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

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 124 by chuckv, Wed Oct 20 20:46:20 2004 UTC vs.
Revision 1940 by gezelter, Fri Nov 1 19:31:41 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	>	#ifdef IS_MPI
51	>	#include <mpi.h>
52	>	#endif
53	>	#include <algorithm>
54	>	#include <set>
55	>	#include <map>
56
57		#include "brains/SimInfo.hpp"
58	<	#define __C
59	<	#include "brains/fSimulation.h"
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 "UseTheForce/DarkSide/simulation_interface.h"
64	<	#include "UseTheForce/notifyCutoffs_interface.h"
63	>	#include "selection/SelectionManager.hpp"
64	>	#include "io/ForceFieldOptions.hpp"
65	>	#include "brains/ForceField.hpp"
66	>	#include "nonbonded/SwitchingFunction.hpp"
67
68	<	//#include "UseTheForce/fortranWrappers.hpp"
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	<	#include "math/MatVec3.h"
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	<	#ifdef IS_MPI
142	<	#include "brains/mpiSimulation.hpp"
143	<	#endif
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
23	–	inline double roundMe( double x ){
24	–	return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
25	–	}
26	–
27	–	inline double min( double a, double b ){
28	–	return (a < b ) ? a : b;
29	–	}
167
168	<	SimInfo* currentInfo;
169	<
170	<	SimInfo::SimInfo(){
171	<
172	<	n_constraints = 0;
173	<	nZconstraints = 0;
174	<	n_oriented = 0;
175	<	n_dipoles = 0;
176	<	ndf = 0;
177	<	ndfRaw = 0;
178	<	nZconstraints = 0;
179	<	the_integrator = NULL;
180	<	setTemp = 0;
181	<	thermalTime = 0.0;
182	<	currentTime = 0.0;
183	<	rCut = 0.0;
184	<	rSw = 0.0;
185	<
186	<	haveRcut = 0;
187	<	haveRsw = 0;
188	<	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;
56	<	orthoTolerance = 1E-6;
57	<	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
79	–	ngroup = 0;
234
235	<	}
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;
89	<
90	<	for(i = properties.begin(); i != properties.end(); i++)
91	<	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();
127	<	calcHmatInv();
128	<
129	<	for(i=0; i < 3; i++) {
130	<	for (j=0; j < 3; j++) {
131	<	FortranHmat[3*j + i] = Hmat[i][j];
132	<	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	<	setFortranBox(FortranHmat, FortranHmatInv, &orthoRhombic);
324	<
325	<	}
326	<
140	<
141	<	void SimInfo::getBoxM (double theBox[3][3]) {
142	<
143	<	int i, j;
144	<	for(i=0; i<3; i++)
145	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
146	<	}
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];
151	<	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 ) {
163	<
164	<	int oldOrtho;
165	<	int i,j;
166	<	double smallDiag;
167	<	double tol;
168	<	double sanity[3][3];
169	<
170	<	invertMat3( Hmat, HmatInv );
171	<
172	<	// check to see if Hmat is orthorhombic
173	<
174	<	oldOrtho = orthoRhombic;
175	<
176	<	smallDiag = fabs(Hmat[0][0]);
177	<	if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
178	<	if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
179	<	tol = smallDiag * orthoTolerance;
180	<
181	<	orthoRhombic = 1;
182	<
183	<	for (i = 0; i < 3; i++ ) {
184	<	for (j = 0 ; j < 3; j++) {
185	<	if (i != j) {
186	<	if (orthoRhombic) {
187	<	if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
188	<	}
338	>	if (sd->isDirectional()) {
339	>	if (sd->isLinear()) {
340	>	ndfRaw_local += 2;
341	>	} else {
342	>	ndfRaw_local += 3;
343	>	}
344	>	}
345	>
346		}
347		}
191	–	}
192	–
193	–	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"
200	<	"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
201	<	"\tvariable ( currently set to %G ) smaller.\n",
202	<	orthoTolerance);
203	<	painCave.severity = OOPSE_INFO;
204	<	simError();
205	<	}
206	<	else {
207	<	sprintf( painCave.errMsg,
208	<	"OOPSE is switching from the faster Orthorhombic to the more\n"
209	<	"\tflexible Non-Orthorhombic periodic boundary computations.\n"
210	<	"\tThis is usually because the box has deformed under\n"
211	<	"\tNPTf integration. If you wan't to live on the edge with\n"
212	<	"\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
213	<	"\tvariable ( currently set to %G ) larger.\n",
214	<	orthoTolerance);
215	<	painCave.severity = OOPSE_WARNING;
216	<	simError();
217	<	}
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		}
219	–	}
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
225	–	// 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];
232	<	dsq = dx*dx + dy*dy + dz*dz;
233	<	boxL[0] = sqrt( dsq );
234	<	//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	<	//calculate the max cutoff
423	<	maxCutoff =  calcMaxCutOff();
424	<
254	<	checkCutOffs();
422	>
423	>	for (bond= mol->beginBond(bondIter); bond != NULL;
424	>	bond = mol->nextBond(bondIter)) {
425
426	<	}
426	>	a = bond->getAtomA()->getGlobalIndex();
427	>	b = bond->getAtomB()->getGlobalIndex();
428
429	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
430	+	oneTwoInteractions_.addPair(a, b);
431	+	} else {
432	+	excludedInteractions_.addPair(a, b);
433	+	}
434	+	}
435
436	<	double SimInfo::calcMaxCutOff(){
436	>	for (bend= mol->beginBend(bendIter); bend != NULL;
437	>	bend = mol->nextBend(bendIter)) {
438
439	<	double ri[3], rj[3], rk[3];
440	<	double rij[3], rjk[3], rki[3];
441	<	double minDist;
439	>	a = bend->getAtomA()->getGlobalIndex();
440	>	b = bend->getAtomB()->getGlobalIndex();
441	>	c = bend->getAtomC()->getGlobalIndex();
442	>
443	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
444	>	oneTwoInteractions_.addPair(a, b);
445	>	oneTwoInteractions_.addPair(b, c);
446	>	} else {
447	>	excludedInteractions_.addPair(a, b);
448	>	excludedInteractions_.addPair(b, c);
449	>	}
450
451	<	ri[0] = Hmat[0][0];
452	<	ri[1] = Hmat[1][0];
453	<	ri[2] = Hmat[2][0];
451	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
452	>	oneThreeInteractions_.addPair(a, c);
453	>	} else {
454	>	excludedInteractions_.addPair(a, c);
455	>	}
456	>	}
457
458	<	rj[0] = Hmat[0][1];
459	<	rj[1] = Hmat[1][1];
271	<	rj[2] = Hmat[2][1];
458	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
459	>	torsion = mol->nextTorsion(torsionIter)) {
460
461	<	rk[0] = Hmat[0][2];
462	<	rk[1] = Hmat[1][2];
463	<	rk[2] = Hmat[2][2];
464	<
277	<	crossProduct3(ri, rj, rij);
278	<	distXY = dotProduct3(rk,rij) / norm3(rij);
461	>	a = torsion->getAtomA()->getGlobalIndex();
462	>	b = torsion->getAtomB()->getGlobalIndex();
463	>	c = torsion->getAtomC()->getGlobalIndex();
464	>	d = torsion->getAtomD()->getGlobalIndex();
465
466	<	crossProduct3(rj,rk, rjk);
467	<	distYZ = dotProduct3(ri,rjk) / norm3(rjk);
466	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
467	>	oneTwoInteractions_.addPair(a, b);
468	>	oneTwoInteractions_.addPair(b, c);
469	>	oneTwoInteractions_.addPair(c, d);
470	>	} else {
471	>	excludedInteractions_.addPair(a, b);
472	>	excludedInteractions_.addPair(b, c);
473	>	excludedInteractions_.addPair(c, d);
474	>	}
475
476	<	crossProduct3(rk,ri, rki);
477	<	distZX = dotProduct3(rj,rki) / norm3(rki);
476	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
477	>	oneThreeInteractions_.addPair(a, c);
478	>	oneThreeInteractions_.addPair(b, d);
479	>	} else {
480	>	excludedInteractions_.addPair(a, c);
481	>	excludedInteractions_.addPair(b, d);
482	>	}
483
484	<	minDist = min(min(distXY, distYZ), distZX);
485	<	return minDist/2;
486	<
487	<	}
484	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
485	>	oneFourInteractions_.addPair(a, d);
486	>	} else {
487	>	excludedInteractions_.addPair(a, d);
488	>	}
489	>	}
490
491	<	void SimInfo::wrapVector( double thePos[3] ){
491	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
492	>	inversion = mol->nextInversion(inversionIter)) {
493
494	<	int i;
495	<	double scaled[3];
494	>	a = inversion->getAtomA()->getGlobalIndex();
495	>	b = inversion->getAtomB()->getGlobalIndex();
496	>	c = inversion->getAtomC()->getGlobalIndex();
497	>	d = inversion->getAtomD()->getGlobalIndex();
498
499	<	if( !orthoRhombic ){
500	<	// calc the scaled coordinates.
501	<
499	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
500	>	oneTwoInteractions_.addPair(a, b);
501	>	oneTwoInteractions_.addPair(a, c);
502	>	oneTwoInteractions_.addPair(a, d);
503	>	} else {
504	>	excludedInteractions_.addPair(a, b);
505	>	excludedInteractions_.addPair(a, c);
506	>	excludedInteractions_.addPair(a, d);
507	>	}
508
509	<	matVecMul3(HmatInv, thePos, scaled);
510	<
511	<	for(i=0; i<3; i++)
512	<	scaled[i] -= roundMe(scaled[i]);
513	<
514	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
515	<
516	<	matVecMul3(Hmat, scaled, thePos);
509	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
510	>	oneThreeInteractions_.addPair(b, c);
511	>	oneThreeInteractions_.addPair(b, d);
512	>	oneThreeInteractions_.addPair(c, d);
513	>	} else {
514	>	excludedInteractions_.addPair(b, c);
515	>	excludedInteractions_.addPair(b, d);
516	>	excludedInteractions_.addPair(c, d);
517	>	}
518	>	}
519
520	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
521	+	rb = mol->nextRigidBody(rbIter)) {
522	+	vector<Atom*> atoms = rb->getAtoms();
523	+	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
524	+	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
525	+	a = atoms[i]->getGlobalIndex();
526	+	b = atoms[j]->getGlobalIndex();
527	+	excludedInteractions_.addPair(a, b);
528	+	}
529	+	}
530	+	}
531	+
532		}
310	–	else{
311	–	// calc the scaled coordinates.
312	–
313	–	for(i=0; i<3; i++)
314	–	scaled[i] = thePos[i]*HmatInv[i][i];
315	–
316	–	// wrap the scaled coordinates
317	–
318	–	for(i=0; i<3; i++)
319	–	scaled[i] -= roundMe(scaled[i]);
320	–
321	–	// calc the wrapped real coordinates from the wrapped scaled coordinates
322	–
323	–	for(i=0; i<3; i++)
324	–	thePos[i] = scaled[i]*Hmat[i][i];
325	–	}
326	–
327	–	}
533
534	+	void SimInfo::removeInteractionPairs(Molecule* mol) {
535	+	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
536	+	vector<Bond*>::iterator bondIter;
537	+	vector<Bend*>::iterator bendIter;
538	+	vector<Torsion*>::iterator torsionIter;
539	+	vector<Inversion*>::iterator inversionIter;
540	+	Bond* bond;
541	+	Bend* bend;
542	+	Torsion* torsion;
543	+	Inversion* inversion;
544	+	int a;
545	+	int b;
546	+	int c;
547	+	int d;
548
549	<	int SimInfo::getNDF(){
550	<	int ndf_local;
551	<
552	<	ndf_local = 0;
553	<
554	<	for(int i = 0; i < integrableObjects.size(); i++){
555	<	ndf_local += 3;
556	<	if (integrableObjects[i]->isDirectional()) {
557	<	if (integrableObjects[i]->isLinear())
558	<	ndf_local += 2;
559	<	else
560	<	ndf_local += 3;
549	>	map<int, set<int> > atomGroups;
550	>	Molecule::RigidBodyIterator rbIter;
551	>	RigidBody* rb;
552	>	Molecule::IntegrableObjectIterator ii;
553	>	StuntDouble* sd;
554	>
555	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
556	>	sd = mol->nextIntegrableObject(ii)) {
557	>
558	>	if (sd->isRigidBody()) {
559	>	rb = static_cast<RigidBody*>(sd);
560	>	vector<Atom*> atoms = rb->getAtoms();
561	>	set<int> rigidAtoms;
562	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
563	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
564	>	}
565	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
566	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
567	>	}
568	>	} else {
569	>	set<int> oneAtomSet;
570	>	oneAtomSet.insert(sd->getGlobalIndex());
571	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
572	>	}
573	>	}
574	>
575	>	for (bond= mol->beginBond(bondIter); bond != NULL;
576	>	bond = mol->nextBond(bondIter)) {
577	>
578	>	a = bond->getAtomA()->getGlobalIndex();
579	>	b = bond->getAtomB()->getGlobalIndex();
580	>
581	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
582	>	oneTwoInteractions_.removePair(a, b);
583	>	} else {
584	>	excludedInteractions_.removePair(a, b);
585	>	}
586		}
343	–	}
587
588	<	// n_constraints is local, so subtract them on each processor:
588	>	for (bend= mol->beginBend(bendIter); bend != NULL;
589	>	bend = mol->nextBend(bendIter)) {
590
591	<	ndf_local -= n_constraints;
591	>	a = bend->getAtomA()->getGlobalIndex();
592	>	b = bend->getAtomB()->getGlobalIndex();
593	>	c = bend->getAtomC()->getGlobalIndex();
594	>
595	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
596	>	oneTwoInteractions_.removePair(a, b);
597	>	oneTwoInteractions_.removePair(b, c);
598	>	} else {
599	>	excludedInteractions_.removePair(a, b);
600	>	excludedInteractions_.removePair(b, c);
601	>	}
602
603	<	#ifdef IS_MPI
604	<	MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
605	<	#else
606	<	ndf = ndf_local;
607	<	#endif
603	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
604	>	oneThreeInteractions_.removePair(a, c);
605	>	} else {
606	>	excludedInteractions_.removePair(a, c);
607	>	}
608	>	}
609
610	<	// nZconstraints is global, as are the 3 COM translations for the
611	<	// entire system:
610	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
611	>	torsion = mol->nextTorsion(torsionIter)) {
612
613	<	ndf = ndf - 3 - nZconstraints;
613	>	a = torsion->getAtomA()->getGlobalIndex();
614	>	b = torsion->getAtomB()->getGlobalIndex();
615	>	c = torsion->getAtomC()->getGlobalIndex();
616	>	d = torsion->getAtomD()->getGlobalIndex();
617	>
618	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
619	>	oneTwoInteractions_.removePair(a, b);
620	>	oneTwoInteractions_.removePair(b, c);
621	>	oneTwoInteractions_.removePair(c, d);
622	>	} else {
623	>	excludedInteractions_.removePair(a, b);
624	>	excludedInteractions_.removePair(b, c);
625	>	excludedInteractions_.removePair(c, d);
626	>	}
627
628	<	return ndf;
629	<	}
628	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
629	>	oneThreeInteractions_.removePair(a, c);
630	>	oneThreeInteractions_.removePair(b, d);
631	>	} else {
632	>	excludedInteractions_.removePair(a, c);
633	>	excludedInteractions_.removePair(b, d);
634	>	}
635
636	<	int SimInfo::getNDFraw() {
637	<	int ndfRaw_local;
636	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
637	>	oneFourInteractions_.removePair(a, d);
638	>	} else {
639	>	excludedInteractions_.removePair(a, d);
640	>	}
641	>	}
642
643	<	// Raw degrees of freedom that we have to set
644	<	ndfRaw_local = 0;
643	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
644	>	inversion = mol->nextInversion(inversionIter)) {
645
646	<	for(int i = 0; i < integrableObjects.size(); i++){
647	<	ndfRaw_local += 3;
648	<	if (integrableObjects[i]->isDirectional()) {
649	<	if (integrableObjects[i]->isLinear())
650	<	ndfRaw_local += 2;
651	<	else
652	<	ndfRaw_local += 3;
646	>	a = inversion->getAtomA()->getGlobalIndex();
647	>	b = inversion->getAtomB()->getGlobalIndex();
648	>	c = inversion->getAtomC()->getGlobalIndex();
649	>	d = inversion->getAtomD()->getGlobalIndex();
650	>
651	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
652	>	oneTwoInteractions_.removePair(a, b);
653	>	oneTwoInteractions_.removePair(a, c);
654	>	oneTwoInteractions_.removePair(a, d);
655	>	} else {
656	>	excludedInteractions_.removePair(a, b);
657	>	excludedInteractions_.removePair(a, c);
658	>	excludedInteractions_.removePair(a, d);
659	>	}
660	>
661	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
662	>	oneThreeInteractions_.removePair(b, c);
663	>	oneThreeInteractions_.removePair(b, d);
664	>	oneThreeInteractions_.removePair(c, d);
665	>	} else {
666	>	excludedInteractions_.removePair(b, c);
667	>	excludedInteractions_.removePair(b, d);
668	>	excludedInteractions_.removePair(c, d);
669	>	}
670		}
671	+
672	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
673	+	rb = mol->nextRigidBody(rbIter)) {
674	+	vector<Atom*> atoms = rb->getAtoms();
675	+	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
676	+	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
677	+	a = atoms[i]->getGlobalIndex();
678	+	b = atoms[j]->getGlobalIndex();
679	+	excludedInteractions_.removePair(a, b);
680	+	}
681	+	}
682	+	}
683	+
684		}
685	+
686	+
687	+	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
688	+	int curStampId;
689
690	<	#ifdef IS_MPI
691	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
381	<	#else
382	<	ndfRaw = ndfRaw_local;
383	<	#endif
690	>	//index from 0
691	>	curStampId = moleculeStamps_.size();
692
693	<	return ndfRaw;
694	<	}
693	>	moleculeStamps_.push_back(molStamp);
694	>	molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
695	>	}
696
388	–	int SimInfo::getNDFtranslational() {
389	–	int ndfTrans_local;
697
698	<	ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
699	<
700	<
698	>	/**
699	>	* update
700	>	*
701	>	*  Performs the global checks and variable settings after the
702	>	*  objects have been created.
703	>	*
704	>	*/
705	>	void SimInfo::update() {
706	>	setupSimVariables();
707	>	calcNdf();
708	>	calcNdfRaw();
709	>	calcNdfTrans();
710	>	}
711	>
712	>	/**
713	>	* getSimulatedAtomTypes
714	>	*
715	>	* Returns an STL set of AtomType* that are actually present in this
716	>	* simulation.  Must query all processors to assemble this information.
717	>	*
718	>	*/
719	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
720	>	SimInfo::MoleculeIterator mi;
721	>	Molecule* mol;
722	>	Molecule::AtomIterator ai;
723	>	Atom* atom;
724	>	set<AtomType*> atomTypes;
725	>
726	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
727	>	for(atom = mol->beginAtom(ai); atom != NULL;
728	>	atom = mol->nextAtom(ai)) {
729	>	atomTypes.insert(atom->getAtomType());
730	>	}
731	>	}
732	>
733		#ifdef IS_MPI
395	–	MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
396	–	#else
397	–	ndfTrans = ndfTrans_local;
398	–	#endif
734
735	<	ndfTrans = ndfTrans - 3 - nZconstraints;
735	>	// loop over the found atom types on this processor, and add their
736	>	// numerical idents to a vector:
737	>
738	>	vector<int> foundTypes;
739	>	set<AtomType*>::iterator i;
740	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
741	>	foundTypes.push_back( (*i)->getIdent() );
742
743	<	return ndfTrans;
744	<	}
743	>	// count_local holds the number of found types on this processor
744	>	int count_local = foundTypes.size();
745
746	<	int SimInfo::getTotIntegrableObjects() {
406	<	int nObjs_local;
407	<	int nObjs;
746	>	int nproc = MPI::COMM_WORLD.Get_size();
747
748	<	nObjs_local =  integrableObjects.size();
748	>	// we need arrays to hold the counts and displacement vectors for
749	>	// all processors
750	>	vector<int> counts(nproc, 0);
751	>	vector<int> disps(nproc, 0);
752
753	+	// fill the counts array
754	+	MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
755	+	1, MPI::INT);
756	+
757	+	// use the processor counts to compute the displacement array
758	+	disps[0] = 0;
759	+	int totalCount = counts[0];
760	+	for (int iproc = 1; iproc < nproc; iproc++) {
761	+	disps[iproc] = disps[iproc-1] + counts[iproc-1];
762	+	totalCount += counts[iproc];
763	+	}
764
765	<	#ifdef IS_MPI
766	<	MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
767	<	#else
768	<	nObjs = nObjs_local;
769	<	#endif
765	>	// we need a (possibly redundant) set of all found types:
766	>	vector<int> ftGlobal(totalCount);
767	>
768	>	// now spray out the foundTypes to all the other processors:
769	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
770	>	&ftGlobal[0], &counts[0], &disps[0],
771	>	MPI::INT);
772
773	+	vector<int>::iterator j;
774
775	<	return nObjs;
776	<	}
775	>	// foundIdents is a stl set, so inserting an already found ident
776	>	// will have no effect.
777	>	set<int> foundIdents;
778
779	<	void SimInfo::refreshSim(){
779	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
780	>	foundIdents.insert((*j));
781	>
782	>	// now iterate over the foundIdents and get the actual atom types
783	>	// that correspond to these:
784	>	set<int>::iterator it;
785	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
786	>	atomTypes.insert( forceField_->getAtomType((*it)) );
787	>
788	>	#endif
789
790	<	simtype fInfo;
791	<	int isError;
426	<	int n_global;
427	<	int* excl;
790	>	return atomTypes;
791	>	}
792
429	–	fInfo.dielect = 0.0;
793
794	<	if( useDipoles ){
795	<	if( useReactionField )fInfo.dielect = dielectric;
794	>	int getGlobalCountOfType(AtomType* atype) {
795	>	/*
796	>	set<AtomType*> atypes = getSimulatedAtomTypes();
797	>	map<AtomType*, int> counts_;
798	>
799	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
800	>	for(atom = mol->beginAtom(ai); atom != NULL;
801	>	atom = mol->nextAtom(ai)) {
802	>	atom->getAtomType();
803	>	}
804	>	}
805	>	*/
806	>	return 0;
807		}
808
809	<	fInfo.SIM_uses_PBC = usePBC;
810	<	//fInfo.SIM_uses_LJ = 0;
811	<	fInfo.SIM_uses_LJ = useLJ;
812	<	fInfo.SIM_uses_sticky = useSticky;
813	<	//fInfo.SIM_uses_sticky = 0;
814	<	fInfo.SIM_uses_charges = useCharges;
815	<	fInfo.SIM_uses_dipoles = useDipoles;
816	<	//fInfo.SIM_uses_dipoles = 0;
817	<	fInfo.SIM_uses_RF = useReactionField;
818	<	//fInfo.SIM_uses_RF = 0;
819	<	fInfo.SIM_uses_GB = useGB;
820	<	fInfo.SIM_uses_EAM = useEAM;
809	>	void SimInfo::setupSimVariables() {
810	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
811	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole
812	>	// parameter is true
813	>	calcBoxDipole_ = false;
814	>	if ( simParams_->haveAccumulateBoxDipole() )
815	>	if ( simParams_->getAccumulateBoxDipole() ) {
816	>	calcBoxDipole_ = true;
817	>	}
818	>
819	>	set<AtomType*>::iterator i;
820	>	set<AtomType*> atomTypes;
821	>	atomTypes = getSimulatedAtomTypes();
822	>	bool usesElectrostatic = false;
823	>	bool usesMetallic = false;
824	>	bool usesDirectional = false;
825	>	bool usesFluctuatingCharges =  false;
826	>	//loop over all of the atom types
827	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
828	>	usesElectrostatic |= (*i)->isElectrostatic();
829	>	usesMetallic |= (*i)->isMetal();
830	>	usesDirectional |= (*i)->isDirectional();
831	>	usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
832	>	}
833
448	–	n_exclude = excludes->getSize();
449	–	excl = excludes->getFortranArray();
450	–
834		#ifdef IS_MPI
835	<	n_global = mpiSim->getNAtomsGlobal();
835	>	bool temp;
836	>	temp = usesDirectional;
837	>	MPI::COMM_WORLD.Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI::BOOL,
838	>	MPI::LOR);
839	>
840	>	temp = usesMetallic;
841	>	MPI::COMM_WORLD.Allreduce(&temp, &usesMetallicAtoms_, 1, MPI::BOOL,
842	>	MPI::LOR);
843	>
844	>	temp = usesElectrostatic;
845	>	MPI::COMM_WORLD.Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI::BOOL,
846	>	MPI::LOR);
847	>
848	>	temp = usesFluctuatingCharges;
849	>	MPI::COMM_WORLD.Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI::BOOL,
850	>	MPI::LOR);
851		#else
852	<	n_global = n_atoms;
852	>
853	>	usesDirectionalAtoms_ = usesDirectional;
854	>	usesMetallicAtoms_ = usesMetallic;
855	>	usesElectrostaticAtoms_ = usesElectrostatic;
856	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
857	>
858		#endif
859	<
860	<	isError = 0;
861	<
862	<	getFortranGroupArrays(this, FglobalGroupMembership, mfact);
863	<	//it may not be a good idea to pass the address of first element in vector
461	<	//since c++ standard does not require vector to be stored continuously in meomory
462	<	//Most of the compilers will organize the memory of vector continuously
463	<	setFortranSim( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
464	<	&nGlobalExcludes, globalExcludes, molMembershipArray,
465	<	&mfact[0], &ngroup, &FglobalGroupMembership[0], &isError);
859	>
860	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
861	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
862	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
863	>	}
864
865	<	if( isError ){
865	>
866	>	vector<int> SimInfo::getGlobalAtomIndices() {
867	>	SimInfo::MoleculeIterator mi;
868	>	Molecule* mol;
869	>	Molecule::AtomIterator ai;
870	>	Atom* atom;
871	>
872	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
873
874	<	sprintf( painCave.errMsg,
875	<	"There was an error setting the simulation information in fortran.\n" );
876	<	painCave.isFatal = 1;
877	<	painCave.severity = OOPSE_ERROR;
878	<	simError();
874	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
875	>
876	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
877	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
878	>	}
879	>	}
880	>	return GlobalAtomIndices;
881		}
475	–
476	–	#ifdef IS_MPI
477	–	sprintf( checkPointMsg,
478	–	"succesfully sent the simulation information to fortran.\n");
479	–	MPIcheckPoint();
480	–	#endif // is_mpi
481	–
482	–	this->ndf = this->getNDF();
483	–	this->ndfRaw = this->getNDFraw();
484	–	this->ndfTrans = this->getNDFtranslational();
485	–	}
882
487	–	void SimInfo::setDefaultRcut( double theRcut ){
488	–
489	–	haveRcut = 1;
490	–	rCut = theRcut;
491	–	rList = rCut + 1.0;
492	–
493	–	notifyFortranCutoffs( &rCut, &rSw, &rList );
494	–	}
883
884	<	void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
884	>	vector<int> SimInfo::getGlobalGroupIndices() {
885	>	SimInfo::MoleculeIterator mi;
886	>	Molecule* mol;
887	>	Molecule::CutoffGroupIterator ci;
888	>	CutoffGroup* cg;
889
890	<	rSw = theRsw;
891	<	setDefaultRcut( theRcut );
892	<	}
890	>	vector<int> GlobalGroupIndices;
891	>
892	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
893	>
894	>	//local index of cutoff group is trivial, it only depends on the
895	>	//order of travesing
896	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
897	>	cg = mol->nextCutoffGroup(ci)) {
898	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
899	>	}
900	>	}
901	>	return GlobalGroupIndices;
902	>	}
903
904
905	<	void SimInfo::checkCutOffs( void ){
906	<
907	<	if( boxIsInit ){
905	>	void SimInfo::prepareTopology() {
906	>
907	>	//calculate mass ratio of cutoff group
908	>	SimInfo::MoleculeIterator mi;
909	>	Molecule* mol;
910	>	Molecule::CutoffGroupIterator ci;
911	>	CutoffGroup* cg;
912	>	Molecule::AtomIterator ai;
913	>	Atom* atom;
914	>	RealType totalMass;
915	>
916	>	/**
917	>	* The mass factor is the relative mass of an atom to the total
918	>	* mass of the cutoff group it belongs to.  By default, all atoms
919	>	* are their own cutoff groups, and therefore have mass factors of
920	>	* 1.  We need some special handling for massless atoms, which
921	>	* will be treated as carrying the entire mass of the cutoff
922	>	* group.
923	>	*/
924	>	massFactors_.clear();
925	>	massFactors_.resize(getNAtoms(), 1.0);
926
927	<	//we need to check cutOffs against the box
928	<
929	<	if( rCut > maxCutoff ){
930	<	sprintf( painCave.errMsg,
931	<	"cutoffRadius is too large for the current periodic box.\n"
932	<	"\tCurrent Value of cutoffRadius = %G at time %G\n "
933	<	"\tThis is larger than half of at least one of the\n"
934	<	"\tperiodic box vectors.  Right now, the Box matrix is:\n"
935	<	"\n"
936	<	"\t[ %G %G %G ]\n"
937	<	"\t[ %G %G %G ]\n"
938	<	"\t[ %G %G %G ]\n",
939	<	rCut, currentTime,
940	<	Hmat[0][0], Hmat[0][1], Hmat[0][2],
941	<	Hmat[1][0], Hmat[1][1], Hmat[1][2],
942	<	Hmat[2][0], Hmat[2][1], Hmat[2][2]);
943	<	painCave.severity = OOPSE_ERROR;
944	<	painCave.isFatal = 1;
945	<	simError();
927	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
928	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
929	>	cg = mol->nextCutoffGroup(ci)) {
930	>
931	>	totalMass = cg->getMass();
932	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
933	>	// Check for massless groups - set mfact to 1 if true
934	>	if (totalMass != 0)
935	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
936	>	else
937	>	massFactors_[atom->getLocalIndex()] = 1.0;
938	>	}
939	>	}
940	>	}
941	>
942	>	// Build the identArray_ and regions_
943	>
944	>	identArray_.clear();
945	>	identArray_.reserve(getNAtoms());
946	>	regions_.clear();
947	>	regions_.reserve(getNAtoms());
948	>
949	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
950	>	int reg = mol->getRegion();
951	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
952	>	identArray_.push_back(atom->getIdent());
953	>	regions_.push_back(reg);
954	>	}
955		}
956	<	} else {
957	<	// initialize this stuff before using it, OK?
529	<	sprintf( painCave.errMsg,
530	<	"Trying to check cutoffs without a box.\n"
531	<	"\tOOPSE should have better programmers than that.\n" );
532	<	painCave.severity = OOPSE_ERROR;
533	<	painCave.isFatal = 1;
534	<	simError();
956	>
957	>	topologyDone_ = true;
958		}
536	–
537	–	}
959
960	<	void SimInfo::addProperty(GenericData* prop){
960	>	void SimInfo::addProperty(GenericData* genData) {
961	>	properties_.addProperty(genData);
962	>	}
963
964	<	map<string, GenericData*>::iterator result;
965	<	result = properties.find(prop->getID());
543	<
544	<	//we can't simply use  properties[prop->getID()] = prop,
545	<	//it will cause memory leak if we already contain a propery which has the same name of prop
546	<
547	<	if(result != properties.end()){
548	<
549	<	delete (*result).second;
550	<	(*result).second = prop;
551	<
964	>	void SimInfo::removeProperty(const string& propName) {
965	>	properties_.removeProperty(propName);
966		}
553	–	else{
967
968	<	properties[prop->getID()] = prop;
968	>	void SimInfo::clearProperties() {
969	>	properties_.clearProperties();
970	>	}
971
972	+	vector<string> SimInfo::getPropertyNames() {
973	+	return properties_.getPropertyNames();
974		}
975	<
976	<	}
975	>
976	>	vector<GenericData*> SimInfo::getProperties() {
977	>	return properties_.getProperties();
978	>	}
979
980	<	GenericData* SimInfo::getProperty(const string& propName){
980	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
981	>	return properties_.getPropertyByName(propName);
982	>	}
983	>
984	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
985	>	if (sman_ == sman) {
986	>	return;
987	>	}
988	>	delete sman_;
989	>	sman_ = sman;
990	>
991	>	Molecule* mol;
992	>	RigidBody* rb;
993	>	Atom* atom;
994	>	CutoffGroup* cg;
995	>	SimInfo::MoleculeIterator mi;
996	>	Molecule::RigidBodyIterator rbIter;
997	>	Molecule::AtomIterator atomIter;
998	>	Molecule::CutoffGroupIterator cgIter;
999
1000	<	map<string, GenericData*>::iterator result;
1001	<
1002	<	//string lowerCaseName = ();
1003	<
1004	<	result = properties.find(propName);
1005	<
1006	<	if(result != properties.end())
1007	<	return (*result).second;
1008	<	else
1009	<	return NULL;
1010	<	}
1000	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1001	>
1002	>	for (atom = mol->beginAtom(atomIter); atom != NULL;
1003	>	atom = mol->nextAtom(atomIter)) {
1004	>	atom->setSnapshotManager(sman_);
1005	>	}
1006	>
1007	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
1008	>	rb = mol->nextRigidBody(rbIter)) {
1009	>	rb->setSnapshotManager(sman_);
1010	>	}
1011
1012	+	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL;
1013	+	cg = mol->nextCutoffGroup(cgIter)) {
1014	+	cg->setSnapshotManager(sman_);
1015	+	}
1016	+	}
1017	+
1018	+	}
1019
1020	<	void SimInfo::getFortranGroupArrays(SimInfo* info,
1021	<	vector<int>& FglobalGroupMembership,
1022	<	vector<double>& mfact){
1020	>
1021	>	ostream& operator <<(ostream& o, SimInfo& info) {
1022	>
1023	>	return o;
1024	>	}
1025	>
1026
1027	<	Molecule* myMols;
1028	<	Atom** myAtoms;
1029	<	int numAtom;
1030	<	double mtot;
1031	<	int numMol;
1032	<	int numCutoffGroups;
1033	<	CutoffGroup* myCutoffGroup;
1034	<	vector<CutoffGroup*>::iterator iterCutoff;
1035	<	Atom* cutoffAtom;
1036	<	vector<Atom*>::iterator iterAtom;
1037	<	int atomIndex;
591	<	double totalMass;
1027	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1028	>	if (index >= int(IOIndexToIntegrableObject.size())) {
1029	>	sprintf(painCave.errMsg,
1030	>	"SimInfo::getIOIndexToIntegrableObject Error: Integrable Object\n"
1031	>	"\tindex exceeds number of known objects!\n");
1032	>	painCave.isFatal = 1;
1033	>	simError();
1034	>	return NULL;
1035	>	} else
1036	>	return IOIndexToIntegrableObject.at(index);
1037	>	}
1038
1039	<	mfact.clear();
1040	<	FglobalGroupMembership.clear();
1041	<
1039	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1040	>	IOIndexToIntegrableObject= v;
1041	>	}
1042
1043	<	// Fix the silly fortran indexing problem
1043	>	int SimInfo::getNGlobalConstraints() {
1044	>	int nGlobalConstraints;
1045		#ifdef IS_MPI
1046	<	numAtom = mpiSim->getNAtomsGlobal();
1046	>	MPI::COMM_WORLD.Allreduce(&nConstraints_, &nGlobalConstraints, 1,
1047	>	MPI::INT, MPI::SUM);
1048		#else
1049	<	numAtom = n_atoms;
1049	>	nGlobalConstraints =  nConstraints_;
1050		#endif
1051	<	for (int i = 0; i < numAtom; i++)
604	<	FglobalGroupMembership.push_back(globalGroupMembership[i] + 1);
605	<
606	<
607	<	myMols = info->molecules;
608	<	numMol = info->n_mol;
609	<	for(int i  = 0; i < numMol; i++){
610	<	numCutoffGroups = myMols[i].getNCutoffGroups();
611	<	for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff);
612	<	myCutoffGroup != NULL;
613	<	myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
614	<
615	<	totalMass = myCutoffGroup->getMass();
616	<
617	<	for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom);
618	<	cutoffAtom != NULL;
619	<	cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
620	<	mfact.push_back(cutoffAtom->getMass()/totalMass);
621	<	}
622	<	}
1051	>	return nGlobalConstraints;
1052		}
1053
1054	<	}
1054	>	}//end namespace OpenMD
1055	>

Comparing trunk/src/brains/SimInfo.cpp (property svn:keywords):
Revision 124 by chuckv, Wed Oct 20 20:46:20 2004 UTC vs.
Revision 1940 by gezelter, Fri Nov 1 19:31:41 2013 UTC

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