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

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 292 by tim, Fri Feb 4 22:44:15 2005 UTC vs.
Revision 629 by chuckv, Mon Sep 26 15:58:17 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 \| namespace oopse {
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;
#	Line 111 \| Line 115 \| *SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp,**
115		int nRigidBodiesInStamp = molStamp->getNRigidBodies();
116
117		for (int j=0; j < nRigidBodiesInStamp; j++) {
118	<	rbStamp = molStamp->getRigidBody(j);
119	<	nAtomsInRigidBodies += rbStamp->getNMembers();
118	>	rbStamp = molStamp->getRigidBody(j);
119	>	nAtomsInRigidBodies += rbStamp->getNMembers();
120		}
121
122		nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
123		nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
124
125	<	}
125	>	}
126
127	<	//every free atom (atom does not belong to cutoff groups) is a cutoff group
128	<	//therefore the total number of cutoff groups in the system is equal to
129	<	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
130	<	//file plus the number of cutoff groups defined in meta-data file
131	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
127	>	//every free atom (atom does not belong to cutoff groups) is a cutoff group
128	>	//therefore the total number of cutoff groups in the system is equal to
129	>	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
130	>	//file plus the number of cutoff groups defined in meta-data file
131	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
132
133	<	//every free atom (atom does not belong to rigid bodies) is an integrable object
134	<	//therefore the total number of integrable objects in the system is equal to
135	<	//the total number of atoms minus number of atoms belong to rigid body defined in meta-data
136	<	//file plus the number of rigid bodies defined in meta-data file
137	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
133	>	//every free atom (atom does not belong to rigid bodies) is an integrable object
134	>	//therefore the total number of integrable objects in the system is equal to
135	>	//the total number of atoms minus number of atoms belong to rigid body defined in meta-data
136	>	//file plus the number of rigid bodies defined in meta-data file
137	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
138
139	<	nGlobalMols_ = molStampIds_.size();
139	>	nGlobalMols_ = molStampIds_.size();
140
141		#ifdef IS_MPI
142	<	molToProcMap_.resize(nGlobalMols_);
142	>	molToProcMap_.resize(nGlobalMols_);
143		#endif
144
145	<	selectMan_ = new SelectionManager(nGlobalAtoms_ + nGlobalRigidBodies_);
142	<	selectMan_->selectAll();
143	<	}
145	>	}
146
147	<	SimInfo::~SimInfo() {
148	<	//MemoryUtils::deleteVectorOfPointer(molecules_);
149	<
150	<	MemoryUtils::deleteVectorOfPointer(moleculeStamps_);
151	<
147	>	SimInfo::~SimInfo() {
148	>	std::map<int, Molecule*>::iterator i;
149	>	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
150	>	delete i->second;
151	>	}
152	>	molecules_.clear();
153	>
154	>	delete stamps_;
155		delete sman_;
156		delete simParams_;
157		delete forceField_;
158	<	delete selectMan_;
154	<	}
158	>	}
159
160	<	int SimInfo::getNGlobalConstraints() {
160	>	int SimInfo::getNGlobalConstraints() {
161		int nGlobalConstraints;
162		#ifdef IS_MPI
163		MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
#	Line 162 \| Line 166 \| int SimInfo::getNGlobalConstraints() {
166		nGlobalConstraints = nConstraints_;
167		#endif
168		return nGlobalConstraints;
169	<	}
169	>	}
170
171	<	bool SimInfo::addMolecule(Molecule* mol) {
171	>	bool SimInfo::addMolecule(Molecule* mol) {
172		MoleculeIterator i;
173
174		i = molecules_.find(mol->getGlobalIndex());
175		if (i == molecules_.end() ) {
176
177	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
177	>	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
178
179	<	nAtoms_ += mol->getNAtoms();
180	<	nBonds_ += mol->getNBonds();
181	<	nBends_ += mol->getNBends();
182	<	nTorsions_ += mol->getNTorsions();
183	<	nRigidBodies_ += mol->getNRigidBodies();
184	<	nIntegrableObjects_ += mol->getNIntegrableObjects();
185	<	nCutoffGroups_ += mol->getNCutoffGroups();
186	<	nConstraints_ += mol->getNConstraintPairs();
179	>	nAtoms_ += mol->getNAtoms();
180	>	nBonds_ += mol->getNBonds();
181	>	nBends_ += mol->getNBends();
182	>	nTorsions_ += mol->getNTorsions();
183	>	nRigidBodies_ += mol->getNRigidBodies();
184	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
185	>	nCutoffGroups_ += mol->getNCutoffGroups();
186	>	nConstraints_ += mol->getNConstraintPairs();
187
188	<	addExcludePairs(mol);
188	>	addExcludePairs(mol);
189
190	<	return true;
190	>	return true;
191		} else {
192	<	return false;
192	>	return false;
193		}
194	<	}
194	>	}
195
196	<	bool SimInfo::removeMolecule(Molecule* mol) {
196	>	bool SimInfo::removeMolecule(Molecule* mol) {
197		MoleculeIterator i;
198		i = molecules_.find(mol->getGlobalIndex());
199
200		if (i != molecules_.end() ) {
201
202	<	assert(mol == i->second);
202	>	assert(mol == i->second);
203
204	<	nAtoms_ -= mol->getNAtoms();
205	<	nBonds_ -= mol->getNBonds();
206	<	nBends_ -= mol->getNBends();
207	<	nTorsions_ -= mol->getNTorsions();
208	<	nRigidBodies_ -= mol->getNRigidBodies();
209	<	nIntegrableObjects_ -= mol->getNIntegrableObjects();
210	<	nCutoffGroups_ -= mol->getNCutoffGroups();
211	<	nConstraints_ -= mol->getNConstraintPairs();
204	>	nAtoms_ -= mol->getNAtoms();
205	>	nBonds_ -= mol->getNBonds();
206	>	nBends_ -= mol->getNBends();
207	>	nTorsions_ -= mol->getNTorsions();
208	>	nRigidBodies_ -= mol->getNRigidBodies();
209	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
210	>	nCutoffGroups_ -= mol->getNCutoffGroups();
211	>	nConstraints_ -= mol->getNConstraintPairs();
212
213	<	removeExcludePairs(mol);
214	<	molecules_.erase(mol->getGlobalIndex());
213	>	removeExcludePairs(mol);
214	>	molecules_.erase(mol->getGlobalIndex());
215
216	<	delete mol;
216	>	delete mol;
217
218	<	return true;
218	>	return true;
219		} else {
220	<	return false;
220	>	return false;
221		}
222
223
224	<	}
224	>	}
225
226
227	<	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
227	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
228		i = molecules_.begin();
229		return i == molecules_.end() ? NULL : i->second;
230	<	}
230	>	}
231
232	<	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
232	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
233		++i;
234		return i == molecules_.end() ? NULL : i->second;
235	<	}
235	>	}
236
237
238	<	void SimInfo::calcNdf() {
238	>	void SimInfo::calcNdf() {
239		int ndf_local;
240		MoleculeIterator i;
241		std::vector<StuntDouble*>::iterator j;
#	Line 241 \| Line 245 \| void SimInfo::calcNdf() {
245		ndf_local = 0;
246
247		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
248	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
249	<	integrableObject = mol->nextIntegrableObject(j)) {
248	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
249	>	integrableObject = mol->nextIntegrableObject(j)) {
250
251	<	ndf_local += 3;
251	>	ndf_local += 3;
252
253	<	if (integrableObject->isDirectional()) {
254	<	if (integrableObject->isLinear()) {
255	<	ndf_local += 2;
256	<	} else {
257	<	ndf_local += 3;
258	<	}
259	<	}
253	>	if (integrableObject->isDirectional()) {
254	>	if (integrableObject->isLinear()) {
255	>	ndf_local += 2;
256	>	} else {
257	>	ndf_local += 3;
258	>	}
259	>	}
260
261	<	}//end for (integrableObject)
261	>	}//end for (integrableObject)
262		}// end for (mol)
263
264		// n_constraints is local, so subtract them on each processor
#	Line 270 \| Line 274 \| void SimInfo::calcNdf() {
274		// entire system:
275		ndf_ = ndf_ - 3 - nZconstraint_;
276
277	<	}
277	>	}
278
279	<	void SimInfo::calcNdfRaw() {
279	>	void SimInfo::calcNdfRaw() {
280		int ndfRaw_local;
281
282		MoleculeIterator i;
#	Line 284 \| Line 288 \| void SimInfo::calcNdfRaw() {
288		ndfRaw_local = 0;
289
290		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
291	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
292	<	integrableObject = mol->nextIntegrableObject(j)) {
291	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
292	>	integrableObject = mol->nextIntegrableObject(j)) {
293
294	<	ndfRaw_local += 3;
294	>	ndfRaw_local += 3;
295
296	<	if (integrableObject->isDirectional()) {
297	<	if (integrableObject->isLinear()) {
298	<	ndfRaw_local += 2;
299	<	} else {
300	<	ndfRaw_local += 3;
301	<	}
302	<	}
296	>	if (integrableObject->isDirectional()) {
297	>	if (integrableObject->isLinear()) {
298	>	ndfRaw_local += 2;
299	>	} else {
300	>	ndfRaw_local += 3;
301	>	}
302	>	}
303
304	<	}
304	>	}
305		}
306
307		#ifdef IS_MPI
#	Line 305 \| Line 309 \| void SimInfo::calcNdfRaw() {
309		#else
310		ndfRaw_ = ndfRaw_local;
311		#endif
312	<	}
312	>	}
313
314	<	void SimInfo::calcNdfTrans() {
314	>	void SimInfo::calcNdfTrans() {
315		int ndfTrans_local;
316
317		ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
#	Line 321 \| Line 325 \| void SimInfo::calcNdfTrans() {
325
326		ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
327
328	<	}
328	>	}
329
330	<	void SimInfo::addExcludePairs(Molecule* mol) {
330	>	void SimInfo::addExcludePairs(Molecule* mol) {
331		std::vector<Bond*>::iterator bondIter;
332		std::vector<Bend*>::iterator bendIter;
333		std::vector<Torsion*>::iterator torsionIter;
#	Line 336 \| Line 340 \| *void SimInfo::addExcludePairs(Molecule mol) {**
340		int d;
341
342		for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
343	<	a = bond->getAtomA()->getGlobalIndex();
344	<	b = bond->getAtomB()->getGlobalIndex();
345	<	exclude_.addPair(a, b);
343	>	a = bond->getAtomA()->getGlobalIndex();
344	>	b = bond->getAtomB()->getGlobalIndex();
345	>	exclude_.addPair(a, b);
346		}
347
348		for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
349	<	a = bend->getAtomA()->getGlobalIndex();
350	<	b = bend->getAtomB()->getGlobalIndex();
351	<	c = bend->getAtomC()->getGlobalIndex();
349	>	a = bend->getAtomA()->getGlobalIndex();
350	>	b = bend->getAtomB()->getGlobalIndex();
351	>	c = bend->getAtomC()->getGlobalIndex();
352
353	<	exclude_.addPair(a, b);
354	<	exclude_.addPair(a, c);
355	<	exclude_.addPair(b, c);
353	>	exclude_.addPair(a, b);
354	>	exclude_.addPair(a, c);
355	>	exclude_.addPair(b, c);
356		}
357
358		for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
359	<	a = torsion->getAtomA()->getGlobalIndex();
360	<	b = torsion->getAtomB()->getGlobalIndex();
361	<	c = torsion->getAtomC()->getGlobalIndex();
362	<	d = torsion->getAtomD()->getGlobalIndex();
359	>	a = torsion->getAtomA()->getGlobalIndex();
360	>	b = torsion->getAtomB()->getGlobalIndex();
361	>	c = torsion->getAtomC()->getGlobalIndex();
362	>	d = torsion->getAtomD()->getGlobalIndex();
363
364	<	exclude_.addPair(a, b);
365	<	exclude_.addPair(a, c);
366	<	exclude_.addPair(a, d);
367	<	exclude_.addPair(b, c);
368	<	exclude_.addPair(b, d);
369	<	exclude_.addPair(c, d);
364	>	exclude_.addPair(a, b);
365	>	exclude_.addPair(a, c);
366	>	exclude_.addPair(a, d);
367	>	exclude_.addPair(b, c);
368	>	exclude_.addPair(b, d);
369	>	exclude_.addPair(c, d);
370		}
371
372	<
373	<	}
372	>	Molecule::RigidBodyIterator rbIter;
373	>	RigidBody* rb;
374	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
375	>	std::vector<Atom*> atoms = rb->getAtoms();
376	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
377	>	for (int j = i + 1; j < atoms.size(); ++j) {
378	>	a = atoms[i]->getGlobalIndex();
379	>	b = atoms[j]->getGlobalIndex();
380	>	exclude_.addPair(a, b);
381	>	}
382	>	}
383	>	}
384
385	<	void SimInfo::removeExcludePairs(Molecule* mol) {
385	>	}
386	>
387	>	void SimInfo::removeExcludePairs(Molecule* mol) {
388		std::vector<Bond*>::iterator bondIter;
389		std::vector<Bend*>::iterator bendIter;
390		std::vector<Torsion*>::iterator torsionIter;
#	Line 381 \| Line 397 \| *void SimInfo::removeExcludePairs(Molecule mol) {**
397		int d;
398
399		for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
400	<	a = bond->getAtomA()->getGlobalIndex();
401	<	b = bond->getAtomB()->getGlobalIndex();
402	<	exclude_.removePair(a, b);
400	>	a = bond->getAtomA()->getGlobalIndex();
401	>	b = bond->getAtomB()->getGlobalIndex();
402	>	exclude_.removePair(a, b);
403		}
404
405		for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
406	<	a = bend->getAtomA()->getGlobalIndex();
407	<	b = bend->getAtomB()->getGlobalIndex();
408	<	c = bend->getAtomC()->getGlobalIndex();
406	>	a = bend->getAtomA()->getGlobalIndex();
407	>	b = bend->getAtomB()->getGlobalIndex();
408	>	c = bend->getAtomC()->getGlobalIndex();
409
410	<	exclude_.removePair(a, b);
411	<	exclude_.removePair(a, c);
412	<	exclude_.removePair(b, c);
410	>	exclude_.removePair(a, b);
411	>	exclude_.removePair(a, c);
412	>	exclude_.removePair(b, c);
413		}
414
415		for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
416	<	a = torsion->getAtomA()->getGlobalIndex();
417	<	b = torsion->getAtomB()->getGlobalIndex();
418	<	c = torsion->getAtomC()->getGlobalIndex();
419	<	d = torsion->getAtomD()->getGlobalIndex();
416	>	a = torsion->getAtomA()->getGlobalIndex();
417	>	b = torsion->getAtomB()->getGlobalIndex();
418	>	c = torsion->getAtomC()->getGlobalIndex();
419	>	d = torsion->getAtomD()->getGlobalIndex();
420
421	<	exclude_.removePair(a, b);
422	<	exclude_.removePair(a, c);
423	<	exclude_.removePair(a, d);
424	<	exclude_.removePair(b, c);
425	<	exclude_.removePair(b, d);
426	<	exclude_.removePair(c, d);
421	>	exclude_.removePair(a, b);
422	>	exclude_.removePair(a, c);
423	>	exclude_.removePair(a, d);
424	>	exclude_.removePair(b, c);
425	>	exclude_.removePair(b, d);
426	>	exclude_.removePair(c, d);
427		}
428
429	<	}
429	>	Molecule::RigidBodyIterator rbIter;
430	>	RigidBody* rb;
431	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
432	>	std::vector<Atom*> atoms = rb->getAtoms();
433	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
434	>	for (int j = i + 1; j < atoms.size(); ++j) {
435	>	a = atoms[i]->getGlobalIndex();
436	>	b = atoms[j]->getGlobalIndex();
437	>	exclude_.removePair(a, b);
438	>	}
439	>	}
440	>	}
441
442	+	}
443
444	<	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
444	>
445	>	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
446		int curStampId;
447
448		//index from 0
#	Line 421 \| Line 450 \| *void SimInfo::addMoleculeStamp(MoleculeStamp molStamp**
450
451		moleculeStamps_.push_back(molStamp);
452		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
453	<	}
453	>	}
454
455	<	void SimInfo::update() {
455	>	void SimInfo::update() {
456
457		setupSimType();
458
#	Line 436 \| Line 465 \| void SimInfo::update() {
465		//setup fortran force field
466		/** @deprecate */
467		int isError = 0;
468	<	initFortranFF( &fInfo_.SIM_uses_RF , &isError );
468	>
469	>	setupElectrostaticSummationMethod( isError );
470	>
471		if(isError){
472	<	sprintf( painCave.errMsg,
473	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
474	<	painCave.isFatal = 1;
475	<	simError();
472	>	sprintf( painCave.errMsg,
473	>	"ForceField error: There was an error initializing the forceField in fortran.\n" );
474	>	painCave.isFatal = 1;
475	>	simError();
476		}
477
478
#	Line 452 \| Line 483 \| void SimInfo::update() {
483		calcNdfTrans();
484
485		fortranInitialized_ = true;
486	<	}
486	>	}
487
488	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
488	>	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
489		SimInfo::MoleculeIterator mi;
490		Molecule* mol;
491		Molecule::AtomIterator ai;
#	Line 463 \| Line 494 \| *std::set<AtomType> SimInfo::getUniqueAtomTypes() {**
494
495		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
496
497	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
498	<	atomTypes.insert(atom->getAtomType());
499	<	}
497	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
498	>	atomTypes.insert(atom->getAtomType());
499	>	}
500
501		}
502
503		return atomTypes;
504	<	}
504	>	}
505
506	<	void SimInfo::setupSimType() {
506	>	void SimInfo::setupSimType() {
507		std::set<AtomType*>::iterator i;
508		std::set<AtomType*> atomTypes;
509		atomTypes = getUniqueAtomTypes();
#	Line 485 \| Line 516 \| void SimInfo::setupSimType() {
516		int useDipole = 0;
517		int useGayBerne = 0;
518		int useSticky = 0;
519	+	int useStickyPower = 0;
520		int useShape = 0;
521		int useFLARB = 0; //it is not in AtomType yet
522		int useDirectionalAtom = 0;
523		int useElectrostatics = 0;
524		//usePBC and useRF are from simParams
525		int usePBC = simParams_->getPBC();
526	<	int useRF = simParams_->getUseRF();
526	>	int useRF;
527
528	+	// set the useRF logical
529	+	std::string myMethod = simParams_->getElectrostaticSummationMethod();
530	+	if (myMethod == "REACTION_FIELD")
531	+	useRF = 1;
532	+	else
533	+	useRF = 0;
534	+
535		//loop over all of the atom types
536		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
537	<	useLennardJones \|= (*i)->isLennardJones();
538	<	useElectrostatic \|= (*i)->isElectrostatic();
539	<	useEAM \|= (*i)->isEAM();
540	<	useCharge \|= (*i)->isCharge();
541	<	useDirectional \|= (*i)->isDirectional();
542	<	useDipole \|= (*i)->isDipole();
543	<	useGayBerne \|= (*i)->isGayBerne();
544	<	useSticky \|= (*i)->isSticky();
545	<	useShape \|= (*i)->isShape();
537	>	useLennardJones \|= (*i)->isLennardJones();
538	>	useElectrostatic \|= (*i)->isElectrostatic();
539	>	useEAM \|= (*i)->isEAM();
540	>	useCharge \|= (*i)->isCharge();
541	>	useDirectional \|= (*i)->isDirectional();
542	>	useDipole \|= (*i)->isDipole();
543	>	useGayBerne \|= (*i)->isGayBerne();
544	>	useSticky \|= (*i)->isSticky();
545	>	useStickyPower \|= (*i)->isStickyPower();
546	>	useShape \|= (*i)->isShape();
547		}
548
549	<	if (useSticky \|\| useDipole \|\| useGayBerne \|\| useShape) {
550	<	useDirectionalAtom = 1;
549	>	if (useSticky \|\| useStickyPower \|\| useDipole \|\| useGayBerne \|\| useShape) {
550	>	useDirectionalAtom = 1;
551		}
552
553		if (useCharge \|\| useDipole) {
554	<	useElectrostatics = 1;
554	>	useElectrostatics = 1;
555		}
556
557		#ifdef IS_MPI
#	Line 538 \| Line 578 \| void SimInfo::setupSimType() {
578		temp = useSticky;
579		MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
580
581	+	temp = useStickyPower;
582	+	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
583	+
584		temp = useGayBerne;
585		MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
586
#	Line 552 \| Line 595 \| void SimInfo::setupSimType() {
595
596		temp = useRF;
597		MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
598	<
598	>
599		#endif
600
601		fInfo_.SIM_uses_PBC = usePBC;
#	Line 562 \| Line 605 \| void SimInfo::setupSimType() {
605		fInfo_.SIM_uses_Charges = useCharge;
606		fInfo_.SIM_uses_Dipoles = useDipole;
607		fInfo_.SIM_uses_Sticky = useSticky;
608	+	fInfo_.SIM_uses_StickyPower = useStickyPower;
609		fInfo_.SIM_uses_GayBerne = useGayBerne;
610		fInfo_.SIM_uses_EAM = useEAM;
611		fInfo_.SIM_uses_Shapes = useShape;
612		fInfo_.SIM_uses_FLARB = useFLARB;
613		fInfo_.SIM_uses_RF = useRF;
614
615	<	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
615	>	if( fInfo_.SIM_uses_Dipoles && myMethod == "REACTION_FIELD") {
616
617	<	if (simParams_->haveDielectric()) {
618	<	fInfo_.dielect = simParams_->getDielectric();
619	<	} else {
620	<	sprintf(painCave.errMsg,
621	<	"SimSetup Error: No Dielectric constant was set.\n"
622	<	"\tYou are trying to use Reaction Field without"
623	<	"\tsetting a dielectric constant!\n");
624	<	painCave.isFatal = 1;
625	<	simError();
626	<	}
617	>	if (simParams_->haveDielectric()) {
618	>	fInfo_.dielect = simParams_->getDielectric();
619	>	} else {
620	>	sprintf(painCave.errMsg,
621	>	"SimSetup Error: No Dielectric constant was set.\n"
622	>	"\tYou are trying to use Reaction Field without"
623	>	"\tsetting a dielectric constant!\n");
624	>	painCave.isFatal = 1;
625	>	simError();
626	>	}
627
628		} else {
629	<	fInfo_.dielect = 0.0;
629	>	fInfo_.dielect = 0.0;
630		}
631
632	<	}
632	>	}
633
634	<	void SimInfo::setupFortranSim() {
634	>	void SimInfo::setupFortranSim() {
635		int isError;
636		int nExclude;
637		std::vector<int> fortranGlobalGroupMembership;
#	Line 597 \| Line 641 \| void SimInfo::setupFortranSim() {
641
642		//globalGroupMembership_ is filled by SimCreator
643		for (int i = 0; i < nGlobalAtoms_; i++) {
644	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
644	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
645		}
646
647		//calculate mass ratio of cutoff group
#	Line 614 \| Line 658 \| void SimInfo::setupFortranSim() {
658		mfact.reserve(getNCutoffGroups());
659
660		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
661	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
661	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
662
663	<	totalMass = cg->getMass();
664	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
665	<	mfact.push_back(atom->getMass()/totalMass);
666	<	}
663	>	totalMass = cg->getMass();
664	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
665	>	mfact.push_back(atom->getMass()/totalMass);
666	>	}
667
668	<	}
668	>	}
669		}
670
671		//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
#	Line 631 \| Line 675 \| void SimInfo::setupFortranSim() {
675		identArray.reserve(getNAtoms());
676
677		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
678	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
679	<	identArray.push_back(atom->getIdent());
680	<	}
678	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
679	>	identArray.push_back(atom->getIdent());
680	>	}
681		}
682
683		//fill molMembershipArray
684		//molMembershipArray is filled by SimCreator
685		std::vector<int> molMembershipArray(nGlobalAtoms_);
686		for (int i = 0; i < nGlobalAtoms_; i++) {
687	<	molMembershipArray[i] = globalMolMembership_[i] + 1;
687	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
688		}
689
690		//setup fortran simulation
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
691		int nGlobalExcludes = 0;
692		int* globalExcludes = NULL;
693		int* excludeList = exclude_.getExcludeList();
694		setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
695	<	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
696	<	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
695	>	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
696	>	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
697
698		if( isError ){
699
700	<	sprintf( painCave.errMsg,
701	<	"There was an error setting the simulation information in fortran.\n" );
702	<	painCave.isFatal = 1;
703	<	painCave.severity = OOPSE_ERROR;
704	<	simError();
700	>	sprintf( painCave.errMsg,
701	>	"There was an error setting the simulation information in fortran.\n" );
702	>	painCave.isFatal = 1;
703	>	painCave.severity = OOPSE_ERROR;
704	>	simError();
705		}
706
707		#ifdef IS_MPI
708		sprintf( checkPointMsg,
709	<	"succesfully sent the simulation information to fortran.\n");
709	>	"succesfully sent the simulation information to fortran.\n");
710		MPIcheckPoint();
711		#endif // is_mpi
712	<	}
712	>	}
713
714
715		#ifdef IS_MPI
716	<	void SimInfo::setupFortranParallel() {
716	>	void SimInfo::setupFortranParallel() {
717
718		//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
719		std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
#	Line 688 \| Line 729 \| void SimInfo::setupFortranParallel() {
729
730		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
731
732	<	//local index(index in DataStorge) of atom is important
733	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
734	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
735	<	}
732	>	//local index(index in DataStorge) of atom is important
733	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
734	>	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
735	>	}
736
737	<	//local index of cutoff group is trivial, it only depends on the order of travesing
738	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
739	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
740	<	}
737	>	//local index of cutoff group is trivial, it only depends on the order of travesing
738	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
739	>	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
740	>	}
741
742		}
743
#	Line 716 \| Line 757 \| void SimInfo::setupFortranParallel() {
757		&localToGlobalCutoffGroupIndex[0], &isError);
758
759		if (isError) {
760	<	sprintf(painCave.errMsg,
761	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
762	<	painCave.isFatal = 1;
763	<	simError();
760	>	sprintf(painCave.errMsg,
761	>	"mpiRefresh errror: fortran didn't like something we gave it.\n");
762	>	painCave.isFatal = 1;
763	>	simError();
764		}
765
766		sprintf(checkPointMsg, " mpiRefresh successful.\n");
767		MPIcheckPoint();
768
769
770	<	}
770	>	}
771
772		#endif
773
774	<	double SimInfo::calcMaxCutoffRadius() {
774	>	double SimInfo::calcMaxCutoffRadius() {
775
776
777		std::set<AtomType*> atomTypes;
#	Line 742 \| Line 783 \| double SimInfo::calcMaxCutoffRadius() {
783
784		//query the max cutoff radius among these atom types
785		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
786	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
786	>	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
787		}
788
789		double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
#	Line 751 \| Line 792 \| double SimInfo::calcMaxCutoffRadius() {
792		#endif
793
794		return maxCutoffRadius;
795	<	}
795	>	}
796
797	<	void SimInfo::setupCutoff() {
757	<	double rcut_; //cutoff radius
758	<	double rsw_; //switching radius
797	>	void SimInfo::getCutoff(double& rcut, double& rsw) {
798
799		if (fInfo_.SIM_uses_Charges \| fInfo_.SIM_uses_Dipoles \| fInfo_.SIM_uses_RF) {
800
801	<	if (!simParams_->haveRcut()){
802	<	sprintf(painCave.errMsg,
801	>	if (!simParams_->haveRcut()){
802	>	sprintf(painCave.errMsg,
803		"SimCreator Warning: No value was set for the cutoffRadius.\n"
804		"\tOOPSE will use a default value of 15.0 angstroms"
805		"\tfor the cutoffRadius.\n");
806	<	painCave.isFatal = 0;
807	<	simError();
808	<	rcut_ = 15.0;
809	<	} else{
810	<	rcut_ = simParams_->getRcut();
811	<	}
806	>	painCave.isFatal = 0;
807	>	simError();
808	>	rcut = 15.0;
809	>	} else{
810	>	rcut = simParams_->getRcut();
811	>	}
812
813	<	if (!simParams_->haveRsw()){
814	<	sprintf(painCave.errMsg,
813	>	if (!simParams_->haveRsw()){
814	>	sprintf(painCave.errMsg,
815		"SimCreator Warning: No value was set for switchingRadius.\n"
816		"\tOOPSE will use a default value of\n"
817		"\t0.95 * cutoffRadius for the switchingRadius\n");
818	<	painCave.isFatal = 0;
819	<	simError();
820	<	rsw_ = 0.95 * rcut_;
821	<	} else{
822	<	rsw_ = simParams_->getRsw();
823	<	}
818	>	painCave.isFatal = 0;
819	>	simError();
820	>	rsw = 0.95 * rcut;
821	>	} else{
822	>	rsw = simParams_->getRsw();
823	>	}
824
825		} else {
826	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
827	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
826	>	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
827	>	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
828
829	<	if (simParams_->haveRcut()) {
830	<	rcut_ = simParams_->getRcut();
831	<	} else {
832	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
833	<	rcut_ = calcMaxCutoffRadius();
834	<	}
829	>	if (simParams_->haveRcut()) {
830	>	rcut = simParams_->getRcut();
831	>	} else {
832	>	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
833	>	rcut = calcMaxCutoffRadius();
834	>	}
835
836	<	if (simParams_->haveRsw()) {
837	<	rsw_ = simParams_->getRsw();
838	<	} else {
839	<	rsw_ = rcut_;
840	<	}
836	>	if (simParams_->haveRsw()) {
837	>	rsw = simParams_->getRsw();
838	>	} else {
839	>	rsw = rcut;
840	>	}
841
842		}
843	<
843	>	}
844	>
845	>	void SimInfo::setupCutoff() {
846	>	getCutoff(rcut_, rsw_);
847		double rnblist = rcut_ + 1; // skin of neighbor list
848
849		//Pass these cutoff radius etc. to fortran. This function should be called once and only once
850	<	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist);
851	<	}
850	>
851	>	int cp = TRADITIONAL_CUTOFF_POLICY;
852	>	if (simParams_->haveCutoffPolicy()) {
853	>	std::string myPolicy = simParams_->getCutoffPolicy();
854	>	if (myPolicy == "MIX") {
855	>	cp = MIX_CUTOFF_POLICY;
856	>	} else {
857	>	if (myPolicy == "MAX") {
858	>	cp = MAX_CUTOFF_POLICY;
859	>	} else {
860	>	if (myPolicy == "TRADITIONAL") {
861	>	cp = TRADITIONAL_CUTOFF_POLICY;
862	>	} else {
863	>	// throw error
864	>	sprintf( painCave.errMsg,
865	>	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
866	>	painCave.isFatal = 1;
867	>	simError();
868	>	}
869	>	}
870	>	}
871	>	}
872
873	<	void SimInfo::addProperty(GenericData* genData) {
873	>
874	>	if (simParams_->haveSkinThickness()) {
875	>	double skinThickness = simParams_->getSkinThickness();
876	>	}
877	>
878	>	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
879	>	// also send cutoff notification to electrostatics
880	>	setElectrostaticCutoffRadius(&rcut_);
881	>	}
882	>
883	>	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
884	>
885	>	int errorOut;
886	>	int esm = NONE;
887	>	double alphaVal;
888	>	double dielectric;
889	>
890	>	errorOut = isError;
891	>	alphaVal = simParams_->getDampingAlpha();
892	>	dielectric = simParams_->getDielectric();
893	>
894	>	if (simParams_->haveElectrostaticSummationMethod()) {
895	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
896	>	if (myMethod == "NONE") {
897	>	esm = NONE;
898	>	} else {
899	>	if (myMethod == "UNDAMPED_WOLF") {
900	>	esm = UNDAMPED_WOLF;
901	>	} else {
902	>	if (myMethod == "DAMPED_WOLF") {
903	>	esm = DAMPED_WOLF;
904	>	if (!simParams_->haveDampingAlpha()) {
905	>	//throw error
906	>	sprintf( painCave.errMsg,
907	>	"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);
908	>	painCave.isFatal = 0;
909	>	simError();
910	>	}
911	>	} else {
912	>	if (myMethod == "REACTION_FIELD") {
913	>	esm = REACTION_FIELD;
914	>	} else {
915	>	// throw error
916	>	sprintf( painCave.errMsg,
917	>	"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() );
918	>	painCave.isFatal = 1;
919	>	simError();
920	>	}
921	>	}
922	>	}
923	>	}
924	>	}
925	>	// let's pass some summation method variables to fortran
926	>	setElectrostaticSummationMethod( &esm );
927	>	setDampedWolfAlpha( &alphaVal );
928	>	setReactionFieldDielectric( &dielectric );
929	>	initFortranFF( &esm, &errorOut );
930	>	}
931	>
932	>	void SimInfo::addProperty(GenericData* genData) {
933		properties_.addProperty(genData);
934	<	}
934	>	}
935
936	<	void SimInfo::removeProperty(const std::string& propName) {
936	>	void SimInfo::removeProperty(const std::string& propName) {
937		properties_.removeProperty(propName);
938	<	}
938	>	}
939
940	<	void SimInfo::clearProperties() {
940	>	void SimInfo::clearProperties() {
941		properties_.clearProperties();
942	<	}
942	>	}
943
944	<	std::vector<std::string> SimInfo::getPropertyNames() {
944	>	std::vector<std::string> SimInfo::getPropertyNames() {
945		return properties_.getPropertyNames();
946	<	}
947	<
948	<	std::vector<GenericData*> SimInfo::getProperties() {
946	>	}
947	>
948	>	std::vector<GenericData*> SimInfo::getProperties() {
949		return properties_.getProperties();
950	<	}
950	>	}
951
952	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
952	>	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
953		return properties_.getPropertyByName(propName);
954	<	}
954	>	}
955
956	<	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
956	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
957	>	if (sman_ == sman) {
958	>	return;
959	>	}
960	>	delete sman_;
961		sman_ = sman;
962
963		Molecule* mol;
#	Line 844 \| Line 969 \| *void SimInfo::setSnapshotManager(SnapshotManager sman**
969
970		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
971
972	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
973	<	atom->setSnapshotManager(sman_);
974	<	}
972	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
973	>	atom->setSnapshotManager(sman_);
974	>	}
975
976	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
977	<	rb->setSnapshotManager(sman_);
978	<	}
976	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
977	>	rb->setSnapshotManager(sman_);
978	>	}
979		}
980
981	<	}
981	>	}
982
983	<	Vector3d SimInfo::getComVel(){
983	>	Vector3d SimInfo::getComVel(){
984		SimInfo::MoleculeIterator i;
985		Molecule* mol;
986
#	Line 864 \| Line 989 \| Vector3d SimInfo::getComVel(){
989
990
991		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
992	<	double mass = mol->getMass();
993	<	totalMass += mass;
994	<	comVel += mass * mol->getComVel();
992	>	double mass = mol->getMass();
993	>	totalMass += mass;
994	>	comVel += mass * mol->getComVel();
995		}
996
997		#ifdef IS_MPI
#	Line 879 \| Line 1004 \| Vector3d SimInfo::getComVel(){
1004		comVel /= totalMass;
1005
1006		return comVel;
1007	<	}
1007	>	}
1008
1009	<	Vector3d SimInfo::getCom(){
1009	>	Vector3d SimInfo::getCom(){
1010		SimInfo::MoleculeIterator i;
1011		Molecule* mol;
1012
#	Line 889 \| Line 1014 \| Vector3d SimInfo::getCom(){
1014		double totalMass = 0.0;
1015
1016		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1017	<	double mass = mol->getMass();
1018	<	totalMass += mass;
1019	<	com += mass * mol->getCom();
1017	>	double mass = mol->getMass();
1018	>	totalMass += mass;
1019	>	com += mass * mol->getCom();
1020		}
1021
1022		#ifdef IS_MPI
#	Line 905 \| Line 1030 \| Vector3d SimInfo::getCom(){
1030
1031		return com;
1032
1033	<	}
1033	>	}
1034
1035	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1035	>	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1036
1037		return o;
1038	<	}
1038	>	}
1039	>
1040	>
1041	>	/*
1042	>	Returns center of mass and center of mass velocity in one function call.
1043	>	*/
1044	>
1045	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1046	>	SimInfo::MoleculeIterator i;
1047	>	Molecule* mol;
1048	>
1049	>
1050	>	double totalMass = 0.0;
1051	>
1052
1053	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1054	+	double mass = mol->getMass();
1055	+	totalMass += mass;
1056	+	com += mass * mol->getCom();
1057	+	comVel += mass * mol->getComVel();
1058	+	}
1059	+
1060	+	#ifdef IS_MPI
1061	+	double tmpMass = totalMass;
1062	+	Vector3d tmpCom(com);
1063	+	Vector3d tmpComVel(comVel);
1064	+	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1065	+	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1066	+	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1067	+	#endif
1068	+
1069	+	com /= totalMass;
1070	+	comVel /= totalMass;
1071	+	}
1072	+
1073	+	/*
1074	+	Return intertia tensor for entire system and angular momentum Vector.
1075	+
1076	+
1077	+	[ Ixx -Ixy -Ixz ]
1078	+	J =\| -Iyx Iyy -Iyz \|
1079	+	[ -Izx -Iyz Izz ]
1080	+	*/
1081	+
1082	+	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1083	+
1084	+
1085	+	double xx = 0.0;
1086	+	double yy = 0.0;
1087	+	double zz = 0.0;
1088	+	double xy = 0.0;
1089	+	double xz = 0.0;
1090	+	double yz = 0.0;
1091	+	Vector3d com(0.0);
1092	+	Vector3d comVel(0.0);
1093	+
1094	+	getComAll(com, comVel);
1095	+
1096	+	SimInfo::MoleculeIterator i;
1097	+	Molecule* mol;
1098	+
1099	+	Vector3d thisq(0.0);
1100	+	Vector3d thisv(0.0);
1101	+
1102	+	double thisMass = 0.0;
1103	+
1104	+
1105	+
1106	+
1107	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1108	+
1109	+	thisq = mol->getCom()-com;
1110	+	thisv = mol->getComVel()-comVel;
1111	+	thisMass = mol->getMass();
1112	+	// Compute moment of intertia coefficients.
1113	+	xx += thisq[0]thisq[0]thisMass;
1114	+	yy += thisq[1]thisq[1]thisMass;
1115	+	zz += thisq[2]thisq[2]thisMass;
1116	+
1117	+	// compute products of intertia
1118	+	xy += thisq[0]thisq[1]thisMass;
1119	+	xz += thisq[0]thisq[2]thisMass;
1120	+	yz += thisq[1]thisq[2]thisMass;
1121	+
1122	+	angularMomentum += cross( thisq, thisv ) * thisMass;
1123	+
1124	+	}
1125	+
1126	+
1127	+	inertiaTensor(0,0) = yy + zz;
1128	+	inertiaTensor(0,1) = -xy;
1129	+	inertiaTensor(0,2) = -xz;
1130	+	inertiaTensor(1,0) = -xy;
1131	+	inertiaTensor(1,1) = xx + zz;
1132	+	inertiaTensor(1,2) = -yz;
1133	+	inertiaTensor(2,0) = -xz;
1134	+	inertiaTensor(2,1) = -yz;
1135	+	inertiaTensor(2,2) = xx + yy;
1136	+
1137	+	#ifdef IS_MPI
1138	+	Mat3x3d tmpI(inertiaTensor);
1139	+	Vector3d tmpAngMom;
1140	+	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1141	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1142	+	#endif
1143	+
1144	+	return;
1145	+	}
1146	+
1147	+	//Returns the angular momentum of the system
1148	+	Vector3d SimInfo::getAngularMomentum(){
1149	+
1150	+	Vector3d com(0.0);
1151	+	Vector3d comVel(0.0);
1152	+	Vector3d angularMomentum(0.0);
1153	+
1154	+	getComAll(com,comVel);
1155	+
1156	+	SimInfo::MoleculeIterator i;
1157	+	Molecule* mol;
1158	+
1159	+	Vector3d thisr(0.0);
1160	+	Vector3d thisp(0.0);
1161	+
1162	+	double thisMass;
1163	+
1164	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1165	+	thisMass = mol->getMass();
1166	+	thisr = mol->getCom()-com;
1167	+	thisp = (mol->getComVel()-comVel)*thisMass;
1168	+
1169	+	angularMomentum += cross( thisr, thisp );
1170	+
1171	+	}
1172	+
1173	+	#ifdef IS_MPI
1174	+	Vector3d tmpAngMom;
1175	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1176	+	#endif
1177	+
1178	+	return angularMomentum;
1179	+	}
1180	+
1181	+
1182		}//end namespace oopse
1183

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Comparing trunk/src/brains/SimInfo.cpp (file contents): Revision 292 by tim, Fri Feb 4 22:44:15 2005 UTC vs. Revision 629 by chuckv, Mon Sep 26 15:58:17 2005 UTC

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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 292 by tim, Fri Feb 4 22:44:15 2005 UTC vs.
Revision 629 by chuckv, Mon Sep 26 15:58:17 2005 UTC