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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 1725 by gezelter, Sat May 26 18:13:43 2012 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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	>	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	>	*/
42	>
43	>	/**
44	>	* @file SimInfo.cpp
45	>	* @author    tlin
46	>	* @date  11/02/2004
47	>	* @version 1.0
48	>	*/
49
50	<	#include <iostream>
51	<	using namespace std;
50	>	#include <algorithm>
51	>	#include <set>
52	>	#include <map>
53
54		#include "brains/SimInfo.hpp"
55	<	#define __C
56	<	#include "brains/fSimulation.h"
55	>	#include "math/Vector3.hpp"
56	>	#include "primitives/Molecule.hpp"
57	>	#include "primitives/StuntDouble.hpp"
58	>	#include "utils/MemoryUtils.hpp"
59		#include "utils/simError.h"
60	<	#include "UseTheForce/DarkSide/simulation_interface.h"
61	<	#include "UseTheForce/notifyCutoffs_interface.h"
62	<
63	<	//#include "UseTheForce/fortranWrappers.hpp"
16	<
17	<	#include "math/MatVec3.h"
18	<
60	>	#include "selection/SelectionManager.hpp"
61	>	#include "io/ForceFieldOptions.hpp"
62	>	#include "brains/ForceField.hpp"
63	>	#include "nonbonded/SwitchingFunction.hpp"
64		#ifdef IS_MPI
65	<	#include "brains/mpiSimulation.hpp"
65	>	#include <mpi.h>
66		#endif
67
68	<	inline double roundMe( double x ){
69	<	return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
70	<	}
71	<
72	<	inline double min( double a, double b ){
73	<	return (a < b ) ? a : b;
74	<	}
68	>	using namespace std;
69	>	namespace OpenMD {
70	>
71	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
72	>	forceField_(ff), simParams_(simParams),
73	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
74	>	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
75	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), nGlobalFluctuatingCharges_(0),
76	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
77	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
78	>	nConstraints_(0), nFluctuatingCharges_(0), sman_(NULL), topologyDone_(false),
79	>	calcBoxDipole_(false), useAtomicVirial_(true) {
80	>
81	>	MoleculeStamp* molStamp;
82	>	int nMolWithSameStamp;
83	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
84	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
85	>	CutoffGroupStamp* cgStamp;
86	>	RigidBodyStamp* rbStamp;
87	>	int nRigidAtoms = 0;
88	>
89	>	vector<Component*> components = simParams->getComponents();
90	>
91	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
92	>	molStamp = (*i)->getMoleculeStamp();
93	>	nMolWithSameStamp = (*i)->getNMol();
94	>
95	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
96	>
97	>	//calculate atoms in molecules
98	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
99	>
100	>	//calculate atoms in cutoff groups
101	>	int nAtomsInGroups = 0;
102	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
103	>
104	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
105	>	cgStamp = molStamp->getCutoffGroupStamp(j);
106	>	nAtomsInGroups += cgStamp->getNMembers();
107	>	}
108	>
109	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
110	>
111	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
112	>
113	>	//calculate atoms in rigid bodies
114	>	int nAtomsInRigidBodies = 0;
115	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
116	>
117	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
118	>	rbStamp = molStamp->getRigidBodyStamp(j);
119	>	nAtomsInRigidBodies += rbStamp->getNMembers();
120	>	}
121	>
122	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
123	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
124	>
125	>	}
126	>
127	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
128	>	//group therefore the total number of cutoff groups in the system is
129	>	//equal to the total number of atoms minus number of atoms belong to
130	>	//cutoff group defined in meta-data file plus the number of cutoff
131	>	//groups defined in meta-data file
132
133	<	SimInfo* currentInfo;
133	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
134	>
135	>	//every free atom (atom does not belong to rigid bodies) is an
136	>	//integrable object therefore the total number of integrable objects
137	>	//in the system is equal to the total number of atoms minus number of
138	>	//atoms belong to rigid body defined in meta-data file plus the number
139	>	//of rigid bodies defined in meta-data file
140	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
141	>	+ nGlobalRigidBodies_;
142	>
143	>	nGlobalMols_ = molStampIds_.size();
144	>	molToProcMap_.resize(nGlobalMols_);
145	>	}
146	>
147	>	SimInfo::~SimInfo() {
148	>	map<int, Molecule*>::iterator i;
149	>	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
150	>	delete i->second;
151	>	}
152	>	molecules_.clear();
153	>
154	>	delete sman_;
155	>	delete simParams_;
156	>	delete forceField_;
157	>	}
158
33	–	SimInfo::SimInfo(){
159
160	<	n_constraints = 0;
161	<	nZconstraints = 0;
162	<	n_oriented = 0;
163	<	n_dipoles = 0;
164	<	ndf = 0;
165	<	ndfRaw = 0;
166	<	nZconstraints = 0;
167	<	the_integrator = NULL;
168	<	setTemp = 0;
169	<	thermalTime = 0.0;
170	<	currentTime = 0.0;
171	<	rCut = 0.0;
172	<	rSw = 0.0;
173	<
174	<	haveRcut = 0;
175	<	haveRsw = 0;
176	<	boxIsInit = 0;
160	>	bool SimInfo::addMolecule(Molecule* mol) {
161	>	MoleculeIterator i;
162	>
163	>	i = molecules_.find(mol->getGlobalIndex());
164	>	if (i == molecules_.end() ) {
165	>
166	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
167	>
168	>	nAtoms_ += mol->getNAtoms();
169	>	nBonds_ += mol->getNBonds();
170	>	nBends_ += mol->getNBends();
171	>	nTorsions_ += mol->getNTorsions();
172	>	nInversions_ += mol->getNInversions();
173	>	nRigidBodies_ += mol->getNRigidBodies();
174	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
175	>	nCutoffGroups_ += mol->getNCutoffGroups();
176	>	nConstraints_ += mol->getNConstraintPairs();
177	>
178	>	addInteractionPairs(mol);
179	>
180	>	return true;
181	>	} else {
182	>	return false;
183	>	}
184	>	}
185
186	<	resetTime = 1e99;
186	>	bool SimInfo::removeMolecule(Molecule* mol) {
187	>	MoleculeIterator i;
188	>	i = molecules_.find(mol->getGlobalIndex());
189
190	<	orthoRhombic = 0;
56	<	orthoTolerance = 1E-6;
57	<	useInitXSstate = true;
190	>	if (i != molecules_.end() ) {
191
192	<	usePBC = 0;
193	<	useDirectionalAtoms = 0;
194	<	useLennardJones = 0;
195	<	useElectrostatics = 0;
196	<	useCharges = 0;
197	<	useDipoles = 0;
198	<	useSticky = 0;
199	<	useGayBerne = 0;
200	<	useEAM = 0;
201	<	useShapes = 0;
202	<	useFLARB = 0;
192	>	assert(mol == i->second);
193	>
194	>	nAtoms_ -= mol->getNAtoms();
195	>	nBonds_ -= mol->getNBonds();
196	>	nBends_ -= mol->getNBends();
197	>	nTorsions_ -= mol->getNTorsions();
198	>	nInversions_ -= mol->getNInversions();
199	>	nRigidBodies_ -= mol->getNRigidBodies();
