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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 143 by chrisfen, Fri Oct 22 22:54:01 2004 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1535 by gezelter, Fri Dec 31 18:31:56 2010 UTC

#	Line 1 | Line 1
1	<	#include <stdlib.h>
2	<	#include <string.h>
3	<	#include <math.h>
1	>	/*
2	>	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	>	*
4	>	* The University of Notre Dame grants you ("Licensee") a
5	>	* non-exclusive, royalty free, license to use, modify and
6	>	* redistribute this software in source and binary code form, provided
7	>	* that the following conditions are met:
8	>	*
9	>	* 1. Redistributions of source code must retain the above copyright
10	>	*    notice, this list of conditions and the following disclaimer.
11	>	*
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.
16	>	*
17	>	* This software is provided "AS IS," without a warranty of any
18	>	* kind. All express or implied conditions, representations and
19	>	* warranties, including any implied warranty of merchantability,
20	>	* fitness for a particular purpose or non-infringement, are hereby
21	>	* excluded.  The University of Notre Dame and its licensors shall not
22	>	* be liable for any damages suffered by licensee as a result of
23	>	* using, modifying or distributing the software or its
24	>	* derivatives. In no event will the University of Notre Dame or its
25	>	* licensors be liable for any lost revenue, profit or data, or for
26	>	* direct, indirect, special, consequential, incidental or punitive
27	>	* damages, however caused and regardless of the theory of liability,
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	>	/**
43	>	* @file SimInfo.cpp
44	>	* @author    tlin
45	>	* @date  11/02/2004
46	>	* @version 1.0
47	>	*/
48
49	<	#include <iostream>
50	<	using namespace std;
49	>	#include <algorithm>
50	>	#include <set>
51	>	#include <map>
52
53		#include "brains/SimInfo.hpp"
54	<	#define __C
55	<	#include "brains/fSimulation.h"
54	>	#include "math/Vector3.hpp"
55	>	#include "primitives/Molecule.hpp"
56	>	#include "primitives/StuntDouble.hpp"
57	>	#include "UseTheForce/DarkSide/neighborLists_interface.h"
58	>	#include "utils/MemoryUtils.hpp"
59		#include "utils/simError.h"
60	<	#include "UseTheForce/DarkSide/simulation_interface.h"
61	<	#include "UseTheForce/notifyCutoffs_interface.h"
60	>	#include "selection/SelectionManager.hpp"
61	>	#include "io/ForceFieldOptions.hpp"
62	>	#include "UseTheForce/ForceField.hpp"
63	>	#include "nonbonded/SwitchingFunction.hpp"
64
65	<	//#include "UseTheForce/fortranWrappers.hpp"
65	>	#ifdef IS_MPI
66	>	#include "UseTheForce/mpiComponentPlan.h"
67	>	#include "UseTheForce/DarkSide/simParallel_interface.h"
68	>	#endif
69
70	<	#include "math/MatVec3.h"
70	>	using namespace std;
71	>	namespace OpenMD {
72	>
73	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
74	>	forceField_(ff), simParams_(simParams),
75	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
76	>	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
77	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
78	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
79	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
80	>	nConstraints_(0), sman_(NULL), fortranInitialized_(false),
81	>	calcBoxDipole_(false), useAtomicVirial_(true) {
82	>
83	>	MoleculeStamp* molStamp;
84	>	int nMolWithSameStamp;
85	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
86	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
87	>	CutoffGroupStamp* cgStamp;
88	>	RigidBodyStamp* rbStamp;
89	>	int nRigidAtoms = 0;
90	>
91	>	vector<Component*> components = simParams->getComponents();
92	>
93	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
94	>	molStamp = (*i)->getMoleculeStamp();
95	>	nMolWithSameStamp = (*i)->getNMol();
96	>
97	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
98	>
99	>	//calculate atoms in molecules
100	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
101	>
102	>	//calculate atoms in cutoff groups
103	>	int nAtomsInGroups = 0;
104	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
105	>
106	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
107	>	cgStamp = molStamp->getCutoffGroupStamp(j);
108	>	nAtomsInGroups += cgStamp->getNMembers();
109	>	}
110	>
111	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
112	>
113	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
114	>
115	>	//calculate atoms in rigid bodies
116	>	int nAtomsInRigidBodies = 0;
117	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
118	>
119	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
120	>	rbStamp = molStamp->getRigidBodyStamp(j);
121	>	nAtomsInRigidBodies += rbStamp->getNMembers();
122	>	}
123	>
124	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
125	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
126	>
127	>	}
128	>
129	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
130	>	//group therefore the total number of cutoff groups in the system is
131	>	//equal to the total number of atoms minus number of atoms belong to
132	>	//cutoff group defined in meta-data file plus the number of cutoff
133	>	//groups defined in meta-data file
134	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
135	>
136	>	//every free atom (atom does not belong to rigid bodies) is an
137	>	//integrable object therefore the total number of integrable objects
138	>	//in the system is equal to the total number of atoms minus number of
139	>	//atoms belong to rigid body defined in meta-data file plus the number
140	>	//of rigid bodies defined in meta-data file
141	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
142	>	+ nGlobalRigidBodies_;
143	>
144	>	nGlobalMols_ = molStampIds_.size();
145	>	molToProcMap_.resize(nGlobalMols_);
146	>	}
147	>
148	>	SimInfo::~SimInfo() {
149	>	map<int, Molecule*>::iterator i;
150	>	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
151	>	delete i->second;
152	>	}
153	>	molecules_.clear();
154	>
155	>	delete sman_;
156	>	delete simParams_;
157	>	delete forceField_;
158	>	}
159
19	–	#ifdef IS_MPI
20	–	#include "brains/mpiSimulation.hpp"
21	–	#endif
160
161	<	inline double roundMe( double x ){
162	<	return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
163	<	}
164	<
165	<	inline double min( double a, double b ){
166	<	return (a < b ) ? a : b;
167	<	}
161	>	bool SimInfo::addMolecule(Molecule* mol) {
162	>	MoleculeIterator i;
163	>
164	>	i = molecules_.find(mol->getGlobalIndex());
165	>	if (i == molecules_.end() ) {
166	>
167	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
168	>
169	>	nAtoms_ += mol->getNAtoms();
170	>	nBonds_ += mol->getNBonds();
171	>	nBends_ += mol->getNBends();
172	>	nTorsions_ += mol->getNTorsions();
173	>	nInversions_ += mol->getNInversions();
174	>	nRigidBodies_ += mol->getNRigidBodies();
175	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
176	>	nCutoffGroups_ += mol->getNCutoffGroups();
177	>	nConstraints_ += mol->getNConstraintPairs();
178	>
179	>	addInteractionPairs(mol);
180	>
181	>	return true;
182	>	} else {
183	>	return false;
184	>	}
185	>	}
186	>
187	>	bool SimInfo::removeMolecule(Molecule* mol) {
188	>	MoleculeIterator i;
189	>	i = molecules_.find(mol->getGlobalIndex());
190
191	<	SimInfo* currentInfo;
191	>	if (i != molecules_.end() ) {
192
