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

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 3 by tim, Fri Sep 24 16:27:58 2004 UTC vs.
Revision 1983 by gezelter, Tue Apr 15 20:36:19 2014 UTC

#	Line 1 | Line 1
1	<	#include <stdlib.h>
2	<	#include <string.h>
3	<	#include <math.h>
1	>	/*
2	>	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	>	*
4	>	* The University of Notre Dame grants you ("Licensee") a
5	>	* non-exclusive, royalty free, license to use, modify and
6	>	* redistribute this software in source and binary code form, provided
7	>	* that the following conditions are met:
8	>	*
9	>	* 1. Redistributions of source code must retain the above copyright
10	>	*    notice, this list of conditions and the following disclaimer.
11	>	*
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13	>	*    notice, this list of conditions and the following disclaimer in the
14	>	*    documentation and/or other materials provided with the
15	>	*    distribution.
16	>	*
17	>	* This software is provided "AS IS," without a warranty of any
18	>	* kind. All express or implied conditions, representations and
19	>	* warranties, including any implied warranty of merchantability,
20	>	* fitness for a particular purpose or non-infringement, are hereby
21	>	* excluded.  The University of Notre Dame and its licensors shall not
22	>	* be liable for any damages suffered by licensee as a result of
23	>	* using, modifying or distributing the software or its
24	>	* derivatives. In no event will the University of Notre Dame or its
25	>	* licensors be liable for any lost revenue, profit or data, or for
26	>	* direct, indirect, special, consequential, incidental or punitive
27	>	* damages, however caused and regardless of the theory of liability,
28	>	* arising out of the use of or inability to use software, even if the
29	>	* University of Notre Dame has been advised of the possibility of
30	>	* such damages.
31	>	*
32	>	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	>	* research, please cite the appropriate papers when you publish your
34	>	* work.  Good starting points are:
35	>	*
36	>	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	>	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	>	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	>	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	>	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	>	*/
42	>
43	>	/**
44	>	* @file SimInfo.cpp
45	>	* @author    tlin
46	>	* @date  11/02/2004
47	>	* @version 1.0
48	>	*/
49
50	<	#include <iostream>
51	<	using namespace std;
50	>	#ifdef IS_MPI
51	>	#include <mpi.h>
52	>	#endif
53	>	#include <algorithm>
54	>	#include <set>
55	>	#include <map>
56
57		#include "brains/SimInfo.hpp"
58	<	#define __C
59	<	#include "brains/fSimulation.h"
58	>	#include "math/Vector3.hpp"
59	>	#include "primitives/Molecule.hpp"
60	>	#include "primitives/StuntDouble.hpp"
61	>	#include "utils/MemoryUtils.hpp"
62		#include "utils/simError.h"
63	+	#include "selection/SelectionManager.hpp"
64	+	#include "io/ForceFieldOptions.hpp"
65	+	#include "brains/ForceField.hpp"
66	+	#include "nonbonded/SwitchingFunction.hpp"
67
68	<	#include "UseTheForce/fortranWrappers.hpp"
68	>	using namespace std;
69	>	namespace OpenMD {
70	>
71	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
72	>	forceField_(ff), simParams_(simParams),
73	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
74	>	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
75	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
76	>	nGlobalFluctuatingCharges_(0), nGlobalBonds_(0), nGlobalBends_(0),
77	>	nGlobalTorsions_(0), nGlobalInversions_(0), nGlobalConstraints_(0),
78	>	nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nInversions_(0),
79	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
80	>	nConstraints_(0), nFluctuatingCharges_(0), sman_(NULL),
81	>	topologyDone_(false), calcBoxDipole_(false), useAtomicVirial_(true),
82	>	hasNGlobalConstraints_(false) {
83	>
84	>	MoleculeStamp* molStamp;
85	>	int nMolWithSameStamp;
86	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
87	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
88	>	CutoffGroupStamp* cgStamp;
89	>	RigidBodyStamp* rbStamp;
90	>	int nRigidAtoms = 0;
91	>
92	>	vector<Component*> components = simParams->getComponents();
93	>
94	>	for (vector<Component*>::iterator i = components.begin();
95	>	i !=components.end(); ++i) {
96	>	molStamp = (*i)->getMoleculeStamp();
97	>	if ( (*i)->haveRegion() ) {
98	>	molStamp->setRegion( (*i)->getRegion() );
99	>	} else {
100	>	// set the region to a disallowed value:
101	>	molStamp->setRegion( -1 );
102	>	}
103
104	<	#include "math/MatVec3.h"
104	>	nMolWithSameStamp = (*i)->getNMol();
105	>
106	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
107	>
108	>	//calculate atoms in molecules
109	>	nGlobalAtoms_ += molStamp->getNAtoms() * nMolWithSameStamp;
110	>	nGlobalBonds_ += molStamp->getNBonds() * nMolWithSameStamp;
111	>	nGlobalBends_ += molStamp->getNBends() * nMolWithSameStamp;
112	>	nGlobalTorsions_ += molStamp->getNTorsions() * nMolWithSameStamp;
113	>	nGlobalInversions_ += molStamp->getNInversions() * nMolWithSameStamp;
114	>
115	>	//calculate atoms in cutoff groups
116	>	int nAtomsInGroups = 0;
117	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
118	>
119	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
120	>	cgStamp = molStamp->getCutoffGroupStamp(j);
121	>	nAtomsInGroups += cgStamp->getNMembers();
122	>	}
123	>
124	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
125	>
126	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
127	>
128	>	//calculate atoms in rigid bodies
129	>	int nAtomsInRigidBodies = 0;
130	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
131	>
132	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
133	>	rbStamp = molStamp->getRigidBodyStamp(j);
134	>	nAtomsInRigidBodies += rbStamp->getNMembers();
135	>	}
136	>
137	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
138	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
139	>
140	>	}
141	>
142	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
143	>	//group therefore the total number of cutoff groups in the system is
144	>	//equal to the total number of atoms minus number of atoms belong to
145	>	//cutoff group defined in meta-data file plus the number of cutoff
146	>	//groups defined in meta-data file
147
148	<	#ifdef IS_MPI
149	<	#include "brains/mpiSimulation.hpp"
150	<	#endif
148	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
149	>
150	>	//every free atom (atom does not belong to rigid bodies) is an
151	>	//integrable object therefore the total number of integrable objects
152	>	//in the system is equal to the total number of atoms minus number of
153	>	//atoms belong to rigid body defined in meta-data file plus the number
154	>	//of rigid bodies defined in meta-data file
155	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
156	>	+ nGlobalRigidBodies_;
157	>
158	>	nGlobalMols_ = molStampIds_.size();
159	>	molToProcMap_.resize(nGlobalMols_);
160	>	}
161	>
162	>	SimInfo::~SimInfo() {
163	>	map<int, Molecule*>::iterator i;
164	>	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
165	>	delete i->second;
166	>	}
167	>	molecules_.clear();
168	>
169	>	delete sman_;
170	>	delete simParams_;
171	>	delete forceField_;
172	>	}
173
21	–	inline double roundMe( double x ){
22	–	return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
23	–	}
24	–
25	–	inline double min( double a, double b ){
26	–	return (a < b ) ? a : b;
27	–	}
174
175	<	SimInfo* currentInfo;
176	<
177	<	SimInfo::SimInfo(){
178	<
179	<	n_constraints = 0;
180	<	nZconstraints = 0;
181	<	n_oriented = 0;
182	<	n_dipoles = 0;
183	<	ndf = 0;
184	<	ndfRaw = 0;
185	<	nZconstraints = 0;
186	<	the_integrator = NULL;
187	<	setTemp = 0;
188	<	thermalTime = 0.0;
189	<	currentTime = 0.0;
190	<	rCut = 0.0;
191	<	rSw = 0.0;
192	<
193	<	haveRcut = 0;
194	<	haveRsw = 0;
195	<	boxIsInit = 0;
175	>	bool SimInfo::addMolecule(Molecule* mol) {
176	>	MoleculeIterator i;
177	>
178	>	i = molecules_.find(mol->getGlobalIndex());
179	>	if (i == molecules_.end() ) {
180	>
181	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
182	>
183	>	nAtoms_ += mol->getNAtoms();
184	>	nBonds_ += mol->getNBonds();
185	>	nBends_ += mol->getNBends();
186	>	nTorsions_ += mol->getNTorsions();
187	>	nInversions_ += mol->getNInversions();
188	>	nRigidBodies_ += mol->getNRigidBodies();
189	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
190	>	nCutoffGroups_ += mol->getNCutoffGroups();
191	>	nConstraints_ += mol->getNConstraintPairs();
192	>
193	>	addInteractionPairs(mol);
194	>
195	>	return true;
196	>	} else {
197	>	return false;
198	>	}
199	>	}
200
201	<	resetTime = 1e99;
201	>	bool SimInfo::removeMolecule(Molecule* mol) {
202	>	MoleculeIterator i;
203	>	i = molecules_.find(mol->getGlobalIndex());
204
205	<	orthoRhombic = 0;
54	<	orthoTolerance = 1E-6;
55	<	useInitXSstate = true;
205	>	if (i != molecules_.end() ) {
206
207	<	usePBC = 0;
208	<	useLJ = 0;
209	<	useSticky = 0;
210	<	useCharges = 0;
211	<	useDipoles = 0;
212	<	useReactionField = 0;
213	<	useGB = 0;
214	<	useEAM = 0;
215	<	useSolidThermInt = 0;
216	<	useLiquidThermInt = 0;
207	>	assert(mol == i->second);
208	>
209	>	nAtoms_ -= mol->getNAtoms();
210	>	nBonds_ -= mol->getNBonds();
211	>	nBends_ -= mol->getNBends();
212	>	nTorsions_ -= mol->getNTorsions();
213	>	nInversions_ -= mol->getNInversions();
214	>	nRigidBodies_ -= mol->getNRigidBodies();
215	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
216	>	nCutoffGroups_ -= mol->getNCutoffGroups();
217	>	nConstraints_ -= mol->getNConstraintPairs();
218
219	<	haveCutoffGroups = false;
219	>	removeInteractionPairs(mol);
220	>	molecules_.erase(mol->getGlobalIndex());
221
222	<	excludes = Exclude::Instance();
222	>	delete mol;
223	>
224	>	return true;
225	>	} else {
226	>	return false;
227	>	}
228	>	}
229
230	<	myConfiguration = new SimState();
230	>
231	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
232	>	i = molecules_.begin();
233	>	return i == molecules_.end() ? NULL : i->second;
234	>	}
235
236	<	has_minimizer = false;
237	<	the_minimizer =NULL;
236	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
237	>	++i;
238	>	return i == molecules_.end() ? NULL : i->second;
239	>	}
240
77	–	ngroup = 0;
241
242	<	wrapMeSimInfo( this );
243	<	}
242	>	void SimInfo::calcNdf() {
243	>	int ndf_local, nfq_local;
244	>	MoleculeIterator i;
245	>	vector<StuntDouble*>::iterator j;
246	>	vector<Atom*>::iterator k;
247
248	+	Molecule* mol;
249	+	StuntDouble* sd;
250	+	Atom* atom;
251
252	<	SimInfo::~SimInfo(){
252	>	ndf_local = 0;
253	>	nfq_local = 0;
254	>
255	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
256
257	<	delete myConfiguration;
257	>	for (sd = mol->beginIntegrableObject(j); sd != NULL;
258	>	sd = mol->nextIntegrableObject(j)) {
259
260	<	map<string, GenericData*>::iterator i;
88	<
89	<	for(i = properties.begin(); i != properties.end(); i++)
90	<	delete (*i).second;
260	>	ndf_local += 3;
261
262	<	}
262	>	if (sd->isDirectional()) {
263	>	if (sd->isLinear()) {
264	>	ndf_local += 2;
265	>	} else {
266	>	ndf_local += 3;
267	>	}
268	>	}
269	>	}
270
271	<	void SimInfo::setBox(double newBox[3]) {
272	<
273	<	int i, j;
274	<	double tempMat[3][3];
271	>	for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
272	>	atom = mol->nextFluctuatingCharge(k)) {
273	>	if (atom->isFluctuatingCharge()) {
274	>	nfq_local++;
275	>	}
276	>	}
277	>	}
278	>
279	>	ndfLocal_ = ndf_local;
280
281	<	for(i=0; i<3; i++)
282	<	for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
281	>	// n_constraints is local, so subtract them on each processor
282	>	ndf_local -= nConstraints_;
283
284	<	tempMat[0][0] = newBox[0];
285	<	tempMat[1][1] = newBox[1];
286	<	tempMat[2][2] = newBox[2];
284	>	#ifdef IS_MPI
285	>	MPI_Allreduce(&ndf_local, &ndf_, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
286	>	MPI_Allreduce(&nfq_local, &nGlobalFluctuatingCharges_, 1,
287	>	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
288	>	#else
289	>	ndf_ = ndf_local;
290	>	nGlobalFluctuatingCharges_ = nfq_local;
291	>	#endif
292
293	<	setBoxM( tempMat );
293	>	// nZconstraints_ is global, as are the 3 COM translations for the
294	>	// entire system:
295	>	ndf_ = ndf_ - 3 - nZconstraint_;
296
297	<	}
297	>	}
298
299	<	void SimInfo::setBoxM( double theBox[3][3] ){
299	>	int SimInfo::getFdf() {
300	>	#ifdef IS_MPI
301	>	MPI_Allreduce(&fdf_local, &fdf_, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
302	>	#else
303	>	fdf_ = fdf_local;
304	>	#endif
305	>	return fdf_;
306	>	}
307
308	<	int i, j;
309	<	double FortranHmat[9]; // to preserve compatibility with Fortran the
310	<	// ordering in the array is as follows:
311	<	// [ 0 3 6 ]
312	<	// [ 1 4 7 ]
313	<	// [ 2 5 8 ]
314	<	double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
315	<
316	<	if( !boxIsInit ) boxIsInit = 1;
317	<
318	<	for(i=0; i < 3; i++)
319	<	for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
320	<
321	<	calcBoxL();
126	<	calcHmatInv();
127	<
128	<	for(i=0; i < 3; i++) {
129	<	for (j=0; j < 3; j++) {
130	<	FortranHmat[3*j + i] = Hmat[i][j];
131	<	FortranHmatInv[3*j + i] = HmatInv[i][j];
308	>	unsigned int SimInfo::getNLocalCutoffGroups(){
309	>	int nLocalCutoffAtoms = 0;
310	>	Molecule* mol;
