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

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 328 by tim, Sun Feb 13 20:36:24 2005 UTC vs.
Revision 586 by gezelter, Wed Sep 7 20:46:46 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 52 \| Line 52
52		#include "brains/SimInfo.hpp"
53		#include "math/Vector3.hpp"
54		#include "primitives/Molecule.hpp"
55	+	#include "UseTheForce/fCutoffPolicy.h"
56		#include "UseTheForce/doForces_interface.h"
57		#include "UseTheForce/notifyCutoffs_interface.h"
58		#include "utils/MemoryUtils.hpp"
#	Line 65 \| Line 66 \| namespace oopse {
66
67		namespace oopse {
68
69	<	SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
70	<	ForceField* ff, Globals* simParams) :
71	<	forceField_(ff), simParams_(simParams),
72	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
73	<	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
74	<	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
75	<	nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nRigidBodies_(0),
76	<	nIntegrableObjects_(0), nCutoffGroups_(0), nConstraints_(0),
77	<	sman_(NULL), fortranInitialized_(false), selectMan_(NULL) {
69	>	SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
70	>	ForceField* ff, Globals* simParams) :
71	>	stamps_(stamps), forceField_(ff), simParams_(simParams),
72	>	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
73	>	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
74	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
75	>	nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nRigidBodies_(0),
76	>	nIntegrableObjects_(0), nCutoffGroups_(0), nConstraints_(0),
77	>	sman_(NULL), fortranInitialized_(false) {
78
79
80	<	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
81	<	MoleculeStamp* molStamp;
82	<	int nMolWithSameStamp;
83	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
84	<	int nGroups = 0; //total cutoff groups defined in meta-data file
85	<	CutoffGroupStamp* cgStamp;
86	<	RigidBodyStamp* rbStamp;
87	<	int nRigidAtoms = 0;
80	>	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
81	>	MoleculeStamp* molStamp;
82	>	int nMolWithSameStamp;
83	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
84	>	int nGroups = 0; //total cutoff groups defined in meta-data file
85	>	CutoffGroupStamp* cgStamp;
86	>	RigidBodyStamp* rbStamp;
87	>	int nRigidAtoms = 0;
88
89	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
89	>	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
90		molStamp = i->first;
91		nMolWithSameStamp = i->second;
92
#	Line 100 \| Line 101 \| *SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp,**
101		int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
102
103		for (int j=0; j < nCutoffGroupsInStamp; j++) {
104	<	cgStamp = molStamp->getCutoffGroup(j);
105	<	nAtomsInGroups += cgStamp->getNMembers();
104	>	cgStamp = molStamp->getCutoffGroup(j);
105	>	nAtomsInGroups += cgStamp->getNMembers();
106		}
107
108		nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
#	Line 112 \| Line 113 \| *SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp,**
113		int nRigidBodiesInStamp = molStamp->getNRigidBodies();
114
115		for (int j=0; j < nRigidBodiesInStamp; j++) {
116	<	rbStamp = molStamp->getRigidBody(j);
117	<	nAtomsInRigidBodies += rbStamp->getNMembers();
116	>	rbStamp = molStamp->getRigidBody(j);
117	>	nAtomsInRigidBodies += rbStamp->getNMembers();
118		}
119
120		nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
121		nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
122
123	<	}
123	>	}
124
125	<	//every free atom (atom does not belong to cutoff groups) is a cutoff group
126	<	//therefore the total number of cutoff groups in the system is equal to
127	<	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
128	<	//file plus the number of cutoff groups defined in meta-data file
129	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
125	>	//every free atom (atom does not belong to cutoff groups) is a cutoff group
126	>	//therefore the total number of cutoff groups in the system is equal to
127	>	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
128	>	//file plus the number of cutoff groups defined in meta-data file
129	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
130
131	<	//every free atom (atom does not belong to rigid bodies) is an integrable object
132	<	//therefore the total number of integrable objects in the system is equal to
133	<	//the total number of atoms minus number of atoms belong to rigid body defined in meta-data
134	<	//file plus the number of rigid bodies defined in meta-data file
135	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
131	>	//every free atom (atom does not belong to rigid bodies) is an integrable object
132	>	//therefore the total number of integrable objects in the system is equal to
133	>	//the total number of atoms minus number of atoms belong to rigid body defined in meta-data
