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

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 430 by tim, Thu Mar 10 23:56:42 2005 UTC vs.
Revision 726 by chrisfen, Fri Nov 11 15:22:11 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/DarkSide/fSwitchingFunctionType.h"
59		#include "UseTheForce/doForces_interface.h"
60	+	#include "UseTheForce/DarkSide/electrostatic_interface.h"
61		#include "UseTheForce/notifyCutoffs_interface.h"
62	+	#include "UseTheForce/DarkSide/switcheroo_interface.h"
63		#include "utils/MemoryUtils.hpp"
64		#include "utils/simError.h"
65		#include "selection/SelectionManager.hpp"
#	Line 65 \| Line 71 \| namespace oopse {
71
72		namespace oopse {
73
74	<	SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
75	<	ForceField* ff, Globals* simParams) :
76	<	forceField_(ff), simParams_(simParams),
77	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
78	<	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
79	<	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
80	<	nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nRigidBodies_(0),
81	<	nIntegrableObjects_(0), nCutoffGroups_(0), nConstraints_(0),
82	<	sman_(NULL), fortranInitialized_(false) {
74	>	SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
75	>	ForceField* ff, Globals* simParams) :
76	>	stamps_(stamps), forceField_(ff), simParams_(simParams),
77	>	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
78	>	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
79	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
80	>	nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nRigidBodies_(0),
81	>	nIntegrableObjects_(0), nCutoffGroups_(0), nConstraints_(0),
82	>	sman_(NULL), fortranInitialized_(false) {
83
84
85	<	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
86	<	MoleculeStamp* molStamp;
87	<	int nMolWithSameStamp;
88	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
89	<	int nGroups = 0; //total cutoff groups defined in meta-data file
90	<	CutoffGroupStamp* cgStamp;
91	<	RigidBodyStamp* rbStamp;
92	<	int nRigidAtoms = 0;
85	>	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
86	>	MoleculeStamp* molStamp;
87	>	int nMolWithSameStamp;
88	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
89	>	int nGroups = 0; //total cutoff groups defined in meta-data file
90	>	CutoffGroupStamp* cgStamp;
91	>	RigidBodyStamp* rbStamp;
92	>	int nRigidAtoms = 0;
93
94	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
94	>	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
95		molStamp = i->first;
96		nMolWithSameStamp = i->second;
97
#	Line 100 \| Line 106 \| *SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp,**
106		int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
107
108		for (int j=0; j < nCutoffGroupsInStamp; j++) {
109	<	cgStamp = molStamp->getCutoffGroup(j);
110	<	nAtomsInGroups += cgStamp->getNMembers();
109	>	cgStamp = molStamp->getCutoffGroup(j);
110	>	nAtomsInGroups += cgStamp->getNMembers();
111		}
112
113		nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
114	+
115		nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
116
117		//calculate atoms in rigid bodies
#	Line 112 \| Line 119 \| *SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp,**
119		int nRigidBodiesInStamp = molStamp->getNRigidBodies();
120
121		for (int j=0; j < nRigidBodiesInStamp; j++) {
122	<	rbStamp = molStamp->getRigidBody(j);
123	<	nAtomsInRigidBodies += rbStamp->getNMembers();
122	>	rbStamp = molStamp->getRigidBody(j);
123	>	nAtomsInRigidBodies += rbStamp->getNMembers();
124		}
125
126		nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
127		nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
128
129	<	}
129	>	}
130
131	<	//every free atom (atom does not belong to cutoff groups) is a cutoff group
132	<	//therefore the total number of cutoff groups in the system is equal to
133	<	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
134	<	//file plus the number of cutoff groups defined in meta-data file
135	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
131	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
132	>	//group therefore the total number of cutoff groups in the system is
133	>	//equal to the total number of atoms minus number of atoms belong to
134	>	//cutoff group defined in meta-data file plus the number of cutoff
135	>	//groups defined in meta-data file
136	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
137
138	<	//every free atom (atom does not belong to rigid bodies) is an integrable object
139	<	//therefore the total number of integrable objects in the system is equal to
140	<	//the total number of atoms minus number of atoms belong to rigid body defined in meta-data
141	<	//file plus the number of rigid bodies defined in meta-data file
142	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
138	>	//every free atom (atom does not belong to rigid bodies) is an
139	>	//integrable object therefore the total number of integrable objects
140	>	//in the system is equal to the total number of atoms minus number of
141	>	//atoms belong to rigid body defined in meta-data file plus the number
142	>	//of rigid bodies defined in meta-data file
143	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
144	>	+ nGlobalRigidBodies_;
145	>
146	>	nGlobalMols_ = molStampIds_.size();
147
136	–	nGlobalMols_ = molStampIds_.size();
137	–
148		#ifdef IS_MPI
149	<	molToProcMap_.resize(nGlobalMols_);
149	>	molToProcMap_.resize(nGlobalMols_);
150		#endif
151
152	<	}
152	>	}
153
154	<	SimInfo::~SimInfo() {
154	>	SimInfo::~SimInfo() {
155		std::map<int, Molecule*>::iterator i;
156		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
157	<	delete i->second;
157	>	delete i->second;
158		}
159		molecules_.clear();
160	<
161	<	MemoryUtils::deletePointers(moleculeStamps_);
152	<
160	>
161	>	delete stamps_;
162		delete sman_;
163		delete simParams_;
164		delete forceField_;
165	<	}
165	>	}
166
167	<	int SimInfo::getNGlobalConstraints() {
167	>	int SimInfo::getNGlobalConstraints() {
168		int nGlobalConstraints;
169		#ifdef IS_MPI
170		MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
#	Line 164 \| Line 173 \| int SimInfo::getNGlobalConstraints() {
173		nGlobalConstraints = nConstraints_;
174		#endif
175		return nGlobalConstraints;
176	<	}
176	>	}
177
178	<	bool SimInfo::addMolecule(Molecule* mol) {
178	>	bool SimInfo::addMolecule(Molecule* mol) {
179		MoleculeIterator i;
180
181		i = molecules_.find(mol->getGlobalIndex());
182		if (i == molecules_.end() ) {
183
184	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
184	>	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
185
186	<	nAtoms_ += mol->getNAtoms();
187	<	nBonds_ += mol->getNBonds();
188	<	nBends_ += mol->getNBends();
189	<	nTorsions_ += mol->getNTorsions();
190	<	nRigidBodies_ += mol->getNRigidBodies();
191	<	nIntegrableObjects_ += mol->getNIntegrableObjects();
192	<	nCutoffGroups_ += mol->getNCutoffGroups();
193	<	nConstraints_ += mol->getNConstraintPairs();
186	>	nAtoms_ += mol->getNAtoms();
187	>	nBonds_ += mol->getNBonds();
188	>	nBends_ += mol->getNBends();
189	>	nTorsions_ += mol->getNTorsions();
190	>	nRigidBodies_ += mol->getNRigidBodies();
191	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
192	>	nCutoffGroups_ += mol->getNCutoffGroups();
193	>	nConstraints_ += mol->getNConstraintPairs();
194
195	<	addExcludePairs(mol);
195	>	addExcludePairs(mol);
196
197	<	return true;
197	>	return true;
198		} else {
199	<	return false;
199	>	return false;
200		}
201	<	}
201	>	}
202
203	<	bool SimInfo::removeMolecule(Molecule* mol) {
203	>	bool SimInfo::removeMolecule(Molecule* mol) {
204		MoleculeIterator i;
205		i = molecules_.find(mol->getGlobalIndex());
206
207		if (i != molecules_.end() ) {
208
209	<	assert(mol == i->second);
209	>	assert(mol == i->second);
210
211	<	nAtoms_ -= mol->getNAtoms();
212	<	nBonds_ -= mol->getNBonds();
213	<	nBends_ -= mol->getNBends();
214	<	nTorsions_ -= mol->getNTorsions();
215	<	nRigidBodies_ -= mol->getNRigidBodies();
216	<	nIntegrableObjects_ -= mol->getNIntegrableObjects();
217	<	nCutoffGroups_ -= mol->getNCutoffGroups();
218	<	nConstraints_ -= mol->getNConstraintPairs();
211	>	nAtoms_ -= mol->getNAtoms();
212	>	nBonds_ -= mol->getNBonds();
213	>	nBends_ -= mol->getNBends();
214	>	nTorsions_ -= mol->getNTorsions();
215	>	nRigidBodies_ -= mol->getNRigidBodies();
216	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
217	>	nCutoffGroups_ -= mol->getNCutoffGroups();
218	>	nConstraints_ -= mol->getNConstraintPairs();
219
220	<	removeExcludePairs(mol);
221	<	molecules_.erase(mol->getGlobalIndex());
220	>	removeExcludePairs(mol);
221	>	molecules_.erase(mol->getGlobalIndex());
222
223	<	delete mol;
223	>	delete mol;
224
225	<	return true;
225	>	return true;
226		} else {
227	<	return false;
227	>	return false;
228		}
229
230
231	<	}
231	>	}
232
233
234	<	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
234	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
235		i = molecules_.begin();
236		return i == molecules_.end() ? NULL : i->second;
237	<	}
237	>	}
238
239	<	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
239	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
240		++i;
241		return i == molecules_.end() ? NULL : i->second;
242	<	}
242	>	}
243
244
245	<	void SimInfo::calcNdf() {
245	>	void SimInfo::calcNdf() {
246		int ndf_local;
247		MoleculeIterator i;
248		std::vector<StuntDouble*>::iterator j;
#	Line 243 \| Line 252 \| void SimInfo::calcNdf() {
252		ndf_local = 0;
253
254		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
255	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
256	<	integrableObject = mol->nextIntegrableObject(j)) {
255	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
256	>	integrableObject = mol->nextIntegrableObject(j)) {
257
258	<	ndf_local += 3;
258	>	ndf_local += 3;
259
260	<	if (integrableObject->isDirectional()) {
261	<	if (integrableObject->isLinear()) {
262	<	ndf_local += 2;
263	<	} else {
264	<	ndf_local += 3;
265	<	}
266	<	}
260	>	if (integrableObject->isDirectional()) {
261	>	if (integrableObject->isLinear()) {
262	>	ndf_local += 2;
263	>	} else {
264	>	ndf_local += 3;
265	>	}
266	>	}
267
268	<	}//end for (integrableObject)
268	>	}//end for (integrableObject)
269		}// end for (mol)
270
271		// n_constraints is local, so subtract them on each processor
#	Line 272 \| Line 281 \| void SimInfo::calcNdf() {
281		// entire system:
282		ndf_ = ndf_ - 3 - nZconstraint_;
283
284	<	}
284	>	}
285
286	<	void SimInfo::calcNdfRaw() {
286	>	void SimInfo::calcNdfRaw() {
287		int ndfRaw_local;
288
289		MoleculeIterator i;
#	Line 286 \| Line 295 \| void SimInfo::calcNdfRaw() {
295		ndfRaw_local = 0;
296
297		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
298	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
299	<	integrableObject = mol->nextIntegrableObject(j)) {
298	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
299	>	integrableObject = mol->nextIntegrableObject(j)) {
300
301	<	ndfRaw_local += 3;
301	>	ndfRaw_local += 3;
302
303	<	if (integrableObject->isDirectional()) {
304	<	if (integrableObject->isLinear()) {
305	<	ndfRaw_local += 2;
306	<	} else {
307	<	ndfRaw_local += 3;
308	<	}
309	<	}
303	>	if (integrableObject->isDirectional()) {
304	>	if (integrableObject->isLinear()) {
305	>	ndfRaw_local += 2;
306	>	} else {
307	>	ndfRaw_local += 3;
308	>	}
309	>	}
310
311	<	}
311	>	}
312		}
313
314		#ifdef IS_MPI
#	Line 307 \| Line 316 \| void SimInfo::calcNdfRaw() {
316		#else
317		ndfRaw_ = ndfRaw_local;
318		#endif
319	<	}
319	>	}
320
321	<	void SimInfo::calcNdfTrans() {
321	>	void SimInfo::calcNdfTrans() {
322		int ndfTrans_local;
323
324		ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
#	Line 323 \| Line 332 \| void SimInfo::calcNdfTrans() {
332
333		ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
334
335	<	}
335	>	}
336
337	<	void SimInfo::addExcludePairs(Molecule* mol) {
337	>	void SimInfo::addExcludePairs(Molecule* mol) {
338		std::vector<Bond*>::iterator bondIter;
339		std::vector<Bend*>::iterator bendIter;
340		std::vector<Torsion*>::iterator torsionIter;
#	Line 338 \| Line 347 \| *void SimInfo::addExcludePairs(Molecule mol) {**
347		int d;
348
349		for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
350	<	a = bond->getAtomA()->getGlobalIndex();
351	<	b = bond->getAtomB()->getGlobalIndex();
352	<	exclude_.addPair(a, b);
350	>	a = bond->getAtomA()->getGlobalIndex();
351	>	b = bond->getAtomB()->getGlobalIndex();
352	>	exclude_.addPair(a, b);
353		}
354
355		for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
356	<	a = bend->getAtomA()->getGlobalIndex();
357	<	b = bend->getAtomB()->getGlobalIndex();
358	<	c = bend->getAtomC()->getGlobalIndex();
356	>	a = bend->getAtomA()->getGlobalIndex();
357	>	b = bend->getAtomB()->getGlobalIndex();
358	>	c = bend->getAtomC()->getGlobalIndex();
359
360	<	exclude_.addPair(a, b);
361	<	exclude_.addPair(a, c);
362	<	exclude_.addPair(b, c);
360	>	exclude_.addPair(a, b);
361	>	exclude_.addPair(a, c);
362	>	exclude_.addPair(b, c);
363		}
364
365		for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
366	<	a = torsion->getAtomA()->getGlobalIndex();
367	<	b = torsion->getAtomB()->getGlobalIndex();
368	<	c = torsion->getAtomC()->getGlobalIndex();
369	<	d = torsion->getAtomD()->getGlobalIndex();
366	>	a = torsion->getAtomA()->getGlobalIndex();
367	>	b = torsion->getAtomB()->getGlobalIndex();
368	>	c = torsion->getAtomC()->getGlobalIndex();
369	>	d = torsion->getAtomD()->getGlobalIndex();
370
371	<	exclude_.addPair(a, b);
372	<	exclude_.addPair(a, c);
373	<	exclude_.addPair(a, d);
374	<	exclude_.addPair(b, c);
375	<	exclude_.addPair(b, d);
376	<	exclude_.addPair(c, d);
371	>	exclude_.addPair(a, b);
372	>	exclude_.addPair(a, c);
373	>	exclude_.addPair(a, d);
374	>	exclude_.addPair(b, c);
375	>	exclude_.addPair(b, d);
376	>	exclude_.addPair(c, d);
377		}
378
379		Molecule::RigidBodyIterator rbIter;
380		RigidBody* rb;
381		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
382	<	std::vector<Atom*> atoms = rb->getAtoms();
383	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
384	<	for (int j = i + 1; j < atoms.size(); ++j) {
385	<	a = atoms[i]->getGlobalIndex();
386	<	b = atoms[j]->getGlobalIndex();
387	<	exclude_.addPair(a, b);
388	<	}
389	<	}
382	>	std::vector<Atom*> atoms = rb->getAtoms();
383	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
384	>	for (int j = i + 1; j < atoms.size(); ++j) {
385	>	a = atoms[i]->getGlobalIndex();
386	>	b = atoms[j]->getGlobalIndex();
387	>	exclude_.addPair(a, b);
388	>	}
389	>	}
390		}
391
392	<	Molecule::CutoffGroupIterator cgIter;
384	<	CutoffGroup* cg;
385	<	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
386	<	std::vector<Atom*> atoms = cg->getAtoms();
387	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
388	<	for (int j = i + 1; j < atoms.size(); ++j) {
389	<	a = atoms[i]->getGlobalIndex();
390	<	b = atoms[j]->getGlobalIndex();
391	<	exclude_.addPair(a, b);
392	<	}
393	<	}
394	<	}
392	>	}
393
394	<	}
397	<
398	<	void SimInfo::removeExcludePairs(Molecule* mol) {
394	>	void SimInfo::removeExcludePairs(Molecule* mol) {
395		std::vector<Bond*>::iterator bondIter;
396		std::vector<Bend*>::iterator bendIter;
397		std::vector<Torsion*>::iterator torsionIter;
#	Line 408 \| Line 404 \| *void SimInfo::removeExcludePairs(Molecule mol) {**
404		int d;
405
406		for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
407	<	a = bond->getAtomA()->getGlobalIndex();
408	<	b = bond->getAtomB()->getGlobalIndex();
409	<	exclude_.removePair(a, b);
407	>	a = bond->getAtomA()->getGlobalIndex();
408	>	b = bond->getAtomB()->getGlobalIndex();
409	>	exclude_.removePair(a, b);
410		}
411
412		for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
413	<	a = bend->getAtomA()->getGlobalIndex();
414	<	b = bend->getAtomB()->getGlobalIndex();
415	<	c = bend->getAtomC()->getGlobalIndex();
413	>	a = bend->getAtomA()->getGlobalIndex();
414	>	b = bend->getAtomB()->getGlobalIndex();
415	>	c = bend->getAtomC()->getGlobalIndex();
416
417	<	exclude_.removePair(a, b);
418	<	exclude_.removePair(a, c);
419	<	exclude_.removePair(b, c);
417	>	exclude_.removePair(a, b);
418	>	exclude_.removePair(a, c);
419	>	exclude_.removePair(b, c);
420		}
421
422		for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
423	<	a = torsion->getAtomA()->getGlobalIndex();
424	<	b = torsion->getAtomB()->getGlobalIndex();
425	<	c = torsion->getAtomC()->getGlobalIndex();
426	<	d = torsion->getAtomD()->getGlobalIndex();
423	>	a = torsion->getAtomA()->getGlobalIndex();
424	>	b = torsion->getAtomB()->getGlobalIndex();
425	>	c = torsion->getAtomC()->getGlobalIndex();
426	>	d = torsion->getAtomD()->getGlobalIndex();
427
428	<	exclude_.removePair(a, b);
429	<	exclude_.removePair(a, c);
430	<	exclude_.removePair(a, d);
431	<	exclude_.removePair(b, c);
432	<	exclude_.removePair(b, d);
433	<	exclude_.removePair(c, d);
428	>	exclude_.removePair(a, b);
429	>	exclude_.removePair(a, c);
430	>	exclude_.removePair(a, d);
431	>	exclude_.removePair(b, c);
432	>	exclude_.removePair(b, d);
433	>	exclude_.removePair(c, d);
434		}
435
436		Molecule::RigidBodyIterator rbIter;
437		RigidBody* rb;
438		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
439	<	std::vector<Atom*> atoms = rb->getAtoms();
440	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
441	<	for (int j = i + 1; j < atoms.size(); ++j) {
442	<	a = atoms[i]->getGlobalIndex();
443	<	b = atoms[j]->getGlobalIndex();
444	<	exclude_.removePair(a, b);
445	<	}
446	<	}
439	>	std::vector<Atom*> atoms = rb->getAtoms();
440	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
441	>	for (int j = i + 1; j < atoms.size(); ++j) {
442	>	a = atoms[i]->getGlobalIndex();
443	>	b = atoms[j]->getGlobalIndex();
444	>	exclude_.removePair(a, b);
445	>	}
446	>	}
447		}
448
449	<	Molecule::CutoffGroupIterator cgIter;
454	<	CutoffGroup* cg;
455	<	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
456	<	std::vector<Atom*> atoms = cg->getAtoms();
457	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
458	<	for (int j = i + 1; j < atoms.size(); ++j) {
459	<	a = atoms[i]->getGlobalIndex();
460	<	b = atoms[j]->getGlobalIndex();
461	<	exclude_.removePair(a, b);
462	<	}
463	<	}
464	<	}
449	>	}
450
466	–	}
451
452	<
469	<	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
452	>	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
453		int curStampId;
454
455		//index from 0
#	Line 474 \| Line 457 \| *void SimInfo::addMoleculeStamp(MoleculeStamp molStamp**
457
458		moleculeStamps_.push_back(molStamp);
459		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
460	<	}
460	>	}
461
462	<	void SimInfo::update() {
462	>	void SimInfo::update() {
463
464		setupSimType();
465
#	Line 489 \| Line 472 \| void SimInfo::update() {
472		//setup fortran force field
473		/** @deprecate */
474		int isError = 0;
475	<	initFortranFF( &fInfo_.SIM_uses_RF , &isError );
475	>
476	>	setupElectrostaticSummationMethod( isError );
477	>	setupSwitchingFunction();
478	>
479		if(isError){
480	<	sprintf( painCave.errMsg,
481	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
482	<	painCave.isFatal = 1;
483	<	simError();
480	>	sprintf( painCave.errMsg,
481	>	"ForceField error: There was an error initializing the forceField in fortran.\n" );
482	>	painCave.isFatal = 1;
483	>	simError();
484		}
485
486
#	Line 505 \| Line 491 \| void SimInfo::update() {
491		calcNdfTrans();
492
493		fortranInitialized_ = true;
494	<	}
494	>	}
495
496	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
496	>	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
497		SimInfo::MoleculeIterator mi;
498		Molecule* mol;
499		Molecule::AtomIterator ai;
#	Line 516 \| Line 502 \| *std::set<AtomType> SimInfo::getUniqueAtomTypes() {**
502
503		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
504
505	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
506	<	atomTypes.insert(atom->getAtomType());
507	<	}
505	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
506	>	atomTypes.insert(atom->getAtomType());
507	>	}
508
509		}
510
511		return atomTypes;
512	<	}
512	>	}
513
514	<	void SimInfo::setupSimType() {
514	>	void SimInfo::setupSimType() {
515		std::set<AtomType*>::iterator i;
516		std::set<AtomType*> atomTypes;
517		atomTypes = getUniqueAtomTypes();
#	Line 538 \| Line 524 \| void SimInfo::setupSimType() {
524		int useDipole = 0;
525		int useGayBerne = 0;
526		int useSticky = 0;
527	+	int useStickyPower = 0;
528		int useShape = 0;
529		int useFLARB = 0; //it is not in AtomType yet
530		int useDirectionalAtom = 0;
531		int useElectrostatics = 0;
532		//usePBC and useRF are from simParams
533	<	int usePBC = simParams_->getPBC();
534	<	int useRF = simParams_->getUseRF();
533	>	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
534	>	int useRF;
535	>	int useSF;
536	>	std::string myMethod;
537
538	+	// set the useRF logical
539	+	useRF = 0;
540	+	useSF = 0;
541	+
542	+
543	+	if (simParams_->haveElectrostaticSummationMethod()) {
544	+	std::string myMethod = simParams_->getElectrostaticSummationMethod();
545	+	toUpper(myMethod);
546	+	if (myMethod == "REACTION_FIELD") {
547	+	useRF=1;
548	+	} else {
549	+	if (myMethod == "SHIFTED_FORCE") {
550	+	useSF = 1;
551	+	}
552	+	}
553	+	}
554	+
555		//loop over all of the atom types
556		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
557	<	useLennardJones \|= (*i)->isLennardJones();
558	<	useElectrostatic \|= (*i)->isElectrostatic();
559	<	useEAM \|= (*i)->isEAM();
560	<	useCharge \|= (*i)->isCharge();
561	<	useDirectional \|= (*i)->isDirectional();
562	<	useDipole \|= (*i)->isDipole();
563	<	useGayBerne \|= (*i)->isGayBerne();
564	<	useSticky \|= (*i)->isSticky();
565	<	useShape \|= (*i)->isShape();
557	>	useLennardJones \|= (*i)->isLennardJones();
558	>	useElectrostatic \|= (*i)->isElectrostatic();
559	>	useEAM \|= (*i)->isEAM();
560	>	useCharge \|= (*i)->isCharge();
561	>	useDirectional \|= (*i)->isDirectional();
562	>	useDipole \|= (*i)->isDipole();
563	>	useGayBerne \|= (*i)->isGayBerne();
564	>	useSticky \|= (*i)->isSticky();
565	>	useStickyPower \|= (*i)->isStickyPower();
566	>	useShape \|= (*i)->isShape();
567		}
568
569	<	if (useSticky \|\| useDipole \|\| useGayBerne \|\| useShape) {
570	<	useDirectionalAtom = 1;
569	>	if (useSticky \|\| useStickyPower \|\| useDipole \|\| useGayBerne \|\| useShape) {
570	>	useDirectionalAtom = 1;
571		}
572
573		if (useCharge \|\| useDipole) {
574	<	useElectrostatics = 1;
574	>	useElectrostatics = 1;
575		}
576
577		#ifdef IS_MPI
#	Line 591 \| Line 598 \| void SimInfo::setupSimType() {
598		temp = useSticky;
599		MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
600
601	+	temp = useStickyPower;
602	+	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
603	+
604		temp = useGayBerne;
605		MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
606
#	Line 605 \| Line 615 \| void SimInfo::setupSimType() {
615
616		temp = useRF;
617		MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
618	<
618	>
619	>	temp = useSF;
620	>	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
621	>
622		#endif
623
624		fInfo_.SIM_uses_PBC = usePBC;
#	Line 615 \| Line 628 \| void SimInfo::setupSimType() {
628		fInfo_.SIM_uses_Charges = useCharge;
629		fInfo_.SIM_uses_Dipoles = useDipole;
630		fInfo_.SIM_uses_Sticky = useSticky;
631	+	fInfo_.SIM_uses_StickyPower = useStickyPower;
632		fInfo_.SIM_uses_GayBerne = useGayBerne;
633		fInfo_.SIM_uses_EAM = useEAM;
634		fInfo_.SIM_uses_Shapes = useShape;
635		fInfo_.SIM_uses_FLARB = useFLARB;
636		fInfo_.SIM_uses_RF = useRF;
637	+	fInfo_.SIM_uses_SF = useSF;
638
639	<	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
640	<
641	<	if (simParams_->haveDielectric()) {
642	<	fInfo_.dielect = simParams_->getDielectric();
643	<	} else {
644	<	sprintf(painCave.errMsg,
645	<	"SimSetup Error: No Dielectric constant was set.\n"
646	<	"\tYou are trying to use Reaction Field without"
647	<	"\tsetting a dielectric constant!\n");
648	<	painCave.isFatal = 1;
649	<	simError();
650	<	}
636	<
637	<	} else {
638	<	fInfo_.dielect = 0.0;
639	>	if( myMethod == "REACTION_FIELD") {
640	>
641	>	if (simParams_->haveDielectric()) {
642	>	fInfo_.dielect = simParams_->getDielectric();
643	>	} else {
644	>	sprintf(painCave.errMsg,
645	>	"SimSetup Error: No Dielectric constant was set.\n"
646	>	"\tYou are trying to use Reaction Field without"
647	>	"\tsetting a dielectric constant!\n");
648	>	painCave.isFatal = 1;
649	>	simError();
650	>	}
651		}
652
653	<	}
653	>	}
654
655	<	void SimInfo::setupFortranSim() {
655	>	void SimInfo::setupFortranSim() {
656		int isError;
657		int nExclude;
658		std::vector<int> fortranGlobalGroupMembership;
#	Line 650 \| Line 662 \| void SimInfo::setupFortranSim() {
662
663		//globalGroupMembership_ is filled by SimCreator
664		for (int i = 0; i < nGlobalAtoms_; i++) {
665	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
665	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
666		}
667
668		//calculate mass ratio of cutoff group
#	Line 667 \| Line 679 \| void SimInfo::setupFortranSim() {
679		mfact.reserve(getNCutoffGroups());
680
681		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
682	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
682	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
683
684	<	totalMass = cg->getMass();
685	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
686	<	mfact.push_back(atom->getMass()/totalMass);
687	<	}
684	>	totalMass = cg->getMass();
685	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
686	>	// Check for massless groups - set mfact to 1 if true
687	>	if (totalMass != 0)
688	>	mfact.push_back(atom->getMass()/totalMass);
689	>	else
690	>	mfact.push_back( 1.0 );
691	>	}
692
693	<	}
693	>	}
694		}
695
696		//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
#	Line 684 \| Line 700 \| void SimInfo::setupFortranSim() {
700		identArray.reserve(getNAtoms());
701
702		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
703	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
704	<	identArray.push_back(atom->getIdent());
705	<	}
703	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
704	>	identArray.push_back(atom->getIdent());
705	>	}
706		}
707
708		//fill molMembershipArray
709		//molMembershipArray is filled by SimCreator
710		std::vector<int> molMembershipArray(nGlobalAtoms_);
711		for (int i = 0; i < nGlobalAtoms_; i++) {
712	<	molMembershipArray[i] = globalMolMembership_[i] + 1;
712	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
713		}
714
715		//setup fortran simulation
700	–	//gloalExcludes and molMembershipArray should go away (They are never used)
701	–	//why the hell fortran need to know molecule?
702	–	//OOPSE = Object-Obfuscated Parallel Simulation Engine
716		int nGlobalExcludes = 0;
717		int* globalExcludes = NULL;
718		int* excludeList = exclude_.getExcludeList();
719		setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
720	<	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
721	<	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
720	>	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
721	>	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
722
723		if( isError ){
724
725	<	sprintf( painCave.errMsg,
726	<	"There was an error setting the simulation information in fortran.\n" );
727	<	painCave.isFatal = 1;
728	<	painCave.severity = OOPSE_ERROR;
729	<	simError();
725	>	sprintf( painCave.errMsg,
726	>	"There was an error setting the simulation information in fortran.\n" );
727	>	painCave.isFatal = 1;
728	>	painCave.severity = OOPSE_ERROR;
729	>	simError();
730		}
731
732		#ifdef IS_MPI
733		sprintf( checkPointMsg,
734	<	"succesfully sent the simulation information to fortran.\n");
734	>	"succesfully sent the simulation information to fortran.\n");
735		MPIcheckPoint();
736		#endif // is_mpi
737	<	}
737	>	}
738
739
740		#ifdef IS_MPI
741	<	void SimInfo::setupFortranParallel() {
741	>	void SimInfo::setupFortranParallel() {
742
743		//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
744		std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
#	Line 741 \| Line 754 \| void SimInfo::setupFortranParallel() {
754
755		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
756
757	<	//local index(index in DataStorge) of atom is important
758	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
759	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
760	<	}
757	>	//local index(index in DataStorge) of atom is important
758	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
759	>	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
760	>	}
761
762	<	//local index of cutoff group is trivial, it only depends on the order of travesing
763	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
764	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
765	<	}
762	>	//local index of cutoff group is trivial, it only depends on the order of travesing
763	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
764	>	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
765	>	}
766
767		}
768
#	Line 769 \| Line 782 \| void SimInfo::setupFortranParallel() {
782		&localToGlobalCutoffGroupIndex[0], &isError);
783
784		if (isError) {
785	<	sprintf(painCave.errMsg,
786	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
787	<	painCave.isFatal = 1;
788	<	simError();
785	>	sprintf(painCave.errMsg,
786	>	"mpiRefresh errror: fortran didn't like something we gave it.\n");
787	>	painCave.isFatal = 1;
788	>	simError();
789		}
790
791		sprintf(checkPointMsg, " mpiRefresh successful.\n");
792		MPIcheckPoint();
793
794
795	<	}
795	>	}
796
797		#endif
798
799	<	double SimInfo::calcMaxCutoffRadius() {
799	>	double SimInfo::calcMaxCutoffRadius() {
800
801
802		std::set<AtomType*> atomTypes;
#	Line 795 \| Line 808 \| double SimInfo::calcMaxCutoffRadius() {
808
809		//query the max cutoff radius among these atom types
810		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
811	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
811	>	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
812		}
813
814		double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
#	Line 804 \| Line 817 \| double SimInfo::calcMaxCutoffRadius() {
817		#endif
818
819		return maxCutoffRadius;
820	<	}
820	>	}
821
822	<	void SimInfo::getCutoff(double& rcut, double& rsw) {
822	>	void SimInfo::getCutoff(double& rcut, double& rsw) {
823
824		if (fInfo_.SIM_uses_Charges \| fInfo_.SIM_uses_Dipoles \| fInfo_.SIM_uses_RF) {
825
826	<	if (!simParams_->haveRcut()){
827	<	sprintf(painCave.errMsg,
826	>	if (!simParams_->haveCutoffRadius()){
827	>	sprintf(painCave.errMsg,
828		"SimCreator Warning: No value was set for the cutoffRadius.\n"
829		"\tOOPSE will use a default value of 15.0 angstroms"
830		"\tfor the cutoffRadius.\n");
831	<	painCave.isFatal = 0;
832	<	simError();
833	<	rcut = 15.0;
834	<	} else{
835	<	rcut = simParams_->getRcut();
836	<	}
831	>	painCave.isFatal = 0;
832	>	simError();
833	>	rcut = 15.0;
834	>	} else{
835	>	rcut = simParams_->getCutoffRadius();
836	>	}
837
838	<	if (!simParams_->haveRsw()){
839	<	sprintf(painCave.errMsg,
838	>	if (!simParams_->haveSwitchingRadius()){
839	>	sprintf(painCave.errMsg,
840		"SimCreator Warning: No value was set for switchingRadius.\n"
841		"\tOOPSE will use a default value of\n"
842	<	"\t0.95 * cutoffRadius for the switchingRadius\n");
843	<	painCave.isFatal = 0;
844	<	simError();
845	<	rsw = 0.95 * rcut;
846	<	} else{
847	<	rsw = simParams_->getRsw();
848	<	}
842	>	"\t0.85 * cutoffRadius for the switchingRadius\n");
843	>	painCave.isFatal = 0;
844	>	simError();
845	>	rsw = 0.85 * rcut;
846	>	} else{
847	>	rsw = simParams_->getSwitchingRadius();
848	>	}
849
850		} else {
851	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
852	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
851	>	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
852	>	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
853
854	<	if (simParams_->haveRcut()) {
855	<	rcut = simParams_->getRcut();
856	<	} else {
857	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
858	<	rcut = calcMaxCutoffRadius();
859	<	}
854	>	if (simParams_->haveCutoffRadius()) {
855	>	rcut = simParams_->getCutoffRadius();
856	>	} else {
857	>	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
858	>	rcut = calcMaxCutoffRadius();
859	>	}
860
861	<	if (simParams_->haveRsw()) {
862	<	rsw = simParams_->getRsw();
863	<	} else {
864	<	rsw = rcut;
865	<	}
861	>	if (simParams_->haveSwitchingRadius()) {
862	>	rsw = simParams_->getSwitchingRadius();
863	>	} else {
864	>	rsw = rcut;
865	>	}
866
867		}
868	<	}
868	>	}
869
870	<	void SimInfo::setupCutoff() {
870	>	void SimInfo::setupCutoff() {
871		getCutoff(rcut_, rsw_);
872		double rnblist = rcut_ + 1; // skin of neighbor list
873
874		//Pass these cutoff radius etc. to fortran. This function should be called once and only once
875	<	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist);
876	<	}
875	>
876	>	int cp = TRADITIONAL_CUTOFF_POLICY;
877	>	if (simParams_->haveCutoffPolicy()) {
878	>	std::string myPolicy = simParams_->getCutoffPolicy();
879	>	toUpper(myPolicy);
880	>	if (myPolicy == "MIX") {
881	>	cp = MIX_CUTOFF_POLICY;
882	>	} else {
883	>	if (myPolicy == "MAX") {
884	>	cp = MAX_CUTOFF_POLICY;
885	>	} else {
886	>	if (myPolicy == "TRADITIONAL") {
887	>	cp = TRADITIONAL_CUTOFF_POLICY;
888	>	} else {
889	>	// throw error
890	>	sprintf( painCave.errMsg,
891	>	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
892	>	painCave.isFatal = 1;
893	>	simError();
894	>	}
895	>	}
896	>	}
897	>	}
898
865	–	void SimInfo::addProperty(GenericData* genData) {
866	–	properties_.addProperty(genData);
867	–	}
899
900	<	void SimInfo::removeProperty(const std::string& propName) {
901	<	properties_.removeProperty(propName);
902	<	}
900	>	if (simParams_->haveSkinThickness()) {
901	>	double skinThickness = simParams_->getSkinThickness();
902	>	}
903
904	<	void SimInfo::clearProperties() {
905	<	properties_.clearProperties();
906	<	}
904	>	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
905	>	// also send cutoff notification to electrostatics
906	>	setElectrostaticCutoffRadius(&rcut_, &rsw_);
907	>	}
908
909	<	std::vector<std::string> SimInfo::getPropertyNames() {
910	<	return properties_.getPropertyNames();
911	<	}
912	<
913	<	std::vector<GenericData*> SimInfo::getProperties() {
914	<	return properties_.getProperties();
915	<	}
909	>	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
910	>
911	>	int errorOut;
912	>	int esm = NONE;
913	>	int sm = UNDAMPED;
914	>	double alphaVal;
915	>	double dielectric;
916
917	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
918	<	return properties_.getPropertyByName(propName);
919	<	}
917	>	errorOut = isError;
918	>	alphaVal = simParams_->getDampingAlpha();
919	>	dielectric = simParams_->getDielectric();
920
921	<	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
922	<	//if (sman_ == sman_) {
923	<	// return;
924	<	//}
921	>	if (simParams_->haveElectrostaticSummationMethod()) {
922	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
923	>	toUpper(myMethod);
924	>	if (myMethod == "NONE") {
925	>	esm = NONE;
926	>	} else {
927	>	if (myMethod == "SWITCHING_FUNCTION") {
928	>	esm = SWITCHING_FUNCTION;
929	>	} else {
930	>	if (myMethod == "SHIFTED_POTENTIAL") {
931	>	esm = SHIFTED_POTENTIAL;
932	>	} else {
933	>	if (myMethod == "SHIFTED_FORCE") {
934	>	esm = SHIFTED_FORCE;
935	>	} else {
936	>	if (myMethod == "REACTION_FIELD") {
937	>	esm = REACTION_FIELD;
938	>	} else {
939	>	// throw error
940	>	sprintf( painCave.errMsg,
941	>	"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() );
942	>	painCave.isFatal = 1;
943	>	simError();
944	>	}
945	>	}
946	>	}
947	>	}
948	>	}
949	>	}
950
951	<	//delete sman_;
951	>	if (simParams_->haveElectrostaticScreeningMethod()) {
952	>	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
953	>	toUpper(myScreen);
954	>	if (myScreen == "UNDAMPED") {
955	>	sm = UNDAMPED;
956	>	} else {
957	>	if (myScreen == "DAMPED") {
958	>	sm = DAMPED;
959	>	if (!simParams_->haveDampingAlpha()) {
960	>	//throw error
961	>	sprintf( painCave.errMsg,
962	>	"SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used.", alphaVal);
963	>	painCave.isFatal = 0;
964	>	simError();
965	>	}
966	>	} else {
967	>	// throw error
968	>	sprintf( painCave.errMsg,
969	>	"SimInfo error: Unknown electrostaticScreeningMethod. (Input file specified %s .)\n\telectrostaticScreeningMethod must be one of: \"undamped\" or \"damped\".", myScreen.c_str() );
970	>	painCave.isFatal = 1;
971	>	simError();
972	>	}
973	>	}
974	>	}
975	>
976	>	// let's pass some summation method variables to fortran
977	>	setElectrostaticSummationMethod( &esm );
978	>	setScreeningMethod( &sm );
979	>	setDampingAlpha( &alphaVal );
980	>	setReactionFieldDielectric( &dielectric );
981	>	initFortranFF( &esm, &errorOut );
982	>	}
983	>
984	>	void SimInfo::setupSwitchingFunction() {
985	>	int ft = CUBIC;
986	>
987	>	if (simParams_->haveSwitchingFunctionType()) {
988	>	std::string funcType = simParams_->getSwitchingFunctionType();
989	>	toUpper(funcType);
990	>	if (funcType == "CUBIC") {
991	>	ft = CUBIC;
992	>	} else {
993	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
994	>	ft = FIFTH_ORDER_POLY;
995	>	} else {
996	>	// throw error
997	>	sprintf( painCave.errMsg,
998	>	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
999	>	painCave.isFatal = 1;
1000	>	simError();
1001	>	}
1002	>	}
1003	>	}
1004	>
1005	>	// send switching function notification to switcheroo
1006	>	setFunctionType(&ft);
1007	>
1008	>	}
1009	>
1010	>	void SimInfo::addProperty(GenericData* genData) {
1011	>	properties_.addProperty(genData);
1012	>	}
1013	>
1014	>	void SimInfo::removeProperty(const std::string& propName) {
1015	>	properties_.removeProperty(propName);
1016	>	}
1017	>
1018	>	void SimInfo::clearProperties() {
1019	>	properties_.clearProperties();
1020	>	}
1021	>
1022	>	std::vector<std::string> SimInfo::getPropertyNames() {
1023	>	return properties_.getPropertyNames();
1024	>	}
1025	>
1026	>	std::vector<GenericData*> SimInfo::getProperties() {
1027	>	return properties_.getProperties();
1028	>	}
1029	>
1030	>	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1031	>	return properties_.getPropertyByName(propName);
1032	>	}
1033	>
1034	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1035	>	if (sman_ == sman) {
1036	>	return;
1037	>	}
1038	>	delete sman_;
1039		sman_ = sman;
1040
1041		Molecule* mol;
#	Line 903 \| Line 1047 \| *void SimInfo::setSnapshotManager(SnapshotManager sman**
1047
1048		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1049
1050	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1051	<	atom->setSnapshotManager(sman_);
1052	<	}
1050	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1051	>	atom->setSnapshotManager(sman_);
1052	>	}
1053
1054	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1055	<	rb->setSnapshotManager(sman_);
1056	<	}
1054	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1055	>	rb->setSnapshotManager(sman_);
1056	>	}
1057		}
1058
1059	<	}
1059	>	}
1060
1061	<	Vector3d SimInfo::getComVel(){
1061	>	Vector3d SimInfo::getComVel(){
1062		SimInfo::MoleculeIterator i;
1063		Molecule* mol;
1064
#	Line 923 \| Line 1067 \| Vector3d SimInfo::getComVel(){
1067
1068
1069		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1070	<	double mass = mol->getMass();
1071	<	totalMass += mass;
1072	<	comVel += mass * mol->getComVel();
1070	>	double mass = mol->getMass();
1071	>	totalMass += mass;
1072	>	comVel += mass * mol->getComVel();
1073		}
1074
1075		#ifdef IS_MPI
#	Line 938 \| Line 1082 \| Vector3d SimInfo::getComVel(){
1082		comVel /= totalMass;
1083
1084		return comVel;
1085	<	}
1085	>	}
1086
1087	<	Vector3d SimInfo::getCom(){
1087	>	Vector3d SimInfo::getCom(){
1088		SimInfo::MoleculeIterator i;
1089		Molecule* mol;
1090
#	Line 948 \| Line 1092 \| Vector3d SimInfo::getCom(){
1092		double totalMass = 0.0;
1093
1094		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1095	<	double mass = mol->getMass();
1096	<	totalMass += mass;
1097	<	com += mass * mol->getCom();
1095	>	double mass = mol->getMass();
1096	>	totalMass += mass;
1097	>	com += mass * mol->getCom();
1098		}
1099
1100		#ifdef IS_MPI
#	Line 964 \| Line 1108 \| Vector3d SimInfo::getCom(){
1108
1109		return com;
1110
1111	<	}
1111	>	}
1112
1113	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1113	>	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1114
1115		return o;
1116	<	}
1116	>	}
1117	>
1118	>
1119	>	/*
1120	>	Returns center of mass and center of mass velocity in one function call.
1121	>	*/
1122	>
1123	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1124	>	SimInfo::MoleculeIterator i;
1125	>	Molecule* mol;
1126	>
1127	>
1128	>	double totalMass = 0.0;
1129	>
1130
1131	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1132	+	double mass = mol->getMass();
1133	+	totalMass += mass;
1134	+	com += mass * mol->getCom();
1135	+	comVel += mass * mol->getComVel();
1136	+	}
1137	+
1138	+	#ifdef IS_MPI
1139	+	double tmpMass = totalMass;
1140	+	Vector3d tmpCom(com);
1141	+	Vector3d tmpComVel(comVel);
1142	+	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1143	+	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1144	+	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1145	+	#endif
1146	+
1147	+	com /= totalMass;
1148	+	comVel /= totalMass;
1149	+	}
1150	+
1151	+	/*
1152	+	Return intertia tensor for entire system and angular momentum Vector.
1153	+
1154	+
1155	+	[ Ixx -Ixy -Ixz ]
1156	+	J =\| -Iyx Iyy -Iyz \|
1157	+	[ -Izx -Iyz Izz ]
1158	+	*/
1159	+
1160	+	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1161	+
1162	+
1163	+	double xx = 0.0;
1164	+	double yy = 0.0;
1165	+	double zz = 0.0;
1166	+	double xy = 0.0;
1167	+	double xz = 0.0;
1168	+	double yz = 0.0;
1169	+	Vector3d com(0.0);
1170	+	Vector3d comVel(0.0);
1171	+
1172	+	getComAll(com, comVel);
1173	+
1174	+	SimInfo::MoleculeIterator i;
1175	+	Molecule* mol;
1176	+
1177	+	Vector3d thisq(0.0);
1178	+	Vector3d thisv(0.0);
1179	+
1180	+	double thisMass = 0.0;
1181	+
1182	+
1183	+
1184	+
1185	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1186	+
1187	+	thisq = mol->getCom()-com;
1188	+	thisv = mol->getComVel()-comVel;
1189	+	thisMass = mol->getMass();
1190	+	// Compute moment of intertia coefficients.
1191	+	xx += thisq[0]thisq[0]thisMass;
1192	+	yy += thisq[1]thisq[1]thisMass;
1193	+	zz += thisq[2]thisq[2]thisMass;
1194	+
1195	+	// compute products of intertia
1196	+	xy += thisq[0]thisq[1]thisMass;
1197	+	xz += thisq[0]thisq[2]thisMass;
1198	+	yz += thisq[1]thisq[2]thisMass;
1199	+
1200	+	angularMomentum += cross( thisq, thisv ) * thisMass;
1201	+
1202	+	}
1203	+
1204	+
1205	+	inertiaTensor(0,0) = yy + zz;
1206	+	inertiaTensor(0,1) = -xy;
1207	+	inertiaTensor(0,2) = -xz;
1208	+	inertiaTensor(1,0) = -xy;
1209	+	inertiaTensor(1,1) = xx + zz;
1210	+	inertiaTensor(1,2) = -yz;
1211	+	inertiaTensor(2,0) = -xz;
1212	+	inertiaTensor(2,1) = -yz;
1213	+	inertiaTensor(2,2) = xx + yy;
1214	+
1215	+	#ifdef IS_MPI
1216	+	Mat3x3d tmpI(inertiaTensor);
1217	+	Vector3d tmpAngMom;
1218	+	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1219	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1220	+	#endif
1221	+
1222	+	return;
1223	+	}
1224	+
1225	+	//Returns the angular momentum of the system
1226	+	Vector3d SimInfo::getAngularMomentum(){
1227	+
1228	+	Vector3d com(0.0);
1229	+	Vector3d comVel(0.0);
1230	+	Vector3d angularMomentum(0.0);
1231	+
1232	+	getComAll(com,comVel);
1233	+
1234	+	SimInfo::MoleculeIterator i;
1235	+	Molecule* mol;
1236	+
1237	+	Vector3d thisr(0.0);
1238	+	Vector3d thisp(0.0);
1239	+
1240	+	double thisMass;
1241	+
1242	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1243	+	thisMass = mol->getMass();
1244	+	thisr = mol->getCom()-com;
1245	+	thisp = (mol->getComVel()-comVel)*thisMass;
1246	+
1247	+	angularMomentum += cross( thisr, thisp );
1248	+
1249	+	}
1250	+
1251	+	#ifdef IS_MPI
1252	+	Vector3d tmpAngMom;
1253	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1254	+	#endif
1255	+
1256	+	return angularMomentum;
1257	+	}
1258	+
1259	+
1260		}//end namespace oopse
1261

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Comparing trunk/src/brains/SimInfo.cpp (file contents): Revision 430 by tim, Thu Mar 10 23:56:42 2005 UTC vs. Revision 726 by chrisfen, Fri Nov 11 15:22:11 2005 UTC

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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 430 by tim, Thu Mar 10 23:56:42 2005 UTC vs.
Revision 726 by chrisfen, Fri Nov 11 15:22:11 2005 UTC