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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 143 by chrisfen, Fri Oct 22 22:54:01 2004 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1577 by gezelter, Wed Jun 8 20:26:56 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"
59	>	#include "selection/SelectionManager.hpp"
60	>	#include "io/ForceFieldOptions.hpp"
61	>	#include "UseTheForce/ForceField.hpp"
62	>	#include "nonbonded/SwitchingFunction.hpp"
63
64	<	//#include "UseTheForce/fortranWrappers.hpp"
64	>	using namespace std;
65	>	namespace OpenMD {
66	>
67	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
68	>	forceField_(ff), simParams_(simParams),
69	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
70	>	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
71	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
72	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
73	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
74	>	nConstraints_(0), sman_(NULL), topologyDone_(false),
75	>	calcBoxDipole_(false), useAtomicVirial_(true) {
76	>
77	>	MoleculeStamp* molStamp;
78	>	int nMolWithSameStamp;
79	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
80	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
81	>	CutoffGroupStamp* cgStamp;
82	>	RigidBodyStamp* rbStamp;
83	>	int nRigidAtoms = 0;
84	>
85	>	vector<Component*> components = simParams->getComponents();
86	>
87	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
88	>	molStamp = (*i)->getMoleculeStamp();
89	>	nMolWithSameStamp = (*i)->getNMol();
90	>
91	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
92	>
93	>	//calculate atoms in molecules
94	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
95	>
96	>	//calculate atoms in cutoff groups
97	>	int nAtomsInGroups = 0;
98	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
99	>
100	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
101	>	cgStamp = molStamp->getCutoffGroupStamp(j);
102	>	nAtomsInGroups += cgStamp->getNMembers();
103	>	}
104	>
105	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
106	>
107	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
108	>
109	>	//calculate atoms in rigid bodies
110	>	int nAtomsInRigidBodies = 0;
111	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
112	>
113	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
114	>	rbStamp = molStamp->getRigidBodyStamp(j);
115	>	nAtomsInRigidBodies += rbStamp->getNMembers();
116	>	}
117	>
118	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
119	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
120	>
121	>	}
122	>
123	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
124	>	//group therefore the total number of cutoff groups in the system is
125	>	//equal to the total number of atoms minus number of atoms belong to
126	>	//cutoff group defined in meta-data file plus the number of cutoff
127	>	//groups defined in meta-data file
128
129	<	#include "math/MatVec3.h"
129	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
130	>
131	>	//every free atom (atom does not belong to rigid bodies) is an
132	>	//integrable object therefore the total number of integrable objects
133	>	//in the system is equal to the total number of atoms minus number of
134	>	//atoms belong to rigid body defined in meta-data file plus the number
135	>	//of rigid bodies defined in meta-data file
136	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
137	>	+ nGlobalRigidBodies_;
138	>
139	>	nGlobalMols_ = molStampIds_.size();
140	>	molToProcMap_.resize(nGlobalMols_);
141	>	}
142	>
143	>	SimInfo::~SimInfo() {
144	>	map<int, Molecule*>::iterator i;
145	>	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
146	>	delete i->second;
147	>	}
148	>	molecules_.clear();
149	>
150	>	delete sman_;
151	>	delete simParams_;
152	>	delete forceField_;
153	>	}
154
19	–	#ifdef IS_MPI
20	–	#include "brains/mpiSimulation.hpp"
21	–	#endif
155
156	<	inline double roundMe( double x ){
157	<	return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
158	<	}
159	<
160	<	inline double min( double a, double b ){
161	<	return (a < b ) ? a : b;
162	<	}
156	>	bool SimInfo::addMolecule(Molecule* mol) {
157	>	MoleculeIterator i;
158	>
159	>	i = molecules_.find(mol->getGlobalIndex());
160	>	if (i == molecules_.end() ) {
161	>
162	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
163	>
164	>	nAtoms_ += mol->getNAtoms();
165	>	nBonds_ += mol->getNBonds();
166	>	nBends_ += mol->getNBends();
167	>	nTorsions_ += mol->getNTorsions();
168	>	nInversions_ += mol->getNInversions();
169	>	nRigidBodies_ += mol->getNRigidBodies();
170	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
171	>	nCutoffGroups_ += mol->getNCutoffGroups();
172	>	nConstraints_ += mol->getNConstraintPairs();
173	>
174	>	addInteractionPairs(mol);
175	>
176	>	return true;
177	>	} else {
178	>	return false;
179	>	}
180	>	}
181	>
182	>	bool SimInfo::removeMolecule(Molecule* mol) {
183	>	MoleculeIterator i;
184	>	i = molecules_.find(mol->getGlobalIndex());
185
186	<	SimInfo* currentInfo;
186	>	if (i != molecules_.end() ) {
187
188	<	SimInfo::SimInfo(){
188	>	assert(mol == i->second);
189	>
190	>	nAtoms_ -= mol->getNAtoms();
191	>	nBonds_ -= mol->getNBonds();
192	>	nBends_ -= mol->getNBends();
193	>	nTorsions_ -= mol->getNTorsions();
194	>	nInversions_ -= mol->getNInversions();
195	>	nRigidBodies_ -= mol->getNRigidBodies();
196	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
197	>	nCutoffGroups_ -= mol->getNCutoffGroups();
198	>	nConstraints_ -= mol->getNConstraintPairs();
199
200	<	n_constraints = 0;
201	<	nZconstraints = 0;
37	<	n_oriented = 0;
38	<	n_dipoles = 0;
39	<	ndf = 0;
40	<	ndfRaw = 0;
41	<	nZconstraints = 0;
42	<	the_integrator = NULL;
43	<	setTemp = 0;
44	<	thermalTime = 0.0;
45	<	currentTime = 0.0;
46	<	rCut = 0.0;
47	<	rSw = 0.0;
200	>	removeInteractionPairs(mol);
201	>	molecules_.erase(mol->getGlobalIndex());
202
203	<	haveRcut = 0;
204	<	haveRsw = 0;
205	<	boxIsInit = 0;
206	<
207	<	resetTime = 1e99;
203	>	delete mol;
204	>
205	>	return true;
206	>	} else {
207	>	return false;
208	>	}
209	>	}
210
211	<	orthoRhombic = 0;
212	<	orthoTolerance = 1E-6;
213	<	useInitXSstate = true;
211	>
