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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 292 by tim, Fri Feb 4 22:44:15 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1535 by gezelter, Fri Dec 31 18:31:56 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 "UseTheForce/doForces_interface.h"
57	<	#include "UseTheForce/notifyCutoffs_interface.h"
56	>	#include "primitives/StuntDouble.hpp"
57	>	#include "UseTheForce/DarkSide/neighborLists_interface.h"
58		#include "utils/MemoryUtils.hpp"
59		#include "utils/simError.h"
60	+	#include "selection/SelectionManager.hpp"
61	+	#include "io/ForceFieldOptions.hpp"
62	+	#include "UseTheForce/ForceField.hpp"
63	+	#include "nonbonded/SwitchingFunction.hpp"
64
65		#ifdef IS_MPI
66		#include "UseTheForce/mpiComponentPlan.h"
67		#include "UseTheForce/DarkSide/simParallel_interface.h"
68		#endif
69
70	<	namespace oopse {
71	<
72	<	SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
73	<	ForceField* ff, Globals* simParams) :
74	<	forceField_(ff), simParams_(simParams),
75	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
76	<	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
77	<	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
78	<	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
79	<	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
80	<	sman_(NULL), fortranInitialized_(false), selectMan_(NULL) {
81	<
82	<
78	<	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
70	>	using namespace std;
71	>	namespace OpenMD {
72	>
73	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
74	>	forceField_(ff), simParams_(simParams),
75	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
76	>	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
77	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
78	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
79	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
80	>	nConstraints_(0), sman_(NULL), fortranInitialized_(false),
81	>	calcBoxDipole_(false), useAtomicVirial_(true) {
82	>
83		MoleculeStamp* molStamp;
84		int nMolWithSameStamp;
85		int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
86	<	int nGroups = 0;          //total cutoff groups defined in meta-data file
86	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
87		CutoffGroupStamp* cgStamp;
88		RigidBodyStamp* rbStamp;
89		int nRigidAtoms = 0;
90
91	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
92	<	molStamp = i->first;
93	<	nMolWithSameStamp = i->second;
94	<
95	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
96	<
97	<	//calculate atoms in molecules
98	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
99	<
100	<
101	<	//calculate atoms in cutoff groups
102	<	int nAtomsInGroups = 0;
103	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
104	<
105	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
106	<	cgStamp = molStamp->getCutoffGroup(j);
107	<	nAtomsInGroups += cgStamp->getNMembers();
108	<	}
109	<
110	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
111	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
112	<
113	<	//calculate atoms in rigid bodies
114	<	int nAtomsInRigidBodies = 0;
115	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
116	<
117	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
118	<	rbStamp = molStamp->getRigidBody(j);
119	<	nAtomsInRigidBodies += rbStamp->getNMembers();
120	<	}
121	<
122	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
123	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
124	<
91	>	vector<Component*> components = simParams->getComponents();
92	>
93	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
94	>	molStamp = (*i)->getMoleculeStamp();
95	>	nMolWithSameStamp = (*i)->getNMol();
96	>
97	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
98	>
99	>	//calculate atoms in molecules
100	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
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->getCutoffGroupStamp(j);
108	>	nAtomsInGroups += cgStamp->getNMembers();
109	>	}
110	>
111	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
112	>
113	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
114	>
115	>	//calculate atoms in rigid bodies
116	>	int nAtomsInRigidBodies = 0;
117	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
118	>
119	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
120	>	rbStamp = molStamp->getRigidBodyStamp(j);
121	>	nAtomsInRigidBodies += rbStamp->getNMembers();
122	>	}
123	>
124	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
125	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
126	>
127		}
128	<
129	<	//every free atom (atom does not belong to cutoff groups) is a cutoff group
130	<	//therefore the total number of cutoff groups in the system is equal to
131	<	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
132	<	//file plus the number of cutoff groups defined in meta-data file
128	>
129	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
130	>	//group therefore the total number of cutoff groups in the system is
131	>	//equal to the total number of atoms minus number of atoms belong to
132	>	//cutoff group defined in meta-data file plus the number of cutoff
133	>	//groups defined in meta-data file
134		nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
135	<
136	<	//every free atom (atom does not belong to rigid bodies) is an integrable object
137	<	//therefore the total number of  integrable objects in the system is equal to
138	<	//the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
139	<	//file plus the number of  rigid bodies defined in meta-data file
140	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
141	<
135	>
136	>	//every free atom (atom does not belong to rigid bodies) is an
137	>	//integrable object therefore the total number of integrable objects
138	>	//in the system is equal to the total number of atoms minus number of
139	>	//atoms belong to rigid body defined in meta-data file plus the number
140	>	//of rigid bodies defined in meta-data file
141	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
142	>	+ nGlobalRigidBodies_;
143	>
144		nGlobalMols_ = molStampIds_.size();
136	–
137	–	#ifdef IS_MPI
145		molToProcMap_.resize(nGlobalMols_);
146	<	#endif
147	<
148	<	selectMan_ = new SelectionManager(nGlobalAtoms_ + nGlobalRigidBodies_);
149	<	selectMan_->selectAll();
150	<	}
151	<
152	<	SimInfo::~SimInfo() {
153	<	//MemoryUtils::deleteVectorOfPointer(molecules_);
154	<
148	<	MemoryUtils::deleteVectorOfPointer(moleculeStamps_);
149	<
146	>	}
147	>
148	>	SimInfo::~SimInfo() {
149	>	map<int, Molecule*>::iterator i;
150	>	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
151	>	delete i->second;
152	>	}
153	>	molecules_.clear();
154	>
155		delete sman_;
156		delete simParams_;
157		delete forceField_;
158	<	delete selectMan_;
154	<	}
158	>	}
159
156	–	int SimInfo::getNGlobalConstraints() {
157	–	int nGlobalConstraints;
158	–	#ifdef IS_MPI
159	–	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
160	–	MPI_COMM_WORLD);
161	–	#else
162	–	nGlobalConstraints =  nConstraints_;
163	–	#endif
164	–	return nGlobalConstraints;
165	–	}
160
161	<	bool SimInfo::addMolecule(Molecule* mol) {
161	>	bool SimInfo::addMolecule(Molecule* mol) {
162		MoleculeIterator i;
163	<
163	>
164		i = molecules_.find(mol->getGlobalIndex());
165		if (i == molecules_.end() ) {
166	<
167	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
168	<
169	<	nAtoms_ += mol->getNAtoms();
170	<	nBonds_ += mol->getNBonds();
171	<	nBends_ += mol->getNBends();
172	<	nTorsions_ += mol->getNTorsions();
173	<	nRigidBodies_ += mol->getNRigidBodies();
174	<	nIntegrableObjects_ += mol->getNIntegrableObjects();
175	<	nCutoffGroups_ += mol->getNCutoffGroups();
176	<	nConstraints_ += mol->getNConstraintPairs();
177	<
178	<	addExcludePairs(mol);
179	<
180	<	return true;
181	<	} else {
182	<	return false;
166	>
167	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
168	>
169	>	nAtoms_ += mol->getNAtoms();
170	>	nBonds_ += mol->getNBonds();
171	>	nBends_ += mol->getNBends();
172	>	nTorsions_ += mol->getNTorsions();
173	>	nInversions_ += mol->getNInversions();
174	>	nRigidBodies_ += mol->getNRigidBodies();
175	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
176	>	nCutoffGroups_ += mol->getNCutoffGroups();
177	>	nConstraints_ += mol->getNConstraintPairs();
178	>
179	>	addInteractionPairs(mol);
180	>
181	>	return true;
182	>	} else {
183	>	return false;
184		}
185	<	}
186	<
187	<	bool SimInfo::removeMolecule(Molecule* mol) {
185	>	}
186	>
187	>	bool SimInfo::removeMolecule(Molecule* mol) {
188		MoleculeIterator i;
189		i = molecules_.find(mol->getGlobalIndex());
190
191		if (i != molecules_.end() ) {
192
193	<	assert(mol == i->second);
193	>	assert(mol == i->second);
194
195	<	nAtoms_ -= mol->getNAtoms();
196	<	nBonds_ -= mol->getNBonds();
197	<	nBends_ -= mol->getNBends();
198	<	nTorsions_ -= mol->getNTorsions();
199	<	nRigidBodies_ -= mol->getNRigidBodies();
200	<	nIntegrableObjects_ -= mol->getNIntegrableObjects();
201	<	nCutoffGroups_ -= mol->getNCutoffGroups();
202	<	nConstraints_ -= mol->getNConstraintPairs();
195	>	nAtoms_ -= mol->getNAtoms();
196	>	nBonds_ -= mol->getNBonds();
197	>	nBends_ -= mol->getNBends();
198	>	nTorsions_ -= mol->getNTorsions();
199	>	nInversions_ -= mol->getNInversions();
200	>	nRigidBodies_ -= mol->getNRigidBodies();
201	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
202	>	nCutoffGroups_ -= mol->getNCutoffGroups();
203	>	nConstraints_ -= mol->getNConstraintPairs();
204
205	<	removeExcludePairs(mol);
206	<	molecules_.erase(mol->getGlobalIndex());
205	>	removeInteractionPairs(mol);
206	>	molecules_.erase(mol->getGlobalIndex());
207
208	<	delete mol;
208	>	delete mol;
209
210	<	return true;
210	>	return true;
211		} else {
212	<	return false;
212	>	return false;
213		}
214	+	}
215
219	–
220	–	}
221	–
216
217	<	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
217	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
218		i = molecules_.begin();
219		return i == molecules_.end() ? NULL : i->second;
220	<	}
220	>	}
221
222	<	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
222	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
223		++i;
224		return i == molecules_.end() ? NULL : i->second;
225	<	}
225	>	}
226
227
228	<	void SimInfo::calcNdf() {
228	>	void SimInfo::calcNdf() {
229		int ndf_local;
230		MoleculeIterator i;
231	<	std::vector<StuntDouble*>::iterator j;
231	>	vector<StuntDouble*>::iterator j;
232		Molecule* mol;
233		StuntDouble* integrableObject;
234
235		ndf_local = 0;
236
237		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
238	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
239	<	integrableObject = mol->nextIntegrableObject(j)) {
238	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
239	>	integrableObject = mol->nextIntegrableObject(j)) {
240
241	<	ndf_local += 3;
241	>	ndf_local += 3;
242
243	<	if (integrableObject->isDirectional()) {
244	<	if (integrableObject->isLinear()) {
245	<	ndf_local += 2;
246	<	} else {
247	<	ndf_local += 3;
248	<	}
249	<	}
243	>	if (integrableObject->isDirectional()) {
244	>	if (integrableObject->isLinear()) {
245	>	ndf_local += 2;
246	>	} else {
247	>	ndf_local += 3;
248	>	}
249	>	}
250
251	<	}//end for (integrableObject)
252	<	}// end for (mol)
251	>	}
252	>	}
253
254		// n_constraints is local, so subtract them on each processor
255		ndf_local -= nConstraints_;
#	Line 270 | Line 264 | void SimInfo::calcNdf() {
264		// entire system:
265		ndf_ = ndf_ - 3 - nZconstraint_;
266
267	<	}
267	>	}
268
269	<	void SimInfo::calcNdfRaw() {
269	>	int SimInfo::getFdf() {
270	>	#ifdef IS_MPI
271	>	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
272	>	#else
273	>	fdf_ = fdf_local;
274	>	#endif
275	>	return fdf_;
276	>	}
277	>
278	>	void SimInfo::calcNdfRaw() {
279		int ndfRaw_local;
280
281		MoleculeIterator i;
282	<	std::vector<StuntDouble*>::iterator j;
282	>	vector<StuntDouble*>::iterator j;
283		Molecule* mol;
284		StuntDouble* integrableObject;
285
#	Line 284 | Line 287 | void SimInfo::calcNdfRaw() {
287		ndfRaw_local = 0;
288
289		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
290	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
291	<	integrableObject = mol->nextIntegrableObject(j)) {
290	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
291	>	integrableObject = mol->nextIntegrableObject(j)) {
292
293	<	ndfRaw_local += 3;
293	>	ndfRaw_local += 3;
294
295	<	if (integrableObject->isDirectional()) {
296	<	if (integrableObject->isLinear()) {
297	<	ndfRaw_local += 2;
298	<	} else {
299	<	ndfRaw_local += 3;
300	<	}
301	<	}
295	>	if (integrableObject->isDirectional()) {
296	>	if (integrableObject->isLinear()) {
297	>	ndfRaw_local += 2;
298	>	} else {
299	>	ndfRaw_local += 3;
300	>	}
301	>	}
302
303	<	}
303	>	}
304		}
305
306		#ifdef IS_MPI
#	Line 305 | Line 308 | void SimInfo::calcNdfRaw() {
308		#else
309		ndfRaw_ = ndfRaw_local;
310		#endif
311	<	}
311	>	}
312
313	<	void SimInfo::calcNdfTrans() {
313	>	void SimInfo::calcNdfTrans() {
314		int ndfTrans_local;
315
316		ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
#	Line 321 | Line 324 | void SimInfo::calcNdfTrans() {
324
325		ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
326
327	<	}
327	>	}
328
329	<	void SimInfo::addExcludePairs(Molecule* mol) {
330	<	std::vector<Bond*>::iterator bondIter;
331	<	std::vector<Bend*>::iterator bendIter;
332	<	std::vector<Torsion*>::iterator torsionIter;
329	>	void SimInfo::addInteractionPairs(Molecule* mol) {
330	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
331	>	vector<Bond*>::iterator bondIter;
332	>	vector<Bend*>::iterator bendIter;
333	>	vector<Torsion*>::iterator torsionIter;
334	>	vector<Inversion*>::iterator inversionIter;
335		Bond* bond;
336		Bend* bend;
337		Torsion* torsion;
338	+	Inversion* inversion;
339		int a;
340		int b;
341		int c;
342		int d;
337	–
338	–	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
339	–	a = bond->getAtomA()->getGlobalIndex();
340	–	b = bond->getAtomB()->getGlobalIndex();
341	–	exclude_.addPair(a, b);
342	–	}
343
344	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
345	<	a = bend->getAtomA()->getGlobalIndex();
346	<	b = bend->getAtomB()->getGlobalIndex();
347	<	c = bend->getAtomC()->getGlobalIndex();
344	>	// atomGroups can be used to add special interaction maps between
345	>	// groups of atoms that are in two separate rigid bodies.
346	>	// However, most site-site interactions between two rigid bodies
347	>	// are probably not special, just the ones between the physically
348	>	// bonded atoms.  Interactions *within* a single rigid body should
349	>	// always be excluded.  These are done at the bottom of this
350	>	// function.
351
352	<	exclude_.addPair(a, b);
353	<	exclude_.addPair(a, c);
354	<	exclude_.addPair(b, c);
355	<	}
356	<
357	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
358	<	a = torsion->getAtomA()->getGlobalIndex();
359	<	b = torsion->getAtomB()->getGlobalIndex();
360	<	c = torsion->getAtomC()->getGlobalIndex();
361	<	d = torsion->getAtomD()->getGlobalIndex();
352	>	map<int, set<int> > atomGroups;
353	>	Molecule::RigidBodyIterator rbIter;
354	>	RigidBody* rb;
355	>	Molecule::IntegrableObjectIterator ii;
356	>	StuntDouble* integrableObject;
357	>
358	>	for (integrableObject = mol->beginIntegrableObject(ii);
359	>	integrableObject != NULL;
360	>	integrableObject = mol->nextIntegrableObject(ii)) {
361	>
362	>	if (integrableObject->isRigidBody()) {
363	>	rb = static_cast<RigidBody*>(integrableObject);
364	>	vector<Atom*> atoms = rb->getAtoms();
365	>	set<int> rigidAtoms;
366	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
367	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
368	>	}
369	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
370	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
371	>	}
372	>	} else {
373	>	set<int> oneAtomSet;
374	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
375	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
376	>	}
377	>	}
378	>
379	>	for (bond= mol->beginBond(bondIter); bond != NULL;
380	>	bond = mol->nextBond(bondIter)) {
381
382	<	exclude_.addPair(a, b);
383	<	exclude_.addPair(a, c);
384	<	exclude_.addPair(a, d);
385	<	exclude_.addPair(b, c);
386	<	exclude_.addPair(b, d);
387	<	exclude_.addPair(c, d);
382	>	a = bond->getAtomA()->getGlobalIndex();
383	>	b = bond->getAtomB()->getGlobalIndex();
384	>
385	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
386	>	oneTwoInteractions_.addPair(a, b);
387	>	} else {
388	>	excludedInteractions_.addPair(a, b);
389	>	}
390		}
391
392	<
393	<	}
392	>	for (bend= mol->beginBend(bendIter); bend != NULL;
393	>	bend = mol->nextBend(bendIter)) {
394
395	<	void SimInfo::removeExcludePairs(Molecule* mol) {
396	<	std::vector<Bond*>::iterator bondIter;
397	<	std::vector<Bend*>::iterator bendIter;
398	<	std::vector<Torsion*>::iterator torsionIter;
395	>	a = bend->getAtomA()->getGlobalIndex();
396	>	b = bend->getAtomB()->getGlobalIndex();
397	>	c = bend->getAtomC()->getGlobalIndex();
398	>
399	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
400	>	oneTwoInteractions_.addPair(a, b);
401	>	oneTwoInteractions_.addPair(b, c);
402	>	} else {
403	>	excludedInteractions_.addPair(a, b);
404	>	excludedInteractions_.addPair(b, c);
405	>	}
406	>
407	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
408	>	oneThreeInteractions_.addPair(a, c);
409	>	} else {
410	>	excludedInteractions_.addPair(a, c);
411	>	}
412	>	}
413	>
414	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
415	>	torsion = mol->nextTorsion(torsionIter)) {
416	>
417	>	a = torsion->getAtomA()->getGlobalIndex();
418	>	b = torsion->getAtomB()->getGlobalIndex();
419	>	c = torsion->getAtomC()->getGlobalIndex();
420	>	d = torsion->getAtomD()->getGlobalIndex();
421	>
422	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
423	>	oneTwoInteractions_.addPair(a, b);
424	>	oneTwoInteractions_.addPair(b, c);
425	>	oneTwoInteractions_.addPair(c, d);
426	>	} else {
427	>	excludedInteractions_.addPair(a, b);
428	>	excludedInteractions_.addPair(b, c);
429	>	excludedInteractions_.addPair(c, d);
430	>	}
431	>
432	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
433	>	oneThreeInteractions_.addPair(a, c);
434	>	oneThreeInteractions_.addPair(b, d);
435	>	} else {
436	>	excludedInteractions_.addPair(a, c);
437	>	excludedInteractions_.addPair(b, d);
438	>	}
439	>
440	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
441	>	oneFourInteractions_.addPair(a, d);
442	>	} else {
443	>	excludedInteractions_.addPair(a, d);
444	>	}
445	>	}
446	>
447	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
448	>	inversion = mol->nextInversion(inversionIter)) {
449	>
450	>	a = inversion->getAtomA()->getGlobalIndex();
451	>	b = inversion->getAtomB()->getGlobalIndex();
452	>	c = inversion->getAtomC()->getGlobalIndex();
453	>	d = inversion->getAtomD()->getGlobalIndex();
454	>
455	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
456	>	oneTwoInteractions_.addPair(a, b);
457	>	oneTwoInteractions_.addPair(a, c);
458	>	oneTwoInteractions_.addPair(a, d);
459	>	} else {
460	>	excludedInteractions_.addPair(a, b);
461	>	excludedInteractions_.addPair(a, c);
462	>	excludedInteractions_.addPair(a, d);
463	>	}
464	>
465	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
466	>	oneThreeInteractions_.addPair(b, c);
467	>	oneThreeInteractions_.addPair(b, d);
468	>	oneThreeInteractions_.addPair(c, d);
469	>	} else {
470	>	excludedInteractions_.addPair(b, c);
471	>	excludedInteractions_.addPair(b, d);
472	>	excludedInteractions_.addPair(c, d);
473	>	}
474	>	}
475	>
476	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
477	>	rb = mol->nextRigidBody(rbIter)) {
478	>	vector<Atom*> atoms = rb->getAtoms();
479	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
480	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
481	>	a = atoms[i]->getGlobalIndex();
482	>	b = atoms[j]->getGlobalIndex();
483	>	excludedInteractions_.addPair(a, b);
484	>	}
485	>	}
486	>	}
487	>
488	>	}
489	>
490	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
491	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
492	>	vector<Bond*>::iterator bondIter;
493	>	vector<Bend*>::iterator bendIter;
494	>	vector<Torsion*>::iterator torsionIter;
495	>	vector<Inversion*>::iterator inversionIter;
496		Bond* bond;
497		Bend* bend;
498		Torsion* torsion;
499	+	Inversion* inversion;
500		int a;
501		int b;
502		int c;
503		int d;
504	+
505	+	map<int, set<int> > atomGroups;
506	+	Molecule::RigidBodyIterator rbIter;
507	+	RigidBody* rb;
508	+	Molecule::IntegrableObjectIterator ii;
509	+	StuntDouble* integrableObject;
510
511	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
512	<	a = bond->getAtomA()->getGlobalIndex();
513	<	b = bond->getAtomB()->getGlobalIndex();
514	<	exclude_.removePair(a, b);
511	>	for (integrableObject = mol->beginIntegrableObject(ii);
512	>	integrableObject != NULL;
513	>	integrableObject = mol->nextIntegrableObject(ii)) {
514	>
515	>	if (integrableObject->isRigidBody()) {
516	>	rb = static_cast<RigidBody*>(integrableObject);
517	>	vector<Atom*> atoms = rb->getAtoms();
518	>	set<int> rigidAtoms;
519	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
520	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
521	>	}
522	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
523	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
524	>	}
525	>	} else {
526	>	set<int> oneAtomSet;
527	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
528	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
529	>	}
530	>	}
531	>
532	>	for (bond= mol->beginBond(bondIter); bond != NULL;
533	>	bond = mol->nextBond(bondIter)) {
534	>
535	>	a = bond->getAtomA()->getGlobalIndex();
536	>	b = bond->getAtomB()->getGlobalIndex();
537	>
538	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
539	>	oneTwoInteractions_.removePair(a, b);
540	>	} else {
541	>	excludedInteractions_.removePair(a, b);
542	>	}
543		}
544
545	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
546	<	a = bend->getAtomA()->getGlobalIndex();
391	<	b = bend->getAtomB()->getGlobalIndex();
392	<	c = bend->getAtomC()->getGlobalIndex();
545	>	for (bend= mol->beginBend(bendIter); bend != NULL;
546	>	bend = mol->nextBend(bendIter)) {
547
548	<	exclude_.removePair(a, b);
549	<	exclude_.removePair(a, c);
550	<	exclude_.removePair(b, c);
548	>	a = bend->getAtomA()->getGlobalIndex();
549	>	b = bend->getAtomB()->getGlobalIndex();
550	>	c = bend->getAtomC()->getGlobalIndex();
551	>
552	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
553	>	oneTwoInteractions_.removePair(a, b);
554	>	oneTwoInteractions_.removePair(b, c);
555	>	} else {
556	>	excludedInteractions_.removePair(a, b);
557	>	excludedInteractions_.removePair(b, c);
558	>	}
559	>
560	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
561	>	oneThreeInteractions_.removePair(a, c);
562	>	} else {
563	>	excludedInteractions_.removePair(a, c);
564	>	}
565		}
566
567	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
568	<	a = torsion->getAtomA()->getGlobalIndex();
401	<	b = torsion->getAtomB()->getGlobalIndex();
402	<	c = torsion->getAtomC()->getGlobalIndex();
403	<	d = torsion->getAtomD()->getGlobalIndex();
567	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
568	>	torsion = mol->nextTorsion(torsionIter)) {
569
570	<	exclude_.removePair(a, b);
571	<	exclude_.removePair(a, c);
572	<	exclude_.removePair(a, d);
573	<	exclude_.removePair(b, c);
574	<	exclude_.removePair(b, d);
575	<	exclude_.removePair(c, d);
570	>	a = torsion->getAtomA()->getGlobalIndex();
571	>	b = torsion->getAtomB()->getGlobalIndex();
572	>	c = torsion->getAtomC()->getGlobalIndex();
573	>	d = torsion->getAtomD()->getGlobalIndex();
574	>
575	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
576	>	oneTwoInteractions_.removePair(a, b);
577	>	oneTwoInteractions_.removePair(b, c);
578	>	oneTwoInteractions_.removePair(c, d);
579	>	} else {
580	>	excludedInteractions_.removePair(a, b);
581	>	excludedInteractions_.removePair(b, c);
582	>	excludedInteractions_.removePair(c, d);
583	>	}
584	>
585	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
586	>	oneThreeInteractions_.removePair(a, c);
587	>	oneThreeInteractions_.removePair(b, d);
588	>	} else {
589	>	excludedInteractions_.removePair(a, c);
590	>	excludedInteractions_.removePair(b, d);
591	>	}
592	>
593	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
594	>	oneFourInteractions_.removePair(a, d);
595	>	} else {
596	>	excludedInteractions_.removePair(a, d);
597	>	}
598		}
599
600	<	}
600	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
601	>	inversion = mol->nextInversion(inversionIter)) {
602
603	+	a = inversion->getAtomA()->getGlobalIndex();
604	+	b = inversion->getAtomB()->getGlobalIndex();
605	+	c = inversion->getAtomC()->getGlobalIndex();
606	+	d = inversion->getAtomD()->getGlobalIndex();
607
608	<	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
609	<	int curStampId;
608	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
609	>	oneTwoInteractions_.removePair(a, b);
610	>	oneTwoInteractions_.removePair(a, c);
611	>	oneTwoInteractions_.removePair(a, d);
612	>	} else {
613	>	excludedInteractions_.removePair(a, b);
614	>	excludedInteractions_.removePair(a, c);
615	>	excludedInteractions_.removePair(a, d);
616	>	}
617
618	+	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
619	+	oneThreeInteractions_.removePair(b, c);
620	+	oneThreeInteractions_.removePair(b, d);
621	+	oneThreeInteractions_.removePair(c, d);
622	+	} else {
623	+	excludedInteractions_.removePair(b, c);
624	+	excludedInteractions_.removePair(b, d);
625	+	excludedInteractions_.removePair(c, d);
626	+	}
627	+	}
628	+
629	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
630	+	rb = mol->nextRigidBody(rbIter)) {
631	+	vector<Atom*> atoms = rb->getAtoms();
632	+	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
633	+	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
634	+	a = atoms[i]->getGlobalIndex();
635	+	b = atoms[j]->getGlobalIndex();
636	+	excludedInteractions_.removePair(a, b);
637	+	}
638	+	}
639	+	}
640	+
641	+	}
642	+
643	+
644	+	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
645	+	int curStampId;
646	+
647		//index from 0
648		curStampId = moleculeStamps_.size();
649
650		moleculeStamps_.push_back(molStamp);
651		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
652	<	}
652	>	}
653
426	–	void SimInfo::update() {
654
655	<	setupSimType();
656	<
657	<	#ifdef IS_MPI
658	<	setupFortranParallel();
659	<	#endif
660	<
661	<	setupFortranSim();
662	<
663	<	//setup fortran force field
437	<	/** @deprecate */
438	<	int isError = 0;
439	<	initFortranFF( &fInfo_.SIM_uses_RF , &isError );
440	<	if(isError){
441	<	sprintf( painCave.errMsg,
442	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
443	<	painCave.isFatal = 1;
444	<	simError();
445	<	}
446	<
447	<
448	<	setupCutoff();
449	<
655	>	/**
656	>	* update
657	>	*
658	>	*  Performs the global checks and variable settings after the
659	>	*  objects have been created.
660	>	*
661	>	*/
662	>	void SimInfo::update() {
663	>	setupSimVariables();
664		calcNdf();
665		calcNdfRaw();
666		calcNdfTrans();
667	<
668	<	fortranInitialized_ = true;
669	<	}
670	<
671	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
667	>	}
668	>
669	>	/**
670	>	* getSimulatedAtomTypes
671	>	*
672	>	* Returns an STL set of AtomType* that are actually present in this
673	>	* simulation.  Must query all processors to assemble this information.
674	>	*
675	>	*/
676	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
677		SimInfo::MoleculeIterator mi;
678		Molecule* mol;
679		Molecule::AtomIterator ai;
680		Atom* atom;
681	<	std::set<AtomType*> atomTypes;
681	>	set<AtomType*> atomTypes;
682	>
683	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
684	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
685	>	atomTypes.insert(atom->getAtomType());
686	>	}
687	>	}
688
689	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
689	>	#ifdef IS_MPI
690
691	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
692	<	atomTypes.insert(atom->getAtomType());
468	<	}
469	<
470	<	}
691	>	// loop over the found atom types on this processor, and add their
692	>	// numerical idents to a vector:
693
694	<	return atomTypes;
695	<	}
696	<
697	<	void SimInfo::setupSimType() {
476	<	std::set<AtomType*>::iterator i;
477	<	std::set<AtomType*> atomTypes;
478	<	atomTypes = getUniqueAtomTypes();
479	<
480	<	int useLennardJones = 0;
481	<	int useElectrostatic = 0;
482	<	int useEAM = 0;
483	<	int useCharge = 0;
484	<	int useDirectional = 0;
485	<	int useDipole = 0;
486	<	int useGayBerne = 0;
487	<	int useSticky = 0;
488	<	int useShape = 0;
489	<	int useFLARB = 0; //it is not in AtomType yet
490	<	int useDirectionalAtom = 0;
491	<	int useElectrostatics = 0;
492	<	//usePBC and useRF are from simParams
493	<	int usePBC = simParams_->getPBC();
494	<	int useRF = simParams_->getUseRF();
694	>	vector<int> foundTypes;
695	>	set<AtomType*>::iterator i;
696	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
697	>	foundTypes.push_back( (*i)->getIdent() );
698
699	<	//loop over all of the atom types
700	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
498	<	useLennardJones |= (*i)->isLennardJones();
499	<	useElectrostatic |= (*i)->isElectrostatic();
500	<	useEAM |= (*i)->isEAM();
501	<	useCharge |= (*i)->isCharge();
502	<	useDirectional |= (*i)->isDirectional();
503	<	useDipole |= (*i)->isDipole();
504	<	useGayBerne |= (*i)->isGayBerne();
505	<	useSticky |= (*i)->isSticky();
506	<	useShape |= (*i)->isShape();
507	<	}
699	>	// count_local holds the number of found types on this processor
700	>	int count_local = foundTypes.size();
701
702	<	if (useSticky || useDipole || useGayBerne || useShape) {
703	<	useDirectionalAtom = 1;
704	<	}
702	>	// count holds the total number of found types on all processors
703	>	// (some will be redundant with the ones found locally):
704	>	int count;
705	>	MPI::COMM_WORLD.Allreduce(&count_local, &count, 1, MPI::INT, MPI::SUM);
706
707	<	if (useCharge || useDipole) {
708	<	useElectrostatics = 1;
709	<	}
707	>	// create a vector to hold the globally found types, and resize it:
708	>	vector<int> ftGlobal;
709	>	ftGlobal.resize(count);
710	>	vector<int> counts;
711
712	<	#ifdef IS_MPI
713	<	int temp;
712	>	int nproc = MPI::COMM_WORLD.Get_size();
713	>	counts.resize(nproc);
714	>	vector<int> disps;
715	>	disps.resize(nproc);
716
717	<	temp = usePBC;
718	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
717	>	// now spray out the foundTypes to all the other processors:
718	>
719	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
720	>	&ftGlobal[0], &counts[0], &disps[0], MPI::INT);
721
722	<	temp = useDirectionalAtom;
723	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
724	<
725	<	temp = useLennardJones;
726	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
727	<
529	<	temp = useElectrostatics;
530	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
531	<
532	<	temp = useCharge;
533	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
534	<
535	<	temp = useDipole;
536	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
537	<
538	<	temp = useSticky;
539	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
540	<
541	<	temp = useGayBerne;
542	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
543	<
544	<	temp = useEAM;
545	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
546	<
547	<	temp = useShape;
548	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
549	<
550	<	temp = useFLARB;
551	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
552	<
553	<	temp = useRF;
554	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
722	>	// foundIdents is a stl set, so inserting an already found ident
723	>	// will have no effect.
724	>	set<int> foundIdents;
725	>	vector<int>::iterator j;
726	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
727	>	foundIdents.insert((*j));
728
729	+	// now iterate over the foundIdents and get the actual atom types
730	+	// that correspond to these:
731	+	set<int>::iterator it;
732	+	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
733	+	atomTypes.insert( forceField_->getAtomType((*it)) );
734	+
735		#endif
736	+
737	+	return atomTypes;
738	+	}
739
740	<	fInfo_.SIM_uses_PBC = usePBC;
741	<	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
742	<	fInfo_.SIM_uses_LennardJones = useLennardJones;
743	<	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
744	<	fInfo_.SIM_uses_Charges = useCharge;
745	<	fInfo_.SIM_uses_Dipoles = useDipole;
746	<	fInfo_.SIM_uses_Sticky = useSticky;
747	<	fInfo_.SIM_uses_GayBerne = useGayBerne;
566	<	fInfo_.SIM_uses_EAM = useEAM;
567	<	fInfo_.SIM_uses_Shapes = useShape;
568	<	fInfo_.SIM_uses_FLARB = useFLARB;
569	<	fInfo_.SIM_uses_RF = useRF;
740	>	void SimInfo::setupSimVariables() {
741	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
742	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
743	>	calcBoxDipole_ = false;
744	>	if ( simParams_->haveAccumulateBoxDipole() )
745	>	if ( simParams_->getAccumulateBoxDipole() ) {
746	>	calcBoxDipole_ = true;
747	>	}
748
749	<	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
750	<
751	<	if (simParams_->haveDielectric()) {
752	<	fInfo_.dielect = simParams_->getDielectric();
753	<	} else {
754	<	sprintf(painCave.errMsg,
755	<	"SimSetup Error: No Dielectric constant was set.\n"
756	<	"\tYou are trying to use Reaction Field without"
757	<	"\tsetting a dielectric constant!\n");
758	<	painCave.isFatal = 1;
759	<	simError();
582	<	}
583	<
584	<	} else {
585	<	fInfo_.dielect = 0.0;
749	>	set<AtomType*>::iterator i;
750	>	set<AtomType*> atomTypes;
751	>	atomTypes = getSimulatedAtomTypes();
752	>	int usesElectrostatic = 0;
753	>	int usesMetallic = 0;
754	>	int usesDirectional = 0;
755	>	//loop over all of the atom types
756	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
757	>	usesElectrostatic |= (*i)->isElectrostatic();
758	>	usesMetallic |= (*i)->isMetal();
759	>	usesDirectional |= (*i)->isDirectional();
760		}
761
762	<	}
762	>	#ifdef IS_MPI
763	>	int temp;
764	>	temp = usesDirectional;
765	>	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
766
767	<	void SimInfo::setupFortranSim() {
767	>	temp = usesMetallic;
768	>	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
769	>
770	>	temp = usesElectrostatic;
771	>	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
772	>	#endif
773	>	fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;
774	>	fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
775	>	fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
776	>	fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
777	>	fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
778	>	fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
779	>	}
780	>
781	>	void SimInfo::setupFortran() {
782		int isError;
783	<	int nExclude;
784	<	std::vector<int> fortranGlobalGroupMembership;
783	>	int nExclude, nOneTwo, nOneThree, nOneFour;
784	>	vector<int> fortranGlobalGroupMembership;
785
595	–	nExclude = exclude_.getSize();
786		isError = 0;
787
788		//globalGroupMembership_ is filled by SimCreator
789		for (int i = 0; i < nGlobalAtoms_; i++) {
790	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
790	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
791		}
792
793		//calculate mass ratio of cutoff group
794	<	std::vector<double> mfact;
794	>	vector<RealType> mfact;
795		SimInfo::MoleculeIterator mi;
796		Molecule* mol;
797		Molecule::CutoffGroupIterator ci;
798		CutoffGroup* cg;
799		Molecule::AtomIterator ai;
800		Atom* atom;
801	<	double totalMass;
801	>	RealType totalMass;
802
803		//to avoid memory reallocation, reserve enough space for mfact
804		mfact.reserve(getNCutoffGroups());
805
806		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
807	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
807	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
808
809	<	totalMass = cg->getMass();
810	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
811	<	mfact.push_back(atom->getMass()/totalMass);
812	<	}
813	<
814	<	}
809	>	totalMass = cg->getMass();
810	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
811	>	// Check for massless groups - set mfact to 1 if true
812	>	if (totalMass != 0)
813	>	mfact.push_back(atom->getMass()/totalMass);
814	>	else
815	>	mfact.push_back( 1.0 );
816	>	}
817	>	}
818		}
819
820	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
821	<	std::vector<int> identArray;
820	>	//fill ident array of local atoms (it is actually ident of
821	>	//AtomType, it is so confusing !!!)
822	>	vector<int> identArray;
823
824		//to avoid memory reallocation, reserve enough space identArray
825		identArray.reserve(getNAtoms());
826
827		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
828	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
829	<	identArray.push_back(atom->getIdent());
830	<	}
828	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
829	>	identArray.push_back(atom->getIdent());
830	>	}
831		}
832
833		//fill molMembershipArray
834		//molMembershipArray is filled by SimCreator
835	<	std::vector<int> molMembershipArray(nGlobalAtoms_);
835	>	vector<int> molMembershipArray(nGlobalAtoms_);
836		for (int i = 0; i < nGlobalAtoms_; i++) {
837	<	molMembershipArray[i] = globalMolMembership_[i] + 1;
837	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
838		}
839
840		//setup fortran simulation
647	–	//gloalExcludes and molMembershipArray should go away (They are never used)
648	–	//why the hell fortran need to know molecule?
649	–	//OOPSE = Object-Obfuscated Parallel Simulation Engine
650	–	int nGlobalExcludes = 0;
651	–	int* globalExcludes = NULL;
652	–	int* excludeList = exclude_.getExcludeList();
653	–	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
654	–	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
655	–	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
841
842	<	if( isError ){
842	>	nExclude = excludedInteractions_.getSize();
843	>	nOneTwo = oneTwoInteractions_.getSize();
844	>	nOneThree = oneThreeInteractions_.getSize();
845	>	nOneFour = oneFourInteractions_.getSize();
846
847	<	sprintf( painCave.errMsg,
848	<	"There was an error setting the simulation information in fortran.\n" );
849	<	painCave.isFatal = 1;
850	<	painCave.severity = OOPSE_ERROR;
663	<	simError();
664	<	}
847	>	int* excludeList = excludedInteractions_.getPairList();
848	>	int* oneTwoList = oneTwoInteractions_.getPairList();
849	>	int* oneThreeList = oneThreeInteractions_.getPairList();
850	>	int* oneFourList = oneFourInteractions_.getPairList();
851
852	<	#ifdef IS_MPI
852	>	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
853	>	&nExclude, excludeList,
854	>	&nOneTwo, oneTwoList,
855	>	&nOneThree, oneThreeList,
856	>	&nOneFour, oneFourList,
857	>	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
858	>	&fortranGlobalGroupMembership[0], &isError);
859	>
860	>	if( isError ){
861	>
862	>	sprintf( painCave.errMsg,
863	>	"There was an error setting the simulation information in fortran.\n" );
864	>	painCave.isFatal = 1;
865	>	painCave.severity = OPENMD_ERROR;
866	>	simError();
867	>	}
868	>
869	>
870		sprintf( checkPointMsg,
871	<	"succesfully sent the simulation information to fortran.\n");
669	<	MPIcheckPoint();
670	<	#endif // is_mpi
671	<	}
672	<
673	<
674	<	#ifdef IS_MPI
675	<	void SimInfo::setupFortranParallel() {
871	>	"succesfully sent the simulation information to fortran.\n");
872
873	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
874	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
875	<	std::vector<int> localToGlobalCutoffGroupIndex;
876	<	SimInfo::MoleculeIterator mi;
877	<	Molecule::AtomIterator ai;
878	<	Molecule::CutoffGroupIterator ci;
879	<	Molecule* mol;
880	<	Atom* atom;
881	<	CutoffGroup* cg;
873	>	errorCheckPoint();
874	>
875	>	// Setup number of neighbors in neighbor list if present
876	>	if (simParams_->haveNeighborListNeighbors()) {
877	>	int nlistNeighbors = simParams_->getNeighborListNeighbors();
878	>	setNeighbors(&nlistNeighbors);
879	>	}
880	>
881	>	#ifdef IS_MPI
882	>	//SimInfo is responsible for creating localToGlobalAtomIndex and
883	>	//localToGlobalGroupIndex
884	>	vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
885	>	vector<int> localToGlobalCutoffGroupIndex;
886		mpiSimData parallelData;
687	–	int isError;
887
888		for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
889
890	<	//local index(index in DataStorge) of atom is important
891	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
892	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
893	<	}
890	>	//local index(index in DataStorge) of atom is important
891	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
892	>	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
893	>	}
894
895	<	//local index of cutoff group is trivial, it only depends on the order of travesing
896	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
897	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
898	<	}
895	>	//local index of cutoff group is trivial, it only depends on the order of travesing
896	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
897	>	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
898	>	}
899
900		}
901
#	Line 716 | Line 915 | void SimInfo::setupFortranParallel() {
915		&localToGlobalCutoffGroupIndex[0], &isError);
916
917		if (isError) {
918	<	sprintf(painCave.errMsg,
919	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
920	<	painCave.isFatal = 1;
921	<	simError();
918	>	sprintf(painCave.errMsg,
919	>	"mpiRefresh errror: fortran didn't like something we gave it.\n");
920	>	painCave.isFatal = 1;
921	>	simError();
922		}
923
924		sprintf(checkPointMsg, " mpiRefresh successful.\n");
925	<	MPIcheckPoint();
727	<
728	<
729	<	}
730	<
925	>	errorCheckPoint();
926		#endif
927	+	fortranInitialized_ = true;
928	+	}
929
930	<	double SimInfo::calcMaxCutoffRadius() {
930	>	void SimInfo::addProperty(GenericData* genData) {
931	>	properties_.addProperty(genData);
932	>	}
933
934	+	void SimInfo::removeProperty(const string& propName) {
935	+	properties_.removeProperty(propName);
936	+	}
937
938	<	std::set<AtomType*> atomTypes;
939	<	std::set<AtomType*>::iterator i;
940	<	std::vector<double> cutoffRadius;
938	>	void SimInfo::clearProperties() {
939	>	properties_.clearProperties();
940	>	}
941
942	<	//get the unique atom types
943	<	atomTypes = getUniqueAtomTypes();
942	>	vector<string> SimInfo::getPropertyNames() {
943	>	return properties_.getPropertyNames();
944	>	}
945	>
946	>	vector<GenericData*> SimInfo::getProperties() {
947	>	return properties_.getProperties();
948	>	}
949
950	<	//query the max cutoff radius among these atom types
951	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
952	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
746	<	}
950	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
951	>	return properties_.getPropertyByName(propName);
952	>	}
953
954	<	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
955	<	#ifdef IS_MPI
956	<	//pick the max cutoff radius among the processors
957	<	#endif
958	<
753	<	return maxCutoffRadius;
754	<	}
755	<
756	<	void SimInfo::setupCutoff() {
757	<	double rcut_;  //cutoff radius
758	<	double rsw_; //switching radius
759	<
760	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
761	<
762	<	if (!simParams_->haveRcut()){
763	<	sprintf(painCave.errMsg,
764	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
765	<	"\tOOPSE will use a default value of 15.0 angstroms"
766	<	"\tfor the cutoffRadius.\n");
767	<	painCave.isFatal = 0;
768	<	simError();
769	<	rcut_ = 15.0;
770	<	} else{
771	<	rcut_ = simParams_->getRcut();
772	<	}
773	<
774	<	if (!simParams_->haveRsw()){
775	<	sprintf(painCave.errMsg,
776	<	"SimCreator Warning: No value was set for switchingRadius.\n"
777	<	"\tOOPSE will use a default value of\n"
778	<	"\t0.95 * cutoffRadius for the switchingRadius\n");
779	<	painCave.isFatal = 0;
780	<	simError();
781	<	rsw_ = 0.95 * rcut_;
782	<	} else{
783	<	rsw_ = simParams_->getRsw();
784	<	}
785	<
786	<	} else {
787	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
788	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
789	<
790	<	if (simParams_->haveRcut()) {
791	<	rcut_ = simParams_->getRcut();
792	<	} else {
793	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
794	<	rcut_ = calcMaxCutoffRadius();
795	<	}
796	<
797	<	if (simParams_->haveRsw()) {
798	<	rsw_  = simParams_->getRsw();
799	<	} else {
800	<	rsw_ = rcut_;
801	<	}
802	<
803	<	}
804	<
805	<	double rnblist = rcut_ + 1; // skin of neighbor list
806	<
807	<	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
808	<	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist);
809	<	}
810	<
811	<	void SimInfo::addProperty(GenericData* genData) {
812	<	properties_.addProperty(genData);
813	<	}
814	<
815	<	void SimInfo::removeProperty(const std::string& propName) {
816	<	properties_.removeProperty(propName);
817	<	}
818	<
819	<	void SimInfo::clearProperties() {
820	<	properties_.clearProperties();
821	<	}
822	<
823	<	std::vector<std::string> SimInfo::getPropertyNames() {
824	<	return properties_.getPropertyNames();
825	<	}
826	<
827	<	std::vector<GenericData*> SimInfo::getProperties() {
828	<	return properties_.getProperties();
829	<	}
830	<
831	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
832	<	return properties_.getPropertyByName(propName);
833	<	}
834	<
835	<	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
954	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
955	>	if (sman_ == sman) {
956	>	return;
957	>	}
958	>	delete sman_;
959		sman_ = sman;
960
961		Molecule* mol;
#	Line 844 | Line 967 | void SimInfo::setSnapshotManager(SnapshotManager* sman
967
968		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
969
970	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
971	<	atom->setSnapshotManager(sman_);
972	<	}
970	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
971	>	atom->setSnapshotManager(sman_);
972	>	}
973
974	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
975	<	rb->setSnapshotManager(sman_);
976	<	}
974	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
975	>	rb->setSnapshotManager(sman_);
976	>	}
977		}
978
979	<	}
979	>	}
980
981	<	Vector3d SimInfo::getComVel(){
981	>	Vector3d SimInfo::getComVel(){
982		SimInfo::MoleculeIterator i;
983		Molecule* mol;
984
985		Vector3d comVel(0.0);
986	<	double totalMass = 0.0;
986	>	RealType totalMass = 0.0;
987
988
989		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
990	<	double mass = mol->getMass();
991	<	totalMass += mass;
992	<	comVel += mass * mol->getComVel();
990	>	RealType mass = mol->getMass();
991	>	totalMass += mass;
992	>	comVel += mass * mol->getComVel();
993		}
994
995		#ifdef IS_MPI
996	<	double tmpMass = totalMass;
996	>	RealType tmpMass = totalMass;
997		Vector3d tmpComVel(comVel);
998	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
999	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
998	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
999	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1000		#endif
1001
1002		comVel /= totalMass;
1003
1004		return comVel;
1005	<	}
1005	>	}
1006
1007	<	Vector3d SimInfo::getCom(){
1007	>	Vector3d SimInfo::getCom(){
1008		SimInfo::MoleculeIterator i;
1009		Molecule* mol;
1010
1011		Vector3d com(0.0);
1012	<	double totalMass = 0.0;
1012	>	RealType totalMass = 0.0;
1013
1014		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1015	<	double mass = mol->getMass();
1016	<	totalMass += mass;
1017	<	com += mass * mol->getCom();
1015	>	RealType mass = mol->getMass();
1016	>	totalMass += mass;
1017	>	com += mass * mol->getCom();
1018		}
1019
1020		#ifdef IS_MPI
1021	<	double tmpMass = totalMass;
1021	>	RealType tmpMass = totalMass;
1022		Vector3d tmpCom(com);
1023	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1024	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1023	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1024	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1025		#endif
1026
1027		com /= totalMass;
1028
1029		return com;
1030
1031	<	}
1031	>	}
1032
1033	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1033	>	ostream& operator <<(ostream& o, SimInfo& info) {
1034
1035		return o;
1036	<	}
1036	>	}
1037	>
1038	>
1039	>	/*
1040	>	Returns center of mass and center of mass velocity in one function call.
1041	>	*/
1042	>
1043	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1044	>	SimInfo::MoleculeIterator i;
1045	>	Molecule* mol;
1046	>
1047	>
1048	>	RealType totalMass = 0.0;
1049	>
1050
1051	<	}//end namespace oopse
1051	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1052	>	RealType mass = mol->getMass();
1053	>	totalMass += mass;
1054	>	com += mass * mol->getCom();
1055	>	comVel += mass * mol->getComVel();
1056	>	}
1057	>
1058	>	#ifdef IS_MPI
1059	>	RealType tmpMass = totalMass;
1060	>	Vector3d tmpCom(com);
1061	>	Vector3d tmpComVel(comVel);
1062	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1063	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1064	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1065	>	#endif
1066	>
1067	>	com /= totalMass;
1068	>	comVel /= totalMass;
1069	>	}
1070	>
1071	>	/*
1072	>	Return intertia tensor for entire system and angular momentum Vector.
1073
1074	+
1075	+	[  Ixx -Ixy  -Ixz ]
1076	+	J =| -Iyx  Iyy  -Iyz |
1077	+	[ -Izx -Iyz   Izz ]
1078	+	*/
1079	+
1080	+	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1081	+
1082	+
1083	+	RealType xx = 0.0;
1084	+	RealType yy = 0.0;
1085	+	RealType zz = 0.0;
1086	+	RealType xy = 0.0;
1087	+	RealType xz = 0.0;
1088	+	RealType yz = 0.0;
1089	+	Vector3d com(0.0);
1090	+	Vector3d comVel(0.0);
1091	+
1092	+	getComAll(com, comVel);
1093	+
1094	+	SimInfo::MoleculeIterator i;
1095	+	Molecule* mol;
1096	+
1097	+	Vector3d thisq(0.0);
1098	+	Vector3d thisv(0.0);
1099	+
1100	+	RealType thisMass = 0.0;
1101	+
1102	+
1103	+
1104	+
1105	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1106	+
1107	+	thisq = mol->getCom()-com;
1108	+	thisv = mol->getComVel()-comVel;
1109	+	thisMass = mol->getMass();
1110	+	// Compute moment of intertia coefficients.
1111	+	xx += thisq[0]*thisq[0]*thisMass;
1112	+	yy += thisq[1]*thisq[1]*thisMass;
1113	+	zz += thisq[2]*thisq[2]*thisMass;
1114	+
1115	+	// compute products of intertia
1116	+	xy += thisq[0]*thisq[1]*thisMass;
1117	+	xz += thisq[0]*thisq[2]*thisMass;
1118	+	yz += thisq[1]*thisq[2]*thisMass;
1119	+
1120	+	angularMomentum += cross( thisq, thisv ) * thisMass;
1121	+
1122	+	}
1123	+
1124	+
1125	+	inertiaTensor(0,0) = yy + zz;
1126	+	inertiaTensor(0,1) = -xy;
1127	+	inertiaTensor(0,2) = -xz;
1128	+	inertiaTensor(1,0) = -xy;
1129	+	inertiaTensor(1,1) = xx + zz;
1130	+	inertiaTensor(1,2) = -yz;
1131	+	inertiaTensor(2,0) = -xz;
1132	+	inertiaTensor(2,1) = -yz;
1133	+	inertiaTensor(2,2) = xx + yy;
1134	+
1135	+	#ifdef IS_MPI
1136	+	Mat3x3d tmpI(inertiaTensor);
1137	+	Vector3d tmpAngMom;
1138	+	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1139	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1140	+	#endif
1141	+
1142	+	return;
1143	+	}
1144	+
1145	+	//Returns the angular momentum of the system
1146	+	Vector3d SimInfo::getAngularMomentum(){
1147	+
1148	+	Vector3d com(0.0);
1149	+	Vector3d comVel(0.0);
1150	+	Vector3d angularMomentum(0.0);
1151	+
1152	+	getComAll(com,comVel);
1153	+
1154	+	SimInfo::MoleculeIterator i;
1155	+	Molecule* mol;
1156	+
1157	+	Vector3d thisr(0.0);
1158	+	Vector3d thisp(0.0);
1159	+
1160	+	RealType thisMass;
1161	+
1162	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1163	+	thisMass = mol->getMass();
1164	+	thisr = mol->getCom()-com;
1165	+	thisp = (mol->getComVel()-comVel)*thisMass;
1166	+
1167	+	angularMomentum += cross( thisr, thisp );
1168	+
1169	+	}
1170	+
1171	+	#ifdef IS_MPI
1172	+	Vector3d tmpAngMom;
1173	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1174	+	#endif
1175	+
1176	+	return angularMomentum;
1177	+	}
1178	+
1179	+	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1180	+	return IOIndexToIntegrableObject.at(index);
1181	+	}
1182	+
1183	+	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1184	+	IOIndexToIntegrableObject= v;
1185	+	}
1186	+
1187	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1188	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1189	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1190	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1191	+	*/
1192	+	void SimInfo::getGyrationalVolume(RealType &volume){
1193	+	Mat3x3d intTensor;
1194	+	RealType det;
1195	+	Vector3d dummyAngMom;
1196	+	RealType sysconstants;
1197	+	RealType geomCnst;
1198	+
1199	+	geomCnst = 3.0/2.0;
1200	+	/* Get the inertial tensor and angular momentum for free*/
1201	+	getInertiaTensor(intTensor,dummyAngMom);
1202	+
1203	+	det = intTensor.determinant();
1204	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1205	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1206	+	return;
1207	+	}
1208	+
1209	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1210	+	Mat3x3d intTensor;
1211	+	Vector3d dummyAngMom;
1212	+	RealType sysconstants;
1213	+	RealType geomCnst;
1214	+
1215	+	geomCnst = 3.0/2.0;
1216	+	/* Get the inertial tensor and angular momentum for free*/
1217	+	getInertiaTensor(intTensor,dummyAngMom);
1218	+
1219	+	detI = intTensor.determinant();
1220	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1221	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1222	+	return;
1223	+	}
1224	+	/*
1225	+	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1226	+	assert( v.size() == nAtoms_ + nRigidBodies_);
1227	+	sdByGlobalIndex_ = v;
1228	+	}
1229	+
1230	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1231	+	//assert(index < nAtoms_ + nRigidBodies_);
1232	+	return sdByGlobalIndex_.at(index);
1233	+	}
1234	+	*/
1235	+	int SimInfo::getNGlobalConstraints() {
1236	+	int nGlobalConstraints;
1237	+	#ifdef IS_MPI
1238	+	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1239	+	MPI_COMM_WORLD);
1240	+	#else
1241	+	nGlobalConstraints =  nConstraints_;
1242	+	#endif
1243	+	return nGlobalConstraints;
1244	+	}
1245	+
1246	+	}//end namespace OpenMD
1247	+

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 292 by tim, Fri Feb 4 22:44:15 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1535 by gezelter, Fri Dec 31 18:31:56 2010 UTC

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