ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

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

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 2 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
Revision 2071 by gezelter, Sat Mar 7 21:41:51 2015 UTC

#	Line 1 | Line 1
1	<	#include <stdlib.h>
2	<	#include <string.h>
3	<	#include <math.h>
1	>	/*
2	>	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	>	*
4	>	* The University of Notre Dame grants you ("Licensee") a
5	>	* non-exclusive, royalty free, license to use, modify and
6	>	* redistribute this software in source and binary code form, provided
7	>	* that the following conditions are met:
8	>	*
9	>	* 1. Redistributions of source code must retain the above copyright
10	>	*    notice, this list of conditions and the following disclaimer.
11	>	*
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13	>	*    notice, this list of conditions and the following disclaimer in the
14	>	*    documentation and/or other materials provided with the
15	>	*    distribution.
16	>	*
17	>	* This software is provided "AS IS," without a warranty of any
18	>	* kind. All express or implied conditions, representations and
19	>	* warranties, including any implied warranty of merchantability,
20	>	* fitness for a particular purpose or non-infringement, are hereby
21	>	* excluded.  The University of Notre Dame and its licensors shall not
22	>	* be liable for any damages suffered by licensee as a result of
23	>	* using, modifying or distributing the software or its
24	>	* derivatives. In no event will the University of Notre Dame or its
25	>	* licensors be liable for any lost revenue, profit or data, or for
26	>	* direct, indirect, special, consequential, incidental or punitive
27	>	* damages, however caused and regardless of the theory of liability,
28	>	* arising out of the use of or inability to use software, even if the
29	>	* University of Notre Dame has been advised of the possibility of
30	>	* such damages.
31	>	*
32	>	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	>	* research, please cite the appropriate papers when you publish your
34	>	* work.  Good starting points are:
35	>	*
36	>	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	>	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	>	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	>	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	>	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	>	*/
42	>
43	>	/**
44	>	* @file SimInfo.cpp
45	>	* @author    tlin
46	>	* @date  11/02/2004
47	>	* @version 1.0
48	>	*/
49
5	–	#include <iostream>
6	–	using namespace std;
7	–
8	–	#include "SimInfo.hpp"
9	–	#define __C
10	–	#include "fSimulation.h"
11	–	#include "simError.h"
12	–
13	–	#include "fortranWrappers.hpp"
14	–
15	–	#include "MatVec3.h"
16	–
50		#ifdef IS_MPI
51	<	#include "mpiSimulation.hpp"
51	>	#include <mpi.h>
52		#endif
53	+	#include <algorithm>
54	+	#include <set>
55	+	#include <map>
56
57	<	inline double roundMe( double x ){
58	<	return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
59	<	}
60	<
61	<	inline double min( double a, double b ){
62	<	return (a < b ) ? a : b;
63	<	}
57	>	#include "brains/SimInfo.hpp"
58	>	#include "math/Vector3.hpp"
59	>	#include "primitives/Molecule.hpp"
60	>	#include "primitives/StuntDouble.hpp"
61	>	#include "utils/MemoryUtils.hpp"
62	>	#include "utils/simError.h"
63	>	#include "selection/SelectionManager.hpp"
64	>	#include "io/ForceFieldOptions.hpp"
65	>	#include "brains/ForceField.hpp"
66	>	#include "nonbonded/SwitchingFunction.hpp"
67
68	<	SimInfo* currentInfo;
68	>	using namespace std;
69	>	namespace OpenMD {
70	>
71	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
72	>	forceField_(ff), simParams_(simParams),
73	>	nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nInversions_(0),
74	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
75	>	nConstraints_(0), nFluctuatingCharges_(0),
76	>	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
77	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
78	>	nGlobalFluctuatingCharges_(0), nGlobalBonds_(0), nGlobalBends_(0),
79	>	nGlobalTorsions_(0), nGlobalInversions_(0), nGlobalConstraints_(0),
80	>	hasNGlobalConstraints_(false),
81	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
82	>	sman_(NULL), topologyDone_(false), calcBoxDipole_(false),
83	>	calcBoxQuadrupole_(false), useAtomicVirial_(true) {
84	>
85	>	MoleculeStamp* molStamp;
86	>	int nMolWithSameStamp;
87	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
88	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
89	>	CutoffGroupStamp* cgStamp;
90	>	RigidBodyStamp* rbStamp;
91	>	int nRigidAtoms = 0;
92	>
93	>	vector<Component*> components = simParams->getComponents();
94	>
95	>	for (vector<Component*>::iterator i = components.begin();
96	>	i !=components.end(); ++i) {
97	>	molStamp = (*i)->getMoleculeStamp();
98	>	if ( (*i)->haveRegion() ) {
99	>	molStamp->setRegion( (*i)->getRegion() );
100	>	} else {
101	>	// set the region to a disallowed value:
102	>	molStamp->setRegion( -1 );
103	>	}
104
105	<	SimInfo::SimInfo(){
105	>	nMolWithSameStamp = (*i)->getNMol();
106	>
107	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
108	>
109	>	//calculate atoms in molecules
110	>	nGlobalAtoms_ += molStamp->getNAtoms() * nMolWithSameStamp;
111	>	nGlobalBonds_ += molStamp->getNBonds() * nMolWithSameStamp;
112	>	nGlobalBends_ += molStamp->getNBends() * nMolWithSameStamp;
113	>	nGlobalTorsions_ += molStamp->getNTorsions() * nMolWithSameStamp;
114	>	nGlobalInversions_ += molStamp->getNInversions() * nMolWithSameStamp;
115	>
116	>	//calculate atoms in cutoff groups
117	>	int nAtomsInGroups = 0;
118	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
119	>
120	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
121	>	cgStamp = molStamp->getCutoffGroupStamp(j);
122	>	nAtomsInGroups += cgStamp->getNMembers();
123	>	}
124	>
125	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
126	>
127	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
128	>
129	>	//calculate atoms in rigid bodies
130	>	int nAtomsInRigidBodies = 0;
131	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
132	>
133	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
134	>	rbStamp = molStamp->getRigidBodyStamp(j);
135	>	nAtomsInRigidBodies += rbStamp->getNMembers();
136	>	}
137	>
138	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
139	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
140	>
141	>	}
142	>
143	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
144	>	//group therefore the total number of cutoff groups in the system is
145	>	//equal to the total number of atoms minus number of atoms belong to
146	>	//cutoff group defined in meta-data file plus the number of cutoff
147	>	//groups defined in meta-data file
148
149	<	n_constraints = 0;
150	<	nZconstraints = 0;
151	<	n_oriented = 0;
152	<	n_dipoles = 0;
153	<	ndf = 0;
154	<	ndfRaw = 0;
155	<	nZconstraints = 0;
156	<	the_integrator = NULL;
157	<	setTemp = 0;
158	<	thermalTime = 0.0;
159	<	currentTime = 0.0;
160	<	rCut = 0.0;
161	<	rSw = 0.0;
46	<
47	<	haveRcut = 0;
48	<	haveRsw = 0;
49	<	boxIsInit = 0;
149	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
150	>
151	>	//every free atom (atom does not belong to rigid bodies) is an
152	>	//integrable object therefore the total number of integrable objects
153	>	//in the system is equal to the total number of atoms minus number of
154	>	//atoms belong to rigid body defined in meta-data file plus the number
155	>	//of rigid bodies defined in meta-data file
156	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
157	>	+ nGlobalRigidBodies_;
158	>
159	>	nGlobalMols_ = molStampIds_.size();
160	>	molToProcMap_.resize(nGlobalMols_);
161	>	}
162
163	<	resetTime = 1e99;
163	>	SimInfo::~SimInfo() {
164	>	map<int, Molecule*>::iterator i;
165	>	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
166	>	delete i->second;
167	>	}
168	>	molecules_.clear();
169	>
170	>	delete sman_;
171	>	delete simParams_;
172	>	delete forceField_;
173	>	}
174
53	–	orthoRhombic = 0;
54	–	orthoTolerance = 1E-6;
55	–	useInitXSstate = true;
175
176	<	usePBC = 0;
177	<	useLJ = 0;
178	<	useSticky = 0;
179	<	useCharges = 0;
180	<	useDipoles = 0;
181	<	useReactionField = 0;
182	<	useGB = 0;
183	<	useEAM = 0;
184	<	useSolidThermInt = 0;
185	<	useLiquidThermInt = 0;
176	>	bool SimInfo::addMolecule(Molecule* mol) {
177	>	MoleculeIterator i;
178	>
179	>	i = molecules_.find(mol->getGlobalIndex());
180	>	if (i == molecules_.end() ) {
181	>
182	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
183	>
184	>	nAtoms_ += mol->getNAtoms();
185	>	nBonds_ += mol->getNBonds();
186	>	nBends_ += mol->getNBends();
187	>	nTorsions_ += mol->getNTorsions();
188	>	nInversions_ += mol->getNInversions();
189	>	nRigidBodies_ += mol->getNRigidBodies();
190	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
191	>	nCutoffGroups_ += mol->getNCutoffGroups();
192	>	nConstraints_ += mol->getNConstraintPairs();
193	>
194	>	addInteractionPairs(mol);
195	>
196	>	return true;
197	>	} else {
198	>	return false;
199	>	}
200	>	}
201	>
202	>	bool SimInfo::removeMolecule(Molecule* mol) {
203	>	MoleculeIterator i;
204	>	i = molecules_.find(mol->getGlobalIndex());
205
206	<	haveCutoffGroups = false;
206	>	if (i != molecules_.end() ) {
207
208	<	excludes = Exclude::Instance();
208	>	assert(mol == i->second);
209	>
210	>	nAtoms_ -= mol->getNAtoms();
211	>	nBonds_ -= mol->getNBonds();
212	>	nBends_ -= mol->getNBends();
213	>	nTorsions_ -= mol->getNTorsions();
214	>	nInversions_ -= mol->getNInversions();
215	>	nRigidBodies_ -= mol->getNRigidBodies();
216	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
217	>	nCutoffGroups_ -= mol->getNCutoffGroups();
218	>	nConstraints_ -= mol->getNConstraintPairs();
219
220	<	myConfiguration = new SimState();
220	>	removeInteractionPairs(mol);
221	>	molecules_.erase(mol->getGlobalIndex());
222
223	<	has_minimizer = false;
224	<	the_minimizer =NULL;
223	>	delete mol;
224	>
225	>	return true;
226	>	} else {
227	>	return false;
228	>	}
229	>	}
230
231	<	ngroup = 0;
231	>
232	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
233	>	i = molecules_.begin();
234	>	return i == molecules_.end() ? NULL : i->second;
235	>	}
236
237	<	wrapMeSimInfo( this );
238	<	}
237	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
238	>	++i;
239	>	return i == molecules_.end() ? NULL : i->second;
240	>	}
241
242
243	<	SimInfo::~SimInfo(){
243	>	void SimInfo::calcNdf() {
244	>	int ndf_local, nfq_local;
245	>	MoleculeIterator i;
246	>	vector<StuntDouble*>::iterator j;
247	>	vector<Atom*>::iterator k;
248
249	<	delete myConfiguration;
249	>	Molecule* mol;
250	>	StuntDouble* sd;
251	>	Atom* atom;
252
253	<	map<string, GenericData*>::iterator i;
254	<
255	<	for(i = properties.begin(); i != properties.end(); i++)
256	<	delete (*i).second;
253	>	ndf_local = 0;
254	>	nfq_local = 0;
255	>
256	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
257
258	<	}
258	>	for (sd = mol->beginIntegrableObject(j); sd != NULL;
259	>	sd = mol->nextIntegrableObject(j)) {
260
261	<	void SimInfo::setBox(double newBox[3]) {
95	<
96	<	int i, j;
97	<	double tempMat[3][3];
261	>	ndf_local += 3;
262
263	<	for(i=0; i<3; i++)
264	<	for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
263	>	if (sd->isDirectional()) {
264	>	if (sd->isLinear()) {
265	>	ndf_local += 2;
266	>	} else {
267	>	ndf_local += 3;
268	>	}
269	>	}
270	>	}
271
272	<	tempMat[0][0] = newBox[0];
273	<	tempMat[1][1] = newBox[1];
274	<	tempMat[2][2] = newBox[2];
272	>	for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
273	>	atom = mol->nextFluctuatingCharge(k)) {
274	>	if (atom->isFluctuatingCharge()) {
275	>	nfq_local++;
276	>	}
277	>	}
278	>	}
279	>
280	>	ndfLocal_ = ndf_local;
281
282	<	setBoxM( tempMat );
282	>	// n_constraints is local, so subtract them on each processor
283	>	ndf_local -= nConstraints_;
284
285	<	}
285	>	#ifdef IS_MPI
286	>	MPI_Allreduce(&ndf_local, &ndf_, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
287	>	MPI_Allreduce(&nfq_local, &nGlobalFluctuatingCharges_, 1,
288	>	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
289	>	#else
290	>	ndf_ = ndf_local;
291	>	nGlobalFluctuatingCharges_ = nfq_local;
292	>	#endif
293
294	<	void SimInfo::setBoxM( double theBox[3][3] ){
295	<
296	<	int i, j;
113	<	double FortranHmat[9]; // to preserve compatibility with Fortran the
114	<	// ordering in the array is as follows:
115	<	// [ 0 3 6 ]
116	<	// [ 1 4 7 ]
117	<	// [ 2 5 8 ]
118	<	double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
294	>	// nZconstraints_ is global, as are the 3 COM translations for the
295	>	// entire system:
296	>	ndf_ = ndf_ - 3 - nZconstraint_;
297
298	<	if( !boxIsInit ) boxIsInit = 1;
298	>	}
299
300	<	for(i=0; i < 3; i++)
301	<	for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
300	>	int SimInfo::getFdf() {
301	>	#ifdef IS_MPI
302	>	MPI_Allreduce(&fdf_local, &fdf_, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
303	>	#else
304	>	fdf_ = fdf_local;
305	>	#endif
306	>	return fdf_;
307	>	}
308
309	<	calcBoxL();
310	<	calcHmatInv();
311	<
312	<	for(i=0; i < 3; i++) {
313	<	for (j=0; j < 3; j++) {
314	<	FortranHmat[3*j + i] = Hmat[i][j];
315	<	FortranHmatInv[3*j + i] = HmatInv[i][j];
309	>	unsigned int SimInfo::getNLocalCutoffGroups(){
310	>	int nLocalCutoffAtoms = 0;
311	>	Molecule* mol;
312	>	MoleculeIterator mi;
313	>	CutoffGroup* cg;
314	>	Molecule::CutoffGroupIterator ci;
315	>
316	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
317	>
318	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
319	>	cg = mol->nextCutoffGroup(ci)) {
320	>	nLocalCutoffAtoms += cg->getNumAtom();
321	>
322	>	}
323		}
324	+
325	+	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
326		}
327	+
328	+	void SimInfo::calcNdfRaw() {
329	+	int ndfRaw_local;
330
331	<	setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
332	<
333	<	}
334	<
331	>	MoleculeIterator i;
332	>	vector<StuntDouble*>::iterator j;
333	>	Molecule* mol;
334	>	StuntDouble* sd;
335
336	<	void SimInfo::getBoxM (double theBox[3][3]) {
336	>	// Raw degrees of freedom that we have to set
337	>	ndfRaw_local = 0;
338	>
339	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
340
341	<	int i, j;
342	<	for(i=0; i<3; i++)
144	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
145	<	}
341	>	for (sd = mol->beginIntegrableObject(j); sd != NULL;
342	>	sd = mol->nextIntegrableObject(j)) {
343
344	+	ndfRaw_local += 3;
345
346	<	void SimInfo::scaleBox(double scale) {
347	<	double theBox[3][3];
348	<	int i, j;
346	>	if (sd->isDirectional()) {
347	>	if (sd->isLinear()) {
348	>	ndfRaw_local += 2;
349	>	} else {
350	>	ndfRaw_local += 3;
351	>	}
352	>	}
353	>
354	>	}
355	>	}
356	>
357	>	#ifdef IS_MPI
358	>	MPI_Allreduce(&ndfRaw_local, &ndfRaw_, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
359	>	#else
360	>	ndfRaw_ = ndfRaw_local;
361	>	#endif
362	>	}
363
364	<	// cerr << "Scaling box by " << scale << "\n";
364	>	void SimInfo::calcNdfTrans() {
365	>	int ndfTrans_local;
366
367	<	for(i=0; i<3; i++)
155	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
367	>	ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
368
369	<	setBoxM(theBox);
369	>	#ifdef IS_MPI
370	>	MPI_Allreduce(&ndfTrans_local, &ndfTrans_, 1, MPI_INT, MPI_SUM,
371	>	MPI_COMM_WORLD);
372	>	#else
373	>	ndfTrans_ = ndfTrans_local;
374	>	#endif
375
376	<	}
376	>	ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
377	>	}
378
379	<	void SimInfo::calcHmatInv( void ) {
380	<
381	<	int oldOrtho;
382	<	int i,j;
383	<	double smallDiag;
384	<	double tol;
385	<	double sanity[3][3];
379	>	void SimInfo::addInteractionPairs(Molecule* mol) {
380	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
381	>	vector<Bond*>::iterator bondIter;
382	>	vector<Bend*>::iterator bendIter;
383	>	vector<Torsion*>::iterator torsionIter;
384	>	vector<Inversion*>::iterator inversionIter;
385	>	Bond* bond;
386	>	Bend* bend;
387	>	Torsion* torsion;
388	>	Inversion* inversion;
389	>	int a;
390	>	int b;
391	>	int c;
392	>	int d;
393
394	<	invertMat3( Hmat, HmatInv );
394	>	// atomGroups can be used to add special interaction maps between
395	>	// groups of atoms that are in two separate rigid bodies.
396	>	// However, most site-site interactions between two rigid bodies
397	>	// are probably not special, just the ones between the physically
398	>	// bonded atoms.  Interactions *within* a single rigid body should
399	>	// always be excluded.  These are done at the bottom of this
400	>	// function.
401
402	<	// check to see if Hmat is orthorhombic
403	<
404	<	oldOrtho = orthoRhombic;
402	>	map<int, set<int> > atomGroups;
403	>	Molecule::RigidBodyIterator rbIter;
404	>	RigidBody* rb;
405	>	Molecule::IntegrableObjectIterator ii;
406	>	StuntDouble* sd;
407	>
408	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
409	>	sd = mol->nextIntegrableObject(ii)) {
410	>
411	>	if (sd->isRigidBody()) {
412	>	rb = static_cast<RigidBody*>(sd);
413	>	vector<Atom*> atoms = rb->getAtoms();
414	>	set<int> rigidAtoms;
415	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
416	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
417	>	}
418	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
419	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
420	>	}
421	>	} else {
422	>	set<int> oneAtomSet;
423	>	oneAtomSet.insert(sd->getGlobalIndex());
424	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
425	>	}
426	>	}
427
428	<	smallDiag = fabs(Hmat[0][0]);
429	<	if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
430	<	if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
178	<	tol = smallDiag * orthoTolerance;
428	>
429	>	for (bond= mol->beginBond(bondIter); bond != NULL;
430	>	bond = mol->nextBond(bondIter)) {
431
432	<	orthoRhombic = 1;
433	<
434	<	for (i = 0; i < 3; i++ ) {
435	<	for (j = 0 ; j < 3; j++) {
436	<	if (i != j) {
437	<	if (orthoRhombic) {
438	<	if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
187	<	}
432	>	a = bond->getAtomA()->getGlobalIndex();
433	>	b = bond->getAtomB()->getGlobalIndex();
434	>
435	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
436	>	oneTwoInteractions_.addPair(a, b);
437	>	} else {
438	>	excludedInteractions_.addPair(a, b);
439		}
440		}
190	–	}
441
442	<	if( oldOrtho != orthoRhombic ){
443	<
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	<	}
442	>	for (bend= mol->beginBend(bendIter); bend != NULL;
443	>	bend = mol->nextBend(bendIter)) {
444
445	<	void SimInfo::calcBoxL( void ){
445	>	a = bend->getAtomA()->getGlobalIndex();
446	>	b = bend->getAtomB()->getGlobalIndex();
447	>	c = bend->getAtomC()->getGlobalIndex();
448	>
449	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
450	>	oneTwoInteractions_.addPair(a, b);
451	>	oneTwoInteractions_.addPair(b, c);
452	>	} else {
453	>	excludedInteractions_.addPair(a, b);
454	>	excludedInteractions_.addPair(b, c);
455	>	}
456
457	<	double dx, dy, dz, dsq;
457	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
458	>	oneThreeInteractions_.addPair(a, c);
459	>	} else {
460	>	excludedInteractions_.addPair(a, c);
461	>	}
462	>	}
463
464	<	// boxVol = Determinant of Hmat
464	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
465	>	torsion = mol->nextTorsion(torsionIter)) {
466
467	<	boxVol = matDet3( Hmat );
467	>	a = torsion->getAtomA()->getGlobalIndex();
468	>	b = torsion->getAtomB()->getGlobalIndex();
469	>	c = torsion->getAtomC()->getGlobalIndex();
470	>	d = torsion->getAtomD()->getGlobalIndex();
471
472	<	// boxLx
473	<
474	<	dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
475	<	dsq = dx*dx + dy*dy + dz*dz;
476	<	boxL[0] = sqrt( dsq );
477	<	//maxCutoff = 0.5 * boxL[0];
472	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
473	>	oneTwoInteractions_.addPair(a, b);
474	>	oneTwoInteractions_.addPair(b, c);
475	>	oneTwoInteractions_.addPair(c, d);
476	>	} else {
477	>	excludedInteractions_.addPair(a, b);
478	>	excludedInteractions_.addPair(b, c);
479	>	excludedInteractions_.addPair(c, d);
480	>	}
481
482	<	// boxLy
483	<
484	<	dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
485	<	dsq = dx*dx + dy*dy + dz*dz;
486	<	boxL[1] = sqrt( dsq );
487	<	//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
482	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
483	>	oneThreeInteractions_.addPair(a, c);
484	>	oneThreeInteractions_.addPair(b, d);
485	>	} else {
486	>	excludedInteractions_.addPair(a, c);
487	>	excludedInteractions_.addPair(b, d);
488	>	}
489
490	+	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
491	+	oneFourInteractions_.addPair(a, d);
492	+	} else {
493	+	excludedInteractions_.addPair(a, d);
494	+	}
495	+	}
496
497	<	// boxLz
498	<
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];
497	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
498	>	inversion = mol->nextInversion(inversionIter)) {
499
500	<	//calculate the max cutoff
501	<	maxCutoff =  calcMaxCutOff();
502	<
503	<	checkCutOffs();
500	>	a = inversion->getAtomA()->getGlobalIndex();
501	>	b = inversion->getAtomB()->getGlobalIndex();
502	>	c = inversion->getAtomC()->getGlobalIndex();
503	>	d = inversion->getAtomD()->getGlobalIndex();
504
505	<	}
505	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
506	>	oneTwoInteractions_.addPair(a, b);
507	>	oneTwoInteractions_.addPair(a, c);
508	>	oneTwoInteractions_.addPair(a, d);
509	>	} else {
510	>	excludedInteractions_.addPair(a, b);
511	>	excludedInteractions_.addPair(a, c);
512	>	excludedInteractions_.addPair(a, d);
513	>	}
514
515	+	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
516	+	oneThreeInteractions_.addPair(b, c);
517	+	oneThreeInteractions_.addPair(b, d);
518	+	oneThreeInteractions_.addPair(c, d);
519	+	} else {
520	+	excludedInteractions_.addPair(b, c);
521	+	excludedInteractions_.addPair(b, d);
522	+	excludedInteractions_.addPair(c, d);
523	+	}
524	+	}
525
526	<	double SimInfo::calcMaxCutOff(){
526	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
527	>	rb = mol->nextRigidBody(rbIter)) {
528	>	vector<Atom*> atoms = rb->getAtoms();
529	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
530	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
531	>	a = atoms[i]->getGlobalIndex();
532	>	b = atoms[j]->getGlobalIndex();
533	>	excludedInteractions_.addPair(a, b);
534	>	}
535	>	}
536	>	}
537
538	<	double ri[3], rj[3], rk[3];
261	<	double rij[3], rjk[3], rki[3];
262	<	double minDist;
538	>	}
539
540	<	ri[0] = Hmat[0][0];
541	<	ri[1] = Hmat[1][0];
542	<	ri[2] = Hmat[2][0];
540	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
541	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
542	>	vector<Bond*>::iterator bondIter;
543	>	vector<Bend*>::iterator bendIter;
544	>	vector<Torsion*>::iterator torsionIter;
545	>	vector<Inversion*>::iterator inversionIter;
546	>	Bond* bond;
547	>	Bend* bend;
548	>	Torsion* torsion;
549	>	Inversion* inversion;
550	>	int a;
551	>	int b;
552	>	int c;
553	>	int d;
554
555	<	rj[0] = Hmat[0][1];
556	<	rj[1] = Hmat[1][1];
557	<	rj[2] = Hmat[2][1];
555	>	map<int, set<int> > atomGroups;
556	>	Molecule::RigidBodyIterator rbIter;
557	>	RigidBody* rb;
558	>	Molecule::IntegrableObjectIterator ii;
559	>	StuntDouble* sd;
560	>
561	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
562	>	sd = mol->nextIntegrableObject(ii)) {
563	>
564	>	if (sd->isRigidBody()) {
565	>	rb = static_cast<RigidBody*>(sd);
566	>	vector<Atom*> atoms = rb->getAtoms();
567	>	set<int> rigidAtoms;
568	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
569	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
570	>	}
571	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
572	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
573	>	}
574	>	} else {
575	>	set<int> oneAtomSet;
576	>	oneAtomSet.insert(sd->getGlobalIndex());
577	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
578	>	}
579	>	}
580
581	<	rk[0] = Hmat[0][2];
582	<	rk[1] = Hmat[1][2];
583	<	rk[2] = Hmat[2][2];
581	>	for (bond= mol->beginBond(bondIter); bond != NULL;
582	>	bond = mol->nextBond(bondIter)) {
583	>
584	>	a = bond->getAtomA()->getGlobalIndex();
585	>	b = bond->getAtomB()->getGlobalIndex();
586
587	<	crossProduct3(ri, rj, rij);
588	<	distXY = dotProduct3(rk,rij) / norm3(rij);
587	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
588	>	oneTwoInteractions_.removePair(a, b);
589	>	} else {
590	>	excludedInteractions_.removePair(a, b);
591	>	}
592	>	}
593
594	<	crossProduct3(rj,rk, rjk);
595	<	distYZ = dotProduct3(ri,rjk) / norm3(rjk);
594	>	for (bend= mol->beginBend(bendIter); bend != NULL;
595	>	bend = mol->nextBend(bendIter)) {
596
597	<	crossProduct3(rk,ri, rki);
598	<	distZX = dotProduct3(rj,rki) / norm3(rki);
597	>	a = bend->getAtomA()->getGlobalIndex();
598	>	b = bend->getAtomB()->getGlobalIndex();
599	>	c = bend->getAtomC()->getGlobalIndex();
600	>
601	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
602	>	oneTwoInteractions_.removePair(a, b);
603	>	oneTwoInteractions_.removePair(b, c);
604	>	} else {
605	>	excludedInteractions_.removePair(a, b);
606	>	excludedInteractions_.removePair(b, c);
607	>	}
608
609	<	minDist = min(min(distXY, distYZ), distZX);
610	<	return minDist/2;
611	<
612	<	}
609	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
610	>	oneThreeInteractions_.removePair(a, c);
611	>	} else {
612	>	excludedInteractions_.removePair(a, c);
613	>	}
614	>	}
615
616	<	void SimInfo::wrapVector( double thePos[3] ){
616	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
617	>	torsion = mol->nextTorsion(torsionIter)) {
618
619	<	int i;
620	<	double scaled[3];
621	<
622	<	if( !orthoRhombic ){
296	<	// calc the scaled coordinates.
619	>	a = torsion->getAtomA()->getGlobalIndex();
620	>	b = torsion->getAtomB()->getGlobalIndex();
621	>	c = torsion->getAtomC()->getGlobalIndex();
622	>	d = torsion->getAtomD()->getGlobalIndex();
623
624	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
625	+	oneTwoInteractions_.removePair(a, b);
626	+	oneTwoInteractions_.removePair(b, c);
627	+	oneTwoInteractions_.removePair(c, d);
628	+	} else {
629	+	excludedInteractions_.removePair(a, b);
630	+	excludedInteractions_.removePair(b, c);
631	+	excludedInteractions_.removePair(c, d);
632	+	}
633
634	<	matVecMul3(HmatInv, thePos, scaled);
635	<
636	<	for(i=0; i<3; i++)
637	<	scaled[i] -= roundMe(scaled[i]);
638	<
639	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
640	<
306	<	matVecMul3(Hmat, scaled, thePos);
634	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
635	>	oneThreeInteractions_.removePair(a, c);
636	>	oneThreeInteractions_.removePair(b, d);
637	>	} else {
638	>	excludedInteractions_.removePair(a, c);
639	>	excludedInteractions_.removePair(b, d);
640	>	}
641
642	<	}
643	<	else{
644	<	// calc the scaled coordinates.
642	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
643	>	oneFourInteractions_.removePair(a, d);
644	>	} else {
645	>	excludedInteractions_.removePair(a, d);
646	>	}
647	>	}
648	>
649	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
650	>	inversion = mol->nextInversion(inversionIter)) {
651	>
652	>	a = inversion->getAtomA()->getGlobalIndex();
653	>	b = inversion->getAtomB()->getGlobalIndex();
654	>	c = inversion->getAtomC()->getGlobalIndex();
655	>	d = inversion->getAtomD()->getGlobalIndex();
656	>
657	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
658	>	oneTwoInteractions_.removePair(a, b);
659	>	oneTwoInteractions_.removePair(a, c);
660	>	oneTwoInteractions_.removePair(a, d);
661	>	} else {
662	>	excludedInteractions_.removePair(a, b);
663	>	excludedInteractions_.removePair(a, c);
664	>	excludedInteractions_.removePair(a, d);
665	>	}
666	>
667	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
668	>	oneThreeInteractions_.removePair(b, c);
669	>	oneThreeInteractions_.removePair(b, d);
670	>	oneThreeInteractions_.removePair(c, d);
671	>	} else {
672	>	excludedInteractions_.removePair(b, c);
673	>	excludedInteractions_.removePair(b, d);
674	>	excludedInteractions_.removePair(c, d);
675	>	}
676	>	}
677	>
678	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
679	>	rb = mol->nextRigidBody(rbIter)) {
680	>	vector<Atom*> atoms = rb->getAtoms();
681	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
682	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
683	>	a = atoms[i]->getGlobalIndex();
684	>	b = atoms[j]->getGlobalIndex();
685	>	excludedInteractions_.removePair(a, b);
686	>	}
687	>	}
688	>	}
689
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];
690		}
691	+
692	+
693	+	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
694	+	int curStampId;
695
696	<	}
696	>	//index from 0
697	>	curStampId = moleculeStamps_.size();
698
699	+	moleculeStamps_.push_back(molStamp);
700	+	molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
701	+	}
702
329	–	int SimInfo::getNDF(){
330	–	int ndf_local;
703
704	<	ndf_local = 0;
705	<
706	<	for(int i = 0; i < integrableObjects.size(); i++){
707	<	ndf_local += 3;
708	<	if (integrableObjects[i]->isDirectional()) {
709	<	if (integrableObjects[i]->isLinear())
710	<	ndf_local += 2;
711	<	else
712	<	ndf_local += 3;
713	<	}
704	>	/**
705	>	* update
706	>	*
707	>	*  Performs the global checks and variable settings after the
708	>	*  objects have been created.
709	>	*
710	>	*/
711	>	void SimInfo::update() {
712	>	setupSimVariables();
713	>	calcNConstraints();
714	>	calcNdf();
715	>	calcNdfRaw();
716	>	calcNdfTrans();
717		}
718	+
719	+	/**
720	+	* getSimulatedAtomTypes
721	+	*
722	+	* Returns an STL set of AtomType* that are actually present in this
723	+	* simulation.  Must query all processors to assemble this information.
724	+	*
725	+	*/
726	+	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
727	+	SimInfo::MoleculeIterator mi;
728	+	Molecule* mol;
729	+	Molecule::AtomIterator ai;
730	+	Atom* atom;
731	+	set<AtomType*> atomTypes;
732	+
733	+	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
734	+	for(atom = mol->beginAtom(ai); atom != NULL;
735	+	atom = mol->nextAtom(ai)) {
736	+	atomTypes.insert(atom->getAtomType());
737	+	}
738	+	}
739	+
740	+	#ifdef IS_MPI
741
742	<	// n_constraints is local, so subtract them on each processor:
742	>	// loop over the found atom types on this processor, and add their
743	>	// numerical idents to a vector:
744	>
745	>	vector<int> foundTypes;
746	>	set<AtomType*>::iterator i;
747	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
748	>	foundTypes.push_back( (*i)->getIdent() );
749
750	<	ndf_local -= n_constraints;
750	>	// count_local holds the number of found types on this processor
751	>	int count_local = foundTypes.size();
752
753	<	#ifdef IS_MPI
754	<	MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
350	<	#else
351	<	ndf = ndf_local;
352	<	#endif
753	>	int nproc;
754	>	MPI_Comm_size( MPI_COMM_WORLD, &nproc);
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	>
765	>	// use the processor counts to compute the displacement array
766	>	disps[0] = 0;
767	>	int totalCount = counts[0];
768	>	for (int iproc = 1; iproc < nproc; iproc++) {
769	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
770	>	totalCount += counts[iproc];
771	>	}
772
773	<	return ndf;
774	<	}
773	>	// we need a (possibly redundant) set of all found types:
774	>	vector<int> ftGlobal(totalCount);
775	>
776	>	// now spray out the foundTypes to all the other processors:
777	>	MPI_Allgatherv(&foundTypes[0], count_local, MPI_INT,
778	>	&ftGlobal[0], &counts[0], &disps[0],
779	>	MPI_INT, MPI_COMM_WORLD);
780
781	<	int SimInfo::getNDFraw() {
363	<	int ndfRaw_local;
781	>	vector<int>::iterator j;
782
783	<	// Raw degrees of freedom that we have to set
784	<	ndfRaw_local = 0;
783	>	// foundIdents is a stl set, so inserting an already found ident
784	>	// will have no effect.
785	>	set<int> foundIdents;
786
787	<	for(int i = 0; i < integrableObjects.size(); i++){
788	<	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	<	}
787	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
788	>	foundIdents.insert((*j));
789
790	<	#ifdef IS_MPI
791	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
792	<	#else
793	<	ndfRaw = ndfRaw_local;
790	>	// now iterate over the foundIdents and get the actual atom types
791	>	// that correspond to these:
792	>	set<int>::iterator it;
793	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
794	>	atomTypes.insert( forceField_->getAtomType((*it)) );
795	>
796		#endif
797
798	<	return ndfRaw;
799	<	}
798	>	return atomTypes;
799	>	}
800
387	–	int SimInfo::getNDFtranslational() {
388	–	int ndfTrans_local;
801
802	<	ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
802	>	int getGlobalCountOfType(AtomType* atype) {
803	>	/*
804	>	set<AtomType*> atypes = getSimulatedAtomTypes();
805	>	map<AtomType*, int> counts_;
806
807	+	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
808	+	for(atom = mol->beginAtom(ai); atom != NULL;
809	+	atom = mol->nextAtom(ai)) {
810	+	atom->getAtomType();
811	+	}
812	+	}
813	+	*/
814	+	return 0;
815	+	}
816
817	+	void SimInfo::setupSimVariables() {
818	+	useAtomicVirial_ = simParams_->getUseAtomicVirial();
819	+	// we only call setAccumulateBoxDipole if the accumulateBoxDipole
820	+	// parameter is true
821	+	calcBoxDipole_ = false;
822	+	if ( simParams_->haveAccumulateBoxDipole() )
823	+	if ( simParams_->getAccumulateBoxDipole() ) {
824	+	calcBoxDipole_ = true;
825	+	}
826	+	// we only call setAccumulateBoxQuadrupole if the accumulateBoxQuadrupole
827	+	// parameter is true
828	+	calcBoxQuadrupole_ = false;
829	+	if ( simParams_->haveAccumulateBoxQuadrupole() )
830	+	if ( simParams_->getAccumulateBoxQuadrupole() ) {
831	+	calcBoxQuadrupole_ = true;
832	+	}
833	+
834	+	set<AtomType*>::iterator i;
835	+	set<AtomType*> atomTypes;
836	+	atomTypes = getSimulatedAtomTypes();
837	+	bool usesElectrostatic = false;
838	+	bool usesMetallic = false;
839	+	bool usesDirectional = false;
840	+	bool usesFluctuatingCharges =  false;
841	+	//loop over all of the atom types
842	+	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
843	+	usesElectrostatic |= (*i)->isElectrostatic();
844	+	usesMetallic |= (*i)->isMetal();
845	+	usesDirectional |= (*i)->isDirectional();
846	+	usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
847	+	}
848	+
849		#ifdef IS_MPI
850	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
395	<	#else
396	<	ndfTrans = ndfTrans_local;
397	<	#endif
850	>	int temp;
851
852	<	ndfTrans = ndfTrans - 3 - nZconstraints;
852	>	temp = usesDirectional;
853	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
854	>	usesDirectionalAtoms_ = (temp == 0) ? false : true;
855	>
856	>	temp = usesMetallic;
857	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
858	>	usesMetallicAtoms_ = (temp == 0) ? false : true;
859
860	<	return ndfTrans;
861	<	}
860	>	temp = usesElectrostatic;
861	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
862	>	usesElectrostaticAtoms_ = (temp == 0) ? false : true;
863
864	<	int SimInfo::getTotIntegrableObjects() {
865	<	int nObjs_local;
866	<	int nObjs;
864	>	temp = usesFluctuatingCharges;
865	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
866	>	usesFluctuatingCharges_ = (temp == 0) ? false : true;
867	>	#else
868
869	<	nObjs_local =  integrableObjects.size();
869	>	usesDirectionalAtoms_ = usesDirectional;
870	>	usesMetallicAtoms_ = usesMetallic;
871	>	usesElectrostaticAtoms_ = usesElectrostatic;
872	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
873
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;
874		#endif
875	+
876	+	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
877	+	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
878	+	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
879	+	}
880
881
882	<	return nObjs;
883	<	}
882	>	vector<int> SimInfo::getGlobalAtomIndices() {
883	>	SimInfo::MoleculeIterator mi;
884	>	Molecule* mol;
885	>	Molecule::AtomIterator ai;
886	>	Atom* atom;
887
888	<	void SimInfo::refreshSim(){
888	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
889	>
890	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
891	>
892	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
893	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
894	>	}
895	>	}
896	>	return GlobalAtomIndices;
897	>	}
898
423	–	simtype fInfo;
424	–	int isError;
425	–	int n_global;
426	–	int* excl;
899
900	<	fInfo.dielect = 0.0;
900	>	vector<int> SimInfo::getGlobalGroupIndices() {
901	>	SimInfo::MoleculeIterator mi;
902	>	Molecule* mol;
903	>	Molecule::CutoffGroupIterator ci;
904	>	CutoffGroup* cg;
905
906	<	if( useDipoles ){
907	<	if( useReactionField )fInfo.dielect = dielectric;
906	>	vector<int> GlobalGroupIndices;
907	>
908	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
909	>
910	>	//local index of cutoff group is trivial, it only depends on the
911	>	//order of travesing
912	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
913	>	cg = mol->nextCutoffGroup(ci)) {
914	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
915	>	}
916	>	}
917	>	return GlobalGroupIndices;
918		}
919
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;
920
921	<	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);
921	>	void SimInfo::prepareTopology() {
922
923	<	if( isError ){
923	>	//calculate mass ratio of cutoff group
924	>	SimInfo::MoleculeIterator mi;
925	>	Molecule* mol;
926	>	Molecule::CutoffGroupIterator ci;
927	>	CutoffGroup* cg;
928	>	Molecule::AtomIterator ai;
929	>	Atom* atom;
930	>	RealType totalMass;
931	>
932	>	/**
933	>	* The mass factor is the relative mass of an atom to the total
934	>	* mass of the cutoff group it belongs to.  By default, all atoms
935	>	* are their own cutoff groups, and therefore have mass factors of
936	>	* 1.  We need some special handling for massless atoms, which
937	>	* will be treated as carrying the entire mass of the cutoff
938	>	* group.
939	>	*/
940	>	massFactors_.clear();
941	>	massFactors_.resize(getNAtoms(), 1.0);
942
943	<	sprintf( painCave.errMsg,
944	<	"There was an error setting the simulation information in fortran.\n" );
945	<	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	<	}
943	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
944	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
945	>	cg = mol->nextCutoffGroup(ci)) {
946
947	<	void SimInfo::setDefaultRcut( double theRcut ){
948	<
949	<	haveRcut = 1;
950	<	rCut = theRcut;
951	<	rList = rCut + 1.0;
952	<
953	<	notifyFortranCutOffs( &rCut, &rSw, &rList );
954	<	}
947	>	totalMass = cg->getMass();
948	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
949	>	// Check for massless groups - set mfact to 1 if true
950	>	if (totalMass != 0)
951	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
952	>	else
953	>	massFactors_[atom->getLocalIndex()] = 1.0;
954	>	}
955	>	}
956	>	}
957
958	<	void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
958	>	// Build the identArray_ and regions_
959
960	<	rSw = theRsw;
961	<	setDefaultRcut( theRcut );
962	<	}
960	>	identArray_.clear();
961	>	identArray_.reserve(getNAtoms());
962	>	regions_.clear();
963	>	regions_.reserve(getNAtoms());
964	>
965	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
966	>	int reg = mol->getRegion();
967	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
968	>	identArray_.push_back(atom->getIdent());
969	>	regions_.push_back(reg);
970	>	}
971	>	}
972	>
973	>	topologyDone_ = true;
974	>	}
975
976	+	void SimInfo::addProperty(GenericData* genData) {
977	+	properties_.addProperty(genData);
978	+	}
979
980	<	void SimInfo::checkCutOffs( void ){
981	<
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();
980	>	void SimInfo::removeProperty(const string& propName) {
981	>	properties_.removeProperty(propName);
982		}
535	–
536	–	}
983
984	<	void SimInfo::addProperty(GenericData* prop){
984	>	void SimInfo::clearProperties() {
985	>	properties_.clearProperties();
986	>	}
987
988	<	map<string, GenericData*>::iterator result;
989	<	result = properties.find(prop->getID());
990	<
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;
988	>	vector<string> SimInfo::getPropertyNames() {
989	>	return properties_.getPropertyNames();
990	>	}
991
992	+	vector<GenericData*> SimInfo::getProperties() {
993	+	return properties_.getProperties();
994		}
552	–	else{
995
996	<	properties[prop->getID()] = prop;
997	<
996	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
997	>	return properties_.getPropertyByName(propName);
998		}
557	–
558	–	}
999
1000	<	GenericData* SimInfo::getProperty(const string& propName){
1000	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1001	>	if (sman_ == sman) {
1002	>	return;
1003	>	}
1004	>	delete sman_;
1005	>	sman_ = sman;
1006	>
1007	>	SimInfo::MoleculeIterator mi;
1008	>	Molecule::AtomIterator ai;
1009	>	Molecule::RigidBodyIterator rbIter;
1010	>	Molecule::CutoffGroupIterator cgIter;
1011	>	Molecule::BondIterator bondIter;
1012	>	Molecule::BendIterator bendIter;
1013	>	Molecule::TorsionIterator torsionIter;
1014	>	Molecule::InversionIterator inversionIter;
1015
1016	<	map<string, GenericData*>::iterator result;
1017	<
1018	<	//string lowerCaseName = ();
1019	<
1020	<	result = properties.find(propName);
1021	<
1022	<	if(result != properties.end())
1023	<	return (*result).second;
570	<	else
571	<	return NULL;
572	<	}
1016	>	Molecule* mol;
1017	>	Atom* atom;
1018	>	RigidBody* rb;
1019	>	CutoffGroup* cg;
1020	>	Bond* bond;
1021	>	Bend* bend;
1022	>	Torsion* torsion;
1023	>	Inversion* inversion;
1024
1025	+	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1026	+
1027	+	for (atom = mol->beginAtom(ai); atom != NULL;
1028	+	atom = mol->nextAtom(ai)) {
1029	+	atom->setSnapshotManager(sman_);
1030	+	}
1031	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
1032	+	rb = mol->nextRigidBody(rbIter)) {
1033	+	rb->setSnapshotManager(sman_);
1034	+	}
1035	+	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL;
1036	+	cg = mol->nextCutoffGroup(cgIter)) {
1037	+	cg->setSnapshotManager(sman_);
1038	+	}
1039	+	for (bond = mol->beginBond(bondIter); bond != NULL;
1040	+	bond = mol->nextBond(bondIter)) {
1041	+	bond->setSnapshotManager(sman_);
1042	+	}
1043	+	for (bend = mol->beginBend(bendIter); bend != NULL;
1044	+	bend = mol->nextBend(bendIter)) {
1045	+	bend->setSnapshotManager(sman_);
1046	+	}
1047	+	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
1048	+	torsion = mol->nextTorsion(torsionIter)) {
1049	+	torsion->setSnapshotManager(sman_);
1050	+	}
1051	+	for (inversion = mol->beginInversion(inversionIter); inversion != NULL;
1052	+	inversion = mol->nextInversion(inversionIter)) {
1053	+	inversion->setSnapshotManager(sman_);
1054	+	}
1055	+	}
1056	+	}
1057
1058	<	void SimInfo::getFortranGroupArrays(SimInfo* info,
1059	<	vector<int>& FglobalGroupMembership,
1060	<	vector<double>& mfact){
1058	>
1059	>	ostream& operator <<(ostream& o, SimInfo& info) {
1060	>
1061	>	return o;
1062	>	}
1063	>
1064
1065	<	Molecule* myMols;
1066	<	Atom** myAtoms;
1067	<	int numAtom;
1068	<	double mtot;
1069	<	int numMol;
1070	<	int numCutoffGroups;
1071	<	CutoffGroup* myCutoffGroup;
1072	<	vector<CutoffGroup*>::iterator iterCutoff;
1073	<	Atom* cutoffAtom;
1074	<	vector<Atom*>::iterator iterAtom;
1075	<	int atomIndex;
590	<	double totalMass;
1065	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1066	>	if (index >= int(IOIndexToIntegrableObject.size())) {
1067	>	sprintf(painCave.errMsg,
1068	>	"SimInfo::getIOIndexToIntegrableObject Error: Integrable Object\n"
1069	>	"\tindex exceeds number of known objects!\n");
1070	>	painCave.isFatal = 1;
1071	>	simError();
1072	>	return NULL;
1073	>	} else
1074	>	return IOIndexToIntegrableObject.at(index);
1075	>	}
1076
1077	<	mfact.clear();
1078	<	FglobalGroupMembership.clear();
1079	<
1077	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1078	>	IOIndexToIntegrableObject= v;
1079	>	}
1080
1081	<	// Fix the silly fortran indexing problem
1081	>	void SimInfo::calcNConstraints() {
1082		#ifdef IS_MPI
1083	<	numAtom = mpiSim->getNAtomsGlobal();
1083	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints_, 1,
1084	>	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
1085		#else
1086	<	numAtom = n_atoms;
1086	>	nGlobalConstraints_ =  nConstraints_;
1087		#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	–	}
1088		}
1089
1090	<	}
1090	>	}//end namespace OpenMD
1091	>

Comparing trunk/src/brains/SimInfo.cpp (property svn:keywords):
Revision 2 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
Revision 2071 by gezelter, Sat Mar 7 21:41:51 2015 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines