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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 1744 by gezelter, Tue Jun 5 18:07:08 2012 UTC

#	Line 1 | Line 1
1	<	#include <stdlib.h>
2	<	#include <string.h>
3	<	#include <math.h>
1	>	/*
2	>	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	>	*
4	>	* The University of Notre Dame grants you ("Licensee") a
5	>	* non-exclusive, royalty free, license to use, modify and
6	>	* redistribute this software in source and binary code form, provided
7	>	* that the following conditions are met:
8	>	*
9	>	* 1. Redistributions of source code must retain the above copyright
10	>	*    notice, this list of conditions and the following disclaimer.
11	>	*
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13	>	*    notice, this list of conditions and the following disclaimer in the
14	>	*    documentation and/or other materials provided with the
15	>	*    distribution.
16	>	*
17	>	* This software is provided "AS IS," without a warranty of any
18	>	* kind. All express or implied conditions, representations and
19	>	* warranties, including any implied warranty of merchantability,
20	>	* fitness for a particular purpose or non-infringement, are hereby
21	>	* excluded.  The University of Notre Dame and its licensors shall not
22	>	* be liable for any damages suffered by licensee as a result of
23	>	* using, modifying or distributing the software or its
24	>	* derivatives. In no event will the University of Notre Dame or its
25	>	* licensors be liable for any lost revenue, profit or data, or for
26	>	* direct, indirect, special, consequential, incidental or punitive
27	>	* damages, however caused and regardless of the theory of liability,
28	>	* arising out of the use of or inability to use software, even if the
29	>	* University of Notre Dame has been advised of the possibility of
30	>	* such damages.
31	>	*
32	>	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	>	* research, please cite the appropriate papers when you publish your
34	>	* work.  Good starting points are:
35	>	*
36	>	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	>	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	>	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	>	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	>	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	>	*/
42	>
43	>	/**
44	>	* @file SimInfo.cpp
45	>	* @author    tlin
46	>	* @date  11/02/2004
47	>	* @version 1.0
48	>	*/
49
50	<	#include <iostream>
51	<	using namespace std;
50	>	#include <algorithm>
51	>	#include <set>
52	>	#include <map>
53
54		#include "brains/SimInfo.hpp"
55	<	#define __C
56	<	#include "brains/fSimulation.h"
55	>	#include "math/Vector3.hpp"
56	>	#include "primitives/Molecule.hpp"
57	>	#include "primitives/StuntDouble.hpp"
58	>	#include "utils/MemoryUtils.hpp"
59		#include "utils/simError.h"
60	<	#include "UseTheForce/DarkSide/simulation_interface.h"
61	<	#include "UseTheForce/notifyCutoffs_interface.h"
62	<
63	<	//#include "UseTheForce/fortranWrappers.hpp"
16	<
17	<	#include "math/MatVec3.h"
18	<
60	>	#include "selection/SelectionManager.hpp"
61	>	#include "io/ForceFieldOptions.hpp"
62	>	#include "brains/ForceField.hpp"
63	>	#include "nonbonded/SwitchingFunction.hpp"
64		#ifdef IS_MPI
65	<	#include "brains/mpiSimulation.hpp"
65	>	#include <mpi.h>
66		#endif
67
68	<	inline double roundMe( double x ){
69	<	return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
70	<	}
71	<
72	<	inline double min( double a, double b ){
73	<	return (a < b ) ? a : b;
74	<	}
68	>	using namespace std;
69	>	namespace OpenMD {
70	>
71	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
72	>	forceField_(ff), simParams_(simParams),
73	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
74	>	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
75	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), nGlobalFluctuatingCharges_(0),
76	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
77	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
78	>	nConstraints_(0), nFluctuatingCharges_(0), sman_(NULL), topologyDone_(false),
79	>	calcBoxDipole_(false), useAtomicVirial_(true) {
80	>
81	>	MoleculeStamp* molStamp;
82	>	int nMolWithSameStamp;
83	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
84	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
85	>	CutoffGroupStamp* cgStamp;
86	>	RigidBodyStamp* rbStamp;
87	>	int nRigidAtoms = 0;
88	>
89	>	vector<Component*> components = simParams->getComponents();
90	>
91	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
92	>	molStamp = (*i)->getMoleculeStamp();
93	>	nMolWithSameStamp = (*i)->getNMol();
94	>
95	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
96	>
97	>	//calculate atoms in molecules
98	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
99	>
100	>	//calculate atoms in cutoff groups
101	>	int nAtomsInGroups = 0;
102	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
103	>
104	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
105	>	cgStamp = molStamp->getCutoffGroupStamp(j);
106	>	nAtomsInGroups += cgStamp->getNMembers();
107	>	}
108	>
109	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
110	>
111	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
112	>
113	>	//calculate atoms in rigid bodies
114	>	int nAtomsInRigidBodies = 0;
115	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
116	>
117	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
118	>	rbStamp = molStamp->getRigidBodyStamp(j);
119	>	nAtomsInRigidBodies += rbStamp->getNMembers();
120	>	}
121	>
122	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
123	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
124	>
125	>	}
126	>
127	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
128	>	//group therefore the total number of cutoff groups in the system is
129	>	//equal to the total number of atoms minus number of atoms belong to
130	>	//cutoff group defined in meta-data file plus the number of cutoff
131	>	//groups defined in meta-data file
132
133	<	SimInfo* currentInfo;
133	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
134	>
135	>	//every free atom (atom does not belong to rigid bodies) is an
136	>	//integrable object therefore the total number of integrable objects
137	>	//in the system is equal to the total number of atoms minus number of
138	>	//atoms belong to rigid body defined in meta-data file plus the number
139	>	//of rigid bodies defined in meta-data file
140	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
141	>	+ nGlobalRigidBodies_;
142	>
143	>	nGlobalMols_ = molStampIds_.size();
144	>	molToProcMap_.resize(nGlobalMols_);
