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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 845 by gezelter, Thu Oct 30 18:59:20 2003 UTC vs.
Revision 1214 by gezelter, Tue Jun 1 18:42:58 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
38	+	/**
39	+	* Check whether dividend is divisble by divisor or not
40	+	*/
41	+	bool isDivisible(double dividend, double divisor){
42	+	double tolerance = 0.000001;
43	+	double quotient;
44	+	double diff;
45	+	int intQuotient;
46	+
47	+	quotient = dividend / divisor;
48	+
49	+	if (quotient < 0)
50	+	quotient = -quotient;
51	+
52	+	intQuotient = int (quotient + tolerance);
53	+
54	+	diff = fabs(fabs(dividend) - intQuotient  * fabs(divisor));
55	+
56	+	if (diff <= tolerance)
57	+	return true;
58	+	else
59	+	return false;
60	+	}
61	+
62		SimSetup::SimSetup(){
63
64		initSuspend = false;
#	Line 103 | Line 132 | void SimSetup::createSim(void){
132
133		sysObjectsCreation();
134
135	+	// check on the post processing info
136	+
137	+	finalInfoCheck();
138	+
139		// initialize the system coordinates
140
141		if ( !initSuspend ){
#	Line 112 | Line 145 | void SimSetup::createSim(void){
145		info[0].currentTime = 0.0;
146		}
147
115	–	// check on the post processing info
116	–
117	–	finalInfoCheck();
118	–
148		// make the output filenames
149
150		makeOutNames();
151	<
123	<	// make the integrator
124	<
125	<	makeIntegrator();
126	<
151	>
152		#ifdef IS_MPI
153		mpiSim->mpiRefresh();
154		#endif
#	Line 131 | 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
158	–
212		// init the atoms
213
214	<	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]);
178	–	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
179	–	molInfo.myBonds = new Bond * [molInfo.nBonds];
180	–	molInfo.myBends = new Bend * [molInfo.nBends];
181	–	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());
273		info[k].n_oriented++;
274		molInfo.myAtoms[j] = dAtom;
275
276	<	ux = currentAtom->getOrntX();
277	<	uy = currentAtom->getOrntY();
278	<	uz = currentAtom->getOrntZ();
276	>	// Directional Atoms have standard unit vectors which are oriented
277	>	// in space using the three Euler angles.  We assume the standard
278	>	// unit vector was originally along the z axis below.
279
280	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
280	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
281	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
282	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
283
284	<	u = sqrt(uSqr);
285	<	ux = ux / u;
205	<	uy = uy / u;
206	<	uz = uz / u;
207	<
208	<	dAtom->setSUx(ux);
209	<	dAtom->setSUy(uy);
210	<	dAtom->setSUz(uz);
284	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
285	>
286		}
287		else{
213	–	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
214	–	info[k].getConfiguration());
215	–	}
216	–	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 228 | 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
234	–	// exclude_I must always be the smaller of the pair
235	–	if (exI > exJ){
236	–	tempEx = exI;
237	–	exI = exJ;
238	–	exJ = tempEx;
239	–	}
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);
247	<	#else  // isn't MPI
248	<
249	<	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
250	<	#endif  //is_mpi
316	>	info[k].excludes->addPair(exI, exJ);
317		}
252	–	excludeOffset += molInfo.nBonds;
318
319		//make the bends
320		for (j = 0; j < molInfo.nBends; j++){
#	Line 299 | 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{
307	<	exI = theBends[j].a;
308	<	exJ = theBends[j].b;
309	<	}
310	<
311	<	// exclude_I must always be the smaller of the pair
312	<	if (exI > exJ){
313	<	tempEx = exI;
314	<	exI = exJ;
315	<	exJ = tempEx;
316	<	}
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		}
328	–	excludeOffset += molInfo.nBends;
402
403		for (j = 0; j < molInfo.nTorsions; j++){
404		currentTorsion = comp_stamps[stampID]->getTorsion(j);
#	Line 334 | 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;
410	>	tempI = theTorsions[j].a;
411	>	tempJ = theTorsions[j].b;
412	>	tempK = theTorsions[j].c;
413	>	tempL = theTorsions[j].d;
414
340	–	// exclude_I must always be the smaller of the pair
341	–	if (exI > exJ){
342	–	tempEx = exI;
343	–	exI = exJ;
344	–	exJ = tempEx;
345	–	}
415		#ifdef IS_MPI
416	<	tempEx = exI;
417	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
418	<	tempEx = exJ;
419	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
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[j + excludeOffset]->setPair(exI, exJ);
428	<	#else  // isn't MPI
429	<	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
430	<	#endif  //is_mpi
431	<	}
432	<	excludeOffset += molInfo.nTorsions;
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	>	}
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[j + groupOffset]);
520	>	#else
521	>	myCutoffGroup->setGlobalIndex(j + 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[j+groupOffset];
535	>	#else
536	>	globalID = info[k].atoms[tempI]->getIndex();
537	>	info[k].globalGroupMembership[globalID] = j + groupOffset;
538	>	#endif
539	>
540	>
541	>
542	>	myCutoffGroup->addAtom(info[k].atoms[tempI]);
543	>
544	>	cutoffAtomSet.insert(tempI);
545	>	}
546	>
547	>	molInfo.myCutoffGroups.push_back(myCutoffGroup);
548	>	groupOffset++;
549	>
550	>	}//end for (j = 0; j < molInfo.nCutoffGroups; j++)
551	>
552	>	//creat a cutoff group for every atom  in current molecule which does not belong to cutoffgroup defined at mdl file
553	>
554	>	for(j = 0; j < molInfo.nAtoms; j++){
555	>
556	>	if(cutoffAtomSet.find(molInfo.myAtoms[j]->getIndex()) == cutoffAtomSet.end()){
557	>	myCutoffGroup = new CutoffGroup();
558	>	myCutoffGroup->addAtom(molInfo.myAtoms[j]);
559	>
560	>	#ifdef IS_MPI
561	>	myCutoffGroup->setGlobalIndex(globalGroupIndex[j + groupOffset]);
562	>	globalID = info[k].atoms[atomOffset + j]->getGlobalIndex();
563	>	info[k].globalGroupMembership[globalID] = globalGroupIndex[j+groupOffset];
564	>	#else
565	>	myCutoffGroup->setGlobalIndex(j + groupOffset);
566	>	globalID = info[k].atoms[atomOffset + j]->getIndex();
567	>	info[k].globalGroupMembership[globalID] = j+groupOffset;
568	>	#endif
569	>	molInfo.myCutoffGroups.push_back(myCutoffGroup);
570	>	groupOffset++;
571	>	}
572	>
573	>	}
574	>
575	>	// After this is all set up, scan through the atoms to
576	>	// see if they can be added to the integrableObjects:
577	>
578	>	molInfo.myIntegrableObjects.clear();
579	>
580	>
581	>	for (j = 0; j < molInfo.nAtoms; j++){
582	>
583	>	#ifdef IS_MPI
584	>	slJ = molInfo.myAtoms[j]->getGlobalIndex();
585	>	#else
586	>	slJ = j+atomOffset;
587	>	#endif
588	>
589	>	// if they aren't on the skip list, then they can be integrated
590	>
591	>	if (skipList.find(slJ) == skipList.end()) {
592	>	mySD = (StuntDouble *) molInfo.myAtoms[j];
593	>	info[k].integrableObjects.push_back(mySD);
594	>	molInfo.myIntegrableObjects.push_back(mySD);
595	>	}
596	>	}
597	>
598	>	// all rigid bodies are integrated:
599	>
600	>	for (j = 0; j < molInfo.nRigidBodies; j++) {
601	>	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
602	>	info[k].integrableObjects.push_back(mySD);
603	>	molInfo.myIntegrableObjects.push_back(mySD);
604	>	}
605	>
606	>
607	>	/*
608	>
609	>	//creat ConstraintPair.
610	>	molInfo.myConstraintPair.clear();
611	>
612	>	for (j = 0; j < molInfo.nBonds; j++){
613	>
614	>	//if both atoms are in the same rigid body, just skip it
615	>	currentBond = comp_stamps[stampID]->getBond(j);
616	>	if(!comp_stamps[stampID]->isBondInSameRigidBody(currentBond)){
617	>
618	>	tempI = currentBond->getA() + atomOffset;
619	>	if( comp_stamps[stampID]->isAtomInRigidBody(currentBond->getA(), whichRigidBody, consAtomIndex))
620	>	consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
621	>	else
622	>	consElement1 = new ConstraintAtom(info[k].atoms[tempI]);
623	>
624	>	tempJ =  currentBond->getB() + atomOffset;
625	>	if(comp_stamps[stampID]->isAtomInRigidBody(currentBond->getB(), whichRigidBody, consAtomIndex))
626	>	consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
627	>	else
628	>	consElement2 = new ConstraintAtom(info[k].atoms[tempJ]);
629	>
630	>	consPair = new DistanceConstraintPair(consElement1, consElement2);
631	>	molInfo.myConstraintPairs.push_back(consPair);
632	>	}
633	>	}
634	>
635	>	//loop over rigid bodies, if two rigid bodies share same joint, creat a HingeConstraintPair
636	>	for (int rb1 = 0; rb1 < molInfo.nRigidBodies -1 ; rb1++){
637	>	for (int rb2 = rb1 + 1; rb2 < molInfo.nRigidBodies ; rb2++){
638	>
639	>	jointAtoms = comp_stamps[stampID]->getJointAtoms(rb1, rb2);
640
641	+	for(size_t m = 0; m < jointAtoms.size(); m++){
642	+	consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[rb1], jointAtoms[m].first);
643	+	consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[rb2], jointAtoms[m].second);
644	+
645	+	consPair = new JointConstraintPair(consElement1, consElement2);
646	+	molInfo.myConstraintPairs.push_back(consPair);
647	+	}
648	+
649	+	}
650	+	}
651	+
652	+	*/
653	+	// send the arrays off to the forceField for init.
654	+
655		the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
656		the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
657		the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
658		the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
659		theTorsions);
660
368	–
661		info[k].molecules[i].initialize(molInfo);
662	<
663	<
662	>
663	>
664		atomOffset += molInfo.nAtoms;
665		delete[] theBonds;
666		delete[] theBends;
667		delete[] theTorsions;
668		}
669	+
670	+
671	+
672	+	#ifdef IS_MPI
673	+	// Since the globalGroupMembership has been zero filled and we've only
674	+	// poked values into the atoms we know, we can do an Allreduce
675	+	// to get the full globalGroupMembership array (We think).
676	+	// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
677	+	// docs said we could.
678	+
679	+	int* ggMjunk = new int[mpiSim->getNAtomsGlobal()];
680	+
681	+	MPI_Allreduce(info[k].globalGroupMembership,
682	+	ggMjunk,
683	+	mpiSim->getNAtomsGlobal(),
684	+	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
685	+
686	+	for (i = 0; i < mpiSim->getNAtomsGlobal(); i++)
687	+	info[k].globalGroupMembership[i] = ggMjunk[i];
688	+
689	+	delete[] ggMjunk;
690	+
691	+	#endif
692	+
693	+
694	+
695		}
696
697		#ifdef IS_MPI
#	Line 381 | Line 699 | void SimSetup::makeMolecules(void){
699		MPIcheckPoint();
700		#endif // is_mpi
701
384	–	// clean up the forcefield
385	–
386	–	the_ff->calcRcut();
387	–	the_ff->cleanMe();
702		}
703
704		void SimSetup::initFromBass(void){
#	Line 585 | Line 899 | void SimSetup::gatherInfo(void){
899		else if (!strcasecmp(force_field, "EAM")){
900		ffCase = FF_EAM;
901		}
902	+	else if (!strcasecmp(force_field, "WATER")){
903	+	ffCase = FF_H2O;
904	+	}
905		else{
906		sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
907		force_field);
#	Line 613 | Line 930 | void SimSetup::gatherInfo(void){
930		}
931		else{
932		sprintf(painCave.errMsg,
933	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
934	<	"reverting to NVE for this simulation.\n",
933	>	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
934	>	"\treverting to NVE for this simulation.\n",
935		ensemble);
936		painCave.isFatal = 0;
937		simError();
#	Line 646 | Line 963 | void SimSetup::gatherInfo(void){
963		if (!the_components[i]->haveNMol()){
964		// we have a problem
965		sprintf(painCave.errMsg,
966	<	"SimSetup Error. No global NMol or component NMol"
967	<	" given. Cannot calculate the number of atoms.\n");
966	>	"SimSetup Error. No global NMol or component NMol given.\n"
967	>	"\tCannot calculate the number of atoms.\n");
968		painCave.isFatal = 1;
969		simError();
970		}
#	Line 667 | Line 984 | void SimSetup::gatherInfo(void){
984		simError();
985		}
986
987	+	//check whether sample time, status time, thermal time and reset time are divisble by dt
988	+	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
989	+	sprintf(painCave.errMsg,
990	+	"Sample time is not divisible by dt.\n"
991	+	"\tThis will result in samples that are not uniformly\n"
992	+	"\tdistributed in time.  If this is a problem, change\n"
993	+	"\tyour sampleTime variable.\n");
994	+	painCave.isFatal = 0;
995	+	simError();
996	+	}
997	+
998	+	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
999	+	sprintf(painCave.errMsg,
1000	+	"Status time is not divisible by dt.\n"
1001	+	"\tThis will result in status reports that are not uniformly\n"
1002	+	"\tdistributed in time.  If this is a problem, change \n"
1003	+	"\tyour statusTime variable.\n");
1004	+	painCave.isFatal = 0;
1005	+	simError();
1006	+	}
1007	+
1008	+	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
1009	+	sprintf(painCave.errMsg,
1010	+	"Thermal time is not divisible by dt.\n"
1011	+	"\tThis will result in thermalizations that are not uniformly\n"
1012	+	"\tdistributed in time.  If this is a problem, change \n"
1013	+	"\tyour thermalTime variable.\n");
1014	+	painCave.isFatal = 0;
1015	+	simError();
1016	+	}
1017	+
1018	+	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
1019	+	sprintf(painCave.errMsg,
1020	+	"Reset time is not divisible by dt.\n"
1021	+	"\tThis will result in integrator resets that are not uniformly\n"
1022	+	"\tdistributed in time.  If this is a problem, change\n"
1023	+	"\tyour resetTime variable.\n");
1024	+	painCave.isFatal = 0;
1025	+	simError();
1026	+	}
1027	+
1028		// set the status, sample, and thermal kick times
1029
1030		for (i = 0; i < nInfo; i++){
1031		if (globals->haveSampleTime()){
1032		info[i].sampleTime = globals->getSampleTime();
1033		info[i].statusTime = info[i].sampleTime;
676	–	info[i].thermalTime = info[i].sampleTime;
1034		}
1035		else{
1036		info[i].sampleTime = globals->getRunTime();
1037		info[i].statusTime = info[i].sampleTime;
681	–	info[i].thermalTime = info[i].sampleTime;
1038		}
1039
1040		if (globals->haveStatusTime()){
#	Line 687 | Line 1043 | void SimSetup::gatherInfo(void){
1043
1044		if (globals->haveThermalTime()){
1045		info[i].thermalTime = globals->getThermalTime();
1046	+	} else {
1047	+	info[i].thermalTime = globals->getRunTime();
1048		}
1049
1050		info[i].resetIntegrator = 0;
#	Line 699 | Line 1057 | void SimSetup::gatherInfo(void){
1057
1058		if (globals->haveTempSet())
1059		info[i].setTemp = globals->getTempSet();
1060	<
1060	>
1061	>	// check for the extended State init
1062	>
1063	>	info[i].useInitXSstate = globals->getUseInitXSstate();
1064	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
1065	>
1066	>	// check for thermodynamic integration
1067	>	if (globals->getUseSolidThermInt() && !globals->getUseLiquidThermInt()) {
1068	>	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1069	>	info[i].useSolidThermInt = globals->getUseSolidThermInt();
1070	>	info[i].thermIntLambda = globals->getThermIntLambda();
1071	>	info[i].thermIntK = globals->getThermIntK();
1072	>
1073	>	Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK);
1074	>	info[i].restraint = myRestraint;
1075	>	}
1076	>	else {
1077	>	sprintf(painCave.errMsg,
1078	>	"SimSetup Error:\n"
1079	>	"\tKeyword useSolidThermInt was set to 'true' but\n"
1080	>	"\tthermodynamicIntegrationLambda (and/or\n"
1081	>	"\tthermodynamicIntegrationK) was not specified.\n"
1082	>	"\tPlease provide a lambda value and k value in your .bass file.\n");
1083	>	painCave.isFatal = 1;
1084	>	simError();
1085	>	}
1086	>	}
1087	>	else if(globals->getUseLiquidThermInt()) {
1088	>	if (globals->getUseSolidThermInt()) {
1089	>	sprintf( painCave.errMsg,
1090	>	"SimSetup Warning: It appears that you have both solid and\n"
1091	>	"\tliquid thermodynamic integration activated in your .bass\n"
1092	>	"\tfile. To avoid confusion, specify only one technique in\n"
1093	>	"\tyour .bass file. Liquid-state thermodynamic integration\n"
1094	>	"\twill be assumed for the current simulation. If this is not\n"
1095	>	"\twhat you desire, set useSolidThermInt to 'true' and\n"
1096	>	"\tuseLiquidThermInt to 'false' in your .bass file.\n");
1097	>	painCave.isFatal = 0;
1098	>	simError();
1099	>	}
1100	>	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1101	>	info[i].useLiquidThermInt = globals->getUseLiquidThermInt();
1102	>	info[i].thermIntLambda = globals->getThermIntLambda();
1103	>	info[i].thermIntK = globals->getThermIntK();
1104	>	}
1105	>	else {
1106	>	sprintf(painCave.errMsg,
1107	>	"SimSetup Error:\n"
1108	>	"\tKeyword useLiquidThermInt was set to 'true' but\n"
1109	>	"\tthermodynamicIntegrationLambda (and/or\n"
1110	>	"\tthermodynamicIntegrationK) was not specified.\n"
1111	>	"\tPlease provide a lambda value and k value in your .bass file.\n");
1112	>	painCave.isFatal = 1;
1113	>	simError();
1114	>	}
1115	>	}
1116	>	else if(globals->haveThermIntLambda() || globals->haveThermIntK()){
1117	>	sprintf(painCave.errMsg,
1118	>	"SimSetup Warning: If you want to use Thermodynamic\n"
1119	>	"\tIntegration, set useSolidThermInt or useLiquidThermInt to\n"
1120	>	"\t'true' in your .bass file.  These keywords are set to\n"
1121	>	"\t'false' by default, so your lambda and/or k values are\n"
1122	>	"\tbeing ignored.\n");
1123	>	painCave.isFatal = 0;
1124	>	simError();
1125	>	}
1126		}
1127
1128		//setup seed for random number generator
#	Line 741 | Line 1164 | void SimSetup::gatherInfo(void){
1164		for (int i = 0; i < nInfo; i++){
1165		info[i].setSeed(seedValue);
1166		}
1167	<
1167	>
1168		#ifdef IS_MPI
1169	<	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
1169	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
1170		MPIcheckPoint();
1171		#endif // is_mpi
1172		}
#	Line 752 | Line 1175 | void SimSetup::finalInfoCheck(void){
1175		void SimSetup::finalInfoCheck(void){
1176		int index;
1177		int usesDipoles;
1178	+	int usesCharges;
1179		int i;
1180
1181		for (i = 0; i < nInfo; i++){
#	Line 763 | Line 1187 | void SimSetup::finalInfoCheck(void){
1187		usesDipoles = (info[i].atoms[index])->hasDipole();
1188		index++;
1189		}
1190	<
1190	>	index = 0;
1191	>	usesCharges = 0;
1192	>	while ((index < info[i].n_atoms) && !usesCharges){
1193	>	usesCharges= (info[i].atoms[index])->hasCharge();
1194	>	index++;
1195	>	}
1196		#ifdef IS_MPI
1197		int myUse = usesDipoles;
1198		MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1199		#endif //is_mpi
1200
1201	<	double theEcr, theEst;
1201	>	double theRcut, theRsw;
1202
1203	<	if (globals->getUseRF()){
1204	<	info[i].useReactionField = 1;
1203	>	if (globals->haveRcut()) {
1204	>	theRcut = globals->getRcut();
1205
1206	<	if (!globals->haveECR()){
1206	>	if (globals->haveRsw())
1207	>	theRsw = globals->getRsw();
1208	>	else
1209	>	theRsw = theRcut;
1210	>
1211	>	info[i].setDefaultRcut(theRcut, theRsw);
1212	>
1213	>	} else {
1214	>
1215	>	the_ff->calcRcut();
1216	>	theRcut = info[i].getRcut();
1217	>
1218	>	if (globals->haveRsw())
1219	>	theRsw = globals->getRsw();
1220	>	else
1221	>	theRsw = theRcut;
1222	>
1223	>	info[i].setDefaultRcut(theRcut, theRsw);
1224	>	}
1225	>
1226	>	if (globals->getUseRF()){
1227	>	info[i].useReactionField = 1;
1228	>
1229	>	if (!globals->haveRcut()){
1230		sprintf(painCave.errMsg,
1231	<	"SimSetup Warning: using default value of 1/2 the smallest "
1232	<	"box length for the electrostaticCutoffRadius.\n"
1233	<	"I hope you have a very fast processor!\n");
1231	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1232	>	"\tOOPSE will use a default value of 15.0 angstroms"
1233	>	"\tfor the cutoffRadius.\n");
1234		painCave.isFatal = 0;
1235		simError();
1236	<	double smallest;
785	<	smallest = info[i].boxL[0];
786	<	if (info[i].boxL[1] <= smallest)
787	<	smallest = info[i].boxL[1];
788	<	if (info[i].boxL[2] <= smallest)
789	<	smallest = info[i].boxL[2];
790	<	theEcr = 0.5 * smallest;
1236	>	theRcut = 15.0;
1237		}
1238		else{
1239	<	theEcr = globals->getECR();
1239	>	theRcut = globals->getRcut();
1240		}
1241
1242	<	if (!globals->haveEST()){
1242	>	if (!globals->haveRsw()){
1243		sprintf(painCave.errMsg,
1244	<	"SimSetup Warning: using default value of 0.05 * the "
1245	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
1244	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1245	>	"\tOOPSE will use a default value of\n"
1246	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1247		painCave.isFatal = 0;
1248		simError();
1249	<	theEst = 0.05 * theEcr;
1249	>	theRsw = 0.95 * theRcut;
1250		}
1251		else{
1252	<	theEst = globals->getEST();
1252	>	theRsw = globals->getRsw();
1253		}
1254
1255	<	info[i].setDefaultEcr(theEcr, theEst);
1255	>	info[i].setDefaultRcut(theRcut, theRsw);
1256
1257		if (!globals->haveDielectric()){
1258		sprintf(painCave.errMsg,
1259	<	"SimSetup Error: You are trying to use Reaction Field without"
1260	<	"setting a dielectric constant!\n");
1259	>	"SimSetup Error: No Dielectric constant was set.\n"
1260	>	"\tYou are trying to use Reaction Field without"
1261	>	"\tsetting a dielectric constant!\n");
1262		painCave.isFatal = 1;
1263		simError();
1264		}
1265		info[i].dielectric = globals->getDielectric();
1266		}
1267		else{
1268	<	if (usesDipoles){
1269	<	if (!globals->haveECR()){
1268	>	if (usesDipoles || usesCharges){
1269	>
1270	>	if (!globals->haveRcut()){
1271		sprintf(painCave.errMsg,
1272	<	"SimSetup Warning: using default value of 1/2 the smallest "
1273	<	"box length for the electrostaticCutoffRadius.\n"
1274	<	"I hope you have a very fast processor!\n");
1272	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1273	>	"\tOOPSE will use a default value of 15.0 angstroms"
1274	>	"\tfor the cutoffRadius.\n");
1275		painCave.isFatal = 0;
1276		simError();
1277	<	double smallest;
1278	<	smallest = info[i].boxL[0];
830	<	if (info[i].boxL[1] <= smallest)
831	<	smallest = info[i].boxL[1];
832	<	if (info[i].boxL[2] <= smallest)
833	<	smallest = info[i].boxL[2];
834	<	theEcr = 0.5 * smallest;
835	<	}
1277	>	theRcut = 15.0;
1278	>	}
1279		else{
1280	<	theEcr = globals->getECR();
1280	>	theRcut = globals->getRcut();
1281		}
1282	<
1283	<	if (!globals->haveEST()){
1282	>
1283	>	if (!globals->haveRsw()){
1284		sprintf(painCave.errMsg,
1285	<	"SimSetup Warning: using default value of 0.05 * the "
1286	<	"electrostaticCutoffRadius for the "
1287	<	"electrostaticSkinThickness\n");
1285	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1286	>	"\tOOPSE will use a default value of\n"
1287	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1288		painCave.isFatal = 0;
1289		simError();
1290	<	theEst = 0.05 * theEcr;
1290	>	theRsw = 0.95 * theRcut;
1291		}
1292		else{
1293	<	theEst = globals->getEST();
1293	>	theRsw = globals->getRsw();
1294		}
1295	<
1296	<	info[i].setDefaultEcr(theEcr, theEst);
1295	>
1296	>	info[i].setDefaultRcut(theRcut, theRsw);
1297	>
1298		}
1299		}
856	–	info[i].checkCutOffs();
1300		}
858	–
1301		#ifdef IS_MPI
1302		strcpy(checkPointMsg, "post processing checks out");
1303		MPIcheckPoint();
1304		#endif // is_mpi
863	–	}
1305
1306	+	// clean up the forcefield
1307	+	the_ff->cleanMe();
1308	+	}
1309	+
1310		void SimSetup::initSystemCoords(void){
1311		int i;
1312
#	Line 889 | Line 1334 | void SimSetup::initSystemCoords(void){
1334		delete fileInit;
1335		}
1336		else{
1337	<	#ifdef IS_MPI
893	<
1337	>
1338		// no init from bass
1339	<
1339	>
1340		sprintf(painCave.errMsg,
1341	<	"Cannot intialize a parallel simulation without an initial configuration file.\n");
1341	>	"Cannot intialize a simulation without an initial configuration file.\n");
1342		painCave.isFatal = 1;;
1343		simError();
1344	<
901	<	#else
902	<
903	<	initFromBass();
904	<
905	<
906	<	#endif
1344	>
1345		}
1346
1347		#ifdef IS_MPI
#	Line 994 | Line 1432 | void SimSetup::makeOutNames(void){
1432		}
1433		else{
1434		strcat(info[k].statusName, ".stat");
1435	+	}
1436	+	}
1437	+
1438	+	strcpy(info[k].rawPotName, inFileName);
1439	+	nameLength = strlen(info[k].rawPotName);
1440	+	endTest = &(info[k].rawPotName[nameLength - 5]);
1441	+	if (!strcmp(endTest, ".bass")){
1442	+	strcpy(endTest, ".raw");
1443	+	}
1444	+	else if (!strcmp(endTest, ".BASS")){
1445	+	strcpy(endTest, ".raw");
1446	+	}
1447	+	else{
1448	+	endTest = &(info[k].rawPotName[nameLength - 4]);
1449	+	if (!strcmp(endTest, ".bss")){
1450	+	strcpy(endTest, ".raw");
1451	+	}
1452	+	else if (!strcmp(endTest, ".mdl")){
1453	+	strcpy(endTest, ".raw");
1454		}
1455	+	else{
1456	+	strcat(info[k].rawPotName, ".raw");
1457	+	}
1458		}
1459
1460		#ifdef IS_MPI
#	Line 1057 | Line 1517 | void SimSetup::createFF(void){
1517		the_ff = new EAM_FF();
1518		break;
1519
1520	+	case FF_H2O:
1521	+	the_ff = new WATER();
1522	+	break;
1523	+
1524		default:
1525		sprintf(painCave.errMsg,
1526		"SimSetup Error. Unrecognized force field in case statement.\n");
#	Line 1077 | Line 1541 | void SimSetup::compList(void){
1541		LinkedMolStamp* headStamp = new LinkedMolStamp();
1542		LinkedMolStamp* currentStamp = NULL;
1543		comp_stamps = new MoleculeStamp * [n_components];
1544	+	bool haveCutoffGroups;
1545
1546	+	haveCutoffGroups = false;
1547	+
1548		// make an array of molecule stamps that match the components used.
1549		// also extract the used stamps out into a separate linked list
1550
#	Line 1112 | Line 1579 | void SimSetup::compList(void){
1579		headStamp->add(currentStamp);
1580		comp_stamps[i] = headStamp->match(id);
1581		}
1582	+
1583	+	if(comp_stamps[i]->getNCutoffGroups() > 0)
1584	+	haveCutoffGroups = true;
1585		}
1586	+
1587	+	for (i = 0; i < nInfo; i++)
1588	+	info[i].haveCutoffGroups = haveCutoffGroups;
1589
1590		#ifdef IS_MPI
1591		strcpy(checkPointMsg, "Component stamps successfully extracted\n");
#	Line 1121 | Line 1594 | void SimSetup::calcSysValues(void){
1594		}
1595
1596		void SimSetup::calcSysValues(void){
1597	<	int i;
1597	>	int i, j;
1598	>	int ncutgroups, atomsingroups, ngroupsinstamp;
1599
1600		int* molMembershipArray;
1601	+	CutoffGroupStamp* cg;
1602
1603		tot_atoms = 0;
1604		tot_bonds = 0;
1605		tot_bends = 0;
1606		tot_torsions = 0;
1607	+	tot_rigid = 0;
1608	+	tot_groups = 0;
1609		for (i = 0; i < n_components; i++){
1610		tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1611		tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1612		tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1613		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1614	<	}
1614	>	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1615
1616	+	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1617	+	atomsingroups = 0;
1618	+	for (j=0; j < ncutgroups; j++) {
1619	+	cg = comp_stamps[i]->getCutoffGroup(j);
1620	+	atomsingroups += cg->getNMembers();
1621	+	}
1622	+	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups + ncutgroups;
1623	+	tot_groups += components_nmol[i] * ngroupsinstamp;
1624	+	}
1625	+
1626		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1627		molMembershipArray = new int[tot_atoms];
1628
#	Line 1146 | Line 1633 | void SimSetup::calcSysValues(void){
1633		info[i].n_torsions = tot_torsions;
1634		info[i].n_SRI = tot_SRI;
1635		info[i].n_mol = tot_nmol;
1636	<
1636	>	info[i].ngroup = tot_groups;
1637		info[i].molMembershipArray = molMembershipArray;
1638		}
1639		}
#	Line 1157 | Line 1644 | void SimSetup::mpiMolDivide(void){
1644		int i, j, k;
1645		int localMol, allMol;
1646		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1647	+	int local_rigid, local_groups;
1648	+	vector<int> globalMolIndex;
1649	+	int ncutgroups, atomsingroups, ngroupsinstamp;
1650	+	CutoffGroupStamp* cg;
1651
1652		mpiSim = new mpiSimulation(info);
1653
1654	<	globalIndex = mpiSim->divideLabor();
1654	>	mpiSim->divideLabor();
1655	>	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1656	>	globalGroupIndex = mpiSim->getGlobalGroupIndex();
1657	>	//globalMolIndex = mpiSim->getGlobalMolIndex();
1658
1659		// set up the local variables
1660
#	Line 1173 | Line 1667 | void SimSetup::mpiMolDivide(void){
1667		local_bonds = 0;
1668		local_bends = 0;
1669		local_torsions = 0;
1670	<	globalAtomIndex = 0;
1670	>	local_rigid = 0;
1671	>	local_groups = 0;
1672	>	globalAtomCounter = 0;
1673
1178	–
1674		for (i = 0; i < n_components; i++){
1675		for (j = 0; j < components_nmol[i]; j++){
1676		if (mol2proc[allMol] == worldRank){
#	Line 1183 | Line 1678 | void SimSetup::mpiMolDivide(void){
1678		local_bonds += comp_stamps[i]->getNBonds();
1679		local_bends += comp_stamps[i]->getNBends();
1680		local_torsions += comp_stamps[i]->getNTorsions();
1681	+	local_rigid += comp_stamps[i]->getNRigidBodies();
1682	+
1683	+	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1684	+	atomsingroups = 0;
1685	+	for (k=0; k < ncutgroups; k++) {
1686	+	cg = comp_stamps[i]->getCutoffGroup(k);
1687	+	atomsingroups += cg->getNMembers();
1688	+	}
1689	+	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups +
1690	+	ncutgroups;
1691	+	local_groups += ngroupsinstamp;
1692	+
1693		localMol++;
1694		}
1695		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1696	<	info[0].molMembershipArray[globalAtomIndex] = allMol;
1697	<	globalAtomIndex++;
1696	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1697	>	globalAtomCounter++;
1698		}
1699
1700		allMol++;
#	Line 1195 | Line 1702 | void SimSetup::mpiMolDivide(void){
1702		}
1703		local_SRI = local_bonds + local_bends + local_torsions;
1704
1705	<	info[0].n_atoms = mpiSim->getMyNlocal();
1706	<
1705	>	info[0].n_atoms = mpiSim->getNAtomsLocal();
1706	>
1707		if (local_atoms != info[0].n_atoms){
1708		sprintf(painCave.errMsg,
1709	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1710	<	" localAtom (%d) are not equal.\n",
1709	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1710	>	"\tlocalAtom (%d) are not equal.\n",
1711		info[0].n_atoms, local_atoms);
1712		painCave.isFatal = 1;
1713		simError();
1714		}
1715
1716	+	info[0].ngroup = mpiSim->getNGroupsLocal();
1717	+	if (local_groups != info[0].ngroup){
1718	+	sprintf(painCave.errMsg,
1719	+	"SimSetup error: mpiSim's localGroups (%d) and SimSetup's\n"
1720	+	"\tlocalGroups (%d) are not equal.\n",
1721	+	info[0].ngroup, local_groups);
1722	+	painCave.isFatal = 1;
1723	+	simError();
1724	+	}
1725	+
1726		info[0].n_bonds = local_bonds;
1727		info[0].n_bends = local_bends;
1728		info[0].n_torsions = local_torsions;
#	Line 1228 | Line 1745 | void SimSetup::makeSysArrays(void){
1745
1746		Atom** the_atoms;
1747		Molecule* the_molecules;
1231	–	Exclude** the_excludes;
1748
1233	–
1749		for (l = 0; l < nInfo; l++){
1750		// create the atom and short range interaction arrays
1751
#	Line 1244 | Line 1759 | void SimSetup::makeSysArrays(void){
1759
1760
1761		molIndex = 0;
1762	<	for (i = 0; i < mpiSim->getTotNmol(); i++){
1762	>	for (i = 0; i < mpiSim->getNMolGlobal(); i++){
1763		if (mol2proc[i] == worldRank){
1764		the_molecules[molIndex].setStampID(molCompType[i]);
1765		the_molecules[molIndex].setMyIndex(molIndex);
#	Line 1256 | Line 1771 | void SimSetup::makeSysArrays(void){
1771		#else // is_mpi
1772
1773		molIndex = 0;
1774	<	globalAtomIndex = 0;
1774	>	globalAtomCounter = 0;
1775		for (i = 0; i < n_components; i++){
1776		for (j = 0; j < components_nmol[i]; j++){
1777		the_molecules[molIndex].setStampID(i);
1778		the_molecules[molIndex].setMyIndex(molIndex);
1779		the_molecules[molIndex].setGlobalIndex(molIndex);
1780		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1781	<	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1782	<	globalAtomIndex++;
1781	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1782	>	globalAtomCounter++;
1783		}
1784		molIndex++;
1785		}
#	Line 1273 | Line 1788 | void SimSetup::makeSysArrays(void){
1788
1789		#endif // is_mpi
1790
1791	<
1792	<	if (info[l].n_SRI){
1793	<	Exclude::createArray(info[l].n_SRI);
1279	<	the_excludes = new Exclude * [info[l].n_SRI];
1280	<	for (int ex = 0; ex < info[l].n_SRI; ex++){
1281	<	the_excludes[ex] = new Exclude(ex);
1282	<	}
1283	<	info[l].globalExcludes = new int;
1284	<	info[l].n_exclude = info[l].n_SRI;
1285	<	}
1286	<	else{
1287	<	Exclude::createArray(1);
1288	<	the_excludes = new Exclude * ;
1289	<	the_excludes[0] = new Exclude(0);
1290	<	the_excludes[0]->setPair(0, 0);
1291	<	info[l].globalExcludes = new int;
1292	<	info[l].globalExcludes[0] = 0;
1293	<	info[l].n_exclude = 0;
1294	<	}
1295	<
1791	>	info[l].globalExcludes = new int;
1792	>	info[l].globalExcludes[0] = 0;
1793	>
1794		// set the arrays into the SimInfo object
1795
1796		info[l].atoms = the_atoms;
1797		info[l].molecules = the_molecules;
1798		info[l].nGlobalExcludes = 0;
1799	<	info[l].excludes = the_excludes;
1302	<
1799	>
1800		the_ff->setSimInfo(info);
1801		}
1802		}
#	Line 1342 | Line 1839 | void SimSetup::makeIntegrator(void){
1839		else{
1840		sprintf(painCave.errMsg,
1841		"SimSetup error: If you use the NVT\n"
1842	<	"    ensemble, you must set tauThermostat.\n");
1842	>	"\tensemble, you must set tauThermostat.\n");
1843		painCave.isFatal = 1;
1844		simError();
1845		}
#	Line 1365 | Line 1862 | void SimSetup::makeIntegrator(void){
1862		else{
1863		sprintf(painCave.errMsg,
1864		"SimSetup error: If you use a constant pressure\n"
1865	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1865	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1866		painCave.isFatal = 1;
1867		simError();
1868		}
#	Line 1375 | Line 1872 | void SimSetup::makeIntegrator(void){
1872		else{
1873		sprintf(painCave.errMsg,
1874		"SimSetup error: If you use an NPT\n"
1875	<	"    ensemble, you must set tauThermostat.\n");
1875	>	"\tensemble, you must set tauThermostat.\n");
1876		painCave.isFatal = 1;
1877		simError();
1878		}
#	Line 1385 | Line 1882 | void SimSetup::makeIntegrator(void){
1882		else{
1883		sprintf(painCave.errMsg,
1884		"SimSetup error: If you use an NPT\n"
1885	<	"    ensemble, you must set tauBarostat.\n");
1885	>	"\tensemble, you must set tauBarostat.\n");
1886		painCave.isFatal = 1;
1887		simError();
1888		}
#	Line 1408 | Line 1905 | void SimSetup::makeIntegrator(void){
1905		else{
1906		sprintf(painCave.errMsg,
1907		"SimSetup error: If you use a constant pressure\n"
1908	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1908	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1909		painCave.isFatal = 1;
1910		simError();
1911		}
#	Line 1419 | Line 1916 | void SimSetup::makeIntegrator(void){
1916		else{
1917		sprintf(painCave.errMsg,
1918		"SimSetup error: If you use an NPT\n"
1919	<	"    ensemble, you must set tauThermostat.\n");
1919	>	"\tensemble, you must set tauThermostat.\n");
1920		painCave.isFatal = 1;
1921		simError();
1922		}
#	Line 1430 | Line 1927 | void SimSetup::makeIntegrator(void){
1927		else{
1928		sprintf(painCave.errMsg,
1929		"SimSetup error: If you use an NPT\n"
1930	<	"    ensemble, you must set tauBarostat.\n");
1930	>	"\tensemble, you must set tauBarostat.\n");
1931		painCave.isFatal = 1;
1932		simError();
1933		}
#	Line 1453 | Line 1950 | void SimSetup::makeIntegrator(void){
1950		else{
1951		sprintf(painCave.errMsg,
1952		"SimSetup error: If you use a constant pressure\n"
1953	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1953	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1954		painCave.isFatal = 1;
1955		simError();
1956		}
#	Line 1463 | Line 1960 | void SimSetup::makeIntegrator(void){
1960		else{
1961		sprintf(painCave.errMsg,
1962		"SimSetup error: If you use an NPT\n"
1963	<	"    ensemble, you must set tauThermostat.\n");
1963	>	"\tensemble, you must set tauThermostat.\n");
1964		painCave.isFatal = 1;
1965		simError();
1966		}
#	Line 1473 | Line 1970 | void SimSetup::makeIntegrator(void){
1970		else{
1971		sprintf(painCave.errMsg,
1972		"SimSetup error: If you use an NPT\n"
1973	<	"    ensemble, you must set tauBarostat.\n");
1973	>	"\tensemble, you must set tauBarostat.\n");
1974		painCave.isFatal = 1;
1975		simError();
1976		}
#	Line 1526 | Line 2023 | void SimSetup::setupZConstraint(SimInfo& theInfo){
2023		}
2024		else{
2025		sprintf(painCave.errMsg,
2026	<	"ZConstraint error: If you use an ZConstraint\n"
2027	<	" , you must set sample time.\n");
2026	>	"ZConstraint error: If you use a ZConstraint,\n"
2027	>	"\tyou must set zconsTime.\n");
2028		painCave.isFatal = 1;
2029		simError();
2030		}
#	Line 1542 | Line 2039 | void SimSetup::setupZConstraint(SimInfo& theInfo){
2039		else{
2040		double defaultZConsTol = 0.01;
2041		sprintf(painCave.errMsg,
2042	<	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
2043	<	" , default value %f is used.\n",
2042	>	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
2043	>	"\tOOPSE will use a default value of %f.\n"
2044	>	"\tTo set the tolerance, use the zconsTol variable.\n",
2045		defaultZConsTol);
2046		painCave.isFatal = 0;
2047		simError();
#	Line 1561 | Line 2059 | void SimSetup::setupZConstraint(SimInfo& theInfo){
2059		}
2060		else{
2061		sprintf(painCave.errMsg,
2062	<	"ZConstraint Warning: User does not set force Subtraction policy, "
2063	<	"PolicyByMass is used\n");
2062	>	"ZConstraint Warning: No force subtraction policy was set.\n"
2063	>	"\tOOPSE will use PolicyByMass.\n"
2064	>	"\tTo set the policy, use the zconsForcePolicy variable.\n");
2065		painCave.isFatal = 0;
2066		simError();
2067		zconsForcePolicy->setData("BYMASS");
#	Line 1570 | Line 2069 | void SimSetup::setupZConstraint(SimInfo& theInfo){
2069
2070		theInfo.addProperty(zconsForcePolicy);
2071
2072	+	//set zcons gap
2073	+	DoubleData* zconsGap = new DoubleData();
2074	+	zconsGap->setID(ZCONSGAP_ID);
2075	+
2076	+	if (globals->haveZConsGap()){
2077	+	zconsGap->setData(globals->getZconsGap());
2078	+	theInfo.addProperty(zconsGap);
2079	+	}
2080	+
2081	+	//set zcons fixtime
2082	+	DoubleData* zconsFixtime = new DoubleData();
2083	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
2084	+
2085	+	if (globals->haveZConsFixTime()){
2086	+	zconsFixtime->setData(globals->getZconsFixtime());
2087	+	theInfo.addProperty(zconsFixtime);
2088	+	}
2089	+
2090	+	//set zconsUsingSMD
2091	+	IntData* zconsUsingSMD = new IntData();
2092	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
2093	+
2094	+	if (globals->haveZConsUsingSMD()){
2095	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
2096	+	theInfo.addProperty(zconsUsingSMD);
2097	+	}
2098	+
2099		//Determine the name of ouput file and add it into SimInfo's property list
2100		//Be careful, do not use inFileName, since it is a pointer which
2101		//point to a string at master node, and slave nodes do not contain that string
#	Line 1599 | Line 2125 | void SimSetup::setupZConstraint(SimInfo& theInfo){
2125		tempParaItem.zPos = zconStamp[i]->getZpos();
2126		tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
2127		tempParaItem.kRatio = zconStamp[i]->getKratio();
2128	<
2128	>	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
2129	>	tempParaItem.cantVel = zconStamp[i]->getCantVel();
2130		zconsParaData->addItem(tempParaItem);
2131		}
2132
2133		//check the uniqueness of index
2134		if(!zconsParaData->isIndexUnique()){
2135		sprintf(painCave.errMsg,
2136	<	"ZConstraint Error: molIndex is not unique\n");
2136	>	"ZConstraint Error: molIndex is not unique!\n");
2137		painCave.isFatal = 1;
2138		simError();
2139		}
#	Line 1616 | Line 2143 | void SimSetup::setupZConstraint(SimInfo& theInfo){
2143
2144		//push data into siminfo, therefore, we can retrieve later
2145		theInfo.addProperty(zconsParaData);
2146	+	}
2147	+
2148	+	void SimSetup::makeMinimizer(){
2149	+
2150	+	OOPSEMinimizer* myOOPSEMinimizer;
2151	+	MinimizerParameterSet* param;
2152	+	char minimizerName[100];
2153	+
2154	+	for (int i = 0; i < nInfo; i++){
2155	+
2156	+	//prepare parameter set for minimizer
2157	+	param = new MinimizerParameterSet();
2158	+	param->setDefaultParameter();
2159	+
2160	+	if (globals->haveMinimizer()){
2161	+	param->setFTol(globals->getMinFTol());
2162	+	}
2163	+
2164	+	if (globals->haveMinGTol()){
2165	+	param->setGTol(globals->getMinGTol());
2166	+	}
2167	+
2168	+	if (globals->haveMinMaxIter()){
2169	+	param->setMaxIteration(globals->getMinMaxIter());
2170	+	}
2171	+
2172	+	if (globals->haveMinWriteFrq()){
2173	+	param->setMaxIteration(globals->getMinMaxIter());
2174	+	}
2175	+
2176	+	if (globals->haveMinWriteFrq()){
2177	+	param->setWriteFrq(globals->getMinWriteFrq());
2178	+	}
2179	+
2180	+	if (globals->haveMinStepSize()){
2181	+	param->setStepSize(globals->getMinStepSize());
2182	+	}
2183	+
2184	+	if (globals->haveMinLSMaxIter()){
2185	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
2186	+	}
2187	+
2188	+	if (globals->haveMinLSTol()){
2189	+	param->setLineSearchTol(globals->getMinLSTol());
2190	+	}
2191	+
2192	+	strcpy(minimizerName, globals->getMinimizer());
2193	+
2194	+	if (!strcasecmp(minimizerName, "CG")){
2195	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2196	+	}
2197	+	else if (!strcasecmp(minimizerName, "SD")){
2198	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
2199	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
2200	+	}
2201	+	else{
2202	+	sprintf(painCave.errMsg,
2203	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
2204	+	painCave.isFatal = 0;
2205	+	simError();
2206	+
2207	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2208	+	}
2209	+	info[i].the_integrator = myOOPSEMinimizer;
2210	+
2211	+	//store the minimizer into simInfo
2212	+	info[i].the_minimizer = myOOPSEMinimizer;
2213	+	info[i].has_minimizer = true;
2214	+	}
2215	+
2216		}

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