ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

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

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 143 by chrisfen, Fri Oct 22 22:54:01 2004 UTC vs.
Revision 1290 by cli2, Wed Sep 10 19:51:45 2008 UTC

#	Line 1 | Line 1
1	<	#include <stdlib.h>
2	<	#include <string.h>
3	<	#include <math.h>
1	>	/*
2	>	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	>	*
4	>	* The University of Notre Dame grants you ("Licensee") a
5	>	* non-exclusive, royalty free, license to use, modify and
6	>	* redistribute this software in source and binary code form, provided
7	>	* that the following conditions are met:
8	>	*
9	>	* 1. Acknowledgement of the program authors must be made in any
10	>	*    publication of scientific results based in part on use of the
11	>	*    program.  An acceptable form of acknowledgement is citation of
12	>	*    the article in which the program was described (Matthew
13	>	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	>	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	>	*    Parallel Simulation Engine for Molecular Dynamics,"
16	>	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	>	*
18	>	* 2. Redistributions of source code must retain the above copyright
19	>	*    notice, this list of conditions and the following disclaimer.
20	>	*
21	>	* 3. Redistributions in binary form must reproduce the above copyright
22	>	*    notice, this list of conditions and the following disclaimer in the
23	>	*    documentation and/or other materials provided with the
24	>	*    distribution.
25	>	*
26	>	* This software is provided "AS IS," without a warranty of any
27	>	* kind. All express or implied conditions, representations and
28	>	* warranties, including any implied warranty of merchantability,
29	>	* fitness for a particular purpose or non-infringement, are hereby
30	>	* excluded.  The University of Notre Dame and its licensors shall not
31	>	* be liable for any damages suffered by licensee as a result of
32	>	* using, modifying or distributing the software or its
33	>	* derivatives. In no event will the University of Notre Dame or its
34	>	* licensors be liable for any lost revenue, profit or data, or for
35	>	* direct, indirect, special, consequential, incidental or punitive
36	>	* damages, however caused and regardless of the theory of liability,
37	>	* arising out of the use of or inability to use software, even if the
38	>	* University of Notre Dame has been advised of the possibility of
39	>	* such damages.
40	>	*/
41	>
42	>	/**
43	>	* @file SimInfo.cpp
44	>	* @author    tlin
45	>	* @date  11/02/2004
46	>	* @version 1.0
47	>	*/
48
49	<	#include <iostream>
50	<	using namespace std;
49	>	#include <algorithm>
50	>	#include <set>
51	>	#include <map>
52
53		#include "brains/SimInfo.hpp"
54	<	#define __C
55	<	#include "brains/fSimulation.h"
54	>	#include "math/Vector3.hpp"
55	>	#include "primitives/Molecule.hpp"
56	>	#include "primitives/StuntDouble.hpp"
57	>	#include "UseTheForce/fCutoffPolicy.h"
58	>	#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
59	>	#include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h"
60	>	#include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
61	>	#include "UseTheForce/doForces_interface.h"
62	>	#include "UseTheForce/DarkSide/neighborLists_interface.h"
63	>	#include "UseTheForce/DarkSide/electrostatic_interface.h"
64	>	#include "UseTheForce/DarkSide/switcheroo_interface.h"
65	>	#include "utils/MemoryUtils.hpp"
66		#include "utils/simError.h"
67	<	#include "UseTheForce/DarkSide/simulation_interface.h"
68	<	#include "UseTheForce/notifyCutoffs_interface.h"
67	>	#include "selection/SelectionManager.hpp"
68	>	#include "io/ForceFieldOptions.hpp"
69	>	#include "UseTheForce/ForceField.hpp"
70
15	–	//#include "UseTheForce/fortranWrappers.hpp"
71
17	–	#include "math/MatVec3.h"
18	–
72		#ifdef IS_MPI
73	<	#include "brains/mpiSimulation.hpp"
74	<	#endif
73	>	#include "UseTheForce/mpiComponentPlan.h"
74	>	#include "UseTheForce/DarkSide/simParallel_interface.h"
75	>	#endif
76
77	<	inline double roundMe( double x ){
78	<	return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
79	<	}
80	<
81	<	inline double min( double a, double b ){
82	<	return (a < b ) ? a : b;
83	<	}
77	>	namespace oopse {
78	>	std::set<int> getRigidSet(int index, std::map<int, std::set<int> >& container) {
79	>	std::map<int, std::set<int> >::iterator i = container.find(index);
80	>	std::set<int> result;
81	>	if (i != container.end()) {
82	>	result = i->second;
83	>	}
84
85	<	SimInfo* currentInfo;
86	<
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;
85	>	return result;
86	>	}
87
88	<	resetTime = 1e99;
88	>	SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
89	>	forceField_(ff), simParams_(simParams),
90	>	ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
91	>	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
92	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
93	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nInversions_(0),
94	>	nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0),
95	>	nConstraints_(0), sman_(NULL), fortranInitialized_(false),
96	>	calcBoxDipole_(false), useAtomicVirial_(true) {
97
55	–	orthoRhombic = 0;
56	–	orthoTolerance = 1E-6;
57	–	useInitXSstate = true;
98
99	<	usePBC = 0;
100	<	useDirectionalAtoms = 0;
101	<	useLennardJones = 0;
102	<	useElectrostatics = 0;
103	<	useCharges = 0;
104	<	useDipoles = 0;
105	<	useSticky = 0;
66	<	useGayBerne = 0;
67	<	useEAM = 0;
68	<	useShapes = 0;
69	<	useFLARB = 0;
99	>	MoleculeStamp* molStamp;
100	>	int nMolWithSameStamp;
101	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
102	>	int nGroups = 0;      //total cutoff groups defined in meta-data file
103	>	CutoffGroupStamp* cgStamp;
104	>	RigidBodyStamp* rbStamp;
105	>	int nRigidAtoms = 0;
106
107	<	useSolidThermInt = 0;
108	<	useLiquidThermInt = 0;
107	>	std::vector<Component*> components = simParams->getComponents();
108	>
109	>	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
110	>	molStamp = (*i)->getMoleculeStamp();
111	>	nMolWithSameStamp = (*i)->getNMol();
112	>
113	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
114
115	<	haveCutoffGroups = false;
115	>	//calculate atoms in molecules
116	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
117
118	<	excludes = Exclude::Instance();
118	>	//calculate atoms in cutoff groups
119	>	int nAtomsInGroups = 0;
120	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
121	>
122	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
123	>	cgStamp = molStamp->getCutoffGroupStamp(j);
124	>	nAtomsInGroups += cgStamp->getNMembers();
125	>	}
126
127	<	myConfiguration = new SimState();
127	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
128
129	<	has_minimizer = false;
81	<	the_minimizer =NULL;
129	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
130
131	<	ngroup = 0;
131	>	//calculate atoms in rigid bodies
132	>	int nAtomsInRigidBodies = 0;
133	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
134	>
135	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
136	>	rbStamp = molStamp->getRigidBodyStamp(j);
137	>	nAtomsInRigidBodies += rbStamp->getNMembers();
138	>	}
139
140	<	}
140	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
141	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
142	>
143	>	}
144
145	+	//every free atom (atom does not belong to cutoff groups) is a cutoff
146	+	//group therefore the total number of cutoff groups in the system is
147	+	//equal to the total number of atoms minus number of atoms belong to
148	+	//cutoff group defined in meta-data file plus the number of cutoff
149	+	//groups defined in meta-data file
150	+	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
151
152	<	SimInfo::~SimInfo(){
153	<
154	<	delete myConfiguration;
155	<
156	<	map<string, GenericData*>::iterator i;
152	>	//every free atom (atom does not belong to rigid bodies) is an
153	>	//integrable object therefore the total number of integrable objects
154	>	//in the system is equal to the total number of atoms minus number of
155	>	//atoms belong to rigid body defined in meta-data file plus the number
156	>	//of rigid bodies defined in meta-data file
157	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
158	>	+ nGlobalRigidBodies_;
159
160	<	for(i = properties.begin(); i != properties.end(); i++)
161	<	delete (*i).second;
160	>	nGlobalMols_ = molStampIds_.size();
161	>	molToProcMap_.resize(nGlobalMols_);
162	>	}
163
164	<	}
164	>	SimInfo::~SimInfo() {
165	>	std::map<int, Molecule*>::iterator i;
166	>	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
