ViewVC Help

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

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

Comparing:
trunk/src/brains/SimInfo.cpp (file contents), Revision 331 by tim, Sun Feb 13 21:18:27 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1668 by gezelter, Fri Jan 6 19:03:05 2012 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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		/**
#	Line 48 | Line 49
49
50		#include <algorithm>
51		#include <set>
52	+	#include <map>
53
54		#include "brains/SimInfo.hpp"
55		#include "math/Vector3.hpp"
56		#include "primitives/Molecule.hpp"
57	<	#include "UseTheForce/doForces_interface.h"
56	<	#include "UseTheForce/notifyCutoffs_interface.h"
57	>	#include "primitives/StuntDouble.hpp"
58		#include "utils/MemoryUtils.hpp"
59		#include "utils/simError.h"
60		#include "selection/SelectionManager.hpp"
61	<
61	>	#include "io/ForceFieldOptions.hpp"
62	>	#include "UseTheForce/ForceField.hpp"
63	>	#include "nonbonded/SwitchingFunction.hpp"
64		#ifdef IS_MPI
65	<	#include "UseTheForce/mpiComponentPlan.h"
66	<	#include "UseTheForce/DarkSide/simParallel_interface.h"
64	<	#endif
65	>	#include <mpi.h>
66	>	#endif
67
68	<	namespace oopse {
69	<
70	<	SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
71	<	ForceField* ff, Globals* simParams) :
72	<	forceField_(ff), simParams_(simParams),
73	<	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
74	<	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
75	<	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
76	<	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
77	<	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
78	<	sman_(NULL), fortranInitialized_(false), selectMan_(NULL) {
79	<
80	<
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	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
77	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
78	>	nConstraints_(0), sman_(NULL), topologyDone_(false),
79	>	calcBoxDipole_(false), useAtomicVirial_(true) {
80	>
81		MoleculeStamp* molStamp;
82		int nMolWithSameStamp;
83		int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
84	<	int nGroups = 0;          //total cutoff groups defined in meta-data file
84	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
85		CutoffGroupStamp* cgStamp;
86		RigidBodyStamp* rbStamp;
87		int nRigidAtoms = 0;
88
89	<	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
90	<	molStamp = i->first;
91	<	nMolWithSameStamp = i->second;
92	<
93	<	addMoleculeStamp(molStamp, nMolWithSameStamp);
94	<
95	<	//calculate atoms in molecules
96	<	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
97	<
98	<
99	<	//calculate atoms in cutoff groups
100	<	int nAtomsInGroups = 0;
101	<	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
102	<
103	<	for (int j=0; j < nCutoffGroupsInStamp; j++) {
104	<	cgStamp = molStamp->getCutoffGroup(j);
105	<	nAtomsInGroups += cgStamp->getNMembers();
106	<	}
107	<
108	<	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
109	<	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
110	<
111	<	//calculate atoms in rigid bodies
112	<	int nAtomsInRigidBodies = 0;
113	<	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
114	<
115	<	for (int j=0; j < nRigidBodiesInStamp; j++) {
116	<	rbStamp = molStamp->getRigidBody(j);
117	<	nAtomsInRigidBodies += rbStamp->getNMembers();
118	<	}
119	<
120	<	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
121	<	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
122	<
89	>	vector<Component*> components = simParams->getComponents();
90	>
91	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
92	>	molStamp = (*i)->getMoleculeStamp();
93	>	nMolWithSameStamp = (*i)->getNMol();
94	>
95	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
96	>
97	>	//calculate atoms in molecules
98	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
99	>
100	>	//calculate atoms in cutoff groups
101	>	int nAtomsInGroups = 0;
102	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
103	>
104	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
105	>	cgStamp = molStamp->getCutoffGroupStamp(j);
106	>	nAtomsInGroups += cgStamp->getNMembers();
107	>	}
108	>
109	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
110	>
111	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
112	>
113	>	//calculate atoms in rigid bodies
114	>	int nAtomsInRigidBodies = 0;
115	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
116	>
117	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
118	>	rbStamp = molStamp->getRigidBodyStamp(j);
119	>	nAtomsInRigidBodies += rbStamp->getNMembers();
120	>	}
121	>
122	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
123	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
124	>
125		}
126	+
127	+	//every free atom (atom does not belong to cutoff groups) is a cutoff
128	+	//group therefore the total number of cutoff groups in the system is
129	+	//equal to the total number of atoms minus number of atoms belong to
130	+	//cutoff group defined in meta-data file plus the number of cutoff
131	+	//groups defined in meta-data file
132
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
133		nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
134	<
135	<	//every free atom (atom does not belong to rigid bodies) is an integrable object
136	<	//therefore the total number of  integrable objects in the system is equal to
137	<	//the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
138	<	//file plus the number of  rigid bodies defined in meta-data file
139	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
140	<
134	>
135	>	//every free atom (atom does not belong to rigid bodies) is an
136	>	//integrable object therefore the total number of integrable objects
137	>	//in the system is equal to the total number of atoms minus number of
138	>	//atoms belong to rigid body defined in meta-data file plus the number
139	>	//of rigid bodies defined in meta-data file
140	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
141	>	+ nGlobalRigidBodies_;
142	>
143		nGlobalMols_ = molStampIds_.size();
137	–
138	–	#ifdef IS_MPI
144		molToProcMap_.resize(nGlobalMols_);
145	<	#endif
146	<
147	<	selectMan_ = new SelectionManager(this);
148	<	selectMan_->selectAll();
149	<	}
150	<
151	<	SimInfo::~SimInfo() {
152	<	//MemoryUtils::deleteVectorOfPointer(molecules_);
153	<
149	<	MemoryUtils::deleteVectorOfPointer(moleculeStamps_);
150	<
145	>	}
146	>
147	>	SimInfo::~SimInfo() {
148	>	map<int, Molecule*>::iterator i;
149	>	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
150	>	delete i->second;
151	>	}
152	>	molecules_.clear();
153	>
154		delete sman_;
155		delete simParams_;
156		delete forceField_;
157	<	delete selectMan_;
155	<	}
157	>	}
158
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	–	}
159
160	<	bool SimInfo::addMolecule(Molecule* mol) {
160	>	bool SimInfo::addMolecule(Molecule* mol) {
161		MoleculeIterator i;
162	<
162	>
163		i = molecules_.find(mol->getGlobalIndex());
164		if (i == molecules_.end() ) {
165	<
166	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
167	<
168	<	nAtoms_ += mol->getNAtoms();
169	<	nBonds_ += mol->getNBonds();
170	<	nBends_ += mol->getNBends();
171	<	nTorsions_ += mol->getNTorsions();
172	<	nRigidBodies_ += mol->getNRigidBodies();
