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

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 2 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
Revision 1908 by gezelter, Fri Jul 19 21:25:45 2013 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, 234107 (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 "SimInfo.hpp"
55	<	#define __C
56	<	#include "fSimulation.h"
57	<	#include "simError.h"
58	<
59	<	#include "fortranWrappers.hpp"
60	<
61	<	#include "MatVec3.h"
62	<
54	>	#include "brains/SimInfo.hpp"
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	>	#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 "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	>	if ( (*i)->haveRegion() ) {
95	>	molStamp->setRegion( (*i)->getRegion() );
96	>	} else {
97	>	// set the region to a disallowed value:
98	>	molStamp->setRegion( -1 );
99	>	}
100
101	<	SimInfo* currentInfo;
101	>	nMolWithSameStamp = (*i)->getNMol();
102	>
103	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
104	>
105	>	//calculate atoms in molecules
106	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
107	>
108	>	//calculate atoms in cutoff groups
109	>	int nAtomsInGroups = 0;
110	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
111	>
112	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
113	>	cgStamp = molStamp->getCutoffGroupStamp(j);
114	>	nAtomsInGroups += cgStamp->getNMembers();
115	>	}
116	>
117	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
118	>
119	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
120	>
121	>	//calculate atoms in rigid bodies
122	>	int nAtomsInRigidBodies = 0;
123	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
124	>
125	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
126	>	rbStamp = molStamp->getRigidBodyStamp(j);
127	>	nAtomsInRigidBodies += rbStamp->getNMembers();
128	>	}
129	>
130	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
131	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
132	>
133	>	}
134	>
135	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
136	>	//group therefore the total number of cutoff groups in the system is
137	>	//equal to the total number of atoms minus number of atoms belong to
138	>	//cutoff group defined in meta-data file plus the number of cutoff
139	>	//groups defined in meta-data file
140
141	<	SimInfo::SimInfo(){
141	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
142	>
143	>	//every free atom (atom does not belong to rigid bodies) is an
144	>	//integrable object therefore the total number of integrable objects
145	>	//in the system is equal to the total number of atoms minus number of
146	>	//atoms belong to rigid body defined in meta-data file plus the number
147	>	//of rigid bodies defined in meta-data file
148	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
149	>	+ nGlobalRigidBodies_;
150	>
151	>	nGlobalMols_ = molStampIds_.size();
152	>	molToProcMap_.resize(nGlobalMols_);
153	>	}
154	>
155	>	SimInfo::~SimInfo() {
156	>	map<int, Molecule*>::iterator i;
157	>	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
158	>	delete i->second;
159	>	}
160	>	molecules_.clear();
161	>
162	>	delete sman_;
163	>	delete simParams_;
164	>	delete forceField_;
165	>	}
166
33	–	n_constraints = 0;
34	–	nZconstraints = 0;
35	–	n_oriented = 0;
36	–	n_dipoles = 0;
37	–	ndf = 0;
38	–	ndfRaw = 0;
39	–	nZconstraints = 0;
40	–	the_integrator = NULL;
41	–	setTemp = 0;
42	–	thermalTime = 0.0;
43	–	currentTime = 0.0;
44	–	rCut = 0.0;
45	–	rSw = 0.0;
167
168	<	haveRcut = 0;
169	<	haveRsw = 0;
170	<	boxIsInit = 0;
168	>	bool SimInfo::addMolecule(Molecule* mol) {
169	>	MoleculeIterator i;
170	>
171	>	i = molecules_.find(mol->getGlobalIndex());
172	>	if (i == molecules_.end() ) {
173	>
174	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
175	>
176	>	nAtoms_ += mol->getNAtoms();
177	>	nBonds_ += mol->getNBonds();
178	>	nBends_ += mol->getNBends();
179	>	nTorsions_ += mol->getNTorsions();
180	>	nInversions_ += mol->getNInversions();
181	>	nRigidBodies_ += mol->getNRigidBodies();
182	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
183	>	nCutoffGroups_ += mol->getNCutoffGroups();
184	>	nConstraints_ += mol->getNConstraintPairs();
185	>
186	>	addInteractionPairs(mol);
187	>
188	>	return true;
189	>	} else {
190	>	return false;
191	>	}
192	>	}
193
194	<	resetTime = 1e99;
194	>	bool SimInfo::removeMolecule(Molecule* mol) {
195	>	MoleculeIterator i;
196	>	i = molecules_.find(mol->getGlobalIndex());
197
198	<	orthoRhombic = 0;
54	<	orthoTolerance = 1E-6;
55	<	useInitXSstate = true;
198	>	if (i != molecules_.end() ) {
199
200	<	usePBC = 0;
201	<	useLJ = 0;
202	<	useSticky = 0;
203	<	useCharges = 0;
204	<	useDipoles = 0;
205	<	useReactionField = 0;
206	<	useGB = 0;
207	<	useEAM = 0;
208	<	useSolidThermInt = 0;
209	<	useLiquidThermInt = 0;
200	>	assert(mol == i->second);
201	>
202	>	nAtoms_ -= mol->getNAtoms();
203	>	nBonds_ -= mol->getNBonds();
204	>	nBends_ -= mol->getNBends();
205	>	nTorsions_ -= mol->getNTorsions();
206	>	nInversions_ -= mol->getNInversions();
207	>	nRigidBodies_ -= mol->getNRigidBodies();
208	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
209	>	nCutoffGroups_ -= mol->getNCutoffGroups();
210	>	nConstraints_ -= mol->getNConstraintPairs();
211
212	<	haveCutoffGroups = false;
212	>	removeInteractionPairs(mol);
213	>	molecules_.erase(mol->getGlobalIndex());
214
215	<	excludes = Exclude::Instance();
215	>	delete mol;
216	>
217	>	return true;
218	>	} else {
219	>	return false;
220	>	}
221	>	}
222
223	<	myConfiguration = new SimState();
223	>
224	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
225	>	i = molecules_.begin();
226	>	return i == molecules_.end() ? NULL : i->second;
227	>	}
228
229	<	has_minimizer = false;
230	<	the_minimizer =NULL;
229	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
230	>	++i;
231	>	return i == molecules_.end() ? NULL : i->second;
232	>	}
233
77	–	ngroup = 0;
234
235	<	wrapMeSimInfo( this );
236	<	}
235	>	void SimInfo::calcNdf() {
236	>	int ndf_local, nfq_local;
237	>	MoleculeIterator i;
238	>	vector<StuntDouble*>::iterator j;
239	>	vector<Atom*>::iterator k;
240
241	+	Molecule* mol;
242	+	StuntDouble* sd;
243	+	Atom* atom;
244
245	<	SimInfo::~SimInfo(){
245	>	ndf_local = 0;
246	>	nfq_local = 0;
247	>
248	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
249
250	<	delete myConfiguration;
250	>	for (sd = mol->beginIntegrableObject(j); sd != NULL;
251	>	sd = mol->nextIntegrableObject(j)) {
252
253	<	map<string, GenericData*>::iterator i;
88	<
89	<	for(i = properties.begin(); i != properties.end(); i++)
90	<	delete (*i).second;
253	>	ndf_local += 3;
254
255	<	}
255	>	if (sd->isDirectional()) {
256	>	if (sd->isLinear()) {
257	>	ndf_local += 2;
258	>	} else {
259	>	ndf_local += 3;
260	>	}
261	>	}
262	>	}
263
264	<	void SimInfo::setBox(double newBox[3]) {
265	<
266	<	int i, j;
267	<	double tempMat[3][3];
264	>	for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
265	>	atom = mol->nextFluctuatingCharge(k)) {
266	>	if (atom->isFluctuatingCharge()) {
267	>	nfq_local++;
268	>	}
269	>	}
270	>	}
271	>
272	>	ndfLocal_ = ndf_local;
273
274	<	for(i=0; i<3; i++)
275	<	for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
274	>	// n_constraints is local, so subtract them on each processor
275	>	ndf_local -= nConstraints_;
276
277	<	tempMat[0][0] = newBox[0];
278	<	tempMat[1][1] = newBox[1];
279	<	tempMat[2][2] = newBox[2];
277	>	#ifdef IS_MPI
278	>	MPI::COMM_WORLD.Allreduce(&ndf_local, &ndf_, 1, MPI::INT,MPI::SUM);
279	>	MPI::COMM_WORLD.Allreduce(&nfq_local, &nGlobalFluctuatingCharges_, 1,
280	>	MPI::INT, MPI::SUM);
281	>	#else
282	>	ndf_ = ndf_local;
283	>	nGlobalFluctuatingCharges_ = nfq_local;
284	>	#endif
285
286	<	setBoxM( tempMat );
286	>	// nZconstraints_ is global, as are the 3 COM translations for the
287	>	// entire system:
288	>	ndf_ = ndf_ - 3 - nZconstraint_;
289
290	<	}
290	>	}
291
292	<	void SimInfo::setBoxM( double theBox[3][3] ){
292	>	int SimInfo::getFdf() {
293	>	#ifdef IS_MPI
294	>	MPI::COMM_WORLD.Allreduce(&fdf_local, &fdf_, 1, MPI::INT, MPI::SUM);
295	>	#else
296	>	fdf_ = fdf_local;
297	>	#endif
298	>	return fdf_;
299	>	}
300
301	<	int i, j;
302	<	double FortranHmat[9]; // to preserve compatibility with Fortran the
303	<	// ordering in the array is as follows:
304	<	// [ 0 3 6 ]
305	<	// [ 1 4 7 ]
306	<	// [ 2 5 8 ]
307	<	double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
308	<
309	<	if( !boxIsInit ) boxIsInit = 1;
310	<
311	<	for(i=0; i < 3; i++)
312	<	for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
313	<
314	<	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];
301	>	unsigned int SimInfo::getNLocalCutoffGroups(){
302	>	int nLocalCutoffAtoms = 0;
303	>	Molecule* mol;
304	>	MoleculeIterator mi;
305	>	CutoffGroup* cg;
306	>	Molecule::CutoffGroupIterator ci;
307	>
308	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
309	>
310	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
311	>	cg = mol->nextCutoffGroup(ci)) {
312	>	nLocalCutoffAtoms += cg->getNumAtom();
313	>
314	>	}
315		}
316	+
317	+	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
318		}
319	+
320	+	void SimInfo::calcNdfRaw() {
321	+	int ndfRaw_local;
322
323	<	setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
324	<
325	<	}
326	<
139	<
140	<	void SimInfo::getBoxM (double theBox[3][3]) {
141	<
142	<	int i, j;
143	<	for(i=0; i<3; i++)
144	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
145	<	}
323	>	MoleculeIterator i;
324	>	vector<StuntDouble*>::iterator j;
325	>	Molecule* mol;
326	>	StuntDouble* sd;
327
328	+	// Raw degrees of freedom that we have to set
329	+	ndfRaw_local = 0;
330	+
331	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
332
333	<	void SimInfo::scaleBox(double scale) {
334	<	double theBox[3][3];
150	<	int i, j;
333	>	for (sd = mol->beginIntegrableObject(j); sd != NULL;
334	>	sd = mol->nextIntegrableObject(j)) {
335
336	<	// cerr << "Scaling box by " << scale << "\n";
336	>	ndfRaw_local += 3;
337
338	<	for(i=0; i<3; i++)
339	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
340	<
