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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 2071 by gezelter, Sat Mar 7 21:41:51 2015 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) {
84	<
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	>	nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nInversions_(0),
74	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
75	>	nConstraints_(0), nFluctuatingCharges_(0),
76	>	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
77	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
78	>	nGlobalFluctuatingCharges_(0), nGlobalBonds_(0), nGlobalBends_(0),
79	>	nGlobalTorsions_(0), nGlobalInversions_(0), nGlobalConstraints_(0),
80	>	hasNGlobalConstraints_(false),
81	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
82	>	sman_(NULL), topologyDone_(false), calcBoxDipole_(false),
83	>	calcBoxQuadrupole_(false), useAtomicVirial_(true) {
84	>
85		MoleculeStamp* molStamp;
86		int nMolWithSameStamp;
87		int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
88	<	int nGroups = 0;          //total cutoff groups defined in meta-data file
88	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
89		CutoffGroupStamp* cgStamp;
90		RigidBodyStamp* rbStamp;
91		int nRigidAtoms = 0;
92
93	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
94	<	molStamp = i->first;
95	<	nMolWithSameStamp = i->second;
96	<
97	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
93	>	vector<Component*> components = simParams->getComponents();
94	>
95	>	for (vector<Component*>::iterator i = components.begin();
96	>	i !=components.end(); ++i) {
97	>	molStamp = (*i)->getMoleculeStamp();
98	>	if ( (*i)->haveRegion() ) {
99	>	molStamp->setRegion( (*i)->getRegion() );
100	>	} else {
101	>	// set the region to a disallowed value:
102	>	molStamp->setRegion( -1 );
103	>	}
104
105	<	//calculate atoms in molecules
106	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
107	<
108	<
109	<	//calculate atoms in cutoff groups
110	<	int nAtomsInGroups = 0;
111	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
112	<
113	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
114	<	cgStamp = molStamp->getCutoffGroup(j);
115	<	nAtomsInGroups += cgStamp->getNMembers();
116	<	}
117	<
118	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
119	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
120	<
121	<	//calculate atoms in rigid bodies
122	<	int nAtomsInRigidBodies = 0;
123	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
124	<
125	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
126	<	rbStamp = molStamp->getRigidBody(j);
127	<	nAtomsInRigidBodies += rbStamp->getNMembers();
128	<	}
129	<
130	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
131	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
132	<
105	>	nMolWithSameStamp = (*i)->getNMol();
106	>
107	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
108	>
109	>	//calculate atoms in molecules
110	>	nGlobalAtoms_ += molStamp->getNAtoms() * nMolWithSameStamp;
111	>	nGlobalBonds_ += molStamp->getNBonds() * nMolWithSameStamp;
112	>	nGlobalBends_ += molStamp->getNBends() * nMolWithSameStamp;
113	>	nGlobalTorsions_ += molStamp->getNTorsions() * nMolWithSameStamp;
114	>	nGlobalInversions_ += molStamp->getNInversions() * nMolWithSameStamp;
115	>
116	>	//calculate atoms in cutoff groups
117	>	int nAtomsInGroups = 0;
118	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
119	>
120	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
121	>	cgStamp = molStamp->getCutoffGroupStamp(j);
122	>	nAtomsInGroups += cgStamp->getNMembers();
123	>	}
