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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 124 by chuckv, Wed Oct 20 20:46:20 2004 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1503 by gezelter, Sat Oct 2 19:54:41 2010 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. Redistributions of source code must retain the above copyright
10	>	*    notice, this list of conditions and the following disclaimer.
11	>	*
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13	>	*    notice, this list of conditions and the following disclaimer in the
14	>	*    documentation and/or other materials provided with the
15	>	*    distribution.
16	>	*
17	>	* This software is provided "AS IS," without a warranty of any
18	>	* kind. All express or implied conditions, representations and
19	>	* warranties, including any implied warranty of merchantability,
20	>	* fitness for a particular purpose or non-infringement, are hereby
21	>	* excluded.  The University of Notre Dame and its licensors shall not
22	>	* be liable for any damages suffered by licensee as a result of
23	>	* using, modifying or distributing the software or its
24	>	* derivatives. In no event will the University of Notre Dame or its
25	>	* licensors be liable for any lost revenue, profit or data, or for
26	>	* direct, indirect, special, consequential, incidental or punitive
27	>	* damages, however caused and regardless of the theory of liability,
28	>	* arising out of the use of or inability to use software, even if the
29	>	* University of Notre Dame has been advised of the possibility of
30	>	* such damages.
31	>	*
32	>	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	>	* research, please cite the appropriate papers when you publish your
34	>	* work.  Good starting points are:
35	>	*
36	>	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	>	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	>	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	>	* [4]  Vardeman & Gezelter, in progress (2009).
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/fSwitchingFunctionType.h"
59	>	#include "UseTheForce/doForces_interface.h"
60	>	#include "UseTheForce/DarkSide/neighborLists_interface.h"
61	>	#include "UseTheForce/DarkSide/switcheroo_interface.h"
62	>	#include "utils/MemoryUtils.hpp"
63		#include "utils/simError.h"
64	<	#include "UseTheForce/DarkSide/simulation_interface.h"
65	<	#include "UseTheForce/notifyCutoffs_interface.h"
64	>	#include "selection/SelectionManager.hpp"
65	>	#include "io/ForceFieldOptions.hpp"
66	>	#include "UseTheForce/ForceField.hpp"
67
15	–	//#include "UseTheForce/fortranWrappers.hpp"
68
17	–	#include "math/MatVec3.h"
18	–
69		#ifdef IS_MPI
70	<	#include "brains/mpiSimulation.hpp"
71	<	#endif
70	>	#include "UseTheForce/mpiComponentPlan.h"
71	>	#include "UseTheForce/DarkSide/simParallel_interface.h"
72	>	#endif
73
74	<	inline double roundMe( double x ){
75	<	return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
76	<	}
77	<
78	<	inline double min( double a, double b ){
79	<	return (a < b ) ? a : b;
80	<	}
74	>	namespace OpenMD {
75	>	std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
76	>	std::map<int, std::set<int> >::iterator i = container.find(index);
77	>	std::set<int> result;
78	>	if (i != container.end()) {
79	>	result = i->second;
80	>	}
81
82	<	SimInfo* currentInfo;
83	<
33	<	SimInfo::SimInfo(){
34	<
35	<	n_constraints = 0;
36	<	nZconstraints = 0;
37	<	n_oriented = 0;
38	<	n_dipoles = 0;
39	<	ndf = 0;
40	<	ndfRaw = 0;
41	<	nZconstraints = 0;
42	<	the_integrator = NULL;
43	<	setTemp = 0;
44	<	thermalTime = 0.0;
45	<	currentTime = 0.0;
46	<	rCut = 0.0;
47	<	rSw = 0.0;
48	<
49	<	haveRcut = 0;
50	<	haveRsw = 0;
51	<	boxIsInit = 0;
82	>	return result;
83	>	}
84
85	<	resetTime = 1e99;
85	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
86	>	forceField_(ff), simParams_(simParams),
87	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
88	>	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
89	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
90	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
91	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
92	>	nConstraints_(0), sman_(NULL), fortranInitialized_(false),
93	>	calcBoxDipole_(false), useAtomicVirial_(true) {
94
55	–	orthoRhombic = 0;
56	–	orthoTolerance = 1E-6;
57	–	useInitXSstate = true;
95
96	<	usePBC = 0;
97	<	useLJ = 0;
98	<	useSticky = 0;
99	<	useCharges = 0;
100	<	useDipoles = 0;
101	<	useReactionField = 0;
102	<	useGB = 0;
66	<	useEAM = 0;
67	<	useSolidThermInt = 0;
68	<	useLiquidThermInt = 0;
96	>	MoleculeStamp* molStamp;
97	>	int nMolWithSameStamp;
98	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
99	>	int nGroups = 0;      //total cutoff groups defined in meta-data file
100	>	CutoffGroupStamp* cgStamp;
101	>	RigidBodyStamp* rbStamp;
102	>	int nRigidAtoms = 0;
103
104	<	haveCutoffGroups = false;
104	>	std::vector<Component*> components = simParams->getComponents();
105	>
106	>	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
107	>	molStamp = (*i)->getMoleculeStamp();
108	>	nMolWithSameStamp = (*i)->getNMol();
109	>
110	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
111
112	<	excludes = Exclude::Instance();
112	>	//calculate atoms in molecules
113	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
114
115	<	myConfiguration = new SimState();
115	>	//calculate atoms in cutoff groups
116	>	int nAtomsInGroups = 0;
117	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
118	>
119	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
120	>	cgStamp = molStamp->getCutoffGroupStamp(j);
121	>	nAtomsInGroups += cgStamp->getNMembers();
122	>	}
123
124	<	has_minimizer = false;
77	<	the_minimizer =NULL;
124	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
125
126	<	ngroup = 0;
126	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
127
128	<	}
128	>	//calculate atoms in rigid bodies
129	>	int nAtomsInRigidBodies = 0;
130	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
131	>
132	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
133	>	rbStamp = molStamp->getRigidBodyStamp(j);
134	>	nAtomsInRigidBodies += rbStamp->getNMembers();
135	>	}
136
137	+	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
138	+	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
139	+
140	+	}
141
142	<	SimInfo::~SimInfo(){
142	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
143	>	//group therefore the total number of cutoff groups in the system is
144	>	//equal to the total number of atoms minus number of atoms belong to
145	>	//cutoff group defined in meta-data file plus the number of cutoff
146	>	//groups defined in meta-data file
147	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
148
149	<	delete myConfiguration;
150	<
151	<	map<string, GenericData*>::iterator i;
149	>	//every free atom (atom does not belong to rigid bodies) is an
150	>	//integrable object therefore the total number of integrable objects
151	>	//in the system is equal to the total number of atoms minus number of
152	>	//atoms belong to rigid body defined in meta-data file plus the number
153	>	//of rigid bodies defined in meta-data file
154	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
155	>	+ nGlobalRigidBodies_;
156
157	<	for(i = properties.begin(); i != properties.end(); i++)
158	<	delete (*i).second;
157	>	nGlobalMols_ = molStampIds_.size();
158	>	molToProcMap_.resize(nGlobalMols_);
159	>	}
160
161	<	}
161	>	SimInfo::~SimInfo() {
162	>	std::map<int, Molecule*>::iterator i;
163	>	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
164	>	delete i->second;
165	>	}
166	>	molecules_.clear();
167	>
168	>	delete sman_;
169	>	delete simParams_;
170	>	delete forceField_;
171	>	}
172
173	<	void SimInfo::setBox(double newBox[3]) {
174	<
175	<	int i, j;
176	<	double tempMat[3][3];
173	>	int SimInfo::getNGlobalConstraints() {
174	>	int nGlobalConstraints;
175	>	#ifdef IS_MPI
176	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
177	>	MPI_COMM_WORLD);
178	>	#else
179	>	nGlobalConstraints =  nConstraints_;
180	>	#endif
181	>	return nGlobalConstraints;
182	>	}