200	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
201	>	nCutoffGroups_ -= mol->getNCutoffGroups();
202	>	nConstraints_ -= mol->getNConstraintPairs();
203
204	<	useSolidThermInt = 0;
205	<	useLiquidThermInt = 0;
204	>	removeInteractionPairs(mol);
205	>	molecules_.erase(mol->getGlobalIndex());
206
207	<	haveCutoffGroups = false;
207	>	delete mol;
208	>
209	>	return true;
210	>	} else {
211	>	return false;
212	>	}
213	>	}
214
215	<	excludes = Exclude::Instance();
215	>
216	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
217	>	i = molecules_.begin();
218	>	return i == molecules_.end() ? NULL : i->second;
219	>	}
220
221	<	myConfiguration = new SimState();
221	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
222	>	++i;
223	>	return i == molecules_.end() ? NULL : i->second;
224	>	}
225
80	–	has_minimizer = false;
81	–	the_minimizer =NULL;
226
227	<	ngroup = 0;
227	>	void SimInfo::calcNdf() {
228	>	int ndf_local, nfq_local;
229	>	MoleculeIterator i;
230	>	vector<StuntDouble*>::iterator j;
231	>	vector<Atom*>::iterator k;
232
233	<	}
233	>	Molecule* mol;
234	>	StuntDouble* integrableObject;
235	>	Atom* atom;
236
237	+	ndf_local = 0;
238	+	nfq_local = 0;
239	+
240	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
241	+	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
242	+	integrableObject = mol->nextIntegrableObject(j)) {
243
244	<	SimInfo::~SimInfo(){
244	>	ndf_local += 3;
245
246	<	delete myConfiguration;
246	>	if (integrableObject->isDirectional()) {
247	>	if (integrableObject->isLinear()) {
248	>	ndf_local += 2;
249	>	} else {
250	>	ndf_local += 3;
251	>	}
252	>	}
253	>	}
254	>	for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
255	>	atom = mol->nextFluctuatingCharge(k)) {
256	>	if (atom->isFluctuatingCharge()) {
257	>	nfq_local++;
258	>	}
259	>	}
260	>	}
261	>
262	>	// n_constraints is local, so subtract them on each processor
263	>	ndf_local -= nConstraints_;
264
265	<	map<string, GenericData*>::iterator i;
266	<
267	<	for(i = properties.begin(); i != properties.end(); i++)
268	<	delete (*i).second;
265	>	#ifdef IS_MPI
266	>	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
267	>	MPI_Allreduce(&nfq_local,&nGlobalFluctuatingCharges_,1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
268	>	#else
269	>	ndf_ = ndf_local;
270	>	nGlobalFluctuatingCharges_ = nfq_local;
271	>	#endif
272
273	<	}
273	>	// nZconstraints_ is global, as are the 3 COM translations for the
274	>	// entire system:
275	>	ndf_ = ndf_ - 3 - nZconstraint_;
276
277	<	void SimInfo::setBox(double newBox[3]) {
100	<
101	<	int i, j;
102	<	double tempMat[3][3];
277	>	}
278
279	<	for(i=0; i<3; i++)
280	<	for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
281	<
282	<	tempMat[0][0] = newBox[0];
283	<	tempMat[1][1] = newBox[1];
284	<	tempMat[2][2] = newBox[2];
285	<
286	<	setBoxM( tempMat );
112	<
113	<	}
114	<
115	<	void SimInfo::setBoxM( double theBox[3][3] ){
279	>	int SimInfo::getFdf() {
280	>	#ifdef IS_MPI
281	>	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
282	>	#else
283	>	fdf_ = fdf_local;
284	>	#endif
285	>	return fdf_;
286	>	}
287
288	<	int i, j;
289	<	double FortranHmat[9]; // to preserve compatibility with Fortran the
290	<	// ordering in the array is as follows:
291	<	// [ 0 3 6 ]
292	<	// [ 1 4 7 ]
293	<	// [ 2 5 8 ]
294	<	double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
295	<
296	<	if( !boxIsInit ) boxIsInit = 1;
297	<
298	<	for(i=0; i < 3; i++)
299	<	for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
300	<
301	<	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];
288	>	unsigned int SimInfo::getNLocalCutoffGroups(){
289	>	int nLocalCutoffAtoms = 0;
290	>	Molecule* mol;
291	>	MoleculeIterator mi;
292	>	CutoffGroup* cg;
293	>	Molecule::CutoffGroupIterator ci;
294	>
295	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
296	>
297	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
298	>	cg = mol->nextCutoffGroup(ci)) {
299	>	nLocalCutoffAtoms += cg->getNumAtom();
300	>
301	>	}
302		}
303	+
304	+	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
305		}
306	+
307	+	void SimInfo::calcNdfRaw() {
308	+	int ndfRaw_local;
309
310	<	setFortranBox(FortranHmat, FortranHmatInv, &orthoRhombic);
311	<
312	<	}
313	<
310	>	MoleculeIterator i;
311	>	vector<StuntDouble*>::iterator j;
312	>	Molecule* mol;
313	>	StuntDouble* integrableObject;
314
315	<	void SimInfo::getBoxM (double theBox[3][3]) {
315	>	// Raw degrees of freedom that we have to set
316	>	ndfRaw_local = 0;
317	>
318	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
319	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
320	>	integrableObject = mol->nextIntegrableObject(j)) {
321
322	<	int i, j;
148	<	for(i=0; i<3; i++)
149	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
150	<	}
322	>	ndfRaw_local += 3;
323
324	+	if (integrableObject->isDirectional()) {
325	+	if (integrableObject->isLinear()) {
326	+	ndfRaw_local += 2;
327	+	} else {
328	+	ndfRaw_local += 3;
329	+	}
330	+	}
331	+
332	+	}
333	+	}
334	+
335	+	#ifdef IS_MPI
336	+	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
337	+	#else
338	+	ndfRaw_ = ndfRaw_local;
339	+	#endif
340	+	}
341
342	<	void SimInfo::scaleBox(double scale) {
343	<	double theBox[3][3];
155	<	int i, j;
342	>	void SimInfo::calcNdfTrans() {
343	>	int ndfTrans_local;
344
345	<	// cerr << "Scaling box by " << scale << "\n";
345	>	ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
346
159	–	for(i=0; i<3; i++)
160	–	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
347
348	<	setBoxM(theBox);
348	>	#ifdef IS_MPI
349	>	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
350	>	#else
351	>	ndfTrans_ = ndfTrans_local;
352	>	#endif
353
354	<	}
354	>	ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
355	>
356	>	}
357
358	<	void SimInfo::calcHmatInv( void ) {
359	<
360	<	int oldOrtho;
361	<	int i,j;
362	<	double smallDiag;
363	<	double tol;
364	<	double sanity[3][3];
365	<
366	<	invertMat3( Hmat, HmatInv );
367	<
368	<	// check to see if Hmat is orthorhombic
369	<
370	<	oldOrtho = orthoRhombic;
358	>	void SimInfo::addInteractionPairs(Molecule* mol) {
359	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
360	>	vector<Bond*>::iterator bondIter;
361	>	vector<Bend*>::iterator bendIter;
362	>	vector<Torsion*>::iterator torsionIter;
363	>	vector<Inversion*>::iterator inversionIter;
364	>	Bond* bond;
365	>	Bend* bend;
366	>	Torsion* torsion;
367	>	Inversion* inversion;
368	>	int a;
369	>	int b;
370	>	int c;
371	>	int d;
372
373	<	smallDiag = fabs(Hmat[0][0]);
374	<	if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
375	<	if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
376	<	tol = smallDiag * orthoTolerance;
373	>	// atomGroups can be used to add special interaction maps between
374	>	// groups of atoms that are in two separate rigid bodies.
