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

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 2 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
Revision 1277 by gezelter, Mon Jul 14 12:35:58 2008 UTC

#	Line 1 | Line 1
1	<	#include <stdlib.h>
2	<	#include <string.h>
3	<	#include <math.h>
1	>	/*
2	>	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	>	*
4	>	* The University of Notre Dame grants you ("Licensee") a
5	>	* non-exclusive, royalty free, license to use, modify and
6	>	* redistribute this software in source and binary code form, provided
7	>	* that the following conditions are met:
8	>	*
9	>	* 1. Acknowledgement of the program authors must be made in any
10	>	*    publication of scientific results based in part on use of the
11	>	*    program.  An acceptable form of acknowledgement is citation of
12	>	*    the article in which the program was described (Matthew
13	>	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	>	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	>	*    Parallel Simulation Engine for Molecular Dynamics,"
16	>	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	>	*
18	>	* 2. Redistributions of source code must retain the above copyright
19	>	*    notice, this list of conditions and the following disclaimer.
20	>	*
21	>	* 3. Redistributions in binary form must reproduce the above copyright
22	>	*    notice, this list of conditions and the following disclaimer in the
23	>	*    documentation and/or other materials provided with the
24	>	*    distribution.
25	>	*
26	>	* This software is provided "AS IS," without a warranty of any
27	>	* kind. All express or implied conditions, representations and
28	>	* warranties, including any implied warranty of merchantability,
29	>	* fitness for a particular purpose or non-infringement, are hereby
30	>	* excluded.  The University of Notre Dame and its licensors shall not
31	>	* be liable for any damages suffered by licensee as a result of
32	>	* using, modifying or distributing the software or its
33	>	* derivatives. In no event will the University of Notre Dame or its
34	>	* licensors be liable for any lost revenue, profit or data, or for
35	>	* direct, indirect, special, consequential, incidental or punitive
36	>	* damages, however caused and regardless of the theory of liability,
37	>	* arising out of the use of or inability to use software, even if the
38	>	* University of Notre Dame has been advised of the possibility of
39	>	* such damages.
40	>	*/
41	>
42	>	/**
43	>	* @file SimInfo.cpp
44	>	* @author    tlin
45	>	* @date  11/02/2004
46	>	* @version 1.0
47	>	*/
48
49	<	#include <iostream>
50	<	using namespace std;
49	>	#include <algorithm>
50	>	#include <set>
51	>	#include <map>
52
53	<	#include "SimInfo.hpp"
54	<	#define __C
55	<	#include "fSimulation.h"
56	<	#include "simError.h"
53	>	#include "brains/SimInfo.hpp"
54	>	#include "math/Vector3.hpp"
55	>	#include "primitives/Molecule.hpp"
56	>	#include "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/neighborLists_interface.h"
63	>	#include "UseTheForce/DarkSide/electrostatic_interface.h"
64	>	#include "UseTheForce/DarkSide/switcheroo_interface.h"
65	>	#include "utils/MemoryUtils.hpp"
66	>	#include "utils/simError.h"
67	>	#include "selection/SelectionManager.hpp"
68	>	#include "io/ForceFieldOptions.hpp"
69	>	#include "UseTheForce/ForceField.hpp"
70
13	–	#include "fortranWrappers.hpp"
71
15	–	#include "MatVec3.h"
16	–
72		#ifdef IS_MPI
73	<	#include "mpiSimulation.hpp"
74	<	#endif
73	>	#include "UseTheForce/mpiComponentPlan.h"
74	>	#include "UseTheForce/DarkSide/simParallel_interface.h"
75	>	#endif
76
77	<	inline double roundMe( double x ){
78	<	return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
79	<	}
80	<
81	<	inline double min( double a, double b ){
82	<	return (a < b ) ? a : b;
83	<	}
77	>	namespace oopse {
78	>	std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
79	>	std::map<int, std::set<int> >::iterator i = container.find(index);
80	>	std::set<int> result;
81	>	if (i != container.end()) {
82	>	result = i->second;
83	>	}
84
85	<	SimInfo* currentInfo;
86	<
31	<	SimInfo::SimInfo(){
32	<
33	<	n_constraints = 0;
34	<	nZconstraints = 0;
35	<	n_oriented = 0;
36	<	n_dipoles = 0;
37	<	ndf = 0;
38	<	ndfRaw = 0;
39	<	nZconstraints = 0;
40	<	the_integrator = NULL;
41	<	setTemp = 0;
42	<	thermalTime = 0.0;
43	<	currentTime = 0.0;
44	<	rCut = 0.0;
45	<	rSw = 0.0;
46	<
47	<	haveRcut = 0;
48	<	haveRsw = 0;
49	<	boxIsInit = 0;
85	>	return result;
86	>	}
87
88	<	resetTime = 1e99;
88	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
89	>	forceField_(ff), simParams_(simParams),
90	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
91	>	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
92	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
93	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
94	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
95	>	nConstraints_(0), sman_(NULL), fortranInitialized_(false),
96	>	calcBoxDipole_(false), useAtomicVirial_(true) {
97
53	–	orthoRhombic = 0;
54	–	orthoTolerance = 1E-6;
55	–	useInitXSstate = true;
98
99	<	usePBC = 0;
100	<	useLJ = 0;
101	<	useSticky = 0;
102	<	useCharges = 0;
103	<	useDipoles = 0;
104	<	useReactionField = 0;
105	<	useGB = 0;
64	<	useEAM = 0;
65	<	useSolidThermInt = 0;
66	<	useLiquidThermInt = 0;
99	>	MoleculeStamp* molStamp;
100	>	int nMolWithSameStamp;
101	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
102	>	int nGroups = 0;      //total cutoff groups defined in meta-data file
103	>	CutoffGroupStamp* cgStamp;
104	>	RigidBodyStamp* rbStamp;
105	>	int nRigidAtoms = 0;
106
107	<	haveCutoffGroups = false;
107	>	std::vector<Component*> components = simParams->getComponents();
108	>
109	>	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
110	>	molStamp = (*i)->getMoleculeStamp();
111	>	nMolWithSameStamp = (*i)->getNMol();
112	>
113	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
114
115	<	excludes = Exclude::Instance();
115	>	//calculate atoms in molecules
116	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
117
118	<	myConfiguration = new SimState();
118	>	//calculate atoms in cutoff groups
119	>	int nAtomsInGroups = 0;
120	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
121	>
122	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
123	>	cgStamp = molStamp->getCutoffGroupStamp(j);
124	>	nAtomsInGroups += cgStamp->getNMembers();
125	>	}
126
127	<	has_minimizer = false;
75	<	the_minimizer =NULL;
127	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
128
129	<	ngroup = 0;
129	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
130
131	<	wrapMeSimInfo( this );
132	<	}
131	>	//calculate atoms in rigid bodies
132	>	int nAtomsInRigidBodies = 0;
133	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
134	>
135	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
136	>	rbStamp = molStamp->getRigidBodyStamp(j);
137	>	nAtomsInRigidBodies += rbStamp->getNMembers();
138	>	}
139
140	+	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
141	+	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
142	+
143	+	}
144
145	<	SimInfo::~SimInfo(){
145	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
146	>	//group therefore the total number of cutoff groups in the system is
147	>	//equal to the total number of atoms minus number of atoms belong to
148	>	//cutoff group defined in meta-data file plus the number of cutoff
149	>	//groups defined in meta-data file
150	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
151
152	<	delete myConfiguration;
153	<
154	<	map<string, GenericData*>::iterator i;
152	>	//every free atom (atom does not belong to rigid bodies) is an
153	>	//integrable object therefore the total number of integrable objects
154	>	//in the system is equal to the total number of atoms minus number of
155	>	//atoms belong to rigid body defined in meta-data file plus the number
156	>	//of rigid bodies defined in meta-data file
157	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
158	>	+ nGlobalRigidBodies_;
159
160	<	for(i = properties.begin(); i != properties.end(); i++)
161	<	delete (*i).second;
160	>	nGlobalMols_ = molStampIds_.size();
161	>	molToProcMap_.resize(nGlobalMols_);
162	>	}
163
164	<	}
164	>	SimInfo::~SimInfo() {
165	>	std::map<int, Molecule*>::iterator i;
