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Comparing trunk/OOPSE-2.0/src/brains/SimInfo.cpp (file contents):
Revision 1617 by chuckv, Wed Oct 20 20:46:20 2004 UTC vs.
Revision 2469 by tim, Fri Dec 2 15:38:03 2005 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 "brains/SimInfo.hpp"
54	<	#define __C
55	<	#include "brains/fSimulation.h"
54	>	#include "math/Vector3.hpp"
55	>	#include "primitives/Molecule.hpp"
56	>	#include "UseTheForce/fCutoffPolicy.h"
57	>	#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
58	>	#include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h"
59	>	#include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
60	>	#include "UseTheForce/doForces_interface.h"
61	>	#include "UseTheForce/DarkSide/electrostatic_interface.h"
62	>	#include "UseTheForce/DarkSide/switcheroo_interface.h"
63	>	#include "utils/MemoryUtils.hpp"
64		#include "utils/simError.h"
65	<	#include "UseTheForce/DarkSide/simulation_interface.h"
13	<	#include "UseTheForce/notifyCutoffs_interface.h"
65	>	#include "selection/SelectionManager.hpp"
66
15	–	//#include "UseTheForce/fortranWrappers.hpp"
16	–
17	–	#include "math/MatVec3.h"
18	–
67		#ifdef IS_MPI
68	<	#include "brains/mpiSimulation.hpp"
69	<	#endif
68	>	#include "UseTheForce/mpiComponentPlan.h"
69	>	#include "UseTheForce/DarkSide/simParallel_interface.h"
70	>	#endif
71
72	<	inline double roundMe( double x ){
73	<	return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
74	<	}
75	<
76	<	inline double min( double a, double b ){
77	<	return (a < b ) ? a : b;
78	<	}
72	>	namespace oopse {
73	>	std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
74	>	std::map<int, std::set<int> >::iterator i = container.find(index);
75	>	std::set<int> result;
76	>	if (i != container.end()) {
77	>	result = i->second;
78	>	}
79
80	<	SimInfo* currentInfo;
81	<
33	<	SimInfo::SimInfo(){
34	<
35	<	n_constraints = 0;
36	<	nZconstraints = 0;
37	<	n_oriented = 0;
38	<	n_dipoles = 0;
39	<	ndf = 0;
40	<	ndfRaw = 0;
41	<	nZconstraints = 0;
42	<	the_integrator = NULL;
43	<	setTemp = 0;
44	<	thermalTime = 0.0;
45	<	currentTime = 0.0;
46	<	rCut = 0.0;
47	<	rSw = 0.0;
48	<
49	<	haveRcut = 0;
50	<	haveRsw = 0;
51	<	boxIsInit = 0;
80	>	return result;
81	>	}
82
83	<	resetTime = 1e99;
83	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
84	>	forceField_(ff), simParams_(simParams),
85	>	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
86	>	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
87	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
88	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
89	>	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
90	>	sman_(NULL), fortranInitialized_(false) {
91
92	<	orthoRhombic = 0;
93	<	orthoTolerance = 1E-6;
94	<	useInitXSstate = true;
92	>	MoleculeStamp* molStamp;
93	>	int nMolWithSameStamp;
94	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
95	>	int nGroups = 0;      //total cutoff groups defined in meta-data file
96	>	CutoffGroupStamp* cgStamp;
97	>	RigidBodyStamp* rbStamp;
98	>	int nRigidAtoms = 0;
99	>	std::vector<Component*> components = simParams->getComponents();
100	>
101	>	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
102	>	molStamp = (*i)->getMoleculeStamp();
103	>	nMolWithSameStamp = (*i)->getNMol();
104	>
105	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
106
107	<	usePBC = 0;
108	<	useLJ = 0;
61	<	useSticky = 0;
62	<	useCharges = 0;
63	<	useDipoles = 0;
64	<	useReactionField = 0;
65	<	useGB = 0;
66	<	useEAM = 0;
67	<	useSolidThermInt = 0;
68	<	useLiquidThermInt = 0;
107	>	//calculate atoms in molecules
108	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
109
110	<	haveCutoffGroups = false;
110	>	//calculate atoms in cutoff groups
111	>	int nAtomsInGroups = 0;
112	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
113	>
114	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
115	>	cgStamp = molStamp->getCutoffGroupStamp(j);
116	>	nAtomsInGroups += cgStamp->getNMembers();
117	>	}
118
119	<	excludes = Exclude::Instance();
119	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
120
121	<	myConfiguration = new SimState();
121	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
122
123	<	has_minimizer = false;
124	<	the_minimizer =NULL;
123	>	//calculate atoms in rigid bodies
124	>	int nAtomsInRigidBodies = 0;
125	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
126	>
127	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
128	>	rbStamp = molStamp->getRigidBodyStamp(j);
129	>	nAtomsInRigidBodies += rbStamp->getNMembers();
130	>	}
131
132	<	ngroup = 0;
132	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
133	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
134	>
135	>	}
136
137	<	}
137	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
138	>	//group therefore the total number of cutoff groups in the system is
139	>	//equal to the total number of atoms minus number of atoms belong to
140	>	//cutoff group defined in meta-data file plus the number of cutoff
141	>	//groups defined in meta-data file
142	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
143
144	+	//every free atom (atom does not belong to rigid bodies) is an
145	+	//integrable object therefore the total number of integrable objects
146	+	//in the system is equal to the total number of atoms minus number of
147	+	//atoms belong to rigid body defined in meta-data file plus the number
148	+	//of rigid bodies defined in meta-data file
149	+	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
150	+	+ nGlobalRigidBodies_;
151	+
152	+	nGlobalMols_ = molStampIds_.size();
153
154	<	SimInfo::~SimInfo(){
154	>	#ifdef IS_MPI
155	>	molToProcMap_.resize(nGlobalMols_);
156	>	#endif
157
158	<	delete myConfiguration;
158	>	}
159
160	<	map<string, GenericData*>::iterator i;
161	<
162	<	for(i = properties.begin(); i != properties.end(); i++)
163	<	delete (*i).second;
160	>	SimInfo::~SimInfo() {
161	>	std::map<int, Molecule*>::iterator i;
162	>	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
163	>	delete i->second;
164	>	}
165	>	molecules_.clear();
166	>
167	>	delete sman_;
168	>	delete simParams_;
169	>	delete forceField_;
170	>	}
171
172	<	}
172	>	int SimInfo::getNGlobalConstraints() {
173	>	int nGlobalConstraints;
174	>	#ifdef IS_MPI
175	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
176	>	MPI_COMM_WORLD);
177	>	#else
178	>	nGlobalConstraints =  nConstraints_;
179	>	#endif
180	>	return nGlobalConstraints;
181	>	}
182
183	<	void SimInfo::setBox(double newBox[3]) {
184	<
97	<	int i, j;
98	<	double tempMat[3][3];
183	>	bool SimInfo::addMolecule(Molecule* mol) {
184	>	MoleculeIterator i;
185
186	<	for(i=0; i<3; i++)
187	<	for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
186	>	i = molecules_.find(mol->getGlobalIndex());
187	>	if (i == molecules_.end() ) {
188
189	<	tempMat[0][0] = newBox[0];
190	<	tempMat[1][1] = newBox[1];
191	<	tempMat[2][2] = newBox[2];
189	>	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
190	>
191	>	nAtoms_ += mol->getNAtoms();
192	>	nBonds_ += mol->getNBonds();
193	>	nBends_ += mol->getNBends();
194	>	nTorsions_ += mol->getNTorsions();
195	>	nRigidBodies_ += mol->getNRigidBodies();
196	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
197	>	nCutoffGroups_ += mol->getNCutoffGroups();
198	>	nConstraints_ += mol->getNConstraintPairs();
199
200	<	setBoxM( tempMat );
200	>	addExcludePairs(mol);
201	>
202	>	return true;
203	>	} else {
204	>	return false;
205	>	}
206	>	}
207
208	<	}
208	>	bool SimInfo::removeMolecule(Molecule* mol) {
209	>	MoleculeIterator i;
