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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 398 by tim, Mon Mar 7 22:39:33 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1549 by gezelter, Wed Apr 27 18:38:15 2011 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/DarkSide/neighborLists_interface.h"
58		#include "UseTheForce/doForces_interface.h"
56	–	#include "UseTheForce/notifyCutoffs_interface.h"
59		#include "utils/MemoryUtils.hpp"
60		#include "utils/simError.h"
61		#include "selection/SelectionManager.hpp"
62	+	#include "io/ForceFieldOptions.hpp"
63	+	#include "UseTheForce/ForceField.hpp"
64	+	#include "nonbonded/SwitchingFunction.hpp"
65
66		#ifdef IS_MPI
67		#include "UseTheForce/mpiComponentPlan.h"
68		#include "UseTheForce/DarkSide/simParallel_interface.h"
69		#endif
70
71	<	namespace oopse {
72	<
73	<	SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
74	<	ForceField* ff, Globals* simParams) :
75	<	forceField_(ff), simParams_(simParams),
76	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
77	<	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
78	<	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
79	<	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
80	<	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
81	<	sman_(NULL), fortranInitialized_(false), selectMan_(NULL) {
82	<
83	<
79	<	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
71	>	using namespace std;
72	>	namespace OpenMD {
73	>
74	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
75	>	forceField_(ff), simParams_(simParams),
76	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
77	>	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
78	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
79	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
80	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
81	>	nConstraints_(0), sman_(NULL), fortranInitialized_(false),
82	>	calcBoxDipole_(false), useAtomicVirial_(true) {
83	>
84		MoleculeStamp* molStamp;
85		int nMolWithSameStamp;
86		int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
87	<	int nGroups = 0;          //total cutoff groups defined in meta-data file
87	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
88		CutoffGroupStamp* cgStamp;
89		RigidBodyStamp* rbStamp;
90		int nRigidAtoms = 0;
91
92	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
93	<	molStamp = i->first;
94	<	nMolWithSameStamp = i->second;
95	<
96	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
97	<
98	<	//calculate atoms in molecules
99	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
100	<
101	<
102	<	//calculate atoms in cutoff groups
103	<	int nAtomsInGroups = 0;
104	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
105	<
106	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
107	<	cgStamp = molStamp->getCutoffGroup(j);
108	<	nAtomsInGroups += cgStamp->getNMembers();
109	<	}
110	<
111	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
112	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
113	<
114	<	//calculate atoms in rigid bodies
115	<	int nAtomsInRigidBodies = 0;
116	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
117	<
118	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
119	<	rbStamp = molStamp->getRigidBody(j);
120	<	nAtomsInRigidBodies += rbStamp->getNMembers();
121	<	}
122	<
123	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
124	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
125	<
92	>	vector<Component*> components = simParams->getComponents();
93	>
94	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
95	>	molStamp = (*i)->getMoleculeStamp();
96	>	nMolWithSameStamp = (*i)->getNMol();
97	>
98	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
99	>
100	>	//calculate atoms in molecules
101	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
102	>
103	>	//calculate atoms in cutoff groups
104	>	int nAtomsInGroups = 0;
105	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
106	>
107	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
108	>	cgStamp = molStamp->getCutoffGroupStamp(j);
109	>	nAtomsInGroups += cgStamp->getNMembers();
110	>	}
111	>
112	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
113	>
114	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
115	>
116	>	//calculate atoms in rigid bodies
117	>	int nAtomsInRigidBodies = 0;
118	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
119	>
120	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
121	>	rbStamp = molStamp->getRigidBodyStamp(j);
122	>	nAtomsInRigidBodies += rbStamp->getNMembers();
123	>	}
124	>
125	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
126	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
127	>
128		}
129	+
130	+	//every free atom (atom does not belong to cutoff groups) is a cutoff
131	+	//group therefore the total number of cutoff groups in the system is
132	+	//equal to the total number of atoms minus number of atoms belong to
133	+	//cutoff group defined in meta-data file plus the number of cutoff
134	+	//groups defined in meta-data file
135	+	std::cerr << "nGA = " << nGlobalAtoms_ << "\n";
136	+	std::cerr << "nCA = " << nCutoffAtoms << "\n";
137	+	std::cerr << "nG = " << nGroups << "\n";
138
124	–	//every free atom (atom does not belong to cutoff groups) is a cutoff group
125	–	//therefore the total number of cutoff groups in the system is equal to
126	–	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
127	–	//file plus the number of cutoff groups defined in meta-data file
139		nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
140
141	<	//every free atom (atom does not belong to rigid bodies) is an integrable object
142	<	//therefore the total number of  integrable objects in the system is equal to
143	<	//the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
144	<	//file plus the number of  rigid bodies defined in meta-data file
145	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
146	<
141	>	std::cerr << "nGCG = " << nGlobalCutoffGroups_ << "\n";
142	>
143	>	//every free atom (atom does not belong to rigid bodies) is an
144	>	//integrable object therefore the total number of integrable objects
145	>	//in the system is equal to the total number of atoms minus number of
146	>	//atoms belong to rigid body defined in meta-data file plus the number
147	>	//of rigid bodies defined in meta-data file
148	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
149	>	+ nGlobalRigidBodies_;
150	>
151		nGlobalMols_ = molStampIds_.size();
137	–
138	–	#ifdef IS_MPI
152		molToProcMap_.resize(nGlobalMols_);
153	<	#endif
154	<
155	<	selectMan_ = new SelectionManager(this);
156	<	selectMan_->selectAll();
144	<	}
145	<
146	<	SimInfo::~SimInfo() {
147	<	std::map<int, Molecule*>::iterator i;
153	>	}
154	>
155	>	SimInfo::~SimInfo() {
156	>	map<int, Molecule*>::iterator i;
157		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
158	<	delete i->second;
158	>	delete i->second;
159		}
160		molecules_.clear();
161	<
153	<	MemoryUtils::deletePointers(moleculeStamps_);
154	<
161	>
162		delete sman_;
163		delete simParams_;
164		delete forceField_;
165	<	delete selectMan_;
159	<	}
165	>	}
166
161	–	int SimInfo::getNGlobalConstraints() {
162	–	int nGlobalConstraints;
163	–	#ifdef IS_MPI
164	–	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
165	–	MPI_COMM_WORLD);
166	–	#else
