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

Comparing trunk/OOPSE-2.0/src/brains/SimInfo.cpp (file contents):
Revision 2119 by tim, Fri Mar 11 15:55:17 2005 UTC vs.
Revision 2404 by chrisfen, Tue Nov 1 19:14:27 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/DarkSide/fElectrostaticSummationMethod.h"
57		#include "UseTheForce/doForces_interface.h"
58	+	#include "UseTheForce/DarkSide/electrostatic_interface.h"
59		#include "UseTheForce/notifyCutoffs_interface.h"
60		#include "utils/MemoryUtils.hpp"
61		#include "utils/simError.h"
#	Line 65 \| Line 68 \| *SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp,**
68
69		namespace oopse {
70
71	<	SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
72	<	ForceField* ff, Globals* simParams) :
73	<	forceField_(ff), simParams_(simParams),
74	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
75	<	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
76	<	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
77	<	nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nRigidBodies_(0),
78	<	nIntegrableObjects_(0), nCutoffGroups_(0), nConstraints_(0),
79	<	sman_(NULL), fortranInitialized_(false) {
71	>	SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
72	>	ForceField* ff, Globals* simParams) :
73	>	stamps_(stamps), forceField_(ff), simParams_(simParams),
74	>	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
75	>	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
76	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
77	>	nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nRigidBodies_(0),
78	>	nIntegrableObjects_(0), nCutoffGroups_(0), nConstraints_(0),
79	>	sman_(NULL), fortranInitialized_(false) {
80
81
82	<	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
83	<	MoleculeStamp* molStamp;
84	<	int nMolWithSameStamp;
85	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
86	<	int nGroups = 0; //total cutoff groups defined in meta-data file
87	<	CutoffGroupStamp* cgStamp;
88	<	RigidBodyStamp* rbStamp;
89	<	int nRigidAtoms = 0;
82	>	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
83	>	MoleculeStamp* molStamp;
84	>	int nMolWithSameStamp;
85	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
86	>	int nGroups = 0; //total cutoff groups defined in meta-data file
87	>	CutoffGroupStamp* cgStamp;
88	>	RigidBodyStamp* rbStamp;
89	>	int nRigidAtoms = 0;
90
91	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
91	>	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
92		molStamp = i->first;
93		nMolWithSameStamp = i->second;
94
#	Line 100 \| Line 103 \| *SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp,**
103		int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
104
105		for (int j=0; j < nCutoffGroupsInStamp; j++) {
106	<	cgStamp = molStamp->getCutoffGroup(j);
107	<	nAtomsInGroups += cgStamp->getNMembers();
106	>	cgStamp = molStamp->getCutoffGroup(j);
107	>	nAtomsInGroups += cgStamp->getNMembers();
108		}
109
110		nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
111	+
112		nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
113
114		//calculate atoms in rigid bodies
#	Line 112 \| Line 116 \| *SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp,**
116		int nRigidBodiesInStamp = molStamp->getNRigidBodies();
117
118		for (int j=0; j < nRigidBodiesInStamp; j++) {
119	<	rbStamp = molStamp->getRigidBody(j);
120	<	nAtomsInRigidBodies += rbStamp->getNMembers();
119	>	rbStamp = molStamp->getRigidBody(j);
120	>	nAtomsInRigidBodies += rbStamp->getNMembers();
121		}
122
123		nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
124		nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
125
126	<	}
126	>	}
127
128	<	//every free atom (atom does not belong to cutoff groups) is a cutoff group
129	<	//therefore the total number of cutoff groups in the system is equal to
130	<	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
131	<	//file plus the number of cutoff groups defined in meta-data file
132	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
128	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
129	>	//group therefore the total number of cutoff groups in the system is
130	>	//equal to the total number of atoms minus number of atoms belong to
131	>	//cutoff group defined in meta-data file plus the number of cutoff
132	>	//groups defined in meta-data file
133	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
134
135	<	//every free atom (atom does not belong to rigid bodies) is an integrable object
136	<	//therefore the total number of integrable objects in the system is equal to
137	<	//the total number of atoms minus number of atoms belong to rigid body defined in meta-data
138	<	//file plus the number of rigid bodies defined in meta-data file
139	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
135	>	//every free atom (atom does not belong to rigid bodies) is an
136	>	//integrable object therefore the total number of integrable objects
137	>	//in the system is equal to the total number of atoms minus number of
138	>	//atoms belong to rigid body defined in meta-data file plus the number
139	>	//of rigid bodies defined in meta-data file
140	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
141	>	+ nGlobalRigidBodies_;
142	>
143	>	nGlobalMols_ = molStampIds_.size();
144
136	–	nGlobalMols_ = molStampIds_.size();
137	–
145		#ifdef IS_MPI
146	<	molToProcMap_.resize(nGlobalMols_);
146	>	molToProcMap_.resize(nGlobalMols_);
147		#endif
148
149	<	}
149	>	}
150
151	<	SimInfo::~SimInfo() {
151	>	SimInfo::~SimInfo() {
152		std::map<int, Molecule*>::iterator i;
153		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
154	<	delete i->second;
154	>	delete i->second;
155		}
156		molecules_.clear();
157	<
158	<	MemoryUtils::deletePointers(moleculeStamps_);
152	<
157	>
158	>	delete stamps_;
159		delete sman_;
160		delete simParams_;
161		delete forceField_;
162	<	}
162	>	}
163
164	<	int SimInfo::getNGlobalConstraints() {
164	>	int SimInfo::getNGlobalConstraints() {
165		int nGlobalConstraints;
166		#ifdef IS_MPI
167		MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
#	Line 164 \| Line 170 \| int SimInfo::getNGlobalConstraints() {
170		nGlobalConstraints = nConstraints_;
171		#endif
172		return nGlobalConstraints;
173	<	}
173	>	}
174
175	<	bool SimInfo::addMolecule(Molecule* mol) {
175	>	bool SimInfo::addMolecule(Molecule* mol) {
176		MoleculeIterator i;
177
178		i = molecules_.find(mol->getGlobalIndex());
179		if (i == molecules_.end() ) {
180
181	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
181	>	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
182
183	<	nAtoms_ += mol->getNAtoms();
184	<	nBonds_ += mol->getNBonds();
185	<	nBends_ += mol->getNBends();
186	<	nTorsions_ += mol->getNTorsions();
187	<	nRigidBodies_ += mol->getNRigidBodies();
188	<	nIntegrableObjects_ += mol->getNIntegrableObjects();
189	<	nCutoffGroups_ += mol->getNCutoffGroups();
190	<	nConstraints_ += mol->getNConstraintPairs();
183	>	nAtoms_ += mol->getNAtoms();
184	>	nBonds_ += mol->getNBonds();
185	>	nBends_ += mol->getNBends();
186	>	nTorsions_ += mol->getNTorsions();
187	>	nRigidBodies_ += mol->getNRigidBodies();
188	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
189	>	nCutoffGroups_ += mol->getNCutoffGroups();
190	>	nConstraints_ += mol->getNConstraintPairs();
191
192	<	addExcludePairs(mol);
192	>	addExcludePairs(mol);
193
194	<	return true;
194	>	return true;
195		} else {
196	<	return false;
196	>	return false;
197		}
198	<	}
198	>	}
199
200	<	bool SimInfo::removeMolecule(Molecule* mol) {
200	>	bool SimInfo::removeMolecule(Molecule* mol) {
201		MoleculeIterator i;
202		i = molecules_.find(mol->getGlobalIndex());
203
204		if (i != molecules_.end() ) {
205
206	<	assert(mol == i->second);
206	>	assert(mol == i->second);
207
208	<	nAtoms_ -= mol->getNAtoms();
209	<	nBonds_ -= mol->getNBonds();
210	<	nBends_ -= mol->getNBends();
211	<	nTorsions_ -= mol->getNTorsions();
212	<	nRigidBodies_ -= mol->getNRigidBodies();
213	<	nIntegrableObjects_ -= mol->getNIntegrableObjects();
214	<	nCutoffGroups_ -= mol->getNCutoffGroups();
215	<	nConstraints_ -= mol->getNConstraintPairs();
208	>	nAtoms_ -= mol->getNAtoms();
209	>	nBonds_ -= mol->getNBonds();
210	>	nBends_ -= mol->getNBends();
211	>	nTorsions_ -= mol->getNTorsions();
212	>	nRigidBodies_ -= mol->getNRigidBodies();
213	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
214	>	nCutoffGroups_ -= mol->getNCutoffGroups();
215	>	nConstraints_ -= mol->getNConstraintPairs();
216
217	<	removeExcludePairs(mol);
218	<	molecules_.erase(mol->getGlobalIndex());
217	>	removeExcludePairs(mol);
218	>	molecules_.erase(mol->getGlobalIndex());
219
220	<	delete mol;
220	>	delete mol;
221
222	<	return true;
222	>	return true;
223		} else {
224	<	return false;
224	>	return false;
225		}
226
227
228	<	}
228	>	}
229
230
231	<	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
231	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
232		i = molecules_.begin();
233		return i == molecules_.end() ? NULL : i->second;
234	<	}
234	>	}
235
236	<	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
236	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
237		++i;
238		return i == molecules_.end() ? NULL : i->second;
239	<	}
239	>	}
240
241
242	<	void SimInfo::calcNdf() {
242	>	void SimInfo::calcNdf() {
243		int ndf_local;
244		MoleculeIterator i;
245		std::vector<StuntDouble*>::iterator j;
#	Line 243 \| Line 249 \| void SimInfo::calcNdf() {
249		ndf_local = 0;
250
251		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
252	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
253	<	integrableObject = mol->nextIntegrableObject(j)) {
252	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
253	>	integrableObject = mol->nextIntegrableObject(j)) {
254
255	<	ndf_local += 3;
255	>	ndf_local += 3;
256
257	<	if (integrableObject->isDirectional()) {
258	<	if (integrableObject->isLinear()) {
259	<	ndf_local += 2;
260	<	} else {
261	<	ndf_local += 3;
262	<	}
263	<	}
257	>	if (integrableObject->isDirectional()) {
258	>	if (integrableObject->isLinear()) {
259	>	ndf_local += 2;
260	>	} else {
261	>	ndf_local += 3;
262	>	}
263	>	}
264
265	<	}//end for (integrableObject)
265	>	}//end for (integrableObject)
266		}// end for (mol)
267
268		// n_constraints is local, so subtract them on each processor
#	Line 272 \| Line 278 \| void SimInfo::calcNdf() {
278		// entire system:
279		ndf_ = ndf_ - 3 - nZconstraint_;
280
281	<	}
281	>	}
282
283	<	void SimInfo::calcNdfRaw() {
283	>	void SimInfo::calcNdfRaw() {
284		int ndfRaw_local;
285
286		MoleculeIterator i;
#	Line 286 \| Line 292 \| void SimInfo::calcNdfRaw() {
292		ndfRaw_local = 0;
293
294		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
295	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
296	<	integrableObject = mol->nextIntegrableObject(j)) {
295	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
296	>	integrableObject = mol->nextIntegrableObject(j)) {
297
298	<	ndfRaw_local += 3;
298	>	ndfRaw_local += 3;
299
300	<	if (integrableObject->isDirectional()) {
301	<	if (integrableObject->isLinear()) {
302	<	ndfRaw_local += 2;
303	<	} else {
304	<	ndfRaw_local += 3;
305	<	}
306	<	}
300	>	if (integrableObject->isDirectional()) {
301	>	if (integrableObject->isLinear()) {
302	>	ndfRaw_local += 2;
303	>	} else {
304	>	ndfRaw_local += 3;
305	>	}
306	>	}
307
308	<	}
308	>	}
309		}
310
311		#ifdef IS_MPI
#	Line 307 \| Line 313 \| void SimInfo::calcNdfRaw() {
313		#else
314		ndfRaw_ = ndfRaw_local;
315		#endif
316	<	}
316	>	}
317
318	<	void SimInfo::calcNdfTrans() {
318	>	void SimInfo::calcNdfTrans() {
319		int ndfTrans_local;
320
321		ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
#	Line 323 \| Line 329 \| void SimInfo::calcNdfTrans() {
329
330		ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
331
332	<	}
332	>	}
333
334	<	void SimInfo::addExcludePairs(Molecule* mol) {
334	>	void SimInfo::addExcludePairs(Molecule* mol) {
335		std::vector<Bond*>::iterator bondIter;
336		std::vector<Bend*>::iterator bendIter;
337		std::vector<Torsion*>::iterator torsionIter;
#	Line 338 \| Line 344 \| *void SimInfo::addExcludePairs(Molecule mol) {**
344		int d;
345
346		for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
347	<	a = bond->getAtomA()->getGlobalIndex();
348	<	b = bond->getAtomB()->getGlobalIndex();
349	<	exclude_.addPair(a, b);
347	>	a = bond->getAtomA()->getGlobalIndex();
348	>	b = bond->getAtomB()->getGlobalIndex();
349	>	exclude_.addPair(a, b);
350		}
351
352		for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
353	<	a = bend->getAtomA()->getGlobalIndex();
354	<	b = bend->getAtomB()->getGlobalIndex();
355	<	c = bend->getAtomC()->getGlobalIndex();
353	>	a = bend->getAtomA()->getGlobalIndex();
354	>	b = bend->getAtomB()->getGlobalIndex();
355	>	c = bend->getAtomC()->getGlobalIndex();
356
357	<	exclude_.addPair(a, b);
358	<	exclude_.addPair(a, c);
359	<	exclude_.addPair(b, c);
357	>	exclude_.addPair(a, b);
358	>	exclude_.addPair(a, c);
359	>	exclude_.addPair(b, c);
360		}
361
362		for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
363	<	a = torsion->getAtomA()->getGlobalIndex();
364	<	b = torsion->getAtomB()->getGlobalIndex();
365	<	c = torsion->getAtomC()->getGlobalIndex();
366	<	d = torsion->getAtomD()->getGlobalIndex();
363	>	a = torsion->getAtomA()->getGlobalIndex();
364	>	b = torsion->getAtomB()->getGlobalIndex();
365	>	c = torsion->getAtomC()->getGlobalIndex();
366	>	d = torsion->getAtomD()->getGlobalIndex();
367
368	<	exclude_.addPair(a, b);
369	<	exclude_.addPair(a, c);
370	<	exclude_.addPair(a, d);
371	<	exclude_.addPair(b, c);
372	<	exclude_.addPair(b, d);
373	<	exclude_.addPair(c, d);
368	>	exclude_.addPair(a, b);
369	>	exclude_.addPair(a, c);
370	>	exclude_.addPair(a, d);
371	>	exclude_.addPair(b, c);
372	>	exclude_.addPair(b, d);
373	>	exclude_.addPair(c, d);
374		}
375
376		Molecule::RigidBodyIterator rbIter;
377		RigidBody* rb;
378		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
379	<	std::vector<Atom*> atoms = rb->getAtoms();
380	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
381	<	for (int j = i + 1; j < atoms.size(); ++j) {
382	<	a = atoms[i]->getGlobalIndex();
383	<	b = atoms[j]->getGlobalIndex();
384	<	exclude_.addPair(a, b);
385	<	}
386	<	}
379	>	std::vector<Atom*> atoms = rb->getAtoms();
380	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
381	>	for (int j = i + 1; j < atoms.size(); ++j) {
382	>	a = atoms[i]->getGlobalIndex();
383	>	b = atoms[j]->getGlobalIndex();
384	>	exclude_.addPair(a, b);
385	>	}
386	>	}
387		}
388
389	<	}
389	>	}
390
391	<	void SimInfo::removeExcludePairs(Molecule* mol) {
391	>	void SimInfo::removeExcludePairs(Molecule* mol) {
392		std::vector<Bond*>::iterator bondIter;
393		std::vector<Bend*>::iterator bendIter;
394		std::vector<Torsion*>::iterator torsionIter;
#	Line 395 \| Line 401 \| *void SimInfo::removeExcludePairs(Molecule mol) {**
401		int d;
402
403		for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
404	<	a = bond->getAtomA()->getGlobalIndex();
405	<	b = bond->getAtomB()->getGlobalIndex();
406	<	exclude_.removePair(a, b);
404	>	a = bond->getAtomA()->getGlobalIndex();
405	>	b = bond->getAtomB()->getGlobalIndex();
406	>	exclude_.removePair(a, b);
407		}
408
409		for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
410	<	a = bend->getAtomA()->getGlobalIndex();
411	<	b = bend->getAtomB()->getGlobalIndex();
412	<	c = bend->getAtomC()->getGlobalIndex();
410	>	a = bend->getAtomA()->getGlobalIndex();
411	>	b = bend->getAtomB()->getGlobalIndex();
412	>	c = bend->getAtomC()->getGlobalIndex();
413
414	<	exclude_.removePair(a, b);
415	<	exclude_.removePair(a, c);
416	<	exclude_.removePair(b, c);
414	>	exclude_.removePair(a, b);
415	>	exclude_.removePair(a, c);
416	>	exclude_.removePair(b, c);
417		}
418
419		for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
420	<	a = torsion->getAtomA()->getGlobalIndex();
421	<	b = torsion->getAtomB()->getGlobalIndex();
422	<	c = torsion->getAtomC()->getGlobalIndex();
423	<	d = torsion->getAtomD()->getGlobalIndex();
420	>	a = torsion->getAtomA()->getGlobalIndex();
421	>	b = torsion->getAtomB()->getGlobalIndex();
422	>	c = torsion->getAtomC()->getGlobalIndex();
423	>	d = torsion->getAtomD()->getGlobalIndex();
424
425	<	exclude_.removePair(a, b);
426	<	exclude_.removePair(a, c);
427	<	exclude_.removePair(a, d);
428	<	exclude_.removePair(b, c);
429	<	exclude_.removePair(b, d);
430	<	exclude_.removePair(c, d);
425	>	exclude_.removePair(a, b);
426	>	exclude_.removePair(a, c);
427	>	exclude_.removePair(a, d);
428	>	exclude_.removePair(b, c);
429	>	exclude_.removePair(b, d);
430	>	exclude_.removePair(c, d);
431		}
432
433		Molecule::RigidBodyIterator rbIter;
434		RigidBody* rb;
435		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
436	<	std::vector<Atom*> atoms = rb->getAtoms();
437	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
438	<	for (int j = i + 1; j < atoms.size(); ++j) {
439	<	a = atoms[i]->getGlobalIndex();
440	<	b = atoms[j]->getGlobalIndex();
441	<	exclude_.removePair(a, b);
442	<	}
443	<	}
436	>	std::vector<Atom*> atoms = rb->getAtoms();
437	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
438	>	for (int j = i + 1; j < atoms.size(); ++j) {
439	>	a = atoms[i]->getGlobalIndex();
440	>	b = atoms[j]->getGlobalIndex();
441	>	exclude_.removePair(a, b);
442	>	}
443	>	}
444		}
445
446	<	}
446	>	}
447
448
449	<	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
449	>	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
450		int curStampId;
451
452		//index from 0
#	Line 448 \| Line 454 \| *void SimInfo::addMoleculeStamp(MoleculeStamp molStamp**
454
455		moleculeStamps_.push_back(molStamp);
456		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
457	<	}
457	>	}
458
459	<	void SimInfo::update() {
459	>	void SimInfo::update() {
460
461		setupSimType();
462
#	Line 463 \| Line 469 \| void SimInfo::update() {
469		//setup fortran force field
470		/** @deprecate */
471		int isError = 0;
472	<	initFortranFF( &fInfo_.SIM_uses_RF , &isError );
472	>
473	>	setupElectrostaticSummationMethod( isError );
474	>
475		if(isError){
476	<	sprintf( painCave.errMsg,
477	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
478	<	painCave.isFatal = 1;
479	<	simError();
476	>	sprintf( painCave.errMsg,
477	>	"ForceField error: There was an error initializing the forceField in fortran.\n" );
478	>	painCave.isFatal = 1;
479	>	simError();
480		}
481
482
#	Line 479 \| Line 487 \| void SimInfo::update() {
487		calcNdfTrans();
488
489		fortranInitialized_ = true;
490	<	}
490	>	}
491
492	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
492	>	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
493		SimInfo::MoleculeIterator mi;
494		Molecule* mol;
495		Molecule::AtomIterator ai;
#	Line 490 \| Line 498 \| *std::set<AtomType> SimInfo::getUniqueAtomTypes() {**
498
499		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
500
501	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
502	<	atomTypes.insert(atom->getAtomType());
503	<	}
501	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
502	>	atomTypes.insert(atom->getAtomType());
503	>	}
504
505		}
506
507		return atomTypes;
508	<	}
508	>	}
509
510	<	void SimInfo::setupSimType() {
510	>	void SimInfo::setupSimType() {
511		std::set<AtomType*>::iterator i;
512		std::set<AtomType*> atomTypes;
513		atomTypes = getUniqueAtomTypes();
#	Line 512 \| Line 520 \| void SimInfo::setupSimType() {
520		int useDipole = 0;
521		int useGayBerne = 0;
522		int useSticky = 0;
523	+	int useStickyPower = 0;
524		int useShape = 0;
525		int useFLARB = 0; //it is not in AtomType yet
526		int useDirectionalAtom = 0;
527		int useElectrostatics = 0;
528		//usePBC and useRF are from simParams
529	<	int usePBC = simParams_->getPBC();
530	<	int useRF = simParams_->getUseRF();
529	>	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
530	>	int useRF;
531	>	int useDW;
532	>	std::string myMethod;
533
534	+	// set the useRF logical
535	+	useRF = 0;
536	+	useDW = 0;
537	+
538	+
539	+	if (simParams_->haveElectrostaticSummationMethod()) {
540	+	std::string myMethod = simParams_->getElectrostaticSummationMethod();
541	+	toUpper(myMethod);
542	+	if (myMethod == "REACTION_FIELD") {
543	+	useRF=1;
544	+	} else {
545	+	if (myMethod == "DAMPED_WOLF") {
546	+	useDW = 1;
547	+	}
548	+	}
549	+	}
550	+
551		//loop over all of the atom types
552		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
553	<	useLennardJones \|= (*i)->isLennardJones();
554	<	useElectrostatic \|= (*i)->isElectrostatic();
555	<	useEAM \|= (*i)->isEAM();
556	<	useCharge \|= (*i)->isCharge();
557	<	useDirectional \|= (*i)->isDirectional();
558	<	useDipole \|= (*i)->isDipole();
559	<	useGayBerne \|= (*i)->isGayBerne();
560	<	useSticky \|= (*i)->isSticky();
561	<	useShape \|= (*i)->isShape();
553	>	useLennardJones \|= (*i)->isLennardJones();
554	>	useElectrostatic \|= (*i)->isElectrostatic();
555	>	useEAM \|= (*i)->isEAM();
556	>	useCharge \|= (*i)->isCharge();
557	>	useDirectional \|= (*i)->isDirectional();
558	>	useDipole \|= (*i)->isDipole();
559	>	useGayBerne \|= (*i)->isGayBerne();
560	>	useSticky \|= (*i)->isSticky();
561	>	useStickyPower \|= (*i)->isStickyPower();
562	>	useShape \|= (*i)->isShape();
563		}
564
565	<	if (useSticky \|\| useDipole \|\| useGayBerne \|\| useShape) {
566	<	useDirectionalAtom = 1;
565	>	if (useSticky \|\| useStickyPower \|\| useDipole \|\| useGayBerne \|\| useShape) {
566	>	useDirectionalAtom = 1;
567		}
568
569		if (useCharge \|\| useDipole) {
570	<	useElectrostatics = 1;
570	>	useElectrostatics = 1;
571		}
572
573		#ifdef IS_MPI
#	Line 565 \| Line 594 \| void SimInfo::setupSimType() {
594		temp = useSticky;
595		MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
596
597	+	temp = useStickyPower;
598	+	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
599	+
600		temp = useGayBerne;
601		MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
602
#	Line 579 \| Line 611 \| void SimInfo::setupSimType() {
611
612		temp = useRF;
613		MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
614	<
614	>
615	>	temp = useDW;
616	>	MPI_Allreduce(&temp, &useDW, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
617	>
618		#endif
619
620		fInfo_.SIM_uses_PBC = usePBC;
#	Line 589 \| Line 624 \| void SimInfo::setupSimType() {
624		fInfo_.SIM_uses_Charges = useCharge;
625		fInfo_.SIM_uses_Dipoles = useDipole;
626		fInfo_.SIM_uses_Sticky = useSticky;
627	+	fInfo_.SIM_uses_StickyPower = useStickyPower;
628		fInfo_.SIM_uses_GayBerne = useGayBerne;
629		fInfo_.SIM_uses_EAM = useEAM;
630		fInfo_.SIM_uses_Shapes = useShape;
631		fInfo_.SIM_uses_FLARB = useFLARB;
632		fInfo_.SIM_uses_RF = useRF;
633	+	fInfo_.SIM_uses_DampedWolf = useDW;
634
635	<	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
636	<
637	<	if (simParams_->haveDielectric()) {
638	<	fInfo_.dielect = simParams_->getDielectric();
639	<	} else {
640	<	sprintf(painCave.errMsg,
641	<	"SimSetup Error: No Dielectric constant was set.\n"
642	<	"\tYou are trying to use Reaction Field without"
643	<	"\tsetting a dielectric constant!\n");
644	<	painCave.isFatal = 1;
645	<	simError();
646	<	}
610	<
611	<	} else {
612	<	fInfo_.dielect = 0.0;
635	>	if( myMethod == "REACTION_FIELD") {
636	>
637	>	if (simParams_->haveDielectric()) {
638	>	fInfo_.dielect = simParams_->getDielectric();
639	>	} else {
640	>	sprintf(painCave.errMsg,
641	>	"SimSetup Error: No Dielectric constant was set.\n"
642	>	"\tYou are trying to use Reaction Field without"
643	>	"\tsetting a dielectric constant!\n");
644	>	painCave.isFatal = 1;
645	>	simError();
646	>	}
647		}
648
649	<	}
649	>	}
650
651	<	void SimInfo::setupFortranSim() {
651	>	void SimInfo::setupFortranSim() {
652		int isError;
653		int nExclude;
654		std::vector<int> fortranGlobalGroupMembership;
#	Line 624 \| Line 658 \| void SimInfo::setupFortranSim() {
658
659		//globalGroupMembership_ is filled by SimCreator
660		for (int i = 0; i < nGlobalAtoms_; i++) {
661	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
661	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
662		}
663
664		//calculate mass ratio of cutoff group
#	Line 641 \| Line 675 \| void SimInfo::setupFortranSim() {
675		mfact.reserve(getNCutoffGroups());
676
677		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
678	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
678	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
679
680	<	totalMass = cg->getMass();
681	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
682	<	mfact.push_back(atom->getMass()/totalMass);
683	<	}
680	>	totalMass = cg->getMass();
681	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
682	>	// Check for massless groups - set mfact to 1 if true
683	>	if (totalMass != 0)
684	>	mfact.push_back(atom->getMass()/totalMass);
685	>	else
686	>	mfact.push_back( 1.0 );
687	>	}
688
689	<	}
689	>	}
690		}
691
692		//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
#	Line 658 \| Line 696 \| void SimInfo::setupFortranSim() {
696		identArray.reserve(getNAtoms());
697
698		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
699	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
700	<	identArray.push_back(atom->getIdent());
701	<	}
699	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
700	>	identArray.push_back(atom->getIdent());
701	>	}
702		}
703
704		//fill molMembershipArray
705		//molMembershipArray is filled by SimCreator
706		std::vector<int> molMembershipArray(nGlobalAtoms_);
707		for (int i = 0; i < nGlobalAtoms_; i++) {
708	<	molMembershipArray[i] = globalMolMembership_[i] + 1;
708	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
709		}
710
711		//setup fortran simulation
#	Line 675 \| Line 713 \| void SimInfo::setupFortranSim() {
713		int* globalExcludes = NULL;
714		int* excludeList = exclude_.getExcludeList();
715		setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
716	<	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
717	<	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
716	>	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
717	>	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
718
719		if( isError ){
720
721	<	sprintf( painCave.errMsg,
722	<	"There was an error setting the simulation information in fortran.\n" );
723	<	painCave.isFatal = 1;
724	<	painCave.severity = OOPSE_ERROR;
725	<	simError();
721	>	sprintf( painCave.errMsg,
722	>	"There was an error setting the simulation information in fortran.\n" );
723	>	painCave.isFatal = 1;
724	>	painCave.severity = OOPSE_ERROR;
725	>	simError();
726		}
727
728		#ifdef IS_MPI
729		sprintf( checkPointMsg,
730	<	"succesfully sent the simulation information to fortran.\n");
730	>	"succesfully sent the simulation information to fortran.\n");
731		MPIcheckPoint();
732		#endif // is_mpi
733	<	}
733	>	}
734
735
736		#ifdef IS_MPI
737	<	void SimInfo::setupFortranParallel() {
737	>	void SimInfo::setupFortranParallel() {
738
739		//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
740		std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
#	Line 712 \| Line 750 \| void SimInfo::setupFortranParallel() {
750
751		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
752
753	<	//local index(index in DataStorge) of atom is important
754	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
755	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
756	<	}
753	>	//local index(index in DataStorge) of atom is important
754	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
755	>	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
756	>	}
757
758	<	//local index of cutoff group is trivial, it only depends on the order of travesing
759	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
760	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
761	<	}
758	>	//local index of cutoff group is trivial, it only depends on the order of travesing
759	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
760	>	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
761	>	}
762
763		}
764
#	Line 740 \| Line 778 \| void SimInfo::setupFortranParallel() {
778		&localToGlobalCutoffGroupIndex[0], &isError);
779
780		if (isError) {
781	<	sprintf(painCave.errMsg,
782	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
783	<	painCave.isFatal = 1;
784	<	simError();
781	>	sprintf(painCave.errMsg,
782	>	"mpiRefresh errror: fortran didn't like something we gave it.\n");
783	>	painCave.isFatal = 1;
784	>	simError();
785		}
786
787		sprintf(checkPointMsg, " mpiRefresh successful.\n");
788		MPIcheckPoint();
789
790
791	<	}
791	>	}
792
793		#endif
794
795	<	double SimInfo::calcMaxCutoffRadius() {
795	>	double SimInfo::calcMaxCutoffRadius() {
796
797
798		std::set<AtomType*> atomTypes;
#	Line 766 \| Line 804 \| double SimInfo::calcMaxCutoffRadius() {
804
805		//query the max cutoff radius among these atom types
806		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
807	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
807	>	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
808		}
809
810		double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
#	Line 775 \| Line 813 \| double SimInfo::calcMaxCutoffRadius() {
813		#endif
814
815		return maxCutoffRadius;
816	<	}
816	>	}
817
818	<	void SimInfo::getCutoff(double& rcut, double& rsw) {
818	>	void SimInfo::getCutoff(double& rcut, double& rsw) {
819
820		if (fInfo_.SIM_uses_Charges \| fInfo_.SIM_uses_Dipoles \| fInfo_.SIM_uses_RF) {
821
822	<	if (!simParams_->haveRcut()){
823	<	sprintf(painCave.errMsg,
822	>	if (!simParams_->haveCutoffRadius()){
823	>	sprintf(painCave.errMsg,
824		"SimCreator Warning: No value was set for the cutoffRadius.\n"
825		"\tOOPSE will use a default value of 15.0 angstroms"
826		"\tfor the cutoffRadius.\n");
827	<	painCave.isFatal = 0;
828	<	simError();
829	<	rcut = 15.0;
830	<	} else{
831	<	rcut = simParams_->getRcut();
832	<	}
827	>	painCave.isFatal = 0;
828	>	simError();
829	>	rcut = 15.0;
830	>	} else{
831	>	rcut = simParams_->getCutoffRadius();
832	>	}
833
834	<	if (!simParams_->haveRsw()){
835	<	sprintf(painCave.errMsg,
834	>	if (!simParams_->haveSwitchingRadius()){
835	>	sprintf(painCave.errMsg,
836		"SimCreator Warning: No value was set for switchingRadius.\n"
837		"\tOOPSE will use a default value of\n"
838	<	"\t0.95 * cutoffRadius for the switchingRadius\n");
839	<	painCave.isFatal = 0;
840	<	simError();
841	<	rsw = 0.95 * rcut;
842	<	} else{
843	<	rsw = simParams_->getRsw();
844	<	}
838	>	"\t0.85 * cutoffRadius for the switchingRadius\n");
839	>	painCave.isFatal = 0;
840	>	simError();
841	>	rsw = 0.85 * rcut;
842	>	} else{
843	>	rsw = simParams_->getSwitchingRadius();
844	>	}
845
846		} else {
847	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
848	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
847	>	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
848	>	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
849
850	<	if (simParams_->haveRcut()) {
851	<	rcut = simParams_->getRcut();
852	<	} else {
853	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
854	<	rcut = calcMaxCutoffRadius();
855	<	}
850	>	if (simParams_->haveCutoffRadius()) {
851	>	rcut = simParams_->getCutoffRadius();
852	>	} else {
853	>	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
854	>	rcut = calcMaxCutoffRadius();
855	>	}
856
857	<	if (simParams_->haveRsw()) {
858	<	rsw = simParams_->getRsw();
859	<	} else {
860	<	rsw = rcut;
861	<	}
857	>	if (simParams_->haveSwitchingRadius()) {
858	>	rsw = simParams_->getSwitchingRadius();
859	>	} else {
860	>	rsw = rcut;
861	>	}
862
863		}
864	<	}
864	>	}
865
866	<	void SimInfo::setupCutoff() {
866	>	void SimInfo::setupCutoff() {
867		getCutoff(rcut_, rsw_);
868		double rnblist = rcut_ + 1; // skin of neighbor list
869
870		//Pass these cutoff radius etc. to fortran. This function should be called once and only once
871	<	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist);
872	<	}
871	>
872	>	int cp = TRADITIONAL_CUTOFF_POLICY;
873	>	if (simParams_->haveCutoffPolicy()) {
874	>	std::string myPolicy = simParams_->getCutoffPolicy();
875	>	toUpper(myPolicy);
876	>	if (myPolicy == "MIX") {
877	>	cp = MIX_CUTOFF_POLICY;
878	>	} else {
879	>	if (myPolicy == "MAX") {
880	>	cp = MAX_CUTOFF_POLICY;
881	>	} else {
882	>	if (myPolicy == "TRADITIONAL") {
883	>	cp = TRADITIONAL_CUTOFF_POLICY;
884	>	} else {
885	>	// throw error
886	>	sprintf( painCave.errMsg,
887	>	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
888	>	painCave.isFatal = 1;
889	>	simError();
890	>	}
891	>	}
892	>	}
893	>	}
894
895	<	void SimInfo::addProperty(GenericData* genData) {
895	>
896	>	if (simParams_->haveSkinThickness()) {
897	>	double skinThickness = simParams_->getSkinThickness();
898	>	}
899	>
900	>	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
901	>	// also send cutoff notification to electrostatics
902	>	setElectrostaticCutoffRadius(&rcut_, &rsw_);
903	>	}
904	>
905	>	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
906	>
907	>	int errorOut;
908	>	int esm = NONE;
909	>	double alphaVal;
910	>	double dielectric;
911	>
912	>	errorOut = isError;
913	>	alphaVal = simParams_->getDampingAlpha();
914	>	dielectric = simParams_->getDielectric();
915	>
916	>	if (simParams_->haveElectrostaticSummationMethod()) {
917	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
918	>	toUpper(myMethod);
919	>	if (myMethod == "NONE") {
920	>	esm = NONE;
921	>	} else {
922	>	if (myMethod == "UNDAMPED_WOLF") {
923	>	esm = UNDAMPED_WOLF;
924	>	} else {
925	>	if (myMethod == "DAMPED_WOLF") {
926	>	esm = DAMPED_WOLF;
927	>	if (!simParams_->haveDampingAlpha()) {
928	>	//throw error
929	>	sprintf( painCave.errMsg,
930	>	"SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used for the Damped Wolf Method.", alphaVal);
931	>	painCave.isFatal = 0;
932	>	simError();
933	>	}
934	>	} else {
935	>	if (myMethod == "REACTION_FIELD") {
936	>	esm = REACTION_FIELD;
937	>	} else {
938	>	// throw error
939	>	sprintf( painCave.errMsg,
940	>	"SimInfo error: Unknown electrostaticSummationMethod. (Input file specified %s .)\n\telectrostaticSummationMethod must be one of: \"none\", \"undamped_wolf\", \"damped_wolf\", or \"reaction_field\".", myMethod.c_str() );
941	>	painCave.isFatal = 1;
942	>	simError();
943	>	}
944	>	}
945	>	}
946	>	}
947	>	}
948	>	// let's pass some summation method variables to fortran
949	>	setElectrostaticSummationMethod( &esm );
950	>	setDampedWolfAlpha( &alphaVal );
951	>	setReactionFieldDielectric( &dielectric );
952	>	initFortranFF( &esm, &errorOut );
953	>	}
954	>
955	>	void SimInfo::addProperty(GenericData* genData) {
956		properties_.addProperty(genData);
957	<	}
957	>	}
958
959	<	void SimInfo::removeProperty(const std::string& propName) {
959	>	void SimInfo::removeProperty(const std::string& propName) {
960		properties_.removeProperty(propName);
961	<	}
961	>	}
962
963	<	void SimInfo::clearProperties() {
963	>	void SimInfo::clearProperties() {
964		properties_.clearProperties();
965	<	}
965	>	}
966
967	<	std::vector<std::string> SimInfo::getPropertyNames() {
967	>	std::vector<std::string> SimInfo::getPropertyNames() {
968		return properties_.getPropertyNames();
969	<	}
969	>	}
970
971	<	std::vector<GenericData*> SimInfo::getProperties() {
971	>	std::vector<GenericData*> SimInfo::getProperties() {
972		return properties_.getProperties();
973	<	}
973	>	}
974
975	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
975	>	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
976		return properties_.getPropertyByName(propName);
977	<	}
977	>	}
978
979	<	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
979	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
980		if (sman_ == sman) {
981	<	return;
981	>	return;
982		}
983		delete sman_;
984		sman_ = sman;
#	Line 873 \| Line 992 \| *void SimInfo::setSnapshotManager(SnapshotManager sman**
992
993		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
994
995	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
996	<	atom->setSnapshotManager(sman_);
997	<	}
995	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
996	>	atom->setSnapshotManager(sman_);
997	>	}
998
999	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1000	<	rb->setSnapshotManager(sman_);
1001	<	}
999	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1000	>	rb->setSnapshotManager(sman_);
1001	>	}
1002		}
1003
1004	<	}
1004	>	}
1005
1006	<	Vector3d SimInfo::getComVel(){
1006	>	Vector3d SimInfo::getComVel(){
1007		SimInfo::MoleculeIterator i;
1008		Molecule* mol;
1009
#	Line 893 \| Line 1012 \| Vector3d SimInfo::getComVel(){
1012
1013
1014		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1015	<	double mass = mol->getMass();
1016	<	totalMass += mass;
1017	<	comVel += mass * mol->getComVel();
1015	>	double mass = mol->getMass();
1016	>	totalMass += mass;
1017	>	comVel += mass * mol->getComVel();
1018		}
1019
1020		#ifdef IS_MPI
#	Line 908 \| Line 1027 \| Vector3d SimInfo::getComVel(){
1027		comVel /= totalMass;
1028
1029		return comVel;
1030	<	}
1030	>	}
1031
1032	<	Vector3d SimInfo::getCom(){
1032	>	Vector3d SimInfo::getCom(){
1033		SimInfo::MoleculeIterator i;
1034		Molecule* mol;
1035
#	Line 918 \| Line 1037 \| Vector3d SimInfo::getCom(){
1037		double totalMass = 0.0;
1038
1039		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1040	<	double mass = mol->getMass();
1041	<	totalMass += mass;
1042	<	com += mass * mol->getCom();
1040	>	double mass = mol->getMass();
1041	>	totalMass += mass;
1042	>	com += mass * mol->getCom();
1043		}
1044
1045		#ifdef IS_MPI
#	Line 934 \| Line 1053 \| Vector3d SimInfo::getCom(){
1053
1054		return com;
1055
1056	<	}
1056	>	}
1057
1058	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1058	>	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1059
1060		return o;
1061	<	}
1061	>	}
1062	>
1063	>
1064	>	/*
1065	>	Returns center of mass and center of mass velocity in one function call.
1066	>	*/
1067	>
1068	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1069	>	SimInfo::MoleculeIterator i;
1070	>	Molecule* mol;
1071	>
1072	>
1073	>	double totalMass = 0.0;
1074	>
1075
1076	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1077	+	double mass = mol->getMass();
1078	+	totalMass += mass;
1079	+	com += mass * mol->getCom();
1080	+	comVel += mass * mol->getComVel();
1081	+	}
1082	+
1083	+	#ifdef IS_MPI
1084	+	double tmpMass = totalMass;
1085	+	Vector3d tmpCom(com);
1086	+	Vector3d tmpComVel(comVel);
1087	+	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1088	+	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1089	+	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1090	+	#endif
1091	+
1092	+	com /= totalMass;
1093	+	comVel /= totalMass;
1094	+	}
1095	+
1096	+	/*
1097	+	Return intertia tensor for entire system and angular momentum Vector.
1098	+
1099	+
1100	+	[ Ixx -Ixy -Ixz ]
1101	+	J =\| -Iyx Iyy -Iyz \|
1102	+	[ -Izx -Iyz Izz ]
1103	+	*/
1104	+
1105	+	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1106	+
1107	+
1108	+	double xx = 0.0;
1109	+	double yy = 0.0;
1110	+	double zz = 0.0;
1111	+	double xy = 0.0;
1112	+	double xz = 0.0;
1113	+	double yz = 0.0;
1114	+	Vector3d com(0.0);
1115	+	Vector3d comVel(0.0);
1116	+
1117	+	getComAll(com, comVel);
1118	+
1119	+	SimInfo::MoleculeIterator i;
1120	+	Molecule* mol;
1121	+
1122	+	Vector3d thisq(0.0);
1123	+	Vector3d thisv(0.0);
1124	+
1125	+	double thisMass = 0.0;
1126	+
1127	+
1128	+
1129	+
1130	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1131	+
1132	+	thisq = mol->getCom()-com;
1133	+	thisv = mol->getComVel()-comVel;
1134	+	thisMass = mol->getMass();
1135	+	// Compute moment of intertia coefficients.
1136	+	xx += thisq[0]thisq[0]thisMass;
1137	+	yy += thisq[1]thisq[1]thisMass;
1138	+	zz += thisq[2]thisq[2]thisMass;
1139	+
1140	+	// compute products of intertia
1141	+	xy += thisq[0]thisq[1]thisMass;
1142	+	xz += thisq[0]thisq[2]thisMass;
1143	+	yz += thisq[1]thisq[2]thisMass;
1144	+
1145	+	angularMomentum += cross( thisq, thisv ) * thisMass;
1146	+
1147	+	}
1148	+
1149	+
1150	+	inertiaTensor(0,0) = yy + zz;
1151	+	inertiaTensor(0,1) = -xy;
1152	+	inertiaTensor(0,2) = -xz;
1153	+	inertiaTensor(1,0) = -xy;
1154	+	inertiaTensor(1,1) = xx + zz;
1155	+	inertiaTensor(1,2) = -yz;
1156	+	inertiaTensor(2,0) = -xz;
1157	+	inertiaTensor(2,1) = -yz;
1158	+	inertiaTensor(2,2) = xx + yy;
1159	+
1160	+	#ifdef IS_MPI
1161	+	Mat3x3d tmpI(inertiaTensor);
1162	+	Vector3d tmpAngMom;
1163	+	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1164	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1165	+	#endif
1166	+
1167	+	return;
1168	+	}
1169	+
1170	+	//Returns the angular momentum of the system
1171	+	Vector3d SimInfo::getAngularMomentum(){
1172	+
1173	+	Vector3d com(0.0);
1174	+	Vector3d comVel(0.0);
1175	+	Vector3d angularMomentum(0.0);
1176	+
1177	+	getComAll(com,comVel);
1178	+
1179	+	SimInfo::MoleculeIterator i;
1180	+	Molecule* mol;
1181	+
1182	+	Vector3d thisr(0.0);
1183	+	Vector3d thisp(0.0);
1184	+
1185	+	double thisMass;
1186	+
1187	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1188	+	thisMass = mol->getMass();
1189	+	thisr = mol->getCom()-com;
1190	+	thisp = (mol->getComVel()-comVel)*thisMass;
1191	+
1192	+	angularMomentum += cross( thisr, thisp );
1193	+
1194	+	}
1195	+
1196	+	#ifdef IS_MPI
1197	+	Vector3d tmpAngMom;
1198	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1199	+	#endif
1200	+
1201	+	return angularMomentum;
1202	+	}
1203	+
1204	+
1205		}//end namespace oopse
1206

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Comparing trunk/OOPSE-2.0/src/brains/SimInfo.cpp (file contents): Revision 2119 by tim, Fri Mar 11 15:55:17 2005 UTC vs. Revision 2404 by chrisfen, Tue Nov 1 19:14:27 2005 UTC

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Comparing trunk/OOPSE-2.0/src/brains/SimInfo.cpp (file contents):
Revision 2119 by tim, Fri Mar 11 15:55:17 2005 UTC vs.
Revision 2404 by chrisfen, Tue Nov 1 19:14:27 2005 UTC