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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 2 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
Revision 1121 by chuckv, Mon Feb 26 04:45:42 2007 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. Acknowledgement of the program authors must be made in any
10	>	*    publication of scientific results based in part on use of the
11	>	*    program.  An acceptable form of acknowledgement is citation of
12	>	*    the article in which the program was described (Matthew
13	>	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	>	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	>	*    Parallel Simulation Engine for Molecular Dynamics,"
16	>	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	>	*
18	>	* 2. Redistributions of source code must retain the above copyright
19	>	*    notice, this list of conditions and the following disclaimer.
20	>	*
21	>	* 3. Redistributions in binary form must reproduce the above copyright
22	>	*    notice, this list of conditions and the following disclaimer in the
23	>	*    documentation and/or other materials provided with the
24	>	*    distribution.
25	>	*
26	>	* This software is provided "AS IS," without a warranty of any
27	>	* kind. All express or implied conditions, representations and
28	>	* warranties, including any implied warranty of merchantability,
29	>	* fitness for a particular purpose or non-infringement, are hereby
30	>	* excluded.  The University of Notre Dame and its licensors shall not
31	>	* be liable for any damages suffered by licensee as a result of
32	>	* using, modifying or distributing the software or its
33	>	* derivatives. In no event will the University of Notre Dame or its
34	>	* licensors be liable for any lost revenue, profit or data, or for
35	>	* direct, indirect, special, consequential, incidental or punitive
36	>	* damages, however caused and regardless of the theory of liability,
37	>	* arising out of the use of or inability to use software, even if the
38	>	* University of Notre Dame has been advised of the possibility of
39	>	* such damages.
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 "SimInfo.hpp"
54	<	#define __C
55	<	#include "fSimulation.h"
56	<	#include "simError.h"
53	>	#include "brains/SimInfo.hpp"
54	>	#include "math/Vector3.hpp"
55	>	#include "primitives/Molecule.hpp"
56	>	#include "primitives/StuntDouble.hpp"
57	>	#include "UseTheForce/fCutoffPolicy.h"
58	>	#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
59	>	#include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h"
60	>	#include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
61	>	#include "UseTheForce/doForces_interface.h"
62	>	#include "UseTheForce/DarkSide/neighborLists_interface.h"
63	>	#include "UseTheForce/DarkSide/electrostatic_interface.h"
64	>	#include "UseTheForce/DarkSide/switcheroo_interface.h"
65	>	#include "utils/MemoryUtils.hpp"
66	>	#include "utils/simError.h"
67	>	#include "selection/SelectionManager.hpp"
68	>	#include "io/ForceFieldOptions.hpp"
69	>	#include "UseTheForce/ForceField.hpp"
70
13	–	#include "fortranWrappers.hpp"
71
15	–	#include "MatVec3.h"
16	–
72		#ifdef IS_MPI
73	<	#include "mpiSimulation.hpp"
74	<	#endif
73	>	#include "UseTheForce/mpiComponentPlan.h"
74	>	#include "UseTheForce/DarkSide/simParallel_interface.h"
75	>	#endif
76
77	<	inline double roundMe( double x ){
78	<	return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
79	<	}
80	<
81	<	inline double min( double a, double b ){
82	<	return (a < b ) ? a : b;
83	<	}
77	>	namespace oopse {
78	>	std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
79	>	std::map<int, std::set<int> >::iterator i = container.find(index);
80	>	std::set<int> result;
81	>	if (i != container.end()) {
82	>	result = i->second;
83	>	}
84
85	<	SimInfo* currentInfo;
86	<
31	<	SimInfo::SimInfo(){
32	<
33	<	n_constraints = 0;
34	<	nZconstraints = 0;
35	<	n_oriented = 0;
36	<	n_dipoles = 0;
37	<	ndf = 0;
38	<	ndfRaw = 0;
39	<	nZconstraints = 0;
40	<	the_integrator = NULL;
41	<	setTemp = 0;
42	<	thermalTime = 0.0;
43	<	currentTime = 0.0;
44	<	rCut = 0.0;
45	<	rSw = 0.0;
46	<
47	<	haveRcut = 0;
48	<	haveRsw = 0;
49	<	boxIsInit = 0;
85	>	return result;
86	>	}
87
88	<	resetTime = 1e99;
88	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
89	>	forceField_(ff), simParams_(simParams),
90	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
91	>	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
92	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
93	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
94	>	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
95	>	sman_(NULL), fortranInitialized_(false), calcBoxDipole_(false) {
96
97	<	orthoRhombic = 0;
98	<	orthoTolerance = 1E-6;
99	<	useInitXSstate = true;
97	>	MoleculeStamp* molStamp;
98	>	int nMolWithSameStamp;
99	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
100	>	int nGroups = 0;      //total cutoff groups defined in meta-data file
101	>	CutoffGroupStamp* cgStamp;
102	>	RigidBodyStamp* rbStamp;
103	>	int nRigidAtoms = 0;
104	>	std::vector<Component*> components = simParams->getComponents();
105	>
106	>	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
107	>	molStamp = (*i)->getMoleculeStamp();
108	>	nMolWithSameStamp = (*i)->getNMol();
109	>
110	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
111
112	<	usePBC = 0;
113	<	useLJ = 0;
59	<	useSticky = 0;
60	<	useCharges = 0;
61	<	useDipoles = 0;
62	<	useReactionField = 0;
63	<	useGB = 0;
64	<	useEAM = 0;
65	<	useSolidThermInt = 0;
66	<	useLiquidThermInt = 0;
112	>	//calculate atoms in molecules
113	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
114
115	<	haveCutoffGroups = false;
115	>	//calculate atoms in cutoff groups
116	>	int nAtomsInGroups = 0;
117	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
118	>
119	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
120	>	cgStamp = molStamp->getCutoffGroupStamp(j);
121	>	nAtomsInGroups += cgStamp->getNMembers();
122	>	}
123
124	<	excludes = Exclude::Instance();
124	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
125
126	<	myConfiguration = new SimState();
126	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
127
128	<	has_minimizer = false;
129	<	the_minimizer =NULL;
128	>	//calculate atoms in rigid bodies
129	>	int nAtomsInRigidBodies = 0;
130	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
131	>
132	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
133	>	rbStamp = molStamp->getRigidBodyStamp(j);
134	>	nAtomsInRigidBodies += rbStamp->getNMembers();
135	>	}
136
137	<	ngroup = 0;
137	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
138	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
139	>
140	>	}
141
142	<	wrapMeSimInfo( this );
143	<	}
142	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
143	>	//group therefore the total number of cutoff groups in the system is
144	>	//equal to the total number of atoms minus number of atoms belong to
145	>	//cutoff group defined in meta-data file plus the number of cutoff
146	>	//groups defined in meta-data file
147	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
148
149	<
150	<	SimInfo::~SimInfo(){
151	<
152	<	delete myConfiguration;
153	<
154	<	map<string, GenericData*>::iterator i;
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	<	for(i = properties.begin(); i != properties.end(); i++)
90	<	delete (*i).second;
157	>	nGlobalMols_ = molStampIds_.size();
158
159	<	}
159	>	#ifdef IS_MPI
160	>	molToProcMap_.resize(nGlobalMols_);
161	>	#endif
162
163	<	void SimInfo::setBox(double newBox[3]) {
95	<
96	<	int i, j;
97	<	double tempMat[3][3];
163	>	}
164
165	<	for(i=0; i<3; i++)
166	<	for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
165	>	SimInfo::~SimInfo() {
166	>	std::map<int, Molecule*>::iterator i;