166	>	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
167	>	delete i->second;
168	>	}
169	>	molecules_.clear();
170	>
171	>	delete sman_;
172	>	delete simParams_;
173	>	delete forceField_;
174	>	}
175
176	<	void SimInfo::setBox(double newBox[3]) {
177	<
178	<	int i, j;
179	<	double tempMat[3][3];
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	<	for(i=0; i<3; i++)
188	<	for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
187	>	bool SimInfo::addMolecule(Molecule* mol) {
188	>	MoleculeIterator i;
189
190	<	tempMat[0][0] = newBox[0];
191	<	tempMat[1][1] = newBox[1];
104	<	tempMat[2][2] = newBox[2];
190	>	i = molecules_.find(mol->getGlobalIndex());
191	>	if (i == molecules_.end() ) {
192
193	<	setBoxM( tempMat );
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	>	nInversions_ += mol->getNInversions();
200	>	nRigidBodies_ += mol->getNRigidBodies();
201	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
202	>	nCutoffGroups_ += mol->getNCutoffGroups();
203	>	nConstraints_ += mol->getNConstraintPairs();
204
205	<	}
205	>	addExcludePairs(mol);
206	>
207	>	return true;
208	>	} else {
209	>	return false;
210	>	}
211	>	}
212
213	<	void SimInfo::setBoxM( double theBox[3][3] ){
214	<
215	<	int i, j;
113	<	double FortranHmat[9]; // to preserve compatibility with Fortran the
114	<	// ordering in the array is as follows:
115	<	// [ 0 3 6 ]
116	<	// [ 1 4 7 ]
117	<	// [ 2 5 8 ]
118	<	double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
213	>	bool SimInfo::removeMolecule(Molecule* mol) {
214	>	MoleculeIterator i;
215	>	i = molecules_.find(mol->getGlobalIndex());
216
217	<	if( !boxIsInit ) boxIsInit = 1;
217	>	if (i != molecules_.end() ) {
218
219	<	for(i=0; i < 3; i++)
220	<	for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
221	<
222	<	calcBoxL();
223	<	calcHmatInv();
224	<
225	<	for(i=0; i < 3; i++) {
226	<	for (j=0; j < 3; j++) {
227	<	FortranHmat[3*j + i] = Hmat[i][j];
228	<	FortranHmatInv[3*j + i] = HmatInv[i][j];
229	<	}
133	<	}
219	>	assert(mol == i->second);
220	>
221	>	nAtoms_ -= mol->getNAtoms();
222	>	nBonds_ -= mol->getNBonds();
223	>	nBends_ -= mol->getNBends();
224	>	nTorsions_ -= mol->getNTorsions();
225	>	nInversions_ -= mol->getNInversions();
226	>	nRigidBodies_ -= mol->getNRigidBodies();
227	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
228	>	nCutoffGroups_ -= mol->getNCutoffGroups();
229	>	nConstraints_ -= mol->getNConstraintPairs();
230
231	<	setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
232	<
137	<	}
138	<
231	>	removeExcludePairs(mol);
232	>	molecules_.erase(mol->getGlobalIndex());
233
234	<	void SimInfo::getBoxM (double theBox[3][3]) {
234	>	delete mol;
235	>
236	>	return true;
237	>	} else {
238	>	return false;
239	>	}
240
142	–	int i, j;
143	–	for(i=0; i<3; i++)
144	–	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
145	–	}
241
242	+	}
243
244	<	void SimInfo::scaleBox(double scale) {
245	<	double theBox[3][3];
246	<	int i, j;
244	>
245	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
246	>	i = molecules_.begin();
247	>	return i == molecules_.end() ? NULL : i->second;
248	>	}
249
250	<	// cerr << "Scaling box by " << scale << "\n";
250	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
251	>	++i;
252	>	return i == molecules_.end() ? NULL : i->second;
253	>	}
254
154	–	for(i=0; i<3; i++)
155	–	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
255
256	<	setBoxM(theBox);
256	>	void SimInfo::calcNdf() {
257	>	int ndf_local;
258	>	MoleculeIterator i;
259	>	std::vector<StuntDouble*>::iterator j;
260	>	Molecule* mol;
261	>	StuntDouble* integrableObject;
262
263	<	}
263	>	ndf_local = 0;
264	>
265	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
266	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
267	>	integrableObject = mol->nextIntegrableObject(j)) {
268
269	<	void SimInfo::calcHmatInv( void ) {
162	<
163	<	int oldOrtho;
164	<	int i,j;
165	<	double smallDiag;
166	<	double tol;
167	<	double sanity[3][3];
269	>	ndf_local += 3;
270
271	<	invertMat3( Hmat, HmatInv );
272	<
273	<	// check to see if Hmat is orthorhombic
274	<
275	<	oldOrtho = orthoRhombic;
276	<
277	<	smallDiag = fabs(Hmat[0][0]);
278	<	if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
177	<	if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
178	<	tol = smallDiag * orthoTolerance;
179	<
180	<	orthoRhombic = 1;
181	<
182	<	for (i = 0; i < 3; i++ ) {
183	<	for (j = 0 ; j < 3; j++) {
184	<	if (i != j) {
185	<	if (orthoRhombic) {
186	<	if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
187	<	}
271	>	if (integrableObject->isDirectional()) {
272	>	if (integrableObject->isLinear()) {
273	>	ndf_local += 2;
274	>	} else {
275	>	ndf_local += 3;
276	>	}
277	>	}
278	>
279		}
280		}
190	–	}
191	–
192	–	if( oldOrtho != orthoRhombic ){
281
282	<	if( orthoRhombic ) {
283	<	sprintf( painCave.errMsg,
196	<	"OOPSE is switching from the default Non-Orthorhombic\n"
197	<	"\tto the faster Orthorhombic periodic boundary computations.\n"
198	<	"\tThis is usually a good thing, but if you wan't the\n"
199	<	"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
200	<	"\tvariable ( currently set to %G ) smaller.\n",
201	<	orthoTolerance);
202	<	painCave.severity = OOPSE_INFO;
203	<	simError();
204	<	}
205	<	else {
206	<	sprintf( painCave.errMsg,
207	<	"OOPSE is switching from the faster Orthorhombic to the more\n"
208	<	"\tflexible Non-Orthorhombic periodic boundary computations.\n"
209	<	"\tThis is usually because the box has deformed under\n"
210	<	"\tNPTf integration. If you wan't to live on the edge with\n"
211	<	"\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
212	<	"\tvariable ( currently set to %G ) larger.\n",
213	<	orthoTolerance);
214	<	painCave.severity = OOPSE_WARNING;
215	<	simError();
216	<	}
217	<	}
218	<	}
282	>	// n_constraints is local, so subtract them on each processor
283	>	ndf_local -= nConstraints_;
284
285	<	void SimInfo::calcBoxL( void ){
285	>	#ifdef IS_MPI
286	>	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
287	>	#else
288	>	ndf_ = ndf_local;
289	>	#endif
290
291	<	double dx, dy, dz, dsq;
291	>	// nZconstraints_ is global, as are the 3 COM translations for the
292	>	// entire system:
293	>	ndf_ = ndf_ - 3 - nZconstraint_;
294
295	<	// boxVol = Determinant of Hmat
295	>	}
296
297	<	boxVol = matDet3( Hmat );
298	<
299	<	// boxLx
300	<
301	<	dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
302	<	dsq = dx*dx + dy*dy + dz*dz;
303	<	boxL[0] = sqrt( dsq );
304	<	//maxCutoff = 0.5 * boxL[0];
234	<
235	<	// boxLy
236	<
237	<	dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
238	<	dsq = dx*dx + dy*dy + dz*dz;
239	<	boxL[1] = sqrt( dsq );
240	<	//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
241	<
242	<
243	<	// boxLz
244	<
245	<	dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
246	<	dsq = dx*dx + dy*dy + dz*dz;
247	<	boxL[2] = sqrt( dsq );
248	<	//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
249	<
250	<	//calculate the max cutoff
251	<	maxCutoff =  calcMaxCutOff();
252	<
253	<	checkCutOffs();
254	<
255	<	}
256	<
257	<
258	<	double SimInfo::calcMaxCutOff(){
259	<
260	<	double ri[3], rj[3], rk[3];
261	<	double rij[3], rjk[3], rki[3];
262	<	double minDist;
263	<
264	<	ri[0] = Hmat[0][0];
265	<	ri[1] = Hmat[1][0];
266	<	ri[2] = Hmat[2][0];
267	<
268	<	rj[0] = Hmat[0][1];
269	<	rj[1] = Hmat[1][1];
270	<	rj[2] = Hmat[2][1];
271	<
272	<	rk[0] = Hmat[0][2];
273	<	rk[1] = Hmat[1][2];
274	<	rk[2] = Hmat[2][2];
297	>	int SimInfo::getFdf() {
298	>	#ifdef IS_MPI
299	>	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
300	>	#else
301	>	fdf_ = fdf_local;
302	>	#endif
303	>	return fdf_;
304	>	}
305
306	<	crossProduct3(ri, rj, rij);
307	<	distXY = dotProduct3(rk,rij) / norm3(rij);
306	>	void SimInfo::calcNdfRaw() {
307	>	int ndfRaw_local;
308
309	<	crossProduct3(rj,rk, rjk);
310	<	distYZ = dotProduct3(ri,rjk) / norm3(rjk);
309	>	MoleculeIterator i;
310	>	std::vector<StuntDouble*>::iterator j;
311	>	Molecule* mol;
312	>	StuntDouble* integrableObject;
313
314	<	crossProduct3(rk,ri, rki);
315	<	distZX = dotProduct3(rj,rki) / norm3(rki);
284	<
285	<	minDist = min(min(distXY, distYZ), distZX);
286	<	return minDist/2;
287	<
288	<	}
289	<
290	<	void SimInfo::wrapVector( double thePos[3] ){
291	<
292	<	int i;
293	<	double scaled[3];
294	<
295	<	if( !orthoRhombic ){
296	<	// calc the scaled coordinates.
297	<
298	<
299	<	matVecMul3(HmatInv, thePos, scaled);
314	>	// Raw degrees of freedom that we have to set
315	>	ndfRaw_local = 0;
316
317	<	for(i=0; i<3; i++)
318	<	scaled[i] -= roundMe(scaled[i]);
319	<
304	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
305	<
306	<	matVecMul3(Hmat, scaled, thePos);
317	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
318	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
319	>	integrableObject = mol->nextIntegrableObject(j)) {
320
321	<	}
309	<	else{
310	<	// calc the scaled coordinates.
311	<
312	<	for(i=0; i<3; i++)
313	<	scaled[i] = thePos[i]*HmatInv[i][i];
314	<
315	<	// wrap the scaled coordinates
316	<
317	<	for(i=0; i<3; i++)
318	<	scaled[i] -= roundMe(scaled[i]);
319	<
320	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
321	<
322	<	for(i=0; i<3; i++)
323	<	thePos[i] = scaled[i]*Hmat[i][i];
324	<	}
325	<
326	<	}
321	>	ndfRaw_local += 3;
322
323	<
324	<	int SimInfo::getNDF(){
325	<	int ndf_local;
326	<
327	<	ndf_local = 0;
328	<
329	<	for(int i = 0; i < integrableObjects.size(); i++){
330	<	ndf_local += 3;
331	<	if (integrableObjects[i]->isDirectional()) {
337	<	if (integrableObjects[i]->isLinear())
338	<	ndf_local += 2;
339	<	else
340	<	ndf_local += 3;
323	>	if (integrableObject->isDirectional()) {
324	>	if (integrableObject->isLinear()) {
325	>	ndfRaw_local += 2;
326	>	} else {
327	>	ndfRaw_local += 3;
328	>	}
329	>	}
330	>
331	>	}
332		}
333	+
334	+	#ifdef IS_MPI
335	+	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
336	+	#else
337	+	ndfRaw_ = ndfRaw_local;
338	+	#endif
339		}
340
341	<	// n_constraints is local, so subtract them on each processor:
341	>	void SimInfo::calcNdfTrans() {
342	>	int ndfTrans_local;
343
344	<	ndf_local -= n_constraints;
344	>	ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
345
346	+
347		#ifdef IS_MPI
348	<	MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
348	>	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
349		#else
350	<	ndf = ndf_local;
350	>	ndfTrans_ = ndfTrans_local;
351		#endif
352
353	<	// nZconstraints is global, as are the 3 COM translations for the
354	<	// entire system:
353	>	ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
354	>
355	>	}
356
357	<	ndf = ndf - 3 - nZconstraints;
357	>	void SimInfo::addExcludePairs(Molecule* mol) {
358	>	std::vector<Bond*>::iterator bondIter;
359	>	std::vector<Bend*>::iterator bendIter;
360	>	std::vector<Torsion*>::iterator torsionIter;
361	>	std::vector<Inversion*>::iterator inversionIter;
362	>	Bond* bond;
363	>	Bend* bend;
364	>	Torsion* torsion;
365	>	Inversion* inversion;
366	>	int a;
367	>	int b;
368	>	int c;
369	>	int d;
370
371	<	return ndf;
360	<	}
371	>	std::map<int, std::set<int> > atomGroups;
372
373	<	int SimInfo::getNDFraw() {
374	<	int ndfRaw_local;
373	>	Molecule::RigidBodyIterator rbIter;
374	>	RigidBody* rb;
375	>	Molecule::IntegrableObjectIterator ii;
376	>	StuntDouble* integrableObject;
377	>
378	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
379	>	integrableObject = mol->nextIntegrableObject(ii)) {
380
381	<	// Raw degrees of freedom that we have to set
382	<	ndfRaw_local = 0;
381	>	if (integrableObject->isRigidBody()) {
382	>	rb = static_cast<RigidBody*>(integrableObject);
383	>	std::vector<Atom*> atoms = rb->getAtoms();
384	>	std::set<int> rigidAtoms;
385	>	for (int i = 0; i < atoms.size(); ++i) {
386	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
387	>	}
388	>	for (int i = 0; i < atoms.size(); ++i) {
389	>	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
390	>	}
391	>	} else {
392	>	std::set<int> oneAtomSet;
393	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
394	>	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
395	>	}
396	>	}
397
368	–	for(int i = 0; i < integrableObjects.size(); i++){
369	–	ndfRaw_local += 3;
370	–	if (integrableObjects[i]->isDirectional()) {
371	–	if (integrableObjects[i]->isLinear())
372	–	ndfRaw_local += 2;
373	–	else
374	–	ndfRaw_local += 3;
375	–	}
376	–	}
398
399	<	#ifdef IS_MPI
400	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
401	<	#else
402	<	ndfRaw = ndfRaw_local;
403	<	#endif
399	>
400	>	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
401	>	a = bond->getAtomA()->getGlobalIndex();
402	>	b = bond->getAtomB()->getGlobalIndex();
403	>	exclude_.addPair(a, b);
404	>	}
405
406	<	return ndfRaw;
407	<	}
406	>	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
407	>	a = bend->getAtomA()->getGlobalIndex();
408	>	b = bend->getAtomB()->getGlobalIndex();
409	>	c = bend->getAtomC()->getGlobalIndex();
410	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
411	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
412	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
413
414	<	int SimInfo::getNDFtranslational() {
415	<	int ndfTrans_local;
414	>	exclude_.addPairs(rigidSetA, rigidSetB);
415	>	exclude_.addPairs(rigidSetA, rigidSetC);
416	>	exclude_.addPairs(rigidSetB, rigidSetC);
417	>
418	>	//exclude_.addPair(a, b);
419	>	//exclude_.addPair(a, c);
420	>	//exclude_.addPair(b, c);
421	>	}
422
423	<	ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
423	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
424	>	a = torsion->getAtomA()->getGlobalIndex();
425	>	b = torsion->getAtomB()->getGlobalIndex();
426	>	c = torsion->getAtomC()->getGlobalIndex();
427	>	d = torsion->getAtomD()->getGlobalIndex();
428	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
429	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
430	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
431	>	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
432
433	+	exclude_.addPairs(rigidSetA, rigidSetB);
434	+	exclude_.addPairs(rigidSetA, rigidSetC);
435	+	exclude_.addPairs(rigidSetA, rigidSetD);
436	+	exclude_.addPairs(rigidSetB, rigidSetC);
437	+	exclude_.addPairs(rigidSetB, rigidSetD);
438	+	exclude_.addPairs(rigidSetC, rigidSetD);
439
440	<	#ifdef IS_MPI
441	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
442	<	#else
443	<	ndfTrans = ndfTrans_local;
444	<	#endif
440	>	/*
441	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
442	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
443	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
444	>	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
445	>	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
446	>	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
447	>
448	>
449	>	exclude_.addPair(a, b);
450	>	exclude_.addPair(a, c);
451	>	exclude_.addPair(a, d);
452	>	exclude_.addPair(b, c);
453	>	exclude_.addPair(b, d);
454	>	exclude_.addPair(c, d);
455	>	*/
456	>	}
457
458	<	ndfTrans = ndfTrans - 3 - nZconstraints;
458	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
459	>	inversion = mol->nextInversion(inversionIter)) {
460	>	a = inversion->getAtomA()->getGlobalIndex();
461	>	b = inversion->getAtomB()->getGlobalIndex();
462	>	c = inversion->getAtomC()->getGlobalIndex();
463	>	d = inversion->getAtomD()->getGlobalIndex();
464	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
465	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
466	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
467	>	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
468
469	<	return ndfTrans;
470	<	}
469	>	exclude_.addPairs(rigidSetA, rigidSetB);
470	>	exclude_.addPairs(rigidSetA, rigidSetC);
471	>	exclude_.addPairs(rigidSetA, rigidSetD);
472	>	exclude_.addPairs(rigidSetB, rigidSetC);
473	>	exclude_.addPairs(rigidSetB, rigidSetD);
474	>	exclude_.addPairs(rigidSetC, rigidSetD);
475
476	<	int SimInfo::getTotIntegrableObjects() {
477	<	int nObjs_local;
478	<	int nObjs;
476	>	/*
477	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
478	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
479	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
480	>	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
481	>	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
482	>	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
483	>
484	>
485	>	exclude_.addPair(a, b);
486	>	exclude_.addPair(a, c);
487	>	exclude_.addPair(a, d);
488	>	exclude_.addPair(b, c);
489	>	exclude_.addPair(b, d);
490	>	exclude_.addPair(c, d);
491	>	*/
492	>	}
493
494	<	nObjs_local =  integrableObjects.size();
494	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
495	>	std::vector<Atom*> atoms = rb->getAtoms();
496	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
497	>	for (int j = i + 1; j < atoms.size(); ++j) {
