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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 1767 by gezelter, Fri Jul 6 22:01:58 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* integrableObject;
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	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
242	>	integrableObject = mol->nextIntegrableObject(j)) {
243
244	<	delete myConfiguration;
244	>	ndf_local += 3;
245
246	<	map<string, GenericData*>::iterator i;
247	<
248	<	for(i = properties.begin(); i != properties.end(); i++)
249	<	delete (*i).second;
246	>	if (integrableObject->isDirectional()) {
247	>	if (integrableObject->isLinear()) {
248	>	ndf_local += 2;
249	>	} else {
250	>	ndf_local += 3;
251	>	}
252	>	}
253	>	}
254	>	for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
255	>	atom = mol->nextFluctuatingCharge(k)) {
256	>	if (atom->isFluctuatingCharge()) {
257	>	nfq_local++;
258	>	}
259	>	}
260	>	}
261	>
262	>	ndfLocal_ = ndf_local;
263
264	<	}
264	>	// n_constraints is local, so subtract them on each processor
265	>	ndf_local -= nConstraints_;
266
267	<	void SimInfo::setBox(double newBox[3]) {
268	<
269	<	int i, j;
270	<	double tempMat[3][3];
267	>	#ifdef IS_MPI
268	>	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
269	>	MPI_Allreduce(&nfq_local,&nGlobalFluctuatingCharges_,1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
270	>	#else
271	>	ndf_ = ndf_local;
272	>	nGlobalFluctuatingCharges_ = nfq_local;
273	>	#endif
274
275	<	for(i=0; i<3; i++)
276	<	for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
275	>	// nZconstraints_ is global, as are the 3 COM translations for the
276	>	// entire system:
277	>	ndf_ = ndf_ - 3 - nZconstraint_;
278
279	<	tempMat[0][0] = newBox[0];
103	<	tempMat[1][1] = newBox[1];
104	<	tempMat[2][2] = newBox[2];
279	>	}
280
281	<	setBoxM( tempMat );
282	<
283	<	}
284	<
285	<	void SimInfo::setBoxM( double theBox[3][3] ){
281	>	int SimInfo::getFdf() {
282	>	#ifdef IS_MPI
283	>	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
284	>	#else
285	>	fdf_ = fdf_local;
286	>	#endif
287	>	return fdf_;
288	>	}
289
290	<	int i, j;
291	<	double FortranHmat[9]; // to preserve compatibility with Fortran the
292	<	// ordering in the array is as follows:
293	<	// [ 0 3 6 ]
294	<	// [ 1 4 7 ]
295	<	// [ 2 5 8 ]
296	<	double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
297	<
298	<	if( !boxIsInit ) boxIsInit = 1;
299	<
300	<	for(i=0; i < 3; i++)
301	<	for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
302	<
303	<	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];
290	>	unsigned int SimInfo::getNLocalCutoffGroups(){
291	>	int nLocalCutoffAtoms = 0;
292	>	Molecule* mol;
293	>	MoleculeIterator mi;
294	>	CutoffGroup* cg;
295	>	Molecule::CutoffGroupIterator ci;
296	>
297	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
298	>
299	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
300	>	cg = mol->nextCutoffGroup(ci)) {
301	>	nLocalCutoffAtoms += cg->getNumAtom();
302	>
303	>	}
304		}
305	+
306	+	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
307		}
308	+
309	+	void SimInfo::calcNdfRaw() {
310	+	int ndfRaw_local;
311
312	<	setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
313	<
314	<	}
315	<
312	>	MoleculeIterator i;
313	>	vector<StuntDouble*>::iterator j;
314	>	Molecule* mol;
315	>	StuntDouble* integrableObject;
316
317	<	void SimInfo::getBoxM (double theBox[3][3]) {
318	<
319	<	int i, j;
320	<	for(i=0; i<3; i++)
321	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
322	<	}
317	>	// Raw degrees of freedom that we have to set
318	>	ndfRaw_local = 0;
319	>
320	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
321	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
322	>	integrableObject = mol->nextIntegrableObject(j)) {
323
324	+	ndfRaw_local += 3;
325
326	<	void SimInfo::scaleBox(double scale) {
327	<	double theBox[3][3];
328	<	int i, j;
329	<
330	<	// cerr << "Scaling box by " << scale << "\n";
331	<
332	<	for(i=0; i<3; i++)
333	<	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	<	}
326	>	if (integrableObject->isDirectional()) {
327	>	if (integrableObject->isLinear()) {
328	>	ndfRaw_local += 2;
329	>	} else {
330	>	ndfRaw_local += 3;
331	>	}
332	>	}
333	>
334		}
335		}
190	–	}
191	–
192	–	if( oldOrtho != orthoRhombic ){
336
337	<	if( orthoRhombic ) {
338	<	sprintf( painCave.errMsg,
339	<	"OOPSE is switching from the default Non-Orthorhombic\n"
340	<	"\tto the faster Orthorhombic periodic boundary computations.\n"
341	<	"\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	<	}
337	>	#ifdef IS_MPI
338	>	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
339	>	#else
340	>	ndfRaw_ = ndfRaw_local;
341	>	#endif
342		}
218	–	}
343
344	<	void SimInfo::calcBoxL( void ){
344	>	void SimInfo::calcNdfTrans() {
345	>	int ndfTrans_local;
346
347	<	double dx, dy, dz, dsq;
347	>	ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
348
224	–	// boxVol = Determinant of Hmat
349
350	<	boxVol = matDet3( Hmat );
350	>	#ifdef IS_MPI
351	>	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
352	>	#else
353	>	ndfTrans_ = ndfTrans_local;
354	>	#endif
355
356	<	// boxLx
357	<
358	<	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];
356	>	ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
357	>
358	>	}
359
360	<	// boxLy
361	<
362	<	dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
363	<	dsq = dx*dx + dy*dy + dz*dz;
364	<	boxL[1] = sqrt( dsq );
365	<	//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
360	>	void SimInfo::addInteractionPairs(Molecule* mol) {
361	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
362	>	vector<Bond*>::iterator bondIter;
363	>	vector<Bend*>::iterator bendIter;
364	>	vector<Torsion*>::iterator torsionIter;
365	>	vector<Inversion*>::iterator inversionIter;
366	>	Bond* bond;
367	>	Bend* bend;
368	>	Torsion* torsion;
369	>	Inversion* inversion;
370	>	int a;
371	>	int b;
372	>	int c;
373	>	int d;
374
375	+	// atomGroups can be used to add special interaction maps between
376	+	// groups of atoms that are in two separate rigid bodies.
377	+	// However, most site-site interactions between two rigid bodies
378	+	// are probably not special, just the ones between the physically
379	+	// bonded atoms.  Interactions *within* a single rigid body should
380	+	// always be excluded.  These are done at the bottom of this
381	+	// function.
382
383	<	// boxLz
384	<
385	<	dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
386	<	dsq = dx*dx + dy*dy + dz*dz;
387	<	boxL[2] = sqrt( dsq );
388	<	//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
383	>	map<int, set<int> > atomGroups;
384	>	Molecule::RigidBodyIterator rbIter;
385	>	RigidBody* rb;
386	>	Molecule::IntegrableObjectIterator ii;
387	>	StuntDouble* integrableObject;
388	>
389	>	for (integrableObject = mol->beginIntegrableObject(ii);
390	>	integrableObject != NULL;
391	>	integrableObject = mol->nextIntegrableObject(ii)) {
392	>
393	>	if (integrableObject->isRigidBody()) {
394	>	rb = static_cast<RigidBody*>(integrableObject);
395	>	vector<Atom*> atoms = rb->getAtoms();
396	>	set<int> rigidAtoms;
397	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
398	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
399	>	}
400	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
401	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
402	>	}
403	>	} else {
404	>	set<int> oneAtomSet;
405	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
406	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
407	>	}
408	>	}
409	>
410	>	for (bond= mol->beginBond(bondIter); bond != NULL;
411	>	bond = mol->nextBond(bondIter)) {
412
413	<	//calculate the max cutoff
414	<	maxCutoff =  calcMaxCutOff();
415	<
416	<	checkCutOffs();
413	>	a = bond->getAtomA()->getGlobalIndex();
414	>	b = bond->getAtomB()->getGlobalIndex();
415	>
416	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
417	>	oneTwoInteractions_.addPair(a, b);
418	>	} else {
419	>	excludedInteractions_.addPair(a, b);
420	>	}
421	>	}
422
423	<	}
423	>	for (bend= mol->beginBend(bendIter); bend != NULL;
424	>	bend = mol->nextBend(bendIter)) {
425
426	+	a = bend->getAtomA()->getGlobalIndex();
427	+	b = bend->getAtomB()->getGlobalIndex();
428	+	c = bend->getAtomC()->getGlobalIndex();
429	+
430	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
431	+	oneTwoInteractions_.addPair(a, b);
432	+	oneTwoInteractions_.addPair(b, c);
433	+	} else {
434	+	excludedInteractions_.addPair(a, b);
435	+	excludedInteractions_.addPair(b, c);
436	+	}
437
438	<	double SimInfo::calcMaxCutOff(){
438	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
439	>	oneThreeInteractions_.addPair(a, c);
440	>	} else {
441	>	excludedInteractions_.addPair(a, c);
442	>	}
443	>	}
444
445	<	double ri[3], rj[3], rk[3];
446	<	double rij[3], rjk[3], rki[3];
262	<	double minDist;
445	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
446	>	torsion = mol->nextTorsion(torsionIter)) {
447
448	<	ri[0] = Hmat[0][0];
449	<	ri[1] = Hmat[1][0];
450	<	ri[2] = Hmat[2][0];
448	>	a = torsion->getAtomA()->getGlobalIndex();
449	>	b = torsion->getAtomB()->getGlobalIndex();
450	>	c = torsion->getAtomC()->getGlobalIndex();
451	>	d = torsion->getAtomD()->getGlobalIndex();
452
453	<	rj[0] = Hmat[0][1];
454	<	rj[1] = Hmat[1][1];
455	<	rj[2] = Hmat[2][1];
453	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
454	>	oneTwoInteractions_.addPair(a, b);
455	>	oneTwoInteractions_.addPair(b, c);
456	>	oneTwoInteractions_.addPair(c, d);
457	>	} else {
458	>	excludedInteractions_.addPair(a, b);
459	>	excludedInteractions_.addPair(b, c);
460	>	excludedInteractions_.addPair(c, d);
461	>	}
462
463	<	rk[0] = Hmat[0][2];
464	<	rk[1] = Hmat[1][2];
465	<	rk[2] = Hmat[2][2];
466	<
467	<	crossProduct3(ri, rj, rij);
468	<	distXY = dotProduct3(rk,rij) / norm3(rij);
463	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
464	>	oneThreeInteractions_.addPair(a, c);
465	>	oneThreeInteractions_.addPair(b, d);
466	>	} else {
467	>	excludedInteractions_.addPair(a, c);
468	>	excludedInteractions_.addPair(b, d);
469	>	}
470
471	<	crossProduct3(rj,rk, rjk);
472	<	distYZ = dotProduct3(ri,rjk) / norm3(rjk);
471	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
472	>	oneFourInteractions_.addPair(a, d);
473	>	} else {
474	>	excludedInteractions_.addPair(a, d);
475	>	}
476	>	}
477
478	<	crossProduct3(rk,ri, rki);
479	<	distZX = dotProduct3(rj,rki) / norm3(rki);
478	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
479	>	inversion = mol->nextInversion(inversionIter)) {
480
481	<	minDist = min(min(distXY, distYZ), distZX);
482	<	return minDist/2;
483	<
484	<	}
481	>	a = inversion->getAtomA()->getGlobalIndex();
482	>	b = inversion->getAtomB()->getGlobalIndex();
483	>	c = inversion->getAtomC()->getGlobalIndex();
484	>	d = inversion->getAtomD()->getGlobalIndex();
485
486	<	void SimInfo::wrapVector( double thePos[3] ){
486	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
487	>	oneTwoInteractions_.addPair(a, b);
488	>	oneTwoInteractions_.addPair(a, c);
489	>	oneTwoInteractions_.addPair(a, d);
490	>	} else {
491	>	excludedInteractions_.addPair(a, b);
492	>	excludedInteractions_.addPair(a, c);
493	>	excludedInteractions_.addPair(a, d);
494	>	}
495
496	<	int i;
497	<	double scaled[3];
496	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
497	>	oneThreeInteractions_.addPair(b, c);
498	>	oneThreeInteractions_.addPair(b, d);
499	>	oneThreeInteractions_.addPair(c, d);
500	>	} else {
501	>	excludedInteractions_.addPair(b, c);
502	>	excludedInteractions_.addPair(b, d);
503	>	excludedInteractions_.addPair(c, d);
504	>	}
505	>	}
506
507	<	if( !orthoRhombic ){
508	<	// calc the scaled coordinates.
509	<
507	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
508	>	rb = mol->nextRigidBody(rbIter)) {
509	>	vector<Atom*> atoms = rb->getAtoms();
510	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
511	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
512	>	a = atoms[i]->getGlobalIndex();
513	>	b = atoms[j]->getGlobalIndex();
514	>	excludedInteractions_.addPair(a, b);
515	>	}
516	>	}
517	>	}
518
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	–
519		}
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	–	}
520
521	+	void SimInfo::removeInteractionPairs(Molecule* mol) {
522	+	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
523	+	vector<Bond*>::iterator bondIter;
524	+	vector<Bend*>::iterator bendIter;
525	+	vector<Torsion*>::iterator torsionIter;
526	+	vector<Inversion*>::iterator inversionIter;
527	+	Bond* bond;
528	+	Bend* bend;
529	+	Torsion* torsion;
530	+	Inversion* inversion;
531	+	int a;
532	+	int b;
533	+	int c;
534	+	int d;
535
536	<	int SimInfo::getNDF(){
537	<	int ndf_local;
538	<
539	<	ndf_local = 0;
540	<
541	<	for(int i = 0; i < integrableObjects.size(); i++){
542	<	ndf_local += 3;
543	<	if (integrableObjects[i]->isDirectional()) {
544	<	if (integrableObjects[i]->isLinear())
545	<	ndf_local += 2;
546	<	else
547	<	ndf_local += 3;
536	>	map<int, set<int> > atomGroups;
537	>	Molecule::RigidBodyIterator rbIter;
538	>	RigidBody* rb;
539	>	Molecule::IntegrableObjectIterator ii;
540	>	StuntDouble* integrableObject;
541	>
542	>	for (integrableObject = mol->beginIntegrableObject(ii);
543	>	integrableObject != NULL;
544	>	integrableObject = mol->nextIntegrableObject(ii)) {
545	>
546	>	if (integrableObject->isRigidBody()) {
547	>	rb = static_cast<RigidBody*>(integrableObject);
548	>	vector<Atom*> atoms = rb->getAtoms();
549	>	set<int> rigidAtoms;
550	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
551	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
552	>	}
553	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
554	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
555	>	}
556	>	} else {
557	>	set<int> oneAtomSet;
558	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
559	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
560	>	}
561	>	}
562	>
563	>	for (bond= mol->beginBond(bondIter); bond != NULL;
564	>	bond = mol->nextBond(bondIter)) {
565	>
566	>	a = bond->getAtomA()->getGlobalIndex();
567	>	b = bond->getAtomB()->getGlobalIndex();
568	>
569	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
570	>	oneTwoInteractions_.removePair(a, b);
571	>	} else {
572	>	excludedInteractions_.removePair(a, b);
573	>	}
574		}
342	–	}
575
576	<	// n_constraints is local, so subtract them on each processor:
576	>	for (bend= mol->beginBend(bendIter); bend != NULL;
577	>	bend = mol->nextBend(bendIter)) {
578
579	<	ndf_local -= n_constraints;
579	>	a = bend->getAtomA()->getGlobalIndex();
580	>	b = bend->getAtomB()->getGlobalIndex();
581	>	c = bend->getAtomC()->getGlobalIndex();
582	>
583	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
584	>	oneTwoInteractions_.removePair(a, b);
585	>	oneTwoInteractions_.removePair(b, c);
586	>	} else {
587	>	excludedInteractions_.removePair(a, b);
588	>	excludedInteractions_.removePair(b, c);
589	>	}
590
591	<	#ifdef IS_MPI
592	<	MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
593	<	#else
594	<	ndf = ndf_local;
595	<	#endif
591	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
592	>	oneThreeInteractions_.removePair(a, c);
593	>	} else {
594	>	excludedInteractions_.removePair(a, c);
595	>	}
596	>	}
597
598	<	// nZconstraints is global, as are the 3 COM translations for the
599	<	// entire system:
598	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
599	>	torsion = mol->nextTorsion(torsionIter)) {
600
601	<	ndf = ndf - 3 - nZconstraints;
601	>	a = torsion->getAtomA()->getGlobalIndex();
602	>	b = torsion->getAtomB()->getGlobalIndex();
603	>	c = torsion->getAtomC()->getGlobalIndex();
604	>	d = torsion->getAtomD()->getGlobalIndex();
605	>
606	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
607	>	oneTwoInteractions_.removePair(a, b);
608	>	oneTwoInteractions_.removePair(b, c);
609	>	oneTwoInteractions_.removePair(c, d);
610	>	} else {
611	>	excludedInteractions_.removePair(a, b);
612	>	excludedInteractions_.removePair(b, c);
613	>	excludedInteractions_.removePair(c, d);
614	>	}
615
616	<	return ndf;
617	<	}
616	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
617	>	oneThreeInteractions_.removePair(a, c);
618	>	oneThreeInteractions_.removePair(b, d);
619	>	} else {
620	>	excludedInteractions_.removePair(a, c);
621	>	excludedInteractions_.removePair(b, d);
622	>	}
623
624	<	int SimInfo::getNDFraw() {
625	<	int ndfRaw_local;
624	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
625	>	oneFourInteractions_.removePair(a, d);
626	>	} else {
627	>	excludedInteractions_.removePair(a, d);
628	>	}
629	>	}
630
631	<	// Raw degrees of freedom that we have to set
632	<	ndfRaw_local = 0;
631	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
632	>	inversion = mol->nextInversion(inversionIter)) {
633
634	<	for(int i = 0; i < integrableObjects.size(); i++){
635	<	ndfRaw_local += 3;
636	<	if (integrableObjects[i]->isDirectional()) {
637	<	if (integrableObjects[i]->isLinear())
638	<	ndfRaw_local += 2;
639	<	else
640	<	ndfRaw_local += 3;
634	>	a = inversion->getAtomA()->getGlobalIndex();
635	>	b = inversion->getAtomB()->getGlobalIndex();
636	>	c = inversion->getAtomC()->getGlobalIndex();
637	>	d = inversion->getAtomD()->getGlobalIndex();
638	>
639	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
640	>	oneTwoInteractions_.removePair(a, b);
641	>	oneTwoInteractions_.removePair(a, c);
642	>	oneTwoInteractions_.removePair(a, d);
643	>	} else {
644	>	excludedInteractions_.removePair(a, b);
645	>	excludedInteractions_.removePair(a, c);
646	>	excludedInteractions_.removePair(a, d);
647	>	}
648	>
649	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
650	>	oneThreeInteractions_.removePair(b, c);
651	>	oneThreeInteractions_.removePair(b, d);
652	>	oneThreeInteractions_.removePair(c, d);
653	>	} else {
654	>	excludedInteractions_.removePair(b, c);
655	>	excludedInteractions_.removePair(b, d);
656	>	excludedInteractions_.removePair(c, d);
657	>	}
658		}
659	+
660	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
661	+	rb = mol->nextRigidBody(rbIter)) {
662	+	vector<Atom*> atoms = rb->getAtoms();
663	+	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
664	+	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
665	+	a = atoms[i]->getGlobalIndex();
666	+	b = atoms[j]->getGlobalIndex();
667	+	excludedInteractions_.removePair(a, b);
668	+	}
669	+	}
670	+	}
671	+
672		}
673	+
674	+
675	+	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
676	+	int curStampId;
677
678	+	//index from 0
679	+	curStampId = moleculeStamps_.size();
680	+
681	+	moleculeStamps_.push_back(molStamp);
682	+	molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
683	+	}
684	+
685	+
686	+	/**
687	+	* update
688	+	*
689	+	*  Performs the global checks and variable settings after the
690	+	*  objects have been created.
691	+	*
692	+	*/
693	+	void SimInfo::update() {
694	+	setupSimVariables();
695	+	calcNdf();
696	+	calcNdfRaw();
697	+	calcNdfTrans();
698	+	}
699	+
700	+	/**
701	+	* getSimulatedAtomTypes
702	+	*
703	+	* Returns an STL set of AtomType* that are actually present in this
704	+	* simulation.  Must query all processors to assemble this information.
705	+	*
706	+	*/
707	+	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
708	+	SimInfo::MoleculeIterator mi;
709	+	Molecule* mol;
710	+	Molecule::AtomIterator ai;
711	+	Atom* atom;
712	+	set<AtomType*> atomTypes;
713	+
714	+	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
715	+	for(atom = mol->beginAtom(ai); atom != NULL;
716	+	atom = mol->nextAtom(ai)) {
717	+	atomTypes.insert(atom->getAtomType());
718	+	}
719	+	}
720	+
721		#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
722
723	<	return ndfRaw;
724	<	}
723	>	// loop over the found atom types on this processor, and add their
724	>	// numerical idents to a vector:
725	>
726	>	vector<int> foundTypes;
727	>	set<AtomType*>::iterator i;
728	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
729	>	foundTypes.push_back( (*i)->getIdent() );
730
731	<	int SimInfo::getNDFtranslational() {
732	<	int ndfTrans_local;
731	>	// count_local holds the number of found types on this processor
732	>	int count_local = foundTypes.size();
733
734	<	ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
734	>	int nproc = MPI::COMM_WORLD.Get_size();
735
736	+	// we need arrays to hold the counts and displacement vectors for
737	+	// all processors
738	+	vector<int> counts(nproc, 0);
739	+	vector<int> disps(nproc, 0);
740
741	<	#ifdef IS_MPI
742	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
743	<	#else
744	<	ndfTrans = ndfTrans_local;
745	<	#endif
741	>	// fill the counts array
742	>	MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
743	>	1, MPI::INT);
744	>
745	>	// use the processor counts to compute the displacement array
746	>	disps[0] = 0;
747	>	int totalCount = counts[0];
748	>	for (int iproc = 1; iproc < nproc; iproc++) {
749	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
750	>	totalCount += counts[iproc];
751	>	}
752
753	<	ndfTrans = ndfTrans - 3 - nZconstraints;
753	>	// we need a (possibly redundant) set of all found types:
754	>	vector<int> ftGlobal(totalCount);
755	>
756	>	// now spray out the foundTypes to all the other processors:
757	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
758	>	&ftGlobal[0], &counts[0], &disps[0],
759	>	MPI::INT);
760
761	<	return ndfTrans;
402	<	}
761	>	vector<int>::iterator j;
762
763	<	int SimInfo::getTotIntegrableObjects() {
764	<	int nObjs_local;
765	<	int nObjs;
763	>	// foundIdents is a stl set, so inserting an already found ident
764	>	// will have no effect.
765	>	set<int> foundIdents;
766
767	<	nObjs_local =  integrableObjects.size();
767	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
768	>	foundIdents.insert((*j));
769	>
770	>	// now iterate over the foundIdents and get the actual atom types
771	>	// that correspond to these:
772	>	set<int>::iterator it;
773	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
774	>	atomTypes.insert( forceField_->getAtomType((*it)) );
775	>
776	>	#endif
777
778	+	return atomTypes;
779	+	}
780
781	+	void SimInfo::setupSimVariables() {
782	+	useAtomicVirial_ = simParams_->getUseAtomicVirial();
783	+	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
784	+	calcBoxDipole_ = false;
785	+	if ( simParams_->haveAccumulateBoxDipole() )
786	+	if ( simParams_->getAccumulateBoxDipole() ) {
787	+	calcBoxDipole_ = true;
788	+	}
789	+
790	+	set<AtomType*>::iterator i;
791	+	set<AtomType*> atomTypes;
792	+	atomTypes = getSimulatedAtomTypes();
793	+	bool usesElectrostatic = false;
794	+	bool usesMetallic = false;
795	+	bool usesDirectional = false;
796	+	bool usesFluctuatingCharges =  false;
797	+	//loop over all of the atom types
798	+	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
799	+	usesElectrostatic |= (*i)->isElectrostatic();
800	+	usesMetallic |= (*i)->isMetal();
801	+	usesDirectional |= (*i)->isDirectional();
802	+	usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
803	+	}
804	+
805		#ifdef IS_MPI
806	<	MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
806	>	bool temp;
807	>	temp = usesDirectional;
808	>	MPI::COMM_WORLD.Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI::BOOL,
809	>	MPI::LOR);
810	>
811	>	temp = usesMetallic;
812	>	MPI::COMM_WORLD.Allreduce(&temp, &usesMetallicAtoms_, 1, MPI::BOOL,
813	>	MPI::LOR);
814	>
815	>	temp = usesElectrostatic;
816	>	MPI::COMM_WORLD.Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI::BOOL,
817	>	MPI::LOR);
818	>
819	>	temp = usesFluctuatingCharges;
820	>	MPI::COMM_WORLD.Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI::BOOL,
821	>	MPI::LOR);
822		#else
823	<	nObjs = nObjs_local;
823	>
824	>	usesDirectionalAtoms_ = usesDirectional;
825	>	usesMetallicAtoms_ = usesMetallic;
826	>	usesElectrostaticAtoms_ = usesElectrostatic;
827	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
828	>
829		#endif
830	+
831	+	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
832	+	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
833	+	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
834	+	}
835
836
837	<	return nObjs;
838	<	}
837	>	vector<int> SimInfo::getGlobalAtomIndices() {
838	>	SimInfo::MoleculeIterator mi;
839	>	Molecule* mol;
840	>	Molecule::AtomIterator ai;
841	>	Atom* atom;
842
843	<	void SimInfo::refreshSim(){
843	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
844	>
845	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
846	>
847	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
848	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
849	>	}
850	>	}
851	>	return GlobalAtomIndices;
852	>	}
853
423	–	simtype fInfo;
424	–	int isError;
425	–	int n_global;
426	–	int* excl;
854
855	<	fInfo.dielect = 0.0;
855	>	vector<int> SimInfo::getGlobalGroupIndices() {
856	>	SimInfo::MoleculeIterator mi;
857	>	Molecule* mol;
858	>	Molecule::CutoffGroupIterator ci;
859	>	CutoffGroup* cg;
860
861	<	if( useDipoles ){
862	<	if( useReactionField )fInfo.dielect = dielectric;
861	>	vector<int> GlobalGroupIndices;
862	>
863	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
864	>
865	>	//local index of cutoff group is trivial, it only depends on the
866	>	//order of travesing
867	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
868	>	cg = mol->nextCutoffGroup(ci)) {
869	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
870	>	}
871	>	}
872	>	return GlobalGroupIndices;
873		}
874
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;
875
876	<	n_exclude = excludes->getSize();
877	<	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);
876	>	void SimInfo::prepareTopology() {
877	>	int nExclude, nOneTwo, nOneThree, nOneFour;
878
879	<	if( isError ){
879	>	//calculate mass ratio of cutoff group
880	>	SimInfo::MoleculeIterator mi;
881	>	Molecule* mol;
882	>	Molecule::CutoffGroupIterator ci;
883	>	CutoffGroup* cg;
884	>	Molecule::AtomIterator ai;
885	>	Atom* atom;
886	>	RealType totalMass;
887	>
888	>	/**
889	>	* The mass factor is the relative mass of an atom to the total
890	>	* mass of the cutoff group it belongs to.  By default, all atoms
891	>	* are their own cutoff groups, and therefore have mass factors of
892	>	* 1.  We need some special handling for massless atoms, which
893	>	* will be treated as carrying the entire mass of the cutoff
894	>	* group.
895	>	*/
896	>	massFactors_.clear();
897	>	massFactors_.resize(getNAtoms(), 1.0);
898
899	<	sprintf( painCave.errMsg,
900	<	"There was an error setting the simulation information in fortran.\n" );
901	<	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	<	}
899	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
900	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
901	>	cg = mol->nextCutoffGroup(ci)) {
902
903	<	void SimInfo::setDefaultRcut( double theRcut ){
904	<
905	<	haveRcut = 1;
906	<	rCut = theRcut;
907	<	rList = rCut + 1.0;
908	<
909	<	notifyFortranCutOffs( &rCut, &rSw, &rList );
910	<	}
903	>	totalMass = cg->getMass();
904	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
905	>	// Check for massless groups - set mfact to 1 if true
906	>	if (totalMass != 0)
907	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
908	>	else
909	>	massFactors_[atom->getLocalIndex()] = 1.0;
910	>	}
911	>	}
912	>	}
913
914	<	void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
914	>	// Build the identArray_
915
916	<	rSw = theRsw;
917	<	setDefaultRcut( theRcut );
918	<	}
916	>	identArray_.clear();
917	>	identArray_.reserve(getNAtoms());
918	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
919	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
920	>	identArray_.push_back(atom->getIdent());
921	>	}
922	>	}
923	>
924	>	//scan topology
925
926	+	nExclude = excludedInteractions_.getSize();
927	+	nOneTwo = oneTwoInteractions_.getSize();
928	+	nOneThree = oneThreeInteractions_.getSize();
929	+	nOneFour = oneFourInteractions_.getSize();
930
931	<	void SimInfo::checkCutOffs( void ){
932	<
933	<	if( boxIsInit ){
934	<
935	<	//we need to check cutOffs against the box
936	<
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();
931	>	int* excludeList = excludedInteractions_.getPairList();
932	>	int* oneTwoList = oneTwoInteractions_.getPairList();
933	>	int* oneThreeList = oneThreeInteractions_.getPairList();
934	>	int* oneFourList = oneFourInteractions_.getPairList();
935	>
936	>	topologyDone_ = true;
937		}
535	–
536	–	}
938
939	<	void SimInfo::addProperty(GenericData* prop){
939	>	void SimInfo::addProperty(GenericData* genData) {
940	>	properties_.addProperty(genData);
941	>	}
942
943	<	map<string, GenericData*>::iterator result;
944	<	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	<
943	>	void SimInfo::removeProperty(const string& propName) {
944	>	properties_.removeProperty(propName);
945		}
552	–	else{
946
947	<	properties[prop->getID()] = prop;
947	>	void SimInfo::clearProperties() {
948	>	properties_.clearProperties();
949	>	}
950
951	+	vector<string> SimInfo::getPropertyNames() {
952	+	return properties_.getPropertyNames();
953		}
954	<
955	<	}
954	>
955	>	vector<GenericData*> SimInfo::getProperties() {
956	>	return properties_.getProperties();
957	>	}
958
959	<	GenericData* SimInfo::getProperty(const string& propName){
959	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
960	>	return properties_.getPropertyByName(propName);
961	>	}
962	>
963	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
964	>	if (sman_ == sman) {
965	>	return;
966	>	}
967	>	delete sman_;
968	>	sman_ = sman;
969	>
970	>	Molecule* mol;
971	>	RigidBody* rb;
972	>	Atom* atom;
973	>	CutoffGroup* cg;
974	>	SimInfo::MoleculeIterator mi;
975	>	Molecule::RigidBodyIterator rbIter;
976	>	Molecule::AtomIterator atomIter;
977	>	Molecule::CutoffGroupIterator cgIter;
978
979	<	map<string, GenericData*>::iterator result;
980	<
981	<	//string lowerCaseName = ();
982	<
983	<	result = properties.find(propName);
984	<
985	<	if(result != properties.end())
986	<	return (*result).second;
987	<	else
571	<	return NULL;
572	<	}
979	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
980	>
981	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
982	>	atom->setSnapshotManager(sman_);
983	>	}
984	>
985	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
986	>	rb->setSnapshotManager(sman_);
987	>	}
988
989	+	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
990	+	cg->setSnapshotManager(sman_);
991	+	}
992	+	}
993	+
994	+	}
995
996	<	void SimInfo::getFortranGroupArrays(SimInfo* info,
997	<	vector<int>& FglobalGroupMembership,
998	<	vector<double>& mfact){
996	>
997	>	ostream& operator <<(ostream& o, SimInfo& info) {
998	>
999	>	return o;
1000	>	}
1001	>
1002
1003	<	Molecule* myMols;
1004	<	Atom** myAtoms;
1005	<	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;
1003	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1004	>	return IOIndexToIntegrableObject.at(index);
1005	>	}
1006
1007	<	mfact.clear();
1008	<	FglobalGroupMembership.clear();
1009	<
1007	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1008	>	IOIndexToIntegrableObject= v;
1009	>	}
1010	>	/*
1011	>	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1012	>	assert( v.size() == nAtoms_ + nRigidBodies_);
1013	>	sdByGlobalIndex_ = v;
1014	>	}
1015
1016	<	// Fix the silly fortran indexing problem
1016	>	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1017	>	//assert(index < nAtoms_ + nRigidBodies_);
1018	>	return sdByGlobalIndex_.at(index);
1019	>	}
1020	>	*/
1021	>	int SimInfo::getNGlobalConstraints() {
1022	>	int nGlobalConstraints;
1023		#ifdef IS_MPI
1024	<	numAtom = mpiSim->getNAtomsGlobal();
1024	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1025	>	MPI_COMM_WORLD);
1026		#else
1027	<	numAtom = n_atoms;
1027	>	nGlobalConstraints =  nConstraints_;
1028		#endif
1029	<	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	<	}
1029	>	return nGlobalConstraints;
1030		}
1031
1032	<	}
1032	>	}//end namespace OpenMD
1033	>

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 1767 by gezelter, Fri Jul 6 22:01:58 2012 UTC

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