311	>	MoleculeIterator mi;
312	>	CutoffGroup* cg;
313	>	Molecule::CutoffGroupIterator ci;
314	>
315	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
316	>
317	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
318	>	cg = mol->nextCutoffGroup(ci)) {
319	>	nLocalCutoffAtoms += cg->getNumAtom();
320	>
321	>	}
322		}
323	+
324	+	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
325		}
326	+
327	+	void SimInfo::calcNdfRaw() {
328	+	int ndfRaw_local;
329
330	<	setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
331	<
332	<	}
333	<
330	>	MoleculeIterator i;
331	>	vector<StuntDouble*>::iterator j;
332	>	Molecule* mol;
333	>	StuntDouble* sd;
334
335	<	void SimInfo::getBoxM (double theBox[3][3]) {
335	>	// Raw degrees of freedom that we have to set
336	>	ndfRaw_local = 0;
337	>
338	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
339
340	<	int i, j;
341	<	for(i=0; i<3; i++)
144	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
145	<	}
340	>	for (sd = mol->beginIntegrableObject(j); sd != NULL;
341	>	sd = mol->nextIntegrableObject(j)) {
342
343	+	ndfRaw_local += 3;
344
345	<	void SimInfo::scaleBox(double scale) {
346	<	double theBox[3][3];
347	<	int i, j;
345	>	if (sd->isDirectional()) {
346	>	if (sd->isLinear()) {
347	>	ndfRaw_local += 2;
348	>	} else {
349	>	ndfRaw_local += 3;
350	>	}
351	>	}
352	>
353	>	}
354	>	}
355	>
356	>	#ifdef IS_MPI
357	>	MPI_Allreduce(&ndfRaw_local, &ndfRaw_, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
358	>	#else
359	>	ndfRaw_ = ndfRaw_local;
360	>	#endif
361	>	}
362
363	<	// cerr << "Scaling box by " << scale << "\n";
363	>	void SimInfo::calcNdfTrans() {
364	>	int ndfTrans_local;
365
366	<	for(i=0; i<3; i++)
155	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
366	>	ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
367
368	<	setBoxM(theBox);
368	>	#ifdef IS_MPI
369	>	MPI_Allreduce(&ndfTrans_local, &ndfTrans_, 1, MPI_INT, MPI_SUM,
370	>	MPI_COMM_WORLD);
371	>	#else
372	>	ndfTrans_ = ndfTrans_local;
373	>	#endif
374
375	<	}
375	>	ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
376	>	}
377
378	<	void SimInfo::calcHmatInv( void ) {
379	<
380	<	int oldOrtho;
381	<	int i,j;
382	<	double smallDiag;
383	<	double tol;
384	<	double sanity[3][3];
378	>	void SimInfo::addInteractionPairs(Molecule* mol) {
379	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
380	>	vector<Bond*>::iterator bondIter;
381	>	vector<Bend*>::iterator bendIter;
382	>	vector<Torsion*>::iterator torsionIter;
383	>	vector<Inversion*>::iterator inversionIter;
384	>	Bond* bond;
385	>	Bend* bend;
386	>	Torsion* torsion;
387	>	Inversion* inversion;
388	>	int a;
389	>	int b;
390	>	int c;
391	>	int d;
392
393	<	invertMat3( Hmat, HmatInv );
393	>	// atomGroups can be used to add special interaction maps between
394	>	// groups of atoms that are in two separate rigid bodies.
395	>	// However, most site-site interactions between two rigid bodies
396	>	// are probably not special, just the ones between the physically
397	>	// bonded atoms.  Interactions *within* a single rigid body should
398	>	// always be excluded.  These are done at the bottom of this
399	>	// function.
400
401	<	// check to see if Hmat is orthorhombic
402	<
403	<	oldOrtho = orthoRhombic;
401	>	map<int, set<int> > atomGroups;
402	>	Molecule::RigidBodyIterator rbIter;
403	>	RigidBody* rb;
404	>	Molecule::IntegrableObjectIterator ii;
405	>	StuntDouble* sd;
406	>
407	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
408	>	sd = mol->nextIntegrableObject(ii)) {
409	>
410	>	if (sd->isRigidBody()) {
411	>	rb = static_cast<RigidBody*>(sd);
412	>	vector<Atom*> atoms = rb->getAtoms();
413	>	set<int> rigidAtoms;
414	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
415	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
416	>	}
417	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
418	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
419	>	}
420	>	} else {
421	>	set<int> oneAtomSet;
422	>	oneAtomSet.insert(sd->getGlobalIndex());
423	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
424	>	}
425	>	}
426
427	<	smallDiag = fabs(Hmat[0][0]);
428	<	if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
429	<	if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
178	<	tol = smallDiag * orthoTolerance;
427	>
428	>	for (bond= mol->beginBond(bondIter); bond != NULL;
429	>	bond = mol->nextBond(bondIter)) {
430
431	<	orthoRhombic = 1;
432	<
433	<	for (i = 0; i < 3; i++ ) {
434	<	for (j = 0 ; j < 3; j++) {
435	<	if (i != j) {
436	<	if (orthoRhombic) {
437	<	if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
187	<	}
431	>	a = bond->getAtomA()->getGlobalIndex();
432	>	b = bond->getAtomB()->getGlobalIndex();
433	>
434	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
435	>	oneTwoInteractions_.addPair(a, b);
436	>	} else {
437	>	excludedInteractions_.addPair(a, b);
438		}
439		}
190	–	}
440
441	<	if( oldOrtho != orthoRhombic ){
442	<
194	<	if( orthoRhombic ) {
195	<	sprintf( painCave.errMsg,
196	<	"OOPSE is switching from the default Non-Orthorhombic\n"
197	<	"\tto the faster Orthorhombic periodic boundary computations.\n"
198	<	"\tThis is usually a good thing, but if you wan't the\n"
199	<	"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
200	<	"\tvariable ( currently set to %G ) smaller.\n",
201	<	orthoTolerance);
202	<	painCave.severity = OOPSE_INFO;
203	<	simError();
204	<	}
205	<	else {
206	<	sprintf( painCave.errMsg,
207	<	"OOPSE is switching from the faster Orthorhombic to the more\n"
208	<	"\tflexible Non-Orthorhombic periodic boundary computations.\n"
209	<	"\tThis is usually because the box has deformed under\n"
210	<	"\tNPTf integration. If you wan't to live on the edge with\n"
211	<	"\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
212	<	"\tvariable ( currently set to %G ) larger.\n",
213	<	orthoTolerance);
214	<	painCave.severity = OOPSE_WARNING;
215	<	simError();
216	<	}
217	<	}
218	<	}
441	>	for (bend= mol->beginBend(bendIter); bend != NULL;
442	>	bend = mol->nextBend(bendIter)) {
443
444	<	void SimInfo::calcBoxL( void ){
444	>	a = bend->getAtomA()->getGlobalIndex();
445	>	b = bend->getAtomB()->getGlobalIndex();
446	>	c = bend->getAtomC()->getGlobalIndex();
447	>
448	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
449	>	oneTwoInteractions_.addPair(a, b);
450	>	oneTwoInteractions_.addPair(b, c);
451	>	} else {
452	>	excludedInteractions_.addPair(a, b);
453	>	excludedInteractions_.addPair(b, c);
454	>	}
455
456	<	double dx, dy, dz, dsq;
456	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
457	>	oneThreeInteractions_.addPair(a, c);
458	>	} else {
459	>	excludedInteractions_.addPair(a, c);
