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root/group/trunk/OOPSE-2.0/src/brains/SimInfo.cpp

Comparing trunk/OOPSE-2.0/src/brains/SimInfo.cpp (file contents):
Revision 1492 by tim, Fri Sep 24 16:27:58 2004 UTC vs.
Revision 2533 by chuckv, Fri Dec 30 23:15:59 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 "selection/SelectionManager.hpp"
66	+	#include "io/ForceFieldOptions.hpp"
67	+	#include "UseTheForce/ForceField.hpp"
68
13	–	#include "UseTheForce/fortranWrappers.hpp"
14	–
15	–	#include "math/MatVec3.h"
16	–
69		#ifdef IS_MPI
70	<	#include "brains/mpiSimulation.hpp"
71	<	#endif
70	>	#include "UseTheForce/mpiComponentPlan.h"
71	>	#include "UseTheForce/DarkSide/simParallel_interface.h"
72	>	#endif
73
74	<	inline double roundMe( double x ){
75	<	return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
76	<	}
77	<
78	<	inline double min( double a, double b ){
79	<	return (a < b ) ? a : b;
80	<	}
74	>	namespace oopse {
75	>	std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
76	>	std::map<int, std::set<int> >::iterator i = container.find(index);
77	>	std::set<int> result;
78	>	if (i != container.end()) {
79	>	result = i->second;
80	>	}
81
82	<	SimInfo* currentInfo;
83	<
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;
82	>	return result;
83	>	}
84
85	<	resetTime = 1e99;
85	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
86	>	forceField_(ff), simParams_(simParams),
87	>	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
88	>	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
89	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
90	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
91	>	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
92	>	sman_(NULL), fortranInitialized_(false) {
93
94	<	orthoRhombic = 0;
95	<	orthoTolerance = 1E-6;
96	<	useInitXSstate = true;
94	>	MoleculeStamp* molStamp;
95	>	int nMolWithSameStamp;
96	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
97	>	int nGroups = 0;      //total cutoff groups defined in meta-data file
98	>	CutoffGroupStamp* cgStamp;
99	>	RigidBodyStamp* rbStamp;
100	>	int nRigidAtoms = 0;
101	>	std::vector<Component*> components = simParams->getComponents();
102	>
103	>	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
104	>	molStamp = (*i)->getMoleculeStamp();
105	>	nMolWithSameStamp = (*i)->getNMol();
106	>
107	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
108
109	<	usePBC = 0;
110	<	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;
109	>	//calculate atoms in molecules
110	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
111
112	<	haveCutoffGroups = false;
112	>	//calculate atoms in cutoff groups
113	>	int nAtomsInGroups = 0;
114	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
115	>
116	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
117	>	cgStamp = molStamp->getCutoffGroupStamp(j);
118	>	nAtomsInGroups += cgStamp->getNMembers();
119	>	}
120
121	<	excludes = Exclude::Instance();
121	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
122
123	<	myConfiguration = new SimState();
123	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
124
125	<	has_minimizer = false;
126	<	the_minimizer =NULL;
125	>	//calculate atoms in rigid bodies
126	>	int nAtomsInRigidBodies = 0;
127	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
128	>
129	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
130	>	rbStamp = molStamp->getRigidBodyStamp(j);
131	>	nAtomsInRigidBodies += rbStamp->getNMembers();
132	>	}
133
134	<	ngroup = 0;
134	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
135	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
136	>
137	>	}
138
139	<	wrapMeSimInfo( this );
140	<	}
139	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
140	>	//group therefore the total number of cutoff groups in the system is
141	>	//equal to the total number of atoms minus number of atoms belong to
142	>	//cutoff group defined in meta-data file plus the number of cutoff
143	>	//groups defined in meta-data file
144	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
145
146	+	//every free atom (atom does not belong to rigid bodies) is an
147	+	//integrable object therefore the total number of integrable objects
148	+	//in the system is equal to the total number of atoms minus number of
149	+	//atoms belong to rigid body defined in meta-data file plus the number
150	+	//of rigid bodies defined in meta-data file
151	+	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
152	+	+ nGlobalRigidBodies_;
153	+
154	+	nGlobalMols_ = molStampIds_.size();
155
156	<	SimInfo::~SimInfo(){
156	>	#ifdef IS_MPI
157	>	molToProcMap_.resize(nGlobalMols_);
158	>	#endif
159
160	<	delete myConfiguration;
160	>	}
161
162	<	map<string, GenericData*>::iterator i;
163	<
164	<	for(i = properties.begin(); i != properties.end(); i++)
165	<	delete (*i).second;
162	>	SimInfo::~SimInfo() {
163	>	std::map<int, Molecule*>::iterator i;
164	>	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
165	>	delete i->second;
166	>	}
167	>	molecules_.clear();
168	>
169	>	delete sman_;
170	>	delete simParams_;
171	>	delete forceField_;
172	>	}
173
174	<	}
174	>	int SimInfo::getNGlobalConstraints() {
175	>	int nGlobalConstraints;
176	>	#ifdef IS_MPI
177	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
178	>	MPI_COMM_WORLD);
179	>	#else
180	>	nGlobalConstraints =  nConstraints_;
181	>	#endif
182	>	return nGlobalConstraints;
183	>	}
184
185	<	void SimInfo::setBox(double newBox[3]) {
186	<
96	<	int i, j;
97	<	double tempMat[3][3];
185	>	bool SimInfo::addMolecule(Molecule* mol) {
186	>	MoleculeIterator i;
187
188	<	for(i=0; i<3; i++)
189	<	for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
188	>	i = molecules_.find(mol->getGlobalIndex());
189	>	if (i == molecules_.end() ) {
190
191	<	tempMat[0][0] = newBox[0];
192	<	tempMat[1][1] = newBox[1];
193	<	tempMat[2][2] = newBox[2];
191	>	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
192	>
193	>	nAtoms_ += mol->getNAtoms();
194	>	nBonds_ += mol->getNBonds();
195	>	nBends_ += mol->getNBends();
196	>	nTorsions_ += mol->getNTorsions();
197	>	nRigidBodies_ += mol->getNRigidBodies();
198	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
199	>	nCutoffGroups_ += mol->getNCutoffGroups();
200	>	nConstraints_ += mol->getNConstraintPairs();
201
202	<	setBoxM( tempMat );
202	>	addExcludePairs(mol);
203	>
204	>	return true;
205	>	} else {
206	>	return false;
207	>	}
208	>	}
209
210	<	}
210	>	bool SimInfo::removeMolecule(Molecule* mol) {
211	>	MoleculeIterator i;
212	>	i = molecules_.find(mol->getGlobalIndex());
213
214	<	void SimInfo::setBoxM( double theBox[3][3] ){
111	<
112	<	int i, j;
113	<	double FortranHmat[9]; // to preserve compatibility with Fortran the
114	<	// ordering in the array is as follows:
115	<	// [ 0 3 6 ]
116	<	// [ 1 4 7 ]
117	<	// [ 2 5 8 ]
118	<	double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
214	>	if (i != molecules_.end() ) {
215
216	<	if( !boxIsInit ) boxIsInit = 1;
216	>	assert(mol == i->second);
217	>
218	>	nAtoms_ -= mol->getNAtoms();
219	>	nBonds_ -= mol->getNBonds();
220	>	nBends_ -= mol->getNBends();
221	>	nTorsions_ -= mol->getNTorsions();
222	>	nRigidBodies_ -= mol->getNRigidBodies();
223	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
224	>	nCutoffGroups_ -= mol->getNCutoffGroups();
225	>	nConstraints_ -= mol->getNConstraintPairs();
226
227	<	for(i=0; i < 3; i++)
228	<	for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
124	<
125	<	calcBoxL();
126	<	calcHmatInv();
227	>	removeExcludePairs(mol);
228	>	molecules_.erase(mol->getGlobalIndex());
229
230	<	for(i=0; i < 3; i++) {
231	<	for (j=0; j < 3; j++) {
232	<	FortranHmat[3*j + i] = Hmat[i][j];
233	<	FortranHmatInv[3*j + i] = HmatInv[i][j];
230	>	delete mol;
231	>
232	>	return true;
233	>	} else {
234	>	return false;
235		}
133	–	}
236
135	–	setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
136	–
137	–	}
138	–
237
238	<	void SimInfo::getBoxM (double theBox[3][3]) {
238	>	}
239
240	<	int i, j;
241	<	for(i=0; i<3; i++)
242	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
243	<	}
240	>
241	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
242	>	i = molecules_.begin();
243	>	return i == molecules_.end() ? NULL : i->second;
244	>	}
245
246	+	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
247	+	++i;
248	+	return i == molecules_.end() ? NULL : i->second;
249	+	}
250
148	–	void SimInfo::scaleBox(double scale) {
149	–	double theBox[3][3];
150	–	int i, j;
251
252	<	// cerr << "Scaling box by " << scale << "\n";
252	>	void SimInfo::calcNdf() {
253	>	int ndf_local;
254	>	MoleculeIterator i;
255	>	std::vector<StuntDouble*>::iterator j;
256	>	Molecule* mol;
257	>	StuntDouble* integrableObject;
258
259	<	for(i=0; i<3; i++)
260	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
259	>	ndf_local = 0;
260	>
261	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
262	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
263	>	integrableObject = mol->nextIntegrableObject(j)) {
264
265	<	setBoxM(theBox);
265	>	ndf_local += 3;
266
267	<	}
268	<
269	<	void SimInfo::calcHmatInv( void ) {
270	<
271	<	int oldOrtho;
272	<	int i,j;
273	<	double smallDiag;
274	<	double tol;
167	<	double sanity[3][3];
168	<
169	<	invertMat3( Hmat, HmatInv );
170	<
171	<	// check to see if Hmat is orthorhombic
172	<
173	<	oldOrtho = orthoRhombic;
174	<
175	<	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;
179	<
180	<	orthoRhombic = 1;
181	<
182	<	for (i = 0; i < 3; i++ ) {
183	<	for (j = 0 ; j < 3; j++) {
184	<	if (i != j) {
185	<	if (orthoRhombic) {
186	<	if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
187	<	}
267	>	if (integrableObject->isDirectional()) {
268	>	if (integrableObject->isLinear()) {
269	>	ndf_local += 2;
270	>	} else {
271	>	ndf_local += 3;
272	>	}
273	>	}
274	>
275		}
276		}
190	–	}
191	–
192	–	if( oldOrtho != orthoRhombic ){
277
278	<	if( orthoRhombic ) {
279	<	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	<	}
278	>	// n_constraints is local, so subtract them on each processor
279	>	ndf_local -= nConstraints_;
280
281	<	void SimInfo::calcBoxL( void ){
281	>	#ifdef IS_MPI
282	>	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
283	>	#else
284	>	ndf_ = ndf_local;
285	>	#endif
286
287	<	double dx, dy, dz, dsq;
287	>	// nZconstraints_ is global, as are the 3 COM translations for the
288	>	// entire system:
289	>	ndf_ = ndf_ - 3 - nZconstraint_;
290
291	<	// boxVol = Determinant of Hmat
291	>	}
292
293	<	boxVol = matDet3( Hmat );
293	>	void SimInfo::calcNdfRaw() {
294	>	int ndfRaw_local;
295
296	<	// boxLx
297	<
298	<	dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
299	<	dsq = dx*dx + dy*dy + dz*dz;
232	<	boxL[0] = sqrt( dsq );
233	<	//maxCutoff = 0.5 * boxL[0];
296	>	MoleculeIterator i;
297	>	std::vector<StuntDouble*>::iterator j;
298	>	Molecule* mol;
299	>	StuntDouble* integrableObject;
300
301	<	// boxLy
302	<
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];
301	>	// Raw degrees of freedom that we have to set
302	>	ndfRaw_local = 0;
303
304	<	crossProduct3(ri, rj, rij);
305	<	distXY = dotProduct3(rk,rij) / norm3(rij);
304	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
305	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
306	>	integrableObject = mol->nextIntegrableObject(j)) {
307
308	<	crossProduct3(rj,rk, rjk);
280	<	distYZ = dotProduct3(ri,rjk) / norm3(rjk);
308	>	ndfRaw_local += 3;
309
310	<	crossProduct3(rk,ri, rki);
311	<	distZX = dotProduct3(rj,rki) / norm3(rki);
312	<
313	<	minDist = min(min(distXY, distYZ), distZX);
314	<	return minDist/2;
315	<
316	<	}
317	<
318	<	void SimInfo::wrapVector( double thePos[3] ){
319	<
292	<	int i;
293	<	double scaled[3];
294	<
295	<	if( !orthoRhombic ){
296	<	// calc the scaled coordinates.