124	>
125	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
126	>
127	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
128	>
129	>	//calculate atoms in rigid bodies
130	>	int nAtomsInRigidBodies = 0;
131	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
132	>
133	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
134	>	rbStamp = molStamp->getRigidBodyStamp(j);
135	>	nAtomsInRigidBodies += rbStamp->getNMembers();
136	>	}
137	>
138	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
139	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
140	>
141		}
142	+
143	+	//every free atom (atom does not belong to cutoff groups) is a cutoff
144	+	//group therefore the total number of cutoff groups in the system is
145	+	//equal to the total number of atoms minus number of atoms belong to
146	+	//cutoff group defined in meta-data file plus the number of cutoff
147	+	//groups defined in meta-data file
148
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
149		nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
150	<
151	<	//every free atom (atom does not belong to rigid bodies) is an integrable object
152	<	//therefore the total number of  integrable objects in the system is equal to
153	<	//the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
154	<	//file plus the number of  rigid bodies defined in meta-data file
155	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
156	<
150	>
151	>	//every free atom (atom does not belong to rigid bodies) is an
152	>	//integrable object therefore the total number of integrable objects
153	>	//in the system is equal to the total number of atoms minus number of
154	>	//atoms belong to rigid body defined in meta-data file plus the number
155	>	//of rigid bodies defined in meta-data file
156	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
157	>	+ nGlobalRigidBodies_;
158	>
159		nGlobalMols_ = molStampIds_.size();
137	–
138	–	#ifdef IS_MPI
160		molToProcMap_.resize(nGlobalMols_);
161	<	#endif
162	<
163	<	selectMan_ = new SelectionManager(this);
164	<	selectMan_->selectAll();
165	<	}
166	<
167	<	SimInfo::~SimInfo() {
168	<	//MemoryUtils::deleteVectorOfPointer(molecules_);
169	<
149	<	MemoryUtils::deleteVectorOfPointer(moleculeStamps_);
150	<
161	>	}
162	>
163	>	SimInfo::~SimInfo() {
164	>	map<int, Molecule*>::iterator i;
165	>	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
166	>	delete i->second;
167	>	}
168	>	molecules_.clear();
169	>
170		delete sman_;
171		delete simParams_;
172		delete forceField_;
173	<	delete selectMan_;
155	<	}
173	>	}
174
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	–	}
175
176	<	bool SimInfo::addMolecule(Molecule* mol) {
176	>	bool SimInfo::addMolecule(Molecule* mol) {
177		MoleculeIterator i;
178	<
178	>
179		i = molecules_.find(mol->getGlobalIndex());
180		if (i == molecules_.end() ) {
181	<
182	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
183	<
184	<	nAtoms_ += mol->getNAtoms();
185	<	nBonds_ += mol->getNBonds();
186	<	nBends_ += mol->getNBends();
187	<	nTorsions_ += mol->getNTorsions();
188	<	nRigidBodies_ += mol->getNRigidBodies();
189	<	nIntegrableObjects_ += mol->getNIntegrableObjects();
190	<	nCutoffGroups_ += mol->getNCutoffGroups();
191	<	nConstraints_ += mol->getNConstraintPairs();
192	<
193	<	addExcludePairs(mol);
194	<
195	<	return true;
181	>
182	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
183	>
184	>	nAtoms_ += mol->getNAtoms();
185	>	nBonds_ += mol->getNBonds();
186	>	nBends_ += mol->getNBends();
187	>	nTorsions_ += mol->getNTorsions();
188	>	nInversions_ += mol->getNInversions();