460	>	}
461	>	}
462
463	<	// boxVol = Determinant of Hmat
463	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
464	>	torsion = mol->nextTorsion(torsionIter)) {
465
466	<	boxVol = matDet3( Hmat );
466	>	a = torsion->getAtomA()->getGlobalIndex();
467	>	b = torsion->getAtomB()->getGlobalIndex();
468	>	c = torsion->getAtomC()->getGlobalIndex();
469	>	d = torsion->getAtomD()->getGlobalIndex();
470
471	<	// boxLx
472	<
473	<	dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
474	<	dsq = dx*dx + dy*dy + dz*dz;
475	<	boxL[0] = sqrt( dsq );
476	<	//maxCutoff = 0.5 * boxL[0];
471	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
472	>	oneTwoInteractions_.addPair(a, b);
473	>	oneTwoInteractions_.addPair(b, c);
474	>	oneTwoInteractions_.addPair(c, d);
475	>	} else {
476	>	excludedInteractions_.addPair(a, b);
477	>	excludedInteractions_.addPair(b, c);
478	>	excludedInteractions_.addPair(c, d);
479	>	}
480
481	<	// boxLy
482	<
483	<	dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
484	<	dsq = dx*dx + dy*dy + dz*dz;
485	<	boxL[1] = sqrt( dsq );
486	<	//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
481	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
482	>	oneThreeInteractions_.addPair(a, c);
483	>	oneThreeInteractions_.addPair(b, d);
484	>	} else {
485	>	excludedInteractions_.addPair(a, c);
486	>	excludedInteractions_.addPair(b, d);
487	>	}
488
489	+	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
490	+	oneFourInteractions_.addPair(a, d);
491	+	} else {
492	+	excludedInteractions_.addPair(a, d);
493	+	}
494	+	}
495
496	<	// boxLz
497	<
245	<	dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
246	<	dsq = dx*dx + dy*dy + dz*dz;
247	<	boxL[2] = sqrt( dsq );
248	<	//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
496	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
497	>	inversion = mol->nextInversion(inversionIter)) {
498
499	<	//calculate the max cutoff
500	<	maxCutoff =  calcMaxCutOff();
501	<
502	<	checkCutOffs();
499	>	a = inversion->getAtomA()->getGlobalIndex();
500	>	b = inversion->getAtomB()->getGlobalIndex();
501	>	c = inversion->getAtomC()->getGlobalIndex();
502	>	d = inversion->getAtomD()->getGlobalIndex();
503
504	<	}
504	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
505	>	oneTwoInteractions_.addPair(a, b);
506	>	oneTwoInteractions_.addPair(a, c);
507	>	oneTwoInteractions_.addPair(a, d);
508	>	} else {
509	>	excludedInteractions_.addPair(a, b);
510	>	excludedInteractions_.addPair(a, c);
511	>	excludedInteractions_.addPair(a, d);
512	>	}
513
514	+	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
515	+	oneThreeInteractions_.addPair(b, c);
516	+	oneThreeInteractions_.addPair(b, d);
517	+	oneThreeInteractions_.addPair(c, d);
518	+	} else {
519	+	excludedInteractions_.addPair(b, c);
520	+	excludedInteractions_.addPair(b, d);
521	+	excludedInteractions_.addPair(c, d);
522	+	}
523	+	}
524
525	<	double SimInfo::calcMaxCutOff(){
525	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
526	>	rb = mol->nextRigidBody(rbIter)) {
527	>	vector<Atom*> atoms = rb->getAtoms();
528	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
529	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
530	>	a = atoms[i]->getGlobalIndex();
531	>	b = atoms[j]->getGlobalIndex();
532	>	excludedInteractions_.addPair(a, b);
533	>	}
534	>	}
535	>	}
536
537	<	double ri[3], rj[3], rk[3];
261	<	double rij[3], rjk[3], rki[3];
262	<	double minDist;
537	>	}
538
539	<	ri[0] = Hmat[0][0];
540	<	ri[1] = Hmat[1][0];
541	<	ri[2] = Hmat[2][0];
539	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
540	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
541	>	vector<Bond*>::iterator bondIter;
542	>	vector<Bend*>::iterator bendIter;
543	>	vector<Torsion*>::iterator torsionIter;
544	>	vector<Inversion*>::iterator inversionIter;
545	>	Bond* bond;
546	>	Bend* bend;
547	>	Torsion* torsion;
548	>	Inversion* inversion;
549	>	int a;
550	>	int b;
551	>	int c;
552	>	int d;
553
554	<	rj[0] = Hmat[0][1];
555	<	rj[1] = Hmat[1][1];
556	<	rj[2] = Hmat[2][1];
554	>	map<int, set<int> > atomGroups;
555	>	Molecule::RigidBodyIterator rbIter;
556	>	RigidBody* rb;
557	>	Molecule::IntegrableObjectIterator ii;
558	>	StuntDouble* sd;
559	>
560	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
561	>	sd = mol->nextIntegrableObject(ii)) {
562	>
563	>	if (sd->isRigidBody()) {
564	>	rb = static_cast<RigidBody*>(sd);
565	>	vector<Atom*> atoms = rb->getAtoms();
566	>	set<int> rigidAtoms;
567	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
568	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
569	>	}
570	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
571	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
572	>	}
573	>	} else {
574	>	set<int> oneAtomSet;
575	>	oneAtomSet.insert(sd->getGlobalIndex());
576	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
577	>	}
578	>	}
579
580	<	rk[0] = Hmat[0][2];
581	<	rk[1] = Hmat[1][2];
582	<	rk[2] = Hmat[2][2];
580	>	for (bond= mol->beginBond(bondIter); bond != NULL;
581	>	bond = mol->nextBond(bondIter)) {
582	>
583	>	a = bond->getAtomA()->getGlobalIndex();
584	>	b = bond->getAtomB()->getGlobalIndex();
585
586	<	crossProduct3(ri, rj, rij);
587	<	distXY = dotProduct3(rk,rij) / norm3(rij);
586	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
587	>	oneTwoInteractions_.removePair(a, b);
588	>	} else {
589	>	excludedInteractions_.removePair(a, b);
590	>	}
591	>	}
592
593	<	crossProduct3(rj,rk, rjk);
594	<	distYZ = dotProduct3(ri,rjk) / norm3(rjk);
593	>	for (bend= mol->beginBend(bendIter); bend != NULL;
594	>	bend = mol->nextBend(bendIter)) {
595
596	<	crossProduct3(rk,ri, rki);
597	<	distZX = dotProduct3(rj,rki) / norm3(rki);
596	>	a = bend->getAtomA()->getGlobalIndex();
597	>	b = bend->getAtomB()->getGlobalIndex();
598	>	c = bend->getAtomC()->getGlobalIndex();
599	>
600	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
601	>	oneTwoInteractions_.removePair(a, b);
602	>	oneTwoInteractions_.removePair(b, c);
603	>	} else {
604	>	excludedInteractions_.removePair(a, b);
605	>	excludedInteractions_.removePair(b, c);
606	>	}
607
608	<	minDist = min(min(distXY, distYZ), distZX);
609	<	return minDist/2;
610	<
611	<	}
608	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
609	>	oneThreeInteractions_.removePair(a, c);
610	>	} else {
611	>	excludedInteractions_.removePair(a, c);
612	>	}
613	>	}
614
615	<	void SimInfo::wrapVector( double thePos[3] ){
615	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
616	>	torsion = mol->nextTorsion(torsionIter)) {
617
618	<	int i;
619	<	double scaled[3];
620	<
621	<	if( !orthoRhombic ){
296	<	// calc the scaled coordinates.
618	>	a = torsion->getAtomA()->getGlobalIndex();
619	>	b = torsion->getAtomB()->getGlobalIndex();
620	>	c = torsion->getAtomC()->getGlobalIndex();
621	>	d = torsion->getAtomD()->getGlobalIndex();
622
623	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
624	+	oneTwoInteractions_.removePair(a, b);
625	+	oneTwoInteractions_.removePair(b, c);
626	+	oneTwoInteractions_.removePair(c, d);
627	+	} else {
628	+	excludedInteractions_.removePair(a, b);
629	+	excludedInteractions_.removePair(b, c);
630	+	excludedInteractions_.removePair(c, d);
631	+	}
632
633	<	matVecMul3(HmatInv, thePos, scaled);
634	<
635	<	for(i=0; i<3; i++)
636	<	scaled[i] -= roundMe(scaled[i]);
637	<
638	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
639	<
306	<	matVecMul3(Hmat, scaled, thePos);
633	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
634	>	oneThreeInteractions_.removePair(a, c);
635	>	oneThreeInteractions_.removePair(b, d);
636	>	} else {
637	>	excludedInteractions_.removePair(a, c);
638	>	excludedInteractions_.removePair(b, d);
639	>	}
640
641	<	}
642	<	else{
643	<	// calc the scaled coordinates.
641	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
642	>	oneFourInteractions_.removePair(a, d);
643	>	} else {
644	>	excludedInteractions_.removePair(a, d);
645	>	}
646	>	}
647	>
648	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
649	>	inversion = mol->nextInversion(inversionIter)) {
650	>
651	>	a = inversion->getAtomA()->getGlobalIndex();
652	>	b = inversion->getAtomB()->getGlobalIndex();
653	>	c = inversion->getAtomC()->getGlobalIndex();
654	>	d = inversion->getAtomD()->getGlobalIndex();
655	>
656	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
657	>	oneTwoInteractions_.removePair(a, b);
658	>	oneTwoInteractions_.removePair(a, c);
659	>	oneTwoInteractions_.removePair(a, d);
660	>	} else {
661	>	excludedInteractions_.removePair(a, b);
662	>	excludedInteractions_.removePair(a, c);
663	>	excludedInteractions_.removePair(a, d);
664	>	}
665	>
666	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
667	>	oneThreeInteractions_.removePair(b, c);
668	>	oneThreeInteractions_.removePair(b, d);
669	>	oneThreeInteractions_.removePair(c, d);
670	>	} else {
671	>	excludedInteractions_.removePair(b, c);
672	>	excludedInteractions_.removePair(b, d);
673	>	excludedInteractions_.removePair(c, d);
674	>	}
675	>	}
676	>
677	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
678	>	rb = mol->nextRigidBody(rbIter)) {
679	>	vector<Atom*> atoms = rb->getAtoms();
680	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
681	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
682	>	a = atoms[i]->getGlobalIndex();
683	>	b = atoms[j]->getGlobalIndex();
684	>	excludedInteractions_.removePair(a, b);
685	>	}
686	>	}
687	>	}
688
312	–	for(i=0; i<3; i++)
313	–	scaled[i] = thePos[i]*HmatInv[i][i];
314	–
315	–	// wrap the scaled coordinates
316	–
317	–	for(i=0; i<3; i++)
318	–	scaled[i] -= roundMe(scaled[i]);
319	–
320	–	// calc the wrapped real coordinates from the wrapped scaled coordinates
321	–
322	–	for(i=0; i<3; i++)
323	–	thePos[i] = scaled[i]*Hmat[i][i];
689		}
690	+
691	+
692	+	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
693	+	int curStampId;
694
695	<	}
695	>	//index from 0
696	>	curStampId = moleculeStamps_.size();
697
698	+	moleculeStamps_.push_back(molStamp);
699	+	molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
700	+	}
701
329	–	int SimInfo::getNDF(){
330	–	int ndf_local;
702
703	<	ndf_local = 0;
704	<
705	<	for(int i = 0; i < integrableObjects.size(); i++){
706	<	ndf_local += 3;
707	<	if (integrableObjects[i]->isDirectional()) {
708	<	if (integrableObjects[i]->isLinear())
709	<	ndf_local += 2;
710	<	else
711	<	ndf_local += 3;
712	<	}
703	>	/**
704	>	* update
705	>	*
706	>	*  Performs the global checks and variable settings after the
707	>	*  objects have been created.
708	>	*
709	>	*/
710	>	void SimInfo::update() {
711	>	setupSimVariables();
712	>	calcNConstraints();
713	>	calcNdf();
714	>	calcNdfRaw();
715	>	calcNdfTrans();
716		}
717	+
718	+	/**
719	+	* getSimulatedAtomTypes
720	+	*
721	+	* Returns an STL set of AtomType* that are actually present in this
722	+	* simulation.  Must query all processors to assemble this information.
723	+	*
724	+	*/
725	+	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
726	+	SimInfo::MoleculeIterator mi;
727	+	Molecule* mol;
728	+	Molecule::AtomIterator ai;
729	+	Atom* atom;
730	+	set<AtomType*> atomTypes;
731	+
732	+	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
733	+	for(atom = mol->beginAtom(ai); atom != NULL;
734	+	atom = mol->nextAtom(ai)) {
735	+	atomTypes.insert(atom->getAtomType());
736	+	}
737	+	}
738	+
739	+	#ifdef IS_MPI
740
741	<	// n_constraints is local, so subtract them on each processor:
741	>	// loop over the found atom types on this processor, and add their
742	>	// numerical idents to a vector:
743	>
744	>	vector<int> foundTypes;
745	>	set<AtomType*>::iterator i;
746	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
747	>	foundTypes.push_back( (*i)->getIdent() );
748
749	<	ndf_local -= n_constraints;
749	>	// count_local holds the number of found types on this processor
750	>	int count_local = foundTypes.size();
751
752	<	#ifdef IS_MPI
753	<	MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
754	<	#else
351	<	ndf = ndf_local;
352	<	#endif
752	>	int nproc;
753	>	MPI_Comm_size( MPI_COMM_WORLD, &nproc);
754	>	// int nproc = MPI::COMM_WORLD.Get_size();
755
756	<	// nZconstraints is global, as are the 3 COM translations for the
757	<	// entire system:
756	>	// we need arrays to hold the counts and displacement vectors for
757	>	// all processors
758	>	vector<int> counts(nproc, 0);
759	>	vector<int> disps(nproc, 0);
760
761	<	ndf = ndf - 3 - nZconstraints;
761	>	// fill the counts array
762	>	MPI_Allgather(&count_local, 1, MPI_INT, &counts[0],
763	>	1, MPI_INT, MPI_COMM_WORLD);
764	>	// MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
765	>	//                           1, MPI::INT);
766	>
767	>	// use the processor counts to compute the displacement array
768	>	disps[0] = 0;
769	>	int totalCount = counts[0];
770	>	for (int iproc = 1; iproc < nproc; iproc++) {
771	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
772	>	totalCount += counts[iproc];
773	>	}
774
775	<	return ndf;
776	<	}
775	>	// we need a (possibly redundant) set of all found types:
776	>	vector<int> ftGlobal(totalCount);
777	>
778	>	// now spray out the foundTypes to all the other processors:
779	>	MPI_Allgatherv(&foundTypes[0], count_local, MPI_INT,
780	>	&ftGlobal[0], &counts[0], &disps[0],
781	>	MPI_INT, MPI_COMM_WORLD);
782	>	// MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
783	>	//                            &ftGlobal[0], &counts[0], &disps[0],
784	>	//                            MPI::INT);
785
786	<	int SimInfo::getNDFraw() {
363	<	int ndfRaw_local;
786	>	vector<int>::iterator j;
787
788	<	// Raw degrees of freedom that we have to set
789	<	ndfRaw_local = 0;
788	>	// foundIdents is a stl set, so inserting an already found ident
789	>	// will have no effect.
790	>	set<int> foundIdents;
791
792	<	for(int i = 0; i < integrableObjects.size(); i++){
793	<	ndfRaw_local += 3;
370	<	if (integrableObjects[i]->isDirectional()) {
371	<	if (integrableObjects[i]->isLinear())
372	<	ndfRaw_local += 2;
373	<	else
374	<	ndfRaw_local += 3;
375	<	}
376	<	}
792	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
793	>	foundIdents.insert((*j));
794
795	<	#ifdef IS_MPI
796	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
797	<	#else
798	<	ndfRaw = ndfRaw_local;
795	>	// now iterate over the foundIdents and get the actual atom types
796	>	// that correspond to these:
797	>	set<int>::iterator it;
798	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
799	>	atomTypes.insert( forceField_->getAtomType((*it)) );
800	>
801		#endif
802
803	<	return ndfRaw;
804	<	}
803	>	return atomTypes;
804	>	}
805
387	–	int SimInfo::getNDFtranslational() {
388	–	int ndfTrans_local;
806
807	<	ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
807	>	int getGlobalCountOfType(AtomType* atype) {
808	>	/*
809	>	set<AtomType*> atypes = getSimulatedAtomTypes();
810	>	map<AtomType*, int> counts_;
811
812	+	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
813	+	for(atom = mol->beginAtom(ai); atom != NULL;
814	+	atom = mol->nextAtom(ai)) {
815	+	atom->getAtomType();
816	+	}
817	+	}
818	+	*/
819	+	return 0;
820	+	}
821
822	+	void SimInfo::setupSimVariables() {
823	+	useAtomicVirial_ = simParams_->getUseAtomicVirial();
824	+	// we only call setAccumulateBoxDipole if the accumulateBoxDipole
825	+	// parameter is true
826	+	calcBoxDipole_ = false;
827	+	if ( simParams_->haveAccumulateBoxDipole() )
828	+	if ( simParams_->getAccumulateBoxDipole() ) {
829	+	calcBoxDipole_ = true;
830	+	}
831	+
832	+	set<AtomType*>::iterator i;
833	+	set<AtomType*> atomTypes;
834	+	atomTypes = getSimulatedAtomTypes();
835	+	bool usesElectrostatic = false;
836	+	bool usesMetallic = false;
837	+	bool usesDirectional = false;
838	+	bool usesFluctuatingCharges =  false;
839	+	//loop over all of the atom types
840	+	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
841	+	usesElectrostatic |= (*i)->isElectrostatic();
842	+	usesMetallic |= (*i)->isMetal();
843	+	usesDirectional |= (*i)->isDirectional();
844	+	usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
845	+	}
846	+
847		#ifdef IS_MPI
848	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
395	<	#else
396	<	ndfTrans = ndfTrans_local;
397	<	#endif
848	>	int temp;
849
850	<	ndfTrans = ndfTrans - 3 - nZconstraints;
850	>	temp = usesDirectional;
851	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
852	>	usesDirectionalAtoms_ = (temp == 0) ? false : true;
853	>
854	>	temp = usesMetallic;
855	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
856	>	usesMetallicAtoms_ = (temp == 0) ? false : true;
857
858	<	return ndfTrans;
859	<	}
858	>	temp = usesElectrostatic;
859	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
860	>	usesElectrostaticAtoms_ = (temp == 0) ? false : true;
861
862	<	int SimInfo::getTotIntegrableObjects() {
863	<	int nObjs_local;
864	<	int nObjs;
862	>	temp = usesFluctuatingCharges;
863	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
864	>	usesFluctuatingCharges_ = (temp == 0) ? false : true;
865	>	#else
866
867	<	nObjs_local =  integrableObjects.size();
867	>	usesDirectionalAtoms_ = usesDirectional;
868	>	usesMetallicAtoms_ = usesMetallic;
869	>	usesElectrostaticAtoms_ = usesElectrostatic;
870	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
871
410	–
411	–	#ifdef IS_MPI
412	–	MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
413	–	#else
414	–	nObjs = nObjs_local;
872		#endif
873	+
874	+	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
875	+	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
876	+	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
877	+	}
878
879
880	<	return nObjs;
881	<	}
880	>	vector<int> SimInfo::getGlobalAtomIndices() {
881	>	SimInfo::MoleculeIterator mi;
882	>	Molecule* mol;
883	>	Molecule::AtomIterator ai;
884	>	Atom* atom;
885
886	<	void SimInfo::refreshSim(){
886	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
887	>
888	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
889	>
890	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
891	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
892	>	}
893	>	}
894	>	return GlobalAtomIndices;
895	>	}
896
423	–	simtype fInfo;
424	–	int isError;
425	–	int n_global;
426	–	int* excl;
897
898	<	fInfo.dielect = 0.0;
898	>	vector<int> SimInfo::getGlobalGroupIndices() {
899	>	SimInfo::MoleculeIterator mi;
900	>	Molecule* mol;
901	>	Molecule::CutoffGroupIterator ci;
902	>	CutoffGroup* cg;
903
904	<	if( useDipoles ){
905	<	if( useReactionField )fInfo.dielect = dielectric;
906	<	}
904	>	vector<int> GlobalGroupIndices;
905	>
906	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
907	>
908	>	//local index of cutoff group is trivial, it only depends on the
909	>	//order of travesing
910	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
911	>	cg = mol->nextCutoffGroup(ci)) {
912	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
913	>	}
914	>	}
915	>	return GlobalGroupIndices;
916	>	}
917
434	–	fInfo.SIM_uses_PBC = usePBC;
435	–	//fInfo.SIM_uses_LJ = 0;
436	–	fInfo.SIM_uses_LJ = useLJ;
437	–	fInfo.SIM_uses_sticky = useSticky;
438	–	//fInfo.SIM_uses_sticky = 0;
439	–	fInfo.SIM_uses_charges = useCharges;
440	–	fInfo.SIM_uses_dipoles = useDipoles;
441	–	//fInfo.SIM_uses_dipoles = 0;
442	–	fInfo.SIM_uses_RF = useReactionField;
443	–	//fInfo.SIM_uses_RF = 0;
444	–	fInfo.SIM_uses_GB = useGB;
445	–	fInfo.SIM_uses_EAM = useEAM;
918
919	<	n_exclude = excludes->getSize();
448	<	excl = excludes->getFortranArray();
449	<
450	<	#ifdef IS_MPI
451	<	n_global = mpiSim->getNAtomsGlobal();
452	<	#else
453	<	n_global = n_atoms;
454	<	#endif
455	<
456	<	isError = 0;
457	<
458	<	getFortranGroupArrays(this, FglobalGroupMembership, mfact);
459	<	//it may not be a good idea to pass the address of first element in vector
460	<	//since c++ standard does not require vector to be stored continuously in meomory
461	<	//Most of the compilers will organize the memory of vector continuously
462	<	setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
463	<	&nGlobalExcludes, globalExcludes, molMembershipArray,
464	<	&mfact[0], &ngroup, &FglobalGroupMembership[0], &isError);
919	>	void SimInfo::prepareTopology() {
920
921	<	if( isError ){
921	>	//calculate mass ratio of cutoff group
922	>	SimInfo::MoleculeIterator mi;
923	>	Molecule* mol;
924	>	Molecule::CutoffGroupIterator ci;
925	>	CutoffGroup* cg;
926	>	Molecule::AtomIterator ai;
927	>	Atom* atom;
928	>	RealType totalMass;
929	>
930	>	/**
931	>	* The mass factor is the relative mass of an atom to the total
932	>	* mass of the cutoff group it belongs to.  By default, all atoms
933	>	* are their own cutoff groups, and therefore have mass factors of
934	>	* 1.  We need some special handling for massless atoms, which
935	>	* will be treated as carrying the entire mass of the cutoff
936	>	* group.
937	>	*/
938	>	massFactors_.clear();
939	>	massFactors_.resize(getNAtoms(), 1.0);
940
941	<	sprintf( painCave.errMsg,
942	<	"There was an error setting the simulation information in fortran.\n" );
943	<	painCave.isFatal = 1;
471	<	painCave.severity = OOPSE_ERROR;
472	<	simError();
473	<	}
474	<
475	<	#ifdef IS_MPI
476	<	sprintf( checkPointMsg,
477	<	"succesfully sent the simulation information to fortran.\n");
478	<	MPIcheckPoint();
479	<	#endif // is_mpi
480	<
481	<	this->ndf = this->getNDF();
482	<	this->ndfRaw = this->getNDFraw();
483	<	this->ndfTrans = this->getNDFtranslational();
484	<	}
941	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
942	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
943	>	cg = mol->nextCutoffGroup(ci)) {
944
945	<	void SimInfo::setDefaultRcut( double theRcut ){
946	<
947	<	haveRcut = 1;
948	<	rCut = theRcut;
949	<	rList = rCut + 1.0;
950	<
951	<	notifyFortranCutOffs( &rCut, &rSw, &rList );
952	<	}
945	>	totalMass = cg->getMass();
946	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
947	>	// Check for massless groups - set mfact to 1 if true
948	>	if (totalMass != 0)
949	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
950	>	else
951	>	massFactors_[atom->getLocalIndex()] = 1.0;
952	>	}
953	>	}
954	>	}
955
956	<	void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
956	>	// Build the identArray_ and regions_
957
958	<	rSw = theRsw;
959	<	setDefaultRcut( theRcut );
960	<	}
958	>	identArray_.clear();
959	>	identArray_.reserve(getNAtoms());
960	>	regions_.clear();
961	>	regions_.reserve(getNAtoms());
962	>
963	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
964	>	int reg = mol->getRegion();
965	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
966	>	identArray_.push_back(atom->getIdent());
967	>	regions_.push_back(reg);
968	>	}
969	>	}
970	>
971	>	topologyDone_ = true;
972	>	}
973
974	+	void SimInfo::addProperty(GenericData* genData) {
975	+	properties_.addProperty(genData);
976	+	}
977
978	<	void SimInfo::checkCutOffs( void ){
979	<
504	<	if( boxIsInit ){
505	<
506	<	//we need to check cutOffs against the box
507	<
508	<	if( rCut > maxCutoff ){
509	<	sprintf( painCave.errMsg,
510	<	"cutoffRadius is too large for the current periodic box.\n"
511	<	"\tCurrent Value of cutoffRadius = %G at time %G\n "
512	<	"\tThis is larger than half of at least one of the\n"
513	<	"\tperiodic box vectors.  Right now, the Box matrix is:\n"
514	<	"\n"
515	<	"\t[ %G %G %G ]\n"
516	<	"\t[ %G %G %G ]\n"
517	<	"\t[ %G %G %G ]\n",
518	<	rCut, currentTime,
519	<	Hmat[0][0], Hmat[0][1], Hmat[0][2],
520	<	Hmat[1][0], Hmat[1][1], Hmat[1][2],
521	<	Hmat[2][0], Hmat[2][1], Hmat[2][2]);
522	<	painCave.severity = OOPSE_ERROR;
523	<	painCave.isFatal = 1;
524	<	simError();
525	<	}
526	<	} else {
527	<	// initialize this stuff before using it, OK?
