ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

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 1969 by gezelter, Wed Feb 26 14:14:50 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),
76	<	sman_(NULL), fortranInitialized_(false), selectMan_(NULL) {
77	<
78	<
79	<	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
68	>	using namespace std;
69	>	namespace OpenMD {
70	>
71	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
72	>	forceField_(ff), simParams_(simParams),
73	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
74	>	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
75	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
76	>	nGlobalFluctuatingCharges_(0), nGlobalBonds_(0), nGlobalBends_(0),
77	>	nGlobalTorsions_(0), nGlobalInversions_(0), nAtoms_(0), nBonds_(0),
78	>	nBends_(0), nTorsions_(0), nInversions_(0), nRigidBodies_(0),
79	>	nIntegrableObjects_(0), nCutoffGroups_(0), nConstraints_(0),
80	>	nFluctuatingCharges_(0), sman_(NULL), topologyDone_(false),
81	>	calcBoxDipole_(false), useAtomicVirial_(true) {
82	>
83		MoleculeStamp* molStamp;
84		int nMolWithSameStamp;
85		int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
86	<	int nGroups = 0;          //total cutoff groups defined in meta-data file
86	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
87		CutoffGroupStamp* cgStamp;
88		RigidBodyStamp* rbStamp;
89		int nRigidAtoms = 0;
90
91	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
92	<	molStamp = i->first;
93	<	nMolWithSameStamp = i->second;
94	<
95	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
91	>	vector<Component*> components = simParams->getComponents();
92	>
93	>	for (vector<Component*>::iterator i = components.begin();
94	>	i !=components.end(); ++i) {
95	>	molStamp = (*i)->getMoleculeStamp();
96	>	if ( (*i)->haveRegion() ) {
97	>	molStamp->setRegion( (*i)->getRegion() );
98	>	} else {
99	>	// set the region to a disallowed value:
100	>	molStamp->setRegion( -1 );
101	>	}
102
103	<	//calculate atoms in molecules
104	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
105	<
106	<
107	<	//calculate atoms in cutoff groups
108	<	int nAtomsInGroups = 0;
109	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
110	<
111	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
112	<	cgStamp = molStamp->getCutoffGroup(j);
113	<	nAtomsInGroups += cgStamp->getNMembers();
114	<	}
115	<
116	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
117	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
118	<
119	<	//calculate atoms in rigid bodies
120	<	int nAtomsInRigidBodies = 0;
121	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
122	<
123	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
124	<	rbStamp = molStamp->getRigidBody(j);
125	<	nAtomsInRigidBodies += rbStamp->getNMembers();
126	<	}
127	<
128	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
129	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
130	<
103	>	nMolWithSameStamp = (*i)->getNMol();
104	>
105	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
106	>
107	>	//calculate atoms in molecules
108	>	nGlobalAtoms_ += molStamp->getNAtoms() * nMolWithSameStamp;
109	>	nGlobalBonds_ += molStamp->getNBonds() * nMolWithSameStamp;
110	>	nGlobalBends_ += molStamp->getNBends() * nMolWithSameStamp;
111	>	nGlobalTorsions_ += molStamp->getNTorsions() * nMolWithSameStamp;
112	>	nGlobalInversions_ += molStamp->getNInversions() * nMolWithSameStamp;
113	>
114	>	//calculate atoms in cutoff groups
115	>	int nAtomsInGroups = 0;
116	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
117	>
118	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
119	>	cgStamp = molStamp->getCutoffGroupStamp(j);
120	>	nAtomsInGroups += cgStamp->getNMembers();
121	>	}
122	>
123	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
124	>
125	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
126	>
127	>	//calculate atoms in rigid bodies
128	>	int nAtomsInRigidBodies = 0;
129	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
130	>
131	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
132	>	rbStamp = molStamp->getRigidBodyStamp(j);
133	>	nAtomsInRigidBodies += rbStamp->getNMembers();
134	>	}
135	>
136	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
137	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
138	>
139		}
140	+
141	+	//every free atom (atom does not belong to cutoff groups) is a cutoff
142	+	//group therefore the total number of cutoff groups in the system is
143	+	//equal to the total number of atoms minus number of atoms belong to
144	+	//cutoff group defined in meta-data file plus the number of cutoff
145	+	//groups defined in meta-data file
146
124	–	//every free atom (atom does not belong to cutoff groups) is a cutoff group
125	–	//therefore the total number of cutoff groups in the system is equal to
126	–	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
127	–	//file plus the number of cutoff groups defined in meta-data file
147		nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
148	<
149	<	//every free atom (atom does not belong to rigid bodies) is an integrable object
150	<	//therefore the total number of  integrable objects in the system is equal to
151	<	//the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
152	<	//file plus the number of  rigid bodies defined in meta-data file
