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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 1569 by gezelter, Thu May 26 13:55:04 2011 UTC

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

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 1569 by gezelter, Thu May 26 13:55:04 2011 UTC

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