167	>	delete i->second;
168	>	}
169	>	molecules_.clear();
170	>
171	>	delete sman_;
172	>	delete simParams_;
173	>	delete forceField_;
174	>	}
175
176	<	void SimInfo::setBox(double newBox[3]) {
177	<
178	<	int i, j;
179	<	double tempMat[3][3];
176	>	int SimInfo::getNGlobalConstraints() {
177	>	int nGlobalConstraints;
178	>	#ifdef IS_MPI
179	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
180	>	MPI_COMM_WORLD);
181	>	#else
182	>	nGlobalConstraints =  nConstraints_;
183	>	#endif
184	>	return nGlobalConstraints;
185	>	}
186
187	<	for(i=0; i<3; i++)
188	<	for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
187	>	bool SimInfo::addMolecule(Molecule* mol) {
188	>	MoleculeIterator i;
189
190	<	tempMat[0][0] = newBox[0];
191	<	tempMat[1][1] = newBox[1];
109	<	tempMat[2][2] = newBox[2];
190	>	i = molecules_.find(mol->getGlobalIndex());
191	>	if (i == molecules_.end() ) {
192
193	<	setBoxM( tempMat );
193	>	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
194	>
195	>	nAtoms_ += mol->getNAtoms();
196	>	nBonds_ += mol->getNBonds();
197	>	nBends_ += mol->getNBends();
198	>	nTorsions_ += mol->getNTorsions();
199	>	nInversions_ += mol->getNInversions();
200	>	nRigidBodies_ += mol->getNRigidBodies();
201	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
202	>	nCutoffGroups_ += mol->getNCutoffGroups();
203	>	nConstraints_ += mol->getNConstraintPairs();
204
205	<	}
114	<
115	<	void SimInfo::setBoxM( double theBox[3][3] ){
205	>	addInteractionPairs(mol);
206
207	<	int i, j;
208	<	double FortranHmat[9]; // to preserve compatibility with Fortran the
209	<	// ordering in the array is as follows:
210	<	// [ 0 3 6 ]
211	<	// [ 1 4 7 ]
122	<	// [ 2 5 8 ]
123	<	double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
207	>	return true;
208	>	} else {
209	>	return false;
210	>	}
211	>	}
212
213	<	if( !boxIsInit ) boxIsInit = 1;
213	>	bool SimInfo::removeMolecule(Molecule* mol) {
214	>	MoleculeIterator i;
215	>	i = molecules_.find(mol->getGlobalIndex());
216
217	<	for(i=0; i < 3; i++)
128	<	for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
129	<
130	<	calcBoxL();
131	<	calcHmatInv();
217	>	if (i != molecules_.end() ) {
218
219	<	for(i=0; i < 3; i++) {
220	<	for (j=0; j < 3; j++) {
221	<	FortranHmat[3*j + i] = Hmat[i][j];
222	<	FortranHmatInv[3*j + i] = HmatInv[i][j];
223	<	}
224	<	}
219	>	assert(mol == i->second);
220	>
221	>	nAtoms_ -= mol->getNAtoms();
222	>	nBonds_ -= mol->getNBonds();
223	>	nBends_ -= mol->getNBends();
224	>	nTorsions_ -= mol->getNTorsions();
225	>	nInversions_ -= mol->getNInversions();
226	>	nRigidBodies_ -= mol->getNRigidBodies();
227	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
228	>	nCutoffGroups_ -= mol->getNCutoffGroups();
229	>	nConstraints_ -= mol->getNConstraintPairs();
230
231	<	setFortranBox(FortranHmat, FortranHmatInv, &orthoRhombic);
232	<
142	<	}
143	<
231	>	removeInteractionPairs(mol);
232	>	molecules_.erase(mol->getGlobalIndex());
233
234	<	void SimInfo::getBoxM (double theBox[3][3]) {
234	>	delete mol;
235	>
236	>	return true;
237	>	} else {
238	>	return false;
239	>	}
240
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	–	}
241
242	+	}
243
244	<	void SimInfo::scaleBox(double scale) {
245	<	double theBox[3][3];
246	<	int i, j;
244	>
245	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
246	>	i = molecules_.begin();
247	>	return i == molecules_.end() ? NULL : i->second;
248	>	}
249
250	<	// cerr << "Scaling box by " << scale << "\n";
250	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
251	>	++i;
252	>	return i == molecules_.end() ? NULL : i->second;
253	>	}
254
159	–	for(i=0; i<3; i++)
160	–	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
255
256	<	setBoxM(theBox);
256	>	void SimInfo::calcNdf() {
257	>	int ndf_local;
258	>	MoleculeIterator i;
259	>	std::vector<StuntDouble*>::iterator j;
260	>	Molecule* mol;
261	>	StuntDouble* integrableObject;
262
263	<	}
263	>	ndf_local = 0;
264	>
265	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
266	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
267	>	integrableObject = mol->nextIntegrableObject(j)) {
268
269	<	void SimInfo::calcHmatInv( void ) {
167	<
168	<	int oldOrtho;
169	<	int i,j;
170	<	double smallDiag;
171	<	double tol;
172	<	double sanity[3][3];
269	>	ndf_local += 3;
270
271	<	invertMat3( Hmat, HmatInv );
272	<
273	<	// check to see if Hmat is orthorhombic
274	<
275	<	oldOrtho = orthoRhombic;
276	<
277	<	smallDiag = fabs(Hmat[0][0]);
278	<	if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
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	<	}
271	>	if (integrableObject->isDirectional()) {
272	>	if (integrableObject->isLinear()) {
273	>	ndf_local += 2;
274	>	} else {
275	>	ndf_local += 3;
276	>	}
277	>	}
278	>
279		}
280		}
195	–	}
196	–
197	–	if( oldOrtho != orthoRhombic ){
281
282	<	if( orthoRhombic ) {
283	<	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	<	}
282	>	// n_constraints is local, so subtract them on each processor
283	>	ndf_local -= nConstraints_;
284
285	<	void SimInfo::calcBoxL( void ){
285	>	#ifdef IS_MPI
286	>	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
287	>	#else
288	>	ndf_ = ndf_local;
289	>	#endif
290
291	<	double dx, dy, dz, dsq;
291	>	// nZconstraints_ is global, as are the 3 COM translations for the
292	>	// entire system:
293	>	ndf_ = ndf_ - 3 - nZconstraint_;
294
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	–
295		}
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	–	}
296
297	<
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	<
297	>	int SimInfo::getFdf() {
298		#ifdef IS_MPI
299	<	MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
299	>	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
300		#else
301	<	ndf = ndf_local;
301	>	fdf_ = fdf_local;
302		#endif
303	+	return fdf_;
304	+	}
305	+
306	+	void SimInfo::calcNdfRaw() {
307	+	int ndfRaw_local;
308
309	<	// nZconstraints is global, as are the 3 COM translations for the
310	<	// entire system:
309	>	MoleculeIterator i;
310	>	std::vector<StuntDouble*>::iterator j;
311	>	Molecule* mol;
312	>	StuntDouble* integrableObject;
313
314	<	ndf = ndf - 3 - nZconstraints;
314	>	// Raw degrees of freedom that we have to set
315	>	ndfRaw_local = 0;
316	>
317	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
318	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
319	>	integrableObject = mol->nextIntegrableObject(j)) {
320
321	<	return ndf;
365	<	}
321	>	ndfRaw_local += 3;
322
323	<	int SimInfo::getNDFraw() {
324	<	int ndfRaw_local;
325	<
326	<	// Raw degrees of freedom that we have to set
327	<	ndfRaw_local = 0;
328	<
329	<	for(int i = 0; i < integrableObjects.size(); i++){
330	<	ndfRaw_local += 3;
331	<	if (integrableObjects[i]->isDirectional()) {
376	<	if (integrableObjects[i]->isLinear())
377	<	ndfRaw_local += 2;
378	<	else
379	<	ndfRaw_local += 3;
323	>	if (integrableObject->isDirectional()) {
324	>	if (integrableObject->isLinear()) {
325	>	ndfRaw_local += 2;
326	>	} else {
327	>	ndfRaw_local += 3;
328	>	}
329	>	}
330	>
331	>	}
332		}
381	–	}
333
334		#ifdef IS_MPI
335	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
335	>	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
336		#else
337	<	ndfRaw = ndfRaw_local;
337	>	ndfRaw_ = ndfRaw_local;
338		#endif
339	+	}
340
341	<	return ndfRaw;
342	<	}
341	>	void SimInfo::calcNdfTrans() {
342	>	int ndfTrans_local;
343
344	<	int SimInfo::getNDFtranslational() {
393	<	int ndfTrans_local;
344	>	ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
345
395	–	ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
346
397	–
347		#ifdef IS_MPI
348	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
348	>	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
349		#else
350	<	ndfTrans = ndfTrans_local;
350	>	ndfTrans_ = ndfTrans_local;
351		#endif
352
353	<	ndfTrans = ndfTrans - 3 - nZconstraints;
353	>	ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
354	>
355	>	}
356
357	<	return ndfTrans;
358	<	}
357	>	void SimInfo::addInteractionPairs(Molecule* mol) {
358	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
359	>	std::vector<Bond*>::iterator bondIter;
360	>	std::vector<Bend*>::iterator bendIter;
361	>	std::vector<Torsion*>::iterator torsionIter;
362	>	std::vector<Inversion*>::iterator inversionIter;
363	>	Bond* bond;
364	>	Bend* bend;
365	>	Torsion* torsion;
366	>	Inversion* inversion;
367	>	int a;
368	>	int b;
369	>	int c;
370	>	int d;
371
372	<	int SimInfo::getTotIntegrableObjects() {
373	<	int nObjs_local;
374	<	int nObjs;
372	>	// atomGroups can be used to add special interaction maps between
373	>	// groups of atoms that are in two separate rigid bodies.
374	>	// However, most site-site interactions between two rigid bodies
375	>	// are probably not special, just the ones between the physically
376	>	// bonded atoms.  Interactions *within* a single rigid body should
377	>	// always be excluded.  These are done at the bottom of this
378	>	// function.
379
380	<	nObjs_local =  integrableObjects.size();
380	>	std::map<int, std::set<int> > atomGroups;
381	>	Molecule::RigidBodyIterator rbIter;
382	>	RigidBody* rb;
383	>	Molecule::IntegrableObjectIterator ii;
384	>	StuntDouble* integrableObject;
385	>
386	>	for (integrableObject = mol->beginIntegrableObject(ii);
387	>	integrableObject != NULL;
388	>	integrableObject = mol->nextIntegrableObject(ii)) {
389	>
390	>	if (integrableObject->isRigidBody()) {
391	>	rb = static_cast<RigidBody*>(integrableObject);
392	>	std::vector<Atom*> atoms = rb->getAtoms();
393	>	std::set<int> rigidAtoms;
394	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
395	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
396	>	}
397	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
398	>	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
399	>	}
400	>	} else {
401	>	std::set<int> oneAtomSet;
402	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
403	>	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
404	>	}
405	>	}
406	>
407	>	for (bond= mol->beginBond(bondIter); bond != NULL;
408	>	bond = mol->nextBond(bondIter)) {
409
410	+	a = bond->getAtomA()->getGlobalIndex();
411	+	b = bond->getAtomB()->getGlobalIndex();
412	+
413	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
414	+	oneTwoInteractions_.addPair(a, b);
415	+	} else {
416	+	excludedInteractions_.addPair(a, b);
417	+	}
418	+	}
419
420	<	#ifdef IS_MPI
421	<	MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
418	<	#else
419	<	nObjs = nObjs_local;
420	<	#endif
420	>	for (bend= mol->beginBend(bendIter); bend != NULL;
421	>	bend = mol->nextBend(bendIter)) {
422
423	+	a = bend->getAtomA()->getGlobalIndex();
424	+	b = bend->getAtomB()->getGlobalIndex();
425	+	c = bend->getAtomC()->getGlobalIndex();
426	+
427	+	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
428	+	oneTwoInteractions_.addPair(a, b);
429	+	oneTwoInteractions_.addPair(b, c);
430	+	} else {
431	+	excludedInteractions_.addPair(a, b);
432	+	excludedInteractions_.addPair(b, c);
433	+	}
434
435	<	return nObjs;
436	<	}
435	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
436	>	oneThreeInteractions_.addPair(a, c);
437	>	} else {
438	>	excludedInteractions_.addPair(a, c);
439	>	}
440	>	}
441
442	<	void SimInfo::refreshSim(){
442	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
443	>	torsion = mol->nextTorsion(torsionIter)) {
444
445	<	simtype fInfo;
446	<	int isError;
447	<	int n_global;
448	<	int* excl;
445	>	a = torsion->getAtomA()->getGlobalIndex();
446	>	b = torsion->getAtomB()->getGlobalIndex();
447	>	c = torsion->getAtomC()->getGlobalIndex();
448	>	d = torsion->getAtomD()->getGlobalIndex();
449
450	<	fInfo.dielect = 0.0;
450	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
451	>	oneTwoInteractions_.addPair(a, b);
452	>	oneTwoInteractions_.addPair(b, c);
453	>	oneTwoInteractions_.addPair(c, d);
454	>	} else {
455	>	excludedInteractions_.addPair(a, b);
456	>	excludedInteractions_.addPair(b, c);
457	>	excludedInteractions_.addPair(c, d);
458	>	}
459
460	<	if( useDipoles ){
461	<	if( useReactionField )fInfo.dielect = dielectric;
462	<	}
460	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
461	>	oneThreeInteractions_.addPair(a, c);
462	>	oneThreeInteractions_.addPair(b, d);
463	>	} else {
464	>	excludedInteractions_.addPair(a, c);
465	>	excludedInteractions_.addPair(b, d);
466	>	}
467
468	<	fInfo.SIM_uses_PBC = usePBC;
468	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
469	>	oneFourInteractions_.addPair(a, d);
470	>	} else {
471	>	excludedInteractions_.addPair(a, d);
472	>	}
473	>	}
474
475	<	if (useSticky || useDipoles || useGayBerne || useShapes) {
476	<	useDirectionalAtoms = 1;
443	<	fInfo.SIM_uses_DirectionalAtoms = useDirectionalAtoms;
444	<	}
475	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
476	>	inversion = mol->nextInversion(inversionIter)) {
477
478	<	fInfo.SIM_uses_LennardJones = useLennardJones;
478	>	a = inversion->getAtomA()->getGlobalIndex();
479	>	b = inversion->getAtomB()->getGlobalIndex();
480	>	c = inversion->getAtomC()->getGlobalIndex();
481	>	d = inversion->getAtomD()->getGlobalIndex();
482
483	<	if (useCharges || useDipoles) {
484	<	useElectrostatics = 1;
485	<	fInfo.SIM_uses_Electrostatics = useElectrostatics;
486	<	}
483	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
484	>	oneTwoInteractions_.addPair(a, b);
485	>	oneTwoInteractions_.addPair(a, c);
486	>	oneTwoInteractions_.addPair(a, d);
487	>	} else {
488	>	excludedInteractions_.addPair(a, b);
489	>	excludedInteractions_.addPair(a, c);
490	>	excludedInteractions_.addPair(a, d);
491	>	}
492
493	<	fInfo.SIM_uses_Charges = useCharges;
494	<	fInfo.SIM_uses_Dipoles = useDipoles;
495	<	fInfo.SIM_uses_Sticky = useSticky;
496	<	fInfo.SIM_uses_GayBerne = useGayBerne;
497	<	fInfo.SIM_uses_EAM = useEAM;
498	<	fInfo.SIM_uses_Shapes = useShapes;
499	<	fInfo.SIM_uses_FLARB = useFLARB;
500	<	fInfo.SIM_uses_RF = useReactionField;
493	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
494	>	oneThreeInteractions_.addPair(b, c);
495	>	oneThreeInteractions_.addPair(b, d);
496	>	oneThreeInteractions_.addPair(c, d);
497	>	} else {
498	>	excludedInteractions_.addPair(b, c);
499	>	excludedInteractions_.addPair(b, d);
500	>	excludedInteractions_.addPair(c, d);
501	>	}
502	>	}
503
504	<	n_exclude = excludes->getSize();
505	<	excl = excludes->getFortranArray();
504	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
505	>	rb = mol->nextRigidBody(rbIter)) {
506	>	std::vector<Atom*> atoms = rb->getAtoms();
507	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
508	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
509	>	a = atoms[i]->getGlobalIndex();
510	>	b = atoms[j]->getGlobalIndex();
511	>	excludedInteractions_.addPair(a, b);
512	>	}
513	>	}
514	>	}
515	>
516	>	}
517	>
518	>	void SimInfo::removeInteractionPairs(Molecule* mol) {
519	>	ForceFieldOptions& options_ = forceField_->getForceFieldOptions();
520	>	std::vector<Bond*>::iterator bondIter;
521	>	std::vector<Bend*>::iterator bendIter;
522	>	std::vector<Torsion*>::iterator torsionIter;
523	>	std::vector<Inversion*>::iterator inversionIter;
524	>	Bond* bond;
525	>	Bend* bend;
526	>	Torsion* torsion;
527	>	Inversion* inversion;
528	>	int a;
529	>	int b;
530	>	int c;
531	>	int d;
532	>
533	>	std::map<int, std::set<int> > atomGroups;
534	>	Molecule::RigidBodyIterator rbIter;
535	>	RigidBody* rb;
536	>	Molecule::IntegrableObjectIterator ii;
537	>	StuntDouble* integrableObject;
538	>
539	>	for (integrableObject = mol->beginIntegrableObject(ii);
540	>	integrableObject != NULL;
541	>	integrableObject = mol->nextIntegrableObject(ii)) {
542	>
543	>	if (integrableObject->isRigidBody()) {
544	>	rb = static_cast<RigidBody*>(integrableObject);
545	>	std::vector<Atom*> atoms = rb->getAtoms();
546	>	std::set<int> rigidAtoms;
547	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
548	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
549	>	}
550	>	for (int i = 0; i < static_cast<int>(atoms.size()); ++i) {
551	>	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
552	>	}
553	>	} else {
554	>	std::set<int> oneAtomSet;
555	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
556	>	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
557	>	}
558	>	}
559	>
560	>	for (bond= mol->beginBond(bondIter); bond != NULL;
