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

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
Revision 716 by chrisfen, Thu Nov 3 23:12:27 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/DarkSide/fElectrostaticScreeningMethod.h"
58		#include "UseTheForce/doForces_interface.h"
59	+	#include "UseTheForce/DarkSide/electrostatic_interface.h"
60		#include "UseTheForce/notifyCutoffs_interface.h"
61		#include "utils/MemoryUtils.hpp"
62		#include "utils/simError.h"
63	+	#include "selection/SelectionManager.hpp"
64
65		#ifdef IS_MPI
66		#include "UseTheForce/mpiComponentPlan.h"
#	Line 64 \| Line 69 \| namespace oopse {
69
70		namespace oopse {
71
72	<	SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
73	<	ForceField* ff, Globals* simParams) :
74	<	forceField_(ff), simParams_(simParams),
75	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
76	<	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
77	<	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
78	<	nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nRigidBodies_(0),
79	<	nIntegrableObjects_(0), nCutoffGroups_(0), nConstraints_(0),
80	<	sman_(NULL), fortranInitialized_(false) {
72	>	SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
73	>	ForceField* ff, Globals* simParams) :
74	>	stamps_(stamps), forceField_(ff), simParams_(simParams),
75	>	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
76	>	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
77	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
78	>	nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nRigidBodies_(0),
79	>	nIntegrableObjects_(0), nCutoffGroups_(0), nConstraints_(0),
80	>	sman_(NULL), fortranInitialized_(false) {
81
82
83	<	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
84	<	MoleculeStamp* molStamp;
85	<	int nMolWithSameStamp;
86	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
87	<	int nGroups = 0; //total cutoff groups defined in meta-data file
88	<	CutoffGroupStamp* cgStamp;
89	<	RigidBodyStamp* rbStamp;
90	<	int nRigidAtoms = 0;
83	>	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
84	>	MoleculeStamp* molStamp;
85	>	int nMolWithSameStamp;
86	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
87	>	int nGroups = 0; //total cutoff groups defined in meta-data file
88	>	CutoffGroupStamp* cgStamp;
89	>	RigidBodyStamp* rbStamp;
90	>	int nRigidAtoms = 0;
91
92	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
92	>	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
93		molStamp = i->first;
94		nMolWithSameStamp = i->second;
95
#	Line 99 \| Line 104 \| *SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp,**
104		int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
105
106		for (int j=0; j < nCutoffGroupsInStamp; j++) {
107	<	cgStamp = molStamp->getCutoffGroup(j);
108	<	nAtomsInGroups += cgStamp->getNMembers();
107	>	cgStamp = molStamp->getCutoffGroup(j);
108	>	nAtomsInGroups += cgStamp->getNMembers();
109		}
110
111		nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
112	+
113		nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
114
115		//calculate atoms in rigid bodies
116		int nAtomsInRigidBodies = 0;
117	<	int nRigidBodiesInStamp = molStamp->getNCutoffGroups();
117	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
118
119		for (int j=0; j < nRigidBodiesInStamp; j++) {
120	<	rbStamp = molStamp->getRigidBody(j);
121	<	nAtomsInRigidBodies += rbStamp->getNMembers();
120	>	rbStamp = molStamp->getRigidBody(j);
121	>	nAtomsInRigidBodies += rbStamp->getNMembers();
122		}
123
124		nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
125		nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
126
127	<	}
127	>	}
128
129	<	//every free atom (atom does not belong to cutoff groups) is a cutoff group
130	<	//therefore the total number of cutoff groups in the system is equal to
131	<	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
132	<	//file plus the number of cutoff groups defined in meta-data file
133	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
129	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
130	>	//group therefore the total number of cutoff groups in the system is
131	>	//equal to the total number of atoms minus number of atoms belong to
132	>	//cutoff group defined in meta-data file plus the number of cutoff
133	>	//groups defined in meta-data file
134	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
135
136	<	//every free atom (atom does not belong to rigid bodies) is an integrable object
137	<	//therefore the total number of integrable objects in the system is equal to
138	<	//the total number of atoms minus number of atoms belong to rigid body defined in meta-data
139	<	//file plus the number of rigid bodies defined in meta-data file
140	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
136	>	//every free atom (atom does not belong to rigid bodies) is an
137	>	//integrable object therefore the total number of integrable objects
138	>	//in the system is equal to the total number of atoms minus number of
139	>	//atoms belong to rigid body defined in meta-data file plus the number
140	>	//of rigid bodies defined in meta-data file
141	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
142	>	+ nGlobalRigidBodies_;
143	>
144	>	nGlobalMols_ = molStampIds_.size();
145
135	–	nGlobalMols_ = molStampIds_.size();
136	–
146		#ifdef IS_MPI
147	<	molToProcMap_.resize(nGlobalMols_);
147	>	molToProcMap_.resize(nGlobalMols_);
148		#endif
140	–
141	–	}
149
150	<	SimInfo::~SimInfo() {
144	<	//MemoryUtils::deleteVectorOfPointer(molecules_);
150	>	}
151
152	<	MemoryUtils::deleteVectorOfPointer(moleculeStamps_);
153	<
152	>	SimInfo::~SimInfo() {
153	>	std::map<int, Molecule*>::iterator i;
154	>	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
155	>	delete i->second;
156	>	}
157	>	molecules_.clear();
158	>
159	>	delete stamps_;
160		delete sman_;
161		delete simParams_;
162		delete forceField_;
163	+	}
164
165	<	}
153	<
154	<	int SimInfo::getNGlobalConstraints() {
165	>	int SimInfo::getNGlobalConstraints() {
166		int nGlobalConstraints;
167		#ifdef IS_MPI
168		MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
#	Line 160 \| Line 171 \| int SimInfo::getNGlobalConstraints() {
171		nGlobalConstraints = nConstraints_;
172		#endif
173		return nGlobalConstraints;
174	<	}
174	>	}
175
176	<	bool SimInfo::addMolecule(Molecule* mol) {
176	>	bool SimInfo::addMolecule(Molecule* mol) {
177		MoleculeIterator i;
178
179		i = molecules_.find(mol->getGlobalIndex());
180		if (i == molecules_.end() ) {
181
182	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
182	>	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
183
184	<	nAtoms_ += mol->getNAtoms();
185	<	nBonds_ += mol->getNBonds();
186	<	nBends_ += mol->getNBends();
187	<	nTorsions_ += mol->getNTorsions();
188	<	nRigidBodies_ += mol->getNRigidBodies();
189	<	nIntegrableObjects_ += mol->getNIntegrableObjects();
190	<	nCutoffGroups_ += mol->getNCutoffGroups();
191	<	nConstraints_ += mol->getNConstraintPairs();
184	>	nAtoms_ += mol->getNAtoms();
185	>	nBonds_ += mol->getNBonds();
186	>	nBends_ += mol->getNBends();
187	>	nTorsions_ += mol->getNTorsions();
188	>	nRigidBodies_ += mol->getNRigidBodies();
189	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
190	>	nCutoffGroups_ += mol->getNCutoffGroups();
191	>	nConstraints_ += mol->getNConstraintPairs();
192
193	<	addExcludePairs(mol);
193	>	addExcludePairs(mol);
194
195	<	return true;
195	>	return true;
196		} else {
197	<	return false;
197	>	return false;
198		}
199	<	}
199	>	}
200
201	<	bool SimInfo::removeMolecule(Molecule* mol) {
201	>	bool SimInfo::removeMolecule(Molecule* mol) {
202		MoleculeIterator i;
203		i = molecules_.find(mol->getGlobalIndex());
204
205		if (i != molecules_.end() ) {
206
207	<	assert(mol == i->second);
207	>	assert(mol == i->second);
208
209	<	nAtoms_ -= mol->getNAtoms();
210	<	nBonds_ -= mol->getNBonds();
211	<	nBends_ -= mol->getNBends();
212	<	nTorsions_ -= mol->getNTorsions();
213	<	nRigidBodies_ -= mol->getNRigidBodies();
214	<	nIntegrableObjects_ -= mol->getNIntegrableObjects();
215	<	nCutoffGroups_ -= mol->getNCutoffGroups();
216	<	nConstraints_ -= mol->getNConstraintPairs();
209	>	nAtoms_ -= mol->getNAtoms();
210	>	nBonds_ -= mol->getNBonds();
211	>	nBends_ -= mol->getNBends();
212	>	nTorsions_ -= mol->getNTorsions();
213	>	nRigidBodies_ -= mol->getNRigidBodies();
214	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
215	>	nCutoffGroups_ -= mol->getNCutoffGroups();
216	>	nConstraints_ -= mol->getNConstraintPairs();
217
218	<	removeExcludePairs(mol);
219	<	molecules_.erase(mol->getGlobalIndex());
218	>	removeExcludePairs(mol);
219	>	molecules_.erase(mol->getGlobalIndex());
220
221	<	delete mol;
221	>	delete mol;
222
223	<	return true;
223	>	return true;
224		} else {
225	<	return false;
225	>	return false;
226		}
227
228
229	<	}
229	>	}
230
231
232	<	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
232	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
233		i = molecules_.begin();
234		return i == molecules_.end() ? NULL : i->second;
235	<	}
235	>	}
236
237	<	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
237	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
238		++i;
239		return i == molecules_.end() ? NULL : i->second;
240	<	}
240	>	}
241
242
243	<	void SimInfo::calcNdf() {
243	>	void SimInfo::calcNdf() {
244		int ndf_local;
245		MoleculeIterator i;
246		std::vector<StuntDouble*>::iterator j;
#	Line 239 \| Line 250 \| void SimInfo::calcNdf() {
250		ndf_local = 0;
251
252		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
253	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
254	<	integrableObject = mol->nextIntegrableObject(j)) {
253	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
254	>	integrableObject = mol->nextIntegrableObject(j)) {
255
256	<	ndf_local += 3;
256	>	ndf_local += 3;
257
258	<	if (integrableObject->isDirectional()) {
259	<	if (integrableObject->isLinear()) {
260	<	ndf_local += 2;
261	<	} else {
262	<	ndf_local += 3;
263	<	}
264	<	}
258	>	if (integrableObject->isDirectional()) {
259	>	if (integrableObject->isLinear()) {
260	>	ndf_local += 2;
261	>	} else {
262	>	ndf_local += 3;
263	>	}
264	>	}
265
266	<	}//end for (integrableObject)
266	>	}//end for (integrableObject)
267		}// end for (mol)
268
269		// n_constraints is local, so subtract them on each processor
#	Line 268 \| Line 279 \| void SimInfo::calcNdf() {
279		// entire system:
280		ndf_ = ndf_ - 3 - nZconstraint_;
281
282	<	}
282	>	}
283
284	<	void SimInfo::calcNdfRaw() {
284	>	void SimInfo::calcNdfRaw() {
285		int ndfRaw_local;
286
287		MoleculeIterator i;
#	Line 282 \| Line 293 \| void SimInfo::calcNdfRaw() {
293		ndfRaw_local = 0;
294
295		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
296	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
297	<	integrableObject = mol->nextIntegrableObject(j)) {
296	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
297	>	integrableObject = mol->nextIntegrableObject(j)) {
298
299	<	ndfRaw_local += 3;
299	>	ndfRaw_local += 3;
300
301	<	if (integrableObject->isDirectional()) {
302	<	if (integrableObject->isLinear()) {
303	<	ndfRaw_local += 2;
304	<	} else {
305	<	ndfRaw_local += 3;
306	<	}
307	<	}
301	>	if (integrableObject->isDirectional()) {
302	>	if (integrableObject->isLinear()) {
303	>	ndfRaw_local += 2;
304	>	} else {
305	>	ndfRaw_local += 3;
306	>	}
307	>	}
308
309	<	}
309	>	}
310		}
311
312		#ifdef IS_MPI
#	Line 303 \| Line 314 \| void SimInfo::calcNdfRaw() {
314		#else
315		ndfRaw_ = ndfRaw_local;
316		#endif
317	<	}
317	>	}
318
319	<	void SimInfo::calcNdfTrans() {
319	>	void SimInfo::calcNdfTrans() {
320		int ndfTrans_local;
321
322		ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
#	Line 319 \| Line 330 \| void SimInfo::calcNdfTrans() {
330
331		ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
332
333	<	}
333	>	}
334
335	<	void SimInfo::addExcludePairs(Molecule* mol) {
335	>	void SimInfo::addExcludePairs(Molecule* mol) {
336		std::vector<Bond*>::iterator bondIter;
337		std::vector<Bend*>::iterator bendIter;
338		std::vector<Torsion*>::iterator torsionIter;
#	Line 334 \| Line 345 \| *void SimInfo::addExcludePairs(Molecule mol) {**
345		int d;
346
347		for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
348	<	a = bond->getAtomA()->getGlobalIndex();
349	<	b = bond->getAtomB()->getGlobalIndex();
350	<	exclude_.addPair(a, b);
348	>	a = bond->getAtomA()->getGlobalIndex();
349	>	b = bond->getAtomB()->getGlobalIndex();
350	>	exclude_.addPair(a, b);
351		}
352
353		for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
354	<	a = bend->getAtomA()->getGlobalIndex();
355	<	b = bend->getAtomB()->getGlobalIndex();
356	<	c = bend->getAtomC()->getGlobalIndex();
354	>	a = bend->getAtomA()->getGlobalIndex();
355	>	b = bend->getAtomB()->getGlobalIndex();
356	>	c = bend->getAtomC()->getGlobalIndex();
357
358	<	exclude_.addPair(a, b);
359	<	exclude_.addPair(a, c);
360	<	exclude_.addPair(b, c);
358	>	exclude_.addPair(a, b);
359	>	exclude_.addPair(a, c);
360	>	exclude_.addPair(b, c);
361		}
362
363		for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
364	<	a = torsion->getAtomA()->getGlobalIndex();
365	<	b = torsion->getAtomB()->getGlobalIndex();
366	<	c = torsion->getAtomC()->getGlobalIndex();
367	<	d = torsion->getAtomD()->getGlobalIndex();
364	>	a = torsion->getAtomA()->getGlobalIndex();
365	>	b = torsion->getAtomB()->getGlobalIndex();
366	>	c = torsion->getAtomC()->getGlobalIndex();
367	>	d = torsion->getAtomD()->getGlobalIndex();
368
369	<	exclude_.addPair(a, b);
370	<	exclude_.addPair(a, c);
371	<	exclude_.addPair(a, d);
372	<	exclude_.addPair(b, c);
373	<	exclude_.addPair(b, d);
374	<	exclude_.addPair(c, d);
369	>	exclude_.addPair(a, b);
370	>	exclude_.addPair(a, c);
371	>	exclude_.addPair(a, d);
372	>	exclude_.addPair(b, c);
373	>	exclude_.addPair(b, d);
374	>	exclude_.addPair(c, d);
375		}
376
377	<
378	<	}
377	>	Molecule::RigidBodyIterator rbIter;
378	>	RigidBody* rb;
379	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
380	>	std::vector<Atom*> atoms = rb->getAtoms();
381	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
382	>	for (int j = i + 1; j < atoms.size(); ++j) {
383	>	a = atoms[i]->getGlobalIndex();
384	>	b = atoms[j]->getGlobalIndex();
385	>	exclude_.addPair(a, b);
386	>	}
387	>	}
388	>	}
389
390	<	void SimInfo::removeExcludePairs(Molecule* mol) {
390	>	}
391	>
392	>	void SimInfo::removeExcludePairs(Molecule* mol) {
393		std::vector<Bond*>::iterator bondIter;
394		std::vector<Bend*>::iterator bendIter;
395		std::vector<Torsion*>::iterator torsionIter;
#	Line 379 \| Line 402 \| *void SimInfo::removeExcludePairs(Molecule mol) {**
402		int d;
403
404		for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
405	<	a = bond->getAtomA()->getGlobalIndex();
406	<	b = bond->getAtomB()->getGlobalIndex();
407	<	exclude_.removePair(a, b);
405	>	a = bond->getAtomA()->getGlobalIndex();
406	>	b = bond->getAtomB()->getGlobalIndex();
407	>	exclude_.removePair(a, b);
408		}
409
410		for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
411	<	a = bend->getAtomA()->getGlobalIndex();
412	<	b = bend->getAtomB()->getGlobalIndex();
413	<	c = bend->getAtomC()->getGlobalIndex();
411	>	a = bend->getAtomA()->getGlobalIndex();
412	>	b = bend->getAtomB()->getGlobalIndex();
413	>	c = bend->getAtomC()->getGlobalIndex();
414
415	<	exclude_.removePair(a, b);
416	<	exclude_.removePair(a, c);
417	<	exclude_.removePair(b, c);
415	>	exclude_.removePair(a, b);
416	>	exclude_.removePair(a, c);
417	>	exclude_.removePair(b, c);
418		}
419
420		for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
421	<	a = torsion->getAtomA()->getGlobalIndex();
422	<	b = torsion->getAtomB()->getGlobalIndex();
423	<	c = torsion->getAtomC()->getGlobalIndex();
424	<	d = torsion->getAtomD()->getGlobalIndex();
421	>	a = torsion->getAtomA()->getGlobalIndex();
422	>	b = torsion->getAtomB()->getGlobalIndex();
423	>	c = torsion->getAtomC()->getGlobalIndex();
424	>	d = torsion->getAtomD()->getGlobalIndex();
425
426	<	exclude_.removePair(a, b);
427	<	exclude_.removePair(a, c);
428	<	exclude_.removePair(a, d);
429	<	exclude_.removePair(b, c);
430	<	exclude_.removePair(b, d);
431	<	exclude_.removePair(c, d);
426	>	exclude_.removePair(a, b);
427	>	exclude_.removePair(a, c);
428	>	exclude_.removePair(a, d);
429	>	exclude_.removePair(b, c);
430	>	exclude_.removePair(b, d);
431	>	exclude_.removePair(c, d);
432		}
433
434	<	}
434	>	Molecule::RigidBodyIterator rbIter;
435	>	RigidBody* rb;
436	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
437	>	std::vector<Atom*> atoms = rb->getAtoms();
438	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
439	>	for (int j = i + 1; j < atoms.size(); ++j) {
440	>	a = atoms[i]->getGlobalIndex();
441	>	b = atoms[j]->getGlobalIndex();
442	>	exclude_.removePair(a, b);
443	>	}
444	>	}
445	>	}
446
447	+	}
448
449	<	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
449	>
450	>	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
451		int curStampId;
452
453		//index from 0
#	Line 419 \| Line 455 \| *void SimInfo::addMoleculeStamp(MoleculeStamp molStamp**
455
456		moleculeStamps_.push_back(molStamp);
457		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
458	<	}
458	>	}
459
460	<	void SimInfo::update() {
460	>	void SimInfo::update() {
461
462		setupSimType();
463
#	Line 434 \| Line 470 \| void SimInfo::update() {
470		//setup fortran force field
471		/** @deprecate */
472		int isError = 0;
473	<	initFortranFF( &fInfo_.SIM_uses_RF , &isError );
473	>
474	>	setupElectrostaticSummationMethod( isError );
475	>
476		if(isError){
477	<	sprintf( painCave.errMsg,
478	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
479	<	painCave.isFatal = 1;
480	<	simError();
477	>	sprintf( painCave.errMsg,
478	>	"ForceField error: There was an error initializing the forceField in fortran.\n" );
479	>	painCave.isFatal = 1;
480	>	simError();
481		}
482
483
#	Line 450 \| Line 488 \| void SimInfo::update() {
488		calcNdfTrans();
489
490		fortranInitialized_ = true;
491	<	}
491	>	}
492
493	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
493	>	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
494		SimInfo::MoleculeIterator mi;
495		Molecule* mol;
496		Molecule::AtomIterator ai;
#	Line 461 \| Line 499 \| *std::set<AtomType> SimInfo::getUniqueAtomTypes() {**
499
500		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
501
502	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
503	<	atomTypes.insert(atom->getAtomType());
504	<	}
502	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
503	>	atomTypes.insert(atom->getAtomType());
504	>	}
505
506		}
507
508		return atomTypes;
509	<	}
509	>	}
510
511	<	void SimInfo::setupSimType() {
511	>	void SimInfo::setupSimType() {
512		std::set<AtomType*>::iterator i;
513		std::set<AtomType*> atomTypes;
514		atomTypes = getUniqueAtomTypes();
#	Line 483 \| Line 521 \| void SimInfo::setupSimType() {
521		int useDipole = 0;
522		int useGayBerne = 0;
523		int useSticky = 0;
524	+	int useStickyPower = 0;
525		int useShape = 0;
526		int useFLARB = 0; //it is not in AtomType yet
527		int useDirectionalAtom = 0;
528		int useElectrostatics = 0;
529		//usePBC and useRF are from simParams
530	<	int usePBC = simParams_->getPBC();
531	<	int useRF = simParams_->getUseRF();
530	>	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
531	>	int useRF;
532	>	int useDW;
533	>	std::string myMethod;
534
535	+	// set the useRF logical
536	+	useRF = 0;
537	+	useDW = 0;
538	+
539	+
540	+	if (simParams_->haveElectrostaticSummationMethod()) {
541	+	std::string myMethod = simParams_->getElectrostaticSummationMethod();
542	+	toUpper(myMethod);
543	+	if (myMethod == "REACTION_FIELD") {
544	+	useRF=1;
545	+	} else {
546	+	if (myMethod == "SHIFTED_POTENTIAL") {
547	+	useDW = 1;
548	+	}
549	+	}
550	+	}
551	+
552		//loop over all of the atom types
553		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
554	<	useLennardJones \|= (*i)->isLennardJones();
555	<	useElectrostatic \|= (*i)->isElectrostatic();
556	<	useEAM \|= (*i)->isEAM();
557	<	useCharge \|= (*i)->isCharge();
558	<	useDirectional \|= (*i)->isDirectional();
559	<	useDipole \|= (*i)->isDipole();
560	<	useGayBerne \|= (*i)->isGayBerne();
561	<	useSticky \|= (*i)->isSticky();
562	<	useShape \|= (*i)->isShape();
554	>	useLennardJones \|= (*i)->isLennardJones();
555	>	useElectrostatic \|= (*i)->isElectrostatic();
556	>	useEAM \|= (*i)->isEAM();
557	>	useCharge \|= (*i)->isCharge();
558	>	useDirectional \|= (*i)->isDirectional();
559	>	useDipole \|= (*i)->isDipole();
560	>	useGayBerne \|= (*i)->isGayBerne();
561	>	useSticky \|= (*i)->isSticky();
562	>	useStickyPower \|= (*i)->isStickyPower();
563	>	useShape \|= (*i)->isShape();
564		}
565
566	<	if (useSticky \|\| useDipole \|\| useGayBerne \|\| useShape) {
567	<	useDirectionalAtom = 1;
566	>	if (useSticky \|\| useStickyPower \|\| useDipole \|\| useGayBerne \|\| useShape) {
567	>	useDirectionalAtom = 1;
568		}
569
570		if (useCharge \|\| useDipole) {
571	<	useElectrostatics = 1;
571	>	useElectrostatics = 1;
572		}
573
574		#ifdef IS_MPI
#	Line 536 \| Line 595 \| void SimInfo::setupSimType() {
595		temp = useSticky;
596		MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
597
598	+	temp = useStickyPower;
599	+	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
600	+
601		temp = useGayBerne;
602		MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
603
#	Line 550 \| Line 612 \| void SimInfo::setupSimType() {
612
613		temp = useRF;
614		MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
615	<
615	>
616	>	temp = useDW;
617	>	MPI_Allreduce(&temp, &useDW, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
618	>
619		#endif
620
621		fInfo_.SIM_uses_PBC = usePBC;
#	Line 560 \| Line 625 \| void SimInfo::setupSimType() {
625		fInfo_.SIM_uses_Charges = useCharge;
626		fInfo_.SIM_uses_Dipoles = useDipole;
627		fInfo_.SIM_uses_Sticky = useSticky;
628	+	fInfo_.SIM_uses_StickyPower = useStickyPower;
629		fInfo_.SIM_uses_GayBerne = useGayBerne;
630		fInfo_.SIM_uses_EAM = useEAM;
631		fInfo_.SIM_uses_Shapes = useShape;
632		fInfo_.SIM_uses_FLARB = useFLARB;
633		fInfo_.SIM_uses_RF = useRF;
634	+	fInfo_.SIM_uses_DampedWolf = useDW;
635
636	<	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
637	<
638	<	if (simParams_->haveDielectric()) {
639	<	fInfo_.dielect = simParams_->getDielectric();
640	<	} else {
641	<	sprintf(painCave.errMsg,
642	<	"SimSetup Error: No Dielectric constant was set.\n"
643	<	"\tYou are trying to use Reaction Field without"
644	<	"\tsetting a dielectric constant!\n");
645	<	painCave.isFatal = 1;
646	<	simError();
647	<	}
581	<
582	<	} else {
583	<	fInfo_.dielect = 0.0;
636	>	if( myMethod == "REACTION_FIELD") {
637	>
638	>	if (simParams_->haveDielectric()) {
639	>	fInfo_.dielect = simParams_->getDielectric();
640	>	} else {
641	>	sprintf(painCave.errMsg,
642	>	"SimSetup Error: No Dielectric constant was set.\n"
643	>	"\tYou are trying to use Reaction Field without"
644	>	"\tsetting a dielectric constant!\n");
645	>	painCave.isFatal = 1;
646	>	simError();
647	>	}
648		}
649
650	<	}
650	>	}
651
652	<	void SimInfo::setupFortranSim() {
652	>	void SimInfo::setupFortranSim() {
653		int isError;
654		int nExclude;
655		std::vector<int> fortranGlobalGroupMembership;
#	Line 595 \| Line 659 \| void SimInfo::setupFortranSim() {
659
660		//globalGroupMembership_ is filled by SimCreator
661		for (int i = 0; i < nGlobalAtoms_; i++) {
662	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
662	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
663		}
664
665		//calculate mass ratio of cutoff group
#	Line 612 \| Line 676 \| void SimInfo::setupFortranSim() {
676		mfact.reserve(getNCutoffGroups());
677
678		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
679	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
679	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
680
681	<	totalMass = cg->getMass();
682	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
683	<	mfact.push_back(atom->getMass()/totalMass);
684	<	}
681	>	totalMass = cg->getMass();
682	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
683	>	// Check for massless groups - set mfact to 1 if true
684	>	if (totalMass != 0)
685	>	mfact.push_back(atom->getMass()/totalMass);
686	>	else
687	>	mfact.push_back( 1.0 );
688	>	}
689
690	<	}
690	>	}
691		}
692
693		//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
#	Line 629 \| Line 697 \| void SimInfo::setupFortranSim() {
697		identArray.reserve(getNAtoms());
698
699		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
700	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
701	<	identArray.push_back(atom->getIdent());
702	<	}
700	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
701	>	identArray.push_back(atom->getIdent());
702	>	}
703		}
704
705		//fill molMembershipArray
706		//molMembershipArray is filled by SimCreator
707		std::vector<int> molMembershipArray(nGlobalAtoms_);
708		for (int i = 0; i < nGlobalAtoms_; i++) {
709	<	molMembershipArray[i] = globalMolMembership_[i] + 1;
709	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
710		}
711
712		//setup fortran simulation
645	–	//gloalExcludes and molMembershipArray should go away (They are never used)
646	–	//why the hell fortran need to know molecule?
647	–	//OOPSE = Object-Obfuscated Parallel Simulation Engine
713		int nGlobalExcludes = 0;
714		int* globalExcludes = NULL;
715		int* excludeList = exclude_.getExcludeList();
716		setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
717	<	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
718	<	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
717	>	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
718	>	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
719
720		if( isError ){
721
722	<	sprintf( painCave.errMsg,
723	<	"There was an error setting the simulation information in fortran.\n" );
724	<	painCave.isFatal = 1;
725	<	painCave.severity = OOPSE_ERROR;
726	<	simError();
722	>	sprintf( painCave.errMsg,
723	>	"There was an error setting the simulation information in fortran.\n" );
724	>	painCave.isFatal = 1;
725	>	painCave.severity = OOPSE_ERROR;
726	>	simError();
727		}
728
729		#ifdef IS_MPI
730		sprintf( checkPointMsg,
731	<	"succesfully sent the simulation information to fortran.\n");
731	>	"succesfully sent the simulation information to fortran.\n");
732		MPIcheckPoint();
733		#endif // is_mpi
734	<	}
734	>	}
735
736
737		#ifdef IS_MPI
738	<	void SimInfo::setupFortranParallel() {
738	>	void SimInfo::setupFortranParallel() {
739
740		//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
741		std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
#	Line 686 \| Line 751 \| void SimInfo::setupFortranParallel() {
751
752		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
753
754	<	//local index(index in DataStorge) of atom is important
755	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
756	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
757	<	}
754	>	//local index(index in DataStorge) of atom is important
755	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
756	>	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
757	>	}
758
759	<	//local index of cutoff group is trivial, it only depends on the order of travesing
760	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
761	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
762	<	}
759	>	//local index of cutoff group is trivial, it only depends on the order of travesing
760	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
761	>	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
762	>	}
763
764		}
765
#	Line 714 \| Line 779 \| void SimInfo::setupFortranParallel() {
779		&localToGlobalCutoffGroupIndex[0], &isError);
780
781		if (isError) {
782	<	sprintf(painCave.errMsg,
783	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
784	<	painCave.isFatal = 1;
785	<	simError();
782	>	sprintf(painCave.errMsg,
783	>	"mpiRefresh errror: fortran didn't like something we gave it.\n");
784	>	painCave.isFatal = 1;
785	>	simError();
786		}
787
788		sprintf(checkPointMsg, " mpiRefresh successful.\n");
789		MPIcheckPoint();
790
791
792	<	}
792	>	}
793
794		#endif
795
796	<	double SimInfo::calcMaxCutoffRadius() {
796	>	double SimInfo::calcMaxCutoffRadius() {
797
798
799		std::set<AtomType*> atomTypes;
#	Line 740 \| Line 805 \| double SimInfo::calcMaxCutoffRadius() {
805
806		//query the max cutoff radius among these atom types
807		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
808	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
808	>	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
809		}
810
811		double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
#	Line 749 \| Line 814 \| double SimInfo::calcMaxCutoffRadius() {
814		#endif
815
816		return maxCutoffRadius;
817	<	}
817	>	}
818
819	<	void SimInfo::setupCutoff() {
755	<	double rcut_; //cutoff radius
756	<	double rsw_; //switching radius
819	>	void SimInfo::getCutoff(double& rcut, double& rsw) {
820
821		if (fInfo_.SIM_uses_Charges \| fInfo_.SIM_uses_Dipoles \| fInfo_.SIM_uses_RF) {
822
823	<	if (!simParams_->haveRcut()){
824	<	sprintf(painCave.errMsg,
823	>	if (!simParams_->haveCutoffRadius()){
824	>	sprintf(painCave.errMsg,
825		"SimCreator Warning: No value was set for the cutoffRadius.\n"
826		"\tOOPSE will use a default value of 15.0 angstroms"
827		"\tfor the cutoffRadius.\n");
828	<	painCave.isFatal = 0;
829	<	simError();
830	<	rcut_ = 15.0;
831	<	} else{
832	<	rcut_ = simParams_->getRcut();
833	<	}
828	>	painCave.isFatal = 0;
829	>	simError();
830	>	rcut = 15.0;
831	>	} else{
832	>	rcut = simParams_->getCutoffRadius();
833	>	}
834
835	<	if (!simParams_->haveRsw()){
836	<	sprintf(painCave.errMsg,
835	>	if (!simParams_->haveSwitchingRadius()){
836	>	sprintf(painCave.errMsg,
837		"SimCreator Warning: No value was set for switchingRadius.\n"
838		"\tOOPSE will use a default value of\n"
839	<	"\t0.95 * cutoffRadius for the switchingRadius\n");
840	<	painCave.isFatal = 0;
841	<	simError();
842	<	rsw_ = 0.95 * rcut_;
843	<	} else{
844	<	rsw_ = simParams_->getRsw();
845	<	}
839	>	"\t0.85 * cutoffRadius for the switchingRadius\n");
840	>	painCave.isFatal = 0;
841	>	simError();
842	>	rsw = 0.85 * rcut;
843	>	} else{
844	>	rsw = simParams_->getSwitchingRadius();
845	>	}
846
847		} else {
848	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
849	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
848	>	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
849	>	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
850
851	<	if (simParams_->haveRcut()) {
852	<	rcut_ = simParams_->getRcut();
853	<	} else {
854	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
855	<	rcut_ = calcMaxCutoffRadius();
856	<	}
851	>	if (simParams_->haveCutoffRadius()) {
852	>	rcut = simParams_->getCutoffRadius();
853	>	} else {
854	>	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
855	>	rcut = calcMaxCutoffRadius();
856	>	}
857
858	<	if (simParams_->haveRsw()) {
859	<	rsw_ = simParams_->getRsw();
860	<	} else {
861	<	rsw_ = rcut_;
862	<	}
858	>	if (simParams_->haveSwitchingRadius()) {
859	>	rsw = simParams_->getSwitchingRadius();
860	>	} else {
861	>	rsw = rcut;
862	>	}
863
864		}
865	<
865	>	}
866	>
867	>	void SimInfo::setupCutoff() {
868	>	getCutoff(rcut_, rsw_);
869		double rnblist = rcut_ + 1; // skin of neighbor list
870
871		//Pass these cutoff radius etc. to fortran. This function should be called once and only once
872	<	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist);
873	<	}
872	>
873	>	int cp = TRADITIONAL_CUTOFF_POLICY;
874	>	if (simParams_->haveCutoffPolicy()) {
875	>	std::string myPolicy = simParams_->getCutoffPolicy();
876	>	toUpper(myPolicy);
877	>	if (myPolicy == "MIX") {
878	>	cp = MIX_CUTOFF_POLICY;
879	>	} else {
880	>	if (myPolicy == "MAX") {
881	>	cp = MAX_CUTOFF_POLICY;
882	>	} else {
883	>	if (myPolicy == "TRADITIONAL") {
884	>	cp = TRADITIONAL_CUTOFF_POLICY;
885	>	} else {
886	>	// throw error
887	>	sprintf( painCave.errMsg,
888	>	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
889	>	painCave.isFatal = 1;
890	>	simError();
891	>	}
892	>	}
893	>	}
894	>	}
895
809	–	void SimInfo::addProperty(GenericData* genData) {
810	–	properties_.addProperty(genData);
811	–	}
896
897	<	void SimInfo::removeProperty(const std::string& propName) {
898	<	properties_.removeProperty(propName);
899	<	}
897	>	if (simParams_->haveSkinThickness()) {
898	>	double skinThickness = simParams_->getSkinThickness();
899	>	}
900
901	<	void SimInfo::clearProperties() {
902	<	properties_.clearProperties();
903	<	}
901	>	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
902	>	// also send cutoff notification to electrostatics
903	>	setElectrostaticCutoffRadius(&rcut_, &rsw_);
904	>	}
905
906	<	std::vector<std::string> SimInfo::getPropertyNames() {
907	<	return properties_.getPropertyNames();
908	<	}
909	<
910	<	std::vector<GenericData*> SimInfo::getProperties() {
911	<	return properties_.getProperties();
912	<	}
906	>	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
907	>
908	>	int errorOut;
909	>	int esm = NONE;
910	>	int sm = UNDAMPED;
911	>	double alphaVal;
912	>	double dielectric;
913
914	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
915	<	return properties_.getPropertyByName(propName);
916	<	}
914	>	errorOut = isError;
915	>	alphaVal = simParams_->getDampingAlpha();
916	>	dielectric = simParams_->getDielectric();
917
918	<	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
918	>	if (simParams_->haveElectrostaticSummationMethod()) {
919	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
920	>	toUpper(myMethod);
921	>	if (myMethod == "NONE") {
922	>	esm = NONE;
923	>	} else {
924	>	if (myMethod == "SWITCHING_FUNCTION") {
925	>	esm = SWITCHING_FUNCTION;
926	>	} else {
927	>	if (myMethod == "SHIFTED_POTENTIAL") {
928	>	esm = SHIFTED_POTENTIAL;
929	>	} else {
930	>	if (myMethod == "SHIFTED_FORCE") {
931	>	esm = SHIFTED_FORCE;
932	>	} else {
933	>	if (myMethod == "REACTION_FIELD") {
934	>	esm = REACTION_FIELD;
935	>	} else {
936	>	// throw error
937	>	sprintf( painCave.errMsg,
938	>	"SimInfo error: Unknown electrostaticSummationMethod. (Input file specified %s .)\n\telectrostaticSummationMethod must be one of: \"none\", \"shifted_potential\", \"shifted_force\", or \"reaction_field\".", myMethod.c_str() );
939	>	painCave.isFatal = 1;
940	>	simError();
941	>	}
942	>	}
943	>	}
944	>	}
945	>	}
946	>	}
947	>
948	>	if (simParams_->haveElectrostaticScreeningMethod()) {
949	>	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
950	>	toUpper(myScreen);
951	>	if (myScreen == "UNDAMPED") {
952	>	sm = UNDAMPED;
953	>	} else {
954	>	if (myScreen == "DAMPED") {
955	>	sm = DAMPED;
956	>	if (!simParams_->haveDampingAlpha()) {
957	>	//throw error
958	>	sprintf( painCave.errMsg,
959	>	"SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used.", alphaVal);
960	>	painCave.isFatal = 0;
961	>	simError();
962	>	}
963	>	} else {
964	>	// throw error
965	>	sprintf( painCave.errMsg,
966	>	"SimInfo error: Unknown electrostaticScreeningMethod. (Input file specified %s .)\n\telectrostaticScreeningMethod must be one of: \"undamped\" or \"damped\".", myScreen.c_str() );
967	>	painCave.isFatal = 1;
968	>	simError();
969	>	}
970	>	}
971	>	}
972	>
973	>	// let's pass some summation method variables to fortran
974	>	setElectrostaticSummationMethod( &esm );
975	>	setScreeningMethod( &sm );
976	>	setDampingAlpha( &alphaVal );
977	>	setReactionFieldDielectric( &dielectric );
978	>	initFortranFF( &esm, &errorOut );
979	>	}
980	>
981	>	void SimInfo::addProperty(GenericData* genData) {
982	>	properties_.addProperty(genData);
983	>	}
984	>
985	>	void SimInfo::removeProperty(const std::string& propName) {
986	>	properties_.removeProperty(propName);
987	>	}
988	>
989	>	void SimInfo::clearProperties() {
990	>	properties_.clearProperties();
991	>	}
992	>
993	>	std::vector<std::string> SimInfo::getPropertyNames() {
994	>	return properties_.getPropertyNames();
995	>	}
996	>
997	>	std::vector<GenericData*> SimInfo::getProperties() {
998	>	return properties_.getProperties();
999	>	}
1000	>
1001	>	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1002	>	return properties_.getPropertyByName(propName);
1003	>	}
1004	>
1005	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1006	>	if (sman_ == sman) {
1007	>	return;
1008	>	}
1009	>	delete sman_;
1010		sman_ = sman;
1011
1012		Molecule* mol;
#	Line 842 \| Line 1018 \| *void SimInfo::setSnapshotManager(SnapshotManager sman**
1018
1019		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1020
1021	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1022	<	atom->setSnapshotManager(sman_);
1023	<	}
1021	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1022	>	atom->setSnapshotManager(sman_);
1023	>	}
1024
1025	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1026	<	rb->setSnapshotManager(sman_);
1027	<	}
1025	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1026	>	rb->setSnapshotManager(sman_);
1027	>	}
1028		}
1029
1030	<	}
1030	>	}
1031
1032	<	Vector3d SimInfo::getComVel(){
1032	>	Vector3d SimInfo::getComVel(){
1033		SimInfo::MoleculeIterator i;
1034		Molecule* mol;
1035
#	Line 862 \| Line 1038 \| Vector3d SimInfo::getComVel(){
1038
1039
1040		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1041	<	double mass = mol->getMass();
1042	<	totalMass += mass;
1043	<	comVel += mass * mol->getComVel();
1041	>	double mass = mol->getMass();
1042	>	totalMass += mass;
1043	>	comVel += mass * mol->getComVel();
1044		}
1045
1046		#ifdef IS_MPI
#	Line 877 \| Line 1053 \| Vector3d SimInfo::getComVel(){
1053		comVel /= totalMass;
1054
1055		return comVel;
1056	<	}
1056	>	}
1057
1058	<	Vector3d SimInfo::getCom(){
1058	>	Vector3d SimInfo::getCom(){
1059		SimInfo::MoleculeIterator i;
1060		Molecule* mol;
1061
#	Line 887 \| Line 1063 \| Vector3d SimInfo::getCom(){
1063		double totalMass = 0.0;
1064
1065		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1066	<	double mass = mol->getMass();
1067	<	totalMass += mass;
1068	<	com += mass * mol->getCom();
1066	>	double mass = mol->getMass();
1067	>	totalMass += mass;
1068	>	com += mass * mol->getCom();
1069		}
1070
1071		#ifdef IS_MPI
#	Line 903 \| Line 1079 \| Vector3d SimInfo::getCom(){
1079
1080		return com;
1081
1082	<	}
1082	>	}
1083
1084	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1084	>	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1085
1086		return o;
1087	<	}
1087	>	}
1088	>
1089	>
1090	>	/*
1091	>	Returns center of mass and center of mass velocity in one function call.
1092	>	*/
1093	>
1094	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1095	>	SimInfo::MoleculeIterator i;
1096	>	Molecule* mol;
1097	>
1098	>
1099	>	double totalMass = 0.0;
1100	>
1101
1102	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1103	+	double mass = mol->getMass();
1104	+	totalMass += mass;
1105	+	com += mass * mol->getCom();
1106	+	comVel += mass * mol->getComVel();
1107	+	}
1108	+
1109	+	#ifdef IS_MPI
1110	+	double tmpMass = totalMass;
1111	+	Vector3d tmpCom(com);
1112	+	Vector3d tmpComVel(comVel);
1113	+	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1114	+	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1115	+	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1116	+	#endif
1117	+
1118	+	com /= totalMass;
1119	+	comVel /= totalMass;
1120	+	}
1121	+
1122	+	/*
1123	+	Return intertia tensor for entire system and angular momentum Vector.
1124	+
1125	+
1126	+	[ Ixx -Ixy -Ixz ]
1127	+	J =\| -Iyx Iyy -Iyz \|
1128	+	[ -Izx -Iyz Izz ]
1129	+	*/
1130	+
1131	+	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1132	+
1133	+
1134	+	double xx = 0.0;
1135	+	double yy = 0.0;
1136	+	double zz = 0.0;
1137	+	double xy = 0.0;
1138	+	double xz = 0.0;
1139	+	double yz = 0.0;
1140	+	Vector3d com(0.0);
1141	+	Vector3d comVel(0.0);
1142	+
1143	+	getComAll(com, comVel);
1144	+
1145	+	SimInfo::MoleculeIterator i;
1146	+	Molecule* mol;
1147	+
1148	+	Vector3d thisq(0.0);
1149	+	Vector3d thisv(0.0);
1150	+
1151	+	double thisMass = 0.0;
1152	+
1153	+
1154	+
1155	+
1156	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1157	+
1158	+	thisq = mol->getCom()-com;
1159	+	thisv = mol->getComVel()-comVel;
1160	+	thisMass = mol->getMass();
1161	+	// Compute moment of intertia coefficients.
1162	+	xx += thisq[0]thisq[0]thisMass;
1163	+	yy += thisq[1]thisq[1]thisMass;
1164	+	zz += thisq[2]thisq[2]thisMass;
1165	+
1166	+	// compute products of intertia
1167	+	xy += thisq[0]thisq[1]thisMass;
1168	+	xz += thisq[0]thisq[2]thisMass;
1169	+	yz += thisq[1]thisq[2]thisMass;
1170	+
1171	+	angularMomentum += cross( thisq, thisv ) * thisMass;
1172	+
1173	+	}
1174	+
1175	+
1176	+	inertiaTensor(0,0) = yy + zz;
1177	+	inertiaTensor(0,1) = -xy;
1178	+	inertiaTensor(0,2) = -xz;
1179	+	inertiaTensor(1,0) = -xy;
1180	+	inertiaTensor(1,1) = xx + zz;
1181	+	inertiaTensor(1,2) = -yz;
1182	+	inertiaTensor(2,0) = -xz;
1183	+	inertiaTensor(2,1) = -yz;
1184	+	inertiaTensor(2,2) = xx + yy;
1185	+
1186	+	#ifdef IS_MPI
1187	+	Mat3x3d tmpI(inertiaTensor);
1188	+	Vector3d tmpAngMom;
1189	+	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1190	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1191	+	#endif
1192	+
1193	+	return;
1194	+	}
1195	+
1196	+	//Returns the angular momentum of the system
1197	+	Vector3d SimInfo::getAngularMomentum(){
1198	+
1199	+	Vector3d com(0.0);
1200	+	Vector3d comVel(0.0);
1201	+	Vector3d angularMomentum(0.0);
1202	+
1203	+	getComAll(com,comVel);
1204	+
1205	+	SimInfo::MoleculeIterator i;
1206	+	Molecule* mol;
1207	+
1208	+	Vector3d thisr(0.0);
1209	+	Vector3d thisp(0.0);
1210	+
1211	+	double thisMass;
1212	+
1213	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1214	+	thisMass = mol->getMass();
1215	+	thisr = mol->getCom()-com;
1216	+	thisp = (mol->getComVel()-comVel)*thisMass;
1217	+
1218	+	angularMomentum += cross( thisr, thisp );
1219	+
1220	+	}
1221	+
1222	+	#ifdef IS_MPI
1223	+	Vector3d tmpAngMom;
1224	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1225	+	#endif
1226	+
1227	+	return angularMomentum;
1228	+	}
1229	+
1230	+
1231		}//end namespace oopse
1232

Diff Legend

-–
+Removed lines
-+
+Added lines
-<
+Changed lines
->
+Changed lines

Comparing trunk/src/brains/SimInfo.cpp (file contents): Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs. Revision 716 by chrisfen, Thu Nov 3 23:12:27 2005 UTC

Diff Legend

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
Revision 716 by chrisfen, Thu Nov 3 23:12:27 2005 UTC