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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 2 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1532 by gezelter, Wed Dec 29 19:59:21 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 "SimInfo.hpp"
54	<	#define __C
55	<	#include "fSimulation.h"
56	<	#include "simError.h"
53	>	#include "brains/SimInfo.hpp"
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 "selection/SelectionManager.hpp"
62	>	#include "io/ForceFieldOptions.hpp"
63	>	#include "UseTheForce/ForceField.hpp"
64	>	#include "nonbonded/SwitchingFunction.hpp"
65
13	–	#include "fortranWrappers.hpp"
66
15	–	#include "MatVec3.h"
16	–
67		#ifdef IS_MPI
68	<	#include "mpiSimulation.hpp"
69	<	#endif
68	>	#include "UseTheForce/mpiComponentPlan.h"
69	>	#include "UseTheForce/DarkSide/simParallel_interface.h"
70	>	#endif
71
72	<	inline double roundMe( double x ){
73	<	return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
74	<	}
75	<
76	<	inline double min( double a, double b ){
77	<	return (a < b ) ? a : b;
78	<	}
72	>	using namespace std;
73	>	namespace OpenMD {
74	>
75	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
76	>	forceField_(ff), simParams_(simParams),
77	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
78	>	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
79	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
80	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
81	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
82	>	nConstraints_(0), sman_(NULL), fortranInitialized_(false),
83	>	calcBoxDipole_(false), useAtomicVirial_(true) {
84	>
85	>	MoleculeStamp* molStamp;
86	>	int nMolWithSameStamp;
87	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
88	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
89	>	CutoffGroupStamp* cgStamp;
90	>	RigidBodyStamp* rbStamp;
91	>	int nRigidAtoms = 0;
92	>
93	>	vector<Component*> components = simParams->getComponents();
94	>
95	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
96	>	molStamp = (*i)->getMoleculeStamp();
97	>	nMolWithSameStamp = (*i)->getNMol();
98	>
99	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
100	>
101	>	//calculate atoms in molecules
102	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
103	>
104	>	//calculate atoms in cutoff groups
105	>	int nAtomsInGroups = 0;
106	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
107	>
108	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
109	>	cgStamp = molStamp->getCutoffGroupStamp(j);
110	>	nAtomsInGroups += cgStamp->getNMembers();
111	>	}
112	>
113	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
114	>
115	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
116	>
117	>	//calculate atoms in rigid bodies
118	>	int nAtomsInRigidBodies = 0;
119	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
120	>
121	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
122	>	rbStamp = molStamp->getRigidBodyStamp(j);
123	>	nAtomsInRigidBodies += rbStamp->getNMembers();
124	>	}
125	>
126	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
127	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
128	>
129	>	}
130	>
131	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
132	>	//group therefore the total number of cutoff groups in the system is
133	>	//equal to the total number of atoms minus number of atoms belong to
134	>	//cutoff group defined in meta-data file plus the number of cutoff
135	>	//groups defined in meta-data file
136	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
137	>
138	>	//every free atom (atom does not belong to rigid bodies) is an
139	>	//integrable object therefore the total number of integrable objects
140	>	//in the system is equal to the total number of atoms minus number of
141	>	//atoms belong to rigid body defined in meta-data file plus the number
142	>	//of rigid bodies defined in meta-data file
143	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
144	>	+ nGlobalRigidBodies_;
145	>
146	>	nGlobalMols_ = molStampIds_.size();
147	>	molToProcMap_.resize(nGlobalMols_);
148	>	}
149	>
150	>	SimInfo::~SimInfo() {
151	>	map<int, Molecule*>::iterator i;
152	>	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
153	>	delete i->second;
154	>	}
155	>	molecules_.clear();
156	>
157	>	delete sman_;
158	>	delete simParams_;
159	>	delete forceField_;
160	>	}
161
29	–	SimInfo* currentInfo;
162
163	<	SimInfo::SimInfo(){
164	<
165	<	n_constraints = 0;
166	<	nZconstraints = 0;
167	<	n_oriented = 0;
168	<	n_dipoles = 0;
169	<	ndf = 0;
170	<	ndfRaw = 0;
171	<	nZconstraints = 0;
172	<	the_integrator = NULL;
173	<	setTemp = 0;
174	<	thermalTime = 0.0;
175	<	currentTime = 0.0;
176	<	rCut = 0.0;
177	<	rSw = 0.0;
178	<
179	<	haveRcut = 0;
180	<	haveRsw = 0;
181	<	boxIsInit = 0;
163	>	bool SimInfo::addMolecule(Molecule* mol) {
164	>	MoleculeIterator i;
165	>
166	>	i = molecules_.find(mol->getGlobalIndex());
167	>	if (i == molecules_.end() ) {
168	>
169	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
170	>
171	>	nAtoms_ += mol->getNAtoms();
172	>	nBonds_ += mol->getNBonds();
173	>	nBends_ += mol->getNBends();
174	>	nTorsions_ += mol->getNTorsions();
175	>	nInversions_ += mol->getNInversions();
176	>	nRigidBodies_ += mol->getNRigidBodies();
177	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
178	>	nCutoffGroups_ += mol->getNCutoffGroups();
179	>	nConstraints_ += mol->getNConstraintPairs();
180	>
181	>	addInteractionPairs(mol);
182	>
183	>	return true;
184	>	} else {
185	>	return false;
186	>	}
187	>	}
188
189	<	resetTime = 1e99;
189	>	bool SimInfo::removeMolecule(Molecule* mol) {
190	>	MoleculeIterator i;
191	>	i = molecules_.find(mol->getGlobalIndex());
192
193	<	orthoRhombic = 0;
54	<	orthoTolerance = 1E-6;
55	<	useInitXSstate = true;
193	>	if (i != molecules_.end() ) {
194
195	<	usePBC = 0;
196	<	useLJ = 0;
197	<	useSticky = 0;
198	<	useCharges = 0;
199	<	useDipoles = 0;
200	<	useReactionField = 0;
201	<	useGB = 0;
202	<	useEAM = 0;
203	<	useSolidThermInt = 0;
204	<	useLiquidThermInt = 0;
195	>	assert(mol == i->second);
196	>
197	>	nAtoms_ -= mol->getNAtoms();
198	>	nBonds_ -= mol->getNBonds();
199	>	nBends_ -= mol->getNBends();
200	>	nTorsions_ -= mol->getNTorsions();
201	>	nInversions_ -= mol->getNInversions();
202	>	nRigidBodies_ -= mol->getNRigidBodies();
203	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
204	>	nCutoffGroups_ -= mol->getNCutoffGroups();
205	>	nConstraints_ -= mol->getNConstraintPairs();
206
207	<	haveCutoffGroups = false;
207	>	removeInteractionPairs(mol);
208	>	molecules_.erase(mol->getGlobalIndex());
209
210	<	excludes = Exclude::Instance();
211	<
212	<	myConfiguration = new SimState();
213	<
214	<	has_minimizer = false;
215	<	the_minimizer =NULL;
216	<
77	<	ngroup = 0;
78	<
79	<	wrapMeSimInfo( this );
80	<	}
210	>	delete mol;
211	>
212	>	return true;
213	>	} else {
214	>	return false;
215	>	}
216	>	}
217
218	+
219	+	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
220	+	i = molecules_.begin();
221	+	return i == molecules_.end() ? NULL : i->second;
222	+	}
223
224	<	SimInfo::~SimInfo(){
224	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
225	>	++i;
