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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 3 by tim, Fri Sep 24 16:27:58 2004 UTC vs.
Revision 1313 by gezelter, Wed Oct 22 20:01:49 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 "brains/SimInfo.hpp"
54	<	#define __C
55	<	#include "brains/fSimulation.h"
54	>	#include "math/Vector3.hpp"
55	>	#include "primitives/Molecule.hpp"
56	>	#include "primitives/StuntDouble.hpp"
57	>	#include "UseTheForce/fCutoffPolicy.h"
58	>	#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
59	>	#include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h"
60	>	#include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
61	>	#include "UseTheForce/doForces_interface.h"
62	>	#include "UseTheForce/DarkSide/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 "UseTheForce/fortranWrappers.hpp"
71
15	–	#include "math/MatVec3.h"
16	–
72		#ifdef IS_MPI
73	<	#include "brains/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	<	}
109	<
110	<	void SimInfo::setBoxM( double theBox[3][3] ){
205	>	addInteractionPairs(mol);
206
207	<	int i, j;
208	<	double FortranHmat[9]; // to preserve compatibility with Fortran the
209	<	// ordering in the array is as follows:
210	<	// [ 0 3 6 ]
211	<	// [ 1 4 7 ]
117	<	// [ 2 5 8 ]
118	<	double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
207	>	return true;
208	>	} else {
209	>	return false;
210	>	}
211	>	}
212
213	<	if( !boxIsInit ) boxIsInit = 1;
213	>	bool SimInfo::removeMolecule(Molecule* mol) {
214	>	MoleculeIterator i;
215	>	i = molecules_.find(mol->getGlobalIndex());
216
217	<	for(i=0; i < 3; i++)
123	<	for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
124	<
125	<	calcBoxL();
126	<	calcHmatInv();
217	>	if (i != molecules_.end() ) {
218
219	<	for(i=0; i < 3; i++) {
220	<	for (j=0; j < 3; j++) {
221	<	FortranHmat[3*j + i] = Hmat[i][j];
222	<	FortranHmatInv[3*j + i] = HmatInv[i][j];
223	<	}
224	<	}
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	>	removeInteractionPairs(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
224	–	// 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	–
295		}
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	–	}
296
297	<
329	<	int SimInfo::getNDF(){
330	<	int ndf_local;
331	<
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	<	}
342	<	}
343	<
344	<	// 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::addInteractionPairs(Molecule* mol) {
358	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
359	>	std::vector<Bond*>::iterator bondIter;
360	>	std::vector<Bend*>::iterator bendIter;
361	>	std::vector<Torsion*>::iterator torsionIter;
362	>	std::vector<Inversion*>::iterator inversionIter;
363	>	Bond* bond;
364	>	Bend* bend;
365	>	Torsion* torsion;
366	>	Inversion* inversion;
367	>	int a;
368	>	int b;
369	>	int c;
370	>	int d;
371
372	<	int SimInfo::getTotIntegrableObjects() {
373	<	int nObjs_local;
374	<	int nObjs;
372	>	// atomGroups can be used to add special interaction maps between
373	>	// groups of atoms that are in two separate rigid bodies.
374	>	// However, most site-site interactions between two rigid bodies
375	>	// are probably not special, just the ones between the physically
376	>	// bonded atoms.  Interactions *within* a single rigid body should
377	>	// always be excluded.  These are done at the bottom of this
378	>	// function.
379
380	<	nObjs_local =  integrableObjects.size();
380	>	std::map<int, std::set<int> > atomGroups;
381	>	Molecule::RigidBodyIterator rbIter;
382	>	RigidBody* rb;
383	>	Molecule::IntegrableObjectIterator ii;
384	>	StuntDouble* integrableObject;
385	>
386	>	for (integrableObject = mol->beginIntegrableObject(ii);
387	>	integrableObject != NULL;
388	>	integrableObject = mol->nextIntegrableObject(ii)) {
389	>
390	>	if (integrableObject->isRigidBody()) {
391	>	rb = static_cast<RigidBody*>(integrableObject);
392	>	std::vector<Atom*> atoms = rb->getAtoms();
393	>	std::set<int> rigidAtoms;
394	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
395	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
396	>	}
397	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
398	>	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
399	>	}
400	>	} else {
401	>	std::set<int> oneAtomSet;
402	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
403	>	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
404	>	}
405	>	}
406	>
407	>	for (bond= mol->beginBond(bondIter); bond != NULL;
408	>	bond = mol->nextBond(bondIter)) {
409
410	+	a = bond->getAtomA()->getGlobalIndex();
411	+	b = bond->getAtomB()->getGlobalIndex();
412	+
413	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
414	+	oneTwoInteractions_.addPair(a, b);
415	+	} else {
416	+	excludedInteractions_.addPair(a, b);
417	+	}
418	+	}
419
420	<	#ifdef IS_MPI
421	<	MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
413	<	#else
414	<	nObjs = nObjs_local;
415	<	#endif
420	>	for (bend= mol->beginBend(bendIter); bend != NULL;
421	>	bend = mol->nextBend(bendIter)) {
422
423	+	a = bend->getAtomA()->getGlobalIndex();
424	+	b = bend->getAtomB()->getGlobalIndex();
425	+	c = bend->getAtomC()->getGlobalIndex();
426	+
427	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
428	+	oneTwoInteractions_.addPair(a, b);
429	+	oneTwoInteractions_.addPair(b, c);
430	+	} else {
431	+	excludedInteractions_.addPair(a, b);
432	+	excludedInteractions_.addPair(b, c);
433	+	}
434
435	<	return nObjs;
436	<	}
435	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
436	>	oneThreeInteractions_.addPair(a, c);
437	>	} else {
438	>	excludedInteractions_.addPair(a, c);
439	>	}
440	>	}
441
442	<	void SimInfo::refreshSim(){
442	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
443	>	torsion = mol->nextTorsion(torsionIter)) {
444
445	<	simtype fInfo;
446	<	int isError;
447	<	int n_global;
448	<	int* excl;
445	>	a = torsion->getAtomA()->getGlobalIndex();
446	>	b = torsion->getAtomB()->getGlobalIndex();
447	>	c = torsion->getAtomC()->getGlobalIndex();
448	>	d = torsion->getAtomD()->getGlobalIndex();
449
450	<	fInfo.dielect = 0.0;
450	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
451	>	oneTwoInteractions_.addPair(a, b);
452	>	oneTwoInteractions_.addPair(b, c);
453	>	oneTwoInteractions_.addPair(c, d);
454	>	} else {
455	>	excludedInteractions_.addPair(a, b);
456	>	excludedInteractions_.addPair(b, c);
457	>	excludedInteractions_.addPair(c, d);
458	>	}
459
460	<	if( useDipoles ){
461	<	if( useReactionField )fInfo.dielect = dielectric;
462	<	}
460	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
461	>	oneThreeInteractions_.addPair(a, c);
462	>	oneThreeInteractions_.addPair(b, d);
463	>	} else {
464	>	excludedInteractions_.addPair(a, c);
465	>	excludedInteractions_.addPair(b, d);
466	>	}
467
468	<	fInfo.SIM_uses_PBC = usePBC;
469	<	//fInfo.SIM_uses_LJ = 0;
470	<	fInfo.SIM_uses_LJ = useLJ;
471	<	fInfo.SIM_uses_sticky = useSticky;
472	<	//fInfo.SIM_uses_sticky = 0;
473	<	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;
468	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
469	>	oneFourInteractions_.addPair(a, d);
470	>	} else {
471	>	excludedInteractions_.addPair(a, d);
472	>	}
473	>	}
474
475	<	n_exclude = excludes->getSize();
476	<	excl = excludes->getFortranArray();
449	<
450	<	#ifdef IS_MPI
451	<	n_global = mpiSim->getNAtomsGlobal();
452	<	#else
453	<	n_global = n_atoms;
454	<	#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);
475	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
476	>	inversion = mol->nextInversion(inversionIter)) {
477
478	<	if( isError ){
479	<
480	<	sprintf( painCave.errMsg,
481	<	"There was an error setting the simulation information in fortran.\n" );
482	<	painCave.isFatal = 1;
483	<	painCave.severity = OOPSE_ERROR;
484	<	simError();
478	>	a = inversion->getAtomA()->getGlobalIndex();
479	>	b = inversion->getAtomB()->getGlobalIndex();
480	>	c = inversion->getAtomC()->getGlobalIndex();
481	>	d = inversion->getAtomD()->getGlobalIndex();
482	>
483	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
484	>	oneTwoInteractions_.addPair(a, b);
485	>	oneTwoInteractions_.addPair(a, c);
486	>	oneTwoInteractions_.addPair(a, d);
487	>	} else {
488	>	excludedInteractions_.addPair(a, b);
489	>	excludedInteractions_.addPair(a, c);
490	>	excludedInteractions_.addPair(a, d);
491	>	}
492	>
493	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
494	>	oneThreeInteractions_.addPair(b, c);
495	>	oneThreeInteractions_.addPair(b, d);
496	>	oneThreeInteractions_.addPair(c, d);
497	>	} else {
498	>	excludedInteractions_.addPair(b, c);
499	>	excludedInteractions_.addPair(b, d);
500	>	excludedInteractions_.addPair(c, d);
501	>	}
502	>	}
503	>
504	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
505	>	rb = mol->nextRigidBody(rbIter)) {
506	>	std::vector<Atom*> atoms = rb->getAtoms();
507	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
508	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
509	>	a = atoms[i]->getGlobalIndex();
510	>	b = atoms[j]->getGlobalIndex();
511	>	excludedInteractions_.addPair(a, b);
512	>	}
513	>	}
514	>	}
515	>
516		}
517	+
518	+	void SimInfo::removeInteractionPairs(Molecule* mol) {
519	+	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
520	+	std::vector<Bond*>::iterator bondIter;
521	+	std::vector<Bend*>::iterator bendIter;
522	+	std::vector<Torsion*>::iterator torsionIter;
523	+	std::vector<Inversion*>::iterator inversionIter;
524	+	Bond* bond;
525	+	Bend* bend;
526	+	Torsion* torsion;
527	+	Inversion* inversion;
528	+	int a;
529	+	int b;
530	+	int c;
531	+	int d;
532	+
533	+	std::map<int, std::set<int> > atomGroups;
534	+	Molecule::RigidBodyIterator rbIter;
535	+	RigidBody* rb;
536	+	Molecule::IntegrableObjectIterator ii;
537	+	StuntDouble* integrableObject;
538	+
539	+	for (integrableObject = mol->beginIntegrableObject(ii);
540	+	integrableObject != NULL;
541	+	integrableObject = mol->nextIntegrableObject(ii)) {
542	+
543	+	if (integrableObject->isRigidBody()) {
544	+	rb = static_cast<RigidBody*>(integrableObject);
545	+	std::vector<Atom*> atoms = rb->getAtoms();
546	+	std::set<int> rigidAtoms;
547	+	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
548	+	rigidAtoms.insert(atoms[i]->getGlobalIndex());
549	+	}
550	+	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
551	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
552	+	}
553	+	} else {
554	+	std::set<int> oneAtomSet;
555	+	oneAtomSet.insert(integrableObject->getGlobalIndex());
556	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
557	+	}
558	+	}
559	+
560	+	for (bond= mol->beginBond(bondIter); bond != NULL;
561	+	bond = mol->nextBond(bondIter)) {
562	+
563	+	a = bond->getAtomA()->getGlobalIndex();
564	+	b = bond->getAtomB()->getGlobalIndex();
565	+
566	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
567	+	oneTwoInteractions_.removePair(a, b);
568	+	} else {
569	+	excludedInteractions_.removePair(a, b);
570	+	}
571	+	}
572	+
573	+	for (bend= mol->beginBend(bendIter); bend != NULL;
574	+	bend = mol->nextBend(bendIter)) {
575	+
576	+	a = bend->getAtomA()->getGlobalIndex();
577	+	b = bend->getAtomB()->getGlobalIndex();
578	+	c = bend->getAtomC()->getGlobalIndex();
579	+
580	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
581	+	oneTwoInteractions_.removePair(a, b);
582	+	oneTwoInteractions_.removePair(b, c);
583	+	} else {
584	+	excludedInteractions_.removePair(a, b);
585	+	excludedInteractions_.removePair(b, c);
586	+	}
587	+
588	+	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
589	+	oneThreeInteractions_.removePair(a, c);
590	+	} else {
591	+	excludedInteractions_.removePair(a, c);
592	+	}
593	+	}
594	+
595	+	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
596	+	torsion = mol->nextTorsion(torsionIter)) {
597	+
598	+	a = torsion->getAtomA()->getGlobalIndex();
599	+	b = torsion->getAtomB()->getGlobalIndex();
600	+	c = torsion->getAtomC()->getGlobalIndex();
601	+	d = torsion->getAtomD()->getGlobalIndex();
602
603	<	#ifdef IS_MPI
604	<	sprintf( checkPointMsg,
605	<	"succesfully sent the simulation information to fortran.\n");
606	<	MPIcheckPoint();
607	<	#endif // is_mpi
608	<
609	<	this->ndf = this->getNDF();
610	<	this->ndfRaw = this->getNDFraw();
611	<	this->ndfTrans = this->getNDFtranslational();
484	<	}
603	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
604	>	oneTwoInteractions_.removePair(a, b);
605	>	oneTwoInteractions_.removePair(b, c);
606	>	oneTwoInteractions_.removePair(c, d);
607	>	} else {
608	>	excludedInteractions_.removePair(a, b);
609	>	excludedInteractions_.removePair(b, c);
610	>	excludedInteractions_.removePair(c, d);
611	>	}
612
613	<	void SimInfo::setDefaultRcut( double theRcut ){
613	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
614	>	oneThreeInteractions_.removePair(a, c);
615	>	oneThreeInteractions_.removePair(b, d);
616	>	} else {
617	>	excludedInteractions_.removePair(a, c);
618	>	excludedInteractions_.removePair(b, d);
619	>	}
620	>
621	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
622	>	oneFourInteractions_.removePair(a, d);
623	>	} else {
624	>	excludedInteractions_.removePair(a, d);
625	>	}
626	>	}
627	>
628	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
629	>	inversion = mol->nextInversion(inversionIter)) {
630	>
631	>	a = inversion->getAtomA()->getGlobalIndex();
632	>	b = inversion->getAtomB()->getGlobalIndex();
633	>	c = inversion->getAtomC()->getGlobalIndex();
634	>	d = inversion->getAtomD()->getGlobalIndex();
635	>
636	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
637	>	oneTwoInteractions_.removePair(a, b);
638	>	oneTwoInteractions_.removePair(a, c);
639	>	oneTwoInteractions_.removePair(a, d);
640	>	} else {
641	>	excludedInteractions_.removePair(a, b);
642	>	excludedInteractions_.removePair(a, c);
643	>	excludedInteractions_.removePair(a, d);
644	>	}
645	>
646	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
647	>	oneThreeInteractions_.removePair(b, c);
648	>	oneThreeInteractions_.removePair(b, d);
649	>	oneThreeInteractions_.removePair(c, d);
650	>	} else {
651	>	excludedInteractions_.removePair(b, c);
652	>	excludedInteractions_.removePair(b, d);
653	>	excludedInteractions_.removePair(c, d);
654	>	}
655	>	}
656	>
657	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
658	>	rb = mol->nextRigidBody(rbIter)) {
659	>	std::vector<Atom*> atoms = rb->getAtoms();
660	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
661	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
662	>	a = atoms[i]->getGlobalIndex();
663	>	b = atoms[j]->getGlobalIndex();
664	>	excludedInteractions_.removePair(a, b);
665	>	}
666	>	}
667	>	}
668	>
669	>	}
670
488	–	haveRcut = 1;
489	–	rCut = theRcut;
490	–	rList = rCut + 1.0;
671
672	<	notifyFortranCutOffs( &rCut, &rSw, &rList );
673	<	}
672	>	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
673	>	int curStampId;
674	>
675	>	//index from 0
676	>	curStampId = moleculeStamps_.size();
677
678	<	void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
678	>	moleculeStamps_.push_back(molStamp);
679	>	molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
680	>	}
681
682	<	rSw = theRsw;
683	<	setDefaultRcut( theRcut );
684	<	}
682	>	void SimInfo::update() {
683	>
684	>	setupSimType();
685	>
686	>	#ifdef IS_MPI
687	>	setupFortranParallel();
688	>	#endif
689	>
690	>	setupFortranSim();
691	>
692	>	//setup fortran force field
693	>	/** @deprecate */
694	>	int isError = 0;
695	>
696	>	setupCutoff();
697	>
698	>	setupElectrostaticSummationMethod( isError );
699	>	setupSwitchingFunction();
700	>	setupAccumulateBoxDipole();
701	>
702	>	if(isError){
703	>	sprintf( painCave.errMsg,
704	>	"ForceField error: There was an error initializing the forceField in fortran.\n" );
705	>	painCave.isFatal = 1;
706	>	simError();
707	>	}
708	>
709	>	calcNdf();
710	>	calcNdfRaw();
711	>	calcNdfTrans();
712	>
713	>	fortranInitialized_ = true;
714	>	}
715	>
716	>	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
717	>	SimInfo::MoleculeIterator mi;
718	>	Molecule* mol;
719	>	Molecule::AtomIterator ai;
720	>	Atom* atom;
721	>	std::set<AtomType*> atomTypes;
722	>
723	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
724	>
725	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
726	>	atomTypes.insert(atom->getAtomType());
727	>	}
728	>
729	>	}
730	>
731	>	return atomTypes;
732	>	}
733	>
734	>	void SimInfo::setupSimType() {
735	>	std::set<AtomType*>::iterator i;
736	>	std::set<AtomType*> atomTypes;
737	>	atomTypes = getUniqueAtomTypes();
738	>
739	>	int useLennardJones = 0;
740	>	int useElectrostatic = 0;
741	>	int useEAM = 0;
742	>	int useSC = 0;
743	>	int useCharge = 0;
744	>	int useDirectional = 0;
745	>	int useDipole = 0;
746	>	int useGayBerne = 0;
747	>	int useSticky = 0;
748	>	int useStickyPower = 0;
749	>	int useShape = 0;
750	>	int useFLARB = 0; //it is not in AtomType yet
751	>	int useDirectionalAtom = 0;
752	>	int useElectrostatics = 0;
753	>	//usePBC and useRF are from simParams
754	>	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
755	>	int useRF;
756	>	int useSF;
757	>	int useSP;
758	>	int useBoxDipole;
759
760	+	std::string myMethod;
761
762	<	void SimInfo::checkCutOffs( void ){
763	<
764	<	if( boxIsInit ){
762	>	// set the useRF logical
763	>	useRF = 0;
764	>	useSF = 0;
765	>	useSP = 0;
766	>	useBoxDipole = 0;
767	>
768	>
769	>	if (simParams_->haveElectrostaticSummationMethod()) {
770	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
771	>	toUpper(myMethod);
772	>	if (myMethod == "REACTION_FIELD"){
773	>	useRF = 1;
774	>	} else if (myMethod == "SHIFTED_FORCE"){
775	>	useSF = 1;
776	>	} else if (myMethod == "SHIFTED_POTENTIAL"){
777	>	useSP = 1;
778	>	}
779	>	}
780
781	<	//we need to check cutOffs against the box
782	<
783	<	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	<	}
781	>	if (simParams_->haveAccumulateBoxDipole())
782	>	if (simParams_->getAccumulateBoxDipole())
783	>	useBoxDipole = 1;
784
785	<	void SimInfo::addProperty(GenericData* prop){
785	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
786
787	<	map<string, GenericData*>::iterator result;
788	<	result = properties.find(prop->getID());
789	<
790	<	//we can't simply use  properties[prop->getID()] = prop,
791	<	//it will cause memory leak if we already contain a propery which has the same name of prop
792	<
793	<	if(result != properties.end()){
787	>	//loop over all of the atom types
788	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
789	>	useLennardJones |= (*i)->isLennardJones();
790	>	useElectrostatic |= (*i)->isElectrostatic();
791	>	useEAM |= (*i)->isEAM();
792	>	useSC |= (*i)->isSC();
793	>	useCharge |= (*i)->isCharge();
794	>	useDirectional |= (*i)->isDirectional();
795	>	useDipole |= (*i)->isDipole();
796	>	useGayBerne |= (*i)->isGayBerne();
797	>	useSticky |= (*i)->isSticky();
798	>	useStickyPower |= (*i)->isStickyPower();
799	>	useShape |= (*i)->isShape();
800	>	}
801	>
802	>	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
803	>	useDirectionalAtom = 1;
804	>	}
805	>
806	>	if (useCharge || useDipole) {
807	>	useElectrostatics = 1;
808	>	}
809	>
810	>	#ifdef IS_MPI
811	>	int temp;
812	>
813	>	temp = usePBC;
814	>	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
815	>
816	>	temp = useDirectionalAtom;
817	>	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
818	>
819	>	temp = useLennardJones;
820	>	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
821	>
822	>	temp = useElectrostatics;
823	>	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
824	>
825	>	temp = useCharge;
826	>	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
827	>
828	>	temp = useDipole;
829	>	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
830	>
831	>	temp = useSticky;
832	>	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
833	>
834	>	temp = useStickyPower;
835	>	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
836
837	<	delete (*result).second;
838	<	(*result).second = prop;
550	<
551	<	}
552	<	else{
837	>	temp = useGayBerne;
838	>	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
839
840	<	properties[prop->getID()] = prop;
840	>	temp = useEAM;
841	>	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
842
843	<	}
843	>	temp = useSC;
844	>	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
845
846	<	}
846	>	temp = useShape;
847	>	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
848
849	<	GenericData* SimInfo::getProperty(const string& propName){
850	<
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	<	}
849	>	temp = useFLARB;
850	>	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
851
852	+	temp = useRF;
853	+	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
854
855	<	void SimInfo::getFortranGroupArrays(SimInfo* info,
856	<	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	<
855	>	temp = useSF;
856	>	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
857
858	<	// Fix the silly fortran indexing problem
859	<	#ifdef IS_MPI
860	<	numAtom = mpiSim->getNAtomsGlobal();
861	<	#else
862	<	numAtom = n_atoms;
858	>	temp = useSP;
859	>	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
860	>
861	>	temp = useBoxDipole;
862	>	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
863	>
864	>	temp = useAtomicVirial_;
865	>	MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
866	>
867		#endif
602	–	for (int i = 0; i < numAtom; i++)
603	–	FglobalGroupMembership.push_back(globalGroupMembership[i] + 1);
604	–
868
869	<	myMols = info->molecules;
870	<	numMol = info->n_mol;
871	<	for(int i  = 0; i < numMol; i++){
872	<	numCutoffGroups = myMols[i].getNCutoffGroups();
873	<	for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff);
874	<	myCutoffGroup != NULL;
875	<	myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
869	>	fInfo_.SIM_uses_PBC = usePBC;
870	>	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
871	>	fInfo_.SIM_uses_LennardJones = useLennardJones;
872	>	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
873	>	fInfo_.SIM_uses_Charges = useCharge;
874	>	fInfo_.SIM_uses_Dipoles = useDipole;
875	>	fInfo_.SIM_uses_Sticky = useSticky;
876	>	fInfo_.SIM_uses_StickyPower = useStickyPower;
877	>	fInfo_.SIM_uses_GayBerne = useGayBerne;
878	>	fInfo_.SIM_uses_EAM = useEAM;
879	>	fInfo_.SIM_uses_SC = useSC;
880	>	fInfo_.SIM_uses_Shapes = useShape;
881	>	fInfo_.SIM_uses_FLARB = useFLARB;
882	>	fInfo_.SIM_uses_RF = useRF;
883	>	fInfo_.SIM_uses_SF = useSF;
884	>	fInfo_.SIM_uses_SP = useSP;
885	>	fInfo_.SIM_uses_BoxDipole = useBoxDipole;
886	>	fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
887	>	}
888
889	<	totalMass = myCutoffGroup->getMass();
889	>	void SimInfo::setupFortranSim() {
890	>	int isError;
891	>	int nExclude, nOneTwo, nOneThree, nOneFour;
892	>	std::vector<int> fortranGlobalGroupMembership;
893	>
894	>	isError = 0;
895	>
896	>	//globalGroupMembership_ is filled by SimCreator
897	>	for (int i = 0; i < nGlobalAtoms_; i++) {
898	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
899	>	}
900	>
901	>	//calculate mass ratio of cutoff group
902	>	std::vector<RealType> mfact;
903	>	SimInfo::MoleculeIterator mi;
904	>	Molecule* mol;
905	>	Molecule::CutoffGroupIterator ci;
906	>	CutoffGroup* cg;
907	>	Molecule::AtomIterator ai;
908	>	Atom* atom;
909	>	RealType totalMass;
910	>
911	>	//to avoid memory reallocation, reserve enough space for mfact
912	>	mfact.reserve(getNCutoffGroups());
913	>
914	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
915	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
916	>
917	>	totalMass = cg->getMass();
918	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
919	>	// Check for massless groups - set mfact to 1 if true
920	>	if (totalMass != 0)
921	>	mfact.push_back(atom->getMass()/totalMass);
922	>	else
923	>	mfact.push_back( 1.0 );
924	>	}
925	>	}
926	>	}
927	>
928	>	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
929	>	std::vector<int> identArray;
930	>
931	>	//to avoid memory reallocation, reserve enough space identArray
932	>	identArray.reserve(getNAtoms());
933	>
934	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
935	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
936	>	identArray.push_back(atom->getIdent());
937	>	}
938	>	}
939	>
940	>	//fill molMembershipArray
941	>	//molMembershipArray is filled by SimCreator
942	>	std::vector<int> molMembershipArray(nGlobalAtoms_);
943	>	for (int i = 0; i < nGlobalAtoms_; i++) {
944	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
945	>	}
946	>
947	>	//setup fortran simulation
948	>
949	>	nExclude = excludedInteractions_.getSize();
950	>	nOneTwo = oneTwoInteractions_.getSize();
951	>	nOneThree = oneThreeInteractions_.getSize();
952	>	nOneFour = oneFourInteractions_.getSize();
953	>
954	>	int* excludeList = excludedInteractions_.getPairList();
955	>	int* oneTwoList = oneTwoInteractions_.getPairList();
956	>	int* oneThreeList = oneThreeInteractions_.getPairList();
957	>	int* oneFourList = oneFourInteractions_.getPairList();
958	>
959	>	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
960	>	&nExclude, excludeList,
961	>	&nOneTwo, oneTwoList,
962	>	&nOneThree, oneThreeList,
963	>	&nOneFour, oneFourList,
964	>	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
965	>	&fortranGlobalGroupMembership[0], &isError);
966	>
967	>	if( isError ){
968
969	<	for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom);
970	<	cutoffAtom != NULL;
971	<	cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
972	<	mfact.push_back(cutoffAtom->getMass()/totalMass);
973	<	}
969	>	sprintf( painCave.errMsg,
970	>	"There was an error setting the simulation information in fortran.\n" );
971	>	painCave.isFatal = 1;
972	>	painCave.severity = OOPSE_ERROR;
973	>	simError();
974	>	}
975	>
976	>
977	>	sprintf( checkPointMsg,
978	>	"succesfully sent the simulation information to fortran.\n");
979	>
980	>	errorCheckPoint();
981	>
982	>	// Setup number of neighbors in neighbor list if present
983	>	if (simParams_->haveNeighborListNeighbors()) {
984	>	int nlistNeighbors = simParams_->getNeighborListNeighbors();
985	>	setNeighbors(&nlistNeighbors);
986	>	}
987	>
988	>
989	>	}
990	>
991	>
992	>	void SimInfo::setupFortranParallel() {
993	>	#ifdef IS_MPI
994	>	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
995	>	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
996	>	std::vector<int> localToGlobalCutoffGroupIndex;
997	>	SimInfo::MoleculeIterator mi;
998	>	Molecule::AtomIterator ai;
999	>	Molecule::CutoffGroupIterator ci;
1000	>	Molecule* mol;
1001	>	Atom* atom;
1002	>	CutoffGroup* cg;
1003	>	mpiSimData parallelData;
1004	>	int isError;
1005	>
1006	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
1007	>
1008	>	//local index(index in DataStorge) of atom is important
1009	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
1010	>	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
1011	>	}
1012	>
1013	>	//local index of cutoff group is trivial, it only depends on the order of travesing
1014	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
1015	>	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
1016	>	}
1017	>
1018	>	}
1019	>
1020	>	//fill up mpiSimData struct
1021	>	parallelData.nMolGlobal = getNGlobalMolecules();
1022	>	parallelData.nMolLocal = getNMolecules();
1023	>	parallelData.nAtomsGlobal = getNGlobalAtoms();
1024	>	parallelData.nAtomsLocal = getNAtoms();
1025	>	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
1026	>	parallelData.nGroupsLocal = getNCutoffGroups();
1027	>	parallelData.myNode = worldRank;
1028	>	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
1029	>
1030	>	//pass mpiSimData struct and index arrays to fortran
1031	>	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
1032	>	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
1033	>	&localToGlobalCutoffGroupIndex[0], &isError);
1034	>
1035	>	if (isError) {
1036	>	sprintf(painCave.errMsg,
1037	>	"mpiRefresh errror: fortran didn't like something we gave it.\n");
1038	>	painCave.isFatal = 1;
1039	>	simError();
1040	>	}
1041	>
1042	>	sprintf(checkPointMsg, " mpiRefresh successful.\n");
1043	>	errorCheckPoint();
1044	>
1045	>	#endif
1046	>	}
1047	>
1048	>	void SimInfo::setupCutoff() {
1049	>
1050	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
1051	>
1052	>	// Check the cutoff policy
1053	>	int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
1054	>
1055	>	// Set LJ shifting bools to false
1056	>	ljsp_ = false;
1057	>	ljsf_ = false;
1058	>
1059	>	std::string myPolicy;
1060	>	if (forceFieldOptions_.haveCutoffPolicy()){
1061	>	myPolicy = forceFieldOptions_.getCutoffPolicy();
1062	>	}else if (simParams_->haveCutoffPolicy()) {
1063	>	myPolicy = simParams_->getCutoffPolicy();
1064	>	}
1065	>
1066	>	if (!myPolicy.empty()){
1067	>	toUpper(myPolicy);
1068	>	if (myPolicy == "MIX") {
1069	>	cp = MIX_CUTOFF_POLICY;
1070	>	} else {
1071	>	if (myPolicy == "MAX") {
1072	>	cp = MAX_CUTOFF_POLICY;
1073	>	} else {
1074	>	if (myPolicy == "TRADITIONAL") {
1075	>	cp = TRADITIONAL_CUTOFF_POLICY;
1076	>	} else {
1077	>	// throw error
1078	>	sprintf( painCave.errMsg,
1079	>	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
1080	>	painCave.isFatal = 1;
1081	>	simError();
1082	>	}
1083	>	}
1084	>	}
1085	>	}
1086	>	notifyFortranCutoffPolicy(&cp);
1087	>
1088	>	// Check the Skin Thickness for neighborlists
1089	>	RealType skin;
1090	>	if (simParams_->haveSkinThickness()) {
1091	>	skin = simParams_->getSkinThickness();
1092	>	notifyFortranSkinThickness(&skin);
1093	>	}
1094	>
1095	>	// Check if the cutoff was set explicitly:
1096	>	if (simParams_->haveCutoffRadius()) {
1097	>	rcut_ = simParams_->getCutoffRadius();
1098	>	if (simParams_->haveSwitchingRadius()) {
1099	>	rsw_  = simParams_->getSwitchingRadius();
1100	>	} else {
1101	>	if (fInfo_.SIM_uses_Charges |
1102	>	fInfo_.SIM_uses_Dipoles |
1103	>	fInfo_.SIM_uses_RF) {
1104	>
1105	>	rsw_ = 0.85 * rcut_;
1106	>	sprintf(painCave.errMsg,
1107	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
1108	>	"\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
1109	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1110	>	painCave.isFatal = 0;
1111	>	simError();
1112	>	} else {
1113	>	rsw_ = rcut_;
1114	>	sprintf(painCave.errMsg,
1115	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
1116	>	"\tOOPSE will use the same value as the cutoffRadius.\n"
1117	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1118	>	painCave.isFatal = 0;
1119	>	simError();
1120	>	}
1121	>	}
1122	>
1123	>	if (simParams_->haveElectrostaticSummationMethod()) {
1124	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1125	>	toUpper(myMethod);
1126	>
1127	>	if (myMethod == "SHIFTED_POTENTIAL") {
1128	>	ljsp_ = true;
1129	>	} else if (myMethod == "SHIFTED_FORCE") {
1130	>	ljsf_ = true;
1131	>	}
1132	>	}
1133	>	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1134	>
1135	>	} else {
1136	>
1137	>	// For electrostatic atoms, we'll assume a large safe value:
1138	>	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1139	>	sprintf(painCave.errMsg,
1140	>	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1141	>	"\tOOPSE will use a default value of 15.0 angstroms"
1142	>	"\tfor the cutoffRadius.\n");
1143	>	painCave.isFatal = 0;
1144	>	simError();
1145	>	rcut_ = 15.0;
1146	>
1147	>	if (simParams_->haveElectrostaticSummationMethod()) {
1148	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1149	>	toUpper(myMethod);
1150	>
1151	>	// For the time being, we're tethering the LJ shifted behavior to the
1152	>	// electrostaticSummationMethod keyword options
1153	>	if (myMethod == "SHIFTED_POTENTIAL") {
1154	>	ljsp_ = true;
1155	>	} else if (myMethod == "SHIFTED_FORCE") {
1156	>	ljsf_ = true;
1157	>	}
1158	>	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1159	>	if (simParams_->haveSwitchingRadius()){
1160	>	sprintf(painCave.errMsg,
1161	>	"SimInfo Warning: A value was set for the switchingRadius\n"
1162	>	"\teven though the electrostaticSummationMethod was\n"
1163	>	"\tset to %s\n", myMethod.c_str());
1164	>	painCave.isFatal = 1;
1165	>	simError();
1166	>	}
1167	>	}
1168	>	}
1169	>
1170	>	if (simParams_->haveSwitchingRadius()){
1171	>	rsw_ = simParams_->getSwitchingRadius();
1172	>	} else {
1173	>	sprintf(painCave.errMsg,
1174	>	"SimCreator Warning: No value was set for switchingRadius.\n"
1175	>	"\tOOPSE will use a default value of\n"
1176	>	"\t0.85 * cutoffRadius for the switchingRadius\n");
1177	>	painCave.isFatal = 0;
1178	>	simError();
1179	>	rsw_ = 0.85 * rcut_;
1180	>	}
1181	>
1182	>	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1183	>
1184	>	} else {
1185	>	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1186	>	// We'll punt and let fortran figure out the cutoffs later.
1187	>
1188	>	notifyFortranYouAreOnYourOwn();
1189	>
1190	>	}
1191		}
1192		}
1193
1194	<	}
1194	>	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1195	>
1196	>	int errorOut;
1197	>	int esm =  NONE;
1198	>	int sm = UNDAMPED;
1199	>	RealType alphaVal;
1200	>	RealType dielectric;
1201	>
1202	>	errorOut = isError;
1203	>
1204	>	if (simParams_->haveElectrostaticSummationMethod()) {
1205	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1206	>	toUpper(myMethod);
1207	>	if (myMethod == "NONE") {
1208	>	esm = NONE;
1209	>	} else {
1210	>	if (myMethod == "SWITCHING_FUNCTION") {
1211	>	esm = SWITCHING_FUNCTION;
1212	>	} else {
1213	>	if (myMethod == "SHIFTED_POTENTIAL") {
1214	>	esm = SHIFTED_POTENTIAL;
1215	>	} else {
1216	>	if (myMethod == "SHIFTED_FORCE") {
1217	>	esm = SHIFTED_FORCE;
1218	>	} else {
1219	>	if (myMethod == "REACTION_FIELD") {
1220	>	esm = REACTION_FIELD;
1221	>	dielectric = simParams_->getDielectric();
1222	>	if (!simParams_->haveDielectric()) {
1223	>	// throw warning
1224	>	sprintf( painCave.errMsg,
1225	>	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1226	>	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1227	>	painCave.isFatal = 0;
1228	>	simError();
1229	>	}
1230	>	} else {
1231	>	// throw error
1232	>	sprintf( painCave.errMsg,
1233	>	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1234	>	"\t(Input file specified %s .)\n"
1235	>	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1236	>	"\t\"shifted_potential\", \"shifted_force\", or \n"
1237	>	"\t\"reaction_field\".\n", myMethod.c_str() );
1238	>	painCave.isFatal = 1;
1239	>	simError();
1240	>	}
1241	>	}
1242	>	}
1243	>	}
1244	>	}
1245	>	}
1246	>
1247	>	if (simParams_->haveElectrostaticScreeningMethod()) {
1248	>	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1249	>	toUpper(myScreen);
1250	>	if (myScreen == "UNDAMPED") {
1251	>	sm = UNDAMPED;
1252	>	} else {
1253	>	if (myScreen == "DAMPED") {
1254	>	sm = DAMPED;
1255	>	if (!simParams_->haveDampingAlpha()) {
1256	>	// first set a cutoff dependent alpha value
1257	>	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1258	>	alphaVal = 0.5125 - rcut_* 0.025;
1259	>	// for values rcut > 20.5, alpha is zero
1260	>	if (alphaVal < 0) alphaVal = 0;
1261	>
1262	>	// throw warning
1263	>	sprintf( painCave.errMsg,
1264	>	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1265	>	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1266	>	painCave.isFatal = 0;
1267	>	simError();
1268	>	} else {
1269	>	alphaVal = simParams_->getDampingAlpha();
1270	>	}
1271	>
1272	>	} else {
1273	>	// throw error
1274	>	sprintf( painCave.errMsg,
1275	>	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1276	>	"\t(Input file specified %s .)\n"
1277	>	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1278	>	"or \"damped\".\n", myScreen.c_str() );
1279	>	painCave.isFatal = 1;
1280	>	simError();
1281	>	}
1282	>	}
1283	>	}
1284	>
1285	>	// let's pass some summation method variables to fortran
1286	>	setElectrostaticSummationMethod( &esm );
1287	>	setFortranElectrostaticMethod( &esm );
1288	>	setScreeningMethod( &sm );
1289	>	setDampingAlpha( &alphaVal );
1290	>	setReactionFieldDielectric( &dielectric );
1291	>	initFortranFF( &errorOut );
1292	>	}
1293	>
1294	>	void SimInfo::setupSwitchingFunction() {
1295	>	int ft = CUBIC;
1296	>
1297	>	if (simParams_->haveSwitchingFunctionType()) {
1298	>	std::string funcType = simParams_->getSwitchingFunctionType();
1299	>	toUpper(funcType);
1300	>	if (funcType == "CUBIC") {
1301	>	ft = CUBIC;
1302	>	} else {
1303	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1304	>	ft = FIFTH_ORDER_POLY;
1305	>	} else {
1306	>	// throw error
1307	>	sprintf( painCave.errMsg,
1308	>	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1309	>	painCave.isFatal = 1;
1310	>	simError();
1311	>	}
1312	>	}
1313	>	}
1314	>
1315	>	// send switching function notification to switcheroo
1316	>	setFunctionType(&ft);
1317	>
1318	>	}
1319	>
1320	>	void SimInfo::setupAccumulateBoxDipole() {
1321	>
1322	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1323	>	if ( simParams_->haveAccumulateBoxDipole() )
1324	>	if ( simParams_->getAccumulateBoxDipole() ) {
1325	>	setAccumulateBoxDipole();
1326	>	calcBoxDipole_ = true;
1327	>	}
1328	>
1329	>	}
1330	>
1331	>	void SimInfo::addProperty(GenericData* genData) {
1332	>	properties_.addProperty(genData);
1333	>	}
1334	>
1335	>	void SimInfo::removeProperty(const std::string& propName) {
1336	>	properties_.removeProperty(propName);
1337	>	}
1338	>
1339	>	void SimInfo::clearProperties() {
1340	>	properties_.clearProperties();
1341	>	}
1342	>
1343	>	std::vector<std::string> SimInfo::getPropertyNames() {
1344	>	return properties_.getPropertyNames();
1345	>	}
1346	>
1347	>	std::vector<GenericData*> SimInfo::getProperties() {
1348	>	return properties_.getProperties();
1349	>	}
1350	>
1351	>	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1352	>	return properties_.getPropertyByName(propName);
1353	>	}
1354	>
1355	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1356	>	if (sman_ == sman) {
1357	>	return;
1358	>	}
1359	>	delete sman_;
1360	>	sman_ = sman;
1361	>
1362	>	Molecule* mol;
1363	>	RigidBody* rb;
1364	>	Atom* atom;
1365	>	SimInfo::MoleculeIterator mi;
1366	>	Molecule::RigidBodyIterator rbIter;
1367	>	Molecule::AtomIterator atomIter;;
1368	>
1369	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1370	>
1371	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1372	>	atom->setSnapshotManager(sman_);
1373	>	}
1374	>
1375	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1376	>	rb->setSnapshotManager(sman_);
1377	>	}
1378	>	}
1379	>
1380	>	}
1381	>
1382	>	Vector3d SimInfo::getComVel(){
1383	>	SimInfo::MoleculeIterator i;
1384	>	Molecule* mol;
1385	>
1386	>	Vector3d comVel(0.0);
1387	>	RealType totalMass = 0.0;
1388	>
1389	>
1390	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1391	>	RealType mass = mol->getMass();
1392	>	totalMass += mass;
1393	>	comVel += mass * mol->getComVel();
1394	>	}
1395	>
1396	>	#ifdef IS_MPI
1397	>	RealType tmpMass = totalMass;
1398	>	Vector3d tmpComVel(comVel);
1399	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1400	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1401	>	#endif
1402	>
1403	>	comVel /= totalMass;
1404	>
1405	>	return comVel;
1406	>	}
1407	>
1408	>	Vector3d SimInfo::getCom(){
1409	>	SimInfo::MoleculeIterator i;
1410	>	Molecule* mol;
1411	>
1412	>	Vector3d com(0.0);
1413	>	RealType totalMass = 0.0;
1414	>
1415	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1416	>	RealType mass = mol->getMass();
1417	>	totalMass += mass;
1418	>	com += mass * mol->getCom();
1419	>	}
1420	>
1421	>	#ifdef IS_MPI
1422	>	RealType tmpMass = totalMass;
1423	>	Vector3d tmpCom(com);
1424	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1425	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1426	>	#endif
1427	>
1428	>	com /= totalMass;
1429	>
1430	>	return com;
1431	>
1432	>	}
1433	>
1434	>	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1435	>
1436	>	return o;
1437	>	}
1438	>
1439	>
1440	>	/*
1441	>	Returns center of mass and center of mass velocity in one function call.
1442	>	*/
1443	>
1444	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1445	>	SimInfo::MoleculeIterator i;
1446	>	Molecule* mol;
1447	>
1448	>
1449	>	RealType totalMass = 0.0;
1450	>
1451	>
1452	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1453	>	RealType mass = mol->getMass();
1454	>	totalMass += mass;
1455	>	com += mass * mol->getCom();
1456	>	comVel += mass * mol->getComVel();
1457	>	}
1458	>
1459	>	#ifdef IS_MPI
1460	>	RealType tmpMass = totalMass;
1461	>	Vector3d tmpCom(com);
1462	>	Vector3d tmpComVel(comVel);
1463	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1464	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1465	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1466	>	#endif
1467	>
1468	>	com /= totalMass;
1469	>	comVel /= totalMass;
1470	>	}
1471	>
1472	>	/*
1473	>	Return intertia tensor for entire system and angular momentum Vector.
1474	>
1475	>
1476	>	[  Ixx -Ixy  -Ixz ]
1477	>	J =| -Iyx  Iyy  -Iyz |
1478	>	[ -Izx -Iyz   Izz ]
1479	>	*/
1480	>
1481	>	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1482	>
1483	>
1484	>	RealType xx = 0.0;
1485	>	RealType yy = 0.0;
1486	>	RealType zz = 0.0;
1487	>	RealType xy = 0.0;
1488	>	RealType xz = 0.0;
1489	>	RealType yz = 0.0;
1490	>	Vector3d com(0.0);
1491	>	Vector3d comVel(0.0);
1492	>
1493	>	getComAll(com, comVel);
1494	>
1495	>	SimInfo::MoleculeIterator i;
1496	>	Molecule* mol;
1497	>
1498	>	Vector3d thisq(0.0);
1499	>	Vector3d thisv(0.0);
1500	>
1501	>	RealType thisMass = 0.0;
1502	>
1503	>
1504	>
1505	>
1506	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1507	>
1508	>	thisq = mol->getCom()-com;
1509	>	thisv = mol->getComVel()-comVel;
1510	>	thisMass = mol->getMass();
1511	>	// Compute moment of intertia coefficients.
1512	>	xx += thisq[0]*thisq[0]*thisMass;
1513	>	yy += thisq[1]*thisq[1]*thisMass;
1514	>	zz += thisq[2]*thisq[2]*thisMass;
1515	>
1516	>	// compute products of intertia
1517	>	xy += thisq[0]*thisq[1]*thisMass;
1518	>	xz += thisq[0]*thisq[2]*thisMass;
1519	>	yz += thisq[1]*thisq[2]*thisMass;
1520	>
1521	>	angularMomentum += cross( thisq, thisv ) * thisMass;
1522	>
1523	>	}
1524	>
1525	>
1526	>	inertiaTensor(0,0) = yy + zz;
1527	>	inertiaTensor(0,1) = -xy;
1528	>	inertiaTensor(0,2) = -xz;
1529	>	inertiaTensor(1,0) = -xy;
1530	>	inertiaTensor(1,1) = xx + zz;
1531	>	inertiaTensor(1,2) = -yz;
1532	>	inertiaTensor(2,0) = -xz;
1533	>	inertiaTensor(2,1) = -yz;
1534	>	inertiaTensor(2,2) = xx + yy;
1535	>
1536	>	#ifdef IS_MPI
1537	>	Mat3x3d tmpI(inertiaTensor);
1538	>	Vector3d tmpAngMom;
1539	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1540	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1541	>	#endif
1542	>
1543	>	return;
1544	>	}
1545	>
1546	>	//Returns the angular momentum of the system
1547	>	Vector3d SimInfo::getAngularMomentum(){
1548	>
1549	>	Vector3d com(0.0);
1550	>	Vector3d comVel(0.0);
1551	>	Vector3d angularMomentum(0.0);
1552	>
1553	>	getComAll(com,comVel);
1554	>
1555	>	SimInfo::MoleculeIterator i;
1556	>	Molecule* mol;
1557	>
1558	>	Vector3d thisr(0.0);
1559	>	Vector3d thisp(0.0);
1560	>
1561	>	RealType thisMass;
1562	>
1563	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1564	>	thisMass = mol->getMass();
1565	>	thisr = mol->getCom()-com;
1566	>	thisp = (mol->getComVel()-comVel)*thisMass;
1567	>
1568	>	angularMomentum += cross( thisr, thisp );
1569	>
1570	>	}
1571	>
1572	>	#ifdef IS_MPI
1573	>	Vector3d tmpAngMom;
1574	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1575	>	#endif
1576	>
1577	>	return angularMomentum;
1578	>	}
1579	>
1580	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1581	>	return IOIndexToIntegrableObject.at(index);
1582	>	}
1583	>
1584	>	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1585	>	IOIndexToIntegrableObject= v;
1586	>	}
1587	>
1588	>	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1589	>	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1590	>	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1591	>	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1592	>	*/
1593	>	void SimInfo::getGyrationalVolume(RealType &volume){
1594	>	Mat3x3d intTensor;
1595	>	RealType det;
1596	>	Vector3d dummyAngMom;
1597	>	RealType sysconstants;
1598	>	RealType geomCnst;
1599	>
1600	>	geomCnst = 3.0/2.0;
1601	>	/* Get the inertial tensor and angular momentum for free*/
1602	>	getInertiaTensor(intTensor,dummyAngMom);
1603	>
1604	>	det = intTensor.determinant();
1605	>	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1606	>	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1607	>	return;
1608	>	}
1609	>
1610	>	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1611	>	Mat3x3d intTensor;
1612	>	Vector3d dummyAngMom;
1613	>	RealType sysconstants;
1614	>	RealType geomCnst;
1615	>
1616	>	geomCnst = 3.0/2.0;
1617	>	/* Get the inertial tensor and angular momentum for free*/
1618	>	getInertiaTensor(intTensor,dummyAngMom);
1619	>
1620	>	detI = intTensor.determinant();
1621	>	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1622	>	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1623	>	return;
1624	>	}
1625	>	/*
1626	>	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1627	>	assert( v.size() == nAtoms_ + nRigidBodies_);
1628	>	sdByGlobalIndex_ = v;
1629	>	}
1630	>
1631	>	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1632	>	//assert(index < nAtoms_ + nRigidBodies_);
1633	>	return sdByGlobalIndex_.at(index);
1634	>	}
1635	>	*/
1636	>	}//end namespace oopse
1637	>

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