ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

root/OpenMD/branches/development/src/brains/SimInfo.cpp

Comparing:
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 1549 by gezelter, Wed Apr 27 18:38:15 2011 UTC

#	Line 1 | Line 1
1	<	#include <stdlib.h>
2	<	#include <string.h>
3	<	#include <math.h>
1	>	/*
2	>	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	>	*
4	>	* The University of Notre Dame grants you ("Licensee") a
5	>	* non-exclusive, royalty free, license to use, modify and
6	>	* redistribute this software in source and binary code form, provided
7	>	* that the following conditions are met:
8	>	*
9	>	* 1. Redistributions of source code must retain the above copyright
10	>	*    notice, this list of conditions and the following disclaimer.
11	>	*
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13	>	*    notice, this list of conditions and the following disclaimer in the
14	>	*    documentation and/or other materials provided with the
15	>	*    distribution.
16	>	*
17	>	* This software is provided "AS IS," without a warranty of any
18	>	* kind. All express or implied conditions, representations and
19	>	* warranties, including any implied warranty of merchantability,
20	>	* fitness for a particular purpose or non-infringement, are hereby
21	>	* excluded.  The University of Notre Dame and its licensors shall not
22	>	* be liable for any damages suffered by licensee as a result of
23	>	* using, modifying or distributing the software or its
24	>	* derivatives. In no event will the University of Notre Dame or its
25	>	* licensors be liable for any lost revenue, profit or data, or for
26	>	* direct, indirect, special, consequential, incidental or punitive
27	>	* damages, however caused and regardless of the theory of liability,
28	>	* arising out of the use of or inability to use software, even if the
29	>	* University of Notre Dame has been advised of the possibility of
30	>	* such damages.
31	>	*
32	>	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	>	* research, please cite the appropriate papers when you publish your
34	>	* work.  Good starting points are:
35	>	*
36	>	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	>	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	>	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	>	* [4]  Vardeman & Gezelter, in progress (2009).
40	>	*/
41	>
42	>	/**
43	>	* @file SimInfo.cpp
44	>	* @author    tlin
45	>	* @date  11/02/2004
46	>	* @version 1.0
47	>	*/
48
49	<	#include <iostream>
50	<	using namespace std;
49	>	#include <algorithm>
50	>	#include <set>
51	>	#include <map>
52
53		#include "brains/SimInfo.hpp"
54	<	#define __C
55	<	#include "brains/fSimulation.h"
54	>	#include "math/Vector3.hpp"
55	>	#include "primitives/Molecule.hpp"
56	>	#include "primitives/StuntDouble.hpp"
57	>	#include "UseTheForce/DarkSide/neighborLists_interface.h"
58	>	#include "UseTheForce/doForces_interface.h"
59	>	#include "utils/MemoryUtils.hpp"
60		#include "utils/simError.h"
61	<	#include "UseTheForce/DarkSide/simulation_interface.h"
62	<	#include "UseTheForce/notifyCutoffs_interface.h"
61	>	#include "selection/SelectionManager.hpp"
62	>	#include "io/ForceFieldOptions.hpp"
63	>	#include "UseTheForce/ForceField.hpp"
64	>	#include "nonbonded/SwitchingFunction.hpp"
65
15	–	//#include "UseTheForce/fortranWrappers.hpp"
16	–
17	–	#include "math/MatVec3.h"
18	–
66		#ifdef IS_MPI
67	<	#include "brains/mpiSimulation.hpp"
68	<	#endif
67	>	#include "UseTheForce/mpiComponentPlan.h"
68	>	#include "UseTheForce/DarkSide/simParallel_interface.h"
69	>	#endif
70
71	<	inline double roundMe( double x ){
72	<	return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
73	<	}
74	<
75	<	inline double min( double a, double b ){
76	<	return (a < b ) ? a : b;
77	<	}
71	>	using namespace std;
72	>	namespace OpenMD {
73	>
74	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
75	>	forceField_(ff), simParams_(simParams),
76	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
77	>	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
78	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
79	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
80	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
81	>	nConstraints_(0), sman_(NULL), fortranInitialized_(false),
82	>	calcBoxDipole_(false), useAtomicVirial_(true) {
83	>
84	>	MoleculeStamp* molStamp;
85	>	int nMolWithSameStamp;
86	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
87	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
88	>	CutoffGroupStamp* cgStamp;
89	>	RigidBodyStamp* rbStamp;
90	>	int nRigidAtoms = 0;
91	>
92	>	vector<Component*> components = simParams->getComponents();
93	>
94	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
95	>	molStamp = (*i)->getMoleculeStamp();
96	>	nMolWithSameStamp = (*i)->getNMol();
97	>
98	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
99	>
100	>	//calculate atoms in molecules
101	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
102	>
103	>	//calculate atoms in cutoff groups
104	>	int nAtomsInGroups = 0;
105	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
106	>
107	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
108	>	cgStamp = molStamp->getCutoffGroupStamp(j);
109	>	nAtomsInGroups += cgStamp->getNMembers();
110	>	}
111	>
112	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
113	>
114	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
115	>
116	>	//calculate atoms in rigid bodies
117	>	int nAtomsInRigidBodies = 0;
118	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
119	>
120	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
121	>	rbStamp = molStamp->getRigidBodyStamp(j);
122	>	nAtomsInRigidBodies += rbStamp->getNMembers();
123	>	}
124	>
125	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
126	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
127	>
128	>	}
129	>
130	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
131	>	//group therefore the total number of cutoff groups in the system is
132	>	//equal to the total number of atoms minus number of atoms belong to
133	>	//cutoff group defined in meta-data file plus the number of cutoff
134	>	//groups defined in meta-data file
135	>	std::cerr << "nGA = " << nGlobalAtoms_ << "\n";
136	>	std::cerr << "nCA = " << nCutoffAtoms << "\n";
137	>	std::cerr << "nG = " << nGroups << "\n";
138
139	<	SimInfo* currentInfo;
139	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
140
