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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 1091 by tim, Tue Mar 16 19:22:56 2004 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 "ConjugateMinimizer.hpp"
12	>	#include "RigidBody.hpp"
13		#include "OOPSEMinimizer.hpp"
14	+	//#include "ConstraintElement.hpp"
15	+	//#include "ConstraintPair.hpp"
16
17		#ifdef IS_MPI
18		#include "mpiBASS.h"
#	Line 146 \| Line 148 \| void SimSetup::createSim(void){
148		// make the output filenames
149
150		makeOutNames();
149	–
150	–	if (globals->haveMinimizer())
151	–	// make minimizer
152	–	makeMinimizer();
153	–	else
154	–	// make the integrator
155	–	makeIntegrator();
151
152		#ifdef IS_MPI
153		mpiSim->mpiRefresh();
#	Line 161 \| 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
187	–
212		// init the atoms
213
214	<	double phi, theta, psi;
191	<	double sux, suy, suz;
192	<	double Axx, Axy, Axz, Ayx, Ayy, Ayz, Azx, Azy, Azz;
193	<	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]);
210	–	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
211	–	molInfo.myBonds = new Bond * [molInfo.nBonds];
212	–	molInfo.myBends = new Bend * [molInfo.nBends];
213	–	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
245
246	+	if (molInfo.nBonds > 0)
247	+	molInfo.myBonds = new Bond*[molInfo.nBonds];
248	+	else
249	+	molInfo.myBonds = NULL;
250	+
251	+	if (molInfo.nBends > 0)
252	+	molInfo.myBends = new Bend*[molInfo.nBends];
253	+	else
254	+	molInfo.myBends = NULL;
255	+
256	+	if (molInfo.nTorsions > 0)
257	+	molInfo.myTorsions = new Torsion *[molInfo.nTorsions];
258	+	else
259	+	molInfo.myTorsions = NULL;
260	+
261		theBonds = new bond_pair[molInfo.nBonds];
262		theBends = new bend_set[molInfo.nBends];
263		theTorsions = new torsion_set[molInfo.nTorsions];
264	<
264	>
265		// make the Atoms
266
267		for (j = 0; j < molInfo.nAtoms; j++){
268		currentAtom = comp_stamps[stampID]->getAtom(j);
269	+
270		if (currentAtom->haveOrientation()){
271		dAtom = new DirectionalAtom((j + atomOffset),
272		info[k].getConfiguration());
#	Line 233 \| Line 280 \| void SimSetup::makeMolecules(void){
280		phi = currentAtom->getEulerPhi() * M_PI / 180.0;
281		theta = currentAtom->getEulerTheta() * M_PI / 180.0;
282		psi = currentAtom->getEulerPsi()* M_PI / 180.0;
236	–
237	–	Axx = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi));
238	–	Axy = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi));
239	–	Axz = sin(theta) * sin(psi);
240	–
241	–	Ayx = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi));
242	–	Ayy = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi));
243	–	Ayz = sin(theta) * cos(psi);
244	–
245	–	Azx = sin(phi) * sin(theta);
246	–	Azy = -cos(phi) * sin(theta);
247	–	Azz = cos(theta);
283
284	<	sux = 0.0;
285	<	suy = 0.0;
251	<	suz = 1.0;
252	<
253	<	ux = (Axx * sux) + (Ayx * suy) + (Azx * suz);
254	<	uy = (Axy * sux) + (Ayy * suy) + (Azy * suz);
255	<	uz = (Axz * sux) + (Ayz * suy) + (Azz * suz);
256	<
257	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
258	<
259	<	u = sqrt(uSqr);
260	<	ux = ux / u;
261	<	uy = uy / u;
262	<	uz = uz / u;
263	<
264	<	dAtom->setSUx(ux);
265	<	dAtom->setSUy(uy);
266	<	dAtom->setSUz(uz);
284	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
285	>
286		}
287		else{
269	–	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
270	–	info[k].getConfiguration());
271	–	}
272	–	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 284 \| 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
290	–	// exclude_I must always be the smaller of the pair
291	–	if (exI > exJ){
292	–	tempEx = exI;
293	–	exI = exJ;
294	–	exJ = tempEx;
295	–	}
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);
303	<	#else // isn't MPI
304	<
305	<	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
306	<	#endif //is_mpi
316	>	info[k].excludes->addPair(exI, exJ);
317		}
308	–	excludeOffset += molInfo.nBonds;
318
319		//make the bends
320		for (j = 0; j < molInfo.nBends; j++){
#	Line 355 \| 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{
363	<	exI = theBends[j].a;
364	<	exJ = theBends[j].b;
365	<	}
366	<