193	<	SimInfo::SimInfo(){
193	>	assert(mol == i->second);
194	>
195	>	nAtoms_ -= mol->getNAtoms();
196	>	nBonds_ -= mol->getNBonds();
197	>	nBends_ -= mol->getNBends();
198	>	nTorsions_ -= mol->getNTorsions();
199	>	nInversions_ -= mol->getNInversions();
200	>	nRigidBodies_ -= mol->getNRigidBodies();
201	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
202	>	nCutoffGroups_ -= mol->getNCutoffGroups();
203	>	nConstraints_ -= mol->getNConstraintPairs();
204
205	<	n_constraints = 0;
206	<	nZconstraints = 0;
37	<	n_oriented = 0;
38	<	n_dipoles = 0;
39	<	ndf = 0;
40	<	ndfRaw = 0;
41	<	nZconstraints = 0;
42	<	the_integrator = NULL;
43	<	setTemp = 0;
44	<	thermalTime = 0.0;
45	<	currentTime = 0.0;
46	<	rCut = 0.0;
47	<	rSw = 0.0;
205	>	removeInteractionPairs(mol);
206	>	molecules_.erase(mol->getGlobalIndex());
207
208	<	haveRcut = 0;
209	<	haveRsw = 0;
210	<	boxIsInit = 0;
211	<
212	<	resetTime = 1e99;
208	>	delete mol;
209	>
210	>	return true;
211	>	} else {
212	>	return false;
213	>	}
214	>	}
215
216	<	orthoRhombic = 0;
217	<	orthoTolerance = 1E-6;
218	<	useInitXSstate = true;
216	>
217	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
218	>	i = molecules_.begin();
219	>	return i == molecules_.end() ? NULL : i->second;
220	>	}
221
222	<	usePBC = 0;
223	<	useDirectionalAtoms = 0;
224	<	useLennardJones = 0;
225	<	useElectrostatics = 0;
63	<	useCharges = 0;
64	<	useDipoles = 0;
65	<	useSticky = 0;
66	<	useGayBerne = 0;
67	<	useEAM = 0;
68	<	useShapes = 0;
69	<	useFLARB = 0;
222	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
223	>	++i;
224	>	return i == molecules_.end() ? NULL : i->second;
225	>	}
226
71	–	useSolidThermInt = 0;
72	–	useLiquidThermInt = 0;
227
228	<	haveCutoffGroups = false;
228	>	void SimInfo::calcNdf() {
229	>	int ndf_local;
230	>	MoleculeIterator i;
231	>	vector<StuntDouble*>::iterator j;
232	>	Molecule* mol;
233	>	StuntDouble* integrableObject;
234
235	<	excludes = Exclude::Instance();
235	>	ndf_local = 0;
236	>
237	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
238	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
239	>	integrableObject = mol->nextIntegrableObject(j)) {
240
241	<	myConfiguration = new SimState();
241	>	ndf_local += 3;
242
243	<	has_minimizer = false;
244	<	the_minimizer =NULL;
243	>	if (integrableObject->isDirectional()) {
244	>	if (integrableObject->isLinear()) {
245	>	ndf_local += 2;
246	>	} else {
247	>	ndf_local += 3;
248	>	}
249	>	}
250	>
251	>	}
252	>	}
253	>
254	>	// n_constraints is local, so subtract them on each processor
255	>	ndf_local -= nConstraints_;
256
257	<	ngroup = 0;
257	>	#ifdef IS_MPI
258	>	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
259	>	#else
260	>	ndf_ = ndf_local;
261	>	#endif
262
263	<	}
263	>	// nZconstraints_ is global, as are the 3 COM translations for the
264	>	// entire system:
265	>	ndf_ = ndf_ - 3 - nZconstraint_;
266
267	+	}
268
269	<	SimInfo::~SimInfo(){
269	>	int SimInfo::getFdf() {
270	>	#ifdef IS_MPI
271	>	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
272	>	#else
273	>	fdf_ = fdf_local;
274	>	#endif
275	>	return fdf_;
276	>	}
277	>
278	>	void SimInfo::calcNdfRaw() {
279	>	int ndfRaw_local;
280
281	<	delete myConfiguration;
281	>	MoleculeIterator i;
282	>	vector<StuntDouble*>::iterator j;
283	>	Molecule* mol;
284	>	StuntDouble* integrableObject;
285
286	<	map<string, GenericData*>::iterator i;
287	<
288	<	for(i = properties.begin(); i != properties.end(); i++)
289	<	delete (*i).second;
286	>	// Raw degrees of freedom that we have to set
287	>	ndfRaw_local = 0;
288	>
289	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
290	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
291	>	integrableObject = mol->nextIntegrableObject(j)) {
292
293	<	}
293	>	ndfRaw_local += 3;
294
295	<	void SimInfo::setBox(double newBox[3]) {
296	<
297	<	int i, j;
298	<	double tempMat[3][3];
299	<
300	<	for(i=0; i<3; i++)
301	<	for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
302	<
303	<	tempMat[0][0] = newBox[0];
108	<	tempMat[1][1] = newBox[1];
109	<	tempMat[2][2] = newBox[2];
110	<
111	<	setBoxM( tempMat );
112	<
113	<	}
114	<
115	<	void SimInfo::setBoxM( double theBox[3][3] ){
116	<
117	<	int i, j;
118	<	double FortranHmat[9]; // to preserve compatibility with Fortran the
119	<	// ordering in the array is as follows:
120	<	// [ 0 3 6 ]
121	<	// [ 1 4 7 ]
122	<	// [ 2 5 8 ]
123	<	double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
124	<
125	<	if( !boxIsInit ) boxIsInit = 1;
126	<
127	<	for(i=0; i < 3; i++)
128	<	for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
129	<
130	<	calcBoxL();
131	<	calcHmatInv();
132	<
133	<	for(i=0; i < 3; i++) {
134	<	for (j=0; j < 3; j++) {
135	<	FortranHmat[3*j + i] = Hmat[i][j];
136	<	FortranHmatInv[3*j + i] = HmatInv[i][j];
295	>	if (integrableObject->isDirectional()) {
296	>	if (integrableObject->isLinear()) {
297	>	ndfRaw_local += 2;
298	>	} else {
299	>	ndfRaw_local += 3;
300	>	}
301	>	}
302	>
303	>	}
304		}
305	+
306	+	#ifdef IS_MPI
307	+	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
308	+	#else
309	+	ndfRaw_ = ndfRaw_local;
310	+	#endif
311		}
312
313	<	setFortranBox(FortranHmat, FortranHmatInv, &orthoRhombic);
314	<
142	<	}
143	<
313	>	void SimInfo::calcNdfTrans() {
314	>	int ndfTrans_local;
315
316	<	void SimInfo::getBoxM (double theBox[3][3]) {
316	>	ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
317
147	–	int i, j;
148	–	for(i=0; i<3; i++)
149	–	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
150	–	}
318
319	+	#ifdef IS_MPI
320	+	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
321	+	#else
322	+	ndfTrans_ = ndfTrans_local;
323	+	#endif
324
325	<	void SimInfo::scaleBox(double scale) {
326	<	double theBox[3][3];
155	<	int i, j;
156	<
157	<	// cerr << "Scaling box by " << scale << "\n";
158	<
159	<	for(i=0; i<3; i++)
160	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
161	<
162	<	setBoxM(theBox);
163	<
164	<	}
165	<
166	<	void SimInfo::calcHmatInv( void ) {
167	<
168	<	int oldOrtho;
169	<	int i,j;
170	<	double smallDiag;
171	<	double tol;
172	<	double sanity[3][3];
173	<
174	<	invertMat3( Hmat, HmatInv );
175	<
176	<	// check to see if Hmat is orthorhombic
177	<
178	<	oldOrtho = orthoRhombic;
179	<
180	<	smallDiag = fabs(Hmat[0][0]);
181	<	if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
182	<	if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
183	<	tol = smallDiag * orthoTolerance;
184	<
185	<	orthoRhombic = 1;
186	<
187	<	for (i = 0; i < 3; i++ ) {
188	<	for (j = 0 ; j < 3; j++) {
189	<	if (i != j) {
190	<	if (orthoRhombic) {
191	<	if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
192	<	}
193	<	}
194	<	}
325	>	ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
326	>
327		}
328
329	<	if( oldOrtho != orthoRhombic ){
329	>	void SimInfo::addInteractionPairs(Molecule* mol) {
330	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
331	>	vector<Bond*>::iterator bondIter;
332	>	vector<Bend*>::iterator bendIter;
333	>	vector<Torsion*>::iterator torsionIter;
334	>	vector<Inversion*>::iterator inversionIter;
335	>	Bond* bond;
336	>	Bend* bend;
337	>	Torsion* torsion;
338	>	Inversion* inversion;
339	>	int a;
340	>	int b;
341	>	int c;
342	>	int d;
343	>
344	>	// atomGroups can be used to add special interaction maps between
345	>	// groups of atoms that are in two separate rigid bodies.
346	>	// However, most site-site interactions between two rigid bodies
347	>	// are probably not special, just the ones between the physically
348	>	// bonded atoms.  Interactions *within* a single rigid body should
349	>	// always be excluded.  These are done at the bottom of this
350	>	// function.
351	>
352	>	map<int, set<int> > atomGroups;
353	>	Molecule::RigidBodyIterator rbIter;
354	>	RigidBody* rb;
355	>	Molecule::IntegrableObjectIterator ii;
356	>	StuntDouble* integrableObject;
357
358	<	if( orthoRhombic ) {
359	<	sprintf( painCave.errMsg,
360	<	"OOPSE is switching from the default Non-Orthorhombic\n"
361	<	"\tto the faster Orthorhombic periodic boundary computations.\n"
362	<	"\tThis is usually a good thing, but if you wan't the\n"
363	<	"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
364	<	"\tvariable ( currently set to %G ) smaller.\n",
365	<	orthoTolerance);
366	<	painCave.severity = OOPSE_INFO;
367	<	simError();
358	>	for (integrableObject = mol->beginIntegrableObject(ii);
359	>	integrableObject != NULL;
360	>	integrableObject = mol->nextIntegrableObject(ii)) {
361	>
362	>	if (integrableObject->isRigidBody()) {
363	>	rb = static_cast<RigidBody*>(integrableObject);
364	>	vector<Atom*> atoms = rb->getAtoms();
365	>	set<int> rigidAtoms;
366	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
367	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
368	>	}
369	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
370	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
371	>	}
372	>	} else {
373	>	set<int> oneAtomSet;
374	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
375	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
376	>	}
377	>	}
378	>
379	>	for (bond= mol->beginBond(bondIter); bond != NULL;
380	>	bond = mol->nextBond(bondIter)) {
381	>
382	>	a = bond->getAtomA()->getGlobalIndex();
383	>	b = bond->getAtomB()->getGlobalIndex();
384	>
385	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
386	>	oneTwoInteractions_.addPair(a, b);
387	>	} else {
388	>	excludedInteractions_.addPair(a, b);
389	>	}
390		}
210	–	else {
211	–	sprintf( painCave.errMsg,
212	–	"OOPSE is switching from the faster Orthorhombic to the more\n"
213	–	"\tflexible Non-Orthorhombic periodic boundary computations.\n"
214	–	"\tThis is usually because the box has deformed under\n"
215	–	"\tNPTf integration. If you wan't to live on the edge with\n"
216	–	"\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
217	–	"\tvariable ( currently set to %G ) larger.\n",
218	–	orthoTolerance);
219	–	painCave.severity = OOPSE_WARNING;
220	–	simError();
221	–	}
222	–	}
223	–	}
391
392	<	void SimInfo::calcBoxL( void ){
392	>	for (bend= mol->beginBend(bendIter); bend != NULL;
393	>	bend = mol->nextBend(bendIter)) {
394
395	<	double dx, dy, dz, dsq;
395	>	a = bend->getAtomA()->getGlobalIndex();
396	>	b = bend->getAtomB()->getGlobalIndex();
397	>	c = bend->getAtomC()->getGlobalIndex();
398	>
399	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
400	>	oneTwoInteractions_.addPair(a, b);
401	>	oneTwoInteractions_.addPair(b, c);
402	>	} else {
403	>	excludedInteractions_.addPair(a, b);
404	>	excludedInteractions_.addPair(b, c);
405	>	}
406
407	<	// boxVol = Determinant of Hmat
407	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
408	>	oneThreeInteractions_.addPair(a, c);
409	>	} else {
410	>	excludedInteractions_.addPair(a, c);
411	>	}
412	>	}
413
414	<	boxVol = matDet3( Hmat );
414	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
415	>	torsion = mol->nextTorsion(torsionIter)) {
416
417	<	// boxLx
418	<
419	<	dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
420	<	dsq = dx*dx + dy*dy + dz*dz;
237	<	boxL[0] = sqrt( dsq );
238	<	//maxCutoff = 0.5 * boxL[0];
417	>	a = torsion->getAtomA()->getGlobalIndex();
418	>	b = torsion->getAtomB()->getGlobalIndex();
419	>	c = torsion->getAtomC()->getGlobalIndex();
420	>	d = torsion->getAtomD()->getGlobalIndex();
421
422	<	// boxLy
423	<
424	<	dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
425	<	dsq = dx*dx + dy*dy + dz*dz;
426	<	boxL[1] = sqrt( dsq );
427	<	//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
422	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
423	>	oneTwoInteractions_.addPair(a, b);
424	>	oneTwoInteractions_.addPair(b, c);
425	>	oneTwoInteractions_.addPair(c, d);
426	>	} else {
427	>	excludedInteractions_.addPair(a, b);
428	>	excludedInteractions_.addPair(b, c);
429	>	excludedInteractions_.addPair(c, d);
430	>	}
431
432	+	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
433	+	oneThreeInteractions_.addPair(a, c);
434	+	oneThreeInteractions_.addPair(b, d);
435	+	} else {
436	+	excludedInteractions_.addPair(a, c);
437	+	excludedInteractions_.addPair(b, d);
438	+	}
439
440	<	// boxLz
441	<
442	<	dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
443	<	dsq = dx*dx + dy*dy + dz*dz;
444	<	boxL[2] = sqrt( dsq );
445	<	//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
440	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
441	>	oneFourInteractions_.addPair(a, d);
442	>	} else {
443	>	excludedInteractions_.addPair(a, d);
444	>	}
445	>	}
446
447	<	//calculate the max cutoff
448	<	maxCutoff =  calcMaxCutOff();
257	<
258	<	checkCutOffs();
447	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
448	>	inversion = mol->nextInversion(inversionIter)) {
449
450	<	}
450	>	a = inversion->getAtomA()->getGlobalIndex();
451	>	b = inversion->getAtomB()->getGlobalIndex();
452	>	c = inversion->getAtomC()->getGlobalIndex();
453	>	d = inversion->getAtomD()->getGlobalIndex();
454
455	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
456	+	oneTwoInteractions_.addPair(a, b);
457	+	oneTwoInteractions_.addPair(a, c);
458	+	oneTwoInteractions_.addPair(a, d);
459	+	} else {
460	+	excludedInteractions_.addPair(a, b);
461	+	excludedInteractions_.addPair(a, c);
462	+	excludedInteractions_.addPair(a, d);
463	+	}
464
465	<	double SimInfo::calcMaxCutOff(){
465	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
466	>	oneThreeInteractions_.addPair(b, c);
467	>	oneThreeInteractions_.addPair(b, d);
468	>	oneThreeInteractions_.addPair(c, d);
469	>	} else {
470	>	excludedInteractions_.addPair(b, c);
471	>	excludedInteractions_.addPair(b, d);
472	>	excludedInteractions_.addPair(c, d);
473	>	}
474	>	}
475
476	<	double ri[3], rj[3], rk[3];
477	<	double rij[3], rjk[3], rki[3];
478	<	double minDist;
476	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
477	>	rb = mol->nextRigidBody(rbIter)) {
478	>	vector<Atom*> atoms = rb->getAtoms();
479	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
480	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
481	>	a = atoms[i]->getGlobalIndex();
482	>	b = atoms[j]->getGlobalIndex();
483	>	excludedInteractions_.addPair(a, b);
484	>	}
485	>	}
486	>	}
487
488	<	ri[0] = Hmat[0][0];
270	<	ri[1] = Hmat[1][0];
271	<	ri[2] = Hmat[2][0];
488	>	}
489
490	<	rj[0] = Hmat[0][1];
491	<	rj[1] = Hmat[1][1];
492	<	rj[2] = Hmat[2][1];
490	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
491	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
492	>	vector<Bond*>::iterator bondIter;
493	>	vector<Bend*>::iterator bendIter;
494	>	vector<Torsion*>::iterator torsionIter;
495	>	vector<Inversion*>::iterator inversionIter;
496	>	Bond* bond;
497	>	Bend* bend;
498	>	Torsion* torsion;
499	>	Inversion* inversion;
500	>	int a;
501	>	int b;
502	>	int c;
503	>	int d;
504
505	<	rk[0] = Hmat[0][2];
506	<	rk[1] = Hmat[1][2];
507	<	rk[2] = Hmat[2][2];
505	>	map<int, set<int> > atomGroups;
506	>	Molecule::RigidBodyIterator rbIter;
507	>	RigidBody* rb;
508	>	Molecule::IntegrableObjectIterator ii;
509	>	StuntDouble* integrableObject;
510
511	<	crossProduct3(ri, rj, rij);
512	<	distXY = dotProduct3(rk,rij) / norm3(rij);
511	>	for (integrableObject = mol->beginIntegrableObject(ii);
512	>	integrableObject != NULL;
513	>	integrableObject = mol->nextIntegrableObject(ii)) {
514	>
515	>	if (integrableObject->isRigidBody()) {
516	>	rb = static_cast<RigidBody*>(integrableObject);
517	>	vector<Atom*> atoms = rb->getAtoms();
518	>	set<int> rigidAtoms;
519	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
520	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
521	>	}
522	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
523	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
524	>	}
525	>	} else {
526	>	set<int> oneAtomSet;
527	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
528	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
529	>	}
530	>	}
531
532	<	crossProduct3(rj,rk, rjk);
533	<	distYZ = dotProduct3(ri,rjk) / norm3(rjk);
532	>	for (bond= mol->beginBond(bondIter); bond != NULL;
533	>	bond = mol->nextBond(bondIter)) {
534	>
535	>	a = bond->getAtomA()->getGlobalIndex();
536	>	b = bond->getAtomB()->getGlobalIndex();
537	>
538	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
539	>	oneTwoInteractions_.removePair(a, b);
540	>	} else {
541	>	excludedInteractions_.removePair(a, b);
542	>	}
543	>	}
544
545	<	crossProduct3(rk,ri, rki);
546	<	distZX = dotProduct3(rj,rki) / norm3(rki);
545	>	for (bend= mol->beginBend(bendIter); bend != NULL;
546	>	bend = mol->nextBend(bendIter)) {
547
548	<	minDist = min(min(distXY, distYZ), distZX);
549	<	return minDist/2;
550	<
551	<	}
548	>	a = bend->getAtomA()->getGlobalIndex();
549	>	b = bend->getAtomB()->getGlobalIndex();
550	>	c = bend->getAtomC()->getGlobalIndex();
551	>
552	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
553	>	oneTwoInteractions_.removePair(a, b);
554	>	oneTwoInteractions_.removePair(b, c);
555	>	} else {
556	>	excludedInteractions_.removePair(a, b);
557	>	excludedInteractions_.removePair(b, c);
558	>	}
559
560	<	void SimInfo::wrapVector( double thePos[3] ){
560	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
561	>	oneThreeInteractions_.removePair(a, c);
562	>	} else {
563	>	excludedInteractions_.removePair(a, c);
564	>	}
565	>	}
566
567	<	int i;
568	<	double scaled[3];
567	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
568	>	torsion = mol->nextTorsion(torsionIter)) {
569
570	<	if( !orthoRhombic ){
571	<	// calc the scaled coordinates.
570	>	a = torsion->getAtomA()->getGlobalIndex();
571	>	b = torsion->getAtomB()->getGlobalIndex();
572	>	c = torsion->getAtomC()->getGlobalIndex();
573	>	d = torsion->getAtomD()->getGlobalIndex();
574
575	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
576	+	oneTwoInteractions_.removePair(a, b);
577	+	oneTwoInteractions_.removePair(b, c);
578	+	oneTwoInteractions_.removePair(c, d);
579	+	} else {
580	+	excludedInteractions_.removePair(a, b);
581	+	excludedInteractions_.removePair(b, c);
582	+	excludedInteractions_.removePair(c, d);
583	+	}
584
585	<	matVecMul3(HmatInv, thePos, scaled);
586	<
587	<	for(i=0; i<3; i++)
588	<	scaled[i] -= roundMe(scaled[i]);
589	<
590	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
591	<
311	<	matVecMul3(Hmat, scaled, thePos);
585	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
586	>	oneThreeInteractions_.removePair(a, c);
587	>	oneThreeInteractions_.removePair(b, d);
588	>	} else {
589	>	excludedInteractions_.removePair(a, c);
590	>	excludedInteractions_.removePair(b, d);
591	>	}
592
593	<	}
594	<	else{
595	<	// calc the scaled coordinates.
