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

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 432 by tim, Fri Mar 11 15:00:20 2005 UTC vs.
Revision 749 by tim, Wed Nov 16 23:10:02 2005 UTC

#	Line 1 | Line 1
1	<	/*
1	>	/*
2		* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
#	Line 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 "UseTheForce/fCutoffPolicy.h"
57	+	#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
58	+	#include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h"
59	+	#include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
60		#include "UseTheForce/doForces_interface.h"
61	+	#include "UseTheForce/DarkSide/electrostatic_interface.h"
62		#include "UseTheForce/notifyCutoffs_interface.h"
63	+	#include "UseTheForce/DarkSide/switcheroo_interface.h"
64		#include "utils/MemoryUtils.hpp"
65		#include "utils/simError.h"
66		#include "selection/SelectionManager.hpp"
#	Line 64 | Line 71 | namespace oopse {
71		#endif
72
73		namespace oopse {
74	+	std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
75	+	std::map<int, std::set<int> >::iterator i = container.find(index);
76	+	std::set<int> result;
77	+	if (i != container.end()) {
78	+	result = i->second;
79	+	}
80
81	<	SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
82	<	ForceField* ff, Globals* simParams) :
83	<	forceField_(ff), simParams_(simParams),
84	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
85	<	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
86	<	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
87	<	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
88	<	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
89	<	sman_(NULL), fortranInitialized_(false) {
81	>	return result;
82	>	}
83	>
84	>	SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
85	>	ForceField* ff, Globals* simParams) :
86	>	stamps_(stamps), forceField_(ff), simParams_(simParams),
87	>	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
88	>	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
89	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
90	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
91	>	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
92	>	sman_(NULL), fortranInitialized_(false) {
93
94
95	<	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
96	<	MoleculeStamp* molStamp;
97	<	int nMolWithSameStamp;
98	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
99	<	int nGroups = 0;          //total cutoff groups defined in meta-data file
100	<	CutoffGroupStamp* cgStamp;
101	<	RigidBodyStamp* rbStamp;
102	<	int nRigidAtoms = 0;
95	>	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
96	>	MoleculeStamp* molStamp;
97	>	int nMolWithSameStamp;
98	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
99	>	int nGroups = 0;      //total cutoff groups defined in meta-data file
100	>	CutoffGroupStamp* cgStamp;
101	>	RigidBodyStamp* rbStamp;
102	>	int nRigidAtoms = 0;
103
104	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
104	>	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
105		molStamp = i->first;
106		nMolWithSameStamp = i->second;
107
#	Line 100 | Line 116 | SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*,
116		int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
117
118		for (int j=0; j < nCutoffGroupsInStamp; j++) {
119	<	cgStamp = molStamp->getCutoffGroup(j);
120	<	nAtomsInGroups += cgStamp->getNMembers();
119	>	cgStamp = molStamp->getCutoffGroup(j);
120	>	nAtomsInGroups += cgStamp->getNMembers();
121		}
122
123		nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
124	+
125		nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
126
127		//calculate atoms in rigid bodies
#	Line 112 | Line 129 | SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*,
129		int nRigidBodiesInStamp = molStamp->getNRigidBodies();
130
131		for (int j=0; j < nRigidBodiesInStamp; j++) {
132	<	rbStamp = molStamp->getRigidBody(j);
133	<	nAtomsInRigidBodies += rbStamp->getNMembers();
132	>	rbStamp = molStamp->getRigidBody(j);
133	>	nAtomsInRigidBodies += rbStamp->getNMembers();
134		}
135
136		nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
137		nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
138
139	<	}
139	>	}
140
141	<	//every free atom (atom does not belong to cutoff groups) is a cutoff group
142	<	//therefore the total number of cutoff groups in the system is equal to
143	<	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
144	<	//file plus the number of cutoff groups defined in meta-data file
145	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
141	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
142	>	//group therefore the total number of cutoff groups in the system is
143	>	//equal to the total number of atoms minus number of atoms belong to
144	>	//cutoff group defined in meta-data file plus the number of cutoff
145	>	//groups defined in meta-data file
146	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
147
148	<	//every free atom (atom does not belong to rigid bodies) is an integrable object
149	<	//therefore the total number of  integrable objects in the system is equal to
150	<	//the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
151	<	//file plus the number of  rigid bodies defined in meta-data file
152	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
148	>	//every free atom (atom does not belong to rigid bodies) is an
149	>	//integrable object therefore the total number of integrable objects
150	>	//in the system is equal to the total number of atoms minus number of
151	>	//atoms belong to rigid body defined in meta-data file plus the number
152	>	//of rigid bodies defined in meta-data file
153	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
154	>	+ nGlobalRigidBodies_;
155	>
156	>	nGlobalMols_ = molStampIds_.size();
157
136	–	nGlobalMols_ = molStampIds_.size();
137	–
158		#ifdef IS_MPI
159	<	molToProcMap_.resize(nGlobalMols_);
159	>	molToProcMap_.resize(nGlobalMols_);
160		#endif
161
162	<	}
162	>	}
163
164	<	SimInfo::~SimInfo() {
164	>	SimInfo::~SimInfo() {
165		std::map<int, Molecule*>::iterator i;
166		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
167	<	delete i->second;
167	>	delete i->second;
168		}
169		molecules_.clear();
170	<
171	<	MemoryUtils::deletePointers(moleculeStamps_);
152	<
170	>
171	>	delete stamps_;
172		delete sman_;
173		delete simParams_;
174		delete forceField_;
175	<	}
175	>	}
176
177	<	int SimInfo::getNGlobalConstraints() {
177	>	int SimInfo::getNGlobalConstraints() {
178		int nGlobalConstraints;
179		#ifdef IS_MPI
180		MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
#	Line 164 | Line 183 | int SimInfo::getNGlobalConstraints() {
183		nGlobalConstraints =  nConstraints_;
184		#endif
185		return nGlobalConstraints;
186	<	}
186	>	}
187
188	<	bool SimInfo::addMolecule(Molecule* mol) {
188	>	bool SimInfo::addMolecule(Molecule* mol) {
189		MoleculeIterator i;
190
191		i = molecules_.find(mol->getGlobalIndex());
192		if (i == molecules_.end() ) {
193
194	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
194	>	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
195
196	<	nAtoms_ += mol->getNAtoms();
197	<	nBonds_ += mol->getNBonds();
198	<	nBends_ += mol->getNBends();
199	<	nTorsions_ += mol->getNTorsions();
200	<	nRigidBodies_ += mol->getNRigidBodies();
201	<	nIntegrableObjects_ += mol->getNIntegrableObjects();
202	<	nCutoffGroups_ += mol->getNCutoffGroups();
203	<	nConstraints_ += mol->getNConstraintPairs();
196	>	nAtoms_ += mol->getNAtoms();
197	>	nBonds_ += mol->getNBonds();
198	>	nBends_ += mol->getNBends();
199	>	nTorsions_ += mol->getNTorsions();
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	>	nRigidBodies_ -= mol->getNRigidBodies();
226	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
227	>	nCutoffGroups_ -= mol->getNCutoffGroups();
228	>	nConstraints_ -= mol->getNConstraintPairs();
229
230	<	removeExcludePairs(mol);
231	<	molecules_.erase(mol->getGlobalIndex());
230	>	removeExcludePairs(mol);
231	>	molecules_.erase(mol->getGlobalIndex());
232
233	<	delete mol;
233	>	delete mol;
234
235	<	return true;
235	>	return true;
236		} else {
237	<	return false;
237	>	return false;
238		}
239
240
241	<	}
241	>	}
242
243
244	<	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
244	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
245		i = molecules_.begin();
246		return i == molecules_.end() ? NULL : i->second;
247	<	}
247	>	}
248
249	<	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
249	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
250		++i;
251		return i == molecules_.end() ? NULL : i->second;
252	<	}
252	>	}
253
254
255	<	void SimInfo::calcNdf() {
255	>	void SimInfo::calcNdf() {
256		int ndf_local;
257		MoleculeIterator i;
258		std::vector<StuntDouble*>::iterator j;
#	Line 243 | Line 262 | void SimInfo::calcNdf() {
262		ndf_local = 0;
263
264		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
265	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
266	<	integrableObject = mol->nextIntegrableObject(j)) {
265	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
266	>	integrableObject = mol->nextIntegrableObject(j)) {
267
268	<	ndf_local += 3;
268	>	ndf_local += 3;
269
270	<	if (integrableObject->isDirectional()) {
271	<	if (integrableObject->isLinear()) {
272	<	ndf_local += 2;
273	<	} else {
274	<	ndf_local += 3;
275	<	}
276	<	}
270	>	if (integrableObject->isDirectional()) {
271	>	if (integrableObject->isLinear()) {
272	>	ndf_local += 2;
273	>	} else {
274	>	ndf_local += 3;
275	>	}
276	>	}
277
278	<	}//end for (integrableObject)
278	>	}//end for (integrableObject)
279		}// end for (mol)
280
281		// n_constraints is local, so subtract them on each processor
#	Line 272 | Line 291 | void SimInfo::calcNdf() {
291		// entire system:
292		ndf_ = ndf_ - 3 - nZconstraint_;
293
294	<	}
294	>	}
295
296	<	void SimInfo::calcNdfRaw() {
296	>	void SimInfo::calcNdfRaw() {
297		int ndfRaw_local;
298
299		MoleculeIterator i;
#	Line 286 | Line 305 | void SimInfo::calcNdfRaw() {
305		ndfRaw_local = 0;
306
307		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
308	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
309	<	integrableObject = mol->nextIntegrableObject(j)) {
308	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
309	>	integrableObject = mol->nextIntegrableObject(j)) {
310
311	<	ndfRaw_local += 3;
311	>	ndfRaw_local += 3;
312
313	<	if (integrableObject->isDirectional()) {
314	<	if (integrableObject->isLinear()) {
315	<	ndfRaw_local += 2;
316	<	} else {
317	<	ndfRaw_local += 3;
318	<	}
319	<	}
313	>	if (integrableObject->isDirectional()) {
314	>	if (integrableObject->isLinear()) {
315	>	ndfRaw_local += 2;
316	>	} else {
317	>	ndfRaw_local += 3;
318	>	}
319	>	}
320
321	<	}
321	>	}
322		}
323
324		#ifdef IS_MPI
#	Line 307 | Line 326 | void SimInfo::calcNdfRaw() {
326		#else
327		ndfRaw_ = ndfRaw_local;
328		#endif
329	<	}
329	>	}
330
331	<	void SimInfo::calcNdfTrans() {
331	>	void SimInfo::calcNdfTrans() {
332		int ndfTrans_local;
333
334		ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
#	Line 323 | Line 342 | void SimInfo::calcNdfTrans() {
342
343		ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
344
345	<	}
345	>	}
346
347	<	void SimInfo::addExcludePairs(Molecule* mol) {
347	>	void SimInfo::addExcludePairs(Molecule* mol) {
348		std::vector<Bond*>::iterator bondIter;
349		std::vector<Bend*>::iterator bendIter;
350		std::vector<Torsion*>::iterator torsionIter;
#	Line 336 | Line 355 | void SimInfo::addExcludePairs(Molecule* mol) {
355		int b;
356		int c;
357		int d;
358	+
359	+	std::map<int, std::set<int> > atomGroups;
360	+
361	+	Molecule::RigidBodyIterator rbIter;
362	+	RigidBody* rb;
363	+	Molecule::IntegrableObjectIterator ii;
364	+	StuntDouble* integrableObject;
365
366	+	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
367	+	integrableObject = mol->nextIntegrableObject(ii)) {
368	+
369	+	if (integrableObject->isRigidBody()) {
370	+	rb = static_cast<RigidBody*>(integrableObject);
371	+	std::vector<Atom*> atoms = rb->getAtoms();
372	+	std::set<int> rigidAtoms;
373	+	for (int i = 0; i < atoms.size(); ++i) {
374	+	rigidAtoms.insert(atoms[i]->getGlobalIndex());
375	+	}
376	+	for (int i = 0; i < atoms.size(); ++i) {
377	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
378	+	}
379	+	} else {
380	+	std::set<int> oneAtomSet;
381	+	oneAtomSet.insert(integrableObject->getGlobalIndex());
382	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
383	+	}
384	+	}
385	+
386	+
387	+
388		for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
389	<	a = bond->getAtomA()->getGlobalIndex();
390	<	b = bond->getAtomB()->getGlobalIndex();
391	<	exclude_.addPair(a, b);
389	>	a = bond->getAtomA()->getGlobalIndex();
390	>	b = bond->getAtomB()->getGlobalIndex();
391	>	exclude_.addPair(a, b);
392		}
393
394		for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
395	<	a = bend->getAtomA()->getGlobalIndex();
396	<	b = bend->getAtomB()->getGlobalIndex();
397	<	c = bend->getAtomC()->getGlobalIndex();
395	>	a = bend->getAtomA()->getGlobalIndex();
396	>	b = bend->getAtomB()->getGlobalIndex();
397	>	c = bend->getAtomC()->getGlobalIndex();
398	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
399	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
400	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
401
402	<	exclude_.addPair(a, b);
403	<	exclude_.addPair(a, c);
404	<	exclude_.addPair(b, c);
402	>	exclude_.addPairs(rigidSetA, rigidSetB);
403	>	exclude_.addPairs(rigidSetA, rigidSetC);
404	>	exclude_.addPairs(rigidSetB, rigidSetC);
405	>
406	>	//exclude_.addPair(a, b);
407	>	//exclude_.addPair(a, c);
408	>	//exclude_.addPair(b, c);
409		}
410
411		for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
412	<	a = torsion->getAtomA()->getGlobalIndex();
413	<	b = torsion->getAtomB()->getGlobalIndex();
414	<	c = torsion->getAtomC()->getGlobalIndex();
415	<	d = torsion->getAtomD()->getGlobalIndex();
412	>	a = torsion->getAtomA()->getGlobalIndex();
413	>	b = torsion->getAtomB()->getGlobalIndex();
414	>	c = torsion->getAtomC()->getGlobalIndex();
415	>	d = torsion->getAtomD()->getGlobalIndex();
416	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
417	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
418	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
419	>	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
420
421	<	exclude_.addPair(a, b);
422	<	exclude_.addPair(a, c);
423	<	exclude_.addPair(a, d);
424	<	exclude_.addPair(b, c);
425	<	exclude_.addPair(b, d);
426	<	exclude_.addPair(c, d);
421	>	exclude_.addPairs(rigidSetA, rigidSetB);
422	>	exclude_.addPairs(rigidSetA, rigidSetC);
423	>	exclude_.addPairs(rigidSetA, rigidSetD);
424	>	exclude_.addPairs(rigidSetB, rigidSetC);
425	>	exclude_.addPairs(rigidSetB, rigidSetD);
426	>	exclude_.addPairs(rigidSetC, rigidSetD);
427	>
428	>	/*
429	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
430	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
431	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
432	>	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
433	>	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
434	>	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
435	>
436	>
437	>	exclude_.addPair(a, b);
438	>	exclude_.addPair(a, c);
439	>	exclude_.addPair(a, d);
440	>	exclude_.addPair(b, c);
441	>	exclude_.addPair(b, d);
442	>	exclude_.addPair(c, d);
443	>	*/
444		}
445
370	–	Molecule::RigidBodyIterator rbIter;
371	–	RigidBody* rb;
446		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
447	<	std::vector<Atom*> atoms = rb->getAtoms();
448	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
449	<	for (int j = i + 1; j < atoms.size(); ++j) {
450	<	a = atoms[i]->getGlobalIndex();
451	<	b = atoms[j]->getGlobalIndex();
452	<	exclude_.addPair(a, b);
453	<	}
454	<	}
447	>	std::vector<Atom*> atoms = rb->getAtoms();
448	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
449	>	for (int j = i + 1; j < atoms.size(); ++j) {
450	>	a = atoms[i]->getGlobalIndex();
451	>	b = atoms[j]->getGlobalIndex();
452	>	exclude_.addPair(a, b);
453	>	}
454	>	}
455		}
456
457	<	Molecule::CutoffGroupIterator cgIter;
384	<	CutoffGroup* cg;
385	<	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
386	<	std::vector<Atom*> atoms = cg->getAtoms();
387	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
388	<	for (int j = i + 1; j < atoms.size(); ++j) {
389	<	a = atoms[i]->getGlobalIndex();
390	<	b = atoms[j]->getGlobalIndex();
391	<	exclude_.addPair(a, b);
392	<	}
393	<	}
394	<	}
457	>	}
458
459	<	}
397	<
398	<	void SimInfo::removeExcludePairs(Molecule* mol) {
459	>	void SimInfo::removeExcludePairs(Molecule* mol) {
460		std::vector<Bond*>::iterator bondIter;
461		std::vector<Bend*>::iterator bendIter;
462		std::vector<Torsion*>::iterator torsionIter;
#	Line 406 | Line 467 | void SimInfo::removeExcludePairs(Molecule* mol) {
467		int b;
468		int c;
469		int d;
470	+
471	+	std::map<int, std::set<int> > atomGroups;
472	+
473	+	Molecule::RigidBodyIterator rbIter;
474	+	RigidBody* rb;
475	+	Molecule::IntegrableObjectIterator ii;
476	+	StuntDouble* integrableObject;
477
478	+	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
479	+	integrableObject = mol->nextIntegrableObject(ii)) {
480	+
481	+	if (integrableObject->isRigidBody()) {
482	+	rb = static_cast<RigidBody*>(integrableObject);
483	+	std::vector<Atom*> atoms = rb->getAtoms();
484	+	std::set<int> rigidAtoms;
485	+	for (int i = 0; i < atoms.size(); ++i) {
486	+	rigidAtoms.insert(atoms[i]->getGlobalIndex());
487	+	}
488	+	for (int i = 0; i < atoms.size(); ++i) {
489	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
490	+	}
491	+	} else {
492	+	std::set<int> oneAtomSet;
493	+	oneAtomSet.insert(integrableObject->getGlobalIndex());
494	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
495	+	}
496	+	}
497	+
498	+
499		for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
500	<	a = bond->getAtomA()->getGlobalIndex();
501	<	b = bond->getAtomB()->getGlobalIndex();
502	<	exclude_.removePair(a, b);
500	>	a = bond->getAtomA()->getGlobalIndex();
501	>	b = bond->getAtomB()->getGlobalIndex();
502	>	exclude_.removePair(a, b);
503		}
504
505		for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
506	<	a = bend->getAtomA()->getGlobalIndex();
507	<	b = bend->getAtomB()->getGlobalIndex();
508	<	c = bend->getAtomC()->getGlobalIndex();
506	>	a = bend->getAtomA()->getGlobalIndex();
507	>	b = bend->getAtomB()->getGlobalIndex();
508	>	c = bend->getAtomC()->getGlobalIndex();
509
510	<	exclude_.removePair(a, b);
511	<	exclude_.removePair(a, c);
512	<	exclude_.removePair(b, c);
510	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
511	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
512	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
513	>
514	>	exclude_.removePairs(rigidSetA, rigidSetB);
515	>	exclude_.removePairs(rigidSetA, rigidSetC);
516	>	exclude_.removePairs(rigidSetB, rigidSetC);
517	>
518	>	//exclude_.removePair(a, b);
519	>	//exclude_.removePair(a, c);
520	>	//exclude_.removePair(b, c);
521		}
522
523		for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
524	<	a = torsion->getAtomA()->getGlobalIndex();
525	<	b = torsion->getAtomB()->getGlobalIndex();
526	<	c = torsion->getAtomC()->getGlobalIndex();
527	<	d = torsion->getAtomD()->getGlobalIndex();
524	>	a = torsion->getAtomA()->getGlobalIndex();
525	>	b = torsion->getAtomB()->getGlobalIndex();
526	>	c = torsion->getAtomC()->getGlobalIndex();
527	>	d = torsion->getAtomD()->getGlobalIndex();
528
529	<	exclude_.removePair(a, b);
530	<	exclude_.removePair(a, c);
531	<	exclude_.removePair(a, d);
532	<	exclude_.removePair(b, c);
436	<	exclude_.removePair(b, d);
437	<	exclude_.removePair(c, d);
438	<	}
529	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
530	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
531	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
532	>	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
533
534	<	Molecule::RigidBodyIterator rbIter;
535	<	RigidBody* rb;
534	>	exclude_.removePairs(rigidSetA, rigidSetB);
535	>	exclude_.removePairs(rigidSetA, rigidSetC);
536	>	exclude_.removePairs(rigidSetA, rigidSetD);
537	>	exclude_.removePairs(rigidSetB, rigidSetC);
538	>	exclude_.removePairs(rigidSetB, rigidSetD);
539	>	exclude_.removePairs(rigidSetC, rigidSetD);
540	>
541	>	/*
542	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
543	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
544	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
545	>	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
546	>	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
547	>	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
548	>
549	>
550	>	exclude_.removePair(a, b);
551	>	exclude_.removePair(a, c);
552	>	exclude_.removePair(a, d);
553	>	exclude_.removePair(b, c);
554	>	exclude_.removePair(b, d);
555	>	exclude_.removePair(c, d);
556	>	*/
557	>	}
558	>
559		for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
560	<	std::vector<Atom*> atoms = rb->getAtoms();
561	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
562	<	for (int j = i + 1; j < atoms.size(); ++j) {
563	<	a = atoms[i]->getGlobalIndex();
564	<	b = atoms[j]->getGlobalIndex();
565	<	exclude_.removePair(a, b);
566	<	}
567	<	}
560	>	std::vector<Atom*> atoms = rb->getAtoms();
561	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
562	>	for (int j = i + 1; j < atoms.size(); ++j) {
563	>	a = atoms[i]->getGlobalIndex();
564	>	b = atoms[j]->getGlobalIndex();
565	>	exclude_.removePair(a, b);
566	>	}
567	>	}
568		}
569
570	<	Molecule::CutoffGroupIterator cgIter;
454	<	CutoffGroup* cg;
455	<	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
456	<	std::vector<Atom*> atoms = cg->getAtoms();
457	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
458	<	for (int j = i + 1; j < atoms.size(); ++j) {
459	<	a = atoms[i]->getGlobalIndex();
460	<	b = atoms[j]->getGlobalIndex();
461	<	exclude_.removePair(a, b);
462	<	}
463	<	}
464	<	}
570	>	}
571
466	–	}
572
573	<
469	<	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
573	>	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
574		int curStampId;
575
576		//index from 0
#	Line 474 | Line 578 | void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp
578
579		moleculeStamps_.push_back(molStamp);
580		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
581	<	}
581	>	}
582
583	<	void SimInfo::update() {
583	>	void SimInfo::update() {
584
585		setupSimType();
586
#	Line 489 | Line 593 | void SimInfo::update() {
593		//setup fortran force field
594		/** @deprecate */
595		int isError = 0;
596	<	initFortranFF( &fInfo_.SIM_uses_RF , &isError );
596	>
597	>	setupElectrostaticSummationMethod( isError );
598	>	setupSwitchingFunction();
599	>
600		if(isError){
601	<	sprintf( painCave.errMsg,
602	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
603	<	painCave.isFatal = 1;
604	<	simError();
601	>	sprintf( painCave.errMsg,
602	>	"ForceField error: There was an error initializing the forceField in fortran.\n" );
603	>	painCave.isFatal = 1;
604	>	simError();
605		}
606
607
#	Line 505 | Line 612 | void SimInfo::update() {
612		calcNdfTrans();
613
614		fortranInitialized_ = true;
615	<	}
615	>	}
616
617	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
617	>	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
618		SimInfo::MoleculeIterator mi;
619		Molecule* mol;
620		Molecule::AtomIterator ai;
#	Line 516 | Line 623 | std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
623
624		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
625
626	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
627	<	atomTypes.insert(atom->getAtomType());
628	<	}
626	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
627	>	atomTypes.insert(atom->getAtomType());
628	>	}
629
630		}
631
632		return atomTypes;
633	<	}
633	>	}
634
635	<	void SimInfo::setupSimType() {
635	>	void SimInfo::setupSimType() {
636		std::set<AtomType*>::iterator i;
637		std::set<AtomType*> atomTypes;
638		atomTypes = getUniqueAtomTypes();
#	Line 533 | Line 640 | void SimInfo::setupSimType() {
640		int useLennardJones = 0;
641		int useElectrostatic = 0;
642		int useEAM = 0;
643	+	int useSC = 0;
644		int useCharge = 0;
645		int useDirectional = 0;
646		int useDipole = 0;
647		int useGayBerne = 0;
648		int useSticky = 0;
649	+	int useStickyPower = 0;
650		int useShape = 0;
651		int useFLARB = 0; //it is not in AtomType yet
652		int useDirectionalAtom = 0;
653		int useElectrostatics = 0;
654		//usePBC and useRF are from simParams
655	<	int usePBC = simParams_->getPBC();
656	<	int useRF = simParams_->getUseRF();
655	>	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
656	>	int useRF;
657	>	int useSF;
658	>	std::string myMethod;
659
660	+	// set the useRF logical
661	+	useRF = 0;
662	+	useSF = 0;
663	+
664	+
665	+	if (simParams_->haveElectrostaticSummationMethod()) {
666	+	std::string myMethod = simParams_->getElectrostaticSummationMethod();
667	+	toUpper(myMethod);
668	+	if (myMethod == "REACTION_FIELD") {
669	+	useRF=1;
670	+	} else {
671	+	if (myMethod == "SHIFTED_FORCE") {
672	+	useSF = 1;
673	+	}
674	+	}
675	+	}
676	+
677		//loop over all of the atom types
678		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
679	<	useLennardJones |= (*i)->isLennardJones();
680	<	useElectrostatic |= (*i)->isElectrostatic();
681	<	useEAM |= (*i)->isEAM();
682	<	useCharge |= (*i)->isCharge();
683	<	useDirectional |= (*i)->isDirectional();
684	<	useDipole |= (*i)->isDipole();
685	<	useGayBerne |= (*i)->isGayBerne();
686	<	useSticky |= (*i)->isSticky();
687	<	useShape |= (*i)->isShape();
679	>	useLennardJones |= (*i)->isLennardJones();
680	>	useElectrostatic |= (*i)->isElectrostatic();
681	>	useEAM |= (*i)->isEAM();
682	>	useSC |= (*i)->isSC();
683	>	useCharge |= (*i)->isCharge();
684	>	useDirectional |= (*i)->isDirectional();
685	>	useDipole |= (*i)->isDipole();
686	>	useGayBerne |= (*i)->isGayBerne();
687	>	useSticky |= (*i)->isSticky();
688	>	useStickyPower |= (*i)->isStickyPower();
689	>	useShape |= (*i)->isShape();
690		}
691
692	<	if (useSticky || useDipole || useGayBerne || useShape) {
693	<	useDirectionalAtom = 1;
692	>	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
693	>	useDirectionalAtom = 1;
694		}
695
696		if (useCharge || useDipole) {
697	<	useElectrostatics = 1;
697	>	useElectrostatics = 1;
698		}
699
700		#ifdef IS_MPI
#	Line 591 | Line 721 | void SimInfo::setupSimType() {
721		temp = useSticky;
722		MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
723
724	+	temp = useStickyPower;
725	+	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
726	+
727		temp = useGayBerne;
728		MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
729
730		temp = useEAM;
731		MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
732
733	+	temp = useSC;
734	+	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
735	+
736		temp = useShape;
737		MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
738
#	Line 605 | Line 741 | void SimInfo::setupSimType() {
741
742		temp = useRF;
743		MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
744	<
744	>
745	>	temp = useSF;
746	>	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
747	>
748		#endif
749
750		fInfo_.SIM_uses_PBC = usePBC;
#	Line 615 | Line 754 | void SimInfo::setupSimType() {
754		fInfo_.SIM_uses_Charges = useCharge;
755		fInfo_.SIM_uses_Dipoles = useDipole;
756		fInfo_.SIM_uses_Sticky = useSticky;
757	+	fInfo_.SIM_uses_StickyPower = useStickyPower;
758		fInfo_.SIM_uses_GayBerne = useGayBerne;
759		fInfo_.SIM_uses_EAM = useEAM;
760	+	fInfo_.SIM_uses_SC = useSC;
761		fInfo_.SIM_uses_Shapes = useShape;
762		fInfo_.SIM_uses_FLARB = useFLARB;
763		fInfo_.SIM_uses_RF = useRF;
764	+	fInfo_.SIM_uses_SF = useSF;
765
766	<	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
767	<
768	<	if (simParams_->haveDielectric()) {
769	<	fInfo_.dielect = simParams_->getDielectric();
770	<	} else {
771	<	sprintf(painCave.errMsg,
772	<	"SimSetup Error: No Dielectric constant was set.\n"
773	<	"\tYou are trying to use Reaction Field without"
774	<	"\tsetting a dielectric constant!\n");
775	<	painCave.isFatal = 1;
776	<	simError();
777	<	}
636	<
637	<	} else {
638	<	fInfo_.dielect = 0.0;
766	>	if( myMethod == "REACTION_FIELD") {
767	>
768	>	if (simParams_->haveDielectric()) {
769	>	fInfo_.dielect = simParams_->getDielectric();
770	>	} else {
771	>	sprintf(painCave.errMsg,
772	>	"SimSetup Error: No Dielectric constant was set.\n"
773	>	"\tYou are trying to use Reaction Field without"
774	>	"\tsetting a dielectric constant!\n");
775	>	painCave.isFatal = 1;
776	>	simError();
777	>	}
778		}
779
780	<	}
780	>	}
781
782	<	void SimInfo::setupFortranSim() {
782	>	void SimInfo::setupFortranSim() {
783		int isError;
784		int nExclude;
785		std::vector<int> fortranGlobalGroupMembership;
#	Line 650 | Line 789 | void SimInfo::setupFortranSim() {
789
790		//globalGroupMembership_ is filled by SimCreator
791		for (int i = 0; i < nGlobalAtoms_; i++) {
792	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
792	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
793		}
794
795		//calculate mass ratio of cutoff group
#	Line 667 | Line 806 | void SimInfo::setupFortranSim() {
806		mfact.reserve(getNCutoffGroups());
807
808		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
809	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
809	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
810
811	<	totalMass = cg->getMass();
812	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
813	<	mfact.push_back(atom->getMass()/totalMass);
814	<	}
811	>	totalMass = cg->getMass();
812	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
813	>	// Check for massless groups - set mfact to 1 if true
814	>	if (totalMass != 0)
815	>	mfact.push_back(atom->getMass()/totalMass);
816	>	else
817	>	mfact.push_back( 1.0 );
818	>	}
819
820	<	}
820	>	}
821		}
822
823		//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
#	Line 684 | Line 827 | void SimInfo::setupFortranSim() {
827		identArray.reserve(getNAtoms());
828
829		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
830	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
831	<	identArray.push_back(atom->getIdent());
832	<	}
830	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
831	>	identArray.push_back(atom->getIdent());
832	>	}
833		}
834
835		//fill molMembershipArray
836		//molMembershipArray is filled by SimCreator
837		std::vector<int> molMembershipArray(nGlobalAtoms_);
838		for (int i = 0; i < nGlobalAtoms_; i++) {
839	<	molMembershipArray[i] = globalMolMembership_[i] + 1;
839	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
840		}
841
842		//setup fortran simulation
#	Line 701 | Line 844 | void SimInfo::setupFortranSim() {
844		int* globalExcludes = NULL;
845		int* excludeList = exclude_.getExcludeList();
846		setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
847	<	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
848	<	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
847	>	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
848	>	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
849
850		if( isError ){
851
852	<	sprintf( painCave.errMsg,
853	<	"There was an error setting the simulation information in fortran.\n" );
854	<	painCave.isFatal = 1;
855	<	painCave.severity = OOPSE_ERROR;
856	<	simError();
852	>	sprintf( painCave.errMsg,
853	>	"There was an error setting the simulation information in fortran.\n" );
854	>	painCave.isFatal = 1;
855	>	painCave.severity = OOPSE_ERROR;
856	>	simError();
857		}
858
859		#ifdef IS_MPI
860		sprintf( checkPointMsg,
861	<	"succesfully sent the simulation information to fortran.\n");
861	>	"succesfully sent the simulation information to fortran.\n");
862		MPIcheckPoint();
863		#endif // is_mpi
864	<	}
864	>	}
865
866
867		#ifdef IS_MPI
868	<	void SimInfo::setupFortranParallel() {
868	>	void SimInfo::setupFortranParallel() {
869
870		//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
871		std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
#	Line 738 | Line 881 | void SimInfo::setupFortranParallel() {
881
882		for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
883
884	<	//local index(index in DataStorge) of atom is important
885	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
886	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
887	<	}
884	>	//local index(index in DataStorge) of atom is important
885	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
886	>	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
887	>	}
888
889	<	//local index of cutoff group is trivial, it only depends on the order of travesing
890	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
891	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
892	<	}
889	>	//local index of cutoff group is trivial, it only depends on the order of travesing
890	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
891	>	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
892	>	}
893
894		}
895
#	Line 766 | Line 909 | void SimInfo::setupFortranParallel() {
909		&localToGlobalCutoffGroupIndex[0], &isError);
910
911		if (isError) {
912	<	sprintf(painCave.errMsg,
913	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
914	<	painCave.isFatal = 1;
915	<	simError();
912	>	sprintf(painCave.errMsg,
913	>	"mpiRefresh errror: fortran didn't like something we gave it.\n");
914	>	painCave.isFatal = 1;
915	>	simError();
916		}
917
918		sprintf(checkPointMsg, " mpiRefresh successful.\n");
919		MPIcheckPoint();
920
921
922	<	}
922	>	}
923
924		#endif
925
926	<	double SimInfo::calcMaxCutoffRadius() {
926	>	double SimInfo::calcMaxCutoffRadius() {
927
928
929		std::set<AtomType*> atomTypes;
#	Line 792 | Line 935 | double SimInfo::calcMaxCutoffRadius() {
935
936		//query the max cutoff radius among these atom types
937		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
938	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
938	>	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
939		}
940
941		double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
#	Line 801 | Line 944 | double SimInfo::calcMaxCutoffRadius() {
944		#endif
945
946		return maxCutoffRadius;
947	<	}
947	>	}
948
949	<	void SimInfo::getCutoff(double& rcut, double& rsw) {
949	>	void SimInfo::getCutoff(double& rcut, double& rsw) {
950
951		if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
952
953	<	if (!simParams_->haveRcut()){
954	<	sprintf(painCave.errMsg,
953	>	if (!simParams_->haveCutoffRadius()){
954	>	sprintf(painCave.errMsg,
955		"SimCreator Warning: No value was set for the cutoffRadius.\n"
956		"\tOOPSE will use a default value of 15.0 angstroms"
957		"\tfor the cutoffRadius.\n");
958	<	painCave.isFatal = 0;
959	<	simError();
960	<	rcut = 15.0;
961	<	} else{
962	<	rcut = simParams_->getRcut();
963	<	}
958	>	painCave.isFatal = 0;
959	>	simError();
960	>	rcut = 15.0;
961	>	} else{
962	>	rcut = simParams_->getCutoffRadius();
963	>	}
964
965	<	if (!simParams_->haveRsw()){
966	<	sprintf(painCave.errMsg,
965	>	if (!simParams_->haveSwitchingRadius()){
966	>	sprintf(painCave.errMsg,
967		"SimCreator Warning: No value was set for switchingRadius.\n"
968		"\tOOPSE will use a default value of\n"
969	<	"\t0.95 * cutoffRadius for the switchingRadius\n");
970	<	painCave.isFatal = 0;
971	<	simError();
972	<	rsw = 0.95 * rcut;
973	<	} else{
974	<	rsw = simParams_->getRsw();
975	<	}
969	>	"\t0.85 * cutoffRadius for the switchingRadius\n");
970	>	painCave.isFatal = 0;
971	>	simError();
972	>	rsw = 0.85 * rcut;
973	>	} else{
974	>	rsw = simParams_->getSwitchingRadius();
975	>	}
976
977		} else {
978	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
979	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
978	>	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
979	>	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
980
981	<	if (simParams_->haveRcut()) {
982	<	rcut = simParams_->getRcut();
983	<	} else {
984	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
985	<	rcut = calcMaxCutoffRadius();
986	<	}
981	>	if (simParams_->haveCutoffRadius()) {
982	>	rcut = simParams_->getCutoffRadius();
983	>	} else {
984	>	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
985	>	rcut = calcMaxCutoffRadius();
986	>	}
987
988	<	if (simParams_->haveRsw()) {
989	<	rsw  = simParams_->getRsw();
990	<	} else {
991	<	rsw = rcut;
992	<	}
988	>	if (simParams_->haveSwitchingRadius()) {
989	>	rsw  = simParams_->getSwitchingRadius();
990	>	} else {
991	>	rsw = rcut;
992	>	}
993
994		}
995	<	}
995	>	}
996
997	<	void SimInfo::setupCutoff() {
997	>	void SimInfo::setupCutoff() {
998		getCutoff(rcut_, rsw_);
999		double rnblist = rcut_ + 1; // skin of neighbor list
1000
1001		//Pass these cutoff radius etc. to fortran. This function should be called once and only once
1002	<	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist);
1003	<	}
1002	>
1003	>	int cp =  TRADITIONAL_CUTOFF_POLICY;
1004	>	if (simParams_->haveCutoffPolicy()) {
1005	>	std::string myPolicy = simParams_->getCutoffPolicy();
1006	>	toUpper(myPolicy);
1007	>	if (myPolicy == "MIX") {
1008	>	cp = MIX_CUTOFF_POLICY;
1009	>	} else {
1010	>	if (myPolicy == "MAX") {
1011	>	cp = MAX_CUTOFF_POLICY;
1012	>	} else {
1013	>	if (myPolicy == "TRADITIONAL") {
1014	>	cp = TRADITIONAL_CUTOFF_POLICY;
1015	>	} else {
1016	>	// throw error
1017	>	sprintf( painCave.errMsg,
1018	>	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
1019	>	painCave.isFatal = 1;
1020	>	simError();
1021	>	}
1022	>	}
1023	>	}
1024	>	}
1025
862	–	void SimInfo::addProperty(GenericData* genData) {
863	–	properties_.addProperty(genData);
864	–	}
1026
1027	<	void SimInfo::removeProperty(const std::string& propName) {
1028	<	properties_.removeProperty(propName);
1029	<	}
1027	>	if (simParams_->haveSkinThickness()) {
1028	>	double skinThickness = simParams_->getSkinThickness();
1029	>	}
1030
1031	<	void SimInfo::clearProperties() {
1032	<	properties_.clearProperties();
1033	<	}
1031	>	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
1032	>	// also send cutoff notification to electrostatics
1033	>	setElectrostaticCutoffRadius(&rcut_, &rsw_);
1034	>	}
1035
1036	<	std::vector<std::string> SimInfo::getPropertyNames() {
1037	<	return properties_.getPropertyNames();
1038	<	}
1039	<
1040	<	std::vector<GenericData*> SimInfo::getProperties() {
1041	<	return properties_.getProperties();
1042	<	}
1036	>	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1037	>
1038	>	int errorOut;
1039	>	int esm =  NONE;
1040	>	int sm = UNDAMPED;
1041	>	double alphaVal;
1042	>	double dielectric;
1043
1044	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1045	<	return properties_.getPropertyByName(propName);
1046	<	}
1044	>	errorOut = isError;
1045	>	alphaVal = simParams_->getDampingAlpha();
1046	>	dielectric = simParams_->getDielectric();
1047
1048	<	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1048	>	if (simParams_->haveElectrostaticSummationMethod()) {
1049	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1050	>	toUpper(myMethod);
1051	>	if (myMethod == "NONE") {
1052	>	esm = NONE;
1053	>	} else {
1054	>	if (myMethod == "SWITCHING_FUNCTION") {
1055	>	esm = SWITCHING_FUNCTION;
1056	>	} else {
1057	>	if (myMethod == "SHIFTED_POTENTIAL") {
1058	>	esm = SHIFTED_POTENTIAL;
1059	>	} else {
1060	>	if (myMethod == "SHIFTED_FORCE") {
1061	>	esm = SHIFTED_FORCE;
1062	>	} else {
1063	>	if (myMethod == "REACTION_FIELD") {
1064	>	esm = REACTION_FIELD;
1065	>	} else {
1066	>	// throw error
1067	>	sprintf( painCave.errMsg,
1068	>	"SimInfo error: Unknown electrostaticSummationMethod. (Input file specified %s .)\n\telectrostaticSummationMethod must be one of: \"none\", \"shifted_potential\", \"shifted_force\", or \"reaction_field\".", myMethod.c_str() );
1069	>	painCave.isFatal = 1;
1070	>	simError();
1071	>	}
1072	>	}
1073	>	}
1074	>	}
1075	>	}
1076	>	}
1077	>
1078	>	if (simParams_->haveElectrostaticScreeningMethod()) {
1079	>	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1080	>	toUpper(myScreen);
1081	>	if (myScreen == "UNDAMPED") {
1082	>	sm = UNDAMPED;
1083	>	} else {
1084	>	if (myScreen == "DAMPED") {
1085	>	sm = DAMPED;
1086	>	if (!simParams_->haveDampingAlpha()) {
1087	>	//throw error
1088	>	sprintf( painCave.errMsg,
1089	>	"SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used.", alphaVal);
1090	>	painCave.isFatal = 0;
1091	>	simError();
1092	>	}
1093	>	} else {
1094	>	// throw error
1095	>	sprintf( painCave.errMsg,
1096	>	"SimInfo error: Unknown electrostaticScreeningMethod. (Input file specified %s .)\n\telectrostaticScreeningMethod must be one of: \"undamped\" or \"damped\".", myScreen.c_str() );
1097	>	painCave.isFatal = 1;
1098	>	simError();
1099	>	}
1100	>	}
1101	>	}
1102	>
1103	>	// let's pass some summation method variables to fortran
1104	>	setElectrostaticSummationMethod( &esm );
1105	>	setScreeningMethod( &sm );
1106	>	setDampingAlpha( &alphaVal );
1107	>	setReactionFieldDielectric( &dielectric );
1108	>	initFortranFF( &esm, &errorOut );
1109	>	}
1110	>
1111	>	void SimInfo::setupSwitchingFunction() {
1112	>	int ft = CUBIC;
1113	>
1114	>	if (simParams_->haveSwitchingFunctionType()) {
1115	>	std::string funcType = simParams_->getSwitchingFunctionType();
1116	>	toUpper(funcType);
1117	>	if (funcType == "CUBIC") {
1118	>	ft = CUBIC;
1119	>	} else {
1120	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1121	>	ft = FIFTH_ORDER_POLY;
1122	>	} else {
1123	>	// throw error
1124	>	sprintf( painCave.errMsg,
1125	>	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1126	>	painCave.isFatal = 1;
1127	>	simError();
1128	>	}
1129	>	}
1130	>	}
1131	>
1132	>	// send switching function notification to switcheroo
1133	>	setFunctionType(&ft);
1134	>
1135	>	}
1136	>
1137	>	void SimInfo::addProperty(GenericData* genData) {
1138	>	properties_.addProperty(genData);
1139	>	}
1140	>
1141	>	void SimInfo::removeProperty(const std::string& propName) {
1142	>	properties_.removeProperty(propName);
1143	>	}
1144	>
1145	>	void SimInfo::clearProperties() {
1146	>	properties_.clearProperties();
1147	>	}
1148	>
1149	>	std::vector<std::string> SimInfo::getPropertyNames() {
1150	>	return properties_.getPropertyNames();
1151	>	}
1152	>
1153	>	std::vector<GenericData*> SimInfo::getProperties() {
1154	>	return properties_.getProperties();
1155	>	}
1156	>
1157	>	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1158	>	return properties_.getPropertyByName(propName);
1159	>	}
1160	>
1161	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1162		if (sman_ == sman) {
1163	<	return;
1163	>	return;
1164		}
1165		delete sman_;
1166		sman_ = sman;
#	Line 899 | Line 1174 | void SimInfo::setSnapshotManager(SnapshotManager* sman
1174
1175		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1176
1177	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1178	<	atom->setSnapshotManager(sman_);
1179	<	}
1177	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1178	>	atom->setSnapshotManager(sman_);
1179	>	}
1180
1181	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1182	<	rb->setSnapshotManager(sman_);
1183	<	}
1181	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1182	>	rb->setSnapshotManager(sman_);
1183	>	}
1184		}
1185
1186	<	}
1186	>	}
1187
1188	<	Vector3d SimInfo::getComVel(){
1188	>	Vector3d SimInfo::getComVel(){
1189		SimInfo::MoleculeIterator i;
1190		Molecule* mol;
1191
#	Line 919 | Line 1194 | Vector3d SimInfo::getComVel(){
1194
1195
1196		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1197	<	double mass = mol->getMass();
1198	<	totalMass += mass;
1199	<	comVel += mass * mol->getComVel();
1197	>	double mass = mol->getMass();
1198	>	totalMass += mass;
1199	>	comVel += mass * mol->getComVel();
1200		}
1201
1202		#ifdef IS_MPI
#	Line 934 | Line 1209 | Vector3d SimInfo::getComVel(){
1209		comVel /= totalMass;
1210
1211		return comVel;
1212	<	}
1212	>	}
1213
1214	<	Vector3d SimInfo::getCom(){
1214	>	Vector3d SimInfo::getCom(){
1215		SimInfo::MoleculeIterator i;
1216		Molecule* mol;
1217
#	Line 944 | Line 1219 | Vector3d SimInfo::getCom(){
1219		double totalMass = 0.0;
1220
1221		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1222	<	double mass = mol->getMass();
1223	<	totalMass += mass;
1224	<	com += mass * mol->getCom();
1222	>	double mass = mol->getMass();
1223	>	totalMass += mass;
1224	>	com += mass * mol->getCom();
1225		}
1226
1227		#ifdef IS_MPI
#	Line 960 | Line 1235 | Vector3d SimInfo::getCom(){
1235
1236		return com;
1237
1238	<	}
1238	>	}
1239
1240	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1240	>	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1241
1242		return o;
1243	<	}
1243	>	}
1244	>
1245	>
1246	>	/*
1247	>	Returns center of mass and center of mass velocity in one function call.
1248	>	*/
1249	>
1250	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1251	>	SimInfo::MoleculeIterator i;
1252	>	Molecule* mol;
1253	>
1254	>
1255	>	double totalMass = 0.0;
1256	>
1257
1258	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1259	+	double mass = mol->getMass();
1260	+	totalMass += mass;
1261	+	com += mass * mol->getCom();
1262	+	comVel += mass * mol->getComVel();
1263	+	}
1264	+
1265	+	#ifdef IS_MPI
1266	+	double tmpMass = totalMass;
1267	+	Vector3d tmpCom(com);
1268	+	Vector3d tmpComVel(comVel);
1269	+	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1270	+	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1271	+	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1272	+	#endif
1273	+
1274	+	com /= totalMass;
1275	+	comVel /= totalMass;
1276	+	}
1277	+
1278	+	/*
1279	+	Return intertia tensor for entire system and angular momentum Vector.
1280	+
1281	+
1282	+	[  Ixx -Ixy  -Ixz ]
1283	+	J =| -Iyx  Iyy  -Iyz |
1284	+	[ -Izx -Iyz   Izz ]
1285	+	*/
1286	+
1287	+	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1288	+
1289	+
1290	+	double xx = 0.0;
1291	+	double yy = 0.0;
1292	+	double zz = 0.0;
1293	+	double xy = 0.0;
1294	+	double xz = 0.0;
1295	+	double yz = 0.0;
1296	+	Vector3d com(0.0);
1297	+	Vector3d comVel(0.0);
1298	+
1299	+	getComAll(com, comVel);
1300	+
1301	+	SimInfo::MoleculeIterator i;
1302	+	Molecule* mol;
1303	+
1304	+	Vector3d thisq(0.0);
1305	+	Vector3d thisv(0.0);
1306	+
1307	+	double thisMass = 0.0;
1308	+
1309	+
1310	+
1311	+
1312	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1313	+
1314	+	thisq = mol->getCom()-com;
1315	+	thisv = mol->getComVel()-comVel;
1316	+	thisMass = mol->getMass();
1317	+	// Compute moment of intertia coefficients.
1318	+	xx += thisq[0]*thisq[0]*thisMass;
1319	+	yy += thisq[1]*thisq[1]*thisMass;
1320	+	zz += thisq[2]*thisq[2]*thisMass;
1321	+
1322	+	// compute products of intertia
1323	+	xy += thisq[0]*thisq[1]*thisMass;
1324	+	xz += thisq[0]*thisq[2]*thisMass;
1325	+	yz += thisq[1]*thisq[2]*thisMass;
1326	+
1327	+	angularMomentum += cross( thisq, thisv ) * thisMass;
1328	+
1329	+	}
1330	+
1331	+
1332	+	inertiaTensor(0,0) = yy + zz;
1333	+	inertiaTensor(0,1) = -xy;
1334	+	inertiaTensor(0,2) = -xz;
1335	+	inertiaTensor(1,0) = -xy;
1336	+	inertiaTensor(1,1) = xx + zz;
1337	+	inertiaTensor(1,2) = -yz;
1338	+	inertiaTensor(2,0) = -xz;
1339	+	inertiaTensor(2,1) = -yz;
1340	+	inertiaTensor(2,2) = xx + yy;
1341	+
1342	+	#ifdef IS_MPI
1343	+	Mat3x3d tmpI(inertiaTensor);
1344	+	Vector3d tmpAngMom;
1345	+	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1346	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1347	+	#endif
1348	+
1349	+	return;
1350	+	}
1351	+
1352	+	//Returns the angular momentum of the system
1353	+	Vector3d SimInfo::getAngularMomentum(){
1354	+
1355	+	Vector3d com(0.0);
1356	+	Vector3d comVel(0.0);
1357	+	Vector3d angularMomentum(0.0);
1358	+
1359	+	getComAll(com,comVel);
1360	+
1361	+	SimInfo::MoleculeIterator i;
1362	+	Molecule* mol;
1363	+
1364	+	Vector3d thisr(0.0);
1365	+	Vector3d thisp(0.0);
1366	+
1367	+	double thisMass;
1368	+
1369	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1370	+	thisMass = mol->getMass();
1371	+	thisr = mol->getCom()-com;
1372	+	thisp = (mol->getComVel()-comVel)*thisMass;
1373	+
1374	+	angularMomentum += cross( thisr, thisp );
1375	+
1376	+	}
1377	+
1378	+	#ifdef IS_MPI
1379	+	Vector3d tmpAngMom;
1380	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1381	+	#endif
1382	+
1383	+	return angularMomentum;
1384	+	}
1385	+
1386	+
1387		}//end namespace oopse
1388

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