167	–	nGlobalConstraints =  nConstraints_;
168	–	#endif
169	–	return nGlobalConstraints;
170	–	}
167
168	<	bool SimInfo::addMolecule(Molecule* mol) {
168	>	bool SimInfo::addMolecule(Molecule* mol) {
169		MoleculeIterator i;
170	<
170	>
171		i = molecules_.find(mol->getGlobalIndex());
172		if (i == molecules_.end() ) {
173	<
174	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
175	<
176	<	nAtoms_ += mol->getNAtoms();
177	<	nBonds_ += mol->getNBonds();
178	<	nBends_ += mol->getNBends();
179	<	nTorsions_ += mol->getNTorsions();
180	<	nRigidBodies_ += mol->getNRigidBodies();
181	<	nIntegrableObjects_ += mol->getNIntegrableObjects();
182	<	nCutoffGroups_ += mol->getNCutoffGroups();
183	<	nConstraints_ += mol->getNConstraintPairs();
184	<
185	<	addExcludePairs(mol);
186	<
187	<	return true;
188	<	} else {
189	<	return false;
173	>
174	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
175	>
176	>	nAtoms_ += mol->getNAtoms();
177	>	nBonds_ += mol->getNBonds();
178	>	nBends_ += mol->getNBends();
179	>	nTorsions_ += mol->getNTorsions();
180	>	nInversions_ += mol->getNInversions();
181	>	nRigidBodies_ += mol->getNRigidBodies();
182	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
183	>	nCutoffGroups_ += mol->getNCutoffGroups();
184	>	nConstraints_ += mol->getNConstraintPairs();
185	>
186	>	addInteractionPairs(mol);
187	>
188	>	return true;
189	>	} else {
190	>	return false;
191		}
192	<	}
193	<
194	<	bool SimInfo::removeMolecule(Molecule* mol) {
192	>	}
193	>
194	>	bool SimInfo::removeMolecule(Molecule* mol) {
195		MoleculeIterator i;
196		i = molecules_.find(mol->getGlobalIndex());
197
198		if (i != molecules_.end() ) {
199
200	<	assert(mol == i->second);
200	>	assert(mol == i->second);
201
202	<	nAtoms_ -= mol->getNAtoms();
203	<	nBonds_ -= mol->getNBonds();
204	<	nBends_ -= mol->getNBends();
205	<	nTorsions_ -= mol->getNTorsions();
206	<	nRigidBodies_ -= mol->getNRigidBodies();
207	<	nIntegrableObjects_ -= mol->getNIntegrableObjects();
208	<	nCutoffGroups_ -= mol->getNCutoffGroups();
209	<	nConstraints_ -= mol->getNConstraintPairs();
202	>	nAtoms_ -= mol->getNAtoms();
203	>	nBonds_ -= mol->getNBonds();
204	>	nBends_ -= mol->getNBends();
205	>	nTorsions_ -= mol->getNTorsions();
206	>	nInversions_ -= mol->getNInversions();
207	>	nRigidBodies_ -= mol->getNRigidBodies();
208	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
209	>	nCutoffGroups_ -= mol->getNCutoffGroups();
210	>	nConstraints_ -= mol->getNConstraintPairs();
211
212	<	removeExcludePairs(mol);
213	<	molecules_.erase(mol->getGlobalIndex());
212	>	removeInteractionPairs(mol);
213	>	molecules_.erase(mol->getGlobalIndex());
214
215	<	delete mol;
215	>	delete mol;
216
217	<	return true;
217	>	return true;
218		} else {
219	<	return false;
219	>	return false;
220		}
221	+	}
222
224	–
225	–	}
226	–
223
224	<	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
224	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
225		i = molecules_.begin();
226		return i == molecules_.end() ? NULL : i->second;
227	<	}
227	>	}
228
229	<	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
229	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
230		++i;
231		return i == molecules_.end() ? NULL : i->second;
232	<	}
232	>	}
233
234
235	<	void SimInfo::calcNdf() {
235	>	void SimInfo::calcNdf() {
236		int ndf_local;
237		MoleculeIterator i;
238	<	std::vector<StuntDouble*>::iterator j;
238	>	vector<StuntDouble*>::iterator j;
239		Molecule* mol;
240		StuntDouble* integrableObject;
241
242		ndf_local = 0;
243
244		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
245	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
246	<	integrableObject = mol->nextIntegrableObject(j)) {
245	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
246	>	integrableObject = mol->nextIntegrableObject(j)) {
247
248	<	ndf_local += 3;
248	>	ndf_local += 3;
249
250	<	if (integrableObject->isDirectional()) {
251	<	if (integrableObject->isLinear()) {
252	<	ndf_local += 2;
253	<	} else {
254	<	ndf_local += 3;
255	<	}
256	<	}
250	>	if (integrableObject->isDirectional()) {
251	>	if (integrableObject->isLinear()) {
252	>	ndf_local += 2;
253	>	} else {
254	>	ndf_local += 3;
255	>	}
256	>	}
257
258	<	}//end for (integrableObject)
259	<	}// end for (mol)
258	>	}
259	>	}
260
261		// n_constraints is local, so subtract them on each processor
262		ndf_local -= nConstraints_;
#	Line 275 | Line 271 | void SimInfo::calcNdf() {
271		// entire system:
272		ndf_ = ndf_ - 3 - nZconstraint_;
273
274	<	}
274	>	}
275
276	<	void SimInfo::calcNdfRaw() {
276	>	int SimInfo::getFdf() {
277	>	#ifdef IS_MPI
278	>	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
279	>	#else
280	>	fdf_ = fdf_local;
281	>	#endif
282	>	return fdf_;
283	>	}
284	>
285	>	void SimInfo::calcNdfRaw() {
286		int ndfRaw_local;
287
288		MoleculeIterator i;
289	<	std::vector<StuntDouble*>::iterator j;
289	>	vector<StuntDouble*>::iterator j;
290		Molecule* mol;
291		StuntDouble* integrableObject;
292
#	Line 289 | Line 294 | void SimInfo::calcNdfRaw() {
294		ndfRaw_local = 0;
295
296		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
297	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
298	<	integrableObject = mol->nextIntegrableObject(j)) {
297	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
298	>	integrableObject = mol->nextIntegrableObject(j)) {
299
300	<	ndfRaw_local += 3;
300	>	ndfRaw_local += 3;
301
302	<	if (integrableObject->isDirectional()) {
303	<	if (integrableObject->isLinear()) {
304	<	ndfRaw_local += 2;
305	<	} else {
306	<	ndfRaw_local += 3;
307	<	}
308	<	}
302	>	if (integrableObject->isDirectional()) {
303	>	if (integrableObject->isLinear()) {
304	>	ndfRaw_local += 2;
305	>	} else {
306	>	ndfRaw_local += 3;
307	>	}
308	>	}
309
310	<	}
310	>	}
311		}
312
313		#ifdef IS_MPI
#	Line 310 | Line 315 | void SimInfo::calcNdfRaw() {
315		#else
316		ndfRaw_ = ndfRaw_local;
317		#endif
318	<	}
318	>	}
319
320	<	void SimInfo::calcNdfTrans() {
320	>	void SimInfo::calcNdfTrans() {
321		int ndfTrans_local;
322
323		ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
#	Line 326 | Line 331 | void SimInfo::calcNdfTrans() {
331
332		ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
333
334	<	}
334	>	}
335
336	<	void SimInfo::addExcludePairs(Molecule* mol) {
337	<	std::vector<Bond*>::iterator bondIter;
338	<	std::vector<Bend*>::iterator bendIter;
339	<	std::vector<Torsion*>::iterator torsionIter;
336	>	void SimInfo::addInteractionPairs(Molecule* mol) {
337	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
338	>	vector<Bond*>::iterator bondIter;
339	>	vector<Bend*>::iterator bendIter;
340	>	vector<Torsion*>::iterator torsionIter;
341	>	vector<Inversion*>::iterator inversionIter;
342		Bond* bond;
343		Bend* bend;
344		Torsion* torsion;
345	+	Inversion* inversion;
346		int a;
347		int b;
348		int c;
349		int d;
342	–
343	–	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
344	–	a = bond->getAtomA()->getGlobalIndex();
345	–	b = bond->getAtomB()->getGlobalIndex();
346	–	exclude_.addPair(a, b);
347	–	}
350
351	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
352	<	a = bend->getAtomA()->getGlobalIndex();
353	<	b = bend->getAtomB()->getGlobalIndex();
354	<	c = bend->getAtomC()->getGlobalIndex();
351	>	// atomGroups can be used to add special interaction maps between
352	>	// groups of atoms that are in two separate rigid bodies.
353	>	// However, most site-site interactions between two rigid bodies
354	>	// are probably not special, just the ones between the physically
355	>	// bonded atoms.  Interactions *within* a single rigid body should
356	>	// always be excluded.  These are done at the bottom of this
357	>	// function.
358
359	<	exclude_.addPair(a, b);
360	<	exclude_.addPair(a, c);
361	<	exclude_.addPair(b, c);
362	<	}
359	>	map<int, set<int> > atomGroups;
360	>	Molecule::RigidBodyIterator rbIter;
361	>	RigidBody* rb;
362	>	Molecule::IntegrableObjectIterator ii;
363	>	StuntDouble* integrableObject;
364	>
365	>	for (integrableObject = mol->beginIntegrableObject(ii);
366	>	integrableObject != NULL;
367	>	integrableObject = mol->nextIntegrableObject(ii)) {
368	>
369	>	if (integrableObject->isRigidBody()) {
370	>	rb = static_cast<RigidBody*>(integrableObject);
371	>	vector<Atom*> atoms = rb->getAtoms();
372	>	set<int> rigidAtoms;
373	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
374	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
375	>	}
376	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
377	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
378	>	}
379	>	} else {
380	>	set<int> oneAtomSet;
381	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
382	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
383	>	}
384	>	}
385	>
386	>	for (bond= mol->beginBond(bondIter); bond != NULL;
387	>	bond = mol->nextBond(bondIter)) {
388
389	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
390	<	a = torsion->getAtomA()->getGlobalIndex();
391	<	b = torsion->getAtomB()->getGlobalIndex();
392	<	c = torsion->getAtomC()->getGlobalIndex();
393	<	d = torsion->getAtomD()->getGlobalIndex();
389	>	a = bond->getAtomA()->getGlobalIndex();
390	>	b = bond->getAtomB()->getGlobalIndex();
391	>
392	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
393	>	oneTwoInteractions_.addPair(a, b);
394	>	} else {
395	>	excludedInteractions_.addPair(a, b);
396	>	}
397	>	}
398
399	<	exclude_.addPair(a, b);
400	<	exclude_.addPair(a, c);
401	<	exclude_.addPair(a, d);
402	<	exclude_.addPair(b, c);
403	<	exclude_.addPair(b, d);
404	<	exclude_.addPair(c, d);
399	>	for (bend= mol->beginBend(bendIter); bend != NULL;
400	>	bend = mol->nextBend(bendIter)) {
401	>
402	>	a = bend->getAtomA()->getGlobalIndex();
403	>	b = bend->getAtomB()->getGlobalIndex();
404	>	c = bend->getAtomC()->getGlobalIndex();
405	>
406	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
407	>	oneTwoInteractions_.addPair(a, b);
408	>	oneTwoInteractions_.addPair(b, c);
409	>	} else {
410	>	excludedInteractions_.addPair(a, b);
411	>	excludedInteractions_.addPair(b, c);
412	>	}
413	>
414	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
415	>	oneThreeInteractions_.addPair(a, c);
416	>	} else {
417	>	excludedInteractions_.addPair(a, c);
418	>	}
419		}
420
421	<
422	<	}
421	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
422	>	torsion = mol->nextTorsion(torsionIter)) {
423
424	<	void SimInfo::removeExcludePairs(Molecule* mol) {
425	<	std::vector<Bond*>::iterator bondIter;
426	<	std::vector<Bend*>::iterator bendIter;
427	<	std::vector<Torsion*>::iterator torsionIter;
424	>	a = torsion->getAtomA()->getGlobalIndex();
425	>	b = torsion->getAtomB()->getGlobalIndex();
426	>	c = torsion->getAtomC()->getGlobalIndex();
427	>	d = torsion->getAtomD()->getGlobalIndex();
428	>
429	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
430	>	oneTwoInteractions_.addPair(a, b);
431	>	oneTwoInteractions_.addPair(b, c);
432	>	oneTwoInteractions_.addPair(c, d);
433	>	} else {
434	>	excludedInteractions_.addPair(a, b);
435	>	excludedInteractions_.addPair(b, c);
436	>	excludedInteractions_.addPair(c, d);
437	>	}
438	>
439	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
440	>	oneThreeInteractions_.addPair(a, c);
441	>	oneThreeInteractions_.addPair(b, d);
442	>	} else {
443	>	excludedInteractions_.addPair(a, c);
444	>	excludedInteractions_.addPair(b, d);
445	>	}
446	>
447	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
448	>	oneFourInteractions_.addPair(a, d);
449	>	} else {
450	>	excludedInteractions_.addPair(a, d);
451	>	}
452	>	}
453	>
454	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
455	>	inversion = mol->nextInversion(inversionIter)) {
456	>
457	>	a = inversion->getAtomA()->getGlobalIndex();
458	>	b = inversion->getAtomB()->getGlobalIndex();
459	>	c = inversion->getAtomC()->getGlobalIndex();
460	>	d = inversion->getAtomD()->getGlobalIndex();
461	>
462	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
463	>	oneTwoInteractions_.addPair(a, b);
464	>	oneTwoInteractions_.addPair(a, c);
465	>	oneTwoInteractions_.addPair(a, d);
466	>	} else {
467	>	excludedInteractions_.addPair(a, b);
468	>	excludedInteractions_.addPair(a, c);
469	>	excludedInteractions_.addPair(a, d);
470	>	}
471	>
472	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
473	>	oneThreeInteractions_.addPair(b, c);
474	>	oneThreeInteractions_.addPair(b, d);
475	>	oneThreeInteractions_.addPair(c, d);
476	>	} else {
477	>	excludedInteractions_.addPair(b, c);
478	>	excludedInteractions_.addPair(b, d);
479	>	excludedInteractions_.addPair(c, d);
480	>	}
481	>	}
482	>
483	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
484	>	rb = mol->nextRigidBody(rbIter)) {
485	>	vector<Atom*> atoms = rb->getAtoms();
486	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
487	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
488	>	a = atoms[i]->getGlobalIndex();
489	>	b = atoms[j]->getGlobalIndex();
490	>	excludedInteractions_.addPair(a, b);
491	>	}
492	>	}
493	>	}
494	>
495	>	}
496	>
497	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
498	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
499	>	vector<Bond*>::iterator bondIter;
500	>	vector<Bend*>::iterator bendIter;
501	>	vector<Torsion*>::iterator torsionIter;
502	>	vector<Inversion*>::iterator inversionIter;
503		Bond* bond;
504		Bend* bend;
505		Torsion* torsion;
506	+	Inversion* inversion;
507		int a;
508		int b;
509		int c;
510		int d;
511	+
512	+	map<int, set<int> > atomGroups;
513	+	Molecule::RigidBodyIterator rbIter;
514	+	RigidBody* rb;
515	+	Molecule::IntegrableObjectIterator ii;
516	+	StuntDouble* integrableObject;
517
518	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
519	<	a = bond->getAtomA()->getGlobalIndex();
520	<	b = bond->getAtomB()->getGlobalIndex();
521	<	exclude_.removePair(a, b);
518	>	for (integrableObject = mol->beginIntegrableObject(ii);
519	>	integrableObject != NULL;
520	>	integrableObject = mol->nextIntegrableObject(ii)) {
