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root/OpenMD/trunk/src/brains/SimInfo.cpp

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 2 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
Revision 945 by gezelter, Tue Apr 25 02:09:01 2006 UTC

#	Line 1 | Line 1
1	<	#include <stdlib.h>
2	<	#include <string.h>
3	<	#include <math.h>
1	>	/*
2	>	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	>	*
4	>	* The University of Notre Dame grants you ("Licensee") a
5	>	* non-exclusive, royalty free, license to use, modify and
6	>	* redistribute this software in source and binary code form, provided
7	>	* that the following conditions are met:
8	>	*
9	>	* 1. Acknowledgement of the program authors must be made in any
10	>	*    publication of scientific results based in part on use of the
11	>	*    program.  An acceptable form of acknowledgement is citation of
12	>	*    the article in which the program was described (Matthew
13	>	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	>	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	>	*    Parallel Simulation Engine for Molecular Dynamics,"
16	>	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	>	*
18	>	* 2. Redistributions of source code must retain the above copyright
19	>	*    notice, this list of conditions and the following disclaimer.
20	>	*
21	>	* 3. Redistributions in binary form must reproduce the above copyright
22	>	*    notice, this list of conditions and the following disclaimer in the
23	>	*    documentation and/or other materials provided with the
24	>	*    distribution.
25	>	*
26	>	* This software is provided "AS IS," without a warranty of any
27	>	* kind. All express or implied conditions, representations and
28	>	* warranties, including any implied warranty of merchantability,
29	>	* fitness for a particular purpose or non-infringement, are hereby
30	>	* excluded.  The University of Notre Dame and its licensors shall not
31	>	* be liable for any damages suffered by licensee as a result of
32	>	* using, modifying or distributing the software or its
33	>	* derivatives. In no event will the University of Notre Dame or its
34	>	* licensors be liable for any lost revenue, profit or data, or for
35	>	* direct, indirect, special, consequential, incidental or punitive
36	>	* damages, however caused and regardless of the theory of liability,
37	>	* arising out of the use of or inability to use software, even if the
38	>	* University of Notre Dame has been advised of the possibility of
39	>	* such damages.
40	>	*/
41	>
42	>	/**
43	>	* @file SimInfo.cpp
44	>	* @author    tlin
45	>	* @date  11/02/2004
46	>	* @version 1.0
47	>	*/
48
49	<	#include <iostream>
50	<	using namespace std;
49	>	#include <algorithm>
50	>	#include <set>
51	>	#include <map>
52
53	<	#include "SimInfo.hpp"
54	<	#define __C
55	<	#include "fSimulation.h"
56	<	#include "simError.h"
53	>	#include "brains/SimInfo.hpp"
54	>	#include "math/Vector3.hpp"
55	>	#include "primitives/Molecule.hpp"
56	>	#include "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 "fortranWrappers.hpp"
14	–
15	–	#include "MatVec3.h"
16	–
69		#ifdef IS_MPI
70	<	#include "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), fdf_local(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	<
147	<	SimInfo::~SimInfo(){
148	<
149	<	delete myConfiguration;
150	<
151	<	map<string, GenericData*>::iterator i;
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	<	for(i = properties.begin(); i != properties.end(); i++)
90	<	delete (*i).second;
154	>	nGlobalMols_ = molStampIds_.size();
155
156	<	}
156	>	#ifdef IS_MPI
157	>	molToProcMap_.resize(nGlobalMols_);
158	>	#endif
159
160	<	void SimInfo::setBox(double newBox[3]) {
95	<
96	<	int i, j;
97	<	double tempMat[3][3];
160	>	}
161
162	<	for(i=0; i<3; i++)
163	<	for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
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	<	tempMat[0][0] = newBox[0];
175	<	tempMat[1][1] = newBox[1];
176	<	tempMat[2][2] = newBox[2];
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	<	setBoxM( tempMat );
185	>	bool SimInfo::addMolecule(Molecule* mol) {
186	>	MoleculeIterator i;
187
188	<	}
188	>	i = molecules_.find(mol->getGlobalIndex());
189	>	if (i == molecules_.end() ) {
190
191	<	void SimInfo::setBoxM( double theBox[3][3] ){
192	<
193	<	int i, j;
194	<	double FortranHmat[9]; // to preserve compatibility with Fortran the
195	<	// ordering in the array is as follows:
196	<	// [ 0 3 6 ]
197	<	// [ 1 4 7 ]
198	<	// [ 2 5 8 ]
199	<	double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
200	<
120	<	if( !boxIsInit ) boxIsInit = 1;
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	<	for(i=0; i < 3; i++)
203	<	for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
204	<
205	<	calcBoxL();
206	<	calcHmatInv();
127	<
128	<	for(i=0; i < 3; i++) {
129	<	for (j=0; j < 3; j++) {
130	<	FortranHmat[3*j + i] = Hmat[i][j];
131	<	FortranHmatInv[3*j + i] = HmatInv[i][j];
202	>	addExcludePairs(mol);
203	>
204	>	return true;
205	>	} else {
206	>	return false;
207		}
208		}
209
210	<	setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
211	<
212	<	}
138	<
210	>	bool SimInfo::removeMolecule(Molecule* mol) {
211	>	MoleculeIterator i;
212	>	i = molecules_.find(mol->getGlobalIndex());
213
214	<	void SimInfo::getBoxM (double theBox[3][3]) {
214	>	if (i != molecules_.end() ) {
215
216	<	int i, j;
217	<	for(i=0; i<3; i++)
218	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
219	<	}
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	+	removeExcludePairs(mol);
228	+	molecules_.erase(mol->getGlobalIndex());
229
230	<	void SimInfo::scaleBox(double scale) {
231	<	double theBox[3][3];
232	<	int i, j;
230	>	delete mol;
231	>
232	>	return true;
233	>	} else {
234	>	return false;
235	>	}
236
152	–	// cerr << "Scaling box by " << scale << "\n";
237
238	<	for(i=0; i<3; i++)
155	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
238	>	}
239
240	<	setBoxM(theBox);
240	>
241	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
242	>	i = molecules_.begin();
243	>	return i == molecules_.end() ? NULL : i->second;
244	>	}
245
246	<	}
246	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
