ViewVC Help

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

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

Comparing:
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 1530 by gezelter, Tue Dec 28 21:47:55 2010 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]  Vardeman & Gezelter, in progress (2009).
40	>	*/
41	>
42	>	/**
43	>	* @file SimInfo.cpp
44	>	* @author    tlin
45	>	* @date  11/02/2004
46	>	* @version 1.0
47	>	*/
48
49	<	#include <iostream>
50	<	using namespace std;
49	>	#include <algorithm>
50	>	#include <set>
51	>	#include <map>
52
53		#include "brains/SimInfo.hpp"
54	<	#define __C
55	<	#include "brains/fSimulation.h"
54	>	#include "math/Vector3.hpp"
55	>	#include "primitives/Molecule.hpp"
56	>	#include "primitives/StuntDouble.hpp"
57	>	#include "UseTheForce/fCutoffPolicy.h"
58	>	#include "UseTheForce/doForces_interface.h"
59	>	#include "UseTheForce/DarkSide/neighborLists_interface.h"
60	>	#include "utils/MemoryUtils.hpp"
61		#include "utils/simError.h"
62	<	#include "UseTheForce/DarkSide/simulation_interface.h"
63	<	#include "UseTheForce/notifyCutoffs_interface.h"
62	>	#include "selection/SelectionManager.hpp"
63	>	#include "io/ForceFieldOptions.hpp"
64	>	#include "UseTheForce/ForceField.hpp"
65	>	#include "nonbonded/SwitchingFunction.hpp"
66
15	–	//#include "UseTheForce/fortranWrappers.hpp"
67
17	–	#include "math/MatVec3.h"
18	–
68		#ifdef IS_MPI
69	<	#include "brains/mpiSimulation.hpp"
70	<	#endif
69	>	#include "UseTheForce/mpiComponentPlan.h"
70	>	#include "UseTheForce/DarkSide/simParallel_interface.h"
71	>	#endif
72
73	<	inline double roundMe( double x ){
74	<	return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
75	<	}
76	<
77	<	inline double min( double a, double b ){
78	<	return (a < b ) ? a : b;
79	<	}
73	>	using namespace std;
74	>	namespace OpenMD {
75	>
76	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
77	>	forceField_(ff), simParams_(simParams),
78	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
79	>	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
80	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
81	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
82	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
83	>	nConstraints_(0), sman_(NULL), fortranInitialized_(false),
84	>	calcBoxDipole_(false), useAtomicVirial_(true) {
85	>
86	>	MoleculeStamp* molStamp;
87	>	int nMolWithSameStamp;
88	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
89	>	int nGroups = 0;       //total cutoff groups defined in meta-data file
90	>	CutoffGroupStamp* cgStamp;
91	>	RigidBodyStamp* rbStamp;
92	>	int nRigidAtoms = 0;
93	>
94	>	vector<Component*> components = simParams->getComponents();
95	>
96	>	for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
97	>	molStamp = (*i)->getMoleculeStamp();
98	>	nMolWithSameStamp = (*i)->getNMol();
99	>
100	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
101	>
102	>	//calculate atoms in molecules
103	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
104	>
105	>	//calculate atoms in cutoff groups
106	>	int nAtomsInGroups = 0;
107	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
108	>
109	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
110	>	cgStamp = molStamp->getCutoffGroupStamp(j);
111	>	nAtomsInGroups += cgStamp->getNMembers();
112	>	}
113	>
114	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
115	>
116	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
117	>
118	>	//calculate atoms in rigid bodies
119	>	int nAtomsInRigidBodies = 0;
120	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
121	>
122	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
123	>	rbStamp = molStamp->getRigidBodyStamp(j);
124	>	nAtomsInRigidBodies += rbStamp->getNMembers();
125	>	}
126	>
127	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
128	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
129	>
130	>	}
131	>
132	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
133	>	//group therefore the total number of cutoff groups in the system is
134	>	//equal to the total number of atoms minus number of atoms belong to
135	>	//cutoff group defined in meta-data file plus the number of cutoff
136	>	//groups defined in meta-data file
137	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
138	>
139	>	//every free atom (atom does not belong to rigid bodies) is an
140	>	//integrable object therefore the total number of integrable objects
141	>	//in the system is equal to the total number of atoms minus number of
142	>	//atoms belong to rigid body defined in meta-data file plus the number
143	>	//of rigid bodies defined in meta-data file
144	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
145	>	+ nGlobalRigidBodies_;
146	>
147	>	nGlobalMols_ = molStampIds_.size();
148	>	molToProcMap_.resize(nGlobalMols_);
149	>	}
150	>
151	>	SimInfo::~SimInfo() {
152	>	map<int, Molecule*>::iterator i;
153	>	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
154	>	delete i->second;
155	>	}
156	>	molecules_.clear();
157	>
158	>	delete sman_;
159	>	delete simParams_;
160	>	delete forceField_;
161	>	}
162
31	–	SimInfo* currentInfo;
163
164	<	SimInfo::SimInfo(){
165	<
166	<	n_constraints = 0;
167	<	nZconstraints = 0;
168	<	n_oriented = 0;
169	<	n_dipoles = 0;
170	<	ndf = 0;
171	<	ndfRaw = 0;
172	<	nZconstraints = 0;
173	<	the_integrator = NULL;
174	<	setTemp = 0;
175	<	thermalTime = 0.0;
176	<	currentTime = 0.0;
177	<	rCut = 0.0;
178	<	rSw = 0.0;
179	<
180	<	haveRcut = 0;
181	<	haveRsw = 0;
182	<	boxIsInit = 0;
164	>	bool SimInfo::addMolecule(Molecule* mol) {
165	>	MoleculeIterator i;
166	>
167	>	i = molecules_.find(mol->getGlobalIndex());
168	>	if (i == molecules_.end() ) {
169	>
170	>	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
171	>
172	>	nAtoms_ += mol->getNAtoms();
173	>	nBonds_ += mol->getNBonds();
174	>	nBends_ += mol->getNBends();
175	>	nTorsions_ += mol->getNTorsions();
176	>	nInversions_ += mol->getNInversions();
177	>	nRigidBodies_ += mol->getNRigidBodies();
178	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
179	>	nCutoffGroups_ += mol->getNCutoffGroups();
180	>	nConstraints_ += mol->getNConstraintPairs();
181	>
182	>	addInteractionPairs(mol);
183	>
184	>	return true;
185	>	} else {
186	>	return false;
187	>	}
188	>	}
189
190	<	resetTime = 1e99;
190	>	bool SimInfo::removeMolecule(Molecule* mol) {
191	>	MoleculeIterator i;
192	>	i = molecules_.find(mol->getGlobalIndex());
193
194	<	orthoRhombic = 0;
56	<	orthoTolerance = 1E-6;
57	<	useInitXSstate = true;
194	>	if (i != molecules_.end() ) {
195
196	<	usePBC = 0;
197	<	useDirectionalAtoms = 0;
198	<	useLennardJones = 0;
199	<	useElectrostatics = 0;
200	<	useCharges = 0;
201	<	useDipoles = 0;
202	<	useSticky = 0;
203	<	useGayBerne = 0;
204	<	useEAM = 0;
205	<	useShapes = 0;
206	<	useFLARB = 0;
196	>	assert(mol == i->second);
197	>
198	>	nAtoms_ -= mol->getNAtoms();
199	>	nBonds_ -= mol->getNBonds();
200	>	nBends_ -= mol->getNBends();
201	>	nTorsions_ -= mol->getNTorsions();
202	>	nInversions_ -= mol->getNInversions();
203	>	nRigidBodies_ -= mol->getNRigidBodies();
204	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
205	>	nCutoffGroups_ -= mol->getNCutoffGroups();
206	>	nConstraints_ -= mol->getNConstraintPairs();
207
208	<	useSolidThermInt = 0;
209	<	useLiquidThermInt = 0;
208	>	removeInteractionPairs(mol);
209	>	molecules_.erase(mol->getGlobalIndex());
210
211	<	haveCutoffGroups = false;
211	>	delete mol;
212	>
213	>	return true;
214	>	} else {
215	>	return false;
216	>	}
217	>	}
218
219	<	excludes = Exclude::Instance();
219	>
220	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
221	>	i = molecules_.begin();
222	>	return i == molecules_.end() ? NULL : i->second;
223	>	}
224
225	<	myConfiguration = new SimState();
225	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
226	>	++i;
227	>	return i == molecules_.end() ? NULL : i->second;
228	>	}
229
80	–	has_minimizer = false;
81	–	the_minimizer =NULL;
230
231	<	ngroup = 0;
231	>	void SimInfo::calcNdf() {
232	>	int ndf_local;
233	>	MoleculeIterator i;
234	>	vector<StuntDouble*>::iterator j;
235	>	Molecule* mol;
236	>	StuntDouble* integrableObject;
237
238	<	}
238	>	ndf_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	+	ndf_local += 3;
245
246	<	SimInfo::~SimInfo(){
246	>	if (integrableObject->isDirectional()) {
247	>	if (integrableObject->isLinear()) {
248	>	ndf_local += 2;
249	>	} else {
250	>	ndf_local += 3;
251	>	}
252	>	}
253	>
254	>	}
255	>	}
256	>
257	>	// n_constraints is local, so subtract them on each processor
258	>	ndf_local -= nConstraints_;
259
260	<	delete myConfiguration;
260	>	#ifdef IS_MPI
261	>	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
262	>	#else
263	>	ndf_ = ndf_local;
264	>	#endif
265
266	<	map<string, GenericData*>::iterator i;
267	<
268	<	for(i = properties.begin(); i != properties.end(); i++)
95	<	delete (*i).second;
266	>	// nZconstraints_ is global, as are the 3 COM translations for the
267	>	// entire system:
268	>	ndf_ = ndf_ - 3 - nZconstraint_;
269
270	<	}
270	>	}
271
272	<	void SimInfo::setBox(double newBox[3]) {
273	<
274	<	int i, j;
275	<	double tempMat[3][3];
276	<
277	<	for(i=0; i<3; i++)
278	<	for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
106	<
107	<	tempMat[0][0] = newBox[0];
108	<	tempMat[1][1] = newBox[1];
109	<	tempMat[2][2] = newBox[2];
110	<
111	<	setBoxM( tempMat );
112	<
113	<	}
114	<
115	<	void SimInfo::setBoxM( double theBox[3][3] ){
116	<
117	<	int i, j;
118	<	double FortranHmat[9]; // to preserve compatibility with Fortran the
119	<	// ordering in the array is as follows:
120	<	// [ 0 3 6 ]
121	<	// [ 1 4 7 ]
122	<	// [ 2 5 8 ]
123	<	double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
124	<
125	<	if( !boxIsInit ) boxIsInit = 1;
126	<
127	<	for(i=0; i < 3; i++)
128	<	for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
129	<
130	<	calcBoxL();
131	<	calcHmatInv();
132	<
133	<	for(i=0; i < 3; i++) {
134	<	for (j=0; j < 3; j++) {
135	<	FortranHmat[3*j + i] = Hmat[i][j];
136	<	FortranHmatInv[3*j + i] = HmatInv[i][j];
137	<	}
272	>	int SimInfo::getFdf() {
273	>	#ifdef IS_MPI
274	>	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
275	>	#else
276	>	fdf_ = fdf_local;
277	>	#endif
278	>	return fdf_;
279		}
280	+
281	+	void SimInfo::calcNdfRaw() {
282	+	int ndfRaw_local;
283
284	<	setFortranBox(FortranHmat, FortranHmatInv, &orthoRhombic);
285	<
286	<	}
287	<
284	>	MoleculeIterator i;
285	>	vector<StuntDouble*>::iterator j;
286	>	Molecule* mol;
287	>	StuntDouble* integrableObject;
288
289	<	void SimInfo::getBoxM (double theBox[3][3]) {
289	>	// Raw degrees of freedom that we have to set
290	>	ndfRaw_local = 0;
291	>
292	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
293	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
294	>	integrableObject = mol->nextIntegrableObject(j)) {
295
296	<	int i, j;
148	<	for(i=0; i<3; i++)
149	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
150	<	}
296	>	ndfRaw_local += 3;
297
298	<
299	<	void SimInfo::scaleBox(double scale) {
300	<	double theBox[3][3];
301	<	int i, j;
302	<
303	<	// cerr << "Scaling box by " << scale << "\n";
304	<
305	<	for(i=0; i<3; i++)
160	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
161	<
162	<	setBoxM(theBox);
163	<
164	<	}
165	<
166	<	void SimInfo::calcHmatInv( void ) {
167	<
168	<	int oldOrtho;
169	<	int i,j;
170	<	double smallDiag;
171	<	double tol;
172	<	double sanity[3][3];
173	<
174	<	invertMat3( Hmat, HmatInv );
175	<
176	<	// check to see if Hmat is orthorhombic
177	<
178	<	oldOrtho = orthoRhombic;
179	<
180	<	smallDiag = fabs(Hmat[0][0]);
181	<	if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
182	<	if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
183	<	tol = smallDiag * orthoTolerance;
184	<
185	<	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	<	}
298	>	if (integrableObject->isDirectional()) {
299	>	if (integrableObject->isLinear()) {
300	>	ndfRaw_local += 2;
301	>	} else {
302	>	ndfRaw_local += 3;
303	>	}
304	>	}
305	>
306		}
307		}
195	–	}
196	–
197	–	if( oldOrtho != orthoRhombic ){
308
309	<	if( orthoRhombic ) {
310	<	sprintf( painCave.errMsg,
311	<	"OOPSE is switching from the default Non-Orthorhombic\n"
312	<	"\tto the faster Orthorhombic periodic boundary computations.\n"
313	<	"\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();
209	<	}
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	<	}
309	>	#ifdef IS_MPI
310	>	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
311	>	#else
312	>	ndfRaw_ = ndfRaw_local;
313	>	#endif
314		}
223	–	}
315
316	<	void SimInfo::calcBoxL( void ){
316	>	void SimInfo::calcNdfTrans() {
317	>	int ndfTrans_local;
318
319	<	double dx, dy, dz, dsq;
319	>	ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
320
229	–	// boxVol = Determinant of Hmat
321
322	<	boxVol = matDet3( Hmat );
322	>	#ifdef IS_MPI
323	>	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
324	>	#else
325	>	ndfTrans_ = ndfTrans_local;
326	>	#endif
327
328	<	// boxLx
329	<
330	<	dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
236	<	dsq = dx*dx + dy*dy + dz*dz;
237	<	boxL[0] = sqrt( dsq );
238	<	//maxCutoff = 0.5 * boxL[0];
328	>	ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
329	>
330	>	}
331
332	<	// boxLy
333	<
334	<	dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
335	<	dsq = dx*dx + dy*dy + dz*dz;
336	<	boxL[1] = sqrt( dsq );
337	<	//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
332	>	void SimInfo::addInteractionPairs(Molecule* mol) {
333	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
334	>	vector<Bond*>::iterator bondIter;
335	>	vector<Bend*>::iterator bendIter;
336	>	vector<Torsion*>::iterator torsionIter;
337	>	vector<Inversion*>::iterator inversionIter;
338	>	Bond* bond;
339	>	Bend* bend;
340	>	Torsion* torsion;
341	>	Inversion* inversion;
342	>	int a;
343	>	int b;
344	>	int c;
345	>	int d;
346
347	+	// atomGroups can be used to add special interaction maps between
348	+	// groups of atoms that are in two separate rigid bodies.
349	+	// However, most site-site interactions between two rigid bodies
350	+	// are probably not special, just the ones between the physically
351	+	// bonded atoms.  Interactions *within* a single rigid body should
352	+	// always be excluded.  These are done at the bottom of this
353	+	// function.
354
355	<	// boxLz
356	<
357	<	dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
358	<	dsq = dx*dx + dy*dy + dz*dz;
359	<	boxL[2] = sqrt( dsq );
360	<	//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
355	>	map<int, set<int> > atomGroups;
356	>	Molecule::RigidBodyIterator rbIter;
357	>	RigidBody* rb;
358	>	Molecule::IntegrableObjectIterator ii;
359	>	StuntDouble* integrableObject;
360	>
361	>	for (integrableObject = mol->beginIntegrableObject(ii);
362	>	integrableObject != NULL;
363	>	integrableObject = mol->nextIntegrableObject(ii)) {
364	>
365	>	if (integrableObject->isRigidBody()) {
366	>	rb = static_cast<RigidBody*>(integrableObject);
367	>	vector<Atom*> atoms = rb->getAtoms();
368	>	set<int> rigidAtoms;
369	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
370	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
371	>	}
372	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
373	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
374	>	}
375	>	} else {
376	>	set<int> oneAtomSet;
377	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
378	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
379	>	}
380	>	}
381	>
382	>	for (bond= mol->beginBond(bondIter); bond != NULL;
383	>	bond = mol->nextBond(bondIter)) {
384
385	<	//calculate the max cutoff
386	<	maxCutoff =  calcMaxCutOff();
387	<
388	<	checkCutOffs();
385	>	a = bond->getAtomA()->getGlobalIndex();
386	>	b = bond->getAtomB()->getGlobalIndex();
387	>
388	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
389	>	oneTwoInteractions_.addPair(a, b);
390	>	} else {
391	>	excludedInteractions_.addPair(a, b);
392	>	}
393	>	}
394
395	<	}
395	>	for (bend= mol->beginBend(bendIter); bend != NULL;
396	>	bend = mol->nextBend(bendIter)) {
397
398	+	a = bend->getAtomA()->getGlobalIndex();
399	+	b = bend->getAtomB()->getGlobalIndex();
400	+	c = bend->getAtomC()->getGlobalIndex();
401	+
402	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
403	+	oneTwoInteractions_.addPair(a, b);
404	+	oneTwoInteractions_.addPair(b, c);
405	+	} else {
406	+	excludedInteractions_.addPair(a, b);
407	+	excludedInteractions_.addPair(b, c);
408	+	}
409
410	<	double SimInfo::calcMaxCutOff(){
410	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
411	>	oneThreeInteractions_.addPair(a, c);
412	>	} else {
413	>	excludedInteractions_.addPair(a, c);
414	>	}
415	>	}
416
417	<	double ri[3], rj[3], rk[3];
418	<	double rij[3], rjk[3], rki[3];
267	<	double minDist;
417	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
418	>	torsion = mol->nextTorsion(torsionIter)) {
419
420	<	ri[0] = Hmat[0][0];
421	<	ri[1] = Hmat[1][0];
422	<	ri[2] = Hmat[2][0];
420	>	a = torsion->getAtomA()->getGlobalIndex();
421	>	b = torsion->getAtomB()->getGlobalIndex();
422	>	c = torsion->getAtomC()->getGlobalIndex();
423	>	d = torsion->getAtomD()->getGlobalIndex();
424
425	<	rj[0] = Hmat[0][1];
426	<	rj[1] = Hmat[1][1];
427	<	rj[2] = Hmat[2][1];
425	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
426	>	oneTwoInteractions_.addPair(a, b);
427	>	oneTwoInteractions_.addPair(b, c);
428	>	oneTwoInteractions_.addPair(c, d);
429	>	} else {
430	>	excludedInteractions_.addPair(a, b);
431	>	excludedInteractions_.addPair(b, c);
432	>	excludedInteractions_.addPair(c, d);
433	>	}
434
435	<	rk[0] = Hmat[0][2];
436	<	rk[1] = Hmat[1][2];
437	<	rk[2] = Hmat[2][2];
438	<
439	<	crossProduct3(ri, rj, rij);
440	<	distXY = dotProduct3(rk,rij) / norm3(rij);
435	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
436	>	oneThreeInteractions_.addPair(a, c);
437	>	oneThreeInteractions_.addPair(b, d);
438	>	} else {
439	>	excludedInteractions_.addPair(a, c);
440	>	excludedInteractions_.addPair(b, d);
441	>	}
442
443	<	crossProduct3(rj,rk, rjk);
444	<	distYZ = dotProduct3(ri,rjk) / norm3(rjk);
443	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
444	>	oneFourInteractions_.addPair(a, d);
445	>	} else {
446	>	excludedInteractions_.addPair(a, d);
447	>	}
448	>	}
449
450	<	crossProduct3(rk,ri, rki);
451	<	distZX = dotProduct3(rj,rki) / norm3(rki);
450	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
451	>	inversion = mol->nextInversion(inversionIter)) {
452
453	<	minDist = min(min(distXY, distYZ), distZX);
454	<	return minDist/2;
455	<
456	<	}
453	>	a = inversion->getAtomA()->getGlobalIndex();
454	>	b = inversion->getAtomB()->getGlobalIndex();
455	>	c = inversion->getAtomC()->getGlobalIndex();
456	>	d = inversion->getAtomD()->getGlobalIndex();
457
458	<	void SimInfo::wrapVector( double thePos[3] ){
458	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
459	>	oneTwoInteractions_.addPair(a, b);
460	>	oneTwoInteractions_.addPair(a, c);
461	>	oneTwoInteractions_.addPair(a, d);
462	>	} else {
463	>	excludedInteractions_.addPair(a, b);
464	>	excludedInteractions_.addPair(a, c);
465	>	excludedInteractions_.addPair(a, d);
466	>	}
467
468	<	int i;
469	<	double scaled[3];
468	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
469	>	oneThreeInteractions_.addPair(b, c);
470	>	oneThreeInteractions_.addPair(b, d);
471	>	oneThreeInteractions_.addPair(c, d);
472	>	} else {
473	>	excludedInteractions_.addPair(b, c);
474	>	excludedInteractions_.addPair(b, d);
475	>	excludedInteractions_.addPair(c, d);
476	>	}
477	>	}
478
479	<	if( !orthoRhombic ){
480	<	// calc the scaled coordinates.
481	<
479	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
480	>	rb = mol->nextRigidBody(rbIter)) {
481	>	vector<Atom*> atoms = rb->getAtoms();
482	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
483	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
484	>	a = atoms[i]->getGlobalIndex();
485	>	b = atoms[j]->getGlobalIndex();
486	>	excludedInteractions_.addPair(a, b);
487	>	}
488	>	}
489	>	}
490
491	<	matVecMul3(HmatInv, thePos, scaled);
491	>	}
492	>
493	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
494	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
495	>	vector<Bond*>::iterator bondIter;
496	>	vector<Bend*>::iterator bendIter;
497	>	vector<Torsion*>::iterator torsionIter;
498	>	vector<Inversion*>::iterator inversionIter;
499	>	Bond* bond;
500	>	Bend* bend;
501	>	Torsion* torsion;
502	>	Inversion* inversion;
503	>	int a;
504	>	int b;
505	>	int c;
506	>	int d;
507	>
508	>	map<int, set<int> > atomGroups;
509	>	Molecule::RigidBodyIterator rbIter;
510	>	RigidBody* rb;
511	>	Molecule::IntegrableObjectIterator ii;
512	>	StuntDouble* integrableObject;
513
514	<	for(i=0; i<3; i++)
515	<	scaled[i] -= roundMe(scaled[i]);
516	<
517	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
518	<
519	<	matVecMul3(Hmat, scaled, thePos);
514	>	for (integrableObject = mol->beginIntegrableObject(ii);
515	>	integrableObject != NULL;
516	>	integrableObject = mol->nextIntegrableObject(ii)) {
517	>
518	>	if (integrableObject->isRigidBody()) {
519	>	rb = static_cast<RigidBody*>(integrableObject);
520	>	vector<Atom*> atoms = rb->getAtoms();
521	>	set<int> rigidAtoms;
522	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
523	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
524	>	}
525	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
526	>	atomGroups.insert(map<int, set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
527	>	}
528	>	} else {
529	>	set<int> oneAtomSet;
530	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
531	>	atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
532	>	}
533	>	}
534
535	<	}
536	<	else{
537	<	// calc the scaled coordinates.
535	>	for (bond= mol->beginBond(bondIter); bond != NULL;
536	>	bond = mol->nextBond(bondIter)) {
537	>
538	>	a = bond->getAtomA()->getGlobalIndex();
539	>	b = bond->getAtomB()->getGlobalIndex();
540
541	<	for(i=0; i<3; i++)
542	<	scaled[i] = thePos[i]*HmatInv[i][i];
543	<
544	<	// wrap the scaled coordinates
545	<
546	<	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	<	}
541	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
542	>	oneTwoInteractions_.removePair(a, b);
543	>	} else {
544	>	excludedInteractions_.removePair(a, b);
545	>	}
546	>	}
547
548	+	for (bend= mol->beginBend(bendIter); bend != NULL;
549	+	bend = mol->nextBend(bendIter)) {
550
551	<	int SimInfo::getNDF(){
552	<	int ndf_local;
551	>	a = bend->getAtomA()->getGlobalIndex();
552	>	b = bend->getAtomB()->getGlobalIndex();
553	>	c = bend->getAtomC()->getGlobalIndex();
554	>
555	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
556	>	oneTwoInteractions_.removePair(a, b);
557	>	oneTwoInteractions_.removePair(b, c);
558	>	} else {
559	>	excludedInteractions_.removePair(a, b);
560	>	excludedInteractions_.removePair(b, c);
561	>	}
562
563	<	ndf_local = 0;
564	<
565	<	for(int i = 0; i < integrableObjects.size(); i++){
566	<	ndf_local += 3;
567	<	if (integrableObjects[i]->isDirectional()) {
342	<	if (integrableObjects[i]->isLinear())
343	<	ndf_local += 2;
344	<	else
345	<	ndf_local += 3;
563	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
564	>	oneThreeInteractions_.removePair(a, c);
565	>	} else {
566	>	excludedInteractions_.removePair(a, c);
567	>	}
568		}
347	–	}
569
570	<	// n_constraints is local, so subtract them on each processor:
570	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
571	>	torsion = mol->nextTorsion(torsionIter)) {
572
573	<	ndf_local -= n_constraints;
573	>	a = torsion->getAtomA()->getGlobalIndex();
574	>	b = torsion->getAtomB()->getGlobalIndex();
575	>	c = torsion->getAtomC()->getGlobalIndex();
576	>	d = torsion->getAtomD()->getGlobalIndex();
577	>
578	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
579	>	oneTwoInteractions_.removePair(a, b);
580	>	oneTwoInteractions_.removePair(b, c);
581	>	oneTwoInteractions_.removePair(c, d);
582	>	} else {
583	>	excludedInteractions_.removePair(a, b);
584	>	excludedInteractions_.removePair(b, c);
585	>	excludedInteractions_.removePair(c, d);
586	>	}
587
588	<	#ifdef IS_MPI
589	<	MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
590	<	#else
591	<	ndf = ndf_local;
592	<	#endif
588	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
589	>	oneThreeInteractions_.removePair(a, c);
590	>	oneThreeInteractions_.removePair(b, d);
591	>	} else {
592	>	excludedInteractions_.removePair(a, c);
593	>	excludedInteractions_.removePair(b, d);
594	>	}
595
596	<	// nZconstraints is global, as are the 3 COM translations for the
597	<	// entire system:
596	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
597	>	oneFourInteractions_.removePair(a, d);
598	>	} else {
599	>	excludedInteractions_.removePair(a, d);
600	>	}
601	>	}
602
603	<	ndf = ndf - 3 - nZconstraints;
603	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
604	>	inversion = mol->nextInversion(inversionIter)) {
605
606	<	return ndf;
607	<	}
606	>	a = inversion->getAtomA()->getGlobalIndex();
607	>	b = inversion->getAtomB()->getGlobalIndex();
608	>	c = inversion->getAtomC()->getGlobalIndex();
609	>	d = inversion->getAtomD()->getGlobalIndex();
610
611	<	int SimInfo::getNDFraw() {
612	<	int ndfRaw_local;
611	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
612	>	oneTwoInteractions_.removePair(a, b);
613	>	oneTwoInteractions_.removePair(a, c);
614	>	oneTwoInteractions_.removePair(a, d);
615	>	} else {
616	>	excludedInteractions_.removePair(a, b);
617	>	excludedInteractions_.removePair(a, c);
618	>	excludedInteractions_.removePair(a, d);
619	>	}
620
621	<	// Raw degrees of freedom that we have to set
622	<	ndfRaw_local = 0;
623	<
624	<	for(int i = 0; i < integrableObjects.size(); i++){
625	<	ndfRaw_local += 3;
626	<	if (integrableObjects[i]->isDirectional()) {
627	<	if (integrableObjects[i]->isLinear())
628	<	ndfRaw_local += 2;
629	<	else
379	<	ndfRaw_local += 3;
621	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
622	>	oneThreeInteractions_.removePair(b, c);
623	>	oneThreeInteractions_.removePair(b, d);
624	>	oneThreeInteractions_.removePair(c, d);
625	>	} else {
626	>	excludedInteractions_.removePair(b, c);
627	>	excludedInteractions_.removePair(b, d);
628	>	excludedInteractions_.removePair(c, d);
629	>	}
630		}
631	+
632	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
633	+	rb = mol->nextRigidBody(rbIter)) {
634	+	vector<Atom*> atoms = rb->getAtoms();
635	+	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
636	+	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
637	+	a = atoms[i]->getGlobalIndex();
638	+	b = atoms[j]->getGlobalIndex();
639	+	excludedInteractions_.removePair(a, b);
640	+	}
641	+	}
642	+	}
643	+
644		}
645	+
646	+
647	+	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
648	+	int curStampId;
649
650	<	#ifdef IS_MPI
651	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
385	<	#else
386	<	ndfRaw = ndfRaw_local;
387	<	#endif
650	>	//index from 0
651	>	curStampId = moleculeStamps_.size();
652
653	<	return ndfRaw;
654	<	}
653	>	moleculeStamps_.push_back(molStamp);
654	>	molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
655	>	}
656
392	–	int SimInfo::getNDFtranslational() {
393	–	int ndfTrans_local;
657
658	<	ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
658	>	/**
659	>	* update
660	>	*
661	>	*  Performs the global checks and variable settings after the objects have been
662	>	*  created.
663	>	*
664	>	*/
665	>	void SimInfo::update() {
666	>
667	>	setupSimVariables();
668	>	setupCutoffs();
669	>	setupSwitching();
670	>	setupElectrostatics();
671	>	setupNeighborlists();
672	>
673	>	#ifdef IS_MPI
674	>	setupFortranParallel();
675	>	#endif
676	>	setupFortranSim();
677	>	fortranInitialized_ = true;
678	>
679	>	calcNdf();
680	>	calcNdfRaw();
681	>	calcNdfTrans();
682	>	}
683	>
684	>	set<AtomType*> SimInfo::getSimulatedAtomTypes() {
685	>	SimInfo::MoleculeIterator mi;
686	>	Molecule* mol;
687	>	Molecule::AtomIterator ai;
688	>	Atom* atom;
689	>	set<AtomType*> atomTypes;
690	>
691	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
692	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
693	>	atomTypes.insert(atom->getAtomType());
694	>	}
695	>	}
696	>	return atomTypes;
697	>	}
698
699	+	/**
700	+	* setupCutoffs
701	+	*
702	+	* Sets the values of cutoffRadius and cutoffMethod
703	+	*
704	+	* cutoffRadius : realType
705	+	*  If the cutoffRadius was explicitly set, use that value.
706	+	*  If the cutoffRadius was not explicitly set:
707	+	*      Are there electrostatic atoms?  Use 12.0 Angstroms.
708	+	*      No electrostatic atoms?  Poll the atom types present in the
709	+	*      simulation for suggested cutoff values (e.g. 2.5 * sigma).
710	+	*      Use the maximum suggested value that was found.
711	+	*
712	+	* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL)
713	+	*      If cutoffMethod was explicitly set, use that choice.
714	+	*      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
715	+	*/
716	+	void SimInfo::setupCutoffs() {
717	+
718	+	if (simParams_->haveCutoffRadius()) {
719	+	cutoffRadius_ = simParams_->getCutoffRadius();
720	+	} else {
721	+	if (usesElectrostaticAtoms_) {
722	+	sprintf(painCave.errMsg,
723	+	"SimInfo: No value was set for the cutoffRadius.\n"
724	+	"\tOpenMD will use a default value of 12.0 angstroms"
725	+	"\tfor the cutoffRadius.\n");
726	+	painCave.isFatal = 0;
727	+	painCave.severity = OPENMD_INFO;
728	+	simError();
729	+	cutoffRadius_ = 12.0;
730	+	} else {
731	+	RealType thisCut;
732	+	set<AtomType*>::iterator i;
733	+	set<AtomType*> atomTypes;
734	+	atomTypes = getSimulatedAtomTypes();
735	+	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
736	+	thisCut = InteractionManager::Instance()->getSuggestedCutoffRadius((*i));
737	+	cutoffRadius_ = max(thisCut, cutoffRadius_);
738	+	}
739	+	sprintf(painCave.errMsg,
740	+	"SimInfo: No value was set for the cutoffRadius.\n"
741	+	"\tOpenMD will use %lf angstroms.\n",
742	+	cutoffRadius_);
743	+	painCave.isFatal = 0;
744	+	painCave.severity = OPENMD_INFO;
745	+	simError();
746	+	}
747	+	}
748
749	<	#ifdef IS_MPI
399	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
400	<	#else
401	<	ndfTrans = ndfTrans_local;
402	<	#endif
749	>	InteractionManager::Instance()->setCutoffRadius(cutoffRadius_);
750
751	<	ndfTrans = ndfTrans - 3 - nZconstraints;
751	>	map<string, CutoffMethod> stringToCutoffMethod;
752	>	stringToCutoffMethod["HARD"] = HARD;
753	>	stringToCutoffMethod["SWITCHING_FUNCTION"] = SWITCHING_FUNCTION;
754	>	stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;
755	>	stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
756	>
757	>	if (simParams_->haveCutoffMethod()) {
758	>	string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
759	>	map<string, CutoffMethod>::iterator i;
760	>	i = stringToCutoffMethod.find(cutMeth);
761	>	if (i == stringToCutoffMethod.end()) {
762	>	sprintf(painCave.errMsg,
763	>	"SimInfo: Could not find chosen cutoffMethod %s\n"
764	>	"\tShould be one of: "
765	>	"HARD, SWITCHING_FUNCTION, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
766	>	cutMeth.c_str());
767	>	painCave.isFatal = 1;
768	>	painCave.severity = OPENMD_ERROR;
769	>	simError();
770	>	} else {
771	>	cutoffMethod_ = i->second;
772	>	}
773	>	} else {
774	>	sprintf(painCave.errMsg,
775	>	"SimInfo: No value was set for the cutoffMethod.\n"
776	>	"\tOpenMD will use SHIFTED_FORCE.\n");
777	>	painCave.isFatal = 0;
778	>	painCave.severity = OPENMD_INFO;
779	>	simError();
780	>	cutoffMethod_ = SHIFTED_FORCE;
781	>	}
782
783	<	return ndfTrans;
784	<	}
783	>	InteractionManager::Instance()->setCutoffMethod(cutoffMethod_);
784	>	}
785	>
786	>	/**
787	>	* setupSwitching
788	>	*
789	>	* Sets the values of switchingRadius and
790	>	*  If the switchingRadius was explicitly set, use that value (but check it)
791	>	*  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
792	>	*/
793	>	void SimInfo::setupSwitching() {
794	>
795	>	if (simParams_->haveSwitchingRadius()) {
796	>	switchingRadius_ = simParams_->getSwitchingRadius();
797	>	if (switchingRadius_ > cutoffRadius_) {
798	>	sprintf(painCave.errMsg,
799	>	"SimInfo: switchingRadius (%f) is larger than cutoffRadius(%f)\n",
800	>	switchingRadius_, cutoffRadius_);
801	>	painCave.isFatal = 1;
802	>	painCave.severity = OPENMD_ERROR;
803	>	simError();
804	>	}
805	>	} else {
806	>	switchingRadius_ = 0.85 * cutoffRadius_;
807	>	sprintf(painCave.errMsg,
808	>	"SimInfo: No value was set for the switchingRadius.\n"
809	>	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
810	>	"\tswitchingRadius = %f. for this simulation\n", switchingRadius_);
811	>	painCave.isFatal = 0;
812	>	painCave.severity = OPENMD_WARNING;
813	>	simError();
814	>	}
815	>
816	>	InteractionManager::Instance()->setSwitchingRadius(switchingRadius_);
817
818	<	int SimInfo::getTotIntegrableObjects() {
819	<	int nObjs_local;
820	<	int nObjs;
818	>	SwitchingFunctionType ft;
819	>
820	>	if (simParams_->haveSwitchingFunctionType()) {
821	>	string funcType = simParams_->getSwitchingFunctionType();
822	>	toUpper(funcType);
823	>	if (funcType == "CUBIC") {
824	>	ft = cubic;
825	>	} else {
826	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
827	>	ft = fifth_order_poly;
828	>	} else {
829	>	// throw error
830	>	sprintf( painCave.errMsg,
831	>	"SimInfo : Unknown switchingFunctionType. (Input file specified %s .)\n"
832	>	"\tswitchingFunctionType must be one of: "
833	>	"\"cubic\" or \"fifth_order_polynomial\".",
834	>	funcType.c_str() );
835	>	painCave.isFatal = 1;
836	>	painCave.severity = OPENMD_ERROR;
837	>	simError();
838	>	}
839	>	}
840	>	}
841
842	<	nObjs_local =  integrableObjects.size();
842	>	InteractionManager::Instance()->setSwitchingFunctionType(ft);
843	>	}
844
845	+	/**
846	+	* setupSkinThickness
847	+	*
848	+	*  If the skinThickness was explicitly set, use that value (but check it)
849	+	*  If the skinThickness was not explicitly set: use 1.0 angstroms
850	+	*/
851	+	void SimInfo::setupSkinThickness() {
852	+	if (simParams_->haveSkinThickness()) {
853	+	skinThickness_ = simParams_->getSkinThickness();
854	+	} else {
855	+	skinThickness_ = 1.0;
856	+	sprintf(painCave.errMsg,
857	+	"SimInfo Warning: No value was set for the skinThickness.\n"
858	+	"\tOpenMD will use a default value of %f Angstroms\n"
859	+	"\tfor this simulation\n", skinThickness_);
860	+	painCave.isFatal = 0;
861	+	simError();
862	+	}
863	+	}
864
865	<	#ifdef IS_MPI
866	<	MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
867	<	#else
868	<	nObjs = nObjs_local;
420	<	#endif
865	>	void SimInfo::setupSimType() {
866	>	set<AtomType*>::iterator i;
867	>	set<AtomType*> atomTypes;
868	>	atomTypes = getSimulatedAtomTypes();
869
870	+	useAtomicVirial_ = simParams_->getUseAtomicVirial();
871
872	<	return nObjs;
873	<	}
872	>	int usesElectrostatic = 0;
873	>	int usesMetallic = 0;
874	>	int usesDirectional = 0;
875	>	//loop over all of the atom types
876	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
877	>	usesElectrostatic |= (*i)->isElectrostatic();
878	>	usesMetallic |= (*i)->isMetal();
879	>	usesDirectional |= (*i)->isDirectional();
880	>	}
881
882	<	void SimInfo::refreshSim(){
882	>	#ifdef IS_MPI
883	>	int temp;
884	>	temp = usesDirectional;
885	>	MPI_Allreduce(&temp, &usesDirectionalAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
886
887	<	simtype fInfo;
888	<	int isError;
430	<	int n_global;
431	<	int* excl;
887	>	temp = usesMetallic;
888	>	MPI_Allreduce(&temp, &usesMetallicAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
889
890	<	fInfo.dielect = 0.0;
891	<
892	<	if( useDipoles ){
893	<	if( useReactionField )fInfo.dielect = dielectric;
890	>	temp = usesElectrostatic;
891	>	MPI_Allreduce(&temp, &usesElectrostaticAtoms_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
892	>	#endif
893	>	fInfo_.SIM_uses_PBC = usesPeriodicBoundaries_;
894	>	fInfo_.SIM_uses_DirectionalAtoms = usesDirectionalAtoms_;
895	>	fInfo_.SIM_uses_MetallicAtoms = usesMetallicAtoms_;
896	>	fInfo_.SIM_requires_SkipCorrection = usesElectrostaticAtoms_;
897	>	fInfo_.SIM_requires_SelfCorrection = usesElectrostaticAtoms_;
898	>	fInfo_.SIM_uses_AtomicVirial = usesAtomicVirial_;
899		}
900
901	<	fInfo.SIM_uses_PBC = usePBC;
901	>	void SimInfo::setupFortranSim() {
902	>	int isError;
903	>	int nExclude, nOneTwo, nOneThree, nOneFour;
904	>	vector<int> fortranGlobalGroupMembership;
905	>
906	>	notifyFortranSkinThickness(&skinThickness_);
907
908	<	if (useSticky || useDipoles || useGayBerne || useShapes) {
909	<	useDirectionalAtoms = 1;
910	<	fInfo.SIM_uses_DirectionalAtoms = useDirectionalAtoms;
444	<	}
908	>	int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0;
909	>	int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0;
910	>	notifyFortranCutoffs(&cutoffRadius_, &switchingRadius_, &ljsp, &ljsf);
911
912	<	fInfo.SIM_uses_LennardJones = useLennardJones;
912	>	isError = 0;
913
914	<	if (useCharges || useDipoles) {
915	<	useElectrostatics = 1;
916	<	fInfo.SIM_uses_Electrostatics = useElectrostatics;
917	<	}
914	>	//globalGroupMembership_ is filled by SimCreator
915	>	for (int i = 0; i < nGlobalAtoms_; i++) {
916	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
917	>	}
918
919	<	fInfo.SIM_uses_Charges = useCharges;
920	<	fInfo.SIM_uses_Dipoles = useDipoles;
921	<	fInfo.SIM_uses_Sticky = useSticky;
922	<	fInfo.SIM_uses_GayBerne = useGayBerne;
923	<	fInfo.SIM_uses_EAM = useEAM;
924	<	fInfo.SIM_uses_Shapes = useShapes;
925	<	fInfo.SIM_uses_FLARB = useFLARB;
926	<	fInfo.SIM_uses_RF = useReactionField;
919	>	//calculate mass ratio of cutoff group
920	>	vector<RealType> mfact;
921	>	SimInfo::MoleculeIterator mi;
922	>	Molecule* mol;
923	>	Molecule::CutoffGroupIterator ci;
924	>	CutoffGroup* cg;
925	>	Molecule::AtomIterator ai;
926	>	Atom* atom;
927	>	RealType totalMass;
928
929	<	n_exclude = excludes->getSize();
930	<	excl = excludes->getFortranArray();
464	<
465	<	#ifdef IS_MPI
466	<	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);
480	<
481	<	if( isError ){
929	>	//to avoid memory reallocation, reserve enough space for mfact
930	>	mfact.reserve(getNCutoffGroups());
931
932	<	sprintf( painCave.errMsg,
933	<	"There was an error setting the simulation information in fortran.\n" );
485	<	painCave.isFatal = 1;
486	<	painCave.severity = OOPSE_ERROR;
487	<	simError();
488	<	}
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	<	}
932	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
933	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
934
935	<	void SimInfo::setDefaultRcut( double theRcut ){
936	<
937	<	haveRcut = 1;
938	<	rCut = theRcut;
939	<	rList = rCut + 1.0;
940	<
941	<	notifyFortranCutoffs( &rCut, &rSw, &rList );
942	<	}
935	>	totalMass = cg->getMass();
936	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
937	>	// Check for massless groups - set mfact to 1 if true
938	>	if (totalMass != 0)
939	>	mfact.push_back(atom->getMass()/totalMass);
940	>	else
941	>	mfact.push_back( 1.0 );
942	>	}
943	>	}
944	>	}
945
946	<	void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
946	>	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
947	>	vector<int> identArray;
948
949	<	rSw = theRsw;
950	<	setDefaultRcut( theRcut );
951	<	}
949	>	//to avoid memory reallocation, reserve enough space identArray
950	>	identArray.reserve(getNAtoms());
951	>
952	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
953	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
954	>	identArray.push_back(atom->getIdent());
955	>	}
956	>	}
957
958	+	//fill molMembershipArray
959	+	//molMembershipArray is filled by SimCreator
960	+	vector<int> molMembershipArray(nGlobalAtoms_);
961	+	for (int i = 0; i < nGlobalAtoms_; i++) {
962	+	molMembershipArray[i] = globalMolMembership_[i] + 1;
963	+	}
964	+
965	+	//setup fortran simulation
966
967	<	void SimInfo::checkCutOffs( void ){
968	<
969	<	if( boxIsInit ){
967	>	nExclude = excludedInteractions_.getSize();
968	>	nOneTwo = oneTwoInteractions_.getSize();
969	>	nOneThree = oneThreeInteractions_.getSize();
970	>	nOneFour = oneFourInteractions_.getSize();
971	>
972	>	int* excludeList = excludedInteractions_.getPairList();
973	>	int* oneTwoList = oneTwoInteractions_.getPairList();
974	>	int* oneThreeList = oneThreeInteractions_.getPairList();
975	>	int* oneFourList = oneFourInteractions_.getPairList();
976	>
977	>	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
978	>	&nExclude, excludeList,
979	>	&nOneTwo, oneTwoList,
980	>	&nOneThree, oneThreeList,
981	>	&nOneFour, oneFourList,
982	>	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
983	>	&fortranGlobalGroupMembership[0], &isError);
984
985	<	//we need to check cutOffs against the box
986	<
523	<	if( rCut > maxCutoff ){
985	>	if( isError ){
986	>
987		sprintf( painCave.errMsg,
988	<	"cutoffRadius is too large for the current periodic box.\n"
526	<	"\tCurrent Value of cutoffRadius = %G at time %G\n "
527	<	"\tThis is larger than half of at least one of the\n"
528	<	"\tperiodic box vectors.  Right now, the Box matrix is:\n"
529	<	"\n"
530	<	"\t[ %G %G %G ]\n"
531	<	"\t[ %G %G %G ]\n"
532	<	"\t[ %G %G %G ]\n",
533	<	rCut, currentTime,
534	<	Hmat[0][0], Hmat[0][1], Hmat[0][2],
535	<	Hmat[1][0], Hmat[1][1], Hmat[1][2],
536	<	Hmat[2][0], Hmat[2][1], Hmat[2][2]);
537	<	painCave.severity = OOPSE_ERROR;
988	>	"There was an error setting the simulation information in fortran.\n" );
989		painCave.isFatal = 1;
990	+	painCave.severity = OPENMD_ERROR;
991		simError();
992	<	}
993	<	} else {
994	<	// initialize this stuff before using it, OK?
995	<	sprintf( painCave.errMsg,
996	<	"Trying to check cutoffs without a box.\n"
997	<	"\tOOPSE should have better programmers than that.\n" );
998	<	painCave.severity = OOPSE_ERROR;
999	<	painCave.isFatal = 1;
1000	<	simError();
992	>	}
993	>
994	>
995	>	sprintf( checkPointMsg,
996	>	"succesfully sent the simulation information to fortran.\n");
997	>
998	>	errorCheckPoint();
999	>
1000	>	// Setup number of neighbors in neighbor list if present
1001	>	if (simParams_->haveNeighborListNeighbors()) {
1002	>	int nlistNeighbors = simParams_->getNeighborListNeighbors();
1003	>	setNeighbors(&nlistNeighbors);
1004	>	}
1005	>
1006	>
1007		}
550	–
551	–	}
1008
553	–	void SimInfo::addProperty(GenericData* prop){
1009
1010	<	map<string, GenericData*>::iterator result;
1011	<	result = properties.find(prop->getID());
1012	<
1013	<	//we can't simply use  properties[prop->getID()] = prop,
1014	<	//it will cause memory leak if we already contain a propery which has the same name of prop
1015	<
1016	<	if(result != properties.end()){
1017	<
1018	<	delete (*result).second;
1019	<	(*result).second = prop;
1020	<
1021	<	}
1022	<	else{
1010	>	void SimInfo::setupFortranParallel() {
1011	>	#ifdef IS_MPI
1012	>	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
1013	>	vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
1014	>	vector<int> localToGlobalCutoffGroupIndex;
1015	>	SimInfo::MoleculeIterator mi;
1016	>	Molecule::AtomIterator ai;
1017	>	Molecule::CutoffGroupIterator ci;
1018	>	Molecule* mol;
1019	>	Atom* atom;
1020	>	CutoffGroup* cg;
1021	>	mpiSimData parallelData;
1022	>	int isError;
1023
1024	<	properties[prop->getID()] = prop;
1024	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
1025
1026	+	//local index(index in DataStorge) of atom is important
1027	+	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
1028	+	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
1029	+	}
1030	+
1031	+	//local index of cutoff group is trivial, it only depends on the order of travesing
1032	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
1033	+	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
1034	+	}
1035	+
1036	+	}
1037	+
1038	+	//fill up mpiSimData struct
1039	+	parallelData.nMolGlobal = getNGlobalMolecules();
1040	+	parallelData.nMolLocal = getNMolecules();
1041	+	parallelData.nAtomsGlobal = getNGlobalAtoms();
1042	+	parallelData.nAtomsLocal = getNAtoms();
1043	+	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
1044	+	parallelData.nGroupsLocal = getNCutoffGroups();
1045	+	parallelData.myNode = worldRank;
1046	+	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
1047	+
1048	+	//pass mpiSimData struct and index arrays to fortran
1049	+	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
1050	+	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
1051	+	&localToGlobalCutoffGroupIndex[0], &isError);
1052	+
1053	+	if (isError) {
1054	+	sprintf(painCave.errMsg,
1055	+	"mpiRefresh errror: fortran didn't like something we gave it.\n");
1056	+	painCave.isFatal = 1;
1057	+	simError();
1058	+	}
1059	+
1060	+	sprintf(checkPointMsg, " mpiRefresh successful.\n");
1061	+	errorCheckPoint();
1062	+
1063	+	#endif
1064		}
1065	+
1066	+
1067	+	void SimInfo::setupSwitchingFunction() {
1068	+
1069	+	}
1070	+
1071	+	void SimInfo::setupAccumulateBoxDipole() {
1072	+
1073	+	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1074	+	if ( simParams_->haveAccumulateBoxDipole() )
1075	+	if ( simParams_->getAccumulateBoxDipole() ) {
1076	+	calcBoxDipole_ = true;
1077	+	}
1078	+
1079	+	}
1080	+
1081	+	void SimInfo::addProperty(GenericData* genData) {
1082	+	properties_.addProperty(genData);
1083	+	}
1084	+
1085	+	void SimInfo::removeProperty(const string& propName) {
1086	+	properties_.removeProperty(propName);
1087	+	}
1088	+
1089	+	void SimInfo::clearProperties() {
1090	+	properties_.clearProperties();
1091	+	}
1092	+
1093	+	vector<string> SimInfo::getPropertyNames() {
1094	+	return properties_.getPropertyNames();
1095	+	}
1096	+
1097	+	vector<GenericData*> SimInfo::getProperties() {
1098	+	return properties_.getProperties();
1099	+	}
1100	+
1101	+	GenericData* SimInfo::getPropertyByName(const string& propName) {
1102	+	return properties_.getPropertyByName(propName);
1103	+	}
1104	+
1105	+	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1106	+	if (sman_ == sman) {
1107	+	return;
1108	+	}
1109	+	delete sman_;
1110	+	sman_ = sman;
1111	+
1112	+	Molecule* mol;
1113	+	RigidBody* rb;
1114	+	Atom* atom;
1115	+	SimInfo::MoleculeIterator mi;
1116	+	Molecule::RigidBodyIterator rbIter;
1117	+	Molecule::AtomIterator atomIter;;
1118	+
1119	+	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1120	+
1121	+	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1122	+	atom->setSnapshotManager(sman_);
1123	+	}
1124	+
1125	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1126	+	rb->setSnapshotManager(sman_);
1127	+	}
1128	+	}
1129
1130	<	}
1130	>	}
1131
1132	<	GenericData* SimInfo::getProperty(const string& propName){
1132	>	Vector3d SimInfo::getComVel(){
1133	>	SimInfo::MoleculeIterator i;
1134	>	Molecule* mol;
1135	>
1136	>	Vector3d comVel(0.0);
1137	>	RealType totalMass = 0.0;
1138	>
1139
1140	<	map<string, GenericData*>::iterator result;
1141	<
1142	<	//string lowerCaseName = ();
1143	<
1144	<	result = properties.find(propName);
582	<
583	<	if(result != properties.end())
584	<	return (*result).second;
585	<	else
586	<	return NULL;
587	<	}
1140	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1141	>	RealType mass = mol->getMass();
1142	>	totalMass += mass;
1143	>	comVel += mass * mol->getComVel();
1144	>	}
1145
1146	+	#ifdef IS_MPI
1147	+	RealType tmpMass = totalMass;
1148	+	Vector3d tmpComVel(comVel);
1149	+	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1150	+	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1151	+	#endif
1152
1153	<	void SimInfo::getFortranGroupArrays(SimInfo* info,
591	<	vector<int>& FglobalGroupMembership,
592	<	vector<double>& mfact){
593	<
594	<	Molecule* myMols;
595	<	Atom** myAtoms;
596	<	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;
606	<
607	<	mfact.clear();
608	<	FglobalGroupMembership.clear();
609	<
1153	>	comVel /= totalMass;
1154
1155	<	// Fix the silly fortran indexing problem
1155	>	return comVel;
1156	>	}
1157	>
1158	>	Vector3d SimInfo::getCom(){
1159	>	SimInfo::MoleculeIterator i;
1160	>	Molecule* mol;
1161	>
1162	>	Vector3d com(0.0);
1163	>	RealType totalMass = 0.0;
1164	>
1165	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1166	>	RealType mass = mol->getMass();
1167	>	totalMass += mass;
1168	>	com += mass * mol->getCom();
1169	>	}
1170	>
1171		#ifdef IS_MPI
1172	<	numAtom = mpiSim->getNAtomsGlobal();
1173	<	#else
1174	<	numAtom = n_atoms;
1172	>	RealType tmpMass = totalMass;
1173	>	Vector3d tmpCom(com);
1174	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1175	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1176		#endif
617	–	for (int i = 0; i < numAtom; i++)
618	–	FglobalGroupMembership.push_back(globalGroupMembership[i] + 1);
619	–
1177
1178	<	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)){
1178	>	com /= totalMass;
1179
1180	<	totalMass = myCutoffGroup->getMass();
1180	>	return com;
1181	>
1182	>	}
1183	>
1184	>	ostream& operator <<(ostream& o, SimInfo& info) {
1185	>
1186	>	return o;
1187	>	}
1188	>
1189	>
1190	>	/*
1191	>	Returns center of mass and center of mass velocity in one function call.
1192	>	*/
1193	>
1194	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1195	>	SimInfo::MoleculeIterator i;
1196	>	Molecule* mol;
1197
1198	<	for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom);
1199	<	cutoffAtom != NULL;
1200	<	cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
1201	<	mfact.push_back(cutoffAtom->getMass()/totalMass);
1198	>
1199	>	RealType totalMass = 0.0;
1200	>
1201	>
1202	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1203	>	RealType mass = mol->getMass();
1204	>	totalMass += mass;
1205	>	com += mass * mol->getCom();
1206	>	comVel += mass * mol->getComVel();
1207		}
1208	+
1209	+	#ifdef IS_MPI
1210	+	RealType tmpMass = totalMass;
1211	+	Vector3d tmpCom(com);
1212	+	Vector3d tmpComVel(comVel);
1213	+	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1214	+	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1215	+	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1216	+	#endif
1217	+
1218	+	com /= totalMass;
1219	+	comVel /= totalMass;
1220	+	}
1221	+
1222	+	/*
1223	+	Return intertia tensor for entire system and angular momentum Vector.
1224	+
1225	+
1226	+	[  Ixx -Ixy  -Ixz ]
1227	+	J =| -Iyx  Iyy  -Iyz |
1228	+	[ -Izx -Iyz   Izz ]
1229	+	*/
1230	+
1231	+	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1232	+
1233	+
1234	+	RealType xx = 0.0;
1235	+	RealType yy = 0.0;
1236	+	RealType zz = 0.0;
1237	+	RealType xy = 0.0;
1238	+	RealType xz = 0.0;
1239	+	RealType yz = 0.0;
1240	+	Vector3d com(0.0);
1241	+	Vector3d comVel(0.0);
1242	+
1243	+	getComAll(com, comVel);
1244	+
1245	+	SimInfo::MoleculeIterator i;
1246	+	Molecule* mol;
1247	+
1248	+	Vector3d thisq(0.0);
1249	+	Vector3d thisv(0.0);
1250	+
1251	+	RealType thisMass = 0.0;
1252	+
1253	+
1254	+
1255	+
1256	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1257	+
1258	+	thisq = mol->getCom()-com;
1259	+	thisv = mol->getComVel()-comVel;
1260	+	thisMass = mol->getMass();
1261	+	// Compute moment of intertia coefficients.
1262	+	xx += thisq[0]*thisq[0]*thisMass;
1263	+	yy += thisq[1]*thisq[1]*thisMass;
1264	+	zz += thisq[2]*thisq[2]*thisMass;
1265	+
1266	+	// compute products of intertia
1267	+	xy += thisq[0]*thisq[1]*thisMass;
1268	+	xz += thisq[0]*thisq[2]*thisMass;
1269	+	yz += thisq[1]*thisq[2]*thisMass;
1270	+
1271	+	angularMomentum += cross( thisq, thisv ) * thisMass;
1272	+
1273	+	}
1274	+
1275	+
1276	+	inertiaTensor(0,0) = yy + zz;
1277	+	inertiaTensor(0,1) = -xy;
1278	+	inertiaTensor(0,2) = -xz;
1279	+	inertiaTensor(1,0) = -xy;
1280	+	inertiaTensor(1,1) = xx + zz;
1281	+	inertiaTensor(1,2) = -yz;
1282	+	inertiaTensor(2,0) = -xz;
1283	+	inertiaTensor(2,1) = -yz;
1284	+	inertiaTensor(2,2) = xx + yy;
1285	+
1286	+	#ifdef IS_MPI
1287	+	Mat3x3d tmpI(inertiaTensor);
1288	+	Vector3d tmpAngMom;
1289	+	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1290	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1291	+	#endif
1292	+
1293	+	return;
1294	+	}
1295	+
1296	+	//Returns the angular momentum of the system
1297	+	Vector3d SimInfo::getAngularMomentum(){
1298	+
1299	+	Vector3d com(0.0);
1300	+	Vector3d comVel(0.0);
1301	+	Vector3d angularMomentum(0.0);
1302	+
1303	+	getComAll(com,comVel);
1304	+
1305	+	SimInfo::MoleculeIterator i;
1306	+	Molecule* mol;
1307	+
1308	+	Vector3d thisr(0.0);
1309	+	Vector3d thisp(0.0);
1310	+
1311	+	RealType thisMass;
1312	+
1313	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1314	+	thisMass = mol->getMass();
1315	+	thisr = mol->getCom()-com;
1316	+	thisp = (mol->getComVel()-comVel)*thisMass;
1317	+
1318	+	angularMomentum += cross( thisr, thisp );
1319	+
1320	+	}
1321	+
1322	+	#ifdef IS_MPI
1323	+	Vector3d tmpAngMom;
1324	+	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1325	+	#endif
1326	+
1327	+	return angularMomentum;
1328	+	}
1329	+
1330	+	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1331	+	return IOIndexToIntegrableObject.at(index);
1332	+	}
1333	+
1334	+	void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) {
1335	+	IOIndexToIntegrableObject= v;
1336	+	}
1337	+
1338	+	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1339	+	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1340	+	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1341	+	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1342	+	*/
1343	+	void SimInfo::getGyrationalVolume(RealType &volume){
1344	+	Mat3x3d intTensor;
1345	+	RealType det;
1346	+	Vector3d dummyAngMom;
1347	+	RealType sysconstants;
1348	+	RealType geomCnst;
1349	+
1350	+	geomCnst = 3.0/2.0;
1351	+	/* Get the inertial tensor and angular momentum for free*/
1352	+	getInertiaTensor(intTensor,dummyAngMom);
1353	+
1354	+	det = intTensor.determinant();
1355	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1356	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1357	+	return;
1358	+	}
1359	+
1360	+	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1361	+	Mat3x3d intTensor;
1362	+	Vector3d dummyAngMom;
1363	+	RealType sysconstants;
1364	+	RealType geomCnst;
1365	+
1366	+	geomCnst = 3.0/2.0;
1367	+	/* Get the inertial tensor and angular momentum for free*/
1368	+	getInertiaTensor(intTensor,dummyAngMom);
1369	+
1370	+	detI = intTensor.determinant();
1371	+	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1372	+	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1373	+	return;
1374	+	}
1375	+	/*
1376	+	void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) {
1377	+	assert( v.size() == nAtoms_ + nRigidBodies_);
1378	+	sdByGlobalIndex_ = v;
1379		}
1380	+
1381	+	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1382	+	//assert(index < nAtoms_ + nRigidBodies_);
1383	+	return sdByGlobalIndex_.at(index);
1384	+	}
1385	+	*/
1386	+	int SimInfo::getNGlobalConstraints() {
1387	+	int nGlobalConstraints;
1388	+	#ifdef IS_MPI
1389	+	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
1390	+	MPI_COMM_WORLD);
1391	+	#else
1392	+	nGlobalConstraints =  nConstraints_;
1393	+	#endif
1394	+	return nGlobalConstraints;
1395		}
1396
1397	<	}
1397	>	}//end namespace OpenMD
1398	>

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 1530 by gezelter, Tue Dec 28 21:47:55 2010 UTC

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

Diff Legend

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