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

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 326 by tim, Sun Feb 13 20:05:42 2005 UTC vs.
Revision 1277 by gezelter, Mon Jul 14 12:35:58 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), selectMan_(NULL) {
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), nInversions_(0),
94	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
95	>	nConstraints_(0), sman_(NULL), fortranInitialized_(false),
96	>	calcBoxDipole_(false), 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;
110	<	nMolWithSameStamp = i->second;
98	>
99	>	MoleculeStamp* molStamp;
100	>	int nMolWithSameStamp;
101	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
102	>	int nGroups = 0;      //total cutoff groups defined in meta-data file
103	>	CutoffGroupStamp* cgStamp;
104	>	RigidBodyStamp* rbStamp;
105	>	int nRigidAtoms = 0;
106	>
107	>	std::vector<Component*> components = simParams->getComponents();
108	>
109	>	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
110	>	molStamp = (*i)->getMoleculeStamp();
111	>	nMolWithSameStamp = (*i)->getNMol();
112
113		addMoleculeStamp(molStamp, nMolWithSameStamp);
114
115		//calculate atoms in molecules
116		nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
117
97	–
118		//calculate atoms in cutoff groups
119		int nAtomsInGroups = 0;
120		int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
121
122		for (int j=0; j < nCutoffGroupsInStamp; j++) {
123	<	cgStamp = molStamp->getCutoffGroup(j);
124	<	nAtomsInGroups += cgStamp->getNMembers();
123	>	cgStamp = molStamp->getCutoffGroupStamp(j);
124	>	nAtomsInGroups += cgStamp->getNMembers();
125		}
126
127		nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
128	+
129		nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
130
131		//calculate atoms in rigid bodies
#	Line 112 | Line 133 | SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*,
133		int nRigidBodiesInStamp = molStamp->getNRigidBodies();
134
135		for (int j=0; j < nRigidBodiesInStamp; j++) {
136	<	rbStamp = molStamp->getRigidBody(j);
137	<	nAtomsInRigidBodies += rbStamp->getNMembers();
136	>	rbStamp = molStamp->getRigidBodyStamp(j);
137	>	nAtomsInRigidBodies += rbStamp->getNMembers();
138		}
139
140		nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
141		nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
142
143	<	}
143	>	}
144
145	<	//every free atom (atom does not belong to cutoff groups) is a cutoff group
146	<	//therefore the total number of cutoff groups in the system is equal to
147	<	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
148	<	//file plus the number of cutoff groups defined in meta-data file
149	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
145	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
146	>	//group therefore the total number of cutoff groups in the system is
147	>	//equal to the total number of atoms minus number of atoms belong to
148	>	//cutoff group defined in meta-data file plus the number of cutoff
149	>	//groups defined in meta-data file
150	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
151
152	<	//every free atom (atom does not belong to rigid bodies) is an integrable object
153	<	//therefore the total number of  integrable objects in the system is equal to
154	<	//the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
155	<	//file plus the number of  rigid bodies defined in meta-data file
156	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
157	<
158	<	nGlobalMols_ = molStampIds_.size();
159	<
160	<	#ifdef IS_MPI
161	<	molToProcMap_.resize(nGlobalMols_);
162	<	#endif
141	<
142	<	selectMan_ = new SelectionManager(this);
143	<	selectMan_->selectAll();
144	<	}
145	<
146	<	SimInfo::~SimInfo() {
147	<	//MemoryUtils::deleteVectorOfPointer(molecules_);
152	>	//every free atom (atom does not belong to rigid bodies) is an
153	>	//integrable object therefore the total number of integrable objects
154	>	//in the system is equal to the total number of atoms minus number of
155	>	//atoms belong to rigid body defined in meta-data file plus the number
156	>	//of rigid bodies defined in meta-data file
157	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
158	>	+ nGlobalRigidBodies_;
159	>
160	>	nGlobalMols_ = molStampIds_.size();
161	>	molToProcMap_.resize(nGlobalMols_);
162	>	}
163
164	<	MemoryUtils::deleteVectorOfPointer(moleculeStamps_);
165	<
164	>	SimInfo::~SimInfo() {
165	>	std::map<int, Molecule*>::iterator i;
166	>	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
167	>	delete i->second;
168	>	}
169	>	molecules_.clear();
170	>
171		delete sman_;
172		delete simParams_;
173		delete forceField_;
174	<	delete selectMan_;
155	<	}
174	>	}
175
176	<	int SimInfo::getNGlobalConstraints() {
176	>	int SimInfo::getNGlobalConstraints() {
177		int nGlobalConstraints;
178		#ifdef IS_MPI
179		MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
#	Line 163 | Line 182 | int SimInfo::getNGlobalConstraints() {
182		nGlobalConstraints =  nConstraints_;
183		#endif
184		return nGlobalConstraints;
185	<	}
185	>	}
186
187	<	bool SimInfo::addMolecule(Molecule* mol) {
187	>	bool SimInfo::addMolecule(Molecule* mol) {
188		MoleculeIterator i;
189
190		i = molecules_.find(mol->getGlobalIndex());
191		if (i == molecules_.end() ) {
192
193	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
193	>	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
194
195	<	nAtoms_ += mol->getNAtoms();
196	<	nBonds_ += mol->getNBonds();
197	<	nBends_ += mol->getNBends();
198	<	nTorsions_ += mol->getNTorsions();
199	<	nRigidBodies_ += mol->getNRigidBodies();
200	<	nIntegrableObjects_ += mol->getNIntegrableObjects();
201	<	nCutoffGroups_ += mol->getNCutoffGroups();
202	<	nConstraints_ += mol->getNConstraintPairs();
195	>	nAtoms_ += mol->getNAtoms();
196	>	nBonds_ += mol->getNBonds();
197	>	nBends_ += mol->getNBends();
198	>	nTorsions_ += mol->getNTorsions();
199	>	nInversions_ += mol->getNInversions();
200	>	nRigidBodies_ += mol->getNRigidBodies();
201	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
202	>	nCutoffGroups_ += mol->getNCutoffGroups();
203	>	nConstraints_ += mol->getNConstraintPairs();
204
205	<	addExcludePairs(mol);
205	>	addExcludePairs(mol);
206
207	<	return true;
207	>	return true;
208		} else {
209	<	return false;
209	>	return false;
210		}
211	<	}
211	>	}
212
213	<	bool SimInfo::removeMolecule(Molecule* mol) {
213	>	bool SimInfo::removeMolecule(Molecule* mol) {
214		MoleculeIterator i;
215		i = molecules_.find(mol->getGlobalIndex());
216
217		if (i != molecules_.end() ) {
218
219	<	assert(mol == i->second);
219	>	assert(mol == i->second);
220
221	<	nAtoms_ -= mol->getNAtoms();
222	<	nBonds_ -= mol->getNBonds();
223	<	nBends_ -= mol->getNBends();
224	<	nTorsions_ -= mol->getNTorsions();
225	<	nRigidBodies_ -= mol->getNRigidBodies();
226	<	nIntegrableObjects_ -= mol->getNIntegrableObjects();
227	<	nCutoffGroups_ -= mol->getNCutoffGroups();
228	<	nConstraints_ -= mol->getNConstraintPairs();
221	>	nAtoms_ -= mol->getNAtoms();
222	>	nBonds_ -= mol->getNBonds();
223	>	nBends_ -= mol->getNBends();
224	>	nTorsions_ -= mol->getNTorsions();
225	>	nInversions_ -= mol->getNInversions();
226	>	nRigidBodies_ -= mol->getNRigidBodies();
227	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
228	>	nCutoffGroups_ -= mol->getNCutoffGroups();
229	>	nConstraints_ -= mol->getNConstraintPairs();
230
231	<	removeExcludePairs(mol);
232	<	molecules_.erase(mol->getGlobalIndex());
231	>	removeExcludePairs(mol);
232	>	molecules_.erase(mol->getGlobalIndex());
233
234	<	delete mol;
234	>	delete mol;
235
236	<	return true;
236	>	return true;
237		} else {
238	<	return false;
238	>	return false;
239		}
240
241
242	<	}
242	>	}
243
244
245	<	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
245	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
246		i = molecules_.begin();
247		return i == molecules_.end() ? NULL : i->second;
248	<	}
248	>	}
249
250	<	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
250	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
251		++i;
252		return i == molecules_.end() ? NULL : i->second;
253	<	}
253	>	}
254
255
256	<	void SimInfo::calcNdf() {
256	>	void SimInfo::calcNdf() {
257		int ndf_local;
258		MoleculeIterator i;
259		std::vector<StuntDouble*>::iterator j;
#	Line 242 | Line 263 | void SimInfo::calcNdf() {
263		ndf_local = 0;
264
265		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
266	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
267	<	integrableObject = mol->nextIntegrableObject(j)) {
247	<
248	<	ndf_local += 3;
266	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
267	>	integrableObject = mol->nextIntegrableObject(j)) {
268
269	<	if (integrableObject->isDirectional()) {
270	<	if (integrableObject->isLinear()) {
271	<	ndf_local += 2;
272	<	} else {
273	<	ndf_local += 3;
274	<	}
275	<	}
269	>	ndf_local += 3;
270	>
271	>	if (integrableObject->isDirectional()) {
272	>	if (integrableObject->isLinear()) {
273	>	ndf_local += 2;
274	>	} else {
275	>	ndf_local += 3;
276	>	}
277	>	}
278
279	<	}//end for (integrableObject)
280	<	}// end for (mol)
279	>	}
280	>	}
281
282		// n_constraints is local, so subtract them on each processor
283		ndf_local -= nConstraints_;
#	Line 271 | Line 292 | void SimInfo::calcNdf() {
292		// entire system:
293		ndf_ = ndf_ - 3 - nZconstraint_;
294
295	<	}
295	>	}
296
297	<	void SimInfo::calcNdfRaw() {
297	>	int SimInfo::getFdf() {
298	>	#ifdef IS_MPI
299	>	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
300	>	#else
301	>	fdf_ = fdf_local;
302	>	#endif
303	>	return fdf_;
304	>	}
305	>
306	>	void SimInfo::calcNdfRaw() {
307		int ndfRaw_local;
308
309		MoleculeIterator i;
#	Line 285 | Line 315 | void SimInfo::calcNdfRaw() {
315		ndfRaw_local = 0;
316
317		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
318	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
319	<	integrableObject = mol->nextIntegrableObject(j)) {
318	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
319	>	integrableObject = mol->nextIntegrableObject(j)) {
320
321	<	ndfRaw_local += 3;
321	>	ndfRaw_local += 3;
322
323	<	if (integrableObject->isDirectional()) {
324	<	if (integrableObject->isLinear()) {
325	<	ndfRaw_local += 2;
326	<	} else {
327	<	ndfRaw_local += 3;
328	<	}
329	<	}
323	>	if (integrableObject->isDirectional()) {
324	>	if (integrableObject->isLinear()) {
325	>	ndfRaw_local += 2;
326	>	} else {
327	>	ndfRaw_local += 3;
328	>	}
329	>	}
330
331	<	}
331	>	}
332		}
333
334		#ifdef IS_MPI
#	Line 306 | Line 336 | void SimInfo::calcNdfRaw() {
336		#else
337		ndfRaw_ = ndfRaw_local;
338		#endif
339	<	}
339	>	}
340
341	<	void SimInfo::calcNdfTrans() {
341	>	void SimInfo::calcNdfTrans() {
342		int ndfTrans_local;
343
344		ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
#	Line 322 | Line 352 | void SimInfo::calcNdfTrans() {
352
353		ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
354
355	<	}
355	>	}
356
357	<	void SimInfo::addExcludePairs(Molecule* mol) {
357	>	void SimInfo::addExcludePairs(Molecule* mol) {
358		std::vector<Bond*>::iterator bondIter;
359		std::vector<Bend*>::iterator bendIter;
360		std::vector<Torsion*>::iterator torsionIter;
361	+	std::vector<Inversion*>::iterator inversionIter;
362		Bond* bond;
363		Bend* bend;
364		Torsion* torsion;
365	+	Inversion* inversion;
366		int a;
367		int b;
368		int c;
369		int d;
370	+
371	+	std::map<int, std::set<int> > atomGroups;
372	+
373	+	Molecule::RigidBodyIterator rbIter;
374	+	RigidBody* rb;
375	+	Molecule::IntegrableObjectIterator ii;
376	+	StuntDouble* integrableObject;
377
378	+	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
379	+	integrableObject = mol->nextIntegrableObject(ii)) {
380	+
381	+	if (integrableObject->isRigidBody()) {
382	+	rb = static_cast<RigidBody*>(integrableObject);
383	+	std::vector<Atom*> atoms = rb->getAtoms();
384	+	std::set<int> rigidAtoms;
385	+	for (int i = 0; i < atoms.size(); ++i) {
386	+	rigidAtoms.insert(atoms[i]->getGlobalIndex());
387	+	}
388	+	for (int i = 0; i < atoms.size(); ++i) {
389	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
390	+	}
391	+	} else {
392	+	std::set<int> oneAtomSet;
393	+	oneAtomSet.insert(integrableObject->getGlobalIndex());
394	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
395	+	}
396	+	}
397	+
398	+
399	+
400		for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
401	<	a = bond->getAtomA()->getGlobalIndex();
402	<	b = bond->getAtomB()->getGlobalIndex();
403	<	exclude_.addPair(a, b);
401	>	a = bond->getAtomA()->getGlobalIndex();
402	>	b = bond->getAtomB()->getGlobalIndex();
403	>	exclude_.addPair(a, b);
404		}
405
406		for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
407	<	a = bend->getAtomA()->getGlobalIndex();
408	<	b = bend->getAtomB()->getGlobalIndex();
409	<	c = bend->getAtomC()->getGlobalIndex();
407	>	a = bend->getAtomA()->getGlobalIndex();
408	>	b = bend->getAtomB()->getGlobalIndex();
409	>	c = bend->getAtomC()->getGlobalIndex();
410	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
411	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
412	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
413
414	<	exclude_.addPair(a, b);
415	<	exclude_.addPair(a, c);
416	<	exclude_.addPair(b, c);
414	>	exclude_.addPairs(rigidSetA, rigidSetB);
415	>	exclude_.addPairs(rigidSetA, rigidSetC);
416	>	exclude_.addPairs(rigidSetB, rigidSetC);
417	>
418	>	//exclude_.addPair(a, b);
419	>	//exclude_.addPair(a, c);
420	>	//exclude_.addPair(b, c);
421		}
422
423		for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
424	<	a = torsion->getAtomA()->getGlobalIndex();
425	<	b = torsion->getAtomB()->getGlobalIndex();
426	<	c = torsion->getAtomC()->getGlobalIndex();
427	<	d = torsion->getAtomD()->getGlobalIndex();
424	>	a = torsion->getAtomA()->getGlobalIndex();
425	>	b = torsion->getAtomB()->getGlobalIndex();
426	>	c = torsion->getAtomC()->getGlobalIndex();
427	>	d = torsion->getAtomD()->getGlobalIndex();
428	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
429	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
430	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
431	>	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
432
433	<	exclude_.addPair(a, b);
434	<	exclude_.addPair(a, c);
435	<	exclude_.addPair(a, d);
436	<	exclude_.addPair(b, c);
437	<	exclude_.addPair(b, d);
438	<	exclude_.addPair(c, d);
433	>	exclude_.addPairs(rigidSetA, rigidSetB);
434	>	exclude_.addPairs(rigidSetA, rigidSetC);
435	>	exclude_.addPairs(rigidSetA, rigidSetD);
436	>	exclude_.addPairs(rigidSetB, rigidSetC);
437	>	exclude_.addPairs(rigidSetB, rigidSetD);
438	>	exclude_.addPairs(rigidSetC, rigidSetD);
439	>
440	>	/*
441	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
442	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
443	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
444	>	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
445	>	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
446	>	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
447	>
448	>
449	>	exclude_.addPair(a, b);
450	>	exclude_.addPair(a, c);
451	>	exclude_.addPair(a, d);
452	>	exclude_.addPair(b, c);
453	>	exclude_.addPair(b, d);
454	>	exclude_.addPair(c, d);
455	>	*/
456		}
457
458	<
459	<	}
458	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
459	>	inversion = mol->nextInversion(inversionIter)) {
460	>	a = inversion->getAtomA()->getGlobalIndex();
461	>	b = inversion->getAtomB()->getGlobalIndex();
462	>	c = inversion->getAtomC()->getGlobalIndex();
463	>	d = inversion->getAtomD()->getGlobalIndex();
464	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
465	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
466	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
467	>	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
468
469	<	void SimInfo::removeExcludePairs(Molecule* mol) {
469	>	exclude_.addPairs(rigidSetA, rigidSetB);
470	>	exclude_.addPairs(rigidSetA, rigidSetC);
471	>	exclude_.addPairs(rigidSetA, rigidSetD);
472	>	exclude_.addPairs(rigidSetB, rigidSetC);
473	>	exclude_.addPairs(rigidSetB, rigidSetD);
474	>	exclude_.addPairs(rigidSetC, rigidSetD);
475	>
476	>	/*
477	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
478	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
479	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
480	>	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
481	>	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
482	>	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
483	>
484	>
485	>	exclude_.addPair(a, b);
486	>	exclude_.addPair(a, c);
487	>	exclude_.addPair(a, d);
488	>	exclude_.addPair(b, c);
489	>	exclude_.addPair(b, d);
490	>	exclude_.addPair(c, d);
491	>	*/
492	>	}
493	>
494	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
495	>	std::vector<Atom*> atoms = rb->getAtoms();
496	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
497	>	for (int j = i + 1; j < atoms.size(); ++j) {
498	>	a = atoms[i]->getGlobalIndex();
499	>	b = atoms[j]->getGlobalIndex();
500	>	exclude_.addPair(a, b);
501	>	}
502	>	}
503	>	}
504	>
505	>	}
506	>
507	>	void SimInfo::removeExcludePairs(Molecule* mol) {
508		std::vector<Bond*>::iterator bondIter;
509		std::vector<Bend*>::iterator bendIter;
510		std::vector<Torsion*>::iterator torsionIter;
511	+	std::vector<Inversion*>::iterator inversionIter;
512		Bond* bond;
513		Bend* bend;
514		Torsion* torsion;
515	+	Inversion* inversion;
516		int a;
517		int b;
518		int c;
519		int d;
520	+
521	+	std::map<int, std::set<int> > atomGroups;
522	+
523	+	Molecule::RigidBodyIterator rbIter;
524	+	RigidBody* rb;
525	+	Molecule::IntegrableObjectIterator ii;
526	+	StuntDouble* integrableObject;
527
528	+	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
529	+	integrableObject = mol->nextIntegrableObject(ii)) {
530	+
531	+	if (integrableObject->isRigidBody()) {
532	+	rb = static_cast<RigidBody*>(integrableObject);
533	+	std::vector<Atom*> atoms = rb->getAtoms();
534	+	std::set<int> rigidAtoms;
535	+	for (int i = 0; i < atoms.size(); ++i) {
536	+	rigidAtoms.insert(atoms[i]->getGlobalIndex());
537	+	}
538	+	for (int i = 0; i < atoms.size(); ++i) {
539	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
540	+	}
541	+	} else {
542	+	std::set<int> oneAtomSet;
543	+	oneAtomSet.insert(integrableObject->getGlobalIndex());
544	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
545	+	}
546	+	}
547	+
548	+
549		for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
550	<	a = bond->getAtomA()->getGlobalIndex();
551	<	b = bond->getAtomB()->getGlobalIndex();
552	<	exclude_.removePair(a, b);
550	>	a = bond->getAtomA()->getGlobalIndex();
551	>	b = bond->getAtomB()->getGlobalIndex();
552	>	exclude_.removePair(a, b);
553		}
554
555		for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
556	<	a = bend->getAtomA()->getGlobalIndex();
557	<	b = bend->getAtomB()->getGlobalIndex();
558	<	c = bend->getAtomC()->getGlobalIndex();
556	>	a = bend->getAtomA()->getGlobalIndex();
557	>	b = bend->getAtomB()->getGlobalIndex();
558	>	c = bend->getAtomC()->getGlobalIndex();
559
560	<	exclude_.removePair(a, b);
561	<	exclude_.removePair(a, c);
562	<	exclude_.removePair(b, c);
560	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
561	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
562	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
563	>
564	>	exclude_.removePairs(rigidSetA, rigidSetB);
565	>	exclude_.removePairs(rigidSetA, rigidSetC);
566	>	exclude_.removePairs(rigidSetB, rigidSetC);
567	>
568	>	//exclude_.removePair(a, b);
569	>	//exclude_.removePair(a, c);
570	>	//exclude_.removePair(b, c);
571		}
572
573		for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
574	<	a = torsion->getAtomA()->getGlobalIndex();
575	<	b = torsion->getAtomB()->getGlobalIndex();
576	<	c = torsion->getAtomC()->getGlobalIndex();
577	<	d = torsion->getAtomD()->getGlobalIndex();
574	>	a = torsion->getAtomA()->getGlobalIndex();
575	>	b = torsion->getAtomB()->getGlobalIndex();
576	>	c = torsion->getAtomC()->getGlobalIndex();
577	>	d = torsion->getAtomD()->getGlobalIndex();
578
579	<	exclude_.removePair(a, b);
580	<	exclude_.removePair(a, c);
581	<	exclude_.removePair(a, d);
582	<	exclude_.removePair(b, c);
583	<	exclude_.removePair(b, d);
584	<	exclude_.removePair(c, d);
579	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
580	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
581	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
582	>	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
583	>
584	>	exclude_.removePairs(rigidSetA, rigidSetB);
585	>	exclude_.removePairs(rigidSetA, rigidSetC);
586	>	exclude_.removePairs(rigidSetA, rigidSetD);
587	>	exclude_.removePairs(rigidSetB, rigidSetC);
588	>	exclude_.removePairs(rigidSetB, rigidSetD);
589	>	exclude_.removePairs(rigidSetC, rigidSetD);
590	>
591	>	/*
592	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
593	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
594	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
595	>	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
596	>	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
597	>	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
598	>
599	>
600	>	exclude_.removePair(a, b);
601	>	exclude_.removePair(a, c);
602	>	exclude_.removePair(a, d);
603	>	exclude_.removePair(b, c);
604	>	exclude_.removePair(b, d);
605	>	exclude_.removePair(c, d);
606	>	*/
607		}
608
609	<	}
609	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL; inversion = mol->nextInversion(inversionIter)) {
610	>	a = inversion->getAtomA()->getGlobalIndex();
611	>	b = inversion->getAtomB()->getGlobalIndex();
612	>	c = inversion->getAtomC()->getGlobalIndex();
613	>	d = inversion->getAtomD()->getGlobalIndex();
614
615	+	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
616	+	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
617	+	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
618	+	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
619
620	<	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
620	>	exclude_.removePairs(rigidSetA, rigidSetB);
621	>	exclude_.removePairs(rigidSetA, rigidSetC);
622	>	exclude_.removePairs(rigidSetA, rigidSetD);
623	>	exclude_.removePairs(rigidSetB, rigidSetC);
624	>	exclude_.removePairs(rigidSetB, rigidSetD);
625	>	exclude_.removePairs(rigidSetC, rigidSetD);
626	>
627	>	/*
628	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
629	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
630	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
631	>	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
632	>	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
633	>	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
634	>
635	>
636	>	exclude_.removePair(a, b);
637	>	exclude_.removePair(a, c);
638	>	exclude_.removePair(a, d);
639	>	exclude_.removePair(b, c);
640	>	exclude_.removePair(b, d);
641	>	exclude_.removePair(c, d);
642	>	*/
643	>	}
644	>
645	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
646	>	std::vector<Atom*> atoms = rb->getAtoms();
647	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
648	>	for (int j = i + 1; j < atoms.size(); ++j) {
649	>	a = atoms[i]->getGlobalIndex();
650	>	b = atoms[j]->getGlobalIndex();
651	>	exclude_.removePair(a, b);
652	>	}
653	>	}
654	>	}
655	>
656	>	}
657	>
658	>
659	>	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
660		int curStampId;
661
662		//index from 0
#	Line 422 | Line 664 | void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp
664
665		moleculeStamps_.push_back(molStamp);
666		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
667	<	}
667	>	}
668
669	<	void SimInfo::update() {
669	>	void SimInfo::update() {
670
671		setupSimType();
672
#	Line 437 | Line 679 | void SimInfo::update() {
679		//setup fortran force field
680		/** @deprecate */
681		int isError = 0;
440	–	initFortranFF( &fInfo_.SIM_uses_RF , &isError );
441	–	if(isError){
442	–	sprintf( painCave.errMsg,
443	–	"ForceField error: There was an error initializing the forceField in fortran.\n" );
444	–	painCave.isFatal = 1;
445	–	simError();
446	–	}
447	–
682
683		setupCutoff();
684	+
685	+	setupElectrostaticSummationMethod( isError );
686	+	setupSwitchingFunction();
687	+	setupAccumulateBoxDipole();
688
689	+	if(isError){
690	+	sprintf( painCave.errMsg,
691	+	"ForceField error: There was an error initializing the forceField in fortran.\n" );
692	+	painCave.isFatal = 1;
693	+	simError();
694	+	}
695	+
696		calcNdf();
697		calcNdfRaw();
698		calcNdfTrans();
699
700		fortranInitialized_ = true;
701	<	}
701	>	}
702
703	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
703	>	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
704		SimInfo::MoleculeIterator mi;
705		Molecule* mol;
706		Molecule::AtomIterator ai;
#	Line 464 | Line 709 | std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
709
710		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
711
712	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
713	<	atomTypes.insert(atom->getAtomType());
714	<	}
712	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
713	>	atomTypes.insert(atom->getAtomType());
714	>	}
715
716		}
717
718		return atomTypes;
719	<	}
719	>	}
720
721	<	void SimInfo::setupSimType() {
721	>	void SimInfo::setupSimType() {
722		std::set<AtomType*>::iterator i;
723		std::set<AtomType*> atomTypes;
724		atomTypes = getUniqueAtomTypes();
#	Line 481 | Line 726 | void SimInfo::setupSimType() {
726		int useLennardJones = 0;
727		int useElectrostatic = 0;
728		int useEAM = 0;
729	+	int useSC = 0;
730		int useCharge = 0;
731		int useDirectional = 0;
732		int useDipole = 0;
733		int useGayBerne = 0;
734		int useSticky = 0;
735	+	int useStickyPower = 0;
736		int useShape = 0;
737		int useFLARB = 0; //it is not in AtomType yet
738		int useDirectionalAtom = 0;
739		int useElectrostatics = 0;
740		//usePBC and useRF are from simParams
741	<	int usePBC = simParams_->getPBC();
742	<	int useRF = simParams_->getUseRF();
741	>	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
742	>	int useRF;
743	>	int useSF;
744	>	int useSP;
745	>	int useBoxDipole;
746
747	+	std::string myMethod;
748	+
749	+	// set the useRF logical
750	+	useRF = 0;
751	+	useSF = 0;
752	+	useSP = 0;
753	+
754	+
755	+	if (simParams_->haveElectrostaticSummationMethod()) {
756	+	std::string myMethod = simParams_->getElectrostaticSummationMethod();
757	+	toUpper(myMethod);
758	+	if (myMethod == "REACTION_FIELD"){
759	+	useRF = 1;
760	+	} else if (myMethod == "SHIFTED_FORCE"){
761	+	useSF = 1;
762	+	} else if (myMethod == "SHIFTED_POTENTIAL"){
763	+	useSP = 1;
764	+	}
765	+	}
766	+
767	+	if (simParams_->haveAccumulateBoxDipole())
768	+	if (simParams_->getAccumulateBoxDipole())
769	+	useBoxDipole = 1;
770	+
771	+	useAtomicVirial_ = simParams_->getUseAtomicVirial();
772	+
773		//loop over all of the atom types
774		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
775	<	useLennardJones |= (*i)->isLennardJones();
776	<	useElectrostatic |= (*i)->isElectrostatic();
777	<	useEAM |= (*i)->isEAM();
778	<	useCharge |= (*i)->isCharge();
779	<	useDirectional |= (*i)->isDirectional();
780	<	useDipole |= (*i)->isDipole();
781	<	useGayBerne |= (*i)->isGayBerne();
782	<	useSticky |= (*i)->isSticky();
783	<	useShape |= (*i)->isShape();
775	>	useLennardJones |= (*i)->isLennardJones();
776	>	useElectrostatic |= (*i)->isElectrostatic();
777	>	useEAM |= (*i)->isEAM();
778	>	useSC |= (*i)->isSC();
779	>	useCharge |= (*i)->isCharge();
780	>	useDirectional |= (*i)->isDirectional();
781	>	useDipole |= (*i)->isDipole();
782	>	useGayBerne |= (*i)->isGayBerne();
783	>	useSticky |= (*i)->isSticky();
784	>	useStickyPower |= (*i)->isStickyPower();
785	>	useShape |= (*i)->isShape();
786		}
787
788	<	if (useSticky || useDipole || useGayBerne || useShape) {
789	<	useDirectionalAtom = 1;
788	>	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
789	>	useDirectionalAtom = 1;
790		}
791
792		if (useCharge || useDipole) {
793	<	useElectrostatics = 1;
793	>	useElectrostatics = 1;
794		}
795
796		#ifdef IS_MPI
#	Line 539 | Line 817 | void SimInfo::setupSimType() {
817		temp = useSticky;
818		MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
819
820	+	temp = useStickyPower;
821	+	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
822	+
823		temp = useGayBerne;
824		MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
825
826		temp = useEAM;
827		MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
828
829	+	temp = useSC;
830	+	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
831	+
832		temp = useShape;
833		MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
834
#	Line 553 | Line 837 | void SimInfo::setupSimType() {
837
838		temp = useRF;
839		MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
840	<
840	>
841	>	temp = useSF;
842	>	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
843	>
844	>	temp = useSP;
845	>	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
846	>
847	>	temp = useBoxDipole;
848	>	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
849	>
850	>	temp = useAtomicVirial_;
851	>	MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
852	>
853		#endif
854
855		fInfo_.SIM_uses_PBC = usePBC;
#	Line 563 | Line 859 | void SimInfo::setupSimType() {
859		fInfo_.SIM_uses_Charges = useCharge;
860		fInfo_.SIM_uses_Dipoles = useDipole;
861		fInfo_.SIM_uses_Sticky = useSticky;
862	+	fInfo_.SIM_uses_StickyPower = useStickyPower;
863		fInfo_.SIM_uses_GayBerne = useGayBerne;
864		fInfo_.SIM_uses_EAM = useEAM;
865	+	fInfo_.SIM_uses_SC = useSC;
866		fInfo_.SIM_uses_Shapes = useShape;
867		fInfo_.SIM_uses_FLARB = useFLARB;
868		fInfo_.SIM_uses_RF = useRF;
869	+	fInfo_.SIM_uses_SF = useSF;
870	+	fInfo_.SIM_uses_SP = useSP;
871	+	fInfo_.SIM_uses_BoxDipole = useBoxDipole;
872	+	fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
873	+	}
874
875	<	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
573	<
574	<	if (simParams_->haveDielectric()) {
575	<	fInfo_.dielect = simParams_->getDielectric();
576	<	} else {
577	<	sprintf(painCave.errMsg,
578	<	"SimSetup Error: No Dielectric constant was set.\n"
579	<	"\tYou are trying to use Reaction Field without"
580	<	"\tsetting a dielectric constant!\n");
581	<	painCave.isFatal = 1;
582	<	simError();
583	<	}
584	<
585	<	} else {
586	<	fInfo_.dielect = 0.0;
587	<	}
588	<
589	<	}
590	<
591	<	void SimInfo::setupFortranSim() {
875	>	void SimInfo::setupFortranSim() {
876		int isError;
877		int nExclude;
878		std::vector<int> fortranGlobalGroupMembership;
#	Line 598 | Line 882 | void SimInfo::setupFortranSim() {
882
883		//globalGroupMembership_ is filled by SimCreator
884		for (int i = 0; i < nGlobalAtoms_; i++) {
885	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
885	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
886		}
887
888		//calculate mass ratio of cutoff group
889	<	std::vector<double> mfact;
889	>	std::vector<RealType> mfact;
890		SimInfo::MoleculeIterator mi;
891		Molecule* mol;
892		Molecule::CutoffGroupIterator ci;
893		CutoffGroup* cg;
894		Molecule::AtomIterator ai;
895		Atom* atom;
896	<	double totalMass;
896	>	RealType totalMass;
897
898		//to avoid memory reallocation, reserve enough space for mfact
899		mfact.reserve(getNCutoffGroups());
900
901		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
902	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
902	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
903
904	<	totalMass = cg->getMass();
905	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
906	<	mfact.push_back(atom->getMass()/totalMass);
907	<	}
904	>	totalMass = cg->getMass();
905	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
906	>	// Check for massless groups - set mfact to 1 if true
907	>	if (totalMass != 0)
908	>	mfact.push_back(atom->getMass()/totalMass);
909	>	else
910	>	mfact.push_back( 1.0 );
911	>	}
912
913	<	}
913	>	}
914		}
915
916		//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
#	Line 632 | Line 920 | void SimInfo::setupFortranSim() {
920		identArray.reserve(getNAtoms());
921
922		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
923	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
924	<	identArray.push_back(atom->getIdent());
925	<	}
923	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
924	>	identArray.push_back(atom->getIdent());
925	>	}
926		}
927
928		//fill molMembershipArray
929		//molMembershipArray is filled by SimCreator
930		std::vector<int> molMembershipArray(nGlobalAtoms_);
931		for (int i = 0; i < nGlobalAtoms_; i++) {
932	<	molMembershipArray[i] = globalMolMembership_[i] + 1;
932	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
933		}
934
935		//setup fortran simulation
648	–	//gloalExcludes and molMembershipArray should go away (They are never used)
649	–	//why the hell fortran need to know molecule?
650	–	//OOPSE = Object-Obfuscated Parallel Simulation Engine
936		int nGlobalExcludes = 0;
937		int* globalExcludes = NULL;
938		int* excludeList = exclude_.getExcludeList();
939	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
940	<	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
941	<	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
942	<
939	>	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
940	>	&nExclude, excludeList , &nGlobalExcludes, globalExcludes,
941	>	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
942	>	&fortranGlobalGroupMembership[0], &isError);
943	>
944		if( isError ){
945	<
946	<	sprintf( painCave.errMsg,
947	<	"There was an error setting the simulation information in fortran.\n" );
948	<	painCave.isFatal = 1;
949	<	painCave.severity = OOPSE_ERROR;
950	<	simError();
945	>
946	>	sprintf( painCave.errMsg,
947	>	"There was an error setting the simulation information in fortran.\n" );
948	>	painCave.isFatal = 1;
949	>	painCave.severity = OOPSE_ERROR;
950	>	simError();
951		}
952	<
953	<	#ifdef IS_MPI
952	>
953	>
954		sprintf( checkPointMsg,
955	<	"succesfully sent the simulation information to fortran.\n");
956	<	MPIcheckPoint();
957	<	#endif // is_mpi
958	<	}
955	>	"succesfully sent the simulation information to fortran.\n");
956	>
957	>	errorCheckPoint();
958	>
959	>	// Setup number of neighbors in neighbor list if present
960	>	if (simParams_->haveNeighborListNeighbors()) {
961	>	int nlistNeighbors = simParams_->getNeighborListNeighbors();
962	>	setNeighbors(&nlistNeighbors);
963	>	}
964	>
965
966	+	}
967
968	<	#ifdef IS_MPI
969	<	void SimInfo::setupFortranParallel() {
970	<
968	>
969	>	void SimInfo::setupFortranParallel() {
970	>	#ifdef IS_MPI
971		//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
972		std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
973		std::vector<int> localToGlobalCutoffGroupIndex;
#	Line 689 | Line 982 | void SimInfo::setupFortranParallel() {
982
983		for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
984
985	<	//local index(index in DataStorge) of atom is important
986	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
987	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
988	<	}
985	>	//local index(index in DataStorge) of atom is important
986	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
987	>	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
988	>	}
989
990	<	//local index of cutoff group is trivial, it only depends on the order of travesing
991	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
992	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
993	<	}
990	>	//local index of cutoff group is trivial, it only depends on the order of travesing
991	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
992	>	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
993	>	}
994
995		}
996
#	Line 717 | Line 1010 | void SimInfo::setupFortranParallel() {
1010		&localToGlobalCutoffGroupIndex[0], &isError);
1011
1012		if (isError) {
1013	<	sprintf(painCave.errMsg,
1014	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
1015	<	painCave.isFatal = 1;
1016	<	simError();
1013	>	sprintf(painCave.errMsg,
1014	>	"mpiRefresh errror: fortran didn't like something we gave it.\n");
1015	>	painCave.isFatal = 1;
1016	>	simError();
1017		}
1018
1019		sprintf(checkPointMsg, " mpiRefresh successful.\n");
1020	<	MPIcheckPoint();
1020	>	errorCheckPoint();
1021
729	–
730	–	}
731	–
1022		#endif
1023	+	}
1024
1025	<	double SimInfo::calcMaxCutoffRadius() {
1025	>	void SimInfo::setupCutoff() {
1026	>
1027	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
1028
1029	+	// Check the cutoff policy
1030	+	int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
1031
1032	<	std::set<AtomType*> atomTypes;
1033	<	std::set<AtomType*>::iterator i;
1034	<	std::vector<double> cutoffRadius;
1032	>	// Set LJ shifting bools to false
1033	>	ljsp_ = false;
1034	>	ljsf_ = false;
1035
1036	<	//get the unique atom types
1037	<	atomTypes = getUniqueAtomTypes();
1038	<
1039	<	//query the max cutoff radius among these atom types
1040	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
746	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
1036	>	std::string myPolicy;
1037	>	if (forceFieldOptions_.haveCutoffPolicy()){
1038	>	myPolicy = forceFieldOptions_.getCutoffPolicy();
1039	>	}else if (simParams_->haveCutoffPolicy()) {
1040	>	myPolicy = simParams_->getCutoffPolicy();
1041		}
1042
1043	<	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
1044	<	#ifdef IS_MPI
1045	<	//pick the max cutoff radius among the processors
1046	<	#endif
1043	>	if (!myPolicy.empty()){
1044	>	toUpper(myPolicy);
1045	>	if (myPolicy == "MIX") {
1046	>	cp = MIX_CUTOFF_POLICY;
1047	>	} else {
1048	>	if (myPolicy == "MAX") {
1049	>	cp = MAX_CUTOFF_POLICY;
1050	>	} else {
1051	>	if (myPolicy == "TRADITIONAL") {
1052	>	cp = TRADITIONAL_CUTOFF_POLICY;
1053	>	} else {
1054	>	// throw error
1055	>	sprintf( painCave.errMsg,
1056	>	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
1057	>	painCave.isFatal = 1;
1058	>	simError();
1059	>	}
1060	>	}
1061	>	}
1062	>	}
1063	>	notifyFortranCutoffPolicy(&cp);
1064
1065	<	return maxCutoffRadius;
1066	<	}
1065	>	// Check the Skin Thickness for neighborlists
1066	>	RealType skin;
1067	>	if (simParams_->haveSkinThickness()) {
1068	>	skin = simParams_->getSkinThickness();
1069	>	notifyFortranSkinThickness(&skin);
1070	>	}
1071	>
1072	>	// Check if the cutoff was set explicitly:
1073	>	if (simParams_->haveCutoffRadius()) {
1074	>	rcut_ = simParams_->getCutoffRadius();
1075	>	if (simParams_->haveSwitchingRadius()) {
1076	>	rsw_  = simParams_->getSwitchingRadius();
1077	>	} else {
1078	>	if (fInfo_.SIM_uses_Charges |
1079	>	fInfo_.SIM_uses_Dipoles |
1080	>	fInfo_.SIM_uses_RF) {
1081	>
1082	>	rsw_ = 0.85 * rcut_;
1083	>	sprintf(painCave.errMsg,
1084	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
1085	>	"\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
1086	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1087	>	painCave.isFatal = 0;
1088	>	simError();
1089	>	} else {
1090	>	rsw_ = rcut_;
1091	>	sprintf(painCave.errMsg,
1092	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
1093	>	"\tOOPSE will use the same value as the cutoffRadius.\n"
1094	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1095	>	painCave.isFatal = 0;
1096	>	simError();
1097	>	}
1098	>	}
1099
1100	<	void SimInfo::getCutoff(double& rcut, double& rsw) {
1101	<
1102	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1100	>	if (simParams_->haveElectrostaticSummationMethod()) {
1101	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1102	>	toUpper(myMethod);
1103
1104	<	if (!simParams_->haveRcut()){
1105	<	sprintf(painCave.errMsg,
1104	>	if (myMethod == "SHIFTED_POTENTIAL") {
1105	>	ljsp_ = true;
1106	>	} else if (myMethod == "SHIFTED_FORCE") {
1107	>	ljsf_ = true;
1108	>	}
1109	>	}
1110	>	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1111	>
1112	>	} else {
1113	>
1114	>	// For electrostatic atoms, we'll assume a large safe value:
1115	>	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1116	>	sprintf(painCave.errMsg,
1117		"SimCreator Warning: No value was set for the cutoffRadius.\n"
1118		"\tOOPSE will use a default value of 15.0 angstroms"
1119		"\tfor the cutoffRadius.\n");
1120	<	painCave.isFatal = 0;
1121	<	simError();
1122	<	rcut_ = 15.0;
1123	<	} else{
1124	<	rcut_ = simParams_->getRcut();
1120	>	painCave.isFatal = 0;
1121	>	simError();
1122	>	rcut_ = 15.0;
1123	>
1124	>	if (simParams_->haveElectrostaticSummationMethod()) {
1125	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1126	>	toUpper(myMethod);
1127	>
1128	>	// For the time being, we're tethering the LJ shifted behavior to the
1129	>	// electrostaticSummationMethod keyword options
1130	>	if (myMethod == "SHIFTED_POTENTIAL") {
1131	>	ljsp_ = true;
1132	>	} else if (myMethod == "SHIFTED_FORCE") {
1133	>	ljsf_ = true;
1134	>	}
1135	>	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1136	>	if (simParams_->haveSwitchingRadius()){
1137	>	sprintf(painCave.errMsg,
1138	>	"SimInfo Warning: A value was set for the switchingRadius\n"
1139	>	"\teven though the electrostaticSummationMethod was\n"
1140	>	"\tset to %s\n", myMethod.c_str());
1141	>	painCave.isFatal = 1;
1142	>	simError();
1143	>	}
1144	>	}
1145		}
1146	<
1147	<	if (!simParams_->haveRsw()){
1148	<	sprintf(painCave.errMsg,
1149	<	"SimCreator Warning: No value was set for switchingRadius.\n"
1150	<	"\tOOPSE will use a default value of\n"
1151	<	"\t0.95 * cutoffRadius for the switchingRadius\n");
1152	<	painCave.isFatal = 0;
1153	<	simError();
1154	<	rsw_ = 0.95 * rcut_;
1155	<	} else{
1156	<	rsw_ = simParams_->getRsw();
1146	>
1147	>	if (simParams_->haveSwitchingRadius()){
1148	>	rsw_ = simParams_->getSwitchingRadius();
1149	>	} else {
1150	>	sprintf(painCave.errMsg,
1151	>	"SimCreator Warning: No value was set for switchingRadius.\n"
1152	>	"\tOOPSE will use a default value of\n"
1153	>	"\t0.85 * cutoffRadius for the switchingRadius\n");
1154	>	painCave.isFatal = 0;
1155	>	simError();
1156	>	rsw_ = 0.85 * rcut_;
1157		}
1158
1159	<	} else {
1160	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
1161	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
1159	>	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1160	>
1161	>	} else {
1162	>	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1163	>	// We'll punt and let fortran figure out the cutoffs later.
1164
1165	<	if (simParams_->haveRcut()) {
790	<	rcut_ = simParams_->getRcut();
791	<	} else {
792	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
793	<	rcut_ = calcMaxCutoffRadius();
794	<	}
1165	>	notifyFortranYouAreOnYourOwn();
1166
1167	<	if (simParams_->haveRsw()) {
797	<	rsw_  = simParams_->getRsw();
798	<	} else {
799	<	rsw_ = rcut_;
800	<	}
801	<
1167	>	}
1168		}
1169	<	}
1169	>	}
1170
1171	<	void SimInfo::setupCutoff() {
1172	<	getCutoff(rcut_, rsw_);
1173	<	double rnblist = rcut_ + 1; // skin of neighbor list
1171	>	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1172	>
1173	>	int errorOut;
1174	>	int esm =  NONE;
1175	>	int sm = UNDAMPED;
1176	>	RealType alphaVal;
1177	>	RealType dielectric;
1178	>
1179	>	errorOut = isError;
1180
1181	<	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
1182	<	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist);
1183	<	}
1181	>	if (simParams_->haveElectrostaticSummationMethod()) {
1182	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1183	>	toUpper(myMethod);
1184	>	if (myMethod == "NONE") {
1185	>	esm = NONE;
1186	>	} else {
1187	>	if (myMethod == "SWITCHING_FUNCTION") {
1188	>	esm = SWITCHING_FUNCTION;
1189	>	} else {
1190	>	if (myMethod == "SHIFTED_POTENTIAL") {
1191	>	esm = SHIFTED_POTENTIAL;
1192	>	} else {
1193	>	if (myMethod == "SHIFTED_FORCE") {
1194	>	esm = SHIFTED_FORCE;
1195	>	} else {
1196	>	if (myMethod == "REACTION_FIELD") {
1197	>	esm = REACTION_FIELD;
1198	>	dielectric = simParams_->getDielectric();
1199	>	if (!simParams_->haveDielectric()) {
1200	>	// throw warning
1201	>	sprintf( painCave.errMsg,
1202	>	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1203	>	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1204	>	painCave.isFatal = 0;
1205	>	simError();
1206	>	}
1207	>	} else {
1208	>	// throw error
1209	>	sprintf( painCave.errMsg,
1210	>	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1211	>	"\t(Input file specified %s .)\n"
1212	>	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1213	>	"\t\"shifted_potential\", \"shifted_force\", or \n"
1214	>	"\t\"reaction_field\".\n", myMethod.c_str() );
1215	>	painCave.isFatal = 1;
1216	>	simError();
1217	>	}
1218	>	}
1219	>	}
1220	>	}
1221	>	}
1222	>	}
1223	>
1224	>	if (simParams_->haveElectrostaticScreeningMethod()) {
1225	>	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1226	>	toUpper(myScreen);
1227	>	if (myScreen == "UNDAMPED") {
1228	>	sm = UNDAMPED;
1229	>	} else {
1230	>	if (myScreen == "DAMPED") {
1231	>	sm = DAMPED;
1232	>	if (!simParams_->haveDampingAlpha()) {
1233	>	// first set a cutoff dependent alpha value
1234	>	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1235	>	alphaVal = 0.5125 - rcut_* 0.025;
1236	>	// for values rcut > 20.5, alpha is zero
1237	>	if (alphaVal < 0) alphaVal = 0;
1238
1239	<	void SimInfo::addProperty(GenericData* genData) {
1240	<	properties_.addProperty(genData);
1241	<	}
1242	<
1243	<	void SimInfo::removeProperty(const std::string& propName) {
1244	<	properties_.removeProperty(propName);
1245	<	}
1246	<
1247	<	void SimInfo::clearProperties() {
1248	<	properties_.clearProperties();
1249	<	}
1250	<
1251	<	std::vector<std::string> SimInfo::getPropertyNames() {
1252	<	return properties_.getPropertyNames();
1253	<	}
1254	<
1255	<	std::vector<GenericData*> SimInfo::getProperties() {
1256	<	return properties_.getProperties();
1257	<	}
1258	<
1259	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1260	<	return properties_.getPropertyByName(propName);
1261	<	}
1239	>	// throw warning
1240	>	sprintf( painCave.errMsg,
1241	>	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1242	>	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1243	>	painCave.isFatal = 0;
1244	>	simError();
1245	>	} else {
1246	>	alphaVal = simParams_->getDampingAlpha();
1247	>	}
1248	>
1249	>	} else {
1250	>	// throw error
1251	>	sprintf( painCave.errMsg,
1252	>	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1253	>	"\t(Input file specified %s .)\n"
1254	>	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1255	>	"or \"damped\".\n", myScreen.c_str() );
1256	>	painCave.isFatal = 1;
1257	>	simError();
1258	>	}
1259	>	}
1260	>	}
1261	>
1262	>	// let's pass some summation method variables to fortran
1263	>	setElectrostaticSummationMethod( &esm );
1264	>	setFortranElectrostaticMethod( &esm );
1265	>	setScreeningMethod( &sm );
1266	>	setDampingAlpha( &alphaVal );
1267	>	setReactionFieldDielectric( &dielectric );
1268	>	initFortranFF( &errorOut );
1269	>	}
1270
1271	<	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1271	>	void SimInfo::setupSwitchingFunction() {
1272	>	int ft = CUBIC;
1273	>
1274	>	if (simParams_->haveSwitchingFunctionType()) {
1275	>	std::string funcType = simParams_->getSwitchingFunctionType();
1276	>	toUpper(funcType);
1277	>	if (funcType == "CUBIC") {
1278	>	ft = CUBIC;
1279	>	} else {
1280	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1281	>	ft = FIFTH_ORDER_POLY;
1282	>	} else {
1283	>	// throw error
1284	>	sprintf( painCave.errMsg,
1285	>	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1286	>	painCave.isFatal = 1;
1287	>	simError();
1288	>	}
1289	>	}
1290	>	}
1291	>
1292	>	// send switching function notification to switcheroo
1293	>	setFunctionType(&ft);
1294	>
1295	>	}
1296	>
1297	>	void SimInfo::setupAccumulateBoxDipole() {
1298	>
1299	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1300	>	if ( simParams_->haveAccumulateBoxDipole() )
1301	>	if ( simParams_->getAccumulateBoxDipole() ) {
1302	>	setAccumulateBoxDipole();
1303	>	calcBoxDipole_ = true;
1304	>	}
1305	>
1306	>	}
1307	>
1308	>	void SimInfo::addProperty(GenericData* genData) {
1309	>	properties_.addProperty(genData);
1310	>	}
1311	>
1312	>	void SimInfo::removeProperty(const std::string& propName) {
1313	>	properties_.removeProperty(propName);
1314	>	}
1315	>
1316	>	void SimInfo::clearProperties() {
1317	>	properties_.clearProperties();
1318	>	}
1319	>
1320	>	std::vector<std::string> SimInfo::getPropertyNames() {
1321	>	return properties_.getPropertyNames();
1322	>	}
1323	>
1324	>	std::vector<GenericData*> SimInfo::getProperties() {
1325	>	return properties_.getProperties();
1326	>	}
1327	>
1328	>	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1329	>	return properties_.getPropertyByName(propName);
1330	>	}
1331	>
1332	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1333	>	if (sman_ == sman) {
1334	>	return;
1335	>	}
1336	>	delete sman_;
1337		sman_ = sman;
1338
1339		Molecule* mol;
#	Line 846 | Line 1345 | void SimInfo::setSnapshotManager(SnapshotManager* sman
1345
1346		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1347
1348	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1349	<	atom->setSnapshotManager(sman_);
1350	<	}
1348	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1349	>	atom->setSnapshotManager(sman_);
1350	>	}
1351
1352	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1353	<	rb->setSnapshotManager(sman_);
1354	<	}
1352	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1353	>	rb->setSnapshotManager(sman_);
1354	>	}
1355		}
1356
1357	<	}
1357	>	}
1358
1359	<	Vector3d SimInfo::getComVel(){
1359	>	Vector3d SimInfo::getComVel(){
1360		SimInfo::MoleculeIterator i;
1361		Molecule* mol;
1362
1363		Vector3d comVel(0.0);
1364	<	double totalMass = 0.0;
1364	>	RealType totalMass = 0.0;
1365
1366
1367		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1368	<	double mass = mol->getMass();
1369	<	totalMass += mass;
1370	<	comVel += mass * mol->getComVel();
1368	>	RealType mass = mol->getMass();
1369	>	totalMass += mass;
1370	>	comVel += mass * mol->getComVel();
1371		}
1372
1373		#ifdef IS_MPI
1374	<	double tmpMass = totalMass;
1374	>	RealType tmpMass = totalMass;
1375		Vector3d tmpComVel(comVel);
1376	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1377	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1376	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1377	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1378		#endif
1379
1380		comVel /= totalMass;
1381
1382		return comVel;
1383	<	}
1383	>	}
1384
1385	<	Vector3d SimInfo::getCom(){
1385	>	Vector3d SimInfo::getCom(){
1386		SimInfo::MoleculeIterator i;
1387		Molecule* mol;
1388
1389		Vector3d com(0.0);
1390	<	double totalMass = 0.0;
1390	>	RealType totalMass = 0.0;
1391
1392		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1393	<	double mass = mol->getMass();
1394	<	totalMass += mass;
1395	<	com += mass * mol->getCom();
1393	>	RealType mass = mol->getMass();
1394	>	totalMass += mass;
1395	>	com += mass * mol->getCom();
1396		}
1397
1398		#ifdef IS_MPI
1399	<	double tmpMass = totalMass;
1399	>	RealType tmpMass = totalMass;
1400		Vector3d tmpCom(com);
1401	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1402	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1401	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1402	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1403		#endif
1404
1405		com /= totalMass;
1406
1407		return com;
1408
1409	<	}
1409	>	}
1410
1411	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1411	>	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1412
1413		return o;
1414	<	}
1414	>	}
1415	>
1416	>
1417	>	/*
1418	>	Returns center of mass and center of mass velocity in one function call.
1419	>	*/
1420	>
1421	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1422	>	SimInfo::MoleculeIterator i;
1423	>	Molecule* mol;
1424	>
1425	>
1426	>	RealType totalMass = 0.0;
1427	>
1428
1429	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1430	+	RealType mass = mol->getMass();
1431	+	totalMass += mass;
1432	+	com += mass * mol->getCom();
1433	+	comVel += mass * mol->getComVel();
1434	+	}
1435	+
1436	+	#ifdef IS_MPI
1437	+	RealType tmpMass = totalMass;
1438	+	Vector3d tmpCom(com);
1439	+	Vector3d tmpComVel(comVel);
1440	+	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1441	+	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1442	+	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1443	+	#endif
1444	+
1445	+	com /= totalMass;
1446	+	comVel /= totalMass;
1447	+	}
1448	+
1449	+	/*
1450	+	Return intertia tensor for entire system and angular momentum Vector.
1451	+
1452	+
1453	+	[  Ixx -Ixy  -Ixz ]
1454	+	J =| -Iyx  Iyy  -Iyz |
1455	+	[ -Izx -Iyz   Izz ]
1456	+	*/
1457	+
1458	+	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1459	+
1460	+
1461	+	RealType xx = 0.0;
1462	+	RealType yy = 0.0;
1463	+	RealType zz = 0.0;
1464	+	RealType xy = 0.0;
1465	+	RealType xz = 0.0;
1466	+	RealType yz = 0.0;
1467	+	Vector3d com(0.0);
1468	+	Vector3d comVel(0.0);
1469	+
1470	+	getComAll(com, comVel);
1471	+
1472	+	SimInfo::MoleculeIterator i;
1473	+	Molecule* mol;
1474	+
1475	+	Vector3d thisq(0.0);
1476	+	Vector3d thisv(0.0);
1477	+
1478	+	RealType thisMass = 0.0;
1479	+
1480	+
1481	+
1482	+
1483	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1484	+
1485	+	thisq = mol->getCom()-com;
1486	+	thisv = mol->getComVel()-comVel;
1487	+	thisMass = mol->getMass();
1488	+	// Compute moment of intertia coefficients.
1489	+	xx += thisq[0]*thisq[0]*thisMass;
1490	+	yy += thisq[1]*thisq[1]*thisMass;
1491	+	zz += thisq[2]*thisq[2]*thisMass;
1492	+
1493	+	// compute products of intertia
1494	+	xy += thisq[0]*thisq[1]*thisMass;
1495	+	xz += thisq[0]*thisq[2]*thisMass;
1496	+	yz += thisq[1]*thisq[2]*thisMass;
1497	+
1498	+	angularMomentum += cross( thisq, thisv ) * thisMass;
1499	+
1500	+	}
1501	+
1502	+
1503	+	inertiaTensor(0,0) = yy + zz;
1504	+	inertiaTensor(0,1) = -xy;
1505	+	inertiaTensor(0,2) = -xz;
1506	+	inertiaTensor(1,0) = -xy;
1507	+	inertiaTensor(1,1) = xx + zz;
1508	+	inertiaTensor(1,2) = -yz;
1509	+	inertiaTensor(2,0) = -xz;
1510	+	inertiaTensor(2,1) = -yz;
1511	+	inertiaTensor(2,2) = xx + yy;
1512	+
1513	+	#ifdef IS_MPI
1514	+	Mat3x3d tmpI(inertiaTensor);
1515	+	Vector3d tmpAngMom;
1516	+	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1517	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1518	+	#endif
1519	+
1520	+	return;
1521	+	}
1522	+
1523	+	//Returns the angular momentum of the system
1524	+	Vector3d SimInfo::getAngularMomentum(){
1525	+
1526	+	Vector3d com(0.0);
1527	+	Vector3d comVel(0.0);
1528	+	Vector3d angularMomentum(0.0);
1529	+
1530	+	getComAll(com,comVel);
1531	+
1532	+	SimInfo::MoleculeIterator i;
1533	+	Molecule* mol;
1534	+
1535	+	Vector3d thisr(0.0);
1536	+	Vector3d thisp(0.0);
1537	+
1538	+	RealType thisMass;
1539	+
1540	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1541	+	thisMass = mol->getMass();
1542	+	thisr = mol->getCom()-com;
1543	+	thisp = (mol->getComVel()-comVel)*thisMass;
1544	+
1545	+	angularMomentum += cross( thisr, thisp );
1546	+
1547	+	}
1548	+
1549	+	#ifdef IS_MPI
1550	+	Vector3d tmpAngMom;
1551	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1552	+	#endif
1553	+
1554	+	return angularMomentum;
1555	+	}
1556	+
1557	+	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1558	+	return IOIndexToIntegrableObject.at(index);
1559	+	}
1560	+
1561	+	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1562	+	IOIndexToIntegrableObject= v;
1563	+	}
1564	+
1565	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1566	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1567	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1568	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1569	+	*/
1570	+	void SimInfo::getGyrationalVolume(RealType &volume){
1571	+	Mat3x3d intTensor;
1572	+	RealType det;
1573	+	Vector3d dummyAngMom;
1574	+	RealType sysconstants;
1575	+	RealType geomCnst;
1576	+
1577	+	geomCnst = 3.0/2.0;
1578	+	/* Get the inertial tensor and angular momentum for free*/
1579	+	getInertiaTensor(intTensor,dummyAngMom);
1580	+
1581	+	det = intTensor.determinant();
1582	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1583	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1584	+	return;
1585	+	}
1586	+
1587	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1588	+	Mat3x3d intTensor;
1589	+	Vector3d dummyAngMom;
1590	+	RealType sysconstants;
1591	+	RealType geomCnst;
1592	+
1593	+	geomCnst = 3.0/2.0;
1594	+	/* Get the inertial tensor and angular momentum for free*/
1595	+	getInertiaTensor(intTensor,dummyAngMom);
1596	+
1597	+	detI = intTensor.determinant();
1598	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1599	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1600	+	return;
1601	+	}
1602	+	/*
1603	+	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1604	+	assert( v.size() == nAtoms_ + nRigidBodies_);
1605	+	sdByGlobalIndex_ = v;
1606	+	}
1607	+
1608	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1609	+	//assert(index < nAtoms_ + nRigidBodies_);
1610	+	return sdByGlobalIndex_.at(index);
1611	+	}
1612	+	*/
1613		}//end namespace oopse
1614

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