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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 1536 by gezelter, Wed Jan 5 14:49:05 2011 UTC

#	Line 1 | Line 1
1	<	#include <stdlib.h>
2	<	#include <string.h>
3	<	#include <math.h>
1	>	/*
2	>	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	>	*
4	>	* The University of Notre Dame grants you ("Licensee") a
5	>	* non-exclusive, royalty free, license to use, modify and
6	>	* redistribute this software in source and binary code form, provided
7	>	* that the following conditions are met:
8	>	*
9	>	* 1. Redistributions of source code must retain the above copyright
10	>	*    notice, this list of conditions and the following disclaimer.
11	>	*
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13	>	*    notice, this list of conditions and the following disclaimer in the
14	>	*    documentation and/or other materials provided with the
15	>	*    distribution.
16	>	*
17	>	* This software is provided "AS IS," without a warranty of any
18	>	* kind. All express or implied conditions, representations and
19	>	* warranties, including any implied warranty of merchantability,
20	>	* fitness for a particular purpose or non-infringement, are hereby
21	>	* excluded.  The University of Notre Dame and its licensors shall not
22	>	* be liable for any damages suffered by licensee as a result of
23	>	* using, modifying or distributing the software or its
24	>	* derivatives. In no event will the University of Notre Dame or its
25	>	* licensors be liable for any lost revenue, profit or data, or for
26	>	* direct, indirect, special, consequential, incidental or punitive
27	>	* damages, however caused and regardless of the theory of liability,
28	>	* arising out of the use of or inability to use software, even if the
29	>	* University of Notre Dame has been advised of the possibility of
30	>	* such damages.
31	>	*
32	>	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	>	* research, please cite the appropriate papers when you publish your
34	>	* work.  Good starting points are:
35	>	*
36	>	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	>	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	>	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	>	* [4]  Vardeman & Gezelter, in progress (2009).
40	>	*/
41	>
42	>	/**
43	>	* @file SimInfo.cpp
44	>	* @author    tlin
45	>	* @date  11/02/2004
46	>	* @version 1.0
47	>	*/
48
49	<	#include <iostream>
50	<	using namespace std;
49	>	#include <algorithm>
50	>	#include <set>
51	>	#include <map>
52
53		#include "brains/SimInfo.hpp"
54	<	#define __C
55	<	#include "brains/fSimulation.h"
54	>	#include "math/Vector3.hpp"
55	>	#include "primitives/Molecule.hpp"
56	>	#include "primitives/StuntDouble.hpp"
57	>	#include "UseTheForce/DarkSide/neighborLists_interface.h"
58	>	#include "UseTheForce/doForces_interface.h"
59	>	#include "utils/MemoryUtils.hpp"
60		#include "utils/simError.h"
61	<	#include "UseTheForce/DarkSide/simulation_interface.h"
62	<	#include "UseTheForce/notifyCutoffs_interface.h"
61	>	#include "selection/SelectionManager.hpp"
62	>	#include "io/ForceFieldOptions.hpp"
63	>	#include "UseTheForce/ForceField.hpp"
64	>	#include "nonbonded/SwitchingFunction.hpp"
65
66	<	//#include "UseTheForce/fortranWrappers.hpp"
66	>	#ifdef IS_MPI
67	>	#include "UseTheForce/mpiComponentPlan.h"
68	>	#include "UseTheForce/DarkSide/simParallel_interface.h"
69	>	#endif
70
71	<	#include "math/MatVec3.h"
71	>	using namespace std;
72	>	namespace OpenMD {
73	>
74	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
75	>	forceField_(ff), simParams_(simParams),
76	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
77	>	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
78	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
79	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
80	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
81	>	nConstraints_(0), sman_(NULL), fortranInitialized_(false),
82	>	calcBoxDipole_(false), useAtomicVirial_(true) {
83	>
84	>	MoleculeStamp* molStamp;
85	>	int nMolWithSameStamp;
86	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
87	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
88	>	CutoffGroupStamp* cgStamp;
89	>	RigidBodyStamp* rbStamp;
90	>	int nRigidAtoms = 0;
91	>
92	>	vector<Component*> components = simParams->getComponents();
93	>
94	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
95	>	molStamp = (*i)->getMoleculeStamp();
96	>	nMolWithSameStamp = (*i)->getNMol();
97	>
98	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
99	>
100	>	//calculate atoms in molecules
101	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
102	>
103	>	//calculate atoms in cutoff groups
104	>	int nAtomsInGroups = 0;
105	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
106	>
107	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
108	>	cgStamp = molStamp->getCutoffGroupStamp(j);
109	>	nAtomsInGroups += cgStamp->getNMembers();
110	>	}
111	>
112	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
113	>
114	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
115	>
116	>	//calculate atoms in rigid bodies
117	>	int nAtomsInRigidBodies = 0;
118	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
119	>
120	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
121	>	rbStamp = molStamp->getRigidBodyStamp(j);
122	>	nAtomsInRigidBodies += rbStamp->getNMembers();
123	>	}
124	>
125	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
126	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
127	>
128	>	}
129	>
130	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
131	>	//group therefore the total number of cutoff groups in the system is