226	>	return i == molecules_.end() ? NULL : i->second;
227	>	}
228
85	–	delete myConfiguration;
229
230	<	map<string, GenericData*>::iterator i;
231	<
232	<	for(i = properties.begin(); i != properties.end(); i++)
233	<	delete (*i).second;
230	>	void SimInfo::calcNdf() {
231	>	int ndf_local;
232	>	MoleculeIterator i;
233	>	vector<StuntDouble*>::iterator j;
234	>	Molecule* mol;
235	>	StuntDouble* integrableObject;
236
237	<	}
237	>	ndf_local = 0;
238	>
239	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
240	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
241	>	integrableObject = mol->nextIntegrableObject(j)) {
242
243	<	void SimInfo::setBox(double newBox[3]) {
95	<
96	<	int i, j;
97	<	double tempMat[3][3];
243	>	ndf_local += 3;
244
245	<	for(i=0; i<3; i++)
246	<	for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
245	>	if (integrableObject->isDirectional()) {
246	>	if (integrableObject->isLinear()) {
247	>	ndf_local += 2;
248	>	} else {
249	>	ndf_local += 3;
250	>	}
251	>	}
252	>
253	>	}
254	>	}
255	>
256	>	// n_constraints is local, so subtract them on each processor
257	>	ndf_local -= nConstraints_;
258
259	<	tempMat[0][0] = newBox[0];
260	<	tempMat[1][1] = newBox[1];
261	<	tempMat[2][2] = newBox[2];
259	>	#ifdef IS_MPI
260	>	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
261	>	#else
262	>	ndf_ = ndf_local;
263	>	#endif
264
265	<	setBoxM( tempMat );
265	>	// nZconstraints_ is global, as are the 3 COM translations for the
266	>	// entire system:
267	>	ndf_ = ndf_ - 3 - nZconstraint_;
268
269	<	}
269	>	}
270
271	<	void SimInfo::setBoxM( double theBox[3][3] ){
272	<
273	<	int i, j;
274	<	double FortranHmat[9]; // to preserve compatibility with Fortran the
275	<	// ordering in the array is as follows:
276	<	// [ 0 3 6 ]
277	<	// [ 1 4 7 ]
117	<	// [ 2 5 8 ]
118	<	double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
119	<
120	<	if( !boxIsInit ) boxIsInit = 1;
121	<
122	<	for(i=0; i < 3; i++)
123	<	for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
124	<
125	<	calcBoxL();
126	<	calcHmatInv();
127	<
128	<	for(i=0; i < 3; i++) {
129	<	for (j=0; j < 3; j++) {
130	<	FortranHmat[3*j + i] = Hmat[i][j];
131	<	FortranHmatInv[3*j + i] = HmatInv[i][j];
132	<	}
271	>	int SimInfo::getFdf() {
272	>	#ifdef IS_MPI
273	>	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
274	>	#else
275	>	fdf_ = fdf_local;
276	>	#endif
277	>	return fdf_;
278		}
279	+
280	+	void SimInfo::calcNdfRaw() {
281	+	int ndfRaw_local;
282
283	<	setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
284	<
285	<	}
286	<
283	>	MoleculeIterator i;
284	>	vector<StuntDouble*>::iterator j;
285	>	Molecule* mol;
286	>	StuntDouble* integrableObject;
287
288	<	void SimInfo::getBoxM (double theBox[3][3]) {
288	>	// Raw degrees of freedom that we have to set
289	>	ndfRaw_local = 0;
290	>
291	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
292	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
293	>	integrableObject = mol->nextIntegrableObject(j)) {
294
295	<	int i, j;
143	<	for(i=0; i<3; i++)
144	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
145	<	}
295	>	ndfRaw_local += 3;
296
297	<
298	<	void SimInfo::scaleBox(double scale) {
299	<	double theBox[3][3];
300	<	int i, j;
301	<
302	<	// cerr << "Scaling box by " << scale << "\n";
303	<
304	<	for(i=0; i<3; i++)
155	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
156	<
157	<	setBoxM(theBox);
158	<
159	<	}
160	<
161	<	void SimInfo::calcHmatInv( void ) {
162	<
163	<	int oldOrtho;
164	<	int i,j;
165	<	double smallDiag;
166	<	double tol;
167	<	double sanity[3][3];
168	<
169	<	invertMat3( Hmat, HmatInv );
170	<
171	<	// check to see if Hmat is orthorhombic
172	<
173	<	oldOrtho = orthoRhombic;
174	<
175	<	smallDiag = fabs(Hmat[0][0]);
176	<	if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
177	<	if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
178	<	tol = smallDiag * orthoTolerance;
179	<
180	<	orthoRhombic = 1;
181	<
182	<	for (i = 0; i < 3; i++ ) {
183	<	for (j = 0 ; j < 3; j++) {
184	<	if (i != j) {
185	<	if (orthoRhombic) {
186	<	if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
187	<	}
297	>	if (integrableObject->isDirectional()) {
298	>	if (integrableObject->isLinear()) {
299	>	ndfRaw_local += 2;
300	>	} else {
301	>	ndfRaw_local += 3;
302	>	}
303	>	}
304	>
305		}
306		}
190	–	}
191	–
192	–	if( oldOrtho != orthoRhombic ){
307
308	<	if( orthoRhombic ) {
309	<	sprintf( painCave.errMsg,
310	<	"OOPSE is switching from the default Non-Orthorhombic\n"
311	<	"\tto the faster Orthorhombic periodic boundary computations.\n"
312	<	"\tThis is usually a good thing, but if you wan't the\n"
199	<	"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
200	<	"\tvariable ( currently set to %G ) smaller.\n",
201	<	orthoTolerance);
202	<	painCave.severity = OOPSE_INFO;
203	<	simError();
204	<	}
205	<	else {
206	<	sprintf( painCave.errMsg,
207	<	"OOPSE is switching from the faster Orthorhombic to the more\n"
208	<	"\tflexible Non-Orthorhombic periodic boundary computations.\n"
209	<	"\tThis is usually because the box has deformed under\n"
210	<	"\tNPTf integration. If you wan't to live on the edge with\n"
211	<	"\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
212	<	"\tvariable ( currently set to %G ) larger.\n",
213	<	orthoTolerance);
214	<	painCave.severity = OOPSE_WARNING;
215	<	simError();
216	<	}
308	>	#ifdef IS_MPI
309	>	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
310	>	#else
311	>	ndfRaw_ = ndfRaw_local;
312	>	#endif
313		}
218	–	}
314
315	<	void SimInfo::calcBoxL( void ){
315	>	void SimInfo::calcNdfTrans() {
316	>	int ndfTrans_local;
317
318	<	double dx, dy, dz, dsq;
318	>	ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
319
224	–	// boxVol = Determinant of Hmat
320
321	<	boxVol = matDet3( Hmat );
321	>	#ifdef IS_MPI
322	>	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
323	>	#else
324	>	ndfTrans_ = ndfTrans_local;
325	>	#endif
326
327	<	// boxLx
328	<
329	<	dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
231	<	dsq = dx*dx + dy*dy + dz*dz;
232	<	boxL[0] = sqrt( dsq );
233	<	//maxCutoff = 0.5 * boxL[0];
234	<
235	<	// boxLy
236	<
237	<	dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
238	<	dsq = dx*dx + dy*dy + dz*dz;
239	<	boxL[1] = sqrt( dsq );
240	<	//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
327	>	ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
328	>
329	>	}
330
331	+	void SimInfo::addInteractionPairs(Molecule* mol) {
332	+	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
333	+	vector<Bond*>::iterator bondIter;
334	+	vector<Bend*>::iterator bendIter;
335	+	vector<Torsion*>::iterator torsionIter;
336	+	vector<Inversion*>::iterator inversionIter;
337	+	Bond* bond;
338	+	Bend* bend;
339	+	Torsion* torsion;
340	+	Inversion* inversion;
341	+	int a;
342	+	int b;
343	+	int c;
344	+	int d;
345
346	<	// boxLz
347	<
348	<	dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
349	<	dsq = dx*dx + dy*dy + dz*dz;
350	<	boxL[2] = sqrt( dsq );
351	<	//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
346	>	// atomGroups can be used to add special interaction maps between
347	>	// groups of atoms that are in two separate rigid bodies.
348	>	// However, most site-site interactions between two rigid bodies
349	>	// are probably not special, just the ones between the physically
350	>	// bonded atoms.  Interactions *within* a single rigid body should
351	>	// always be excluded.  These are done at the bottom of this
352	>	// function.
353
354	<	//calculate the max cutoff
355	<	maxCutoff =  calcMaxCutOff();
356	<
357	<	checkCutOffs();
354	>	map<int, set<int> > atomGroups;
355	>	Molecule::RigidBodyIterator rbIter;
356	>	RigidBody* rb;
357	>	Molecule::IntegrableObjectIterator ii;
358	>	StuntDouble* integrableObject;
359	>
360	>	for (integrableObject = mol->beginIntegrableObject(ii);
361	>	integrableObject != NULL;
362	>	integrableObject = mol->nextIntegrableObject(ii)) {
363	>
364	>	if (integrableObject->isRigidBody()) {
365	>	rb = static_cast<RigidBody*>(integrableObject);
366	>	vector<Atom*> atoms = rb->getAtoms();
367	>	set<int> rigidAtoms;
368	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
369	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
370	>	}
371	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
372	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
373	>	}
374	>	} else {
375	>	set<int> oneAtomSet;
376	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
377	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
378	>	}
379	>	}
380	>
381	>	for (bond= mol->beginBond(bondIter); bond != NULL;
382	>	bond = mol->nextBond(bondIter)) {
383
384	<	}
384	>	a = bond->getAtomA()->getGlobalIndex();
385	>	b = bond->getAtomB()->getGlobalIndex();
386	>
387	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
388	>	oneTwoInteractions_.addPair(a, b);
389	>	} else {
390	>	excludedInteractions_.addPair(a, b);
391	>	}
392	>	}
393
394	+	for (bend= mol->beginBend(bendIter); bend != NULL;
395	+	bend = mol->nextBend(bendIter)) {
396
397	<	double SimInfo::calcMaxCutOff(){
397	>	a = bend->getAtomA()->getGlobalIndex();
398	>	b = bend->getAtomB()->getGlobalIndex();
399	>	c = bend->getAtomC()->getGlobalIndex();
400	>
401	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
402	>	oneTwoInteractions_.addPair(a, b);
403	>	oneTwoInteractions_.addPair(b, c);
404	>	} else {
405	>	excludedInteractions_.addPair(a, b);
406	>	excludedInteractions_.addPair(b, c);
407	>	}
408
409	<	double ri[3], rj[3], rk[3];
410	<	double rij[3], rjk[3], rki[3];
411	<	double minDist;
409	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
410	>	oneThreeInteractions_.addPair(a, c);
411	>	} else {
412	>	excludedInteractions_.addPair(a, c);
413	>	}
414	>	}
415
416	<	ri[0] = Hmat[0][0];
417	<	ri[1] = Hmat[1][0];
266	<	ri[2] = Hmat[2][0];
416	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
417	>	torsion = mol->nextTorsion(torsionIter)) {
418
419	<	rj[0] = Hmat[0][1];
420	<	rj[1] = Hmat[1][1];
421	<	rj[2] = Hmat[2][1];
419	>	a = torsion->getAtomA()->getGlobalIndex();
420	>	b = torsion->getAtomB()->getGlobalIndex();
421	>	c = torsion->getAtomC()->getGlobalIndex();
422	>	d = torsion->getAtomD()->getGlobalIndex();
423
424	<	rk[0] = Hmat[0][2];
425	<	rk[1] = Hmat[1][2];
426	<	rk[2] = Hmat[2][2];
427	<
428	<	crossProduct3(ri, rj, rij);
429	<	distXY = dotProduct3(rk,rij) / norm3(rij);
424	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
425	>	oneTwoInteractions_.addPair(a, b);
426	>	oneTwoInteractions_.addPair(b, c);
427	>	oneTwoInteractions_.addPair(c, d);
428	>	} else {
429	>	excludedInteractions_.addPair(a, b);
430	>	excludedInteractions_.addPair(b, c);
431	>	excludedInteractions_.addPair(c, d);
432	>	}
433
434	<	crossProduct3(rj,rk, rjk);
435	<	distYZ = dotProduct3(ri,rjk) / norm3(rjk);
434	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
435	>	oneThreeInteractions_.addPair(a, c);
436	>	oneThreeInteractions_.addPair(b, d);
437	>	} else {
438	>	excludedInteractions_.addPair(a, c);
439	>	excludedInteractions_.addPair(b, d);
440	>	}
441
442	<	crossProduct3(rk,ri, rki);
443	<	distZX = dotProduct3(rj,rki) / norm3(rki);
442	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
443	>	oneFourInteractions_.addPair(a, d);
444	>	} else {
445	>	excludedInteractions_.addPair(a, d);
446	>	}
447	>	}
448
449	<	minDist = min(min(distXY, distYZ), distZX);
450	<	return minDist/2;
287	<
288	<	}
449	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
450	>	inversion = mol->nextInversion(inversionIter)) {
451
452	<	void SimInfo::wrapVector( double thePos[3] ){
452	>	a = inversion->getAtomA()->getGlobalIndex();
453	>	b = inversion->getAtomB()->getGlobalIndex();
454	>	c = inversion->getAtomC()->getGlobalIndex();
455	>	d = inversion->getAtomD()->getGlobalIndex();
456
457	<	int i;
458	<	double scaled[3];
457	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
458	>	oneTwoInteractions_.addPair(a, b);
459	>	oneTwoInteractions_.addPair(a, c);
460	>	oneTwoInteractions_.addPair(a, d);
461	>	} else {
462	>	excludedInteractions_.addPair(a, b);
463	>	excludedInteractions_.addPair(a, c);
464	>	excludedInteractions_.addPair(a, d);
465	>	}
466
467	<	if( !orthoRhombic ){
468	<	// calc the scaled coordinates.
469	<
467	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
468	>	oneThreeInteractions_.addPair(b, c);
469	>	oneThreeInteractions_.addPair(b, d);
470	>	oneThreeInteractions_.addPair(c, d);
471	>	} else {
472	>	excludedInteractions_.addPair(b, c);
473	>	excludedInteractions_.addPair(b, d);
474	>	excludedInteractions_.addPair(c, d);
475	>	}
476	>	}
477
478	<	matVecMul3(HmatInv, thePos, scaled);
479	<
480	<	for(i=0; i<3; i++)
481	<	scaled[i] -= roundMe(scaled[i]);
482	<
483	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
484	<
485	<	matVecMul3(Hmat, scaled, thePos);
478	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
479	>	rb = mol->nextRigidBody(rbIter)) {
480	>	vector<Atom*> atoms = rb->getAtoms();
481	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
482	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
483	>	a = atoms[i]->getGlobalIndex();
484	>	b = atoms[j]->getGlobalIndex();
485	>	excludedInteractions_.addPair(a, b);
486	>	}
487	>	}
488	>	}
489
490		}
491	<	else{
492	<	// calc the scaled coordinates.
