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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 1550 by gezelter, Wed Apr 27 21:49:59 2011 UTC

#	Line 1 | Line 1
1	<	#include <stdlib.h>
2	<	#include <string.h>
3	<	#include <math.h>
1	>	/*
2	>	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	>	*
4	>	* The University of Notre Dame grants you ("Licensee") a
5	>	* non-exclusive, royalty free, license to use, modify and
6	>	* redistribute this software in source and binary code form, provided
7	>	* that the following conditions are met:
8	>	*
9	>	* 1. Redistributions of source code must retain the above copyright
10	>	*    notice, this list of conditions and the following disclaimer.
11	>	*
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13	>	*    notice, this list of conditions and the following disclaimer in the
14	>	*    documentation and/or other materials provided with the
15	>	*    distribution.
16	>	*
17	>	* This software is provided "AS IS," without a warranty of any
18	>	* kind. All express or implied conditions, representations and
19	>	* warranties, including any implied warranty of merchantability,
20	>	* fitness for a particular purpose or non-infringement, are hereby
21	>	* excluded.  The University of Notre Dame and its licensors shall not
22	>	* be liable for any damages suffered by licensee as a result of
23	>	* using, modifying or distributing the software or its
24	>	* derivatives. In no event will the University of Notre Dame or its
25	>	* licensors be liable for any lost revenue, profit or data, or for
26	>	* direct, indirect, special, consequential, incidental or punitive
27	>	* damages, however caused and regardless of the theory of liability,
28	>	* arising out of the use of or inability to use software, even if the
29	>	* University of Notre Dame has been advised of the possibility of
30	>	* such damages.
31	>	*
32	>	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	>	* research, please cite the appropriate papers when you publish your
34	>	* work.  Good starting points are:
35	>	*
36	>	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	>	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	>	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	>	* [4]  Vardeman & Gezelter, in progress (2009).
40	>	*/
41	>
42	>	/**
43	>	* @file SimInfo.cpp
44	>	* @author    tlin
45	>	* @date  11/02/2004
46	>	* @version 1.0
47	>	*/
48
49	<	#include <iostream>
50	<	using namespace std;
49	>	#include <algorithm>
50	>	#include <set>
51	>	#include <map>
52
53		#include "brains/SimInfo.hpp"
54	<	#define __C
55	<	#include "brains/fSimulation.h"
54	>	#include "math/Vector3.hpp"
55	>	#include "primitives/Molecule.hpp"
56	>	#include "primitives/StuntDouble.hpp"
57	>	#include "utils/MemoryUtils.hpp"
58		#include "utils/simError.h"
59	<	#include "UseTheForce/DarkSide/simulation_interface.h"
60	<	#include "UseTheForce/notifyCutoffs_interface.h"
59	>	#include "selection/SelectionManager.hpp"
60	>	#include "io/ForceFieldOptions.hpp"
61	>	#include "UseTheForce/ForceField.hpp"
62	>	#include "nonbonded/SwitchingFunction.hpp"
63
64	<	//#include "UseTheForce/fortranWrappers.hpp"
64	>	using namespace std;
65	>	namespace OpenMD {
66	>
67	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
68	>	forceField_(ff), simParams_(simParams),
69	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
70	>	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
71	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
72	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
73	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
74	>	nConstraints_(0), sman_(NULL), fortranInitialized_(false),
75	>	calcBoxDipole_(false), useAtomicVirial_(true) {
76	>
77	>	MoleculeStamp* molStamp;
78	>	int nMolWithSameStamp;
79	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
80	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
81	>	CutoffGroupStamp* cgStamp;
82	>	RigidBodyStamp* rbStamp;
83	>	int nRigidAtoms = 0;
84	>
85	>	vector<Component*> components = simParams->getComponents();
86	>
87	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
88	>	molStamp = (*i)->getMoleculeStamp();
89	>	nMolWithSameStamp = (*i)->getNMol();
90	>
91	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
92	>
93	>	//calculate atoms in molecules
94	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
95	>
96	>	//calculate atoms in cutoff groups
97	>	int nAtomsInGroups = 0;
98	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
99	>
100	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
101	>	cgStamp = molStamp->getCutoffGroupStamp(j);
102	>	nAtomsInGroups += cgStamp->getNMembers();
103	>	}
104	>
105	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
106	>
107	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
108	>
109	>	//calculate atoms in rigid bodies
110	>	int nAtomsInRigidBodies = 0;
111	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
112	>
113	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
114	>	rbStamp = molStamp->getRigidBodyStamp(j);
115	>	nAtomsInRigidBodies += rbStamp->getNMembers();
116	>	}
117	>
118	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
119	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
120	>
121	>	}
122	>
123	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
124	>	//group therefore the total number of cutoff groups in the system is
125	>	//equal to the total number of atoms minus number of atoms belong to
126	>	//cutoff group defined in meta-data file plus the number of cutoff
127	>	//groups defined in meta-data file
128	>	std::cerr << "nGA = " << nGlobalAtoms_ << "\n";
129	>	std::cerr << "nCA = " << nCutoffAtoms << "\n";
130	>	std::cerr << "nG = " << nGroups << "\n";
131
132	<	#include "math/MatVec3.h"
132	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
133
134	<	#ifdef IS_MPI
135	<	#include "brains/mpiSimulation.hpp"
136	<	#endif
134	>	std::cerr << "nGCG = " << nGlobalCutoffGroups_ << "\n";
135	>
136	>	//every free atom (atom does not belong to rigid bodies) is an
137	>	//integrable object therefore the total number of integrable objects
138	>	//in the system is equal to the total number of atoms minus number of
139	>	//atoms belong to rigid body defined in meta-data file plus the number
140	>	//of rigid bodies defined in meta-data file
141	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
142	>	+ nGlobalRigidBodies_;
143	>
144	>	nGlobalMols_ = molStampIds_.size();
145	>	molToProcMap_.resize(nGlobalMols_);
146	>	}
147	>
148	>	SimInfo::~SimInfo() {
149	>	map<int, Molecule*>::iterator i;
150	>	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
151	>	delete i->second;
152	>	}
153	>	molecules_.clear();
154	>
155	>	delete sman_;
156	>	delete simParams_;
157	>	delete forceField_;
158	>	}
159
23	–	inline double roundMe( double x ){
24	–	return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
25	–	}
26	–
27	–	inline double min( double a, double b ){
28	–	return (a < b ) ? a : b;
29	–	}
160
161	<	SimInfo* currentInfo;
162	<
163	<	SimInfo::SimInfo(){
164	<
165	<	n_constraints = 0;
166	<	nZconstraints = 0;
167	<	n_oriented = 0;
168	<	n_dipoles = 0;
169	<	ndf = 0;
170	<	ndfRaw = 0;
171	<	nZconstraints = 0;
172	<	the_integrator = NULL;
173	<	setTemp = 0;
174	<	thermalTime = 0.0;
175	<	currentTime = 0.0;
176	<	rCut = 0.0;
177	<	rSw = 0.0;
178	<
179	<	haveRcut = 0;
180	<	haveRsw = 0;
181	<	boxIsInit = 0;
161	>	bool SimInfo::addMolecule(Molecule* mol) {
162	>	MoleculeIterator i;
163	>
164	>	i = molecules_.find(mol->getGlobalIndex());
165	>	if (i == molecules_.end() ) {
166	>
167	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
168	>
169	>	nAtoms_ += mol->getNAtoms();
170	>	nBonds_ += mol->getNBonds();
171	>	nBends_ += mol->getNBends();
172	>	nTorsions_ += mol->getNTorsions();
173	>	nInversions_ += mol->getNInversions();
174	>	nRigidBodies_ += mol->getNRigidBodies();
175	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
176	>	nCutoffGroups_ += mol->getNCutoffGroups();
177	>	nConstraints_ += mol->getNConstraintPairs();
178	>
179	>	addInteractionPairs(mol);
180	>
181	>	return true;
182	>	} else {
183	>	return false;
184	>	}
185	>	}
186
187	<	resetTime = 1e99;
187	>	bool SimInfo::removeMolecule(Molecule* mol) {
188	>	MoleculeIterator i;
189	>	i = molecules_.find(mol->getGlobalIndex());
190
191	<	orthoRhombic = 0;
56	<	orthoTolerance = 1E-6;
57	<	useInitXSstate = true;
191	>	if (i != molecules_.end() ) {
192
193	<	usePBC = 0;
194	<	useDirectionalAtoms = 0;
195	<	useLennardJones = 0;
196	<	useElectrostatics = 0;
197	<	useCharges = 0;
198	<	useDipoles = 0;
199	<	useSticky = 0;
200	<	useGayBerne = 0;
201	<	useEAM = 0;
202	<	useShapes = 0;
203	<	useFLARB = 0;
193	>	assert(mol == i->second);
194	>
195	>	nAtoms_ -= mol->getNAtoms();
196	>	nBonds_ -= mol->getNBonds();
197	>	nBends_ -= mol->getNBends();
198	>	nTorsions_ -= mol->getNTorsions();
199	>	nInversions_ -= mol->getNInversions();
200	>	nRigidBodies_ -= mol->getNRigidBodies();
201	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
202	>	nCutoffGroups_ -= mol->getNCutoffGroups();
203	>	nConstraints_ -= mol->getNConstraintPairs();
204
205	<	useSolidThermInt = 0;
206	<	useLiquidThermInt = 0;
205	>	removeInteractionPairs(mol);
206	>	molecules_.erase(mol->getGlobalIndex());
207
208	<	haveCutoffGroups = false;
209	<
210	<	excludes = Exclude::Instance();
208	>	delete mol;
209	>
210	>	return true;
211	>	} else {
212	>	return false;
213	>	}
214	>	}
215
216	<	myConfiguration = new SimState();
216	>
217	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
218	>	i = molecules_.begin();
219	>	return i == molecules_.end() ? NULL : i->second;
220	>	}
221
222	<	has_minimizer = false;
223	<	the_minimizer =NULL;
222	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
223	>	++i;
224	>	return i == molecules_.end() ? NULL : i->second;
225	>	}
226
83	–	ngroup = 0;
227
228	<	}
228	>	void SimInfo::calcNdf() {
229	>	int ndf_local;
230	>	MoleculeIterator i;
231	>	vector<StuntDouble*>::iterator j;
232	>	Molecule* mol;
233	>	StuntDouble* integrableObject;
234
235	+	ndf_local = 0;
236	+
237	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
238	+	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
239	+	integrableObject = mol->nextIntegrableObject(j)) {
240
241	<	SimInfo::~SimInfo(){
241	>	ndf_local += 3;
242
243	<	delete myConfiguration;
243	>	if (integrableObject->isDirectional()) {
244	>	if (integrableObject->isLinear()) {
245	>	ndf_local += 2;
246	>	} else {
247	>	ndf_local += 3;
248	>	}
249	>	}
250	>
251	>	}
252	>	}
253	>
254	>	// n_constraints is local, so subtract them on each processor
255	>	ndf_local -= nConstraints_;
256
257	<	map<string, GenericData*>::iterator i;
258	<
259	<	for(i = properties.begin(); i != properties.end(); i++)
260	<	delete (*i).second;
257	>	#ifdef IS_MPI
258	>	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
259	>	#else
260	>	ndf_ = ndf_local;
261	>	#endif
262
263	<	}
263	>	// nZconstraints_ is global, as are the 3 COM translations for the
264	>	// entire system:
265	>	ndf_ = ndf_ - 3 - nZconstraint_;
266
267	<	void SimInfo::setBox(double newBox[3]) {
100	<
101	<	int i, j;
102	<	double tempMat[3][3];
267	>	}
268
269	<	for(i=0; i<3; i++)
270	<	for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
269	>	int SimInfo::getFdf() {
270	>	#ifdef IS_MPI
271	>	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
272	>	#else
273	>	fdf_ = fdf_local;
274	>	#endif
275	>	return fdf_;
276	>	}
277	>
278	>	void SimInfo::calcNdfRaw() {
279	>	int ndfRaw_local;
280
281	<	tempMat[0][0] = newBox[0];
282	<	tempMat[1][1] = newBox[1];
283	<	tempMat[2][2] = newBox[2];
281	>	MoleculeIterator i;
282	>	vector<StuntDouble*>::iterator j;
283	>	Molecule* mol;
284	>	StuntDouble* integrableObject;
285
286	<	setBoxM( tempMat );
286	>	// Raw degrees of freedom that we have to set
287	>	ndfRaw_local = 0;
288	>
289	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
290	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
291	>	integrableObject = mol->nextIntegrableObject(j)) {
292
293	<	}
293	>	ndfRaw_local += 3;
294
295	<	void SimInfo::setBoxM( double theBox[3][3] ){
296	<
297	<	int i, j;
298	<	double FortranHmat[9]; // to preserve compatibility with Fortran the
299	<	// ordering in the array is as follows:
300	<	// [ 0 3 6 ]
301	<	// [ 1 4 7 ]
302	<	// [ 2 5 8 ]
303	<	double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
124	<
125	<	if( !boxIsInit ) boxIsInit = 1;
126	<
127	<	for(i=0; i < 3; i++)
128	<	for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
129	<
130	<	calcBoxL();
131	<	calcHmatInv();
132	<
133	<	for(i=0; i < 3; i++) {
134	<	for (j=0; j < 3; j++) {
135	<	FortranHmat[3*j + i] = Hmat[i][j];
136	<	FortranHmatInv[3*j + i] = HmatInv[i][j];
295	>	if (integrableObject->isDirectional()) {
296	>	if (integrableObject->isLinear()) {
297	>	ndfRaw_local += 2;
298	>	} else {
299	>	ndfRaw_local += 3;
300	>	}
301	>	}
302	>
303	>	}
304		}
305	+
306	+	#ifdef IS_MPI
307	+	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
308	+	#else
309	+	ndfRaw_ = ndfRaw_local;
310	+	#endif
311		}
312
313	<	setFortranBox(FortranHmat, FortranHmatInv, &orthoRhombic);
314	<
142	<	}
143	<
313	>	void SimInfo::calcNdfTrans() {
314	>	int ndfTrans_local;
315
316	<	void SimInfo::getBoxM (double theBox[3][3]) {
316	>	ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
317
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	–	}
318
319	+	#ifdef IS_MPI
320	+	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
321	+	#else
322	+	ndfTrans_ = ndfTrans_local;
323	+	#endif
324
325	<	void SimInfo::scaleBox(double scale) {
326	<	double theBox[3][3];
327	<	int i, j;
325	>	ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
326	>
327	>	}
328
329	<	// cerr << "Scaling box by " << scale << "\n";
329	>	void SimInfo::addInteractionPairs(Molecule* mol) {
330	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
331	>	vector<Bond*>::iterator bondIter;
332	>	vector<Bend*>::iterator bendIter;
333	>	vector<Torsion*>::iterator torsionIter;
334	>	vector<Inversion*>::iterator inversionIter;
335	>	Bond* bond;
336	>	Bend* bend;
337	>	Torsion* torsion;
338	>	Inversion* inversion;
339	>	int a;
340	>	int b;
341	>	int c;
342	>	int d;
343
344	<	for(i=0; i<3; i++)
345	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
346	<
347	<	setBoxM(theBox);
348	<
349	<	}
350	<
351	<	void SimInfo::calcHmatInv( void ) {
352	<
353	<	int oldOrtho;
354	<	int i,j;
355	<	double smallDiag;
356	<	double tol;
357	<	double sanity[3][3];
358	<
359	<	invertMat3( Hmat, HmatInv );
360	<
361	<	// check to see if Hmat is orthorhombic
362	<
363	<	oldOrtho = orthoRhombic;
364	<
365	<	smallDiag = fabs(Hmat[0][0]);
366	<	if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
367	<	if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
368	<	tol = smallDiag * orthoTolerance;
369	<
370	<	orthoRhombic = 1;
371	<
372	<	for (i = 0; i < 3; i++ ) {
373	<	for (j = 0 ; j < 3; j++) {
374	<	if (i != j) {
375	<	if (orthoRhombic) {
191	<	if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
192	<	}
344	>	// atomGroups can be used to add special interaction maps between
345	>	// groups of atoms that are in two separate rigid bodies.
346	>	// However, most site-site interactions between two rigid bodies
347	>	// are probably not special, just the ones between the physically
348	>	// bonded atoms.  Interactions *within* a single rigid body should
349	>	// always be excluded.  These are done at the bottom of this
350	>	// function.
351	>
352	>	map<int, set<int> > atomGroups;
353	>	Molecule::RigidBodyIterator rbIter;
354	>	RigidBody* rb;
355	>	Molecule::IntegrableObjectIterator ii;
356	>	StuntDouble* integrableObject;
357	>
358	>	for (integrableObject = mol->beginIntegrableObject(ii);
359	>	integrableObject != NULL;
360	>	integrableObject = mol->nextIntegrableObject(ii)) {
361	>
362	>	if (integrableObject->isRigidBody()) {
363	>	rb = static_cast<RigidBody*>(integrableObject);
364	>	vector<Atom*> atoms = rb->getAtoms();
365	>	set<int> rigidAtoms;
366	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
367	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
368	>	}
369	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
370	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
371	>	}
372	>	} else {
373	>	set<int> oneAtomSet;
374	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
375	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
376		}
377	<	}
378	<	}
377	>	}
378	>
379	>	for (bond= mol->beginBond(bondIter); bond != NULL;
380	>	bond = mol->nextBond(bondIter)) {
381
382	<	if( oldOrtho != orthoRhombic ){
382	>	a = bond->getAtomA()->getGlobalIndex();
383	>	b = bond->getAtomB()->getGlobalIndex();
384
385	<	if( orthoRhombic ) {
386	<	sprintf( painCave.errMsg,
387	<	"OOPSE is switching from the default Non-Orthorhombic\n"
388	<	"\tto the faster Orthorhombic periodic boundary computations.\n"
389	<	"\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();
385	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
386	>	oneTwoInteractions_.addPair(a, b);
387	>	} else {
388	>	excludedInteractions_.addPair(a, b);
389	>	}
390		}
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	–	}
391
392	<	void SimInfo::calcBoxL( void ){
392	>	for (bend= mol->beginBend(bendIter); bend != NULL;
393	>	bend = mol->nextBend(bendIter)) {
394
395	<	double dx, dy, dz, dsq;
395	>	a = bend->getAtomA()->getGlobalIndex();
396	>	b = bend->getAtomB()->getGlobalIndex();
397	>	c = bend->getAtomC()->getGlobalIndex();
398	>
399	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
400	>	oneTwoInteractions_.addPair(a, b);
401	>	oneTwoInteractions_.addPair(b, c);
402	>	} else {
403	>	excludedInteractions_.addPair(a, b);
404	>	excludedInteractions_.addPair(b, c);
405	>	}
406
407	<	// boxVol = Determinant of Hmat
407	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
408	>	oneThreeInteractions_.addPair(a, c);
409	>	} else {
410	>	excludedInteractions_.addPair(a, c);
411	>	}
412	>	}
413
414	<	boxVol = matDet3( Hmat );
414	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
415	>	torsion = mol->nextTorsion(torsionIter)) {
416
417	<	// boxLx
418	<
419	<	dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
420	<	dsq = dx*dx + dy*dy + dz*dz;
237	<	boxL[0] = sqrt( dsq );
238	<	//maxCutoff = 0.5 * boxL[0];
417	>	a = torsion->getAtomA()->getGlobalIndex();
418	>	b = torsion->getAtomB()->getGlobalIndex();
419	>	c = torsion->getAtomC()->getGlobalIndex();
420	>	d = torsion->getAtomD()->getGlobalIndex();
421
422	<	// boxLy
423	<
424	<	dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
425	<	dsq = dx*dx + dy*dy + dz*dz;
426	<	boxL[1] = sqrt( dsq );
427	<	//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
422	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
423	>	oneTwoInteractions_.addPair(a, b);
424	>	oneTwoInteractions_.addPair(b, c);
425	>	oneTwoInteractions_.addPair(c, d);
426	>	} else {
427	>	excludedInteractions_.addPair(a, b);
428	>	excludedInteractions_.addPair(b, c);
429	>	excludedInteractions_.addPair(c, d);
430	>	}
431
432	+	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
433	+	oneThreeInteractions_.addPair(a, c);
434	+	oneThreeInteractions_.addPair(b, d);
435	+	} else {
436	+	excludedInteractions_.addPair(a, c);
437	+	excludedInteractions_.addPair(b, d);
438	+	}
439
440	<	// boxLz
441	<
442	<	dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
443	<	dsq = dx*dx + dy*dy + dz*dz;
444	<	boxL[2] = sqrt( dsq );
445	<	//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
440	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
441	>	oneFourInteractions_.addPair(a, d);
442	>	} else {
443	>	excludedInteractions_.addPair(a, d);
444	>	}
445	>	}
446
447	<	//calculate the max cutoff
448	<	maxCutoff =  calcMaxCutOff();
257	<
258	<	checkCutOffs();
447	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
448	>	inversion = mol->nextInversion(inversionIter)) {
449
450	<	}
450	>	a = inversion->getAtomA()->getGlobalIndex();
451	>	b = inversion->getAtomB()->getGlobalIndex();
452	>	c = inversion->getAtomC()->getGlobalIndex();
453	>	d = inversion->getAtomD()->getGlobalIndex();
454
455	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
456	+	oneTwoInteractions_.addPair(a, b);
457	+	oneTwoInteractions_.addPair(a, c);
458	+	oneTwoInteractions_.addPair(a, d);
459	+	} else {
460	+	excludedInteractions_.addPair(a, b);
461	+	excludedInteractions_.addPair(a, c);
462	+	excludedInteractions_.addPair(a, d);
463	+	}
464
465	<	double SimInfo::calcMaxCutOff(){
465	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
466	>	oneThreeInteractions_.addPair(b, c);
467	>	oneThreeInteractions_.addPair(b, d);
468	>	oneThreeInteractions_.addPair(c, d);
469	>	} else {
470	>	excludedInteractions_.addPair(b, c);
471	>	excludedInteractions_.addPair(b, d);
472	>	excludedInteractions_.addPair(c, d);
473	>	}
474	>	}
475
476	<	double ri[3], rj[3], rk[3];
477	<	double rij[3], rjk[3], rki[3];
478	<	double minDist;
476	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
477	>	rb = mol->nextRigidBody(rbIter)) {
478	>	vector<Atom*> atoms = rb->getAtoms();
479	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
480	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
481	>	a = atoms[i]->getGlobalIndex();
482	>	b = atoms[j]->getGlobalIndex();
483	>	excludedInteractions_.addPair(a, b);
484	>	}
485	>	}
486	>	}
487
488	<	ri[0] = Hmat[0][0];
270	<	ri[1] = Hmat[1][0];
271	<	ri[2] = Hmat[2][0];
488	>	}
489
490	<	rj[0] = Hmat[0][1];
491	<	rj[1] = Hmat[1][1];
492	<	rj[2] = Hmat[2][1];
490	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
491	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
492	>	vector<Bond*>::iterator bondIter;
493	>	vector<Bend*>::iterator bendIter;
494	>	vector<Torsion*>::iterator torsionIter;
495	>	vector<Inversion*>::iterator inversionIter;
496	>	Bond* bond;
497	>	Bend* bend;
498	>	Torsion* torsion;
499	>	Inversion* inversion;
500	>	int a;
501	>	int b;
502	>	int c;
503	>	int d;
504
505	<	rk[0] = Hmat[0][2];
506	<	rk[1] = Hmat[1][2];
507	<	rk[2] = Hmat[2][2];
505	>	map<int, set<int> > atomGroups;
506	>	Molecule::RigidBodyIterator rbIter;
507	>	RigidBody* rb;
508	>	Molecule::IntegrableObjectIterator ii;
509	>	StuntDouble* integrableObject;
510
511	<	crossProduct3(ri, rj, rij);
512	<	distXY = dotProduct3(rk,rij) / norm3(rij);
511	>	for (integrableObject = mol->beginIntegrableObject(ii);
512	>	integrableObject != NULL;
513	>	integrableObject = mol->nextIntegrableObject(ii)) {
514	>
515	>	if (integrableObject->isRigidBody()) {
516	>	rb = static_cast<RigidBody*>(integrableObject);
517	>	vector<Atom*> atoms = rb->getAtoms();
518	>	set<int> rigidAtoms;
519	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
520	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
521	>	}
522	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
523	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
524	>	}
525	>	} else {
526	>	set<int> oneAtomSet;
527	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
528	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
529	>	}
530	>	}
531
532	<	crossProduct3(rj,rk, rjk);
533	<	distYZ = dotProduct3(ri,rjk) / norm3(rjk);
532	>	for (bond= mol->beginBond(bondIter); bond != NULL;
533	>	bond = mol->nextBond(bondIter)) {
534	>
535	>	a = bond->getAtomA()->getGlobalIndex();
536	>	b = bond->getAtomB()->getGlobalIndex();
537	>
538	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
539	>	oneTwoInteractions_.removePair(a, b);
540	>	} else {
541	>	excludedInteractions_.removePair(a, b);
542	>	}
543	>	}
544
545	<	crossProduct3(rk,ri, rki);
546	<	distZX = dotProduct3(rj,rki) / norm3(rki);
545	>	for (bend= mol->beginBend(bendIter); bend != NULL;
546	>	bend = mol->nextBend(bendIter)) {
547
548	<	minDist = min(min(distXY, distYZ), distZX);
549	<	return minDist/2;
550	<
551	<	}
548	>	a = bend->getAtomA()->getGlobalIndex();
549	>	b = bend->getAtomB()->getGlobalIndex();
550	>	c = bend->getAtomC()->getGlobalIndex();
551	>
552	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
553	>	oneTwoInteractions_.removePair(a, b);
554	>	oneTwoInteractions_.removePair(b, c);
555	>	} else {
556	>	excludedInteractions_.removePair(a, b);
557	>	excludedInteractions_.removePair(b, c);
558	>	}
559
560	<	void SimInfo::wrapVector( double thePos[3] ){
560	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
561	>	oneThreeInteractions_.removePair(a, c);
562	>	} else {
563	>	excludedInteractions_.removePair(a, c);
564	>	}
565	>	}
566
567	<	int i;
568	<	double scaled[3];
567	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
568	>	torsion = mol->nextTorsion(torsionIter)) {
569
570	<	if( !orthoRhombic ){
571	<	// calc the scaled coordinates.
570	>	a = torsion->getAtomA()->getGlobalIndex();
571	>	b = torsion->getAtomB()->getGlobalIndex();
572	>	c = torsion->getAtomC()->getGlobalIndex();
573	>	d = torsion->getAtomD()->getGlobalIndex();
574
575	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
576	+	oneTwoInteractions_.removePair(a, b);
577	+	oneTwoInteractions_.removePair(b, c);
578	+	oneTwoInteractions_.removePair(c, d);
579	+	} else {
580	+	excludedInteractions_.removePair(a, b);
581	+	excludedInteractions_.removePair(b, c);
582	+	excludedInteractions_.removePair(c, d);
583	+	}
584
585	<	matVecMul3(HmatInv, thePos, scaled);
586	<
587	<	for(i=0; i<3; i++)
588	<	scaled[i] -= roundMe(scaled[i]);
589	<
590	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
591	<
311	<	matVecMul3(Hmat, scaled, thePos);
585	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
586	>	oneThreeInteractions_.removePair(a, c);
587	>	oneThreeInteractions_.removePair(b, d);
588	>	} else {
589	>	excludedInteractions_.removePair(a, c);
590	>	excludedInteractions_.removePair(b, d);
591	>	}
592
593	<	}
594	<	else{
595	<	// calc the scaled coordinates.
596	<
597	<	for(i=0; i<3; i++)
598	<	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	<	}
593	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
594	>	oneFourInteractions_.removePair(a, d);
595	>	} else {
596	>	excludedInteractions_.removePair(a, d);
597	>	}
598	>	}
599
600	+	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
601	+	inversion = mol->nextInversion(inversionIter)) {
602
603	<	int SimInfo::getNDF(){
604	<	int ndf_local;
603	>	a = inversion->getAtomA()->getGlobalIndex();
604	>	b = inversion->getAtomB()->getGlobalIndex();
605	>	c = inversion->getAtomC()->getGlobalIndex();
606	>	d = inversion->getAtomD()->getGlobalIndex();
607
608	<	ndf_local = 0;
609	<
610	<	for(int i = 0; i < integrableObjects.size(); i++){
611	<	ndf_local += 3;
612	<	if (integrableObjects[i]->isDirectional()) {
613	<	if (integrableObjects[i]->isLinear())
614	<	ndf_local += 2;
615	<	else
616	<	ndf_local += 3;
608	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
609	>	oneTwoInteractions_.removePair(a, b);
610	>	oneTwoInteractions_.removePair(a, c);
611	>	oneTwoInteractions_.removePair(a, d);
612	>	} else {
613	>	excludedInteractions_.removePair(a, b);
614	>	excludedInteractions_.removePair(a, c);
615	>	excludedInteractions_.removePair(a, d);
616	>	}
617	>
618	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
619	>	oneThreeInteractions_.removePair(b, c);
620	>	oneThreeInteractions_.removePair(b, d);
621	>	oneThreeInteractions_.removePair(c, d);
622	>	} else {
623	>	excludedInteractions_.removePair(b, c);
624	>	excludedInteractions_.removePair(b, d);
625	>	excludedInteractions_.removePair(c, d);
626	>	}
627		}
628	+
629	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
630	+	rb = mol->nextRigidBody(rbIter)) {
631	+	vector<Atom*> atoms = rb->getAtoms();
632	+	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
633	+	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
634	+	a = atoms[i]->getGlobalIndex();
635	+	b = atoms[j]->getGlobalIndex();
636	+	excludedInteractions_.removePair(a, b);
637	+	}
638	+	}
639	+	}
640	+
641		}
642	+
643	+
644	+	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
645	+	int curStampId;
646	+
647	+	//index from 0
648	+	curStampId = moleculeStamps_.size();
649
650	<	// n_constraints is local, so subtract them on each processor:
650	>	moleculeStamps_.push_back(molStamp);
651	>	molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
652	>	}
653
654	<	ndf_local -= n_constraints;
654	>
655	>	/**
656	>	* update
657	>	*
658	>	*  Performs the global checks and variable settings after the
659	>	*  objects have been created.
660	>	*
661	>	*/
662	>	void SimInfo::update() {
663	>	setupSimVariables();
664	>	calcNdf();
665	>	calcNdfRaw();
666	>	calcNdfTrans();
667	>	}
668	>
669	>	/**
670	>	* getSimulatedAtomTypes
671	>	*
672	>	* Returns an STL set of AtomType* that are actually present in this
673	>	* simulation.  Must query all processors to assemble this information.
674	>	*
675	>	*/
676	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
677	>	SimInfo::MoleculeIterator mi;
678	>	Molecule* mol;
679	>	Molecule::AtomIterator ai;
680	>	Atom* atom;
681	>	set<AtomType*> atomTypes;
682	>
683	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
684	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
685	>	atomTypes.insert(atom->getAtomType());
686	>	}
687	>	}
688
689		#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
690
691	<	// nZconstraints is global, as are the 3 COM translations for the
692	<	// entire system:
691	>	// loop over the found atom types on this processor, and add their
692	>	// numerical idents to a vector:
693
694	<	ndf = ndf - 3 - nZconstraints;
694	>	vector<int> foundTypes;
695	>	set<AtomType*>::iterator i;
696	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
697	>	foundTypes.push_back( (*i)->getIdent() );
698
699	<	return ndf;
700	<	}
699	>	// count_local holds the number of found types on this processor
700	>	int count_local = foundTypes.size();
701
702	<	int SimInfo::getNDFraw() {
703	<	int ndfRaw_local;
702	>	// count holds the total number of found types on all processors
703	>	// (some will be redundant with the ones found locally):
704	>	int count;
705	>	MPI::COMM_WORLD.Allreduce(&count_local, &count, 1, MPI::INT, MPI::SUM);
706
707	<	// Raw degrees of freedom that we have to set
708	<	ndfRaw_local = 0;
707	>	// create a vector to hold the globally found types, and resize it:
708	>	vector<int> ftGlobal;
709	>	ftGlobal.resize(count);
710	>	vector<int> counts;
711
712	<	for(int i = 0; i < integrableObjects.size(); i++){
713	<	ndfRaw_local += 3;
714	<	if (integrableObjects[i]->isDirectional()) {
715	<	if (integrableObjects[i]->isLinear())
716	<	ndfRaw_local += 2;
717	<	else
379	<	ndfRaw_local += 3;
380	<	}
381	<	}
712	>	int nproc = MPI::COMM_WORLD.Get_size();
713	>	counts.resize(nproc);
714	>	vector<int> disps;
715	>	disps.resize(nproc);
716	>
717	>	// now spray out the foundTypes to all the other processors:
718
719	<	#ifdef IS_MPI
720	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
385	<	#else
386	<	ndfRaw = ndfRaw_local;
387	<	#endif
719	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
720	>	&ftGlobal[0], &counts[0], &disps[0], MPI::INT);
721
722	<	return ndfRaw;
723	<	}
724	<
725	<	int SimInfo::getNDFtranslational() {
726	<	int ndfTrans_local;
727	<
728	<	ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
729	<
730	<
731	<	#ifdef IS_MPI
732	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
733	<	#else
734	<	ndfTrans = ndfTrans_local;
722	>	// foundIdents is a stl set, so inserting an already found ident
723	>	// will have no effect.
724	>	set<int> foundIdents;
725	>	vector<int>::iterator j;
726	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
727	>	foundIdents.insert((*j));
728	>
729	>	// now iterate over the foundIdents and get the actual atom types
730	>	// that correspond to these:
731	>	set<int>::iterator it;
732	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
733	>	atomTypes.insert( forceField_->getAtomType((*it)) );
734	>
735		#endif
736	+
737	+	return atomTypes;
738	+	}
739
740	<	ndfTrans = ndfTrans - 3 - nZconstraints;
740	>	void SimInfo::setupSimVariables() {
741	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
742	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
743	>	calcBoxDipole_ = false;
744	>	if ( simParams_->haveAccumulateBoxDipole() )
745	>	if ( simParams_->getAccumulateBoxDipole() ) {
746	>	calcBoxDipole_ = true;
747	>	}
748
749	<	return ndfTrans;
750	<	}
749	>	set<AtomType*>::iterator i;
750	>	set<AtomType*> atomTypes;
751	>	atomTypes = getSimulatedAtomTypes();
752	>	int usesElectrostatic = 0;
753	>	int usesMetallic = 0;
754	>	int usesDirectional = 0;
755	>	//loop over all of the atom types
756	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
757	>	usesElectrostatic |= (*i)->isElectrostatic();
758	>	usesMetallic |= (*i)->isMetal();
759	>	usesDirectional |= (*i)->isDirectional();
760	>	}
761
762	<	int SimInfo::getTotIntegrableObjects() {
763	<	int nObjs_local;
764	<	int nObjs;
762	>	#ifdef IS_MPI
763	>	int temp;
764	>	temp = usesDirectional;
765	>	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
766
767	<	nObjs_local =  integrableObjects.size();
767	>	temp = usesMetallic;
768	>	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
769
770	<
771	<	#ifdef IS_MPI
417	<	MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
418	<	#else
419	<	nObjs = nObjs_local;
770	>	temp = usesElectrostatic;
771	>	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
772		#endif
773	<
774	<
775	<	return nObjs;
776	<	}
777	<
778	<	void SimInfo::refreshSim(){
427	<
428	<	simtype fInfo;
429	<	int isError;
430	<	int n_global;
431	<	int* excl;
432	<
433	<	fInfo.dielect = 0.0;
434	<
435	<	if( useDipoles ){
436	<	if( useReactionField )fInfo.dielect = dielectric;
773	>	fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;
774	>	fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
775	>	fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
776	>	fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
777	>	fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
778	>	fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
779		}
780
439	–	fInfo.SIM_uses_PBC = usePBC;
781
782	<	if (useSticky || useDipoles || useGayBerne || useShapes) {
783	<	useDirectionalAtoms = 1;
784	<	fInfo.SIM_uses_DirectionalAtoms = useDirectionalAtoms;
785	<	}
782	>	vector<int> SimInfo::getGlobalAtomIndices() {
783	>	SimInfo::MoleculeIterator mi;
784	>	Molecule* mol;
785	>	Molecule::AtomIterator ai;
786	>	Atom* atom;
787
788	<	fInfo.SIM_uses_LennardJones = useLennardJones;
789	<
790	<	if (useCharges || useDipoles) {
791	<	useElectrostatics = 1;
792	<	fInfo.SIM_uses_Electrostatics = useElectrostatics;
788	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
789	>
790	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
791	>
792	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
793	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
794	>	}
795	>	}
796	>	return GlobalAtomIndices;
797		}
798
453	–	fInfo.SIM_uses_Charges = useCharges;
454	–	fInfo.SIM_uses_Dipoles = useDipoles;
455	–	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;
799
800	<	n_exclude = excludes->getSize();
801	<	excl = excludes->getFortranArray();
802	<
803	<	#ifdef IS_MPI
804	<	n_global = mpiSim->getNAtomsGlobal();
467	<	#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);
800	>	vector<int> SimInfo::getGlobalGroupIndices() {
801	>	SimInfo::MoleculeIterator mi;
802	>	Molecule* mol;
803	>	Molecule::CutoffGroupIterator ci;
804	>	CutoffGroup* cg;
805
806	<	if( isError ){
806	>	vector<int> GlobalGroupIndices;
807
808	<	sprintf( painCave.errMsg,
809	<	"There was an error setting the simulation information in fortran.\n" );
810	<	painCave.isFatal = 1;
811	<	painCave.severity = OOPSE_ERROR;
812	<	simError();
808	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
809	>
810	>	//local index of cutoff group is trivial, it only depends on the
811	>	//order of travesing
812	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
813	>	cg = mol->nextCutoffGroup(ci)) {
814	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
815	>	}
816	>	}
817	>	return GlobalGroupIndices;
818		}
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	–	}
819
501	–	void SimInfo::setDefaultRcut( double theRcut ){
502	–
503	–	haveRcut = 1;
504	–	rCut = theRcut;
505	–	rList = rCut + 1.0;
506	–
507	–	notifyFortranCutoffs( &rCut, &rSw, &rList );
508	–	}
820
821	<	void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
821	>	void SimInfo::setupFortran() {
822	>	int isError;
823	>	int nExclude, nOneTwo, nOneThree, nOneFour;
824	>	vector<int> fortranGlobalGroupMembership;
825	>
826	>	isError = 0;
827
828	<	rSw = theRsw;
829	<	setDefaultRcut( theRcut );
830	<	}
828	>	//globalGroupMembership_ is filled by SimCreator
829	>	for (int i = 0; i < nGlobalAtoms_; i++) {
830	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
831	>	}
832
833	+	//calculate mass ratio of cutoff group
834	+	vector<RealType> mfact;
835	+	SimInfo::MoleculeIterator mi;
836	+	Molecule* mol;
837	+	Molecule::CutoffGroupIterator ci;
838	+	CutoffGroup* cg;
839	+	Molecule::AtomIterator ai;
840	+	Atom* atom;
841	+	RealType totalMass;
842
843	<	void SimInfo::checkCutOffs( void ){
844	<
519	<	if( boxIsInit ){
843	>	//to avoid memory reallocation, reserve enough space for mfact
844	>	mfact.reserve(getNCutoffGroups());
845
846	<	//we need to check cutOffs against the box
847	<
523	<	if( rCut > maxCutoff ){
524	<	sprintf( painCave.errMsg,
525	<	"cutoffRadius is too large for the current periodic box.\n"
526	<	"\tCurrent Value of cutoffRadius = %G at time %G\n "
527	<	"\tThis is larger than half of at least one of the\n"
528	<	"\tperiodic box vectors.  Right now, the Box matrix is:\n"
529	<	"\n"
530	<	"\t[ %G %G %G ]\n"
531	<	"\t[ %G %G %G ]\n"
532	<	"\t[ %G %G %G ]\n",
533	<	rCut, currentTime,
534	<	Hmat[0][0], Hmat[0][1], Hmat[0][2],
535	<	Hmat[1][0], Hmat[1][1], Hmat[1][2],
536	<	Hmat[2][0], Hmat[2][1], Hmat[2][2]);
537	<	painCave.severity = OOPSE_ERROR;
538	<	painCave.isFatal = 1;
539	<	simError();
540	<	}
541	<	} else {
542	<	// initialize this stuff before using it, OK?
543	<	sprintf( painCave.errMsg,
544	<	"Trying to check cutoffs without a box.\n"
545	<	"\tOOPSE should have better programmers than that.\n" );
546	<	painCave.severity = OOPSE_ERROR;
547	<	painCave.isFatal = 1;
548	<	simError();
549	<	}
550	<
551	<	}
846	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
847	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
848
849	<	void SimInfo::addProperty(GenericData* prop){
849	>	totalMass = cg->getMass();
850	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
851	>	// Check for massless groups - set mfact to 1 if true
852	>	if (totalMass != 0)
853	>	mfact.push_back(atom->getMass()/totalMass);
854	>	else
855	>	mfact.push_back( 1.0 );
856	>	}
857	>	}
858	>	}
859
860	<	map<string, GenericData*>::iterator result;
556	<	result = properties.find(prop->getID());
557	<
558	<	//we can't simply use  properties[prop->getID()] = prop,
559	<	//it will cause memory leak if we already contain a propery which has the same name of prop
560	<
561	<	if(result != properties.end()){
562	<
563	<	delete (*result).second;
564	<	(*result).second = prop;
565	<
566	<	}
567	<	else{
860	>	// Build the identArray_
861
862	<	properties[prop->getID()] = prop;
862	>	identArray_.clear();
863	>	identArray_.reserve(getNAtoms());
864	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
865	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
866	>	identArray_.push_back(atom->getIdent());
867	>	}
868	>	}
869
870	<	}
870	>	//fill molMembershipArray
871	>	//molMembershipArray is filled by SimCreator
872	>	vector<int> molMembershipArray(nGlobalAtoms_);
873	>	for (int i = 0; i < nGlobalAtoms_; i++) {
874	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
875	>	}
876
877	<	}
877	>	//setup fortran simulation
878
879	<	GenericData* SimInfo::getProperty(const string& propName){
880	<
881	<	map<string, GenericData*>::iterator result;
882	<
579	<	//string lowerCaseName = ();
580	<
581	<	result = properties.find(propName);
582	<
583	<	if(result != properties.end())
584	<	return (*result).second;
585	<	else
586	<	return NULL;
587	<	}
879	>	nExclude = excludedInteractions_.getSize();
880	>	nOneTwo = oneTwoInteractions_.getSize();
881	>	nOneThree = oneThreeInteractions_.getSize();
882	>	nOneFour = oneFourInteractions_.getSize();
883
884	+	int* excludeList = excludedInteractions_.getPairList();
885	+	int* oneTwoList = oneTwoInteractions_.getPairList();
886	+	int* oneThreeList = oneThreeInteractions_.getPairList();
887	+	int* oneFourList = oneFourInteractions_.getPairList();
888
889	<	void SimInfo::getFortranGroupArrays(SimInfo* info,
890	<	vector<int>& FglobalGroupMembership,
891	<	vector<double>& mfact){
892	<
893	<	Molecule* myMols;
894	<	Atom** myAtoms;
895	<	int numAtom;
896	<	double mtot;
897	<	int numMol;
898	<	int numCutoffGroups;
899	<	CutoffGroup* myCutoffGroup;
900	<	vector<CutoffGroup*>::iterator iterCutoff;
901	<	Atom* cutoffAtom;
902	<	vector<Atom*>::iterator iterAtom;
903	<	int atomIndex;
904	<	double totalMass;
905	<
906	<	mfact.clear();
907	<	FglobalGroupMembership.clear();
908	<
909	<
910	<	// Fix the silly fortran indexing problem
911	<	#ifdef IS_MPI
912	<	numAtom = mpiSim->getNAtomsGlobal();
913	<	#else
914	<	numAtom = n_atoms;
889	>	//setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray_[0],
890	>	//               &nExclude, excludeList,
891	>	//               &nOneTwo, oneTwoList,
892	>	//               &nOneThree, oneThreeList,
893	>	//               &nOneFour, oneFourList,
894	>	//               &molMembershipArray[0], &mfact[0], &nCutoffGroups_,
895	>	//               &fortranGlobalGroupMembership[0], &isError);
896	>
897	>	// if( isError ){
898	>	//
899	>	//  sprintf( painCave.errMsg,
900	>	//         "There was an error setting the simulation information in fortran.\n" );
901	>	//  painCave.isFatal = 1;
902	>	//  painCave.severity = OPENMD_ERROR;
903	>	//  simError();
904	>	//}
905	>
906	>
907	>	// sprintf( checkPointMsg,
908	>	//          "succesfully sent the simulation information to fortran.\n");
909	>
910	>	// errorCheckPoint();
911	>
912	>	// Setup number of neighbors in neighbor list if present
913	>	//if (simParams_->haveNeighborListNeighbors()) {
914	>	//  int nlistNeighbors = simParams_->getNeighborListNeighbors();
915	>	//  setNeighbors(&nlistNeighbors);
916	>	//}
917	>
918	>	#ifdef IS_MPI
919	>	// mpiSimData parallelData;
920	>
921	>	//fill up mpiSimData struct
922	>	// parallelData.nMolGlobal = getNGlobalMolecules();
923	>	// parallelData.nMolLocal = getNMolecules();
924	>	// parallelData.nAtomsGlobal = getNGlobalAtoms();
925	>	// parallelData.nAtomsLocal = getNAtoms();
926	>	// parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
927	>	// parallelData.nGroupsLocal = getNCutoffGroups();
928	>	// parallelData.myNode = worldRank;
929	>	// MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
930	>
931	>	//pass mpiSimData struct and index arrays to fortran
932	>	//setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
933	>	//                &localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
934	>	//                &localToGlobalCutoffGroupIndex[0], &isError);
935	>
936	>	// if (isError) {
937	>	//   sprintf(painCave.errMsg,
938	>	//           "mpiRefresh errror: fortran didn't like something we gave it.\n");
939	>	//   painCave.isFatal = 1;
940	>	//   simError();
941	>	// }
942	>
943	>	// sprintf(checkPointMsg, " mpiRefresh successful.\n");
944	>	// errorCheckPoint();
945		#endif
617	–	for (int i = 0; i < numAtom; i++)
618	–	FglobalGroupMembership.push_back(globalGroupMembership[i] + 1);
619	–
946
947	<	myMols = info->molecules;
948	<	numMol = info->n_mol;
949	<	for(int i  = 0; i < numMol; i++){
950	<	numCutoffGroups = myMols[i].getNCutoffGroups();
951	<	for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff);
952	<	myCutoffGroup != NULL;
953	<	myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
947	>	// initFortranFF(&isError);
948	>	// if (isError) {
949	>	//   sprintf(painCave.errMsg,
950	>	//           "initFortranFF errror: fortran didn't like something we gave it.\n");
951	>	//   painCave.isFatal = 1;
952	>	//   simError();
953	>	// }
954	>	// fortranInitialized_ = true;
955	>	}
956
957	<	totalMass = myCutoffGroup->getMass();
957	>	void SimInfo::addProperty(GenericData* genData) {
958	>	properties_.addProperty(genData);
959	>	}
960	>
961	>	void SimInfo::removeProperty(const string& propName) {
962	>	properties_.removeProperty(propName);
963	>	}
964	>
965	>	void SimInfo::clearProperties() {
966	>	properties_.clearProperties();
967	>	}
968	>
969	>	vector<string> SimInfo::getPropertyNames() {
970	>	return properties_.getPropertyNames();
971	>	}
972
973	<	for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom);
974	<	cutoffAtom != NULL;
975	<	cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
976	<	mfact.push_back(cutoffAtom->getMass()/totalMass);
973	>	vector<GenericData*> SimInfo::getProperties() {
974	>	return properties_.getProperties();
975	>	}
976	>
977	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
978	>	return properties_.getPropertyByName(propName);
979	>	}
980	>
981	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
982	>	if (sman_ == sman) {
983	>	return;
984	>	}
985	>	delete sman_;
986	>	sman_ = sman;
987	>
988	>	Molecule* mol;
989	>	RigidBody* rb;
990	>	Atom* atom;
991	>	CutoffGroup* cg;
992	>	SimInfo::MoleculeIterator mi;
993	>	Molecule::RigidBodyIterator rbIter;
994	>	Molecule::AtomIterator atomIter;
995	>	Molecule::CutoffGroupIterator cgIter;
996	>
997	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
998	>
999	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1000	>	atom->setSnapshotManager(sman_);
1001	>	}
1002	>
1003	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1004	>	rb->setSnapshotManager(sman_);
1005	>	}
1006	>
1007	>	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
1008	>	cg->setSnapshotManager(sman_);
1009	>	}
1010	>	}
1011	>
1012	>	}
1013	>
1014	>	Vector3d SimInfo::getComVel(){
1015	>	SimInfo::MoleculeIterator i;
1016	>	Molecule* mol;
1017	>
1018	>	Vector3d comVel(0.0);
1019	>	RealType totalMass = 0.0;
1020	>
1021	>
1022	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1023	>	RealType mass = mol->getMass();
1024	>	totalMass += mass;
1025	>	comVel += mass * mol->getComVel();
1026	>	}
1027	>
1028	>	#ifdef IS_MPI
1029	>	RealType tmpMass = totalMass;
1030	>	Vector3d tmpComVel(comVel);
1031	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1032	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1033	>	#endif
1034	>
1035	>	comVel /= totalMass;
1036	>
1037	>	return comVel;
1038	>	}
1039	>
1040	>	Vector3d SimInfo::getCom(){
1041	>	SimInfo::MoleculeIterator i;
1042	>	Molecule* mol;
1043	>
1044	>	Vector3d com(0.0);
1045	>	RealType totalMass = 0.0;
1046	>
1047	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1048	>	RealType mass = mol->getMass();
1049	>	totalMass += mass;
1050	>	com += mass * mol->getCom();
1051	>	}
1052	>
1053	>	#ifdef IS_MPI
1054	>	RealType tmpMass = totalMass;
1055	>	Vector3d tmpCom(com);
1056	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1057	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1058	>	#endif
1059	>
1060	>	com /= totalMass;
1061	>
1062	>	return com;
1063	>
1064	>	}
1065	>
1066	>	ostream& operator <<(ostream& o, SimInfo& info) {
1067	>
1068	>	return o;
1069	>	}
1070	>
1071	>
1072	>	/*
1073	>	Returns center of mass and center of mass velocity in one function call.
1074	>	*/
1075	>
1076	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1077	>	SimInfo::MoleculeIterator i;
1078	>	Molecule* mol;
1079	>
1080	>
1081	>	RealType totalMass = 0.0;
1082	>
1083	>
1084	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1085	>	RealType mass = mol->getMass();
1086	>	totalMass += mass;
1087	>	com += mass * mol->getCom();
1088	>	comVel += mass * mol->getComVel();
1089		}
1090	+
1091	+	#ifdef IS_MPI
1092	+	RealType tmpMass = totalMass;
1093	+	Vector3d tmpCom(com);
1094	+	Vector3d tmpComVel(comVel);
1095	+	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1096	+	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1097	+	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1098	+	#endif
1099	+
1100	+	com /= totalMass;
1101	+	comVel /= totalMass;
1102	+	}
1103	+
1104	+	/*
1105	+	Return intertia tensor for entire system and angular momentum Vector.
1106	+
1107	+
1108	+	[  Ixx -Ixy  -Ixz ]
1109	+	J =| -Iyx  Iyy  -Iyz |
1110	+	[ -Izx -Iyz   Izz ]
1111	+	*/
1112	+
1113	+	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1114	+
1115	+
1116	+	RealType xx = 0.0;
1117	+	RealType yy = 0.0;
1118	+	RealType zz = 0.0;
1119	+	RealType xy = 0.0;
1120	+	RealType xz = 0.0;
1121	+	RealType yz = 0.0;
1122	+	Vector3d com(0.0);
1123	+	Vector3d comVel(0.0);
1124	+
1125	+	getComAll(com, comVel);
1126	+
1127	+	SimInfo::MoleculeIterator i;
1128	+	Molecule* mol;
1129	+
1130	+	Vector3d thisq(0.0);
1131	+	Vector3d thisv(0.0);
1132	+
1133	+	RealType thisMass = 0.0;
1134	+
1135	+
1136	+
1137	+
1138	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1139	+
1140	+	thisq = mol->getCom()-com;
1141	+	thisv = mol->getComVel()-comVel;
1142	+	thisMass = mol->getMass();
1143	+	// Compute moment of intertia coefficients.
1144	+	xx += thisq[0]*thisq[0]*thisMass;
1145	+	yy += thisq[1]*thisq[1]*thisMass;
1146	+	zz += thisq[2]*thisq[2]*thisMass;
1147	+
1148	+	// compute products of intertia
1149	+	xy += thisq[0]*thisq[1]*thisMass;
1150	+	xz += thisq[0]*thisq[2]*thisMass;
1151	+	yz += thisq[1]*thisq[2]*thisMass;
1152	+
1153	+	angularMomentum += cross( thisq, thisv ) * thisMass;
1154	+
1155	+	}
1156	+
1157	+
1158	+	inertiaTensor(0,0) = yy + zz;
1159	+	inertiaTensor(0,1) = -xy;
1160	+	inertiaTensor(0,2) = -xz;
1161	+	inertiaTensor(1,0) = -xy;
1162	+	inertiaTensor(1,1) = xx + zz;
1163	+	inertiaTensor(1,2) = -yz;
1164	+	inertiaTensor(2,0) = -xz;
1165	+	inertiaTensor(2,1) = -yz;
1166	+	inertiaTensor(2,2) = xx + yy;
1167	+
1168	+	#ifdef IS_MPI
1169	+	Mat3x3d tmpI(inertiaTensor);
1170	+	Vector3d tmpAngMom;
1171	+	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1172	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1173	+	#endif
1174	+
1175	+	return;
1176	+	}
1177	+
1178	+	//Returns the angular momentum of the system
1179	+	Vector3d SimInfo::getAngularMomentum(){
1180	+
1181	+	Vector3d com(0.0);
1182	+	Vector3d comVel(0.0);
1183	+	Vector3d angularMomentum(0.0);
1184	+
1185	+	getComAll(com,comVel);
1186	+
1187	+	SimInfo::MoleculeIterator i;
1188	+	Molecule* mol;
1189	+
1190	+	Vector3d thisr(0.0);
1191	+	Vector3d thisp(0.0);
1192	+
1193	+	RealType thisMass;
1194	+
1195	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1196	+	thisMass = mol->getMass();
1197	+	thisr = mol->getCom()-com;
1198	+	thisp = (mol->getComVel()-comVel)*thisMass;
1199	+
1200	+	angularMomentum += cross( thisr, thisp );
1201	+
1202	+	}
1203	+
1204	+	#ifdef IS_MPI
1205	+	Vector3d tmpAngMom;
1206	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1207	+	#endif
1208	+
1209	+	return angularMomentum;
1210	+	}
1211	+
1212	+	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1213	+	return IOIndexToIntegrableObject.at(index);
1214	+	}
1215	+
1216	+	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1217	+	IOIndexToIntegrableObject= v;
1218	+	}
1219	+
1220	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1221	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1222	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1223	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1224	+	*/
1225	+	void SimInfo::getGyrationalVolume(RealType &volume){
1226	+	Mat3x3d intTensor;
1227	+	RealType det;
1228	+	Vector3d dummyAngMom;
1229	+	RealType sysconstants;
1230	+	RealType geomCnst;
1231	+
1232	+	geomCnst = 3.0/2.0;
1233	+	/* Get the inertial tensor and angular momentum for free*/
1234	+	getInertiaTensor(intTensor,dummyAngMom);
1235	+
1236	+	det = intTensor.determinant();
1237	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1238	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1239	+	return;
1240	+	}
1241	+
1242	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1243	+	Mat3x3d intTensor;
1244	+	Vector3d dummyAngMom;
1245	+	RealType sysconstants;
1246	+	RealType geomCnst;
1247	+
1248	+	geomCnst = 3.0/2.0;
1249	+	/* Get the inertial tensor and angular momentum for free*/
1250	+	getInertiaTensor(intTensor,dummyAngMom);
1251	+
1252	+	detI = intTensor.determinant();
1253	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1254	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1255	+	return;
1256	+	}
1257	+	/*
1258	+	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1259	+	assert( v.size() == nAtoms_ + nRigidBodies_);
1260	+	sdByGlobalIndex_ = v;
1261		}
1262	+
1263	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1264	+	//assert(index < nAtoms_ + nRigidBodies_);
1265	+	return sdByGlobalIndex_.at(index);
1266	+	}
1267	+	*/
1268	+	int SimInfo::getNGlobalConstraints() {
1269	+	int nGlobalConstraints;
1270	+	#ifdef IS_MPI
1271	+	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1272	+	MPI_COMM_WORLD);
1273	+	#else
1274	+	nGlobalConstraints =  nConstraints_;
1275	+	#endif
1276	+	return nGlobalConstraints;
1277		}
1278
1279	<	}
1279	>	}//end namespace OpenMD
1280	>

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 1550 by gezelter, Wed Apr 27 21:49:59 2011 UTC

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