528	<	sprintf( painCave.errMsg,
529	<	"Trying to check cutoffs without a box.\n"
530	<	"\tOOPSE should have better programmers than that.\n" );
531	<	painCave.severity = OOPSE_ERROR;
532	<	painCave.isFatal = 1;
533	<	simError();
978	>	void SimInfo::removeProperty(const string& propName) {
979	>	properties_.removeProperty(propName);
980		}
535	–
536	–	}
981
982	<	void SimInfo::addProperty(GenericData* prop){
982	>	void SimInfo::clearProperties() {
983	>	properties_.clearProperties();
984	>	}
985
986	<	map<string, GenericData*>::iterator result;
987	<	result = properties.find(prop->getID());
988	<
543	<	//we can't simply use  properties[prop->getID()] = prop,
544	<	//it will cause memory leak if we already contain a propery which has the same name of prop
545	<
546	<	if(result != properties.end()){
547	<
548	<	delete (*result).second;
549	<	(*result).second = prop;
986	>	vector<string> SimInfo::getPropertyNames() {
987	>	return properties_.getPropertyNames();
988	>	}
989
990	+	vector<GenericData*> SimInfo::getProperties() {
991	+	return properties_.getProperties();
992		}
552	–	else{
993
994	<	properties[prop->getID()] = prop;
995	<
994	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
995	>	return properties_.getPropertyByName(propName);
996		}
557	–
558	–	}
997
998	<	GenericData* SimInfo::getProperty(const string& propName){
998	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
999	>	if (sman_ == sman) {
1000	>	return;
1001	>	}
1002	>	delete sman_;
1003	>	sman_ = sman;
1004	>
1005	>	SimInfo::MoleculeIterator mi;
1006	>	Molecule::AtomIterator ai;
1007	>	Molecule::RigidBodyIterator rbIter;
1008	>	Molecule::CutoffGroupIterator cgIter;
1009	>	Molecule::BondIterator bondIter;
1010	>	Molecule::BendIterator bendIter;
1011	>	Molecule::TorsionIterator torsionIter;
1012	>	Molecule::InversionIterator inversionIter;
1013
1014	<	map<string, GenericData*>::iterator result;
1015	<
1016	<	//string lowerCaseName = ();
1017	<
1018	<	result = properties.find(propName);
1019	<
1020	<	if(result != properties.end())
1021	<	return (*result).second;
570	<	else
571	<	return NULL;
572	<	}
1014	>	Molecule* mol;
1015	>	Atom* atom;
1016	>	RigidBody* rb;
1017	>	CutoffGroup* cg;
1018	>	Bond* bond;
1019	>	Bend* bend;
1020	>	Torsion* torsion;
1021	>	Inversion* inversion;
1022
1023	+	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1024	+
1025	+	for (atom = mol->beginAtom(ai); atom != NULL;
1026	+	atom = mol->nextAtom(ai)) {
1027	+	atom->setSnapshotManager(sman_);
1028	+	}
1029	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
1030	+	rb = mol->nextRigidBody(rbIter)) {
1031	+	rb->setSnapshotManager(sman_);
1032	+	}
1033	+	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL;
1034	+	cg = mol->nextCutoffGroup(cgIter)) {
1035	+	cg->setSnapshotManager(sman_);
1036	+	}
1037	+	for (bond = mol->beginBond(bondIter); bond != NULL;
1038	+	bond = mol->nextBond(bondIter)) {
1039	+	bond->setSnapshotManager(sman_);
1040	+	}
1041	+	for (bend = mol->beginBend(bendIter); bend != NULL;
1042	+	bend = mol->nextBend(bendIter)) {
1043	+	bend->setSnapshotManager(sman_);
1044	+	}
1045	+	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
1046	+	torsion = mol->nextTorsion(torsionIter)) {
1047	+	torsion->setSnapshotManager(sman_);
1048	+	}
1049	+	for (inversion = mol->beginInversion(inversionIter); inversion != NULL;
1050	+	inversion = mol->nextInversion(inversionIter)) {
1051	+	inversion->setSnapshotManager(sman_);
1052	+	}
1053	+	}
1054	+	}
1055
1056	<	void SimInfo::getFortranGroupArrays(SimInfo* info,
1057	<	vector<int>& FglobalGroupMembership,
1058	<	vector<double>& mfact){
1056	>
1057	>	ostream& operator <<(ostream& o, SimInfo& info) {
1058	>
1059	>	return o;
1060	>	}
1061	>
1062
1063	<	Molecule* myMols;
1064	<	Atom** myAtoms;
1065	<	int numAtom;
1066	<	double mtot;
1067	<	int numMol;
1068	<	int numCutoffGroups;
1069	<	CutoffGroup* myCutoffGroup;
1070	<	vector<CutoffGroup*>::iterator iterCutoff;
1071	<	Atom* cutoffAtom;
1072	<	vector<Atom*>::iterator iterAtom;
1073	<	int atomIndex;
590	<	double totalMass;
1063	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1064	>	if (index >= int(IOIndexToIntegrableObject.size())) {
1065	>	sprintf(painCave.errMsg,
1066	>	"SimInfo::getIOIndexToIntegrableObject Error: Integrable Object\n"
1067	>	"\tindex exceeds number of known objects!\n");
1068	>	painCave.isFatal = 1;
1069	>	simError();
1070	>	return NULL;
1071	>	} else
1072	>	return IOIndexToIntegrableObject.at(index);
1073	>	}
1074
1075	<	mfact.clear();
1076	<	FglobalGroupMembership.clear();
1077	<
1075	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1076	>	IOIndexToIntegrableObject= v;
1077	>	}
1078
1079	<	// Fix the silly fortran indexing problem
1079	>	void SimInfo::calcNConstraints() {
1080		#ifdef IS_MPI
1081	<	numAtom = mpiSim->getNAtomsGlobal();
1081	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints_, 1,
1082	>	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
1083		#else
1084	<	numAtom = n_atoms;
1084	>	nGlobalConstraints_ =  nConstraints_;
1085		#endif
602	–	for (int i = 0; i < numAtom; i++)
603	–	FglobalGroupMembership.push_back(globalGroupMembership[i] + 1);
604	–
605	–
606	–	myMols = info->molecules;
607	–	numMol = info->n_mol;
608	–	for(int i  = 0; i < numMol; i++){
609	–	numCutoffGroups = myMols[i].getNCutoffGroups();
610	–	for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff);
611	–	myCutoffGroup != NULL;
612	–	myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
613	–
614	–	totalMass = myCutoffGroup->getMass();
615	–
616	–	for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom);
617	–	cutoffAtom != NULL;
618	–	cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
619	–	mfact.push_back(cutoffAtom->getMass()/totalMass);
620	–	}
621	–	}
1086		}
1087
1088	<	}
1088	>	}//end namespace OpenMD
1089	>

Comparing trunk/src/brains/SimInfo.cpp (property svn:keywords):
Revision 3 by tim, Fri Sep 24 16:27:58 2004 UTC vs.
Revision 1983 by gezelter, Tue Apr 15 20:36:19 2014 UTC

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