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

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 331 by tim, Sun Feb 13 21:18:27 2005 UTC vs.
Revision 1987 by gezelter, Thu Apr 17 19:07:31 2014 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),
83	<	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), nGlobalConstraints_(0),
78	>	nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nInversions_(0),
79	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
80	>	nConstraints_(0), nFluctuatingCharges_(0), sman_(NULL),
81	>	topologyDone_(false), calcBoxDipole_(false), useAtomicVirial_(true),
82	>	hasNGlobalConstraints_(false) {
83	>
84		MoleculeStamp* molStamp;
85		int nMolWithSameStamp;
86		int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
87	<	int nGroups = 0;          //total cutoff groups defined in meta-data file
87	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
88		CutoffGroupStamp* cgStamp;
89		RigidBodyStamp* rbStamp;
90		int nRigidAtoms = 0;
91
92	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
93	<	molStamp = i->first;
94	<	nMolWithSameStamp = i->second;
95	<
96	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
92	>	vector<Component*> components = simParams->getComponents();
93	>
94	>	for (vector<Component*>::iterator i = components.begin();
95	>	i !=components.end(); ++i) {
96	>	molStamp = (*i)->getMoleculeStamp();
97	>	if ( (*i)->haveRegion() ) {
98	>	molStamp->setRegion( (*i)->getRegion() );
99	>	} else {
100	>	// set the region to a disallowed value:
101	>	molStamp->setRegion( -1 );
102	>	}
103
104	<	//calculate atoms in molecules
105	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
106	<
107	<
108	<	//calculate atoms in cutoff groups
109	<	int nAtomsInGroups = 0;
110	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
111	<
112	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
113	<	cgStamp = molStamp->getCutoffGroup(j);
114	<	nAtomsInGroups += cgStamp->getNMembers();
115	<	}
116	<
117	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
118	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
119	<
120	<	//calculate atoms in rigid bodies
121	<	int nAtomsInRigidBodies = 0;
122	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
123	<
124	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
125	<	rbStamp = molStamp->getRigidBody(j);
126	<	nAtomsInRigidBodies += rbStamp->getNMembers();
127	<	}
128	<
129	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
130	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
131	<
104	>	nMolWithSameStamp = (*i)->getNMol();
105	>
106	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
107	>
108	>	//calculate atoms in molecules
109	>	nGlobalAtoms_ += molStamp->getNAtoms() * nMolWithSameStamp;
110	>	nGlobalBonds_ += molStamp->getNBonds() * nMolWithSameStamp;
111	>	nGlobalBends_ += molStamp->getNBends() * nMolWithSameStamp;
112	>	nGlobalTorsions_ += molStamp->getNTorsions() * nMolWithSameStamp;
113	>	nGlobalInversions_ += molStamp->getNInversions() * nMolWithSameStamp;
114	>
115	>	//calculate atoms in cutoff groups
116	>	int nAtomsInGroups = 0;
117	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
118	>
119	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
120	>	cgStamp = molStamp->getCutoffGroupStamp(j);
121	>	nAtomsInGroups += cgStamp->getNMembers();
122	>	}
123	>
124	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
125	>
126	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
127	>
128	>	//calculate atoms in rigid bodies
129	>	int nAtomsInRigidBodies = 0;
130	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
131	>
132	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
133	>	rbStamp = molStamp->getRigidBodyStamp(j);
134	>	nAtomsInRigidBodies += rbStamp->getNMembers();
135	>	}
136	>
137	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
138	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
139	>
140		}
141	+
142	+	//every free atom (atom does not belong to cutoff groups) is a cutoff
143	+	//group therefore the total number of cutoff groups in the system is
144	+	//equal to the total number of atoms minus number of atoms belong to
145	+	//cutoff group defined in meta-data file plus the number of cutoff
146	+	//groups defined in meta-data file
147
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
148		nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
149	<
150	<	//every free atom (atom does not belong to rigid bodies) is an integrable object
151	<	//therefore the total number of  integrable objects in the system is equal to
152	<	//the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
153	<	//file plus the number of  rigid bodies defined in meta-data file
154	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
155	<
149	>
150	>	//every free atom (atom does not belong to rigid bodies) is an
151	>	//integrable object therefore the total number of integrable objects
152	>	//in the system is equal to the total number of atoms minus number of
153	>	//atoms belong to rigid body defined in meta-data file plus the number
154	>	//of rigid bodies defined in meta-data file
155	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
156	>	+ nGlobalRigidBodies_;
157	>
158		nGlobalMols_ = molStampIds_.size();
137	–
138	–	#ifdef IS_MPI
159		molToProcMap_.resize(nGlobalMols_);
160	<	#endif
161	<
162	<	selectMan_ = new SelectionManager(this);
163	<	selectMan_->selectAll();
164	<	}
165	<
166	<	SimInfo::~SimInfo() {
167	<	//MemoryUtils::deleteVectorOfPointer(molecules_);
168	<
149	<	MemoryUtils::deleteVectorOfPointer(moleculeStamps_);
150	<
160	>	}
161	>
162	>	SimInfo::~SimInfo() {
163	>	map<int, Molecule*>::iterator i;
164	>	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
165	>	delete i->second;
166	>	}
167	>	molecules_.clear();
168	>
169		delete sman_;
170		delete simParams_;
171		delete forceField_;
172	<	delete selectMan_;
155	<	}
172	>	}
173
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	–	}
174
175	<	bool SimInfo::addMolecule(Molecule* mol) {
175	>	bool SimInfo::addMolecule(Molecule* mol) {
176		MoleculeIterator i;
177	<
177	>
178		i = molecules_.find(mol->getGlobalIndex());
179		if (i == molecules_.end() ) {
180	<
181	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
182	<
183	<	nAtoms_ += mol->getNAtoms();
184	<	nBonds_ += mol->getNBonds();
185	<	nBends_ += mol->getNBends();
186	<	nTorsions_ += mol->getNTorsions();
187	<	nRigidBodies_ += mol->getNRigidBodies();
188	<	nIntegrableObjects_ += mol->getNIntegrableObjects();
189	<	nCutoffGroups_ += mol->getNCutoffGroups();
190	<	nConstraints_ += mol->getNConstraintPairs();
191	<
192	<	addExcludePairs(mol);
193	<
194	<	return true;
180	>
181	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
182	>
183	>	nAtoms_ += mol->getNAtoms();
184	>	nBonds_ += mol->getNBonds();
185	>	nBends_ += mol->getNBends();
186	>	nTorsions_ += mol->getNTorsions();
187	>	nInversions_ += mol->getNInversions();
188	>	nRigidBodies_ += mol->getNRigidBodies();
189	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
190	>	nCutoffGroups_ += mol->getNCutoffGroups();
191	>	nConstraints_ += mol->getNConstraintPairs();
192	>
193	>	addInteractionPairs(mol);
194	>
195	>	return true;
196		} else {
197	<	return false;
197	>	return false;
198		}
199	<	}
200	<
201	<	bool SimInfo::removeMolecule(Molecule* mol) {
199	>	}
200	>
201	>	bool SimInfo::removeMolecule(Molecule* mol) {
202		MoleculeIterator i;
203		i = molecules_.find(mol->getGlobalIndex());
204
205		if (i != molecules_.end() ) {
206
207	<	assert(mol == i->second);
207	>	assert(mol == i->second);
208
209	<	nAtoms_ -= mol->getNAtoms();
210	<	nBonds_ -= mol->getNBonds();
211	<	nBends_ -= mol->getNBends();
212	<	nTorsions_ -= mol->getNTorsions();
213	<	nRigidBodies_ -= mol->getNRigidBodies();
214	<	nIntegrableObjects_ -= mol->getNIntegrableObjects();
215	<	nCutoffGroups_ -= mol->getNCutoffGroups();
216	<	nConstraints_ -= mol->getNConstraintPairs();
209	>	nAtoms_ -= mol->getNAtoms();
210	>	nBonds_ -= mol->getNBonds();
211	>	nBends_ -= mol->getNBends();
212	>	nTorsions_ -= mol->getNTorsions();
213	>	nInversions_ -= mol->getNInversions();
214	>	nRigidBodies_ -= mol->getNRigidBodies();
215	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
216	>	nCutoffGroups_ -= mol->getNCutoffGroups();
217	>	nConstraints_ -= mol->getNConstraintPairs();
218
219	<	removeExcludePairs(mol);
220	<	molecules_.erase(mol->getGlobalIndex());
219	>	removeInteractionPairs(mol);
220	>	molecules_.erase(mol->getGlobalIndex());
221
222	<	delete mol;
222	>	delete mol;
223
224	<	return true;
224	>	return true;
225		} else {
226	<	return false;
226	>	return false;
227		}
228	+	}
229
220	–
221	–	}
222	–
230
231	<	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
231	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
232		i = molecules_.begin();
233		return i == molecules_.end() ? NULL : i->second;
234	<	}
234	>	}
235
236	<	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
236	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
237		++i;
238		return i == molecules_.end() ? NULL : i->second;
239	<	}
239	>	}
240
241
242	<	void SimInfo::calcNdf() {
243	<	int ndf_local;
242	>	void SimInfo::calcNdf() {
243	>	int ndf_local, nfq_local;
244		MoleculeIterator i;
245	<	std::vector<StuntDouble*>::iterator j;
245	>	vector<StuntDouble*>::iterator j;
246	>	vector<Atom*>::iterator k;
247	>
248		Molecule* mol;
249	<	StuntDouble* integrableObject;
249	>	StuntDouble* sd;
250	>	Atom* atom;
251
252		ndf_local = 0;
253	+	nfq_local = 0;
254
255		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
245	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
246	–	integrableObject = mol->nextIntegrableObject(j)) {
256
257	<	ndf_local += 3;
257	>	for (sd = mol->beginIntegrableObject(j); sd != NULL;
258	>	sd = mol->nextIntegrableObject(j)) {
259
260	<	if (integrableObject->isDirectional()) {
261	<	if (integrableObject->isLinear()) {
262	<	ndf_local += 2;
263	<	} else {
264	<	ndf_local += 3;
265	<	}
266	<	}
267	<
268	<	}//end for (integrableObject)
269	<	}// end for (mol)
260	>	ndf_local += 3;
261	>
262	>	if (sd->isDirectional()) {
263	>	if (sd->isLinear()) {
264	>	ndf_local += 2;
265	>	} else {
266	>	ndf_local += 3;
267	>	}
268	>	}
269	>	}
270	>
271	>	for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
272	>	atom = mol->nextFluctuatingCharge(k)) {
273	>	if (atom->isFluctuatingCharge()) {
274	>	nfq_local++;
275	>	}
276	>	}
277	>	}
278
279	+	ndfLocal_ = ndf_local;
280	+
281		// n_constraints is local, so subtract them on each processor
282		ndf_local -= nConstraints_;
283
284		#ifdef IS_MPI
285	<	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
285	>	MPI_Allreduce(&ndf_local, &ndf_, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
286	>	MPI_Allreduce(&nfq_local, &nGlobalFluctuatingCharges_, 1,
287	>	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
288		#else
289		ndf_ = ndf_local;
290	+	nGlobalFluctuatingCharges_ = nfq_local;
291		#endif
292
293		// nZconstraints_ is global, as are the 3 COM translations for the
294		// entire system:
295		ndf_ = ndf_ - 3 - nZconstraint_;
296
297	<	}
297	>	}
298
299	<	void SimInfo::calcNdfRaw() {
299	>	int SimInfo::getFdf() {
300	>	#ifdef IS_MPI
301	>	MPI_Allreduce(&fdf_local, &fdf_, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
302	>	#else
303	>	fdf_ = fdf_local;
304	>	#endif
305	>	return fdf_;
306	>	}
307	>
308	>	unsigned int SimInfo::getNLocalCutoffGroups(){
309	>	int nLocalCutoffAtoms = 0;
310	>	Molecule* mol;
311	>	MoleculeIterator mi;
312	>	CutoffGroup* cg;
313	>	Molecule::CutoffGroupIterator ci;
314	>
315	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
316	>
317	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
318	>	cg = mol->nextCutoffGroup(ci)) {
319	>	nLocalCutoffAtoms += cg->getNumAtom();
320	>
321	>	}
322	>	}
323	>
324	>	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
325	>	}
326	>
327	>	void SimInfo::calcNdfRaw() {
328		int ndfRaw_local;
329
330		MoleculeIterator i;
331	<	std::vector<StuntDouble*>::iterator j;
331	>	vector<StuntDouble*>::iterator j;
332		Molecule* mol;
333	<	StuntDouble* integrableObject;
333	>	StuntDouble* sd;
334
335		// Raw degrees of freedom that we have to set
336		ndfRaw_local = 0;
337
338		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
288	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
289	–	integrableObject = mol->nextIntegrableObject(j)) {
339
340	<	ndfRaw_local += 3;
340	>	for (sd = mol->beginIntegrableObject(j); sd != NULL;
341	>	sd = mol->nextIntegrableObject(j)) {
342
343	<	if (integrableObject->isDirectional()) {
344	<	if (integrableObject->isLinear()) {
345	<	ndfRaw_local += 2;
346	<	} else {
347	<	ndfRaw_local += 3;
348	<	}
349	<	}
343	>	ndfRaw_local += 3;
344	>
345	>	if (sd->isDirectional()) {
346	>	if (sd->isLinear()) {
347	>	ndfRaw_local += 2;
348	>	} else {
349	>	ndfRaw_local += 3;
350	>	}
351	>	}
352
353	<	}
353	>	}
354		}
355
356		#ifdef IS_MPI
357	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
357	>	MPI_Allreduce(&ndfRaw_local, &ndfRaw_, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
358		#else
359		ndfRaw_ = ndfRaw_local;
360		#endif
361	<	}
361	>	}
362
363	<	void SimInfo::calcNdfTrans() {
363	>	void SimInfo::calcNdfTrans() {
364		int ndfTrans_local;
365
366		ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
367
316	–
368		#ifdef IS_MPI
369	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
369	>	MPI_Allreduce(&ndfTrans_local, &ndfTrans_, 1, MPI_INT, MPI_SUM,
370	>	MPI_COMM_WORLD);
371		#else
372		ndfTrans_ = ndfTrans_local;
373		#endif
374
375		ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
376	<
325	<	}
376	>	}
377
378	<	void SimInfo::addExcludePairs(Molecule* mol) {
379	<	std::vector<Bond*>::iterator bondIter;
380	<	std::vector<Bend*>::iterator bendIter;
381	<	std::vector<Torsion*>::iterator torsionIter;
378	>	void SimInfo::addInteractionPairs(Molecule* mol) {
379	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
380	>	vector<Bond*>::iterator bondIter;
381	>	vector<Bend*>::iterator bendIter;
382	>	vector<Torsion*>::iterator torsionIter;
383	>	vector<Inversion*>::iterator inversionIter;
384		Bond* bond;
385		Bend* bend;
386		Torsion* torsion;
387	+	Inversion* inversion;
388		int a;
389		int b;
390		int c;
391		int d;
392	+
393	+	// atomGroups can be used to add special interaction maps between
394	+	// groups of atoms that are in two separate rigid bodies.
395	+	// However, most site-site interactions between two rigid bodies
396	+	// are probably not special, just the ones between the physically
397	+	// bonded atoms.  Interactions *within* a single rigid body should
398	+	// always be excluded.  These are done at the bottom of this
399	+	// function.