132	>	//equal to the total number of atoms minus number of atoms belong to
133	>	//cutoff group defined in meta-data file plus the number of cutoff
134	>	//groups defined in meta-data file
135	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
136	>
137	>	//every free atom (atom does not belong to rigid bodies) is an
138	>	//integrable object therefore the total number of integrable objects
139	>	//in the system is equal to the total number of atoms minus number of
140	>	//atoms belong to rigid body defined in meta-data file plus the number
141	>	//of rigid bodies defined in meta-data file
142	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
143	>	+ nGlobalRigidBodies_;
144	>
145	>	nGlobalMols_ = molStampIds_.size();
146	>	molToProcMap_.resize(nGlobalMols_);
147	>	}
148	>
149	>	SimInfo::~SimInfo() {
150	>	map<int, Molecule*>::iterator i;
151	>	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
152	>	delete i->second;
153	>	}
154	>	molecules_.clear();
155	>
156	>	delete sman_;
157	>	delete simParams_;
158	>	delete forceField_;
159	>	}
160
19	–	#ifdef IS_MPI
20	–	#include "brains/mpiSimulation.hpp"
21	–	#endif
161
162	<	inline double roundMe( double x ){
163	<	return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
164	<	}
165	<
166	<	inline double min( double a, double b ){
167	<	return (a < b ) ? a : b;
168	<	}
162	>	bool SimInfo::addMolecule(Molecule* mol) {
163	>	MoleculeIterator i;
164	>
165	>	i = molecules_.find(mol->getGlobalIndex());
166	>	if (i == molecules_.end() ) {
167	>
168	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
169	>
170	>	nAtoms_ += mol->getNAtoms();
171	>	nBonds_ += mol->getNBonds();
172	>	nBends_ += mol->getNBends();
173	>	nTorsions_ += mol->getNTorsions();
174	>	nInversions_ += mol->getNInversions();
175	>	nRigidBodies_ += mol->getNRigidBodies();
176	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
177	>	nCutoffGroups_ += mol->getNCutoffGroups();
178	>	nConstraints_ += mol->getNConstraintPairs();
179	>
180	>	addInteractionPairs(mol);
181	>
182	>	return true;
183	>	} else {
184	>	return false;
185	>	}
186	>	}
187	>
188	>	bool SimInfo::removeMolecule(Molecule* mol) {
189	>	MoleculeIterator i;
190	>	i = molecules_.find(mol->getGlobalIndex());
191
192	<	SimInfo* currentInfo;
192	>	if (i != molecules_.end() ) {
193
194	<	SimInfo::SimInfo(){
194	>	assert(mol == i->second);
195	>
196	>	nAtoms_ -= mol->getNAtoms();
197	>	nBonds_ -= mol->getNBonds();
198	>	nBends_ -= mol->getNBends();
199	>	nTorsions_ -= mol->getNTorsions();
200	>	nInversions_ -= mol->getNInversions();
201	>	nRigidBodies_ -= mol->getNRigidBodies();
202	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
203	>	nCutoffGroups_ -= mol->getNCutoffGroups();
204	>	nConstraints_ -= mol->getNConstraintPairs();
205
206	<	n_constraints = 0;
207	<	nZconstraints = 0;
37	<	n_oriented = 0;
38	<	n_dipoles = 0;
39	<	ndf = 0;
40	<	ndfRaw = 0;
41	<	nZconstraints = 0;
42	<	the_integrator = NULL;
43	<	setTemp = 0;
44	<	thermalTime = 0.0;
45	<	currentTime = 0.0;
46	<	rCut = 0.0;
47	<	rSw = 0.0;
206	>	removeInteractionPairs(mol);
207	>	molecules_.erase(mol->getGlobalIndex());
208
209	<	haveRcut = 0;
210	<	haveRsw = 0;
211	<	boxIsInit = 0;
212	<
213	<	resetTime = 1e99;
209	>	delete mol;
210	>
211	>	return true;
212	>	} else {
213	>	return false;
214	>	}
215	>	}
216
217	<	orthoRhombic = 0;
218	<	orthoTolerance = 1E-6;
219	<	useInitXSstate = true;
217	>
218	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
219	>	i = molecules_.begin();
220	>	return i == molecules_.end() ? NULL : i->second;
221	>	}
222
223	<	usePBC = 0;
224	<	useDirectionalAtoms = 0;
225	<	useLennardJones = 0;
226	<	useElectrostatics = 0;
63	<	useCharges = 0;
64	<	useDipoles = 0;
65	<	useSticky = 0;
66	<	useGayBerne = 0;
67	<	useEAM = 0;
68	<	useShapes = 0;
69	<	useFLARB = 0;
223	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
224	>	++i;
225	>	return i == molecules_.end() ? NULL : i->second;
226	>	}
227
71	–	useSolidThermInt = 0;
72	–	useLiquidThermInt = 0;
228
229	<	haveCutoffGroups = false;
229	>	void SimInfo::calcNdf() {
230	>	int ndf_local;
231	>	MoleculeIterator i;
232	>	vector<StuntDouble*>::iterator j;
233	>	Molecule* mol;
234	>	StuntDouble* integrableObject;
235
236	<	excludes = Exclude::Instance();
236	>	ndf_local = 0;
237	>
238	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
239	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
240	>	integrableObject = mol->nextIntegrableObject(j)) {
241
242	<	myConfiguration = new SimState();
242	>	ndf_local += 3;
243
244	<	has_minimizer = false;
245	<	the_minimizer =NULL;
244	>	if (integrableObject->isDirectional()) {
245	>	if (integrableObject->isLinear()) {
246	>	ndf_local += 2;
247	>	} else {
248	>	ndf_local += 3;
249	>	}
250	>	}
251	>
252	>	}
253	>	}
254	>
255	>	// n_constraints is local, so subtract them on each processor
256	>	ndf_local -= nConstraints_;
257
258	<	ngroup = 0;
258	>	#ifdef IS_MPI
259	>	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
260	>	#else
261	>	ndf_ = ndf_local;
262	>	#endif
263
264	<	}
264	>	// nZconstraints_ is global, as are the 3 COM translations for the
265	>	// entire system:
266	>	ndf_ = ndf_ - 3 - nZconstraint_;
267
268	+	}
269
270	<	SimInfo::~SimInfo(){
270	>	int SimInfo::getFdf() {
271	>	#ifdef IS_MPI
272	>	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
273	>	#else
274	>	fdf_ = fdf_local;
275	>	#endif
276	>	return fdf_;
277	>	}
278	>
279	>	void SimInfo::calcNdfRaw() {
280	>	int ndfRaw_local;
281
282	<	delete myConfiguration;
282	>	MoleculeIterator i;
283	>	vector<StuntDouble*>::iterator j;
284	>	Molecule* mol;
285	>	StuntDouble* integrableObject;
286
287	<	map<string, GenericData*>::iterator i;
288	<
289	<	for(i = properties.begin(); i != properties.end(); i++)
290	<	delete (*i).second;
287	>	// Raw degrees of freedom that we have to set
288	>	ndfRaw_local = 0;
289	>
290	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
291	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
292	>	integrableObject = mol->nextIntegrableObject(j)) {
293
294	<	}
294	>	ndfRaw_local += 3;
295
296	<	void SimInfo::setBox(double newBox[3]) {
297	<
298	<	int i, j;
299	<	double tempMat[3][3];
300	<
301	<	for(i=0; i<3; i++)
302	<	for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
303	<
304	<	tempMat[0][0] = newBox[0];
108	<	tempMat[1][1] = newBox[1];
109	<	tempMat[2][2] = newBox[2];
110	<
111	<	setBoxM( tempMat );
112	<
113	<	}
114	<
115	<	void SimInfo::setBoxM( double theBox[3][3] ){
116	<
117	<	int i, j;
118	<	double FortranHmat[9]; // to preserve compatibility with Fortran the
119	<	// ordering in the array is as follows:
120	<	// [ 0 3 6 ]
121	<	// [ 1 4 7 ]
122	<	// [ 2 5 8 ]
123	<	double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
124	<
125	<	if( !boxIsInit ) boxIsInit = 1;
126	<
127	<	for(i=0; i < 3; i++)
128	<	for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
129	<
130	<	calcBoxL();
131	<	calcHmatInv();
132	<
133	<	for(i=0; i < 3; i++) {
134	<	for (j=0; j < 3; j++) {
135	<	FortranHmat[3*j + i] = Hmat[i][j];
136	<	FortranHmatInv[3*j + i] = HmatInv[i][j];
296	>	if (integrableObject->isDirectional()) {
297	>	if (integrableObject->isLinear()) {
298	>	ndfRaw_local += 2;
299	>	} else {
300	>	ndfRaw_local += 3;
301	>	}
302	>	}
303	>
304	>	}
305		}
306	+
307	+	#ifdef IS_MPI
308	+	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
309	+	#else
310	+	ndfRaw_ = ndfRaw_local;
311	+	#endif
312		}
313
314	<	setFortranBox(FortranHmat, FortranHmatInv, &orthoRhombic);
315	<
142	<	}
143	<
314	>	void SimInfo::calcNdfTrans() {
315	>	int ndfTrans_local;
316
317	<	void SimInfo::getBoxM (double theBox[3][3]) {
317	>	ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
318
147	–	int i, j;
148	–	for(i=0; i<3; i++)
149	–	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
150	–	}
319
320	+	#ifdef IS_MPI
321	+	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
322	+	#else
323	+	ndfTrans_ = ndfTrans_local;
324	+	#endif
325
326	<	void SimInfo::scaleBox(double scale) {
327	<	double theBox[3][3];
328	<	int i, j;
326	>	ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
327	>
328	>	}
329
330	<	// cerr << "Scaling box by " << scale << "\n";
330	>	void SimInfo::addInteractionPairs(Molecule* mol) {
331	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
332	>	vector<Bond*>::iterator bondIter;
333	>	vector<Bend*>::iterator bendIter;
334	>	vector<Torsion*>::iterator torsionIter;
335	>	vector<Inversion*>::iterator inversionIter;
336	>	Bond* bond;
337	>	Bend* bend;
338	>	Torsion* torsion;
339	>	Inversion* inversion;
340	>	int a;
341	>	int b;
342	>	int c;
343	>	int d;
344
345	<	for(i=0; i<3; i++)
346	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
345	>	// atomGroups can be used to add special interaction maps between
346	>	// groups of atoms that are in two separate rigid bodies.
347	>	// However, most site-site interactions between two rigid bodies
348	>	// are probably not special, just the ones between the physically
349	>	// bonded atoms.  Interactions *within* a single rigid body should
350	>	// always be excluded.  These are done at the bottom of this
351	>	// function.
352
353	<	setBoxM(theBox);
354	<
355	<	}
356	<
357	<	void SimInfo::calcHmatInv( void ) {
358	<
359	<	int oldOrtho;
360	<	int i,j;
361	<	double smallDiag;
362	<	double tol;
363	<	double sanity[3][3];
364	<
365	<	invertMat3( Hmat, HmatInv );
366	<
367	<	// check to see if Hmat is orthorhombic
368	<
369	<	oldOrtho = orthoRhombic;
370	<
371	<	smallDiag = fabs(Hmat[0][0]);
372	<	if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
373	<	if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
374	<	tol = smallDiag * orthoTolerance;
375	<
376	<	orthoRhombic = 1;
186	<
187	<	for (i = 0; i < 3; i++ ) {
188	<	for (j = 0 ; j < 3; j++) {
189	<	if (i != j) {
190	<	if (orthoRhombic) {
191	<	if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
192	<	}
353	>	map<int, set<int> > atomGroups;
354	>	Molecule::RigidBodyIterator rbIter;
355	>	RigidBody* rb;
356	>	Molecule::IntegrableObjectIterator ii;
357	>	StuntDouble* integrableObject;
358	>
359	>	for (integrableObject = mol->beginIntegrableObject(ii);
360	>	integrableObject != NULL;
361	>	integrableObject = mol->nextIntegrableObject(ii)) {
362	>
363	>	if (integrableObject->isRigidBody()) {
364	>	rb = static_cast<RigidBody*>(integrableObject);
365	>	vector<Atom*> atoms = rb->getAtoms();
366	>	set<int> rigidAtoms;
367	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
368	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
369	>	}
370	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
371	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
372	>	}
373	>	} else {
374	>	set<int> oneAtomSet;
375	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
376	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
377		}
378	<	}
379	<	}
378	>	}
379	>
380	>	for (bond= mol->beginBond(bondIter); bond != NULL;
381	>	bond = mol->nextBond(bondIter)) {
382
383	<	if( oldOrtho != orthoRhombic ){
383	>	a = bond->getAtomA()->getGlobalIndex();
384	>	b = bond->getAtomB()->getGlobalIndex();
385
386	<	if( orthoRhombic ) {
387	<	sprintf( painCave.errMsg,
388	<	"OOPSE is switching from the default Non-Orthorhombic\n"
389	<	"\tto the faster Orthorhombic periodic boundary computations.\n"
390	<	"\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();
386	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