367	<	// exclude_I must always be the smaller of the pair
368	<	if (exI > exJ){
369	<	tempEx = exI;
370	<	exI = exJ;
371	<	exJ = tempEx;
372	<	}
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		}
384	–	excludeOffset += molInfo.nBends;
402
403		for (j = 0; j < molInfo.nTorsions; j++){
404		currentTorsion = comp_stamps[stampID]->getTorsion(j);
#	Line 390 \| 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
415	<	// exclude_I must always be the smaller of the pair
416	<	if (exI > exJ){
417	<	tempEx = exI;
418	<	exI = exJ;
419	<	exJ = tempEx;
415	>	#ifdef IS_MPI
416	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
417	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
418	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
419	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
420	>	#else
421	>	exI = tempI + 1;
422	>	exJ = tempJ + 1;
423	>	exK = tempK + 1;
424	>	exL = tempL + 1;
425	>	#endif
426	>
427	>	info[k].excludes->addPair(exI, exJ);
428	>	info[k].excludes->addPair(exI, exK);
429	>	info[k].excludes->addPair(exI, exL);
430	>	info[k].excludes->addPair(exJ, exK);
431	>	info[k].excludes->addPair(exJ, exL);
432	>	info[k].excludes->addPair(exK, exL);
433	>	}
434	>
435	>
436	>	molInfo.myRigidBodies.clear();
437	>
438	>	for (j = 0; j < molInfo.nRigidBodies; j++){
439	>
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	<	tempEx = exI;
490	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
491	<	tempEx = exJ;
492	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
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	<	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
502	<	#else // isn't MPI
410	<	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
411	<	#endif //is_mpi
501	>	molInfo.myRigidBodies.push_back(myRB);
502	>	info[k].rigidBodies.push_back(myRB);
503		}
504	<	excludeOffset += molInfo.nTorsions;
504	>
505
506	+	//create cutoff group for molecule
507
508	<	// send the arrays off to the forceField for init.
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
424	–
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 437 \| Line 699 \| void SimSetup::makeMolecules(void){
699		MPIcheckPoint();
700		#endif // is_mpi
701
440	–	// clean up the forcefield
441	–
442	–	the_ff->calcRcut();
443	–	the_ff->cleanMe();
702		}
703
704		void SimSetup::initFromBass(void){
#	Line 727 \| Line 985 \| void SimSetup::gatherInfo(void){
985		}
986
987		//check whether sample time, status time, thermal time and reset time are divisble by dt
988	<	if (!isDivisible(globals->getSampleTime(), globals->getDt())){
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"
#	Line 737 \| Line 995 \| void SimSetup::gatherInfo(void){
995		simError();
996		}
997
998	<	if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
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"
#	Line 773 \| Line 1031 \| void SimSetup::gatherInfo(void){
1031		if (globals->haveSampleTime()){
1032		info[i].sampleTime = globals->getSampleTime();
1033		info[i].statusTime = info[i].sampleTime;
776	–	info[i].thermalTime = info[i].sampleTime;
1034		}
1035		else{
1036		info[i].sampleTime = globals->getRunTime();
1037		info[i].statusTime = info[i].sampleTime;
781	–	info[i].thermalTime = info[i].sampleTime;
1038		}
1039
1040		if (globals->haveStatusTime()){
#	Line 787 \| 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 804 \| Line 1062 \| void SimSetup::gatherInfo(void){
1062
1063		info[i].useInitXSstate = globals->getUseInitXSstate();
1064		info[i].orthoTolerance = globals->getOrthoBoxTolerance();
1065	<
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 857 \| 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 868 \| 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->haveRcut()) {
1204	+	theRcut = globals->getRcut();
1205	+
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->haveECR()){
1228	>
1229	>	if (!globals->haveRcut()){
1230		sprintf(painCave.errMsg,
1231	<	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\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 electrostaticCutoffRadius.\n");
1233	>	"\tfor the cutoffRadius.\n");
1234		painCave.isFatal = 0;
1235		simError();
1236	<	theEcr = 15.0;
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: No value was set for electrostaticSkinThickness.\n"
1244	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1245		"\tOOPSE will use a default value of\n"
1246	<	"\t0.05 * electrostaticCutoffRadius\n"
900	<	"\tfor the electrostaticSkinThickness\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,
#	Line 919 \| Line 1265 \| void SimSetup::finalInfoCheck(void){
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: No value was set for electrostaticCutoffRadius.\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 electrostaticCutoffRadius.\n");
1275	<	painCave.isFatal = 0;
1276	<	simError();
1277	<	theEcr = 15.0;
1278	<	}
1274	>	"\tfor the cutoffRadius.\n");
1275	>	painCave.isFatal = 0;
1276	>	simError();
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: No value was set for electrostaticSkinThickness.\n"
1285	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1286		"\tOOPSE will use a default value of\n"
1287	<	"\t0.05 * electrostaticCutoffRadius\n"
941	<	"\tfor the electrostaticSkinThickness\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].setDefaultRcut(theRcut, theRsw);
1297
950	–	info[i].setDefaultEcr(theEcr, theEst);
1298		}
1299		}
1300		}
#	Line 955 \| Line 1302 \| void SimSetup::finalInfoCheck(void){
1302		strcpy(checkPointMsg, "post processing checks out");
1303		MPIcheckPoint();
1304		#endif // is_mpi
1305	+
1306	+	// clean up the forcefield
1307	+	the_ff->cleanMe();
1308		}
1309
1310		void SimSetup::initSystemCoords(void){
#	Line 1082 \| 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 1169 \| 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 1204 \| 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 1213 \| 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 1238 \| 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 1249 \| 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 1265 \| 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
1270	–
1674		for (i = 0; i < n_components; i++){
1675		for (j = 0; j < components_nmol[i]; j++){
1676		if (mol2proc[allMol] == worldRank){
#	Line 1275 \| 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 1287 \| 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\n"
#	Line 1298 \| Line 1713 \| void SimSetup::mpiMolDivide(void){
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 1320 \| Line 1745 \| void SimSetup::makeSysArrays(void){
1745
1746		Atom** the_atoms;
1747		Molecule* the_molecules;
1323	–	Exclude** the_excludes;
1748
1325	–
1749		for (l = 0; l < nInfo; l++){
1750		// create the atom and short range interaction arrays
1751
#	Line 1336 \| 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 1348 \| 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 1365 \| 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);
1371	<	the_excludes = new Exclude * [info[l].n_SRI];
1372	<	for (int ex = 0; ex < info[l].n_SRI; ex++){
1373	<	the_excludes[ex] = new Exclude(ex);
1374	<	}
1375	<	info[l].globalExcludes = new int;
1376	<	info[l].n_exclude = info[l].n_SRI;
1377	<	}
1378	<	else{
1379	<	Exclude::createArray(1);
1380	<	the_excludes = new Exclude * ;
1381	<	the_excludes[0] = new Exclude(0);
1382	<	the_excludes[0]->setPair(0, 0);
1383	<	info[l].globalExcludes = new int;
1384	<	info[l].globalExcludes[0] = 0;
1385	<	info[l].n_exclude = 0;
1386	<	}
1387	<
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;
1394	<
1799	>
1800		the_ff->setSimInfo(info);
1801		}
1802		}
#	Line 1682 \| Line 2087 \| void SimSetup::setupZConstraint(SimInfo& theInfo){
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 1712 \| 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

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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents): Revision 1091 by tim, Tue Mar 16 19:22:56 2004 UTC vs. Revision 1214 by gezelter, Tue Jun 1 18:42:58 2004 UTC

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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 1091 by tim, Tue Mar 16 19:22:56 2004 UTC vs.
Revision 1214 by gezelter, Tue Jun 1 18:42:58 2004 UTC