[ViewVC] Diff of: OpenMD/trunk/src/brains/SimInfo.cpp

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 432 by tim, Fri Mar 11 15:00:20 2005 UTC vs.
Revision 555 by chuckv, Mon May 30 14:01:52 2005 UTC

#	Line 1 \| Line 1
1	<	/*
1	>	/*
2		* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
#	Line 65 \| Line 65 \| namespace oopse {
65
66		namespace oopse {
67
68	<	SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
69	<	ForceField* ff, Globals* simParams) :
70	<	forceField_(ff), simParams_(simParams),
71	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
72	<	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
73	<	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
74	<	nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nRigidBodies_(0),
75	<	nIntegrableObjects_(0), nCutoffGroups_(0), nConstraints_(0),
76	<	sman_(NULL), fortranInitialized_(false) {
68	>	SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
69	>	ForceField* ff, Globals* simParams) :
70	>	stamps_(stamps), forceField_(ff), simParams_(simParams),
71	>	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
72	>	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
73	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
74	>	nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nRigidBodies_(0),
75	>	nIntegrableObjects_(0), nCutoffGroups_(0), nConstraints_(0),
76	>	sman_(NULL), fortranInitialized_(false) {
77
78
79	<	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
80	<	MoleculeStamp* molStamp;
81	<	int nMolWithSameStamp;
82	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
83	<	int nGroups = 0; //total cutoff groups defined in meta-data file
84	<	CutoffGroupStamp* cgStamp;
85	<	RigidBodyStamp* rbStamp;
86	<	int nRigidAtoms = 0;
79	>	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
80	>	MoleculeStamp* molStamp;
81	>	int nMolWithSameStamp;
82	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
83	>	int nGroups = 0; //total cutoff groups defined in meta-data file
84	>	CutoffGroupStamp* cgStamp;
85	>	RigidBodyStamp* rbStamp;
86	>	int nRigidAtoms = 0;
87
88	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
88	>	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
89		molStamp = i->first;
90		nMolWithSameStamp = i->second;
91
#	Line 100 \| Line 100 \| *SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp,**
100		int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
101
102		for (int j=0; j < nCutoffGroupsInStamp; j++) {
103	<	cgStamp = molStamp->getCutoffGroup(j);
104	<	nAtomsInGroups += cgStamp->getNMembers();
103	>	cgStamp = molStamp->getCutoffGroup(j);
104	>	nAtomsInGroups += cgStamp->getNMembers();
105		}
106
107		nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
#	Line 112 \| Line 112 \| *SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp,**
112		int nRigidBodiesInStamp = molStamp->getNRigidBodies();
113
114		for (int j=0; j < nRigidBodiesInStamp; j++) {
115	<	rbStamp = molStamp->getRigidBody(j);
116	<	nAtomsInRigidBodies += rbStamp->getNMembers();
115	>	rbStamp = molStamp->getRigidBody(j);
116	>	nAtomsInRigidBodies += rbStamp->getNMembers();
117		}
118
119		nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
120		nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
121
122	<	}
122	>	}
123
124	<	//every free atom (atom does not belong to cutoff groups) is a cutoff group
125	<	//therefore the total number of cutoff groups in the system is equal to
126	<	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
127	<	//file plus the number of cutoff groups defined in meta-data file
128	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
124	>	//every free atom (atom does not belong to cutoff groups) is a cutoff group
125	>	//therefore the total number of cutoff groups in the system is equal to
126	>	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
127	>	//file plus the number of cutoff groups defined in meta-data file
128	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
129
130	<	//every free atom (atom does not belong to rigid bodies) is an integrable object
131	<	//therefore the total number of integrable objects in the system is equal to
132	<	//the total number of atoms minus number of atoms belong to rigid body defined in meta-data
133	<	//file plus the number of rigid bodies defined in meta-data file
134	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
130	>	//every free atom (atom does not belong to rigid bodies) is an integrable object
131	>	//therefore the total number of integrable objects in the system is equal to
132	>	//the total number of atoms minus number of atoms belong to rigid body defined in meta-data
133	>	//file plus the number of rigid bodies defined in meta-data file
134	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
135
136	<	nGlobalMols_ = molStampIds_.size();
136	>	nGlobalMols_ = molStampIds_.size();
137
138		#ifdef IS_MPI