134	>	//file plus the number of rigid bodies defined in meta-data file
135	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
136
137	<	nGlobalMols_ = molStampIds_.size();
137	>	nGlobalMols_ = molStampIds_.size();
138
139		#ifdef IS_MPI
140	<	molToProcMap_.resize(nGlobalMols_);
140	>	molToProcMap_.resize(nGlobalMols_);
141		#endif
142
143	<	selectMan_ = new SelectionManager(this);
143	<	selectMan_->selectAll();
144	<	}
143	>	}
144
145	<	SimInfo::~SimInfo() {
146	<	//MemoryUtils::deleteVectorOfPointer(molecules_);
147	<
148	<	MemoryUtils::deleteVectorOfPointer(moleculeStamps_);
149	<
145	>	SimInfo::~SimInfo() {
146	>	std::map<int, Molecule*>::iterator i;
147	>	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
148	>	delete i->second;
149	>	}
150	>	molecules_.clear();
151	>
152	>	delete stamps_;
153		delete sman_;
154		delete simParams_;
155		delete forceField_;
156	<	delete selectMan_;
155	<	}
156	>	}
157
158	<	int SimInfo::getNGlobalConstraints() {
158	>	int SimInfo::getNGlobalConstraints() {
159		int nGlobalConstraints;
160		#ifdef IS_MPI
161		MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
#	Line 163 \| Line 164 \| int SimInfo::getNGlobalConstraints() {
164		nGlobalConstraints = nConstraints_;
165		#endif
166		return nGlobalConstraints;
167	<	}
167	>	}
168
169	<	bool SimInfo::addMolecule(Molecule* mol) {
169	>	bool SimInfo::addMolecule(Molecule* mol) {
170		MoleculeIterator i;
171
172		i = molecules_.find(mol->getGlobalIndex());
173		if (i == molecules_.end() ) {
174
175	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
175	>	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
176
177	<	nAtoms_ += mol->getNAtoms();
178	<	nBonds_ += mol->getNBonds();
179	<	nBends_ += mol->getNBends();
180	<	nTorsions_ += mol->getNTorsions();
181	<	nRigidBodies_ += mol->getNRigidBodies();
182	<	nIntegrableObjects_ += mol->getNIntegrableObjects();
183	<	nCutoffGroups_ += mol->getNCutoffGroups();
184	<	nConstraints_ += mol->getNConstraintPairs();
177	>	nAtoms_ += mol->getNAtoms();
178	>	nBonds_ += mol->getNBonds();
179	>	nBends_ += mol->getNBends();
180	>	nTorsions_ += mol->getNTorsions();
181	>	nRigidBodies_ += mol->getNRigidBodies();
182	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
183	>	nCutoffGroups_ += mol->getNCutoffGroups();
184	>	nConstraints_ += mol->getNConstraintPairs();
185
186	<	addExcludePairs(mol);
186	>	addExcludePairs(mol);
187
188	<	return true;
188	>	return true;
189		} else {
190	<	return false;
190	>	return false;
191		}
192	<	}
192	>	}
193
194	<	bool SimInfo::removeMolecule(Molecule* mol) {
194	>	bool SimInfo::removeMolecule(Molecule* mol) {
195		MoleculeIterator i;
196		i = molecules_.find(mol->getGlobalIndex());
197
198		if (i != molecules_.end() ) {
199
200	<	assert(mol == i->second);
200	>	assert(mol == i->second);
201
202	<	nAtoms_ -= mol->getNAtoms();
203	<	nBonds_ -= mol->getNBonds();
204	<	nBends_ -= mol->getNBends();
205	<	nTorsions_ -= mol->getNTorsions();
206	<	nRigidBodies_ -= mol->getNRigidBodies();
207	<	nIntegrableObjects_ -= mol->getNIntegrableObjects();
208	<	nCutoffGroups_ -= mol->getNCutoffGroups();
209	<	nConstraints_ -= mol->getNConstraintPairs();
202	>	nAtoms_ -= mol->getNAtoms();
203	>	nBonds_ -= mol->getNBonds();
204	>	nBends_ -= mol->getNBends();
205	>	nTorsions_ -= mol->getNTorsions();
206	>	nRigidBodies_ -= mol->getNRigidBodies();
207	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
208	>	nCutoffGroups_ -= mol->getNCutoffGroups();
209	>	nConstraints_ -= mol->getNConstraintPairs();
210
211	<	removeExcludePairs(mol);
212	<	molecules_.erase(mol->getGlobalIndex());
211	>	removeExcludePairs(mol);
212	>	molecules_.erase(mol->getGlobalIndex());
213
214	<	delete mol;
214	>	delete mol;
215
216	<	return true;
216	>	return true;
217		} else {
218	<	return false;
218	>	return false;
219		}
220
221
222	<	}
222	>	}
223
224
225	<	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
225	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
226		i = molecules_.begin();
227		return i == molecules_.end() ? NULL : i->second;
228	<	}
228	>	}
229
230	<	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
230	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
231		++i;
232		return i == molecules_.end() ? NULL : i->second;
233	<	}
233	>	}
234
235
236	<	void SimInfo::calcNdf() {
236	>	void SimInfo::calcNdf() {
237		int ndf_local;
238		MoleculeIterator i;
239		std::vector<StuntDouble*>::iterator j;
#	Line 242 \| Line 243 \| void SimInfo::calcNdf() {
243		ndf_local = 0;
244
245		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
246	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
247	<	integrableObject = mol->nextIntegrableObject(j)) {
246	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
247	>	integrableObject = mol->nextIntegrableObject(j)) {
248
249	<	ndf_local += 3;
249	>	ndf_local += 3;
250
251	<	if (integrableObject->isDirectional()) {
252	<	if (integrableObject->isLinear()) {
253	<	ndf_local += 2;
254	<	} else {
255	<	ndf_local += 3;
256	<	}
257	<	}
251	>	if (integrableObject->isDirectional()) {
252	>	if (integrableObject->isLinear()) {
253	>	ndf_local += 2;
254	>	} else {
255	>	ndf_local += 3;
256	>	}
257	>	}
258
259	<	}//end for (integrableObject)
259	>	}//end for (integrableObject)
260		}// end for (mol)
261
262		// n_constraints is local, so subtract them on each processor
#	Line 271 \| Line 272 \| void SimInfo::calcNdf() {
272		// entire system:
273		ndf_ = ndf_ - 3 - nZconstraint_;
274
275	<	}
275	>	}
276
277	<	void SimInfo::calcNdfRaw() {
277	>	void SimInfo::calcNdfRaw() {
278		int ndfRaw_local;
279
280		MoleculeIterator i;
#	Line 285 \| Line 286 \| void SimInfo::calcNdfRaw() {
286		ndfRaw_local = 0;
287
288		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
289	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
290	<	integrableObject = mol->nextIntegrableObject(j)) {
289	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
290	>	integrableObject = mol->nextIntegrableObject(j)) {
291
292	<	ndfRaw_local += 3;
292	>	ndfRaw_local += 3;
293
294	<	if (integrableObject->isDirectional()) {
295	<	if (integrableObject->isLinear()) {
296	<	ndfRaw_local += 2;
297	<	} else {
298	<	ndfRaw_local += 3;
299	<	}
300	<	}
294	>	if (integrableObject->isDirectional()) {
295	>	if (integrableObject->isLinear()) {
296	>	ndfRaw_local += 2;
297	>	} else {
298	>	ndfRaw_local += 3;
299	>	}
300	>	}
301
302	<	}
302	>	}
303		}
304
305		#ifdef IS_MPI
#	Line 306 \| Line 307 \| void SimInfo::calcNdfRaw() {
307		#else
308		ndfRaw_ = ndfRaw_local;
309		#endif
310	<	}
310	>	}
311
312	<	void SimInfo::calcNdfTrans() {
312	>	void SimInfo::calcNdfTrans() {
313		int ndfTrans_local;
314
315		ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
#	Line 322 \| Line 323 \| void SimInfo::calcNdfTrans() {
323
324		ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
325
326	<	}
326	>	}
327
328	<	void SimInfo::addExcludePairs(Molecule* mol) {
328	>	void SimInfo::addExcludePairs(Molecule* mol) {
329		std::vector<Bond*>::iterator bondIter;
330		std::vector<Bend*>::iterator bendIter;
331		std::vector<Torsion*>::iterator torsionIter;
#	Line 337 \| Line 338 \| *void SimInfo::addExcludePairs(Molecule mol) {**
338		int d;
339
340		for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
341	<	a = bond->getAtomA()->getGlobalIndex();
342	<	b = bond->getAtomB()->getGlobalIndex();
343	<	exclude_.addPair(a, b);
341	>	a = bond->getAtomA()->getGlobalIndex();
342	>	b = bond->getAtomB()->getGlobalIndex();
343	>	exclude_.addPair(a, b);
344		}
345
346		for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
347	<	a = bend->getAtomA()->getGlobalIndex();
348	<	b = bend->getAtomB()->getGlobalIndex();
349	<	c = bend->getAtomC()->getGlobalIndex();
350	<
351	<	exclude_.addPair(a, b);
352	<	exclude_.addPair(a, c);
353	<	exclude_.addPair(b, c);
347	>	a = bend->getAtomA()->getGlobalIndex();
348	>	b = bend->getAtomB()->getGlobalIndex();
349	>	c = bend->getAtomC()->getGlobalIndex();
350	>
351	>	exclude_.addPair(a, b);
352	>	exclude_.addPair(a, c);
353	>	exclude_.addPair(b, c);
354		}
355
356		for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
357	<	a = torsion->getAtomA()->getGlobalIndex();
358	<	b = torsion->getAtomB()->getGlobalIndex();
359	<	c = torsion->getAtomC()->getGlobalIndex();
360	<	d = torsion->getAtomD()->getGlobalIndex();
357	>	a = torsion->getAtomA()->getGlobalIndex();
358	>	b = torsion->getAtomB()->getGlobalIndex();
359	>	c = torsion->getAtomC()->getGlobalIndex();
360	>	d = torsion->getAtomD()->getGlobalIndex();
361
362	<	exclude_.addPair(a, b);
363	<	exclude_.addPair(a, c);
364	<	exclude_.addPair(a, d);
365	<	exclude_.addPair(b, c);
366	<	exclude_.addPair(b, d);
367	<	exclude_.addPair(c, d);
362	>	exclude_.addPair(a, b);
363	>	exclude_.addPair(a, c);
364	>	exclude_.addPair(a, d);
365	>	exclude_.addPair(b, c);
366	>	exclude_.addPair(b, d);
367	>	exclude_.addPair(c, d);
368		}
369
370	<
371	<	}
370	>	Molecule::RigidBodyIterator rbIter;
371	>	RigidBody* rb;
372	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
373	>	std::vector<Atom*> atoms = rb->getAtoms();
374	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
375	>	for (int j = i + 1; j < atoms.size(); ++j) {
376	>	a = atoms[i]->getGlobalIndex();
377	>	b = atoms[j]->getGlobalIndex();
378	>	exclude_.addPair(a, b);
379	>	}
380	>	}
381	>	}
382
383	<	void SimInfo::removeExcludePairs(Molecule* mol) {
383	>	}
384	>
385	>	void SimInfo::removeExcludePairs(Molecule* mol) {
386		std::vector<Bond*>::iterator bondIter;
387		std::vector<Bend*>::iterator bendIter;
388		std::vector<Torsion*>::iterator torsionIter;
#	Line 382 \| Line 395 \| *void SimInfo::removeExcludePairs(Molecule mol) {**
395		int d;
396
397		for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
398	<	a = bond->getAtomA()->getGlobalIndex();
399	<	b = bond->getAtomB()->getGlobalIndex();
400	<	exclude_.removePair(a, b);
398	>	a = bond->getAtomA()->getGlobalIndex();
399	>	b = bond->getAtomB()->getGlobalIndex();
400	>	exclude_.removePair(a, b);
401		}
402
403		for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
404	<	a = bend->getAtomA()->getGlobalIndex();
405	<	b = bend->getAtomB()->getGlobalIndex();
406	<	c = bend->getAtomC()->getGlobalIndex();
404	>	a = bend->getAtomA()->getGlobalIndex();
405	>	b = bend->getAtomB()->getGlobalIndex();
406	>	c = bend->getAtomC()->getGlobalIndex();
407
408	<	exclude_.removePair(a, b);
409	<	exclude_.removePair(a, c);
410	<	exclude_.removePair(b, c);
408	>	exclude_.removePair(a, b);
409	>	exclude_.removePair(a, c);
410	>	exclude_.removePair(b, c);
411		}
412
413		for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
414	<	a = torsion->getAtomA()->getGlobalIndex();
415	<	b = torsion->getAtomB()->getGlobalIndex();
416	<	c = torsion->getAtomC()->getGlobalIndex();
417	<	d = torsion->getAtomD()->getGlobalIndex();
414	>	a = torsion->getAtomA()->getGlobalIndex();
415	>	b = torsion->getAtomB()->getGlobalIndex();
416	>	c = torsion->getAtomC()->getGlobalIndex();
417	>	d = torsion->getAtomD()->getGlobalIndex();
418
419	<	exclude_.removePair(a, b);
420	<	exclude_.removePair(a, c);
421	<	exclude_.removePair(a, d);
422	<	exclude_.removePair(b, c);
423	<	exclude_.removePair(b, d);
424	<	exclude_.removePair(c, d);
419	>	exclude_.removePair(a, b);
420	>	exclude_.removePair(a, c);
421	>	exclude_.removePair(a, d);
422	>	exclude_.removePair(b, c);
423	>	exclude_.removePair(b, d);
424	>	exclude_.removePair(c, d);
425		}
426
427	<	}
427	>	Molecule::RigidBodyIterator rbIter;
428	>	RigidBody* rb;
429	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
430	>	std::vector<Atom*> atoms = rb->getAtoms();
431	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
432	>	for (int j = i + 1; j < atoms.size(); ++j) {
433	>	a = atoms[i]->getGlobalIndex();
434	>	b = atoms[j]->getGlobalIndex();
435	>	exclude_.removePair(a, b);
436	>	}
437	>	}
438	>	}
439
440	+	}
441
442	<	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
442	>
443	>	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
444		int curStampId;
445
446		//index from 0
#	Line 422 \| Line 448 \| *void SimInfo::addMoleculeStamp(MoleculeStamp molStamp**
448
449		moleculeStamps_.push_back(molStamp);
450		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
451	<	}
451	>	}
452
453	<	void SimInfo::update() {
453	>	void SimInfo::update() {
454
455		setupSimType();
456
#	Line 437 \| Line 463 \| void SimInfo::update() {
463		//setup fortran force field
464		/** @deprecate */
465		int isError = 0;
466	<	initFortranFF( &fInfo_.SIM_uses_RF , &isError );
466	>	initFortranFF( &fInfo_.SIM_uses_RF, &fInfo_.SIM_uses_UW,
467	>	&fInfo_.SIM_uses_DW, &isError );
468		if(isError){
469	<	sprintf( painCave.errMsg,
470	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
471	<	painCave.isFatal = 1;
472	<	simError();
469	>	sprintf( painCave.errMsg,
470	>	"ForceField error: There was an error initializing the forceField in fortran.\n" );
471	>	painCave.isFatal = 1;
472	>	simError();
473		}
474
475
#	Line 453 \| Line 480 \| void SimInfo::update() {
480		calcNdfTrans();
481
482		fortranInitialized_ = true;
483	<	}
483	>	}
484
485	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
485	>	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
486		SimInfo::MoleculeIterator mi;
487		Molecule* mol;
488		Molecule::AtomIterator ai;
#	Line 464 \| Line 491 \| *std::set<AtomType> SimInfo::getUniqueAtomTypes() {**
491
492		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
493
494	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
495	<	atomTypes.insert(atom->getAtomType());
496	<	}
494	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
495	>	atomTypes.insert(atom->getAtomType());
496	>	}
497
498		}
499
500		return atomTypes;
501	<	}
501	>	}
502
503	<	void SimInfo::setupSimType() {
503	>	void SimInfo::setupSimType() {
504		std::set<AtomType*>::iterator i;
505		std::set<AtomType*> atomTypes;
506		atomTypes = getUniqueAtomTypes();
#	Line 486 \| Line 513 \| void SimInfo::setupSimType() {
513		int useDipole = 0;
514		int useGayBerne = 0;
515		int useSticky = 0;
516	+	int useStickyPower = 0;
517		int useShape = 0;
518		int useFLARB = 0; //it is not in AtomType yet
519		int useDirectionalAtom = 0;
#	Line 493 \| Line 521 \| void SimInfo::setupSimType() {
521		//usePBC and useRF are from simParams
522		int usePBC = simParams_->getPBC();
523		int useRF = simParams_->getUseRF();
524	+	int useUW = simParams_->getUseUndampedWolf();
525	+	int useDW = simParams_->getUseDampedWolf();
526
527		//loop over all of the atom types
528		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
529	<	useLennardJones \|= (*i)->isLennardJones();
530	<	useElectrostatic \|= (*i)->isElectrostatic();
531	<	useEAM \|= (*i)->isEAM();
532	<	useCharge \|= (*i)->isCharge();
533	<	useDirectional \|= (*i)->isDirectional();
534	<	useDipole \|= (*i)->isDipole();
535	<	useGayBerne \|= (*i)->isGayBerne();
536	<	useSticky \|= (*i)->isSticky();
537	<	useShape \|= (*i)->isShape();
529	>	useLennardJones \|= (*i)->isLennardJones();
530	>	useElectrostatic \|= (*i)->isElectrostatic();
531	>	useEAM \|= (*i)->isEAM();
532	>	useCharge \|= (*i)->isCharge();
533	>	useDirectional \|= (*i)->isDirectional();
534	>	useDipole \|= (*i)->isDipole();
535	>	useGayBerne \|= (*i)->isGayBerne();
536	>	useSticky \|= (*i)->isSticky();
537	>	useStickyPower \|= (*i)->isStickyPower();
538	>	useShape \|= (*i)->isShape();
539		}
540
541	<	if (useSticky \|\| useDipole \|\| useGayBerne \|\| useShape) {
542	<	useDirectionalAtom = 1;
541	>	if (useSticky \|\| useStickyPower \|\| useDipole \|\| useGayBerne \|\| useShape) {
542	>	useDirectionalAtom = 1;
543		}
544
545		if (useCharge \|\| useDipole) {
546	<	useElectrostatics = 1;
546	>	useElectrostatics = 1;
547		}
548
549		#ifdef IS_MPI
#	Line 539 \| Line 570 \| void SimInfo::setupSimType() {
570		temp = useSticky;
571		MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
572
573	+	temp = useStickyPower;
574	+	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
575	+
576		temp = useGayBerne;
577		MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
578
#	Line 553 \| Line 587 \| void SimInfo::setupSimType() {
587
588		temp = useRF;
589		MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
590	+
591	+	temp = useUW;
592	+	MPI_Allreduce(&temp, &useUW, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
593	+
594	+	temp = useDW;
595	+	MPI_Allreduce(&temp, &useDW, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
596
597		#endif
598
#	Line 563 \| Line 603 \| void SimInfo::setupSimType() {
603		fInfo_.SIM_uses_Charges = useCharge;
604		fInfo_.SIM_uses_Dipoles = useDipole;
605		fInfo_.SIM_uses_Sticky = useSticky;
606	+	fInfo_.SIM_uses_StickyPower = useStickyPower;
607		fInfo_.SIM_uses_GayBerne = useGayBerne;
608		fInfo_.SIM_uses_EAM = useEAM;
609		fInfo_.SIM_uses_Shapes = useShape;
610		fInfo_.SIM_uses_FLARB = useFLARB;
611		fInfo_.SIM_uses_RF = useRF;
612	+	fInfo_.SIM_uses_UW = useUW;
613	+	fInfo_.SIM_uses_DW = useDW;
614
615		if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
616
617	<	if (simParams_->haveDielectric()) {
618	<	fInfo_.dielect = simParams_->getDielectric();
619	<	} else {
620	<	sprintf(painCave.errMsg,
621	<	"SimSetup Error: No Dielectric constant was set.\n"
622	<	"\tYou are trying to use Reaction Field without"
623	<	"\tsetting a dielectric constant!\n");
624	<	painCave.isFatal = 1;
625	<	simError();
626	<	}
617	>	if (simParams_->haveDielectric()) {
618	>	fInfo_.dielect = simParams_->getDielectric();
619	>	} else {
620	>	sprintf(painCave.errMsg,
621	>	"SimSetup Error: No Dielectric constant was set.\n"
622	>	"\tYou are trying to use Reaction Field without"
623	>	"\tsetting a dielectric constant!\n");
624	>	painCave.isFatal = 1;
625	>	simError();
626	>	}
627
628		} else {
629	<	fInfo_.dielect = 0.0;
629	>	fInfo_.dielect = 0.0;
630		}
631
632	<	}
632	>	}
633
634	<	void SimInfo::setupFortranSim() {
634	>	void SimInfo::setupFortranSim() {
635		int isError;
636		int nExclude;
637		std::vector<int> fortranGlobalGroupMembership;
#	Line 598 \| Line 641 \| void SimInfo::setupFortranSim() {
641
642		//globalGroupMembership_ is filled by SimCreator
643		for (int i = 0; i < nGlobalAtoms_; i++) {
644	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
644	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
645		}
646
647		//calculate mass ratio of cutoff group
#	Line 615 \| Line 658 \| void SimInfo::setupFortranSim() {
658		mfact.reserve(getNCutoffGroups());
659
660		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
661	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
661	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
662
663	<	totalMass = cg->getMass();
664	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
665	<	mfact.push_back(atom->getMass()/totalMass);
666	<	}
663	>	totalMass = cg->getMass();
664	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
665	>	mfact.push_back(atom->getMass()/totalMass);
666	>	}
667
668	<	}
668	>	}
669		}
670
671		//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
#	Line 632 \| Line 675 \| void SimInfo::setupFortranSim() {
675		identArray.reserve(getNAtoms());
676
677		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
678	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
679	<	identArray.push_back(atom->getIdent());
680	<	}
678	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
679	>	identArray.push_back(atom->getIdent());
680	>	}
681		}
682
683		//fill molMembershipArray
684		//molMembershipArray is filled by SimCreator
685		std::vector<int> molMembershipArray(nGlobalAtoms_);
686		for (int i = 0; i < nGlobalAtoms_; i++) {
687	<	molMembershipArray[i] = globalMolMembership_[i] + 1;
687	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
688		}
689
690		//setup fortran simulation
648	–	//gloalExcludes and molMembershipArray should go away (They are never used)
649	–	//why the hell fortran need to know molecule?
650	–	//OOPSE = Object-Obfuscated Parallel Simulation Engine
691		int nGlobalExcludes = 0;
692		int* globalExcludes = NULL;
693		int* excludeList = exclude_.getExcludeList();
694		setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
695	<	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
696	<	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
695	>	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
696	>	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
697
698		if( isError ){
699
700	<	sprintf( painCave.errMsg,
701	<	"There was an error setting the simulation information in fortran.\n" );
702	<	painCave.isFatal = 1;
703	<	painCave.severity = OOPSE_ERROR;
704	<	simError();
700	>	sprintf( painCave.errMsg,
701	>	"There was an error setting the simulation information in fortran.\n" );
702	>	painCave.isFatal = 1;
703	>	painCave.severity = OOPSE_ERROR;
704	>	simError();
705		}
706
707		#ifdef IS_MPI
708		sprintf( checkPointMsg,
709	<	"succesfully sent the simulation information to fortran.\n");
709	>	"succesfully sent the simulation information to fortran.\n");
710		MPIcheckPoint();
711		#endif // is_mpi
712	<	}
712	>	}
713
714
715		#ifdef IS_MPI
716	<	void SimInfo::setupFortranParallel() {
716	>	void SimInfo::setupFortranParallel() {
717
718		//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
719		std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
#	Line 689 \| Line 729 \| void SimInfo::setupFortranParallel() {
729
730		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
731
732	<	//local index(index in DataStorge) of atom is important
733	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
734	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
735	<	}
732	>	//local index(index in DataStorge) of atom is important
733	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
734	>	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
735	>	}
736
737	<	//local index of cutoff group is trivial, it only depends on the order of travesing
738	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
739	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
740	<	}
737	>	//local index of cutoff group is trivial, it only depends on the order of travesing
738	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
739	>	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
740	>	}
741
742		}
743
#	Line 717 \| Line 757 \| void SimInfo::setupFortranParallel() {
757		&localToGlobalCutoffGroupIndex[0], &isError);
758
759		if (isError) {
760	<	sprintf(painCave.errMsg,
761	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
762	<	painCave.isFatal = 1;
763	<	simError();
760	>	sprintf(painCave.errMsg,
761	>	"mpiRefresh errror: fortran didn't like something we gave it.\n");
762	>	painCave.isFatal = 1;
763	>	simError();
764		}
765
766		sprintf(checkPointMsg, " mpiRefresh successful.\n");
767		MPIcheckPoint();
768
769
770	<	}
770	>	}
771
772		#endif
773
774	<	double SimInfo::calcMaxCutoffRadius() {
774	>	double SimInfo::calcMaxCutoffRadius() {
775
776
777		std::set<AtomType*> atomTypes;
#	Line 743 \| Line 783 \| double SimInfo::calcMaxCutoffRadius() {
783
784		//query the max cutoff radius among these atom types
785		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
786	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
786	>	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
787		}
788
789		double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
#	Line 752 \| Line 792 \| double SimInfo::calcMaxCutoffRadius() {
792		#endif
793
794		return maxCutoffRadius;
795	<	}
795	>	}
796
797	<	void SimInfo::getCutoff(double& rcut, double& rsw) {
797	>	void SimInfo::getCutoff(double& rcut, double& rsw) {
798
799		if (fInfo_.SIM_uses_Charges \| fInfo_.SIM_uses_Dipoles \| fInfo_.SIM_uses_RF) {
800
801	<	if (!simParams_->haveRcut()){
802	<	sprintf(painCave.errMsg,
801	>	if (!simParams_->haveRcut()){
802	>	sprintf(painCave.errMsg,
803		"SimCreator Warning: No value was set for the cutoffRadius.\n"
804		"\tOOPSE will use a default value of 15.0 angstroms"
805		"\tfor the cutoffRadius.\n");
806	<	painCave.isFatal = 0;
807	<	simError();
808	<	rcut = 15.0;
809	<	} else{
810	<	rcut = simParams_->getRcut();
811	<	}
806	>	painCave.isFatal = 0;
807	>	simError();
808	>	rcut = 15.0;
809	>	} else{
810	>	rcut = simParams_->getRcut();
811	>	}
812
813	<	if (!simParams_->haveRsw()){
814	<	sprintf(painCave.errMsg,
813	>	if (!simParams_->haveRsw()){
814	>	sprintf(painCave.errMsg,
815		"SimCreator Warning: No value was set for switchingRadius.\n"
816		"\tOOPSE will use a default value of\n"
817		"\t0.95 * cutoffRadius for the switchingRadius\n");
818	<	painCave.isFatal = 0;
819	<	simError();
820	<	rsw = 0.95 * rcut;
821	<	} else{
822	<	rsw = simParams_->getRsw();
823	<	}
818	>	painCave.isFatal = 0;
819	>	simError();
820	>	rsw = 0.95 * rcut;
821	>	} else{
822	>	rsw = simParams_->getRsw();
823	>	}
824
825		} else {
826	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
827	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
826	>	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
827	>	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
828
829	<	if (simParams_->haveRcut()) {
830	<	rcut = simParams_->getRcut();
831	<	} else {
832	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
833	<	rcut = calcMaxCutoffRadius();
834	<	}
829	>	if (simParams_->haveRcut()) {
830	>	rcut = simParams_->getRcut();
831	>	} else {
832	>	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
833	>	rcut = calcMaxCutoffRadius();
834	>	}
835
836	<	if (simParams_->haveRsw()) {
837	<	rsw = simParams_->getRsw();
838	<	} else {
839	<	rsw = rcut;
840	<	}
836	>	if (simParams_->haveRsw()) {
837	>	rsw = simParams_->getRsw();
838	>	} else {
839	>	rsw = rcut;
840	>	}
841
842		}
843	<	}
843	>	}
844
845	<	void SimInfo::setupCutoff() {
845	>	void SimInfo::setupCutoff() {
846		getCutoff(rcut_, rsw_);
847		double rnblist = rcut_ + 1; // skin of neighbor list
848
849		//Pass these cutoff radius etc. to fortran. This function should be called once and only once
850	<	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist);
851	<	}
850	>
851	>	int cp = TRADITIONAL_CUTOFF_POLICY;
852	>	if (simParams_->haveCutoffPolicy()) {
853	>	std::string myPolicy = simParams_->getCutoffPolicy();
854	>	if (myPolicy == "MIX") {
855	>	cp = MIX_CUTOFF_POLICY;
856	>	} else {
857	>	if (myPolicy == "MAX") {
858	>	cp = MAX_CUTOFF_POLICY;
859	>	} else {
860	>	if (myPolicy == "TRADITIONAL") {
861	>	cp = TRADITIONAL_CUTOFF_POLICY;
862	>	} else {
863	>	// throw error
864	>	sprintf( painCave.errMsg,
865	>	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
866	>	painCave.isFatal = 1;
867	>	simError();
868	>	}
869	>	}
870	>	}
871	>	}
872	>	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
873	>	}
874
875	<	void SimInfo::addProperty(GenericData* genData) {
875	>	void SimInfo::addProperty(GenericData* genData) {
876		properties_.addProperty(genData);
877	<	}
877	>	}
878
879	<	void SimInfo::removeProperty(const std::string& propName) {
879	>	void SimInfo::removeProperty(const std::string& propName) {
880		properties_.removeProperty(propName);
881	<	}
881	>	}
882
883	<	void SimInfo::clearProperties() {
883	>	void SimInfo::clearProperties() {
884		properties_.clearProperties();
885	<	}
885	>	}
886
887	<	std::vector<std::string> SimInfo::getPropertyNames() {
887	>	std::vector<std::string> SimInfo::getPropertyNames() {
888		return properties_.getPropertyNames();
889	<	}
889	>	}
890
891	<	std::vector<GenericData*> SimInfo::getProperties() {
891	>	std::vector<GenericData*> SimInfo::getProperties() {
892		return properties_.getProperties();
893	<	}
893	>	}
894
895	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
895	>	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
896		return properties_.getPropertyByName(propName);
897	<	}
897	>	}
898
899	<	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
899	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
900	>	if (sman_ == sman) {
901	>	return;
902	>	}
903	>	delete sman_;
904		sman_ = sman;
905
906		Molecule* mol;
#	Line 846 \| Line 912 \| *void SimInfo::setSnapshotManager(SnapshotManager sman**
912
913		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
914
915	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
916	<	atom->setSnapshotManager(sman_);
917	<	}
915	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
916	>	atom->setSnapshotManager(sman_);
917	>	}
918
919	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
920	<	rb->setSnapshotManager(sman_);
921	<	}
919	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
920	>	rb->setSnapshotManager(sman_);
921	>	}
922		}
923
924	<	}
924	>	}
925
926	<	Vector3d SimInfo::getComVel(){
926	>	Vector3d SimInfo::getComVel(){
927		SimInfo::MoleculeIterator i;
928		Molecule* mol;
929
#	Line 866 \| Line 932 \| Vector3d SimInfo::getComVel(){
932
933
934		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
935	<	double mass = mol->getMass();
936	<	totalMass += mass;
937	<	comVel += mass * mol->getComVel();
935	>	double mass = mol->getMass();
936	>	totalMass += mass;
937	>	comVel += mass * mol->getComVel();
938		}
939
940		#ifdef IS_MPI
#	Line 881 \| Line 947 \| Vector3d SimInfo::getComVel(){
947		comVel /= totalMass;
948
949		return comVel;
950	<	}
950	>	}
951
952	<	Vector3d SimInfo::getCom(){
952	>	Vector3d SimInfo::getCom(){
953		SimInfo::MoleculeIterator i;
954		Molecule* mol;
955
#	Line 891 \| Line 957 \| Vector3d SimInfo::getCom(){
957		double totalMass = 0.0;
958
959		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
960	<	double mass = mol->getMass();
961	<	totalMass += mass;
962	<	com += mass * mol->getCom();
960	>	double mass = mol->getMass();
961	>	totalMass += mass;
962	>	com += mass * mol->getCom();
963		}
964
965		#ifdef IS_MPI
#	Line 907 \| Line 973 \| Vector3d SimInfo::getCom(){
973
974		return com;
975
976	<	}
976	>	}
977
978	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
978	>	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
979
980		return o;
981	<	}
981	>	}
982	>
983	>
984	>	/*
985	>	Returns center of mass and center of mass velocity in one function call.
986	>	*/
987	>
988	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
989	>	SimInfo::MoleculeIterator i;
990	>	Molecule* mol;
991	>
992	>
993	>	double totalMass = 0.0;
994	>
995
996	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
997	+	double mass = mol->getMass();
998	+	totalMass += mass;
999	+	com += mass * mol->getCom();
1000	+	comVel += mass * mol->getComVel();
1001	+	}
1002	+
1003	+	#ifdef IS_MPI
1004	+	double tmpMass = totalMass;
1005	+	Vector3d tmpCom(com);
1006	+	Vector3d tmpComVel(comVel);
1007	+	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1008	+	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1009	+	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1010	+	#endif
1011	+
1012	+	com /= totalMass;
1013	+	comVel /= totalMass;
1014	+	}
1015	+
1016	+	/*
1017	+	Return intertia tensor for entire system and angular momentum Vector.
1018	+
1019	+
1020	+	[ Ixx -Ixy -Ixz ]
1021	+	J =\| -Iyx Iyy -Iyz \|
1022	+	[ -Izx -Iyz Izz ]
1023	+	*/
1024	+
1025	+	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1026	+
1027	+
1028	+	double xx = 0.0;
1029	+	double yy = 0.0;
1030	+	double zz = 0.0;
1031	+	double xy = 0.0;
1032	+	double xz = 0.0;
1033	+	double yz = 0.0;
1034	+	Vector3d com(0.0);
1035	+	Vector3d comVel(0.0);
1036	+
1037	+	getComAll(com, comVel);
1038	+
1039	+	SimInfo::MoleculeIterator i;
1040	+	Molecule* mol;
1041	+
1042	+	Vector3d thisq(0.0);
1043	+	Vector3d thisv(0.0);
1044	+
1045	+	double thisMass = 0.0;
1046	+
1047	+
1048	+
1049	+
1050	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1051	+
1052	+	thisq = mol->getCom()-com;
1053	+	thisv = mol->getComVel()-comVel;
1054	+	thisMass = mol->getMass();
1055	+	// Compute moment of intertia coefficients.
1056	+	xx += thisq[0]thisq[0]thisMass;
1057	+	yy += thisq[1]thisq[1]thisMass;
1058	+	zz += thisq[2]thisq[2]thisMass;
1059	+
1060	+	// compute products of intertia
1061	+	xy += thisq[0]thisq[1]thisMass;
1062	+	xz += thisq[0]thisq[2]thisMass;
1063	+	yz += thisq[1]thisq[2]thisMass;
1064	+
1065	+	angularMomentum += cross( thisq, thisv ) * thisMass;
1066	+
1067	+	}
1068	+
1069	+
1070	+	inertiaTensor(0,0) = yy + zz;
1071	+	inertiaTensor(0,1) = -xy;
1072	+	inertiaTensor(0,2) = -xz;
1073	+	inertiaTensor(1,0) = -xy;
1074	+	inertiaTensor(1,1) = xx + zz;
1075	+	inertiaTensor(1,2) = -yz;
1076	+	inertiaTensor(2,0) = -xz;
1077	+	inertiaTensor(2,1) = -yz;
1078	+	inertiaTensor(2,2) = xx + yy;
1079	+
1080	+	#ifdef IS_MPI
1081	+	Mat3x3d tmpI(inertiaTensor);
1082	+	Vector3d tmpAngMom;
1083	+	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1084	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1085	+	#endif
1086	+
1087	+	return;
1088	+	}
1089	+
1090	+	//Returns the angular momentum of the system
1091	+	Vector3d SimInfo::getAngularMomentum(){
1092	+
1093	+	Vector3d com(0.0);
1094	+	Vector3d comVel(0.0);
1095	+	Vector3d angularMomentum(0.0);
1096	+
1097	+	getComAll(com,comVel);
1098	+
1099	+	SimInfo::MoleculeIterator i;
1100	+	Molecule* mol;
1101	+
1102	+	Vector3d thisr(0.0);
1103	+	Vector3d thisp(0.0);
1104	+
1105	+	double thisMass;
1106	+
1107	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1108	+	thisMass = mol->getMass();
1109	+	thisr = mol->getCom()-com;
1110	+	thisp = (mol->getComVel()-comVel)*thisMass;
1111	+
1112	+	angularMomentum += cross( thisr, thisp );
1113	+
1114	+	}
1115	+
1116	+	#ifdef IS_MPI
1117	+	Vector3d tmpAngMom;
1118	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1119	+	#endif
1120	+
1121	+	return angularMomentum;
1122	+	}
1123	+
1124	+
1125		}//end namespace oopse
1126

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Comparing trunk/src/brains/SimInfo.cpp (file contents): Revision 328 by tim, Sun Feb 13 20:36:24 2005 UTC vs. Revision 586 by gezelter, Wed Sep 7 20:46:46 2005 UTC

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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 328 by tim, Sun Feb 13 20:36:24 2005 UTC vs.
Revision 586 by gezelter, Wed Sep 7 20:46:46 2005 UTC