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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 143 by chrisfen, Fri Oct 22 22:54:01 2004 UTC vs.
Revision 1241 by gezelter, Fri Apr 25 15:14:47 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), nRigidBodies_(0),
94	>	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
95	>	sman_(NULL), fortranInitialized_(false), calcBoxDipole_(false),
96	>	useAtomicVirial_(true) {
97
98	<	orthoRhombic = 0;
99	<	orthoTolerance = 1E-6;
100	<	useInitXSstate = true;
98	>	MoleculeStamp* molStamp;
99	>	int nMolWithSameStamp;
100	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
101	>	int nGroups = 0;      //total cutoff groups defined in meta-data file
102	>	CutoffGroupStamp* cgStamp;
103	>	RigidBodyStamp* rbStamp;
104	>	int nRigidAtoms = 0;
105	>	std::vector<Component*> components = simParams->getComponents();
106	>
107	>	for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
108	>	molStamp = (*i)->getMoleculeStamp();
109	>	nMolWithSameStamp = (*i)->getNMol();
110	>
111	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
112
113	<	usePBC = 0;
114	<	useDirectionalAtoms = 0;
61	<	useLennardJones = 0;
62	<	useElectrostatics = 0;
63	<	useCharges = 0;
64	<	useDipoles = 0;
65	<	useSticky = 0;
66	<	useGayBerne = 0;
67	<	useEAM = 0;
68	<	useShapes = 0;
69	<	useFLARB = 0;
113	>	//calculate atoms in molecules
114	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
115
116	<	useSolidThermInt = 0;
117	<	useLiquidThermInt = 0;
116	>	//calculate atoms in cutoff groups
117	>	int nAtomsInGroups = 0;
118	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
119	>
120	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
121	>	cgStamp = molStamp->getCutoffGroupStamp(j);
122	>	nAtomsInGroups += cgStamp->getNMembers();
123	>	}
124
125	<	haveCutoffGroups = false;
125	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
126
127	<	excludes = Exclude::Instance();
127	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
128
129	<	myConfiguration = new SimState();
129	>	//calculate atoms in rigid bodies
130	>	int nAtomsInRigidBodies = 0;
131	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
132	>
133	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
134	>	rbStamp = molStamp->getRigidBodyStamp(j);
135	>	nAtomsInRigidBodies += rbStamp->getNMembers();
136	>	}
137
138	<	has_minimizer = false;
139	<	the_minimizer =NULL;
138	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
139	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
140	>
141	>	}
142
143	<	ngroup = 0;
143	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
144	>	//group therefore the total number of cutoff groups in the system is
145	>	//equal to the total number of atoms minus number of atoms belong to
146	>	//cutoff group defined in meta-data file plus the number of cutoff
147	>	//groups defined in meta-data file
148	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
149
150	<	}
150	>	//every free atom (atom does not belong to rigid bodies) is an
151	>	//integrable object therefore the total number of integrable objects
152	>	//in the system is equal to the total number of atoms minus number of
153	>	//atoms belong to rigid body defined in meta-data file plus the number
154	>	//of rigid bodies defined in meta-data file
155	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
156	>	+ nGlobalRigidBodies_;
157	>
158	>	nGlobalMols_ = molStampIds_.size();
159	>	molToProcMap_.resize(nGlobalMols_);
160	>	}
161
162	+	SimInfo::~SimInfo() {
163	+	std::map<int, Molecule*>::iterator i;
164	+	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
165	+	delete i->second;
166	+	}
167	+	molecules_.clear();
168	+
169	+	delete sman_;
170	+	delete simParams_;
171	+	delete forceField_;
172	+	}
173
174	<	SimInfo::~SimInfo(){
174	>	int SimInfo::getNGlobalConstraints() {
175	>	int nGlobalConstraints;
176	>	#ifdef IS_MPI
177	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
178	>	MPI_COMM_WORLD);
179	>	#else
180	>	nGlobalConstraints =  nConstraints_;
181	>	#endif
182	>	return nGlobalConstraints;
183	>	}
184
185	<	delete myConfiguration;
185	>	bool SimInfo::addMolecule(Molecule* mol) {
186	>	MoleculeIterator i;
187
188	<	map<string, GenericData*>::iterator i;
189	<
94	<	for(i = properties.begin(); i != properties.end(); i++)
95	<	delete (*i).second;
188	>	i = molecules_.find(mol->getGlobalIndex());
189	>	if (i == molecules_.end() ) {
190
191	<	}
191	>	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
192	>
193	>	nAtoms_ += mol->getNAtoms();
194	>	nBonds_ += mol->getNBonds();
195	>	nBends_ += mol->getNBends();
196	>	nTorsions_ += mol->getNTorsions();
197	>	nRigidBodies_ += mol->getNRigidBodies();
198	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
199	>	nCutoffGroups_ += mol->getNCutoffGroups();
200	>	nConstraints_ += mol->getNConstraintPairs();
201
202	<	void SimInfo::setBox(double newBox[3]) {
203	<
204	<	int i, j;
205	<	double tempMat[3][3];
202	>	addExcludePairs(mol);
203	>
204	>	return true;
205	>	} else {
206	>	return false;
207	>	}
208	>	}
209
210	<	for(i=0; i<3; i++)
211	<	for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
210	>	bool SimInfo::removeMolecule(Molecule* mol) {
211	>	MoleculeIterator i;
212	>	i = molecules_.find(mol->getGlobalIndex());
213
214	<	tempMat[0][0] = newBox[0];
108	<	tempMat[1][1] = newBox[1];
109	<	tempMat[2][2] = newBox[2];
214	>	if (i != molecules_.end() ) {
215
216	<	setBoxM( tempMat );
216	>	assert(mol == i->second);
217	>
218	>	nAtoms_ -= mol->getNAtoms();
219	>	nBonds_ -= mol->getNBonds();
220	>	nBends_ -= mol->getNBends();
221	>	nTorsions_ -= mol->getNTorsions();
222	>	nRigidBodies_ -= mol->getNRigidBodies();
223	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
224	>	nCutoffGroups_ -= mol->getNCutoffGroups();
225	>	nConstraints_ -= mol->getNConstraintPairs();
226
227	<	}
227	>	removeExcludePairs(mol);
228	>	molecules_.erase(mol->getGlobalIndex());
229
230	<	void SimInfo::setBoxM( double theBox[3][3] ){
231	<
232	<	int i, j;
233	<	double FortranHmat[9]; // to preserve compatibility with Fortran the
234	<	// ordering in the array is as follows:
120	<	// [ 0 3 6 ]
121	<	// [ 1 4 7 ]
122	<	// [ 2 5 8 ]
123	<	double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
124	<
125	<	if( !boxIsInit ) boxIsInit = 1;
126	<
127	<	for(i=0; i < 3; i++)
128	<	for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
129	<
130	<	calcBoxL();
131	<	calcHmatInv();
132	<
133	<	for(i=0; i < 3; i++) {
134	<	for (j=0; j < 3; j++) {
135	<	FortranHmat[3*j + i] = Hmat[i][j];
136	<	FortranHmatInv[3*j + i] = HmatInv[i][j];
230	>	delete mol;
231	>
232	>	return true;
233	>	} else {
234	>	return false;
235		}
138	–	}
236
140	–	setFortranBox(FortranHmat, FortranHmatInv, &orthoRhombic);
141	–
142	–	}
143	–
237
238	<	void SimInfo::getBoxM (double theBox[3][3]) {
238	>	}
239
240	<	int i, j;
241	<	for(i=0; i<3; i++)
242	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
243	<	}
240	>
241	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
242	>	i = molecules_.begin();
243	>	return i == molecules_.end() ? NULL : i->second;
244	>	}
245
246	+	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
247	+	++i;
248	+	return i == molecules_.end() ? NULL : i->second;
249	+	}
250
153	–	void SimInfo::scaleBox(double scale) {
154	–	double theBox[3][3];
155	–	int i, j;
251
252	<	// cerr << "Scaling box by " << scale << "\n";
252	>	void SimInfo::calcNdf() {
253	>	int ndf_local;
254	>	MoleculeIterator i;
255	>	std::vector<StuntDouble*>::iterator j;
256	>	Molecule* mol;
257	>	StuntDouble* integrableObject;
258
259	<	for(i=0; i<3; i++)
260	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
259	>	ndf_local = 0;
260	>
261	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
262	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
263	>	integrableObject = mol->nextIntegrableObject(j)) {
264
265	<	setBoxM(theBox);
265	>	ndf_local += 3;
266
267	<	}
268	<
269	<	void SimInfo::calcHmatInv( void ) {
270	<
271	<	int oldOrtho;
272	<	int i,j;
273	<	double smallDiag;
274	<	double tol;
172	<	double sanity[3][3];
173	<
174	<	invertMat3( Hmat, HmatInv );
175	<
176	<	// check to see if Hmat is orthorhombic
177	<
178	<	oldOrtho = orthoRhombic;
179	<
180	<	smallDiag = fabs(Hmat[0][0]);
181	<	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	<	}
267	>	if (integrableObject->isDirectional()) {
268	>	if (integrableObject->isLinear()) {
269	>	ndf_local += 2;
270	>	} else {
271	>	ndf_local += 3;
272	>	}
273	>	}
274	>
275		}
276		}
195	–	}
196	–
197	–	if( oldOrtho != orthoRhombic ){
277
278	<	if( orthoRhombic ) {
279	<	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	<	}
278	>	// n_constraints is local, so subtract them on each processor
279	>	ndf_local -= nConstraints_;
280
281	<	void SimInfo::calcBoxL( void ){
281	>	#ifdef IS_MPI
282	>	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
283	>	#else
284	>	ndf_ = ndf_local;
285	>	#endif
286
287	<	double dx, dy, dz, dsq;
287	>	// nZconstraints_ is global, as are the 3 COM translations for the
288	>	// entire system:
289	>	ndf_ = ndf_ - 3 - nZconstraint_;
290
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	–
313	–	}
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	–	}
332	–
333	–
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	–	}
291		}
292
293	<	// n_constraints is local, so subtract them on each processor:
350	<
351	<	ndf_local -= n_constraints;
352	<
293	>	int SimInfo::getFdf() {
294		#ifdef IS_MPI
295	<	MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
295	>	MPI_Allreduce(&fdf_local,&fdf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
296		#else
297	<	ndf = ndf_local;
297	>	fdf_ = fdf_local;
298		#endif
299	+	return fdf_;
300	+	}
301	+
302	+	void SimInfo::calcNdfRaw() {
303	+	int ndfRaw_local;
304
305	<	// nZconstraints is global, as are the 3 COM translations for the
306	<	// entire system:
305	>	MoleculeIterator i;
306	>	std::vector<StuntDouble*>::iterator j;
307	>	Molecule* mol;
308	>	StuntDouble* integrableObject;
309
310	<	ndf = ndf - 3 - nZconstraints;
310	>	// Raw degrees of freedom that we have to set
311	>	ndfRaw_local = 0;
312	>
313	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
314	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
315	>	integrableObject = mol->nextIntegrableObject(j)) {
316
317	<	return ndf;
365	<	}
317	>	ndfRaw_local += 3;
318
319	<	int SimInfo::getNDFraw() {
320	<	int ndfRaw_local;
321	<
322	<	// Raw degrees of freedom that we have to set
323	<	ndfRaw_local = 0;
324	<
325	<	for(int i = 0; i < integrableObjects.size(); i++){
326	<	ndfRaw_local += 3;
327	<	if (integrableObjects[i]->isDirectional()) {
376	<	if (integrableObjects[i]->isLinear())
377	<	ndfRaw_local += 2;
378	<	else
379	<	ndfRaw_local += 3;
319	>	if (integrableObject->isDirectional()) {
320	>	if (integrableObject->isLinear()) {
321	>	ndfRaw_local += 2;
322	>	} else {
323	>	ndfRaw_local += 3;
324	>	}
325	>	}
326	>
327	>	}
328		}
381	–	}
329
330		#ifdef IS_MPI
331	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
331	>	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
332		#else
333	<	ndfRaw = ndfRaw_local;
333	>	ndfRaw_ = ndfRaw_local;
334		#endif
335	+	}
336
337	<	return ndfRaw;
338	<	}
337	>	void SimInfo::calcNdfTrans() {
338	>	int ndfTrans_local;
339
340	<	int SimInfo::getNDFtranslational() {
393	<	int ndfTrans_local;
340	>	ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
341
395	–	ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
342
397	–
343		#ifdef IS_MPI
344	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
344	>	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
345		#else
346	<	ndfTrans = ndfTrans_local;
346	>	ndfTrans_ = ndfTrans_local;
347		#endif
348
349	<	ndfTrans = ndfTrans - 3 - nZconstraints;
349	>	ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
350	>
351	>	}
352
353	<	return ndfTrans;
354	<	}
353	>	void SimInfo::addExcludePairs(Molecule* mol) {
354	>	std::vector<Bond*>::iterator bondIter;
355	>	std::vector<Bend*>::iterator bendIter;
356	>	std::vector<Torsion*>::iterator torsionIter;
357	>	Bond* bond;
358	>	Bend* bend;
359	>	Torsion* torsion;
360	>	int a;
361	>	int b;
362	>	int c;
363	>	int d;
364
365	<	int SimInfo::getTotIntegrableObjects() {
410	<	int nObjs_local;
411	<	int nObjs;
365	>	std::map<int, std::set<int> > atomGroups;
366
367	<	nObjs_local =  integrableObjects.size();
367	>	Molecule::RigidBodyIterator rbIter;
368	>	RigidBody* rb;
369	>	Molecule::IntegrableObjectIterator ii;
370	>	StuntDouble* integrableObject;
371	>
372	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
373	>	integrableObject = mol->nextIntegrableObject(ii)) {
374
375	+	if (integrableObject->isRigidBody()) {
376	+	rb = static_cast<RigidBody*>(integrableObject);
377	+	std::vector<Atom*> atoms = rb->getAtoms();
378	+	std::set<int> rigidAtoms;
379	+	for (int i = 0; i < atoms.size(); ++i) {
380	+	rigidAtoms.insert(atoms[i]->getGlobalIndex());
381	+	}
382	+	for (int i = 0; i < atoms.size(); ++i) {
383	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
384	+	}
385	+	} else {
386	+	std::set<int> oneAtomSet;
387	+	oneAtomSet.insert(integrableObject->getGlobalIndex());
388	+	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
389	+	}
390	+	}
391
392	<	#ifdef IS_MPI
393	<	MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
394	<	#else
395	<	nObjs = nObjs_local;
396	<	#endif
392	>
393	>
394	>	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
395	>	a = bond->getAtomA()->getGlobalIndex();
396	>	b = bond->getAtomB()->getGlobalIndex();
397	>	exclude_.addPair(a, b);
398	>	}
399
400	+	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
401	+	a = bend->getAtomA()->getGlobalIndex();
402	+	b = bend->getAtomB()->getGlobalIndex();
403	+	c = bend->getAtomC()->getGlobalIndex();
404	+	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
405	+	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
406	+	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
407
408	<	return nObjs;
409	<	}
408	>	exclude_.addPairs(rigidSetA, rigidSetB);
409	>	exclude_.addPairs(rigidSetA, rigidSetC);
410	>	exclude_.addPairs(rigidSetB, rigidSetC);
411	>
412	>	//exclude_.addPair(a, b);
413	>	//exclude_.addPair(a, c);
414	>	//exclude_.addPair(b, c);
415	>	}
416
417	<	void SimInfo::refreshSim(){
417	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
418	>	a = torsion->getAtomA()->getGlobalIndex();
419	>	b = torsion->getAtomB()->getGlobalIndex();
420	>	c = torsion->getAtomC()->getGlobalIndex();
421	>	d = torsion->getAtomD()->getGlobalIndex();
422	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
423	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
424	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
425	>	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
426
427	<	simtype fInfo;
428	<	int isError;
429	<	int n_global;
430	<	int* excl;
427	>	exclude_.addPairs(rigidSetA, rigidSetB);
428	>	exclude_.addPairs(rigidSetA, rigidSetC);
429	>	exclude_.addPairs(rigidSetA, rigidSetD);
430	>	exclude_.addPairs(rigidSetB, rigidSetC);
431	>	exclude_.addPairs(rigidSetB, rigidSetD);
432	>	exclude_.addPairs(rigidSetC, rigidSetD);
433
434	<	fInfo.dielect = 0.0;
434	>	/*
435	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
436	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
437	>	exclude_.addPairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
438	>	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
439	>	exclude_.addPairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
440	>	exclude_.addPairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
441	>
442	>
443	>	exclude_.addPair(a, b);
444	>	exclude_.addPair(a, c);
445	>	exclude_.addPair(a, d);
446	>	exclude_.addPair(b, c);
447	>	exclude_.addPair(b, d);
448	>	exclude_.addPair(c, d);
449	>	*/
450	>	}
451
452	<	if( useDipoles ){
453	<	if( useReactionField )fInfo.dielect = dielectric;
452	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
453	>	std::vector<Atom*> atoms = rb->getAtoms();
454	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
455	>	for (int j = i + 1; j < atoms.size(); ++j) {
456	>	a = atoms[i]->getGlobalIndex();
457	>	b = atoms[j]->getGlobalIndex();
458	>	exclude_.addPair(a, b);
459	>	}
460	>	}
461	>	}
462	>
463	>	}
464	>
465	>	void SimInfo::removeExcludePairs(Molecule* mol) {
466	>	std::vector<Bond*>::iterator bondIter;
467	>	std::vector<Bend*>::iterator bendIter;
468	>	std::vector<Torsion*>::iterator torsionIter;
469	>	Bond* bond;
470	>	Bend* bend;
471	>	Torsion* torsion;
472	>	int a;
473	>	int b;
474	>	int c;
475	>	int d;
476	>
477	>	std::map<int, std::set<int> > atomGroups;
478	>
479	>	Molecule::RigidBodyIterator rbIter;
480	>	RigidBody* rb;
481	>	Molecule::IntegrableObjectIterator ii;
482	>	StuntDouble* integrableObject;
483	>
484	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
485	>	integrableObject = mol->nextIntegrableObject(ii)) {
486	>
487	>	if (integrableObject->isRigidBody()) {
488	>	rb = static_cast<RigidBody*>(integrableObject);
489	>	std::vector<Atom*> atoms = rb->getAtoms();
490	>	std::set<int> rigidAtoms;
491	>	for (int i = 0; i < atoms.size(); ++i) {
492	>	rigidAtoms.insert(atoms[i]->getGlobalIndex());
493	>	}
494	>	for (int i = 0; i < atoms.size(); ++i) {
495	>	atomGroups.insert(std::map<int, std::set<int> >::value_type(atoms[i]->getGlobalIndex(), rigidAtoms));
496	>	}
497	>	} else {
498	>	std::set<int> oneAtomSet;
499	>	oneAtomSet.insert(integrableObject->getGlobalIndex());
500	>	atomGroups.insert(std::map<int, std::set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet));
501	>	}
502	>	}
503	>
504	>
505	>	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
506	>	a = bond->getAtomA()->getGlobalIndex();
507	>	b = bond->getAtomB()->getGlobalIndex();
508	>	exclude_.removePair(a, b);
509	>	}
510	>
511	>	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
512	>	a = bend->getAtomA()->getGlobalIndex();
513	>	b = bend->getAtomB()->getGlobalIndex();
514	>	c = bend->getAtomC()->getGlobalIndex();
515	>
516	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
517	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
518	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
519	>
520	>	exclude_.removePairs(rigidSetA, rigidSetB);
521	>	exclude_.removePairs(rigidSetA, rigidSetC);
522	>	exclude_.removePairs(rigidSetB, rigidSetC);
523	>
524	>	//exclude_.removePair(a, b);
525	>	//exclude_.removePair(a, c);
526	>	//exclude_.removePair(b, c);
527	>	}
528	>
529	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
530	>	a = torsion->getAtomA()->getGlobalIndex();
531	>	b = torsion->getAtomB()->getGlobalIndex();
532	>	c = torsion->getAtomC()->getGlobalIndex();
533	>	d = torsion->getAtomD()->getGlobalIndex();
534	>
535	>	std::set<int> rigidSetA = getRigidSet(a, atomGroups);
536	>	std::set<int> rigidSetB = getRigidSet(b, atomGroups);
537	>	std::set<int> rigidSetC = getRigidSet(c, atomGroups);
538	>	std::set<int> rigidSetD = getRigidSet(d, atomGroups);
539	>
540	>	exclude_.removePairs(rigidSetA, rigidSetB);
541	>	exclude_.removePairs(rigidSetA, rigidSetC);
542	>	exclude_.removePairs(rigidSetA, rigidSetD);
543	>	exclude_.removePairs(rigidSetB, rigidSetC);
544	>	exclude_.removePairs(rigidSetB, rigidSetD);
545	>	exclude_.removePairs(rigidSetC, rigidSetD);
546	>
547	>	/*
548	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetB.begin(), rigidSetB.end());
549	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetC.begin(), rigidSetC.end());
550	>	exclude_.removePairs(rigidSetA.begin(), rigidSetA.end(), rigidSetD.begin(), rigidSetD.end());
551	>	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetC.begin(), rigidSetC.end());
552	>	exclude_.removePairs(rigidSetB.begin(), rigidSetB.end(), rigidSetD.begin(), rigidSetD.end());
553	>	exclude_.removePairs(rigidSetC.begin(), rigidSetC.end(), rigidSetD.begin(), rigidSetD.end());
554	>
555	>
556	>	exclude_.removePair(a, b);
557	>	exclude_.removePair(a, c);
558	>	exclude_.removePair(a, d);
559	>	exclude_.removePair(b, c);
560	>	exclude_.removePair(b, d);
561	>	exclude_.removePair(c, d);
562	>	*/
563	>	}
564	>
565	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
566	>	std::vector<Atom*> atoms = rb->getAtoms();
567	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
568	>	for (int j = i + 1; j < atoms.size(); ++j) {
569	>	a = atoms[i]->getGlobalIndex();
570	>	b = atoms[j]->getGlobalIndex();
571	>	exclude_.removePair(a, b);
572	>	}
573	>	}
574	>	}
575	>
576		}
577
578	<	fInfo.SIM_uses_PBC = usePBC;
578	>
579	>	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
580	>	int curStampId;
581	>
582	>	//index from 0
583	>	curStampId = moleculeStamps_.size();
584	>
585	>	moleculeStamps_.push_back(molStamp);
586	>	molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
587	>	}
588	>
589	>	void SimInfo::update() {
590	>
591	>	setupSimType();
592	>
593	>	#ifdef IS_MPI
594	>	setupFortranParallel();
595	>	#endif
596	>
597	>	setupFortranSim();
598	>
599	>	//setup fortran force field
600	>	/** @deprecate */
601	>	int isError = 0;
602	>
603	>	setupCutoff();
604	>
605	>	setupElectrostaticSummationMethod( isError );
606	>	setupSwitchingFunction();
607	>	setupAccumulateBoxDipole();
608	>
609	>	if(isError){
610	>	sprintf( painCave.errMsg,
611	>	"ForceField error: There was an error initializing the forceField in fortran.\n" );
612	>	painCave.isFatal = 1;
613	>	simError();
614	>	}
615	>
616	>	calcNdf();
617	>	calcNdfRaw();
618	>	calcNdfTrans();
619	>
620	>	fortranInitialized_ = true;
621	>	}
622	>
623	>	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
624	>	SimInfo::MoleculeIterator mi;
625	>	Molecule* mol;
626	>	Molecule::AtomIterator ai;
627	>	Atom* atom;
628	>	std::set<AtomType*> atomTypes;
629	>
630	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
631	>
632	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
633	>	atomTypes.insert(atom->getAtomType());
634	>	}
635	>
636	>	}
637	>
638	>	return atomTypes;
639	>	}
640	>
641	>	void SimInfo::setupSimType() {
642	>	std::set<AtomType*>::iterator i;
643	>	std::set<AtomType*> atomTypes;
644	>	atomTypes = getUniqueAtomTypes();
645	>
646	>	int useLennardJones = 0;
647	>	int useElectrostatic = 0;
648	>	int useEAM = 0;
649	>	int useSC = 0;
650	>	int useCharge = 0;
651	>	int useDirectional = 0;
652	>	int useDipole = 0;
653	>	int useGayBerne = 0;
654	>	int useSticky = 0;
655	>	int useStickyPower = 0;
656	>	int useShape = 0;
657	>	int useFLARB = 0; //it is not in AtomType yet
658	>	int useDirectionalAtom = 0;
659	>	int useElectrostatics = 0;
660	>	//usePBC and useRF are from simParams
661	>	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
662	>	int useRF;
663	>	int useSF;
664	>	int useSP;
665	>	int useBoxDipole;
666	>
667	>	std::string myMethod;
668	>
669	>	// set the useRF logical
670	>	useRF = 0;
671	>	useSF = 0;
672	>	useSP = 0;
673	>
674	>
675	>	if (simParams_->haveElectrostaticSummationMethod()) {
676	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
677	>	toUpper(myMethod);
678	>	if (myMethod == "REACTION_FIELD"){
679	>	useRF = 1;
680	>	} else if (myMethod == "SHIFTED_FORCE"){
681	>	useSF = 1;
682	>	} else if (myMethod == "SHIFTED_POTENTIAL"){
683	>	useSP = 1;
684	>	}
685	>	}
686	>
687	>	if (simParams_->haveAccumulateBoxDipole())
688	>	if (simParams_->getAccumulateBoxDipole())
689	>	useBoxDipole = 1;
690	>
691	>	useAtomicVirial_ = simParams_->getUseAtomicVirial();
692	>
693	>	//loop over all of the atom types
694	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
695	>	useLennardJones |= (*i)->isLennardJones();
696	>	useElectrostatic |= (*i)->isElectrostatic();
697	>	useEAM |= (*i)->isEAM();
698	>	useSC |= (*i)->isSC();
699	>	useCharge |= (*i)->isCharge();
700	>	useDirectional |= (*i)->isDirectional();
701	>	useDipole |= (*i)->isDipole();
702	>	useGayBerne |= (*i)->isGayBerne();
703	>	useSticky |= (*i)->isSticky();
704	>	useStickyPower |= (*i)->isStickyPower();
705	>	useShape |= (*i)->isShape();
706	>	}
707	>
708	>	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
709	>	useDirectionalAtom = 1;
710	>	}
711	>
712	>	if (useCharge || useDipole) {
713	>	useElectrostatics = 1;
714	>	}
715	>
716	>	#ifdef IS_MPI
717	>	int temp;
718	>
719	>	temp = usePBC;
720	>	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
721	>
722	>	temp = useDirectionalAtom;
723	>	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
724	>
725	>	temp = useLennardJones;
726	>	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
727	>
728	>	temp = useElectrostatics;
729	>	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
730	>
731	>	temp = useCharge;
732	>	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
733	>
734	>	temp = useDipole;
735	>	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
736	>
737	>	temp = useSticky;
738	>	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
739	>
740	>	temp = useStickyPower;
741	>	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
742	>
743	>	temp = useGayBerne;
744	>	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
745	>
746	>	temp = useEAM;
747	>	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
748	>
749	>	temp = useSC;
750	>	MPI_Allreduce(&temp, &useSC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
751	>
752	>	temp = useShape;
753	>	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
754	>
755	>	temp = useFLARB;
756	>	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
757	>
758	>	temp = useRF;
759	>	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
760	>
761	>	temp = useSF;
762	>	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
763
764	<	if (useSticky || useDipoles || useGayBerne || useShapes) {
765	<	useDirectionalAtoms = 1;
443	<	fInfo.SIM_uses_DirectionalAtoms = useDirectionalAtoms;
444	<	}
764	>	temp = useSP;
765	>	MPI_Allreduce(&temp, &useSP, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
766
767	<	fInfo.SIM_uses_LennardJones = useLennardJones;
767	>	temp = useBoxDipole;
768	>	MPI_Allreduce(&temp, &useBoxDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
769
770	<	if (useCharges || useDipoles) {
771	<	useElectrostatics = 1;
772	<	fInfo.SIM_uses_Electrostatics = useElectrostatics;
770	>	temp = useAtomicVirial_;
771	>	MPI_Allreduce(&temp, &useAtomicVirial_, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
772	>
773	>	#endif
774	>
775	>	fInfo_.SIM_uses_PBC = usePBC;
776	>	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
777	>	fInfo_.SIM_uses_LennardJones = useLennardJones;
778	>	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
779	>	fInfo_.SIM_uses_Charges = useCharge;
780	>	fInfo_.SIM_uses_Dipoles = useDipole;
781	>	fInfo_.SIM_uses_Sticky = useSticky;
782	>	fInfo_.SIM_uses_StickyPower = useStickyPower;
783	>	fInfo_.SIM_uses_GayBerne = useGayBerne;
784	>	fInfo_.SIM_uses_EAM = useEAM;
785	>	fInfo_.SIM_uses_SC = useSC;
786	>	fInfo_.SIM_uses_Shapes = useShape;
787	>	fInfo_.SIM_uses_FLARB = useFLARB;
788	>	fInfo_.SIM_uses_RF = useRF;
789	>	fInfo_.SIM_uses_SF = useSF;
790	>	fInfo_.SIM_uses_SP = useSP;
791	>	fInfo_.SIM_uses_BoxDipole = useBoxDipole;
792	>	fInfo_.SIM_uses_AtomicVirial = useAtomicVirial_;
793		}
794
795	<	fInfo.SIM_uses_Charges = useCharges;
796	<	fInfo.SIM_uses_Dipoles = useDipoles;
797	<	fInfo.SIM_uses_Sticky = useSticky;
798	<	fInfo.SIM_uses_GayBerne = useGayBerne;
799	<	fInfo.SIM_uses_EAM = useEAM;
800	<	fInfo.SIM_uses_Shapes = useShapes;
801	<	fInfo.SIM_uses_FLARB = useFLARB;
460	<	fInfo.SIM_uses_RF = useReactionField;
795	>	void SimInfo::setupFortranSim() {
796	>	int isError;
797	>	int nExclude;
798	>	std::vector<int> fortranGlobalGroupMembership;
799	>
800	>	nExclude = exclude_.getSize();
801	>	isError = 0;
802
803	<	n_exclude = excludes->getSize();
804	<	excl = excludes->getFortranArray();
805	<
806	<	#ifdef IS_MPI
466	<	n_global = mpiSim->getNAtomsGlobal();
467	<	#else
468	<	n_global = n_atoms;
469	<	#endif
470	<
471	<	isError = 0;
472	<
473	<	getFortranGroupArrays(this, FglobalGroupMembership, mfact);
474	<	//it may not be a good idea to pass the address of first element in vector
475	<	//since c++ standard does not require vector to be stored continuously in meomory
476	<	//Most of the compilers will organize the memory of vector continuously
477	<	setFortranSim( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
478	<	&nGlobalExcludes, globalExcludes, molMembershipArray,
479	<	&mfact[0], &ngroup, &FglobalGroupMembership[0], &isError);
803	>	//globalGroupMembership_ is filled by SimCreator
804	>	for (int i = 0; i < nGlobalAtoms_; i++) {
805	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
806	>	}
807
808	<	if( isError ){
808	>	//calculate mass ratio of cutoff group
809	>	std::vector<RealType> mfact;
810	>	SimInfo::MoleculeIterator mi;
811	>	Molecule* mol;
812	>	Molecule::CutoffGroupIterator ci;
813	>	CutoffGroup* cg;
814	>	Molecule::AtomIterator ai;
815	>	Atom* atom;
816	>	RealType totalMass;
817	>
818	>	//to avoid memory reallocation, reserve enough space for mfact
819	>	mfact.reserve(getNCutoffGroups());
820
821	<	sprintf( painCave.errMsg,
822	<	"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	<	}
821	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
822	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
823
824	<	void SimInfo::setDefaultRcut( double theRcut ){
825	<
826	<	haveRcut = 1;
827	<	rCut = theRcut;
828	<	rList = rCut + 1.0;
829	<
830	<	notifyFortranCutoffs( &rCut, &rSw, &rList );
831	<	}
824	>	totalMass = cg->getMass();
825	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
826	>	// Check for massless groups - set mfact to 1 if true
827	>	if (totalMass != 0)
828	>	mfact.push_back(atom->getMass()/totalMass);
829	>	else
830	>	mfact.push_back( 1.0 );
831	>	}
832
833	<	void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
833	>	}
834	>	}
835
836	<	rSw = theRsw;
837	<	setDefaultRcut( theRcut );
514	<	}
836	>	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
837	>	std::vector<int> identArray;
838
839	+	//to avoid memory reallocation, reserve enough space identArray
840	+	identArray.reserve(getNAtoms());
841	+
842	+	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
843	+	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
844	+	identArray.push_back(atom->getIdent());
845	+	}
846	+	}
847
848	<	void SimInfo::checkCutOffs( void ){
849	<
850	<	if( boxIsInit ){
848	>	//fill molMembershipArray
849	>	//molMembershipArray is filled by SimCreator
850	>	std::vector<int> molMembershipArray(nGlobalAtoms_);
851	>	for (int i = 0; i < nGlobalAtoms_; i++) {
852	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
853	>	}
854
855	<	//we need to check cutOffs against the box
855	>	//setup fortran simulation
856	>	int nGlobalExcludes = 0;
857	>	int* globalExcludes = NULL;
858	>	int* excludeList = exclude_.getExcludeList();
859	>	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0],
860	>	&nExclude, excludeList , &nGlobalExcludes, globalExcludes,
861	>	&molMembershipArray[0], &mfact[0], &nCutoffGroups_,
862	>	&fortranGlobalGroupMembership[0], &isError);
863
864	<	if( rCut > maxCutoff ){
864	>	if( isError ){
865	>
866		sprintf( painCave.errMsg,
867	<	"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;
867	>	"There was an error setting the simulation information in fortran.\n" );
868		painCave.isFatal = 1;
869	+	painCave.severity = OOPSE_ERROR;
870		simError();
871	<	}
872	<	} else {
873	<	// initialize this stuff before using it, OK?
874	<	sprintf( painCave.errMsg,
875	<	"Trying to check cutoffs without a box.\n"
876	<	"\tOOPSE should have better programmers than that.\n" );
877	<	painCave.severity = OOPSE_ERROR;
878	<	painCave.isFatal = 1;
879	<	simError();
871	>	}
872	>
873	>
874	>	sprintf( checkPointMsg,
875	>	"succesfully sent the simulation information to fortran.\n");
876	>
877	>	errorCheckPoint();
878	>
879	>	// Setup number of neighbors in neighbor list if present
880	>	if (simParams_->haveNeighborListNeighbors()) {
881	>	int nlistNeighbors = simParams_->getNeighborListNeighbors();
882	>	setNeighbors(&nlistNeighbors);
883	>	}
884	>
885	>
886		}
550	–
551	–	}
887
553	–	void SimInfo::addProperty(GenericData* prop){
888
889	<	map<string, GenericData*>::iterator result;
890	<	result = properties.find(prop->getID());
891	<
892	<	//we can't simply use  properties[prop->getID()] = prop,
893	<	//it will cause memory leak if we already contain a propery which has the same name of prop
894	<
895	<	if(result != properties.end()){
896	<
897	<	delete (*result).second;
898	<	(*result).second = prop;
899	<
900	<	}
901	<	else{
889	>	void SimInfo::setupFortranParallel() {
890	>	#ifdef IS_MPI
891	>	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
892	>	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
893	>	std::vector<int> localToGlobalCutoffGroupIndex;
894	>	SimInfo::MoleculeIterator mi;
895	>	Molecule::AtomIterator ai;
896	>	Molecule::CutoffGroupIterator ci;
897	>	Molecule* mol;
898	>	Atom* atom;
899	>	CutoffGroup* cg;
900	>	mpiSimData parallelData;
901	>	int isError;
902
903	<	properties[prop->getID()] = prop;
903	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
904	>
905	>	//local index(index in DataStorge) of atom is important
906	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
907	>	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
908	>	}
909
910	+	//local index of cutoff group is trivial, it only depends on the order of travesing
911	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
912	+	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
913	+	}
914	+
915	+	}
916	+
917	+	//fill up mpiSimData struct
918	+	parallelData.nMolGlobal = getNGlobalMolecules();
919	+	parallelData.nMolLocal = getNMolecules();
920	+	parallelData.nAtomsGlobal = getNGlobalAtoms();
921	+	parallelData.nAtomsLocal = getNAtoms();
922	+	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
923	+	parallelData.nGroupsLocal = getNCutoffGroups();
924	+	parallelData.myNode = worldRank;
925	+	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
926	+
927	+	//pass mpiSimData struct and index arrays to fortran
928	+	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
929	+	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
930	+	&localToGlobalCutoffGroupIndex[0], &isError);
931	+
932	+	if (isError) {
933	+	sprintf(painCave.errMsg,
934	+	"mpiRefresh errror: fortran didn't like something we gave it.\n");
935	+	painCave.isFatal = 1;
936	+	simError();
937	+	}
938	+
939	+	sprintf(checkPointMsg, " mpiRefresh successful.\n");
940	+	errorCheckPoint();
941	+
942	+	#endif
943		}
944	+
945	+	void SimInfo::setupCutoff() {
946
947	<	}
947	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
948
949	<	GenericData* SimInfo::getProperty(const string& propName){
950	<
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	<	}
949	>	// Check the cutoff policy
950	>	int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
951
952	+	// Set LJ shifting bools to false
953	+	ljsp_ = false;
954	+	ljsf_ = false;
955
956	<	void SimInfo::getFortranGroupArrays(SimInfo* info,
957	<	vector<int>& FglobalGroupMembership,
958	<	vector<double>& mfact){
959	<
960	<	Molecule* myMols;
961	<	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	<
956	>	std::string myPolicy;
957	>	if (forceFieldOptions_.haveCutoffPolicy()){
958	>	myPolicy = forceFieldOptions_.getCutoffPolicy();
959	>	}else if (simParams_->haveCutoffPolicy()) {
960	>	myPolicy = simParams_->getCutoffPolicy();
961	>	}
962
963	<	// Fix the silly fortran indexing problem
964	<	#ifdef IS_MPI
965	<	numAtom = mpiSim->getNAtomsGlobal();
966	<	#else
967	<	numAtom = n_atoms;
968	<	#endif
969	<	for (int i = 0; i < numAtom; i++)
970	<	FglobalGroupMembership.push_back(globalGroupMembership[i] + 1);
971	<
963	>	if (!myPolicy.empty()){
964	>	toUpper(myPolicy);
965	>	if (myPolicy == "MIX") {
966	>	cp = MIX_CUTOFF_POLICY;
967	>	} else {
968	>	if (myPolicy == "MAX") {
969	>	cp = MAX_CUTOFF_POLICY;
970	>	} else {
971	>	if (myPolicy == "TRADITIONAL") {
972	>	cp = TRADITIONAL_CUTOFF_POLICY;
973	>	} else {
974	>	// throw error
975	>	sprintf( painCave.errMsg,
976	>	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
977	>	painCave.isFatal = 1;
978	>	simError();
979	>	}
980	>	}
981	>	}
982	>	}
983	>	notifyFortranCutoffPolicy(&cp);
984
985	<	myMols = info->molecules;
986	<	numMol = info->n_mol;
987	<	for(int i  = 0; i < numMol; i++){
988	<	numCutoffGroups = myMols[i].getNCutoffGroups();
989	<	for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff);
990	<	myCutoffGroup != NULL;
991	<	myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
985	>	// Check the Skin Thickness for neighborlists
986	>	RealType skin;
987	>	if (simParams_->haveSkinThickness()) {
988	>	skin = simParams_->getSkinThickness();
989	>	notifyFortranSkinThickness(&skin);
990	>	}
991	>
992	>	// Check if the cutoff was set explicitly:
993	>	if (simParams_->haveCutoffRadius()) {
994	>	rcut_ = simParams_->getCutoffRadius();
995	>	if (simParams_->haveSwitchingRadius()) {
996	>	rsw_  = simParams_->getSwitchingRadius();
997	>	} else {
998	>	if (fInfo_.SIM_uses_Charges |
999	>	fInfo_.SIM_uses_Dipoles |
1000	>	fInfo_.SIM_uses_RF) {
1001	>
1002	>	rsw_ = 0.85 * rcut_;
1003	>	sprintf(painCave.errMsg,
1004	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
1005	>	"\tOOPSE will use a default value of 85 percent of the cutoffRadius.\n"
1006	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1007	>	painCave.isFatal = 0;
1008	>	simError();
1009	>	} else {
1010	>	rsw_ = rcut_;
1011	>	sprintf(painCave.errMsg,
1012	>	"SimCreator Warning: No value was set for the switchingRadius.\n"
1013	>	"\tOOPSE will use the same value as the cutoffRadius.\n"
1014	>	"\tswitchingRadius = %f. for this simulation\n", rsw_);
1015	>	painCave.isFatal = 0;
1016	>	simError();
1017	>	}
1018	>	}
1019
1020	<	totalMass = myCutoffGroup->getMass();
1020	>	if (simParams_->haveElectrostaticSummationMethod()) {
1021	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1022	>	toUpper(myMethod);
1023	>
1024	>	if (myMethod == "SHIFTED_POTENTIAL") {
1025	>	ljsp_ = true;
1026	>	} else if (myMethod == "SHIFTED_FORCE") {
1027	>	ljsf_ = true;
1028	>	}
1029	>	}
1030	>	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1031
1032	<	for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom);
1033	<	cutoffAtom != NULL;
1034	<	cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
1035	<	mfact.push_back(cutoffAtom->getMass()/totalMass);
1036	<	}
1032	>	} else {
1033	>
1034	>	// For electrostatic atoms, we'll assume a large safe value:
1035	>	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
1036	>	sprintf(painCave.errMsg,
1037	>	"SimCreator Warning: No value was set for the cutoffRadius.\n"
1038	>	"\tOOPSE will use a default value of 15.0 angstroms"
1039	>	"\tfor the cutoffRadius.\n");
1040	>	painCave.isFatal = 0;
1041	>	simError();
1042	>	rcut_ = 15.0;
1043	>
1044	>	if (simParams_->haveElectrostaticSummationMethod()) {
1045	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1046	>	toUpper(myMethod);
1047	>
1048	>	// For the time being, we're tethering the LJ shifted behavior to the
1049	>	// electrostaticSummationMethod keyword options
1050	>	if (myMethod == "SHIFTED_POTENTIAL") {
1051	>	ljsp_ = true;
1052	>	} else if (myMethod == "SHIFTED_FORCE") {
1053	>	ljsf_ = true;
1054	>	}
1055	>	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
1056	>	if (simParams_->haveSwitchingRadius()){
1057	>	sprintf(painCave.errMsg,
1058	>	"SimInfo Warning: A value was set for the switchingRadius\n"
1059	>	"\teven though the electrostaticSummationMethod was\n"
1060	>	"\tset to %s\n", myMethod.c_str());
1061	>	painCave.isFatal = 1;
1062	>	simError();
1063	>	}
1064	>	}
1065	>	}
1066	>
1067	>	if (simParams_->haveSwitchingRadius()){
1068	>	rsw_ = simParams_->getSwitchingRadius();
1069	>	} else {
1070	>	sprintf(painCave.errMsg,
1071	>	"SimCreator Warning: No value was set for switchingRadius.\n"
1072	>	"\tOOPSE will use a default value of\n"
1073	>	"\t0.85 * cutoffRadius for the switchingRadius\n");
1074	>	painCave.isFatal = 0;
1075	>	simError();
1076	>	rsw_ = 0.85 * rcut_;
1077	>	}
1078	>
1079	>	notifyFortranCutoffs(&rcut_, &rsw_, &ljsp_, &ljsf_);
1080	>
1081	>	} else {
1082	>	// We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1083	>	// We'll punt and let fortran figure out the cutoffs later.
1084	>
1085	>	notifyFortranYouAreOnYourOwn();
1086	>
1087	>	}
1088		}
1089		}
1090
1091	<	}
1091	>	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
1092	>
1093	>	int errorOut;
1094	>	int esm =  NONE;
1095	>	int sm = UNDAMPED;
1096	>	RealType alphaVal;
1097	>	RealType dielectric;
1098	>
1099	>	errorOut = isError;
1100	>
1101	>	if (simParams_->haveElectrostaticSummationMethod()) {
1102	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
1103	>	toUpper(myMethod);
1104	>	if (myMethod == "NONE") {
1105	>	esm = NONE;
1106	>	} else {
1107	>	if (myMethod == "SWITCHING_FUNCTION") {
1108	>	esm = SWITCHING_FUNCTION;
1109	>	} else {
1110	>	if (myMethod == "SHIFTED_POTENTIAL") {
1111	>	esm = SHIFTED_POTENTIAL;
1112	>	} else {
1113	>	if (myMethod == "SHIFTED_FORCE") {
1114	>	esm = SHIFTED_FORCE;
1115	>	} else {
1116	>	if (myMethod == "REACTION_FIELD") {
1117	>	esm = REACTION_FIELD;
1118	>	dielectric = simParams_->getDielectric();
1119	>	if (!simParams_->haveDielectric()) {
1120	>	// throw warning
1121	>	sprintf( painCave.errMsg,
1122	>	"SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n"
1123	>	"\tA default value of %f will be used for the dielectric.\n", dielectric);
1124	>	painCave.isFatal = 0;
1125	>	simError();
1126	>	}
1127	>	} else {
1128	>	// throw error
1129	>	sprintf( painCave.errMsg,
1130	>	"SimInfo error: Unknown electrostaticSummationMethod.\n"
1131	>	"\t(Input file specified %s .)\n"
1132	>	"\telectrostaticSummationMethod must be one of: \"none\",\n"
1133	>	"\t\"shifted_potential\", \"shifted_force\", or \n"
1134	>	"\t\"reaction_field\".\n", myMethod.c_str() );
1135	>	painCave.isFatal = 1;
1136	>	simError();
1137	>	}
1138	>	}
1139	>	}
1140	>	}
1141	>	}
1142	>	}
1143	>
1144	>	if (simParams_->haveElectrostaticScreeningMethod()) {
1145	>	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
1146	>	toUpper(myScreen);
1147	>	if (myScreen == "UNDAMPED") {
1148	>	sm = UNDAMPED;
1149	>	} else {
1150	>	if (myScreen == "DAMPED") {
1151	>	sm = DAMPED;
1152	>	if (!simParams_->haveDampingAlpha()) {
1153	>	// first set a cutoff dependent alpha value
1154	>	// we assume alpha depends linearly with rcut from 0 to 20.5 ang
1155	>	alphaVal = 0.5125 - rcut_* 0.025;
1156	>	// for values rcut > 20.5, alpha is zero
1157	>	if (alphaVal < 0) alphaVal = 0;
1158	>
1159	>	// throw warning
1160	>	sprintf( painCave.errMsg,
1161	>	"SimInfo warning: dampingAlpha was not specified in the input file.\n"
1162	>	"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_);
1163	>	painCave.isFatal = 0;
1164	>	simError();
1165	>	} else {
1166	>	alphaVal = simParams_->getDampingAlpha();
1167	>	}
1168	>
1169	>	} else {
1170	>	// throw error
1171	>	sprintf( painCave.errMsg,
1172	>	"SimInfo error: Unknown electrostaticScreeningMethod.\n"
1173	>	"\t(Input file specified %s .)\n"
1174	>	"\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1175	>	"or \"damped\".\n", myScreen.c_str() );
1176	>	painCave.isFatal = 1;
1177	>	simError();
1178	>	}
1179	>	}
1180	>	}
1181	>
1182	>	// let's pass some summation method variables to fortran
1183	>	setElectrostaticSummationMethod( &esm );
1184	>	setFortranElectrostaticMethod( &esm );
1185	>	setScreeningMethod( &sm );
1186	>	setDampingAlpha( &alphaVal );
1187	>	setReactionFieldDielectric( &dielectric );
1188	>	initFortranFF( &errorOut );
1189	>	}
1190	>
1191	>	void SimInfo::setupSwitchingFunction() {
1192	>	int ft = CUBIC;
1193	>
1194	>	if (simParams_->haveSwitchingFunctionType()) {
1195	>	std::string funcType = simParams_->getSwitchingFunctionType();
1196	>	toUpper(funcType);
1197	>	if (funcType == "CUBIC") {
1198	>	ft = CUBIC;
1199	>	} else {
1200	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1201	>	ft = FIFTH_ORDER_POLY;
1202	>	} else {
1203	>	// throw error
1204	>	sprintf( painCave.errMsg,
1205	>	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1206	>	painCave.isFatal = 1;
1207	>	simError();
1208	>	}
1209	>	}
1210	>	}
1211	>
1212	>	// send switching function notification to switcheroo
1213	>	setFunctionType(&ft);
1214	>
1215	>	}
1216	>
1217	>	void SimInfo::setupAccumulateBoxDipole() {
1218	>
1219	>	// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true
1220	>	if ( simParams_->haveAccumulateBoxDipole() )
1221	>	if ( simParams_->getAccumulateBoxDipole() ) {
1222	>	setAccumulateBoxDipole();
1223	>	calcBoxDipole_ = true;
1224	>	}
1225	>
1226	>	}
1227	>
1228	>	void SimInfo::addProperty(GenericData* genData) {
1229	>	properties_.addProperty(genData);
1230	>	}
1231	>
1232	>	void SimInfo::removeProperty(const std::string& propName) {
1233	>	properties_.removeProperty(propName);
1234	>	}
1235	>
1236	>	void SimInfo::clearProperties() {
1237	>	properties_.clearProperties();
1238	>	}
1239	>
1240	>	std::vector<std::string> SimInfo::getPropertyNames() {
1241	>	return properties_.getPropertyNames();
1242	>	}
1243	>
1244	>	std::vector<GenericData*> SimInfo::getProperties() {
1245	>	return properties_.getProperties();
1246	>	}
1247	>
1248	>	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1249	>	return properties_.getPropertyByName(propName);
1250	>	}
1251	>
1252	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1253	>	if (sman_ == sman) {
1254	>	return;
1255	>	}
1256	>	delete sman_;
1257	>	sman_ = sman;
1258	>
1259	>	Molecule* mol;
1260	>	RigidBody* rb;
1261	>	Atom* atom;
1262	>	SimInfo::MoleculeIterator mi;
1263	>	Molecule::RigidBodyIterator rbIter;
1264	>	Molecule::AtomIterator atomIter;;
1265	>
1266	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1267	>
1268	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1269	>	atom->setSnapshotManager(sman_);
1270	>	}
1271	>
1272	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1273	>	rb->setSnapshotManager(sman_);
1274	>	}
1275	>	}
1276	>
1277	>	}
1278	>
1279	>	Vector3d SimInfo::getComVel(){
1280	>	SimInfo::MoleculeIterator i;
1281	>	Molecule* mol;
1282	>
1283	>	Vector3d comVel(0.0);
1284	>	RealType totalMass = 0.0;
1285	>
1286	>
1287	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1288	>	RealType mass = mol->getMass();
1289	>	totalMass += mass;
1290	>	comVel += mass * mol->getComVel();
1291	>	}
1292	>
1293	>	#ifdef IS_MPI
1294	>	RealType tmpMass = totalMass;
1295	>	Vector3d tmpComVel(comVel);
1296	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1297	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1298	>	#endif
1299	>
1300	>	comVel /= totalMass;
1301	>
1302	>	return comVel;
1303	>	}
1304	>
1305	>	Vector3d SimInfo::getCom(){
1306	>	SimInfo::MoleculeIterator i;
1307	>	Molecule* mol;
1308	>
1309	>	Vector3d com(0.0);
1310	>	RealType totalMass = 0.0;
1311	>
1312	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1313	>	RealType mass = mol->getMass();
1314	>	totalMass += mass;
1315	>	com += mass * mol->getCom();
1316	>	}
1317	>
1318	>	#ifdef IS_MPI
1319	>	RealType tmpMass = totalMass;
1320	>	Vector3d tmpCom(com);
1321	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1322	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1323	>	#endif
1324	>
1325	>	com /= totalMass;
1326	>
1327	>	return com;
1328	>
1329	>	}
1330	>
1331	>	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1332	>
1333	>	return o;
1334	>	}
1335	>
1336	>
1337	>	/*
1338	>	Returns center of mass and center of mass velocity in one function call.
1339	>	*/
1340	>
1341	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1342	>	SimInfo::MoleculeIterator i;
1343	>	Molecule* mol;
1344	>
1345	>
1346	>	RealType totalMass = 0.0;
1347	>
1348	>
1349	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1350	>	RealType mass = mol->getMass();
1351	>	totalMass += mass;
1352	>	com += mass * mol->getCom();
1353	>	comVel += mass * mol->getComVel();
1354	>	}
1355	>
1356	>	#ifdef IS_MPI
1357	>	RealType tmpMass = totalMass;
1358	>	Vector3d tmpCom(com);
1359	>	Vector3d tmpComVel(comVel);
1360	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1361	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1362	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1363	>	#endif
1364	>
1365	>	com /= totalMass;
1366	>	comVel /= totalMass;
1367	>	}
1368	>
1369	>	/*
1370	>	Return intertia tensor for entire system and angular momentum Vector.
1371	>
1372	>
1373	>	[  Ixx -Ixy  -Ixz ]
1374	>	J =| -Iyx  Iyy  -Iyz |
1375	>	[ -Izx -Iyz   Izz ]
1376	>	*/
1377	>
1378	>	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1379	>
1380	>
1381	>	RealType xx = 0.0;
1382	>	RealType yy = 0.0;
1383	>	RealType zz = 0.0;
1384	>	RealType xy = 0.0;
1385	>	RealType xz = 0.0;
1386	>	RealType yz = 0.0;
1387	>	Vector3d com(0.0);
1388	>	Vector3d comVel(0.0);
1389	>
1390	>	getComAll(com, comVel);
1391	>
1392	>	SimInfo::MoleculeIterator i;
1393	>	Molecule* mol;
1394	>
1395	>	Vector3d thisq(0.0);
1396	>	Vector3d thisv(0.0);
1397	>
1398	>	RealType thisMass = 0.0;
1399	>
1400	>
1401	>
1402	>
1403	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1404	>
1405	>	thisq = mol->getCom()-com;
1406	>	thisv = mol->getComVel()-comVel;
1407	>	thisMass = mol->getMass();
1408	>	// Compute moment of intertia coefficients.
1409	>	xx += thisq[0]*thisq[0]*thisMass;
1410	>	yy += thisq[1]*thisq[1]*thisMass;
1411	>	zz += thisq[2]*thisq[2]*thisMass;
1412	>
1413	>	// compute products of intertia
1414	>	xy += thisq[0]*thisq[1]*thisMass;
1415	>	xz += thisq[0]*thisq[2]*thisMass;
1416	>	yz += thisq[1]*thisq[2]*thisMass;
1417	>
1418	>	angularMomentum += cross( thisq, thisv ) * thisMass;
1419	>
1420	>	}
1421	>
1422	>
1423	>	inertiaTensor(0,0) = yy + zz;
1424	>	inertiaTensor(0,1) = -xy;
1425	>	inertiaTensor(0,2) = -xz;
1426	>	inertiaTensor(1,0) = -xy;
1427	>	inertiaTensor(1,1) = xx + zz;
1428	>	inertiaTensor(1,2) = -yz;
1429	>	inertiaTensor(2,0) = -xz;
1430	>	inertiaTensor(2,1) = -yz;
1431	>	inertiaTensor(2,2) = xx + yy;
1432	>
1433	>	#ifdef IS_MPI
1434	>	Mat3x3d tmpI(inertiaTensor);
1435	>	Vector3d tmpAngMom;
1436	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1437	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1438	>	#endif
1439	>
1440	>	return;
1441	>	}
1442	>
1443	>	//Returns the angular momentum of the system
1444	>	Vector3d SimInfo::getAngularMomentum(){
1445	>
1446	>	Vector3d com(0.0);
1447	>	Vector3d comVel(0.0);
1448	>	Vector3d angularMomentum(0.0);
1449	>
1450	>	getComAll(com,comVel);
1451	>
1452	>	SimInfo::MoleculeIterator i;
1453	>	Molecule* mol;
1454	>
1455	>	Vector3d thisr(0.0);
1456	>	Vector3d thisp(0.0);
1457	>
1458	>	RealType thisMass;
1459	>
1460	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1461	>	thisMass = mol->getMass();
1462	>	thisr = mol->getCom()-com;
1463	>	thisp = (mol->getComVel()-comVel)*thisMass;
1464	>
1465	>	angularMomentum += cross( thisr, thisp );
1466	>
1467	>	}
1468	>
1469	>	#ifdef IS_MPI
1470	>	Vector3d tmpAngMom;
1471	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_REALTYPE,MPI_SUM, MPI_COMM_WORLD);
1472	>	#endif
1473	>
1474	>	return angularMomentum;
1475	>	}
1476	>
1477	>	StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) {
1478	>	return IOIndexToIntegrableObject.at(index);
1479	>	}
1480	>
1481	>	void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) {
1482	>	IOIndexToIntegrableObject= v;
1483	>	}
1484	>
1485	>	/* Returns the Volume of the simulation based on a ellipsoid with semi-axes
1486	>	based on the radius of gyration V=4/3*Pi*R_1*R_2*R_3
1487	>	where R_i are related to the principle inertia moments R_i = sqrt(C*I_i/N), this reduces to
1488	>	V = 4/3*Pi*(C/N)^3/2*sqrt(det(I)). See S.E. Baltazar et. al. Comp. Mat. Sci. 37 (2006) 526-536.
1489	>	*/
1490	>	void SimInfo::getGyrationalVolume(RealType &volume){
1491	>	Mat3x3d intTensor;
1492	>	RealType det;
1493	>	Vector3d dummyAngMom;
1494	>	RealType sysconstants;
1495	>	RealType geomCnst;
1496	>
1497	>	geomCnst = 3.0/2.0;
1498	>	/* Get the inertial tensor and angular momentum for free*/
1499	>	getInertiaTensor(intTensor,dummyAngMom);
1500	>
1501	>	det = intTensor.determinant();
1502	>	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1503	>	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(det);
1504	>	return;
1505	>	}
1506	>
1507	>	void SimInfo::getGyrationalVolume(RealType &volume, RealType &detI){
1508	>	Mat3x3d intTensor;
1509	>	Vector3d dummyAngMom;
1510	>	RealType sysconstants;
1511	>	RealType geomCnst;
1512	>
1513	>	geomCnst = 3.0/2.0;
1514	>	/* Get the inertial tensor and angular momentum for free*/
1515	>	getInertiaTensor(intTensor,dummyAngMom);
1516	>
1517	>	detI = intTensor.determinant();
1518	>	sysconstants = geomCnst/(RealType)nGlobalIntegrableObjects_;
1519	>	volume = 4.0/3.0*NumericConstant::PI*pow(sysconstants,3.0/2.0)*sqrt(detI);
1520	>	return;
1521	>	}
1522	>	/*
1523	>	void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) {
1524	>	assert( v.size() == nAtoms_ + nRigidBodies_);
1525	>	sdByGlobalIndex_ = v;
1526	>	}
1527	>
1528	>	StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) {
1529	>	//assert(index < nAtoms_ + nRigidBodies_);
1530	>	return sdByGlobalIndex_.at(index);
1531	>	}
1532	>	*/
1533	>	}//end namespace oopse
1534	>

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