297	<
298	<
299	<	matVecMul3(HmatInv, thePos, scaled);
310	>	if (integrableObject->isDirectional()) {
311	>	if (integrableObject->isLinear()) {
312	>	ndfRaw_local += 2;
313	>	} else {
314	>	ndfRaw_local += 3;
315	>	}
316	>	}
317	>
318	>	}
319	>	}
320
321	<	for(i=0; i<3; i++)
322	<	scaled[i] -= roundMe(scaled[i]);
323	<
324	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
325	<
306	<	matVecMul3(Hmat, scaled, thePos);
307	<
321	>	#ifdef IS_MPI
322	>	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
323	>	#else
324	>	ndfRaw_ = ndfRaw_local;
325	>	#endif
326		}
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
328	+	void SimInfo::calcNdfTrans() {
329	+	int ndfTrans_local;
330
331	<	int SimInfo::getNDF(){
330	<	int ndf_local;
331	>	ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
332
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	–	}
342	–	}
333
344	–	// n_constraints is local, so subtract them on each processor:
345	–
346	–	ndf_local -= n_constraints;
347	–
334		#ifdef IS_MPI
335	<	MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
335	>	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
336		#else
337	<	ndf = ndf_local;
337	>	ndfTrans_ = ndfTrans_local;
338		#endif
339
340	<	// nZconstraints is global, as are the 3 COM translations for the
341	<	// entire system:
340	>	ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
341	>
342	>	}
343
344	<	ndf = ndf - 3 - nZconstraints;
344	>	void SimInfo::addExcludePairs(Molecule* mol) {
345	>	std::vector<Bond*>::iterator bondIter;
346	>	std::vector<Bend*>::iterator bendIter;
347	>	std::vector<Torsion*>::iterator torsionIter;
348	>	Bond* bond;
349	>	Bend* bend;
350	>	Torsion* torsion;
351	>	int a;
352	>	int b;
353	>	int c;
354	>	int d;
355
356	<	return ndf;
360	<	}
356	>	std::map<int, std::set<int> > atomGroups;
357
358	<	int SimInfo::getNDFraw() {
359	<	int ndfRaw_local;
358	>	Molecule::RigidBodyIterator rbIter;
359	>	RigidBody* rb;
360	>	Molecule::IntegrableObjectIterator ii;
361	>	StuntDouble* integrableObject;
362	>
363	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
364	>	integrableObject = mol->nextIntegrableObject(ii)) {
365
366	<	// Raw degrees of freedom that we have to set
367	<	ndfRaw_local = 0;
366	>	if (integrableObject->isRigidBody()) {
367	>	rb = static_cast<RigidBody*>(integrableObject);
368	>	std::vector<Atom*> atoms = rb->getAtoms();
369	>	std::set<int> rigidAtoms;
370	>	for (int i = 0; i < atoms.size(); ++i) {
371	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
372	>	}
373	>	for (int i = 0; i < atoms.size(); ++i) {
374	>	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
375	>	}
376	>	} else {
377	>	std::set<int> oneAtomSet;
378	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
379	>	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
380	>	}
381	>	}
382
368	–	for(int i = 0; i < integrableObjects.size(); i++){
369	–	ndfRaw_local += 3;
370	–	if (integrableObjects[i]->isDirectional()) {
371	–	if (integrableObjects[i]->isLinear())
372	–	ndfRaw_local += 2;
373	–	else
374	–	ndfRaw_local += 3;
375	–	}
376	–	}
383
384	<	#ifdef IS_MPI
385	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
386	<	#else
387	<	ndfRaw = ndfRaw_local;
388	<	#endif
384	>
385	>	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
386	>	a = bond->getAtomA()->getGlobalIndex();
387	>	b = bond->getAtomB()->getGlobalIndex();
388	>	exclude_.addPair(a, b);
389	>	}
390
391	<	return ndfRaw;
392	<	}
391	>	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
392	>	a = bend->getAtomA()->getGlobalIndex();
393	>	b = bend->getAtomB()->getGlobalIndex();
394	>	c = bend->getAtomC()->getGlobalIndex();
395	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
396	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
397	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
398
399	<	int SimInfo::getNDFtranslational() {
400	<	int ndfTrans_local;
399	>	exclude_.addPairs(rigidSetA, rigidSetB);
400	>	exclude_.addPairs(rigidSetA, rigidSetC);
401	>	exclude_.addPairs(rigidSetB, rigidSetC);
402	>
403	>	//exclude_.addPair(a, b);
404	>	//exclude_.addPair(a, c);
405	>	//exclude_.addPair(b, c);
406	>	}
407
408	<	ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
408	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
409	>	a = torsion->getAtomA()->getGlobalIndex();
410	>	b = torsion->getAtomB()->getGlobalIndex();
411	>	c = torsion->getAtomC()->getGlobalIndex();
412	>	d = torsion->getAtomD()->getGlobalIndex();
413	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
414	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
415	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
416	>	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
417
418	+	exclude_.addPairs(rigidSetA, rigidSetB);
419	+	exclude_.addPairs(rigidSetA, rigidSetC);
420	+	exclude_.addPairs(rigidSetA, rigidSetD);
421	+	exclude_.addPairs(rigidSetB, rigidSetC);
422	+	exclude_.addPairs(rigidSetB, rigidSetD);
423	+	exclude_.addPairs(rigidSetC, rigidSetD);
424
425	<	#ifdef IS_MPI
426	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
427	<	#else
428	<	ndfTrans = ndfTrans_local;
429	<	#endif
425	>	/*
426	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
427	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
428	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
429	>	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
430	>	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
431	>	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
432	>
433	>
434	>	exclude_.addPair(a, b);
435	>	exclude_.addPair(a, c);
436	>	exclude_.addPair(a, d);
437	>	exclude_.addPair(b, c);
438	>	exclude_.addPair(b, d);
439	>	exclude_.addPair(c, d);
440	>	*/
441	>	}
442
443	<	ndfTrans = ndfTrans - 3 - nZconstraints;
443	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
444	>	std::vector<Atom*> atoms = rb->getAtoms();
445	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
446	>	for (int j = i + 1; j < atoms.size(); ++j) {
447	>	a = atoms[i]->getGlobalIndex();
448	>	b = atoms[j]->getGlobalIndex();
449	>	exclude_.addPair(a, b);
450	>	}
451	>	}
452	>	}
453
454	<	return ndfTrans;
402	<	}
454	>	}
455
456	<	int SimInfo::getTotIntegrableObjects() {
457	<	int nObjs_local;
458	<	int nObjs;
459	<
460	<	nObjs_local =  integrableObjects.size();
456	>	void SimInfo::removeExcludePairs(Molecule* mol) {
457	>	std::vector<Bond*>::iterator bondIter;
458	>	std::vector<Bend*>::iterator bendIter;
459	>	std::vector<Torsion*>::iterator torsionIter;
460	>	Bond* bond;
461	>	Bend* bend;
462	>	Torsion* torsion;
463	>	int a;
464	>	int b;
465	>	int c;
466	>	int d;
467
468	+	std::map<int, std::set<int> > atomGroups;
469
470	<	#ifdef IS_MPI
471	<	MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
472	<	#else
473	<	nObjs = nObjs_local;
474	<	#endif
470	>	Molecule::RigidBodyIterator rbIter;
471	>	RigidBody* rb;
472	>	Molecule::IntegrableObjectIterator ii;
473	>	StuntDouble* integrableObject;
474	>
475	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
476	>	integrableObject = mol->nextIntegrableObject(ii)) {
477
478	+	if (integrableObject->isRigidBody()) {
479	+	rb = static_cast<RigidBody*>(integrableObject);
480	+	std::vector<Atom*> atoms = rb->getAtoms();
481	+	std::set<int> rigidAtoms;
482	+	for (int i = 0; i < atoms.size(); ++i) {
483	+	rigidAtoms.insert(atoms[i]->getGlobalIndex());
484	+	}
485	+	for (int i = 0; i < atoms.size(); ++i) {
486	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
487	+	}
488	+	} else {
489	+	std::set<int> oneAtomSet;
490	+	oneAtomSet.insert(integrableObject->getGlobalIndex());
491	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
492	+	}
493	+	}
494
495	<	return nObjs;
496	<	}
495	>
496	>	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
497	>	a = bond->getAtomA()->getGlobalIndex();
498	>	b = bond->getAtomB()->getGlobalIndex();
499	>	exclude_.removePair(a, b);
500	>	}
501
502	<	void SimInfo::refreshSim(){
502	>	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
503	>	a = bend->getAtomA()->getGlobalIndex();
504	>	b = bend->getAtomB()->getGlobalIndex();
505	>	c = bend->getAtomC()->getGlobalIndex();
506
507	<	simtype fInfo;
508	<	int isError;
509	<	int n_global;
426	<	int* excl;
507	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
508	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
509	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
510
511	<	fInfo.dielect = 0.0;
511	>	exclude_.removePairs(rigidSetA, rigidSetB);
512	>	exclude_.removePairs(rigidSetA, rigidSetC);
513	>	exclude_.removePairs(rigidSetB, rigidSetC);
514	>
515	>	//exclude_.removePair(a, b);
516	>	//exclude_.removePair(a, c);
517	>	//exclude_.removePair(b, c);
518	>	}
519
520	<	if( useDipoles ){
521	<	if( useReactionField )fInfo.dielect = dielectric;
520	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
521	>	a = torsion->getAtomA()->getGlobalIndex();
522	>	b = torsion->getAtomB()->getGlobalIndex();
523	>	c = torsion->getAtomC()->getGlobalIndex();
524	>	d = torsion->getAtomD()->getGlobalIndex();
525	>
526	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
527	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
528	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
529	>	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
530	>
531	>	exclude_.removePairs(rigidSetA, rigidSetB);
532	>	exclude_.removePairs(rigidSetA, rigidSetC);
533	>	exclude_.removePairs(rigidSetA, rigidSetD);
534	>	exclude_.removePairs(rigidSetB, rigidSetC);
535	>	exclude_.removePairs(rigidSetB, rigidSetD);
536	>	exclude_.removePairs(rigidSetC, rigidSetD);
537	>
538	>	/*
539	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
540	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
541	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
542	>	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
543	>	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
544	>	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
545	>
546	>
547	>	exclude_.removePair(a, b);
548	>	exclude_.removePair(a, c);
549	>	exclude_.removePair(a, d);
550	>	exclude_.removePair(b, c);
551	>	exclude_.removePair(b, d);
552	>	exclude_.removePair(c, d);
553	>	*/
554	>	}
555	>
556	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
557	>	std::vector<Atom*> atoms = rb->getAtoms();
558	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
559	>	for (int j = i + 1; j < atoms.size(); ++j) {
560	>	a = atoms[i]->getGlobalIndex();
561	>	b = atoms[j]->getGlobalIndex();
562	>	exclude_.removePair(a, b);
563	>	}
564	>	}
565	>	}
566	>
567		}
568
434	–	fInfo.SIM_uses_PBC = usePBC;
435	–	//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;
569
570	<	n_exclude = excludes->getSize();
571	<	excl = excludes->getFortranArray();
449	<
450	<	#ifdef IS_MPI
451	<	n_global = mpiSim->getNAtomsGlobal();
452	<	#else
453	<	n_global = n_atoms;
454	<	#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);
570	>	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
571	>	int curStampId;
572
573	<	if( isError ){
574	<
575	<	sprintf( painCave.errMsg,
576	<	"There was an error setting the simulation information in fortran.\n" );
577	<	painCave.isFatal = 1;
471	<	painCave.severity = OOPSE_ERROR;
472	<	simError();
573	>	//index from 0
574	>	curStampId = moleculeStamps_.size();
575	>
576	>	moleculeStamps_.push_back(molStamp);
577	>	molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
578		}
579	<
579	>
580	>	void SimInfo::update() {
581	>
582	>	setupSimType();
583	>
584		#ifdef IS_MPI
585	<	sprintf( checkPointMsg,
586	<	"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	<	}
585	>	setupFortranParallel();
586	>	#endif
587
588	<	void SimInfo::setDefaultRcut( double theRcut ){
487	<
488	<	haveRcut = 1;
489	<	rCut = theRcut;
490	<	rList = rCut + 1.0;
491	<
492	<	notifyFortranCutOffs( &rCut, &rSw, &rList );
493	<	}
588	>	setupFortranSim();
589
590	<	void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
590	>	//setup fortran force field
591	>	/** @deprecate */
592	>	int isError = 0;
593	>
594	>	setupElectrostaticSummationMethod( isError );
595	>	setupSwitchingFunction();
596
597	<	rSw = theRsw;
598	<	setDefaultRcut( theRcut );
599	<	}
597	>	if(isError){
598	>	sprintf( painCave.errMsg,
599	>	"ForceField error: There was an error initializing the forceField in fortran.\n" );
600	>	painCave.isFatal = 1;
601	>	simError();
602	>	}
603	>
604	>
605	>	setupCutoff();
606
607	+	calcNdf();
608	+	calcNdfRaw();
609	+	calcNdfTrans();
610
611	<	void SimInfo::checkCutOffs( void ){
612	<
613	<	if( boxIsInit ){
611	>	fortranInitialized_ = true;
612	>	}
613	>
614	>	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
615	>	SimInfo::MoleculeIterator mi;
616	>	Molecule* mol;
617	>	Molecule::AtomIterator ai;
618	>	Atom* atom;
619	>	std::set<AtomType*> atomTypes;
620	>
621	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
622	>
623	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
624	>	atomTypes.insert(atom->getAtomType());
625	>	}
626	>
627	>	}
628	>
629	>	return atomTypes;
630	>	}
631	>
632	>	void SimInfo::setupSimType() {
633	>	std::set<AtomType*>::iterator i;
634	>	std::set<AtomType*> atomTypes;
635	>	atomTypes = getUniqueAtomTypes();
636
637	<	//we need to check cutOffs against the box
637	>	int useLennardJones = 0;
638	>	int useElectrostatic = 0;
639	>	int useEAM = 0;
640	>	int useSC = 0;
641	>	int useCharge = 0;
642	>	int useDirectional = 0;
643	>	int useDipole = 0;
644	>	int useGayBerne = 0;
645	>	int useSticky = 0;
646	>	int useStickyPower = 0;
647	>	int useShape = 0;
648	>	int useFLARB = 0; //it is not in AtomType yet
649	>	int useDirectionalAtom = 0;
650	>	int useElectrostatics = 0;
651	>	//usePBC and useRF are from simParams
652	>	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
653	>	int useRF;
654	>	int useSF;
655	>	std::string myMethod;
656	>
657	>	// set the useRF logical
658	>	useRF = 0;
659	>	useSF = 0;
660	>
661	>
662	>	if (simParams_->haveElectrostaticSummationMethod()) {
663	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
664	>	toUpper(myMethod);
665	>	if (myMethod == "REACTION_FIELD") {
666	>	useRF=1;
667	>	} else {
668	>	if (myMethod == "SHIFTED_FORCE") {
669	>	useSF = 1;
670	>	}
671	>	}
672	>	}
673	>
674	>	//loop over all of the atom types
675	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
676	>	useLennardJones |= (*i)->isLennardJones();
677	>	useElectrostatic |= (*i)->isElectrostatic();
678	>	useEAM |= (*i)->isEAM();
679	>	useSC |= (*i)->isSC();
680	>	useCharge |= (*i)->isCharge();
681	>	useDirectional |= (*i)->isDirectional();
682	>	useDipole |= (*i)->isDipole();
683	>	useGayBerne |= (*i)->isGayBerne();
684	>	useSticky |= (*i)->isSticky();
685	>	useStickyPower |= (*i)->isStickyPower();
686	>	useShape |= (*i)->isShape();
687	>	}
688	>
689	>	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
690	>	useDirectionalAtom = 1;
691	>	}
692	>
693	>	if (useCharge || useDipole) {
694	>	useElectrostatics = 1;
695	>	}
696	>
697	>	#ifdef IS_MPI
698	>	int temp;
699	>
700	>	temp = usePBC;
701	>	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
702	>
703	>	temp = useDirectionalAtom;
704	>	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
705	>
706	>	temp = useLennardJones;
707	>	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
708	>
709	>	temp = useElectrostatics;
710	>	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
711	>
712	>	temp = useCharge;
713	>	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
714	>
715	>	temp = useDipole;
716	>	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
717	>
718	>	temp = useSticky;
719	>	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
720	>
721	>	temp = useStickyPower;
722	>	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
723
724	<	if( rCut > maxCutoff ){
725	<	sprintf( painCave.errMsg,
510	<	"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;
523	<	painCave.isFatal = 1;
524	<	simError();
525	<	}
526	<	} else {
527	<	// initialize this stuff before using it, OK?
528	<	sprintf( painCave.errMsg,
529	<	"Trying to check cutoffs without a box.\n"
530	<	"\tOOPSE should have better programmers than that.\n" );
531	<	painCave.severity = OOPSE_ERROR;
532	<	painCave.isFatal = 1;
533	<	simError();
534	<	}
535	<
536	<	}
724	>	temp = useGayBerne;
725	>	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
726
727	<	void SimInfo::addProperty(GenericData* prop){
727	>	temp = useEAM;
728	>	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
729
730	<	map<string, GenericData*>::iterator result;
731	<	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()){
730	>	temp = useSC;
731	>	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
732
733	<	delete (*result).second;
734	<	(*result).second = prop;
733	>	temp = useShape;
734	>	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
735	>
736	>	temp = useFLARB;
737	>	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
738	>
739	>	temp = useRF;
740	>	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
741	>
742	>	temp = useSF;
743	>	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
744	>
745	>	#endif
746	>
747	>	fInfo_.SIM_uses_PBC = usePBC;
748	>	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
749	>	fInfo_.SIM_uses_LennardJones = useLennardJones;
750	>	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
751	>	fInfo_.SIM_uses_Charges = useCharge;
752	>	fInfo_.SIM_uses_Dipoles = useDipole;
753	>	fInfo_.SIM_uses_Sticky = useSticky;
754	>	fInfo_.SIM_uses_StickyPower = useStickyPower;
755	>	fInfo_.SIM_uses_GayBerne = useGayBerne;
756	>	fInfo_.SIM_uses_EAM = useEAM;
757	>	fInfo_.SIM_uses_SC = useSC;
758	>	fInfo_.SIM_uses_Shapes = useShape;
759	>	fInfo_.SIM_uses_FLARB = useFLARB;
760	>	fInfo_.SIM_uses_RF = useRF;
761	>	fInfo_.SIM_uses_SF = useSF;
762	>
763	>	if( myMethod == "REACTION_FIELD") {
764
765	+	if (simParams_->haveDielectric()) {
766	+	fInfo_.dielect = simParams_->getDielectric();
767	+	} else {
768	+	sprintf(painCave.errMsg,
769	+	"SimSetup Error: No Dielectric constant was set.\n"
770	+	"\tYou are trying to use Reaction Field without"
771	+	"\tsetting a dielectric constant!\n");
772	+	painCave.isFatal = 1;
773	+	simError();
774	+	}
775	+	}
776	+
777		}
552	–	else{
778
779	<	properties[prop->getID()] = prop;
779	>	void SimInfo::setupFortranSim() {
780	>	int isError;
781	>	int nExclude;
782	>	std::vector<int> fortranGlobalGroupMembership;
783	>
784	>	nExclude = exclude_.getSize();
785	>	isError = 0;
786
787	<	}
787	>	//globalGroupMembership_ is filled by SimCreator
788	>	for (int i = 0; i < nGlobalAtoms_; i++) {
789	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
790	>	}
791	>
792	>	//calculate mass ratio of cutoff group
793	>	std::vector<double> mfact;
794	>	SimInfo::MoleculeIterator mi;
795	>	Molecule* mol;
796	>	Molecule::CutoffGroupIterator ci;
797	>	CutoffGroup* cg;
798	>	Molecule::AtomIterator ai;
799	>	Atom* atom;
800	>	double totalMass;
801	>
802	>	//to avoid memory reallocation, reserve enough space for mfact
803	>	mfact.reserve(getNCutoffGroups());
804
805	<	}
805	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
806	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
807
808	<	GenericData* SimInfo::getProperty(const string& propName){
809	<
810	<	map<string, GenericData*>::iterator result;
811	<
812	<	//string lowerCaseName = ();
813	<
814	<	result = properties.find(propName);
815	<
568	<	if(result != properties.end())
569	<	return (*result).second;
570	<	else
571	<	return NULL;
572	<	}
808	>	totalMass = cg->getMass();
809	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
810	>	// Check for massless groups - set mfact to 1 if true
811	>	if (totalMass != 0)
812	>	mfact.push_back(atom->getMass()/totalMass);
813	>	else
814	>	mfact.push_back( 1.0 );
815	>	}
816
817	+	}
818	+	}
819
820	<	void SimInfo::getFortranGroupArrays(SimInfo* info,
821	<	vector<int>& FglobalGroupMembership,
577	<	vector<double>& mfact){
578	<
579	<	Molecule* myMols;
580	<	Atom** myAtoms;
581	<	int numAtom;
582	<	double mtot;
583	<	int numMol;
584	<	int numCutoffGroups;
585	<	CutoffGroup* myCutoffGroup;
586	<	vector<CutoffGroup*>::iterator iterCutoff;
587	<	Atom* cutoffAtom;
588	<	vector<Atom*>::iterator iterAtom;
589	<	int atomIndex;
590	<	double totalMass;
591	<
592	<	mfact.clear();
593	<	FglobalGroupMembership.clear();
594	<
820	>	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
821	>	std::vector<int> identArray;
822
823	<	// Fix the silly fortran indexing problem
823	>	//to avoid memory reallocation, reserve enough space identArray
824	>	identArray.reserve(getNAtoms());
825	>
826	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
827	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
828	>	identArray.push_back(atom->getIdent());
829	>	}
830	>	}
831	>
832	>	//fill molMembershipArray
833	>	//molMembershipArray is filled by SimCreator
834	>	std::vector<int> molMembershipArray(nGlobalAtoms_);
835	>	for (int i = 0; i < nGlobalAtoms_; i++) {
836	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
837	>	}
838	>
839	>	//setup fortran simulation
840	>	int nGlobalExcludes = 0;
841	>	int* globalExcludes = NULL;
842	>	int* excludeList = exclude_.getExcludeList();
843	>	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
844	>	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
845	>	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
846	>
847	>	if( isError ){
848	>
849	>	sprintf( painCave.errMsg,
850	>	"There was an error setting the simulation information in fortran.\n" );
851	>	painCave.isFatal = 1;
852	>	painCave.severity = OOPSE_ERROR;
853	>	simError();
854	>	}
855	>
856		#ifdef IS_MPI
857	<	numAtom = mpiSim->getNAtomsGlobal();
858	<	#else
859	<	numAtom = n_atoms;
857	>	sprintf( checkPointMsg,
858	>	"succesfully sent the simulation information to fortran.\n");
859	>	MPIcheckPoint();
860	>	#endif // is_mpi
861	>	}
862	>
863	>
864	>	#ifdef IS_MPI
865	>	void SimInfo::setupFortranParallel() {
866	>
867	>	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
868	>	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
869	>	std::vector<int> localToGlobalCutoffGroupIndex;
870	>	SimInfo::MoleculeIterator mi;
871	>	Molecule::AtomIterator ai;
872	>	Molecule::CutoffGroupIterator ci;
873	>	Molecule* mol;
874	>	Atom* atom;
875	>	CutoffGroup* cg;
876	>	mpiSimData parallelData;
877	>	int isError;
878	>
879	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
880	>
881	>	//local index(index in DataStorge) of atom is important
882	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
883	>	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
884	>	}
885	>
886	>	//local index of cutoff group is trivial, it only depends on the order of travesing
887	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
888	>	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
889	>	}
890	>
891	>	}
892	>
893	>	//fill up mpiSimData struct
894	>	parallelData.nMolGlobal = getNGlobalMolecules();
895	>	parallelData.nMolLocal = getNMolecules();
896	>	parallelData.nAtomsGlobal = getNGlobalAtoms();
897	>	parallelData.nAtomsLocal = getNAtoms();
898	>	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
899	>	parallelData.nGroupsLocal = getNCutoffGroups();
900	>	parallelData.myNode = worldRank;
901	>	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
902	>
903	>	//pass mpiSimData struct and index arrays to fortran
904	>	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
905	>	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
906	>	&localToGlobalCutoffGroupIndex[0], &isError);
907	>
908	>	if (isError) {
909	>	sprintf(painCave.errMsg,
910	>	"mpiRefresh errror: fortran didn't like something we gave it.\n");
911	>	painCave.isFatal = 1;
912	>	simError();
913	>	}
914	>
915	>	sprintf(checkPointMsg, " mpiRefresh successful.\n");
916	>	MPIcheckPoint();
917	>
918	>
919	>	}
920	>
921		#endif
602	–	for (int i = 0; i < numAtom; i++)
603	–	FglobalGroupMembership.push_back(globalGroupMembership[i] + 1);
604	–
922
923	<	myMols = info->molecules;
924	<	numMol = info->n_mol;
925	<	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)){
923	>	void SimInfo::setupCutoff() {
924	>
925	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
926
927	<	totalMass = myCutoffGroup->getMass();
928	<
929	<	for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom);
930	<	cutoffAtom != NULL;
931	<	cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
932	<	mfact.push_back(cutoffAtom->getMass()/totalMass);
933	<	}
927	>	// Check the cutoff policy
928	>	int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
929	>
930	>	std::string myPolicy;
931	>	if (forceFieldOptions_.haveCutoffPolicy()){
932	>	myPolicy = forceFieldOptions_.getCutoffPolicy();
933	>	}else if (simParams_->haveCutoffPolicy()) {
934	>	myPolicy = simParams_->getCutoffPolicy();
935	>	}
936	>
937	>	if (!myPolicy.empty()){
938	>	toUpper(myPolicy);
939	>	if (myPolicy == "MIX") {
940	>	cp = MIX_CUTOFF_POLICY;
941	>	} else {
942	>	if (myPolicy == "MAX") {
943	>	cp = MAX_CUTOFF_POLICY;
944	>	} else {
945	>	if (myPolicy == "TRADITIONAL") {
946	>	cp = TRADITIONAL_CUTOFF_POLICY;
947	>	} else {
948	>	// throw error
949	>	sprintf( painCave.errMsg,
950	>	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
951	>	painCave.isFatal = 1;
952	>	simError();
953	>	}
954	>	}
955	>	}
956	>	}
957	>	notifyFortranCutoffPolicy(&cp);
958	>
959	>	// Check the Skin Thickness for neighborlists
960	>	double skin;
961	>	if (simParams_->haveSkinThickness()) {
962	>	skin = simParams_->getSkinThickness();
963	>	notifyFortranSkinThickness(&skin);
964	>	}
965	>
966	>	// Check if the cutoff was set explicitly:
967	>	if (simParams_->haveCutoffRadius()) {
968	>	rcut_ = simParams_->getCutoffRadius();
969	>	if (simParams_->haveSwitchingRadius()) {
970	>	rsw_  = simParams_->getSwitchingRadius();
971	>	} else {
972	>	rsw_ = rcut_;
973	>	}
974	>	notifyFortranCutoffs(&rcut_, &rsw_);
975	>
976	>	} else {
977	>
978	>	// For electrostatic atoms, we'll assume a large safe value:
979	>	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
980	>	sprintf(painCave.errMsg,
981	>	"SimCreator Warning: No value was set for the cutoffRadius.\n"
982	>	"\tOOPSE will use a default value of 15.0 angstroms"
983	>	"\tfor the cutoffRadius.\n");
984	>	painCave.isFatal = 0;
985	>	simError();
986	>	rcut_ = 15.0;
987	>
988	>	if (simParams_->haveElectrostaticSummationMethod()) {
989	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
990	>	toUpper(myMethod);
991	>	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
992	>	if (simParams_->haveSwitchingRadius()){
993	>	sprintf(painCave.errMsg,
994	>	"SimInfo Warning: A value was set for the switchingRadius\n"
995	>	"\teven though the electrostaticSummationMethod was\n"
996	>	"\tset to %s\n", myMethod.c_str());
997	>	painCave.isFatal = 1;
998	>	simError();
999	>	}
1000	>	}
1001	>	}
1002	>
1003	>	if (simParams_->haveSwitchingRadius()){
1004	>	rsw_ = simParams_->getSwitchingRadius();
1005	>	} else {
1006	>	sprintf(painCave.errMsg,
1007	>	"SimCreator Warning: No value was set for switchingRadius.\n"
1008	>	"\tOOPSE will use a default value of\n"
1009	>	"\t0.85 * cutoffRadius for the switchingRadius\n");
1010	>	painCave.isFatal = 0;
1011	>	simError();
1012	>	rsw_ = 0.85 * rcut_;
1013	>	}
1014	>	notifyFortranCutoffs(&rcut_, &rsw_);
1015	>	} else {
1016	>	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1017	>	// We'll punt and let fortran figure out the cutoffs later.
1018	>
1019	>	notifyFortranYouAreOnYourOwn();
1020	>
1021	>	}
1022		}
1023		}
1024
1025	<	}
1025	>	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1026	>
1027	>	int errorOut;
1028	>	int esm =  NONE;
1029	>	int sm = UNDAMPED;
1030	>	double alphaVal;
1031	>	double dielectric;
1032	>
1033	>	errorOut = isError;
1034	>	alphaVal = simParams_->getDampingAlpha();
1035	>	dielectric = simParams_->getDielectric();
1036	>
1037	>	if (simParams_->haveElectrostaticSummationMethod()) {
1038	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1039	>	toUpper(myMethod);
1040	>	if (myMethod == "NONE") {
1041	>	esm = NONE;
1042	>	} else {
1043	>	if (myMethod == "SWITCHING_FUNCTION") {
1044	>	esm = SWITCHING_FUNCTION;
1045	>	} else {
1046	>	if (myMethod == "SHIFTED_POTENTIAL") {
1047	>	esm = SHIFTED_POTENTIAL;
1048	>	} else {
1049	>	if (myMethod == "SHIFTED_FORCE") {
1050	>	esm = SHIFTED_FORCE;
1051	>	} else {
1052	>	if (myMethod == "REACTION_FIELD") {
1053	>	esm = REACTION_FIELD;
1054	>	} else {
1055	>	// throw error
1056	>	sprintf( painCave.errMsg,
1057	>	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1058	>	"\t(Input file specified %s .)\n"
1059	>	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1060	>	"\t\"shifted_potential\", \"shifted_force\", or \n"
1061	>	"\t\"reaction_field\".\n", myMethod.c_str() );
1062	>	painCave.isFatal = 1;
1063	>	simError();
1064	>	}
1065	>	}
1066	>	}
1067	>	}
1068	>	}
1069	>	}
1070	>
1071	>	if (simParams_->haveElectrostaticScreeningMethod()) {
1072	>	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1073	>	toUpper(myScreen);
1074	>	if (myScreen == "UNDAMPED") {
1075	>	sm = UNDAMPED;
1076	>	} else {
1077	>	if (myScreen == "DAMPED") {
1078	>	sm = DAMPED;
1079	>	if (!simParams_->haveDampingAlpha()) {
1080	>	//throw error
1081	>	sprintf( painCave.errMsg,
1082	>	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1083	>	"\tA default value of %f (1/ang) will be used.\n", alphaVal);
1084	>	painCave.isFatal = 0;
1085	>	simError();
1086	>	}
1087	>	} else {
1088	>	// throw error
1089	>	sprintf( painCave.errMsg,
1090	>	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1091	>	"\t(Input file specified %s .)\n"
1092	>	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1093	>	"or \"damped\".\n", myScreen.c_str() );
1094	>	painCave.isFatal = 1;
1095	>	simError();
1096	>	}
1097	>	}
1098	>	}
1099	>
1100	>	// let's pass some summation method variables to fortran
1101	>	setElectrostaticSumMethod( &esm );
1102	>	setFortranElectrostaticMethod( &esm );
1103	>	setScreeningMethod( &sm );
1104	>	setDampingAlpha( &alphaVal );
1105	>	setReactionFieldDielectric( &dielectric );
1106	>	initFortranFF( &errorOut );
1107	>	}
1108	>
1109	>	void SimInfo::setupSwitchingFunction() {
1110	>	int ft = CUBIC;
1111	>
1112	>	if (simParams_->haveSwitchingFunctionType()) {
1113	>	std::string funcType = simParams_->getSwitchingFunctionType();
1114	>	toUpper(funcType);
1115	>	if (funcType == "CUBIC") {
1116	>	ft = CUBIC;
1117	>	} else {
1118	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1119	>	ft = FIFTH_ORDER_POLY;
1120	>	} else {
1121	>	// throw error
1122	>	sprintf( painCave.errMsg,
1123	>	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1124	>	painCave.isFatal = 1;
1125	>	simError();
1126	>	}
1127	>	}
1128	>	}
1129	>
1130	>	// send switching function notification to switcheroo
1131	>	setFunctionType(&ft);
1132	>
1133	>	}
1134	>
1135	>	void SimInfo::addProperty(GenericData* genData) {
1136	>	properties_.addProperty(genData);
1137	>	}
1138	>
1139	>	void SimInfo::removeProperty(const std::string& propName) {
1140	>	properties_.removeProperty(propName);
1141	>	}
1142	>
1143	>	void SimInfo::clearProperties() {
1144	>	properties_.clearProperties();
1145	>	}
1146	>
1147	>	std::vector<std::string> SimInfo::getPropertyNames() {
1148	>	return properties_.getPropertyNames();
1149	>	}
1150	>
1151	>	std::vector<GenericData*> SimInfo::getProperties() {
1152	>	return properties_.getProperties();
1153	>	}
1154	>
1155	>	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1156	>	return properties_.getPropertyByName(propName);
1157	>	}
1158	>
1159	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1160	>	if (sman_ == sman) {
1161	>	return;
1162	>	}
1163	>	delete sman_;
1164	>	sman_ = sman;
1165	>
1166	>	Molecule* mol;
1167	>	RigidBody* rb;
1168	>	Atom* atom;
1169	>	SimInfo::MoleculeIterator mi;
1170	>	Molecule::RigidBodyIterator rbIter;
1171	>	Molecule::AtomIterator atomIter;;
1172	>
1173	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1174	>
1175	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1176	>	atom->setSnapshotManager(sman_);
1177	>	}
1178	>
1179	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1180	>	rb->setSnapshotManager(sman_);
1181	>	}
1182	>	}
1183	>
1184	>	}
1185	>
1186	>	Vector3d SimInfo::getComVel(){
1187	>	SimInfo::MoleculeIterator i;
1188	>	Molecule* mol;
1189	>
1190	>	Vector3d comVel(0.0);
1191	>	double totalMass = 0.0;
1192	>
1193	>
1194	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1195	>	double mass = mol->getMass();
1196	>	totalMass += mass;
1197	>	comVel += mass * mol->getComVel();
1198	>	}
1199	>
1200	>	#ifdef IS_MPI
1201	>	double tmpMass = totalMass;
1202	>	Vector3d tmpComVel(comVel);
1203	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1204	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1205	>	#endif
1206	>
1207	>	comVel /= totalMass;
1208	>
1209	>	return comVel;
1210	>	}
1211	>
1212	>	Vector3d SimInfo::getCom(){
1213	>	SimInfo::MoleculeIterator i;
1214	>	Molecule* mol;
1215	>
1216	>	Vector3d com(0.0);
1217	>	double totalMass = 0.0;
1218	>
1219	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1220	>	double mass = mol->getMass();
1221	>	totalMass += mass;
1222	>	com += mass * mol->getCom();
1223	>	}
1224	>
1225	>	#ifdef IS_MPI
1226	>	double tmpMass = totalMass;
1227	>	Vector3d tmpCom(com);
1228	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1229	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1230	>	#endif
1231	>
1232	>	com /= totalMass;
1233	>
1234	>	return com;
1235	>
1236	>	}
1237	>
1238	>	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1239	>
1240	>	return o;
1241	>	}
1242	>
1243	>
1244	>	/*
1245	>	Returns center of mass and center of mass velocity in one function call.
1246	>	*/
1247	>
1248	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1249	>	SimInfo::MoleculeIterator i;
1250	>	Molecule* mol;
1251	>
1252	>
1253	>	double totalMass = 0.0;
1254	>
1255	>
1256	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1257	>	double mass = mol->getMass();
1258	>	totalMass += mass;
1259	>	com += mass * mol->getCom();
1260	>	comVel += mass * mol->getComVel();
1261	>	}
1262	>
1263	>	#ifdef IS_MPI
1264	>	double tmpMass = totalMass;
1265	>	Vector3d tmpCom(com);
1266	>	Vector3d tmpComVel(comVel);
1267	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1268	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1269	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1270	>	#endif
1271	>
1272	>	com /= totalMass;
1273	>	comVel /= totalMass;
1274	>	}
1275	>
1276	>	/*
1277	>	Return intertia tensor for entire system and angular momentum Vector.
1278	>
1279	>
1280	>	[  Ixx -Ixy  -Ixz ]
1281	>	J =| -Iyx  Iyy  -Iyz |
1282	>	[ -Izx -Iyz   Izz ]
1283	>	*/
1284	>
1285	>	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1286	>
1287	>
1288	>	double xx = 0.0;
1289	>	double yy = 0.0;
1290	>	double zz = 0.0;
1291	>	double xy = 0.0;
1292	>	double xz = 0.0;
1293	>	double yz = 0.0;
1294	>	Vector3d com(0.0);
1295	>	Vector3d comVel(0.0);
1296	>
1297	>	getComAll(com, comVel);
1298	>
1299	>	SimInfo::MoleculeIterator i;
1300	>	Molecule* mol;
1301	>
1302	>	Vector3d thisq(0.0);
1303	>	Vector3d thisv(0.0);
1304	>
1305	>	double thisMass = 0.0;
1306	>
1307	>
1308	>
1309	>
1310	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1311	>
1312	>	thisq = mol->getCom()-com;
1313	>	thisv = mol->getComVel()-comVel;
1314	>	thisMass = mol->getMass();
1315	>	// Compute moment of intertia coefficients.
1316	>	xx += thisq[0]*thisq[0]*thisMass;
1317	>	yy += thisq[1]*thisq[1]*thisMass;
1318	>	zz += thisq[2]*thisq[2]*thisMass;
1319	>
1320	>	// compute products of intertia
1321	>	xy += thisq[0]*thisq[1]*thisMass;
1322	>	xz += thisq[0]*thisq[2]*thisMass;
1323	>	yz += thisq[1]*thisq[2]*thisMass;
1324	>
1325	>	angularMomentum += cross( thisq, thisv ) * thisMass;
1326	>
1327	>	}
1328	>
1329	>
1330	>	inertiaTensor(0,0) = yy + zz;
1331	>	inertiaTensor(0,1) = -xy;
1332	>	inertiaTensor(0,2) = -xz;
1333	>	inertiaTensor(1,0) = -xy;
1334	>	inertiaTensor(1,1) = xx + zz;
1335	>	inertiaTensor(1,2) = -yz;
1336	>	inertiaTensor(2,0) = -xz;
1337	>	inertiaTensor(2,1) = -yz;
1338	>	inertiaTensor(2,2) = xx + yy;
1339	>
1340	>	#ifdef IS_MPI
1341	>	Mat3x3d tmpI(inertiaTensor);
1342	>	Vector3d tmpAngMom;
1343	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1344	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1345	>	#endif
1346	>
1347	>	return;
1348	>	}
1349	>
1350	>	//Returns the angular momentum of the system
1351	>	Vector3d SimInfo::getAngularMomentum(){
1352	>
1353	>	Vector3d com(0.0);
1354	>	Vector3d comVel(0.0);
1355	>	Vector3d angularMomentum(0.0);
1356	>
1357	>	getComAll(com,comVel);
1358	>
1359	>	SimInfo::MoleculeIterator i;
1360	>	Molecule* mol;
1361	>
1362	>	Vector3d thisr(0.0);
1363	>	Vector3d thisp(0.0);
1364	>
1365	>	double thisMass;
1366	>
1367	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1368	>	thisMass = mol->getMass();
1369	>	thisr = mol->getCom()-com;
1370	>	thisp = (mol->getComVel()-comVel)*thisMass;
1371	>
1372	>	angularMomentum += cross( thisr, thisp );
1373	>
1374	>	}
1375	>
1376	>	#ifdef IS_MPI
1377	>	Vector3d tmpAngMom;
1378	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1379	>	#endif
1380	>
1381	>	return angularMomentum;
1382	>	}
1383	>
1384	>
1385	>	}//end namespace oopse
1386	>

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