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

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 124 by chuckv, Wed Oct 20 20:46:20 2004 UTC vs.
Revision 1969 by gezelter, Wed Feb 26 14:14:50 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 "UseTheForce/DarkSide/simulation_interface.h"
64	<	#include "UseTheForce/notifyCutoffs_interface.h"
63	>	#include "selection/SelectionManager.hpp"
64	>	#include "io/ForceFieldOptions.hpp"
65	>	#include "brains/ForceField.hpp"
66	>	#include "nonbonded/SwitchingFunction.hpp"
67
68	<	//#include "UseTheForce/fortranWrappers.hpp"
68	>	using namespace std;
69	>	namespace OpenMD {
70	>
71	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
72	>	forceField_(ff), simParams_(simParams),
73	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
74	>	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
75	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
76	>	nGlobalFluctuatingCharges_(0), nGlobalBonds_(0), nGlobalBends_(0),
77	>	nGlobalTorsions_(0), nGlobalInversions_(0), nAtoms_(0), nBonds_(0),
78	>	nBends_(0), nTorsions_(0), nInversions_(0), nRigidBodies_(0),
79	>	nIntegrableObjects_(0), nCutoffGroups_(0), nConstraints_(0),
80	>	nFluctuatingCharges_(0), sman_(NULL), topologyDone_(false),
81	>	calcBoxDipole_(false), useAtomicVirial_(true) {
82	>
83	>	MoleculeStamp* molStamp;
84	>	int nMolWithSameStamp;
85	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
86	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
87	>	CutoffGroupStamp* cgStamp;
88	>	RigidBodyStamp* rbStamp;
89	>	int nRigidAtoms = 0;
90	>
91	>	vector<Component*> components = simParams->getComponents();
92	>
93	>	for (vector<Component*>::iterator i = components.begin();
94	>	i !=components.end(); ++i) {
95	>	molStamp = (*i)->getMoleculeStamp();
96	>	if ( (*i)->haveRegion() ) {
97	>	molStamp->setRegion( (*i)->getRegion() );
98	>	} else {
99	>	// set the region to a disallowed value:
100	>	molStamp->setRegion( -1 );
101	>	}
102
103	<	#include "math/MatVec3.h"
103	>	nMolWithSameStamp = (*i)->getNMol();
104	>
105	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
106	>
107	>	//calculate atoms in molecules
108	>	nGlobalAtoms_ += molStamp->getNAtoms() * nMolWithSameStamp;
109	>	nGlobalBonds_ += molStamp->getNBonds() * nMolWithSameStamp;
110	>	nGlobalBends_ += molStamp->getNBends() * nMolWithSameStamp;
111	>	nGlobalTorsions_ += molStamp->getNTorsions() * nMolWithSameStamp;
112	>	nGlobalInversions_ += molStamp->getNInversions() * nMolWithSameStamp;
113	>
114	>	//calculate atoms in cutoff groups
115	>	int nAtomsInGroups = 0;
116	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
117	>
118	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
119	>	cgStamp = molStamp->getCutoffGroupStamp(j);
120	>	nAtomsInGroups += cgStamp->getNMembers();
121	>	}
122	>
123	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
124	>
125	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
126	>
127	>	//calculate atoms in rigid bodies
128	>	int nAtomsInRigidBodies = 0;
129	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
130	>
131	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
132	>	rbStamp = molStamp->getRigidBodyStamp(j);
133	>	nAtomsInRigidBodies += rbStamp->getNMembers();
134	>	}
135	>
136	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
137	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
138	>
139	>	}
140	>
141	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
142	>	//group therefore the total number of cutoff groups in the system is
143	>	//equal to the total number of atoms minus number of atoms belong to
144	>	//cutoff group defined in meta-data file plus the number of cutoff
145	>	//groups defined in meta-data file
146
147	<	#ifdef IS_MPI
148	<	#include "brains/mpiSimulation.hpp"
149	<	#endif
147	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
148	>
149	>	//every free atom (atom does not belong to rigid bodies) is an
150	>	//integrable object therefore the total number of integrable objects
151	>	//in the system is equal to the total number of atoms minus number of
152	>	//atoms belong to rigid body defined in meta-data file plus the number
153	>	//of rigid bodies defined in meta-data file
154	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
155	>	+ nGlobalRigidBodies_;
156	>
157	>	nGlobalMols_ = molStampIds_.size();
158	>	molToProcMap_.resize(nGlobalMols_);
159	>	}
160	>
161	>	SimInfo::~SimInfo() {
162	>	map<int, Molecule*>::iterator i;
163	>	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
164	>	delete i->second;
165	>	}
166	>	molecules_.clear();
167	>
168	>	delete sman_;
169	>	delete simParams_;
170	>	delete forceField_;
171	>	}
172
23	–	inline double roundMe( double x ){
24	–	return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
25	–	}
26	–
27	–	inline double min( double a, double b ){
28	–	return (a < b ) ? a : b;
29	–	}
173
174	<	SimInfo* currentInfo;
175	<
176	<	SimInfo::SimInfo(){
177	<
178	<	n_constraints = 0;
179	<	nZconstraints = 0;
180	<	n_oriented = 0;
181	<	n_dipoles = 0;
182	<	ndf = 0;
183	<	ndfRaw = 0;
184	<	nZconstraints = 0;
185	<	the_integrator = NULL;
186	<	setTemp = 0;
187	<	thermalTime = 0.0;
188	<	currentTime = 0.0;
189	<	rCut = 0.0;
190	<	rSw = 0.0;
191	<
192	<	haveRcut = 0;
193	<	haveRsw = 0;
194	<	boxIsInit = 0;
174	>	bool SimInfo::addMolecule(Molecule* mol) {
175	>	MoleculeIterator i;
176	>
177	>	i = molecules_.find(mol->getGlobalIndex());
178	>	if (i == molecules_.end() ) {
179	>
180	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
181	>
182	>	nAtoms_ += mol->getNAtoms();
183	>	nBonds_ += mol->getNBonds();
184	>	nBends_ += mol->getNBends();
185	>	nTorsions_ += mol->getNTorsions();
186	>	nInversions_ += mol->getNInversions();
187	>	nRigidBodies_ += mol->getNRigidBodies();
188	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
189	>	nCutoffGroups_ += mol->getNCutoffGroups();
190	>	nConstraints_ += mol->getNConstraintPairs();
191	>
192	>	addInteractionPairs(mol);
193	>
194	>	return true;
195	>	} else {
196	>	return false;
197	>	}
198	>	}
199
200	<	resetTime = 1e99;
200	>	bool SimInfo::removeMolecule(Molecule* mol) {
201	>	MoleculeIterator i;
202	>	i = molecules_.find(mol->getGlobalIndex());
203
204	<	orthoRhombic = 0;
56	<	orthoTolerance = 1E-6;
57	<	useInitXSstate = true;
204	>	if (i != molecules_.end() ) {
205
206	<	usePBC = 0;
207	<	useLJ = 0;
208	<	useSticky = 0;
209	<	useCharges = 0;
210	<	useDipoles = 0;
211	<	useReactionField = 0;
212	<	useGB = 0;
213	<	useEAM = 0;
214	<	useSolidThermInt = 0;
215	<	useLiquidThermInt = 0;
206	>	assert(mol == i->second);
207	>
208	>	nAtoms_ -= mol->getNAtoms();
209	>	nBonds_ -= mol->getNBonds();
210	>	nBends_ -= mol->getNBends();
211	>	nTorsions_ -= mol->getNTorsions();
212	>	nInversions_ -= mol->getNInversions();
213	>	nRigidBodies_ -= mol->getNRigidBodies();
214	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
215	>	nCutoffGroups_ -= mol->getNCutoffGroups();
216	>	nConstraints_ -= mol->getNConstraintPairs();
217
218	<	haveCutoffGroups = false;
218	>	removeInteractionPairs(mol);
219	>	molecules_.erase(mol->getGlobalIndex());
220
221	<	excludes = Exclude::Instance();
221	>	delete mol;
222	>
223	>	return true;
224	>	} else {
225	>	return false;
226	>	}
227	>	}
228
229	<	myConfiguration = new SimState();
229	>
230	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
231	>	i = molecules_.begin();
232	>	return i == molecules_.end() ? NULL : i->second;
233	>	}
234
235	<	has_minimizer = false;
236	<	the_minimizer =NULL;
235	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
236	>	++i;
237	>	return i == molecules_.end() ? NULL : i->second;
238	>	}
239
79	–	ngroup = 0;
240
241	<	}
241	>	void SimInfo::calcNdf() {
242	>	int ndf_local, nfq_local;
243	>	MoleculeIterator i;
244	>	vector<StuntDouble*>::iterator j;
245	>	vector<Atom*>::iterator k;
246
247	+	Molecule* mol;
248	+	StuntDouble* sd;
249	+	Atom* atom;
250
251	<	SimInfo::~SimInfo(){
251	>	ndf_local = 0;
252	>	nfq_local = 0;
253	>
254	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
255
256	<	delete myConfiguration;
256	>	for (sd = mol->beginIntegrableObject(j); sd != NULL;
257	>	sd = mol->nextIntegrableObject(j)) {
258
259	<	map<string, GenericData*>::iterator i;
89	<
90	<	for(i = properties.begin(); i != properties.end(); i++)
91	<	delete (*i).second;
259	>	ndf_local += 3;
260
261	<	}
261	>	if (sd->isDirectional()) {
262	>	if (sd->isLinear()) {
263	>	ndf_local += 2;
264	>	} else {
265	>	ndf_local += 3;
266	>	}
267	>	}
268	>	}
269
270	<	void SimInfo::setBox(double newBox[3]) {
271	<
272	<	int i, j;
273	<	double tempMat[3][3];
270	>	for (atom = mol->beginFluctuatingCharge(k); atom != NULL;
271	>	atom = mol->nextFluctuatingCharge(k)) {
272	>	if (atom->isFluctuatingCharge()) {
273	>	nfq_local++;
274	>	}
275	>	}
276	>	}
277	>
278	>	ndfLocal_ = ndf_local;
279
280	<	for(i=0; i<3; i++)
281	<	for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
280	>	// n_constraints is local, so subtract them on each processor
281	>	ndf_local -= nConstraints_;
282
283	<	tempMat[0][0] = newBox[0];
284	<	tempMat[1][1] = newBox[1];
285	<	tempMat[2][2] = newBox[2];
283	>	#ifdef IS_MPI
284	>	MPI_Allreduce(&ndf_local, &ndf_, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
285	>	MPI_Allreduce(&nfq_local, &nGlobalFluctuatingCharges_, 1,
286	>	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
287	>	// MPI::COMM_WORLD.Allreduce(&ndf_local, &ndf_, 1, MPI::INT,MPI::SUM);
288	>	// MPI::COMM_WORLD.Allreduce(&nfq_local, &nGlobalFluctuatingCharges_, 1,
289	>	//                           MPI::INT, MPI::SUM);
290	>	#else
291	>	ndf_ = ndf_local;
292	>	nGlobalFluctuatingCharges_ = nfq_local;
293	>	#endif
294
295	<	setBoxM( tempMat );
295	>	// nZconstraints_ is global, as are the 3 COM translations for the
296	>	// entire system:
297	>	ndf_ = ndf_ - 3 - nZconstraint_;
298
299	<	}
299	>	}
300
301	<	void SimInfo::setBoxM( double theBox[3][3] ){
301	>	int SimInfo::getFdf() {
302	>	#ifdef IS_MPI
303	>	MPI_Allreduce(&fdf_local, &fdf_, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
304	>	// MPI::COMM_WORLD.Allreduce(&fdf_local, &fdf_, 1, MPI::INT, MPI::SUM);
305	>	#else
306	>	fdf_ = fdf_local;
307	>	#endif
308	>	return fdf_;
309	>	}
310
311	<	int i, j;
312	<	double FortranHmat[9]; // to preserve compatibility with Fortran the
313	<	// ordering in the array is as follows:
314	<	// [ 0 3 6 ]
315	<	// [ 1 4 7 ]
316	<	// [ 2 5 8 ]
317	<	double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
318	<
319	<	if( !boxIsInit ) boxIsInit = 1;
320	<
321	<	for(i=0; i < 3; i++)
322	<	for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
323	<
324	<	calcBoxL();
127	<	calcHmatInv();
128	<
129	<	for(i=0; i < 3; i++) {
130	<	for (j=0; j < 3; j++) {
131	<	FortranHmat[3*j + i] = Hmat[i][j];
132	<	FortranHmatInv[3*j + i] = HmatInv[i][j];
311	>	unsigned int SimInfo::getNLocalCutoffGroups(){
312	>	int nLocalCutoffAtoms = 0;
313	>	Molecule* mol;
314	>	MoleculeIterator mi;
315	>	CutoffGroup* cg;
316	>	Molecule::CutoffGroupIterator ci;
317	>
318	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
319	>
320	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
321	>	cg = mol->nextCutoffGroup(ci)) {
322	>	nLocalCutoffAtoms += cg->getNumAtom();
323	>
324	>	}
325		}
326	+
327	+	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
328		}
329	+
330	+	void SimInfo::calcNdfRaw() {
331	+	int ndfRaw_local;
332
333	<	setFortranBox(FortranHmat, FortranHmatInv, &orthoRhombic);
334	<
335	<	}
336	<
333	>	MoleculeIterator i;
334	>	vector<StuntDouble*>::iterator j;
335	>	Molecule* mol;
336	>	StuntDouble* sd;
337
338	<	void SimInfo::getBoxM (double theBox[3][3]) {
338	>	// Raw degrees of freedom that we have to set
339	>	ndfRaw_local = 0;
340	>
341	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
342
343	<	int i, j;
344	<	for(i=0; i<3; i++)
145	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
146	<	}
343	>	for (sd = mol->beginIntegrableObject(j); sd != NULL;
344	>	sd = mol->nextIntegrableObject(j)) {
345
346	+	ndfRaw_local += 3;
347
348	<	void SimInfo::scaleBox(double scale) {
349	<	double theBox[3][3];
350	<	int i, j;
348	>	if (sd->isDirectional()) {
349	>	if (sd->isLinear()) {
350	>	ndfRaw_local += 2;
351	>	} else {
352	>	ndfRaw_local += 3;
353	>	}
354	>	}
355	>
356	>	}
357	>	}
358	>
359	>	#ifdef IS_MPI
360	>	MPI_Allreduce(&ndfRaw_local, &ndfRaw_, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
361	>	// MPI::COMM_WORLD.Allreduce(&ndfRaw_local, &ndfRaw_, 1, MPI::INT, MPI::SUM);
362	>	#else
363	>	ndfRaw_ = ndfRaw_local;
364	>	#endif
365	>	}
366
367	<	// cerr << "Scaling box by " << scale << "\n";
367	>	void SimInfo::calcNdfTrans() {
368	>	int ndfTrans_local;
369
370	<	for(i=0; i<3; i++)
156	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
370	>	ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
371
158	–	setBoxM(theBox);
372
373	<	}
373	>	#ifdef IS_MPI
374	>	MPI_Allreduce(&ndfTrans_local, &ndfTrans_, 1,
375	>	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
376	>	// MPI::COMM_WORLD.Allreduce(&ndfTrans_local, &ndfTrans_, 1,
377	>	//                           MPI::INT, MPI::SUM);
378	>	#else
379	>	ndfTrans_ = ndfTrans_local;
380	>	#endif
381
382	<	void SimInfo::calcHmatInv( void ) {
383	<
384	<	int oldOrtho;
165	<	int i,j;
166	<	double smallDiag;
167	<	double tol;
168	<	double sanity[3][3];
382	>	ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
383	>
384	>	}
385
386	<	invertMat3( Hmat, HmatInv );
386	>	void SimInfo::addInteractionPairs(Molecule* mol) {
387	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
388	>	vector<Bond*>::iterator bondIter;
389	>	vector<Bend*>::iterator bendIter;
390	>	vector<Torsion*>::iterator torsionIter;
391	>	vector<Inversion*>::iterator inversionIter;
392	>	Bond* bond;
393	>	Bend* bend;
394	>	Torsion* torsion;
395	>	Inversion* inversion;
396	>	int a;
397	>	int b;
398	>	int c;
399	>	int d;
400
401	<	// check to see if Hmat is orthorhombic
402	<
403	<	oldOrtho = orthoRhombic;
401	>	// atomGroups can be used to add special interaction maps between
402	>	// groups of atoms that are in two separate rigid bodies.
403	>	// However, most site-site interactions between two rigid bodies
404	>	// are probably not special, just the ones between the physically
405	>	// bonded atoms.  Interactions *within* a single rigid body should
406	>	// always be excluded.  These are done at the bottom of this
407	>	// function.
408
409	<	smallDiag = fabs(Hmat[0][0]);
410	<	if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
411	<	if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
412	<	tol = smallDiag * orthoTolerance;
409	>	map<int, set<int> > atomGroups;
410	>	Molecule::RigidBodyIterator rbIter;
411	>	RigidBody* rb;
412	>	Molecule::IntegrableObjectIterator ii;
413	>	StuntDouble* sd;
414	>
415	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
416	>	sd = mol->nextIntegrableObject(ii)) {
417	>
418	>	if (sd->isRigidBody()) {
419	>	rb = static_cast<RigidBody*>(sd);
420	>	vector<Atom*> atoms = rb->getAtoms();
421	>	set<int> rigidAtoms;
422	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
423	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
424	>	}
425	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
426	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
427	>	}
428	>	} else {
429	>	set<int> oneAtomSet;
430	>	oneAtomSet.insert(sd->getGlobalIndex());
431	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
432	>	}
433	>	}
434
435	<	orthoRhombic = 1;
436	<
437	<	for (i = 0; i < 3; i++ ) {
438	<	for (j = 0 ; j < 3; j++) {
439	<	if (i != j) {
440	<	if (orthoRhombic) {
441	<	if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
442	<	}
435	>
436	>	for (bond= mol->beginBond(bondIter); bond != NULL;
437	>	bond = mol->nextBond(bondIter)) {
438	>
439	>	a = bond->getAtomA()->getGlobalIndex();
440	>	b = bond->getAtomB()->getGlobalIndex();
441	>
442	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
443	>	oneTwoInteractions_.addPair(a, b);
444	>	} else {
445	>	excludedInteractions_.addPair(a, b);
446		}
447		}
191	–	}
448
449	<	if( oldOrtho != orthoRhombic ){
450	<
195	<	if( orthoRhombic ) {
196	<	sprintf( painCave.errMsg,
197	<	"OOPSE is switching from the default Non-Orthorhombic\n"
198	<	"\tto the faster Orthorhombic periodic boundary computations.\n"
199	<	"\tThis is usually a good thing, but if you wan't the\n"
200	<	"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
201	<	"\tvariable ( currently set to %G ) smaller.\n",
202	<	orthoTolerance);
203	<	painCave.severity = OOPSE_INFO;
204	<	simError();
205	<	}
206	<	else {
207	<	sprintf( painCave.errMsg,
208	<	"OOPSE is switching from the faster Orthorhombic to the more\n"
209	<	"\tflexible Non-Orthorhombic periodic boundary computations.\n"
210	<	"\tThis is usually because the box has deformed under\n"
211	<	"\tNPTf integration. If you wan't to live on the edge with\n"
212	<	"\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
213	<	"\tvariable ( currently set to %G ) larger.\n",
214	<	orthoTolerance);
215	<	painCave.severity = OOPSE_WARNING;
216	<	simError();
217	<	}
218	<	}
219	<	}
449	>	for (bend= mol->beginBend(bendIter); bend != NULL;
450	>	bend = mol->nextBend(bendIter)) {
451
452	<	void SimInfo::calcBoxL( void ){
452	>	a = bend->getAtomA()->getGlobalIndex();
453	>	b = bend->getAtomB()->getGlobalIndex();
454	>	c = bend->getAtomC()->getGlobalIndex();
455	>
456	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
457	>	oneTwoInteractions_.addPair(a, b);
458	>	oneTwoInteractions_.addPair(b, c);
459	>	} else {
460	>	excludedInteractions_.addPair(a, b);
461	>	excludedInteractions_.addPair(b, c);
462	>	}
463
464	<	double dx, dy, dz, dsq;
464	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
465	>	oneThreeInteractions_.addPair(a, c);
466	>	} else {
467	>	excludedInteractions_.addPair(a, c);
468	>	}
469	>	}
470
471	<	// boxVol = Determinant of Hmat
471	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
472	>	torsion = mol->nextTorsion(torsionIter)) {
473
474	<	boxVol = matDet3( Hmat );
474	>	a = torsion->getAtomA()->getGlobalIndex();
475	>	b = torsion->getAtomB()->getGlobalIndex();
476	>	c = torsion->getAtomC()->getGlobalIndex();
477	>	d = torsion->getAtomD()->getGlobalIndex();
478
479	<	// boxLx
480	<
481	<	dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
482	<	dsq = dx*dx + dy*dy + dz*dz;
483	<	boxL[0] = sqrt( dsq );
484	<	//maxCutoff = 0.5 * boxL[0];
479	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
480	>	oneTwoInteractions_.addPair(a, b);
481	>	oneTwoInteractions_.addPair(b, c);
482	>	oneTwoInteractions_.addPair(c, d);
483	>	} else {
484	>	excludedInteractions_.addPair(a, b);
485	>	excludedInteractions_.addPair(b, c);
486	>	excludedInteractions_.addPair(c, d);
487	>	}
488
489	<	// boxLy
490	<
491	<	dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
492	<	dsq = dx*dx + dy*dy + dz*dz;
493	<	boxL[1] = sqrt( dsq );
494	<	//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
489	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
490	>	oneThreeInteractions_.addPair(a, c);
491	>	oneThreeInteractions_.addPair(b, d);
492	>	} else {
493	>	excludedInteractions_.addPair(a, c);
494	>	excludedInteractions_.addPair(b, d);
495	>	}
496
497	+	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
498	+	oneFourInteractions_.addPair(a, d);
499	+	} else {
500	+	excludedInteractions_.addPair(a, d);
501	+	}
502	+	}
503
504	<	// boxLz
505	<
246	<	dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
247	<	dsq = dx*dx + dy*dy + dz*dz;
248	<	boxL[2] = sqrt( dsq );
249	<	//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
504	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
505	>	inversion = mol->nextInversion(inversionIter)) {
506
507	<	//calculate the max cutoff
508	<	maxCutoff =  calcMaxCutOff();
509	<
510	<	checkCutOffs();
507	>	a = inversion->getAtomA()->getGlobalIndex();
508	>	b = inversion->getAtomB()->getGlobalIndex();
509	>	c = inversion->getAtomC()->getGlobalIndex();
510	>	d = inversion->getAtomD()->getGlobalIndex();
511
512	<	}
512	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
513	>	oneTwoInteractions_.addPair(a, b);
514	>	oneTwoInteractions_.addPair(a, c);
515	>	oneTwoInteractions_.addPair(a, d);
516	>	} else {
517	>	excludedInteractions_.addPair(a, b);
518	>	excludedInteractions_.addPair(a, c);
519	>	excludedInteractions_.addPair(a, d);
520	>	}
521
522	+	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
523	+	oneThreeInteractions_.addPair(b, c);
524	+	oneThreeInteractions_.addPair(b, d);
525	+	oneThreeInteractions_.addPair(c, d);
526	+	} else {
527	+	excludedInteractions_.addPair(b, c);
528	+	excludedInteractions_.addPair(b, d);
529	+	excludedInteractions_.addPair(c, d);
530	+	}
531	+	}
532
533	<	double SimInfo::calcMaxCutOff(){
533	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
534	>	rb = mol->nextRigidBody(rbIter)) {
535	>	vector<Atom*> atoms = rb->getAtoms();
536	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
537	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
538	>	a = atoms[i]->getGlobalIndex();
539	>	b = atoms[j]->getGlobalIndex();
540	>	excludedInteractions_.addPair(a, b);
541	>	}
542	>	}
543	>	}
544
545	<	double ri[3], rj[3], rk[3];
262	<	double rij[3], rjk[3], rki[3];
263	<	double minDist;
545	>	}
546
547	<	ri[0] = Hmat[0][0];
548	<	ri[1] = Hmat[1][0];
549	<	ri[2] = Hmat[2][0];
547	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
548	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
549	>	vector<Bond*>::iterator bondIter;
550	>	vector<Bend*>::iterator bendIter;
551	>	vector<Torsion*>::iterator torsionIter;
552	>	vector<Inversion*>::iterator inversionIter;
553	>	Bond* bond;
554	>	Bend* bend;
555	>	Torsion* torsion;
556	>	Inversion* inversion;
557	>	int a;
558	>	int b;
559	>	int c;
560	>	int d;
561
562	<	rj[0] = Hmat[0][1];
563	<	rj[1] = Hmat[1][1];
564	<	rj[2] = Hmat[2][1];
562	>	map<int, set<int> > atomGroups;
563	>	Molecule::RigidBodyIterator rbIter;
564	>	RigidBody* rb;
565	>	Molecule::IntegrableObjectIterator ii;
566	>	StuntDouble* sd;
567	>
568	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
569	>	sd = mol->nextIntegrableObject(ii)) {
570	>
571	>	if (sd->isRigidBody()) {
572	>	rb = static_cast<RigidBody*>(sd);
573	>	vector<Atom*> atoms = rb->getAtoms();
574	>	set<int> rigidAtoms;
575	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
576	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
577	>	}
578	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
579	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
580	>	}
581	>	} else {
582	>	set<int> oneAtomSet;
583	>	oneAtomSet.insert(sd->getGlobalIndex());
584	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
585	>	}
586	>	}
587
588	<	rk[0] = Hmat[0][2];
589	<	rk[1] = Hmat[1][2];
590	<	rk[2] = Hmat[2][2];
588	>	for (bond= mol->beginBond(bondIter); bond != NULL;
589	>	bond = mol->nextBond(bondIter)) {
590	>
591	>	a = bond->getAtomA()->getGlobalIndex();
592	>	b = bond->getAtomB()->getGlobalIndex();
593
594	<	crossProduct3(ri, rj, rij);
595	<	distXY = dotProduct3(rk,rij) / norm3(rij);
594	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
595	>	oneTwoInteractions_.removePair(a, b);
596	>	} else {
597	>	excludedInteractions_.removePair(a, b);
598	>	}
599	>	}
600
601	<	crossProduct3(rj,rk, rjk);
602	<	distYZ = dotProduct3(ri,rjk) / norm3(rjk);
601	>	for (bend= mol->beginBend(bendIter); bend != NULL;
602	>	bend = mol->nextBend(bendIter)) {
603
604	<	crossProduct3(rk,ri, rki);
605	<	distZX = dotProduct3(rj,rki) / norm3(rki);
604	>	a = bend->getAtomA()->getGlobalIndex();
605	>	b = bend->getAtomB()->getGlobalIndex();
606	>	c = bend->getAtomC()->getGlobalIndex();
607	>
608	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
609	>	oneTwoInteractions_.removePair(a, b);
610	>	oneTwoInteractions_.removePair(b, c);
611	>	} else {
612	>	excludedInteractions_.removePair(a, b);
613	>	excludedInteractions_.removePair(b, c);
614	>	}
615
616	<	minDist = min(min(distXY, distYZ), distZX);
617	<	return minDist/2;
618	<
619	<	}
616	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
617	>	oneThreeInteractions_.removePair(a, c);
618	>	} else {
619	>	excludedInteractions_.removePair(a, c);
620	>	}
621	>	}
622
623	<	void SimInfo::wrapVector( double thePos[3] ){
623	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
624	>	torsion = mol->nextTorsion(torsionIter)) {
625
626	<	int i;
627	<	double scaled[3];
626	>	a = torsion->getAtomA()->getGlobalIndex();
627	>	b = torsion->getAtomB()->getGlobalIndex();
628	>	c = torsion->getAtomC()->getGlobalIndex();
629	>	d = torsion->getAtomD()->getGlobalIndex();
630	>
631	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
632	>	oneTwoInteractions_.removePair(a, b);
633	>	oneTwoInteractions_.removePair(b, c);
634	>	oneTwoInteractions_.removePair(c, d);
635	>	} else {
636	>	excludedInteractions_.removePair(a, b);
637	>	excludedInteractions_.removePair(b, c);
638	>	excludedInteractions_.removePair(c, d);
639	>	}
640
641	<	if( !orthoRhombic ){
642	<	// calc the scaled coordinates.
643	<
641	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
642	>	oneThreeInteractions_.removePair(a, c);
643	>	oneThreeInteractions_.removePair(b, d);
644	>	} else {
645	>	excludedInteractions_.removePair(a, c);
646	>	excludedInteractions_.removePair(b, d);
647	>	}
648
649	<	matVecMul3(HmatInv, thePos, scaled);
650	<
651	<	for(i=0; i<3; i++)
652	<	scaled[i] -= roundMe(scaled[i]);
653	<
654	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
306	<
307	<	matVecMul3(Hmat, scaled, thePos);
649	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
650	>	oneFourInteractions_.removePair(a, d);
651	>	} else {
652	>	excludedInteractions_.removePair(a, d);
653	>	}
654	>	}
655
656	<	}
657	<	else{
658	<	// calc the scaled coordinates.
656	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
657	>	inversion = mol->nextInversion(inversionIter)) {
658	>
659	>	a = inversion->getAtomA()->getGlobalIndex();
660	>	b = inversion->getAtomB()->getGlobalIndex();
661	>	c = inversion->getAtomC()->getGlobalIndex();
662	>	d = inversion->getAtomD()->getGlobalIndex();
663	>
664	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
665	>	oneTwoInteractions_.removePair(a, b);
666	>	oneTwoInteractions_.removePair(a, c);
667	>	oneTwoInteractions_.removePair(a, d);
668	>	} else {
669	>	excludedInteractions_.removePair(a, b);
670	>	excludedInteractions_.removePair(a, c);
671	>	excludedInteractions_.removePair(a, d);
672	>	}
673	>
674	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
675	>	oneThreeInteractions_.removePair(b, c);
676	>	oneThreeInteractions_.removePair(b, d);
677	>	oneThreeInteractions_.removePair(c, d);
678	>	} else {
679	>	excludedInteractions_.removePair(b, c);
680	>	excludedInteractions_.removePair(b, d);
681	>	excludedInteractions_.removePair(c, d);
682	>	}
683	>	}
684	>
685	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
686	>	rb = mol->nextRigidBody(rbIter)) {
687	>	vector<Atom*> atoms = rb->getAtoms();
688	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
689	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
690	>	a = atoms[i]->getGlobalIndex();
691	>	b = atoms[j]->getGlobalIndex();
692	>	excludedInteractions_.removePair(a, b);
693	>	}
694	>	}
695	>	}
696
313	–	for(i=0; i<3; i++)
314	–	scaled[i] = thePos[i]*HmatInv[i][i];
315	–
316	–	// wrap the scaled coordinates
317	–
318	–	for(i=0; i<3; i++)
319	–	scaled[i] -= roundMe(scaled[i]);
320	–
321	–	// calc the wrapped real coordinates from the wrapped scaled coordinates
322	–
323	–	for(i=0; i<3; i++)
324	–	thePos[i] = scaled[i]*Hmat[i][i];
697		}
698	+
699	+
700	+	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
701	+	int curStampId;
702
703	<	}
703	>	//index from 0
704	>	curStampId = moleculeStamps_.size();
705
706	+	moleculeStamps_.push_back(molStamp);
707	+	molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
708	+	}
709
330	–	int SimInfo::getNDF(){
331	–	int ndf_local;
710
711	<	ndf_local = 0;
712	<
713	<	for(int i = 0; i < integrableObjects.size(); i++){
714	<	ndf_local += 3;
715	<	if (integrableObjects[i]->isDirectional()) {
716	<	if (integrableObjects[i]->isLinear())
717	<	ndf_local += 2;
718	<	else
719	<	ndf_local += 3;
720	<	}
711	>	/**
712	>	* update
713	>	*
714	>	*  Performs the global checks and variable settings after the
715	>	*  objects have been created.
716	>	*
717	>	*/
718	>	void SimInfo::update() {
719	>	setupSimVariables();
720	>	calcNdf();
721	>	calcNdfRaw();
722	>	calcNdfTrans();
723		}
724	+
725	+	/**
726	+	* getSimulatedAtomTypes
727	+	*
728	+	* Returns an STL set of AtomType* that are actually present in this
729	+	* simulation.  Must query all processors to assemble this information.
730	+	*
731	+	*/
732	+	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
733	+	SimInfo::MoleculeIterator mi;
734	+	Molecule* mol;
735	+	Molecule::AtomIterator ai;
736	+	Atom* atom;
737	+	set<AtomType*> atomTypes;
738	+
739	+	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
740	+	for(atom = mol->beginAtom(ai); atom != NULL;
741	+	atom = mol->nextAtom(ai)) {
742	+	atomTypes.insert(atom->getAtomType());
743	+	}
744	+	}
745	+
746	+	#ifdef IS_MPI
747
748	<	// n_constraints is local, so subtract them on each processor:
748	>	// loop over the found atom types on this processor, and add their
749	>	// numerical idents to a vector:
750	>
751	>	vector<int> foundTypes;
752	>	set<AtomType*>::iterator i;
753	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
754	>	foundTypes.push_back( (*i)->getIdent() );
755
756	<	ndf_local -= n_constraints;
756	>	// count_local holds the number of found types on this processor
757	>	int count_local = foundTypes.size();
758
759	<	#ifdef IS_MPI
760	<	MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
761	<	#else
352	<	ndf = ndf_local;
353	<	#endif
759	>	int nproc;
760	>	MPI_Comm_size( MPI_COMM_WORLD, &nproc);
761	>	// int nproc = MPI::COMM_WORLD.Get_size();
762
763	<	// nZconstraints is global, as are the 3 COM translations for the
764	<	// entire system:
763	>	// we need arrays to hold the counts and displacement vectors for
764	>	// all processors
765	>	vector<int> counts(nproc, 0);
766	>	vector<int> disps(nproc, 0);
767
768	<	ndf = ndf - 3 - nZconstraints;
768	>	// fill the counts array
769	>	MPI_Allgather(&count_local, 1, MPI_INT, &counts[0],
770	>	1, MPI_INT, MPI_COMM_WORLD);
771	>	// MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
772	>	//                           1, MPI::INT);
773	>
774	>	// use the processor counts to compute the displacement array
775	>	disps[0] = 0;
776	>	int totalCount = counts[0];
777	>	for (int iproc = 1; iproc < nproc; iproc++) {
778	>	disps[iproc] = disps[iproc-1] + counts[iproc-1];
779	>	totalCount += counts[iproc];
780	>	}
781
782	<	return ndf;
783	<	}
782	>	// we need a (possibly redundant) set of all found types:
783	>	vector<int> ftGlobal(totalCount);
784	>
785	>	// now spray out the foundTypes to all the other processors:
786	>	MPI_Allgatherv(&foundTypes[0], count_local, MPI_INT,
787	>	&ftGlobal[0], &counts[0], &disps[0],
788	>	MPI_INT, MPI_COMM_WORLD);
789	>	// MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
790	>	//                            &ftGlobal[0], &counts[0], &disps[0],
791	>	//                            MPI::INT);
792
793	<	int SimInfo::getNDFraw() {
364	<	int ndfRaw_local;
793	>	vector<int>::iterator j;
794
795	<	// Raw degrees of freedom that we have to set
796	<	ndfRaw_local = 0;
795	>	// foundIdents is a stl set, so inserting an already found ident
796	>	// will have no effect.
797	>	set<int> foundIdents;
798
799	<	for(int i = 0; i < integrableObjects.size(); i++){
800	<	ndfRaw_local += 3;
371	<	if (integrableObjects[i]->isDirectional()) {
372	<	if (integrableObjects[i]->isLinear())
373	<	ndfRaw_local += 2;
374	<	else
375	<	ndfRaw_local += 3;
376	<	}
377	<	}
799	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
800	>	foundIdents.insert((*j));
801
802	<	#ifdef IS_MPI
803	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
804	<	#else
805	<	ndfRaw = ndfRaw_local;
802	>	// now iterate over the foundIdents and get the actual atom types
803	>	// that correspond to these:
804	>	set<int>::iterator it;
805	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
806	>	atomTypes.insert( forceField_->getAtomType((*it)) );
807	>
808		#endif
809
810	<	return ndfRaw;
811	<	}
810	>	return atomTypes;
811	>	}
812
388	–	int SimInfo::getNDFtranslational() {
389	–	int ndfTrans_local;
813
814	<	ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
814	>	int getGlobalCountOfType(AtomType* atype) {
815	>	/*
816	>	set<AtomType*> atypes = getSimulatedAtomTypes();
817	>	map<AtomType*, int> counts_;
818
819	+	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
820	+	for(atom = mol->beginAtom(ai); atom != NULL;
821	+	atom = mol->nextAtom(ai)) {
822	+	atom->getAtomType();
823	+	}
824	+	}
825	+	*/
826	+	return 0;
827	+	}
828
829	+	void SimInfo::setupSimVariables() {
830	+	useAtomicVirial_ = simParams_->getUseAtomicVirial();
831	+	// we only call setAccumulateBoxDipole if the accumulateBoxDipole
832	+	// parameter is true
833	+	calcBoxDipole_ = false;
834	+	if ( simParams_->haveAccumulateBoxDipole() )
835	+	if ( simParams_->getAccumulateBoxDipole() ) {
836	+	calcBoxDipole_ = true;
837	+	}
838	+
839	+	set<AtomType*>::iterator i;
840	+	set<AtomType*> atomTypes;
841	+	atomTypes = getSimulatedAtomTypes();
842	+	bool usesElectrostatic = false;
843	+	bool usesMetallic = false;
844	+	bool usesDirectional = false;
845	+	bool usesFluctuatingCharges =  false;
846	+	//loop over all of the atom types
847	+	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
848	+	usesElectrostatic |= (*i)->isElectrostatic();
849	+	usesMetallic |= (*i)->isMetal();
850	+	usesDirectional |= (*i)->isDirectional();
851	+	usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
852	+	}
853	+
854		#ifdef IS_MPI
855	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
396	<	#else
397	<	ndfTrans = ndfTrans_local;
398	<	#endif
855	>	int temp;
856
857	<	ndfTrans = ndfTrans - 3 - nZconstraints;
857	>	temp = usesDirectional;
858	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
859	>	usesDirectionalAtoms_ = (temp == 0) ? false : true;
860
861	<	return ndfTrans;
862	<	}
861	>	// MPI::COMM_WORLD.Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI::BOOL,
862	>	//                           MPI::LOR);
863	>
864	>	temp = usesMetallic;
865	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
866	>	usesMetallicAtoms_ = (temp == 0) ? false : true;
867
868	<	int SimInfo::getTotIntegrableObjects() {
869	<	int nObjs_local;
870	<	int nObjs;
868	>	// MPI::COMM_WORLD.Allreduce(&temp, &usesMetallicAtoms_, 1, MPI::BOOL,
869	>	//                           MPI::LOR);
870	>
871	>	temp = usesElectrostatic;
872	>	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
873	>	usesElectrostaticAtoms_ = (temp == 0) ? false : true;
874
875	<	nObjs_local =  integrableObjects.size();
875	>	// MPI::COMM_WORLD.Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI::BOOL,
876	>	//                           MPI::LOR);
877
878	+	temp = usesFluctuatingCharges;
879	+	MPI_Allreduce(MPI_IN_PLACE, &temp, 1, MPI_INT,  MPI_LOR, MPI_COMM_WORLD);
880	+	usesFluctuatingCharges_ = (temp == 0) ? false : true;
881
882	<	#ifdef IS_MPI
883	<	MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
882	>	// MPI::COMM_WORLD.Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI::BOOL,
883	>	//                           MPI::LOR);
884	>
885		#else
415	–	nObjs = nObjs_local;
416	–	#endif
886
887	+	usesDirectionalAtoms_ = usesDirectional;
888	+	usesMetallicAtoms_ = usesMetallic;
889	+	usesElectrostaticAtoms_ = usesElectrostatic;
890	+	usesFluctuatingCharges_ = usesFluctuatingCharges;
891
892	<	return nObjs;
893	<	}
892	>	#endif
893	>
894	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
895	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
896	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
897	>	}
898
422	–	void SimInfo::refreshSim(){
899
900	<	simtype fInfo;
901	<	int isError;
902	<	int n_global;
903	<	int* excl;
900	>	vector<int> SimInfo::getGlobalAtomIndices() {
901	>	SimInfo::MoleculeIterator mi;
902	>	Molecule* mol;
903	>	Molecule::AtomIterator ai;
904	>	Atom* atom;
905
906	<	fInfo.dielect = 0.0;
907	<
908	<	if( useDipoles ){
909	<	if( useReactionField )fInfo.dielect = dielectric;
906	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
907	>
908	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
909	>
910	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
911	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
912	>	}
913	>	}
914	>	return GlobalAtomIndices;
915		}
916
435	–	fInfo.SIM_uses_PBC = usePBC;
436	–	//fInfo.SIM_uses_LJ = 0;
437	–	fInfo.SIM_uses_LJ = useLJ;
438	–	fInfo.SIM_uses_sticky = useSticky;
439	–	//fInfo.SIM_uses_sticky = 0;
440	–	fInfo.SIM_uses_charges = useCharges;
441	–	fInfo.SIM_uses_dipoles = useDipoles;
442	–	//fInfo.SIM_uses_dipoles = 0;
443	–	fInfo.SIM_uses_RF = useReactionField;
444	–	//fInfo.SIM_uses_RF = 0;
445	–	fInfo.SIM_uses_GB = useGB;
446	–	fInfo.SIM_uses_EAM = useEAM;
917
918	<	n_exclude = excludes->getSize();
919	<	excl = excludes->getFortranArray();
920	<
921	<	#ifdef IS_MPI
922	<	n_global = mpiSim->getNAtomsGlobal();
453	<	#else
454	<	n_global = n_atoms;
455	<	#endif
456	<
457	<	isError = 0;
458	<
459	<	getFortranGroupArrays(this, FglobalGroupMembership, mfact);
460	<	//it may not be a good idea to pass the address of first element in vector
461	<	//since c++ standard does not require vector to be stored continuously in meomory
462	<	//Most of the compilers will organize the memory of vector continuously
463	<	setFortranSim( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
464	<	&nGlobalExcludes, globalExcludes, molMembershipArray,
465	<	&mfact[0], &ngroup, &FglobalGroupMembership[0], &isError);
918	>	vector<int> SimInfo::getGlobalGroupIndices() {
919	>	SimInfo::MoleculeIterator mi;
920	>	Molecule* mol;
921	>	Molecule::CutoffGroupIterator ci;
922	>	CutoffGroup* cg;
923
924	<	if( isError ){
924	>	vector<int> GlobalGroupIndices;
925
926	<	sprintf( painCave.errMsg,
927	<	"There was an error setting the simulation information in fortran.\n" );
928	<	painCave.isFatal = 1;
929	<	painCave.severity = OOPSE_ERROR;
930	<	simError();
926	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
927	>
928	>	//local index of cutoff group is trivial, it only depends on the
929	>	//order of travesing
930	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
931	>	cg = mol->nextCutoffGroup(ci)) {
932	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
933	>	}
934	>	}
935	>	return GlobalGroupIndices;
936		}
475	–
476	–	#ifdef IS_MPI
477	–	sprintf( checkPointMsg,
478	–	"succesfully sent the simulation information to fortran.\n");
479	–	MPIcheckPoint();
480	–	#endif // is_mpi
481	–
482	–	this->ndf = this->getNDF();
483	–	this->ndfRaw = this->getNDFraw();
484	–	this->ndfTrans = this->getNDFtranslational();
485	–	}
937
487	–	void SimInfo::setDefaultRcut( double theRcut ){
488	–
489	–	haveRcut = 1;
490	–	rCut = theRcut;
491	–	rList = rCut + 1.0;
492	–
493	–	notifyFortranCutoffs( &rCut, &rSw, &rList );
494	–	}
938
939	<	void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
939	>	void SimInfo::prepareTopology() {
940
941	<	rSw = theRsw;
942	<	setDefaultRcut( theRcut );
943	<	}
941	>	//calculate mass ratio of cutoff group
942	>	SimInfo::MoleculeIterator mi;
943	>	Molecule* mol;
944	>	Molecule::CutoffGroupIterator ci;
945	>	CutoffGroup* cg;
946	>	Molecule::AtomIterator ai;
947	>	Atom* atom;
948	>	RealType totalMass;
949
950	<
951	<	void SimInfo::checkCutOffs( void ){
952	<
953	<	if( boxIsInit ){
950	>	/**
951	>	* The mass factor is the relative mass of an atom to the total
952	>	* mass of the cutoff group it belongs to.  By default, all atoms
953	>	* are their own cutoff groups, and therefore have mass factors of
954	>	* 1.  We need some special handling for massless atoms, which
955	>	* will be treated as carrying the entire mass of the cutoff
956	>	* group.
957	>	*/
958	>	massFactors_.clear();
959	>	massFactors_.resize(getNAtoms(), 1.0);
960
961	<	//we need to check cutOffs against the box
962	<
963	<	if( rCut > maxCutoff ){
964	<	sprintf( painCave.errMsg,
965	<	"cutoffRadius is too large for the current periodic box.\n"
966	<	"\tCurrent Value of cutoffRadius = %G at time %G\n "
967	<	"\tThis is larger than half of at least one of the\n"
968	<	"\tperiodic box vectors.  Right now, the Box matrix is:\n"
969	<	"\n"
970	<	"\t[ %G %G %G ]\n"
971	<	"\t[ %G %G %G ]\n"
972	<	"\t[ %G %G %G ]\n",
973	<	rCut, currentTime,
974	<	Hmat[0][0], Hmat[0][1], Hmat[0][2],
975	<	Hmat[1][0], Hmat[1][1], Hmat[1][2],
976	<	Hmat[2][0], Hmat[2][1], Hmat[2][2]);
977	<	painCave.severity = OOPSE_ERROR;
978	<	painCave.isFatal = 1;
979	<	simError();
961	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
962	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
963	>	cg = mol->nextCutoffGroup(ci)) {
964	>
965	>	totalMass = cg->getMass();
966	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
967	>	// Check for massless groups - set mfact to 1 if true
968	>	if (totalMass != 0)
969	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
970	>	else
971	>	massFactors_[atom->getLocalIndex()] = 1.0;
972	>	}
973	>	}
974	>	}
975	>
976	>	// Build the identArray_ and regions_
977	>
978	>	identArray_.clear();
979	>	identArray_.reserve(getNAtoms());
980	>	regions_.clear();
981	>	regions_.reserve(getNAtoms());
982	>
983	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
984	>	int reg = mol->getRegion();
985	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
986	>	identArray_.push_back(atom->getIdent());
987	>	regions_.push_back(reg);
988	>	}
989		}
990	<	} else {
991	<	// initialize this stuff before using it, OK?
529	<	sprintf( painCave.errMsg,
530	<	"Trying to check cutoffs without a box.\n"
531	<	"\tOOPSE should have better programmers than that.\n" );
532	<	painCave.severity = OOPSE_ERROR;
533	<	painCave.isFatal = 1;
534	<	simError();
990	>
991	>	topologyDone_ = true;
992		}
536	–
537	–	}
993
994	<	void SimInfo::addProperty(GenericData* prop){
994	>	void SimInfo::addProperty(GenericData* genData) {
995	>	properties_.addProperty(genData);
996	>	}
997
998	<	map<string, GenericData*>::iterator result;
999	<	result = properties.find(prop->getID());
543	<
544	<	//we can't simply use  properties[prop->getID()] = prop,
545	<	//it will cause memory leak if we already contain a propery which has the same name of prop
546	<
547	<	if(result != properties.end()){
548	<
549	<	delete (*result).second;
550	<	(*result).second = prop;
551	<
998	>	void SimInfo::removeProperty(const string& propName) {
999	>	properties_.removeProperty(propName);
1000		}
553	–	else{
1001
1002	<	properties[prop->getID()] = prop;
1002	>	void SimInfo::clearProperties() {
1003	>	properties_.clearProperties();
1004	>	}
1005
1006	+	vector<string> SimInfo::getPropertyNames() {
1007	+	return properties_.getPropertyNames();
1008		}
1009	<
1010	<	}
1009	>
1010	>	vector<GenericData*> SimInfo::getProperties() {
1011	>	return properties_.getProperties();
1012	>	}
1013
1014	<	GenericData* SimInfo::getProperty(const string& propName){
1014	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
1015	>	return properties_.getPropertyByName(propName);
1016	>	}
1017	>
1018	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1019	>	if (sman_ == sman) {
1020	>	return;
1021	>	}
1022	>	delete sman_;
1023	>	sman_ = sman;
1024	>
1025	>	SimInfo::MoleculeIterator mi;
1026	>	Molecule::AtomIterator ai;
1027	>	Molecule::RigidBodyIterator rbIter;
1028	>	Molecule::CutoffGroupIterator cgIter;
1029	>	Molecule::BondIterator bondIter;
1030	>	Molecule::BendIterator bendIter;
1031	>	Molecule::TorsionIterator torsionIter;
1032	>	Molecule::InversionIterator inversionIter;
1033
1034	<	map<string, GenericData*>::iterator result;
1035	<
1036	<	//string lowerCaseName = ();
1037	<
1038	<	result = properties.find(propName);
1039	<
1040	<	if(result != properties.end())
1041	<	return (*result).second;
571	<	else
572	<	return NULL;
573	<	}
1034	>	Molecule* mol;
1035	>	Atom* atom;
1036	>	RigidBody* rb;
1037	>	CutoffGroup* cg;
1038	>	Bond* bond;
1039	>	Bend* bend;
1040	>	Torsion* torsion;
1041	>	Inversion* inversion;
1042
1043	+	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1044	+
1045	+	for (atom = mol->beginAtom(ai); atom != NULL;
1046	+	atom = mol->nextAtom(ai)) {
1047	+	atom->setSnapshotManager(sman_);
1048	+	}
1049	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
1050	+	rb = mol->nextRigidBody(rbIter)) {
1051	+	rb->setSnapshotManager(sman_);
1052	+	}
1053	+	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL;
1054	+	cg = mol->nextCutoffGroup(cgIter)) {
1055	+	cg->setSnapshotManager(sman_);
1056	+	}
1057	+	for (bond = mol->beginBond(bondIter); bond != NULL;
1058	+	bond = mol->nextBond(bondIter)) {
1059	+	bond->setSnapshotManager(sman_);
1060	+	}
1061	+	for (bend = mol->beginBend(bendIter); bend != NULL;
1062	+	bend = mol->nextBend(bendIter)) {
1063	+	bend->setSnapshotManager(sman_);
1064	+	}
1065	+	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
1066	+	torsion = mol->nextTorsion(torsionIter)) {
1067	+	torsion->setSnapshotManager(sman_);
1068	+	}
1069	+	for (inversion = mol->beginInversion(inversionIter); inversion != NULL;
1070	+	inversion = mol->nextInversion(inversionIter)) {
1071	+	inversion->setSnapshotManager(sman_);
1072	+	}
1073	+	}
1074	+	}
1075
1076	<	void SimInfo::getFortranGroupArrays(SimInfo* info,
1077	<	vector<int>& FglobalGroupMembership,
1078	<	vector<double>& mfact){
1076	>
1077	>	ostream& operator <<(ostream& o, SimInfo& info) {
1078	>
1079	>	return o;
1080	>	}
1081	>
1082
1083	<	Molecule* myMols;
1084	<	Atom** myAtoms;
1085	<	int numAtom;
1086	<	double mtot;
1087	<	int numMol;
1088	<	int numCutoffGroups;
1089	<	CutoffGroup* myCutoffGroup;
1090	<	vector<CutoffGroup*>::iterator iterCutoff;
1091	<	Atom* cutoffAtom;
1092	<	vector<Atom*>::iterator iterAtom;
1093	<	int atomIndex;
591	<	double totalMass;
1083	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1084	>	if (index >= int(IOIndexToIntegrableObject.size())) {
1085	>	sprintf(painCave.errMsg,
1086	>	"SimInfo::getIOIndexToIntegrableObject Error: Integrable Object\n"
1087	>	"\tindex exceeds number of known objects!\n");
1088	>	painCave.isFatal = 1;
1089	>	simError();
1090	>	return NULL;
1091	>	} else
1092	>	return IOIndexToIntegrableObject.at(index);
1093	>	}
1094
1095	<	mfact.clear();
1096	<	FglobalGroupMembership.clear();
1097	<
1095	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1096	>	IOIndexToIntegrableObject= v;
1097	>	}
1098
1099	<	// Fix the silly fortran indexing problem
1099	>	int SimInfo::getNGlobalConstraints() {
1100	>	int nGlobalConstraints;
1101		#ifdef IS_MPI
1102	<	numAtom = mpiSim->getNAtomsGlobal();
1102	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1,
1103	>	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
1104	>	// MPI::COMM_WORLD.Allreduce(&nConstraints_, &nGlobalConstraints, 1,
1105	>	//                           MPI::INT, MPI::SUM);
1106		#else
1107	<	numAtom = n_atoms;
1107	>	nGlobalConstraints =  nConstraints_;
1108		#endif
1109	<	for (int i = 0; i < numAtom; i++)
604	<	FglobalGroupMembership.push_back(globalGroupMembership[i] + 1);
605	<
606	<
607	<	myMols = info->molecules;
608	<	numMol = info->n_mol;
609	<	for(int i  = 0; i < numMol; i++){
610	<	numCutoffGroups = myMols[i].getNCutoffGroups();
611	<	for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff);
612	<	myCutoffGroup != NULL;
613	<	myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
614	<
615	<	totalMass = myCutoffGroup->getMass();
616	<
617	<	for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom);
618	<	cutoffAtom != NULL;
619	<	cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
620	<	mfact.push_back(cutoffAtom->getMass()/totalMass);
621	<	}
622	<	}
1109	>	return nGlobalConstraints;
1110		}
1111
1112	<	}
1112	>	}//end namespace OpenMD
1113	>

Comparing trunk/src/brains/SimInfo.cpp (property svn:keywords):
Revision 124 by chuckv, Wed Oct 20 20:46:20 2004 UTC vs.
Revision 1969 by gezelter, Wed Feb 26 14:14:50 2014 UTC

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