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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 124 by chuckv, Wed Oct 20 20:46:20 2004 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1534 by gezelter, Wed Dec 29 21:53:28 2010 UTC

#	Line 1 | Line 1
1	<	#include <stdlib.h>
2	<	#include <string.h>
3	<	#include <math.h>
1	>	/*
2	>	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	>	*
4	>	* The University of Notre Dame grants you ("Licensee") a
5	>	* non-exclusive, royalty free, license to use, modify and
6	>	* redistribute this software in source and binary code form, provided
7	>	* that the following conditions are met:
8	>	*
9	>	* 1. Redistributions of source code must retain the above copyright
10	>	*    notice, this list of conditions and the following disclaimer.
11	>	*
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13	>	*    notice, this list of conditions and the following disclaimer in the
14	>	*    documentation and/or other materials provided with the
15	>	*    distribution.
16	>	*
17	>	* This software is provided "AS IS," without a warranty of any
18	>	* kind. All express or implied conditions, representations and
19	>	* warranties, including any implied warranty of merchantability,
20	>	* fitness for a particular purpose or non-infringement, are hereby
21	>	* excluded.  The University of Notre Dame and its licensors shall not
22	>	* be liable for any damages suffered by licensee as a result of
23	>	* using, modifying or distributing the software or its
24	>	* derivatives. In no event will the University of Notre Dame or its
25	>	* licensors be liable for any lost revenue, profit or data, or for
26	>	* direct, indirect, special, consequential, incidental or punitive
27	>	* damages, however caused and regardless of the theory of liability,
28	>	* arising out of the use of or inability to use software, even if the
29	>	* University of Notre Dame has been advised of the possibility of
30	>	* such damages.
31	>	*
32	>	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	>	* research, please cite the appropriate papers when you publish your
34	>	* work.  Good starting points are:
35	>	*
36	>	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	>	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	>	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	>	* [4]  Vardeman & Gezelter, in progress (2009).
40	>	*/
41	>
42	>	/**
43	>	* @file SimInfo.cpp
44	>	* @author    tlin
45	>	* @date  11/02/2004
46	>	* @version 1.0
47	>	*/
48
49	<	#include <iostream>
50	<	using namespace std;
49	>	#include <algorithm>
50	>	#include <set>
51	>	#include <map>
52
53		#include "brains/SimInfo.hpp"
54	<	#define __C
55	<	#include "brains/fSimulation.h"
54	>	#include "math/Vector3.hpp"
55	>	#include "primitives/Molecule.hpp"
56	>	#include "primitives/StuntDouble.hpp"
57	>	#include "UseTheForce/doForces_interface.h"
58	>	#include "UseTheForce/DarkSide/neighborLists_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	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
136	>
137	>	//every free atom (atom does not belong to rigid bodies) is an
138	>	//integrable object therefore the total number of integrable objects
139	>	//in the system is equal to the total number of atoms minus number of
140	>	//atoms belong to rigid body defined in meta-data file plus the number
141	>	//of rigid bodies defined in meta-data file
142	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
143	>	+ nGlobalRigidBodies_;
144	>
145	>	nGlobalMols_ = molStampIds_.size();
146	>	molToProcMap_.resize(nGlobalMols_);
147	>	}
148	>
149	>	SimInfo::~SimInfo() {
150	>	map<int, Molecule*>::iterator i;
151	>	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
152	>	delete i->second;
153	>	}
154	>	molecules_.clear();
155	>
156	>	delete sman_;
157	>	delete simParams_;
158	>	delete forceField_;
159	>	}
160
31	–	SimInfo* currentInfo;
161
162	<	SimInfo::SimInfo(){
163	<
164	<	n_constraints = 0;
165	<	nZconstraints = 0;
166	<	n_oriented = 0;
167	<	n_dipoles = 0;
168	<	ndf = 0;
169	<	ndfRaw = 0;
170	<	nZconstraints = 0;
171	<	the_integrator = NULL;
172	<	setTemp = 0;
173	<	thermalTime = 0.0;
174	<	currentTime = 0.0;
175	<	rCut = 0.0;
176	<	rSw = 0.0;
177	<
178	<	haveRcut = 0;
179	<	haveRsw = 0;
180	<	boxIsInit = 0;
162	>	bool SimInfo::addMolecule(Molecule* mol) {
163	>	MoleculeIterator i;
164	>
165	>	i = molecules_.find(mol->getGlobalIndex());
166	>	if (i == molecules_.end() ) {
167	>
168	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
169	>
170	>	nAtoms_ += mol->getNAtoms();
171	>	nBonds_ += mol->getNBonds();
172	>	nBends_ += mol->getNBends();
173	>	nTorsions_ += mol->getNTorsions();
174	>	nInversions_ += mol->getNInversions();
175	>	nRigidBodies_ += mol->getNRigidBodies();
176	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
177	>	nCutoffGroups_ += mol->getNCutoffGroups();
178	>	nConstraints_ += mol->getNConstraintPairs();
179	>
180	>	addInteractionPairs(mol);
181	>
182	>	return true;
183	>	} else {
184	>	return false;
185	>	}
186	>	}
187
188	<	resetTime = 1e99;
188	>	bool SimInfo::removeMolecule(Molecule* mol) {
189	>	MoleculeIterator i;
190	>	i = molecules_.find(mol->getGlobalIndex());
191
192	<	orthoRhombic = 0;
56	<	orthoTolerance = 1E-6;
57	<	useInitXSstate = true;
192	>	if (i != molecules_.end() ) {
193
194	<	usePBC = 0;
195	<	useLJ = 0;
196	<	useSticky = 0;
197	<	useCharges = 0;
198	<	useDipoles = 0;
199	<	useReactionField = 0;
200	<	useGB = 0;
201	<	useEAM = 0;
202	<	useSolidThermInt = 0;
203	<	useLiquidThermInt = 0;
194	>	assert(mol == i->second);
195	>
196	>	nAtoms_ -= mol->getNAtoms();
197	>	nBonds_ -= mol->getNBonds();
198	>	nBends_ -= mol->getNBends();
199	>	nTorsions_ -= mol->getNTorsions();
200	>	nInversions_ -= mol->getNInversions();
201	>	nRigidBodies_ -= mol->getNRigidBodies();
202	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
203	>	nCutoffGroups_ -= mol->getNCutoffGroups();
204	>	nConstraints_ -= mol->getNConstraintPairs();
205
206	<	haveCutoffGroups = false;
206	>	removeInteractionPairs(mol);
207	>	molecules_.erase(mol->getGlobalIndex());
208
209	<	excludes = Exclude::Instance();
210	<
211	<	myConfiguration = new SimState();
212	<
213	<	has_minimizer = false;
214	<	the_minimizer =NULL;
215	<
79	<	ngroup = 0;
80	<
81	<	}
209	>	delete mol;
210	>
211	>	return true;
212	>	} else {
213	>	return false;
214	>	}
215	>	}
216
217	+
218	+	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
219	+	i = molecules_.begin();
220	+	return i == molecules_.end() ? NULL : i->second;
221	+	}
222
223	<	SimInfo::~SimInfo(){
223	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
224	>	++i;
225	>	return i == molecules_.end() ? NULL : i->second;
226	>	}
227
86	–	delete myConfiguration;
228
229	<	map<string, GenericData*>::iterator i;
230	<
231	<	for(i = properties.begin(); i != properties.end(); i++)
232	<	delete (*i).second;
229	>	void SimInfo::calcNdf() {
230	>	int ndf_local;
231	>	MoleculeIterator i;
232	>	vector<StuntDouble*>::iterator j;
233	>	Molecule* mol;
234	>	StuntDouble* integrableObject;
235
236	<	}
236	>	ndf_local = 0;
237	>
238	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
239	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
240	>	integrableObject = mol->nextIntegrableObject(j)) {
241
242	<	void SimInfo::setBox(double newBox[3]) {
96	<
97	<	int i, j;
98	<	double tempMat[3][3];
242	>	ndf_local += 3;
243
244	<	for(i=0; i<3; i++)
245	<	for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
244	>	if (integrableObject->isDirectional()) {
245	>	if (integrableObject->isLinear()) {
246	>	ndf_local += 2;
247	>	} else {
248	>	ndf_local += 3;
249	>	}
250	>	}
251	>
252	>	}
253	>	}
254	>
255	>	// n_constraints is local, so subtract them on each processor
256	>	ndf_local -= nConstraints_;
257
258	<	tempMat[0][0] = newBox[0];
259	<	tempMat[1][1] = newBox[1];
260	<	tempMat[2][2] = newBox[2];
258	>	#ifdef IS_MPI
259	>	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
260	>	#else
261	>	ndf_ = ndf_local;
262	>	#endif
263
264	<	setBoxM( tempMat );
264	>	// nZconstraints_ is global, as are the 3 COM translations for the
265	>	// entire system:
266	>	ndf_ = ndf_ - 3 - nZconstraint_;
267
268	<	}
268	>	}
269
270	<	void SimInfo::setBoxM( double theBox[3][3] ){
271	<
272	<	int i, j;
273	<	double FortranHmat[9]; // to preserve compatibility with Fortran the
274	<	// ordering in the array is as follows:
275	<	// [ 0 3 6 ]
276	<	// [ 1 4 7 ]
118	<	// [ 2 5 8 ]
119	<	double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
120	<
121	<	if( !boxIsInit ) boxIsInit = 1;
122	<
123	<	for(i=0; i < 3; i++)
124	<	for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
125	<
126	<	calcBoxL();
127	<	calcHmatInv();
128	<
129	<	for(i=0; i < 3; i++) {
130	<	for (j=0; j < 3; j++) {
131	<	FortranHmat[3*j + i] = Hmat[i][j];
132	<	FortranHmatInv[3*j + i] = HmatInv[i][j];
133	<	}
270	>	int SimInfo::getFdf() {
271	>	#ifdef IS_MPI
272	>	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
273	>	#else
274	>	fdf_ = fdf_local;
275	>	#endif
276	>	return fdf_;
277		}
278	+
279	+	void SimInfo::calcNdfRaw() {
280	+	int ndfRaw_local;
281
282	<	setFortranBox(FortranHmat, FortranHmatInv, &orthoRhombic);
283	<
284	<	}
285	<
282	>	MoleculeIterator i;
283	>	vector<StuntDouble*>::iterator j;
284	>	Molecule* mol;
285	>	StuntDouble* integrableObject;
286
287	<	void SimInfo::getBoxM (double theBox[3][3]) {
287	>	// Raw degrees of freedom that we have to set
288	>	ndfRaw_local = 0;
289	>
290	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
291	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
292	>	integrableObject = mol->nextIntegrableObject(j)) {
293
294	<	int i, j;
144	<	for(i=0; i<3; i++)
145	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
146	<	}
294	>	ndfRaw_local += 3;
295
296	<
297	<	void SimInfo::scaleBox(double scale) {
298	<	double theBox[3][3];
299	<	int i, j;
300	<
301	<	// cerr << "Scaling box by " << scale << "\n";
302	<
303	<	for(i=0; i<3; i++)
156	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
157	<
158	<	setBoxM(theBox);
159	<
160	<	}
161	<
162	<	void SimInfo::calcHmatInv( void ) {
163	<
164	<	int oldOrtho;
165	<	int i,j;
166	<	double smallDiag;
167	<	double tol;
168	<	double sanity[3][3];
169	<
170	<	invertMat3( Hmat, HmatInv );
171	<
172	<	// check to see if Hmat is orthorhombic
173	<
174	<	oldOrtho = orthoRhombic;
175	<
176	<	smallDiag = fabs(Hmat[0][0]);
177	<	if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
178	<	if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
179	<	tol = smallDiag * orthoTolerance;
180	<
181	<	orthoRhombic = 1;
182	<
183	<	for (i = 0; i < 3; i++ ) {
184	<	for (j = 0 ; j < 3; j++) {
185	<	if (i != j) {
186	<	if (orthoRhombic) {
187	<	if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
188	<	}
296	>	if (integrableObject->isDirectional()) {
297	>	if (integrableObject->isLinear()) {
298	>	ndfRaw_local += 2;
299	>	} else {
300	>	ndfRaw_local += 3;
301	>	}
302	>	}
303	>
304		}
305		}
191	–	}
192	–
193	–	if( oldOrtho != orthoRhombic ){
306
307	<	if( orthoRhombic ) {
308	<	sprintf( painCave.errMsg,
309	<	"OOPSE is switching from the default Non-Orthorhombic\n"
310	<	"\tto the faster Orthorhombic periodic boundary computations.\n"
311	<	"\tThis is usually a good thing, but if you wan't the\n"
200	<	"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
201	<	"\tvariable ( currently set to %G ) smaller.\n",
202	<	orthoTolerance);
203	<	painCave.severity = OOPSE_INFO;
204	<	simError();
205	<	}
206	<	else {
207	<	sprintf( painCave.errMsg,
208	<	"OOPSE is switching from the faster Orthorhombic to the more\n"
209	<	"\tflexible Non-Orthorhombic periodic boundary computations.\n"
210	<	"\tThis is usually because the box has deformed under\n"
211	<	"\tNPTf integration. If you wan't to live on the edge with\n"
212	<	"\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
213	<	"\tvariable ( currently set to %G ) larger.\n",
214	<	orthoTolerance);
215	<	painCave.severity = OOPSE_WARNING;
216	<	simError();
217	<	}
307	>	#ifdef IS_MPI
308	>	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
309	>	#else
310	>	ndfRaw_ = ndfRaw_local;
311	>	#endif
312		}
219	–	}
313
314	<	void SimInfo::calcBoxL( void ){
314	>	void SimInfo::calcNdfTrans() {
315	>	int ndfTrans_local;
316
317	<	double dx, dy, dz, dsq;
317	>	ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
318
225	–	// boxVol = Determinant of Hmat
319
320	<	boxVol = matDet3( Hmat );
320	>	#ifdef IS_MPI
321	>	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
322	>	#else
323	>	ndfTrans_ = ndfTrans_local;
324	>	#endif
325
326	<	// boxLx
327	<
328	<	dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
232	<	dsq = dx*dx + dy*dy + dz*dz;
233	<	boxL[0] = sqrt( dsq );
234	<	//maxCutoff = 0.5 * boxL[0];
326	>	ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
327	>
328	>	}
329
330	<	// boxLy
331	<
332	<	dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
333	<	dsq = dx*dx + dy*dy + dz*dz;
334	<	boxL[1] = sqrt( dsq );
335	<	//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
330	>	void SimInfo::addInteractionPairs(Molecule* mol) {
331	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
332	>	vector<Bond*>::iterator bondIter;
333	>	vector<Bend*>::iterator bendIter;
334	>	vector<Torsion*>::iterator torsionIter;
335	>	vector<Inversion*>::iterator inversionIter;
336	>	Bond* bond;
337	>	Bend* bend;
338	>	Torsion* torsion;
339	>	Inversion* inversion;
340	>	int a;
341	>	int b;
342	>	int c;
343	>	int d;
344
345	+	// atomGroups can be used to add special interaction maps between
346	+	// groups of atoms that are in two separate rigid bodies.
347	+	// However, most site-site interactions between two rigid bodies
348	+	// are probably not special, just the ones between the physically
349	+	// bonded atoms.  Interactions *within* a single rigid body should
350	+	// always be excluded.  These are done at the bottom of this
351	+	// function.
352
353	<	// boxLz
354	<
355	<	dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
356	<	dsq = dx*dx + dy*dy + dz*dz;
357	<	boxL[2] = sqrt( dsq );
358	<	//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
353	>	map<int, set<int> > atomGroups;
354	>	Molecule::RigidBodyIterator rbIter;
355	>	RigidBody* rb;
356	>	Molecule::IntegrableObjectIterator ii;
357	>	StuntDouble* integrableObject;
358	>
359	>	for (integrableObject = mol->beginIntegrableObject(ii);
360	>	integrableObject != NULL;
361	>	integrableObject = mol->nextIntegrableObject(ii)) {
362	>
363	>	if (integrableObject->isRigidBody()) {
364	>	rb = static_cast<RigidBody*>(integrableObject);
365	>	vector<Atom*> atoms = rb->getAtoms();
366	>	set<int> rigidAtoms;
367	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
368	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
369	>	}
370	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
371	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
372	>	}
373	>	} else {
374	>	set<int> oneAtomSet;
375	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
376	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
377	>	}
378	>	}
379	>
380	>	for (bond= mol->beginBond(bondIter); bond != NULL;
381	>	bond = mol->nextBond(bondIter)) {
382
383	<	//calculate the max cutoff
384	<	maxCutoff =  calcMaxCutOff();
385	<
386	<	checkCutOffs();
383	>	a = bond->getAtomA()->getGlobalIndex();
384	>	b = bond->getAtomB()->getGlobalIndex();
385	>
386	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
387	>	oneTwoInteractions_.addPair(a, b);
388	>	} else {
389	>	excludedInteractions_.addPair(a, b);
390	>	}
391	>	}
392
393	<	}
393	>	for (bend= mol->beginBend(bendIter); bend != NULL;
394	>	bend = mol->nextBend(bendIter)) {
395
396	+	a = bend->getAtomA()->getGlobalIndex();
397	+	b = bend->getAtomB()->getGlobalIndex();
398	+	c = bend->getAtomC()->getGlobalIndex();
399	+
400	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
401	+	oneTwoInteractions_.addPair(a, b);
402	+	oneTwoInteractions_.addPair(b, c);
403	+	} else {
404	+	excludedInteractions_.addPair(a, b);
405	+	excludedInteractions_.addPair(b, c);
406	+	}
407
408	<	double SimInfo::calcMaxCutOff(){
408	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
409	>	oneThreeInteractions_.addPair(a, c);
410	>	} else {
411	>	excludedInteractions_.addPair(a, c);
412	>	}
413	>	}
414
415	<	double ri[3], rj[3], rk[3];
416	<	double rij[3], rjk[3], rki[3];
263	<	double minDist;
415	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
416	>	torsion = mol->nextTorsion(torsionIter)) {
417
418	<	ri[0] = Hmat[0][0];
419	<	ri[1] = Hmat[1][0];
420	<	ri[2] = Hmat[2][0];
418	>	a = torsion->getAtomA()->getGlobalIndex();
419	>	b = torsion->getAtomB()->getGlobalIndex();
420	>	c = torsion->getAtomC()->getGlobalIndex();
421	>	d = torsion->getAtomD()->getGlobalIndex();
422
423	<	rj[0] = Hmat[0][1];
424	<	rj[1] = Hmat[1][1];
425	<	rj[2] = Hmat[2][1];
423	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
424	>	oneTwoInteractions_.addPair(a, b);
425	>	oneTwoInteractions_.addPair(b, c);
426	>	oneTwoInteractions_.addPair(c, d);
427	>	} else {
428	>	excludedInteractions_.addPair(a, b);
429	>	excludedInteractions_.addPair(b, c);
430	>	excludedInteractions_.addPair(c, d);
431	>	}
432
433	<	rk[0] = Hmat[0][2];
434	<	rk[1] = Hmat[1][2];
435	<	rk[2] = Hmat[2][2];
436	<
437	<	crossProduct3(ri, rj, rij);
438	<	distXY = dotProduct3(rk,rij) / norm3(rij);
433	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
434	>	oneThreeInteractions_.addPair(a, c);
435	>	oneThreeInteractions_.addPair(b, d);
436	>	} else {
437	>	excludedInteractions_.addPair(a, c);
438	>	excludedInteractions_.addPair(b, d);
439	>	}
440
441	<	crossProduct3(rj,rk, rjk);
442	<	distYZ = dotProduct3(ri,rjk) / norm3(rjk);
441	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
442	>	oneFourInteractions_.addPair(a, d);
443	>	} else {
444	>	excludedInteractions_.addPair(a, d);
445	>	}
446	>	}
447
448	<	crossProduct3(rk,ri, rki);
449	<	distZX = dotProduct3(rj,rki) / norm3(rki);
448	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
449	>	inversion = mol->nextInversion(inversionIter)) {
450
451	<	minDist = min(min(distXY, distYZ), distZX);
452	<	return minDist/2;
453	<
454	<	}
451	>	a = inversion->getAtomA()->getGlobalIndex();
452	>	b = inversion->getAtomB()->getGlobalIndex();
453	>	c = inversion->getAtomC()->getGlobalIndex();
454	>	d = inversion->getAtomD()->getGlobalIndex();
455
456	<	void SimInfo::wrapVector( double thePos[3] ){
456	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
457	>	oneTwoInteractions_.addPair(a, b);
458	>	oneTwoInteractions_.addPair(a, c);
459	>	oneTwoInteractions_.addPair(a, d);
460	>	} else {
461	>	excludedInteractions_.addPair(a, b);
462	>	excludedInteractions_.addPair(a, c);
463	>	excludedInteractions_.addPair(a, d);
464	>	}
465
466	<	int i;
467	<	double scaled[3];
466	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
467	>	oneThreeInteractions_.addPair(b, c);
468	>	oneThreeInteractions_.addPair(b, d);
469	>	oneThreeInteractions_.addPair(c, d);
470	>	} else {
471	>	excludedInteractions_.addPair(b, c);
472	>	excludedInteractions_.addPair(b, d);
473	>	excludedInteractions_.addPair(c, d);
474	>	}
475	>	}
476
477	<	if( !orthoRhombic ){
478	<	// calc the scaled coordinates.
479	<
477	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
478	>	rb = mol->nextRigidBody(rbIter)) {
479	>	vector<Atom*> atoms = rb->getAtoms();
480	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
481	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
482	>	a = atoms[i]->getGlobalIndex();
483	>	b = atoms[j]->getGlobalIndex();
484	>	excludedInteractions_.addPair(a, b);
485	>	}
486	>	}
487	>	}
488
489	<	matVecMul3(HmatInv, thePos, scaled);
489	>	}
490	>
491	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
492	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
493	>	vector<Bond*>::iterator bondIter;
494	>	vector<Bend*>::iterator bendIter;
495	>	vector<Torsion*>::iterator torsionIter;
496	>	vector<Inversion*>::iterator inversionIter;
497	>	Bond* bond;
498	>	Bend* bend;
499	>	Torsion* torsion;
500	>	Inversion* inversion;
501	>	int a;
502	>	int b;
503	>	int c;
504	>	int d;
505	>
506	>	map<int, set<int> > atomGroups;
507	>	Molecule::RigidBodyIterator rbIter;
508	>	RigidBody* rb;
509	>	Molecule::IntegrableObjectIterator ii;
510	>	StuntDouble* integrableObject;
511
512	<	for(i=0; i<3; i++)
513	<	scaled[i] -= roundMe(scaled[i]);
514	<
515	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
516	<
517	<	matVecMul3(Hmat, scaled, thePos);
512	>	for (integrableObject = mol->beginIntegrableObject(ii);
513	>	integrableObject != NULL;
514	>	integrableObject = mol->nextIntegrableObject(ii)) {
515	>
516	>	if (integrableObject->isRigidBody()) {
517	>	rb = static_cast<RigidBody*>(integrableObject);
518	>	vector<Atom*> atoms = rb->getAtoms();
519	>	set<int> rigidAtoms;
520	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
521	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
522	>	}
523	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
524	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
525	>	}
526	>	} else {
527	>	set<int> oneAtomSet;
528	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
529	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
530	>	}
531	>	}
532
533	<	}
534	<	else{
535	<	// calc the scaled coordinates.
533	>	for (bond= mol->beginBond(bondIter); bond != NULL;
534	>	bond = mol->nextBond(bondIter)) {
535	>
536	>	a = bond->getAtomA()->getGlobalIndex();
537	>	b = bond->getAtomB()->getGlobalIndex();
538
539	<	for(i=0; i<3; i++)
540	<	scaled[i] = thePos[i]*HmatInv[i][i];
541	<
542	<	// wrap the scaled coordinates
543	<
544	<	for(i=0; i<3; i++)
319	<	scaled[i] -= roundMe(scaled[i]);
320	<
321	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
322	<
323	<	for(i=0; i<3; i++)
324	<	thePos[i] = scaled[i]*Hmat[i][i];
325	<	}
326	<
327	<	}
539	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
540	>	oneTwoInteractions_.removePair(a, b);
541	>	} else {
542	>	excludedInteractions_.removePair(a, b);
543	>	}
544	>	}
545
546	+	for (bend= mol->beginBend(bendIter); bend != NULL;
547	+	bend = mol->nextBend(bendIter)) {
548
549	<	int SimInfo::getNDF(){
550	<	int ndf_local;
549	>	a = bend->getAtomA()->getGlobalIndex();
550	>	b = bend->getAtomB()->getGlobalIndex();
551	>	c = bend->getAtomC()->getGlobalIndex();
552	>
553	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
554	>	oneTwoInteractions_.removePair(a, b);
555	>	oneTwoInteractions_.removePair(b, c);
556	>	} else {
557	>	excludedInteractions_.removePair(a, b);
558	>	excludedInteractions_.removePair(b, c);
559	>	}
560
561	<	ndf_local = 0;
561	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
562	>	oneThreeInteractions_.removePair(a, c);
563	>	} else {
564	>	excludedInteractions_.removePair(a, c);
565	>	}
566	>	}
567	>
568	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
569	>	torsion = mol->nextTorsion(torsionIter)) {
570	>
571	>	a = torsion->getAtomA()->getGlobalIndex();
572	>	b = torsion->getAtomB()->getGlobalIndex();
573	>	c = torsion->getAtomC()->getGlobalIndex();
574	>	d = torsion->getAtomD()->getGlobalIndex();
575
576	<	for(int i = 0; i < integrableObjects.size(); i++){
577	<	ndf_local += 3;
578	<	if (integrableObjects[i]->isDirectional()) {
579	<	if (integrableObjects[i]->isLinear())
580	<	ndf_local += 2;
581	<	else
582	<	ndf_local += 3;
576	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
577	>	oneTwoInteractions_.removePair(a, b);
578	>	oneTwoInteractions_.removePair(b, c);
579	>	oneTwoInteractions_.removePair(c, d);
580	>	} else {
581	>	excludedInteractions_.removePair(a, b);
582	>	excludedInteractions_.removePair(b, c);
583	>	excludedInteractions_.removePair(c, d);
584	>	}
585	>
586	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
587	>	oneThreeInteractions_.removePair(a, c);
588	>	oneThreeInteractions_.removePair(b, d);
589	>	} else {
590	>	excludedInteractions_.removePair(a, c);
591	>	excludedInteractions_.removePair(b, d);
592	>	}
593	>
594	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
595	>	oneFourInteractions_.removePair(a, d);
596	>	} else {
597	>	excludedInteractions_.removePair(a, d);
598	>	}
599		}
343	–	}
600
601	<	// n_constraints is local, so subtract them on each processor:
601	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
602	>	inversion = mol->nextInversion(inversionIter)) {
603
604	<	ndf_local -= n_constraints;
604	>	a = inversion->getAtomA()->getGlobalIndex();
605	>	b = inversion->getAtomB()->getGlobalIndex();
606	>	c = inversion->getAtomC()->getGlobalIndex();
607	>	d = inversion->getAtomD()->getGlobalIndex();
608
609	<	#ifdef IS_MPI
610	<	MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
611	<	#else
612	<	ndf = ndf_local;
613	<	#endif
609	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
610	>	oneTwoInteractions_.removePair(a, b);
611	>	oneTwoInteractions_.removePair(a, c);
612	>	oneTwoInteractions_.removePair(a, d);
613	>	} else {
614	>	excludedInteractions_.removePair(a, b);
615	>	excludedInteractions_.removePair(a, c);
616	>	excludedInteractions_.removePair(a, d);
617	>	}
618
619	<	// nZconstraints is global, as are the 3 COM translations for the
620	<	// entire system:
619	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
620	>	oneThreeInteractions_.removePair(b, c);
621	>	oneThreeInteractions_.removePair(b, d);
622	>	oneThreeInteractions_.removePair(c, d);
623	>	} else {
624	>	excludedInteractions_.removePair(b, c);
625	>	excludedInteractions_.removePair(b, d);
626	>	excludedInteractions_.removePair(c, d);
627	>	}
628	>	}
629
630	<	ndf = ndf - 3 - nZconstraints;
630	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
631	>	rb = mol->nextRigidBody(rbIter)) {
632	>	vector<Atom*> atoms = rb->getAtoms();
633	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
634	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
635	>	a = atoms[i]->getGlobalIndex();
636	>	b = atoms[j]->getGlobalIndex();
637	>	excludedInteractions_.removePair(a, b);
638	>	}
639	>	}
640	>	}
641	>
642	>	}
643	>
644	>
645	>	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
646	>	int curStampId;
647	>
648	>	//index from 0
649	>	curStampId = moleculeStamps_.size();
650
651	<	return ndf;
652	<	}
651	>	moleculeStamps_.push_back(molStamp);
652	>	molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
653	>	}
654
363	–	int SimInfo::getNDFraw() {
364	–	int ndfRaw_local;
655
656	<	// Raw degrees of freedom that we have to set
657	<	ndfRaw_local = 0;
656	>	/**
657	>	* update
658	>	*
659	>	*  Performs the global checks and variable settings after the objects have been
660	>	*  created.
661	>	*
662	>	*/
663	>	void SimInfo::update() {
664	>
665	>	setupSimVariables();
666	>	setupCutoffs();
667	>	setupSwitching();
668	>	setupElectrostatics();
669	>	setupNeighborlists();
670
671	<	for(int i = 0; i < integrableObjects.size(); i++){
672	<	ndfRaw_local += 3;
673	<	if (integrableObjects[i]->isDirectional()) {
674	<	if (integrableObjects[i]->isLinear())
675	<	ndfRaw_local += 2;
676	<	else
677	<	ndfRaw_local += 3;
671	>	#ifdef IS_MPI
672	>	setupFortranParallel();
673	>	#endif
674	>	setupFortranSim();
675	>	fortranInitialized_ = true;
676	>
677	>	calcNdf();
678	>	calcNdfRaw();
679	>	calcNdfTrans();
680	>	}
681	>
682	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
683	>	SimInfo::MoleculeIterator mi;
684	>	Molecule* mol;
685	>	Molecule::AtomIterator ai;
686	>	Atom* atom;
687	>	set<AtomType*> atomTypes;
688	>
689	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
690	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
691	>	atomTypes.insert(atom->getAtomType());
692	>	}
693	>	}
694	>	return atomTypes;
695	>	}
696	>
697	>	/**
698	>	* setupCutoffs
699	>	*
700	>	* Sets the values of cutoffRadius and cutoffMethod
701	>	*
702	>	* cutoffRadius : realType
703	>	*  If the cutoffRadius was explicitly set, use that value.
704	>	*  If the cutoffRadius was not explicitly set:
705	>	*      Are there electrostatic atoms?  Use 12.0 Angstroms.
706	>	*      No electrostatic atoms?  Poll the atom types present in the
707	>	*      simulation for suggested cutoff values (e.g. 2.5 * sigma).
708	>	*      Use the maximum suggested value that was found.
709	>	*
710	>	* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL)
711	>	*      If cutoffMethod was explicitly set, use that choice.
712	>	*      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
713	>	*/
714	>	void SimInfo::setupCutoffs() {
715	>
716	>	if (simParams_->haveCutoffRadius()) {
717	>	cutoffRadius_ = simParams_->getCutoffRadius();
718	>	} else {
719	>	if (usesElectrostaticAtoms_) {
720	>	sprintf(painCave.errMsg,
721	>	"SimInfo: No value was set for the cutoffRadius.\n"
722	>	"\tOpenMD will use a default value of 12.0 angstroms"
723	>	"\tfor the cutoffRadius.\n");
724	>	painCave.isFatal = 0;
725	>	painCave.severity = OPENMD_INFO;
726	>	simError();
727	>	cutoffRadius_ = 12.0;
728	>	} else {
729	>	RealType thisCut;
730	>	set<AtomType*>::iterator i;
731	>	set<AtomType*> atomTypes;
732	>	atomTypes = getSimulatedAtomTypes();
733	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
734	>	thisCut = InteractionManager::Instance()->getSuggestedCutoffRadius((*i));
735	>	cutoffRadius_ = max(thisCut, cutoffRadius_);
736	>	}
737	>	sprintf(painCave.errMsg,
738	>	"SimInfo: No value was set for the cutoffRadius.\n"
739	>	"\tOpenMD will use %lf angstroms.\n",
740	>	cutoffRadius_);
741	>	painCave.isFatal = 0;
742	>	painCave.severity = OPENMD_INFO;
743	>	simError();
744	>	}
745		}
746	+
747	+	map<string, CutoffMethod> stringToCutoffMethod;
748	+	stringToCutoffMethod["HARD"] = HARD;
749	+	stringToCutoffMethod["SWITCHING_FUNCTION"] = SWITCHING_FUNCTION;
750	+	stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;
751	+	stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
752	+
753	+	if (simParams_->haveCutoffMethod()) {
754	+	string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
755	+	map<string, CutoffMethod>::iterator i;
756	+	i = stringToCutoffMethod.find(cutMeth);
757	+	if (i == stringToCutoffMethod.end()) {
758	+	sprintf(painCave.errMsg,
759	+	"SimInfo: Could not find chosen cutoffMethod %s\n"
760	+	"\tShould be one of: "
761	+	"HARD, SWITCHING_FUNCTION, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
762	+	cutMeth.c_str());
763	+	painCave.isFatal = 1;
764	+	painCave.severity = OPENMD_ERROR;
765	+	simError();
766	+	} else {
767	+	cutoffMethod_ = i->second;
768	+	}
769	+	} else {
770	+	sprintf(painCave.errMsg,
771	+	"SimInfo: No value was set for the cutoffMethod.\n"
772	+	"\tOpenMD will use SHIFTED_FORCE.\n");
773	+	painCave.isFatal = 0;
774	+	painCave.severity = OPENMD_INFO;
775	+	simError();
776	+	cutoffMethod_ = SHIFTED_FORCE;
777	+	}
778		}
779	+
780	+	/**
781	+	* setupSwitching
782	+	*
783	+	* Sets the values of switchingRadius and
784	+	*  If the switchingRadius was explicitly set, use that value (but check it)
785	+	*  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
786	+	*/
787	+	void SimInfo::setupSwitching() {
788
789	<	#ifdef IS_MPI
790	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
791	<	#else
792	<	ndfRaw = ndfRaw_local;
793	<	#endif
789	>	if (simParams_->haveSwitchingRadius()) {
790	>	switchingRadius_ = simParams_->getSwitchingRadius();
791	>	if (switchingRadius_ > cutoffRadius_) {
792	>	sprintf(painCave.errMsg,
793	>	"SimInfo: switchingRadius (%f) is larger than cutoffRadius(%f)\n",
794	>	switchingRadius_, cutoffRadius_);
795	>	painCave.isFatal = 1;
796	>	painCave.severity = OPENMD_ERROR;
797	>	simError();
798	>	}
799	>	} else {
800	>	switchingRadius_ = 0.85 * cutoffRadius_;
801	>	sprintf(painCave.errMsg,
802	>	"SimInfo: No value was set for the switchingRadius.\n"
803	>	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
804	>	"\tswitchingRadius = %f. for this simulation\n", switchingRadius_);
805	>	painCave.isFatal = 0;
806	>	painCave.severity = OPENMD_WARNING;
807	>	simError();
808	>	}
809	>
810	>	if (simParams_->haveSwitchingFunctionType()) {
811	>	string funcType = simParams_->getSwitchingFunctionType();
812	>	toUpper(funcType);
813	>	if (funcType == "CUBIC") {
814	>	sft_ = cubic;
815	>	} else {
816	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
817	>	sft_ = fifth_order_poly;
818	>	} else {
819	>	// throw error
820	>	sprintf( painCave.errMsg,
821	>	"SimInfo : Unknown switchingFunctionType. (Input file specified %s .)\n"
822	>	"\tswitchingFunctionType must be one of: "
823	>	"\"cubic\" or \"fifth_order_polynomial\".",
824	>	funcType.c_str() );
825	>	painCave.isFatal = 1;
826	>	painCave.severity = OPENMD_ERROR;
827	>	simError();
828	>	}
829	>	}
830	>	}
831	>	}
832
833	<	return ndfRaw;
834	<	}
833	>	/**
834	>	* setupNeighborlists
835	>	*
836	>	*  If the skinThickness was explicitly set, use that value (but check it)
837	>	*  If the skinThickness was not explicitly set: use 1.0 angstroms
838	>	*/
839	>	void SimInfo::setupNeighborlists() {
840	>	if (simParams_->haveSkinThickness()) {
841	>	skinThickness_ = simParams_->getSkinThickness();
842	>	} else {
843	>	skinThickness_ = 1.0;
844	>	sprintf(painCave.errMsg,
845	>	"SimInfo: No value was set for the skinThickness.\n"
846	>	"\tOpenMD will use a default value of %f Angstroms\n"
847	>	"\tfor this simulation\n", skinThickness_);
848	>	painCave.severity = OPENMD_INFO;
849	>	painCave.isFatal = 0;
850	>	simError();
851	>	}
852	>	}
853
854	<	int SimInfo::getNDFtranslational() {
855	<	int ndfTrans_local;
854	>	void SimInfo::setupSimVariables() {
855	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
856	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
857	>	calcBoxDipole_ = false;
858	>	if ( simParams_->haveAccumulateBoxDipole() )
859	>	if ( simParams_->getAccumulateBoxDipole() ) {
860	>	calcBoxDipole_ = true;
861	>	}
862
863	<	ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
863	>	set<AtomType*>::iterator i;
864	>	set<AtomType*> atomTypes;
865	>	atomTypes = getSimulatedAtomTypes();
866	>	int usesElectrostatic = 0;
867	>	int usesMetallic = 0;
868	>	int usesDirectional = 0;
869	>	//loop over all of the atom types
870	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
871	>	usesElectrostatic |= (*i)->isElectrostatic();
872	>	usesMetallic |= (*i)->isMetal();
873	>	usesDirectional |= (*i)->isDirectional();
874	>	}
875
876	+	#ifdef IS_MPI
877	+	int temp;
878	+	temp = usesDirectional;
879	+	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
880
881	<	#ifdef IS_MPI
882	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
396	<	#else
397	<	ndfTrans = ndfTrans_local;
398	<	#endif
881	>	temp = usesMetallic;
882	>	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
883
884	<	ndfTrans = ndfTrans - 3 - nZconstraints;
885	<
402	<	return ndfTrans;
403	<	}
404	<
405	<	int SimInfo::getTotIntegrableObjects() {
406	<	int nObjs_local;
407	<	int nObjs;
408	<
409	<	nObjs_local =  integrableObjects.size();
410	<
411	<
412	<	#ifdef IS_MPI
413	<	MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
414	<	#else
415	<	nObjs = nObjs_local;
884	>	temp = usesElectrostatic;
885	>	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
886		#endif
887	+	fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;
888	+	fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
889	+	fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
890	+	fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
891	+	fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
892	+	fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
893	+	}
894
895	+	void SimInfo::setupFortranSim() {
896	+	int isError;
897	+	int nExclude, nOneTwo, nOneThree, nOneFour;
898	+	vector<int> fortranGlobalGroupMembership;
899	+
900	+	notifyFortranSkinThickness(&skinThickness_);
901
902	<	return nObjs;
903	<	}
902	>	int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0;
903	>	int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0;
904	>	notifyFortranCutoffs(&cutoffRadius_, &switchingRadius_, &ljsp, &ljsf);
905
906	<	void SimInfo::refreshSim(){
906	>	isError = 0;
907
908	<	simtype fInfo;
909	<	int isError;
910	<	int n_global;
911	<	int* excl;
908	>	//globalGroupMembership_ is filled by SimCreator
909	>	for (int i = 0; i < nGlobalAtoms_; i++) {
910	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
911	>	}
912
913	<	fInfo.dielect = 0.0;
913	>	//calculate mass ratio of cutoff group
914	>	vector<RealType> mfact;
915	>	SimInfo::MoleculeIterator mi;
916	>	Molecule* mol;
917	>	Molecule::CutoffGroupIterator ci;
918	>	CutoffGroup* cg;
919	>	Molecule::AtomIterator ai;
920	>	Atom* atom;
921	>	RealType totalMass;
922
923	<	if( useDipoles ){
924	<	if( useReactionField )fInfo.dielect = dielectric;
925	<	}
923	>	//to avoid memory reallocation, reserve enough space for mfact
924	>	mfact.reserve(getNCutoffGroups());
925	>
926	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
927	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
928
929	<	fInfo.SIM_uses_PBC = usePBC;
930	<	//fInfo.SIM_uses_LJ = 0;
931	<	fInfo.SIM_uses_LJ = useLJ;
932	<	fInfo.SIM_uses_sticky = useSticky;
933	<	//fInfo.SIM_uses_sticky = 0;
934	<	fInfo.SIM_uses_charges = useCharges;
935	<	fInfo.SIM_uses_dipoles = useDipoles;
936	<	//fInfo.SIM_uses_dipoles = 0;
937	<	fInfo.SIM_uses_RF = useReactionField;
938	<	//fInfo.SIM_uses_RF = 0;
445	<	fInfo.SIM_uses_GB = useGB;
446	<	fInfo.SIM_uses_EAM = useEAM;
929	>	totalMass = cg->getMass();
930	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
931	>	// Check for massless groups - set mfact to 1 if true
932	>	if (totalMass != 0)
933	>	mfact.push_back(atom->getMass()/totalMass);
934	>	else
935	>	mfact.push_back( 1.0 );
936	>	}
937	>	}
938	>	}
939
940	<	n_exclude = excludes->getSize();
941	<	excl = excludes->getFortranArray();
450	<
451	<	#ifdef IS_MPI
452	<	n_global = mpiSim->getNAtomsGlobal();
453	<	#else
454	<	n_global = n_atoms;
455	<	#endif
456	<
457	<	isError = 0;
458	<
459	<	getFortranGroupArrays(this, FglobalGroupMembership, mfact);
460	<	//it may not be a good idea to pass the address of first element in vector
461	<	//since c++ standard does not require vector to be stored continuously in meomory
462	<	//Most of the compilers will organize the memory of vector continuously
463	<	setFortranSim( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
464	<	&nGlobalExcludes, globalExcludes, molMembershipArray,
465	<	&mfact[0], &ngroup, &FglobalGroupMembership[0], &isError);
940	>	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
941	>	vector<int> identArray;
942
943	<	if( isError ){
943	>	//to avoid memory reallocation, reserve enough space identArray
944	>	identArray.reserve(getNAtoms());
945
946	<	sprintf( painCave.errMsg,
947	<	"There was an error setting the simulation information in fortran.\n" );
948	<	painCave.isFatal = 1;
949	<	painCave.severity = OOPSE_ERROR;
950	<	simError();
474	<	}
475	<
476	<	#ifdef IS_MPI
477	<	sprintf( checkPointMsg,
478	<	"succesfully sent the simulation information to fortran.\n");
479	<	MPIcheckPoint();
480	<	#endif // is_mpi
481	<
482	<	this->ndf = this->getNDF();
483	<	this->ndfRaw = this->getNDFraw();
484	<	this->ndfTrans = this->getNDFtranslational();
485	<	}
946	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
947	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
948	>	identArray.push_back(atom->getIdent());
949	>	}
950	>	}
951
952	<	void SimInfo::setDefaultRcut( double theRcut ){
953	<
954	<	haveRcut = 1;
955	<	rCut = theRcut;
956	<	rList = rCut + 1.0;
957	<
958	<	notifyFortranCutoffs( &rCut, &rSw, &rList );
959	<	}
952	>	//fill molMembershipArray
953	>	//molMembershipArray is filled by SimCreator
954	>	vector<int> molMembershipArray(nGlobalAtoms_);
955	>	for (int i = 0; i < nGlobalAtoms_; i++) {
956	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
957	>	}
958	>
959	>	//setup fortran simulation
960
961	<	void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
961	>	nExclude = excludedInteractions_.getSize();
962	>	nOneTwo = oneTwoInteractions_.getSize();
963	>	nOneThree = oneThreeInteractions_.getSize();
964	>	nOneFour = oneFourInteractions_.getSize();
965
966	<	rSw = theRsw;
967	<	setDefaultRcut( theRcut );
968	<	}
966	>	int* excludeList = excludedInteractions_.getPairList();
967	>	int* oneTwoList = oneTwoInteractions_.getPairList();
968	>	int* oneThreeList = oneThreeInteractions_.getPairList();
969	>	int* oneFourList = oneFourInteractions_.getPairList();
970
971	<
972	<	void SimInfo::checkCutOffs( void ){
973	<
974	<	if( boxIsInit ){
971	>	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
972	>	&nExclude, excludeList,
973	>	&nOneTwo, oneTwoList,
974	>	&nOneThree, oneThreeList,
975	>	&nOneFour, oneFourList,
976	>	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
977	>	&fortranGlobalGroupMembership[0], &isError);
978
979	<	//we need to check cutOffs against the box
980	<
509	<	if( rCut > maxCutoff ){
979	>	if( isError ){
980	>
981		sprintf( painCave.errMsg,
982	<	"cutoffRadius is too large for the current periodic box.\n"
512	<	"\tCurrent Value of cutoffRadius = %G at time %G\n "
513	<	"\tThis is larger than half of at least one of the\n"
514	<	"\tperiodic box vectors.  Right now, the Box matrix is:\n"
515	<	"\n"
516	<	"\t[ %G %G %G ]\n"
517	<	"\t[ %G %G %G ]\n"
518	<	"\t[ %G %G %G ]\n",
519	<	rCut, currentTime,
520	<	Hmat[0][0], Hmat[0][1], Hmat[0][2],
521	<	Hmat[1][0], Hmat[1][1], Hmat[1][2],
522	<	Hmat[2][0], Hmat[2][1], Hmat[2][2]);
523	<	painCave.severity = OOPSE_ERROR;
982	>	"There was an error setting the simulation information in fortran.\n" );
983		painCave.isFatal = 1;
984	+	painCave.severity = OPENMD_ERROR;
985		simError();
986	<	}
527	<	} else {
528	<	// initialize this stuff before using it, OK?
529	<	sprintf( painCave.errMsg,
530	<	"Trying to check cutoffs without a box.\n"
531	<	"\tOOPSE should have better programmers than that.\n" );
532	<	painCave.severity = OOPSE_ERROR;
533	<	painCave.isFatal = 1;
534	<	simError();
535	<	}
536	<
537	<	}
538	<
539	<	void SimInfo::addProperty(GenericData* prop){
540	<
541	<	map<string, GenericData*>::iterator result;
542	<	result = properties.find(prop->getID());
543	<
544	<	//we can't simply use  properties[prop->getID()] = prop,
545	<	//it will cause memory leak if we already contain a propery which has the same name of prop
546	<
547	<	if(result != properties.end()){
986	>	}
987
549	–	delete (*result).second;
550	–	(*result).second = prop;
551	–
552	–	}
553	–	else{
554	–
555	–	properties[prop->getID()] = prop;
556	–
557	–	}
988
989	<	}
990	<
991	<	GenericData* SimInfo::getProperty(const string& propName){
992	<
993	<	map<string, GenericData*>::iterator result;
994	<
995	<	//string lowerCaseName = ();
996	<
997	<	result = properties.find(propName);
998	<
999	<	if(result != properties.end())
570	<	return (*result).second;
571	<	else
572	<	return NULL;
573	<	}
989	>	sprintf( checkPointMsg,
990	>	"succesfully sent the simulation information to fortran.\n");
991	>
992	>	errorCheckPoint();
993	>
994	>	// Setup number of neighbors in neighbor list if present
995	>	if (simParams_->haveNeighborListNeighbors()) {
996	>	int nlistNeighbors = simParams_->getNeighborListNeighbors();
997	>	setNeighbors(&nlistNeighbors);
998	>	}
999	>
1000
1001	+	}
1002
576	–	void SimInfo::getFortranGroupArrays(SimInfo* info,
577	–	vector<int>& FglobalGroupMembership,
578	–	vector<double>& mfact){
579	–
580	–	Molecule* myMols;
581	–	Atom** myAtoms;
582	–	int numAtom;
583	–	double mtot;
584	–	int numMol;
585	–	int numCutoffGroups;
586	–	CutoffGroup* myCutoffGroup;
587	–	vector<CutoffGroup*>::iterator iterCutoff;
588	–	Atom* cutoffAtom;
589	–	vector<Atom*>::iterator iterAtom;
590	–	int atomIndex;
591	–	double totalMass;
592	–
593	–	mfact.clear();
594	–	FglobalGroupMembership.clear();
595	–
1003
1004	<	// Fix the silly fortran indexing problem
1004	>	void SimInfo::setupFortranParallel() {
1005	>	#ifdef IS_MPI
1006	>	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
1007	>	vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
1008	>	vector<int> localToGlobalCutoffGroupIndex;
1009	>	SimInfo::MoleculeIterator mi;
1010	>	Molecule::AtomIterator ai;
1011	>	Molecule::CutoffGroupIterator ci;
1012	>	Molecule* mol;
1013	>	Atom* atom;
1014	>	CutoffGroup* cg;
1015	>	mpiSimData parallelData;
1016	>	int isError;
1017	>
1018	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
1019	>
1020	>	//local index(index in DataStorge) of atom is important
1021	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
1022	>	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
1023	>	}
1024	>
1025	>	//local index of cutoff group is trivial, it only depends on the order of travesing
1026	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
1027	>	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
1028	>	}
1029	>
1030	>	}
1031	>
1032	>	//fill up mpiSimData struct
1033	>	parallelData.nMolGlobal = getNGlobalMolecules();
1034	>	parallelData.nMolLocal = getNMolecules();
1035	>	parallelData.nAtomsGlobal = getNGlobalAtoms();
1036	>	parallelData.nAtomsLocal = getNAtoms();
1037	>	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
1038	>	parallelData.nGroupsLocal = getNCutoffGroups();
1039	>	parallelData.myNode = worldRank;
1040	>	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
1041	>
1042	>	//pass mpiSimData struct and index arrays to fortran
1043	>	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
1044	>	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
1045	>	&localToGlobalCutoffGroupIndex[0], &isError);
1046	>
1047	>	if (isError) {
1048	>	sprintf(painCave.errMsg,
1049	>	"mpiRefresh errror: fortran didn't like something we gave it.\n");
1050	>	painCave.isFatal = 1;
1051	>	simError();
1052	>	}
1053	>
1054	>	sprintf(checkPointMsg, " mpiRefresh successful.\n");
1055	>	errorCheckPoint();
1056	>
1057	>	#endif
1058	>	}
1059	>
1060	>
1061	>	void SimInfo::setupAccumulateBoxDipole() {
1062	>
1063	>
1064	>	}
1065	>
1066	>	void SimInfo::addProperty(GenericData* genData) {
1067	>	properties_.addProperty(genData);
1068	>	}
1069	>
1070	>	void SimInfo::removeProperty(const string& propName) {
1071	>	properties_.removeProperty(propName);
1072	>	}
1073	>
1074	>	void SimInfo::clearProperties() {
1075	>	properties_.clearProperties();
1076	>	}
1077	>
1078	>	vector<string> SimInfo::getPropertyNames() {
1079	>	return properties_.getPropertyNames();
1080	>	}
1081	>
1082	>	vector<GenericData*> SimInfo::getProperties() {
1083	>	return properties_.getProperties();
1084	>	}
1085	>
1086	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
1087	>	return properties_.getPropertyByName(propName);
1088	>	}
1089	>
1090	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1091	>	if (sman_ == sman) {
1092	>	return;
1093	>	}
1094	>	delete sman_;
1095	>	sman_ = sman;
1096	>
1097	>	Molecule* mol;
1098	>	RigidBody* rb;
1099	>	Atom* atom;
1100	>	SimInfo::MoleculeIterator mi;
1101	>	Molecule::RigidBodyIterator rbIter;
1102	>	Molecule::AtomIterator atomIter;;
1103	>
1104	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1105	>
1106	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1107	>	atom->setSnapshotManager(sman_);
1108	>	}
1109	>
1110	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1111	>	rb->setSnapshotManager(sman_);
1112	>	}
1113	>	}
1114	>
1115	>	}
1116	>
1117	>	Vector3d SimInfo::getComVel(){
1118	>	SimInfo::MoleculeIterator i;
1119	>	Molecule* mol;
1120	>
1121	>	Vector3d comVel(0.0);
1122	>	RealType totalMass = 0.0;
1123	>
1124	>
1125	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1126	>	RealType mass = mol->getMass();
1127	>	totalMass += mass;
1128	>	comVel += mass * mol->getComVel();
1129	>	}
1130	>
1131		#ifdef IS_MPI
1132	<	numAtom = mpiSim->getNAtomsGlobal();
1133	<	#else
1134	<	numAtom = n_atoms;
1132	>	RealType tmpMass = totalMass;
1133	>	Vector3d tmpComVel(comVel);
1134	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1135	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1136		#endif
603	–	for (int i = 0; i < numAtom; i++)
604	–	FglobalGroupMembership.push_back(globalGroupMembership[i] + 1);
605	–
1137
1138	<	myMols = info->molecules;
608	<	numMol = info->n_mol;
609	<	for(int i  = 0; i < numMol; i++){
610	<	numCutoffGroups = myMols[i].getNCutoffGroups();
611	<	for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff);
612	<	myCutoffGroup != NULL;
613	<	myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
1138	>	comVel /= totalMass;
1139
1140	<	totalMass = myCutoffGroup->getMass();
1140	>	return comVel;
1141	>	}
1142	>
1143	>	Vector3d SimInfo::getCom(){
1144	>	SimInfo::MoleculeIterator i;
1145	>	Molecule* mol;
1146	>
1147	>	Vector3d com(0.0);
1148	>	RealType totalMass = 0.0;
1149	>
1150	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1151	>	RealType mass = mol->getMass();
1152	>	totalMass += mass;
1153	>	com += mass * mol->getCom();
1154	>	}
1155	>
1156	>	#ifdef IS_MPI
1157	>	RealType tmpMass = totalMass;
1158	>	Vector3d tmpCom(com);
1159	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1160	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1161	>	#endif
1162	>
1163	>	com /= totalMass;
1164	>
1165	>	return com;
1166	>
1167	>	}
1168	>
1169	>	ostream& operator <<(ostream& o, SimInfo& info) {
1170	>
1171	>	return o;
1172	>	}
1173	>
1174	>
1175	>	/*
1176	>	Returns center of mass and center of mass velocity in one function call.
1177	>	*/
1178	>
1179	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1180	>	SimInfo::MoleculeIterator i;
1181	>	Molecule* mol;
1182
1183	<	for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom);
1184	<	cutoffAtom != NULL;
1185	<	cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
1186	<	mfact.push_back(cutoffAtom->getMass()/totalMass);
1183	>
1184	>	RealType totalMass = 0.0;
1185	>
1186	>
1187	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1188	>	RealType mass = mol->getMass();
1189	>	totalMass += mass;
1190	>	com += mass * mol->getCom();
1191	>	comVel += mass * mol->getComVel();
1192		}
1193	+
1194	+	#ifdef IS_MPI
1195	+	RealType tmpMass = totalMass;
1196	+	Vector3d tmpCom(com);
1197	+	Vector3d tmpComVel(comVel);
1198	+	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1199	+	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1200	+	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1201	+	#endif
1202	+
1203	+	com /= totalMass;
1204	+	comVel /= totalMass;
1205	+	}
1206	+
1207	+	/*
1208	+	Return intertia tensor for entire system and angular momentum Vector.
1209	+
1210	+
1211	+	[  Ixx -Ixy  -Ixz ]
1212	+	J =| -Iyx  Iyy  -Iyz |
1213	+	[ -Izx -Iyz   Izz ]
1214	+	*/
1215	+
1216	+	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1217	+
1218	+
1219	+	RealType xx = 0.0;
1220	+	RealType yy = 0.0;
1221	+	RealType zz = 0.0;
1222	+	RealType xy = 0.0;
1223	+	RealType xz = 0.0;
1224	+	RealType yz = 0.0;
1225	+	Vector3d com(0.0);
1226	+	Vector3d comVel(0.0);
1227	+
1228	+	getComAll(com, comVel);
1229	+
1230	+	SimInfo::MoleculeIterator i;
1231	+	Molecule* mol;
1232	+
1233	+	Vector3d thisq(0.0);
1234	+	Vector3d thisv(0.0);
1235	+
1236	+	RealType thisMass = 0.0;
1237	+
1238	+
1239	+
1240	+
1241	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1242	+
1243	+	thisq = mol->getCom()-com;
1244	+	thisv = mol->getComVel()-comVel;
1245	+	thisMass = mol->getMass();
1246	+	// Compute moment of intertia coefficients.
1247	+	xx += thisq[0]*thisq[0]*thisMass;
1248	+	yy += thisq[1]*thisq[1]*thisMass;
1249	+	zz += thisq[2]*thisq[2]*thisMass;
1250	+
1251	+	// compute products of intertia
1252	+	xy += thisq[0]*thisq[1]*thisMass;
1253	+	xz += thisq[0]*thisq[2]*thisMass;
1254	+	yz += thisq[1]*thisq[2]*thisMass;
1255	+
1256	+	angularMomentum += cross( thisq, thisv ) * thisMass;
1257	+
1258	+	}
1259	+
1260	+
1261	+	inertiaTensor(0,0) = yy + zz;
1262	+	inertiaTensor(0,1) = -xy;
1263	+	inertiaTensor(0,2) = -xz;
1264	+	inertiaTensor(1,0) = -xy;
1265	+	inertiaTensor(1,1) = xx + zz;
1266	+	inertiaTensor(1,2) = -yz;
1267	+	inertiaTensor(2,0) = -xz;
1268	+	inertiaTensor(2,1) = -yz;
1269	+	inertiaTensor(2,2) = xx + yy;
1270	+
1271	+	#ifdef IS_MPI
1272	+	Mat3x3d tmpI(inertiaTensor);
1273	+	Vector3d tmpAngMom;
1274	+	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1275	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1276	+	#endif
1277	+
1278	+	return;
1279	+	}
1280	+
1281	+	//Returns the angular momentum of the system
1282	+	Vector3d SimInfo::getAngularMomentum(){
1283	+
1284	+	Vector3d com(0.0);
1285	+	Vector3d comVel(0.0);
1286	+	Vector3d angularMomentum(0.0);
1287	+
1288	+	getComAll(com,comVel);
1289	+
1290	+	SimInfo::MoleculeIterator i;
1291	+	Molecule* mol;
1292	+
1293	+	Vector3d thisr(0.0);
1294	+	Vector3d thisp(0.0);
1295	+
1296	+	RealType thisMass;
1297	+
1298	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1299	+	thisMass = mol->getMass();
1300	+	thisr = mol->getCom()-com;
1301	+	thisp = (mol->getComVel()-comVel)*thisMass;
1302	+
1303	+	angularMomentum += cross( thisr, thisp );
1304	+
1305	+	}
1306	+
1307	+	#ifdef IS_MPI
1308	+	Vector3d tmpAngMom;
1309	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1310	+	#endif
1311	+
1312	+	return angularMomentum;
1313	+	}
1314	+
1315	+	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1316	+	return IOIndexToIntegrableObject.at(index);
1317	+	}
1318	+
1319	+	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1320	+	IOIndexToIntegrableObject= v;
1321	+	}
1322	+
1323	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1324	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1325	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1326	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1327	+	*/
1328	+	void SimInfo::getGyrationalVolume(RealType &volume){
1329	+	Mat3x3d intTensor;
1330	+	RealType det;
1331	+	Vector3d dummyAngMom;
1332	+	RealType sysconstants;
1333	+	RealType geomCnst;
1334	+
1335	+	geomCnst = 3.0/2.0;
1336	+	/* Get the inertial tensor and angular momentum for free*/
1337	+	getInertiaTensor(intTensor,dummyAngMom);
1338	+
1339	+	det = intTensor.determinant();
1340	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1341	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1342	+	return;
1343	+	}
1344	+
1345	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1346	+	Mat3x3d intTensor;
1347	+	Vector3d dummyAngMom;
1348	+	RealType sysconstants;
1349	+	RealType geomCnst;
1350	+
1351	+	geomCnst = 3.0/2.0;
1352	+	/* Get the inertial tensor and angular momentum for free*/
1353	+	getInertiaTensor(intTensor,dummyAngMom);
1354	+
1355	+	detI = intTensor.determinant();
1356	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1357	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1358	+	return;
1359	+	}
1360	+	/*
1361	+	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1362	+	assert( v.size() == nAtoms_ + nRigidBodies_);
1363	+	sdByGlobalIndex_ = v;
1364		}
1365	+
1366	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1367	+	//assert(index < nAtoms_ + nRigidBodies_);
1368	+	return sdByGlobalIndex_.at(index);
1369	+	}
1370	+	*/
1371	+	int SimInfo::getNGlobalConstraints() {
1372	+	int nGlobalConstraints;
1373	+	#ifdef IS_MPI
1374	+	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1375	+	MPI_COMM_WORLD);
1376	+	#else
1377	+	nGlobalConstraints =  nConstraints_;
1378	+	#endif
1379	+	return nGlobalConstraints;
1380		}
1381
1382	<	}
1382	>	}//end namespace OpenMD
1383	>

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 124 by chuckv, Wed Oct 20 20:46:20 2004 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1534 by gezelter, Wed Dec 29 21:53:28 2010 UTC

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