593	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
594	>	oneFourInteractions_.removePair(a, d);
595	>	} else {
596	>	excludedInteractions_.removePair(a, d);
597	>	}
598	>	}
599	>
600	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
601	>	inversion = mol->nextInversion(inversionIter)) {
602	>
603	>	a = inversion->getAtomA()->getGlobalIndex();
604	>	b = inversion->getAtomB()->getGlobalIndex();
605	>	c = inversion->getAtomC()->getGlobalIndex();
606	>	d = inversion->getAtomD()->getGlobalIndex();
607	>
608	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
609	>	oneTwoInteractions_.removePair(a, b);
610	>	oneTwoInteractions_.removePair(a, c);
611	>	oneTwoInteractions_.removePair(a, d);
612	>	} else {
613	>	excludedInteractions_.removePair(a, b);
614	>	excludedInteractions_.removePair(a, c);
615	>	excludedInteractions_.removePair(a, d);
616	>	}
617	>
618	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
619	>	oneThreeInteractions_.removePair(b, c);
620	>	oneThreeInteractions_.removePair(b, d);
621	>	oneThreeInteractions_.removePair(c, d);
622	>	} else {
623	>	excludedInteractions_.removePair(b, c);
624	>	excludedInteractions_.removePair(b, d);
625	>	excludedInteractions_.removePair(c, d);
626	>	}
627	>	}
628	>
629	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
630	>	rb = mol->nextRigidBody(rbIter)) {
631	>	vector<Atom*> atoms = rb->getAtoms();
632	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
633	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
634	>	a = atoms[i]->getGlobalIndex();
635	>	b = atoms[j]->getGlobalIndex();
636	>	excludedInteractions_.removePair(a, b);
637	>	}
638	>	}
639	>	}
640
317	–	for(i=0; i<3; i++)
318	–	scaled[i] = thePos[i]*HmatInv[i][i];
319	–
320	–	// wrap the scaled coordinates
321	–
322	–	for(i=0; i<3; i++)
323	–	scaled[i] -= roundMe(scaled[i]);
324	–
325	–	// calc the wrapped real coordinates from the wrapped scaled coordinates
326	–
327	–	for(i=0; i<3; i++)
328	–	thePos[i] = scaled[i]*Hmat[i][i];
641		}
642	+
643	+
644	+	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
645	+	int curStampId;
646
647	<	}
647	>	//index from 0
648	>	curStampId = moleculeStamps_.size();
649
650	+	moleculeStamps_.push_back(molStamp);
651	+	molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
652	+	}
653
334	–	int SimInfo::getNDF(){
335	–	int ndf_local;
654
655	<	ndf_local = 0;
656	<
657	<	for(int i = 0; i < integrableObjects.size(); i++){
658	<	ndf_local += 3;
659	<	if (integrableObjects[i]->isDirectional()) {
660	<	if (integrableObjects[i]->isLinear())
661	<	ndf_local += 2;
662	<	else
663	<	ndf_local += 3;
664	<	}
655	>	/**
656	>	* update
657	>	*
658	>	*  Performs the global checks and variable settings after the
659	>	*  objects have been created.
660	>	*
661	>	*/
662	>	void SimInfo::update() {
663	>	setupSimVariables();
664	>	calcNdf();
665	>	calcNdfRaw();
666	>	calcNdfTrans();
667		}
668	+
669	+	/**
670	+	* getSimulatedAtomTypes
671	+	*
672	+	* Returns an STL set of AtomType* that are actually present in this
673	+	* simulation.  Must query all processors to assemble this information.
674	+	*
675	+	*/
676	+	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
677	+	SimInfo::MoleculeIterator mi;
678	+	Molecule* mol;
679	+	Molecule::AtomIterator ai;
680	+	Atom* atom;
681	+	set<AtomType*> atomTypes;
682	+
683	+	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
684	+	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
685	+	atomTypes.insert(atom->getAtomType());
686	+	}
687	+	}
688
689	<	// n_constraints is local, so subtract them on each processor:
689	>	#ifdef IS_MPI
690
691	<	ndf_local -= n_constraints;
691	>	// loop over the found atom types on this processor, and add their
692	>	// numerical idents to a vector:
693
694	<	#ifdef IS_MPI
695	<	MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
696	<	#else
697	<	ndf = ndf_local;
357	<	#endif
694	>	vector<int> foundTypes;
695	>	set<AtomType*>::iterator i;
696	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
697	>	foundTypes.push_back( (*i)->getIdent() );
698
699	<	// nZconstraints is global, as are the 3 COM translations for the
700	<	// entire system:
699	>	// count_local holds the number of found types on this processor
700	>	int count_local = foundTypes.size();
701
702	<	ndf = ndf - 3 - nZconstraints;
702	>	// count holds the total number of found types on all processors
703	>	// (some will be redundant with the ones found locally):
704	>	int count;
705	>	MPI::COMM_WORLD.Allreduce(&count_local, &count, 1, MPI::INT, MPI::SUM);
706
707	<	return ndf;
708	<	}
707	>	// create a vector to hold the globally found types, and resize it:
708	>	vector<int> ftGlobal;
709	>	ftGlobal.resize(count);
710	>	vector<int> counts;
711
712	<	int SimInfo::getNDFraw() {
713	<	int ndfRaw_local;
712	>	int nproc = MPI::COMM_WORLD.Get_size();
713	>	counts.resize(nproc);
714	>	vector<int> disps;
715	>	disps.resize(nproc);
716
717	<	// Raw degrees of freedom that we have to set
718	<	ndfRaw_local = 0;
717	>	// now spray out the foundTypes to all the other processors:
718	>
719	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
720	>	&ftGlobal[0], &counts[0], &disps[0], MPI::INT);
721
722	<	for(int i = 0; i < integrableObjects.size(); i++){
723	<	ndfRaw_local += 3;
724	<	if (integrableObjects[i]->isDirectional()) {
725	<	if (integrableObjects[i]->isLinear())
726	<	ndfRaw_local += 2;
727	<	else
379	<	ndfRaw_local += 3;
380	<	}
381	<	}
722	>	// foundIdents is a stl set, so inserting an already found ident
723	>	// will have no effect.
724	>	set<int> foundIdents;
725	>	vector<int>::iterator j;
726	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
727	>	foundIdents.insert((*j));
728
729	<	#ifdef IS_MPI
730	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
731	<	#else
732	<	ndfRaw = ndfRaw_local;
729	>	// now iterate over the foundIdents and get the actual atom types
730	>	// that correspond to these:
731	>	set<int>::iterator it;
732	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
733	>	atomTypes.insert( forceField_->getAtomType((*it)) );
734	>
735		#endif
736	+
737	+	return atomTypes;
738	+	}
739
740	<	return ndfRaw;
741	<	}
740	>	void SimInfo::setupSimVariables() {
741	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
742	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
743	>	calcBoxDipole_ = false;
744	>	if ( simParams_->haveAccumulateBoxDipole() )
745	>	if ( simParams_->getAccumulateBoxDipole() ) {
746	>	calcBoxDipole_ = true;
747	>	}
748
749	<	int SimInfo::getNDFtranslational() {
750	<	int ndfTrans_local;
749	>	set<AtomType*>::iterator i;
750	>	set<AtomType*> atomTypes;
751	>	atomTypes = getSimulatedAtomTypes();
752	>	int usesElectrostatic = 0;
753	>	int usesMetallic = 0;
754	>	int usesDirectional = 0;
755	>	//loop over all of the atom types
756	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
757	>	usesElectrostatic |= (*i)->isElectrostatic();
758	>	usesMetallic |= (*i)->isMetal();
759	>	usesDirectional |= (*i)->isDirectional();
760	>	}
761
762	<	ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
762	>	#ifdef IS_MPI
763	>	int temp;
764	>	temp = usesDirectional;
765	>	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
766
767	+	temp = usesMetallic;
768	+	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
769
770	<	#ifdef IS_MPI
771	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
400	<	#else
401	<	ndfTrans = ndfTrans_local;
770	>	temp = usesElectrostatic;
771	>	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
772		#endif
773	+	fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;
774	+	fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
775	+	fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
776	+	fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
777	+	fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
778	+	fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
779	+	}
780
781	<	ndfTrans = ndfTrans - 3 - nZconstraints;
781	>	void SimInfo::setupFortran() {
782	>	int isError;
783	>	int nExclude, nOneTwo, nOneThree, nOneFour;
784	>	vector<int> fortranGlobalGroupMembership;
785	>
786	>	isError = 0;
787
788	<	return ndfTrans;
789	<	}
788	>	//globalGroupMembership_ is filled by SimCreator
789	>	for (int i = 0; i < nGlobalAtoms_; i++) {
790	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
791	>	}
792
793	<	int SimInfo::getTotIntegrableObjects() {
794	<	int nObjs_local;
795	<	int nObjs;
793	>	//calculate mass ratio of cutoff group
794	>	vector<RealType> mfact;
795	>	SimInfo::MoleculeIterator mi;
796	>	Molecule* mol;
797	>	Molecule::CutoffGroupIterator ci;
798	>	CutoffGroup* cg;
799	>	Molecule::AtomIterator ai;
800	>	Atom* atom;
801	>	RealType totalMass;
802
803	<	nObjs_local =  integrableObjects.size();
803	>	//to avoid memory reallocation, reserve enough space for mfact
804	>	mfact.reserve(getNCutoffGroups());
805	>
806	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
807	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
808
809	+	totalMass = cg->getMass();
810	+	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
811	+	// Check for massless groups - set mfact to 1 if true
812	+	if (totalMass != 0)
813	+	mfact.push_back(atom->getMass()/totalMass);
814	+	else
815	+	mfact.push_back( 1.0 );
816	+	}
817	+	}
818	+	}
819
820	<	#ifdef IS_MPI
821	<	MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
822	<	#else
419	<	nObjs = nObjs_local;
420	<	#endif
820	>	//fill ident array of local atoms (it is actually ident of
821	>	//AtomType, it is so confusing !!!)
822	>	vector<int> identArray;
823
824	+	//to avoid memory reallocation, reserve enough space identArray
825	+	identArray.reserve(getNAtoms());
826	+
827	+	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
828	+	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
829	+	identArray.push_back(atom->getIdent());
830	+	}
831	+	}
832
833	<	return nObjs;
834	<	}
833	>	//fill molMembershipArray
834	>	//molMembershipArray is filled by SimCreator
835	>	vector<int> molMembershipArray(nGlobalAtoms_);
836	>	for (int i = 0; i < nGlobalAtoms_; i++) {
837	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
838	>	}
839	>
840	>	//setup fortran simulation
841
842	<	void SimInfo::refreshSim(){
842	>	nExclude = excludedInteractions_.getSize();
843	>	nOneTwo = oneTwoInteractions_.getSize();
844	>	nOneThree = oneThreeInteractions_.getSize();
845	>	nOneFour = oneFourInteractions_.getSize();
846
847	<	simtype fInfo;
848	<	int isError;
849	<	int n_global;
850	<	int* excl;
847	>	int* excludeList = excludedInteractions_.getPairList();
848	>	int* oneTwoList = oneTwoInteractions_.getPairList();
849	>	int* oneThreeList = oneThreeInteractions_.getPairList();
850	>	int* oneFourList = oneFourInteractions_.getPairList();
851
852	<	fInfo.dielect = 0.0;
852	>	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
853	>	&nExclude, excludeList,
854	>	&nOneTwo, oneTwoList,
855	>	&nOneThree, oneThreeList,
856	>	&nOneFour, oneFourList,
857	>	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
858	>	&fortranGlobalGroupMembership[0], &isError);
859	>
860	>	if( isError ){
861	>
862	>	sprintf( painCave.errMsg,
863	>	"There was an error setting the simulation information in fortran.\n" );
864	>	painCave.isFatal = 1;
865	>	painCave.severity = OPENMD_ERROR;
866	>	simError();
867	>	}
868	>
869	>
870	>	sprintf( checkPointMsg,
871	>	"succesfully sent the simulation information to fortran.\n");
872	>
873	>	errorCheckPoint();
874	>
875	>	// Setup number of neighbors in neighbor list if present
876	>	if (simParams_->haveNeighborListNeighbors()) {
877	>	int nlistNeighbors = simParams_->getNeighborListNeighbors();
878	>	setNeighbors(&nlistNeighbors);
879	>	}
880	>
881	>	#ifdef IS_MPI
882	>	//SimInfo is responsible for creating localToGlobalAtomIndex and
883	>	//localToGlobalGroupIndex
884	>	vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
885	>	vector<int> localToGlobalCutoffGroupIndex;
886	>	mpiSimData parallelData;
887
888	<	if( useDipoles ){
436	<	if( useReactionField )fInfo.dielect = dielectric;
437	<	}
888	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
889
890	<	fInfo.SIM_uses_PBC = usePBC;
890	>	//local index(index in DataStorge) of atom is important
891	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
892	>	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
893	>	}
894
895	<	if (useSticky || useDipoles || useGayBerne || useShapes) {
896	<	useDirectionalAtoms = 1;
897	<	fInfo.SIM_uses_DirectionalAtoms = useDirectionalAtoms;
898	<	}
895	>	//local index of cutoff group is trivial, it only depends on the order of travesing
896	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
897	>	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
898	>	}
899	>
900	>	}
901
902	<	fInfo.SIM_uses_LennardJones = useLennardJones;
902	>	//fill up mpiSimData struct
903	>	parallelData.nMolGlobal = getNGlobalMolecules();
904	>	parallelData.nMolLocal = getNMolecules();
905	>	parallelData.nAtomsGlobal = getNGlobalAtoms();
906	>	parallelData.nAtomsLocal = getNAtoms();
907	>	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
908	>	parallelData.nGroupsLocal = getNCutoffGroups();
909	>	parallelData.myNode = worldRank;
910	>	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
911
912	<	if (useCharges || useDipoles) {
913	<	useElectrostatics = 1;
914	<	fInfo.SIM_uses_Electrostatics = useElectrostatics;
915	<	}
912	>	//pass mpiSimData struct and index arrays to fortran
913	>	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
914	>	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
915	>	&localToGlobalCutoffGroupIndex[0], &isError);
916
917	<	fInfo.SIM_uses_Charges = useCharges;
918	<	fInfo.SIM_uses_Dipoles = useDipoles;
919	<	fInfo.SIM_uses_Sticky = useSticky;
920	<	fInfo.SIM_uses_GayBerne = useGayBerne;
921	<	fInfo.SIM_uses_EAM = useEAM;
922	<	fInfo.SIM_uses_Shapes = useShapes;
459	<	fInfo.SIM_uses_FLARB = useFLARB;
460	<	fInfo.SIM_uses_RF = useReactionField;
917	>	if (isError) {
918	>	sprintf(painCave.errMsg,
919	>	"mpiRefresh errror: fortran didn't like something we gave it.\n");
920	>	painCave.isFatal = 1;
921	>	simError();
922	>	}
923
924	<	n_exclude = excludes->getSize();
925	<	excl = excludes->getFortranArray();
464	<
465	<	#ifdef IS_MPI
466	<	n_global = mpiSim->getNAtomsGlobal();
467	<	#else
468	<	n_global = n_atoms;
924	>	sprintf(checkPointMsg, " mpiRefresh successful.\n");
925	>	errorCheckPoint();
926		#endif
927	<
928	<	isError = 0;
472	<
473	<	getFortranGroupArrays(this, FglobalGroupMembership, mfact);
474	<	//it may not be a good idea to pass the address of first element in vector
475	<	//since c++ standard does not require vector to be stored continuously in meomory
476	<	//Most of the compilers will organize the memory of vector continuously
477	<	setFortranSim( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
478	<	&nGlobalExcludes, globalExcludes, molMembershipArray,
479	<	&mfact[0], &ngroup, &FglobalGroupMembership[0], &isError);
927	>	fortranInitialized_ = true;
928	>	}
929
930	<	if( isError ){
931	<
483	<	sprintf( painCave.errMsg,
484	<	"There was an error setting the simulation information in fortran.\n" );
485	<	painCave.isFatal = 1;
486	<	painCave.severity = OOPSE_ERROR;
487	<	simError();
930	>	void SimInfo::addProperty(GenericData* genData) {
931	>	properties_.addProperty(genData);
932		}
489	–
490	–	#ifdef IS_MPI
491	–	sprintf( checkPointMsg,
492	–	"succesfully sent the simulation information to fortran.\n");
493	–	MPIcheckPoint();
494	–	#endif // is_mpi
495	–
496	–	this->ndf = this->getNDF();
497	–	this->ndfRaw = this->getNDFraw();
498	–	this->ndfTrans = this->getNDFtranslational();
499	–	}
933
934	<	void SimInfo::setDefaultRcut( double theRcut ){
935	<
936	<	haveRcut = 1;
504	<	rCut = theRcut;
505	<	rList = rCut + 1.0;
506	<
507	<	notifyFortranCutoffs( &rCut, &rSw, &rList );
508	<	}
934	>	void SimInfo::removeProperty(const string& propName) {
935	>	properties_.removeProperty(propName);
936	>	}
937
938	<	void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
938	>	void SimInfo::clearProperties() {
939	>	properties_.clearProperties();
940	>	}
941
942	<	rSw = theRsw;
943	<	setDefaultRcut( theRcut );
944	<	}
942	>	vector<string> SimInfo::getPropertyNames() {
943	>	return properties_.getPropertyNames();
944	>	}
945	>
946	>	vector<GenericData*> SimInfo::getProperties() {
947	>	return properties_.getProperties();
948	>	}
949
950	+	GenericData* SimInfo::getPropertyByName(const string& propName) {
951	+	return properties_.getPropertyByName(propName);
952	+	}
953
954	<	void SimInfo::checkCutOffs( void ){
955	<
956	<	if( boxIsInit ){
957	<
958	<	//we need to check cutOffs against the box
959	<
960	<	if( rCut > maxCutoff ){
961	<	sprintf( painCave.errMsg,
962	<	"cutoffRadius is too large for the current periodic box.\n"
963	<	"\tCurrent Value of cutoffRadius = %G at time %G\n "
964	<	"\tThis is larger than half of at least one of the\n"
965	<	"\tperiodic box vectors.  Right now, the Box matrix is:\n"
966	<	"\n"
967	<	"\t[ %G %G %G ]\n"
968	<	"\t[ %G %G %G ]\n"
969	<	"\t[ %G %G %G ]\n",
970	<	rCut, currentTime,
971	<	Hmat[0][0], Hmat[0][1], Hmat[0][2],
972	<	Hmat[1][0], Hmat[1][1], Hmat[1][2],
973	<	Hmat[2][0], Hmat[2][1], Hmat[2][2]);
974	<	painCave.severity = OOPSE_ERROR;
975	<	painCave.isFatal = 1;
976	<	simError();
954	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
955	>	if (sman_ == sman) {
956	>	return;
957	>	}
958	>	delete sman_;
959	>	sman_ = sman;
960	>
961	>	Molecule* mol;
962	>	RigidBody* rb;
963	>	Atom* atom;
964	>	SimInfo::MoleculeIterator mi;
965	>	Molecule::RigidBodyIterator rbIter;
966	>	Molecule::AtomIterator atomIter;;
967	>
968	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
969	>
970	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
971	>	atom->setSnapshotManager(sman_);
972	>	}
973	>
974	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
975	>	rb->setSnapshotManager(sman_);
976	>	}
977		}
978	<	} else {
542	<	// initialize this stuff before using it, OK?
543	<	sprintf( painCave.errMsg,
544	<	"Trying to check cutoffs without a box.\n"
545	<	"\tOOPSE should have better programmers than that.\n" );
546	<	painCave.severity = OOPSE_ERROR;
547	<	painCave.isFatal = 1;
548	<	simError();
978	>
979		}
550	–
551	–	}
980
981	<	void SimInfo::addProperty(GenericData* prop){
981	>	Vector3d SimInfo::getComVel(){
982	>	SimInfo::MoleculeIterator i;
983	>	Molecule* mol;
984
985	<	map<string, GenericData*>::iterator result;
986	<	result = properties.find(prop->getID());
557	<
558	<	//we can't simply use  properties[prop->getID()] = prop,
559	<	//it will cause memory leak if we already contain a propery which has the same name of prop
560	<
561	<	if(result != properties.end()){
985	>	Vector3d comVel(0.0);
986	>	RealType totalMass = 0.0;
987
988	<	delete (*result).second;
989	<	(*result).second = prop;
990	<
988	>
989	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
990	>	RealType mass = mol->getMass();
991	>	totalMass += mass;
992	>	comVel += mass * mol->getComVel();
993	>	}
994	>
995	>	#ifdef IS_MPI
996	>	RealType tmpMass = totalMass;
997	>	Vector3d tmpComVel(comVel);
998	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
999	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1000	>	#endif
1001	>
1002	>	comVel /= totalMass;
1003	>
1004	>	return comVel;
1005		}
567	–	else{
1006
1007	<	properties[prop->getID()] = prop;
1007	>	Vector3d SimInfo::getCom(){
1008	>	SimInfo::MoleculeIterator i;
1009	>	Molecule* mol;
1010
1011	+	Vector3d com(0.0);
1012	+	RealType totalMass = 0.0;
1013	+
1014	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1015	+	RealType mass = mol->getMass();
1016	+	totalMass += mass;
1017	+	com += mass * mol->getCom();
1018	+	}
1019	+
1020	+	#ifdef IS_MPI
1021	+	RealType tmpMass = totalMass;
1022	+	Vector3d tmpCom(com);
1023	+	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1024	+	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1025	+	#endif
1026	+
1027	+	com /= totalMass;
1028	+
1029	+	return com;
1030	+
1031	+	}
1032	+
1033	+	ostream& operator <<(ostream& o, SimInfo& info) {
1034	+
1035	+	return o;
1036		}
1037	+
1038	+
1039	+	/*
1040	+	Returns center of mass and center of mass velocity in one function call.
1041	+	*/
1042	+
1043	+	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1044	+	SimInfo::MoleculeIterator i;
1045	+	Molecule* mol;
1046	+
1047
1048	<	}
1048	>	RealType totalMass = 0.0;
1049	>
1050
1051	<	GenericData* SimInfo::getProperty(const string& propName){
1052	<
1053	<	map<string, GenericData*>::iterator result;
1054	<
1055	<	//string lowerCaseName = ();
1056	<
1057	<	result = properties.find(propName);
1058	<
1059	<	if(result != properties.end())
1060	<	return (*result).second;
1061	<	else
1062	<	return NULL;
1063	<	}
1051	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1052	>	RealType mass = mol->getMass();
1053	>	totalMass += mass;
1054	>	com += mass * mol->getCom();
1055	>	comVel += mass * mol->getComVel();
1056	>	}
1057	>
1058	>	#ifdef IS_MPI
1059	>	RealType tmpMass = totalMass;
1060	>	Vector3d tmpCom(com);
1061	>	Vector3d tmpComVel(comVel);
1062	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1063	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1064	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1065	>	#endif
1066	>
1067	>	com /= totalMass;
1068	>	comVel /= totalMass;
1069	>	}
1070	>
1071	>	/*
1072	>	Return intertia tensor for entire system and angular momentum Vector.
1073
1074
1075	<	void SimInfo::getFortranGroupArrays(SimInfo* info,
1076	<	vector<int>& FglobalGroupMembership,
1077	<	vector<double>& mfact){
1078	<
594	<	Molecule* myMols;
595	<	Atom** myAtoms;
596	<	int numAtom;
597	<	double mtot;
598	<	int numMol;
599	<	int numCutoffGroups;
600	<	CutoffGroup* myCutoffGroup;
601	<	vector<CutoffGroup*>::iterator iterCutoff;
602	<	Atom* cutoffAtom;
603	<	vector<Atom*>::iterator iterAtom;
604	<	int atomIndex;
605	<	double totalMass;
606	<
607	<	mfact.clear();
608	<	FglobalGroupMembership.clear();
609	<
1075	>	[  Ixx -Ixy  -Ixz ]
1076	>	J =| -Iyx  Iyy  -Iyz |
1077	>	[ -Izx -Iyz   Izz ]
1078	>	*/
1079
1080	<	// Fix the silly fortran indexing problem
1080	>	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1081	>
1082	>
1083	>	RealType xx = 0.0;
1084	>	RealType yy = 0.0;
1085	>	RealType zz = 0.0;
1086	>	RealType xy = 0.0;
1087	>	RealType xz = 0.0;
1088	>	RealType yz = 0.0;
1089	>	Vector3d com(0.0);
1090	>	Vector3d comVel(0.0);
1091	>
1092	>	getComAll(com, comVel);
1093	>
1094	>	SimInfo::MoleculeIterator i;
1095	>	Molecule* mol;
1096	>
1097	>	Vector3d thisq(0.0);
1098	>	Vector3d thisv(0.0);
1099	>
1100	>	RealType thisMass = 0.0;
1101	>
1102	>
1103	>
1104	>
1105	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1106	>
1107	>	thisq = mol->getCom()-com;
1108	>	thisv = mol->getComVel()-comVel;
1109	>	thisMass = mol->getMass();
1110	>	// Compute moment of intertia coefficients.
1111	>	xx += thisq[0]*thisq[0]*thisMass;
1112	>	yy += thisq[1]*thisq[1]*thisMass;
1113	>	zz += thisq[2]*thisq[2]*thisMass;
1114	>
1115	>	// compute products of intertia
1116	>	xy += thisq[0]*thisq[1]*thisMass;
1117	>	xz += thisq[0]*thisq[2]*thisMass;
1118	>	yz += thisq[1]*thisq[2]*thisMass;
1119	>
1120	>	angularMomentum += cross( thisq, thisv ) * thisMass;
1121	>
1122	>	}
1123	>
1124	>
1125	>	inertiaTensor(0,0) = yy + zz;
1126	>	inertiaTensor(0,1) = -xy;
1127	>	inertiaTensor(0,2) = -xz;
1128	>	inertiaTensor(1,0) = -xy;
1129	>	inertiaTensor(1,1) = xx + zz;
1130	>	inertiaTensor(1,2) = -yz;
1131	>	inertiaTensor(2,0) = -xz;
1132	>	inertiaTensor(2,1) = -yz;
1133	>	inertiaTensor(2,2) = xx + yy;
1134	>
1135		#ifdef IS_MPI
1136	<	numAtom = mpiSim->getNAtomsGlobal();
1137	<	#else
1138	<	numAtom = n_atoms;
1136	>	Mat3x3d tmpI(inertiaTensor);
1137	>	Vector3d tmpAngMom;
1138	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1139	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1140		#endif
1141	<	for (int i = 0; i < numAtom; i++)
1142	<	FglobalGroupMembership.push_back(globalGroupMembership[i] + 1);
1143	<
1141	>
1142	>	return;
1143	>	}
1144
1145	<	myMols = info->molecules;
1146	<	numMol = info->n_mol;
623	<	for(int i  = 0; i < numMol; i++){
624	<	numCutoffGroups = myMols[i].getNCutoffGroups();
625	<	for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff);
626	<	myCutoffGroup != NULL;
627	<	myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
628	<
629	<	totalMass = myCutoffGroup->getMass();
1145	>	//Returns the angular momentum of the system
1146	>	Vector3d SimInfo::getAngularMomentum(){
1147
1148	<	for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom);
1149	<	cutoffAtom != NULL;
1150	<	cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
1151	<	mfact.push_back(cutoffAtom->getMass()/totalMass);
1148	>	Vector3d com(0.0);
1149	>	Vector3d comVel(0.0);
1150	>	Vector3d angularMomentum(0.0);
1151	>
1152	>	getComAll(com,comVel);
1153	>
1154	>	SimInfo::MoleculeIterator i;
1155	>	Molecule* mol;
1156	>
1157	>	Vector3d thisr(0.0);
1158	>	Vector3d thisp(0.0);
1159	>
1160	>	RealType thisMass;
1161	>
1162	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1163	>	thisMass = mol->getMass();
1164	>	thisr = mol->getCom()-com;
1165	>	thisp = (mol->getComVel()-comVel)*thisMass;
1166	>
1167	>	angularMomentum += cross( thisr, thisp );
1168	>
1169		}
1170	+
1171	+	#ifdef IS_MPI
1172	+	Vector3d tmpAngMom;
1173	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1174	+	#endif
1175	+
1176	+	return angularMomentum;
1177	+	}
1178	+
1179	+	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1180	+	return IOIndexToIntegrableObject.at(index);
1181	+	}
1182	+
1183	+	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1184	+	IOIndexToIntegrableObject= v;
1185	+	}
1186	+
1187	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1188	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1189	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1190	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1191	+	*/
1192	+	void SimInfo::getGyrationalVolume(RealType &volume){
1193	+	Mat3x3d intTensor;
1194	+	RealType det;
1195	+	Vector3d dummyAngMom;
1196	+	RealType sysconstants;
1197	+	RealType geomCnst;
1198	+
1199	+	geomCnst = 3.0/2.0;
1200	+	/* Get the inertial tensor and angular momentum for free*/
1201	+	getInertiaTensor(intTensor,dummyAngMom);
1202	+
1203	+	det = intTensor.determinant();
1204	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1205	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1206	+	return;
1207	+	}
1208	+
1209	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1210	+	Mat3x3d intTensor;
1211	+	Vector3d dummyAngMom;
1212	+	RealType sysconstants;
1213	+	RealType geomCnst;
1214	+
1215	+	geomCnst = 3.0/2.0;
1216	+	/* Get the inertial tensor and angular momentum for free*/
1217	+	getInertiaTensor(intTensor,dummyAngMom);
1218	+
1219	+	detI = intTensor.determinant();
1220	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1221	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1222	+	return;
1223	+	}
1224	+	/*
1225	+	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1226	+	assert( v.size() == nAtoms_ + nRigidBodies_);
1227	+	sdByGlobalIndex_ = v;
1228		}
1229	+
1230	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1231	+	//assert(index < nAtoms_ + nRigidBodies_);
1232	+	return sdByGlobalIndex_.at(index);
1233	+	}
1234	+	*/
1235	+	int SimInfo::getNGlobalConstraints() {
1236	+	int nGlobalConstraints;
1237	+	#ifdef IS_MPI
1238	+	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1239	+	MPI_COMM_WORLD);
1240	+	#else
1241	+	nGlobalConstraints =  nConstraints_;
1242	+	#endif
1243	+	return nGlobalConstraints;
1244		}
1245
1246	<	}
1246	>	}//end namespace OpenMD
1247	>

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 143 by chrisfen, Fri Oct 22 22:54:01 2004 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1535 by gezelter, Fri Dec 31 18:31:56 2010 UTC

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