145	>	}
146	>
147	>	SimInfo::~SimInfo() {
148	>	map<int, Molecule*>::iterator i;
149	>	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
150	>	delete i->second;
151	>	}
152	>	molecules_.clear();
153	>
154	>	delete sman_;
155	>	delete simParams_;
156	>	delete forceField_;
157	>	}
158
33	–	SimInfo::SimInfo(){
159
160	<	n_constraints = 0;
161	<	nZconstraints = 0;
162	<	n_oriented = 0;
163	<	n_dipoles = 0;
164	<	ndf = 0;
165	<	ndfRaw = 0;
166	<	nZconstraints = 0;
167	<	the_integrator = NULL;
168	<	setTemp = 0;
169	<	thermalTime = 0.0;
170	<	currentTime = 0.0;
171	<	rCut = 0.0;
172	<	rSw = 0.0;
173	<
174	<	haveRcut = 0;
175	<	haveRsw = 0;
176	<	boxIsInit = 0;
160	>	bool SimInfo::addMolecule(Molecule* mol) {
161	>	MoleculeIterator i;
162	>
163	>	i = molecules_.find(mol->getGlobalIndex());
164	>	if (i == molecules_.end() ) {
165	>
166	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
167	>
168	>	nAtoms_ += mol->getNAtoms();
169	>	nBonds_ += mol->getNBonds();
170	>	nBends_ += mol->getNBends();
171	>	nTorsions_ += mol->getNTorsions();
172	>	nInversions_ += mol->getNInversions();
173	>	nRigidBodies_ += mol->getNRigidBodies();
174	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
175	>	nCutoffGroups_ += mol->getNCutoffGroups();
176	>	nConstraints_ += mol->getNConstraintPairs();
177	>
178	>	addInteractionPairs(mol);
179	>
180	>	return true;
181	>	} else {
182	>	return false;
183	>	}
184	>	}
185
186	<	resetTime = 1e99;
186	>	bool SimInfo::removeMolecule(Molecule* mol) {
187	>	MoleculeIterator i;
188	>	i = molecules_.find(mol->getGlobalIndex());
189
190	<	orthoRhombic = 0;
56	<	orthoTolerance = 1E-6;
57	<	useInitXSstate = true;
190	>	if (i != molecules_.end() ) {
191
192	<	usePBC = 0;
193	<	useDirectionalAtoms = 0;
194	<	useLennardJones = 0;
195	<	useElectrostatics = 0;
196	<	useCharges = 0;
197	<	useDipoles = 0;
198	<	useSticky = 0;
199	<	useGayBerne = 0;
200	<	useEAM = 0;
201	<	useShapes = 0;
202	<	useFLARB = 0;
192	>	assert(mol == i->second);
193	>
194	>	nAtoms_ -= mol->getNAtoms();
195	>	nBonds_ -= mol->getNBonds();
196	>	nBends_ -= mol->getNBends();
197	>	nTorsions_ -= mol->getNTorsions();
198	>	nInversions_ -= mol->getNInversions();
199	>	nRigidBodies_ -= mol->getNRigidBodies();
200	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
201	>	nCutoffGroups_ -= mol->getNCutoffGroups();
202	>	nConstraints_ -= mol->getNConstraintPairs();
203
204	<	useSolidThermInt = 0;
205	<	useLiquidThermInt = 0;
204	>	removeInteractionPairs(mol);
205	>	molecules_.erase(mol->getGlobalIndex());
206
207	<	haveCutoffGroups = false;
208	<
209	<	excludes = Exclude::Instance();
207	>	delete mol;
208	>
209	>	return true;
210	>	} else {
211	>	return false;
212	>	}
213	>	}
214
215	<	myConfiguration = new SimState();
215	>
216	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
217	>	i = molecules_.begin();
218	>	return i == molecules_.end() ? NULL : i->second;
219	>	}
220
221	<	has_minimizer = false;
222	<	the_minimizer =NULL;
221	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
222	>	++i;
223	>	return i == molecules_.end() ? NULL : i->second;
224	>	}
225
83	–	ngroup = 0;
226
227	<	}
227	>	void SimInfo::calcNdf() {
228	>	int ndf_local, nfq_local;
229	>	MoleculeIterator i;
230	>	vector<StuntDouble*>::iterator j;
231	>	vector<Atom*>::iterator k;
232
233	+	Molecule* mol;
234	+	StuntDouble* integrableObject;
235	+	Atom* atom;
236
237	<	SimInfo::~SimInfo(){
237	>	ndf_local = 0;
238	>	nfq_local = 0;
239	>
240	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
241	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
242	>	integrableObject = mol->nextIntegrableObject(j)) {
243
244	<	delete myConfiguration;
244	>	ndf_local += 3;
245
246	<	map<string, GenericData*>::iterator i;
247	<
248	<	for(i = properties.begin(); i != properties.end(); i++)
249	<	delete (*i).second;
246	>	if (integrableObject->isDirectional()) {
247	>	if (integrableObject->isLinear()) {
248	>	ndf_local += 2;
249	>	} else {
250	>	ndf_local += 3;
251	>	}
252	>	}
253	>	}
254	>	for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
255	>	atom = mol->nextFluctuatingCharge(k)) {
256	>	if (atom->isFluctuatingCharge()) {
257	>	nfq_local++;
258	>	}
259	>	}
260	>	}
261	>
262	>	ndfLocal_ = ndf_local;
263	>	cerr << "ndfLocal_ = " << ndfLocal_ << "\n";
264
265	<	}
265	>	// n_constraints is local, so subtract them on each processor
266	>	ndf_local -= nConstraints_;
267
268	<	void SimInfo::setBox(double newBox[3]) {
269	<
270	<	int i, j;
271	<	double tempMat[3][3];
268	>	#ifdef IS_MPI
269	>	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
270	>	MPI_Allreduce(&nfq_local,&nGlobalFluctuatingCharges_,1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
271	>	#else
272	>	ndf_ = ndf_local;
273	>	nGlobalFluctuatingCharges_ = nfq_local;
274	>	#endif
275
276	<	for(i=0; i<3; i++)
277	<	for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
276	>	// nZconstraints_ is global, as are the 3 COM translations for the
277	>	// entire system:
278	>	ndf_ = ndf_ - 3 - nZconstraint_;
279
280	<	tempMat[0][0] = newBox[0];
108	<	tempMat[1][1] = newBox[1];
109	<	tempMat[2][2] = newBox[2];
280	>	}
281
282	<	setBoxM( tempMat );
283	<
284	<	}
285	<
286	<	void SimInfo::setBoxM( double theBox[3][3] ){
282	>	int SimInfo::getFdf() {
283	>	#ifdef IS_MPI
284	>	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
285	>	#else
286	>	fdf_ = fdf_local;
287	>	#endif
288	>	return fdf_;
289	>	}
290
291	<	int i, j;
292	<	double FortranHmat[9]; // to preserve compatibility with Fortran the
293	<	// ordering in the array is as follows:
294	<	// [ 0 3 6 ]
295	<	// [ 1 4 7 ]
296	<	// [ 2 5 8 ]
297	<	double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
298	<
299	<	if( !boxIsInit ) boxIsInit = 1;
300	<
301	<	for(i=0; i < 3; i++)
302	<	for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
303	<
304	<	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];
291	>	unsigned int SimInfo::getNLocalCutoffGroups(){
292	>	int nLocalCutoffAtoms = 0;
293	>	Molecule* mol;
294	>	MoleculeIterator mi;
295	>	CutoffGroup* cg;
296	>	Molecule::CutoffGroupIterator ci;
297	>
298	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
299	>
300	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
301	>	cg = mol->nextCutoffGroup(ci)) {
302	>	nLocalCutoffAtoms += cg->getNumAtom();
303	>
304	>	}
305		}
306	+
307	+	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
308		}
309	+
310	+	void SimInfo::calcNdfRaw() {
311	+	int ndfRaw_local;
312
313	<	setFortranBox(FortranHmat, FortranHmatInv, &orthoRhombic);
314	<
315	<	}
316	<
313	>	MoleculeIterator i;
314	>	vector<StuntDouble*>::iterator j;
315	>	Molecule* mol;