210	>	i = molecules_.find(mol->getGlobalIndex());
211
212	<	void SimInfo::setBoxM( double theBox[3][3] ){
112	<
113	<	int i, j;
114	<	double FortranHmat[9]; // to preserve compatibility with Fortran the
115	<	// ordering in the array is as follows:
116	<	// [ 0 3 6 ]
117	<	// [ 1 4 7 ]
118	<	// [ 2 5 8 ]
119	<	double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
212	>	if (i != molecules_.end() ) {
213
214	<	if( !boxIsInit ) boxIsInit = 1;
214	>	assert(mol == i->second);
215	>
216	>	nAtoms_ -= mol->getNAtoms();
217	>	nBonds_ -= mol->getNBonds();
218	>	nBends_ -= mol->getNBends();
219	>	nTorsions_ -= mol->getNTorsions();
220	>	nRigidBodies_ -= mol->getNRigidBodies();
221	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
222	>	nCutoffGroups_ -= mol->getNCutoffGroups();
223	>	nConstraints_ -= mol->getNConstraintPairs();
224
225	<	for(i=0; i < 3; i++)
226	<	for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
125	<
126	<	calcBoxL();
127	<	calcHmatInv();
225	>	removeExcludePairs(mol);
226	>	molecules_.erase(mol->getGlobalIndex());
227
228	<	for(i=0; i < 3; i++) {
229	<	for (j=0; j < 3; j++) {
230	<	FortranHmat[3*j + i] = Hmat[i][j];
231	<	FortranHmatInv[3*j + i] = HmatInv[i][j];
228	>	delete mol;
229	>
230	>	return true;
231	>	} else {
232	>	return false;
233		}
134	–	}
234
136	–	setFortranBox(FortranHmat, FortranHmatInv, &orthoRhombic);
137	–
138	–	}
139	–
235
236	<	void SimInfo::getBoxM (double theBox[3][3]) {
236	>	}
237
238	<	int i, j;
239	<	for(i=0; i<3; i++)
240	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
241	<	}
238	>
239	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
240	>	i = molecules_.begin();
241	>	return i == molecules_.end() ? NULL : i->second;
242	>	}
243
244	+	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
245	+	++i;
246	+	return i == molecules_.end() ? NULL : i->second;
247	+	}
248
149	–	void SimInfo::scaleBox(double scale) {
150	–	double theBox[3][3];
151	–	int i, j;
249
250	<	// cerr << "Scaling box by " << scale << "\n";
250	>	void SimInfo::calcNdf() {
251	>	int ndf_local;
252	>	MoleculeIterator i;
253	>	std::vector<StuntDouble*>::iterator j;
254	>	Molecule* mol;
255	>	StuntDouble* integrableObject;
256
257	<	for(i=0; i<3; i++)
258	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
257	>	ndf_local = 0;
258	>
259	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
260	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
261	>	integrableObject = mol->nextIntegrableObject(j)) {
262
263	<	setBoxM(theBox);
263	>	ndf_local += 3;
264
265	<	}
266	<
267	<	void SimInfo::calcHmatInv( void ) {
268	<
269	<	int oldOrtho;
270	<	int i,j;
271	<	double smallDiag;
272	<	double tol;
168	<	double sanity[3][3];
169	<
170	<	invertMat3( Hmat, HmatInv );
171	<
172	<	// check to see if Hmat is orthorhombic
173	<
174	<	oldOrtho = orthoRhombic;
175	<
176	<	smallDiag = fabs(Hmat[0][0]);
177	<	if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
178	<	if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
179	<	tol = smallDiag * orthoTolerance;
180	<
181	<	orthoRhombic = 1;
182	<
183	<	for (i = 0; i < 3; i++ ) {
184	<	for (j = 0 ; j < 3; j++) {
185	<	if (i != j) {
186	<	if (orthoRhombic) {
187	<	if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
188	<	}
265	>	if (integrableObject->isDirectional()) {
266	>	if (integrableObject->isLinear()) {
267	>	ndf_local += 2;
268	>	} else {
269	>	ndf_local += 3;
270	>	}
271	>	}
272	>
273		}
274		}
191	–	}
192	–
193	–	if( oldOrtho != orthoRhombic ){
275
276	<	if( orthoRhombic ) {
277	<	sprintf( painCave.errMsg,
197	<	"OOPSE is switching from the default Non-Orthorhombic\n"
198	<	"\tto the faster Orthorhombic periodic boundary computations.\n"
199	<	"\tThis is usually a good thing, but if you wan't the\n"
200	<	"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
201	<	"\tvariable ( currently set to %G ) smaller.\n",
202	<	orthoTolerance);
203	<	painCave.severity = OOPSE_INFO;
204	<	simError();
205	<	}
206	<	else {
207	<	sprintf( painCave.errMsg,
208	<	"OOPSE is switching from the faster Orthorhombic to the more\n"
209	<	"\tflexible Non-Orthorhombic periodic boundary computations.\n"
210	<	"\tThis is usually because the box has deformed under\n"
211	<	"\tNPTf integration. If you wan't to live on the edge with\n"
212	<	"\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
213	<	"\tvariable ( currently set to %G ) larger.\n",
214	<	orthoTolerance);
215	<	painCave.severity = OOPSE_WARNING;
216	<	simError();
217	<	}
218	<	}
219	<	}
276	>	// n_constraints is local, so subtract them on each processor
277	>	ndf_local -= nConstraints_;
278
279	<	void SimInfo::calcBoxL( void ){
279	>	#ifdef IS_MPI
280	>	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
281	>	#else
282	>	ndf_ = ndf_local;
283	>	#endif
284
285	<	double dx, dy, dz, dsq;
285	>	// nZconstraints_ is global, as are the 3 COM translations for the
286	>	// entire system:
287	>	ndf_ = ndf_ - 3 - nZconstraint_;
288
289	<	// boxVol = Determinant of Hmat
289	>	}
290
291	<	boxVol = matDet3( Hmat );
291	>	void SimInfo::calcNdfRaw() {
292	>	int ndfRaw_local;
293
294	<	// boxLx
295	<
296	<	dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
297	<	dsq = dx*dx + dy*dy + dz*dz;
233	<	boxL[0] = sqrt( dsq );
234	<	//maxCutoff = 0.5 * boxL[0];
294	>	MoleculeIterator i;
295	>	std::vector<StuntDouble*>::iterator j;
296	>	Molecule* mol;
297	>	StuntDouble* integrableObject;
298
299	<	// boxLy
300	<
238	<	dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
239	<	dsq = dx*dx + dy*dy + dz*dz;
240	<	boxL[1] = sqrt( dsq );
241	<	//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
242	<
243	<
244	<	// boxLz
245	<
246	<	dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
247	<	dsq = dx*dx + dy*dy + dz*dz;
248	<	boxL[2] = sqrt( dsq );
249	<	//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
250	<
251	<	//calculate the max cutoff
252	<	maxCutoff =  calcMaxCutOff();
253	<
254	<	checkCutOffs();
255	<
256	<	}
257	<
258	<
259	<	double SimInfo::calcMaxCutOff(){
260	<
261	<	double ri[3], rj[3], rk[3];
262	<	double rij[3], rjk[3], rki[3];
263	<	double minDist;
264	<
265	<	ri[0] = Hmat[0][0];
266	<	ri[1] = Hmat[1][0];
267	<	ri[2] = Hmat[2][0];
268	<
269	<	rj[0] = Hmat[0][1];
270	<	rj[1] = Hmat[1][1];
271	<	rj[2] = Hmat[2][1];
272	<
273	<	rk[0] = Hmat[0][2];
274	<	rk[1] = Hmat[1][2];
275	<	rk[2] = Hmat[2][2];
299	>	// Raw degrees of freedom that we have to set
300	>	ndfRaw_local = 0;
301
302	<	crossProduct3(ri, rj, rij);
303	<	distXY = dotProduct3(rk,rij) / norm3(rij);
302	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
303	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
304	>	integrableObject = mol->nextIntegrableObject(j)) {
305
306	<	crossProduct3(rj,rk, rjk);
281	<	distYZ = dotProduct3(ri,rjk) / norm3(rjk);
306	>	ndfRaw_local += 3;
307
308	<	crossProduct3(rk,ri, rki);
309	<	distZX = dotProduct3(rj,rki) / norm3(rki);
308	>	if (integrableObject->isDirectional()) {
309	>	if (integrableObject->isLinear()) {
310	>	ndfRaw_local += 2;
311	>	} else {
312	>	ndfRaw_local += 3;
313	>	}
314	>	}
315	>
316	>	}
317	>	}
318	>
319	>	#ifdef IS_MPI
320	>	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
321	>	#else
322	>	ndfRaw_ = ndfRaw_local;
323	>	#endif
324	>	}
325
326	<	minDist = min(min(distXY, distYZ), distZX);
327	<	return minDist/2;
288	<
289	<	}
326	>	void SimInfo::calcNdfTrans() {
327	>	int ndfTrans_local;
328
329	<	void SimInfo::wrapVector( double thePos[3] ){
329	>	ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
330
293	–	int i;
294	–	double scaled[3];
331
332	<	if( !orthoRhombic ){
333	<	// calc the scaled coordinates.
334	<
332	>	#ifdef IS_MPI
333	>	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
334	>	#else
335	>	ndfTrans_ = ndfTrans_local;
336	>	#endif
337
338	<	matVecMul3(HmatInv, thePos, scaled);
338	>	ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
339	>
340	>	}
341	>
342	>	void SimInfo::addExcludePairs(Molecule* mol) {
343	>	std::vector<Bond*>::iterator bondIter;
344	>	std::vector<Bend*>::iterator bendIter;
345	>	std::vector<Torsion*>::iterator torsionIter;
346	>	Bond* bond;
347	>	Bend* bend;
348	>	Torsion* torsion;
349	>	int a;
350	>	int b;
351	>	int c;
352	>	int d;
353	>
354	>	std::map<int, std::set<int> > atomGroups;
355	>
356	>	Molecule::RigidBodyIterator rbIter;
357	>	RigidBody* rb;
358	>	Molecule::IntegrableObjectIterator ii;
359	>	StuntDouble* integrableObject;
360
361	<	for(i=0; i<3; i++)
362	<	scaled[i] -= roundMe(scaled[i]);
304	<
305	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
306	<
307	<	matVecMul3(Hmat, scaled, thePos);
361	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
362	>	integrableObject = mol->nextIntegrableObject(ii)) {
363
364	<	}
365	<	else{
366	<	// calc the scaled coordinates.
364	>	if (integrableObject->isRigidBody()) {
365	>	rb = static_cast<RigidBody*>(integrableObject);
366	>	std::vector<Atom*> atoms = rb->getAtoms();
367	>	std::set<int> rigidAtoms;
368	>	for (int i = 0; i < atoms.size(); ++i) {
369	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
370	>	}
371	>	for (int i = 0; i < atoms.size(); ++i) {
372	>	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
373	>	}
374	>	} else {
375	>	std::set<int> oneAtomSet;
376	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
377	>	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
378	>	}
379	>	}
380	>
381
313	–	for(i=0; i<3; i++)
314	–	scaled[i] = thePos[i]*HmatInv[i][i];
382
383	<	// wrap the scaled coordinates
384	<
385	<	for(i=0; i<3; i++)
386	<	scaled[i] -= roundMe(scaled[i]);
387	<
321	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
322	<
323	<	for(i=0; i<3; i++)
324	<	thePos[i] = scaled[i]*Hmat[i][i];
325	<	}
326	<
327	<	}
383	>	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
384	>	a = bond->getAtomA()->getGlobalIndex();
385	>	b = bond->getAtomB()->getGlobalIndex();
386	>	exclude_.addPair(a, b);
387	>	}
388
389	+	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
390	+	a = bend->getAtomA()->getGlobalIndex();
391	+	b = bend->getAtomB()->getGlobalIndex();
392	+	c = bend->getAtomC()->getGlobalIndex();
393	+	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
394	+	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
395	+	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
396
397	<	int SimInfo::getNDF(){
398	<	int ndf_local;
399	<
400	<	ndf_local = 0;
401	<
402	<	for(int i = 0; i < integrableObjects.size(); i++){
403	<	ndf_local += 3;
337	<	if (integrableObjects[i]->isDirectional()) {
338	<	if (integrableObjects[i]->isLinear())
339	<	ndf_local += 2;
340	<	else
341	<	ndf_local += 3;
397	>	exclude_.addPairs(rigidSetA, rigidSetB);
398	>	exclude_.addPairs(rigidSetA, rigidSetC);
399	>	exclude_.addPairs(rigidSetB, rigidSetC);
400	>
401	>	//exclude_.addPair(a, b);
402	>	//exclude_.addPair(a, c);
403	>	//exclude_.addPair(b, c);
404		}
343	–	}
405
406	<	// n_constraints is local, so subtract them on each processor:
406	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
407	>	a = torsion->getAtomA()->getGlobalIndex();
408	>	b = torsion->getAtomB()->getGlobalIndex();
409	>	c = torsion->getAtomC()->getGlobalIndex();
410	>	d = torsion->getAtomD()->getGlobalIndex();
411	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
412	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
413	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
414	>	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
415
416	<	ndf_local -= n_constraints;
416	>	exclude_.addPairs(rigidSetA, rigidSetB);
417	>	exclude_.addPairs(rigidSetA, rigidSetC);
418	>	exclude_.addPairs(rigidSetA, rigidSetD);
419	>	exclude_.addPairs(rigidSetB, rigidSetC);
420	>	exclude_.addPairs(rigidSetB, rigidSetD);
421	>	exclude_.addPairs(rigidSetC, rigidSetD);
422
423	<	#ifdef IS_MPI
424	<	MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
425	<	#else
426	<	ndf = ndf_local;
427	<	#endif
423	>	/*
424	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
425	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
426	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
427	>	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
428	>	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
429	>	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
430	>
431	>
432	>	exclude_.addPair(a, b);
433	>	exclude_.addPair(a, c);
434	>	exclude_.addPair(a, d);
435	>	exclude_.addPair(b, c);
436	>	exclude_.addPair(b, d);
437	>	exclude_.addPair(c, d);
438	>	*/
439	>	}
440
441	<	// nZconstraints is global, as are the 3 COM translations for the
442	<	// entire system:
441	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
442	>	std::vector<Atom*> atoms = rb->getAtoms();
443	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
444	>	for (int j = i + 1; j < atoms.size(); ++j) {
445	>	a = atoms[i]->getGlobalIndex();
446	>	b = atoms[j]->getGlobalIndex();
447	>	exclude_.addPair(a, b);
448	>	}
449	>	}
450	>	}
451
452	<	ndf = ndf - 3 - nZconstraints;
452	>	}
453
454	<	return ndf;
455	<	}
454	>	void SimInfo::removeExcludePairs(Molecule* mol) {
455	>	std::vector<Bond*>::iterator bondIter;
456	>	std::vector<Bend*>::iterator bendIter;
457	>	std::vector<Torsion*>::iterator torsionIter;
458	>	Bond* bond;
459	>	Bend* bend;
460	>	Torsion* torsion;
461	>	int a;
462	>	int b;
463	>	int c;
464	>	int d;
465
466	<	int SimInfo::getNDFraw() {
364	<	int ndfRaw_local;
466	>	std::map<int, std::set<int> > atomGroups;
467
468	<	// Raw degrees of freedom that we have to set
469	<	ndfRaw_local = 0;
470	<
471	<	for(int i = 0; i < integrableObjects.size(); i++){
370	<	ndfRaw_local += 3;
371	<	if (integrableObjects[i]->isDirectional()) {
372	<	if (integrableObjects[i]->isLinear())
373	<	ndfRaw_local += 2;
374	<	else
375	<	ndfRaw_local += 3;
376	<	}
377	<	}
468	>	Molecule::RigidBodyIterator rbIter;
469	>	RigidBody* rb;
470	>	Molecule::IntegrableObjectIterator ii;
471	>	StuntDouble* integrableObject;
472
473	<	#ifdef IS_MPI
474	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
381	<	#else
382	<	ndfRaw = ndfRaw_local;
383	<	#endif
473	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
474	>	integrableObject = mol->nextIntegrableObject(ii)) {
475
476	<	return ndfRaw;
477	<	}
476	>	if (integrableObject->isRigidBody()) {
477	>	rb = static_cast<RigidBody*>(integrableObject);
478	>	std::vector<Atom*> atoms = rb->getAtoms();
479	>	std::set<int> rigidAtoms;
480	>	for (int i = 0; i < atoms.size(); ++i) {
481	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
482	>	}
483	>	for (int i = 0; i < atoms.size(); ++i) {
484	>	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
485	>	}
486	>	} else {
487	>	std::set<int> oneAtomSet;
488	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
489	>	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
490	>	}
491	>	}
492
493	<	int SimInfo::getNDFtranslational() {
494	<	int ndfTrans_local;
493	>
494	>	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
495	>	a = bond->getAtomA()->getGlobalIndex();
496	>	b = bond->getAtomB()->getGlobalIndex();
497	>	exclude_.removePair(a, b);
498	>	}
499
500	<	ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
500	>	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
501	>	a = bend->getAtomA()->getGlobalIndex();
502	>	b = bend->getAtomB()->getGlobalIndex();
503	>	c = bend->getAtomC()->getGlobalIndex();
504
505	+	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
506	+	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
507	+	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
508
509	<	#ifdef IS_MPI
510	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
511	<	#else
512	<	ndfTrans = ndfTrans_local;
513	<	#endif
509	>	exclude_.removePairs(rigidSetA, rigidSetB);
510	>	exclude_.removePairs(rigidSetA, rigidSetC);
511	>	exclude_.removePairs(rigidSetB, rigidSetC);
512	>
513	>	//exclude_.removePair(a, b);
514	>	//exclude_.removePair(a, c);
515	>	//exclude_.removePair(b, c);
516	>	}
517
518	<	ndfTrans = ndfTrans - 3 - nZconstraints;
518	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
519	>	a = torsion->getAtomA()->getGlobalIndex();
520	>	b = torsion->getAtomB()->getGlobalIndex();
521	>	c = torsion->getAtomC()->getGlobalIndex();
522	>	d = torsion->getAtomD()->getGlobalIndex();
523
524	<	return ndfTrans;
525	<	}
524	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
525	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
526	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
527	>	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
528
529	<	int SimInfo::getTotIntegrableObjects() {
530	<	int nObjs_local;
531	<	int nObjs;
529	>	exclude_.removePairs(rigidSetA, rigidSetB);
530	>	exclude_.removePairs(rigidSetA, rigidSetC);
531	>	exclude_.removePairs(rigidSetA, rigidSetD);
532	>	exclude_.removePairs(rigidSetB, rigidSetC);
533	>	exclude_.removePairs(rigidSetB, rigidSetD);
534	>	exclude_.removePairs(rigidSetC, rigidSetD);
535
536	<	nObjs_local =  integrableObjects.size();
536	>	/*
537	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
538	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
539	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
540	>	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
541	>	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
542	>	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
543
544	+
545	+	exclude_.removePair(a, b);
546	+	exclude_.removePair(a, c);
547	+	exclude_.removePair(a, d);
548	+	exclude_.removePair(b, c);
549	+	exclude_.removePair(b, d);
550	+	exclude_.removePair(c, d);
551	+	*/
552	+	}
553
554	<	#ifdef IS_MPI
555	<	MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
556	<	#else
557	<	nObjs = nObjs_local;
558	<	#endif
554	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
555	>	std::vector<Atom*> atoms = rb->getAtoms();
556	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
557	>	for (int j = i + 1; j < atoms.size(); ++j) {
558	>	a = atoms[i]->getGlobalIndex();
559	>	b = atoms[j]->getGlobalIndex();
560	>	exclude_.removePair(a, b);
561	>	}
562	>	}
563	>	}
564
565	+	}
566
419	–	return nObjs;
420	–	}
567
568	<	void SimInfo::refreshSim(){
568	>	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
569	>	int curStampId;
570
571	<	simtype fInfo;
572	<	int isError;
426	<	int n_global;
427	<	int* excl;
571	>	//index from 0
572	>	curStampId = moleculeStamps_.size();
573
574	<	fInfo.dielect = 0.0;
575	<
431	<	if( useDipoles ){
432	<	if( useReactionField )fInfo.dielect = dielectric;
574	>	moleculeStamps_.push_back(molStamp);
575	>	molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
576		}
577
578	<	fInfo.SIM_uses_PBC = usePBC;
436	<	//fInfo.SIM_uses_LJ = 0;
437	<	fInfo.SIM_uses_LJ = useLJ;
438	<	fInfo.SIM_uses_sticky = useSticky;
439	<	//fInfo.SIM_uses_sticky = 0;
440	<	fInfo.SIM_uses_charges = useCharges;
441	<	fInfo.SIM_uses_dipoles = useDipoles;
442	<	//fInfo.SIM_uses_dipoles = 0;
443	<	fInfo.SIM_uses_RF = useReactionField;
444	<	//fInfo.SIM_uses_RF = 0;
445	<	fInfo.SIM_uses_GB = useGB;
446	<	fInfo.SIM_uses_EAM = useEAM;
578	>	void SimInfo::update() {
579
580	<	n_exclude = excludes->getSize();
581	<	excl = excludes->getFortranArray();
450	<
580	>	setupSimType();
581	>
582		#ifdef IS_MPI
583	<	n_global = mpiSim->getNAtomsGlobal();
453	<	#else
454	<	n_global = n_atoms;
583	>	setupFortranParallel();
584		#endif
456	–
457	–	isError = 0;
458	–
459	–	getFortranGroupArrays(this, FglobalGroupMembership, mfact);
460	–	//it may not be a good idea to pass the address of first element in vector
461	–	//since c++ standard does not require vector to be stored continuously in meomory
462	–	//Most of the compilers will organize the memory of vector continuously
463	–	setFortranSim( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
464	–	&nGlobalExcludes, globalExcludes, molMembershipArray,
465	–	&mfact[0], &ngroup, &FglobalGroupMembership[0], &isError);
585
586	<	if( isError ){
586	>	setupFortranSim();
587	>
588	>	//setup fortran force field
589	>	/** @deprecate */
590	>	int isError = 0;
591
592	<	sprintf( painCave.errMsg,
593	<	"There was an error setting the simulation information in fortran.\n" );
471	<	painCave.isFatal = 1;
472	<	painCave.severity = OOPSE_ERROR;
473	<	simError();
474	<	}
475	<
476	<	#ifdef IS_MPI
477	<	sprintf( checkPointMsg,
478	<	"succesfully sent the simulation information to fortran.\n");
479	<	MPIcheckPoint();
480	<	#endif // is_mpi
481	<
482	<	this->ndf = this->getNDF();
483	<	this->ndfRaw = this->getNDFraw();
484	<	this->ndfTrans = this->getNDFtranslational();
485	<	}
592	>	setupElectrostaticSummationMethod( isError );
593	>	setupSwitchingFunction();
594
595	<	void SimInfo::setDefaultRcut( double theRcut ){
596	<
597	<	haveRcut = 1;
598	<	rCut = theRcut;
599	<	rList = rCut + 1.0;
600	<
601	<	notifyFortranCutoffs( &rCut, &rSw, &rList );
602	<	}
603	<
496	<	void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
497	<
498	<	rSw = theRsw;
499	<	setDefaultRcut( theRcut );
500	<	}
595	>	if(isError){
596	>	sprintf( painCave.errMsg,
597	>	"ForceField error: There was an error initializing the forceField in fortran.\n" );
598	>	painCave.isFatal = 1;
599	>	simError();
600	>	}
601	>
602	>
603	>	setupCutoff();
604
605	+	calcNdf();
606	+	calcNdfRaw();
607	+	calcNdfTrans();
608
609	<	void SimInfo::checkCutOffs( void ){
610	<
611	<	if( boxIsInit ){
609	>	fortranInitialized_ = true;
610	>	}
611	>
612	>	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
613	>	SimInfo::MoleculeIterator mi;
614	>	Molecule* mol;
615	>	Molecule::AtomIterator ai;
616	>	Atom* atom;
617	>	std::set<AtomType*> atomTypes;
618	>
619	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
620	>
621	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
622	>	atomTypes.insert(atom->getAtomType());
623	>	}
624	>
625	>	}
626	>
627	>	return atomTypes;
628	>	}
629	>
630	>	void SimInfo::setupSimType() {
631	>	std::set<AtomType*>::iterator i;
632	>	std::set<AtomType*> atomTypes;
633	>	atomTypes = getUniqueAtomTypes();
634
635	<	//we need to check cutOffs against the box
635	>	int useLennardJones = 0;
636	>	int useElectrostatic = 0;
637	>	int useEAM = 0;
638	>	int useSC = 0;
639	>	int useCharge = 0;
640	>	int useDirectional = 0;
641	>	int useDipole = 0;
642	>	int useGayBerne = 0;
643	>	int useSticky = 0;
644	>	int useStickyPower = 0;
645	>	int useShape = 0;
646	>	int useFLARB = 0; //it is not in AtomType yet
647	>	int useDirectionalAtom = 0;
648	>	int useElectrostatics = 0;
649	>	//usePBC and useRF are from simParams
650	>	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
651	>	int useRF;
652	>	int useSF;
653	>	std::string myMethod;
654	>
655	>	// set the useRF logical
656	>	useRF = 0;
657	>	useSF = 0;
658	>
659	>
660	>	if (simParams_->haveElectrostaticSummationMethod()) {
661	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
662	>	toUpper(myMethod);
663	>	if (myMethod == "REACTION_FIELD") {
664	>	useRF=1;
665	>	} else {
666	>	if (myMethod == "SHIFTED_FORCE") {
667	>	useSF = 1;
668	>	}
669	>	}
670	>	}
671	>
672	>	//loop over all of the atom types
673	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
674	>	useLennardJones |= (*i)->isLennardJones();
675	>	useElectrostatic |= (*i)->isElectrostatic();
676	>	useEAM |= (*i)->isEAM();
677	>	useSC |= (*i)->isSC();
678	>	useCharge |= (*i)->isCharge();
679	>	useDirectional |= (*i)->isDirectional();
680	>	useDipole |= (*i)->isDipole();
681	>	useGayBerne |= (*i)->isGayBerne();
682	>	useSticky |= (*i)->isSticky();
683	>	useStickyPower |= (*i)->isStickyPower();
684	>	useShape |= (*i)->isShape();
685	>	}
686	>
687	>	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
688	>	useDirectionalAtom = 1;
689	>	}
690	>
691	>	if (useCharge || useDipole) {
692	>	useElectrostatics = 1;
693	>	}
694	>
695	>	#ifdef IS_MPI
696	>	int temp;
697	>
698	>	temp = usePBC;
699	>	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
700	>
701	>	temp = useDirectionalAtom;
702	>	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
703	>
704	>	temp = useLennardJones;
705	>	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
706	>
707	>	temp = useElectrostatics;
708	>	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
709	>
710	>	temp = useCharge;
711	>	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
712	>
713	>	temp = useDipole;
714	>	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
715	>
716	>	temp = useSticky;
717	>	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
718	>
719	>	temp = useStickyPower;
720	>	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
721
722	<	if( rCut > maxCutoff ){
723	<	sprintf( painCave.errMsg,
511	<	"cutoffRadius is too large for the current periodic box.\n"
512	<	"\tCurrent Value of cutoffRadius = %G at time %G\n "
513	<	"\tThis is larger than half of at least one of the\n"
514	<	"\tperiodic box vectors.  Right now, the Box matrix is:\n"
515	<	"\n"
516	<	"\t[ %G %G %G ]\n"
517	<	"\t[ %G %G %G ]\n"
518	<	"\t[ %G %G %G ]\n",
519	<	rCut, currentTime,
520	<	Hmat[0][0], Hmat[0][1], Hmat[0][2],
521	<	Hmat[1][0], Hmat[1][1], Hmat[1][2],
522	<	Hmat[2][0], Hmat[2][1], Hmat[2][2]);
523	<	painCave.severity = OOPSE_ERROR;
524	<	painCave.isFatal = 1;
525	<	simError();
526	<	}
527	<	} else {
528	<	// initialize this stuff before using it, OK?
529	<	sprintf( painCave.errMsg,
530	<	"Trying to check cutoffs without a box.\n"
531	<	"\tOOPSE should have better programmers than that.\n" );
532	<	painCave.severity = OOPSE_ERROR;
533	<	painCave.isFatal = 1;
534	<	simError();
535	<	}
536	<
537	<	}
722	>	temp = useGayBerne;
723	>	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
724
725	<	void SimInfo::addProperty(GenericData* prop){
725	>	temp = useEAM;
726	>	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
727
728	<	map<string, GenericData*>::iterator result;
729	<	result = properties.find(prop->getID());
543	<
544	<	//we can't simply use  properties[prop->getID()] = prop,
545	<	//it will cause memory leak if we already contain a propery which has the same name of prop
546	<
547	<	if(result != properties.end()){
728	>	temp = useSC;
729	>	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
730
731	<	delete (*result).second;
732	<	(*result).second = prop;
731	>	temp = useShape;
732	>	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
733	>
734	>	temp = useFLARB;
735	>	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
736	>
737	>	temp = useRF;
738	>	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
739	>
740	>	temp = useSF;
741	>	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
742	>
743	>	#endif
744	>
745	>	fInfo_.SIM_uses_PBC = usePBC;
746	>	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
747	>	fInfo_.SIM_uses_LennardJones = useLennardJones;
748	>	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
749	>	fInfo_.SIM_uses_Charges = useCharge;
750	>	fInfo_.SIM_uses_Dipoles = useDipole;
751	>	fInfo_.SIM_uses_Sticky = useSticky;
752	>	fInfo_.SIM_uses_StickyPower = useStickyPower;
753	>	fInfo_.SIM_uses_GayBerne = useGayBerne;
754	>	fInfo_.SIM_uses_EAM = useEAM;
755	>	fInfo_.SIM_uses_SC = useSC;
756	>	fInfo_.SIM_uses_Shapes = useShape;
757	>	fInfo_.SIM_uses_FLARB = useFLARB;
758	>	fInfo_.SIM_uses_RF = useRF;
759	>	fInfo_.SIM_uses_SF = useSF;
760	>
761	>	if( myMethod == "REACTION_FIELD") {
762
763	+	if (simParams_->haveDielectric()) {
764	+	fInfo_.dielect = simParams_->getDielectric();
765	+	} else {
766	+	sprintf(painCave.errMsg,
767	+	"SimSetup Error: No Dielectric constant was set.\n"
768	+	"\tYou are trying to use Reaction Field without"
769	+	"\tsetting a dielectric constant!\n");
770	+	painCave.isFatal = 1;
771	+	simError();
772	+	}
773	+	}
774	+
775		}
553	–	else{
776
777	<	properties[prop->getID()] = prop;
777	>	void SimInfo::setupFortranSim() {
778	>	int isError;
779	>	int nExclude;
780	>	std::vector<int> fortranGlobalGroupMembership;
781	>
782	>	nExclude = exclude_.getSize();
783	>	isError = 0;
784
785	<	}
785	>	//globalGroupMembership_ is filled by SimCreator
786	>	for (int i = 0; i < nGlobalAtoms_; i++) {
787	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
788	>	}
789	>
790	>	//calculate mass ratio of cutoff group
791	>	std::vector<double> mfact;
792	>	SimInfo::MoleculeIterator mi;
793	>	Molecule* mol;
794	>	Molecule::CutoffGroupIterator ci;
795	>	CutoffGroup* cg;
796	>	Molecule::AtomIterator ai;
797	>	Atom* atom;
798	>	double totalMass;
799	>
800	>	//to avoid memory reallocation, reserve enough space for mfact
801	>	mfact.reserve(getNCutoffGroups());
802
803	<	}
803	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
804	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
805
806	<	GenericData* SimInfo::getProperty(const string& propName){
807	<
808	<	map<string, GenericData*>::iterator result;
809	<
810	<	//string lowerCaseName = ();
811	<
812	<	result = properties.find(propName);
813	<
569	<	if(result != properties.end())
570	<	return (*result).second;
571	<	else
572	<	return NULL;
573	<	}
806	>	totalMass = cg->getMass();
807	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
808	>	// Check for massless groups - set mfact to 1 if true
809	>	if (totalMass != 0)
810	>	mfact.push_back(atom->getMass()/totalMass);
811	>	else
812	>	mfact.push_back( 1.0 );
813	>	}
814
815	+	}
816	+	}
817
818	<	void SimInfo::getFortranGroupArrays(SimInfo* info,
819	<	vector<int>& FglobalGroupMembership,
578	<	vector<double>& mfact){
579	<
580	<	Molecule* myMols;
581	<	Atom** myAtoms;
582	<	int numAtom;
583	<	double mtot;
584	<	int numMol;
585	<	int numCutoffGroups;
586	<	CutoffGroup* myCutoffGroup;
587	<	vector<CutoffGroup*>::iterator iterCutoff;
588	<	Atom* cutoffAtom;
589	<	vector<Atom*>::iterator iterAtom;
590	<	int atomIndex;
591	<	double totalMass;
592	<
593	<	mfact.clear();
594	<	FglobalGroupMembership.clear();
595	<
818	>	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
819	>	std::vector<int> identArray;
820
821	<	// Fix the silly fortran indexing problem
821	>	//to avoid memory reallocation, reserve enough space identArray
822	>	identArray.reserve(getNAtoms());
823	>
824	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
825	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
826	>	identArray.push_back(atom->getIdent());
827	>	}
828	>	}
829	>
830	>	//fill molMembershipArray
831	>	//molMembershipArray is filled by SimCreator
832	>	std::vector<int> molMembershipArray(nGlobalAtoms_);
833	>	for (int i = 0; i < nGlobalAtoms_; i++) {
834	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
835	>	}
836	>
837	>	//setup fortran simulation
838	>	int nGlobalExcludes = 0;
839	>	int* globalExcludes = NULL;
840	>	int* excludeList = exclude_.getExcludeList();
841	>	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
842	>	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
843	>	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
844	>
845	>	if( isError ){
846	>
847	>	sprintf( painCave.errMsg,
848	>	"There was an error setting the simulation information in fortran.\n" );
849	>	painCave.isFatal = 1;
850	>	painCave.severity = OOPSE_ERROR;
851	>	simError();
852	>	}
853	>
854		#ifdef IS_MPI
855	<	numAtom = mpiSim->getNAtomsGlobal();
856	<	#else
857	<	numAtom = n_atoms;
858	<	#endif
859	<	for (int i = 0; i < numAtom; i++)
604	<	FglobalGroupMembership.push_back(globalGroupMembership[i] + 1);
605	<
855	>	sprintf( checkPointMsg,
856	>	"succesfully sent the simulation information to fortran.\n");
857	>	MPIcheckPoint();
858	>	#endif // is_mpi
859	>	}
860
607	–	myMols = info->molecules;
608	–	numMol = info->n_mol;
609	–	for(int i  = 0; i < numMol; i++){
610	–	numCutoffGroups = myMols[i].getNCutoffGroups();
611	–	for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff);
612	–	myCutoffGroup != NULL;
613	–	myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
861
862	<	totalMass = myCutoffGroup->getMass();
863	<
864	<	for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom);
865	<	cutoffAtom != NULL;
866	<	cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
867	<	mfact.push_back(cutoffAtom->getMass()/totalMass);
868	<	}
862	>	#ifdef IS_MPI
863	>	void SimInfo::setupFortranParallel() {
864	>
865	>	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
866	>	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
867	>	std::vector<int> localToGlobalCutoffGroupIndex;
868	>	SimInfo::MoleculeIterator mi;
869	>	Molecule::AtomIterator ai;
870	>	Molecule::CutoffGroupIterator ci;
871	>	Molecule* mol;
872	>	Atom* atom;
873	>	CutoffGroup* cg;
874	>	mpiSimData parallelData;
875	>	int isError;
876	>
877	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
878	>
879	>	//local index(index in DataStorge) of atom is important
880	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
881	>	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
882	>	}
883	>
884	>	//local index of cutoff group is trivial, it only depends on the order of travesing
885	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
886	>	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
887	>	}
888	>
889		}
890	+
891	+	//fill up mpiSimData struct
892	+	parallelData.nMolGlobal = getNGlobalMolecules();
893	+	parallelData.nMolLocal = getNMolecules();
894	+	parallelData.nAtomsGlobal = getNGlobalAtoms();
895	+	parallelData.nAtomsLocal = getNAtoms();
896	+	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
897	+	parallelData.nGroupsLocal = getNCutoffGroups();
898	+	parallelData.myNode = worldRank;
899	+	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
900	+
901	+	//pass mpiSimData struct and index arrays to fortran
902	+	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
903	+	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
904	+	&localToGlobalCutoffGroupIndex[0], &isError);
905	+
906	+	if (isError) {
907	+	sprintf(painCave.errMsg,
908	+	"mpiRefresh errror: fortran didn't like something we gave it.\n");
909	+	painCave.isFatal = 1;
910	+	simError();
911	+	}
912	+
913	+	sprintf(checkPointMsg, " mpiRefresh successful.\n");
914	+	MPIcheckPoint();
915	+
916	+
917		}
918
919	<	}
919	>	#endif
920	>
921	>	void SimInfo::setupCutoff() {
922	>
923	>	// Check the cutoff policy
924	>	int cp =  TRADITIONAL_CUTOFF_POLICY;
925	>	if (simParams_->haveCutoffPolicy()) {
926	>	std::string myPolicy = simParams_->getCutoffPolicy();
927	>	toUpper(myPolicy);
928	>	if (myPolicy == "MIX") {
929	>	cp = MIX_CUTOFF_POLICY;
930	>	} else {
931	>	if (myPolicy == "MAX") {
932	>	cp = MAX_CUTOFF_POLICY;
933	>	} else {
934	>	if (myPolicy == "TRADITIONAL") {
935	>	cp = TRADITIONAL_CUTOFF_POLICY;
936	>	} else {
937	>	// throw error
938	>	sprintf( painCave.errMsg,
939	>	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
940	>	painCave.isFatal = 1;
941	>	simError();
942	>	}
943	>	}
944	>	}
945	>	}
946	>	notifyFortranCutoffPolicy(&cp);
947	>
948	>	// Check the Skin Thickness for neighborlists
949	>	double skin;
950	>	if (simParams_->haveSkinThickness()) {
951	>	skin = simParams_->getSkinThickness();
952	>	notifyFortranSkinThickness(&skin);
953	>	}
954	>
955	>	// Check if the cutoff was set explicitly:
956	>	if (simParams_->haveCutoffRadius()) {
957	>	rcut_ = simParams_->getCutoffRadius();
958	>	if (simParams_->haveSwitchingRadius()) {
959	>	rsw_  = simParams_->getSwitchingRadius();
960	>	} else {
961	>	rsw_ = rcut_;
962	>	}
963	>	notifyFortranCutoffs(&rcut_, &rsw_);
964	>
965	>	} else {
966	>
967	>	// For electrostatic atoms, we'll assume a large safe value:
968	>	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
969	>	sprintf(painCave.errMsg,
970	>	"SimCreator Warning: No value was set for the cutoffRadius.\n"
971	>	"\tOOPSE will use a default value of 15.0 angstroms"
972	>	"\tfor the cutoffRadius.\n");
973	>	painCave.isFatal = 0;
974	>	simError();
975	>	rcut_ = 15.0;
976	>
977	>	if (simParams_->haveElectrostaticSummationMethod()) {
978	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
979	>	toUpper(myMethod);
980	>	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
981	>	if (simParams_->haveSwitchingRadius()){
982	>	sprintf(painCave.errMsg,
983	>	"SimInfo Warning: A value was set for the switchingRadius\n"
984	>	"\teven though the electrostaticSummationMethod was\n"
985	>	"\tset to %s\n", myMethod.c_str());
986	>	painCave.isFatal = 1;
987	>	simError();
988	>	}
989	>	}
990	>	}
991	>
992	>	if (simParams_->haveSwitchingRadius()){
993	>	rsw_ = simParams_->getSwitchingRadius();
994	>	} else {
995	>	sprintf(painCave.errMsg,
996	>	"SimCreator Warning: No value was set for switchingRadius.\n"
997	>	"\tOOPSE will use a default value of\n"
998	>	"\t0.85 * cutoffRadius for the switchingRadius\n");
999	>	painCave.isFatal = 0;
1000	>	simError();
1001	>	rsw_ = 0.85 * rcut_;
1002	>	}
1003	>	notifyFortranCutoffs(&rcut_, &rsw_);
1004	>	} else {
1005	>	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1006	>	// We'll punt and let fortran figure out the cutoffs later.
1007	>
1008	>	notifyFortranYouAreOnYourOwn();
1009	>
1010	>	}
1011	>	}
1012	>	}
1013	>
1014	>	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1015	>
1016	>	int errorOut;
1017	>	int esm =  NONE;
1018	>	int sm = UNDAMPED;
1019	>	double alphaVal;
1020	>	double dielectric;
1021	>
1022	>	errorOut = isError;
1023	>	alphaVal = simParams_->getDampingAlpha();
1024	>	dielectric = simParams_->getDielectric();
1025	>
1026	>	if (simParams_->haveElectrostaticSummationMethod()) {
1027	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1028	>	toUpper(myMethod);
1029	>	if (myMethod == "NONE") {
1030	>	esm = NONE;
1031	>	} else {
1032	>	if (myMethod == "SWITCHING_FUNCTION") {
1033	>	esm = SWITCHING_FUNCTION;
1034	>	} else {
1035	>	if (myMethod == "SHIFTED_POTENTIAL") {
1036	>	esm = SHIFTED_POTENTIAL;
1037	>	} else {
1038	>	if (myMethod == "SHIFTED_FORCE") {
1039	>	esm = SHIFTED_FORCE;
1040	>	} else {
1041	>	if (myMethod == "REACTION_FIELD") {
1042	>	esm = REACTION_FIELD;
1043	>	} else {
1044	>	// throw error
1045	>	sprintf( painCave.errMsg,
1046	>	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1047	>	"\t(Input file specified %s .)\n"
1048	>	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1049	>	"\t\"shifted_potential\", \"shifted_force\", or \n"
1050	>	"\t\"reaction_field\".\n", myMethod.c_str() );
1051	>	painCave.isFatal = 1;
1052	>	simError();
1053	>	}
1054	>	}
1055	>	}
1056	>	}
1057	>	}
1058	>	}
1059	>
1060	>	if (simParams_->haveElectrostaticScreeningMethod()) {
1061	>	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1062	>	toUpper(myScreen);
1063	>	if (myScreen == "UNDAMPED") {
1064	>	sm = UNDAMPED;
1065	>	} else {
1066	>	if (myScreen == "DAMPED") {
1067	>	sm = DAMPED;
1068	>	if (!simParams_->haveDampingAlpha()) {
1069	>	//throw error
1070	>	sprintf( painCave.errMsg,
1071	>	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1072	>	"\tA default value of %f (1/ang) will be used.\n", alphaVal);
1073	>	painCave.isFatal = 0;
1074	>	simError();
1075	>	}
1076	>	} else {
1077	>	// throw error
1078	>	sprintf( painCave.errMsg,
1079	>	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1080	>	"\t(Input file specified %s .)\n"
1081	>	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1082	>	"or \"damped\".\n", myScreen.c_str() );
1083	>	painCave.isFatal = 1;
1084	>	simError();
1085	>	}
1086	>	}
1087	>	}
1088	>
1089	>	// let's pass some summation method variables to fortran
1090	>	setElectrostaticSummationMethod( &esm );
1091	>	notifyFortranElectrostaticMethod( &esm );
1092	>	setScreeningMethod( &sm );
1093	>	setDampingAlpha( &alphaVal );
1094	>	setReactionFieldDielectric( &dielectric );
1095	>	initFortranFF( &errorOut );
1096	>	}
1097	>
1098	>	void SimInfo::setupSwitchingFunction() {
1099	>	int ft = CUBIC;
1100	>
1101	>	if (simParams_->haveSwitchingFunctionType()) {
1102	>	std::string funcType = simParams_->getSwitchingFunctionType();
1103	>	toUpper(funcType);
1104	>	if (funcType == "CUBIC") {
1105	>	ft = CUBIC;
1106	>	} else {
1107	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1108	>	ft = FIFTH_ORDER_POLY;
1109	>	} else {
1110	>	// throw error
1111	>	sprintf( painCave.errMsg,
1112	>	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1113	>	painCave.isFatal = 1;
1114	>	simError();
1115	>	}
1116	>	}
1117	>	}
1118	>
1119	>	// send switching function notification to switcheroo
1120	>	setFunctionType(&ft);
1121	>
1122	>	}
1123	>
1124	>	void SimInfo::addProperty(GenericData* genData) {
1125	>	properties_.addProperty(genData);
1126	>	}
1127	>
1128	>	void SimInfo::removeProperty(const std::string& propName) {
1129	>	properties_.removeProperty(propName);
1130	>	}
1131	>
1132	>	void SimInfo::clearProperties() {
1133	>	properties_.clearProperties();
1134	>	}
1135	>
1136	>	std::vector<std::string> SimInfo::getPropertyNames() {
1137	>	return properties_.getPropertyNames();
1138	>	}
1139	>
1140	>	std::vector<GenericData*> SimInfo::getProperties() {
1141	>	return properties_.getProperties();
1142	>	}
1143	>
1144	>	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1145	>	return properties_.getPropertyByName(propName);
1146	>	}
1147	>
1148	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1149	>	if (sman_ == sman) {
1150	>	return;
1151	>	}
1152	>	delete sman_;
1153	>	sman_ = sman;
1154	>
1155	>	Molecule* mol;
1156	>	RigidBody* rb;
1157	>	Atom* atom;
1158	>	SimInfo::MoleculeIterator mi;
1159	>	Molecule::RigidBodyIterator rbIter;
1160	>	Molecule::AtomIterator atomIter;;
1161	>
1162	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1163	>
1164	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1165	>	atom->setSnapshotManager(sman_);
1166	>	}
1167	>
1168	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1169	>	rb->setSnapshotManager(sman_);
1170	>	}
1171	>	}
1172	>
1173	>	}
1174	>
1175	>	Vector3d SimInfo::getComVel(){
1176	>	SimInfo::MoleculeIterator i;
1177	>	Molecule* mol;
1178	>
1179	>	Vector3d comVel(0.0);
1180	>	double totalMass = 0.0;
1181	>
1182	>
1183	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1184	>	double mass = mol->getMass();
1185	>	totalMass += mass;
1186	>	comVel += mass * mol->getComVel();
1187	>	}
1188	>
1189	>	#ifdef IS_MPI
1190	>	double tmpMass = totalMass;
1191	>	Vector3d tmpComVel(comVel);
1192	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1193	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1194	>	#endif
1195	>
1196	>	comVel /= totalMass;
1197	>
1198	>	return comVel;
1199	>	}
1200	>
1201	>	Vector3d SimInfo::getCom(){
1202	>	SimInfo::MoleculeIterator i;
1203	>	Molecule* mol;
1204	>
1205	>	Vector3d com(0.0);
1206	>	double totalMass = 0.0;
1207	>
1208	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1209	>	double mass = mol->getMass();
1210	>	totalMass += mass;
1211	>	com += mass * mol->getCom();
1212	>	}
1213	>
1214	>	#ifdef IS_MPI
1215	>	double tmpMass = totalMass;
1216	>	Vector3d tmpCom(com);
1217	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1218	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1219	>	#endif
1220	>
1221	>	com /= totalMass;
1222	>
1223	>	return com;
1224	>
1225	>	}
1226	>
1227	>	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1228	>
1229	>	return o;
1230	>	}
1231	>
1232	>
1233	>	/*
1234	>	Returns center of mass and center of mass velocity in one function call.
1235	>	*/
1236	>
1237	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1238	>	SimInfo::MoleculeIterator i;
1239	>	Molecule* mol;
1240	>
1241	>
1242	>	double totalMass = 0.0;
1243	>
1244	>
1245	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1246	>	double mass = mol->getMass();
1247	>	totalMass += mass;
1248	>	com += mass * mol->getCom();
1249	>	comVel += mass * mol->getComVel();
1250	>	}
1251	>
1252	>	#ifdef IS_MPI
1253	>	double tmpMass = totalMass;
1254	>	Vector3d tmpCom(com);
1255	>	Vector3d tmpComVel(comVel);
1256	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1257	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1258	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1259	>	#endif
1260	>
1261	>	com /= totalMass;
1262	>	comVel /= totalMass;
1263	>	}
1264	>
1265	>	/*
1266	>	Return intertia tensor for entire system and angular momentum Vector.
1267	>
1268	>
1269	>	[  Ixx -Ixy  -Ixz ]
1270	>	J =| -Iyx  Iyy  -Iyz |
1271	>	[ -Izx -Iyz   Izz ]
1272	>	*/
1273	>
1274	>	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1275	>
1276	>
1277	>	double xx = 0.0;
1278	>	double yy = 0.0;
1279	>	double zz = 0.0;
1280	>	double xy = 0.0;
1281	>	double xz = 0.0;
1282	>	double yz = 0.0;
1283	>	Vector3d com(0.0);
1284	>	Vector3d comVel(0.0);
1285	>
1286	>	getComAll(com, comVel);
1287	>
1288	>	SimInfo::MoleculeIterator i;
1289	>	Molecule* mol;
1290	>
1291	>	Vector3d thisq(0.0);
1292	>	Vector3d thisv(0.0);
1293	>
1294	>	double thisMass = 0.0;
1295	>
1296	>
1297	>
1298	>
1299	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1300	>
1301	>	thisq = mol->getCom()-com;
1302	>	thisv = mol->getComVel()-comVel;
1303	>	thisMass = mol->getMass();
1304	>	// Compute moment of intertia coefficients.
1305	>	xx += thisq[0]*thisq[0]*thisMass;
1306	>	yy += thisq[1]*thisq[1]*thisMass;
1307	>	zz += thisq[2]*thisq[2]*thisMass;
1308	>
1309	>	// compute products of intertia
1310	>	xy += thisq[0]*thisq[1]*thisMass;
1311	>	xz += thisq[0]*thisq[2]*thisMass;
1312	>	yz += thisq[1]*thisq[2]*thisMass;
1313	>
1314	>	angularMomentum += cross( thisq, thisv ) * thisMass;
1315	>
1316	>	}
1317	>
1318	>
1319	>	inertiaTensor(0,0) = yy + zz;
1320	>	inertiaTensor(0,1) = -xy;
1321	>	inertiaTensor(0,2) = -xz;
1322	>	inertiaTensor(1,0) = -xy;
1323	>	inertiaTensor(1,1) = xx + zz;
1324	>	inertiaTensor(1,2) = -yz;
1325	>	inertiaTensor(2,0) = -xz;
1326	>	inertiaTensor(2,1) = -yz;
1327	>	inertiaTensor(2,2) = xx + yy;
1328	>
1329	>	#ifdef IS_MPI
1330	>	Mat3x3d tmpI(inertiaTensor);
1331	>	Vector3d tmpAngMom;
1332	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1333	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1334	>	#endif
1335	>
1336	>	return;
1337	>	}
1338	>
1339	>	//Returns the angular momentum of the system
1340	>	Vector3d SimInfo::getAngularMomentum(){
1341	>
1342	>	Vector3d com(0.0);
1343	>	Vector3d comVel(0.0);
1344	>	Vector3d angularMomentum(0.0);
1345	>
1346	>	getComAll(com,comVel);
1347	>
1348	>	SimInfo::MoleculeIterator i;
1349	>	Molecule* mol;
1350	>
1351	>	Vector3d thisr(0.0);
1352	>	Vector3d thisp(0.0);
1353	>
1354	>	double thisMass;
1355	>
1356	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1357	>	thisMass = mol->getMass();
1358	>	thisr = mol->getCom()-com;
1359	>	thisp = (mol->getComVel()-comVel)*thisMass;
1360	>
1361	>	angularMomentum += cross( thisr, thisp );
1362	>
1363	>	}
1364	>
1365	>	#ifdef IS_MPI
1366	>	Vector3d tmpAngMom;
1367	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1368	>	#endif
1369	>
1370	>	return angularMomentum;
1371	>	}
1372	>
1373	>
1374	>	}//end namespace oopse
1375	>

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