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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 1938 by gezelter, Thu Oct 31 15:32:17 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
5	–	#include <iostream>
6	–	using namespace std;
7	–
8	–	#include "SimInfo.hpp"
9	–	#define __C
10	–	#include "fSimulation.h"
11	–	#include "simError.h"
12	–
13	–	#include "fortranWrappers.hpp"
14	–
15	–	#include "MatVec3.h"
16	–
50		#ifdef IS_MPI
51	<	#include "mpiSimulation.hpp"
51	>	#include <mpi.h>
52		#endif
53	+	#include <algorithm>
54	+	#include <set>
55	+	#include <map>
56
57	<	inline double roundMe( double x ){
58	<	return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
59	<	}
60	<
61	<	inline double min( double a, double b ){
62	<	return (a < b ) ? a : b;
63	<	}
57	>	#include "brains/SimInfo.hpp"
58	>	#include "math/Vector3.hpp"
59	>	#include "primitives/Molecule.hpp"
60	>	#include "primitives/StuntDouble.hpp"
61	>	#include "utils/MemoryUtils.hpp"
62	>	#include "utils/simError.h"
63	>	#include "selection/SelectionManager.hpp"
64	>	#include "io/ForceFieldOptions.hpp"
65	>	#include "brains/ForceField.hpp"
66	>	#include "nonbonded/SwitchingFunction.hpp"
67
68	<	SimInfo* currentInfo;
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::SimInfo(){
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	<	n_constraints = 0;
142	<	nZconstraints = 0;
143	<	n_oriented = 0;
144	<	n_dipoles = 0;
145	<	ndf = 0;
146	<	ndfRaw = 0;
147	<	nZconstraints = 0;
148	<	the_integrator = NULL;
149	<	setTemp = 0;
150	<	thermalTime = 0.0;
151	<	currentTime = 0.0;
152	<	rCut = 0.0;
153	<	rSw = 0.0;
46	<
47	<	haveRcut = 0;
48	<	haveRsw = 0;
49	<	boxIsInit = 0;
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	<	resetTime = 1e99;
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
53	–	orthoRhombic = 0;
54	–	orthoTolerance = 1E-6;
55	–	useInitXSstate = true;
167
168	<	usePBC = 0;
169	<	useLJ = 0;
170	<	useSticky = 0;
171	<	useCharges = 0;
172	<	useDipoles = 0;
173	<	useReactionField = 0;
174	<	useGB = 0;
175	<	useEAM = 0;
176	<	useSolidThermInt = 0;
177	<	useLiquidThermInt = 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	>	bool SimInfo::removeMolecule(Molecule* mol) {
195	>	MoleculeIterator i;
196	>	i = molecules_.find(mol->getGlobalIndex());
197
198	<	haveCutoffGroups = false;
198	>	if (i != molecules_.end() ) {
199
200	<	excludes = Exclude::Instance();
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	<	myConfiguration = new SimState();
212	>	removeInteractionPairs(mol);
213	>	molecules_.erase(mol->getGlobalIndex());
214
215	<	has_minimizer = false;
216	<	the_minimizer =NULL;
215	>	delete mol;
216	>
217	>	return true;
218	>	} else {
219	>	return false;
220	>	}
221	>	}
222
223	<	ngroup = 0;
223	>
224	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
225	>	i = molecules_.begin();
226	>	return i == molecules_.end() ? NULL : i->second;
227	>	}
228
229	<	wrapMeSimInfo( this );
230	<	}
229	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
230	>	++i;
231	>	return i == molecules_.end() ? NULL : i->second;
232	>	}
233
234
235	<	SimInfo::~SimInfo(){
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	<	delete myConfiguration;
241	>	Molecule* mol;
242	>	StuntDouble* sd;
243	>	Atom* atom;
244
245	<	map<string, GenericData*>::iterator i;
246	<
247	<	for(i = properties.begin(); i != properties.end(); i++)
248	<	delete (*i).second;
245	>	ndf_local = 0;
246	>	nfq_local = 0;
247	>
248	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
249
250	<	}
250	>	for (sd = mol->beginIntegrableObject(j); sd != NULL;
251	>	sd = mol->nextIntegrableObject(j)) {
252
253	<	void SimInfo::setBox(double newBox[3]) {
95	<
96	<	int i, j;
97	<	double tempMat[3][3];
253	>	ndf_local += 3;
254
255	<	for(i=0; i<3; i++)
256	<	for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
255	>	if (sd->isDirectional()) {
256	>	if (sd->isLinear()) {
257	>	ndf_local += 2;
258	>	} else {
259	>	ndf_local += 3;
260	>	}
261	>	}
262	>	}
263
264	<	tempMat[0][0] = newBox[0];
265	<	tempMat[1][1] = newBox[1];
266	<	tempMat[2][2] = newBox[2];
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	<	setBoxM( tempMat );
274	>	// n_constraints is local, so subtract them on each processor
275	>	ndf_local -= nConstraints_;
276
277	<	}
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	<	void SimInfo::setBoxM( double theBox[3][3] ){
287	<
288	<	int i, j;
113	<	double FortranHmat[9]; // to preserve compatibility with Fortran the
114	<	// ordering in the array is as follows:
115	<	// [ 0 3 6 ]
116	<	// [ 1 4 7 ]
117	<	// [ 2 5 8 ]
118	<	double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
286	>	// nZconstraints_ is global, as are the 3 COM translations for the
287	>	// entire system:
288	>	ndf_ = ndf_ - 3 - nZconstraint_;
289
290	<	if( !boxIsInit ) boxIsInit = 1;
290	>	}
291
292	<	for(i=0; i < 3; i++)
293	<	for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
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	<	calcBoxL();
302	<	calcHmatInv();
303	<
304	<	for(i=0; i < 3; i++) {
305	<	for (j=0; j < 3; j++) {
306	<	FortranHmat[3*j + i] = Hmat[i][j];
307	<	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	<
323	>	MoleculeIterator i;
324	>	vector<StuntDouble*>::iterator j;
325	>	Molecule* mol;
326	>	StuntDouble* sd;
327
328	<	void SimInfo::getBoxM (double theBox[3][3]) {
329	<
330	<	int i, j;
331	<	for(i=0; i<3; i++)
144	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
145	<	}
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	+	for (sd = mol->beginIntegrableObject(j); sd != NULL;
334	+	sd = mol->nextIntegrableObject(j)) {
335
336	<	void SimInfo::scaleBox(double scale) {
149	<	double theBox[3][3];
150	<	int i, j;
336	>	ndfRaw_local += 3;
337
338	<	// cerr << "Scaling box by " << scale << "\n";
339	<
340	<	for(i=0; i<3; i++)
341	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
342	<
343	<	setBoxM(theBox);
344	<
345	<	}
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	<	}
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<Atom*>::iterator atomIter;
376	>	vector<Bond*>::iterator bondIter;
377	>	vector<Bend*>::iterator bendIter;
378	>	vector<Torsion*>::iterator torsionIter;
379	>	vector<Inversion*>::iterator inversionIter;
380	>	Atom* atom;
381	>	Bond* bond;
382	>	Bend* bend;
383	>	Torsion* torsion;
384	>	Inversion* inversion;
385	>	int a;
386	>	int b;
387	>	int c;
388	>	int d;
389
390	+	// atomGroups can be used to add special interaction maps between
391	+	// groups of atoms that are in two separate rigid bodies.
392	+	// However, most site-site interactions between two rigid bodies
393	+	// are probably not special, just the ones between the physically
394	+	// bonded atoms.  Interactions *within* a single rigid body should
395	+	// always be excluded.  These are done at the bottom of this
396	+	// function.
397
398	<	// boxLz
399	<
400	<	dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
401	<	dsq = dx*dx + dy*dy + dz*dz;
402	<	boxL[2] = sqrt( dsq );
403	<	//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
398	>	map<int, set<int> > atomGroups;
399	>	Molecule::RigidBodyIterator rbIter;
400	>	RigidBody* rb;
401	>	Molecule::IntegrableObjectIterator ii;
402	>	StuntDouble* sd;
403	>
404	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
405	>	sd = mol->nextIntegrableObject(ii)) {
406	>
407	>	if (sd->isRigidBody()) {
408	>	rb = static_cast<RigidBody*>(sd);
409	>	vector<Atom*> atoms = rb->getAtoms();
410	>	set<int> rigidAtoms;
411	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
412	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
413	>	}
414	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
415	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
416	>	}
417	>	} else {
418	>	set<int> oneAtomSet;
419	>	oneAtomSet.insert(sd->getGlobalIndex());
420	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
421	>	}
422	>	}
423
424	<	//calculate the max cutoff
425	<	maxCutoff =  calcMaxCutOff();
426	<
253	<	checkCutOffs();
424	>
425	>	for (bond= mol->beginBond(bondIter); bond != NULL;
426	>	bond = mol->nextBond(bondIter)) {
427
428	<	}
428	>	a = bond->getAtomA()->getGlobalIndex();
429	>	b = bond->getAtomB()->getGlobalIndex();
430
431	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
432	+	oneTwoInteractions_.addPair(a, b);
433	+	} else {
434	+	excludedInteractions_.addPair(a, b);
435	+	}
436	+	}
437
438	<	double SimInfo::calcMaxCutOff(){
438	>	for (bend= mol->beginBend(bendIter); bend != NULL;
439	>	bend = mol->nextBend(bendIter)) {
440
441	<	double ri[3], rj[3], rk[3];
442	<	double rij[3], rjk[3], rki[3];
443	<	double minDist;
441	>	a = bend->getAtomA()->getGlobalIndex();
442	>	b = bend->getAtomB()->getGlobalIndex();
443	>	c = bend->getAtomC()->getGlobalIndex();
444	>
445	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
446	>	oneTwoInteractions_.addPair(a, b);
447	>	oneTwoInteractions_.addPair(b, c);
448	>	} else {
449	>	excludedInteractions_.addPair(a, b);
450	>	excludedInteractions_.addPair(b, c);
451	>	}
452
453	<	ri[0] = Hmat[0][0];
454	<	ri[1] = Hmat[1][0];
455	<	ri[2] = Hmat[2][0];
453	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
454	>	oneThreeInteractions_.addPair(a, c);
455	>	} else {
456	>	excludedInteractions_.addPair(a, c);
457	>	}
458	>	}
459
460	<	rj[0] = Hmat[0][1];
461	<	rj[1] = Hmat[1][1];
270	<	rj[2] = Hmat[2][1];
460	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
461	>	torsion = mol->nextTorsion(torsionIter)) {
462
463	<	rk[0] = Hmat[0][2];
464	<	rk[1] = Hmat[1][2];
465	<	rk[2] = Hmat[2][2];
466	<
276	<	crossProduct3(ri, rj, rij);
277	<	distXY = dotProduct3(rk,rij) / norm3(rij);
463	>	a = torsion->getAtomA()->getGlobalIndex();
464	>	b = torsion->getAtomB()->getGlobalIndex();
465	>	c = torsion->getAtomC()->getGlobalIndex();
466	>	d = torsion->getAtomD()->getGlobalIndex();
467
468	<	crossProduct3(rj,rk, rjk);
469	<	distYZ = dotProduct3(ri,rjk) / norm3(rjk);
468	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
469	>	oneTwoInteractions_.addPair(a, b);
470	>	oneTwoInteractions_.addPair(b, c);
471	>	oneTwoInteractions_.addPair(c, d);
472	>	} else {
473	>	excludedInteractions_.addPair(a, b);
474	>	excludedInteractions_.addPair(b, c);
475	>	excludedInteractions_.addPair(c, d);
476	>	}
477
478	<	crossProduct3(rk,ri, rki);
479	<	distZX = dotProduct3(rj,rki) / norm3(rki);
478	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
479	>	oneThreeInteractions_.addPair(a, c);
480	>	oneThreeInteractions_.addPair(b, d);
481	>	} else {
482	>	excludedInteractions_.addPair(a, c);
483	>	excludedInteractions_.addPair(b, d);
484	>	}
485
486	<	minDist = min(min(distXY, distYZ), distZX);
487	<	return minDist/2;
488	<
489	<	}
486	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
487	>	oneFourInteractions_.addPair(a, d);
488	>	} else {
489	>	excludedInteractions_.addPair(a, d);
490	>	}
491	>	}
492
493	<	void SimInfo::wrapVector( double thePos[3] ){
493	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
494	>	inversion = mol->nextInversion(inversionIter)) {
495
496	<	int i;
497	<	double scaled[3];
496	>	a = inversion->getAtomA()->getGlobalIndex();
497	>	b = inversion->getAtomB()->getGlobalIndex();
498	>	c = inversion->getAtomC()->getGlobalIndex();
499	>	d = inversion->getAtomD()->getGlobalIndex();
500
501	<	if( !orthoRhombic ){
502	<	// calc the scaled coordinates.