316	>	StuntDouble* integrableObject;
317
318	<	void SimInfo::getBoxM (double theBox[3][3]) {
318	>	// Raw degrees of freedom that we have to set
319	>	ndfRaw_local = 0;
320	>
321	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
322	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
323	>	integrableObject = mol->nextIntegrableObject(j)) {
324
325	<	int i, j;
148	<	for(i=0; i<3; i++)
149	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
150	<	}
325	>	ndfRaw_local += 3;
326
327	+	if (integrableObject->isDirectional()) {
328	+	if (integrableObject->isLinear()) {
329	+	ndfRaw_local += 2;
330	+	} else {
331	+	ndfRaw_local += 3;
332	+	}
333	+	}
334	+
335	+	}
336	+	}
337	+
338	+	#ifdef IS_MPI
339	+	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
340	+	#else
341	+	ndfRaw_ = ndfRaw_local;
342	+	#endif
343	+	}
344
345	<	void SimInfo::scaleBox(double scale) {
346	<	double theBox[3][3];
155	<	int i, j;
345	>	void SimInfo::calcNdfTrans() {
346	>	int ndfTrans_local;
347
348	<	// cerr << "Scaling box by " << scale << "\n";
348	>	ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
349
159	–	for(i=0; i<3; i++)
160	–	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
350
351	<	setBoxM(theBox);
351	>	#ifdef IS_MPI
352	>	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
353	>	#else
354	>	ndfTrans_ = ndfTrans_local;
355	>	#endif
356
357	<	}
357	>	ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
358	>
359	>	}
360
361	<	void SimInfo::calcHmatInv( void ) {
362	<
363	<	int oldOrtho;
364	<	int i,j;
365	<	double smallDiag;
366	<	double tol;
367	<	double sanity[3][3];
368	<
369	<	invertMat3( Hmat, HmatInv );
370	<
371	<	// check to see if Hmat is orthorhombic
372	<
373	<	oldOrtho = orthoRhombic;
361	>	void SimInfo::addInteractionPairs(Molecule* mol) {
362	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
363	>	vector<Bond*>::iterator bondIter;
364	>	vector<Bend*>::iterator bendIter;
365	>	vector<Torsion*>::iterator torsionIter;
366	>	vector<Inversion*>::iterator inversionIter;
367	>	Bond* bond;
368	>	Bend* bend;
369	>	Torsion* torsion;
370	>	Inversion* inversion;
371	>	int a;
372	>	int b;
373	>	int c;
374	>	int d;
375
376	<	smallDiag = fabs(Hmat[0][0]);
377	<	if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
378	<	if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
379	<	tol = smallDiag * orthoTolerance;
376	>	// atomGroups can be used to add special interaction maps between
377	>	// groups of atoms that are in two separate rigid bodies.
378	>	// However, most site-site interactions between two rigid bodies
379	>	// are probably not special, just the ones between the physically
380	>	// bonded atoms.  Interactions *within* a single rigid body should
381	>	// always be excluded.  These are done at the bottom of this
382	>	// function.
383
384	<	orthoRhombic = 1;
385	<
386	<	for (i = 0; i < 3; i++ ) {
387	<	for (j = 0 ; j < 3; j++) {
388	<	if (i != j) {
389	<	if (orthoRhombic) {
390	<	if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
391	<	}
384	>	map<int, set<int> > atomGroups;
385	>	Molecule::RigidBodyIterator rbIter;
386	>	RigidBody* rb;
387	>	Molecule::IntegrableObjectIterator ii;
388	>	StuntDouble* integrableObject;
389	>
390	>	for (integrableObject = mol->beginIntegrableObject(ii);
391	>	integrableObject != NULL;
392	>	integrableObject = mol->nextIntegrableObject(ii)) {
393	>
394	>	if (integrableObject->isRigidBody()) {
395	>	rb = static_cast<RigidBody*>(integrableObject);
396	>	vector<Atom*> atoms = rb->getAtoms();
397	>	set<int> rigidAtoms;
398	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
399	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
400	>	}
401	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
402	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
403	>	}
404	>	} else {
405	>	set<int> oneAtomSet;
406	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
407	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
408		}
409	<	}
410	<	}
409	>	}
410	>
411	>	for (bond= mol->beginBond(bondIter); bond != NULL;
412	>	bond = mol->nextBond(bondIter)) {
413
414	<	if( oldOrtho != orthoRhombic ){
414	>	a = bond->getAtomA()->getGlobalIndex();
415	>	b = bond->getAtomB()->getGlobalIndex();
416
417	<	if( orthoRhombic ) {
418	<	sprintf( painCave.errMsg,
419	<	"OOPSE is switching from the default Non-Orthorhombic\n"
420	<	"\tto the faster Orthorhombic periodic boundary computations.\n"
421	<	"\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();
417	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
418	>	oneTwoInteractions_.addPair(a, b);
419	>	} else {
420	>	excludedInteractions_.addPair(a, b);
421	>	}
422		}
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	–	}
423
424	<	void SimInfo::calcBoxL( void ){
424	>	for (bend= mol->beginBend(bendIter); bend != NULL;
425	>	bend = mol->nextBend(bendIter)) {
426
427	<	double dx, dy, dz, dsq;
427	>	a = bend->getAtomA()->getGlobalIndex();
428	>	b = bend->getAtomB()->getGlobalIndex();
429	>	c = bend->getAtomC()->getGlobalIndex();
430	>
431	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
432	>	oneTwoInteractions_.addPair(a, b);
433	>	oneTwoInteractions_.addPair(b, c);
434	>	} else {
435	>	excludedInteractions_.addPair(a, b);
436	>	excludedInteractions_.addPair(b, c);
437	>	}
438
439	<	// boxVol = Determinant of Hmat
439	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
440	>	oneThreeInteractions_.addPair(a, c);
441	>	} else {
442	>	excludedInteractions_.addPair(a, c);
443	>	}
444	>	}
445
446	<	boxVol = matDet3( Hmat );
446	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
447	>	torsion = mol->nextTorsion(torsionIter)) {
448
449	<	// boxLx
450	<
451	<	dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
452	<	dsq = dx*dx + dy*dy + dz*dz;
237	<	boxL[0] = sqrt( dsq );
238	<	//maxCutoff = 0.5 * boxL[0];
449	>	a = torsion->getAtomA()->getGlobalIndex();
450	>	b = torsion->getAtomB()->getGlobalIndex();
451	>	c = torsion->getAtomC()->getGlobalIndex();
452	>	d = torsion->getAtomD()->getGlobalIndex();
453
454	<	// boxLy
455	<
456	<	dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
457	<	dsq = dx*dx + dy*dy + dz*dz;
458	<	boxL[1] = sqrt( dsq );
459	<	//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
454	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
455	>	oneTwoInteractions_.addPair(a, b);
456	>	oneTwoInteractions_.addPair(b, c);
457	>	oneTwoInteractions_.addPair(c, d);
458	>	} else {
459	>	excludedInteractions_.addPair(a, b);
460	>	excludedInteractions_.addPair(b, c);
461	>	excludedInteractions_.addPair(c, d);
462	>	}
463
464	+	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
465	+	oneThreeInteractions_.addPair(a, c);
466	+	oneThreeInteractions_.addPair(b, d);
467	+	} else {
468	+	excludedInteractions_.addPair(a, c);
469	+	excludedInteractions_.addPair(b, d);
470	+	}
471
472	<	// boxLz
473	<
474	<	dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
475	<	dsq = dx*dx + dy*dy + dz*dz;
476	<	boxL[2] = sqrt( dsq );
477	<	//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
472	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
473	>	oneFourInteractions_.addPair(a, d);
474	>	} else {
475	>	excludedInteractions_.addPair(a, d);
476	>	}
477	>	}
478
479	<	//calculate the max cutoff
480	<	maxCutoff =  calcMaxCutOff();
257	<
258	<	checkCutOffs();
479	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
480	>	inversion = mol->nextInversion(inversionIter)) {
481
482	<	}
482	>	a = inversion->getAtomA()->getGlobalIndex();
483	>	b = inversion->getAtomB()->getGlobalIndex();
484	>	c = inversion->getAtomC()->getGlobalIndex();
485	>	d = inversion->getAtomD()->getGlobalIndex();
486
487	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
488	+	oneTwoInteractions_.addPair(a, b);
489	+	oneTwoInteractions_.addPair(a, c);
490	+	oneTwoInteractions_.addPair(a, d);
491	+	} else {
492	+	excludedInteractions_.addPair(a, b);
493	+	excludedInteractions_.addPair(a, c);
494	+	excludedInteractions_.addPair(a, d);
495	+	}
496
497	<	double SimInfo::calcMaxCutOff(){
497	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
498	>	oneThreeInteractions_.addPair(b, c);
499	>	oneThreeInteractions_.addPair(b, d);
500	>	oneThreeInteractions_.addPair(c, d);
501	>	} else {
502	>	excludedInteractions_.addPair(b, c);
503	>	excludedInteractions_.addPair(b, d);
504	>	excludedInteractions_.addPair(c, d);
505	>	}
506	>	}
507
508	<	double ri[3], rj[3], rk[3];
509	<	double rij[3], rjk[3], rki[3];
510	<	double minDist;
508	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
509	>	rb = mol->nextRigidBody(rbIter)) {
510	>	vector<Atom*> atoms = rb->getAtoms();
511	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
512	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
513	>	a = atoms[i]->getGlobalIndex();
514	>	b = atoms[j]->getGlobalIndex();
515	>	excludedInteractions_.addPair(a, b);
516	>	}
517	>	}
518	>	}
519
520	<	ri[0] = Hmat[0][0];
270	<	ri[1] = Hmat[1][0];
271	<	ri[2] = Hmat[2][0];
520	>	}
521
522	<	rj[0] = Hmat[0][1];
523	<	rj[1] = Hmat[1][1];
524	<	rj[2] = Hmat[2][1];
522	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
523	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
524	>	vector<Bond*>::iterator bondIter;
525	>	vector<Bend*>::iterator bendIter;
526	>	vector<Torsion*>::iterator torsionIter;
527	>	vector<Inversion*>::iterator inversionIter;
528	>	Bond* bond;
529	>	Bend* bend;
530	>	Torsion* torsion;
531	>	Inversion* inversion;
532	>	int a;
533	>	int b;
534	>	int c;
535	>	int d;
536
537	<	rk[0] = Hmat[0][2];
538	<	rk[1] = Hmat[1][2];
539	<	rk[2] = Hmat[2][2];
537	>	map<int, set<int> > atomGroups;
538	>	Molecule::RigidBodyIterator rbIter;
539	>	RigidBody* rb;
540	>	Molecule::IntegrableObjectIterator ii;
541	>	StuntDouble* integrableObject;
542
543	<	crossProduct3(ri, rj, rij);
544	<	distXY = dotProduct3(rk,rij) / norm3(rij);
543	>	for (integrableObject = mol->beginIntegrableObject(ii);
544	>	integrableObject != NULL;
545	>	integrableObject = mol->nextIntegrableObject(ii)) {
546	>
547	>	if (integrableObject->isRigidBody()) {
548	>	rb = static_cast<RigidBody*>(integrableObject);
549	>	vector<Atom*> atoms = rb->getAtoms();
550	>	set<int> rigidAtoms;
551	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
552	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
553	>	}
554	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
555	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
556	>	}
557	>	} else {
558	>	set<int> oneAtomSet;
559	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
560	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
561	>	}
562	>	}
563
564	<	crossProduct3(rj,rk, rjk);
565	<	distYZ = dotProduct3(ri,rjk) / norm3(rjk);
564	>	for (bond= mol->beginBond(bondIter); bond != NULL;
565	>	bond = mol->nextBond(bondIter)) {
566	>
567	>	a = bond->getAtomA()->getGlobalIndex();
568	>	b = bond->getAtomB()->getGlobalIndex();
569	>
570	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
571	>	oneTwoInteractions_.removePair(a, b);
572	>	} else {
573	>	excludedInteractions_.removePair(a, b);
574	>	}
575	>	}
576
577	<	crossProduct3(rk,ri, rki);
578	<	distZX = dotProduct3(rj,rki) / norm3(rki);
577	>	for (bend= mol->beginBend(bendIter); bend != NULL;
578	>	bend = mol->nextBend(bendIter)) {
579
580	<	minDist = min(min(distXY, distYZ), distZX);
581	<	return minDist/2;
582	<
583	<	}
580	>	a = bend->getAtomA()->getGlobalIndex();
581	>	b = bend->getAtomB()->getGlobalIndex();
582	>	c = bend->getAtomC()->getGlobalIndex();
583	>
584	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
585	>	oneTwoInteractions_.removePair(a, b);
586	>	oneTwoInteractions_.removePair(b, c);
587	>	} else {
588	>	excludedInteractions_.removePair(a, b);
589	>	excludedInteractions_.removePair(b, c);
590	>	}
591
592	<	void SimInfo::wrapVector( double thePos[3] ){
592	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
593	>	oneThreeInteractions_.removePair(a, c);
594	>	} else {
595	>	excludedInteractions_.removePair(a, c);
596	>	}
597	>	}
598
599	<	int i;
600	<	double scaled[3];
599	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
600	>	torsion = mol->nextTorsion(torsionIter)) {
601
602	<	if( !orthoRhombic ){
603	<	// calc the scaled coordinates.
602	>	a = torsion->getAtomA()->getGlobalIndex();
603	>	b = torsion->getAtomB()->getGlobalIndex();
604	>	c = torsion->getAtomC()->getGlobalIndex();
605	>	d = torsion->getAtomD()->getGlobalIndex();
606
607	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
608	+	oneTwoInteractions_.removePair(a, b);
609	+	oneTwoInteractions_.removePair(b, c);
610	+	oneTwoInteractions_.removePair(c, d);
611	+	} else {
612	+	excludedInteractions_.removePair(a, b);
613	+	excludedInteractions_.removePair(b, c);
614	+	excludedInteractions_.removePair(c, d);
615	+	}
616
617	<	matVecMul3(HmatInv, thePos, scaled);
618	<
619	<	for(i=0; i<3; i++)
620	<	scaled[i] -= roundMe(scaled[i]);
621	<
622	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
623	<
311	<	matVecMul3(Hmat, scaled, thePos);
617	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
618	>	oneThreeInteractions_.removePair(a, c);
619	>	oneThreeInteractions_.removePair(b, d);
620	>	} else {
621	>	excludedInteractions_.removePair(a, c);
622	>	excludedInteractions_.removePair(b, d);
623	>	}
624
625	<	}
626	<	else{
627	<	// calc the scaled coordinates.
628	<
629	<	for(i=0; i<3; i++)
630	<	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	<	}
625	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
626	>	oneFourInteractions_.removePair(a, d);
627	>	} else {
628	>	excludedInteractions_.removePair(a, d);
629	>	}
630	>	}
631
632	+	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
633	+	inversion = mol->nextInversion(inversionIter)) {
634
635	<	int SimInfo::getNDF(){
636	<	int ndf_local;
635	>	a = inversion->getAtomA()->getGlobalIndex();
636	>	b = inversion->getAtomB()->getGlobalIndex();
637	>	c = inversion->getAtomC()->getGlobalIndex();
638	>	d = inversion->getAtomD()->getGlobalIndex();
639
640	<	ndf_local = 0;
641	<
642	<	for(int i = 0; i < integrableObjects.size(); i++){
643	<	ndf_local += 3;
644	<	if (integrableObjects[i]->isDirectional()) {
645	<	if (integrableObjects[i]->isLinear())
646	<	ndf_local += 2;
647	<	else
648	<	ndf_local += 3;
649	<	}
640	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
641	>	oneTwoInteractions_.removePair(a, b);
642	>	oneTwoInteractions_.removePair(a, c);
643	>	oneTwoInteractions_.removePair(a, d);
644	>	} else {
645	>	excludedInteractions_.removePair(a, b);
646	>	excludedInteractions_.removePair(a, c);
647	>	excludedInteractions_.removePair(a, d);
648	>	}
649	>
650	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
651	>	oneThreeInteractions_.removePair(b, c);
652	>	oneThreeInteractions_.removePair(b, d);
653	>	oneThreeInteractions_.removePair(c, d);
654	>	} else {
655	>	excludedInteractions_.removePair(b, c);
656	>	excludedInteractions_.removePair(b, d);
657	>	excludedInteractions_.removePair(c, d);
658	>	}
659	>	}
660	>
661	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
662	>	rb = mol->nextRigidBody(rbIter)) {
663	>	vector<Atom*> atoms = rb->getAtoms();
664	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
665	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
666	>	a = atoms[i]->getGlobalIndex();
667	>	b = atoms[j]->getGlobalIndex();
668	>	excludedInteractions_.removePair(a, b);
669	>	}
670	>	}
671	>	}
672	>
673		}
674	+
675	+
676	+	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
677	+	int curStampId;
678	+
679	+	//index from 0
680	+	curStampId = moleculeStamps_.size();
681
682	<	// n_constraints is local, so subtract them on each processor:
682	>	moleculeStamps_.push_back(molStamp);
683	>	molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
684	>	}
685
351	–	ndf_local -= n_constraints;
686
687	+	/**
688	+	* update
689	+	*
690	+	*  Performs the global checks and variable settings after the
691	+	*  objects have been created.
692	+	*
693	+	*/
694	+	void SimInfo::update() {
695	+	setupSimVariables();
696	+	calcNdf();
697	+	calcNdfRaw();
698	+	calcNdfTrans();
699	+	}
700	+
701	+	/**
702	+	* getSimulatedAtomTypes
703	+	*
704	+	* Returns an STL set of AtomType* that are actually present in this
705	+	* simulation.  Must query all processors to assemble this information.
706	+	*
707	+	*/
708	+	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
709	+	SimInfo::MoleculeIterator mi;
710	+	Molecule* mol;
711	+	Molecule::AtomIterator ai;
712	+	Atom* atom;
713	+	set<AtomType*> atomTypes;
714	+
715	+	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
716	+	for(atom = mol->beginAtom(ai); atom != NULL;
717	+	atom = mol->nextAtom(ai)) {
718	+	atomTypes.insert(atom->getAtomType());
719	+	}
720	+	}
721	+
722		#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
723
724	<	// nZconstraints is global, as are the 3 COM translations for the
725	<	// entire system:
724	>	// loop over the found atom types on this processor, and add their
725	>	// numerical idents to a vector:
726	>
727	>	vector<int> foundTypes;
728	>	set<AtomType*>::iterator i;
729	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
730	>	foundTypes.push_back( (*i)->getIdent() );
731
732	<	ndf = ndf - 3 - nZconstraints;
732	>	// count_local holds the number of found types on this processor
733	>	int count_local = foundTypes.size();
734
735	<	return ndf;
365	<	}
735	>	int nproc = MPI::COMM_WORLD.Get_size();
736
737	<	int SimInfo::getNDFraw() {
738	<	int ndfRaw_local;
737	>	// we need arrays to hold the counts and displacement vectors for
738	>	// all processors
739	>	vector<int> counts(nproc, 0);
740	>	vector<int> disps(nproc, 0);
741
742	<	// Raw degrees of freedom that we have to set
743	<	ndfRaw_local = 0;
744	<
745	<	for(int i = 0; i < integrableObjects.size(); i++){
746	<	ndfRaw_local += 3;
747	<	if (integrableObjects[i]->isDirectional()) {
748	<	if (integrableObjects[i]->isLinear())
749	<	ndfRaw_local += 2;
750	<	else
751	<	ndfRaw_local += 3;
742	>	// fill the counts array
743	>	MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
744	>	1, MPI::INT);
745	>
746	>	// use the processor counts to compute the displacement array
747	>	disps[0] = 0;
748	>	int totalCount = counts[0];
749	>	for (int iproc = 1; iproc < nproc; iproc++) {
750	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
751	>	totalCount += counts[iproc];
752		}
753	+
754	+	// we need a (possibly redundant) set of all found types:
755	+	vector<int> ftGlobal(totalCount);
756	+
757	+	// now spray out the foundTypes to all the other processors:
758	+	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
759	+	&ftGlobal[0], &counts[0], &disps[0],
760	+	MPI::INT);
761	+
762	+	vector<int>::iterator j;
763	+
764	+	// foundIdents is a stl set, so inserting an already found ident
765	+	// will have no effect.
766	+	set<int> foundIdents;
767	+
768	+	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
769	+	foundIdents.insert((*j));
770	+
771	+	// now iterate over the foundIdents and get the actual atom types
772	+	// that correspond to these:
773	+	set<int>::iterator it;
774	+	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
775	+	atomTypes.insert( forceField_->getAtomType((*it)) );
776	+
777	+	#endif
778	+
779	+	return atomTypes;
780		}
781	+
782	+	void SimInfo::setupSimVariables() {
783	+	useAtomicVirial_ = simParams_->getUseAtomicVirial();
784	+	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
785	+	calcBoxDipole_ = false;
786	+	if ( simParams_->haveAccumulateBoxDipole() )
787	+	if ( simParams_->getAccumulateBoxDipole() ) {
788	+	calcBoxDipole_ = true;
789	+	}
790
791	<	#ifdef IS_MPI
792	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
791	>	set<AtomType*>::iterator i;
792	>	set<AtomType*> atomTypes;
793	>	atomTypes = getSimulatedAtomTypes();
794	>	int usesElectrostatic = 0;
795	>	int usesMetallic = 0;
796	>	int usesDirectional = 0;
797	>	int usesFluctuatingCharges =  0;
798	>	//loop over all of the atom types
799	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
800	>	usesElectrostatic |= (*i)->isElectrostatic();
801	>	usesMetallic |= (*i)->isMetal();
802	>	usesDirectional |= (*i)->isDirectional();
803	>	usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
804	>	}
805	>
806	>	#ifdef IS_MPI
807	>	int temp;
808	>	temp = usesDirectional;
809	>	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
810	>
811	>	temp = usesMetallic;
812	>	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
813	>
814	>	temp = usesElectrostatic;
815	>	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
816	>
817	>	temp = usesFluctuatingCharges;
818	>	MPI_Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
819		#else
820	<	ndfRaw = ndfRaw_local;
820	>
821	>	usesDirectionalAtoms_ = usesDirectional;
822	>	usesMetallicAtoms_ = usesMetallic;
823	>	usesElectrostaticAtoms_ = usesElectrostatic;
824	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
825	>
826		#endif
827	+
828	+	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
829	+	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
830	+	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
831	+	}
832
389	–	return ndfRaw;
390	–	}
833
834	<	int SimInfo::getNDFtranslational() {
835	<	int ndfTrans_local;
834	>	vector<int> SimInfo::getGlobalAtomIndices() {
835	>	SimInfo::MoleculeIterator mi;
836	>	Molecule* mol;
837	>	Molecule::AtomIterator ai;
838	>	Atom* atom;
839
840	<	ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
840	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
841	>
842	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
843	>
844	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
845	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
846	>	}
847	>	}
848	>	return GlobalAtomIndices;
849	>	}
850
851
852	<	#ifdef IS_MPI
853	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
854	<	#else
855	<	ndfTrans = ndfTrans_local;
856	<	#endif
852	>	vector<int> SimInfo::getGlobalGroupIndices() {
853	>	SimInfo::MoleculeIterator mi;
854	>	Molecule* mol;
855	>	Molecule::CutoffGroupIterator ci;
856	>	CutoffGroup* cg;
857
858	<	ndfTrans = ndfTrans - 3 - nZconstraints;
858	>	vector<int> GlobalGroupIndices;
859	>
860	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
861	>
862	>	//local index of cutoff group is trivial, it only depends on the
863	>	//order of travesing
864	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
865	>	cg = mol->nextCutoffGroup(ci)) {
866	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
867	>	}
868	>	}
869	>	return GlobalGroupIndices;
870	>	}
871
406	–	return ndfTrans;
407	–	}
872
873	<	int SimInfo::getTotIntegrableObjects() {
874	<	int nObjs_local;
411	<	int nObjs;
873	>	void SimInfo::prepareTopology() {
874	>	int nExclude, nOneTwo, nOneThree, nOneFour;
875
876	<	nObjs_local =  integrableObjects.size();
876	>	//calculate mass ratio of cutoff group
877	>	SimInfo::MoleculeIterator mi;
878	>	Molecule* mol;
879	>	Molecule::CutoffGroupIterator ci;
880	>	CutoffGroup* cg;
881	>	Molecule::AtomIterator ai;
882	>	Atom* atom;
883	>	RealType totalMass;
884
885	+	/**
886	+	* The mass factor is the relative mass of an atom to the total
887	+	* mass of the cutoff group it belongs to.  By default, all atoms
888	+	* are their own cutoff groups, and therefore have mass factors of
889	+	* 1.  We need some special handling for massless atoms, which
890	+	* will be treated as carrying the entire mass of the cutoff
891	+	* group.
892	+	*/
893	+	massFactors_.clear();
894	+	massFactors_.resize(getNAtoms(), 1.0);
895	+
896	+	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
897	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
898	+	cg = mol->nextCutoffGroup(ci)) {
899
900	<	#ifdef IS_MPI
901	<	MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
902	<	#else
903	<	nObjs = nObjs_local;
904	<	#endif
900	>	totalMass = cg->getMass();
901	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
902	>	// Check for massless groups - set mfact to 1 if true
903	>	if (totalMass != 0)
904	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
905	>	else
906	>	massFactors_[atom->getLocalIndex()] = 1.0;
907	>	}
908	>	}
909	>	}
910
911	+	// Build the identArray_
912
913	<	return nObjs;
914	<	}
913	>	identArray_.clear();
914	>	identArray_.reserve(getNAtoms());
915	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
916	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
917	>	identArray_.push_back(atom->getIdent());
918	>	}
919	>	}
920	>
921	>	//scan topology
922
923	<	void SimInfo::refreshSim(){
923	>	nExclude = excludedInteractions_.getSize();
924	>	nOneTwo = oneTwoInteractions_.getSize();
925	>	nOneThree = oneThreeInteractions_.getSize();
926	>	nOneFour = oneFourInteractions_.getSize();
927
928	<	simtype fInfo;
929	<	int isError;
930	<	int n_global;
931	<	int* excl;
928	>	int* excludeList = excludedInteractions_.getPairList();
929	>	int* oneTwoList = oneTwoInteractions_.getPairList();
930	>	int* oneThreeList = oneThreeInteractions_.getPairList();
931	>	int* oneFourList = oneFourInteractions_.getPairList();
932
933	<	fInfo.dielect = 0.0;
933	>	topologyDone_ = true;
934	>	}
935
936	<	if( useDipoles ){
937	<	if( useReactionField )fInfo.dielect = dielectric;
936	>	void SimInfo::addProperty(GenericData* genData) {
937	>	properties_.addProperty(genData);
938		}
939
940	<	fInfo.SIM_uses_PBC = usePBC;
940	>	void SimInfo::removeProperty(const string& propName) {
941	>	properties_.removeProperty(propName);
942	>	}
943
944	<	if (useSticky || useDipoles || useGayBerne || useShapes) {
945	<	useDirectionalAtoms = 1;
443	<	fInfo.SIM_uses_DirectionalAtoms = useDirectionalAtoms;
944	>	void SimInfo::clearProperties() {
945	>	properties_.clearProperties();
946		}
947
948	<	fInfo.SIM_uses_LennardJones = useLennardJones;
948	>	vector<string> SimInfo::getPropertyNames() {
949	>	return properties_.getPropertyNames();
950	>	}
951	>
952	>	vector<GenericData*> SimInfo::getProperties() {
953	>	return properties_.getProperties();
954	>	}
955
956	<	if (useCharges || useDipoles) {
957	<	useElectrostatics = 1;
450	<	fInfo.SIM_uses_Electrostatics = useElectrostatics;
956	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
957	>	return properties_.getPropertyByName(propName);
958		}
959
960	<	fInfo.SIM_uses_Charges = useCharges;
961	<	fInfo.SIM_uses_Dipoles = useDipoles;
962	<	fInfo.SIM_uses_Sticky = useSticky;
963	<	fInfo.SIM_uses_GayBerne = useGayBerne;
964	<	fInfo.SIM_uses_EAM = useEAM;
965	<	fInfo.SIM_uses_Shapes = useShapes;
459	<	fInfo.SIM_uses_FLARB = useFLARB;
460	<	fInfo.SIM_uses_RF = useReactionField;
960	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
961	>	if (sman_ == sman) {
962	>	return;
963	>	}
964	>	delete sman_;
965	>	sman_ = sman;
966
967	<	n_exclude = excludes->getSize();
968	<	excl = excludes->getFortranArray();
969	<
970	<	#ifdef IS_MPI
971	<	n_global = mpiSim->getNAtomsGlobal();
972	<	#else
973	<	n_global = n_atoms;
974	<	#endif
975	<
976	<	isError = 0;
977	<
978	<	getFortranGroupArrays(this, FglobalGroupMembership, mfact);
979	<	//it may not be a good idea to pass the address of first element in vector
980	<	//since c++ standard does not require vector to be stored continuously in meomory
981	<	//Most of the compilers will organize the memory of vector continuously
982	<	setFortranSim( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
983	<	&nGlobalExcludes, globalExcludes, molMembershipArray,
984	<	&mfact[0], &ngroup, &FglobalGroupMembership[0], &isError);
967	>	Molecule* mol;
968	>	RigidBody* rb;
969	>	Atom* atom;
970	>	CutoffGroup* cg;
971	>	SimInfo::MoleculeIterator mi;
972	>	Molecule::RigidBodyIterator rbIter;
973	>	Molecule::AtomIterator atomIter;
974	>	Molecule::CutoffGroupIterator cgIter;
975	>
976	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
977	>
978	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
979	>	atom->setSnapshotManager(sman_);
980	>	}
981	>
982	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
983	>	rb->setSnapshotManager(sman_);
984	>	}
985
986	<	if( isError ){
986	>	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
987	>	cg->setSnapshotManager(sman_);
988	>	}
989	>	}
990
483	–	sprintf( painCave.errMsg,
484	–	"There was an error setting the simulation information in fortran.\n" );
485	–	painCave.isFatal = 1;
486	–	painCave.severity = OOPSE_ERROR;
487	–	simError();
991		}
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	–	}
992
993	<	void SimInfo::setDefaultRcut( double theRcut ){
994	<
995	<	haveRcut = 1;
504	<	rCut = theRcut;
505	<	rList = rCut + 1.0;
506	<
507	<	notifyFortranCutoffs( &rCut, &rSw, &rList );
508	<	}
993	>	Vector3d SimInfo::getComVel(){
994	>	SimInfo::MoleculeIterator i;
995	>	Molecule* mol;
996
997	<	void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
997	>	Vector3d comVel(0.0);
998	>	RealType totalMass = 0.0;
999	>
1000	>
1001	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1002	>	RealType mass = mol->getMass();
1003	>	totalMass += mass;
1004	>	comVel += mass * mol->getComVel();
1005	>	}
1006
1007	<	rSw = theRsw;
1008	<	setDefaultRcut( theRcut );
1009	<	}
1007	>	#ifdef IS_MPI
1008	>	RealType tmpMass = totalMass;
1009	>	Vector3d tmpComVel(comVel);
1010	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1011	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1012	>	#endif
1013
1014	+	comVel /= totalMass;
1015
1016	<	void SimInfo::checkCutOffs( void ){
518	<
519	<	if( boxIsInit ){
520	<
521	<	//we need to check cutOffs against the box
522	<
523	<	if( rCut > maxCutoff ){
524	<	sprintf( painCave.errMsg,
525	<	"cutoffRadius is too large for the current periodic box.\n"
526	<	"\tCurrent Value of cutoffRadius = %G at time %G\n "
527	<	"\tThis is larger than half of at least one of the\n"
528	<	"\tperiodic box vectors.  Right now, the Box matrix is:\n"
529	<	"\n"
530	<	"\t[ %G %G %G ]\n"
531	<	"\t[ %G %G %G ]\n"
532	<	"\t[ %G %G %G ]\n",
533	<	rCut, currentTime,
534	<	Hmat[0][0], Hmat[0][1], Hmat[0][2],
535	<	Hmat[1][0], Hmat[1][1], Hmat[1][2],
536	<	Hmat[2][0], Hmat[2][1], Hmat[2][2]);
537	<	painCave.severity = OOPSE_ERROR;
538	<	painCave.isFatal = 1;
539	<	simError();
540	<	}
541	<	} else {
542	<	// initialize this stuff before using it, OK?
543	<	sprintf( painCave.errMsg,
544	<	"Trying to check cutoffs without a box.\n"
545	<	"\tOOPSE should have better programmers than that.\n" );
546	<	painCave.severity = OOPSE_ERROR;
547	<	painCave.isFatal = 1;
548	<	simError();
1016	>	return comVel;
1017		}
550	–
551	–	}
1018
1019	<	void SimInfo::addProperty(GenericData* prop){
1019	>	Vector3d SimInfo::getCom(){
1020	>	SimInfo::MoleculeIterator i;
1021	>	Molecule* mol;
1022
1023	<	map<string, GenericData*>::iterator result;
1024	<	result = properties.find(prop->getID());
1025	<
1026	<	//we can't simply use  properties[prop->getID()] = prop,
1027	<	//it will cause memory leak if we already contain a propery which has the same name of prop
1028	<
1029	<	if(result != properties.end()){
1030	<
563	<	delete (*result).second;
564	<	(*result).second = prop;
565	<
566	<	}
567	<	else{
1023	>	Vector3d com(0.0);
1024	>	RealType totalMass = 0.0;
1025	>
1026	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1027	>	RealType mass = mol->getMass();
1028	>	totalMass += mass;
1029	>	com += mass * mol->getCom();
1030	>	}
1031
1032	<	properties[prop->getID()] = prop;
1032	>	#ifdef IS_MPI
1033	>	RealType tmpMass = totalMass;
1034	>	Vector3d tmpCom(com);
1035	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1036	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1037	>	#endif
1038
1039	+	com /= totalMass;
1040	+
1041	+	return com;
1042	+
1043	+	}
1044	+
1045	+	ostream& operator <<(ostream& o, SimInfo& info) {
1046	+
1047	+	return o;
1048		}
1049	+
1050	+
1051	+	/*
1052	+	Returns center of mass and center of mass velocity in one function call.
1053	+	*/
1054	+
1055	+	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1056	+	SimInfo::MoleculeIterator i;
1057	+	Molecule* mol;
1058	+
1059
1060	<	}
1060	>	RealType totalMass = 0.0;
1061	>
1062
1063	<	GenericData* SimInfo::getProperty(const string& propName){
1064	<
1065	<	map<string, GenericData*>::iterator result;
1066	<
1067	<	//string lowerCaseName = ();
1068	<
1069	<	result = properties.find(propName);
1070	<
1071	<	if(result != properties.end())
1072	<	return (*result).second;
1073	<	else
1074	<	return NULL;
1075	<	}
1063	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1064	>	RealType mass = mol->getMass();
1065	>	totalMass += mass;
1066	>	com += mass * mol->getCom();
1067	>	comVel += mass * mol->getComVel();
1068	>	}
1069	>
1070	>	#ifdef IS_MPI
1071	>	RealType tmpMass = totalMass;
1072	>	Vector3d tmpCom(com);
1073	>	Vector3d tmpComVel(comVel);
1074	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1075	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1076	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1077	>	#endif
1078	>
1079	>	com /= totalMass;
1080	>	comVel /= totalMass;
1081	>	}
1082	>
1083	>	/*
1084	>	Return intertia tensor for entire system and angular momentum Vector.
1085
1086
1087	<	void SimInfo::getFortranGroupArrays(SimInfo* info,
1088	<	vector<int>& FglobalGroupMembership,
1089	<	vector<double>& mfact){
1090	<
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	<
1087	>	[  Ixx -Ixy  -Ixz ]
1088	>	J =| -Iyx  Iyy  -Iyz |
1089	>	[ -Izx -Iyz   Izz ]
1090	>	*/
1091
1092	<	// Fix the silly fortran indexing problem
1092	>	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1093	>
1094	>
1095	>	RealType xx = 0.0;
1096	>	RealType yy = 0.0;
1097	>	RealType zz = 0.0;
1098	>	RealType xy = 0.0;
1099	>	RealType xz = 0.0;
1100	>	RealType yz = 0.0;
1101	>	Vector3d com(0.0);
1102	>	Vector3d comVel(0.0);
1103	>
1104	>	getComAll(com, comVel);
1105	>
1106	>	SimInfo::MoleculeIterator i;
1107	>	Molecule* mol;
1108	>
1109	>	Vector3d thisq(0.0);
1110	>	Vector3d thisv(0.0);
1111	>
1112	>	RealType thisMass = 0.0;
1113	>
1114	>
1115	>
1116	>
1117	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1118	>
1119	>	thisq = mol->getCom()-com;
1120	>	thisv = mol->getComVel()-comVel;
1121	>	thisMass = mol->getMass();
1122	>	// Compute moment of intertia coefficients.
1123	>	xx += thisq[0]*thisq[0]*thisMass;
1124	>	yy += thisq[1]*thisq[1]*thisMass;
1125	>	zz += thisq[2]*thisq[2]*thisMass;
1126	>
1127	>	// compute products of intertia
1128	>	xy += thisq[0]*thisq[1]*thisMass;
1129	>	xz += thisq[0]*thisq[2]*thisMass;
1130	>	yz += thisq[1]*thisq[2]*thisMass;
1131	>
1132	>	angularMomentum += cross( thisq, thisv ) * thisMass;
1133	>
1134	>	}
1135	>
1136	>
1137	>	inertiaTensor(0,0) = yy + zz;
1138	>	inertiaTensor(0,1) = -xy;
1139	>	inertiaTensor(0,2) = -xz;
1140	>	inertiaTensor(1,0) = -xy;
1141	>	inertiaTensor(1,1) = xx + zz;
1142	>	inertiaTensor(1,2) = -yz;
1143	>	inertiaTensor(2,0) = -xz;
1144	>	inertiaTensor(2,1) = -yz;
1145	>	inertiaTensor(2,2) = xx + yy;
1146	>
1147		#ifdef IS_MPI
1148	<	numAtom = mpiSim->getNAtomsGlobal();
1149	<	#else
1150	<	numAtom = n_atoms;
1148	>	Mat3x3d tmpI(inertiaTensor);
1149	>	Vector3d tmpAngMom;
1150	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1151	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1152		#endif
1153	<	for (int i = 0; i < numAtom; i++)
1154	<	FglobalGroupMembership.push_back(globalGroupMembership[i] + 1);
1155	<
1153	>
1154	>	return;
1155	>	}
1156
1157	<	myMols = info->molecules;
1158	<	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();
1157	>	//Returns the angular momentum of the system
1158	>	Vector3d SimInfo::getAngularMomentum(){
1159
1160	<	for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom);
1161	<	cutoffAtom != NULL;
1162	<	cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
1163	<	mfact.push_back(cutoffAtom->getMass()/totalMass);
1160	>	Vector3d com(0.0);
1161	>	Vector3d comVel(0.0);
1162	>	Vector3d angularMomentum(0.0);
1163	>
1164	>	getComAll(com,comVel);
1165	>
1166	>	SimInfo::MoleculeIterator i;
1167	>	Molecule* mol;
1168	>
1169	>	Vector3d thisr(0.0);
1170	>	Vector3d thisp(0.0);
1171	>
1172	>	RealType thisMass;
1173	>
1174	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1175	>	thisMass = mol->getMass();
1176	>	thisr = mol->getCom()-com;
1177	>	thisp = (mol->getComVel()-comVel)*thisMass;
1178	>
1179	>	angularMomentum += cross( thisr, thisp );
1180	>
1181		}
1182	+
1183	+	#ifdef IS_MPI
1184	+	Vector3d tmpAngMom;
1185	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1186	+	#endif
1187	+
1188	+	return angularMomentum;
1189	+	}
1190	+
1191	+	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1192	+	return IOIndexToIntegrableObject.at(index);
1193	+	}
1194	+
1195	+	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1196	+	IOIndexToIntegrableObject= v;
1197	+	}
1198	+
1199	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1200	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1201	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1202	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1203	+	*/
1204	+	void SimInfo::getGyrationalVolume(RealType &volume){
1205	+	Mat3x3d intTensor;
1206	+	RealType det;
1207	+	Vector3d dummyAngMom;
1208	+	RealType sysconstants;
1209	+	RealType geomCnst;
1210	+
1211	+	geomCnst = 3.0/2.0;
1212	+	/* Get the inertial tensor and angular momentum for free*/
1213	+	getInertiaTensor(intTensor,dummyAngMom);
1214	+
1215	+	det = intTensor.determinant();
1216	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1217	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(det);
1218	+	return;
1219	+	}
1220	+
1221	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1222	+	Mat3x3d intTensor;
1223	+	Vector3d dummyAngMom;
1224	+	RealType sysconstants;
1225	+	RealType geomCnst;
1226	+
1227	+	geomCnst = 3.0/2.0;
1228	+	/* Get the inertial tensor and angular momentum for free*/
1229	+	getInertiaTensor(intTensor,dummyAngMom);
1230	+
1231	+	detI = intTensor.determinant();
1232	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1233	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,geomCnst)*sqrt(detI);
1234	+	return;
1235	+	}
1236	+	/*
1237	+	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1238	+	assert( v.size() == nAtoms_ + nRigidBodies_);
1239	+	sdByGlobalIndex_ = v;
1240		}
1241	+
1242	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1243	+	//assert(index < nAtoms_ + nRigidBodies_);
1244	+	return sdByGlobalIndex_.at(index);
1245	+	}
1246	+	*/
1247	+	int SimInfo::getNGlobalConstraints() {
1248	+	int nGlobalConstraints;
1249	+	#ifdef IS_MPI
1250	+	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1251	+	MPI_COMM_WORLD);
1252	+	#else
1253	+	nGlobalConstraints =  nConstraints_;
1254	+	#endif
1255	+	return nGlobalConstraints;
1256		}
1257
1258	<	}
1258	>	}//end namespace OpenMD
1259	>

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 1744 by gezelter, Tue Jun 5 18:07:08 2012 UTC

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