173	<	nIntegrableObjects_ += mol->getNIntegrableObjects();
174	<	nCutoffGroups_ += mol->getNCutoffGroups();
175	<	nConstraints_ += mol->getNConstraintPairs();
176	<
177	<	addExcludePairs(mol);
178	<
179	<	return true;
180	<	} else {
181	<	return false;
165	>
166	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
167	>
168	>	nAtoms_ += mol->getNAtoms();
169	>	nBonds_ += mol->getNBonds();
170	>	nBends_ += mol->getNBends();
171	>	nTorsions_ += mol->getNTorsions();
172	>	nInversions_ += mol->getNInversions();
173	>	nRigidBodies_ += mol->getNRigidBodies();
174	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
175	>	nCutoffGroups_ += mol->getNCutoffGroups();
176	>	nConstraints_ += mol->getNConstraintPairs();
177	>
178	>	addInteractionPairs(mol);
179	>
180	>	return true;
181	>	} else {
182	>	return false;
183		}
184	<	}
185	<
186	<	bool SimInfo::removeMolecule(Molecule* mol) {
184	>	}
185	>
186	>	bool SimInfo::removeMolecule(Molecule* mol) {
187		MoleculeIterator i;
188		i = molecules_.find(mol->getGlobalIndex());
189
190		if (i != molecules_.end() ) {
191
192	<	assert(mol == i->second);
192	>	assert(mol == i->second);
193
194	<	nAtoms_ -= mol->getNAtoms();
195	<	nBonds_ -= mol->getNBonds();
196	<	nBends_ -= mol->getNBends();
197	<	nTorsions_ -= mol->getNTorsions();
198	<	nRigidBodies_ -= mol->getNRigidBodies();
199	<	nIntegrableObjects_ -= mol->getNIntegrableObjects();
200	<	nCutoffGroups_ -= mol->getNCutoffGroups();
201	<	nConstraints_ -= mol->getNConstraintPairs();
194	>	nAtoms_ -= mol->getNAtoms();
195	>	nBonds_ -= mol->getNBonds();
196	>	nBends_ -= mol->getNBends();
197	>	nTorsions_ -= mol->getNTorsions();
198	>	nInversions_ -= mol->getNInversions();
199	>	nRigidBodies_ -= mol->getNRigidBodies();
200	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
201	>	nCutoffGroups_ -= mol->getNCutoffGroups();
202	>	nConstraints_ -= mol->getNConstraintPairs();
203
204	<	removeExcludePairs(mol);
205	<	molecules_.erase(mol->getGlobalIndex());
204	>	removeInteractionPairs(mol);
205	>	molecules_.erase(mol->getGlobalIndex());
206
207	<	delete mol;
207	>	delete mol;
208
209	<	return true;
209	>	return true;
210		} else {
211	<	return false;
211	>	return false;
212		}
213	+	}
214
220	–
221	–	}
222	–
215
216	<	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
216	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
217		i = molecules_.begin();
218		return i == molecules_.end() ? NULL : i->second;
219	<	}
219	>	}
220
221	<	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
221	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
222		++i;
223		return i == molecules_.end() ? NULL : i->second;
224	<	}
224	>	}
225
226
227	<	void SimInfo::calcNdf() {
227	>	void SimInfo::calcNdf() {
228		int ndf_local;
229		MoleculeIterator i;
230	<	std::vector<StuntDouble*>::iterator j;
230	>	vector<StuntDouble*>::iterator j;
231		Molecule* mol;
232		StuntDouble* integrableObject;
233
234		ndf_local = 0;
235
236		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
237	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
238	<	integrableObject = mol->nextIntegrableObject(j)) {
237	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
238	>	integrableObject = mol->nextIntegrableObject(j)) {
239
240	<	ndf_local += 3;
240	>	ndf_local += 3;
241
242	<	if (integrableObject->isDirectional()) {
243	<	if (integrableObject->isLinear()) {
244	<	ndf_local += 2;
245	<	} else {
246	<	ndf_local += 3;
247	<	}
248	<	}
242	>	if (integrableObject->isDirectional()) {
243	>	if (integrableObject->isLinear()) {
244	>	ndf_local += 2;
245	>	} else {
246	>	ndf_local += 3;
247	>	}
248	>	}
249
250	<	}//end for (integrableObject)
251	<	}// end for (mol)
250	>	}
251	>	}
252
253		// n_constraints is local, so subtract them on each processor
254		ndf_local -= nConstraints_;
#	Line 271 | Line 263 | void SimInfo::calcNdf() {
263		// entire system:
264		ndf_ = ndf_ - 3 - nZconstraint_;
265
266	<	}
266	>	}
267
268	<	void SimInfo::calcNdfRaw() {
268	>	int SimInfo::getFdf() {
269	>	#ifdef IS_MPI
270	>	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
271	>	#else
272	>	fdf_ = fdf_local;
273	>	#endif
274	>	return fdf_;
275	>	}
276	>
277	>	unsigned int SimInfo::getNLocalCutoffGroups(){
278	>	int nLocalCutoffAtoms = 0;
279	>	Molecule* mol;
280	>	MoleculeIterator mi;
281	>	CutoffGroup* cg;
282	>	Molecule::CutoffGroupIterator ci;
283	>
284	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
285	>
286	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
287	>	cg = mol->nextCutoffGroup(ci)) {
288	>	nLocalCutoffAtoms += cg->getNumAtom();
289	>
290	>	}
291	>	}
292	>
293	>	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
294	>	}
295	>
296	>	void SimInfo::calcNdfRaw() {
297		int ndfRaw_local;
298
299		MoleculeIterator i;
300	<	std::vector<StuntDouble*>::iterator j;
300	>	vector<StuntDouble*>::iterator j;
301		Molecule* mol;
302		StuntDouble* integrableObject;
303
#	Line 285 | Line 305 | void SimInfo::calcNdfRaw() {
305		ndfRaw_local = 0;
306
307		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
308	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
309	<	integrableObject = mol->nextIntegrableObject(j)) {
308	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
309	>	integrableObject = mol->nextIntegrableObject(j)) {
310
311	<	ndfRaw_local += 3;
311	>	ndfRaw_local += 3;
312
313	<	if (integrableObject->isDirectional()) {
314	<	if (integrableObject->isLinear()) {
315	<	ndfRaw_local += 2;
316	<	} else {
317	<	ndfRaw_local += 3;
318	<	}
319	<	}
313	>	if (integrableObject->isDirectional()) {
314	>	if (integrableObject->isLinear()) {
315	>	ndfRaw_local += 2;
316	>	} else {
317	>	ndfRaw_local += 3;
318	>	}
319	>	}
320
321	<	}
321	>	}
322		}
323
324		#ifdef IS_MPI
#	Line 306 | Line 326 | void SimInfo::calcNdfRaw() {
326		#else
327		ndfRaw_ = ndfRaw_local;
328		#endif
329	<	}
329	>	}
330
331	<	void SimInfo::calcNdfTrans() {
331	>	void SimInfo::calcNdfTrans() {
332		int ndfTrans_local;
333
334		ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
#	Line 322 | Line 342 | void SimInfo::calcNdfTrans() {
342
343		ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
344
345	<	}
345	>	}
346
347	<	void SimInfo::addExcludePairs(Molecule* mol) {
348	<	std::vector<Bond*>::iterator bondIter;
349	<	std::vector<Bend*>::iterator bendIter;
350	<	std::vector<Torsion*>::iterator torsionIter;
347	>	void SimInfo::addInteractionPairs(Molecule* mol) {
348	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
349	>	vector<Bond*>::iterator bondIter;
350	>	vector<Bend*>::iterator bendIter;
351	>	vector<Torsion*>::iterator torsionIter;
352	>	vector<Inversion*>::iterator inversionIter;
353		Bond* bond;
354		Bend* bend;
355		Torsion* torsion;
356	+	Inversion* inversion;
357		int a;
358		int b;
359		int c;
360		int d;
338	–
339	–	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
340	–	a = bond->getAtomA()->getGlobalIndex();
341	–	b = bond->getAtomB()->getGlobalIndex();
342	–	exclude_.addPair(a, b);
343	–	}
361
362	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
363	<	a = bend->getAtomA()->getGlobalIndex();
364	<	b = bend->getAtomB()->getGlobalIndex();
365	<	c = bend->getAtomC()->getGlobalIndex();
362	>	// atomGroups can be used to add special interaction maps between
363	>	// groups of atoms that are in two separate rigid bodies.
364	>	// However, most site-site interactions between two rigid bodies
365	>	// are probably not special, just the ones between the physically
366	>	// bonded atoms.  Interactions *within* a single rigid body should
367	>	// always be excluded.  These are done at the bottom of this
368	>	// function.
369
370	<	exclude_.addPair(a, b);
371	<	exclude_.addPair(a, c);
372	<	exclude_.addPair(b, c);
373	<	}
374	<
375	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
376	<	a = torsion->getAtomA()->getGlobalIndex();
377	<	b = torsion->getAtomB()->getGlobalIndex();
378	<	c = torsion->getAtomC()->getGlobalIndex();
379	<	d = torsion->getAtomD()->getGlobalIndex();
370	>	map<int, set<int> > atomGroups;
371	>	Molecule::RigidBodyIterator rbIter;
372	>	RigidBody* rb;
373	>	Molecule::IntegrableObjectIterator ii;
374	>	StuntDouble* integrableObject;
375	>
376	>	for (integrableObject = mol->beginIntegrableObject(ii);
377	>	integrableObject != NULL;
378	>	integrableObject = mol->nextIntegrableObject(ii)) {
379	>
380	>	if (integrableObject->isRigidBody()) {
381	>	rb = static_cast<RigidBody*>(integrableObject);
382	>	vector<Atom*> atoms = rb->getAtoms();
383	>	set<int> rigidAtoms;
384	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
385	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
386	>	}
387	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
388	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
389	>	}
390	>	} else {
391	>	set<int> oneAtomSet;
392	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
393	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
394	>	}
395	>	}
396	>
397	>	for (bond= mol->beginBond(bondIter); bond != NULL;
398	>	bond = mol->nextBond(bondIter)) {
399
400	<	exclude_.addPair(a, b);
401	<	exclude_.addPair(a, c);
402	<	exclude_.addPair(a, d);
403	<	exclude_.addPair(b, c);
404	<	exclude_.addPair(b, d);
405	<	exclude_.addPair(c, d);
400	>	a = bond->getAtomA()->getGlobalIndex();
401	>	b = bond->getAtomB()->getGlobalIndex();
402	>
403	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
404	>	oneTwoInteractions_.addPair(a, b);
405	>	} else {
406	>	excludedInteractions_.addPair(a, b);
407	>	}
408		}
409
410	<
411	<	}
410	>	for (bend= mol->beginBend(bendIter); bend != NULL;
411	>	bend = mol->nextBend(bendIter)) {
412
413	<	void SimInfo::removeExcludePairs(Molecule* mol) {
414	<	std::vector<Bond*>::iterator bondIter;
415	<	std::vector<Bend*>::iterator bendIter;
416	<	std::vector<Torsion*>::iterator torsionIter;
413	>	a = bend->getAtomA()->getGlobalIndex();
414	>	b = bend->getAtomB()->getGlobalIndex();
415	>	c = bend->getAtomC()->getGlobalIndex();
416	>
417	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
418	>	oneTwoInteractions_.addPair(a, b);
419	>	oneTwoInteractions_.addPair(b, c);
420	>	} else {
421	>	excludedInteractions_.addPair(a, b);
422	>	excludedInteractions_.addPair(b, c);
423	>	}
424	>
425	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
426	>	oneThreeInteractions_.addPair(a, c);
427	>	} else {
428	>	excludedInteractions_.addPair(a, c);
429	>	}
430	>	}
431	>
432	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
433	>	torsion = mol->nextTorsion(torsionIter)) {
434	>
435	>	a = torsion->getAtomA()->getGlobalIndex();
436	>	b = torsion->getAtomB()->getGlobalIndex();
437	>	c = torsion->getAtomC()->getGlobalIndex();
438	>	d = torsion->getAtomD()->getGlobalIndex();
439	>
440	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
441	>	oneTwoInteractions_.addPair(a, b);
442	>	oneTwoInteractions_.addPair(b, c);
443	>	oneTwoInteractions_.addPair(c, d);
444	>	} else {
445	>	excludedInteractions_.addPair(a, b);
446	>	excludedInteractions_.addPair(b, c);
447	>	excludedInteractions_.addPair(c, d);
448	>	}
449	>
450	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
451	>	oneThreeInteractions_.addPair(a, c);
452	>	oneThreeInteractions_.addPair(b, d);
453	>	} else {
454	>	excludedInteractions_.addPair(a, c);
455	>	excludedInteractions_.addPair(b, d);
456	>	}
457	>
458	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
459	>	oneFourInteractions_.addPair(a, d);
460	>	} else {
461	>	excludedInteractions_.addPair(a, d);
462	>	}
463	>	}
464	>
465	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
466	>	inversion = mol->nextInversion(inversionIter)) {
467	>
468	>	a = inversion->getAtomA()->getGlobalIndex();
469	>	b = inversion->getAtomB()->getGlobalIndex();
470	>	c = inversion->getAtomC()->getGlobalIndex();
471	>	d = inversion->getAtomD()->getGlobalIndex();
472	>
473	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
474	>	oneTwoInteractions_.addPair(a, b);
475	>	oneTwoInteractions_.addPair(a, c);
476	>	oneTwoInteractions_.addPair(a, d);
477	>	} else {
478	>	excludedInteractions_.addPair(a, b);
479	>	excludedInteractions_.addPair(a, c);
480	>	excludedInteractions_.addPair(a, d);
481	>	}
482	>
483	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
484	>	oneThreeInteractions_.addPair(b, c);
485	>	oneThreeInteractions_.addPair(b, d);
486	>	oneThreeInteractions_.addPair(c, d);
487	>	} else {
488	>	excludedInteractions_.addPair(b, c);
489	>	excludedInteractions_.addPair(b, d);
490	>	excludedInteractions_.addPair(c, d);
491	>	}
492	>	}
493	>
494	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
495	>	rb = mol->nextRigidBody(rbIter)) {
496	>	vector<Atom*> atoms = rb->getAtoms();
497	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
498	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
499	>	a = atoms[i]->getGlobalIndex();
500	>	b = atoms[j]->getGlobalIndex();
501	>	excludedInteractions_.addPair(a, b);
502	>	}
503	>	}
504	>	}
505	>
506	>	}
507	>
508	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
509	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
510	>	vector<Bond*>::iterator bondIter;
511	>	vector<Bend*>::iterator bendIter;
512	>	vector<Torsion*>::iterator torsionIter;
513	>	vector<Inversion*>::iterator inversionIter;
514		Bond* bond;
515		Bend* bend;
516		Torsion* torsion;
517	+	Inversion* inversion;
518		int a;
519		int b;
520		int c;
521		int d;
522	+
523	+	map<int, set<int> > atomGroups;
524	+	Molecule::RigidBodyIterator rbIter;
525	+	RigidBody* rb;
526	+	Molecule::IntegrableObjectIterator ii;
527	+	StuntDouble* integrableObject;
528
529	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
530	<	a = bond->getAtomA()->getGlobalIndex();
531	<	b = bond->getAtomB()->getGlobalIndex();
532	<	exclude_.removePair(a, b);
529	>	for (integrableObject = mol->beginIntegrableObject(ii);
530	>	integrableObject != NULL;
531	>	integrableObject = mol->nextIntegrableObject(ii)) {
532	>
533	>	if (integrableObject->isRigidBody()) {
534	>	rb = static_cast<RigidBody*>(integrableObject);
535	>	vector<Atom*> atoms = rb->getAtoms();
536	>	set<int> rigidAtoms;
537	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
538	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
539	>	}
540	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
541	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
542	>	}
543	>	} else {
544	>	set<int> oneAtomSet;
545	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
546	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
547	>	}
548	>	}
549	>
550	>	for (bond= mol->beginBond(bondIter); bond != NULL;
551	>	bond = mol->nextBond(bondIter)) {
552	>
553	>	a = bond->getAtomA()->getGlobalIndex();
554	>	b = bond->getAtomB()->getGlobalIndex();
555	>
556	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
557	>	oneTwoInteractions_.removePair(a, b);
558	>	} else {
559	>	excludedInteractions_.removePair(a, b);
560	>	}
561		}
562
563	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
564	<	a = bend->getAtomA()->getGlobalIndex();
392	<	b = bend->getAtomB()->getGlobalIndex();
393	<	c = bend->getAtomC()->getGlobalIndex();
563	>	for (bend= mol->beginBend(bendIter); bend != NULL;
564	>	bend = mol->nextBend(bendIter)) {
565
566	<	exclude_.removePair(a, b);
567	<	exclude_.removePair(a, c);
568	<	exclude_.removePair(b, c);
566	>	a = bend->getAtomA()->getGlobalIndex();
567	>	b = bend->getAtomB()->getGlobalIndex();
568	>	c = bend->getAtomC()->getGlobalIndex();
569	>
570	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
571	>	oneTwoInteractions_.removePair(a, b);
572	>	oneTwoInteractions_.removePair(b, c);
573	>	} else {
574	>	excludedInteractions_.removePair(a, b);
575	>	excludedInteractions_.removePair(b, c);
576	>	}
577	>
578	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
579	>	oneThreeInteractions_.removePair(a, c);
580	>	} else {
581	>	excludedInteractions_.removePair(a, c);
582	>	}
583		}
584
585	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
586	<	a = torsion->getAtomA()->getGlobalIndex();
402	<	b = torsion->getAtomB()->getGlobalIndex();
403	<	c = torsion->getAtomC()->getGlobalIndex();
404	<	d = torsion->getAtomD()->getGlobalIndex();
585	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
586	>	torsion = mol->nextTorsion(torsionIter)) {
587
588	<	exclude_.removePair(a, b);
589	<	exclude_.removePair(a, c);
590	<	exclude_.removePair(a, d);
591	<	exclude_.removePair(b, c);
592	<	exclude_.removePair(b, d);
593	<	exclude_.removePair(c, d);
588	>	a = torsion->getAtomA()->getGlobalIndex();
589	>	b = torsion->getAtomB()->getGlobalIndex();
590	>	c = torsion->getAtomC()->getGlobalIndex();
591	>	d = torsion->getAtomD()->getGlobalIndex();
592	>
593	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
594	>	oneTwoInteractions_.removePair(a, b);
595	>	oneTwoInteractions_.removePair(b, c);
596	>	oneTwoInteractions_.removePair(c, d);
597	>	} else {
598	>	excludedInteractions_.removePair(a, b);
599	>	excludedInteractions_.removePair(b, c);
600	>	excludedInteractions_.removePair(c, d);
601	>	}
602	>
603	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
604	>	oneThreeInteractions_.removePair(a, c);
605	>	oneThreeInteractions_.removePair(b, d);
606	>	} else {
607	>	excludedInteractions_.removePair(a, c);
608	>	excludedInteractions_.removePair(b, d);
609	>	}
610	>
611	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
612	>	oneFourInteractions_.removePair(a, d);
613	>	} else {
614	>	excludedInteractions_.removePair(a, d);
615	>	}
616		}
617
618	<	}
618	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
619	>	inversion = mol->nextInversion(inversionIter)) {
620
621	+	a = inversion->getAtomA()->getGlobalIndex();
622	+	b = inversion->getAtomB()->getGlobalIndex();
623	+	c = inversion->getAtomC()->getGlobalIndex();
624	+	d = inversion->getAtomD()->getGlobalIndex();
625
626	<	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
627	<	int curStampId;
626	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
627	>	oneTwoInteractions_.removePair(a, b);
628	>	oneTwoInteractions_.removePair(a, c);
629	>	oneTwoInteractions_.removePair(a, d);
630	>	} else {
631	>	excludedInteractions_.removePair(a, b);
632	>	excludedInteractions_.removePair(a, c);
633	>	excludedInteractions_.removePair(a, d);
634	>	}
635
636	+	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
637	+	oneThreeInteractions_.removePair(b, c);
638	+	oneThreeInteractions_.removePair(b, d);
639	+	oneThreeInteractions_.removePair(c, d);
640	+	} else {
641	+	excludedInteractions_.removePair(b, c);
642	+	excludedInteractions_.removePair(b, d);
643	+	excludedInteractions_.removePair(c, d);
644	+	}
645	+	}
646	+
647	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
648	+	rb = mol->nextRigidBody(rbIter)) {
649	+	vector<Atom*> atoms = rb->getAtoms();
650	+	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
651	+	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
652	+	a = atoms[i]->getGlobalIndex();
653	+	b = atoms[j]->getGlobalIndex();
654	+	excludedInteractions_.removePair(a, b);
655	+	}
656	+	}
657	+	}
658	+
659	+	}
660	+
661	+
662	+	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
663	+	int curStampId;
664	+
665		//index from 0
666		curStampId = moleculeStamps_.size();
667
668		moleculeStamps_.push_back(molStamp);
669		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
670	<	}
670	>	}
671
427	–	void SimInfo::update() {
672
673	<	setupSimType();
674	<
675	<	#ifdef IS_MPI
676	<	setupFortranParallel();
677	<	#endif
678	<
679	<	setupFortranSim();
680	<
681	<	//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	<
673	>	/**
674	>	* update
675	>	*
676	>	*  Performs the global checks and variable settings after the
677	>	*  objects have been created.
678	>	*
679	>	*/
680	>	void SimInfo::update() {
681	>	setupSimVariables();
682		calcNdf();
683		calcNdfRaw();
684		calcNdfTrans();
685	<
686	<	fortranInitialized_ = true;
687	<	}
688	<
689	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
685	>	}
686	>
687	>	/**
688	>	* getSimulatedAtomTypes
689	>	*
690	>	* Returns an STL set of AtomType* that are actually present in this
691	>	* simulation.  Must query all processors to assemble this information.
692	>	*
693	>	*/
694	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
695		SimInfo::MoleculeIterator mi;
696		Molecule* mol;
697		Molecule::AtomIterator ai;
698		Atom* atom;
699	<	std::set<AtomType*> atomTypes;
700	<
699	>	set<AtomType*> atomTypes;
700	>
701		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
702	+	for(atom = mol->beginAtom(ai); atom != NULL;
703	+	atom = mol->nextAtom(ai)) {
704	+	atomTypes.insert(atom->getAtomType());
705	+	}
706	+	}
707	+
708	+	#ifdef IS_MPI
709
710	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
711	<	atomTypes.insert(atom->getAtomType());
712	<	}
713	<
714	<	}
710	>	// loop over the found atom types on this processor, and add their
711	>	// numerical idents to a vector:
712	>
713	>	vector<int> foundTypes;
714	>	set<AtomType*>::iterator i;
715	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
716	>	foundTypes.push_back( (*i)->getIdent() );
717
718	<	return atomTypes;
719	<	}
718	>	// count_local holds the number of found types on this processor
719	>	int count_local = foundTypes.size();
720
721	<	void SimInfo::setupSimType() {
722	<	std::set<AtomType*>::iterator i;
723	<	std::set<AtomType*> atomTypes;
724	<	atomTypes = getUniqueAtomTypes();
725	<
726	<	int useLennardJones = 0;
727	<	int useElectrostatic = 0;
728	<	int useEAM = 0;
729	<	int useCharge = 0;
730	<	int useDirectional = 0;
731	<	int useDipole = 0;
732	<	int useGayBerne = 0;
733	<	int useSticky = 0;
734	<	int useShape = 0;
735	<	int useFLARB = 0; //it is not in AtomType yet
736	<	int useDirectionalAtom = 0;
737	<	int useElectrostatics = 0;
493	<	//usePBC and useRF are from simParams
494	<	int usePBC = simParams_->getPBC();
495	<	int useRF = simParams_->getUseRF();
496	<
497	<	//loop over all of the atom types
498	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
499	<	useLennardJones |= (*i)->isLennardJones();
500	<	useElectrostatic |= (*i)->isElectrostatic();
501	<	useEAM |= (*i)->isEAM();
502	<	useCharge |= (*i)->isCharge();
503	<	useDirectional |= (*i)->isDirectional();
504	<	useDipole |= (*i)->isDipole();
505	<	useGayBerne |= (*i)->isGayBerne();
506	<	useSticky |= (*i)->isSticky();
507	<	useShape |= (*i)->isShape();
721	>	int nproc = MPI::COMM_WORLD.Get_size();
722	>
723	>	// we need arrays to hold the counts and displacement vectors for
724	>	// all processors
725	>	vector<int> counts(nproc, 0);
726	>	vector<int> disps(nproc, 0);
727	>
728	>	// fill the counts array
729	>	MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
730	>	1, MPI::INT);
731	>
732	>	// use the processor counts to compute the displacement array
733	>	disps[0] = 0;
734	>	int totalCount = counts[0];
735	>	for (int iproc = 1; iproc < nproc; iproc++) {
736	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
737	>	totalCount += counts[iproc];
738		}
739
740	<	if (useSticky || useDipole || useGayBerne || useShape) {
741	<	useDirectionalAtom = 1;
742	<	}
740	>	// we need a (possibly redundant) set of all found types:
741	>	vector<int> ftGlobal(totalCount);
742	>
743	>	// now spray out the foundTypes to all the other processors:
744	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
745	>	&ftGlobal[0], &counts[0], &disps[0],
746	>	MPI::INT);
747
748	<	if (useCharge || useDipole) {
515	<	useElectrostatics = 1;
516	<	}
748	>	vector<int>::iterator j;
749
750	<	#ifdef IS_MPI
751	<	int temp;
750	>	// foundIdents is a stl set, so inserting an already found ident
751	>	// will have no effect.
752	>	set<int> foundIdents;
753
754	<	temp = usePBC;
755	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
523	<
524	<	temp = useDirectionalAtom;
525	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
526	<
527	<	temp = useLennardJones;
528	<	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
529	<
530	<	temp = useElectrostatics;
531	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
532	<
533	<	temp = useCharge;
534	<	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
535	<
536	<	temp = useDipole;
537	<	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
538	<
539	<	temp = useSticky;
540	<	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
541	<
542	<	temp = useGayBerne;
543	<	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
544	<
545	<	temp = useEAM;
546	<	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
547	<
548	<	temp = useShape;
549	<	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
550	<
551	<	temp = useFLARB;
552	<	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
553	<
554	<	temp = useRF;
555	<	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
754	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
755	>	foundIdents.insert((*j));
756
757	+	// now iterate over the foundIdents and get the actual atom types
758	+	// that correspond to these:
759	+	set<int>::iterator it;
760	+	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
761	+	atomTypes.insert( forceField_->getAtomType((*it)) );
762	+
763		#endif
764
765	<	fInfo_.SIM_uses_PBC = usePBC;
766	<	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;
765	>	return atomTypes;
766	>	}
767
768	<	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
769	<
770	<	if (simParams_->haveDielectric()) {
771	<	fInfo_.dielect = simParams_->getDielectric();
772	<	} else {
773	<	sprintf(painCave.errMsg,
774	<	"SimSetup Error: No Dielectric constant was set.\n"
775	<	"\tYou are trying to use Reaction Field without"
776	<	"\tsetting a dielectric constant!\n");
777	<	painCave.isFatal = 1;
778	<	simError();
779	<	}
780	<
781	<	} else {
782	<	fInfo_.dielect = 0.0;
768	>	void SimInfo::setupSimVariables() {
769	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
770	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
771	>	calcBoxDipole_ = false;
772	>	if ( simParams_->haveAccumulateBoxDipole() )
773	>	if ( simParams_->getAccumulateBoxDipole() ) {
774	>	calcBoxDipole_ = true;
775	>	}
776	>
777	>	set<AtomType*>::iterator i;
778	>	set<AtomType*> atomTypes;
779	>	atomTypes = getSimulatedAtomTypes();
780	>	int usesElectrostatic = 0;
781	>	int usesMetallic = 0;
782	>	int usesDirectional = 0;
783	>	//loop over all of the atom types
784	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
785	>	usesElectrostatic |= (*i)->isElectrostatic();
786	>	usesMetallic |= (*i)->isMetal();
787	>	usesDirectional |= (*i)->isDirectional();
788		}
789	+
790	+	#ifdef IS_MPI
791	+	int temp;
792	+	temp = usesDirectional;
793	+	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
794	+
795	+	temp = usesMetallic;
796	+	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
797	+
798	+	temp = usesElectrostatic;
799	+	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
800	+	#else
801
802	<	}
802	>	usesDirectionalAtoms_ = usesDirectional;
803	>	usesMetallicAtoms_ = usesMetallic;
804	>	usesElectrostaticAtoms_ = usesElectrostatic;
805
806	<	void SimInfo::setupFortranSim() {
592	<	int isError;
593	<	int nExclude;
594	<	std::vector<int> fortranGlobalGroupMembership;
806	>	#endif
807
808	<	nExclude = exclude_.getSize();
809	<	isError = 0;
808	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
809	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
810	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
811	>	}
812
599	–	//globalGroupMembership_ is filled by SimCreator
600	–	for (int i = 0; i < nGlobalAtoms_; i++) {
601	–	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
602	–	}
813
814	<	//calculate mass ratio of cutoff group
605	<	std::vector<double> mfact;
814	>	vector<int> SimInfo::getGlobalAtomIndices() {
815		SimInfo::MoleculeIterator mi;
816		Molecule* mol;
608	–	Molecule::CutoffGroupIterator ci;
609	–	CutoffGroup* cg;
817		Molecule::AtomIterator ai;
818		Atom* atom;
612	–	double totalMass;
819
820	<	//to avoid memory reallocation, reserve enough space for mfact
615	<	mfact.reserve(getNCutoffGroups());
820	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
821
822	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
823	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
824	<
825	<	totalMass = cg->getMass();
826	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
622	<	mfact.push_back(atom->getMass()/totalMass);
623	<	}
624	<
625	<	}
822	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
823	>
824	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
825	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
826	>	}
827		}
828	+	return GlobalAtomIndices;
829	+	}
830
628	–	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
629	–	std::vector<int> identArray;
831
832	<	//to avoid memory reallocation, reserve enough space identArray
833	<	identArray.reserve(getNAtoms());
834	<
835	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
836	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
636	<	identArray.push_back(atom->getIdent());
637	<	}
638	<	}
832	>	vector<int> SimInfo::getGlobalGroupIndices() {
833	>	SimInfo::MoleculeIterator mi;
834	>	Molecule* mol;
835	>	Molecule::CutoffGroupIterator ci;
836	>	CutoffGroup* cg;
837
838	<	//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	<	}
838	>	vector<int> GlobalGroupIndices;
839
840	<	//setup fortran simulation
841	<	//gloalExcludes and molMembershipArray should go away (They are never used)
842	<	//why the hell fortran need to know molecule?
843	<	//OOPSE = Object-Obfuscated Parallel Simulation Engine
844	<	int nGlobalExcludes = 0;
845	<	int* globalExcludes = NULL;
846	<	int* excludeList = exclude_.getExcludeList();
847	<	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();
840	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
841	>
842	>	//local index of cutoff group is trivial, it only depends on the
843	>	//order of travesing
844	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
845	>	cg = mol->nextCutoffGroup(ci)) {
846	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
847	>	}
848		}
849	+	return GlobalGroupIndices;
850	+	}
851
667	–	#ifdef IS_MPI
668	–	sprintf( checkPointMsg,
669	–	"succesfully sent the simulation information to fortran.\n");
670	–	MPIcheckPoint();
671	–	#endif // is_mpi
672	–	}
852
853	+	void SimInfo::prepareTopology() {
854	+	int nExclude, nOneTwo, nOneThree, nOneFour;
855
856	<	#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;
856	>	//calculate mass ratio of cutoff group
857		SimInfo::MoleculeIterator mi;
682	–	Molecule::AtomIterator ai;
683	–	Molecule::CutoffGroupIterator ci;
858		Molecule* mol;
859	<	Atom* atom;
859	>	Molecule::CutoffGroupIterator ci;
860		CutoffGroup* cg;
861	<	mpiSimData parallelData;
862	<	int isError;
861	>	Molecule::AtomIterator ai;
862	>	Atom* atom;
863	>	RealType totalMass;
864
865	<	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
865	>	/**
866	>	* The mass factor is the relative mass of an atom to the total
867	>	* mass of the cutoff group it belongs to.  By default, all atoms
868	>	* are their own cutoff groups, and therefore have mass factors of
869	>	* 1.  We need some special handling for massless atoms, which
870	>	* will be treated as carrying the entire mass of the cutoff
871	>	* group.
872	>	*/
873	>	massFactors_.clear();
874	>	massFactors_.resize(getNAtoms(), 1.0);
875	>
876	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
877	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
878	>	cg = mol->nextCutoffGroup(ci)) {
879
880	<	//local index(index in DataStorge) of atom is important
881	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
882	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
883	<	}
884	<
885	<	//local index of cutoff group is trivial, it only depends on the order of travesing
886	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
887	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
888	<	}
701	<
880	>	totalMass = cg->getMass();
881	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
882	>	// Check for massless groups - set mfact to 1 if true
883	>	if (totalMass != 0)
884	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
885	>	else
886	>	massFactors_[atom->getLocalIndex()] = 1.0;
887	>	}
888	>	}
889		}
890
891	<	//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));
891	>	// Build the identArray_
892
893	<	//pass mpiSimData struct and index arrays to fortran
894	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
895	<	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
896	<	&localToGlobalCutoffGroupIndex[0], &isError);
893	>	identArray_.clear();
894	>	identArray_.reserve(getNAtoms());
895	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
896	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
897	>	identArray_.push_back(atom->getIdent());
898	>	}
899	>	}
900	>
901	>	//scan topology
902
903	<	if (isError) {
904	<	sprintf(painCave.errMsg,
905	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
906	<	painCave.isFatal = 1;
723	<	simError();
724	<	}
903	>	nExclude = excludedInteractions_.getSize();
904	>	nOneTwo = oneTwoInteractions_.getSize();
905	>	nOneThree = oneThreeInteractions_.getSize();
906	>	nOneFour = oneFourInteractions_.getSize();
907
908	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
909	<	MPIcheckPoint();
908	>	int* excludeList = excludedInteractions_.getPairList();
909	>	int* oneTwoList = oneTwoInteractions_.getPairList();
910	>	int* oneThreeList = oneThreeInteractions_.getPairList();
911	>	int* oneFourList = oneFourInteractions_.getPairList();
912
913	+	topologyDone_ = true;
914	+	}
915
916	<	}
916	>	void SimInfo::addProperty(GenericData* genData) {
917	>	properties_.addProperty(genData);
918	>	}
919
920	<	#endif
920	>	void SimInfo::removeProperty(const string& propName) {
921	>	properties_.removeProperty(propName);
922	>	}
923
924	<	double SimInfo::calcMaxCutoffRadius() {
924	>	void SimInfo::clearProperties() {
925	>	properties_.clearProperties();
926	>	}
927
928	+	vector<string> SimInfo::getPropertyNames() {
929	+	return properties_.getPropertyNames();
930	+	}
931	+
932	+	vector<GenericData*> SimInfo::getProperties() {
933	+	return properties_.getProperties();
934	+	}
935
936	<	std::set<AtomType*> atomTypes;
937	<	std::set<AtomType*>::iterator i;
938	<	std::vector<double> cutoffRadius;
936	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
937	>	return properties_.getPropertyByName(propName);
938	>	}
939
940	<	//get the unique atom types
941	<	atomTypes = getUniqueAtomTypes();
942	<
943	<	//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) {
814	<	properties_.addProperty(genData);
815	<	}
816	<
817	<	void SimInfo::removeProperty(const std::string& propName) {
818	<	properties_.removeProperty(propName);
819	<	}
820	<
821	<	void SimInfo::clearProperties() {
822	<	properties_.clearProperties();
823	<	}
824	<
825	<	std::vector<std::string> SimInfo::getPropertyNames() {
826	<	return properties_.getPropertyNames();
827	<	}
828	<
829	<	std::vector<GenericData*> SimInfo::getProperties() {
830	<	return properties_.getProperties();
831	<	}
832	<
833	<	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
834	<	return properties_.getPropertyByName(propName);
835	<	}
836	<
837	<	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
838	<	if (sman_ == sman_) {
839	<	return;
840	<	}
841	<
940	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
941	>	if (sman_ == sman) {
942	>	return;
943	>	}
944		delete sman_;
945		sman_ = sman;
946
947		Molecule* mol;
948		RigidBody* rb;
949		Atom* atom;
950	+	CutoffGroup* cg;
951		SimInfo::MoleculeIterator mi;
952		Molecule::RigidBodyIterator rbIter;
953	<	Molecule::AtomIterator atomIter;;
953	>	Molecule::AtomIterator atomIter;
954	>	Molecule::CutoffGroupIterator cgIter;
955
956		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
957
958	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
959	<	atom->setSnapshotManager(sman_);
960	<	}
958	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
959	>	atom->setSnapshotManager(sman_);
960	>	}
961
962	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
963	<	rb->setSnapshotManager(sman_);
964	<	}
962	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
963	>	rb->setSnapshotManager(sman_);
964	>	}
965	>
966	>	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
967	>	cg->setSnapshotManager(sman_);
968	>	}
969		}
970
971	<	}
971	>	}
972
973	<	Vector3d SimInfo::getComVel(){
973	>	Vector3d SimInfo::getComVel(){
974		SimInfo::MoleculeIterator i;
975		Molecule* mol;
976
977		Vector3d comVel(0.0);
978	<	double totalMass = 0.0;
978	>	RealType totalMass = 0.0;
979
980
981		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
982	<	double mass = mol->getMass();
983	<	totalMass += mass;
984	<	comVel += mass * mol->getComVel();
982	>	RealType mass = mol->getMass();
983	>	totalMass += mass;
984	>	comVel += mass * mol->getComVel();
985		}
986
987		#ifdef IS_MPI
988	<	double tmpMass = totalMass;
988	>	RealType tmpMass = totalMass;
989		Vector3d tmpComVel(comVel);
990	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
991	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
990	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
991	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
992		#endif
993
994		comVel /= totalMass;
995
996		return comVel;
997	<	}
997	>	}
998
999	<	Vector3d SimInfo::getCom(){
999	>	Vector3d SimInfo::getCom(){
1000		SimInfo::MoleculeIterator i;
1001		Molecule* mol;
1002
1003		Vector3d com(0.0);
1004	<	double totalMass = 0.0;
1004	>	RealType totalMass = 0.0;
1005
1006		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1007	<	double mass = mol->getMass();
1008	<	totalMass += mass;
1009	<	com += mass * mol->getCom();
1007	>	RealType mass = mol->getMass();
1008	>	totalMass += mass;
1009	>	com += mass * mol->getCom();
1010		}
1011
1012		#ifdef IS_MPI
1013	<	double tmpMass = totalMass;
1013	>	RealType tmpMass = totalMass;
1014		Vector3d tmpCom(com);
1015	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1016	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1015	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1016	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1017		#endif
1018
1019		com /= totalMass;
1020
1021		return com;
1022
1023	<	}
1023	>	}
1024
1025	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1025	>	ostream& operator <<(ostream& o, SimInfo& info) {
1026
1027		return o;
1028	<	}
1028	>	}
1029	>
1030	>
1031	>	/*
1032	>	Returns center of mass and center of mass velocity in one function call.
1033	>	*/
1034	>
1035	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1036	>	SimInfo::MoleculeIterator i;
1037	>	Molecule* mol;
1038	>
1039	>
1040	>	RealType totalMass = 0.0;
1041	>
1042
1043	<	}//end namespace oopse
1043	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1044	>	RealType mass = mol->getMass();
1045	>	totalMass += mass;
1046	>	com += mass * mol->getCom();
1047	>	comVel += mass * mol->getComVel();
1048	>	}
1049	>
1050	>	#ifdef IS_MPI
1051	>	RealType tmpMass = totalMass;
1052	>	Vector3d tmpCom(com);
1053	>	Vector3d tmpComVel(comVel);
1054	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1055	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1056	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1057	>	#endif
1058	>
1059	>	com /= totalMass;
1060	>	comVel /= totalMass;
1061	>	}
1062	>
1063	>	/*
1064	>	Return intertia tensor for entire system and angular momentum Vector.
1065
1066	+
1067	+	[  Ixx -Ixy  -Ixz ]
1068	+	J =| -Iyx  Iyy  -Iyz |
1069	+	[ -Izx -Iyz   Izz ]
1070	+	*/
1071	+
1072	+	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1073	+
1074	+
1075	+	RealType xx = 0.0;
1076	+	RealType yy = 0.0;
1077	+	RealType zz = 0.0;
1078	+	RealType xy = 0.0;
1079	+	RealType xz = 0.0;
1080	+	RealType yz = 0.0;
1081	+	Vector3d com(0.0);
1082	+	Vector3d comVel(0.0);
1083	+
1084	+	getComAll(com, comVel);
1085	+
1086	+	SimInfo::MoleculeIterator i;
1087	+	Molecule* mol;
1088	+
1089	+	Vector3d thisq(0.0);
1090	+	Vector3d thisv(0.0);
1091	+
1092	+	RealType thisMass = 0.0;
1093	+
1094	+
1095	+
1096	+
1097	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1098	+
1099	+	thisq = mol->getCom()-com;
1100	+	thisv = mol->getComVel()-comVel;
1101	+	thisMass = mol->getMass();
1102	+	// Compute moment of intertia coefficients.
1103	+	xx += thisq[0]*thisq[0]*thisMass;
1104	+	yy += thisq[1]*thisq[1]*thisMass;
1105	+	zz += thisq[2]*thisq[2]*thisMass;
1106	+
1107	+	// compute products of intertia
1108	+	xy += thisq[0]*thisq[1]*thisMass;
1109	+	xz += thisq[0]*thisq[2]*thisMass;
1110	+	yz += thisq[1]*thisq[2]*thisMass;
1111	+
1112	+	angularMomentum += cross( thisq, thisv ) * thisMass;
1113	+
1114	+	}
1115	+
1116	+
1117	+	inertiaTensor(0,0) = yy + zz;
1118	+	inertiaTensor(0,1) = -xy;
1119	+	inertiaTensor(0,2) = -xz;
1120	+	inertiaTensor(1,0) = -xy;
1121	+	inertiaTensor(1,1) = xx + zz;
1122	+	inertiaTensor(1,2) = -yz;
1123	+	inertiaTensor(2,0) = -xz;
1124	+	inertiaTensor(2,1) = -yz;
1125	+	inertiaTensor(2,2) = xx + yy;
1126	+
1127	+	#ifdef IS_MPI
1128	+	Mat3x3d tmpI(inertiaTensor);
1129	+	Vector3d tmpAngMom;
1130	+	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1131	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1132	+	#endif
1133	+
1134	+	return;
1135	+	}
1136	+
1137	+	//Returns the angular momentum of the system
1138	+	Vector3d SimInfo::getAngularMomentum(){
1139	+
1140	+	Vector3d com(0.0);
1141	+	Vector3d comVel(0.0);
1142	+	Vector3d angularMomentum(0.0);
1143	+
1144	+	getComAll(com,comVel);
1145	+
1146	+	SimInfo::MoleculeIterator i;
1147	+	Molecule* mol;
1148	+
1149	+	Vector3d thisr(0.0);
1150	+	Vector3d thisp(0.0);
1151	+
1152	+	RealType thisMass;
1153	+
1154	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1155	+	thisMass = mol->getMass();
1156	+	thisr = mol->getCom()-com;
1157	+	thisp = (mol->getComVel()-comVel)*thisMass;
1158	+
1159	+	angularMomentum += cross( thisr, thisp );
1160	+
1161	+	}
1162	+
1163	+	#ifdef IS_MPI
1164	+	Vector3d tmpAngMom;
1165	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1166	+	#endif
1167	+
1168	+	return angularMomentum;
1169	+	}
1170	+
1171	+	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1172	+	return IOIndexToIntegrableObject.at(index);
1173	+	}
1174	+
1175	+	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1176	+	IOIndexToIntegrableObject= v;
1177	+	}
1178	+
1179	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1180	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1181	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1182	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1183	+	*/
1184	+	void SimInfo::getGyrationalVolume(RealType &volume){
1185	+	Mat3x3d intTensor;
1186	+	RealType det;
1187	+	Vector3d dummyAngMom;
1188	+	RealType sysconstants;
1189	+	RealType geomCnst;
1190	+
1191	+	geomCnst = 3.0/2.0;
1192	+	/* Get the inertial tensor and angular momentum for free*/
1193	+	getInertiaTensor(intTensor,dummyAngMom);
1194	+
1195	+	det = intTensor.determinant();
1196	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1197	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(det);
1198	+	return;
1199	+	}
1200	+
1201	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1202	+	Mat3x3d intTensor;
1203	+	Vector3d dummyAngMom;
1204	+	RealType sysconstants;
1205	+	RealType geomCnst;
1206	+
1207	+	geomCnst = 3.0/2.0;
1208	+	/* Get the inertial tensor and angular momentum for free*/
1209	+	getInertiaTensor(intTensor,dummyAngMom);
1210	+
1211	+	detI = intTensor.determinant();
1212	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1213	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(detI);
1214	+	return;
1215	+	}
1216	+	/*
1217	+	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1218	+	assert( v.size() == nAtoms_ + nRigidBodies_);
1219	+	sdByGlobalIndex_ = v;
1220	+	}
1221	+
1222	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1223	+	//assert(index < nAtoms_ + nRigidBodies_);
1224	+	return sdByGlobalIndex_.at(index);
1225	+	}
1226	+	*/
1227	+	int SimInfo::getNGlobalConstraints() {
1228	+	int nGlobalConstraints;
1229	+	#ifdef IS_MPI
1230	+	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1231	+	MPI_COMM_WORLD);
1232	+	#else
1233	+	nGlobalConstraints =  nConstraints_;
1234	+	#endif
1235	+	return nGlobalConstraints;
1236	+	}
1237	+
1238	+	}//end namespace OpenMD
1239	+

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 331 by tim, Sun Feb 13 21:18:27 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1668 by gezelter, Fri Jan 6 19:03:05 2012 UTC

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

Diff Legend

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