503	<
501	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
502	>	oneTwoInteractions_.addPair(a, b);
503	>	oneTwoInteractions_.addPair(a, c);
504	>	oneTwoInteractions_.addPair(a, d);
505	>	} else {
506	>	excludedInteractions_.addPair(a, b);
507	>	excludedInteractions_.addPair(a, c);
508	>	excludedInteractions_.addPair(a, d);
509	>	}
510
511	<	matVecMul3(HmatInv, thePos, scaled);
512	<
513	<	for(i=0; i<3; i++)
514	<	scaled[i] -= roundMe(scaled[i]);
515	<
516	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
517	<
518	<	matVecMul3(Hmat, scaled, thePos);
511	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
512	>	oneThreeInteractions_.addPair(b, c);
513	>	oneThreeInteractions_.addPair(b, d);
514	>	oneThreeInteractions_.addPair(c, d);
515	>	} else {
516	>	excludedInteractions_.addPair(b, c);
517	>	excludedInteractions_.addPair(b, d);
518	>	excludedInteractions_.addPair(c, d);
519	>	}
520	>	}
521
522	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
523	+	rb = mol->nextRigidBody(rbIter)) {
524	+	vector<Atom*> atoms = rb->getAtoms();
525	+	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
526	+	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
527	+	a = atoms[i]->getGlobalIndex();
528	+	b = atoms[j]->getGlobalIndex();
529	+	excludedInteractions_.addPair(a, b);
530	+	}
531	+	}
532	+	}
533	+
534		}
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	–	}
535
536	+	void SimInfo::removeInteractionPairs(Molecule* mol) {
537	+	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
538	+	vector<Bond*>::iterator bondIter;
539	+	vector<Bend*>::iterator bendIter;
540	+	vector<Torsion*>::iterator torsionIter;
541	+	vector<Inversion*>::iterator inversionIter;
542	+	Bond* bond;
543	+	Bend* bend;
544	+	Torsion* torsion;
545	+	Inversion* inversion;
546	+	int a;
547	+	int b;
548	+	int c;
549	+	int d;
550
551	<	int SimInfo::getNDF(){
552	<	int ndf_local;
553	<
554	<	ndf_local = 0;
555	<
556	<	for(int i = 0; i < integrableObjects.size(); i++){
557	<	ndf_local += 3;
558	<	if (integrableObjects[i]->isDirectional()) {
559	<	if (integrableObjects[i]->isLinear())
560	<	ndf_local += 2;
561	<	else
562	<	ndf_local += 3;
551	>	map<int, set<int> > atomGroups;
552	>	Molecule::RigidBodyIterator rbIter;
553	>	RigidBody* rb;
554	>	Molecule::IntegrableObjectIterator ii;
555	>	StuntDouble* sd;
556	>
557	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
558	>	sd = mol->nextIntegrableObject(ii)) {
559	>
560	>	if (sd->isRigidBody()) {
561	>	rb = static_cast<RigidBody*>(sd);
562	>	vector<Atom*> atoms = rb->getAtoms();
563	>	set<int> rigidAtoms;
564	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
565	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
566	>	}
567	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
568	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
569	>	}
570	>	} else {
571	>	set<int> oneAtomSet;
572	>	oneAtomSet.insert(sd->getGlobalIndex());
573	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
574	>	}
575	>	}
576	>
577	>	for (bond= mol->beginBond(bondIter); bond != NULL;
578	>	bond = mol->nextBond(bondIter)) {
579	>
580	>	a = bond->getAtomA()->getGlobalIndex();
581	>	b = bond->getAtomB()->getGlobalIndex();
582	>
583	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
584	>	oneTwoInteractions_.removePair(a, b);
585	>	} else {
586	>	excludedInteractions_.removePair(a, b);
587	>	}
588		}
342	–	}
589
590	<	// n_constraints is local, so subtract them on each processor:
590	>	for (bend= mol->beginBend(bendIter); bend != NULL;
591	>	bend = mol->nextBend(bendIter)) {
592
593	<	ndf_local -= n_constraints;
593	>	a = bend->getAtomA()->getGlobalIndex();
594	>	b = bend->getAtomB()->getGlobalIndex();
595	>	c = bend->getAtomC()->getGlobalIndex();
596	>
597	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
598	>	oneTwoInteractions_.removePair(a, b);
599	>	oneTwoInteractions_.removePair(b, c);
600	>	} else {
601	>	excludedInteractions_.removePair(a, b);
602	>	excludedInteractions_.removePair(b, c);
603	>	}
604
605	<	#ifdef IS_MPI
606	<	MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
607	<	#else
608	<	ndf = ndf_local;
609	<	#endif
605	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
606	>	oneThreeInteractions_.removePair(a, c);
607	>	} else {
608	>	excludedInteractions_.removePair(a, c);
609	>	}
610	>	}
611
612	<	// nZconstraints is global, as are the 3 COM translations for the
613	<	// entire system:
612	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
613	>	torsion = mol->nextTorsion(torsionIter)) {
614
615	<	ndf = ndf - 3 - nZconstraints;
615	>	a = torsion->getAtomA()->getGlobalIndex();
616	>	b = torsion->getAtomB()->getGlobalIndex();
617	>	c = torsion->getAtomC()->getGlobalIndex();
618	>	d = torsion->getAtomD()->getGlobalIndex();
619	>
620	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
621	>	oneTwoInteractions_.removePair(a, b);
622	>	oneTwoInteractions_.removePair(b, c);
623	>	oneTwoInteractions_.removePair(c, d);
624	>	} else {
625	>	excludedInteractions_.removePair(a, b);
626	>	excludedInteractions_.removePair(b, c);
627	>	excludedInteractions_.removePair(c, d);
628	>	}
629
630	<	return ndf;
631	<	}
630	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
631	>	oneThreeInteractions_.removePair(a, c);
632	>	oneThreeInteractions_.removePair(b, d);
633	>	} else {
634	>	excludedInteractions_.removePair(a, c);
635	>	excludedInteractions_.removePair(b, d);
636	>	}
637
638	<	int SimInfo::getNDFraw() {
639	<	int ndfRaw_local;
638	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
639	>	oneFourInteractions_.removePair(a, d);
640	>	} else {
641	>	excludedInteractions_.removePair(a, d);
642	>	}
643	>	}
644
645	<	// Raw degrees of freedom that we have to set
646	<	ndfRaw_local = 0;
645	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
646	>	inversion = mol->nextInversion(inversionIter)) {
647
648	<	for(int i = 0; i < integrableObjects.size(); i++){
649	<	ndfRaw_local += 3;
650	<	if (integrableObjects[i]->isDirectional()) {
651	<	if (integrableObjects[i]->isLinear())
652	<	ndfRaw_local += 2;
653	<	else
654	<	ndfRaw_local += 3;
648	>	a = inversion->getAtomA()->getGlobalIndex();
649	>	b = inversion->getAtomB()->getGlobalIndex();
650	>	c = inversion->getAtomC()->getGlobalIndex();
651	>	d = inversion->getAtomD()->getGlobalIndex();
652	>
653	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
654	>	oneTwoInteractions_.removePair(a, b);
655	>	oneTwoInteractions_.removePair(a, c);
656	>	oneTwoInteractions_.removePair(a, d);
657	>	} else {
658	>	excludedInteractions_.removePair(a, b);
659	>	excludedInteractions_.removePair(a, c);
660	>	excludedInteractions_.removePair(a, d);
661	>	}
662	>
663	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
664	>	oneThreeInteractions_.removePair(b, c);
665	>	oneThreeInteractions_.removePair(b, d);
666	>	oneThreeInteractions_.removePair(c, d);
667	>	} else {
668	>	excludedInteractions_.removePair(b, c);
669	>	excludedInteractions_.removePair(b, d);
670	>	excludedInteractions_.removePair(c, d);
671	>	}
672		}
673	+
674	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
675	+	rb = mol->nextRigidBody(rbIter)) {
676	+	vector<Atom*> atoms = rb->getAtoms();
677	+	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
678	+	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
679	+	a = atoms[i]->getGlobalIndex();
680	+	b = atoms[j]->getGlobalIndex();
681	+	excludedInteractions_.removePair(a, b);
682	+	}
683	+	}
684	+	}
685	+
686		}
687	+
688	+
689	+	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
690	+	int curStampId;
691
692	<	#ifdef IS_MPI
693	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
380	<	#else
381	<	ndfRaw = ndfRaw_local;
382	<	#endif
692	>	//index from 0
693	>	curStampId = moleculeStamps_.size();
694
695	<	return ndfRaw;
696	<	}
695	>	moleculeStamps_.push_back(molStamp);
696	>	molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
697	>	}
698
387	–	int SimInfo::getNDFtranslational() {
388	–	int ndfTrans_local;
699
700	<	ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
701	<
702	<
700	>	/**
701	>	* update
702	>	*
703	>	*  Performs the global checks and variable settings after the
704	>	*  objects have been created.
705	>	*
706	>	*/
707	>	void SimInfo::update() {
708	>	setupSimVariables();
709	>	calcNdf();
710	>	calcNdfRaw();
711	>	calcNdfTrans();
712	>	}
713	>
714	>	/**
715	>	* getSimulatedAtomTypes
716	>	*
717	>	* Returns an STL set of AtomType* that are actually present in this
718	>	* simulation.  Must query all processors to assemble this information.
719	>	*
720	>	*/
721	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
722	>	SimInfo::MoleculeIterator mi;
723	>	Molecule* mol;
724	>	Molecule::AtomIterator ai;
725	>	Atom* atom;
726	>	set<AtomType*> atomTypes;
727	>
728	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
729	>	for(atom = mol->beginAtom(ai); atom != NULL;
730	>	atom = mol->nextAtom(ai)) {
731	>	atomTypes.insert(atom->getAtomType());
732	>	}
733	>	}
734	>
735		#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
736
737	<	ndfTrans = ndfTrans - 3 - nZconstraints;
737	>	// loop over the found atom types on this processor, and add their
738	>	// numerical idents to a vector:
739	>
740	>	vector<int> foundTypes;
741	>	set<AtomType*>::iterator i;
742	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
743	>	foundTypes.push_back( (*i)->getIdent() );
744
745	<	return ndfTrans;
746	<	}
745	>	// count_local holds the number of found types on this processor
746	>	int count_local = foundTypes.size();
747
748	<	int SimInfo::getTotIntegrableObjects() {
405	<	int nObjs_local;
406	<	int nObjs;
748	>	int nproc = MPI::COMM_WORLD.Get_size();
749
750	<	nObjs_local =  integrableObjects.size();
750	>	// we need arrays to hold the counts and displacement vectors for
751	>	// all processors
752	>	vector<int> counts(nproc, 0);
753	>	vector<int> disps(nproc, 0);
754
755	+	// fill the counts array
756	+	MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
757	+	1, MPI::INT);
758	+
759	+	// use the processor counts to compute the displacement array
760	+	disps[0] = 0;
761	+	int totalCount = counts[0];
762	+	for (int iproc = 1; iproc < nproc; iproc++) {
763	+	disps[iproc] = disps[iproc-1] + counts[iproc-1];
764	+	totalCount += counts[iproc];
765	+	}
766
767	<	#ifdef IS_MPI
768	<	MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
769	<	#else
770	<	nObjs = nObjs_local;
771	<	#endif
767	>	// we need a (possibly redundant) set of all found types:
768	>	vector<int> ftGlobal(totalCount);
769	>
770	>	// now spray out the foundTypes to all the other processors:
771	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
772	>	&ftGlobal[0], &counts[0], &disps[0],
773	>	MPI::INT);
774
775	+	vector<int>::iterator j;
776
777	<	return nObjs;
778	<	}
777	>	// foundIdents is a stl set, so inserting an already found ident
778	>	// will have no effect.
779	>	set<int> foundIdents;
780
781	<	void SimInfo::refreshSim(){
781	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
782	>	foundIdents.insert((*j));
783	>
784	>	// now iterate over the foundIdents and get the actual atom types
785	>	// that correspond to these:
786	>	set<int>::iterator it;
787	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
788	>	atomTypes.insert( forceField_->getAtomType((*it)) );
789	>
790	>	#endif
791
792	<	simtype fInfo;
793	<	int isError;
425	<	int n_global;
426	<	int* excl;
792	>	return atomTypes;
793	>	}
794
428	–	fInfo.dielect = 0.0;
795
796	<	if( useDipoles ){
797	<	if( useReactionField )fInfo.dielect = dielectric;
796	>	int getGlobalCountOfType(AtomType* atype) {
797	>	/*
798	>	set<AtomType*> atypes = getSimulatedAtomTypes();
799	>	map<AtomType*, int> counts_;
800	>
801	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
802	>	for(atom = mol->beginAtom(ai); atom != NULL;
803	>	atom = mol->nextAtom(ai)) {
804	>	atom->getAtomType();
805	>	}
806	>	}
807	>	*/
808	>	return 0;
809		}
810
811	<	fInfo.SIM_uses_PBC = usePBC;
812	<	//fInfo.SIM_uses_LJ = 0;
813	<	fInfo.SIM_uses_LJ = useLJ;
814	<	fInfo.SIM_uses_sticky = useSticky;
815	<	//fInfo.SIM_uses_sticky = 0;
816	<	fInfo.SIM_uses_charges = useCharges;
817	<	fInfo.SIM_uses_dipoles = useDipoles;
818	<	//fInfo.SIM_uses_dipoles = 0;
819	<	fInfo.SIM_uses_RF = useReactionField;
820	<	//fInfo.SIM_uses_RF = 0;
821	<	fInfo.SIM_uses_GB = useGB;
822	<	fInfo.SIM_uses_EAM = useEAM;
811	>	void SimInfo::setupSimVariables() {
812	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
813	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole
814	>	// parameter is true
815	>	calcBoxDipole_ = false;
816	>	if ( simParams_->haveAccumulateBoxDipole() )
817	>	if ( simParams_->getAccumulateBoxDipole() ) {
818	>	calcBoxDipole_ = true;
819	>	}
820	>
821	>	set<AtomType*>::iterator i;
822	>	set<AtomType*> atomTypes;
823	>	atomTypes = getSimulatedAtomTypes();
824	>	bool usesElectrostatic = false;
825	>	bool usesMetallic = false;
826	>	bool usesDirectional = false;
827	>	bool usesFluctuatingCharges =  false;
828	>	//loop over all of the atom types
829	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
830	>	usesElectrostatic |= (*i)->isElectrostatic();
831	>	usesMetallic |= (*i)->isMetal();
832	>	usesDirectional |= (*i)->isDirectional();
833	>	usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
834	>	}
835
447	–	n_exclude = excludes->getSize();
448	–	excl = excludes->getFortranArray();
449	–
836		#ifdef IS_MPI
837	<	n_global = mpiSim->getNAtomsGlobal();
837	>	bool temp;
838	>	temp = usesDirectional;
839	>	MPI::COMM_WORLD.Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI::BOOL,
840	>	MPI::LOR);
841	>
842	>	temp = usesMetallic;
843	>	MPI::COMM_WORLD.Allreduce(&temp, &usesMetallicAtoms_, 1, MPI::BOOL,
844	>	MPI::LOR);
845	>
846	>	temp = usesElectrostatic;
847	>	MPI::COMM_WORLD.Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI::BOOL,
848	>	MPI::LOR);
849	>
850	>	temp = usesFluctuatingCharges;
851	>	MPI::COMM_WORLD.Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI::BOOL,
852	>	MPI::LOR);
853		#else
854	<	n_global = n_atoms;
854	>
855	>	usesDirectionalAtoms_ = usesDirectional;
856	>	usesMetallicAtoms_ = usesMetallic;
857	>	usesElectrostaticAtoms_ = usesElectrostatic;
858	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
859	>
860		#endif
861	<
862	<	isError = 0;
863	<
864	<	getFortranGroupArrays(this, FglobalGroupMembership, mfact);
865	<	//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);
861	>
862	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
863	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
864	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
865	>	}
866
867	<	if( isError ){
867	>
868	>	vector<int> SimInfo::getGlobalAtomIndices() {
869	>	SimInfo::MoleculeIterator mi;
870	>	Molecule* mol;
871	>	Molecule::AtomIterator ai;
872	>	Atom* atom;
873	>
874	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
875
876	<	sprintf( painCave.errMsg,
877	<	"There was an error setting the simulation information in fortran.\n" );
878	<	painCave.isFatal = 1;
879	<	painCave.severity = OOPSE_ERROR;
880	<	simError();
876	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
877	>
878	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
879	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
880	>	}
881	>	}
882	>	return GlobalAtomIndices;
883		}
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	–	}
884
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	–	}
885
886	<	void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
886	>	vector<int> SimInfo::getGlobalGroupIndices() {
887	>	SimInfo::MoleculeIterator mi;
888	>	Molecule* mol;
889	>	Molecule::CutoffGroupIterator ci;
890	>	CutoffGroup* cg;
891
892	<	rSw = theRsw;
893	<	setDefaultRcut( theRcut );
894	<	}
892	>	vector<int> GlobalGroupIndices;
893	>
894	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
895	>
896	>	//local index of cutoff group is trivial, it only depends on the
897	>	//order of travesing
898	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
899	>	cg = mol->nextCutoffGroup(ci)) {
900	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
901	>	}
902	>	}
903	>	return GlobalGroupIndices;
904	>	}
905
906
907	<	void SimInfo::checkCutOffs( void ){
908	<
909	<	if( boxIsInit ){
907	>	void SimInfo::prepareTopology() {
908	>
909	>	//calculate mass ratio of cutoff group
910	>	SimInfo::MoleculeIterator mi;
911	>	Molecule* mol;
912	>	Molecule::CutoffGroupIterator ci;
913	>	CutoffGroup* cg;
914	>	Molecule::AtomIterator ai;
915	>	Atom* atom;
916	>	RealType totalMass;
917	>
918	>	/**
919	>	* The mass factor is the relative mass of an atom to the total
920	>	* mass of the cutoff group it belongs to.  By default, all atoms
921	>	* are their own cutoff groups, and therefore have mass factors of
922	>	* 1.  We need some special handling for massless atoms, which
923	>	* will be treated as carrying the entire mass of the cutoff
924	>	* group.
925	>	*/
926	>	massFactors_.clear();
927	>	massFactors_.resize(getNAtoms(), 1.0);
928
929	<	//we need to check cutOffs against the box
930	<
931	<	if( rCut > maxCutoff ){
932	<	sprintf( painCave.errMsg,
933	<	"cutoffRadius is too large for the current periodic box.\n"
934	<	"\tCurrent Value of cutoffRadius = %G at time %G\n "
935	<	"\tThis is larger than half of at least one of the\n"
936	<	"\tperiodic box vectors.  Right now, the Box matrix is:\n"
937	<	"\n"
938	<	"\t[ %G %G %G ]\n"
939	<	"\t[ %G %G %G ]\n"
940	<	"\t[ %G %G %G ]\n",
941	<	rCut, currentTime,
942	<	Hmat[0][0], Hmat[0][1], Hmat[0][2],
943	<	Hmat[1][0], Hmat[1][1], Hmat[1][2],
944	<	Hmat[2][0], Hmat[2][1], Hmat[2][2]);
945	<	painCave.severity = OOPSE_ERROR;
946	<	painCave.isFatal = 1;
947	<	simError();
929	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
930	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
931	>	cg = mol->nextCutoffGroup(ci)) {
932	>
933	>	totalMass = cg->getMass();
934	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
935	>	// Check for massless groups - set mfact to 1 if true
936	>	if (totalMass != 0)
937	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
938	>	else
939	>	massFactors_[atom->getLocalIndex()] = 1.0;
940	>	}
941	>	}
942	>	}
943	>
944	>	// Build the identArray_ and regions_
945	>
946	>	identArray_.clear();
947	>	identArray_.reserve(getNAtoms());
948	>	regions_.clear();
949	>	regions_.reserve(getNAtoms());
950	>
951	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
952	>	int reg = mol->getRegion();
953	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
954	>	identArray_.push_back(atom->getIdent());
955	>	regions_.push_back(reg);
956	>	}
957		}
958	<	} else {
959	<	// 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();
958	>
959	>	topologyDone_ = true;
960		}
535	–
536	–	}
961
962	<	void SimInfo::addProperty(GenericData* prop){
962	>	void SimInfo::addProperty(GenericData* genData) {
963	>	properties_.addProperty(genData);
964	>	}
965
966	<	map<string, GenericData*>::iterator result;
967	<	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	<
966	>	void SimInfo::removeProperty(const string& propName) {
967	>	properties_.removeProperty(propName);
968		}
552	–	else{
969
970	<	properties[prop->getID()] = prop;
970	>	void SimInfo::clearProperties() {
971	>	properties_.clearProperties();
972	>	}
973
974	+	vector<string> SimInfo::getPropertyNames() {
975	+	return properties_.getPropertyNames();
976		}
977	<
978	<	}
977	>
978	>	vector<GenericData*> SimInfo::getProperties() {
979	>	return properties_.getProperties();
980	>	}
981
982	<	GenericData* SimInfo::getProperty(const string& propName){
982	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
983	>	return properties_.getPropertyByName(propName);
984	>	}
985	>
986	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
987	>	if (sman_ == sman) {
988	>	return;
989	>	}
990	>	delete sman_;
991	>	sman_ = sman;
992	>
993	>	Molecule* mol;
994	>	RigidBody* rb;
995	>	Atom* atom;
996	>	CutoffGroup* cg;
997	>	SimInfo::MoleculeIterator mi;
998	>	Molecule::RigidBodyIterator rbIter;
999	>	Molecule::AtomIterator atomIter;
1000	>	Molecule::CutoffGroupIterator cgIter;
1001
1002	<	map<string, GenericData*>::iterator result;
1003	<
1004	<	//string lowerCaseName = ();
1005	<
1006	<	result = properties.find(propName);
1007	<
1008	<	if(result != properties.end())
1009	<	return (*result).second;
1010	<	else
1011	<	return NULL;
1012	<	}
1002	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1003	>
1004	>	for (atom = mol->beginAtom(atomIter); atom != NULL;
1005	>	atom = mol->nextAtom(atomIter)) {
1006	>	atom->setSnapshotManager(sman_);
1007	>	}
1008	>
1009	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
1010	>	rb = mol->nextRigidBody(rbIter)) {
1011	>	rb->setSnapshotManager(sman_);
1012	>	}
1013
1014	+	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL;
1015	+	cg = mol->nextCutoffGroup(cgIter)) {
1016	+	cg->setSnapshotManager(sman_);
1017	+	}
1018	+	}
1019	+
1020	+	}
1021
1022	<	void SimInfo::getFortranGroupArrays(SimInfo* info,
1023	<	vector<int>& FglobalGroupMembership,
1024	<	vector<double>& mfact){
1022	>
1023	>	ostream& operator <<(ostream& o, SimInfo& info) {
1024	>
1025	>	return o;
1026	>	}
1027	>
1028
1029	<	Molecule* myMols;
1030	<	Atom** myAtoms;
1031	<	int numAtom;
1032	<	double mtot;
1033	<	int numMol;
1034	<	int numCutoffGroups;
1035	<	CutoffGroup* myCutoffGroup;
1036	<	vector<CutoffGroup*>::iterator iterCutoff;
1037	<	Atom* cutoffAtom;
1038	<	vector<Atom*>::iterator iterAtom;
1039	<	int atomIndex;
590	<	double totalMass;
1029	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1030	>	if (index >= int(IOIndexToIntegrableObject.size())) {
1031	>	sprintf(painCave.errMsg,
1032	>	"SimInfo::getIOIndexToIntegrableObject Error: Integrable Object\n"
1033	>	"\tindex exceeds number of known objects!\n");
1034	>	painCave.isFatal = 1;
1035	>	simError();
1036	>	return NULL;
1037	>	} else
1038	>	return IOIndexToIntegrableObject.at(index);
1039	>	}
1040
1041	<	mfact.clear();
1042	<	FglobalGroupMembership.clear();
1043	<
1041	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1042	>	IOIndexToIntegrableObject= v;
1043	>	}
1044
1045	<	// Fix the silly fortran indexing problem
1045	>	int SimInfo::getNGlobalConstraints() {
1046	>	int nGlobalConstraints;
1047		#ifdef IS_MPI
1048	<	numAtom = mpiSim->getNAtomsGlobal();
1048	>	MPI::COMM_WORLD.Allreduce(&nConstraints_, &nGlobalConstraints, 1,
1049	>	MPI::INT, MPI::SUM);
1050		#else
1051	<	numAtom = n_atoms;
1051	>	nGlobalConstraints =  nConstraints_;
1052		#endif
1053	<	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	<	}
1053	>	return nGlobalConstraints;
1054		}
1055
1056	<	}
1056	>	}//end namespace OpenMD
1057	>

Comparing trunk/src/brains/SimInfo.cpp (property svn:keywords):
Revision 2 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
Revision 1938 by gezelter, Thu Oct 31 15:32:17 2013 UTC

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