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root/OpenMD/branches/development/src/brains/SimInfo.cpp

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 143 by chrisfen, Fri Oct 22 22:54:01 2004 UTC vs.
Revision 1078 by gezelter, Wed Oct 18 21:58:48 2006 UTC

#	Line 1 | Line 1
1	<	#include <stdlib.h>
2	<	#include <string.h>
3	<	#include <math.h>
1	>	/*
2	>	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	>	*
4	>	* The University of Notre Dame grants you ("Licensee") a
5	>	* non-exclusive, royalty free, license to use, modify and
6	>	* redistribute this software in source and binary code form, provided
7	>	* that the following conditions are met:
8	>	*
9	>	* 1. Acknowledgement of the program authors must be made in any
10	>	*    publication of scientific results based in part on use of the
11	>	*    program.  An acceptable form of acknowledgement is citation of
12	>	*    the article in which the program was described (Matthew
13	>	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	>	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	>	*    Parallel Simulation Engine for Molecular Dynamics,"
16	>	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	>	*
18	>	* 2. Redistributions of source code must retain the above copyright
19	>	*    notice, this list of conditions and the following disclaimer.
20	>	*
21	>	* 3. Redistributions in binary form must reproduce the above copyright
22	>	*    notice, this list of conditions and the following disclaimer in the
23	>	*    documentation and/or other materials provided with the
24	>	*    distribution.
25	>	*
26	>	* This software is provided "AS IS," without a warranty of any
27	>	* kind. All express or implied conditions, representations and
28	>	* warranties, including any implied warranty of merchantability,
29	>	* fitness for a particular purpose or non-infringement, are hereby
30	>	* excluded.  The University of Notre Dame and its licensors shall not
31	>	* be liable for any damages suffered by licensee as a result of
32	>	* using, modifying or distributing the software or its
33	>	* derivatives. In no event will the University of Notre Dame or its
34	>	* licensors be liable for any lost revenue, profit or data, or for
35	>	* direct, indirect, special, consequential, incidental or punitive
36	>	* damages, however caused and regardless of the theory of liability,
37	>	* arising out of the use of or inability to use software, even if the
38	>	* University of Notre Dame has been advised of the possibility of
39	>	* such damages.
40	>	*/
41	>
42	>	/**
43	>	* @file SimInfo.cpp
44	>	* @author    tlin
45	>	* @date  11/02/2004
46	>	* @version 1.0
47	>	*/
48
49	<	#include <iostream>
50	<	using namespace std;
49	>	#include <algorithm>
50	>	#include <set>
51	>	#include <map>
52
53		#include "brains/SimInfo.hpp"
54	<	#define __C
55	<	#include "brains/fSimulation.h"
54	>	#include "math/Vector3.hpp"
55	>	#include "primitives/Molecule.hpp"
56	>	#include "primitives/StuntDouble.hpp"
57	>	#include "UseTheForce/fCutoffPolicy.h"
58	>	#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
59	>	#include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h"
60	>	#include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
61	>	#include "UseTheForce/doForces_interface.h"
62	>	#include "UseTheForce/DarkSide/electrostatic_interface.h"
63	>	#include "UseTheForce/DarkSide/switcheroo_interface.h"
64	>	#include "utils/MemoryUtils.hpp"
65		#include "utils/simError.h"
66	<	#include "UseTheForce/DarkSide/simulation_interface.h"
67	<	#include "UseTheForce/notifyCutoffs_interface.h"
66	>	#include "selection/SelectionManager.hpp"
67	>	#include "io/ForceFieldOptions.hpp"
68	>	#include "UseTheForce/ForceField.hpp"
69
15	–	//#include "UseTheForce/fortranWrappers.hpp"
16	–
17	–	#include "math/MatVec3.h"
18	–
70		#ifdef IS_MPI
71	<	#include "brains/mpiSimulation.hpp"
72	<	#endif
71	>	#include "UseTheForce/mpiComponentPlan.h"
72	>	#include "UseTheForce/DarkSide/simParallel_interface.h"
73	>	#endif
74
75	<	inline double roundMe( double x ){
76	<	return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
77	<	}
78	<
79	<	inline double min( double a, double b ){
80	<	return (a < b ) ? a : b;
81	<	}
75	>	namespace oopse {
76	>	std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
77	>	std::map<int, std::set<int> >::iterator i = container.find(index);
78	>	std::set<int> result;
79	>	if (i != container.end()) {
80	>	result = i->second;
81	>	}
82
83	<	SimInfo* currentInfo;
84	<
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;
83	>	return result;
84	>	}
85
86	<	resetTime = 1e99;
86	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
87	>	forceField_(ff), simParams_(simParams),
88	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
89	>	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
90	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
91	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
92	>	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
93	>	sman_(NULL), fortranInitialized_(false), calcBoxDipole_(false) {
94
95	<	orthoRhombic = 0;
96	<	orthoTolerance = 1E-6;
97	<	useInitXSstate = true;
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	>	std::vector<Component*> components = simParams->getComponents();
103	>
104	>	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
105	>	molStamp = (*i)->getMoleculeStamp();
106	>	nMolWithSameStamp = (*i)->getNMol();
107	>
108	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
109
110	<	usePBC = 0;
111	<	useDirectionalAtoms = 0;
61	<	useLennardJones = 0;
62	<	useElectrostatics = 0;
63	<	useCharges = 0;
64	<	useDipoles = 0;
65	<	useSticky = 0;
66	<	useGayBerne = 0;
67	<	useEAM = 0;
68	<	useShapes = 0;
69	<	useFLARB = 0;
110	>	//calculate atoms in molecules
111	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
112
113	<	useSolidThermInt = 0;
114	<	useLiquidThermInt = 0;
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->getCutoffGroupStamp(j);
119	>	nAtomsInGroups += cgStamp->getNMembers();
120	>	}
121
122	<	haveCutoffGroups = false;
122	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
123
124	<	excludes = Exclude::Instance();
124	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
125
126	<	myConfiguration = new SimState();
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->getRigidBodyStamp(j);
132	>	nAtomsInRigidBodies += rbStamp->getNMembers();
133	>	}
134
135	<	has_minimizer = false;
136	<	the_minimizer =NULL;
135	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
136	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
137	>
138	>	}
139
140	<	ngroup = 0;
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	<	}
148	<
149	<
150	<	SimInfo::~SimInfo(){
151	<
152	<	delete myConfiguration;
153	<
92	<	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++)
95	<	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]) {
100	<
101	<	int i, j;
102	<	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 sman_;
171	>	delete simParams_;
172	>	delete forceField_;
173	>	}
174
175	<	tempMat[0][0] = newBox[0];
176	<	tempMat[1][1] = newBox[1];
177	<	tempMat[2][2] = newBox[2];
175	>	int SimInfo::getNGlobalConstraints() {
176	>	int nGlobalConstraints;
177	>	#ifdef IS_MPI
178	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
179	>	MPI_COMM_WORLD);
180	>	#else
181	>	nGlobalConstraints =  nConstraints_;
182	>	#endif
183	>	return nGlobalConstraints;
184	>	}
185
186	<	setBoxM( tempMat );
186	>	bool SimInfo::addMolecule(Molecule* mol) {
187	>	MoleculeIterator i;
188
189	<	}
189	>	i = molecules_.find(mol->getGlobalIndex());