139	<	molToProcMap_.resize(nGlobalMols_);
139	>	molToProcMap_.resize(nGlobalMols_);
140		#endif
141
142	<	}
142	>	}
143
144	<	SimInfo::~SimInfo() {
144	>	SimInfo::~SimInfo() {
145		std::map<int, Molecule*>::iterator i;
146		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
147	<	delete i->second;
147	>	delete i->second;
148		}
149		molecules_.clear();
150	<
151	<	MemoryUtils::deletePointers(moleculeStamps_);
152	<
150	>
151	>	delete stamps_;
152		delete sman_;
153		delete simParams_;
154		delete forceField_;
155	<	}
155	>	}
156
157	<	int SimInfo::getNGlobalConstraints() {
157	>	int SimInfo::getNGlobalConstraints() {
158		int nGlobalConstraints;
159		#ifdef IS_MPI
160		MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
#	Line 164 \| Line 163 \| int SimInfo::getNGlobalConstraints() {
163		nGlobalConstraints = nConstraints_;
164		#endif
165		return nGlobalConstraints;
166	<	}
166	>	}
167
168	<	bool SimInfo::addMolecule(Molecule* mol) {
168	>	bool SimInfo::addMolecule(Molecule* mol) {
169		MoleculeIterator i;
170
171		i = molecules_.find(mol->getGlobalIndex());
172		if (i == molecules_.end() ) {
173
174	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
174	>	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
175
176	<	nAtoms_ += mol->getNAtoms();
177	<	nBonds_ += mol->getNBonds();
178	<	nBends_ += mol->getNBends();
179	<	nTorsions_ += mol->getNTorsions();
180	<	nRigidBodies_ += mol->getNRigidBodies();
181	<	nIntegrableObjects_ += mol->getNIntegrableObjects();
182	<	nCutoffGroups_ += mol->getNCutoffGroups();
183	<	nConstraints_ += mol->getNConstraintPairs();
176	>	nAtoms_ += mol->getNAtoms();
177	>	nBonds_ += mol->getNBonds();
178	>	nBends_ += mol->getNBends();
179	>	nTorsions_ += mol->getNTorsions();
180	>	nRigidBodies_ += mol->getNRigidBodies();
181	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
182	>	nCutoffGroups_ += mol->getNCutoffGroups();
183	>	nConstraints_ += mol->getNConstraintPairs();
184
185	<	addExcludePairs(mol);
185	>	addExcludePairs(mol);
186
187	<	return true;
187	>	return true;
188		} else {
189	<	return false;
189	>	return false;
190		}
191	<	}
191	>	}
192
193	<	bool SimInfo::removeMolecule(Molecule* mol) {
193	>	bool SimInfo::removeMolecule(Molecule* mol) {
194		MoleculeIterator i;
195		i = molecules_.find(mol->getGlobalIndex());
196
197		if (i != molecules_.end() ) {
198
199	<	assert(mol == i->second);
199	>	assert(mol == i->second);
200
201	<	nAtoms_ -= mol->getNAtoms();
202	<	nBonds_ -= mol->getNBonds();
203	<	nBends_ -= mol->getNBends();
204	<	nTorsions_ -= mol->getNTorsions();
205	<	nRigidBodies_ -= mol->getNRigidBodies();
206	<	nIntegrableObjects_ -= mol->getNIntegrableObjects();
207	<	nCutoffGroups_ -= mol->getNCutoffGroups();
208	<	nConstraints_ -= mol->getNConstraintPairs();
201	>	nAtoms_ -= mol->getNAtoms();
202	>	nBonds_ -= mol->getNBonds();
203	>	nBends_ -= mol->getNBends();
204	>	nTorsions_ -= mol->getNTorsions();
205	>	nRigidBodies_ -= mol->getNRigidBodies();
206	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
207	>	nCutoffGroups_ -= mol->getNCutoffGroups();
208	>	nConstraints_ -= mol->getNConstraintPairs();
209
210	<	removeExcludePairs(mol);
211	<	molecules_.erase(mol->getGlobalIndex());
210	>	removeExcludePairs(mol);
211	>	molecules_.erase(mol->getGlobalIndex());
212
213	<	delete mol;
213	>	delete mol;
214
215	<	return true;
215	>	return true;
216		} else {
217	<	return false;
217	>	return false;
218		}
219
220
221	<	}
221	>	}
222
223
224	<	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
224	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
225		i = molecules_.begin();
226		return i == molecules_.end() ? NULL : i->second;
227	<	}
227	>	}
228
229	<	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
229	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
230		++i;
231		return i == molecules_.end() ? NULL : i->second;
232	<	}
232	>	}
233
234
235	<	void SimInfo::calcNdf() {
235	>	void SimInfo::calcNdf() {
236		int ndf_local;
237		MoleculeIterator i;
238		std::vector<StuntDouble*>::iterator j;
#	Line 243 \| Line 242 \| void SimInfo::calcNdf() {
242		ndf_local = 0;
243
244		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
245	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
246	<	integrableObject = mol->nextIntegrableObject(j)) {
245	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
246	>	integrableObject = mol->nextIntegrableObject(j)) {
247
248	<	ndf_local += 3;
248	>	ndf_local += 3;
249
250	<	if (integrableObject->isDirectional()) {
251	<	if (integrableObject->isLinear()) {
252	<	ndf_local += 2;
253	<	} else {
254	<	ndf_local += 3;
255	<	}
256	<	}
250	>	if (integrableObject->isDirectional()) {
251	>	if (integrableObject->isLinear()) {
252	>	ndf_local += 2;
253	>	} else {
254	>	ndf_local += 3;
255	>	}
256	>	}
257
258	<	}//end for (integrableObject)
258	>	}//end for (integrableObject)
259		}// end for (mol)
260
261		// n_constraints is local, so subtract them on each processor
#	Line 272 \| Line 271 \| void SimInfo::calcNdf() {
271		// entire system:
272		ndf_ = ndf_ - 3 - nZconstraint_;
273
274	<	}
274	>	}
275
276	<	void SimInfo::calcNdfRaw() {
276	>	void SimInfo::calcNdfRaw() {
277		int ndfRaw_local;
278
279		MoleculeIterator i;
#	Line 286 \| Line 285 \| void SimInfo::calcNdfRaw() {
285		ndfRaw_local = 0;
286
287		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
288	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
289	<	integrableObject = mol->nextIntegrableObject(j)) {
288	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
289	>	integrableObject = mol->nextIntegrableObject(j)) {
290
291	<	ndfRaw_local += 3;
291	>	ndfRaw_local += 3;
292
293	<	if (integrableObject->isDirectional()) {
294	<	if (integrableObject->isLinear()) {
295	<	ndfRaw_local += 2;
296	<	} else {
297	<	ndfRaw_local += 3;
298	<	}
299	<	}
293	>	if (integrableObject->isDirectional()) {
294	>	if (integrableObject->isLinear()) {
295	>	ndfRaw_local += 2;
296	>	} else {
297	>	ndfRaw_local += 3;
298	>	}
299	>	}
300
301	<	}
301	>	}
302		}
303
304		#ifdef IS_MPI
#	Line 307 \| Line 306 \| void SimInfo::calcNdfRaw() {
306		#else
307		ndfRaw_ = ndfRaw_local;
308		#endif
309	<	}
309	>	}
310
311	<	void SimInfo::calcNdfTrans() {
311	>	void SimInfo::calcNdfTrans() {
312		int ndfTrans_local;
313
314		ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
#	Line 323 \| Line 322 \| void SimInfo::calcNdfTrans() {
322
323		ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
324
325	<	}
325	>	}
326
327	<	void SimInfo::addExcludePairs(Molecule* mol) {
327	>	void SimInfo::addExcludePairs(Molecule* mol) {
328		std::vector<Bond*>::iterator bondIter;
329		std::vector<Bend*>::iterator bendIter;
330		std::vector<Torsion*>::iterator torsionIter;
#	Line 338 \| Line 337 \| *void SimInfo::addExcludePairs(Molecule mol) {**
337		int d;
338
339		for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
340	<	a = bond->getAtomA()->getGlobalIndex();
341	<	b = bond->getAtomB()->getGlobalIndex();
342	<	exclude_.addPair(a, b);
340	>	a = bond->getAtomA()->getGlobalIndex();
341	>	b = bond->getAtomB()->getGlobalIndex();
342	>	exclude_.addPair(a, b);
343		}
344
345		for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
346	<	a = bend->getAtomA()->getGlobalIndex();
347	<	b = bend->getAtomB()->getGlobalIndex();
348	<	c = bend->getAtomC()->getGlobalIndex();
346	>	a = bend->getAtomA()->getGlobalIndex();
347	>	b = bend->getAtomB()->getGlobalIndex();
348	>	c = bend->getAtomC()->getGlobalIndex();
349
350	<	exclude_.addPair(a, b);
351	<	exclude_.addPair(a, c);
352	<	exclude_.addPair(b, c);
350	>	exclude_.addPair(a, b);
351	>	exclude_.addPair(a, c);
352	>	exclude_.addPair(b, c);
353		}
354
355		for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
356	<	a = torsion->getAtomA()->getGlobalIndex();
357	<	b = torsion->getAtomB()->getGlobalIndex();
358	<	c = torsion->getAtomC()->getGlobalIndex();
359	<	d = torsion->getAtomD()->getGlobalIndex();
356	>	a = torsion->getAtomA()->getGlobalIndex();
357	>	b = torsion->getAtomB()->getGlobalIndex();
358	>	c = torsion->getAtomC()->getGlobalIndex();
359	>	d = torsion->getAtomD()->getGlobalIndex();
360
361	<	exclude_.addPair(a, b);
362	<	exclude_.addPair(a, c);
363	<	exclude_.addPair(a, d);
364	<	exclude_.addPair(b, c);
365	<	exclude_.addPair(b, d);
366	<	exclude_.addPair(c, d);
361	>	exclude_.addPair(a, b);
362	>	exclude_.addPair(a, c);
363	>	exclude_.addPair(a, d);
364	>	exclude_.addPair(b, c);
365	>	exclude_.addPair(b, d);
366	>	exclude_.addPair(c, d);
367		}
368
369		Molecule::RigidBodyIterator rbIter;
370		RigidBody* rb;
371		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
372	<	std::vector<Atom*> atoms = rb->getAtoms();
373	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
374	<	for (int j = i + 1; j < atoms.size(); ++j) {
375	<	a = atoms[i]->getGlobalIndex();
376	<	b = atoms[j]->getGlobalIndex();
377	<	exclude_.addPair(a, b);
378	<	}
379	<	}
372	>	std::vector<Atom*> atoms = rb->getAtoms();
373	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
374	>	for (int j = i + 1; j < atoms.size(); ++j) {
375	>	a = atoms[i]->getGlobalIndex();
376	>	b = atoms[j]->getGlobalIndex();
377	>	exclude_.addPair(a, b);
378	>	}
379	>	}
380		}
381
382	<	Molecule::CutoffGroupIterator cgIter;
384	<	CutoffGroup* cg;
385	<	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
386	<	std::vector<Atom*> atoms = cg->getAtoms();
387	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
388	<	for (int j = i + 1; j < atoms.size(); ++j) {
389	<	a = atoms[i]->getGlobalIndex();
390	<	b = atoms[j]->getGlobalIndex();
391	<	exclude_.addPair(a, b);
392	<	}
393	<	}
394	<	}
382	>	}
383
384	<	}
397	<
398	<	void SimInfo::removeExcludePairs(Molecule* mol) {
384	>	void SimInfo::removeExcludePairs(Molecule* mol) {
385		std::vector<Bond*>::iterator bondIter;
386		std::vector<Bend*>::iterator bendIter;
387		std::vector<Torsion*>::iterator torsionIter;
#	Line 408 \| Line 394 \| *void SimInfo::removeExcludePairs(Molecule mol) {**
394		int d;
395
396		for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
397	<	a = bond->getAtomA()->getGlobalIndex();
398	<	b = bond->getAtomB()->getGlobalIndex();
399	<	exclude_.removePair(a, b);
397	>	a = bond->getAtomA()->getGlobalIndex();
398	>	b = bond->getAtomB()->getGlobalIndex();
399	>	exclude_.removePair(a, b);
400		}
401
402		for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
403	<	a = bend->getAtomA()->getGlobalIndex();
404	<	b = bend->getAtomB()->getGlobalIndex();
405	<	c = bend->getAtomC()->getGlobalIndex();
403	>	a = bend->getAtomA()->getGlobalIndex();
404	>	b = bend->getAtomB()->getGlobalIndex();
405	>	c = bend->getAtomC()->getGlobalIndex();
406
407	<	exclude_.removePair(a, b);
408	<	exclude_.removePair(a, c);
409	<	exclude_.removePair(b, c);
407	>	exclude_.removePair(a, b);
408	>	exclude_.removePair(a, c);
409	>	exclude_.removePair(b, c);
410		}
411
412		for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
413	<	a = torsion->getAtomA()->getGlobalIndex();
414	<	b = torsion->getAtomB()->getGlobalIndex();
415	<	c = torsion->getAtomC()->getGlobalIndex();
416	<	d = torsion->getAtomD()->getGlobalIndex();
413	>	a = torsion->getAtomA()->getGlobalIndex();
414	>	b = torsion->getAtomB()->getGlobalIndex();
415	>	c = torsion->getAtomC()->getGlobalIndex();
416	>	d = torsion->getAtomD()->getGlobalIndex();
417
418	<	exclude_.removePair(a, b);
419	<	exclude_.removePair(a, c);
420	<	exclude_.removePair(a, d);
421	<	exclude_.removePair(b, c);
422	<	exclude_.removePair(b, d);
423	<	exclude_.removePair(c, d);
418	>	exclude_.removePair(a, b);
419	>	exclude_.removePair(a, c);
420	>	exclude_.removePair(a, d);
421	>	exclude_.removePair(b, c);
422	>	exclude_.removePair(b, d);
423	>	exclude_.removePair(c, d);
424		}
425
426		Molecule::RigidBodyIterator rbIter;
427		RigidBody* rb;
428		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
429	<	std::vector<Atom*> atoms = rb->getAtoms();
430	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
431	<	for (int j = i + 1; j < atoms.size(); ++j) {
432	<	a = atoms[i]->getGlobalIndex();
433	<	b = atoms[j]->getGlobalIndex();
434	<	exclude_.removePair(a, b);
435	<	}
436	<	}
429	>	std::vector<Atom*> atoms = rb->getAtoms();
430	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
431	>	for (int j = i + 1; j < atoms.size(); ++j) {
432	>	a = atoms[i]->getGlobalIndex();
433	>	b = atoms[j]->getGlobalIndex();
434	>	exclude_.removePair(a, b);
435	>	}
436	>	}
437		}
438
439	<	Molecule::CutoffGroupIterator cgIter;
454	<	CutoffGroup* cg;
455	<	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
456	<	std::vector<Atom*> atoms = cg->getAtoms();
457	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
458	<	for (int j = i + 1; j < atoms.size(); ++j) {
459	<	a = atoms[i]->getGlobalIndex();
460	<	b = atoms[j]->getGlobalIndex();
461	<	exclude_.removePair(a, b);
462	<	}
463	<	}
464	<	}
439	>	}
440
466	–	}
441
442	<
469	<	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
442	>	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
443		int curStampId;
444
445		//index from 0
#	Line 474 \| Line 447 \| *void SimInfo::addMoleculeStamp(MoleculeStamp molStamp**
447
448		moleculeStamps_.push_back(molStamp);
449		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
450	<	}
450	>	}
451
452	<	void SimInfo::update() {
452	>	void SimInfo::update() {
453
454		setupSimType();
455
#	Line 491 \| Line 464 \| void SimInfo::update() {
464		int isError = 0;
465		initFortranFF( &fInfo_.SIM_uses_RF , &isError );
466		if(isError){
467	<	sprintf( painCave.errMsg,
468	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
469	<	painCave.isFatal = 1;
470	<	simError();
467	>	sprintf( painCave.errMsg,
468	>	"ForceField error: There was an error initializing the forceField in fortran.\n" );
469	>	painCave.isFatal = 1;
470	>	simError();
471		}
472
473
#	Line 505 \| Line 478 \| void SimInfo::update() {
478		calcNdfTrans();
479
480		fortranInitialized_ = true;
481	<	}
481	>	}
482
483	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
483	>	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
484		SimInfo::MoleculeIterator mi;
485		Molecule* mol;
486		Molecule::AtomIterator ai;
#	Line 516 \| Line 489 \| *std::set<AtomType> SimInfo::getUniqueAtomTypes() {**
489
490		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
491
492	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
493	<	atomTypes.insert(atom->getAtomType());
494	<	}
492	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
493	>	atomTypes.insert(atom->getAtomType());
494	>	}
495
496		}
497
498		return atomTypes;
499	<	}
499	>	}
500
501	<	void SimInfo::setupSimType() {
501	>	void SimInfo::setupSimType() {
502		std::set<AtomType*>::iterator i;
503		std::set<AtomType*> atomTypes;
504		atomTypes = getUniqueAtomTypes();
#	Line 538 \| Line 511 \| void SimInfo::setupSimType() {
511		int useDipole = 0;
512		int useGayBerne = 0;
513		int useSticky = 0;
514	+	int useStickyPower = 0;
515		int useShape = 0;
516		int useFLARB = 0; //it is not in AtomType yet
517		int useDirectionalAtom = 0;
#	Line 548 \| Line 522 \| void SimInfo::setupSimType() {
522
523		//loop over all of the atom types
524		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
525	<	useLennardJones \|= (*i)->isLennardJones();
526	<	useElectrostatic \|= (*i)->isElectrostatic();
527	<	useEAM \|= (*i)->isEAM();
528	<	useCharge \|= (*i)->isCharge();
529	<	useDirectional \|= (*i)->isDirectional();
530	<	useDipole \|= (*i)->isDipole();
531	<	useGayBerne \|= (*i)->isGayBerne();
532	<	useSticky \|= (*i)->isSticky();
533	<	useShape \|= (*i)->isShape();
525	>	useLennardJones \|= (*i)->isLennardJones();
526	>	useElectrostatic \|= (*i)->isElectrostatic();
527	>	useEAM \|= (*i)->isEAM();
528	>	useCharge \|= (*i)->isCharge();
529	>	useDirectional \|= (*i)->isDirectional();
530	>	useDipole \|= (*i)->isDipole();
531	>	useGayBerne \|= (*i)->isGayBerne();
532	>	useSticky \|= (*i)->isSticky();
533	>	useStickyPower \|= (*i)->isStickyPower();
534	>	useShape \|= (*i)->isShape();
535		}
536
537	<	if (useSticky \|\| useDipole \|\| useGayBerne \|\| useShape) {
538	<	useDirectionalAtom = 1;
537	>	if (useSticky \|\| useStickyPower \|\| useDipole \|\| useGayBerne \|\| useShape) {
538	>	useDirectionalAtom = 1;
539		}
540
541		if (useCharge \|\| useDipole) {
542	<	useElectrostatics = 1;
542	>	useElectrostatics = 1;
543		}
544
545		#ifdef IS_MPI
#	Line 591 \| Line 566 \| void SimInfo::setupSimType() {
566		temp = useSticky;
567		MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
568
569	+	temp = useStickyPower;
570	+	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
571	+
572		temp = useGayBerne;
573		MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
574
#	Line 615 \| Line 593 \| void SimInfo::setupSimType() {
593		fInfo_.SIM_uses_Charges = useCharge;
594		fInfo_.SIM_uses_Dipoles = useDipole;
595		fInfo_.SIM_uses_Sticky = useSticky;
596	+	fInfo_.SIM_uses_StickyPower = useStickyPower;
597		fInfo_.SIM_uses_GayBerne = useGayBerne;
598		fInfo_.SIM_uses_EAM = useEAM;
599		fInfo_.SIM_uses_Shapes = useShape;
#	Line 623 \| Line 602 \| void SimInfo::setupSimType() {
602
603		if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
604
605	<	if (simParams_->haveDielectric()) {
606	<	fInfo_.dielect = simParams_->getDielectric();
607	<	} else {
608	<	sprintf(painCave.errMsg,
609	<	"SimSetup Error: No Dielectric constant was set.\n"
610	<	"\tYou are trying to use Reaction Field without"
611	<	"\tsetting a dielectric constant!\n");
612	<	painCave.isFatal = 1;
613	<	simError();
614	<	}
605	>	if (simParams_->haveDielectric()) {
606	>	fInfo_.dielect = simParams_->getDielectric();
607	>	} else {
608	>	sprintf(painCave.errMsg,
609	>	"SimSetup Error: No Dielectric constant was set.\n"
610	>	"\tYou are trying to use Reaction Field without"
611	>	"\tsetting a dielectric constant!\n");
612	>	painCave.isFatal = 1;
613	>	simError();
614	>	}
615
616		} else {
617	<	fInfo_.dielect = 0.0;
617	>	fInfo_.dielect = 0.0;
618		}
619
620	<	}
620	>	}
621
622	<	void SimInfo::setupFortranSim() {
622	>	void SimInfo::setupFortranSim() {
623		int isError;
624		int nExclude;
625		std::vector<int> fortranGlobalGroupMembership;
#	Line 650 \| Line 629 \| void SimInfo::setupFortranSim() {
629
630		//globalGroupMembership_ is filled by SimCreator
631		for (int i = 0; i < nGlobalAtoms_; i++) {
632	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
632	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
633		}
634
635		//calculate mass ratio of cutoff group
#	Line 667 \| Line 646 \| void SimInfo::setupFortranSim() {
646		mfact.reserve(getNCutoffGroups());
647
648		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
649	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
649	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
650
651	<	totalMass = cg->getMass();
652	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
653	<	mfact.push_back(atom->getMass()/totalMass);
654	<	}
651	>	totalMass = cg->getMass();
652	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
653	>	mfact.push_back(atom->getMass()/totalMass);
654	>	}
655
656	<	}
656	>	}
657		}
658
659		//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
#	Line 684 \| Line 663 \| void SimInfo::setupFortranSim() {
663		identArray.reserve(getNAtoms());
664
665		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
666	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
667	<	identArray.push_back(atom->getIdent());
668	<	}
666	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
667	>	identArray.push_back(atom->getIdent());
668	>	}
669		}
670
671		//fill molMembershipArray
672		//molMembershipArray is filled by SimCreator
673		std::vector<int> molMembershipArray(nGlobalAtoms_);
674		for (int i = 0; i < nGlobalAtoms_; i++) {
675	<	molMembershipArray[i] = globalMolMembership_[i] + 1;
675	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
676		}
677
678		//setup fortran simulation
#	Line 701 \| Line 680 \| void SimInfo::setupFortranSim() {
680		int* globalExcludes = NULL;
681		int* excludeList = exclude_.getExcludeList();
682		setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
683	<	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
684	<	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
683	>	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
684	>	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
685
686		if( isError ){
687
688	<	sprintf( painCave.errMsg,
689	<	"There was an error setting the simulation information in fortran.\n" );
690	<	painCave.isFatal = 1;
691	<	painCave.severity = OOPSE_ERROR;
692	<	simError();
688	>	sprintf( painCave.errMsg,
689	>	"There was an error setting the simulation information in fortran.\n" );
690	>	painCave.isFatal = 1;
691	>	painCave.severity = OOPSE_ERROR;
692	>	simError();
693		}
694
695		#ifdef IS_MPI
696		sprintf( checkPointMsg,
697	<	"succesfully sent the simulation information to fortran.\n");
697	>	"succesfully sent the simulation information to fortran.\n");
698		MPIcheckPoint();
699		#endif // is_mpi
700	<	}
700	>	}
701
702
703		#ifdef IS_MPI
704	<	void SimInfo::setupFortranParallel() {
704	>	void SimInfo::setupFortranParallel() {
705
706		//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
707		std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
#	Line 738 \| Line 717 \| void SimInfo::setupFortranParallel() {
717
718		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
719
720	<	//local index(index in DataStorge) of atom is important
721	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
722	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
723	<	}
720	>	//local index(index in DataStorge) of atom is important
721	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
722	>	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
723	>	}
724
725	<	//local index of cutoff group is trivial, it only depends on the order of travesing
726	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
727	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
728	<	}
725	>	//local index of cutoff group is trivial, it only depends on the order of travesing
726	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
727	>	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
728	>	}
729
730		}
731
#	Line 766 \| Line 745 \| void SimInfo::setupFortranParallel() {
745		&localToGlobalCutoffGroupIndex[0], &isError);
746
747		if (isError) {
748	<	sprintf(painCave.errMsg,
749	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
750	<	painCave.isFatal = 1;
751	<	simError();
748	>	sprintf(painCave.errMsg,
749	>	"mpiRefresh errror: fortran didn't like something we gave it.\n");
750	>	painCave.isFatal = 1;
751	>	simError();
752		}
753
754		sprintf(checkPointMsg, " mpiRefresh successful.\n");
755		MPIcheckPoint();
756
757
758	<	}
758	>	}
759
760		#endif
761
762	<	double SimInfo::calcMaxCutoffRadius() {
762	>	double SimInfo::calcMaxCutoffRadius() {
763
764
765		std::set<AtomType*> atomTypes;
#	Line 792 \| Line 771 \| double SimInfo::calcMaxCutoffRadius() {
771
772		//query the max cutoff radius among these atom types
773		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
774	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
774	>	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
775		}
776
777		double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
#	Line 801 \| Line 780 \| double SimInfo::calcMaxCutoffRadius() {
780		#endif
781
782		return maxCutoffRadius;
783	<	}
783	>	}
784
785	<	void SimInfo::getCutoff(double& rcut, double& rsw) {
785	>	void SimInfo::getCutoff(double& rcut, double& rsw) {
786
787		if (fInfo_.SIM_uses_Charges \| fInfo_.SIM_uses_Dipoles \| fInfo_.SIM_uses_RF) {
788
789	<	if (!simParams_->haveRcut()){
790	<	sprintf(painCave.errMsg,
789	>	if (!simParams_->haveRcut()){
790	>	sprintf(painCave.errMsg,
791		"SimCreator Warning: No value was set for the cutoffRadius.\n"
792		"\tOOPSE will use a default value of 15.0 angstroms"
793		"\tfor the cutoffRadius.\n");
794	<	painCave.isFatal = 0;
795	<	simError();
796	<	rcut = 15.0;
797	<	} else{
798	<	rcut = simParams_->getRcut();
799	<	}
794	>	painCave.isFatal = 0;
795	>	simError();
796	>	rcut = 15.0;
797	>	} else{
798	>	rcut = simParams_->getRcut();
799	>	}
800
801	<	if (!simParams_->haveRsw()){
802	<	sprintf(painCave.errMsg,
801	>	if (!simParams_->haveRsw()){
802	>	sprintf(painCave.errMsg,
803		"SimCreator Warning: No value was set for switchingRadius.\n"
804		"\tOOPSE will use a default value of\n"
805		"\t0.95 * cutoffRadius for the switchingRadius\n");
806	<	painCave.isFatal = 0;
807	<	simError();
808	<	rsw = 0.95 * rcut;
809	<	} else{
810	<	rsw = simParams_->getRsw();
811	<	}
806	>	painCave.isFatal = 0;
807	>	simError();
808	>	rsw = 0.95 * rcut;
809	>	} else{
810	>	rsw = simParams_->getRsw();
811	>	}
812
813		} else {
814	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
815	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
814	>	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
815	>	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
816
817	<	if (simParams_->haveRcut()) {
818	<	rcut = simParams_->getRcut();
819	<	} else {
820	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
821	<	rcut = calcMaxCutoffRadius();
822	<	}
817	>	if (simParams_->haveRcut()) {
818	>	rcut = simParams_->getRcut();
819	>	} else {
820	>	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
821	>	rcut = calcMaxCutoffRadius();
822	>	}
823
824	<	if (simParams_->haveRsw()) {
825	<	rsw = simParams_->getRsw();
826	<	} else {
827	<	rsw = rcut;
828	<	}
824	>	if (simParams_->haveRsw()) {
825	>	rsw = simParams_->getRsw();
826	>	} else {
827	>	rsw = rcut;
828	>	}
829
830		}
831	<	}
831	>	}
832
833	<	void SimInfo::setupCutoff() {
833	>	void SimInfo::setupCutoff() {
834		getCutoff(rcut_, rsw_);
835		double rnblist = rcut_ + 1; // skin of neighbor list
836
837		//Pass these cutoff radius etc. to fortran. This function should be called once and only once
838		notifyFortranCutoffs(&rcut_, &rsw_, &rnblist);
839	<	}
839	>	}
840
841	<	void SimInfo::addProperty(GenericData* genData) {
841	>	void SimInfo::addProperty(GenericData* genData) {
842		properties_.addProperty(genData);
843	<	}
843	>	}
844
845	<	void SimInfo::removeProperty(const std::string& propName) {
845	>	void SimInfo::removeProperty(const std::string& propName) {
846		properties_.removeProperty(propName);
847	<	}
847	>	}
848
849	<	void SimInfo::clearProperties() {
849	>	void SimInfo::clearProperties() {
850		properties_.clearProperties();
851	<	}
851	>	}
852
853	<	std::vector<std::string> SimInfo::getPropertyNames() {
853	>	std::vector<std::string> SimInfo::getPropertyNames() {
854		return properties_.getPropertyNames();
855	<	}
855	>	}
856
857	<	std::vector<GenericData*> SimInfo::getProperties() {
857	>	std::vector<GenericData*> SimInfo::getProperties() {
858		return properties_.getProperties();
859	<	}
859	>	}
860
861	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
861	>	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
862		return properties_.getPropertyByName(propName);
863	<	}
863	>	}
864
865	<	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
865	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
866		if (sman_ == sman) {
867	<	return;
867	>	return;
868		}
869		delete sman_;
870		sman_ = sman;
#	Line 899 \| Line 878 \| *void SimInfo::setSnapshotManager(SnapshotManager sman**
878
879		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
880
881	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
882	<	atom->setSnapshotManager(sman_);
883	<	}
881	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
882	>	atom->setSnapshotManager(sman_);
883	>	}
884
885	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
886	<	rb->setSnapshotManager(sman_);
887	<	}
885	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
886	>	rb->setSnapshotManager(sman_);
887	>	}
888		}
889
890	<	}
890	>	}
891
892	<	Vector3d SimInfo::getComVel(){
892	>	Vector3d SimInfo::getComVel(){
893		SimInfo::MoleculeIterator i;
894		Molecule* mol;
895
#	Line 919 \| Line 898 \| Vector3d SimInfo::getComVel(){
898
899
900		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
901	<	double mass = mol->getMass();
902	<	totalMass += mass;
903	<	comVel += mass * mol->getComVel();
901	>	double mass = mol->getMass();
902	>	totalMass += mass;
903	>	comVel += mass * mol->getComVel();
904		}
905
906		#ifdef IS_MPI
#	Line 934 \| Line 913 \| Vector3d SimInfo::getComVel(){
913		comVel /= totalMass;
914
915		return comVel;
916	<	}
916	>	}
917
918	<	Vector3d SimInfo::getCom(){
918	>	Vector3d SimInfo::getCom(){
919		SimInfo::MoleculeIterator i;
920		Molecule* mol;
921
#	Line 944 \| Line 923 \| Vector3d SimInfo::getCom(){
923		double totalMass = 0.0;
924
925		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
926	<	double mass = mol->getMass();
927	<	totalMass += mass;
928	<	com += mass * mol->getCom();
926	>	double mass = mol->getMass();
927	>	totalMass += mass;
928	>	com += mass * mol->getCom();
929		}
930
931		#ifdef IS_MPI
#	Line 960 \| Line 939 \| Vector3d SimInfo::getCom(){
939
940		return com;
941
942	<	}
942	>	}
943
944	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
944	>	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
945
946		return o;
947	<	}
947	>	}
948	>
949	>
950	>	/*
951	>	Returns center of mass and center of mass velocity in one function call.
952	>	*/
953	>
954	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
955	>	SimInfo::MoleculeIterator i;
956	>	Molecule* mol;
957	>
958	>
959	>	double totalMass = 0.0;
960	>
961
962	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
963	+	double mass = mol->getMass();
964	+	totalMass += mass;
965	+	com += mass * mol->getCom();
966	+	comVel += mass * mol->getComVel();
967	+	}
968	+
969	+	#ifdef IS_MPI
970	+	double tmpMass = totalMass;
971	+	Vector3d tmpCom(com);
972	+	Vector3d tmpComVel(comVel);
973	+	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
974	+	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
975	+	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
976	+	#endif
977	+
978	+	com /= totalMass;
979	+	comVel /= totalMass;
980	+	}
981	+
982	+	/*
983	+	Return intertia tensor for entire system and angular momentum Vector.
984	+	*/
985	+
986	+	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
987	+
988	+
989	+	double xx = 0.0;
990	+	double yy = 0.0;
991	+	double zz = 0.0;
992	+	double xy = 0.0;
993	+	double xz = 0.0;
994	+	double yz = 0.0;
995	+	Vector3d com(0.0);
996	+	Vector3d comVel(0.0);
997	+
998	+	getComAll(com, comVel);
999	+
1000	+	SimInfo::MoleculeIterator i;
1001	+	Molecule* mol;
1002	+
1003	+	Vector3d thisq(0.0);
1004	+	Vector3d thisv(0.0);
1005	+
1006	+	double thisMass = 0.0;
1007	+
1008	+
1009	+
1010	+
1011	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1012	+
1013	+	thisq = mol->getCom()-com;
1014	+	thisv = mol->getComVel()-comVel;
1015	+	thisMass = mol->getMass();
1016	+	// Compute moment of intertia coefficients.
1017	+	xx += thisq[0]thisq[0]thisMass;
1018	+	yy += thisq[1]thisq[1]thisMass;
1019	+	zz += thisq[2]thisq[2]thisMass;
1020	+
1021	+	// compute products of intertia
1022	+	xy += thisq[0]thisq[1]thisMass;
1023	+	xz += thisq[0]thisq[2]thisMass;
1024	+	yz += thisq[1]thisq[2]thisMass;
1025	+
1026	+	angularMomentum += cross( thisq, thisv ) * thisMass;
1027	+
1028	+	}
1029	+
1030	+
1031	+	inertiaTensor(0,0) = yy + zz;
1032	+	inertiaTensor(0,1) = -xy;
1033	+	inertiaTensor(0,2) = -xz;
1034	+	inertiaTensor(1,0) = -xy;
1035	+	inertiaTensor(2,0) = xx + zz;
1036	+	inertiaTensor(1,2) = -yz;
1037	+	inertiaTensor(2,0) = -xz;
1038	+	inertiaTensor(2,1) = -yz;
1039	+	inertiaTensor(2,2) = xx + yy;
1040	+
1041	+	#ifdef IS_MPI
1042	+	Mat3x3d tmpI(inertiaTensor);
1043	+	Vector3d tmpAngMom;
1044	+	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1045	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1046	+	#endif
1047	+
1048	+	return;
1049	+	}
1050	+
1051	+	//Returns the angular momentum of the system
1052	+	Vector3d SimInfo::getAngularMomentum(){
1053	+
1054	+	Vector3d com(0.0);
1055	+	Vector3d comVel(0.0);
1056	+	Vector3d angularMomentum(0.0);
1057	+
1058	+	getComAll(com,comVel);
1059	+
1060	+	SimInfo::MoleculeIterator i;
1061	+	Molecule* mol;
1062	+
1063	+	Vector3d thisq(0.0);
1064	+	Vector3d thisv(0.0);
1065	+
1066	+	double thisMass = 0.0;
1067	+
1068	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1069	+	thisq = mol->getCom()-com;
1070	+	thisv = mol->getComVel()-comVel;
1071	+	thisMass = mol->getMass();
1072	+	angularMomentum += cross( thisq, thisv ) * thisMass;
1073	+
1074	+	}
1075	+
1076	+	#ifdef IS_MPI
1077	+	Vector3d tmpAngMom;
1078	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1079	+	#endif
1080	+
1081	+	return angularMomentum;
1082	+	}
1083	+
1084	+
1085		}//end namespace oopse
1086

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Comparing trunk/src/brains/SimInfo.cpp (file contents): Revision 432 by tim, Fri Mar 11 15:00:20 2005 UTC vs. Revision 555 by chuckv, Mon May 30 14:01:52 2005 UTC

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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 432 by tim, Fri Mar 11 15:00:20 2005 UTC vs.
Revision 555 by chuckv, Mon May 30 14:01:52 2005 UTC