400	+
401	+	map<int, set<int> > atomGroups;
402	+	Molecule::RigidBodyIterator rbIter;
403	+	RigidBody* rb;
404	+	Molecule::IntegrableObjectIterator ii;
405	+	StuntDouble* sd;
406
407	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
408	<	a = bond->getAtomA()->getGlobalIndex();
409	<	b = bond->getAtomB()->getGlobalIndex();
410	<	exclude_.addPair(a, b);
407	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
408	>	sd = mol->nextIntegrableObject(ii)) {
409	>
410	>	if (sd->isRigidBody()) {
411	>	rb = static_cast<RigidBody*>(sd);
412	>	vector<Atom*> atoms = rb->getAtoms();
413	>	set<int> rigidAtoms;
414	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
415	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
416	>	}
417	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
418	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
419	>	}
420	>	} else {
421	>	set<int> oneAtomSet;
422	>	oneAtomSet.insert(sd->getGlobalIndex());
423	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
424	>	}
425	>	}
426	>
427	>
428	>	for (bond= mol->beginBond(bondIter); bond != NULL;
429	>	bond = mol->nextBond(bondIter)) {
430	>
431	>	a = bond->getAtomA()->getGlobalIndex();
432	>	b = bond->getAtomB()->getGlobalIndex();
433	>
434	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
435	>	oneTwoInteractions_.addPair(a, b);
436	>	} else {
437	>	excludedInteractions_.addPair(a, b);
438	>	}
439		}
440
441	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
442	<	a = bend->getAtomA()->getGlobalIndex();
347	<	b = bend->getAtomB()->getGlobalIndex();
348	<	c = bend->getAtomC()->getGlobalIndex();
441	>	for (bend= mol->beginBend(bendIter); bend != NULL;
442	>	bend = mol->nextBend(bendIter)) {
443
444	<	exclude_.addPair(a, b);
445	<	exclude_.addPair(a, c);
446	<	exclude_.addPair(b, c);
444	>	a = bend->getAtomA()->getGlobalIndex();
445	>	b = bend->getAtomB()->getGlobalIndex();
446	>	c = bend->getAtomC()->getGlobalIndex();
447	>
448	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
449	>	oneTwoInteractions_.addPair(a, b);
450	>	oneTwoInteractions_.addPair(b, c);
451	>	} else {
452	>	excludedInteractions_.addPair(a, b);
453	>	excludedInteractions_.addPair(b, c);
454	>	}
455	>
456	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
457	>	oneThreeInteractions_.addPair(a, c);
458	>	} else {
459	>	excludedInteractions_.addPair(a, c);
460	>	}
461		}
462
463	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
464	<	a = torsion->getAtomA()->getGlobalIndex();
357	<	b = torsion->getAtomB()->getGlobalIndex();
358	<	c = torsion->getAtomC()->getGlobalIndex();
359	<	d = torsion->getAtomD()->getGlobalIndex();
463	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
464	>	torsion = mol->nextTorsion(torsionIter)) {
465
466	<	exclude_.addPair(a, b);
467	<	exclude_.addPair(a, c);
468	<	exclude_.addPair(a, d);
469	<	exclude_.addPair(b, c);
470	<	exclude_.addPair(b, d);
471	<	exclude_.addPair(c, d);
466	>	a = torsion->getAtomA()->getGlobalIndex();
467	>	b = torsion->getAtomB()->getGlobalIndex();
468	>	c = torsion->getAtomC()->getGlobalIndex();
469	>	d = torsion->getAtomD()->getGlobalIndex();
470	>
471	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
472	>	oneTwoInteractions_.addPair(a, b);
473	>	oneTwoInteractions_.addPair(b, c);
474	>	oneTwoInteractions_.addPair(c, d);
475	>	} else {
476	>	excludedInteractions_.addPair(a, b);
477	>	excludedInteractions_.addPair(b, c);
478	>	excludedInteractions_.addPair(c, d);
479	>	}
480	>
481	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
482	>	oneThreeInteractions_.addPair(a, c);
483	>	oneThreeInteractions_.addPair(b, d);
484	>	} else {
485	>	excludedInteractions_.addPair(a, c);
486	>	excludedInteractions_.addPair(b, d);
487	>	}
488	>
489	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
490	>	oneFourInteractions_.addPair(a, d);
491	>	} else {
492	>	excludedInteractions_.addPair(a, d);
493	>	}
494		}
495
496	<
497	<	}
496	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
497	>	inversion = mol->nextInversion(inversionIter)) {
498
499	<	void SimInfo::removeExcludePairs(Molecule* mol) {
500	<	std::vector<Bond*>::iterator bondIter;
501	<	std::vector<Bend*>::iterator bendIter;
502	<	std::vector<Torsion*>::iterator torsionIter;
499	>	a = inversion->getAtomA()->getGlobalIndex();
500	>	b = inversion->getAtomB()->getGlobalIndex();
501	>	c = inversion->getAtomC()->getGlobalIndex();
502	>	d = inversion->getAtomD()->getGlobalIndex();
503	>
504	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
505	>	oneTwoInteractions_.addPair(a, b);
506	>	oneTwoInteractions_.addPair(a, c);
507	>	oneTwoInteractions_.addPair(a, d);
508	>	} else {
509	>	excludedInteractions_.addPair(a, b);
510	>	excludedInteractions_.addPair(a, c);
511	>	excludedInteractions_.addPair(a, d);
512	>	}
513	>
514	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
515	>	oneThreeInteractions_.addPair(b, c);
516	>	oneThreeInteractions_.addPair(b, d);
517	>	oneThreeInteractions_.addPair(c, d);
518	>	} else {
519	>	excludedInteractions_.addPair(b, c);
520	>	excludedInteractions_.addPair(b, d);
521	>	excludedInteractions_.addPair(c, d);
522	>	}
523	>	}
524	>
525	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
526	>	rb = mol->nextRigidBody(rbIter)) {
527	>	vector<Atom*> atoms = rb->getAtoms();
528	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
529	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
530	>	a = atoms[i]->getGlobalIndex();
531	>	b = atoms[j]->getGlobalIndex();
532	>	excludedInteractions_.addPair(a, b);
533	>	}
534	>	}
535	>	}
536	>
537	>	}
538	>
539	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
540	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
541	>	vector<Bond*>::iterator bondIter;
542	>	vector<Bend*>::iterator bendIter;
543	>	vector<Torsion*>::iterator torsionIter;
544	>	vector<Inversion*>::iterator inversionIter;
545		Bond* bond;
546		Bend* bend;
547		Torsion* torsion;
548	+	Inversion* inversion;
549		int a;
550		int b;
551		int c;
552		int d;
553	+
554	+	map<int, set<int> > atomGroups;
555	+	Molecule::RigidBodyIterator rbIter;
556	+	RigidBody* rb;
557	+	Molecule::IntegrableObjectIterator ii;
558	+	StuntDouble* sd;
559
560	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
561	<	a = bond->getAtomA()->getGlobalIndex();
562	<	b = bond->getAtomB()->getGlobalIndex();
563	<	exclude_.removePair(a, b);
560	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
561	>	sd = mol->nextIntegrableObject(ii)) {
562	>
563	>	if (sd->isRigidBody()) {
564	>	rb = static_cast<RigidBody*>(sd);
565	>	vector<Atom*> atoms = rb->getAtoms();
566	>	set<int> rigidAtoms;
567	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
568	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
569	>	}
570	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
571	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
572	>	}
573	>	} else {
574	>	set<int> oneAtomSet;
575	>	oneAtomSet.insert(sd->getGlobalIndex());
576	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
577	>	}
578	>	}
579	>
580	>	for (bond= mol->beginBond(bondIter); bond != NULL;
581	>	bond = mol->nextBond(bondIter)) {
582	>
583	>	a = bond->getAtomA()->getGlobalIndex();
584	>	b = bond->getAtomB()->getGlobalIndex();
585	>
586	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
587	>	oneTwoInteractions_.removePair(a, b);
588	>	} else {
589	>	excludedInteractions_.removePair(a, b);
590	>	}
591		}
592
593	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
594	<	a = bend->getAtomA()->getGlobalIndex();
392	<	b = bend->getAtomB()->getGlobalIndex();
393	<	c = bend->getAtomC()->getGlobalIndex();
593	>	for (bend= mol->beginBend(bendIter); bend != NULL;
594	>	bend = mol->nextBend(bendIter)) {
595
596	<	exclude_.removePair(a, b);
597	<	exclude_.removePair(a, c);
598	<	exclude_.removePair(b, c);
596	>	a = bend->getAtomA()->getGlobalIndex();
597	>	b = bend->getAtomB()->getGlobalIndex();
598	>	c = bend->getAtomC()->getGlobalIndex();
599	>
600	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
601	>	oneTwoInteractions_.removePair(a, b);
602	>	oneTwoInteractions_.removePair(b, c);
603	>	} else {
604	>	excludedInteractions_.removePair(a, b);
605	>	excludedInteractions_.removePair(b, c);
606	>	}
607	>
608	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
609	>	oneThreeInteractions_.removePair(a, c);
610	>	} else {
611	>	excludedInteractions_.removePair(a, c);
612	>	}
613		}
614
615	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
616	<	a = torsion->getAtomA()->getGlobalIndex();
402	<	b = torsion->getAtomB()->getGlobalIndex();
403	<	c = torsion->getAtomC()->getGlobalIndex();
404	<	d = torsion->getAtomD()->getGlobalIndex();
615	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
616	>	torsion = mol->nextTorsion(torsionIter)) {
617
618	<	exclude_.removePair(a, b);
619	<	exclude_.removePair(a, c);
620	<	exclude_.removePair(a, d);
621	<	exclude_.removePair(b, c);
622	<	exclude_.removePair(b, d);
623	<	exclude_.removePair(c, d);
618	>	a = torsion->getAtomA()->getGlobalIndex();
619	>	b = torsion->getAtomB()->getGlobalIndex();
620	>	c = torsion->getAtomC()->getGlobalIndex();
621	>	d = torsion->getAtomD()->getGlobalIndex();
622	>
623	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
624	>	oneTwoInteractions_.removePair(a, b);
625	>	oneTwoInteractions_.removePair(b, c);
626	>	oneTwoInteractions_.removePair(c, d);
627	>	} else {
628	>	excludedInteractions_.removePair(a, b);
629	>	excludedInteractions_.removePair(b, c);
630	>	excludedInteractions_.removePair(c, d);
631	>	}
632	>
633	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
634	>	oneThreeInteractions_.removePair(a, c);
635	>	oneThreeInteractions_.removePair(b, d);
636	>	} else {
637	>	excludedInteractions_.removePair(a, c);
638	>	excludedInteractions_.removePair(b, d);
639	>	}
640	>
641	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
642	>	oneFourInteractions_.removePair(a, d);
643	>	} else {
644	>	excludedInteractions_.removePair(a, d);
645	>	}
646		}
647
648	<	}
648	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
649	>	inversion = mol->nextInversion(inversionIter)) {
650
651	+	a = inversion->getAtomA()->getGlobalIndex();
652	+	b = inversion->getAtomB()->getGlobalIndex();
653	+	c = inversion->getAtomC()->getGlobalIndex();
654	+	d = inversion->getAtomD()->getGlobalIndex();
655
656	<	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
657	<	int curStampId;
656	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
657	>	oneTwoInteractions_.removePair(a, b);
658	>	oneTwoInteractions_.removePair(a, c);
659	>	oneTwoInteractions_.removePair(a, d);
660	>	} else {
661	>	excludedInteractions_.removePair(a, b);
662	>	excludedInteractions_.removePair(a, c);
663	>	excludedInteractions_.removePair(a, d);
664	>	}
665
666	+	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
667	+	oneThreeInteractions_.removePair(b, c);
668	+	oneThreeInteractions_.removePair(b, d);
669	+	oneThreeInteractions_.removePair(c, d);
670	+	} else {
671	+	excludedInteractions_.removePair(b, c);
672	+	excludedInteractions_.removePair(b, d);
673	+	excludedInteractions_.removePair(c, d);
674	+	}
675	+	}
676	+
677	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
678	+	rb = mol->nextRigidBody(rbIter)) {
679	+	vector<Atom*> atoms = rb->getAtoms();
680	+	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
681	+	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
682	+	a = atoms[i]->getGlobalIndex();
683	+	b = atoms[j]->getGlobalIndex();
684	+	excludedInteractions_.removePair(a, b);
685	+	}
686	+	}
687	+	}
688	+
689	+	}
690	+
691	+
692	+	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
693	+	int curStampId;
694	+
695		//index from 0
696		curStampId = moleculeStamps_.size();
697
698		moleculeStamps_.push_back(molStamp);
699		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
700	<	}
700	>	}
701
427	–	void SimInfo::update() {
702
703	<	setupSimType();
704	<
705	<	#ifdef IS_MPI
706	<	setupFortranParallel();
707	<	#endif
708	<
709	<	setupFortranSim();
710	<
711	<	//setup fortran force field
712	<	/** @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	<
703	>	/**
704	>	* update
705	>	*
706	>	*  Performs the global checks and variable settings after the
707	>	*  objects have been created.
708	>	*
709	>	*/
710	>	void SimInfo::update() {
711	>	setupSimVariables();
712	>	calcNConstraints();
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() {
753	<	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;
753	>	MPI_Comm_size( MPI_COMM_WORLD, &nproc);
754
755	<	//loop over all of the atom types
756	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
757	<	useLennardJones |= (*i)->isLennardJones();
758	<	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	<	}
755	>	// we need arrays to hold the counts and displacement vectors for
756	>	// all processors
757	>	vector<int> counts(nproc, 0);
758	>	vector<int> disps(nproc, 0);
759
760	<	if (useSticky || useDipole || useGayBerne || useShape) {
761	<	useDirectionalAtom = 1;
760	>	// fill the counts array
761	>	MPI_Allgather(&count_local, 1, MPI_INT, &counts[0],
762	>	1, MPI_INT, MPI_COMM_WORLD);
763	>
764	>	// use the processor counts to compute the displacement array
765	>	disps[0] = 0;
766	>	int totalCount = counts[0];
767	>	for (int iproc = 1; iproc < nproc; iproc++) {
768	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
769	>	totalCount += counts[iproc];
770		}
771
772	<	if (useCharge || useDipole) {
773	<	useElectrostatics = 1;
774	<	}
772	>	// we need a (possibly redundant) set of all found types:
773	>	vector<int> ftGlobal(totalCount);
774	>
775	>	// now spray out the foundTypes to all the other processors:
776	>	MPI_Allgatherv(&foundTypes[0], count_local, MPI_INT,
777	>	&ftGlobal[0], &counts[0], &disps[0],
778	>	MPI_INT, MPI_COMM_WORLD);
779
780	<	#ifdef IS_MPI
519	<	int temp;
780	>	vector<int>::iterator j;
781
782	<	temp = usePBC;
783	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
782	>	// foundIdents is a stl set, so inserting an already found ident
783	>	// will have no effect.
784	>	set<int> foundIdents;
785
786	<	temp = useDirectionalAtom;
787	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
786	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
787	>	foundIdents.insert((*j));
788	>
789	>	// now iterate over the foundIdents and get the actual atom types
790	>	// that correspond to these:
791	>	set<int>::iterator it;
792	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
793	>	atomTypes.insert( forceField_->getAtomType((*it)) );
794	>
795	>	#endif
796
797	<	temp = useLennardJones;
798	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
797	>	return atomTypes;
798	>	}
799
530	–	temp = useElectrostatics;
531	–	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
800
801	<	temp = useCharge;
802	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
801	>	int getGlobalCountOfType(AtomType* atype) {
802	>	/*
803	>	set<AtomType*> atypes = getSimulatedAtomTypes();
804	>	map<AtomType*, int> counts_;
805
806	<	temp = useDipole;
807	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
806	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
807	>	for(atom = mol->beginAtom(ai); atom != NULL;
808	>	atom = mol->nextAtom(ai)) {
809	>	atom->getAtomType();
810	>	}
811	>	}
812	>	*/
813	>	return 0;
814	>	}
815
816	<	temp = useSticky;
817	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
816	>	void SimInfo::setupSimVariables() {
817	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
818	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole
819	>	// parameter is true
820	>	calcBoxDipole_ = false;
821	>	if ( simParams_->haveAccumulateBoxDipole() )
822	>	if ( simParams_->getAccumulateBoxDipole() ) {
823	>	calcBoxDipole_ = true;
824	>	}
825	>
826	>	set<AtomType*>::iterator i;
827	>	set<AtomType*> atomTypes;
828	>	atomTypes = getSimulatedAtomTypes();
829	>	bool usesElectrostatic = false;
830	>	bool usesMetallic = false;
831	>	bool usesDirectional = false;
832	>	bool usesFluctuatingCharges =  false;
833	>	//loop over all of the atom types
834	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
835	>	usesElectrostatic |= (*i)->isElectrostatic();
836	>	usesMetallic |= (*i)->isMetal();
837	>	usesDirectional |= (*i)->isDirectional();
838	>	usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
839	>	}
840
841	<	temp = useGayBerne;
842	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
841	>	#ifdef IS_MPI
842	>	int temp;
843
844	<	temp = useEAM;
845	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
844	>	temp = usesDirectional;
845	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
846	>	usesDirectionalAtoms_ = (temp == 0) ? false : true;
847	>
848	>	temp = usesMetallic;
849	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
850	>	usesMetallicAtoms_ = (temp == 0) ? false : true;
851
852	<	temp = useShape;
853	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
852	>	temp = usesElectrostatic;
853	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
854	>	usesElectrostaticAtoms_ = (temp == 0) ? false : true;
855
856	<	temp = useFLARB;
857	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
856	>	temp = usesFluctuatingCharges;
857	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
858	>	usesFluctuatingCharges_ = (temp == 0) ? false : true;
859	>	#else
860
861	<	temp = useRF;
862	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
863	<
861	>	usesDirectionalAtoms_ = usesDirectional;
862	>	usesMetallicAtoms_ = usesMetallic;
863	>	usesElectrostaticAtoms_ = usesElectrostatic;
864	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
865	>
866		#endif
867	+
868	+	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
869	+	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
870	+	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
871	+	}
872
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;
873
874	<	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
874	>	vector<int> SimInfo::getGlobalAtomIndices() {
875	>	SimInfo::MoleculeIterator mi;
876	>	Molecule* mol;
877	>	Molecule::AtomIterator ai;
878	>	Atom* atom;
879
880	<	if (simParams_->haveDielectric()) {
881	<	fInfo_.dielect = simParams_->getDielectric();
882	<	} else {
883	<	sprintf(painCave.errMsg,
884	<	"SimSetup Error: No Dielectric constant was set.\n"
885	<	"\tYou are trying to use Reaction Field without"
886	<	"\tsetting a dielectric constant!\n");
581	<	painCave.isFatal = 1;
582	<	simError();
583	<	}
584	<
585	<	} else {
586	<	fInfo_.dielect = 0.0;
880	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
881	>
882	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
883	>
884	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
885	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
886	>	}
887		}
888	+	return GlobalAtomIndices;
889	+	}
890
589	–	}
891
892	<	void SimInfo::setupFortranSim() {
893	<	int isError;
894	<	int nExclude;
895	<	std::vector<int> fortranGlobalGroupMembership;
896	<
596	<	nExclude = exclude_.getSize();
597	<	isError = 0;
892	>	vector<int> SimInfo::getGlobalGroupIndices() {
893	>	SimInfo::MoleculeIterator mi;
894	>	Molecule* mol;
895	>	Molecule::CutoffGroupIterator ci;
896	>	CutoffGroup* cg;
897
898	<	//globalGroupMembership_ is filled by SimCreator
899	<	for (int i = 0; i < nGlobalAtoms_; i++) {
900	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
898	>	vector<int> GlobalGroupIndices;
899	>
900	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
901	>
902	>	//local index of cutoff group is trivial, it only depends on the
903	>	//order of travesing
904	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
905	>	cg = mol->nextCutoffGroup(ci)) {
906	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
907	>	}
908		}
909	+	return GlobalGroupIndices;
910	+	}
911
912	+
913	+	void SimInfo::prepareTopology() {
914	+
915		//calculate mass ratio of cutoff group
605	–	std::vector<double> mfact;
916		SimInfo::MoleculeIterator mi;
917		Molecule* mol;
918		Molecule::CutoffGroupIterator ci;
919		CutoffGroup* cg;
920		Molecule::AtomIterator ai;
921		Atom* atom;
922	<	double totalMass;
922	>	RealType totalMass;
923
924	<	//to avoid memory reallocation, reserve enough space for mfact
925	<	mfact.reserve(getNCutoffGroups());
924	>	/**
925	>	* The mass factor is the relative mass of an atom to the total
926	>	* mass of the cutoff group it belongs to.  By default, all atoms
927	>	* are their own cutoff groups, and therefore have mass factors of
928	>	* 1.  We need some special handling for massless atoms, which
929	>	* will be treated as carrying the entire mass of the cutoff
930	>	* group.
931	>	*/
932	>	massFactors_.clear();
933	>	massFactors_.resize(getNAtoms(), 1.0);
934
935		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
936	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
936	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
937	>	cg = mol->nextCutoffGroup(ci)) {
938
939	<	totalMass = cg->getMass();
940	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
941	<	mfact.push_back(atom->getMass()/totalMass);
942	<	}
943	<
944	<	}
939	>	totalMass = cg->getMass();
940	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
941	>	// Check for massless groups - set mfact to 1 if true
942	>	if (totalMass != 0)
943	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
944	>	else
945	>	massFactors_[atom->getLocalIndex()] = 1.0;
946	>	}
947	>	}
948		}
949
950	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
629	<	std::vector<int> identArray;
950	>	// Build the identArray_ and regions_
951
952	<	//to avoid memory reallocation, reserve enough space identArray
953	<	identArray.reserve(getNAtoms());
954	<
955	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
956	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
957	<	identArray.push_back(atom->getIdent());
958	<	}
952	>	identArray_.clear();
953	>	identArray_.reserve(getNAtoms());
954	>	regions_.clear();
955	>	regions_.reserve(getNAtoms());
956	>
957	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
958	>	int reg = mol->getRegion();
959	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
960	>	identArray_.push_back(atom->getIdent());
961	>	regions_.push_back(reg);
962	>	}
963		}
964	+
965	+	topologyDone_ = true;
966	+	}
967
968	<	//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) {
968	>	void SimInfo::addProperty(GenericData* genData) {
969		properties_.addProperty(genData);
970	<	}
970	>	}
971
972	<	void SimInfo::removeProperty(const std::string& propName) {
972	>	void SimInfo::removeProperty(const string& propName) {
973		properties_.removeProperty(propName);
974	<	}
974	>	}
975
976	<	void SimInfo::clearProperties() {
976	>	void SimInfo::clearProperties() {
977		properties_.clearProperties();
978	<	}
978	>	}
979
980	<	std::vector<std::string> SimInfo::getPropertyNames() {
980	>	vector<string> SimInfo::getPropertyNames() {
981		return properties_.getPropertyNames();
982	<	}
982	>	}
983
984	<	std::vector<GenericData*> SimInfo::getProperties() {
984	>	vector<GenericData*> SimInfo::getProperties() {
985		return properties_.getProperties();
986	<	}
986	>	}
987
988	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
988	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
989		return properties_.getPropertyByName(propName);
990	<	}
990	>	}
991
992	<	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
993	<	if (sman_ == sman_) {
994	<	return;
995	<	}
841	<
992	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
993	>	if (sman_ == sman) {
994	>	return;
995	>	}
996		delete sman_;
997		sman_ = sman;
998
845	–	Molecule* mol;
846	–	RigidBody* rb;
847	–	Atom* atom;
999		SimInfo::MoleculeIterator mi;
1000	+	Molecule::AtomIterator ai;
1001		Molecule::RigidBodyIterator rbIter;
1002	<	Molecule::AtomIterator atomIter;;
1002	>	Molecule::CutoffGroupIterator cgIter;
1003	>	Molecule::BondIterator bondIter;
1004	>	Molecule::BendIterator bendIter;
1005	>	Molecule::TorsionIterator torsionIter;
1006	>	Molecule::InversionIterator inversionIter;
1007
1008	+	Molecule* mol;
1009	+	Atom* atom;
1010	+	RigidBody* rb;
1011	+	CutoffGroup* cg;
1012	+	Bond* bond;
1013	+	Bend* bend;
1014	+	Torsion* torsion;
1015	+	Inversion* inversion;
1016	+
1017		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1018
1019	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1020	<	atom->setSnapshotManager(sman_);
1021	<	}
1022	<
1023	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1024	<	rb->setSnapshotManager(sman_);
1025	<	}
1026	<	}
1027	<
1028	<	}
1019	>	for (atom = mol->beginAtom(ai); atom != NULL;
1020	>	atom = mol->nextAtom(ai)) {
1021	>	atom->setSnapshotManager(sman_);
1022	>	}
1023	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
1024	>	rb = mol->nextRigidBody(rbIter)) {
1025	>	rb->setSnapshotManager(sman_);
1026	>	}
1027	>	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL;
1028	>	cg = mol->nextCutoffGroup(cgIter)) {
1029	>	cg->setSnapshotManager(sman_);
1030	>	}
1031	>	for (bond = mol->beginBond(bondIter); bond != NULL;
1032	>	bond = mol->nextBond(bondIter)) {
1033	>	bond->setSnapshotManager(sman_);
1034	>	}
1035	>	for (bend = mol->beginBend(bendIter); bend != NULL;
1036	>	bend = mol->nextBend(bendIter)) {
1037	>	bend->setSnapshotManager(sman_);
1038	>	}
1039	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
1040	>	torsion = mol->nextTorsion(torsionIter)) {
1041	>	torsion->setSnapshotManager(sman_);
1042	>	}
1043	>	for (inversion = mol->beginInversion(inversionIter); inversion != NULL;
1044	>	inversion = mol->nextInversion(inversionIter)) {
1045	>	inversion->setSnapshotManager(sman_);
1046	>	}
1047	>	}
1048	>	}
1049
865	–	Vector3d SimInfo::getComVel(){
866	–	SimInfo::MoleculeIterator i;
867	–	Molecule* mol;
1050
1051	<	Vector3d comVel(0.0);
870	<	double totalMass = 0.0;
871	<
872	<
873	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
874	<	double mass = mol->getMass();
875	<	totalMass += mass;
876	<	comVel += mass * mol->getComVel();
877	<	}
1051	>	ostream& operator <<(ostream& o, SimInfo& info) {
1052
1053	<	#ifdef IS_MPI
1054	<	double tmpMass = totalMass;
1055	<	Vector3d tmpComVel(comVel);
1056	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1057	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1058	<	#endif
1053	>	return o;
1054	>	}
1055	>
1056	>
1057	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1058	>	if (index >= int(IOIndexToIntegrableObject.size())) {
1059	>	sprintf(painCave.errMsg,
1060	>	"SimInfo::getIOIndexToIntegrableObject Error: Integrable Object\n"
1061	>	"\tindex exceeds number of known objects!\n");
1062	>	painCave.isFatal = 1;
1063	>	simError();
1064	>	return NULL;
1065	>	} else
1066	>	return IOIndexToIntegrableObject.at(index);
1067	>	}
1068	>
1069	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1070	>	IOIndexToIntegrableObject= v;
1071	>	}
1072
1073	<	comVel /= totalMass;
887	<
888	<	return comVel;
889	<	}
890	<
891	<	Vector3d SimInfo::getCom(){
892	<	SimInfo::MoleculeIterator i;
893	<	Molecule* mol;
894	<
895	<	Vector3d com(0.0);
896	<	double totalMass = 0.0;
897	<
898	<	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
899	<	double mass = mol->getMass();
900	<	totalMass += mass;
901	<	com += mass * mol->getCom();
902	<	}
903	<
1073	>	void SimInfo::calcNConstraints() {
1074		#ifdef IS_MPI
1075	<	double tmpMass = totalMass;
1076	<	Vector3d tmpCom(com);
1077	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1078	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1075	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints_, 1,
1076	>	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
1077	>	#else
1078	>	nGlobalConstraints_ =  nConstraints_;
1079		#endif
1080	+	}
1081
1082	<	com /= totalMass;
1082	>	}//end namespace OpenMD
1083
913	–	return com;
914	–
915	–	}
916	–
917	–	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
918	–
919	–	return o;
920	–	}
921	–
922	–	}//end namespace oopse
923	–

Comparing trunk/src/brains/SimInfo.cpp (property svn:keywords):
Revision 331 by tim, Sun Feb 13 21:18:27 2005 UTC vs.
Revision 1987 by gezelter, Thu Apr 17 19:07:31 2014 UTC

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