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root/OpenMD/branches/development/src/brains/SimInfo.cpp

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 413 by tim, Wed Mar 9 17:30:29 2005 UTC vs.
Revision 1241 by gezelter, Fri Apr 25 15:14:47 2008 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 48 | Line 48
48
49		#include <algorithm>
50		#include <set>
51	+	#include <map>
52
53		#include "brains/SimInfo.hpp"
54		#include "math/Vector3.hpp"
55		#include "primitives/Molecule.hpp"
56	+	#include "primitives/StuntDouble.hpp"
57	+	#include "UseTheForce/fCutoffPolicy.h"
58	+	#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
59	+	#include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h"
60	+	#include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
61		#include "UseTheForce/doForces_interface.h"
62	<	#include "UseTheForce/notifyCutoffs_interface.h"
62	>	#include "UseTheForce/DarkSide/neighborLists_interface.h"
63	>	#include "UseTheForce/DarkSide/electrostatic_interface.h"
64	>	#include "UseTheForce/DarkSide/switcheroo_interface.h"
65		#include "utils/MemoryUtils.hpp"
66		#include "utils/simError.h"
67		#include "selection/SelectionManager.hpp"
68	+	#include "io/ForceFieldOptions.hpp"
69	+	#include "UseTheForce/ForceField.hpp"
70
71	+
72		#ifdef IS_MPI
73		#include "UseTheForce/mpiComponentPlan.h"
74		#include "UseTheForce/DarkSide/simParallel_interface.h"
75		#endif
76
77		namespace oopse {
78	+	std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
79	+	std::map<int, std::set<int> >::iterator i = container.find(index);
80	+	std::set<int> result;
81	+	if (i != container.end()) {
82	+	result = i->second;
83	+	}
84
85	<	SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
86	<	ForceField* ff, Globals* simParams) :
87	<	forceField_(ff), simParams_(simParams),
88	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
89	<	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
90	<	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
91	<	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
92	<	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
93	<	sman_(NULL), fortranInitialized_(false) {
85	>	return result;
86	>	}
87	>
88	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
89	>	forceField_(ff), simParams_(simParams),
90	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
91	>	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
92	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
93	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
94	>	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
95	>	sman_(NULL), fortranInitialized_(false), calcBoxDipole_(false),
96	>	useAtomicVirial_(true) {
97
98	<
99	<	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
100	<	MoleculeStamp* molStamp;
101	<	int nMolWithSameStamp;
102	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
103	<	int nGroups = 0;          //total cutoff groups defined in meta-data file
104	<	CutoffGroupStamp* cgStamp;
105	<	RigidBodyStamp* rbStamp;
106	<	int nRigidAtoms = 0;
107	<
108	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
109	<	molStamp = i->first;
90	<	nMolWithSameStamp = i->second;
98	>	MoleculeStamp* molStamp;
99	>	int nMolWithSameStamp;
100	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
101	>	int nGroups = 0;      //total cutoff groups defined in meta-data file
102	>	CutoffGroupStamp* cgStamp;
103	>	RigidBodyStamp* rbStamp;
104	>	int nRigidAtoms = 0;
105	>	std::vector<Component*> components = simParams->getComponents();
106	>
107	>	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
108	>	molStamp = (*i)->getMoleculeStamp();
109	>	nMolWithSameStamp = (*i)->getNMol();
110
111		addMoleculeStamp(molStamp, nMolWithSameStamp);
112
113		//calculate atoms in molecules
114		nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
115
97	–
116		//calculate atoms in cutoff groups
117		int nAtomsInGroups = 0;
118		int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
119
120		for (int j=0; j < nCutoffGroupsInStamp; j++) {
121	<	cgStamp = molStamp->getCutoffGroup(j);
122	<	nAtomsInGroups += cgStamp->getNMembers();
121	>	cgStamp = molStamp->getCutoffGroupStamp(j);
122	>	nAtomsInGroups += cgStamp->getNMembers();
123		}
124
125		nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
126	+
127		nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
128
129		//calculate atoms in rigid bodies
#	Line 112 | Line 131 | SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*,
131		int nRigidBodiesInStamp = molStamp->getNRigidBodies();
132
133		for (int j=0; j < nRigidBodiesInStamp; j++) {
134	<	rbStamp = molStamp->getRigidBody(j);
135	<	nAtomsInRigidBodies += rbStamp->getNMembers();
134	>	rbStamp = molStamp->getRigidBodyStamp(j);
135	>	nAtomsInRigidBodies += rbStamp->getNMembers();
136		}
137
138		nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
139		nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
140
141	<	}
141	>	}
142
143	<	//every free atom (atom does not belong to cutoff groups) is a cutoff group
144	<	//therefore the total number of cutoff groups in the system is equal to
145	<	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
146	<	//file plus the number of cutoff groups defined in meta-data file
147	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
143	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
144	>	//group therefore the total number of cutoff groups in the system is
145	>	//equal to the total number of atoms minus number of atoms belong to
146	>	//cutoff group defined in meta-data file plus the number of cutoff
147	>	//groups defined in meta-data file
148	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
149
150	<	//every free atom (atom does not belong to rigid bodies) is an integrable object
151	<	//therefore the total number of  integrable objects in the system is equal to
152	<	//the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
153	<	//file plus the number of  rigid bodies defined in meta-data file
154	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
150	>	//every free atom (atom does not belong to rigid bodies) is an
151	>	//integrable object therefore the total number of integrable objects
152	>	//in the system is equal to the total number of atoms minus number of
153	>	//atoms belong to rigid body defined in meta-data file plus the number
154	>	//of rigid bodies defined in meta-data file
155	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
156	>	+ nGlobalRigidBodies_;
157	>
158	>	nGlobalMols_ = molStampIds_.size();
159	>	molToProcMap_.resize(nGlobalMols_);
160	>	}
161
162	<	nGlobalMols_ = molStampIds_.size();
137	<
138	<	#ifdef IS_MPI
139	<	molToProcMap_.resize(nGlobalMols_);
140	<	#endif
141	<
142	<	}
143	<
144	<	SimInfo::~SimInfo() {
162	>	SimInfo::~SimInfo() {
163		std::map<int, Molecule*>::iterator i;
164		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
165	<	delete i->second;