141	<	SimInfo::SimInfo(){
141	>	std::cerr << "nGCG = " << nGlobalCutoffGroups_ << "\n";
142	>
143	>	//every free atom (atom does not belong to rigid bodies) is an
144	>	//integrable object therefore the total number of integrable objects
145	>	//in the system is equal to the total number of atoms minus number of
146	>	//atoms belong to rigid body defined in meta-data file plus the number
147	>	//of rigid bodies defined in meta-data file
148	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
149	>	+ nGlobalRigidBodies_;
150	>
151	>	nGlobalMols_ = molStampIds_.size();
152	>	molToProcMap_.resize(nGlobalMols_);
153	>	}
154	>
155	>	SimInfo::~SimInfo() {
156	>	map<int, Molecule*>::iterator i;
157	>	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
158	>	delete i->second;
159	>	}
160	>	molecules_.clear();
161	>
162	>	delete sman_;
163	>	delete simParams_;
164	>	delete forceField_;
165	>	}
166
35	–	n_constraints = 0;
36	–	nZconstraints = 0;
37	–	n_oriented = 0;
38	–	n_dipoles = 0;
39	–	ndf = 0;
40	–	ndfRaw = 0;
41	–	nZconstraints = 0;
42	–	the_integrator = NULL;
43	–	setTemp = 0;
44	–	thermalTime = 0.0;
45	–	currentTime = 0.0;
46	–	rCut = 0.0;
47	–	rSw = 0.0;
167
168	<	haveRcut = 0;
169	<	haveRsw = 0;
170	<	boxIsInit = 0;
168	>	bool SimInfo::addMolecule(Molecule* mol) {
169	>	MoleculeIterator i;
170	>
171	>	i = molecules_.find(mol->getGlobalIndex());
172	>	if (i == molecules_.end() ) {
173	>
174	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
175	>
176	>	nAtoms_ += mol->getNAtoms();
177	>	nBonds_ += mol->getNBonds();
178	>	nBends_ += mol->getNBends();
179	>	nTorsions_ += mol->getNTorsions();
180	>	nInversions_ += mol->getNInversions();
181	>	nRigidBodies_ += mol->getNRigidBodies();
182	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
183	>	nCutoffGroups_ += mol->getNCutoffGroups();
184	>	nConstraints_ += mol->getNConstraintPairs();
185	>
186	>	addInteractionPairs(mol);
187	>
188	>	return true;
189	>	} else {
190	>	return false;
191	>	}
192	>	}
193
194	<	resetTime = 1e99;
194	>	bool SimInfo::removeMolecule(Molecule* mol) {
195	>	MoleculeIterator i;
196	>	i = molecules_.find(mol->getGlobalIndex());
197
198	<	orthoRhombic = 0;
56	<	orthoTolerance = 1E-6;
57	<	useInitXSstate = true;
198	>	if (i != molecules_.end() ) {
199
200	<	usePBC = 0;
201	<	useDirectionalAtoms = 0;
202	<	useLennardJones = 0;
203	<	useElectrostatics = 0;
204	<	useCharges = 0;
205	<	useDipoles = 0;
206	<	useSticky = 0;
207	<	useGayBerne = 0;
208	<	useEAM = 0;
209	<	useShapes = 0;
210	<	useFLARB = 0;
70	<
71	<	useSolidThermInt = 0;
72	<	useLiquidThermInt = 0;
73	<
74	<	haveCutoffGroups = false;
75	<
76	<	excludes = Exclude::Instance();
77	<
78	<	myConfiguration = new SimState();
79	<
80	<	has_minimizer = false;
81	<	the_minimizer =NULL;
82	<
83	<	ngroup = 0;
84	<
85	<	}
200	>	assert(mol == i->second);
201	>
202	>	nAtoms_ -= mol->getNAtoms();
203	>	nBonds_ -= mol->getNBonds();
204	>	nBends_ -= mol->getNBends();
205	>	nTorsions_ -= mol->getNTorsions();
206	>	nInversions_ -= mol->getNInversions();
207	>	nRigidBodies_ -= mol->getNRigidBodies();
208	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
209	>	nCutoffGroups_ -= mol->getNCutoffGroups();
210	>	nConstraints_ -= mol->getNConstraintPairs();
211
212	+	removeInteractionPairs(mol);
213	+	molecules_.erase(mol->getGlobalIndex());
214
215	<	SimInfo::~SimInfo(){
215	>	delete mol;
216	>
217	>	return true;
218	>	} else {
219	>	return false;
220	>	}
221	>	}
222
223	<	delete myConfiguration;
223	>
224	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
225	>	i = molecules_.begin();
226	>	return i == molecules_.end() ? NULL : i->second;
227	>	}
228
229	<	map<string, GenericData*>::iterator i;
230	<
231	<	for(i = properties.begin(); i != properties.end(); i++)
232	<	delete (*i).second;
229	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
230	>	++i;
231	>	return i == molecules_.end() ? NULL : i->second;
232	>	}
233
97	–	}
234
235	<	void SimInfo::setBox(double newBox[3]) {
236	<
237	<	int i, j;
238	<	double tempMat[3][3];
235	>	void SimInfo::calcNdf() {
236	>	int ndf_local;
237	>	MoleculeIterator i;
238	>	vector<StuntDouble*>::iterator j;
239	>	Molecule* mol;
240	>	StuntDouble* integrableObject;
241
242	<	for(i=0; i<3; i++)
243	<	for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
242	>	ndf_local = 0;
243	>
244	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
245	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
246	>	integrableObject = mol->nextIntegrableObject(j)) {
247
248	<	tempMat[0][0] = newBox[0];
108	<	tempMat[1][1] = newBox[1];
109	<	tempMat[2][2] = newBox[2];
248	>	ndf_local += 3;
249
250	<	setBoxM( tempMat );
250	>	if (integrableObject->isDirectional()) {
251	>	if (integrableObject->isLinear()) {
252	>	ndf_local += 2;
253	>	} else {
254	>	ndf_local += 3;
255	>	}
256	>	}
257	>
258	>	}
259	>	}
260	>
261	>	// n_constraints is local, so subtract them on each processor
262	>	ndf_local -= nConstraints_;
263
264	<	}
264	>	#ifdef IS_MPI
265	>	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
266	>	#else
267	>	ndf_ = ndf_local;
268	>	#endif
269
270	<	void SimInfo::setBoxM( double theBox[3][3] ){
271	<
272	<	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);
270	>	// nZconstraints_ is global, as are the 3 COM translations for the
271	>	// entire system:
272	>	ndf_ = ndf_ - 3 - nZconstraint_;
273
274	<	if( !boxIsInit ) boxIsInit = 1;
274	>	}
275
276	<	for(i=0; i < 3; i++)
277	<	for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
278	<
279	<	calcBoxL();
280	<	calcHmatInv();
281	<
282	<	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];
137	<	}
276	>	int SimInfo::getFdf() {
277	>	#ifdef IS_MPI
278	>	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
279	>	#else
280	>	fdf_ = fdf_local;
281	>	#endif
282	>	return fdf_;
283		}
284	+
285	+	void SimInfo::calcNdfRaw() {
286	+	int ndfRaw_local;
287
288	<	setFortranBox(FortranHmat, FortranHmatInv, &orthoRhombic);
289	<
290	<	}
291	<
288	>	MoleculeIterator i;
289	>	vector<StuntDouble*>::iterator j;
290	>	Molecule* mol;
291	>	StuntDouble* integrableObject;
292
293	<	void SimInfo::getBoxM (double theBox[3][3]) {
293	>	// Raw degrees of freedom that we have to set
294	>	ndfRaw_local = 0;
295	>
296	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
297	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
298	>	integrableObject = mol->nextIntegrableObject(j)) {
299
300	<	int i, j;
148	<	for(i=0; i<3; i++)