212	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
213	>	i = molecules_.begin();
214	>	return i == molecules_.end() ? NULL : i->second;
215	>	}
216
217	<	usePBC = 0;
218	<	useDirectionalAtoms = 0;
219	<	useLennardJones = 0;
220	<	useElectrostatics = 0;
63	<	useCharges = 0;
64	<	useDipoles = 0;
65	<	useSticky = 0;
66	<	useGayBerne = 0;
67	<	useEAM = 0;
68	<	useShapes = 0;
69	<	useFLARB = 0;
217	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
218	>	++i;
219	>	return i == molecules_.end() ? NULL : i->second;
220	>	}
221
71	–	useSolidThermInt = 0;
72	–	useLiquidThermInt = 0;
222
223	<	haveCutoffGroups = false;
223	>	void SimInfo::calcNdf() {
224	>	int ndf_local;
225	>	MoleculeIterator i;
226	>	vector<StuntDouble*>::iterator j;
227	>	Molecule* mol;
228	>	StuntDouble* integrableObject;
229
230	<	excludes = Exclude::Instance();
230	>	ndf_local = 0;
231	>
232	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
233	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
234	>	integrableObject = mol->nextIntegrableObject(j)) {
235
236	<	myConfiguration = new SimState();
236	>	ndf_local += 3;
237
238	<	has_minimizer = false;
239	<	the_minimizer =NULL;
238	>	if (integrableObject->isDirectional()) {
239	>	if (integrableObject->isLinear()) {
240	>	ndf_local += 2;
241	>	} else {
242	>	ndf_local += 3;
243	>	}
244	>	}
245	>
246	>	}
247	>	}
248	>
249	>	// n_constraints is local, so subtract them on each processor
250	>	ndf_local -= nConstraints_;
251
252	<	ngroup = 0;
252	>	#ifdef IS_MPI
253	>	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
254	>	#else
255	>	ndf_ = ndf_local;
256	>	#endif
257
258	<	}
258	>	// nZconstraints_ is global, as are the 3 COM translations for the
259	>	// entire system:
260	>	ndf_ = ndf_ - 3 - nZconstraint_;
261
262	+	}
263
264	<	SimInfo::~SimInfo(){
265	<
266	<	delete myConfiguration;
267	<
268	<	map<string, GenericData*>::iterator i;
264	>	int SimInfo::getFdf() {
265	>	#ifdef IS_MPI
266	>	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
267	>	#else
268	>	fdf_ = fdf_local;
269	>	#endif
270	>	return fdf_;
271	>	}
272
273	<	for(i = properties.begin(); i != properties.end(); i++)
274	<	delete (*i).second;
273	>	unsigned int SimInfo::getNLocalCutoffGroups(){
274	>	int nLocalCutoffAtoms = 0;
275	>	Molecule* mol;
276	>	MoleculeIterator mi;
277	>	CutoffGroup* cg;
278	>	Molecule::CutoffGroupIterator ci;
279	>
280	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
281	>
282	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
283	>	cg = mol->nextCutoffGroup(ci)) {
284	>	nLocalCutoffAtoms += cg->getNumAtom();
285	>
286	>	}
287	>	}
288	>
289	>	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
290	>	}
291	>
292	>	void SimInfo::calcNdfRaw() {
293	>	int ndfRaw_local;
294
295	<	}
295	>	MoleculeIterator i;
296	>	vector<StuntDouble*>::iterator j;
297	>	Molecule* mol;
298	>	StuntDouble* integrableObject;
299
300	<	void SimInfo::setBox(double newBox[3]) {
301	<
302	<	int i, j;
303	<	double tempMat[3][3];
300	>	// Raw degrees of freedom that we have to set
301	>	ndfRaw_local = 0;
302	>
303	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
304	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
305	>	integrableObject = mol->nextIntegrableObject(j)) {
306
307	<	for(i=0; i<3; i++)
105	<	for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
307	>	ndfRaw_local += 3;
308
309	<	tempMat[0][0] = newBox[0];
310	<	tempMat[1][1] = newBox[1];
311	<	tempMat[2][2] = newBox[2];
312	<
313	<	setBoxM( tempMat );
314	<
315	<	}
316	<
317	<	void SimInfo::setBoxM( double theBox[3][3] ){
116	<
117	<	int i, j;
118	<	double FortranHmat[9]; // to preserve compatibility with Fortran the
119	<	// ordering in the array is as follows:
120	<	// [ 0 3 6 ]
121	<	// [ 1 4 7 ]
122	<	// [ 2 5 8 ]
123	<	double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
124	<
125	<	if( !boxIsInit ) boxIsInit = 1;
126	<
127	<	for(i=0; i < 3; i++)
128	<	for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
129	<
130	<	calcBoxL();
131	<	calcHmatInv();
132	<
133	<	for(i=0; i < 3; i++) {
134	<	for (j=0; j < 3; j++) {
135	<	FortranHmat[3*j + i] = Hmat[i][j];
136	<	FortranHmatInv[3*j + i] = HmatInv[i][j];
309	>	if (integrableObject->isDirectional()) {
310	>	if (integrableObject->isLinear()) {
311	>	ndfRaw_local += 2;
312	>	} else {
313	>	ndfRaw_local += 3;
314	>	}
315	>	}
316	>
317	>	}
318		}
319	+
320	+	#ifdef IS_MPI
321	+	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
322	+	#else
323	+	ndfRaw_ = ndfRaw_local;
324	+	#endif
325		}
326
327	<	setFortranBox(FortranHmat, FortranHmatInv, &orthoRhombic);
328	<
142	<	}
143	<
327	>	void SimInfo::calcNdfTrans() {
328	>	int ndfTrans_local;
329
330	<	void SimInfo::getBoxM (double theBox[3][3]) {
330	>	ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
331
147	–	int i, j;
148	–	for(i=0; i<3; i++)
149	–	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
150	–	}
332
333	+	#ifdef IS_MPI
334	+	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
335	+	#else
336	+	ndfTrans_ = ndfTrans_local;
337	+	#endif
338
339	<	void SimInfo::scaleBox(double scale) {
340	<	double theBox[3][3];
341	<	int i, j;
339	>	ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
340	>
341	>	}
342
343	<	// cerr << "Scaling box by " << scale << "\n";
343	>	void SimInfo::addInteractionPairs(Molecule* mol) {
344	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
345	>	vector<Bond*>::iterator bondIter;
346	>	vector<Bend*>::iterator bendIter;
347	>	vector<Torsion*>::iterator torsionIter;
348	>	vector<Inversion*>::iterator inversionIter;
349	>	Bond* bond;
350	>	Bend* bend;
351	>	Torsion* torsion;
352	>	Inversion* inversion;
353	>	int a;
354	>	int b;
355	>	int c;
356	>	int d;
357
358	<	for(i=0; i<3; i++)
359	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
358	>	// atomGroups can be used to add special interaction maps between
359	>	// groups of atoms that are in two separate rigid bodies.
360	>	// However, most site-site interactions between two rigid bodies
361	>	// are probably not special, just the ones between the physically
362	>	// bonded atoms.  Interactions *within* a single rigid body should
363	>	// always be excluded.  These are done at the bottom of this
364	>	// function.
365
366	<	setBoxM(theBox);
367	<
368	<	}
369	<
370	<	void SimInfo::calcHmatInv( void ) {
371	<
372	<	int oldOrtho;
373	<	int i,j;
374	<	double smallDiag;
375	<	double tol;
376	<	double sanity[3][3];
377	<
378	<	invertMat3( Hmat, HmatInv );
379	<
380	<	// check to see if Hmat is orthorhombic
381	<
382	<	oldOrtho = orthoRhombic;
383	<
384	<	smallDiag = fabs(Hmat[0][0]);
385	<	if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
386	<	if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
387	<	tol = smallDiag * orthoTolerance;
388	<
389	<	orthoRhombic = 1;
186	<
187	<	for (i = 0; i < 3; i++ ) {
188	<	for (j = 0 ; j < 3; j++) {
189	<	if (i != j) {
190	<	if (orthoRhombic) {
191	<	if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
192	<	}
366	>	map<int, set<int> > atomGroups;
367	>	Molecule::RigidBodyIterator rbIter;
368	>	RigidBody* rb;
369	>	Molecule::IntegrableObjectIterator ii;
370	>	StuntDouble* integrableObject;
371	>
372	>	for (integrableObject = mol->beginIntegrableObject(ii);
373	>	integrableObject != NULL;
374	>	integrableObject = mol->nextIntegrableObject(ii)) {
375	>
376	>	if (integrableObject->isRigidBody()) {
377	>	rb = static_cast<RigidBody*>(integrableObject);
378	>	vector<Atom*> atoms = rb->getAtoms();
379	>	set<int> rigidAtoms;
380	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
381	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
382	>	}
383	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
384	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
385	>	}
386	>	} else {
387	>	set<int> oneAtomSet;
388	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
389	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
390		}
391	<	}
392	<	}
391	>	}
392	>
393	>	for (bond= mol->beginBond(bondIter); bond != NULL;
394	>	bond = mol->nextBond(bondIter)) {
395
396	<	if( oldOrtho != orthoRhombic ){
396	>	a = bond->getAtomA()->getGlobalIndex();
397	>	b = bond->getAtomB()->getGlobalIndex();
398
399	<	if( orthoRhombic ) {
400	<	sprintf( painCave.errMsg,
401	<	"OOPSE is switching from the default Non-Orthorhombic\n"
402	<	"\tto the faster Orthorhombic periodic boundary computations.\n"
403	<	"\tThis is usually a good thing, but if you wan't the\n"
204	<	"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
205	<	"\tvariable ( currently set to %G ) smaller.\n",
206	<	orthoTolerance);
207	<	painCave.severity = OOPSE_INFO;
208	<	simError();
399	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
400	>	oneTwoInteractions_.addPair(a, b);
401	>	} else {
402	>	excludedInteractions_.addPair(a, b);
403	>	}
404		}
210	–	else {
211	–	sprintf( painCave.errMsg,
212	–	"OOPSE is switching from the faster Orthorhombic to the more\n"
213	–	"\tflexible Non-Orthorhombic periodic boundary computations.\n"
214	–	"\tThis is usually because the box has deformed under\n"
215	–	"\tNPTf integration. If you wan't to live on the edge with\n"
216	–	"\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
217	–	"\tvariable ( currently set to %G ) larger.\n",
218	–	orthoTolerance);
219	–	painCave.severity = OOPSE_WARNING;
220	–	simError();
221	–	}
222	–	}
223	–	}
405
406	<	void SimInfo::calcBoxL( void ){
406	>	for (bend= mol->beginBend(bendIter); bend != NULL;
407	>	bend = mol->nextBend(bendIter)) {
408
409	<	double dx, dy, dz, dsq;
409	>	a = bend->getAtomA()->getGlobalIndex();
410	>	b = bend->getAtomB()->getGlobalIndex();
411	>	c = bend->getAtomC()->getGlobalIndex();
412	>
413	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
414	>	oneTwoInteractions_.addPair(a, b);
415	>	oneTwoInteractions_.addPair(b, c);
416	>	} else {
417	>	excludedInteractions_.addPair(a, b);
418	>	excludedInteractions_.addPair(b, c);
419	>	}
420
421	<	// boxVol = Determinant of Hmat
421	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
422	>	oneThreeInteractions_.addPair(a, c);
423	>	} else {
424	>	excludedInteractions_.addPair(a, c);
425	>	}
426	>	}
427
428	<	boxVol = matDet3( Hmat );
428	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
429	>	torsion = mol->nextTorsion(torsionIter)) {
430
431	<	// boxLx
432	<
433	<	dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
434	<	dsq = dx*dx + dy*dy + dz*dz;
237	<	boxL[0] = sqrt( dsq );
238	<	//maxCutoff = 0.5 * boxL[0];
431	>	a = torsion->getAtomA()->getGlobalIndex();
432	>	b = torsion->getAtomB()->getGlobalIndex();
433	>	c = torsion->getAtomC()->getGlobalIndex();
434	>	d = torsion->getAtomD()->getGlobalIndex();
435
436	<	// boxLy
437	<
438	<	dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
439	<	dsq = dx*dx + dy*dy + dz*dz;
440	<	boxL[1] = sqrt( dsq );
441	<	//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
436	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
437	>	oneTwoInteractions_.addPair(a, b);
438	>	oneTwoInteractions_.addPair(b, c);
439	>	oneTwoInteractions_.addPair(c, d);
440	>	} else {
441	>	excludedInteractions_.addPair(a, b);
442	>	excludedInteractions_.addPair(b, c);
443	>	excludedInteractions_.addPair(c, d);
444	>	}
445
446	+	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
447	+	oneThreeInteractions_.addPair(a, c);
448	+	oneThreeInteractions_.addPair(b, d);
449	+	} else {
450	+	excludedInteractions_.addPair(a, c);
451	+	excludedInteractions_.addPair(b, d);
452	+	}
453
454	<	// boxLz
455	<
456	<	dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
457	<	dsq = dx*dx + dy*dy + dz*dz;
458	<	boxL[2] = sqrt( dsq );
459	<	//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
454	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
455	>	oneFourInteractions_.addPair(a, d);
456	>	} else {
457	>	excludedInteractions_.addPair(a, d);
458	>	}
459	>	}
460
461	<	//calculate the max cutoff
462	<	maxCutoff =  calcMaxCutOff();
257	<
258	<	checkCutOffs();
461	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
462	>	inversion = mol->nextInversion(inversionIter)) {
463
464	<	}
