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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 326 by tim, Sun Feb 13 20:05:42 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1583 by gezelter, Thu Jun 16 22:00:08 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), selectMan_(NULL) {
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), topologyDone_(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
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
129		nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
130	<
131	<	//every free atom (atom does not belong to rigid bodies) is an integrable object
132	<	//therefore the total number of  integrable objects in the system is equal to
133	<	//the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
134	<	//file plus the number of  rigid bodies defined in meta-data file
135	<	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
136	<
130	>
131	>	//every free atom (atom does not belong to rigid bodies) is an
132	>	//integrable object therefore the total number of integrable objects
133	>	//in the system is equal to the total number of atoms minus number of
134	>	//atoms belong to rigid body defined in meta-data file plus the number
135	>	//of rigid bodies defined in meta-data file
136	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
137	>	+ nGlobalRigidBodies_;
138	>
139		nGlobalMols_ = molStampIds_.size();
137	–
138	–	#ifdef IS_MPI
140		molToProcMap_.resize(nGlobalMols_);
141	<	#endif
142	<
143	<	selectMan_ = new SelectionManager(this);
144	<	selectMan_->selectAll();
145	<	}
146	<
147	<	SimInfo::~SimInfo() {
148	<	//MemoryUtils::deleteVectorOfPointer(molecules_);
149	<
149	<	MemoryUtils::deleteVectorOfPointer(moleculeStamps_);
150	<
141	>	}
142	>
143	>	SimInfo::~SimInfo() {
144	>	map<int, Molecule*>::iterator i;
145	>	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
146	>	delete i->second;
147	>	}
148	>	molecules_.clear();
149	>
150		delete sman_;
151		delete simParams_;
152		delete forceField_;
153	<	delete selectMan_;
155	<	}
153	>	}
154
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	–	}
155
156	<	bool SimInfo::addMolecule(Molecule* mol) {
156	>	bool SimInfo::addMolecule(Molecule* mol) {
157		MoleculeIterator i;
158	<
158	>
159		i = molecules_.find(mol->getGlobalIndex());
160		if (i == molecules_.end() ) {
161	<
162	<	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
163	<
164	<	nAtoms_ += mol->getNAtoms();
165	<	nBonds_ += mol->getNBonds();
166	<	nBends_ += mol->getNBends();
167	<	nTorsions_ += mol->getNTorsions();
168	<	nRigidBodies_ += mol->getNRigidBodies();
169	<	nIntegrableObjects_ += mol->getNIntegrableObjects();
170	<	nCutoffGroups_ += mol->getNCutoffGroups();
171	<	nConstraints_ += mol->getNConstraintPairs();
172	<
173	<	addExcludePairs(mol);
174	<
175	<	return true;
176	<	} else {
177	<	return false;
161	>
162	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
163	>
164	>	nAtoms_ += mol->getNAtoms();
165	>	nBonds_ += mol->getNBonds();
166	>	nBends_ += mol->getNBends();
167	>	nTorsions_ += mol->getNTorsions();
168	>	nInversions_ += mol->getNInversions();
169	>	nRigidBodies_ += mol->getNRigidBodies();
170	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
171	>	nCutoffGroups_ += mol->getNCutoffGroups();
172	>	nConstraints_ += mol->getNConstraintPairs();
173	>
174	>	addInteractionPairs(mol);
175	>
176	>	return true;
177	>	} else {
178	>	return false;
179		}
180	<	}
181	<
182	<	bool SimInfo::removeMolecule(Molecule* mol) {
180	>	}
181	>
182	>	bool SimInfo::removeMolecule(Molecule* mol) {
183		MoleculeIterator i;
184		i = molecules_.find(mol->getGlobalIndex());
185
186		if (i != molecules_.end() ) {
187
188	<	assert(mol == i->second);
188	>	assert(mol == i->second);
189
190	<	nAtoms_ -= mol->getNAtoms();
191	<	nBonds_ -= mol->getNBonds();
192	<	nBends_ -= mol->getNBends();
193	<	nTorsions_ -= mol->getNTorsions();
194	<	nRigidBodies_ -= mol->getNRigidBodies();
195	<	nIntegrableObjects_ -= mol->getNIntegrableObjects();
196	<	nCutoffGroups_ -= mol->getNCutoffGroups();
197	<	nConstraints_ -= mol->getNConstraintPairs();
190	>	nAtoms_ -= mol->getNAtoms();
191	>	nBonds_ -= mol->getNBonds();
192	>	nBends_ -= mol->getNBends();
193	>	nTorsions_ -= mol->getNTorsions();
194	>	nInversions_ -= mol->getNInversions();
195	>	nRigidBodies_ -= mol->getNRigidBodies();
196	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
197	>	nCutoffGroups_ -= mol->getNCutoffGroups();
198	>	nConstraints_ -= mol->getNConstraintPairs();
199
200	<	removeExcludePairs(mol);
201	<	molecules_.erase(mol->getGlobalIndex());
200	>	removeInteractionPairs(mol);
201	>	molecules_.erase(mol->getGlobalIndex());
202
203	<	delete mol;
203	>	delete mol;
204
205	<	return true;
205	>	return true;
206		} else {
207	<	return false;
207	>	return false;
208		}
209	+	}
210
220	–
221	–	}
222	–
211
212	<	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
212	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
213		i = molecules_.begin();
214		return i == molecules_.end() ? NULL : i->second;
