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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 1953 by gezelter, Thu Dec 5 18:19:26 2013 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::COMM_WORLD.Allreduce(&ndf_local, &ndf_, 1, MPI::INT,MPI::SUM);
285	>	MPI::COMM_WORLD.Allreduce(&nfq_local, &nGlobalFluctuatingCharges_, 1,
286	>	MPI::INT, MPI::SUM);
287	>	#else
288	>	ndf_ = ndf_local;
289	>	nGlobalFluctuatingCharges_ = nfq_local;
290	>	#endif
291
292	<	setBoxM( tempMat );
292	>	// nZconstraints_ is global, as are the 3 COM translations for the
293	>	// entire system:
294	>	ndf_ = ndf_ - 3 - nZconstraint_;
295
296	<	}
296	>	}
297
298	<	void SimInfo::setBoxM( double theBox[3][3] ){
298	>	int SimInfo::getFdf() {
299	>	#ifdef IS_MPI
300	>	MPI::COMM_WORLD.Allreduce(&fdf_local, &fdf_, 1, MPI::INT, MPI::SUM);
301	>	#else
302	>	fdf_ = fdf_local;
303	>	#endif
304	>	return fdf_;
305	>	}
306
307	<	int i, j;
308	<	double FortranHmat[9]; // to preserve compatibility with Fortran the
309	<	// ordering in the array is as follows:
310	<	// [ 0 3 6 ]
311	<	// [ 1 4 7 ]
312	<	// [ 2 5 8 ]
313	<	double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
314	<
315	<	if( !boxIsInit ) boxIsInit = 1;
316	<
317	<	for(i=0; i < 3; i++)
318	<	for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
319	<
320	<	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];
307	>	unsigned int SimInfo::getNLocalCutoffGroups(){
308	>	int nLocalCutoffAtoms = 0;
309	>	Molecule* mol;
310	>	MoleculeIterator mi;
311	>	CutoffGroup* cg;
312	>	Molecule::CutoffGroupIterator ci;
313	>
314	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
315	>
316	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
317	>	cg = mol->nextCutoffGroup(ci)) {
318	>	nLocalCutoffAtoms += cg->getNumAtom();
319	>
320	>	}
321		}
322	+
323	+	return nAtoms_ - nLocalCutoffAtoms + nCutoffGroups_;
324		}
325	+
326	+	void SimInfo::calcNdfRaw() {
327	+	int ndfRaw_local;
328
329	<	setFortranBox(FortranHmat, FortranHmatInv, &orthoRhombic);
330	<
331	<	}
332	<
329	>	MoleculeIterator i;
330	>	vector<StuntDouble*>::iterator j;
331	>	Molecule* mol;
332	>	StuntDouble* sd;
333
334	<	void SimInfo::getBoxM (double theBox[3][3]) {
334	>	// Raw degrees of freedom that we have to set
335	>	ndfRaw_local = 0;
336	>
337	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
338
339	<	int i, j;
340	<	for(i=0; i<3; i++)
145	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
146	<	}
339	>	for (sd = mol->beginIntegrableObject(j); sd != NULL;
340	>	sd = mol->nextIntegrableObject(j)) {
341
342	+	ndfRaw_local += 3;
343
344	<	void SimInfo::scaleBox(double scale) {
345	<	double theBox[3][3];
346	<	int i, j;
347	<
348	<	// cerr << "Scaling box by " << scale << "\n";
349	<
350	<	for(i=0; i<3; i++)
351	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
157	<
158	<	setBoxM(theBox);
159	<
160	<	}
161	<
162	<	void SimInfo::calcHmatInv( void ) {
163	<
164	<	int oldOrtho;
165	<	int i,j;
166	<	double smallDiag;
167	<	double tol;
168	<	double sanity[3][3];
169	<
170	<	invertMat3( Hmat, HmatInv );
171	<
172	<	// check to see if Hmat is orthorhombic
173	<
174	<	oldOrtho = orthoRhombic;
175	<
176	<	smallDiag = fabs(Hmat[0][0]);
177	<	if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
178	<	if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
179	<	tol = smallDiag * orthoTolerance;
180	<
181	<	orthoRhombic = 1;
182	<
183	<	for (i = 0; i < 3; i++ ) {
184	<	for (j = 0 ; j < 3; j++) {
185	<	if (i != j) {
186	<	if (orthoRhombic) {
187	<	if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
188	<	}
344	>	if (sd->isDirectional()) {
345	>	if (sd->isLinear()) {
346	>	ndfRaw_local += 2;
347	>	} else {
348	>	ndfRaw_local += 3;
349	>	}
350	>	}
351	>
352		}
353		}
191	–	}
192	–
193	–	if( oldOrtho != orthoRhombic ){
354
355	<	if( orthoRhombic ) {
356	<	sprintf( painCave.errMsg,
357	<	"OOPSE is switching from the default Non-Orthorhombic\n"
358	<	"\tto the faster Orthorhombic periodic boundary computations.\n"
359	<	"\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	<	}
355	>	#ifdef IS_MPI
356	>	MPI::COMM_WORLD.Allreduce(&ndfRaw_local, &ndfRaw_, 1, MPI::INT, MPI::SUM);
357	>	#else
358	>	ndfRaw_ = ndfRaw_local;
359	>	#endif
360		}
219	–	}
361
362	<	void SimInfo::calcBoxL( void ){
362	>	void SimInfo::calcNdfTrans() {
363	>	int ndfTrans_local;
364
365	<	double dx, dy, dz, dsq;
365	>	ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
366
225	–	// boxVol = Determinant of Hmat
367
368	<	boxVol = matDet3( Hmat );
368	>	#ifdef IS_MPI
369	>	MPI::COMM_WORLD.Allreduce(&ndfTrans_local, &ndfTrans_, 1,
370	>	MPI::INT, MPI::SUM);
371	>	#else
372	>	ndfTrans_ = ndfTrans_local;
373	>	#endif
374
375	<	// boxLx
376	<
377	<	dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
232	<	dsq = dx*dx + dy*dy + dz*dz;
233	<	boxL[0] = sqrt( dsq );
234	<	//maxCutoff = 0.5 * boxL[0];
375	>	ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
376	>
377	>	}
378
379	<	// boxLy
380	<
381	<	dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
382	<	dsq = dx*dx + dy*dy + dz*dz;
383	<	boxL[1] = sqrt( dsq );
384	<	//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
379	>	void SimInfo::addInteractionPairs(Molecule* mol) {
380	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
381	>	vector<Bond*>::iterator bondIter;
382	>	vector<Bend*>::iterator bendIter;
383	>	vector<Torsion*>::iterator torsionIter;
384	>	vector<Inversion*>::iterator inversionIter;
385	>	Bond* bond;
386	>	Bend* bend;
387	>	Torsion* torsion;
388	>	Inversion* inversion;
389	>	int a;
390	>	int b;
391	>	int c;
392	>	int d;
393
394	+	// atomGroups can be used to add special interaction maps between
395	+	// groups of atoms that are in two separate rigid bodies.
396	+	// However, most site-site interactions between two rigid bodies
397	+	// are probably not special, just the ones between the physically
398	+	// bonded atoms.  Interactions *within* a single rigid body should
399	+	// always be excluded.  These are done at the bottom of this
400	+	// function.
401
402	<	// boxLz
403	<
404	<	dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
405	<	dsq = dx*dx + dy*dy + dz*dz;
406	<	boxL[2] = sqrt( dsq );
407	<	//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
402	>	map<int, set<int> > atomGroups;
403	>	Molecule::RigidBodyIterator rbIter;
404	>	RigidBody* rb;
405	>	Molecule::IntegrableObjectIterator ii;
406	>	StuntDouble* sd;
407	>
408	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
409	>	sd = mol->nextIntegrableObject(ii)) {
410	>
411	>	if (sd->isRigidBody()) {
412	>	rb = static_cast<RigidBody*>(sd);
413	>	vector<Atom*> atoms = rb->getAtoms();
414	>	set<int> rigidAtoms;
415	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
416	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
417	>	}
418	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
419	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
420	>	}
421	>	} else {
422	>	set<int> oneAtomSet;
423	>	oneAtomSet.insert(sd->getGlobalIndex());
424	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
425	>	}
426	>	}
427
428	<	//calculate the max cutoff
429	<	maxCutoff =  calcMaxCutOff();
430	<
254	<	checkCutOffs();
428	>
429	>	for (bond= mol->beginBond(bondIter); bond != NULL;
430	>	bond = mol->nextBond(bondIter)) {
431
432	<	}
432	>	a = bond->getAtomA()->getGlobalIndex();
433	>	b = bond->getAtomB()->getGlobalIndex();
434
435	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
436	+	oneTwoInteractions_.addPair(a, b);
437	+	} else {
438	+	excludedInteractions_.addPair(a, b);
439	+	}
440	+	}
441
442	<	double SimInfo::calcMaxCutOff(){
442	>	for (bend= mol->beginBend(bendIter); bend != NULL;
443	>	bend = mol->nextBend(bendIter)) {
444
445	<	double ri[3], rj[3], rk[3];
446	<	double rij[3], rjk[3], rki[3];
447	<	double minDist;
445	>	a = bend->getAtomA()->getGlobalIndex();
446	>	b = bend->getAtomB()->getGlobalIndex();
447	>	c = bend->getAtomC()->getGlobalIndex();
448	>
449	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
450	>	oneTwoInteractions_.addPair(a, b);
451	>	oneTwoInteractions_.addPair(b, c);
452	>	} else {
453	>	excludedInteractions_.addPair(a, b);
454	>	excludedInteractions_.addPair(b, c);
455	>	}
456
457	<	ri[0] = Hmat[0][0];
458	<	ri[1] = Hmat[1][0];
459	<	ri[2] = Hmat[2][0];
457	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
458	>	oneThreeInteractions_.addPair(a, c);
459	>	} else {
460	>	excludedInteractions_.addPair(a, c);
461	>	}
462	>	}
463
464	<	rj[0] = Hmat[0][1];
465	<	rj[1] = Hmat[1][1];
271	<	rj[2] = Hmat[2][1];
464	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
465	>	torsion = mol->nextTorsion(torsionIter)) {
466
467	<	rk[0] = Hmat[0][2];
468	<	rk[1] = Hmat[1][2];
469	<	rk[2] = Hmat[2][2];
470	<
277	<	crossProduct3(ri, rj, rij);
278	<	distXY = dotProduct3(rk,rij) / norm3(rij);
467	>	a = torsion->getAtomA()->getGlobalIndex();
468	>	b = torsion->getAtomB()->getGlobalIndex();
469	>	c = torsion->getAtomC()->getGlobalIndex();
470	>	d = torsion->getAtomD()->getGlobalIndex();
471
472	<	crossProduct3(rj,rk, rjk);
473	<	distYZ = dotProduct3(ri,rjk) / norm3(rjk);
472	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
473	>	oneTwoInteractions_.addPair(a, b);
474	>	oneTwoInteractions_.addPair(b, c);
475	>	oneTwoInteractions_.addPair(c, d);
476	>	} else {
477	>	excludedInteractions_.addPair(a, b);
478	>	excludedInteractions_.addPair(b, c);
479	>	excludedInteractions_.addPair(c, d);
480	>	}
481
482	<	crossProduct3(rk,ri, rki);
483	<	distZX = dotProduct3(rj,rki) / norm3(rki);
482	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
483	>	oneThreeInteractions_.addPair(a, c);
484	>	oneThreeInteractions_.addPair(b, d);
485	>	} else {
486	>	excludedInteractions_.addPair(a, c);
487	>	excludedInteractions_.addPair(b, d);
488	>	}
489
490	<	minDist = min(min(distXY, distYZ), distZX);
491	<	return minDist/2;
492	<
493	<	}
490	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
491	>	oneFourInteractions_.addPair(a, d);
492	>	} else {
493	>	excludedInteractions_.addPair(a, d);
494	>	}
495	>	}
496
497	<	void SimInfo::wrapVector( double thePos[3] ){
497	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
498	>	inversion = mol->nextInversion(inversionIter)) {
499
500	<	int i;
501	<	double scaled[3];
500	>	a = inversion->getAtomA()->getGlobalIndex();
501	>	b = inversion->getAtomB()->getGlobalIndex();
502	>	c = inversion->getAtomC()->getGlobalIndex();
503	>	d = inversion->getAtomD()->getGlobalIndex();
504
505	<	if( !orthoRhombic ){
506	<	// calc the scaled coordinates.
507	<
505	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
506	>	oneTwoInteractions_.addPair(a, b);
507	>	oneTwoInteractions_.addPair(a, c);
508	>	oneTwoInteractions_.addPair(a, d);
509	>	} else {
510	>	excludedInteractions_.addPair(a, b);
511	>	excludedInteractions_.addPair(a, c);
512	>	excludedInteractions_.addPair(a, d);
513	>	}
514
515	<	matVecMul3(HmatInv, thePos, scaled);
516	<
517	<	for(i=0; i<3; i++)
518	<	scaled[i] -= roundMe(scaled[i]);
519	<
520	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
521	<
522	<	matVecMul3(Hmat, scaled, thePos);
515	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
516	>	oneThreeInteractions_.addPair(b, c);
517	>	oneThreeInteractions_.addPair(b, d);
518	>	oneThreeInteractions_.addPair(c, d);
519	>	} else {
520	>	excludedInteractions_.addPair(b, c);
521	>	excludedInteractions_.addPair(b, d);
522	>	excludedInteractions_.addPair(c, d);
523	>	}
524	>	}
525
526	<	}
527	<	else{
528	<	// calc the scaled coordinates.
529	<
530	<	for(i=0; i<3; i++)
531	<	scaled[i] = thePos[i]*HmatInv[i][i];
532	<
533	<	// wrap the scaled coordinates
534	<
535	<	for(i=0; i<3; i++)
536	<	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];
325	<	}
326	<
327	<	}
526	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
527	>	rb = mol->nextRigidBody(rbIter)) {
528	>	vector<Atom*> atoms = rb->getAtoms();
529	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
530	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
531	>	a = atoms[i]->getGlobalIndex();
532	>	b = atoms[j]->getGlobalIndex();
533	>	excludedInteractions_.addPair(a, b);
534	>	}
535	>	}
536	>	}
537
329	–
330	–	int SimInfo::getNDF(){
331	–	int ndf_local;
332	–
333	–	ndf_local = 0;
334	–
335	–	for(int i = 0; i < integrableObjects.size(); i++){
336	–	ndf_local += 3;
337	–	if (integrableObjects[i]->isDirectional()) {
338	–	if (integrableObjects[i]->isLinear())
339	–	ndf_local += 2;
340	–	else
341	–	ndf_local += 3;
342	–	}
538		}
539
540	<	// n_constraints is local, so subtract them on each processor:
540	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
541	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
542	>	vector<Bond*>::iterator bondIter;
543	>	vector<Bend*>::iterator bendIter;
544	>	vector<Torsion*>::iterator torsionIter;
545	>	vector<Inversion*>::iterator inversionIter;
546	>	Bond* bond;
547	>	Bend* bend;
548	>	Torsion* torsion;
549	>	Inversion* inversion;
550	>	int a;
551	>	int b;
552	>	int c;
553	>	int d;
554
555	<	ndf_local -= n_constraints;
555	>	map<int, set<int> > atomGroups;
556	>	Molecule::RigidBodyIterator rbIter;
557	>	RigidBody* rb;
558	>	Molecule::IntegrableObjectIterator ii;
559	>	StuntDouble* sd;
560	>
561	>	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
562	>	sd = mol->nextIntegrableObject(ii)) {
563	>
564	>	if (sd->isRigidBody()) {
565	>	rb = static_cast<RigidBody*>(sd);
566	>	vector<Atom*> atoms = rb->getAtoms();
567	>	set<int> rigidAtoms;
568	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
569	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
570	>	}
571	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
572	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
573	>	}
574	>	} else {
575	>	set<int> oneAtomSet;
576	>	oneAtomSet.insert(sd->getGlobalIndex());
577	>	atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet));
578	>	}
579	>	}
580
581	<	#ifdef IS_MPI
582	<	MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
583	<	#else
584	<	ndf = ndf_local;
585	<	#endif
581	>	for (bond= mol->beginBond(bondIter); bond != NULL;
582	>	bond = mol->nextBond(bondIter)) {
583	>
584	>	a = bond->getAtomA()->getGlobalIndex();
585	>	b = bond->getAtomB()->getGlobalIndex();
586	>
587	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
588	>	oneTwoInteractions_.removePair(a, b);
589	>	} else {
590	>	excludedInteractions_.removePair(a, b);
591	>	}
592	>	}
593
594	<	// nZconstraints is global, as are the 3 COM translations for the
595	<	// entire system:
594	>	for (bend= mol->beginBend(bendIter); bend != NULL;
595	>	bend = mol->nextBend(bendIter)) {
596
597	<	ndf = ndf - 3 - nZconstraints;
597	>	a = bend->getAtomA()->getGlobalIndex();
598	>	b = bend->getAtomB()->getGlobalIndex();
599	>	c = bend->getAtomC()->getGlobalIndex();
600	>
601	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
602	>	oneTwoInteractions_.removePair(a, b);
603	>	oneTwoInteractions_.removePair(b, c);
604	>	} else {
605	>	excludedInteractions_.removePair(a, b);
606	>	excludedInteractions_.removePair(b, c);
607	>	}
608
609	<	return ndf;
610	<	}
609	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
610	>	oneThreeInteractions_.removePair(a, c);
611	>	} else {
612	>	excludedInteractions_.removePair(a, c);
613	>	}
614	>	}
615
616	<	int SimInfo::getNDFraw() {
617	<	int ndfRaw_local;
616	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
617	>	torsion = mol->nextTorsion(torsionIter)) {
618
619	<	// Raw degrees of freedom that we have to set
620	<	ndfRaw_local = 0;
619	>	a = torsion->getAtomA()->getGlobalIndex();
620	>	b = torsion->getAtomB()->getGlobalIndex();
621	>	c = torsion->getAtomC()->getGlobalIndex();
622	>	d = torsion->getAtomD()->getGlobalIndex();
623	>
624	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
625	>	oneTwoInteractions_.removePair(a, b);
626	>	oneTwoInteractions_.removePair(b, c);
627	>	oneTwoInteractions_.removePair(c, d);
628	>	} else {
629	>	excludedInteractions_.removePair(a, b);
630	>	excludedInteractions_.removePair(b, c);
631	>	excludedInteractions_.removePair(c, d);
632	>	}
633
634	<	for(int i = 0; i < integrableObjects.size(); i++){
635	<	ndfRaw_local += 3;
636	<	if (integrableObjects[i]->isDirectional()) {
637	<	if (integrableObjects[i]->isLinear())
638	<	ndfRaw_local += 2;
639	<	else
640	<	ndfRaw_local += 3;
634	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
635	>	oneThreeInteractions_.removePair(a, c);
636	>	oneThreeInteractions_.removePair(b, d);
637	>	} else {
638	>	excludedInteractions_.removePair(a, c);
639	>	excludedInteractions_.removePair(b, d);
640	>	}
641	>
642	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
643	>	oneFourInteractions_.removePair(a, d);
644	>	} else {
645	>	excludedInteractions_.removePair(a, d);
646	>	}
647		}
377	–	}
378	–
379	–	#ifdef IS_MPI
380	–	MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
381	–	#else
382	–	ndfRaw = ndfRaw_local;
383	–	#endif
648
649	<	return ndfRaw;
650	<	}
649	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
650	>	inversion = mol->nextInversion(inversionIter)) {
651
652	<	int SimInfo::getNDFtranslational() {
653	<	int ndfTrans_local;
652	>	a = inversion->getAtomA()->getGlobalIndex();
653	>	b = inversion->getAtomB()->getGlobalIndex();
654	>	c = inversion->getAtomC()->getGlobalIndex();
655	>	d = inversion->getAtomD()->getGlobalIndex();
656
657	<	ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
657	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
658	>	oneTwoInteractions_.removePair(a, b);
659	>	oneTwoInteractions_.removePair(a, c);
660	>	oneTwoInteractions_.removePair(a, d);
661	>	} else {
662	>	excludedInteractions_.removePair(a, b);
663	>	excludedInteractions_.removePair(a, c);
664	>	excludedInteractions_.removePair(a, d);
665	>	}
666
667	+	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
668	+	oneThreeInteractions_.removePair(b, c);
669	+	oneThreeInteractions_.removePair(b, d);
670	+	oneThreeInteractions_.removePair(c, d);
671	+	} else {
672	+	excludedInteractions_.removePair(b, c);
673	+	excludedInteractions_.removePair(b, d);
674	+	excludedInteractions_.removePair(c, d);
675	+	}
676	+	}
677
678	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
679	+	rb = mol->nextRigidBody(rbIter)) {
680	+	vector<Atom*> atoms = rb->getAtoms();
681	+	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
682	+	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
683	+	a = atoms[i]->getGlobalIndex();
684	+	b = atoms[j]->getGlobalIndex();
685	+	excludedInteractions_.removePair(a, b);
686	+	}
687	+	}
688	+	}
689	+
690	+	}
691	+
692	+
693	+	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
694	+	int curStampId;
695	+
696	+	//index from 0
697	+	curStampId = moleculeStamps_.size();
698	+
699	+	moleculeStamps_.push_back(molStamp);
700	+	molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
701	+	}
702	+
703	+
704	+	/**
705	+	* update
706	+	*
707	+	*  Performs the global checks and variable settings after the
708	+	*  objects have been created.
709	+	*
710	+	*/
711	+	void SimInfo::update() {
712	+	setupSimVariables();
713	+	calcNdf();
714	+	calcNdfRaw();
715	+	calcNdfTrans();
716	+	}
717	+
718	+	/**
719	+	* getSimulatedAtomTypes
720	+	*
721	+	* Returns an STL set of AtomType* that are actually present in this
722	+	* simulation.  Must query all processors to assemble this information.
723	+	*
724	+	*/
725	+	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
726	+	SimInfo::MoleculeIterator mi;
727	+	Molecule* mol;
728	+	Molecule::AtomIterator ai;
729	+	Atom* atom;
730	+	set<AtomType*> atomTypes;
731	+
732	+	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
733	+	for(atom = mol->beginAtom(ai); atom != NULL;
734	+	atom = mol->nextAtom(ai)) {
735	+	atomTypes.insert(atom->getAtomType());
736	+	}
737	+	}
738	+
739		#ifdef IS_MPI
395	–	MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
396	–	#else
397	–	ndfTrans = ndfTrans_local;
398	–	#endif
740
741	<	ndfTrans = ndfTrans - 3 - nZconstraints;
741	>	// loop over the found atom types on this processor, and add their
742	>	// numerical idents to a vector:
743	>
744	>	vector<int> foundTypes;
745	>	set<AtomType*>::iterator i;
746	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
747	>	foundTypes.push_back( (*i)->getIdent() );
748
749	<	return ndfTrans;
750	<	}
749	>	// count_local holds the number of found types on this processor
750	>	int count_local = foundTypes.size();
751
752	<	int SimInfo::getTotIntegrableObjects() {
406	<	int nObjs_local;
407	<	int nObjs;
752	>	int nproc = MPI::COMM_WORLD.Get_size();
753
754	<	nObjs_local =  integrableObjects.size();
754	>	// we need arrays to hold the counts and displacement vectors for
755	>	// all processors
756	>	vector<int> counts(nproc, 0);
757	>	vector<int> disps(nproc, 0);
758
759	+	// fill the counts array
760	+	MPI::COMM_WORLD.Allgather(&count_local, 1, MPI::INT, &counts[0],
761	+	1, MPI::INT);
762	+
763	+	// use the processor counts to compute the displacement array
764	+	disps[0] = 0;
765	+	int totalCount = counts[0];
766	+	for (int iproc = 1; iproc < nproc; iproc++) {
767	+	disps[iproc] = disps[iproc-1] + counts[iproc-1];
768	+	totalCount += counts[iproc];
769	+	}
770
771	<	#ifdef IS_MPI
772	<	MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
773	<	#else
774	<	nObjs = nObjs_local;
775	<	#endif
771	>	// we need a (possibly redundant) set of all found types:
772	>	vector<int> ftGlobal(totalCount);
773	>
774	>	// now spray out the foundTypes to all the other processors:
775	>	MPI::COMM_WORLD.Allgatherv(&foundTypes[0], count_local, MPI::INT,
776	>	&ftGlobal[0], &counts[0], &disps[0],
777	>	MPI::INT);
778
779	+	vector<int>::iterator j;
780
781	<	return nObjs;
782	<	}
781	>	// foundIdents is a stl set, so inserting an already found ident
782	>	// will have no effect.
783	>	set<int> foundIdents;
784
785	<	void SimInfo::refreshSim(){
785	>	for (j = ftGlobal.begin(); j != ftGlobal.end(); ++j)
786	>	foundIdents.insert((*j));
787	>
788	>	// now iterate over the foundIdents and get the actual atom types
789	>	// that correspond to these:
790	>	set<int>::iterator it;
791	>	for (it = foundIdents.begin(); it != foundIdents.end(); ++it)
792	>	atomTypes.insert( forceField_->getAtomType((*it)) );
793	>
794	>	#endif
795
796	<	simtype fInfo;
797	<	int isError;
426	<	int n_global;
427	<	int* excl;
796	>	return atomTypes;
797	>	}
798
429	–	fInfo.dielect = 0.0;
799
800	<	if( useDipoles ){
801	<	if( useReactionField )fInfo.dielect = dielectric;
800	>	int getGlobalCountOfType(AtomType* atype) {
801	>	/*
802	>	set<AtomType*> atypes = getSimulatedAtomTypes();
803	>	map<AtomType*, int> counts_;
804	>
805	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
806	>	for(atom = mol->beginAtom(ai); atom != NULL;
807	>	atom = mol->nextAtom(ai)) {
808	>	atom->getAtomType();
809	>	}
810	>	}
811	>	*/
812	>	return 0;
813		}
814
815	<	fInfo.SIM_uses_PBC = usePBC;
816	<	//fInfo.SIM_uses_LJ = 0;
817	<	fInfo.SIM_uses_LJ = useLJ;
818	<	fInfo.SIM_uses_sticky = useSticky;
819	<	//fInfo.SIM_uses_sticky = 0;
820	<	fInfo.SIM_uses_charges = useCharges;
821	<	fInfo.SIM_uses_dipoles = useDipoles;
822	<	//fInfo.SIM_uses_dipoles = 0;
823	<	fInfo.SIM_uses_RF = useReactionField;
824	<	//fInfo.SIM_uses_RF = 0;
825	<	fInfo.SIM_uses_GB = useGB;
826	<	fInfo.SIM_uses_EAM = useEAM;
815	>	void SimInfo::setupSimVariables() {
816	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
817	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole
818	>	// parameter is true
819	>	calcBoxDipole_ = false;
820	>	if ( simParams_->haveAccumulateBoxDipole() )
821	>	if ( simParams_->getAccumulateBoxDipole() ) {
822	>	calcBoxDipole_ = true;
823	>	}
824	>
825	>	set<AtomType*>::iterator i;
826	>	set<AtomType*> atomTypes;
827	>	atomTypes = getSimulatedAtomTypes();
828	>	bool usesElectrostatic = false;
829	>	bool usesMetallic = false;
830	>	bool usesDirectional = false;
831	>	bool usesFluctuatingCharges =  false;
832	>	//loop over all of the atom types
833	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
834	>	usesElectrostatic |= (*i)->isElectrostatic();
835	>	usesMetallic |= (*i)->isMetal();
836	>	usesDirectional |= (*i)->isDirectional();
837	>	usesFluctuatingCharges |= (*i)->isFluctuatingCharge();
838	>	}
839
448	–	n_exclude = excludes->getSize();
449	–	excl = excludes->getFortranArray();
450	–
840		#ifdef IS_MPI
841	<	n_global = mpiSim->getNAtomsGlobal();
841	>	bool temp;
842	>	temp = usesDirectional;
843	>	MPI::COMM_WORLD.Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI::BOOL,
844	>	MPI::LOR);
845	>
846	>	temp = usesMetallic;
847	>	MPI::COMM_WORLD.Allreduce(&temp, &usesMetallicAtoms_, 1, MPI::BOOL,
848	>	MPI::LOR);
849	>
850	>	temp = usesElectrostatic;
851	>	MPI::COMM_WORLD.Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI::BOOL,
852	>	MPI::LOR);
853	>
854	>	temp = usesFluctuatingCharges;
855	>	MPI::COMM_WORLD.Allreduce(&temp, &usesFluctuatingCharges_, 1, MPI::BOOL,
856	>	MPI::LOR);
857		#else
858	<	n_global = n_atoms;
858	>
859	>	usesDirectionalAtoms_ = usesDirectional;
860	>	usesMetallicAtoms_ = usesMetallic;
861	>	usesElectrostaticAtoms_ = usesElectrostatic;
862	>	usesFluctuatingCharges_ = usesFluctuatingCharges;
863	>
864		#endif
865	<
866	<	isError = 0;
867	<
868	<	getFortranGroupArrays(this, FglobalGroupMembership, mfact);
869	<	//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);
865	>
866	>	requiresPrepair_ = usesMetallicAtoms_ ? true : false;
867	>	requiresSkipCorrection_ = usesElectrostaticAtoms_ ? true : false;
868	>	requiresSelfCorrection_ = usesElectrostaticAtoms_ ? true : false;
869	>	}
870
871	<	if( isError ){
871	>
872	>	vector<int> SimInfo::getGlobalAtomIndices() {
873	>	SimInfo::MoleculeIterator mi;
874	>	Molecule* mol;
875	>	Molecule::AtomIterator ai;
876	>	Atom* atom;
877	>
878	>	vector<int> GlobalAtomIndices(getNAtoms(), 0);
879
880	<	sprintf( painCave.errMsg,
881	<	"There was an error setting the simulation information in fortran.\n" );
882	<	painCave.isFatal = 1;
883	<	painCave.severity = OOPSE_ERROR;
884	<	simError();
880	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
881	>
882	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
883	>	GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex();
884	>	}
885	>	}
886	>	return GlobalAtomIndices;
887		}
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	–	}
888
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	–	}
889
890	<	void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
890	>	vector<int> SimInfo::getGlobalGroupIndices() {
891	>	SimInfo::MoleculeIterator mi;
892	>	Molecule* mol;
893	>	Molecule::CutoffGroupIterator ci;
894	>	CutoffGroup* cg;
895
896	<	rSw = theRsw;
897	<	setDefaultRcut( theRcut );
898	<	}
896	>	vector<int> GlobalGroupIndices;
897	>
898	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
899	>
900	>	//local index of cutoff group is trivial, it only depends on the
901	>	//order of travesing
902	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
903	>	cg = mol->nextCutoffGroup(ci)) {
904	>	GlobalGroupIndices.push_back(cg->getGlobalIndex());
905	>	}
906	>	}
907	>	return GlobalGroupIndices;
908	>	}
909
910
911	<	void SimInfo::checkCutOffs( void ){
912	<
913	<	if( boxIsInit ){
911	>	void SimInfo::prepareTopology() {
912	>
913	>	//calculate mass ratio of cutoff group
914	>	SimInfo::MoleculeIterator mi;
915	>	Molecule* mol;
916	>	Molecule::CutoffGroupIterator ci;
917	>	CutoffGroup* cg;
918	>	Molecule::AtomIterator ai;
919	>	Atom* atom;
920	>	RealType totalMass;
921	>
922	>	/**
923	>	* The mass factor is the relative mass of an atom to the total
924	>	* mass of the cutoff group it belongs to.  By default, all atoms
925	>	* are their own cutoff groups, and therefore have mass factors of
926	>	* 1.  We need some special handling for massless atoms, which
927	>	* will be treated as carrying the entire mass of the cutoff
928	>	* group.
929	>	*/
930	>	massFactors_.clear();
931	>	massFactors_.resize(getNAtoms(), 1.0);
932
933	<	//we need to check cutOffs against the box
934	<
935	<	if( rCut > maxCutoff ){
936	<	sprintf( painCave.errMsg,
937	<	"cutoffRadius is too large for the current periodic box.\n"
938	<	"\tCurrent Value of cutoffRadius = %G at time %G\n "
939	<	"\tThis is larger than half of at least one of the\n"
940	<	"\tperiodic box vectors.  Right now, the Box matrix is:\n"
941	<	"\n"
942	<	"\t[ %G %G %G ]\n"
943	<	"\t[ %G %G %G ]\n"
944	<	"\t[ %G %G %G ]\n",
945	<	rCut, currentTime,
946	<	Hmat[0][0], Hmat[0][1], Hmat[0][2],
947	<	Hmat[1][0], Hmat[1][1], Hmat[1][2],
948	<	Hmat[2][0], Hmat[2][1], Hmat[2][2]);
949	<	painCave.severity = OOPSE_ERROR;
950	<	painCave.isFatal = 1;
951	<	simError();
933	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
934	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
935	>	cg = mol->nextCutoffGroup(ci)) {
936	>
937	>	totalMass = cg->getMass();
938	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
939	>	// Check for massless groups - set mfact to 1 if true
940	>	if (totalMass != 0)
941	>	massFactors_[atom->getLocalIndex()] = atom->getMass()/totalMass;
942	>	else
943	>	massFactors_[atom->getLocalIndex()] = 1.0;
944	>	}
945	>	}
946	>	}
947	>
948	>	// Build the identArray_ and regions_
949	>
950	>	identArray_.clear();
951	>	identArray_.reserve(getNAtoms());
952	>	regions_.clear();
953	>	regions_.reserve(getNAtoms());
954	>
955	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
956	>	int reg = mol->getRegion();
957	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
958	>	identArray_.push_back(atom->getIdent());
959	>	regions_.push_back(reg);
960	>	}
961		}
962	<	} else {
963	<	// 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();
962	>
963	>	topologyDone_ = true;
964		}
536	–
537	–	}
965
966	<	void SimInfo::addProperty(GenericData* prop){
966	>	void SimInfo::addProperty(GenericData* genData) {
967	>	properties_.addProperty(genData);
968	>	}
969
970	<	map<string, GenericData*>::iterator result;
971	<	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	<
970	>	void SimInfo::removeProperty(const string& propName) {
971	>	properties_.removeProperty(propName);
972		}
553	–	else{
973
974	<	properties[prop->getID()] = prop;
974	>	void SimInfo::clearProperties() {
975	>	properties_.clearProperties();
976	>	}
977
978	+	vector<string> SimInfo::getPropertyNames() {
979	+	return properties_.getPropertyNames();
980		}
981	<
982	<	}
981	>
982	>	vector<GenericData*> SimInfo::getProperties() {
983	>	return properties_.getProperties();
984	>	}
985
986	<	GenericData* SimInfo::getProperty(const string& propName){
986	>	GenericData* SimInfo::getPropertyByName(const string& propName) {
987	>	return properties_.getPropertyByName(propName);
988	>	}
989	>
990	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
991	>	if (sman_ == sman) {
992	>	return;
993	>	}
994	>	delete sman_;
995	>	sman_ = sman;
996	>
997	>	SimInfo::MoleculeIterator mi;
998	>	Molecule::AtomIterator ai;
999	>	Molecule::RigidBodyIterator rbIter;
1000	>	Molecule::CutoffGroupIterator cgIter;
1001	>	Molecule::BondIterator bondIter;
1002	>	Molecule::BendIterator bendIter;
1003	>	Molecule::TorsionIterator torsionIter;
1004	>	Molecule::InversionIterator inversionIter;
1005
1006	<	map<string, GenericData*>::iterator result;
1007	<
1008	<	//string lowerCaseName = ();
1009	<
1010	<	result = properties.find(propName);
1011	<
1012	<	if(result != properties.end())
1013	<	return (*result).second;
571	<	else
572	<	return NULL;
573	<	}
1006	>	Molecule* mol;
1007	>	Atom* atom;
1008	>	RigidBody* rb;
1009	>	CutoffGroup* cg;
1010	>	Bond* bond;
1011	>	Bend* bend;
1012	>	Torsion* torsion;
1013	>	Inversion* inversion;
1014
1015	+	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1016	+
1017	+	for (atom = mol->beginAtom(ai); atom != NULL;
1018	+	atom = mol->nextAtom(ai)) {
1019	+	atom->setSnapshotManager(sman_);
1020	+	}
1021	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
1022	+	rb = mol->nextRigidBody(rbIter)) {
1023	+	rb->setSnapshotManager(sman_);
1024	+	}
1025	+	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL;
1026	+	cg = mol->nextCutoffGroup(cgIter)) {
1027	+	cg->setSnapshotManager(sman_);
1028	+	}
1029	+	for (bond = mol->beginBond(bondIter); bond != NULL;
1030	+	bond = mol->nextBond(bondIter)) {
1031	+	bond->setSnapshotManager(sman_);
1032	+	}
1033	+	for (bend = mol->beginBend(bendIter); bend != NULL;
1034	+	bend = mol->nextBend(bendIter)) {
1035	+	bend->setSnapshotManager(sman_);
1036	+	}
1037	+	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
1038	+	torsion = mol->nextTorsion(torsionIter)) {
1039	+	torsion->setSnapshotManager(sman_);
1040	+	}
1041	+	for (inversion = mol->beginInversion(inversionIter); inversion != NULL;
1042	+	inversion = mol->nextInversion(inversionIter)) {
1043	+	inversion->setSnapshotManager(sman_);
1044	+	}
1045	+	}
1046	+	}
1047
1048	<	void SimInfo::getFortranGroupArrays(SimInfo* info,
1049	<	vector<int>& FglobalGroupMembership,
1050	<	vector<double>& mfact){
1048	>
1049	>	ostream& operator <<(ostream& o, SimInfo& info) {
1050	>
1051	>	return o;
1052	>	}
1053	>
1054
1055	<	Molecule* myMols;
1056	<	Atom** myAtoms;
1057	<	int numAtom;
1058	<	double mtot;
1059	<	int numMol;
1060	<	int numCutoffGroups;
1061	<	CutoffGroup* myCutoffGroup;
1062	<	vector<CutoffGroup*>::iterator iterCutoff;
1063	<	Atom* cutoffAtom;
1064	<	vector<Atom*>::iterator iterAtom;
1065	<	int atomIndex;
591	<	double totalMass;
1055	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1056	>	if (index >= int(IOIndexToIntegrableObject.size())) {
1057	>	sprintf(painCave.errMsg,
1058	>	"SimInfo::getIOIndexToIntegrableObject Error: Integrable Object\n"
1059	>	"\tindex exceeds number of known objects!\n");
1060	>	painCave.isFatal = 1;
1061	>	simError();
1062	>	return NULL;
1063	>	} else
1064	>	return IOIndexToIntegrableObject.at(index);
1065	>	}
1066
1067	<	mfact.clear();
1068	<	FglobalGroupMembership.clear();
1069	<
1067	>	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1068	>	IOIndexToIntegrableObject= v;
1069	>	}
1070
1071	<	// Fix the silly fortran indexing problem
1071	>	int SimInfo::getNGlobalConstraints() {
1072	>	int nGlobalConstraints;
1073		#ifdef IS_MPI
1074	<	numAtom = mpiSim->getNAtomsGlobal();
1074	>	MPI::COMM_WORLD.Allreduce(&nConstraints_, &nGlobalConstraints, 1,
1075	>	MPI::INT, MPI::SUM);
1076		#else
1077	<	numAtom = n_atoms;
1077	>	nGlobalConstraints =  nConstraints_;
1078		#endif
1079	<	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	<	}
1079	>	return nGlobalConstraints;
1080		}
1081
1082	<	}
1082	>	}//end namespace OpenMD
1083	>

Comparing trunk/src/brains/SimInfo.cpp (property svn:keywords):
Revision 124 by chuckv, Wed Oct 20 20:46:20 2004 UTC vs.
Revision 1953 by gezelter, Thu Dec 5 18:19:26 2013 UTC

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