149	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
150	<	}
300	>	ndfRaw_local += 3;
301
302	+	if (integrableObject->isDirectional()) {
303	+	if (integrableObject->isLinear()) {
304	+	ndfRaw_local += 2;
305	+	} else {
306	+	ndfRaw_local += 3;
307	+	}
308	+	}
309	+
310	+	}
311	+	}
312	+
313	+	#ifdef IS_MPI
314	+	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
315	+	#else
316	+	ndfRaw_ = ndfRaw_local;
317	+	#endif
318	+	}
319
320	<	void SimInfo::scaleBox(double scale) {
321	<	double theBox[3][3];
155	<	int i, j;
320	>	void SimInfo::calcNdfTrans() {
321	>	int ndfTrans_local;
322
323	<	// cerr << "Scaling box by " << scale << "\n";
323	>	ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
324
159	–	for(i=0; i<3; i++)
160	–	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
325
326	<	setBoxM(theBox);
326	>	#ifdef IS_MPI
327	>	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
328	>	#else
329	>	ndfTrans_ = ndfTrans_local;
330	>	#endif
331
332	<	}
332	>	ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
333	>
334	>	}
335
336	<	void SimInfo::calcHmatInv( void ) {
337	<
338	<	int oldOrtho;
339	<	int i,j;
340	<	double smallDiag;
341	<	double tol;
342	<	double sanity[3][3];
336	>	void SimInfo::addInteractionPairs(Molecule* mol) {
337	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
338	>	vector<Bond*>::iterator bondIter;
339	>	vector<Bend*>::iterator bendIter;
340	>	vector<Torsion*>::iterator torsionIter;
341	>	vector<Inversion*>::iterator inversionIter;
342	>	Bond* bond;
343	>	Bend* bend;
344	>	Torsion* torsion;
345	>	Inversion* inversion;
346	>	int a;
347	>	int b;
348	>	int c;
349	>	int d;
350
351	<	invertMat3( Hmat, HmatInv );
352	<
353	<	// check to see if Hmat is orthorhombic
354	<
355	<	oldOrtho = orthoRhombic;
356	<
357	<	smallDiag = fabs(Hmat[0][0]);
358	<	if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
359	<	if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
360	<	tol = smallDiag * orthoTolerance;
361	<
362	<	orthoRhombic = 1;
363	<
364	<	for (i = 0; i < 3; i++ ) {
365	<	for (j = 0 ; j < 3; j++) {
366	<	if (i != j) {
367	<	if (orthoRhombic) {
368	<	if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
369	<	}
351	>	// atomGroups can be used to add special interaction maps between
352	>	// groups of atoms that are in two separate rigid bodies.
353	>	// However, most site-site interactions between two rigid bodies
354	>	// are probably not special, just the ones between the physically
355	>	// bonded atoms.  Interactions *within* a single rigid body should
356	>	// always be excluded.  These are done at the bottom of this
357	>	// function.
358	>
359	>	map<int, set<int> > atomGroups;
360	>	Molecule::RigidBodyIterator rbIter;
361	>	RigidBody* rb;
362	>	Molecule::IntegrableObjectIterator ii;
363	>	StuntDouble* integrableObject;
364	>
365	>	for (integrableObject = mol->beginIntegrableObject(ii);
366	>	integrableObject != NULL;
367	>	integrableObject = mol->nextIntegrableObject(ii)) {
368	>
369	>	if (integrableObject->isRigidBody()) {
370	>	rb = static_cast<RigidBody*>(integrableObject);
371	>	vector<Atom*> atoms = rb->getAtoms();
372	>	set<int> rigidAtoms;
373	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
374	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
375	>	}
376	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
377	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
378	>	}
379	>	} else {
380	>	set<int> oneAtomSet;
381	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
382	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
383		}
384	<	}
385	<	}
384	>	}
385	>
386	>	for (bond= mol->beginBond(bondIter); bond != NULL;
387	>	bond = mol->nextBond(bondIter)) {
388
389	<	if( oldOrtho != orthoRhombic ){
389	>	a = bond->getAtomA()->getGlobalIndex();
390	>	b = bond->getAtomB()->getGlobalIndex();
391
392	<	if( orthoRhombic ) {
393	<	sprintf( painCave.errMsg,
394	<	"OOPSE is switching from the default Non-Orthorhombic\n"
395	<	"\tto the faster Orthorhombic periodic boundary computations.\n"
396	<	"\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();
392	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
393	>	oneTwoInteractions_.addPair(a, b);
394	>	} else {
395	>	excludedInteractions_.addPair(a, b);
396	>	}
397		}
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	–	}
398
399	<	void SimInfo::calcBoxL( void ){
399	>	for (bend= mol->beginBend(bendIter); bend != NULL;
400	>	bend = mol->nextBend(bendIter)) {
401
402	<	double dx, dy, dz, dsq;
402	>	a = bend->getAtomA()->getGlobalIndex();
403	>	b = bend->getAtomB()->getGlobalIndex();
404	>	c = bend->getAtomC()->getGlobalIndex();
405	>
406	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
407	>	oneTwoInteractions_.addPair(a, b);
408	>	oneTwoInteractions_.addPair(b, c);
409	>	} else {
410	>	excludedInteractions_.addPair(a, b);
411	>	excludedInteractions_.addPair(b, c);
412	>	}
413
414	<	// boxVol = Determinant of Hmat
414	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
415	>	oneThreeInteractions_.addPair(a, c);
416	>	} else {
417	>	excludedInteractions_.addPair(a, c);
418	>	}
419	>	}
420
421	<	boxVol = matDet3( Hmat );
421	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
422	>	torsion = mol->nextTorsion(torsionIter)) {
423
424	<	// boxLx
425	<
426	<	dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
427	<	dsq = dx*dx + dy*dy + dz*dz;
237	<	boxL[0] = sqrt( dsq );
238	<	//maxCutoff = 0.5 * boxL[0];
424	>	a = torsion->getAtomA()->getGlobalIndex();
425	>	b = torsion->getAtomB()->getGlobalIndex();
426	>	c = torsion->getAtomC()->getGlobalIndex();
427	>	d = torsion->getAtomD()->getGlobalIndex();
428
429	<	// boxLy
430	<
431	<	dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
432	<	dsq = dx*dx + dy*dy + dz*dz;
433	<	boxL[1] = sqrt( dsq );
434	<	//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
429	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
430	>	oneTwoInteractions_.addPair(a, b);
431	>	oneTwoInteractions_.addPair(b, c);
432	>	oneTwoInteractions_.addPair(c, d);
433	>	} else {
434	>	excludedInteractions_.addPair(a, b);
435	>	excludedInteractions_.addPair(b, c);
436	>	excludedInteractions_.addPair(c, d);
437	>	}
438
439	+	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
440	+	oneThreeInteractions_.addPair(a, c);
441	+	oneThreeInteractions_.addPair(b, d);
442	+	} else {
443	+	excludedInteractions_.addPair(a, c);
444	+	excludedInteractions_.addPair(b, d);
445	+	}
446
447	<	// boxLz
448	<
449	<	dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
450	<	dsq = dx*dx + dy*dy + dz*dz;
451	<	boxL[2] = sqrt( dsq );
452	<	//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
447	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
448	>	oneFourInteractions_.addPair(a, d);
449	>	} else {
450	>	excludedInteractions_.addPair(a, d);
451	>	}
452	>	}
453
454	<	//calculate the max cutoff
455	<	maxCutoff =  calcMaxCutOff();
257	<
258	<	checkCutOffs();
454	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
455	>	inversion = mol->nextInversion(inversionIter)) {
456
457	<	}
457	>	a = inversion->getAtomA()->getGlobalIndex();
458	>	b = inversion->getAtomB()->getGlobalIndex();
459	>	c = inversion->getAtomC()->getGlobalIndex();
460	>	d = inversion->getAtomD()->getGlobalIndex();
461
462	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
463	+	oneTwoInteractions_.addPair(a, b);
464	+	oneTwoInteractions_.addPair(a, c);
465	+	oneTwoInteractions_.addPair(a, d);
466	+	} else {
467	+	excludedInteractions_.addPair(a, b);
468	+	excludedInteractions_.addPair(a, c);
469	+	excludedInteractions_.addPair(a, d);
470	+	}
471
472	<	double SimInfo::calcMaxCutOff(){
472	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
473	>	oneThreeInteractions_.addPair(b, c);
474	>	oneThreeInteractions_.addPair(b, d);
475	>	oneThreeInteractions_.addPair(c, d);
476	>	} else {
477	>	excludedInteractions_.addPair(b, c);
478	>	excludedInteractions_.addPair(b, d);
479	>	excludedInteractions_.addPair(c, d);
480	>	}
481	>	}
482
483	<	double ri[3], rj[3], rk[3];
484	<	double rij[3], rjk[3], rki[3];
485	<	double minDist;
483	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
484	>	rb = mol->nextRigidBody(rbIter)) {
485	>	vector<Atom*> atoms = rb->getAtoms();
486	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
487	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
488	>	a = atoms[i]->getGlobalIndex();
489	>	b = atoms[j]->getGlobalIndex();
490	>	excludedInteractions_.addPair(a, b);
491	>	}
492	>	}
493	>	}
494
495	<	ri[0] = Hmat[0][0];
270	<	ri[1] = Hmat[1][0];
271	<	ri[2] = Hmat[2][0];
495	>	}
496
497	<	rj[0] = Hmat[0][1];
498	<	rj[1] = Hmat[1][1];
499	<	rj[2] = Hmat[2][1];
497	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
498	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
499	>	vector<Bond*>::iterator bondIter;
500	>	vector<Bend*>::iterator bendIter;
501	>	vector<Torsion*>::iterator torsionIter;
502	>	vector<Inversion*>::iterator inversionIter;
503	>	Bond* bond;
504	>	Bend* bend;
505	>	Torsion* torsion;
506	>	Inversion* inversion;
507	>	int a;
508	>	int b;
509	>	int c;
510	>	int d;
511
512	<	rk[0] = Hmat[0][2];
513	<	rk[1] = Hmat[1][2];
514	<	rk[2] = Hmat[2][2];
512	>	map<int, set<int> > atomGroups;
513	>	Molecule::RigidBodyIterator rbIter;
514	>	RigidBody* rb;
515	>	Molecule::IntegrableObjectIterator ii;
516	>	StuntDouble* integrableObject;
517
518	<	crossProduct3(ri, rj, rij);
519	<	distXY = dotProduct3(rk,rij) / norm3(rij);
518	>	for (integrableObject = mol->beginIntegrableObject(ii);
519	>	integrableObject != NULL;
520	>	integrableObject = mol->nextIntegrableObject(ii)) {
521	>
522	>	if (integrableObject->isRigidBody()) {
523	>	rb = static_cast<RigidBody*>(integrableObject);
524	>	vector<Atom*> atoms = rb->getAtoms();
525	>	set<int> rigidAtoms;
526	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
527	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
528	>	}
529	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
530	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
531	>	}
532	>	} else {
533	>	set<int> oneAtomSet;
534	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
535	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
536	>	}
537	>	}
538
539	<	crossProduct3(rj,rk, rjk);
540	<	distYZ = dotProduct3(ri,rjk) / norm3(rjk);
539	>	for (bond= mol->beginBond(bondIter); bond != NULL;
540	>	bond = mol->nextBond(bondIter)) {
541	>
542	>	a = bond->getAtomA()->getGlobalIndex();
543	>	b = bond->getAtomB()->getGlobalIndex();
544	>
545	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
546	>	oneTwoInteractions_.removePair(a, b);
547	>	} else {
548	>	excludedInteractions_.removePair(a, b);
549	>	}
550	>	}
551
552	<	crossProduct3(rk,ri, rki);
553	<	distZX = dotProduct3(rj,rki) / norm3(rki);
552	>	for (bend= mol->beginBend(bendIter); bend != NULL;
553	>	bend = mol->nextBend(bendIter)) {
554
555	<	minDist = min(min(distXY, distYZ), distZX);
556	<	return minDist/2;
557	<
558	<	}
555	>	a = bend->getAtomA()->getGlobalIndex();
556	>	b = bend->getAtomB()->getGlobalIndex();
557	>	c = bend->getAtomC()->getGlobalIndex();
558	>
559	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
560	>	oneTwoInteractions_.removePair(a, b);
561	>	oneTwoInteractions_.removePair(b, c);
562	>	} else {
563	>	excludedInteractions_.removePair(a, b);
564	>	excludedInteractions_.removePair(b, c);
565	>	}
566
567	<	void SimInfo::wrapVector( double thePos[3] ){
567	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
568	>	oneThreeInteractions_.removePair(a, c);
569	>	} else {
570	>	excludedInteractions_.removePair(a, c);
571	>	}
572	>	}
573
574	<	int i;
575	<	double scaled[3];
574	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
575	>	torsion = mol->nextTorsion(torsionIter)) {
576
577	<	if( !orthoRhombic ){
578	<	// calc the scaled coordinates.
577	>	a = torsion->getAtomA()->getGlobalIndex();
578	>	b = torsion->getAtomB()->getGlobalIndex();
579	>	c = torsion->getAtomC()->getGlobalIndex();
580	>	d = torsion->getAtomD()->getGlobalIndex();
581
582	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
583	+	oneTwoInteractions_.removePair(a, b);
584	+	oneTwoInteractions_.removePair(b, c);
585	+	oneTwoInteractions_.removePair(c, d);
586	+	} else {
587	+	excludedInteractions_.removePair(a, b);
588	+	excludedInteractions_.removePair(b, c);
589	+	excludedInteractions_.removePair(c, d);
590	+	}
591
592	<	matVecMul3(HmatInv, thePos, scaled);
593	<
594	<	for(i=0; i<3; i++)
595	<	scaled[i] -= roundMe(scaled[i]);
596	<
597	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
598	<
311	<	matVecMul3(Hmat, scaled, thePos);
592	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
593	>	oneThreeInteractions_.removePair(a, c);
594	>	oneThreeInteractions_.removePair(b, d);
595	>	} else {
596	>	excludedInteractions_.removePair(a, c);
597	>	excludedInteractions_.removePair(b, d);
598	>	}
599
600	<	}
601	<	else{
602	<	// calc the scaled coordinates.