215	<	}
215	>	}
216
217	<	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
217	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
218		++i;
219		return i == molecules_.end() ? NULL : i->second;
220	<	}
220	>	}
221
222
223	<	void SimInfo::calcNdf() {
223	>	void SimInfo::calcNdf() {
224		int ndf_local;
225		MoleculeIterator i;
226	<	std::vector<StuntDouble*>::iterator j;
226	>	vector<StuntDouble*>::iterator j;
227		Molecule* mol;
228		StuntDouble* integrableObject;
229
230		ndf_local = 0;
231
232		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
233	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
234	<	integrableObject = mol->nextIntegrableObject(j)) {
233	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
234	>	integrableObject = mol->nextIntegrableObject(j)) {
235
236	<	ndf_local += 3;
236	>	ndf_local += 3;
237
238	<	if (integrableObject->isDirectional()) {
239	<	if (integrableObject->isLinear()) {
240	<	ndf_local += 2;
241	<	} else {
242	<	ndf_local += 3;
243	<	}
244	<	}
238	>	if (integrableObject->isDirectional()) {
239	>	if (integrableObject->isLinear()) {
240	>	ndf_local += 2;
241	>	} else {
242	>	ndf_local += 3;
243	>	}
244	>	}
245
246	<	}//end for (integrableObject)
247	<	}// end for (mol)
246	>	}
247	>	}
248
249		// n_constraints is local, so subtract them on each processor
250		ndf_local -= nConstraints_;
#	Line 271 | Line 259 | void SimInfo::calcNdf() {
259		// entire system:
260		ndf_ = ndf_ - 3 - nZconstraint_;
261
262	<	}
262	>	}
263
264	<	void SimInfo::calcNdfRaw() {
264	>	int SimInfo::getFdf() {
265	>	#ifdef IS_MPI
266	>	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
267	>	#else
268	>	fdf_ = fdf_local;
269	>	#endif
270	>	return fdf_;
271	>	}
272	>
273	>	unsigned int SimInfo::getNLocalCutoffGroups(){
274	>	int nLocalCutoffAtoms = 0;
275	>	Molecule* mol;
276	>	MoleculeIterator mi;
277	>	CutoffGroup* cg;
278	>	Molecule::CutoffGroupIterator ci;
279	>
280	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
281	>
282	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
283	>	cg = mol->nextCutoffGroup(ci)) {
284	>	nLocalCutoffAtoms += cg->getNumAtom();
285	>
286	>	}
287	>	}
288	>
289	>	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
290	>	}
291	>
292	>	void SimInfo::calcNdfRaw() {
293		int ndfRaw_local;
294
295		MoleculeIterator i;
296	<	std::vector<StuntDouble*>::iterator j;
296	>	vector<StuntDouble*>::iterator j;
297		Molecule* mol;
298		StuntDouble* integrableObject;
299
#	Line 285 | Line 301 | void SimInfo::calcNdfRaw() {
301		ndfRaw_local = 0;
302
303		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
304	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
305	<	integrableObject = mol->nextIntegrableObject(j)) {
304	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
305	>	integrableObject = mol->nextIntegrableObject(j)) {
306
307	<	ndfRaw_local += 3;
307	>	ndfRaw_local += 3;
308
309	<	if (integrableObject->isDirectional()) {
310	<	if (integrableObject->isLinear()) {
311	<	ndfRaw_local += 2;
312	<	} else {
313	<	ndfRaw_local += 3;
314	<	}
315	<	}
309	>	if (integrableObject->isDirectional()) {
310	>	if (integrableObject->isLinear()) {
311	>	ndfRaw_local += 2;
312	>	} else {
313	>	ndfRaw_local += 3;
314	>	}
315	>	}
316
317	<	}
317	>	}
318		}
319
320		#ifdef IS_MPI
#	Line 306 | Line 322 | void SimInfo::calcNdfRaw() {
322		#else
323		ndfRaw_ = ndfRaw_local;
324		#endif
325	<	}
325	>	}
326
327	<	void SimInfo::calcNdfTrans() {
327	>	void SimInfo::calcNdfTrans() {
328		int ndfTrans_local;
329
330		ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
#	Line 322 | Line 338 | void SimInfo::calcNdfTrans() {
338
339		ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
340
341	<	}
341	>	}
342
343	<	void SimInfo::addExcludePairs(Molecule* mol) {
344	<	std::vector<Bond*>::iterator bondIter;
345	<	std::vector<Bend*>::iterator bendIter;
346	<	std::vector<Torsion*>::iterator torsionIter;
343	>	void SimInfo::addInteractionPairs(Molecule* mol) {
344	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
345	>	vector<Bond*>::iterator bondIter;
346	>	vector<Bend*>::iterator bendIter;
347	>	vector<Torsion*>::iterator torsionIter;
348	>	vector<Inversion*>::iterator inversionIter;
349		Bond* bond;
350		Bend* bend;
351		Torsion* torsion;
352	+	Inversion* inversion;
353		int a;
354		int b;
355		int c;
356		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	–	}
357
358	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
359	<	a = bend->getAtomA()->getGlobalIndex();
360	<	b = bend->getAtomB()->getGlobalIndex();
361	<	c = bend->getAtomC()->getGlobalIndex();
358	>	// atomGroups can be used to add special interaction maps between
359	>	// groups of atoms that are in two separate rigid bodies.
360	>	// However, most site-site interactions between two rigid bodies
361	>	// are probably not special, just the ones between the physically
362	>	// bonded atoms.  Interactions *within* a single rigid body should
363	>	// always be excluded.  These are done at the bottom of this
364	>	// function.
