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

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trunk/src/brains/SimInfo.cpp (file contents), Revision 143 by chrisfen, Fri Oct 22 22:54:01 2004 UTC vs.
branches/development/src/brains/SimInfo.cpp (file contents), Revision 1505 by gezelter, Sun Oct 3 22:18:59 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	<	useDirectionalAtoms = 0;
98	<	useLennardJones = 0;
99	<	useElectrostatics = 0;
100	<	useCharges = 0;
101	<	useDipoles = 0;
102	<	useSticky = 0;
66	<	useGayBerne = 0;
67	<	useEAM = 0;
68	<	useShapes = 0;
69	<	useFLARB = 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	<	useSolidThermInt = 0;
105	<	useLiquidThermInt = 0;
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	<	haveCutoffGroups = false;
112	>	//calculate atoms in molecules
113	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
114
115	<	excludes = Exclude::Instance();
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	<	myConfiguration = new SimState();
124	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
125
126	<	has_minimizer = false;
81	<	the_minimizer =NULL;
126	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
127
128	<	ngroup = 0;
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	<	}
137	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
138	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
139	>
140	>	}
141
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	<	SimInfo::~SimInfo(){
150	<
151	<	delete myConfiguration;
152	<
153	<	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];
109	<	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	<	}
114	<
115	<	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 ]
122	<	// [ 2 5 8 ]
123	<	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++)
128	<	for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
129	<
130	<	calcBoxL();
131	<	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	<
142	<	}
143	<
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
147	–	int i, j;
148	–	for(i=0; i<3; i++)
149	–	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
150	–	}
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
159	–	for(i=0; i<3; i++)
160	–	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 ) {
167	<
168	<	int oldOrtho;
169	<	int i,j;
170	<	double smallDiag;
171	<	double tol;
172	<	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]);
182	<	if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
183	<	tol = smallDiag * orthoTolerance;
184	<
185	<	orthoRhombic = 1;
186	<
187	<	for (i = 0; i < 3; i++ ) {
188	<	for (j = 0 ; j < 3; j++) {
189	<	if (i != j) {
190	<	if (orthoRhombic) {
191	<	if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
192	<	}
268	>	if (integrableObject->isDirectional()) {
269	>	if (integrableObject->isLinear()) {
270	>	ndf_local += 2;
271	>	} else {
272	>	ndf_local += 3;
273	>	}
274	>	}
275	>
276		}
277		}
195	–	}
196	–
197	–	if( oldOrtho != orthoRhombic ){
278
279	<	if( orthoRhombic ) {
280	<	sprintf( painCave.errMsg,
201	<	"OOPSE is switching from the default Non-Orthorhombic\n"
202	<	"\tto the faster Orthorhombic periodic boundary computations.\n"
203	<	"\tThis is usually a good thing, but if you wan't the\n"
204	<	"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
205	<	"\tvariable ( currently set to %G ) smaller.\n",
206	<	orthoTolerance);
207	<	painCave.severity = OOPSE_INFO;
208	<	simError();
209	<	}
210	<	else {
211	<	sprintf( painCave.errMsg,
212	<	"OOPSE is switching from the faster Orthorhombic to the more\n"
213	<	"\tflexible Non-Orthorhombic periodic boundary computations.\n"
214	<	"\tThis is usually because the box has deformed under\n"
215	<	"\tNPTf integration. If you wan't to live on the edge with\n"
216	<	"\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
217	<	"\tvariable ( currently set to %G ) larger.\n",
218	<	orthoTolerance);
219	<	painCave.severity = OOPSE_WARNING;
220	<	simError();
221	<	}
222	<	}
223	<	}
279	>	// n_constraints is local, so subtract them on each processor
280	>	ndf_local -= nConstraints_;
281
282	<	void SimInfo::calcBoxL( void ){
282	>	#ifdef IS_MPI
283	>	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
284	>	#else
285	>	ndf_ = ndf_local;
286	>	#endif
287
288	<	double dx, dy, dz, dsq;
288	>	// nZconstraints_ is global, as are the 3 COM translations for the
289	>	// entire system:
290	>	ndf_ = ndf_ - 3 - nZconstraint_;
291
229	–	// boxVol = Determinant of Hmat
230	–
231	–	boxVol = matDet3( Hmat );
232	–
233	–	// boxLx
234	–
235	–	dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
236	–	dsq = dx*dx + dy*dy + dz*dz;
237	–	boxL[0] = sqrt( dsq );
238	–	//maxCutoff = 0.5 * boxL[0];
239	–
240	–	// boxLy
241	–
242	–	dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
243	–	dsq = dx*dx + dy*dy + dz*dz;
244	–	boxL[1] = sqrt( dsq );
245	–	//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
246	–
247	–
248	–	// boxLz
249	–
250	–	dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
251	–	dsq = dx*dx + dy*dy + dz*dz;
252	–	boxL[2] = sqrt( dsq );
253	–	//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
254	–
255	–	//calculate the max cutoff
256	–	maxCutoff =  calcMaxCutOff();
257	–
258	–	checkCutOffs();
259	–
260	–	}
261	–
262	–
263	–	double SimInfo::calcMaxCutOff(){
264	–
265	–	double ri[3], rj[3], rk[3];
266	–	double rij[3], rjk[3], rki[3];
267	–	double minDist;
268	–
269	–	ri[0] = Hmat[0][0];
270	–	ri[1] = Hmat[1][0];
271	–	ri[2] = Hmat[2][0];
272	–
273	–	rj[0] = Hmat[0][1];
274	–	rj[1] = Hmat[1][1];
275	–	rj[2] = Hmat[2][1];
276	–
277	–	rk[0] = Hmat[0][2];
278	–	rk[1] = Hmat[1][2];
279	–	rk[2] = Hmat[2][2];
280	–
281	–	crossProduct3(ri, rj, rij);
282	–	distXY = dotProduct3(rk,rij) / norm3(rij);
283	–
284	–	crossProduct3(rj,rk, rjk);
285	–	distYZ = dotProduct3(ri,rjk) / norm3(rjk);
286	–
287	–	crossProduct3(rk,ri, rki);
288	–	distZX = dotProduct3(rj,rki) / norm3(rki);
289	–
290	–	minDist = min(min(distXY, distYZ), distZX);
291	–	return minDist/2;
292	–
293	–	}
294	–
295	–	void SimInfo::wrapVector( double thePos[3] ){
296	–
297	–	int i;
298	–	double scaled[3];
299	–
300	–	if( !orthoRhombic ){
301	–	// calc the scaled coordinates.
302	–
303	–
304	–	matVecMul3(HmatInv, thePos, scaled);
305	–
306	–	for(i=0; i<3; i++)
307	–	scaled[i] -= roundMe(scaled[i]);
308	–
309	–	// calc the wrapped real coordinates from the wrapped scaled coordinates
310	–
311	–	matVecMul3(Hmat, scaled, thePos);
312	–
292		}
314	–	else{
315	–	// calc the scaled coordinates.
316	–
317	–	for(i=0; i<3; i++)
318	–	scaled[i] = thePos[i]*HmatInv[i][i];
319	–
320	–	// wrap the scaled coordinates
321	–
322	–	for(i=0; i<3; i++)
323	–	scaled[i] -= roundMe(scaled[i]);
324	–
325	–	// calc the wrapped real coordinates from the wrapped scaled coordinates
326	–
327	–	for(i=0; i<3; i++)
328	–	thePos[i] = scaled[i]*Hmat[i][i];
329	–	}
330	–
331	–	}
293
294	<
334	<	int SimInfo::getNDF(){
335	<	int ndf_local;
336	<
337	<	ndf_local = 0;
338	<
339	<	for(int i = 0; i < integrableObjects.size(); i++){
340	<	ndf_local += 3;
341	<	if (integrableObjects[i]->isDirectional()) {
342	<	if (integrableObjects[i]->isLinear())
343	<	ndf_local += 2;
344	<	else
345	<	ndf_local += 3;
346	<	}
347	<	}
348	<
349	<	// n_constraints is local, so subtract them on each processor:
350	<
351	<	ndf_local -= n_constraints;
352	<
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	+	return fdf_;
301	+	}
302	+
303	+	void SimInfo::calcNdfRaw() {
304	+	int ndfRaw_local;
305
306	<	// nZconstraints is global, as are the 3 COM translations for the
307	<	// entire system:
306	>	MoleculeIterator i;
307	>	std::vector<StuntDouble*>::iterator j;
308	>	Molecule* mol;
309	>	StuntDouble* integrableObject;
310
311	<	ndf = ndf - 3 - nZconstraints;
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	<	return ndf;
365	<	}
318	>	ndfRaw_local += 3;
319
320	<	int SimInfo::getNDFraw() {
321	<	int ndfRaw_local;
322	<
323	<	// Raw degrees of freedom that we have to set
324	<	ndfRaw_local = 0;
325	<
326	<	for(int i = 0; i < integrableObjects.size(); i++){
327	<	ndfRaw_local += 3;
328	<	if (integrableObjects[i]->isDirectional()) {
376	<	if (integrableObjects[i]->isLinear())
377	<	ndfRaw_local += 2;
378	<	else
379	<	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		}
381	–	}
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() {
393	<	int ndfTrans_local;
341	>	ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
342
395	–	ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
343
397	–
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);
418	<	#else
419	<	nObjs = nObjs_local;
420	<	#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;
465	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
466	>	oneFourInteractions_.addPair(a, d);
467	>	} else {
468	>	excludedInteractions_.addPair(a, d);
469	>	}
470	>	}
471
472	<	if (useSticky || useDipoles || useGayBerne || useShapes) {
473	<	useDirectionalAtoms = 1;
443	<	fInfo.SIM_uses_DirectionalAtoms = useDirectionalAtoms;
444	<	}
472	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
473	>	inversion = mol->nextInversion(inversionIter)) {
474
475	<	fInfo.SIM_uses_LennardJones = useLennardJones;
475	>	a = inversion->getAtomA()->getGlobalIndex();
476	>	b = inversion->getAtomB()->getGlobalIndex();
477	>	c = inversion->getAtomC()->getGlobalIndex();
478	>	d = inversion->getAtomD()->getGlobalIndex();
479
480	<	if (useCharges || useDipoles) {
481	<	useElectrostatics = 1;
482	<	fInfo.SIM_uses_Electrostatics = useElectrostatics;
483	<	}
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	<	fInfo.SIM_uses_Charges = useCharges;
491	<	fInfo.SIM_uses_Dipoles = useDipoles;
492	<	fInfo.SIM_uses_Sticky = useSticky;
493	<	fInfo.SIM_uses_GayBerne = useGayBerne;
494	<	fInfo.SIM_uses_EAM = useEAM;
495	<	fInfo.SIM_uses_Shapes = useShapes;
496	<	fInfo.SIM_uses_FLARB = useFLARB;
497	<	fInfo.SIM_uses_RF = useReactionField;
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	<	n_exclude = excludes->getSize();
502	<	excl = excludes->getFortranArray();
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	<	n_global = mpiSim->getNAtomsGlobal();
602	<	#else
603	<	n_global = n_atoms;
604	<	#endif
605	<
606	<	isError = 0;
607	<
608	<	getFortranGroupArrays(this, FglobalGroupMembership, mfact);
609	<	//it may not be a good idea to pass the address of first element in vector
610	<	//since c++ standard does not require vector to be stored continuously in meomory
611	<	//Most of the compilers will organize the memory of vector continuously
612	<	setFortranSim( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
613	<	&nGlobalExcludes, globalExcludes, molMembershipArray,
614	<	&mfact[0], &ngroup, &FglobalGroupMembership[0], &isError);
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	>	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	>
668	>
669	>	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
670	>	int curStampId;
671	>
672	>	//index from 0
673	>	curStampId = moleculeStamps_.size();
674	>
675	>	moleculeStamps_.push_back(molStamp);
676	>	molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
677	>	}
678	>
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	>	// set the useRF logical
760	>	useRF = 0;
761	>	useSF = 0;
762	>	useSP = 0;
763	>	useBoxDipole = 0;
764	>
765	>	if (simParams_->haveElectrostaticSummationMethod()) {
766	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
767	>	toUpper(myMethod);
768	>	if (myMethod == "REACTION_FIELD"){
769	>	useRF = 1;
770	>	} else if (myMethod == "SHIFTED_FORCE"){
771	>	useSF = 1;
772	>	} else if (myMethod == "SHIFTED_POTENTIAL"){
773	>	useSP = 1;
774	>	}
775	>	}
776	>
777	>	if (simParams_->haveAccumulateBoxDipole())
778	>	if (simParams_->getAccumulateBoxDipole())
779	>	useBoxDipole = 1;
780	>
781	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
782	>
783	>	//loop over all of the atom types
784	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
785	>	useLennardJones |= (*i)->isLennardJones();
786	>	useElectrostatic |= (*i)->isElectrostatic();
787	>	useEAM |= (*i)->isEAM();
788	>	useSC |= (*i)->isSC();
789	>	useCharge |= (*i)->isCharge();
790	>	useDirectional |= (*i)->isDirectional();
791	>	useDipole |= (*i)->isDipole();
792	>	useGayBerne |= (*i)->isGayBerne();
793	>	useSticky |= (*i)->isSticky();
794	>	useStickyPower |= (*i)->isStickyPower();
795	>	useShape |= (*i)->isShape();
796	>	}
797
798	<	if( isError ){
799	<
800	<	sprintf( painCave.errMsg,
484	<	"There was an error setting the simulation information in fortran.\n" );
485	<	painCave.isFatal = 1;
486	<	painCave.severity = OOPSE_ERROR;
487	<	simError();
488	<	}
489	<
490	<	#ifdef IS_MPI
491	<	sprintf( checkPointMsg,
492	<	"succesfully sent the simulation information to fortran.\n");
493	<	MPIcheckPoint();
494	<	#endif // is_mpi
495	<
496	<	this->ndf = this->getNDF();
497	<	this->ndfRaw = this->getNDFraw();
498	<	this->ndfTrans = this->getNDFtranslational();
499	<	}
798	>	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
799	>	useDirectionalAtom = 1;
800	>	}
801
802	<	void SimInfo::setDefaultRcut( double theRcut ){
803	<
804	<	haveRcut = 1;
504	<	rCut = theRcut;
505	<	rList = rCut + 1.0;
506	<
507	<	notifyFortranCutoffs( &rCut, &rSw, &rList );
508	<	}
802	>	if (useCharge || useDipole) {
803	>	useElectrostatics = 1;
804	>	}
805
806	<	void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
806	>	#ifdef IS_MPI
807	>	int temp;
808
809	<	rSw = theRsw;
810	<	setDefaultRcut( theRcut );
514	<	}
809	>	temp = usePBC;
810	>	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
811
812	+	temp = useDirectionalAtom;
813	+	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
814
815	<	void SimInfo::checkCutOffs( void ){
816	<
519	<	if( boxIsInit ){
520	<
521	<	//we need to check cutOffs against the box
522	<
523	<	if( rCut > maxCutoff ){
524	<	sprintf( painCave.errMsg,
525	<	"cutoffRadius is too large for the current periodic box.\n"
526	<	"\tCurrent Value of cutoffRadius = %G at time %G\n "
527	<	"\tThis is larger than half of at least one of the\n"
528	<	"\tperiodic box vectors.  Right now, the Box matrix is:\n"
529	<	"\n"
530	<	"\t[ %G %G %G ]\n"
531	<	"\t[ %G %G %G ]\n"
532	<	"\t[ %G %G %G ]\n",
533	<	rCut, currentTime,
534	<	Hmat[0][0], Hmat[0][1], Hmat[0][2],
535	<	Hmat[1][0], Hmat[1][1], Hmat[1][2],
536	<	Hmat[2][0], Hmat[2][1], Hmat[2][2]);
537	<	painCave.severity = OOPSE_ERROR;
538	<	painCave.isFatal = 1;
539	<	simError();
540	<	}
541	<	} else {
542	<	// initialize this stuff before using it, OK?
543	<	sprintf( painCave.errMsg,
544	<	"Trying to check cutoffs without a box.\n"
545	<	"\tOOPSE should have better programmers than that.\n" );
546	<	painCave.severity = OOPSE_ERROR;
547	<	painCave.isFatal = 1;
548	<	simError();
549	<	}
550	<
551	<	}
815	>	temp = useLennardJones;
816	>	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
817
818	<	void SimInfo::addProperty(GenericData* prop){
818	>	temp = useElectrostatics;
819	>	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
820
821	<	map<string, GenericData*>::iterator result;
822	<	result = properties.find(prop->getID());
823	<
824	<	//we can't simply use  properties[prop->getID()] = prop,
825	<	//it will cause memory leak if we already contain a propery which has the same name of prop
826	<
827	<	if(result != properties.end()){
821	>	temp = useCharge;
822	>	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
823	>
824	>	temp = useDipole;
825	>	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
826	>
827	>	temp = useSticky;
828	>	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
829	>
830	>	temp = useStickyPower;
831	>	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
832
833	<	delete (*result).second;
834	<	(*result).second = prop;
565	<
566	<	}
567	<	else{
833	>	temp = useGayBerne;
834	>	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
835
836	<	properties[prop->getID()] = prop;
836	>	temp = useEAM;
837	>	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
838
839	<	}
839	>	temp = useSC;
840	>	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
841
842	<	}
842	>	temp = useShape;
843	>	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
844
845	<	GenericData* SimInfo::getProperty(const string& propName){
846	<
577	<	map<string, GenericData*>::iterator result;
578	<
579	<	//string lowerCaseName = ();
580	<
581	<	result = properties.find(propName);
582	<
583	<	if(result != properties.end())
584	<	return (*result).second;
585	<	else
586	<	return NULL;
587	<	}
845	>	temp = useFLARB;
846	>	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
847
848	+	temp = useRF;
849	+	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
850
851	<	void SimInfo::getFortranGroupArrays(SimInfo* info,
852	<	vector<int>& FglobalGroupMembership,
592	<	vector<double>& mfact){
593	<
594	<	Molecule* myMols;
595	<	Atom** myAtoms;
596	<	int numAtom;
597	<	double mtot;
598	<	int numMol;
599	<	int numCutoffGroups;
600	<	CutoffGroup* myCutoffGroup;
601	<	vector<CutoffGroup*>::iterator iterCutoff;
602	<	Atom* cutoffAtom;
603	<	vector<Atom*>::iterator iterAtom;
604	<	int atomIndex;
605	<	double totalMass;
606	<
607	<	mfact.clear();
608	<	FglobalGroupMembership.clear();
609	<
851	>	temp = useSF;
852	>	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
853
854	<	// Fix the silly fortran indexing problem
855	<	#ifdef IS_MPI
856	<	numAtom = mpiSim->getNAtomsGlobal();
857	<	#else
858	<	numAtom = n_atoms;
854	>	temp = useSP;
855	>	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
856	>
857	>	temp = useBoxDipole;
858	>	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
859	>
860	>	temp = useAtomicVirial_;
861	>	MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
862	>
863		#endif
864	<	for (int i = 0; i < numAtom; i++)
865	<	FglobalGroupMembership.push_back(globalGroupMembership[i] + 1);
866	<
864	>	fInfo_.SIM_uses_PBC = usePBC;
865	>	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
866	>	fInfo_.SIM_uses_LennardJones = useLennardJones;
867	>	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
868	>	fInfo_.SIM_uses_Charges = useCharge;
869	>	fInfo_.SIM_uses_Dipoles = useDipole;
870	>	fInfo_.SIM_uses_Sticky = useSticky;
871	>	fInfo_.SIM_uses_StickyPower = useStickyPower;
872	>	fInfo_.SIM_uses_GayBerne = useGayBerne;
873	>	fInfo_.SIM_uses_EAM = useEAM;
874	>	fInfo_.SIM_uses_SC = useSC;
875	>	fInfo_.SIM_uses_Shapes = useShape;
876	>	fInfo_.SIM_uses_FLARB = useFLARB;
877	>	fInfo_.SIM_uses_RF = useRF;
878	>	fInfo_.SIM_uses_SF = useSF;
879	>	fInfo_.SIM_uses_SP = useSP;
880	>	fInfo_.SIM_uses_BoxDipole = useBoxDipole;
881	>	fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
882	>	}
883
884	<	myMols = info->molecules;
885	<	numMol = info->n_mol;
886	<	for(int i  = 0; i < numMol; i++){
887	<	numCutoffGroups = myMols[i].getNCutoffGroups();
888	<	for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff);
889	<	myCutoffGroup != NULL;
627	<	myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
884	>	void SimInfo::setupFortranSim() {
885	>	int isError;
886	>	int nExclude, nOneTwo, nOneThree, nOneFour;
887	>	std::vector<int> fortranGlobalGroupMembership;
888	>
889	>	isError = 0;
890
891	<	totalMass = myCutoffGroup->getMass();
891	>	//globalGroupMembership_ is filled by SimCreator
892	>	for (int i = 0; i < nGlobalAtoms_; i++) {
893	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
894	>	}
895	>
896	>	//calculate mass ratio of cutoff group
897	>	std::vector<RealType> mfact;
898	>	SimInfo::MoleculeIterator mi;
899	>	Molecule* mol;
900	>	Molecule::CutoffGroupIterator ci;
901	>	CutoffGroup* cg;
902	>	Molecule::AtomIterator ai;
903	>	Atom* atom;
904	>	RealType totalMass;
905	>
906	>	//to avoid memory reallocation, reserve enough space for mfact
907	>	mfact.reserve(getNCutoffGroups());
908	>
909	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
910	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
911	>
912	>	totalMass = cg->getMass();
913	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
914	>	// Check for massless groups - set mfact to 1 if true
915	>	if (totalMass != 0)
916	>	mfact.push_back(atom->getMass()/totalMass);
917	>	else
918	>	mfact.push_back( 1.0 );
919	>	}
920	>	}
921	>	}
922	>
923	>	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
924	>	std::vector<int> identArray;
925	>
926	>	//to avoid memory reallocation, reserve enough space identArray
927	>	identArray.reserve(getNAtoms());
928	>
929	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
930	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
931	>	identArray.push_back(atom->getIdent());
932	>	}
933	>	}
934	>
935	>	//fill molMembershipArray
936	>	//molMembershipArray is filled by SimCreator
937	>	std::vector<int> molMembershipArray(nGlobalAtoms_);
938	>	for (int i = 0; i < nGlobalAtoms_; i++) {
939	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
940	>	}
941	>
942	>	//setup fortran simulation
943	>
944	>	nExclude = excludedInteractions_.getSize();
945	>	nOneTwo = oneTwoInteractions_.getSize();
946	>	nOneThree = oneThreeInteractions_.getSize();
947	>	nOneFour = oneFourInteractions_.getSize();
948	>
949	>	int* excludeList = excludedInteractions_.getPairList();
950	>	int* oneTwoList = oneTwoInteractions_.getPairList();
951	>	int* oneThreeList = oneThreeInteractions_.getPairList();
952	>	int* oneFourList = oneFourInteractions_.getPairList();
953	>
954	>	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
955	>	&nExclude, excludeList,
956	>	&nOneTwo, oneTwoList,
957	>	&nOneThree, oneThreeList,
958	>	&nOneFour, oneFourList,
959	>	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
960	>	&fortranGlobalGroupMembership[0], &isError);
961	>
962	>	if( isError ){
963
964	<	for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom);
965	<	cutoffAtom != NULL;
966	<	cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
967	<	mfact.push_back(cutoffAtom->getMass()/totalMass);
968	<	}
964	>	sprintf( painCave.errMsg,
965	>	"There was an error setting the simulation information in fortran.\n" );
966	>	painCave.isFatal = 1;
967	>	painCave.severity = OPENMD_ERROR;
968	>	simError();
969	>	}
970	>
971	>
972	>	sprintf( checkPointMsg,
973	>	"succesfully sent the simulation information to fortran.\n");
974	>
975	>	errorCheckPoint();
976	>
977	>	// Setup number of neighbors in neighbor list if present
978	>	if (simParams_->haveNeighborListNeighbors()) {
979	>	int nlistNeighbors = simParams_->getNeighborListNeighbors();
980	>	setNeighbors(&nlistNeighbors);
981	>	}
982	>
983	>
984	>	}
985	>
986	>
987	>	void SimInfo::setupFortranParallel() {
988	>	#ifdef IS_MPI
989	>	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
990	>	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
991	>	std::vector<int> localToGlobalCutoffGroupIndex;
992	>	SimInfo::MoleculeIterator mi;
993	>	Molecule::AtomIterator ai;
994	>	Molecule::CutoffGroupIterator ci;
995	>	Molecule* mol;
996	>	Atom* atom;
997	>	CutoffGroup* cg;
998	>	mpiSimData parallelData;
999	>	int isError;
1000	>
1001	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
1002	>
1003	>	//local index(index in DataStorge) of atom is important
1004	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
1005	>	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
1006	>	}
1007	>
1008	>	//local index of cutoff group is trivial, it only depends on the order of travesing
1009	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
1010	>	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
1011	>	}
1012	>
1013	>	}
1014	>
1015	>	//fill up mpiSimData struct
1016	>	parallelData.nMolGlobal = getNGlobalMolecules();
1017	>	parallelData.nMolLocal = getNMolecules();
1018	>	parallelData.nAtomsGlobal = getNGlobalAtoms();
1019	>	parallelData.nAtomsLocal = getNAtoms();
1020	>	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
1021	>	parallelData.nGroupsLocal = getNCutoffGroups();
1022	>	parallelData.myNode = worldRank;
1023	>	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
1024	>
1025	>	//pass mpiSimData struct and index arrays to fortran
1026	>	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
1027	>	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
1028	>	&localToGlobalCutoffGroupIndex[0], &isError);
1029	>
1030	>	if (isError) {
1031	>	sprintf(painCave.errMsg,
1032	>	"mpiRefresh errror: fortran didn't like something we gave it.\n");
1033	>	painCave.isFatal = 1;
1034	>	simError();
1035	>	}
1036	>
1037	>	sprintf(checkPointMsg, " mpiRefresh successful.\n");
1038	>	errorCheckPoint();
1039	>
1040	>	#endif
1041	>	}
1042	>
1043	>	void SimInfo::setupCutoff() {
1044	>
1045	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
1046	>
1047	>	// Check the cutoff policy
1048	>	int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
1049	>
1050	>	// Set LJ shifting bools to false
1051	>	ljsp_ = 0;
1052	>	ljsf_ = 0;
1053	>
1054	>	std::string myPolicy;
1055	>	if (forceFieldOptions_.haveCutoffPolicy()){
1056	>	myPolicy = forceFieldOptions_.getCutoffPolicy();
1057	>	}else if (simParams_->haveCutoffPolicy()) {
1058	>	myPolicy = simParams_->getCutoffPolicy();
1059	>	}
1060	>
1061	>	if (!myPolicy.empty()){
1062	>	toUpper(myPolicy);
1063	>	if (myPolicy == "MIX") {
1064	>	cp = MIX_CUTOFF_POLICY;
1065	>	} else {
1066	>	if (myPolicy == "MAX") {
1067	>	cp = MAX_CUTOFF_POLICY;
1068	>	} else {
1069	>	if (myPolicy == "TRADITIONAL") {
1070	>	cp = TRADITIONAL_CUTOFF_POLICY;
1071	>	} else {
1072	>	// throw error
1073	>	sprintf( painCave.errMsg,
1074	>	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
1075	>	painCave.isFatal = 1;
1076	>	simError();
1077	>	}
1078	>	}
1079	>	}
1080	>	}
1081	>	notifyFortranCutoffPolicy(&cp);
1082	>
1083	>	// Check the Skin Thickness for neighborlists
1084	>	RealType skin;
1085	>	if (simParams_->haveSkinThickness()) {
1086	>	skin = simParams_->getSkinThickness();
1087	>	notifyFortranSkinThickness(&skin);
1088	>	}
1089	>
1090	>	// Check if the cutoff was set explicitly:
1091	>	if (simParams_->haveCutoffRadius()) {
1092	>	rcut_ = simParams_->getCutoffRadius();
1093	>	if (simParams_->haveSwitchingRadius()) {
1094	>	rsw_  = simParams_->getSwitchingRadius();
1095	>	} else {
1096	>	if (fInfo_.SIM_uses_Charges |
1097	>	fInfo_.SIM_uses_Dipoles |
1098	>	fInfo_.SIM_uses_RF) {
1099	>
1100	>	rsw_ = 0.85 * rcut_;
1101	>	sprintf(painCave.errMsg,
1102	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
1103	>	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
1104	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1105	>	painCave.isFatal = 0;
1106	>	simError();
1107	>	} else {
1108	>	rsw_ = rcut_;
1109	>	sprintf(painCave.errMsg,
1110	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
1111	>	"\tOpenMD will use the same value as the cutoffRadius.\n"
1112	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1113	>	painCave.isFatal = 0;
1114	>	simError();
1115	>	}
1116	>	}
1117	>
1118	>	if (simParams_->haveElectrostaticSummationMethod()) {
1119	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1120	>	toUpper(myMethod);
1121	>
1122	>	if (myMethod == "SHIFTED_POTENTIAL") {
1123	>	ljsp_ = 1;
1124	>	} else if (myMethod == "SHIFTED_FORCE") {
1125	>	ljsf_ = 1;
1126	>	}
1127	>	}
1128	>
1129	>	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1130	>
1131	>	} else {
1132	>
1133	>	// For electrostatic atoms, we'll assume a large safe value:
1134	>	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1135	>	sprintf(painCave.errMsg,
1136	>	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1137	>	"\tOpenMD will use a default value of 15.0 angstroms"
1138	>	"\tfor the cutoffRadius.\n");
1139	>	painCave.isFatal = 0;
1140	>	simError();
1141	>	rcut_ = 15.0;
1142	>
1143	>	if (simParams_->haveElectrostaticSummationMethod()) {
1144	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1145	>	toUpper(myMethod);
1146	>
1147	>	// For the time being, we're tethering the LJ shifted behavior to the
1148	>	// electrostaticSummationMethod keyword options
1149	>	if (myMethod == "SHIFTED_POTENTIAL") {
1150	>	ljsp_ = 1;
1151	>	} else if (myMethod == "SHIFTED_FORCE") {
1152	>	ljsf_ = 1;
1153	>	}
1154	>	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1155	>	if (simParams_->haveSwitchingRadius()){
1156	>	sprintf(painCave.errMsg,
1157	>	"SimInfo Warning: A value was set for the switchingRadius\n"
1158	>	"\teven though the electrostaticSummationMethod was\n"
1159	>	"\tset to %s\n", myMethod.c_str());
1160	>	painCave.isFatal = 1;
1161	>	simError();
1162	>	}
1163	>	}
1164	>	}
1165	>
1166	>	if (simParams_->haveSwitchingRadius()){
1167	>	rsw_ = simParams_->getSwitchingRadius();
1168	>	} else {
1169	>	sprintf(painCave.errMsg,
1170	>	"SimCreator Warning: No value was set for switchingRadius.\n"
1171	>	"\tOpenMD will use a default value of\n"
1172	>	"\t0.85 * cutoffRadius for the switchingRadius\n");
1173	>	painCave.isFatal = 0;
1174	>	simError();
1175	>	rsw_ = 0.85 * rcut_;
1176	>	}
1177	>
1178	>	Electrostatic::setElectrostaticCutoffRadius(rcut_, rsw_);
1179	>	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1180	>
1181	>	} else {
1182	>	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1183	>	// We'll punt and let fortran figure out the cutoffs later.
1184	>
1185	>	notifyFortranYouAreOnYourOwn();
1186	>
1187	>	}
1188		}
1189		}
1190
1191	<	}
1191	>	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1192	>
1193	>	int errorOut;
1194	>	ElectrostaticSummationMethod esm = NONE;
1195	>	ElectrostaticScreeningMethod sm = UNDAMPED;
1196	>	RealType alphaVal;
1197	>	RealType dielectric;
1198	>
1199	>	errorOut = isError;
1200	>
1201	>	if (simParams_->haveElectrostaticSummationMethod()) {
1202	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1203	>	toUpper(myMethod);
1204	>	if (myMethod == "NONE") {
1205	>	esm = NONE;
1206	>	} else {
1207	>	if (myMethod == "SWITCHING_FUNCTION") {
1208	>	esm = SWITCHING_FUNCTION;
1209	>	} else {
1210	>	if (myMethod == "SHIFTED_POTENTIAL") {
1211	>	esm = SHIFTED_POTENTIAL;
1212	>	} else {
1213	>	if (myMethod == "SHIFTED_FORCE") {
1214	>	esm = SHIFTED_FORCE;
1215	>	} else {
1216	>	if (myMethod == "REACTION_FIELD") {
1217	>	esm = REACTION_FIELD;
1218	>	dielectric = simParams_->getDielectric();
1219	>	if (!simParams_->haveDielectric()) {
1220	>	// throw warning
1221	>	sprintf( painCave.errMsg,
1222	>	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1223	>	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1224	>	painCave.isFatal = 0;
1225	>	simError();
1226	>	}
1227	>	} else {
1228	>	// throw error
1229	>	sprintf( painCave.errMsg,
1230	>	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1231	>	"\t(Input file specified %s .)\n"
1232	>	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1233	>	"\t\"shifted_potential\", \"shifted_force\", or \n"
1234	>	"\t\"reaction_field\".\n", myMethod.c_str() );
1235	>	painCave.isFatal = 1;
1236	>	simError();
1237	>	}
1238	>	}
1239	>	}
1240	>	}
1241	>	}
1242	>	}
1243	>
1244	>	if (simParams_->haveElectrostaticScreeningMethod()) {
1245	>	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1246	>	toUpper(myScreen);
1247	>	if (myScreen == "UNDAMPED") {
1248	>	sm = UNDAMPED;
1249	>	} else {
1250	>	if (myScreen == "DAMPED") {
1251	>	sm = DAMPED;
1252	>	if (!simParams_->haveDampingAlpha()) {
1253	>	// first set a cutoff dependent alpha value
1254	>	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1255	>	alphaVal = 0.5125 - rcut_* 0.025;
1256	>	// for values rcut > 20.5, alpha is zero
1257	>	if (alphaVal < 0) alphaVal = 0;
1258	>
1259	>	// throw warning
1260	>	sprintf( painCave.errMsg,
1261	>	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1262	>	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1263	>	painCave.isFatal = 0;
1264	>	simError();
1265	>	} else {
1266	>	alphaVal = simParams_->getDampingAlpha();
1267	>	}
1268	>
1269	>	} else {
1270	>	// throw error
1271	>	sprintf( painCave.errMsg,
1272	>	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1273	>	"\t(Input file specified %s .)\n"
1274	>	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1275	>	"or \"damped\".\n", myScreen.c_str() );
1276	>	painCave.isFatal = 1;
1277	>	simError();
1278	>	}
1279	>	}
1280	>	}
1281	>
1282	>
1283	>	Electrostatic::setElectrostaticSummationMethod( esm );
1284	>	Electrostatic::setElectrostaticScreeningMethod( sm );
1285	>	Electrostatic::setDampingAlpha( alphaVal );
1286	>	Electrostatic::setReactionFieldDielectric( dielectric );
1287	>	initFortranFF( &errorOut );
1288	>	}
1289	>
1290	>	void SimInfo::setupSwitchingFunction() {
1291	>	int ft = CUBIC;
1292	>
1293	>	if (simParams_->haveSwitchingFunctionType()) {
1294	>	std::string funcType = simParams_->getSwitchingFunctionType();
1295	>	toUpper(funcType);
1296	>	if (funcType == "CUBIC") {
1297	>	ft = CUBIC;
1298	>	} else {
1299	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1300	>	ft = FIFTH_ORDER_POLY;
1301	>	} else {
1302	>	// throw error
1303	>	sprintf( painCave.errMsg,
1304	>	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1305	>	painCave.isFatal = 1;
1306	>	simError();
1307	>	}
1308	>	}
1309	>	}
1310	>
1311	>	// send switching function notification to switcheroo
1312	>	setFunctionType(&ft);
1313	>
1314	>	}
1315	>
1316	>	void SimInfo::setupAccumulateBoxDipole() {
1317	>
1318	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1319	>	if ( simParams_->haveAccumulateBoxDipole() )
1320	>	if ( simParams_->getAccumulateBoxDipole() ) {
1321	>	setAccumulateBoxDipole();
1322	>	calcBoxDipole_ = true;
1323	>	}
1324	>
1325	>	}
1326	>
1327	>	void SimInfo::addProperty(GenericData* genData) {
1328	>	properties_.addProperty(genData);
1329	>	}
1330	>
1331	>	void SimInfo::removeProperty(const std::string& propName) {
1332	>	properties_.removeProperty(propName);
1333	>	}
1334	>
1335	>	void SimInfo::clearProperties() {
1336	>	properties_.clearProperties();
1337	>	}
1338	>
1339	>	std::vector<std::string> SimInfo::getPropertyNames() {
1340	>	return properties_.getPropertyNames();
1341	>	}
1342	>
1343	>	std::vector<GenericData*> SimInfo::getProperties() {
1344	>	return properties_.getProperties();
1345	>	}
1346	>
1347	>	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1348	>	return properties_.getPropertyByName(propName);
1349	>	}
1350	>
1351	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1352	>	if (sman_ == sman) {
1353	>	return;
1354	>	}
1355	>	delete sman_;
1356	>	sman_ = sman;
1357	>
1358	>	Molecule* mol;
1359	>	RigidBody* rb;
1360	>	Atom* atom;
1361	>	SimInfo::MoleculeIterator mi;
1362	>	Molecule::RigidBodyIterator rbIter;
1363	>	Molecule::AtomIterator atomIter;;
1364	>
1365	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1366	>
1367	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1368	>	atom->setSnapshotManager(sman_);
1369	>	}
1370	>
1371	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1372	>	rb->setSnapshotManager(sman_);
1373	>	}
1374	>	}
1375	>
1376	>	}
1377	>
1378	>	Vector3d SimInfo::getComVel(){
1379	>	SimInfo::MoleculeIterator i;
1380	>	Molecule* mol;
1381	>
1382	>	Vector3d comVel(0.0);
1383	>	RealType totalMass = 0.0;
1384	>
1385	>
1386	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1387	>	RealType mass = mol->getMass();
1388	>	totalMass += mass;
1389	>	comVel += mass * mol->getComVel();
1390	>	}
1391	>
1392	>	#ifdef IS_MPI
1393	>	RealType tmpMass = totalMass;
1394	>	Vector3d tmpComVel(comVel);
1395	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1396	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1397	>	#endif
1398	>
1399	>	comVel /= totalMass;
1400	>
1401	>	return comVel;
1402	>	}
1403	>
1404	>	Vector3d SimInfo::getCom(){
1405	>	SimInfo::MoleculeIterator i;
1406	>	Molecule* mol;
1407	>
1408	>	Vector3d com(0.0);
1409	>	RealType totalMass = 0.0;
1410	>
1411	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1412	>	RealType mass = mol->getMass();
1413	>	totalMass += mass;
1414	>	com += mass * mol->getCom();
1415	>	}
1416	>
1417	>	#ifdef IS_MPI
1418	>	RealType tmpMass = totalMass;
1419	>	Vector3d tmpCom(com);
1420	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1421	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1422	>	#endif
1423	>
1424	>	com /= totalMass;
1425	>
1426	>	return com;
1427	>
1428	>	}
1429	>
1430	>	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1431	>
1432	>	return o;
1433	>	}
1434	>
1435	>
1436	>	/*
1437	>	Returns center of mass and center of mass velocity in one function call.
1438	>	*/
1439	>
1440	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1441	>	SimInfo::MoleculeIterator i;
1442	>	Molecule* mol;
1443	>
1444	>
1445	>	RealType totalMass = 0.0;
1446	>
1447	>
1448	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1449	>	RealType mass = mol->getMass();
1450	>	totalMass += mass;
1451	>	com += mass * mol->getCom();
1452	>	comVel += mass * mol->getComVel();
1453	>	}
1454	>
1455	>	#ifdef IS_MPI
1456	>	RealType tmpMass = totalMass;
1457	>	Vector3d tmpCom(com);
1458	>	Vector3d tmpComVel(comVel);
1459	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1460	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1461	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1462	>	#endif
1463	>
1464	>	com /= totalMass;
1465	>	comVel /= totalMass;
1466	>	}
1467	>
1468	>	/*
1469	>	Return intertia tensor for entire system and angular momentum Vector.
1470	>
1471	>
1472	>	[  Ixx -Ixy  -Ixz ]
1473	>	J =| -Iyx  Iyy  -Iyz |
1474	>	[ -Izx -Iyz   Izz ]
1475	>	*/
1476	>
1477	>	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1478	>
1479	>
1480	>	RealType xx = 0.0;
1481	>	RealType yy = 0.0;
1482	>	RealType zz = 0.0;
1483	>	RealType xy = 0.0;
1484	>	RealType xz = 0.0;
1485	>	RealType yz = 0.0;
1486	>	Vector3d com(0.0);
1487	>	Vector3d comVel(0.0);
1488	>
1489	>	getComAll(com, comVel);
1490	>
1491	>	SimInfo::MoleculeIterator i;
1492	>	Molecule* mol;
1493	>
1494	>	Vector3d thisq(0.0);
1495	>	Vector3d thisv(0.0);
1496	>
1497	>	RealType thisMass = 0.0;
1498	>
1499	>
1500	>
1501	>
1502	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1503	>
1504	>	thisq = mol->getCom()-com;
1505	>	thisv = mol->getComVel()-comVel;
1506	>	thisMass = mol->getMass();
1507	>	// Compute moment of intertia coefficients.
1508	>	xx += thisq[0]*thisq[0]*thisMass;
1509	>	yy += thisq[1]*thisq[1]*thisMass;
1510	>	zz += thisq[2]*thisq[2]*thisMass;
1511	>
1512	>	// compute products of intertia
1513	>	xy += thisq[0]*thisq[1]*thisMass;
1514	>	xz += thisq[0]*thisq[2]*thisMass;
1515	>	yz += thisq[1]*thisq[2]*thisMass;
1516	>
1517	>	angularMomentum += cross( thisq, thisv ) * thisMass;
1518	>
1519	>	}
1520	>
1521	>
1522	>	inertiaTensor(0,0) = yy + zz;
1523	>	inertiaTensor(0,1) = -xy;
1524	>	inertiaTensor(0,2) = -xz;
1525	>	inertiaTensor(1,0) = -xy;
1526	>	inertiaTensor(1,1) = xx + zz;
1527	>	inertiaTensor(1,2) = -yz;
1528	>	inertiaTensor(2,0) = -xz;
1529	>	inertiaTensor(2,1) = -yz;
1530	>	inertiaTensor(2,2) = xx + yy;
1531	>
1532	>	#ifdef IS_MPI
1533	>	Mat3x3d tmpI(inertiaTensor);
1534	>	Vector3d tmpAngMom;
1535	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1536	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1537	>	#endif
1538	>
1539	>	return;
1540	>	}
1541	>
1542	>	//Returns the angular momentum of the system
1543	>	Vector3d SimInfo::getAngularMomentum(){
1544	>
1545	>	Vector3d com(0.0);
1546	>	Vector3d comVel(0.0);
1547	>	Vector3d angularMomentum(0.0);
1548	>
1549	>	getComAll(com,comVel);
1550	>
1551	>	SimInfo::MoleculeIterator i;
1552	>	Molecule* mol;
1553	>
1554	>	Vector3d thisr(0.0);
1555	>	Vector3d thisp(0.0);
1556	>
1557	>	RealType thisMass;
1558	>
1559	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1560	>	thisMass = mol->getMass();
1561	>	thisr = mol->getCom()-com;
1562	>	thisp = (mol->getComVel()-comVel)*thisMass;
1563	>
1564	>	angularMomentum += cross( thisr, thisp );
1565	>
1566	>	}
1567	>
1568	>	#ifdef IS_MPI
1569	>	Vector3d tmpAngMom;
1570	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1571	>	#endif
1572	>
1573	>	return angularMomentum;
1574	>	}
1575	>
1576	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1577	>	return IOIndexToIntegrableObject.at(index);
1578	>	}
1579	>
1580	>	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1581	>	IOIndexToIntegrableObject= v;
1582	>	}
1583	>
1584	>	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1585	>	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1586	>	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1587	>	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1588	>	*/
1589	>	void SimInfo::getGyrationalVolume(RealType &volume){
1590	>	Mat3x3d intTensor;
1591	>	RealType det;
1592	>	Vector3d dummyAngMom;
1593	>	RealType sysconstants;
1594	>	RealType geomCnst;
1595	>
1596	>	geomCnst = 3.0/2.0;
1597	>	/* Get the inertial tensor and angular momentum for free*/
1598	>	getInertiaTensor(intTensor,dummyAngMom);
1599	>
1600	>	det = intTensor.determinant();
1601	>	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1602	>	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1603	>	return;
1604	>	}
1605	>
1606	>	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1607	>	Mat3x3d intTensor;
1608	>	Vector3d dummyAngMom;
1609	>	RealType sysconstants;
1610	>	RealType geomCnst;
1611	>
1612	>	geomCnst = 3.0/2.0;
1613	>	/* Get the inertial tensor and angular momentum for free*/
1614	>	getInertiaTensor(intTensor,dummyAngMom);
1615	>
1616	>	detI = intTensor.determinant();
1617	>	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1618	>	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1619	>	return;
1620	>	}
1621	>	/*
1622	>	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1623	>	assert( v.size() == nAtoms_ + nRigidBodies_);
1624	>	sdByGlobalIndex_ = v;
1625	>	}
1626	>
1627	>	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1628	>	//assert(index < nAtoms_ + nRigidBodies_);
1629	>	return sdByGlobalIndex_.at(index);
1630	>	}
1631	>	*/
1632	>	}//end namespace OpenMD
1633	>

Comparing:
trunk/src/brains/SimInfo.cpp (property svn:keywords), Revision 143 by chrisfen, Fri Oct 22 22:54:01 2004 UTC vs.
branches/development/src/brains/SimInfo.cpp (property svn:keywords), Revision 1505 by gezelter, Sun Oct 3 22:18:59 2010 UTC

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