464	>	a = inversion->getAtomA()->getGlobalIndex();
465	>	b = inversion->getAtomB()->getGlobalIndex();
466	>	c = inversion->getAtomC()->getGlobalIndex();
467	>	d = inversion->getAtomD()->getGlobalIndex();
468
469	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
470	+	oneTwoInteractions_.addPair(a, b);
471	+	oneTwoInteractions_.addPair(a, c);
472	+	oneTwoInteractions_.addPair(a, d);
473	+	} else {
474	+	excludedInteractions_.addPair(a, b);
475	+	excludedInteractions_.addPair(a, c);
476	+	excludedInteractions_.addPair(a, d);
477	+	}
478
479	<	double SimInfo::calcMaxCutOff(){
479	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
480	>	oneThreeInteractions_.addPair(b, c);
481	>	oneThreeInteractions_.addPair(b, d);
482	>	oneThreeInteractions_.addPair(c, d);
483	>	} else {
484	>	excludedInteractions_.addPair(b, c);
485	>	excludedInteractions_.addPair(b, d);
486	>	excludedInteractions_.addPair(c, d);
487	>	}
488	>	}
489
490	<	double ri[3], rj[3], rk[3];
491	<	double rij[3], rjk[3], rki[3];
492	<	double minDist;
490	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
491	>	rb = mol->nextRigidBody(rbIter)) {
492	>	vector<Atom*> atoms = rb->getAtoms();
493	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
494	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
495	>	a = atoms[i]->getGlobalIndex();
496	>	b = atoms[j]->getGlobalIndex();
497	>	excludedInteractions_.addPair(a, b);
498	>	}
499	>	}
500	>	}
501
502	<	ri[0] = Hmat[0][0];
270	<	ri[1] = Hmat[1][0];
271	<	ri[2] = Hmat[2][0];
502	>	}
503
504	<	rj[0] = Hmat[0][1];
505	<	rj[1] = Hmat[1][1];
506	<	rj[2] = Hmat[2][1];
504	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
505	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
506	>	vector<Bond*>::iterator bondIter;
507	>	vector<Bend*>::iterator bendIter;
508	>	vector<Torsion*>::iterator torsionIter;
509	>	vector<Inversion*>::iterator inversionIter;
510	>	Bond* bond;
511	>	Bend* bend;
512	>	Torsion* torsion;
513	>	Inversion* inversion;
514	>	int a;
515	>	int b;
516	>	int c;
517	>	int d;
518
519	<	rk[0] = Hmat[0][2];
520	<	rk[1] = Hmat[1][2];
521	<	rk[2] = Hmat[2][2];
519	>	map<int, set<int> > atomGroups;
520	>	Molecule::RigidBodyIterator rbIter;
521	>	RigidBody* rb;
522	>	Molecule::IntegrableObjectIterator ii;
523	>	StuntDouble* integrableObject;
524
525	<	crossProduct3(ri, rj, rij);
526	<	distXY = dotProduct3(rk,rij) / norm3(rij);
525	>	for (integrableObject = mol->beginIntegrableObject(ii);
526	>	integrableObject != NULL;
527	>	integrableObject = mol->nextIntegrableObject(ii)) {
528	>
529	>	if (integrableObject->isRigidBody()) {
530	>	rb = static_cast<RigidBody*>(integrableObject);
531	>	vector<Atom*> atoms = rb->getAtoms();
532	>	set<int> rigidAtoms;
533	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
534	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
535	>	}
536	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
537	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
538	>	}
539	>	} else {
540	>	set<int> oneAtomSet;
541	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
542	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
543	>	}
544	>	}
545
546	<	crossProduct3(rj,rk, rjk);
547	<	distYZ = dotProduct3(ri,rjk) / norm3(rjk);
546	>	for (bond= mol->beginBond(bondIter); bond != NULL;
547	>	bond = mol->nextBond(bondIter)) {
548	>
549	>	a = bond->getAtomA()->getGlobalIndex();
550	>	b = bond->getAtomB()->getGlobalIndex();
551	>
552	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
553	>	oneTwoInteractions_.removePair(a, b);
554	>	} else {
555	>	excludedInteractions_.removePair(a, b);
556	>	}
557	>	}
558
559	<	crossProduct3(rk,ri, rki);
560	<	distZX = dotProduct3(rj,rki) / norm3(rki);
559	>	for (bend= mol->beginBend(bendIter); bend != NULL;
560	>	bend = mol->nextBend(bendIter)) {
561
562	<	minDist = min(min(distXY, distYZ), distZX);
563	<	return minDist/2;
564	<
565	<	}
562	>	a = bend->getAtomA()->getGlobalIndex();
563	>	b = bend->getAtomB()->getGlobalIndex();
564	>	c = bend->getAtomC()->getGlobalIndex();
565	>
566	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
567	>	oneTwoInteractions_.removePair(a, b);
568	>	oneTwoInteractions_.removePair(b, c);
569	>	} else {
570	>	excludedInteractions_.removePair(a, b);
571	>	excludedInteractions_.removePair(b, c);
572	>	}
573
574	<	void SimInfo::wrapVector( double thePos[3] ){
574	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
575	>	oneThreeInteractions_.removePair(a, c);
576	>	} else {
577	>	excludedInteractions_.removePair(a, c);
578	>	}
579	>	}
580
581	<	int i;
582	<	double scaled[3];
581	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
582	>	torsion = mol->nextTorsion(torsionIter)) {
583
584	<	if( !orthoRhombic ){
585	<	// calc the scaled coordinates.
584	>	a = torsion->getAtomA()->getGlobalIndex();
585	>	b = torsion->getAtomB()->getGlobalIndex();
586	>	c = torsion->getAtomC()->getGlobalIndex();
587	>	d = torsion->getAtomD()->getGlobalIndex();
588
589	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
590	+	oneTwoInteractions_.removePair(a, b);
591	+	oneTwoInteractions_.removePair(b, c);
592	+	oneTwoInteractions_.removePair(c, d);
593	+	} else {
594	+	excludedInteractions_.removePair(a, b);
595	+	excludedInteractions_.removePair(b, c);
596	+	excludedInteractions_.removePair(c, d);
597	+	}
598
599	<	matVecMul3(HmatInv, thePos, scaled);
600	<
601	<	for(i=0; i<3; i++)
602	<	scaled[i] -= roundMe(scaled[i]);
603	<
604	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
605	<
311	<	matVecMul3(Hmat, scaled, thePos);
599	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
600	>	oneThreeInteractions_.removePair(a, c);
601	>	oneThreeInteractions_.removePair(b, d);
602	>	} else {
603	>	excludedInteractions_.removePair(a, c);
604	>	excludedInteractions_.removePair(b, d);
605	>	}
606
607	<	}
608	<	else{
609	<	// calc the scaled coordinates.
610	<
611	<	for(i=0; i<3; i++)
318	<	scaled[i] = thePos[i]*HmatInv[i][i];
319	<
320	<	// wrap the scaled coordinates
321	<
322	<	for(i=0; i<3; i++)
323	<	scaled[i] -= roundMe(scaled[i]);
324	<
325	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
326	<
327	<	for(i=0; i<3; i++)
328	<	thePos[i] = scaled[i]*Hmat[i][i];
329	<	}
330	<
331	<	}
332	<
333	<
334	<	int SimInfo::getNDF(){
335	<	int ndf_local;
336	<
337	<	ndf_local = 0;
338	<
339	<	for(int i = 0; i < integrableObjects.size(); i++){
340	<	ndf_local += 3;
341	<	if (integrableObjects[i]->isDirectional()) {
342	<	if (integrableObjects[i]->isLinear())
343	<	ndf_local += 2;
344	<	else
345	<	ndf_local += 3;
607	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
608	>	oneFourInteractions_.removePair(a, d);
609	>	} else {
610	>	excludedInteractions_.removePair(a, d);
611	>	}
612		}
347	–	}
613
614	<	// n_constraints is local, so subtract them on each processor:
614	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
615	>	inversion = mol->nextInversion(inversionIter)) {
616
617	<	ndf_local -= n_constraints;
617	>	a = inversion->getAtomA()->getGlobalIndex();
618	>	b = inversion->getAtomB()->getGlobalIndex();
619	>	c = inversion->getAtomC()->getGlobalIndex();
620	>	d = inversion->getAtomD()->getGlobalIndex();
621
622	<	#ifdef IS_MPI
623	<	MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
624	<	#else
625	<	ndf = ndf_local;
626	<	#endif
627	<
628	<	// nZconstraints is global, as are the 3 COM translations for the
629	<	// entire system:
622	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
623	>	oneTwoInteractions_.removePair(a, b);
624	>	oneTwoInteractions_.removePair(a, c);
625	>	oneTwoInteractions_.removePair(a, d);
626	>	} else {
627	>	excludedInteractions_.removePair(a, b);
628	>	excludedInteractions_.removePair(a, c);
629	>	excludedInteractions_.removePair(a, d);
630	>	}
631
632	<	ndf = ndf - 3 - nZconstraints;
632	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
633	>	oneThreeInteractions_.removePair(b, c);
634	>	oneThreeInteractions_.removePair(b, d);
635	>	oneThreeInteractions_.removePair(c, d);
636	>	} else {
637	>	excludedInteractions_.removePair(b, c);
638	>	excludedInteractions_.removePair(b, d);
639	>	excludedInteractions_.removePair(c, d);
640	>	}
641	>	}
642
643	<	return ndf;
644	<	}
643	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
644	>	rb = mol->nextRigidBody(rbIter)) {
645	>	vector<Atom*> atoms = rb->getAtoms();
646	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
647	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
648	>	a = atoms[i]->getGlobalIndex();
649	>	b = atoms[j]->getGlobalIndex();
650	>	excludedInteractions_.removePair(a, b);
651	>	}
652	>	}
653	>	}
654	>
655	>	}
656	>
657	>
658	>	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
659	>	int curStampId;
660	>
661	>	//index from 0
662	>	curStampId = moleculeStamps_.size();
663
664	<	int SimInfo::getNDFraw() {
665	<	int ndfRaw_local;
664	>	moleculeStamps_.push_back(molStamp);
665	>	molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
666	>	}
667
370	–	// Raw degrees of freedom that we have to set
371	–	ndfRaw_local = 0;
668
669	<	for(int i = 0; i < integrableObjects.size(); i++){
670	<	ndfRaw_local += 3;
671	<	if (integrableObjects[i]->isDirectional()) {
672	<	if (integrableObjects[i]->isLinear())
673	<	ndfRaw_local += 2;
674	<	else
675	<	ndfRaw_local += 3;
676	<	}
669	>	/**
670	>	* update
671	>	*
672	>	*  Performs the global checks and variable settings after the
673	>	*  objects have been created.
674	>	*
675	>	*/
676	>	void SimInfo::update() {
677	>	setupSimVariables();
678	>	calcNdf();
679	>	calcNdfRaw();
680	>	calcNdfTrans();
681		}
682	+
683	+	/**
684	+	* getSimulatedAtomTypes
685	+	*
686	+	* Returns an STL set of AtomType* that are actually present in this
687	+	* simulation.  Must query all processors to assemble this information.
688	+	*
689	+	*/
690	+	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
691	+	SimInfo::MoleculeIterator mi;
692	+	Molecule* mol;
693	+	Molecule::AtomIterator ai;
694	+	Atom* atom;
695	+	set<AtomType*> atomTypes;
696
697	+	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
698	+	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
699	+	atomTypes.insert(atom->getAtomType());
700	+	}
701	+	}
702	+
703		#ifdef IS_MPI
384	–	MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
385	–	#else
386	–	ndfRaw = ndfRaw_local;
387	–	#endif
704
705	<	return ndfRaw;
706	<	}
705	>	// loop over the found atom types on this processor, and add their
706	>	// numerical idents to a vector:
707
708	<	int SimInfo::getNDFtranslational() {
709	<	int ndfTrans_local;
708	>	vector<int> foundTypes;
709	>	set<AtomType*>::iterator i;
710	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
711	>	foundTypes.push_back( (*i)->getIdent() );
712
713	<	ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
713	>	// count_local holds the number of found types on this processor
714	>	int count_local = foundTypes.size();
715
716	+	// count holds the total number of found types on all processors
717	+	// (some will be redundant with the ones found locally):
718	+	int count;
719	+	MPI::COMM_WORLD.Allreduce(&count_local, &count, 1, MPI::INT, MPI::SUM);
720
721	<	#ifdef IS_MPI
722	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
723	<	#else
724	<	ndfTrans = ndfTrans_local;
402	<	#endif
721	>	// create a vector to hold the globally found types, and resize it:
722	>	vector<int> ftGlobal;
723	>	ftGlobal.resize(count);
724	>	vector<int> counts;
725
726	<	ndfTrans = ndfTrans - 3 - nZconstraints;
726	>	int nproc = MPI::COMM_WORLD.Get_size();
727	>	counts.resize(nproc);
728	>	vector<int> disps;
729	>	disps.resize(nproc);
730
731	<	return ndfTrans;
732	<	}
731	>	// now spray out the foundTypes to all the other processors:
732	>
733	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
734	>	&ftGlobal[0], &counts[0], &disps[0], MPI::INT);
735
736	<	int SimInfo::getTotIntegrableObjects() {
737	<	int nObjs_local;
738	<	int nObjs;
739	<
740	<	nObjs_local =  integrableObjects.size();
741	<
742	<
743	<	#ifdef IS_MPI
744	<	MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
745	<	#else
746	<	nObjs = nObjs_local;
736	>	// foundIdents is a stl set, so inserting an already found ident
737	>	// will have no effect.
738	>	set<int> foundIdents;
739	>	vector<int>::iterator j;
740	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
741	>	foundIdents.insert((*j));
742	>
743	>	// now iterate over the foundIdents and get the actual atom types
744	>	// that correspond to these:
745	>	set<int>::iterator it;
746	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
747	>	atomTypes.insert( forceField_->getAtomType((*it)) );
748	>
749		#endif
750	+
751	+	return atomTypes;
752	+	}
753
754	+	void SimInfo::setupSimVariables() {
755	+	useAtomicVirial_ = simParams_->getUseAtomicVirial();
756	+	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
757	+	calcBoxDipole_ = false;
758	+	if ( simParams_->haveAccumulateBoxDipole() )
759	+	if ( simParams_->getAccumulateBoxDipole() ) {
760	+	calcBoxDipole_ = true;
761	+	}
762
763	<	return nObjs;
764	<	}
763	>	set<AtomType*>::iterator i;
764	>	set<AtomType*> atomTypes;
765	>	atomTypes = getSimulatedAtomTypes();
766	>	int usesElectrostatic = 0;
767	>	int usesMetallic = 0;
768	>	int usesDirectional = 0;
769	>	//loop over all of the atom types
770	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
771	>	usesElectrostatic |= (*i)->isElectrostatic();
772	>	usesMetallic |= (*i)->isMetal();
773	>	usesDirectional |= (*i)->isDirectional();
774	>	}
775
776	<	void SimInfo::refreshSim(){
776	>	#ifdef IS_MPI
777	>	int temp;
778	>	temp = usesDirectional;
779	>	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
780
781	<	simtype fInfo;
782	<	int isError;
430	<	int n_global;
431	<	int* excl;
781	>	temp = usesMetallic;
782	>	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
783
784	<	fInfo.dielect = 0.0;
785	<
786	<	if( useDipoles ){
436	<	if( useReactionField )fInfo.dielect = dielectric;
784	>	temp = usesElectrostatic;
785	>	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
786	>	#endif
787		}
788
439	–	fInfo.SIM_uses_PBC = usePBC;
789
790	<	if (useSticky || useDipoles || useGayBerne || useShapes) {
791	<	useDirectionalAtoms = 1;
792	<	fInfo.SIM_uses_DirectionalAtoms = useDirectionalAtoms;
790	>	vector<int> SimInfo::getGlobalAtomIndices() {
791	>	SimInfo::MoleculeIterator mi;
792	>	Molecule* mol;
793	>	Molecule::AtomIterator ai;
794	>	Atom* atom;
795	>
796	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
797	>
798	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
799	>
800	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
801	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
802	>	}
803	>	}
804	>	return GlobalAtomIndices;
805		}
806
446	–	fInfo.SIM_uses_LennardJones = useLennardJones;
807
808	<	if (useCharges || useDipoles) {
809	<	useElectrostatics = 1;
810	<	fInfo.SIM_uses_Electrostatics = useElectrostatics;
808	>	vector<int> SimInfo::getGlobalGroupIndices() {
809	>	SimInfo::MoleculeIterator mi;
810	>	Molecule* mol;
811	>	Molecule::CutoffGroupIterator ci;
812	>	CutoffGroup* cg;
813	>
814	>	vector<int> GlobalGroupIndices;
815	>
816	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
817	>
818	>	//local index of cutoff group is trivial, it only depends on the
819	>	//order of travesing
820	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
821	>	cg = mol->nextCutoffGroup(ci)) {
822	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
823	>	}
824	>	}
825	>	return GlobalGroupIndices;
826		}
827
453	–	fInfo.SIM_uses_Charges = useCharges;
454	–	fInfo.SIM_uses_Dipoles = useDipoles;
455	–	fInfo.SIM_uses_Sticky = useSticky;
456	–	fInfo.SIM_uses_GayBerne = useGayBerne;
457	–	fInfo.SIM_uses_EAM = useEAM;
458	–	fInfo.SIM_uses_Shapes = useShapes;
459	–	fInfo.SIM_uses_FLARB = useFLARB;
460	–	fInfo.SIM_uses_RF = useReactionField;
828
829	<	n_exclude = excludes->getSize();
830	<	excl = excludes->getFortranArray();
464	<
465	<	#ifdef IS_MPI
466	<	n_global = mpiSim->getNAtomsGlobal();
467	<	#else
468	<	n_global = n_atoms;
469	<	#endif
470	<
471	<	isError = 0;
472	<
473	<	getFortranGroupArrays(this, FglobalGroupMembership, mfact);
474	<	//it may not be a good idea to pass the address of first element in vector
475	<	//since c++ standard does not require vector to be stored continuously in meomory
476	<	//Most of the compilers will organize the memory of vector continuously
477	<	setFortranSim( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
478	<	&nGlobalExcludes, globalExcludes, molMembershipArray,
479	<	&mfact[0], &ngroup, &FglobalGroupMembership[0], &isError);
829	>	void SimInfo::prepareTopology() {
830	>	int nExclude, nOneTwo, nOneThree, nOneFour;
831
832	<	if( isError ){
832	>	//calculate mass ratio of cutoff group
833	>	SimInfo::MoleculeIterator mi;
834	>	Molecule* mol;
835	>	Molecule::CutoffGroupIterator ci;
836	>	CutoffGroup* cg;
837	>	Molecule::AtomIterator ai;
838	>	Atom* atom;
839	>	RealType totalMass;
840	>
841	>	//to avoid memory reallocation, reserve enough space for massFactors_
842	>	massFactors_.clear();
843	>	massFactors_.reserve(getNCutoffGroups());
844
845	<	sprintf( painCave.errMsg,
846	<	"There was an error setting the simulation information in fortran.\n" );
847	<	painCave.isFatal = 1;
486	<	painCave.severity = OOPSE_ERROR;
487	<	simError();
488	<	}
489	<
490	<	#ifdef IS_MPI
491	<	sprintf( checkPointMsg,
492	<	"succesfully sent the simulation information to fortran.\n");
493	<	MPIcheckPoint();
494	<	#endif // is_mpi
495	<
496	<	this->ndf = this->getNDF();
497	<	this->ndfRaw = this->getNDFraw();
498	<	this->ndfTrans = this->getNDFtranslational();
499	<	}
845	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
846	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
847	>	cg = mol->nextCutoffGroup(ci)) {
848
849	<	void SimInfo::setDefaultRcut( double theRcut ){
850	<
851	<	haveRcut = 1;
852	<	rCut = theRcut;
853	<	rList = rCut + 1.0;
854	<
855	<	notifyFortranCutoffs( &rCut, &rSw, &rList );
856	<	}
849	>	totalMass = cg->getMass();
850	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
851	>	// Check for massless groups - set mfact to 1 if true
852	>	if (totalMass != 0)
853	>	massFactors_.push_back(atom->getMass()/totalMass);
854	>	else
855	>	massFactors_.push_back( 1.0 );
856	>	}
857	>	}
858	>	}
859
860	<	void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
860	>	// Build the identArray_
861
862	<	rSw = theRsw;
863	<	setDefaultRcut( theRcut );
864	<	}
862	>	identArray_.clear();
863	>	identArray_.reserve(getNAtoms());
864	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
865	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
866	>	identArray_.push_back(atom->getIdent());
867	>	}
868	>	}
869	>
870	>	//scan topology
871
872	+	nExclude = excludedInteractions_.getSize();
873	+	nOneTwo = oneTwoInteractions_.getSize();
874	+	nOneThree = oneThreeInteractions_.getSize();
875	+	nOneFour = oneFourInteractions_.getSize();
876
877	<	void SimInfo::checkCutOffs( void ){
878	<
879	<	if( boxIsInit ){
877	>	int* excludeList = excludedInteractions_.getPairList();
878	>	int* oneTwoList = oneTwoInteractions_.getPairList();
879	>	int* oneThreeList = oneThreeInteractions_.getPairList();
880	>	int* oneFourList = oneFourInteractions_.getPairList();
881	>
882	>	//setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray_[0],
883	>	//               &nExclude, excludeList,
884	>	//               &nOneTwo, oneTwoList,
885	>	//               &nOneThree, oneThreeList,
886	>	//               &nOneFour, oneFourList,
887	>	//               &molMembershipArray[0], &mfact[0], &nCutoffGroups_,
888	>	//               &fortranGlobalGroupMembership[0], &isError);
889
890	<	//we need to check cutOffs against the box
522	<
523	<	if( rCut > maxCutoff ){
524	<	sprintf( painCave.errMsg,
525	<	"cutoffRadius is too large for the current periodic box.\n"
526	<	"\tCurrent Value of cutoffRadius = %G at time %G\n "
527	<	"\tThis is larger than half of at least one of the\n"
528	<	"\tperiodic box vectors.  Right now, the Box matrix is:\n"
529	<	"\n"
530	<	"\t[ %G %G %G ]\n"
531	<	"\t[ %G %G %G ]\n"
532	<	"\t[ %G %G %G ]\n",
533	<	rCut, currentTime,
534	<	Hmat[0][0], Hmat[0][1], Hmat[0][2],
535	<	Hmat[1][0], Hmat[1][1], Hmat[1][2],
536	<	Hmat[2][0], Hmat[2][1], Hmat[2][2]);
537	<	painCave.severity = OOPSE_ERROR;
538	<	painCave.isFatal = 1;
539	<	simError();
540	<	}
541	<	} else {
542	<	// initialize this stuff before using it, OK?
543	<	sprintf( painCave.errMsg,
544	<	"Trying to check cutoffs without a box.\n"
545	<	"\tOOPSE should have better programmers than that.\n" );
546	<	painCave.severity = OOPSE_ERROR;
547	<	painCave.isFatal = 1;
548	<	simError();
890	>	topologyDone_ = true;
891		}
550	–
551	–	}
892
893	<	void SimInfo::addProperty(GenericData* prop){
893	>	void SimInfo::addProperty(GenericData* genData) {
894	>	properties_.addProperty(genData);
895	>	}
896
897	<	map<string, GenericData*>::iterator result;
898	<	result = properties.find(prop->getID());
557	<
558	<	//we can't simply use  properties[prop->getID()] = prop,
559	<	//it will cause memory leak if we already contain a propery which has the same name of prop
560	<
561	<	if(result != properties.end()){
562	<
563	<	delete (*result).second;
564	<	(*result).second = prop;
565	<
897	>	void SimInfo::removeProperty(const string& propName) {
898	>	properties_.removeProperty(propName);
899		}
567	–	else{
900
901	<	properties[prop->getID()] = prop;
901	>	void SimInfo::clearProperties() {
902	>	properties_.clearProperties();
903	>	}
904
905	+	vector<string> SimInfo::getPropertyNames() {
906	+	return properties_.getPropertyNames();
907		}
908	+
909	+	vector<GenericData*> SimInfo::getProperties() {
910	+	return properties_.getProperties();
911	+	}
912	+
913	+	GenericData* SimInfo::getPropertyByName(const string& propName) {
914	+	return properties_.getPropertyByName(propName);
915	+	}
916	+
917	+	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
918	+	if (sman_ == sman) {
919	+	return;
920	+	}
921	+	delete sman_;
922	+	sman_ = sman;
923	+
924	+	Molecule* mol;
925	+	RigidBody* rb;
926	+	Atom* atom;
927	+	CutoffGroup* cg;
928	+	SimInfo::MoleculeIterator mi;
929	+	Molecule::RigidBodyIterator rbIter;
930	+	Molecule::AtomIterator atomIter;
931	+	Molecule::CutoffGroupIterator cgIter;
932	+
933	+	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
934	+
935	+	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
936	+	atom->setSnapshotManager(sman_);
937	+	}
938	+
939	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
940	+	rb->setSnapshotManager(sman_);
941	+	}
942	+
943	+	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
944	+	cg->setSnapshotManager(sman_);
945	+	}
946	+	}
947
948	<	}
948	>	}
949
950	<	GenericData* SimInfo::getProperty(const string& propName){
950	>	Vector3d SimInfo::getComVel(){
951	>	SimInfo::MoleculeIterator i;
952	>	Molecule* mol;
953	>
954	>	Vector3d comVel(0.0);
955	>	RealType totalMass = 0.0;
956	>
957
958	<	map<string, GenericData*>::iterator result;
959	<
960	<	//string lowerCaseName = ();
961	<
962	<	result = properties.find(propName);
582	<
583	<	if(result != properties.end())
584	<	return (*result).second;
585	<	else
586	<	return NULL;
587	<	}
958	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
959	>	RealType mass = mol->getMass();
960	>	totalMass += mass;
961	>	comVel += mass * mol->getComVel();
962	>	}
963
964	+	#ifdef IS_MPI
965	+	RealType tmpMass = totalMass;
966	+	Vector3d tmpComVel(comVel);
967	+	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
968	+	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
969	+	#endif
970
971	<	void SimInfo::getFortranGroupArrays(SimInfo* info,
591	<	vector<int>& FglobalGroupMembership,
592	<	vector<double>& mfact){
593	<
594	<	Molecule* myMols;
595	<	Atom** myAtoms;
596	<	int numAtom;
597	<	double mtot;
598	<	int numMol;
599	<	int numCutoffGroups;
600	<	CutoffGroup* myCutoffGroup;
601	<	vector<CutoffGroup*>::iterator iterCutoff;
602	<	Atom* cutoffAtom;
603	<	vector<Atom*>::iterator iterAtom;
604	<	int atomIndex;
605	<	double totalMass;
606	<
607	<	mfact.clear();
608	<	FglobalGroupMembership.clear();
609	<
971	>	comVel /= totalMass;
972
973	<	// Fix the silly fortran indexing problem
973	>	return comVel;
974	>	}
975	>
976	>	Vector3d SimInfo::getCom(){
977	>	SimInfo::MoleculeIterator i;
978	>	Molecule* mol;
979	>
980	>	Vector3d com(0.0);
981	>	RealType totalMass = 0.0;
982	>
983	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
984	>	RealType mass = mol->getMass();
985	>	totalMass += mass;
986	>	com += mass * mol->getCom();
987	>	}
988	>
989		#ifdef IS_MPI
990	<	numAtom = mpiSim->getNAtomsGlobal();
991	<	#else
992	<	numAtom = n_atoms;
990	>	RealType tmpMass = totalMass;
991	>	Vector3d tmpCom(com);
992	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
993	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
994		#endif
617	–	for (int i = 0; i < numAtom; i++)
618	–	FglobalGroupMembership.push_back(globalGroupMembership[i] + 1);
619	–
995
996	<	myMols = info->molecules;
622	<	numMol = info->n_mol;
623	<	for(int i  = 0; i < numMol; i++){
624	<	numCutoffGroups = myMols[i].getNCutoffGroups();
625	<	for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff);
626	<	myCutoffGroup != NULL;
627	<	myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
996	>	com /= totalMass;
997
998	<	totalMass = myCutoffGroup->getMass();
998	>	return com;
999	>
1000	>	}
1001	>
1002	>	ostream& operator <<(ostream& o, SimInfo& info) {
1003	>
1004	>	return o;
1005	>	}
1006	>
1007	>
1008	>	/*
1009	>	Returns center of mass and center of mass velocity in one function call.
1010	>	*/
1011	>
1012	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1013	>	SimInfo::MoleculeIterator i;
1014	>	Molecule* mol;
1015
1016	<	for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom);
1017	<	cutoffAtom != NULL;
1018	<	cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
1019	<	mfact.push_back(cutoffAtom->getMass()/totalMass);
1016	>
1017	>	RealType totalMass = 0.0;
1018	>
1019	>
1020	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1021	>	RealType mass = mol->getMass();
1022	>	totalMass += mass;
1023	>	com += mass * mol->getCom();
1024	>	comVel += mass * mol->getComVel();
1025		}
1026	+
1027	+	#ifdef IS_MPI
1028	+	RealType tmpMass = totalMass;
1029	+	Vector3d tmpCom(com);
1030	+	Vector3d tmpComVel(comVel);
1031	+	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1032	+	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1033	+	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1034	+	#endif
1035	+
1036	+	com /= totalMass;
1037	+	comVel /= totalMass;
1038	+	}
1039	+
1040	+	/*
1041	+	Return intertia tensor for entire system and angular momentum Vector.
1042	+
1043	+
1044	+	[  Ixx -Ixy  -Ixz ]
1045	+	J =| -Iyx  Iyy  -Iyz |
1046	+	[ -Izx -Iyz   Izz ]
1047	+	*/
1048	+
1049	+	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1050	+
1051	+
1052	+	RealType xx = 0.0;
1053	+	RealType yy = 0.0;
1054	+	RealType zz = 0.0;
1055	+	RealType xy = 0.0;
1056	+	RealType xz = 0.0;
1057	+	RealType yz = 0.0;
1058	+	Vector3d com(0.0);
1059	+	Vector3d comVel(0.0);
1060	+
1061	+	getComAll(com, comVel);
1062	+
1063	+	SimInfo::MoleculeIterator i;
1064	+	Molecule* mol;
1065	+
1066	+	Vector3d thisq(0.0);
1067	+	Vector3d thisv(0.0);
1068	+
1069	+	RealType thisMass = 0.0;
1070	+
1071	+
1072	+
1073	+
1074	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1075	+
1076	+	thisq = mol->getCom()-com;
1077	+	thisv = mol->getComVel()-comVel;
1078	+	thisMass = mol->getMass();
1079	+	// Compute moment of intertia coefficients.
1080	+	xx += thisq[0]*thisq[0]*thisMass;
1081	+	yy += thisq[1]*thisq[1]*thisMass;
1082	+	zz += thisq[2]*thisq[2]*thisMass;
1083	+
1084	+	// compute products of intertia
1085	+	xy += thisq[0]*thisq[1]*thisMass;
1086	+	xz += thisq[0]*thisq[2]*thisMass;
1087	+	yz += thisq[1]*thisq[2]*thisMass;
1088	+
1089	+	angularMomentum += cross( thisq, thisv ) * thisMass;
1090	+
1091	+	}
1092	+
1093	+
1094	+	inertiaTensor(0,0) = yy + zz;
1095	+	inertiaTensor(0,1) = -xy;
1096	+	inertiaTensor(0,2) = -xz;
1097	+	inertiaTensor(1,0) = -xy;
1098	+	inertiaTensor(1,1) = xx + zz;
1099	+	inertiaTensor(1,2) = -yz;
1100	+	inertiaTensor(2,0) = -xz;
1101	+	inertiaTensor(2,1) = -yz;
1102	+	inertiaTensor(2,2) = xx + yy;
1103	+
1104	+	#ifdef IS_MPI
1105	+	Mat3x3d tmpI(inertiaTensor);
1106	+	Vector3d tmpAngMom;
1107	+	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1108	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1109	+	#endif
1110	+
1111	+	return;
1112	+	}
1113	+
1114	+	//Returns the angular momentum of the system
1115	+	Vector3d SimInfo::getAngularMomentum(){
1116	+
1117	+	Vector3d com(0.0);
1118	+	Vector3d comVel(0.0);
1119	+	Vector3d angularMomentum(0.0);
1120	+
1121	+	getComAll(com,comVel);
1122	+
1123	+	SimInfo::MoleculeIterator i;
1124	+	Molecule* mol;
1125	+
1126	+	Vector3d thisr(0.0);
1127	+	Vector3d thisp(0.0);
1128	+
1129	+	RealType thisMass;
1130	+
1131	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1132	+	thisMass = mol->getMass();
1133	+	thisr = mol->getCom()-com;
1134	+	thisp = (mol->getComVel()-comVel)*thisMass;
1135	+
1136	+	angularMomentum += cross( thisr, thisp );
1137	+
1138	+	}
1139	+
1140	+	#ifdef IS_MPI
1141	+	Vector3d tmpAngMom;
1142	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1143	+	#endif
1144	+
1145	+	return angularMomentum;
1146	+	}
1147	+
1148	+	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1149	+	return IOIndexToIntegrableObject.at(index);
1150	+	}
1151	+
1152	+	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1153	+	IOIndexToIntegrableObject= v;
1154	+	}
1155	+
1156	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1157	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1158	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1159	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1160	+	*/
1161	+	void SimInfo::getGyrationalVolume(RealType &volume){
1162	+	Mat3x3d intTensor;
1163	+	RealType det;
1164	+	Vector3d dummyAngMom;
1165	+	RealType sysconstants;
1166	+	RealType geomCnst;
1167	+
1168	+	geomCnst = 3.0/2.0;
1169	+	/* Get the inertial tensor and angular momentum for free*/
1170	+	getInertiaTensor(intTensor,dummyAngMom);
1171	+
1172	+	det = intTensor.determinant();
1173	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1174	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1175	+	return;
1176	+	}
1177	+
1178	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1179	+	Mat3x3d intTensor;
1180	+	Vector3d dummyAngMom;
1181	+	RealType sysconstants;
1182	+	RealType geomCnst;
1183	+
1184	+	geomCnst = 3.0/2.0;
1185	+	/* Get the inertial tensor and angular momentum for free*/
1186	+	getInertiaTensor(intTensor,dummyAngMom);
1187	+
1188	+	detI = intTensor.determinant();
1189	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1190	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1191	+	return;
1192	+	}
1193	+	/*
1194	+	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1195	+	assert( v.size() == nAtoms_ + nRigidBodies_);
1196	+	sdByGlobalIndex_ = v;
1197		}
1198	+
1199	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1200	+	//assert(index < nAtoms_ + nRigidBodies_);
1201	+	return sdByGlobalIndex_.at(index);
1202	+	}
1203	+	*/
1204	+	int SimInfo::getNGlobalConstraints() {
1205	+	int nGlobalConstraints;
1206	+	#ifdef IS_MPI
1207	+	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1208	+	MPI_COMM_WORLD);
1209	+	#else
1210	+	nGlobalConstraints =  nConstraints_;
1211	+	#endif
1212	+	return nGlobalConstraints;
1213		}
1214
1215	<	}
1215	>	}//end namespace OpenMD
1216	>

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 143 by chrisfen, Fri Oct 22 22:54:01 2004 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1577 by gezelter, Wed Jun 8 20:26:56 2011 UTC

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