603	<
604	<	for(i=0; i<3; i++)
605	<	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	<	}
600	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
601	>	oneFourInteractions_.removePair(a, d);
602	>	} else {
603	>	excludedInteractions_.removePair(a, d);
604	>	}
605	>	}
606
607	+	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
608	+	inversion = mol->nextInversion(inversionIter)) {
609
610	<	int SimInfo::getNDF(){
611	<	int ndf_local;
610	>	a = inversion->getAtomA()->getGlobalIndex();
611	>	b = inversion->getAtomB()->getGlobalIndex();
612	>	c = inversion->getAtomC()->getGlobalIndex();
613	>	d = inversion->getAtomD()->getGlobalIndex();
614
615	<	ndf_local = 0;
616	<
617	<	for(int i = 0; i < integrableObjects.size(); i++){
618	<	ndf_local += 3;
619	<	if (integrableObjects[i]->isDirectional()) {
620	<	if (integrableObjects[i]->isLinear())
621	<	ndf_local += 2;
622	<	else
623	<	ndf_local += 3;
615	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
616	>	oneTwoInteractions_.removePair(a, b);
617	>	oneTwoInteractions_.removePair(a, c);
618	>	oneTwoInteractions_.removePair(a, d);
619	>	} else {
620	>	excludedInteractions_.removePair(a, b);
621	>	excludedInteractions_.removePair(a, c);
622	>	excludedInteractions_.removePair(a, d);
623	>	}
624	>
625	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
626	>	oneThreeInteractions_.removePair(b, c);
627	>	oneThreeInteractions_.removePair(b, d);
628	>	oneThreeInteractions_.removePair(c, d);
629	>	} else {
630	>	excludedInteractions_.removePair(b, c);
631	>	excludedInteractions_.removePair(b, d);
632	>	excludedInteractions_.removePair(c, d);
633	>	}
634		}
635	+
636	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
637	+	rb = mol->nextRigidBody(rbIter)) {
638	+	vector<Atom*> atoms = rb->getAtoms();
639	+	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
640	+	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
641	+	a = atoms[i]->getGlobalIndex();
642	+	b = atoms[j]->getGlobalIndex();
643	+	excludedInteractions_.removePair(a, b);
644	+	}
645	+	}
646	+	}
647	+
648		}
649	+
650	+
651	+	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
652	+	int curStampId;
653	+
654	+	//index from 0
655	+	curStampId = moleculeStamps_.size();
656
657	<	// n_constraints is local, so subtract them on each processor:
657	>	moleculeStamps_.push_back(molStamp);
658	>	molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
659	>	}
660
661	<	ndf_local -= n_constraints;
661	>
662	>	/**
663	>	* update
664	>	*
665	>	*  Performs the global checks and variable settings after the
666	>	*  objects have been created.
667	>	*
668	>	*/
669	>	void SimInfo::update() {
670	>	setupSimVariables();
671	>	calcNdf();
672	>	calcNdfRaw();
673	>	calcNdfTrans();
674	>	}
675	>
676	>	/**
677	>	* getSimulatedAtomTypes
678	>	*
679	>	* Returns an STL set of AtomType* that are actually present in this
680	>	* simulation.  Must query all processors to assemble this information.
681	>	*
682	>	*/
683	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
684	>	SimInfo::MoleculeIterator mi;
685	>	Molecule* mol;
686	>	Molecule::AtomIterator ai;
687	>	Atom* atom;
688	>	set<AtomType*> atomTypes;
689	>
690	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
691	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
692	>	atomTypes.insert(atom->getAtomType());
693	>	}
694	>	}
695
696		#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
697
698	<	// nZconstraints is global, as are the 3 COM translations for the
699	<	// entire system:
698	>	// loop over the found atom types on this processor, and add their
699	>	// numerical idents to a vector:
700
701	<	ndf = ndf - 3 - nZconstraints;
701	>	vector<int> foundTypes;
702	>	set<AtomType*>::iterator i;
703	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
704	>	foundTypes.push_back( (*i)->getIdent() );
705
706	<	return ndf;
707	<	}
706	>	// count_local holds the number of found types on this processor
707	>	int count_local = foundTypes.size();
708
709	<	int SimInfo::getNDFraw() {
710	<	int ndfRaw_local;
709	>	// count holds the total number of found types on all processors
710	>	// (some will be redundant with the ones found locally):
711	>	int count;
712	>	MPI::COMM_WORLD.Allreduce(&count_local, &count, 1, MPI::INT, MPI::SUM);
713
714	<	// Raw degrees of freedom that we have to set
715	<	ndfRaw_local = 0;
714	>	// create a vector to hold the globally found types, and resize it:
715	>	vector<int> ftGlobal;
716	>	ftGlobal.resize(count);
717	>	vector<int> counts;
718
719	<	for(int i = 0; i < integrableObjects.size(); i++){
720	<	ndfRaw_local += 3;
721	<	if (integrableObjects[i]->isDirectional()) {
722	<	if (integrableObjects[i]->isLinear())
723	<	ndfRaw_local += 2;
724	<	else
379	<	ndfRaw_local += 3;
380	<	}
381	<	}
719	>	int nproc = MPI::COMM_WORLD.Get_size();
720	>	counts.resize(nproc);
721	>	vector<int> disps;
722	>	disps.resize(nproc);
723	>
724	>	// now spray out the foundTypes to all the other processors:
725
726	<	#ifdef IS_MPI
727	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
385	<	#else
386	<	ndfRaw = ndfRaw_local;
387	<	#endif
726	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
727	>	&ftGlobal[0], &counts[0], &disps[0], MPI::INT);
728
729	<	return ndfRaw;
730	<	}
731	<
732	<	int SimInfo::getNDFtranslational() {
733	<	int ndfTrans_local;
734	<
735	<	ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
736	<
737	<
738	<	#ifdef IS_MPI
739	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
740	<	#else
741	<	ndfTrans = ndfTrans_local;
729	>	// foundIdents is a stl set, so inserting an already found ident
730	>	// will have no effect.
731	>	set<int> foundIdents;
732	>	vector<int>::iterator j;
733	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
734	>	foundIdents.insert((*j));
735	>
736	>	// now iterate over the foundIdents and get the actual atom types
737	>	// that correspond to these:
738	>	set<int>::iterator it;
739	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
740	>	atomTypes.insert( forceField_->getAtomType((*it)) );
741	>
742		#endif
743	+
744	+	return atomTypes;
745	+	}
746
747	<	ndfTrans = ndfTrans - 3 - nZconstraints;
747	>	void SimInfo::setupSimVariables() {
748	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
749	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
750	>	calcBoxDipole_ = false;
751	>	if ( simParams_->haveAccumulateBoxDipole() )
752	>	if ( simParams_->getAccumulateBoxDipole() ) {
753	>	calcBoxDipole_ = true;
754	>	}
755
756	<	return ndfTrans;
757	<	}
756	>	set<AtomType*>::iterator i;
757	>	set<AtomType*> atomTypes;
758	>	atomTypes = getSimulatedAtomTypes();
759	>	int usesElectrostatic = 0;
760	>	int usesMetallic = 0;
761	>	int usesDirectional = 0;
762	>	//loop over all of the atom types
763	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
764	>	usesElectrostatic |= (*i)->isElectrostatic();
765	>	usesMetallic |= (*i)->isMetal();
766	>	usesDirectional |= (*i)->isDirectional();
767	>	}
768
769	<	int SimInfo::getTotIntegrableObjects() {
770	<	int nObjs_local;
771	<	int nObjs;
769	>	#ifdef IS_MPI
770	>	int temp;
771	>	temp = usesDirectional;
772	>	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
773
774	<	nObjs_local =  integrableObjects.size();
774	>	temp = usesMetallic;
775	>	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
776
777	<
778	<	#ifdef IS_MPI
417	<	MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
418	<	#else
419	<	nObjs = nObjs_local;
777	>	temp = usesElectrostatic;
778	>	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
779		#endif
780	+	fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;
781	+	fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
782	+	fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
783	+	fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
784	+	fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
785	+	fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
786	+	}
787
788
789	<	return nObjs;
790	<	}
789	>	vector<int> SimInfo::getGlobalAtomIndices() {
790	>	SimInfo::MoleculeIterator mi;
791	>	Molecule* mol;
792	>	Molecule::AtomIterator ai;
793	>	Atom* atom;
794
795	<	void SimInfo::refreshSim(){
795	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
796	>
797	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
798	>
799	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
800	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
801	>	}
802	>	}
803	>	return GlobalAtomIndices;
804	>	}
805
428	–	simtype fInfo;
429	–	int isError;
430	–	int n_global;
431	–	int* excl;
806
807	<	fInfo.dielect = 0.0;
807	>	vector<int> SimInfo::getGlobalGroupIndices() {
808	>	SimInfo::MoleculeIterator mi;
809	>	Molecule* mol;
810	>	Molecule::CutoffGroupIterator ci;
811	>	CutoffGroup* cg;
812
813	<	if( useDipoles ){
814	<	if( useReactionField )fInfo.dielect = dielectric;
813	>	vector<int> GlobalGroupIndices;
814	>
815	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
816	>
817	>	//local index of cutoff group is trivial, it only depends on the
818	>	//order of travesing
819	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
820	>	cg = mol->nextCutoffGroup(ci)) {
821	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
822	>	}
823	>	}
824	>	return GlobalGroupIndices;
825		}
826
439	–	fInfo.SIM_uses_PBC = usePBC;
827
828	<	if (useSticky || useDipoles || useGayBerne || useShapes) {
829	<	useDirectionalAtoms = 1;
830	<	fInfo.SIM_uses_DirectionalAtoms = useDirectionalAtoms;
831	<	}
828	>	void SimInfo::setupFortran() {
829	>	int isError;
830	>	int nExclude, nOneTwo, nOneThree, nOneFour;
831	>	vector<int> fortranGlobalGroupMembership;
832	>
833	>	isError = 0;
834
835	<	fInfo.SIM_uses_LennardJones = useLennardJones;
835	>	//globalGroupMembership_ is filled by SimCreator
836	>	for (int i = 0; i < nGlobalAtoms_; i++) {
837	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
838	>	}
839
840	<	if (useCharges || useDipoles) {
841	<	useElectrostatics = 1;
842	<	fInfo.SIM_uses_Electrostatics = useElectrostatics;
843	<	}
840	>	//calculate mass ratio of cutoff group
841	>	vector<RealType> mfact;
842	>	SimInfo::MoleculeIterator mi;
843	>	Molecule* mol;
844	>	Molecule::CutoffGroupIterator ci;
845	>	CutoffGroup* cg;
846	>	Molecule::AtomIterator ai;
847	>	Atom* atom;
848	>	RealType totalMass;
849
850	<	fInfo.SIM_uses_Charges = useCharges;
851	<	fInfo.SIM_uses_Dipoles = useDipoles;
852	<	fInfo.SIM_uses_Sticky = useSticky;
853	<	fInfo.SIM_uses_GayBerne = useGayBerne;
854	<	fInfo.SIM_uses_EAM = useEAM;
458	<	fInfo.SIM_uses_Shapes = useShapes;
459	<	fInfo.SIM_uses_FLARB = useFLARB;
460	<	fInfo.SIM_uses_RF = useReactionField;
850	>	//to avoid memory reallocation, reserve enough space for mfact
851	>	mfact.reserve(getNCutoffGroups());
852	>
853	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
854	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
855
856	<	n_exclude = excludes->getSize();
857	<	excl = excludes->getFortranArray();
858	<
859	<	#ifdef IS_MPI
860	<	n_global = mpiSim->getNAtomsGlobal();
861	<	#else
862	<	n_global = n_atoms;
863	<	#endif
864	<
865	<	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);
856	>	totalMass = cg->getMass();
857	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
858	>	// Check for massless groups - set mfact to 1 if true
859	>	if (totalMass != 0)
860	>	mfact.push_back(atom->getMass()/totalMass);
861	>	else
862	>	mfact.push_back( 1.0 );
863	>	}
864	>	}
865	>	}
866
867	<	if( isError ){
482	<
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();
488	<	}
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	<	}
867	>	// Build the identArray_
868
869	<	void SimInfo::setDefaultRcut( double theRcut ){
870	<
871	<	haveRcut = 1;
872	<	rCut = theRcut;
873	<	rList = rCut + 1.0;
874	<
875	<	notifyFortranCutoffs( &rCut, &rSw, &rList );
508	<	}
869	>	identArray_.clear();
870	>	identArray_.reserve(getNAtoms());
871	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
872	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
873	>	identArray_.push_back(atom->getIdent());
874	>	}
875	>	}
876
877	<	void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
877	>	//fill molMembershipArray
878	>	//molMembershipArray is filled by SimCreator
879	>	vector<int> molMembershipArray(nGlobalAtoms_);
880	>	for (int i = 0; i < nGlobalAtoms_; i++) {
881	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
882	>	}
883	>
884	>	//setup fortran simulation
885
886	<	rSw = theRsw;
887	<	setDefaultRcut( theRcut );
888	<	}
886	>	nExclude = excludedInteractions_.getSize();
887	>	nOneTwo = oneTwoInteractions_.getSize();
888	>	nOneThree = oneThreeInteractions_.getSize();
889	>	nOneFour = oneFourInteractions_.getSize();
890
891	+	int* excludeList = excludedInteractions_.getPairList();
892	+	int* oneTwoList = oneTwoInteractions_.getPairList();
893	+	int* oneThreeList = oneThreeInteractions_.getPairList();
894	+	int* oneFourList = oneFourInteractions_.getPairList();
895
896	<	void SimInfo::checkCutOffs( void ){
897	<
898	<	if( boxIsInit ){
896	>	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray_[0],
897	>	&nExclude, excludeList,
898	>	&nOneTwo, oneTwoList,
899	>	&nOneThree, oneThreeList,
900	>	&nOneFour, oneFourList,
901	>	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
902	>	&fortranGlobalGroupMembership[0], &isError);
903
904	<	//we need to check cutOffs against the box
905	<
523	<	if( rCut > maxCutoff ){
904	>	if( isError ){
905	>
906		sprintf( painCave.errMsg,
907	<	"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;
907	>	"There was an error setting the simulation information in fortran.\n" );
908		painCave.isFatal = 1;
909	+	painCave.severity = OPENMD_ERROR;
910		simError();
911	<	}
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	<	}
552	<
553	<	void SimInfo::addProperty(GenericData* prop){
554	<
555	<	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()){
911	>	}
912
563	–	delete (*result).second;
564	–	(*result).second = prop;
565	–
566	–	}
567	–	else{
568	–
569	–	properties[prop->getID()] = prop;
570	–
571	–	}
913
914	<	}
915	<
916	<	GenericData* SimInfo::getProperty(const string& propName){
917	<
918	<	map<string, GenericData*>::iterator result;
919	<
920	<	//string lowerCaseName = ();
921	<
922	<	result = properties.find(propName);
923	<
924	<	if(result != properties.end())
925	<	return (*result).second;
926	<	else
586	<	return NULL;
587	<	}
914	>	sprintf( checkPointMsg,
915	>	"succesfully sent the simulation information to fortran.\n");
916	>
917	>	errorCheckPoint();
918	>
919	>	// Setup number of neighbors in neighbor list if present
920	>	if (simParams_->haveNeighborListNeighbors()) {
921	>	int nlistNeighbors = simParams_->getNeighborListNeighbors();
922	>	setNeighbors(&nlistNeighbors);
923	>	}
924	>
925	>	#ifdef IS_MPI
926	>	mpiSimData parallelData;
927
928	+	//fill up mpiSimData struct
929	+	parallelData.nMolGlobal = getNGlobalMolecules();
930	+	parallelData.nMolLocal = getNMolecules();
931	+	parallelData.nAtomsGlobal = getNGlobalAtoms();
932	+	parallelData.nAtomsLocal = getNAtoms();
933	+	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
934	+	parallelData.nGroupsLocal = getNCutoffGroups();
935	+	parallelData.myNode = worldRank;
936	+	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
937
938	<	void SimInfo::getFortranGroupArrays(SimInfo* info,
939	<	vector<int>& FglobalGroupMembership,
940	<	vector<double>& mfact){
941	<
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	<
938	>	//pass mpiSimData struct and index arrays to fortran
939	>	//setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
940	>	//                &localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
941	>	//                &localToGlobalCutoffGroupIndex[0], &isError);
942
943	<	// Fix the silly fortran indexing problem
943	>	if (isError) {
944	>	sprintf(painCave.errMsg,
945	>	"mpiRefresh errror: fortran didn't like something we gave it.\n");
946	>	painCave.isFatal = 1;
947	>	simError();
948	>	}
949	>
950	>	sprintf(checkPointMsg, " mpiRefresh successful.\n");
951	>	errorCheckPoint();
952	>	#endif
953	>
954	>	initFortranFF(&isError);
955	>	if (isError) {
956	>	sprintf(painCave.errMsg,
957	>	"initFortranFF errror: fortran didn't like something we gave it.\n");
958	>	painCave.isFatal = 1;
959	>	simError();
960	>	}
961	>	fortranInitialized_ = true;
962	>	}
963	>
964	>	void SimInfo::addProperty(GenericData* genData) {
965	>	properties_.addProperty(genData);
966	>	}
967	>
968	>	void SimInfo::removeProperty(const string& propName) {
969	>	properties_.removeProperty(propName);
970	>	}
971	>
972	>	void SimInfo::clearProperties() {
973	>	properties_.clearProperties();
974	>	}
975	>
976	>	vector<string> SimInfo::getPropertyNames() {
977	>	return properties_.getPropertyNames();
978	>	}
979	>
980	>	vector<GenericData*> SimInfo::getProperties() {
981	>	return properties_.getProperties();
982	>	}
983	>
984	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
985	>	return properties_.getPropertyByName(propName);
986	>	}
987	>
988	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
989	>	if (sman_ == sman) {
990	>	return;
991	>	}
992	>	delete sman_;
993	>	sman_ = sman;
994	>
995	>	Molecule* mol;
996	>	RigidBody* rb;
997	>	Atom* atom;
998	>	CutoffGroup* cg;
999	>	SimInfo::MoleculeIterator mi;
1000	>	Molecule::RigidBodyIterator rbIter;
1001	>	Molecule::AtomIterator atomIter;
1002	>	Molecule::CutoffGroupIterator cgIter;
1003	>
1004	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1005	>
1006	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1007	>	atom->setSnapshotManager(sman_);
1008	>	}
1009	>
1010	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1011	>	rb->setSnapshotManager(sman_);
1012	>	}
1013	>
1014	>	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
1015	>	cg->setSnapshotManager(sman_);
1016	>	}
1017	>	}
1018	>
1019	>	}
1020	>
1021	>	Vector3d SimInfo::getComVel(){
1022	>	SimInfo::MoleculeIterator i;
1023	>	Molecule* mol;
1024	>
1025	>	Vector3d comVel(0.0);
1026	>	RealType totalMass = 0.0;
1027	>
1028	>
1029	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1030	>	RealType mass = mol->getMass();
1031	>	totalMass += mass;
1032	>	comVel += mass * mol->getComVel();
1033	>	}
1034	>
1035		#ifdef IS_MPI
1036	<	numAtom = mpiSim->getNAtomsGlobal();
1037	<	#else
1038	<	numAtom = n_atoms;
1036	>	RealType tmpMass = totalMass;
1037	>	Vector3d tmpComVel(comVel);
1038	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1039	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1040		#endif
617	–	for (int i = 0; i < numAtom; i++)
618	–	FglobalGroupMembership.push_back(globalGroupMembership[i] + 1);
619	–
1041
1042	<	myMols = info->molecules;
622	<	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)){
1042	>	comVel /= totalMass;
1043
1044	<	totalMass = myCutoffGroup->getMass();
1044	>	return comVel;
1045	>	}
1046	>
1047	>	Vector3d SimInfo::getCom(){
1048	>	SimInfo::MoleculeIterator i;
1049	>	Molecule* mol;
1050	>
1051	>	Vector3d com(0.0);
1052	>	RealType totalMass = 0.0;
1053	>
1054	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1055	>	RealType mass = mol->getMass();
1056	>	totalMass += mass;
1057	>	com += mass * mol->getCom();
1058	>	}
1059	>
1060	>	#ifdef IS_MPI
1061	>	RealType tmpMass = totalMass;
1062	>	Vector3d tmpCom(com);
1063	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1064	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1065	>	#endif
1066	>
1067	>	com /= totalMass;
1068	>
1069	>	return com;
1070	>
1071	>	}
1072	>
1073	>	ostream& operator <<(ostream& o, SimInfo& info) {
1074	>
1075	>	return o;
1076	>	}
1077	>
1078	>
1079	>	/*
1080	>	Returns center of mass and center of mass velocity in one function call.
1081	>	*/
1082	>
1083	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1084	>	SimInfo::MoleculeIterator i;
1085	>	Molecule* mol;
1086
1087	<	for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom);
1088	<	cutoffAtom != NULL;
1089	<	cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
1090	<	mfact.push_back(cutoffAtom->getMass()/totalMass);
1087	>
1088	>	RealType totalMass = 0.0;
1089	>
1090	>
1091	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1092	>	RealType mass = mol->getMass();
1093	>	totalMass += mass;
1094	>	com += mass * mol->getCom();
1095	>	comVel += mass * mol->getComVel();
1096		}
1097	+
1098	+	#ifdef IS_MPI
1099	+	RealType tmpMass = totalMass;
1100	+	Vector3d tmpCom(com);
1101	+	Vector3d tmpComVel(comVel);
1102	+	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1103	+	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1104	+	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1105	+	#endif
1106	+
1107	+	com /= totalMass;
1108	+	comVel /= totalMass;
1109	+	}
1110	+
1111	+	/*
1112	+	Return intertia tensor for entire system and angular momentum Vector.
1113	+
1114	+
1115	+	[  Ixx -Ixy  -Ixz ]
1116	+	J =| -Iyx  Iyy  -Iyz |
1117	+	[ -Izx -Iyz   Izz ]
1118	+	*/
1119	+
1120	+	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1121	+
1122	+
1123	+	RealType xx = 0.0;
1124	+	RealType yy = 0.0;
1125	+	RealType zz = 0.0;
1126	+	RealType xy = 0.0;
1127	+	RealType xz = 0.0;
1128	+	RealType yz = 0.0;
1129	+	Vector3d com(0.0);
1130	+	Vector3d comVel(0.0);
1131	+
1132	+	getComAll(com, comVel);
1133	+
1134	+	SimInfo::MoleculeIterator i;
1135	+	Molecule* mol;
1136	+
1137	+	Vector3d thisq(0.0);
1138	+	Vector3d thisv(0.0);
1139	+
1140	+	RealType thisMass = 0.0;
1141	+
1142	+
1143	+
1144	+
1145	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1146	+
1147	+	thisq = mol->getCom()-com;
1148	+	thisv = mol->getComVel()-comVel;
1149	+	thisMass = mol->getMass();
1150	+	// Compute moment of intertia coefficients.
1151	+	xx += thisq[0]*thisq[0]*thisMass;
1152	+	yy += thisq[1]*thisq[1]*thisMass;
1153	+	zz += thisq[2]*thisq[2]*thisMass;
1154	+
1155	+	// compute products of intertia
1156	+	xy += thisq[0]*thisq[1]*thisMass;
1157	+	xz += thisq[0]*thisq[2]*thisMass;
1158	+	yz += thisq[1]*thisq[2]*thisMass;
1159	+
1160	+	angularMomentum += cross( thisq, thisv ) * thisMass;
1161	+
1162	+	}
1163	+
1164	+
1165	+	inertiaTensor(0,0) = yy + zz;
1166	+	inertiaTensor(0,1) = -xy;
1167	+	inertiaTensor(0,2) = -xz;
1168	+	inertiaTensor(1,0) = -xy;
1169	+	inertiaTensor(1,1) = xx + zz;
1170	+	inertiaTensor(1,2) = -yz;
1171	+	inertiaTensor(2,0) = -xz;
1172	+	inertiaTensor(2,1) = -yz;
1173	+	inertiaTensor(2,2) = xx + yy;
1174	+
1175	+	#ifdef IS_MPI
1176	+	Mat3x3d tmpI(inertiaTensor);
1177	+	Vector3d tmpAngMom;
1178	+	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1179	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1180	+	#endif
1181	+
1182	+	return;
1183	+	}
1184	+
1185	+	//Returns the angular momentum of the system
1186	+	Vector3d SimInfo::getAngularMomentum(){
1187	+
1188	+	Vector3d com(0.0);
1189	+	Vector3d comVel(0.0);
1190	+	Vector3d angularMomentum(0.0);
1191	+
1192	+	getComAll(com,comVel);
1193	+
1194	+	SimInfo::MoleculeIterator i;
1195	+	Molecule* mol;
1196	+
1197	+	Vector3d thisr(0.0);
1198	+	Vector3d thisp(0.0);
1199	+
1200	+	RealType thisMass;
1201	+
1202	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1203	+	thisMass = mol->getMass();
1204	+	thisr = mol->getCom()-com;
1205	+	thisp = (mol->getComVel()-comVel)*thisMass;
1206	+
1207	+	angularMomentum += cross( thisr, thisp );
1208	+
1209	+	}
1210	+
1211	+	#ifdef IS_MPI
1212	+	Vector3d tmpAngMom;
1213	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1214	+	#endif
1215	+
1216	+	return angularMomentum;
1217	+	}
1218	+
1219	+	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1220	+	return IOIndexToIntegrableObject.at(index);
1221	+	}
1222	+
1223	+	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1224	+	IOIndexToIntegrableObject= v;
1225	+	}
1226	+
1227	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1228	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1229	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1230	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1231	+	*/
1232	+	void SimInfo::getGyrationalVolume(RealType &volume){
1233	+	Mat3x3d intTensor;
1234	+	RealType det;
1235	+	Vector3d dummyAngMom;
1236	+	RealType sysconstants;
1237	+	RealType geomCnst;
1238	+
1239	+	geomCnst = 3.0/2.0;
1240	+	/* Get the inertial tensor and angular momentum for free*/
1241	+	getInertiaTensor(intTensor,dummyAngMom);
1242	+
1243	+	det = intTensor.determinant();
1244	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1245	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1246	+	return;
1247	+	}
1248	+
1249	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1250	+	Mat3x3d intTensor;
1251	+	Vector3d dummyAngMom;
1252	+	RealType sysconstants;
1253	+	RealType geomCnst;
1254	+
1255	+	geomCnst = 3.0/2.0;
1256	+	/* Get the inertial tensor and angular momentum for free*/
1257	+	getInertiaTensor(intTensor,dummyAngMom);
1258	+
1259	+	detI = intTensor.determinant();
1260	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1261	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1262	+	return;
1263	+	}
1264	+	/*
1265	+	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1266	+	assert( v.size() == nAtoms_ + nRigidBodies_);
1267	+	sdByGlobalIndex_ = v;
1268		}
1269	+
1270	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1271	+	//assert(index < nAtoms_ + nRigidBodies_);
1272	+	return sdByGlobalIndex_.at(index);
1273	+	}
1274	+	*/
1275	+	int SimInfo::getNGlobalConstraints() {
1276	+	int nGlobalConstraints;
1277	+	#ifdef IS_MPI
1278	+	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1279	+	MPI_COMM_WORLD);
1280	+	#else
1281	+	nGlobalConstraints =  nConstraints_;
1282	+	#endif
1283	+	return nGlobalConstraints;
1284		}
1285
1286	<	}
1286	>	}//end namespace OpenMD
1287	>

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 1549 by gezelter, Wed Apr 27 18:38:15 2011 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines