[ViewVC] Diff of: group/trunk/OOPSE-2.0/src/brains/SimInfo.cpp

Comparing trunk/OOPSE-2.0/src/brains/SimInfo.cpp (file contents):
Revision 2116 by tim, Fri Mar 11 15:00:20 2005 UTC vs.
Revision 2297 by chrisfen, Thu Sep 15 00:14:35 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/fCoulombicCorrection.h"
57		#include "UseTheForce/doForces_interface.h"
58		#include "UseTheForce/notifyCutoffs_interface.h"
59		#include "utils/MemoryUtils.hpp"
#	Line 65 \| Line 67 \| *SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp,**
67
68		namespace oopse {
69
70	<	SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
71	<	ForceField* ff, Globals* simParams) :
72	<	forceField_(ff), simParams_(simParams),
73	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
74	<	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
75	<	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
76	<	nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nRigidBodies_(0),
77	<	nIntegrableObjects_(0), nCutoffGroups_(0), nConstraints_(0),
78	<	sman_(NULL), fortranInitialized_(false) {
70	>	SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
71	>	ForceField* ff, Globals* simParams) :
72	>	stamps_(stamps), forceField_(ff), simParams_(simParams),
73	>	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
74	>	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
75	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
76	>	nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nRigidBodies_(0),
77	>	nIntegrableObjects_(0), nCutoffGroups_(0), nConstraints_(0),
78	>	sman_(NULL), fortranInitialized_(false) {
79
80
81	<	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
82	<	MoleculeStamp* molStamp;
83	<	int nMolWithSameStamp;
84	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
85	<	int nGroups = 0; //total cutoff groups defined in meta-data file
86	<	CutoffGroupStamp* cgStamp;
87	<	RigidBodyStamp* rbStamp;
88	<	int nRigidAtoms = 0;
81	>	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
82	>	MoleculeStamp* molStamp;
83	>	int nMolWithSameStamp;
84	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
85	>	int nGroups = 0; //total cutoff groups defined in meta-data file
86	>	CutoffGroupStamp* cgStamp;
87	>	RigidBodyStamp* rbStamp;
88	>	int nRigidAtoms = 0;
89
90	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
90	>	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
91		molStamp = i->first;
92		nMolWithSameStamp = i->second;
93
#	Line 100 \| Line 102 \| *SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp,**
102		int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
103
104		for (int j=0; j < nCutoffGroupsInStamp; j++) {
105	<	cgStamp = molStamp->getCutoffGroup(j);
106	<	nAtomsInGroups += cgStamp->getNMembers();
105	>	cgStamp = molStamp->getCutoffGroup(j);
106	>	nAtomsInGroups += cgStamp->getNMembers();
107		}
108
109		nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
#	Line 112 \| Line 114 \| *SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp,**
114		int nRigidBodiesInStamp = molStamp->getNRigidBodies();
115
116		for (int j=0; j < nRigidBodiesInStamp; j++) {
117	<	rbStamp = molStamp->getRigidBody(j);
118	<	nAtomsInRigidBodies += rbStamp->getNMembers();
117	>	rbStamp = molStamp->getRigidBody(j);
118	>	nAtomsInRigidBodies += rbStamp->getNMembers();
119		}
120
121		nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
122		nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
123
124	<	}
124	>	}
125
126	<	//every free atom (atom does not belong to cutoff groups) is a cutoff group
127	<	//therefore the total number of cutoff groups in the system is equal to
128	<	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
129	<	//file plus the number of cutoff groups defined in meta-data file
130	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
126	>	//every free atom (atom does not belong to cutoff groups) is a cutoff group
127	>	//therefore the total number of cutoff groups in the system is equal to
128	>	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
129	>	//file plus the number of cutoff groups defined in meta-data file
130	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
131
132	<	//every free atom (atom does not belong to rigid bodies) is an integrable object
133	<	//therefore the total number of integrable objects in the system is equal to
134	<	//the total number of atoms minus number of atoms belong to rigid body defined in meta-data
135	<	//file plus the number of rigid bodies defined in meta-data file
136	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
132	>	//every free atom (atom does not belong to rigid bodies) is an integrable object
133	>	//therefore the total number of integrable objects in the system is equal to
134	>	//the total number of atoms minus number of atoms belong to rigid body defined in meta-data
135	>	//file plus the number of rigid bodies defined in meta-data file
136	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
137
138	<	nGlobalMols_ = molStampIds_.size();
138	>	nGlobalMols_ = molStampIds_.size();
139
140		#ifdef IS_MPI
141	<	molToProcMap_.resize(nGlobalMols_);
141	>	molToProcMap_.resize(nGlobalMols_);
142		#endif
143
144	<	}
144	>	}
145
146	<	SimInfo::~SimInfo() {
146	>	SimInfo::~SimInfo() {
147		std::map<int, Molecule*>::iterator i;
148		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
149	<	delete i->second;
149	>	delete i->second;
150		}
151		molecules_.clear();
152	<
153	<	MemoryUtils::deletePointers(moleculeStamps_);
152	<
152	>
153	>	delete stamps_;
154		delete sman_;
155		delete simParams_;
156		delete forceField_;
157	<	}
157	>	}
158
159	<	int SimInfo::getNGlobalConstraints() {
159	>	int SimInfo::getNGlobalConstraints() {
160		int nGlobalConstraints;
161		#ifdef IS_MPI
162		MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
#	Line 164 \| Line 165 \| int SimInfo::getNGlobalConstraints() {
165		nGlobalConstraints = nConstraints_;
166		#endif
167		return nGlobalConstraints;
168	<	}
168	>	}
169
170	<	bool SimInfo::addMolecule(Molecule* mol) {
170	>	bool SimInfo::addMolecule(Molecule* mol) {
171		MoleculeIterator i;
172
173		i = molecules_.find(mol->getGlobalIndex());
174		if (i == molecules_.end() ) {
175
176	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
176	>	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
177
178	<	nAtoms_ += mol->getNAtoms();
179	<	nBonds_ += mol->getNBonds();
180	<	nBends_ += mol->getNBends();
181	<	nTorsions_ += mol->getNTorsions();
182	<	nRigidBodies_ += mol->getNRigidBodies();
183	<	nIntegrableObjects_ += mol->getNIntegrableObjects();
184	<	nCutoffGroups_ += mol->getNCutoffGroups();
185	<	nConstraints_ += mol->getNConstraintPairs();
178	>	nAtoms_ += mol->getNAtoms();
179	>	nBonds_ += mol->getNBonds();
180	>	nBends_ += mol->getNBends();
181	>	nTorsions_ += mol->getNTorsions();
182	>	nRigidBodies_ += mol->getNRigidBodies();
183	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
184	>	nCutoffGroups_ += mol->getNCutoffGroups();
185	>	nConstraints_ += mol->getNConstraintPairs();
186
187	<	addExcludePairs(mol);
187	>	addExcludePairs(mol);
188
189	<	return true;
189	>	return true;
190		} else {
191	<	return false;
191	>	return false;
192		}
193	<	}
193	>	}
194
195	<	bool SimInfo::removeMolecule(Molecule* mol) {
195	>	bool SimInfo::removeMolecule(Molecule* mol) {
196		MoleculeIterator i;
197		i = molecules_.find(mol->getGlobalIndex());
198
199		if (i != molecules_.end() ) {
200
201	<	assert(mol == i->second);
201	>	assert(mol == i->second);
202
203	<	nAtoms_ -= mol->getNAtoms();
204	<	nBonds_ -= mol->getNBonds();
205	<	nBends_ -= mol->getNBends();
206	<	nTorsions_ -= mol->getNTorsions();
207	<	nRigidBodies_ -= mol->getNRigidBodies();
208	<	nIntegrableObjects_ -= mol->getNIntegrableObjects();
209	<	nCutoffGroups_ -= mol->getNCutoffGroups();
210	<	nConstraints_ -= mol->getNConstraintPairs();
210	<
211	<	removeExcludePairs(mol);
212	<	molecules_.erase(mol->getGlobalIndex());
203	>	nAtoms_ -= mol->getNAtoms();
204	>	nBonds_ -= mol->getNBonds();
205	>	nBends_ -= mol->getNBends();
206	>	nTorsions_ -= mol->getNTorsions();
207	>	nRigidBodies_ -= mol->getNRigidBodies();
208	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
209	>	nCutoffGroups_ -= mol->getNCutoffGroups();
210	>	nConstraints_ -= mol->getNConstraintPairs();
211
212	<	delete mol;
212	>	removeExcludePairs(mol);
213	>	molecules_.erase(mol->getGlobalIndex());
214	>
215	>	delete mol;
216
217	<	return true;
217	>	return true;
218		} else {
219	<	return false;
219	>	return false;
220		}
221
222
223	<	}
223	>	}
224
225
226	<	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
226	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
227		i = molecules_.begin();
228		return i == molecules_.end() ? NULL : i->second;
229	<	}
229	>	}
230
231	<	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
231	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
232		++i;
233		return i == molecules_.end() ? NULL : i->second;
234	<	}
234	>	}
235
236
237	<	void SimInfo::calcNdf() {
237	>	void SimInfo::calcNdf() {
238		int ndf_local;
239		MoleculeIterator i;
240		std::vector<StuntDouble*>::iterator j;
#	Line 243 \| Line 244 \| void SimInfo::calcNdf() {
244		ndf_local = 0;
245
246		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
247	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
248	<	integrableObject = mol->nextIntegrableObject(j)) {
247	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
248	>	integrableObject = mol->nextIntegrableObject(j)) {
249
250	<	ndf_local += 3;
250	>	ndf_local += 3;
251
252	<	if (integrableObject->isDirectional()) {
253	<	if (integrableObject->isLinear()) {
254	<	ndf_local += 2;
255	<	} else {
256	<	ndf_local += 3;
257	<	}
258	<	}
252	>	if (integrableObject->isDirectional()) {
253	>	if (integrableObject->isLinear()) {
254	>	ndf_local += 2;
255	>	} else {
256	>	ndf_local += 3;
257	>	}
258	>	}
259
260	<	}//end for (integrableObject)
260	>	}//end for (integrableObject)
261		}// end for (mol)
262
263		// n_constraints is local, so subtract them on each processor
#	Line 272 \| Line 273 \| void SimInfo::calcNdf() {
273		// entire system:
274		ndf_ = ndf_ - 3 - nZconstraint_;
275
276	<	}
276	>	}
277
278	<	void SimInfo::calcNdfRaw() {
278	>	void SimInfo::calcNdfRaw() {
279		int ndfRaw_local;
280
281		MoleculeIterator i;
#	Line 286 \| Line 287 \| void SimInfo::calcNdfRaw() {
287		ndfRaw_local = 0;
288
289		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
290	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
291	<	integrableObject = mol->nextIntegrableObject(j)) {
290	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
291	>	integrableObject = mol->nextIntegrableObject(j)) {
292
293	<	ndfRaw_local += 3;
293	>	ndfRaw_local += 3;
294
295	<	if (integrableObject->isDirectional()) {
296	<	if (integrableObject->isLinear()) {
297	<	ndfRaw_local += 2;
298	<	} else {
299	<	ndfRaw_local += 3;
300	<	}
301	<	}
295	>	if (integrableObject->isDirectional()) {
296	>	if (integrableObject->isLinear()) {
297	>	ndfRaw_local += 2;
298	>	} else {
299	>	ndfRaw_local += 3;
300	>	}
301	>	}
302
303	<	}
303	>	}
304		}
305
306		#ifdef IS_MPI
#	Line 307 \| Line 308 \| void SimInfo::calcNdfRaw() {
308		#else
309		ndfRaw_ = ndfRaw_local;
310		#endif
311	<	}
311	>	}
312
313	<	void SimInfo::calcNdfTrans() {
313	>	void SimInfo::calcNdfTrans() {
314		int ndfTrans_local;
315
316		ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
#	Line 323 \| Line 324 \| void SimInfo::calcNdfTrans() {
324
325		ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
326
327	<	}
327	>	}
328
329	<	void SimInfo::addExcludePairs(Molecule* mol) {
329	>	void SimInfo::addExcludePairs(Molecule* mol) {
330		std::vector<Bond*>::iterator bondIter;
331		std::vector<Bend*>::iterator bendIter;
332		std::vector<Torsion*>::iterator torsionIter;
#	Line 338 \| Line 339 \| *void SimInfo::addExcludePairs(Molecule mol) {**
339		int d;
340
341		for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
342	<	a = bond->getAtomA()->getGlobalIndex();
343	<	b = bond->getAtomB()->getGlobalIndex();
344	<	exclude_.addPair(a, b);
342	>	a = bond->getAtomA()->getGlobalIndex();
343	>	b = bond->getAtomB()->getGlobalIndex();
344	>	exclude_.addPair(a, b);
345		}
346
347		for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
348	<	a = bend->getAtomA()->getGlobalIndex();
349	<	b = bend->getAtomB()->getGlobalIndex();
350	<	c = bend->getAtomC()->getGlobalIndex();
348	>	a = bend->getAtomA()->getGlobalIndex();
349	>	b = bend->getAtomB()->getGlobalIndex();
350	>	c = bend->getAtomC()->getGlobalIndex();
351
352	<	exclude_.addPair(a, b);
353	<	exclude_.addPair(a, c);
354	<	exclude_.addPair(b, c);
352	>	exclude_.addPair(a, b);
353	>	exclude_.addPair(a, c);
354	>	exclude_.addPair(b, c);
355		}
356
357		for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
358	<	a = torsion->getAtomA()->getGlobalIndex();
359	<	b = torsion->getAtomB()->getGlobalIndex();
360	<	c = torsion->getAtomC()->getGlobalIndex();
361	<	d = torsion->getAtomD()->getGlobalIndex();
358	>	a = torsion->getAtomA()->getGlobalIndex();
359	>	b = torsion->getAtomB()->getGlobalIndex();
360	>	c = torsion->getAtomC()->getGlobalIndex();
361	>	d = torsion->getAtomD()->getGlobalIndex();
362
363	<	exclude_.addPair(a, b);
364	<	exclude_.addPair(a, c);
365	<	exclude_.addPair(a, d);
366	<	exclude_.addPair(b, c);
367	<	exclude_.addPair(b, d);
368	<	exclude_.addPair(c, d);
363	>	exclude_.addPair(a, b);
364	>	exclude_.addPair(a, c);
365	>	exclude_.addPair(a, d);
366	>	exclude_.addPair(b, c);
367	>	exclude_.addPair(b, d);
368	>	exclude_.addPair(c, d);
369		}
370
371		Molecule::RigidBodyIterator rbIter;
372		RigidBody* rb;
373		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
374	<	std::vector<Atom*> atoms = rb->getAtoms();
375	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
376	<	for (int j = i + 1; j < atoms.size(); ++j) {
377	<	a = atoms[i]->getGlobalIndex();
378	<	b = atoms[j]->getGlobalIndex();
379	<	exclude_.addPair(a, b);
380	<	}
381	<	}
374	>	std::vector<Atom*> atoms = rb->getAtoms();
375	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
376	>	for (int j = i + 1; j < atoms.size(); ++j) {
377	>	a = atoms[i]->getGlobalIndex();
378	>	b = atoms[j]->getGlobalIndex();
379	>	exclude_.addPair(a, b);
380	>	}
381	>	}
382		}
383
384	<	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	<	}
384	>	}
385
386	<	}
397	<
398	<	void SimInfo::removeExcludePairs(Molecule* mol) {
386	>	void SimInfo::removeExcludePairs(Molecule* mol) {
387		std::vector<Bond*>::iterator bondIter;
388		std::vector<Bend*>::iterator bendIter;
389		std::vector<Torsion*>::iterator torsionIter;
#	Line 408 \| Line 396 \| *void SimInfo::removeExcludePairs(Molecule mol) {**
396		int d;
397
398		for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
399	<	a = bond->getAtomA()->getGlobalIndex();
400	<	b = bond->getAtomB()->getGlobalIndex();
401	<	exclude_.removePair(a, b);
399	>	a = bond->getAtomA()->getGlobalIndex();
400	>	b = bond->getAtomB()->getGlobalIndex();
401	>	exclude_.removePair(a, b);
402		}
403
404		for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
405	<	a = bend->getAtomA()->getGlobalIndex();
406	<	b = bend->getAtomB()->getGlobalIndex();
407	<	c = bend->getAtomC()->getGlobalIndex();
405	>	a = bend->getAtomA()->getGlobalIndex();
406	>	b = bend->getAtomB()->getGlobalIndex();
407	>	c = bend->getAtomC()->getGlobalIndex();
408
409	<	exclude_.removePair(a, b);
410	<	exclude_.removePair(a, c);
411	<	exclude_.removePair(b, c);
409	>	exclude_.removePair(a, b);
410	>	exclude_.removePair(a, c);
411	>	exclude_.removePair(b, c);
412		}
413
414		for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
415	<	a = torsion->getAtomA()->getGlobalIndex();
416	<	b = torsion->getAtomB()->getGlobalIndex();
417	<	c = torsion->getAtomC()->getGlobalIndex();
418	<	d = torsion->getAtomD()->getGlobalIndex();
415	>	a = torsion->getAtomA()->getGlobalIndex();
416	>	b = torsion->getAtomB()->getGlobalIndex();
417	>	c = torsion->getAtomC()->getGlobalIndex();
418	>	d = torsion->getAtomD()->getGlobalIndex();
419
420	<	exclude_.removePair(a, b);
421	<	exclude_.removePair(a, c);
422	<	exclude_.removePair(a, d);
423	<	exclude_.removePair(b, c);
424	<	exclude_.removePair(b, d);
425	<	exclude_.removePair(c, d);
420	>	exclude_.removePair(a, b);
421	>	exclude_.removePair(a, c);
422	>	exclude_.removePair(a, d);
423	>	exclude_.removePair(b, c);
424	>	exclude_.removePair(b, d);
425	>	exclude_.removePair(c, d);
426		}
427
428		Molecule::RigidBodyIterator rbIter;
429		RigidBody* rb;
430		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
431	<	std::vector<Atom*> atoms = rb->getAtoms();
432	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
433	<	for (int j = i + 1; j < atoms.size(); ++j) {
434	<	a = atoms[i]->getGlobalIndex();
435	<	b = atoms[j]->getGlobalIndex();
436	<	exclude_.removePair(a, b);
437	<	}
438	<	}
431	>	std::vector<Atom*> atoms = rb->getAtoms();
432	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
433	>	for (int j = i + 1; j < atoms.size(); ++j) {
434	>	a = atoms[i]->getGlobalIndex();
435	>	b = atoms[j]->getGlobalIndex();
436	>	exclude_.removePair(a, b);
437	>	}
438	>	}
439		}
440
441	<	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	<	}
441	>	}
442
466	–	}
443
444	<
469	<	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
444	>	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
445		int curStampId;
446
447		//index from 0
#	Line 474 \| Line 449 \| *void SimInfo::addMoleculeStamp(MoleculeStamp molStamp**
449
450		moleculeStamps_.push_back(molStamp);
451		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
452	<	}
452	>	}
453
454	<	void SimInfo::update() {
454	>	void SimInfo::update() {
455
456		setupSimType();
457
#	Line 489 \| Line 464 \| void SimInfo::update() {
464		//setup fortran force field
465		/** @deprecate */
466		int isError = 0;
467	<	initFortranFF( &fInfo_.SIM_uses_RF , &isError );
467	>
468	>	setupCoulombicCorrection( isError );
469	>
470		if(isError){
471	<	sprintf( painCave.errMsg,
472	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
473	<	painCave.isFatal = 1;
474	<	simError();
471	>	sprintf( painCave.errMsg,
472	>	"ForceField error: There was an error initializing the forceField in fortran.\n" );
473	>	painCave.isFatal = 1;
474	>	simError();
475		}
476
477
#	Line 505 \| Line 482 \| void SimInfo::update() {
482		calcNdfTrans();
483
484		fortranInitialized_ = true;
485	<	}
485	>	}
486
487	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
487	>	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
488		SimInfo::MoleculeIterator mi;
489		Molecule* mol;
490		Molecule::AtomIterator ai;
#	Line 516 \| Line 493 \| *std::set<AtomType> SimInfo::getUniqueAtomTypes() {**
493
494		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
495
496	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
497	<	atomTypes.insert(atom->getAtomType());
498	<	}
496	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
497	>	atomTypes.insert(atom->getAtomType());
498	>	}
499
500		}
501
502		return atomTypes;
503	<	}
503	>	}
504
505	<	void SimInfo::setupSimType() {
505	>	void SimInfo::setupSimType() {
506		std::set<AtomType*>::iterator i;
507		std::set<AtomType*> atomTypes;
508		atomTypes = getUniqueAtomTypes();
#	Line 538 \| Line 515 \| void SimInfo::setupSimType() {
515		int useDipole = 0;
516		int useGayBerne = 0;
517		int useSticky = 0;
518	+	int useStickyPower = 0;
519		int useShape = 0;
520		int useFLARB = 0; //it is not in AtomType yet
521		int useDirectionalAtom = 0;
#	Line 548 \| Line 526 \| void SimInfo::setupSimType() {
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 591 \| 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 605 \| 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 615 \| 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;
#	Line 623 \| Line 612 \| void SimInfo::setupSimType() {
612
613		if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
614
615	<	if (simParams_->haveDielectric()) {
616	<	fInfo_.dielect = simParams_->getDielectric();
617	<	} else {
618	<	sprintf(painCave.errMsg,
619	<	"SimSetup Error: No Dielectric constant was set.\n"
620	<	"\tYou are trying to use Reaction Field without"
621	<	"\tsetting a dielectric constant!\n");
622	<	painCave.isFatal = 1;
623	<	simError();
624	<	}
615	>	if (simParams_->haveDielectric()) {
616	>	fInfo_.dielect = simParams_->getDielectric();
617	>	} else {
618	>	sprintf(painCave.errMsg,
619	>	"SimSetup Error: No Dielectric constant was set.\n"
620	>	"\tYou are trying to use Reaction Field without"
621	>	"\tsetting a dielectric constant!\n");
622	>	painCave.isFatal = 1;
623	>	simError();
624	>	}
625
626		} else {
627	<	fInfo_.dielect = 0.0;
627	>	fInfo_.dielect = 0.0;
628		}
629
630	<	}
630	>	}
631
632	<	void SimInfo::setupFortranSim() {
632	>	void SimInfo::setupFortranSim() {
633		int isError;
634		int nExclude;
635		std::vector<int> fortranGlobalGroupMembership;
#	Line 650 \| Line 639 \| void SimInfo::setupFortranSim() {
639
640		//globalGroupMembership_ is filled by SimCreator
641		for (int i = 0; i < nGlobalAtoms_; i++) {
642	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
642	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
643		}
644
645		//calculate mass ratio of cutoff group
#	Line 667 \| Line 656 \| void SimInfo::setupFortranSim() {
656		mfact.reserve(getNCutoffGroups());
657
658		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
659	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
659	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
660
661	<	totalMass = cg->getMass();
662	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
663	<	mfact.push_back(atom->getMass()/totalMass);
664	<	}
661	>	totalMass = cg->getMass();
662	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
663	>	mfact.push_back(atom->getMass()/totalMass);
664	>	}
665
666	<	}
666	>	}
667		}
668
669		//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
#	Line 684 \| Line 673 \| void SimInfo::setupFortranSim() {
673		identArray.reserve(getNAtoms());
674
675		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
676	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
677	<	identArray.push_back(atom->getIdent());
678	<	}
676	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
677	>	identArray.push_back(atom->getIdent());
678	>	}
679		}
680
681		//fill molMembershipArray
682		//molMembershipArray is filled by SimCreator
683		std::vector<int> molMembershipArray(nGlobalAtoms_);
684		for (int i = 0; i < nGlobalAtoms_; i++) {
685	<	molMembershipArray[i] = globalMolMembership_[i] + 1;
685	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
686		}
687
688		//setup fortran simulation
#	Line 701 \| Line 690 \| void SimInfo::setupFortranSim() {
690		int* globalExcludes = NULL;
691		int* excludeList = exclude_.getExcludeList();
692		setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
693	<	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
694	<	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
693	>	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
694	>	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
695
696		if( isError ){
697
698	<	sprintf( painCave.errMsg,
699	<	"There was an error setting the simulation information in fortran.\n" );
700	<	painCave.isFatal = 1;
701	<	painCave.severity = OOPSE_ERROR;
702	<	simError();
698	>	sprintf( painCave.errMsg,
699	>	"There was an error setting the simulation information in fortran.\n" );
700	>	painCave.isFatal = 1;
701	>	painCave.severity = OOPSE_ERROR;
702	>	simError();
703		}
704
705		#ifdef IS_MPI
706		sprintf( checkPointMsg,
707	<	"succesfully sent the simulation information to fortran.\n");
707	>	"succesfully sent the simulation information to fortran.\n");
708		MPIcheckPoint();
709		#endif // is_mpi
710	<	}
710	>	}
711
712
713		#ifdef IS_MPI
714	<	void SimInfo::setupFortranParallel() {
714	>	void SimInfo::setupFortranParallel() {
715
716		//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
717		std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
#	Line 738 \| Line 727 \| void SimInfo::setupFortranParallel() {
727
728		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
729
730	<	//local index(index in DataStorge) of atom is important
731	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
732	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
733	<	}
730	>	//local index(index in DataStorge) of atom is important
731	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
732	>	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
733	>	}
734
735	<	//local index of cutoff group is trivial, it only depends on the order of travesing
736	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
737	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
738	<	}
735	>	//local index of cutoff group is trivial, it only depends on the order of travesing
736	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
737	>	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
738	>	}
739
740		}
741
#	Line 766 \| Line 755 \| void SimInfo::setupFortranParallel() {
755		&localToGlobalCutoffGroupIndex[0], &isError);
756
757		if (isError) {
758	<	sprintf(painCave.errMsg,
759	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
760	<	painCave.isFatal = 1;
761	<	simError();
758	>	sprintf(painCave.errMsg,
759	>	"mpiRefresh errror: fortran didn't like something we gave it.\n");
760	>	painCave.isFatal = 1;
761	>	simError();
762		}
763
764		sprintf(checkPointMsg, " mpiRefresh successful.\n");
765		MPIcheckPoint();
766
767
768	<	}
768	>	}
769
770		#endif
771
772	<	double SimInfo::calcMaxCutoffRadius() {
772	>	double SimInfo::calcMaxCutoffRadius() {
773
774
775		std::set<AtomType*> atomTypes;
#	Line 792 \| Line 781 \| double SimInfo::calcMaxCutoffRadius() {
781
782		//query the max cutoff radius among these atom types
783		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
784	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
784	>	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
785		}
786
787		double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
#	Line 801 \| Line 790 \| double SimInfo::calcMaxCutoffRadius() {
790		#endif
791
792		return maxCutoffRadius;
793	<	}
793	>	}
794
795	<	void SimInfo::getCutoff(double& rcut, double& rsw) {
795	>	void SimInfo::getCutoff(double& rcut, double& rsw) {
796
797		if (fInfo_.SIM_uses_Charges \| fInfo_.SIM_uses_Dipoles \| fInfo_.SIM_uses_RF) {
798
799	<	if (!simParams_->haveRcut()){
800	<	sprintf(painCave.errMsg,
799	>	if (!simParams_->haveRcut()){
800	>	sprintf(painCave.errMsg,
801		"SimCreator Warning: No value was set for the cutoffRadius.\n"
802		"\tOOPSE will use a default value of 15.0 angstroms"
803		"\tfor the cutoffRadius.\n");
804	<	painCave.isFatal = 0;
805	<	simError();
806	<	rcut = 15.0;
807	<	} else{
808	<	rcut = simParams_->getRcut();
809	<	}
804	>	painCave.isFatal = 0;
805	>	simError();
806	>	rcut = 15.0;
807	>	} else{
808	>	rcut = simParams_->getRcut();
809	>	}
810
811	<	if (!simParams_->haveRsw()){
812	<	sprintf(painCave.errMsg,
811	>	if (!simParams_->haveRsw()){
812	>	sprintf(painCave.errMsg,
813		"SimCreator Warning: No value was set for switchingRadius.\n"
814		"\tOOPSE will use a default value of\n"
815		"\t0.95 * cutoffRadius for the switchingRadius\n");
816	<	painCave.isFatal = 0;
817	<	simError();
818	<	rsw = 0.95 * rcut;
819	<	} else{
820	<	rsw = simParams_->getRsw();
821	<	}
816	>	painCave.isFatal = 0;
817	>	simError();
818	>	rsw = 0.95 * rcut;
819	>	} else{
820	>	rsw = simParams_->getRsw();
821	>	}
822
823		} else {
824	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
825	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
824	>	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
825	>	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
826
827	<	if (simParams_->haveRcut()) {
828	<	rcut = simParams_->getRcut();
829	<	} else {
830	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
831	<	rcut = calcMaxCutoffRadius();
832	<	}
827	>	if (simParams_->haveRcut()) {
828	>	rcut = simParams_->getRcut();
829	>	} else {
830	>	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
831	>	rcut = calcMaxCutoffRadius();
832	>	}
833
834	<	if (simParams_->haveRsw()) {
835	<	rsw = simParams_->getRsw();
836	<	} else {
837	<	rsw = rcut;
838	<	}
834	>	if (simParams_->haveRsw()) {
835	>	rsw = simParams_->getRsw();
836	>	} else {
837	>	rsw = rcut;
838	>	}
839
840		}
841	<	}
841	>	}
842
843	<	void SimInfo::setupCutoff() {
843	>	void SimInfo::setupCutoff() {
844		getCutoff(rcut_, rsw_);
845		double rnblist = rcut_ + 1; // skin of neighbor list
846
847		//Pass these cutoff radius etc. to fortran. This function should be called once and only once
848	<	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist);
849	<	}
848	>
849	>	int cp = TRADITIONAL_CUTOFF_POLICY;
850	>	if (simParams_->haveCutoffPolicy()) {
851	>	std::string myPolicy = simParams_->getCutoffPolicy();
852	>	if (myPolicy == "MIX") {
853	>	cp = MIX_CUTOFF_POLICY;
854	>	} else {
855	>	if (myPolicy == "MAX") {
856	>	cp = MAX_CUTOFF_POLICY;
857	>	} else {
858	>	if (myPolicy == "TRADITIONAL") {
859	>	cp = TRADITIONAL_CUTOFF_POLICY;
860	>	} else {
861	>	// throw error
862	>	sprintf( painCave.errMsg,
863	>	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
864	>	painCave.isFatal = 1;
865	>	simError();
866	>	}
867	>	}
868	>	}
869	>	}
870	>	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
871	>	}
872
873	<	void SimInfo::addProperty(GenericData* genData) {
873	>	void SimInfo::setupCoulombicCorrection( int isError ) {
874	>
875	>	int errorOut;
876	>	int cc = NONE;
877	>	double alphaVal;
878	>
879	>	errorOut = isError;
880	>
881	>	if (simParams_->haveCoulombicCorrection()) {
882	>	std::string myCorrection = simParams_->getCoulombicCorrection();
883	>	if (myCorrection == "NONE") {
884	>	cc = NONE;
885	>	} else {
886	>	if (myCorrection == "UNDAMPED_WOLF") {
887	>	cc = UNDAMPED_WOLF;
888	>	} else {
889	>	if (myCorrection == "WOLF") {
890	>	cc = WOLF;
891	>	if (!simParams_->haveDampingAlpha()) {
892	>	//throw error
893	>	sprintf( painCave.errMsg,
894	>	"SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used for the Wolf Coulombic Correction.", simParams_->getDampingAlpha());
895	>	painCave.isFatal = 0;
896	>	simError();
897	>	}
898	>	alphaVal = simParams_->getDampingAlpha();
899	>	} else {
900	>	if (myCorrection == "REACTION_FIELD") {
901	>	cc = REACTION_FIELD;
902	>	} else {
903	>	// throw error
904	>	sprintf( painCave.errMsg,
905	>	"SimInfo error: Unknown coulombicCorrection. (Input file specified %s .)\n\tcoulombicCorrection must be one of: \"none\", \"undamped_wolf\", \"wolf\", or \"reaction_field\".", myCorrection.c_str() );
906	>	painCave.isFatal = 1;
907	>	simError();
908	>	}
909	>	}
910	>	}
911	>	}
912	>	}
913	>	initFortranFF( &fInfo_.SIM_uses_RF, &cc, &alphaVal, &errorOut );
914	>	}
915	>
916	>	void SimInfo::addProperty(GenericData* genData) {
917		properties_.addProperty(genData);
918	<	}
918	>	}
919
920	<	void SimInfo::removeProperty(const std::string& propName) {
920	>	void SimInfo::removeProperty(const std::string& propName) {
921		properties_.removeProperty(propName);
922	<	}
922	>	}
923
924	<	void SimInfo::clearProperties() {
924	>	void SimInfo::clearProperties() {
925		properties_.clearProperties();
926	<	}
926	>	}
927
928	<	std::vector<std::string> SimInfo::getPropertyNames() {
928	>	std::vector<std::string> SimInfo::getPropertyNames() {
929		return properties_.getPropertyNames();
930	<	}
930	>	}
931
932	<	std::vector<GenericData*> SimInfo::getProperties() {
933	<	return properties_.getProperties();
934	<	}
932	>	std::vector<GenericData*> SimInfo::getProperties() {
933	>	return properties_.getProperties();
934	>	}
935
936	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
936	>	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
937		return properties_.getPropertyByName(propName);
938	<	}
938	>	}
939
940	<	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
940	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
941		if (sman_ == sman) {
942	<	return;
942	>	return;
943		}
944		delete sman_;
945		sman_ = sman;
#	Line 899 \| Line 953 \| *void SimInfo::setSnapshotManager(SnapshotManager sman**
953
954		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
955
956	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
957	<	atom->setSnapshotManager(sman_);
958	<	}
956	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
957	>	atom->setSnapshotManager(sman_);
958	>	}
959
960	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
961	<	rb->setSnapshotManager(sman_);
962	<	}
960	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
961	>	rb->setSnapshotManager(sman_);
962	>	}
963		}
964
965	<	}
965	>	}
966
967	<	Vector3d SimInfo::getComVel(){
967	>	Vector3d SimInfo::getComVel(){
968		SimInfo::MoleculeIterator i;
969		Molecule* mol;
970
#	Line 919 \| Line 973 \| Vector3d SimInfo::getComVel(){
973
974
975		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
976	<	double mass = mol->getMass();
977	<	totalMass += mass;
978	<	comVel += mass * mol->getComVel();
976	>	double mass = mol->getMass();
977	>	totalMass += mass;
978	>	comVel += mass * mol->getComVel();
979		}
980
981		#ifdef IS_MPI
#	Line 934 \| Line 988 \| Vector3d SimInfo::getComVel(){
988		comVel /= totalMass;
989
990		return comVel;
991	<	}
991	>	}
992
993	<	Vector3d SimInfo::getCom(){
993	>	Vector3d SimInfo::getCom(){
994		SimInfo::MoleculeIterator i;
995		Molecule* mol;
996
#	Line 944 \| Line 998 \| Vector3d SimInfo::getCom(){
998		double totalMass = 0.0;
999
1000		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1001	<	double mass = mol->getMass();
1002	<	totalMass += mass;
1003	<	com += mass * mol->getCom();
1001	>	double mass = mol->getMass();
1002	>	totalMass += mass;
1003	>	com += mass * mol->getCom();
1004		}
1005
1006		#ifdef IS_MPI
#	Line 960 \| Line 1014 \| Vector3d SimInfo::getCom(){
1014
1015		return com;
1016
1017	<	}
1017	>	}
1018
1019	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1019	>	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1020
1021		return o;
1022	<	}
1022	>	}
1023	>
1024	>
1025	>	/*
1026	>	Returns center of mass and center of mass velocity in one function call.
1027	>	*/
1028	>
1029	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1030	>	SimInfo::MoleculeIterator i;
1031	>	Molecule* mol;
1032	>
1033	>
1034	>	double totalMass = 0.0;
1035	>
1036
1037	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1038	+	double mass = mol->getMass();
1039	+	totalMass += mass;
1040	+	com += mass * mol->getCom();
1041	+	comVel += mass * mol->getComVel();
1042	+	}
1043	+
1044	+	#ifdef IS_MPI
1045	+	double tmpMass = totalMass;
1046	+	Vector3d tmpCom(com);
1047	+	Vector3d tmpComVel(comVel);
1048	+	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1049	+	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1050	+	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1051	+	#endif
1052	+
1053	+	com /= totalMass;
1054	+	comVel /= totalMass;
1055	+	}
1056	+
1057	+	/*
1058	+	Return intertia tensor for entire system and angular momentum Vector.
1059	+
1060	+
1061	+	[ Ixx -Ixy -Ixz ]
1062	+	J =\| -Iyx Iyy -Iyz \|
1063	+	[ -Izx -Iyz Izz ]
1064	+	*/
1065	+
1066	+	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1067	+
1068	+
1069	+	double xx = 0.0;
1070	+	double yy = 0.0;
1071	+	double zz = 0.0;
1072	+	double xy = 0.0;
1073	+	double xz = 0.0;
1074	+	double yz = 0.0;
1075	+	Vector3d com(0.0);
1076	+	Vector3d comVel(0.0);
1077	+
1078	+	getComAll(com, comVel);
1079	+
1080	+	SimInfo::MoleculeIterator i;
1081	+	Molecule* mol;
1082	+
1083	+	Vector3d thisq(0.0);
1084	+	Vector3d thisv(0.0);
1085	+
1086	+	double thisMass = 0.0;
1087	+
1088	+
1089	+
1090	+
1091	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1092	+
1093	+	thisq = mol->getCom()-com;
1094	+	thisv = mol->getComVel()-comVel;
1095	+	thisMass = mol->getMass();
1096	+	// Compute moment of intertia coefficients.
1097	+	xx += thisq[0]thisq[0]thisMass;
1098	+	yy += thisq[1]thisq[1]thisMass;
1099	+	zz += thisq[2]thisq[2]thisMass;
1100	+
1101	+	// compute products of intertia
1102	+	xy += thisq[0]thisq[1]thisMass;
1103	+	xz += thisq[0]thisq[2]thisMass;
1104	+	yz += thisq[1]thisq[2]thisMass;
1105	+
1106	+	angularMomentum += cross( thisq, thisv ) * thisMass;
1107	+
1108	+	}
1109	+
1110	+
1111	+	inertiaTensor(0,0) = yy + zz;
1112	+	inertiaTensor(0,1) = -xy;
1113	+	inertiaTensor(0,2) = -xz;
1114	+	inertiaTensor(1,0) = -xy;
1115	+	inertiaTensor(1,1) = xx + zz;
1116	+	inertiaTensor(1,2) = -yz;
1117	+	inertiaTensor(2,0) = -xz;
1118	+	inertiaTensor(2,1) = -yz;
1119	+	inertiaTensor(2,2) = xx + yy;
1120	+
1121	+	#ifdef IS_MPI
1122	+	Mat3x3d tmpI(inertiaTensor);
1123	+	Vector3d tmpAngMom;
1124	+	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1125	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1126	+	#endif
1127	+
1128	+	return;
1129	+	}
1130	+
1131	+	//Returns the angular momentum of the system
1132	+	Vector3d SimInfo::getAngularMomentum(){
1133	+
1134	+	Vector3d com(0.0);
1135	+	Vector3d comVel(0.0);
1136	+	Vector3d angularMomentum(0.0);
1137	+
1138	+	getComAll(com,comVel);
1139	+
1140	+	SimInfo::MoleculeIterator i;
1141	+	Molecule* mol;
1142	+
1143	+	Vector3d thisr(0.0);
1144	+	Vector3d thisp(0.0);
1145	+
1146	+	double thisMass;
1147	+
1148	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1149	+	thisMass = mol->getMass();
1150	+	thisr = mol->getCom()-com;
1151	+	thisp = (mol->getComVel()-comVel)*thisMass;
1152	+
1153	+	angularMomentum += cross( thisr, thisp );
1154	+
1155	+	}
1156	+
1157	+	#ifdef IS_MPI
1158	+	Vector3d tmpAngMom;
1159	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1160	+	#endif
1161	+
1162	+	return angularMomentum;
1163	+	}
1164	+
1165	+
1166		}//end namespace oopse
1167

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Comparing trunk/OOPSE-2.0/src/brains/SimInfo.cpp (file contents): Revision 2116 by tim, Fri Mar 11 15:00:20 2005 UTC vs. Revision 2297 by chrisfen, Thu Sep 15 00:14:35 2005 UTC

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Comparing trunk/OOPSE-2.0/src/brains/SimInfo.cpp (file contents):
Revision 2116 by tim, Fri Mar 11 15:00:20 2005 UTC vs.
Revision 2297 by chrisfen, Thu Sep 15 00:14:35 2005 UTC