561	>	bond = mol->nextBond(bondIter)) {
562	>
563	>	a = bond->getAtomA()->getGlobalIndex();
564	>	b = bond->getAtomB()->getGlobalIndex();
565	>
566	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
567	>	oneTwoInteractions_.removePair(a, b);
568	>	} else {
569	>	excludedInteractions_.removePair(a, b);
570	>	}
571	>	}
572	>
573	>	for (bend= mol->beginBend(bendIter); bend != NULL;
574	>	bend = mol->nextBend(bendIter)) {
575	>
576	>	a = bend->getAtomA()->getGlobalIndex();
577	>	b = bend->getAtomB()->getGlobalIndex();
578	>	c = bend->getAtomC()->getGlobalIndex();
579	>
580	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
581	>	oneTwoInteractions_.removePair(a, b);
582	>	oneTwoInteractions_.removePair(b, c);
583	>	} else {
584	>	excludedInteractions_.removePair(a, b);
585	>	excludedInteractions_.removePair(b, c);
586	>	}
587	>
588	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
589	>	oneThreeInteractions_.removePair(a, c);
590	>	} else {
591	>	excludedInteractions_.removePair(a, c);
592	>	}
593	>	}
594	>
595	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL;
596	>	torsion = mol->nextTorsion(torsionIter)) {
597	>
598	>	a = torsion->getAtomA()->getGlobalIndex();
599	>	b = torsion->getAtomB()->getGlobalIndex();
600	>	c = torsion->getAtomC()->getGlobalIndex();
601	>	d = torsion->getAtomD()->getGlobalIndex();
602
603	<	#ifdef IS_MPI
604	<	n_global = mpiSim->getNAtomsGlobal();
605	<	#else
606	<	n_global = n_atoms;
607	<	#endif
608	<
609	<	isError = 0;
610	<
611	<	getFortranGroupArrays(this, FglobalGroupMembership, mfact);
612	<	//it may not be a good idea to pass the address of first element in vector
613	<	//since c++ standard does not require vector to be stored continuously in meomory
614	<	//Most of the compilers will organize the memory of vector continuously
615	<	setFortranSim( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
616	<	&nGlobalExcludes, globalExcludes, molMembershipArray,
617	<	&mfact[0], &ngroup, &FglobalGroupMembership[0], &isError);
603	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
604	>	oneTwoInteractions_.removePair(a, b);
605	>	oneTwoInteractions_.removePair(b, c);
606	>	oneTwoInteractions_.removePair(c, d);
607	>	} else {
608	>	excludedInteractions_.removePair(a, b);
609	>	excludedInteractions_.removePair(b, c);
610	>	excludedInteractions_.removePair(c, d);
611	>	}
612	>
613	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
614	>	oneThreeInteractions_.removePair(a, c);
615	>	oneThreeInteractions_.removePair(b, d);
616	>	} else {
617	>	excludedInteractions_.removePair(a, c);
618	>	excludedInteractions_.removePair(b, d);
619	>	}
620	>
621	>	if (options_.havevdw14scale() || options_.haveelectrostatic14scale()) {
622	>	oneFourInteractions_.removePair(a, d);
623	>	} else {
624	>	excludedInteractions_.removePair(a, d);
625	>	}
626	>	}
627	>
628	>	for (inversion= mol->beginInversion(inversionIter); inversion != NULL;
629	>	inversion = mol->nextInversion(inversionIter)) {
630	>
631	>	a = inversion->getAtomA()->getGlobalIndex();
632	>	b = inversion->getAtomB()->getGlobalIndex();
633	>	c = inversion->getAtomC()->getGlobalIndex();
634	>	d = inversion->getAtomD()->getGlobalIndex();
635	>
636	>	if (options_.havevdw12scale() || options_.haveelectrostatic12scale()) {
637	>	oneTwoInteractions_.removePair(a, b);
638	>	oneTwoInteractions_.removePair(a, c);
639	>	oneTwoInteractions_.removePair(a, d);
640	>	} else {
641	>	excludedInteractions_.removePair(a, b);
642	>	excludedInteractions_.removePair(a, c);
643	>	excludedInteractions_.removePair(a, d);
644	>	}
645	>
646	>	if (options_.havevdw13scale() || options_.haveelectrostatic13scale()) {
647	>	oneThreeInteractions_.removePair(b, c);
648	>	oneThreeInteractions_.removePair(b, d);
649	>	oneThreeInteractions_.removePair(c, d);
650	>	} else {
651	>	excludedInteractions_.removePair(b, c);
652	>	excludedInteractions_.removePair(b, d);
653	>	excludedInteractions_.removePair(c, d);
654	>	}
655	>	}
656	>
657	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
658	>	rb = mol->nextRigidBody(rbIter)) {
659	>	std::vector<Atom*> atoms = rb->getAtoms();
660	>	for (int i = 0; i < static_cast<int>(atoms.size()) -1 ; ++i) {
661	>	for (int j = i + 1; j < static_cast<int>(atoms.size()); ++j) {
662	>	a = atoms[i]->getGlobalIndex();
663	>	b = atoms[j]->getGlobalIndex();
664	>	excludedInteractions_.removePair(a, b);
665	>	}
666	>	}
667	>	}
668	>
669	>	}
670	>
671	>
672	>	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
673	>	int curStampId;
674	>
675	>	//index from 0
676	>	curStampId = moleculeStamps_.size();
677	>
678	>	moleculeStamps_.push_back(molStamp);
679	>	molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
680	>	}
681	>
682	>	void SimInfo::update() {
683	>
684	>	setupSimType();
685	>
686	>	#ifdef IS_MPI
687	>	setupFortranParallel();
688	>	#endif
689	>
690	>	setupFortranSim();
691	>
692	>	//setup fortran force field
693	>	/** @deprecate */
694	>	int isError = 0;
695	>
696	>	setupCutoff();
697	>
698	>	setupElectrostaticSummationMethod( isError );
699	>	setupSwitchingFunction();
700	>	setupAccumulateBoxDipole();
701	>
702	>	if(isError){
703	>	sprintf( painCave.errMsg,
704	>	"ForceField error: There was an error initializing the forceField in fortran.\n" );
705	>	painCave.isFatal = 1;
706	>	simError();
707	>	}
708	>
709	>	calcNdf();
710	>	calcNdfRaw();
711	>	calcNdfTrans();
712	>
713	>	fortranInitialized_ = true;
714	>	}
715	>
716	>	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
717	>	SimInfo::MoleculeIterator mi;
718	>	Molecule* mol;
719	>	Molecule::AtomIterator ai;
720	>	Atom* atom;
721	>	std::set<AtomType*> atomTypes;
722	>
723	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
724	>
725	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
726	>	atomTypes.insert(atom->getAtomType());
727	>	}
728	>
729	>	}
730	>
731	>	return atomTypes;
732	>	}
733	>
734	>	void SimInfo::setupSimType() {
735	>	std::set<AtomType*>::iterator i;
736	>	std::set<AtomType*> atomTypes;
737	>	atomTypes = getUniqueAtomTypes();
738	>
739	>	int useLennardJones = 0;
740	>	int useElectrostatic = 0;
741	>	int useEAM = 0;
742	>	int useSC = 0;
743	>	int useCharge = 0;
744	>	int useDirectional = 0;
745	>	int useDipole = 0;
746	>	int useGayBerne = 0;
747	>	int useSticky = 0;
748	>	int useStickyPower = 0;
749	>	int useShape = 0;
750	>	int useFLARB = 0; //it is not in AtomType yet
751	>	int useDirectionalAtom = 0;
752	>	int useElectrostatics = 0;
753	>	//usePBC and useRF are from simParams
754	>	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
755	>	int useRF;
756	>	int useSF;
757	>	int useSP;
758	>	int useBoxDipole;
759	>
760	>	std::string myMethod;
761	>
762	>	// set the useRF logical
763	>	useRF = 0;
764	>	useSF = 0;
765	>	useSP = 0;
766	>
767	>
768	>	if (simParams_->haveElectrostaticSummationMethod()) {
769	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
770	>	toUpper(myMethod);
771	>	if (myMethod == "REACTION_FIELD"){
772	>	useRF = 1;
773	>	} else if (myMethod == "SHIFTED_FORCE"){
774	>	useSF = 1;
775	>	} else if (myMethod == "SHIFTED_POTENTIAL"){
776	>	useSP = 1;
777	>	}
778	>	}
779	>
780	>	if (simParams_->haveAccumulateBoxDipole())
781	>	if (simParams_->getAccumulateBoxDipole())
782	>	useBoxDipole = 1;
783	>
784	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
785	>
786	>	//loop over all of the atom types
787	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
788	>	useLennardJones |= (*i)->isLennardJones();
789	>	useElectrostatic |= (*i)->isElectrostatic();
790	>	useEAM |= (*i)->isEAM();
791	>	useSC |= (*i)->isSC();
792	>	useCharge |= (*i)->isCharge();
793	>	useDirectional |= (*i)->isDirectional();
794	>	useDipole |= (*i)->isDipole();
795	>	useGayBerne |= (*i)->isGayBerne();
796	>	useSticky |= (*i)->isSticky();
797	>	useStickyPower |= (*i)->isStickyPower();
798	>	useShape |= (*i)->isShape();
799	>	}
800
801	<	if( isError ){
802	<
803	<	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	<	}
801	>	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
802	>	useDirectionalAtom = 1;
803	>	}
804
805	<	void SimInfo::setDefaultRcut( double theRcut ){
806	<
807	<	haveRcut = 1;
504	<	rCut = theRcut;
505	<	rList = rCut + 1.0;
506	<
507	<	notifyFortranCutoffs( &rCut, &rSw, &rList );
508	<	}
805	>	if (useCharge || useDipole) {
806	>	useElectrostatics = 1;
807	>	}
808
809	<	void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
809	>	#ifdef IS_MPI
810	>	int temp;
811
812	<	rSw = theRsw;
813	<	setDefaultRcut( theRcut );
514	<	}
812	>	temp = usePBC;
813	>	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
814
815	+	temp = useDirectionalAtom;
816	+	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
817
818	<	void SimInfo::checkCutOffs( void ){
819	<
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	<	}
818	>	temp = useLennardJones;
819	>	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
820
821	<	void SimInfo::addProperty(GenericData* prop){
821	>	temp = useElectrostatics;
822	>	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
823
824	<	map<string, GenericData*>::iterator result;
825	<	result = properties.find(prop->getID());
826	<
827	<	//we can't simply use  properties[prop->getID()] = prop,
828	<	//it will cause memory leak if we already contain a propery which has the same name of prop
829	<
830	<	if(result != properties.end()){
824	>	temp = useCharge;
825	>	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
826	>
827	>	temp = useDipole;
828	>	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
829	>
830	>	temp = useSticky;
831	>	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
832	>
833	>	temp = useStickyPower;
834	>	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
835
836	<	delete (*result).second;
837	<	(*result).second = prop;
565	<
566	<	}
567	<	else{
836	>	temp = useGayBerne;
837	>	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
838
839	<	properties[prop->getID()] = prop;
839	>	temp = useEAM;
840	>	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
841
842	<	}
842	>	temp = useSC;
843	>	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
844
845	<	}
845	>	temp = useShape;
846	>	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
847
848	<	GenericData* SimInfo::getProperty(const string& propName){
849	<
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	<	}
848	>	temp = useFLARB;
849	>	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
850
851	+	temp = useRF;
852	+	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
853
854	<	void SimInfo::getFortranGroupArrays(SimInfo* info,
855	<	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	<
854	>	temp = useSF;
855	>	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
856
857	<	// Fix the silly fortran indexing problem
858	<	#ifdef IS_MPI
859	<	numAtom = mpiSim->getNAtomsGlobal();
860	<	#else
861	<	numAtom = n_atoms;
857	>	temp = useSP;
858	>	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
859	>
860	>	temp = useBoxDipole;
861	>	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
862	>
863	>	temp = useAtomicVirial_;
864	>	MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
865	>
866		#endif
617	–	for (int i = 0; i < numAtom; i++)
618	–	FglobalGroupMembership.push_back(globalGroupMembership[i] + 1);
619	–
867
868	<	myMols = info->molecules;
869	<	numMol = info->n_mol;
870	<	for(int i  = 0; i < numMol; i++){
871	<	numCutoffGroups = myMols[i].getNCutoffGroups();
872	<	for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff);
873	<	myCutoffGroup != NULL;
874	<	myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
868	>	fInfo_.SIM_uses_PBC = usePBC;
869	>	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
870	>	fInfo_.SIM_uses_LennardJones = useLennardJones;
871	>	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
872	>	fInfo_.SIM_uses_Charges = useCharge;
873	>	fInfo_.SIM_uses_Dipoles = useDipole;
874	>	fInfo_.SIM_uses_Sticky = useSticky;
875	>	fInfo_.SIM_uses_StickyPower = useStickyPower;
876	>	fInfo_.SIM_uses_GayBerne = useGayBerne;
877	>	fInfo_.SIM_uses_EAM = useEAM;
878	>	fInfo_.SIM_uses_SC = useSC;
879	>	fInfo_.SIM_uses_Shapes = useShape;
880	>	fInfo_.SIM_uses_FLARB = useFLARB;
881	>	fInfo_.SIM_uses_RF = useRF;
882	>	fInfo_.SIM_uses_SF = useSF;
883	>	fInfo_.SIM_uses_SP = useSP;
884	>	fInfo_.SIM_uses_BoxDipole = useBoxDipole;
885	>	fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
886	>	}
887
888	<	totalMass = myCutoffGroup->getMass();
888	>	void SimInfo::setupFortranSim() {
889	>	int isError;
890	>	int nExclude, nOneTwo, nOneThree, nOneFour;
891	>	std::vector<int> fortranGlobalGroupMembership;
892	>
893	>	isError = 0;
894	>
895	>	//globalGroupMembership_ is filled by SimCreator
896	>	for (int i = 0; i < nGlobalAtoms_; i++) {
897	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
898	>	}
899	>
900	>	//calculate mass ratio of cutoff group
901	>	std::vector<RealType> mfact;
902	>	SimInfo::MoleculeIterator mi;
903	>	Molecule* mol;
904	>	Molecule::CutoffGroupIterator ci;
905	>	CutoffGroup* cg;
906	>	Molecule::AtomIterator ai;
907	>	Atom* atom;
908	>	RealType totalMass;
909	>
910	>	//to avoid memory reallocation, reserve enough space for mfact
911	>	mfact.reserve(getNCutoffGroups());
912	>
913	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
914	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
915	>
916	>	totalMass = cg->getMass();
917	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
918	>	// Check for massless groups - set mfact to 1 if true
919	>	if (totalMass != 0)
920	>	mfact.push_back(atom->getMass()/totalMass);
921	>	else
922	>	mfact.push_back( 1.0 );
923	>	}
924	>	}
925	>	}
926	>
927	>	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
928	>	std::vector<int> identArray;
929	>
930	>	//to avoid memory reallocation, reserve enough space identArray
931	>	identArray.reserve(getNAtoms());
932	>
933	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
934	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
935	>	identArray.push_back(atom->getIdent());
936	>	}
937	>	}
938	>
939	>	//fill molMembershipArray
940	>	//molMembershipArray is filled by SimCreator
941	>	std::vector<int> molMembershipArray(nGlobalAtoms_);
942	>	for (int i = 0; i < nGlobalAtoms_; i++) {
943	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
944	>	}
945	>
946	>	//setup fortran simulation
947	>
948	>	nExclude = excludedInteractions_.getSize();
949	>	nOneTwo = oneTwoInteractions_.getSize();
950	>	nOneThree = oneThreeInteractions_.getSize();
951	>	nOneFour = oneFourInteractions_.getSize();
952	>
953	>	std::cerr << "excludedInteractions contains: " << excludedInteractions_.getSize() << " pairs \n";
954	>	std::cerr << "oneTwoInteractions contains: " << oneTwoInteractions_.getSize() << " pairs \n";
955	>	std::cerr << "oneThreeInteractions contains: " << oneThreeInteractions_.getSize() << " pairs \n";
956	>	std::cerr << "oneFourInteractions contains: " << oneFourInteractions_.getSize() << " pairs \n";
957	>
958	>	int* excludeList = excludedInteractions_.getPairList();
959	>	int* oneTwoList = oneTwoInteractions_.getPairList();
960	>	int* oneThreeList = oneThreeInteractions_.getPairList();
961	>	int* oneFourList = oneFourInteractions_.getPairList();
962	>
963	>	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
964	>	&nExclude, excludeList,
