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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 1668 by gezelter, Fri Jan 6 19:03:05 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 "UseTheForce/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),
76	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
77	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
78	>	nConstraints_(0), sman_(NULL), topologyDone_(false),
79	>	calcBoxDipole_(false), useAtomicVirial_(true) {
80	>
81	>	MoleculeStamp* molStamp;
82	>	int nMolWithSameStamp;
83	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
84	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
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;
70	<
71	<	useSolidThermInt = 0;
72	<	useLiquidThermInt = 0;
73	<
74	<	haveCutoffGroups = false;
75	<
76	<	excludes = Exclude::Instance();
77	<
78	<	myConfiguration = new SimState();
79	<
80	<	has_minimizer = false;
81	<	the_minimizer =NULL;
82	<
83	<	ngroup = 0;
84	<
85	<	}
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	+	removeInteractionPairs(mol);
205	+	molecules_.erase(mol->getGlobalIndex());
206
207	<	SimInfo::~SimInfo(){
207	>	delete mol;
208	>
209	>	return true;
210	>	} else {
211	>	return false;
212	>	}
213	>	}
214
215	<	delete myConfiguration;
215	>
216	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
217	>	i = molecules_.begin();
218	>	return i == molecules_.end() ? NULL : i->second;
219	>	}
220
221	<	map<string, GenericData*>::iterator i;
222	<
223	<	for(i = properties.begin(); i != properties.end(); i++)
224	<	delete (*i).second;
221	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
222	>	++i;
223	>	return i == molecules_.end() ? NULL : i->second;
224	>	}
225
97	–	}
226
227	<	void SimInfo::setBox(double newBox[3]) {
228	<
229	<	int i, j;
230	<	double tempMat[3][3];
227	>	void SimInfo::calcNdf() {
228	>	int ndf_local;
229	>	MoleculeIterator i;
230	>	vector<StuntDouble*>::iterator j;
231	>	Molecule* mol;
232	>	StuntDouble* integrableObject;
233
234	<	for(i=0; i<3; i++)
235	<	for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
234	>	ndf_local = 0;
235	>
236	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
237	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
238	>	integrableObject = mol->nextIntegrableObject(j)) {
239
240	<	tempMat[0][0] = newBox[0];
108	<	tempMat[1][1] = newBox[1];
109	<	tempMat[2][2] = newBox[2];
240	>	ndf_local += 3;
241
242	<	setBoxM( tempMat );
242	>	if (integrableObject->isDirectional()) {
243	>	if (integrableObject->isLinear()) {
244	>	ndf_local += 2;
245	>	} else {
246	>	ndf_local += 3;
247	>	}
248	>	}
249	>
250	>	}
251	>	}
252	>
253	>	// n_constraints is local, so subtract them on each processor
254	>	ndf_local -= nConstraints_;
255
256	<	}
256	>	#ifdef IS_MPI
257	>	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
258	>	#else
259	>	ndf_ = ndf_local;
260	>	#endif
261
262	<	void SimInfo::setBoxM( double theBox[3][3] ){
263	<
264	<	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);
262	>	// nZconstraints_ is global, as are the 3 COM translations for the
263	>	// entire system:
264	>	ndf_ = ndf_ - 3 - nZconstraint_;
265
266	<	if( !boxIsInit ) boxIsInit = 1;
266	>	}
267
268	<	for(i=0; i < 3; i++)
269	<	for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
268	>	int SimInfo::getFdf() {
269	>	#ifdef IS_MPI
270	>	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
271	>	#else
272	>	fdf_ = fdf_local;
273	>	#endif
274	>	return fdf_;
275	>	}
276
277	<	calcBoxL();
278	<	calcHmatInv();
279	<
280	<	for(i=0; i < 3; i++) {
281	<	for (j=0; j < 3; j++) {
282	<	FortranHmat[3*j + i] = Hmat[i][j];
283	<	FortranHmatInv[3*j + i] = HmatInv[i][j];
277	>	unsigned int SimInfo::getNLocalCutoffGroups(){
278	>	int nLocalCutoffAtoms = 0;
279	>	Molecule* mol;
280	>	MoleculeIterator mi;
281	>	CutoffGroup* cg;
282	>	Molecule::CutoffGroupIterator ci;
283	>
284	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
285	>
286	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
287	>	cg = mol->nextCutoffGroup(ci)) {
288	>	nLocalCutoffAtoms += cg->getNumAtom();
289	>
290	>	}
291		}
292	+
293	+	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
294		}
295	+
296	+	void SimInfo::calcNdfRaw() {
297	+	int ndfRaw_local;
298
299	<	setFortranBox(FortranHmat, FortranHmatInv, &orthoRhombic);
300	<
301	<	}
302	<
299	>	MoleculeIterator i;
300	>	vector<StuntDouble*>::iterator j;
301	>	Molecule* mol;
302	>	StuntDouble* integrableObject;
303
304	<	void SimInfo::getBoxM (double theBox[3][3]) {
304	>	// Raw degrees of freedom that we have to set
305	>	ndfRaw_local = 0;
306	>
307	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
308	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
309	>	integrableObject = mol->nextIntegrableObject(j)) {
310
311	<	int i, j;
148	<	for(i=0; i<3; i++)
149	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
150	<	}
311	>	ndfRaw_local += 3;
312
313	+	if (integrableObject->isDirectional()) {
314	+	if (integrableObject->isLinear()) {
315	+	ndfRaw_local += 2;
316	+	} else {
317	+	ndfRaw_local += 3;
318	+	}
319	+	}
320	+
321	+	}
322	+	}
323	+
324	+	#ifdef IS_MPI
325	+	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
326	+	#else
327	+	ndfRaw_ = ndfRaw_local;
328	+	#endif
329	+	}
330
331	<	void SimInfo::scaleBox(double scale) {
332	<	double theBox[3][3];
155	<	int i, j;
331	>	void SimInfo::calcNdfTrans() {
332	>	int ndfTrans_local;
333
334	<	// cerr << "Scaling box by " << scale << "\n";
334	>	ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
335
159	–	for(i=0; i<3; i++)
160	–	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
336
337	<	setBoxM(theBox);
337	>	#ifdef IS_MPI
338	>	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
339	>	#else
340	>	ndfTrans_ = ndfTrans_local;
341	>	#endif
342
343	<	}
343	>	ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
344	>
345	>	}
346
347	<	void SimInfo::calcHmatInv( void ) {
348	<
349	<	int oldOrtho;
350	<	int i,j;
351	<	double smallDiag;
352	<	double tol;
353	<	double sanity[3][3];
354	<
355	<	invertMat3( Hmat, HmatInv );
356	<
357	<	// check to see if Hmat is orthorhombic
358	<
359	<	oldOrtho = orthoRhombic;
360	<
361	<	smallDiag = fabs(Hmat[0][0]);
362	<	if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
363	<	if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
364	<	tol = smallDiag * orthoTolerance;
365	<
366	<	orthoRhombic = 1;
367	<
368	<	for (i = 0; i < 3; i++ ) {
369	<	for (j = 0 ; j < 3; j++) {
370	<	if (i != j) {
371	<	if (orthoRhombic) {
372	<	if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
373	<	}
347	>	void SimInfo::addInteractionPairs(Molecule* mol) {
348	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
349	>	vector<Bond*>::iterator bondIter;
350	>	vector<Bend*>::iterator bendIter;
351	>	vector<Torsion*>::iterator torsionIter;
352	>	vector<Inversion*>::iterator inversionIter;
353	>	Bond* bond;
354	>	Bend* bend;
355	>	Torsion* torsion;
356	>	Inversion* inversion;
357	>	int a;
358	>	int b;
359	>	int c;
360	>	int d;
361	>
362	>	// atomGroups can be used to add special interaction maps between
363	>	// groups of atoms that are in two separate rigid bodies.
364	>	// However, most site-site interactions between two rigid bodies
365	>	// are probably not special, just the ones between the physically
366	>	// bonded atoms.  Interactions *within* a single rigid body should
367	>	// always be excluded.  These are done at the bottom of this
368	>	// function.
369	>
370	>	map<int, set<int> > atomGroups;
371	>	Molecule::RigidBodyIterator rbIter;
372	>	RigidBody* rb;
373	>	Molecule::IntegrableObjectIterator ii;
374	>	StuntDouble* integrableObject;
375	>
376	>	for (integrableObject = mol->beginIntegrableObject(ii);
377	>	integrableObject != NULL;
378	>	integrableObject = mol->nextIntegrableObject(ii)) {
379	>
380	>	if (integrableObject->isRigidBody()) {
381	>	rb = static_cast<RigidBody*>(integrableObject);
382	>	vector<Atom*> atoms = rb->getAtoms();
383	>	set<int> rigidAtoms;
384	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
385	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
386	>	}
387	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
388	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
389	>	}
390	>	} else {
391	>	set<int> oneAtomSet;
392	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
393	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
394		}
395	<	}
396	<	}
395	>	}
396	>
397	>	for (bond= mol->beginBond(bondIter); bond != NULL;
398	>	bond = mol->nextBond(bondIter)) {
399
400	<	if( oldOrtho != orthoRhombic ){
400	>	a = bond->getAtomA()->getGlobalIndex();
401	>	b = bond->getAtomB()->getGlobalIndex();
402
403	<	if( orthoRhombic ) {
404	<	sprintf( painCave.errMsg,
405	<	"OOPSE is switching from the default Non-Orthorhombic\n"
406	<	"\tto the faster Orthorhombic periodic boundary computations.\n"
407	<	"\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();
403	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
404	>	oneTwoInteractions_.addPair(a, b);
405	>	} else {
406	>	excludedInteractions_.addPair(a, b);
407	>	}
408		}
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	–	}
409
410	<	void SimInfo::calcBoxL( void ){
410	>	for (bend= mol->beginBend(bendIter); bend != NULL;
411	>	bend = mol->nextBend(bendIter)) {
412
413	<	double dx, dy, dz, dsq;
413	>	a = bend->getAtomA()->getGlobalIndex();
414	>	b = bend->getAtomB()->getGlobalIndex();
415	>	c = bend->getAtomC()->getGlobalIndex();
416	>
417	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
418	>	oneTwoInteractions_.addPair(a, b);
419	>	oneTwoInteractions_.addPair(b, c);
420	>	} else {
421	>	excludedInteractions_.addPair(a, b);
422	>	excludedInteractions_.addPair(b, c);
423	>	}
424
425	<	// boxVol = Determinant of Hmat
425	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
426	>	oneThreeInteractions_.addPair(a, c);
427	>	} else {
428	>	excludedInteractions_.addPair(a, c);
429	>	}
430	>	}
431
432	<	boxVol = matDet3( Hmat );
432	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
433	>	torsion = mol->nextTorsion(torsionIter)) {
434
435	<	// boxLx
436	<
437	<	dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
438	<	dsq = dx*dx + dy*dy + dz*dz;
237	<	boxL[0] = sqrt( dsq );
238	<	//maxCutoff = 0.5 * boxL[0];
435	>	a = torsion->getAtomA()->getGlobalIndex();
436	>	b = torsion->getAtomB()->getGlobalIndex();
437	>	c = torsion->getAtomC()->getGlobalIndex();
438	>	d = torsion->getAtomD()->getGlobalIndex();
439
440	<	// boxLy
441	<
442	<	dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
443	<	dsq = dx*dx + dy*dy + dz*dz;
444	<	boxL[1] = sqrt( dsq );
445	<	//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
440	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
441	>	oneTwoInteractions_.addPair(a, b);
442	>	oneTwoInteractions_.addPair(b, c);
443	>	oneTwoInteractions_.addPair(c, d);
444	>	} else {
445	>	excludedInteractions_.addPair(a, b);
446	>	excludedInteractions_.addPair(b, c);
447	>	excludedInteractions_.addPair(c, d);
448	>	}
449
450	+	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
451	+	oneThreeInteractions_.addPair(a, c);
452	+	oneThreeInteractions_.addPair(b, d);
453	+	} else {
454	+	excludedInteractions_.addPair(a, c);
455	+	excludedInteractions_.addPair(b, d);
456	+	}
457
458	<	// boxLz
459	<
460	<	dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
461	<	dsq = dx*dx + dy*dy + dz*dz;
462	<	boxL[2] = sqrt( dsq );
463	<	//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
458	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
459	>	oneFourInteractions_.addPair(a, d);
460	>	} else {
461	>	excludedInteractions_.addPair(a, d);
462	>	}
463	>	}
464
465	<	//calculate the max cutoff
466	<	maxCutoff =  calcMaxCutOff();
257	<
258	<	checkCutOffs();
465	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
466	>	inversion = mol->nextInversion(inversionIter)) {
467
468	<	}
468	>	a = inversion->getAtomA()->getGlobalIndex();
469	>	b = inversion->getAtomB()->getGlobalIndex();
470	>	c = inversion->getAtomC()->getGlobalIndex();
471	>	d = inversion->getAtomD()->getGlobalIndex();
472
473	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
474	+	oneTwoInteractions_.addPair(a, b);
475	+	oneTwoInteractions_.addPair(a, c);
476	+	oneTwoInteractions_.addPair(a, d);
477	+	} else {
478	+	excludedInteractions_.addPair(a, b);
479	+	excludedInteractions_.addPair(a, c);
480	+	excludedInteractions_.addPair(a, d);
481	+	}
482
483	<	double SimInfo::calcMaxCutOff(){
483	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
484	>	oneThreeInteractions_.addPair(b, c);
485	>	oneThreeInteractions_.addPair(b, d);
486	>	oneThreeInteractions_.addPair(c, d);
487	>	} else {
488	>	excludedInteractions_.addPair(b, c);
489	>	excludedInteractions_.addPair(b, d);
490	>	excludedInteractions_.addPair(c, d);
491	>	}
492	>	}
493
494	<	double ri[3], rj[3], rk[3];
495	<	double rij[3], rjk[3], rki[3];
496	<	double minDist;
494	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
495	>	rb = mol->nextRigidBody(rbIter)) {
496	>	vector<Atom*> atoms = rb->getAtoms();
497	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
498	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
499	>	a = atoms[i]->getGlobalIndex();
500	>	b = atoms[j]->getGlobalIndex();
501	>	excludedInteractions_.addPair(a, b);
502	>	}
503	>	}
504	>	}
505
506	<	ri[0] = Hmat[0][0];
270	<	ri[1] = Hmat[1][0];
271	<	ri[2] = Hmat[2][0];
506	>	}
507
508	<	rj[0] = Hmat[0][1];
509	<	rj[1] = Hmat[1][1];
510	<	rj[2] = Hmat[2][1];
508	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
509	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
510	>	vector<Bond*>::iterator bondIter;
511	>	vector<Bend*>::iterator bendIter;
512	>	vector<Torsion*>::iterator torsionIter;
513	>	vector<Inversion*>::iterator inversionIter;
514	>	Bond* bond;
515	>	Bend* bend;
516	>	Torsion* torsion;
517	>	Inversion* inversion;
518	>	int a;
519	>	int b;
520	>	int c;
521	>	int d;
522
523	<	rk[0] = Hmat[0][2];
524	<	rk[1] = Hmat[1][2];
525	<	rk[2] = Hmat[2][2];
523	>	map<int, set<int> > atomGroups;
524	>	Molecule::RigidBodyIterator rbIter;
525	>	RigidBody* rb;
526	>	Molecule::IntegrableObjectIterator ii;
527	>	StuntDouble* integrableObject;
528
529	<	crossProduct3(ri, rj, rij);
530	<	distXY = dotProduct3(rk,rij) / norm3(rij);
529	>	for (integrableObject = mol->beginIntegrableObject(ii);
530	>	integrableObject != NULL;
531	>	integrableObject = mol->nextIntegrableObject(ii)) {
532	>
533	>	if (integrableObject->isRigidBody()) {
534	>	rb = static_cast<RigidBody*>(integrableObject);
535	>	vector<Atom*> atoms = rb->getAtoms();
536	>	set<int> rigidAtoms;
537	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
538	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
539	>	}
540	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
541	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
542	>	}
543	>	} else {
544	>	set<int> oneAtomSet;
545	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
546	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
547	>	}
548	>	}
549
550	<	crossProduct3(rj,rk, rjk);
551	<	distYZ = dotProduct3(ri,rjk) / norm3(rjk);
550	>	for (bond= mol->beginBond(bondIter); bond != NULL;
551	>	bond = mol->nextBond(bondIter)) {
552	>
553	>	a = bond->getAtomA()->getGlobalIndex();
554	>	b = bond->getAtomB()->getGlobalIndex();
555	>
556	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
557	>	oneTwoInteractions_.removePair(a, b);
558	>	} else {
559	>	excludedInteractions_.removePair(a, b);
560	>	}
561	>	}
562
563	<	crossProduct3(rk,ri, rki);
564	<	distZX = dotProduct3(rj,rki) / norm3(rki);
563	>	for (bend= mol->beginBend(bendIter); bend != NULL;
564	>	bend = mol->nextBend(bendIter)) {
565
566	<	minDist = min(min(distXY, distYZ), distZX);
567	<	return minDist/2;
568	<
569	<	}
566	>	a = bend->getAtomA()->getGlobalIndex();
567	>	b = bend->getAtomB()->getGlobalIndex();
568	>	c = bend->getAtomC()->getGlobalIndex();
569	>
570	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
571	>	oneTwoInteractions_.removePair(a, b);
572	>	oneTwoInteractions_.removePair(b, c);
573	>	} else {
574	>	excludedInteractions_.removePair(a, b);
575	>	excludedInteractions_.removePair(b, c);
576	>	}
577
578	<	void SimInfo::wrapVector( double thePos[3] ){
578	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
579	>	oneThreeInteractions_.removePair(a, c);
580	>	} else {
581	>	excludedInteractions_.removePair(a, c);
582	>	}
583	>	}
584
585	<	int i;
586	<	double scaled[3];
585	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
586	>	torsion = mol->nextTorsion(torsionIter)) {
587
588	<	if( !orthoRhombic ){
589	<	// calc the scaled coordinates.
588	>	a = torsion->getAtomA()->getGlobalIndex();
589	>	b = torsion->getAtomB()->getGlobalIndex();
590	>	c = torsion->getAtomC()->getGlobalIndex();
591	>	d = torsion->getAtomD()->getGlobalIndex();
592
593	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
594	+	oneTwoInteractions_.removePair(a, b);
595	+	oneTwoInteractions_.removePair(b, c);
596	+	oneTwoInteractions_.removePair(c, d);
597	+	} else {
598	+	excludedInteractions_.removePair(a, b);
599	+	excludedInteractions_.removePair(b, c);
600	+	excludedInteractions_.removePair(c, d);
601	+	}
602
603	<	matVecMul3(HmatInv, thePos, scaled);
604	<
605	<	for(i=0; i<3; i++)
606	<	scaled[i] -= roundMe(scaled[i]);
607	<
608	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
609	<
311	<	matVecMul3(Hmat, scaled, thePos);
603	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
604	>	oneThreeInteractions_.removePair(a, c);
605	>	oneThreeInteractions_.removePair(b, d);
606	>	} else {
607	>	excludedInteractions_.removePair(a, c);
608	>	excludedInteractions_.removePair(b, d);
609	>	}
610
611	<	}
612	<	else{
613	<	// calc the scaled coordinates.
614	<
615	<	for(i=0; i<3; i++)
616	<	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	<	}
611	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
612	>	oneFourInteractions_.removePair(a, d);
613	>	} else {
614	>	excludedInteractions_.removePair(a, d);
615	>	}
616	>	}
617
618	+	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
619	+	inversion = mol->nextInversion(inversionIter)) {
620
621	<	int SimInfo::getNDF(){
622	<	int ndf_local;
621	>	a = inversion->getAtomA()->getGlobalIndex();
622	>	b = inversion->getAtomB()->getGlobalIndex();
623	>	c = inversion->getAtomC()->getGlobalIndex();
624	>	d = inversion->getAtomD()->getGlobalIndex();
625
626	<	ndf_local = 0;
627	<
628	<	for(int i = 0; i < integrableObjects.size(); i++){
629	<	ndf_local += 3;
630	<	if (integrableObjects[i]->isDirectional()) {
631	<	if (integrableObjects[i]->isLinear())
632	<	ndf_local += 2;
633	<	else
634	<	ndf_local += 3;
626	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
627	>	oneTwoInteractions_.removePair(a, b);
628	>	oneTwoInteractions_.removePair(a, c);
629	>	oneTwoInteractions_.removePair(a, d);
630	>	} else {
631	>	excludedInteractions_.removePair(a, b);
632	>	excludedInteractions_.removePair(a, c);
633	>	excludedInteractions_.removePair(a, d);
634	>	}
635	>
636	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
637	>	oneThreeInteractions_.removePair(b, c);
638	>	oneThreeInteractions_.removePair(b, d);
639	>	oneThreeInteractions_.removePair(c, d);
640	>	} else {
641	>	excludedInteractions_.removePair(b, c);
642	>	excludedInteractions_.removePair(b, d);
643	>	excludedInteractions_.removePair(c, d);
644	>	}
645		}
347	–	}
646
647	<	// n_constraints is local, so subtract them on each processor:
647	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
648	>	rb = mol->nextRigidBody(rbIter)) {
649	>	vector<Atom*> atoms = rb->getAtoms();
650	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
651	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
652	>	a = atoms[i]->getGlobalIndex();
653	>	b = atoms[j]->getGlobalIndex();
654	>	excludedInteractions_.removePair(a, b);
655	>	}
656	>	}
657	>	}
658	>
659	>	}
660	>
661	>
662	>	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
663	>	int curStampId;
664	>
665	>	//index from 0
666	>	curStampId = moleculeStamps_.size();
667
668	<	ndf_local -= n_constraints;
668	>	moleculeStamps_.push_back(molStamp);
669	>	molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
670	>	}
671
672	+
673	+	/**
674	+	* update
675	+	*
676	+	*  Performs the global checks and variable settings after the
677	+	*  objects have been created.
678	+	*
679	+	*/
680	+	void SimInfo::update() {
681	+	setupSimVariables();
682	+	calcNdf();
683	+	calcNdfRaw();
684	+	calcNdfTrans();
685	+	}
686	+
687	+	/**
688	+	* getSimulatedAtomTypes
689	+	*
690	+	* Returns an STL set of AtomType* that are actually present in this
691	+	* simulation.  Must query all processors to assemble this information.
692	+	*
693	+	*/
694	+	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
695	+	SimInfo::MoleculeIterator mi;
696	+	Molecule* mol;
697	+	Molecule::AtomIterator ai;
698	+	Atom* atom;
699	+	set<AtomType*> atomTypes;
700	+
701	+	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
702	+	for(atom = mol->beginAtom(ai); atom != NULL;
703	+	atom = mol->nextAtom(ai)) {
704	+	atomTypes.insert(atom->getAtomType());
705	+	}
706	+	}
707	+
708		#ifdef IS_MPI
354	–	MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
355	–	#else
356	–	ndf = ndf_local;
357	–	#endif
709
710	<	// nZconstraints is global, as are the 3 COM translations for the
711	<	// entire system:
710	>	// loop over the found atom types on this processor, and add their
711	>	// numerical idents to a vector:
712	>
713	>	vector<int> foundTypes;
714	>	set<AtomType*>::iterator i;
715	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
716	>	foundTypes.push_back( (*i)->getIdent() );
717
718	<	ndf = ndf - 3 - nZconstraints;
718	>	// count_local holds the number of found types on this processor
719	>	int count_local = foundTypes.size();
720
721	<	return ndf;
365	<	}
721	>	int nproc = MPI::COMM_WORLD.Get_size();
722
723	<	int SimInfo::getNDFraw() {
724	<	int ndfRaw_local;
723	>	// we need arrays to hold the counts and displacement vectors for
724	>	// all processors
725	>	vector<int> counts(nproc, 0);
726	>	vector<int> disps(nproc, 0);
727
728	<	// Raw degrees of freedom that we have to set
729	<	ndfRaw_local = 0;
730	<
731	<	for(int i = 0; i < integrableObjects.size(); i++){
732	<	ndfRaw_local += 3;
733	<	if (integrableObjects[i]->isDirectional()) {
734	<	if (integrableObjects[i]->isLinear())
735	<	ndfRaw_local += 2;
736	<	else
737	<	ndfRaw_local += 3;
728	>	// fill the counts array
729	>	MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
730	>	1, MPI::INT);
731	>
732	>	// use the processor counts to compute the displacement array
733	>	disps[0] = 0;
734	>	int totalCount = counts[0];
735	>	for (int iproc = 1; iproc < nproc; iproc++) {
736	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
737	>	totalCount += counts[iproc];
738		}
739	+
740	+	// we need a (possibly redundant) set of all found types:
741	+	vector<int> ftGlobal(totalCount);
742	+
743	+	// now spray out the foundTypes to all the other processors:
744	+	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
745	+	&ftGlobal[0], &counts[0], &disps[0],
746	+	MPI::INT);
747	+
748	+	vector<int>::iterator j;
749	+
750	+	// foundIdents is a stl set, so inserting an already found ident
751	+	// will have no effect.
752	+	set<int> foundIdents;
753	+
754	+	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
755	+	foundIdents.insert((*j));
756	+
757	+	// now iterate over the foundIdents and get the actual atom types
758	+	// that correspond to these:
759	+	set<int>::iterator it;
760	+	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
761	+	atomTypes.insert( forceField_->getAtomType((*it)) );
762	+
763	+	#endif
764	+
765	+	return atomTypes;
766		}
767	+
768	+	void SimInfo::setupSimVariables() {
769	+	useAtomicVirial_ = simParams_->getUseAtomicVirial();
770	+	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
771	+	calcBoxDipole_ = false;
772	+	if ( simParams_->haveAccumulateBoxDipole() )
773	+	if ( simParams_->getAccumulateBoxDipole() ) {
774	+	calcBoxDipole_ = true;
775	+	}
776
777	<	#ifdef IS_MPI
778	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
777	>	set<AtomType*>::iterator i;
778	>	set<AtomType*> atomTypes;
779	>	atomTypes = getSimulatedAtomTypes();
780	>	int usesElectrostatic = 0;
781	>	int usesMetallic = 0;
782	>	int usesDirectional = 0;
783	>	//loop over all of the atom types
784	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
785	>	usesElectrostatic |= (*i)->isElectrostatic();
786	>	usesMetallic |= (*i)->isMetal();
787	>	usesDirectional |= (*i)->isDirectional();
788	>	}
789	>
790	>	#ifdef IS_MPI
791	>	int temp;
792	>	temp = usesDirectional;
793	>	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
794	>
795	>	temp = usesMetallic;
796	>	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
797	>
798	>	temp = usesElectrostatic;
799	>	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
800		#else
801	<	ndfRaw = ndfRaw_local;
801	>
802	>	usesDirectionalAtoms_ = usesDirectional;
803	>	usesMetallicAtoms_ = usesMetallic;
804	>	usesElectrostaticAtoms_ = usesElectrostatic;
805	>
806		#endif
807	+
808	+	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
809	+	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
810	+	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
811	+	}
812
389	–	return ndfRaw;
390	–	}
813
814	<	int SimInfo::getNDFtranslational() {
815	<	int ndfTrans_local;
814	>	vector<int> SimInfo::getGlobalAtomIndices() {
815	>	SimInfo::MoleculeIterator mi;
816	>	Molecule* mol;
817	>	Molecule::AtomIterator ai;
818	>	Atom* atom;
819
820	<	ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
820	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
821	>
822	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
823	>
824	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
825	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
826	>	}
827	>	}
828	>	return GlobalAtomIndices;
829	>	}
830
831
832	<	#ifdef IS_MPI
833	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
834	<	#else
835	<	ndfTrans = ndfTrans_local;
836	<	#endif
832	>	vector<int> SimInfo::getGlobalGroupIndices() {
833	>	SimInfo::MoleculeIterator mi;
834	>	Molecule* mol;
835	>	Molecule::CutoffGroupIterator ci;
836	>	CutoffGroup* cg;
837
838	<	ndfTrans = ndfTrans - 3 - nZconstraints;
838	>	vector<int> GlobalGroupIndices;
839	>
840	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
841	>
842	>	//local index of cutoff group is trivial, it only depends on the
843	>	//order of travesing
844	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
845	>	cg = mol->nextCutoffGroup(ci)) {
846	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
847	>	}
848	>	}
849	>	return GlobalGroupIndices;
850	>	}
851
406	–	return ndfTrans;
407	–	}
852
853	<	int SimInfo::getTotIntegrableObjects() {
854	<	int nObjs_local;
411	<	int nObjs;
853	>	void SimInfo::prepareTopology() {
854	>	int nExclude, nOneTwo, nOneThree, nOneFour;
855
856	<	nObjs_local =  integrableObjects.size();
856	>	//calculate mass ratio of cutoff group
857	>	SimInfo::MoleculeIterator mi;
858	>	Molecule* mol;
859	>	Molecule::CutoffGroupIterator ci;
860	>	CutoffGroup* cg;
861	>	Molecule::AtomIterator ai;
862	>	Atom* atom;
863	>	RealType totalMass;
864
865	+	/**
866	+	* The mass factor is the relative mass of an atom to the total
867	+	* mass of the cutoff group it belongs to.  By default, all atoms
868	+	* are their own cutoff groups, and therefore have mass factors of
869	+	* 1.  We need some special handling for massless atoms, which
870	+	* will be treated as carrying the entire mass of the cutoff
871	+	* group.
872	+	*/
873	+	massFactors_.clear();
874	+	massFactors_.resize(getNAtoms(), 1.0);
875	+
876	+	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
877	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
878	+	cg = mol->nextCutoffGroup(ci)) {
879
880	<	#ifdef IS_MPI
881	<	MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
882	<	#else
883	<	nObjs = nObjs_local;
884	<	#endif
880	>	totalMass = cg->getMass();
881	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
882	>	// Check for massless groups - set mfact to 1 if true
883	>	if (totalMass != 0)
884	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
885	>	else
886	>	massFactors_[atom->getLocalIndex()] = 1.0;
887	>	}
888	>	}
889	>	}
890
891	+	// Build the identArray_
892
893	<	return nObjs;
894	<	}
893	>	identArray_.clear();
894	>	identArray_.reserve(getNAtoms());
895	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
896	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
897	>	identArray_.push_back(atom->getIdent());
898	>	}
899	>	}
900	>
901	>	//scan topology
902
903	<	void SimInfo::refreshSim(){
903	>	nExclude = excludedInteractions_.getSize();
904	>	nOneTwo = oneTwoInteractions_.getSize();
905	>	nOneThree = oneThreeInteractions_.getSize();
906	>	nOneFour = oneFourInteractions_.getSize();
907
908	<	simtype fInfo;
909	<	int isError;
910	<	int n_global;
911	<	int* excl;
908	>	int* excludeList = excludedInteractions_.getPairList();
909	>	int* oneTwoList = oneTwoInteractions_.getPairList();
910	>	int* oneThreeList = oneThreeInteractions_.getPairList();
911	>	int* oneFourList = oneFourInteractions_.getPairList();
912
913	<	fInfo.dielect = 0.0;
913	>	topologyDone_ = true;
914	>	}
915
916	<	if( useDipoles ){
917	<	if( useReactionField )fInfo.dielect = dielectric;
916	>	void SimInfo::addProperty(GenericData* genData) {
917	>	properties_.addProperty(genData);
918		}
919
920	<	fInfo.SIM_uses_PBC = usePBC;
920	>	void SimInfo::removeProperty(const string& propName) {
921	>	properties_.removeProperty(propName);
922	>	}
923
924	<	if (useSticky || useDipoles || useGayBerne || useShapes) {
925	<	useDirectionalAtoms = 1;
443	<	fInfo.SIM_uses_DirectionalAtoms = useDirectionalAtoms;
924	>	void SimInfo::clearProperties() {
925	>	properties_.clearProperties();
926		}
927
928	<	fInfo.SIM_uses_LennardJones = useLennardJones;
928	>	vector<string> SimInfo::getPropertyNames() {
929	>	return properties_.getPropertyNames();
930	>	}
931	>
932	>	vector<GenericData*> SimInfo::getProperties() {
933	>	return properties_.getProperties();
934	>	}
935
936	<	if (useCharges || useDipoles) {
937	<	useElectrostatics = 1;
450	<	fInfo.SIM_uses_Electrostatics = useElectrostatics;
936	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
937	>	return properties_.getPropertyByName(propName);
938		}
939
940	<	fInfo.SIM_uses_Charges = useCharges;
941	<	fInfo.SIM_uses_Dipoles = useDipoles;
942	<	fInfo.SIM_uses_Sticky = useSticky;
943	<	fInfo.SIM_uses_GayBerne = useGayBerne;
944	<	fInfo.SIM_uses_EAM = useEAM;
945	<	fInfo.SIM_uses_Shapes = useShapes;
459	<	fInfo.SIM_uses_FLARB = useFLARB;
460	<	fInfo.SIM_uses_RF = useReactionField;
940	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
941	>	if (sman_ == sman) {
942	>	return;
943	>	}
944	>	delete sman_;
945	>	sman_ = sman;
946
947	<	n_exclude = excludes->getSize();
948	<	excl = excludes->getFortranArray();
949	<
947	>	Molecule* mol;
948	>	RigidBody* rb;
949	>	Atom* atom;
950	>	CutoffGroup* cg;
951	>	SimInfo::MoleculeIterator mi;
952	>	Molecule::RigidBodyIterator rbIter;
953	>	Molecule::AtomIterator atomIter;
954	>	Molecule::CutoffGroupIterator cgIter;
955	>
956	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
957	>
958	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
959	>	atom->setSnapshotManager(sman_);
960	>	}
961	>
962	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
963	>	rb->setSnapshotManager(sman_);
964	>	}
965	>
966	>	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
967	>	cg->setSnapshotManager(sman_);
968	>	}
969	>	}
970	>
971	>	}
972	>
973	>	Vector3d SimInfo::getComVel(){
974	>	SimInfo::MoleculeIterator i;
975	>	Molecule* mol;
976	>
977	>	Vector3d comVel(0.0);
978	>	RealType totalMass = 0.0;
979	>
980	>
981	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
982	>	RealType mass = mol->getMass();
983	>	totalMass += mass;
984	>	comVel += mass * mol->getComVel();
985	>	}
986	>
987		#ifdef IS_MPI
988	<	n_global = mpiSim->getNAtomsGlobal();
989	<	#else
990	<	n_global = n_atoms;
988	>	RealType tmpMass = totalMass;
989	>	Vector3d tmpComVel(comVel);
990	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
991	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
992		#endif
470	–
471	–	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);
993
994	<	if( isError ){
995	<
996	<	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();
994	>	comVel /= totalMass;
995	>
996	>	return comVel;
997		}
998	<
998	>
999	>	Vector3d SimInfo::getCom(){
1000	>	SimInfo::MoleculeIterator i;
1001	>	Molecule* mol;
1002	>
1003	>	Vector3d com(0.0);
1004	>	RealType totalMass = 0.0;
1005	>
1006	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1007	>	RealType mass = mol->getMass();
1008	>	totalMass += mass;
1009	>	com += mass * mol->getCom();
1010	>	}
1011	>
1012		#ifdef IS_MPI
1013	<	sprintf( checkPointMsg,
1014	<	"succesfully sent the simulation information to fortran.\n");
1015	<	MPIcheckPoint();
1016	<	#endif // is_mpi
1017	<
496	<	this->ndf = this->getNDF();
497	<	this->ndfRaw = this->getNDFraw();
498	<	this->ndfTrans = this->getNDFtranslational();
499	<	}
1013	>	RealType tmpMass = totalMass;
1014	>	Vector3d tmpCom(com);
1015	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1016	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1017	>	#endif
1018
1019	<	void SimInfo::setDefaultRcut( double theRcut ){
502	<
503	<	haveRcut = 1;
504	<	rCut = theRcut;
505	<	rList = rCut + 1.0;
506	<
507	<	notifyFortranCutoffs( &rCut, &rSw, &rList );
508	<	}
1019	>	com /= totalMass;
1020
1021	<	void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
1021	>	return com;
1022
1023	<	rSw = theRsw;
513	<	setDefaultRcut( theRcut );
514	<	}
1023	>	}
1024
1025	+	ostream& operator <<(ostream& o, SimInfo& info) {
1026
1027	<	void SimInfo::checkCutOffs( void ){
1028	<
1029	<	if( boxIsInit ){
1027	>	return o;
1028	>	}
1029	>
1030	>
1031	>	/*
1032	>	Returns center of mass and center of mass velocity in one function call.
1033	>	*/
1034	>
1035	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1036	>	SimInfo::MoleculeIterator i;
1037	>	Molecule* mol;
1038	>
1039
1040	<	//we need to check cutOffs against the box
1040	>	RealType totalMass = 0.0;
1041
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();
549	–	}
550	–
551	–	}
1042
1043	<	void SimInfo::addProperty(GenericData* prop){
1044	<
1045	<	map<string, GenericData*>::iterator result;
1046	<	result = properties.find(prop->getID());
1047	<
1048	<	//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()){
562	<
563	<	delete (*result).second;
564	<	(*result).second = prop;
1043	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1044	>	RealType mass = mol->getMass();
1045	>	totalMass += mass;
1046	>	com += mass * mol->getCom();
1047	>	comVel += mass * mol->getComVel();
1048	>	}
1049
1050	<	}
1051	<	else{
1050	>	#ifdef IS_MPI
1051	>	RealType tmpMass = totalMass;
1052	>	Vector3d tmpCom(com);
1053	>	Vector3d tmpComVel(comVel);
1054	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1055	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1056	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1057	>	#endif
1058	>
1059	>	com /= totalMass;
1060	>	comVel /= totalMass;
1061	>	}
1062	>
1063	>	/*
1064	>	Return intertia tensor for entire system and angular momentum Vector.
1065
569	–	properties[prop->getID()] = prop;
1066
1067	<	}
1068	<
1069	<	}
1067	>	[  Ixx -Ixy  -Ixz ]
1068	>	J =| -Iyx  Iyy  -Iyz |
1069	>	[ -Izx -Iyz   Izz ]
1070	>	*/
1071
1072	<	GenericData* SimInfo::getProperty(const string& propName){
1072	>	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1073	>
1074
1075	<	map<string, GenericData*>::iterator result;
1076	<
1077	<	//string lowerCaseName = ();
1078	<
1079	<	result = properties.find(propName);
1080	<
1081	<	if(result != properties.end())
1082	<	return (*result).second;
1083	<	else
1084	<	return NULL;
1085	<	}
1075	>	RealType xx = 0.0;
1076	>	RealType yy = 0.0;
1077	>	RealType zz = 0.0;
1078	>	RealType xy = 0.0;
1079	>	RealType xz = 0.0;
1080	>	RealType yz = 0.0;
1081	>	Vector3d com(0.0);
1082	>	Vector3d comVel(0.0);
1083	>
1084	>	getComAll(com, comVel);
1085	>
1086	>	SimInfo::MoleculeIterator i;
1087	>	Molecule* mol;
1088	>
1089	>	Vector3d thisq(0.0);
1090	>	Vector3d thisv(0.0);
1091
1092	+	RealType thisMass = 0.0;
1093	+
1094	+
1095	+
1096	+
1097	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1098	+
1099	+	thisq = mol->getCom()-com;
1100	+	thisv = mol->getComVel()-comVel;
1101	+	thisMass = mol->getMass();
1102	+	// Compute moment of intertia coefficients.
1103	+	xx += thisq[0]*thisq[0]*thisMass;
1104	+	yy += thisq[1]*thisq[1]*thisMass;
1105	+	zz += thisq[2]*thisq[2]*thisMass;
1106	+
1107	+	// compute products of intertia
1108	+	xy += thisq[0]*thisq[1]*thisMass;
1109	+	xz += thisq[0]*thisq[2]*thisMass;
1110	+	yz += thisq[1]*thisq[2]*thisMass;
1111	+
1112	+	angularMomentum += cross( thisq, thisv ) * thisMass;
1113	+
1114	+	}
1115	+
1116	+
1117	+	inertiaTensor(0,0) = yy + zz;
1118	+	inertiaTensor(0,1) = -xy;
1119	+	inertiaTensor(0,2) = -xz;
1120	+	inertiaTensor(1,0) = -xy;
1121	+	inertiaTensor(1,1) = xx + zz;
1122	+	inertiaTensor(1,2) = -yz;
1123	+	inertiaTensor(2,0) = -xz;
1124	+	inertiaTensor(2,1) = -yz;
1125	+	inertiaTensor(2,2) = xx + yy;
1126	+
1127	+	#ifdef IS_MPI
1128	+	Mat3x3d tmpI(inertiaTensor);
1129	+	Vector3d tmpAngMom;
1130	+	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1131	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1132	+	#endif
1133	+
1134	+	return;
1135	+	}
1136
1137	<	void SimInfo::getFortranGroupArrays(SimInfo* info,
1138	<	vector<int>& FglobalGroupMembership,
1139	<	vector<double>& mfact){
1140	<
1141	<	Molecule* myMols;
1142	<	Atom** myAtoms;
1143	<	int numAtom;
1144	<	double mtot;
1145	<	int numMol;
1146	<	int numCutoffGroups;
1147	<	CutoffGroup* myCutoffGroup;
1148	<	vector<CutoffGroup*>::iterator iterCutoff;
1149	<	Atom* cutoffAtom;
1150	<	vector<Atom*>::iterator iterAtom;
1151	<	int atomIndex;
1152	<	double totalMass;
1153	<
1154	<	mfact.clear();
1155	<	FglobalGroupMembership.clear();
1156	<
1157	<
1158	<	// Fix the silly fortran indexing problem
1137	>	//Returns the angular momentum of the system
1138	>	Vector3d SimInfo::getAngularMomentum(){
1139	>
1140	>	Vector3d com(0.0);
1141	>	Vector3d comVel(0.0);
1142	>	Vector3d angularMomentum(0.0);
1143	>
1144	>	getComAll(com,comVel);
1145	>
1146	>	SimInfo::MoleculeIterator i;
1147	>	Molecule* mol;
1148	>
1149	>	Vector3d thisr(0.0);
1150	>	Vector3d thisp(0.0);
1151	>
1152	>	RealType thisMass;
1153	>
1154	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1155	>	thisMass = mol->getMass();
1156	>	thisr = mol->getCom()-com;
1157	>	thisp = (mol->getComVel()-comVel)*thisMass;
1158	>
1159	>	angularMomentum += cross( thisr, thisp );
1160	>
1161	>	}
1162	>
1163		#ifdef IS_MPI
1164	<	numAtom = mpiSim->getNAtomsGlobal();
1165	<	#else
615	<	numAtom = n_atoms;
1164	>	Vector3d tmpAngMom;
1165	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1166		#endif
1167	<	for (int i = 0; i < numAtom; i++)
1168	<	FglobalGroupMembership.push_back(globalGroupMembership[i] + 1);
1167	>
1168	>	return angularMomentum;
1169	>	}
1170	>
1171	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1172	>	return IOIndexToIntegrableObject.at(index);
1173	>	}
1174
1175	+	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1176	+	IOIndexToIntegrableObject= v;
1177	+	}
1178
1179	<	myMols = info->molecules;
1180	<	numMol = info->n_mol;
1181	<	for(int i  = 0; i < numMol; i++){
1182	<	numCutoffGroups = myMols[i].getNCutoffGroups();
1183	<	for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff);
1184	<	myCutoffGroup != NULL;
1185	<	myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
1179	>	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1180	>	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1181	>	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1182	>	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1183	>	*/
1184	>	void SimInfo::getGyrationalVolume(RealType &volume){
1185	>	Mat3x3d intTensor;
1186	>	RealType det;
1187	>	Vector3d dummyAngMom;
1188	>	RealType sysconstants;
1189	>	RealType geomCnst;
1190
1191	<	totalMass = myCutoffGroup->getMass();
1192	<
1193	<	for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom);
1194	<	cutoffAtom != NULL;
1195	<	cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
1196	<	mfact.push_back(cutoffAtom->getMass()/totalMass);
1197	<	}
1191	>	geomCnst = 3.0/2.0;
1192	>	/* Get the inertial tensor and angular momentum for free*/
1193	>	getInertiaTensor(intTensor,dummyAngMom);
1194	>
1195	>	det = intTensor.determinant();
1196	>	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1197	>	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(det);
1198	>	return;
1199	>	}
1200	>
1201	>	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1202	>	Mat3x3d intTensor;
1203	>	Vector3d dummyAngMom;
1204	>	RealType sysconstants;
1205	>	RealType geomCnst;
1206	>
1207	>	geomCnst = 3.0/2.0;
1208	>	/* Get the inertial tensor and angular momentum for free*/
1209	>	getInertiaTensor(intTensor,dummyAngMom);
1210	>
1211	>	detI = intTensor.determinant();
1212	>	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1213	>	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(detI);
1214	>	return;
1215	>	}
1216	>	/*
1217	>	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1218	>	assert( v.size() == nAtoms_ + nRigidBodies_);
1219	>	sdByGlobalIndex_ = v;
1220		}
1221	+
1222	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1223	+	//assert(index < nAtoms_ + nRigidBodies_);
1224	+	return sdByGlobalIndex_.at(index);
1225	+	}
1226	+	*/
1227	+	int SimInfo::getNGlobalConstraints() {
1228	+	int nGlobalConstraints;
1229	+	#ifdef IS_MPI
1230	+	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1231	+	MPI_COMM_WORLD);
1232	+	#else
1233	+	nGlobalConstraints =  nConstraints_;
1234	+	#endif
1235	+	return nGlobalConstraints;
1236		}
1237
1238	<	}
1238	>	}//end namespace OpenMD
1239	>

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 1668 by gezelter, Fri Jan 6 19:03:05 2012 UTC

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