341	<	setBoxM(theBox);
342	<
343	<	}
344	<
345	<	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	<	}
338	>	if (sd->isDirectional()) {
339	>	if (sd->isLinear()) {
340	>	ndfRaw_local += 2;
341	>	} else {
342	>	ndfRaw_local += 3;
343	>	}
344	>	}
345	>
346		}
347		}
190	–	}
191	–
192	–	if( oldOrtho != orthoRhombic ){
348
349	<	if( orthoRhombic ) {
350	<	sprintf( painCave.errMsg,
351	<	"OOPSE is switching from the default Non-Orthorhombic\n"
352	<	"\tto the faster Orthorhombic periodic boundary computations.\n"
353	<	"\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	<	}
349	>	#ifdef IS_MPI
350	>	MPI::COMM_WORLD.Allreduce(&ndfRaw_local, &ndfRaw_, 1, MPI::INT, MPI::SUM);
351	>	#else
352	>	ndfRaw_ = ndfRaw_local;
353	>	#endif
354		}
218	–	}
355
356	<	void SimInfo::calcBoxL( void ){
356	>	void SimInfo::calcNdfTrans() {
357	>	int ndfTrans_local;
358
359	<	double dx, dy, dz, dsq;
359	>	ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
360
224	–	// boxVol = Determinant of Hmat
361
362	<	boxVol = matDet3( Hmat );
362	>	#ifdef IS_MPI
363	>	MPI::COMM_WORLD.Allreduce(&ndfTrans_local, &ndfTrans_, 1,
364	>	MPI::INT, MPI::SUM);
365	>	#else
366	>	ndfTrans_ = ndfTrans_local;
367	>	#endif
368
369	<	// boxLx
370	<
371	<	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];
369	>	ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
370	>
371	>	}
372
373	<	// boxLy
374	<
375	<	dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
376	<	dsq = dx*dx + dy*dy + dz*dz;
377	<	boxL[1] = sqrt( dsq );
378	<	//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
373	>	void SimInfo::addInteractionPairs(Molecule* mol) {
374	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
375	>	vector<Bond*>::iterator bondIter;
376	>	vector<Bend*>::iterator bendIter;
377	>	vector<Torsion*>::iterator torsionIter;
378	>	vector<Inversion*>::iterator inversionIter;
379	>	Bond* bond;
380	>	Bend* bend;
381	>	Torsion* torsion;
382	>	Inversion* inversion;
383	>	int a;
384	>	int b;
385	>	int c;
386	>	int d;
387
388	+	// atomGroups can be used to add special interaction maps between
389	+	// groups of atoms that are in two separate rigid bodies.
390	+	// However, most site-site interactions between two rigid bodies
391	+	// are probably not special, just the ones between the physically
392	+	// bonded atoms.  Interactions *within* a single rigid body should
393	+	// always be excluded.  These are done at the bottom of this
394	+	// function.
395
396	<	// boxLz
397	<
398	<	dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
399	<	dsq = dx*dx + dy*dy + dz*dz;
400	<	boxL[2] = sqrt( dsq );
401	<	//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
396	>	map<int, set<int> > atomGroups;
397	>	Molecule::RigidBodyIterator rbIter;
398	>	RigidBody* rb;
399	>	Molecule::IntegrableObjectIterator ii;
400	>	StuntDouble* sd;
401	>
402	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
403	>	sd = mol->nextIntegrableObject(ii)) {
404	>
405	>	if (sd->isRigidBody()) {
406	>	rb = static_cast<RigidBody*>(sd);
407	>	vector<Atom*> atoms = rb->getAtoms();
408	>	set<int> rigidAtoms;
409	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
410	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
411	>	}
412	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
413	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
414	>	}
415	>	} else {
416	>	set<int> oneAtomSet;
417	>	oneAtomSet.insert(sd->getGlobalIndex());
418	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
419	>	}
420	>	}
421	>
422	>	for (bond= mol->beginBond(bondIter); bond != NULL;
423	>	bond = mol->nextBond(bondIter)) {
424
425	<	//calculate the max cutoff
426	<	maxCutoff =  calcMaxCutOff();
252	<
253	<	checkCutOffs();
425	>	a = bond->getAtomA()->getGlobalIndex();
426	>	b = bond->getAtomB()->getGlobalIndex();
427
428	<	}
428	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
429	>	oneTwoInteractions_.addPair(a, b);
430	>	} else {
431	>	excludedInteractions_.addPair(a, b);
432	>	}
433	>	}
434
435	+	for (bend= mol->beginBend(bendIter); bend != NULL;
436	+	bend = mol->nextBend(bendIter)) {
437
438	<	double SimInfo::calcMaxCutOff(){
438	>	a = bend->getAtomA()->getGlobalIndex();
439	>	b = bend->getAtomB()->getGlobalIndex();
440	>	c = bend->getAtomC()->getGlobalIndex();
441	>
442	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
443	>	oneTwoInteractions_.addPair(a, b);
444	>	oneTwoInteractions_.addPair(b, c);
445	>	} else {
446	>	excludedInteractions_.addPair(a, b);
447	>	excludedInteractions_.addPair(b, c);
448	>	}
449
450	<	double ri[3], rj[3], rk[3];
451	<	double rij[3], rjk[3], rki[3];
452	<	double minDist;
450	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
451	>	oneThreeInteractions_.addPair(a, c);
452	>	} else {
453	>	excludedInteractions_.addPair(a, c);
454	>	}
455	>	}
456
457	<	ri[0] = Hmat[0][0];
458	<	ri[1] = Hmat[1][0];
266	<	ri[2] = Hmat[2][0];
457	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
458	>	torsion = mol->nextTorsion(torsionIter)) {
459
460	<	rj[0] = Hmat[0][1];
461	<	rj[1] = Hmat[1][1];
462	<	rj[2] = Hmat[2][1];
460	>	a = torsion->getAtomA()->getGlobalIndex();
461	>	b = torsion->getAtomB()->getGlobalIndex();
462	>	c = torsion->getAtomC()->getGlobalIndex();
463	>	d = torsion->getAtomD()->getGlobalIndex();
464
465	<	rk[0] = Hmat[0][2];
466	<	rk[1] = Hmat[1][2];
467	<	rk[2] = Hmat[2][2];
468	<
469	<	crossProduct3(ri, rj, rij);
470	<	distXY = dotProduct3(rk,rij) / norm3(rij);
465	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
466	>	oneTwoInteractions_.addPair(a, b);
467	>	oneTwoInteractions_.addPair(b, c);
468	>	oneTwoInteractions_.addPair(c, d);
469	>	} else {
470	>	excludedInteractions_.addPair(a, b);
471	>	excludedInteractions_.addPair(b, c);
472	>	excludedInteractions_.addPair(c, d);
473	>	}
474
475	<	crossProduct3(rj,rk, rjk);
476	<	distYZ = dotProduct3(ri,rjk) / norm3(rjk);
475	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
476	>	oneThreeInteractions_.addPair(a, c);
477	>	oneThreeInteractions_.addPair(b, d);
478	>	} else {
479	>	excludedInteractions_.addPair(a, c);
480	>	excludedInteractions_.addPair(b, d);
481	>	}
482
483	<	crossProduct3(rk,ri, rki);
484	<	distZX = dotProduct3(rj,rki) / norm3(rki);
483	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
484	>	oneFourInteractions_.addPair(a, d);
485	>	} else {
486	>	excludedInteractions_.addPair(a, d);
487	>	}
488	>	}
489
490	<	minDist = min(min(distXY, distYZ), distZX);
491	<	return minDist/2;
287	<
288	<	}
490	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
491	>	inversion = mol->nextInversion(inversionIter)) {
492
493	<	void SimInfo::wrapVector( double thePos[3] ){
493	>	a = inversion->getAtomA()->getGlobalIndex();
494	>	b = inversion->getAtomB()->getGlobalIndex();
495	>	c = inversion->getAtomC()->getGlobalIndex();
496	>	d = inversion->getAtomD()->getGlobalIndex();
497
498	<	int i;
499	<	double scaled[3];
498	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
499	>	oneTwoInteractions_.addPair(a, b);
500	>	oneTwoInteractions_.addPair(a, c);
501	>	oneTwoInteractions_.addPair(a, d);
502	>	} else {
503	>	excludedInteractions_.addPair(a, b);
504	>	excludedInteractions_.addPair(a, c);
505	>	excludedInteractions_.addPair(a, d);
506	>	}
507
508	<	if( !orthoRhombic ){
509	<	// calc the scaled coordinates.
510	<
508	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
509	>	oneThreeInteractions_.addPair(b, c);
510	>	oneThreeInteractions_.addPair(b, d);
511	>	oneThreeInteractions_.addPair(c, d);
512	>	} else {
513	>	excludedInteractions_.addPair(b, c);
514	>	excludedInteractions_.addPair(b, d);
515	>	excludedInteractions_.addPair(c, d);
516	>	}
517	>	}
518
519	<	matVecMul3(HmatInv, thePos, scaled);
520	<
521	<	for(i=0; i<3; i++)
522	<	scaled[i] -= roundMe(scaled[i]);
523	<
524	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
525	<
526	<	matVecMul3(Hmat, scaled, thePos);
519	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
520	>	rb = mol->nextRigidBody(rbIter)) {
521	>	vector<Atom*> atoms = rb->getAtoms();
522	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
523	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
524	>	a = atoms[i]->getGlobalIndex();
525	>	b = atoms[j]->getGlobalIndex();
526	>	excludedInteractions_.addPair(a, b);
527	>	}
528	>	}
529	>	}
530
531		}
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	–	}
532
533	+	void SimInfo::removeInteractionPairs(Molecule* mol) {
534	+	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
535	+	vector<Bond*>::iterator bondIter;
536	+	vector<Bend*>::iterator bendIter;
537	+	vector<Torsion*>::iterator torsionIter;
538	+	vector<Inversion*>::iterator inversionIter;
539	+	Bond* bond;
540	+	Bend* bend;
541	+	Torsion* torsion;
542	+	Inversion* inversion;
543	+	int a;
544	+	int b;
545	+	int c;
546	+	int d;
547
548	<	int SimInfo::getNDF(){
549	<	int ndf_local;
550	<
551	<	ndf_local = 0;
552	<
553	<	for(int i = 0; i < integrableObjects.size(); i++){
554	<	ndf_local += 3;
555	<	if (integrableObjects[i]->isDirectional()) {
556	<	if (integrableObjects[i]->isLinear())
557	<	ndf_local += 2;
558	<	else
559	<	ndf_local += 3;
548	>	map<int, set<int> > atomGroups;
549	>	Molecule::RigidBodyIterator rbIter;
550	>	RigidBody* rb;
551	>	Molecule::IntegrableObjectIterator ii;
552	>	StuntDouble* sd;
553	>
554	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
555	>	sd = mol->nextIntegrableObject(ii)) {
556	>
557	>	if (sd->isRigidBody()) {
558	>	rb = static_cast<RigidBody*>(sd);
559	>	vector<Atom*> atoms = rb->getAtoms();
560	>	set<int> rigidAtoms;
561	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
562	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
563	>	}
564	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
565	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
566	>	}
567	>	} else {
568	>	set<int> oneAtomSet;
569	>	oneAtomSet.insert(sd->getGlobalIndex());
570	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
571	>	}
572	>	}
573	>
574	>	for (bond= mol->beginBond(bondIter); bond != NULL;
575	>	bond = mol->nextBond(bondIter)) {
576	>
577	>	a = bond->getAtomA()->getGlobalIndex();
578	>	b = bond->getAtomB()->getGlobalIndex();
579	>
580	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
581	>	oneTwoInteractions_.removePair(a, b);
582	>	} else {
583	>	excludedInteractions_.removePair(a, b);
584	>	}
585		}
342	–	}
586
587	<	// n_constraints is local, so subtract them on each processor:
587	>	for (bend= mol->beginBend(bendIter); bend != NULL;
588	>	bend = mol->nextBend(bendIter)) {
589
590	<	ndf_local -= n_constraints;
590	>	a = bend->getAtomA()->getGlobalIndex();
591	>	b = bend->getAtomB()->getGlobalIndex();
592	>	c = bend->getAtomC()->getGlobalIndex();
593	>
594	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
595	>	oneTwoInteractions_.removePair(a, b);
596	>	oneTwoInteractions_.removePair(b, c);
597	>	} else {
598	>	excludedInteractions_.removePair(a, b);
599	>	excludedInteractions_.removePair(b, c);
600	>	}
601
602	<	#ifdef IS_MPI
603	<	MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
604	<	#else
605	<	ndf = ndf_local;
606	<	#endif
602	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
603	>	oneThreeInteractions_.removePair(a, c);
604	>	} else {
605	>	excludedInteractions_.removePair(a, c);
606	>	}
607	>	}
608
609	<	// nZconstraints is global, as are the 3 COM translations for the
610	<	// entire system:
609	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
610	>	torsion = mol->nextTorsion(torsionIter)) {
611
612	<	ndf = ndf - 3 - nZconstraints;
612	>	a = torsion->getAtomA()->getGlobalIndex();
613	>	b = torsion->getAtomB()->getGlobalIndex();
614	>	c = torsion->getAtomC()->getGlobalIndex();
615	>	d = torsion->getAtomD()->getGlobalIndex();
616	>
617	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
618	>	oneTwoInteractions_.removePair(a, b);
619	>	oneTwoInteractions_.removePair(b, c);
620	>	oneTwoInteractions_.removePair(c, d);
621	>	} else {
622	>	excludedInteractions_.removePair(a, b);
623	>	excludedInteractions_.removePair(b, c);
624	>	excludedInteractions_.removePair(c, d);
625	>	}
626
627	<	return ndf;
628	<	}
627	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
628	>	oneThreeInteractions_.removePair(a, c);
629	>	oneThreeInteractions_.removePair(b, d);
630	>	} else {
631	>	excludedInteractions_.removePair(a, c);
632	>	excludedInteractions_.removePair(b, d);
633	>	}
634
635	<	int SimInfo::getNDFraw() {
636	<	int ndfRaw_local;
635	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
636	>	oneFourInteractions_.removePair(a, d);
637	>	} else {
638	>	excludedInteractions_.removePair(a, d);
639	>	}
640	>	}
641
642	<	// Raw degrees of freedom that we have to set
643	<	ndfRaw_local = 0;
642	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
643	>	inversion = mol->nextInversion(inversionIter)) {
644
645	<	for(int i = 0; i < integrableObjects.size(); i++){
646	<	ndfRaw_local += 3;
647	<	if (integrableObjects[i]->isDirectional()) {
648	<	if (integrableObjects[i]->isLinear())
649	<	ndfRaw_local += 2;
650	<	else
651	<	ndfRaw_local += 3;
645	>	a = inversion->getAtomA()->getGlobalIndex();
646	>	b = inversion->getAtomB()->getGlobalIndex();
647	>	c = inversion->getAtomC()->getGlobalIndex();
648	>	d = inversion->getAtomD()->getGlobalIndex();
649	>
650	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
651	>	oneTwoInteractions_.removePair(a, b);
652	>	oneTwoInteractions_.removePair(a, c);
653	>	oneTwoInteractions_.removePair(a, d);
654	>	} else {
655	>	excludedInteractions_.removePair(a, b);
656	>	excludedInteractions_.removePair(a, c);
657	>	excludedInteractions_.removePair(a, d);
658	>	}
659	>
660	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
661	>	oneThreeInteractions_.removePair(b, c);
662	>	oneThreeInteractions_.removePair(b, d);
663	>	oneThreeInteractions_.removePair(c, d);
664	>	} else {
665	>	excludedInteractions_.removePair(b, c);
666	>	excludedInteractions_.removePair(b, d);
667	>	excludedInteractions_.removePair(c, d);
668	>	}
669		}
670	+
671	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
672	+	rb = mol->nextRigidBody(rbIter)) {
673	+	vector<Atom*> atoms = rb->getAtoms();
674	+	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
675	+	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
676	+	a = atoms[i]->getGlobalIndex();
677	+	b = atoms[j]->getGlobalIndex();
678	+	excludedInteractions_.removePair(a, b);
679	+	}
680	+	}
681	+	}
682	+
683		}
684	+
685	+
686	+	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
687	+	int curStampId;
688
689	<	#ifdef IS_MPI
690	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
380	<	#else
381	<	ndfRaw = ndfRaw_local;
382	<	#endif
689	>	//index from 0
690	>	curStampId = moleculeStamps_.size();
691
692	<	return ndfRaw;
693	<	}
692	>	moleculeStamps_.push_back(molStamp);
693	>	molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
694	>	}
695
387	–	int SimInfo::getNDFtranslational() {
388	–	int ndfTrans_local;
696
697	<	ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
698	<
699	<
697	>	/**
698	>	* update
699	>	*
700	>	*  Performs the global checks and variable settings after the
701	>	*  objects have been created.
702	>	*
703	>	*/
704	>	void SimInfo::update() {
705	>	setupSimVariables();
706	>	calcNdf();
707	>	calcNdfRaw();
708	>	calcNdfTrans();
709	>	}
710	>
711	>	/**
712	>	* getSimulatedAtomTypes
713	>	*
714	>	* Returns an STL set of AtomType* that are actually present in this
715	>	* simulation.  Must query all processors to assemble this information.
716	>	*
717	>	*/
718	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
719	>	SimInfo::MoleculeIterator mi;
720	>	Molecule* mol;
721	>	Molecule::AtomIterator ai;
722	>	Atom* atom;
723	>	set<AtomType*> atomTypes;
724	>
725	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
726	>	for(atom = mol->beginAtom(ai); atom != NULL;
727	>	atom = mol->nextAtom(ai)) {
728	>	atomTypes.insert(atom->getAtomType());
729	>	}
730	>	}
731	>
732		#ifdef IS_MPI
394	–	MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
395	–	#else
396	–	ndfTrans = ndfTrans_local;
397	–	#endif
733
734	<	ndfTrans = ndfTrans - 3 - nZconstraints;
734	>	// loop over the found atom types on this processor, and add their
735	>	// numerical idents to a vector:
736	>
737	>	vector<int> foundTypes;
738	>	set<AtomType*>::iterator i;
739	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
740	>	foundTypes.push_back( (*i)->getIdent() );
741
742	<	return ndfTrans;
743	<	}
742	>	// count_local holds the number of found types on this processor
743	>	int count_local = foundTypes.size();
744
745	<	int SimInfo::getTotIntegrableObjects() {
405	<	int nObjs_local;
406	<	int nObjs;
745	>	int nproc = MPI::COMM_WORLD.Get_size();
746
747	<	nObjs_local =  integrableObjects.size();
747	>	// we need arrays to hold the counts and displacement vectors for
748	>	// all processors
749	>	vector<int> counts(nproc, 0);
750	>	vector<int> disps(nproc, 0);
751
752	+	// fill the counts array
753	+	MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
754	+	1, MPI::INT);
755	+
756	+	// use the processor counts to compute the displacement array
757	+	disps[0] = 0;
758	+	int totalCount = counts[0];
759	+	for (int iproc = 1; iproc < nproc; iproc++) {
760	+	disps[iproc] = disps[iproc-1] + counts[iproc-1];
761	+	totalCount += counts[iproc];
762	+	}
763
764	<	#ifdef IS_MPI
765	<	MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
766	<	#else
767	<	nObjs = nObjs_local;
768	<	#endif
764	>	// we need a (possibly redundant) set of all found types:
765	>	vector<int> ftGlobal(totalCount);
766	>
767	>	// now spray out the foundTypes to all the other processors:
768	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
769	>	&ftGlobal[0], &counts[0], &disps[0],
770	>	MPI::INT);
771
772	+	vector<int>::iterator j;
773
774	<	return nObjs;
775	<	}
774	>	// foundIdents is a stl set, so inserting an already found ident
775	>	// will have no effect.
776	>	set<int> foundIdents;
777
778	<	void SimInfo::refreshSim(){
778	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
779	>	foundIdents.insert((*j));
780	>
781	>	// now iterate over the foundIdents and get the actual atom types
782	>	// that correspond to these:
783	>	set<int>::iterator it;
784	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
785	>	atomTypes.insert( forceField_->getAtomType((*it)) );
786	>
787	>	#endif
788
789	<	simtype fInfo;
790	<	int isError;
425	<	int n_global;
426	<	int* excl;
789	>	return atomTypes;
790	>	}
791
428	–	fInfo.dielect = 0.0;
792
793	<	if( useDipoles ){
794	<	if( useReactionField )fInfo.dielect = dielectric;
793	>	int getGlobalCountOfType(AtomType* atype) {
794	>	/*
795	>	set<AtomType*> atypes = getSimulatedAtomTypes();
796	>	map<AtomType*, int> counts_;
797	>
798	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
799	>	for(atom = mol->beginAtom(ai); atom != NULL;
800	>	atom = mol->nextAtom(ai)) {
801	>	atom->getAtomType();
802	>	}
803	>	}
804	>	*/
805	>	return 0;
806		}
807
808	<	fInfo.SIM_uses_PBC = usePBC;
809	<	//fInfo.SIM_uses_LJ = 0;
810	<	fInfo.SIM_uses_LJ = useLJ;
811	<	fInfo.SIM_uses_sticky = useSticky;
812	<	//fInfo.SIM_uses_sticky = 0;
813	<	fInfo.SIM_uses_charges = useCharges;
814	<	fInfo.SIM_uses_dipoles = useDipoles;
815	<	//fInfo.SIM_uses_dipoles = 0;
816	<	fInfo.SIM_uses_RF = useReactionField;
817	<	//fInfo.SIM_uses_RF = 0;
818	<	fInfo.SIM_uses_GB = useGB;
819	<	fInfo.SIM_uses_EAM = useEAM;
808	>	void SimInfo::setupSimVariables() {
809	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
810	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole
811	>	// parameter is true
812	>	calcBoxDipole_ = false;
813	>	if ( simParams_->haveAccumulateBoxDipole() )
814	>	if ( simParams_->getAccumulateBoxDipole() ) {
815	>	calcBoxDipole_ = true;
816	>	}
817	>
818	>	set<AtomType*>::iterator i;
819	>	set<AtomType*> atomTypes;
820	>	atomTypes = getSimulatedAtomTypes();
821	>	bool usesElectrostatic = false;
822	>	bool usesMetallic = false;
823	>	bool usesDirectional = false;
824	>	bool usesFluctuatingCharges =  false;
825	>	//loop over all of the atom types
826	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
827	>	usesElectrostatic |= (*i)->isElectrostatic();
828	>	usesMetallic |= (*i)->isMetal();
829	>	usesDirectional |= (*i)->isDirectional();
830	>	usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
831	>	}
832
447	–	n_exclude = excludes->getSize();
448	–	excl = excludes->getFortranArray();
449	–
833		#ifdef IS_MPI
834	<	n_global = mpiSim->getNAtomsGlobal();
834	>	bool temp;
835	>	temp = usesDirectional;
836	>	MPI::COMM_WORLD.Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI::BOOL,
837	>	MPI::LOR);
838	>
839	>	temp = usesMetallic;
840	>	MPI::COMM_WORLD.Allreduce(&temp, &usesMetallicAtoms_, 1, MPI::BOOL,
841	>	MPI::LOR);
842	>
843	>	temp = usesElectrostatic;
844	>	MPI::COMM_WORLD.Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI::BOOL,
845	>	MPI::LOR);
846	>
847	>	temp = usesFluctuatingCharges;
848	>	MPI::COMM_WORLD.Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI::BOOL,
849	>	MPI::LOR);
850		#else
851	<	n_global = n_atoms;
851	>
852	>	usesDirectionalAtoms_ = usesDirectional;
853	>	usesMetallicAtoms_ = usesMetallic;
854	>	usesElectrostaticAtoms_ = usesElectrostatic;
855	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
856	>
857		#endif
858	<
859	<	isError = 0;
860	<
861	<	getFortranGroupArrays(this, FglobalGroupMembership, mfact);
862	<	//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);
858	>
859	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
860	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
861	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
862	>	}
863
864	<	if( isError ){
864	>
865	>	vector<int> SimInfo::getGlobalAtomIndices() {
866	>	SimInfo::MoleculeIterator mi;
867	>	Molecule* mol;
868	>	Molecule::AtomIterator ai;
869	>	Atom* atom;
870	>
871	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
872
873	<	sprintf( painCave.errMsg,
874	<	"There was an error setting the simulation information in fortran.\n" );
875	<	painCave.isFatal = 1;
876	<	painCave.severity = OOPSE_ERROR;
877	<	simError();
873	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
874	>
875	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
876	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
877	>	}
878	>	}
879	>	return GlobalAtomIndices;
880		}
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	–	}
881
486	–	void SimInfo::setDefaultRcut( double theRcut ){
487	–
488	–	haveRcut = 1;
489	–	rCut = theRcut;
490	–	rList = rCut + 1.0;
491	–
492	–	notifyFortranCutOffs( &rCut, &rSw, &rList );
493	–	}
882
883	<	void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
883	>	vector<int> SimInfo::getGlobalGroupIndices() {
884	>	SimInfo::MoleculeIterator mi;
885	>	Molecule* mol;
886	>	Molecule::CutoffGroupIterator ci;
887	>	CutoffGroup* cg;
888
889	<	rSw = theRsw;
890	<	setDefaultRcut( theRcut );
891	<	}
889	>	vector<int> GlobalGroupIndices;
890	>
891	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
892	>
893	>	//local index of cutoff group is trivial, it only depends on the
894	>	//order of travesing
895	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
896	>	cg = mol->nextCutoffGroup(ci)) {
897	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
898	>	}
899	>	}
900	>	return GlobalGroupIndices;
901	>	}
902
903
904	<	void SimInfo::checkCutOffs( void ){
905	<
906	<	if( boxIsInit ){
904	>	void SimInfo::prepareTopology() {
905	>
906	>	//calculate mass ratio of cutoff group
907	>	SimInfo::MoleculeIterator mi;
908	>	Molecule* mol;
909	>	Molecule::CutoffGroupIterator ci;
910	>	CutoffGroup* cg;
911	>	Molecule::AtomIterator ai;
912	>	Atom* atom;
913	>	RealType totalMass;
914	>
915	>	/**
916	>	* The mass factor is the relative mass of an atom to the total
917	>	* mass of the cutoff group it belongs to.  By default, all atoms
918	>	* are their own cutoff groups, and therefore have mass factors of
919	>	* 1.  We need some special handling for massless atoms, which
920	>	* will be treated as carrying the entire mass of the cutoff
921	>	* group.
922	>	*/
923	>	massFactors_.clear();
924	>	massFactors_.resize(getNAtoms(), 1.0);
925
926	<	//we need to check cutOffs against the box
927	<
928	<	if( rCut > maxCutoff ){
929	<	sprintf( painCave.errMsg,
930	<	"cutoffRadius is too large for the current periodic box.\n"
931	<	"\tCurrent Value of cutoffRadius = %G at time %G\n "
932	<	"\tThis is larger than half of at least one of the\n"
933	<	"\tperiodic box vectors.  Right now, the Box matrix is:\n"
934	<	"\n"
935	<	"\t[ %G %G %G ]\n"
936	<	"\t[ %G %G %G ]\n"
937	<	"\t[ %G %G %G ]\n",
938	<	rCut, currentTime,
939	<	Hmat[0][0], Hmat[0][1], Hmat[0][2],
940	<	Hmat[1][0], Hmat[1][1], Hmat[1][2],
941	<	Hmat[2][0], Hmat[2][1], Hmat[2][2]);
942	<	painCave.severity = OOPSE_ERROR;
943	<	painCave.isFatal = 1;
944	<	simError();
926	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
927	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
928	>	cg = mol->nextCutoffGroup(ci)) {
929	>
930	>	totalMass = cg->getMass();
931	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
932	>	// Check for massless groups - set mfact to 1 if true
933	>	if (totalMass != 0)
934	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
935	>	else
936	>	massFactors_[atom->getLocalIndex()] = 1.0;
937	>	}
938	>	}
939	>	}
940	>
941	>	// Build the identArray_
942	>
943	>	identArray_.clear();
944	>	identArray_.reserve(getNAtoms());
945	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
946	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
947	>	identArray_.push_back(atom->getIdent());
948	>	}
949		}
950	<	} else {
951	<	// 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();
950	>
951	>	topologyDone_ = true;
952		}
535	–
536	–	}
953
954	<	void SimInfo::addProperty(GenericData* prop){
954	>	void SimInfo::addProperty(GenericData* genData) {
955	>	properties_.addProperty(genData);
956	>	}
957
958	<	map<string, GenericData*>::iterator result;
959	<	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	<
958	>	void SimInfo::removeProperty(const string& propName) {
959	>	properties_.removeProperty(propName);
960		}
552	–	else{
961
962	<	properties[prop->getID()] = prop;
962	>	void SimInfo::clearProperties() {
963	>	properties_.clearProperties();
964	>	}
965
966	+	vector<string> SimInfo::getPropertyNames() {
967	+	return properties_.getPropertyNames();
968		}
969	<
970	<	}
969	>
970	>	vector<GenericData*> SimInfo::getProperties() {
971	>	return properties_.getProperties();
972	>	}
973
974	<	GenericData* SimInfo::getProperty(const string& propName){
974	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
975	>	return properties_.getPropertyByName(propName);
976	>	}
977	>
978	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
979	>	if (sman_ == sman) {
980	>	return;
981	>	}
982	>	delete sman_;
983	>	sman_ = sman;
984	>
985	>	Molecule* mol;
986	>	RigidBody* rb;
987	>	Atom* atom;
988	>	CutoffGroup* cg;
989	>	SimInfo::MoleculeIterator mi;
990	>	Molecule::RigidBodyIterator rbIter;
991	>	Molecule::AtomIterator atomIter;
992	>	Molecule::CutoffGroupIterator cgIter;
993
994	<	map<string, GenericData*>::iterator result;
995	<
996	<	//string lowerCaseName = ();
997	<
998	<	result = properties.find(propName);
999	<
1000	<	if(result != properties.end())
1001	<	return (*result).second;
1002	<	else
1003	<	return NULL;
1004	<	}
994	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
995	>
996	>	for (atom = mol->beginAtom(atomIter); atom != NULL;
997	>	atom = mol->nextAtom(atomIter)) {
998	>	atom->setSnapshotManager(sman_);
999	>	}
1000	>
1001	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
1002	>	rb = mol->nextRigidBody(rbIter)) {
1003	>	rb->setSnapshotManager(sman_);
1004	>	}
1005
1006	+	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL;
1007	+	cg = mol->nextCutoffGroup(cgIter)) {
1008	+	cg->setSnapshotManager(sman_);
1009	+	}
1010	+	}
1011	+
1012	+	}
1013
1014	<	void SimInfo::getFortranGroupArrays(SimInfo* info,
1015	<	vector<int>& FglobalGroupMembership,
1016	<	vector<double>& mfact){
1014	>
1015	>	ostream& operator <<(ostream& o, SimInfo& info) {
1016	>
1017	>	return o;
1018	>	}
1019	>
1020
1021	<	Molecule* myMols;
1022	<	Atom** myAtoms;
1023	<	int numAtom;
1024	<	double mtot;
1025	<	int numMol;
1026	<	int numCutoffGroups;
1027	<	CutoffGroup* myCutoffGroup;
1028	<	vector<CutoffGroup*>::iterator iterCutoff;
1029	<	Atom* cutoffAtom;
1030	<	vector<Atom*>::iterator iterAtom;
1031	<	int atomIndex;
590	<	double totalMass;
1021	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1022	>	if (index >= int(IOIndexToIntegrableObject.size())) {
1023	>	sprintf(painCave.errMsg,
1024	>	"SimInfo::getIOIndexToIntegrableObject Error: Integrable Object\n"
1025	>	"\tindex exceeds number of known objects!\n");
1026	>	painCave.isFatal = 1;
1027	>	simError();
1028	>	return NULL;
1029	>	} else
1030	>	return IOIndexToIntegrableObject.at(index);
1031	>	}
1032
1033	<	mfact.clear();
1034	<	FglobalGroupMembership.clear();
1035	<
1033	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1034	>	IOIndexToIntegrableObject= v;
1035	>	}
1036
1037	<	// Fix the silly fortran indexing problem
1037	>	int SimInfo::getNGlobalConstraints() {
1038	>	int nGlobalConstraints;
1039		#ifdef IS_MPI
1040	<	numAtom = mpiSim->getNAtomsGlobal();
1040	>	MPI::COMM_WORLD.Allreduce(&nConstraints_, &nGlobalConstraints, 1,
1041	>	MPI::INT, MPI::SUM);
1042		#else
1043	<	numAtom = n_atoms;
1043	>	nGlobalConstraints =  nConstraints_;
1044		#endif
1045	<	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	<	}
1045	>	return nGlobalConstraints;
1046		}
1047
1048	<	}
1048	>	}//end namespace OpenMD
1049	>

Comparing trunk/src/brains/SimInfo.cpp (property svn:keywords):
Revision 2 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
Revision 1908 by gezelter, Fri Jul 19 21:25:45 2013 UTC

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