153	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
154	<
148	>
149	>	//every free atom (atom does not belong to rigid bodies) is an
150	>	//integrable object therefore the total number of integrable objects
151	>	//in the system is equal to the total number of atoms minus number of
152	>	//atoms belong to rigid body defined in meta-data file plus the number
153	>	//of rigid bodies defined in meta-data file
154	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
155	>	+ nGlobalRigidBodies_;
156	>
157		nGlobalMols_ = molStampIds_.size();
137	–
138	–	#ifdef IS_MPI
158		molToProcMap_.resize(nGlobalMols_);
159	<	#endif
160	<
161	<	selectMan_ = new SelectionManager(this);
162	<	selectMan_->selectAll();
163	<	}
164	<
165	<	SimInfo::~SimInfo() {
166	<	//MemoryUtils::deleteVectorOfPointer(molecules_);
167	<
149	<	MemoryUtils::deleteVectorOfPointer(moleculeStamps_);
150	<
159	>	}
160	>
161	>	SimInfo::~SimInfo() {
162	>	map<int, Molecule*>::iterator i;
163	>	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
164	>	delete i->second;
165	>	}
166	>	molecules_.clear();
167	>
168		delete sman_;
169		delete simParams_;
170		delete forceField_;
171	<	delete selectMan_;
155	<	}
171	>	}
172
157	–	int SimInfo::getNGlobalConstraints() {
158	–	int nGlobalConstraints;
159	–	#ifdef IS_MPI
160	–	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
161	–	MPI_COMM_WORLD);
162	–	#else
163	–	nGlobalConstraints =  nConstraints_;
164	–	#endif
165	–	return nGlobalConstraints;
166	–	}
173
174	<	bool SimInfo::addMolecule(Molecule* mol) {
174	>	bool SimInfo::addMolecule(Molecule* mol) {
175		MoleculeIterator i;
176	<
176	>
177		i = molecules_.find(mol->getGlobalIndex());
178		if (i == molecules_.end() ) {
179	<
180	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
181	<
182	<	nAtoms_ += mol->getNAtoms();
183	<	nBonds_ += mol->getNBonds();
184	<	nBends_ += mol->getNBends();
185	<	nTorsions_ += mol->getNTorsions();
186	<	nRigidBodies_ += mol->getNRigidBodies();
187	<	nIntegrableObjects_ += mol->getNIntegrableObjects();
188	<	nCutoffGroups_ += mol->getNCutoffGroups();
189	<	nConstraints_ += mol->getNConstraintPairs();
190	<
191	<	addExcludePairs(mol);
192	<
193	<	return true;
179	>
180	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
181	>
182	>	nAtoms_ += mol->getNAtoms();
183	>	nBonds_ += mol->getNBonds();
184	>	nBends_ += mol->getNBends();
185	>	nTorsions_ += mol->getNTorsions();
186	>	nInversions_ += mol->getNInversions();
187	>	nRigidBodies_ += mol->getNRigidBodies();
188	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
189	>	nCutoffGroups_ += mol->getNCutoffGroups();
190	>	nConstraints_ += mol->getNConstraintPairs();
191	>
192	>	addInteractionPairs(mol);
193	>
194	>	return true;
195		} else {
196	<	return false;
196	>	return false;
197		}
198	<	}
199	<
200	<	bool SimInfo::removeMolecule(Molecule* mol) {
198	>	}
199	>
200	>	bool SimInfo::removeMolecule(Molecule* mol) {
201		MoleculeIterator i;
202		i = molecules_.find(mol->getGlobalIndex());
203
204		if (i != molecules_.end() ) {
205
206	<	assert(mol == i->second);
206	>	assert(mol == i->second);
207
208	<	nAtoms_ -= mol->getNAtoms();
209	<	nBonds_ -= mol->getNBonds();
210	<	nBends_ -= mol->getNBends();
211	<	nTorsions_ -= mol->getNTorsions();
212	<	nRigidBodies_ -= mol->getNRigidBodies();
213	<	nIntegrableObjects_ -= mol->getNIntegrableObjects();
214	<	nCutoffGroups_ -= mol->getNCutoffGroups();
215	<	nConstraints_ -= mol->getNConstraintPairs();
208	>	nAtoms_ -= mol->getNAtoms();
209	>	nBonds_ -= mol->getNBonds();
210	>	nBends_ -= mol->getNBends();
211	>	nTorsions_ -= mol->getNTorsions();
212	>	nInversions_ -= mol->getNInversions();
213	>	nRigidBodies_ -= mol->getNRigidBodies();
214	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
215	>	nCutoffGroups_ -= mol->getNCutoffGroups();
216	>	nConstraints_ -= mol->getNConstraintPairs();
217
218	<	removeExcludePairs(mol);
219	<	molecules_.erase(mol->getGlobalIndex());
218	>	removeInteractionPairs(mol);
219	>	molecules_.erase(mol->getGlobalIndex());
220
221	<	delete mol;
221	>	delete mol;
222
223	<	return true;
223	>	return true;
224		} else {
225	<	return false;
225	>	return false;
226		}
227	+	}
228
220	–
221	–	}
222	–
229
230	<	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
230	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
231		i = molecules_.begin();
232		return i == molecules_.end() ? NULL : i->second;
233	<	}
233	>	}
234
235	<	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
235	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
236		++i;
237		return i == molecules_.end() ? NULL : i->second;
238	<	}
238	>	}
239
240
241	<	void SimInfo::calcNdf() {
242	<	int ndf_local;
241	>	void SimInfo::calcNdf() {
242	>	int ndf_local, nfq_local;
243		MoleculeIterator i;
244	<	std::vector<StuntDouble*>::iterator j;
244	>	vector<StuntDouble*>::iterator j;
245	>	vector<Atom*>::iterator k;
246	>
247		Molecule* mol;
248	<	StuntDouble* integrableObject;
248	>	StuntDouble* sd;
249	>	Atom* atom;
250
251		ndf_local = 0;
252	+	nfq_local = 0;
253
254		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
245	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
246	–	integrableObject = mol->nextIntegrableObject(j)) {
255
256	<	ndf_local += 3;
256	>	for (sd = mol->beginIntegrableObject(j); sd != NULL;
257	>	sd = mol->nextIntegrableObject(j)) {
258
259	<	if (integrableObject->isDirectional()) {
260	<	if (integrableObject->isLinear()) {
261	<	ndf_local += 2;
262	<	} else {
263	<	ndf_local += 3;
264	<	}
265	<	}
266	<
267	<	}//end for (integrableObject)
268	<	}// end for (mol)
259	>	ndf_local += 3;
260	>
261	>	if (sd->isDirectional()) {
262	>	if (sd->isLinear()) {
263	>	ndf_local += 2;
264	>	} else {
265	>	ndf_local += 3;
266	>	}
267	>	}
268	>	}
269	>
270	>	for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
271	>	atom = mol->nextFluctuatingCharge(k)) {
272	>	if (atom->isFluctuatingCharge()) {
273	>	nfq_local++;
274	>	}
275	>	}
276	>	}
277
278	+	ndfLocal_ = ndf_local;
279	+
280		// n_constraints is local, so subtract them on each processor
281		ndf_local -= nConstraints_;
282
283		#ifdef IS_MPI
284	<	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
284	>	MPI_Allreduce(&ndf_local, &ndf_, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
285	>	MPI_Allreduce(&nfq_local, &nGlobalFluctuatingCharges_, 1,
286	>	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
287	>	// MPI::COMM_WORLD.Allreduce(&ndf_local, &ndf_, 1, MPI::INT,MPI::SUM);
288	>	// MPI::COMM_WORLD.Allreduce(&nfq_local, &nGlobalFluctuatingCharges_, 1,
289	>	//                           MPI::INT, MPI::SUM);
290		#else
291		ndf_ = ndf_local;
292	+	nGlobalFluctuatingCharges_ = nfq_local;
293		#endif
294
295		// nZconstraints_ is global, as are the 3 COM translations for the
296		// entire system:
297		ndf_ = ndf_ - 3 - nZconstraint_;
298
299	<	}
299	>	}
300
301	<	void SimInfo::calcNdfRaw() {
301	>	int SimInfo::getFdf() {
302	>	#ifdef IS_MPI
303	>	MPI_Allreduce(&fdf_local, &fdf_, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
304	>	// MPI::COMM_WORLD.Allreduce(&fdf_local, &fdf_, 1, MPI::INT, MPI::SUM);
305	>	#else
306	>	fdf_ = fdf_local;
307	>	#endif
308	>	return fdf_;
309	>	}
310	>
311	>	unsigned int SimInfo::getNLocalCutoffGroups(){
312	>	int nLocalCutoffAtoms = 0;
313	>	Molecule* mol;
314	>	MoleculeIterator mi;
315	>	CutoffGroup* cg;
316	>	Molecule::CutoffGroupIterator ci;
317	>
318	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
319	>
320	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
321	>	cg = mol->nextCutoffGroup(ci)) {
322	>	nLocalCutoffAtoms += cg->getNumAtom();
323	>
324	>	}
325	>	}
326	>
327	>	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
328	>	}
329	>
330	>	void SimInfo::calcNdfRaw() {
331		int ndfRaw_local;
332
333		MoleculeIterator i;
334	<	std::vector<StuntDouble*>::iterator j;
334	>	vector<StuntDouble*>::iterator j;
335		Molecule* mol;
336	<	StuntDouble* integrableObject;
336	>	StuntDouble* sd;
337
338		// Raw degrees of freedom that we have to set
339		ndfRaw_local = 0;
340
341		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
288	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
289	–	integrableObject = mol->nextIntegrableObject(j)) {
342
343	<	ndfRaw_local += 3;
343	>	for (sd = mol->beginIntegrableObject(j); sd != NULL;
344	>	sd = mol->nextIntegrableObject(j)) {
345
346	<	if (integrableObject->isDirectional()) {
347	<	if (integrableObject->isLinear()) {
348	<	ndfRaw_local += 2;
349	<	} else {
350	<	ndfRaw_local += 3;
351	<	}
352	<	}
346	>	ndfRaw_local += 3;
347	>
348	>	if (sd->isDirectional()) {
349	>	if (sd->isLinear()) {
350	>	ndfRaw_local += 2;
351	>	} else {
352	>	ndfRaw_local += 3;
353	>	}
354	>	}
355
356	<	}
356	>	}
357		}
358
359		#ifdef IS_MPI
360	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
360	>	MPI_Allreduce(&ndfRaw_local, &ndfRaw_, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
361	>	// MPI::COMM_WORLD.Allreduce(&ndfRaw_local, &ndfRaw_, 1, MPI::INT, MPI::SUM);
362		#else
363		ndfRaw_ = ndfRaw_local;
364		#endif
365	<	}
365	>	}
366
367	<	void SimInfo::calcNdfTrans() {
367	>	void SimInfo::calcNdfTrans() {
368		int ndfTrans_local;
369
370		ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
371
372
373		#ifdef IS_MPI
374	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
374	>	MPI_Allreduce(&ndfTrans_local, &ndfTrans_, 1,
375	>	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
376	>	// MPI::COMM_WORLD.Allreduce(&ndfTrans_local, &ndfTrans_, 1,
377	>	//                           MPI::INT, MPI::SUM);
378		#else
379		ndfTrans_ = ndfTrans_local;
380		#endif
381
382		ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
383
384	<	}
384	>	}
385
386	<	void SimInfo::addExcludePairs(Molecule* mol) {
387	<	std::vector<Bond*>::iterator bondIter;
388	<	std::vector<Bend*>::iterator bendIter;
389	<	std::vector<Torsion*>::iterator torsionIter;
386	>	void SimInfo::addInteractionPairs(Molecule* mol) {
387	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
388	>	vector<Bond*>::iterator bondIter;
389	>	vector<Bend*>::iterator bendIter;
390	>	vector<Torsion*>::iterator torsionIter;
391	>	vector<Inversion*>::iterator inversionIter;
392		Bond* bond;
393		Bend* bend;
394		Torsion* torsion;
395	+	Inversion* inversion;
396		int a;
397		int b;
398		int c;
399		int d;
400	+
401	+	// atomGroups can be used to add special interaction maps between
402	+	// groups of atoms that are in two separate rigid bodies.
403	+	// However, most site-site interactions between two rigid bodies
404	+	// are probably not special, just the ones between the physically
405	+	// bonded atoms.  Interactions *within* a single rigid body should
406	+	// always be excluded.  These are done at the bottom of this
407	+	// function.