183
184	<	for(i=0; i<3; i++)
185	<	for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
184	>	bool SimInfo::addMolecule(Molecule* mol) {
185	>	MoleculeIterator i;
186
187	<	tempMat[0][0] = newBox[0];
188	<	tempMat[1][1] = newBox[1];
105	<	tempMat[2][2] = newBox[2];
187	>	i = molecules_.find(mol->getGlobalIndex());
188	>	if (i == molecules_.end() ) {
189
190	<	setBoxM( tempMat );
190	>	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
191	>
192	>	nAtoms_ += mol->getNAtoms();
193	>	nBonds_ += mol->getNBonds();
194	>	nBends_ += mol->getNBends();
195	>	nTorsions_ += mol->getNTorsions();
196	>	nInversions_ += mol->getNInversions();
197	>	nRigidBodies_ += mol->getNRigidBodies();
198	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
199	>	nCutoffGroups_ += mol->getNCutoffGroups();
200	>	nConstraints_ += mol->getNConstraintPairs();
201
202	<	}
110	<
111	<	void SimInfo::setBoxM( double theBox[3][3] ){
202	>	addInteractionPairs(mol);
203
204	<	int i, j;
205	<	double FortranHmat[9]; // to preserve compatibility with Fortran the
206	<	// ordering in the array is as follows:
207	<	// [ 0 3 6 ]
208	<	// [ 1 4 7 ]
118	<	// [ 2 5 8 ]
119	<	double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
204	>	return true;
205	>	} else {
206	>	return false;
207	>	}
208	>	}
209
210	<	if( !boxIsInit ) boxIsInit = 1;
210	>	bool SimInfo::removeMolecule(Molecule* mol) {
211	>	MoleculeIterator i;
212	>	i = molecules_.find(mol->getGlobalIndex());
213
214	<	for(i=0; i < 3; i++)
124	<	for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
125	<
126	<	calcBoxL();
127	<	calcHmatInv();
214	>	if (i != molecules_.end() ) {
215
216	<	for(i=0; i < 3; i++) {
217	<	for (j=0; j < 3; j++) {
218	<	FortranHmat[3*j + i] = Hmat[i][j];
219	<	FortranHmatInv[3*j + i] = HmatInv[i][j];
220	<	}
221	<	}
216	>	assert(mol == i->second);
217	>
218	>	nAtoms_ -= mol->getNAtoms();
219	>	nBonds_ -= mol->getNBonds();
220	>	nBends_ -= mol->getNBends();
221	>	nTorsions_ -= mol->getNTorsions();
222	>	nInversions_ -= mol->getNInversions();
223	>	nRigidBodies_ -= mol->getNRigidBodies();
224	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
225	>	nCutoffGroups_ -= mol->getNCutoffGroups();
226	>	nConstraints_ -= mol->getNConstraintPairs();
227
228	<	setFortranBox(FortranHmat, FortranHmatInv, &orthoRhombic);
229	<
138	<	}
139	<
228	>	removeInteractionPairs(mol);
229	>	molecules_.erase(mol->getGlobalIndex());
230
231	<	void SimInfo::getBoxM (double theBox[3][3]) {
231	>	delete mol;
232	>
233	>	return true;
234	>	} else {
235	>	return false;
236	>	}
237
143	–	int i, j;
144	–	for(i=0; i<3; i++)
145	–	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
146	–	}
238
239	+	}
240
241	<	void SimInfo::scaleBox(double scale) {
242	<	double theBox[3][3];
243	<	int i, j;
241	>
242	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
243	>	i = molecules_.begin();
244	>	return i == molecules_.end() ? NULL : i->second;
245	>	}
246
247	<	// cerr << "Scaling box by " << scale << "\n";
247	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
248	>	++i;
249	>	return i == molecules_.end() ? NULL : i->second;
250	>	}
251
155	–	for(i=0; i<3; i++)
156	–	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
252
253	<	setBoxM(theBox);
253	>	void SimInfo::calcNdf() {
254	>	int ndf_local;
255	>	MoleculeIterator i;
256	>	std::vector<StuntDouble*>::iterator j;
257	>	Molecule* mol;
258	>	StuntDouble* integrableObject;
259
260	<	}
260	>	ndf_local = 0;
261	>
262	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
263	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
264	>	integrableObject = mol->nextIntegrableObject(j)) {
265
266	<	void SimInfo::calcHmatInv( void ) {
163	<
164	<	int oldOrtho;
165	<	int i,j;
166	<	double smallDiag;
167	<	double tol;
168	<	double sanity[3][3];
266	>	ndf_local += 3;
267
268	<	invertMat3( Hmat, HmatInv );
269	<
270	<	// check to see if Hmat is orthorhombic
271	<
272	<	oldOrtho = orthoRhombic;
273	<
274	<	smallDiag = fabs(Hmat[0][0]);
275	<	if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
178	<	if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
179	<	tol = smallDiag * orthoTolerance;
180	<
181	<	orthoRhombic = 1;
182	<
183	<	for (i = 0; i < 3; i++ ) {
184	<	for (j = 0 ; j < 3; j++) {
185	<	if (i != j) {
186	<	if (orthoRhombic) {
187	<	if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
188	<	}
268	>	if (integrableObject->isDirectional()) {
269	>	if (integrableObject->isLinear()) {
270	>	ndf_local += 2;
271	>	} else {
272	>	ndf_local += 3;
273	>	}
274	>	}
275	>
276		}
277		}
191	–	}
192	–
193	–	if( oldOrtho != orthoRhombic ){
278
279	<	if( orthoRhombic ) {
280	<	sprintf( painCave.errMsg,
197	<	"OOPSE is switching from the default Non-Orthorhombic\n"
198	<	"\tto the faster Orthorhombic periodic boundary computations.\n"
199	<	"\tThis is usually a good thing, but if you wan't the\n"
200	<	"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
201	<	"\tvariable ( currently set to %G ) smaller.\n",
202	<	orthoTolerance);
203	<	painCave.severity = OOPSE_INFO;
204	<	simError();
205	<	}
206	<	else {
207	<	sprintf( painCave.errMsg,
208	<	"OOPSE is switching from the faster Orthorhombic to the more\n"
209	<	"\tflexible Non-Orthorhombic periodic boundary computations.\n"
210	<	"\tThis is usually because the box has deformed under\n"
211	<	"\tNPTf integration. If you wan't to live on the edge with\n"
212	<	"\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
213	<	"\tvariable ( currently set to %G ) larger.\n",
214	<	orthoTolerance);
215	<	painCave.severity = OOPSE_WARNING;
216	<	simError();
217	<	}
218	<	}
219	<	}
279	>	// n_constraints is local, so subtract them on each processor
280	>	ndf_local -= nConstraints_;
281
282	<	void SimInfo::calcBoxL( void ){
282	>	#ifdef IS_MPI
283	>	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
284	>	#else
285	>	ndf_ = ndf_local;
286	>	#endif
287
288	<	double dx, dy, dz, dsq;
288	>	// nZconstraints_ is global, as are the 3 COM translations for the
289	>	// entire system:
290	>	ndf_ = ndf_ - 3 - nZconstraint_;
291
225	–	// boxVol = Determinant of Hmat
226	–
227	–	boxVol = matDet3( Hmat );
228	–
229	–	// boxLx
230	–
231	–	dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
232	–	dsq = dx*dx + dy*dy + dz*dz;
233	–	boxL[0] = sqrt( dsq );
234	–	//maxCutoff = 0.5 * boxL[0];
235	–
236	–	// boxLy
237	–
238	–	dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
239	–	dsq = dx*dx + dy*dy + dz*dz;
240	–	boxL[1] = sqrt( dsq );
241	–	//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
242	–
243	–
244	–	// boxLz
245	–
246	–	dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
247	–	dsq = dx*dx + dy*dy + dz*dz;
248	–	boxL[2] = sqrt( dsq );
249	–	//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
250	–
251	–	//calculate the max cutoff
252	–	maxCutoff =  calcMaxCutOff();
253	–
254	–	checkCutOffs();
255	–
256	–	}
257	–
258	–
259	–	double SimInfo::calcMaxCutOff(){
260	–
261	–	double ri[3], rj[3], rk[3];
262	–	double rij[3], rjk[3], rki[3];
263	–	double minDist;
264	–
265	–	ri[0] = Hmat[0][0];
266	–	ri[1] = Hmat[1][0];
267	–	ri[2] = Hmat[2][0];
268	–
269	–	rj[0] = Hmat[0][1];
270	–	rj[1] = Hmat[1][1];
271	–	rj[2] = Hmat[2][1];
272	–
273	–	rk[0] = Hmat[0][2];
274	–	rk[1] = Hmat[1][2];
275	–	rk[2] = Hmat[2][2];
276	–
277	–	crossProduct3(ri, rj, rij);
278	–	distXY = dotProduct3(rk,rij) / norm3(rij);
279	–
280	–	crossProduct3(rj,rk, rjk);
281	–	distYZ = dotProduct3(ri,rjk) / norm3(rjk);
282	–
283	–	crossProduct3(rk,ri, rki);
284	–	distZX = dotProduct3(rj,rki) / norm3(rki);
285	–
286	–	minDist = min(min(distXY, distYZ), distZX);
287	–	return minDist/2;
288	–
289	–	}
290	–
291	–	void SimInfo::wrapVector( double thePos[3] ){
292	–
293	–	int i;
294	–	double scaled[3];
295	–
296	–	if( !orthoRhombic ){
297	–	// calc the scaled coordinates.
298	–
299	–
300	–	matVecMul3(HmatInv, thePos, scaled);
301	–
302	–	for(i=0; i<3; i++)
303	–	scaled[i] -= roundMe(scaled[i]);
304	–
305	–	// calc the wrapped real coordinates from the wrapped scaled coordinates
306	–
307	–	matVecMul3(Hmat, scaled, thePos);
308	–
292		}
310	–	else{
311	–	// calc the scaled coordinates.
