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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 430 by tim, Thu Mar 10 23:56:42 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1553 by gezelter, Fri Apr 29 17:25:12 2011 UTC

#	Line 1 | Line 1
1	<	/*
1	>	/*
2		* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		/**
#	Line 48 | Line 48
48
49		#include <algorithm>
50		#include <set>
51	+	#include <map>
52
53		#include "brains/SimInfo.hpp"
54		#include "math/Vector3.hpp"
55		#include "primitives/Molecule.hpp"
56	<	#include "UseTheForce/doForces_interface.h"
56	<	#include "UseTheForce/notifyCutoffs_interface.h"
56	>	#include "primitives/StuntDouble.hpp"
57		#include "utils/MemoryUtils.hpp"
58		#include "utils/simError.h"
59		#include "selection/SelectionManager.hpp"
60	+	#include "io/ForceFieldOptions.hpp"
61	+	#include "UseTheForce/ForceField.hpp"
62	+	#include "nonbonded/SwitchingFunction.hpp"
63
64	<	#ifdef IS_MPI
65	<	#include "UseTheForce/mpiComponentPlan.h"
66	<	#include "UseTheForce/DarkSide/simParallel_interface.h"
67	<	#endif
68	<
69	<	namespace oopse {
70	<
71	<	SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
72	<	ForceField* ff, Globals* simParams) :
73	<	forceField_(ff), simParams_(simParams),
74	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
75	<	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
76	<	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
74	<	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
75	<	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
76	<	sman_(NULL), fortranInitialized_(false) {
77	<
78	<
79	<	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
64	>	using namespace std;
65	>	namespace OpenMD {
66	>
67	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
68	>	forceField_(ff), simParams_(simParams),
69	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
70	>	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
71	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
72	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
73	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
74	>	nConstraints_(0), sman_(NULL), fortranInitialized_(false),
75	>	calcBoxDipole_(false), useAtomicVirial_(true) {
76	>
77		MoleculeStamp* molStamp;
78		int nMolWithSameStamp;
79		int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
80	<	int nGroups = 0;          //total cutoff groups defined in meta-data file
80	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
81		CutoffGroupStamp* cgStamp;
82		RigidBodyStamp* rbStamp;
83		int nRigidAtoms = 0;
84
85	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
86	<	molStamp = i->first;
87	<	nMolWithSameStamp = i->second;
88	<
89	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
90	<
91	<	//calculate atoms in molecules
92	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
93	<
94	<
95	<	//calculate atoms in cutoff groups
96	<	int nAtomsInGroups = 0;
97	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
98	<
99	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
100	<	cgStamp = molStamp->getCutoffGroup(j);
101	<	nAtomsInGroups += cgStamp->getNMembers();
102	<	}
103	<
104	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
105	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
106	<
107	<	//calculate atoms in rigid bodies
108	<	int nAtomsInRigidBodies = 0;
109	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
110	<
111	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
112	<	rbStamp = molStamp->getRigidBody(j);
113	<	nAtomsInRigidBodies += rbStamp->getNMembers();
114	<	}
115	<
116	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
117	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
118	<
85	>	vector<Component*> components = simParams->getComponents();
86	>
87	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
88	>	molStamp = (*i)->getMoleculeStamp();
89	>	nMolWithSameStamp = (*i)->getNMol();
90	>
91	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
92	>
93	>	//calculate atoms in molecules
94	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
95	>
96	>	//calculate atoms in cutoff groups
97	>	int nAtomsInGroups = 0;
98	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
99	>
100	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
101	>	cgStamp = molStamp->getCutoffGroupStamp(j);
102	>	nAtomsInGroups += cgStamp->getNMembers();
103	>	}
104	>
105	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
106	>
107	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
108	>
109	>	//calculate atoms in rigid bodies
110	>	int nAtomsInRigidBodies = 0;
111	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
112	>
113	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
114	>	rbStamp = molStamp->getRigidBodyStamp(j);
115	>	nAtomsInRigidBodies += rbStamp->getNMembers();
116	>	}
117	>
118	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
119	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
120	>
121		}
122	+
123	+	//every free atom (atom does not belong to cutoff groups) is a cutoff
124	+	//group therefore the total number of cutoff groups in the system is
125	+	//equal to the total number of atoms minus number of atoms belong to
126	+	//cutoff group defined in meta-data file plus the number of cutoff
127	+	//groups defined in meta-data file
128	+	std::cerr << "nGA = " << nGlobalAtoms_ << "\n";
129	+	std::cerr << "nCA = " << nCutoffAtoms << "\n";
130	+	std::cerr << "nG = " << nGroups << "\n";
131
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
132		nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
133
134	<	//every free atom (atom does not belong to rigid bodies) is an integrable object
135	<	//therefore the total number of  integrable objects in the system is equal to
136	<	//the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
137	<	//file plus the number of  rigid bodies defined in meta-data file
138	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
139	<
134	>	std::cerr << "nGCG = " << nGlobalCutoffGroups_ << "\n";
135	>
136	>	//every free atom (atom does not belong to rigid bodies) is an
137	>	//integrable object therefore the total number of integrable objects
138	>	//in the system is equal to the total number of atoms minus number of
139	>	//atoms belong to rigid body defined in meta-data file plus the number
140	>	//of rigid bodies defined in meta-data file
141	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
142	>	+ nGlobalRigidBodies_;
143	>
144		nGlobalMols_ = molStampIds_.size();
137	–
138	–	#ifdef IS_MPI
145		molToProcMap_.resize(nGlobalMols_);
146	<	#endif
147	<
148	<	}
149	<
144	<	SimInfo::~SimInfo() {
145	<	std::map<int, Molecule*>::iterator i;
146	>	}
147	>
148	>	SimInfo::~SimInfo() {
149	>	map<int, Molecule*>::iterator i;
150		for (i = molecules_.begin(); i != molecules_.end(); ++i) {
151	<	delete i->second;
151	>	delete i->second;
152		}
153		molecules_.clear();
154	<
151	<	MemoryUtils::deletePointers(moleculeStamps_);
152	<
154	>
155		delete sman_;
156		delete simParams_;
157		delete forceField_;
158	<	}
158	>	}
159
158	–	int SimInfo::getNGlobalConstraints() {
159	–	int nGlobalConstraints;
160	–	#ifdef IS_MPI
161	–	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
162	–	MPI_COMM_WORLD);
163	–	#else