190	>	if (i == molecules_.end() ) {
191
192	<	void SimInfo::setBoxM( double theBox[3][3] ){
193	<
194	<	int i, j;
195	<	double FortranHmat[9]; // to preserve compatibility with Fortran the
196	<	// ordering in the array is as follows:
197	<	// [ 0 3 6 ]
198	<	// [ 1 4 7 ]
199	<	// [ 2 5 8 ]
200	<	double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
192	>	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
193	>
194	>	nAtoms_ += mol->getNAtoms();
195	>	nBonds_ += mol->getNBonds();
196	>	nBends_ += mol->getNBends();
197	>	nTorsions_ += mol->getNTorsions();
198	>	nRigidBodies_ += mol->getNRigidBodies();
199	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
200	>	nCutoffGroups_ += mol->getNCutoffGroups();
201	>	nConstraints_ += mol->getNConstraintPairs();
202
203	<	if( !boxIsInit ) boxIsInit = 1;
204	<
205	<	for(i=0; i < 3; i++)
206	<	for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
207	<
130	<	calcBoxL();
131	<	calcHmatInv();
132	<
133	<	for(i=0; i < 3; i++) {
134	<	for (j=0; j < 3; j++) {
135	<	FortranHmat[3*j + i] = Hmat[i][j];
136	<	FortranHmatInv[3*j + i] = HmatInv[i][j];
203	>	addExcludePairs(mol);
204	>
205	>	return true;
206	>	} else {
207	>	return false;
208		}
209		}
210
211	<	setFortranBox(FortranHmat, FortranHmatInv, &orthoRhombic);
212	<
213	<	}
143	<
211	>	bool SimInfo::removeMolecule(Molecule* mol) {
212	>	MoleculeIterator i;
213	>	i = molecules_.find(mol->getGlobalIndex());
214
215	<	void SimInfo::getBoxM (double theBox[3][3]) {
215	>	if (i != molecules_.end() ) {
216
217	<	int i, j;
218	<	for(i=0; i<3; i++)
219	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
220	<	}
217	>	assert(mol == i->second);
218	>
219	>	nAtoms_ -= mol->getNAtoms();
220	>	nBonds_ -= mol->getNBonds();
221	>	nBends_ -= mol->getNBends();
222	>	nTorsions_ -= mol->getNTorsions();
223	>	nRigidBodies_ -= mol->getNRigidBodies();
224	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
225	>	nCutoffGroups_ -= mol->getNCutoffGroups();
226	>	nConstraints_ -= mol->getNConstraintPairs();
227
228	+	removeExcludePairs(mol);
229	+	molecules_.erase(mol->getGlobalIndex());
230
231	<	void SimInfo::scaleBox(double scale) {
232	<	double theBox[3][3];
233	<	int i, j;
231	>	delete mol;
232	>
233	>	return true;
234	>	} else {
235	>	return false;
236	>	}
237
157	–	// cerr << "Scaling box by " << scale << "\n";
238
239	<	for(i=0; i<3; i++)
160	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
239	>	}
240
241	<	setBoxM(theBox);
241	>
242	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
243	>	i = molecules_.begin();
244	>	return i == molecules_.end() ? NULL : i->second;
245	>	}
246
247	<	}
247	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
248	>	++i;
249	>	return i == molecules_.end() ? NULL : i->second;
250	>	}
251
166	–	void SimInfo::calcHmatInv( void ) {
167	–
168	–	int oldOrtho;
169	–	int i,j;
170	–	double smallDiag;
171	–	double tol;
172	–	double sanity[3][3];
252
253	<	invertMat3( Hmat, HmatInv );
253	>	void SimInfo::calcNdf() {
254	>	int ndf_local;
255	>	MoleculeIterator i;
256	>	std::vector<StuntDouble*>::iterator j;
257	>	Molecule* mol;
258	>	StuntDouble* integrableObject;
259
260	<	// check to see if Hmat is orthorhombic
261	<
262	<	oldOrtho = orthoRhombic;
260	>	ndf_local = 0;
261	>
262	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
263	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
264	>	integrableObject = mol->nextIntegrableObject(j)) {
265
266	<	smallDiag = fabs(Hmat[0][0]);
181	<	if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
182	<	if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
183	<	tol = smallDiag * orthoTolerance;
266	>	ndf_local += 3;
267
268	<	orthoRhombic = 1;
269	<
270	<	for (i = 0; i < 3; i++ ) {
271	<	for (j = 0 ; j < 3; j++) {
272	<	if (i != j) {
273	<	if (orthoRhombic) {
274	<	if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
275	<	}
268	>	if (integrableObject->isDirectional()) {
269	>	if (integrableObject->isLinear()) {
270	>	ndf_local += 2;
271	>	} else {
272	>	ndf_local += 3;
273	>	}
274	>	}
275	>
276		}
277		}
195	–	}
196	–
197	–	if( oldOrtho != orthoRhombic ){
278
279	<	if( orthoRhombic ) {
280	<	sprintf( painCave.errMsg,
201	<	"OOPSE is switching from the default Non-Orthorhombic\n"
202	<	"\tto the faster Orthorhombic periodic boundary computations.\n"
203	<	"\tThis is usually a good thing, but if you wan't the\n"
204	<	"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
205	<	"\tvariable ( currently set to %G ) smaller.\n",
206	<	orthoTolerance);
207	<	painCave.severity = OOPSE_INFO;
208	<	simError();
209	<	}
210	<	else {
211	<	sprintf( painCave.errMsg,
212	<	"OOPSE is switching from the faster Orthorhombic to the more\n"
213	<	"\tflexible Non-Orthorhombic periodic boundary computations.\n"
214	<	"\tThis is usually because the box has deformed under\n"
215	<	"\tNPTf integration. If you wan't to live on the edge with\n"
216	<	"\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
217	<	"\tvariable ( currently set to %G ) larger.\n",
218	<	orthoTolerance);
219	<	painCave.severity = OOPSE_WARNING;
220	<	simError();
221	<	}
222	<	}
223	<	}
279	>	// n_constraints is local, so subtract them on each processor
280	>	ndf_local -= nConstraints_;
281
282	<	void SimInfo::calcBoxL( void ){
282	>	#ifdef IS_MPI
283	>	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
284	>	#else
285	>	ndf_ = ndf_local;
286	>	#endif
287
288	<	double dx, dy, dz, dsq;
288	>	// nZconstraints_ is global, as are the 3 COM translations for the
289	>	// entire system:
290	>	ndf_ = ndf_ - 3 - nZconstraint_;
291
292	<	// boxVol = Determinant of Hmat
292	>	}
293
294	<	boxVol = matDet3( Hmat );
294	>	int SimInfo::getFdf() {
295	>	#ifdef IS_MPI
296	>	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
297	>	#else
298	>	fdf_ = fdf_local;
299	>	#endif
300	>	return fdf_;
301	>	}
302	>
303	>	void SimInfo::calcNdfRaw() {
304	>	int ndfRaw_local;
305
306	<	// boxLx
307	<
308	<	dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
309	<	dsq = dx*dx + dy*dy + dz*dz;
237	<	boxL[0] = sqrt( dsq );
238	<	//maxCutoff = 0.5 * boxL[0];
306	>	MoleculeIterator i;
307	>	std::vector<StuntDouble*>::iterator j;
308	>	Molecule* mol;
309	>	StuntDouble* integrableObject;
310
311	<	// boxLy
312	<
313	<	dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
314	<	dsq = dx*dx + dy*dy + dz*dz;
315	<	boxL[1] = sqrt( dsq );
316	<	//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
311	>	// Raw degrees of freedom that we have to set
312	>	ndfRaw_local = 0;
313	>
314	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
315	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
316	>	integrableObject = mol->nextIntegrableObject(j)) {
317
318	+	ndfRaw_local += 3;
319
320	<	// boxLz
321	<
322	<	dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
323	<	dsq = dx*dx + dy*dy + dz*dz;
324	<	boxL[2] = sqrt( dsq );
325	<	//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
320	>	if (integrableObject->isDirectional()) {
321	>	if (integrableObject->isLinear()) {
322	>	ndfRaw_local += 2;
323	>	} else {
324	>	ndfRaw_local += 3;
325	>	}
326	>	}
327	>
328	>	}
329	>	}
330	>
331	>	#ifdef IS_MPI
332	>	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
333	>	#else
334	>	ndfRaw_ = ndfRaw_local;
335	>	#endif
336	>	}
337
338	<	//calculate the max cutoff
339	<	maxCutoff =  calcMaxCutOff();
257	<
258	<	checkCutOffs();
338	>	void SimInfo::calcNdfTrans() {
339	>	int ndfTrans_local;
340
341	<	}
341	>	ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
342
343
344	<	double SimInfo::calcMaxCutOff(){
344	>	#ifdef IS_MPI
345	>	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
346	>	#else
347	>	ndfTrans_ = ndfTrans_local;
348	>	#endif
349
350	<	double ri[3], rj[3], rk[3];
351	<	double rij[3], rjk[3], rki[3];
352	<	double minDist;
350	>	ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
351	>
352	>	}
353
354	<	ri[0] = Hmat[0][0];
355	<	ri[1] = Hmat[1][0];
356	<	ri[2] = Hmat[2][0];
354	>	void SimInfo::addExcludePairs(Molecule* mol) {
355	>	std::vector<Bond*>::iterator bondIter;
356	>	std::vector<Bend*>::iterator bendIter;
357	>	std::vector<Torsion*>::iterator torsionIter;
358	>	Bond* bond;
359	>	Bend* bend;
360	>	Torsion* torsion;
361	>	int a;
362	>	int b;
363	>	int c;
364	>	int d;
365
366	<	rj[0] = Hmat[0][1];
274	<	rj[1] = Hmat[1][1];
275	<	rj[2] = Hmat[2][1];
366	>	std::map<int, std::set<int> > atomGroups;
367
368	<	rk[0] = Hmat[0][2];
369	<	rk[1] = Hmat[1][2];
370	<	rk[2] = Hmat[2][2];
368	>	Molecule::RigidBodyIterator rbIter;
369	>	RigidBody* rb;
370	>	Molecule::IntegrableObjectIterator ii;
371	>	StuntDouble* integrableObject;
372
373	<	crossProduct3(ri, rj, rij);
374	<	distXY = dotProduct3(rk,rij) / norm3(rij);
373	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
374	>	integrableObject = mol->nextIntegrableObject(ii)) {
375
376	<	crossProduct3(rj,rk, rjk);
377	<	distYZ = dotProduct3(ri,rjk) / norm3(rjk);
376	>	if (integrableObject->isRigidBody()) {
377	>	rb = static_cast<RigidBody*>(integrableObject);
378	>	std::vector<Atom*> atoms = rb->getAtoms();
379	>	std::set<int> rigidAtoms;
380	>	for (int i = 0; i < atoms.size(); ++i) {
381	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
382	>	}
383	>	for (int i = 0; i < atoms.size(); ++i) {
384	>	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
385	>	}
386	>	} else {
387	>	std::set<int> oneAtomSet;
388	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
389	>	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
390	>	}
391	>	}
392
287	–	crossProduct3(rk,ri, rki);
288	–	distZX = dotProduct3(rj,rki) / norm3(rki);
289	–
290	–	minDist = min(min(distXY, distYZ), distZX);
291	–	return minDist/2;
292	–
293	–	}
294	–
295	–	void SimInfo::wrapVector( double thePos[3] ){
296	–
297	–	int i;
298	–	double scaled[3];
299	–
300	–	if( !orthoRhombic ){
301	–	// calc the scaled coordinates.
302	–
303	–
304	–	matVecMul3(HmatInv, thePos, scaled);
393
306	–	for(i=0; i<3; i++)
307	–	scaled[i] -= roundMe(scaled[i]);
394
395	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
396	<
397	<	matVecMul3(Hmat, scaled, thePos);
395	>	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
396	>	a = bond->getAtomA()->getGlobalIndex();
397	>	b = bond->getAtomB()->getGlobalIndex();
398	>	exclude_.addPair(a, b);
399	>	}
400
401	<	}
402	<	else{
403	<	// calc the scaled coordinates.
404	<
405	<	for(i=0; i<3; i++)
406	<	scaled[i] = thePos[i]*HmatInv[i][i];
407	<
320	<	// wrap the scaled coordinates
321	<
322	<	for(i=0; i<3; i++)
323	<	scaled[i] -= roundMe(scaled[i]);
324	<
325	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
326	<
327	<	for(i=0; i<3; i++)
328	<	thePos[i] = scaled[i]*Hmat[i][i];
329	<	}
330	<
331	<	}
401	>	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
402	>	a = bend->getAtomA()->getGlobalIndex();
403	>	b = bend->getAtomB()->getGlobalIndex();
404	>	c = bend->getAtomC()->getGlobalIndex();
405	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
406	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
407	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
408
409	+	exclude_.addPairs(rigidSetA, rigidSetB);
410	+	exclude_.addPairs(rigidSetA, rigidSetC);
411	+	exclude_.addPairs(rigidSetB, rigidSetC);
412	+
413	+	//exclude_.addPair(a, b);
414	+	//exclude_.addPair(a, c);
415	+	//exclude_.addPair(b, c);
416	+	}
417
418	<	int SimInfo::getNDF(){
419	<	int ndf_local;
418	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
419	>	a = torsion->getAtomA()->getGlobalIndex();
420	>	b = torsion->getAtomB()->getGlobalIndex();
421	>	c = torsion->getAtomC()->getGlobalIndex();
422	>	d = torsion->getAtomD()->getGlobalIndex();
423	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
424	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
425	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
426	>	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
427
428	<	ndf_local = 0;
429	<
430	<	for(int i = 0; i < integrableObjects.size(); i++){
431	<	ndf_local += 3;
432	<	if (integrableObjects[i]->isDirectional()) {
433	<	if (integrableObjects[i]->isLinear())
434	<	ndf_local += 2;
435	<	else
436	<	ndf_local += 3;
428	>	exclude_.addPairs(rigidSetA, rigidSetB);
429	>	exclude_.addPairs(rigidSetA, rigidSetC);
430	>	exclude_.addPairs(rigidSetA, rigidSetD);
431	>	exclude_.addPairs(rigidSetB, rigidSetC);
432	>	exclude_.addPairs(rigidSetB, rigidSetD);
433	>	exclude_.addPairs(rigidSetC, rigidSetD);
434	>
435	>	/*
436	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
437	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
438	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
439	>	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
440	>	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
441	>	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
442	>
443	>
444	>	exclude_.addPair(a, b);
445	>	exclude_.addPair(a, c);
446	>	exclude_.addPair(a, d);
447	>	exclude_.addPair(b, c);
448	>	exclude_.addPair(b, d);
449	>	exclude_.addPair(c, d);
450	>	*/
451		}
452	+
453	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
454	+	std::vector<Atom*> atoms = rb->getAtoms();
455	+	for (int i = 0; i < atoms.size() -1 ; ++i) {
456	+	for (int j = i + 1; j < atoms.size(); ++j) {
457	+	a = atoms[i]->getGlobalIndex();
458	+	b = atoms[j]->getGlobalIndex();
459	+	exclude_.addPair(a, b);
460	+	}
461	+	}
462	+	}
463	+
464		}
465
466	<	// n_constraints is local, so subtract them on each processor:
466	>	void SimInfo::removeExcludePairs(Molecule* mol) {
467	>	std::vector<Bond*>::iterator bondIter;
468	>	std::vector<Bend*>::iterator bendIter;
469	>	std::vector<Torsion*>::iterator torsionIter;
470	>	Bond* bond;
471	>	Bend* bend;
472	>	Torsion* torsion;
473	>	int a;
474	>	int b;
475	>	int c;
476	>	int d;
477
478	<	ndf_local -= n_constraints;
478	>	std::map<int, std::set<int> > atomGroups;
479
480	<	#ifdef IS_MPI
481	<	MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
482	<	#else
483	<	ndf = ndf_local;
484	<	#endif
480	>	Molecule::RigidBodyIterator rbIter;
481	>	RigidBody* rb;
482	>	Molecule::IntegrableObjectIterator ii;
483	>	StuntDouble* integrableObject;
484	>
485	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
486	>	integrableObject = mol->nextIntegrableObject(ii)) {
487
488	<	// nZconstraints is global, as are the 3 COM translations for the
489	<	// entire system:
488	>	if (integrableObject->isRigidBody()) {
489	>	rb = static_cast<RigidBody*>(integrableObject);
490	>	std::vector<Atom*> atoms = rb->getAtoms();
491	>	std::set<int> rigidAtoms;
492	>	for (int i = 0; i < atoms.size(); ++i) {
493	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
494	>	}
495	>	for (int i = 0; i < atoms.size(); ++i) {
496	>	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
497	>	}
498	>	} else {
499	>	std::set<int> oneAtomSet;
500	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
501	>	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
502	>	}
503	>	}
504
505	<	ndf = ndf - 3 - nZconstraints;
505	>
506	>	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
507	>	a = bond->getAtomA()->getGlobalIndex();
508	>	b = bond->getAtomB()->getGlobalIndex();
509	>	exclude_.removePair(a, b);
510	>	}
511
512	<	return ndf;
513	<	}
512	>	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
513	>	a = bend->getAtomA()->getGlobalIndex();
514	>	b = bend->getAtomB()->getGlobalIndex();
515	>	c = bend->getAtomC()->getGlobalIndex();
516
517	<	int SimInfo::getNDFraw() {
518	<	int ndfRaw_local;
517	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
518	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
519	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
520
521	<	// Raw degrees of freedom that we have to set
522	<	ndfRaw_local = 0;
521	>	exclude_.removePairs(rigidSetA, rigidSetB);
522	>	exclude_.removePairs(rigidSetA, rigidSetC);
523	>	exclude_.removePairs(rigidSetB, rigidSetC);
524	>
525	>	//exclude_.removePair(a, b);
526	>	//exclude_.removePair(a, c);
527	>	//exclude_.removePair(b, c);
528	>	}
529
530	<	for(int i = 0; i < integrableObjects.size(); i++){
531	<	ndfRaw_local += 3;
532	<	if (integrableObjects[i]->isDirectional()) {
533	<	if (integrableObjects[i]->isLinear())
534	<	ndfRaw_local += 2;
378	<	else
379	<	ndfRaw_local += 3;
380	<	}
381	<	}
382	<
383	<	#ifdef IS_MPI
384	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
385	<	#else
386	<	ndfRaw = ndfRaw_local;
387	<	#endif
530	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
531	>	a = torsion->getAtomA()->getGlobalIndex();
532	>	b = torsion->getAtomB()->getGlobalIndex();
533	>	c = torsion->getAtomC()->getGlobalIndex();
534	>	d = torsion->getAtomD()->getGlobalIndex();
535
536	<	return ndfRaw;
537	<	}
536	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
537	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
538	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
539	>	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
540
541	<	int SimInfo::getNDFtranslational() {
542	<	int ndfTrans_local;
541	>	exclude_.removePairs(rigidSetA, rigidSetB);
542	>	exclude_.removePairs(rigidSetA, rigidSetC);
543	>	exclude_.removePairs(rigidSetA, rigidSetD);
544	>	exclude_.removePairs(rigidSetB, rigidSetC);
545	>	exclude_.removePairs(rigidSetB, rigidSetD);
546	>	exclude_.removePairs(rigidSetC, rigidSetD);
547
548	<	ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
548	>	/*
549	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
550	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
551	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
552	>	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
553	>	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
554	>	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
555
556	+
557	+	exclude_.removePair(a, b);
558	+	exclude_.removePair(a, c);
559	+	exclude_.removePair(a, d);
560	+	exclude_.removePair(b, c);
561	+	exclude_.removePair(b, d);
562	+	exclude_.removePair(c, d);
563	+	*/
564	+	}
565
566	<	#ifdef IS_MPI
567	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
568	<	#else
569	<	ndfTrans = ndfTrans_local;
570	<	#endif
566	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
567	>	std::vector<Atom*> atoms = rb->getAtoms();
568	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
569	>	for (int j = i + 1; j < atoms.size(); ++j) {
570	>	a = atoms[i]->getGlobalIndex();
571	>	b = atoms[j]->getGlobalIndex();
572	>	exclude_.removePair(a, b);
573	>	}
574	>	}
575	>	}
576
577	<	ndfTrans = ndfTrans - 3 - nZconstraints;
577	>	}
578
406	–	return ndfTrans;
407	–	}
579
580	<	int SimInfo::getTotIntegrableObjects() {
581	<	int nObjs_local;
411	<	int nObjs;
580	>	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
581	>	int curStampId;
582
583	<	nObjs_local =  integrableObjects.size();
583	>	//index from 0
584	>	curStampId = moleculeStamps_.size();
585
586	+	moleculeStamps_.push_back(molStamp);
587	+	molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
588	+	}
589
590	+	void SimInfo::update() {
591	+
592	+	setupSimType();
593	+
594		#ifdef IS_MPI
595	<	MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
418	<	#else
419	<	nObjs = nObjs_local;
595	>	setupFortranParallel();
596		#endif
597
598	+	setupFortranSim();
599
600	<	return nObjs;
601	<	}
600	>	//setup fortran force field
601	>	/** @deprecate */
602	>	int isError = 0;
603	>
604	>	setupCutoff();
605	>
606	>	setupElectrostaticSummationMethod( isError );
607	>	setupSwitchingFunction();
608	>	setupAccumulateBoxDipole();
609
610	<	void SimInfo::refreshSim(){
610	>	if(isError){
611	>	sprintf( painCave.errMsg,
612	>	"ForceField error: There was an error initializing the forceField in fortran.\n" );
613	>	painCave.isFatal = 1;
614	>	simError();
615	>	}
616
617	<	simtype fInfo;
618	<	int isError;
619	<	int n_global;
431	<	int* excl;
617	>	calcNdf();
618	>	calcNdfRaw();
619	>	calcNdfTrans();
620
621	<	fInfo.dielect = 0.0;
434	<
435	<	if( useDipoles ){
436	<	if( useReactionField )fInfo.dielect = dielectric;
621	>	fortranInitialized_ = true;
622		}
623
624	<	fInfo.SIM_uses_PBC = usePBC;
624	>	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
625	>	SimInfo::MoleculeIterator mi;
626	>	Molecule* mol;
627	>	Molecule::AtomIterator ai;
628	>	Atom* atom;
629	>	std::set<AtomType*> atomTypes;
630
631	<	if (useSticky || useDipoles || useGayBerne || useShapes) {
442	<	useDirectionalAtoms = 1;
443	<	fInfo.SIM_uses_DirectionalAtoms = useDirectionalAtoms;
444	<	}
631	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
632
633	<	fInfo.SIM_uses_LennardJones = useLennardJones;
633	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
634	>	atomTypes.insert(atom->getAtomType());
635	>	}
636	>
637	>	}
638
639	<	if (useCharges || useDipoles) {
449	<	useElectrostatics = 1;
450	<	fInfo.SIM_uses_Electrostatics = useElectrostatics;
639	>	return atomTypes;
640		}
641
642	<	fInfo.SIM_uses_Charges = useCharges;
643	<	fInfo.SIM_uses_Dipoles = useDipoles;
644	<	fInfo.SIM_uses_Sticky = useSticky;
645	<	fInfo.SIM_uses_GayBerne = useGayBerne;
646	<	fInfo.SIM_uses_EAM = useEAM;
647	<	fInfo.SIM_uses_Shapes = useShapes;
648	<	fInfo.SIM_uses_FLARB = useFLARB;
649	<	fInfo.SIM_uses_RF = useReactionField;
642	>	void SimInfo::setupSimType() {
643	>	std::set<AtomType*>::iterator i;
644	>	std::set<AtomType*> atomTypes;
645	>	atomTypes = getUniqueAtomTypes();
646	>
647	>	int useLennardJones = 0;
648	>	int useElectrostatic = 0;
649	>	int useEAM = 0;
650	>	int useSC = 0;
651	>	int useCharge = 0;
652	>	int useDirectional = 0;
653	>	int useDipole = 0;
654	>	int useGayBerne = 0;
655	>	int useSticky = 0;
656	>	int useStickyPower = 0;
657	>	int useShape = 0;
658	>	int useFLARB = 0; //it is not in AtomType yet
659	>	int useDirectionalAtom = 0;
660	>	int useElectrostatics = 0;
661	>	//usePBC and useRF are from simParams
662	>	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
663	>	int useRF;
664	>	int useSF;
665	>	int useSP;
666	>	int useBoxDipole;
667	>	std::string myMethod;
668
669	<	n_exclude = excludes->getSize();
670	<	excl = excludes->getFortranArray();
671	<
672	<	#ifdef IS_MPI
673	<	n_global = mpiSim->getNAtomsGlobal();
674	<	#else
675	<	n_global = n_atoms;
676	<	#endif
677	<
678	<	isError = 0;
679	<
680	<	getFortranGroupArrays(this, FglobalGroupMembership, mfact);
681	<	//it may not be a good idea to pass the address of first element in vector
682	<	//since c++ standard does not require vector to be stored continuously in meomory
683	<	//Most of the compilers will organize the memory of vector continuously
684	<	setFortranSim( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
685	<	&nGlobalExcludes, globalExcludes, molMembershipArray,
686	<	&mfact[0], &ngroup, &FglobalGroupMembership[0], &isError);
669	>	// set the useRF logical
670	>	useRF = 0;
671	>	useSF = 0;
672	>	useSP = 0;
673	>
674	>
675	>	if (simParams_->haveElectrostaticSummationMethod()) {
676	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
677	>	toUpper(myMethod);
678	>	if (myMethod == "REACTION_FIELD"){
679	>	useRF = 1;
680	>	} else if (myMethod == "SHIFTED_FORCE"){
681	>	useSF = 1;
682	>	} else if (myMethod == "SHIFTED_POTENTIAL"){
683	>	useSP = 1;
684	>	}
685	>	}
686	>
687	>	if (simParams_->haveAccumulateBoxDipole())
688	>	if (simParams_->getAccumulateBoxDipole())
689	>	useBoxDipole = 1;
690	>
691	>	//loop over all of the atom types
692	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
693	>	useLennardJones |= (*i)->isLennardJones();
694	>	useElectrostatic |= (*i)->isElectrostatic();
695	>	useEAM |= (*i)->isEAM();
696	>	useSC |= (*i)->isSC();
697	>	useCharge |= (*i)->isCharge();
698	>	useDirectional |= (*i)->isDirectional();
699	>	useDipole |= (*i)->isDipole();
700	>	useGayBerne |= (*i)->isGayBerne();
701	>	useSticky |= (*i)->isSticky();
702	>	useStickyPower |= (*i)->isStickyPower();
703	>	useShape |= (*i)->isShape();
704	>	}
705
706	<	if( isError ){
706	>	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
707	>	useDirectionalAtom = 1;
708	>	}
709	>
710	>	if (useCharge || useDipole) {
711	>	useElectrostatics = 1;
712	>	}
713	>
714	>	#ifdef IS_MPI
715	>	int temp;
716	>
717	>	temp = usePBC;
718	>	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
719	>
720	>	temp = useDirectionalAtom;
721	>	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
722	>
723	>	temp = useLennardJones;
724	>	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
725	>
726	>	temp = useElectrostatics;
727	>	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
728	>
729	>	temp = useCharge;
730	>	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
731	>
732	>	temp = useDipole;
733	>	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
734	>
735	>	temp = useSticky;
736	>	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
737	>
738	>	temp = useStickyPower;
739	>	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
740
741	<	sprintf( painCave.errMsg,
742	<	"There was an error setting the simulation information in fortran.\n" );
743	<	painCave.isFatal = 1;
744	<	painCave.severity = OOPSE_ERROR;
745	<	simError();
741	>	temp = useGayBerne;
742	>	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
743	>
744	>	temp = useEAM;
745	>	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
746	>
747	>	temp = useSC;
748	>	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
749	>
750	>	temp = useShape;
751	>	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
752	>
753	>	temp = useFLARB;
754	>	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
755	>
756	>	temp = useRF;
757	>	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
758	>
759	>	temp = useSF;
760	>	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
761	>
762	>	temp = useSP;
763	>	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
764	>
765	>	temp = useBoxDipole;
766	>	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
767	>
768	>	#endif
769	>
770	>	fInfo_.SIM_uses_PBC = usePBC;
771	>	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
772	>	fInfo_.SIM_uses_LennardJones = useLennardJones;
773	>	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
774	>	fInfo_.SIM_uses_Charges = useCharge;
775	>	fInfo_.SIM_uses_Dipoles = useDipole;
776	>	fInfo_.SIM_uses_Sticky = useSticky;
777	>	fInfo_.SIM_uses_StickyPower = useStickyPower;
778	>	fInfo_.SIM_uses_GayBerne = useGayBerne;
779	>	fInfo_.SIM_uses_EAM = useEAM;
780	>	fInfo_.SIM_uses_SC = useSC;
781	>	fInfo_.SIM_uses_Shapes = useShape;
782	>	fInfo_.SIM_uses_FLARB = useFLARB;
783	>	fInfo_.SIM_uses_RF = useRF;
784	>	fInfo_.SIM_uses_SF = useSF;
785	>	fInfo_.SIM_uses_SP = useSP;
786	>	fInfo_.SIM_uses_BoxDipole = useBoxDipole;
787		}
489	–
490	–	#ifdef IS_MPI
491	–	sprintf( checkPointMsg,
492	–	"succesfully sent the simulation information to fortran.\n");
493	–	MPIcheckPoint();
494	–	#endif // is_mpi
495	–
496	–	this->ndf = this->getNDF();
497	–	this->ndfRaw = this->getNDFraw();
498	–	this->ndfTrans = this->getNDFtranslational();
499	–	}
788
789	<	void SimInfo::setDefaultRcut( double theRcut ){
790	<
791	<	haveRcut = 1;
792	<	rCut = theRcut;
793	<	rList = rCut + 1.0;
794	<
795	<	notifyFortranCutoffs( &rCut, &rSw, &rList );
508	<	}
789	>	void SimInfo::setupFortranSim() {
790	>	int isError;
791	>	int nExclude;
792	>	std::vector<int> fortranGlobalGroupMembership;
793	>
794	>	nExclude = exclude_.getSize();
795	>	isError = 0;
796
797	<	void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
797	>	//globalGroupMembership_ is filled by SimCreator
798	>	for (int i = 0; i < nGlobalAtoms_; i++) {
799	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
800	>	}
801
802	<	rSw = theRsw;
803	<	setDefaultRcut( theRcut );
804	<	}
802	>	//calculate mass ratio of cutoff group
803	>	std::vector<RealType> mfact;
804	>	SimInfo::MoleculeIterator mi;
805	>	Molecule* mol;
806	>	Molecule::CutoffGroupIterator ci;
807	>	CutoffGroup* cg;
808	>	Molecule::AtomIterator ai;
809	>	Atom* atom;
810	>	RealType totalMass;
811
812	+	//to avoid memory reallocation, reserve enough space for mfact
813	+	mfact.reserve(getNCutoffGroups());
814	+
815	+	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
816	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
817
818	<	void SimInfo::checkCutOffs( void ){
819	<
820	<	if( boxIsInit ){
818	>	totalMass = cg->getMass();
819	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
820	>	// Check for massless groups - set mfact to 1 if true
821	>	if (totalMass != 0)
822	>	mfact.push_back(atom->getMass()/totalMass);
823	>	else
824	>	mfact.push_back( 1.0 );
825	>	}
826	>
827	>	}
828	>	}
829	>
830	>	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
831	>	std::vector<int> identArray;
832	>
833	>	//to avoid memory reallocation, reserve enough space identArray
834	>	identArray.reserve(getNAtoms());
835
836	<	//we need to check cutOffs against the box
836	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
837	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
838	>	identArray.push_back(atom->getIdent());
839	>	}
840	>	}
841	>
842	>	//fill molMembershipArray
843	>	//molMembershipArray is filled by SimCreator
844	>	std::vector<int> molMembershipArray(nGlobalAtoms_);
845	>	for (int i = 0; i < nGlobalAtoms_; i++) {
846	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
847	>	}
848
849	<	if( rCut > maxCutoff ){
849	>	//setup fortran simulation
850	>	int nGlobalExcludes = 0;
851	>	int* globalExcludes = NULL;
852	>	int* excludeList = exclude_.getExcludeList();
853	>	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
854	>	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
855	>	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
856	>
857	>	if( isError ){
858	>
859		sprintf( painCave.errMsg,
860	<	"cutoffRadius is too large for the current periodic box.\n"
526	<	"\tCurrent Value of cutoffRadius = %G at time %G\n "
527	<	"\tThis is larger than half of at least one of the\n"
528	<	"\tperiodic box vectors.  Right now, the Box matrix is:\n"
529	<	"\n"
530	<	"\t[ %G %G %G ]\n"
531	<	"\t[ %G %G %G ]\n"
532	<	"\t[ %G %G %G ]\n",
533	<	rCut, currentTime,
534	<	Hmat[0][0], Hmat[0][1], Hmat[0][2],
535	<	Hmat[1][0], Hmat[1][1], Hmat[1][2],
536	<	Hmat[2][0], Hmat[2][1], Hmat[2][2]);
537	<	painCave.severity = OOPSE_ERROR;
860	>	"There was an error setting the simulation information in fortran.\n" );
861		painCave.isFatal = 1;
862	+	painCave.severity = OOPSE_ERROR;
863		simError();
864	<	}
865	<	} else {
866	<	// initialize this stuff before using it, OK?
867	<	sprintf( painCave.errMsg,
868	<	"Trying to check cutoffs without a box.\n"
869	<	"\tOOPSE should have better programmers than that.\n" );
870	<	painCave.severity = OOPSE_ERROR;
547	<	painCave.isFatal = 1;
548	<	simError();
864	>	}
865	>
866	>	#ifdef IS_MPI
867	>	sprintf( checkPointMsg,
868	>	"succesfully sent the simulation information to fortran.\n");
869	>	MPIcheckPoint();
870	>	#endif // is_mpi
871		}
550	–
551	–	}
872
553	–	void SimInfo::addProperty(GenericData* prop){
873
874	<	map<string, GenericData*>::iterator result;
875	<	result = properties.find(prop->getID());
557	<
558	<	//we can't simply use  properties[prop->getID()] = prop,
559	<	//it will cause memory leak if we already contain a propery which has the same name of prop
560	<
561	<	if(result != properties.end()){
874	>	#ifdef IS_MPI
875	>	void SimInfo::setupFortranParallel() {
876
877	<	delete (*result).second;
878	<	(*result).second = prop;
879	<
880	<	}
881	<	else{
877	>	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
878	>	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
879	>	std::vector<int> localToGlobalCutoffGroupIndex;
880	>	SimInfo::MoleculeIterator mi;
881	>	Molecule::AtomIterator ai;
882	>	Molecule::CutoffGroupIterator ci;
883	>	Molecule* mol;
884	>	Atom* atom;
885	>	CutoffGroup* cg;
886	>	mpiSimData parallelData;
887	>	int isError;
888
889	<	properties[prop->getID()] = prop;
889	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
890
891	<	}
892	<
893	<	}
891	>	//local index(index in DataStorge) of atom is important
892	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
893	>	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
894	>	}
895
896	<	GenericData* SimInfo::getProperty(const string& propName){
897	<
898	<	map<string, GenericData*>::iterator result;
899	<
900	<	//string lowerCaseName = ();
901	<
581	<	result = properties.find(propName);
582	<
583	<	if(result != properties.end())
584	<	return (*result).second;
585	<	else
586	<	return NULL;
587	<	}
896	>	//local index of cutoff group is trivial, it only depends on the order of travesing
897	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
898	>	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
899	>	}
900	>
901	>	}
902
903	+	//fill up mpiSimData struct
904	+	parallelData.nMolGlobal = getNGlobalMolecules();
905	+	parallelData.nMolLocal = getNMolecules();
906	+	parallelData.nAtomsGlobal = getNGlobalAtoms();
907	+	parallelData.nAtomsLocal = getNAtoms();
908	+	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
909	+	parallelData.nGroupsLocal = getNCutoffGroups();
910	+	parallelData.myNode = worldRank;
911	+	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
912
913	<	void SimInfo::getFortranGroupArrays(SimInfo* info,
914	<	vector<int>& FglobalGroupMembership,
915	<	vector<double>& mfact){
916	<
594	<	Molecule* myMols;
595	<	Atom** myAtoms;
596	<	int numAtom;
597	<	double mtot;
598	<	int numMol;
599	<	int numCutoffGroups;
600	<	CutoffGroup* myCutoffGroup;
601	<	vector<CutoffGroup*>::iterator iterCutoff;
602	<	Atom* cutoffAtom;
603	<	vector<Atom*>::iterator iterAtom;
604	<	int atomIndex;
605	<	double totalMass;
606	<
607	<	mfact.clear();
608	<	FglobalGroupMembership.clear();
609	<
913	>	//pass mpiSimData struct and index arrays to fortran
914	>	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
915	>	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
916	>	&localToGlobalCutoffGroupIndex[0], &isError);
917
918	<	// Fix the silly fortran indexing problem
919	<	#ifdef IS_MPI
920	<	numAtom = mpiSim->getNAtomsGlobal();
921	<	#else
922	<	numAtom = n_atoms;
918	>	if (isError) {
919	>	sprintf(painCave.errMsg,
920	>	"mpiRefresh errror: fortran didn't like something we gave it.\n");
921	>	painCave.isFatal = 1;
922	>	simError();
923	>	}
924	>
925	>	sprintf(checkPointMsg, " mpiRefresh successful.\n");
926	>	MPIcheckPoint();
927	>
928	>
929	>	}
930	>
931		#endif
617	–	for (int i = 0; i < numAtom; i++)
618	–	FglobalGroupMembership.push_back(globalGroupMembership[i] + 1);
619	–
932
933	<	myMols = info->molecules;
934	<	numMol = info->n_mol;
935	<	for(int i  = 0; i < numMol; i++){
624	<	numCutoffGroups = myMols[i].getNCutoffGroups();
625	<	for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff);
626	<	myCutoffGroup != NULL;
627	<	myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
933	>	void SimInfo::setupCutoff() {
934	>
935	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
936
937	<	totalMass = myCutoffGroup->getMass();
937	>	// Check the cutoff policy
938	>	int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
939	>
940	>	std::string myPolicy;
941	>	if (forceFieldOptions_.haveCutoffPolicy()){
942	>	myPolicy = forceFieldOptions_.getCutoffPolicy();
943	>	}else if (simParams_->haveCutoffPolicy()) {
944	>	myPolicy = simParams_->getCutoffPolicy();
945	>	}
946	>
947	>	if (!myPolicy.empty()){
948	>	toUpper(myPolicy);
949	>	if (myPolicy == "MIX") {
950	>	cp = MIX_CUTOFF_POLICY;
951	>	} else {
952	>	if (myPolicy == "MAX") {
953	>	cp = MAX_CUTOFF_POLICY;
954	>	} else {
955	>	if (myPolicy == "TRADITIONAL") {
956	>	cp = TRADITIONAL_CUTOFF_POLICY;
957	>	} else {
958	>	// throw error
959	>	sprintf( painCave.errMsg,
960	>	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
961	>	painCave.isFatal = 1;
962	>	simError();
963	>	}
964	>	}
965	>	}
966	>	}
967	>	notifyFortranCutoffPolicy(&cp);
968	>
969	>	// Check the Skin Thickness for neighborlists
970	>	RealType skin;
971	>	if (simParams_->haveSkinThickness()) {
972	>	skin = simParams_->getSkinThickness();
973	>	notifyFortranSkinThickness(&skin);
974	>	}
975	>
976	>	// Check if the cutoff was set explicitly:
977	>	if (simParams_->haveCutoffRadius()) {
978	>	rcut_ = simParams_->getCutoffRadius();
979	>	if (simParams_->haveSwitchingRadius()) {
980	>	rsw_  = simParams_->getSwitchingRadius();
981	>	} else {
982	>	if (fInfo_.SIM_uses_Charges |
983	>	fInfo_.SIM_uses_Dipoles |
984	>	fInfo_.SIM_uses_RF) {
985	>
986	>	rsw_ = 0.85 * rcut_;
987	>	sprintf(painCave.errMsg,
988	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
989	>	"\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
990	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
991	>	painCave.isFatal = 0;
992	>	simError();
993	>	} else {
994	>	rsw_ = rcut_;
995	>	sprintf(painCave.errMsg,
996	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
997	>	"\tOOPSE will use the same value as the cutoffRadius.\n"
998	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
999	>	painCave.isFatal = 0;
1000	>	simError();
1001	>	}
1002	>	}
1003
1004	<	for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom);
1005	<	cutoffAtom != NULL;
1006	<	cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
1007	<	mfact.push_back(cutoffAtom->getMass()/totalMass);
1008	<	}
1004	>	notifyFortranCutoffs(&rcut_, &rsw_);
1005	>
1006	>	} else {
1007	>
1008	>	// For electrostatic atoms, we'll assume a large safe value:
1009	>	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1010	>	sprintf(painCave.errMsg,
1011	>	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1012	>	"\tOOPSE will use a default value of 15.0 angstroms"
1013	>	"\tfor the cutoffRadius.\n");
1014	>	painCave.isFatal = 0;
1015	>	simError();
1016	>	rcut_ = 15.0;
1017	>
1018	>	if (simParams_->haveElectrostaticSummationMethod()) {
1019	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1020	>	toUpper(myMethod);
1021	>	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1022	>	if (simParams_->haveSwitchingRadius()){
1023	>	sprintf(painCave.errMsg,
1024	>	"SimInfo Warning: A value was set for the switchingRadius\n"
1025	>	"\teven though the electrostaticSummationMethod was\n"
1026	>	"\tset to %s\n", myMethod.c_str());
1027	>	painCave.isFatal = 1;
1028	>	simError();
1029	>	}
1030	>	}
1031	>	}
1032	>
1033	>	if (simParams_->haveSwitchingRadius()){
1034	>	rsw_ = simParams_->getSwitchingRadius();
1035	>	} else {
1036	>	sprintf(painCave.errMsg,
1037	>	"SimCreator Warning: No value was set for switchingRadius.\n"
1038	>	"\tOOPSE will use a default value of\n"
1039	>	"\t0.85 * cutoffRadius for the switchingRadius\n");
1040	>	painCave.isFatal = 0;
1041	>	simError();
1042	>	rsw_ = 0.85 * rcut_;
1043	>	}
1044	>	notifyFortranCutoffs(&rcut_, &rsw_);
1045	>	} else {
1046	>	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1047	>	// We'll punt and let fortran figure out the cutoffs later.
1048	>
1049	>	notifyFortranYouAreOnYourOwn();
1050	>
1051	>	}
1052		}
1053		}
1054
1055	<	}
1055	>	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1056	>
1057	>	int errorOut;
1058	>	int esm =  NONE;
1059	>	int sm = UNDAMPED;
1060	>	RealType alphaVal;
1061	>	RealType dielectric;
1062	>
1063	>	errorOut = isError;
1064	>
1065	>	if (simParams_->haveElectrostaticSummationMethod()) {
1066	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1067	>	toUpper(myMethod);
1068	>	if (myMethod == "NONE") {
1069	>	esm = NONE;
1070	>	} else {
1071	>	if (myMethod == "SWITCHING_FUNCTION") {
1072	>	esm = SWITCHING_FUNCTION;
1073	>	} else {
1074	>	if (myMethod == "SHIFTED_POTENTIAL") {
1075	>	esm = SHIFTED_POTENTIAL;
1076	>	} else {
1077	>	if (myMethod == "SHIFTED_FORCE") {
1078	>	esm = SHIFTED_FORCE;
1079	>	} else {
1080	>	if (myMethod == "REACTION_FIELD") {
1081	>	esm = REACTION_FIELD;
1082	>	dielectric = simParams_->getDielectric();
1083	>	if (!simParams_->haveDielectric()) {
1084	>	// throw warning
1085	>	sprintf( painCave.errMsg,
1086	>	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1087	>	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1088	>	painCave.isFatal = 0;
1089	>	simError();
1090	>	}
1091	>	} else {
1092	>	// throw error
1093	>	sprintf( painCave.errMsg,
1094	>	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1095	>	"\t(Input file specified %s .)\n"
1096	>	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1097	>	"\t\"shifted_potential\", \"shifted_force\", or \n"
1098	>	"\t\"reaction_field\".\n", myMethod.c_str() );
1099	>	painCave.isFatal = 1;
1100	>	simError();
1101	>	}
1102	>	}
1103	>	}
1104	>	}
1105	>	}
1106	>	}
1107	>
1108	>	if (simParams_->haveElectrostaticScreeningMethod()) {
1109	>	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1110	>	toUpper(myScreen);
1111	>	if (myScreen == "UNDAMPED") {
1112	>	sm = UNDAMPED;
1113	>	} else {
1114	>	if (myScreen == "DAMPED") {
1115	>	sm = DAMPED;
1116	>	if (!simParams_->haveDampingAlpha()) {
1117	>	// first set a cutoff dependent alpha value
1118	>	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1119	>	alphaVal = 0.5125 - rcut_* 0.025;
1120	>	// for values rcut > 20.5, alpha is zero
1121	>	if (alphaVal < 0) alphaVal = 0;
1122	>
1123	>	// throw warning
1124	>	sprintf( painCave.errMsg,
1125	>	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1126	>	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1127	>	painCave.isFatal = 0;
1128	>	simError();
1129	>	}
1130	>	} else {
1131	>	// throw error
1132	>	sprintf( painCave.errMsg,
1133	>	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1134	>	"\t(Input file specified %s .)\n"
1135	>	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1136	>	"or \"damped\".\n", myScreen.c_str() );
1137	>	painCave.isFatal = 1;
1138	>	simError();
1139	>	}
1140	>	}
1141	>	}
1142	>
1143	>	// let's pass some summation method variables to fortran
1144	>	setElectrostaticSummationMethod( &esm );
1145	>	setFortranElectrostaticMethod( &esm );
1146	>	setScreeningMethod( &sm );
1147	>	setDampingAlpha( &alphaVal );
1148	>	setReactionFieldDielectric( &dielectric );
1149	>	initFortranFF( &errorOut );
1150	>	}
1151	>
1152	>	void SimInfo::setupSwitchingFunction() {
1153	>	int ft = CUBIC;
1154	>
1155	>	if (simParams_->haveSwitchingFunctionType()) {
1156	>	std::string funcType = simParams_->getSwitchingFunctionType();
1157	>	toUpper(funcType);
1158	>	if (funcType == "CUBIC") {
1159	>	ft = CUBIC;
1160	>	} else {
1161	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1162	>	ft = FIFTH_ORDER_POLY;
1163	>	} else {
1164	>	// throw error
1165	>	sprintf( painCave.errMsg,
1166	>	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1167	>	painCave.isFatal = 1;
1168	>	simError();
1169	>	}
1170	>	}
1171	>	}
1172	>
1173	>	// send switching function notification to switcheroo
1174	>	setFunctionType(&ft);
1175	>
1176	>	}
1177	>
1178	>	void SimInfo::setupAccumulateBoxDipole() {
1179	>
1180	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1181	>	if ( simParams_->haveAccumulateBoxDipole() )
1182	>	if ( simParams_->getAccumulateBoxDipole() ) {
1183	>	setAccumulateBoxDipole();
1184	>	calcBoxDipole_ = true;
1185	>	}
1186	>
1187	>	}
1188	>
1189	>	void SimInfo::addProperty(GenericData* genData) {
1190	>	properties_.addProperty(genData);
1191	>	}
1192	>
1193	>	void SimInfo::removeProperty(const std::string& propName) {
1194	>	properties_.removeProperty(propName);
1195	>	}
1196	>
1197	>	void SimInfo::clearProperties() {
1198	>	properties_.clearProperties();
1199	>	}
1200	>
1201	>	std::vector<std::string> SimInfo::getPropertyNames() {
1202	>	return properties_.getPropertyNames();
1203	>	}
1204	>
1205	>	std::vector<GenericData*> SimInfo::getProperties() {
1206	>	return properties_.getProperties();
1207	>	}
1208	>
1209	>	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1210	>	return properties_.getPropertyByName(propName);
1211	>	}
1212	>
1213	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1214	>	if (sman_ == sman) {
1215	>	return;
1216	>	}
1217	>	delete sman_;
1218	>	sman_ = sman;
1219	>
1220	>	Molecule* mol;
1221	>	RigidBody* rb;
1222	>	Atom* atom;
1223	>	SimInfo::MoleculeIterator mi;
1224	>	Molecule::RigidBodyIterator rbIter;
1225	>	Molecule::AtomIterator atomIter;;
1226	>
1227	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1228	>
1229	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1230	>	atom->setSnapshotManager(sman_);
1231	>	}
1232	>
1233	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1234	>	rb->setSnapshotManager(sman_);
1235	>	}
1236	>	}
1237	>
1238	>	}
1239	>
1240	>	Vector3d SimInfo::getComVel(){
1241	>	SimInfo::MoleculeIterator i;
1242	>	Molecule* mol;
1243	>
1244	>	Vector3d comVel(0.0);
1245	>	RealType totalMass = 0.0;
1246	>
1247	>
1248	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1249	>	RealType mass = mol->getMass();
1250	>	totalMass += mass;
1251	>	comVel += mass * mol->getComVel();
1252	>	}
1253	>
1254	>	#ifdef IS_MPI
1255	>	RealType tmpMass = totalMass;
1256	>	Vector3d tmpComVel(comVel);
1257	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1258	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1259	>	#endif
1260	>
1261	>	comVel /= totalMass;
1262	>
1263	>	return comVel;
1264	>	}
1265	>
1266	>	Vector3d SimInfo::getCom(){
1267	>	SimInfo::MoleculeIterator i;
1268	>	Molecule* mol;
1269	>
1270	>	Vector3d com(0.0);
1271	>	RealType totalMass = 0.0;
1272	>
1273	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1274	>	RealType mass = mol->getMass();
1275	>	totalMass += mass;
1276	>	com += mass * mol->getCom();
1277	>	}
1278	>
1279	>	#ifdef IS_MPI
1280	>	RealType tmpMass = totalMass;
1281	>	Vector3d tmpCom(com);
1282	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1283	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1284	>	#endif
1285	>
1286	>	com /= totalMass;
1287	>
1288	>	return com;
1289	>
1290	>	}
1291	>
1292	>	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1293	>
1294	>	return o;
1295	>	}
1296	>
1297	>
1298	>	/*
1299	>	Returns center of mass and center of mass velocity in one function call.
1300	>	*/
1301	>
1302	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1303	>	SimInfo::MoleculeIterator i;
1304	>	Molecule* mol;
1305	>
1306	>
1307	>	RealType totalMass = 0.0;
1308	>
1309	>
1310	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1311	>	RealType mass = mol->getMass();
1312	>	totalMass += mass;
1313	>	com += mass * mol->getCom();
1314	>	comVel += mass * mol->getComVel();
1315	>	}
1316	>
1317	>	#ifdef IS_MPI
1318	>	RealType tmpMass = totalMass;
1319	>	Vector3d tmpCom(com);
1320	>	Vector3d tmpComVel(comVel);
1321	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1322	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1323	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1324	>	#endif
1325	>
1326	>	com /= totalMass;
1327	>	comVel /= totalMass;
1328	>	}
1329	>
1330	>	/*
1331	>	Return intertia tensor for entire system and angular momentum Vector.
1332	>
1333	>
1334	>	[  Ixx -Ixy  -Ixz ]
1335	>	J =| -Iyx  Iyy  -Iyz |
1336	>	[ -Izx -Iyz   Izz ]
1337	>	*/
1338	>
1339	>	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1340	>
1341	>
1342	>	RealType xx = 0.0;
1343	>	RealType yy = 0.0;
1344	>	RealType zz = 0.0;
1345	>	RealType xy = 0.0;
1346	>	RealType xz = 0.0;
1347	>	RealType yz = 0.0;
1348	>	Vector3d com(0.0);
1349	>	Vector3d comVel(0.0);
1350	>
1351	>	getComAll(com, comVel);
1352	>
1353	>	SimInfo::MoleculeIterator i;
1354	>	Molecule* mol;
1355	>
1356	>	Vector3d thisq(0.0);
1357	>	Vector3d thisv(0.0);
1358	>
1359	>	RealType thisMass = 0.0;
1360	>
1361	>
1362	>
1363	>
1364	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1365	>
1366	>	thisq = mol->getCom()-com;
1367	>	thisv = mol->getComVel()-comVel;
1368	>	thisMass = mol->getMass();
1369	>	// Compute moment of intertia coefficients.
1370	>	xx += thisq[0]*thisq[0]*thisMass;
1371	>	yy += thisq[1]*thisq[1]*thisMass;
1372	>	zz += thisq[2]*thisq[2]*thisMass;
1373	>
1374	>	// compute products of intertia
1375	>	xy += thisq[0]*thisq[1]*thisMass;
1376	>	xz += thisq[0]*thisq[2]*thisMass;
1377	>	yz += thisq[1]*thisq[2]*thisMass;
1378	>
1379	>	angularMomentum += cross( thisq, thisv ) * thisMass;
1380	>
1381	>	}
1382	>
1383	>
1384	>	inertiaTensor(0,0) = yy + zz;
1385	>	inertiaTensor(0,1) = -xy;
1386	>	inertiaTensor(0,2) = -xz;
1387	>	inertiaTensor(1,0) = -xy;
1388	>	inertiaTensor(1,1) = xx + zz;
1389	>	inertiaTensor(1,2) = -yz;
1390	>	inertiaTensor(2,0) = -xz;
1391	>	inertiaTensor(2,1) = -yz;
1392	>	inertiaTensor(2,2) = xx + yy;
1393	>
1394	>	#ifdef IS_MPI
1395	>	Mat3x3d tmpI(inertiaTensor);
1396	>	Vector3d tmpAngMom;
1397	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1398	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1399	>	#endif
1400	>
1401	>	return;
1402	>	}
1403	>
1404	>	//Returns the angular momentum of the system
1405	>	Vector3d SimInfo::getAngularMomentum(){
1406	>
1407	>	Vector3d com(0.0);
1408	>	Vector3d comVel(0.0);
1409	>	Vector3d angularMomentum(0.0);
1410	>
1411	>	getComAll(com,comVel);
1412	>
1413	>	SimInfo::MoleculeIterator i;
1414	>	Molecule* mol;
1415	>
1416	>	Vector3d thisr(0.0);
1417	>	Vector3d thisp(0.0);
1418	>
1419	>	RealType thisMass;
1420	>
1421	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1422	>	thisMass = mol->getMass();
1423	>	thisr = mol->getCom()-com;
1424	>	thisp = (mol->getComVel()-comVel)*thisMass;
1425	>
1426	>	angularMomentum += cross( thisr, thisp );
1427	>
1428	>	}
1429	>
1430	>	#ifdef IS_MPI
1431	>	Vector3d tmpAngMom;
1432	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1433	>	#endif
1434	>
1435	>	return angularMomentum;
1436	>	}
1437	>
1438	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1439	>	return IOIndexToIntegrableObject.at(index);
1440	>	}
1441	>
1442	>	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1443	>	IOIndexToIntegrableObject= v;
1444	>	}
1445	>
1446	>	/*
1447	>	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1448	>	assert( v.size() == nAtoms_ + nRigidBodies_);
1449	>	sdByGlobalIndex_ = v;
1450	>	}
1451	>
1452	>	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1453	>	//assert(index < nAtoms_ + nRigidBodies_);
1454	>	return sdByGlobalIndex_.at(index);
1455	>	}
1456	>	*/
1457	>	}//end namespace oopse
1458	>

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