521	>
522	>	if (integrableObject->isRigidBody()) {
523	>	rb = static_cast<RigidBody*>(integrableObject);
524	>	vector<Atom*> atoms = rb->getAtoms();
525	>	set<int> rigidAtoms;
526	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
527	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
528	>	}
529	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
530	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
531	>	}
532	>	} else {
533	>	set<int> oneAtomSet;
534	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
535	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
536	>	}
537	>	}
538	>
539	>	for (bond= mol->beginBond(bondIter); bond != NULL;
540	>	bond = mol->nextBond(bondIter)) {
541	>
542	>	a = bond->getAtomA()->getGlobalIndex();
543	>	b = bond->getAtomB()->getGlobalIndex();
544	>
545	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
546	>	oneTwoInteractions_.removePair(a, b);
547	>	} else {
548	>	excludedInteractions_.removePair(a, b);
549	>	}
550		}
551
552	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
553	<	a = bend->getAtomA()->getGlobalIndex();
396	<	b = bend->getAtomB()->getGlobalIndex();
397	<	c = bend->getAtomC()->getGlobalIndex();
552	>	for (bend= mol->beginBend(bendIter); bend != NULL;
553	>	bend = mol->nextBend(bendIter)) {
554
555	<	exclude_.removePair(a, b);
556	<	exclude_.removePair(a, c);
557	<	exclude_.removePair(b, c);
555	>	a = bend->getAtomA()->getGlobalIndex();
556	>	b = bend->getAtomB()->getGlobalIndex();
557	>	c = bend->getAtomC()->getGlobalIndex();
558	>
559	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
560	>	oneTwoInteractions_.removePair(a, b);
561	>	oneTwoInteractions_.removePair(b, c);
562	>	} else {
563	>	excludedInteractions_.removePair(a, b);
564	>	excludedInteractions_.removePair(b, c);
565	>	}
566	>
567	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
568	>	oneThreeInteractions_.removePair(a, c);
569	>	} else {
570	>	excludedInteractions_.removePair(a, c);
571	>	}
572		}
573
574	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
575	<	a = torsion->getAtomA()->getGlobalIndex();
406	<	b = torsion->getAtomB()->getGlobalIndex();
407	<	c = torsion->getAtomC()->getGlobalIndex();
408	<	d = torsion->getAtomD()->getGlobalIndex();
574	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
575	>	torsion = mol->nextTorsion(torsionIter)) {
576
577	<	exclude_.removePair(a, b);
578	<	exclude_.removePair(a, c);
579	<	exclude_.removePair(a, d);
580	<	exclude_.removePair(b, c);
581	<	exclude_.removePair(b, d);
582	<	exclude_.removePair(c, d);
577	>	a = torsion->getAtomA()->getGlobalIndex();
578	>	b = torsion->getAtomB()->getGlobalIndex();
579	>	c = torsion->getAtomC()->getGlobalIndex();
580	>	d = torsion->getAtomD()->getGlobalIndex();
581	>
582	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
583	>	oneTwoInteractions_.removePair(a, b);
584	>	oneTwoInteractions_.removePair(b, c);
585	>	oneTwoInteractions_.removePair(c, d);
586	>	} else {
587	>	excludedInteractions_.removePair(a, b);
588	>	excludedInteractions_.removePair(b, c);
589	>	excludedInteractions_.removePair(c, d);
590	>	}
591	>
592	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
593	>	oneThreeInteractions_.removePair(a, c);
594	>	oneThreeInteractions_.removePair(b, d);
595	>	} else {
596	>	excludedInteractions_.removePair(a, c);
597	>	excludedInteractions_.removePair(b, d);
598	>	}
599	>
600	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
601	>	oneFourInteractions_.removePair(a, d);
602	>	} else {
603	>	excludedInteractions_.removePair(a, d);
604	>	}
605		}
606
607	<	}
607	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
608	>	inversion = mol->nextInversion(inversionIter)) {
609
610	+	a = inversion->getAtomA()->getGlobalIndex();
611	+	b = inversion->getAtomB()->getGlobalIndex();
612	+	c = inversion->getAtomC()->getGlobalIndex();
613	+	d = inversion->getAtomD()->getGlobalIndex();
614
615	<	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
616	<	int curStampId;
615	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
616	>	oneTwoInteractions_.removePair(a, b);
617	>	oneTwoInteractions_.removePair(a, c);
618	>	oneTwoInteractions_.removePair(a, d);
619	>	} else {
620	>	excludedInteractions_.removePair(a, b);
621	>	excludedInteractions_.removePair(a, c);
622	>	excludedInteractions_.removePair(a, d);
623	>	}
624
625	+	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
626	+	oneThreeInteractions_.removePair(b, c);
627	+	oneThreeInteractions_.removePair(b, d);
628	+	oneThreeInteractions_.removePair(c, d);
629	+	} else {
630	+	excludedInteractions_.removePair(b, c);
631	+	excludedInteractions_.removePair(b, d);
632	+	excludedInteractions_.removePair(c, d);
633	+	}
634	+	}
635	+
636	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
637	+	rb = mol->nextRigidBody(rbIter)) {
638	+	vector<Atom*> atoms = rb->getAtoms();
639	+	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
640	+	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
641	+	a = atoms[i]->getGlobalIndex();
642	+	b = atoms[j]->getGlobalIndex();
643	+	excludedInteractions_.removePair(a, b);
644	+	}
645	+	}
646	+	}
647	+
648	+	}
649	+
650	+
651	+	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
652	+	int curStampId;
653	+
654		//index from 0
655		curStampId = moleculeStamps_.size();
656
657		moleculeStamps_.push_back(molStamp);
658		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
659	<	}
659	>	}
660
431	–	void SimInfo::update() {
661
662	<	setupSimType();
663	<
664	<	#ifdef IS_MPI
665	<	setupFortranParallel();
666	<	#endif
667	<
668	<	setupFortranSim();
669	<
670	<	//setup fortran force field
442	<	/** @deprecate */
443	<	int isError = 0;
444	<	initFortranFF( &fInfo_.SIM_uses_RF , &isError );
445	<	if(isError){
446	<	sprintf( painCave.errMsg,
447	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
448	<	painCave.isFatal = 1;
449	<	simError();
450	<	}
451	<
452	<
453	<	setupCutoff();
454	<
662	>	/**
663	>	* update
664	>	*
665	>	*  Performs the global checks and variable settings after the
666	>	*  objects have been created.
667	>	*
668	>	*/
669	>	void SimInfo::update() {
670	>	setupSimVariables();
671		calcNdf();
672		calcNdfRaw();
673		calcNdfTrans();
674	<
675	<	fortranInitialized_ = true;
676	<	}
677	<
678	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
674	>	}
675	>
676	>	/**
677	>	* getSimulatedAtomTypes
678	>	*
679	>	* Returns an STL set of AtomType* that are actually present in this
680	>	* simulation.  Must query all processors to assemble this information.
681	>	*
682	>	*/
683	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
684		SimInfo::MoleculeIterator mi;
685		Molecule* mol;
686		Molecule::AtomIterator ai;
687		Atom* atom;
688	<	std::set<AtomType*> atomTypes;
688	>	set<AtomType*> atomTypes;
689	>
690	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
691	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
692	>	atomTypes.insert(atom->getAtomType());
693	>	}
694	>	}
695
696	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
696	>	#ifdef IS_MPI
697
698	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
699	<	atomTypes.insert(atom->getAtomType());
473	<	}
474	<
475	<	}
698	>	// loop over the found atom types on this processor, and add their
699	>	// numerical idents to a vector:
700
701	<	return atomTypes;
702	<	}
701	>	vector<int> foundTypes;
702	>	set<AtomType*>::iterator i;
703	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
704	>	foundTypes.push_back( (*i)->getIdent() );
705
706	<	void SimInfo::setupSimType() {
707	<	std::set<AtomType*>::iterator i;
708	<	std::set<AtomType*> atomTypes;
709	<	atomTypes = getUniqueAtomTypes();
706	>	// count_local holds the number of found types on this processor
707	>	int count_local = foundTypes.size();
708	>
709	>	// count holds the total number of found types on all processors
710	>	// (some will be redundant with the ones found locally):
711	>	int count;
712	>	MPI::COMM_WORLD.Allreduce(&count_local, &count, 1, MPI::INT, MPI::SUM);
713	>
714	>	// create a vector to hold the globally found types, and resize it:
715	>	vector<int> ftGlobal;
716	>	ftGlobal.resize(count);
717	>	vector<int> counts;
718	>
719	>	int nproc = MPI::COMM_WORLD.Get_size();
720	>	counts.resize(nproc);
721	>	vector<int> disps;
722	>	disps.resize(nproc);
723	>
724	>	// now spray out the foundTypes to all the other processors:
725
726	<	int useLennardJones = 0;
727	<	int useElectrostatic = 0;
487	<	int useEAM = 0;
488	<	int useCharge = 0;
489	<	int useDirectional = 0;
490	<	int useDipole = 0;
491	<	int useGayBerne = 0;
492	<	int useSticky = 0;
493	<	int useShape = 0;
494	<	int useFLARB = 0; //it is not in AtomType yet
495	<	int useDirectionalAtom = 0;
496	<	int useElectrostatics = 0;
497	<	//usePBC and useRF are from simParams
498	<	int usePBC = simParams_->getPBC();
499	<	int useRF = simParams_->getUseRF();
726	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
727	>	&ftGlobal[0], &counts[0], &disps[0], MPI::INT);
728
729	+	// foundIdents is a stl set, so inserting an already found ident
730	+	// will have no effect.
731	+	set<int> foundIdents;
732	+	vector<int>::iterator j;
733	+	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
734	+	foundIdents.insert((*j));
735	+
736	+	// now iterate over the foundIdents and get the actual atom types
737	+	// that correspond to these:
738	+	set<int>::iterator it;
739	+	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
740	+	atomTypes.insert( forceField_->getAtomType((*it)) );
741	+
742	+	#endif
743	+
744	+	return atomTypes;
745	+	}
746	+
747	+	void SimInfo::setupSimVariables() {
748	+	useAtomicVirial_ = simParams_->getUseAtomicVirial();
749	+	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
750	+	calcBoxDipole_ = false;
751	+	if ( simParams_->haveAccumulateBoxDipole() )
752	+	if ( simParams_->getAccumulateBoxDipole() ) {
753	+	calcBoxDipole_ = true;
754	+	}
755	+
756	+	set<AtomType*>::iterator i;
757	+	set<AtomType*> atomTypes;
758	+	atomTypes = getSimulatedAtomTypes();
759	+	int usesElectrostatic = 0;
760	+	int usesMetallic = 0;
761	+	int usesDirectional = 0;
762		//loop over all of the atom types
763		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
764	<	useLennardJones |= (*i)->isLennardJones();
765	<	useElectrostatic |= (*i)->isElectrostatic();
766	<	useEAM |= (*i)->isEAM();
506	<	useCharge |= (*i)->isCharge();
507	<	useDirectional |= (*i)->isDirectional();
508	<	useDipole |= (*i)->isDipole();
509	<	useGayBerne |= (*i)->isGayBerne();
510	<	useSticky |= (*i)->isSticky();
511	<	useShape |= (*i)->isShape();
764	>	usesElectrostatic |= (*i)->isElectrostatic();
765	>	usesMetallic |= (*i)->isMetal();
766	>	usesDirectional |= (*i)->isDirectional();
767		}
768
514	–	if (useSticky || useDipole || useGayBerne || useShape) {
515	–	useDirectionalAtom = 1;
516	–	}
517	–
518	–	if (useCharge || useDipole) {
519	–	useElectrostatics = 1;
520	–	}
521	–
769		#ifdef IS_MPI
770		int temp;
771	+	temp = usesDirectional;
772	+	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
773
774	<	temp = usePBC;
775	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
774	>	temp = usesMetallic;
775	>	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
776
777	<	temp = useDirectionalAtom;
778	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
777	>	temp = usesElectrostatic;
778	>	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
779	>	#endif
780	>	fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;
781	>	fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
782	>	fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
783	>	fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
784	>	fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
785	>	fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
786	>	}
787
531	–	temp = useLennardJones;
532	–	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
788
789	<	temp = useElectrostatics;
790	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
789	>	vector<int> SimInfo::getGlobalAtomIndices() {
790	>	SimInfo::MoleculeIterator mi;
791	>	Molecule* mol;
792	>	Molecule::AtomIterator ai;
793	>	Atom* atom;
794
795	<	temp = useCharge;
538	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
539	<
540	<	temp = useDipole;
541	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
542	<
543	<	temp = useSticky;
544	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
545	<
546	<	temp = useGayBerne;
547	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
548	<
549	<	temp = useEAM;
550	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
551	<
552	<	temp = useShape;
553	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
554	<
555	<	temp = useFLARB;
556	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
557	<
558	<	temp = useRF;
559	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
795	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
796
797	<	#endif
797	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
798	>
799	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
800	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
801	>	}
802	>	}
803	>	return GlobalAtomIndices;
804	>	}
805
563	–	fInfo_.SIM_uses_PBC = usePBC;
564	–	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
565	–	fInfo_.SIM_uses_LennardJones = useLennardJones;
566	–	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
567	–	fInfo_.SIM_uses_Charges = useCharge;
568	–	fInfo_.SIM_uses_Dipoles = useDipole;
569	–	fInfo_.SIM_uses_Sticky = useSticky;
570	–	fInfo_.SIM_uses_GayBerne = useGayBerne;
571	–	fInfo_.SIM_uses_EAM = useEAM;
572	–	fInfo_.SIM_uses_Shapes = useShape;
573	–	fInfo_.SIM_uses_FLARB = useFLARB;
574	–	fInfo_.SIM_uses_RF = useRF;
806
807	<	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
807	>	vector<int> SimInfo::getGlobalGroupIndices() {
808	>	SimInfo::MoleculeIterator mi;
809	>	Molecule* mol;
810	>	Molecule::CutoffGroupIterator ci;
811	>	CutoffGroup* cg;
812
813	<	if (simParams_->haveDielectric()) {
814	<	fInfo_.dielect = simParams_->getDielectric();
815	<	} else {
816	<	sprintf(painCave.errMsg,
817	<	"SimSetup Error: No Dielectric constant was set.\n"
818	<	"\tYou are trying to use Reaction Field without"
819	<	"\tsetting a dielectric constant!\n");
820	<	painCave.isFatal = 1;
821	<	simError();
822	<	}
588	<
589	<	} else {
590	<	fInfo_.dielect = 0.0;
813	>	vector<int> GlobalGroupIndices;
814	>
815	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
816	>
817	>	//local index of cutoff group is trivial, it only depends on the
818	>	//order of travesing
819	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
820	>	cg = mol->nextCutoffGroup(ci)) {
821	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
822	>	}
823		}
824	+	return GlobalGroupIndices;
825	+	}
826
593	–	}
827
828	<	void SimInfo::setupFortranSim() {
828	>	void SimInfo::setupFortran() {
829		int isError;
830	<	int nExclude;
831	<	std::vector<int> fortranGlobalGroupMembership;
830	>	int nExclude, nOneTwo, nOneThree, nOneFour;
831	>	vector<int> fortranGlobalGroupMembership;
832
600	–	nExclude = exclude_.getSize();
833		isError = 0;
834
835		//globalGroupMembership_ is filled by SimCreator
836		for (int i = 0; i < nGlobalAtoms_; i++) {
837	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
837	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
838		}
839
840		//calculate mass ratio of cutoff group
841	<	std::vector<double> mfact;
841	>	vector<RealType> mfact;
842		SimInfo::MoleculeIterator mi;
843		Molecule* mol;
844		Molecule::CutoffGroupIterator ci;
845		CutoffGroup* cg;
846		Molecule::AtomIterator ai;
847		Atom* atom;
848	<	double totalMass;
848	>	RealType totalMass;
849
850		//to avoid memory reallocation, reserve enough space for mfact
851		mfact.reserve(getNCutoffGroups());
852
853		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
854	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
854	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
855
856	<	totalMass = cg->getMass();
857	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
858	<	mfact.push_back(atom->getMass()/totalMass);
859	<	}
860	<
861	<	}
856	>	totalMass = cg->getMass();
857	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
858	>	// Check for massless groups - set mfact to 1 if true
859	>	if (totalMass != 0)
860	>	mfact.push_back(atom->getMass()/totalMass);
861	>	else
862	>	mfact.push_back( 1.0 );
863	>	}
864	>	}
865		}
866
867	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
633	<	std::vector<int> identArray;
867	>	// Build the identArray_
868
869	<	//to avoid memory reallocation, reserve enough space identArray
870	<	identArray.reserve(getNAtoms());
637	<
869	>	identArray_.clear();
870	>	identArray_.reserve(getNAtoms());
871		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
872	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
873	<	identArray.push_back(atom->getIdent());
874	<	}
872	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
873	>	identArray_.push_back(atom->getIdent());
874	>	}
875		}
876
877		//fill molMembershipArray
878		//molMembershipArray is filled by SimCreator
879	<	std::vector<int> molMembershipArray(nGlobalAtoms_);
879	>	vector<int> molMembershipArray(nGlobalAtoms_);
880		for (int i = 0; i < nGlobalAtoms_; i++) {
881	<	molMembershipArray[i] = globalMolMembership_[i] + 1;
881	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
882		}
883
884		//setup fortran simulation
652	–	//gloalExcludes and molMembershipArray should go away (They are never used)
653	–	//why the hell fortran need to know molecule?
654	–	//OOPSE = Object-Obfuscated Parallel Simulation Engine
655	–	int nGlobalExcludes = 0;
656	–	int* globalExcludes = NULL;
657	–	int* excludeList = exclude_.getExcludeList();
658	–	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
659	–	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
660	–	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
885
886	<	if( isError ){
886	>	nExclude = excludedInteractions_.getSize();
887	>	nOneTwo = oneTwoInteractions_.getSize();
888	>	nOneThree = oneThreeInteractions_.getSize();
889	>	nOneFour = oneFourInteractions_.getSize();
890
891	<	sprintf( painCave.errMsg,
892	<	"There was an error setting the simulation information in fortran.\n" );
893	<	painCave.isFatal = 1;
894	<	painCave.severity = OOPSE_ERROR;
668	<	simError();
669	<	}
891	>	int* excludeList = excludedInteractions_.getPairList();
892	>	int* oneTwoList = oneTwoInteractions_.getPairList();
893	>	int* oneThreeList = oneThreeInteractions_.getPairList();
894	>	int* oneFourList = oneFourInteractions_.getPairList();
895
896	<	#ifdef IS_MPI
896	>	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray_[0],
897	>	&nExclude, excludeList,
898	>	&nOneTwo, oneTwoList,
899	>	&nOneThree, oneThreeList,
900	>	&nOneFour, oneFourList,
901	>	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
902	>	&fortranGlobalGroupMembership[0], &isError);
903	>
904	>	if( isError ){
905	>
906	>	sprintf( painCave.errMsg,
907	>	"There was an error setting the simulation information in fortran.\n" );
908	>	painCave.isFatal = 1;
909	>	painCave.severity = OPENMD_ERROR;
910	>	simError();
911	>	}
912	>
913	>
914		sprintf( checkPointMsg,
915	<	"succesfully sent the simulation information to fortran.\n");
674	<	MPIcheckPoint();
675	<	#endif // is_mpi
676	<	}
677	<
678	<
679	<	#ifdef IS_MPI
680	<	void SimInfo::setupFortranParallel() {
915	>	"succesfully sent the simulation information to fortran.\n");
916
917	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
918	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
919	<	std::vector<int> localToGlobalCutoffGroupIndex;
920	<	SimInfo::MoleculeIterator mi;
921	<	Molecule::AtomIterator ai;
922	<	Molecule::CutoffGroupIterator ci;
923	<	Molecule* mol;
924	<	Atom* atom;
925	<	CutoffGroup* cg;
917	>	errorCheckPoint();
918	>
919	>	// Setup number of neighbors in neighbor list if present
920	>	if (simParams_->haveNeighborListNeighbors()) {
921	>	int nlistNeighbors = simParams_->getNeighborListNeighbors();
922	>	setNeighbors(&nlistNeighbors);
923	>	}
924	>
925	>	#ifdef IS_MPI
926		mpiSimData parallelData;
692	–	int isError;
927
694	–	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
695	–
696	–	//local index(index in DataStorge) of atom is important
697	–	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
698	–	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
699	–	}
700	–
701	–	//local index of cutoff group is trivial, it only depends on the order of travesing
702	–	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
703	–	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
704	–	}
705	–
706	–	}
707	–
928		//fill up mpiSimData struct
929		parallelData.nMolGlobal = getNGlobalMolecules();
930		parallelData.nMolLocal = getNMolecules();
#	Line 716 | Line 936 | void SimInfo::setupFortranParallel() {
936		MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
937
938		//pass mpiSimData struct and index arrays to fortran
939	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
940	<	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
941	<	&localToGlobalCutoffGroupIndex[0], &isError);
939	>	//setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
940	>	//                &localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
941	>	//                &localToGlobalCutoffGroupIndex[0], &isError);
942
943		if (isError) {
944	<	sprintf(painCave.errMsg,
945	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
946	<	painCave.isFatal = 1;
947	<	simError();
944	>	sprintf(painCave.errMsg,
945	>	"mpiRefresh errror: fortran didn't like something we gave it.\n");
946	>	painCave.isFatal = 1;
947	>	simError();
948		}
949
950		sprintf(checkPointMsg, " mpiRefresh successful.\n");
951	<	MPIcheckPoint();
732	<
733	<
734	<	}
735	<
951	>	errorCheckPoint();
952		#endif
953
954	<	double SimInfo::calcMaxCutoffRadius() {
954	>	initFortranFF(&isError);
955	>	if (isError) {
956	>	sprintf(painCave.errMsg,
957	>	"initFortranFF errror: fortran didn't like something we gave it.\n");
958	>	painCave.isFatal = 1;
959	>	simError();
960	>	}
961	>	fortranInitialized_ = true;
962	>	}
963
964	+	void SimInfo::addProperty(GenericData* genData) {
965	+	properties_.addProperty(genData);
966	+	}
967
968	<	std::set<AtomType*> atomTypes;
969	<	std::set<AtomType*>::iterator i;
970	<	std::vector<double> cutoffRadius;
968	>	void SimInfo::removeProperty(const string& propName) {
969	>	properties_.removeProperty(propName);
970	>	}
971
972	<	//get the unique atom types
973	<	atomTypes = getUniqueAtomTypes();
972	>	void SimInfo::clearProperties() {
973	>	properties_.clearProperties();
974	>	}
975
976	<	//query the max cutoff radius among these atom types
977	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
978	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
979	<	}
976	>	vector<string> SimInfo::getPropertyNames() {
977	>	return properties_.getPropertyNames();
978	>	}
979	>
980	>	vector<GenericData*> SimInfo::getProperties() {
981	>	return properties_.getProperties();
982	>	}
983
984	<	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
754	<	#ifdef IS_MPI
755	<	//pick the max cutoff radius among the processors
756	<	#endif
757	<
758	<	return maxCutoffRadius;
759	<	}
760	<
761	<	void SimInfo::getCutoff(double& rcut, double& rsw) {
762	<
763	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
764	<
765	<	if (!simParams_->haveRcut()){
766	<	sprintf(painCave.errMsg,
767	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
768	<	"\tOOPSE will use a default value of 15.0 angstroms"
769	<	"\tfor the cutoffRadius.\n");
770	<	painCave.isFatal = 0;
771	<	simError();
772	<	rcut = 15.0;
773	<	} else{
774	<	rcut = simParams_->getRcut();
775	<	}
776	<
777	<	if (!simParams_->haveRsw()){
778	<	sprintf(painCave.errMsg,
779	<	"SimCreator Warning: No value was set for switchingRadius.\n"
780	<	"\tOOPSE will use a default value of\n"
781	<	"\t0.95 * cutoffRadius for the switchingRadius\n");
782	<	painCave.isFatal = 0;
783	<	simError();
784	<	rsw = 0.95 * rcut;
785	<	} else{
786	<	rsw = simParams_->getRsw();
787	<	}
788	<
789	<	} else {
790	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
791	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
792	<
793	<	if (simParams_->haveRcut()) {
794	<	rcut = simParams_->getRcut();
795	<	} else {
796	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
797	<	rcut = calcMaxCutoffRadius();
798	<	}
799	<
800	<	if (simParams_->haveRsw()) {
801	<	rsw  = simParams_->getRsw();
802	<	} else {
803	<	rsw = rcut;
804	<	}
805	<
806	<	}
807	<	}
808	<
809	<	void SimInfo::setupCutoff() {
810	<	getCutoff(rcut_, rsw_);
811	<	double rnblist = rcut_ + 1; // skin of neighbor list
812	<
813	<	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
814	<	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist);
815	<	}
816	<
817	<	void SimInfo::addProperty(GenericData* genData) {
818	<	properties_.addProperty(genData);
819	<	}
820	<
821	<	void SimInfo::removeProperty(const std::string& propName) {
822	<	properties_.removeProperty(propName);
823	<	}
824	<
825	<	void SimInfo::clearProperties() {
826	<	properties_.clearProperties();
827	<	}
828	<
829	<	std::vector<std::string> SimInfo::getPropertyNames() {
830	<	return properties_.getPropertyNames();
831	<	}
832	<
833	<	std::vector<GenericData*> SimInfo::getProperties() {
834	<	return properties_.getProperties();
835	<	}
836	<
837	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
984	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
985		return properties_.getPropertyByName(propName);
986	<	}
986	>	}
987
988	<	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
989	<	//if (sman_ == sman_) {
990	<	//    return;
991	<	//}
992	<
846	<	//delete sman_;
988	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
989	>	if (sman_ == sman) {
990	>	return;
991	>	}
992	>	delete sman_;
993		sman_ = sman;
994
995		Molecule* mol;
996		RigidBody* rb;
997		Atom* atom;
998	+	CutoffGroup* cg;
999		SimInfo::MoleculeIterator mi;
1000		Molecule::RigidBodyIterator rbIter;
1001	<	Molecule::AtomIterator atomIter;;
1001	>	Molecule::AtomIterator atomIter;
1002	>	Molecule::CutoffGroupIterator cgIter;
1003
1004		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1005
1006	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1007	<	atom->setSnapshotManager(sman_);
1008	<	}
1006	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1007	>	atom->setSnapshotManager(sman_);
1008	>	}
1009
1010	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1011	<	rb->setSnapshotManager(sman_);
1012	<	}
1010	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1011	>	rb->setSnapshotManager(sman_);
1012	>	}
1013	>
1014	>	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
1015	>	cg->setSnapshotManager(sman_);
1016	>	}
1017		}
1018
1019	<	}
1019	>	}
1020
1021	<	Vector3d SimInfo::getComVel(){
1021	>	Vector3d SimInfo::getComVel(){
1022		SimInfo::MoleculeIterator i;
1023		Molecule* mol;
1024
1025		Vector3d comVel(0.0);
1026	<	double totalMass = 0.0;
1026	>	RealType totalMass = 0.0;
1027
1028
1029		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1030	<	double mass = mol->getMass();
1031	<	totalMass += mass;
1032	<	comVel += mass * mol->getComVel();
1030	>	RealType mass = mol->getMass();
1031	>	totalMass += mass;
1032	>	comVel += mass * mol->getComVel();
1033		}
1034
1035		#ifdef IS_MPI
1036	<	double tmpMass = totalMass;
1036	>	RealType tmpMass = totalMass;
1037		Vector3d tmpComVel(comVel);
1038	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1039	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1038	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1039	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1040		#endif
1041
1042		comVel /= totalMass;
1043
1044		return comVel;
1045	<	}
1045	>	}
1046
1047	<	Vector3d SimInfo::getCom(){
1047	>	Vector3d SimInfo::getCom(){
1048		SimInfo::MoleculeIterator i;
1049		Molecule* mol;
1050
1051		Vector3d com(0.0);
1052	<	double totalMass = 0.0;
1052	>	RealType totalMass = 0.0;
1053
1054		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1055	<	double mass = mol->getMass();
1056	<	totalMass += mass;
1057	<	com += mass * mol->getCom();
1055	>	RealType mass = mol->getMass();
1056	>	totalMass += mass;
1057	>	com += mass * mol->getCom();
1058		}
1059
1060		#ifdef IS_MPI
1061	<	double tmpMass = totalMass;
1061	>	RealType tmpMass = totalMass;
1062		Vector3d tmpCom(com);
1063	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1064	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1063	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1064	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1065		#endif
1066
1067		com /= totalMass;
1068
1069		return com;
1070
1071	<	}
1071	>	}
1072
1073	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1073	>	ostream& operator <<(ostream& o, SimInfo& info) {
1074
1075		return o;
1076	<	}
1076	>	}
1077	>
1078	>
1079	>	/*
1080	>	Returns center of mass and center of mass velocity in one function call.
1081	>	*/
1082	>
1083	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1084	>	SimInfo::MoleculeIterator i;
1085	>	Molecule* mol;
1086	>
1087	>
1088	>	RealType totalMass = 0.0;
1089	>
1090
1091	<	}//end namespace oopse
1091	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1092	>	RealType mass = mol->getMass();
1093	>	totalMass += mass;
1094	>	com += mass * mol->getCom();
1095	>	comVel += mass * mol->getComVel();
1096	>	}
1097	>
1098	>	#ifdef IS_MPI
1099	>	RealType tmpMass = totalMass;
1100	>	Vector3d tmpCom(com);
1101	>	Vector3d tmpComVel(comVel);
1102	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1103	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1104	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1105	>	#endif
1106	>
1107	>	com /= totalMass;
1108	>	comVel /= totalMass;
1109	>	}
1110	>
1111	>	/*
1112	>	Return intertia tensor for entire system and angular momentum Vector.
1113
1114	+
1115	+	[  Ixx -Ixy  -Ixz ]
1116	+	J =| -Iyx  Iyy  -Iyz |
1117	+	[ -Izx -Iyz   Izz ]
1118	+	*/
1119	+
1120	+	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1121	+
1122	+
1123	+	RealType xx = 0.0;
1124	+	RealType yy = 0.0;
1125	+	RealType zz = 0.0;
1126	+	RealType xy = 0.0;
1127	+	RealType xz = 0.0;
1128	+	RealType yz = 0.0;
1129	+	Vector3d com(0.0);
1130	+	Vector3d comVel(0.0);
1131	+
1132	+	getComAll(com, comVel);
1133	+
1134	+	SimInfo::MoleculeIterator i;
1135	+	Molecule* mol;
1136	+
1137	+	Vector3d thisq(0.0);
1138	+	Vector3d thisv(0.0);
1139	+
1140	+	RealType thisMass = 0.0;
1141	+
1142	+
1143	+
1144	+
1145	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1146	+
1147	+	thisq = mol->getCom()-com;
1148	+	thisv = mol->getComVel()-comVel;
1149	+	thisMass = mol->getMass();
1150	+	// Compute moment of intertia coefficients.
1151	+	xx += thisq[0]*thisq[0]*thisMass;
1152	+	yy += thisq[1]*thisq[1]*thisMass;
1153	+	zz += thisq[2]*thisq[2]*thisMass;
1154	+
1155	+	// compute products of intertia
1156	+	xy += thisq[0]*thisq[1]*thisMass;
1157	+	xz += thisq[0]*thisq[2]*thisMass;
1158	+	yz += thisq[1]*thisq[2]*thisMass;
1159	+
1160	+	angularMomentum += cross( thisq, thisv ) * thisMass;
1161	+
1162	+	}
1163	+
1164	+
1165	+	inertiaTensor(0,0) = yy + zz;
1166	+	inertiaTensor(0,1) = -xy;
1167	+	inertiaTensor(0,2) = -xz;
1168	+	inertiaTensor(1,0) = -xy;
1169	+	inertiaTensor(1,1) = xx + zz;
1170	+	inertiaTensor(1,2) = -yz;
1171	+	inertiaTensor(2,0) = -xz;
1172	+	inertiaTensor(2,1) = -yz;
1173	+	inertiaTensor(2,2) = xx + yy;
1174	+
1175	+	#ifdef IS_MPI
1176	+	Mat3x3d tmpI(inertiaTensor);
1177	+	Vector3d tmpAngMom;
1178	+	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1179	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1180	+	#endif
1181	+
1182	+	return;
1183	+	}
1184	+
1185	+	//Returns the angular momentum of the system
1186	+	Vector3d SimInfo::getAngularMomentum(){
1187	+
1188	+	Vector3d com(0.0);
1189	+	Vector3d comVel(0.0);
1190	+	Vector3d angularMomentum(0.0);
1191	+
1192	+	getComAll(com,comVel);
1193	+
1194	+	SimInfo::MoleculeIterator i;
1195	+	Molecule* mol;
1196	+
1197	+	Vector3d thisr(0.0);
1198	+	Vector3d thisp(0.0);
1199	+
1200	+	RealType thisMass;
1201	+
1202	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1203	+	thisMass = mol->getMass();
1204	+	thisr = mol->getCom()-com;
1205	+	thisp = (mol->getComVel()-comVel)*thisMass;
1206	+
1207	+	angularMomentum += cross( thisr, thisp );
1208	+
1209	+	}
1210	+
1211	+	#ifdef IS_MPI
1212	+	Vector3d tmpAngMom;
1213	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1214	+	#endif
1215	+
1216	+	return angularMomentum;
1217	+	}
1218	+
1219	+	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1220	+	return IOIndexToIntegrableObject.at(index);
1221	+	}
1222	+
1223	+	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1224	+	IOIndexToIntegrableObject= v;
1225	+	}
1226	+
1227	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1228	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1229	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1230	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1231	+	*/
1232	+	void SimInfo::getGyrationalVolume(RealType &volume){
1233	+	Mat3x3d intTensor;
1234	+	RealType det;
1235	+	Vector3d dummyAngMom;
1236	+	RealType sysconstants;
1237	+	RealType geomCnst;
1238	+
1239	+	geomCnst = 3.0/2.0;
1240	+	/* Get the inertial tensor and angular momentum for free*/
1241	+	getInertiaTensor(intTensor,dummyAngMom);
1242	+
1243	+	det = intTensor.determinant();
1244	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1245	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1246	+	return;
1247	+	}
1248	+
1249	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1250	+	Mat3x3d intTensor;
1251	+	Vector3d dummyAngMom;
1252	+	RealType sysconstants;
1253	+	RealType geomCnst;
1254	+
1255	+	geomCnst = 3.0/2.0;
1256	+	/* Get the inertial tensor and angular momentum for free*/
1257	+	getInertiaTensor(intTensor,dummyAngMom);
1258	+
1259	+	detI = intTensor.determinant();
1260	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1261	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1262	+	return;
1263	+	}
1264	+	/*
1265	+	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1266	+	assert( v.size() == nAtoms_ + nRigidBodies_);
1267	+	sdByGlobalIndex_ = v;
1268	+	}
1269	+
1270	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1271	+	//assert(index < nAtoms_ + nRigidBodies_);
1272	+	return sdByGlobalIndex_.at(index);
1273	+	}
1274	+	*/
1275	+	int SimInfo::getNGlobalConstraints() {
1276	+	int nGlobalConstraints;
1277	+	#ifdef IS_MPI
1278	+	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1279	+	MPI_COMM_WORLD);
1280	+	#else
1281	+	nGlobalConstraints =  nConstraints_;
1282	+	#endif
1283	+	return nGlobalConstraints;
1284	+	}
1285	+
1286	+	}//end namespace OpenMD
1287	+

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 398 by tim, Mon Mar 7 22:39:33 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1549 by gezelter, Wed Apr 27 18:38:15 2011 UTC

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