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root/OpenMD/trunk/src/brains/SimInfo.cpp

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 328 by tim, Sun Feb 13 20:36:24 2005 UTC vs.
Revision 1953 by gezelter, Thu Dec 5 18:19:26 2013 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, 234107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		/**
#	Line 46 | Line 47
47		* @version 1.0
48		*/
49
50	+	#ifdef IS_MPI
51	+	#include <mpi.h>
52	+	#endif
53		#include <algorithm>
54		#include <set>
55	+	#include <map>
56
57		#include "brains/SimInfo.hpp"
58		#include "math/Vector3.hpp"
59		#include "primitives/Molecule.hpp"
60	<	#include "UseTheForce/doForces_interface.h"
56	<	#include "UseTheForce/notifyCutoffs_interface.h"
60	>	#include "primitives/StuntDouble.hpp"
61		#include "utils/MemoryUtils.hpp"
62		#include "utils/simError.h"
63		#include "selection/SelectionManager.hpp"
64	+	#include "io/ForceFieldOptions.hpp"
65	+	#include "brains/ForceField.hpp"
66	+	#include "nonbonded/SwitchingFunction.hpp"
67
68	<	#ifdef IS_MPI
69	<	#include "UseTheForce/mpiComponentPlan.h"
70	<	#include "UseTheForce/DarkSide/simParallel_interface.h"
71	<	#endif
72	<
73	<	namespace oopse {
74	<
75	<	SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
76	<	ForceField* ff, Globals* simParams) :
77	<	forceField_(ff), simParams_(simParams),
78	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
79	<	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
80	<	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
81	<	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
82	<	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
76	<	sman_(NULL), fortranInitialized_(false), selectMan_(NULL) {
77	<
78	<
79	<	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
68	>	using namespace std;
69	>	namespace OpenMD {
70	>
71	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
72	>	forceField_(ff), simParams_(simParams),
73	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
74	>	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
75	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
76	>	nGlobalFluctuatingCharges_(0), nGlobalBonds_(0), nGlobalBends_(0),
77	>	nGlobalTorsions_(0), nGlobalInversions_(0), nAtoms_(0), nBonds_(0),
78	>	nBends_(0), nTorsions_(0), nInversions_(0), nRigidBodies_(0),
79	>	nIntegrableObjects_(0), nCutoffGroups_(0), nConstraints_(0),
80	>	nFluctuatingCharges_(0), sman_(NULL), topologyDone_(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);
91	>	vector<Component*> components = simParams->getComponents();
92	>
93	>	for (vector<Component*>::iterator i = components.begin();
94	>	i !=components.end(); ++i) {
95	>	molStamp = (*i)->getMoleculeStamp();
96	>	if ( (*i)->haveRegion() ) {
97	>	molStamp->setRegion( (*i)->getRegion() );
98	>	} else {
99	>	// set the region to a disallowed value:
100	>	molStamp->setRegion( -1 );
101	>	}
102
103	<	//calculate atoms in molecules
104	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
105	<
106	<
107	<	//calculate atoms in cutoff groups
108	<	int nAtomsInGroups = 0;
109	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
110	<
111	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
112	<	cgStamp = molStamp->getCutoffGroup(j);
113	<	nAtomsInGroups += cgStamp->getNMembers();
114	<	}
115	<
116	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
117	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
118	<
119	<	//calculate atoms in rigid bodies
120	<	int nAtomsInRigidBodies = 0;
121	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
122	<
123	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
124	<	rbStamp = molStamp->getRigidBody(j);
125	<	nAtomsInRigidBodies += rbStamp->getNMembers();
126	<	}
127	<
128	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
129	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
130	<
103	>	nMolWithSameStamp = (*i)->getNMol();
104	>
105	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
106	>
107	>	//calculate atoms in molecules
108	>	nGlobalAtoms_ += molStamp->getNAtoms() * nMolWithSameStamp;
109	>	nGlobalBonds_ += molStamp->getNBonds() * nMolWithSameStamp;
110	>	nGlobalBends_ += molStamp->getNBends() * nMolWithSameStamp;
111	>	nGlobalTorsions_ += molStamp->getNTorsions() * nMolWithSameStamp;
112	>	nGlobalInversions_ += molStamp->getNInversions() * nMolWithSameStamp;
113	>
114	>	//calculate atoms in cutoff groups
115	>	int nAtomsInGroups = 0;
116	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
117	>
118	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
119	>	cgStamp = molStamp->getCutoffGroupStamp(j);
120	>	nAtomsInGroups += cgStamp->getNMembers();
121	>	}
122	>
123	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
124	>
125	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
126	>
127	>	//calculate atoms in rigid bodies
128	>	int nAtomsInRigidBodies = 0;
129	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
130	>
131	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
132	>	rbStamp = molStamp->getRigidBodyStamp(j);
133	>	nAtomsInRigidBodies += rbStamp->getNMembers();
134	>	}
135	>
136	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
137	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
138	>
139		}
140	+
141	+	//every free atom (atom does not belong to cutoff groups) is a cutoff
142	+	//group therefore the total number of cutoff groups in the system is
143	+	//equal to the total number of atoms minus number of atoms belong to
144	+	//cutoff group defined in meta-data file plus the number of cutoff
145	+	//groups defined in meta-data file
146
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
147		nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
148	<
149	<	//every free atom (atom does not belong to rigid bodies) is an integrable object
150	<	//therefore the total number of  integrable objects in the system is equal to
151	<	//the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
152	<	//file plus the number of  rigid bodies defined in meta-data file
153	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
154	<
148	>
149	>	//every free atom (atom does not belong to rigid bodies) is an
150	>	//integrable object therefore the total number of integrable objects
151	>	//in the system is equal to the total number of atoms minus number of
152	>	//atoms belong to rigid body defined in meta-data file plus the number
153	>	//of rigid bodies defined in meta-data file
154	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
155	>	+ nGlobalRigidBodies_;
156	>
157		nGlobalMols_ = molStampIds_.size();
137	–
138	–	#ifdef IS_MPI
158		molToProcMap_.resize(nGlobalMols_);
159	<	#endif
160	<
161	<	selectMan_ = new SelectionManager(this);
162	<	selectMan_->selectAll();
163	<	}
164	<
165	<	SimInfo::~SimInfo() {
166	<	//MemoryUtils::deleteVectorOfPointer(molecules_);
167	<
149	<	MemoryUtils::deleteVectorOfPointer(moleculeStamps_);
150	<
159	>	}
160	>
161	>	SimInfo::~SimInfo() {
162	>	map<int, Molecule*>::iterator i;
163	>	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
164	>	delete i->second;
165	>	}
166	>	molecules_.clear();
167	>
168		delete sman_;
169		delete simParams_;
170		delete forceField_;
171	<	delete selectMan_;
155	<	}
171	>	}
172
157	–	int SimInfo::getNGlobalConstraints() {
158	–	int nGlobalConstraints;
159	–	#ifdef IS_MPI
160	–	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
161	–	MPI_COMM_WORLD);
162	–	#else
163	–	nGlobalConstraints =  nConstraints_;
164	–	#endif
165	–	return nGlobalConstraints;
166	–	}
173
174	<	bool SimInfo::addMolecule(Molecule* mol) {
174	>	bool SimInfo::addMolecule(Molecule* mol) {
175		MoleculeIterator i;
176	<
176	>
177		i = molecules_.find(mol->getGlobalIndex());
178		if (i == molecules_.end() ) {
179	<
180	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
181	<
182	<	nAtoms_ += mol->getNAtoms();
183	<	nBonds_ += mol->getNBonds();
184	<	nBends_ += mol->getNBends();
185	<	nTorsions_ += mol->getNTorsions();
186	<	nRigidBodies_ += mol->getNRigidBodies();
187	<	nIntegrableObjects_ += mol->getNIntegrableObjects();
188	<	nCutoffGroups_ += mol->getNCutoffGroups();
189	<	nConstraints_ += mol->getNConstraintPairs();
190	<
191	<	addExcludePairs(mol);
192	<
193	<	return true;
179	>
180	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
181	>
182	>	nAtoms_ += mol->getNAtoms();
183	>	nBonds_ += mol->getNBonds();
184	>	nBends_ += mol->getNBends();
185	>	nTorsions_ += mol->getNTorsions();
186	>	nInversions_ += mol->getNInversions();
187	>	nRigidBodies_ += mol->getNRigidBodies();
188	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
189	>	nCutoffGroups_ += mol->getNCutoffGroups();
190	>	nConstraints_ += mol->getNConstraintPairs();
191	>
192	>	addInteractionPairs(mol);
193	>
194	>	return true;
195		} else {
196	<	return false;
196	>	return false;
197		}
198	<	}
199	<
200	<	bool SimInfo::removeMolecule(Molecule* mol) {
198	>	}
199	>
200	>	bool SimInfo::removeMolecule(Molecule* mol) {
201		MoleculeIterator i;
202		i = molecules_.find(mol->getGlobalIndex());
203
204		if (i != molecules_.end() ) {
205
206	<	assert(mol == i->second);
206	>	assert(mol == i->second);
207
208	<	nAtoms_ -= mol->getNAtoms();
209	<	nBonds_ -= mol->getNBonds();
210	<	nBends_ -= mol->getNBends();
211	<	nTorsions_ -= mol->getNTorsions();
212	<	nRigidBodies_ -= mol->getNRigidBodies();
213	<	nIntegrableObjects_ -= mol->getNIntegrableObjects();
214	<	nCutoffGroups_ -= mol->getNCutoffGroups();
215	<	nConstraints_ -= mol->getNConstraintPairs();
208	>	nAtoms_ -= mol->getNAtoms();
209	>	nBonds_ -= mol->getNBonds();
210	>	nBends_ -= mol->getNBends();
211	>	nTorsions_ -= mol->getNTorsions();
212	>	nInversions_ -= mol->getNInversions();
213	>	nRigidBodies_ -= mol->getNRigidBodies();
214	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
215	>	nCutoffGroups_ -= mol->getNCutoffGroups();
216	>	nConstraints_ -= mol->getNConstraintPairs();
217
218	<	removeExcludePairs(mol);
219	<	molecules_.erase(mol->getGlobalIndex());
218	>	removeInteractionPairs(mol);
219	>	molecules_.erase(mol->getGlobalIndex());
220
221	<	delete mol;
221	>	delete mol;
222
223	<	return true;
223	>	return true;
224		} else {
225	<	return false;
225	>	return false;
226		}
227	+	}
228
220	–
221	–	}
222	–
229
230	<	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
230	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
231		i = molecules_.begin();
232		return i == molecules_.end() ? NULL : i->second;
233	<	}
233	>	}
234
235	<	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
235	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
236		++i;
237		return i == molecules_.end() ? NULL : i->second;
238	<	}
238	>	}
239
240
241	<	void SimInfo::calcNdf() {
242	<	int ndf_local;
241	>	void SimInfo::calcNdf() {
242	>	int ndf_local, nfq_local;
243		MoleculeIterator i;
244	<	std::vector<StuntDouble*>::iterator j;
244	>	vector<StuntDouble*>::iterator j;
245	>	vector<Atom*>::iterator k;
246	>
247		Molecule* mol;
248	<	StuntDouble* integrableObject;
248	>	StuntDouble* sd;
249	>	Atom* atom;
250
251		ndf_local = 0;
252	+	nfq_local = 0;
253
254		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
245	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
246	–	integrableObject = mol->nextIntegrableObject(j)) {
255
256	<	ndf_local += 3;
256	>	for (sd = mol->beginIntegrableObject(j); sd != NULL;
257	>	sd = mol->nextIntegrableObject(j)) {
258
259	<	if (integrableObject->isDirectional()) {
260	<	if (integrableObject->isLinear()) {
261	<	ndf_local += 2;
262	<	} else {
263	<	ndf_local += 3;
264	<	}
265	<	}
266	<
267	<	}//end for (integrableObject)
268	<	}// end for (mol)
259	>	ndf_local += 3;
260	>
261	>	if (sd->isDirectional()) {
262	>	if (sd->isLinear()) {
263	>	ndf_local += 2;
264	>	} else {
265	>	ndf_local += 3;
266	>	}
267	>	}
268	>	}
269	>
270	>	for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
271	>	atom = mol->nextFluctuatingCharge(k)) {
272	>	if (atom->isFluctuatingCharge()) {
273	>	nfq_local++;
274	>	}
275	>	}
276	>	}
277
278	+	ndfLocal_ = ndf_local;
279	+
280		// n_constraints is local, so subtract them on each processor
281		ndf_local -= nConstraints_;
282
283		#ifdef IS_MPI
284	<	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
284	>	MPI::COMM_WORLD.Allreduce(&ndf_local, &ndf_, 1, MPI::INT,MPI::SUM);
285	>	MPI::COMM_WORLD.Allreduce(&nfq_local, &nGlobalFluctuatingCharges_, 1,
286	>	MPI::INT, MPI::SUM);
287		#else
288		ndf_ = ndf_local;
289	+	nGlobalFluctuatingCharges_ = nfq_local;
290		#endif
291
292		// nZconstraints_ is global, as are the 3 COM translations for the
293		// entire system:
294		ndf_ = ndf_ - 3 - nZconstraint_;
295
296	<	}
296	>	}
297
298	<	void SimInfo::calcNdfRaw() {
298	>	int SimInfo::getFdf() {
299	>	#ifdef IS_MPI
300	>	MPI::COMM_WORLD.Allreduce(&fdf_local, &fdf_, 1, MPI::INT, MPI::SUM);
301	>	#else
302	>	fdf_ = fdf_local;
303	>	#endif
304	>	return fdf_;
305	>	}
306	>
307	>	unsigned int SimInfo::getNLocalCutoffGroups(){
308	>	int nLocalCutoffAtoms = 0;
309	>	Molecule* mol;
310	>	MoleculeIterator mi;
311	>	CutoffGroup* cg;
312	>	Molecule::CutoffGroupIterator ci;
313	>
314	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
315	>
316	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
317	>	cg = mol->nextCutoffGroup(ci)) {
318	>	nLocalCutoffAtoms += cg->getNumAtom();
319	>
320	>	}
321	>	}
322	>
323	>	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
324	>	}
325	>
326	>	void SimInfo::calcNdfRaw() {
327		int ndfRaw_local;
328
329		MoleculeIterator i;
330	<	std::vector<StuntDouble*>::iterator j;
330	>	vector<StuntDouble*>::iterator j;
331		Molecule* mol;
332	<	StuntDouble* integrableObject;
332	>	StuntDouble* sd;
333
334		// Raw degrees of freedom that we have to set
335		ndfRaw_local = 0;
336
337		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
288	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
289	–	integrableObject = mol->nextIntegrableObject(j)) {
338
339	<	ndfRaw_local += 3;
339	>	for (sd = mol->beginIntegrableObject(j); sd != NULL;
340	>	sd = mol->nextIntegrableObject(j)) {
341
342	<	if (integrableObject->isDirectional()) {
343	<	if (integrableObject->isLinear()) {
344	<	ndfRaw_local += 2;
345	<	} else {
346	<	ndfRaw_local += 3;
347	<	}
348	<	}
342	>	ndfRaw_local += 3;
343	>
344	>	if (sd->isDirectional()) {
345	>	if (sd->isLinear()) {
346	>	ndfRaw_local += 2;
347	>	} else {
348	>	ndfRaw_local += 3;
349	>	}
350	>	}
351
352	<	}
352	>	}
353		}
354
355		#ifdef IS_MPI
356	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
356	>	MPI::COMM_WORLD.Allreduce(&ndfRaw_local, &ndfRaw_, 1, MPI::INT, MPI::SUM);
357		#else
358		ndfRaw_ = ndfRaw_local;
359		#endif
360	<	}
360	>	}
361
362	<	void SimInfo::calcNdfTrans() {
362	>	void SimInfo::calcNdfTrans() {
363		int ndfTrans_local;
364
365		ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
366
367
368		#ifdef IS_MPI
369	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
369	>	MPI::COMM_WORLD.Allreduce(&ndfTrans_local, &ndfTrans_, 1,
370	>	MPI::INT, MPI::SUM);
371		#else
372		ndfTrans_ = ndfTrans_local;
373		#endif
374
375		ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
376
377	<	}
377	>	}
378
379	<	void SimInfo::addExcludePairs(Molecule* mol) {
380	<	std::vector<Bond*>::iterator bondIter;
381	<	std::vector<Bend*>::iterator bendIter;
382	<	std::vector<Torsion*>::iterator torsionIter;
379	>	void SimInfo::addInteractionPairs(Molecule* mol) {
380	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
381	>	vector<Bond*>::iterator bondIter;
382	>	vector<Bend*>::iterator bendIter;
383	>	vector<Torsion*>::iterator torsionIter;
384	>	vector<Inversion*>::iterator inversionIter;
385		Bond* bond;
386		Bend* bend;
387		Torsion* torsion;
388	+	Inversion* inversion;
389		int a;
390		int b;
391		int c;
392		int d;
393	+
394	+	// atomGroups can be used to add special interaction maps between
395	+	// groups of atoms that are in two separate rigid bodies.
396	+	// However, most site-site interactions between two rigid bodies
397	+	// are probably not special, just the ones between the physically
398	+	// bonded atoms.  Interactions *within* a single rigid body should
399	+	// always be excluded.  These are done at the bottom of this
400	+	// function.
401	+
402	+	map<int, set<int> > atomGroups;
403	+	Molecule::RigidBodyIterator rbIter;
404	+	RigidBody* rb;
405	+	Molecule::IntegrableObjectIterator ii;
406	+	StuntDouble* sd;
407
408	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
409	<	a = bond->getAtomA()->getGlobalIndex();
410	<	b = bond->getAtomB()->getGlobalIndex();
411	<	exclude_.addPair(a, b);
408	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
409	>	sd = mol->nextIntegrableObject(ii)) {
410	>
411	>	if (sd->isRigidBody()) {
412	>	rb = static_cast<RigidBody*>(sd);
413	>	vector<Atom*> atoms = rb->getAtoms();
414	>	set<int> rigidAtoms;
415	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
416	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
417	>	}
418	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
419	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
420	>	}
421	>	} else {
422	>	set<int> oneAtomSet;
423	>	oneAtomSet.insert(sd->getGlobalIndex());
424	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
425	>	}
426	>	}
427	>
428	>
429	>	for (bond= mol->beginBond(bondIter); bond != NULL;
430	>	bond = mol->nextBond(bondIter)) {
431	>
432	>	a = bond->getAtomA()->getGlobalIndex();
433	>	b = bond->getAtomB()->getGlobalIndex();
434	>
435	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
436	>	oneTwoInteractions_.addPair(a, b);
437	>	} else {
438	>	excludedInteractions_.addPair(a, b);
439	>	}
440		}
441
442	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
443	<	a = bend->getAtomA()->getGlobalIndex();
347	<	b = bend->getAtomB()->getGlobalIndex();
348	<	c = bend->getAtomC()->getGlobalIndex();
442	>	for (bend= mol->beginBend(bendIter); bend != NULL;
443	>	bend = mol->nextBend(bendIter)) {
444
445	<	exclude_.addPair(a, b);
446	<	exclude_.addPair(a, c);
447	<	exclude_.addPair(b, c);
445	>	a = bend->getAtomA()->getGlobalIndex();
446	>	b = bend->getAtomB()->getGlobalIndex();
447	>	c = bend->getAtomC()->getGlobalIndex();
448	>
449	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
450	>	oneTwoInteractions_.addPair(a, b);
451	>	oneTwoInteractions_.addPair(b, c);
452	>	} else {
453	>	excludedInteractions_.addPair(a, b);
454	>	excludedInteractions_.addPair(b, c);
455	>	}
456	>
457	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
458	>	oneThreeInteractions_.addPair(a, c);
459	>	} else {
460	>	excludedInteractions_.addPair(a, c);
461	>	}
462		}
463
464	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
465	<	a = torsion->getAtomA()->getGlobalIndex();
357	<	b = torsion->getAtomB()->getGlobalIndex();
358	<	c = torsion->getAtomC()->getGlobalIndex();
359	<	d = torsion->getAtomD()->getGlobalIndex();
464	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
465	>	torsion = mol->nextTorsion(torsionIter)) {
466
467	<	exclude_.addPair(a, b);
468	<	exclude_.addPair(a, c);
469	<	exclude_.addPair(a, d);
470	<	exclude_.addPair(b, c);
471	<	exclude_.addPair(b, d);
472	<	exclude_.addPair(c, d);
467	>	a = torsion->getAtomA()->getGlobalIndex();
468	>	b = torsion->getAtomB()->getGlobalIndex();
469	>	c = torsion->getAtomC()->getGlobalIndex();
470	>	d = torsion->getAtomD()->getGlobalIndex();
471	>
472	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
473	>	oneTwoInteractions_.addPair(a, b);
474	>	oneTwoInteractions_.addPair(b, c);
475	>	oneTwoInteractions_.addPair(c, d);
476	>	} else {
477	>	excludedInteractions_.addPair(a, b);
478	>	excludedInteractions_.addPair(b, c);
479	>	excludedInteractions_.addPair(c, d);
480	>	}
481	>
482	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
483	>	oneThreeInteractions_.addPair(a, c);
484	>	oneThreeInteractions_.addPair(b, d);
485	>	} else {
486	>	excludedInteractions_.addPair(a, c);
487	>	excludedInteractions_.addPair(b, d);
488	>	}
489	>
490	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
491	>	oneFourInteractions_.addPair(a, d);
492	>	} else {
493	>	excludedInteractions_.addPair(a, d);
494	>	}
495		}
496
497	<
498	<	}
497	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
498	>	inversion = mol->nextInversion(inversionIter)) {
499
500	<	void SimInfo::removeExcludePairs(Molecule* mol) {
501	<	std::vector<Bond*>::iterator bondIter;
502	<	std::vector<Bend*>::iterator bendIter;
503	<	std::vector<Torsion*>::iterator torsionIter;
500	>	a = inversion->getAtomA()->getGlobalIndex();
501	>	b = inversion->getAtomB()->getGlobalIndex();
502	>	c = inversion->getAtomC()->getGlobalIndex();
503	>	d = inversion->getAtomD()->getGlobalIndex();
504	>
505	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
506	>	oneTwoInteractions_.addPair(a, b);
507	>	oneTwoInteractions_.addPair(a, c);
508	>	oneTwoInteractions_.addPair(a, d);
509	>	} else {
510	>	excludedInteractions_.addPair(a, b);
511	>	excludedInteractions_.addPair(a, c);
512	>	excludedInteractions_.addPair(a, d);
513	>	}
514	>
515	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
516	>	oneThreeInteractions_.addPair(b, c);
517	>	oneThreeInteractions_.addPair(b, d);
518	>	oneThreeInteractions_.addPair(c, d);
519	>	} else {
520	>	excludedInteractions_.addPair(b, c);
521	>	excludedInteractions_.addPair(b, d);
522	>	excludedInteractions_.addPair(c, d);
523	>	}
524	>	}
525	>
526	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
527	>	rb = mol->nextRigidBody(rbIter)) {
528	>	vector<Atom*> atoms = rb->getAtoms();
529	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
530	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
531	>	a = atoms[i]->getGlobalIndex();
532	>	b = atoms[j]->getGlobalIndex();
533	>	excludedInteractions_.addPair(a, b);
534	>	}
535	>	}
536	>	}
537	>
538	>	}
539	>
540	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
541	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
542	>	vector<Bond*>::iterator bondIter;
543	>	vector<Bend*>::iterator bendIter;
544	>	vector<Torsion*>::iterator torsionIter;
545	>	vector<Inversion*>::iterator inversionIter;
546		Bond* bond;
547		Bend* bend;
548		Torsion* torsion;
549	+	Inversion* inversion;
550		int a;
551		int b;
552		int c;
553		int d;
554	+
555	+	map<int, set<int> > atomGroups;
556	+	Molecule::RigidBodyIterator rbIter;
557	+	RigidBody* rb;
558	+	Molecule::IntegrableObjectIterator ii;
559	+	StuntDouble* sd;
560
561	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
562	<	a = bond->getAtomA()->getGlobalIndex();
563	<	b = bond->getAtomB()->getGlobalIndex();
564	<	exclude_.removePair(a, b);
561	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
562	>	sd = mol->nextIntegrableObject(ii)) {
563	>
564	>	if (sd->isRigidBody()) {
565	>	rb = static_cast<RigidBody*>(sd);
566	>	vector<Atom*> atoms = rb->getAtoms();
567	>	set<int> rigidAtoms;
568	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
569	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
570	>	}
571	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
572	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
573	>	}
574	>	} else {
575	>	set<int> oneAtomSet;
576	>	oneAtomSet.insert(sd->getGlobalIndex());
577	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
578	>	}
579	>	}
580	>
581	>	for (bond= mol->beginBond(bondIter); bond != NULL;
582	>	bond = mol->nextBond(bondIter)) {
583	>
584	>	a = bond->getAtomA()->getGlobalIndex();
585	>	b = bond->getAtomB()->getGlobalIndex();
586	>
587	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
588	>	oneTwoInteractions_.removePair(a, b);
589	>	} else {
590	>	excludedInteractions_.removePair(a, b);
591	>	}
592		}
593
594	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
595	<	a = bend->getAtomA()->getGlobalIndex();
392	<	b = bend->getAtomB()->getGlobalIndex();
393	<	c = bend->getAtomC()->getGlobalIndex();
594	>	for (bend= mol->beginBend(bendIter); bend != NULL;
595	>	bend = mol->nextBend(bendIter)) {
596
597	<	exclude_.removePair(a, b);
598	<	exclude_.removePair(a, c);
599	<	exclude_.removePair(b, c);
597	>	a = bend->getAtomA()->getGlobalIndex();
598	>	b = bend->getAtomB()->getGlobalIndex();
599	>	c = bend->getAtomC()->getGlobalIndex();
600	>
601	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
602	>	oneTwoInteractions_.removePair(a, b);
603	>	oneTwoInteractions_.removePair(b, c);
604	>	} else {
605	>	excludedInteractions_.removePair(a, b);
606	>	excludedInteractions_.removePair(b, c);
607	>	}
608	>
609	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
610	>	oneThreeInteractions_.removePair(a, c);
611	>	} else {
612	>	excludedInteractions_.removePair(a, c);
613	>	}
614		}
615
616	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
617	<	a = torsion->getAtomA()->getGlobalIndex();
402	<	b = torsion->getAtomB()->getGlobalIndex();
403	<	c = torsion->getAtomC()->getGlobalIndex();
404	<	d = torsion->getAtomD()->getGlobalIndex();
616	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
617	>	torsion = mol->nextTorsion(torsionIter)) {
618
619	<	exclude_.removePair(a, b);
620	<	exclude_.removePair(a, c);
621	<	exclude_.removePair(a, d);
622	<	exclude_.removePair(b, c);
623	<	exclude_.removePair(b, d);
624	<	exclude_.removePair(c, d);
619	>	a = torsion->getAtomA()->getGlobalIndex();
620	>	b = torsion->getAtomB()->getGlobalIndex();
621	>	c = torsion->getAtomC()->getGlobalIndex();
622	>	d = torsion->getAtomD()->getGlobalIndex();
623	>
624	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
625	>	oneTwoInteractions_.removePair(a, b);
626	>	oneTwoInteractions_.removePair(b, c);
627	>	oneTwoInteractions_.removePair(c, d);
628	>	} else {
629	>	excludedInteractions_.removePair(a, b);
630	>	excludedInteractions_.removePair(b, c);
631	>	excludedInteractions_.removePair(c, d);
632	>	}
633	>
634	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
635	>	oneThreeInteractions_.removePair(a, c);
636	>	oneThreeInteractions_.removePair(b, d);
637	>	} else {
638	>	excludedInteractions_.removePair(a, c);
639	>	excludedInteractions_.removePair(b, d);
640	>	}
641	>
642	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
643	>	oneFourInteractions_.removePair(a, d);
644	>	} else {
645	>	excludedInteractions_.removePair(a, d);
646	>	}
647		}
648
649	<	}
649	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
650	>	inversion = mol->nextInversion(inversionIter)) {
651
652	+	a = inversion->getAtomA()->getGlobalIndex();
653	+	b = inversion->getAtomB()->getGlobalIndex();
654	+	c = inversion->getAtomC()->getGlobalIndex();
655	+	d = inversion->getAtomD()->getGlobalIndex();
656
657	<	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
658	<	int curStampId;
657	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
658	>	oneTwoInteractions_.removePair(a, b);
659	>	oneTwoInteractions_.removePair(a, c);
660	>	oneTwoInteractions_.removePair(a, d);
661	>	} else {
662	>	excludedInteractions_.removePair(a, b);
663	>	excludedInteractions_.removePair(a, c);
664	>	excludedInteractions_.removePair(a, d);
665	>	}
666
667	+	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
668	+	oneThreeInteractions_.removePair(b, c);
669	+	oneThreeInteractions_.removePair(b, d);
670	+	oneThreeInteractions_.removePair(c, d);
671	+	} else {
672	+	excludedInteractions_.removePair(b, c);
673	+	excludedInteractions_.removePair(b, d);
674	+	excludedInteractions_.removePair(c, d);
675	+	}
676	+	}
677	+
678	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
679	+	rb = mol->nextRigidBody(rbIter)) {
680	+	vector<Atom*> atoms = rb->getAtoms();
681	+	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
682	+	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
683	+	a = atoms[i]->getGlobalIndex();
684	+	b = atoms[j]->getGlobalIndex();
685	+	excludedInteractions_.removePair(a, b);
686	+	}
687	+	}
688	+	}
689	+
690	+	}
691	+
692	+
693	+	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
694	+	int curStampId;
695	+
696		//index from 0
697		curStampId = moleculeStamps_.size();
698
699		moleculeStamps_.push_back(molStamp);
700		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
701	<	}
701	>	}
702
427	–	void SimInfo::update() {
703
704	<	setupSimType();
705	<
706	<	#ifdef IS_MPI
707	<	setupFortranParallel();
708	<	#endif
709	<
710	<	setupFortranSim();
711	<
712	<	//setup fortran force field
438	<	/** @deprecate */
439	<	int isError = 0;
440	<	initFortranFF( &fInfo_.SIM_uses_RF , &isError );
441	<	if(isError){
442	<	sprintf( painCave.errMsg,
443	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
444	<	painCave.isFatal = 1;
445	<	simError();
446	<	}
447	<
448	<
449	<	setupCutoff();
450	<
704	>	/**
705	>	* update
706	>	*
707	>	*  Performs the global checks and variable settings after the
708	>	*  objects have been created.
709	>	*
710	>	*/
711	>	void SimInfo::update() {
712	>	setupSimVariables();
713		calcNdf();
714		calcNdfRaw();
715		calcNdfTrans();
716	<
717	<	fortranInitialized_ = true;
718	<	}
719	<
720	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
716	>	}
717	>
718	>	/**
719	>	* getSimulatedAtomTypes
720	>	*
721	>	* Returns an STL set of AtomType* that are actually present in this
722	>	* simulation.  Must query all processors to assemble this information.
723	>	*
724	>	*/
725	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
726		SimInfo::MoleculeIterator mi;
727		Molecule* mol;
728		Molecule::AtomIterator ai;
729		Atom* atom;
730	<	std::set<AtomType*> atomTypes;
731	<
730	>	set<AtomType*> atomTypes;
731	>
732		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
733	+	for(atom = mol->beginAtom(ai); atom != NULL;
734	+	atom = mol->nextAtom(ai)) {
735	+	atomTypes.insert(atom->getAtomType());
736	+	}
737	+	}
738	+
739	+	#ifdef IS_MPI
740
741	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
742	<	atomTypes.insert(atom->getAtomType());
743	<	}
744	<
745	<	}
741	>	// loop over the found atom types on this processor, and add their
742	>	// numerical idents to a vector:
743	>
744	>	vector<int> foundTypes;
745	>	set<AtomType*>::iterator i;
746	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
747	>	foundTypes.push_back( (*i)->getIdent() );
748
749	<	return atomTypes;
750	<	}
749	>	// count_local holds the number of found types on this processor
750	>	int count_local = foundTypes.size();
751
752	<	void SimInfo::setupSimType() {
477	<	std::set<AtomType*>::iterator i;
478	<	std::set<AtomType*> atomTypes;
479	<	atomTypes = getUniqueAtomTypes();
480	<
481	<	int useLennardJones = 0;
482	<	int useElectrostatic = 0;
483	<	int useEAM = 0;
484	<	int useCharge = 0;
485	<	int useDirectional = 0;
486	<	int useDipole = 0;
487	<	int useGayBerne = 0;
488	<	int useSticky = 0;
489	<	int useShape = 0;
490	<	int useFLARB = 0; //it is not in AtomType yet
491	<	int useDirectionalAtom = 0;
492	<	int useElectrostatics = 0;
493	<	//usePBC and useRF are from simParams
494	<	int usePBC = simParams_->getPBC();
495	<	int useRF = simParams_->getUseRF();
752	>	int nproc = MPI::COMM_WORLD.Get_size();
753
754	<	//loop over all of the atom types
755	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
756	<	useLennardJones |= (*i)->isLennardJones();
757	<	useElectrostatic |= (*i)->isElectrostatic();
501	<	useEAM |= (*i)->isEAM();
502	<	useCharge |= (*i)->isCharge();
503	<	useDirectional |= (*i)->isDirectional();
504	<	useDipole |= (*i)->isDipole();
505	<	useGayBerne |= (*i)->isGayBerne();
506	<	useSticky |= (*i)->isSticky();
507	<	useShape |= (*i)->isShape();
508	<	}
754	>	// we need arrays to hold the counts and displacement vectors for
755	>	// all processors
756	>	vector<int> counts(nproc, 0);
757	>	vector<int> disps(nproc, 0);
758
759	<	if (useSticky || useDipole || useGayBerne || useShape) {
760	<	useDirectionalAtom = 1;
759	>	// fill the counts array
760	>	MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
761	>	1, MPI::INT);
762	>
763	>	// use the processor counts to compute the displacement array
764	>	disps[0] = 0;
765	>	int totalCount = counts[0];
766	>	for (int iproc = 1; iproc < nproc; iproc++) {
767	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
768	>	totalCount += counts[iproc];
769		}
770
771	<	if (useCharge || useDipole) {
772	<	useElectrostatics = 1;
773	<	}
771	>	// we need a (possibly redundant) set of all found types:
772	>	vector<int> ftGlobal(totalCount);
773	>
774	>	// now spray out the foundTypes to all the other processors:
775	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
776	>	&ftGlobal[0], &counts[0], &disps[0],
777	>	MPI::INT);
778
779	<	#ifdef IS_MPI
519	<	int temp;
779	>	vector<int>::iterator j;
780
781	<	temp = usePBC;
782	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
781	>	// foundIdents is a stl set, so inserting an already found ident
782	>	// will have no effect.
783	>	set<int> foundIdents;
784
785	<	temp = useDirectionalAtom;
786	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
785	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
786	>	foundIdents.insert((*j));
787	>
788	>	// now iterate over the foundIdents and get the actual atom types
789	>	// that correspond to these:
790	>	set<int>::iterator it;
791	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
792	>	atomTypes.insert( forceField_->getAtomType((*it)) );
793	>
794	>	#endif
795
796	<	temp = useLennardJones;
797	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
796	>	return atomTypes;
797	>	}
798
530	–	temp = useElectrostatics;
531	–	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
799
800	<	temp = useCharge;
801	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
800	>	int getGlobalCountOfType(AtomType* atype) {
801	>	/*
802	>	set<AtomType*> atypes = getSimulatedAtomTypes();
803	>	map<AtomType*, int> counts_;
804
805	<	temp = useDipole;
806	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
805	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
806	>	for(atom = mol->beginAtom(ai); atom != NULL;
807	>	atom = mol->nextAtom(ai)) {
808	>	atom->getAtomType();
809	>	}
810	>	}
811	>	*/
812	>	return 0;
813	>	}
814
815	<	temp = useSticky;
816	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
815	>	void SimInfo::setupSimVariables() {
816	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
817	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole
818	>	// parameter is true
819	>	calcBoxDipole_ = false;
820	>	if ( simParams_->haveAccumulateBoxDipole() )
821	>	if ( simParams_->getAccumulateBoxDipole() ) {
822	>	calcBoxDipole_ = true;
823	>	}
824	>
825	>	set<AtomType*>::iterator i;
826	>	set<AtomType*> atomTypes;
827	>	atomTypes = getSimulatedAtomTypes();
828	>	bool usesElectrostatic = false;
829	>	bool usesMetallic = false;
830	>	bool usesDirectional = false;
831	>	bool usesFluctuatingCharges =  false;
832	>	//loop over all of the atom types
833	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
834	>	usesElectrostatic |= (*i)->isElectrostatic();
835	>	usesMetallic |= (*i)->isMetal();
836	>	usesDirectional |= (*i)->isDirectional();
837	>	usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
838	>	}
839
840	<	temp = useGayBerne;
841	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
840	>	#ifdef IS_MPI
841	>	bool temp;
842	>	temp = usesDirectional;
843	>	MPI::COMM_WORLD.Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI::BOOL,
844	>	MPI::LOR);
845	>
846	>	temp = usesMetallic;
847	>	MPI::COMM_WORLD.Allreduce(&temp, &usesMetallicAtoms_, 1, MPI::BOOL,
848	>	MPI::LOR);
849	>
850	>	temp = usesElectrostatic;
851	>	MPI::COMM_WORLD.Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI::BOOL,
852	>	MPI::LOR);
853
854	<	temp = useEAM;
855	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
854	>	temp = usesFluctuatingCharges;
855	>	MPI::COMM_WORLD.Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI::BOOL,
856	>	MPI::LOR);
857	>	#else
858
859	<	temp = useShape;
860	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
859	>	usesDirectionalAtoms_ = usesDirectional;
860	>	usesMetallicAtoms_ = usesMetallic;
861	>	usesElectrostaticAtoms_ = usesElectrostatic;
862	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
863
551	–	temp = useFLARB;
552	–	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
553	–
554	–	temp = useRF;
555	–	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
556	–
864		#endif
865	+
866	+	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
867	+	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
868	+	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
869	+	}
870
559	–	fInfo_.SIM_uses_PBC = usePBC;
560	–	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
561	–	fInfo_.SIM_uses_LennardJones = useLennardJones;
562	–	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
563	–	fInfo_.SIM_uses_Charges = useCharge;
564	–	fInfo_.SIM_uses_Dipoles = useDipole;
565	–	fInfo_.SIM_uses_Sticky = useSticky;
566	–	fInfo_.SIM_uses_GayBerne = useGayBerne;
567	–	fInfo_.SIM_uses_EAM = useEAM;
568	–	fInfo_.SIM_uses_Shapes = useShape;
569	–	fInfo_.SIM_uses_FLARB = useFLARB;
570	–	fInfo_.SIM_uses_RF = useRF;
871
872	<	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
872	>	vector<int> SimInfo::getGlobalAtomIndices() {
873	>	SimInfo::MoleculeIterator mi;
874	>	Molecule* mol;
875	>	Molecule::AtomIterator ai;
876	>	Atom* atom;
877
878	<	if (simParams_->haveDielectric()) {
879	<	fInfo_.dielect = simParams_->getDielectric();
880	<	} else {
881	<	sprintf(painCave.errMsg,
882	<	"SimSetup Error: No Dielectric constant was set.\n"
883	<	"\tYou are trying to use Reaction Field without"
884	<	"\tsetting a dielectric constant!\n");
581	<	painCave.isFatal = 1;
582	<	simError();
583	<	}
584	<
585	<	} else {
586	<	fInfo_.dielect = 0.0;
878	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
879	>
880	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
881	>
882	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
883	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
884	>	}
885		}
886	+	return GlobalAtomIndices;
887	+	}
888
589	–	}
889
890	<	void SimInfo::setupFortranSim() {
891	<	int isError;
892	<	int nExclude;
893	<	std::vector<int> fortranGlobalGroupMembership;
894	<
596	<	nExclude = exclude_.getSize();
597	<	isError = 0;
890	>	vector<int> SimInfo::getGlobalGroupIndices() {
891	>	SimInfo::MoleculeIterator mi;
892	>	Molecule* mol;
893	>	Molecule::CutoffGroupIterator ci;
894	>	CutoffGroup* cg;
895
896	<	//globalGroupMembership_ is filled by SimCreator
897	<	for (int i = 0; i < nGlobalAtoms_; i++) {
898	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
896	>	vector<int> GlobalGroupIndices;
897	>
898	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
899	>
900	>	//local index of cutoff group is trivial, it only depends on the
901	>	//order of travesing
902	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
903	>	cg = mol->nextCutoffGroup(ci)) {
904	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
905	>	}
906		}
907	+	return GlobalGroupIndices;
908	+	}
909
910	+
911	+	void SimInfo::prepareTopology() {
912	+
913		//calculate mass ratio of cutoff group
605	–	std::vector<double> mfact;
914		SimInfo::MoleculeIterator mi;
915		Molecule* mol;
916		Molecule::CutoffGroupIterator ci;
917		CutoffGroup* cg;
918		Molecule::AtomIterator ai;
919		Atom* atom;
920	<	double totalMass;
920	>	RealType totalMass;
921
922	<	//to avoid memory reallocation, reserve enough space for mfact
923	<	mfact.reserve(getNCutoffGroups());
922	>	/**
923	>	* The mass factor is the relative mass of an atom to the total
924	>	* mass of the cutoff group it belongs to.  By default, all atoms
925	>	* are their own cutoff groups, and therefore have mass factors of
926	>	* 1.  We need some special handling for massless atoms, which
927	>	* will be treated as carrying the entire mass of the cutoff
928	>	* group.
929	>	*/
930	>	massFactors_.clear();
931	>	massFactors_.resize(getNAtoms(), 1.0);
932
933		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
934	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
934	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
935	>	cg = mol->nextCutoffGroup(ci)) {
936
937	<	totalMass = cg->getMass();
938	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
939	<	mfact.push_back(atom->getMass()/totalMass);
940	<	}
941	<
942	<	}
937	>	totalMass = cg->getMass();
938	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
939	>	// Check for massless groups - set mfact to 1 if true
940	>	if (totalMass != 0)
941	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
942	>	else
943	>	massFactors_[atom->getLocalIndex()] = 1.0;
944	>	}
945	>	}
946		}
947
948	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
629	<	std::vector<int> identArray;
948	>	// Build the identArray_ and regions_
949
950	<	//to avoid memory reallocation, reserve enough space identArray
951	<	identArray.reserve(getNAtoms());
952	<
953	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
954	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
955	<	identArray.push_back(atom->getIdent());
956	<	}
950	>	identArray_.clear();
951	>	identArray_.reserve(getNAtoms());
952	>	regions_.clear();
953	>	regions_.reserve(getNAtoms());
954	>
955	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
956	>	int reg = mol->getRegion();
957	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
958	>	identArray_.push_back(atom->getIdent());
959	>	regions_.push_back(reg);
960	>	}
961		}
962	+
963	+	topologyDone_ = true;
964	+	}
965
966	<	//fill molMembershipArray
641	<	//molMembershipArray is filled by SimCreator
642	<	std::vector<int> molMembershipArray(nGlobalAtoms_);
643	<	for (int i = 0; i < nGlobalAtoms_; i++) {
644	<	molMembershipArray[i] = globalMolMembership_[i] + 1;
645	<	}
646	<
647	<	//setup fortran simulation
648	<	//gloalExcludes and molMembershipArray should go away (They are never used)
649	<	//why the hell fortran need to know molecule?
650	<	//OOPSE = Object-Obfuscated Parallel Simulation Engine
651	<	int nGlobalExcludes = 0;
652	<	int* globalExcludes = NULL;
653	<	int* excludeList = exclude_.getExcludeList();
654	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
655	<	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
656	<	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
657	<
658	<	if( isError ){
659	<
660	<	sprintf( painCave.errMsg,
661	<	"There was an error setting the simulation information in fortran.\n" );
662	<	painCave.isFatal = 1;
663	<	painCave.severity = OOPSE_ERROR;
664	<	simError();
665	<	}
666	<
667	<	#ifdef IS_MPI
668	<	sprintf( checkPointMsg,
669	<	"succesfully sent the simulation information to fortran.\n");
670	<	MPIcheckPoint();
671	<	#endif // is_mpi
672	<	}
673	<
674	<
675	<	#ifdef IS_MPI
676	<	void SimInfo::setupFortranParallel() {
677	<
678	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
679	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
680	<	std::vector<int> localToGlobalCutoffGroupIndex;
681	<	SimInfo::MoleculeIterator mi;
682	<	Molecule::AtomIterator ai;
683	<	Molecule::CutoffGroupIterator ci;
684	<	Molecule* mol;
685	<	Atom* atom;
686	<	CutoffGroup* cg;
687	<	mpiSimData parallelData;
688	<	int isError;
689	<
690	<	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
691	<
692	<	//local index(index in DataStorge) of atom is important
693	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
694	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
695	<	}
696	<
697	<	//local index of cutoff group is trivial, it only depends on the order of travesing
698	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
699	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
700	<	}
701	<
702	<	}
703	<
704	<	//fill up mpiSimData struct
705	<	parallelData.nMolGlobal = getNGlobalMolecules();
706	<	parallelData.nMolLocal = getNMolecules();
707	<	parallelData.nAtomsGlobal = getNGlobalAtoms();
708	<	parallelData.nAtomsLocal = getNAtoms();
709	<	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
710	<	parallelData.nGroupsLocal = getNCutoffGroups();
711	<	parallelData.myNode = worldRank;
712	<	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
713	<
714	<	//pass mpiSimData struct and index arrays to fortran
715	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
716	<	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
717	<	&localToGlobalCutoffGroupIndex[0], &isError);
718	<
719	<	if (isError) {
720	<	sprintf(painCave.errMsg,
721	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
722	<	painCave.isFatal = 1;
723	<	simError();
724	<	}
725	<
726	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
727	<	MPIcheckPoint();
728	<
729	<
730	<	}
731	<
732	<	#endif
733	<
734	<	double SimInfo::calcMaxCutoffRadius() {
735	<
736	<
737	<	std::set<AtomType*> atomTypes;
738	<	std::set<AtomType*>::iterator i;
739	<	std::vector<double> cutoffRadius;
740	<
741	<	//get the unique atom types
742	<	atomTypes = getUniqueAtomTypes();
743	<
744	<	//query the max cutoff radius among these atom types
745	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
746	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
747	<	}
748	<
749	<	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
750	<	#ifdef IS_MPI
751	<	//pick the max cutoff radius among the processors
752	<	#endif
753	<
754	<	return maxCutoffRadius;
755	<	}
756	<
757	<	void SimInfo::getCutoff(double& rcut, double& rsw) {
758	<
759	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
760	<
761	<	if (!simParams_->haveRcut()){
762	<	sprintf(painCave.errMsg,
763	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
764	<	"\tOOPSE will use a default value of 15.0 angstroms"
765	<	"\tfor the cutoffRadius.\n");
766	<	painCave.isFatal = 0;
767	<	simError();
768	<	rcut = 15.0;
769	<	} else{
770	<	rcut = simParams_->getRcut();
771	<	}
772	<
773	<	if (!simParams_->haveRsw()){
774	<	sprintf(painCave.errMsg,
775	<	"SimCreator Warning: No value was set for switchingRadius.\n"
776	<	"\tOOPSE will use a default value of\n"
777	<	"\t0.95 * cutoffRadius for the switchingRadius\n");
778	<	painCave.isFatal = 0;
779	<	simError();
780	<	rsw = 0.95 * rcut;
781	<	} else{
782	<	rsw = simParams_->getRsw();
783	<	}
784	<
785	<	} else {
786	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
787	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
788	<
789	<	if (simParams_->haveRcut()) {
790	<	rcut = simParams_->getRcut();
791	<	} else {
792	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
793	<	rcut = calcMaxCutoffRadius();
794	<	}
795	<
796	<	if (simParams_->haveRsw()) {
797	<	rsw  = simParams_->getRsw();
798	<	} else {
799	<	rsw = rcut;
800	<	}
801	<
802	<	}
803	<	}
804	<
805	<	void SimInfo::setupCutoff() {
806	<	getCutoff(rcut_, rsw_);
807	<	double rnblist = rcut_ + 1; // skin of neighbor list
808	<
809	<	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
810	<	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist);
811	<	}
812	<
813	<	void SimInfo::addProperty(GenericData* genData) {
966	>	void SimInfo::addProperty(GenericData* genData) {
967		properties_.addProperty(genData);
968	<	}
968	>	}
969
970	<	void SimInfo::removeProperty(const std::string& propName) {
970	>	void SimInfo::removeProperty(const string& propName) {
971		properties_.removeProperty(propName);
972	<	}
972	>	}
973
974	<	void SimInfo::clearProperties() {
974	>	void SimInfo::clearProperties() {
975		properties_.clearProperties();
976	<	}
976	>	}
977
978	<	std::vector<std::string> SimInfo::getPropertyNames() {
978	>	vector<string> SimInfo::getPropertyNames() {
979		return properties_.getPropertyNames();
980	<	}
980	>	}
981
982	<	std::vector<GenericData*> SimInfo::getProperties() {
982	>	vector<GenericData*> SimInfo::getProperties() {
983		return properties_.getProperties();
984	<	}
984	>	}
985
986	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
986	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
987		return properties_.getPropertyByName(propName);
988	<	}
988	>	}
989
990	<	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
990	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
991	>	if (sman_ == sman) {
992	>	return;
993	>	}
994	>	delete sman_;
995		sman_ = sman;
996
840	–	Molecule* mol;
841	–	RigidBody* rb;
842	–	Atom* atom;
997		SimInfo::MoleculeIterator mi;
998	+	Molecule::AtomIterator ai;
999		Molecule::RigidBodyIterator rbIter;
1000	<	Molecule::AtomIterator atomIter;;
1000	>	Molecule::CutoffGroupIterator cgIter;
1001	>	Molecule::BondIterator bondIter;
1002	>	Molecule::BendIterator bendIter;
1003	>	Molecule::TorsionIterator torsionIter;
1004	>	Molecule::InversionIterator inversionIter;
1005
1006	+	Molecule* mol;
1007	+	Atom* atom;
1008	+	RigidBody* rb;
1009	+	CutoffGroup* cg;
1010	+	Bond* bond;
1011	+	Bend* bend;
1012	+	Torsion* torsion;
1013	+	Inversion* inversion;
1014	+
1015		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1016
1017	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1018	<	atom->setSnapshotManager(sman_);
1019	<	}
1020	<
1021	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1022	<	rb->setSnapshotManager(sman_);
1023	<	}
1024	<	}
1025	<
1026	<	}
1017	>	for (atom = mol->beginAtom(ai); atom != NULL;
1018	>	atom = mol->nextAtom(ai)) {
1019	>	atom->setSnapshotManager(sman_);
1020	>	}
1021	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
1022	>	rb = mol->nextRigidBody(rbIter)) {
1023	>	rb->setSnapshotManager(sman_);
1024	>	}
1025	>	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL;
1026	>	cg = mol->nextCutoffGroup(cgIter)) {
1027	>	cg->setSnapshotManager(sman_);
1028	>	}
1029	>	for (bond = mol->beginBond(bondIter); bond != NULL;
1030	>	bond = mol->nextBond(bondIter)) {
1031	>	bond->setSnapshotManager(sman_);
1032	>	}
1033	>	for (bend = mol->beginBend(bendIter); bend != NULL;
1034	>	bend = mol->nextBend(bendIter)) {
1035	>	bend->setSnapshotManager(sman_);
1036	>	}
1037	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
1038	>	torsion = mol->nextTorsion(torsionIter)) {
1039	>	torsion->setSnapshotManager(sman_);
1040	>	}
1041	>	for (inversion = mol->beginInversion(inversionIter); inversion != NULL;
1042	>	inversion = mol->nextInversion(inversionIter)) {
1043	>	inversion->setSnapshotManager(sman_);
1044	>	}
1045	>	}
1046	>	}
1047
860	–	Vector3d SimInfo::getComVel(){
861	–	SimInfo::MoleculeIterator i;
862	–	Molecule* mol;
1048
1049	<	Vector3d comVel(0.0);
865	<	double totalMass = 0.0;
866	<
867	<
868	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
869	<	double mass = mol->getMass();
870	<	totalMass += mass;
871	<	comVel += mass * mol->getComVel();
872	<	}
1049	>	ostream& operator <<(ostream& o, SimInfo& info) {
1050
1051	<	#ifdef IS_MPI
1052	<	double tmpMass = totalMass;
1053	<	Vector3d tmpComVel(comVel);
1054	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1055	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1056	<	#endif
1051	>	return o;
1052	>	}
1053	>
1054	>
1055	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1056	>	if (index >= int(IOIndexToIntegrableObject.size())) {
1057	>	sprintf(painCave.errMsg,
1058	>	"SimInfo::getIOIndexToIntegrableObject Error: Integrable Object\n"
1059	>	"\tindex exceeds number of known objects!\n");
1060	>	painCave.isFatal = 1;
1061	>	simError();
1062	>	return NULL;
1063	>	} else
1064	>	return IOIndexToIntegrableObject.at(index);
1065	>	}
1066	>
1067	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1068	>	IOIndexToIntegrableObject= v;
1069	>	}
1070
1071	<	comVel /= totalMass;
1072	<
883	<	return comVel;
884	<	}
885	<
886	<	Vector3d SimInfo::getCom(){
887	<	SimInfo::MoleculeIterator i;
888	<	Molecule* mol;
889	<
890	<	Vector3d com(0.0);
891	<	double totalMass = 0.0;
892	<
893	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
894	<	double mass = mol->getMass();
895	<	totalMass += mass;
896	<	com += mass * mol->getCom();
897	<	}
898	<
1071	>	int SimInfo::getNGlobalConstraints() {
1072	>	int nGlobalConstraints;
1073		#ifdef IS_MPI
1074	<	double tmpMass = totalMass;
1075	<	Vector3d tmpCom(com);
1076	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1077	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1074	>	MPI::COMM_WORLD.Allreduce(&nConstraints_, &nGlobalConstraints, 1,
1075	>	MPI::INT, MPI::SUM);
1076	>	#else
1077	>	nGlobalConstraints =  nConstraints_;
1078		#endif
1079	+	return nGlobalConstraints;
1080	+	}
1081
1082	<	com /= totalMass;
1082	>	}//end namespace OpenMD
1083
908	–	return com;
909	–
910	–	}
911	–
912	–	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
913	–
914	–	return o;
915	–	}
916	–
917	–	}//end namespace oopse
918	–

Comparing trunk/src/brains/SimInfo.cpp (property svn:keywords):
Revision 328 by tim, Sun Feb 13 20:36:24 2005 UTC vs.
Revision 1953 by gezelter, Thu Dec 5 18:19:26 2013 UTC

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