167	>	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
168	>	delete i->second;
169	>	}
170	>	molecules_.clear();
171	>
172	>	delete sman_;
173	>	delete simParams_;
174	>	delete forceField_;
175	>	}
176
177	<	tempMat[0][0] = newBox[0];
178	<	tempMat[1][1] = newBox[1];
179	<	tempMat[2][2] = newBox[2];
177	>	int SimInfo::getNGlobalConstraints() {
178	>	int nGlobalConstraints;
179	>	#ifdef IS_MPI
180	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
181	>	MPI_COMM_WORLD);
182	>	#else
183	>	nGlobalConstraints =  nConstraints_;
184	>	#endif
185	>	return nGlobalConstraints;
186	>	}
187
188	<	setBoxM( tempMat );
188	>	bool SimInfo::addMolecule(Molecule* mol) {
189	>	MoleculeIterator i;
190
191	<	}
191	>	i = molecules_.find(mol->getGlobalIndex());
192	>	if (i == molecules_.end() ) {
193
194	<	void SimInfo::setBoxM( double theBox[3][3] ){
195	<
196	<	int i, j;
197	<	double FortranHmat[9]; // to preserve compatibility with Fortran the
198	<	// ordering in the array is as follows:
199	<	// [ 0 3 6 ]
200	<	// [ 1 4 7 ]
201	<	// [ 2 5 8 ]
202	<	double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
203	<
204	<	if( !boxIsInit ) boxIsInit = 1;
205	<
206	<	for(i=0; i < 3; i++)
207	<	for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
208	<
209	<	calcBoxL();
126	<	calcHmatInv();
127	<
128	<	for(i=0; i < 3; i++) {
129	<	for (j=0; j < 3; j++) {
130	<	FortranHmat[3*j + i] = Hmat[i][j];
131	<	FortranHmatInv[3*j + i] = HmatInv[i][j];
194	>	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
195	>
196	>	nAtoms_ += mol->getNAtoms();
197	>	nBonds_ += mol->getNBonds();
198	>	nBends_ += mol->getNBends();
199	>	nTorsions_ += mol->getNTorsions();
200	>	nRigidBodies_ += mol->getNRigidBodies();
201	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
202	>	nCutoffGroups_ += mol->getNCutoffGroups();
203	>	nConstraints_ += mol->getNConstraintPairs();
204	>
205	>	addExcludePairs(mol);
206	>
207	>	return true;
208	>	} else {
209	>	return false;
210		}
211		}
212
213	<	setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
214	<
215	<	}
138	<
213	>	bool SimInfo::removeMolecule(Molecule* mol) {
214	>	MoleculeIterator i;
215	>	i = molecules_.find(mol->getGlobalIndex());
216
217	<	void SimInfo::getBoxM (double theBox[3][3]) {
217	>	if (i != molecules_.end() ) {
218
219	<	int i, j;
220	<	for(i=0; i<3; i++)
221	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
222	<	}
219	>	assert(mol == i->second);
220	>
221	>	nAtoms_ -= mol->getNAtoms();
222	>	nBonds_ -= mol->getNBonds();
223	>	nBends_ -= mol->getNBends();
224	>	nTorsions_ -= mol->getNTorsions();
225	>	nRigidBodies_ -= mol->getNRigidBodies();
226	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
227	>	nCutoffGroups_ -= mol->getNCutoffGroups();
228	>	nConstraints_ -= mol->getNConstraintPairs();
229
230	+	removeExcludePairs(mol);
231	+	molecules_.erase(mol->getGlobalIndex());
232
233	<	void SimInfo::scaleBox(double scale) {
234	<	double theBox[3][3];
235	<	int i, j;
233	>	delete mol;
234	>
235	>	return true;
236	>	} else {
237	>	return false;
238	>	}
239
152	–	// cerr << "Scaling box by " << scale << "\n";
240
241	<	for(i=0; i<3; i++)
155	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
241	>	}
242
243	<	setBoxM(theBox);
243	>
244	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
245	>	i = molecules_.begin();
246	>	return i == molecules_.end() ? NULL : i->second;
247	>	}
248
249	<	}
249	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
250	>	++i;
251	>	return i == molecules_.end() ? NULL : i->second;
252	>	}
253
161	–	void SimInfo::calcHmatInv( void ) {
162	–
163	–	int oldOrtho;
164	–	int i,j;
165	–	double smallDiag;
166	–	double tol;
167	–	double sanity[3][3];
254
255	<	invertMat3( Hmat, HmatInv );
255	>	void SimInfo::calcNdf() {
256	>	int ndf_local;
257	>	MoleculeIterator i;
258	>	std::vector<StuntDouble*>::iterator j;
259	>	Molecule* mol;
260	>	StuntDouble* integrableObject;
261
262	<	// check to see if Hmat is orthorhombic
263	<
264	<	oldOrtho = orthoRhombic;
262	>	ndf_local = 0;
263	>
264	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
265	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
266	>	integrableObject = mol->nextIntegrableObject(j)) {
267
268	<	smallDiag = fabs(Hmat[0][0]);
176	<	if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
177	<	if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
178	<	tol = smallDiag * orthoTolerance;
268	>	ndf_local += 3;
269
270	<	orthoRhombic = 1;
271	<
272	<	for (i = 0; i < 3; i++ ) {
273	<	for (j = 0 ; j < 3; j++) {
274	<	if (i != j) {
275	<	if (orthoRhombic) {
276	<	if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
277	<	}
270	>	if (integrableObject->isDirectional()) {
271	>	if (integrableObject->isLinear()) {
272	>	ndf_local += 2;
273	>	} else {
274	>	ndf_local += 3;
275	>	}
276	>	}
277	>
278		}
279		}
190	–	}
191	–
192	–	if( oldOrtho != orthoRhombic ){
280
281	<	if( orthoRhombic ) {
282	<	sprintf( painCave.errMsg,
196	<	"OOPSE is switching from the default Non-Orthorhombic\n"
197	<	"\tto the faster Orthorhombic periodic boundary computations.\n"
198	<	"\tThis is usually a good thing, but if you wan't the\n"
199	<	"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
200	<	"\tvariable ( currently set to %G ) smaller.\n",
201	<	orthoTolerance);
202	<	painCave.severity = OOPSE_INFO;
203	<	simError();
204	<	}
205	<	else {
206	<	sprintf( painCave.errMsg,
207	<	"OOPSE is switching from the faster Orthorhombic to the more\n"
208	<	"\tflexible Non-Orthorhombic periodic boundary computations.\n"
209	<	"\tThis is usually because the box has deformed under\n"
210	<	"\tNPTf integration. If you wan't to live on the edge with\n"
211	<	"\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
212	<	"\tvariable ( currently set to %G ) larger.\n",
213	<	orthoTolerance);
214	<	painCave.severity = OOPSE_WARNING;
215	<	simError();
216	<	}
217	<	}
218	<	}
281	>	// n_constraints is local, so subtract them on each processor
282	>	ndf_local -= nConstraints_;
283
284	<	void SimInfo::calcBoxL( void ){
285	<
286	<	double dx, dy, dz, dsq;
287	<
288	<	// boxVol = Determinant of Hmat
225	<
226	<	boxVol = matDet3( Hmat );
227	<
228	<	// boxLx
229	<
230	<	dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
231	<	dsq = dx*dx + dy*dy + dz*dz;
232	<	boxL[0] = sqrt( dsq );
233	<	//maxCutoff = 0.5 * boxL[0];
234	<
235	<	// boxLy
236	<
237	<	dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
238	<	dsq = dx*dx + dy*dy + dz*dz;
239	<	boxL[1] = sqrt( dsq );
240	<	//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
241	<
242	<
243	<	// boxLz
244	<
245	<	dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
246	<	dsq = dx*dx + dy*dy + dz*dz;
247	<	boxL[2] = sqrt( dsq );
248	<	//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
249	<
250	<	//calculate the max cutoff
251	<	maxCutoff =  calcMaxCutOff();
252	<
253	<	checkCutOffs();
254	<
255	<	}
256	<
257	<
258	<	double SimInfo::calcMaxCutOff(){
259	<
260	<	double ri[3], rj[3], rk[3];
261	<	double rij[3], rjk[3], rki[3];
262	<	double minDist;
263	<
264	<	ri[0] = Hmat[0][0];
265	<	ri[1] = Hmat[1][0];
266	<	ri[2] = Hmat[2][0];
267	<
268	<	rj[0] = Hmat[0][1];
269	<	rj[1] = Hmat[1][1];
270	<	rj[2] = Hmat[2][1];
271	<
272	<	rk[0] = Hmat[0][2];
273	<	rk[1] = Hmat[1][2];
274	<	rk[2] = Hmat[2][2];
275	<
276	<	crossProduct3(ri, rj, rij);
277	<	distXY = dotProduct3(rk,rij) / norm3(rij);
278	<
279	<	crossProduct3(rj,rk, rjk);
280	<	distYZ = dotProduct3(ri,rjk) / norm3(rjk);
281	<
282	<	crossProduct3(rk,ri, rki);
283	<	distZX = dotProduct3(rj,rki) / norm3(rki);
284	<
285	<	minDist = min(min(distXY, distYZ), distZX);
286	<	return minDist/2;
287	<
288	<	}
289	<
290	<	void SimInfo::wrapVector( double thePos[3] ){
291	<
292	<	int i;
293	<	double scaled[3];
294	<
295	<	if( !orthoRhombic ){
296	<	// calc the scaled coordinates.
297	<
298	<
299	<	matVecMul3(HmatInv, thePos, scaled);
300	<
301	<	for(i=0; i<3; i++)
302	<	scaled[i] -= roundMe(scaled[i]);
303	<
304	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
305	<
306	<	matVecMul3(Hmat, scaled, thePos);
307	<
308	<	}
309	<	else{
310	<	// calc the scaled coordinates.
311	<
312	<	for(i=0; i<3; i++)
313	<	scaled[i] = thePos[i]*HmatInv[i][i];
314	<
315	<	// wrap the scaled coordinates
316	<
317	<	for(i=0; i<3; i++)
318	<	scaled[i] -= roundMe(scaled[i]);
319	<
320	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
321	<
322	<	for(i=0; i<3; i++)
323	<	thePos[i] = scaled[i]*Hmat[i][i];
324	<	}
325	<
326	<	}
327	<
284	>	#ifdef IS_MPI
285	>	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
286	>	#else
287	>	ndf_ = ndf_local;
288	>	#endif
289
290	<	int SimInfo::getNDF(){
291	<	int ndf_local;
290	>	// nZconstraints_ is global, as are the 3 COM translations for the
291	>	// entire system:
292	>	ndf_ = ndf_ - 3 - nZconstraint_;
293
332	–	ndf_local = 0;
333	–
334	–	for(int i = 0; i < integrableObjects.size(); i++){
335	–	ndf_local += 3;
336	–	if (integrableObjects[i]->isDirectional()) {
337	–	if (integrableObjects[i]->isLinear())
338	–	ndf_local += 2;
339	–	else
340	–	ndf_local += 3;
341	–	}
294		}
295
296	<	// n_constraints is local, so subtract them on each processor:
345	<
346	<	ndf_local -= n_constraints;
347	<
296	>	int SimInfo::getFdf() {
297		#ifdef IS_MPI
298	<	MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
298	>	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
299		#else
300	<	ndf = ndf_local;
300	>	fdf_ = fdf_local;
301		#endif
302	+	return fdf_;
303	+	}
304	+
305	+	void SimInfo::calcNdfRaw() {
306	+	int ndfRaw_local;
307
308	<	// nZconstraints is global, as are the 3 COM translations for the
309	<	// entire system:
308	>	MoleculeIterator i;
309	>	std::vector<StuntDouble*>::iterator j;
310	>	Molecule* mol;
311	>	StuntDouble* integrableObject;
312
313	<	ndf = ndf - 3 - nZconstraints;
313	>	// Raw degrees of freedom that we have to set
314	>	ndfRaw_local = 0;
315	>
316	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
317	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
318	>	integrableObject = mol->nextIntegrableObject(j)) {
319
320	<	return ndf;
360	<	}
320	>	ndfRaw_local += 3;
321
322	<	int SimInfo::getNDFraw() {
323	<	int ndfRaw_local;
324	<
325	<	// Raw degrees of freedom that we have to set
326	<	ndfRaw_local = 0;
327	<
328	<	for(int i = 0; i < integrableObjects.size(); i++){
329	<	ndfRaw_local += 3;
330	<	if (integrableObjects[i]->isDirectional()) {
371	<	if (integrableObjects[i]->isLinear())
372	<	ndfRaw_local += 2;
373	<	else
374	<	ndfRaw_local += 3;
322	>	if (integrableObject->isDirectional()) {
323	>	if (integrableObject->isLinear()) {
324	>	ndfRaw_local += 2;
325	>	} else {
326	>	ndfRaw_local += 3;
327	>	}
328	>	}
329	>
330	>	}
331		}
376	–	}
332
333		#ifdef IS_MPI
334	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
334	>	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
335		#else
336	<	ndfRaw = ndfRaw_local;
336	>	ndfRaw_ = ndfRaw_local;
337		#endif
338	+	}
339
340	<	return ndfRaw;
341	<	}
340	>	void SimInfo::calcNdfTrans() {
341	>	int ndfTrans_local;
342
343	<	int SimInfo::getNDFtranslational() {
388	<	int ndfTrans_local;
343	>	ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
344
390	–	ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
345
392	–
346		#ifdef IS_MPI
347	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
347	>	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
348		#else
349	<	ndfTrans = ndfTrans_local;
349	>	ndfTrans_ = ndfTrans_local;
350		#endif
351
352	<	ndfTrans = ndfTrans - 3 - nZconstraints;
352	>	ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
353	>
354	>	}
355
356	<	return ndfTrans;
357	<	}
356	>	void SimInfo::addExcludePairs(Molecule* mol) {
357	>	std::vector<Bond*>::iterator bondIter;
358	>	std::vector<Bend*>::iterator bendIter;
359	>	std::vector<Torsion*>::iterator torsionIter;
360	>	Bond* bond;
361	>	Bend* bend;
362	>	Torsion* torsion;
363	>	int a;
364	>	int b;
365	>	int c;
366	>	int d;
367
368	<	int SimInfo::getTotIntegrableObjects() {
405	<	int nObjs_local;
406	<	int nObjs;
368	>	std::map<int, std::set<int> > atomGroups;
369
370	<	nObjs_local =  integrableObjects.size();
370	>	Molecule::RigidBodyIterator rbIter;
371	>	RigidBody* rb;
372	>	Molecule::IntegrableObjectIterator ii;
373	>	StuntDouble* integrableObject;
374	>
375	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
376	>	integrableObject = mol->nextIntegrableObject(ii)) {
377
378	+	if (integrableObject->isRigidBody()) {
379	+	rb = static_cast<RigidBody*>(integrableObject);
380	+	std::vector<Atom*> atoms = rb->getAtoms();
381	+	std::set<int> rigidAtoms;
382	+	for (int i = 0; i < atoms.size(); ++i) {
383	+	rigidAtoms.insert(atoms[i]->getGlobalIndex());
384	+	}
385	+	for (int i = 0; i < atoms.size(); ++i) {
386	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
387	+	}
388	+	} else {
389	+	std::set<int> oneAtomSet;
390	+	oneAtomSet.insert(integrableObject->getGlobalIndex());
391	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
392	+	}
393	+	}
394
395	<	#ifdef IS_MPI
396	<	MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
397	<	#else
398	<	nObjs = nObjs_local;
399	<	#endif
395	>
396	>
397	>	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
398	>	a = bond->getAtomA()->getGlobalIndex();
399	>	b = bond->getAtomB()->getGlobalIndex();
400	>	exclude_.addPair(a, b);
401	>	}
402
403	+	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
404	+	a = bend->getAtomA()->getGlobalIndex();
405	+	b = bend->getAtomB()->getGlobalIndex();
406	+	c = bend->getAtomC()->getGlobalIndex();
407	+	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
408	+	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
409	+	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
410
411	<	return nObjs;
412	<	}
411	>	exclude_.addPairs(rigidSetA, rigidSetB);
412	>	exclude_.addPairs(rigidSetA, rigidSetC);
413	>	exclude_.addPairs(rigidSetB, rigidSetC);
414	>
415	>	//exclude_.addPair(a, b);
416	>	//exclude_.addPair(a, c);
417	>	//exclude_.addPair(b, c);
418	>	}
419
420	<	void SimInfo::refreshSim(){
420	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
421	>	a = torsion->getAtomA()->getGlobalIndex();
422	>	b = torsion->getAtomB()->getGlobalIndex();
423	>	c = torsion->getAtomC()->getGlobalIndex();
424	>	d = torsion->getAtomD()->getGlobalIndex();
425	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
426	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
427	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
428	>	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
429
430	<	simtype fInfo;
431	<	int isError;
432	<	int n_global;
433	<	int* excl;
430	>	exclude_.addPairs(rigidSetA, rigidSetB);
431	>	exclude_.addPairs(rigidSetA, rigidSetC);
432	>	exclude_.addPairs(rigidSetA, rigidSetD);
433	>	exclude_.addPairs(rigidSetB, rigidSetC);
434	>	exclude_.addPairs(rigidSetB, rigidSetD);
435	>	exclude_.addPairs(rigidSetC, rigidSetD);
436
437	<	fInfo.dielect = 0.0;
437	>	/*
438	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
439	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
440	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
441	>	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
442	>	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
443	>	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
444	>
445	>
446	>	exclude_.addPair(a, b);
447	>	exclude_.addPair(a, c);
448	>	exclude_.addPair(a, d);
449	>	exclude_.addPair(b, c);
450	>	exclude_.addPair(b, d);
451	>	exclude_.addPair(c, d);
452	>	*/
453	>	}
454	>
455	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
456	>	std::vector<Atom*> atoms = rb->getAtoms();
457	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
458	>	for (int j = i + 1; j < atoms.size(); ++j) {
459	>	a = atoms[i]->getGlobalIndex();
460	>	b = atoms[j]->getGlobalIndex();
461	>	exclude_.addPair(a, b);
462	>	}
463	>	}
464	>	}
465	>
466	>	}
467	>
468	>	void SimInfo::removeExcludePairs(Molecule* mol) {
469	>	std::vector<Bond*>::iterator bondIter;
470	>	std::vector<Bend*>::iterator bendIter;
471	>	std::vector<Torsion*>::iterator torsionIter;
472	>	Bond* bond;
473	>	Bend* bend;
474	>	Torsion* torsion;
475	>	int a;
476	>	int b;
477	>	int c;
478	>	int d;
479	>
480	>	std::map<int, std::set<int> > atomGroups;
481	>
482	>	Molecule::RigidBodyIterator rbIter;
483	>	RigidBody* rb;
484	>	Molecule::IntegrableObjectIterator ii;
485	>	StuntDouble* integrableObject;
486	>
487	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
488	>	integrableObject = mol->nextIntegrableObject(ii)) {
489	>
490	>	if (integrableObject->isRigidBody()) {
491	>	rb = static_cast<RigidBody*>(integrableObject);
492	>	std::vector<Atom*> atoms = rb->getAtoms();
493	>	std::set<int> rigidAtoms;
494	>	for (int i = 0; i < atoms.size(); ++i) {
495	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
496	>	}
497	>	for (int i = 0; i < atoms.size(); ++i) {
498	>	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
499	>	}
500	>	} else {
501	>	std::set<int> oneAtomSet;
502	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
503	>	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
504	>	}
505	>	}
506	>
507	>
508	>	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
509	>	a = bond->getAtomA()->getGlobalIndex();
510	>	b = bond->getAtomB()->getGlobalIndex();
511	>	exclude_.removePair(a, b);
512	>	}
513	>
514	>	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
515	>	a = bend->getAtomA()->getGlobalIndex();
516	>	b = bend->getAtomB()->getGlobalIndex();
517	>	c = bend->getAtomC()->getGlobalIndex();
518	>
519	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
520	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
521	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
522	>
523	>	exclude_.removePairs(rigidSetA, rigidSetB);
524	>	exclude_.removePairs(rigidSetA, rigidSetC);
525	>	exclude_.removePairs(rigidSetB, rigidSetC);
526	>
527	>	//exclude_.removePair(a, b);
528	>	//exclude_.removePair(a, c);
529	>	//exclude_.removePair(b, c);
530	>	}
531	>
532	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
533	>	a = torsion->getAtomA()->getGlobalIndex();
534	>	b = torsion->getAtomB()->getGlobalIndex();
535	>	c = torsion->getAtomC()->getGlobalIndex();
536	>	d = torsion->getAtomD()->getGlobalIndex();
537	>
538	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
539	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
540	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
541	>	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
542	>
543	>	exclude_.removePairs(rigidSetA, rigidSetB);
544	>	exclude_.removePairs(rigidSetA, rigidSetC);
545	>	exclude_.removePairs(rigidSetA, rigidSetD);
546	>	exclude_.removePairs(rigidSetB, rigidSetC);
547	>	exclude_.removePairs(rigidSetB, rigidSetD);
548	>	exclude_.removePairs(rigidSetC, rigidSetD);
549	>
550	>	/*
551	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
552	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
553	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
554	>	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
555	>	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
556	>	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
557	>
558	>
559	>	exclude_.removePair(a, b);
560	>	exclude_.removePair(a, c);
561	>	exclude_.removePair(a, d);
562	>	exclude_.removePair(b, c);
563	>	exclude_.removePair(b, d);
564	>	exclude_.removePair(c, d);
565	>	*/
566	>	}
567	>
568	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
569	>	std::vector<Atom*> atoms = rb->getAtoms();
570	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
571	>	for (int j = i + 1; j < atoms.size(); ++j) {
572	>	a = atoms[i]->getGlobalIndex();
573	>	b = atoms[j]->getGlobalIndex();
574	>	exclude_.removePair(a, b);
575	>	}
576	>	}
577	>	}
578	>
579	>	}
580	>
581	>
582	>	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
583	>	int curStampId;
584	>
585	>	//index from 0
586	>	curStampId = moleculeStamps_.size();
587	>
588	>	moleculeStamps_.push_back(molStamp);
589	>	molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
590	>	}
591	>
592	>	void SimInfo::update() {
593	>
594	>	setupSimType();
595	>
596	>	#ifdef IS_MPI
597	>	setupFortranParallel();
598	>	#endif
599	>
600	>	setupFortranSim();
601	>
602	>	//setup fortran force field
603	>	/** @deprecate */
604	>	int isError = 0;
605	>
606	>	setupCutoff();
607	>
608	>	setupElectrostaticSummationMethod( isError );
609	>	setupSwitchingFunction();
610	>	setupAccumulateBoxDipole();
611	>
612	>	if(isError){
613	>	sprintf( painCave.errMsg,
614	>	"ForceField error: There was an error initializing the forceField in fortran.\n" );
615	>	painCave.isFatal = 1;
616	>	simError();
617	>	}
618	>
619	>	calcNdf();
620	>	calcNdfRaw();
621	>	calcNdfTrans();
622	>
623	>	fortranInitialized_ = true;
624	>	}
625	>
626	>	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
627	>	SimInfo::MoleculeIterator mi;
628	>	Molecule* mol;
629	>	Molecule::AtomIterator ai;
630	>	Atom* atom;
631	>	std::set<AtomType*> atomTypes;
632	>
633	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
634	>
635	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
636	>	atomTypes.insert(atom->getAtomType());
637	>	}
638	>
639	>	}
640	>
641	>	return atomTypes;
642	>	}
643	>
644	>	void SimInfo::setupSimType() {
645	>	std::set<AtomType*>::iterator i;
646	>	std::set<AtomType*> atomTypes;
647	>	atomTypes = getUniqueAtomTypes();
648	>
649	>	int useLennardJones = 0;
650	>	int useElectrostatic = 0;
651	>	int useEAM = 0;
652	>	int useSC = 0;
653	>	int useCharge = 0;
654	>	int useDirectional = 0;
655	>	int useDipole = 0;
656	>	int useGayBerne = 0;
657	>	int useSticky = 0;
658	>	int useStickyPower = 0;
659	>	int useShape = 0;
660	>	int useFLARB = 0; //it is not in AtomType yet
661	>	int useDirectionalAtom = 0;
662	>	int useElectrostatics = 0;
663	>	//usePBC and useRF are from simParams
664	>	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
665	>	int useRF;
666	>	int useSF;
667	>	int useSP;
668	>	int useBoxDipole;
669	>	std::string myMethod;
670	>
671	>	// set the useRF logical
672	>	useRF = 0;
673	>	useSF = 0;
674	>	useSP = 0;
675	>
676	>
677	>	if (simParams_->haveElectrostaticSummationMethod()) {
678	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
679	>	toUpper(myMethod);
680	>	if (myMethod == "REACTION_FIELD"){
681	>	useRF = 1;
682	>	} else if (myMethod == "SHIFTED_FORCE"){
683	>	useSF = 1;
684	>	} else if (myMethod == "SHIFTED_POTENTIAL"){
685	>	useSP = 1;
686	>	}
687	>	}
688	>
689	>	if (simParams_->haveAccumulateBoxDipole())
690	>	if (simParams_->getAccumulateBoxDipole())
691	>	useBoxDipole = 1;
692	>
693	>	//loop over all of the atom types
694	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
695	>	useLennardJones |= (*i)->isLennardJones();
696	>	useElectrostatic |= (*i)->isElectrostatic();
697	>	useEAM |= (*i)->isEAM();
698	>	useSC |= (*i)->isSC();
699	>	useCharge |= (*i)->isCharge();
700	>	useDirectional |= (*i)->isDirectional();
701	>	useDipole |= (*i)->isDipole();
702	>	useGayBerne |= (*i)->isGayBerne();
703	>	useSticky |= (*i)->isSticky();
704	>	useStickyPower |= (*i)->isStickyPower();
705	>	useShape |= (*i)->isShape();
706	>	}
707	>
708	>	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
709	>	useDirectionalAtom = 1;
710	>	}
711	>
712	>	if (useCharge || useDipole) {
713	>	useElectrostatics = 1;
714	>	}
715	>
716	>	#ifdef IS_MPI
717	>	int temp;
718	>
719	>	temp = usePBC;
720	>	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
721	>
722	>	temp = useDirectionalAtom;
723	>	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
724	>
725	>	temp = useLennardJones;
726	>	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
727	>
728	>	temp = useElectrostatics;
729	>	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
730	>
731	>	temp = useCharge;
732	>	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
733	>
734	>	temp = useDipole;
735	>	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
736	>
737	>	temp = useSticky;
738	>	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
739	>
740	>	temp = useStickyPower;
741	>	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
742	>
743	>	temp = useGayBerne;
744	>	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
745	>
746	>	temp = useEAM;
747	>	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
748
749	<	if( useDipoles ){
750	<	if( useReactionField )fInfo.dielect = dielectric;
751	<	}
749	>	temp = useSC;
750	>	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
751	>
752	>	temp = useShape;
753	>	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
754
755	<	fInfo.SIM_uses_PBC = usePBC;
756	<	//fInfo.SIM_uses_LJ = 0;
436	<	fInfo.SIM_uses_LJ = useLJ;
437	<	fInfo.SIM_uses_sticky = useSticky;
438	<	//fInfo.SIM_uses_sticky = 0;
439	<	fInfo.SIM_uses_charges = useCharges;
440	<	fInfo.SIM_uses_dipoles = useDipoles;
441	<	//fInfo.SIM_uses_dipoles = 0;
442	<	fInfo.SIM_uses_RF = useReactionField;
443	<	//fInfo.SIM_uses_RF = 0;
444	<	fInfo.SIM_uses_GB = useGB;
445	<	fInfo.SIM_uses_EAM = useEAM;
755	>	temp = useFLARB;
756	>	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
757
758	<	n_exclude = excludes->getSize();
759	<	excl = excludes->getFortranArray();
760	<
761	<	#ifdef IS_MPI
762	<	n_global = mpiSim->getNAtomsGlobal();
763	<	#else
764	<	n_global = n_atoms;
758	>	temp = useRF;
759	>	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
760	>
761	>	temp = useSF;
762	>	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
763	>
764	>	temp = useSP;
765	>	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
766	>
767	>	temp = useBoxDipole;
768	>	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
769	>
770		#endif
455	–
456	–	isError = 0;
457	–
458	–	getFortranGroupArrays(this, FglobalGroupMembership, mfact);
459	–	//it may not be a good idea to pass the address of first element in vector
460	–	//since c++ standard does not require vector to be stored continuously in meomory
461	–	//Most of the compilers will organize the memory of vector continuously
462	–	setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
463	–	&nGlobalExcludes, globalExcludes, molMembershipArray,
464	–	&mfact[0], &ngroup, &FglobalGroupMembership[0], &isError);
771
772	<	if( isError ){
773	<
774	<	sprintf( painCave.errMsg,
775	<	"There was an error setting the simulation information in fortran.\n" );
776	<	painCave.isFatal = 1;
777	<	painCave.severity = OOPSE_ERROR;
778	<	simError();
772	>	fInfo_.SIM_uses_PBC = usePBC;
773	>	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
774	>	fInfo_.SIM_uses_LennardJones = useLennardJones;
775	>	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
776	>	fInfo_.SIM_uses_Charges = useCharge;
777	>	fInfo_.SIM_uses_Dipoles = useDipole;
778	>	fInfo_.SIM_uses_Sticky = useSticky;
779	>	fInfo_.SIM_uses_StickyPower = useStickyPower;
780	>	fInfo_.SIM_uses_GayBerne = useGayBerne;
781	>	fInfo_.SIM_uses_EAM = useEAM;
782	>	fInfo_.SIM_uses_SC = useSC;
783	>	fInfo_.SIM_uses_Shapes = useShape;
784	>	fInfo_.SIM_uses_FLARB = useFLARB;
785	>	fInfo_.SIM_uses_RF = useRF;
786	>	fInfo_.SIM_uses_SF = useSF;
787	>	fInfo_.SIM_uses_SP = useSP;
788	>	fInfo_.SIM_uses_BoxDipole = useBoxDipole;
789		}
474	–
475	–	#ifdef IS_MPI
476	–	sprintf( checkPointMsg,
477	–	"succesfully sent the simulation information to fortran.\n");
478	–	MPIcheckPoint();
479	–	#endif // is_mpi
480	–
481	–	this->ndf = this->getNDF();
482	–	this->ndfRaw = this->getNDFraw();
483	–	this->ndfTrans = this->getNDFtranslational();
484	–	}
790
791	<	void SimInfo::setDefaultRcut( double theRcut ){
792	<
793	<	haveRcut = 1;
794	<	rCut = theRcut;
795	<	rList = rCut + 1.0;
796	<
797	<	notifyFortranCutOffs( &rCut, &rSw, &rList );
493	<	}
791	>	void SimInfo::setupFortranSim() {
792	>	int isError;
793	>	int nExclude;
794	>	std::vector<int> fortranGlobalGroupMembership;
795	>
796	>	nExclude = exclude_.getSize();
797	>	isError = 0;
798
799	<	void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
799	>	//globalGroupMembership_ is filled by SimCreator
800	>	for (int i = 0; i < nGlobalAtoms_; i++) {
801	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
802	>	}
803
804	<	rSw = theRsw;
805	<	setDefaultRcut( theRcut );
806	<	}
804	>	//calculate mass ratio of cutoff group
805	>	std::vector<RealType> mfact;
806	>	SimInfo::MoleculeIterator mi;
807	>	Molecule* mol;
808	>	Molecule::CutoffGroupIterator ci;
809	>	CutoffGroup* cg;
810	>	Molecule::AtomIterator ai;
811	>	Atom* atom;
812	>	RealType totalMass;
813
814	+	//to avoid memory reallocation, reserve enough space for mfact
815	+	mfact.reserve(getNCutoffGroups());
816	+
817	+	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
818	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
819
820	<	void SimInfo::checkCutOffs( void ){
821	<
822	<	if( boxIsInit ){
820	>	totalMass = cg->getMass();
821	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
822	>	// Check for massless groups - set mfact to 1 if true
823	>	if (totalMass != 0)
824	>	mfact.push_back(atom->getMass()/totalMass);
825	>	else
826	>	mfact.push_back( 1.0 );
827	>	}
828	>
829	>	}
830	>	}
831	>
832	>	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
833	>	std::vector<int> identArray;
834	>
835	>	//to avoid memory reallocation, reserve enough space identArray
836	>	identArray.reserve(getNAtoms());
837
838	<	//we need to check cutOffs against the box
838	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
839	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
840	>	identArray.push_back(atom->getIdent());
841	>	}
842	>	}
843	>
844	>	//fill molMembershipArray
845	>	//molMembershipArray is filled by SimCreator
846	>	std::vector<int> molMembershipArray(nGlobalAtoms_);
847	>	for (int i = 0; i < nGlobalAtoms_; i++) {
848	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
849	>	}
850
851	<	if( rCut > maxCutoff ){
851	>	//setup fortran simulation
852	>	int nGlobalExcludes = 0;
853	>	int* globalExcludes = NULL;
854	>	int* excludeList = exclude_.getExcludeList();
855	>	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
856	>	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
857	>	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
858	>
859	>	if( isError ){
860	>
861		sprintf( painCave.errMsg,
862	<	"cutoffRadius is too large for the current periodic box.\n"
511	<	"\tCurrent Value of cutoffRadius = %G at time %G\n "
512	<	"\tThis is larger than half of at least one of the\n"
513	<	"\tperiodic box vectors.  Right now, the Box matrix is:\n"
514	<	"\n"
515	<	"\t[ %G %G %G ]\n"
516	<	"\t[ %G %G %G ]\n"
517	<	"\t[ %G %G %G ]\n",
518	<	rCut, currentTime,
519	<	Hmat[0][0], Hmat[0][1], Hmat[0][2],
520	<	Hmat[1][0], Hmat[1][1], Hmat[1][2],
521	<	Hmat[2][0], Hmat[2][1], Hmat[2][2]);
522	<	painCave.severity = OOPSE_ERROR;
862	>	"There was an error setting the simulation information in fortran.\n" );
863		painCave.isFatal = 1;
864	+	painCave.severity = OOPSE_ERROR;
865		simError();
866	<	}
867	<	} else {
868	<	// initialize this stuff before using it, OK?
869	<	sprintf( painCave.errMsg,
870	<	"Trying to check cutoffs without a box.\n"
871	<	"\tOOPSE should have better programmers than that.\n" );
872	<	painCave.severity = OOPSE_ERROR;
873	<	painCave.isFatal = 1;
874	<	simError();
866	>	}
867	>
868	>	#ifdef IS_MPI
869	>	sprintf( checkPointMsg,
870	>	"succesfully sent the simulation information to fortran.\n");
871	>	MPIcheckPoint();
872	>	#endif // is_mpi
873	>
874	>	// Setup number of neighbors in neighbor list if present
875	>	if (simParams_->haveNeighborListNeighbors()) {
876	>	int nlistNeighbors = simParams_->getNeighborListNeighbors();
877	>	setNeighbors(&nlistNeighbors);
878	>	}
879	>
880	>
881		}
535	–
536	–	}
882
538	–	void SimInfo::addProperty(GenericData* prop){
883
884	<	map<string, GenericData*>::iterator result;
885	<	result = properties.find(prop->getID());
542	<
543	<	//we can't simply use  properties[prop->getID()] = prop,
544	<	//it will cause memory leak if we already contain a propery which has the same name of prop
545	<
546	<	if(result != properties.end()){
884	>	#ifdef IS_MPI
885	>	void SimInfo::setupFortranParallel() {
886
887	<	delete (*result).second;
888	<	(*result).second = prop;
889	<
890	<	}
891	<	else{
887	>	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
888	>	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
889	>	std::vector<int> localToGlobalCutoffGroupIndex;
890	>	SimInfo::MoleculeIterator mi;
891	>	Molecule::AtomIterator ai;
892	>	Molecule::CutoffGroupIterator ci;
893	>	Molecule* mol;
894	>	Atom* atom;
895	>	CutoffGroup* cg;
896	>	mpiSimData parallelData;
897	>	int isError;
898
899	<	properties[prop->getID()] = prop;
899	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
900
901	+	//local index(index in DataStorge) of atom is important
902	+	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
903	+	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
904	+	}
905	+
906	+	//local index of cutoff group is trivial, it only depends on the order of travesing
907	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
908	+	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
909	+	}
910	+
911	+	}
912	+
913	+	//fill up mpiSimData struct
914	+	parallelData.nMolGlobal = getNGlobalMolecules();
915	+	parallelData.nMolLocal = getNMolecules();
916	+	parallelData.nAtomsGlobal = getNGlobalAtoms();
917	+	parallelData.nAtomsLocal = getNAtoms();
918	+	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
919	+	parallelData.nGroupsLocal = getNCutoffGroups();
920	+	parallelData.myNode = worldRank;
921	+	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
922	+
923	+	//pass mpiSimData struct and index arrays to fortran
924	+	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
925	+	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
926	+	&localToGlobalCutoffGroupIndex[0], &isError);
927	+
928	+	if (isError) {
929	+	sprintf(painCave.errMsg,
930	+	"mpiRefresh errror: fortran didn't like something we gave it.\n");
931	+	painCave.isFatal = 1;
932	+	simError();
933	+	}
934	+
935	+	sprintf(checkPointMsg, " mpiRefresh successful.\n");
936	+	MPIcheckPoint();
937	+
938	+
939		}
940	+
941	+	#endif
942	+
943	+	void SimInfo::setupCutoff() {
944
945	<	}
945	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
946
947	<	GenericData* SimInfo::getProperty(const string& propName){
948	<
562	<	map<string, GenericData*>::iterator result;
563	<
564	<	//string lowerCaseName = ();
565	<
566	<	result = properties.find(propName);
567	<
568	<	if(result != properties.end())
569	<	return (*result).second;
570	<	else
571	<	return NULL;
572	<	}
947	>	// Check the cutoff policy
948	>	int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
949
950	+	std::string myPolicy;
951	+	if (forceFieldOptions_.haveCutoffPolicy()){
952	+	myPolicy = forceFieldOptions_.getCutoffPolicy();
953	+	}else if (simParams_->haveCutoffPolicy()) {
954	+	myPolicy = simParams_->getCutoffPolicy();
955	+	}
956
957	<	void SimInfo::getFortranGroupArrays(SimInfo* info,
958	<	vector<int>& FglobalGroupMembership,
959	<	vector<double>& mfact){
960	<
961	<	Molecule* myMols;
962	<	Atom** myAtoms;
963	<	int numAtom;
964	<	double mtot;
965	<	int numMol;
966	<	int numCutoffGroups;
967	<	CutoffGroup* myCutoffGroup;
968	<	vector<CutoffGroup*>::iterator iterCutoff;
969	<	Atom* cutoffAtom;
970	<	vector<Atom*>::iterator iterAtom;
971	<	int atomIndex;
972	<	double totalMass;
973	<
974	<	mfact.clear();
975	<	FglobalGroupMembership.clear();
976	<
957	>	if (!myPolicy.empty()){
958	>	toUpper(myPolicy);
959	>	if (myPolicy == "MIX") {
960	>	cp = MIX_CUTOFF_POLICY;
961	>	} else {
962	>	if (myPolicy == "MAX") {
963	>	cp = MAX_CUTOFF_POLICY;
964	>	} else {
965	>	if (myPolicy == "TRADITIONAL") {
966	>	cp = TRADITIONAL_CUTOFF_POLICY;
967	>	} else {
968	>	// throw error
969	>	sprintf( painCave.errMsg,
970	>	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
971	>	painCave.isFatal = 1;
972	>	simError();
973	>	}
974	>	}
975	>	}
976	>	}
977	>	notifyFortranCutoffPolicy(&cp);
978
979	<	// Fix the silly fortran indexing problem
980	<	#ifdef IS_MPI
981	<	numAtom = mpiSim->getNAtomsGlobal();
982	<	#else
983	<	numAtom = n_atoms;
984	<	#endif
985	<	for (int i = 0; i < numAtom; i++)
986	<	FglobalGroupMembership.push_back(globalGroupMembership[i] + 1);
987	<
979	>	// Check the Skin Thickness for neighborlists
980	>	RealType skin;
981	>	if (simParams_->haveSkinThickness()) {
982	>	skin = simParams_->getSkinThickness();
983	>	notifyFortranSkinThickness(&skin);
984	>	}
985	>
986	>	// Check if the cutoff was set explicitly:
987	>	if (simParams_->haveCutoffRadius()) {
988	>	rcut_ = simParams_->getCutoffRadius();
989	>	if (simParams_->haveSwitchingRadius()) {
990	>	rsw_  = simParams_->getSwitchingRadius();
991	>	} else {
992	>	if (fInfo_.SIM_uses_Charges |
993	>	fInfo_.SIM_uses_Dipoles |
994	>	fInfo_.SIM_uses_RF) {
995	>
996	>	rsw_ = 0.85 * rcut_;
997	>	sprintf(painCave.errMsg,
998	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
999	>	"\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
1000	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1001	>	painCave.isFatal = 0;
1002	>	simError();
1003	>	} else {
1004	>	rsw_ = rcut_;
1005	>	sprintf(painCave.errMsg,
1006	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
1007	>	"\tOOPSE will use the same value as the cutoffRadius.\n"
1008	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1009	>	painCave.isFatal = 0;
1010	>	simError();
1011	>	}
1012	>	}
1013	>
1014	>	notifyFortranCutoffs(&rcut_, &rsw_);
1015	>
1016	>	} else {
1017	>
1018	>	// For electrostatic atoms, we'll assume a large safe value:
1019	>	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1020	>	sprintf(painCave.errMsg,
1021	>	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1022	>	"\tOOPSE will use a default value of 15.0 angstroms"
1023	>	"\tfor the cutoffRadius.\n");
1024	>	painCave.isFatal = 0;
1025	>	simError();
1026	>	rcut_ = 15.0;
1027	>
1028	>	if (simParams_->haveElectrostaticSummationMethod()) {
1029	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1030	>	toUpper(myMethod);
1031	>	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1032	>	if (simParams_->haveSwitchingRadius()){
1033	>	sprintf(painCave.errMsg,
1034	>	"SimInfo Warning: A value was set for the switchingRadius\n"
1035	>	"\teven though the electrostaticSummationMethod was\n"
1036	>	"\tset to %s\n", myMethod.c_str());
1037	>	painCave.isFatal = 1;
1038	>	simError();
1039	>	}
1040	>	}
1041	>	}
1042	>
1043	>	if (simParams_->haveSwitchingRadius()){
1044	>	rsw_ = simParams_->getSwitchingRadius();
1045	>	} else {
1046	>	sprintf(painCave.errMsg,
1047	>	"SimCreator Warning: No value was set for switchingRadius.\n"
1048	>	"\tOOPSE will use a default value of\n"
1049	>	"\t0.85 * cutoffRadius for the switchingRadius\n");
1050	>	painCave.isFatal = 0;
1051	>	simError();
1052	>	rsw_ = 0.85 * rcut_;
1053	>	}
1054	>	notifyFortranCutoffs(&rcut_, &rsw_);
1055	>	} else {
1056	>	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1057	>	// We'll punt and let fortran figure out the cutoffs later.
1058	>
1059	>	notifyFortranYouAreOnYourOwn();
1060
1061	<	myMols = info->molecules;
1062	<	numMol = info->n_mol;
1063	<	for(int i  = 0; i < numMol; i++){
609	<	numCutoffGroups = myMols[i].getNCutoffGroups();
610	<	for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff);
611	<	myCutoffGroup != NULL;
612	<	myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
1061	>	}
1062	>	}
1063	>	}
1064
1065	<	totalMass = myCutoffGroup->getMass();
1065	>	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1066	>
1067	>	int errorOut;
1068	>	int esm =  NONE;
1069	>	int sm = UNDAMPED;
1070	>	RealType alphaVal;
1071	>	RealType dielectric;
1072	>
1073	>	errorOut = isError;
1074	>
1075	>	if (simParams_->haveElectrostaticSummationMethod()) {
1076	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1077	>	toUpper(myMethod);
1078	>	if (myMethod == "NONE") {
1079	>	esm = NONE;
1080	>	} else {
1081	>	if (myMethod == "SWITCHING_FUNCTION") {
1082	>	esm = SWITCHING_FUNCTION;
1083	>	} else {
1084	>	if (myMethod == "SHIFTED_POTENTIAL") {
1085	>	esm = SHIFTED_POTENTIAL;
1086	>	} else {
1087	>	if (myMethod == "SHIFTED_FORCE") {
1088	>	esm = SHIFTED_FORCE;
1089	>	} else {
1090	>	if (myMethod == "REACTION_FIELD") {
1091	>	esm = REACTION_FIELD;
1092	>	dielectric = simParams_->getDielectric();
1093	>	if (!simParams_->haveDielectric()) {
1094	>	// throw warning
1095	>	sprintf( painCave.errMsg,
1096	>	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1097	>	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1098	>	painCave.isFatal = 0;
1099	>	simError();
1100	>	}
1101	>	} else {
1102	>	// throw error
1103	>	sprintf( painCave.errMsg,
1104	>	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1105	>	"\t(Input file specified %s .)\n"
1106	>	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1107	>	"\t\"shifted_potential\", \"shifted_force\", or \n"
1108	>	"\t\"reaction_field\".\n", myMethod.c_str() );
1109	>	painCave.isFatal = 1;
1110	>	simError();
1111	>	}
1112	>	}
1113	>	}
1114	>	}
1115	>	}
1116	>	}
1117	>
1118	>	if (simParams_->haveElectrostaticScreeningMethod()) {
1119	>	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1120	>	toUpper(myScreen);
1121	>	if (myScreen == "UNDAMPED") {
1122	>	sm = UNDAMPED;
1123	>	} else {
1124	>	if (myScreen == "DAMPED") {
1125	>	sm = DAMPED;
1126	>	if (!simParams_->haveDampingAlpha()) {
1127	>	// first set a cutoff dependent alpha value
1128	>	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1129	>	alphaVal = 0.5125 - rcut_* 0.025;
1130	>	// for values rcut > 20.5, alpha is zero
1131	>	if (alphaVal < 0) alphaVal = 0;
1132	>
1133	>	// throw warning
1134	>	sprintf( painCave.errMsg,
1135	>	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1136	>	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1137	>	painCave.isFatal = 0;
1138	>	simError();
1139	>	} else {
1140	>	alphaVal = simParams_->getDampingAlpha();
1141	>	}
1142	>
1143	>	} else {
1144	>	// throw error
1145	>	sprintf( painCave.errMsg,
1146	>	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1147	>	"\t(Input file specified %s .)\n"
1148	>	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1149	>	"or \"damped\".\n", myScreen.c_str() );
1150	>	painCave.isFatal = 1;
1151	>	simError();
1152	>	}
1153	>	}
1154	>	}
1155	>
1156	>	// let's pass some summation method variables to fortran
1157	>	setElectrostaticSummationMethod( &esm );
1158	>	setFortranElectrostaticMethod( &esm );
1159	>	setScreeningMethod( &sm );
1160	>	setDampingAlpha( &alphaVal );
1161	>	setReactionFieldDielectric( &dielectric );
1162	>	initFortranFF( &errorOut );
1163	>	}
1164	>
1165	>	void SimInfo::setupSwitchingFunction() {
1166	>	int ft = CUBIC;
1167	>
1168	>	if (simParams_->haveSwitchingFunctionType()) {
1169	>	std::string funcType = simParams_->getSwitchingFunctionType();
1170	>	toUpper(funcType);
1171	>	if (funcType == "CUBIC") {
1172	>	ft = CUBIC;
1173	>	} else {
1174	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1175	>	ft = FIFTH_ORDER_POLY;
1176	>	} else {
1177	>	// throw error
1178	>	sprintf( painCave.errMsg,
1179	>	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1180	>	painCave.isFatal = 1;
1181	>	simError();
1182	>	}
1183	>	}
1184	>	}
1185	>
1186	>	// send switching function notification to switcheroo
1187	>	setFunctionType(&ft);
1188	>
1189	>	}
1190	>
1191	>	void SimInfo::setupAccumulateBoxDipole() {
1192	>
1193	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1194	>	if ( simParams_->haveAccumulateBoxDipole() )
1195	>	if ( simParams_->getAccumulateBoxDipole() ) {
1196	>	setAccumulateBoxDipole();
1197	>	calcBoxDipole_ = true;
1198	>	}
1199	>
1200	>	}
1201	>
1202	>	void SimInfo::addProperty(GenericData* genData) {
1203	>	properties_.addProperty(genData);
1204	>	}
1205	>
1206	>	void SimInfo::removeProperty(const std::string& propName) {
1207	>	properties_.removeProperty(propName);
1208	>	}
1209	>
1210	>	void SimInfo::clearProperties() {
1211	>	properties_.clearProperties();
1212	>	}
1213	>
1214	>	std::vector<std::string> SimInfo::getPropertyNames() {
1215	>	return properties_.getPropertyNames();
1216	>	}
1217
1218	<	for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom);
1219	<	cutoffAtom != NULL;
1220	<	cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
1221	<	mfact.push_back(cutoffAtom->getMass()/totalMass);
1218	>	std::vector<GenericData*> SimInfo::getProperties() {
1219	>	return properties_.getProperties();
1220	>	}
1221	>
1222	>	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1223	>	return properties_.getPropertyByName(propName);
1224	>	}
1225	>
1226	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1227	>	if (sman_ == sman) {
1228	>	return;
1229	>	}
1230	>	delete sman_;
1231	>	sman_ = sman;
1232	>
1233	>	Molecule* mol;
1234	>	RigidBody* rb;
1235	>	Atom* atom;
1236	>	SimInfo::MoleculeIterator mi;
1237	>	Molecule::RigidBodyIterator rbIter;
1238	>	Molecule::AtomIterator atomIter;;
1239	>
1240	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1241	>
1242	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1243	>	atom->setSnapshotManager(sman_);
1244	>	}
1245	>
1246	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1247	>	rb->setSnapshotManager(sman_);
1248	>	}
1249	>	}
1250	>
1251	>	}
1252	>
1253	>	Vector3d SimInfo::getComVel(){
1254	>	SimInfo::MoleculeIterator i;
1255	>	Molecule* mol;
1256	>
1257	>	Vector3d comVel(0.0);
1258	>	RealType totalMass = 0.0;
1259	>
1260	>
1261	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1262	>	RealType mass = mol->getMass();
1263	>	totalMass += mass;
1264	>	comVel += mass * mol->getComVel();
1265	>	}
1266	>
1267	>	#ifdef IS_MPI
1268	>	RealType tmpMass = totalMass;
1269	>	Vector3d tmpComVel(comVel);
1270	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1271	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1272	>	#endif
1273	>
1274	>	comVel /= totalMass;
1275	>
1276	>	return comVel;
1277	>	}
1278	>
1279	>	Vector3d SimInfo::getCom(){
1280	>	SimInfo::MoleculeIterator i;
1281	>	Molecule* mol;
1282	>
1283	>	Vector3d com(0.0);
1284	>	RealType totalMass = 0.0;
1285	>
1286	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1287	>	RealType mass = mol->getMass();
1288	>	totalMass += mass;
1289	>	com += mass * mol->getCom();
1290	>	}
1291	>
1292	>	#ifdef IS_MPI
1293	>	RealType tmpMass = totalMass;
1294	>	Vector3d tmpCom(com);
1295	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1296	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1297	>	#endif
1298	>
1299	>	com /= totalMass;
1300	>
1301	>	return com;
1302	>
1303	>	}
1304	>
1305	>	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1306	>
1307	>	return o;
1308	>	}
1309	>
1310	>
1311	>	/*
1312	>	Returns center of mass and center of mass velocity in one function call.
1313	>	*/
1314	>
1315	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1316	>	SimInfo::MoleculeIterator i;
1317	>	Molecule* mol;
1318	>
1319	>
1320	>	RealType totalMass = 0.0;
1321	>
1322	>
1323	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1324	>	RealType mass = mol->getMass();
1325	>	totalMass += mass;
1326	>	com += mass * mol->getCom();
1327	>	comVel += mass * mol->getComVel();
1328		}
1329	<	}
1329	>
1330	>	#ifdef IS_MPI
1331	>	RealType tmpMass = totalMass;
1332	>	Vector3d tmpCom(com);
1333	>	Vector3d tmpComVel(comVel);
1334	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1335	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1336	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1337	>	#endif
1338	>
1339	>	com /= totalMass;
1340	>	comVel /= totalMass;
1341	>	}
1342	>
1343	>	/*
1344	>	Return intertia tensor for entire system and angular momentum Vector.
1345	>
1346	>
1347	>	[  Ixx -Ixy  -Ixz ]
1348	>	J =| -Iyx  Iyy  -Iyz |
1349	>	[ -Izx -Iyz   Izz ]
1350	>	*/
1351	>
1352	>	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1353	>
1354	>
1355	>	RealType xx = 0.0;
1356	>	RealType yy = 0.0;
1357	>	RealType zz = 0.0;
1358	>	RealType xy = 0.0;
1359	>	RealType xz = 0.0;
1360	>	RealType yz = 0.0;
1361	>	Vector3d com(0.0);
1362	>	Vector3d comVel(0.0);
1363	>
1364	>	getComAll(com, comVel);
1365	>
1366	>	SimInfo::MoleculeIterator i;
1367	>	Molecule* mol;
1368	>
1369	>	Vector3d thisq(0.0);
1370	>	Vector3d thisv(0.0);
1371	>
1372	>	RealType thisMass = 0.0;
1373	>
1374	>
1375	>
1376	>
1377	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1378	>
1379	>	thisq = mol->getCom()-com;
1380	>	thisv = mol->getComVel()-comVel;
1381	>	thisMass = mol->getMass();
1382	>	// Compute moment of intertia coefficients.
1383	>	xx += thisq[0]*thisq[0]*thisMass;
1384	>	yy += thisq[1]*thisq[1]*thisMass;
1385	>	zz += thisq[2]*thisq[2]*thisMass;
1386	>
1387	>	// compute products of intertia
1388	>	xy += thisq[0]*thisq[1]*thisMass;
1389	>	xz += thisq[0]*thisq[2]*thisMass;
1390	>	yz += thisq[1]*thisq[2]*thisMass;
1391	>
1392	>	angularMomentum += cross( thisq, thisv ) * thisMass;
1393	>
1394	>	}
1395	>
1396	>
1397	>	inertiaTensor(0,0) = yy + zz;
1398	>	inertiaTensor(0,1) = -xy;
1399	>	inertiaTensor(0,2) = -xz;
1400	>	inertiaTensor(1,0) = -xy;
1401	>	inertiaTensor(1,1) = xx + zz;
1402	>	inertiaTensor(1,2) = -yz;
1403	>	inertiaTensor(2,0) = -xz;
1404	>	inertiaTensor(2,1) = -yz;
1405	>	inertiaTensor(2,2) = xx + yy;
1406	>
1407	>	#ifdef IS_MPI
1408	>	Mat3x3d tmpI(inertiaTensor);
1409	>	Vector3d tmpAngMom;
1410	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1411	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1412	>	#endif
1413	>
1414	>	return;
1415	>	}
1416	>
1417	>	//Returns the angular momentum of the system
1418	>	Vector3d SimInfo::getAngularMomentum(){
1419	>
1420	>	Vector3d com(0.0);
1421	>	Vector3d comVel(0.0);
1422	>	Vector3d angularMomentum(0.0);
1423	>
1424	>	getComAll(com,comVel);
1425	>
1426	>	SimInfo::MoleculeIterator i;
1427	>	Molecule* mol;
1428	>
1429	>	Vector3d thisr(0.0);
1430	>	Vector3d thisp(0.0);
1431	>
1432	>	RealType thisMass;
1433	>
1434	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1435	>	thisMass = mol->getMass();
1436	>	thisr = mol->getCom()-com;
1437	>	thisp = (mol->getComVel()-comVel)*thisMass;
1438	>
1439	>	angularMomentum += cross( thisr, thisp );
1440	>
1441	>	}
1442	>
1443	>	#ifdef IS_MPI
1444	>	Vector3d tmpAngMom;
1445	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1446	>	#endif
1447	>
1448	>	return angularMomentum;
1449	>	}
1450	>
1451	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1452	>	return IOIndexToIntegrableObject.at(index);
1453		}
1454	+
1455	+	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1456	+	IOIndexToIntegrableObject= v;
1457	+	}
1458
1459	<	}
1459	>	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1460	>	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1461	>	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1462	>	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1463	>	*/
1464	>	void SimInfo::getGyrationalVolume(RealType &volume){
1465	>	Mat3x3d intTensor;
1466	>	RealType det;
1467	>	Vector3d dummyAngMom;
1468	>	RealType sysconstants;
1469	>	RealType geomCnst;
1470	>
1471	>	geomCnst = 3.0/2.0;
1472	>	/* Get the inertial tensor and angular momentum for free*/
1473	>	getInertiaTensor(intTensor,dummyAngMom);
1474	>
1475	>	det = intTensor.determinant();
1476	>	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1477	>	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1478	>	return;
1479	>	}
1480	>
1481	>	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1482	>	Mat3x3d intTensor;
1483	>	Vector3d dummyAngMom;
1484	>	RealType sysconstants;
1485	>	RealType geomCnst;
1486	>
1487	>	geomCnst = 3.0/2.0;
1488	>	/* Get the inertial tensor and angular momentum for free*/
1489	>	getInertiaTensor(intTensor,dummyAngMom);
1490	>
1491	>	detI = intTensor.determinant();
1492	>	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1493	>	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1494	>	return;
1495	>	}
1496	>	/*
1497	>	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1498	>	assert( v.size() == nAtoms_ + nRigidBodies_);
1499	>	sdByGlobalIndex_ = v;
1500	>	}
1501	>
1502	>	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1503	>	//assert(index < nAtoms_ + nRigidBodies_);
1504	>	return sdByGlobalIndex_.at(index);
1505	>	}
1506	>	*/
1507	>	}//end namespace oopse
1508	>

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