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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 3 by tim, Fri Sep 24 16:27:58 2004 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1769 by gezelter, Mon Jul 9 14:15:52 2012 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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	>	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	>	*/
42	>
43	>	/**
44	>	* @file SimInfo.cpp
45	>	* @author    tlin
46	>	* @date  11/02/2004
47	>	* @version 1.0
48	>	*/
49
50	<	#include <iostream>
51	<	using namespace std;
50	>	#include <algorithm>
51	>	#include <set>
52	>	#include <map>
53
54		#include "brains/SimInfo.hpp"
55	<	#define __C
56	<	#include "brains/fSimulation.h"
55	>	#include "math/Vector3.hpp"
56	>	#include "primitives/Molecule.hpp"
57	>	#include "primitives/StuntDouble.hpp"
58	>	#include "utils/MemoryUtils.hpp"
59		#include "utils/simError.h"
60	<
61	<	#include "UseTheForce/fortranWrappers.hpp"
62	<
63	<	#include "math/MatVec3.h"
16	<
60	>	#include "selection/SelectionManager.hpp"
61	>	#include "io/ForceFieldOptions.hpp"
62	>	#include "brains/ForceField.hpp"
63	>	#include "nonbonded/SwitchingFunction.hpp"
64		#ifdef IS_MPI
65	<	#include "brains/mpiSimulation.hpp"
65	>	#include <mpi.h>
66		#endif
67
68	<	inline double roundMe( double x ){
69	<	return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
70	<	}
71	<
72	<	inline double min( double a, double b ){
73	<	return (a < b ) ? a : b;
74	<	}
68	>	using namespace std;
69	>	namespace OpenMD {
70	>
71	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
72	>	forceField_(ff), simParams_(simParams),
73	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
74	>	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
75	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), nGlobalFluctuatingCharges_(0),
76	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
77	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
78	>	nConstraints_(0), nFluctuatingCharges_(0), sman_(NULL), topologyDone_(false),
79	>	calcBoxDipole_(false), useAtomicVirial_(true) {
80	>
81	>	MoleculeStamp* molStamp;
82	>	int nMolWithSameStamp;
83	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
84	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
85	>	CutoffGroupStamp* cgStamp;
86	>	RigidBodyStamp* rbStamp;
87	>	int nRigidAtoms = 0;
88	>
89	>	vector<Component*> components = simParams->getComponents();
90	>
91	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
92	>	molStamp = (*i)->getMoleculeStamp();
93	>	nMolWithSameStamp = (*i)->getNMol();
94	>
95	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
96	>
97	>	//calculate atoms in molecules
98	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
99	>
100	>	//calculate atoms in cutoff groups
101	>	int nAtomsInGroups = 0;
102	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
103	>
104	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
105	>	cgStamp = molStamp->getCutoffGroupStamp(j);
106	>	nAtomsInGroups += cgStamp->getNMembers();
107	>	}
108	>
109	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
110	>
111	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
112	>
113	>	//calculate atoms in rigid bodies
114	>	int nAtomsInRigidBodies = 0;
115	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
116	>
117	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
118	>	rbStamp = molStamp->getRigidBodyStamp(j);
119	>	nAtomsInRigidBodies += rbStamp->getNMembers();
120	>	}
121	>
122	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
123	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
124	>
125	>	}
126	>
127	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
128	>	//group therefore the total number of cutoff groups in the system is
129	>	//equal to the total number of atoms minus number of atoms belong to
130	>	//cutoff group defined in meta-data file plus the number of cutoff
131	>	//groups defined in meta-data file
132
133	<	SimInfo* currentInfo;
133	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
134	>
135	>	//every free atom (atom does not belong to rigid bodies) is an
136	>	//integrable object therefore the total number of integrable objects
137	>	//in the system is equal to the total number of atoms minus number of
138	>	//atoms belong to rigid body defined in meta-data file plus the number
139	>	//of rigid bodies defined in meta-data file
140	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
141	>	+ nGlobalRigidBodies_;
142	>
143	>	nGlobalMols_ = molStampIds_.size();
144	>	molToProcMap_.resize(nGlobalMols_);
145	>	}
146	>
147	>	SimInfo::~SimInfo() {
148	>	map<int, Molecule*>::iterator i;
