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Comparing trunk/OOPSE-2.0/src/brains/SimInfo.cpp (file contents):
Revision 1617 by chuckv, Wed Oct 20 20:46:20 2004 UTC vs.
Revision 2448 by tim, Wed Nov 16 23:10:02 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"
56	<	#include "utils/simError.h"
57	<	#include "UseTheForce/DarkSide/simulation_interface.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/notifyCutoffs_interface.h"
63	+	#include "UseTheForce/DarkSide/switcheroo_interface.h"
64	+	#include "utils/MemoryUtils.hpp"
65	+	#include "utils/simError.h"
66	+	#include "selection/SelectionManager.hpp"
67
15	–	//#include "UseTheForce/fortranWrappers.hpp"
16	–
17	–	#include "math/MatVec3.h"
18	–
68		#ifdef IS_MPI
69	<	#include "brains/mpiSimulation.hpp"
70	<	#endif
69	>	#include "UseTheForce/mpiComponentPlan.h"
70	>	#include "UseTheForce/DarkSide/simParallel_interface.h"
71	>	#endif
72
73	<	inline double roundMe( double x ){
74	<	return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
75	<	}
76	<
77	<	inline double min( double a, double b ){
78	<	return (a < b ) ? a : b;
79	<	}
73	>	namespace oopse {
74	>	std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
75	>	std::map<int, std::set<int> >::iterator i = container.find(index);
76	>	std::set<int> result;
77	>	if (i != container.end()) {
78	>	result = i->second;
79	>	}
80
81	<	SimInfo* currentInfo;
82	<
33	<	SimInfo::SimInfo(){
34	<
35	<	n_constraints = 0;
36	<	nZconstraints = 0;
37	<	n_oriented = 0;
38	<	n_dipoles = 0;
39	<	ndf = 0;
40	<	ndfRaw = 0;
41	<	nZconstraints = 0;
42	<	the_integrator = NULL;
43	<	setTemp = 0;
44	<	thermalTime = 0.0;
45	<	currentTime = 0.0;
46	<	rCut = 0.0;
47	<	rSw = 0.0;
48	<
49	<	haveRcut = 0;
50	<	haveRsw = 0;
51	<	boxIsInit = 0;
81	>	return result;
82	>	}
83
84	<	resetTime = 1e99;
84	>	SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
85	>	ForceField* ff, Globals* simParams) :
86	>	stamps_(stamps), 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	>
95	>	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
96	>	MoleculeStamp* molStamp;
97	>	int nMolWithSameStamp;
98	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
99	>	int nGroups = 0;      //total cutoff groups defined in meta-data file
100	>	CutoffGroupStamp* cgStamp;
101	>	RigidBodyStamp* rbStamp;
102	>	int nRigidAtoms = 0;
103	>
104	>	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
105	>	molStamp = i->first;
106	>	nMolWithSameStamp = i->second;
107	>
108	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
109
110	<	usePBC = 0;
111	<	useLJ = 0;
61	<	useSticky = 0;
62	<	useCharges = 0;
63	<	useDipoles = 0;
64	<	useReactionField = 0;
65	<	useGB = 0;
66	<	useEAM = 0;
67	<	useSolidThermInt = 0;
68	<	useLiquidThermInt = 0;
110	>	//calculate atoms in molecules
111	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
112
70	–	haveCutoffGroups = false;
113
114	<	excludes = Exclude::Instance();
114	>	//calculate atoms in cutoff groups
115	>	int nAtomsInGroups = 0;
116	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
117	>
118	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
119	>	cgStamp = molStamp->getCutoffGroup(j);
120	>	nAtomsInGroups += cgStamp->getNMembers();
121	>	}
122
123	<	myConfiguration = new SimState();
123	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
124
125	<	has_minimizer = false;
77	<	the_minimizer =NULL;
125	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
126
127	<	ngroup = 0;
127	>	//calculate atoms in rigid bodies
128	>	int nAtomsInRigidBodies = 0;
129	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
130	>
131	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
132	>	rbStamp = molStamp->getRigidBody(j);
133	>	nAtomsInRigidBodies += rbStamp->getNMembers();
134	>	}
135
136	<	}
136	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
137	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
138	>
139	>	}
140
141	+	//every free atom (atom does not belong to cutoff groups) is a cutoff
142	+	//group therefore the total number of cutoff groups in the system is
143	+	//equal to the total number of atoms minus number of atoms belong to
144	+	//cutoff group defined in meta-data file plus the number of cutoff
145	+	//groups defined in meta-data file
146	+	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
147
148	<	SimInfo::~SimInfo(){
149	<
150	<	delete myConfiguration;
151	<
152	<	map<string, GenericData*>::iterator i;
148	>	//every free atom (atom does not belong to rigid bodies) is an
149	>	//integrable object therefore the total number of integrable objects
150	>	//in the system is equal to the total number of atoms minus number of
151	>	//atoms belong to rigid body defined in meta-data file plus the number
152	>	//of rigid bodies defined in meta-data file
153	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
154	>	+ nGlobalRigidBodies_;
155
156	<	for(i = properties.begin(); i != properties.end(); i++)
91	<	delete (*i).second;
156	>	nGlobalMols_ = molStampIds_.size();
157
158	<	}
158	>	#ifdef IS_MPI
159	>	molToProcMap_.resize(nGlobalMols_);
160	>	#endif
161
162	<	void SimInfo::setBox(double newBox[3]) {
96	<
97	<	int i, j;
98	<	double tempMat[3][3];
162	>	}
163
164	<	for(i=0; i<3; i++)
165	<	for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
164	>	SimInfo::~SimInfo() {
165	>	std::map<int, Molecule*>::iterator i;
166	>	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
167	>	delete i->second;
168	>	}
169	>	molecules_.clear();
170	>
171	>	delete stamps_;
172	>	delete sman_;
173	>	delete simParams_;
174	>	delete forceField_;
175	>	}
176
177	<	tempMat[0][0] = newBox[0];
178	<	tempMat[1][1] = newBox[1];
179	<	tempMat[2][2] = newBox[2];
177	>	int SimInfo::getNGlobalConstraints() {
178	>	int nGlobalConstraints;
179	>	#ifdef IS_MPI
180	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
181	>	MPI_COMM_WORLD);
182	>	#else
183	>	nGlobalConstraints =  nConstraints_;
184	>	#endif
185	>	return nGlobalConstraints;
186	>	}
187
188	<	setBoxM( tempMat );
188	>	bool SimInfo::addMolecule(Molecule* mol) {
189	>	MoleculeIterator i;
190
191	<	}
191	>	i = molecules_.find(mol->getGlobalIndex());
192	>	if (i == molecules_.end() ) {
193
194	<	void SimInfo::setBoxM( double theBox[3][3] ){
195	<
196	<	int i, j;
197	<	double FortranHmat[9]; // to preserve compatibility with Fortran the
198	<	// ordering in the array is as follows:
199	<	// [ 0 3 6 ]
200	<	// [ 1 4 7 ]
201	<	// [ 2 5 8 ]
202	<	double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
203	<
121	<	if( !boxIsInit ) boxIsInit = 1;
194	>	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
195	>
196	>	nAtoms_ += mol->getNAtoms();
197	>	nBonds_ += mol->getNBonds();
198	>	nBends_ += mol->getNBends();
199	>	nTorsions_ += mol->getNTorsions();
200	>	nRigidBodies_ += mol->getNRigidBodies();
201	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
202	>	nCutoffGroups_ += mol->getNCutoffGroups();
203	>	nConstraints_ += mol->getNConstraintPairs();
204
205	<	for(i=0; i < 3; i++)