189	>	nRigidBodies_ += mol->getNRigidBodies();
190	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
191	>	nCutoffGroups_ += mol->getNCutoffGroups();
192	>	nConstraints_ += mol->getNConstraintPairs();
193	>
194	>	addInteractionPairs(mol);
195	>
196	>	return true;
197		} else {
198	<	return false;
198	>	return false;
199		}
200	<	}
201	<
202	<	bool SimInfo::removeMolecule(Molecule* mol) {
200	>	}
201	>
202	>	bool SimInfo::removeMolecule(Molecule* mol) {
203		MoleculeIterator i;
204		i = molecules_.find(mol->getGlobalIndex());
205
206		if (i != molecules_.end() ) {
207
208	<	assert(mol == i->second);
208	>	assert(mol == i->second);
209
210	<	nAtoms_ -= mol->getNAtoms();
211	<	nBonds_ -= mol->getNBonds();
212	<	nBends_ -= mol->getNBends();
213	<	nTorsions_ -= mol->getNTorsions();
214	<	nRigidBodies_ -= mol->getNRigidBodies();
215	<	nIntegrableObjects_ -= mol->getNIntegrableObjects();
216	<	nCutoffGroups_ -= mol->getNCutoffGroups();
217	<	nConstraints_ -= mol->getNConstraintPairs();
210	>	nAtoms_ -= mol->getNAtoms();
211	>	nBonds_ -= mol->getNBonds();
212	>	nBends_ -= mol->getNBends();
213	>	nTorsions_ -= mol->getNTorsions();
214	>	nInversions_ -= mol->getNInversions();
215	>	nRigidBodies_ -= mol->getNRigidBodies();
216	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
217	>	nCutoffGroups_ -= mol->getNCutoffGroups();
218	>	nConstraints_ -= mol->getNConstraintPairs();
219
220	<	removeExcludePairs(mol);
221	<	molecules_.erase(mol->getGlobalIndex());
220	>	removeInteractionPairs(mol);
221	>	molecules_.erase(mol->getGlobalIndex());
222
223	<	delete mol;
223	>	delete mol;
224
225	<	return true;
225	>	return true;
226		} else {
227	<	return false;
227	>	return false;
228		}
229	+	}
230
220	–
221	–	}
222	–
231
232	<	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
232	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
233		i = molecules_.begin();
234		return i == molecules_.end() ? NULL : i->second;
235	<	}
235	>	}
236
237	<	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
237	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
238		++i;
239		return i == molecules_.end() ? NULL : i->second;
240	<	}
240	>	}
241
242
243	<	void SimInfo::calcNdf() {
244	<	int ndf_local;
243	>	void SimInfo::calcNdf() {
244	>	int ndf_local, nfq_local;
245		MoleculeIterator i;
246	<	std::vector<StuntDouble*>::iterator j;
246	>	vector<StuntDouble*>::iterator j;
247	>	vector<Atom*>::iterator k;
248	>
249		Molecule* mol;
250	<	StuntDouble* integrableObject;
250	>	StuntDouble* sd;
251	>	Atom* atom;
252
253		ndf_local = 0;
254	+	nfq_local = 0;
255
256		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
245	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
246	–	integrableObject = mol->nextIntegrableObject(j)) {
257
258	<	ndf_local += 3;
258	>	for (sd = mol->beginIntegrableObject(j); sd != NULL;
259	>	sd = mol->nextIntegrableObject(j)) {
260
261	<	if (integrableObject->isDirectional()) {
262	<	if (integrableObject->isLinear()) {
263	<	ndf_local += 2;
264	<	} else {
265	<	ndf_local += 3;
266	<	}
267	<	}
268	<
269	<	}//end for (integrableObject)
270	<	}// end for (mol)
261	>	ndf_local += 3;
262	>
263	>	if (sd->isDirectional()) {
264	>	if (sd->isLinear()) {
265	>	ndf_local += 2;
266	>	} else {
267	>	ndf_local += 3;
268	>	}
269	>	}
270	>	}
271	>
272	>	for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
273	>	atom = mol->nextFluctuatingCharge(k)) {
274	>	if (atom->isFluctuatingCharge()) {
275	>	nfq_local++;
276	>	}
277	>	}
278	>	}
279
280	+	ndfLocal_ = ndf_local;
281	+
282		// n_constraints is local, so subtract them on each processor
283		ndf_local -= nConstraints_;
284
285		#ifdef IS_MPI
286	<	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
286	>	MPI_Allreduce(&ndf_local, &ndf_, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
287	>	MPI_Allreduce(&nfq_local, &nGlobalFluctuatingCharges_, 1,
288	>	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
289		#else
290		ndf_ = ndf_local;
291	+	nGlobalFluctuatingCharges_ = nfq_local;
292		#endif
293
294		// nZconstraints_ is global, as are the 3 COM translations for the
295		// entire system:
296		ndf_ = ndf_ - 3 - nZconstraint_;
297
298	<	}
298	>	}
299
300	<	void SimInfo::calcNdfRaw() {
300	>	int SimInfo::getFdf() {
301	>	#ifdef IS_MPI
302	>	MPI_Allreduce(&fdf_local, &fdf_, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
303	>	#else
304	>	fdf_ = fdf_local;
305	>	#endif
306	>	return fdf_;
307	>	}
308	>
309	>	unsigned int SimInfo::getNLocalCutoffGroups(){
310	>	int nLocalCutoffAtoms = 0;
311	>	Molecule* mol;
312	>	MoleculeIterator mi;
313	>	CutoffGroup* cg;
314	>	Molecule::CutoffGroupIterator ci;
315	>
316	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
317	>
318	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
319	>	cg = mol->nextCutoffGroup(ci)) {
320	>	nLocalCutoffAtoms += cg->getNumAtom();
321	>
322	>	}
323	>	}
324	>
325	>	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
326	>	}
327	>
328	>	void SimInfo::calcNdfRaw() {
329		int ndfRaw_local;
330
331		MoleculeIterator i;
332	<	std::vector<StuntDouble*>::iterator j;
332	>	vector<StuntDouble*>::iterator j;
333		Molecule* mol;
334	<	StuntDouble* integrableObject;
334	>	StuntDouble* sd;
335
336		// Raw degrees of freedom that we have to set
337		ndfRaw_local = 0;
338
339		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
288	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
289	–	integrableObject = mol->nextIntegrableObject(j)) {
340
341	<	ndfRaw_local += 3;
341	>	for (sd = mol->beginIntegrableObject(j); sd != NULL;
342	>	sd = mol->nextIntegrableObject(j)) {
343
344	<	if (integrableObject->isDirectional()) {
345	<	if (integrableObject->isLinear()) {
346	<	ndfRaw_local += 2;
347	<	} else {
348	<	ndfRaw_local += 3;
349	<	}
350	<	}
344	>	ndfRaw_local += 3;
345	>
346	>	if (sd->isDirectional()) {
347	>	if (sd->isLinear()) {
348	>	ndfRaw_local += 2;
349	>	} else {
350	>	ndfRaw_local += 3;
351	>	}
352	>	}
353
354	<	}
354	>	}
355		}
356
357		#ifdef IS_MPI
358	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
358	>	MPI_Allreduce(&ndfRaw_local, &ndfRaw_, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
359		#else
360		ndfRaw_ = ndfRaw_local;
361		#endif
362	<	}
362	>	}
363
364	<	void SimInfo::calcNdfTrans() {
364	>	void SimInfo::calcNdfTrans() {
365		int ndfTrans_local;
366
367		ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
368
316	–
369		#ifdef IS_MPI
370	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
370	>	MPI_Allreduce(&ndfTrans_local, &ndfTrans_, 1, MPI_INT, MPI_SUM,
371	>	MPI_COMM_WORLD);
372		#else
373		ndfTrans_ = ndfTrans_local;
374		#endif
375
376		ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
377	<
325	<	}
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
713	<	/** @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	>	calcNConstraints();
714		calcNdf();
715		calcNdfRaw();
716		calcNdfTrans();
717	<
718	<	fortranInitialized_ = true;
719	<	}
720	<
721	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
717	>	}
718	>
719	>	/**
720	>	* getSimulatedAtomTypes
721	>	*
722	>	* Returns an STL set of AtomType* that are actually present in this
723	>	* simulation.  Must query all processors to assemble this information.
724	>	*
725	>	*/
726	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
727		SimInfo::MoleculeIterator mi;
728		Molecule* mol;
729		Molecule::AtomIterator ai;
730		Atom* atom;
731	<	std::set<AtomType*> atomTypes;
732	<
731	>	set<AtomType*> atomTypes;
732	>
733		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
734	+	for(atom = mol->beginAtom(ai); atom != NULL;
735	+	atom = mol->nextAtom(ai)) {
736	+	atomTypes.insert(atom->getAtomType());
737	+	}
738	+	}
739	+
740	+	#ifdef IS_MPI
741
742	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
743	<	atomTypes.insert(atom->getAtomType());
744	<	}
745	<
746	<	}
742	>	// loop over the found atom types on this processor, and add their
743	>	// numerical idents to a vector:
744	>
745	>	vector<int> foundTypes;
746	>	set<AtomType*>::iterator i;
747	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
748	>	foundTypes.push_back( (*i)->getIdent() );
749
750	<	return atomTypes;
751	<	}
750	>	// count_local holds the number of found types on this processor
751	>	int count_local = foundTypes.size();
752
753	<	void SimInfo::setupSimType() {
754	<	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();
753	>	int nproc;
754	>	MPI_Comm_size( MPI_COMM_WORLD, &nproc);
755
756	<	//loop over all of the atom types
757	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
758	<	useLennardJones |= (*i)->isLennardJones();
759	<	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	<	}
756	>	// we need arrays to hold the counts and displacement vectors for
757	>	// all processors
758	>	vector<int> counts(nproc, 0);
759	>	vector<int> disps(nproc, 0);
760
761	<	if (useSticky || useDipole || useGayBerne || useShape) {
762	<	useDirectionalAtom = 1;
761	>	// fill the counts array
762	>	MPI_Allgather(&count_local, 1, MPI_INT, &counts[0],
763	>	1, MPI_INT, MPI_COMM_WORLD);
764	>
765	>	// use the processor counts to compute the displacement array
766	>	disps[0] = 0;
767	>	int totalCount = counts[0];
768	>	for (int iproc = 1; iproc < nproc; iproc++) {
769	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
770	>	totalCount += counts[iproc];
771		}
772
773	<	if (useCharge || useDipole) {
774	<	useElectrostatics = 1;
775	<	}
773	>	// we need a (possibly redundant) set of all found types:
774	>	vector<int> ftGlobal(totalCount);
775	>
776	>	// now spray out the foundTypes to all the other processors:
777	>	MPI_Allgatherv(&foundTypes[0], count_local, MPI_INT,
778	>	&ftGlobal[0], &counts[0], &disps[0],
779	>	MPI_INT, MPI_COMM_WORLD);
780
781	<	#ifdef IS_MPI
519	<	int temp;
781	>	vector<int>::iterator j;
782
783	<	temp = usePBC;
784	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
783	>	// foundIdents is a stl set, so inserting an already found ident
784	>	// will have no effect.
785	>	set<int> foundIdents;
786
787	<	temp = useDirectionalAtom;
788	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
787	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
788	>	foundIdents.insert((*j));
789	>
790	>	// now iterate over the foundIdents and get the actual atom types
791	>	// that correspond to these:
792	>	set<int>::iterator it;
793	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
794	>	atomTypes.insert( forceField_->getAtomType((*it)) );
795	>
796	>	#endif
797
798	<	temp = useLennardJones;
799	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
798	>	return atomTypes;
799	>	}
800
530	–	temp = useElectrostatics;
531	–	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
801
802	<	temp = useCharge;
803	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
802	>	int getGlobalCountOfType(AtomType* atype) {
803	>	/*
804	>	set<AtomType*> atypes = getSimulatedAtomTypes();
805	>	map<AtomType*, int> counts_;
806
807	<	temp = useDipole;
808	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
807	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
808	>	for(atom = mol->beginAtom(ai); atom != NULL;
809	>	atom = mol->nextAtom(ai)) {
810	>	atom->getAtomType();
811	>	}
812	>	}
813	>	*/
814	>	return 0;
815	>	}
816
817	<	temp = useSticky;
818	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
817	>	void SimInfo::setupSimVariables() {
818	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
819	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole
820	>	// parameter is true
821	>	calcBoxDipole_ = false;
822	>	if ( simParams_->haveAccumulateBoxDipole() )
823	>	if ( simParams_->getAccumulateBoxDipole() ) {
824	>	calcBoxDipole_ = true;
825	>	}
826	>	// we only call setAccumulateBoxQuadrupole if the accumulateBoxQuadrupole
827	>	// parameter is true
828	>	calcBoxQuadrupole_ = false;
829	>	if ( simParams_->haveAccumulateBoxQuadrupole() )
830	>	if ( simParams_->getAccumulateBoxQuadrupole() ) {
831	>	calcBoxQuadrupole_ = true;
832	>	}
833	>
834	>	set<AtomType*>::iterator i;
835	>	set<AtomType*> atomTypes;
836	>	atomTypes = getSimulatedAtomTypes();
837	>	bool usesElectrostatic = false;
838	>	bool usesMetallic = false;
839	>	bool usesDirectional = false;
840	>	bool usesFluctuatingCharges =  false;
841	>	//loop over all of the atom types
842	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
843	>	usesElectrostatic |= (*i)->isElectrostatic();
844	>	usesMetallic |= (*i)->isMetal();
845	>	usesDirectional |= (*i)->isDirectional();
846	>	usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
847	>	}
848
849	<	temp = useGayBerne;
850	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
849	>	#ifdef IS_MPI
850	>	int temp;
851
852	<	temp = useEAM;
853	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
852	>	temp = usesDirectional;
853	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
854	>	usesDirectionalAtoms_ = (temp == 0) ? false : true;
855	>
856	>	temp = usesMetallic;
857	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
858	>	usesMetallicAtoms_ = (temp == 0) ? false : true;
859
860	<	temp = useShape;
861	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
860	>	temp = usesElectrostatic;
861	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
862	>	usesElectrostaticAtoms_ = (temp == 0) ? false : true;
863
864	<	temp = useFLARB;
865	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
864	>	temp = usesFluctuatingCharges;
865	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
866	>	usesFluctuatingCharges_ = (temp == 0) ? false : true;
867	>	#else
868
869	<	temp = useRF;
870	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
871	<
869	>	usesDirectionalAtoms_ = usesDirectional;
870	>	usesMetallicAtoms_ = usesMetallic;
871	>	usesElectrostaticAtoms_ = usesElectrostatic;
872	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
873	>
874		#endif
875	+
876	+	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
877	+	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
878	+	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
879	+	}
880
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;
881
882	<	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
882	>	vector<int> SimInfo::getGlobalAtomIndices() {
883	>	SimInfo::MoleculeIterator mi;
884	>	Molecule* mol;
885	>	Molecule::AtomIterator ai;
886	>	Atom* atom;
887
888	<	if (simParams_->haveDielectric()) {
889	<	fInfo_.dielect = simParams_->getDielectric();
890	<	} else {
891	<	sprintf(painCave.errMsg,
892	<	"SimSetup Error: No Dielectric constant was set.\n"
893	<	"\tYou are trying to use Reaction Field without"
894	<	"\tsetting a dielectric constant!\n");
581	<	painCave.isFatal = 1;
582	<	simError();
583	<	}
584	<
585	<	} else {
586	<	fInfo_.dielect = 0.0;
888	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
889	>
890	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
891	>
892	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
893	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
894	>	}
895		}
896	+	return GlobalAtomIndices;
897	+	}
898
589	–	}
899
900	<	void SimInfo::setupFortranSim() {
901	<	int isError;
902	<	int nExclude;
903	<	std::vector<int> fortranGlobalGroupMembership;
904	<
596	<	nExclude = exclude_.getSize();
597	<	isError = 0;
900	>	vector<int> SimInfo::getGlobalGroupIndices() {
901	>	SimInfo::MoleculeIterator mi;
902	>	Molecule* mol;
903	>	Molecule::CutoffGroupIterator ci;
904	>	CutoffGroup* cg;
905
906	<	//globalGroupMembership_ is filled by SimCreator
907	<	for (int i = 0; i < nGlobalAtoms_; i++) {
908	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
906	>	vector<int> GlobalGroupIndices;
907	>
908	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
909	>
910	>	//local index of cutoff group is trivial, it only depends on the
911	>	//order of travesing
912	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
913	>	cg = mol->nextCutoffGroup(ci)) {
914	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
915	>	}
916		}
917	+	return GlobalGroupIndices;
918	+	}
919
920	+
921	+	void SimInfo::prepareTopology() {
922	+
923		//calculate mass ratio of cutoff group
605	–	std::vector<double> mfact;
924		SimInfo::MoleculeIterator mi;
925		Molecule* mol;
926		Molecule::CutoffGroupIterator ci;
927		CutoffGroup* cg;
928		Molecule::AtomIterator ai;
929		Atom* atom;
930	<	double totalMass;
930	>	RealType totalMass;
931
932	<	//to avoid memory reallocation, reserve enough space for mfact
933	<	mfact.reserve(getNCutoffGroups());
932	>	/**
933	>	* The mass factor is the relative mass of an atom to the total
934	>	* mass of the cutoff group it belongs to.  By default, all atoms
935	>	* are their own cutoff groups, and therefore have mass factors of
936	>	* 1.  We need some special handling for massless atoms, which
937	>	* will be treated as carrying the entire mass of the cutoff
938	>	* group.
939	>	*/
940	>	massFactors_.clear();
941	>	massFactors_.resize(getNAtoms(), 1.0);
942
943		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
944	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
944	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
945	>	cg = mol->nextCutoffGroup(ci)) {
946
947	<	totalMass = cg->getMass();
948	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
949	<	mfact.push_back(atom->getMass()/totalMass);
950	<	}
951	<
952	<	}
947	>	totalMass = cg->getMass();
948	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
949	>	// Check for massless groups - set mfact to 1 if true
950	>	if (totalMass != 0)
951	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
952	>	else
953	>	massFactors_[atom->getLocalIndex()] = 1.0;
954	>	}
955	>	}
956		}
957
958	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
629	<	std::vector<int> identArray;
958	>	// Build the identArray_ and regions_
959
960	<	//to avoid memory reallocation, reserve enough space identArray
961	<	identArray.reserve(getNAtoms());
962	<
963	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
964	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
965	<	identArray.push_back(atom->getIdent());
966	<	}
960	>	identArray_.clear();
961	>	identArray_.reserve(getNAtoms());
962	>	regions_.clear();
963	>	regions_.reserve(getNAtoms());
964	>
965	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
966	>	int reg = mol->getRegion();
967	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
968	>	identArray_.push_back(atom->getIdent());
969	>	regions_.push_back(reg);
970	>	}
971		}
972	+
973	+	topologyDone_ = true;
974	+	}
975
976	<	//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) {
976	>	void SimInfo::addProperty(GenericData* genData) {
977		properties_.addProperty(genData);
978	<	}
978	>	}
979
980	<	void SimInfo::removeProperty(const std::string& propName) {
980	>	void SimInfo::removeProperty(const string& propName) {
981		properties_.removeProperty(propName);
982	<	}
982	>	}
983
984	<	void SimInfo::clearProperties() {
984	>	void SimInfo::clearProperties() {
985		properties_.clearProperties();
986	<	}
986	>	}
987
988	<	std::vector<std::string> SimInfo::getPropertyNames() {
988	>	vector<string> SimInfo::getPropertyNames() {
989		return properties_.getPropertyNames();
990	<	}
990	>	}
991
992	<	std::vector<GenericData*> SimInfo::getProperties() {
992	>	vector<GenericData*> SimInfo::getProperties() {
993		return properties_.getProperties();
994	<	}
994	>	}
995
996	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
996	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
997		return properties_.getPropertyByName(propName);
998	<	}
998	>	}
999
1000	<	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1000	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1001	>	if (sman_ == sman) {
1002	>	return;
1003	>	}
1004	>	delete sman_;
1005		sman_ = sman;
1006
840	–	Molecule* mol;
841	–	RigidBody* rb;
842	–	Atom* atom;
1007		SimInfo::MoleculeIterator mi;
1008	+	Molecule::AtomIterator ai;
1009		Molecule::RigidBodyIterator rbIter;
1010	<	Molecule::AtomIterator atomIter;;
1010	>	Molecule::CutoffGroupIterator cgIter;
1011	>	Molecule::BondIterator bondIter;
1012	>	Molecule::BendIterator bendIter;
1013	>	Molecule::TorsionIterator torsionIter;
1014	>	Molecule::InversionIterator inversionIter;
1015
1016	+	Molecule* mol;
1017	+	Atom* atom;
1018	+	RigidBody* rb;
1019	+	CutoffGroup* cg;
1020	+	Bond* bond;
1021	+	Bend* bend;
1022	+	Torsion* torsion;
1023	+	Inversion* inversion;
1024	+
1025		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1026
1027	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1028	<	atom->setSnapshotManager(sman_);
1029	<	}
1030	<
1031	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1032	<	rb->setSnapshotManager(sman_);
1033	<	}
1034	<	}
1035	<
1036	<	}
1027	>	for (atom = mol->beginAtom(ai); atom != NULL;
1028	>	atom = mol->nextAtom(ai)) {
1029	>	atom->setSnapshotManager(sman_);
1030	>	}
1031	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
1032	>	rb = mol->nextRigidBody(rbIter)) {
1033	>	rb->setSnapshotManager(sman_);
1034	>	}
1035	>	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL;
1036	>	cg = mol->nextCutoffGroup(cgIter)) {
1037	>	cg->setSnapshotManager(sman_);
1038	>	}
1039	>	for (bond = mol->beginBond(bondIter); bond != NULL;
1040	>	bond = mol->nextBond(bondIter)) {
1041	>	bond->setSnapshotManager(sman_);
1042	>	}
1043	>	for (bend = mol->beginBend(bendIter); bend != NULL;
1044	>	bend = mol->nextBend(bendIter)) {
1045	>	bend->setSnapshotManager(sman_);
1046	>	}
1047	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
1048	>	torsion = mol->nextTorsion(torsionIter)) {
1049	>	torsion->setSnapshotManager(sman_);
1050	>	}
1051	>	for (inversion = mol->beginInversion(inversionIter); inversion != NULL;
1052	>	inversion = mol->nextInversion(inversionIter)) {
1053	>	inversion->setSnapshotManager(sman_);
1054	>	}
1055	>	}
1056	>	}
1057
860	–	Vector3d SimInfo::getComVel(){
861	–	SimInfo::MoleculeIterator i;
862	–	Molecule* mol;
1058
1059	<	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	<	}
1059	>	ostream& operator <<(ostream& o, SimInfo& info) {
1060
1061	<	#ifdef IS_MPI
1062	<	double tmpMass = totalMass;
1063	<	Vector3d tmpComVel(comVel);
1064	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1065	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1066	<	#endif
1061	>	return o;
1062	>	}
1063	>
1064	>
1065	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1066	>	if (index >= int(IOIndexToIntegrableObject.size())) {
1067	>	sprintf(painCave.errMsg,
1068	>	"SimInfo::getIOIndexToIntegrableObject Error: Integrable Object\n"
1069	>	"\tindex exceeds number of known objects!\n");
1070	>	painCave.isFatal = 1;
1071	>	simError();
1072	>	return NULL;
1073	>	} else
1074	>	return IOIndexToIntegrableObject.at(index);
1075	>	}
1076	>
1077	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1078	>	IOIndexToIntegrableObject= v;
1079	>	}
1080
1081	<	comVel /= totalMass;
882	<
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	<
1081	>	void SimInfo::calcNConstraints() {
1082		#ifdef IS_MPI
1083	<	double tmpMass = totalMass;
1084	<	Vector3d tmpCom(com);
1085	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1086	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1083	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints_, 1,
1084	>	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
1085	>	#else
1086	>	nGlobalConstraints_ =  nConstraints_;
1087		#endif
1088	+	}
1089
1090	<	com /= totalMass;
1090	>	}//end namespace OpenMD
1091
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 2071 by gezelter, Sat Mar 7 21:41:51 2015 UTC

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