247	>	++i;
248	>	return i == molecules_.end() ? NULL : i->second;
249	>	}
250
161	–	void SimInfo::calcHmatInv( void ) {
162	–
163	–	int oldOrtho;
164	–	int i,j;
165	–	double smallDiag;
166	–	double tol;
167	–	double sanity[3][3];
251
252	<	invertMat3( Hmat, HmatInv );
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	<	// check to see if Hmat is orthorhombic
260	<
261	<	oldOrtho = orthoRhombic;
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	<	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;
265	>	ndf_local += 3;
266
267	<	orthoRhombic = 1;
268	<
269	<	for (i = 0; i < 3; i++ ) {
270	<	for (j = 0 ; j < 3; j++) {
271	<	if (i != j) {
272	<	if (orthoRhombic) {
273	<	if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
274	<	}
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 ){
282	<
283	<	double dx, dy, dz, dsq;
284	<
285	<	// boxVol = Determinant of Hmat
225	<
226	<	boxVol = matDet3( Hmat );
227	<
228	<	// boxLx
229	<
230	<	dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
231	<	dsq = dx*dx + dy*dy + dz*dz;
232	<	boxL[0] = sqrt( dsq );
233	<	//maxCutoff = 0.5 * boxL[0];
234	<
235	<	// boxLy
236	<
237	<	dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
238	<	dsq = dx*dx + dy*dy + dz*dz;
239	<	boxL[1] = sqrt( dsq );
240	<	//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
241	<
242	<
243	<	// boxLz
244	<
245	<	dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
246	<	dsq = dx*dx + dy*dy + dz*dz;
247	<	boxL[2] = sqrt( dsq );
248	<	//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
249	<
250	<	//calculate the max cutoff
251	<	maxCutoff =  calcMaxCutOff();
252	<
253	<	checkCutOffs();
254	<
255	<	}
256	<
257	<
258	<	double SimInfo::calcMaxCutOff(){
259	<
260	<	double ri[3], rj[3], rk[3];
261	<	double rij[3], rjk[3], rki[3];
262	<	double minDist;
263	<
264	<	ri[0] = Hmat[0][0];
265	<	ri[1] = Hmat[1][0];
266	<	ri[2] = Hmat[2][0];
267	<
268	<	rj[0] = Hmat[0][1];
269	<	rj[1] = Hmat[1][1];
270	<	rj[2] = Hmat[2][1];
271	<
272	<	rk[0] = Hmat[0][2];
273	<	rk[1] = Hmat[1][2];
274	<	rk[2] = Hmat[2][2];
275	<
276	<	crossProduct3(ri, rj, rij);
277	<	distXY = dotProduct3(rk,rij) / norm3(rij);
278	<
279	<	crossProduct3(rj,rk, rjk);
280	<	distYZ = dotProduct3(ri,rjk) / norm3(rjk);
281	<
282	<	crossProduct3(rk,ri, rki);
283	<	distZX = dotProduct3(rj,rki) / norm3(rki);
284	<
285	<	minDist = min(min(distXY, distYZ), distZX);
286	<	return minDist/2;
287	<
288	<	}
289	<
290	<	void SimInfo::wrapVector( double thePos[3] ){
291	<
292	<	int i;
293	<	double scaled[3];
294	<
295	<	if( !orthoRhombic ){
296	<	// calc the scaled coordinates.
297	<
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	<	matVecMul3(HmatInv, thePos, scaled);
288	<
289	<	for(i=0; i<3; i++)
302	<	scaled[i] -= roundMe(scaled[i]);
303	<
304	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
305	<
306	<	matVecMul3(Hmat, scaled, thePos);
287	>	// nZconstraints_ is global, as are the 3 COM translations for the
288	>	// entire system:
289	>	ndf_ = ndf_ - 3 - nZconstraint_;
290
291		}
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	–	}
292
293	<
329	<	int SimInfo::getNDF(){
330	<	int ndf_local;
331	<
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	<	}
343	<
344	<	// n_constraints is local, so subtract them on each processor:
345	<
346	<	ndf_local -= n_constraints;
347	<
293	>	int SimInfo::getFdf() {
294		#ifdef IS_MPI
295	<	MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
295	>	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
296		#else
297	<	ndf = ndf_local;
297	>	fdf_ = fdf_local;
298		#endif
299	+	return fdf_;
300	+	}
301	+
302	+	void SimInfo::calcNdfRaw() {
303	+	int ndfRaw_local;
304
305	<	// nZconstraints is global, as are the 3 COM translations for the
306	<	// entire system:
305	>	MoleculeIterator i;
306	>	std::vector<StuntDouble*>::iterator j;
307	>	Molecule* mol;
308	>	StuntDouble* integrableObject;
309
310	<	ndf = ndf - 3 - nZconstraints;
310	>	// Raw degrees of freedom that we have to set
311	>	ndfRaw_local = 0;
312	>
313	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
314	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
315	>	integrableObject = mol->nextIntegrableObject(j)) {
316
317	<	return ndf;
360	<	}
317	>	ndfRaw_local += 3;
318
319	<	int SimInfo::getNDFraw() {
320	<	int ndfRaw_local;
321	<
322	<	// Raw degrees of freedom that we have to set
323	<	ndfRaw_local = 0;
324	<
325	<	for(int i = 0; i < integrableObjects.size(); i++){
326	<	ndfRaw_local += 3;
327	<	if (integrableObjects[i]->isDirectional()) {
371	<	if (integrableObjects[i]->isLinear())
372	<	ndfRaw_local += 2;
373	<	else
374	<	ndfRaw_local += 3;
319	>	if (integrableObject->isDirectional()) {
320	>	if (integrableObject->isLinear()) {
321	>	ndfRaw_local += 2;
322	>	} else {
323	>	ndfRaw_local += 3;
324	>	}
325	>	}
326	>
327	>	}
328		}
376	–	}
329
330		#ifdef IS_MPI
331	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
331	>	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
332		#else
333	<	ndfRaw = ndfRaw_local;
333	>	ndfRaw_ = ndfRaw_local;
334		#endif
335	+	}
336
337	<	return ndfRaw;
338	<	}
337	>	void SimInfo::calcNdfTrans() {
338	>	int ndfTrans_local;
339
340	<	int SimInfo::getNDFtranslational() {
388	<	int ndfTrans_local;
340	>	ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
341
390	–	ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
342
392	–
343		#ifdef IS_MPI
344	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
344	>	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
345		#else
346	<	ndfTrans = ndfTrans_local;
346	>	ndfTrans_ = ndfTrans_local;
347		#endif
348
349	<	ndfTrans = ndfTrans - 3 - nZconstraints;
349	>	ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
350	>
351	>	}
352
353	<	return ndfTrans;
354	<	}
353	>	void SimInfo::addExcludePairs(Molecule* mol) {
354	>	std::vector<Bond*>::iterator bondIter;
355	>	std::vector<Bend*>::iterator bendIter;
356	>	std::vector<Torsion*>::iterator torsionIter;
357	>	Bond* bond;
358	>	Bend* bend;
359	>	Torsion* torsion;
360	>	int a;
361	>	int b;
362	>	int c;
363	>	int d;
364
365	<	int SimInfo::getTotIntegrableObjects() {
405	<	int nObjs_local;
406	<	int nObjs;
365	>	std::map<int, std::set<int> > atomGroups;
366
367	<	nObjs_local =  integrableObjects.size();
367	>	Molecule::RigidBodyIterator rbIter;
368	>	RigidBody* rb;
369	>	Molecule::IntegrableObjectIterator ii;
370	>	StuntDouble* integrableObject;
371	>
372	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
373	>	integrableObject = mol->nextIntegrableObject(ii)) {
374
375	+	if (integrableObject->isRigidBody()) {
376	+	rb = static_cast<RigidBody*>(integrableObject);
377	+	std::vector<Atom*> atoms = rb->getAtoms();
378	+	std::set<int> rigidAtoms;
379	+	for (int i = 0; i < atoms.size(); ++i) {
380	+	rigidAtoms.insert(atoms[i]->getGlobalIndex());
381	+	}
382	+	for (int i = 0; i < atoms.size(); ++i) {
383	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
384	+	}
385	+	} else {
386	+	std::set<int> oneAtomSet;
387	+	oneAtomSet.insert(integrableObject->getGlobalIndex());
388	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
389	+	}
390	+	}
391
392	<	#ifdef IS_MPI
393	<	MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
394	<	#else
395	<	nObjs = nObjs_local;
396	<	#endif
392	>
393	>
394	>	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
395	>	a = bond->getAtomA()->getGlobalIndex();
396	>	b = bond->getAtomB()->getGlobalIndex();
397	>	exclude_.addPair(a, b);
398	>	}
399
400	+	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
401	+	a = bend->getAtomA()->getGlobalIndex();
402	+	b = bend->getAtomB()->getGlobalIndex();
403	+	c = bend->getAtomC()->getGlobalIndex();
404	+	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
405	+	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
406	+	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
407
408	<	return nObjs;
409	<	}
408	>	exclude_.addPairs(rigidSetA, rigidSetB);
409	>	exclude_.addPairs(rigidSetA, rigidSetC);
410	>	exclude_.addPairs(rigidSetB, rigidSetC);
411	>
412	>	//exclude_.addPair(a, b);
413	>	//exclude_.addPair(a, c);
414	>	//exclude_.addPair(b, c);
415	>	}
416
417	<	void SimInfo::refreshSim(){
417	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
418	>	a = torsion->getAtomA()->getGlobalIndex();
419	>	b = torsion->getAtomB()->getGlobalIndex();
420	>	c = torsion->getAtomC()->getGlobalIndex();
421	>	d = torsion->getAtomD()->getGlobalIndex();
422	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
423	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
424	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
425	>	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
426
427	<	simtype fInfo;
428	<	int isError;
429	<	int n_global;
430	<	int* excl;
427	>	exclude_.addPairs(rigidSetA, rigidSetB);
428	>	exclude_.addPairs(rigidSetA, rigidSetC);
429	>	exclude_.addPairs(rigidSetA, rigidSetD);
430	>	exclude_.addPairs(rigidSetB, rigidSetC);
431	>	exclude_.addPairs(rigidSetB, rigidSetD);
432	>	exclude_.addPairs(rigidSetC, rigidSetD);
433
434	<	fInfo.dielect = 0.0;
434	>	/*
435	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
436	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
437	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
438	>	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
439	>	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
440	>	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
441	>
442	>
443	>	exclude_.addPair(a, b);
444	>	exclude_.addPair(a, c);
445	>	exclude_.addPair(a, d);
446	>	exclude_.addPair(b, c);
447	>	exclude_.addPair(b, d);
448	>	exclude_.addPair(c, d);
449	>	*/
450	>	}
451
452	<	if( useDipoles ){
453	<	if( useReactionField )fInfo.dielect = dielectric;
452	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
453	>	std::vector<Atom*> atoms = rb->getAtoms();
454	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
455	>	for (int j = i + 1; j < atoms.size(); ++j) {
456	>	a = atoms[i]->getGlobalIndex();
457	>	b = atoms[j]->getGlobalIndex();
458	>	exclude_.addPair(a, b);
459	>	}
460	>	}
461	>	}
462	>
463		}
464
465	<	fInfo.SIM_uses_PBC = usePBC;
466	<	//fInfo.SIM_uses_LJ = 0;
467	<	fInfo.SIM_uses_LJ = useLJ;
468	<	fInfo.SIM_uses_sticky = useSticky;
469	<	//fInfo.SIM_uses_sticky = 0;
470	<	fInfo.SIM_uses_charges = useCharges;
471	<	fInfo.SIM_uses_dipoles = useDipoles;
472	<	//fInfo.SIM_uses_dipoles = 0;
473	<	fInfo.SIM_uses_RF = useReactionField;
474	<	//fInfo.SIM_uses_RF = 0;
475	<	fInfo.SIM_uses_GB = useGB;
445	<	fInfo.SIM_uses_EAM = useEAM;
465	>	void SimInfo::removeExcludePairs(Molecule* mol) {
466	>	std::vector<Bond*>::iterator bondIter;
467	>	std::vector<Bend*>::iterator bendIter;
468	>	std::vector<Torsion*>::iterator torsionIter;
469	>	Bond* bond;
470	>	Bend* bend;
471	>	Torsion* torsion;
472	>	int a;
473	>	int b;
474	>	int c;
475	>	int d;
476
477	<	n_exclude = excludes->getSize();
448	<	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);
477	>	std::map<int, std::set<int> > atomGroups;
478
479	<	if( isError ){
479	>	Molecule::RigidBodyIterator rbIter;
480	>	RigidBody* rb;
481	>	Molecule::IntegrableObjectIterator ii;
482	>	StuntDouble* integrableObject;
483
484	<	sprintf( painCave.errMsg,
485	<	"There was an error setting the simulation information in fortran.\n" );
486	<	painCave.isFatal = 1;
487	<	painCave.severity = OOPSE_ERROR;
488	<	simError();
484	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
485	>	integrableObject = mol->nextIntegrableObject(ii)) {
486	>
487	>	if (integrableObject->isRigidBody()) {
488	>	rb = static_cast<RigidBody*>(integrableObject);
489	>	std::vector<Atom*> atoms = rb->getAtoms();
490	>	std::set<int> rigidAtoms;
491	>	for (int i = 0; i < atoms.size(); ++i) {
492	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
493	>	}
494	>	for (int i = 0; i < atoms.size(); ++i) {
495	>	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
496	>	}
497	>	} else {
498	>	std::set<int> oneAtomSet;
499	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
500	>	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
501	>	}
502	>	}
503	>
504	>
505	>	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
506	>	a = bond->getAtomA()->getGlobalIndex();
507	>	b = bond->getAtomB()->getGlobalIndex();
508	>	exclude_.removePair(a, b);
509	>	}
510	>
511	>	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
512	>	a = bend->getAtomA()->getGlobalIndex();
513	>	b = bend->getAtomB()->getGlobalIndex();
514	>	c = bend->getAtomC()->getGlobalIndex();
515	>
516	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
517	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
518	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
519	>
520	>	exclude_.removePairs(rigidSetA, rigidSetB);
521	>	exclude_.removePairs(rigidSetA, rigidSetC);
522	>	exclude_.removePairs(rigidSetB, rigidSetC);
523	>
524	>	//exclude_.removePair(a, b);
525	>	//exclude_.removePair(a, c);
526	>	//exclude_.removePair(b, c);
527	>	}
528	>
529	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
530	>	a = torsion->getAtomA()->getGlobalIndex();
531	>	b = torsion->getAtomB()->getGlobalIndex();
532	>	c = torsion->getAtomC()->getGlobalIndex();
533	>	d = torsion->getAtomD()->getGlobalIndex();
534	>
535	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
536	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
537	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
538	>	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
539	>
540	>	exclude_.removePairs(rigidSetA, rigidSetB);
541	>	exclude_.removePairs(rigidSetA, rigidSetC);
542	>	exclude_.removePairs(rigidSetA, rigidSetD);
543	>	exclude_.removePairs(rigidSetB, rigidSetC);
544	>	exclude_.removePairs(rigidSetB, rigidSetD);
545	>	exclude_.removePairs(rigidSetC, rigidSetD);
546	>
547	>	/*
548	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
549	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
550	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
551	>	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
552	>	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
553	>	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
554	>
555	>
556	>	exclude_.removePair(a, b);
557	>	exclude_.removePair(a, c);
558	>	exclude_.removePair(a, d);
559	>	exclude_.removePair(b, c);
560	>	exclude_.removePair(b, d);
561	>	exclude_.removePair(c, d);
562	>	*/
563	>	}
564	>
565	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
566	>	std::vector<Atom*> atoms = rb->getAtoms();
567	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
568	>	for (int j = i + 1; j < atoms.size(); ++j) {
569	>	a = atoms[i]->getGlobalIndex();
570	>	b = atoms[j]->getGlobalIndex();
571	>	exclude_.removePair(a, b);
572	>	}
573	>	}
574	>	}
575	>
576		}
577	<
577	>
578	>
579	>	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
580	>	int curStampId;
581	>
582	>	//index from 0
583	>	curStampId = moleculeStamps_.size();
584	>
585	>	moleculeStamps_.push_back(molStamp);
586	>	molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
587	>	}
588	>
589	>	void SimInfo::update() {
590	>
591	>	setupSimType();
592	>
593		#ifdef IS_MPI
594	<	sprintf( checkPointMsg,
595	<	"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	<	}
594	>	setupFortranParallel();
595	>	#endif
596
597	<	void SimInfo::setDefaultRcut( double theRcut ){
597	>	setupFortranSim();
598	>
599	>	//setup fortran force field
600	>	/** @deprecate */
601	>	int isError = 0;
602	>
603	>	setupElectrostaticSummationMethod( isError );
604	>	setupSwitchingFunction();
605	>
606	>	if(isError){
607	>	sprintf( painCave.errMsg,
608	>	"ForceField error: There was an error initializing the forceField in fortran.\n" );
609	>	painCave.isFatal = 1;
610	>	simError();
611	>	}
612
613	<	haveRcut = 1;
614	<	rCut = theRcut;
490	<	rList = rCut + 1.0;
491	<
492	<	notifyFortranCutOffs( &rCut, &rSw, &rList );
493	<	}
613	>
614	>	setupCutoff();
615
616	<	void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
616	>	calcNdf();
617	>	calcNdfRaw();
618	>	calcNdfTrans();
619
620	<	rSw = theRsw;
621	<	setDefaultRcut( theRcut );
499	<	}
620	>	fortranInitialized_ = true;
621	>	}
622
623	+	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
624	+	SimInfo::MoleculeIterator mi;
625	+	Molecule* mol;
626	+	Molecule::AtomIterator ai;
627	+	Atom* atom;
628	+	std::set<AtomType*> atomTypes;
629
630	<	void SimInfo::checkCutOffs( void ){
631	<
632	<	if( boxIsInit ){
630	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
631	>
632	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
633	>	atomTypes.insert(atom->getAtomType());
634	>	}
635	>
636	>	}
637	>
638	>	return atomTypes;
639	>	}
640	>
641	>	void SimInfo::setupSimType() {
642	>	std::set<AtomType*>::iterator i;
643	>	std::set<AtomType*> atomTypes;
644	>	atomTypes = getUniqueAtomTypes();
645
646	<	//we need to check cutOffs against the box
646	>	int useLennardJones = 0;
647	>	int useElectrostatic = 0;
648	>	int useEAM = 0;
649	>	int useSC = 0;
650	>	int useCharge = 0;
651	>	int useDirectional = 0;
652	>	int useDipole = 0;
653	>	int useGayBerne = 0;
654	>	int useSticky = 0;
655	>	int useStickyPower = 0;
656	>	int useShape = 0;
657	>	int useFLARB = 0; //it is not in AtomType yet
658	>	int useDirectionalAtom = 0;
659	>	int useElectrostatics = 0;
660	>	//usePBC and useRF are from simParams
661	>	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
662	>	int useRF;
663	>	int useSF;
664	>	std::string myMethod;
665	>
666	>	// set the useRF logical
667	>	useRF = 0;
668	>	useSF = 0;
669	>
670	>
671	>	if (simParams_->haveElectrostaticSummationMethod()) {
672	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
673	>	toUpper(myMethod);
674	>	if (myMethod == "REACTION_FIELD") {
675	>	useRF=1;
676	>	} else {
677	>	if (myMethod == "SHIFTED_FORCE") {
678	>	useSF = 1;
679	>	}
680	>	}
681	>	}
682	>
683	>	//loop over all of the atom types
684	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
685	>	useLennardJones |= (*i)->isLennardJones();
686	>	useElectrostatic |= (*i)->isElectrostatic();
687	>	useEAM |= (*i)->isEAM();
688	>	useSC |= (*i)->isSC();
689	>	useCharge |= (*i)->isCharge();
690	>	useDirectional |= (*i)->isDirectional();
691	>	useDipole |= (*i)->isDipole();
692	>	useGayBerne |= (*i)->isGayBerne();
693	>	useSticky |= (*i)->isSticky();
694	>	useStickyPower |= (*i)->isStickyPower();
695	>	useShape |= (*i)->isShape();
696	>	}
697	>
698	>	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
699	>	useDirectionalAtom = 1;
700	>	}
701	>
702	>	if (useCharge || useDipole) {
703	>	useElectrostatics = 1;
704	>	}
705	>
706	>	#ifdef IS_MPI
707	>	int temp;
708	>
709	>	temp = usePBC;
710	>	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
711	>
712	>	temp = useDirectionalAtom;
713	>	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
714	>
715	>	temp = useLennardJones;
716	>	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
717	>
718	>	temp = useElectrostatics;
719	>	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
720	>
721	>	temp = useCharge;
722	>	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
723	>
724	>	temp = useDipole;
725	>	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
726	>
727	>	temp = useSticky;
728	>	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
729	>
730	>	temp = useStickyPower;
731	>	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
732
733	<	if( rCut > maxCutoff ){
734	<	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	<	}
733	>	temp = useGayBerne;
734	>	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
735
736	<	void SimInfo::addProperty(GenericData* prop){
736	>	temp = useEAM;
737	>	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
738
739	<	map<string, GenericData*>::iterator result;
740	<	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()){
739	>	temp = useSC;
740	>	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
741
742	<	delete (*result).second;
743	<	(*result).second = prop;
742	>	temp = useShape;
743	>	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
744	>
745	>	temp = useFLARB;
746	>	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
747	>
748	>	temp = useRF;
749	>	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
750	>
751	>	temp = useSF;
752	>	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
753	>
754	>	#endif
755	>
756	>	fInfo_.SIM_uses_PBC = usePBC;
757	>	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
758	>	fInfo_.SIM_uses_LennardJones = useLennardJones;
759	>	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
760	>	fInfo_.SIM_uses_Charges = useCharge;
761	>	fInfo_.SIM_uses_Dipoles = useDipole;
762	>	fInfo_.SIM_uses_Sticky = useSticky;
763	>	fInfo_.SIM_uses_StickyPower = useStickyPower;
764	>	fInfo_.SIM_uses_GayBerne = useGayBerne;
765	>	fInfo_.SIM_uses_EAM = useEAM;
766	>	fInfo_.SIM_uses_SC = useSC;
767	>	fInfo_.SIM_uses_Shapes = useShape;
768	>	fInfo_.SIM_uses_FLARB = useFLARB;
769	>	fInfo_.SIM_uses_RF = useRF;
770	>	fInfo_.SIM_uses_SF = useSF;
771	>
772	>	if( myMethod == "REACTION_FIELD") {
773
774	+	if (simParams_->haveDielectric()) {
775	+	fInfo_.dielect = simParams_->getDielectric();
776	+	} else {
777	+	sprintf(painCave.errMsg,
778	+	"SimSetup Error: No Dielectric constant was set.\n"
779	+	"\tYou are trying to use Reaction Field without"
780	+	"\tsetting a dielectric constant!\n");
781	+	painCave.isFatal = 1;
782	+	simError();
783	+	}
784	+	}
785	+
786		}
552	–	else{
787
788	<	properties[prop->getID()] = prop;
788	>	void SimInfo::setupFortranSim() {
789	>	int isError;
790	>	int nExclude;
791	>	std::vector<int> fortranGlobalGroupMembership;
792	>
793	>	nExclude = exclude_.getSize();
794	>	isError = 0;
795
796	<	}
796	>	//globalGroupMembership_ is filled by SimCreator
797	>	for (int i = 0; i < nGlobalAtoms_; i++) {
798	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
799	>	}
800	>
801	>	//calculate mass ratio of cutoff group
802	>	std::vector<double> mfact;
803	>	SimInfo::MoleculeIterator mi;
804	>	Molecule* mol;
805	>	Molecule::CutoffGroupIterator ci;
806	>	CutoffGroup* cg;
807	>	Molecule::AtomIterator ai;
808	>	Atom* atom;
809	>	double totalMass;
810	>
811	>	//to avoid memory reallocation, reserve enough space for mfact
812	>	mfact.reserve(getNCutoffGroups());
813
814	<	}
814	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
815	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
816
817	<	GenericData* SimInfo::getProperty(const string& propName){
818	<
819	<	map<string, GenericData*>::iterator result;
820	<
821	<	//string lowerCaseName = ();
822	<
823	<	result = properties.find(propName);
824	<
568	<	if(result != properties.end())
569	<	return (*result).second;
570	<	else
571	<	return NULL;
572	<	}
817	>	totalMass = cg->getMass();
818	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
819	>	// Check for massless groups - set mfact to 1 if true
820	>	if (totalMass != 0)
821	>	mfact.push_back(atom->getMass()/totalMass);
822	>	else
823	>	mfact.push_back( 1.0 );
824	>	}
825
826	+	}
827	+	}
828
829	<	void SimInfo::getFortranGroupArrays(SimInfo* info,
830	<	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	<
829	>	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
830	>	std::vector<int> identArray;
831
832	<	// Fix the silly fortran indexing problem
832	>	//to avoid memory reallocation, reserve enough space identArray
833	>	identArray.reserve(getNAtoms());
834	>
835	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
836	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
837	>	identArray.push_back(atom->getIdent());
838	>	}
839	>	}
840	>
841	>	//fill molMembershipArray
842	>	//molMembershipArray is filled by SimCreator
843	>	std::vector<int> molMembershipArray(nGlobalAtoms_);
844	>	for (int i = 0; i < nGlobalAtoms_; i++) {
845	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
846	>	}
847	>
848	>	//setup fortran simulation
849	>	int nGlobalExcludes = 0;
850	>	int* globalExcludes = NULL;
851	>	int* excludeList = exclude_.getExcludeList();
852	>	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
853	>	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
854	>	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
855	>
856	>	if( isError ){
857	>
858	>	sprintf( painCave.errMsg,
859	>	"There was an error setting the simulation information in fortran.\n" );
860	>	painCave.isFatal = 1;
861	>	painCave.severity = OOPSE_ERROR;
862	>	simError();
863	>	}
864	>
865		#ifdef IS_MPI
866	<	numAtom = mpiSim->getNAtomsGlobal();
867	<	#else
868	<	numAtom = n_atoms;
866	>	sprintf( checkPointMsg,
867	>	"succesfully sent the simulation information to fortran.\n");
868	>	MPIcheckPoint();
869	>	#endif // is_mpi
870	>	}
871	>
872	>
873	>	#ifdef IS_MPI
874	>	void SimInfo::setupFortranParallel() {
875	>
876	>	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
877	>	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
878	>	std::vector<int> localToGlobalCutoffGroupIndex;
879	>	SimInfo::MoleculeIterator mi;
880	>	Molecule::AtomIterator ai;
881	>	Molecule::CutoffGroupIterator ci;
882	>	Molecule* mol;
883	>	Atom* atom;
884	>	CutoffGroup* cg;
885	>	mpiSimData parallelData;
886	>	int isError;
887	>
888	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
889	>
890	>	//local index(index in DataStorge) of atom is important
891	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
892	>	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
893	>	}
894	>
895	>	//local index of cutoff group is trivial, it only depends on the order of travesing
896	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
897	>	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
898	>	}
899	>
900	>	}
901	>
902	>	//fill up mpiSimData struct
903	>	parallelData.nMolGlobal = getNGlobalMolecules();
904	>	parallelData.nMolLocal = getNMolecules();
905	>	parallelData.nAtomsGlobal = getNGlobalAtoms();
906	>	parallelData.nAtomsLocal = getNAtoms();
907	>	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
908	>	parallelData.nGroupsLocal = getNCutoffGroups();
909	>	parallelData.myNode = worldRank;
910	>	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
911	>
912	>	//pass mpiSimData struct and index arrays to fortran
913	>	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
914	>	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
915	>	&localToGlobalCutoffGroupIndex[0], &isError);
916	>
917	>	if (isError) {
918	>	sprintf(painCave.errMsg,
919	>	"mpiRefresh errror: fortran didn't like something we gave it.\n");
920	>	painCave.isFatal = 1;
921	>	simError();
922	>	}
923	>
924	>	sprintf(checkPointMsg, " mpiRefresh successful.\n");
925	>	MPIcheckPoint();
926	>
927	>
928	>	}
929	>
930		#endif
602	–	for (int i = 0; i < numAtom; i++)
603	–	FglobalGroupMembership.push_back(globalGroupMembership[i] + 1);
604	–
931
932	<	myMols = info->molecules;
933	<	numMol = info->n_mol;
934	<	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)){
932	>	void SimInfo::setupCutoff() {
933	>
934	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
935
936	<	totalMass = myCutoffGroup->getMass();
937	<
938	<	for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom);
939	<	cutoffAtom != NULL;
940	<	cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
941	<	mfact.push_back(cutoffAtom->getMass()/totalMass);
942	<	}
936	>	// Check the cutoff policy
937	>	int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
938	>
939	>	std::string myPolicy;
940	>	if (forceFieldOptions_.haveCutoffPolicy()){
941	>	myPolicy = forceFieldOptions_.getCutoffPolicy();
942	>	}else if (simParams_->haveCutoffPolicy()) {
943	>	myPolicy = simParams_->getCutoffPolicy();
944		}
945	+
946	+	if (!myPolicy.empty()){
947	+	toUpper(myPolicy);
948	+	if (myPolicy == "MIX") {
949	+	cp = MIX_CUTOFF_POLICY;
950	+	} else {
951	+	if (myPolicy == "MAX") {
952	+	cp = MAX_CUTOFF_POLICY;
953	+	} else {
954	+	if (myPolicy == "TRADITIONAL") {
955	+	cp = TRADITIONAL_CUTOFF_POLICY;
956	+	} else {
957	+	// throw error
958	+	sprintf( painCave.errMsg,
959	+	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
960	+	painCave.isFatal = 1;
961	+	simError();
962	+	}
963	+	}
964	+	}
965	+	}
966	+	notifyFortranCutoffPolicy(&cp);
967	+
968	+	// Check the Skin Thickness for neighborlists
969	+	double skin;
970	+	if (simParams_->haveSkinThickness()) {
971	+	skin = simParams_->getSkinThickness();
972	+	notifyFortranSkinThickness(&skin);
973	+	}
974	+
975	+	// Check if the cutoff was set explicitly:
976	+	if (simParams_->haveCutoffRadius()) {
977	+	rcut_ = simParams_->getCutoffRadius();
978	+	if (simParams_->haveSwitchingRadius()) {
979	+	rsw_  = simParams_->getSwitchingRadius();
980	+	} else {
981	+	if (fInfo_.SIM_uses_Charges |
982	+	fInfo_.SIM_uses_Dipoles |
983	+	fInfo_.SIM_uses_RF) {
984	+
985	+	rsw_ = 0.85 * rcut_;
986	+	sprintf(painCave.errMsg,
987	+	"SimCreator Warning: No value was set for the switchingRadius.\n"
988	+	"\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
989	+	"\tswitchingRadius = %f. for this simulation\n", rsw_);
990	+	painCave.isFatal = 0;
991	+	simError();
992	+	} else {
993	+	rsw_ = rcut_;
994	+	sprintf(painCave.errMsg,
995	+	"SimCreator Warning: No value was set for the switchingRadius.\n"
996	+	"\tOOPSE will use the same value as the cutoffRadius.\n"
997	+	"\tswitchingRadius = %f. for this simulation\n", rsw_);
998	+	painCave.isFatal = 0;
999	+	simError();
1000	+	}
1001	+	}
1002	+
1003	+	notifyFortranCutoffs(&rcut_, &rsw_);
1004	+
1005	+	} else {
1006	+
1007	+	// For electrostatic atoms, we'll assume a large safe value:
1008	+	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1009	+	sprintf(painCave.errMsg,
1010	+	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1011	+	"\tOOPSE will use a default value of 15.0 angstroms"
1012	+	"\tfor the cutoffRadius.\n");
1013	+	painCave.isFatal = 0;
1014	+	simError();
1015	+	rcut_ = 15.0;
1016	+
1017	+	if (simParams_->haveElectrostaticSummationMethod()) {
1018	+	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1019	+	toUpper(myMethod);
1020	+	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1021	+	if (simParams_->haveSwitchingRadius()){
1022	+	sprintf(painCave.errMsg,
1023	+	"SimInfo Warning: A value was set for the switchingRadius\n"
1024	+	"\teven though the electrostaticSummationMethod was\n"
1025	+	"\tset to %s\n", myMethod.c_str());
1026	+	painCave.isFatal = 1;
1027	+	simError();
1028	+	}
1029	+	}
1030	+	}
1031	+
1032	+	if (simParams_->haveSwitchingRadius()){
1033	+	rsw_ = simParams_->getSwitchingRadius();
1034	+	} else {
1035	+	sprintf(painCave.errMsg,
1036	+	"SimCreator Warning: No value was set for switchingRadius.\n"
1037	+	"\tOOPSE will use a default value of\n"
1038	+	"\t0.85 * cutoffRadius for the switchingRadius\n");
1039	+	painCave.isFatal = 0;
1040	+	simError();
1041	+	rsw_ = 0.85 * rcut_;
1042	+	}
1043	+	notifyFortranCutoffs(&rcut_, &rsw_);
1044	+	} else {
1045	+	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1046	+	// We'll punt and let fortran figure out the cutoffs later.
1047	+
1048	+	notifyFortranYouAreOnYourOwn();
1049	+
1050	+	}
1051	+	}
1052		}
1053
1054	<	}
1054	>	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1055	>
1056	>	int errorOut;
1057	>	int esm =  NONE;
1058	>	int sm = UNDAMPED;
1059	>	double alphaVal;
1060	>	double dielectric;
1061	>
1062	>	errorOut = isError;
1063	>	alphaVal = simParams_->getDampingAlpha();
1064	>	dielectric = simParams_->getDielectric();
1065	>
1066	>	if (simParams_->haveElectrostaticSummationMethod()) {
1067	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1068	>	toUpper(myMethod);
1069	>	if (myMethod == "NONE") {
1070	>	esm = NONE;
1071	>	} else {
1072	>	if (myMethod == "SWITCHING_FUNCTION") {
1073	>	esm = SWITCHING_FUNCTION;
1074	>	} else {
1075	>	if (myMethod == "SHIFTED_POTENTIAL") {
1076	>	esm = SHIFTED_POTENTIAL;
1077	>	} else {
1078	>	if (myMethod == "SHIFTED_FORCE") {
1079	>	esm = SHIFTED_FORCE;
1080	>	} else {
1081	>	if (myMethod == "REACTION_FIELD") {
1082	>	esm = REACTION_FIELD;
1083	>	} else {
1084	>	// throw error
1085	>	sprintf( painCave.errMsg,
1086	>	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1087	>	"\t(Input file specified %s .)\n"
1088	>	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1089	>	"\t\"shifted_potential\", \"shifted_force\", or \n"
1090	>	"\t\"reaction_field\".\n", myMethod.c_str() );
1091	>	painCave.isFatal = 1;
1092	>	simError();
1093	>	}
1094	>	}
1095	>	}
1096	>	}
1097	>	}
1098	>	}
1099	>
1100	>	if (simParams_->haveElectrostaticScreeningMethod()) {
1101	>	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1102	>	toUpper(myScreen);
1103	>	if (myScreen == "UNDAMPED") {
1104	>	sm = UNDAMPED;
1105	>	} else {
1106	>	if (myScreen == "DAMPED") {
1107	>	sm = DAMPED;
1108	>	if (!simParams_->haveDampingAlpha()) {
1109	>	//throw error
1110	>	sprintf( painCave.errMsg,
1111	>	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1112	>	"\tA default value of %f (1/ang) will be used.\n", alphaVal);
1113	>	painCave.isFatal = 0;
1114	>	simError();
1115	>	}
1116	>	} else {
1117	>	// throw error
1118	>	sprintf( painCave.errMsg,
1119	>	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1120	>	"\t(Input file specified %s .)\n"
1121	>	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1122	>	"or \"damped\".\n", myScreen.c_str() );
1123	>	painCave.isFatal = 1;
1124	>	simError();
1125	>	}
1126	>	}
1127	>	}
1128	>
1129	>	// let's pass some summation method variables to fortran
1130	>	setElectrostaticSummationMethod( &esm );
1131	>	setFortranElectrostaticMethod( &esm );
1132	>	setScreeningMethod( &sm );
1133	>	setDampingAlpha( &alphaVal );
1134	>	setReactionFieldDielectric( &dielectric );
1135	>	initFortranFF( &errorOut );
1136	>	}
1137	>
1138	>	void SimInfo::setupSwitchingFunction() {
1139	>	int ft = CUBIC;
1140	>
1141	>	if (simParams_->haveSwitchingFunctionType()) {
1142	>	std::string funcType = simParams_->getSwitchingFunctionType();
1143	>	toUpper(funcType);
1144	>	if (funcType == "CUBIC") {
1145	>	ft = CUBIC;
1146	>	} else {
1147	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1148	>	ft = FIFTH_ORDER_POLY;
1149	>	} else {
1150	>	// throw error
1151	>	sprintf( painCave.errMsg,
1152	>	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1153	>	painCave.isFatal = 1;
1154	>	simError();
1155	>	}
1156	>	}
1157	>	}
1158	>
1159	>	// send switching function notification to switcheroo
1160	>	setFunctionType(&ft);
1161	>
1162	>	}
1163	>
1164	>	void SimInfo::addProperty(GenericData* genData) {
1165	>	properties_.addProperty(genData);
1166	>	}
1167	>
1168	>	void SimInfo::removeProperty(const std::string& propName) {
1169	>	properties_.removeProperty(propName);
1170	>	}
1171	>
1172	>	void SimInfo::clearProperties() {
1173	>	properties_.clearProperties();
1174	>	}
1175	>
1176	>	std::vector<std::string> SimInfo::getPropertyNames() {
1177	>	return properties_.getPropertyNames();
1178	>	}
1179	>
1180	>	std::vector<GenericData*> SimInfo::getProperties() {
1181	>	return properties_.getProperties();
1182	>	}
1183	>
1184	>	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1185	>	return properties_.getPropertyByName(propName);
1186	>	}
1187	>
1188	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1189	>	if (sman_ == sman) {
1190	>	return;
1191	>	}
1192	>	delete sman_;
1193	>	sman_ = sman;
1194	>
1195	>	Molecule* mol;
1196	>	RigidBody* rb;
1197	>	Atom* atom;
1198	>	SimInfo::MoleculeIterator mi;
1199	>	Molecule::RigidBodyIterator rbIter;
1200	>	Molecule::AtomIterator atomIter;;
1201	>
1202	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1203	>
1204	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1205	>	atom->setSnapshotManager(sman_);
1206	>	}
1207	>
1208	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1209	>	rb->setSnapshotManager(sman_);
1210	>	}
1211	>	}
1212	>
1213	>	}
1214	>
1215	>	Vector3d SimInfo::getComVel(){
1216	>	SimInfo::MoleculeIterator i;
1217	>	Molecule* mol;
1218	>
1219	>	Vector3d comVel(0.0);
1220	>	double totalMass = 0.0;
1221	>
1222	>
1223	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1224	>	double mass = mol->getMass();
1225	>	totalMass += mass;
1226	>	comVel += mass * mol->getComVel();
1227	>	}
1228	>
1229	>	#ifdef IS_MPI
1230	>	double tmpMass = totalMass;
1231	>	Vector3d tmpComVel(comVel);
1232	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1233	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1234	>	#endif
1235	>
1236	>	comVel /= totalMass;
1237	>
1238	>	return comVel;
1239	>	}
1240	>
1241	>	Vector3d SimInfo::getCom(){
1242	>	SimInfo::MoleculeIterator i;
1243	>	Molecule* mol;
1244	>
1245	>	Vector3d com(0.0);
1246	>	double totalMass = 0.0;
1247	>
1248	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1249	>	double mass = mol->getMass();
1250	>	totalMass += mass;
1251	>	com += mass * mol->getCom();
1252	>	}
1253	>
1254	>	#ifdef IS_MPI
1255	>	double tmpMass = totalMass;
1256	>	Vector3d tmpCom(com);
1257	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1258	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1259	>	#endif
1260	>
1261	>	com /= totalMass;
1262	>
1263	>	return com;
1264	>
1265	>	}
1266	>
1267	>	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1268	>
1269	>	return o;
1270	>	}
1271	>
1272	>
1273	>	/*
1274	>	Returns center of mass and center of mass velocity in one function call.
1275	>	*/
1276	>
1277	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1278	>	SimInfo::MoleculeIterator i;
1279	>	Molecule* mol;
1280	>
1281	>
1282	>	double totalMass = 0.0;
1283	>
1284	>
1285	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1286	>	double mass = mol->getMass();
1287	>	totalMass += mass;
1288	>	com += mass * mol->getCom();
1289	>	comVel += mass * mol->getComVel();
1290	>	}
1291	>
1292	>	#ifdef IS_MPI
1293	>	double tmpMass = totalMass;
1294	>	Vector3d tmpCom(com);
1295	>	Vector3d tmpComVel(comVel);
1296	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1297	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1298	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1299	>	#endif
1300	>
1301	>	com /= totalMass;
1302	>	comVel /= totalMass;
1303	>	}
1304	>
1305	>	/*
1306	>	Return intertia tensor for entire system and angular momentum Vector.
1307	>
1308	>
1309	>	[  Ixx -Ixy  -Ixz ]
1310	>	J =| -Iyx  Iyy  -Iyz |
1311	>	[ -Izx -Iyz   Izz ]
1312	>	*/
1313	>
1314	>	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1315	>
1316	>
1317	>	double xx = 0.0;
1318	>	double yy = 0.0;
1319	>	double zz = 0.0;
1320	>	double xy = 0.0;
1321	>	double xz = 0.0;
1322	>	double yz = 0.0;
1323	>	Vector3d com(0.0);
1324	>	Vector3d comVel(0.0);
1325	>
1326	>	getComAll(com, comVel);
1327	>
1328	>	SimInfo::MoleculeIterator i;
1329	>	Molecule* mol;
1330	>
1331	>	Vector3d thisq(0.0);
1332	>	Vector3d thisv(0.0);
1333	>
1334	>	double thisMass = 0.0;
1335	>
1336	>
1337	>
1338	>
1339	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1340	>
1341	>	thisq = mol->getCom()-com;
1342	>	thisv = mol->getComVel()-comVel;
1343	>	thisMass = mol->getMass();
1344	>	// Compute moment of intertia coefficients.
1345	>	xx += thisq[0]*thisq[0]*thisMass;
1346	>	yy += thisq[1]*thisq[1]*thisMass;
1347	>	zz += thisq[2]*thisq[2]*thisMass;
1348	>
1349	>	// compute products of intertia
1350	>	xy += thisq[0]*thisq[1]*thisMass;
1351	>	xz += thisq[0]*thisq[2]*thisMass;
1352	>	yz += thisq[1]*thisq[2]*thisMass;
1353	>
1354	>	angularMomentum += cross( thisq, thisv ) * thisMass;
1355	>
1356	>	}
1357	>
1358	>
1359	>	inertiaTensor(0,0) = yy + zz;
1360	>	inertiaTensor(0,1) = -xy;
1361	>	inertiaTensor(0,2) = -xz;
1362	>	inertiaTensor(1,0) = -xy;
1363	>	inertiaTensor(1,1) = xx + zz;
1364	>	inertiaTensor(1,2) = -yz;
1365	>	inertiaTensor(2,0) = -xz;
1366	>	inertiaTensor(2,1) = -yz;
1367	>	inertiaTensor(2,2) = xx + yy;
1368	>
1369	>	#ifdef IS_MPI
1370	>	Mat3x3d tmpI(inertiaTensor);
1371	>	Vector3d tmpAngMom;
1372	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1373	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1374	>	#endif
1375	>
1376	>	return;
1377	>	}
1378	>
1379	>	//Returns the angular momentum of the system
1380	>	Vector3d SimInfo::getAngularMomentum(){
1381	>
1382	>	Vector3d com(0.0);
1383	>	Vector3d comVel(0.0);
1384	>	Vector3d angularMomentum(0.0);
1385	>
1386	>	getComAll(com,comVel);
1387	>
1388	>	SimInfo::MoleculeIterator i;
1389	>	Molecule* mol;
1390	>
1391	>	Vector3d thisr(0.0);
1392	>	Vector3d thisp(0.0);
1393	>
1394	>	double thisMass;
1395	>
1396	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1397	>	thisMass = mol->getMass();
1398	>	thisr = mol->getCom()-com;
1399	>	thisp = (mol->getComVel()-comVel)*thisMass;
1400	>
1401	>	angularMomentum += cross( thisr, thisp );
1402	>
1403	>	}
1404	>
1405	>	#ifdef IS_MPI
1406	>	Vector3d tmpAngMom;
1407	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1408	>	#endif
1409	>
1410	>	return angularMomentum;
1411	>	}
1412	>
1413	>
1414	>	}//end namespace oopse
1415	>

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