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

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 274 by tim, Tue Jan 25 21:59:18 2005 UTC vs.
Revision 734 by chuckv, Tue Nov 15 16:05:38 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"
66
67		#ifdef IS_MPI
68		#include "UseTheForce/mpiComponentPlan.h"
#	Line 64 \| 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 99 \| 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 111 \| 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
135	–	nGlobalMols_ = molStampIds_.size();
136	–
148		#ifdef IS_MPI
149	<	molToProcMap_.resize(nGlobalMols_);
149	>	molToProcMap_.resize(nGlobalMols_);
150		#endif
140	–
141	–	}
151
152	<	SimInfo::~SimInfo() {
144	<	//MemoryUtils::deleteVectorOfPointer(molecules_);
152	>	}
153
154	<	MemoryUtils::deleteVectorOfPointer(moleculeStamps_);
155	<
154	>	SimInfo::~SimInfo() {
155	>	std::map<int, Molecule*>::iterator i;
156	>	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
157	>	delete i->second;
158	>	}
159	>	molecules_.clear();
160	>
161	>	delete stamps_;
162		delete sman_;
163		delete simParams_;
164		delete forceField_;
165	+	}
166
167	<	}
153	<
154	<	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 160 \| 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();
219	<
220	<	removeExcludePairs(mol);
221	<	molecules_.erase(mol->getGlobalIndex());
222	<
223	<	delete mol;
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());
222	>
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 239 \| 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 268 \| 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 282 \| 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 303 \| 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 319 \| 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 334 \| 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	<
380	<	}
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	>	}
390	>	}
391
392	<	void SimInfo::removeExcludePairs(Molecule* mol) {
392	>	}
393	>
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 379 \| 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	<	}
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	>	}
447	>	}
448
449	+	}
450
451	<	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
451	>
452	>	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
453		int curStampId;
454
455		//index from 0
#	Line 419 \| 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 434 \| 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 450 \| 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 461 \| 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 478 \| Line 519 \| void SimInfo::setupSimType() {
519		int useLennardJones = 0;
520		int useElectrostatic = 0;
521		int useEAM = 0;
522	+	int useSC = 0;
523		int useCharge = 0;
524		int useDirectional = 0;
525		int useDipole = 0;
526		int useGayBerne = 0;
527		int useSticky = 0;
528	+	int useStickyPower = 0;
529		int useShape = 0;
530		int useFLARB = 0; //it is not in AtomType yet
531		int useDirectionalAtom = 0;
532		int useElectrostatics = 0;
533		//usePBC and useRF are from simParams
534	<	int usePBC = simParams_->getPBC();
535	<	int useRF = simParams_->getUseRF();
534	>	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
535	>	int useRF;
536	>	int useSF;
537	>	std::string myMethod;
538	>
539	>	// set the useRF logical
540	>	useRF = 0;
541	>	useSF = 0;
542	>
543	>
544	>	if (simParams_->haveElectrostaticSummationMethod()) {
545	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
546	>	toUpper(myMethod);
547	>	if (myMethod == "REACTION_FIELD") {
548	>	useRF=1;
549	>	} else {
550	>	if (myMethod == "SHIFTED_FORCE") {
551	>	useSF = 1;
552	>	}
553	>	}
554	>	}
555
556		//loop over all of the atom types
557		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
558	<	useLennardJones \|= (*i)->isLennardJones();
559	<	useElectrostatic \|= (*i)->isElectrostatic();
560	<	useEAM \|= (*i)->isEAM();
561	<	useCharge \|= (*i)->isCharge();
562	<	useDirectional \|= (*i)->isDirectional();
563	<	useDipole \|= (*i)->isDipole();
564	<	useGayBerne \|= (*i)->isGayBerne();
565	<	useSticky \|= (*i)->isSticky();
566	<	useShape \|= (*i)->isShape();
558	>	useLennardJones \|= (*i)->isLennardJones();
559	>	useElectrostatic \|= (*i)->isElectrostatic();
560	>	useEAM \|= (*i)->isEAM();
561	>	useSC \|= (*i)->isSC();
562	>	useCharge \|= (*i)->isCharge();
563	>	useDirectional \|= (*i)->isDirectional();
564	>	useDipole \|= (*i)->isDipole();
565	>	useGayBerne \|= (*i)->isGayBerne();
566	>	useSticky \|= (*i)->isSticky();
567	>	useStickyPower \|= (*i)->isStickyPower();
568	>	useShape \|= (*i)->isShape();
569		}
570
571	<	if (useSticky \|\| useDipole \|\| useGayBerne \|\| useShape) {
572	<	useDirectionalAtom = 1;
571	>	if (useSticky \|\| useStickyPower \|\| useDipole \|\| useGayBerne \|\| useShape) {
572	>	useDirectionalAtom = 1;
573		}
574
575		if (useCharge \|\| useDipole) {
576	<	useElectrostatics = 1;
576	>	useElectrostatics = 1;
577		}
578
579		#ifdef IS_MPI
#	Line 536 \| Line 600 \| void SimInfo::setupSimType() {
600		temp = useSticky;
601		MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
602
603	+	temp = useStickyPower;
604	+	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
605	+
606		temp = useGayBerne;
607		MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
608
609		temp = useEAM;
610		MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
611
612	+	temp = useSC;
613	+	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
614	+
615		temp = useShape;
616		MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
617
#	Line 550 \| Line 620 \| void SimInfo::setupSimType() {
620
621		temp = useRF;
622		MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
623	<
623	>
624	>	temp = useSF;
625	>	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
626	>
627		#endif
628
629		fInfo_.SIM_uses_PBC = usePBC;
#	Line 560 \| Line 633 \| void SimInfo::setupSimType() {
633		fInfo_.SIM_uses_Charges = useCharge;
634		fInfo_.SIM_uses_Dipoles = useDipole;
635		fInfo_.SIM_uses_Sticky = useSticky;
636	+	fInfo_.SIM_uses_StickyPower = useStickyPower;
637		fInfo_.SIM_uses_GayBerne = useGayBerne;
638		fInfo_.SIM_uses_EAM = useEAM;
639	+	fInfo_.SIM_uses_SC = useSC;
640		fInfo_.SIM_uses_Shapes = useShape;
641		fInfo_.SIM_uses_FLARB = useFLARB;
642		fInfo_.SIM_uses_RF = useRF;
643	+	fInfo_.SIM_uses_SF = useSF;
644
645	<	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
646	<
647	<	if (simParams_->haveDielectric()) {
648	<	fInfo_.dielect = simParams_->getDielectric();
649	<	} else {
650	<	sprintf(painCave.errMsg,
651	<	"SimSetup Error: No Dielectric constant was set.\n"
652	<	"\tYou are trying to use Reaction Field without"
653	<	"\tsetting a dielectric constant!\n");
654	<	painCave.isFatal = 1;
655	<	simError();
656	<	}
581	<
582	<	} else {
583	<	fInfo_.dielect = 0.0;
645	>	if( myMethod == "REACTION_FIELD") {
646	>
647	>	if (simParams_->haveDielectric()) {
648	>	fInfo_.dielect = simParams_->getDielectric();
649	>	} else {
650	>	sprintf(painCave.errMsg,
651	>	"SimSetup Error: No Dielectric constant was set.\n"
652	>	"\tYou are trying to use Reaction Field without"
653	>	"\tsetting a dielectric constant!\n");
654	>	painCave.isFatal = 1;
655	>	simError();
656	>	}
657		}
658
659	<	}
659	>	}
660
661	<	void SimInfo::setupFortranSim() {
661	>	void SimInfo::setupFortranSim() {
662		int isError;
663		int nExclude;
664		std::vector<int> fortranGlobalGroupMembership;
#	Line 595 \| Line 668 \| void SimInfo::setupFortranSim() {
668
669		//globalGroupMembership_ is filled by SimCreator
670		for (int i = 0; i < nGlobalAtoms_; i++) {
671	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
671	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
672		}
673
674		//calculate mass ratio of cutoff group
#	Line 612 \| Line 685 \| void SimInfo::setupFortranSim() {
685		mfact.reserve(getNCutoffGroups());
686
687		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
688	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
688	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
689
690	<	totalMass = cg->getMass();
691	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
692	<	mfact.push_back(atom->getMass()/totalMass);
693	<	}
690	>	totalMass = cg->getMass();
691	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
692	>	// Check for massless groups - set mfact to 1 if true
693	>	if (totalMass != 0)
694	>	mfact.push_back(atom->getMass()/totalMass);
695	>	else
696	>	mfact.push_back( 1.0 );
697	>	}
698
699	<	}
699	>	}
700		}
701
702		//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
#	Line 629 \| Line 706 \| void SimInfo::setupFortranSim() {
706		identArray.reserve(getNAtoms());
707
708		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
709	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
710	<	identArray.push_back(atom->getIdent());
711	<	}
709	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
710	>	identArray.push_back(atom->getIdent());
711	>	}
712		}
713
714		//fill molMembershipArray
715		//molMembershipArray is filled by SimCreator
716		std::vector<int> molMembershipArray(nGlobalAtoms_);
717		for (int i = 0; i < nGlobalAtoms_; i++) {
718	<	molMembershipArray[i] = globalMolMembership_[i] + 1;
718	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
719		}
720
721		//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
722		int nGlobalExcludes = 0;
723		int* globalExcludes = NULL;
724		int* excludeList = exclude_.getExcludeList();
725		setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
726	<	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
727	<	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
726	>	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
727	>	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
728
729		if( isError ){
730
731	<	sprintf( painCave.errMsg,
732	<	"There was an error setting the simulation information in fortran.\n" );
733	<	painCave.isFatal = 1;
734	<	painCave.severity = OOPSE_ERROR;
735	<	simError();
731	>	sprintf( painCave.errMsg,
732	>	"There was an error setting the simulation information in fortran.\n" );
733	>	painCave.isFatal = 1;
734	>	painCave.severity = OOPSE_ERROR;
735	>	simError();
736		}
737
738		#ifdef IS_MPI
739		sprintf( checkPointMsg,
740	<	"succesfully sent the simulation information to fortran.\n");
740	>	"succesfully sent the simulation information to fortran.\n");
741		MPIcheckPoint();
742		#endif // is_mpi
743	<	}
743	>	}
744
745
746		#ifdef IS_MPI
747	<	void SimInfo::setupFortranParallel() {
747	>	void SimInfo::setupFortranParallel() {
748
749		//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
750		std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
#	Line 686 \| Line 760 \| void SimInfo::setupFortranParallel() {
760
761		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
762
763	<	//local index(index in DataStorge) of atom is important
764	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
765	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
766	<	}
763	>	//local index(index in DataStorge) of atom is important
764	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
765	>	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
766	>	}
767
768	<	//local index of cutoff group is trivial, it only depends on the order of travesing
769	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
770	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
771	<	}
768	>	//local index of cutoff group is trivial, it only depends on the order of travesing
769	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
770	>	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
771	>	}
772
773		}
774
#	Line 714 \| Line 788 \| void SimInfo::setupFortranParallel() {
788		&localToGlobalCutoffGroupIndex[0], &isError);
789
790		if (isError) {
791	<	sprintf(painCave.errMsg,
792	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
793	<	painCave.isFatal = 1;
794	<	simError();
791	>	sprintf(painCave.errMsg,
792	>	"mpiRefresh errror: fortran didn't like something we gave it.\n");
793	>	painCave.isFatal = 1;
794	>	simError();
795		}
796
797		sprintf(checkPointMsg, " mpiRefresh successful.\n");
798		MPIcheckPoint();
799
800
801	<	}
801	>	}
802
803		#endif
804
805	<	double SimInfo::calcMaxCutoffRadius() {
805	>	double SimInfo::calcMaxCutoffRadius() {
806
807
808		std::set<AtomType*> atomTypes;
#	Line 740 \| Line 814 \| double SimInfo::calcMaxCutoffRadius() {
814
815		//query the max cutoff radius among these atom types
816		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
817	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
817	>	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
818		}
819
820		double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
#	Line 749 \| Line 823 \| double SimInfo::calcMaxCutoffRadius() {
823		#endif
824
825		return maxCutoffRadius;
826	<	}
826	>	}
827
828	<	void SimInfo::setupCutoff() {
755	<	double rcut_; //cutoff radius
756	<	double rsw_; //switching radius
828	>	void SimInfo::getCutoff(double& rcut, double& rsw) {
829
830		if (fInfo_.SIM_uses_Charges \| fInfo_.SIM_uses_Dipoles \| fInfo_.SIM_uses_RF) {
831
832	<	if (!simParams_->haveRcut()){
833	<	sprintf(painCave.errMsg,
832	>	if (!simParams_->haveCutoffRadius()){
833	>	sprintf(painCave.errMsg,
834		"SimCreator Warning: No value was set for the cutoffRadius.\n"
835		"\tOOPSE will use a default value of 15.0 angstroms"
836		"\tfor the cutoffRadius.\n");
837	<	painCave.isFatal = 0;
838	<	simError();
839	<	rcut_ = 15.0;
840	<	} else{
841	<	rcut_ = simParams_->getRcut();
842	<	}
837	>	painCave.isFatal = 0;
838	>	simError();
839	>	rcut = 15.0;
840	>	} else{
841	>	rcut = simParams_->getCutoffRadius();
842	>	}
843
844	<	if (!simParams_->haveRsw()){
845	<	sprintf(painCave.errMsg,
844	>	if (!simParams_->haveSwitchingRadius()){
845	>	sprintf(painCave.errMsg,
846		"SimCreator Warning: No value was set for switchingRadius.\n"
847		"\tOOPSE will use a default value of\n"
848	<	"\t0.95 * cutoffRadius for the switchingRadius\n");
849	<	painCave.isFatal = 0;
850	<	simError();
851	<	rsw_ = 0.95 * rcut_;
852	<	} else{
853	<	rsw_ = simParams_->getRsw();
854	<	}
848	>	"\t0.85 * cutoffRadius for the switchingRadius\n");
849	>	painCave.isFatal = 0;
850	>	simError();
851	>	rsw = 0.85 * rcut;
852	>	} else{
853	>	rsw = simParams_->getSwitchingRadius();
854	>	}
855
856		} else {
857	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
858	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
857	>	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
858	>	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
859
860	<	if (simParams_->haveRcut()) {
861	<	rcut_ = simParams_->getRcut();
862	<	} else {
863	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
864	<	rcut_ = calcMaxCutoffRadius();
865	<	}
860	>	if (simParams_->haveCutoffRadius()) {
861	>	rcut = simParams_->getCutoffRadius();
862	>	} else {
863	>	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
864	>	rcut = calcMaxCutoffRadius();
865	>	}
866
867	<	if (simParams_->haveRsw()) {
868	<	rsw_ = simParams_->getRsw();
869	<	} else {
870	<	rsw_ = rcut_;
871	<	}
867	>	if (simParams_->haveSwitchingRadius()) {
868	>	rsw = simParams_->getSwitchingRadius();
869	>	} else {
870	>	rsw = rcut;
871	>	}
872
873		}
874	<
874	>	}
875	>
876	>	void SimInfo::setupCutoff() {
877	>	getCutoff(rcut_, rsw_);
878		double rnblist = rcut_ + 1; // skin of neighbor list
879
880		//Pass these cutoff radius etc. to fortran. This function should be called once and only once
881	<	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist);
882	<	}
881	>
882	>	int cp = TRADITIONAL_CUTOFF_POLICY;
883	>	if (simParams_->haveCutoffPolicy()) {
884	>	std::string myPolicy = simParams_->getCutoffPolicy();
885	>	toUpper(myPolicy);
886	>	if (myPolicy == "MIX") {
887	>	cp = MIX_CUTOFF_POLICY;
888	>	} else {
889	>	if (myPolicy == "MAX") {
890	>	cp = MAX_CUTOFF_POLICY;
891	>	} else {
892	>	if (myPolicy == "TRADITIONAL") {
893	>	cp = TRADITIONAL_CUTOFF_POLICY;
894	>	} else {
895	>	// throw error
896	>	sprintf( painCave.errMsg,
897	>	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
898	>	painCave.isFatal = 1;
899	>	simError();
900	>	}
901	>	}
902	>	}
903	>	}
904
809	–	void SimInfo::addProperty(GenericData* genData) {
810	–	properties_.addProperty(genData);
811	–	}
905
906	<	void SimInfo::removeProperty(const std::string& propName) {
907	<	properties_.removeProperty(propName);
908	<	}
906	>	if (simParams_->haveSkinThickness()) {
907	>	double skinThickness = simParams_->getSkinThickness();
908	>	}
909
910	<	void SimInfo::clearProperties() {
911	<	properties_.clearProperties();
912	<	}
910	>	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
911	>	// also send cutoff notification to electrostatics
912	>	setElectrostaticCutoffRadius(&rcut_, &rsw_);
913	>	}
914
915	<	std::vector<std::string> SimInfo::getPropertyNames() {
916	<	return properties_.getPropertyNames();
917	<	}
918	<
919	<	std::vector<GenericData*> SimInfo::getProperties() {
920	<	return properties_.getProperties();
921	<	}
915	>	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
916	>
917	>	int errorOut;
918	>	int esm = NONE;
919	>	int sm = UNDAMPED;
920	>	double alphaVal;
921	>	double dielectric;
922
923	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
924	<	return properties_.getPropertyByName(propName);
925	<	}
923	>	errorOut = isError;
924	>	alphaVal = simParams_->getDampingAlpha();
925	>	dielectric = simParams_->getDielectric();
926
927	<	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
927	>	if (simParams_->haveElectrostaticSummationMethod()) {
928	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
929	>	toUpper(myMethod);
930	>	if (myMethod == "NONE") {
931	>	esm = NONE;
932	>	} else {
933	>	if (myMethod == "SWITCHING_FUNCTION") {
934	>	esm = SWITCHING_FUNCTION;
935	>	} else {
936	>	if (myMethod == "SHIFTED_POTENTIAL") {
937	>	esm = SHIFTED_POTENTIAL;
938	>	} else {
939	>	if (myMethod == "SHIFTED_FORCE") {
940	>	esm = SHIFTED_FORCE;
941	>	} else {
942	>	if (myMethod == "REACTION_FIELD") {
943	>	esm = REACTION_FIELD;
944	>	} else {
945	>	// throw error
946	>	sprintf( painCave.errMsg,
947	>	"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() );
948	>	painCave.isFatal = 1;
949	>	simError();
950	>	}
951	>	}
952	>	}
953	>	}
954	>	}
955	>	}
956	>
957	>	if (simParams_->haveElectrostaticScreeningMethod()) {
958	>	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
959	>	toUpper(myScreen);
960	>	if (myScreen == "UNDAMPED") {
961	>	sm = UNDAMPED;
962	>	} else {
963	>	if (myScreen == "DAMPED") {
964	>	sm = DAMPED;
965	>	if (!simParams_->haveDampingAlpha()) {
966	>	//throw error
967	>	sprintf( painCave.errMsg,
968	>	"SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used.", alphaVal);
969	>	painCave.isFatal = 0;
970	>	simError();
971	>	}
972	>	} else {
973	>	// throw error
974	>	sprintf( painCave.errMsg,
975	>	"SimInfo error: Unknown electrostaticScreeningMethod. (Input file specified %s .)\n\telectrostaticScreeningMethod must be one of: \"undamped\" or \"damped\".", myScreen.c_str() );
976	>	painCave.isFatal = 1;
977	>	simError();
978	>	}
979	>	}
980	>	}
981	>
982	>	// let's pass some summation method variables to fortran
983	>	setElectrostaticSummationMethod( &esm );
984	>	setScreeningMethod( &sm );
985	>	setDampingAlpha( &alphaVal );
986	>	setReactionFieldDielectric( &dielectric );
987	>	initFortranFF( &esm, &errorOut );
988	>	}
989	>
990	>	void SimInfo::setupSwitchingFunction() {
991	>	int ft = CUBIC;
992	>
993	>	if (simParams_->haveSwitchingFunctionType()) {
994	>	std::string funcType = simParams_->getSwitchingFunctionType();
995	>	toUpper(funcType);
996	>	if (funcType == "CUBIC") {
997	>	ft = CUBIC;
998	>	} else {
999	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1000	>	ft = FIFTH_ORDER_POLY;
1001	>	} else {
1002	>	// throw error
1003	>	sprintf( painCave.errMsg,
1004	>	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1005	>	painCave.isFatal = 1;
1006	>	simError();
1007	>	}
1008	>	}
1009	>	}
1010	>
1011	>	// send switching function notification to switcheroo
1012	>	setFunctionType(&ft);
1013	>
1014	>	}
1015	>
1016	>	void SimInfo::addProperty(GenericData* genData) {
1017	>	properties_.addProperty(genData);
1018	>	}
1019	>
1020	>	void SimInfo::removeProperty(const std::string& propName) {
1021	>	properties_.removeProperty(propName);
1022	>	}
1023	>
1024	>	void SimInfo::clearProperties() {
1025	>	properties_.clearProperties();
1026	>	}
1027	>
1028	>	std::vector<std::string> SimInfo::getPropertyNames() {
1029	>	return properties_.getPropertyNames();
1030	>	}
1031	>
1032	>	std::vector<GenericData*> SimInfo::getProperties() {
1033	>	return properties_.getProperties();
1034	>	}
1035	>
1036	>	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1037	>	return properties_.getPropertyByName(propName);
1038	>	}
1039	>
1040	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1041	>	if (sman_ == sman) {
1042	>	return;
1043	>	}
1044	>	delete sman_;
1045		sman_ = sman;
1046
1047		Molecule* mol;
#	Line 842 \| Line 1053 \| *void SimInfo::setSnapshotManager(SnapshotManager sman**
1053
1054		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1055
1056	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1057	<	atom->setSnapshotManager(sman_);
1058	<	}
1056	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1057	>	atom->setSnapshotManager(sman_);
1058	>	}
1059
1060	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1061	<	rb->setSnapshotManager(sman_);
1062	<	}
1060	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1061	>	rb->setSnapshotManager(sman_);
1062	>	}
1063		}
1064
1065	<	}
1065	>	}
1066
1067	<	Vector3d SimInfo::getComVel(){
1067	>	Vector3d SimInfo::getComVel(){
1068		SimInfo::MoleculeIterator i;
1069		Molecule* mol;
1070
#	Line 862 \| Line 1073 \| Vector3d SimInfo::getComVel(){
1073
1074
1075		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1076	<	double mass = mol->getMass();
1077	<	totalMass += mass;
1078	<	comVel += mass * mol->getComVel();
1076	>	double mass = mol->getMass();
1077	>	totalMass += mass;
1078	>	comVel += mass * mol->getComVel();
1079		}
1080
1081		#ifdef IS_MPI
#	Line 877 \| Line 1088 \| Vector3d SimInfo::getComVel(){
1088		comVel /= totalMass;
1089
1090		return comVel;
1091	<	}
1091	>	}
1092
1093	<	Vector3d SimInfo::getCom(){
1093	>	Vector3d SimInfo::getCom(){
1094		SimInfo::MoleculeIterator i;
1095		Molecule* mol;
1096
#	Line 887 \| Line 1098 \| Vector3d SimInfo::getCom(){
1098		double totalMass = 0.0;
1099
1100		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1101	<	double mass = mol->getMass();
1102	<	totalMass += mass;
1103	<	com += mass * mol->getCom();
1101	>	double mass = mol->getMass();
1102	>	totalMass += mass;
1103	>	com += mass * mol->getCom();
1104		}
1105
1106		#ifdef IS_MPI
#	Line 903 \| Line 1114 \| Vector3d SimInfo::getCom(){
1114
1115		return com;
1116
1117	<	}
1117	>	}
1118
1119	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1119	>	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1120
1121		return o;
1122	<	}
1122	>	}
1123	>
1124	>
1125	>	/*
1126	>	Returns center of mass and center of mass velocity in one function call.
1127	>	*/
1128	>
1129	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1130	>	SimInfo::MoleculeIterator i;
1131	>	Molecule* mol;
1132	>
1133	>
1134	>	double totalMass = 0.0;
1135	>
1136
1137	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1138	+	double mass = mol->getMass();
1139	+	totalMass += mass;
1140	+	com += mass * mol->getCom();
1141	+	comVel += mass * mol->getComVel();
1142	+	}
1143	+
1144	+	#ifdef IS_MPI
1145	+	double tmpMass = totalMass;
1146	+	Vector3d tmpCom(com);
1147	+	Vector3d tmpComVel(comVel);
1148	+	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1149	+	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1150	+	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1151	+	#endif
1152	+
1153	+	com /= totalMass;
1154	+	comVel /= totalMass;
1155	+	}
1156	+
1157	+	/*
1158	+	Return intertia tensor for entire system and angular momentum Vector.
1159	+
1160	+
1161	+	[ Ixx -Ixy -Ixz ]
1162	+	J =\| -Iyx Iyy -Iyz \|
1163	+	[ -Izx -Iyz Izz ]
1164	+	*/
1165	+
1166	+	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1167	+
1168	+
1169	+	double xx = 0.0;
1170	+	double yy = 0.0;
1171	+	double zz = 0.0;
1172	+	double xy = 0.0;
1173	+	double xz = 0.0;
1174	+	double yz = 0.0;
1175	+	Vector3d com(0.0);
1176	+	Vector3d comVel(0.0);
1177	+
1178	+	getComAll(com, comVel);
1179	+
1180	+	SimInfo::MoleculeIterator i;
1181	+	Molecule* mol;
1182	+
1183	+	Vector3d thisq(0.0);
1184	+	Vector3d thisv(0.0);
1185	+
1186	+	double thisMass = 0.0;
1187	+
1188	+
1189	+
1190	+
1191	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1192	+
1193	+	thisq = mol->getCom()-com;
1194	+	thisv = mol->getComVel()-comVel;
1195	+	thisMass = mol->getMass();
1196	+	// Compute moment of intertia coefficients.
1197	+	xx += thisq[0]thisq[0]thisMass;
1198	+	yy += thisq[1]thisq[1]thisMass;
1199	+	zz += thisq[2]thisq[2]thisMass;
1200	+
1201	+	// compute products of intertia
1202	+	xy += thisq[0]thisq[1]thisMass;
1203	+	xz += thisq[0]thisq[2]thisMass;
1204	+	yz += thisq[1]thisq[2]thisMass;
1205	+
1206	+	angularMomentum += cross( thisq, thisv ) * thisMass;
1207	+
1208	+	}
1209	+
1210	+
1211	+	inertiaTensor(0,0) = yy + zz;
1212	+	inertiaTensor(0,1) = -xy;
1213	+	inertiaTensor(0,2) = -xz;
1214	+	inertiaTensor(1,0) = -xy;
1215	+	inertiaTensor(1,1) = xx + zz;
1216	+	inertiaTensor(1,2) = -yz;
1217	+	inertiaTensor(2,0) = -xz;
1218	+	inertiaTensor(2,1) = -yz;
1219	+	inertiaTensor(2,2) = xx + yy;
1220	+
1221	+	#ifdef IS_MPI
1222	+	Mat3x3d tmpI(inertiaTensor);
1223	+	Vector3d tmpAngMom;
1224	+	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1225	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1226	+	#endif
1227	+
1228	+	return;
1229	+	}
1230	+
1231	+	//Returns the angular momentum of the system
1232	+	Vector3d SimInfo::getAngularMomentum(){
1233	+
1234	+	Vector3d com(0.0);
1235	+	Vector3d comVel(0.0);
1236	+	Vector3d angularMomentum(0.0);
1237	+
1238	+	getComAll(com,comVel);
1239	+
1240	+	SimInfo::MoleculeIterator i;
1241	+	Molecule* mol;
1242	+
1243	+	Vector3d thisr(0.0);
1244	+	Vector3d thisp(0.0);
1245	+
1246	+	double thisMass;
1247	+
1248	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1249	+	thisMass = mol->getMass();
1250	+	thisr = mol->getCom()-com;
1251	+	thisp = (mol->getComVel()-comVel)*thisMass;
1252	+
1253	+	angularMomentum += cross( thisr, thisp );
1254	+
1255	+	}
1256	+
1257	+	#ifdef IS_MPI
1258	+	Vector3d tmpAngMom;
1259	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1260	+	#endif
1261	+
1262	+	return angularMomentum;
1263	+	}
1264	+
1265	+
1266		}//end namespace oopse
1267

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Comparing trunk/src/brains/SimInfo.cpp (file contents): Revision 274 by tim, Tue Jan 25 21:59:18 2005 UTC vs. Revision 734 by chuckv, Tue Nov 15 16:05:38 2005 UTC

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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 274 by tim, Tue Jan 25 21:59:18 2005 UTC vs.
Revision 734 by chuckv, Tue Nov 15 16:05:38 2005 UTC