491	>
492	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
493	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
494	>	vector<Bond*>::iterator bondIter;
495	>	vector<Bend*>::iterator bendIter;
496	>	vector<Torsion*>::iterator torsionIter;
497	>	vector<Inversion*>::iterator inversionIter;
498	>	Bond* bond;
499	>	Bend* bend;
500	>	Torsion* torsion;
501	>	Inversion* inversion;
502	>	int a;
503	>	int b;
504	>	int c;
505	>	int d;
506	>
507	>	map<int, set<int> > atomGroups;
508	>	Molecule::RigidBodyIterator rbIter;
509	>	RigidBody* rb;
510	>	Molecule::IntegrableObjectIterator ii;
511	>	StuntDouble* integrableObject;
512
513	<	for(i=0; i<3; i++)
514	<	scaled[i] = thePos[i]*HmatInv[i][i];
513	>	for (integrableObject = mol->beginIntegrableObject(ii);
514	>	integrableObject != NULL;
515	>	integrableObject = mol->nextIntegrableObject(ii)) {
516	>
517	>	if (integrableObject->isRigidBody()) {
518	>	rb = static_cast<RigidBody*>(integrableObject);
519	>	vector<Atom*> atoms = rb->getAtoms();
520	>	set<int> rigidAtoms;
521	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
522	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
523	>	}
524	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
525	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
526	>	}
527	>	} else {
528	>	set<int> oneAtomSet;
529	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
530	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
531	>	}
532	>	}
533	>
534	>	for (bond= mol->beginBond(bondIter); bond != NULL;
535	>	bond = mol->nextBond(bondIter)) {
536	>
537	>	a = bond->getAtomA()->getGlobalIndex();
538	>	b = bond->getAtomB()->getGlobalIndex();
539
540	<	// wrap the scaled coordinates
541	<
542	<	for(i=0; i<3; i++)
543	<	scaled[i] -= roundMe(scaled[i]);
544	<
545	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
321	<
322	<	for(i=0; i<3; i++)
323	<	thePos[i] = scaled[i]*Hmat[i][i];
324	<	}
325	<
326	<	}
540	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
541	>	oneTwoInteractions_.removePair(a, b);
542	>	} else {
543	>	excludedInteractions_.removePair(a, b);
544	>	}
545	>	}
546
547	+	for (bend= mol->beginBend(bendIter); bend != NULL;
548	+	bend = mol->nextBend(bendIter)) {
549
550	<	int SimInfo::getNDF(){
551	<	int ndf_local;
550	>	a = bend->getAtomA()->getGlobalIndex();
551	>	b = bend->getAtomB()->getGlobalIndex();
552	>	c = bend->getAtomC()->getGlobalIndex();
553	>
554	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
555	>	oneTwoInteractions_.removePair(a, b);
556	>	oneTwoInteractions_.removePair(b, c);
557	>	} else {
558	>	excludedInteractions_.removePair(a, b);
559	>	excludedInteractions_.removePair(b, c);
560	>	}
561
562	<	ndf_local = 0;
562	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
563	>	oneThreeInteractions_.removePair(a, c);
564	>	} else {
565	>	excludedInteractions_.removePair(a, c);
566	>	}
567	>	}
568	>
569	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
570	>	torsion = mol->nextTorsion(torsionIter)) {
571	>
572	>	a = torsion->getAtomA()->getGlobalIndex();
573	>	b = torsion->getAtomB()->getGlobalIndex();
574	>	c = torsion->getAtomC()->getGlobalIndex();
575	>	d = torsion->getAtomD()->getGlobalIndex();
576
577	<	for(int i = 0; i < integrableObjects.size(); i++){
578	<	ndf_local += 3;
579	<	if (integrableObjects[i]->isDirectional()) {
580	<	if (integrableObjects[i]->isLinear())
581	<	ndf_local += 2;
582	<	else
583	<	ndf_local += 3;
577	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
578	>	oneTwoInteractions_.removePair(a, b);
579	>	oneTwoInteractions_.removePair(b, c);
580	>	oneTwoInteractions_.removePair(c, d);
581	>	} else {
582	>	excludedInteractions_.removePair(a, b);
583	>	excludedInteractions_.removePair(b, c);
584	>	excludedInteractions_.removePair(c, d);
585	>	}
586	>
587	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
588	>	oneThreeInteractions_.removePair(a, c);
589	>	oneThreeInteractions_.removePair(b, d);
590	>	} else {
591	>	excludedInteractions_.removePair(a, c);
592	>	excludedInteractions_.removePair(b, d);
593	>	}
594	>
595	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
596	>	oneFourInteractions_.removePair(a, d);
597	>	} else {
598	>	excludedInteractions_.removePair(a, d);
599	>	}
600		}
342	–	}
601
602	<	// n_constraints is local, so subtract them on each processor:
602	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
603	>	inversion = mol->nextInversion(inversionIter)) {
604
605	<	ndf_local -= n_constraints;
605	>	a = inversion->getAtomA()->getGlobalIndex();
606	>	b = inversion->getAtomB()->getGlobalIndex();
607	>	c = inversion->getAtomC()->getGlobalIndex();
608	>	d = inversion->getAtomD()->getGlobalIndex();
609
610	<	#ifdef IS_MPI
611	<	MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
612	<	#else
613	<	ndf = ndf_local;
614	<	#endif
610	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
611	>	oneTwoInteractions_.removePair(a, b);
612	>	oneTwoInteractions_.removePair(a, c);
613	>	oneTwoInteractions_.removePair(a, d);
614	>	} else {
615	>	excludedInteractions_.removePair(a, b);
616	>	excludedInteractions_.removePair(a, c);
617	>	excludedInteractions_.removePair(a, d);
618	>	}
619
620	<	// nZconstraints is global, as are the 3 COM translations for the
621	<	// entire system:
620	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
621	>	oneThreeInteractions_.removePair(b, c);
622	>	oneThreeInteractions_.removePair(b, d);
623	>	oneThreeInteractions_.removePair(c, d);
624	>	} else {
625	>	excludedInteractions_.removePair(b, c);
626	>	excludedInteractions_.removePair(b, d);
627	>	excludedInteractions_.removePair(c, d);
628	>	}
629	>	}
630
631	<	ndf = ndf - 3 - nZconstraints;
631	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
632	>	rb = mol->nextRigidBody(rbIter)) {
633	>	vector<Atom*> atoms = rb->getAtoms();
634	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
635	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
636	>	a = atoms[i]->getGlobalIndex();
637	>	b = atoms[j]->getGlobalIndex();
638	>	excludedInteractions_.removePair(a, b);
639	>	}
640	>	}
641	>	}
642	>
643	>	}
644	>
645	>
646	>	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
647	>	int curStampId;
648	>
649	>	//index from 0
650	>	curStampId = moleculeStamps_.size();
651
652	<	return ndf;
653	<	}
652	>	moleculeStamps_.push_back(molStamp);
653	>	molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
654	>	}
655
362	–	int SimInfo::getNDFraw() {
363	–	int ndfRaw_local;
656
657	<	// Raw degrees of freedom that we have to set
658	<	ndfRaw_local = 0;
657	>	/**
658	>	* update
659	>	*
660	>	*  Performs the global checks and variable settings after the objects have been
661	>	*  created.
662	>	*
663	>	*/
664	>	void SimInfo::update() {
665	>
666	>	setupSimVariables();
667	>	setupCutoffs();
668	>	setupSwitching();
669	>	setupElectrostatics();
670	>	setupNeighborlists();
671
672	<	for(int i = 0; i < integrableObjects.size(); i++){
673	<	ndfRaw_local += 3;
674	<	if (integrableObjects[i]->isDirectional()) {
675	<	if (integrableObjects[i]->isLinear())
676	<	ndfRaw_local += 2;
677	<	else
678	<	ndfRaw_local += 3;
679	<	}
680	<	}
672	>	#ifdef IS_MPI
673	>	setupFortranParallel();
674	>	#endif
675	>	setupFortranSim();
676	>	fortranInitialized_ = true;
677	>
678	>	calcNdf();
679	>	calcNdfRaw();
680	>	calcNdfTrans();
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	>	return atomTypes;
696	>	}
697	>
698	>	/**
699	>	* setupCutoffs
700	>	*
701	>	* Sets the values of cutoffRadius and cutoffMethod
702	>	*
703	>	* cutoffRadius : realType
704	>	*  If the cutoffRadius was explicitly set, use that value.
705	>	*  If the cutoffRadius was not explicitly set:
706	>	*      Are there electrostatic atoms?  Use 12.0 Angstroms.
707	>	*      No electrostatic atoms?  Poll the atom types present in the
708	>	*      simulation for suggested cutoff values (e.g. 2.5 * sigma).
709	>	*      Use the maximum suggested value that was found.
710	>	*
711	>	* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL)
712	>	*      If cutoffMethod was explicitly set, use that choice.
713	>	*      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
714	>	*/
715	>	void SimInfo::setupCutoffs() {
716
717	<	#ifdef IS_MPI
718	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
719	<	#else
720	<	ndfRaw = ndfRaw_local;
721	<	#endif
717	>	if (simParams_->haveCutoffRadius()) {
718	>	cutoffRadius_ = simParams_->getCutoffRadius();
719	>	} else {
720	>	if (usesElectrostaticAtoms_) {
721	>	sprintf(painCave.errMsg,
722	>	"SimInfo: No value was set for the cutoffRadius.\n"
723	>	"\tOpenMD will use a default value of 12.0 angstroms"
724	>	"\tfor the cutoffRadius.\n");
725	>	painCave.isFatal = 0;
726	>	painCave.severity = OPENMD_INFO;
727	>	simError();
728	>	cutoffRadius_ = 12.0;
729	>	} else {
730	>	RealType thisCut;
731	>	set<AtomType*>::iterator i;
732	>	set<AtomType*> atomTypes;
733	>	atomTypes = getSimulatedAtomTypes();
734	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
735	>	thisCut = InteractionManager::Instance()->getSuggestedCutoffRadius((*i));
736	>	cutoffRadius_ = max(thisCut, cutoffRadius_);
737	>	}
738	>	sprintf(painCave.errMsg,
739	>	"SimInfo: No value was set for the cutoffRadius.\n"
740	>	"\tOpenMD will use %lf angstroms.\n",
741	>	cutoffRadius_);
742	>	painCave.isFatal = 0;
743	>	painCave.severity = OPENMD_INFO;
744	>	simError();
745	>	}
746	>	}
747
748	<	return ndfRaw;
385	<	}
748	>	InteractionManager::Instance()->setCutoffRadius(cutoffRadius_);
749
750	<	int SimInfo::getNDFtranslational() {
751	<	int ndfTrans_local;
750	>	map<string, CutoffMethod> stringToCutoffMethod;
751	>	stringToCutoffMethod["HARD"] = HARD;
752	>	stringToCutoffMethod["SWITCHING_FUNCTION"] = SWITCHING_FUNCTION;
753	>	stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;
754	>	stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
755	>
756	>	if (simParams_->haveCutoffMethod()) {
757	>	string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
758	>	map<string, CutoffMethod>::iterator i;
759	>	i = stringToCutoffMethod.find(cutMeth);
760	>	if (i == stringToCutoffMethod.end()) {
761	>	sprintf(painCave.errMsg,
762	>	"SimInfo: Could not find chosen cutoffMethod %s\n"
763	>	"\tShould be one of: "
764	>	"HARD, SWITCHING_FUNCTION, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
765	>	cutMeth.c_str());
766	>	painCave.isFatal = 1;
767	>	painCave.severity = OPENMD_ERROR;
768	>	simError();
769	>	} else {
770	>	cutoffMethod_ = i->second;
771	>	}
772	>	} else {
773	>	sprintf(painCave.errMsg,
774	>	"SimInfo: No value was set for the cutoffMethod.\n"
775	>	"\tOpenMD will use SHIFTED_FORCE.\n");
776	>	painCave.isFatal = 0;
777	>	painCave.severity = OPENMD_INFO;
778	>	simError();
779	>	cutoffMethod_ = SHIFTED_FORCE;
780	>	}
781
782	<	ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
782	>	InteractionManager::Instance()->setCutoffMethod(cutoffMethod_);
783	>	}
784	>
785	>	/**
786	>	* setupSwitching
787	>	*
788	>	* Sets the values of switchingRadius and
789	>	*  If the switchingRadius was explicitly set, use that value (but check it)
790	>	*  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
791	>	*/
792	>	void SimInfo::setupSwitching() {
793	>
794	>	if (simParams_->haveSwitchingRadius()) {
795	>	switchingRadius_ = simParams_->getSwitchingRadius();
796	>	if (switchingRadius_ > cutoffRadius_) {
797	>	sprintf(painCave.errMsg,
798	>	"SimInfo: switchingRadius (%f) is larger than cutoffRadius(%f)\n",
799	>	switchingRadius_, cutoffRadius_);
800	>	painCave.isFatal = 1;
801	>	painCave.severity = OPENMD_ERROR;
802	>	simError();
803	>	}
804	>	} else {
805	>	switchingRadius_ = 0.85 * cutoffRadius_;
806	>	sprintf(painCave.errMsg,
807	>	"SimInfo: No value was set for the switchingRadius.\n"
808	>	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
809	>	"\tswitchingRadius = %f. for this simulation\n", switchingRadius_);
810	>	painCave.isFatal = 0;
811	>	painCave.severity = OPENMD_WARNING;
812	>	simError();
813	>	}
814	>
815	>	InteractionManager::Instance()->setSwitchingRadius(switchingRadius_);
816
817	+	SwitchingFunctionType ft;
818	+
819	+	if (simParams_->haveSwitchingFunctionType()) {
820	+	string funcType = simParams_->getSwitchingFunctionType();
821	+	toUpper(funcType);
822	+	if (funcType == "CUBIC") {
823	+	ft = cubic;
824	+	} else {
825	+	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
826	+	ft = fifth_order_poly;
827	+	} else {
828	+	// throw error
829	+	sprintf( painCave.errMsg,
830	+	"SimInfo : Unknown switchingFunctionType. (Input file specified %s .)\n"
831	+	"\tswitchingFunctionType must be one of: "
832	+	"\"cubic\" or \"fifth_order_polynomial\".",
833	+	funcType.c_str() );
834	+	painCave.isFatal = 1;
835	+	painCave.severity = OPENMD_ERROR;
836	+	simError();
837	+	}
838	+	}
839	+	}
840
841	<	#ifdef IS_MPI
842	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
395	<	#else
396	<	ndfTrans = ndfTrans_local;
397	<	#endif
841	>	InteractionManager::Instance()->setSwitchingFunctionType(ft);
842	>	}
843
844	<	ndfTrans = ndfTrans - 3 - nZconstraints;
844	>	/**
845	>	* setupSkinThickness
846	>	*
847	>	*  If the skinThickness was explicitly set, use that value (but check it)
848	>	*  If the skinThickness was not explicitly set: use 1.0 angstroms
849	>	*/
850	>	void SimInfo::setupSkinThickness() {
851	>	if (simParams_->haveSkinThickness()) {
852	>	skinThickness_ = simParams_->getSkinThickness();
853	>	} else {
854	>	skinThickness_ = 1.0;
855	>	sprintf(painCave.errMsg,
856	>	"SimInfo Warning: No value was set for the skinThickness.\n"
857	>	"\tOpenMD will use a default value of %f Angstroms\n"
858	>	"\tfor this simulation\n", skinThickness_);
859	>	painCave.isFatal = 0;
860	>	simError();
861	>	}
862	>	}
863
864	<	return ndfTrans;
865	<	}
864	>	void SimInfo::setupSimType() {
865	>	set<AtomType*>::iterator i;
866	>	set<AtomType*> atomTypes;
867	>	atomTypes = getSimulatedAtomTypes();
868
869	<	int SimInfo::getTotIntegrableObjects() {
405	<	int nObjs_local;
406	<	int nObjs;
869	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
870
871	<	nObjs_local =  integrableObjects.size();
871	>	int usesElectrostatic = 0;
872	>	int usesMetallic = 0;
873	>	int usesDirectional = 0;
874	>	//loop over all of the atom types
875	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
876	>	usesElectrostatic |= (*i)->isElectrostatic();
877	>	usesMetallic |= (*i)->isMetal();
878	>	usesDirectional |= (*i)->isDirectional();
879	>	}
880
881	+	#ifdef IS_MPI
882	+	int temp;
883	+	temp = usesDirectional;
884	+	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
885
886	<	#ifdef IS_MPI
887	<	MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
888	<	#else
889	<	nObjs = nObjs_local;
886	>	temp = usesMetallic;
887	>	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
888	>
889	>	temp = usesElectrostatic;
890	>	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
891		#endif
892	+	fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;
893	+	fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
894	+	fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
895	+	fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
896	+	fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
897	+	fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
898	+	}
899
900	+	void SimInfo::setupFortranSim() {
901	+	int isError;
902	+	int nExclude, nOneTwo, nOneThree, nOneFour;
903	+	vector<int> fortranGlobalGroupMembership;
904	+
905	+	notifyFortranSkinThickness(&skinThickness_);
906
907	<	return nObjs;
908	<	}
907	>	int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0;
908	>	int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0;
909	>	notifyFortranCutoffs(&cutoffRadius_, &switchingRadius_, &ljsp, &ljsf);
910
911	<	void SimInfo::refreshSim(){
911	>	isError = 0;
912
913	<	simtype fInfo;
914	<	int isError;
915	<	int n_global;
916	<	int* excl;
913	>	//globalGroupMembership_ is filled by SimCreator
914	>	for (int i = 0; i < nGlobalAtoms_; i++) {
915	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
916	>	}
917
918	<	fInfo.dielect = 0.0;
918	>	//calculate mass ratio of cutoff group
919	>	vector<RealType> mfact;
920	>	SimInfo::MoleculeIterator mi;
921	>	Molecule* mol;
922	>	Molecule::CutoffGroupIterator ci;
923	>	CutoffGroup* cg;
924	>	Molecule::AtomIterator ai;
925	>	Atom* atom;
926	>	RealType totalMass;
927
928	<	if( useDipoles ){
929	<	if( useReactionField )fInfo.dielect = dielectric;
930	<	}
928	>	//to avoid memory reallocation, reserve enough space for mfact
929	>	mfact.reserve(getNCutoffGroups());
930	>
931	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
932	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
933
934	<	fInfo.SIM_uses_PBC = usePBC;
935	<	//fInfo.SIM_uses_LJ = 0;
936	<	fInfo.SIM_uses_LJ = useLJ;
937	<	fInfo.SIM_uses_sticky = useSticky;
938	<	//fInfo.SIM_uses_sticky = 0;
939	<	fInfo.SIM_uses_charges = useCharges;
940	<	fInfo.SIM_uses_dipoles = useDipoles;
941	<	//fInfo.SIM_uses_dipoles = 0;
942	<	fInfo.SIM_uses_RF = useReactionField;
943	<	//fInfo.SIM_uses_RF = 0;
444	<	fInfo.SIM_uses_GB = useGB;
445	<	fInfo.SIM_uses_EAM = useEAM;
934	>	totalMass = cg->getMass();
935	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
936	>	// Check for massless groups - set mfact to 1 if true
937	>	if (totalMass != 0)
938	>	mfact.push_back(atom->getMass()/totalMass);
939	>	else
940	>	mfact.push_back( 1.0 );
941	>	}
942	>	}
943	>	}
944
945	<	n_exclude = excludes->getSize();
946	<	excl = excludes->getFortranArray();
449	<
450	<	#ifdef IS_MPI
451	<	n_global = mpiSim->getNAtomsGlobal();
452	<	#else
453	<	n_global = n_atoms;
454	<	#endif
455	<
456	<	isError = 0;
457	<
458	<	getFortranGroupArrays(this, FglobalGroupMembership, mfact);
459	<	//it may not be a good idea to pass the address of first element in vector
460	<	//since c++ standard does not require vector to be stored continuously in meomory
461	<	//Most of the compilers will organize the memory of vector continuously
462	<	setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
463	<	&nGlobalExcludes, globalExcludes, molMembershipArray,
464	<	&mfact[0], &ngroup, &FglobalGroupMembership[0], &isError);
945	>	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
946	>	vector<int> identArray;
947
948	<	if( isError ){
948	>	//to avoid memory reallocation, reserve enough space identArray
949	>	identArray.reserve(getNAtoms());
950
951	<	sprintf( painCave.errMsg,
952	<	"There was an error setting the simulation information in fortran.\n" );
953	<	painCave.isFatal = 1;
954	<	painCave.severity = OOPSE_ERROR;
955	<	simError();
473	<	}
474	<
475	<	#ifdef IS_MPI
476	<	sprintf( checkPointMsg,
477	<	"succesfully sent the simulation information to fortran.\n");
478	<	MPIcheckPoint();
479	<	#endif // is_mpi
480	<
481	<	this->ndf = this->getNDF();
482	<	this->ndfRaw = this->getNDFraw();
483	<	this->ndfTrans = this->getNDFtranslational();
484	<	}
951	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
952	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
953	>	identArray.push_back(atom->getIdent());
954	>	}
955	>	}
956
957	<	void SimInfo::setDefaultRcut( double theRcut ){
958	<
959	<	haveRcut = 1;
960	<	rCut = theRcut;
961	<	rList = rCut + 1.0;
962	<
963	<	notifyFortranCutOffs( &rCut, &rSw, &rList );
964	<	}
957	>	//fill molMembershipArray
958	>	//molMembershipArray is filled by SimCreator
959	>	vector<int> molMembershipArray(nGlobalAtoms_);
960	>	for (int i = 0; i < nGlobalAtoms_; i++) {
961	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
962	>	}
963	>
964	>	//setup fortran simulation
965
966	<	void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
966	>	nExclude = excludedInteractions_.getSize();
967	>	nOneTwo = oneTwoInteractions_.getSize();
968	>	nOneThree = oneThreeInteractions_.getSize();
969	>	nOneFour = oneFourInteractions_.getSize();
970
971	<	rSw = theRsw;
972	<	setDefaultRcut( theRcut );
973	<	}
971	>	int* excludeList = excludedInteractions_.getPairList();
972	>	int* oneTwoList = oneTwoInteractions_.getPairList();
973	>	int* oneThreeList = oneThreeInteractions_.getPairList();
974	>	int* oneFourList = oneFourInteractions_.getPairList();
975
976	<
977	<	void SimInfo::checkCutOffs( void ){
978	<
979	<	if( boxIsInit ){
976	>	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
977	>	&nExclude, excludeList,
978	>	&nOneTwo, oneTwoList,
979	>	&nOneThree, oneThreeList,
980	>	&nOneFour, oneFourList,
981	>	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
982	>	&fortranGlobalGroupMembership[0], &isError);
983
984	<	//we need to check cutOffs against the box
985	<
508	<	if( rCut > maxCutoff ){
984	>	if( isError ){
985	>
986		sprintf( painCave.errMsg,
987	<	"cutoffRadius is too large for the current periodic box.\n"
511	<	"\tCurrent Value of cutoffRadius = %G at time %G\n "
512	<	"\tThis is larger than half of at least one of the\n"
513	<	"\tperiodic box vectors.  Right now, the Box matrix is:\n"
514	<	"\n"
515	<	"\t[ %G %G %G ]\n"
516	<	"\t[ %G %G %G ]\n"
517	<	"\t[ %G %G %G ]\n",
518	<	rCut, currentTime,
519	<	Hmat[0][0], Hmat[0][1], Hmat[0][2],
520	<	Hmat[1][0], Hmat[1][1], Hmat[1][2],
521	<	Hmat[2][0], Hmat[2][1], Hmat[2][2]);
522	<	painCave.severity = OOPSE_ERROR;
987	>	"There was an error setting the simulation information in fortran.\n" );
988		painCave.isFatal = 1;
989	+	painCave.severity = OPENMD_ERROR;
990		simError();
991	<	}
992	<	} else {
993	<	// initialize this stuff before using it, OK?