149	>	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
150	>	delete i->second;
151	>	}
152	>	molecules_.clear();
153	>
154	>	delete sman_;
155	>	delete simParams_;
156	>	delete forceField_;
157	>	}
158
31	–	SimInfo::SimInfo(){
159
160	<	n_constraints = 0;
161	<	nZconstraints = 0;
162	<	n_oriented = 0;
163	<	n_dipoles = 0;
164	<	ndf = 0;
165	<	ndfRaw = 0;
166	<	nZconstraints = 0;
167	<	the_integrator = NULL;
168	<	setTemp = 0;
169	<	thermalTime = 0.0;
170	<	currentTime = 0.0;
171	<	rCut = 0.0;
172	<	rSw = 0.0;
173	<
174	<	haveRcut = 0;
175	<	haveRsw = 0;
176	<	boxIsInit = 0;
160	>	bool SimInfo::addMolecule(Molecule* mol) {
161	>	MoleculeIterator i;
162	>
163	>	i = molecules_.find(mol->getGlobalIndex());
164	>	if (i == molecules_.end() ) {
165	>
166	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
167	>
168	>	nAtoms_ += mol->getNAtoms();
169	>	nBonds_ += mol->getNBonds();
170	>	nBends_ += mol->getNBends();
171	>	nTorsions_ += mol->getNTorsions();
172	>	nInversions_ += mol->getNInversions();
173	>	nRigidBodies_ += mol->getNRigidBodies();
174	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
175	>	nCutoffGroups_ += mol->getNCutoffGroups();
176	>	nConstraints_ += mol->getNConstraintPairs();
177	>
178	>	addInteractionPairs(mol);
179	>
180	>	return true;
181	>	} else {
182	>	return false;
183	>	}
184	>	}
185
186	<	resetTime = 1e99;
186	>	bool SimInfo::removeMolecule(Molecule* mol) {
187	>	MoleculeIterator i;
188	>	i = molecules_.find(mol->getGlobalIndex());
189
190	<	orthoRhombic = 0;
54	<	orthoTolerance = 1E-6;
55	<	useInitXSstate = true;
190	>	if (i != molecules_.end() ) {
191
192	<	usePBC = 0;
193	<	useLJ = 0;
194	<	useSticky = 0;
195	<	useCharges = 0;
196	<	useDipoles = 0;
197	<	useReactionField = 0;
198	<	useGB = 0;
199	<	useEAM = 0;
200	<	useSolidThermInt = 0;
201	<	useLiquidThermInt = 0;
192	>	assert(mol == i->second);
193	>
194	>	nAtoms_ -= mol->getNAtoms();
195	>	nBonds_ -= mol->getNBonds();
196	>	nBends_ -= mol->getNBends();
197	>	nTorsions_ -= mol->getNTorsions();
198	>	nInversions_ -= mol->getNInversions();
199	>	nRigidBodies_ -= mol->getNRigidBodies();
200	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
201	>	nCutoffGroups_ -= mol->getNCutoffGroups();
202	>	nConstraints_ -= mol->getNConstraintPairs();
203
204	<	haveCutoffGroups = false;
204	>	removeInteractionPairs(mol);
205	>	molecules_.erase(mol->getGlobalIndex());
206
207	<	excludes = Exclude::Instance();
207	>	delete mol;
208	>
209	>	return true;
210	>	} else {
211	>	return false;
212	>	}
213	>	}
214
215	<	myConfiguration = new SimState();
215	>
216	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
217	>	i = molecules_.begin();
218	>	return i == molecules_.end() ? NULL : i->second;
219	>	}
220
221	<	has_minimizer = false;
222	<	the_minimizer =NULL;
221	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
222	>	++i;
223	>	return i == molecules_.end() ? NULL : i->second;
224	>	}
225
77	–	ngroup = 0;
226
227	<	wrapMeSimInfo( this );
228	<	}
227	>	void SimInfo::calcNdf() {
228	>	int ndf_local, nfq_local;
229	>	MoleculeIterator i;
230	>	vector<StuntDouble*>::iterator j;
231	>	vector<Atom*>::iterator k;
232
233	+	Molecule* mol;
234	+	StuntDouble* sd;
235	+	Atom* atom;
236
237	<	SimInfo::~SimInfo(){
237	>	ndf_local = 0;
238	>	nfq_local = 0;
239	>
240	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
241
242	<	delete myConfiguration;
242	>	for (sd = mol->beginIntegrableObject(j); sd != NULL;
243	>	sd = mol->nextIntegrableObject(j)) {
244
245	<	map<string, GenericData*>::iterator i;
88	<
89	<	for(i = properties.begin(); i != properties.end(); i++)
90	<	delete (*i).second;
245	>	ndf_local += 3;
246
247	<	}
247	>	if (sd->isDirectional()) {
248	>	if (sd->isLinear()) {
249	>	ndf_local += 2;
250	>	} else {
251	>	ndf_local += 3;
252	>	}
253	>	}
254	>	}
255
256	<	void SimInfo::setBox(double newBox[3]) {
257	<
258	<	int i, j;
259	<	double tempMat[3][3];
256	>	for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
257	>	atom = mol->nextFluctuatingCharge(k)) {
258	>	if (atom->isFluctuatingCharge()) {
259	>	nfq_local++;
260	>	}
261	>	}
262	>	}
263	>
264	>	ndfLocal_ = ndf_local;
265
266	<	for(i=0; i<3; i++)
267	<	for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
266	>	// n_constraints is local, so subtract them on each processor
267	>	ndf_local -= nConstraints_;
268
269	<	tempMat[0][0] = newBox[0];
270	<	tempMat[1][1] = newBox[1];
271	<	tempMat[2][2] = newBox[2];
269	>	#ifdef IS_MPI
270	>	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
271	>	MPI_Allreduce(&nfq_local,&nGlobalFluctuatingCharges_,1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
272	>	#else
273	>	ndf_ = ndf_local;
274	>	nGlobalFluctuatingCharges_ = nfq_local;
275	>	#endif
276
277	<	setBoxM( tempMat );
277	>	// nZconstraints_ is global, as are the 3 COM translations for the
278	>	// entire system:
279	>	ndf_ = ndf_ - 3 - nZconstraint_;
280
281	<	}
281	>	}
282
283	<	void SimInfo::setBoxM( double theBox[3][3] ){
283	>	int SimInfo::getFdf() {
284	>	#ifdef IS_MPI
285	>	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
286	>	#else
287	>	fdf_ = fdf_local;
288	>	#endif
289	>	return fdf_;
290	>	}
291
292	<	int i, j;
293	<	double FortranHmat[9]; // to preserve compatibility with Fortran the
294	<	// ordering in the array is as follows:
295	<	// [ 0 3 6 ]
296	<	// [ 1 4 7 ]
297	<	// [ 2 5 8 ]
298	<	double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
299	<
300	<	if( !boxIsInit ) boxIsInit = 1;
301	<
302	<	for(i=0; i < 3; i++)
303	<	for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
304	<
305	<	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];
292	>	unsigned int SimInfo::getNLocalCutoffGroups(){
293	>	int nLocalCutoffAtoms = 0;
294	>	Molecule* mol;
295	>	MoleculeIterator mi;
296	>	CutoffGroup* cg;
297	>	Molecule::CutoffGroupIterator ci;
298	>
299	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
300	>
301	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
302	>	cg = mol->nextCutoffGroup(ci)) {
303	>	nLocalCutoffAtoms += cg->getNumAtom();
304	>
305	>	}
306		}
307	+
308	+	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
309		}
310	+
311	+	void SimInfo::calcNdfRaw() {
312	+	int ndfRaw_local;
313
314	<	setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
315	<
316	<	}
317	<
314	>	MoleculeIterator i;
315	>	vector<StuntDouble*>::iterator j;
316	>	Molecule* mol;
317	>	StuntDouble* sd;
318
319	<	void SimInfo::getBoxM (double theBox[3][3]) {
319	>	// Raw degrees of freedom that we have to set
320	>	ndfRaw_local = 0;
321	>
322	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
323
324	<	int i, j;
325	<	for(i=0; i<3; i++)
144	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
145	<	}
324	>	for (sd = mol->beginIntegrableObject(j); sd != NULL;
325	>	sd = mol->nextIntegrableObject(j)) {
326
327	+	ndfRaw_local += 3;
328
329	<	void SimInfo::scaleBox(double scale) {
330	<	double theBox[3][3];
331	<	int i, j;
332	<
333	<	// cerr << "Scaling box by " << scale << "\n";
334	<
335	<	for(i=0; i<3; i++)
336	<	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	<	}
329	>	if (sd->isDirectional()) {
330	>	if (sd->isLinear()) {
331	>	ndfRaw_local += 2;
332	>	} else {
333	>	ndfRaw_local += 3;
334	>	}
335	>	}
336	>
337		}
338		}
190	–	}
191	–
192	–	if( oldOrtho != orthoRhombic ){
339
340	<	if( orthoRhombic ) {
341	<	sprintf( painCave.errMsg,
342	<	"OOPSE is switching from the default Non-Orthorhombic\n"
343	<	"\tto the faster Orthorhombic periodic boundary computations.\n"
344	<	"\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	<	}
340	>	#ifdef IS_MPI
341	>	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
342	>	#else
343	>	ndfRaw_ = ndfRaw_local;
344	>	#endif
345		}
218	–	}
346
347	<	void SimInfo::calcBoxL( void ){
347	>	void SimInfo::calcNdfTrans() {
348	>	int ndfTrans_local;
349
350	<	double dx, dy, dz, dsq;
350	>	ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
351
224	–	// boxVol = Determinant of Hmat
352
353	<	boxVol = matDet3( Hmat );
353	>	#ifdef IS_MPI
354	>	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
355	>	#else
356	>	ndfTrans_ = ndfTrans_local;
357	>	#endif
358
359	<	// boxLx
360	<
361	<	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];
359	>	ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
360	>
361	>	}
362
363	<	// boxLy
364	<
365	<	dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
366	<	dsq = dx*dx + dy*dy + dz*dz;
367	<	boxL[1] = sqrt( dsq );
368	<	//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
363	>	void SimInfo::addInteractionPairs(Molecule* mol) {
364	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
365	>	vector<Bond*>::iterator bondIter;
366	>	vector<Bend*>::iterator bendIter;
367	>	vector<Torsion*>::iterator torsionIter;
368	>	vector<Inversion*>::iterator inversionIter;
369	>	Bond* bond;
370	>	Bend* bend;
371	>	Torsion* torsion;
372	>	Inversion* inversion;
373	>	int a;
374	>	int b;
375	>	int c;
376	>	int d;
377
378	+	// atomGroups can be used to add special interaction maps between
379	+	// groups of atoms that are in two separate rigid bodies.
380	+	// However, most site-site interactions between two rigid bodies
381	+	// are probably not special, just the ones between the physically
382	+	// bonded atoms.  Interactions *within* a single rigid body should
383	+	// always be excluded.  These are done at the bottom of this
384	+	// function.
385
386	<	// boxLz
387	<
388	<	dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
389	<	dsq = dx*dx + dy*dy + dz*dz;
390	<	boxL[2] = sqrt( dsq );
391	<	//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
386	>	map<int, set<int> > atomGroups;
387	>	Molecule::RigidBodyIterator rbIter;
388	>	RigidBody* rb;
389	>	Molecule::IntegrableObjectIterator ii;
390	>	StuntDouble* sd;
391	>
392	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
393	>	sd = mol->nextIntegrableObject(ii)) {
394	>
395	>	if (sd->isRigidBody()) {
396	>	rb = static_cast<RigidBody*>(sd);
397	>	vector<Atom*> atoms = rb->getAtoms();
398	>	set<int> rigidAtoms;
399	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
400	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
401	>	}
402	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
403	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
404	>	}
405	>	} else {
406	>	set<int> oneAtomSet;
407	>	oneAtomSet.insert(sd->getGlobalIndex());
408	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
409	>	}
410	>	}
411	>
412	>	for (bond= mol->beginBond(bondIter); bond != NULL;
413	>	bond = mol->nextBond(bondIter)) {
414
415	<	//calculate the max cutoff
416	<	maxCutoff =  calcMaxCutOff();
417	<
418	<	checkCutOffs();
415	>	a = bond->getAtomA()->getGlobalIndex();
416	>	b = bond->getAtomB()->getGlobalIndex();
417	>
418	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
419	>	oneTwoInteractions_.addPair(a, b);
420	>	} else {
421	>	excludedInteractions_.addPair(a, b);
422	>	}
423	>	}
424
425	<	}
425	>	for (bend= mol->beginBend(bendIter); bend != NULL;
426	>	bend = mol->nextBend(bendIter)) {
427
428	+	a = bend->getAtomA()->getGlobalIndex();
429	+	b = bend->getAtomB()->getGlobalIndex();
430	+	c = bend->getAtomC()->getGlobalIndex();
431	+
432	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
433	+	oneTwoInteractions_.addPair(a, b);
434	+	oneTwoInteractions_.addPair(b, c);
435	+	} else {
436	+	excludedInteractions_.addPair(a, b);
437	+	excludedInteractions_.addPair(b, c);
438	+	}
439
440	<	double SimInfo::calcMaxCutOff(){
440	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
441	>	oneThreeInteractions_.addPair(a, c);
442	>	} else {
443	>	excludedInteractions_.addPair(a, c);
444	>	}
445	>	}
446
447	<	double ri[3], rj[3], rk[3];
448	<	double rij[3], rjk[3], rki[3];
262	<	double minDist;
447	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
448	>	torsion = mol->nextTorsion(torsionIter)) {
449
450	<	ri[0] = Hmat[0][0];
451	<	ri[1] = Hmat[1][0];
452	<	ri[2] = Hmat[2][0];
450	>	a = torsion->getAtomA()->getGlobalIndex();
451	>	b = torsion->getAtomB()->getGlobalIndex();
452	>	c = torsion->getAtomC()->getGlobalIndex();
453	>	d = torsion->getAtomD()->getGlobalIndex();
454
455	<	rj[0] = Hmat[0][1];
456	<	rj[1] = Hmat[1][1];
457	<	rj[2] = Hmat[2][1];
455	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
456	>	oneTwoInteractions_.addPair(a, b);
457	>	oneTwoInteractions_.addPair(b, c);
458	>	oneTwoInteractions_.addPair(c, d);
459	>	} else {
460	>	excludedInteractions_.addPair(a, b);
461	>	excludedInteractions_.addPair(b, c);
462	>	excludedInteractions_.addPair(c, d);
463	>	}
464
465	<	rk[0] = Hmat[0][2];
466	<	rk[1] = Hmat[1][2];
467	<	rk[2] = Hmat[2][2];
468	<
469	<	crossProduct3(ri, rj, rij);
470	<	distXY = dotProduct3(rk,rij) / norm3(rij);
465	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
466	>	oneThreeInteractions_.addPair(a, c);
467	>	oneThreeInteractions_.addPair(b, d);
468	>	} else {
469	>	excludedInteractions_.addPair(a, c);
470	>	excludedInteractions_.addPair(b, d);
471	>	}
472
473	<	crossProduct3(rj,rk, rjk);
474	<	distYZ = dotProduct3(ri,rjk) / norm3(rjk);
473	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
474	>	oneFourInteractions_.addPair(a, d);
475	>	} else {
476	>	excludedInteractions_.addPair(a, d);
477	>	}
478	>	}
479
480	<	crossProduct3(rk,ri, rki);
481	<	distZX = dotProduct3(rj,rki) / norm3(rki);
480	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
481	>	inversion = mol->nextInversion(inversionIter)) {
482
483	<	minDist = min(min(distXY, distYZ), distZX);
484	<	return minDist/2;
485	<
486	<	}
483	>	a = inversion->getAtomA()->getGlobalIndex();
484	>	b = inversion->getAtomB()->getGlobalIndex();
485	>	c = inversion->getAtomC()->getGlobalIndex();
486	>	d = inversion->getAtomD()->getGlobalIndex();
487
488	<	void SimInfo::wrapVector( double thePos[3] ){
488	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
489	>	oneTwoInteractions_.addPair(a, b);
490	>	oneTwoInteractions_.addPair(a, c);
491	>	oneTwoInteractions_.addPair(a, d);
492	>	} else {
493	>	excludedInteractions_.addPair(a, b);
494	>	excludedInteractions_.addPair(a, c);
495	>	excludedInteractions_.addPair(a, d);
496	>	}
497
498	<	int i;
499	<	double scaled[3];
498	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
499	>	oneThreeInteractions_.addPair(b, c);
500	>	oneThreeInteractions_.addPair(b, d);
501	>	oneThreeInteractions_.addPair(c, d);
502	>	} else {
503	>	excludedInteractions_.addPair(b, c);
504	>	excludedInteractions_.addPair(b, d);
505	>	excludedInteractions_.addPair(c, d);
506	>	}
507	>	}
508
509	<	if( !orthoRhombic ){
510	<	// calc the scaled coordinates.
511	<
509	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
510	>	rb = mol->nextRigidBody(rbIter)) {
511	>	vector<Atom*> atoms = rb->getAtoms();
512	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
513	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
514	>	a = atoms[i]->getGlobalIndex();
515	>	b = atoms[j]->getGlobalIndex();
516	>	excludedInteractions_.addPair(a, b);
517	>	}
518	>	}
519	>	}
520
299	–	matVecMul3(HmatInv, thePos, scaled);
300	–
301	–	for(i=0; i<3; i++)
302	–	scaled[i] -= roundMe(scaled[i]);
303	–
304	–	// calc the wrapped real coordinates from the wrapped scaled coordinates
305	–
306	–	matVecMul3(Hmat, scaled, thePos);
307	–
521		}
309	–	else{
310	–	// calc the scaled coordinates.
311	–
312	–	for(i=0; i<3; i++)
313	–	scaled[i] = thePos[i]*HmatInv[i][i];
314	–
315	–	// wrap the scaled coordinates
316	–
317	–	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	–	}
522
523	+	void SimInfo::removeInteractionPairs(Molecule* mol) {
524	+	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
525	+	vector<Bond*>::iterator bondIter;
526	+	vector<Bend*>::iterator bendIter;
527	+	vector<Torsion*>::iterator torsionIter;
528	+	vector<Inversion*>::iterator inversionIter;
529	+	Bond* bond;
530	+	Bend* bend;
531	+	Torsion* torsion;
532	+	Inversion* inversion;
533	+	int a;
534	+	int b;
535	+	int c;
536	+	int d;
537
538	<	int SimInfo::getNDF(){
539	<	int ndf_local;
540	<
541	<	ndf_local = 0;
542	<
543	<	for(int i = 0; i < integrableObjects.size(); i++){
544	<	ndf_local += 3;
545	<	if (integrableObjects[i]->isDirectional()) {
546	<	if (integrableObjects[i]->isLinear())
547	<	ndf_local += 2;
548	<	else
549	<	ndf_local += 3;
538	>	map<int, set<int> > atomGroups;
539	>	Molecule::RigidBodyIterator rbIter;
540	>	RigidBody* rb;
541	>	Molecule::IntegrableObjectIterator ii;
542	>	StuntDouble* sd;
543	>
544	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
545	>	sd = mol->nextIntegrableObject(ii)) {
546	>
547	>	if (sd->isRigidBody()) {
548	>	rb = static_cast<RigidBody*>(sd);
549	>	vector<Atom*> atoms = rb->getAtoms();
550	>	set<int> rigidAtoms;
551	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
552	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
553	>	}
554	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
555	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
556	>	}
557	>	} else {
558	>	set<int> oneAtomSet;
559	>	oneAtomSet.insert(sd->getGlobalIndex());
560	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
561	>	}
562	>	}
563	>
564	>	for (bond= mol->beginBond(bondIter); bond != NULL;
565	>	bond = mol->nextBond(bondIter)) {
566	>
567	>	a = bond->getAtomA()->getGlobalIndex();
568	>	b = bond->getAtomB()->getGlobalIndex();
569	>
570	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
571	>	oneTwoInteractions_.removePair(a, b);
572	>	} else {
573	>	excludedInteractions_.removePair(a, b);
574	>	}
575		}
342	–	}
576
577	<	// n_constraints is local, so subtract them on each processor:
577	>	for (bend= mol->beginBend(bendIter); bend != NULL;
578	>	bend = mol->nextBend(bendIter)) {
579
580	<	ndf_local -= n_constraints;
580	>	a = bend->getAtomA()->getGlobalIndex();
581	>	b = bend->getAtomB()->getGlobalIndex();
582	>	c = bend->getAtomC()->getGlobalIndex();
583	>
584	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
585	>	oneTwoInteractions_.removePair(a, b);
586	>	oneTwoInteractions_.removePair(b, c);
587	>	} else {
588	>	excludedInteractions_.removePair(a, b);
589	>	excludedInteractions_.removePair(b, c);
590	>	}
591
592	<	#ifdef IS_MPI
593	<	MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
594	<	#else
595	<	ndf = ndf_local;
596	<	#endif
592	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
593	>	oneThreeInteractions_.removePair(a, c);
594	>	} else {
595	>	excludedInteractions_.removePair(a, c);
596	>	}
597	>	}
598
599	<	// nZconstraints is global, as are the 3 COM translations for the
600	<	// entire system:
599	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
600	>	torsion = mol->nextTorsion(torsionIter)) {
601
602	<	ndf = ndf - 3 - nZconstraints;
602	>	a = torsion->getAtomA()->getGlobalIndex();
603	>	b = torsion->getAtomB()->getGlobalIndex();
604	>	c = torsion->getAtomC()->getGlobalIndex();
605	>	d = torsion->getAtomD()->getGlobalIndex();
606	>
607	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
608	>	oneTwoInteractions_.removePair(a, b);
609	>	oneTwoInteractions_.removePair(b, c);
610	>	oneTwoInteractions_.removePair(c, d);
611	>	} else {
612	>	excludedInteractions_.removePair(a, b);
613	>	excludedInteractions_.removePair(b, c);
614	>	excludedInteractions_.removePair(c, d);
615	>	}
616
617	<	return ndf;
618	<	}
617	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
618	>	oneThreeInteractions_.removePair(a, c);
619	>	oneThreeInteractions_.removePair(b, d);
620	>	} else {
621	>	excludedInteractions_.removePair(a, c);
622	>	excludedInteractions_.removePair(b, d);
623	>	}
624
625	<	int SimInfo::getNDFraw() {
626	<	int ndfRaw_local;
625	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
626	>	oneFourInteractions_.removePair(a, d);
627	>	} else {
628	>	excludedInteractions_.removePair(a, d);
629	>	}
630	>	}
631
632	<	// Raw degrees of freedom that we have to set
633	<	ndfRaw_local = 0;
632	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
633	>	inversion = mol->nextInversion(inversionIter)) {
634
635	<	for(int i = 0; i < integrableObjects.size(); i++){
636	<	ndfRaw_local += 3;
637	<	if (integrableObjects[i]->isDirectional()) {
638	<	if (integrableObjects[i]->isLinear())
639	<	ndfRaw_local += 2;
640	<	else
641	<	ndfRaw_local += 3;
635	>	a = inversion->getAtomA()->getGlobalIndex();
636	>	b = inversion->getAtomB()->getGlobalIndex();
637	>	c = inversion->getAtomC()->getGlobalIndex();
638	>	d = inversion->getAtomD()->getGlobalIndex();
639	>
640	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
641	>	oneTwoInteractions_.removePair(a, b);
642	>	oneTwoInteractions_.removePair(a, c);
643	>	oneTwoInteractions_.removePair(a, d);
644	>	} else {
645	>	excludedInteractions_.removePair(a, b);
646	>	excludedInteractions_.removePair(a, c);
647	>	excludedInteractions_.removePair(a, d);
648	>	}
649	>
650	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
651	>	oneThreeInteractions_.removePair(b, c);
652	>	oneThreeInteractions_.removePair(b, d);
653	>	oneThreeInteractions_.removePair(c, d);
654	>	} else {
655	>	excludedInteractions_.removePair(b, c);
656	>	excludedInteractions_.removePair(b, d);
657	>	excludedInteractions_.removePair(c, d);
658	>	}
659		}
660	+
661	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
662	+	rb = mol->nextRigidBody(rbIter)) {
663	+	vector<Atom*> atoms = rb->getAtoms();
664	+	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
665	+	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
666	+	a = atoms[i]->getGlobalIndex();
667	+	b = atoms[j]->getGlobalIndex();
668	+	excludedInteractions_.removePair(a, b);
669	+	}
670	+	}
671	+	}
672	+
673		}
674	+
675	+
676	+	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
677	+	int curStampId;
678
679	+	//index from 0
680	+	curStampId = moleculeStamps_.size();
681	+
682	+	moleculeStamps_.push_back(molStamp);
683	+	molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
684	+	}
685	+
686	+
687	+	/**
688	+	* update
689	+	*
690	+	*  Performs the global checks and variable settings after the
691	+	*  objects have been created.
692	+	*
693	+	*/
694	+	void SimInfo::update() {
695	+	setupSimVariables();
696	+	calcNdf();
697	+	calcNdfRaw();
698	+	calcNdfTrans();
699	+	}
700	+
701	+	/**
702	+	* getSimulatedAtomTypes
703	+	*
704	+	* Returns an STL set of AtomType* that are actually present in this
705	+	* simulation.  Must query all processors to assemble this information.
706	+	*
707	+	*/
708	+	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
709	+	SimInfo::MoleculeIterator mi;
710	+	Molecule* mol;
711	+	Molecule::AtomIterator ai;
712	+	Atom* atom;
713	+	set<AtomType*> atomTypes;
714	+
715	+	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
716	+	for(atom = mol->beginAtom(ai); atom != NULL;
717	+	atom = mol->nextAtom(ai)) {
718	+	atomTypes.insert(atom->getAtomType());
719	+	}
720	+	}
721	+
722		#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
723
724	<	return ndfRaw;
725	<	}
724	>	// loop over the found atom types on this processor, and add their
725	>	// numerical idents to a vector:
726	>
727	>	vector<int> foundTypes;
728	>	set<AtomType*>::iterator i;
729	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
730	>	foundTypes.push_back( (*i)->getIdent() );
731
732	<	int SimInfo::getNDFtranslational() {
733	<	int ndfTrans_local;
732	>	// count_local holds the number of found types on this processor
733	>	int count_local = foundTypes.size();
734
735	<	ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
735	>	int nproc = MPI::COMM_WORLD.Get_size();
736
737	+	// we need arrays to hold the counts and displacement vectors for
738	+	// all processors
739	+	vector<int> counts(nproc, 0);
740	+	vector<int> disps(nproc, 0);
741
742	<	#ifdef IS_MPI
743	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
744	<	#else
745	<	ndfTrans = ndfTrans_local;
746	<	#endif
742	>	// fill the counts array
743	>	MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
744	>	1, MPI::INT);
745	>
746	>	// use the processor counts to compute the displacement array
747	>	disps[0] = 0;
748	>	int totalCount = counts[0];
749	>	for (int iproc = 1; iproc < nproc; iproc++) {
750	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
751	>	totalCount += counts[iproc];
752	>	}
753
754	<	ndfTrans = ndfTrans - 3 - nZconstraints;
754	>	// we need a (possibly redundant) set of all found types:
755	>	vector<int> ftGlobal(totalCount);
756	>
757	>	// now spray out the foundTypes to all the other processors:
758	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
759	>	&ftGlobal[0], &counts[0], &disps[0],
760	>	MPI::INT);
761
762	<	return ndfTrans;
402	<	}
762	>	vector<int>::iterator j;
763
764	<	int SimInfo::getTotIntegrableObjects() {
765	<	int nObjs_local;
766	<	int nObjs;
764	>	// foundIdents is a stl set, so inserting an already found ident
765	>	// will have no effect.
766	>	set<int> foundIdents;
767
768	<	nObjs_local =  integrableObjects.size();
768	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
769	>	foundIdents.insert((*j));
770	>
771	>	// now iterate over the foundIdents and get the actual atom types
772	>	// that correspond to these:
773	>	set<int>::iterator it;
774	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
775	>	atomTypes.insert( forceField_->getAtomType((*it)) );
776	>
777	>	#endif
778
779	+	return atomTypes;
780	+	}
781
782	+	void SimInfo::setupSimVariables() {
783	+	useAtomicVirial_ = simParams_->getUseAtomicVirial();
784	+	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
785	+	calcBoxDipole_ = false;
786	+	if ( simParams_->haveAccumulateBoxDipole() )
787	+	if ( simParams_->getAccumulateBoxDipole() ) {
788	+	calcBoxDipole_ = true;
789	+	}
790	+
791	+	set<AtomType*>::iterator i;
792	+	set<AtomType*> atomTypes;
793	+	atomTypes = getSimulatedAtomTypes();
794	+	bool usesElectrostatic = false;
795	+	bool usesMetallic = false;
796	+	bool usesDirectional = false;
797	+	bool usesFluctuatingCharges =  false;
798	+	//loop over all of the atom types
799	+	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
800	+	usesElectrostatic |= (*i)->isElectrostatic();
801	+	usesMetallic |= (*i)->isMetal();
802	+	usesDirectional |= (*i)->isDirectional();
803	+	usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
804	+	}
805	+
806		#ifdef IS_MPI
807	<	MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
807	>	bool temp;
808	>	temp = usesDirectional;
809	>	MPI::COMM_WORLD.Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI::BOOL,
810	>	MPI::LOR);
811	>
812	>	temp = usesMetallic;
813	>	MPI::COMM_WORLD.Allreduce(&temp, &usesMetallicAtoms_, 1, MPI::BOOL,
814	>	MPI::LOR);
815	>
816	>	temp = usesElectrostatic;
817	>	MPI::COMM_WORLD.Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI::BOOL,
818	>	MPI::LOR);
819	>
820	>	temp = usesFluctuatingCharges;
821	>	MPI::COMM_WORLD.Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI::BOOL,
822	>	MPI::LOR);
823		#else
824	<	nObjs = nObjs_local;
824	>
825	>	usesDirectionalAtoms_ = usesDirectional;
826	>	usesMetallicAtoms_ = usesMetallic;
827	>	usesElectrostaticAtoms_ = usesElectrostatic;
828	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
829	>
830		#endif
831	+
832	+	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
833	+	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
834	+	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
835	+	}
836
837
838	<	return nObjs;
839	<	}
838	>	vector<int> SimInfo::getGlobalAtomIndices() {
839	>	SimInfo::MoleculeIterator mi;
840	>	Molecule* mol;
841	>	Molecule::AtomIterator ai;
842	>	Atom* atom;
843
844	<	void SimInfo::refreshSim(){
844	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
845	>
846	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
847	>
848	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
849	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
850	>	}
851	>	}
852	>	return GlobalAtomIndices;
853	>	}
854
423	–	simtype fInfo;
424	–	int isError;
425	–	int n_global;
426	–	int* excl;
855
856	<	fInfo.dielect = 0.0;
856	>	vector<int> SimInfo::getGlobalGroupIndices() {
857	>	SimInfo::MoleculeIterator mi;
858	>	Molecule* mol;
859	>	Molecule::CutoffGroupIterator ci;
860	>	CutoffGroup* cg;
861
862	<	if( useDipoles ){
863	<	if( useReactionField )fInfo.dielect = dielectric;
862	>	vector<int> GlobalGroupIndices;
863	>
864	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
865	>
866	>	//local index of cutoff group is trivial, it only depends on the
867	>	//order of travesing
868	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
869	>	cg = mol->nextCutoffGroup(ci)) {
870	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
871	>	}
872	>	}
873	>	return GlobalGroupIndices;
874		}
875
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;
876
877	<	n_exclude = excludes->getSize();
878	<	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);
877	>	void SimInfo::prepareTopology() {
878	>	int nExclude, nOneTwo, nOneThree, nOneFour;
879
880	<	if( isError ){
880	>	//calculate mass ratio of cutoff group
881	>	SimInfo::MoleculeIterator mi;
882	>	Molecule* mol;
883	>	Molecule::CutoffGroupIterator ci;
884	>	CutoffGroup* cg;
885	>	Molecule::AtomIterator ai;
886	>	Atom* atom;
887	>	RealType totalMass;
888	>
889	>	/**
890	>	* The mass factor is the relative mass of an atom to the total
891	>	* mass of the cutoff group it belongs to.  By default, all atoms
892	>	* are their own cutoff groups, and therefore have mass factors of
893	>	* 1.  We need some special handling for massless atoms, which
894	>	* will be treated as carrying the entire mass of the cutoff
895	>	* group.
896	>	*/
897	>	massFactors_.clear();
898	>	massFactors_.resize(getNAtoms(), 1.0);
899
900	<	sprintf( painCave.errMsg,
901	<	"There was an error setting the simulation information in fortran.\n" );
902	<	painCave.isFatal = 1;
471	<	painCave.severity = OOPSE_ERROR;
472	<	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	<	}
900	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
901	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
902	>	cg = mol->nextCutoffGroup(ci)) {
903
904	<	void SimInfo::setDefaultRcut( double theRcut ){
905	<
906	<	haveRcut = 1;
907	<	rCut = theRcut;
908	<	rList = rCut + 1.0;
909	<
910	<	notifyFortranCutOffs( &rCut, &rSw, &rList );
911	<	}
904	>	totalMass = cg->getMass();
905	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
906	>	// Check for massless groups - set mfact to 1 if true
907	>	if (totalMass != 0)
908	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
909	>	else
910	>	massFactors_[atom->getLocalIndex()] = 1.0;
911	>	}
912	>	}
913	>	}
914
915	<	void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
915	>	// Build the identArray_
916
917	<	rSw = theRsw;
918	<	setDefaultRcut( theRcut );
919	<	}
917	>	identArray_.clear();
918	>	identArray_.reserve(getNAtoms());
919	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
920	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
921	>	identArray_.push_back(atom->getIdent());
922	>	}
923	>	}
924	>
925	>	//scan topology
926
927	+	nExclude = excludedInteractions_.getSize();
928	+	nOneTwo = oneTwoInteractions_.getSize();
929	+	nOneThree = oneThreeInteractions_.getSize();
930	+	nOneFour = oneFourInteractions_.getSize();
931
932	<	void SimInfo::checkCutOffs( void ){
933	<
934	<	if( boxIsInit ){
935	<
936	<	//we need to check cutOffs against the box
937	<
508	<	if( rCut > maxCutoff ){
509	<	sprintf( painCave.errMsg,
510	<	"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;
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();
932	>	int* excludeList = excludedInteractions_.getPairList();
933	>	int* oneTwoList = oneTwoInteractions_.getPairList();
934	>	int* oneThreeList = oneThreeInteractions_.getPairList();
935	>	int* oneFourList = oneFourInteractions_.getPairList();
936	>
937	>	topologyDone_ = true;
938		}
535	–
536	–	}
939
940	<	void SimInfo::addProperty(GenericData* prop){
940	>	void SimInfo::addProperty(GenericData* genData) {
941	>	properties_.addProperty(genData);
942	>	}
943
944	<	map<string, GenericData*>::iterator result;
945	<	result = properties.find(prop->getID());
542	<
543	<	//we can't simply use  properties[prop->getID()] = prop,
544	<	//it will cause memory leak if we already contain a propery which has the same name of prop
545	<
546	<	if(result != properties.end()){
547	<
548	<	delete (*result).second;
549	<	(*result).second = prop;
550	<
944	>	void SimInfo::removeProperty(const string& propName) {
945	>	properties_.removeProperty(propName);
946		}
552	–	else{
947
948	<	properties[prop->getID()] = prop;
948	>	void SimInfo::clearProperties() {
949	>	properties_.clearProperties();
950	>	}
951
952	+	vector<string> SimInfo::getPropertyNames() {
953	+	return properties_.getPropertyNames();
954		}
955	<
956	<	}
955	>
956	>	vector<GenericData*> SimInfo::getProperties() {
957	>	return properties_.getProperties();
958	>	}
959
960	<	GenericData* SimInfo::getProperty(const string& propName){
960	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
961	>	return properties_.getPropertyByName(propName);
962	>	}
963	>
964	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
965	>	if (sman_ == sman) {
966	>	return;
967	>	}
968	>	delete sman_;
969	>	sman_ = sman;
970	>
971	>	Molecule* mol;
972	>	RigidBody* rb;
973	>	Atom* atom;
974	>	CutoffGroup* cg;
975	>	SimInfo::MoleculeIterator mi;
976	>	Molecule::RigidBodyIterator rbIter;
977	>	Molecule::AtomIterator atomIter;
978	>	Molecule::CutoffGroupIterator cgIter;
979
980	<	map<string, GenericData*>::iterator result;
981	<
982	<	//string lowerCaseName = ();
983	<
984	<	result = properties.find(propName);
985	<
986	<	if(result != properties.end())
987	<	return (*result).second;
988	<	else
571	<	return NULL;
572	<	}
980	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
981	>
982	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
983	>	atom->setSnapshotManager(sman_);
984	>	}
985	>
986	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
987	>	rb->setSnapshotManager(sman_);
988	>	}
989
990	+	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
991	+	cg->setSnapshotManager(sman_);
992	+	}
993	+	}
994	+
995	+	}
996
997	<	void SimInfo::getFortranGroupArrays(SimInfo* info,
998	<	vector<int>& FglobalGroupMembership,
999	<	vector<double>& mfact){
997	>
998	>	ostream& operator <<(ostream& o, SimInfo& info) {
999	>
1000	>	return o;
1001	>	}
1002	>
1003
1004	<	Molecule* myMols;
1005	<	Atom** myAtoms;
1006	<	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;
1004	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1005	>	return IOIndexToIntegrableObject.at(index);
1006	>	}
1007
1008	<	mfact.clear();
1009	<	FglobalGroupMembership.clear();
1010	<
1008	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1009	>	IOIndexToIntegrableObject= v;
1010	>	}
1011	>	/*
1012	>	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1013	>	assert( v.size() == nAtoms_ + nRigidBodies_);
1014	>	sdByGlobalIndex_ = v;
1015	>	}
1016
1017	<	// Fix the silly fortran indexing problem
1017	>	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1018	>	//assert(index < nAtoms_ + nRigidBodies_);
1019	>	return sdByGlobalIndex_.at(index);
1020	>	}
1021	>	*/
1022	>	int SimInfo::getNGlobalConstraints() {
1023	>	int nGlobalConstraints;
1024		#ifdef IS_MPI
1025	<	numAtom = mpiSim->getNAtomsGlobal();
1025	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1026	>	MPI_COMM_WORLD);
1027		#else
1028	<	numAtom = n_atoms;
1028	>	nGlobalConstraints =  nConstraints_;
1029		#endif
1030	<	for (int i = 0; i < numAtom; i++)
603	<	FglobalGroupMembership.push_back(globalGroupMembership[i] + 1);
604	<
605	<
606	<	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)){
613	<
614	<	totalMass = myCutoffGroup->getMass();
615	<
616	<	for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom);
617	<	cutoffAtom != NULL;
618	<	cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
619	<	mfact.push_back(cutoffAtom->getMass()/totalMass);
620	<	}
621	<	}
1030	>	return nGlobalConstraints;
1031		}
1032
1033	<	}
1033	>	}//end namespace OpenMD
1034	>

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 3 by tim, Fri Sep 24 16:27:58 2004 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1769 by gezelter, Mon Jul 9 14:15:52 2012 UTC

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