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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 316 by tim, Fri Feb 11 22:41:02 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1503 by gezelter, Sat Oct 2 19:54:41 2010 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 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		/**
#	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/fSwitchingFunctionType.h"
59		#include "UseTheForce/doForces_interface.h"
60	<	#include "UseTheForce/notifyCutoffs_interface.h"
60	>	#include "UseTheForce/DarkSide/neighborLists_interface.h"
61	>	#include "UseTheForce/DarkSide/switcheroo_interface.h"
62		#include "utils/MemoryUtils.hpp"
63		#include "utils/simError.h"
64		#include "selection/SelectionManager.hpp"
65	+	#include "io/ForceFieldOptions.hpp"
66	+	#include "UseTheForce/ForceField.hpp"
67
68	+
69		#ifdef IS_MPI
70		#include "UseTheForce/mpiComponentPlan.h"
71		#include "UseTheForce/DarkSide/simParallel_interface.h"
72		#endif
73
74	<	namespace oopse {
74	>	namespace OpenMD {
75	>	std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
76	>	std::map<int, std::set<int> >::iterator i = container.find(index);
77	>	std::set<int> result;
78	>	if (i != container.end()) {
79	>	result = i->second;
80	>	}
81
82	<	SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
83	<	ForceField* ff, Globals* simParams) :
84	<	forceField_(ff), simParams_(simParams),
85	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
86	<	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
87	<	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
88	<	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
89	<	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
90	<	sman_(NULL), fortranInitialized_(false), selectMan_(NULL) {
82	>	return result;
83	>	}
84	>
85	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
86	>	forceField_(ff), simParams_(simParams),
87	>	ndf_(0), fdf_local(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), nInversions_(0),
91	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
92	>	nConstraints_(0), sman_(NULL), fortranInitialized_(false),
93	>	calcBoxDipole_(false), useAtomicVirial_(true) {
94
95	<
96	<	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
97	<	MoleculeStamp* molStamp;
98	<	int nMolWithSameStamp;
99	<	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
100	<	int nGroups = 0;          //total cutoff groups defined in meta-data file
101	<	CutoffGroupStamp* cgStamp;
102	<	RigidBodyStamp* rbStamp;
103	<	int nRigidAtoms = 0;
104	<
105	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
106	<	molStamp = i->first;
107	<	nMolWithSameStamp = i->second;
95	>
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	>	std::vector<Component*> components = simParams->getComponents();
105	>
106	>	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
107	>	molStamp = (*i)->getMoleculeStamp();
108	>	nMolWithSameStamp = (*i)->getNMol();
109
110		addMoleculeStamp(molStamp, nMolWithSameStamp);
111
112		//calculate atoms in molecules
113		nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
114
97	–
115		//calculate atoms in cutoff groups
116		int nAtomsInGroups = 0;
117		int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
118
119		for (int j=0; j < nCutoffGroupsInStamp; j++) {
120	<	cgStamp = molStamp->getCutoffGroup(j);
121	<	nAtomsInGroups += cgStamp->getNMembers();
120	>	cgStamp = molStamp->getCutoffGroupStamp(j);
121	>	nAtomsInGroups += cgStamp->getNMembers();
122		}
123
124		nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
125	+
126		nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
127
128		//calculate atoms in rigid bodies
#	Line 112 | Line 130 | SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*,
130		int nRigidBodiesInStamp = molStamp->getNRigidBodies();
131
132		for (int j=0; j < nRigidBodiesInStamp; j++) {
133	<	rbStamp = molStamp->getRigidBody(j);
134	<	nAtomsInRigidBodies += rbStamp->getNMembers();
133	>	rbStamp = molStamp->getRigidBodyStamp(j);
134	>	nAtomsInRigidBodies += rbStamp->getNMembers();
135		}
136
137		nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
138		nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
139
140	<	}
140	>	}
141
142	<	//every free atom (atom does not belong to cutoff groups) is a cutoff group
143	<	//therefore the total number of cutoff groups in the system is equal to
144	<	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
145	<	//file plus the number of cutoff groups defined in meta-data file
146	<	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
142	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
143	>	//group therefore the total number of cutoff groups in the system is
144	>	//equal to the total number of atoms minus number of atoms belong to
145	>	//cutoff group defined in meta-data file plus the number of cutoff
146	>	//groups defined in meta-data file
147	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
148
149	<	//every free atom (atom does not belong to rigid bodies) is an integrable object
150	<	//therefore the total number of  integrable objects in the system is equal to
151	<	//the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
152	<	//file plus the number of  rigid bodies defined in meta-data file
153	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
149	>	//every free atom (atom does not belong to rigid bodies) is an
150	>	//integrable object therefore the total number of integrable objects
151	>	//in the system is equal to the total number of atoms minus number of
152	>	//atoms belong to rigid body defined in meta-data file plus the number
153	>	//of rigid bodies defined in meta-data file
154	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
155	>	+ nGlobalRigidBodies_;
156	>
157	>	nGlobalMols_ = molStampIds_.size();
158	>	molToProcMap_.resize(nGlobalMols_);
159	>	}
160
161	<	nGlobalMols_ = molStampIds_.size();
162	<
163	<	#ifdef IS_MPI
164	<	molToProcMap_.resize(nGlobalMols_);
165	<	#endif
166	<
167	<	selectMan_ = new SelectionManager(this);
143	<	selectMan_->selectAll();
144	<	}
145	<
146	<	SimInfo::~SimInfo() {
147	<	//MemoryUtils::deleteVectorOfPointer(molecules_);
148	<
149	<	MemoryUtils::deleteVectorOfPointer(moleculeStamps_);
150	<
161	>	SimInfo::~SimInfo() {
162	>	std::map<int, Molecule*>::iterator i;
163	>	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
164	>	delete i->second;
165	>	}
166	>	molecules_.clear();
167	>
168		delete sman_;
169		delete simParams_;
170		delete forceField_;
171	<	delete selectMan_;
155	<	}
171	>	}
172
173	<	int SimInfo::getNGlobalConstraints() {
173	>	int SimInfo::getNGlobalConstraints() {
174		int nGlobalConstraints;
175		#ifdef IS_MPI
176		MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
#	Line 163 | Line 179 | int SimInfo::getNGlobalConstraints() {
179		nGlobalConstraints =  nConstraints_;
180		#endif
181		return nGlobalConstraints;
182	<	}
182	>	}
183
184	<	bool SimInfo::addMolecule(Molecule* mol) {
184	>	bool SimInfo::addMolecule(Molecule* mol) {
185		MoleculeIterator i;
186
187		i = molecules_.find(mol->getGlobalIndex());
188		if (i == molecules_.end() ) {
189
190	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
190	>	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
191
192	<	nAtoms_ += mol->getNAtoms();
193	<	nBonds_ += mol->getNBonds();
194	<	nBends_ += mol->getNBends();
195	<	nTorsions_ += mol->getNTorsions();
196	<	nRigidBodies_ += mol->getNRigidBodies();
197	<	nIntegrableObjects_ += mol->getNIntegrableObjects();
198	<	nCutoffGroups_ += mol->getNCutoffGroups();
199	<	nConstraints_ += mol->getNConstraintPairs();
192	>	nAtoms_ += mol->getNAtoms();
193	>	nBonds_ += mol->getNBonds();
194	>	nBends_ += mol->getNBends();
195	>	nTorsions_ += mol->getNTorsions();
196	>	nInversions_ += mol->getNInversions();
197	>	nRigidBodies_ += mol->getNRigidBodies();
198	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
199	>	nCutoffGroups_ += mol->getNCutoffGroups();
200	>	nConstraints_ += mol->getNConstraintPairs();
201
202	<	addExcludePairs(mol);
203	<
204	<	return true;
202	>	addInteractionPairs(mol);
203	>
204	>	return true;
205		} else {
206	<	return false;
206	>	return false;
207		}
208	<	}
208	>	}
209
210	<	bool SimInfo::removeMolecule(Molecule* mol) {
210	>	bool SimInfo::removeMolecule(Molecule* mol) {
211		MoleculeIterator i;
212		i = molecules_.find(mol->getGlobalIndex());
213
214		if (i != molecules_.end() ) {
215
216	<	assert(mol == i->second);
216	>	assert(mol == i->second);
217
218	<	nAtoms_ -= mol->getNAtoms();
219	<	nBonds_ -= mol->getNBonds();
220	<	nBends_ -= mol->getNBends();
221	<	nTorsions_ -= mol->getNTorsions();
222	<	nRigidBodies_ -= mol->getNRigidBodies();
223	<	nIntegrableObjects_ -= mol->getNIntegrableObjects();
224	<	nCutoffGroups_ -= mol->getNCutoffGroups();
225	<	nConstraints_ -= mol->getNConstraintPairs();
218	>	nAtoms_ -= mol->getNAtoms();
219	>	nBonds_ -= mol->getNBonds();
220	>	nBends_ -= mol->getNBends();
221	>	nTorsions_ -= mol->getNTorsions();
222	>	nInversions_ -= mol->getNInversions();
223	>	nRigidBodies_ -= mol->getNRigidBodies();
224	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
225	>	nCutoffGroups_ -= mol->getNCutoffGroups();
226	>	nConstraints_ -= mol->getNConstraintPairs();
227
228	<	removeExcludePairs(mol);
229	<	molecules_.erase(mol->getGlobalIndex());
228	>	removeInteractionPairs(mol);
229	>	molecules_.erase(mol->getGlobalIndex());
230
231	<	delete mol;
231	>	delete mol;
232
233	<	return true;
233	>	return true;
234		} else {
235	<	return false;
235	>	return false;
236		}
237
238
239	<	}
239	>	}
240
241
242	<	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
242	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
243		i = molecules_.begin();
244		return i == molecules_.end() ? NULL : i->second;
245	<	}
245	>	}
246
247	<	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
247	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
248		++i;
249		return i == molecules_.end() ? NULL : i->second;
250	<	}
250	>	}
251
252
253	<	void SimInfo::calcNdf() {
253	>	void SimInfo::calcNdf() {
254		int ndf_local;
255		MoleculeIterator i;
256		std::vector<StuntDouble*>::iterator j;
#	Line 242 | Line 260 | void SimInfo::calcNdf() {
260		ndf_local = 0;
261
262		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
263	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
264	<	integrableObject = mol->nextIntegrableObject(j)) {
263	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
264	>	integrableObject = mol->nextIntegrableObject(j)) {
265
266	<	ndf_local += 3;
266	>	ndf_local += 3;
267
268	<	if (integrableObject->isDirectional()) {
269	<	if (integrableObject->isLinear()) {
270	<	ndf_local += 2;
271	<	} else {
272	<	ndf_local += 3;
273	<	}
274	<	}
268	>	if (integrableObject->isDirectional()) {
269	>	if (integrableObject->isLinear()) {
270	>	ndf_local += 2;
271	>	} else {
272	>	ndf_local += 3;
273	>	}
274	>	}
275
276	<	}//end for (integrableObject)
277	<	}// end for (mol)
276	>	}
277	>	}
278
279		// n_constraints is local, so subtract them on each processor
280		ndf_local -= nConstraints_;
#	Line 271 | Line 289 | void SimInfo::calcNdf() {
289		// entire system:
290		ndf_ = ndf_ - 3 - nZconstraint_;
291
292	<	}
292	>	}
293
294	<	void SimInfo::calcNdfRaw() {
294	>	int SimInfo::getFdf() {
295	>	#ifdef IS_MPI
296	>	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
297	>	#else
298	>	fdf_ = fdf_local;
299	>	#endif
300	>	return fdf_;
301	>	}
302	>
303	>	void SimInfo::calcNdfRaw() {
304		int ndfRaw_local;
305
306		MoleculeIterator i;
#	Line 285 | Line 312 | void SimInfo::calcNdfRaw() {
312		ndfRaw_local = 0;
313
314		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
315	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
316	<	integrableObject = mol->nextIntegrableObject(j)) {
315	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
316	>	integrableObject = mol->nextIntegrableObject(j)) {
317
318	<	ndfRaw_local += 3;
318	>	ndfRaw_local += 3;
319
320	<	if (integrableObject->isDirectional()) {
321	<	if (integrableObject->isLinear()) {
322	<	ndfRaw_local += 2;
323	<	} else {
324	<	ndfRaw_local += 3;
325	<	}
326	<	}
320	>	if (integrableObject->isDirectional()) {
321	>	if (integrableObject->isLinear()) {
322	>	ndfRaw_local += 2;
323	>	} else {
324	>	ndfRaw_local += 3;
325	>	}
326	>	}
327
328	<	}
328	>	}
329		}
330
331		#ifdef IS_MPI
#	Line 306 | Line 333 | void SimInfo::calcNdfRaw() {
333		#else
334		ndfRaw_ = ndfRaw_local;
335		#endif
336	<	}
336	>	}
337
338	<	void SimInfo::calcNdfTrans() {
338	>	void SimInfo::calcNdfTrans() {
339		int ndfTrans_local;
340
341		ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
#	Line 322 | Line 349 | void SimInfo::calcNdfTrans() {
349
350		ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
351
352	<	}
352	>	}
353
354	<	void SimInfo::addExcludePairs(Molecule* mol) {
354	>	void SimInfo::addInteractionPairs(Molecule* mol) {
355	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
356		std::vector<Bond*>::iterator bondIter;
357		std::vector<Bend*>::iterator bendIter;
358		std::vector<Torsion*>::iterator torsionIter;
359	+	std::vector<Inversion*>::iterator inversionIter;
360		Bond* bond;
361		Bend* bend;
362		Torsion* torsion;
363	+	Inversion* inversion;
364		int a;
365		int b;
366		int c;
367		int d;
368	+
369	+	// atomGroups can be used to add special interaction maps between
370	+	// groups of atoms that are in two separate rigid bodies.
371	+	// However, most site-site interactions between two rigid bodies
372	+	// are probably not special, just the ones between the physically
373	+	// bonded atoms.  Interactions *within* a single rigid body should
374	+	// always be excluded.  These are done at the bottom of this
375	+	// function.
376	+
377	+	std::map<int, std::set<int> > atomGroups;
378	+	Molecule::RigidBodyIterator rbIter;
379	+	RigidBody* rb;
380	+	Molecule::IntegrableObjectIterator ii;
381	+	StuntDouble* integrableObject;
382
383	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
384	<	a = bond->getAtomA()->getGlobalIndex();
385	<	b = bond->getAtomB()->getGlobalIndex();
386	<	exclude_.addPair(a, b);
383	>	for (integrableObject = mol->beginIntegrableObject(ii);
384	>	integrableObject != NULL;
385	>	integrableObject = mol->nextIntegrableObject(ii)) {
386	>
387	>	if (integrableObject->isRigidBody()) {
388	>	rb = static_cast<RigidBody*>(integrableObject);
389	>	std::vector<Atom*> atoms = rb->getAtoms();
390	>	std::set<int> rigidAtoms;
391	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
392	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
393	>	}
394	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
395	>	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
396	>	}
397	>	} else {
398	>	std::set<int> oneAtomSet;
399	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
400	>	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
401	>	}
402	>	}
403	>
404	>	for (bond= mol->beginBond(bondIter); bond != NULL;
405	>	bond = mol->nextBond(bondIter)) {
406	>
407	>	a = bond->getAtomA()->getGlobalIndex();
408	>	b = bond->getAtomB()->getGlobalIndex();
409	>
410	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
411	>	oneTwoInteractions_.addPair(a, b);
412	>	} else {
413	>	excludedInteractions_.addPair(a, b);
414	>	}
415		}
416
417	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
418	<	a = bend->getAtomA()->getGlobalIndex();
347	<	b = bend->getAtomB()->getGlobalIndex();
348	<	c = bend->getAtomC()->getGlobalIndex();
417	>	for (bend= mol->beginBend(bendIter); bend != NULL;
418	>	bend = mol->nextBend(bendIter)) {
419
420	<	exclude_.addPair(a, b);
421	<	exclude_.addPair(a, c);
422	<	exclude_.addPair(b, c);
420	>	a = bend->getAtomA()->getGlobalIndex();
421	>	b = bend->getAtomB()->getGlobalIndex();
422	>	c = bend->getAtomC()->getGlobalIndex();
423	>
424	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
425	>	oneTwoInteractions_.addPair(a, b);
426	>	oneTwoInteractions_.addPair(b, c);
427	>	} else {
428	>	excludedInteractions_.addPair(a, b);
429	>	excludedInteractions_.addPair(b, c);
430	>	}
431	>
432	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
433	>	oneThreeInteractions_.addPair(a, c);
434	>	} else {
435	>	excludedInteractions_.addPair(a, c);
436	>	}
437		}
438
439	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
440	<	a = torsion->getAtomA()->getGlobalIndex();
357	<	b = torsion->getAtomB()->getGlobalIndex();
358	<	c = torsion->getAtomC()->getGlobalIndex();
359	<	d = torsion->getAtomD()->getGlobalIndex();
439	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
440	>	torsion = mol->nextTorsion(torsionIter)) {
441
442	<	exclude_.addPair(a, b);
443	<	exclude_.addPair(a, c);
444	<	exclude_.addPair(a, d);
445	<	exclude_.addPair(b, c);
365	<	exclude_.addPair(b, d);
366	<	exclude_.addPair(c, d);
367	<	}
442	>	a = torsion->getAtomA()->getGlobalIndex();
443	>	b = torsion->getAtomB()->getGlobalIndex();
444	>	c = torsion->getAtomC()->getGlobalIndex();
445	>	d = torsion->getAtomD()->getGlobalIndex();
446
447	<
448	<	}
447	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
448	>	oneTwoInteractions_.addPair(a, b);
449	>	oneTwoInteractions_.addPair(b, c);
450	>	oneTwoInteractions_.addPair(c, d);
451	>	} else {
452	>	excludedInteractions_.addPair(a, b);
453	>	excludedInteractions_.addPair(b, c);
454	>	excludedInteractions_.addPair(c, d);
455	>	}
456
457	<	void SimInfo::removeExcludePairs(Molecule* mol) {
457	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
458	>	oneThreeInteractions_.addPair(a, c);
459	>	oneThreeInteractions_.addPair(b, d);
460	>	} else {
461	>	excludedInteractions_.addPair(a, c);
462	>	excludedInteractions_.addPair(b, d);
463	>	}
464	>
465	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
466	>	oneFourInteractions_.addPair(a, d);
467	>	} else {
468	>	excludedInteractions_.addPair(a, d);
469	>	}
470	>	}
471	>
472	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
473	>	inversion = mol->nextInversion(inversionIter)) {
474	>
475	>	a = inversion->getAtomA()->getGlobalIndex();
476	>	b = inversion->getAtomB()->getGlobalIndex();
477	>	c = inversion->getAtomC()->getGlobalIndex();
478	>	d = inversion->getAtomD()->getGlobalIndex();
479	>
480	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
481	>	oneTwoInteractions_.addPair(a, b);
482	>	oneTwoInteractions_.addPair(a, c);
483	>	oneTwoInteractions_.addPair(a, d);
484	>	} else {
485	>	excludedInteractions_.addPair(a, b);
486	>	excludedInteractions_.addPair(a, c);
487	>	excludedInteractions_.addPair(a, d);
488	>	}
489	>
490	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
491	>	oneThreeInteractions_.addPair(b, c);
492	>	oneThreeInteractions_.addPair(b, d);
493	>	oneThreeInteractions_.addPair(c, d);
494	>	} else {
495	>	excludedInteractions_.addPair(b, c);
496	>	excludedInteractions_.addPair(b, d);
497	>	excludedInteractions_.addPair(c, d);
498	>	}
499	>	}
500	>
501	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
502	>	rb = mol->nextRigidBody(rbIter)) {
503	>	std::vector<Atom*> atoms = rb->getAtoms();
504	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
505	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
506	>	a = atoms[i]->getGlobalIndex();
507	>	b = atoms[j]->getGlobalIndex();
508	>	excludedInteractions_.addPair(a, b);
509	>	}
510	>	}
511	>	}
512	>
513	>	}
514	>
515	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
516	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
517		std::vector<Bond*>::iterator bondIter;
518		std::vector<Bend*>::iterator bendIter;
519		std::vector<Torsion*>::iterator torsionIter;
520	+	std::vector<Inversion*>::iterator inversionIter;
521		Bond* bond;
522		Bend* bend;
523		Torsion* torsion;
524	+	Inversion* inversion;
525		int a;
526		int b;
527		int c;
528		int d;
529	+
530	+	std::map<int, std::set<int> > atomGroups;
531	+	Molecule::RigidBodyIterator rbIter;
532	+	RigidBody* rb;
533	+	Molecule::IntegrableObjectIterator ii;
534	+	StuntDouble* integrableObject;
535
536	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
537	<	a = bond->getAtomA()->getGlobalIndex();
538	<	b = bond->getAtomB()->getGlobalIndex();
539	<	exclude_.removePair(a, b);
536	>	for (integrableObject = mol->beginIntegrableObject(ii);
537	>	integrableObject != NULL;
538	>	integrableObject = mol->nextIntegrableObject(ii)) {
539	>
540	>	if (integrableObject->isRigidBody()) {
541	>	rb = static_cast<RigidBody*>(integrableObject);
542	>	std::vector<Atom*> atoms = rb->getAtoms();
543	>	std::set<int> rigidAtoms;
544	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
545	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
546	>	}
547	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
548	>	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
549	>	}
550	>	} else {
551	>	std::set<int> oneAtomSet;
552	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
553	>	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
554	>	}
555	>	}
556	>
557	>	for (bond= mol->beginBond(bondIter); bond != NULL;
558	>	bond = mol->nextBond(bondIter)) {
559	>
560	>	a = bond->getAtomA()->getGlobalIndex();
561	>	b = bond->getAtomB()->getGlobalIndex();
562	>
563	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
564	>	oneTwoInteractions_.removePair(a, b);
565	>	} else {
566	>	excludedInteractions_.removePair(a, b);
567	>	}
568		}
569
570	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
571	<	a = bend->getAtomA()->getGlobalIndex();
392	<	b = bend->getAtomB()->getGlobalIndex();
393	<	c = bend->getAtomC()->getGlobalIndex();
570	>	for (bend= mol->beginBend(bendIter); bend != NULL;
571	>	bend = mol->nextBend(bendIter)) {
572
573	<	exclude_.removePair(a, b);
574	<	exclude_.removePair(a, c);
575	<	exclude_.removePair(b, c);
573	>	a = bend->getAtomA()->getGlobalIndex();
574	>	b = bend->getAtomB()->getGlobalIndex();
575	>	c = bend->getAtomC()->getGlobalIndex();
576	>
577	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
578	>	oneTwoInteractions_.removePair(a, b);
579	>	oneTwoInteractions_.removePair(b, c);
580	>	} else {
581	>	excludedInteractions_.removePair(a, b);
582	>	excludedInteractions_.removePair(b, c);
583	>	}
584	>
585	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
586	>	oneThreeInteractions_.removePair(a, c);
587	>	} else {
588	>	excludedInteractions_.removePair(a, c);
589	>	}
590		}
591
592	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
593	<	a = torsion->getAtomA()->getGlobalIndex();
402	<	b = torsion->getAtomB()->getGlobalIndex();
403	<	c = torsion->getAtomC()->getGlobalIndex();
404	<	d = torsion->getAtomD()->getGlobalIndex();
592	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
593	>	torsion = mol->nextTorsion(torsionIter)) {
594
595	<	exclude_.removePair(a, b);
596	<	exclude_.removePair(a, c);
597	<	exclude_.removePair(a, d);
598	<	exclude_.removePair(b, c);
599	<	exclude_.removePair(b, d);
600	<	exclude_.removePair(c, d);
595	>	a = torsion->getAtomA()->getGlobalIndex();
596	>	b = torsion->getAtomB()->getGlobalIndex();
597	>	c = torsion->getAtomC()->getGlobalIndex();
598	>	d = torsion->getAtomD()->getGlobalIndex();
599	>
600	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
601	>	oneTwoInteractions_.removePair(a, b);
602	>	oneTwoInteractions_.removePair(b, c);
603	>	oneTwoInteractions_.removePair(c, d);
604	>	} else {
605	>	excludedInteractions_.removePair(a, b);
606	>	excludedInteractions_.removePair(b, c);
607	>	excludedInteractions_.removePair(c, d);
608	>	}
609	>
610	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
611	>	oneThreeInteractions_.removePair(a, c);
612	>	oneThreeInteractions_.removePair(b, d);
613	>	} else {
614	>	excludedInteractions_.removePair(a, c);
615	>	excludedInteractions_.removePair(b, d);
616	>	}
617	>
618	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
619	>	oneFourInteractions_.removePair(a, d);
620	>	} else {
621	>	excludedInteractions_.removePair(a, d);
622	>	}
623		}
624
625	<	}
625	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
626	>	inversion = mol->nextInversion(inversionIter)) {
627
628	+	a = inversion->getAtomA()->getGlobalIndex();
629	+	b = inversion->getAtomB()->getGlobalIndex();
630	+	c = inversion->getAtomC()->getGlobalIndex();
631	+	d = inversion->getAtomD()->getGlobalIndex();
632
633	<	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
634	<	int curStampId;
633	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
634	>	oneTwoInteractions_.removePair(a, b);
635	>	oneTwoInteractions_.removePair(a, c);
636	>	oneTwoInteractions_.removePair(a, d);
637	>	} else {
638	>	excludedInteractions_.removePair(a, b);
639	>	excludedInteractions_.removePair(a, c);
640	>	excludedInteractions_.removePair(a, d);
641	>	}
642
643	+	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
644	+	oneThreeInteractions_.removePair(b, c);
645	+	oneThreeInteractions_.removePair(b, d);
646	+	oneThreeInteractions_.removePair(c, d);
647	+	} else {
648	+	excludedInteractions_.removePair(b, c);
649	+	excludedInteractions_.removePair(b, d);
650	+	excludedInteractions_.removePair(c, d);
651	+	}
652	+	}
653	+
654	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
655	+	rb = mol->nextRigidBody(rbIter)) {
656	+	std::vector<Atom*> atoms = rb->getAtoms();
657	+	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
658	+	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
659	+	a = atoms[i]->getGlobalIndex();
660	+	b = atoms[j]->getGlobalIndex();
661	+	excludedInteractions_.removePair(a, b);
662	+	}
663	+	}
664	+	}
665	+
666	+	}
667	+
668	+
669	+	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
670	+	int curStampId;
671	+
672		//index from 0
673		curStampId = moleculeStamps_.size();
674
675		moleculeStamps_.push_back(molStamp);
676		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
677	<	}
677	>	}
678
679	<	void SimInfo::update() {
679	>	void SimInfo::update() {
680
681		setupSimType();
682
#	Line 437 | Line 689 | void SimInfo::update() {
689		//setup fortran force field
690		/** @deprecate */
691		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	–
692
693		setupCutoff();
694	+
695	+	setupElectrostaticSummationMethod( isError );
696	+	setupSwitchingFunction();
697	+	setupAccumulateBoxDipole();
698
699	+	if(isError){
700	+	sprintf( painCave.errMsg,
701	+	"ForceField error: There was an error initializing the forceField in fortran.\n" );
702	+	painCave.isFatal = 1;
703	+	simError();
704	+	}
705	+
706		calcNdf();
707		calcNdfRaw();
708		calcNdfTrans();
709
710		fortranInitialized_ = true;
711	<	}
711	>	}
712
713	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
713	>	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
714		SimInfo::MoleculeIterator mi;
715		Molecule* mol;
716		Molecule::AtomIterator ai;
#	Line 464 | Line 719 | std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
719
720		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
721
722	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
723	<	atomTypes.insert(atom->getAtomType());
724	<	}
722	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
723	>	atomTypes.insert(atom->getAtomType());
724	>	}
725
726		}
727
728		return atomTypes;
729	<	}
729	>	}
730
731	<	void SimInfo::setupSimType() {
731	>	void SimInfo::setupSimType() {
732		std::set<AtomType*>::iterator i;
733		std::set<AtomType*> atomTypes;
734		atomTypes = getUniqueAtomTypes();
#	Line 481 | Line 736 | void SimInfo::setupSimType() {
736		int useLennardJones = 0;
737		int useElectrostatic = 0;
738		int useEAM = 0;
739	+	int useSC = 0;
740		int useCharge = 0;
741		int useDirectional = 0;
742		int useDipole = 0;
743		int useGayBerne = 0;
744		int useSticky = 0;
745	+	int useStickyPower = 0;
746		int useShape = 0;
747		int useFLARB = 0; //it is not in AtomType yet
748		int useDirectionalAtom = 0;
749		int useElectrostatics = 0;
750		//usePBC and useRF are from simParams
751	<	int usePBC = simParams_->getPBC();
752	<	int useRF = simParams_->getUseRF();
751	>	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
752	>	int useRF;
753	>	int useSF;
754	>	int useSP;
755	>	int useBoxDipole;
756
757	+	std::string myMethod;
758	+
759	+	// set the useRF logical
760	+	useRF = 0;
761	+	useSF = 0;
762	+	useSP = 0;
763	+	useBoxDipole = 0;
764	+
765	+
766	+	if (simParams_->haveElectrostaticSummationMethod()) {
767	+	std::string myMethod = simParams_->getElectrostaticSummationMethod();
768	+	toUpper(myMethod);
769	+	if (myMethod == "REACTION_FIELD"){
770	+	useRF = 1;
771	+	} else if (myMethod == "SHIFTED_FORCE"){
772	+	useSF = 1;
773	+	} else if (myMethod == "SHIFTED_POTENTIAL"){
774	+	useSP = 1;
775	+	}
776	+	}
777	+
778	+	if (simParams_->haveAccumulateBoxDipole())
779	+	if (simParams_->getAccumulateBoxDipole())
780	+	useBoxDipole = 1;
781	+
782	+	useAtomicVirial_ = simParams_->getUseAtomicVirial();
783	+
784		//loop over all of the atom types
785		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
786	<	useLennardJones |= (*i)->isLennardJones();
787	<	useElectrostatic |= (*i)->isElectrostatic();
788	<	useEAM |= (*i)->isEAM();
789	<	useCharge |= (*i)->isCharge();
790	<	useDirectional |= (*i)->isDirectional();
791	<	useDipole |= (*i)->isDipole();
792	<	useGayBerne |= (*i)->isGayBerne();
793	<	useSticky |= (*i)->isSticky();
794	<	useShape |= (*i)->isShape();
786	>	useLennardJones |= (*i)->isLennardJones();
787	>	useElectrostatic |= (*i)->isElectrostatic();
788	>	useEAM |= (*i)->isEAM();
789	>	useSC |= (*i)->isSC();
790	>	useCharge |= (*i)->isCharge();
791	>	useDirectional |= (*i)->isDirectional();
792	>	useDipole |= (*i)->isDipole();
793	>	useGayBerne |= (*i)->isGayBerne();
794	>	useSticky |= (*i)->isSticky();
795	>	useStickyPower |= (*i)->isStickyPower();
796	>	useShape |= (*i)->isShape();
797		}
798
799	<	if (useSticky || useDipole || useGayBerne || useShape) {
800	<	useDirectionalAtom = 1;
799	>	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
800	>	useDirectionalAtom = 1;
801		}
802
803		if (useCharge || useDipole) {
804	<	useElectrostatics = 1;
804	>	useElectrostatics = 1;
805		}
806
807		#ifdef IS_MPI
#	Line 539 | Line 828 | void SimInfo::setupSimType() {
828		temp = useSticky;
829		MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
830
831	+	temp = useStickyPower;
832	+	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
833	+
834		temp = useGayBerne;
835		MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
836
837		temp = useEAM;
838		MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
839
840	+	temp = useSC;
841	+	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
842	+
843		temp = useShape;
844		MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
845
#	Line 553 | Line 848 | void SimInfo::setupSimType() {
848
849		temp = useRF;
850		MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
851	<
851	>
852	>	temp = useSF;
853	>	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
854	>
855	>	temp = useSP;
856	>	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
857	>
858	>	temp = useBoxDipole;
859	>	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
860	>
861	>	temp = useAtomicVirial_;
862	>	MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
863	>
864		#endif
865
866		fInfo_.SIM_uses_PBC = usePBC;
#	Line 563 | Line 870 | void SimInfo::setupSimType() {
870		fInfo_.SIM_uses_Charges = useCharge;
871		fInfo_.SIM_uses_Dipoles = useDipole;
872		fInfo_.SIM_uses_Sticky = useSticky;
873	+	fInfo_.SIM_uses_StickyPower = useStickyPower;
874		fInfo_.SIM_uses_GayBerne = useGayBerne;
875		fInfo_.SIM_uses_EAM = useEAM;
876	+	fInfo_.SIM_uses_SC = useSC;
877		fInfo_.SIM_uses_Shapes = useShape;
878		fInfo_.SIM_uses_FLARB = useFLARB;
879		fInfo_.SIM_uses_RF = useRF;
880	+	fInfo_.SIM_uses_SF = useSF;
881	+	fInfo_.SIM_uses_SP = useSP;
882	+	fInfo_.SIM_uses_BoxDipole = useBoxDipole;
883	+	fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
884	+	}
885
886	<	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() {
886	>	void SimInfo::setupFortranSim() {
887		int isError;
888	<	int nExclude;
888	>	int nExclude, nOneTwo, nOneThree, nOneFour;
889		std::vector<int> fortranGlobalGroupMembership;
890
596	–	nExclude = exclude_.getSize();
891		isError = 0;
892
893		//globalGroupMembership_ is filled by SimCreator
894		for (int i = 0; i < nGlobalAtoms_; i++) {
895	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
895	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
896		}
897
898		//calculate mass ratio of cutoff group
899	<	std::vector<double> mfact;
899	>	std::vector<RealType> mfact;
900		SimInfo::MoleculeIterator mi;
901		Molecule* mol;
902		Molecule::CutoffGroupIterator ci;
903		CutoffGroup* cg;
904		Molecule::AtomIterator ai;
905		Atom* atom;
906	<	double totalMass;
906	>	RealType totalMass;
907
908		//to avoid memory reallocation, reserve enough space for mfact
909		mfact.reserve(getNCutoffGroups());
910
911		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
912	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
912	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
913
914	<	totalMass = cg->getMass();
915	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
916	<	mfact.push_back(atom->getMass()/totalMass);
917	<	}
918	<
919	<	}
914	>	totalMass = cg->getMass();
915	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
916	>	// Check for massless groups - set mfact to 1 if true
917	>	if (totalMass != 0)
918	>	mfact.push_back(atom->getMass()/totalMass);
919	>	else
920	>	mfact.push_back( 1.0 );
921	>	}
922	>	}
923		}
924
925		//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
#	Line 632 | Line 929 | void SimInfo::setupFortranSim() {
929		identArray.reserve(getNAtoms());
930
931		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
932	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
933	<	identArray.push_back(atom->getIdent());
934	<	}
932	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
933	>	identArray.push_back(atom->getIdent());
934	>	}
935		}
936
937		//fill molMembershipArray
938		//molMembershipArray is filled by SimCreator
939		std::vector<int> molMembershipArray(nGlobalAtoms_);
940		for (int i = 0; i < nGlobalAtoms_; i++) {
941	<	molMembershipArray[i] = globalMolMembership_[i] + 1;
941	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
942		}
943
944		//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
651	–	int nGlobalExcludes = 0;
652	–	int* globalExcludes = NULL;
653	–	int* excludeList = exclude_.getExcludeList();
654	–	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
655	–	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
656	–	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
945
946	<	if( isError ){
946	>	nExclude = excludedInteractions_.getSize();
947	>	nOneTwo = oneTwoInteractions_.getSize();
948	>	nOneThree = oneThreeInteractions_.getSize();
949	>	nOneFour = oneFourInteractions_.getSize();
950
951	<	sprintf( painCave.errMsg,
952	<	"There was an error setting the simulation information in fortran.\n" );
953	<	painCave.isFatal = 1;
954	<	painCave.severity = OOPSE_ERROR;
664	<	simError();
665	<	}
951	>	int* excludeList = excludedInteractions_.getPairList();
952	>	int* oneTwoList = oneTwoInteractions_.getPairList();
953	>	int* oneThreeList = oneThreeInteractions_.getPairList();
954	>	int* oneFourList = oneFourInteractions_.getPairList();
955
956	<	#ifdef IS_MPI
956	>	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
957	>	&nExclude, excludeList,
958	>	&nOneTwo, oneTwoList,
959	>	&nOneThree, oneThreeList,
960	>	&nOneFour, oneFourList,
961	>	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
962	>	&fortranGlobalGroupMembership[0], &isError);
963	>
964	>	if( isError ){
965	>
966	>	sprintf( painCave.errMsg,
967	>	"There was an error setting the simulation information in fortran.\n" );
968	>	painCave.isFatal = 1;
969	>	painCave.severity = OPENMD_ERROR;
970	>	simError();
971	>	}
972	>
973	>
974		sprintf( checkPointMsg,
975	<	"succesfully sent the simulation information to fortran.\n");
976	<	MPIcheckPoint();
977	<	#endif // is_mpi
978	<	}
975	>	"succesfully sent the simulation information to fortran.\n");
976	>
977	>	errorCheckPoint();
978	>
979	>	// Setup number of neighbors in neighbor list if present
980	>	if (simParams_->haveNeighborListNeighbors()) {
981	>	int nlistNeighbors = simParams_->getNeighborListNeighbors();
982	>	setNeighbors(&nlistNeighbors);
983	>	}
984	>
985
986	+	}
987
988	<	#ifdef IS_MPI
989	<	void SimInfo::setupFortranParallel() {
990	<
988	>
989	>	void SimInfo::setupFortranParallel() {
990	>	#ifdef IS_MPI
991		//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
992		std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
993		std::vector<int> localToGlobalCutoffGroupIndex;
#	Line 689 | Line 1002 | void SimInfo::setupFortranParallel() {
1002
1003		for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
1004
1005	<	//local index(index in DataStorge) of atom is important
1006	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
1007	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
1008	<	}
1005	>	//local index(index in DataStorge) of atom is important
1006	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
1007	>	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
1008	>	}
1009
1010	<	//local index of cutoff group is trivial, it only depends on the order of travesing
1011	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
1012	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
1013	<	}
1010	>	//local index of cutoff group is trivial, it only depends on the order of travesing
1011	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
1012	>	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
1013	>	}
1014
1015		}
1016
#	Line 717 | Line 1030 | void SimInfo::setupFortranParallel() {
1030		&localToGlobalCutoffGroupIndex[0], &isError);
1031
1032		if (isError) {
1033	<	sprintf(painCave.errMsg,
1034	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
1035	<	painCave.isFatal = 1;
1036	<	simError();
1033	>	sprintf(painCave.errMsg,
1034	>	"mpiRefresh errror: fortran didn't like something we gave it.\n");
1035	>	painCave.isFatal = 1;
1036	>	simError();
1037		}
1038
1039		sprintf(checkPointMsg, " mpiRefresh successful.\n");
1040	<	MPIcheckPoint();
1040	>	errorCheckPoint();
1041
729	–
730	–	}
731	–
1042		#endif
1043	+	}
1044
1045	<	double SimInfo::calcMaxCutoffRadius() {
1045	>	void SimInfo::setupCutoff() {
1046	>
1047	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
1048
1049	+	// Check the cutoff policy
1050	+	int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
1051
1052	<	std::set<AtomType*> atomTypes;
1053	<	std::set<AtomType*>::iterator i;
1054	<	std::vector<double> cutoffRadius;
1052	>	// Set LJ shifting bools to false
1053	>	ljsp_ = 0;
1054	>	ljsf_ = 0;
1055
1056	<	//get the unique atom types
1057	<	atomTypes = getUniqueAtomTypes();
1058	<
1059	<	//query the max cutoff radius among these atom types
1060	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
746	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
1056	>	std::string myPolicy;
1057	>	if (forceFieldOptions_.haveCutoffPolicy()){
1058	>	myPolicy = forceFieldOptions_.getCutoffPolicy();
1059	>	}else if (simParams_->haveCutoffPolicy()) {
1060	>	myPolicy = simParams_->getCutoffPolicy();
1061		}
1062
1063	<	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
1064	<	#ifdef IS_MPI
1065	<	//pick the max cutoff radius among the processors
1066	<	#endif
1067	<
1068	<	return maxCutoffRadius;
1069	<	}
1070	<
1071	<	void SimInfo::setupCutoff() {
1072	<	double rcut_;  //cutoff radius
1073	<	double rsw_; //switching radius
1074	<
1075	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1076	<
1077	<	if (!simParams_->haveRcut()){
764	<	sprintf(painCave.errMsg,
765	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
766	<	"\tOOPSE will use a default value of 15.0 angstroms"
767	<	"\tfor the cutoffRadius.\n");
768	<	painCave.isFatal = 0;
1063	>	if (!myPolicy.empty()){
1064	>	toUpper(myPolicy);
1065	>	if (myPolicy == "MIX") {
1066	>	cp = MIX_CUTOFF_POLICY;
1067	>	} else {
1068	>	if (myPolicy == "MAX") {
1069	>	cp = MAX_CUTOFF_POLICY;
1070	>	} else {
1071	>	if (myPolicy == "TRADITIONAL") {
1072	>	cp = TRADITIONAL_CUTOFF_POLICY;
1073	>	} else {
1074	>	// throw error
1075	>	sprintf( painCave.errMsg,
1076	>	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
1077	>	painCave.isFatal = 1;
1078		simError();
1079	<	rcut_ = 15.0;
1080	<	} else{
1081	<	rcut_ = simParams_->getRcut();
1082	<	}
1079	>	}
1080	>	}
1081	>	}
1082	>	}
1083	>	notifyFortranCutoffPolicy(&cp);
1084
1085	<	if (!simParams_->haveRsw()){
1086	<	sprintf(painCave.errMsg,
1087	<	"SimCreator Warning: No value was set for switchingRadius.\n"
1088	<	"\tOOPSE will use a default value of\n"
1089	<	"\t0.95 * cutoffRadius for the switchingRadius\n");
1090	<	painCave.isFatal = 0;
781	<	simError();
782	<	rsw_ = 0.95 * rcut_;
783	<	} else{
784	<	rsw_ = simParams_->getRsw();
785	<	}
786	<
787	<	} else {
788	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
789	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
1085	>	// Check the Skin Thickness for neighborlists
1086	>	RealType skin;
1087	>	if (simParams_->haveSkinThickness()) {
1088	>	skin = simParams_->getSkinThickness();
1089	>	notifyFortranSkinThickness(&skin);
1090	>	}
1091
1092	<	if (simParams_->haveRcut()) {
1093	<	rcut_ = simParams_->getRcut();
1094	<	} else {
1095	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
1096	<	rcut_ = calcMaxCutoffRadius();
1097	<	}
1092	>	// Check if the cutoff was set explicitly:
1093	>	if (simParams_->haveCutoffRadius()) {
1094	>	rcut_ = simParams_->getCutoffRadius();
1095	>	if (simParams_->haveSwitchingRadius()) {
1096	>	rsw_  = simParams_->getSwitchingRadius();
1097	>	} else {
1098	>	if (fInfo_.SIM_uses_Charges |
1099	>	fInfo_.SIM_uses_Dipoles |
1100	>	fInfo_.SIM_uses_RF) {
1101	>
1102	>	rsw_ = 0.85 * rcut_;
1103	>	sprintf(painCave.errMsg,
1104	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
1105	>	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
1106	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1107	>	painCave.isFatal = 0;
1108	>	simError();
1109	>	} else {
1110	>	rsw_ = rcut_;
1111	>	sprintf(painCave.errMsg,
1112	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
1113	>	"\tOpenMD will use the same value as the cutoffRadius.\n"
1114	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1115	>	painCave.isFatal = 0;
1116	>	simError();
1117	>	}
1118	>	}
1119
1120	<	if (simParams_->haveRsw()) {
1121	<	rsw_  = simParams_->getRsw();
1122	<	} else {
801	<	rsw_ = rcut_;
802	<	}
803	<
804	<	}
1120	>	if (simParams_->haveElectrostaticSummationMethod()) {
1121	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1122	>	toUpper(myMethod);
1123
1124	<	double rnblist = rcut_ + 1; // skin of neighbor list
1124	>	if (myMethod == "SHIFTED_POTENTIAL") {
1125	>	ljsp_ = 1;
1126	>	} else if (myMethod == "SHIFTED_FORCE") {
1127	>	ljsf_ = 1;
1128	>	}
1129	>	}
1130
1131	<	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
1132	<	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist);
1133	<	}
1131	>	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1132	>
1133	>	} else {
1134	>
1135	>	// For electrostatic atoms, we'll assume a large safe value:
1136	>	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1137	>	sprintf(painCave.errMsg,
1138	>	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1139	>	"\tOpenMD will use a default value of 15.0 angstroms"
1140	>	"\tfor the cutoffRadius.\n");
1141	>	painCave.isFatal = 0;
1142	>	simError();
1143	>	rcut_ = 15.0;
1144	>
1145	>	if (simParams_->haveElectrostaticSummationMethod()) {
1146	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1147	>	toUpper(myMethod);
1148	>
1149	>	// For the time being, we're tethering the LJ shifted behavior to the
1150	>	// electrostaticSummationMethod keyword options
1151	>	if (myMethod == "SHIFTED_POTENTIAL") {
1152	>	ljsp_ = 1;
1153	>	} else if (myMethod == "SHIFTED_FORCE") {
1154	>	ljsf_ = 1;
1155	>	}
1156	>	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1157	>	if (simParams_->haveSwitchingRadius()){
1158	>	sprintf(painCave.errMsg,
1159	>	"SimInfo Warning: A value was set for the switchingRadius\n"
1160	>	"\teven though the electrostaticSummationMethod was\n"
1161	>	"\tset to %s\n", myMethod.c_str());
1162	>	painCave.isFatal = 1;
1163	>	simError();
1164	>	}
1165	>	}
1166	>	}
1167	>
1168	>	if (simParams_->haveSwitchingRadius()){
1169	>	rsw_ = simParams_->getSwitchingRadius();
1170	>	} else {
1171	>	sprintf(painCave.errMsg,
1172	>	"SimCreator Warning: No value was set for switchingRadius.\n"
1173	>	"\tOpenMD will use a default value of\n"
1174	>	"\t0.85 * cutoffRadius for the switchingRadius\n");
1175	>	painCave.isFatal = 0;
1176	>	simError();
1177	>	rsw_ = 0.85 * rcut_;
1178	>	}
1179
1180	<	void SimInfo::addProperty(GenericData* genData) {
1181	<	properties_.addProperty(genData);
814	<	}
1180	>	Electrostatic::setElectrostaticCutoffRadius(rcut_, rsw_);
1181	>	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1182
1183	<	void SimInfo::removeProperty(const std::string& propName) {
1184	<	properties_.removeProperty(propName);
1185	<	}
1183	>	} else {
1184	>	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1185	>	// We'll punt and let fortran figure out the cutoffs later.
1186	>
1187	>	notifyFortranYouAreOnYourOwn();
1188
1189	<	void SimInfo::clearProperties() {
1190	<	properties_.clearProperties();
1191	<	}
1189	>	}
1190	>	}
1191	>	}
1192
1193	<	std::vector<std::string> SimInfo::getPropertyNames() {
1194	<	return properties_.getPropertyNames();
1195	<	}
1196	<
1197	<	std::vector<GenericData*> SimInfo::getProperties() {
1193	>	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1194	>
1195	>	int errorOut;
1196	>	ElectrostaticSummationMethod esm = NONE;
1197	>	ElectrostaticScreeningMethod sm = UNDAMPED;
1198	>	RealType alphaVal;
1199	>	RealType dielectric;
1200	>
1201	>	errorOut = isError;
1202	>
1203	>	if (simParams_->haveElectrostaticSummationMethod()) {
1204	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1205	>	toUpper(myMethod);
1206	>	if (myMethod == "NONE") {
1207	>	esm = NONE;
1208	>	} else {
1209	>	if (myMethod == "SWITCHING_FUNCTION") {
1210	>	esm = SWITCHING_FUNCTION;
1211	>	} else {
1212	>	if (myMethod == "SHIFTED_POTENTIAL") {
1213	>	esm = SHIFTED_POTENTIAL;
1214	>	} else {
1215	>	if (myMethod == "SHIFTED_FORCE") {
1216	>	esm = SHIFTED_FORCE;
1217	>	} else {
1218	>	if (myMethod == "REACTION_FIELD") {
1219	>	esm = REACTION_FIELD;
1220	>	dielectric = simParams_->getDielectric();
1221	>	if (!simParams_->haveDielectric()) {
1222	>	// throw warning
1223	>	sprintf( painCave.errMsg,
1224	>	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1225	>	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1226	>	painCave.isFatal = 0;
1227	>	simError();
1228	>	}
1229	>	} else {
1230	>	// throw error
1231	>	sprintf( painCave.errMsg,
1232	>	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1233	>	"\t(Input file specified %s .)\n"
1234	>	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1235	>	"\t\"shifted_potential\", \"shifted_force\", or \n"
1236	>	"\t\"reaction_field\".\n", myMethod.c_str() );
1237	>	painCave.isFatal = 1;
1238	>	simError();
1239	>	}
1240	>	}
1241	>	}
1242	>	}
1243	>	}
1244	>	}
1245	>
1246	>	if (simParams_->haveElectrostaticScreeningMethod()) {
1247	>	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1248	>	toUpper(myScreen);
1249	>	if (myScreen == "UNDAMPED") {
1250	>	sm = UNDAMPED;
1251	>	} else {
1252	>	if (myScreen == "DAMPED") {
1253	>	sm = DAMPED;
1254	>	if (!simParams_->haveDampingAlpha()) {
1255	>	// first set a cutoff dependent alpha value
1256	>	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1257	>	alphaVal = 0.5125 - rcut_* 0.025;
1258	>	// for values rcut > 20.5, alpha is zero
1259	>	if (alphaVal < 0) alphaVal = 0;
1260	>
1261	>	// throw warning
1262	>	sprintf( painCave.errMsg,
1263	>	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1264	>	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1265	>	painCave.isFatal = 0;
1266	>	simError();
1267	>	} else {
1268	>	alphaVal = simParams_->getDampingAlpha();
1269	>	}
1270	>
1271	>	} else {
1272	>	// throw error
1273	>	sprintf( painCave.errMsg,
1274	>	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1275	>	"\t(Input file specified %s .)\n"
1276	>	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1277	>	"or \"damped\".\n", myScreen.c_str() );
1278	>	painCave.isFatal = 1;
1279	>	simError();
1280	>	}
1281	>	}
1282	>	}
1283	>
1284	>
1285	>	Electrostatic::setElectrostaticSummationMethod( esm );
1286	>	Electrostatic::setElectrostaticScreeningMethod( sm );
1287	>	Electrostatic::setDampingAlpha( alphaVal );
1288	>	Electrostatic::setReactionFieldDielectric( dielectric );
1289	>	initFortranFF( &errorOut );
1290	>	}
1291	>
1292	>	void SimInfo::setupSwitchingFunction() {
1293	>	int ft = CUBIC;
1294	>
1295	>	if (simParams_->haveSwitchingFunctionType()) {
1296	>	std::string funcType = simParams_->getSwitchingFunctionType();
1297	>	toUpper(funcType);
1298	>	if (funcType == "CUBIC") {
1299	>	ft = CUBIC;
1300	>	} else {
1301	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1302	>	ft = FIFTH_ORDER_POLY;
1303	>	} else {
1304	>	// throw error
1305	>	sprintf( painCave.errMsg,
1306	>	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1307	>	painCave.isFatal = 1;
1308	>	simError();
1309	>	}
1310	>	}
1311	>	}
1312	>
1313	>	// send switching function notification to switcheroo
1314	>	setFunctionType(&ft);
1315	>
1316	>	}
1317	>
1318	>	void SimInfo::setupAccumulateBoxDipole() {
1319	>
1320	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1321	>	if ( simParams_->haveAccumulateBoxDipole() )
1322	>	if ( simParams_->getAccumulateBoxDipole() ) {
1323	>	setAccumulateBoxDipole();
1324	>	calcBoxDipole_ = true;
1325	>	}
1326	>
1327	>	}
1328	>
1329	>	void SimInfo::addProperty(GenericData* genData) {
1330	>	properties_.addProperty(genData);
1331	>	}
1332	>
1333	>	void SimInfo::removeProperty(const std::string& propName) {
1334	>	properties_.removeProperty(propName);
1335	>	}
1336	>
1337	>	void SimInfo::clearProperties() {
1338	>	properties_.clearProperties();
1339	>	}
1340	>
1341	>	std::vector<std::string> SimInfo::getPropertyNames() {
1342	>	return properties_.getPropertyNames();
1343	>	}
1344	>
1345	>	std::vector<GenericData*> SimInfo::getProperties() {
1346		return properties_.getProperties();
1347	<	}
1347	>	}
1348
1349	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1349	>	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1350		return properties_.getPropertyByName(propName);
1351	<	}
1351	>	}
1352
1353	<	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1353	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1354	>	if (sman_ == sman) {
1355	>	return;
1356	>	}
1357	>	delete sman_;
1358		sman_ = sman;
1359
1360		Molecule* mol;
#	Line 845 | Line 1366 | void SimInfo::setSnapshotManager(SnapshotManager* sman
1366
1367		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1368
1369	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1370	<	atom->setSnapshotManager(sman_);
1371	<	}
1369	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1370	>	atom->setSnapshotManager(sman_);
1371	>	}
1372
1373	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1374	<	rb->setSnapshotManager(sman_);
1375	<	}
1373	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1374	>	rb->setSnapshotManager(sman_);
1375	>	}
1376		}
1377
1378	<	}
1378	>	}
1379
1380	<	Vector3d SimInfo::getComVel(){
1380	>	Vector3d SimInfo::getComVel(){
1381		SimInfo::MoleculeIterator i;
1382		Molecule* mol;
1383
1384		Vector3d comVel(0.0);
1385	<	double totalMass = 0.0;
1385	>	RealType totalMass = 0.0;
1386
1387
1388		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1389	<	double mass = mol->getMass();
1390	<	totalMass += mass;
1391	<	comVel += mass * mol->getComVel();
1389	>	RealType mass = mol->getMass();
1390	>	totalMass += mass;
1391	>	comVel += mass * mol->getComVel();
1392		}
1393
1394		#ifdef IS_MPI
1395	<	double tmpMass = totalMass;
1395	>	RealType tmpMass = totalMass;
1396		Vector3d tmpComVel(comVel);
1397	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1398	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1397	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1398	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1399		#endif
1400
1401		comVel /= totalMass;
1402
1403		return comVel;
1404	<	}
1404	>	}
1405
1406	<	Vector3d SimInfo::getCom(){
1406	>	Vector3d SimInfo::getCom(){
1407		SimInfo::MoleculeIterator i;
1408		Molecule* mol;
1409
1410		Vector3d com(0.0);
1411	<	double totalMass = 0.0;
1411	>	RealType totalMass = 0.0;
1412
1413		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1414	<	double mass = mol->getMass();
1415	<	totalMass += mass;
1416	<	com += mass * mol->getCom();
1414	>	RealType mass = mol->getMass();
1415	>	totalMass += mass;
1416	>	com += mass * mol->getCom();
1417		}
1418
1419		#ifdef IS_MPI
1420	<	double tmpMass = totalMass;
1420	>	RealType tmpMass = totalMass;
1421		Vector3d tmpCom(com);
1422	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1423	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1422	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1423	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1424		#endif
1425
1426		com /= totalMass;
1427
1428		return com;
1429
1430	<	}
1430	>	}
1431
1432	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1432	>	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1433
1434		return o;
1435	<	}
1435	>	}
1436	>
1437	>
1438	>	/*
1439	>	Returns center of mass and center of mass velocity in one function call.
1440	>	*/
1441	>
1442	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1443	>	SimInfo::MoleculeIterator i;
1444	>	Molecule* mol;
1445	>
1446	>
1447	>	RealType totalMass = 0.0;
1448	>
1449
1450	<	}//end namespace oopse
1450	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1451	>	RealType mass = mol->getMass();
1452	>	totalMass += mass;
1453	>	com += mass * mol->getCom();
1454	>	comVel += mass * mol->getComVel();
1455	>	}
1456	>
1457	>	#ifdef IS_MPI
1458	>	RealType tmpMass = totalMass;
1459	>	Vector3d tmpCom(com);
1460	>	Vector3d tmpComVel(comVel);
1461	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1462	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1463	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1464	>	#endif
1465	>
1466	>	com /= totalMass;
1467	>	comVel /= totalMass;
1468	>	}
1469	>
1470	>	/*
1471	>	Return intertia tensor for entire system and angular momentum Vector.
1472
1473	+
1474	+	[  Ixx -Ixy  -Ixz ]
1475	+	J =| -Iyx  Iyy  -Iyz |
1476	+	[ -Izx -Iyz   Izz ]
1477	+	*/
1478	+
1479	+	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1480	+
1481	+
1482	+	RealType xx = 0.0;
1483	+	RealType yy = 0.0;
1484	+	RealType zz = 0.0;
1485	+	RealType xy = 0.0;
1486	+	RealType xz = 0.0;
1487	+	RealType yz = 0.0;
1488	+	Vector3d com(0.0);
1489	+	Vector3d comVel(0.0);
1490	+
1491	+	getComAll(com, comVel);
1492	+
1493	+	SimInfo::MoleculeIterator i;
1494	+	Molecule* mol;
1495	+
1496	+	Vector3d thisq(0.0);
1497	+	Vector3d thisv(0.0);
1498	+
1499	+	RealType thisMass = 0.0;
1500	+
1501	+
1502	+
1503	+
1504	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1505	+
1506	+	thisq = mol->getCom()-com;
1507	+	thisv = mol->getComVel()-comVel;
1508	+	thisMass = mol->getMass();
1509	+	// Compute moment of intertia coefficients.
1510	+	xx += thisq[0]*thisq[0]*thisMass;
1511	+	yy += thisq[1]*thisq[1]*thisMass;
1512	+	zz += thisq[2]*thisq[2]*thisMass;
1513	+
1514	+	// compute products of intertia
1515	+	xy += thisq[0]*thisq[1]*thisMass;
1516	+	xz += thisq[0]*thisq[2]*thisMass;
1517	+	yz += thisq[1]*thisq[2]*thisMass;
1518	+
1519	+	angularMomentum += cross( thisq, thisv ) * thisMass;
1520	+
1521	+	}
1522	+
1523	+
1524	+	inertiaTensor(0,0) = yy + zz;
1525	+	inertiaTensor(0,1) = -xy;
1526	+	inertiaTensor(0,2) = -xz;
1527	+	inertiaTensor(1,0) = -xy;
1528	+	inertiaTensor(1,1) = xx + zz;
1529	+	inertiaTensor(1,2) = -yz;
1530	+	inertiaTensor(2,0) = -xz;
1531	+	inertiaTensor(2,1) = -yz;
1532	+	inertiaTensor(2,2) = xx + yy;
1533	+
1534	+	#ifdef IS_MPI
1535	+	Mat3x3d tmpI(inertiaTensor);
1536	+	Vector3d tmpAngMom;
1537	+	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1538	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1539	+	#endif
1540	+
1541	+	return;
1542	+	}
1543	+
1544	+	//Returns the angular momentum of the system
1545	+	Vector3d SimInfo::getAngularMomentum(){
1546	+
1547	+	Vector3d com(0.0);
1548	+	Vector3d comVel(0.0);
1549	+	Vector3d angularMomentum(0.0);
1550	+
1551	+	getComAll(com,comVel);
1552	+
1553	+	SimInfo::MoleculeIterator i;
1554	+	Molecule* mol;
1555	+
1556	+	Vector3d thisr(0.0);
1557	+	Vector3d thisp(0.0);
1558	+
1559	+	RealType thisMass;
1560	+
1561	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1562	+	thisMass = mol->getMass();
1563	+	thisr = mol->getCom()-com;
1564	+	thisp = (mol->getComVel()-comVel)*thisMass;
1565	+
1566	+	angularMomentum += cross( thisr, thisp );
1567	+
1568	+	}
1569	+
1570	+	#ifdef IS_MPI
1571	+	Vector3d tmpAngMom;
1572	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1573	+	#endif
1574	+
1575	+	return angularMomentum;
1576	+	}
1577	+
1578	+	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1579	+	return IOIndexToIntegrableObject.at(index);
1580	+	}
1581	+
1582	+	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1583	+	IOIndexToIntegrableObject= v;
1584	+	}
1585	+
1586	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1587	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1588	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1589	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1590	+	*/
1591	+	void SimInfo::getGyrationalVolume(RealType &volume){
1592	+	Mat3x3d intTensor;
1593	+	RealType det;
1594	+	Vector3d dummyAngMom;
1595	+	RealType sysconstants;
1596	+	RealType geomCnst;
1597	+
1598	+	geomCnst = 3.0/2.0;
1599	+	/* Get the inertial tensor and angular momentum for free*/
1600	+	getInertiaTensor(intTensor,dummyAngMom);
1601	+
1602	+	det = intTensor.determinant();
1603	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1604	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1605	+	return;
1606	+	}
1607	+
1608	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1609	+	Mat3x3d intTensor;
1610	+	Vector3d dummyAngMom;
1611	+	RealType sysconstants;
1612	+	RealType geomCnst;
1613	+
1614	+	geomCnst = 3.0/2.0;
1615	+	/* Get the inertial tensor and angular momentum for free*/
1616	+	getInertiaTensor(intTensor,dummyAngMom);
1617	+
1618	+	detI = intTensor.determinant();
1619	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1620	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1621	+	return;
1622	+	}
1623	+	/*
1624	+	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1625	+	assert( v.size() == nAtoms_ + nRigidBodies_);
1626	+	sdByGlobalIndex_ = v;
1627	+	}
1628	+
1629	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1630	+	//assert(index < nAtoms_ + nRigidBodies_);
1631	+	return sdByGlobalIndex_.at(index);
1632	+	}
1633	+	*/
1634	+	}//end namespace OpenMD
1635	+

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 316 by tim, Fri Feb 11 22:41:02 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1503 by gezelter, Sat Oct 2 19:54:41 2010 UTC

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