994	<	sprintf( painCave.errMsg,
995	<	"Trying to check cutoffs without a box.\n"
996	<	"\tOOPSE should have better programmers than that.\n" );
997	<	painCave.severity = OOPSE_ERROR;
998	<	painCave.isFatal = 1;
999	<	simError();
991	>	}
992	>
993	>
994	>	sprintf( checkPointMsg,
995	>	"succesfully sent the simulation information to fortran.\n");
996	>
997	>	errorCheckPoint();
998	>
999	>	// Setup number of neighbors in neighbor list if present
1000	>	if (simParams_->haveNeighborListNeighbors()) {
1001	>	int nlistNeighbors = simParams_->getNeighborListNeighbors();
1002	>	setNeighbors(&nlistNeighbors);
1003	>	}
1004	>
1005	>
1006		}
535	–
536	–	}
1007
538	–	void SimInfo::addProperty(GenericData* prop){
1008
1009	<	map<string, GenericData*>::iterator result;
1010	<	result = properties.find(prop->getID());
1011	<
1012	<	//we can't simply use  properties[prop->getID()] = prop,
1013	<	//it will cause memory leak if we already contain a propery which has the same name of prop
1014	<
1015	<	if(result != properties.end()){
1016	<
1017	<	delete (*result).second;
1018	<	(*result).second = prop;
1019	<
1020	<	}
1021	<	else{
1009	>	void SimInfo::setupFortranParallel() {
1010	>	#ifdef IS_MPI
1011	>	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
1012	>	vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
1013	>	vector<int> localToGlobalCutoffGroupIndex;
1014	>	SimInfo::MoleculeIterator mi;
1015	>	Molecule::AtomIterator ai;
1016	>	Molecule::CutoffGroupIterator ci;
1017	>	Molecule* mol;
1018	>	Atom* atom;
1019	>	CutoffGroup* cg;
1020	>	mpiSimData parallelData;
1021	>	int isError;
1022
1023	<	properties[prop->getID()] = prop;
1023	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
1024
1025	+	//local index(index in DataStorge) of atom is important
1026	+	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
1027	+	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
1028	+	}
1029	+
1030	+	//local index of cutoff group is trivial, it only depends on the order of travesing
1031	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
1032	+	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
1033	+	}
1034	+
1035	+	}
1036	+
1037	+	//fill up mpiSimData struct
1038	+	parallelData.nMolGlobal = getNGlobalMolecules();
1039	+	parallelData.nMolLocal = getNMolecules();
1040	+	parallelData.nAtomsGlobal = getNGlobalAtoms();
1041	+	parallelData.nAtomsLocal = getNAtoms();
1042	+	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
1043	+	parallelData.nGroupsLocal = getNCutoffGroups();
1044	+	parallelData.myNode = worldRank;
1045	+	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
1046	+
1047	+	//pass mpiSimData struct and index arrays to fortran
1048	+	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
1049	+	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
1050	+	&localToGlobalCutoffGroupIndex[0], &isError);
1051	+
1052	+	if (isError) {
1053	+	sprintf(painCave.errMsg,
1054	+	"mpiRefresh errror: fortran didn't like something we gave it.\n");
1055	+	painCave.isFatal = 1;
1056	+	simError();
1057	+	}
1058	+
1059	+	sprintf(checkPointMsg, " mpiRefresh successful.\n");
1060	+	errorCheckPoint();
1061	+
1062	+	#endif
1063		}
1064	+
1065	+
1066	+	void SimInfo::setupSwitchingFunction() {
1067	+
1068	+	}
1069	+
1070	+	void SimInfo::setupAccumulateBoxDipole() {
1071	+
1072	+	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1073	+	if ( simParams_->haveAccumulateBoxDipole() )
1074	+	if ( simParams_->getAccumulateBoxDipole() ) {
1075	+	calcBoxDipole_ = true;
1076	+	}
1077	+
1078	+	}
1079	+
1080	+	void SimInfo::addProperty(GenericData* genData) {
1081	+	properties_.addProperty(genData);
1082	+	}
1083	+
1084	+	void SimInfo::removeProperty(const string& propName) {
1085	+	properties_.removeProperty(propName);
1086	+	}
1087	+
1088	+	void SimInfo::clearProperties() {
1089	+	properties_.clearProperties();
1090	+	}
1091	+
1092	+	vector<string> SimInfo::getPropertyNames() {
1093	+	return properties_.getPropertyNames();
1094	+	}
1095	+
1096	+	vector<GenericData*> SimInfo::getProperties() {
1097	+	return properties_.getProperties();
1098	+	}
1099	+
1100	+	GenericData* SimInfo::getPropertyByName(const string& propName) {
1101	+	return properties_.getPropertyByName(propName);
1102	+	}
1103	+
1104	+	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1105	+	if (sman_ == sman) {
1106	+	return;
1107	+	}
1108	+	delete sman_;
1109	+	sman_ = sman;
1110	+
1111	+	Molecule* mol;
1112	+	RigidBody* rb;
1113	+	Atom* atom;
1114	+	SimInfo::MoleculeIterator mi;
1115	+	Molecule::RigidBodyIterator rbIter;
1116	+	Molecule::AtomIterator atomIter;;
1117	+
1118	+	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1119	+
1120	+	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1121	+	atom->setSnapshotManager(sman_);
1122	+	}
1123	+
1124	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1125	+	rb->setSnapshotManager(sman_);
1126	+	}
1127	+	}
1128
1129	<	}
1129	>	}
1130
1131	<	GenericData* SimInfo::getProperty(const string& propName){
1131	>	Vector3d SimInfo::getComVel(){
1132	>	SimInfo::MoleculeIterator i;
1133	>	Molecule* mol;
1134	>
1135	>	Vector3d comVel(0.0);
1136	>	RealType totalMass = 0.0;
1137	>
1138
1139	<	map<string, GenericData*>::iterator result;
1140	<
1141	<	//string lowerCaseName = ();
1142	<
1143	<	result = properties.find(propName);
567	<
568	<	if(result != properties.end())
569	<	return (*result).second;
570	<	else
571	<	return NULL;
572	<	}
1139	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1140	>	RealType mass = mol->getMass();
1141	>	totalMass += mass;
1142	>	comVel += mass * mol->getComVel();
1143	>	}
1144
1145	+	#ifdef IS_MPI
1146	+	RealType tmpMass = totalMass;
1147	+	Vector3d tmpComVel(comVel);
1148	+	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1149	+	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1150	+	#endif
1151
1152	<	void SimInfo::getFortranGroupArrays(SimInfo* info,
576	<	vector<int>& FglobalGroupMembership,
577	<	vector<double>& mfact){
578	<
579	<	Molecule* myMols;
580	<	Atom** myAtoms;
581	<	int numAtom;
582	<	double mtot;
583	<	int numMol;
584	<	int numCutoffGroups;
585	<	CutoffGroup* myCutoffGroup;
586	<	vector<CutoffGroup*>::iterator iterCutoff;
587	<	Atom* cutoffAtom;
588	<	vector<Atom*>::iterator iterAtom;
589	<	int atomIndex;
590	<	double totalMass;
591	<
592	<	mfact.clear();
593	<	FglobalGroupMembership.clear();
594	<
1152	>	comVel /= totalMass;
1153
1154	<	// Fix the silly fortran indexing problem
1154	>	return comVel;
1155	>	}
1156	>
1157	>	Vector3d SimInfo::getCom(){
1158	>	SimInfo::MoleculeIterator i;
1159	>	Molecule* mol;
1160	>
1161	>	Vector3d com(0.0);
1162	>	RealType totalMass = 0.0;
1163	>
1164	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1165	>	RealType mass = mol->getMass();
1166	>	totalMass += mass;
1167	>	com += mass * mol->getCom();
1168	>	}
1169	>
1170		#ifdef IS_MPI
1171	<	numAtom = mpiSim->getNAtomsGlobal();
1172	<	#else
1173	<	numAtom = n_atoms;
1171	>	RealType tmpMass = totalMass;
1172	>	Vector3d tmpCom(com);
1173	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1174	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1175		#endif
602	–	for (int i = 0; i < numAtom; i++)
603	–	FglobalGroupMembership.push_back(globalGroupMembership[i] + 1);
604	–
1176
1177	<	myMols = info->molecules;
607	<	numMol = info->n_mol;
608	<	for(int i  = 0; i < numMol; i++){
609	<	numCutoffGroups = myMols[i].getNCutoffGroups();
610	<	for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff);
611	<	myCutoffGroup != NULL;
612	<	myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
1177	>	com /= totalMass;
1178
1179	<	totalMass = myCutoffGroup->getMass();
1179	>	return com;
1180	>
1181	>	}
1182	>
1183	>	ostream& operator <<(ostream& o, SimInfo& info) {
1184	>
1185	>	return o;
1186	>	}
1187	>
1188	>
1189	>	/*
1190	>	Returns center of mass and center of mass velocity in one function call.
1191	>	*/
1192	>
1193	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1194	>	SimInfo::MoleculeIterator i;
1195	>	Molecule* mol;
1196
1197	<	for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom);
1198	<	cutoffAtom != NULL;
1199	<	cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
1200	<	mfact.push_back(cutoffAtom->getMass()/totalMass);
1197	>
1198	>	RealType totalMass = 0.0;
1199	>
1200	>
1201	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1202	>	RealType mass = mol->getMass();
1203	>	totalMass += mass;
1204	>	com += mass * mol->getCom();
1205	>	comVel += mass * mol->getComVel();
1206		}
1207	+
1208	+	#ifdef IS_MPI
1209	+	RealType tmpMass = totalMass;
1210	+	Vector3d tmpCom(com);
1211	+	Vector3d tmpComVel(comVel);
1212	+	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1213	+	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1214	+	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1215	+	#endif
1216	+
1217	+	com /= totalMass;
1218	+	comVel /= totalMass;
1219	+	}
1220	+
1221	+	/*
1222	+	Return intertia tensor for entire system and angular momentum Vector.
1223	+
1224	+
1225	+	[  Ixx -Ixy  -Ixz ]
1226	+	J =| -Iyx  Iyy  -Iyz |
1227	+	[ -Izx -Iyz   Izz ]
1228	+	*/
1229	+
1230	+	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1231	+
1232	+
1233	+	RealType xx = 0.0;
1234	+	RealType yy = 0.0;
1235	+	RealType zz = 0.0;
1236	+	RealType xy = 0.0;
1237	+	RealType xz = 0.0;
1238	+	RealType yz = 0.0;
1239	+	Vector3d com(0.0);
1240	+	Vector3d comVel(0.0);
1241	+
1242	+	getComAll(com, comVel);
1243	+
1244	+	SimInfo::MoleculeIterator i;
1245	+	Molecule* mol;
1246	+
1247	+	Vector3d thisq(0.0);
1248	+	Vector3d thisv(0.0);
1249	+
1250	+	RealType thisMass = 0.0;
1251	+
1252	+
1253	+
1254	+
1255	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1256	+
1257	+	thisq = mol->getCom()-com;
1258	+	thisv = mol->getComVel()-comVel;
1259	+	thisMass = mol->getMass();
1260	+	// Compute moment of intertia coefficients.
1261	+	xx += thisq[0]*thisq[0]*thisMass;
1262	+	yy += thisq[1]*thisq[1]*thisMass;
1263	+	zz += thisq[2]*thisq[2]*thisMass;
1264	+
1265	+	// compute products of intertia
1266	+	xy += thisq[0]*thisq[1]*thisMass;
1267	+	xz += thisq[0]*thisq[2]*thisMass;
1268	+	yz += thisq[1]*thisq[2]*thisMass;
1269	+
1270	+	angularMomentum += cross( thisq, thisv ) * thisMass;
1271	+
1272	+	}
1273	+
1274	+
1275	+	inertiaTensor(0,0) = yy + zz;
1276	+	inertiaTensor(0,1) = -xy;
1277	+	inertiaTensor(0,2) = -xz;
1278	+	inertiaTensor(1,0) = -xy;
1279	+	inertiaTensor(1,1) = xx + zz;
1280	+	inertiaTensor(1,2) = -yz;
1281	+	inertiaTensor(2,0) = -xz;
1282	+	inertiaTensor(2,1) = -yz;
1283	+	inertiaTensor(2,2) = xx + yy;
1284	+
1285	+	#ifdef IS_MPI
1286	+	Mat3x3d tmpI(inertiaTensor);
1287	+	Vector3d tmpAngMom;
1288	+	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1289	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1290	+	#endif
1291	+
1292	+	return;
1293	+	}
1294	+
1295	+	//Returns the angular momentum of the system
1296	+	Vector3d SimInfo::getAngularMomentum(){
1297	+
1298	+	Vector3d com(0.0);
1299	+	Vector3d comVel(0.0);
1300	+	Vector3d angularMomentum(0.0);
1301	+
1302	+	getComAll(com,comVel);
1303	+
1304	+	SimInfo::MoleculeIterator i;
1305	+	Molecule* mol;
1306	+
1307	+	Vector3d thisr(0.0);
1308	+	Vector3d thisp(0.0);
1309	+
1310	+	RealType thisMass;
1311	+
1312	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1313	+	thisMass = mol->getMass();
1314	+	thisr = mol->getCom()-com;
1315	+	thisp = (mol->getComVel()-comVel)*thisMass;
1316	+
1317	+	angularMomentum += cross( thisr, thisp );
1318	+
1319	+	}
1320	+
1321	+	#ifdef IS_MPI
1322	+	Vector3d tmpAngMom;
1323	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1324	+	#endif
1325	+
1326	+	return angularMomentum;
1327	+	}
1328	+
1329	+	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1330	+	return IOIndexToIntegrableObject.at(index);
1331	+	}
1332	+
1333	+	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1334	+	IOIndexToIntegrableObject= v;
1335	+	}
1336	+
1337	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1338	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1339	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1340	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1341	+	*/
1342	+	void SimInfo::getGyrationalVolume(RealType &volume){
1343	+	Mat3x3d intTensor;
1344	+	RealType det;
1345	+	Vector3d dummyAngMom;
1346	+	RealType sysconstants;
1347	+	RealType geomCnst;
1348	+
1349	+	geomCnst = 3.0/2.0;
1350	+	/* Get the inertial tensor and angular momentum for free*/
1351	+	getInertiaTensor(intTensor,dummyAngMom);
1352	+
1353	+	det = intTensor.determinant();
1354	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1355	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1356	+	return;
1357	+	}
1358	+
1359	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1360	+	Mat3x3d intTensor;
1361	+	Vector3d dummyAngMom;
1362	+	RealType sysconstants;
1363	+	RealType geomCnst;
1364	+
1365	+	geomCnst = 3.0/2.0;
1366	+	/* Get the inertial tensor and angular momentum for free*/
1367	+	getInertiaTensor(intTensor,dummyAngMom);
1368	+
1369	+	detI = intTensor.determinant();
1370	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1371	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1372	+	return;
1373	+	}
1374	+	/*
1375	+	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1376	+	assert( v.size() == nAtoms_ + nRigidBodies_);
1377	+	sdByGlobalIndex_ = v;
1378		}
1379	+
1380	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1381	+	//assert(index < nAtoms_ + nRigidBodies_);
1382	+	return sdByGlobalIndex_.at(index);
1383	+	}
1384	+	*/
1385	+	int SimInfo::getNGlobalConstraints() {
1386	+	int nGlobalConstraints;
1387	+	#ifdef IS_MPI
1388	+	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1389	+	MPI_COMM_WORLD);
1390	+	#else
1391	+	nGlobalConstraints =  nConstraints_;
1392	+	#endif
1393	+	return nGlobalConstraints;
1394		}
1395
1396	<	}
1396	>	}//end namespace OpenMD
1397	>

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 2 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1532 by gezelter, Wed Dec 29 19:59:21 2010 UTC

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