965	>	&nOneTwo, oneTwoList,
966	>	&nOneThree, oneThreeList,
967	>	&nOneFour, oneFourList,
968	>	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
969	>	&fortranGlobalGroupMembership[0], &isError);
970	>
971	>	if( isError ){
972
973	<	for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom);
974	<	cutoffAtom != NULL;
975	<	cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
976	<	mfact.push_back(cutoffAtom->getMass()/totalMass);
977	<	}
973	>	sprintf( painCave.errMsg,
974	>	"There was an error setting the simulation information in fortran.\n" );
975	>	painCave.isFatal = 1;
976	>	painCave.severity = OOPSE_ERROR;
977	>	simError();
978	>	}
979	>
980	>
981	>	sprintf( checkPointMsg,
982	>	"succesfully sent the simulation information to fortran.\n");
983	>
984	>	errorCheckPoint();
985	>
986	>	// Setup number of neighbors in neighbor list if present
987	>	if (simParams_->haveNeighborListNeighbors()) {
988	>	int nlistNeighbors = simParams_->getNeighborListNeighbors();
989	>	setNeighbors(&nlistNeighbors);
990	>	}
991	>
992	>
993	>	}
994	>
995	>
996	>	void SimInfo::setupFortranParallel() {
997	>	#ifdef IS_MPI
998	>	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
999	>	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
1000	>	std::vector<int> localToGlobalCutoffGroupIndex;
1001	>	SimInfo::MoleculeIterator mi;
1002	>	Molecule::AtomIterator ai;
1003	>	Molecule::CutoffGroupIterator ci;
1004	>	Molecule* mol;
1005	>	Atom* atom;
1006	>	CutoffGroup* cg;
1007	>	mpiSimData parallelData;
1008	>	int isError;
1009	>
1010	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
1011	>
1012	>	//local index(index in DataStorge) of atom is important
1013	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
1014	>	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
1015	>	}
1016	>
1017	>	//local index of cutoff group is trivial, it only depends on the order of travesing
1018	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
1019	>	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
1020	>	}
1021	>
1022	>	}
1023	>
1024	>	//fill up mpiSimData struct
1025	>	parallelData.nMolGlobal = getNGlobalMolecules();
1026	>	parallelData.nMolLocal = getNMolecules();
1027	>	parallelData.nAtomsGlobal = getNGlobalAtoms();
1028	>	parallelData.nAtomsLocal = getNAtoms();
1029	>	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
1030	>	parallelData.nGroupsLocal = getNCutoffGroups();
1031	>	parallelData.myNode = worldRank;
1032	>	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
1033	>
1034	>	//pass mpiSimData struct and index arrays to fortran
1035	>	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
1036	>	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
1037	>	&localToGlobalCutoffGroupIndex[0], &isError);
1038	>
1039	>	if (isError) {
1040	>	sprintf(painCave.errMsg,
1041	>	"mpiRefresh errror: fortran didn't like something we gave it.\n");
1042	>	painCave.isFatal = 1;
1043	>	simError();
1044	>	}
1045	>
1046	>	sprintf(checkPointMsg, " mpiRefresh successful.\n");
1047	>	errorCheckPoint();
1048	>
1049	>	#endif
1050	>	}
1051	>
1052	>	void SimInfo::setupCutoff() {
1053	>
1054	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
1055	>
1056	>	// Check the cutoff policy
1057	>	int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
1058	>
1059	>	// Set LJ shifting bools to false
1060	>	ljsp_ = false;
1061	>	ljsf_ = false;
1062	>
1063	>	std::string myPolicy;
1064	>	if (forceFieldOptions_.haveCutoffPolicy()){
1065	>	myPolicy = forceFieldOptions_.getCutoffPolicy();
1066	>	}else if (simParams_->haveCutoffPolicy()) {
1067	>	myPolicy = simParams_->getCutoffPolicy();
1068	>	}
1069	>
1070	>	if (!myPolicy.empty()){
1071	>	toUpper(myPolicy);
1072	>	if (myPolicy == "MIX") {
1073	>	cp = MIX_CUTOFF_POLICY;
1074	>	} else {
1075	>	if (myPolicy == "MAX") {
1076	>	cp = MAX_CUTOFF_POLICY;
1077	>	} else {
1078	>	if (myPolicy == "TRADITIONAL") {
1079	>	cp = TRADITIONAL_CUTOFF_POLICY;
1080	>	} else {
1081	>	// throw error
1082	>	sprintf( painCave.errMsg,
1083	>	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
1084	>	painCave.isFatal = 1;
1085	>	simError();
1086	>	}
1087	>	}
1088	>	}
1089	>	}
1090	>	notifyFortranCutoffPolicy(&cp);
1091	>
1092	>	// Check the Skin Thickness for neighborlists
1093	>	RealType skin;
1094	>	if (simParams_->haveSkinThickness()) {
1095	>	skin = simParams_->getSkinThickness();
1096	>	notifyFortranSkinThickness(&skin);
1097	>	}
1098	>
1099	>	// Check if the cutoff was set explicitly:
1100	>	if (simParams_->haveCutoffRadius()) {
1101	>	rcut_ = simParams_->getCutoffRadius();
1102	>	if (simParams_->haveSwitchingRadius()) {
1103	>	rsw_  = simParams_->getSwitchingRadius();
1104	>	} else {
1105	>	if (fInfo_.SIM_uses_Charges |
1106	>	fInfo_.SIM_uses_Dipoles |
1107	>	fInfo_.SIM_uses_RF) {
1108	>
1109	>	rsw_ = 0.85 * rcut_;
1110	>	sprintf(painCave.errMsg,
1111	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
1112	>	"\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
1113	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1114	>	painCave.isFatal = 0;
1115	>	simError();
1116	>	} else {
1117	>	rsw_ = rcut_;
1118	>	sprintf(painCave.errMsg,
1119	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
1120	>	"\tOOPSE will use the same value as the cutoffRadius.\n"
1121	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1122	>	painCave.isFatal = 0;
1123	>	simError();
1124	>	}
1125	>	}
1126	>
1127	>	if (simParams_->haveElectrostaticSummationMethod()) {
1128	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1129	>	toUpper(myMethod);
1130	>
1131	>	if (myMethod == "SHIFTED_POTENTIAL") {
1132	>	ljsp_ = true;
1133	>	} else if (myMethod == "SHIFTED_FORCE") {
1134	>	ljsf_ = true;
1135	>	}
1136	>	}
1137	>	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1138	>
1139	>	} else {
1140	>
1141	>	// For electrostatic atoms, we'll assume a large safe value:
1142	>	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1143	>	sprintf(painCave.errMsg,
1144	>	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1145	>	"\tOOPSE will use a default value of 15.0 angstroms"
1146	>	"\tfor the cutoffRadius.\n");
1147	>	painCave.isFatal = 0;
1148	>	simError();
1149	>	rcut_ = 15.0;
1150	>
1151	>	if (simParams_->haveElectrostaticSummationMethod()) {
1152	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1153	>	toUpper(myMethod);
1154	>
1155	>	// For the time being, we're tethering the LJ shifted behavior to the
1156	>	// electrostaticSummationMethod keyword options
1157	>	if (myMethod == "SHIFTED_POTENTIAL") {
1158	>	ljsp_ = true;
1159	>	} else if (myMethod == "SHIFTED_FORCE") {
1160	>	ljsf_ = true;
1161	>	}
1162	>	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1163	>	if (simParams_->haveSwitchingRadius()){
1164	>	sprintf(painCave.errMsg,
1165	>	"SimInfo Warning: A value was set for the switchingRadius\n"
1166	>	"\teven though the electrostaticSummationMethod was\n"
1167	>	"\tset to %s\n", myMethod.c_str());
1168	>	painCave.isFatal = 1;
1169	>	simError();
1170	>	}
1171	>	}
1172	>	}
1173	>
1174	>	if (simParams_->haveSwitchingRadius()){
1175	>	rsw_ = simParams_->getSwitchingRadius();
1176	>	} else {
1177	>	sprintf(painCave.errMsg,
1178	>	"SimCreator Warning: No value was set for switchingRadius.\n"
1179	>	"\tOOPSE will use a default value of\n"
1180	>	"\t0.85 * cutoffRadius for the switchingRadius\n");
1181	>	painCave.isFatal = 0;
1182	>	simError();
1183	>	rsw_ = 0.85 * rcut_;
1184	>	}
1185	>
1186	>	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1187	>
1188	>	} else {
1189	>	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1190	>	// We'll punt and let fortran figure out the cutoffs later.
1191	>
1192	>	notifyFortranYouAreOnYourOwn();
1193	>
1194	>	}
1195		}
1196		}
1197
1198	<	}
1198	>	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1199	>
1200	>	int errorOut;
1201	>	int esm =  NONE;
1202	>	int sm = UNDAMPED;
1203	>	RealType alphaVal;
1204	>	RealType dielectric;
1205	>
1206	>	errorOut = isError;
1207	>
1208	>	if (simParams_->haveElectrostaticSummationMethod()) {
1209	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1210	>	toUpper(myMethod);
1211	>	if (myMethod == "NONE") {
1212	>	esm = NONE;
1213	>	} else {
1214	>	if (myMethod == "SWITCHING_FUNCTION") {
1215	>	esm = SWITCHING_FUNCTION;
1216	>	} else {
1217	>	if (myMethod == "SHIFTED_POTENTIAL") {
1218	>	esm = SHIFTED_POTENTIAL;
1219	>	} else {
1220	>	if (myMethod == "SHIFTED_FORCE") {
1221	>	esm = SHIFTED_FORCE;
1222	>	} else {
1223	>	if (myMethod == "REACTION_FIELD") {
1224	>	esm = REACTION_FIELD;
1225	>	dielectric = simParams_->getDielectric();
1226	>	if (!simParams_->haveDielectric()) {
1227	>	// throw warning
1228	>	sprintf( painCave.errMsg,
1229	>	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1230	>	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1231	>	painCave.isFatal = 0;
1232	>	simError();
1233	>	}
1234	>	} else {
1235	>	// throw error
1236	>	sprintf( painCave.errMsg,
1237	>	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1238	>	"\t(Input file specified %s .)\n"
1239	>	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1240	>	"\t\"shifted_potential\", \"shifted_force\", or \n"
1241	>	"\t\"reaction_field\".\n", myMethod.c_str() );
1242	>	painCave.isFatal = 1;
1243	>	simError();
1244	>	}
1245	>	}
1246	>	}
1247	>	}
1248	>	}
1249	>	}
1250	>
1251	>	if (simParams_->haveElectrostaticScreeningMethod()) {
1252	>	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1253	>	toUpper(myScreen);
1254	>	if (myScreen == "UNDAMPED") {
1255	>	sm = UNDAMPED;
1256	>	} else {
1257	>	if (myScreen == "DAMPED") {
1258	>	sm = DAMPED;
1259	>	if (!simParams_->haveDampingAlpha()) {
1260	>	// first set a cutoff dependent alpha value
1261	>	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1262	>	alphaVal = 0.5125 - rcut_* 0.025;
1263	>	// for values rcut > 20.5, alpha is zero
1264	>	if (alphaVal < 0) alphaVal = 0;
1265	>
1266	>	// throw warning
1267	>	sprintf( painCave.errMsg,
1268	>	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1269	>	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1270	>	painCave.isFatal = 0;
1271	>	simError();
1272	>	} else {
1273	>	alphaVal = simParams_->getDampingAlpha();
1274	>	}
1275	>
1276	>	} else {
1277	>	// throw error
1278	>	sprintf( painCave.errMsg,
1279	>	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1280	>	"\t(Input file specified %s .)\n"
1281	>	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1282	>	"or \"damped\".\n", myScreen.c_str() );
1283	>	painCave.isFatal = 1;
1284	>	simError();
1285	>	}
1286	>	}
1287	>	}
1288	>
1289	>	// let's pass some summation method variables to fortran
1290	>	setElectrostaticSummationMethod( &esm );
1291	>	setFortranElectrostaticMethod( &esm );
1292	>	setScreeningMethod( &sm );
1293	>	setDampingAlpha( &alphaVal );
1294	>	setReactionFieldDielectric( &dielectric );
1295	>	initFortranFF( &errorOut );
1296	>	}
1297	>
1298	>	void SimInfo::setupSwitchingFunction() {
1299	>	int ft = CUBIC;
1300	>
1301	>	if (simParams_->haveSwitchingFunctionType()) {
1302	>	std::string funcType = simParams_->getSwitchingFunctionType();
1303	>	toUpper(funcType);
1304	>	if (funcType == "CUBIC") {
1305	>	ft = CUBIC;
1306	>	} else {
1307	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1308	>	ft = FIFTH_ORDER_POLY;
1309	>	} else {
1310	>	// throw error
1311	>	sprintf( painCave.errMsg,
1312	>	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1313	>	painCave.isFatal = 1;
1314	>	simError();
1315	>	}
1316	>	}
1317	>	}
1318	>
1319	>	// send switching function notification to switcheroo
1320	>	setFunctionType(&ft);
1321	>
1322	>	}
1323	>
1324	>	void SimInfo::setupAccumulateBoxDipole() {
1325	>
1326	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1327	>	if ( simParams_->haveAccumulateBoxDipole() )
1328	>	if ( simParams_->getAccumulateBoxDipole() ) {
1329	>	setAccumulateBoxDipole();
1330	>	calcBoxDipole_ = true;
1331	>	}
1332	>
1333	>	}
1334	>
1335	>	void SimInfo::addProperty(GenericData* genData) {
1336	>	properties_.addProperty(genData);
1337	>	}
1338	>
1339	>	void SimInfo::removeProperty(const std::string& propName) {
1340	>	properties_.removeProperty(propName);
1341	>	}
1342	>
1343	>	void SimInfo::clearProperties() {
1344	>	properties_.clearProperties();
1345	>	}
1346	>
1347	>	std::vector<std::string> SimInfo::getPropertyNames() {
1348	>	return properties_.getPropertyNames();
1349	>	}
1350	>
1351	>	std::vector<GenericData*> SimInfo::getProperties() {
1352	>	return properties_.getProperties();
1353	>	}
1354	>
1355	>	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1356	>	return properties_.getPropertyByName(propName);
1357	>	}
1358	>
1359	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1360	>	if (sman_ == sman) {
1361	>	return;
1362	>	}
1363	>	delete sman_;
1364	>	sman_ = sman;
1365	>
1366	>	Molecule* mol;
1367	>	RigidBody* rb;
1368	>	Atom* atom;
1369	>	SimInfo::MoleculeIterator mi;
1370	>	Molecule::RigidBodyIterator rbIter;
1371	>	Molecule::AtomIterator atomIter;;
1372	>
1373	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1374	>
1375	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1376	>	atom->setSnapshotManager(sman_);
1377	>	}
1378	>
1379	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1380	>	rb->setSnapshotManager(sman_);
1381	>	}
1382	>	}
1383	>
1384	>	}
1385	>
1386	>	Vector3d SimInfo::getComVel(){
1387	>	SimInfo::MoleculeIterator i;
1388	>	Molecule* mol;
1389	>
1390	>	Vector3d comVel(0.0);
1391	>	RealType totalMass = 0.0;
1392	>
1393	>
1394	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1395	>	RealType mass = mol->getMass();
1396	>	totalMass += mass;
1397	>	comVel += mass * mol->getComVel();
1398	>	}
1399	>
1400	>	#ifdef IS_MPI
1401	>	RealType tmpMass = totalMass;
1402	>	Vector3d tmpComVel(comVel);
1403	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1404	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1405	>	#endif
1406	>
1407	>	comVel /= totalMass;
1408	>
1409	>	return comVel;
1410	>	}
1411	>
1412	>	Vector3d SimInfo::getCom(){
1413	>	SimInfo::MoleculeIterator i;
1414	>	Molecule* mol;
1415	>
1416	>	Vector3d com(0.0);
1417	>	RealType totalMass = 0.0;
1418	>
1419	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1420	>	RealType mass = mol->getMass();
1421	>	totalMass += mass;
1422	>	com += mass * mol->getCom();
1423	>	}
1424	>
1425	>	#ifdef IS_MPI
1426	>	RealType tmpMass = totalMass;
1427	>	Vector3d tmpCom(com);
1428	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1429	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1430	>	#endif
1431	>
1432	>	com /= totalMass;
1433	>
1434	>	return com;
1435	>
1436	>	}
1437	>
1438	>	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1439	>
1440	>	return o;
1441	>	}
1442	>
1443	>
1444	>	/*
1445	>	Returns center of mass and center of mass velocity in one function call.
1446	>	*/
1447	>
1448	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1449	>	SimInfo::MoleculeIterator i;
1450	>	Molecule* mol;
1451	>
1452	>
1453	>	RealType totalMass = 0.0;
1454	>
1455	>
1456	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1457	>	RealType mass = mol->getMass();
1458	>	totalMass += mass;
1459	>	com += mass * mol->getCom();
1460	>	comVel += mass * mol->getComVel();
1461	>	}
1462	>
1463	>	#ifdef IS_MPI
1464	>	RealType tmpMass = totalMass;
1465	>	Vector3d tmpCom(com);
1466	>	Vector3d tmpComVel(comVel);
1467	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1468	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1469	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1470	>	#endif
1471	>
1472	>	com /= totalMass;
1473	>	comVel /= totalMass;
1474	>	}
1475	>
1476	>	/*
1477	>	Return intertia tensor for entire system and angular momentum Vector.
1478	>
1479	>
1480	>	[  Ixx -Ixy  -Ixz ]
1481	>	J =| -Iyx  Iyy  -Iyz |
1482	>	[ -Izx -Iyz   Izz ]
1483	>	*/
1484	>
1485	>	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1486	>
1487	>
1488	>	RealType xx = 0.0;
1489	>	RealType yy = 0.0;
1490	>	RealType zz = 0.0;
1491	>	RealType xy = 0.0;
1492	>	RealType xz = 0.0;
1493	>	RealType yz = 0.0;
1494	>	Vector3d com(0.0);
1495	>	Vector3d comVel(0.0);
1496	>
1497	>	getComAll(com, comVel);
1498	>
1499	>	SimInfo::MoleculeIterator i;
1500	>	Molecule* mol;
1501	>
1502	>	Vector3d thisq(0.0);
1503	>	Vector3d thisv(0.0);
1504	>
1505	>	RealType thisMass = 0.0;
1506	>
1507	>
1508	>
1509	>
1510	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1511	>
1512	>	thisq = mol->getCom()-com;
1513	>	thisv = mol->getComVel()-comVel;
1514	>	thisMass = mol->getMass();
1515	>	// Compute moment of intertia coefficients.
1516	>	xx += thisq[0]*thisq[0]*thisMass;
1517	>	yy += thisq[1]*thisq[1]*thisMass;
1518	>	zz += thisq[2]*thisq[2]*thisMass;
1519	>
1520	>	// compute products of intertia
1521	>	xy += thisq[0]*thisq[1]*thisMass;
1522	>	xz += thisq[0]*thisq[2]*thisMass;
1523	>	yz += thisq[1]*thisq[2]*thisMass;
1524	>
1525	>	angularMomentum += cross( thisq, thisv ) * thisMass;
1526	>
1527	>	}
1528	>
1529	>
1530	>	inertiaTensor(0,0) = yy + zz;
1531	>	inertiaTensor(0,1) = -xy;
1532	>	inertiaTensor(0,2) = -xz;
1533	>	inertiaTensor(1,0) = -xy;
1534	>	inertiaTensor(1,1) = xx + zz;
1535	>	inertiaTensor(1,2) = -yz;
1536	>	inertiaTensor(2,0) = -xz;
1537	>	inertiaTensor(2,1) = -yz;
1538	>	inertiaTensor(2,2) = xx + yy;
1539	>
1540	>	#ifdef IS_MPI
1541	>	Mat3x3d tmpI(inertiaTensor);
1542	>	Vector3d tmpAngMom;
1543	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1544	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1545	>	#endif
1546	>
1547	>	return;
1548	>	}
1549	>
1550	>	//Returns the angular momentum of the system
1551	>	Vector3d SimInfo::getAngularMomentum(){
1552	>
1553	>	Vector3d com(0.0);
1554	>	Vector3d comVel(0.0);
1555	>	Vector3d angularMomentum(0.0);
1556	>
1557	>	getComAll(com,comVel);
1558	>
1559	>	SimInfo::MoleculeIterator i;
1560	>	Molecule* mol;
1561	>
1562	>	Vector3d thisr(0.0);
1563	>	Vector3d thisp(0.0);
1564	>
1565	>	RealType thisMass;
1566	>
1567	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1568	>	thisMass = mol->getMass();
1569	>	thisr = mol->getCom()-com;
1570	>	thisp = (mol->getComVel()-comVel)*thisMass;
1571	>
1572	>	angularMomentum += cross( thisr, thisp );
1573	>
1574	>	}
1575	>
1576	>	#ifdef IS_MPI
1577	>	Vector3d tmpAngMom;
1578	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1579	>	#endif
1580	>
1581	>	return angularMomentum;
1582	>	}
1583	>
1584	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1585	>	return IOIndexToIntegrableObject.at(index);
1586	>	}
1587	>
1588	>	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1589	>	IOIndexToIntegrableObject= v;
1590	>	}
1591	>
1592	>	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1593	>	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1594	>	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1595	>	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1596	>	*/
1597	>	void SimInfo::getGyrationalVolume(RealType &volume){
1598	>	Mat3x3d intTensor;
1599	>	RealType det;
1600	>	Vector3d dummyAngMom;
1601	>	RealType sysconstants;
1602	>	RealType geomCnst;
1603	>
1604	>	geomCnst = 3.0/2.0;
1605	>	/* Get the inertial tensor and angular momentum for free*/
1606	>	getInertiaTensor(intTensor,dummyAngMom);
1607	>
1608	>	det = intTensor.determinant();
1609	>	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1610	>	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1611	>	return;
1612	>	}
1613	>
1614	>	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1615	>	Mat3x3d intTensor;
1616	>	Vector3d dummyAngMom;
1617	>	RealType sysconstants;
1618	>	RealType geomCnst;
1619	>
1620	>	geomCnst = 3.0/2.0;
1621	>	/* Get the inertial tensor and angular momentum for free*/
1622	>	getInertiaTensor(intTensor,dummyAngMom);
1623	>
1624	>	detI = intTensor.determinant();
1625	>	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1626	>	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1627	>	return;
1628	>	}
1629	>	/*
1630	>	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1631	>	assert( v.size() == nAtoms_ + nRigidBodies_);
1632	>	sdByGlobalIndex_ = v;
1633	>	}
1634	>
1635	>	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1636	>	//assert(index < nAtoms_ + nRigidBodies_);
1637	>	return sdByGlobalIndex_.at(index);
1638	>	}
1639	>	*/
1640	>	}//end namespace oopse
1641	>

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines