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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 2 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
Revision 1129 by chrisfen, Fri Apr 20 18:15:48 2007 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;
85	>	return result;
86	>	}
87	>
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), nRigidBodies_(0),
94	>	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
95	>	sman_(NULL), fortranInitialized_(false), calcBoxDipole_(false),
96	>	useAtomicVirial_(true) {
97
98	<	SimInfo::SimInfo(){
98	>	MoleculeStamp* molStamp;
99	>	int nMolWithSameStamp;
100	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
101	>	int nGroups = 0;      //total cutoff groups defined in meta-data file
102	>	CutoffGroupStamp* cgStamp;
103	>	RigidBodyStamp* rbStamp;
104	>	int nRigidAtoms = 0;
105	>	std::vector<Component*> components = simParams->getComponents();
106	>
107	>	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
108	>	molStamp = (*i)->getMoleculeStamp();
109	>	nMolWithSameStamp = (*i)->getNMol();
110	>
111	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
112
113	<	n_constraints = 0;
114	<	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;
113	>	//calculate atoms in molecules
114	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
115
116	<	haveRcut = 0;
117	<	haveRsw = 0;
118	<	boxIsInit = 0;
119	<
120	<	resetTime = 1e99;
116	>	//calculate atoms in cutoff groups
117	>	int nAtomsInGroups = 0;
118	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
119	>
120	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
121	>	cgStamp = molStamp->getCutoffGroupStamp(j);
122	>	nAtomsInGroups += cgStamp->getNMembers();
123	>	}
124
125	<	orthoRhombic = 0;
54	<	orthoTolerance = 1E-6;
55	<	useInitXSstate = true;
125	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
126
127	<	usePBC = 0;
58	<	useLJ = 0;
59	<	useSticky = 0;
60	<	useCharges = 0;
61	<	useDipoles = 0;
62	<	useReactionField = 0;
63	<	useGB = 0;
64	<	useEAM = 0;
65	<	useSolidThermInt = 0;
66	<	useLiquidThermInt = 0;
127	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
128
129	<	haveCutoffGroups = false;
129	>	//calculate atoms in rigid bodies
130	>	int nAtomsInRigidBodies = 0;
131	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
132	>
133	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
134	>	rbStamp = molStamp->getRigidBodyStamp(j);
135	>	nAtomsInRigidBodies += rbStamp->getNMembers();
136	>	}
137
138	<	excludes = Exclude::Instance();
138	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
139	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
140	>
141	>	}
142
143	<	myConfiguration = new SimState();
143	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
144	>	//group therefore the total number of cutoff groups in the system is
145	>	//equal to the total number of atoms minus number of atoms belong to
146	>	//cutoff group defined in meta-data file plus the number of cutoff
147	>	//groups defined in meta-data file
148	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
149
150	<	has_minimizer = false;
151	<	the_minimizer =NULL;
150	>	//every free atom (atom does not belong to rigid bodies) is an
151	>	//integrable object therefore the total number of integrable objects
152	>	//in the system is equal to the total number of atoms minus number of
153	>	//atoms belong to rigid body defined in meta-data file plus the number
154	>	//of rigid bodies defined in meta-data file
155	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
156	>	+ nGlobalRigidBodies_;
157	>
158	>	nGlobalMols_ = molStampIds_.size();
159
160	<	ngroup = 0;
160	>	#ifdef IS_MPI
161	>	molToProcMap_.resize(nGlobalMols_);
162	>	#endif
163
164	<	wrapMeSimInfo( this );
80	<	}
164	>	}
165
166	+	SimInfo::~SimInfo() {
167	+	std::map<int, Molecule*>::iterator i;
168	+	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
169	+	delete i->second;
170	+	}
171	+	molecules_.clear();
172	+
173	+	delete sman_;
174	+	delete simParams_;
175	+	delete forceField_;
176	+	}
177
178	<	SimInfo::~SimInfo(){
178	>	int SimInfo::getNGlobalConstraints() {
179	>	int nGlobalConstraints;
180	>	#ifdef IS_MPI
181	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
182	>	MPI_COMM_WORLD);
183	>	#else
184	>	nGlobalConstraints =  nConstraints_;
185	>	#endif
186	>	return nGlobalConstraints;
187	>	}
188
189	<	delete myConfiguration;
189	>	bool SimInfo::addMolecule(Molecule* mol) {
190	>	MoleculeIterator i;
191
192	<	map<string, GenericData*>::iterator i;
193	<
89	<	for(i = properties.begin(); i != properties.end(); i++)
90	<	delete (*i).second;
192	>	i = molecules_.find(mol->getGlobalIndex());
193	>	if (i == molecules_.end() ) {
194
195	<	}
195	>	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
196	>
197	>	nAtoms_ += mol->getNAtoms();
198	>	nBonds_ += mol->getNBonds();
199	>	nBends_ += mol->getNBends();
200	>	nTorsions_ += mol->getNTorsions();
201	>	nRigidBodies_ += mol->getNRigidBodies();
202	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
203	>	nCutoffGroups_ += mol->getNCutoffGroups();
204	>	nConstraints_ += mol->getNConstraintPairs();
205
206	<	void SimInfo::setBox(double newBox[3]) {
207	<
208	<	int i, j;
209	<	double tempMat[3][3];
206	>	addExcludePairs(mol);
207	>
208	>	return true;
209	>	} else {
210	>	return false;
211	>	}
212	>	}
213
214	<	for(i=0; i<3; i++)
215	<	for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
214	>	bool SimInfo::removeMolecule(Molecule* mol) {
215	>	MoleculeIterator i;
216	>	i = molecules_.find(mol->getGlobalIndex());
217
218	<	tempMat[0][0] = newBox[0];
103	<	tempMat[1][1] = newBox[1];
104	<	tempMat[2][2] = newBox[2];
218	>	if (i != molecules_.end() ) {
219
220	<	setBoxM( tempMat );
220	>	assert(mol == i->second);
221	>
222	>	nAtoms_ -= mol->getNAtoms();
223	>	nBonds_ -= mol->getNBonds();
224	>	nBends_ -= mol->getNBends();
225	>	nTorsions_ -= mol->getNTorsions();
226	>	nRigidBodies_ -= mol->getNRigidBodies();
227	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
228	>	nCutoffGroups_ -= mol->getNCutoffGroups();
229	>	nConstraints_ -= mol->getNConstraintPairs();
230
231	<	}
231	>	removeExcludePairs(mol);
232	>	molecules_.erase(mol->getGlobalIndex());
233
234	<	void SimInfo::setBoxM( double theBox[3][3] ){
235	<
236	<	int i, j;
237	<	double FortranHmat[9]; // to preserve compatibility with Fortran the
238	<	// 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);
119	<
120	<	if( !boxIsInit ) boxIsInit = 1;
121	<
122	<	for(i=0; i < 3; i++)
123	<	for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
124	<
125	<	calcBoxL();
126	<	calcHmatInv();
127	<
128	<	for(i=0; i < 3; i++) {
129	<	for (j=0; j < 3; j++) {
130	<	FortranHmat[3*j + i] = Hmat[i][j];
131	<	FortranHmatInv[3*j + i] = HmatInv[i][j];
234	>	delete mol;
235	>
236	>	return true;
237	>	} else {
238	>	return false;
239		}
133	–	}
240
135	–	setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
136	–
137	–	}
138	–
241
242	<	void SimInfo::getBoxM (double theBox[3][3]) {
242	>	}
243
244	<	int i, j;
245	<	for(i=0; i<3; i++)
246	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
247	<	}
244	>
245	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
246	>	i = molecules_.begin();
247	>	return i == molecules_.end() ? NULL : i->second;
248	>	}
249
250	+	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
251	+	++i;
252	+	return i == molecules_.end() ? NULL : i->second;
253	+	}
254
148	–	void SimInfo::scaleBox(double scale) {
149	–	double theBox[3][3];
150	–	int i, j;
255
256	<	// cerr << "Scaling box by " << scale << "\n";
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	<	for(i=0; i<3; i++)
264	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
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	<	setBoxM(theBox);
269	>	ndf_local += 3;
270
271	<	}
272	<
273	<	void SimInfo::calcHmatInv( void ) {
274	<
275	<	int oldOrtho;
276	<	int i,j;
277	<	double smallDiag;
278	<	double tol;
167	<	double sanity[3][3];
168	<
169	<	invertMat3( Hmat, HmatInv );
170	<
171	<	// check to see if Hmat is orthorhombic
172	<
173	<	oldOrtho = orthoRhombic;
174	<
175	<	smallDiag = fabs(Hmat[0][0]);
176	<	if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
177	<	if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
178	<	tol = smallDiag * orthoTolerance;
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;
292	<
293	<	// boxVol = Determinant of Hmat
225	<
226	<	boxVol = matDet3( Hmat );
227	<
228	<	// boxLx
229	<
230	<	dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
231	<	dsq = dx*dx + dy*dy + dz*dz;
232	<	boxL[0] = sqrt( dsq );
233	<	//maxCutoff = 0.5 * boxL[0];
234	<
235	<	// boxLy
236	<
237	<	dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
238	<	dsq = dx*dx + dy*dy + dz*dz;
239	<	boxL[1] = sqrt( dsq );
240	<	//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
241	<
242	<
243	<	// boxLz
244	<
245	<	dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
246	<	dsq = dx*dx + dy*dy + dz*dz;
247	<	boxL[2] = sqrt( dsq );
248	<	//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
249	<
250	<	//calculate the max cutoff
251	<	maxCutoff =  calcMaxCutOff();
252	<
253	<	checkCutOffs();
254	<
255	<	}
256	<
257	<
258	<	double SimInfo::calcMaxCutOff(){
259	<
260	<	double ri[3], rj[3], rk[3];
261	<	double rij[3], rjk[3], rki[3];
262	<	double minDist;
263	<
264	<	ri[0] = Hmat[0][0];
265	<	ri[1] = Hmat[1][0];
266	<	ri[2] = Hmat[2][0];
267	<
268	<	rj[0] = Hmat[0][1];
269	<	rj[1] = Hmat[1][1];
270	<	rj[2] = Hmat[2][1];
271	<
272	<	rk[0] = Hmat[0][2];
273	<	rk[1] = Hmat[1][2];
274	<	rk[2] = Hmat[2][2];
275	<
276	<	crossProduct3(ri, rj, rij);
277	<	distXY = dotProduct3(rk,rij) / norm3(rij);
278	<
279	<	crossProduct3(rj,rk, rjk);
280	<	distYZ = dotProduct3(ri,rjk) / norm3(rjk);
281	<
282	<	crossProduct3(rk,ri, rki);
283	<	distZX = dotProduct3(rj,rki) / norm3(rki);
284	<
285	<	minDist = min(min(distXY, distYZ), distZX);
286	<	return minDist/2;
287	<
288	<	}
289	<
290	<	void SimInfo::wrapVector( double thePos[3] ){
291	<
292	<	int i;
293	<	double scaled[3];
294	<
295	<	if( !orthoRhombic ){
296	<	// calc the scaled coordinates.
297	<
298	<
299	<	matVecMul3(HmatInv, thePos, scaled);
300	<
301	<	for(i=0; i<3; i++)
302	<	scaled[i] -= roundMe(scaled[i]);
303	<
304	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
305	<
306	<	matVecMul3(Hmat, scaled, thePos);
307	<
308	<	}
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	<	}
327	<
328	<
329	<	int SimInfo::getNDF(){
330	<	int ndf_local;
291	>	// nZconstraints_ is global, as are the 3 COM translations for the
292	>	// entire system:
293	>	ndf_ = ndf_ - 3 - nZconstraint_;
294
332	–	ndf_local = 0;
333	–
334	–	for(int i = 0; i < integrableObjects.size(); i++){
335	–	ndf_local += 3;
336	–	if (integrableObjects[i]->isDirectional()) {
337	–	if (integrableObjects[i]->isLinear())
338	–	ndf_local += 2;
339	–	else
340	–	ndf_local += 3;
341	–	}
295		}
296
297	<	// n_constraints is local, so subtract them on each processor:
345	<
346	<	ndf_local -= n_constraints;
347	<
297	>	int SimInfo::getFdf() {
298		#ifdef IS_MPI
299	<	MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
299	>	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
300		#else
301	<	ndf = ndf_local;
301	>	fdf_ = fdf_local;
302		#endif
303	+	return fdf_;
304	+	}
305	+
306	+	void SimInfo::calcNdfRaw() {
307	+	int ndfRaw_local;
308
309	<	// nZconstraints is global, as are the 3 COM translations for the
310	<	// entire system:
309	>	MoleculeIterator i;
310	>	std::vector<StuntDouble*>::iterator j;
311	>	Molecule* mol;
312	>	StuntDouble* integrableObject;
313
314	<	ndf = ndf - 3 - nZconstraints;
314	>	// Raw degrees of freedom that we have to set
315	>	ndfRaw_local = 0;
316	>
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	<	return ndf;
360	<	}
321	>	ndfRaw_local += 3;
322
323	<	int SimInfo::getNDFraw() {
324	<	int ndfRaw_local;
325	<
326	<	// Raw degrees of freedom that we have to set
327	<	ndfRaw_local = 0;
328	<
329	<	for(int i = 0; i < integrableObjects.size(); i++){
330	<	ndfRaw_local += 3;
331	<	if (integrableObjects[i]->isDirectional()) {
371	<	if (integrableObjects[i]->isLinear())
372	<	ndfRaw_local += 2;
373	<	else
374	<	ndfRaw_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		}
376	–	}
333
334		#ifdef IS_MPI
335	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
335	>	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
336		#else
337	<	ndfRaw = ndfRaw_local;
337	>	ndfRaw_ = ndfRaw_local;
338		#endif
339	+	}
340
341	<	return ndfRaw;
342	<	}
341	>	void SimInfo::calcNdfTrans() {
342	>	int ndfTrans_local;
343
344	<	int SimInfo::getNDFtranslational() {
388	<	int ndfTrans_local;
344	>	ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
345
390	–	ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
346
392	–
347		#ifdef IS_MPI
348	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans,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	<	ndfTrans = ndfTrans_local;
350	>	ndfTrans_ = ndfTrans_local;
351		#endif
352
353	<	ndfTrans = ndfTrans - 3 - nZconstraints;
353	>	ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
354	>
355	>	}
356
357	<	return ndfTrans;
358	<	}
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	>	Bond* bond;
362	>	Bend* bend;
363	>	Torsion* torsion;
364	>	int a;
365	>	int b;
366	>	int c;
367	>	int d;
368
369	<	int SimInfo::getTotIntegrableObjects() {
405	<	int nObjs_local;
406	<	int nObjs;
369	>	std::map<int, std::set<int> > atomGroups;
370
371	<	nObjs_local =  integrableObjects.size();
371	>	Molecule::RigidBodyIterator rbIter;
372	>	RigidBody* rb;
373	>	Molecule::IntegrableObjectIterator ii;
374	>	StuntDouble* integrableObject;
375	>
376	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
377	>	integrableObject = mol->nextIntegrableObject(ii)) {
378
379	+	if (integrableObject->isRigidBody()) {
380	+	rb = static_cast<RigidBody*>(integrableObject);
381	+	std::vector<Atom*> atoms = rb->getAtoms();
382	+	std::set<int> rigidAtoms;
383	+	for (int i = 0; i < atoms.size(); ++i) {
384	+	rigidAtoms.insert(atoms[i]->getGlobalIndex());
385	+	}
386	+	for (int i = 0; i < atoms.size(); ++i) {
387	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
388	+	}
389	+	} else {
390	+	std::set<int> oneAtomSet;
391	+	oneAtomSet.insert(integrableObject->getGlobalIndex());
392	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
393	+	}
394	+	}
395
396	<	#ifdef IS_MPI
397	<	MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
398	<	#else
399	<	nObjs = nObjs_local;
400	<	#endif
396	>
397	>
398	>	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
399	>	a = bond->getAtomA()->getGlobalIndex();
400	>	b = bond->getAtomB()->getGlobalIndex();
401	>	exclude_.addPair(a, b);
402	>	}
403
404	+	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
405	+	a = bend->getAtomA()->getGlobalIndex();
406	+	b = bend->getAtomB()->getGlobalIndex();
407	+	c = bend->getAtomC()->getGlobalIndex();
408	+	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
409	+	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
410	+	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
411
412	<	return nObjs;
413	<	}
412	>	exclude_.addPairs(rigidSetA, rigidSetB);
413	>	exclude_.addPairs(rigidSetA, rigidSetC);
414	>	exclude_.addPairs(rigidSetB, rigidSetC);
415	>
416	>	//exclude_.addPair(a, b);
417	>	//exclude_.addPair(a, c);
418	>	//exclude_.addPair(b, c);
419	>	}
420
421	<	void SimInfo::refreshSim(){
421	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
422	>	a = torsion->getAtomA()->getGlobalIndex();
423	>	b = torsion->getAtomB()->getGlobalIndex();
424	>	c = torsion->getAtomC()->getGlobalIndex();
425	>	d = torsion->getAtomD()->getGlobalIndex();
426	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
427	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
428	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
429	>	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
430
431	<	simtype fInfo;
432	<	int isError;
433	<	int n_global;
434	<	int* excl;
431	>	exclude_.addPairs(rigidSetA, rigidSetB);
432	>	exclude_.addPairs(rigidSetA, rigidSetC);
433	>	exclude_.addPairs(rigidSetA, rigidSetD);
434	>	exclude_.addPairs(rigidSetB, rigidSetC);
435	>	exclude_.addPairs(rigidSetB, rigidSetD);
436	>	exclude_.addPairs(rigidSetC, rigidSetD);
437
438	<	fInfo.dielect = 0.0;
438	>	/*
439	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
440	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
441	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
442	>	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
443	>	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
444	>	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
445	>
446	>
447	>	exclude_.addPair(a, b);
448	>	exclude_.addPair(a, c);
449	>	exclude_.addPair(a, d);
450	>	exclude_.addPair(b, c);
451	>	exclude_.addPair(b, d);
452	>	exclude_.addPair(c, d);
453	>	*/
454	>	}
455
456	<	if( useDipoles ){
457	<	if( useReactionField )fInfo.dielect = dielectric;
458	<	}
456	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
457	>	std::vector<Atom*> atoms = rb->getAtoms();
458	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
459	>	for (int j = i + 1; j < atoms.size(); ++j) {
460	>	a = atoms[i]->getGlobalIndex();
461	>	b = atoms[j]->getGlobalIndex();
462	>	exclude_.addPair(a, b);
463	>	}
464	>	}
465	>	}
466	>
467	>	}
468	>
469	>	void SimInfo::removeExcludePairs(Molecule* mol) {
470	>	std::vector<Bond*>::iterator bondIter;
471	>	std::vector<Bend*>::iterator bendIter;
472	>	std::vector<Torsion*>::iterator torsionIter;
473	>	Bond* bond;
474	>	Bend* bend;
475	>	Torsion* torsion;
476	>	int a;
477	>	int b;
478	>	int c;
479	>	int d;
480	>
481	>	std::map<int, std::set<int> > atomGroups;
482	>
483	>	Molecule::RigidBodyIterator rbIter;
484	>	RigidBody* rb;
485	>	Molecule::IntegrableObjectIterator ii;
486	>	StuntDouble* integrableObject;
487	>
488	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
489	>	integrableObject = mol->nextIntegrableObject(ii)) {
490	>
491	>	if (integrableObject->isRigidBody()) {
492	>	rb = static_cast<RigidBody*>(integrableObject);
493	>	std::vector<Atom*> atoms = rb->getAtoms();
494	>	std::set<int> rigidAtoms;
495	>	for (int i = 0; i < atoms.size(); ++i) {
496	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
497	>	}
498	>	for (int i = 0; i < atoms.size(); ++i) {
499	>	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
500	>	}
501	>	} else {
502	>	std::set<int> oneAtomSet;
503	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
504	>	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
505	>	}
506	>	}
507	>
508	>
509	>	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
510	>	a = bond->getAtomA()->getGlobalIndex();
511	>	b = bond->getAtomB()->getGlobalIndex();
512	>	exclude_.removePair(a, b);
513	>	}
514	>
515	>	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
516	>	a = bend->getAtomA()->getGlobalIndex();
517	>	b = bend->getAtomB()->getGlobalIndex();
518	>	c = bend->getAtomC()->getGlobalIndex();
519	>
520	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
521	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
522	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
523	>
524	>	exclude_.removePairs(rigidSetA, rigidSetB);
525	>	exclude_.removePairs(rigidSetA, rigidSetC);
526	>	exclude_.removePairs(rigidSetB, rigidSetC);
527	>
528	>	//exclude_.removePair(a, b);
529	>	//exclude_.removePair(a, c);
530	>	//exclude_.removePair(b, c);
531	>	}
532	>
533	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
534	>	a = torsion->getAtomA()->getGlobalIndex();
535	>	b = torsion->getAtomB()->getGlobalIndex();
536	>	c = torsion->getAtomC()->getGlobalIndex();
537	>	d = torsion->getAtomD()->getGlobalIndex();
538	>
539	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
540	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
541	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
542	>	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
543	>
544	>	exclude_.removePairs(rigidSetA, rigidSetB);
545	>	exclude_.removePairs(rigidSetA, rigidSetC);
546	>	exclude_.removePairs(rigidSetA, rigidSetD);
547	>	exclude_.removePairs(rigidSetB, rigidSetC);
548	>	exclude_.removePairs(rigidSetB, rigidSetD);
549	>	exclude_.removePairs(rigidSetC, rigidSetD);
550	>
551	>	/*
552	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
553	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
554	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
555	>	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
556	>	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
557	>	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
558	>
559	>
560	>	exclude_.removePair(a, b);
561	>	exclude_.removePair(a, c);
562	>	exclude_.removePair(a, d);
563	>	exclude_.removePair(b, c);
564	>	exclude_.removePair(b, d);
565	>	exclude_.removePair(c, d);
566	>	*/
567	>	}
568	>
569	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
570	>	std::vector<Atom*> atoms = rb->getAtoms();
571	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
572	>	for (int j = i + 1; j < atoms.size(); ++j) {
573	>	a = atoms[i]->getGlobalIndex();
574	>	b = atoms[j]->getGlobalIndex();
575	>	exclude_.removePair(a, b);
576	>	}
577	>	}
578	>	}
579	>
580	>	}
581	>
582	>
583	>	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
584	>	int curStampId;
585	>
586	>	//index from 0
587	>	curStampId = moleculeStamps_.size();
588	>
589	>	moleculeStamps_.push_back(molStamp);
590	>	molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
591	>	}
592	>
593	>	void SimInfo::update() {
594	>
595	>	setupSimType();
596	>
597	>	#ifdef IS_MPI
598	>	setupFortranParallel();
599	>	#endif
600	>
601	>	setupFortranSim();
602	>
603	>	//setup fortran force field
604	>	/** @deprecate */
605	>	int isError = 0;
606	>
607	>	setupCutoff();
608	>
609	>	setupElectrostaticSummationMethod( isError );
610	>	setupSwitchingFunction();
611	>	setupAccumulateBoxDipole();
612	>
613	>	if(isError){
614	>	sprintf( painCave.errMsg,
615	>	"ForceField error: There was an error initializing the forceField in fortran.\n" );
616	>	painCave.isFatal = 1;
617	>	simError();
618	>	}
619	>
620	>	calcNdf();
621	>	calcNdfRaw();
622	>	calcNdfTrans();
623	>
624	>	fortranInitialized_ = true;
625	>	}
626	>
627	>	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
628	>	SimInfo::MoleculeIterator mi;
629	>	Molecule* mol;
630	>	Molecule::AtomIterator ai;
631	>	Atom* atom;
632	>	std::set<AtomType*> atomTypes;
633	>
634	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
635	>
636	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
637	>	atomTypes.insert(atom->getAtomType());
638	>	}
639	>
640	>	}
641	>
642	>	return atomTypes;
643	>	}
644	>
645	>	void SimInfo::setupSimType() {
646	>	std::set<AtomType*>::iterator i;
647	>	std::set<AtomType*> atomTypes;
648	>	atomTypes = getUniqueAtomTypes();
649	>
650	>	int useLennardJones = 0;
651	>	int useElectrostatic = 0;
652	>	int useEAM = 0;
653	>	int useSC = 0;
654	>	int useCharge = 0;
655	>	int useDirectional = 0;
656	>	int useDipole = 0;
657	>	int useGayBerne = 0;
658	>	int useSticky = 0;
659	>	int useStickyPower = 0;
660	>	int useShape = 0;
661	>	int useFLARB = 0; //it is not in AtomType yet
662	>	int useDirectionalAtom = 0;
663	>	int useElectrostatics = 0;
664	>	//usePBC and useRF are from simParams
665	>	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
666	>	int useRF;
667	>	int useSF;
668	>	int useSP;
669	>	int useBoxDipole;
670	>
671	>	std::string myMethod;
672	>
673	>	// set the useRF logical
674	>	useRF = 0;
675	>	useSF = 0;
676	>	useSP = 0;
677	>
678	>
679	>	if (simParams_->haveElectrostaticSummationMethod()) {
680	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
681	>	toUpper(myMethod);
682	>	if (myMethod == "REACTION_FIELD"){
683	>	useRF = 1;
684	>	} else if (myMethod == "SHIFTED_FORCE"){
685	>	useSF = 1;
686	>	} else if (myMethod == "SHIFTED_POTENTIAL"){
687	>	useSP = 1;
688	>	}
689	>	}
690	>
691	>	if (simParams_->haveAccumulateBoxDipole())
692	>	if (simParams_->getAccumulateBoxDipole())
693	>	useBoxDipole = 1;
694	>
695	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
696	>
697	>	//loop over all of the atom types
698	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
699	>	useLennardJones |= (*i)->isLennardJones();
700	>	useElectrostatic |= (*i)->isElectrostatic();
701	>	useEAM |= (*i)->isEAM();
702	>	useSC |= (*i)->isSC();
703	>	useCharge |= (*i)->isCharge();
704	>	useDirectional |= (*i)->isDirectional();
705	>	useDipole |= (*i)->isDipole();
706	>	useGayBerne |= (*i)->isGayBerne();
707	>	useSticky |= (*i)->isSticky();
708	>	useStickyPower |= (*i)->isStickyPower();
709	>	useShape |= (*i)->isShape();
710	>	}
711	>
712	>	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
713	>	useDirectionalAtom = 1;
714	>	}
715	>
716	>	if (useCharge || useDipole) {
717	>	useElectrostatics = 1;
718	>	}
719	>
720	>	#ifdef IS_MPI
721	>	int temp;
722	>
723	>	temp = usePBC;
724	>	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
725	>
726	>	temp = useDirectionalAtom;
727	>	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
728	>
729	>	temp = useLennardJones;
730	>	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
731	>
732	>	temp = useElectrostatics;
733	>	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
734	>
735	>	temp = useCharge;
736	>	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
737	>
738	>	temp = useDipole;
739	>	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
740	>
741	>	temp = useSticky;
742	>	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
743	>
744	>	temp = useStickyPower;
745	>	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
746	>
747	>	temp = useGayBerne;
748	>	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
749	>
750	>	temp = useEAM;
751	>	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
752	>
753	>	temp = useSC;
754	>	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
755	>
756	>	temp = useShape;
757	>	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
758	>
759	>	temp = useFLARB;
760	>	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
761	>
762	>	temp = useRF;
763	>	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
764
765	<	fInfo.SIM_uses_PBC = usePBC;
766	<	//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;
765	>	temp = useSF;
766	>	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
767
768	<	n_exclude = excludes->getSize();
769	<	excl = excludes->getFortranArray();
770	<
771	<	#ifdef IS_MPI
772	<	n_global = mpiSim->getNAtomsGlobal();
773	<	#else
774	<	n_global = n_atoms;
768	>	temp = useSP;
769	>	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
770	>
771	>	temp = useBoxDipole;
772	>	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
773	>
774	>	temp = useAtomicVirial_;
775	>	MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
776	>
777		#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);
778
779	<	if( isError ){
780	<
781	<	sprintf( painCave.errMsg,
782	<	"There was an error setting the simulation information in fortran.\n" );
783	<	painCave.isFatal = 1;
784	<	painCave.severity = OOPSE_ERROR;
785	<	simError();
779	>	fInfo_.SIM_uses_PBC = usePBC;
780	>	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
781	>	fInfo_.SIM_uses_LennardJones = useLennardJones;
782	>	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
783	>	fInfo_.SIM_uses_Charges = useCharge;
784	>	fInfo_.SIM_uses_Dipoles = useDipole;
785	>	fInfo_.SIM_uses_Sticky = useSticky;
786	>	fInfo_.SIM_uses_StickyPower = useStickyPower;
787	>	fInfo_.SIM_uses_GayBerne = useGayBerne;
788	>	fInfo_.SIM_uses_EAM = useEAM;
789	>	fInfo_.SIM_uses_SC = useSC;
790	>	fInfo_.SIM_uses_Shapes = useShape;
791	>	fInfo_.SIM_uses_FLARB = useFLARB;
792	>	fInfo_.SIM_uses_RF = useRF;
793	>	fInfo_.SIM_uses_SF = useSF;
794	>	fInfo_.SIM_uses_SP = useSP;
795	>	fInfo_.SIM_uses_BoxDipole = useBoxDipole;
796	>	fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
797		}
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	–	}
798
799	<	void SimInfo::setDefaultRcut( double theRcut ){
800	<
801	<	haveRcut = 1;
802	<	rCut = theRcut;
803	<	rList = rCut + 1.0;
804	<
805	<	notifyFortranCutOffs( &rCut, &rSw, &rList );
493	<	}
799	>	void SimInfo::setupFortranSim() {
800	>	int isError;
801	>	int nExclude;
802	>	std::vector<int> fortranGlobalGroupMembership;
803	>
804	>	nExclude = exclude_.getSize();
805	>	isError = 0;
806
807	<	void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
807	>	//globalGroupMembership_ is filled by SimCreator
808	>	for (int i = 0; i < nGlobalAtoms_; i++) {
809	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
810	>	}
811
812	<	rSw = theRsw;
813	<	setDefaultRcut( theRcut );
814	<	}
812	>	//calculate mass ratio of cutoff group
813	>	std::vector<RealType> mfact;
814	>	SimInfo::MoleculeIterator mi;
815	>	Molecule* mol;
816	>	Molecule::CutoffGroupIterator ci;
817	>	CutoffGroup* cg;
818	>	Molecule::AtomIterator ai;
819	>	Atom* atom;
820	>	RealType totalMass;
821
822	+	//to avoid memory reallocation, reserve enough space for mfact
823	+	mfact.reserve(getNCutoffGroups());
824	+
825	+	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
826	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
827
828	<	void SimInfo::checkCutOffs( void ){
829	<
830	<	if( boxIsInit ){
828	>	totalMass = cg->getMass();
829	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
830	>	// Check for massless groups - set mfact to 1 if true
831	>	if (totalMass != 0)
832	>	mfact.push_back(atom->getMass()/totalMass);
833	>	else
834	>	mfact.push_back( 1.0 );
835	>	}
836	>
837	>	}
838	>	}
839	>
840	>	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
841	>	std::vector<int> identArray;
842	>
843	>	//to avoid memory reallocation, reserve enough space identArray
844	>	identArray.reserve(getNAtoms());
845
846	<	//we need to check cutOffs against the box
846	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
847	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
848	>	identArray.push_back(atom->getIdent());
849	>	}
850	>	}
851	>
852	>	//fill molMembershipArray
853	>	//molMembershipArray is filled by SimCreator
854	>	std::vector<int> molMembershipArray(nGlobalAtoms_);
855	>	for (int i = 0; i < nGlobalAtoms_; i++) {
856	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
857	>	}
858
859	<	if( rCut > maxCutoff ){
859	>	//setup fortran simulation
860	>	int nGlobalExcludes = 0;
861	>	int* globalExcludes = NULL;
862	>	int* excludeList = exclude_.getExcludeList();
863	>	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
864	>	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
865	>	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
866	>
867	>	if( isError ){
868	>
869		sprintf( painCave.errMsg,
870	<	"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;
870	>	"There was an error setting the simulation information in fortran.\n" );
871		painCave.isFatal = 1;
872	+	painCave.severity = OOPSE_ERROR;
873		simError();
874	<	}
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	<	}
874	>	}
875
876	<	void SimInfo::addProperty(GenericData* prop){
876	>	#ifdef IS_MPI
877	>	sprintf( checkPointMsg,
878	>	"succesfully sent the simulation information to fortran.\n");
879	>	MPIcheckPoint();
880	>	#endif // is_mpi
881
882	<	map<string, GenericData*>::iterator result;
883	<	result = properties.find(prop->getID());
884	<
885	<	//we can't simply use  properties[prop->getID()] = prop,
886	<	//it will cause memory leak if we already contain a propery which has the same name of prop
887	<
888	<	if(result != properties.end()){
547	<
548	<	delete (*result).second;
549	<	(*result).second = prop;
550	<
882	>	// Setup number of neighbors in neighbor list if present
883	>	if (simParams_->haveNeighborListNeighbors()) {
884	>	int nlistNeighbors = simParams_->getNeighborListNeighbors();
885	>	setNeighbors(&nlistNeighbors);
886	>	}
887	>
888	>
889		}
552	–	else{
890
554	–	properties[prop->getID()] = prop;
891
892	<	}
892	>	#ifdef IS_MPI
893	>	void SimInfo::setupFortranParallel() {
894
895	<	}
896	<
897	<	GenericData* SimInfo::getProperty(const string& propName){
898	<
899	<	map<string, GenericData*>::iterator result;
900	<
901	<	//string lowerCaseName = ();
902	<
903	<	result = properties.find(propName);
904	<
905	<	if(result != properties.end())
569	<	return (*result).second;
570	<	else
571	<	return NULL;
572	<	}
895	>	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
896	>	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
897	>	std::vector<int> localToGlobalCutoffGroupIndex;
898	>	SimInfo::MoleculeIterator mi;
899	>	Molecule::AtomIterator ai;
900	>	Molecule::CutoffGroupIterator ci;
901	>	Molecule* mol;
902	>	Atom* atom;
903	>	CutoffGroup* cg;
904	>	mpiSimData parallelData;
905	>	int isError;
906
907	+	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
908
909	<	void SimInfo::getFortranGroupArrays(SimInfo* info,
910	<	vector<int>& FglobalGroupMembership,
911	<	vector<double>& mfact){
912	<
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	<
909	>	//local index(index in DataStorge) of atom is important
910	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
911	>	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
912	>	}
913
914	<	// Fix the silly fortran indexing problem
915	<	#ifdef IS_MPI
916	<	numAtom = mpiSim->getNAtomsGlobal();
917	<	#else
918	<	numAtom = n_atoms;
914	>	//local index of cutoff group is trivial, it only depends on the order of travesing
915	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
916	>	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
917	>	}
918	>
919	>	}
920	>
921	>	//fill up mpiSimData struct
922	>	parallelData.nMolGlobal = getNGlobalMolecules();
923	>	parallelData.nMolLocal = getNMolecules();
924	>	parallelData.nAtomsGlobal = getNGlobalAtoms();
925	>	parallelData.nAtomsLocal = getNAtoms();
926	>	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
927	>	parallelData.nGroupsLocal = getNCutoffGroups();
928	>	parallelData.myNode = worldRank;
929	>	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
930	>
931	>	//pass mpiSimData struct and index arrays to fortran
932	>	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
933	>	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
934	>	&localToGlobalCutoffGroupIndex[0], &isError);
935	>
936	>	if (isError) {
937	>	sprintf(painCave.errMsg,
938	>	"mpiRefresh errror: fortran didn't like something we gave it.\n");
939	>	painCave.isFatal = 1;
940	>	simError();
941	>	}
942	>
943	>	sprintf(checkPointMsg, " mpiRefresh successful.\n");
944	>	MPIcheckPoint();
945	>
946	>
947	>	}
948	>
949		#endif
602	–	for (int i = 0; i < numAtom; i++)
603	–	FglobalGroupMembership.push_back(globalGroupMembership[i] + 1);
604	–
950
951	<	myMols = info->molecules;
952	<	numMol = info->n_mol;
953	<	for(int i  = 0; i < numMol; i++){
609	<	numCutoffGroups = myMols[i].getNCutoffGroups();
610	<	for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff);
611	<	myCutoffGroup != NULL;
612	<	myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
951	>	void SimInfo::setupCutoff() {
952	>
953	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
954
955	<	totalMass = myCutoffGroup->getMass();
955	>	// Check the cutoff policy
956	>	int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
957	>
958	>	// Set LJ shifting bools to false
959	>	ljsp_ = false;
960	>	ljsf_ = false;
961	>
962	>	std::string myPolicy;
963	>	if (forceFieldOptions_.haveCutoffPolicy()){
964	>	myPolicy = forceFieldOptions_.getCutoffPolicy();
965	>	}else if (simParams_->haveCutoffPolicy()) {
966	>	myPolicy = simParams_->getCutoffPolicy();
967	>	}
968	>
969	>	if (!myPolicy.empty()){
970	>	toUpper(myPolicy);
971	>	if (myPolicy == "MIX") {
972	>	cp = MIX_CUTOFF_POLICY;
973	>	} else {
974	>	if (myPolicy == "MAX") {
975	>	cp = MAX_CUTOFF_POLICY;
976	>	} else {
977	>	if (myPolicy == "TRADITIONAL") {
978	>	cp = TRADITIONAL_CUTOFF_POLICY;
979	>	} else {
980	>	// throw error
981	>	sprintf( painCave.errMsg,
982	>	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
983	>	painCave.isFatal = 1;
984	>	simError();
985	>	}
986	>	}
987	>	}
988	>	}
989	>	notifyFortranCutoffPolicy(&cp);
990	>
991	>	// Check the Skin Thickness for neighborlists
992	>	RealType skin;
993	>	if (simParams_->haveSkinThickness()) {
994	>	skin = simParams_->getSkinThickness();
995	>	notifyFortranSkinThickness(&skin);
996	>	}
997	>
998	>	// Check if the cutoff was set explicitly:
999	>	if (simParams_->haveCutoffRadius()) {
1000	>	rcut_ = simParams_->getCutoffRadius();
1001	>	if (simParams_->haveSwitchingRadius()) {
1002	>	rsw_  = simParams_->getSwitchingRadius();
1003	>	} else {
1004	>	if (fInfo_.SIM_uses_Charges |
1005	>	fInfo_.SIM_uses_Dipoles |
1006	>	fInfo_.SIM_uses_RF) {
1007	>
1008	>	rsw_ = 0.85 * rcut_;
1009	>	sprintf(painCave.errMsg,
1010	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
1011	>	"\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
1012	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1013	>	painCave.isFatal = 0;
1014	>	simError();
1015	>	} else {
1016	>	rsw_ = rcut_;
1017	>	sprintf(painCave.errMsg,
1018	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
1019	>	"\tOOPSE will use the same value as the cutoffRadius.\n"
1020	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1021	>	painCave.isFatal = 0;
1022	>	simError();
1023	>	}
1024	>	}
1025	>
1026	>	if (simParams_->haveElectrostaticSummationMethod()) {
1027	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1028	>	toUpper(myMethod);
1029	>
1030	>	if (myMethod == "SHIFTED_POTENTIAL") {
1031	>	ljsp_ = true;
1032	>	} else if (myMethod == "SHIFTED_FORCE") {
1033	>	ljsf_ = true;
1034	>	}
1035	>	}
1036	>	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1037
1038	<	for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom);
1039	<	cutoffAtom != NULL;
1040	<	cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
1041	<	mfact.push_back(cutoffAtom->getMass()/totalMass);
1042	<	}
1038	>	} else {
1039	>
1040	>	// For electrostatic atoms, we'll assume a large safe value:
1041	>	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1042	>	sprintf(painCave.errMsg,
1043	>	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1044	>	"\tOOPSE will use a default value of 15.0 angstroms"
1045	>	"\tfor the cutoffRadius.\n");
1046	>	painCave.isFatal = 0;
1047	>	simError();
1048	>	rcut_ = 15.0;
1049	>
1050	>	if (simParams_->haveElectrostaticSummationMethod()) {
1051	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1052	>	toUpper(myMethod);
1053	>
1054	>	// For the time being, we're tethering the LJ shifted behavior to the
1055	>	// electrostaticSummationMethod keyword options
1056	>	if (myMethod == "SHIFTED_POTENTIAL") {
1057	>	ljsp_ = true;
1058	>	} else if (myMethod == "SHIFTED_FORCE") {
1059	>	ljsf_ = true;
1060	>	}
1061	>	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1062	>	if (simParams_->haveSwitchingRadius()){
1063	>	sprintf(painCave.errMsg,
1064	>	"SimInfo Warning: A value was set for the switchingRadius\n"
1065	>	"\teven though the electrostaticSummationMethod was\n"
1066	>	"\tset to %s\n", myMethod.c_str());
1067	>	painCave.isFatal = 1;
1068	>	simError();
1069	>	}
1070	>	}
1071	>	}
1072	>
1073	>	if (simParams_->haveSwitchingRadius()){
1074	>	rsw_ = simParams_->getSwitchingRadius();
1075	>	} else {
1076	>	sprintf(painCave.errMsg,
1077	>	"SimCreator Warning: No value was set for switchingRadius.\n"
1078	>	"\tOOPSE will use a default value of\n"
1079	>	"\t0.85 * cutoffRadius for the switchingRadius\n");
1080	>	painCave.isFatal = 0;
1081	>	simError();
1082	>	rsw_ = 0.85 * rcut_;
1083	>	}
1084	>
1085	>	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1086	>
1087	>	} else {
1088	>	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1089	>	// We'll punt and let fortran figure out the cutoffs later.
1090	>
1091	>	notifyFortranYouAreOnYourOwn();
1092	>
1093	>	}
1094		}
1095		}
1096
1097	<	}
1097	>	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1098	>
1099	>	int errorOut;
1100	>	int esm =  NONE;
1101	>	int sm = UNDAMPED;
1102	>	RealType alphaVal;
1103	>	RealType dielectric;
1104	>
1105	>	errorOut = isError;
1106	>
1107	>	if (simParams_->haveElectrostaticSummationMethod()) {
1108	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1109	>	toUpper(myMethod);
1110	>	if (myMethod == "NONE") {
1111	>	esm = NONE;
1112	>	} else {
1113	>	if (myMethod == "SWITCHING_FUNCTION") {
1114	>	esm = SWITCHING_FUNCTION;
1115	>	} else {
1116	>	if (myMethod == "SHIFTED_POTENTIAL") {
1117	>	esm = SHIFTED_POTENTIAL;
1118	>	} else {
1119	>	if (myMethod == "SHIFTED_FORCE") {
1120	>	esm = SHIFTED_FORCE;
1121	>	} else {
1122	>	if (myMethod == "REACTION_FIELD") {
1123	>	esm = REACTION_FIELD;
1124	>	dielectric = simParams_->getDielectric();
1125	>	if (!simParams_->haveDielectric()) {
1126	>	// throw warning
1127	>	sprintf( painCave.errMsg,
1128	>	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1129	>	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1130	>	painCave.isFatal = 0;
1131	>	simError();
1132	>	}
1133	>	} else {
1134	>	// throw error
1135	>	sprintf( painCave.errMsg,
1136	>	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1137	>	"\t(Input file specified %s .)\n"
1138	>	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1139	>	"\t\"shifted_potential\", \"shifted_force\", or \n"
1140	>	"\t\"reaction_field\".\n", myMethod.c_str() );
1141	>	painCave.isFatal = 1;
1142	>	simError();
1143	>	}
1144	>	}
1145	>	}
1146	>	}
1147	>	}
1148	>	}
1149	>
1150	>	if (simParams_->haveElectrostaticScreeningMethod()) {
1151	>	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1152	>	toUpper(myScreen);
1153	>	if (myScreen == "UNDAMPED") {
1154	>	sm = UNDAMPED;
1155	>	} else {
1156	>	if (myScreen == "DAMPED") {
1157	>	sm = DAMPED;
1158	>	if (!simParams_->haveDampingAlpha()) {
1159	>	// first set a cutoff dependent alpha value
1160	>	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1161	>	alphaVal = 0.5125 - rcut_* 0.025;
1162	>	// for values rcut > 20.5, alpha is zero
1163	>	if (alphaVal < 0) alphaVal = 0;
1164	>
1165	>	// throw warning
1166	>	sprintf( painCave.errMsg,
1167	>	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1168	>	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1169	>	painCave.isFatal = 0;
1170	>	simError();
1171	>	} else {
1172	>	alphaVal = simParams_->getDampingAlpha();
1173	>	}
1174	>
1175	>	} else {
1176	>	// throw error
1177	>	sprintf( painCave.errMsg,
1178	>	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1179	>	"\t(Input file specified %s .)\n"
1180	>	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1181	>	"or \"damped\".\n", myScreen.c_str() );
1182	>	painCave.isFatal = 1;
1183	>	simError();
1184	>	}
1185	>	}
1186	>	}
1187	>
1188	>	// let's pass some summation method variables to fortran
1189	>	setElectrostaticSummationMethod( &esm );
1190	>	setFortranElectrostaticMethod( &esm );
1191	>	setScreeningMethod( &sm );
1192	>	setDampingAlpha( &alphaVal );
1193	>	setReactionFieldDielectric( &dielectric );
1194	>	initFortranFF( &errorOut );
1195	>	}
1196	>
1197	>	void SimInfo::setupSwitchingFunction() {
1198	>	int ft = CUBIC;
1199	>
1200	>	if (simParams_->haveSwitchingFunctionType()) {
1201	>	std::string funcType = simParams_->getSwitchingFunctionType();
1202	>	toUpper(funcType);
1203	>	if (funcType == "CUBIC") {
1204	>	ft = CUBIC;
1205	>	} else {
1206	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1207	>	ft = FIFTH_ORDER_POLY;
1208	>	} else {
1209	>	// throw error
1210	>	sprintf( painCave.errMsg,
1211	>	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1212	>	painCave.isFatal = 1;
1213	>	simError();
1214	>	}
1215	>	}
1216	>	}
1217	>
1218	>	// send switching function notification to switcheroo
1219	>	setFunctionType(&ft);
1220	>
1221	>	}
1222	>
1223	>	void SimInfo::setupAccumulateBoxDipole() {
1224	>
1225	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1226	>	if ( simParams_->haveAccumulateBoxDipole() )
1227	>	if ( simParams_->getAccumulateBoxDipole() ) {
1228	>	setAccumulateBoxDipole();
1229	>	calcBoxDipole_ = true;
1230	>	}
1231	>
1232	>	}
1233	>
1234	>	void SimInfo::addProperty(GenericData* genData) {
1235	>	properties_.addProperty(genData);
1236	>	}
1237	>
1238	>	void SimInfo::removeProperty(const std::string& propName) {
1239	>	properties_.removeProperty(propName);
1240	>	}
1241	>
1242	>	void SimInfo::clearProperties() {
1243	>	properties_.clearProperties();
1244	>	}
1245	>
1246	>	std::vector<std::string> SimInfo::getPropertyNames() {
1247	>	return properties_.getPropertyNames();
1248	>	}
1249	>
1250	>	std::vector<GenericData*> SimInfo::getProperties() {
1251	>	return properties_.getProperties();
1252	>	}
1253	>
1254	>	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1255	>	return properties_.getPropertyByName(propName);
1256	>	}
1257	>
1258	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1259	>	if (sman_ == sman) {
1260	>	return;
1261	>	}
1262	>	delete sman_;
1263	>	sman_ = sman;
1264	>
1265	>	Molecule* mol;
1266	>	RigidBody* rb;
1267	>	Atom* atom;
1268	>	SimInfo::MoleculeIterator mi;
1269	>	Molecule::RigidBodyIterator rbIter;
1270	>	Molecule::AtomIterator atomIter;;
1271	>
1272	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1273	>
1274	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1275	>	atom->setSnapshotManager(sman_);
1276	>	}
1277	>
1278	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1279	>	rb->setSnapshotManager(sman_);
1280	>	}
1281	>	}
1282	>
1283	>	}
1284	>
1285	>	Vector3d SimInfo::getComVel(){
1286	>	SimInfo::MoleculeIterator i;
1287	>	Molecule* mol;
1288	>
1289	>	Vector3d comVel(0.0);
1290	>	RealType totalMass = 0.0;
1291	>
1292	>
1293	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1294	>	RealType mass = mol->getMass();
1295	>	totalMass += mass;
1296	>	comVel += mass * mol->getComVel();
1297	>	}
1298	>
1299	>	#ifdef IS_MPI
1300	>	RealType tmpMass = totalMass;
1301	>	Vector3d tmpComVel(comVel);
1302	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1303	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1304	>	#endif
1305	>
1306	>	comVel /= totalMass;
1307	>
1308	>	return comVel;
1309	>	}
1310	>
1311	>	Vector3d SimInfo::getCom(){
1312	>	SimInfo::MoleculeIterator i;
1313	>	Molecule* mol;
1314	>
1315	>	Vector3d com(0.0);
1316	>	RealType totalMass = 0.0;
1317	>
1318	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1319	>	RealType mass = mol->getMass();
1320	>	totalMass += mass;
1321	>	com += mass * mol->getCom();
1322	>	}
1323	>
1324	>	#ifdef IS_MPI
1325	>	RealType tmpMass = totalMass;
1326	>	Vector3d tmpCom(com);
1327	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1328	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1329	>	#endif
1330	>
1331	>	com /= totalMass;
1332	>
1333	>	return com;
1334	>
1335	>	}
1336	>
1337	>	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1338	>
1339	>	return o;
1340	>	}
1341	>
1342	>
1343	>	/*
1344	>	Returns center of mass and center of mass velocity in one function call.
1345	>	*/
1346	>
1347	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1348	>	SimInfo::MoleculeIterator i;
1349	>	Molecule* mol;
1350	>
1351	>
1352	>	RealType totalMass = 0.0;
1353	>
1354	>
1355	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1356	>	RealType mass = mol->getMass();
1357	>	totalMass += mass;
1358	>	com += mass * mol->getCom();
1359	>	comVel += mass * mol->getComVel();
1360	>	}
1361	>
1362	>	#ifdef IS_MPI
1363	>	RealType tmpMass = totalMass;
1364	>	Vector3d tmpCom(com);
1365	>	Vector3d tmpComVel(comVel);
1366	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1367	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1368	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1369	>	#endif
1370	>
1371	>	com /= totalMass;
1372	>	comVel /= totalMass;
1373	>	}
1374	>
1375	>	/*
1376	>	Return intertia tensor for entire system and angular momentum Vector.
1377	>
1378	>
1379	>	[  Ixx -Ixy  -Ixz ]
1380	>	J =| -Iyx  Iyy  -Iyz |
1381	>	[ -Izx -Iyz   Izz ]
1382	>	*/
1383	>
1384	>	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1385	>
1386	>
1387	>	RealType xx = 0.0;
1388	>	RealType yy = 0.0;
1389	>	RealType zz = 0.0;
1390	>	RealType xy = 0.0;
1391	>	RealType xz = 0.0;
1392	>	RealType yz = 0.0;
1393	>	Vector3d com(0.0);
1394	>	Vector3d comVel(0.0);
1395	>
1396	>	getComAll(com, comVel);
1397	>
1398	>	SimInfo::MoleculeIterator i;
1399	>	Molecule* mol;
1400	>
1401	>	Vector3d thisq(0.0);
1402	>	Vector3d thisv(0.0);
1403	>
1404	>	RealType thisMass = 0.0;
1405	>
1406	>
1407	>
1408	>
1409	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1410	>
1411	>	thisq = mol->getCom()-com;
1412	>	thisv = mol->getComVel()-comVel;
1413	>	thisMass = mol->getMass();
1414	>	// Compute moment of intertia coefficients.
1415	>	xx += thisq[0]*thisq[0]*thisMass;
1416	>	yy += thisq[1]*thisq[1]*thisMass;
1417	>	zz += thisq[2]*thisq[2]*thisMass;
1418	>
1419	>	// compute products of intertia
1420	>	xy += thisq[0]*thisq[1]*thisMass;
1421	>	xz += thisq[0]*thisq[2]*thisMass;
1422	>	yz += thisq[1]*thisq[2]*thisMass;
1423	>
1424	>	angularMomentum += cross( thisq, thisv ) * thisMass;
1425	>
1426	>	}
1427	>
1428	>
1429	>	inertiaTensor(0,0) = yy + zz;
1430	>	inertiaTensor(0,1) = -xy;
1431	>	inertiaTensor(0,2) = -xz;
1432	>	inertiaTensor(1,0) = -xy;
1433	>	inertiaTensor(1,1) = xx + zz;
1434	>	inertiaTensor(1,2) = -yz;
1435	>	inertiaTensor(2,0) = -xz;
1436	>	inertiaTensor(2,1) = -yz;
1437	>	inertiaTensor(2,2) = xx + yy;
1438	>
1439	>	#ifdef IS_MPI
1440	>	Mat3x3d tmpI(inertiaTensor);
1441	>	Vector3d tmpAngMom;
1442	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1443	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1444	>	#endif
1445	>
1446	>	return;
1447	>	}
1448	>
1449	>	//Returns the angular momentum of the system
1450	>	Vector3d SimInfo::getAngularMomentum(){
1451	>
1452	>	Vector3d com(0.0);
1453	>	Vector3d comVel(0.0);
1454	>	Vector3d angularMomentum(0.0);
1455	>
1456	>	getComAll(com,comVel);
1457	>
1458	>	SimInfo::MoleculeIterator i;
1459	>	Molecule* mol;
1460	>
1461	>	Vector3d thisr(0.0);
1462	>	Vector3d thisp(0.0);
1463	>
1464	>	RealType thisMass;
1465	>
1466	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1467	>	thisMass = mol->getMass();
1468	>	thisr = mol->getCom()-com;
1469	>	thisp = (mol->getComVel()-comVel)*thisMass;
1470	>
1471	>	angularMomentum += cross( thisr, thisp );
1472	>
1473	>	}
1474	>
1475	>	#ifdef IS_MPI
1476	>	Vector3d tmpAngMom;
1477	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1478	>	#endif
1479	>
1480	>	return angularMomentum;
1481	>	}
1482	>
1483	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1484	>	return IOIndexToIntegrableObject.at(index);
1485	>	}
1486	>
1487	>	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1488	>	IOIndexToIntegrableObject= v;
1489	>	}
1490	>
1491	>	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1492	>	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1493	>	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1494	>	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1495	>	*/
1496	>	void SimInfo::getGyrationalVolume(RealType &volume){
1497	>	Mat3x3d intTensor;
1498	>	RealType det;
1499	>	Vector3d dummyAngMom;
1500	>	RealType sysconstants;
1501	>	RealType geomCnst;
1502	>
1503	>	geomCnst = 3.0/2.0;
1504	>	/* Get the inertial tensor and angular momentum for free*/
1505	>	getInertiaTensor(intTensor,dummyAngMom);
1506	>
1507	>	det = intTensor.determinant();
1508	>	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1509	>	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1510	>	return;
1511	>	}
1512	>
1513	>	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1514	>	Mat3x3d intTensor;
1515	>	Vector3d dummyAngMom;
1516	>	RealType sysconstants;
1517	>	RealType geomCnst;
1518	>
1519	>	geomCnst = 3.0/2.0;
1520	>	/* Get the inertial tensor and angular momentum for free*/
1521	>	getInertiaTensor(intTensor,dummyAngMom);
1522	>
1523	>	detI = intTensor.determinant();
1524	>	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1525	>	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1526	>	return;
1527	>	}
1528	>	/*
1529	>	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1530	>	assert( v.size() == nAtoms_ + nRigidBodies_);
1531	>	sdByGlobalIndex_ = v;
1532	>	}
1533	>
1534	>	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1535	>	//assert(index < nAtoms_ + nRigidBodies_);
1536	>	return sdByGlobalIndex_.at(index);
1537	>	}
1538	>	*/
1539	>	}//end namespace oopse
1540	>

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