365
366	<	exclude_.addPair(a, b);
367	<	exclude_.addPair(a, c);
368	<	exclude_.addPair(b, c);
369	<	}
370	<
371	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
372	<	a = torsion->getAtomA()->getGlobalIndex();
373	<	b = torsion->getAtomB()->getGlobalIndex();
374	<	c = torsion->getAtomC()->getGlobalIndex();
375	<	d = torsion->getAtomD()->getGlobalIndex();
366	>	map<int, set<int> > atomGroups;
367	>	Molecule::RigidBodyIterator rbIter;
368	>	RigidBody* rb;
369	>	Molecule::IntegrableObjectIterator ii;
370	>	StuntDouble* integrableObject;
371	>
372	>	for (integrableObject = mol->beginIntegrableObject(ii);
373	>	integrableObject != NULL;
374	>	integrableObject = mol->nextIntegrableObject(ii)) {
375	>
376	>	if (integrableObject->isRigidBody()) {
377	>	rb = static_cast<RigidBody*>(integrableObject);
378	>	vector<Atom*> atoms = rb->getAtoms();
379	>	set<int> rigidAtoms;
380	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
381	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
382	>	}
383	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
384	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
385	>	}
386	>	} else {
387	>	set<int> oneAtomSet;
388	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
389	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
390	>	}
391	>	}
392	>
393	>	for (bond= mol->beginBond(bondIter); bond != NULL;
394	>	bond = mol->nextBond(bondIter)) {
395
396	<	exclude_.addPair(a, b);
397	<	exclude_.addPair(a, c);
398	<	exclude_.addPair(a, d);
399	<	exclude_.addPair(b, c);
400	<	exclude_.addPair(b, d);
401	<	exclude_.addPair(c, d);
396	>	a = bond->getAtomA()->getGlobalIndex();
397	>	b = bond->getAtomB()->getGlobalIndex();
398	>
399	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
400	>	oneTwoInteractions_.addPair(a, b);
401	>	} else {
402	>	excludedInteractions_.addPair(a, b);
403	>	}
404		}
405
406	<
407	<	}
406	>	for (bend= mol->beginBend(bendIter); bend != NULL;
407	>	bend = mol->nextBend(bendIter)) {
408
409	<	void SimInfo::removeExcludePairs(Molecule* mol) {
410	<	std::vector<Bond*>::iterator bondIter;
411	<	std::vector<Bend*>::iterator bendIter;
412	<	std::vector<Torsion*>::iterator torsionIter;
409	>	a = bend->getAtomA()->getGlobalIndex();
410	>	b = bend->getAtomB()->getGlobalIndex();
411	>	c = bend->getAtomC()->getGlobalIndex();
412	>
413	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
414	>	oneTwoInteractions_.addPair(a, b);
415	>	oneTwoInteractions_.addPair(b, c);
416	>	} else {
417	>	excludedInteractions_.addPair(a, b);
418	>	excludedInteractions_.addPair(b, c);
419	>	}
420	>
421	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
422	>	oneThreeInteractions_.addPair(a, c);
423	>	} else {
424	>	excludedInteractions_.addPair(a, c);
425	>	}
426	>	}
427	>
428	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
429	>	torsion = mol->nextTorsion(torsionIter)) {
430	>
431	>	a = torsion->getAtomA()->getGlobalIndex();
432	>	b = torsion->getAtomB()->getGlobalIndex();
433	>	c = torsion->getAtomC()->getGlobalIndex();
434	>	d = torsion->getAtomD()->getGlobalIndex();
435	>
436	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
437	>	oneTwoInteractions_.addPair(a, b);
438	>	oneTwoInteractions_.addPair(b, c);
439	>	oneTwoInteractions_.addPair(c, d);
440	>	} else {
441	>	excludedInteractions_.addPair(a, b);
442	>	excludedInteractions_.addPair(b, c);
443	>	excludedInteractions_.addPair(c, d);
444	>	}
445	>
446	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
447	>	oneThreeInteractions_.addPair(a, c);
448	>	oneThreeInteractions_.addPair(b, d);
449	>	} else {
450	>	excludedInteractions_.addPair(a, c);
451	>	excludedInteractions_.addPair(b, d);
452	>	}
453	>
454	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
455	>	oneFourInteractions_.addPair(a, d);
456	>	} else {
457	>	excludedInteractions_.addPair(a, d);
458	>	}
459	>	}
460	>
461	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
462	>	inversion = mol->nextInversion(inversionIter)) {
463	>
464	>	a = inversion->getAtomA()->getGlobalIndex();
465	>	b = inversion->getAtomB()->getGlobalIndex();
466	>	c = inversion->getAtomC()->getGlobalIndex();
467	>	d = inversion->getAtomD()->getGlobalIndex();
468	>
469	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
470	>	oneTwoInteractions_.addPair(a, b);
471	>	oneTwoInteractions_.addPair(a, c);
472	>	oneTwoInteractions_.addPair(a, d);
473	>	} else {
474	>	excludedInteractions_.addPair(a, b);
475	>	excludedInteractions_.addPair(a, c);
476	>	excludedInteractions_.addPair(a, d);
477	>	}
478	>
479	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
480	>	oneThreeInteractions_.addPair(b, c);
481	>	oneThreeInteractions_.addPair(b, d);
482	>	oneThreeInteractions_.addPair(c, d);
483	>	} else {
484	>	excludedInteractions_.addPair(b, c);
485	>	excludedInteractions_.addPair(b, d);
486	>	excludedInteractions_.addPair(c, d);
487	>	}
488	>	}
489	>
490	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
491	>	rb = mol->nextRigidBody(rbIter)) {
492	>	vector<Atom*> atoms = rb->getAtoms();
493	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
494	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
495	>	a = atoms[i]->getGlobalIndex();
496	>	b = atoms[j]->getGlobalIndex();
497	>	excludedInteractions_.addPair(a, b);
498	>	}
499	>	}
500	>	}
501	>
502	>	}
503	>
504	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
505	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
506	>	vector<Bond*>::iterator bondIter;
507	>	vector<Bend*>::iterator bendIter;
508	>	vector<Torsion*>::iterator torsionIter;
509	>	vector<Inversion*>::iterator inversionIter;
510		Bond* bond;
511		Bend* bend;
512		Torsion* torsion;
513	+	Inversion* inversion;
514		int a;
515		int b;
516		int c;
517		int d;
518	+
519	+	map<int, set<int> > atomGroups;
520	+	Molecule::RigidBodyIterator rbIter;
521	+	RigidBody* rb;
522	+	Molecule::IntegrableObjectIterator ii;
523	+	StuntDouble* integrableObject;
524
525	<	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
526	<	a = bond->getAtomA()->getGlobalIndex();
527	<	b = bond->getAtomB()->getGlobalIndex();
528	<	exclude_.removePair(a, b);
525	>	for (integrableObject = mol->beginIntegrableObject(ii);
526	>	integrableObject != NULL;
527	>	integrableObject = mol->nextIntegrableObject(ii)) {