312	–
313	–	for(i=0; i<3; i++)
314	–	scaled[i] = thePos[i]*HmatInv[i][i];
315	–
316	–	// wrap the scaled coordinates
317	–
318	–	for(i=0; i<3; i++)
319	–	scaled[i] -= roundMe(scaled[i]);
320	–
321	–	// calc the wrapped real coordinates from the wrapped scaled coordinates
322	–
323	–	for(i=0; i<3; i++)
324	–	thePos[i] = scaled[i]*Hmat[i][i];
325	–	}
326	–
327	–	}
293
294	<
330	<	int SimInfo::getNDF(){
331	<	int ndf_local;
332	<
333	<	ndf_local = 0;
334	<
335	<	for(int i = 0; i < integrableObjects.size(); i++){
336	<	ndf_local += 3;
337	<	if (integrableObjects[i]->isDirectional()) {
338	<	if (integrableObjects[i]->isLinear())
339	<	ndf_local += 2;
340	<	else
341	<	ndf_local += 3;
342	<	}
343	<	}
344	<
345	<	// n_constraints is local, so subtract them on each processor:
346	<
347	<	ndf_local -= n_constraints;
348	<
294	>	int SimInfo::getFdf() {
295		#ifdef IS_MPI
296	<	MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
296	>	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
297		#else
298	<	ndf = ndf_local;
298	>	fdf_ = fdf_local;
299		#endif
300	<
301	<	// nZconstraints is global, as are the 3 COM translations for the
302	<	// entire system:
303	<
304	<	ndf = ndf - 3 - nZconstraints;
300	>	return fdf_;
301	>	}
302	>
303	>	void SimInfo::calcNdfRaw() {
304	>	int ndfRaw_local;
305
306	<	return ndf;
307	<	}
306	>	MoleculeIterator i;
307	>	std::vector<StuntDouble*>::iterator j;
308	>	Molecule* mol;
309	>	StuntDouble* integrableObject;
310
311	<	int SimInfo::getNDFraw() {
312	<	int ndfRaw_local;
311	>	// Raw degrees of freedom that we have to set
312	>	ndfRaw_local = 0;
313	>
314	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
315	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
316	>	integrableObject = mol->nextIntegrableObject(j)) {
317
318	<	// Raw degrees of freedom that we have to set
367	<	ndfRaw_local = 0;
318	>	ndfRaw_local += 3;
319
320	<	for(int i = 0; i < integrableObjects.size(); i++){
321	<	ndfRaw_local += 3;
322	<	if (integrableObjects[i]->isDirectional()) {
323	<	if (integrableObjects[i]->isLinear())
324	<	ndfRaw_local += 2;
325	<	else
326	<	ndfRaw_local += 3;
320	>	if (integrableObject->isDirectional()) {
321	>	if (integrableObject->isLinear()) {
322	>	ndfRaw_local += 2;
323	>	} else {
324	>	ndfRaw_local += 3;
325	>	}
326	>	}
327	>
328	>	}
329		}
377	–	}
330
331		#ifdef IS_MPI
332	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
332	>	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
333		#else
334	<	ndfRaw = ndfRaw_local;
334	>	ndfRaw_ = ndfRaw_local;
335		#endif
336	+	}
337
338	<	return ndfRaw;
339	<	}
338	>	void SimInfo::calcNdfTrans() {
339	>	int ndfTrans_local;
340
341	<	int SimInfo::getNDFtranslational() {
389	<	int ndfTrans_local;
341	>	ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
342
391	–	ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
343
393	–
344		#ifdef IS_MPI
345	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
345	>	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
346		#else
347	<	ndfTrans = ndfTrans_local;
347	>	ndfTrans_ = ndfTrans_local;
348		#endif
349
350	<	ndfTrans = ndfTrans - 3 - nZconstraints;
350	>	ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
351	>
352	>	}
353
354	<	return ndfTrans;
355	<	}
354	>	void SimInfo::addInteractionPairs(Molecule* mol) {
355	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
356	>	std::vector<Bond*>::iterator bondIter;
357	>	std::vector<Bend*>::iterator bendIter;
358	>	std::vector<Torsion*>::iterator torsionIter;
359	>	std::vector<Inversion*>::iterator inversionIter;
360	>	Bond* bond;
361	>	Bend* bend;
362	>	Torsion* torsion;
363	>	Inversion* inversion;
364	>	int a;
365	>	int b;
366	>	int c;
367	>	int d;
368
369	<	int SimInfo::getTotIntegrableObjects() {
370	<	int nObjs_local;
371	<	int nObjs;
369	>	// atomGroups can be used to add special interaction maps between
370	>	// groups of atoms that are in two separate rigid bodies.
371	>	// However, most site-site interactions between two rigid bodies
372	>	// are probably not special, just the ones between the physically
373	>	// bonded atoms.  Interactions *within* a single rigid body should
374	>	// always be excluded.  These are done at the bottom of this
375	>	// function.
376
377	<	nObjs_local =  integrableObjects.size();
377	>	std::map<int, std::set<int> > atomGroups;
378	>	Molecule::RigidBodyIterator rbIter;
379	>	RigidBody* rb;
380	>	Molecule::IntegrableObjectIterator ii;
381	>	StuntDouble* integrableObject;
382	>
383	>	for (integrableObject = mol->beginIntegrableObject(ii);
384	>	integrableObject != NULL;
385	>	integrableObject = mol->nextIntegrableObject(ii)) {
386	>
387	>	if (integrableObject->isRigidBody()) {
388	>	rb = static_cast<RigidBody*>(integrableObject);
389	>	std::vector<Atom*> atoms = rb->getAtoms();
390	>	std::set<int> rigidAtoms;
391	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
392	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
393	>	}
394	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
395	>	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
396	>	}
397	>	} else {
398	>	std::set<int> oneAtomSet;
399	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
400	>	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
401	>	}
402	>	}
403	>
404	>	for (bond= mol->beginBond(bondIter); bond != NULL;
405	>	bond = mol->nextBond(bondIter)) {
406
407	+	a = bond->getAtomA()->getGlobalIndex();
408	+	b = bond->getAtomB()->getGlobalIndex();
409	+
410	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
411	+	oneTwoInteractions_.addPair(a, b);
412	+	} else {
413	+	excludedInteractions_.addPair(a, b);
414	+	}
415	+	}
416
417	<	#ifdef IS_MPI
418	<	MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
414	<	#else
415	<	nObjs = nObjs_local;
416	<	#endif
417	>	for (bend= mol->beginBend(bendIter); bend != NULL;
418	>	bend = mol->nextBend(bendIter)) {
419
420	+	a = bend->getAtomA()->getGlobalIndex();
421	+	b = bend->getAtomB()->getGlobalIndex();
422	+	c = bend->getAtomC()->getGlobalIndex();
423	+
424	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
425	+	oneTwoInteractions_.addPair(a, b);
426	+	oneTwoInteractions_.addPair(b, c);
427	+	} else {
428	+	excludedInteractions_.addPair(a, b);
429	+	excludedInteractions_.addPair(b, c);
430	+	}
431
432	<	return nObjs;
433	<	}
432	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
433	>	oneThreeInteractions_.addPair(a, c);
434	>	} else {
435	>	excludedInteractions_.addPair(a, c);
436	>	}
437	>	}
438
439	<	void SimInfo::refreshSim(){
439	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
440	>	torsion = mol->nextTorsion(torsionIter)) {
441
442	<	simtype fInfo;
443	<	int isError;
444	<	int n_global;
445	<	int* excl;
442	>	a = torsion->getAtomA()->getGlobalIndex();
443	>	b = torsion->getAtomB()->getGlobalIndex();
444	>	c = torsion->getAtomC()->getGlobalIndex();
445	>	d = torsion->getAtomD()->getGlobalIndex();
446
447	<	fInfo.dielect = 0.0;
447	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
448	>	oneTwoInteractions_.addPair(a, b);
449	>	oneTwoInteractions_.addPair(b, c);
450	>	oneTwoInteractions_.addPair(c, d);
451	>	} else {
452	>	excludedInteractions_.addPair(a, b);
453	>	excludedInteractions_.addPair(b, c);
454	>	excludedInteractions_.addPair(c, d);
455	>	}
456
457	<	if( useDipoles ){
458	<	if( useReactionField )fInfo.dielect = dielectric;
459	<	}
457	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
458	>	oneThreeInteractions_.addPair(a, c);
459	>	oneThreeInteractions_.addPair(b, d);
460	>	} else {
461	>	excludedInteractions_.addPair(a, c);
462	>	excludedInteractions_.addPair(b, d);
463	>	}
464
465	<	fInfo.SIM_uses_PBC = usePBC;
466	<	//fInfo.SIM_uses_LJ = 0;
467	<	fInfo.SIM_uses_LJ = useLJ;
468	<	fInfo.SIM_uses_sticky = useSticky;
469	<	//fInfo.SIM_uses_sticky = 0;
470	<	fInfo.SIM_uses_charges = useCharges;
441	<	fInfo.SIM_uses_dipoles = useDipoles;
442	<	//fInfo.SIM_uses_dipoles = 0;
443	<	fInfo.SIM_uses_RF = useReactionField;
444	<	//fInfo.SIM_uses_RF = 0;
445	<	fInfo.SIM_uses_GB = useGB;
446	<	fInfo.SIM_uses_EAM = useEAM;
465	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
466	>	oneFourInteractions_.addPair(a, d);
467	>	} else {
468	>	excludedInteractions_.addPair(a, d);
469	>	}
470	>	}
471
472	<	n_exclude = excludes->getSize();
473	<	excl = excludes->getFortranArray();
450	<
451	<	#ifdef IS_MPI
452	<	n_global = mpiSim->getNAtomsGlobal();
453	<	#else
454	<	n_global = n_atoms;
455	<	#endif
456	<
457	<	isError = 0;
458	<
459	<	getFortranGroupArrays(this, FglobalGroupMembership, mfact);
460	<	//it may not be a good idea to pass the address of first element in vector
461	<	//since c++ standard does not require vector to be stored continuously in meomory
462	<	//Most of the compilers will organize the memory of vector continuously
463	<	setFortranSim( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
464	<	&nGlobalExcludes, globalExcludes, molMembershipArray,
465	<	&mfact[0], &ngroup, &FglobalGroupMembership[0], &isError);
472	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
473	>	inversion = mol->nextInversion(inversionIter)) {
474
475	<	if( isError ){
476	<
477	<	sprintf( painCave.errMsg,
478	<	"There was an error setting the simulation information in fortran.\n" );
479	<	painCave.isFatal = 1;
480	<	painCave.severity = OOPSE_ERROR;
481	<	simError();
475	>	a = inversion->getAtomA()->getGlobalIndex();
476	>	b = inversion->getAtomB()->getGlobalIndex();
477	>	c = inversion->getAtomC()->getGlobalIndex();
478	>	d = inversion->getAtomD()->getGlobalIndex();
479	>
480	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
481	>	oneTwoInteractions_.addPair(a, b);
482	>	oneTwoInteractions_.addPair(a, c);
483	>	oneTwoInteractions_.addPair(a, d);
484	>	} else {
485	>	excludedInteractions_.addPair(a, b);
486	>	excludedInteractions_.addPair(a, c);
487	>	excludedInteractions_.addPair(a, d);
488	>	}
489	>
490	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
491	>	oneThreeInteractions_.addPair(b, c);
492	>	oneThreeInteractions_.addPair(b, d);
493	>	oneThreeInteractions_.addPair(c, d);
494	>	} else {
495	>	excludedInteractions_.addPair(b, c);
496	>	excludedInteractions_.addPair(b, d);
497	>	excludedInteractions_.addPair(c, d);
498	>	}
499	>	}
500	>
501	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
502	>	rb = mol->nextRigidBody(rbIter)) {
503	>	std::vector<Atom*> atoms = rb->getAtoms();
504	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
505	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
506	>	a = atoms[i]->getGlobalIndex();
507	>	b = atoms[j]->getGlobalIndex();
508	>	excludedInteractions_.addPair(a, b);
509	>	}
510	>	}
511	>	}
512	>
513		}
514	+
515	+	void SimInfo::removeInteractionPairs(Molecule* mol) {
516	+	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
517	+	std::vector<Bond*>::iterator bondIter;
518	+	std::vector<Bend*>::iterator bendIter;
519	+	std::vector<Torsion*>::iterator torsionIter;
520	+	std::vector<Inversion*>::iterator inversionIter;
521	+	Bond* bond;
522	+	Bend* bend;
523	+	Torsion* torsion;
524	+	Inversion* inversion;
525	+	int a;
526	+	int b;
527	+	int c;
528	+	int d;
529	+
530	+	std::map<int, std::set<int> > atomGroups;
531	+	Molecule::RigidBodyIterator rbIter;
532	+	RigidBody* rb;
533	+	Molecule::IntegrableObjectIterator ii;
534	+	StuntDouble* integrableObject;
535	+
536	+	for (integrableObject = mol->beginIntegrableObject(ii);
537	+	integrableObject != NULL;
538	+	integrableObject = mol->nextIntegrableObject(ii)) {
539	+
540	+	if (integrableObject->isRigidBody()) {
541	+	rb = static_cast<RigidBody*>(integrableObject);
542	+	std::vector<Atom*> atoms = rb->getAtoms();
543	+	std::set<int> rigidAtoms;
544	+	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
545	+	rigidAtoms.insert(atoms[i]->getGlobalIndex());
546	+	}
547	+	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
548	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
549	+	}
550	+	} else {
551	+	std::set<int> oneAtomSet;
552	+	oneAtomSet.insert(integrableObject->getGlobalIndex());
553	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
554	+	}
555	+	}
556	+
557	+	for (bond= mol->beginBond(bondIter); bond != NULL;
558	+	bond = mol->nextBond(bondIter)) {
559	+
560	+	a = bond->getAtomA()->getGlobalIndex();
561	+	b = bond->getAtomB()->getGlobalIndex();
562	+
563	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
564	+	oneTwoInteractions_.removePair(a, b);
565	+	} else {
566	+	excludedInteractions_.removePair(a, b);
567	+	}
568	+	}
569	+
570	+	for (bend= mol->beginBend(bendIter); bend != NULL;
571	+	bend = mol->nextBend(bendIter)) {
572	+
573	+	a = bend->getAtomA()->getGlobalIndex();
574	+	b = bend->getAtomB()->getGlobalIndex();
575	+	c = bend->getAtomC()->getGlobalIndex();
576	+
577	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
578	+	oneTwoInteractions_.removePair(a, b);
579	+	oneTwoInteractions_.removePair(b, c);
580	+	} else {
581	+	excludedInteractions_.removePair(a, b);
582	+	excludedInteractions_.removePair(b, c);
583	+	}
584	+
585	+	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
586	+	oneThreeInteractions_.removePair(a, c);
587	+	} else {
588	+	excludedInteractions_.removePair(a, c);
589	+	}
590	+	}
591	+
592	+	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
593	+	torsion = mol->nextTorsion(torsionIter)) {
594	+
595	+	a = torsion->getAtomA()->getGlobalIndex();
596	+	b = torsion->getAtomB()->getGlobalIndex();
597	+	c = torsion->getAtomC()->getGlobalIndex();
598	+	d = torsion->getAtomD()->getGlobalIndex();
599
600	<	#ifdef IS_MPI
601	<	sprintf( checkPointMsg,
602	<	"succesfully sent the simulation information to fortran.\n");
603	<	MPIcheckPoint();
604	<	#endif // is_mpi
605	<
606	<	this->ndf = this->getNDF();
607	<	this->ndfRaw = this->getNDFraw();
608	<	this->ndfTrans = this->getNDFtranslational();
485	<	}
600	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
601	>	oneTwoInteractions_.removePair(a, b);
602	>	oneTwoInteractions_.removePair(b, c);
603	>	oneTwoInteractions_.removePair(c, d);
604	>	} else {
605	>	excludedInteractions_.removePair(a, b);
606	>	excludedInteractions_.removePair(b, c);
607	>	excludedInteractions_.removePair(c, d);
608	>	}
609
610	<	void SimInfo::setDefaultRcut( double theRcut ){
610	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
611	>	oneThreeInteractions_.removePair(a, c);
612	>	oneThreeInteractions_.removePair(b, d);
613	>	} else {
614	>	excludedInteractions_.removePair(a, c);
615	>	excludedInteractions_.removePair(b, d);
616	>	}
617	>
618	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
619	>	oneFourInteractions_.removePair(a, d);
620	>	} else {
621	>	excludedInteractions_.removePair(a, d);
622	>	}
623	>	}
624	>
625	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
626	>	inversion = mol->nextInversion(inversionIter)) {
627	>
628	>	a = inversion->getAtomA()->getGlobalIndex();
629	>	b = inversion->getAtomB()->getGlobalIndex();
630	>	c = inversion->getAtomC()->getGlobalIndex();
631	>	d = inversion->getAtomD()->getGlobalIndex();
632	>
633	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
634	>	oneTwoInteractions_.removePair(a, b);
635	>	oneTwoInteractions_.removePair(a, c);
636	>	oneTwoInteractions_.removePair(a, d);
637	>	} else {
638	>	excludedInteractions_.removePair(a, b);
639	>	excludedInteractions_.removePair(a, c);
640	>	excludedInteractions_.removePair(a, d);
641	>	}
642	>
643	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
644	>	oneThreeInteractions_.removePair(b, c);
645	>	oneThreeInteractions_.removePair(b, d);
646	>	oneThreeInteractions_.removePair(c, d);
647	>	} else {
648	>	excludedInteractions_.removePair(b, c);
649	>	excludedInteractions_.removePair(b, d);
650	>	excludedInteractions_.removePair(c, d);
651	>	}
652	>	}
653	>
654	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
655	>	rb = mol->nextRigidBody(rbIter)) {
656	>	std::vector<Atom*> atoms = rb->getAtoms();
657	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
658	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
659	>	a = atoms[i]->getGlobalIndex();
660	>	b = atoms[j]->getGlobalIndex();
661	>	excludedInteractions_.removePair(a, b);
662	>	}
663	>	}
664	>	}
665	>
666	>	}
667
489	–	haveRcut = 1;
490	–	rCut = theRcut;
491	–	rList = rCut + 1.0;
668
669	<	notifyFortranCutoffs( &rCut, &rSw, &rList );
670	<	}
669	>	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
670	>	int curStampId;
671	>
672	>	//index from 0
673	>	curStampId = moleculeStamps_.size();
674
675	<	void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
675	>	moleculeStamps_.push_back(molStamp);
676	>	molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
677	>	}
678
679	<	rSw = theRsw;
680	<	setDefaultRcut( theRcut );
681	<	}
679	>	void SimInfo::update() {
680	>
681	>	setupSimType();
682	>
683	>	#ifdef IS_MPI
684	>	setupFortranParallel();
685	>	#endif
686	>
687	>	setupFortranSim();
688	>
689	>	//setup fortran force field
690	>	/** @deprecate */
691	>	int isError = 0;
692	>
693	>	setupCutoff();
694	>
695	>	setupElectrostaticSummationMethod( isError );
696	>	setupSwitchingFunction();
697	>	setupAccumulateBoxDipole();
698	>
699	>	if(isError){
700	>	sprintf( painCave.errMsg,
701	>	"ForceField error: There was an error initializing the forceField in fortran.\n" );
702	>	painCave.isFatal = 1;
703	>	simError();
704	>	}
705	>
706	>	calcNdf();
707	>	calcNdfRaw();
708	>	calcNdfTrans();
709	>
710	>	fortranInitialized_ = true;
711	>	}
712	>
713	>	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
714	>	SimInfo::MoleculeIterator mi;
715	>	Molecule* mol;
716	>	Molecule::AtomIterator ai;
717	>	Atom* atom;
718	>	std::set<AtomType*> atomTypes;
719	>
720	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
721	>
722	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
723	>	atomTypes.insert(atom->getAtomType());
724	>	}
725	>
726	>	}
727	>
728	>	return atomTypes;
729	>	}
730	>
731	>	void SimInfo::setupSimType() {
732	>	std::set<AtomType*>::iterator i;
733	>	std::set<AtomType*> atomTypes;
734	>	atomTypes = getUniqueAtomTypes();
735	>
736	>	int useLennardJones = 0;
737	>	int useElectrostatic = 0;
738	>	int useEAM = 0;
739	>	int useSC = 0;
740	>	int useCharge = 0;
741	>	int useDirectional = 0;
742	>	int useDipole = 0;
743	>	int useGayBerne = 0;
744	>	int useSticky = 0;
745	>	int useStickyPower = 0;
746	>	int useShape = 0;
747	>	int useFLARB = 0; //it is not in AtomType yet
748	>	int useDirectionalAtom = 0;
749	>	int useElectrostatics = 0;
750	>	//usePBC and useRF are from simParams
751	>	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
752	>	int useRF;
753	>	int useSF;
754	>	int useSP;
755	>	int useBoxDipole;
756
757	+	std::string myMethod;
758
759	<	void SimInfo::checkCutOffs( void ){
760	<
761	<	if( boxIsInit ){
759	>	// set the useRF logical
760	>	useRF = 0;
761	>	useSF = 0;
762	>	useSP = 0;
763	>	useBoxDipole = 0;
764	>
765	>
766	>	if (simParams_->haveElectrostaticSummationMethod()) {
767	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
768	>	toUpper(myMethod);
769	>	if (myMethod == "REACTION_FIELD"){
770	>	useRF = 1;
771	>	} else if (myMethod == "SHIFTED_FORCE"){
772	>	useSF = 1;
773	>	} else if (myMethod == "SHIFTED_POTENTIAL"){
774	>	useSP = 1;
775	>	}
776	>	}
777
778	<	//we need to check cutOffs against the box
779	<
780	<	if( rCut > maxCutoff ){
510	<	sprintf( painCave.errMsg,
511	<	"cutoffRadius is too large for the current periodic box.\n"
512	<	"\tCurrent Value of cutoffRadius = %G at time %G\n "
513	<	"\tThis is larger than half of at least one of the\n"
514	<	"\tperiodic box vectors.  Right now, the Box matrix is:\n"
515	<	"\n"
516	<	"\t[ %G %G %G ]\n"
517	<	"\t[ %G %G %G ]\n"
518	<	"\t[ %G %G %G ]\n",
519	<	rCut, currentTime,
520	<	Hmat[0][0], Hmat[0][1], Hmat[0][2],
521	<	Hmat[1][0], Hmat[1][1], Hmat[1][2],
522	<	Hmat[2][0], Hmat[2][1], Hmat[2][2]);
523	<	painCave.severity = OOPSE_ERROR;
524	<	painCave.isFatal = 1;
525	<	simError();
526	<	}
527	<	} else {
528	<	// initialize this stuff before using it, OK?
529	<	sprintf( painCave.errMsg,
530	<	"Trying to check cutoffs without a box.\n"
531	<	"\tOOPSE should have better programmers than that.\n" );
532	<	painCave.severity = OOPSE_ERROR;
533	<	painCave.isFatal = 1;
534	<	simError();
535	<	}
536	<
537	<	}
778	>	if (simParams_->haveAccumulateBoxDipole())
779	>	if (simParams_->getAccumulateBoxDipole())
780	>	useBoxDipole = 1;
781
782	<	void SimInfo::addProperty(GenericData* prop){
782	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
783
784	<	map<string, GenericData*>::iterator result;
785	<	result = properties.find(prop->getID());
786	<
787	<	//we can't simply use  properties[prop->getID()] = prop,
788	<	//it will cause memory leak if we already contain a propery which has the same name of prop
789	<
790	<	if(result != properties.end()){
784	>	//loop over all of the atom types
785	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
786	>	useLennardJones |= (*i)->isLennardJones();
787	>	useElectrostatic |= (*i)->isElectrostatic();
788	>	useEAM |= (*i)->isEAM();
789	>	useSC |= (*i)->isSC();
790	>	useCharge |= (*i)->isCharge();
791	>	useDirectional |= (*i)->isDirectional();
792	>	useDipole |= (*i)->isDipole();
793	>	useGayBerne |= (*i)->isGayBerne();
794	>	useSticky |= (*i)->isSticky();
795	>	useStickyPower |= (*i)->isStickyPower();
796	>	useShape |= (*i)->isShape();
797	>	}
798	>
799	>	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
800	>	useDirectionalAtom = 1;
801	>	}
802	>
803	>	if (useCharge || useDipole) {
804	>	useElectrostatics = 1;
805	>	}
806	>
807	>	#ifdef IS_MPI
808	>	int temp;
809	>
810	>	temp = usePBC;
811	>	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
812	>
813	>	temp = useDirectionalAtom;
814	>	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
815	>
816	>	temp = useLennardJones;
817	>	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
818	>
819	>	temp = useElectrostatics;
820	>	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
821	>
822	>	temp = useCharge;
823	>	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
824	>
825	>	temp = useDipole;
826	>	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
827	>
828	>	temp = useSticky;
829	>	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
830	>
831	>	temp = useStickyPower;
832	>	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
833
834	<	delete (*result).second;
835	<	(*result).second = prop;
551	<
552	<	}
553	<	else{
834	>	temp = useGayBerne;
835	>	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
836
837	<	properties[prop->getID()] = prop;
837	>	temp = useEAM;
838	>	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
839
840	<	}
840	>	temp = useSC;
841	>	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
842
843	<	}
843	>	temp = useShape;
844	>	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
845
846	<	GenericData* SimInfo::getProperty(const string& propName){
847	<
563	<	map<string, GenericData*>::iterator result;
564	<
565	<	//string lowerCaseName = ();
566	<
567	<	result = properties.find(propName);
568	<
569	<	if(result != properties.end())
570	<	return (*result).second;
571	<	else
572	<	return NULL;
573	<	}
846	>	temp = useFLARB;
847	>	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
848
849	+	temp = useRF;
850	+	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
851
852	<	void SimInfo::getFortranGroupArrays(SimInfo* info,
853	<	vector<int>& FglobalGroupMembership,
578	<	vector<double>& mfact){
579	<
580	<	Molecule* myMols;
581	<	Atom** myAtoms;
582	<	int numAtom;
583	<	double mtot;
584	<	int numMol;
585	<	int numCutoffGroups;
586	<	CutoffGroup* myCutoffGroup;
587	<	vector<CutoffGroup*>::iterator iterCutoff;
588	<	Atom* cutoffAtom;
589	<	vector<Atom*>::iterator iterAtom;
590	<	int atomIndex;
591	<	double totalMass;
592	<
593	<	mfact.clear();
594	<	FglobalGroupMembership.clear();
595	<
852	>	temp = useSF;
853	>	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
854
855	<	// Fix the silly fortran indexing problem
856	<	#ifdef IS_MPI
857	<	numAtom = mpiSim->getNAtomsGlobal();
858	<	#else
859	<	numAtom = n_atoms;
855	>	temp = useSP;
856	>	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
857	>
858	>	temp = useBoxDipole;
859	>	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
860	>
861	>	temp = useAtomicVirial_;
862	>	MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
863	>
864		#endif
603	–	for (int i = 0; i < numAtom; i++)
604	–	FglobalGroupMembership.push_back(globalGroupMembership[i] + 1);
605	–
865
866	<	myMols = info->molecules;
867	<	numMol = info->n_mol;
868	<	for(int i  = 0; i < numMol; i++){
869	<	numCutoffGroups = myMols[i].getNCutoffGroups();
870	<	for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff);
871	<	myCutoffGroup != NULL;
872	<	myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
866	>	fInfo_.SIM_uses_PBC = usePBC;
867	>	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
868	>	fInfo_.SIM_uses_LennardJones = useLennardJones;
869	>	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
870	>	fInfo_.SIM_uses_Charges = useCharge;
871	>	fInfo_.SIM_uses_Dipoles = useDipole;
872	>	fInfo_.SIM_uses_Sticky = useSticky;
873	>	fInfo_.SIM_uses_StickyPower = useStickyPower;
874	>	fInfo_.SIM_uses_GayBerne = useGayBerne;
875	>	fInfo_.SIM_uses_EAM = useEAM;
876	>	fInfo_.SIM_uses_SC = useSC;
877	>	fInfo_.SIM_uses_Shapes = useShape;
878	>	fInfo_.SIM_uses_FLARB = useFLARB;
879	>	fInfo_.SIM_uses_RF = useRF;
880	>	fInfo_.SIM_uses_SF = useSF;
881	>	fInfo_.SIM_uses_SP = useSP;
882	>	fInfo_.SIM_uses_BoxDipole = useBoxDipole;
883	>	fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
884	>	}
885
886	<	totalMass = myCutoffGroup->getMass();
886	>	void SimInfo::setupFortranSim() {
887	>	int isError;
888	>	int nExclude, nOneTwo, nOneThree, nOneFour;
889	>	std::vector<int> fortranGlobalGroupMembership;
890	>
891	>	isError = 0;
892	>
893	>	//globalGroupMembership_ is filled by SimCreator
894	>	for (int i = 0; i < nGlobalAtoms_; i++) {
895	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
896	>	}
897	>
898	>	//calculate mass ratio of cutoff group
899	>	std::vector<RealType> mfact;
900	>	SimInfo::MoleculeIterator mi;
901	>	Molecule* mol;
902	>	Molecule::CutoffGroupIterator ci;
903	>	CutoffGroup* cg;
904	>	Molecule::AtomIterator ai;
905	>	Atom* atom;
906	>	RealType totalMass;
907	>
908	>	//to avoid memory reallocation, reserve enough space for mfact
909	>	mfact.reserve(getNCutoffGroups());
910	>
911	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
912	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
913	>
914	>	totalMass = cg->getMass();
915	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
916	>	// Check for massless groups - set mfact to 1 if true
917	>	if (totalMass != 0)
918	>	mfact.push_back(atom->getMass()/totalMass);
919	>	else
920	>	mfact.push_back( 1.0 );
921	>	}
922	>	}
923	>	}
924	>
925	>	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
926	>	std::vector<int> identArray;
927	>
928	>	//to avoid memory reallocation, reserve enough space identArray
929	>	identArray.reserve(getNAtoms());
930	>
931	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
932	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
933	>	identArray.push_back(atom->getIdent());
934	>	}
935	>	}
936	>
937	>	//fill molMembershipArray
938	>	//molMembershipArray is filled by SimCreator
939	>	std::vector<int> molMembershipArray(nGlobalAtoms_);
940	>	for (int i = 0; i < nGlobalAtoms_; i++) {
941	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
942	>	}
943	>
944	>	//setup fortran simulation
945	>
946	>	nExclude = excludedInteractions_.getSize();
947	>	nOneTwo = oneTwoInteractions_.getSize();
948	>	nOneThree = oneThreeInteractions_.getSize();
949	>	nOneFour = oneFourInteractions_.getSize();
950	>
951	>	int* excludeList = excludedInteractions_.getPairList();
952	>	int* oneTwoList = oneTwoInteractions_.getPairList();
953	>	int* oneThreeList = oneThreeInteractions_.getPairList();
954	>	int* oneFourList = oneFourInteractions_.getPairList();
955	>
956	>	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
957	>	&nExclude, excludeList,
958	>	&nOneTwo, oneTwoList,
959	>	&nOneThree, oneThreeList,
960	>	&nOneFour, oneFourList,
961	>	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
962	>	&fortranGlobalGroupMembership[0], &isError);
963	>
964	>	if( isError ){
965
966	<	for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom);
967	<	cutoffAtom != NULL;
968	<	cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
969	<	mfact.push_back(cutoffAtom->getMass()/totalMass);
970	<	}
966	>	sprintf( painCave.errMsg,
967	>	"There was an error setting the simulation information in fortran.\n" );
968	>	painCave.isFatal = 1;
969	>	painCave.severity = OPENMD_ERROR;
970	>	simError();
971	>	}
972	>
973	>
974	>	sprintf( checkPointMsg,
975	>	"succesfully sent the simulation information to fortran.\n");
976	>
977	>	errorCheckPoint();
978	>
979	>	// Setup number of neighbors in neighbor list if present
980	>	if (simParams_->haveNeighborListNeighbors()) {
981	>	int nlistNeighbors = simParams_->getNeighborListNeighbors();
982	>	setNeighbors(&nlistNeighbors);
983	>	}
984	>
985	>
986	>	}
987	>
988	>
989	>	void SimInfo::setupFortranParallel() {
990	>	#ifdef IS_MPI
991	>	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
992	>	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
993	>	std::vector<int> localToGlobalCutoffGroupIndex;
994	>	SimInfo::MoleculeIterator mi;
995	>	Molecule::AtomIterator ai;
996	>	Molecule::CutoffGroupIterator ci;
997	>	Molecule* mol;
998	>	Atom* atom;
999	>	CutoffGroup* cg;
1000	>	mpiSimData parallelData;
1001	>	int isError;
1002	>
1003	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
1004	>
1005	>	//local index(index in DataStorge) of atom is important
1006	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
1007	>	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
1008	>	}
1009	>
1010	>	//local index of cutoff group is trivial, it only depends on the order of travesing
1011	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
1012	>	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
1013	>	}
1014	>
1015	>	}
1016	>
1017	>	//fill up mpiSimData struct
1018	>	parallelData.nMolGlobal = getNGlobalMolecules();
1019	>	parallelData.nMolLocal = getNMolecules();
1020	>	parallelData.nAtomsGlobal = getNGlobalAtoms();
1021	>	parallelData.nAtomsLocal = getNAtoms();
1022	>	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
1023	>	parallelData.nGroupsLocal = getNCutoffGroups();
1024	>	parallelData.myNode = worldRank;
1025	>	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
1026	>
1027	>	//pass mpiSimData struct and index arrays to fortran
1028	>	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
1029	>	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
1030	>	&localToGlobalCutoffGroupIndex[0], &isError);
1031	>
1032	>	if (isError) {
1033	>	sprintf(painCave.errMsg,
1034	>	"mpiRefresh errror: fortran didn't like something we gave it.\n");
1035	>	painCave.isFatal = 1;
1036	>	simError();
1037	>	}
1038	>
1039	>	sprintf(checkPointMsg, " mpiRefresh successful.\n");
1040	>	errorCheckPoint();
1041	>
1042	>	#endif
1043	>	}
1044	>
1045	>	void SimInfo::setupCutoff() {
1046	>
1047	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
1048	>
1049	>	// Check the cutoff policy
1050	>	int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
1051	>
1052	>	// Set LJ shifting bools to false
1053	>	ljsp_ = 0;
1054	>	ljsf_ = 0;
1055	>
1056	>	std::string myPolicy;
1057	>	if (forceFieldOptions_.haveCutoffPolicy()){
1058	>	myPolicy = forceFieldOptions_.getCutoffPolicy();
1059	>	}else if (simParams_->haveCutoffPolicy()) {
1060	>	myPolicy = simParams_->getCutoffPolicy();
1061	>	}
1062	>
1063	>	if (!myPolicy.empty()){
1064	>	toUpper(myPolicy);
1065	>	if (myPolicy == "MIX") {
1066	>	cp = MIX_CUTOFF_POLICY;
1067	>	} else {
1068	>	if (myPolicy == "MAX") {
1069	>	cp = MAX_CUTOFF_POLICY;
1070	>	} else {
1071	>	if (myPolicy == "TRADITIONAL") {
1072	>	cp = TRADITIONAL_CUTOFF_POLICY;
1073	>	} else {
1074	>	// throw error
1075	>	sprintf( painCave.errMsg,
1076	>	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
1077	>	painCave.isFatal = 1;
1078	>	simError();
1079	>	}
1080	>	}
1081	>	}
1082	>	}
1083	>	notifyFortranCutoffPolicy(&cp);
1084	>
1085	>	// Check the Skin Thickness for neighborlists
1086	>	RealType skin;
1087	>	if (simParams_->haveSkinThickness()) {
1088	>	skin = simParams_->getSkinThickness();
1089	>	notifyFortranSkinThickness(&skin);
1090	>	}
1091	>
1092	>	// Check if the cutoff was set explicitly:
1093	>	if (simParams_->haveCutoffRadius()) {
1094	>	rcut_ = simParams_->getCutoffRadius();
1095	>	if (simParams_->haveSwitchingRadius()) {
1096	>	rsw_  = simParams_->getSwitchingRadius();
1097	>	} else {
1098	>	if (fInfo_.SIM_uses_Charges |
1099	>	fInfo_.SIM_uses_Dipoles |
1100	>	fInfo_.SIM_uses_RF) {
1101	>
1102	>	rsw_ = 0.85 * rcut_;
1103	>	sprintf(painCave.errMsg,
1104	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
1105	>	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
1106	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1107	>	painCave.isFatal = 0;
1108	>	simError();
1109	>	} else {
1110	>	rsw_ = rcut_;
1111	>	sprintf(painCave.errMsg,
1112	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
1113	>	"\tOpenMD will use the same value as the cutoffRadius.\n"
1114	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1115	>	painCave.isFatal = 0;
1116	>	simError();
1117	>	}
1118	>	}
1119	>
1120	>	if (simParams_->haveElectrostaticSummationMethod()) {
1121	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1122	>	toUpper(myMethod);
1123	>
1124	>	if (myMethod == "SHIFTED_POTENTIAL") {
1125	>	ljsp_ = 1;
1126	>	} else if (myMethod == "SHIFTED_FORCE") {
1127	>	ljsf_ = 1;
1128	>	}
1129	>	}
1130	>
1131	>	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1132	>
1133	>	} else {
1134	>
1135	>	// For electrostatic atoms, we'll assume a large safe value:
1136	>	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1137	>	sprintf(painCave.errMsg,
1138	>	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1139	>	"\tOpenMD will use a default value of 15.0 angstroms"
1140	>	"\tfor the cutoffRadius.\n");
1141	>	painCave.isFatal = 0;
1142	>	simError();
1143	>	rcut_ = 15.0;
1144	>
1145	>	if (simParams_->haveElectrostaticSummationMethod()) {
1146	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1147	>	toUpper(myMethod);
1148	>
1149	>	// For the time being, we're tethering the LJ shifted behavior to the
1150	>	// electrostaticSummationMethod keyword options
1151	>	if (myMethod == "SHIFTED_POTENTIAL") {
1152	>	ljsp_ = 1;
1153	>	} else if (myMethod == "SHIFTED_FORCE") {
1154	>	ljsf_ = 1;
1155	>	}
1156	>	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1157	>	if (simParams_->haveSwitchingRadius()){
1158	>	sprintf(painCave.errMsg,
1159	>	"SimInfo Warning: A value was set for the switchingRadius\n"
1160	>	"\teven though the electrostaticSummationMethod was\n"
1161	>	"\tset to %s\n", myMethod.c_str());
1162	>	painCave.isFatal = 1;
1163	>	simError();
1164	>	}
1165	>	}
1166	>	}
1167	>
1168	>	if (simParams_->haveSwitchingRadius()){
1169	>	rsw_ = simParams_->getSwitchingRadius();
1170	>	} else {
1171	>	sprintf(painCave.errMsg,
1172	>	"SimCreator Warning: No value was set for switchingRadius.\n"
1173	>	"\tOpenMD will use a default value of\n"
1174	>	"\t0.85 * cutoffRadius for the switchingRadius\n");
1175	>	painCave.isFatal = 0;
1176	>	simError();
1177	>	rsw_ = 0.85 * rcut_;
1178	>	}
1179	>
1180	>	Electrostatic::setElectrostaticCutoffRadius(rcut_, rsw_);
1181	>	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1182	>
1183	>	} else {
1184	>	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1185	>	// We'll punt and let fortran figure out the cutoffs later.
1186	>
1187	>	notifyFortranYouAreOnYourOwn();
1188	>
1189	>	}
1190		}
1191		}
1192
1193	<	}
1193	>	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1194	>
1195	>	int errorOut;
1196	>	ElectrostaticSummationMethod esm = NONE;
1197	>	ElectrostaticScreeningMethod sm = UNDAMPED;
1198	>	RealType alphaVal;
1199	>	RealType dielectric;
1200	>
1201	>	errorOut = isError;
1202	>
1203	>	if (simParams_->haveElectrostaticSummationMethod()) {
1204	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1205	>	toUpper(myMethod);
1206	>	if (myMethod == "NONE") {
1207	>	esm = NONE;
1208	>	} else {
1209	>	if (myMethod == "SWITCHING_FUNCTION") {
1210	>	esm = SWITCHING_FUNCTION;
1211	>	} else {
1212	>	if (myMethod == "SHIFTED_POTENTIAL") {
1213	>	esm = SHIFTED_POTENTIAL;
1214	>	} else {
1215	>	if (myMethod == "SHIFTED_FORCE") {
1216	>	esm = SHIFTED_FORCE;
1217	>	} else {
1218	>	if (myMethod == "REACTION_FIELD") {
1219	>	esm = REACTION_FIELD;
1220	>	dielectric = simParams_->getDielectric();
1221	>	if (!simParams_->haveDielectric()) {
1222	>	// throw warning
1223	>	sprintf( painCave.errMsg,
1224	>	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1225	>	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1226	>	painCave.isFatal = 0;
1227	>	simError();
1228	>	}
1229	>	} else {
1230	>	// throw error
1231	>	sprintf( painCave.errMsg,
1232	>	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1233	>	"\t(Input file specified %s .)\n"
1234	>	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1235	>	"\t\"shifted_potential\", \"shifted_force\", or \n"
1236	>	"\t\"reaction_field\".\n", myMethod.c_str() );
1237	>	painCave.isFatal = 1;
1238	>	simError();
1239	>	}
1240	>	}
1241	>	}
1242	>	}
1243	>	}
1244	>	}
1245	>
1246	>	if (simParams_->haveElectrostaticScreeningMethod()) {
1247	>	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1248	>	toUpper(myScreen);
1249	>	if (myScreen == "UNDAMPED") {
1250	>	sm = UNDAMPED;
1251	>	} else {
1252	>	if (myScreen == "DAMPED") {
1253	>	sm = DAMPED;
1254	>	if (!simParams_->haveDampingAlpha()) {
1255	>	// first set a cutoff dependent alpha value
1256	>	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1257	>	alphaVal = 0.5125 - rcut_* 0.025;
1258	>	// for values rcut > 20.5, alpha is zero
1259	>	if (alphaVal < 0) alphaVal = 0;
1260	>
1261	>	// throw warning
1262	>	sprintf( painCave.errMsg,
1263	>	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1264	>	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1265	>	painCave.isFatal = 0;
1266	>	simError();
1267	>	} else {
1268	>	alphaVal = simParams_->getDampingAlpha();
1269	>	}
1270	>
1271	>	} else {
1272	>	// throw error
1273	>	sprintf( painCave.errMsg,
1274	>	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1275	>	"\t(Input file specified %s .)\n"
1276	>	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1277	>	"or \"damped\".\n", myScreen.c_str() );
1278	>	painCave.isFatal = 1;
1279	>	simError();
1280	>	}
1281	>	}
1282	>	}
1283	>
1284	>
1285	>	Electrostatic::setElectrostaticSummationMethod( esm );
1286	>	Electrostatic::setElectrostaticScreeningMethod( sm );
1287	>	Electrostatic::setDampingAlpha( alphaVal );
1288	>	Electrostatic::setReactionFieldDielectric( dielectric );
1289	>	initFortranFF( &errorOut );
1290	>	}
1291	>
1292	>	void SimInfo::setupSwitchingFunction() {
1293	>	int ft = CUBIC;
1294	>
1295	>	if (simParams_->haveSwitchingFunctionType()) {
1296	>	std::string funcType = simParams_->getSwitchingFunctionType();
1297	>	toUpper(funcType);
1298	>	if (funcType == "CUBIC") {
1299	>	ft = CUBIC;
1300	>	} else {
1301	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1302	>	ft = FIFTH_ORDER_POLY;
1303	>	} else {
1304	>	// throw error
1305	>	sprintf( painCave.errMsg,
1306	>	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1307	>	painCave.isFatal = 1;
1308	>	simError();
1309	>	}
1310	>	}
1311	>	}
1312	>
1313	>	// send switching function notification to switcheroo
1314	>	setFunctionType(&ft);
1315	>
1316	>	}
1317	>
1318	>	void SimInfo::setupAccumulateBoxDipole() {
1319	>
1320	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1321	>	if ( simParams_->haveAccumulateBoxDipole() )
1322	>	if ( simParams_->getAccumulateBoxDipole() ) {
1323	>	setAccumulateBoxDipole();
1324	>	calcBoxDipole_ = true;
1325	>	}
1326	>
1327	>	}
1328	>
1329	>	void SimInfo::addProperty(GenericData* genData) {
1330	>	properties_.addProperty(genData);
1331	>	}
1332	>
1333	>	void SimInfo::removeProperty(const std::string& propName) {
1334	>	properties_.removeProperty(propName);
1335	>	}
1336	>
1337	>	void SimInfo::clearProperties() {
1338	>	properties_.clearProperties();
1339	>	}
1340	>
1341	>	std::vector<std::string> SimInfo::getPropertyNames() {
1342	>	return properties_.getPropertyNames();
1343	>	}
1344	>
1345	>	std::vector<GenericData*> SimInfo::getProperties() {
1346	>	return properties_.getProperties();
1347	>	}
1348	>
1349	>	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1350	>	return properties_.getPropertyByName(propName);
1351	>	}
1352	>
1353	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1354	>	if (sman_ == sman) {
1355	>	return;
1356	>	}
1357	>	delete sman_;
1358	>	sman_ = sman;
1359	>
1360	>	Molecule* mol;
1361	>	RigidBody* rb;
1362	>	Atom* atom;
1363	>	SimInfo::MoleculeIterator mi;
1364	>	Molecule::RigidBodyIterator rbIter;
1365	>	Molecule::AtomIterator atomIter;;
1366	>
1367	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1368	>
1369	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1370	>	atom->setSnapshotManager(sman_);
1371	>	}
1372	>
1373	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1374	>	rb->setSnapshotManager(sman_);
1375	>	}
1376	>	}
1377	>
1378	>	}
1379	>
1380	>	Vector3d SimInfo::getComVel(){
1381	>	SimInfo::MoleculeIterator i;
1382	>	Molecule* mol;
1383	>
1384	>	Vector3d comVel(0.0);
1385	>	RealType totalMass = 0.0;
1386	>
1387	>
1388	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1389	>	RealType mass = mol->getMass();
1390	>	totalMass += mass;
1391	>	comVel += mass * mol->getComVel();
1392	>	}
1393	>
1394	>	#ifdef IS_MPI
1395	>	RealType tmpMass = totalMass;
1396	>	Vector3d tmpComVel(comVel);
1397	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1398	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1399	>	#endif
1400	>
1401	>	comVel /= totalMass;
1402	>
1403	>	return comVel;
1404	>	}
1405	>
1406	>	Vector3d SimInfo::getCom(){
1407	>	SimInfo::MoleculeIterator i;
1408	>	Molecule* mol;
1409	>
1410	>	Vector3d com(0.0);
1411	>	RealType totalMass = 0.0;
1412	>
1413	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1414	>	RealType mass = mol->getMass();
1415	>	totalMass += mass;
1416	>	com += mass * mol->getCom();
1417	>	}
1418	>
1419	>	#ifdef IS_MPI
1420	>	RealType tmpMass = totalMass;
1421	>	Vector3d tmpCom(com);
1422	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1423	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1424	>	#endif
1425	>
1426	>	com /= totalMass;
1427	>
1428	>	return com;
1429	>
1430	>	}
1431	>
1432	>	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1433	>
1434	>	return o;
1435	>	}
1436	>
1437	>
1438	>	/*
1439	>	Returns center of mass and center of mass velocity in one function call.
1440	>	*/
1441	>
1442	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1443	>	SimInfo::MoleculeIterator i;
1444	>	Molecule* mol;
1445	>
1446	>
1447	>	RealType totalMass = 0.0;
1448	>
1449	>
1450	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1451	>	RealType mass = mol->getMass();
1452	>	totalMass += mass;
1453	>	com += mass * mol->getCom();
1454	>	comVel += mass * mol->getComVel();
1455	>	}
1456	>
1457	>	#ifdef IS_MPI
1458	>	RealType tmpMass = totalMass;
1459	>	Vector3d tmpCom(com);
1460	>	Vector3d tmpComVel(comVel);
1461	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1462	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1463	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1464	>	#endif
1465	>
1466	>	com /= totalMass;
1467	>	comVel /= totalMass;
1468	>	}
1469	>
1470	>	/*
1471	>	Return intertia tensor for entire system and angular momentum Vector.
1472	>
1473	>
1474	>	[  Ixx -Ixy  -Ixz ]
1475	>	J =| -Iyx  Iyy  -Iyz |
1476	>	[ -Izx -Iyz   Izz ]
1477	>	*/
1478	>
1479	>	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1480	>
1481	>
1482	>	RealType xx = 0.0;
1483	>	RealType yy = 0.0;
1484	>	RealType zz = 0.0;
1485	>	RealType xy = 0.0;
1486	>	RealType xz = 0.0;
1487	>	RealType yz = 0.0;
1488	>	Vector3d com(0.0);
1489	>	Vector3d comVel(0.0);
1490	>
1491	>	getComAll(com, comVel);
1492	>
1493	>	SimInfo::MoleculeIterator i;
1494	>	Molecule* mol;
1495	>
1496	>	Vector3d thisq(0.0);
1497	>	Vector3d thisv(0.0);
1498	>
1499	>	RealType thisMass = 0.0;
1500	>
1501	>
1502	>
1503	>
1504	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1505	>
1506	>	thisq = mol->getCom()-com;
1507	>	thisv = mol->getComVel()-comVel;
1508	>	thisMass = mol->getMass();
1509	>	// Compute moment of intertia coefficients.
1510	>	xx += thisq[0]*thisq[0]*thisMass;
1511	>	yy += thisq[1]*thisq[1]*thisMass;
1512	>	zz += thisq[2]*thisq[2]*thisMass;
1513	>
1514	>	// compute products of intertia
1515	>	xy += thisq[0]*thisq[1]*thisMass;
1516	>	xz += thisq[0]*thisq[2]*thisMass;
1517	>	yz += thisq[1]*thisq[2]*thisMass;
1518	>
1519	>	angularMomentum += cross( thisq, thisv ) * thisMass;
1520	>
1521	>	}
1522	>
1523	>
1524	>	inertiaTensor(0,0) = yy + zz;
1525	>	inertiaTensor(0,1) = -xy;
1526	>	inertiaTensor(0,2) = -xz;
1527	>	inertiaTensor(1,0) = -xy;
1528	>	inertiaTensor(1,1) = xx + zz;
1529	>	inertiaTensor(1,2) = -yz;
1530	>	inertiaTensor(2,0) = -xz;
1531	>	inertiaTensor(2,1) = -yz;
1532	>	inertiaTensor(2,2) = xx + yy;
1533	>
1534	>	#ifdef IS_MPI
1535	>	Mat3x3d tmpI(inertiaTensor);
1536	>	Vector3d tmpAngMom;
1537	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1538	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1539	>	#endif
1540	>
1541	>	return;
1542	>	}
1543	>
1544	>	//Returns the angular momentum of the system
1545	>	Vector3d SimInfo::getAngularMomentum(){
1546	>
1547	>	Vector3d com(0.0);
1548	>	Vector3d comVel(0.0);
1549	>	Vector3d angularMomentum(0.0);
1550	>
1551	>	getComAll(com,comVel);
1552	>
1553	>	SimInfo::MoleculeIterator i;
1554	>	Molecule* mol;
1555	>
1556	>	Vector3d thisr(0.0);
1557	>	Vector3d thisp(0.0);
1558	>
1559	>	RealType thisMass;
1560	>
1561	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1562	>	thisMass = mol->getMass();
1563	>	thisr = mol->getCom()-com;
1564	>	thisp = (mol->getComVel()-comVel)*thisMass;
1565	>
1566	>	angularMomentum += cross( thisr, thisp );
1567	>
1568	>	}
1569	>
1570	>	#ifdef IS_MPI
1571	>	Vector3d tmpAngMom;
1572	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1573	>	#endif
1574	>
1575	>	return angularMomentum;
1576	>	}
1577	>
1578	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1579	>	return IOIndexToIntegrableObject.at(index);
1580	>	}
1581	>
1582	>	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1583	>	IOIndexToIntegrableObject= v;
1584	>	}
1585	>
1586	>	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1587	>	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1588	>	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1589	>	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1590	>	*/
1591	>	void SimInfo::getGyrationalVolume(RealType &volume){
1592	>	Mat3x3d intTensor;
1593	>	RealType det;
1594	>	Vector3d dummyAngMom;
1595	>	RealType sysconstants;
1596	>	RealType geomCnst;
1597	>
1598	>	geomCnst = 3.0/2.0;
1599	>	/* Get the inertial tensor and angular momentum for free*/
1600	>	getInertiaTensor(intTensor,dummyAngMom);
1601	>
1602	>	det = intTensor.determinant();
1603	>	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1604	>	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1605	>	return;
1606	>	}
1607	>
1608	>	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1609	>	Mat3x3d intTensor;
1610	>	Vector3d dummyAngMom;
1611	>	RealType sysconstants;
1612	>	RealType geomCnst;
1613	>
1614	>	geomCnst = 3.0/2.0;
1615	>	/* Get the inertial tensor and angular momentum for free*/
1616	>	getInertiaTensor(intTensor,dummyAngMom);
1617	>
1618	>	detI = intTensor.determinant();
1619	>	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1620	>	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1621	>	return;
1622	>	}
1623	>	/*
1624	>	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1625	>	assert( v.size() == nAtoms_ + nRigidBodies_);
1626	>	sdByGlobalIndex_ = v;
1627	>	}
1628	>
1629	>	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1630	>	//assert(index < nAtoms_ + nRigidBodies_);
1631	>	return sdByGlobalIndex_.at(index);
1632	>	}
1633	>	*/
1634	>	}//end namespace OpenMD
1635	>

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 124 by chuckv, Wed Oct 20 20:46:20 2004 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1503 by gezelter, Sat Oct 2 19:54:41 2010 UTC

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