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

Comparing trunk/OOPSE-2.0/src/brains/SimInfo.cpp (file contents):
Revision 1976 by tim, Fri Feb 4 22:44:15 2005 UTC vs.
Revision 2344 by chrisfen, Tue Oct 4 19:34:03 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"
62	+	#include "selection/SelectionManager.hpp"
63
64		#ifdef IS_MPI
65		#include "UseTheForce/mpiComponentPlan.h"
#	Line 64 \| 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), selectMan_(NULL) {
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 99 \| 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 111 \| 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
135	–	nGlobalMols_ = molStampIds_.size();
136	–
145		#ifdef IS_MPI
146	<	molToProcMap_.resize(nGlobalMols_);
146	>	molToProcMap_.resize(nGlobalMols_);
147		#endif
148
149	<	selectMan_ = new SelectionManager(nGlobalAtoms_ + nGlobalRigidBodies_);
142	<	selectMan_->selectAll();
143	<	}
149	>	}
150
151	<	SimInfo::~SimInfo() {
152	<	//MemoryUtils::deleteVectorOfPointer(molecules_);
153	<
154	<	MemoryUtils::deleteVectorOfPointer(moleculeStamps_);
155	<
151	>	SimInfo::~SimInfo() {
152	>	std::map<int, Molecule*>::iterator i;
153	>	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
154	>	delete i->second;
155	>	}
156	>	molecules_.clear();
157	>
158	>	delete stamps_;
159		delete sman_;
160		delete simParams_;
161		delete forceField_;
162	<	delete selectMan_;
154	<	}
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 162 \| 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 241 \| 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 270 \| 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 284 \| 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 305 \| 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 321 \| 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 336 \| 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);
360	<	}
353	<
354	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
355	<	a = torsion->getAtomA()->getGlobalIndex();
356	<	b = torsion->getAtomB()->getGlobalIndex();
357	<	c = torsion->getAtomC()->getGlobalIndex();
358	<	d = torsion->getAtomD()->getGlobalIndex();
357	>	exclude_.addPair(a, b);
358	>	exclude_.addPair(a, c);
359	>	exclude_.addPair(b, c);
360	>	}
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	>	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();
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);
374		}
375
376	<
377	<	}
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	>	}
387	>	}
388
389	<	void SimInfo::removeExcludePairs(Molecule* mol) {
389	>	}
390	>
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 381 \| 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	<	}
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	>	}
444	>	}
445
446	+	}
447
448	<	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
448	>
449	>	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
450		int curStampId;
451
452		//index from 0
#	Line 421 \| 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 436 \| 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 452 \| 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 463 \| 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 485 \| 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();
530	>	int useRF;
531
532	+	// set the useRF logical
533	+	std::string myMethod = simParams_->getElectrostaticSummationMethod();
534	+	if (myMethod == "REACTION_FIELD")
535	+	useRF = 1;
536	+	else
537	+	useRF = 0;
538	+
539		//loop over all of the atom types
540		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
541	<	useLennardJones \|= (*i)->isLennardJones();
542	<	useElectrostatic \|= (*i)->isElectrostatic();
543	<	useEAM \|= (*i)->isEAM();
544	<	useCharge \|= (*i)->isCharge();
545	<	useDirectional \|= (*i)->isDirectional();
546	<	useDipole \|= (*i)->isDipole();
547	<	useGayBerne \|= (*i)->isGayBerne();
548	<	useSticky \|= (*i)->isSticky();
549	<	useShape \|= (*i)->isShape();
541	>	useLennardJones \|= (*i)->isLennardJones();
542	>	useElectrostatic \|= (*i)->isElectrostatic();
543	>	useEAM \|= (*i)->isEAM();
544	>	useCharge \|= (*i)->isCharge();
545	>	useDirectional \|= (*i)->isDirectional();
546	>	useDipole \|= (*i)->isDipole();
547	>	useGayBerne \|= (*i)->isGayBerne();
548	>	useSticky \|= (*i)->isSticky();
549	>	useStickyPower \|= (*i)->isStickyPower();
550	>	useShape \|= (*i)->isShape();
551		}
552
553	<	if (useSticky \|\| useDipole \|\| useGayBerne \|\| useShape) {
554	<	useDirectionalAtom = 1;
553	>	if (useSticky \|\| useStickyPower \|\| useDipole \|\| useGayBerne \|\| useShape) {
554	>	useDirectionalAtom = 1;
555		}
556
557		if (useCharge \|\| useDipole) {
558	<	useElectrostatics = 1;
558	>	useElectrostatics = 1;
559		}
560
561		#ifdef IS_MPI
#	Line 538 \| Line 582 \| void SimInfo::setupSimType() {
582		temp = useSticky;
583		MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
584
585	+	temp = useStickyPower;
586	+	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
587	+
588		temp = useGayBerne;
589		MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
590
#	Line 552 \| Line 599 \| void SimInfo::setupSimType() {
599
600		temp = useRF;
601		MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
602	<
602	>
603		#endif
604
605		fInfo_.SIM_uses_PBC = usePBC;
#	Line 562 \| Line 609 \| void SimInfo::setupSimType() {
609		fInfo_.SIM_uses_Charges = useCharge;
610		fInfo_.SIM_uses_Dipoles = useDipole;
611		fInfo_.SIM_uses_Sticky = useSticky;
612	+	fInfo_.SIM_uses_StickyPower = useStickyPower;
613		fInfo_.SIM_uses_GayBerne = useGayBerne;
614		fInfo_.SIM_uses_EAM = useEAM;
615		fInfo_.SIM_uses_Shapes = useShape;
616		fInfo_.SIM_uses_FLARB = useFLARB;
617		fInfo_.SIM_uses_RF = useRF;
618
619	<	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
619	>	if( fInfo_.SIM_uses_Dipoles && myMethod == "REACTION_FIELD") {
620
621	<	if (simParams_->haveDielectric()) {
622	<	fInfo_.dielect = simParams_->getDielectric();
623	<	} else {
624	<	sprintf(painCave.errMsg,
625	<	"SimSetup Error: No Dielectric constant was set.\n"
626	<	"\tYou are trying to use Reaction Field without"
627	<	"\tsetting a dielectric constant!\n");
628	<	painCave.isFatal = 1;
629	<	simError();
630	<	}
621	>	if (simParams_->haveDielectric()) {
622	>	fInfo_.dielect = simParams_->getDielectric();
623	>	} else {
624	>	sprintf(painCave.errMsg,
625	>	"SimSetup Error: No Dielectric constant was set.\n"
626	>	"\tYou are trying to use Reaction Field without"
627	>	"\tsetting a dielectric constant!\n");
628	>	painCave.isFatal = 1;
629	>	simError();
630	>	}
631
632		} else {
633	<	fInfo_.dielect = 0.0;
633	>	fInfo_.dielect = 0.0;
634		}
635
636	<	}
636	>	}
637
638	<	void SimInfo::setupFortranSim() {
638	>	void SimInfo::setupFortranSim() {
639		int isError;
640		int nExclude;
641		std::vector<int> fortranGlobalGroupMembership;
#	Line 597 \| Line 645 \| void SimInfo::setupFortranSim() {
645
646		//globalGroupMembership_ is filled by SimCreator
647		for (int i = 0; i < nGlobalAtoms_; i++) {
648	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
648	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
649		}
650
651		//calculate mass ratio of cutoff group
#	Line 614 \| Line 662 \| void SimInfo::setupFortranSim() {
662		mfact.reserve(getNCutoffGroups());
663
664		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
665	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
665	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
666
667	<	totalMass = cg->getMass();
668	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
669	<	mfact.push_back(atom->getMass()/totalMass);
670	<	}
667	>	totalMass = cg->getMass();
668	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
669	>	// Check for massless groups - set mfact to 1 if true
670	>	if (totalMass != 0)
671	>	mfact.push_back(atom->getMass()/totalMass);
672	>	else
673	>	mfact.push_back( 1.0 );
674	>	}
675
676	<	}
676	>	}
677		}
678
679		//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
#	Line 631 \| Line 683 \| void SimInfo::setupFortranSim() {
683		identArray.reserve(getNAtoms());
684
685		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
686	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
687	<	identArray.push_back(atom->getIdent());
688	<	}
686	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
687	>	identArray.push_back(atom->getIdent());
688	>	}
689		}
690
691		//fill molMembershipArray
692		//molMembershipArray is filled by SimCreator
693		std::vector<int> molMembershipArray(nGlobalAtoms_);
694		for (int i = 0; i < nGlobalAtoms_; i++) {
695	<	molMembershipArray[i] = globalMolMembership_[i] + 1;
695	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
696		}
697
698		//setup fortran simulation
647	–	//gloalExcludes and molMembershipArray should go away (They are never used)
648	–	//why the hell fortran need to know molecule?
649	–	//OOPSE = Object-Obfuscated Parallel Simulation Engine
699		int nGlobalExcludes = 0;
700		int* globalExcludes = NULL;
701		int* excludeList = exclude_.getExcludeList();
702		setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
703	<	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
704	<	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
703	>	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
704	>	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
705
706		if( isError ){
707
708	<	sprintf( painCave.errMsg,
709	<	"There was an error setting the simulation information in fortran.\n" );
710	<	painCave.isFatal = 1;
711	<	painCave.severity = OOPSE_ERROR;
712	<	simError();
708	>	sprintf( painCave.errMsg,
709	>	"There was an error setting the simulation information in fortran.\n" );
710	>	painCave.isFatal = 1;
711	>	painCave.severity = OOPSE_ERROR;
712	>	simError();
713		}
714
715		#ifdef IS_MPI
716		sprintf( checkPointMsg,
717	<	"succesfully sent the simulation information to fortran.\n");
717	>	"succesfully sent the simulation information to fortran.\n");
718		MPIcheckPoint();
719		#endif // is_mpi
720	<	}
720	>	}
721
722
723		#ifdef IS_MPI
724	<	void SimInfo::setupFortranParallel() {
724	>	void SimInfo::setupFortranParallel() {
725
726		//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
727		std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
#	Line 688 \| Line 737 \| void SimInfo::setupFortranParallel() {
737
738		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
739
740	<	//local index(index in DataStorge) of atom is important
741	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
742	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
743	<	}
740	>	//local index(index in DataStorge) of atom is important
741	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
742	>	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
743	>	}
744
745	<	//local index of cutoff group is trivial, it only depends on the order of travesing
746	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
747	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
748	<	}
745	>	//local index of cutoff group is trivial, it only depends on the order of travesing
746	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
747	>	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
748	>	}
749
750		}
751
#	Line 716 \| Line 765 \| void SimInfo::setupFortranParallel() {
765		&localToGlobalCutoffGroupIndex[0], &isError);
766
767		if (isError) {
768	<	sprintf(painCave.errMsg,
769	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
770	<	painCave.isFatal = 1;
771	<	simError();
768	>	sprintf(painCave.errMsg,
769	>	"mpiRefresh errror: fortran didn't like something we gave it.\n");
770	>	painCave.isFatal = 1;
771	>	simError();
772		}
773
774		sprintf(checkPointMsg, " mpiRefresh successful.\n");
775		MPIcheckPoint();
776
777
778	<	}
778	>	}
779
780		#endif
781
782	<	double SimInfo::calcMaxCutoffRadius() {
782	>	double SimInfo::calcMaxCutoffRadius() {
783
784
785		std::set<AtomType*> atomTypes;
#	Line 742 \| Line 791 \| double SimInfo::calcMaxCutoffRadius() {
791
792		//query the max cutoff radius among these atom types
793		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
794	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
794	>	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
795		}
796
797		double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
#	Line 751 \| Line 800 \| double SimInfo::calcMaxCutoffRadius() {
800		#endif
801
802		return maxCutoffRadius;
803	<	}
803	>	}
804
805	<	void SimInfo::setupCutoff() {
757	<	double rcut_; //cutoff radius
758	<	double rsw_; //switching radius
805	>	void SimInfo::getCutoff(double& rcut, double& rsw) {
806
807		if (fInfo_.SIM_uses_Charges \| fInfo_.SIM_uses_Dipoles \| fInfo_.SIM_uses_RF) {
808
809	<	if (!simParams_->haveRcut()){
810	<	sprintf(painCave.errMsg,
809	>	if (!simParams_->haveRcut()){
810	>	sprintf(painCave.errMsg,
811		"SimCreator Warning: No value was set for the cutoffRadius.\n"
812		"\tOOPSE will use a default value of 15.0 angstroms"
813		"\tfor the cutoffRadius.\n");
814	<	painCave.isFatal = 0;
815	<	simError();
816	<	rcut_ = 15.0;
817	<	} else{
818	<	rcut_ = simParams_->getRcut();
819	<	}
814	>	painCave.isFatal = 0;
815	>	simError();
816	>	rcut = 15.0;
817	>	} else{
818	>	rcut = simParams_->getRcut();
819	>	}
820
821	<	if (!simParams_->haveRsw()){
822	<	sprintf(painCave.errMsg,
821	>	if (!simParams_->haveRsw()){
822	>	sprintf(painCave.errMsg,
823		"SimCreator Warning: No value was set for switchingRadius.\n"
824		"\tOOPSE will use a default value of\n"
825		"\t0.95 * cutoffRadius for the switchingRadius\n");
826	<	painCave.isFatal = 0;
827	<	simError();
828	<	rsw_ = 0.95 * rcut_;
829	<	} else{
830	<	rsw_ = simParams_->getRsw();
831	<	}
826	>	painCave.isFatal = 0;
827	>	simError();
828	>	rsw = 0.95 * rcut;
829	>	} else{
830	>	rsw = simParams_->getRsw();
831	>	}
832
833		} else {
834	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
835	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
834	>	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
835	>	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
836
837	<	if (simParams_->haveRcut()) {
838	<	rcut_ = simParams_->getRcut();
839	<	} else {
840	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
841	<	rcut_ = calcMaxCutoffRadius();
842	<	}
837	>	if (simParams_->haveRcut()) {
838	>	rcut = simParams_->getRcut();
839	>	} else {
840	>	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
841	>	rcut = calcMaxCutoffRadius();
842	>	}
843
844	<	if (simParams_->haveRsw()) {
845	<	rsw_ = simParams_->getRsw();
846	<	} else {
847	<	rsw_ = rcut_;
848	<	}
844	>	if (simParams_->haveRsw()) {
845	>	rsw = simParams_->getRsw();
846	>	} else {
847	>	rsw = rcut;
848	>	}
849
850		}
851	<
851	>	}
852	>
853	>	void SimInfo::setupCutoff() {
854	>	getCutoff(rcut_, rsw_);
855		double rnblist = rcut_ + 1; // skin of neighbor list
856
857		//Pass these cutoff radius etc. to fortran. This function should be called once and only once
858	<	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist);
859	<	}
858	>
859	>	int cp = TRADITIONAL_CUTOFF_POLICY;
860	>	if (simParams_->haveCutoffPolicy()) {
861	>	std::string myPolicy = simParams_->getCutoffPolicy();
862	>	if (myPolicy == "MIX") {
863	>	cp = MIX_CUTOFF_POLICY;
864	>	} else {
865	>	if (myPolicy == "MAX") {
866	>	cp = MAX_CUTOFF_POLICY;
867	>	} else {
868	>	if (myPolicy == "TRADITIONAL") {
869	>	cp = TRADITIONAL_CUTOFF_POLICY;
870	>	} else {
871	>	// throw error
872	>	sprintf( painCave.errMsg,
873	>	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
874	>	painCave.isFatal = 1;
875	>	simError();
876	>	}
877	>	}
878	>	}
879	>	}
880
881	<	void SimInfo::addProperty(GenericData* genData) {
881	>
882	>	if (simParams_->haveSkinThickness()) {
883	>	double skinThickness = simParams_->getSkinThickness();
884	>	}
885	>
886	>	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
887	>	// also send cutoff notification to electrostatics
888	>	setElectrostaticCutoffRadius(&rcut_);
889	>	}
890	>
891	>	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
892	>
893	>	int errorOut;
894	>	int esm = NONE;
895	>	double alphaVal;
896	>	double dielectric;
897	>
898	>	errorOut = isError;
899	>	alphaVal = simParams_->getDampingAlpha();
900	>	dielectric = simParams_->getDielectric();
901	>
902	>	if (simParams_->haveElectrostaticSummationMethod()) {
903	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
904	>	if (myMethod == "NONE") {
905	>	esm = NONE;
906	>	} else {
907	>	if (myMethod == "UNDAMPED_WOLF") {
908	>	esm = UNDAMPED_WOLF;
909	>	} else {
910	>	if (myMethod == "DAMPED_WOLF") {
911	>	esm = DAMPED_WOLF;
912	>	if (!simParams_->haveDampingAlpha()) {
913	>	//throw error
914	>	sprintf( painCave.errMsg,
915	>	"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);
916	>	painCave.isFatal = 0;
917	>	simError();
918	>	}
919	>	} else {
920	>	if (myMethod == "REACTION_FIELD") {
921	>	esm = REACTION_FIELD;
922	>	} else {
923	>	// throw error
924	>	sprintf( painCave.errMsg,
925	>	"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() );
926	>	painCave.isFatal = 1;
927	>	simError();
928	>	}
929	>	}
930	>	}
931	>	}
932	>	}
933	>	// let's pass some summation method variables to fortran
934	>	setElectrostaticSummationMethod( &esm );
935	>	setDampedWolfAlpha( &alphaVal );
936	>	setReactionFieldDielectric( &dielectric );
937	>	initFortranFF( &esm, &errorOut );
938	>	}
939	>
940	>	void SimInfo::addProperty(GenericData* genData) {
941		properties_.addProperty(genData);
942	<	}
942	>	}
943
944	<	void SimInfo::removeProperty(const std::string& propName) {
944	>	void SimInfo::removeProperty(const std::string& propName) {
945		properties_.removeProperty(propName);
946	<	}
946	>	}
947
948	<	void SimInfo::clearProperties() {
948	>	void SimInfo::clearProperties() {
949		properties_.clearProperties();
950	<	}
950	>	}
951
952	<	std::vector<std::string> SimInfo::getPropertyNames() {
953	<	return properties_.getPropertyNames();
954	<	}
952	>	std::vector<std::string> SimInfo::getPropertyNames() {
953	>	return properties_.getPropertyNames();
954	>	}
955
956	<	std::vector<GenericData*> SimInfo::getProperties() {
956	>	std::vector<GenericData*> SimInfo::getProperties() {
957		return properties_.getProperties();
958	<	}
958	>	}
959
960	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
960	>	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
961		return properties_.getPropertyByName(propName);
962	<	}
962	>	}
963
964	<	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
964	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
965	>	if (sman_ == sman) {
966	>	return;
967	>	}
968	>	delete sman_;
969		sman_ = sman;
970
971		Molecule* mol;
#	Line 844 \| Line 977 \| *void SimInfo::setSnapshotManager(SnapshotManager sman**
977
978		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
979
980	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
981	<	atom->setSnapshotManager(sman_);
982	<	}
980	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
981	>	atom->setSnapshotManager(sman_);
982	>	}
983
984	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
985	<	rb->setSnapshotManager(sman_);
986	<	}
984	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
985	>	rb->setSnapshotManager(sman_);
986	>	}
987		}
988
989	<	}
989	>	}
990
991	<	Vector3d SimInfo::getComVel(){
991	>	Vector3d SimInfo::getComVel(){
992		SimInfo::MoleculeIterator i;
993		Molecule* mol;
994
#	Line 864 \| Line 997 \| Vector3d SimInfo::getComVel(){
997
998
999		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1000	<	double mass = mol->getMass();
1001	<	totalMass += mass;
1002	<	comVel += mass * mol->getComVel();
1000	>	double mass = mol->getMass();
1001	>	totalMass += mass;
1002	>	comVel += mass * mol->getComVel();
1003		}
1004
1005		#ifdef IS_MPI
#	Line 879 \| Line 1012 \| Vector3d SimInfo::getComVel(){
1012		comVel /= totalMass;
1013
1014		return comVel;
1015	<	}
1015	>	}
1016
1017	<	Vector3d SimInfo::getCom(){
1017	>	Vector3d SimInfo::getCom(){
1018		SimInfo::MoleculeIterator i;
1019		Molecule* mol;
1020
#	Line 889 \| Line 1022 \| Vector3d SimInfo::getCom(){
1022		double totalMass = 0.0;
1023
1024		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1025	<	double mass = mol->getMass();
1026	<	totalMass += mass;
1027	<	com += mass * mol->getCom();
1025	>	double mass = mol->getMass();
1026	>	totalMass += mass;
1027	>	com += mass * mol->getCom();
1028		}
1029
1030		#ifdef IS_MPI
#	Line 905 \| Line 1038 \| Vector3d SimInfo::getCom(){
1038
1039		return com;
1040
1041	<	}
1041	>	}
1042
1043	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1043	>	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1044
1045		return o;
1046	<	}
1046	>	}
1047	>
1048	>
1049	>	/*
1050	>	Returns center of mass and center of mass velocity in one function call.
1051	>	*/
1052	>
1053	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1054	>	SimInfo::MoleculeIterator i;
1055	>	Molecule* mol;
1056	>
1057	>
1058	>	double totalMass = 0.0;
1059	>
1060
1061	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1062	+	double mass = mol->getMass();
1063	+	totalMass += mass;
1064	+	com += mass * mol->getCom();
1065	+	comVel += mass * mol->getComVel();
1066	+	}
1067	+
1068	+	#ifdef IS_MPI
1069	+	double tmpMass = totalMass;
1070	+	Vector3d tmpCom(com);
1071	+	Vector3d tmpComVel(comVel);
1072	+	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1073	+	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1074	+	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1075	+	#endif
1076	+
1077	+	com /= totalMass;
1078	+	comVel /= totalMass;
1079	+	}
1080	+
1081	+	/*
1082	+	Return intertia tensor for entire system and angular momentum Vector.
1083	+
1084	+
1085	+	[ Ixx -Ixy -Ixz ]
1086	+	J =\| -Iyx Iyy -Iyz \|
1087	+	[ -Izx -Iyz Izz ]
1088	+	*/
1089	+
1090	+	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1091	+
1092	+
1093	+	double xx = 0.0;
1094	+	double yy = 0.0;
1095	+	double zz = 0.0;
1096	+	double xy = 0.0;
1097	+	double xz = 0.0;
1098	+	double yz = 0.0;
1099	+	Vector3d com(0.0);
1100	+	Vector3d comVel(0.0);
1101	+
1102	+	getComAll(com, comVel);
1103	+
1104	+	SimInfo::MoleculeIterator i;
1105	+	Molecule* mol;
1106	+
1107	+	Vector3d thisq(0.0);
1108	+	Vector3d thisv(0.0);
1109	+
1110	+	double thisMass = 0.0;
1111	+
1112	+
1113	+
1114	+
1115	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1116	+
1117	+	thisq = mol->getCom()-com;
1118	+	thisv = mol->getComVel()-comVel;
1119	+	thisMass = mol->getMass();
1120	+	// Compute moment of intertia coefficients.
1121	+	xx += thisq[0]thisq[0]thisMass;
1122	+	yy += thisq[1]thisq[1]thisMass;
1123	+	zz += thisq[2]thisq[2]thisMass;
1124	+
1125	+	// compute products of intertia
1126	+	xy += thisq[0]thisq[1]thisMass;
1127	+	xz += thisq[0]thisq[2]thisMass;
1128	+	yz += thisq[1]thisq[2]thisMass;
1129	+
1130	+	angularMomentum += cross( thisq, thisv ) * thisMass;
1131	+
1132	+	}
1133	+
1134	+
1135	+	inertiaTensor(0,0) = yy + zz;
1136	+	inertiaTensor(0,1) = -xy;
1137	+	inertiaTensor(0,2) = -xz;
1138	+	inertiaTensor(1,0) = -xy;
1139	+	inertiaTensor(1,1) = xx + zz;
1140	+	inertiaTensor(1,2) = -yz;
1141	+	inertiaTensor(2,0) = -xz;
1142	+	inertiaTensor(2,1) = -yz;
1143	+	inertiaTensor(2,2) = xx + yy;
1144	+
1145	+	#ifdef IS_MPI
1146	+	Mat3x3d tmpI(inertiaTensor);
1147	+	Vector3d tmpAngMom;
1148	+	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1149	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1150	+	#endif
1151	+
1152	+	return;
1153	+	}
1154	+
1155	+	//Returns the angular momentum of the system
1156	+	Vector3d SimInfo::getAngularMomentum(){
1157	+
1158	+	Vector3d com(0.0);
1159	+	Vector3d comVel(0.0);
1160	+	Vector3d angularMomentum(0.0);
1161	+
1162	+	getComAll(com,comVel);
1163	+
1164	+	SimInfo::MoleculeIterator i;
1165	+	Molecule* mol;
1166	+
1167	+	Vector3d thisr(0.0);
1168	+	Vector3d thisp(0.0);
1169	+
1170	+	double thisMass;
1171	+
1172	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1173	+	thisMass = mol->getMass();
1174	+	thisr = mol->getCom()-com;
1175	+	thisp = (mol->getComVel()-comVel)*thisMass;
1176	+
1177	+	angularMomentum += cross( thisr, thisp );
1178	+
1179	+	}
1180	+
1181	+	#ifdef IS_MPI
1182	+	Vector3d tmpAngMom;
1183	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1184	+	#endif
1185	+
1186	+	return angularMomentum;
1187	+	}
1188	+
1189	+
1190		}//end namespace oopse
1191

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Comparing trunk/OOPSE-2.0/src/brains/SimInfo.cpp (file contents): Revision 1976 by tim, Fri Feb 4 22:44:15 2005 UTC vs. Revision 2344 by chrisfen, Tue Oct 4 19:34:03 2005 UTC

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Comparing trunk/OOPSE-2.0/src/brains/SimInfo.cpp (file contents):
Revision 1976 by tim, Fri Feb 4 22:44:15 2005 UTC vs.
Revision 2344 by chrisfen, Tue Oct 4 19:34:03 2005 UTC