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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 143 by chrisfen, Fri Oct 22 22:54:01 2004 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1764 by gezelter, Tue Jul 3 18:32:27 2012 UTC

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

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 143 by chrisfen, Fri Oct 22 22:54:01 2004 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1764 by gezelter, Tue Jul 3 18:32:27 2012 UTC

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