206	<	for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
207	<
208	<	calcBoxL();
209	<	calcHmatInv();
128	<
129	<	for(i=0; i < 3; i++) {
130	<	for (j=0; j < 3; j++) {
131	<	FortranHmat[3*j + i] = Hmat[i][j];
132	<	FortranHmatInv[3*j + i] = HmatInv[i][j];
205	>	addExcludePairs(mol);
206	>
207	>	return true;
208	>	} else {
209	>	return false;
210		}
211		}
212
213	<	setFortranBox(FortranHmat, FortranHmatInv, &orthoRhombic);
214	<
215	<	}
139	<
213	>	bool SimInfo::removeMolecule(Molecule* mol) {
214	>	MoleculeIterator i;
215	>	i = molecules_.find(mol->getGlobalIndex());
216
217	<	void SimInfo::getBoxM (double theBox[3][3]) {
217	>	if (i != molecules_.end() ) {
218
219	<	int i, j;
220	<	for(i=0; i<3; i++)
221	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
222	<	}
219	>	assert(mol == i->second);
220	>
221	>	nAtoms_ -= mol->getNAtoms();
222	>	nBonds_ -= mol->getNBonds();
223	>	nBends_ -= mol->getNBends();
224	>	nTorsions_ -= mol->getNTorsions();
225	>	nRigidBodies_ -= mol->getNRigidBodies();
226	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
227	>	nCutoffGroups_ -= mol->getNCutoffGroups();
228	>	nConstraints_ -= mol->getNConstraintPairs();
229
230	+	removeExcludePairs(mol);
231	+	molecules_.erase(mol->getGlobalIndex());
232
233	<	void SimInfo::scaleBox(double scale) {
234	<	double theBox[3][3];
235	<	int i, j;
233	>	delete mol;
234	>
235	>	return true;
236	>	} else {
237	>	return false;
238	>	}
239
153	–	// cerr << "Scaling box by " << scale << "\n";
240
241	<	for(i=0; i<3; i++)
156	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
241	>	}
242
243	<	setBoxM(theBox);
243	>
244	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
245	>	i = molecules_.begin();
246	>	return i == molecules_.end() ? NULL : i->second;
247	>	}
248
249	<	}
249	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
250	>	++i;
251	>	return i == molecules_.end() ? NULL : i->second;
252	>	}
253
162	–	void SimInfo::calcHmatInv( void ) {
163	–
164	–	int oldOrtho;
165	–	int i,j;
166	–	double smallDiag;
167	–	double tol;
168	–	double sanity[3][3];
254
255	<	invertMat3( Hmat, HmatInv );
255	>	void SimInfo::calcNdf() {
256	>	int ndf_local;
257	>	MoleculeIterator i;
258	>	std::vector<StuntDouble*>::iterator j;
259	>	Molecule* mol;
260	>	StuntDouble* integrableObject;
261
262	<	// check to see if Hmat is orthorhombic
263	<
264	<	oldOrtho = orthoRhombic;
262	>	ndf_local = 0;
263	>
264	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
265	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
266	>	integrableObject = mol->nextIntegrableObject(j)) {
267
268	<	smallDiag = fabs(Hmat[0][0]);
177	<	if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
178	<	if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
179	<	tol = smallDiag * orthoTolerance;
268	>	ndf_local += 3;
269
270	<	orthoRhombic = 1;
271	<
272	<	for (i = 0; i < 3; i++ ) {
273	<	for (j = 0 ; j < 3; j++) {
274	<	if (i != j) {
275	<	if (orthoRhombic) {
276	<	if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
277	<	}
278	<	}
279	<	}
191	<	}
192	<
193	<	if( oldOrtho != orthoRhombic ){
270	>	if (integrableObject->isDirectional()) {
271	>	if (integrableObject->isLinear()) {
272	>	ndf_local += 2;
273	>	} else {
274	>	ndf_local += 3;
275	>	}
276	>	}
277	>
278	>	}//end for (integrableObject)
279	>	}// end for (mol)
280
281	<	if( orthoRhombic ) {
282	<	sprintf( painCave.errMsg,
197	<	"OOPSE is switching from the default Non-Orthorhombic\n"
198	<	"\tto the faster Orthorhombic periodic boundary computations.\n"
199	<	"\tThis is usually a good thing, but if you wan't the\n"
200	<	"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
201	<	"\tvariable ( currently set to %G ) smaller.\n",
202	<	orthoTolerance);
203	<	painCave.severity = OOPSE_INFO;
204	<	simError();
205	<	}
206	<	else {
207	<	sprintf( painCave.errMsg,
208	<	"OOPSE is switching from the faster Orthorhombic to the more\n"
209	<	"\tflexible Non-Orthorhombic periodic boundary computations.\n"
210	<	"\tThis is usually because the box has deformed under\n"
211	<	"\tNPTf integration. If you wan't to live on the edge with\n"
212	<	"\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
213	<	"\tvariable ( currently set to %G ) larger.\n",
214	<	orthoTolerance);
215	<	painCave.severity = OOPSE_WARNING;
216	<	simError();
217	<	}
218	<	}
219	<	}
281	>	// n_constraints is local, so subtract them on each processor
282	>	ndf_local -= nConstraints_;
283
284	<	void SimInfo::calcBoxL( void ){
284	>	#ifdef IS_MPI
285	>	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
286	>	#else
287	>	ndf_ = ndf_local;
288	>	#endif
289
290	<	double dx, dy, dz, dsq;
290	>	// nZconstraints_ is global, as are the 3 COM translations for the
291	>	// entire system:
292	>	ndf_ = ndf_ - 3 - nZconstraint_;
293
294	<	// boxVol = Determinant of Hmat
294	>	}
295
296	<	boxVol = matDet3( Hmat );
296	>	void SimInfo::calcNdfRaw() {
297	>	int ndfRaw_local;
298
299	<	// boxLx
300	<
301	<	dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
302	<	dsq = dx*dx + dy*dy + dz*dz;
233	<	boxL[0] = sqrt( dsq );
234	<	//maxCutoff = 0.5 * boxL[0];
299	>	MoleculeIterator i;
300	>	std::vector<StuntDouble*>::iterator j;
301	>	Molecule* mol;
302	>	StuntDouble* integrableObject;
303
304	<	// boxLy
305	<
238	<	dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
239	<	dsq = dx*dx + dy*dy + dz*dz;
240	<	boxL[1] = sqrt( dsq );
241	<	//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
242	<
243	<
244	<	// boxLz
245	<
246	<	dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
247	<	dsq = dx*dx + dy*dy + dz*dz;
248	<	boxL[2] = sqrt( dsq );
249	<	//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
250	<
251	<	//calculate the max cutoff
252	<	maxCutoff =  calcMaxCutOff();
253	<
254	<	checkCutOffs();
255	<
256	<	}
257	<
258	<
259	<	double SimInfo::calcMaxCutOff(){
260	<
261	<	double ri[3], rj[3], rk[3];
262	<	double rij[3], rjk[3], rki[3];
263	<	double minDist;
264	<
265	<	ri[0] = Hmat[0][0];
266	<	ri[1] = Hmat[1][0];
267	<	ri[2] = Hmat[2][0];
268	<
269	<	rj[0] = Hmat[0][1];
270	<	rj[1] = Hmat[1][1];
271	<	rj[2] = Hmat[2][1];
272	<
273	<	rk[0] = Hmat[0][2];
274	<	rk[1] = Hmat[1][2];
275	<	rk[2] = Hmat[2][2];
304	>	// Raw degrees of freedom that we have to set
305	>	ndfRaw_local = 0;
306
307	<	crossProduct3(ri, rj, rij);
308	<	distXY = dotProduct3(rk,rij) / norm3(rij);
307	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
308	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
309	>	integrableObject = mol->nextIntegrableObject(j)) {
310
311	<	crossProduct3(rj,rk, rjk);
281	<	distYZ = dotProduct3(ri,rjk) / norm3(rjk);
311	>	ndfRaw_local += 3;
312
313	<	crossProduct3(rk,ri, rki);
314	<	distZX = dotProduct3(rj,rki) / norm3(rki);
315	<
316	<	minDist = min(min(distXY, distYZ), distZX);
317	<	return minDist/2;
318	<
319	<	}
320	<
321	<	void SimInfo::wrapVector( double thePos[3] ){
322	<
293	<	int i;
294	<	double scaled[3];
295	<
296	<	if( !orthoRhombic ){
297	<	// calc the scaled coordinates.
298	<
299	<
300	<	matVecMul3(HmatInv, thePos, scaled);
313	>	if (integrableObject->isDirectional()) {
314	>	if (integrableObject->isLinear()) {
315	>	ndfRaw_local += 2;
316	>	} else {
317	>	ndfRaw_local += 3;
318	>	}
319	>	}
320	>
321	>	}
322	>	}
323
324	<	for(i=0; i<3; i++)
325	<	scaled[i] -= roundMe(scaled[i]);
326	<
327	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
328	<
307	<	matVecMul3(Hmat, scaled, thePos);
308	<
324	>	#ifdef IS_MPI
325	>	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
326	>	#else
327	>	ndfRaw_ = ndfRaw_local;
328	>	#endif
329		}
310	–	else{
311	–	// calc the scaled coordinates.
312	–
313	–	for(i=0; i<3; i++)
314	–	scaled[i] = thePos[i]*HmatInv[i][i];
315	–
316	–	// wrap the scaled coordinates
317	–
318	–	for(i=0; i<3; i++)
319	–	scaled[i] -= roundMe(scaled[i]);
320	–
321	–	// calc the wrapped real coordinates from the wrapped scaled coordinates
322	–
323	–	for(i=0; i<3; i++)
324	–	thePos[i] = scaled[i]*Hmat[i][i];
325	–	}
326	–
327	–	}
330
331	+	void SimInfo::calcNdfTrans() {
332	+	int ndfTrans_local;
333
334	<	int SimInfo::getNDF(){
331	<	int ndf_local;
334	>	ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
335
333	–	ndf_local = 0;
334	–
335	–	for(int i = 0; i < integrableObjects.size(); i++){
336	–	ndf_local += 3;
337	–	if (integrableObjects[i]->isDirectional()) {
338	–	if (integrableObjects[i]->isLinear())
339	–	ndf_local += 2;
340	–	else
341	–	ndf_local += 3;
342	–	}
343	–	}
336
345	–	// n_constraints is local, so subtract them on each processor:
346	–
347	–	ndf_local -= n_constraints;
348	–
337		#ifdef IS_MPI
338	<	MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
338	>	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
339		#else
340	<	ndf = ndf_local;
340	>	ndfTrans_ = ndfTrans_local;
341		#endif
342
343	<	// nZconstraints is global, as are the 3 COM translations for the
344	<	// entire system:
343	>	ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
344	>
345	>	}
346
347	<	ndf = ndf - 3 - nZconstraints;
347	>	void SimInfo::addExcludePairs(Molecule* mol) {
348	>	std::vector<Bond*>::iterator bondIter;
349	>	std::vector<Bend*>::iterator bendIter;
350	>	std::vector<Torsion*>::iterator torsionIter;
351	>	Bond* bond;
352	>	Bend* bend;
353	>	Torsion* torsion;
354	>	int a;
355	>	int b;
356	>	int c;
357	>	int d;
358
359	<	return ndf;
361	<	}
359	>	std::map<int, std::set<int> > atomGroups;
360
361	<	int SimInfo::getNDFraw() {
362	<	int ndfRaw_local;
361	>	Molecule::RigidBodyIterator rbIter;
362	>	RigidBody* rb;
363	>	Molecule::IntegrableObjectIterator ii;
364	>	StuntDouble* integrableObject;
365	>
366	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
367	>	integrableObject = mol->nextIntegrableObject(ii)) {
368
369	<	// Raw degrees of freedom that we have to set
370	<	ndfRaw_local = 0;
369	>	if (integrableObject->isRigidBody()) {
370	>	rb = static_cast<RigidBody*>(integrableObject);
371	>	std::vector<Atom*> atoms = rb->getAtoms();
372	>	std::set<int> rigidAtoms;
373	>	for (int i = 0; i < atoms.size(); ++i) {
374	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
375	>	}
376	>	for (int i = 0; i < atoms.size(); ++i) {
377	>	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
378	>	}
379	>	} else {
380	>	std::set<int> oneAtomSet;
381	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
382	>	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
383	>	}
384	>	}
385
369	–	for(int i = 0; i < integrableObjects.size(); i++){
370	–	ndfRaw_local += 3;
371	–	if (integrableObjects[i]->isDirectional()) {
372	–	if (integrableObjects[i]->isLinear())
373	–	ndfRaw_local += 2;
374	–	else
375	–	ndfRaw_local += 3;
376	–	}
377	–	}
386
387	<	#ifdef IS_MPI
388	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
389	<	#else
390	<	ndfRaw = ndfRaw_local;
391	<	#endif
387	>
388	>	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
389	>	a = bond->getAtomA()->getGlobalIndex();
390	>	b = bond->getAtomB()->getGlobalIndex();
391	>	exclude_.addPair(a, b);
392	>	}
393
394	<	return ndfRaw;
395	<	}
394	>	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
395	>	a = bend->getAtomA()->getGlobalIndex();
396	>	b = bend->getAtomB()->getGlobalIndex();
397	>	c = bend->getAtomC()->getGlobalIndex();
398	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
399	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
400	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
401
402	<	int SimInfo::getNDFtranslational() {
403	<	int ndfTrans_local;
402	>	exclude_.addPairs(rigidSetA, rigidSetB);
403	>	exclude_.addPairs(rigidSetA, rigidSetC);
404	>	exclude_.addPairs(rigidSetB, rigidSetC);
405	>
406	>	//exclude_.addPair(a, b);
407	>	//exclude_.addPair(a, c);
408	>	//exclude_.addPair(b, c);
409	>	}
410
411	<	ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
411	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
412	>	a = torsion->getAtomA()->getGlobalIndex();
413	>	b = torsion->getAtomB()->getGlobalIndex();
414	>	c = torsion->getAtomC()->getGlobalIndex();
415	>	d = torsion->getAtomD()->getGlobalIndex();
416	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
417	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
418	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
419	>	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
420
421	+	exclude_.addPairs(rigidSetA, rigidSetB);
422	+	exclude_.addPairs(rigidSetA, rigidSetC);
423	+	exclude_.addPairs(rigidSetA, rigidSetD);
424	+	exclude_.addPairs(rigidSetB, rigidSetC);
425	+	exclude_.addPairs(rigidSetB, rigidSetD);
426	+	exclude_.addPairs(rigidSetC, rigidSetD);
427
428	<	#ifdef IS_MPI
429	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
430	<	#else
431	<	ndfTrans = ndfTrans_local;
432	<	#endif
428	>	/*
429	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
430	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
431	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
432	>	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
433	>	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
434	>	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
435	>
436	>
437	>	exclude_.addPair(a, b);
438	>	exclude_.addPair(a, c);
439	>	exclude_.addPair(a, d);
440	>	exclude_.addPair(b, c);
441	>	exclude_.addPair(b, d);
442	>	exclude_.addPair(c, d);
443	>	*/
444	>	}
445
446	<	ndfTrans = ndfTrans - 3 - nZconstraints;
446	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
447	>	std::vector<Atom*> atoms = rb->getAtoms();
448	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
449	>	for (int j = i + 1; j < atoms.size(); ++j) {
450	>	a = atoms[i]->getGlobalIndex();
451	>	b = atoms[j]->getGlobalIndex();
452	>	exclude_.addPair(a, b);
453	>	}
454	>	}
455	>	}
456
457	<	return ndfTrans;
403	<	}
457	>	}
458
459	<	int SimInfo::getTotIntegrableObjects() {
460	<	int nObjs_local;
461	<	int nObjs;
462	<
463	<	nObjs_local =  integrableObjects.size();
459	>	void SimInfo::removeExcludePairs(Molecule* mol) {
460	>	std::vector<Bond*>::iterator bondIter;
461	>	std::vector<Bend*>::iterator bendIter;
462	>	std::vector<Torsion*>::iterator torsionIter;
463	>	Bond* bond;
464	>	Bend* bend;
465	>	Torsion* torsion;
466	>	int a;
467	>	int b;
468	>	int c;
469	>	int d;
470
471	+	std::map<int, std::set<int> > atomGroups;
472
473	+	Molecule::RigidBodyIterator rbIter;
474	+	RigidBody* rb;
475	+	Molecule::IntegrableObjectIterator ii;
476	+	StuntDouble* integrableObject;
477	+
478	+	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
479	+	integrableObject = mol->nextIntegrableObject(ii)) {
480	+
481	+	if (integrableObject->isRigidBody()) {
482	+	rb = static_cast<RigidBody*>(integrableObject);
483	+	std::vector<Atom*> atoms = rb->getAtoms();
484	+	std::set<int> rigidAtoms;
485	+	for (int i = 0; i < atoms.size(); ++i) {
486	+	rigidAtoms.insert(atoms[i]->getGlobalIndex());
487	+	}
488	+	for (int i = 0; i < atoms.size(); ++i) {
489	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
490	+	}
491	+	} else {
492	+	std::set<int> oneAtomSet;
493	+	oneAtomSet.insert(integrableObject->getGlobalIndex());
494	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
495	+	}
496	+	}
497	+
498	+
499	+	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
500	+	a = bond->getAtomA()->getGlobalIndex();
501	+	b = bond->getAtomB()->getGlobalIndex();
502	+	exclude_.removePair(a, b);
503	+	}
504	+
505	+	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
506	+	a = bend->getAtomA()->getGlobalIndex();
507	+	b = bend->getAtomB()->getGlobalIndex();
508	+	c = bend->getAtomC()->getGlobalIndex();
509	+
510	+	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
511	+	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
512	+	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
513	+
514	+	exclude_.removePairs(rigidSetA, rigidSetB);
515	+	exclude_.removePairs(rigidSetA, rigidSetC);
516	+	exclude_.removePairs(rigidSetB, rigidSetC);
517	+
518	+	//exclude_.removePair(a, b);
519	+	//exclude_.removePair(a, c);
520	+	//exclude_.removePair(b, c);
521	+	}
522	+
523	+	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
524	+	a = torsion->getAtomA()->getGlobalIndex();
525	+	b = torsion->getAtomB()->getGlobalIndex();
526	+	c = torsion->getAtomC()->getGlobalIndex();
527	+	d = torsion->getAtomD()->getGlobalIndex();
528	+
529	+	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
530	+	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
531	+	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
532	+	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
533	+
534	+	exclude_.removePairs(rigidSetA, rigidSetB);
535	+	exclude_.removePairs(rigidSetA, rigidSetC);
536	+	exclude_.removePairs(rigidSetA, rigidSetD);
537	+	exclude_.removePairs(rigidSetB, rigidSetC);
538	+	exclude_.removePairs(rigidSetB, rigidSetD);
539	+	exclude_.removePairs(rigidSetC, rigidSetD);
540	+
541	+	/*
542	+	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
543	+	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
544	+	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
545	+	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
546	+	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
547	+	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
548	+
549	+
550	+	exclude_.removePair(a, b);
551	+	exclude_.removePair(a, c);
552	+	exclude_.removePair(a, d);
553	+	exclude_.removePair(b, c);
554	+	exclude_.removePair(b, d);
555	+	exclude_.removePair(c, d);
556	+	*/
557	+	}
558	+
559	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
560	+	std::vector<Atom*> atoms = rb->getAtoms();
561	+	for (int i = 0; i < atoms.size() -1 ; ++i) {
562	+	for (int j = i + 1; j < atoms.size(); ++j) {
563	+	a = atoms[i]->getGlobalIndex();
564	+	b = atoms[j]->getGlobalIndex();
565	+	exclude_.removePair(a, b);
566	+	}
567	+	}
568	+	}
569	+
570	+	}
571	+
572	+
573	+	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
574	+	int curStampId;
575	+
576	+	//index from 0
577	+	curStampId = moleculeStamps_.size();
578	+
579	+	moleculeStamps_.push_back(molStamp);
580	+	molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
581	+	}
582	+
583	+	void SimInfo::update() {
584	+
585	+	setupSimType();
586	+
587		#ifdef IS_MPI
588	<	MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
414	<	#else
415	<	nObjs = nObjs_local;
588	>	setupFortranParallel();
589		#endif
590
591	+	setupFortranSim();
592
593	<	return nObjs;
594	<	}
593	>	//setup fortran force field
594	>	/** @deprecate */
595	>	int isError = 0;
596	>
597	>	setupElectrostaticSummationMethod( isError );
598	>	setupSwitchingFunction();
599
600	<	void SimInfo::refreshSim(){
600	>	if(isError){
601	>	sprintf( painCave.errMsg,
602	>	"ForceField error: There was an error initializing the forceField in fortran.\n" );
603	>	painCave.isFatal = 1;
604	>	simError();
605	>	}
606	>
607	>
608	>	setupCutoff();
609
610	<	simtype fInfo;
611	<	int isError;
612	<	int n_global;
427	<	int* excl;
610	>	calcNdf();
611	>	calcNdfRaw();
612	>	calcNdfTrans();
613
614	<	fInfo.dielect = 0.0;
614	>	fortranInitialized_ = true;
615	>	}
616
617	<	if( useDipoles ){
618	<	if( useReactionField )fInfo.dielect = dielectric;
617	>	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
618	>	SimInfo::MoleculeIterator mi;
619	>	Molecule* mol;
620	>	Molecule::AtomIterator ai;
621	>	Atom* atom;
622	>	std::set<AtomType*> atomTypes;
623	>
624	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
625	>
626	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
627	>	atomTypes.insert(atom->getAtomType());
628	>	}
629	>
630	>	}
631	>
632	>	return atomTypes;
633		}
634
635	<	fInfo.SIM_uses_PBC = usePBC;
636	<	//fInfo.SIM_uses_LJ = 0;
637	<	fInfo.SIM_uses_LJ = useLJ;
638	<	fInfo.SIM_uses_sticky = useSticky;
639	<	//fInfo.SIM_uses_sticky = 0;
640	<	fInfo.SIM_uses_charges = useCharges;
641	<	fInfo.SIM_uses_dipoles = useDipoles;
642	<	//fInfo.SIM_uses_dipoles = 0;
643	<	fInfo.SIM_uses_RF = useReactionField;
644	<	//fInfo.SIM_uses_RF = 0;
645	<	fInfo.SIM_uses_GB = useGB;
646	<	fInfo.SIM_uses_EAM = useEAM;
635	>	void SimInfo::setupSimType() {
636	>	std::set<AtomType*>::iterator i;
637	>	std::set<AtomType*> atomTypes;
638	>	atomTypes = getUniqueAtomTypes();
639	>
640	>	int useLennardJones = 0;
641	>	int useElectrostatic = 0;
642	>	int useEAM = 0;
643	>	int useSC = 0;
644	>	int useCharge = 0;
645	>	int useDirectional = 0;
646	>	int useDipole = 0;
647	>	int useGayBerne = 0;
648	>	int useSticky = 0;
649	>	int useStickyPower = 0;
650	>	int useShape = 0;
651	>	int useFLARB = 0; //it is not in AtomType yet
652	>	int useDirectionalAtom = 0;
653	>	int useElectrostatics = 0;
654	>	//usePBC and useRF are from simParams
655	>	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
656	>	int useRF;
657	>	int useSF;
658	>	std::string myMethod;
659	>
660	>	// set the useRF logical
661	>	useRF = 0;
662	>	useSF = 0;
663	>
664	>
665	>	if (simParams_->haveElectrostaticSummationMethod()) {
666	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
667	>	toUpper(myMethod);
668	>	if (myMethod == "REACTION_FIELD") {
669	>	useRF=1;
670	>	} else {
671	>	if (myMethod == "SHIFTED_FORCE") {
672	>	useSF = 1;
673	>	}
674	>	}
675	>	}
676
677	<	n_exclude = excludes->getSize();
678	<	excl = excludes->getFortranArray();
679	<
680	<	#ifdef IS_MPI
681	<	n_global = mpiSim->getNAtomsGlobal();
682	<	#else
683	<	n_global = n_atoms;
684	<	#endif
685	<
686	<	isError = 0;
687	<
688	<	getFortranGroupArrays(this, FglobalGroupMembership, mfact);
689	<	//it may not be a good idea to pass the address of first element in vector
690	<	//since c++ standard does not require vector to be stored continuously in meomory
462	<	//Most of the compilers will organize the memory of vector continuously
463	<	setFortranSim( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
464	<	&nGlobalExcludes, globalExcludes, molMembershipArray,
465	<	&mfact[0], &ngroup, &FglobalGroupMembership[0], &isError);
677	>	//loop over all of the atom types
678	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
679	>	useLennardJones |= (*i)->isLennardJones();
680	>	useElectrostatic |= (*i)->isElectrostatic();
681	>	useEAM |= (*i)->isEAM();
682	>	useSC |= (*i)->isSC();
683	>	useCharge |= (*i)->isCharge();
684	>	useDirectional |= (*i)->isDirectional();
685	>	useDipole |= (*i)->isDipole();
686	>	useGayBerne |= (*i)->isGayBerne();
687	>	useSticky |= (*i)->isSticky();
688	>	useStickyPower |= (*i)->isStickyPower();
689	>	useShape |= (*i)->isShape();
690	>	}
691
692	<	if( isError ){
692	>	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
693	>	useDirectionalAtom = 1;
694	>	}
695	>
696	>	if (useCharge || useDipole) {
697	>	useElectrostatics = 1;
698	>	}
699	>
700	>	#ifdef IS_MPI
701	>	int temp;
702	>
703	>	temp = usePBC;
704	>	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
705	>
706	>	temp = useDirectionalAtom;
707	>	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
708	>
709	>	temp = useLennardJones;
710	>	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
711	>
712	>	temp = useElectrostatics;
713	>	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
714	>
715	>	temp = useCharge;
716	>	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
717	>
718	>	temp = useDipole;
719	>	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
720	>
721	>	temp = useSticky;
722	>	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
723	>
724	>	temp = useStickyPower;
725	>	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
726
727	<	sprintf( painCave.errMsg,
728	<	"There was an error setting the simulation information in fortran.\n" );
729	<	painCave.isFatal = 1;
730	<	painCave.severity = OOPSE_ERROR;
731	<	simError();
727	>	temp = useGayBerne;
728	>	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
729	>
730	>	temp = useEAM;
731	>	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
732	>
733	>	temp = useSC;
734	>	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
735	>
736	>	temp = useShape;
737	>	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
738	>
739	>	temp = useFLARB;
740	>	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
741	>
742	>	temp = useRF;
743	>	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
744	>
745	>	temp = useSF;
746	>	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
747	>
748	>	#endif
749	>
750	>	fInfo_.SIM_uses_PBC = usePBC;
751	>	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
752	>	fInfo_.SIM_uses_LennardJones = useLennardJones;
753	>	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
754	>	fInfo_.SIM_uses_Charges = useCharge;
755	>	fInfo_.SIM_uses_Dipoles = useDipole;
756	>	fInfo_.SIM_uses_Sticky = useSticky;
757	>	fInfo_.SIM_uses_StickyPower = useStickyPower;
758	>	fInfo_.SIM_uses_GayBerne = useGayBerne;
759	>	fInfo_.SIM_uses_EAM = useEAM;
760	>	fInfo_.SIM_uses_SC = useSC;
761	>	fInfo_.SIM_uses_Shapes = useShape;
762	>	fInfo_.SIM_uses_FLARB = useFLARB;
763	>	fInfo_.SIM_uses_RF = useRF;
764	>	fInfo_.SIM_uses_SF = useSF;
765	>
766	>	if( myMethod == "REACTION_FIELD") {
767	>
768	>	if (simParams_->haveDielectric()) {
769	>	fInfo_.dielect = simParams_->getDielectric();
770	>	} else {
771	>	sprintf(painCave.errMsg,
772	>	"SimSetup Error: No Dielectric constant was set.\n"
773	>	"\tYou are trying to use Reaction Field without"
774	>	"\tsetting a dielectric constant!\n");
775	>	painCave.isFatal = 1;
776	>	simError();
777	>	}
778	>	}
779	>
780		}
475	–
476	–	#ifdef IS_MPI
477	–	sprintf( checkPointMsg,
478	–	"succesfully sent the simulation information to fortran.\n");
479	–	MPIcheckPoint();
480	–	#endif // is_mpi
481	–
482	–	this->ndf = this->getNDF();
483	–	this->ndfRaw = this->getNDFraw();
484	–	this->ndfTrans = this->getNDFtranslational();
485	–	}
781
782	<	void SimInfo::setDefaultRcut( double theRcut ){
783	<
784	<	haveRcut = 1;
785	<	rCut = theRcut;
786	<	rList = rCut + 1.0;
787	<
788	<	notifyFortranCutoffs( &rCut, &rSw, &rList );
494	<	}
782	>	void SimInfo::setupFortranSim() {
783	>	int isError;
784	>	int nExclude;
785	>	std::vector<int> fortranGlobalGroupMembership;
786	>
787	>	nExclude = exclude_.getSize();
788	>	isError = 0;
789
790	<	void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
790	>	//globalGroupMembership_ is filled by SimCreator
791	>	for (int i = 0; i < nGlobalAtoms_; i++) {
792	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
793	>	}
794
795	<	rSw = theRsw;
796	<	setDefaultRcut( theRcut );
797	<	}
795	>	//calculate mass ratio of cutoff group
796	>	std::vector<double> mfact;
797	>	SimInfo::MoleculeIterator mi;
798	>	Molecule* mol;
799	>	Molecule::CutoffGroupIterator ci;
800	>	CutoffGroup* cg;
801	>	Molecule::AtomIterator ai;
802	>	Atom* atom;
803	>	double totalMass;
804
805	+	//to avoid memory reallocation, reserve enough space for mfact
806	+	mfact.reserve(getNCutoffGroups());
807	+
808	+	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
809	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
810
811	<	void SimInfo::checkCutOffs( void ){
812	<
813	<	if( boxIsInit ){
811	>	totalMass = cg->getMass();
812	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
813	>	// Check for massless groups - set mfact to 1 if true
814	>	if (totalMass != 0)
815	>	mfact.push_back(atom->getMass()/totalMass);
816	>	else
817	>	mfact.push_back( 1.0 );
818	>	}
819	>
820	>	}
821	>	}
822	>
823	>	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
824	>	std::vector<int> identArray;
825	>
826	>	//to avoid memory reallocation, reserve enough space identArray
827	>	identArray.reserve(getNAtoms());
828
829	<	//we need to check cutOffs against the box
829	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
830	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
831	>	identArray.push_back(atom->getIdent());
832	>	}
833	>	}
834	>
835	>	//fill molMembershipArray
836	>	//molMembershipArray is filled by SimCreator
837	>	std::vector<int> molMembershipArray(nGlobalAtoms_);
838	>	for (int i = 0; i < nGlobalAtoms_; i++) {
839	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
840	>	}
841
842	<	if( rCut > maxCutoff ){
842	>	//setup fortran simulation
843	>	int nGlobalExcludes = 0;
844	>	int* globalExcludes = NULL;
845	>	int* excludeList = exclude_.getExcludeList();
846	>	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
847	>	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
848	>	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
849	>
850	>	if( isError ){
851	>
852		sprintf( painCave.errMsg,
853	<	"cutoffRadius is too large for the current periodic box.\n"
512	<	"\tCurrent Value of cutoffRadius = %G at time %G\n "
513	<	"\tThis is larger than half of at least one of the\n"
514	<	"\tperiodic box vectors.  Right now, the Box matrix is:\n"
515	<	"\n"
516	<	"\t[ %G %G %G ]\n"
517	<	"\t[ %G %G %G ]\n"
518	<	"\t[ %G %G %G ]\n",
519	<	rCut, currentTime,
520	<	Hmat[0][0], Hmat[0][1], Hmat[0][2],
521	<	Hmat[1][0], Hmat[1][1], Hmat[1][2],
522	<	Hmat[2][0], Hmat[2][1], Hmat[2][2]);
523	<	painCave.severity = OOPSE_ERROR;
853	>	"There was an error setting the simulation information in fortran.\n" );
854		painCave.isFatal = 1;
855	+	painCave.severity = OOPSE_ERROR;
856		simError();
857	<	}
858	<	} else {
859	<	// initialize this stuff before using it, OK?
860	<	sprintf( painCave.errMsg,
861	<	"Trying to check cutoffs without a box.\n"
862	<	"\tOOPSE should have better programmers than that.\n" );
863	<	painCave.severity = OOPSE_ERROR;
533	<	painCave.isFatal = 1;
534	<	simError();
857	>	}
858	>
859	>	#ifdef IS_MPI
860	>	sprintf( checkPointMsg,
861	>	"succesfully sent the simulation information to fortran.\n");
862	>	MPIcheckPoint();
863	>	#endif // is_mpi
864		}
536	–
537	–	}
865
539	–	void SimInfo::addProperty(GenericData* prop){
866
867	<	map<string, GenericData*>::iterator result;
868	<	result = properties.find(prop->getID());
543	<
544	<	//we can't simply use  properties[prop->getID()] = prop,
545	<	//it will cause memory leak if we already contain a propery which has the same name of prop
546	<
547	<	if(result != properties.end()){
867	>	#ifdef IS_MPI
868	>	void SimInfo::setupFortranParallel() {
869
870	<	delete (*result).second;
871	<	(*result).second = prop;
872	<
873	<	}
874	<	else{
870	>	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
871	>	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
872	>	std::vector<int> localToGlobalCutoffGroupIndex;
873	>	SimInfo::MoleculeIterator mi;
874	>	Molecule::AtomIterator ai;
875	>	Molecule::CutoffGroupIterator ci;
876	>	Molecule* mol;
877	>	Atom* atom;
878	>	CutoffGroup* cg;
879	>	mpiSimData parallelData;
880	>	int isError;
881
882	<	properties[prop->getID()] = prop;
882	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
883
884	+	//local index(index in DataStorge) of atom is important
885	+	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
886	+	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
887	+	}
888	+
889	+	//local index of cutoff group is trivial, it only depends on the order of travesing
890	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
891	+	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
892	+	}
893	+
894	+	}
895	+
896	+	//fill up mpiSimData struct
897	+	parallelData.nMolGlobal = getNGlobalMolecules();
898	+	parallelData.nMolLocal = getNMolecules();
899	+	parallelData.nAtomsGlobal = getNGlobalAtoms();
900	+	parallelData.nAtomsLocal = getNAtoms();
901	+	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
902	+	parallelData.nGroupsLocal = getNCutoffGroups();
903	+	parallelData.myNode = worldRank;
904	+	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
905	+
906	+	//pass mpiSimData struct and index arrays to fortran
907	+	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
908	+	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
909	+	&localToGlobalCutoffGroupIndex[0], &isError);
910	+
911	+	if (isError) {
912	+	sprintf(painCave.errMsg,
913	+	"mpiRefresh errror: fortran didn't like something we gave it.\n");
914	+	painCave.isFatal = 1;
915	+	simError();
916	+	}
917	+
918	+	sprintf(checkPointMsg, " mpiRefresh successful.\n");
919	+	MPIcheckPoint();
920	+
921	+
922		}
558	–
559	–	}
923
924	<	GenericData* SimInfo::getProperty(const string& propName){
562	<
563	<	map<string, GenericData*>::iterator result;
564	<
565	<	//string lowerCaseName = ();
566	<
567	<	result = properties.find(propName);
568	<
569	<	if(result != properties.end())
570	<	return (*result).second;
571	<	else
572	<	return NULL;
573	<	}
924	>	#endif
925
926	+	double SimInfo::calcMaxCutoffRadius() {
927
576	–	void SimInfo::getFortranGroupArrays(SimInfo* info,
577	–	vector<int>& FglobalGroupMembership,
578	–	vector<double>& mfact){
579	–
580	–	Molecule* myMols;
581	–	Atom** myAtoms;
582	–	int numAtom;
583	–	double mtot;
584	–	int numMol;
585	–	int numCutoffGroups;
586	–	CutoffGroup* myCutoffGroup;
587	–	vector<CutoffGroup*>::iterator iterCutoff;
588	–	Atom* cutoffAtom;
589	–	vector<Atom*>::iterator iterAtom;
590	–	int atomIndex;
591	–	double totalMass;
592	–
593	–	mfact.clear();
594	–	FglobalGroupMembership.clear();
595	–
928
929	<	// Fix the silly fortran indexing problem
929	>	std::set<AtomType*> atomTypes;
930	>	std::set<AtomType*>::iterator i;
931	>	std::vector<double> cutoffRadius;
932	>
933	>	//get the unique atom types
934	>	atomTypes = getUniqueAtomTypes();
935	>
936	>	//query the max cutoff radius among these atom types
937	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
938	>	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
939	>	}
940	>
941	>	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
942		#ifdef IS_MPI
943	<	numAtom = mpiSim->getNAtomsGlobal();
600	<	#else
601	<	numAtom = n_atoms;
943	>	//pick the max cutoff radius among the processors
944		#endif
603	–	for (int i = 0; i < numAtom; i++)
604	–	FglobalGroupMembership.push_back(globalGroupMembership[i] + 1);
605	–
945
946	<	myMols = info->molecules;
947	<	numMol = info->n_mol;
609	<	for(int i  = 0; i < numMol; i++){
610	<	numCutoffGroups = myMols[i].getNCutoffGroups();
611	<	for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff);
612	<	myCutoffGroup != NULL;
613	<	myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
946	>	return maxCutoffRadius;
947	>	}
948
949	<	totalMass = myCutoffGroup->getMass();
950	<
951	<	for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom);
952	<	cutoffAtom != NULL;
953	<	cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
954	<	mfact.push_back(cutoffAtom->getMass()/totalMass);
955	<	}
949	>	void SimInfo::getCutoff(double& rcut, double& rsw) {
950	>
951	>	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
952	>
953	>	if (!simParams_->haveCutoffRadius()){
954	>	sprintf(painCave.errMsg,
955	>	"SimCreator Warning: No value was set for the cutoffRadius.\n"
956	>	"\tOOPSE will use a default value of 15.0 angstroms"
957	>	"\tfor the cutoffRadius.\n");
958	>	painCave.isFatal = 0;
959	>	simError();
960	>	rcut = 15.0;
961	>	} else{
962	>	rcut = simParams_->getCutoffRadius();
963	>	}
964	>
965	>	if (!simParams_->haveSwitchingRadius()){
966	>	sprintf(painCave.errMsg,
967	>	"SimCreator Warning: No value was set for switchingRadius.\n"
968	>	"\tOOPSE will use a default value of\n"
969	>	"\t0.85 * cutoffRadius for the switchingRadius\n");
970	>	painCave.isFatal = 0;
971	>	simError();
972	>	rsw = 0.85 * rcut;
973	>	} else{
974	>	rsw = simParams_->getSwitchingRadius();
975	>	}
976	>
977	>	} else {
978	>	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
979	>	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
980	>
981	>	if (simParams_->haveCutoffRadius()) {
982	>	rcut = simParams_->getCutoffRadius();
983	>	} else {
984	>	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
985	>	rcut = calcMaxCutoffRadius();
986	>	}
987	>
988	>	if (simParams_->haveSwitchingRadius()) {
989	>	rsw  = simParams_->getSwitchingRadius();
990	>	} else {
991	>	rsw = rcut;
992	>	}
993	>
994		}
995		}
996
997	<	}
997	>	void SimInfo::setupCutoff() {
998	>	getCutoff(rcut_, rsw_);
999	>	double rnblist = rcut_ + 1; // skin of neighbor list
1000	>
1001	>	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
1002	>
1003	>	int cp =  TRADITIONAL_CUTOFF_POLICY;
1004	>	if (simParams_->haveCutoffPolicy()) {
1005	>	std::string myPolicy = simParams_->getCutoffPolicy();
1006	>	toUpper(myPolicy);
1007	>	if (myPolicy == "MIX") {
1008	>	cp = MIX_CUTOFF_POLICY;
1009	>	} else {
1010	>	if (myPolicy == "MAX") {
1011	>	cp = MAX_CUTOFF_POLICY;
1012	>	} else {
1013	>	if (myPolicy == "TRADITIONAL") {
1014	>	cp = TRADITIONAL_CUTOFF_POLICY;
1015	>	} else {
1016	>	// throw error
1017	>	sprintf( painCave.errMsg,
1018	>	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
1019	>	painCave.isFatal = 1;
1020	>	simError();
1021	>	}
1022	>	}
1023	>	}
1024	>	}
1025	>
1026	>
1027	>	if (simParams_->haveSkinThickness()) {
1028	>	double skinThickness = simParams_->getSkinThickness();
1029	>	}
1030	>
1031	>	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
1032	>	// also send cutoff notification to electrostatics
1033	>	setElectrostaticCutoffRadius(&rcut_, &rsw_);
1034	>	}
1035	>
1036	>	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1037	>
1038	>	int errorOut;
1039	>	int esm =  NONE;
1040	>	int sm = UNDAMPED;
1041	>	double alphaVal;
1042	>	double dielectric;
1043	>
1044	>	errorOut = isError;
1045	>	alphaVal = simParams_->getDampingAlpha();
1046	>	dielectric = simParams_->getDielectric();
1047	>
1048	>	if (simParams_->haveElectrostaticSummationMethod()) {
1049	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1050	>	toUpper(myMethod);
1051	>	if (myMethod == "NONE") {
1052	>	esm = NONE;
1053	>	} else {
1054	>	if (myMethod == "SWITCHING_FUNCTION") {
1055	>	esm = SWITCHING_FUNCTION;
1056	>	} else {
1057	>	if (myMethod == "SHIFTED_POTENTIAL") {
1058	>	esm = SHIFTED_POTENTIAL;
1059	>	} else {
1060	>	if (myMethod == "SHIFTED_FORCE") {
1061	>	esm = SHIFTED_FORCE;
1062	>	} else {
1063	>	if (myMethod == "REACTION_FIELD") {
1064	>	esm = REACTION_FIELD;
1065	>	} else {
1066	>	// throw error
1067	>	sprintf( painCave.errMsg,
1068	>	"SimInfo error: Unknown electrostaticSummationMethod. (Input file specified %s .)\n\telectrostaticSummationMethod must be one of: \"none\", \"shifted_potential\", \"shifted_force\", or \"reaction_field\".", myMethod.c_str() );
1069	>	painCave.isFatal = 1;
1070	>	simError();
1071	>	}
1072	>	}
1073	>	}
1074	>	}
1075	>	}
1076	>	}
1077	>
1078	>	if (simParams_->haveElectrostaticScreeningMethod()) {
1079	>	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1080	>	toUpper(myScreen);
1081	>	if (myScreen == "UNDAMPED") {
1082	>	sm = UNDAMPED;
1083	>	} else {
1084	>	if (myScreen == "DAMPED") {
1085	>	sm = DAMPED;
1086	>	if (!simParams_->haveDampingAlpha()) {
1087	>	//throw error
1088	>	sprintf( painCave.errMsg,
1089	>	"SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used.", alphaVal);
1090	>	painCave.isFatal = 0;
1091	>	simError();
1092	>	}
1093	>	} else {
1094	>	// throw error
1095	>	sprintf( painCave.errMsg,
1096	>	"SimInfo error: Unknown electrostaticScreeningMethod. (Input file specified %s .)\n\telectrostaticScreeningMethod must be one of: \"undamped\" or \"damped\".", myScreen.c_str() );
1097	>	painCave.isFatal = 1;
1098	>	simError();
1099	>	}
1100	>	}
1101	>	}
1102	>
1103	>	// let's pass some summation method variables to fortran
1104	>	setElectrostaticSummationMethod( &esm );
1105	>	setScreeningMethod( &sm );
1106	>	setDampingAlpha( &alphaVal );
1107	>	setReactionFieldDielectric( &dielectric );
1108	>	initFortranFF( &esm, &errorOut );
1109	>	}
1110	>
1111	>	void SimInfo::setupSwitchingFunction() {
1112	>	int ft = CUBIC;
1113	>
1114	>	if (simParams_->haveSwitchingFunctionType()) {
1115	>	std::string funcType = simParams_->getSwitchingFunctionType();
1116	>	toUpper(funcType);
1117	>	if (funcType == "CUBIC") {
1118	>	ft = CUBIC;
1119	>	} else {
1120	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1121	>	ft = FIFTH_ORDER_POLY;
1122	>	} else {
1123	>	// throw error
1124	>	sprintf( painCave.errMsg,
1125	>	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1126	>	painCave.isFatal = 1;
1127	>	simError();
1128	>	}
1129	>	}
1130	>	}
1131	>
1132	>	// send switching function notification to switcheroo
1133	>	setFunctionType(&ft);
1134	>
1135	>	}
1136	>
1137	>	void SimInfo::addProperty(GenericData* genData) {
1138	>	properties_.addProperty(genData);
1139	>	}
1140	>
1141	>	void SimInfo::removeProperty(const std::string& propName) {
1142	>	properties_.removeProperty(propName);
1143	>	}
1144	>
1145	>	void SimInfo::clearProperties() {
1146	>	properties_.clearProperties();
1147	>	}
1148	>
1149	>	std::vector<std::string> SimInfo::getPropertyNames() {
1150	>	return properties_.getPropertyNames();
1151	>	}
1152	>
1153	>	std::vector<GenericData*> SimInfo::getProperties() {
1154	>	return properties_.getProperties();
1155	>	}
1156	>
1157	>	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1158	>	return properties_.getPropertyByName(propName);
1159	>	}
1160	>
1161	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1162	>	if (sman_ == sman) {
1163	>	return;
1164	>	}
1165	>	delete sman_;
1166	>	sman_ = sman;
1167	>
1168	>	Molecule* mol;
1169	>	RigidBody* rb;
1170	>	Atom* atom;
1171	>	SimInfo::MoleculeIterator mi;
1172	>	Molecule::RigidBodyIterator rbIter;
1173	>	Molecule::AtomIterator atomIter;;
1174	>
1175	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1176	>
1177	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1178	>	atom->setSnapshotManager(sman_);
1179	>	}
1180	>
1181	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1182	>	rb->setSnapshotManager(sman_);
1183	>	}
1184	>	}
1185	>
1186	>	}
1187	>
1188	>	Vector3d SimInfo::getComVel(){
1189	>	SimInfo::MoleculeIterator i;
1190	>	Molecule* mol;
1191	>
1192	>	Vector3d comVel(0.0);
1193	>	double totalMass = 0.0;
1194	>
1195	>
1196	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1197	>	double mass = mol->getMass();
1198	>	totalMass += mass;
1199	>	comVel += mass * mol->getComVel();
1200	>	}
1201	>
1202	>	#ifdef IS_MPI
1203	>	double tmpMass = totalMass;
1204	>	Vector3d tmpComVel(comVel);
1205	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1206	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1207	>	#endif
1208	>
1209	>	comVel /= totalMass;
1210	>
1211	>	return comVel;
1212	>	}
1213	>
1214	>	Vector3d SimInfo::getCom(){
1215	>	SimInfo::MoleculeIterator i;
1216	>	Molecule* mol;
1217	>
1218	>	Vector3d com(0.0);
1219	>	double totalMass = 0.0;
1220	>
1221	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1222	>	double mass = mol->getMass();
1223	>	totalMass += mass;
1224	>	com += mass * mol->getCom();
1225	>	}
1226	>
1227	>	#ifdef IS_MPI
1228	>	double tmpMass = totalMass;
1229	>	Vector3d tmpCom(com);
1230	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1231	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1232	>	#endif
1233	>
1234	>	com /= totalMass;
1235	>
1236	>	return com;
1237	>
1238	>	}
1239	>
1240	>	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1241	>
1242	>	return o;
1243	>	}
1244	>
1245	>
1246	>	/*
1247	>	Returns center of mass and center of mass velocity in one function call.
1248	>	*/
1249	>
1250	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1251	>	SimInfo::MoleculeIterator i;
1252	>	Molecule* mol;
1253	>
1254	>
1255	>	double totalMass = 0.0;
1256	>
1257	>
1258	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1259	>	double mass = mol->getMass();
1260	>	totalMass += mass;
1261	>	com += mass * mol->getCom();
1262	>	comVel += mass * mol->getComVel();
1263	>	}
1264	>
1265	>	#ifdef IS_MPI
1266	>	double tmpMass = totalMass;
1267	>	Vector3d tmpCom(com);
1268	>	Vector3d tmpComVel(comVel);
1269	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1270	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1271	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1272	>	#endif
1273	>
1274	>	com /= totalMass;
1275	>	comVel /= totalMass;
1276	>	}
1277	>
1278	>	/*
1279	>	Return intertia tensor for entire system and angular momentum Vector.
1280	>
1281	>
1282	>	[  Ixx -Ixy  -Ixz ]
1283	>	J =| -Iyx  Iyy  -Iyz |
1284	>	[ -Izx -Iyz   Izz ]
1285	>	*/
1286	>
1287	>	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1288	>
1289	>
1290	>	double xx = 0.0;
1291	>	double yy = 0.0;
1292	>	double zz = 0.0;
1293	>	double xy = 0.0;
1294	>	double xz = 0.0;
1295	>	double yz = 0.0;
1296	>	Vector3d com(0.0);
1297	>	Vector3d comVel(0.0);
1298	>
1299	>	getComAll(com, comVel);
1300	>
1301	>	SimInfo::MoleculeIterator i;
1302	>	Molecule* mol;
1303	>
1304	>	Vector3d thisq(0.0);
1305	>	Vector3d thisv(0.0);
1306	>
1307	>	double thisMass = 0.0;
1308	>
1309	>
1310	>
1311	>
1312	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1313	>
1314	>	thisq = mol->getCom()-com;
1315	>	thisv = mol->getComVel()-comVel;
1316	>	thisMass = mol->getMass();
1317	>	// Compute moment of intertia coefficients.
1318	>	xx += thisq[0]*thisq[0]*thisMass;
1319	>	yy += thisq[1]*thisq[1]*thisMass;
1320	>	zz += thisq[2]*thisq[2]*thisMass;
1321	>
1322	>	// compute products of intertia
1323	>	xy += thisq[0]*thisq[1]*thisMass;
1324	>	xz += thisq[0]*thisq[2]*thisMass;
1325	>	yz += thisq[1]*thisq[2]*thisMass;
1326	>
1327	>	angularMomentum += cross( thisq, thisv ) * thisMass;
1328	>
1329	>	}
1330	>
1331	>
1332	>	inertiaTensor(0,0) = yy + zz;
1333	>	inertiaTensor(0,1) = -xy;
1334	>	inertiaTensor(0,2) = -xz;
1335	>	inertiaTensor(1,0) = -xy;
1336	>	inertiaTensor(1,1) = xx + zz;
1337	>	inertiaTensor(1,2) = -yz;
1338	>	inertiaTensor(2,0) = -xz;
1339	>	inertiaTensor(2,1) = -yz;
1340	>	inertiaTensor(2,2) = xx + yy;
1341	>
1342	>	#ifdef IS_MPI
1343	>	Mat3x3d tmpI(inertiaTensor);
1344	>	Vector3d tmpAngMom;
1345	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1346	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1347	>	#endif
1348	>
1349	>	return;
1350	>	}
1351	>
1352	>	//Returns the angular momentum of the system
1353	>	Vector3d SimInfo::getAngularMomentum(){
1354	>
1355	>	Vector3d com(0.0);
1356	>	Vector3d comVel(0.0);
1357	>	Vector3d angularMomentum(0.0);
1358	>
1359	>	getComAll(com,comVel);
1360	>
1361	>	SimInfo::MoleculeIterator i;
1362	>	Molecule* mol;
1363	>
1364	>	Vector3d thisr(0.0);
1365	>	Vector3d thisp(0.0);
1366	>
1367	>	double thisMass;
1368	>
1369	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1370	>	thisMass = mol->getMass();
1371	>	thisr = mol->getCom()-com;
1372	>	thisp = (mol->getComVel()-comVel)*thisMass;
1373	>
1374	>	angularMomentum += cross( thisr, thisp );
1375	>
1376	>	}
1377	>
1378	>	#ifdef IS_MPI
1379	>	Vector3d tmpAngMom;
1380	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1381	>	#endif
1382	>
1383	>	return angularMomentum;
1384	>	}
1385	>
1386	>
1387	>	}//end namespace oopse
1388	>

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