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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 1529 by gezelter, Mon Dec 27 18:35:59 2010 UTC

#	Line 1 | Line 1
1	<	#include <stdlib.h>
2	<	#include <string.h>
3	<	#include <math.h>
1	>	/*
2	>	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	>	*
4	>	* The University of Notre Dame grants you ("Licensee") a
5	>	* non-exclusive, royalty free, license to use, modify and
6	>	* redistribute this software in source and binary code form, provided
7	>	* that the following conditions are met:
8	>	*
9	>	* 1. Redistributions of source code must retain the above copyright
10	>	*    notice, this list of conditions and the following disclaimer.
11	>	*
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13	>	*    notice, this list of conditions and the following disclaimer in the
14	>	*    documentation and/or other materials provided with the
15	>	*    distribution.
16	>	*
17	>	* This software is provided "AS IS," without a warranty of any
18	>	* kind. All express or implied conditions, representations and
19	>	* warranties, including any implied warranty of merchantability,
20	>	* fitness for a particular purpose or non-infringement, are hereby
21	>	* excluded.  The University of Notre Dame and its licensors shall not
22	>	* be liable for any damages suffered by licensee as a result of
23	>	* using, modifying or distributing the software or its
24	>	* derivatives. In no event will the University of Notre Dame or its
25	>	* licensors be liable for any lost revenue, profit or data, or for
26	>	* direct, indirect, special, consequential, incidental or punitive
27	>	* damages, however caused and regardless of the theory of liability,
28	>	* arising out of the use of or inability to use software, even if the
29	>	* University of Notre Dame has been advised of the possibility of
30	>	* such damages.
31	>	*
32	>	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	>	* research, please cite the appropriate papers when you publish your
34	>	* work.  Good starting points are:
35	>	*
36	>	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	>	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	>	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	>	* [4]  Vardeman & Gezelter, in progress (2009).
40	>	*/
41	>
42	>	/**
43	>	* @file SimInfo.cpp
44	>	* @author    tlin
45	>	* @date  11/02/2004
46	>	* @version 1.0
47	>	*/
48
49	<	#include <iostream>
50	<	using namespace std;
49	>	#include <algorithm>
50	>	#include <set>
51	>	#include <map>
52
53		#include "brains/SimInfo.hpp"
54	<	#define __C
55	<	#include "brains/fSimulation.h"
54	>	#include "math/Vector3.hpp"
55	>	#include "primitives/Molecule.hpp"
56	>	#include "primitives/StuntDouble.hpp"
57	>	#include "UseTheForce/fCutoffPolicy.h"
58	>	#include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
59	>	#include "UseTheForce/doForces_interface.h"
60	>	#include "UseTheForce/DarkSide/neighborLists_interface.h"
61	>	#include "UseTheForce/DarkSide/switcheroo_interface.h"
62	>	#include "utils/MemoryUtils.hpp"
63		#include "utils/simError.h"
64	<	#include "UseTheForce/DarkSide/simulation_interface.h"
65	<	#include "UseTheForce/notifyCutoffs_interface.h"
64	>	#include "selection/SelectionManager.hpp"
65	>	#include "io/ForceFieldOptions.hpp"
66	>	#include "UseTheForce/ForceField.hpp"
67	>	#include "nonbonded/InteractionManager.hpp"
68
15	–	//#include "UseTheForce/fortranWrappers.hpp"
69
17	–	#include "math/MatVec3.h"
18	–
70		#ifdef IS_MPI
71	<	#include "brains/mpiSimulation.hpp"
72	<	#endif
71	>	#include "UseTheForce/mpiComponentPlan.h"
72	>	#include "UseTheForce/DarkSide/simParallel_interface.h"
73	>	#endif
74
75	<	inline double roundMe( double x ){
76	<	return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
77	<	}
78	<
79	<	inline double min( double a, double b ){
80	<	return (a < b ) ? a : b;
81	<	}
75	>	using namespace std;
76	>	namespace OpenMD {
77	>
78	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
79	>	forceField_(ff), simParams_(simParams),
80	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
81	>	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
82	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
83	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
84	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
85	>	nConstraints_(0), sman_(NULL), fortranInitialized_(false),
86	>	calcBoxDipole_(false), useAtomicVirial_(true) {
87	>
88	>	MoleculeStamp* molStamp;
89	>	int nMolWithSameStamp;
90	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
91	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
92	>	CutoffGroupStamp* cgStamp;
93	>	RigidBodyStamp* rbStamp;
94	>	int nRigidAtoms = 0;
95	>
96	>	vector<Component*> components = simParams->getComponents();
97	>
98	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
99	>	molStamp = (*i)->getMoleculeStamp();
100	>	nMolWithSameStamp = (*i)->getNMol();
101	>
102	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
103	>
104	>	//calculate atoms in molecules
105	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
106	>
107	>	//calculate atoms in cutoff groups
108	>	int nAtomsInGroups = 0;
109	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
110	>
111	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
112	>	cgStamp = molStamp->getCutoffGroupStamp(j);
113	>	nAtomsInGroups += cgStamp->getNMembers();
114	>	}
115	>
116	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
117	>
118	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
119	>
120	>	//calculate atoms in rigid bodies
121	>	int nAtomsInRigidBodies = 0;
122	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
123	>
124	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
125	>	rbStamp = molStamp->getRigidBodyStamp(j);
126	>	nAtomsInRigidBodies += rbStamp->getNMembers();
127	>	}
128	>
129	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
130	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
131	>
132	>	}
133	>
134	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
135	>	//group therefore the total number of cutoff groups in the system is
136	>	//equal to the total number of atoms minus number of atoms belong to
137	>	//cutoff group defined in meta-data file plus the number of cutoff
138	>	//groups defined in meta-data file
139	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
140	>
141	>	//every free atom (atom does not belong to rigid bodies) is an
142	>	//integrable object therefore the total number of integrable objects
143	>	//in the system is equal to the total number of atoms minus number of
144	>	//atoms belong to rigid body defined in meta-data file plus the number
145	>	//of rigid bodies defined in meta-data file
146	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
147	>	+ nGlobalRigidBodies_;
148	>
149	>	nGlobalMols_ = molStampIds_.size();
150	>	molToProcMap_.resize(nGlobalMols_);
151	>	}
152	>
153	>	SimInfo::~SimInfo() {
154	>	map<int, Molecule*>::iterator i;
155	>	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
156	>	delete i->second;
157	>	}
158	>	molecules_.clear();
159	>
160	>	delete sman_;
161	>	delete simParams_;
162	>	delete forceField_;
163	>	}
164
31	–	SimInfo* currentInfo;
165
166	<	SimInfo::SimInfo(){
167	<
168	<	n_constraints = 0;
169	<	nZconstraints = 0;
170	<	n_oriented = 0;
171	<	n_dipoles = 0;
172	<	ndf = 0;
173	<	ndfRaw = 0;
174	<	nZconstraints = 0;
175	<	the_integrator = NULL;
176	<	setTemp = 0;
177	<	thermalTime = 0.0;
178	<	currentTime = 0.0;
179	<	rCut = 0.0;
180	<	rSw = 0.0;
181	<
182	<	haveRcut = 0;
183	<	haveRsw = 0;
184	<	boxIsInit = 0;
166	>	bool SimInfo::addMolecule(Molecule* mol) {
167	>	MoleculeIterator i;
168	>
169	>	i = molecules_.find(mol->getGlobalIndex());
170	>	if (i == molecules_.end() ) {
171	>
172	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
173	>
174	>	nAtoms_ += mol->getNAtoms();
175	>	nBonds_ += mol->getNBonds();
176	>	nBends_ += mol->getNBends();
177	>	nTorsions_ += mol->getNTorsions();
178	>	nInversions_ += mol->getNInversions();
179	>	nRigidBodies_ += mol->getNRigidBodies();
180	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
181	>	nCutoffGroups_ += mol->getNCutoffGroups();
182	>	nConstraints_ += mol->getNConstraintPairs();
183	>
184	>	addInteractionPairs(mol);
185	>
186	>	return true;
187	>	} else {
188	>	return false;
189	>	}
190	>	}
191
192	<	resetTime = 1e99;
192	>	bool SimInfo::removeMolecule(Molecule* mol) {
193	>	MoleculeIterator i;
194	>	i = molecules_.find(mol->getGlobalIndex());
195
196	<	orthoRhombic = 0;
56	<	orthoTolerance = 1E-6;
57	<	useInitXSstate = true;
196	>	if (i != molecules_.end() ) {
197
198	<	usePBC = 0;
199	<	useDirectionalAtoms = 0;
200	<	useLennardJones = 0;
201	<	useElectrostatics = 0;
202	<	useCharges = 0;
203	<	useDipoles = 0;
204	<	useSticky = 0;
205	<	useGayBerne = 0;
206	<	useEAM = 0;
207	<	useShapes = 0;
208	<	useFLARB = 0;
198	>	assert(mol == i->second);
199	>
200	>	nAtoms_ -= mol->getNAtoms();
201	>	nBonds_ -= mol->getNBonds();
202	>	nBends_ -= mol->getNBends();
203	>	nTorsions_ -= mol->getNTorsions();
204	>	nInversions_ -= mol->getNInversions();
205	>	nRigidBodies_ -= mol->getNRigidBodies();
206	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
207	>	nCutoffGroups_ -= mol->getNCutoffGroups();
208	>	nConstraints_ -= mol->getNConstraintPairs();
209
210	<	useSolidThermInt = 0;
211	<	useLiquidThermInt = 0;
210	>	removeInteractionPairs(mol);
211	>	molecules_.erase(mol->getGlobalIndex());
212
213	<	haveCutoffGroups = false;
214	<
215	<	excludes = Exclude::Instance();
216	<
217	<	myConfiguration = new SimState();
213	>	delete mol;
214	>
215	>	return true;
216	>	} else {
217	>	return false;
218	>	}
219	>	}
220
221	<	has_minimizer = false;
222	<	the_minimizer =NULL;
221	>
222	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
223	>	i = molecules_.begin();
224	>	return i == molecules_.end() ? NULL : i->second;
225	>	}
226
227	<	ngroup = 0;
227	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
228	>	++i;
229	>	return i == molecules_.end() ? NULL : i->second;
230	>	}
231
85	–	}
232
233	+	void SimInfo::calcNdf() {
234	+	int ndf_local;
235	+	MoleculeIterator i;
236	+	vector<StuntDouble*>::iterator j;
237	+	Molecule* mol;
238	+	StuntDouble* integrableObject;
239
240	<	SimInfo::~SimInfo(){
240	>	ndf_local = 0;
241	>
242	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
243	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
244	>	integrableObject = mol->nextIntegrableObject(j)) {
245
246	<	delete myConfiguration;
246	>	ndf_local += 3;
247
248	<	map<string, GenericData*>::iterator i;
249	<
250	<	for(i = properties.begin(); i != properties.end(); i++)
251	<	delete (*i).second;
248	>	if (integrableObject->isDirectional()) {
249	>	if (integrableObject->isLinear()) {
250	>	ndf_local += 2;
251	>	} else {
252	>	ndf_local += 3;
253	>	}
254	>	}
255	>
256	>	}
257	>	}
258	>
259	>	// n_constraints is local, so subtract them on each processor
260	>	ndf_local -= nConstraints_;
261
262	<	}
262	>	#ifdef IS_MPI
263	>	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
264	>	#else
265	>	ndf_ = ndf_local;
266	>	#endif
267
268	<	void SimInfo::setBox(double newBox[3]) {
269	<
270	<	int i, j;
102	<	double tempMat[3][3];
268	>	// nZconstraints_ is global, as are the 3 COM translations for the
269	>	// entire system:
270	>	ndf_ = ndf_ - 3 - nZconstraint_;
271
272	<	for(i=0; i<3; i++)
105	<	for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
272	>	}
273
274	<	tempMat[0][0] = newBox[0];
275	<	tempMat[1][1] = newBox[1];
276	<	tempMat[2][2] = newBox[2];
274	>	int SimInfo::getFdf() {
275	>	#ifdef IS_MPI
276	>	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
277	>	#else
278	>	fdf_ = fdf_local;
279	>	#endif
280	>	return fdf_;
281	>	}
282	>
283	>	void SimInfo::calcNdfRaw() {
284	>	int ndfRaw_local;
285
286	<	setBoxM( tempMat );
286	>	MoleculeIterator i;
287	>	vector<StuntDouble*>::iterator j;
288	>	Molecule* mol;
289	>	StuntDouble* integrableObject;
290
291	<	}
291	>	// Raw degrees of freedom that we have to set
292	>	ndfRaw_local = 0;
293	>
294	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
295	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
296	>	integrableObject = mol->nextIntegrableObject(j)) {
297
298	<	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);
298	>	ndfRaw_local += 3;
299
300	<	if( !boxIsInit ) boxIsInit = 1;
301	<
302	<	for(i=0; i < 3; i++)
303	<	for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
304	<
305	<	calcBoxL();
306	<	calcHmatInv();
307	<
308	<	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];
300	>	if (integrableObject->isDirectional()) {
301	>	if (integrableObject->isLinear()) {
302	>	ndfRaw_local += 2;
303	>	} else {
304	>	ndfRaw_local += 3;
305	>	}
306	>	}
307	>
308	>	}
309		}
310	+
311	+	#ifdef IS_MPI
312	+	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
313	+	#else
314	+	ndfRaw_ = ndfRaw_local;
315	+	#endif
316		}
317
318	<	setFortranBox(FortranHmat, FortranHmatInv, &orthoRhombic);
319	<
142	<	}
143	<
318	>	void SimInfo::calcNdfTrans() {
319	>	int ndfTrans_local;
320
321	<	void SimInfo::getBoxM (double theBox[3][3]) {
321	>	ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
322
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	–	}
323
324	+	#ifdef IS_MPI
325	+	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
326	+	#else
327	+	ndfTrans_ = ndfTrans_local;
328	+	#endif
329
330	<	void SimInfo::scaleBox(double scale) {
331	<	double theBox[3][3];
332	<	int i, j;
330	>	ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
331	>
332	>	}
333
334	<	// cerr << "Scaling box by " << scale << "\n";
334	>	void SimInfo::addInteractionPairs(Molecule* mol) {
335	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
336	>	vector<Bond*>::iterator bondIter;
337	>	vector<Bend*>::iterator bendIter;
338	>	vector<Torsion*>::iterator torsionIter;
339	>	vector<Inversion*>::iterator inversionIter;
340	>	Bond* bond;
341	>	Bend* bend;
342	>	Torsion* torsion;
343	>	Inversion* inversion;
344	>	int a;
345	>	int b;
346	>	int c;
347	>	int d;
348
349	<	for(i=0; i<3; i++)
350	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
349	>	// atomGroups can be used to add special interaction maps between
350	>	// groups of atoms that are in two separate rigid bodies.
351	>	// However, most site-site interactions between two rigid bodies
352	>	// are probably not special, just the ones between the physically
353	>	// bonded atoms.  Interactions *within* a single rigid body should
354	>	// always be excluded.  These are done at the bottom of this
355	>	// function.
356
357	<	setBoxM(theBox);
357	>	map<int, set<int> > atomGroups;
358	>	Molecule::RigidBodyIterator rbIter;
359	>	RigidBody* rb;
360	>	Molecule::IntegrableObjectIterator ii;
361	>	StuntDouble* integrableObject;
362	>
363	>	for (integrableObject = mol->beginIntegrableObject(ii);
364	>	integrableObject != NULL;
365	>	integrableObject = mol->nextIntegrableObject(ii)) {
366	>
367	>	if (integrableObject->isRigidBody()) {
368	>	rb = static_cast<RigidBody*>(integrableObject);
369	>	vector<Atom*> atoms = rb->getAtoms();
370	>	set<int> rigidAtoms;
371	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
372	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
373	>	}
374	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
375	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
376	>	}
377	>	} else {
378	>	set<int> oneAtomSet;
379	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
380	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
381	>	}
382	>	}
383	>
384	>	for (bond= mol->beginBond(bondIter); bond != NULL;
385	>	bond = mol->nextBond(bondIter)) {
386
387	<	}
387	>	a = bond->getAtomA()->getGlobalIndex();
388	>	b = bond->getAtomB()->getGlobalIndex();
389	>
390	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
391	>	oneTwoInteractions_.addPair(a, b);
392	>	} else {
393	>	excludedInteractions_.addPair(a, b);
394	>	}
395	>	}
396
397	<	void SimInfo::calcHmatInv( void ) {
398	<
168	<	int oldOrtho;
169	<	int i,j;
170	<	double smallDiag;
171	<	double tol;
172	<	double sanity[3][3];
397	>	for (bend= mol->beginBend(bendIter); bend != NULL;
398	>	bend = mol->nextBend(bendIter)) {
399
400	<	invertMat3( Hmat, HmatInv );
400	>	a = bend->getAtomA()->getGlobalIndex();
401	>	b = bend->getAtomB()->getGlobalIndex();
402	>	c = bend->getAtomC()->getGlobalIndex();
403	>
404	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
405	>	oneTwoInteractions_.addPair(a, b);
406	>	oneTwoInteractions_.addPair(b, c);
407	>	} else {
408	>	excludedInteractions_.addPair(a, b);
409	>	excludedInteractions_.addPair(b, c);
410	>	}
411
412	<	// check to see if Hmat is orthorhombic
413	<
414	<	oldOrtho = orthoRhombic;
415	<
180	<	smallDiag = fabs(Hmat[0][0]);
181	<	if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
182	<	if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
183	<	tol = smallDiag * orthoTolerance;
184	<
185	<	orthoRhombic = 1;
186	<
187	<	for (i = 0; i < 3; i++ ) {
188	<	for (j = 0 ; j < 3; j++) {
189	<	if (i != j) {
190	<	if (orthoRhombic) {
191	<	if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
192	<	}
412	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
413	>	oneThreeInteractions_.addPair(a, c);
414	>	} else {
415	>	excludedInteractions_.addPair(a, c);
416		}
417		}
195	–	}
418
419	<	if( oldOrtho != orthoRhombic ){
420	<
199	<	if( orthoRhombic ) {
200	<	sprintf( painCave.errMsg,
201	<	"OOPSE is switching from the default Non-Orthorhombic\n"
202	<	"\tto the faster Orthorhombic periodic boundary computations.\n"
203	<	"\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();
209	<	}
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	<	}
419	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
420	>	torsion = mol->nextTorsion(torsionIter)) {
421
422	<	void SimInfo::calcBoxL( void ){
422	>	a = torsion->getAtomA()->getGlobalIndex();
423	>	b = torsion->getAtomB()->getGlobalIndex();
424	>	c = torsion->getAtomC()->getGlobalIndex();
425	>	d = torsion->getAtomD()->getGlobalIndex();
426
427	<	double dx, dy, dz, dsq;
427	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
428	>	oneTwoInteractions_.addPair(a, b);
429	>	oneTwoInteractions_.addPair(b, c);
430	>	oneTwoInteractions_.addPair(c, d);
431	>	} else {
432	>	excludedInteractions_.addPair(a, b);
433	>	excludedInteractions_.addPair(b, c);
434	>	excludedInteractions_.addPair(c, d);
435	>	}
436
437	<	// boxVol = Determinant of Hmat
437	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
438	>	oneThreeInteractions_.addPair(a, c);
439	>	oneThreeInteractions_.addPair(b, d);
440	>	} else {
441	>	excludedInteractions_.addPair(a, c);
442	>	excludedInteractions_.addPair(b, d);
443	>	}
444
445	<	boxVol = matDet3( Hmat );
445	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
446	>	oneFourInteractions_.addPair(a, d);
447	>	} else {
448	>	excludedInteractions_.addPair(a, d);
449	>	}
450	>	}
451
452	<	// boxLx
453	<
235	<	dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
236	<	dsq = dx*dx + dy*dy + dz*dz;
237	<	boxL[0] = sqrt( dsq );
238	<	//maxCutoff = 0.5 * boxL[0];
452	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
453	>	inversion = mol->nextInversion(inversionIter)) {
454
455	<	// boxLy
456	<
457	<	dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
458	<	dsq = dx*dx + dy*dy + dz*dz;
244	<	boxL[1] = sqrt( dsq );
245	<	//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
455	>	a = inversion->getAtomA()->getGlobalIndex();
456	>	b = inversion->getAtomB()->getGlobalIndex();
457	>	c = inversion->getAtomC()->getGlobalIndex();
458	>	d = inversion->getAtomD()->getGlobalIndex();
459
460	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
461	+	oneTwoInteractions_.addPair(a, b);
462	+	oneTwoInteractions_.addPair(a, c);
463	+	oneTwoInteractions_.addPair(a, d);
464	+	} else {
465	+	excludedInteractions_.addPair(a, b);
466	+	excludedInteractions_.addPair(a, c);
467	+	excludedInteractions_.addPair(a, d);
468	+	}
469
470	<	// boxLz
471	<
472	<	dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
473	<	dsq = dx*dx + dy*dy + dz*dz;
474	<	boxL[2] = sqrt( dsq );
475	<	//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
470	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
471	>	oneThreeInteractions_.addPair(b, c);
472	>	oneThreeInteractions_.addPair(b, d);
473	>	oneThreeInteractions_.addPair(c, d);
474	>	} else {
475	>	excludedInteractions_.addPair(b, c);
476	>	excludedInteractions_.addPair(b, d);
477	>	excludedInteractions_.addPair(c, d);
478	>	}
479	>	}
480
481	<	//calculate the max cutoff
482	<	maxCutoff =  calcMaxCutOff();
483	<
484	<	checkCutOffs();
481	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
482	>	rb = mol->nextRigidBody(rbIter)) {
483	>	vector<Atom*> atoms = rb->getAtoms();
484	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
485	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
486	>	a = atoms[i]->getGlobalIndex();
487	>	b = atoms[j]->getGlobalIndex();
488	>	excludedInteractions_.addPair(a, b);
489	>	}
490	>	}
491	>	}
492
493	<	}
493	>	}
494
495	+	void SimInfo::removeInteractionPairs(Molecule* mol) {
496	+	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
497	+	vector<Bond*>::iterator bondIter;
498	+	vector<Bend*>::iterator bendIter;
499	+	vector<Torsion*>::iterator torsionIter;
500	+	vector<Inversion*>::iterator inversionIter;
501	+	Bond* bond;
502	+	Bend* bend;
503	+	Torsion* torsion;
504	+	Inversion* inversion;
505	+	int a;
506	+	int b;
507	+	int c;
508	+	int d;
509
510	<	double SimInfo::calcMaxCutOff(){
510	>	map<int, set<int> > atomGroups;
511	>	Molecule::RigidBodyIterator rbIter;
512	>	RigidBody* rb;
513	>	Molecule::IntegrableObjectIterator ii;
514	>	StuntDouble* integrableObject;
515	>
516	>	for (integrableObject = mol->beginIntegrableObject(ii);
517	>	integrableObject != NULL;
518	>	integrableObject = mol->nextIntegrableObject(ii)) {
519	>
520	>	if (integrableObject->isRigidBody()) {
521	>	rb = static_cast<RigidBody*>(integrableObject);
522	>	vector<Atom*> atoms = rb->getAtoms();
523	>	set<int> rigidAtoms;
524	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
525	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
526	>	}
527	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
528	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
529	>	}
530	>	} else {
531	>	set<int> oneAtomSet;
532	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
533	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
534	>	}
535	>	}
536
537	<	double ri[3], rj[3], rk[3];
538	<	double rij[3], rjk[3], rki[3];
539	<	double minDist;
537	>	for (bond= mol->beginBond(bondIter); bond != NULL;
538	>	bond = mol->nextBond(bondIter)) {
539	>
540	>	a = bond->getAtomA()->getGlobalIndex();
541	>	b = bond->getAtomB()->getGlobalIndex();
542	>
543	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
544	>	oneTwoInteractions_.removePair(a, b);
545	>	} else {
546	>	excludedInteractions_.removePair(a, b);
547	>	}
548	>	}
549
550	<	ri[0] = Hmat[0][0];
551	<	ri[1] = Hmat[1][0];
271	<	ri[2] = Hmat[2][0];
550	>	for (bend= mol->beginBend(bendIter); bend != NULL;
551	>	bend = mol->nextBend(bendIter)) {
552
553	<	rj[0] = Hmat[0][1];
554	<	rj[1] = Hmat[1][1];
555	<	rj[2] = Hmat[2][1];
553	>	a = bend->getAtomA()->getGlobalIndex();
554	>	b = bend->getAtomB()->getGlobalIndex();
555	>	c = bend->getAtomC()->getGlobalIndex();
556	>
557	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
558	>	oneTwoInteractions_.removePair(a, b);
559	>	oneTwoInteractions_.removePair(b, c);
560	>	} else {
561	>	excludedInteractions_.removePair(a, b);
562	>	excludedInteractions_.removePair(b, c);
563	>	}
564
565	<	rk[0] = Hmat[0][2];
566	<	rk[1] = Hmat[1][2];
567	<	rk[2] = Hmat[2][2];
568	<
569	<	crossProduct3(ri, rj, rij);
570	<	distXY = dotProduct3(rk,rij) / norm3(rij);
565	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
566	>	oneThreeInteractions_.removePair(a, c);
567	>	} else {
568	>	excludedInteractions_.removePair(a, c);
569	>	}
570	>	}
571
572	<	crossProduct3(rj,rk, rjk);
573	<	distYZ = dotProduct3(ri,rjk) / norm3(rjk);
572	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
573	>	torsion = mol->nextTorsion(torsionIter)) {
574
575	<	crossProduct3(rk,ri, rki);
576	<	distZX = dotProduct3(rj,rki) / norm3(rki);
577	<
578	<	minDist = min(min(distXY, distYZ), distZX);
291	<	return minDist/2;
575	>	a = torsion->getAtomA()->getGlobalIndex();
576	>	b = torsion->getAtomB()->getGlobalIndex();
577	>	c = torsion->getAtomC()->getGlobalIndex();
578	>	d = torsion->getAtomD()->getGlobalIndex();
579
580	<	}
580	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
581	>	oneTwoInteractions_.removePair(a, b);
582	>	oneTwoInteractions_.removePair(b, c);
583	>	oneTwoInteractions_.removePair(c, d);
584	>	} else {
585	>	excludedInteractions_.removePair(a, b);
586	>	excludedInteractions_.removePair(b, c);
587	>	excludedInteractions_.removePair(c, d);
588	>	}
589
590	<	void SimInfo::wrapVector( double thePos[3] ){
590	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
591	>	oneThreeInteractions_.removePair(a, c);
592	>	oneThreeInteractions_.removePair(b, d);
593	>	} else {
594	>	excludedInteractions_.removePair(a, c);
595	>	excludedInteractions_.removePair(b, d);
596	>	}
597
598	<	int i;
599	<	double scaled[3];
598	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
599	>	oneFourInteractions_.removePair(a, d);
600	>	} else {
601	>	excludedInteractions_.removePair(a, d);
602	>	}
603	>	}
604
605	<	if( !orthoRhombic ){
606	<	// calc the scaled coordinates.
302	<
605	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
606	>	inversion = mol->nextInversion(inversionIter)) {
607
608	<	matVecMul3(HmatInv, thePos, scaled);
609	<
610	<	for(i=0; i<3; i++)
611	<	scaled[i] -= roundMe(scaled[i]);
308	<
309	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
310	<
311	<	matVecMul3(Hmat, scaled, thePos);
608	>	a = inversion->getAtomA()->getGlobalIndex();
609	>	b = inversion->getAtomB()->getGlobalIndex();
610	>	c = inversion->getAtomC()->getGlobalIndex();
611	>	d = inversion->getAtomD()->getGlobalIndex();
612
613	<	}
614	<	else{
615	<	// calc the scaled coordinates.
613	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
614	>	oneTwoInteractions_.removePair(a, b);
615	>	oneTwoInteractions_.removePair(a, c);
616	>	oneTwoInteractions_.removePair(a, d);
617	>	} else {
618	>	excludedInteractions_.removePair(a, b);
619	>	excludedInteractions_.removePair(a, c);
620	>	excludedInteractions_.removePair(a, d);
621	>	}
622	>
623	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
624	>	oneThreeInteractions_.removePair(b, c);
625	>	oneThreeInteractions_.removePair(b, d);
626	>	oneThreeInteractions_.removePair(c, d);
627	>	} else {
628	>	excludedInteractions_.removePair(b, c);
629	>	excludedInteractions_.removePair(b, d);
630	>	excludedInteractions_.removePair(c, d);
631	>	}
632	>	}
633	>
634	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
635	>	rb = mol->nextRigidBody(rbIter)) {
636	>	vector<Atom*> atoms = rb->getAtoms();
637	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
638	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
639	>	a = atoms[i]->getGlobalIndex();
640	>	b = atoms[j]->getGlobalIndex();
641	>	excludedInteractions_.removePair(a, b);
642	>	}
643	>	}
644	>	}
645
317	–	for(i=0; i<3; i++)
318	–	scaled[i] = thePos[i]*HmatInv[i][i];
319	–
320	–	// wrap the scaled coordinates
321	–
322	–	for(i=0; i<3; i++)
323	–	scaled[i] -= roundMe(scaled[i]);
324	–
325	–	// calc the wrapped real coordinates from the wrapped scaled coordinates
326	–
327	–	for(i=0; i<3; i++)
328	–	thePos[i] = scaled[i]*Hmat[i][i];
646		}
647	+
648	+
649	+	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
650	+	int curStampId;
651
652	<	}
652	>	//index from 0
653	>	curStampId = moleculeStamps_.size();
654
655	+	moleculeStamps_.push_back(molStamp);
656	+	molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
657	+	}
658
659	<	int SimInfo::getNDF(){
335	<	int ndf_local;
659	>	void SimInfo::update() {
660
661	<	ndf_local = 0;
661	>	setupSimType();
662	>	setupCutoffRadius();
663	>	setupSwitchingRadius();
664	>	setupCutoffMethod();
665	>	setupSkinThickness();
666	>	setupSwitchingFunction();
667	>	setupAccumulateBoxDipole();
668	>
669	>	#ifdef IS_MPI
670	>	setupFortranParallel();
671	>	#endif
672	>	setupFortranSim();
673	>	fortranInitialized_ = true;
674	>
675	>	calcNdf();
676	>	calcNdfRaw();
677	>	calcNdfTrans();
678	>	}
679
680	<	for(int i = 0; i < integrableObjects.size(); i++){
681	<	ndf_local += 3;
682	<	if (integrableObjects[i]->isDirectional()) {
683	<	if (integrableObjects[i]->isLinear())
684	<	ndf_local += 2;
685	<	else
686	<	ndf_local += 3;
680	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
681	>	SimInfo::MoleculeIterator mi;
682	>	Molecule* mol;
683	>	Molecule::AtomIterator ai;
684	>	Atom* atom;
685	>	set<AtomType*> atomTypes;
686	>
687	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
688	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
689	>	atomTypes.insert(atom->getAtomType());
690	>	}
691	>	}
692	>	return atomTypes;
693	>	}
694	>
695	>	/**
696	>	* setupCutoffRadius
697	>	*
698	>	*  If the cutoffRadius was explicitly set, use that value.
699	>	*  If the cutoffRadius was not explicitly set:
700	>	*      Are there electrostatic atoms?  Use 12.0 Angstroms.
701	>	*      No electrostatic atoms?  Poll the atom types present in the
702	>	*      simulation for suggested cutoff values (e.g. 2.5 * sigma).
703	>	*      Use the maximum suggested value that was found.
704	>	*/
705	>	void SimInfo::setupCutoffRadius() {
706	>
707	>	if (simParams_->haveCutoffRadius()) {
708	>	cutoffRadius_ = simParams_->getCutoffRadius();
709	>	} else {
710	>	if (usesElectrostaticAtoms_) {
711	>	sprintf(painCave.errMsg,
712	>	"SimInfo Warning: No value was set for the cutoffRadius.\n"
713	>	"\tOpenMD will use a default value of 12.0 angstroms"
714	>	"\tfor the cutoffRadius.\n");
715	>	painCave.isFatal = 0;
716	>	simError();
717	>	cutoffRadius_ = 12.0;
718	>	} else {
719	>	RealType thisCut;
720	>	set<AtomType*>::iterator i;
721	>	set<AtomType*> atomTypes;
722	>	atomTypes = getSimulatedAtomTypes();
723	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
724	>	thisCut = InteractionManager::Instance()->getSuggestedCutoffRadius((*i));
725	>	cutoffRadius_ = max(thisCut, cutoffRadius_);
726	>	}
727	>	sprintf(painCave.errMsg,
728	>	"SimInfo Warning: No value was set for the cutoffRadius.\n"
729	>	"\tOpenMD will use %lf angstroms.\n",
730	>	cutoffRadius_);
731	>	painCave.isFatal = 0;
732	>	simError();
733	>	}
734		}
735	+
736	+	InteractionManager::Instance()->setCutoffRadius(cutoffRadius_);
737		}
738	+
739	+	/**
740	+	* setupSwitchingRadius
741	+	*
742	+	*  If the switchingRadius was explicitly set, use that value (but check it)
743	+	*  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
744	+	*/
745	+	void SimInfo::setupSwitchingRadius() {
746	+
747	+	if (simParams_->haveSwitchingRadius()) {
748	+	switchingRadius_ = simParams_->getSwitchingRadius();
749	+	if (switchingRadius_ > cutoffRadius_) {
750	+	sprintf(painCave.errMsg,
751	+	"SimInfo Error: switchingRadius (%f) is larger than cutoffRadius(%f)\n",
752	+	switchingRadius_, cutoffRadius_);
753	+	painCave.isFatal = 1;
754	+	simError();
755
756	<	// n_constraints is local, so subtract them on each processor:
756	>	}
757	>	} else {
758	>	switchingRadius_ = 0.85 * cutoffRadius_;
759	>	sprintf(painCave.errMsg,
760	>	"SimInfo Warning: No value was set for the switchingRadius.\n"
761	>	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
762	>	"\tswitchingRadius = %f. for this simulation\n", switchingRadius_);
763	>	painCave.isFatal = 0;
764	>	simError();
765	>	}
766	>	InteractionManager::Instance()->setSwitchingRadius(switchingRadius_);
767	>	}
768
769	<	ndf_local -= n_constraints;
769	>	/**
770	>	* setupSkinThickness
771	>	*
772	>	*  If the skinThickness was explicitly set, use that value (but check it)
773	>	*  If the skinThickness was not explicitly set: use 1.0 angstroms
774	>	*/
775	>	void SimInfo::setupSkinThickness() {
776	>	if (simParams_->haveSkinThickness()) {
777	>	skinThickness_ = simParams_->getSkinThickness();
778	>	} else {
779	>	skinThickness_ = 1.0;
780	>	sprintf(painCave.errMsg,
781	>	"SimInfo Warning: No value was set for the skinThickness.\n"
782	>	"\tOpenMD will use a default value of %f Angstroms\n"
783	>	"\tfor this simulation\n", skinThickness_);
784	>	painCave.isFatal = 0;
785	>	simError();
786	>	}
787	>	}
788
789	<	#ifdef IS_MPI
790	<	MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
791	<	#else
792	<	ndf = ndf_local;
789	>	void SimInfo::setupSimType() {
790	>	set<AtomType*>::iterator i;
791	>	set<AtomType*> atomTypes;
792	>	atomTypes = getSimulatedAtomTypes();
793	>
794	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
795	>
796	>	int usesElectrostatic = 0;
797	>	int usesMetallic = 0;
798	>	int usesDirectional = 0;
799	>	//loop over all of the atom types
800	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
801	>	usesElectrostatic |= (*i)->isElectrostatic();
802	>	usesMetallic |= (*i)->isMetal();
803	>	usesDirectional |= (*i)->isDirectional();
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		#endif
817	+	fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;
818	+	fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
819	+	fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
820	+	fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
821	+	fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
822	+	fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
823	+	}
824
825	<	// nZconstraints is global, as are the 3 COM translations for the
826	<	// entire system:
825	>	void SimInfo::setupFortranSim() {
826	>	int isError;
827	>	int nExclude, nOneTwo, nOneThree, nOneFour;
828	>	vector<int> fortranGlobalGroupMembership;
829	>
830	>	notifyFortranSkinThickness(&skinThickness_);
831
832	<	ndf = ndf - 3 - nZconstraints;
832	>	int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0;
833	>	int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0;
834	>	notifyFortranCutoffs(&cutoffRadius_, &switchingRadius_, &ljsp, &ljsf);
835
836	<	return ndf;
365	<	}
836	>	isError = 0;
837
838	<	int SimInfo::getNDFraw() {
839	<	int ndfRaw_local;
838	>	//globalGroupMembership_ is filled by SimCreator
839	>	for (int i = 0; i < nGlobalAtoms_; i++) {
840	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
841	>	}
842
843	<	// Raw degrees of freedom that we have to set
844	<	ndfRaw_local = 0;
843	>	//calculate mass ratio of cutoff group
844	>	vector<RealType> mfact;
845	>	SimInfo::MoleculeIterator mi;
846	>	Molecule* mol;
847	>	Molecule::CutoffGroupIterator ci;
848	>	CutoffGroup* cg;
849	>	Molecule::AtomIterator ai;
850	>	Atom* atom;
851	>	RealType totalMass;
852
853	<	for(int i = 0; i < integrableObjects.size(); i++){
854	<	ndfRaw_local += 3;
855	<	if (integrableObjects[i]->isDirectional()) {
856	<	if (integrableObjects[i]->isLinear())
857	<	ndfRaw_local += 2;
858	<	else
859	<	ndfRaw_local += 3;
853	>	//to avoid memory reallocation, reserve enough space for mfact
854	>	mfact.reserve(getNCutoffGroups());
855	>
856	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
857	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
858	>
859	>	totalMass = cg->getMass();
860	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
861	>	// Check for massless groups - set mfact to 1 if true
862	>	if (totalMass != 0)
863	>	mfact.push_back(atom->getMass()/totalMass);
864	>	else
865	>	mfact.push_back( 1.0 );
866	>	}
867	>	}
868		}
869	<	}
869	>
870	>	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
871	>	vector<int> identArray;
872	>
873	>	//to avoid memory reallocation, reserve enough space identArray
874	>	identArray.reserve(getNAtoms());
875
876	<	#ifdef IS_MPI
877	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
878	<	#else
879	<	ndfRaw = ndfRaw_local;
880	<	#endif
876	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
877	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
878	>	identArray.push_back(atom->getIdent());
879	>	}
880	>	}
881
882	<	return ndfRaw;
883	<	}
882	>	//fill molMembershipArray
883	>	//molMembershipArray is filled by SimCreator
884	>	vector<int> molMembershipArray(nGlobalAtoms_);
885	>	for (int i = 0; i < nGlobalAtoms_; i++) {
886	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
887	>	}
888	>
889	>	//setup fortran simulation
890
891	<	int SimInfo::getNDFtranslational() {
892	<	int ndfTrans_local;
891	>	nExclude = excludedInteractions_.getSize();
892	>	nOneTwo = oneTwoInteractions_.getSize();
893	>	nOneThree = oneThreeInteractions_.getSize();
894	>	nOneFour = oneFourInteractions_.getSize();
895
896	<	ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
896	>	int* excludeList = excludedInteractions_.getPairList();
897	>	int* oneTwoList = oneTwoInteractions_.getPairList();
898	>	int* oneThreeList = oneThreeInteractions_.getPairList();
899	>	int* oneFourList = oneFourInteractions_.getPairList();
900
901	+	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
902	+	&nExclude, excludeList,
903	+	&nOneTwo, oneTwoList,
904	+	&nOneThree, oneThreeList,
905	+	&nOneFour, oneFourList,
906	+	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
907	+	&fortranGlobalGroupMembership[0], &isError);
908	+
909	+	if( isError ){
910	+
911	+	sprintf( painCave.errMsg,
912	+	"There was an error setting the simulation information in fortran.\n" );
913	+	painCave.isFatal = 1;
914	+	painCave.severity = OPENMD_ERROR;
915	+	simError();
916	+	}
917	+
918	+
919	+	sprintf( checkPointMsg,
920	+	"succesfully sent the simulation information to fortran.\n");
921	+
922	+	errorCheckPoint();
923	+
924	+	// Setup number of neighbors in neighbor list if present
925	+	if (simParams_->haveNeighborListNeighbors()) {
926	+	int nlistNeighbors = simParams_->getNeighborListNeighbors();
927	+	setNeighbors(&nlistNeighbors);
928	+	}
929	+
930
931	<	#ifdef IS_MPI
399	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
400	<	#else
401	<	ndfTrans = ndfTrans_local;
402	<	#endif
931	>	}
932
404	–	ndfTrans = ndfTrans - 3 - nZconstraints;
933
934	<	return ndfTrans;
935	<	}
934	>	void SimInfo::setupFortranParallel() {
935	>	#ifdef IS_MPI
936	>	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
937	>	vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
938	>	vector<int> localToGlobalCutoffGroupIndex;
939	>	SimInfo::MoleculeIterator mi;
940	>	Molecule::AtomIterator ai;
941	>	Molecule::CutoffGroupIterator ci;
942	>	Molecule* mol;
943	>	Atom* atom;
944	>	CutoffGroup* cg;
945	>	mpiSimData parallelData;
946	>	int isError;
947
948	<	int SimInfo::getTotIntegrableObjects() {
410	<	int nObjs_local;
411	<	int nObjs;
948	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
949
950	<	nObjs_local =  integrableObjects.size();
950	>	//local index(index in DataStorge) of atom is important
951	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
952	>	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
953	>	}
954
955	+	//local index of cutoff group is trivial, it only depends on the order of travesing
956	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
957	+	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
958	+	}
959	+
960	+	}
961
962	<	#ifdef IS_MPI
963	<	MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
964	<	#else
965	<	nObjs = nObjs_local;
962	>	//fill up mpiSimData struct
963	>	parallelData.nMolGlobal = getNGlobalMolecules();
964	>	parallelData.nMolLocal = getNMolecules();
965	>	parallelData.nAtomsGlobal = getNGlobalAtoms();
966	>	parallelData.nAtomsLocal = getNAtoms();
967	>	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
968	>	parallelData.nGroupsLocal = getNCutoffGroups();
969	>	parallelData.myNode = worldRank;
970	>	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
971	>
972	>	//pass mpiSimData struct and index arrays to fortran
973	>	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
974	>	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
975	>	&localToGlobalCutoffGroupIndex[0], &isError);
976	>
977	>	if (isError) {
978	>	sprintf(painCave.errMsg,
979	>	"mpiRefresh errror: fortran didn't like something we gave it.\n");
980	>	painCave.isFatal = 1;
981	>	simError();
982	>	}
983	>
984	>	sprintf(checkPointMsg, " mpiRefresh successful.\n");
985	>	errorCheckPoint();
986	>
987		#endif
988	+	}
989
990
991	<	return nObjs;
992	<	}
991	>	void SimInfo::setupSwitchingFunction() {
992	>	int ft = CUBIC;
993	>
994	>	if (simParams_->haveSwitchingFunctionType()) {
995	>	string funcType = simParams_->getSwitchingFunctionType();
996	>	toUpper(funcType);
997	>	if (funcType == "CUBIC") {
998	>	ft = CUBIC;
999	>	} else {
1000	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1001	>	ft = FIFTH_ORDER_POLY;
1002	>	} else {
1003	>	// throw error
1004	>	sprintf( painCave.errMsg,
1005	>	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n"
1006	>	"\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".",
1007	>	funcType.c_str() );
1008	>	painCave.isFatal = 1;
1009	>	simError();
1010	>	}
1011	>	}
1012	>	}
1013
1014	<	void SimInfo::refreshSim(){
1014	>	// send switching function notification to switcheroo
1015	>	setFunctionType(&ft);
1016
1017	<	simtype fInfo;
429	<	int isError;
430	<	int n_global;
431	<	int* excl;
1017	>	}
1018
1019	<	fInfo.dielect = 0.0;
1019	>	void SimInfo::setupAccumulateBoxDipole() {
1020
1021	<	if( useDipoles ){
1022	<	if( useReactionField )fInfo.dielect = dielectric;
1021	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1022	>	if ( simParams_->haveAccumulateBoxDipole() )
1023	>	if ( simParams_->getAccumulateBoxDipole() ) {
1024	>	calcBoxDipole_ = true;
1025	>	}
1026	>
1027		}
1028
1029	<	fInfo.SIM_uses_PBC = usePBC;
1029	>	void SimInfo::addProperty(GenericData* genData) {
1030	>	properties_.addProperty(genData);
1031	>	}
1032
1033	<	if (useSticky || useDipoles || useGayBerne || useShapes) {
1034	<	useDirectionalAtoms = 1;
443	<	fInfo.SIM_uses_DirectionalAtoms = useDirectionalAtoms;
1033	>	void SimInfo::removeProperty(const string& propName) {
1034	>	properties_.removeProperty(propName);
1035		}
1036
1037	<	fInfo.SIM_uses_LennardJones = useLennardJones;
1037	>	void SimInfo::clearProperties() {
1038	>	properties_.clearProperties();
1039	>	}
1040
1041	<	if (useCharges || useDipoles) {
1042	<	useElectrostatics = 1;
450	<	fInfo.SIM_uses_Electrostatics = useElectrostatics;
1041	>	vector<string> SimInfo::getPropertyNames() {
1042	>	return properties_.getPropertyNames();
1043		}
1044	+
1045	+	vector<GenericData*> SimInfo::getProperties() {
1046	+	return properties_.getProperties();
1047	+	}
1048
1049	<	fInfo.SIM_uses_Charges = useCharges;
1050	<	fInfo.SIM_uses_Dipoles = useDipoles;
1051	<	fInfo.SIM_uses_Sticky = useSticky;
456	<	fInfo.SIM_uses_GayBerne = useGayBerne;
457	<	fInfo.SIM_uses_EAM = useEAM;
458	<	fInfo.SIM_uses_Shapes = useShapes;
459	<	fInfo.SIM_uses_FLARB = useFLARB;
460	<	fInfo.SIM_uses_RF = useReactionField;
1049	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
1050	>	return properties_.getPropertyByName(propName);
1051	>	}
1052
1053	<	n_exclude = excludes->getSize();
1054	<	excl = excludes->getFortranArray();
1055	<
1056	<	#ifdef IS_MPI
1057	<	n_global = mpiSim->getNAtomsGlobal();
1058	<	#else
468	<	n_global = n_atoms;
469	<	#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);
1053	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1054	>	if (sman_ == sman) {
1055	>	return;
1056	>	}
1057	>	delete sman_;
1058	>	sman_ = sman;
1059
1060	<	if( isError ){
1060	>	Molecule* mol;
1061	>	RigidBody* rb;
1062	>	Atom* atom;
1063	>	SimInfo::MoleculeIterator mi;
1064	>	Molecule::RigidBodyIterator rbIter;
1065	>	Molecule::AtomIterator atomIter;;
1066	>
1067	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1068	>
1069	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1070	>	atom->setSnapshotManager(sman_);
1071	>	}
1072	>
1073	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1074	>	rb->setSnapshotManager(sman_);
1075	>	}
1076	>	}
1077
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();
1078		}
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	–	}
1079
1080	<	void SimInfo::setDefaultRcut( double theRcut ){
1081	<
1082	<	haveRcut = 1;
504	<	rCut = theRcut;
505	<	rList = rCut + 1.0;
506	<
507	<	notifyFortranCutoffs( &rCut, &rSw, &rList );
508	<	}
1080	>	Vector3d SimInfo::getComVel(){
1081	>	SimInfo::MoleculeIterator i;
1082	>	Molecule* mol;
1083
1084	<	void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
1084	>	Vector3d comVel(0.0);
1085	>	RealType totalMass = 0.0;
1086	>
1087	>
1088	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1089	>	RealType mass = mol->getMass();
1090	>	totalMass += mass;
1091	>	comVel += mass * mol->getComVel();
1092	>	}
1093
1094	<	rSw = theRsw;
1095	<	setDefaultRcut( theRcut );
1096	<	}
1094	>	#ifdef IS_MPI
1095	>	RealType tmpMass = totalMass;
1096	>	Vector3d tmpComVel(comVel);
1097	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1098	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1099	>	#endif
1100
1101	+	comVel /= totalMass;
1102
1103	<	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();
1103	>	return comVel;
1104		}
550	–
551	–	}
1105
1106	<	void SimInfo::addProperty(GenericData* prop){
1106	>	Vector3d SimInfo::getCom(){
1107	>	SimInfo::MoleculeIterator i;
1108	>	Molecule* mol;
1109
1110	<	map<string, GenericData*>::iterator result;
1111	<	result = properties.find(prop->getID());
1112	<
1113	<	//we can't simply use  properties[prop->getID()] = prop,
1114	<	//it will cause memory leak if we already contain a propery which has the same name of prop
1115	<
1116	<	if(result != properties.end()){
1117	<
563	<	delete (*result).second;
564	<	(*result).second = prop;
565	<
566	<	}
567	<	else{
1110	>	Vector3d com(0.0);
1111	>	RealType totalMass = 0.0;
1112	>
1113	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1114	>	RealType mass = mol->getMass();
1115	>	totalMass += mass;
1116	>	com += mass * mol->getCom();
1117	>	}
1118
1119	<	properties[prop->getID()] = prop;
1119	>	#ifdef IS_MPI
1120	>	RealType tmpMass = totalMass;
1121	>	Vector3d tmpCom(com);
1122	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1123	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1124	>	#endif
1125
1126	+	com /= totalMass;
1127	+
1128	+	return com;
1129	+
1130	+	}
1131	+
1132	+	ostream& operator <<(ostream& o, SimInfo& info) {
1133	+
1134	+	return o;
1135		}
1136	+
1137	+
1138	+	/*
1139	+	Returns center of mass and center of mass velocity in one function call.
1140	+	*/
1141	+
1142	+	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1143	+	SimInfo::MoleculeIterator i;
1144	+	Molecule* mol;
1145	+
1146
1147	<	}
1147	>	RealType totalMass = 0.0;
1148	>
1149
1150	<	GenericData* SimInfo::getProperty(const string& propName){
1151	<
1152	<	map<string, GenericData*>::iterator result;
1153	<
1154	<	//string lowerCaseName = ();
1155	<
1156	<	result = properties.find(propName);
1157	<
1158	<	if(result != properties.end())
1159	<	return (*result).second;
1160	<	else
1161	<	return NULL;
1162	<	}
1150	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1151	>	RealType mass = mol->getMass();
1152	>	totalMass += mass;
1153	>	com += mass * mol->getCom();
1154	>	comVel += mass * mol->getComVel();
1155	>	}
1156	>
1157	>	#ifdef IS_MPI
1158	>	RealType tmpMass = totalMass;
1159	>	Vector3d tmpCom(com);
1160	>	Vector3d tmpComVel(comVel);
1161	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1162	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1163	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1164	>	#endif
1165	>
1166	>	com /= totalMass;
1167	>	comVel /= totalMass;
1168	>	}
1169	>
1170	>	/*
1171	>	Return intertia tensor for entire system and angular momentum Vector.
1172
1173
1174	<	void SimInfo::getFortranGroupArrays(SimInfo* info,
1175	<	vector<int>& FglobalGroupMembership,
1176	<	vector<double>& mfact){
1177	<
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	<
1174	>	[  Ixx -Ixy  -Ixz ]
1175	>	J =| -Iyx  Iyy  -Iyz |
1176	>	[ -Izx -Iyz   Izz ]
1177	>	*/
1178
1179	<	// Fix the silly fortran indexing problem
1179	>	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1180	>
1181	>
1182	>	RealType xx = 0.0;
1183	>	RealType yy = 0.0;
1184	>	RealType zz = 0.0;
1185	>	RealType xy = 0.0;
1186	>	RealType xz = 0.0;
1187	>	RealType yz = 0.0;
1188	>	Vector3d com(0.0);
1189	>	Vector3d comVel(0.0);
1190	>
1191	>	getComAll(com, comVel);
1192	>
1193	>	SimInfo::MoleculeIterator i;
1194	>	Molecule* mol;
1195	>
1196	>	Vector3d thisq(0.0);
1197	>	Vector3d thisv(0.0);
1198	>
1199	>	RealType thisMass = 0.0;
1200	>
1201	>
1202	>
1203	>
1204	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1205	>
1206	>	thisq = mol->getCom()-com;
1207	>	thisv = mol->getComVel()-comVel;
1208	>	thisMass = mol->getMass();
1209	>	// Compute moment of intertia coefficients.
1210	>	xx += thisq[0]*thisq[0]*thisMass;
1211	>	yy += thisq[1]*thisq[1]*thisMass;
1212	>	zz += thisq[2]*thisq[2]*thisMass;
1213	>
1214	>	// compute products of intertia
1215	>	xy += thisq[0]*thisq[1]*thisMass;
1216	>	xz += thisq[0]*thisq[2]*thisMass;
1217	>	yz += thisq[1]*thisq[2]*thisMass;
1218	>
1219	>	angularMomentum += cross( thisq, thisv ) * thisMass;
1220	>
1221	>	}
1222	>
1223	>
1224	>	inertiaTensor(0,0) = yy + zz;
1225	>	inertiaTensor(0,1) = -xy;
1226	>	inertiaTensor(0,2) = -xz;
1227	>	inertiaTensor(1,0) = -xy;
1228	>	inertiaTensor(1,1) = xx + zz;
1229	>	inertiaTensor(1,2) = -yz;
1230	>	inertiaTensor(2,0) = -xz;
1231	>	inertiaTensor(2,1) = -yz;
1232	>	inertiaTensor(2,2) = xx + yy;
1233	>
1234		#ifdef IS_MPI
1235	<	numAtom = mpiSim->getNAtomsGlobal();
1236	<	#else
1237	<	numAtom = n_atoms;
1235	>	Mat3x3d tmpI(inertiaTensor);
1236	>	Vector3d tmpAngMom;
1237	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1238	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1239		#endif
1240	<	for (int i = 0; i < numAtom; i++)
1241	<	FglobalGroupMembership.push_back(globalGroupMembership[i] + 1);
1242	<
1240	>
1241	>	return;
1242	>	}
1243
1244	<	myMols = info->molecules;
1245	<	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();
1244	>	//Returns the angular momentum of the system
1245	>	Vector3d SimInfo::getAngularMomentum(){
1246
1247	<	for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom);
1248	<	cutoffAtom != NULL;
1249	<	cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
1250	<	mfact.push_back(cutoffAtom->getMass()/totalMass);
1247	>	Vector3d com(0.0);
1248	>	Vector3d comVel(0.0);
1249	>	Vector3d angularMomentum(0.0);
1250	>
1251	>	getComAll(com,comVel);
1252	>
1253	>	SimInfo::MoleculeIterator i;
1254	>	Molecule* mol;
1255	>
1256	>	Vector3d thisr(0.0);
1257	>	Vector3d thisp(0.0);
1258	>
1259	>	RealType thisMass;
1260	>
1261	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1262	>	thisMass = mol->getMass();
1263	>	thisr = mol->getCom()-com;
1264	>	thisp = (mol->getComVel()-comVel)*thisMass;
1265	>
1266	>	angularMomentum += cross( thisr, thisp );
1267	>
1268		}
1269	+
1270	+	#ifdef IS_MPI
1271	+	Vector3d tmpAngMom;
1272	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1273	+	#endif
1274	+
1275	+	return angularMomentum;
1276	+	}
1277	+
1278	+	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1279	+	return IOIndexToIntegrableObject.at(index);
1280	+	}
1281	+
1282	+	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1283	+	IOIndexToIntegrableObject= v;
1284	+	}
1285	+
1286	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1287	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1288	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1289	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1290	+	*/
1291	+	void SimInfo::getGyrationalVolume(RealType &volume){
1292	+	Mat3x3d intTensor;
1293	+	RealType det;
1294	+	Vector3d dummyAngMom;
1295	+	RealType sysconstants;
1296	+	RealType geomCnst;
1297	+
1298	+	geomCnst = 3.0/2.0;
1299	+	/* Get the inertial tensor and angular momentum for free*/
1300	+	getInertiaTensor(intTensor,dummyAngMom);
1301	+
1302	+	det = intTensor.determinant();
1303	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1304	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1305	+	return;
1306	+	}
1307	+
1308	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1309	+	Mat3x3d intTensor;
1310	+	Vector3d dummyAngMom;
1311	+	RealType sysconstants;
1312	+	RealType geomCnst;
1313	+
1314	+	geomCnst = 3.0/2.0;
1315	+	/* Get the inertial tensor and angular momentum for free*/
1316	+	getInertiaTensor(intTensor,dummyAngMom);
1317	+
1318	+	detI = intTensor.determinant();
1319	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1320	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1321	+	return;
1322	+	}
1323	+	/*
1324	+	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1325	+	assert( v.size() == nAtoms_ + nRigidBodies_);
1326	+	sdByGlobalIndex_ = v;
1327		}
1328	+
1329	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1330	+	//assert(index < nAtoms_ + nRigidBodies_);
1331	+	return sdByGlobalIndex_.at(index);
1332	+	}
1333	+	*/
1334	+	int SimInfo::getNGlobalConstraints() {
1335	+	int nGlobalConstraints;
1336	+	#ifdef IS_MPI
1337	+	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1338	+	MPI_COMM_WORLD);
1339	+	#else
1340	+	nGlobalConstraints =  nConstraints_;
1341	+	#endif
1342	+	return nGlobalConstraints;
1343		}
1344
1345	<	}
1345	>	}//end namespace OpenMD
1346	>

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 1529 by gezelter, Mon Dec 27 18:35:59 2010 UTC

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