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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 2463 by gezelter, Mon Nov 21 22:59:21 2005 UTC

#	Line 1 | Line 1
1	<	#include <stdlib.h>
2	<	#include <string.h>
3	<	#include <math.h>
1	>	/*
2	>	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	>	*
4	>	* The University of Notre Dame grants you ("Licensee") a
5	>	* non-exclusive, royalty free, license to use, modify and
6	>	* redistribute this software in source and binary code form, provided
7	>	* that the following conditions are met:
8	>	*
9	>	* 1. Acknowledgement of the program authors must be made in any
10	>	*    publication of scientific results based in part on use of the
11	>	*    program.  An acceptable form of acknowledgement is citation of
12	>	*    the article in which the program was described (Matthew
13	>	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	>	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	>	*    Parallel Simulation Engine for Molecular Dynamics,"
16	>	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	>	*
18	>	* 2. Redistributions of source code must retain the above copyright
19	>	*    notice, this list of conditions and the following disclaimer.
20	>	*
21	>	* 3. Redistributions in binary form must reproduce the above copyright
22	>	*    notice, this list of conditions and the following disclaimer in the
23	>	*    documentation and/or other materials provided with the
24	>	*    distribution.
25	>	*
26	>	* This software is provided "AS IS," without a warranty of any
27	>	* kind. All express or implied conditions, representations and
28	>	* warranties, including any implied warranty of merchantability,
29	>	* fitness for a particular purpose or non-infringement, are hereby
30	>	* excluded.  The University of Notre Dame and its licensors shall not
31	>	* be liable for any damages suffered by licensee as a result of
32	>	* using, modifying or distributing the software or its
33	>	* derivatives. In no event will the University of Notre Dame or its
34	>	* licensors be liable for any lost revenue, profit or data, or for
35	>	* direct, indirect, special, consequential, incidental or punitive
36	>	* damages, however caused and regardless of the theory of liability,
37	>	* arising out of the use of or inability to use software, even if the
38	>	* University of Notre Dame has been advised of the possibility of
39	>	* such damages.
40	>	*/
41	>
42	>	/**
43	>	* @file SimInfo.cpp
44	>	* @author    tlin
45	>	* @date  11/02/2004
46	>	* @version 1.0
47	>	*/
48
49	<	#include <iostream>
50	<	using namespace std;
49	>	#include <algorithm>
50	>	#include <set>
51	>	#include <map>
52
53		#include "brains/SimInfo.hpp"
54	<	#define __C
55	<	#include "brains/fSimulation.h"
54	>	#include "math/Vector3.hpp"
55	>	#include "primitives/Molecule.hpp"
56	>	#include "UseTheForce/fCutoffPolicy.h"
57	>	#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
58	>	#include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h"
59	>	#include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
60	>	#include "UseTheForce/doForces_interface.h"
61	>	#include "UseTheForce/DarkSide/electrostatic_interface.h"
62	>	#include "UseTheForce/DarkSide/switcheroo_interface.h"
63	>	#include "utils/MemoryUtils.hpp"
64		#include "utils/simError.h"
65	<	#include "UseTheForce/DarkSide/simulation_interface.h"
13	<	#include "UseTheForce/notifyCutoffs_interface.h"
65	>	#include "selection/SelectionManager.hpp"
66
15	–	//#include "UseTheForce/fortranWrappers.hpp"
16	–
17	–	#include "math/MatVec3.h"
18	–
67		#ifdef IS_MPI
68	<	#include "brains/mpiSimulation.hpp"
69	<	#endif
68	>	#include "UseTheForce/mpiComponentPlan.h"
69	>	#include "UseTheForce/DarkSide/simParallel_interface.h"
70	>	#endif
71
72	<	inline double roundMe( double x ){
73	<	return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
74	<	}
75	<
76	<	inline double min( double a, double b ){
77	<	return (a < b ) ? a : b;
78	<	}
72	>	namespace oopse {
73	>	std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
74	>	std::map<int, std::set<int> >::iterator i = container.find(index);
75	>	std::set<int> result;
76	>	if (i != container.end()) {
77	>	result = i->second;
78	>	}
79
80	<	SimInfo* currentInfo;
81	<
33	<	SimInfo::SimInfo(){
34	<
35	<	n_constraints = 0;
36	<	nZconstraints = 0;
37	<	n_oriented = 0;
38	<	n_dipoles = 0;
39	<	ndf = 0;
40	<	ndfRaw = 0;
41	<	nZconstraints = 0;
42	<	the_integrator = NULL;
43	<	setTemp = 0;
44	<	thermalTime = 0.0;
45	<	currentTime = 0.0;
46	<	rCut = 0.0;
47	<	rSw = 0.0;
48	<
49	<	haveRcut = 0;
50	<	haveRsw = 0;
51	<	boxIsInit = 0;
80	>	return result;
81	>	}
82
83	<	resetTime = 1e99;
83	>	SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
84	>	ForceField* ff, Globals* simParams) :
85	>	stamps_(stamps), forceField_(ff), simParams_(simParams),
86	>	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
87	>	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
88	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
89	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
90	>	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
91	>	sman_(NULL), fortranInitialized_(false) {
92
93	<	orthoRhombic = 0;
94	<	orthoTolerance = 1E-6;
95	<	useInitXSstate = true;
93	>
94	>	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
95	>	MoleculeStamp* molStamp;
96	>	int nMolWithSameStamp;
97	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
98	>	int nGroups = 0;      //total cutoff groups defined in meta-data file
99	>	CutoffGroupStamp* cgStamp;
100	>	RigidBodyStamp* rbStamp;
101	>	int nRigidAtoms = 0;
102	>
103	>	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
104	>	molStamp = i->first;
105	>	nMolWithSameStamp = i->second;
106	>
107	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
108
109	<	usePBC = 0;
110	<	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;
109	>	//calculate atoms in molecules
110	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
111
70	–	haveCutoffGroups = false;
112
113	<	excludes = Exclude::Instance();
113	>	//calculate atoms in cutoff groups
114	>	int nAtomsInGroups = 0;
115	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
116	>
117	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
118	>	cgStamp = molStamp->getCutoffGroup(j);
119	>	nAtomsInGroups += cgStamp->getNMembers();
120	>	}
121
122	<	myConfiguration = new SimState();
122	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
123
124	<	has_minimizer = false;
77	<	the_minimizer =NULL;
124	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
125
126	<	ngroup = 0;
126	>	//calculate atoms in rigid bodies
127	>	int nAtomsInRigidBodies = 0;
128	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
129	>
130	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
131	>	rbStamp = molStamp->getRigidBody(j);
132	>	nAtomsInRigidBodies += rbStamp->getNMembers();
133	>	}
134
135	<	}
135	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
136	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
137	>
138	>	}
139
140	+	//every free atom (atom does not belong to cutoff groups) is a cutoff
141	+	//group therefore the total number of cutoff groups in the system is
142	+	//equal to the total number of atoms minus number of atoms belong to
143	+	//cutoff group defined in meta-data file plus the number of cutoff
144	+	//groups defined in meta-data file
145	+	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
146
147	<	SimInfo::~SimInfo(){