165	>	delete i->second;
166		}
167		molecules_.clear();
168	<
151	<	MemoryUtils::deletePointers(moleculeStamps_);
152	<
168	>
169		delete sman_;
170		delete simParams_;
171		delete forceField_;
172	<	}
172	>	}
173
174	<	int SimInfo::getNGlobalConstraints() {
174	>	int SimInfo::getNGlobalConstraints() {
175		int nGlobalConstraints;
176		#ifdef IS_MPI
177		MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
#	Line 164 | Line 180 | int SimInfo::getNGlobalConstraints() {
180		nGlobalConstraints =  nConstraints_;
181		#endif
182		return nGlobalConstraints;
183	<	}
183	>	}
184
185	<	bool SimInfo::addMolecule(Molecule* mol) {
185	>	bool SimInfo::addMolecule(Molecule* mol) {
186		MoleculeIterator i;
187
188		i = molecules_.find(mol->getGlobalIndex());
189		if (i == molecules_.end() ) {
190
191	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
191	>	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
192
193	<	nAtoms_ += mol->getNAtoms();
194	<	nBonds_ += mol->getNBonds();
195	<	nBends_ += mol->getNBends();
196	<	nTorsions_ += mol->getNTorsions();
197	<	nRigidBodies_ += mol->getNRigidBodies();
198	<	nIntegrableObjects_ += mol->getNIntegrableObjects();
199	<	nCutoffGroups_ += mol->getNCutoffGroups();
200	<	nConstraints_ += mol->getNConstraintPairs();
193	>	nAtoms_ += mol->getNAtoms();
194	>	nBonds_ += mol->getNBonds();
195	>	nBends_ += mol->getNBends();
196	>	nTorsions_ += mol->getNTorsions();
197	>	nRigidBodies_ += mol->getNRigidBodies();
198	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
199	>	nCutoffGroups_ += mol->getNCutoffGroups();
200	>	nConstraints_ += mol->getNConstraintPairs();
201
202	<	addExcludePairs(mol);
202	>	addExcludePairs(mol);
203
204	<	return true;
204	>	return true;
205		} else {
206	<	return false;
206	>	return false;
207		}
208	<	}
208	>	}
209
210	<	bool SimInfo::removeMolecule(Molecule* mol) {
210	>	bool SimInfo::removeMolecule(Molecule* mol) {
211		MoleculeIterator i;
212		i = molecules_.find(mol->getGlobalIndex());
213
214		if (i != molecules_.end() ) {
215
216	<	assert(mol == i->second);
216	>	assert(mol == i->second);
217
218	<	nAtoms_ -= mol->getNAtoms();
219	<	nBonds_ -= mol->getNBonds();
220	<	nBends_ -= mol->getNBends();
221	<	nTorsions_ -= mol->getNTorsions();
222	<	nRigidBodies_ -= mol->getNRigidBodies();
223	<	nIntegrableObjects_ -= mol->getNIntegrableObjects();
224	<	nCutoffGroups_ -= mol->getNCutoffGroups();
225	<	nConstraints_ -= mol->getNConstraintPairs();
218	>	nAtoms_ -= mol->getNAtoms();
219	>	nBonds_ -= mol->getNBonds();
220	>	nBends_ -= mol->getNBends();
221	>	nTorsions_ -= mol->getNTorsions();
222	>	nRigidBodies_ -= mol->getNRigidBodies();
223	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
224	>	nCutoffGroups_ -= mol->getNCutoffGroups();
225	>	nConstraints_ -= mol->getNConstraintPairs();
226
227	<	removeExcludePairs(mol);
228	<	molecules_.erase(mol->getGlobalIndex());
227	>	removeExcludePairs(mol);
228	>	molecules_.erase(mol->getGlobalIndex());
229
230	<	delete mol;
230	>	delete mol;
231
232	<	return true;
232	>	return true;
233		} else {
234	<	return false;
234	>	return false;
235		}
236
237
238	<	}
238	>	}
239
240
241	<	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
241	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
242		i = molecules_.begin();
243		return i == molecules_.end() ? NULL : i->second;
244	<	}
244	>	}
245
246	<	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
246	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
247		++i;
248		return i == molecules_.end() ? NULL : i->second;
249	<	}
249	>	}
250
251
252	<	void SimInfo::calcNdf() {
252	>	void SimInfo::calcNdf() {
253		int ndf_local;
254		MoleculeIterator i;
255		std::vector<StuntDouble*>::iterator j;
#	Line 243 | Line 259 | void SimInfo::calcNdf() {
259		ndf_local = 0;
260
261		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
262	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
263	<	integrableObject = mol->nextIntegrableObject(j)) {
262	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
263	>	integrableObject = mol->nextIntegrableObject(j)) {
264
265	<	ndf_local += 3;
265	>	ndf_local += 3;
266
267	<	if (integrableObject->isDirectional()) {
268	<	if (integrableObject->isLinear()) {
269	<	ndf_local += 2;
270	<	} else {
271	<	ndf_local += 3;
272	<	}
273	<	}
267	>	if (integrableObject->isDirectional()) {
268	>	if (integrableObject->isLinear()) {
269	>	ndf_local += 2;
270	>	} else {
271	>	ndf_local += 3;
272	>	}
273	>	}
274
275	<	}//end for (integrableObject)
276	<	}// end for (mol)
275	>	}
276	>	}
277
278		// n_constraints is local, so subtract them on each processor
279		ndf_local -= nConstraints_;
#	Line 272 | Line 288 | void SimInfo::calcNdf() {
288		// entire system:
289		ndf_ = ndf_ - 3 - nZconstraint_;
290
291	<	}
291	>	}
292
293	<	void SimInfo::calcNdfRaw() {
293	>	int SimInfo::getFdf() {
294	>	#ifdef IS_MPI
295	>	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
296	>	#else
297	>	fdf_ = fdf_local;
298	>	#endif
299	>	return fdf_;
300	>	}
301	>
302	>	void SimInfo::calcNdfRaw() {
303		int ndfRaw_local;
304
305		MoleculeIterator i;
#	Line 286 | Line 311 | void SimInfo::calcNdfRaw() {
311		ndfRaw_local = 0;
312
313		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
314	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
315	<	integrableObject = mol->nextIntegrableObject(j)) {
314	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
315	>	integrableObject = mol->nextIntegrableObject(j)) {
316
317	<	ndfRaw_local += 3;
317	>	ndfRaw_local += 3;
318
319	<	if (integrableObject->isDirectional()) {
320	<	if (integrableObject->isLinear()) {
321	<	ndfRaw_local += 2;
322	<	} else {
323	<	ndfRaw_local += 3;
324	<	}
325	<	}
319	>	if (integrableObject->isDirectional()) {
320	>	if (integrableObject->isLinear()) {
321	>	ndfRaw_local += 2;
322	>	} else {
323	>	ndfRaw_local += 3;
324	>	}
325	>	}
326
327	<	}
327	>	}
328		}
329
330		#ifdef IS_MPI
#	Line 307 | Line 332 | void SimInfo::calcNdfRaw() {
332		#else
333		ndfRaw_ = ndfRaw_local;
334		#endif
335	<	}
335	>	}
336
337	<	void SimInfo::calcNdfTrans() {
337	>	void SimInfo::calcNdfTrans() {
338		int ndfTrans_local;
339
340		ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
#	Line 323 | Line 348 | void SimInfo::calcNdfTrans() {
348
349		ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
350
351	<	}
351	>	}
352
353	<	void SimInfo::addExcludePairs(Molecule* mol) {
353	>	void SimInfo::addExcludePairs(Molecule* mol) {
354		std::vector<Bond*>::iterator bondIter;
355		std::vector<Bend*>::iterator bendIter;
356		std::vector<Torsion*>::iterator torsionIter;
#	Line 336 | Line 361 | void SimInfo::addExcludePairs(Molecule* mol) {
361		int b;
362		int c;
363		int d;
364	+
365	+	std::map<int, std::set<int> > atomGroups;
366	+
367	+	Molecule::RigidBodyIterator rbIter;
368	+	RigidBody* rb;
369	+	Molecule::IntegrableObjectIterator ii;
370	+	StuntDouble* integrableObject;
371
372	+	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
373	+	integrableObject = mol->nextIntegrableObject(ii)) {
374	+
375	+	if (integrableObject->isRigidBody()) {
376	+	rb = static_cast<RigidBody*>(integrableObject);
377	+	std::vector<Atom*> atoms = rb->getAtoms();
378	+	std::set<int> rigidAtoms;
379	+	for (int i = 0; i < atoms.size(); ++i) {
380	+	rigidAtoms.insert(atoms[i]->getGlobalIndex());
381	+	}
382	+	for (int i = 0; i < atoms.size(); ++i) {
383	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
384	+	}
385	+	} else {
386	+	std::set<int> oneAtomSet;
387	+	oneAtomSet.insert(integrableObject->getGlobalIndex());
388	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
389	+	}
390	+	}
391	+
392	+
393	+
394		for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
395	<	a = bond->getAtomA()->getGlobalIndex();
396	<	b = bond->getAtomB()->getGlobalIndex();
397	<	exclude_.addPair(a, b);
395	>	a = bond->getAtomA()->getGlobalIndex();
396	>	b = bond->getAtomB()->getGlobalIndex();
397	>	exclude_.addPair(a, b);
398		}
399
400		for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
401	<	a = bend->getAtomA()->getGlobalIndex();
402	<	b = bend->getAtomB()->getGlobalIndex();
403	<	c = bend->getAtomC()->getGlobalIndex();
401	>	a = bend->getAtomA()->getGlobalIndex();
402	>	b = bend->getAtomB()->getGlobalIndex();
403	>	c = bend->getAtomC()->getGlobalIndex();
404	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
405	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
406	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
407
408	<	exclude_.addPair(a, b);
409	<	exclude_.addPair(a, c);
410	<	exclude_.addPair(b, c);
408	>	exclude_.addPairs(rigidSetA, rigidSetB);
409	>	exclude_.addPairs(rigidSetA, rigidSetC);
410	>	exclude_.addPairs(rigidSetB, rigidSetC);
411	>
412	>	//exclude_.addPair(a, b);
413	>	//exclude_.addPair(a, c);
414	>	//exclude_.addPair(b, c);
415		}
416
417		for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
418	<	a = torsion->getAtomA()->getGlobalIndex();
419	<	b = torsion->getAtomB()->getGlobalIndex();
420	<	c = torsion->getAtomC()->getGlobalIndex();
421	<	d = torsion->getAtomD()->getGlobalIndex();
418	>	a = torsion->getAtomA()->getGlobalIndex();
419	>	b = torsion->getAtomB()->getGlobalIndex();
420	>	c = torsion->getAtomC()->getGlobalIndex();
421	>	d = torsion->getAtomD()->getGlobalIndex();
422	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
423	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
424	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
425	>	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
426
427	<	exclude_.addPair(a, b);
428	<	exclude_.addPair(a, c);
429	<	exclude_.addPair(a, d);
430	<	exclude_.addPair(b, c);
431	<	exclude_.addPair(b, d);
432	<	exclude_.addPair(c, d);
427	>	exclude_.addPairs(rigidSetA, rigidSetB);
428	>	exclude_.addPairs(rigidSetA, rigidSetC);
429	>	exclude_.addPairs(rigidSetA, rigidSetD);
430	>	exclude_.addPairs(rigidSetB, rigidSetC);
431	>	exclude_.addPairs(rigidSetB, rigidSetD);
432	>	exclude_.addPairs(rigidSetC, rigidSetD);
433	>
434	>	/*
435	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
436	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
437	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
438	>	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
439	>	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
440	>	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
441	>
442	>
443	>	exclude_.addPair(a, b);
444	>	exclude_.addPair(a, c);
445	>	exclude_.addPair(a, d);
446	>	exclude_.addPair(b, c);
447	>	exclude_.addPair(b, d);
448	>	exclude_.addPair(c, d);
449	>	*/
450		}
451
452	<
453	<	}
452	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
453	>	std::vector<Atom*> atoms = rb->getAtoms();
454	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
455	>	for (int j = i + 1; j < atoms.size(); ++j) {
456	>	a = atoms[i]->getGlobalIndex();
457	>	b = atoms[j]->getGlobalIndex();
458	>	exclude_.addPair(a, b);
459	>	}
460	>	}
461	>	}
462
463	<	void SimInfo::removeExcludePairs(Molecule* mol) {
463	>	}
464	>
465	>	void SimInfo::removeExcludePairs(Molecule* mol) {
466		std::vector<Bond*>::iterator bondIter;
467		std::vector<Bend*>::iterator bendIter;
468		std::vector<Torsion*>::iterator torsionIter;
#	Line 381 | Line 473 | void SimInfo::removeExcludePairs(Molecule* mol) {
473		int b;
474		int c;
475		int d;
476	+
477	+	std::map<int, std::set<int> > atomGroups;
478	+
479	+	Molecule::RigidBodyIterator rbIter;
480	+	RigidBody* rb;
481	+	Molecule::IntegrableObjectIterator ii;
482	+	StuntDouble* integrableObject;
483
484	+	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
485	+	integrableObject = mol->nextIntegrableObject(ii)) {
486	+
487	+	if (integrableObject->isRigidBody()) {
488	+	rb = static_cast<RigidBody*>(integrableObject);
489	+	std::vector<Atom*> atoms = rb->getAtoms();
490	+	std::set<int> rigidAtoms;
491	+	for (int i = 0; i < atoms.size(); ++i) {
492	+	rigidAtoms.insert(atoms[i]->getGlobalIndex());
493	+	}
494	+	for (int i = 0; i < atoms.size(); ++i) {
495	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
496	+	}
497	+	} else {
498	+	std::set<int> oneAtomSet;
499	+	oneAtomSet.insert(integrableObject->getGlobalIndex());
500	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
501	+	}
502	+	}
503	+
504	+
505		for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
506	<	a = bond->getAtomA()->getGlobalIndex();
507	<	b = bond->getAtomB()->getGlobalIndex();
508	<	exclude_.removePair(a, b);
506	>	a = bond->getAtomA()->getGlobalIndex();
507	>	b = bond->getAtomB()->getGlobalIndex();
508	>	exclude_.removePair(a, b);
509		}
510
511		for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
512	<	a = bend->getAtomA()->getGlobalIndex();
513	<	b = bend->getAtomB()->getGlobalIndex();
514	<	c = bend->getAtomC()->getGlobalIndex();
512	>	a = bend->getAtomA()->getGlobalIndex();
513	>	b = bend->getAtomB()->getGlobalIndex();
514	>	c = bend->getAtomC()->getGlobalIndex();
515
516	<	exclude_.removePair(a, b);
517	<	exclude_.removePair(a, c);
518	<	exclude_.removePair(b, c);
516	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
517	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
518	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
519	>
520	>	exclude_.removePairs(rigidSetA, rigidSetB);
521	>	exclude_.removePairs(rigidSetA, rigidSetC);
522	>	exclude_.removePairs(rigidSetB, rigidSetC);
523	>
524	>	//exclude_.removePair(a, b);
525	>	//exclude_.removePair(a, c);
526	>	//exclude_.removePair(b, c);
527		}
528
529		for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
530	<	a = torsion->getAtomA()->getGlobalIndex();
531	<	b = torsion->getAtomB()->getGlobalIndex();
532	<	c = torsion->getAtomC()->getGlobalIndex();
533	<	d = torsion->getAtomD()->getGlobalIndex();
530	>	a = torsion->getAtomA()->getGlobalIndex();
531	>	b = torsion->getAtomB()->getGlobalIndex();
532	>	c = torsion->getAtomC()->getGlobalIndex();
533	>	d = torsion->getAtomD()->getGlobalIndex();
534
535	<	exclude_.removePair(a, b);
536	<	exclude_.removePair(a, c);
537	<	exclude_.removePair(a, d);
538	<	exclude_.removePair(b, c);
539	<	exclude_.removePair(b, d);
540	<	exclude_.removePair(c, d);
535	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
536	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
537	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
538	>	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
539	>
540	>	exclude_.removePairs(rigidSetA, rigidSetB);
541	>	exclude_.removePairs(rigidSetA, rigidSetC);
542	>	exclude_.removePairs(rigidSetA, rigidSetD);
543	>	exclude_.removePairs(rigidSetB, rigidSetC);
544	>	exclude_.removePairs(rigidSetB, rigidSetD);
545	>	exclude_.removePairs(rigidSetC, rigidSetD);
546	>
547	>	/*
548	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
549	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
550	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
551	>	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
552	>	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
553	>	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
554	>
555	>
556	>	exclude_.removePair(a, b);
557	>	exclude_.removePair(a, c);
558	>	exclude_.removePair(a, d);
559	>	exclude_.removePair(b, c);
560	>	exclude_.removePair(b, d);
561	>	exclude_.removePair(c, d);
562	>	*/
563		}
564
565	<	}
565	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
566	>	std::vector<Atom*> atoms = rb->getAtoms();
567	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
568	>	for (int j = i + 1; j < atoms.size(); ++j) {
569	>	a = atoms[i]->getGlobalIndex();
570	>	b = atoms[j]->getGlobalIndex();
571	>	exclude_.removePair(a, b);
572	>	}
573	>	}
574	>	}
575
576	+	}
577
578	<	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
578	>
579	>	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
580		int curStampId;
581
582		//index from 0
#	Line 423 | Line 584 | void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp
584
585		moleculeStamps_.push_back(molStamp);
586		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
587	<	}
587	>	}
588
589	<	void SimInfo::update() {
589	>	void SimInfo::update() {
590
591		setupSimType();
592
#	Line 438 | Line 599 | void SimInfo::update() {
599		//setup fortran force field
600		/** @deprecate */
601		int isError = 0;
441	–	initFortranFF( &fInfo_.SIM_uses_RF , &isError );
442	–	if(isError){
443	–	sprintf( painCave.errMsg,
444	–	"ForceField error: There was an error initializing the forceField in fortran.\n" );
445	–	painCave.isFatal = 1;
446	–	simError();
447	–	}
448	–
602
603		setupCutoff();
604	+
605	+	setupElectrostaticSummationMethod( isError );
606	+	setupSwitchingFunction();
607	+	setupAccumulateBoxDipole();
608
609	+	if(isError){
610	+	sprintf( painCave.errMsg,
611	+	"ForceField error: There was an error initializing the forceField in fortran.\n" );
612	+	painCave.isFatal = 1;
613	+	simError();
614	+	}
615	+
616		calcNdf();
617		calcNdfRaw();
618		calcNdfTrans();
619
620		fortranInitialized_ = true;
621	<	}
621	>	}
622
623	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
623	>	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
624		SimInfo::MoleculeIterator mi;
625		Molecule* mol;
626		Molecule::AtomIterator ai;
#	Line 465 | Line 629 | std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
629
630		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
631
632	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
633	<	atomTypes.insert(atom->getAtomType());
634	<	}
632	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
633	>	atomTypes.insert(atom->getAtomType());
634	>	}
635
636		}
637
638		return atomTypes;
639	<	}
639	>	}
640
641	<	void SimInfo::setupSimType() {
641	>	void SimInfo::setupSimType() {
642		std::set<AtomType*>::iterator i;
643		std::set<AtomType*> atomTypes;
644		atomTypes = getUniqueAtomTypes();
#	Line 482 | Line 646 | void SimInfo::setupSimType() {
646		int useLennardJones = 0;
647		int useElectrostatic = 0;
648		int useEAM = 0;
649	+	int useSC = 0;
650		int useCharge = 0;
651		int useDirectional = 0;
652		int useDipole = 0;
653		int useGayBerne = 0;
654		int useSticky = 0;
655	+	int useStickyPower = 0;
656		int useShape = 0;
657		int useFLARB = 0; //it is not in AtomType yet
658		int useDirectionalAtom = 0;
659		int useElectrostatics = 0;
660		//usePBC and useRF are from simParams
661	<	int usePBC = simParams_->getPBC();
662	<	int useRF = simParams_->getUseRF();
661	>	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
662	>	int useRF;
663	>	int useSF;
664	>	int useSP;
665	>	int useBoxDipole;
666	>
667	>	std::string myMethod;
668	>
669	>	// set the useRF logical
670	>	useRF = 0;
671	>	useSF = 0;
672	>	useSP = 0;
673	>
674	>
675	>	if (simParams_->haveElectrostaticSummationMethod()) {
676	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
677	>	toUpper(myMethod);
678	>	if (myMethod == "REACTION_FIELD"){
679	>	useRF = 1;
680	>	} else if (myMethod == "SHIFTED_FORCE"){
681	>	useSF = 1;
682	>	} else if (myMethod == "SHIFTED_POTENTIAL"){
683	>	useSP = 1;
684	>	}
685	>	}
686	>
687	>	if (simParams_->haveAccumulateBoxDipole())
688	>	if (simParams_->getAccumulateBoxDipole())
689	>	useBoxDipole = 1;
690
691	+	useAtomicVirial_ = simParams_->getUseAtomicVirial();
692	+
693		//loop over all of the atom types
694		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
695	<	useLennardJones |= (*i)->isLennardJones();
696	<	useElectrostatic |= (*i)->isElectrostatic();
697	<	useEAM |= (*i)->isEAM();
698	<	useCharge |= (*i)->isCharge();
699	<	useDirectional |= (*i)->isDirectional();
700	<	useDipole |= (*i)->isDipole();
701	<	useGayBerne |= (*i)->isGayBerne();
702	<	useSticky |= (*i)->isSticky();
703	<	useShape |= (*i)->isShape();
695	>	useLennardJones |= (*i)->isLennardJones();
696	>	useElectrostatic |= (*i)->isElectrostatic();
697	>	useEAM |= (*i)->isEAM();
698	>	useSC |= (*i)->isSC();
699	>	useCharge |= (*i)->isCharge();
700	>	useDirectional |= (*i)->isDirectional();
701	>	useDipole |= (*i)->isDipole();
702	>	useGayBerne |= (*i)->isGayBerne();
703	>	useSticky |= (*i)->isSticky();
704	>	useStickyPower |= (*i)->isStickyPower();
705	>	useShape |= (*i)->isShape();
706		}
707
708	<	if (useSticky || useDipole || useGayBerne || useShape) {
709	<	useDirectionalAtom = 1;
708	>	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
709	>	useDirectionalAtom = 1;
710		}
711
712		if (useCharge || useDipole) {
713	<	useElectrostatics = 1;
713	>	useElectrostatics = 1;
714		}
715
716		#ifdef IS_MPI
#	Line 540 | Line 737 | void SimInfo::setupSimType() {
737		temp = useSticky;
738		MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
739
740	+	temp = useStickyPower;
741	+	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
742	+
743		temp = useGayBerne;
744		MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
745
746		temp = useEAM;
747		MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
748
749	+	temp = useSC;
750	+	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
751	+
752		temp = useShape;
753		MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
754
#	Line 554 | Line 757 | void SimInfo::setupSimType() {
757
758		temp = useRF;
759		MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
760	<
760	>
761	>	temp = useSF;
762	>	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
763	>
764	>	temp = useSP;
765	>	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
766	>
767	>	temp = useBoxDipole;
768	>	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
769	>
770	>	temp = useAtomicVirial_;
771	>	MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
772	>
773		#endif
774
775		fInfo_.SIM_uses_PBC = usePBC;
#	Line 564 | Line 779 | void SimInfo::setupSimType() {
779		fInfo_.SIM_uses_Charges = useCharge;
780		fInfo_.SIM_uses_Dipoles = useDipole;
781		fInfo_.SIM_uses_Sticky = useSticky;
782	+	fInfo_.SIM_uses_StickyPower = useStickyPower;
783		fInfo_.SIM_uses_GayBerne = useGayBerne;
784		fInfo_.SIM_uses_EAM = useEAM;
785	+	fInfo_.SIM_uses_SC = useSC;
786		fInfo_.SIM_uses_Shapes = useShape;
787		fInfo_.SIM_uses_FLARB = useFLARB;
788		fInfo_.SIM_uses_RF = useRF;
789	+	fInfo_.SIM_uses_SF = useSF;
790	+	fInfo_.SIM_uses_SP = useSP;
791	+	fInfo_.SIM_uses_BoxDipole = useBoxDipole;
792	+	fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
793	+	}
794
795	<	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
574	<
575	<	if (simParams_->haveDielectric()) {
576	<	fInfo_.dielect = simParams_->getDielectric();
577	<	} else {
578	<	sprintf(painCave.errMsg,
579	<	"SimSetup Error: No Dielectric constant was set.\n"
580	<	"\tYou are trying to use Reaction Field without"
581	<	"\tsetting a dielectric constant!\n");
582	<	painCave.isFatal = 1;
583	<	simError();
584	<	}
585	<
586	<	} else {
587	<	fInfo_.dielect = 0.0;
588	<	}
589	<
590	<	}
591	<
592	<	void SimInfo::setupFortranSim() {
795	>	void SimInfo::setupFortranSim() {
796		int isError;
797		int nExclude;
798		std::vector<int> fortranGlobalGroupMembership;
#	Line 599 | Line 802 | void SimInfo::setupFortranSim() {
802
803		//globalGroupMembership_ is filled by SimCreator
804		for (int i = 0; i < nGlobalAtoms_; i++) {
805	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
805	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
806		}
807
808		//calculate mass ratio of cutoff group
809	<	std::vector<double> mfact;
809	>	std::vector<RealType> mfact;
810		SimInfo::MoleculeIterator mi;
811		Molecule* mol;
812		Molecule::CutoffGroupIterator ci;
813		CutoffGroup* cg;
814		Molecule::AtomIterator ai;
815		Atom* atom;
816	<	double totalMass;
816	>	RealType totalMass;
817
818		//to avoid memory reallocation, reserve enough space for mfact
819		mfact.reserve(getNCutoffGroups());
820
821		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
822	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
822	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
823
824	<	totalMass = cg->getMass();
825	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
826	<	mfact.push_back(atom->getMass()/totalMass);
827	<	}
824	>	totalMass = cg->getMass();
825	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
826	>	// Check for massless groups - set mfact to 1 if true
827	>	if (totalMass != 0)
828	>	mfact.push_back(atom->getMass()/totalMass);
829	>	else
830	>	mfact.push_back( 1.0 );
831	>	}
832
833	<	}
833	>	}
834		}
835
836		//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
#	Line 633 | Line 840 | void SimInfo::setupFortranSim() {
840		identArray.reserve(getNAtoms());
841
842		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
843	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
844	<	identArray.push_back(atom->getIdent());
845	<	}
843	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
844	>	identArray.push_back(atom->getIdent());
845	>	}
846		}
847
848		//fill molMembershipArray
849		//molMembershipArray is filled by SimCreator
850		std::vector<int> molMembershipArray(nGlobalAtoms_);
851		for (int i = 0; i < nGlobalAtoms_; i++) {
852	<	molMembershipArray[i] = globalMolMembership_[i] + 1;
852	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
853		}
854
855		//setup fortran simulation
649	–	//gloalExcludes and molMembershipArray should go away (They are never used)
650	–	//why the hell fortran need to know molecule?
651	–	//OOPSE = Object-Obfuscated Parallel Simulation Engine
856		int nGlobalExcludes = 0;
857		int* globalExcludes = NULL;
858		int* excludeList = exclude_.getExcludeList();
859	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
860	<	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
861	<	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
862	<
859	>	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
860	>	&nExclude, excludeList , &nGlobalExcludes, globalExcludes,
861	>	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
862	>	&fortranGlobalGroupMembership[0], &isError);
863	>
864		if( isError ){
865	<
866	<	sprintf( painCave.errMsg,
867	<	"There was an error setting the simulation information in fortran.\n" );
868	<	painCave.isFatal = 1;
869	<	painCave.severity = OOPSE_ERROR;
870	<	simError();
865	>
866	>	sprintf( painCave.errMsg,
867	>	"There was an error setting the simulation information in fortran.\n" );
868	>	painCave.isFatal = 1;
869	>	painCave.severity = OOPSE_ERROR;
870	>	simError();
871		}
872	<
873	<	#ifdef IS_MPI
872	>
873	>
874		sprintf( checkPointMsg,
875	<	"succesfully sent the simulation information to fortran.\n");
876	<	MPIcheckPoint();
877	<	#endif // is_mpi
878	<	}
875	>	"succesfully sent the simulation information to fortran.\n");
876	>
877	>	errorCheckPoint();
878	>
879	>	// Setup number of neighbors in neighbor list if present
880	>	if (simParams_->haveNeighborListNeighbors()) {
881	>	int nlistNeighbors = simParams_->getNeighborListNeighbors();
882	>	setNeighbors(&nlistNeighbors);
883	>	}
884	>
885
886	+	}
887
888	<	#ifdef IS_MPI
889	<	void SimInfo::setupFortranParallel() {
890	<
888	>
889	>	void SimInfo::setupFortranParallel() {
890	>	#ifdef IS_MPI
891		//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
892		std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
893		std::vector<int> localToGlobalCutoffGroupIndex;
#	Line 690 | Line 902 | void SimInfo::setupFortranParallel() {
902
903		for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
904
905	<	//local index(index in DataStorge) of atom is important
906	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
907	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
908	<	}
905	>	//local index(index in DataStorge) of atom is important
906	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
907	>	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
908	>	}
909
910	<	//local index of cutoff group is trivial, it only depends on the order of travesing
911	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
912	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
913	<	}
910	>	//local index of cutoff group is trivial, it only depends on the order of travesing
911	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
912	>	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
913	>	}
914
915		}
916
#	Line 718 | Line 930 | void SimInfo::setupFortranParallel() {
930		&localToGlobalCutoffGroupIndex[0], &isError);
931
932		if (isError) {
933	<	sprintf(painCave.errMsg,
934	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
935	<	painCave.isFatal = 1;
936	<	simError();
933	>	sprintf(painCave.errMsg,
934	>	"mpiRefresh errror: fortran didn't like something we gave it.\n");
935	>	painCave.isFatal = 1;
936	>	simError();
937		}
938
939		sprintf(checkPointMsg, " mpiRefresh successful.\n");
940	<	MPIcheckPoint();
940	>	errorCheckPoint();
941
730	–
731	–	}
732	–
942		#endif
943	+	}
944
945	<	double SimInfo::calcMaxCutoffRadius() {
945	>	void SimInfo::setupCutoff() {
946	>
947	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
948
949	+	// Check the cutoff policy
950	+	int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
951
952	<	std::set<AtomType*> atomTypes;
953	<	std::set<AtomType*>::iterator i;
954	<	std::vector<double> cutoffRadius;
952	>	// Set LJ shifting bools to false
953	>	ljsp_ = false;
954	>	ljsf_ = false;
955
956	<	//get the unique atom types
957	<	atomTypes = getUniqueAtomTypes();
958	<
959	<	//query the max cutoff radius among these atom types
960	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
747	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
956	>	std::string myPolicy;
957	>	if (forceFieldOptions_.haveCutoffPolicy()){
958	>	myPolicy = forceFieldOptions_.getCutoffPolicy();
959	>	}else if (simParams_->haveCutoffPolicy()) {
960	>	myPolicy = simParams_->getCutoffPolicy();
961		}
962
963	<	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
964	<	#ifdef IS_MPI
965	<	//pick the max cutoff radius among the processors
966	<	#endif
963	>	if (!myPolicy.empty()){
964	>	toUpper(myPolicy);
965	>	if (myPolicy == "MIX") {
966	>	cp = MIX_CUTOFF_POLICY;
967	>	} else {
968	>	if (myPolicy == "MAX") {
969	>	cp = MAX_CUTOFF_POLICY;
970	>	} else {
971	>	if (myPolicy == "TRADITIONAL") {
972	>	cp = TRADITIONAL_CUTOFF_POLICY;
973	>	} else {
974	>	// throw error
975	>	sprintf( painCave.errMsg,
976	>	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
977	>	painCave.isFatal = 1;
978	>	simError();
979	>	}
980	>	}
981	>	}
982	>	}
983	>	notifyFortranCutoffPolicy(&cp);
984
985	<	return maxCutoffRadius;
986	<	}
985	>	// Check the Skin Thickness for neighborlists
986	>	RealType skin;
987	>	if (simParams_->haveSkinThickness()) {
988	>	skin = simParams_->getSkinThickness();
989	>	notifyFortranSkinThickness(&skin);
990	>	}
991	>
992	>	// Check if the cutoff was set explicitly:
993	>	if (simParams_->haveCutoffRadius()) {
994	>	rcut_ = simParams_->getCutoffRadius();
995	>	if (simParams_->haveSwitchingRadius()) {
996	>	rsw_  = simParams_->getSwitchingRadius();
997	>	} else {
998	>	if (fInfo_.SIM_uses_Charges |
999	>	fInfo_.SIM_uses_Dipoles |
1000	>	fInfo_.SIM_uses_RF) {
1001	>
1002	>	rsw_ = 0.85 * rcut_;
1003	>	sprintf(painCave.errMsg,
1004	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
1005	>	"\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
1006	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1007	>	painCave.isFatal = 0;
1008	>	simError();
1009	>	} else {
1010	>	rsw_ = rcut_;
1011	>	sprintf(painCave.errMsg,
1012	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
1013	>	"\tOOPSE will use the same value as the cutoffRadius.\n"
1014	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1015	>	painCave.isFatal = 0;
1016	>	simError();
1017	>	}
1018	>	}
1019
1020	<	void SimInfo::getCutoff(double& rcut, double& rsw) {
1021	<
1022	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1020	>	if (simParams_->haveElectrostaticSummationMethod()) {
1021	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1022	>	toUpper(myMethod);
1023
1024	<	if (!simParams_->haveRcut()){
1025	<	sprintf(painCave.errMsg,
1024	>	if (myMethod == "SHIFTED_POTENTIAL") {
1025	>	ljsp_ = true;
1026	>	} else if (myMethod == "SHIFTED_FORCE") {
1027	>	ljsf_ = true;
1028	>	}
1029	>	}
1030	>	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1031	>
1032	>	} else {
1033	>
1034	>	// For electrostatic atoms, we'll assume a large safe value:
1035	>	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1036	>	sprintf(painCave.errMsg,
1037		"SimCreator Warning: No value was set for the cutoffRadius.\n"
1038		"\tOOPSE will use a default value of 15.0 angstroms"
1039		"\tfor the cutoffRadius.\n");
1040	<	painCave.isFatal = 0;
1041	<	simError();
1042	<	rcut = 15.0;
1043	<	} else{
1044	<	rcut = simParams_->getRcut();
1040	>	painCave.isFatal = 0;
1041	>	simError();
1042	>	rcut_ = 15.0;
1043	>
1044	>	if (simParams_->haveElectrostaticSummationMethod()) {
1045	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1046	>	toUpper(myMethod);
1047	>
1048	>	// For the time being, we're tethering the LJ shifted behavior to the
1049	>	// electrostaticSummationMethod keyword options
1050	>	if (myMethod == "SHIFTED_POTENTIAL") {
1051	>	ljsp_ = true;
1052	>	} else if (myMethod == "SHIFTED_FORCE") {
1053	>	ljsf_ = true;
1054	>	}
1055	>	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1056	>	if (simParams_->haveSwitchingRadius()){
1057	>	sprintf(painCave.errMsg,
1058	>	"SimInfo Warning: A value was set for the switchingRadius\n"
1059	>	"\teven though the electrostaticSummationMethod was\n"
1060	>	"\tset to %s\n", myMethod.c_str());
1061	>	painCave.isFatal = 1;
1062	>	simError();
1063	>	}
1064	>	}
1065		}
1066	<
1067	<	if (!simParams_->haveRsw()){
1068	<	sprintf(painCave.errMsg,
1069	<	"SimCreator Warning: No value was set for switchingRadius.\n"
1070	<	"\tOOPSE will use a default value of\n"
1071	<	"\t0.95 * cutoffRadius for the switchingRadius\n");
1072	<	painCave.isFatal = 0;
1073	<	simError();
1074	<	rsw = 0.95 * rcut;
1075	<	} else{
1076	<	rsw = simParams_->getRsw();
1066	>
1067	>	if (simParams_->haveSwitchingRadius()){
1068	>	rsw_ = simParams_->getSwitchingRadius();
1069	>	} else {
1070	>	sprintf(painCave.errMsg,
1071	>	"SimCreator Warning: No value was set for switchingRadius.\n"
1072	>	"\tOOPSE will use a default value of\n"
1073	>	"\t0.85 * cutoffRadius for the switchingRadius\n");
1074	>	painCave.isFatal = 0;
1075	>	simError();
1076	>	rsw_ = 0.85 * rcut_;
1077		}
1078
1079	<	} else {
1080	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
1081	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
1079	>	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1080	>
1081	>	} else {
1082	>	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1083	>	// We'll punt and let fortran figure out the cutoffs later.
1084
1085	<	if (simParams_->haveRcut()) {
791	<	rcut = simParams_->getRcut();
792	<	} else {
793	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
794	<	rcut = calcMaxCutoffRadius();
795	<	}
1085	>	notifyFortranYouAreOnYourOwn();
1086
1087	<	if (simParams_->haveRsw()) {
1088	<	rsw  = simParams_->getRsw();
1087	>	}
1088	>	}
1089	>	}
1090	>
1091	>	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1092	>
1093	>	int errorOut;
1094	>	int esm =  NONE;
1095	>	int sm = UNDAMPED;
1096	>	RealType alphaVal;
1097	>	RealType dielectric;
1098	>
1099	>	errorOut = isError;
1100	>
1101	>	if (simParams_->haveElectrostaticSummationMethod()) {
1102	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1103	>	toUpper(myMethod);
1104	>	if (myMethod == "NONE") {
1105	>	esm = NONE;
1106	>	} else {
1107	>	if (myMethod == "SWITCHING_FUNCTION") {
1108	>	esm = SWITCHING_FUNCTION;
1109		} else {
1110	<	rsw = rcut;
1111	<	}
1110	>	if (myMethod == "SHIFTED_POTENTIAL") {
1111	>	esm = SHIFTED_POTENTIAL;
1112	>	} else {
1113	>	if (myMethod == "SHIFTED_FORCE") {
1114	>	esm = SHIFTED_FORCE;
1115	>	} else {
1116	>	if (myMethod == "REACTION_FIELD") {
1117	>	esm = REACTION_FIELD;
1118	>	dielectric = simParams_->getDielectric();
1119	>	if (!simParams_->haveDielectric()) {
1120	>	// throw warning
1121	>	sprintf( painCave.errMsg,
1122	>	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1123	>	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1124	>	painCave.isFatal = 0;
1125	>	simError();
1126	>	}
1127	>	} else {
1128	>	// throw error
1129	>	sprintf( painCave.errMsg,
1130	>	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1131	>	"\t(Input file specified %s .)\n"
1132	>	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1133	>	"\t\"shifted_potential\", \"shifted_force\", or \n"
1134	>	"\t\"reaction_field\".\n", myMethod.c_str() );
1135	>	painCave.isFatal = 1;
1136	>	simError();
1137	>	}
1138	>	}
1139	>	}
1140	>	}
1141	>	}
1142	>	}
1143
1144	+	if (simParams_->haveElectrostaticScreeningMethod()) {
1145	+	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1146	+	toUpper(myScreen);
1147	+	if (myScreen == "UNDAMPED") {
1148	+	sm = UNDAMPED;
1149	+	} else {
1150	+	if (myScreen == "DAMPED") {
1151	+	sm = DAMPED;
1152	+	if (!simParams_->haveDampingAlpha()) {
1153	+	// first set a cutoff dependent alpha value
1154	+	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1155	+	alphaVal = 0.5125 - rcut_* 0.025;
1156	+	// for values rcut > 20.5, alpha is zero
1157	+	if (alphaVal < 0) alphaVal = 0;
1158	+
1159	+	// throw warning
1160	+	sprintf( painCave.errMsg,
1161	+	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1162	+	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1163	+	painCave.isFatal = 0;
1164	+	simError();
1165	+	} else {
1166	+	alphaVal = simParams_->getDampingAlpha();
1167	+	}
1168	+
1169	+	} else {
1170	+	// throw error
1171	+	sprintf( painCave.errMsg,
1172	+	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1173	+	"\t(Input file specified %s .)\n"
1174	+	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1175	+	"or \"damped\".\n", myScreen.c_str() );
1176	+	painCave.isFatal = 1;
1177	+	simError();
1178	+	}
1179	+	}
1180		}
1181	<	}
1181	>
1182	>	// let's pass some summation method variables to fortran
1183	>	setElectrostaticSummationMethod( &esm );
1184	>	setFortranElectrostaticMethod( &esm );
1185	>	setScreeningMethod( &sm );
1186	>	setDampingAlpha( &alphaVal );
1187	>	setReactionFieldDielectric( &dielectric );
1188	>	initFortranFF( &errorOut );
1189	>	}
1190
1191	<	void SimInfo::setupCutoff() {
1192	<	getCutoff(rcut_, rsw_);
808	<	double rnblist = rcut_ + 1; // skin of neighbor list
1191	>	void SimInfo::setupSwitchingFunction() {
1192	>	int ft = CUBIC;
1193
1194	<	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
1195	<	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist);
1196	<	}
1194	>	if (simParams_->haveSwitchingFunctionType()) {
1195	>	std::string funcType = simParams_->getSwitchingFunctionType();
1196	>	toUpper(funcType);
1197	>	if (funcType == "CUBIC") {
1198	>	ft = CUBIC;
1199	>	} else {
1200	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1201	>	ft = FIFTH_ORDER_POLY;
1202	>	} else {
1203	>	// throw error
1204	>	sprintf( painCave.errMsg,
1205	>	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1206	>	painCave.isFatal = 1;
1207	>	simError();
1208	>	}
1209	>	}
1210	>	}
1211
1212	<	void SimInfo::addProperty(GenericData* genData) {
1213	<	properties_.addProperty(genData);
816	<	}
1212	>	// send switching function notification to switcheroo
1213	>	setFunctionType(&ft);
1214
1215	<	void SimInfo::removeProperty(const std::string& propName) {
1215	>	}
1216	>
1217	>	void SimInfo::setupAccumulateBoxDipole() {
1218	>
1219	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1220	>	if ( simParams_->haveAccumulateBoxDipole() )
1221	>	if ( simParams_->getAccumulateBoxDipole() ) {
1222	>	setAccumulateBoxDipole();
1223	>	calcBoxDipole_ = true;
1224	>	}
1225	>
1226	>	}
1227	>
1228	>	void SimInfo::addProperty(GenericData* genData) {
1229	>	properties_.addProperty(genData);
1230	>	}
1231	>
1232	>	void SimInfo::removeProperty(const std::string& propName) {
1233		properties_.removeProperty(propName);
1234	<	}
1234	>	}
1235
1236	<	void SimInfo::clearProperties() {
1236	>	void SimInfo::clearProperties() {
1237		properties_.clearProperties();
1238	<	}
1238	>	}
1239
1240	<	std::vector<std::string> SimInfo::getPropertyNames() {
1240	>	std::vector<std::string> SimInfo::getPropertyNames() {
1241		return properties_.getPropertyNames();
1242	<	}
1242	>	}
1243
1244	<	std::vector<GenericData*> SimInfo::getProperties() {
1244	>	std::vector<GenericData*> SimInfo::getProperties() {
1245		return properties_.getProperties();
1246	<	}
1246	>	}
1247
1248	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1248	>	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1249		return properties_.getPropertyByName(propName);
1250	<	}
1250	>	}
1251
1252	<	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1253	<	//if (sman_ == sman_) {
1254	<	//    return;
1255	<	//}
1256	<
843	<	//delete sman_;
1252	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1253	>	if (sman_ == sman) {
1254	>	return;
1255	>	}
1256	>	delete sman_;
1257		sman_ = sman;
1258
1259		Molecule* mol;
#	Line 852 | Line 1265 | void SimInfo::setSnapshotManager(SnapshotManager* sman
1265
1266		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1267
1268	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1269	<	atom->setSnapshotManager(sman_);
1270	<	}
1268	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1269	>	atom->setSnapshotManager(sman_);
1270	>	}
1271
1272	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1273	<	rb->setSnapshotManager(sman_);
1274	<	}
1272	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1273	>	rb->setSnapshotManager(sman_);
1274	>	}
1275		}
1276
1277	<	}
1277	>	}
1278
1279	<	Vector3d SimInfo::getComVel(){
1279	>	Vector3d SimInfo::getComVel(){
1280		SimInfo::MoleculeIterator i;
1281		Molecule* mol;
1282
1283		Vector3d comVel(0.0);
1284	<	double totalMass = 0.0;
1284	>	RealType totalMass = 0.0;
1285
1286
1287		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1288	<	double mass = mol->getMass();
1289	<	totalMass += mass;
1290	<	comVel += mass * mol->getComVel();
1288	>	RealType mass = mol->getMass();
1289	>	totalMass += mass;
1290	>	comVel += mass * mol->getComVel();
1291		}
1292
1293		#ifdef IS_MPI
1294	<	double tmpMass = totalMass;
1294	>	RealType tmpMass = totalMass;
1295		Vector3d tmpComVel(comVel);
1296	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1297	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1296	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1297	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1298		#endif
1299
1300		comVel /= totalMass;
1301
1302		return comVel;
1303	<	}
1303	>	}
1304
1305	<	Vector3d SimInfo::getCom(){
1305	>	Vector3d SimInfo::getCom(){
1306		SimInfo::MoleculeIterator i;
1307		Molecule* mol;
1308
1309		Vector3d com(0.0);
1310	<	double totalMass = 0.0;
1310	>	RealType totalMass = 0.0;
1311
1312		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1313	<	double mass = mol->getMass();
1314	<	totalMass += mass;
1315	<	com += mass * mol->getCom();
1313	>	RealType mass = mol->getMass();
1314	>	totalMass += mass;
1315	>	com += mass * mol->getCom();
1316		}
1317
1318		#ifdef IS_MPI
1319	<	double tmpMass = totalMass;
1319	>	RealType tmpMass = totalMass;
1320		Vector3d tmpCom(com);
1321	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1322	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1321	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1322	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1323		#endif
1324
1325		com /= totalMass;
1326
1327		return com;
1328
1329	<	}
1329	>	}
1330
1331	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1331	>	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1332
1333		return o;
1334	<	}
1334	>	}
1335	>
1336	>
1337	>	/*
1338	>	Returns center of mass and center of mass velocity in one function call.
1339	>	*/
1340	>
1341	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1342	>	SimInfo::MoleculeIterator i;
1343	>	Molecule* mol;
1344	>
1345	>
1346	>	RealType totalMass = 0.0;
1347	>
1348
1349	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1350	+	RealType mass = mol->getMass();
1351	+	totalMass += mass;
1352	+	com += mass * mol->getCom();
1353	+	comVel += mass * mol->getComVel();
1354	+	}
1355	+
1356	+	#ifdef IS_MPI
1357	+	RealType tmpMass = totalMass;
1358	+	Vector3d tmpCom(com);
1359	+	Vector3d tmpComVel(comVel);
1360	+	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1361	+	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1362	+	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1363	+	#endif
1364	+
1365	+	com /= totalMass;
1366	+	comVel /= totalMass;
1367	+	}
1368	+
1369	+	/*
1370	+	Return intertia tensor for entire system and angular momentum Vector.
1371	+
1372	+
1373	+	[  Ixx -Ixy  -Ixz ]
1374	+	J =| -Iyx  Iyy  -Iyz |
1375	+	[ -Izx -Iyz   Izz ]
1376	+	*/
1377	+
1378	+	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1379	+
1380	+
1381	+	RealType xx = 0.0;
1382	+	RealType yy = 0.0;
1383	+	RealType zz = 0.0;
1384	+	RealType xy = 0.0;
1385	+	RealType xz = 0.0;
1386	+	RealType yz = 0.0;
1387	+	Vector3d com(0.0);
1388	+	Vector3d comVel(0.0);
1389	+
1390	+	getComAll(com, comVel);
1391	+
1392	+	SimInfo::MoleculeIterator i;
1393	+	Molecule* mol;
1394	+
1395	+	Vector3d thisq(0.0);
1396	+	Vector3d thisv(0.0);
1397	+
1398	+	RealType thisMass = 0.0;
1399	+
1400	+
1401	+
1402	+
1403	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1404	+
1405	+	thisq = mol->getCom()-com;
1406	+	thisv = mol->getComVel()-comVel;
1407	+	thisMass = mol->getMass();
1408	+	// Compute moment of intertia coefficients.
1409	+	xx += thisq[0]*thisq[0]*thisMass;
1410	+	yy += thisq[1]*thisq[1]*thisMass;
1411	+	zz += thisq[2]*thisq[2]*thisMass;
1412	+
1413	+	// compute products of intertia
1414	+	xy += thisq[0]*thisq[1]*thisMass;
1415	+	xz += thisq[0]*thisq[2]*thisMass;
1416	+	yz += thisq[1]*thisq[2]*thisMass;
1417	+
1418	+	angularMomentum += cross( thisq, thisv ) * thisMass;
1419	+
1420	+	}
1421	+
1422	+
1423	+	inertiaTensor(0,0) = yy + zz;
1424	+	inertiaTensor(0,1) = -xy;
1425	+	inertiaTensor(0,2) = -xz;
1426	+	inertiaTensor(1,0) = -xy;
1427	+	inertiaTensor(1,1) = xx + zz;
1428	+	inertiaTensor(1,2) = -yz;
1429	+	inertiaTensor(2,0) = -xz;
1430	+	inertiaTensor(2,1) = -yz;
1431	+	inertiaTensor(2,2) = xx + yy;
1432	+
1433	+	#ifdef IS_MPI
1434	+	Mat3x3d tmpI(inertiaTensor);
1435	+	Vector3d tmpAngMom;
1436	+	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1437	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1438	+	#endif
1439	+
1440	+	return;
1441	+	}
1442	+
1443	+	//Returns the angular momentum of the system
1444	+	Vector3d SimInfo::getAngularMomentum(){
1445	+
1446	+	Vector3d com(0.0);
1447	+	Vector3d comVel(0.0);
1448	+	Vector3d angularMomentum(0.0);
1449	+
1450	+	getComAll(com,comVel);
1451	+
1452	+	SimInfo::MoleculeIterator i;
1453	+	Molecule* mol;
1454	+
1455	+	Vector3d thisr(0.0);
1456	+	Vector3d thisp(0.0);
1457	+
1458	+	RealType thisMass;
1459	+
1460	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1461	+	thisMass = mol->getMass();
1462	+	thisr = mol->getCom()-com;
1463	+	thisp = (mol->getComVel()-comVel)*thisMass;
1464	+
1465	+	angularMomentum += cross( thisr, thisp );
1466	+
1467	+	}
1468	+
1469	+	#ifdef IS_MPI
1470	+	Vector3d tmpAngMom;
1471	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1472	+	#endif
1473	+
1474	+	return angularMomentum;
1475	+	}
1476	+
1477	+	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1478	+	return IOIndexToIntegrableObject.at(index);
1479	+	}
1480	+
1481	+	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1482	+	IOIndexToIntegrableObject= v;
1483	+	}
1484	+
1485	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1486	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1487	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1488	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1489	+	*/
1490	+	void SimInfo::getGyrationalVolume(RealType &volume){
1491	+	Mat3x3d intTensor;
1492	+	RealType det;
1493	+	Vector3d dummyAngMom;
1494	+	RealType sysconstants;
1495	+	RealType geomCnst;
1496	+
1497	+	geomCnst = 3.0/2.0;
1498	+	/* Get the inertial tensor and angular momentum for free*/
1499	+	getInertiaTensor(intTensor,dummyAngMom);
1500	+
1501	+	det = intTensor.determinant();
1502	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1503	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1504	+	return;
1505	+	}
1506	+
1507	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1508	+	Mat3x3d intTensor;
1509	+	Vector3d dummyAngMom;
1510	+	RealType sysconstants;
1511	+	RealType geomCnst;
1512	+
1513	+	geomCnst = 3.0/2.0;
1514	+	/* Get the inertial tensor and angular momentum for free*/
1515	+	getInertiaTensor(intTensor,dummyAngMom);
1516	+
1517	+	detI = intTensor.determinant();
1518	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1519	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1520	+	return;
1521	+	}
1522	+	/*
1523	+	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1524	+	assert( v.size() == nAtoms_ + nRigidBodies_);
1525	+	sdByGlobalIndex_ = v;
1526	+	}
1527	+
1528	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1529	+	//assert(index < nAtoms_ + nRigidBodies_);
1530	+	return sdByGlobalIndex_.at(index);
1531	+	}
1532	+	*/
1533		}//end namespace oopse
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