164	–	nGlobalConstraints =  nConstraints_;
165	–	#endif
166	–	return nGlobalConstraints;
167	–	}
160
161	<	bool SimInfo::addMolecule(Molecule* mol) {
161	>	bool SimInfo::addMolecule(Molecule* mol) {
162		MoleculeIterator i;
163	<
163	>
164		i = molecules_.find(mol->getGlobalIndex());
165		if (i == molecules_.end() ) {
166	<
167	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
168	<
169	<	nAtoms_ += mol->getNAtoms();
170	<	nBonds_ += mol->getNBonds();
171	<	nBends_ += mol->getNBends();
172	<	nTorsions_ += mol->getNTorsions();
173	<	nRigidBodies_ += mol->getNRigidBodies();
174	<	nIntegrableObjects_ += mol->getNIntegrableObjects();
175	<	nCutoffGroups_ += mol->getNCutoffGroups();
176	<	nConstraints_ += mol->getNConstraintPairs();
177	<
178	<	addExcludePairs(mol);
179	<
180	<	return true;
166	>
167	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
168	>
169	>	nAtoms_ += mol->getNAtoms();
170	>	nBonds_ += mol->getNBonds();
171	>	nBends_ += mol->getNBends();
172	>	nTorsions_ += mol->getNTorsions();
173	>	nInversions_ += mol->getNInversions();
174	>	nRigidBodies_ += mol->getNRigidBodies();
175	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
176	>	nCutoffGroups_ += mol->getNCutoffGroups();
177	>	nConstraints_ += mol->getNConstraintPairs();
178	>
179	>	addInteractionPairs(mol);
180	>
181	>	return true;
182		} else {
183	<	return false;
183	>	return false;
184		}
185	<	}
186	<
187	<	bool SimInfo::removeMolecule(Molecule* mol) {
185	>	}
186	>
187	>	bool SimInfo::removeMolecule(Molecule* mol) {
188		MoleculeIterator i;
189		i = molecules_.find(mol->getGlobalIndex());
190
191		if (i != molecules_.end() ) {
192
193	<	assert(mol == i->second);
193	>	assert(mol == i->second);
194
195	<	nAtoms_ -= mol->getNAtoms();
196	<	nBonds_ -= mol->getNBonds();
197	<	nBends_ -= mol->getNBends();
198	<	nTorsions_ -= mol->getNTorsions();
199	<	nRigidBodies_ -= mol->getNRigidBodies();
200	<	nIntegrableObjects_ -= mol->getNIntegrableObjects();
201	<	nCutoffGroups_ -= mol->getNCutoffGroups();
202	<	nConstraints_ -= mol->getNConstraintPairs();
195	>	nAtoms_ -= mol->getNAtoms();
196	>	nBonds_ -= mol->getNBonds();
197	>	nBends_ -= mol->getNBends();
198	>	nTorsions_ -= mol->getNTorsions();
199	>	nInversions_ -= mol->getNInversions();
200	>	nRigidBodies_ -= mol->getNRigidBodies();
201	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
202	>	nCutoffGroups_ -= mol->getNCutoffGroups();
203	>	nConstraints_ -= mol->getNConstraintPairs();
204
205	<	removeExcludePairs(mol);
206	<	molecules_.erase(mol->getGlobalIndex());
205	>	removeInteractionPairs(mol);
206	>	molecules_.erase(mol->getGlobalIndex());
207
208	<	delete mol;
208	>	delete mol;
209
210	<	return true;
210	>	return true;
211		} else {
212	<	return false;
212	>	return false;
213		}
214	+	}
215
221	–
222	–	}
223	–
216
217	<	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
217	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
218		i = molecules_.begin();
219		return i == molecules_.end() ? NULL : i->second;
220	<	}
220	>	}
221
222	<	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
222	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
223		++i;
224		return i == molecules_.end() ? NULL : i->second;
225	<	}
225	>	}
226
227
228	<	void SimInfo::calcNdf() {
228	>	void SimInfo::calcNdf() {
229		int ndf_local;
230		MoleculeIterator i;
231	<	std::vector<StuntDouble*>::iterator j;
231	>	vector<StuntDouble*>::iterator j;
232		Molecule* mol;
233		StuntDouble* integrableObject;
234
235		ndf_local = 0;
236
237		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
238	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
239	<	integrableObject = mol->nextIntegrableObject(j)) {
238	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
239	>	integrableObject = mol->nextIntegrableObject(j)) {
240
241	<	ndf_local += 3;
241	>	ndf_local += 3;
242
243	<	if (integrableObject->isDirectional()) {
244	<	if (integrableObject->isLinear()) {
245	<	ndf_local += 2;
246	<	} else {
247	<	ndf_local += 3;
248	<	}
249	<	}
243	>	if (integrableObject->isDirectional()) {
244	>	if (integrableObject->isLinear()) {
245	>	ndf_local += 2;
246	>	} else {
247	>	ndf_local += 3;
248	>	}
249	>	}
250
251	<	}//end for (integrableObject)
252	<	}// end for (mol)
251	>	}
252	>	}
253
254		// n_constraints is local, so subtract them on each processor
255		ndf_local -= nConstraints_;
#	Line 272 | Line 264 | void SimInfo::calcNdf() {
264		// entire system:
265		ndf_ = ndf_ - 3 - nZconstraint_;
266
267	<	}
267	>	}
268
269	<	void SimInfo::calcNdfRaw() {
269	>	int SimInfo::getFdf() {
270	>	#ifdef IS_MPI
271	>	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
272	>	#else
273	>	fdf_ = fdf_local;
274	>	#endif
275	>	return fdf_;
276	>	}
277	>
278	>	void SimInfo::calcNdfRaw() {
279		int ndfRaw_local;
280
281		MoleculeIterator i;
282	<	std::vector<StuntDouble*>::iterator j;
282	>	vector<StuntDouble*>::iterator j;
283		Molecule* mol;
284		StuntDouble* integrableObject;
285
#	Line 286 | Line 287 | void SimInfo::calcNdfRaw() {
287		ndfRaw_local = 0;
288
289		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
290	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
291	<	integrableObject = mol->nextIntegrableObject(j)) {
290	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
291	>	integrableObject = mol->nextIntegrableObject(j)) {
292
293	<	ndfRaw_local += 3;
293	>	ndfRaw_local += 3;
294
295	<	if (integrableObject->isDirectional()) {
296	<	if (integrableObject->isLinear()) {
297	<	ndfRaw_local += 2;
298	<	} else {
299	<	ndfRaw_local += 3;
300	<	}
301	<	}
295	>	if (integrableObject->isDirectional()) {
296	>	if (integrableObject->isLinear()) {
297	>	ndfRaw_local += 2;
298	>	} else {
299	>	ndfRaw_local += 3;
300	>	}
301	>	}
302
303	<	}
303	>	}
304		}
305
306		#ifdef IS_MPI
#	Line 307 | Line 308 | void SimInfo::calcNdfRaw() {
308		#else
309		ndfRaw_ = ndfRaw_local;
310		#endif
311	<	}
311	>	}
312
313	<	void SimInfo::calcNdfTrans() {
313	>	void SimInfo::calcNdfTrans() {
314		int ndfTrans_local;
315
316		ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
#	Line 323 | Line 324 | void SimInfo::calcNdfTrans() {
324
325		ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
326
327	<	}
327	>	}
328
329	<	void SimInfo::addExcludePairs(Molecule* mol) {
330	<	std::vector<Bond*>::iterator bondIter;
331	<	std::vector<Bend*>::iterator bendIter;
332	<	std::vector<Torsion*>::iterator torsionIter;
329	>	void SimInfo::addInteractionPairs(Molecule* mol) {
330	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
331	>	vector<Bond*>::iterator bondIter;
332	>	vector<Bend*>::iterator bendIter;
333	>	vector<Torsion*>::iterator torsionIter;
334	>	vector<Inversion*>::iterator inversionIter;
335		Bond* bond;
336		Bend* bend;
337		Torsion* torsion;
338	+	Inversion* inversion;
339		int a;
340		int b;
341		int c;
342		int d;
343	+
344	+	// atomGroups can be used to add special interaction maps between
345	+	// groups of atoms that are in two separate rigid bodies.
346	+	// However, most site-site interactions between two rigid bodies
347	+	// are probably not special, just the ones between the physically
348	+	// bonded atoms.  Interactions *within* a single rigid body should
349	+	// always be excluded.  These are done at the bottom of this
350	+	// function.
351	+
352	+	map<int, set<int> > atomGroups;
353	+	Molecule::RigidBodyIterator rbIter;
354	+	RigidBody* rb;
355	+	Molecule::IntegrableObjectIterator ii;
356	+	StuntDouble* integrableObject;
357
358	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
359	<	a = bond->getAtomA()->getGlobalIndex();
360	<	b = bond->getAtomB()->getGlobalIndex();
361	<	exclude_.addPair(a, b);
358	>	for (integrableObject = mol->beginIntegrableObject(ii);
359	>	integrableObject != NULL;
360	>	integrableObject = mol->nextIntegrableObject(ii)) {
361	>
362	>	if (integrableObject->isRigidBody()) {
363	>	rb = static_cast<RigidBody*>(integrableObject);
364	>	vector<Atom*> atoms = rb->getAtoms();
365	>	set<int> rigidAtoms;
366	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
367	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
368	>	}
369	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
370	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
371	>	}
372	>	} else {
373	>	set<int> oneAtomSet;
374	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
375	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
376	>	}
377	>	}
378	>
379	>	for (bond= mol->beginBond(bondIter); bond != NULL;
380	>	bond = mol->nextBond(bondIter)) {
381	>
382	>	a = bond->getAtomA()->getGlobalIndex();
383	>	b = bond->getAtomB()->getGlobalIndex();
384	>
385	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
386	>	oneTwoInteractions_.addPair(a, b);
387	>	} else {
388	>	excludedInteractions_.addPair(a, b);
389	>	}
390		}
391
392	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
393	<	a = bend->getAtomA()->getGlobalIndex();
348	<	b = bend->getAtomB()->getGlobalIndex();
349	<	c = bend->getAtomC()->getGlobalIndex();
392	>	for (bend= mol->beginBend(bendIter); bend != NULL;
393	>	bend = mol->nextBend(bendIter)) {
394
395	<	exclude_.addPair(a, b);
396	<	exclude_.addPair(a, c);
397	<	exclude_.addPair(b, c);
395	>	a = bend->getAtomA()->getGlobalIndex();
396	>	b = bend->getAtomB()->getGlobalIndex();
397	>	c = bend->getAtomC()->getGlobalIndex();
398	>
399	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
400	>	oneTwoInteractions_.addPair(a, b);
401	>	oneTwoInteractions_.addPair(b, c);
402	>	} else {
403	>	excludedInteractions_.addPair(a, b);
404	>	excludedInteractions_.addPair(b, c);
405	>	}
406	>
407	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
408	>	oneThreeInteractions_.addPair(a, c);
409	>	} else {
410	>	excludedInteractions_.addPair(a, c);
411	>	}
412		}
413
414	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
415	<	a = torsion->getAtomA()->getGlobalIndex();
358	<	b = torsion->getAtomB()->getGlobalIndex();
359	<	c = torsion->getAtomC()->getGlobalIndex();
360	<	d = torsion->getAtomD()->getGlobalIndex();
414	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
415	>	torsion = mol->nextTorsion(torsionIter)) {
416
417	<	exclude_.addPair(a, b);
418	<	exclude_.addPair(a, c);
419	<	exclude_.addPair(a, d);
420	<	exclude_.addPair(b, c);
421	<	exclude_.addPair(b, d);
422	<	exclude_.addPair(c, d);
417	>	a = torsion->getAtomA()->getGlobalIndex();
418	>	b = torsion->getAtomB()->getGlobalIndex();
419	>	c = torsion->getAtomC()->getGlobalIndex();
420	>	d = torsion->getAtomD()->getGlobalIndex();
421	>
422	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
423	>	oneTwoInteractions_.addPair(a, b);
424	>	oneTwoInteractions_.addPair(b, c);
425	>	oneTwoInteractions_.addPair(c, d);
426	>	} else {
427	>	excludedInteractions_.addPair(a, b);
428	>	excludedInteractions_.addPair(b, c);
429	>	excludedInteractions_.addPair(c, d);
430	>	}
431	>
432	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
433	>	oneThreeInteractions_.addPair(a, c);
434	>	oneThreeInteractions_.addPair(b, d);
435	>	} else {
436	>	excludedInteractions_.addPair(a, c);
437	>	excludedInteractions_.addPair(b, d);
438	>	}
439	>
440	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
441	>	oneFourInteractions_.addPair(a, d);
442	>	} else {
443	>	excludedInteractions_.addPair(a, d);
444	>	}
445		}
446
447	<	Molecule::RigidBodyIterator rbIter;
448	<	RigidBody* rb;
372	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
373	<	std::vector<Atom*> atoms = rb->getAtoms();
374	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
375	<	for (int j = i + 1; j < atoms.size(); ++j) {
376	<	a = atoms[i]->getGlobalIndex();
377	<	b = atoms[j]->getGlobalIndex();
378	<	exclude_.addPair(a, b);
379	<	}
380	<	}
381	<	}
447	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
448	>	inversion = mol->nextInversion(inversionIter)) {
449
450	<	Molecule::CutoffGroupIterator cgIter;
451	<	CutoffGroup* cg;
452	<	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
453	<	std::vector<Atom*> atoms = cg->getAtoms();
387	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
388	<	for (int j = i + 1; j < atoms.size(); ++j) {
389	<	a = atoms[i]->getGlobalIndex();
390	<	b = atoms[j]->getGlobalIndex();
391	<	exclude_.addPair(a, b);
392	<	}
393	<	}
394	<	}
450	>	a = inversion->getAtomA()->getGlobalIndex();
451	>	b = inversion->getAtomB()->getGlobalIndex();
452	>	c = inversion->getAtomC()->getGlobalIndex();
453	>	d = inversion->getAtomD()->getGlobalIndex();
454
455	<	}
455	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
456	>	oneTwoInteractions_.addPair(a, b);
457	>	oneTwoInteractions_.addPair(a, c);
458	>	oneTwoInteractions_.addPair(a, d);
459	>	} else {
460	>	excludedInteractions_.addPair(a, b);
461	>	excludedInteractions_.addPair(a, c);
462	>	excludedInteractions_.addPair(a, d);
463	>	}
464
465	<	void SimInfo::removeExcludePairs(Molecule* mol) {
466	<	std::vector<Bond*>::iterator bondIter;
467	<	std::vector<Bend*>::iterator bendIter;
468	<	std::vector<Torsion*>::iterator torsionIter;
465	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
466	>	oneThreeInteractions_.addPair(b, c);
467	>	oneThreeInteractions_.addPair(b, d);
468	>	oneThreeInteractions_.addPair(c, d);
469	>	} else {
470	>	excludedInteractions_.addPair(b, c);
471	>	excludedInteractions_.addPair(b, d);
472	>	excludedInteractions_.addPair(c, d);
473	>	}
474	>	}
475	>
476	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
477	>	rb = mol->nextRigidBody(rbIter)) {
478	>	vector<Atom*> atoms = rb->getAtoms();
479	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
480	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
481	>	a = atoms[i]->getGlobalIndex();
482	>	b = atoms[j]->getGlobalIndex();
483	>	excludedInteractions_.addPair(a, b);
484	>	}
485	>	}
486	>	}
487	>
488	>	}
489	>
490	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
491	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
492	>	vector<Bond*>::iterator bondIter;
493	>	vector<Bend*>::iterator bendIter;
494	>	vector<Torsion*>::iterator torsionIter;
495	>	vector<Inversion*>::iterator inversionIter;
496		Bond* bond;
497		Bend* bend;
498		Torsion* torsion;
499	+	Inversion* inversion;
500		int a;
501		int b;
502		int c;
503		int d;
504	+
505	+	map<int, set<int> > atomGroups;
506	+	Molecule::RigidBodyIterator rbIter;
507	+	RigidBody* rb;
508	+	Molecule::IntegrableObjectIterator ii;
509	+	StuntDouble* integrableObject;
510
511	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
512	<	a = bond->getAtomA()->getGlobalIndex();
513	<	b = bond->getAtomB()->getGlobalIndex();
514	<	exclude_.removePair(a, b);
511	>	for (integrableObject = mol->beginIntegrableObject(ii);
512	>	integrableObject != NULL;
513	>	integrableObject = mol->nextIntegrableObject(ii)) {
514	>
515	>	if (integrableObject->isRigidBody()) {
516	>	rb = static_cast<RigidBody*>(integrableObject);
517	>	vector<Atom*> atoms = rb->getAtoms();
518	>	set<int> rigidAtoms;
519	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
520	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
521	>	}
522	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
523	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
524	>	}
525	>	} else {
526	>	set<int> oneAtomSet;
527	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
528	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
529	>	}
530	>	}
531	>
532	>	for (bond= mol->beginBond(bondIter); bond != NULL;
533	>	bond = mol->nextBond(bondIter)) {
534	>
535	>	a = bond->getAtomA()->getGlobalIndex();
536	>	b = bond->getAtomB()->getGlobalIndex();
537	>
538	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
539	>	oneTwoInteractions_.removePair(a, b);
540	>	} else {
541	>	excludedInteractions_.removePair(a, b);
542	>	}
543		}
544
545	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
546	<	a = bend->getAtomA()->getGlobalIndex();
418	<	b = bend->getAtomB()->getGlobalIndex();
419	<	c = bend->getAtomC()->getGlobalIndex();
545	>	for (bend= mol->beginBend(bendIter); bend != NULL;
546	>	bend = mol->nextBend(bendIter)) {
547
548	<	exclude_.removePair(a, b);
549	<	exclude_.removePair(a, c);
550	<	exclude_.removePair(b, c);
548	>	a = bend->getAtomA()->getGlobalIndex();
549	>	b = bend->getAtomB()->getGlobalIndex();
550	>	c = bend->getAtomC()->getGlobalIndex();
551	>
552	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
553	>	oneTwoInteractions_.removePair(a, b);
554	>	oneTwoInteractions_.removePair(b, c);
555	>	} else {
556	>	excludedInteractions_.removePair(a, b);
557	>	excludedInteractions_.removePair(b, c);
558	>	}
559	>
560	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
561	>	oneThreeInteractions_.removePair(a, c);
562	>	} else {
563	>	excludedInteractions_.removePair(a, c);
564	>	}
565		}
566
567	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
568	<	a = torsion->getAtomA()->getGlobalIndex();
428	<	b = torsion->getAtomB()->getGlobalIndex();
429	<	c = torsion->getAtomC()->getGlobalIndex();
430	<	d = torsion->getAtomD()->getGlobalIndex();
567	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
568	>	torsion = mol->nextTorsion(torsionIter)) {
569
570	<	exclude_.removePair(a, b);
571	<	exclude_.removePair(a, c);
572	<	exclude_.removePair(a, d);
573	<	exclude_.removePair(b, c);
574	<	exclude_.removePair(b, d);
575	<	exclude_.removePair(c, d);
570	>	a = torsion->getAtomA()->getGlobalIndex();
571	>	b = torsion->getAtomB()->getGlobalIndex();
572	>	c = torsion->getAtomC()->getGlobalIndex();
573	>	d = torsion->getAtomD()->getGlobalIndex();
574	>
575	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
576	>	oneTwoInteractions_.removePair(a, b);
577	>	oneTwoInteractions_.removePair(b, c);
578	>	oneTwoInteractions_.removePair(c, d);
579	>	} else {
580	>	excludedInteractions_.removePair(a, b);
581	>	excludedInteractions_.removePair(b, c);
582	>	excludedInteractions_.removePair(c, d);
583	>	}
584	>
585	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
586	>	oneThreeInteractions_.removePair(a, c);
587	>	oneThreeInteractions_.removePair(b, d);
588	>	} else {
589	>	excludedInteractions_.removePair(a, c);
590	>	excludedInteractions_.removePair(b, d);
591	>	}
592	>
593	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
594	>	oneFourInteractions_.removePair(a, d);
595	>	} else {
596	>	excludedInteractions_.removePair(a, d);
597	>	}
598		}
599
600	<	Molecule::RigidBodyIterator rbIter;
601	<	RigidBody* rb;
442	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
443	<	std::vector<Atom*> atoms = rb->getAtoms();
444	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
445	<	for (int j = i + 1; j < atoms.size(); ++j) {
446	<	a = atoms[i]->getGlobalIndex();
447	<	b = atoms[j]->getGlobalIndex();
448	<	exclude_.removePair(a, b);
449	<	}
450	<	}
451	<	}
600	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
601	>	inversion = mol->nextInversion(inversionIter)) {
602
603	<	Molecule::CutoffGroupIterator cgIter;
604	<	CutoffGroup* cg;
605	<	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
606	<	std::vector<Atom*> atoms = cg->getAtoms();
457	<	for (int i = 0; i < atoms.size() -1 ; ++i) {
458	<	for (int j = i + 1; j < atoms.size(); ++j) {
459	<	a = atoms[i]->getGlobalIndex();
460	<	b = atoms[j]->getGlobalIndex();
461	<	exclude_.removePair(a, b);
462	<	}
463	<	}
464	<	}
603	>	a = inversion->getAtomA()->getGlobalIndex();
604	>	b = inversion->getAtomB()->getGlobalIndex();
605	>	c = inversion->getAtomC()->getGlobalIndex();
606	>	d = inversion->getAtomD()->getGlobalIndex();
607
608	<	}
608	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
609	>	oneTwoInteractions_.removePair(a, b);
610	>	oneTwoInteractions_.removePair(a, c);
611	>	oneTwoInteractions_.removePair(a, d);
612	>	} else {
613	>	excludedInteractions_.removePair(a, b);
614	>	excludedInteractions_.removePair(a, c);
615	>	excludedInteractions_.removePair(a, d);
616	>	}
617
618	+	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
619	+	oneThreeInteractions_.removePair(b, c);
620	+	oneThreeInteractions_.removePair(b, d);
621	+	oneThreeInteractions_.removePair(c, d);
622	+	} else {
623	+	excludedInteractions_.removePair(b, c);
624	+	excludedInteractions_.removePair(b, d);
625	+	excludedInteractions_.removePair(c, d);
626	+	}
627	+	}
628
629	<	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
629	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
630	>	rb = mol->nextRigidBody(rbIter)) {
631	>	vector<Atom*> atoms = rb->getAtoms();
632	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
633	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
634	>	a = atoms[i]->getGlobalIndex();
635	>	b = atoms[j]->getGlobalIndex();
636	>	excludedInteractions_.removePair(a, b);
637	>	}
638	>	}
639	>	}
640	>
641	>	}
642	>
643	>
644	>	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
645		int curStampId;
646	<
646	>
647		//index from 0
648		curStampId = moleculeStamps_.size();
649
650		moleculeStamps_.push_back(molStamp);
651		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
652	<	}
652	>	}
653
479	–	void SimInfo::update() {
654
655	<	setupSimType();
656	<
657	<	#ifdef IS_MPI
658	<	setupFortranParallel();
659	<	#endif
660	<
661	<	setupFortranSim();
662	<
663	<	//setup fortran force field
490	<	/** @deprecate */
491	<	int isError = 0;
492	<	initFortranFF( &fInfo_.SIM_uses_RF , &isError );
493	<	if(isError){
494	<	sprintf( painCave.errMsg,
495	<	"ForceField error: There was an error initializing the forceField in fortran.\n" );
496	<	painCave.isFatal = 1;
497	<	simError();
498	<	}
499	<
500	<
501	<	setupCutoff();
502	<
655	>	/**
656	>	* update
657	>	*
658	>	*  Performs the global checks and variable settings after the
659	>	*  objects have been created.
660	>	*
661	>	*/
662	>	void SimInfo::update() {
663	>	setupSimVariables();
664		calcNdf();
665		calcNdfRaw();
666		calcNdfTrans();
667	<
668	<	fortranInitialized_ = true;
669	<	}
670	<
671	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
667	>	}
668	>
669	>	/**
670	>	* getSimulatedAtomTypes
671	>	*
672	>	* Returns an STL set of AtomType* that are actually present in this
673	>	* simulation.  Must query all processors to assemble this information.
674	>	*
675	>	*/
676	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
677		SimInfo::MoleculeIterator mi;
678		Molecule* mol;
679		Molecule::AtomIterator ai;
680		Atom* atom;
681	<	std::set<AtomType*> atomTypes;
681	>	set<AtomType*> atomTypes;
682	>
683	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
684	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
685	>	atomTypes.insert(atom->getAtomType());
686	>	}
687	>	}
688
689	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
689	>	#ifdef IS_MPI
690
691	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
692	<	atomTypes.insert(atom->getAtomType());
521	<	}
522	<
523	<	}
691	>	// loop over the found atom types on this processor, and add their
692	>	// numerical idents to a vector:
693
694	<	return atomTypes;
695	<	}
694	>	vector<int> foundTypes;
695	>	set<AtomType*>::iterator i;
696	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
697	>	foundTypes.push_back( (*i)->getIdent() );
698
699	<	void SimInfo::setupSimType() {
700	<	std::set<AtomType*>::iterator i;
530	<	std::set<AtomType*> atomTypes;
531	<	atomTypes = getUniqueAtomTypes();
532	<
533	<	int useLennardJones = 0;
534	<	int useElectrostatic = 0;
535	<	int useEAM = 0;
536	<	int useCharge = 0;
537	<	int useDirectional = 0;
538	<	int useDipole = 0;
539	<	int useGayBerne = 0;
540	<	int useSticky = 0;
541	<	int useShape = 0;
542	<	int useFLARB = 0; //it is not in AtomType yet
543	<	int useDirectionalAtom = 0;
544	<	int useElectrostatics = 0;
545	<	//usePBC and useRF are from simParams
546	<	int usePBC = simParams_->getPBC();
547	<	int useRF = simParams_->getUseRF();
699	>	// count_local holds the number of found types on this processor
700	>	int count_local = foundTypes.size();
701
702	+	// count holds the total number of found types on all processors
703	+	// (some will be redundant with the ones found locally):
704	+	int count;
705	+	MPI::COMM_WORLD.Allreduce(&count_local, &count, 1, MPI::INT, MPI::SUM);
706	+
707	+	// create a vector to hold the globally found types, and resize it:
708	+	vector<int> ftGlobal;
709	+	ftGlobal.resize(count);
710	+	vector<int> counts;
711	+
712	+	int nproc = MPI::COMM_WORLD.Get_size();
713	+	counts.resize(nproc);
714	+	vector<int> disps;
715	+	disps.resize(nproc);
716	+
717	+	// now spray out the foundTypes to all the other processors:
718	+
719	+	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
720	+	&ftGlobal[0], &counts[0], &disps[0], MPI::INT);
721	+
722	+	// foundIdents is a stl set, so inserting an already found ident
723	+	// will have no effect.
724	+	set<int> foundIdents;
725	+	vector<int>::iterator j;
726	+	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
727	+	foundIdents.insert((*j));
728	+
729	+	// now iterate over the foundIdents and get the actual atom types
730	+	// that correspond to these:
731	+	set<int>::iterator it;
732	+	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
733	+	atomTypes.insert( forceField_->getAtomType((*it)) );
734	+
735	+	#endif
736	+
737	+	return atomTypes;
738	+	}
739	+
740	+	void SimInfo::setupSimVariables() {
741	+	useAtomicVirial_ = simParams_->getUseAtomicVirial();
742	+	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
743	+	calcBoxDipole_ = false;
744	+	if ( simParams_->haveAccumulateBoxDipole() )
745	+	if ( simParams_->getAccumulateBoxDipole() ) {
746	+	calcBoxDipole_ = true;
747	+	}
748	+
749	+	set<AtomType*>::iterator i;
750	+	set<AtomType*> atomTypes;
751	+	atomTypes = getSimulatedAtomTypes();
752	+	int usesElectrostatic = 0;
753	+	int usesMetallic = 0;
754	+	int usesDirectional = 0;
755		//loop over all of the atom types
756		for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
757	<	useLennardJones |= (*i)->isLennardJones();
758	<	useElectrostatic |= (*i)->isElectrostatic();
759	<	useEAM |= (*i)->isEAM();
554	<	useCharge |= (*i)->isCharge();
555	<	useDirectional |= (*i)->isDirectional();
556	<	useDipole |= (*i)->isDipole();
557	<	useGayBerne |= (*i)->isGayBerne();
558	<	useSticky |= (*i)->isSticky();
559	<	useShape |= (*i)->isShape();
757	>	usesElectrostatic |= (*i)->isElectrostatic();
758	>	usesMetallic |= (*i)->isMetal();
759	>	usesDirectional |= (*i)->isDirectional();
760		}
761
562	–	if (useSticky || useDipole || useGayBerne || useShape) {
563	–	useDirectionalAtom = 1;
564	–	}
565	–
566	–	if (useCharge || useDipole) {
567	–	useElectrostatics = 1;
568	–	}
569	–
762		#ifdef IS_MPI
763		int temp;
764	+	temp = usesDirectional;
765	+	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
766
767	<	temp = usePBC;
768	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
767	>	temp = usesMetallic;
768	>	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
769
770	<	temp = useDirectionalAtom;
771	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
770	>	temp = usesElectrostatic;
771	>	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
772	>	#endif
773	>	}
774
579	–	temp = useLennardJones;
580	–	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
775
776	<	temp = useElectrostatics;
777	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
776	>	vector<int> SimInfo::getGlobalAtomIndices() {
777	>	SimInfo::MoleculeIterator mi;
778	>	Molecule* mol;
779	>	Molecule::AtomIterator ai;
780	>	Atom* atom;
781
782	<	temp = useCharge;
586	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
587	<
588	<	temp = useDipole;
589	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
590	<
591	<	temp = useSticky;
592	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
593	<
594	<	temp = useGayBerne;
595	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
596	<
597	<	temp = useEAM;
598	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
599	<
600	<	temp = useShape;
601	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
602	<
603	<	temp = useFLARB;
604	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
605	<
606	<	temp = useRF;
607	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
782	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
783
784	<	#endif
784	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
785	>
786	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
787	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
788	>	}
789	>	}
790	>	return GlobalAtomIndices;
791	>	}
792
611	–	fInfo_.SIM_uses_PBC = usePBC;
612	–	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
613	–	fInfo_.SIM_uses_LennardJones = useLennardJones;
614	–	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
615	–	fInfo_.SIM_uses_Charges = useCharge;
616	–	fInfo_.SIM_uses_Dipoles = useDipole;
617	–	fInfo_.SIM_uses_Sticky = useSticky;
618	–	fInfo_.SIM_uses_GayBerne = useGayBerne;
619	–	fInfo_.SIM_uses_EAM = useEAM;
620	–	fInfo_.SIM_uses_Shapes = useShape;
621	–	fInfo_.SIM_uses_FLARB = useFLARB;
622	–	fInfo_.SIM_uses_RF = useRF;
793
794	<	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
794	>	vector<int> SimInfo::getGlobalGroupIndices() {
795	>	SimInfo::MoleculeIterator mi;
796	>	Molecule* mol;
797	>	Molecule::CutoffGroupIterator ci;
798	>	CutoffGroup* cg;
799
800	<	if (simParams_->haveDielectric()) {
801	<	fInfo_.dielect = simParams_->getDielectric();
802	<	} else {
803	<	sprintf(painCave.errMsg,
804	<	"SimSetup Error: No Dielectric constant was set.\n"
805	<	"\tYou are trying to use Reaction Field without"
806	<	"\tsetting a dielectric constant!\n");
807	<	painCave.isFatal = 1;
808	<	simError();
809	<	}
636	<
637	<	} else {
638	<	fInfo_.dielect = 0.0;
800	>	vector<int> GlobalGroupIndices;
801	>
802	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
803	>
804	>	//local index of cutoff group is trivial, it only depends on the
805	>	//order of travesing
806	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
807	>	cg = mol->nextCutoffGroup(ci)) {
808	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
809	>	}
810		}
811	+	return GlobalGroupIndices;
812	+	}
813
641	–	}
814
815	<	void SimInfo::setupFortranSim() {
815	>	void SimInfo::setupFortran() {
816		int isError;
817	<	int nExclude;
818	<	std::vector<int> fortranGlobalGroupMembership;
817	>	int nExclude, nOneTwo, nOneThree, nOneFour;
818	>	vector<int> fortranGlobalGroupMembership;
819
648	–	nExclude = exclude_.getSize();
820		isError = 0;
821
822		//globalGroupMembership_ is filled by SimCreator
823		for (int i = 0; i < nGlobalAtoms_; i++) {
824	<	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
824	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
825		}
826
827		//calculate mass ratio of cutoff group
828	<	std::vector<double> mfact;
828	>	vector<RealType> mfact;
829		SimInfo::MoleculeIterator mi;
830		Molecule* mol;
831		Molecule::CutoffGroupIterator ci;
832		CutoffGroup* cg;
833		Molecule::AtomIterator ai;
834		Atom* atom;
835	<	double totalMass;
835	>	RealType totalMass;
836
837		//to avoid memory reallocation, reserve enough space for mfact
838		mfact.reserve(getNCutoffGroups());
839
840		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
841	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
841	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
842
843	<	totalMass = cg->getMass();
844	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
845	<	mfact.push_back(atom->getMass()/totalMass);
846	<	}
847	<
848	<	}
843	>	totalMass = cg->getMass();
844	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
845	>	// Check for massless groups - set mfact to 1 if true
846	>	if (totalMass != 0)
847	>	mfact.push_back(atom->getMass()/totalMass);
848	>	else
849	>	mfact.push_back( 1.0 );
850	>	}
851	>	}
852		}
853
854	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
681	<	std::vector<int> identArray;
854	>	// Build the identArray_
855
856	<	//to avoid memory reallocation, reserve enough space identArray
857	<	identArray.reserve(getNAtoms());
685	<
856	>	identArray_.clear();
857	>	identArray_.reserve(getNAtoms());
858		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
859	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
860	<	identArray.push_back(atom->getIdent());
861	<	}
859	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
860	>	identArray_.push_back(atom->getIdent());
861	>	}
862		}
863
864		//fill molMembershipArray
865		//molMembershipArray is filled by SimCreator
866	<	std::vector<int> molMembershipArray(nGlobalAtoms_);
866	>	vector<int> molMembershipArray(nGlobalAtoms_);
867		for (int i = 0; i < nGlobalAtoms_; i++) {
868	<	molMembershipArray[i] = globalMolMembership_[i] + 1;
868	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
869		}
870
871		//setup fortran simulation
700	–	//gloalExcludes and molMembershipArray should go away (They are never used)
701	–	//why the hell fortran need to know molecule?
702	–	//OOPSE = Object-Obfuscated Parallel Simulation Engine
703	–	int nGlobalExcludes = 0;
704	–	int* globalExcludes = NULL;
705	–	int* excludeList = exclude_.getExcludeList();
706	–	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
707	–	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
708	–	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
872
873	<	if( isError ){
873	>	nExclude = excludedInteractions_.getSize();
874	>	nOneTwo = oneTwoInteractions_.getSize();
875	>	nOneThree = oneThreeInteractions_.getSize();
876	>	nOneFour = oneFourInteractions_.getSize();
877
878	<	sprintf( painCave.errMsg,
879	<	"There was an error setting the simulation information in fortran.\n" );
880	<	painCave.isFatal = 1;
881	<	painCave.severity = OOPSE_ERROR;
716	<	simError();
717	<	}
878	>	int* excludeList = excludedInteractions_.getPairList();
879	>	int* oneTwoList = oneTwoInteractions_.getPairList();
880	>	int* oneThreeList = oneThreeInteractions_.getPairList();
881	>	int* oneFourList = oneFourInteractions_.getPairList();
882
883	<	#ifdef IS_MPI
884	<	sprintf( checkPointMsg,
885	<	"succesfully sent the simulation information to fortran.\n");
886	<	MPIcheckPoint();
887	<	#endif // is_mpi
888	<	}
889	<
726	<
727	<	#ifdef IS_MPI
728	<	void SimInfo::setupFortranParallel() {
883	>	//setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray_[0],
884	>	//               &nExclude, excludeList,
885	>	//               &nOneTwo, oneTwoList,
886	>	//               &nOneThree, oneThreeList,
887	>	//               &nOneFour, oneFourList,
888	>	//               &molMembershipArray[0], &mfact[0], &nCutoffGroups_,
889	>	//               &fortranGlobalGroupMembership[0], &isError);
890
891	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
892	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
893	<	std::vector<int> localToGlobalCutoffGroupIndex;
894	<	SimInfo::MoleculeIterator mi;
895	<	Molecule::AtomIterator ai;
896	<	Molecule::CutoffGroupIterator ci;
897	<	Molecule* mol;
898	<	Atom* atom;
899	<	CutoffGroup* cg;
900	<	mpiSimData parallelData;
901	<	int isError;
891	>	// if( isError ){
892	>	//
893	>	//  sprintf( painCave.errMsg,
894	>	//         "There was an error setting the simulation information in fortran.\n" );
895	>	//  painCave.isFatal = 1;
896	>	//  painCave.severity = OPENMD_ERROR;
897	>	//  simError();
898	>	//}
899	>
900	>
901	>	// sprintf( checkPointMsg,
902	>	//          "succesfully sent the simulation information to fortran.\n");
903	>
904	>	// errorCheckPoint();
905	>
906	>	// Setup number of neighbors in neighbor list if present
907	>	//if (simParams_->haveNeighborListNeighbors()) {
908	>	//  int nlistNeighbors = simParams_->getNeighborListNeighbors();
909	>	//  setNeighbors(&nlistNeighbors);
910	>	//}
911	>
912	>	#ifdef IS_MPI
913	>	// mpiSimData parallelData;
914
742	–	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
743	–
744	–	//local index(index in DataStorge) of atom is important
745	–	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
746	–	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
747	–	}
748	–
749	–	//local index of cutoff group is trivial, it only depends on the order of travesing
750	–	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
751	–	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
752	–	}
753	–
754	–	}
755	–
915		//fill up mpiSimData struct
916	<	parallelData.nMolGlobal = getNGlobalMolecules();
917	<	parallelData.nMolLocal = getNMolecules();
918	<	parallelData.nAtomsGlobal = getNGlobalAtoms();
919	<	parallelData.nAtomsLocal = getNAtoms();
920	<	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
921	<	parallelData.nGroupsLocal = getNCutoffGroups();
922	<	parallelData.myNode = worldRank;
923	<	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
916	>	// parallelData.nMolGlobal = getNGlobalMolecules();
917	>	// parallelData.nMolLocal = getNMolecules();
918	>	// parallelData.nAtomsGlobal = getNGlobalAtoms();
919	>	// parallelData.nAtomsLocal = getNAtoms();
920	>	// parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
921	>	// parallelData.nGroupsLocal = getNCutoffGroups();
922	>	// parallelData.myNode = worldRank;
923	>	// MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
924
925		//pass mpiSimData struct and index arrays to fortran
926	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
927	<	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
928	<	&localToGlobalCutoffGroupIndex[0], &isError);
926	>	//setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
927	>	//                &localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
928	>	//                &localToGlobalCutoffGroupIndex[0], &isError);
929
930	<	if (isError) {
931	<	sprintf(painCave.errMsg,
932	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
933	<	painCave.isFatal = 1;
934	<	simError();
935	<	}
930	>	// if (isError) {
931	>	//   sprintf(painCave.errMsg,
932	>	//           "mpiRefresh errror: fortran didn't like something we gave it.\n");
933	>	//   painCave.isFatal = 1;
934	>	//   simError();
935	>	// }
936
937	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
938	<	MPIcheckPoint();
780	<
781	<
782	<	}
783	<
937	>	// sprintf(checkPointMsg, " mpiRefresh successful.\n");
938	>	// errorCheckPoint();
939		#endif
940
941	<	double SimInfo::calcMaxCutoffRadius() {
941	>	// initFortranFF(&isError);
942	>	// if (isError) {
943	>	//   sprintf(painCave.errMsg,
944	>	//           "initFortranFF errror: fortran didn't like something we gave it.\n");
945	>	//   painCave.isFatal = 1;
946	>	//   simError();
947	>	// }
948	>	// fortranInitialized_ = true;
949	>	}
950
951	+	void SimInfo::addProperty(GenericData* genData) {
952	+	properties_.addProperty(genData);
953	+	}
954
955	<	std::set<AtomType*> atomTypes;
956	<	std::set<AtomType*>::iterator i;
957	<	std::vector<double> cutoffRadius;
955	>	void SimInfo::removeProperty(const string& propName) {
956	>	properties_.removeProperty(propName);
957	>	}
958
959	<	//get the unique atom types
960	<	atomTypes = getUniqueAtomTypes();
959	>	void SimInfo::clearProperties() {
960	>	properties_.clearProperties();
961	>	}
962
963	<	//query the max cutoff radius among these atom types
964	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
965	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
966	<	}
963	>	vector<string> SimInfo::getPropertyNames() {
964	>	return properties_.getPropertyNames();
965	>	}
966	>
967	>	vector<GenericData*> SimInfo::getProperties() {
968	>	return properties_.getProperties();
969	>	}
970
971	<	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
972	<	#ifdef IS_MPI
973	<	//pick the max cutoff radius among the processors
804	<	#endif
805	<
806	<	return maxCutoffRadius;
807	<	}
971	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
972	>	return properties_.getPropertyByName(propName);
973	>	}
974
975	<	void SimInfo::getCutoff(double& rcut, double& rsw) {
976	<
977	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
978	<
979	<	if (!simParams_->haveRcut()){
814	<	sprintf(painCave.errMsg,
815	<	"SimCreator Warning: No value was set for the cutoffRadius.\n"
816	<	"\tOOPSE will use a default value of 15.0 angstroms"
817	<	"\tfor the cutoffRadius.\n");
818	<	painCave.isFatal = 0;
819	<	simError();
820	<	rcut = 15.0;
821	<	} else{
822	<	rcut = simParams_->getRcut();
823	<	}
824	<
825	<	if (!simParams_->haveRsw()){
826	<	sprintf(painCave.errMsg,
827	<	"SimCreator Warning: No value was set for switchingRadius.\n"
828	<	"\tOOPSE will use a default value of\n"
829	<	"\t0.95 * cutoffRadius for the switchingRadius\n");
830	<	painCave.isFatal = 0;
831	<	simError();
832	<	rsw = 0.95 * rcut;
833	<	} else{
834	<	rsw = simParams_->getRsw();
835	<	}
836	<
837	<	} else {
838	<	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
839	<	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
840	<
841	<	if (simParams_->haveRcut()) {
842	<	rcut = simParams_->getRcut();
843	<	} else {
844	<	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
845	<	rcut = calcMaxCutoffRadius();
846	<	}
847	<
848	<	if (simParams_->haveRsw()) {
849	<	rsw  = simParams_->getRsw();
850	<	} else {
851	<	rsw = rcut;
852	<	}
853	<
854	<	}
855	<	}
856	<
857	<	void SimInfo::setupCutoff() {
858	<	getCutoff(rcut_, rsw_);
859	<	double rnblist = rcut_ + 1; // skin of neighbor list
860	<
861	<	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
862	<	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist);
863	<	}
864	<
865	<	void SimInfo::addProperty(GenericData* genData) {
866	<	properties_.addProperty(genData);
867	<	}
868	<
869	<	void SimInfo::removeProperty(const std::string& propName) {
870	<	properties_.removeProperty(propName);
871	<	}
872	<
873	<	void SimInfo::clearProperties() {
874	<	properties_.clearProperties();
875	<	}
876	<
877	<	std::vector<std::string> SimInfo::getPropertyNames() {
878	<	return properties_.getPropertyNames();
879	<	}
880	<
881	<	std::vector<GenericData*> SimInfo::getProperties() {
882	<	return properties_.getProperties();
883	<	}
884	<
885	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
886	<	return properties_.getPropertyByName(propName);
887	<	}
888	<
889	<	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
890	<	//if (sman_ == sman_) {
891	<	//    return;
892	<	//}
893	<
894	<	//delete sman_;
975	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
976	>	if (sman_ == sman) {
977	>	return;
978	>	}
979	>	delete sman_;
980		sman_ = sman;
981
982		Molecule* mol;
983		RigidBody* rb;
984		Atom* atom;
985	+	CutoffGroup* cg;
986		SimInfo::MoleculeIterator mi;
987		Molecule::RigidBodyIterator rbIter;
988	<	Molecule::AtomIterator atomIter;;
988	>	Molecule::AtomIterator atomIter;
989	>	Molecule::CutoffGroupIterator cgIter;
990
991		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
992
993	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
994	<	atom->setSnapshotManager(sman_);
995	<	}
993	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
994	>	atom->setSnapshotManager(sman_);
995	>	}
996
997	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
998	<	rb->setSnapshotManager(sman_);
999	<	}
997	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
998	>	rb->setSnapshotManager(sman_);
999	>	}
1000	>
1001	>	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
1002	>	cg->setSnapshotManager(sman_);
1003	>	}
1004		}
1005
1006	<	}
1006	>	}
1007
1008	<	Vector3d SimInfo::getComVel(){
1008	>	Vector3d SimInfo::getComVel(){
1009		SimInfo::MoleculeIterator i;
1010		Molecule* mol;
1011
1012		Vector3d comVel(0.0);
1013	<	double totalMass = 0.0;
1013	>	RealType totalMass = 0.0;
1014
1015
1016		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1017	<	double mass = mol->getMass();
1018	<	totalMass += mass;
1019	<	comVel += mass * mol->getComVel();
1017	>	RealType mass = mol->getMass();
1018	>	totalMass += mass;
1019	>	comVel += mass * mol->getComVel();
1020		}
1021
1022		#ifdef IS_MPI
1023	<	double tmpMass = totalMass;
1023	>	RealType tmpMass = totalMass;
1024		Vector3d tmpComVel(comVel);
1025	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1026	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1025	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1026	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1027		#endif
1028
1029		comVel /= totalMass;
1030
1031		return comVel;
1032	<	}
1032	>	}
1033
1034	<	Vector3d SimInfo::getCom(){
1034	>	Vector3d SimInfo::getCom(){
1035		SimInfo::MoleculeIterator i;
1036		Molecule* mol;
1037
1038		Vector3d com(0.0);
1039	<	double totalMass = 0.0;
1039	>	RealType totalMass = 0.0;
1040
1041		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1042	<	double mass = mol->getMass();
1043	<	totalMass += mass;
1044	<	com += mass * mol->getCom();
1042	>	RealType mass = mol->getMass();
1043	>	totalMass += mass;
1044	>	com += mass * mol->getCom();
1045		}
1046
1047		#ifdef IS_MPI
1048	<	double tmpMass = totalMass;
1048	>	RealType tmpMass = totalMass;
1049		Vector3d tmpCom(com);
1050	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1051	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1050	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1051	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1052		#endif
1053
1054		com /= totalMass;
1055
1056		return com;
1057
1058	<	}
1058	>	}
1059
1060	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1060	>	ostream& operator <<(ostream& o, SimInfo& info) {
1061
1062		return o;
1063	<	}
1063	>	}
1064	>
1065	>
1066	>	/*
1067	>	Returns center of mass and center of mass velocity in one function call.
1068	>	*/
1069	>
1070	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1071	>	SimInfo::MoleculeIterator i;
1072	>	Molecule* mol;
1073	>
1074	>
1075	>	RealType totalMass = 0.0;
1076	>
1077
1078	<	}//end namespace oopse
1078	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1079	>	RealType mass = mol->getMass();
1080	>	totalMass += mass;
1081	>	com += mass * mol->getCom();
1082	>	comVel += mass * mol->getComVel();
1083	>	}
1084	>
1085	>	#ifdef IS_MPI
1086	>	RealType tmpMass = totalMass;
1087	>	Vector3d tmpCom(com);
1088	>	Vector3d tmpComVel(comVel);
1089	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1090	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1091	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1092	>	#endif
1093	>
1094	>	com /= totalMass;
1095	>	comVel /= totalMass;
1096	>	}
1097	>
1098	>	/*
1099	>	Return intertia tensor for entire system and angular momentum Vector.
1100
1101	+
1102	+	[  Ixx -Ixy  -Ixz ]
1103	+	J =| -Iyx  Iyy  -Iyz |
1104	+	[ -Izx -Iyz   Izz ]
1105	+	*/
1106	+
1107	+	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1108	+
1109	+
1110	+	RealType xx = 0.0;
1111	+	RealType yy = 0.0;
1112	+	RealType zz = 0.0;
1113	+	RealType xy = 0.0;
1114	+	RealType xz = 0.0;
1115	+	RealType yz = 0.0;
1116	+	Vector3d com(0.0);
1117	+	Vector3d comVel(0.0);
1118	+
1119	+	getComAll(com, comVel);
1120	+
1121	+	SimInfo::MoleculeIterator i;
1122	+	Molecule* mol;
1123	+
1124	+	Vector3d thisq(0.0);
1125	+	Vector3d thisv(0.0);
1126	+
1127	+	RealType thisMass = 0.0;
1128	+
1129	+
1130	+
1131	+
1132	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1133	+
1134	+	thisq = mol->getCom()-com;
1135	+	thisv = mol->getComVel()-comVel;
1136	+	thisMass = mol->getMass();
1137	+	// Compute moment of intertia coefficients.
1138	+	xx += thisq[0]*thisq[0]*thisMass;
1139	+	yy += thisq[1]*thisq[1]*thisMass;
1140	+	zz += thisq[2]*thisq[2]*thisMass;
1141	+
1142	+	// compute products of intertia
1143	+	xy += thisq[0]*thisq[1]*thisMass;
1144	+	xz += thisq[0]*thisq[2]*thisMass;
1145	+	yz += thisq[1]*thisq[2]*thisMass;
1146	+
1147	+	angularMomentum += cross( thisq, thisv ) * thisMass;
1148	+
1149	+	}
1150	+
1151	+
1152	+	inertiaTensor(0,0) = yy + zz;
1153	+	inertiaTensor(0,1) = -xy;
1154	+	inertiaTensor(0,2) = -xz;
1155	+	inertiaTensor(1,0) = -xy;
1156	+	inertiaTensor(1,1) = xx + zz;
1157	+	inertiaTensor(1,2) = -yz;
1158	+	inertiaTensor(2,0) = -xz;
1159	+	inertiaTensor(2,1) = -yz;
1160	+	inertiaTensor(2,2) = xx + yy;
1161	+
1162	+	#ifdef IS_MPI
1163	+	Mat3x3d tmpI(inertiaTensor);
1164	+	Vector3d tmpAngMom;
1165	+	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1166	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1167	+	#endif
1168	+
1169	+	return;
1170	+	}
1171	+
1172	+	//Returns the angular momentum of the system
1173	+	Vector3d SimInfo::getAngularMomentum(){
1174	+
1175	+	Vector3d com(0.0);
1176	+	Vector3d comVel(0.0);
1177	+	Vector3d angularMomentum(0.0);
1178	+
1179	+	getComAll(com,comVel);
1180	+
1181	+	SimInfo::MoleculeIterator i;
1182	+	Molecule* mol;
1183	+
1184	+	Vector3d thisr(0.0);
1185	+	Vector3d thisp(0.0);
1186	+
1187	+	RealType thisMass;
1188	+
1189	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1190	+	thisMass = mol->getMass();
1191	+	thisr = mol->getCom()-com;
1192	+	thisp = (mol->getComVel()-comVel)*thisMass;
1193	+
1194	+	angularMomentum += cross( thisr, thisp );
1195	+
1196	+	}
1197	+
1198	+	#ifdef IS_MPI
1199	+	Vector3d tmpAngMom;
1200	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1201	+	#endif
1202	+
1203	+	return angularMomentum;
1204	+	}
1205	+
1206	+	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1207	+	return IOIndexToIntegrableObject.at(index);
1208	+	}
1209	+
1210	+	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1211	+	IOIndexToIntegrableObject= v;
1212	+	}
1213	+
1214	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1215	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1216	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1217	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1218	+	*/
1219	+	void SimInfo::getGyrationalVolume(RealType &volume){
1220	+	Mat3x3d intTensor;
1221	+	RealType det;
1222	+	Vector3d dummyAngMom;
1223	+	RealType sysconstants;
1224	+	RealType geomCnst;
1225	+
1226	+	geomCnst = 3.0/2.0;
1227	+	/* Get the inertial tensor and angular momentum for free*/
1228	+	getInertiaTensor(intTensor,dummyAngMom);
1229	+
1230	+	det = intTensor.determinant();
1231	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1232	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1233	+	return;
1234	+	}
1235	+
1236	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1237	+	Mat3x3d intTensor;
1238	+	Vector3d dummyAngMom;
1239	+	RealType sysconstants;
1240	+	RealType geomCnst;
1241	+
1242	+	geomCnst = 3.0/2.0;
1243	+	/* Get the inertial tensor and angular momentum for free*/
1244	+	getInertiaTensor(intTensor,dummyAngMom);
1245	+
1246	+	detI = intTensor.determinant();
1247	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1248	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1249	+	return;
1250	+	}
1251	+	/*
1252	+	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1253	+	assert( v.size() == nAtoms_ + nRigidBodies_);
1254	+	sdByGlobalIndex_ = v;
1255	+	}
1256	+
1257	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1258	+	//assert(index < nAtoms_ + nRigidBodies_);
1259	+	return sdByGlobalIndex_.at(index);
1260	+	}
1261	+	*/
1262	+	int SimInfo::getNGlobalConstraints() {
1263	+	int nGlobalConstraints;
1264	+	#ifdef IS_MPI
1265	+	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1266	+	MPI_COMM_WORLD);
1267	+	#else
1268	+	nGlobalConstraints =  nConstraints_;
1269	+	#endif
1270	+	return nGlobalConstraints;
1271	+	}
1272	+
1273	+	}//end namespace OpenMD
1274	+

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 430 by tim, Thu Mar 10 23:56:42 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1553 by gezelter, Fri Apr 29 17:25:12 2011 UTC

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