148	<
149	<	delete myConfiguration;
150	<
151	<	map<string, GenericData*>::iterator i;
147	>	//every free atom (atom does not belong to rigid bodies) is an
148	>	//integrable object therefore the total number of integrable objects
149	>	//in the system is equal to the total number of atoms minus number of
150	>	//atoms belong to rigid body defined in meta-data file plus the number
151	>	//of rigid bodies defined in meta-data file
152	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
153	>	+ nGlobalRigidBodies_;
154
155	<	for(i = properties.begin(); i != properties.end(); i++)
91	<	delete (*i).second;
155	>	nGlobalMols_ = molStampIds_.size();
156
157	<	}
157	>	#ifdef IS_MPI
158	>	molToProcMap_.resize(nGlobalMols_);
159	>	#endif
160
161	<	void SimInfo::setBox(double newBox[3]) {
96	<
97	<	int i, j;
98	<	double tempMat[3][3];
161	>	}
162
163	<	for(i=0; i<3; i++)
164	<	for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
163	>	SimInfo::~SimInfo() {
164	>	std::map<int, Molecule*>::iterator i;
165	>	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
166	>	delete i->second;
167	>	}
168	>	molecules_.clear();
169	>
170	>	delete stamps_;
171	>	delete sman_;
172	>	delete simParams_;
173	>	delete forceField_;
174	>	}
175
176	<	tempMat[0][0] = newBox[0];
177	<	tempMat[1][1] = newBox[1];
178	<	tempMat[2][2] = newBox[2];
176	>	int SimInfo::getNGlobalConstraints() {
177	>	int nGlobalConstraints;
178	>	#ifdef IS_MPI
179	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
180	>	MPI_COMM_WORLD);
181	>	#else
182	>	nGlobalConstraints =  nConstraints_;
183	>	#endif
184	>	return nGlobalConstraints;
185	>	}
186
187	<	setBoxM( tempMat );
187	>	bool SimInfo::addMolecule(Molecule* mol) {
188	>	MoleculeIterator i;
189
190	<	}
190	>	i = molecules_.find(mol->getGlobalIndex());
191	>	if (i == molecules_.end() ) {
192
193	<	void SimInfo::setBoxM( double theBox[3][3] ){
194	<
195	<	int i, j;
196	<	double FortranHmat[9]; // to preserve compatibility with Fortran the
197	<	// ordering in the array is as follows:
198	<	// [ 0 3 6 ]
199	<	// [ 1 4 7 ]
200	<	// [ 2 5 8 ]
201	<	double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
202	<
121	<	if( !boxIsInit ) boxIsInit = 1;
122	<
123	<	for(i=0; i < 3; i++)
124	<	for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
125	<
126	<	calcBoxL();
127	<	calcHmatInv();
193	>	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
194	>
195	>	nAtoms_ += mol->getNAtoms();
196	>	nBonds_ += mol->getNBonds();
197	>	nBends_ += mol->getNBends();
198	>	nTorsions_ += mol->getNTorsions();
199	>	nRigidBodies_ += mol->getNRigidBodies();
200	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
201	>	nCutoffGroups_ += mol->getNCutoffGroups();
202	>	nConstraints_ += mol->getNConstraintPairs();
203
204	<	for(i=0; i < 3; i++) {
205	<	for (j=0; j < 3; j++) {
206	<	FortranHmat[3*j + i] = Hmat[i][j];
207	<	FortranHmatInv[3*j + i] = HmatInv[i][j];
204	>	addExcludePairs(mol);
205	>
206	>	return true;
207	>	} else {
208	>	return false;
209		}
210		}
211
212	<	setFortranBox(FortranHmat, FortranHmatInv, &orthoRhombic);
213	<
214	<	}
139	<
212	>	bool SimInfo::removeMolecule(Molecule* mol) {
213	>	MoleculeIterator i;
214	>	i = molecules_.find(mol->getGlobalIndex());
215
216	<	void SimInfo::getBoxM (double theBox[3][3]) {
216	>	if (i != molecules_.end() ) {
217
218	<	int i, j;
219	<	for(i=0; i<3; i++)
220	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
221	<	}
218	>	assert(mol == i->second);
219	>
220	>	nAtoms_ -= mol->getNAtoms();
221	>	nBonds_ -= mol->getNBonds();
222	>	nBends_ -= mol->getNBends();
223	>	nTorsions_ -= mol->getNTorsions();
224	>	nRigidBodies_ -= mol->getNRigidBodies();
225	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
226	>	nCutoffGroups_ -= mol->getNCutoffGroups();
227	>	nConstraints_ -= mol->getNConstraintPairs();
228
229	+	removeExcludePairs(mol);
230	+	molecules_.erase(mol->getGlobalIndex());
231
232	<	void SimInfo::scaleBox(double scale) {
233	<	double theBox[3][3];
234	<	int i, j;
232	>	delete mol;
233	>
234	>	return true;
235	>	} else {
236	>	return false;
237	>	}
238
153	–	// cerr << "Scaling box by " << scale << "\n";
239
240	<	for(i=0; i<3; i++)
156	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
240	>	}
241
242	<	setBoxM(theBox);
242	>
243	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
244	>	i = molecules_.begin();
245	>	return i == molecules_.end() ? NULL : i->second;
246	>	}
247
248	<	}
248	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
249	>	++i;
250	>	return i == molecules_.end() ? NULL : i->second;
251	>	}
252
162	–	void SimInfo::calcHmatInv( void ) {
163	–
164	–	int oldOrtho;
165	–	int i,j;
166	–	double smallDiag;
167	–	double tol;
168	–	double sanity[3][3];
253
254	<	invertMat3( Hmat, HmatInv );
254	>	void SimInfo::calcNdf() {
255	>	int ndf_local;
256	>	MoleculeIterator i;
257	>	std::vector<StuntDouble*>::iterator j;
258	>	Molecule* mol;
259	>	StuntDouble* integrableObject;
260
261	<	// check to see if Hmat is orthorhombic
262	<
263	<	oldOrtho = orthoRhombic;
261	>	ndf_local = 0;
262	>
263	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
264	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
265	>	integrableObject = mol->nextIntegrableObject(j)) {
266
267	<	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;
267	>	ndf_local += 3;
268
269	<	orthoRhombic = 1;
270	<
271	<	for (i = 0; i < 3; i++ ) {
272	<	for (j = 0 ; j < 3; j++) {
273	<	if (i != j) {
274	<	if (orthoRhombic) {
275	<	if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
276	<	}
277	<	}
278	<	}
269	>	if (integrableObject->isDirectional()) {
270	>	if (integrableObject->isLinear()) {
271	>	ndf_local += 2;
272	>	} else {
273	>	ndf_local += 3;
274	>	}
275	>	}
276	>
277	>	}//end for (integrableObject)
278	>	}// end for (mol)
279	>
280	>	// n_constraints is local, so subtract them on each processor
281	>	ndf_local -= nConstraints_;
282	>
283	>	#ifdef IS_MPI
284	>	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
285	>	#else
286	>	ndf_ = ndf_local;
287	>	#endif
288	>
289	>	// nZconstraints_ is global, as are the 3 COM translations for the
290	>	// entire system:
291	>	ndf_ = ndf_ - 3 - nZconstraint_;
292	>
293		}
294
295	<	if( oldOrtho != orthoRhombic ){
295	>	void SimInfo::calcNdfRaw() {
296	>	int ndfRaw_local;
297	>
298	>	MoleculeIterator i;
299	>	std::vector<StuntDouble*>::iterator j;
300	>	Molecule* mol;
301	>	StuntDouble* integrableObject;
302	>
303	>	// Raw degrees of freedom that we have to set
304	>	ndfRaw_local = 0;
305
306	<	if( orthoRhombic ) {
307	<	sprintf( painCave.errMsg,
308	<	"OOPSE is switching from the default Non-Orthorhombic\n"
309	<	"\tto the faster Orthorhombic periodic boundary computations.\n"
310	<	"\tThis is usually a good thing, but if you wan't the\n"
311	<	"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
312	<	"\tvariable ( currently set to %G ) smaller.\n",
313	<	orthoTolerance);
314	<	painCave.severity = OOPSE_INFO;
315	<	simError();
306	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
307	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
308	>	integrableObject = mol->nextIntegrableObject(j)) {
309	>
310	>	ndfRaw_local += 3;
311	>
312	>	if (integrableObject->isDirectional()) {
313	>	if (integrableObject->isLinear()) {
314	>	ndfRaw_local += 2;
315	>	} else {
316	>	ndfRaw_local += 3;
317	>	}
318	>	}
319	>
320	>	}
321		}
322	<	else {
323	<	sprintf( painCave.errMsg,
324	<	"OOPSE is switching from the faster Orthorhombic to the more\n"
325	<	"\tflexible Non-Orthorhombic periodic boundary computations.\n"
326	<	"\tThis is usually because the box has deformed under\n"
327	<	"\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	<	}
322	>
323	>	#ifdef IS_MPI
324	>	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
325	>	#else
326	>	ndfRaw_ = ndfRaw_local;
327	>	#endif
328		}
219	–	}
329
330	<	void SimInfo::calcBoxL( void ){
330	>	void SimInfo::calcNdfTrans() {
331	>	int ndfTrans_local;
332
333	<	double dx, dy, dz, dsq;
333	>	ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
334
225	–	// boxVol = Determinant of Hmat
335
336	<	boxVol = matDet3( Hmat );
336	>	#ifdef IS_MPI
337	>	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
338	>	#else
339	>	ndfTrans_ = ndfTrans_local;
340	>	#endif
341
342	<	// boxLx
343	<
344	<	dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
232	<	dsq = dx*dx + dy*dy + dz*dz;
233	<	boxL[0] = sqrt( dsq );
234	<	//maxCutoff = 0.5 * boxL[0];
342	>	ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
343	>
344	>	}
345
346	<	// boxLy
347	<
348	<	dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
349	<	dsq = dx*dx + dy*dy + dz*dz;
350	<	boxL[1] = sqrt( dsq );
351	<	//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
346	>	void SimInfo::addExcludePairs(Molecule* mol) {
347	>	std::vector<Bond*>::iterator bondIter;
348	>	std::vector<Bend*>::iterator bendIter;
349	>	std::vector<Torsion*>::iterator torsionIter;
350	>	Bond* bond;
351	>	Bend* bend;
352	>	Torsion* torsion;
353	>	int a;
354	>	int b;
355	>	int c;
356	>	int d;
357
358	+	std::map<int, std::set<int> > atomGroups;
359
360	<	// boxLz
361	<
362	<	dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
363	<	dsq = dx*dx + dy*dy + dz*dz;
364	<	boxL[2] = sqrt( dsq );
365	<	//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
360	>	Molecule::RigidBodyIterator rbIter;
361	>	RigidBody* rb;
362	>	Molecule::IntegrableObjectIterator ii;
363	>	StuntDouble* integrableObject;
364	>
365	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
366	>	integrableObject = mol->nextIntegrableObject(ii)) {
367
368	<	//calculate the max cutoff
369	<	maxCutoff =  calcMaxCutOff();
370	<
371	<	checkCutOffs();
368	>	if (integrableObject->isRigidBody()) {
369	>	rb = static_cast<RigidBody*>(integrableObject);
370	>	std::vector<Atom*> atoms = rb->getAtoms();
371	>	std::set<int> rigidAtoms;
372	>	for (int i = 0; i < atoms.size(); ++i) {
373	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
374	>	}
375	>	for (int i = 0; i < atoms.size(); ++i) {
376	>	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
377	>	}
378	>	} else {
379	>	std::set<int> oneAtomSet;
380	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
381	>	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
382	>	}
383	>	}
384
385	<	}
385	>
386	>
387	>	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
388	>	a = bond->getAtomA()->getGlobalIndex();
389	>	b = bond->getAtomB()->getGlobalIndex();
390	>	exclude_.addPair(a, b);
391	>	}
392
393	+	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
394	+	a = bend->getAtomA()->getGlobalIndex();
395	+	b = bend->getAtomB()->getGlobalIndex();
396	+	c = bend->getAtomC()->getGlobalIndex();
397	+	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
398	+	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
399	+	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
400
401	<	double SimInfo::calcMaxCutOff(){
401	>	exclude_.addPairs(rigidSetA, rigidSetB);
402	>	exclude_.addPairs(rigidSetA, rigidSetC);
403	>	exclude_.addPairs(rigidSetB, rigidSetC);
404	>
405	>	//exclude_.addPair(a, b);
406	>	//exclude_.addPair(a, c);
407	>	//exclude_.addPair(b, c);
408	>	}
409
410	<	double ri[3], rj[3], rk[3];
411	<	double rij[3], rjk[3], rki[3];
412	<	double minDist;
410	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
411	>	a = torsion->getAtomA()->getGlobalIndex();
412	>	b = torsion->getAtomB()->getGlobalIndex();
413	>	c = torsion->getAtomC()->getGlobalIndex();
414	>	d = torsion->getAtomD()->getGlobalIndex();
415	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
416	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
417	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
418	>	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
419
420	<	ri[0] = Hmat[0][0];
421	<	ri[1] = Hmat[1][0];
422	<	ri[2] = Hmat[2][0];
420	>	exclude_.addPairs(rigidSetA, rigidSetB);
421	>	exclude_.addPairs(rigidSetA, rigidSetC);
422	>	exclude_.addPairs(rigidSetA, rigidSetD);
423	>	exclude_.addPairs(rigidSetB, rigidSetC);
424	>	exclude_.addPairs(rigidSetB, rigidSetD);
425	>	exclude_.addPairs(rigidSetC, rigidSetD);
426
427	<	rj[0] = Hmat[0][1];
428	<	rj[1] = Hmat[1][1];
429	<	rj[2] = Hmat[2][1];
427	>	/*
428	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
429	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
430	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
431	>	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
432	>	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
433	>	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
434	>
435	>
436	>	exclude_.addPair(a, b);
437	>	exclude_.addPair(a, c);
438	>	exclude_.addPair(a, d);
439	>	exclude_.addPair(b, c);
440	>	exclude_.addPair(b, d);
441	>	exclude_.addPair(c, d);
442	>	*/
443	>	}
444
445	<	rk[0] = Hmat[0][2];
446	<	rk[1] = Hmat[1][2];
447	<	rk[2] = Hmat[2][2];
448	<
449	<	crossProduct3(ri, rj, rij);
450	<	distXY = dotProduct3(rk,rij) / norm3(rij);
445	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
446	>	std::vector<Atom*> atoms = rb->getAtoms();
447	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
448	>	for (int j = i + 1; j < atoms.size(); ++j) {
449	>	a = atoms[i]->getGlobalIndex();
450	>	b = atoms[j]->getGlobalIndex();
451	>	exclude_.addPair(a, b);
452	>	}
453	>	}
454	>	}
455
456	<	crossProduct3(rj,rk, rjk);
281	<	distYZ = dotProduct3(ri,rjk) / norm3(rjk);
456	>	}
457
458	<	crossProduct3(rk,ri, rki);
459	<	distZX = dotProduct3(rj,rki) / norm3(rki);
458	>	void SimInfo::removeExcludePairs(Molecule* mol) {
459	>	std::vector<Bond*>::iterator bondIter;
460	>	std::vector<Bend*>::iterator bendIter;
461	>	std::vector<Torsion*>::iterator torsionIter;
462	>	Bond* bond;
463	>	Bend* bend;
464	>	Torsion* torsion;
465	>	int a;
466	>	int b;
467	>	int c;
468	>	int d;
469
470	<	minDist = min(min(distXY, distYZ), distZX);
287	<	return minDist/2;
288	<
289	<	}
470	>	std::map<int, std::set<int> > atomGroups;
471
472	<	void SimInfo::wrapVector( double thePos[3] ){
472	>	Molecule::RigidBodyIterator rbIter;
473	>	RigidBody* rb;
474	>	Molecule::IntegrableObjectIterator ii;
475	>	StuntDouble* integrableObject;
476	>
477	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
478	>	integrableObject = mol->nextIntegrableObject(ii)) {
479
480	<	int i;
481	<	double scaled[3];
480	>	if (integrableObject->isRigidBody()) {
481	>	rb = static_cast<RigidBody*>(integrableObject);
482	>	std::vector<Atom*> atoms = rb->getAtoms();
483	>	std::set<int> rigidAtoms;
484	>	for (int i = 0; i < atoms.size(); ++i) {
485	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
486	>	}
487	>	for (int i = 0; i < atoms.size(); ++i) {
488	>	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
489	>	}
490	>	} else {
491	>	std::set<int> oneAtomSet;
492	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
493	>	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
494	>	}
495	>	}
496
296	–	if( !orthoRhombic ){
297	–	// calc the scaled coordinates.
298	–
299	–
300	–	matVecMul3(HmatInv, thePos, scaled);
497
498	<	for(i=0; i<3; i++)
499	<	scaled[i] -= roundMe(scaled[i]);
500	<
501	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
502	<
307	<	matVecMul3(Hmat, scaled, thePos);
498	>	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
499	>	a = bond->getAtomA()->getGlobalIndex();
500	>	b = bond->getAtomB()->getGlobalIndex();
501	>	exclude_.removePair(a, b);
502	>	}
503
504	<	}
505	<	else{
506	<	// calc the scaled coordinates.
507	<
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	<	}
504	>	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
505	>	a = bend->getAtomA()->getGlobalIndex();
506	>	b = bend->getAtomB()->getGlobalIndex();
507	>	c = bend->getAtomC()->getGlobalIndex();
508
509	+	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
510	+	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
511	+	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
512
513	<	int SimInfo::getNDF(){
514	<	int ndf_local;
515	<
516	<	ndf_local = 0;
517	<
518	<	for(int i = 0; i < integrableObjects.size(); i++){
519	<	ndf_local += 3;
337	<	if (integrableObjects[i]->isDirectional()) {
338	<	if (integrableObjects[i]->isLinear())
339	<	ndf_local += 2;
340	<	else
341	<	ndf_local += 3;
513	>	exclude_.removePairs(rigidSetA, rigidSetB);
514	>	exclude_.removePairs(rigidSetA, rigidSetC);
515	>	exclude_.removePairs(rigidSetB, rigidSetC);
516	>
517	>	//exclude_.removePair(a, b);
518	>	//exclude_.removePair(a, c);
519	>	//exclude_.removePair(b, c);
520		}
343	–	}
521
522	<	// n_constraints is local, so subtract them on each processor:
522	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
523	>	a = torsion->getAtomA()->getGlobalIndex();
524	>	b = torsion->getAtomB()->getGlobalIndex();
525	>	c = torsion->getAtomC()->getGlobalIndex();
526	>	d = torsion->getAtomD()->getGlobalIndex();
527
528	<	ndf_local -= n_constraints;
528	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
529	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
530	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
531	>	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
532
533	<	#ifdef IS_MPI
534	<	MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
535	<	#else
536	<	ndf = ndf_local;
537	<	#endif
533	>	exclude_.removePairs(rigidSetA, rigidSetB);
534	>	exclude_.removePairs(rigidSetA, rigidSetC);
535	>	exclude_.removePairs(rigidSetA, rigidSetD);
536	>	exclude_.removePairs(rigidSetB, rigidSetC);
537	>	exclude_.removePairs(rigidSetB, rigidSetD);
538	>	exclude_.removePairs(rigidSetC, rigidSetD);
539
540	<	// nZconstraints is global, as are the 3 COM translations for the
541	<	// entire system:
540	>	/*
541	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
542	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
543	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
544	>	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
545	>	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
546	>	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
547
548	<	ndf = ndf - 3 - nZconstraints;
548	>
549	>	exclude_.removePair(a, b);
550	>	exclude_.removePair(a, c);
551	>	exclude_.removePair(a, d);
552	>	exclude_.removePair(b, c);
553	>	exclude_.removePair(b, d);
554	>	exclude_.removePair(c, d);
555	>	*/
556	>	}
557
558	<	return ndf;
559	<	}
558	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
559	>	std::vector<Atom*> atoms = rb->getAtoms();
560	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
561	>	for (int j = i + 1; j < atoms.size(); ++j) {
562	>	a = atoms[i]->getGlobalIndex();
563	>	b = atoms[j]->getGlobalIndex();
564	>	exclude_.removePair(a, b);
565	>	}
566	>	}
567	>	}
568
569	<	int SimInfo::getNDFraw() {
364	<	int ndfRaw_local;
569	>	}
570
366	–	// Raw degrees of freedom that we have to set
367	–	ndfRaw_local = 0;
571
572	<	for(int i = 0; i < integrableObjects.size(); i++){
573	<	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	<	}
378	<
379	<	#ifdef IS_MPI
380	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
381	<	#else
382	<	ndfRaw = ndfRaw_local;
383	<	#endif
572	>	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
573	>	int curStampId;
574
575	<	return ndfRaw;
576	<	}
575	>	//index from 0
576	>	curStampId = moleculeStamps_.size();
577
578	<	int SimInfo::getNDFtranslational() {
579	<	int ndfTrans_local;
578	>	moleculeStamps_.push_back(molStamp);
579	>	molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
580	>	}
581
582	<	ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
582	>	void SimInfo::update() {
583
584	+	setupSimType();
585
586		#ifdef IS_MPI
587	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
396	<	#else
397	<	ndfTrans = ndfTrans_local;
587	>	setupFortranParallel();
588		#endif
589
590	<	ndfTrans = ndfTrans - 3 - nZconstraints;
590	>	setupFortranSim();
591
592	<	return ndfTrans;
593	<	}
592	>	//setup fortran force field
593	>	/** @deprecate */
594	>	int isError = 0;
595	>
596	>	setupElectrostaticSummationMethod( isError );
597	>	setupSwitchingFunction();
598
599	<	int SimInfo::getTotIntegrableObjects() {
600	<	int nObjs_local;
601	<	int nObjs;
599	>	if(isError){
600	>	sprintf( painCave.errMsg,
601	>	"ForceField error: There was an error initializing the forceField in fortran.\n" );
602	>	painCave.isFatal = 1;
603	>	simError();
604	>	}
605	>
606	>
607	>	setupCutoff();
608
609	<	nObjs_local =  integrableObjects.size();
609	>	calcNdf();
610	>	calcNdfRaw();
611	>	calcNdfTrans();
612
613	+	fortranInitialized_ = true;
614	+	}
615
616	<	#ifdef IS_MPI
617	<	MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
618	<	#else
619	<	nObjs = nObjs_local;
620	<	#endif
616	>	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
617	>	SimInfo::MoleculeIterator mi;
618	>	Molecule* mol;
619	>	Molecule::AtomIterator ai;
620	>	Atom* atom;
621	>	std::set<AtomType*> atomTypes;
622
623	+	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
624
625	<	return nObjs;
626	<	}
625	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
626	>	atomTypes.insert(atom->getAtomType());
627	>	}
628	>
629	>	}
630
631	<	void SimInfo::refreshSim(){
631	>	return atomTypes;
632	>	}
633
634	<	simtype fInfo;
635	<	int isError;
636	<	int n_global;
637	<	int* excl;
634	>	void SimInfo::setupSimType() {
635	>	std::set<AtomType*>::iterator i;
636	>	std::set<AtomType*> atomTypes;
637	>	atomTypes = getUniqueAtomTypes();
638	>
639	>	int useLennardJones = 0;
640	>	int useElectrostatic = 0;
641	>	int useEAM = 0;
642	>	int useSC = 0;
643	>	int useCharge = 0;
644	>	int useDirectional = 0;
645	>	int useDipole = 0;
646	>	int useGayBerne = 0;
647	>	int useSticky = 0;
648	>	int useStickyPower = 0;
649	>	int useShape = 0;
650	>	int useFLARB = 0; //it is not in AtomType yet
651	>	int useDirectionalAtom = 0;
652	>	int useElectrostatics = 0;
653	>	//usePBC and useRF are from simParams
654	>	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
655	>	int useRF;
656	>	int useSF;
657	>	std::string myMethod;
658
659	<	fInfo.dielect = 0.0;
659	>	// set the useRF logical
660	>	useRF = 0;
661	>	useSF = 0;
662
663	<	if( useDipoles ){
664	<	if( useReactionField )fInfo.dielect = dielectric;
665	<	}
663	>
664	>	if (simParams_->haveElectrostaticSummationMethod()) {
665	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
666	>	toUpper(myMethod);
667	>	if (myMethod == "REACTION_FIELD") {
668	>	useRF=1;
669	>	} else {
670	>	if (myMethod == "SHIFTED_FORCE") {
671	>	useSF = 1;
672	>	}
673	>	}
674	>	}
675	>
676	>	//loop over all of the atom types
677	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
678	>	useLennardJones |= (*i)->isLennardJones();
679	>	useElectrostatic |= (*i)->isElectrostatic();
680	>	useEAM |= (*i)->isEAM();
681	>	useSC |= (*i)->isSC();
682	>	useCharge |= (*i)->isCharge();
683	>	useDirectional |= (*i)->isDirectional();
684	>	useDipole |= (*i)->isDipole();
685	>	useGayBerne |= (*i)->isGayBerne();
686	>	useSticky |= (*i)->isSticky();
687	>	useStickyPower |= (*i)->isStickyPower();
688	>	useShape |= (*i)->isShape();
689	>	}
690
691	<	fInfo.SIM_uses_PBC = usePBC;
692	<	//fInfo.SIM_uses_LJ = 0;
693	<	fInfo.SIM_uses_LJ = useLJ;
438	<	fInfo.SIM_uses_sticky = useSticky;
439	<	//fInfo.SIM_uses_sticky = 0;
440	<	fInfo.SIM_uses_charges = useCharges;
441	<	fInfo.SIM_uses_dipoles = useDipoles;
442	<	//fInfo.SIM_uses_dipoles = 0;
443	<	fInfo.SIM_uses_RF = useReactionField;
444	<	//fInfo.SIM_uses_RF = 0;
445	<	fInfo.SIM_uses_GB = useGB;
446	<	fInfo.SIM_uses_EAM = useEAM;
691	>	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
692	>	useDirectionalAtom = 1;
693	>	}
694
695	<	n_exclude = excludes->getSize();
696	<	excl = excludes->getFortranArray();
697	<
451	<	#ifdef IS_MPI
452	<	n_global = mpiSim->getNAtomsGlobal();
453	<	#else
454	<	n_global = n_atoms;
455	<	#endif
456	<
457	<	isError = 0;
458	<
459	<	getFortranGroupArrays(this, FglobalGroupMembership, mfact);
460	<	//it may not be a good idea to pass the address of first element in vector
461	<	//since c++ standard does not require vector to be stored continuously in meomory
462	<	//Most of the compilers will organize the memory of vector continuously
463	<	setFortranSim( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
464	<	&nGlobalExcludes, globalExcludes, molMembershipArray,
465	<	&mfact[0], &ngroup, &FglobalGroupMembership[0], &isError);
695	>	if (useCharge || useDipole) {
696	>	useElectrostatics = 1;
697	>	}
698
699	<	if( isError ){
699	>	#ifdef IS_MPI
700	>	int temp;
701	>
702	>	temp = usePBC;
703	>	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
704	>
705	>	temp = useDirectionalAtom;
706	>	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
707	>
708	>	temp = useLennardJones;
709	>	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
710	>
711	>	temp = useElectrostatics;
712	>	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
713	>
714	>	temp = useCharge;
715	>	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
716	>
717	>	temp = useDipole;
718	>	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
719	>
720	>	temp = useSticky;
721	>	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
722	>
723	>	temp = useStickyPower;
724	>	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
725
726	<	sprintf( painCave.errMsg,
727	<	"There was an error setting the simulation information in fortran.\n" );
728	<	painCave.isFatal = 1;
729	<	painCave.severity = OOPSE_ERROR;
730	<	simError();
726	>	temp = useGayBerne;
727	>	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
728	>
729	>	temp = useEAM;
730	>	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
731	>
732	>	temp = useSC;
733	>	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
734	>
735	>	temp = useShape;
736	>	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
737	>
738	>	temp = useFLARB;
739	>	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
740	>
741	>	temp = useRF;
742	>	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
743	>
744	>	temp = useSF;
745	>	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
746	>
747	>	#endif
748	>
749	>	fInfo_.SIM_uses_PBC = usePBC;
750	>	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
751	>	fInfo_.SIM_uses_LennardJones = useLennardJones;
752	>	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
753	>	fInfo_.SIM_uses_Charges = useCharge;
754	>	fInfo_.SIM_uses_Dipoles = useDipole;
755	>	fInfo_.SIM_uses_Sticky = useSticky;
756	>	fInfo_.SIM_uses_StickyPower = useStickyPower;
757	>	fInfo_.SIM_uses_GayBerne = useGayBerne;
758	>	fInfo_.SIM_uses_EAM = useEAM;
759	>	fInfo_.SIM_uses_SC = useSC;
760	>	fInfo_.SIM_uses_Shapes = useShape;
761	>	fInfo_.SIM_uses_FLARB = useFLARB;
762	>	fInfo_.SIM_uses_RF = useRF;
763	>	fInfo_.SIM_uses_SF = useSF;
764	>
765	>	if( myMethod == "REACTION_FIELD") {
766	>
767	>	if (simParams_->haveDielectric()) {
768	>	fInfo_.dielect = simParams_->getDielectric();
769	>	} else {
770	>	sprintf(painCave.errMsg,
771	>	"SimSetup Error: No Dielectric constant was set.\n"
772	>	"\tYou are trying to use Reaction Field without"
773	>	"\tsetting a dielectric constant!\n");
774	>	painCave.isFatal = 1;
775	>	simError();
776	>	}
777	>	}
778	>
779		}
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	–	}
780
781	<	void SimInfo::setDefaultRcut( double theRcut ){
782	<
783	<	haveRcut = 1;
784	<	rCut = theRcut;
785	<	rList = rCut + 1.0;
786	<
787	<	notifyFortranCutoffs( &rCut, &rSw, &rList );
494	<	}
781	>	void SimInfo::setupFortranSim() {
782	>	int isError;
783	>	int nExclude;
784	>	std::vector<int> fortranGlobalGroupMembership;
785	>
786	>	nExclude = exclude_.getSize();
787	>	isError = 0;
788
789	<	void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
789	>	//globalGroupMembership_ is filled by SimCreator
790	>	for (int i = 0; i < nGlobalAtoms_; i++) {
791	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
792	>	}
793
794	<	rSw = theRsw;
795	<	setDefaultRcut( theRcut );
796	<	}
794	>	//calculate mass ratio of cutoff group
795	>	std::vector<double> mfact;
796	>	SimInfo::MoleculeIterator mi;
797	>	Molecule* mol;
798	>	Molecule::CutoffGroupIterator ci;
799	>	CutoffGroup* cg;
800	>	Molecule::AtomIterator ai;
801	>	Atom* atom;
802	>	double totalMass;
803
804	+	//to avoid memory reallocation, reserve enough space for mfact
805	+	mfact.reserve(getNCutoffGroups());
806	+
807	+	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
808	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
809
810	<	void SimInfo::checkCutOffs( void ){
811	<
812	<	if( boxIsInit ){
810	>	totalMass = cg->getMass();
811	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
812	>	// Check for massless groups - set mfact to 1 if true
813	>	if (totalMass != 0)
814	>	mfact.push_back(atom->getMass()/totalMass);
815	>	else
816	>	mfact.push_back( 1.0 );
817	>	}
818	>
819	>	}
820	>	}
821	>
822	>	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
823	>	std::vector<int> identArray;
824	>
825	>	//to avoid memory reallocation, reserve enough space identArray
826	>	identArray.reserve(getNAtoms());
827
828	<	//we need to check cutOffs against the box
828	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
829	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
830	>	identArray.push_back(atom->getIdent());
831	>	}
832	>	}
833	>
834	>	//fill molMembershipArray
835	>	//molMembershipArray is filled by SimCreator
836	>	std::vector<int> molMembershipArray(nGlobalAtoms_);
837	>	for (int i = 0; i < nGlobalAtoms_; i++) {
838	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
839	>	}
840
841	<	if( rCut > maxCutoff ){
841	>	//setup fortran simulation
842	>	int nGlobalExcludes = 0;
843	>	int* globalExcludes = NULL;
844	>	int* excludeList = exclude_.getExcludeList();
845	>	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
846	>	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
847	>	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
848	>
849	>	if( isError ){
850	>
851		sprintf( painCave.errMsg,
852	<	"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;
852	>	"There was an error setting the simulation information in fortran.\n" );
853		painCave.isFatal = 1;
854	+	painCave.severity = OOPSE_ERROR;
855		simError();
856	<	}
857	<	} else {
858	<	// initialize this stuff before using it, OK?
859	<	sprintf( painCave.errMsg,
860	<	"Trying to check cutoffs without a box.\n"
861	<	"\tOOPSE should have better programmers than that.\n" );
862	<	painCave.severity = OOPSE_ERROR;
533	<	painCave.isFatal = 1;
534	<	simError();
856	>	}
857	>
858	>	#ifdef IS_MPI
859	>	sprintf( checkPointMsg,
860	>	"succesfully sent the simulation information to fortran.\n");
861	>	MPIcheckPoint();
862	>	#endif // is_mpi
863		}
536	–
537	–	}
864
539	–	void SimInfo::addProperty(GenericData* prop){
865
866	<	map<string, GenericData*>::iterator result;
867	<	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()){
866	>	#ifdef IS_MPI
867	>	void SimInfo::setupFortranParallel() {
868
869	<	delete (*result).second;
870	<	(*result).second = prop;
871	<
872	<	}
873	<	else{
869	>	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
870	>	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
871	>	std::vector<int> localToGlobalCutoffGroupIndex;
872	>	SimInfo::MoleculeIterator mi;
873	>	Molecule::AtomIterator ai;
874	>	Molecule::CutoffGroupIterator ci;
875	>	Molecule* mol;
876	>	Atom* atom;
877	>	CutoffGroup* cg;
878	>	mpiSimData parallelData;
879	>	int isError;
880
881	<	properties[prop->getID()] = prop;
881	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
882
883	<	}
884	<
885	<	}
883	>	//local index(index in DataStorge) of atom is important
884	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
885	>	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
886	>	}
887
888	<	GenericData* SimInfo::getProperty(const string& propName){
889	<
890	<	map<string, GenericData*>::iterator result;
891	<
892	<	//string lowerCaseName = ();
893	<
567	<	result = properties.find(propName);
568	<
569	<	if(result != properties.end())
570	<	return (*result).second;
571	<	else
572	<	return NULL;
573	<	}
888	>	//local index of cutoff group is trivial, it only depends on the order of travesing
889	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
890	>	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
891	>	}
892	>
893	>	}
894
895	+	//fill up mpiSimData struct
896	+	parallelData.nMolGlobal = getNGlobalMolecules();
897	+	parallelData.nMolLocal = getNMolecules();
898	+	parallelData.nAtomsGlobal = getNGlobalAtoms();
899	+	parallelData.nAtomsLocal = getNAtoms();
900	+	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
901	+	parallelData.nGroupsLocal = getNCutoffGroups();
902	+	parallelData.myNode = worldRank;
903	+	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
904
905	<	void SimInfo::getFortranGroupArrays(SimInfo* info,
906	<	vector<int>& FglobalGroupMembership,
907	<	vector<double>& mfact){
908	<
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	<
905	>	//pass mpiSimData struct and index arrays to fortran
906	>	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
907	>	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
908	>	&localToGlobalCutoffGroupIndex[0], &isError);
909
910	<	// Fix the silly fortran indexing problem
911	<	#ifdef IS_MPI
912	<	numAtom = mpiSim->getNAtomsGlobal();
913	<	#else
914	<	numAtom = n_atoms;
910	>	if (isError) {
911	>	sprintf(painCave.errMsg,
912	>	"mpiRefresh errror: fortran didn't like something we gave it.\n");
913	>	painCave.isFatal = 1;
914	>	simError();
915	>	}
916	>
917	>	sprintf(checkPointMsg, " mpiRefresh successful.\n");
918	>	MPIcheckPoint();
919	>
920	>
921	>	}
922	>
923		#endif
603	–	for (int i = 0; i < numAtom; i++)
604	–	FglobalGroupMembership.push_back(globalGroupMembership[i] + 1);
605	–
924
925	<	myMols = info->molecules;
926	<	numMol = info->n_mol;
927	<	for(int i  = 0; i < numMol; i++){
928	<	numCutoffGroups = myMols[i].getNCutoffGroups();
929	<	for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff);
930	<	myCutoffGroup != NULL;
931	<	myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
925	>	void SimInfo::setupCutoff() {
926	>
927	>	// Check the cutoff policy
928	>	int cp =  TRADITIONAL_CUTOFF_POLICY;
929	>	if (simParams_->haveCutoffPolicy()) {
930	>	std::string myPolicy = simParams_->getCutoffPolicy();
931	>	toUpper(myPolicy);
932	>	if (myPolicy == "MIX") {
933	>	cp = MIX_CUTOFF_POLICY;
934	>	} else {
935	>	if (myPolicy == "MAX") {
936	>	cp = MAX_CUTOFF_POLICY;
937	>	} else {
938	>	if (myPolicy == "TRADITIONAL") {
939	>	cp = TRADITIONAL_CUTOFF_POLICY;
940	>	} else {
941	>	// throw error
942	>	sprintf( painCave.errMsg,
943	>	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
944	>	painCave.isFatal = 1;
945	>	simError();
946	>	}
947	>	}
948	>	}
949	>	}
950	>	notifyFortranCutoffPolicy(&cp);
951
952	<	totalMass = myCutoffGroup->getMass();
953	<
954	<	for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom);
955	<	cutoffAtom != NULL;
956	<	cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
957	<	mfact.push_back(cutoffAtom->getMass()/totalMass);
958	<	}
952	>	// Check the Skin Thickness for neighborlists
953	>	double skin;
954	>	if (simParams_->haveSkinThickness()) {
955	>	skin = simParams_->getSkinThickness();
956	>	notifyFortranSkinThickness(&skin);
957	>	}
958	>
959	>	// Check if the cutoff was set explicitly:
960	>	if (simParams_->haveCutoffRadius()) {
961	>	rcut_ = simParams_->getCutoffRadius();
962	>	if (simParams_->haveSwitchingRadius()) {
963	>	rsw_  = simParams_->getSwitchingRadius();
964	>	} else {
965	>	rsw_ = rcut_;
966	>	}
967	>	notifyFortranCutoffs(&rcut_, &rsw_);
968	>
969	>	} else {
970	>
971	>	// For electrostatic atoms, we'll assume a large safe value:
972	>	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
973	>	sprintf(painCave.errMsg,
974	>	"SimCreator Warning: No value was set for the cutoffRadius.\n"
975	>	"\tOOPSE will use a default value of 15.0 angstroms"
976	>	"\tfor the cutoffRadius.\n");
977	>	painCave.isFatal = 0;
978	>	simError();
979	>	rcut_ = 15.0;
980	>
981	>	if (simParams_->haveElectrostaticSummationMethod()) {
982	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
983	>	toUpper(myMethod);
984	>	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
985	>	if (simParams_->haveSwitchingRadius()){
986	>	sprintf(painCave.errMsg,
987	>	"SimInfo Warning: A value was set for the switchingRadius\n"
988	>	"\teven though the electrostaticSummationMethod was\n"
989	>	"\tset to %s\n", myMethod.c_str());
990	>	painCave.isFatal = 1;
991	>	simError();
992	>	}
993	>	}
994	>	}
995	>
996	>	if (simParams_->haveSwitchingRadius()){
997	>	rsw_ = simParams_->getSwitchingRadius();
998	>	} else {
999	>	sprintf(painCave.errMsg,
1000	>	"SimCreator Warning: No value was set for switchingRadius.\n"
1001	>	"\tOOPSE will use a default value of\n"
1002	>	"\t0.85 * cutoffRadius for the switchingRadius\n");
1003	>	painCave.isFatal = 0;
1004	>	simError();
1005	>	rsw_ = 0.85 * rcut_;
1006	>	}
1007	>	notifyFortranCutoffs(&rcut_, &rsw_);
1008	>	} else {
1009	>	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1010	>	// We'll punt and let fortran figure out the cutoffs later.
1011	>
1012	>	notifyFortranYouAreOnYourOwn();
1013	>
1014	>	}
1015		}
1016		}
1017
1018	<	}
1018	>	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1019	>
1020	>	int errorOut;
1021	>	int esm =  NONE;
1022	>	int sm = UNDAMPED;
1023	>	double alphaVal;
1024	>	double dielectric;
1025	>
1026	>	errorOut = isError;
1027	>	alphaVal = simParams_->getDampingAlpha();
1028	>	dielectric = simParams_->getDielectric();
1029	>
1030	>	if (simParams_->haveElectrostaticSummationMethod()) {
1031	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1032	>	toUpper(myMethod);
1033	>	if (myMethod == "NONE") {
1034	>	esm = NONE;
1035	>	} else {
1036	>	if (myMethod == "SWITCHING_FUNCTION") {
1037	>	esm = SWITCHING_FUNCTION;
1038	>	} else {
1039	>	if (myMethod == "SHIFTED_POTENTIAL") {
1040	>	esm = SHIFTED_POTENTIAL;
1041	>	} else {
1042	>	if (myMethod == "SHIFTED_FORCE") {
1043	>	esm = SHIFTED_FORCE;
1044	>	} else {
1045	>	if (myMethod == "REACTION_FIELD") {
1046	>	esm = REACTION_FIELD;
1047	>	} else {
1048	>	// throw error
1049	>	sprintf( painCave.errMsg,
1050	>	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1051	>	"\t(Input file specified %s .)\n"
1052	>	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1053	>	"\t\"shifted_potential\", \"shifted_force\", or \n"
1054	>	"\t\"reaction_field\".\n", myMethod.c_str() );
1055	>	painCave.isFatal = 1;
1056	>	simError();
1057	>	}
1058	>	}
1059	>	}
1060	>	}
1061	>	}
1062	>	}
1063	>
1064	>	if (simParams_->haveElectrostaticScreeningMethod()) {
1065	>	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1066	>	toUpper(myScreen);
1067	>	if (myScreen == "UNDAMPED") {
1068	>	sm = UNDAMPED;
1069	>	} else {
1070	>	if (myScreen == "DAMPED") {
1071	>	sm = DAMPED;
1072	>	if (!simParams_->haveDampingAlpha()) {
1073	>	//throw error
1074	>	sprintf( painCave.errMsg,
1075	>	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1076	>	"\tA default value of %f (1/ang) will be used.\n", alphaVal);
1077	>	painCave.isFatal = 0;
1078	>	simError();
1079	>	}
1080	>	} else {
1081	>	// throw error
1082	>	sprintf( painCave.errMsg,
1083	>	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1084	>	"\t(Input file specified %s .)\n"
1085	>	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1086	>	"or \"damped\".\n", myScreen.c_str() );
1087	>	painCave.isFatal = 1;
1088	>	simError();
1089	>	}
1090	>	}
1091	>	}
1092	>
1093	>	// let's pass some summation method variables to fortran
1094	>	setElectrostaticSummationMethod( &esm );
1095	>	notifyFortranElectrostaticMethod( &esm );
1096	>	setScreeningMethod( &sm );
1097	>	setDampingAlpha( &alphaVal );
1098	>	setReactionFieldDielectric( &dielectric );
1099	>	initFortranFF( &errorOut );
1100	>	}
1101	>
1102	>	void SimInfo::setupSwitchingFunction() {
1103	>	int ft = CUBIC;
1104	>
1105	>	if (simParams_->haveSwitchingFunctionType()) {
1106	>	std::string funcType = simParams_->getSwitchingFunctionType();
1107	>	toUpper(funcType);
1108	>	if (funcType == "CUBIC") {
1109	>	ft = CUBIC;
1110	>	} else {
1111	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1112	>	ft = FIFTH_ORDER_POLY;
1113	>	} else {
1114	>	// throw error
1115	>	sprintf( painCave.errMsg,
1116	>	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1117	>	painCave.isFatal = 1;
1118	>	simError();
1119	>	}
1120	>	}
1121	>	}
1122	>
1123	>	// send switching function notification to switcheroo
1124	>	setFunctionType(&ft);
1125	>
1126	>	}
1127	>
1128	>	void SimInfo::addProperty(GenericData* genData) {
1129	>	properties_.addProperty(genData);
1130	>	}
1131	>
1132	>	void SimInfo::removeProperty(const std::string& propName) {
1133	>	properties_.removeProperty(propName);
1134	>	}
1135	>
1136	>	void SimInfo::clearProperties() {
1137	>	properties_.clearProperties();
1138	>	}
1139	>
1140	>	std::vector<std::string> SimInfo::getPropertyNames() {
1141	>	return properties_.getPropertyNames();
1142	>	}
1143	>
1144	>	std::vector<GenericData*> SimInfo::getProperties() {
1145	>	return properties_.getProperties();
1146	>	}
1147	>
1148	>	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1149	>	return properties_.getPropertyByName(propName);
1150	>	}
1151	>
1152	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1153	>	if (sman_ == sman) {
1154	>	return;
1155	>	}
1156	>	delete sman_;
1157	>	sman_ = sman;
1158	>
1159	>	Molecule* mol;
1160	>	RigidBody* rb;
1161	>	Atom* atom;
1162	>	SimInfo::MoleculeIterator mi;
1163	>	Molecule::RigidBodyIterator rbIter;
1164	>	Molecule::AtomIterator atomIter;;
1165	>
1166	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1167	>
1168	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1169	>	atom->setSnapshotManager(sman_);
1170	>	}
1171	>
1172	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1173	>	rb->setSnapshotManager(sman_);
1174	>	}
1175	>	}
1176	>
1177	>	}
1178	>
1179	>	Vector3d SimInfo::getComVel(){
1180	>	SimInfo::MoleculeIterator i;
1181	>	Molecule* mol;
1182	>
1183	>	Vector3d comVel(0.0);
1184	>	double totalMass = 0.0;
1185	>
1186	>
1187	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1188	>	double mass = mol->getMass();
1189	>	totalMass += mass;
1190	>	comVel += mass * mol->getComVel();
1191	>	}
1192	>
1193	>	#ifdef IS_MPI
1194	>	double tmpMass = totalMass;
1195	>	Vector3d tmpComVel(comVel);
1196	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1197	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1198	>	#endif
1199	>
1200	>	comVel /= totalMass;
1201	>
1202	>	return comVel;
1203	>	}
1204	>
1205	>	Vector3d SimInfo::getCom(){
1206	>	SimInfo::MoleculeIterator i;
1207	>	Molecule* mol;
1208	>
1209	>	Vector3d com(0.0);
1210	>	double totalMass = 0.0;
1211	>
1212	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1213	>	double mass = mol->getMass();
1214	>	totalMass += mass;
1215	>	com += mass * mol->getCom();
1216	>	}
1217	>
1218	>	#ifdef IS_MPI
1219	>	double tmpMass = totalMass;
1220	>	Vector3d tmpCom(com);
1221	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1222	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1223	>	#endif
1224	>
1225	>	com /= totalMass;
1226	>
1227	>	return com;
1228	>
1229	>	}
1230	>
1231	>	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1232	>
1233	>	return o;
1234	>	}
1235	>
1236	>
1237	>	/*
1238	>	Returns center of mass and center of mass velocity in one function call.
1239	>	*/
1240	>
1241	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1242	>	SimInfo::MoleculeIterator i;
1243	>	Molecule* mol;
1244	>
1245	>
1246	>	double totalMass = 0.0;
1247	>
1248	>
1249	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1250	>	double mass = mol->getMass();
1251	>	totalMass += mass;
1252	>	com += mass * mol->getCom();
1253	>	comVel += mass * mol->getComVel();
1254	>	}
1255	>
1256	>	#ifdef IS_MPI
1257	>	double tmpMass = totalMass;
1258	>	Vector3d tmpCom(com);
1259	>	Vector3d tmpComVel(comVel);
1260	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1261	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1262	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1263	>	#endif
1264	>
1265	>	com /= totalMass;
1266	>	comVel /= totalMass;
1267	>	}
1268	>
1269	>	/*
1270	>	Return intertia tensor for entire system and angular momentum Vector.
1271	>
1272	>
1273	>	[  Ixx -Ixy  -Ixz ]
1274	>	J =| -Iyx  Iyy  -Iyz |
1275	>	[ -Izx -Iyz   Izz ]
1276	>	*/
1277	>
1278	>	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1279	>
1280	>
1281	>	double xx = 0.0;
1282	>	double yy = 0.0;
1283	>	double zz = 0.0;
1284	>	double xy = 0.0;
1285	>	double xz = 0.0;
1286	>	double yz = 0.0;
1287	>	Vector3d com(0.0);
1288	>	Vector3d comVel(0.0);
1289	>
1290	>	getComAll(com, comVel);
1291	>
1292	>	SimInfo::MoleculeIterator i;
1293	>	Molecule* mol;
1294	>
1295	>	Vector3d thisq(0.0);
1296	>	Vector3d thisv(0.0);
1297	>
1298	>	double thisMass = 0.0;
1299	>
1300	>
1301	>
1302	>
1303	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1304	>
1305	>	thisq = mol->getCom()-com;
1306	>	thisv = mol->getComVel()-comVel;
1307	>	thisMass = mol->getMass();
1308	>	// Compute moment of intertia coefficients.
1309	>	xx += thisq[0]*thisq[0]*thisMass;
1310	>	yy += thisq[1]*thisq[1]*thisMass;
1311	>	zz += thisq[2]*thisq[2]*thisMass;
1312	>
1313	>	// compute products of intertia
1314	>	xy += thisq[0]*thisq[1]*thisMass;
1315	>	xz += thisq[0]*thisq[2]*thisMass;
1316	>	yz += thisq[1]*thisq[2]*thisMass;
1317	>
1318	>	angularMomentum += cross( thisq, thisv ) * thisMass;
1319	>
1320	>	}
1321	>
1322	>
1323	>	inertiaTensor(0,0) = yy + zz;
1324	>	inertiaTensor(0,1) = -xy;
1325	>	inertiaTensor(0,2) = -xz;
1326	>	inertiaTensor(1,0) = -xy;
1327	>	inertiaTensor(1,1) = xx + zz;
1328	>	inertiaTensor(1,2) = -yz;
1329	>	inertiaTensor(2,0) = -xz;
1330	>	inertiaTensor(2,1) = -yz;
1331	>	inertiaTensor(2,2) = xx + yy;
1332	>
1333	>	#ifdef IS_MPI
1334	>	Mat3x3d tmpI(inertiaTensor);
1335	>	Vector3d tmpAngMom;
1336	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1337	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1338	>	#endif
1339	>
1340	>	return;
1341	>	}
1342	>
1343	>	//Returns the angular momentum of the system
1344	>	Vector3d SimInfo::getAngularMomentum(){
1345	>
1346	>	Vector3d com(0.0);
1347	>	Vector3d comVel(0.0);
1348	>	Vector3d angularMomentum(0.0);
1349	>
1350	>	getComAll(com,comVel);
1351	>
1352	>	SimInfo::MoleculeIterator i;
1353	>	Molecule* mol;
1354	>
1355	>	Vector3d thisr(0.0);
1356	>	Vector3d thisp(0.0);
1357	>
1358	>	double thisMass;
1359	>
1360	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1361	>	thisMass = mol->getMass();
1362	>	thisr = mol->getCom()-com;
1363	>	thisp = (mol->getComVel()-comVel)*thisMass;
1364	>
1365	>	angularMomentum += cross( thisr, thisp );
1366	>
1367	>	}
1368	>
1369	>	#ifdef IS_MPI
1370	>	Vector3d tmpAngMom;
1371	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1372	>	#endif
1373	>
1374	>	return angularMomentum;
1375	>	}
1376	>
1377	>
1378	>	}//end namespace oopse
1379	>

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