498	>	a = atoms[i]->getGlobalIndex();
499	>	b = atoms[j]->getGlobalIndex();
500	>	exclude_.addPair(a, b);
501	>	}
502	>	}
503	>	}
504
505	+	}
506
507	<	#ifdef IS_MPI
508	<	MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
509	<	#else
510	<	nObjs = nObjs_local;
511	<	#endif
507	>	void SimInfo::removeExcludePairs(Molecule* mol) {
508	>	std::vector<Bond*>::iterator bondIter;
509	>	std::vector<Bend*>::iterator bendIter;
510	>	std::vector<Torsion*>::iterator torsionIter;
511	>	std::vector<Inversion*>::iterator inversionIter;
512	>	Bond* bond;
513	>	Bend* bend;
514	>	Torsion* torsion;
515	>	Inversion* inversion;
516	>	int a;
517	>	int b;
518	>	int c;
519	>	int d;
520
521	+	std::map<int, std::set<int> > atomGroups;
522
523	<	return nObjs;
524	<	}
523	>	Molecule::RigidBodyIterator rbIter;
524	>	RigidBody* rb;
525	>	Molecule::IntegrableObjectIterator ii;
526	>	StuntDouble* integrableObject;
527	>
528	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
529	>	integrableObject = mol->nextIntegrableObject(ii)) {
530
531	<	void SimInfo::refreshSim(){
532	<
533	<	simtype fInfo;
534	<	int isError;
535	<	int n_global;
536	<	int* excl;
537	<
538	<	fInfo.dielect = 0.0;
531	>	if (integrableObject->isRigidBody()) {
532	>	rb = static_cast<RigidBody*>(integrableObject);
533	>	std::vector<Atom*> atoms = rb->getAtoms();
534	>	std::set<int> rigidAtoms;
535	>	for (int i = 0; i < atoms.size(); ++i) {
536	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
537	>	}
538	>	for (int i = 0; i < atoms.size(); ++i) {
539	>	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
540	>	}
541	>	} else {
542	>	std::set<int> oneAtomSet;
543	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
544	>	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
545	>	}
546	>	}
547
548	<	if( useDipoles ){
549	<	if( useReactionField )fInfo.dielect = dielectric;
548	>
549	>	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
550	>	a = bond->getAtomA()->getGlobalIndex();
551	>	b = bond->getAtomB()->getGlobalIndex();
552	>	exclude_.removePair(a, b);
553	>	}
554	>
555	>	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
556	>	a = bend->getAtomA()->getGlobalIndex();
557	>	b = bend->getAtomB()->getGlobalIndex();
558	>	c = bend->getAtomC()->getGlobalIndex();
559	>
560	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
561	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
562	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
563	>
564	>	exclude_.removePairs(rigidSetA, rigidSetB);
565	>	exclude_.removePairs(rigidSetA, rigidSetC);
566	>	exclude_.removePairs(rigidSetB, rigidSetC);
567	>
568	>	//exclude_.removePair(a, b);
569	>	//exclude_.removePair(a, c);
570	>	//exclude_.removePair(b, c);
571	>	}
572	>
573	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
574	>	a = torsion->getAtomA()->getGlobalIndex();
575	>	b = torsion->getAtomB()->getGlobalIndex();
576	>	c = torsion->getAtomC()->getGlobalIndex();
577	>	d = torsion->getAtomD()->getGlobalIndex();
578	>
579	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
580	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
581	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
582	>	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
583	>
584	>	exclude_.removePairs(rigidSetA, rigidSetB);
585	>	exclude_.removePairs(rigidSetA, rigidSetC);
586	>	exclude_.removePairs(rigidSetA, rigidSetD);
587	>	exclude_.removePairs(rigidSetB, rigidSetC);
588	>	exclude_.removePairs(rigidSetB, rigidSetD);
589	>	exclude_.removePairs(rigidSetC, rigidSetD);
590	>
591	>	/*
592	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
593	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
594	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
595	>	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
596	>	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
597	>	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
598	>
599	>
600	>	exclude_.removePair(a, b);
601	>	exclude_.removePair(a, c);
602	>	exclude_.removePair(a, d);
603	>	exclude_.removePair(b, c);
604	>	exclude_.removePair(b, d);
605	>	exclude_.removePair(c, d);
606	>	*/
607	>	}
608	>
609	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL; inversion = mol->nextInversion(inversionIter)) {
610	>	a = inversion->getAtomA()->getGlobalIndex();
611	>	b = inversion->getAtomB()->getGlobalIndex();
612	>	c = inversion->getAtomC()->getGlobalIndex();
613	>	d = inversion->getAtomD()->getGlobalIndex();
614	>
615	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
616	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
617	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
618	>	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
619	>
620	>	exclude_.removePairs(rigidSetA, rigidSetB);
621	>	exclude_.removePairs(rigidSetA, rigidSetC);
622	>	exclude_.removePairs(rigidSetA, rigidSetD);
623	>	exclude_.removePairs(rigidSetB, rigidSetC);
624	>	exclude_.removePairs(rigidSetB, rigidSetD);
625	>	exclude_.removePairs(rigidSetC, rigidSetD);
626	>
627	>	/*
628	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
629	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
630	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
631	>	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
632	>	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
633	>	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
634	>
635	>
636	>	exclude_.removePair(a, b);
637	>	exclude_.removePair(a, c);
638	>	exclude_.removePair(a, d);
639	>	exclude_.removePair(b, c);
640	>	exclude_.removePair(b, d);
641	>	exclude_.removePair(c, d);
642	>	*/
643	>	}
644	>
645	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
646	>	std::vector<Atom*> atoms = rb->getAtoms();
647	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
648	>	for (int j = i + 1; j < atoms.size(); ++j) {
649	>	a = atoms[i]->getGlobalIndex();
650	>	b = atoms[j]->getGlobalIndex();
651	>	exclude_.removePair(a, b);
652	>	}
653	>	}
654	>	}
655	>
656		}
657
434	–	fInfo.SIM_uses_PBC = usePBC;
435	–	//fInfo.SIM_uses_LJ = 0;
436	–	fInfo.SIM_uses_LJ = useLJ;
437	–	fInfo.SIM_uses_sticky = useSticky;
438	–	//fInfo.SIM_uses_sticky = 0;
439	–	fInfo.SIM_uses_charges = useCharges;
440	–	fInfo.SIM_uses_dipoles = useDipoles;
441	–	//fInfo.SIM_uses_dipoles = 0;
442	–	fInfo.SIM_uses_RF = useReactionField;
443	–	//fInfo.SIM_uses_RF = 0;
444	–	fInfo.SIM_uses_GB = useGB;
445	–	fInfo.SIM_uses_EAM = useEAM;
658
659	<	n_exclude = excludes->getSize();
660	<	excl = excludes->getFortranArray();
661	<
659	>	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
660	>	int curStampId;
661	>
662	>	//index from 0
663	>	curStampId = moleculeStamps_.size();
664	>
665	>	moleculeStamps_.push_back(molStamp);
666	>	molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
667	>	}
668	>
669	>	void SimInfo::update() {
670	>
671	>	setupSimType();
672	>
673		#ifdef IS_MPI
674	<	n_global = mpiSim->getNAtomsGlobal();
452	<	#else
453	<	n_global = n_atoms;
674	>	setupFortranParallel();
675		#endif
455	–
456	–	isError = 0;
457	–
458	–	getFortranGroupArrays(this, FglobalGroupMembership, mfact);
459	–	//it may not be a good idea to pass the address of first element in vector
460	–	//since c++ standard does not require vector to be stored continuously in meomory
461	–	//Most of the compilers will organize the memory of vector continuously
462	–	setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
463	–	&nGlobalExcludes, globalExcludes, molMembershipArray,
464	–	&mfact[0], &ngroup, &FglobalGroupMembership[0], &isError);
676
677	<	if( isError ){
677	>	setupFortranSim();
678	>
679	>	//setup fortran force field
680	>	/** @deprecate */
681	>	int isError = 0;
682
683	<	sprintf( painCave.errMsg,
684	<	"There was an error setting the simulation information in fortran.\n" );
685	<	painCave.isFatal = 1;
686	<	painCave.severity = OOPSE_ERROR;
687	<	simError();
683	>	setupCutoff();
684	>
685	>	setupElectrostaticSummationMethod( isError );
686	>	setupSwitchingFunction();
687	>	setupAccumulateBoxDipole();
688	>
689	>	if(isError){
690	>	sprintf( painCave.errMsg,
691	>	"ForceField error: There was an error initializing the forceField in fortran.\n" );
692	>	painCave.isFatal = 1;
693	>	simError();
694	>	}
695	>
696	>	calcNdf();
697	>	calcNdfRaw();
698	>	calcNdfTrans();
699	>
700	>	fortranInitialized_ = true;
701		}
474	–
475	–	#ifdef IS_MPI
476	–	sprintf( checkPointMsg,
477	–	"succesfully sent the simulation information to fortran.\n");
478	–	MPIcheckPoint();
479	–	#endif // is_mpi
480	–
481	–	this->ndf = this->getNDF();
482	–	this->ndfRaw = this->getNDFraw();
483	–	this->ndfTrans = this->getNDFtranslational();
484	–	}
702
703	<	void SimInfo::setDefaultRcut( double theRcut ){
704	<
705	<	haveRcut = 1;
706	<	rCut = theRcut;
707	<	rList = rCut + 1.0;
708	<
492	<	notifyFortranCutOffs( &rCut, &rSw, &rList );
493	<	}
703	>	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
704	>	SimInfo::MoleculeIterator mi;
705	>	Molecule* mol;
706	>	Molecule::AtomIterator ai;
707	>	Atom* atom;
708	>	std::set<AtomType*> atomTypes;
709
710	<	void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
710	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
711
712	<	rSw = theRsw;
713	<	setDefaultRcut( theRcut );
714	<	}
712	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
713	>	atomTypes.insert(atom->getAtomType());
714	>	}
715	>
716	>	}
717	>
718	>	return atomTypes;
719	>	}
720	>
721	>	void SimInfo::setupSimType() {
722	>	std::set<AtomType*>::iterator i;
723	>	std::set<AtomType*> atomTypes;
724	>	atomTypes = getUniqueAtomTypes();
725	>
726	>	int useLennardJones = 0;
727	>	int useElectrostatic = 0;
728	>	int useEAM = 0;
729	>	int useSC = 0;
730	>	int useCharge = 0;
731	>	int useDirectional = 0;
732	>	int useDipole = 0;
733	>	int useGayBerne = 0;
734	>	int useSticky = 0;
735	>	int useStickyPower = 0;
736	>	int useShape = 0;
737	>	int useFLARB = 0; //it is not in AtomType yet
738	>	int useDirectionalAtom = 0;
739	>	int useElectrostatics = 0;
740	>	//usePBC and useRF are from simParams
741	>	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
742	>	int useRF;
743	>	int useSF;
744	>	int useSP;
745	>	int useBoxDipole;
746
747	+	std::string myMethod;
748
749	<	void SimInfo::checkCutOffs( void ){
750	<
751	<	if( boxIsInit ){
749	>	// set the useRF logical
750	>	useRF = 0;
751	>	useSF = 0;
752	>	useSP = 0;
753	>
754	>
755	>	if (simParams_->haveElectrostaticSummationMethod()) {
756	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
757	>	toUpper(myMethod);
758	>	if (myMethod == "REACTION_FIELD"){
759	>	useRF = 1;
760	>	} else if (myMethod == "SHIFTED_FORCE"){
761	>	useSF = 1;
762	>	} else if (myMethod == "SHIFTED_POTENTIAL"){
763	>	useSP = 1;
764	>	}
765	>	}
766
767	<	//we need to check cutOffs against the box
768	<
769	<	if( rCut > maxCutoff ){
509	<	sprintf( painCave.errMsg,
510	<	"cutoffRadius is too large for the current periodic box.\n"
511	<	"\tCurrent Value of cutoffRadius = %G at time %G\n "
512	<	"\tThis is larger than half of at least one of the\n"
513	<	"\tperiodic box vectors.  Right now, the Box matrix is:\n"
514	<	"\n"
515	<	"\t[ %G %G %G ]\n"
516	<	"\t[ %G %G %G ]\n"
517	<	"\t[ %G %G %G ]\n",
518	<	rCut, currentTime,
519	<	Hmat[0][0], Hmat[0][1], Hmat[0][2],
520	<	Hmat[1][0], Hmat[1][1], Hmat[1][2],
521	<	Hmat[2][0], Hmat[2][1], Hmat[2][2]);
522	<	painCave.severity = OOPSE_ERROR;
523	<	painCave.isFatal = 1;
524	<	simError();
525	<	}
526	<	} else {
527	<	// initialize this stuff before using it, OK?
528	<	sprintf( painCave.errMsg,
529	<	"Trying to check cutoffs without a box.\n"
530	<	"\tOOPSE should have better programmers than that.\n" );
531	<	painCave.severity = OOPSE_ERROR;
532	<	painCave.isFatal = 1;
533	<	simError();
534	<	}
535	<
536	<	}
767	>	if (simParams_->haveAccumulateBoxDipole())
768	>	if (simParams_->getAccumulateBoxDipole())
769	>	useBoxDipole = 1;
770
771	<	void SimInfo::addProperty(GenericData* prop){
771	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
772
773	<	map<string, GenericData*>::iterator result;
774	<	result = properties.find(prop->getID());
775	<
776	<	//we can't simply use  properties[prop->getID()] = prop,
777	<	//it will cause memory leak if we already contain a propery which has the same name of prop
778	<
779	<	if(result != properties.end()){
773	>	//loop over all of the atom types
774	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
775	>	useLennardJones |= (*i)->isLennardJones();
776	>	useElectrostatic |= (*i)->isElectrostatic();
777	>	useEAM |= (*i)->isEAM();
778	>	useSC |= (*i)->isSC();
779	>	useCharge |= (*i)->isCharge();
780	>	useDirectional |= (*i)->isDirectional();
781	>	useDipole |= (*i)->isDipole();
782	>	useGayBerne |= (*i)->isGayBerne();
783	>	useSticky |= (*i)->isSticky();
784	>	useStickyPower |= (*i)->isStickyPower();
785	>	useShape |= (*i)->isShape();
786	>	}
787	>
788	>	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
789	>	useDirectionalAtom = 1;
790	>	}
791	>
792	>	if (useCharge || useDipole) {
793	>	useElectrostatics = 1;
794	>	}
795	>
796	>	#ifdef IS_MPI
797	>	int temp;
798	>
799	>	temp = usePBC;
800	>	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
801	>
802	>	temp = useDirectionalAtom;
803	>	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
804	>
805	>	temp = useLennardJones;
806	>	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
807	>
808	>	temp = useElectrostatics;
809	>	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
810	>
811	>	temp = useCharge;
812	>	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
813	>
814	>	temp = useDipole;
815	>	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
816	>
817	>	temp = useSticky;
818	>	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
819	>
820	>	temp = useStickyPower;
821	>	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
822
823	<	delete (*result).second;
824	<	(*result).second = prop;
550	<
551	<	}
552	<	else{
823	>	temp = useGayBerne;
824	>	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
825
826	<	properties[prop->getID()] = prop;
826	>	temp = useEAM;
827	>	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
828
829	<	}
829	>	temp = useSC;
830	>	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
831
832	<	}
832	>	temp = useShape;
833	>	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
834
835	<	GenericData* SimInfo::getProperty(const string& propName){
836	<
562	<	map<string, GenericData*>::iterator result;
563	<
564	<	//string lowerCaseName = ();
565	<
566	<	result = properties.find(propName);
567	<
568	<	if(result != properties.end())
569	<	return (*result).second;
570	<	else
571	<	return NULL;
572	<	}
835	>	temp = useFLARB;
836	>	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
837
838	+	temp = useRF;
839	+	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
840
841	<	void SimInfo::getFortranGroupArrays(SimInfo* info,
842	<	vector<int>& FglobalGroupMembership,
577	<	vector<double>& mfact){
578	<
579	<	Molecule* myMols;
580	<	Atom** myAtoms;
581	<	int numAtom;
582	<	double mtot;
583	<	int numMol;
584	<	int numCutoffGroups;
585	<	CutoffGroup* myCutoffGroup;
586	<	vector<CutoffGroup*>::iterator iterCutoff;
587	<	Atom* cutoffAtom;
588	<	vector<Atom*>::iterator iterAtom;
589	<	int atomIndex;
590	<	double totalMass;
591	<
592	<	mfact.clear();
593	<	FglobalGroupMembership.clear();
594	<
841	>	temp = useSF;
842	>	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
843
844	<	// Fix the silly fortran indexing problem
845	<	#ifdef IS_MPI
846	<	numAtom = mpiSim->getNAtomsGlobal();
847	<	#else
848	<	numAtom = n_atoms;
844	>	temp = useSP;
845	>	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
846	>
847	>	temp = useBoxDipole;
848	>	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
849	>
850	>	temp = useAtomicVirial_;
851	>	MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
852	>
853		#endif
602	–	for (int i = 0; i < numAtom; i++)
603	–	FglobalGroupMembership.push_back(globalGroupMembership[i] + 1);
604	–
854
855	<	myMols = info->molecules;
856	<	numMol = info->n_mol;
857	<	for(int i  = 0; i < numMol; i++){
858	<	numCutoffGroups = myMols[i].getNCutoffGroups();
859	<	for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff);
860	<	myCutoffGroup != NULL;
861	<	myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
855	>	fInfo_.SIM_uses_PBC = usePBC;
856	>	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
857	>	fInfo_.SIM_uses_LennardJones = useLennardJones;
858	>	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
859	>	fInfo_.SIM_uses_Charges = useCharge;
860	>	fInfo_.SIM_uses_Dipoles = useDipole;
861	>	fInfo_.SIM_uses_Sticky = useSticky;
862	>	fInfo_.SIM_uses_StickyPower = useStickyPower;
863	>	fInfo_.SIM_uses_GayBerne = useGayBerne;
864	>	fInfo_.SIM_uses_EAM = useEAM;
865	>	fInfo_.SIM_uses_SC = useSC;
866	>	fInfo_.SIM_uses_Shapes = useShape;
867	>	fInfo_.SIM_uses_FLARB = useFLARB;
868	>	fInfo_.SIM_uses_RF = useRF;
869	>	fInfo_.SIM_uses_SF = useSF;
870	>	fInfo_.SIM_uses_SP = useSP;
871	>	fInfo_.SIM_uses_BoxDipole = useBoxDipole;
872	>	fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
873	>	}
874
875	<	totalMass = myCutoffGroup->getMass();
875	>	void SimInfo::setupFortranSim() {
876	>	int isError;
877	>	int nExclude;
878	>	std::vector<int> fortranGlobalGroupMembership;
879	>
880	>	nExclude = exclude_.getSize();
881	>	isError = 0;
882	>
883	>	//globalGroupMembership_ is filled by SimCreator
884	>	for (int i = 0; i < nGlobalAtoms_; i++) {
885	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
886	>	}
887	>
888	>	//calculate mass ratio of cutoff group
889	>	std::vector<RealType> mfact;
890	>	SimInfo::MoleculeIterator mi;
891	>	Molecule* mol;
892	>	Molecule::CutoffGroupIterator ci;
893	>	CutoffGroup* cg;
894	>	Molecule::AtomIterator ai;
895	>	Atom* atom;
896	>	RealType totalMass;
897	>
898	>	//to avoid memory reallocation, reserve enough space for mfact
899	>	mfact.reserve(getNCutoffGroups());
900	>
901	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
902	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
903	>
904	>	totalMass = cg->getMass();
905	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
906	>	// Check for massless groups - set mfact to 1 if true
907	>	if (totalMass != 0)
908	>	mfact.push_back(atom->getMass()/totalMass);
909	>	else
910	>	mfact.push_back( 1.0 );
911	>	}
912	>
913	>	}
914	>	}
915	>
916	>	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
917	>	std::vector<int> identArray;
918	>
919	>	//to avoid memory reallocation, reserve enough space identArray
920	>	identArray.reserve(getNAtoms());
921	>
922	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
923	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
924	>	identArray.push_back(atom->getIdent());
925	>	}
926	>	}
927	>
928	>	//fill molMembershipArray
929	>	//molMembershipArray is filled by SimCreator
930	>	std::vector<int> molMembershipArray(nGlobalAtoms_);
931	>	for (int i = 0; i < nGlobalAtoms_; i++) {
932	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
933	>	}
934	>
935	>	//setup fortran simulation
936	>	int nGlobalExcludes = 0;
937	>	int* globalExcludes = NULL;
938	>	int* excludeList = exclude_.getExcludeList();
939	>	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
940	>	&nExclude, excludeList , &nGlobalExcludes, globalExcludes,
941	>	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
942	>	&fortranGlobalGroupMembership[0], &isError);
943	>
944	>	if( isError ){
945
946	<	for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom);
947	<	cutoffAtom != NULL;
948	<	cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
949	<	mfact.push_back(cutoffAtom->getMass()/totalMass);
950	<	}
946	>	sprintf( painCave.errMsg,
947	>	"There was an error setting the simulation information in fortran.\n" );
948	>	painCave.isFatal = 1;
949	>	painCave.severity = OOPSE_ERROR;
950	>	simError();
951	>	}
952	>
953	>
954	>	sprintf( checkPointMsg,
955	>	"succesfully sent the simulation information to fortran.\n");
956	>
957	>	errorCheckPoint();
958	>
959	>	// Setup number of neighbors in neighbor list if present
960	>	if (simParams_->haveNeighborListNeighbors()) {
961	>	int nlistNeighbors = simParams_->getNeighborListNeighbors();
962	>	setNeighbors(&nlistNeighbors);
963	>	}
964	>
965	>
966	>	}
967	>
968	>
969	>	void SimInfo::setupFortranParallel() {
970	>	#ifdef IS_MPI
971	>	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
972	>	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
973	>	std::vector<int> localToGlobalCutoffGroupIndex;
974	>	SimInfo::MoleculeIterator mi;
975	>	Molecule::AtomIterator ai;
976	>	Molecule::CutoffGroupIterator ci;
977	>	Molecule* mol;
978	>	Atom* atom;
979	>	CutoffGroup* cg;
980	>	mpiSimData parallelData;
981	>	int isError;
982	>
983	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
984	>
985	>	//local index(index in DataStorge) of atom is important
986	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
987	>	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
988	>	}
989	>
990	>	//local index of cutoff group is trivial, it only depends on the order of travesing
991	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
992	>	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
993	>	}
994	>
995	>	}
996	>
997	>	//fill up mpiSimData struct
998	>	parallelData.nMolGlobal = getNGlobalMolecules();
999	>	parallelData.nMolLocal = getNMolecules();
1000	>	parallelData.nAtomsGlobal = getNGlobalAtoms();
1001	>	parallelData.nAtomsLocal = getNAtoms();
1002	>	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
1003	>	parallelData.nGroupsLocal = getNCutoffGroups();
1004	>	parallelData.myNode = worldRank;
1005	>	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
1006	>
1007	>	//pass mpiSimData struct and index arrays to fortran
1008	>	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
1009	>	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
1010	>	&localToGlobalCutoffGroupIndex[0], &isError);
1011	>
1012	>	if (isError) {
1013	>	sprintf(painCave.errMsg,
1014	>	"mpiRefresh errror: fortran didn't like something we gave it.\n");
1015	>	painCave.isFatal = 1;
1016	>	simError();
1017	>	}
1018	>
1019	>	sprintf(checkPointMsg, " mpiRefresh successful.\n");
1020	>	errorCheckPoint();
1021	>
1022	>	#endif
1023	>	}
1024	>
1025	>	void SimInfo::setupCutoff() {
1026	>
1027	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
1028	>
1029	>	// Check the cutoff policy
1030	>	int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
1031	>
1032	>	// Set LJ shifting bools to false
1033	>	ljsp_ = false;
1034	>	ljsf_ = false;
1035	>
1036	>	std::string myPolicy;
1037	>	if (forceFieldOptions_.haveCutoffPolicy()){
1038	>	myPolicy = forceFieldOptions_.getCutoffPolicy();
1039	>	}else if (simParams_->haveCutoffPolicy()) {
1040	>	myPolicy = simParams_->getCutoffPolicy();
1041	>	}
1042	>
1043	>	if (!myPolicy.empty()){
1044	>	toUpper(myPolicy);
1045	>	if (myPolicy == "MIX") {
1046	>	cp = MIX_CUTOFF_POLICY;
1047	>	} else {
1048	>	if (myPolicy == "MAX") {
1049	>	cp = MAX_CUTOFF_POLICY;
1050	>	} else {
1051	>	if (myPolicy == "TRADITIONAL") {
1052	>	cp = TRADITIONAL_CUTOFF_POLICY;
1053	>	} else {
1054	>	// throw error
1055	>	sprintf( painCave.errMsg,
1056	>	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
1057	>	painCave.isFatal = 1;
1058	>	simError();
1059	>	}
1060	>	}
1061	>	}
1062	>	}
1063	>	notifyFortranCutoffPolicy(&cp);
1064	>
1065	>	// Check the Skin Thickness for neighborlists
1066	>	RealType skin;
1067	>	if (simParams_->haveSkinThickness()) {
1068	>	skin = simParams_->getSkinThickness();
1069	>	notifyFortranSkinThickness(&skin);
1070	>	}
1071	>
1072	>	// Check if the cutoff was set explicitly:
1073	>	if (simParams_->haveCutoffRadius()) {
1074	>	rcut_ = simParams_->getCutoffRadius();
1075	>	if (simParams_->haveSwitchingRadius()) {
1076	>	rsw_  = simParams_->getSwitchingRadius();
1077	>	} else {
1078	>	if (fInfo_.SIM_uses_Charges |
1079	>	fInfo_.SIM_uses_Dipoles |
1080	>	fInfo_.SIM_uses_RF) {
1081	>
1082	>	rsw_ = 0.85 * rcut_;
1083	>	sprintf(painCave.errMsg,
1084	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
1085	>	"\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
1086	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1087	>	painCave.isFatal = 0;
1088	>	simError();
1089	>	} else {
1090	>	rsw_ = rcut_;
1091	>	sprintf(painCave.errMsg,
1092	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
1093	>	"\tOOPSE will use the same value as the cutoffRadius.\n"
1094	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1095	>	painCave.isFatal = 0;
1096	>	simError();
1097	>	}
1098	>	}
1099	>
1100	>	if (simParams_->haveElectrostaticSummationMethod()) {
1101	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1102	>	toUpper(myMethod);
1103	>
1104	>	if (myMethod == "SHIFTED_POTENTIAL") {
1105	>	ljsp_ = true;
1106	>	} else if (myMethod == "SHIFTED_FORCE") {
1107	>	ljsf_ = true;
1108	>	}
1109	>	}
1110	>	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1111	>
1112	>	} else {
1113	>
1114	>	// For electrostatic atoms, we'll assume a large safe value:
1115	>	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1116	>	sprintf(painCave.errMsg,
1117	>	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1118	>	"\tOOPSE will use a default value of 15.0 angstroms"
1119	>	"\tfor the cutoffRadius.\n");
1120	>	painCave.isFatal = 0;
1121	>	simError();
1122	>	rcut_ = 15.0;
1123	>
1124	>	if (simParams_->haveElectrostaticSummationMethod()) {
1125	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1126	>	toUpper(myMethod);
1127	>
1128	>	// For the time being, we're tethering the LJ shifted behavior to the
1129	>	// electrostaticSummationMethod keyword options
1130	>	if (myMethod == "SHIFTED_POTENTIAL") {
1131	>	ljsp_ = true;
1132	>	} else if (myMethod == "SHIFTED_FORCE") {
1133	>	ljsf_ = true;
1134	>	}
1135	>	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1136	>	if (simParams_->haveSwitchingRadius()){
1137	>	sprintf(painCave.errMsg,
1138	>	"SimInfo Warning: A value was set for the switchingRadius\n"
1139	>	"\teven though the electrostaticSummationMethod was\n"
1140	>	"\tset to %s\n", myMethod.c_str());
1141	>	painCave.isFatal = 1;
1142	>	simError();
1143	>	}
1144	>	}
1145	>	}
1146	>
1147	>	if (simParams_->haveSwitchingRadius()){
1148	>	rsw_ = simParams_->getSwitchingRadius();
1149	>	} else {
1150	>	sprintf(painCave.errMsg,
1151	>	"SimCreator Warning: No value was set for switchingRadius.\n"
1152	>	"\tOOPSE will use a default value of\n"
1153	>	"\t0.85 * cutoffRadius for the switchingRadius\n");
1154	>	painCave.isFatal = 0;
1155	>	simError();
1156	>	rsw_ = 0.85 * rcut_;
1157	>	}
1158	>
1159	>	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1160	>
1161	>	} else {
1162	>	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1163	>	// We'll punt and let fortran figure out the cutoffs later.
1164	>
1165	>	notifyFortranYouAreOnYourOwn();
1166	>
1167	>	}
1168		}
1169		}
1170
1171	<	}
1171	>	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1172	>
1173	>	int errorOut;
1174	>	int esm =  NONE;
1175	>	int sm = UNDAMPED;
1176	>	RealType alphaVal;
1177	>	RealType dielectric;
1178	>
1179	>	errorOut = isError;
1180	>
1181	>	if (simParams_->haveElectrostaticSummationMethod()) {
1182	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1183	>	toUpper(myMethod);
1184	>	if (myMethod == "NONE") {
1185	>	esm = NONE;
1186	>	} else {
1187	>	if (myMethod == "SWITCHING_FUNCTION") {
1188	>	esm = SWITCHING_FUNCTION;
1189	>	} else {
1190	>	if (myMethod == "SHIFTED_POTENTIAL") {
1191	>	esm = SHIFTED_POTENTIAL;
1192	>	} else {
1193	>	if (myMethod == "SHIFTED_FORCE") {
1194	>	esm = SHIFTED_FORCE;
1195	>	} else {
1196	>	if (myMethod == "REACTION_FIELD") {
1197	>	esm = REACTION_FIELD;
1198	>	dielectric = simParams_->getDielectric();
1199	>	if (!simParams_->haveDielectric()) {
1200	>	// throw warning
1201	>	sprintf( painCave.errMsg,
1202	>	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1203	>	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1204	>	painCave.isFatal = 0;
1205	>	simError();
1206	>	}
1207	>	} else {
1208	>	// throw error
1209	>	sprintf( painCave.errMsg,
1210	>	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1211	>	"\t(Input file specified %s .)\n"
1212	>	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1213	>	"\t\"shifted_potential\", \"shifted_force\", or \n"
1214	>	"\t\"reaction_field\".\n", myMethod.c_str() );
1215	>	painCave.isFatal = 1;
1216	>	simError();
1217	>	}
1218	>	}
1219	>	}
1220	>	}
1221	>	}
1222	>	}
1223	>
1224	>	if (simParams_->haveElectrostaticScreeningMethod()) {
1225	>	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1226	>	toUpper(myScreen);
1227	>	if (myScreen == "UNDAMPED") {
1228	>	sm = UNDAMPED;
1229	>	} else {
1230	>	if (myScreen == "DAMPED") {
1231	>	sm = DAMPED;
1232	>	if (!simParams_->haveDampingAlpha()) {
1233	>	// first set a cutoff dependent alpha value
1234	>	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1235	>	alphaVal = 0.5125 - rcut_* 0.025;
1236	>	// for values rcut > 20.5, alpha is zero
1237	>	if (alphaVal < 0) alphaVal = 0;
1238	>
1239	>	// throw warning
1240	>	sprintf( painCave.errMsg,
1241	>	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1242	>	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1243	>	painCave.isFatal = 0;
1244	>	simError();
1245	>	} else {
1246	>	alphaVal = simParams_->getDampingAlpha();
1247	>	}
1248	>
1249	>	} else {
1250	>	// throw error
1251	>	sprintf( painCave.errMsg,
1252	>	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1253	>	"\t(Input file specified %s .)\n"
1254	>	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1255	>	"or \"damped\".\n", myScreen.c_str() );
1256	>	painCave.isFatal = 1;
1257	>	simError();
1258	>	}
1259	>	}
1260	>	}
1261	>
1262	>	// let's pass some summation method variables to fortran
1263	>	setElectrostaticSummationMethod( &esm );
1264	>	setFortranElectrostaticMethod( &esm );
1265	>	setScreeningMethod( &sm );
1266	>	setDampingAlpha( &alphaVal );
1267	>	setReactionFieldDielectric( &dielectric );
1268	>	initFortranFF( &errorOut );
1269	>	}
1270	>
1271	>	void SimInfo::setupSwitchingFunction() {
1272	>	int ft = CUBIC;
1273	>
1274	>	if (simParams_->haveSwitchingFunctionType()) {
1275	>	std::string funcType = simParams_->getSwitchingFunctionType();
1276	>	toUpper(funcType);
1277	>	if (funcType == "CUBIC") {
1278	>	ft = CUBIC;
1279	>	} else {
1280	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1281	>	ft = FIFTH_ORDER_POLY;
1282	>	} else {
1283	>	// throw error
1284	>	sprintf( painCave.errMsg,
1285	>	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1286	>	painCave.isFatal = 1;
1287	>	simError();
1288	>	}
1289	>	}
1290	>	}
1291	>
1292	>	// send switching function notification to switcheroo
1293	>	setFunctionType(&ft);
1294	>
1295	>	}
1296	>
1297	>	void SimInfo::setupAccumulateBoxDipole() {
1298	>
1299	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1300	>	if ( simParams_->haveAccumulateBoxDipole() )
1301	>	if ( simParams_->getAccumulateBoxDipole() ) {
1302	>	setAccumulateBoxDipole();
1303	>	calcBoxDipole_ = true;
1304	>	}
1305	>
1306	>	}
1307	>
1308	>	void SimInfo::addProperty(GenericData* genData) {
1309	>	properties_.addProperty(genData);
1310	>	}
1311	>
1312	>	void SimInfo::removeProperty(const std::string& propName) {
1313	>	properties_.removeProperty(propName);
1314	>	}
1315	>
1316	>	void SimInfo::clearProperties() {
1317	>	properties_.clearProperties();
1318	>	}
1319	>
1320	>	std::vector<std::string> SimInfo::getPropertyNames() {
1321	>	return properties_.getPropertyNames();
1322	>	}
1323	>
1324	>	std::vector<GenericData*> SimInfo::getProperties() {
1325	>	return properties_.getProperties();
1326	>	}
1327	>
1328	>	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1329	>	return properties_.getPropertyByName(propName);
1330	>	}
1331	>
1332	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1333	>	if (sman_ == sman) {
1334	>	return;
1335	>	}
1336	>	delete sman_;
1337	>	sman_ = sman;
1338	>
1339	>	Molecule* mol;
1340	>	RigidBody* rb;
1341	>	Atom* atom;
1342	>	SimInfo::MoleculeIterator mi;
1343	>	Molecule::RigidBodyIterator rbIter;
1344	>	Molecule::AtomIterator atomIter;;
1345	>
1346	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1347	>
1348	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1349	>	atom->setSnapshotManager(sman_);
1350	>	}
1351	>
1352	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1353	>	rb->setSnapshotManager(sman_);
1354	>	}
1355	>	}
1356	>
1357	>	}
1358	>
1359	>	Vector3d SimInfo::getComVel(){
1360	>	SimInfo::MoleculeIterator i;
1361	>	Molecule* mol;
1362	>
1363	>	Vector3d comVel(0.0);
1364	>	RealType totalMass = 0.0;
1365	>
1366	>
1367	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1368	>	RealType mass = mol->getMass();
1369	>	totalMass += mass;
1370	>	comVel += mass * mol->getComVel();
1371	>	}
1372	>
1373	>	#ifdef IS_MPI
1374	>	RealType tmpMass = totalMass;
1375	>	Vector3d tmpComVel(comVel);
1376	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1377	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1378	>	#endif
1379	>
1380	>	comVel /= totalMass;
1381	>
1382	>	return comVel;
1383	>	}
1384	>
1385	>	Vector3d SimInfo::getCom(){
1386	>	SimInfo::MoleculeIterator i;
1387	>	Molecule* mol;
1388	>
1389	>	Vector3d com(0.0);
1390	>	RealType totalMass = 0.0;
1391	>
1392	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1393	>	RealType mass = mol->getMass();
1394	>	totalMass += mass;
1395	>	com += mass * mol->getCom();
1396	>	}
1397	>
1398	>	#ifdef IS_MPI
1399	>	RealType tmpMass = totalMass;
1400	>	Vector3d tmpCom(com);
1401	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1402	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1403	>	#endif
1404	>
1405	>	com /= totalMass;
1406	>
1407	>	return com;
1408	>
1409	>	}
1410	>
1411	>	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1412	>
1413	>	return o;
1414	>	}
1415	>
1416	>
1417	>	/*
1418	>	Returns center of mass and center of mass velocity in one function call.
1419	>	*/
1420	>
1421	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1422	>	SimInfo::MoleculeIterator i;
1423	>	Molecule* mol;
1424	>
1425	>
1426	>	RealType totalMass = 0.0;
1427	>
1428	>
1429	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1430	>	RealType mass = mol->getMass();
1431	>	totalMass += mass;
1432	>	com += mass * mol->getCom();
1433	>	comVel += mass * mol->getComVel();
1434	>	}
1435	>
1436	>	#ifdef IS_MPI
1437	>	RealType tmpMass = totalMass;
1438	>	Vector3d tmpCom(com);
1439	>	Vector3d tmpComVel(comVel);
1440	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1441	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1442	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1443	>	#endif
1444	>
1445	>	com /= totalMass;
1446	>	comVel /= totalMass;
1447	>	}
1448	>
1449	>	/*
1450	>	Return intertia tensor for entire system and angular momentum Vector.
1451	>
1452	>
1453	>	[  Ixx -Ixy  -Ixz ]
1454	>	J =| -Iyx  Iyy  -Iyz |
1455	>	[ -Izx -Iyz   Izz ]
1456	>	*/
1457	>
1458	>	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1459	>
1460	>
1461	>	RealType xx = 0.0;
1462	>	RealType yy = 0.0;
1463	>	RealType zz = 0.0;
1464	>	RealType xy = 0.0;
1465	>	RealType xz = 0.0;
1466	>	RealType yz = 0.0;
1467	>	Vector3d com(0.0);
1468	>	Vector3d comVel(0.0);
1469	>
1470	>	getComAll(com, comVel);
1471	>
1472	>	SimInfo::MoleculeIterator i;
1473	>	Molecule* mol;
1474	>
1475	>	Vector3d thisq(0.0);
1476	>	Vector3d thisv(0.0);
1477	>
1478	>	RealType thisMass = 0.0;
1479	>
1480	>
1481	>
1482	>
1483	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1484	>
1485	>	thisq = mol->getCom()-com;
1486	>	thisv = mol->getComVel()-comVel;
1487	>	thisMass = mol->getMass();
1488	>	// Compute moment of intertia coefficients.
1489	>	xx += thisq[0]*thisq[0]*thisMass;
1490	>	yy += thisq[1]*thisq[1]*thisMass;
1491	>	zz += thisq[2]*thisq[2]*thisMass;
1492	>
1493	>	// compute products of intertia
1494	>	xy += thisq[0]*thisq[1]*thisMass;
1495	>	xz += thisq[0]*thisq[2]*thisMass;
1496	>	yz += thisq[1]*thisq[2]*thisMass;
1497	>
1498	>	angularMomentum += cross( thisq, thisv ) * thisMass;
1499	>
1500	>	}
1501	>
1502	>
1503	>	inertiaTensor(0,0) = yy + zz;
1504	>	inertiaTensor(0,1) = -xy;
1505	>	inertiaTensor(0,2) = -xz;
1506	>	inertiaTensor(1,0) = -xy;
1507	>	inertiaTensor(1,1) = xx + zz;
1508	>	inertiaTensor(1,2) = -yz;
1509	>	inertiaTensor(2,0) = -xz;
1510	>	inertiaTensor(2,1) = -yz;
1511	>	inertiaTensor(2,2) = xx + yy;
1512	>
1513	>	#ifdef IS_MPI
1514	>	Mat3x3d tmpI(inertiaTensor);
1515	>	Vector3d tmpAngMom;
1516	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1517	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1518	>	#endif
1519	>
1520	>	return;
1521	>	}
1522	>
1523	>	//Returns the angular momentum of the system
1524	>	Vector3d SimInfo::getAngularMomentum(){
1525	>
1526	>	Vector3d com(0.0);
1527	>	Vector3d comVel(0.0);
1528	>	Vector3d angularMomentum(0.0);
1529	>
1530	>	getComAll(com,comVel);
1531	>
1532	>	SimInfo::MoleculeIterator i;
1533	>	Molecule* mol;
1534	>
1535	>	Vector3d thisr(0.0);
1536	>	Vector3d thisp(0.0);
1537	>
1538	>	RealType thisMass;
1539	>
1540	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1541	>	thisMass = mol->getMass();
1542	>	thisr = mol->getCom()-com;
1543	>	thisp = (mol->getComVel()-comVel)*thisMass;
1544	>
1545	>	angularMomentum += cross( thisr, thisp );
1546	>
1547	>	}
1548	>
1549	>	#ifdef IS_MPI
1550	>	Vector3d tmpAngMom;
1551	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1552	>	#endif
1553	>
1554	>	return angularMomentum;
1555	>	}
1556	>
1557	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1558	>	return IOIndexToIntegrableObject.at(index);
1559	>	}
1560	>
1561	>	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1562	>	IOIndexToIntegrableObject= v;
1563	>	}
1564	>
1565	>	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1566	>	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1567	>	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1568	>	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1569	>	*/
1570	>	void SimInfo::getGyrationalVolume(RealType &volume){
1571	>	Mat3x3d intTensor;
1572	>	RealType det;
1573	>	Vector3d dummyAngMom;
1574	>	RealType sysconstants;
1575	>	RealType geomCnst;
1576	>
1577	>	geomCnst = 3.0/2.0;
1578	>	/* Get the inertial tensor and angular momentum for free*/
1579	>	getInertiaTensor(intTensor,dummyAngMom);
1580	>
1581	>	det = intTensor.determinant();
1582	>	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1583	>	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1584	>	return;
1585	>	}
1586	>
1587	>	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1588	>	Mat3x3d intTensor;
1589	>	Vector3d dummyAngMom;
1590	>	RealType sysconstants;
1591	>	RealType geomCnst;
1592	>
1593	>	geomCnst = 3.0/2.0;
1594	>	/* Get the inertial tensor and angular momentum for free*/
1595	>	getInertiaTensor(intTensor,dummyAngMom);
1596	>
1597	>	detI = intTensor.determinant();
1598	>	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1599	>	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1600	>	return;
1601	>	}
1602	>	/*
1603	>	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1604	>	assert( v.size() == nAtoms_ + nRigidBodies_);
1605	>	sdByGlobalIndex_ = v;
1606	>	}
1607	>
1608	>	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1609	>	//assert(index < nAtoms_ + nRigidBodies_);
1610	>	return sdByGlobalIndex_.at(index);
1611	>	}
1612	>	*/
1613	>	}//end namespace oopse
1614	>

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