408	+
409	+	map<int, set<int> > atomGroups;
410	+	Molecule::RigidBodyIterator rbIter;
411	+	RigidBody* rb;
412	+	Molecule::IntegrableObjectIterator ii;
413	+	StuntDouble* sd;
414
415	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
416	<	a = bond->getAtomA()->getGlobalIndex();
417	<	b = bond->getAtomB()->getGlobalIndex();
418	<	exclude_.addPair(a, b);
415	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
416	>	sd = mol->nextIntegrableObject(ii)) {
417	>
418	>	if (sd->isRigidBody()) {
419	>	rb = static_cast<RigidBody*>(sd);
420	>	vector<Atom*> atoms = rb->getAtoms();
421	>	set<int> rigidAtoms;
422	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
423	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
424	>	}
425	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
426	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
427	>	}
428	>	} else {
429	>	set<int> oneAtomSet;
430	>	oneAtomSet.insert(sd->getGlobalIndex());
431	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
432	>	}
433	>	}
434	>
435	>
436	>	for (bond= mol->beginBond(bondIter); bond != NULL;
437	>	bond = mol->nextBond(bondIter)) {
438	>
439	>	a = bond->getAtomA()->getGlobalIndex();
440	>	b = bond->getAtomB()->getGlobalIndex();
441	>
442	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
443	>	oneTwoInteractions_.addPair(a, b);
444	>	} else {
445	>	excludedInteractions_.addPair(a, b);
446	>	}
447		}
448
449	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
450	<	a = bend->getAtomA()->getGlobalIndex();
347	<	b = bend->getAtomB()->getGlobalIndex();
348	<	c = bend->getAtomC()->getGlobalIndex();
449	>	for (bend= mol->beginBend(bendIter); bend != NULL;
450	>	bend = mol->nextBend(bendIter)) {
451
452	<	exclude_.addPair(a, b);
453	<	exclude_.addPair(a, c);
454	<	exclude_.addPair(b, c);
452	>	a = bend->getAtomA()->getGlobalIndex();
453	>	b = bend->getAtomB()->getGlobalIndex();
454	>	c = bend->getAtomC()->getGlobalIndex();
455	>
456	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
457	>	oneTwoInteractions_.addPair(a, b);
458	>	oneTwoInteractions_.addPair(b, c);
459	>	} else {
460	>	excludedInteractions_.addPair(a, b);
461	>	excludedInteractions_.addPair(b, c);
462	>	}
463	>
464	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
465	>	oneThreeInteractions_.addPair(a, c);
466	>	} else {
467	>	excludedInteractions_.addPair(a, c);
468	>	}
469		}
470
471	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
472	<	a = torsion->getAtomA()->getGlobalIndex();
357	<	b = torsion->getAtomB()->getGlobalIndex();
358	<	c = torsion->getAtomC()->getGlobalIndex();
359	<	d = torsion->getAtomD()->getGlobalIndex();
471	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
472	>	torsion = mol->nextTorsion(torsionIter)) {
473
474	<	exclude_.addPair(a, b);
475	<	exclude_.addPair(a, c);
476	<	exclude_.addPair(a, d);
477	<	exclude_.addPair(b, c);
478	<	exclude_.addPair(b, d);
479	<	exclude_.addPair(c, d);
474	>	a = torsion->getAtomA()->getGlobalIndex();
475	>	b = torsion->getAtomB()->getGlobalIndex();
476	>	c = torsion->getAtomC()->getGlobalIndex();
477	>	d = torsion->getAtomD()->getGlobalIndex();
478	>
479	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
480	>	oneTwoInteractions_.addPair(a, b);
481	>	oneTwoInteractions_.addPair(b, c);
482	>	oneTwoInteractions_.addPair(c, d);
483	>	} else {
484	>	excludedInteractions_.addPair(a, b);
485	>	excludedInteractions_.addPair(b, c);
486	>	excludedInteractions_.addPair(c, d);
487	>	}
488	>
489	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
490	>	oneThreeInteractions_.addPair(a, c);
491	>	oneThreeInteractions_.addPair(b, d);
492	>	} else {
493	>	excludedInteractions_.addPair(a, c);
494	>	excludedInteractions_.addPair(b, d);
495	>	}
496	>
497	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
498	>	oneFourInteractions_.addPair(a, d);
499	>	} else {
500	>	excludedInteractions_.addPair(a, d);
501	>	}
502		}
503
504	<
505	<	}
504	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
505	>	inversion = mol->nextInversion(inversionIter)) {
506
507	<	void SimInfo::removeExcludePairs(Molecule* mol) {
508	<	std::vector<Bond*>::iterator bondIter;
509	<	std::vector<Bend*>::iterator bendIter;
510	<	std::vector<Torsion*>::iterator torsionIter;
507	>	a = inversion->getAtomA()->getGlobalIndex();
508	>	b = inversion->getAtomB()->getGlobalIndex();
509	>	c = inversion->getAtomC()->getGlobalIndex();
510	>	d = inversion->getAtomD()->getGlobalIndex();
511	>
512	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
513	>	oneTwoInteractions_.addPair(a, b);
514	>	oneTwoInteractions_.addPair(a, c);
515	>	oneTwoInteractions_.addPair(a, d);
516	>	} else {
517	>	excludedInteractions_.addPair(a, b);
518	>	excludedInteractions_.addPair(a, c);
519	>	excludedInteractions_.addPair(a, d);
520	>	}
521	>
522	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
523	>	oneThreeInteractions_.addPair(b, c);
524	>	oneThreeInteractions_.addPair(b, d);
525	>	oneThreeInteractions_.addPair(c, d);
526	>	} else {
527	>	excludedInteractions_.addPair(b, c);
528	>	excludedInteractions_.addPair(b, d);
529	>	excludedInteractions_.addPair(c, d);
530	>	}
531	>	}
532	>
533	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
534	>	rb = mol->nextRigidBody(rbIter)) {
535	>	vector<Atom*> atoms = rb->getAtoms();
536	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
537	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
538	>	a = atoms[i]->getGlobalIndex();
539	>	b = atoms[j]->getGlobalIndex();
540	>	excludedInteractions_.addPair(a, b);
541	>	}
542	>	}
543	>	}
544	>
545	>	}
546	>
547	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
548	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
549	>	vector<Bond*>::iterator bondIter;
550	>	vector<Bend*>::iterator bendIter;
551	>	vector<Torsion*>::iterator torsionIter;
552	>	vector<Inversion*>::iterator inversionIter;
553		Bond* bond;
554		Bend* bend;
555		Torsion* torsion;
556	+	Inversion* inversion;
557		int a;
558		int b;
559		int c;
560		int d;
561	+
562	+	map<int, set<int> > atomGroups;
563	+	Molecule::RigidBodyIterator rbIter;
564	+	RigidBody* rb;
565	+	Molecule::IntegrableObjectIterator ii;
566	+	StuntDouble* sd;
567
568	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
569	<	a = bond->getAtomA()->getGlobalIndex();
570	<	b = bond->getAtomB()->getGlobalIndex();
571	<	exclude_.removePair(a, b);
568	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
569	>	sd = mol->nextIntegrableObject(ii)) {
570	>
571	>	if (sd->isRigidBody()) {
572	>	rb = static_cast<RigidBody*>(sd);
573	>	vector<Atom*> atoms = rb->getAtoms();
574	>	set<int> rigidAtoms;
575	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
576	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
577	>	}
578	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
579	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
580	>	}
581	>	} else {
582	>	set<int> oneAtomSet;
583	>	oneAtomSet.insert(sd->getGlobalIndex());
584	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
585	>	}
586	>	}
587	>
588	>	for (bond= mol->beginBond(bondIter); bond != NULL;
589	>	bond = mol->nextBond(bondIter)) {
590	>
591	>	a = bond->getAtomA()->getGlobalIndex();
592	>	b = bond->getAtomB()->getGlobalIndex();
593	>
594	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
595	>	oneTwoInteractions_.removePair(a, b);
596	>	} else {
597	>	excludedInteractions_.removePair(a, b);
598	>	}
599		}
600
601	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
602	<	a = bend->getAtomA()->getGlobalIndex();
392	<	b = bend->getAtomB()->getGlobalIndex();
393	<	c = bend->getAtomC()->getGlobalIndex();
601	>	for (bend= mol->beginBend(bendIter); bend != NULL;
602	>	bend = mol->nextBend(bendIter)) {
603
604	<	exclude_.removePair(a, b);
605	<	exclude_.removePair(a, c);
606	<	exclude_.removePair(b, c);
604	>	a = bend->getAtomA()->getGlobalIndex();
605	>	b = bend->getAtomB()->getGlobalIndex();
606	>	c = bend->getAtomC()->getGlobalIndex();
607	>
608	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
609	>	oneTwoInteractions_.removePair(a, b);
610	>	oneTwoInteractions_.removePair(b, c);
611	>	} else {
612	>	excludedInteractions_.removePair(a, b);
613	>	excludedInteractions_.removePair(b, c);
614	>	}
615	>
616	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
617	>	oneThreeInteractions_.removePair(a, c);
618	>	} else {
619	>	excludedInteractions_.removePair(a, c);
620	>	}
621		}
622
623	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
624	<	a = torsion->getAtomA()->getGlobalIndex();
402	<	b = torsion->getAtomB()->getGlobalIndex();
403	<	c = torsion->getAtomC()->getGlobalIndex();
404	<	d = torsion->getAtomD()->getGlobalIndex();
623	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
624	>	torsion = mol->nextTorsion(torsionIter)) {
625
626	<	exclude_.removePair(a, b);
627	<	exclude_.removePair(a, c);
628	<	exclude_.removePair(a, d);
629	<	exclude_.removePair(b, c);
630	<	exclude_.removePair(b, d);
631	<	exclude_.removePair(c, d);
626	>	a = torsion->getAtomA()->getGlobalIndex();
627	>	b = torsion->getAtomB()->getGlobalIndex();
628	>	c = torsion->getAtomC()->getGlobalIndex();
629	>	d = torsion->getAtomD()->getGlobalIndex();
630	>
631	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
632	>	oneTwoInteractions_.removePair(a, b);
633	>	oneTwoInteractions_.removePair(b, c);
634	>	oneTwoInteractions_.removePair(c, d);
635	>	} else {
636	>	excludedInteractions_.removePair(a, b);
637	>	excludedInteractions_.removePair(b, c);
638	>	excludedInteractions_.removePair(c, d);
639	>	}
640	>
641	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
642	>	oneThreeInteractions_.removePair(a, c);
643	>	oneThreeInteractions_.removePair(b, d);
644	>	} else {
645	>	excludedInteractions_.removePair(a, c);
646	>	excludedInteractions_.removePair(b, d);
647	>	}
648	>
649	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
650	>	oneFourInteractions_.removePair(a, d);
651	>	} else {
652	>	excludedInteractions_.removePair(a, d);
653	>	}
654		}
655
656	<	}
656	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
657	>	inversion = mol->nextInversion(inversionIter)) {
658
659	+	a = inversion->getAtomA()->getGlobalIndex();
660	+	b = inversion->getAtomB()->getGlobalIndex();
661	+	c = inversion->getAtomC()->getGlobalIndex();
662	+	d = inversion->getAtomD()->getGlobalIndex();
663
664	<	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
665	<	int curStampId;
664	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
665	>	oneTwoInteractions_.removePair(a, b);
666	>	oneTwoInteractions_.removePair(a, c);
667	>	oneTwoInteractions_.removePair(a, d);
668	>	} else {
669	>	excludedInteractions_.removePair(a, b);
670	>	excludedInteractions_.removePair(a, c);
671	>	excludedInteractions_.removePair(a, d);
672	>	}
673
674	+	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
675	+	oneThreeInteractions_.removePair(b, c);
676	+	oneThreeInteractions_.removePair(b, d);
677	+	oneThreeInteractions_.removePair(c, d);
678	+	} else {
679	+	excludedInteractions_.removePair(b, c);
680	+	excludedInteractions_.removePair(b, d);
681	+	excludedInteractions_.removePair(c, d);
682	+	}
683	+	}
684	+
685	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
686	+	rb = mol->nextRigidBody(rbIter)) {
687	+	vector<Atom*> atoms = rb->getAtoms();
688	+	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
689	+	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
690	+	a = atoms[i]->getGlobalIndex();
691	+	b = atoms[j]->getGlobalIndex();
692	+	excludedInteractions_.removePair(a, b);
693	+	}
694	+	}
695	+	}
696	+
697	+	}
698	+
699	+
700	+	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
701	+	int curStampId;
702	+
703		//index from 0
704		curStampId = moleculeStamps_.size();
705
706		moleculeStamps_.push_back(molStamp);
707		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
708	<	}
708	>	}
709
427	–	void SimInfo::update() {
710
711	<	setupSimType();
712	<
713	<	#ifdef IS_MPI
714	<	setupFortranParallel();
715	<	#endif
716	<
717	<	setupFortranSim();
718	<
719	<	//setup fortran force field
438	<	/** @deprecate */
439	<	int isError = 0;
440	<	initFortranFF( &fInfo_.SIM_uses_RF , &isError );
441	<	if(isError){
442	<	sprintf( painCave.errMsg,
443	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
444	<	painCave.isFatal = 1;
445	<	simError();
446	<	}
447	<
448	<
449	<	setupCutoff();
450	<
711	>	/**
712	>	* update
713	>	*
714	>	*  Performs the global checks and variable settings after the
715	>	*  objects have been created.
716	>	*
717	>	*/
718	>	void SimInfo::update() {
719	>	setupSimVariables();
720		calcNdf();
721		calcNdfRaw();
722		calcNdfTrans();
723	<
724	<	fortranInitialized_ = true;
725	<	}
726	<
727	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
723	>	}
724	>
725	>	/**
726	>	* getSimulatedAtomTypes
727	>	*
728	>	* Returns an STL set of AtomType* that are actually present in this
729	>	* simulation.  Must query all processors to assemble this information.
730	>	*
731	>	*/
732	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
733		SimInfo::MoleculeIterator mi;
734		Molecule* mol;
735		Molecule::AtomIterator ai;
736		Atom* atom;
737	<	std::set<AtomType*> atomTypes;
738	<
737	>	set<AtomType*> atomTypes;
738	>
739		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
740	+	for(atom = mol->beginAtom(ai); atom != NULL;
741	+	atom = mol->nextAtom(ai)) {
742	+	atomTypes.insert(atom->getAtomType());
743	+	}
744	+	}
745	+
746	+	#ifdef IS_MPI
747
748	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
749	<	atomTypes.insert(atom->getAtomType());
750	<	}
751	<
748	>	// loop over the found atom types on this processor, and add their
749	>	// numerical idents to a vector:
750	>
751	>	vector<int> foundTypes;
752	>	set<AtomType*>::iterator i;
753	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
754	>	foundTypes.push_back( (*i)->getIdent() );
755	>
756	>	// count_local holds the number of found types on this processor
757	>	int count_local = foundTypes.size();
758	>
759	>	int nproc;
760	>	MPI_Comm_size( MPI_COMM_WORLD, &nproc);
761	>	// int nproc = MPI::COMM_WORLD.Get_size();
762	>
763	>	// we need arrays to hold the counts and displacement vectors for
764	>	// all processors
765	>	vector<int> counts(nproc, 0);
766	>	vector<int> disps(nproc, 0);
767	>
768	>	// fill the counts array
769	>	MPI_Allgather(&count_local, 1, MPI_INT, &counts[0],
770	>	1, MPI_INT, MPI_COMM_WORLD);
771	>	// MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
772	>	//                           1, MPI::INT);
773	>
774	>	// use the processor counts to compute the displacement array
775	>	disps[0] = 0;
776	>	int totalCount = counts[0];
777	>	for (int iproc = 1; iproc < nproc; iproc++) {
778	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
779	>	totalCount += counts[iproc];
780		}
781
782	<	return atomTypes;
783	<	}
782	>	// we need a (possibly redundant) set of all found types:
783	>	vector<int> ftGlobal(totalCount);
784	>
785	>	// now spray out the foundTypes to all the other processors:
786	>	MPI_Allgatherv(&foundTypes[0], count_local, MPI_INT,
787	>	&ftGlobal[0], &counts[0], &disps[0],
788	>	MPI_INT, MPI_COMM_WORLD);
789	>	// MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
790	>	//                            &ftGlobal[0], &counts[0], &disps[0],
791	>	//                            MPI::INT);
792
793	<	void SimInfo::setupSimType() {
794	<	std::set<AtomType*>::iterator i;
795	<	std::set<AtomType*> atomTypes;
796	<	atomTypes = getUniqueAtomTypes();
793	>	vector<int>::iterator j;
794	>
795	>	// foundIdents is a stl set, so inserting an already found ident
796	>	// will have no effect.
797	>	set<int> foundIdents;
798	>
799	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
800	>	foundIdents.insert((*j));
801
802	<	int useLennardJones = 0;
803	<	int useElectrostatic = 0;
804	<	int useEAM = 0;
805	<	int useCharge = 0;
806	<	int useDirectional = 0;
807	<	int useDipole = 0;
808	<	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();
802	>	// now iterate over the foundIdents and get the actual atom types
803	>	// that correspond to these:
804	>	set<int>::iterator it;
805	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
806	>	atomTypes.insert( forceField_->getAtomType((*it)) );
807	>
808	>	#endif
809
810	+	return atomTypes;
811	+	}
812	+
813	+
814	+	int getGlobalCountOfType(AtomType* atype) {
815	+	/*
816	+	set<AtomType*> atypes = getSimulatedAtomTypes();
817	+	map<AtomType*, int> counts_;
818	+
819	+	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
820	+	for(atom = mol->beginAtom(ai); atom != NULL;
821	+	atom = mol->nextAtom(ai)) {
822	+	atom->getAtomType();
823	+	}
824	+	}
825	+	*/
826	+	return 0;
827	+	}
828	+
829	+	void SimInfo::setupSimVariables() {
830	+	useAtomicVirial_ = simParams_->getUseAtomicVirial();
831	+	// we only call setAccumulateBoxDipole if the accumulateBoxDipole
832	+	// parameter is true
833	+	calcBoxDipole_ = false;
834	+	if ( simParams_->haveAccumulateBoxDipole() )
835	+	if ( simParams_->getAccumulateBoxDipole() ) {
836	+	calcBoxDipole_ = true;
837	+	}
838	+
839	+	set<AtomType*>::iterator i;
840	+	set<AtomType*> atomTypes;
841	+	atomTypes = getSimulatedAtomTypes();
842	+	bool usesElectrostatic = false;
843	+	bool usesMetallic = false;
844	+	bool usesDirectional = false;
845	+	bool usesFluctuatingCharges =  false;
846		//loop over all of the atom types
847		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
848	<	useLennardJones |= (*i)->isLennardJones();
849	<	useElectrostatic |= (*i)->isElectrostatic();
850	<	useEAM |= (*i)->isEAM();
851	<	useCharge |= (*i)->isCharge();
503	<	useDirectional |= (*i)->isDirectional();
504	<	useDipole |= (*i)->isDipole();
505	<	useGayBerne |= (*i)->isGayBerne();
506	<	useSticky |= (*i)->isSticky();
507	<	useShape |= (*i)->isShape();
848	>	usesElectrostatic |= (*i)->isElectrostatic();
849	>	usesMetallic |= (*i)->isMetal();
850	>	usesDirectional |= (*i)->isDirectional();
851	>	usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
852		}
853
854	<	if (useSticky || useDipole || useGayBerne || useShape) {
511	<	useDirectionalAtom = 1;
512	<	}
513	<
514	<	if (useCharge || useDipole) {
515	<	useElectrostatics = 1;
516	<	}
517	<
518	<	#ifdef IS_MPI
854	>	#ifdef IS_MPI
855		int temp;
856
857	<	temp = usePBC;
858	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
857	>	temp = usesDirectional;
858	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
859	>	usesDirectionalAtoms_ = (temp == 0) ? false : true;
860
861	<	temp = useDirectionalAtom;
862	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
861	>	// MPI::COMM_WORLD.Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI::BOOL,
862	>	//                           MPI::LOR);
863	>
864	>	temp = usesMetallic;
865	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
866	>	usesMetallicAtoms_ = (temp == 0) ? false : true;
867
868	<	temp = useLennardJones;
869	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
868	>	// MPI::COMM_WORLD.Allreduce(&temp, &usesMetallicAtoms_, 1, MPI::BOOL,
869	>	//                           MPI::LOR);
870	>
871	>	temp = usesElectrostatic;
872	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
873	>	usesElectrostaticAtoms_ = (temp == 0) ? false : true;
874
875	<	temp = useElectrostatics;
876	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
875	>	// MPI::COMM_WORLD.Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI::BOOL,
876	>	//                           MPI::LOR);
877
878	<	temp = useCharge;
879	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
878	>	temp = usesFluctuatingCharges;
879	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
880	>	usesFluctuatingCharges_ = (temp == 0) ? false : true;
881
882	<	temp = useDipole;
883	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
882	>	// MPI::COMM_WORLD.Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI::BOOL,
883	>	//                           MPI::LOR);
884
885	<	temp = useSticky;
540	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
885	>	#else
886
887	<	temp = useGayBerne;
888	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
887	>	usesDirectionalAtoms_ = usesDirectional;
888	>	usesMetallicAtoms_ = usesMetallic;
889	>	usesElectrostaticAtoms_ = usesElectrostatic;
890	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
891
892	<	temp = useEAM;
893	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
892	>	#endif
893	>
894	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
895	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
896	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
897	>	}
898
548	–	temp = useShape;
549	–	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
899
900	<	temp = useFLARB;
901	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
900	>	vector<int> SimInfo::getGlobalAtomIndices() {
901	>	SimInfo::MoleculeIterator mi;
902	>	Molecule* mol;
903	>	Molecule::AtomIterator ai;
904	>	Atom* atom;
905
906	<	temp = useRF;
555	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
906	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
907
908	<	#endif
908	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
909	>
910	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
911	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
912	>	}
913	>	}
914	>	return GlobalAtomIndices;
915	>	}
916
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;
917
918	<	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
918	>	vector<int> SimInfo::getGlobalGroupIndices() {
919	>	SimInfo::MoleculeIterator mi;
920	>	Molecule* mol;
921	>	Molecule::CutoffGroupIterator ci;
922	>	CutoffGroup* cg;
923
924	<	if (simParams_->haveDielectric()) {
925	<	fInfo_.dielect = simParams_->getDielectric();
926	<	} else {
927	<	sprintf(painCave.errMsg,
928	<	"SimSetup Error: No Dielectric constant was set.\n"
929	<	"\tYou are trying to use Reaction Field without"
930	<	"\tsetting a dielectric constant!\n");
931	<	painCave.isFatal = 1;
932	<	simError();
933	<	}
584	<
585	<	} else {
586	<	fInfo_.dielect = 0.0;
924	>	vector<int> GlobalGroupIndices;
925	>
926	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
927	>
928	>	//local index of cutoff group is trivial, it only depends on the
929	>	//order of travesing
930	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
931	>	cg = mol->nextCutoffGroup(ci)) {
932	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
933	>	}
934		}
935	+	return GlobalGroupIndices;
936	+	}
937
589	–	}
938
939	<	void SimInfo::setupFortranSim() {
592	<	int isError;
593	<	int nExclude;
594	<	std::vector<int> fortranGlobalGroupMembership;
595	<
596	<	nExclude = exclude_.getSize();
597	<	isError = 0;
939	>	void SimInfo::prepareTopology() {
940
599	–	//globalGroupMembership_ is filled by SimCreator
600	–	for (int i = 0; i < nGlobalAtoms_; i++) {
601	–	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
602	–	}
603	–
941		//calculate mass ratio of cutoff group
605	–	std::vector<double> mfact;
942		SimInfo::MoleculeIterator mi;
943		Molecule* mol;
944		Molecule::CutoffGroupIterator ci;
945		CutoffGroup* cg;
946		Molecule::AtomIterator ai;
947		Atom* atom;
948	<	double totalMass;
948	>	RealType totalMass;
949
950	<	//to avoid memory reallocation, reserve enough space for mfact
951	<	mfact.reserve(getNCutoffGroups());
950	>	/**
951	>	* The mass factor is the relative mass of an atom to the total
952	>	* mass of the cutoff group it belongs to.  By default, all atoms
953	>	* are their own cutoff groups, and therefore have mass factors of
954	>	* 1.  We need some special handling for massless atoms, which
955	>	* will be treated as carrying the entire mass of the cutoff
956	>	* group.
957	>	*/
958	>	massFactors_.clear();
959	>	massFactors_.resize(getNAtoms(), 1.0);
960
961		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
962	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
962	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
963	>	cg = mol->nextCutoffGroup(ci)) {
964
965	<	totalMass = cg->getMass();
966	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
967	<	mfact.push_back(atom->getMass()/totalMass);
968	<	}
969	<
970	<	}
965	>	totalMass = cg->getMass();
966	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
967	>	// Check for massless groups - set mfact to 1 if true
968	>	if (totalMass != 0)
969	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
970	>	else
971	>	massFactors_[atom->getLocalIndex()] = 1.0;
972	>	}
973	>	}
974		}
975
976	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
629	<	std::vector<int> identArray;
976	>	// Build the identArray_ and regions_
977
978	<	//to avoid memory reallocation, reserve enough space identArray
979	<	identArray.reserve(getNAtoms());
980	<
981	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
982	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
983	<	identArray.push_back(atom->getIdent());
984	<	}
978	>	identArray_.clear();
979	>	identArray_.reserve(getNAtoms());
980	>	regions_.clear();
981	>	regions_.reserve(getNAtoms());
982	>
983	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
984	>	int reg = mol->getRegion();
985	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
986	>	identArray_.push_back(atom->getIdent());
987	>	regions_.push_back(reg);
988	>	}
989		}
990	+
991	+	topologyDone_ = true;
992	+	}
993
994	<	//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) {
994	>	void SimInfo::addProperty(GenericData* genData) {
995		properties_.addProperty(genData);
996	<	}
996	>	}
997
998	<	void SimInfo::removeProperty(const std::string& propName) {
998	>	void SimInfo::removeProperty(const string& propName) {
999		properties_.removeProperty(propName);
1000	<	}
1000	>	}
1001
1002	<	void SimInfo::clearProperties() {
1002	>	void SimInfo::clearProperties() {
1003		properties_.clearProperties();
1004	<	}
1004	>	}
1005
1006	<	std::vector<std::string> SimInfo::getPropertyNames() {
1006	>	vector<string> SimInfo::getPropertyNames() {
1007		return properties_.getPropertyNames();
1008	<	}
1008	>	}
1009
1010	<	std::vector<GenericData*> SimInfo::getProperties() {
1010	>	vector<GenericData*> SimInfo::getProperties() {
1011		return properties_.getProperties();
1012	<	}
1012	>	}
1013
1014	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1014	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
1015		return properties_.getPropertyByName(propName);
1016	<	}
1016	>	}
1017
1018	<	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1018	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1019	>	if (sman_ == sman) {
1020	>	return;
1021	>	}
1022	>	delete sman_;
1023		sman_ = sman;
1024
840	–	Molecule* mol;
841	–	RigidBody* rb;
842	–	Atom* atom;
1025		SimInfo::MoleculeIterator mi;
1026	+	Molecule::AtomIterator ai;
1027		Molecule::RigidBodyIterator rbIter;
1028	<	Molecule::AtomIterator atomIter;;
1028	>	Molecule::CutoffGroupIterator cgIter;
1029	>	Molecule::BondIterator bondIter;
1030	>	Molecule::BendIterator bendIter;
1031	>	Molecule::TorsionIterator torsionIter;
1032	>	Molecule::InversionIterator inversionIter;
1033
1034	+	Molecule* mol;
1035	+	Atom* atom;
1036	+	RigidBody* rb;
1037	+	CutoffGroup* cg;
1038	+	Bond* bond;
1039	+	Bend* bend;
1040	+	Torsion* torsion;
1041	+	Inversion* inversion;
1042	+
1043		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1044
1045	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1046	<	atom->setSnapshotManager(sman_);
1047	<	}
1048	<
1049	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1050	<	rb->setSnapshotManager(sman_);
1051	<	}
1052	<	}
1053	<
1054	<	}
1045	>	for (atom = mol->beginAtom(ai); atom != NULL;
1046	>	atom = mol->nextAtom(ai)) {
1047	>	atom->setSnapshotManager(sman_);
1048	>	}
1049	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
1050	>	rb = mol->nextRigidBody(rbIter)) {
1051	>	rb->setSnapshotManager(sman_);
1052	>	}
1053	>	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL;
1054	>	cg = mol->nextCutoffGroup(cgIter)) {
1055	>	cg->setSnapshotManager(sman_);
1056	>	}
1057	>	for (bond = mol->beginBond(bondIter); bond != NULL;
1058	>	bond = mol->nextBond(bondIter)) {
1059	>	bond->setSnapshotManager(sman_);
1060	>	}
1061	>	for (bend = mol->beginBend(bendIter); bend != NULL;
1062	>	bend = mol->nextBend(bendIter)) {
1063	>	bend->setSnapshotManager(sman_);
1064	>	}
1065	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
1066	>	torsion = mol->nextTorsion(torsionIter)) {
1067	>	torsion->setSnapshotManager(sman_);
1068	>	}
1069	>	for (inversion = mol->beginInversion(inversionIter); inversion != NULL;
1070	>	inversion = mol->nextInversion(inversionIter)) {
1071	>	inversion->setSnapshotManager(sman_);
1072	>	}
1073	>	}
1074	>	}
1075
860	–	Vector3d SimInfo::getComVel(){
861	–	SimInfo::MoleculeIterator i;
862	–	Molecule* mol;
1076
1077	<	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	<	}
1077	>	ostream& operator <<(ostream& o, SimInfo& info) {
1078
1079	<	#ifdef IS_MPI
1080	<	double tmpMass = totalMass;
1081	<	Vector3d tmpComVel(comVel);
1082	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1083	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1084	<	#endif
1079	>	return o;
1080	>	}
1081	>
1082	>
1083	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1084	>	if (index >= int(IOIndexToIntegrableObject.size())) {
1085	>	sprintf(painCave.errMsg,
1086	>	"SimInfo::getIOIndexToIntegrableObject Error: Integrable Object\n"
1087	>	"\tindex exceeds number of known objects!\n");
1088	>	painCave.isFatal = 1;
1089	>	simError();
1090	>	return NULL;
1091	>	} else
1092	>	return IOIndexToIntegrableObject.at(index);
1093	>	}
1094	>
1095	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1096	>	IOIndexToIntegrableObject= v;
1097	>	}
1098
1099	<	comVel /= totalMass;
1100	<
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	<
1099	>	int SimInfo::getNGlobalConstraints() {
1100	>	int nGlobalConstraints;
1101		#ifdef IS_MPI
1102	<	double tmpMass = totalMass;
1103	<	Vector3d tmpCom(com);
1104	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1105	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1102	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1,
1103	>	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
1104	>	// MPI::COMM_WORLD.Allreduce(&nConstraints_, &nGlobalConstraints, 1,
1105	>	//                           MPI::INT, MPI::SUM);
1106	>	#else
1107	>	nGlobalConstraints =  nConstraints_;
1108		#endif
1109	+	return nGlobalConstraints;
1110	+	}
1111
1112	<	com /= totalMass;
1112	>	}//end namespace OpenMD
1113
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 1969 by gezelter, Wed Feb 26 14:14:50 2014 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines