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root/OpenMD/trunk/src/brains/SimInfo.cpp

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 3 by tim, Fri Sep 24 16:27:58 2004 UTC vs.
Revision 1796 by gezelter, Mon Sep 10 18:38:44 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();
92	>	i !=components.end(); ++i) {
93	>	molStamp = (*i)->getMoleculeStamp();
94	>	nMolWithSameStamp = (*i)->getNMol();
95	>
96	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
97	>
98	>	//calculate atoms in molecules
99	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
100	>
101	>	//calculate atoms in cutoff groups
102	>	int nAtomsInGroups = 0;
103	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
104	>
105	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
106	>	cgStamp = molStamp->getCutoffGroupStamp(j);
107	>	nAtomsInGroups += cgStamp->getNMembers();
108	>	}
109	>
110	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
111	>
112	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
113	>
114	>	//calculate atoms in rigid bodies
115	>	int nAtomsInRigidBodies = 0;
116	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
117	>
118	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
119	>	rbStamp = molStamp->getRigidBodyStamp(j);
120	>	nAtomsInRigidBodies += rbStamp->getNMembers();
121	>	}
122	>
123	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
124	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
125	>
126	>	}
127	>
128	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
129	>	//group therefore the total number of cutoff groups in the system is
130	>	//equal to the total number of atoms minus number of atoms belong to
131	>	//cutoff group defined in meta-data file plus the number of cutoff
132	>	//groups defined in meta-data file
133
134	<	SimInfo* currentInfo;
134	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
135	>
136	>	//every free atom (atom does not belong to rigid bodies) is an
137	>	//integrable object therefore the total number of integrable objects
138	>	//in the system is equal to the total number of atoms minus number of
139	>	//atoms belong to rigid body defined in meta-data file plus the number
140	>	//of rigid bodies defined in meta-data file
141	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
142	>	+ nGlobalRigidBodies_;
143	>
144	>	nGlobalMols_ = molStampIds_.size();
145	>	molToProcMap_.resize(nGlobalMols_);
146	>	}
147	>
148	>	SimInfo::~SimInfo() {
149	>	map<int, Molecule*>::iterator i;
150	>	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
151	>	delete i->second;
152	>	}
153	>	molecules_.clear();
154	>
155	>	delete sman_;
156	>	delete simParams_;
157	>	delete forceField_;
158	>	}
159
31	–	SimInfo::SimInfo(){
160
161	<	n_constraints = 0;
162	<	nZconstraints = 0;
163	<	n_oriented = 0;
164	<	n_dipoles = 0;
165	<	ndf = 0;
166	<	ndfRaw = 0;
167	<	nZconstraints = 0;
168	<	the_integrator = NULL;
169	<	setTemp = 0;
170	<	thermalTime = 0.0;
171	<	currentTime = 0.0;
172	<	rCut = 0.0;
173	<	rSw = 0.0;
174	<
175	<	haveRcut = 0;
176	<	haveRsw = 0;
177	<	boxIsInit = 0;
161	>	bool SimInfo::addMolecule(Molecule* mol) {
162	>	MoleculeIterator i;
163	>
164	>	i = molecules_.find(mol->getGlobalIndex());
165	>	if (i == molecules_.end() ) {
166	>
167	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
168	>
169	>	nAtoms_ += mol->getNAtoms();
170	>	nBonds_ += mol->getNBonds();
171	>	nBends_ += mol->getNBends();
172	>	nTorsions_ += mol->getNTorsions();
173	>	nInversions_ += mol->getNInversions();
174	>	nRigidBodies_ += mol->getNRigidBodies();
175	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
176	>	nCutoffGroups_ += mol->getNCutoffGroups();
177	>	nConstraints_ += mol->getNConstraintPairs();
178	>
179	>	addInteractionPairs(mol);
180	>
181	>	return true;
182	>	} else {
183	>	return false;
184	>	}
185	>	}
186
187	<	resetTime = 1e99;
187	>	bool SimInfo::removeMolecule(Molecule* mol) {
188	>	MoleculeIterator i;
189	>	i = molecules_.find(mol->getGlobalIndex());
190
191	<	orthoRhombic = 0;
54	<	orthoTolerance = 1E-6;
55	<	useInitXSstate = true;
191	>	if (i != molecules_.end() ) {
192
193	<	usePBC = 0;
194	<	useLJ = 0;
195	<	useSticky = 0;
196	<	useCharges = 0;
197	<	useDipoles = 0;
198	<	useReactionField = 0;
199	<	useGB = 0;
200	<	useEAM = 0;
201	<	useSolidThermInt = 0;
202	<	useLiquidThermInt = 0;
193	>	assert(mol == i->second);
194	>
195	>	nAtoms_ -= mol->getNAtoms();
196	>	nBonds_ -= mol->getNBonds();
197	>	nBends_ -= mol->getNBends();
198	>	nTorsions_ -= mol->getNTorsions();
199	>	nInversions_ -= mol->getNInversions();
200	>	nRigidBodies_ -= mol->getNRigidBodies();
201	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
202	>	nCutoffGroups_ -= mol->getNCutoffGroups();
203	>	nConstraints_ -= mol->getNConstraintPairs();
204
205	<	haveCutoffGroups = false;
205	>	removeInteractionPairs(mol);
206	>	molecules_.erase(mol->getGlobalIndex());
207
208	<	excludes = Exclude::Instance();
208	>	delete mol;
209	>
210	>	return true;
211	>	} else {
212	>	return false;
213	>	}
214	>	}
215
216	<	myConfiguration = new SimState();
216	>
217	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
218	>	i = molecules_.begin();
219	>	return i == molecules_.end() ? NULL : i->second;
220	>	}
221
222	<	has_minimizer = false;
223	<	the_minimizer =NULL;
222	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
223	>	++i;
224	>	return i == molecules_.end() ? NULL : i->second;
225	>	}
226
77	–	ngroup = 0;
227
228	<	wrapMeSimInfo( this );
229	<	}
228	>	void SimInfo::calcNdf() {
229	>	int ndf_local, nfq_local;
230	>	MoleculeIterator i;
231	>	vector<StuntDouble*>::iterator j;
232	>	vector<Atom*>::iterator k;
233
234	+	Molecule* mol;
235	+	StuntDouble* sd;
236	+	Atom* atom;
237
238	<	SimInfo::~SimInfo(){
238	>	ndf_local = 0;
239	>	nfq_local = 0;
240	>
241	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
242
243	<	delete myConfiguration;
243	>	for (sd = mol->beginIntegrableObject(j); sd != NULL;
244	>	sd = mol->nextIntegrableObject(j)) {
245
246	<	map<string, GenericData*>::iterator i;
88	<
89	<	for(i = properties.begin(); i != properties.end(); i++)
90	<	delete (*i).second;
246	>	ndf_local += 3;
247
248	<	}
248	>	if (sd->isDirectional()) {
249	>	if (sd->isLinear()) {
250	>	ndf_local += 2;
251	>	} else {
252	>	ndf_local += 3;
253	>	}
254	>	}
255	>	}
256
257	<	void SimInfo::setBox(double newBox[3]) {
258	<
259	<	int i, j;
260	<	double tempMat[3][3];
257	>	for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
258	>	atom = mol->nextFluctuatingCharge(k)) {
259	>	if (atom->isFluctuatingCharge()) {
260	>	nfq_local++;
261	>	}
262	>	}
263	>	}
264	>
265	>	ndfLocal_ = ndf_local;
266
267	<	for(i=0; i<3; i++)
268	<	for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
267	>	// n_constraints is local, so subtract them on each processor
268	>	ndf_local -= nConstraints_;
269
270	<	tempMat[0][0] = newBox[0];
271	<	tempMat[1][1] = newBox[1];
272	<	tempMat[2][2] = newBox[2];
270	>	#ifdef IS_MPI
271	>	MPI::COMM_WORLD.Allreduce(&ndf_local, &ndf_, 1, MPI::INT,MPI::SUM);
272	>	MPI::COMM_WORLD.Allreduce(&nfq_local, &nGlobalFluctuatingCharges_, 1,
273	>	MPI::INT, MPI::SUM);
274	>	#else
275	>	ndf_ = ndf_local;
276	>	nGlobalFluctuatingCharges_ = nfq_local;
277	>	#endif
278
279	<	setBoxM( tempMat );
279	>	// nZconstraints_ is global, as are the 3 COM translations for the
280	>	// entire system:
281	>	ndf_ = ndf_ - 3 - nZconstraint_;
282
283	<	}
283	>	}
284
285	<	void SimInfo::setBoxM( double theBox[3][3] ){
285	>	int SimInfo::getFdf() {
286	>	#ifdef IS_MPI
287	>	MPI::COMM_WORLD.Allreduce(&fdf_local, &fdf_, 1, MPI::INT, MPI::SUM);
288	>	#else
289	>	fdf_ = fdf_local;
290	>	#endif
291	>	return fdf_;
292	>	}
293
294	<	int i, j;
295	<	double FortranHmat[9]; // to preserve compatibility with Fortran the
296	<	// ordering in the array is as follows:
297	<	// [ 0 3 6 ]
298	<	// [ 1 4 7 ]
299	<	// [ 2 5 8 ]
300	<	double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
301	<
302	<	if( !boxIsInit ) boxIsInit = 1;
303	<
304	<	for(i=0; i < 3; i++)
305	<	for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
306	<
307	<	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];
294	>	unsigned int SimInfo::getNLocalCutoffGroups(){
295	>	int nLocalCutoffAtoms = 0;
296	>	Molecule* mol;
297	>	MoleculeIterator mi;
298	>	CutoffGroup* cg;
299	>	Molecule::CutoffGroupIterator ci;
300	>
301	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
302	>
303	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
304	>	cg = mol->nextCutoffGroup(ci)) {
305	>	nLocalCutoffAtoms += cg->getNumAtom();
306	>
307	>	}
308		}
309	+
310	+	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
311		}
312	+
313	+	void SimInfo::calcNdfRaw() {
314	+	int ndfRaw_local;
315
316	<	setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
317	<
318	<	}
319	<
316	>	MoleculeIterator i;
317	>	vector<StuntDouble*>::iterator j;
318	>	Molecule* mol;
319	>	StuntDouble* sd;
320
321	<	void SimInfo::getBoxM (double theBox[3][3]) {
322	<
323	<	int i, j;
324	<	for(i=0; i<3; i++)
144	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
145	<	}
321	>	// Raw degrees of freedom that we have to set
322	>	ndfRaw_local = 0;
323	>
324	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
325
326	+	for (sd = mol->beginIntegrableObject(j); sd != NULL;
327	+	sd = mol->nextIntegrableObject(j)) {
328
329	<	void SimInfo::scaleBox(double scale) {
149	<	double theBox[3][3];
150	<	int i, j;
329	>	ndfRaw_local += 3;
330
331	<	// cerr << "Scaling box by " << scale << "\n";
332	<
333	<	for(i=0; i<3; i++)
334	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
335	<
336	<	setBoxM(theBox);
337	<
338	<	}
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	<	}
331	>	if (sd->isDirectional()) {
332	>	if (sd->isLinear()) {
333	>	ndfRaw_local += 2;
334	>	} else {
335	>	ndfRaw_local += 3;
336	>	}
337	>	}
338	>
339		}
340		}
190	–	}
191	–
192	–	if( oldOrtho != orthoRhombic ){
341
342	<	if( orthoRhombic ) {
343	<	sprintf( painCave.errMsg,
344	<	"OOPSE is switching from the default Non-Orthorhombic\n"
345	<	"\tto the faster Orthorhombic periodic boundary computations.\n"
346	<	"\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	<	}
342	>	#ifdef IS_MPI
343	>	MPI::COMM_WORLD.Allreduce(&ndfRaw_local, &ndfRaw_, 1, MPI::INT, MPI::SUM);
344	>	#else
345	>	ndfRaw_ = ndfRaw_local;
346	>	#endif
347		}
218	–	}
348
349	<	void SimInfo::calcBoxL( void ){
349	>	void SimInfo::calcNdfTrans() {
350	>	int ndfTrans_local;
351
352	<	double dx, dy, dz, dsq;
352	>	ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
353
224	–	// boxVol = Determinant of Hmat
354
355	<	boxVol = matDet3( Hmat );
355	>	#ifdef IS_MPI
356	>	MPI::COMM_WORLD.Allreduce(&ndfTrans_local, &ndfTrans_, 1,
357	>	MPI::INT, MPI::SUM);
358	>	#else
359	>	ndfTrans_ = ndfTrans_local;
360	>	#endif
361
362	<	// boxLx
363	<
364	<	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];
362	>	ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
363	>
364	>	}
365
366	<	// boxLy
367	<
368	<	dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
369	<	dsq = dx*dx + dy*dy + dz*dz;
370	<	boxL[1] = sqrt( dsq );
371	<	//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
366	>	void SimInfo::addInteractionPairs(Molecule* mol) {
367	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
368	>	vector<Bond*>::iterator bondIter;
369	>	vector<Bend*>::iterator bendIter;
370	>	vector<Torsion*>::iterator torsionIter;
371	>	vector<Inversion*>::iterator inversionIter;
372	>	Bond* bond;
373	>	Bend* bend;
374	>	Torsion* torsion;
375	>	Inversion* inversion;
376	>	int a;
377	>	int b;
378	>	int c;
379	>	int d;
380
381	+	// atomGroups can be used to add special interaction maps between
382	+	// groups of atoms that are in two separate rigid bodies.
383	+	// However, most site-site interactions between two rigid bodies
384	+	// are probably not special, just the ones between the physically
385	+	// bonded atoms.  Interactions *within* a single rigid body should
386	+	// always be excluded.  These are done at the bottom of this
387	+	// function.
388
389	<	// boxLz
390	<
391	<	dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
392	<	dsq = dx*dx + dy*dy + dz*dz;
393	<	boxL[2] = sqrt( dsq );
394	<	//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
389	>	map<int, set<int> > atomGroups;
390	>	Molecule::RigidBodyIterator rbIter;
391	>	RigidBody* rb;
392	>	Molecule::IntegrableObjectIterator ii;
393	>	StuntDouble* sd;
394	>
395	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
396	>	sd = mol->nextIntegrableObject(ii)) {
397	>
398	>	if (sd->isRigidBody()) {
399	>	rb = static_cast<RigidBody*>(sd);
400	>	vector<Atom*> atoms = rb->getAtoms();
401	>	set<int> rigidAtoms;
402	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
403	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
404	>	}
405	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
406	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
407	>	}
408	>	} else {
409	>	set<int> oneAtomSet;
410	>	oneAtomSet.insert(sd->getGlobalIndex());
411	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
412	>	}
413	>	}
414	>
415	>	for (bond= mol->beginBond(bondIter); bond != NULL;
416	>	bond = mol->nextBond(bondIter)) {
417
418	<	//calculate the max cutoff
419	<	maxCutoff =  calcMaxCutOff();
252	<
253	<	checkCutOffs();
418	>	a = bond->getAtomA()->getGlobalIndex();
419	>	b = bond->getAtomB()->getGlobalIndex();
420
421	<	}
421	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
422	>	oneTwoInteractions_.addPair(a, b);
423	>	} else {
424	>	excludedInteractions_.addPair(a, b);
425	>	}
426	>	}
427
428	+	for (bend= mol->beginBend(bendIter); bend != NULL;
429	+	bend = mol->nextBend(bendIter)) {
430
431	<	double SimInfo::calcMaxCutOff(){
431	>	a = bend->getAtomA()->getGlobalIndex();
432	>	b = bend->getAtomB()->getGlobalIndex();
433	>	c = bend->getAtomC()->getGlobalIndex();
434	>
435	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
436	>	oneTwoInteractions_.addPair(a, b);
437	>	oneTwoInteractions_.addPair(b, c);
438	>	} else {
439	>	excludedInteractions_.addPair(a, b);
440	>	excludedInteractions_.addPair(b, c);
441	>	}
442
443	<	double ri[3], rj[3], rk[3];
444	<	double rij[3], rjk[3], rki[3];
445	<	double minDist;
443	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
444	>	oneThreeInteractions_.addPair(a, c);
445	>	} else {
446	>	excludedInteractions_.addPair(a, c);
447	>	}
448	>	}
449
450	<	ri[0] = Hmat[0][0];
451	<	ri[1] = Hmat[1][0];
266	<	ri[2] = Hmat[2][0];
450	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
451	>	torsion = mol->nextTorsion(torsionIter)) {
452
453	<	rj[0] = Hmat[0][1];
454	<	rj[1] = Hmat[1][1];
455	<	rj[2] = Hmat[2][1];
453	>	a = torsion->getAtomA()->getGlobalIndex();
454	>	b = torsion->getAtomB()->getGlobalIndex();
455	>	c = torsion->getAtomC()->getGlobalIndex();
456	>	d = torsion->getAtomD()->getGlobalIndex();
457
458	<	rk[0] = Hmat[0][2];
459	<	rk[1] = Hmat[1][2];
460	<	rk[2] = Hmat[2][2];
461	<
462	<	crossProduct3(ri, rj, rij);
463	<	distXY = dotProduct3(rk,rij) / norm3(rij);
458	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
459	>	oneTwoInteractions_.addPair(a, b);
460	>	oneTwoInteractions_.addPair(b, c);
461	>	oneTwoInteractions_.addPair(c, d);
462	>	} else {
463	>	excludedInteractions_.addPair(a, b);
464	>	excludedInteractions_.addPair(b, c);
465	>	excludedInteractions_.addPair(c, d);
466	>	}
467
468	<	crossProduct3(rj,rk, rjk);
469	<	distYZ = dotProduct3(ri,rjk) / norm3(rjk);
468	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
469	>	oneThreeInteractions_.addPair(a, c);
470	>	oneThreeInteractions_.addPair(b, d);
471	>	} else {
472	>	excludedInteractions_.addPair(a, c);
473	>	excludedInteractions_.addPair(b, d);
474	>	}
475
476	<	crossProduct3(rk,ri, rki);
477	<	distZX = dotProduct3(rj,rki) / norm3(rki);
476	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
477	>	oneFourInteractions_.addPair(a, d);
478	>	} else {
479	>	excludedInteractions_.addPair(a, d);
480	>	}
481	>	}
482
483	<	minDist = min(min(distXY, distYZ), distZX);
484	<	return minDist/2;
287	<
288	<	}
483	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
484	>	inversion = mol->nextInversion(inversionIter)) {
485
486	<	void SimInfo::wrapVector( double thePos[3] ){
486	>	a = inversion->getAtomA()->getGlobalIndex();
487	>	b = inversion->getAtomB()->getGlobalIndex();
488	>	c = inversion->getAtomC()->getGlobalIndex();
489	>	d = inversion->getAtomD()->getGlobalIndex();
490
491	<	int i;
492	<	double scaled[3];
491	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
492	>	oneTwoInteractions_.addPair(a, b);
493	>	oneTwoInteractions_.addPair(a, c);
494	>	oneTwoInteractions_.addPair(a, d);
495	>	} else {
496	>	excludedInteractions_.addPair(a, b);
497	>	excludedInteractions_.addPair(a, c);
498	>	excludedInteractions_.addPair(a, d);
499	>	}
500
501	<	if( !orthoRhombic ){
502	<	// calc the scaled coordinates.
503	<
501	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
502	>	oneThreeInteractions_.addPair(b, c);
503	>	oneThreeInteractions_.addPair(b, d);
504	>	oneThreeInteractions_.addPair(c, d);
505	>	} else {
506	>	excludedInteractions_.addPair(b, c);
507	>	excludedInteractions_.addPair(b, d);
508	>	excludedInteractions_.addPair(c, d);
509	>	}
510	>	}
511
512	<	matVecMul3(HmatInv, thePos, scaled);
513	<
514	<	for(i=0; i<3; i++)
515	<	scaled[i] -= roundMe(scaled[i]);
516	<
517	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
518	<
519	<	matVecMul3(Hmat, scaled, thePos);
512	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
513	>	rb = mol->nextRigidBody(rbIter)) {
514	>	vector<Atom*> atoms = rb->getAtoms();
515	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
516	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
517	>	a = atoms[i]->getGlobalIndex();
518	>	b = atoms[j]->getGlobalIndex();
519	>	excludedInteractions_.addPair(a, b);
520	>	}
521	>	}
522	>	}
523
524		}
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	–	}
525
526	+	void SimInfo::removeInteractionPairs(Molecule* mol) {
527	+	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
528	+	vector<Bond*>::iterator bondIter;
529	+	vector<Bend*>::iterator bendIter;
530	+	vector<Torsion*>::iterator torsionIter;
531	+	vector<Inversion*>::iterator inversionIter;
532	+	Bond* bond;
533	+	Bend* bend;
534	+	Torsion* torsion;
535	+	Inversion* inversion;
536	+	int a;
537	+	int b;
538	+	int c;
539	+	int d;
540
541	<	int SimInfo::getNDF(){
542	<	int ndf_local;
543	<
544	<	ndf_local = 0;
545	<
546	<	for(int i = 0; i < integrableObjects.size(); i++){
547	<	ndf_local += 3;
548	<	if (integrableObjects[i]->isDirectional()) {
549	<	if (integrableObjects[i]->isLinear())
550	<	ndf_local += 2;
551	<	else
552	<	ndf_local += 3;
541	>	map<int, set<int> > atomGroups;
542	>	Molecule::RigidBodyIterator rbIter;
543	>	RigidBody* rb;
544	>	Molecule::IntegrableObjectIterator ii;
545	>	StuntDouble* sd;
546	>
547	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
548	>	sd = mol->nextIntegrableObject(ii)) {
549	>
550	>	if (sd->isRigidBody()) {
551	>	rb = static_cast<RigidBody*>(sd);
552	>	vector<Atom*> atoms = rb->getAtoms();
553	>	set<int> rigidAtoms;
554	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
555	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
556	>	}
557	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
558	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
559	>	}
560	>	} else {
561	>	set<int> oneAtomSet;
562	>	oneAtomSet.insert(sd->getGlobalIndex());
563	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
564	>	}
565	>	}
566	>
567	>	for (bond= mol->beginBond(bondIter); bond != NULL;
568	>	bond = mol->nextBond(bondIter)) {
569	>
570	>	a = bond->getAtomA()->getGlobalIndex();
571	>	b = bond->getAtomB()->getGlobalIndex();
572	>
573	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
574	>	oneTwoInteractions_.removePair(a, b);
575	>	} else {
576	>	excludedInteractions_.removePair(a, b);
577	>	}
578		}
342	–	}
579
580	<	// n_constraints is local, so subtract them on each processor:
580	>	for (bend= mol->beginBend(bendIter); bend != NULL;
581	>	bend = mol->nextBend(bendIter)) {
582
583	<	ndf_local -= n_constraints;
583	>	a = bend->getAtomA()->getGlobalIndex();
584	>	b = bend->getAtomB()->getGlobalIndex();
585	>	c = bend->getAtomC()->getGlobalIndex();
586	>
587	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
588	>	oneTwoInteractions_.removePair(a, b);
589	>	oneTwoInteractions_.removePair(b, c);
590	>	} else {
591	>	excludedInteractions_.removePair(a, b);
592	>	excludedInteractions_.removePair(b, c);
593	>	}
594
595	<	#ifdef IS_MPI
596	<	MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
597	<	#else
598	<	ndf = ndf_local;
599	<	#endif
595	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
596	>	oneThreeInteractions_.removePair(a, c);
597	>	} else {
598	>	excludedInteractions_.removePair(a, c);
599	>	}
600	>	}
601
602	<	// nZconstraints is global, as are the 3 COM translations for the
603	<	// entire system:
602	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
603	>	torsion = mol->nextTorsion(torsionIter)) {
604
605	<	ndf = ndf - 3 - nZconstraints;
605	>	a = torsion->getAtomA()->getGlobalIndex();
606	>	b = torsion->getAtomB()->getGlobalIndex();
607	>	c = torsion->getAtomC()->getGlobalIndex();
608	>	d = torsion->getAtomD()->getGlobalIndex();
609	>
610	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
611	>	oneTwoInteractions_.removePair(a, b);
612	>	oneTwoInteractions_.removePair(b, c);
613	>	oneTwoInteractions_.removePair(c, d);
614	>	} else {
615	>	excludedInteractions_.removePair(a, b);
616	>	excludedInteractions_.removePair(b, c);
617	>	excludedInteractions_.removePair(c, d);
618	>	}
619
620	<	return ndf;
621	<	}
620	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
621	>	oneThreeInteractions_.removePair(a, c);
622	>	oneThreeInteractions_.removePair(b, d);
623	>	} else {
624	>	excludedInteractions_.removePair(a, c);
625	>	excludedInteractions_.removePair(b, d);
626	>	}
627
628	<	int SimInfo::getNDFraw() {
629	<	int ndfRaw_local;
628	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
629	>	oneFourInteractions_.removePair(a, d);
630	>	} else {
631	>	excludedInteractions_.removePair(a, d);
632	>	}
633	>	}
634
635	<	// Raw degrees of freedom that we have to set
636	<	ndfRaw_local = 0;
635	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
636	>	inversion = mol->nextInversion(inversionIter)) {
637
638	<	for(int i = 0; i < integrableObjects.size(); i++){
639	<	ndfRaw_local += 3;
640	<	if (integrableObjects[i]->isDirectional()) {
641	<	if (integrableObjects[i]->isLinear())
642	<	ndfRaw_local += 2;
643	<	else
644	<	ndfRaw_local += 3;
638	>	a = inversion->getAtomA()->getGlobalIndex();
639	>	b = inversion->getAtomB()->getGlobalIndex();
640	>	c = inversion->getAtomC()->getGlobalIndex();
641	>	d = inversion->getAtomD()->getGlobalIndex();
642	>
643	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
644	>	oneTwoInteractions_.removePair(a, b);
645	>	oneTwoInteractions_.removePair(a, c);
646	>	oneTwoInteractions_.removePair(a, d);
647	>	} else {
648	>	excludedInteractions_.removePair(a, b);
649	>	excludedInteractions_.removePair(a, c);
650	>	excludedInteractions_.removePair(a, d);
651	>	}
652	>
653	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
654	>	oneThreeInteractions_.removePair(b, c);
655	>	oneThreeInteractions_.removePair(b, d);
656	>	oneThreeInteractions_.removePair(c, d);
657	>	} else {
658	>	excludedInteractions_.removePair(b, c);
659	>	excludedInteractions_.removePair(b, d);
660	>	excludedInteractions_.removePair(c, d);
661	>	}
662		}
663	+
664	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
665	+	rb = mol->nextRigidBody(rbIter)) {
666	+	vector<Atom*> atoms = rb->getAtoms();
667	+	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
668	+	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
669	+	a = atoms[i]->getGlobalIndex();
670	+	b = atoms[j]->getGlobalIndex();
671	+	excludedInteractions_.removePair(a, b);
672	+	}
673	+	}
674	+	}
675	+
676		}
677	+
678	+
679	+	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
680	+	int curStampId;
681
682	+	//index from 0
683	+	curStampId = moleculeStamps_.size();
684	+
685	+	moleculeStamps_.push_back(molStamp);
686	+	molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
687	+	}
688	+
689	+
690	+	/**
691	+	* update
692	+	*
693	+	*  Performs the global checks and variable settings after the
694	+	*  objects have been created.
695	+	*
696	+	*/
697	+	void SimInfo::update() {
698	+	setupSimVariables();
699	+	calcNdf();
700	+	calcNdfRaw();
701	+	calcNdfTrans();
702	+	}
703	+
704	+	/**
705	+	* getSimulatedAtomTypes
706	+	*
707	+	* Returns an STL set of AtomType* that are actually present in this
708	+	* simulation.  Must query all processors to assemble this information.
709	+	*
710	+	*/
711	+	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
712	+	SimInfo::MoleculeIterator mi;
713	+	Molecule* mol;
714	+	Molecule::AtomIterator ai;
715	+	Atom* atom;
716	+	set<AtomType*> atomTypes;
717	+
718	+	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
719	+	for(atom = mol->beginAtom(ai); atom != NULL;
720	+	atom = mol->nextAtom(ai)) {
721	+	atomTypes.insert(atom->getAtomType());
722	+	}
723	+	}
724	+
725		#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
726
727	<	return ndfRaw;
728	<	}
727	>	// loop over the found atom types on this processor, and add their
728	>	// numerical idents to a vector:
729	>
730	>	vector<int> foundTypes;
731	>	set<AtomType*>::iterator i;
732	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
733	>	foundTypes.push_back( (*i)->getIdent() );
734
735	<	int SimInfo::getNDFtranslational() {
736	<	int ndfTrans_local;
735	>	// count_local holds the number of found types on this processor
736	>	int count_local = foundTypes.size();
737
738	<	ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
738	>	int nproc = MPI::COMM_WORLD.Get_size();
739
740	+	// we need arrays to hold the counts and displacement vectors for
741	+	// all processors
742	+	vector<int> counts(nproc, 0);
743	+	vector<int> disps(nproc, 0);
744
745	<	#ifdef IS_MPI
746	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
747	<	#else
748	<	ndfTrans = ndfTrans_local;
749	<	#endif
745	>	// fill the counts array
746	>	MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
747	>	1, MPI::INT);
748	>
749	>	// use the processor counts to compute the displacement array
750	>	disps[0] = 0;
751	>	int totalCount = counts[0];
752	>	for (int iproc = 1; iproc < nproc; iproc++) {
753	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
754	>	totalCount += counts[iproc];
755	>	}
756
757	<	ndfTrans = ndfTrans - 3 - nZconstraints;
757	>	// we need a (possibly redundant) set of all found types:
758	>	vector<int> ftGlobal(totalCount);
759	>
760	>	// now spray out the foundTypes to all the other processors:
761	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
762	>	&ftGlobal[0], &counts[0], &disps[0],
763	>	MPI::INT);
764
765	<	return ndfTrans;
402	<	}
765	>	vector<int>::iterator j;
766
767	<	int SimInfo::getTotIntegrableObjects() {
768	<	int nObjs_local;
769	<	int nObjs;
767	>	// foundIdents is a stl set, so inserting an already found ident
768	>	// will have no effect.
769	>	set<int> foundIdents;
770
771	<	nObjs_local =  integrableObjects.size();
771	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
772	>	foundIdents.insert((*j));
773	>
774	>	// now iterate over the foundIdents and get the actual atom types
775	>	// that correspond to these:
776	>	set<int>::iterator it;
777	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
778	>	atomTypes.insert( forceField_->getAtomType((*it)) );
779	>
780	>	#endif
781
782	+	return atomTypes;
783	+	}
784
785	+	void SimInfo::setupSimVariables() {
786	+	useAtomicVirial_ = simParams_->getUseAtomicVirial();
787	+	// we only call setAccumulateBoxDipole if the accumulateBoxDipole
788	+	// parameter is true
789	+	calcBoxDipole_ = false;
790	+	if ( simParams_->haveAccumulateBoxDipole() )
791	+	if ( simParams_->getAccumulateBoxDipole() ) {
792	+	calcBoxDipole_ = true;
793	+	}
794	+
795	+	set<AtomType*>::iterator i;
796	+	set<AtomType*> atomTypes;
797	+	atomTypes = getSimulatedAtomTypes();
798	+	bool usesElectrostatic = false;
799	+	bool usesMetallic = false;
800	+	bool usesDirectional = false;
801	+	bool usesFluctuatingCharges =  false;
802	+	//loop over all of the atom types
803	+	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
804	+	usesElectrostatic |= (*i)->isElectrostatic();
805	+	usesMetallic |= (*i)->isMetal();
806	+	usesDirectional |= (*i)->isDirectional();
807	+	usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
808	+	}
809	+
810		#ifdef IS_MPI
811	<	MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
811	>	bool temp;
812	>	temp = usesDirectional;
813	>	MPI::COMM_WORLD.Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI::BOOL,
814	>	MPI::LOR);
815	>
816	>	temp = usesMetallic;
817	>	MPI::COMM_WORLD.Allreduce(&temp, &usesMetallicAtoms_, 1, MPI::BOOL,
818	>	MPI::LOR);
819	>
820	>	temp = usesElectrostatic;
821	>	MPI::COMM_WORLD.Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI::BOOL,
822	>	MPI::LOR);
823	>
824	>	temp = usesFluctuatingCharges;
825	>	MPI::COMM_WORLD.Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI::BOOL,
826	>	MPI::LOR);
827		#else
828	<	nObjs = nObjs_local;
828	>
829	>	usesDirectionalAtoms_ = usesDirectional;
830	>	usesMetallicAtoms_ = usesMetallic;
831	>	usesElectrostaticAtoms_ = usesElectrostatic;
832	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
833	>
834		#endif
835	+
836	+	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
837	+	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
838	+	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
839	+	}
840
841
842	<	return nObjs;
843	<	}
842	>	vector<int> SimInfo::getGlobalAtomIndices() {
843	>	SimInfo::MoleculeIterator mi;
844	>	Molecule* mol;
845	>	Molecule::AtomIterator ai;
846	>	Atom* atom;
847
848	<	void SimInfo::refreshSim(){
848	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
849	>
850	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
851	>
852	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
853	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
854	>	}
855	>	}
856	>	return GlobalAtomIndices;
857	>	}
858
423	–	simtype fInfo;
424	–	int isError;
425	–	int n_global;
426	–	int* excl;
859
860	<	fInfo.dielect = 0.0;
860	>	vector<int> SimInfo::getGlobalGroupIndices() {
861	>	SimInfo::MoleculeIterator mi;
862	>	Molecule* mol;
863	>	Molecule::CutoffGroupIterator ci;
864	>	CutoffGroup* cg;
865
866	<	if( useDipoles ){
867	<	if( useReactionField )fInfo.dielect = dielectric;
866	>	vector<int> GlobalGroupIndices;
867	>
868	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
869	>
870	>	//local index of cutoff group is trivial, it only depends on the
871	>	//order of travesing
872	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
873	>	cg = mol->nextCutoffGroup(ci)) {
874	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
875	>	}
876	>	}
877	>	return GlobalGroupIndices;
878		}
879
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;
880
881	<	n_exclude = excludes->getSize();
448	<	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);
881	>	void SimInfo::prepareTopology() {
882
883	<	if( isError ){
883	>	//calculate mass ratio of cutoff group
884	>	SimInfo::MoleculeIterator mi;
885	>	Molecule* mol;
886	>	Molecule::CutoffGroupIterator ci;
887	>	CutoffGroup* cg;
888	>	Molecule::AtomIterator ai;
889	>	Atom* atom;
890	>	RealType totalMass;
891	>
892	>	/**
893	>	* The mass factor is the relative mass of an atom to the total
894	>	* mass of the cutoff group it belongs to.  By default, all atoms
895	>	* are their own cutoff groups, and therefore have mass factors of
896	>	* 1.  We need some special handling for massless atoms, which
897	>	* will be treated as carrying the entire mass of the cutoff
898	>	* group.
899	>	*/
900	>	massFactors_.clear();
901	>	massFactors_.resize(getNAtoms(), 1.0);
902
903	<	sprintf( painCave.errMsg,
904	<	"There was an error setting the simulation information in fortran.\n" );
905	<	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	<	}
903	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
904	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
905	>	cg = mol->nextCutoffGroup(ci)) {
906
907	<	void SimInfo::setDefaultRcut( double theRcut ){
908	<
909	<	haveRcut = 1;
910	<	rCut = theRcut;
911	<	rList = rCut + 1.0;
912	<
913	<	notifyFortranCutOffs( &rCut, &rSw, &rList );
914	<	}
907	>	totalMass = cg->getMass();
908	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
909	>	// Check for massless groups - set mfact to 1 if true
910	>	if (totalMass != 0)
911	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
912	>	else
913	>	massFactors_[atom->getLocalIndex()] = 1.0;
914	>	}
915	>	}
916	>	}
917
918	<	void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
918	>	// Build the identArray_
919
920	<	rSw = theRsw;
921	<	setDefaultRcut( theRcut );
922	<	}
920	>	identArray_.clear();
921	>	identArray_.reserve(getNAtoms());
922	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
923	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
924	>	identArray_.push_back(atom->getIdent());
925	>	}
926	>	}
927	>
928	>	//scan topology
929
930	+	int* excludeList = excludedInteractions_.getPairList();
931	+	int* oneTwoList = oneTwoInteractions_.getPairList();
932	+	int* oneThreeList = oneThreeInteractions_.getPairList();
933	+	int* oneFourList = oneFourInteractions_.getPairList();
934
935	<	void SimInfo::checkCutOffs( void ){
503	<
504	<	if( boxIsInit ){
505	<
506	<	//we need to check cutOffs against the box
507	<
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();
935	>	topologyDone_ = true;
936		}
535	–
536	–	}
937
938	<	void SimInfo::addProperty(GenericData* prop){
938	>	void SimInfo::addProperty(GenericData* genData) {
939	>	properties_.addProperty(genData);
940	>	}
941
942	<	map<string, GenericData*>::iterator result;
943	<	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	<
942	>	void SimInfo::removeProperty(const string& propName) {
943	>	properties_.removeProperty(propName);
944		}
552	–	else{
945
946	<	properties[prop->getID()] = prop;
946	>	void SimInfo::clearProperties() {
947	>	properties_.clearProperties();
948	>	}
949
950	+	vector<string> SimInfo::getPropertyNames() {
951	+	return properties_.getPropertyNames();
952		}
953	<
954	<	}
953	>
954	>	vector<GenericData*> SimInfo::getProperties() {
955	>	return properties_.getProperties();
956	>	}
957
958	<	GenericData* SimInfo::getProperty(const string& propName){
958	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
959	>	return properties_.getPropertyByName(propName);
960	>	}
961	>
962	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
963	>	if (sman_ == sman) {
964	>	return;
965	>	}
966	>	delete sman_;
967	>	sman_ = sman;
968	>
969	>	Molecule* mol;
970	>	RigidBody* rb;
971	>	Atom* atom;
972	>	CutoffGroup* cg;
973	>	SimInfo::MoleculeIterator mi;
974	>	Molecule::RigidBodyIterator rbIter;
975	>	Molecule::AtomIterator atomIter;
976	>	Molecule::CutoffGroupIterator cgIter;
977
978	<	map<string, GenericData*>::iterator result;
979	<
980	<	//string lowerCaseName = ();
981	<
982	<	result = properties.find(propName);
983	<
984	<	if(result != properties.end())
985	<	return (*result).second;
986	<	else
987	<	return NULL;
988	<	}
978	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
979	>
980	>	for (atom = mol->beginAtom(atomIter); atom != NULL;
981	>	atom = mol->nextAtom(atomIter)) {
982	>	atom->setSnapshotManager(sman_);
983	>	}
984	>
985	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
986	>	rb = mol->nextRigidBody(rbIter)) {
987	>	rb->setSnapshotManager(sman_);
988	>	}
989
990	+	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL;
991	+	cg = mol->nextCutoffGroup(cgIter)) {
992	+	cg->setSnapshotManager(sman_);
993	+	}
994	+	}
995	+
996	+	}
997
998	<	void SimInfo::getFortranGroupArrays(SimInfo* info,
999	<	vector<int>& FglobalGroupMembership,
1000	<	vector<double>& mfact){
998	>
999	>	ostream& operator <<(ostream& o, SimInfo& info) {
1000	>
1001	>	return o;
1002	>	}
1003	>
1004
1005	<	Molecule* myMols;
1006	<	Atom** myAtoms;
1007	<	int numAtom;
1008	<	double mtot;
1009	<	int numMol;
1010	<	int numCutoffGroups;
1011	<	CutoffGroup* myCutoffGroup;
1012	<	vector<CutoffGroup*>::iterator iterCutoff;
1013	<	Atom* cutoffAtom;
1014	<	vector<Atom*>::iterator iterAtom;
1015	<	int atomIndex;
590	<	double totalMass;
1005	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1006	>	if (index >= IOIndexToIntegrableObject.size()) {
1007	>	sprintf(painCave.errMsg,
1008	>	"SimInfo::getIOIndexToIntegrableObject Error: Integrable Object\n"
1009	>	"\tindex exceeds number of known objects!\n");
1010	>	painCave.isFatal = 1;
1011	>	simError();
1012	>	return NULL;
1013	>	} else
1014	>	return IOIndexToIntegrableObject.at(index);
1015	>	}
1016
1017	<	mfact.clear();
1018	<	FglobalGroupMembership.clear();
1019	<
1017	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1018	>	IOIndexToIntegrableObject= v;
1019	>	}
1020
1021	<	// Fix the silly fortran indexing problem
1021	>	int SimInfo::getNGlobalConstraints() {
1022	>	int nGlobalConstraints;
1023		#ifdef IS_MPI
1024	<	numAtom = mpiSim->getNAtomsGlobal();
1024	>	MPI::COMM_WORLD.Allreduce(&nConstraints_, &nGlobalConstraints, 1,
1025	>	MPI::INT, MPI::SUM);
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.
Revision 1796 by gezelter, Mon Sep 10 18:38:44 2012 UTC

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