set useSolidThermInt to 'true' and\n"
1104	>	"\tuseLiquidThermInt to 'false' in your .bass file.\n");
1105	>	painCave.isFatal = 0;
1106	>	simError();
1107	>	}
1108	>	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1109	>	info[i].useLiquidThermInt = globals->getUseLiquidThermInt();
1110	>	info[i].thermIntLambda = globals->getThermIntLambda();
1111	>	info[i].thermIntK = globals->getThermIntK();
1112	>	}
1113	>	else {
1114	>	sprintf(painCave.errMsg,
1115	>	"SimSetup Error:\n"
1116	>	"\tKeyword useLiquidThermInt was set to 'true' but\n"
1117	>	"\tthermodynamicIntegrationLambda (and/or\n"
1118	>	"\tthermodynamicIntegrationK) was not specified.\n"
1119	>	"\tPlease provide a lambda value and k value in your .bass file.\n");
1120	>	painCave.isFatal = 1;
1121	>	simError();
1122	>	}
1123	>	}
1124	>	else if(globals->haveThermIntLambda() || globals->haveThermIntK()){
1125	>	sprintf(painCave.errMsg,
1126	>	"SimSetup Warning: If you want to use Thermodynamic\n"
1127	>	"\tIntegration, set useSolidThermInt or useLiquidThermInt to\n"
1128	>	"\t'true' in your .bass file.  These keywords are set to\n"
1129	>	"\t'false' by default, so your lambda and/or k values are\n"
1130	>	"\tbeing ignored.\n");
1131	>	painCave.isFatal = 0;
1132	>	simError();
1133	>	}
1134		}
1135
1136		//setup seed for random number generator
#	Line 799 | Line 1172 | void SimSetup::gatherInfo(void){
1172		for (int i = 0; i < nInfo; i++){
1173		info[i].setSeed(seedValue);
1174		}
1175	<
1175	>
1176		#ifdef IS_MPI
1177	<	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
1177	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
1178		MPIcheckPoint();
1179		#endif // is_mpi
1180		}
#	Line 810 | Line 1183 | void SimSetup::finalInfoCheck(void){
1183		void SimSetup::finalInfoCheck(void){
1184		int index;
1185		int usesDipoles;
1186	+	int usesCharges;
1187		int i;
1188
1189		for (i = 0; i < nInfo; i++){
#	Line 821 | Line 1195 | void SimSetup::finalInfoCheck(void){
1195		usesDipoles = (info[i].atoms[index])->hasDipole();
1196		index++;
1197		}
1198	<
1198	>	index = 0;
1199	>	usesCharges = 0;
1200	>	while ((index < info[i].n_atoms) && !usesCharges){
1201	>	usesCharges= (info[i].atoms[index])->hasCharge();
1202	>	index++;
1203	>	}
1204		#ifdef IS_MPI
1205		int myUse = usesDipoles;
1206		MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1207		#endif //is_mpi
1208
1209	<	double theEcr, theEst;
1209	>	double theRcut, theRsw;
1210
1211	<	if (globals->getUseRF()){
1212	<	info[i].useReactionField = 1;
1211	>	if (globals->haveRcut()) {
1212	>	theRcut = globals->getRcut();
1213
1214	<	if (!globals->haveECR()){
1214	>	if (globals->haveRsw())
1215	>	theRsw = globals->getRsw();
1216	>	else
1217	>	theRsw = theRcut;
1218	>
1219	>	info[i].setDefaultRcut(theRcut, theRsw);
1220	>
1221	>	} else {
1222	>
1223	>	the_ff->calcRcut();
1224	>	theRcut = info[i].getRcut();
1225	>
1226	>	if (globals->haveRsw())
1227	>	theRsw = globals->getRsw();
1228	>	else
1229	>	theRsw = theRcut;
1230	>
1231	>	info[i].setDefaultRcut(theRcut, theRsw);
1232	>	}
1233	>
1234	>	if (globals->getUseRF()){
1235	>	info[i].useReactionField = 1;
1236	>
1237	>	if (!globals->haveRcut()){
1238		sprintf(painCave.errMsg,
1239	<	"SimSetup Warning: using default value of 15.0 angstroms"
1240	<	"box length for the electrostaticCutoffRadius.\n");
1239	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1240	>	"\tOOPSE will use a default value of 15.0 angstroms"
1241	>	"\tfor the cutoffRadius.\n");
1242		painCave.isFatal = 0;
1243		simError();
1244	<	theEcr = 15.0;
1244	>	theRcut = 15.0;
1245		}
1246		else{
1247	<	theEcr = globals->getECR();
1247	>	theRcut = globals->getRcut();
1248		}
1249
1250	<	if (!globals->haveEST()){
1250	>	if (!globals->haveRsw()){
1251		sprintf(painCave.errMsg,
1252	<	"SimSetup Warning: using default value of 0.05 * the "
1253	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
1252	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1253	>	"\tOOPSE will use a default value of\n"
1254	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1255		painCave.isFatal = 0;
1256		simError();
1257	<	theEst = 0.05 * theEcr;
1257	>	theRsw = 0.95 * theRcut;
1258		}
1259		else{
1260	<	theEst = globals->getEST();
1260	>	theRsw = globals->getRsw();
1261		}
1262
1263	<	info[i].setDefaultEcr(theEcr, theEst);
1263	>	info[i].setDefaultRcut(theRcut, theRsw);
1264
1265		if (!globals->haveDielectric()){
1266		sprintf(painCave.errMsg,
1267	<	"SimSetup Error: You are trying to use Reaction Field without"
1268	<	"setting a dielectric constant!\n");
1267	>	"SimSetup Error: No Dielectric constant was set.\n"
1268	>	"\tYou are trying to use Reaction Field without"
1269	>	"\tsetting a dielectric constant!\n");
1270		painCave.isFatal = 1;
1271		simError();
1272		}
1273		info[i].dielectric = globals->getDielectric();
1274		}
1275		else{
1276	<	if (usesDipoles){
1277	<	if (!globals->haveECR()){
1276	>	if (usesDipoles || usesCharges){
1277	>
1278	>	if (!globals->haveRcut()){
1279		sprintf(painCave.errMsg,
1280	<	"SimSetup Warning: using default value of 15.0 angstroms"
1281	<	"box length for the electrostaticCutoffRadius.\n");
1282	<	painCave.isFatal = 0;
1283	<	simError();
1284	<	theEcr = 15.0;
1285	<	}
1280	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1281	>	"\tOOPSE will use a default value of 15.0 angstroms"
1282	>	"\tfor the cutoffRadius.\n");
1283	>	painCave.isFatal = 0;
1284	>	simError();
1285	>	theRcut = 15.0;
1286	>	}
1287		else{
1288	<	theEcr = globals->getECR();
1288	>	theRcut = globals->getRcut();
1289		}
1290	<
1291	<	if (!globals->haveEST()){
1290	>
1291	>	if (!globals->haveRsw()){
1292		sprintf(painCave.errMsg,
1293	<	"SimSetup Warning: using default value of 0.05 * the "
1294	<	"electrostaticCutoffRadius for the "
1295	<	"electrostaticSkinThickness\n");
1293	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1294	>	"\tOOPSE will use a default value of\n"
1295	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1296		painCave.isFatal = 0;
1297		simError();
1298	<	theEst = 0.05 * theEcr;
1298	>	theRsw = 0.95 * theRcut;
1299		}
1300		else{
1301	<	theEst = globals->getEST();
1301	>	theRsw = globals->getRsw();
1302		}
1303	+
1304	+	info[i].setDefaultRcut(theRcut, theRsw);
1305
897	–	info[i].setDefaultEcr(theEcr, theEst);
1306		}
1307		}
1308		}
#	Line 902 | Line 1310 | void SimSetup::finalInfoCheck(void){
1310		strcpy(checkPointMsg, "post processing checks out");
1311		MPIcheckPoint();
1312		#endif // is_mpi
1313	+
1314	+	// clean up the forcefield
1315	+	the_ff->cleanMe();
1316		}
1317
1318		void SimSetup::initSystemCoords(void){
#	Line 1032 | Line 1443 | void SimSetup::makeOutNames(void){
1443		}
1444		}
1445
1446	+	strcpy(info[k].rawPotName, inFileName);
1447	+	nameLength = strlen(info[k].rawPotName);
1448	+	endTest = &(info[k].rawPotName[nameLength - 5]);
1449	+	if (!strcmp(endTest, ".bass")){
1450	+	strcpy(endTest, ".raw");
1451	+	}
1452	+	else if (!strcmp(endTest, ".BASS")){
1453	+	strcpy(endTest, ".raw");
1454	+	}
1455	+	else{
1456	+	endTest = &(info[k].rawPotName[nameLength - 4]);
1457	+	if (!strcmp(endTest, ".bss")){
1458	+	strcpy(endTest, ".raw");
1459	+	}
1460	+	else if (!strcmp(endTest, ".mdl")){
1461	+	strcpy(endTest, ".raw");
1462	+	}
1463	+	else{
1464	+	strcat(info[k].rawPotName, ".raw");
1465	+	}
1466	+	}
1467	+
1468		#ifdef IS_MPI
1469
1470		}
#	Line 1092 | Line 1525 | void SimSetup::createFF(void){
1525		the_ff = new EAM_FF();
1526		break;
1527
1528	+	case FF_H2O:
1529	+	the_ff = new WATER();
1530	+	break;
1531	+
1532		default:
1533		sprintf(painCave.errMsg,
1534		"SimSetup Error. Unrecognized force field in case statement.\n");
#	Line 1112 | Line 1549 | void SimSetup::compList(void){
1549		LinkedMolStamp* headStamp = new LinkedMolStamp();
1550		LinkedMolStamp* currentStamp = NULL;
1551		comp_stamps = new MoleculeStamp * [n_components];
1552	+	bool haveCutoffGroups;
1553
1554	+	haveCutoffGroups = false;
1555	+
1556		// make an array of molecule stamps that match the components used.
1557		// also extract the used stamps out into a separate linked list
1558
#	Line 1147 | Line 1587 | void SimSetup::compList(void){
1587		headStamp->add(currentStamp);
1588		comp_stamps[i] = headStamp->match(id);
1589		}
1590	+
1591	+	if(comp_stamps[i]->getNCutoffGroups() > 0)
1592	+	haveCutoffGroups = true;
1593		}
1594	+
1595	+	for (i = 0; i < nInfo; i++)
1596	+	info[i].haveCutoffGroups = haveCutoffGroups;
1597
1598		#ifdef IS_MPI
1599		strcpy(checkPointMsg, "Component stamps successfully extracted\n");
#	Line 1156 | Line 1602 | void SimSetup::calcSysValues(void){
1602		}
1603
1604		void SimSetup::calcSysValues(void){
1605	<	int i;
1605	>	int i, j;
1606	>	int ncutgroups, atomsingroups, ngroupsinstamp;
1607
1608		int* molMembershipArray;
1609	+	CutoffGroupStamp* cg;
1610
1611		tot_atoms = 0;
1612		tot_bonds = 0;
1613		tot_bends = 0;
1614		tot_torsions = 0;
1615	+	tot_rigid = 0;
1616	+	tot_groups = 0;
1617		for (i = 0; i < n_components; i++){
1618		tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1619		tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1620		tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1621		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1622	<	}
1622	>	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1623
1624	+	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1625	+	atomsingroups = 0;
1626	+	for (j=0; j < ncutgroups; j++) {
1627	+	cg = comp_stamps[i]->getCutoffGroup(j);
1628	+	atomsingroups += cg->getNMembers();
1629	+	}
1630	+	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups + ncutgroups;
1631	+	tot_groups += components_nmol[i] * ngroupsinstamp;
1632	+	}
1633	+
1634		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1635		molMembershipArray = new int[tot_atoms];
1636
#	Line 1181 | Line 1641 | void SimSetup::calcSysValues(void){
1641		info[i].n_torsions = tot_torsions;
1642		info[i].n_SRI = tot_SRI;
1643		info[i].n_mol = tot_nmol;
1644	<
1644	>	info[i].ngroup = tot_groups;
1645		info[i].molMembershipArray = molMembershipArray;
1646		}
1647		}
#	Line 1192 | Line 1652 | void SimSetup::mpiMolDivide(void){
1652		int i, j, k;
1653		int localMol, allMol;
1654		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1655	+	int local_rigid, local_groups;
1656	+	vector<int> globalMolIndex;
1657	+	int ncutgroups, atomsingroups, ngroupsinstamp;
1658	+	CutoffGroupStamp* cg;
1659
1660		mpiSim = new mpiSimulation(info);
1661
1662	<	globalIndex = mpiSim->divideLabor();
1662	>	mpiSim->divideLabor();
1663	>	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1664	>	globalGroupIndex = mpiSim->getGlobalGroupIndex();
1665	>	//globalMolIndex = mpiSim->getGlobalMolIndex();
1666
1667		// set up the local variables
1668
#	Line 1208 | Line 1675 | void SimSetup::mpiMolDivide(void){
1675		local_bonds = 0;
1676		local_bends = 0;
1677		local_torsions = 0;
1678	<	globalAtomIndex = 0;
1678	>	local_rigid = 0;
1679	>	local_groups = 0;
1680	>	globalAtomCounter = 0;
1681
1213	–
1682		for (i = 0; i < n_components; i++){
1683		for (j = 0; j < components_nmol[i]; j++){
1684		if (mol2proc[allMol] == worldRank){
#	Line 1218 | Line 1686 | void SimSetup::mpiMolDivide(void){
1686		local_bonds += comp_stamps[i]->getNBonds();
1687		local_bends += comp_stamps[i]->getNBends();
1688		local_torsions += comp_stamps[i]->getNTorsions();
1689	+	local_rigid += comp_stamps[i]->getNRigidBodies();
1690	+
1691	+	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1692	+	atomsingroups = 0;
1693	+	for (k=0; k < ncutgroups; k++) {
1694	+	cg = comp_stamps[i]->getCutoffGroup(k);
1695	+	atomsingroups += cg->getNMembers();
1696	+	}
1697	+	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups +
1698	+	ncutgroups;
1699	+	local_groups += ngroupsinstamp;
1700	+
1701		localMol++;
1702		}
1703		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1704	<	info[0].molMembershipArray[globalAtomIndex] = allMol;
1705	<	globalAtomIndex++;
1704	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1705	>	globalAtomCounter++;
1706		}
1707
1708		allMol++;
#	Line 1230 | Line 1710 | void SimSetup::mpiMolDivide(void){
1710		}
1711		local_SRI = local_bonds + local_bends + local_torsions;
1712
1713	<	info[0].n_atoms = mpiSim->getMyNlocal();
1714	<
1713	>	info[0].n_atoms = mpiSim->getNAtomsLocal();
1714	>
1715		if (local_atoms != info[0].n_atoms){
1716		sprintf(painCave.errMsg,
1717	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1718	<	" localAtom (%d) are not equal.\n",
1717	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1718	>	"\tlocalAtom (%d) are not equal.\n",
1719		info[0].n_atoms, local_atoms);
1720		painCave.isFatal = 1;
1721		simError();
1722		}
1723
1724	+	info[0].ngroup = mpiSim->getNGroupsLocal();
1725	+	if (local_groups != info[0].ngroup){
1726	+	sprintf(painCave.errMsg,
1727	+	"SimSetup error: mpiSim's localGroups (%d) and SimSetup's\n"
1728	+	"\tlocalGroups (%d) are not equal.\n",
1729	+	info[0].ngroup, local_groups);
1730	+	painCave.isFatal = 1;
1731	+	simError();
1732	+	}
1733	+
1734		info[0].n_bonds = local_bonds;
1735		info[0].n_bends = local_bends;
1736		info[0].n_torsions = local_torsions;
#	Line 1263 | Line 1753 | void SimSetup::makeSysArrays(void){
1753
1754		Atom** the_atoms;
1755		Molecule* the_molecules;
1266	–	Exclude** the_excludes;
1756
1268	–
1757		for (l = 0; l < nInfo; l++){
1758		// create the atom and short range interaction arrays
1759
#	Line 1279 | Line 1767 | void SimSetup::makeSysArrays(void){
1767
1768
1769		molIndex = 0;
1770	<	for (i = 0; i < mpiSim->getTotNmol(); i++){
1770	>	for (i = 0; i < mpiSim->getNMolGlobal(); i++){
1771		if (mol2proc[i] == worldRank){
1772		the_molecules[molIndex].setStampID(molCompType[i]);
1773		the_molecules[molIndex].setMyIndex(molIndex);
#	Line 1291 | Line 1779 | void SimSetup::makeSysArrays(void){
1779		#else // is_mpi
1780
1781		molIndex = 0;
1782	<	globalAtomIndex = 0;
1782	>	globalAtomCounter = 0;
1783		for (i = 0; i < n_components; i++){
1784		for (j = 0; j < components_nmol[i]; j++){
1785		the_molecules[molIndex].setStampID(i);
1786		the_molecules[molIndex].setMyIndex(molIndex);
1787		the_molecules[molIndex].setGlobalIndex(molIndex);
1788		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1789	<	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1790	<	globalAtomIndex++;
1789	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1790	>	globalAtomCounter++;
1791		}
1792		molIndex++;
1793		}
#	Line 1308 | Line 1796 | void SimSetup::makeSysArrays(void){
1796
1797		#endif // is_mpi
1798
1799	<
1800	<	if (info[l].n_SRI){
1801	<	Exclude::createArray(info[l].n_SRI);
1314	<	the_excludes = new Exclude * [info[l].n_SRI];
1315	<	for (int ex = 0; ex < info[l].n_SRI; ex++){
1316	<	the_excludes[ex] = new Exclude(ex);
1317	<	}
1318	<	info[l].globalExcludes = new int;
1319	<	info[l].n_exclude = info[l].n_SRI;
1320	<	}
1321	<	else{
1322	<	Exclude::createArray(1);
1323	<	the_excludes = new Exclude * ;
1324	<	the_excludes[0] = new Exclude(0);
1325	<	the_excludes[0]->setPair(0, 0);
1326	<	info[l].globalExcludes = new int;
1327	<	info[l].globalExcludes[0] = 0;
1328	<	info[l].n_exclude = 0;
1329	<	}
1330	<
1799	>	info[l].globalExcludes = new int;
1800	>	info[l].globalExcludes[0] = 0;
1801	>
1802		// set the arrays into the SimInfo object
1803
1804		info[l].atoms = the_atoms;
1805		info[l].molecules = the_molecules;
1806		info[l].nGlobalExcludes = 0;
1807	<	info[l].excludes = the_excludes;
1337	<
1807	>
1808		the_ff->setSimInfo(info);
1809		}
1810		}
#	Line 1377 | Line 1847 | void SimSetup::makeIntegrator(void){
1847		else{
1848		sprintf(painCave.errMsg,
1849		"SimSetup error: If you use the NVT\n"
1850	<	"    ensemble, you must set tauThermostat.\n");
1850	>	"\tensemble, you must set tauThermostat.\n");
1851		painCave.isFatal = 1;
1852		simError();
1853		}
#	Line 1400 | Line 1870 | void SimSetup::makeIntegrator(void){
1870		else{
1871		sprintf(painCave.errMsg,
1872		"SimSetup error: If you use a constant pressure\n"
1873	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1873	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1874		painCave.isFatal = 1;
1875		simError();
1876		}
#	Line 1410 | Line 1880 | void SimSetup::makeIntegrator(void){
1880		else{
1881		sprintf(painCave.errMsg,
1882		"SimSetup error: If you use an NPT\n"
1883	<	"    ensemble, you must set tauThermostat.\n");
1883	>	"\tensemble, you must set tauThermostat.\n");
1884		painCave.isFatal = 1;
1885		simError();
1886		}
#	Line 1420 | Line 1890 | void SimSetup::makeIntegrator(void){
1890		else{
1891		sprintf(painCave.errMsg,
1892		"SimSetup error: If you use an NPT\n"
1893	<	"    ensemble, you must set tauBarostat.\n");
1893	>	"\tensemble, you must set tauBarostat.\n");
1894		painCave.isFatal = 1;
1895		simError();
1896		}
#	Line 1443 | Line 1913 | void SimSetup::makeIntegrator(void){
1913		else{
1914		sprintf(painCave.errMsg,
1915		"SimSetup error: If you use a constant pressure\n"
1916	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1916	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1917		painCave.isFatal = 1;
1918		simError();
1919		}
#	Line 1454 | Line 1924 | void SimSetup::makeIntegrator(void){
1924		else{
1925		sprintf(painCave.errMsg,
1926		"SimSetup error: If you use an NPT\n"
1927	<	"    ensemble, you must set tauThermostat.\n");
1927	>	"\tensemble, you must set tauThermostat.\n");
1928		painCave.isFatal = 1;
1929		simError();
1930		}
#	Line 1465 | Line 1935 | void SimSetup::makeIntegrator(void){
1935		else{
1936		sprintf(painCave.errMsg,
1937		"SimSetup error: If you use an NPT\n"
1938	<	"    ensemble, you must set tauBarostat.\n");
1938	>	"\tensemble, you must set tauBarostat.\n");
1939		painCave.isFatal = 1;
1940		simError();
1941		}
#	Line 1488 | Line 1958 | void SimSetup::makeIntegrator(void){
1958		else{
1959		sprintf(painCave.errMsg,
1960		"SimSetup error: If you use a constant pressure\n"
1961	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1961	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1962		painCave.isFatal = 1;
1963		simError();
1964		}
#	Line 1498 | Line 1968 | void SimSetup::makeIntegrator(void){
1968		else{
1969		sprintf(painCave.errMsg,
1970		"SimSetup error: If you use an NPT\n"
1971	<	"    ensemble, you must set tauThermostat.\n");
1971	>	"\tensemble, you must set tauThermostat.\n");
1972		painCave.isFatal = 1;
1973		simError();
1974		}
#	Line 1508 | Line 1978 | void SimSetup::makeIntegrator(void){
1978		else{
1979		sprintf(painCave.errMsg,
1980		"SimSetup error: If you use an NPT\n"
1981	<	"    ensemble, you must set tauBarostat.\n");
1981	>	"\tensemble, you must set tauBarostat.\n");
1982		painCave.isFatal = 1;
1983		simError();
1984		}
#	Line 1561 | Line 2031 | void SimSetup::setupZConstraint(SimInfo& theInfo){
2031		}
2032		else{
2033		sprintf(painCave.errMsg,
2034	<	"ZConstraint error: If you use an ZConstraint\n"
2035	<	" , you must set sample time.\n");
2034	>	"ZConstraint error: If you use a ZConstraint,\n"
2035	>	"\tyou must set zconsTime.\n");
2036		painCave.isFatal = 1;
2037		simError();
2038		}
#	Line 1577 | Line 2047 | void SimSetup::setupZConstraint(SimInfo& theInfo){
2047		else{
2048		double defaultZConsTol = 0.01;
2049		sprintf(painCave.errMsg,
2050	<	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
2051	<	" , default value %f is used.\n",
2050	>	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
2051	>	"\tOOPSE will use a default value of %f.\n"
2052	>	"\tTo set the tolerance, use the zconsTol variable.\n",
2053		defaultZConsTol);
2054		painCave.isFatal = 0;
2055		simError();
#	Line 1596 | Line 2067 | void SimSetup::setupZConstraint(SimInfo& theInfo){
2067		}
2068		else{
2069		sprintf(painCave.errMsg,
2070	<	"ZConstraint Warning: User does not set force Subtraction policy, "
2071	<	"PolicyByMass is used\n");
2070	>	"ZConstraint Warning: No force subtraction policy was set.\n"
2071	>	"\tOOPSE will use PolicyByMass.\n"
2072	>	"\tTo set the policy, use the zconsForcePolicy variable.\n");
2073		painCave.isFatal = 0;
2074		simError();
2075		zconsForcePolicy->setData("BYMASS");
#	Line 1605 | Line 2077 | void SimSetup::setupZConstraint(SimInfo& theInfo){
2077
2078		theInfo.addProperty(zconsForcePolicy);
2079
2080	+	//set zcons gap
2081	+	DoubleData* zconsGap = new DoubleData();
2082	+	zconsGap->setID(ZCONSGAP_ID);
2083	+
2084	+	if (globals->haveZConsGap()){
2085	+	zconsGap->setData(globals->getZconsGap());
2086	+	theInfo.addProperty(zconsGap);
2087	+	}
2088	+
2089	+	//set zcons fixtime
2090	+	DoubleData* zconsFixtime = new DoubleData();
2091	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
2092	+
2093	+	if (globals->haveZConsFixTime()){
2094	+	zconsFixtime->setData(globals->getZconsFixtime());
2095	+	theInfo.addProperty(zconsFixtime);
2096	+	}
2097	+
2098	+	//set zconsUsingSMD
2099	+	IntData* zconsUsingSMD = new IntData();
2100	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
2101	+
2102	+	if (globals->haveZConsUsingSMD()){
2103	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
2104	+	theInfo.addProperty(zconsUsingSMD);
2105	+	}
2106	+
2107		//Determine the name of ouput file and add it into SimInfo's property list
2108		//Be careful, do not use inFileName, since it is a pointer which
2109		//point to a string at master node, and slave nodes do not contain that string
#	Line 1634 | Line 2133 | void SimSetup::setupZConstraint(SimInfo& theInfo){
2133		tempParaItem.zPos = zconStamp[i]->getZpos();
2134		tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
2135		tempParaItem.kRatio = zconStamp[i]->getKratio();
2136	<
2136	>	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
2137	>	tempParaItem.cantVel = zconStamp[i]->getCantVel();
2138		zconsParaData->addItem(tempParaItem);
2139		}
2140
2141		//check the uniqueness of index
2142		if(!zconsParaData->isIndexUnique()){
2143		sprintf(painCave.errMsg,
2144	<	"ZConstraint Error: molIndex is not unique\n");
2144	>	"ZConstraint Error: molIndex is not unique!\n");
2145		painCave.isFatal = 1;
2146		simError();
2147		}
#	Line 1652 | Line 2152 | void SimSetup::setupZConstraint(SimInfo& theInfo){
2152		//push data into siminfo, therefore, we can retrieve later
2153		theInfo.addProperty(zconsParaData);
2154		}
2155	+
2156	+	void SimSetup::makeMinimizer(){
2157	+
2158	+	OOPSEMinimizer* myOOPSEMinimizer;
2159	+	MinimizerParameterSet* param;
2160	+	char minimizerName[100];
2161	+
2162	+	for (int i = 0; i < nInfo; i++){
2163	+
2164	+	//prepare parameter set for minimizer
2165	+	param = new MinimizerParameterSet();
2166	+	param->setDefaultParameter();
2167	+
2168	+	if (globals->haveMinimizer()){
2169	+	param->setFTol(globals->getMinFTol());
2170	+	}
2171	+
2172	+	if (globals->haveMinGTol()){
2173	+	param->setGTol(globals->getMinGTol());
2174	+	}
2175	+
2176	+	if (globals->haveMinMaxIter()){
2177	+	param->setMaxIteration(globals->getMinMaxIter());
2178	+	}
2179	+
2180	+	if (globals->haveMinWriteFrq()){
2181	+	param->setMaxIteration(globals->getMinMaxIter());
2182	+	}
2183	+
2184	+	if (globals->haveMinWriteFrq()){
2185	+	param->setWriteFrq(globals->getMinWriteFrq());
2186	+	}
2187	+
2188	+	if (globals->haveMinStepSize()){
2189	+	param->setStepSize(globals->getMinStepSize());
2190	+	}
2191	+
2192	+	if (globals->haveMinLSMaxIter()){
2193	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
2194	+	}
2195	+
2196	+	if (globals->haveMinLSTol()){
2197	+	param->setLineSearchTol(globals->getMinLSTol());
2198	+	}
2199	+
2200	+	strcpy(minimizerName, globals->getMinimizer());
2201	+
2202	+	if (!strcasecmp(minimizerName, "CG")){
2203	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2204	+	}
2205	+	else if (!strcasecmp(minimizerName, "SD")){
2206	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
2207	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
2208	+	}
2209	+	else{
2210	+	sprintf(painCave.errMsg,
2211	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
2212	+	painCave.isFatal = 0;
2213	+	simError();
2214	+
2215	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2216	+	}
2217	+	info[i].the_integrator = myOOPSEMinimizer;
2218	+
2219	+	//store the minimizer into simInfo
2220	+	info[i].the_minimizer = myOOPSEMinimizer;
2221	+	info[i].has_minimizer = true;
2222	+	}
2223	+
2224	+	}

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