375	>	// However, most site-site interactions between two rigid bodies
376	>	// are probably not special, just the ones between the physically
377	>	// bonded atoms.  Interactions *within* a single rigid body should
378	>	// always be excluded.  These are done at the bottom of this
379	>	// function.
380
381	<	orthoRhombic = 1;
382	<
383	<	for (i = 0; i < 3; i++ ) {
384	<	for (j = 0 ; j < 3; j++) {
385	<	if (i != j) {
386	<	if (orthoRhombic) {
387	<	if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
388	<	}
381	>	map<int, set<int> > atomGroups;
382	>	Molecule::RigidBodyIterator rbIter;
383	>	RigidBody* rb;
384	>	Molecule::IntegrableObjectIterator ii;
385	>	StuntDouble* integrableObject;
386	>
387	>	for (integrableObject = mol->beginIntegrableObject(ii);
388	>	integrableObject != NULL;
389	>	integrableObject = mol->nextIntegrableObject(ii)) {
390	>
391	>	if (integrableObject->isRigidBody()) {
392	>	rb = static_cast<RigidBody*>(integrableObject);
393	>	vector<Atom*> atoms = rb->getAtoms();
394	>	set<int> rigidAtoms;
395	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
396	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
397	>	}
398	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
399	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
400	>	}
401	>	} else {
402	>	set<int> oneAtomSet;
403	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
404	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
405		}
406	<	}
407	<	}
406	>	}
407	>
408	>	for (bond= mol->beginBond(bondIter); bond != NULL;
409	>	bond = mol->nextBond(bondIter)) {
410
411	<	if( oldOrtho != orthoRhombic ){
411	>	a = bond->getAtomA()->getGlobalIndex();
412	>	b = bond->getAtomB()->getGlobalIndex();
413
414	<	if( orthoRhombic ) {
415	<	sprintf( painCave.errMsg,
416	<	"OOPSE is switching from the default Non-Orthorhombic\n"
417	<	"\tto the faster Orthorhombic periodic boundary computations.\n"
418	<	"\tThis is usually a good thing, but if you wan't the\n"
204	<	"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
205	<	"\tvariable ( currently set to %G ) smaller.\n",
206	<	orthoTolerance);
207	<	painCave.severity = OOPSE_INFO;
208	<	simError();
414	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
415	>	oneTwoInteractions_.addPair(a, b);
416	>	} else {
417	>	excludedInteractions_.addPair(a, b);
418	>	}
419		}
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	–	}
420
421	<	void SimInfo::calcBoxL( void ){
421	>	for (bend= mol->beginBend(bendIter); bend != NULL;
422	>	bend = mol->nextBend(bendIter)) {
423
424	<	double dx, dy, dz, dsq;
424	>	a = bend->getAtomA()->getGlobalIndex();
425	>	b = bend->getAtomB()->getGlobalIndex();
426	>	c = bend->getAtomC()->getGlobalIndex();
427	>
428	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
429	>	oneTwoInteractions_.addPair(a, b);
430	>	oneTwoInteractions_.addPair(b, c);
431	>	} else {
432	>	excludedInteractions_.addPair(a, b);
433	>	excludedInteractions_.addPair(b, c);
434	>	}
435
436	<	// boxVol = Determinant of Hmat
436	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
437	>	oneThreeInteractions_.addPair(a, c);
438	>	} else {
439	>	excludedInteractions_.addPair(a, c);
440	>	}
441	>	}
442
443	<	boxVol = matDet3( Hmat );
443	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
444	>	torsion = mol->nextTorsion(torsionIter)) {
445
446	<	// boxLx
447	<
448	<	dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
449	<	dsq = dx*dx + dy*dy + dz*dz;
237	<	boxL[0] = sqrt( dsq );
238	<	//maxCutoff = 0.5 * boxL[0];
446	>	a = torsion->getAtomA()->getGlobalIndex();
447	>	b = torsion->getAtomB()->getGlobalIndex();
448	>	c = torsion->getAtomC()->getGlobalIndex();
449	>	d = torsion->getAtomD()->getGlobalIndex();
450
451	<	// boxLy
452	<
453	<	dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
454	<	dsq = dx*dx + dy*dy + dz*dz;
455	<	boxL[1] = sqrt( dsq );
456	<	//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
451	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
452	>	oneTwoInteractions_.addPair(a, b);
453	>	oneTwoInteractions_.addPair(b, c);
454	>	oneTwoInteractions_.addPair(c, d);
455	>	} else {
456	>	excludedInteractions_.addPair(a, b);
457	>	excludedInteractions_.addPair(b, c);
458	>	excludedInteractions_.addPair(c, d);
459	>	}
460
461	+	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
462	+	oneThreeInteractions_.addPair(a, c);
463	+	oneThreeInteractions_.addPair(b, d);
464	+	} else {
465	+	excludedInteractions_.addPair(a, c);
466	+	excludedInteractions_.addPair(b, d);
467	+	}
468
469	<	// boxLz
470	<
471	<	dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
472	<	dsq = dx*dx + dy*dy + dz*dz;
473	<	boxL[2] = sqrt( dsq );
474	<	//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
469	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
470	>	oneFourInteractions_.addPair(a, d);
471	>	} else {
472	>	excludedInteractions_.addPair(a, d);
473	>	}
474	>	}
475
476	<	//calculate the max cutoff
477	<	maxCutoff =  calcMaxCutOff();
257	<
258	<	checkCutOffs();
476	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
477	>	inversion = mol->nextInversion(inversionIter)) {
478
479	<	}
479	>	a = inversion->getAtomA()->getGlobalIndex();
480	>	b = inversion->getAtomB()->getGlobalIndex();
481	>	c = inversion->getAtomC()->getGlobalIndex();
482	>	d = inversion->getAtomD()->getGlobalIndex();
483
484	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
485	+	oneTwoInteractions_.addPair(a, b);
486	+	oneTwoInteractions_.addPair(a, c);
487	+	oneTwoInteractions_.addPair(a, d);
488	+	} else {
489	+	excludedInteractions_.addPair(a, b);
490	+	excludedInteractions_.addPair(a, c);
491	+	excludedInteractions_.addPair(a, d);
492	+	}
493
494	<	double SimInfo::calcMaxCutOff(){
494	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
495	>	oneThreeInteractions_.addPair(b, c);
496	>	oneThreeInteractions_.addPair(b, d);
497	>	oneThreeInteractions_.addPair(c, d);
498	>	} else {
499	>	excludedInteractions_.addPair(b, c);
500	>	excludedInteractions_.addPair(b, d);
501	>	excludedInteractions_.addPair(c, d);
502	>	}
503	>	}
504
505	<	double ri[3], rj[3], rk[3];
506	<	double rij[3], rjk[3], rki[3];
507	<	double minDist;
505	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
506	>	rb = mol->nextRigidBody(rbIter)) {
507	>	vector<Atom*> atoms = rb->getAtoms();
508	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
509	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
510	>	a = atoms[i]->getGlobalIndex();
511	>	b = atoms[j]->getGlobalIndex();
512	>	excludedInteractions_.addPair(a, b);
513	>	}
514	>	}
515	>	}
516
517	<	ri[0] = Hmat[0][0];
270	<	ri[1] = Hmat[1][0];
271	<	ri[2] = Hmat[2][0];
517	>	}
518
519	<	rj[0] = Hmat[0][1];
520	<	rj[1] = Hmat[1][1];
521	<	rj[2] = Hmat[2][1];
519	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
520	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
521	>	vector<Bond*>::iterator bondIter;
522	>	vector<Bend*>::iterator bendIter;
523	>	vector<Torsion*>::iterator torsionIter;
524	>	vector<Inversion*>::iterator inversionIter;
525	>	Bond* bond;
526	>	Bend* bend;
527	>	Torsion* torsion;
528	>	Inversion* inversion;
529	>	int a;
530	>	int b;
531	>	int c;
532	>	int d;
533
534	<	rk[0] = Hmat[0][2];
535	<	rk[1] = Hmat[1][2];
536	<	rk[2] = Hmat[2][2];
534	>	map<int, set<int> > atomGroups;
535	>	Molecule::RigidBodyIterator rbIter;
536	>	RigidBody* rb;
537	>	Molecule::IntegrableObjectIterator ii;
538	>	StuntDouble* integrableObject;
539
540	<	crossProduct3(ri, rj, rij);
541	<	distXY = dotProduct3(rk,rij) / norm3(rij);
540	>	for (integrableObject = mol->beginIntegrableObject(ii);
541	>	integrableObject != NULL;
542	>	integrableObject = mol->nextIntegrableObject(ii)) {
543	>
544	>	if (integrableObject->isRigidBody()) {
545	>	rb = static_cast<RigidBody*>(integrableObject);
546	>	vector<Atom*> atoms = rb->getAtoms();
547	>	set<int> rigidAtoms;
548	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
549	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
550	>	}
551	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
552	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
553	>	}
554	>	} else {
555	>	set<int> oneAtomSet;
556	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
557	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
558	>	}
559	>	}
560
561	<	crossProduct3(rj,rk, rjk);
562	<	distYZ = dotProduct3(ri,rjk) / norm3(rjk);
561	>	for (bond= mol->beginBond(bondIter); bond != NULL;
562	>	bond = mol->nextBond(bondIter)) {
563	>
564	>	a = bond->getAtomA()->getGlobalIndex();
565	>	b = bond->getAtomB()->getGlobalIndex();
566	>
567	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
568	>	oneTwoInteractions_.removePair(a, b);
569	>	} else {
570	>	excludedInteractions_.removePair(a, b);
571	>	}
572	>	}
573
574	<	crossProduct3(rk,ri, rki);
575	<	distZX = dotProduct3(rj,rki) / norm3(rki);
574	>	for (bend= mol->beginBend(bendIter); bend != NULL;
575	>	bend = mol->nextBend(bendIter)) {
576
577	<	minDist = min(min(distXY, distYZ), distZX);
578	<	return minDist/2;
579	<
580	<	}
577	>	a = bend->getAtomA()->getGlobalIndex();
578	>	b = bend->getAtomB()->getGlobalIndex();
579	>	c = bend->getAtomC()->getGlobalIndex();
580	>
581	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
582	>	oneTwoInteractions_.removePair(a, b);
583	>	oneTwoInteractions_.removePair(b, c);
584	>	} else {
585	>	excludedInteractions_.removePair(a, b);
586	>	excludedInteractions_.removePair(b, c);
587	>	}
588
589	<	void SimInfo::wrapVector( double thePos[3] ){
589	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
590	>	oneThreeInteractions_.removePair(a, c);
591	>	} else {
592	>	excludedInteractions_.removePair(a, c);
593	>	}
594	>	}
595
596	<	int i;
597	<	double scaled[3];
596	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
597	>	torsion = mol->nextTorsion(torsionIter)) {
598
599	<	if( !orthoRhombic ){
600	<	// calc the scaled coordinates.
599	>	a = torsion->getAtomA()->getGlobalIndex();
600	>	b = torsion->getAtomB()->getGlobalIndex();
601	>	c = torsion->getAtomC()->getGlobalIndex();
602	>	d = torsion->getAtomD()->getGlobalIndex();
603
604	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
605	+	oneTwoInteractions_.removePair(a, b);
606	+	oneTwoInteractions_.removePair(b, c);
607	+	oneTwoInteractions_.removePair(c, d);
608	+	} else {
609	+	excludedInteractions_.removePair(a, b);
610	+	excludedInteractions_.removePair(b, c);
611	+	excludedInteractions_.removePair(c, d);
612	+	}
613
614	<	matVecMul3(HmatInv, thePos, scaled);
615	<
616	<	for(i=0; i<3; i++)
617	<	scaled[i] -= roundMe(scaled[i]);
618	<
619	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
620	<
311	<	matVecMul3(Hmat, scaled, thePos);
614	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
615	>	oneThreeInteractions_.removePair(a, c);
616	>	oneThreeInteractions_.removePair(b, d);
617	>	} else {
618	>	excludedInteractions_.removePair(a, c);
619	>	excludedInteractions_.removePair(b, d);
620	>	}
621
622	<	}
623	<	else{
624	<	// calc the scaled coordinates.
625	<
626	<	for(i=0; i<3; i++)
627	<	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];
329	<	}
330	<
331	<	}
622	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
623	>	oneFourInteractions_.removePair(a, d);
624	>	} else {
625	>	excludedInteractions_.removePair(a, d);
626	>	}
627	>	}
628
629	+	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
630	+	inversion = mol->nextInversion(inversionIter)) {
631
632	<	int SimInfo::getNDF(){
633	<	int ndf_local;
632	>	a = inversion->getAtomA()->getGlobalIndex();
633	>	b = inversion->getAtomB()->getGlobalIndex();
634	>	c = inversion->getAtomC()->getGlobalIndex();
635	>	d = inversion->getAtomD()->getGlobalIndex();
636
637	<	ndf_local = 0;
638	<
639	<	for(int i = 0; i < integrableObjects.size(); i++){
640	<	ndf_local += 3;
641	<	if (integrableObjects[i]->isDirectional()) {
642	<	if (integrableObjects[i]->isLinear())
643	<	ndf_local += 2;
644	<	else
645	<	ndf_local += 3;
637	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
638	>	oneTwoInteractions_.removePair(a, b);
639	>	oneTwoInteractions_.removePair(a, c);
640	>	oneTwoInteractions_.removePair(a, d);
641	>	} else {
642	>	excludedInteractions_.removePair(a, b);
643	>	excludedInteractions_.removePair(a, c);
644	>	excludedInteractions_.removePair(a, d);
645	>	}
646	>
647	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
648	>	oneThreeInteractions_.removePair(b, c);
649	>	oneThreeInteractions_.removePair(b, d);
650	>	oneThreeInteractions_.removePair(c, d);
651	>	} else {
652	>	excludedInteractions_.removePair(b, c);
653	>	excludedInteractions_.removePair(b, d);
654	>	excludedInteractions_.removePair(c, d);
655	>	}
656		}
347	–	}
657
658	<	// n_constraints is local, so subtract them on each processor:
658	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
659	>	rb = mol->nextRigidBody(rbIter)) {
660	>	vector<Atom*> atoms = rb->getAtoms();
661	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
662	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
663	>	a = atoms[i]->getGlobalIndex();
664	>	b = atoms[j]->getGlobalIndex();
665	>	excludedInteractions_.removePair(a, b);
666	>	}
667	>	}
668	>	}
669	>
670	>	}
671	>
672	>
673	>	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
674	>	int curStampId;
675	>
676	>	//index from 0
677	>	curStampId = moleculeStamps_.size();
678
679	<	ndf_local -= n_constraints;
679	>	moleculeStamps_.push_back(molStamp);
680	>	molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
681	>	}
682
683	+
684	+	/**
685	+	* update
686	+	*
687	+	*  Performs the global checks and variable settings after the
688	+	*  objects have been created.
689	+	*
690	+	*/
691	+	void SimInfo::update() {
692	+	setupSimVariables();
693	+	calcNdf();
694	+	calcNdfRaw();
695	+	calcNdfTrans();
696	+	}
697	+
698	+	/**
699	+	* getSimulatedAtomTypes
700	+	*
701	+	* Returns an STL set of AtomType* that are actually present in this
702	+	* simulation.  Must query all processors to assemble this information.
703	+	*
704	+	*/
705	+	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
706	+	SimInfo::MoleculeIterator mi;
707	+	Molecule* mol;
708	+	Molecule::AtomIterator ai;
709	+	Atom* atom;
710	+	set<AtomType*> atomTypes;
711	+
712	+	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
713	+	for(atom = mol->beginAtom(ai); atom != NULL;
714	+	atom = mol->nextAtom(ai)) {
715	+	atomTypes.insert(atom->getAtomType());
716	+	}
717	+	}
718	+
719		#ifdef IS_MPI
354	–	MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
355	–	#else
356	–	ndf = ndf_local;
357	–	#endif
720
721	<	// nZconstraints is global, as are the 3 COM translations for the
722	<	// entire system:
721	>	// loop over the found atom types on this processor, and add their
722	>	// numerical idents to a vector:
723	>
724	>	vector<int> foundTypes;
725	>	set<AtomType*>::iterator i;
726	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
727	>	foundTypes.push_back( (*i)->getIdent() );
728
729	<	ndf = ndf - 3 - nZconstraints;
729	>	// count_local holds the number of found types on this processor
730	>	int count_local = foundTypes.size();
731
732	<	return ndf;
365	<	}
732	>	int nproc = MPI::COMM_WORLD.Get_size();
733
734	<	int SimInfo::getNDFraw() {
735	<	int ndfRaw_local;
734	>	// we need arrays to hold the counts and displacement vectors for
735	>	// all processors
736	>	vector<int> counts(nproc, 0);
737	>	vector<int> disps(nproc, 0);
738
739	<	// Raw degrees of freedom that we have to set
740	<	ndfRaw_local = 0;
741	<
742	<	for(int i = 0; i < integrableObjects.size(); i++){
743	<	ndfRaw_local += 3;
744	<	if (integrableObjects[i]->isDirectional()) {
745	<	if (integrableObjects[i]->isLinear())
746	<	ndfRaw_local += 2;
747	<	else
748	<	ndfRaw_local += 3;
739	>	// fill the counts array
740	>	MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
741	>	1, MPI::INT);
742	>
743	>	// use the processor counts to compute the displacement array
744	>	disps[0] = 0;
745	>	int totalCount = counts[0];
746	>	for (int iproc = 1; iproc < nproc; iproc++) {
747	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
748	>	totalCount += counts[iproc];
749		}
750	+
751	+	// we need a (possibly redundant) set of all found types:
752	+	vector<int> ftGlobal(totalCount);
753	+
754	+	// now spray out the foundTypes to all the other processors:
755	+	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
756	+	&ftGlobal[0], &counts[0], &disps[0],
757	+	MPI::INT);
758	+
759	+	vector<int>::iterator j;
760	+
761	+	// foundIdents is a stl set, so inserting an already found ident
762	+	// will have no effect.
763	+	set<int> foundIdents;
764	+
765	+	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
766	+	foundIdents.insert((*j));
767	+
768	+	// now iterate over the foundIdents and get the actual atom types
769	+	// that correspond to these:
770	+	set<int>::iterator it;
771	+	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
772	+	atomTypes.insert( forceField_->getAtomType((*it)) );
773	+
774	+	#endif
775	+
776	+	return atomTypes;
777		}
778	+
779	+	void SimInfo::setupSimVariables() {
780	+	useAtomicVirial_ = simParams_->getUseAtomicVirial();
781	+	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
782	+	calcBoxDipole_ = false;
783	+	if ( simParams_->haveAccumulateBoxDipole() )
784	+	if ( simParams_->getAccumulateBoxDipole() ) {
785	+	calcBoxDipole_ = true;
786	+	}
787
788	<	#ifdef IS_MPI
789	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
788	>	set<AtomType*>::iterator i;
789	>	set<AtomType*> atomTypes;
790	>	atomTypes = getSimulatedAtomTypes();
791	>	int usesElectrostatic = 0;
792	>	int usesMetallic = 0;
793	>	int usesDirectional = 0;
794	>	int usesFluctuatingCharges =  0;
795	>	//loop over all of the atom types
796	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
797	>	usesElectrostatic |= (*i)->isElectrostatic();
798	>	usesMetallic |= (*i)->isMetal();
799	>	usesDirectional |= (*i)->isDirectional();
800	>	usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
801	>	}
802	>
803	>	#ifdef IS_MPI
804	>	int temp;
805	>	temp = usesDirectional;
806	>	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
807	>
808	>	temp = usesMetallic;
809	>	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
810	>
811	>	temp = usesElectrostatic;
812	>	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
813	>
814	>	temp = usesFluctuatingCharges;
815	>	MPI_Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
816		#else
817	<	ndfRaw = ndfRaw_local;
817	>
818	>	usesDirectionalAtoms_ = usesDirectional;
819	>	usesMetallicAtoms_ = usesMetallic;
820	>	usesElectrostaticAtoms_ = usesElectrostatic;
821	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
822	>
823		#endif
824	+
825	+	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
826	+	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
827	+	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
828	+	}
829
389	–	return ndfRaw;
390	–	}
830
831	<	int SimInfo::getNDFtranslational() {
832	<	int ndfTrans_local;
831	>	vector<int> SimInfo::getGlobalAtomIndices() {
832	>	SimInfo::MoleculeIterator mi;
833	>	Molecule* mol;
834	>	Molecule::AtomIterator ai;
835	>	Atom* atom;
836
837	<	ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
837	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
838	>
839	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
840	>
841	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
842	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
843	>	}
844	>	}
845	>	return GlobalAtomIndices;
846	>	}
847
848
849	<	#ifdef IS_MPI
850	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
851	<	#else
852	<	ndfTrans = ndfTrans_local;
853	<	#endif
849	>	vector<int> SimInfo::getGlobalGroupIndices() {
850	>	SimInfo::MoleculeIterator mi;
851	>	Molecule* mol;
852	>	Molecule::CutoffGroupIterator ci;
853	>	CutoffGroup* cg;
854
855	<	ndfTrans = ndfTrans - 3 - nZconstraints;
855	>	vector<int> GlobalGroupIndices;
856	>
857	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
858	>
859	>	//local index of cutoff group is trivial, it only depends on the
860	>	//order of travesing
861	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
862	>	cg = mol->nextCutoffGroup(ci)) {
863	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
864	>	}
865	>	}
866	>	return GlobalGroupIndices;
867	>	}
868
406	–	return ndfTrans;
407	–	}
869
870	<	int SimInfo::getTotIntegrableObjects() {
871	<	int nObjs_local;
411	<	int nObjs;
870	>	void SimInfo::prepareTopology() {
871	>	int nExclude, nOneTwo, nOneThree, nOneFour;
872
873	<	nObjs_local =  integrableObjects.size();
873	>	//calculate mass ratio of cutoff group
874	>	SimInfo::MoleculeIterator mi;
875	>	Molecule* mol;
876	>	Molecule::CutoffGroupIterator ci;
877	>	CutoffGroup* cg;
878	>	Molecule::AtomIterator ai;
879	>	Atom* atom;
880	>	RealType totalMass;
881
882	+	/**
883	+	* The mass factor is the relative mass of an atom to the total
884	+	* mass of the cutoff group it belongs to.  By default, all atoms
885	+	* are their own cutoff groups, and therefore have mass factors of
886	+	* 1.  We need some special handling for massless atoms, which
887	+	* will be treated as carrying the entire mass of the cutoff
888	+	* group.
889	+	*/
890	+	massFactors_.clear();
891	+	massFactors_.resize(getNAtoms(), 1.0);
892	+
893	+	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
894	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
895	+	cg = mol->nextCutoffGroup(ci)) {
896
897	<	#ifdef IS_MPI
898	<	MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
899	<	#else
900	<	nObjs = nObjs_local;
901	<	#endif
897	>	totalMass = cg->getMass();
898	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
899	>	// Check for massless groups - set mfact to 1 if true
900	>	if (totalMass != 0)
901	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
902	>	else
903	>	massFactors_[atom->getLocalIndex()] = 1.0;
904	>	}
905	>	}
906	>	}
907
908	+	// Build the identArray_
909
910	<	return nObjs;
911	<	}
910	>	identArray_.clear();
911	>	identArray_.reserve(getNAtoms());
912	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
913	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
914	>	identArray_.push_back(atom->getIdent());
915	>	}
916	>	}
917	>
918	>	//scan topology
919
920	<	void SimInfo::refreshSim(){
920	>	nExclude = excludedInteractions_.getSize();
921	>	nOneTwo = oneTwoInteractions_.getSize();
922	>	nOneThree = oneThreeInteractions_.getSize();
923	>	nOneFour = oneFourInteractions_.getSize();
924
925	<	simtype fInfo;
926	<	int isError;
927	<	int n_global;
928	<	int* excl;
925	>	int* excludeList = excludedInteractions_.getPairList();
926	>	int* oneTwoList = oneTwoInteractions_.getPairList();
927	>	int* oneThreeList = oneThreeInteractions_.getPairList();
928	>	int* oneFourList = oneFourInteractions_.getPairList();
929
930	<	fInfo.dielect = 0.0;
930	>	topologyDone_ = true;
931	>	}
932
933	<	if( useDipoles ){
934	<	if( useReactionField )fInfo.dielect = dielectric;
933	>	void SimInfo::addProperty(GenericData* genData) {
934	>	properties_.addProperty(genData);
935		}
936
937	<	fInfo.SIM_uses_PBC = usePBC;
937	>	void SimInfo::removeProperty(const string& propName) {
938	>	properties_.removeProperty(propName);
939	>	}
940
941	<	if (useSticky || useDipoles || useGayBerne || useShapes) {
942	<	useDirectionalAtoms = 1;
443	<	fInfo.SIM_uses_DirectionalAtoms = useDirectionalAtoms;
941	>	void SimInfo::clearProperties() {
942	>	properties_.clearProperties();
943		}
944
945	<	fInfo.SIM_uses_LennardJones = useLennardJones;
945	>	vector<string> SimInfo::getPropertyNames() {
946	>	return properties_.getPropertyNames();
947	>	}
948	>
949	>	vector<GenericData*> SimInfo::getProperties() {
950	>	return properties_.getProperties();
951	>	}
952
953	<	if (useCharges || useDipoles) {
954	<	useElectrostatics = 1;
450	<	fInfo.SIM_uses_Electrostatics = useElectrostatics;
953	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
954	>	return properties_.getPropertyByName(propName);
955		}
956
957	<	fInfo.SIM_uses_Charges = useCharges;
958	<	fInfo.SIM_uses_Dipoles = useDipoles;
959	<	fInfo.SIM_uses_Sticky = useSticky;
960	<	fInfo.SIM_uses_GayBerne = useGayBerne;
961	<	fInfo.SIM_uses_EAM = useEAM;
962	<	fInfo.SIM_uses_Shapes = useShapes;
459	<	fInfo.SIM_uses_FLARB = useFLARB;
460	<	fInfo.SIM_uses_RF = useReactionField;
957	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
958	>	if (sman_ == sman) {
959	>	return;
960	>	}
961	>	delete sman_;
962	>	sman_ = sman;
963
964	<	n_exclude = excludes->getSize();
965	<	excl = excludes->getFortranArray();
966	<
967	<	#ifdef IS_MPI
968	<	n_global = mpiSim->getNAtomsGlobal();
969	<	#else
970	<	n_global = n_atoms;
971	<	#endif
972	<
973	<	isError = 0;
974	<
975	<	getFortranGroupArrays(this, FglobalGroupMembership, mfact);
976	<	//it may not be a good idea to pass the address of first element in vector
977	<	//since c++ standard does not require vector to be stored continuously in meomory
978	<	//Most of the compilers will organize the memory of vector continuously
979	<	setFortranSim( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
980	<	&nGlobalExcludes, globalExcludes, molMembershipArray,
981	<	&mfact[0], &ngroup, &FglobalGroupMembership[0], &isError);
964	>	Molecule* mol;
965	>	RigidBody* rb;
966	>	Atom* atom;
967	>	CutoffGroup* cg;
968	>	SimInfo::MoleculeIterator mi;
969	>	Molecule::RigidBodyIterator rbIter;
970	>	Molecule::AtomIterator atomIter;
971	>	Molecule::CutoffGroupIterator cgIter;
972	>
973	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
974	>
975	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
976	>	atom->setSnapshotManager(sman_);
977	>	}
978	>
979	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
980	>	rb->setSnapshotManager(sman_);
981	>	}
982
983	<	if( isError ){
983	>	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
984	>	cg->setSnapshotManager(sman_);
985	>	}
986	>	}
987
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();
988		}
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	–	}
989
990	<	void SimInfo::setDefaultRcut( double theRcut ){
991	<
992	<	haveRcut = 1;
504	<	rCut = theRcut;
505	<	rList = rCut + 1.0;
506	<
507	<	notifyFortranCutoffs( &rCut, &rSw, &rList );
508	<	}
990	>	Vector3d SimInfo::getComVel(){
991	>	SimInfo::MoleculeIterator i;
992	>	Molecule* mol;
993
994	<	void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
994	>	Vector3d comVel(0.0);
995	>	RealType totalMass = 0.0;
996	>
997	>
998	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
999	>	RealType mass = mol->getMass();
1000	>	totalMass += mass;
1001	>	comVel += mass * mol->getComVel();
1002	>	}
1003
1004	<	rSw = theRsw;
1005	<	setDefaultRcut( theRcut );
1006	<	}
1004	>	#ifdef IS_MPI
1005	>	RealType tmpMass = totalMass;
1006	>	Vector3d tmpComVel(comVel);
1007	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1008	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1009	>	#endif
1010
1011	+	comVel /= totalMass;
1012
1013	<	void SimInfo::checkCutOffs( void ){
518	<
519	<	if( boxIsInit ){
520	<
521	<	//we need to check cutOffs against the box
522	<
523	<	if( rCut > maxCutoff ){
524	<	sprintf( painCave.errMsg,
525	<	"cutoffRadius is too large for the current periodic box.\n"
526	<	"\tCurrent Value of cutoffRadius = %G at time %G\n "
527	<	"\tThis is larger than half of at least one of the\n"
528	<	"\tperiodic box vectors.  Right now, the Box matrix is:\n"
529	<	"\n"
530	<	"\t[ %G %G %G ]\n"
531	<	"\t[ %G %G %G ]\n"
532	<	"\t[ %G %G %G ]\n",
533	<	rCut, currentTime,
534	<	Hmat[0][0], Hmat[0][1], Hmat[0][2],
535	<	Hmat[1][0], Hmat[1][1], Hmat[1][2],
536	<	Hmat[2][0], Hmat[2][1], Hmat[2][2]);
537	<	painCave.severity = OOPSE_ERROR;
538	<	painCave.isFatal = 1;
539	<	simError();
540	<	}
541	<	} 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();
1013	>	return comVel;
1014		}
550	–
551	–	}
1015
1016	<	void SimInfo::addProperty(GenericData* prop){
1016	>	Vector3d SimInfo::getCom(){
1017	>	SimInfo::MoleculeIterator i;
1018	>	Molecule* mol;
1019
1020	<	map<string, GenericData*>::iterator result;
1021	<	result = properties.find(prop->getID());
1022	<
1023	<	//we can't simply use  properties[prop->getID()] = prop,
1024	<	//it will cause memory leak if we already contain a propery which has the same name of prop
1025	<
1026	<	if(result != properties.end()){
1027	<
563	<	delete (*result).second;
564	<	(*result).second = prop;
565	<
566	<	}
567	<	else{
1020	>	Vector3d com(0.0);
1021	>	RealType totalMass = 0.0;
1022	>
1023	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1024	>	RealType mass = mol->getMass();
1025	>	totalMass += mass;
1026	>	com += mass * mol->getCom();
1027	>	}
1028
1029	<	properties[prop->getID()] = prop;
1029	>	#ifdef IS_MPI
1030	>	RealType tmpMass = totalMass;
1031	>	Vector3d tmpCom(com);
1032	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1033	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1034	>	#endif
1035
1036	+	com /= totalMass;
1037	+
1038	+	return com;
1039	+
1040	+	}
1041	+
1042	+	ostream& operator <<(ostream& o, SimInfo& info) {
1043	+
1044	+	return o;
1045		}
1046	+
1047	+
1048	+	/*
1049	+	Returns center of mass and center of mass velocity in one function call.
1050	+	*/
1051	+
1052	+	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1053	+	SimInfo::MoleculeIterator i;
1054	+	Molecule* mol;
1055	+
1056
1057	<	}
1057	>	RealType totalMass = 0.0;
1058	>
1059
1060	<	GenericData* SimInfo::getProperty(const string& propName){
1061	<
1062	<	map<string, GenericData*>::iterator result;
1063	<
1064	<	//string lowerCaseName = ();
1065	<
1066	<	result = properties.find(propName);
1067	<
1068	<	if(result != properties.end())
1069	<	return (*result).second;
1070	<	else
1071	<	return NULL;
1072	<	}
1060	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1061	>	RealType mass = mol->getMass();
1062	>	totalMass += mass;
1063	>	com += mass * mol->getCom();
1064	>	comVel += mass * mol->getComVel();
1065	>	}
1066	>
1067	>	#ifdef IS_MPI
1068	>	RealType tmpMass = totalMass;
1069	>	Vector3d tmpCom(com);
1070	>	Vector3d tmpComVel(comVel);
1071	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1072	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1073	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1074	>	#endif
1075	>
1076	>	com /= totalMass;
1077	>	comVel /= totalMass;
1078	>	}
1079	>
1080	>	/*
1081	>	Return intertia tensor for entire system and angular momentum Vector.
1082
1083
1084	<	void SimInfo::getFortranGroupArrays(SimInfo* info,
1085	<	vector<int>& FglobalGroupMembership,
1086	<	vector<double>& mfact){
1087	<
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	<
1084	>	[  Ixx -Ixy  -Ixz ]
1085	>	J =| -Iyx  Iyy  -Iyz |
1086	>	[ -Izx -Iyz   Izz ]
1087	>	*/
1088
1089	<	// Fix the silly fortran indexing problem
1089	>	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1090	>
1091	>
1092	>	RealType xx = 0.0;
1093	>	RealType yy = 0.0;
1094	>	RealType zz = 0.0;
1095	>	RealType xy = 0.0;
1096	>	RealType xz = 0.0;
1097	>	RealType yz = 0.0;
1098	>	Vector3d com(0.0);
1099	>	Vector3d comVel(0.0);
1100	>
1101	>	getComAll(com, comVel);
1102	>
1103	>	SimInfo::MoleculeIterator i;
1104	>	Molecule* mol;
1105	>
1106	>	Vector3d thisq(0.0);
1107	>	Vector3d thisv(0.0);
1108	>
1109	>	RealType thisMass = 0.0;
1110	>
1111	>
1112	>
1113	>
1114	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1115	>
1116	>	thisq = mol->getCom()-com;
1117	>	thisv = mol->getComVel()-comVel;
1118	>	thisMass = mol->getMass();
1119	>	// Compute moment of intertia coefficients.
1120	>	xx += thisq[0]*thisq[0]*thisMass;
1121	>	yy += thisq[1]*thisq[1]*thisMass;
1122	>	zz += thisq[2]*thisq[2]*thisMass;
1123	>
1124	>	// compute products of intertia
1125	>	xy += thisq[0]*thisq[1]*thisMass;
1126	>	xz += thisq[0]*thisq[2]*thisMass;
1127	>	yz += thisq[1]*thisq[2]*thisMass;
1128	>
1129	>	angularMomentum += cross( thisq, thisv ) * thisMass;
1130	>
1131	>	}
1132	>
1133	>
1134	>	inertiaTensor(0,0) = yy + zz;
1135	>	inertiaTensor(0,1) = -xy;
1136	>	inertiaTensor(0,2) = -xz;
1137	>	inertiaTensor(1,0) = -xy;
1138	>	inertiaTensor(1,1) = xx + zz;
1139	>	inertiaTensor(1,2) = -yz;
1140	>	inertiaTensor(2,0) = -xz;
1141	>	inertiaTensor(2,1) = -yz;
1142	>	inertiaTensor(2,2) = xx + yy;
1143	>
1144		#ifdef IS_MPI
1145	<	numAtom = mpiSim->getNAtomsGlobal();
1146	<	#else
1147	<	numAtom = n_atoms;
1145	>	Mat3x3d tmpI(inertiaTensor);
1146	>	Vector3d tmpAngMom;
1147	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1148	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1149		#endif
1150	<	for (int i = 0; i < numAtom; i++)
1151	<	FglobalGroupMembership.push_back(globalGroupMembership[i] + 1);
1152	<
1150	>
1151	>	return;
1152	>	}
1153
1154	<	myMols = info->molecules;
1155	<	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();
1154	>	//Returns the angular momentum of the system
1155	>	Vector3d SimInfo::getAngularMomentum(){
1156
1157	<	for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom);
1158	<	cutoffAtom != NULL;
1159	<	cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
1160	<	mfact.push_back(cutoffAtom->getMass()/totalMass);
1157	>	Vector3d com(0.0);
1158	>	Vector3d comVel(0.0);
1159	>	Vector3d angularMomentum(0.0);
1160	>
1161	>	getComAll(com,comVel);
1162	>
1163	>	SimInfo::MoleculeIterator i;
1164	>	Molecule* mol;
1165	>
1166	>	Vector3d thisr(0.0);
1167	>	Vector3d thisp(0.0);
1168	>
1169	>	RealType thisMass;
1170	>
1171	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1172	>	thisMass = mol->getMass();
1173	>	thisr = mol->getCom()-com;
1174	>	thisp = (mol->getComVel()-comVel)*thisMass;
1175	>
1176	>	angularMomentum += cross( thisr, thisp );
1177	>
1178		}
1179	+
1180	+	#ifdef IS_MPI
1181	+	Vector3d tmpAngMom;
1182	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1183	+	#endif
1184	+
1185	+	return angularMomentum;
1186	+	}
1187	+
1188	+	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1189	+	return IOIndexToIntegrableObject.at(index);
1190	+	}
1191	+
1192	+	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1193	+	IOIndexToIntegrableObject= v;
1194	+	}
1195	+
1196	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1197	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1198	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1199	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1200	+	*/
1201	+	void SimInfo::getGyrationalVolume(RealType &volume){
1202	+	Mat3x3d intTensor;
1203	+	RealType det;
1204	+	Vector3d dummyAngMom;
1205	+	RealType sysconstants;
1206	+	RealType geomCnst;
1207	+
1208	+	geomCnst = 3.0/2.0;
1209	+	/* Get the inertial tensor and angular momentum for free*/
1210	+	getInertiaTensor(intTensor,dummyAngMom);
1211	+
1212	+	det = intTensor.determinant();
1213	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1214	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(det);
1215	+	return;
1216	+	}
1217	+
1218	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1219	+	Mat3x3d intTensor;
1220	+	Vector3d dummyAngMom;
1221	+	RealType sysconstants;
1222	+	RealType geomCnst;
1223	+
1224	+	geomCnst = 3.0/2.0;
1225	+	/* Get the inertial tensor and angular momentum for free*/
1226	+	getInertiaTensor(intTensor,dummyAngMom);
1227	+
1228	+	detI = intTensor.determinant();
1229	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1230	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(detI);
1231	+	return;
1232	+	}
1233	+	/*
1234	+	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1235	+	assert( v.size() == nAtoms_ + nRigidBodies_);
1236	+	sdByGlobalIndex_ = v;
1237		}
1238	+
1239	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1240	+	//assert(index < nAtoms_ + nRigidBodies_);
1241	+	return sdByGlobalIndex_.at(index);
1242	+	}
1243	+	*/
1244	+	int SimInfo::getNGlobalConstraints() {
1245	+	int nGlobalConstraints;
1246	+	#ifdef IS_MPI
1247	+	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1248	+	MPI_COMM_WORLD);
1249	+	#else
1250	+	nGlobalConstraints =  nConstraints_;
1251	+	#endif
1252	+	return nGlobalConstraints;
1253		}
1254
1255	<	}
1255	>	}//end namespace OpenMD
1256	>

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 1725 by gezelter, Sat May 26 18:13:43 2012 UTC

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