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

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 435 by tim, Fri Mar 11 15:55:17 2005 UTC vs.
Revision 580 by chrisfen, Tue Aug 30 18:23:50 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	<	}
382	>	}
383
384	<	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 395 \| 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	<	}
439	>	}
440
441
442	<	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
442	>	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
443		int curStampId;
444
445		//index from 0
#	Line 448 \| 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 463 \| Line 462 \| void SimInfo::update() {
462		//setup fortran force field
463		/** @deprecate */
464		int isError = 0;
465	<	initFortranFF( &fInfo_.SIM_uses_RF , &isError );
465	>	initFortranFF( &fInfo_.SIM_uses_RF, &fInfo_.SIM_uses_UW,
466	>	&fInfo_.SIM_uses_DW, &isError );
467		if(isError){
468	<	sprintf( painCave.errMsg,
469	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
470	<	painCave.isFatal = 1;
471	<	simError();
468	>	sprintf( painCave.errMsg,
469	>	"ForceField error: There was an error initializing the forceField in fortran.\n" );
470	>	painCave.isFatal = 1;
471	>	simError();
472		}
473
474
#	Line 479 \| Line 479 \| void SimInfo::update() {
479		calcNdfTrans();
480
481		fortranInitialized_ = true;
482	<	}
482	>	}
483
484	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
484	>	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
485		SimInfo::MoleculeIterator mi;
486		Molecule* mol;
487		Molecule::AtomIterator ai;
#	Line 490 \| Line 490 \| *std::set<AtomType> SimInfo::getUniqueAtomTypes() {**
490
491		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
492
493	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
494	<	atomTypes.insert(atom->getAtomType());
495	<	}
493	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
494	>	atomTypes.insert(atom->getAtomType());
495	>	}
496
497		}
498
499		return atomTypes;
500	<	}
500	>	}
501
502	<	void SimInfo::setupSimType() {
502	>	void SimInfo::setupSimType() {
503		std::set<AtomType*>::iterator i;
504		std::set<AtomType*> atomTypes;
505		atomTypes = getUniqueAtomTypes();
#	Line 512 \| Line 512 \| void SimInfo::setupSimType() {
512		int useDipole = 0;
513		int useGayBerne = 0;
514		int useSticky = 0;
515	+	int useStickyPower = 0;
516		int useShape = 0;
517		int useFLARB = 0; //it is not in AtomType yet
518		int useDirectionalAtom = 0;
#	Line 519 \| Line 520 \| void SimInfo::setupSimType() {
520		//usePBC and useRF are from simParams
521		int usePBC = simParams_->getPBC();
522		int useRF = simParams_->getUseRF();
523	+	int useUW = simParams_->getUseUndampedWolf();
524	+	int useDW = simParams_->getUseDampedWolf();
525
526		//loop over all of the atom types
527		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
528	<	useLennardJones \|= (*i)->isLennardJones();
529	<	useElectrostatic \|= (*i)->isElectrostatic();
530	<	useEAM \|= (*i)->isEAM();
531	<	useCharge \|= (*i)->isCharge();
532	<	useDirectional \|= (*i)->isDirectional();
533	<	useDipole \|= (*i)->isDipole();
534	<	useGayBerne \|= (*i)->isGayBerne();
535	<	useSticky \|= (*i)->isSticky();
536	<	useShape \|= (*i)->isShape();
528	>	useLennardJones \|= (*i)->isLennardJones();
529	>	useElectrostatic \|= (*i)->isElectrostatic();
530	>	useEAM \|= (*i)->isEAM();
531	>	useCharge \|= (*i)->isCharge();
532	>	useDirectional \|= (*i)->isDirectional();
533	>	useDipole \|= (*i)->isDipole();
534	>	useGayBerne \|= (*i)->isGayBerne();
535	>	useSticky \|= (*i)->isSticky();
536	>	useStickyPower \|= (*i)->isStickyPower();
537	>	useShape \|= (*i)->isShape();
538		}
539
540	<	if (useSticky \|\| useDipole \|\| useGayBerne \|\| useShape) {
541	<	useDirectionalAtom = 1;
540	>	if (useSticky \|\| useStickyPower \|\| useDipole \|\| useGayBerne \|\| useShape) {
541	>	useDirectionalAtom = 1;
542		}
543
544		if (useCharge \|\| useDipole) {
545	<	useElectrostatics = 1;
545	>	useElectrostatics = 1;
546		}
547
548		#ifdef IS_MPI
#	Line 565 \| Line 569 \| void SimInfo::setupSimType() {
569		temp = useSticky;
570		MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
571
572	+	temp = useStickyPower;
573	+	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
574	+
575		temp = useGayBerne;
576		MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
577
#	Line 579 \| Line 586 \| void SimInfo::setupSimType() {
586
587		temp = useRF;
588		MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
589	+
590	+	temp = useUW;
591	+	MPI_Allreduce(&temp, &useUW, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
592	+
593	+	temp = useDW;
594	+	MPI_Allreduce(&temp, &useDW, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
595
596		#endif
597
#	Line 589 \| Line 602 \| void SimInfo::setupSimType() {
602		fInfo_.SIM_uses_Charges = useCharge;
603		fInfo_.SIM_uses_Dipoles = useDipole;
604		fInfo_.SIM_uses_Sticky = useSticky;
605	+	fInfo_.SIM_uses_StickyPower = useStickyPower;
606		fInfo_.SIM_uses_GayBerne = useGayBerne;
607		fInfo_.SIM_uses_EAM = useEAM;
608		fInfo_.SIM_uses_Shapes = useShape;
609		fInfo_.SIM_uses_FLARB = useFLARB;
610		fInfo_.SIM_uses_RF = useRF;
611	+	fInfo_.SIM_uses_UW = useUW;
612	+	fInfo_.SIM_uses_DW = useDW;
613
614		if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
615
616	<	if (simParams_->haveDielectric()) {
617	<	fInfo_.dielect = simParams_->getDielectric();
618	<	} else {
619	<	sprintf(painCave.errMsg,
620	<	"SimSetup Error: No Dielectric constant was set.\n"
621	<	"\tYou are trying to use Reaction Field without"
622	<	"\tsetting a dielectric constant!\n");
623	<	painCave.isFatal = 1;
624	<	simError();
625	<	}
616	>	if (simParams_->haveDielectric()) {
617	>	fInfo_.dielect = simParams_->getDielectric();
618	>	} else {
619	>	sprintf(painCave.errMsg,
620	>	"SimSetup Error: No Dielectric constant was set.\n"
621	>	"\tYou are trying to use Reaction Field without"
622	>	"\tsetting a dielectric constant!\n");
623	>	painCave.isFatal = 1;
624	>	simError();
625	>	}
626
627		} else {
628	<	fInfo_.dielect = 0.0;
628	>	fInfo_.dielect = 0.0;
629		}
630
631	<	}
631	>	}
632
633	<	void SimInfo::setupFortranSim() {
633	>	void SimInfo::setupFortranSim() {
634		int isError;
635		int nExclude;
636		std::vector<int> fortranGlobalGroupMembership;
#	Line 624 \| Line 640 \| void SimInfo::setupFortranSim() {
640
641		//globalGroupMembership_ is filled by SimCreator
642		for (int i = 0; i < nGlobalAtoms_; i++) {
643	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
643	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
644		}
645
646		//calculate mass ratio of cutoff group
#	Line 641 \| Line 657 \| void SimInfo::setupFortranSim() {
657		mfact.reserve(getNCutoffGroups());
658
659		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
660	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
660	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
661
662	<	totalMass = cg->getMass();
663	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
664	<	mfact.push_back(atom->getMass()/totalMass);
665	<	}
662	>	totalMass = cg->getMass();
663	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
664	>	mfact.push_back(atom->getMass()/totalMass);
665	>	}
666
667	<	}
667	>	}
668		}
669
670		//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
#	Line 658 \| Line 674 \| void SimInfo::setupFortranSim() {
674		identArray.reserve(getNAtoms());
675
676		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
677	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
678	<	identArray.push_back(atom->getIdent());
679	<	}
677	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
678	>	identArray.push_back(atom->getIdent());
679	>	}
680		}
681
682		//fill molMembershipArray
683		//molMembershipArray is filled by SimCreator
684		std::vector<int> molMembershipArray(nGlobalAtoms_);
685		for (int i = 0; i < nGlobalAtoms_; i++) {
686	<	molMembershipArray[i] = globalMolMembership_[i] + 1;
686	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
687		}
688
689		//setup fortran simulation
#	Line 675 \| Line 691 \| void SimInfo::setupFortranSim() {
691		int* globalExcludes = NULL;
692		int* excludeList = exclude_.getExcludeList();
693		setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
694	<	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
695	<	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
694	>	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
695	>	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
696
697		if( isError ){
698
699	<	sprintf( painCave.errMsg,
700	<	"There was an error setting the simulation information in fortran.\n" );
701	<	painCave.isFatal = 1;
702	<	painCave.severity = OOPSE_ERROR;
703	<	simError();
699	>	sprintf( painCave.errMsg,
700	>	"There was an error setting the simulation information in fortran.\n" );
701	>	painCave.isFatal = 1;
702	>	painCave.severity = OOPSE_ERROR;
703	>	simError();
704		}
705
706		#ifdef IS_MPI
707		sprintf( checkPointMsg,
708	<	"succesfully sent the simulation information to fortran.\n");
708	>	"succesfully sent the simulation information to fortran.\n");
709		MPIcheckPoint();
710		#endif // is_mpi
711	<	}
711	>	}
712
713
714		#ifdef IS_MPI
715	<	void SimInfo::setupFortranParallel() {
715	>	void SimInfo::setupFortranParallel() {
716
717		//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
718		std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
#	Line 712 \| Line 728 \| void SimInfo::setupFortranParallel() {
728
729		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
730
731	<	//local index(index in DataStorge) of atom is important
732	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
733	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
734	<	}
731	>	//local index(index in DataStorge) of atom is important
732	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
733	>	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
734	>	}
735
736	<	//local index of cutoff group is trivial, it only depends on the order of travesing
737	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
738	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
739	<	}
736	>	//local index of cutoff group is trivial, it only depends on the order of travesing
737	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
738	>	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
739	>	}
740
741		}
742
#	Line 740 \| Line 756 \| void SimInfo::setupFortranParallel() {
756		&localToGlobalCutoffGroupIndex[0], &isError);
757
758		if (isError) {
759	<	sprintf(painCave.errMsg,
760	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
761	<	painCave.isFatal = 1;
762	<	simError();
759	>	sprintf(painCave.errMsg,
760	>	"mpiRefresh errror: fortran didn't like something we gave it.\n");
761	>	painCave.isFatal = 1;
762	>	simError();
763		}
764
765		sprintf(checkPointMsg, " mpiRefresh successful.\n");
766		MPIcheckPoint();
767
768
769	<	}
769	>	}
770
771		#endif
772
773	<	double SimInfo::calcMaxCutoffRadius() {
773	>	double SimInfo::calcMaxCutoffRadius() {
774
775
776		std::set<AtomType*> atomTypes;
#	Line 766 \| Line 782 \| double SimInfo::calcMaxCutoffRadius() {
782
783		//query the max cutoff radius among these atom types
784		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
785	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
785	>	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
786		}
787
788		double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
#	Line 775 \| Line 791 \| double SimInfo::calcMaxCutoffRadius() {
791		#endif
792
793		return maxCutoffRadius;
794	<	}
794	>	}
795
796	<	void SimInfo::getCutoff(double& rcut, double& rsw) {
796	>	void SimInfo::getCutoff(double& rcut, double& rsw) {
797
798		if (fInfo_.SIM_uses_Charges \| fInfo_.SIM_uses_Dipoles \| fInfo_.SIM_uses_RF) {
799
800	<	if (!simParams_->haveRcut()){
801	<	sprintf(painCave.errMsg,
800	>	if (!simParams_->haveRcut()){
801	>	sprintf(painCave.errMsg,
802		"SimCreator Warning: No value was set for the cutoffRadius.\n"
803		"\tOOPSE will use a default value of 15.0 angstroms"
804		"\tfor the cutoffRadius.\n");
805	<	painCave.isFatal = 0;
806	<	simError();
807	<	rcut = 15.0;
808	<	} else{
809	<	rcut = simParams_->getRcut();
810	<	}
805	>	painCave.isFatal = 0;
806	>	simError();
807	>	rcut = 15.0;
808	>	} else{
809	>	rcut = simParams_->getRcut();
810	>	}
811
812	<	if (!simParams_->haveRsw()){
813	<	sprintf(painCave.errMsg,
812	>	if (!simParams_->haveRsw()){
813	>	sprintf(painCave.errMsg,
814		"SimCreator Warning: No value was set for switchingRadius.\n"
815		"\tOOPSE will use a default value of\n"
816		"\t0.95 * cutoffRadius for the switchingRadius\n");
817	<	painCave.isFatal = 0;
818	<	simError();
819	<	rsw = 0.95 * rcut;
820	<	} else{
821	<	rsw = simParams_->getRsw();
822	<	}
817	>	painCave.isFatal = 0;
818	>	simError();
819	>	rsw = 0.95 * rcut;
820	>	} else{
821	>	rsw = simParams_->getRsw();
822	>	}
823
824		} else {
825	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
826	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
825	>	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
826	>	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
827
828	<	if (simParams_->haveRcut()) {
829	<	rcut = simParams_->getRcut();
830	<	} else {
831	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
832	<	rcut = calcMaxCutoffRadius();
833	<	}
828	>	if (simParams_->haveRcut()) {
829	>	rcut = simParams_->getRcut();
830	>	} else {
831	>	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
832	>	rcut = calcMaxCutoffRadius();
833	>	}
834
835	<	if (simParams_->haveRsw()) {
836	<	rsw = simParams_->getRsw();
837	<	} else {
838	<	rsw = rcut;
839	<	}
835	>	if (simParams_->haveRsw()) {
836	>	rsw = simParams_->getRsw();
837	>	} else {
838	>	rsw = rcut;
839	>	}
840
841		}
842	<	}
842	>	}
843
844	<	void SimInfo::setupCutoff() {
844	>	void SimInfo::setupCutoff() {
845		getCutoff(rcut_, rsw_);
846		double rnblist = rcut_ + 1; // skin of neighbor list
847
848		//Pass these cutoff radius etc. to fortran. This function should be called once and only once
849		notifyFortranCutoffs(&rcut_, &rsw_, &rnblist);
850	<	}
850	>	}
851
852	<	void SimInfo::addProperty(GenericData* genData) {
852	>	void SimInfo::addProperty(GenericData* genData) {
853		properties_.addProperty(genData);
854	<	}
854	>	}
855
856	<	void SimInfo::removeProperty(const std::string& propName) {
856	>	void SimInfo::removeProperty(const std::string& propName) {
857		properties_.removeProperty(propName);
858	<	}
858	>	}
859
860	<	void SimInfo::clearProperties() {
860	>	void SimInfo::clearProperties() {
861		properties_.clearProperties();
862	<	}
862	>	}
863
864	<	std::vector<std::string> SimInfo::getPropertyNames() {
864	>	std::vector<std::string> SimInfo::getPropertyNames() {
865		return properties_.getPropertyNames();
866	<	}
866	>	}
867
868	<	std::vector<GenericData*> SimInfo::getProperties() {
868	>	std::vector<GenericData*> SimInfo::getProperties() {
869		return properties_.getProperties();
870	<	}
870	>	}
871
872	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
872	>	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
873		return properties_.getPropertyByName(propName);
874	<	}
874	>	}
875
876	<	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
876	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
877		if (sman_ == sman) {
878	<	return;
878	>	return;
879		}
880		delete sman_;
881		sman_ = sman;
#	Line 873 \| Line 889 \| *void SimInfo::setSnapshotManager(SnapshotManager sman**
889
890		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
891
892	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
893	<	atom->setSnapshotManager(sman_);
894	<	}
892	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
893	>	atom->setSnapshotManager(sman_);
894	>	}
895
896	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
897	<	rb->setSnapshotManager(sman_);
898	<	}
896	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
897	>	rb->setSnapshotManager(sman_);
898	>	}
899		}
900
901	<	}
901	>	}
902
903	<	Vector3d SimInfo::getComVel(){
903	>	Vector3d SimInfo::getComVel(){
904		SimInfo::MoleculeIterator i;
905		Molecule* mol;
906
#	Line 893 \| Line 909 \| Vector3d SimInfo::getComVel(){
909
910
911		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
912	<	double mass = mol->getMass();
913	<	totalMass += mass;
914	<	comVel += mass * mol->getComVel();
912	>	double mass = mol->getMass();
913	>	totalMass += mass;
914	>	comVel += mass * mol->getComVel();
915		}
916
917		#ifdef IS_MPI
#	Line 908 \| Line 924 \| Vector3d SimInfo::getComVel(){
924		comVel /= totalMass;
925
926		return comVel;
927	<	}
927	>	}
928
929	<	Vector3d SimInfo::getCom(){
929	>	Vector3d SimInfo::getCom(){
930		SimInfo::MoleculeIterator i;
931		Molecule* mol;
932
#	Line 918 \| Line 934 \| Vector3d SimInfo::getCom(){
934		double totalMass = 0.0;
935
936		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
937	<	double mass = mol->getMass();
938	<	totalMass += mass;
939	<	com += mass * mol->getCom();
937	>	double mass = mol->getMass();
938	>	totalMass += mass;
939	>	com += mass * mol->getCom();
940		}
941
942		#ifdef IS_MPI
#	Line 934 \| Line 950 \| Vector3d SimInfo::getCom(){
950
951		return com;
952
953	<	}
953	>	}
954
955	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
955	>	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
956
957		return o;
958	<	}
958	>	}
959	>
960	>
961	>	/*
962	>	Returns center of mass and center of mass velocity in one function call.
963	>	*/
964	>
965	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
966	>	SimInfo::MoleculeIterator i;
967	>	Molecule* mol;
968	>
969	>
970	>	double totalMass = 0.0;
971	>
972
973	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
974	+	double mass = mol->getMass();
975	+	totalMass += mass;
976	+	com += mass * mol->getCom();
977	+	comVel += mass * mol->getComVel();
978	+	}
979	+
980	+	#ifdef IS_MPI
981	+	double tmpMass = totalMass;
982	+	Vector3d tmpCom(com);
983	+	Vector3d tmpComVel(comVel);
984	+	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
985	+	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
986	+	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
987	+	#endif
988	+
989	+	com /= totalMass;
990	+	comVel /= totalMass;
991	+	}
992	+
993	+	/*
994	+	Return intertia tensor for entire system and angular momentum Vector.
995	+
996	+
997	+	[ Ixx -Ixy -Ixz ]
998	+	J =\| -Iyx Iyy -Iyz \|
999	+	[ -Izx -Iyz Izz ]
1000	+	*/
1001	+
1002	+	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1003	+
1004	+
1005	+	double xx = 0.0;
1006	+	double yy = 0.0;
1007	+	double zz = 0.0;
1008	+	double xy = 0.0;
1009	+	double xz = 0.0;
1010	+	double yz = 0.0;
1011	+	Vector3d com(0.0);
1012	+	Vector3d comVel(0.0);
1013	+
1014	+	getComAll(com, comVel);
1015	+
1016	+	SimInfo::MoleculeIterator i;
1017	+	Molecule* mol;
1018	+
1019	+	Vector3d thisq(0.0);
1020	+	Vector3d thisv(0.0);
1021	+
1022	+	double thisMass = 0.0;
1023	+
1024	+
1025	+
1026	+
1027	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1028	+
1029	+	thisq = mol->getCom()-com;
1030	+	thisv = mol->getComVel()-comVel;
1031	+	thisMass = mol->getMass();
1032	+	// Compute moment of intertia coefficients.
1033	+	xx += thisq[0]thisq[0]thisMass;
1034	+	yy += thisq[1]thisq[1]thisMass;
1035	+	zz += thisq[2]thisq[2]thisMass;
1036	+
1037	+	// compute products of intertia
1038	+	xy += thisq[0]thisq[1]thisMass;
1039	+	xz += thisq[0]thisq[2]thisMass;
1040	+	yz += thisq[1]thisq[2]thisMass;
1041	+
1042	+	angularMomentum += cross( thisq, thisv ) * thisMass;
1043	+
1044	+	}
1045	+
1046	+
1047	+	inertiaTensor(0,0) = yy + zz;
1048	+	inertiaTensor(0,1) = -xy;
1049	+	inertiaTensor(0,2) = -xz;
1050	+	inertiaTensor(1,0) = -xy;
1051	+	inertiaTensor(1,1) = xx + zz;
1052	+	inertiaTensor(1,2) = -yz;
1053	+	inertiaTensor(2,0) = -xz;
1054	+	inertiaTensor(2,1) = -yz;
1055	+	inertiaTensor(2,2) = xx + yy;
1056	+
1057	+	#ifdef IS_MPI
1058	+	Mat3x3d tmpI(inertiaTensor);
1059	+	Vector3d tmpAngMom;
1060	+	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1061	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1062	+	#endif
1063	+
1064	+	return;
1065	+	}
1066	+
1067	+	//Returns the angular momentum of the system
1068	+	Vector3d SimInfo::getAngularMomentum(){
1069	+
1070	+	Vector3d com(0.0);
1071	+	Vector3d comVel(0.0);
1072	+	Vector3d angularMomentum(0.0);
1073	+
1074	+	getComAll(com,comVel);
1075	+
1076	+	SimInfo::MoleculeIterator i;
1077	+	Molecule* mol;
1078	+
1079	+	Vector3d thisr(0.0);
1080	+	Vector3d thisp(0.0);
1081	+
1082	+	double thisMass;
1083	+
1084	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1085	+	thisMass = mol->getMass();
1086	+	thisr = mol->getCom()-com;
1087	+	thisp = (mol->getComVel()-comVel)*thisMass;
1088	+
1089	+	angularMomentum += cross( thisr, thisp );
1090	+
1091	+	}
1092	+
1093	+	#ifdef IS_MPI
1094	+	Vector3d tmpAngMom;
1095	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1096	+	#endif
1097	+
1098	+	return angularMomentum;
1099	+	}
1100	+
1101	+
1102		}//end namespace oopse
1103

Diff Legend

-–
+Removed lines
-+
+Added lines
-<
+Changed lines
->
+Changed lines

Comparing trunk/src/brains/SimInfo.cpp (file contents): Revision 435 by tim, Fri Mar 11 15:55:17 2005 UTC vs. Revision 580 by chrisfen, Tue Aug 30 18:23:50 2005 UTC

Diff Legend

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 435 by tim, Fri Mar 11 15:55:17 2005 UTC vs.
Revision 580 by chrisfen, Tue Aug 30 18:23:50 2005 UTC