528	>
529	>	if (integrableObject->isRigidBody()) {
530	>	rb = static_cast<RigidBody*>(integrableObject);
531	>	vector<Atom*> atoms = rb->getAtoms();
532	>	set<int> rigidAtoms;
533	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
534	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
535	>	}
536	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
537	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
538	>	}
539	>	} else {
540	>	set<int> oneAtomSet;
541	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
542	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
543	>	}
544	>	}
545	>
546	>	for (bond= mol->beginBond(bondIter); bond != NULL;
547	>	bond = mol->nextBond(bondIter)) {
548	>
549	>	a = bond->getAtomA()->getGlobalIndex();
550	>	b = bond->getAtomB()->getGlobalIndex();
551	>
552	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
553	>	oneTwoInteractions_.removePair(a, b);
554	>	} else {
555	>	excludedInteractions_.removePair(a, b);
556	>	}
557		}
558
559	<	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
560	<	a = bend->getAtomA()->getGlobalIndex();
392	<	b = bend->getAtomB()->getGlobalIndex();
393	<	c = bend->getAtomC()->getGlobalIndex();
559	>	for (bend= mol->beginBend(bendIter); bend != NULL;
560	>	bend = mol->nextBend(bendIter)) {
561
562	<	exclude_.removePair(a, b);
563	<	exclude_.removePair(a, c);
564	<	exclude_.removePair(b, c);
562	>	a = bend->getAtomA()->getGlobalIndex();
563	>	b = bend->getAtomB()->getGlobalIndex();
564	>	c = bend->getAtomC()->getGlobalIndex();
565	>
566	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
567	>	oneTwoInteractions_.removePair(a, b);
568	>	oneTwoInteractions_.removePair(b, c);
569	>	} else {
570	>	excludedInteractions_.removePair(a, b);
571	>	excludedInteractions_.removePair(b, c);
572	>	}
573	>
574	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
575	>	oneThreeInteractions_.removePair(a, c);
576	>	} else {
577	>	excludedInteractions_.removePair(a, c);
578	>	}
579		}
580
581	<	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
582	<	a = torsion->getAtomA()->getGlobalIndex();
402	<	b = torsion->getAtomB()->getGlobalIndex();
403	<	c = torsion->getAtomC()->getGlobalIndex();
404	<	d = torsion->getAtomD()->getGlobalIndex();
581	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
582	>	torsion = mol->nextTorsion(torsionIter)) {
583
584	<	exclude_.removePair(a, b);
585	<	exclude_.removePair(a, c);
586	<	exclude_.removePair(a, d);
587	<	exclude_.removePair(b, c);
588	<	exclude_.removePair(b, d);
589	<	exclude_.removePair(c, d);
584	>	a = torsion->getAtomA()->getGlobalIndex();
585	>	b = torsion->getAtomB()->getGlobalIndex();
586	>	c = torsion->getAtomC()->getGlobalIndex();
587	>	d = torsion->getAtomD()->getGlobalIndex();
588	>
589	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
590	>	oneTwoInteractions_.removePair(a, b);
591	>	oneTwoInteractions_.removePair(b, c);
592	>	oneTwoInteractions_.removePair(c, d);
593	>	} else {
594	>	excludedInteractions_.removePair(a, b);
595	>	excludedInteractions_.removePair(b, c);
596	>	excludedInteractions_.removePair(c, d);
597	>	}
598	>
599	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
600	>	oneThreeInteractions_.removePair(a, c);
601	>	oneThreeInteractions_.removePair(b, d);
602	>	} else {
603	>	excludedInteractions_.removePair(a, c);
604	>	excludedInteractions_.removePair(b, d);
605	>	}
606	>
607	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
608	>	oneFourInteractions_.removePair(a, d);
609	>	} else {
610	>	excludedInteractions_.removePair(a, d);
611	>	}
612		}
613
614	<	}
614	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
615	>	inversion = mol->nextInversion(inversionIter)) {
616
617	+	a = inversion->getAtomA()->getGlobalIndex();
618	+	b = inversion->getAtomB()->getGlobalIndex();
619	+	c = inversion->getAtomC()->getGlobalIndex();
620	+	d = inversion->getAtomD()->getGlobalIndex();
621
622	<	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
623	<	int curStampId;
622	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
623	>	oneTwoInteractions_.removePair(a, b);
624	>	oneTwoInteractions_.removePair(a, c);
625	>	oneTwoInteractions_.removePair(a, d);
626	>	} else {
627	>	excludedInteractions_.removePair(a, b);
628	>	excludedInteractions_.removePair(a, c);
629	>	excludedInteractions_.removePair(a, d);
630	>	}
631
632	+	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
633	+	oneThreeInteractions_.removePair(b, c);
634	+	oneThreeInteractions_.removePair(b, d);
635	+	oneThreeInteractions_.removePair(c, d);
636	+	} else {
637	+	excludedInteractions_.removePair(b, c);
638	+	excludedInteractions_.removePair(b, d);
639	+	excludedInteractions_.removePair(c, d);
640	+	}
641	+	}
642	+
643	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
644	+	rb = mol->nextRigidBody(rbIter)) {
645	+	vector<Atom*> atoms = rb->getAtoms();
646	+	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
647	+	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
648	+	a = atoms[i]->getGlobalIndex();
649	+	b = atoms[j]->getGlobalIndex();
650	+	excludedInteractions_.removePair(a, b);
651	+	}
652	+	}
653	+	}
654	+
655	+	}
656	+
657	+
658	+	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
659	+	int curStampId;
660	+
661		//index from 0
662		curStampId = moleculeStamps_.size();
663
664		moleculeStamps_.push_back(molStamp);
665		molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
666	<	}
666	>	}
667
427	–	void SimInfo::update() {
668
669	<	setupSimType();
670	<
671	<	#ifdef IS_MPI
672	<	setupFortranParallel();
673	<	#endif
674	<
675	<	setupFortranSim();
676	<
677	<	//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	<
669	>	/**
670	>	* update
671	>	*
672	>	*  Performs the global checks and variable settings after the
673	>	*  objects have been created.
674	>	*
675	>	*/
676	>	void SimInfo::update() {
677	>	setupSimVariables();
678		calcNdf();
679		calcNdfRaw();
680		calcNdfTrans();
681	<
682	<	fortranInitialized_ = true;
683	<	}
684	<
685	<	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
681	>	}
682	>
683	>	/**
684	>	* getSimulatedAtomTypes
685	>	*
686	>	* Returns an STL set of AtomType* that are actually present in this
687	>	* simulation.  Must query all processors to assemble this information.
688	>	*
689	>	*/
690	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
691		SimInfo::MoleculeIterator mi;
692		Molecule* mol;
693		Molecule::AtomIterator ai;
694		Atom* atom;
695	<	std::set<AtomType*> atomTypes;
695	>	set<AtomType*> atomTypes;
696	>
697	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
698	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
699	>	atomTypes.insert(atom->getAtomType());
700	>	}
701	>	}
702
703	<	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
703	>	#ifdef IS_MPI
704
705	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
706	<	atomTypes.insert(atom->getAtomType());
469	<	}
470	<
471	<	}
705	>	// loop over the found atom types on this processor, and add their
706	>	// numerical idents to a vector:
707
708	<	return atomTypes;
709	<	}
708	>	vector<int> foundTypes;
709	>	set<AtomType*>::iterator i;
710	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
711	>	foundTypes.push_back( (*i)->getIdent() );
712
713	<	void SimInfo::setupSimType() {
714	<	std::set<AtomType*>::iterator i;
478	<	std::set<AtomType*> atomTypes;
479	<	atomTypes = getUniqueAtomTypes();
480	<
481	<	int useLennardJones = 0;
482	<	int useElectrostatic = 0;
483	<	int useEAM = 0;
484	<	int useCharge = 0;
485	<	int useDirectional = 0;
486	<	int useDipole = 0;
487	<	int useGayBerne = 0;
488	<	int useSticky = 0;
489	<	int useShape = 0;
490	<	int useFLARB = 0; //it is not in AtomType yet
491	<	int useDirectionalAtom = 0;
492	<	int useElectrostatics = 0;
493	<	//usePBC and useRF are from simParams
494	<	int usePBC = simParams_->getPBC();
495	<	int useRF = simParams_->getUseRF();
713	>	// count_local holds the number of found types on this processor
714	>	int count_local = foundTypes.size();
715
716	<	//loop over all of the atom types
717	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
718	<	useLennardJones |= (*i)->isLennardJones();
719	<	useElectrostatic |= (*i)->isElectrostatic();
720	<	useEAM |= (*i)->isEAM();
721	<	useCharge |= (*i)->isCharge();
722	<	useDirectional |= (*i)->isDirectional();
723	<	useDipole |= (*i)->isDipole();
724	<	useGayBerne |= (*i)->isGayBerne();
506	<	useSticky |= (*i)->isSticky();
507	<	useShape |= (*i)->isShape();
508	<	}
716	>	// count holds the total number of found types on all processors
717	>	// (some will be redundant with the ones found locally):
718	>	int count;
719	>	MPI::COMM_WORLD.Allreduce(&count_local, &count, 1, MPI::INT, MPI::SUM);
720	>
721	>	// create a vector to hold the globally found types, and resize it:
722	>	vector<int> ftGlobal;
723	>	ftGlobal.resize(count);
724	>	vector<int> counts;
725
726	<	if (useSticky || useDipole || useGayBerne || useShape) {
727	<	useDirectionalAtom = 1;
728	<	}
726	>	int nproc = MPI::COMM_WORLD.Get_size();
727	>	counts.resize(nproc);
728	>	vector<int> disps;
729	>	disps.resize(nproc);
730
731	<	if (useCharge || useDipole) {
732	<	useElectrostatics = 1;
733	<	}
731	>	// now spray out the foundTypes to all the other processors:
732	>
733	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
734	>	&ftGlobal[0], &counts[0], &disps[0], MPI::INT);
735
736	+	// foundIdents is a stl set, so inserting an already found ident
737	+	// will have no effect.
738	+	set<int> foundIdents;
739	+	vector<int>::iterator j;
740	+	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
741	+	foundIdents.insert((*j));
742	+
743	+	// now iterate over the foundIdents and get the actual atom types
744	+	// that correspond to these:
745	+	set<int>::iterator it;
746	+	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
747	+	atomTypes.insert( forceField_->getAtomType((*it)) );
748	+
749	+	#endif
750	+
751	+	return atomTypes;
752	+	}
753	+
754	+	void SimInfo::setupSimVariables() {
755	+	useAtomicVirial_ = simParams_->getUseAtomicVirial();
756	+	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
757	+	calcBoxDipole_ = false;
758	+	if ( simParams_->haveAccumulateBoxDipole() )
759	+	if ( simParams_->getAccumulateBoxDipole() ) {
760	+	calcBoxDipole_ = true;
761	+	}
762	+
763	+	set<AtomType*>::iterator i;
764	+	set<AtomType*> atomTypes;
765	+	atomTypes = getSimulatedAtomTypes();
766	+	int usesElectrostatic = 0;
767	+	int usesMetallic = 0;
768	+	int usesDirectional = 0;
769	+	//loop over all of the atom types
770	+	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
771	+	usesElectrostatic |= (*i)->isElectrostatic();
772	+	usesMetallic |= (*i)->isMetal();
773	+	usesDirectional |= (*i)->isDirectional();
774	+	}
775	+
776		#ifdef IS_MPI
777		int temp;
778	+	temp = usesDirectional;
779	+	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
780	+
781	+	temp = usesMetallic;
782	+	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
783	+
784	+	temp = usesElectrostatic;
785	+	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
786	+	#else
787
788	<	temp = usePBC;
789	<	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
788	>	usesDirectionalAtoms_ = usesDirectional;
789	>	usesMetallicAtoms_ = usesMetallic;
790	>	usesElectrostaticAtoms_ = usesElectrostatic;
791
792	<	temp = useDirectionalAtom;
793	<	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
792	>	#endif
793	>
794	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
795	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
796	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
797	>	}
798
527	–	temp = useLennardJones;
528	–	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
799
800	<	temp = useElectrostatics;
801	<	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
800	>	vector<int> SimInfo::getGlobalAtomIndices() {
801	>	SimInfo::MoleculeIterator mi;
802	>	Molecule* mol;
803	>	Molecule::AtomIterator ai;
804	>	Atom* atom;
805
806	<	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);
806	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
807
808	<	#endif
808	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
809	>
810	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
811	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
812	>	}
813	>	}
814	>	return GlobalAtomIndices;
815	>	}
816
559	–	fInfo_.SIM_uses_PBC = usePBC;
560	–	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
561	–	fInfo_.SIM_uses_LennardJones = useLennardJones;
562	–	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
563	–	fInfo_.SIM_uses_Charges = useCharge;
564	–	fInfo_.SIM_uses_Dipoles = useDipole;
565	–	fInfo_.SIM_uses_Sticky = useSticky;
566	–	fInfo_.SIM_uses_GayBerne = useGayBerne;
567	–	fInfo_.SIM_uses_EAM = useEAM;
568	–	fInfo_.SIM_uses_Shapes = useShape;
569	–	fInfo_.SIM_uses_FLARB = useFLARB;
570	–	fInfo_.SIM_uses_RF = useRF;
817
818	<	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
818	>	vector<int> SimInfo::getGlobalGroupIndices() {
819	>	SimInfo::MoleculeIterator mi;
820	>	Molecule* mol;
821	>	Molecule::CutoffGroupIterator ci;
822	>	CutoffGroup* cg;
823
824	<	if (simParams_->haveDielectric()) {
825	<	fInfo_.dielect = simParams_->getDielectric();
826	<	} else {
827	<	sprintf(painCave.errMsg,
828	<	"SimSetup Error: No Dielectric constant was set.\n"
829	<	"\tYou are trying to use Reaction Field without"
830	<	"\tsetting a dielectric constant!\n");
831	<	painCave.isFatal = 1;
832	<	simError();
833	<	}
584	<
585	<	} else {
586	<	fInfo_.dielect = 0.0;
824	>	vector<int> GlobalGroupIndices;
825	>
826	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
827	>
828	>	//local index of cutoff group is trivial, it only depends on the
829	>	//order of travesing
830	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
831	>	cg = mol->nextCutoffGroup(ci)) {
832	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
833	>	}
834		}
835	+	return GlobalGroupIndices;
836	+	}
837
589	–	}
838
839	<	void SimInfo::setupFortranSim() {
840	<	int isError;
593	<	int nExclude;
594	<	std::vector<int> fortranGlobalGroupMembership;
595	<
596	<	nExclude = exclude_.getSize();
597	<	isError = 0;
839	>	void SimInfo::prepareTopology() {
840	>	int nExclude, nOneTwo, nOneThree, nOneFour;
841
599	–	//globalGroupMembership_ is filled by SimCreator
600	–	for (int i = 0; i < nGlobalAtoms_; i++) {
601	–	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
602	–	}
603	–
842		//calculate mass ratio of cutoff group
605	–	std::vector<double> mfact;
843		SimInfo::MoleculeIterator mi;
844		Molecule* mol;
845		Molecule::CutoffGroupIterator ci;
846		CutoffGroup* cg;
847		Molecule::AtomIterator ai;
848		Atom* atom;
849	<	double totalMass;
849	>	RealType totalMass;
850
851	<	//to avoid memory reallocation, reserve enough space for mfact
852	<	mfact.reserve(getNCutoffGroups());
851	>	/**
852	>	* The mass factor is the relative mass of an atom to the total
853	>	* mass of the cutoff group it belongs to.  By default, all atoms
854	>	* are their own cutoff groups, and therefore have mass factors of
855	>	* 1.  We need some special handling for massless atoms, which
856	>	* will be treated as carrying the entire mass of the cutoff
857	>	* group.
858	>	*/
859	>	massFactors_.clear();
860	>	massFactors_.resize(getNAtoms(), 1.0);
861
862		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
863	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
863	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
864	>	cg = mol->nextCutoffGroup(ci)) {
865
866	<	totalMass = cg->getMass();
867	<	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
868	<	mfact.push_back(atom->getMass()/totalMass);
869	<	}
870	<
871	<	}
866	>	totalMass = cg->getMass();
867	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
868	>	// Check for massless groups - set mfact to 1 if true
869	>	if (totalMass != 0)
870	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
871	>	else
872	>	massFactors_[atom->getLocalIndex()] = 1.0;
873	>	}
874	>	}
875		}
876
877	<	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
629	<	std::vector<int> identArray;
877	>	// Build the identArray_
878
879	<	//to avoid memory reallocation, reserve enough space identArray
880	<	identArray.reserve(getNAtoms());
633	<
879	>	identArray_.clear();
880	>	identArray_.reserve(getNAtoms());
881		for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
882	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
883	<	identArray.push_back(atom->getIdent());
884	<	}
882	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
883	>	identArray_.push_back(atom->getIdent());
884	>	}
885		}
639	–
640	–	//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	–	}
886
887	<	//setup fortran simulation
648	<	//gloalExcludes and molMembershipArray should go away (They are never used)
649	<	//why the hell fortran need to know molecule?
650	<	//OOPSE = Object-Obfuscated Parallel Simulation Engine
651	<	int nGlobalExcludes = 0;
652	<	int* globalExcludes = NULL;
653	<	int* excludeList = exclude_.getExcludeList();
654	<	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
655	<	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
656	<	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
887	>	//scan topology
888
889	<	if( isError ){
889	>	nExclude = excludedInteractions_.getSize();
890	>	nOneTwo = oneTwoInteractions_.getSize();
891	>	nOneThree = oneThreeInteractions_.getSize();
892	>	nOneFour = oneFourInteractions_.getSize();
893
894	<	sprintf( painCave.errMsg,
895	<	"There was an error setting the simulation information in fortran.\n" );
896	<	painCave.isFatal = 1;
897	<	painCave.severity = OOPSE_ERROR;
664	<	simError();
665	<	}
894	>	int* excludeList = excludedInteractions_.getPairList();
895	>	int* oneTwoList = oneTwoInteractions_.getPairList();
896	>	int* oneThreeList = oneThreeInteractions_.getPairList();
897	>	int* oneFourList = oneFourInteractions_.getPairList();
898
899	<	#ifdef IS_MPI
900	<	sprintf( checkPointMsg,
669	<	"succesfully sent the simulation information to fortran.\n");
670	<	MPIcheckPoint();
671	<	#endif // is_mpi
672	<	}
899	>	topologyDone_ = true;
900	>	}
901
902	+	void SimInfo::addProperty(GenericData* genData) {
903	+	properties_.addProperty(genData);
904	+	}
905
906	<	#ifdef IS_MPI
907	<	void SimInfo::setupFortranParallel() {
908	<
678	<	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
679	<	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
680	<	std::vector<int> localToGlobalCutoffGroupIndex;
681	<	SimInfo::MoleculeIterator mi;
682	<	Molecule::AtomIterator ai;
683	<	Molecule::CutoffGroupIterator ci;
684	<	Molecule* mol;
685	<	Atom* atom;
686	<	CutoffGroup* cg;
687	<	mpiSimData parallelData;
688	<	int isError;
906	>	void SimInfo::removeProperty(const string& propName) {
907	>	properties_.removeProperty(propName);
908	>	}
909
910	<	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
910	>	void SimInfo::clearProperties() {
911	>	properties_.clearProperties();
912	>	}
913
914	<	//local index(index in DataStorge) of atom is important
915	<	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
916	<	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
917	<	}
914	>	vector<string> SimInfo::getPropertyNames() {
915	>	return properties_.getPropertyNames();
916	>	}
917	>
918	>	vector<GenericData*> SimInfo::getProperties() {
919	>	return properties_.getProperties();
920	>	}
921
922	<	//local index of cutoff group is trivial, it only depends on the order of travesing
923	<	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
924	<	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
700	<	}
701	<
702	<	}
703	<
704	<	//fill up mpiSimData struct
705	<	parallelData.nMolGlobal = getNGlobalMolecules();
706	<	parallelData.nMolLocal = getNMolecules();
707	<	parallelData.nAtomsGlobal = getNGlobalAtoms();
708	<	parallelData.nAtomsLocal = getNAtoms();
709	<	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
710	<	parallelData.nGroupsLocal = getNCutoffGroups();
711	<	parallelData.myNode = worldRank;
712	<	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
713	<
714	<	//pass mpiSimData struct and index arrays to fortran
715	<	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
716	<	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
717	<	&localToGlobalCutoffGroupIndex[0], &isError);
718	<
719	<	if (isError) {
720	<	sprintf(painCave.errMsg,
721	<	"mpiRefresh errror: fortran didn't like something we gave it.\n");
722	<	painCave.isFatal = 1;
723	<	simError();
724	<	}
725	<
726	<	sprintf(checkPointMsg, " mpiRefresh successful.\n");
727	<	MPIcheckPoint();
728	<
729	<
730	<	}
731	<
732	<	#endif
733	<
734	<	double SimInfo::calcMaxCutoffRadius() {
735	<
736	<
737	<	std::set<AtomType*> atomTypes;
738	<	std::set<AtomType*>::iterator i;
739	<	std::vector<double> cutoffRadius;
740	<
741	<	//get the unique atom types
742	<	atomTypes = getUniqueAtomTypes();
743	<
744	<	//query the max cutoff radius among these atom types
745	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
746	<	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
747	<	}
748	<
749	<	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
750	<	#ifdef IS_MPI
751	<	//pick the max cutoff radius among the processors
752	<	#endif
753	<
754	<	return maxCutoffRadius;
755	<	}
922	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
923	>	return properties_.getPropertyByName(propName);
924	>	}
925
926	<	void SimInfo::getCutoff(double& rcut, double& rsw) {
927	<
928	<	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
929	<
930	<	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) {
926	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
927	>	if (sman_ == sman) {
928	>	return;
929	>	}
930	>	delete sman_;
931		sman_ = sman;
932
933		Molecule* mol;
934		RigidBody* rb;
935		Atom* atom;
936	+	CutoffGroup* cg;
937		SimInfo::MoleculeIterator mi;
938		Molecule::RigidBodyIterator rbIter;
939	<	Molecule::AtomIterator atomIter;;
939	>	Molecule::AtomIterator atomIter;
940	>	Molecule::CutoffGroupIterator cgIter;
941
942		for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
943
944	<	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
945	<	atom->setSnapshotManager(sman_);
946	<	}
944	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
945	>	atom->setSnapshotManager(sman_);
946	>	}
947
948	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
949	<	rb->setSnapshotManager(sman_);
950	<	}
948	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
949	>	rb->setSnapshotManager(sman_);
950	>	}
951	>
952	>	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
953	>	cg->setSnapshotManager(sman_);
954	>	}
955		}
956
957	<	}
957	>	}
958
959	<	Vector3d SimInfo::getComVel(){
959	>	Vector3d SimInfo::getComVel(){
960		SimInfo::MoleculeIterator i;
961		Molecule* mol;
962
963		Vector3d comVel(0.0);
964	<	double totalMass = 0.0;
964	>	RealType totalMass = 0.0;
965
966
967		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
968	<	double mass = mol->getMass();
969	<	totalMass += mass;
970	<	comVel += mass * mol->getComVel();
968	>	RealType mass = mol->getMass();
969	>	totalMass += mass;
970	>	comVel += mass * mol->getComVel();
971		}
972
973		#ifdef IS_MPI
974	<	double tmpMass = totalMass;
974	>	RealType tmpMass = totalMass;
975		Vector3d tmpComVel(comVel);
976	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
977	<	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
976	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
977	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
978		#endif
979
980		comVel /= totalMass;
981
982		return comVel;
983	<	}
983	>	}
984
985	<	Vector3d SimInfo::getCom(){
985	>	Vector3d SimInfo::getCom(){
986		SimInfo::MoleculeIterator i;
987		Molecule* mol;
988
989		Vector3d com(0.0);
990	<	double totalMass = 0.0;
990	>	RealType totalMass = 0.0;
991
992		for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
993	<	double mass = mol->getMass();
994	<	totalMass += mass;
995	<	com += mass * mol->getCom();
993	>	RealType mass = mol->getMass();
994	>	totalMass += mass;
995	>	com += mass * mol->getCom();
996		}
997
998		#ifdef IS_MPI
999	<	double tmpMass = totalMass;
999	>	RealType tmpMass = totalMass;
1000		Vector3d tmpCom(com);
1001	<	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1002	<	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1001	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1002	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1003		#endif
1004
1005		com /= totalMass;
1006
1007		return com;
1008
1009	<	}
1009	>	}
1010
1011	<	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1011	>	ostream& operator <<(ostream& o, SimInfo& info) {
1012
1013		return o;
1014	<	}
1014	>	}
1015	>
1016	>
1017	>	/*
1018	>	Returns center of mass and center of mass velocity in one function call.
1019	>	*/
1020	>
1021	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1022	>	SimInfo::MoleculeIterator i;
1023	>	Molecule* mol;
1024	>
1025	>
1026	>	RealType totalMass = 0.0;
1027	>
1028
1029	<	}//end namespace oopse
1029	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1030	>	RealType mass = mol->getMass();
1031	>	totalMass += mass;
1032	>	com += mass * mol->getCom();
1033	>	comVel += mass * mol->getComVel();
1034	>	}
1035	>
1036	>	#ifdef IS_MPI
1037	>	RealType tmpMass = totalMass;
1038	>	Vector3d tmpCom(com);
1039	>	Vector3d tmpComVel(comVel);
1040	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1041	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1042	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1043	>	#endif
1044	>
1045	>	com /= totalMass;
1046	>	comVel /= totalMass;
1047	>	}
1048	>
1049	>	/*
1050	>	Return intertia tensor for entire system and angular momentum Vector.
1051
1052	+
1053	+	[  Ixx -Ixy  -Ixz ]
1054	+	J =| -Iyx  Iyy  -Iyz |
1055	+	[ -Izx -Iyz   Izz ]
1056	+	*/
1057	+
1058	+	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1059	+
1060	+
1061	+	RealType xx = 0.0;
1062	+	RealType yy = 0.0;
1063	+	RealType zz = 0.0;
1064	+	RealType xy = 0.0;
1065	+	RealType xz = 0.0;
1066	+	RealType yz = 0.0;
1067	+	Vector3d com(0.0);
1068	+	Vector3d comVel(0.0);
1069	+
1070	+	getComAll(com, comVel);
1071	+
1072	+	SimInfo::MoleculeIterator i;
1073	+	Molecule* mol;
1074	+
1075	+	Vector3d thisq(0.0);
1076	+	Vector3d thisv(0.0);
1077	+
1078	+	RealType thisMass = 0.0;
1079	+
1080	+
1081	+
1082	+
1083	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1084	+
1085	+	thisq = mol->getCom()-com;
1086	+	thisv = mol->getComVel()-comVel;
1087	+	thisMass = mol->getMass();
1088	+	// Compute moment of intertia coefficients.
1089	+	xx += thisq[0]*thisq[0]*thisMass;
1090	+	yy += thisq[1]*thisq[1]*thisMass;
1091	+	zz += thisq[2]*thisq[2]*thisMass;
1092	+
1093	+	// compute products of intertia
1094	+	xy += thisq[0]*thisq[1]*thisMass;
1095	+	xz += thisq[0]*thisq[2]*thisMass;
1096	+	yz += thisq[1]*thisq[2]*thisMass;
1097	+
1098	+	angularMomentum += cross( thisq, thisv ) * thisMass;
1099	+
1100	+	}
1101	+
1102	+
1103	+	inertiaTensor(0,0) = yy + zz;
1104	+	inertiaTensor(0,1) = -xy;
1105	+	inertiaTensor(0,2) = -xz;
1106	+	inertiaTensor(1,0) = -xy;
1107	+	inertiaTensor(1,1) = xx + zz;
1108	+	inertiaTensor(1,2) = -yz;
1109	+	inertiaTensor(2,0) = -xz;
1110	+	inertiaTensor(2,1) = -yz;
1111	+	inertiaTensor(2,2) = xx + yy;
1112	+
1113	+	#ifdef IS_MPI
1114	+	Mat3x3d tmpI(inertiaTensor);
1115	+	Vector3d tmpAngMom;
1116	+	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1117	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1118	+	#endif
1119	+
1120	+	return;
1121	+	}
1122	+
1123	+	//Returns the angular momentum of the system
1124	+	Vector3d SimInfo::getAngularMomentum(){
1125	+
1126	+	Vector3d com(0.0);
1127	+	Vector3d comVel(0.0);
1128	+	Vector3d angularMomentum(0.0);
1129	+
1130	+	getComAll(com,comVel);
1131	+
1132	+	SimInfo::MoleculeIterator i;
1133	+	Molecule* mol;
1134	+
1135	+	Vector3d thisr(0.0);
1136	+	Vector3d thisp(0.0);
1137	+
1138	+	RealType thisMass;
1139	+
1140	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1141	+	thisMass = mol->getMass();
1142	+	thisr = mol->getCom()-com;
1143	+	thisp = (mol->getComVel()-comVel)*thisMass;
1144	+
1145	+	angularMomentum += cross( thisr, thisp );
1146	+
1147	+	}
1148	+
1149	+	#ifdef IS_MPI
1150	+	Vector3d tmpAngMom;
1151	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1152	+	#endif
1153	+
1154	+	return angularMomentum;
1155	+	}
1156	+
1157	+	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1158	+	return IOIndexToIntegrableObject.at(index);
1159	+	}
1160	+
1161	+	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1162	+	IOIndexToIntegrableObject= v;
1163	+	}
1164	+
1165	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1166	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1167	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1168	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1169	+	*/
1170	+	void SimInfo::getGyrationalVolume(RealType &volume){
1171	+	Mat3x3d intTensor;
1172	+	RealType det;
1173	+	Vector3d dummyAngMom;
1174	+	RealType sysconstants;
1175	+	RealType geomCnst;
1176	+
1177	+	geomCnst = 3.0/2.0;
1178	+	/* Get the inertial tensor and angular momentum for free*/
1179	+	getInertiaTensor(intTensor,dummyAngMom);
1180	+
1181	+	det = intTensor.determinant();
1182	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1183	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1184	+	return;
1185	+	}
1186	+
1187	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1188	+	Mat3x3d intTensor;
1189	+	Vector3d dummyAngMom;
1190	+	RealType sysconstants;
1191	+	RealType geomCnst;
1192	+
1193	+	geomCnst = 3.0/2.0;
1194	+	/* Get the inertial tensor and angular momentum for free*/
1195	+	getInertiaTensor(intTensor,dummyAngMom);
1196	+
1197	+	detI = intTensor.determinant();
1198	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1199	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1200	+	return;
1201	+	}
1202	+	/*
1203	+	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1204	+	assert( v.size() == nAtoms_ + nRigidBodies_);
1205	+	sdByGlobalIndex_ = v;
1206	+	}
1207	+
1208	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1209	+	//assert(index < nAtoms_ + nRigidBodies_);
1210	+	return sdByGlobalIndex_.at(index);
1211	+	}
1212	+	*/
1213	+	int SimInfo::getNGlobalConstraints() {
1214	+	int nGlobalConstraints;
1215	+	#ifdef IS_MPI
1216	+	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1217	+	MPI_COMM_WORLD);
1218	+	#else
1219	+	nGlobalConstraints =  nConstraints_;
1220	+	#endif
1221	+	return nGlobalConstraints;
1222	+	}
1223	+
1224	+	}//end namespace OpenMD
1225	+

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 326 by tim, Sun Feb 13 20:05:42 2005 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1583 by gezelter, Thu Jun 16 22:00:08 2011 UTC

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