387	>	oneTwoInteractions_.addPair(a, b);
388	>	} else {
389	>	excludedInteractions_.addPair(a, b);
390	>	}
391		}
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	–	}
392
393	<	void SimInfo::calcBoxL( void ){
393	>	for (bend= mol->beginBend(bendIter); bend != NULL;
394	>	bend = mol->nextBend(bendIter)) {
395
396	<	double dx, dy, dz, dsq;
396	>	a = bend->getAtomA()->getGlobalIndex();
397	>	b = bend->getAtomB()->getGlobalIndex();
398	>	c = bend->getAtomC()->getGlobalIndex();
399	>
400	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
401	>	oneTwoInteractions_.addPair(a, b);
402	>	oneTwoInteractions_.addPair(b, c);
403	>	} else {
404	>	excludedInteractions_.addPair(a, b);
405	>	excludedInteractions_.addPair(b, c);
406	>	}
407
408	<	// boxVol = Determinant of Hmat
408	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
409	>	oneThreeInteractions_.addPair(a, c);
410	>	} else {
411	>	excludedInteractions_.addPair(a, c);
412	>	}
413	>	}
414
415	<	boxVol = matDet3( Hmat );
415	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
416	>	torsion = mol->nextTorsion(torsionIter)) {
417
418	<	// boxLx
419	<
420	<	dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
421	<	dsq = dx*dx + dy*dy + dz*dz;
237	<	boxL[0] = sqrt( dsq );
238	<	//maxCutoff = 0.5 * boxL[0];
418	>	a = torsion->getAtomA()->getGlobalIndex();
419	>	b = torsion->getAtomB()->getGlobalIndex();
420	>	c = torsion->getAtomC()->getGlobalIndex();
421	>	d = torsion->getAtomD()->getGlobalIndex();
422
423	<	// boxLy
424	<
425	<	dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
426	<	dsq = dx*dx + dy*dy + dz*dz;
427	<	boxL[1] = sqrt( dsq );
428	<	//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
423	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
424	>	oneTwoInteractions_.addPair(a, b);
425	>	oneTwoInteractions_.addPair(b, c);
426	>	oneTwoInteractions_.addPair(c, d);
427	>	} else {
428	>	excludedInteractions_.addPair(a, b);
429	>	excludedInteractions_.addPair(b, c);
430	>	excludedInteractions_.addPair(c, d);
431	>	}
432
433	+	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
434	+	oneThreeInteractions_.addPair(a, c);
435	+	oneThreeInteractions_.addPair(b, d);
436	+	} else {
437	+	excludedInteractions_.addPair(a, c);
438	+	excludedInteractions_.addPair(b, d);
439	+	}
440
441	<	// boxLz
442	<
443	<	dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
444	<	dsq = dx*dx + dy*dy + dz*dz;
445	<	boxL[2] = sqrt( dsq );
446	<	//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
441	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
442	>	oneFourInteractions_.addPair(a, d);
443	>	} else {
444	>	excludedInteractions_.addPair(a, d);
445	>	}
446	>	}
447
448	<	//calculate the max cutoff
449	<	maxCutoff =  calcMaxCutOff();
257	<
258	<	checkCutOffs();
448	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
449	>	inversion = mol->nextInversion(inversionIter)) {
450
451	<	}
451	>	a = inversion->getAtomA()->getGlobalIndex();
452	>	b = inversion->getAtomB()->getGlobalIndex();
453	>	c = inversion->getAtomC()->getGlobalIndex();
454	>	d = inversion->getAtomD()->getGlobalIndex();
455
456	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
457	+	oneTwoInteractions_.addPair(a, b);
458	+	oneTwoInteractions_.addPair(a, c);
459	+	oneTwoInteractions_.addPair(a, d);
460	+	} else {
461	+	excludedInteractions_.addPair(a, b);
462	+	excludedInteractions_.addPair(a, c);
463	+	excludedInteractions_.addPair(a, d);
464	+	}
465
466	<	double SimInfo::calcMaxCutOff(){
466	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
467	>	oneThreeInteractions_.addPair(b, c);
468	>	oneThreeInteractions_.addPair(b, d);
469	>	oneThreeInteractions_.addPair(c, d);
470	>	} else {
471	>	excludedInteractions_.addPair(b, c);
472	>	excludedInteractions_.addPair(b, d);
473	>	excludedInteractions_.addPair(c, d);
474	>	}
475	>	}
476
477	<	double ri[3], rj[3], rk[3];
478	<	double rij[3], rjk[3], rki[3];
479	<	double minDist;
477	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
478	>	rb = mol->nextRigidBody(rbIter)) {
479	>	vector<Atom*> atoms = rb->getAtoms();
480	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
481	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
482	>	a = atoms[i]->getGlobalIndex();
483	>	b = atoms[j]->getGlobalIndex();
484	>	excludedInteractions_.addPair(a, b);
485	>	}
486	>	}
487	>	}
488
489	<	ri[0] = Hmat[0][0];
270	<	ri[1] = Hmat[1][0];
271	<	ri[2] = Hmat[2][0];
489	>	}
490
491	<	rj[0] = Hmat[0][1];
492	<	rj[1] = Hmat[1][1];
493	<	rj[2] = Hmat[2][1];
491	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
492	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
493	>	vector<Bond*>::iterator bondIter;
494	>	vector<Bend*>::iterator bendIter;
495	>	vector<Torsion*>::iterator torsionIter;
496	>	vector<Inversion*>::iterator inversionIter;
497	>	Bond* bond;
498	>	Bend* bend;
499	>	Torsion* torsion;
500	>	Inversion* inversion;
501	>	int a;
502	>	int b;
503	>	int c;
504	>	int d;
505
506	<	rk[0] = Hmat[0][2];
507	<	rk[1] = Hmat[1][2];
508	<	rk[2] = Hmat[2][2];
506	>	map<int, set<int> > atomGroups;
507	>	Molecule::RigidBodyIterator rbIter;
508	>	RigidBody* rb;
509	>	Molecule::IntegrableObjectIterator ii;
510	>	StuntDouble* integrableObject;
511
512	<	crossProduct3(ri, rj, rij);
513	<	distXY = dotProduct3(rk,rij) / norm3(rij);
512	>	for (integrableObject = mol->beginIntegrableObject(ii);
513	>	integrableObject != NULL;
514	>	integrableObject = mol->nextIntegrableObject(ii)) {
515	>
516	>	if (integrableObject->isRigidBody()) {
517	>	rb = static_cast<RigidBody*>(integrableObject);
518	>	vector<Atom*> atoms = rb->getAtoms();
519	>	set<int> rigidAtoms;
520	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
521	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
522	>	}
523	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
524	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
525	>	}
526	>	} else {
527	>	set<int> oneAtomSet;
528	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
529	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
530	>	}
531	>	}
532
533	<	crossProduct3(rj,rk, rjk);
534	<	distYZ = dotProduct3(ri,rjk) / norm3(rjk);
533	>	for (bond= mol->beginBond(bondIter); bond != NULL;
534	>	bond = mol->nextBond(bondIter)) {
535	>
536	>	a = bond->getAtomA()->getGlobalIndex();
537	>	b = bond->getAtomB()->getGlobalIndex();
538	>
539	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
540	>	oneTwoInteractions_.removePair(a, b);
541	>	} else {
542	>	excludedInteractions_.removePair(a, b);
543	>	}
544	>	}
545
546	<	crossProduct3(rk,ri, rki);
547	<	distZX = dotProduct3(rj,rki) / norm3(rki);
546	>	for (bend= mol->beginBend(bendIter); bend != NULL;
547	>	bend = mol->nextBend(bendIter)) {
548
549	<	minDist = min(min(distXY, distYZ), distZX);
550	<	return minDist/2;
551	<
552	<	}
549	>	a = bend->getAtomA()->getGlobalIndex();
550	>	b = bend->getAtomB()->getGlobalIndex();
551	>	c = bend->getAtomC()->getGlobalIndex();
552	>
553	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
554	>	oneTwoInteractions_.removePair(a, b);
555	>	oneTwoInteractions_.removePair(b, c);
556	>	} else {
557	>	excludedInteractions_.removePair(a, b);
558	>	excludedInteractions_.removePair(b, c);
559	>	}
560
561	<	void SimInfo::wrapVector( double thePos[3] ){
561	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
562	>	oneThreeInteractions_.removePair(a, c);
563	>	} else {
564	>	excludedInteractions_.removePair(a, c);
565	>	}
566	>	}
567
568	<	int i;
569	<	double scaled[3];
568	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
569	>	torsion = mol->nextTorsion(torsionIter)) {
570
571	<	if( !orthoRhombic ){
572	<	// calc the scaled coordinates.
571	>	a = torsion->getAtomA()->getGlobalIndex();
572	>	b = torsion->getAtomB()->getGlobalIndex();
573	>	c = torsion->getAtomC()->getGlobalIndex();
574	>	d = torsion->getAtomD()->getGlobalIndex();
575
576	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
577	+	oneTwoInteractions_.removePair(a, b);
578	+	oneTwoInteractions_.removePair(b, c);
579	+	oneTwoInteractions_.removePair(c, d);
580	+	} else {
581	+	excludedInteractions_.removePair(a, b);
582	+	excludedInteractions_.removePair(b, c);
583	+	excludedInteractions_.removePair(c, d);
584	+	}
585
586	<	matVecMul3(HmatInv, thePos, scaled);
587	<
588	<	for(i=0; i<3; i++)
589	<	scaled[i] -= roundMe(scaled[i]);
590	<
591	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
592	<
311	<	matVecMul3(Hmat, scaled, thePos);
586	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
587	>	oneThreeInteractions_.removePair(a, c);
588	>	oneThreeInteractions_.removePair(b, d);
589	>	} else {
590	>	excludedInteractions_.removePair(a, c);
591	>	excludedInteractions_.removePair(b, d);
592	>	}
593
594	<	}
595	<	else{
596	<	// calc the scaled coordinates.
597	<
598	<	for(i=0; i<3; i++)
599	<	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	<	}
594	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
595	>	oneFourInteractions_.removePair(a, d);
596	>	} else {
597	>	excludedInteractions_.removePair(a, d);
598	>	}
599	>	}
600
601	+	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
602	+	inversion = mol->nextInversion(inversionIter)) {
603
604	<	int SimInfo::getNDF(){
605	<	int ndf_local;
604	>	a = inversion->getAtomA()->getGlobalIndex();
605	>	b = inversion->getAtomB()->getGlobalIndex();
606	>	c = inversion->getAtomC()->getGlobalIndex();
607	>	d = inversion->getAtomD()->getGlobalIndex();
608
609	<	ndf_local = 0;
610	<
611	<	for(int i = 0; i < integrableObjects.size(); i++){
612	<	ndf_local += 3;
613	<	if (integrableObjects[i]->isDirectional()) {
614	<	if (integrableObjects[i]->isLinear())
615	<	ndf_local += 2;
616	<	else
617	<	ndf_local += 3;
609	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
610	>	oneTwoInteractions_.removePair(a, b);
611	>	oneTwoInteractions_.removePair(a, c);
612	>	oneTwoInteractions_.removePair(a, d);
613	>	} else {
614	>	excludedInteractions_.removePair(a, b);
615	>	excludedInteractions_.removePair(a, c);
616	>	excludedInteractions_.removePair(a, d);
617	>	}
618	>
619	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
620	>	oneThreeInteractions_.removePair(b, c);
621	>	oneThreeInteractions_.removePair(b, d);
622	>	oneThreeInteractions_.removePair(c, d);
623	>	} else {
624	>	excludedInteractions_.removePair(b, c);
625	>	excludedInteractions_.removePair(b, d);
626	>	excludedInteractions_.removePair(c, d);
627	>	}
628		}
629	+
630	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
631	+	rb = mol->nextRigidBody(rbIter)) {
632	+	vector<Atom*> atoms = rb->getAtoms();
633	+	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
634	+	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
635	+	a = atoms[i]->getGlobalIndex();
636	+	b = atoms[j]->getGlobalIndex();
637	+	excludedInteractions_.removePair(a, b);
638	+	}
639	+	}
640	+	}
641	+
642		}
643	+
644	+
645	+	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
646	+	int curStampId;
647	+
648	+	//index from 0
649	+	curStampId = moleculeStamps_.size();
650
651	<	// n_constraints is local, so subtract them on each processor:
651	>	moleculeStamps_.push_back(molStamp);
652	>	molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
653	>	}
654
655	<	ndf_local -= n_constraints;
655	>
656	>	/**
657	>	* update
658	>	*
659	>	*  Performs the global checks and variable settings after the
660	>	*  objects have been created.
661	>	*
662	>	*/
663	>	void SimInfo::update() {
664	>	setupSimVariables();
665	>	calcNdf();
666	>	calcNdfRaw();
667	>	calcNdfTrans();
668	>	}
669	>
670	>	/**
671	>	* getSimulatedAtomTypes
672	>	*
673	>	* Returns an STL set of AtomType* that are actually present in this
674	>	* simulation.  Must query all processors to assemble this information.
675	>	*
676	>	*/
677	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
678	>	SimInfo::MoleculeIterator mi;
679	>	Molecule* mol;
680	>	Molecule::AtomIterator ai;
681	>	Atom* atom;
682	>	set<AtomType*> atomTypes;
683	>
684	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
685	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
686	>	atomTypes.insert(atom->getAtomType());
687	>	}
688	>	}
689
690		#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
691
692	<	// nZconstraints is global, as are the 3 COM translations for the
693	<	// entire system:
692	>	// loop over the found atom types on this processor, and add their
693	>	// numerical idents to a vector:
694
695	<	ndf = ndf - 3 - nZconstraints;
695	>	vector<int> foundTypes;
696	>	set<AtomType*>::iterator i;
697	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
698	>	foundTypes.push_back( (*i)->getIdent() );
699
700	<	return ndf;
701	<	}
700	>	// count_local holds the number of found types on this processor
701	>	int count_local = foundTypes.size();
702
703	<	int SimInfo::getNDFraw() {
704	<	int ndfRaw_local;
703	>	// count holds the total number of found types on all processors
704	>	// (some will be redundant with the ones found locally):
705	>	int count;
706	>	MPI::COMM_WORLD.Allreduce(&count_local, &count, 1, MPI::INT, MPI::SUM);
707
708	<	// Raw degrees of freedom that we have to set
709	<	ndfRaw_local = 0;
708	>	// create a vector to hold the globally found types, and resize it:
709	>	vector<int> ftGlobal;
710	>	ftGlobal.resize(count);
711	>	vector<int> counts;
712
713	<	for(int i = 0; i < integrableObjects.size(); i++){
714	<	ndfRaw_local += 3;
715	<	if (integrableObjects[i]->isDirectional()) {
716	<	if (integrableObjects[i]->isLinear())
717	<	ndfRaw_local += 2;
718	<	else
379	<	ndfRaw_local += 3;
380	<	}
381	<	}
713	>	int nproc = MPI::COMM_WORLD.Get_size();
714	>	counts.resize(nproc);
715	>	vector<int> disps;
716	>	disps.resize(nproc);
717	>
718	>	// now spray out the foundTypes to all the other processors:
719
720	<	#ifdef IS_MPI
721	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
722	<	#else
723	<	ndfRaw = ndfRaw_local;
720	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
721	>	&ftGlobal[0], &counts[0], &disps[0], MPI::INT);
722	>
723	>	// foundIdents is a stl set, so inserting an already found ident
724	>	// will have no effect.
725	>	set<int> foundIdents;
726	>	vector<int>::iterator j;
727	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
728	>	foundIdents.insert((*j));
729	>
730	>	// now iterate over the foundIdents and get the actual atom types
731	>	// that correspond to these:
732	>	set<int>::iterator it;
733	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
734	>	atomTypes.insert( forceField_->getAtomType((*it)) );
735	>
736		#endif
737	+
738	+	return atomTypes;
739	+	}
740
741	<	return ndfRaw;
742	<	}
741	>	void SimInfo::setupSimVariables() {
742	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
743	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
744	>	calcBoxDipole_ = false;
745	>	if ( simParams_->haveAccumulateBoxDipole() )
746	>	if ( simParams_->getAccumulateBoxDipole() ) {
747	>	calcBoxDipole_ = true;
748	>	}
749
750	<	int SimInfo::getNDFtranslational() {
751	<	int ndfTrans_local;
750	>	set<AtomType*>::iterator i;
751	>	set<AtomType*> atomTypes;
752	>	atomTypes = getSimulatedAtomTypes();
753	>	int usesElectrostatic = 0;
754	>	int usesMetallic = 0;
755	>	int usesDirectional = 0;
756	>	//loop over all of the atom types
757	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
758	>	usesElectrostatic |= (*i)->isElectrostatic();
759	>	usesMetallic |= (*i)->isMetal();
760	>	usesDirectional |= (*i)->isDirectional();
761	>	}
762
763	<	ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
763	>	#ifdef IS_MPI
764	>	int temp;
765	>	temp = usesDirectional;
766	>	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
767
768	+	temp = usesMetallic;
769	+	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
770
771	<	#ifdef IS_MPI
772	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
400	<	#else
401	<	ndfTrans = ndfTrans_local;
771	>	temp = usesElectrostatic;
772	>	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
773		#endif
774	+	fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;
775	+	fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
776	+	fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
777	+	fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
778	+	fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
779	+	fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
780	+	}
781
782	<	ndfTrans = ndfTrans - 3 - nZconstraints;
782	>	void SimInfo::setupFortran() {
783	>	int isError;
784	>	int nExclude, nOneTwo, nOneThree, nOneFour;
785	>	vector<int> fortranGlobalGroupMembership;
786	>
787	>	isError = 0;
788
789	<	return ndfTrans;
790	<	}
789	>	//globalGroupMembership_ is filled by SimCreator
790	>	for (int i = 0; i < nGlobalAtoms_; i++) {
791	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
792	>	}
793
794	<	int SimInfo::getTotIntegrableObjects() {
795	<	int nObjs_local;
796	<	int nObjs;
794	>	//calculate mass ratio of cutoff group
795	>	vector<RealType> mfact;
796	>	SimInfo::MoleculeIterator mi;
797	>	Molecule* mol;
798	>	Molecule::CutoffGroupIterator ci;
799	>	CutoffGroup* cg;
800	>	Molecule::AtomIterator ai;
801	>	Atom* atom;
802	>	RealType totalMass;
803
804	<	nObjs_local =  integrableObjects.size();
804	>	//to avoid memory reallocation, reserve enough space for mfact
805	>	mfact.reserve(getNCutoffGroups());
806	>
807	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
808	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
809
810	+	totalMass = cg->getMass();
811	+	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
812	+	// Check for massless groups - set mfact to 1 if true
813	+	if (totalMass != 0)
814	+	mfact.push_back(atom->getMass()/totalMass);
815	+	else
816	+	mfact.push_back( 1.0 );
817	+	}
818	+	}
819	+	}
820
821	<	#ifdef IS_MPI
822	<	MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
823	<	#else
419	<	nObjs = nObjs_local;
420	<	#endif
821	>	//fill ident array of local atoms (it is actually ident of
822	>	//AtomType, it is so confusing !!!)
823	>	vector<int> identArray;
824
825	+	//to avoid memory reallocation, reserve enough space identArray
826	+	identArray.reserve(getNAtoms());
827	+
828	+	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
829	+	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
830	+	identArray.push_back(atom->getIdent());
831	+	}
832	+	}
833
834	<	return nObjs;
835	<	}
834	>	//fill molMembershipArray
835	>	//molMembershipArray is filled by SimCreator
836	>	vector<int> molMembershipArray(nGlobalAtoms_);
837	>	for (int i = 0; i < nGlobalAtoms_; i++) {
838	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
839	>	}
840	>
841	>	//setup fortran simulation
842
843	<	void SimInfo::refreshSim(){
843	>	nExclude = excludedInteractions_.getSize();
844	>	nOneTwo = oneTwoInteractions_.getSize();
845	>	nOneThree = oneThreeInteractions_.getSize();
846	>	nOneFour = oneFourInteractions_.getSize();
847
848	<	simtype fInfo;
849	<	int isError;
850	<	int n_global;
851	<	int* excl;
848	>	int* excludeList = excludedInteractions_.getPairList();
849	>	int* oneTwoList = oneTwoInteractions_.getPairList();
850	>	int* oneThreeList = oneThreeInteractions_.getPairList();
851	>	int* oneFourList = oneFourInteractions_.getPairList();
852
853	<	fInfo.dielect = 0.0;
853	>	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
854	>	&nExclude, excludeList,
855	>	&nOneTwo, oneTwoList,
856	>	&nOneThree, oneThreeList,
857	>	&nOneFour, oneFourList,
858	>	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
859	>	&fortranGlobalGroupMembership[0], &isError);
860	>
861	>	if( isError ){
862	>
863	>	sprintf( painCave.errMsg,
864	>	"There was an error setting the simulation information in fortran.\n" );
865	>	painCave.isFatal = 1;
866	>	painCave.severity = OPENMD_ERROR;
867	>	simError();
868	>	}
869	>
870	>
871	>	sprintf( checkPointMsg,
872	>	"succesfully sent the simulation information to fortran.\n");
873	>
874	>	errorCheckPoint();
875	>
876	>	// Setup number of neighbors in neighbor list if present
877	>	if (simParams_->haveNeighborListNeighbors()) {
878	>	int nlistNeighbors = simParams_->getNeighborListNeighbors();
879	>	setNeighbors(&nlistNeighbors);
880	>	}
881	>
882	>	#ifdef IS_MPI
883	>	//SimInfo is responsible for creating localToGlobalAtomIndex and
884	>	//localToGlobalGroupIndex
885	>	vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
886	>	vector<int> localToGlobalCutoffGroupIndex;
887	>	mpiSimData parallelData;
888
889	<	if( useDipoles ){
436	<	if( useReactionField )fInfo.dielect = dielectric;
437	<	}
889	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
890
891	<	fInfo.SIM_uses_PBC = usePBC;
891	>	//local index(index in DataStorge) of atom is important
892	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
893	>	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
894	>	}
895
896	<	if (useSticky || useDipoles || useGayBerne || useShapes) {
897	<	useDirectionalAtoms = 1;
898	<	fInfo.SIM_uses_DirectionalAtoms = useDirectionalAtoms;
899	<	}
896	>	//local index of cutoff group is trivial, it only depends on the order of travesing
897	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
898	>	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
899	>	}
900	>
901	>	}
902
903	<	fInfo.SIM_uses_LennardJones = useLennardJones;
903	>	//fill up mpiSimData struct
904	>	parallelData.nMolGlobal = getNGlobalMolecules();
905	>	parallelData.nMolLocal = getNMolecules();
906	>	parallelData.nAtomsGlobal = getNGlobalAtoms();
907	>	parallelData.nAtomsLocal = getNAtoms();
908	>	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
909	>	parallelData.nGroupsLocal = getNCutoffGroups();
910	>	parallelData.myNode = worldRank;
911	>	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
912
913	<	if (useCharges || useDipoles) {
914	<	useElectrostatics = 1;
915	<	fInfo.SIM_uses_Electrostatics = useElectrostatics;
916	<	}
913	>	//pass mpiSimData struct and index arrays to fortran
914	>	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
915	>	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
916	>	&localToGlobalCutoffGroupIndex[0], &isError);
917
918	<	fInfo.SIM_uses_Charges = useCharges;
919	<	fInfo.SIM_uses_Dipoles = useDipoles;
920	<	fInfo.SIM_uses_Sticky = useSticky;
921	<	fInfo.SIM_uses_GayBerne = useGayBerne;
922	<	fInfo.SIM_uses_EAM = useEAM;
923	<	fInfo.SIM_uses_Shapes = useShapes;
459	<	fInfo.SIM_uses_FLARB = useFLARB;
460	<	fInfo.SIM_uses_RF = useReactionField;
918	>	if (isError) {
919	>	sprintf(painCave.errMsg,
920	>	"mpiRefresh errror: fortran didn't like something we gave it.\n");
921	>	painCave.isFatal = 1;
922	>	simError();
923	>	}
924
925	<	n_exclude = excludes->getSize();
926	<	excl = excludes->getFortranArray();
464	<
465	<	#ifdef IS_MPI
466	<	n_global = mpiSim->getNAtomsGlobal();
467	<	#else
468	<	n_global = n_atoms;
925	>	sprintf(checkPointMsg, " mpiRefresh successful.\n");
926	>	errorCheckPoint();
927		#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);
928
929	<	if( isError ){
930	<
931	<	sprintf( painCave.errMsg,
932	<	"There was an error setting the simulation information in fortran.\n" );
933	<	painCave.isFatal = 1;
934	<	painCave.severity = OOPSE_ERROR;
935	<	simError();
929	>	initFortranFF(&isError);
930	>	if (isError) {
931	>	sprintf(painCave.errMsg,
932	>	"initFortranFF errror: fortran didn't like something we gave it.\n");
933	>	painCave.isFatal = 1;
934	>	simError();
935	>	}
936	>	fortranInitialized_ = true;
937		}
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	–	}
938
939	<	void SimInfo::setDefaultRcut( double theRcut ){
940	<
941	<	haveRcut = 1;
504	<	rCut = theRcut;
505	<	rList = rCut + 1.0;
506	<
507	<	notifyFortranCutoffs( &rCut, &rSw, &rList );
508	<	}
939	>	void SimInfo::addProperty(GenericData* genData) {
940	>	properties_.addProperty(genData);
941	>	}
942
943	<	void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
943	>	void SimInfo::removeProperty(const string& propName) {
944	>	properties_.removeProperty(propName);
945	>	}
946
947	<	rSw = theRsw;
948	<	setDefaultRcut( theRcut );
949	<	}
947	>	void SimInfo::clearProperties() {
948	>	properties_.clearProperties();
949	>	}
950
951	+	vector<string> SimInfo::getPropertyNames() {
952	+	return properties_.getPropertyNames();
953	+	}
954	+
955	+	vector<GenericData*> SimInfo::getProperties() {
956	+	return properties_.getProperties();
957	+	}
958
959	<	void SimInfo::checkCutOffs( void ){
960	<
961	<	if( boxIsInit ){
962	<
963	<	//we need to check cutOffs against the box
964	<
965	<	if( rCut > maxCutoff ){
966	<	sprintf( painCave.errMsg,
967	<	"cutoffRadius is too large for the current periodic box.\n"
968	<	"\tCurrent Value of cutoffRadius = %G at time %G\n "
969	<	"\tThis is larger than half of at least one of the\n"
970	<	"\tperiodic box vectors.  Right now, the Box matrix is:\n"
971	<	"\n"
972	<	"\t[ %G %G %G ]\n"
973	<	"\t[ %G %G %G ]\n"
974	<	"\t[ %G %G %G ]\n",
975	<	rCut, currentTime,
976	<	Hmat[0][0], Hmat[0][1], Hmat[0][2],
977	<	Hmat[1][0], Hmat[1][1], Hmat[1][2],
978	<	Hmat[2][0], Hmat[2][1], Hmat[2][2]);
979	<	painCave.severity = OOPSE_ERROR;
980	<	painCave.isFatal = 1;
981	<	simError();
959	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
960	>	return properties_.getPropertyByName(propName);
961	>	}
962	>
963	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
964	>	if (sman_ == sman) {
965	>	return;
966	>	}
967	>	delete sman_;
968	>	sman_ = sman;
969	>
970	>	Molecule* mol;
971	>	RigidBody* rb;
972	>	Atom* atom;
973	>	SimInfo::MoleculeIterator mi;
974	>	Molecule::RigidBodyIterator rbIter;
975	>	Molecule::AtomIterator atomIter;;
976	>
977	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
978	>
979	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
980	>	atom->setSnapshotManager(sman_);
981	>	}
982	>
983	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
984	>	rb->setSnapshotManager(sman_);
985	>	}
986		}
987	<	} 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();
987	>
988		}
550	–
551	–	}
989
990	<	void SimInfo::addProperty(GenericData* prop){
990	>	Vector3d SimInfo::getComVel(){
991	>	SimInfo::MoleculeIterator i;
992	>	Molecule* mol;
993
994	<	map<string, GenericData*>::iterator result;
995	<	result = properties.find(prop->getID());
557	<
558	<	//we can't simply use  properties[prop->getID()] = prop,
559	<	//it will cause memory leak if we already contain a propery which has the same name of prop
560	<
561	<	if(result != properties.end()){
994	>	Vector3d comVel(0.0);
995	>	RealType totalMass = 0.0;
996
997	<	delete (*result).second;
998	<	(*result).second = prop;
999	<
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	>	#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	>	return comVel;
1014		}
567	–	else{
1015
1016	<	properties[prop->getID()] = prop;
1016	>	Vector3d SimInfo::getCom(){
1017	>	SimInfo::MoleculeIterator i;
1018	>	Molecule* mol;
1019
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	+	#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,3.0/2.0)*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,3.0/2.0)*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 1536 by gezelter, Wed Jan 5 14:49:05 2011 UTC

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