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root/OpenMD/branches/development/src/brains/SimInfo.cpp

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trunk/src/brains/SimInfo.cpp (file contents), Revision 124 by chuckv, Wed Oct 20 20:46:20 2004 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1627 by gezelter, Tue Sep 13 22:05:04 2011 UTC

#	Line 1 | Line 1
1	<	#include <stdlib.h>
2	<	#include <string.h>
3	<	#include <math.h>
1	>	/*
2	>	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	>	*
4	>	* The University of Notre Dame grants you ("Licensee") a
5	>	* non-exclusive, royalty free, license to use, modify and
6	>	* redistribute this software in source and binary code form, provided
7	>	* that the following conditions are met:
8	>	*
9	>	* 1. Redistributions of source code must retain the above copyright
10	>	*    notice, this list of conditions and the following disclaimer.
11	>	*
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13	>	*    notice, this list of conditions and the following disclaimer in the
14	>	*    documentation and/or other materials provided with the
15	>	*    distribution.
16	>	*
17	>	* This software is provided "AS IS," without a warranty of any
18	>	* kind. All express or implied conditions, representations and
19	>	* warranties, including any implied warranty of merchantability,
20	>	* fitness for a particular purpose or non-infringement, are hereby
21	>	* excluded.  The University of Notre Dame and its licensors shall not
22	>	* be liable for any damages suffered by licensee as a result of
23	>	* using, modifying or distributing the software or its
24	>	* derivatives. In no event will the University of Notre Dame or its
25	>	* licensors be liable for any lost revenue, profit or data, or for
26	>	* direct, indirect, special, consequential, incidental or punitive
27	>	* damages, however caused and regardless of the theory of liability,
28	>	* arising out of the use of or inability to use software, even if the
29	>	* University of Notre Dame has been advised of the possibility of
30	>	* such damages.
31	>	*
32	>	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	>	* research, please cite the appropriate papers when you publish your
34	>	* work.  Good starting points are:
35	>	*
36	>	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	>	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	>	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	>	* [4]  Vardeman & Gezelter, in progress (2009).
40	>	*/
41	>
42	>	/**
43	>	* @file SimInfo.cpp
44	>	* @author    tlin
45	>	* @date  11/02/2004
46	>	* @version 1.0
47	>	*/
48
49	<	#include <iostream>
50	<	using namespace std;
49	>	#include <algorithm>
50	>	#include <set>
51	>	#include <map>
52
53		#include "brains/SimInfo.hpp"
54	<	#define __C
55	<	#include "brains/fSimulation.h"
54	>	#include "math/Vector3.hpp"
55	>	#include "primitives/Molecule.hpp"
56	>	#include "primitives/StuntDouble.hpp"
57	>	#include "utils/MemoryUtils.hpp"
58		#include "utils/simError.h"
59	<	#include "UseTheForce/DarkSide/simulation_interface.h"
60	<	#include "UseTheForce/notifyCutoffs_interface.h"
61	<
62	<	//#include "UseTheForce/fortranWrappers.hpp"
16	<
17	<	#include "math/MatVec3.h"
18	<
59	>	#include "selection/SelectionManager.hpp"
60	>	#include "io/ForceFieldOptions.hpp"
61	>	#include "UseTheForce/ForceField.hpp"
62	>	#include "nonbonded/SwitchingFunction.hpp"
63		#ifdef IS_MPI
64	<	#include "brains/mpiSimulation.hpp"
64	>	#include <mpi.h>
65		#endif
66
67	<	inline double roundMe( double x ){
68	<	return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
69	<	}
70	<
71	<	inline double min( double a, double b ){
72	<	return (a < b ) ? a : b;
73	<	}
67	>	using namespace std;
68	>	namespace OpenMD {
69	>
70	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
71	>	forceField_(ff), simParams_(simParams),
72	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
73	>	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
74	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
75	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
76	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
77	>	nConstraints_(0), sman_(NULL), topologyDone_(false),
78	>	calcBoxDipole_(false), useAtomicVirial_(true) {
79	>
80	>	MoleculeStamp* molStamp;
81	>	int nMolWithSameStamp;
82	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
83	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
84	>	CutoffGroupStamp* cgStamp;
85	>	RigidBodyStamp* rbStamp;
86	>	int nRigidAtoms = 0;
87	>
88	>	vector<Component*> components = simParams->getComponents();
89	>
90	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
91	>	molStamp = (*i)->getMoleculeStamp();
92	>	nMolWithSameStamp = (*i)->getNMol();
93	>
94	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
95	>
96	>	//calculate atoms in molecules
97	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
98	>
99	>	//calculate atoms in cutoff groups
100	>	int nAtomsInGroups = 0;
101	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
102	>
103	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
104	>	cgStamp = molStamp->getCutoffGroupStamp(j);
105	>	nAtomsInGroups += cgStamp->getNMembers();
106	>	}
107	>
108	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
109	>
110	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
111	>
112	>	//calculate atoms in rigid bodies
113	>	int nAtomsInRigidBodies = 0;
114	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
115	>
116	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
117	>	rbStamp = molStamp->getRigidBodyStamp(j);
118	>	nAtomsInRigidBodies += rbStamp->getNMembers();
119	>	}
120	>
121	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
122	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
123	>
124	>	}
125	>
126	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
127	>	//group therefore the total number of cutoff groups in the system is
128	>	//equal to the total number of atoms minus number of atoms belong to
129	>	//cutoff group defined in meta-data file plus the number of cutoff
130	>	//groups defined in meta-data file
131
132	<	SimInfo* currentInfo;
132	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
133	>
134	>	//every free atom (atom does not belong to rigid bodies) is an
135	>	//integrable object therefore the total number of integrable objects
136	>	//in the system is equal to the total number of atoms minus number of
137	>	//atoms belong to rigid body defined in meta-data file plus the number
138	>	//of rigid bodies defined in meta-data file
139	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
140	>	+ nGlobalRigidBodies_;
141	>
142	>	nGlobalMols_ = molStampIds_.size();
143	>	molToProcMap_.resize(nGlobalMols_);
144	>	}
145	>
146	>	SimInfo::~SimInfo() {
147	>	map<int, Molecule*>::iterator i;
148	>	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
149	>	delete i->second;
150	>	}
151	>	molecules_.clear();
152	>
153	>	delete sman_;
154	>	delete simParams_;
155	>	delete forceField_;
156	>	}
157
33	–	SimInfo::SimInfo(){
158
159	<	n_constraints = 0;
160	<	nZconstraints = 0;
161	<	n_oriented = 0;
162	<	n_dipoles = 0;
163	<	ndf = 0;
164	<	ndfRaw = 0;
165	<	nZconstraints = 0;
166	<	the_integrator = NULL;
167	<	setTemp = 0;
168	<	thermalTime = 0.0;
169	<	currentTime = 0.0;
170	<	rCut = 0.0;
171	<	rSw = 0.0;
172	<
173	<	haveRcut = 0;
174	<	haveRsw = 0;
175	<	boxIsInit = 0;
159	>	bool SimInfo::addMolecule(Molecule* mol) {
160	>	MoleculeIterator i;
161	>
162	>	i = molecules_.find(mol->getGlobalIndex());
163	>	if (i == molecules_.end() ) {
164	>
165	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
166	>
167	>	nAtoms_ += mol->getNAtoms();
168	>	nBonds_ += mol->getNBonds();
169	>	nBends_ += mol->getNBends();
170	>	nTorsions_ += mol->getNTorsions();
171	>	nInversions_ += mol->getNInversions();
172	>	nRigidBodies_ += mol->getNRigidBodies();
173	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
174	>	nCutoffGroups_ += mol->getNCutoffGroups();
175	>	nConstraints_ += mol->getNConstraintPairs();
176	>
177	>	addInteractionPairs(mol);
178	>
179	>	return true;
180	>	} else {
181	>	return false;
182	>	}
183	>	}
184
185	<	resetTime = 1e99;
185	>	bool SimInfo::removeMolecule(Molecule* mol) {
186	>	MoleculeIterator i;
187	>	i = molecules_.find(mol->getGlobalIndex());
188
189	<	orthoRhombic = 0;
56	<	orthoTolerance = 1E-6;
57	<	useInitXSstate = true;
189	>	if (i != molecules_.end() ) {
190
191	<	usePBC = 0;
192	<	useLJ = 0;
193	<	useSticky = 0;
194	<	useCharges = 0;
195	<	useDipoles = 0;
196	<	useReactionField = 0;
197	<	useGB = 0;
198	<	useEAM = 0;
199	<	useSolidThermInt = 0;
200	<	useLiquidThermInt = 0;
201	<
70	<	haveCutoffGroups = false;
71	<
72	<	excludes = Exclude::Instance();
73	<
74	<	myConfiguration = new SimState();
75	<
76	<	has_minimizer = false;
77	<	the_minimizer =NULL;
78	<
79	<	ngroup = 0;
80	<
81	<	}
191	>	assert(mol == i->second);
192	>
193	>	nAtoms_ -= mol->getNAtoms();
194	>	nBonds_ -= mol->getNBonds();
195	>	nBends_ -= mol->getNBends();
196	>	nTorsions_ -= mol->getNTorsions();
197	>	nInversions_ -= mol->getNInversions();
198	>	nRigidBodies_ -= mol->getNRigidBodies();
199	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
200	>	nCutoffGroups_ -= mol->getNCutoffGroups();
201	>	nConstraints_ -= mol->getNConstraintPairs();
202
203	+	removeInteractionPairs(mol);
204	+	molecules_.erase(mol->getGlobalIndex());
205
206	<	SimInfo::~SimInfo(){
206	>	delete mol;
207	>
208	>	return true;
209	>	} else {
210	>	return false;
211	>	}
212	>	}
213
214	<	delete myConfiguration;
214	>
215	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
216	>	i = molecules_.begin();
217	>	return i == molecules_.end() ? NULL : i->second;
218	>	}
219
220	<	map<string, GenericData*>::iterator i;
221	<
222	<	for(i = properties.begin(); i != properties.end(); i++)
223	<	delete (*i).second;
220	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
221	>	++i;
222	>	return i == molecules_.end() ? NULL : i->second;
223	>	}
224
93	–	}
225
226	<	void SimInfo::setBox(double newBox[3]) {
227	<
228	<	int i, j;
229	<	double tempMat[3][3];
226	>	void SimInfo::calcNdf() {
227	>	int ndf_local;
228	>	MoleculeIterator i;
229	>	vector<StuntDouble*>::iterator j;
230	>	Molecule* mol;
231	>	StuntDouble* integrableObject;
232
233	<	for(i=0; i<3; i++)
234	<	for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
233	>	ndf_local = 0;
234	>
235	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
236	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
237	>	integrableObject = mol->nextIntegrableObject(j)) {
238
239	<	tempMat[0][0] = newBox[0];
104	<	tempMat[1][1] = newBox[1];
105	<	tempMat[2][2] = newBox[2];
239	>	ndf_local += 3;
240
241	<	setBoxM( tempMat );
241	>	if (integrableObject->isDirectional()) {
242	>	if (integrableObject->isLinear()) {
243	>	ndf_local += 2;
244	>	} else {
245	>	ndf_local += 3;
246	>	}
247	>	}
248	>
249	>	}
250	>	}
251	>
252	>	// n_constraints is local, so subtract them on each processor
253	>	ndf_local -= nConstraints_;
254
255	<	}
255	>	#ifdef IS_MPI
256	>	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
257	>	#else
258	>	ndf_ = ndf_local;
259	>	#endif
260
261	<	void SimInfo::setBoxM( double theBox[3][3] ){
262	<
263	<	int i, j;
114	<	double FortranHmat[9]; // to preserve compatibility with Fortran the
115	<	// ordering in the array is as follows:
116	<	// [ 0 3 6 ]
117	<	// [ 1 4 7 ]
118	<	// [ 2 5 8 ]
119	<	double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
261	>	// nZconstraints_ is global, as are the 3 COM translations for the
262	>	// entire system:
263	>	ndf_ = ndf_ - 3 - nZconstraint_;
264
265	<	if( !boxIsInit ) boxIsInit = 1;
265	>	}
266
267	<	for(i=0; i < 3; i++)
268	<	for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
267	>	int SimInfo::getFdf() {
268	>	#ifdef IS_MPI
269	>	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
270	>	#else
271	>	fdf_ = fdf_local;
272	>	#endif
273	>	return fdf_;
274	>	}
275
276	<	calcBoxL();
277	<	calcHmatInv();
278	<
279	<	for(i=0; i < 3; i++) {
280	<	for (j=0; j < 3; j++) {
281	<	FortranHmat[3*j + i] = Hmat[i][j];
282	<	FortranHmatInv[3*j + i] = HmatInv[i][j];
276	>	unsigned int SimInfo::getNLocalCutoffGroups(){
277	>	int nLocalCutoffAtoms = 0;
278	>	Molecule* mol;
279	>	MoleculeIterator mi;
280	>	CutoffGroup* cg;
281	>	Molecule::CutoffGroupIterator ci;
282	>
283	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
284	>
285	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
286	>	cg = mol->nextCutoffGroup(ci)) {
287	>	nLocalCutoffAtoms += cg->getNumAtom();
288	>
289	>	}
290		}
291	+
292	+	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
293		}
294	+
295	+	void SimInfo::calcNdfRaw() {
296	+	int ndfRaw_local;
297
298	<	setFortranBox(FortranHmat, FortranHmatInv, &orthoRhombic);
299	<
300	<	}
301	<
298	>	MoleculeIterator i;
299	>	vector<StuntDouble*>::iterator j;
300	>	Molecule* mol;
301	>	StuntDouble* integrableObject;
302
303	<	void SimInfo::getBoxM (double theBox[3][3]) {
303	>	// Raw degrees of freedom that we have to set
304	>	ndfRaw_local = 0;
305	>
306	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
307	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
308	>	integrableObject = mol->nextIntegrableObject(j)) {
309
310	<	int i, j;
144	<	for(i=0; i<3; i++)
145	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
146	<	}
310	>	ndfRaw_local += 3;
311
312	+	if (integrableObject->isDirectional()) {
313	+	if (integrableObject->isLinear()) {
314	+	ndfRaw_local += 2;
315	+	} else {
316	+	ndfRaw_local += 3;
317	+	}
318	+	}
319	+
320	+	}
321	+	}
322	+
323	+	#ifdef IS_MPI
324	+	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
325	+	#else
326	+	ndfRaw_ = ndfRaw_local;
327	+	#endif
328	+	}
329
330	<	void SimInfo::scaleBox(double scale) {
331	<	double theBox[3][3];
151	<	int i, j;
330	>	void SimInfo::calcNdfTrans() {
331	>	int ndfTrans_local;
332
333	<	// cerr << "Scaling box by " << scale << "\n";
333	>	ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
334
155	–	for(i=0; i<3; i++)
156	–	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
335
336	<	setBoxM(theBox);
336	>	#ifdef IS_MPI
337	>	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
338	>	#else
339	>	ndfTrans_ = ndfTrans_local;
340	>	#endif
341
342	<	}
342	>	ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
343	>
344	>	}
345
346	<	void SimInfo::calcHmatInv( void ) {
347	<
348	<	int oldOrtho;
349	<	int i,j;
350	<	double smallDiag;
351	<	double tol;
352	<	double sanity[3][3];
346	>	void SimInfo::addInteractionPairs(Molecule* mol) {
347	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
348	>	vector<Bond*>::iterator bondIter;
349	>	vector<Bend*>::iterator bendIter;
350	>	vector<Torsion*>::iterator torsionIter;
351	>	vector<Inversion*>::iterator inversionIter;
352	>	Bond* bond;
353	>	Bend* bend;
354	>	Torsion* torsion;
355	>	Inversion* inversion;
356	>	int a;
357	>	int b;
358	>	int c;
359	>	int d;
360
361	<	invertMat3( Hmat, HmatInv );
361	>	// atomGroups can be used to add special interaction maps between
362	>	// groups of atoms that are in two separate rigid bodies.
363	>	// However, most site-site interactions between two rigid bodies
364	>	// are probably not special, just the ones between the physically
365	>	// bonded atoms.  Interactions *within* a single rigid body should
366	>	// always be excluded.  These are done at the bottom of this
367	>	// function.
368
369	<	// check to see if Hmat is orthorhombic
370	<
371	<	oldOrtho = orthoRhombic;
372	<
373	<	smallDiag = fabs(Hmat[0][0]);
374	<	if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
375	<	if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
376	<	tol = smallDiag * orthoTolerance;
377	<
378	<	orthoRhombic = 1;
379	<
380	<	for (i = 0; i < 3; i++ ) {
381	<	for (j = 0 ; j < 3; j++) {
382	<	if (i != j) {
383	<	if (orthoRhombic) {
384	<	if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
385	<	}
369	>	map<int, set<int> > atomGroups;
370	>	Molecule::RigidBodyIterator rbIter;
371	>	RigidBody* rb;
372	>	Molecule::IntegrableObjectIterator ii;
373	>	StuntDouble* integrableObject;
374	>
375	>	for (integrableObject = mol->beginIntegrableObject(ii);
376	>	integrableObject != NULL;
377	>	integrableObject = mol->nextIntegrableObject(ii)) {
378	>
379	>	if (integrableObject->isRigidBody()) {
380	>	rb = static_cast<RigidBody*>(integrableObject);
381	>	vector<Atom*> atoms = rb->getAtoms();
382	>	set<int> rigidAtoms;
383	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
384	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
385	>	}
386	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
387	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
388	>	}
389	>	} else {
390	>	set<int> oneAtomSet;
391	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
392	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
393		}
394	<	}
395	<	}
394	>	}
395	>
396	>	for (bond= mol->beginBond(bondIter); bond != NULL;
397	>	bond = mol->nextBond(bondIter)) {
398
399	<	if( oldOrtho != orthoRhombic ){
399	>	a = bond->getAtomA()->getGlobalIndex();
400	>	b = bond->getAtomB()->getGlobalIndex();
401
402	<	if( orthoRhombic ) {
403	<	sprintf( painCave.errMsg,
404	<	"OOPSE is switching from the default Non-Orthorhombic\n"
405	<	"\tto the faster Orthorhombic periodic boundary computations.\n"
406	<	"\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();
402	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
403	>	oneTwoInteractions_.addPair(a, b);
404	>	} else {
405	>	excludedInteractions_.addPair(a, b);
406	>	}
407		}
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	–	}
218	–	}
219	–	}
408
409	<	void SimInfo::calcBoxL( void ){
409	>	for (bend= mol->beginBend(bendIter); bend != NULL;
410	>	bend = mol->nextBend(bendIter)) {
411
412	<	double dx, dy, dz, dsq;
412	>	a = bend->getAtomA()->getGlobalIndex();
413	>	b = bend->getAtomB()->getGlobalIndex();
414	>	c = bend->getAtomC()->getGlobalIndex();
415	>
416	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
417	>	oneTwoInteractions_.addPair(a, b);
418	>	oneTwoInteractions_.addPair(b, c);
419	>	} else {
420	>	excludedInteractions_.addPair(a, b);
421	>	excludedInteractions_.addPair(b, c);
422	>	}
423
424	<	// boxVol = Determinant of Hmat
424	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
425	>	oneThreeInteractions_.addPair(a, c);
426	>	} else {
427	>	excludedInteractions_.addPair(a, c);
428	>	}
429	>	}
430
431	<	boxVol = matDet3( Hmat );
431	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
432	>	torsion = mol->nextTorsion(torsionIter)) {
433
434	<	// boxLx
435	<
436	<	dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
437	<	dsq = dx*dx + dy*dy + dz*dz;
233	<	boxL[0] = sqrt( dsq );
234	<	//maxCutoff = 0.5 * boxL[0];
434	>	a = torsion->getAtomA()->getGlobalIndex();
435	>	b = torsion->getAtomB()->getGlobalIndex();
436	>	c = torsion->getAtomC()->getGlobalIndex();
437	>	d = torsion->getAtomD()->getGlobalIndex();
438
439	<	// boxLy
440	<
441	<	dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
442	<	dsq = dx*dx + dy*dy + dz*dz;
443	<	boxL[1] = sqrt( dsq );
444	<	//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
439	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
440	>	oneTwoInteractions_.addPair(a, b);
441	>	oneTwoInteractions_.addPair(b, c);
442	>	oneTwoInteractions_.addPair(c, d);
443	>	} else {
444	>	excludedInteractions_.addPair(a, b);
445	>	excludedInteractions_.addPair(b, c);
446	>	excludedInteractions_.addPair(c, d);
447	>	}
448
449	+	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
450	+	oneThreeInteractions_.addPair(a, c);
451	+	oneThreeInteractions_.addPair(b, d);
452	+	} else {
453	+	excludedInteractions_.addPair(a, c);
454	+	excludedInteractions_.addPair(b, d);
455	+	}
456
457	<	// boxLz
458	<
459	<	dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
460	<	dsq = dx*dx + dy*dy + dz*dz;
461	<	boxL[2] = sqrt( dsq );
462	<	//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
457	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
458	>	oneFourInteractions_.addPair(a, d);
459	>	} else {
460	>	excludedInteractions_.addPair(a, d);
461	>	}
462	>	}
463
464	<	//calculate the max cutoff
465	<	maxCutoff =  calcMaxCutOff();
253	<
254	<	checkCutOffs();
464	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
465	>	inversion = mol->nextInversion(inversionIter)) {
466
467	<	}
467	>	a = inversion->getAtomA()->getGlobalIndex();
468	>	b = inversion->getAtomB()->getGlobalIndex();
469	>	c = inversion->getAtomC()->getGlobalIndex();
470	>	d = inversion->getAtomD()->getGlobalIndex();
471
472	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
473	+	oneTwoInteractions_.addPair(a, b);
474	+	oneTwoInteractions_.addPair(a, c);
475	+	oneTwoInteractions_.addPair(a, d);
476	+	} else {
477	+	excludedInteractions_.addPair(a, b);
478	+	excludedInteractions_.addPair(a, c);
479	+	excludedInteractions_.addPair(a, d);
480	+	}
481
482	<	double SimInfo::calcMaxCutOff(){
482	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
483	>	oneThreeInteractions_.addPair(b, c);
484	>	oneThreeInteractions_.addPair(b, d);
485	>	oneThreeInteractions_.addPair(c, d);
486	>	} else {
487	>	excludedInteractions_.addPair(b, c);
488	>	excludedInteractions_.addPair(b, d);
489	>	excludedInteractions_.addPair(c, d);
490	>	}
491	>	}
492
493	<	double ri[3], rj[3], rk[3];
494	<	double rij[3], rjk[3], rki[3];
495	<	double minDist;
493	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
494	>	rb = mol->nextRigidBody(rbIter)) {
495	>	vector<Atom*> atoms = rb->getAtoms();
496	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
497	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
498	>	a = atoms[i]->getGlobalIndex();
499	>	b = atoms[j]->getGlobalIndex();
500	>	excludedInteractions_.addPair(a, b);
501	>	}
502	>	}
503	>	}
504
505	<	ri[0] = Hmat[0][0];
266	<	ri[1] = Hmat[1][0];
267	<	ri[2] = Hmat[2][0];
505	>	}
506
507	<	rj[0] = Hmat[0][1];
508	<	rj[1] = Hmat[1][1];
509	<	rj[2] = Hmat[2][1];
507	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
508	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
509	>	vector<Bond*>::iterator bondIter;
510	>	vector<Bend*>::iterator bendIter;
511	>	vector<Torsion*>::iterator torsionIter;
512	>	vector<Inversion*>::iterator inversionIter;
513	>	Bond* bond;
514	>	Bend* bend;
515	>	Torsion* torsion;
516	>	Inversion* inversion;
517	>	int a;
518	>	int b;
519	>	int c;
520	>	int d;
521
522	<	rk[0] = Hmat[0][2];
523	<	rk[1] = Hmat[1][2];
524	<	rk[2] = Hmat[2][2];
522	>	map<int, set<int> > atomGroups;
523	>	Molecule::RigidBodyIterator rbIter;
524	>	RigidBody* rb;
525	>	Molecule::IntegrableObjectIterator ii;
526	>	StuntDouble* integrableObject;
527
528	<	crossProduct3(ri, rj, rij);
529	<	distXY = dotProduct3(rk,rij) / norm3(rij);
528	>	for (integrableObject = mol->beginIntegrableObject(ii);
529	>	integrableObject != NULL;
530	>	integrableObject = mol->nextIntegrableObject(ii)) {
531	>
532	>	if (integrableObject->isRigidBody()) {
533	>	rb = static_cast<RigidBody*>(integrableObject);
534	>	vector<Atom*> atoms = rb->getAtoms();
535	>	set<int> rigidAtoms;
536	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
537	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
538	>	}
539	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
540	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
541	>	}
542	>	} else {
543	>	set<int> oneAtomSet;
544	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
545	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
546	>	}
547	>	}
548
549	<	crossProduct3(rj,rk, rjk);
550	<	distYZ = dotProduct3(ri,rjk) / norm3(rjk);
549	>	for (bond= mol->beginBond(bondIter); bond != NULL;
550	>	bond = mol->nextBond(bondIter)) {
551	>
552	>	a = bond->getAtomA()->getGlobalIndex();
553	>	b = bond->getAtomB()->getGlobalIndex();
554	>
555	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
556	>	oneTwoInteractions_.removePair(a, b);
557	>	} else {
558	>	excludedInteractions_.removePair(a, b);
559	>	}
560	>	}
561
562	<	crossProduct3(rk,ri, rki);
563	<	distZX = dotProduct3(rj,rki) / norm3(rki);
562	>	for (bend= mol->beginBend(bendIter); bend != NULL;
563	>	bend = mol->nextBend(bendIter)) {
564
565	<	minDist = min(min(distXY, distYZ), distZX);
566	<	return minDist/2;
567	<
568	<	}
565	>	a = bend->getAtomA()->getGlobalIndex();
566	>	b = bend->getAtomB()->getGlobalIndex();
567	>	c = bend->getAtomC()->getGlobalIndex();
568	>
569	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
570	>	oneTwoInteractions_.removePair(a, b);
571	>	oneTwoInteractions_.removePair(b, c);
572	>	} else {
573	>	excludedInteractions_.removePair(a, b);
574	>	excludedInteractions_.removePair(b, c);
575	>	}
576
577	<	void SimInfo::wrapVector( double thePos[3] ){
577	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
578	>	oneThreeInteractions_.removePair(a, c);
579	>	} else {
580	>	excludedInteractions_.removePair(a, c);
581	>	}
582	>	}
583
584	<	int i;
585	<	double scaled[3];
584	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
585	>	torsion = mol->nextTorsion(torsionIter)) {
586
587	<	if( !orthoRhombic ){
588	<	// calc the scaled coordinates.
587	>	a = torsion->getAtomA()->getGlobalIndex();
588	>	b = torsion->getAtomB()->getGlobalIndex();
589	>	c = torsion->getAtomC()->getGlobalIndex();
590	>	d = torsion->getAtomD()->getGlobalIndex();
591
592	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
593	+	oneTwoInteractions_.removePair(a, b);
594	+	oneTwoInteractions_.removePair(b, c);
595	+	oneTwoInteractions_.removePair(c, d);
596	+	} else {
597	+	excludedInteractions_.removePair(a, b);
598	+	excludedInteractions_.removePair(b, c);
599	+	excludedInteractions_.removePair(c, d);
600	+	}
601
602	<	matVecMul3(HmatInv, thePos, scaled);
603	<
604	<	for(i=0; i<3; i++)
605	<	scaled[i] -= roundMe(scaled[i]);
606	<
607	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
608	<
307	<	matVecMul3(Hmat, scaled, thePos);
602	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
603	>	oneThreeInteractions_.removePair(a, c);
604	>	oneThreeInteractions_.removePair(b, d);
605	>	} else {
606	>	excludedInteractions_.removePair(a, c);
607	>	excludedInteractions_.removePair(b, d);
608	>	}
609
610	<	}
611	<	else{
612	<	// calc the scaled coordinates.
613	<
614	<	for(i=0; i<3; i++)
615	<	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	<	}
610	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
611	>	oneFourInteractions_.removePair(a, d);
612	>	} else {
613	>	excludedInteractions_.removePair(a, d);
614	>	}
615	>	}
616
617	+	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
618	+	inversion = mol->nextInversion(inversionIter)) {
619
620	<	int SimInfo::getNDF(){
621	<	int ndf_local;
620	>	a = inversion->getAtomA()->getGlobalIndex();
621	>	b = inversion->getAtomB()->getGlobalIndex();
622	>	c = inversion->getAtomC()->getGlobalIndex();
623	>	d = inversion->getAtomD()->getGlobalIndex();
624
625	<	ndf_local = 0;
626	<
627	<	for(int i = 0; i < integrableObjects.size(); i++){
628	<	ndf_local += 3;
629	<	if (integrableObjects[i]->isDirectional()) {
630	<	if (integrableObjects[i]->isLinear())
631	<	ndf_local += 2;
632	<	else
633	<	ndf_local += 3;
625	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
626	>	oneTwoInteractions_.removePair(a, b);
627	>	oneTwoInteractions_.removePair(a, c);
628	>	oneTwoInteractions_.removePair(a, d);
629	>	} else {
630	>	excludedInteractions_.removePair(a, b);
631	>	excludedInteractions_.removePair(a, c);
632	>	excludedInteractions_.removePair(a, d);
633	>	}
634	>
635	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
636	>	oneThreeInteractions_.removePair(b, c);
637	>	oneThreeInteractions_.removePair(b, d);
638	>	oneThreeInteractions_.removePair(c, d);
639	>	} else {
640	>	excludedInteractions_.removePair(b, c);
641	>	excludedInteractions_.removePair(b, d);
642	>	excludedInteractions_.removePair(c, d);
643	>	}
644		}
645	+
646	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
647	+	rb = mol->nextRigidBody(rbIter)) {
648	+	vector<Atom*> atoms = rb->getAtoms();
649	+	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
650	+	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
651	+	a = atoms[i]->getGlobalIndex();
652	+	b = atoms[j]->getGlobalIndex();
653	+	excludedInteractions_.removePair(a, b);
654	+	}
655	+	}
656	+	}
657	+
658		}
659	+
660	+
661	+	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
662	+	int curStampId;
663	+
664	+	//index from 0
665	+	curStampId = moleculeStamps_.size();
666
667	<	// n_constraints is local, so subtract them on each processor:
667	>	moleculeStamps_.push_back(molStamp);
668	>	molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
669	>	}
670
347	–	ndf_local -= n_constraints;
671
672	<	#ifdef IS_MPI
673	<	MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
674	<	#else
675	<	ndf = ndf_local;
676	<	#endif
677	<
678	<	// nZconstraints is global, as are the 3 COM translations for the
679	<	// entire system:
680	<
681	<	ndf = ndf - 3 - nZconstraints;
682	<
683	<	return ndf;
361	<	}
362	<
363	<	int SimInfo::getNDFraw() {
364	<	int ndfRaw_local;
365	<
366	<	// Raw degrees of freedom that we have to set
367	<	ndfRaw_local = 0;
368	<
369	<	for(int i = 0; i < integrableObjects.size(); i++){
370	<	ndfRaw_local += 3;
371	<	if (integrableObjects[i]->isDirectional()) {
372	<	if (integrableObjects[i]->isLinear())
373	<	ndfRaw_local += 2;
374	<	else
375	<	ndfRaw_local += 3;
376	<	}
672	>	/**
673	>	* update
674	>	*
675	>	*  Performs the global checks and variable settings after the
676	>	*  objects have been created.
677	>	*
678	>	*/
679	>	void SimInfo::update() {
680	>	setupSimVariables();
681	>	calcNdf();
682	>	calcNdfRaw();
683	>	calcNdfTrans();
684		}
685	+
686	+	/**
687	+	* getSimulatedAtomTypes
688	+	*
689	+	* Returns an STL set of AtomType* that are actually present in this
690	+	* simulation.  Must query all processors to assemble this information.
691	+	*
692	+	*/
693	+	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
694	+	SimInfo::MoleculeIterator mi;
695	+	Molecule* mol;
696	+	Molecule::AtomIterator ai;
697	+	Atom* atom;
698	+	set<AtomType*> atomTypes;
699
700	+	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
701	+	for(atom = mol->beginAtom(ai); atom != NULL;
702	+	atom = mol->nextAtom(ai)) {
703	+	atomTypes.insert(atom->getAtomType());
704	+	}
705	+	}
706	+
707		#ifdef IS_MPI
380	–	MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
381	–	#else
382	–	ndfRaw = ndfRaw_local;
383	–	#endif
708
709	<	return ndfRaw;
710	<	}
709	>	// loop over the found atom types on this processor, and add their
710	>	// numerical idents to a vector:
711	>
712	>	vector<int> foundTypes;
713	>	set<AtomType*>::iterator i;
714	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
715	>	foundTypes.push_back( (*i)->getIdent() );
716
717	<	int SimInfo::getNDFtranslational() {
718	<	int ndfTrans_local;
717	>	// count_local holds the number of found types on this processor
718	>	int count_local = foundTypes.size();
719
720	<	ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
720	>	int nproc = MPI::COMM_WORLD.Get_size();
721
722	+	// we need arrays to hold the counts and displacement vectors for
723	+	// all processors
724	+	vector<int> counts(nproc, 0);
725	+	vector<int> disps(nproc, 0);
726
727	<	#ifdef IS_MPI
728	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
729	<	#else
730	<	ndfTrans = ndfTrans_local;
731	<	#endif
727	>	// fill the counts array
728	>	MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
729	>	1, MPI::INT);
730	>
731	>	// use the processor counts to compute the displacement array
732	>	disps[0] = 0;
733	>	int totalCount = counts[0];
734	>	for (int iproc = 1; iproc < nproc; iproc++) {
735	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
736	>	totalCount += counts[iproc];
737	>	}
738
739	<	ndfTrans = ndfTrans - 3 - nZconstraints;
739	>	// we need a (possibly redundant) set of all found types:
740	>	vector<int> ftGlobal(totalCount);
741	>
742	>	// now spray out the foundTypes to all the other processors:
743	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
744	>	&ftGlobal[0], &counts[0], &disps[0],
745	>	MPI::INT);
746
747	<	return ndfTrans;
403	<	}
747	>	vector<int>::iterator j;
748
749	<	int SimInfo::getTotIntegrableObjects() {
750	<	int nObjs_local;
751	<	int nObjs;
749	>	// foundIdents is a stl set, so inserting an already found ident
750	>	// will have no effect.
751	>	set<int> foundIdents;
752
753	<	nObjs_local =  integrableObjects.size();
754	<
755	<
756	<	#ifdef IS_MPI
757	<	MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
758	<	#else
759	<	nObjs = nObjs_local;
753	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
754	>	foundIdents.insert((*j));
755	>
756	>	// now iterate over the foundIdents and get the actual atom types
757	>	// that correspond to these:
758	>	set<int>::iterator it;
759	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
760	>	atomTypes.insert( forceField_->getAtomType((*it)) );
761	>
762		#endif
763
764	<
419	<	return nObjs;
420	<	}
421	<
422	<	void SimInfo::refreshSim(){
423	<
424	<	simtype fInfo;
425	<	int isError;
426	<	int n_global;
427	<	int* excl;
428	<
429	<	fInfo.dielect = 0.0;
430	<
431	<	if( useDipoles ){
432	<	if( useReactionField )fInfo.dielect = dielectric;
764	>	return atomTypes;
765		}
766
767	<	fInfo.SIM_uses_PBC = usePBC;
768	<	//fInfo.SIM_uses_LJ = 0;
769	<	fInfo.SIM_uses_LJ = useLJ;
770	<	fInfo.SIM_uses_sticky = useSticky;
771	<	//fInfo.SIM_uses_sticky = 0;
772	<	fInfo.SIM_uses_charges = useCharges;
773	<	fInfo.SIM_uses_dipoles = useDipoles;
774	<	//fInfo.SIM_uses_dipoles = 0;
775	<	fInfo.SIM_uses_RF = useReactionField;
776	<	//fInfo.SIM_uses_RF = 0;
777	<	fInfo.SIM_uses_GB = useGB;
778	<	fInfo.SIM_uses_EAM = useEAM;
779	<
780	<	n_exclude = excludes->getSize();
781	<	excl = excludes->getFortranArray();
782	<
783	<	#ifdef IS_MPI
784	<	n_global = mpiSim->getNAtomsGlobal();
767	>	void SimInfo::setupSimVariables() {
768	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
769	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
770	>	calcBoxDipole_ = false;
771	>	if ( simParams_->haveAccumulateBoxDipole() )
772	>	if ( simParams_->getAccumulateBoxDipole() ) {
773	>	calcBoxDipole_ = true;
774	>	}
775	>
776	>	set<AtomType*>::iterator i;
777	>	set<AtomType*> atomTypes;
778	>	atomTypes = getSimulatedAtomTypes();
779	>	int usesElectrostatic = 0;
780	>	int usesMetallic = 0;
781	>	int usesDirectional = 0;
782	>	//loop over all of the atom types
783	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
784	>	usesElectrostatic |= (*i)->isElectrostatic();
785	>	usesMetallic |= (*i)->isMetal();
786	>	usesDirectional |= (*i)->isDirectional();
787	>	}
788	>
789	>	#ifdef IS_MPI
790	>	int temp;
791	>	temp = usesDirectional;
792	>	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
793	>
794	>	temp = usesMetallic;
795	>	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
796	>
797	>	temp = usesElectrostatic;
798	>	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
799		#else
454	–	n_global = n_atoms;
455	–	#endif
456	–
457	–	isError = 0;
458	–
459	–	getFortranGroupArrays(this, FglobalGroupMembership, mfact);
460	–	//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);
800
801	<	if( isError ){
801	>	usesDirectionalAtoms_ = usesDirectional;
802	>	usesMetallicAtoms_ = usesMetallic;
803	>	usesElectrostaticAtoms_ = usesElectrostatic;
804	>
805	>	#endif
806
807	<	sprintf( painCave.errMsg,
808	<	"There was an error setting the simulation information in fortran.\n" );
809	<	painCave.isFatal = 1;
472	<	painCave.severity = OOPSE_ERROR;
473	<	simError();
807	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
808	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
809	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
810		}
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	–	}
811
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	–	}
812
813	<	void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
813	>	vector<int> SimInfo::getGlobalAtomIndices() {
814	>	SimInfo::MoleculeIterator mi;
815	>	Molecule* mol;
816	>	Molecule::AtomIterator ai;
817	>	Atom* atom;
818
819	<	rSw = theRsw;
499	<	setDefaultRcut( theRcut );
500	<	}
501	<
502	<
503	<	void SimInfo::checkCutOffs( void ){
504	<
505	<	if( boxIsInit ){
819	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
820
821	<	//we need to check cutOffs against the box
822	<
823	<	if( rCut > maxCutoff ){
824	<	sprintf( painCave.errMsg,
825	<	"cutoffRadius is too large for the current periodic box.\n"
826	<	"\tCurrent Value of cutoffRadius = %G at time %G\n "
827	<	"\tThis is larger than half of at least one of the\n"
514	<	"\tperiodic box vectors.  Right now, the Box matrix is:\n"
515	<	"\n"
516	<	"\t[ %G %G %G ]\n"
517	<	"\t[ %G %G %G ]\n"
518	<	"\t[ %G %G %G ]\n",
519	<	rCut, currentTime,
520	<	Hmat[0][0], Hmat[0][1], Hmat[0][2],
521	<	Hmat[1][0], Hmat[1][1], Hmat[1][2],
522	<	Hmat[2][0], Hmat[2][1], Hmat[2][2]);
523	<	painCave.severity = OOPSE_ERROR;
524	<	painCave.isFatal = 1;
525	<	simError();
526	<	}
527	<	} else {
528	<	// 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();
821	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
822	>
823	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
824	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
825	>	}
826	>	}
827	>	return GlobalAtomIndices;
828		}
536	–
537	–	}
829
539	–	void SimInfo::addProperty(GenericData* prop){
830
831	<	map<string, GenericData*>::iterator result;
832	<	result = properties.find(prop->getID());
833	<
834	<	//we can't simply use  properties[prop->getID()] = prop,
835	<	//it will cause memory leak if we already contain a propery which has the same name of prop
836	<
837	<	if(result != properties.end()){
831	>	vector<int> SimInfo::getGlobalGroupIndices() {
832	>	SimInfo::MoleculeIterator mi;
833	>	Molecule* mol;
834	>	Molecule::CutoffGroupIterator ci;
835	>	CutoffGroup* cg;
836	>
837	>	vector<int> GlobalGroupIndices;
838
839	<	delete (*result).second;
550	<	(*result).second = prop;
839	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
840
841	+	//local index of cutoff group is trivial, it only depends on the
842	+	//order of travesing
843	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
844	+	cg = mol->nextCutoffGroup(ci)) {
845	+	GlobalGroupIndices.push_back(cg->getGlobalIndex());
846	+	}
847	+	}
848	+	return GlobalGroupIndices;
849		}
553	–	else{
850
555	–	properties[prop->getID()] = prop;
851
852	<	}
852	>	void SimInfo::prepareTopology() {
853	>	int nExclude, nOneTwo, nOneThree, nOneFour;
854	>
855	>	//calculate mass ratio of cutoff group
856	>	SimInfo::MoleculeIterator mi;
857	>	Molecule* mol;
858	>	Molecule::CutoffGroupIterator ci;
859	>	CutoffGroup* cg;
860	>	Molecule::AtomIterator ai;
861	>	Atom* atom;
862	>	RealType totalMass;
863	>
864	>	/**
865	>	* The mass factor is the relative mass of an atom to the total
866	>	* mass of the cutoff group it belongs to.  By default, all atoms
867	>	* are their own cutoff groups, and therefore have mass factors of
868	>	* 1.  We need some special handling for massless atoms, which
869	>	* will be treated as carrying the entire mass of the cutoff
870	>	* group.
871	>	*/
872	>	massFactors_.clear();
873	>	massFactors_.resize(getNAtoms(), 1.0);
874
875	<	}
875	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
876	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
877	>	cg = mol->nextCutoffGroup(ci)) {
878
879	<	GenericData* SimInfo::getProperty(const string& propName){
880	<
881	<	map<string, GenericData*>::iterator result;
882	<
883	<	//string lowerCaseName = ();
884	<
885	<	result = properties.find(propName);
886	<
887	<	if(result != properties.end())
888	<	return (*result).second;
571	<	else
572	<	return NULL;
573	<	}
879	>	totalMass = cg->getMass();
880	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
881	>	// Check for massless groups - set mfact to 1 if true
882	>	if (totalMass != 0)
883	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
884	>	else
885	>	massFactors_[atom->getLocalIndex()] = 1.0;
886	>	}
887	>	}
888	>	}
889
890	+	// Build the identArray_
891
892	<	void SimInfo::getFortranGroupArrays(SimInfo* info,
893	<	vector<int>& FglobalGroupMembership,
894	<	vector<double>& mfact){
895	<
896	<	Molecule* myMols;
897	<	Atom** myAtoms;
898	<	int numAtom;
899	<	double mtot;
900	<	int numMol;
585	<	int numCutoffGroups;
586	<	CutoffGroup* myCutoffGroup;
587	<	vector<CutoffGroup*>::iterator iterCutoff;
588	<	Atom* cutoffAtom;
589	<	vector<Atom*>::iterator iterAtom;
590	<	int atomIndex;
591	<	double totalMass;
592	<
593	<	mfact.clear();
594	<	FglobalGroupMembership.clear();
595	<
892	>	identArray_.clear();
893	>	identArray_.reserve(getNAtoms());
894	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
895	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
896	>	identArray_.push_back(atom->getIdent());
897	>	}
898	>	}
899	>
900	>	//scan topology
901
902	<	// Fix the silly fortran indexing problem
902	>	nExclude = excludedInteractions_.getSize();
903	>	nOneTwo = oneTwoInteractions_.getSize();
904	>	nOneThree = oneThreeInteractions_.getSize();
905	>	nOneFour = oneFourInteractions_.getSize();
906	>
907	>	int* excludeList = excludedInteractions_.getPairList();
908	>	int* oneTwoList = oneTwoInteractions_.getPairList();
909	>	int* oneThreeList = oneThreeInteractions_.getPairList();
910	>	int* oneFourList = oneFourInteractions_.getPairList();
911	>
912	>	topologyDone_ = true;
913	>	}
914	>
915	>	void SimInfo::addProperty(GenericData* genData) {
916	>	properties_.addProperty(genData);
917	>	}
918	>
919	>	void SimInfo::removeProperty(const string& propName) {
920	>	properties_.removeProperty(propName);
921	>	}
922	>
923	>	void SimInfo::clearProperties() {
924	>	properties_.clearProperties();
925	>	}
926	>
927	>	vector<string> SimInfo::getPropertyNames() {
928	>	return properties_.getPropertyNames();
929	>	}
930	>
931	>	vector<GenericData*> SimInfo::getProperties() {
932	>	return properties_.getProperties();
933	>	}
934	>
935	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
936	>	return properties_.getPropertyByName(propName);
937	>	}
938	>
939	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
940	>	if (sman_ == sman) {
941	>	return;
942	>	}
943	>	delete sman_;
944	>	sman_ = sman;
945	>
946	>	Molecule* mol;
947	>	RigidBody* rb;
948	>	Atom* atom;
949	>	CutoffGroup* cg;
950	>	SimInfo::MoleculeIterator mi;
951	>	Molecule::RigidBodyIterator rbIter;
952	>	Molecule::AtomIterator atomIter;
953	>	Molecule::CutoffGroupIterator cgIter;
954	>
955	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
956	>
957	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
958	>	atom->setSnapshotManager(sman_);
959	>	}
960	>
961	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
962	>	rb->setSnapshotManager(sman_);
963	>	}
964	>
965	>	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
966	>	cg->setSnapshotManager(sman_);
967	>	}
968	>	}
969	>
970	>	}
971	>
972	>	Vector3d SimInfo::getComVel(){
973	>	SimInfo::MoleculeIterator i;
974	>	Molecule* mol;
975	>
976	>	Vector3d comVel(0.0);
977	>	RealType totalMass = 0.0;
978	>
979	>
980	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
981	>	RealType mass = mol->getMass();
982	>	totalMass += mass;
983	>	comVel += mass * mol->getComVel();
984	>	}
985	>
986		#ifdef IS_MPI
987	<	numAtom = mpiSim->getNAtomsGlobal();
988	<	#else
989	<	numAtom = n_atoms;
987	>	RealType tmpMass = totalMass;
988	>	Vector3d tmpComVel(comVel);
989	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
990	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
991		#endif
603	–	for (int i = 0; i < numAtom; i++)
604	–	FglobalGroupMembership.push_back(globalGroupMembership[i] + 1);
605	–
992
993	<	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)){
993	>	comVel /= totalMass;
994
995	<	totalMass = myCutoffGroup->getMass();
995	>	return comVel;
996	>	}
997	>
998	>	Vector3d SimInfo::getCom(){
999	>	SimInfo::MoleculeIterator i;
1000	>	Molecule* mol;
1001	>
1002	>	Vector3d com(0.0);
1003	>	RealType totalMass = 0.0;
1004	>
1005	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1006	>	RealType mass = mol->getMass();
1007	>	totalMass += mass;
1008	>	com += mass * mol->getCom();
1009	>	}
1010	>
1011	>	#ifdef IS_MPI
1012	>	RealType tmpMass = totalMass;
1013	>	Vector3d tmpCom(com);
1014	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1015	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1016	>	#endif
1017	>
1018	>	com /= totalMass;
1019	>
1020	>	return com;
1021	>
1022	>	}
1023	>
1024	>	ostream& operator <<(ostream& o, SimInfo& info) {
1025	>
1026	>	return o;
1027	>	}
1028	>
1029	>
1030	>	/*
1031	>	Returns center of mass and center of mass velocity in one function call.
1032	>	*/
1033	>
1034	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1035	>	SimInfo::MoleculeIterator i;
1036	>	Molecule* mol;
1037
1038	<	for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom);
1039	<	cutoffAtom != NULL;
1040	<	cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
1041	<	mfact.push_back(cutoffAtom->getMass()/totalMass);
1038	>
1039	>	RealType totalMass = 0.0;
1040	>
1041	>
1042	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1043	>	RealType mass = mol->getMass();
1044	>	totalMass += mass;
1045	>	com += mass * mol->getCom();
1046	>	comVel += mass * mol->getComVel();
1047		}
1048	+
1049	+	#ifdef IS_MPI
1050	+	RealType tmpMass = totalMass;
1051	+	Vector3d tmpCom(com);
1052	+	Vector3d tmpComVel(comVel);
1053	+	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1054	+	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1055	+	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1056	+	#endif
1057	+
1058	+	com /= totalMass;
1059	+	comVel /= totalMass;
1060	+	}
1061	+
1062	+	/*
1063	+	Return intertia tensor for entire system and angular momentum Vector.
1064	+
1065	+
1066	+	[  Ixx -Ixy  -Ixz ]
1067	+	J =| -Iyx  Iyy  -Iyz |
1068	+	[ -Izx -Iyz   Izz ]
1069	+	*/
1070	+
1071	+	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1072	+
1073	+
1074	+	RealType xx = 0.0;
1075	+	RealType yy = 0.0;
1076	+	RealType zz = 0.0;
1077	+	RealType xy = 0.0;
1078	+	RealType xz = 0.0;
1079	+	RealType yz = 0.0;
1080	+	Vector3d com(0.0);
1081	+	Vector3d comVel(0.0);
1082	+
1083	+	getComAll(com, comVel);
1084	+
1085	+	SimInfo::MoleculeIterator i;
1086	+	Molecule* mol;
1087	+
1088	+	Vector3d thisq(0.0);
1089	+	Vector3d thisv(0.0);
1090	+
1091	+	RealType thisMass = 0.0;
1092	+
1093	+
1094	+
1095	+
1096	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1097	+
1098	+	thisq = mol->getCom()-com;
1099	+	thisv = mol->getComVel()-comVel;
1100	+	thisMass = mol->getMass();
1101	+	// Compute moment of intertia coefficients.
1102	+	xx += thisq[0]*thisq[0]*thisMass;
1103	+	yy += thisq[1]*thisq[1]*thisMass;
1104	+	zz += thisq[2]*thisq[2]*thisMass;
1105	+
1106	+	// compute products of intertia
1107	+	xy += thisq[0]*thisq[1]*thisMass;
1108	+	xz += thisq[0]*thisq[2]*thisMass;
1109	+	yz += thisq[1]*thisq[2]*thisMass;
1110	+
1111	+	angularMomentum += cross( thisq, thisv ) * thisMass;
1112	+
1113	+	}
1114	+
1115	+
1116	+	inertiaTensor(0,0) = yy + zz;
1117	+	inertiaTensor(0,1) = -xy;
1118	+	inertiaTensor(0,2) = -xz;
1119	+	inertiaTensor(1,0) = -xy;
1120	+	inertiaTensor(1,1) = xx + zz;
1121	+	inertiaTensor(1,2) = -yz;
1122	+	inertiaTensor(2,0) = -xz;
1123	+	inertiaTensor(2,1) = -yz;
1124	+	inertiaTensor(2,2) = xx + yy;
1125	+
1126	+	#ifdef IS_MPI
1127	+	Mat3x3d tmpI(inertiaTensor);
1128	+	Vector3d tmpAngMom;
1129	+	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1130	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1131	+	#endif
1132	+
1133	+	return;
1134	+	}
1135	+
1136	+	//Returns the angular momentum of the system
1137	+	Vector3d SimInfo::getAngularMomentum(){
1138	+
1139	+	Vector3d com(0.0);
1140	+	Vector3d comVel(0.0);
1141	+	Vector3d angularMomentum(0.0);
1142	+
1143	+	getComAll(com,comVel);
1144	+
1145	+	SimInfo::MoleculeIterator i;
1146	+	Molecule* mol;
1147	+
1148	+	Vector3d thisr(0.0);
1149	+	Vector3d thisp(0.0);
1150	+
1151	+	RealType thisMass;
1152	+
1153	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1154	+	thisMass = mol->getMass();
1155	+	thisr = mol->getCom()-com;
1156	+	thisp = (mol->getComVel()-comVel)*thisMass;
1157	+
1158	+	angularMomentum += cross( thisr, thisp );
1159	+
1160	+	}
1161	+
1162	+	#ifdef IS_MPI
1163	+	Vector3d tmpAngMom;
1164	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1165	+	#endif
1166	+
1167	+	return angularMomentum;
1168	+	}
1169	+
1170	+	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1171	+	return IOIndexToIntegrableObject.at(index);
1172	+	}
1173	+
1174	+	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1175	+	IOIndexToIntegrableObject= v;
1176	+	}
1177	+
1178	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1179	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1180	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1181	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1182	+	*/
1183	+	void SimInfo::getGyrationalVolume(RealType &volume){
1184	+	Mat3x3d intTensor;
1185	+	RealType det;
1186	+	Vector3d dummyAngMom;
1187	+	RealType sysconstants;
1188	+	RealType geomCnst;
1189	+
1190	+	geomCnst = 3.0/2.0;
1191	+	/* Get the inertial tensor and angular momentum for free*/
1192	+	getInertiaTensor(intTensor,dummyAngMom);
1193	+
1194	+	det = intTensor.determinant();
1195	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1196	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1197	+	return;
1198	+	}
1199	+
1200	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1201	+	Mat3x3d intTensor;
1202	+	Vector3d dummyAngMom;
1203	+	RealType sysconstants;
1204	+	RealType geomCnst;
1205	+
1206	+	geomCnst = 3.0/2.0;
1207	+	/* Get the inertial tensor and angular momentum for free*/
1208	+	getInertiaTensor(intTensor,dummyAngMom);
1209	+
1210	+	detI = intTensor.determinant();
1211	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1212	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1213	+	return;
1214	+	}
1215	+	/*
1216	+	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1217	+	assert( v.size() == nAtoms_ + nRigidBodies_);
1218	+	sdByGlobalIndex_ = v;
1219		}
1220	+
1221	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1222	+	//assert(index < nAtoms_ + nRigidBodies_);
1223	+	return sdByGlobalIndex_.at(index);
1224	+	}
1225	+	*/
1226	+	int SimInfo::getNGlobalConstraints() {
1227	+	int nGlobalConstraints;
1228	+	#ifdef IS_MPI
1229	+	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1230	+	MPI_COMM_WORLD);
1231	+	#else
1232	+	nGlobalConstraints =  nConstraints_;
1233	+	#endif
1234	+	return nGlobalConstraints;
1235		}
1236
1237	<	}
1237	>	}//end namespace OpenMD
1238	>

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 124 by chuckv, Wed Oct 20 20:46:20 2004 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1627 by gezelter, Tue Sep 13 22:05:04 2011 UTC

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