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Comparing trunk/OOPSE-2.0/src/brains/SimInfo.cpp (file contents):
Revision 1617 by chuckv, Wed Oct 20 20:46:20 2004 UTC vs.
Revision 2425 by chrisfen, Fri Nov 11 15:22:11 2005 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
52		#include "brains/SimInfo.hpp"
53	<	#define __C
54	<	#include "brains/fSimulation.h"
55	<	#include "utils/simError.h"
56	<	#include "UseTheForce/DarkSide/simulation_interface.h"
53	>	#include "math/Vector3.hpp"
54	>	#include "primitives/Molecule.hpp"
55	>	#include "UseTheForce/fCutoffPolicy.h"
56	>	#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
57	>	#include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h"
58	>	#include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
59	>	#include "UseTheForce/doForces_interface.h"
60	>	#include "UseTheForce/DarkSide/electrostatic_interface.h"
61		#include "UseTheForce/notifyCutoffs_interface.h"
62	+	#include "UseTheForce/DarkSide/switcheroo_interface.h"
63	+	#include "utils/MemoryUtils.hpp"
64	+	#include "utils/simError.h"
65	+	#include "selection/SelectionManager.hpp"
66
15	–	//#include "UseTheForce/fortranWrappers.hpp"
16	–
17	–	#include "math/MatVec3.h"
18	–
67		#ifdef IS_MPI
68	<	#include "brains/mpiSimulation.hpp"
69	<	#endif
68	>	#include "UseTheForce/mpiComponentPlan.h"
69	>	#include "UseTheForce/DarkSide/simParallel_interface.h"
70	>	#endif
71
72	<	inline double roundMe( double x ){
24	<	return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
25	<	}
26	<
27	<	inline double min( double a, double b ){
28	<	return (a < b ) ? a : b;
29	<	}
72	>	namespace oopse {
73
74	<	SimInfo* currentInfo;
74	>	SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
75	>	ForceField* ff, Globals* simParams) :
76	>	stamps_(stamps), forceField_(ff), simParams_(simParams),
77	>	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
78	>	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
79	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
80	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
81	>	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
82	>	sman_(NULL), fortranInitialized_(false) {
83
84	<	SimInfo::SimInfo(){
84	>
85	>	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
86	>	MoleculeStamp* molStamp;
87	>	int nMolWithSameStamp;
88	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
89	>	int nGroups = 0;      //total cutoff groups defined in meta-data file
90	>	CutoffGroupStamp* cgStamp;
91	>	RigidBodyStamp* rbStamp;
92	>	int nRigidAtoms = 0;
93	>
94	>	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
95	>	molStamp = i->first;
96	>	nMolWithSameStamp = i->second;
97	>
98	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
99
100	<	n_constraints = 0;
101	<	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;
100	>	//calculate atoms in molecules
101	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
102
49	–	haveRcut = 0;
50	–	haveRsw = 0;
51	–	boxIsInit = 0;
52	–
53	–	resetTime = 1e99;
103
104	<	orthoRhombic = 0;
105	<	orthoTolerance = 1E-6;
106	<	useInitXSstate = true;
104	>	//calculate atoms in cutoff groups
105	>	int nAtomsInGroups = 0;
106	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
107	>
108	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
109	>	cgStamp = molStamp->getCutoffGroup(j);
110	>	nAtomsInGroups += cgStamp->getNMembers();
111	>	}
112
113	<	usePBC = 0;
60	<	useLJ = 0;
61	<	useSticky = 0;
62	<	useCharges = 0;
63	<	useDipoles = 0;
64	<	useReactionField = 0;
65	<	useGB = 0;
66	<	useEAM = 0;
67	<	useSolidThermInt = 0;
68	<	useLiquidThermInt = 0;
113	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
114
115	<	haveCutoffGroups = false;
115	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
116
117	<	excludes = Exclude::Instance();
117	>	//calculate atoms in rigid bodies
118	>	int nAtomsInRigidBodies = 0;
119	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
120	>
121	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
122	>	rbStamp = molStamp->getRigidBody(j);
123	>	nAtomsInRigidBodies += rbStamp->getNMembers();
124	>	}
125
126	<	myConfiguration = new SimState();
126	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
127	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
128	>
129	>	}
130
131	<	has_minimizer = false;
132	<	the_minimizer =NULL;
131	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
132	>	//group therefore the total number of cutoff groups in the system is
133	>	//equal to the total number of atoms minus number of atoms belong to
134	>	//cutoff group defined in meta-data file plus the number of cutoff
135	>	//groups defined in meta-data file
136	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
137
138	<	ngroup = 0;
138	>	//every free atom (atom does not belong to rigid bodies) is an
139	>	//integrable object therefore the total number of integrable objects
140	>	//in the system is equal to the total number of atoms minus number of
141	>	//atoms belong to rigid body defined in meta-data file plus the number
142	>	//of rigid bodies defined in meta-data file
143	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
144	>	+ nGlobalRigidBodies_;
145	>
146	>	nGlobalMols_ = molStampIds_.size();
147
148	<	}
148	>	#ifdef IS_MPI
149	>	molToProcMap_.resize(nGlobalMols_);
150	>	#endif
151
152	+	}
153
154	<	SimInfo::~SimInfo(){
154	>	SimInfo::~SimInfo() {
155	>	std::map<int, Molecule*>::iterator i;
156	>	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
157	>	delete i->second;
158	>	}
159	>	molecules_.clear();
160	>
161	>	delete stamps_;
162	>	delete sman_;
163	>	delete simParams_;
164	>	delete forceField_;
165	>	}
166
167	<	delete myConfiguration;
167	>	int SimInfo::getNGlobalConstraints() {
168	>	int nGlobalConstraints;
169	>	#ifdef IS_MPI
170	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
171	>	MPI_COMM_WORLD);
172	>	#else
173	>	nGlobalConstraints =  nConstraints_;
174	>	#endif
175	>	return nGlobalConstraints;
176	>	}
177
178	<	map<string, GenericData*>::iterator i;
179	<
90	<	for(i = properties.begin(); i != properties.end(); i++)
91	<	delete (*i).second;
178	>	bool SimInfo::addMolecule(Molecule* mol) {
179	>	MoleculeIterator i;
180
181	<	}
181	>	i = molecules_.find(mol->getGlobalIndex());
182	>	if (i == molecules_.end() ) {
183
184	<	void SimInfo::setBox(double newBox[3]) {
185	<
186	<	int i, j;
187	<	double tempMat[3][3];
184	>	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
185	>
186	>	nAtoms_ += mol->getNAtoms();
187	>	nBonds_ += mol->getNBonds();
188	>	nBends_ += mol->getNBends();
189	>	nTorsions_ += mol->getNTorsions();
190	>	nRigidBodies_ += mol->getNRigidBodies();
191	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
192	>	nCutoffGroups_ += mol->getNCutoffGroups();
193	>	nConstraints_ += mol->getNConstraintPairs();
194
195	<	for(i=0; i<3; i++)
196	<	for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
197	<
198	<	tempMat[0][0] = newBox[0];
199	<	tempMat[1][1] = newBox[1];
105	<	tempMat[2][2] = newBox[2];
106	<
107	<	setBoxM( tempMat );
108	<
109	<	}
110	<
111	<	void SimInfo::setBoxM( double theBox[3][3] ){
112	<
113	<	int i, j;
114	<	double FortranHmat[9]; // to preserve compatibility with Fortran the
115	<	// ordering in the array is as follows:
116	<	// [ 0 3 6 ]
117	<	// [ 1 4 7 ]
118	<	// [ 2 5 8 ]
119	<	double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
120	<
121	<	if( !boxIsInit ) boxIsInit = 1;
122	<
123	<	for(i=0; i < 3; i++)
124	<	for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
125	<
126	<	calcBoxL();
127	<	calcHmatInv();
128	<
129	<	for(i=0; i < 3; i++) {
130	<	for (j=0; j < 3; j++) {
131	<	FortranHmat[3*j + i] = Hmat[i][j];
132	<	FortranHmatInv[3*j + i] = HmatInv[i][j];
195	>	addExcludePairs(mol);
196	>
197	>	return true;
198	>	} else {
199	>	return false;
200		}
201		}
202
203	<	setFortranBox(FortranHmat, FortranHmatInv, &orthoRhombic);
204	<
205	<	}
139	<
203	>	bool SimInfo::removeMolecule(Molecule* mol) {
204	>	MoleculeIterator i;
205	>	i = molecules_.find(mol->getGlobalIndex());
206
207	<	void SimInfo::getBoxM (double theBox[3][3]) {
207	>	if (i != molecules_.end() ) {
208
209	<	int i, j;
210	<	for(i=0; i<3; i++)
211	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
212	<	}
209	>	assert(mol == i->second);
210	>
211	>	nAtoms_ -= mol->getNAtoms();
212	>	nBonds_ -= mol->getNBonds();
213	>	nBends_ -= mol->getNBends();
214	>	nTorsions_ -= mol->getNTorsions();
215	>	nRigidBodies_ -= mol->getNRigidBodies();
216	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
217	>	nCutoffGroups_ -= mol->getNCutoffGroups();
218	>	nConstraints_ -= mol->getNConstraintPairs();
219
220	+	removeExcludePairs(mol);
221	+	molecules_.erase(mol->getGlobalIndex());
222
223	<	void SimInfo::scaleBox(double scale) {
224	<	double theBox[3][3];
225	<	int i, j;
223	>	delete mol;
224	>
225	>	return true;
226	>	} else {
227	>	return false;
228	>	}
229
153	–	// cerr << "Scaling box by " << scale << "\n";
230
231	<	for(i=0; i<3; i++)
156	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
231	>	}
232
233	<	setBoxM(theBox);
233	>
234	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
235	>	i = molecules_.begin();
236	>	return i == molecules_.end() ? NULL : i->second;
237	>	}
238
239	<	}
239	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
240	>	++i;
241	>	return i == molecules_.end() ? NULL : i->second;
242	>	}
243
162	–	void SimInfo::calcHmatInv( void ) {
163	–
164	–	int oldOrtho;
165	–	int i,j;
166	–	double smallDiag;
167	–	double tol;
168	–	double sanity[3][3];
244
245	<	invertMat3( Hmat, HmatInv );
245	>	void SimInfo::calcNdf() {
246	>	int ndf_local;
247	>	MoleculeIterator i;
248	>	std::vector<StuntDouble*>::iterator j;
249	>	Molecule* mol;
250	>	StuntDouble* integrableObject;
251
252	<	// check to see if Hmat is orthorhombic
253	<
254	<	oldOrtho = orthoRhombic;
252	>	ndf_local = 0;
253	>
254	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
255	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
256	>	integrableObject = mol->nextIntegrableObject(j)) {
257
258	<	smallDiag = fabs(Hmat[0][0]);
177	<	if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
178	<	if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
179	<	tol = smallDiag * orthoTolerance;
258	>	ndf_local += 3;
259
260	<	orthoRhombic = 1;
261	<
262	<	for (i = 0; i < 3; i++ ) {
263	<	for (j = 0 ; j < 3; j++) {
264	<	if (i != j) {
265	<	if (orthoRhombic) {
266	<	if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
267	<	}
268	<	}
269	<	}
191	<	}
192	<
193	<	if( oldOrtho != orthoRhombic ){
260	>	if (integrableObject->isDirectional()) {
261	>	if (integrableObject->isLinear()) {
262	>	ndf_local += 2;
263	>	} else {
264	>	ndf_local += 3;
265	>	}
266	>	}
267	>
268	>	}//end for (integrableObject)
269	>	}// end for (mol)
270
271	<	if( orthoRhombic ) {
272	<	sprintf( painCave.errMsg,
197	<	"OOPSE is switching from the default Non-Orthorhombic\n"
198	<	"\tto the faster Orthorhombic periodic boundary computations.\n"
199	<	"\tThis is usually a good thing, but if you wan't the\n"
200	<	"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
201	<	"\tvariable ( currently set to %G ) smaller.\n",
202	<	orthoTolerance);
203	<	painCave.severity = OOPSE_INFO;
204	<	simError();
205	<	}
206	<	else {
207	<	sprintf( painCave.errMsg,
208	<	"OOPSE is switching from the faster Orthorhombic to the more\n"
209	<	"\tflexible Non-Orthorhombic periodic boundary computations.\n"
210	<	"\tThis is usually because the box has deformed under\n"
211	<	"\tNPTf integration. If you wan't to live on the edge with\n"
212	<	"\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
213	<	"\tvariable ( currently set to %G ) larger.\n",
214	<	orthoTolerance);
215	<	painCave.severity = OOPSE_WARNING;
216	<	simError();
217	<	}
218	<	}
219	<	}
271	>	// n_constraints is local, so subtract them on each processor
272	>	ndf_local -= nConstraints_;
273
274	<	void SimInfo::calcBoxL( void ){
274	>	#ifdef IS_MPI
275	>	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
276	>	#else
277	>	ndf_ = ndf_local;
278	>	#endif
279
280	<	double dx, dy, dz, dsq;
280	>	// nZconstraints_ is global, as are the 3 COM translations for the
281	>	// entire system:
282	>	ndf_ = ndf_ - 3 - nZconstraint_;
283
284	<	// boxVol = Determinant of Hmat
284	>	}
285
286	<	boxVol = matDet3( Hmat );
286	>	void SimInfo::calcNdfRaw() {
287	>	int ndfRaw_local;
288
289	<	// boxLx
290	<
291	<	dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
292	<	dsq = dx*dx + dy*dy + dz*dz;
233	<	boxL[0] = sqrt( dsq );
234	<	//maxCutoff = 0.5 * boxL[0];
289	>	MoleculeIterator i;
290	>	std::vector<StuntDouble*>::iterator j;
291	>	Molecule* mol;
292	>	StuntDouble* integrableObject;
293
294	<	// boxLy
295	<
296	<	dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
297	<	dsq = dx*dx + dy*dy + dz*dz;
298	<	boxL[1] = sqrt( dsq );
299	<	//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
294	>	// Raw degrees of freedom that we have to set
295	>	ndfRaw_local = 0;
296	>
297	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
298	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
299	>	integrableObject = mol->nextIntegrableObject(j)) {
300
301	+	ndfRaw_local += 3;
302
303	<	// boxLz
304	<
305	<	dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
306	<	dsq = dx*dx + dy*dy + dz*dz;
307	<	boxL[2] = sqrt( dsq );
308	<	//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
309	<
310	<	//calculate the max cutoff
311	<	maxCutoff =  calcMaxCutOff();
312	<
313	<	checkCutOffs();
314	<
315	<	}
316	<
317	<
318	<	double SimInfo::calcMaxCutOff(){
303	>	if (integrableObject->isDirectional()) {
304	>	if (integrableObject->isLinear()) {
305	>	ndfRaw_local += 2;
306	>	} else {
307	>	ndfRaw_local += 3;
308	>	}
309	>	}
310	>
311	>	}
312	>	}
313	>
314	>	#ifdef IS_MPI
315	>	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
316	>	#else
317	>	ndfRaw_ = ndfRaw_local;
318	>	#endif
319	>	}
320
321	<	double ri[3], rj[3], rk[3];
322	<	double rij[3], rjk[3], rki[3];
263	<	double minDist;
321	>	void SimInfo::calcNdfTrans() {
322	>	int ndfTrans_local;
323
324	<	ri[0] = Hmat[0][0];
266	<	ri[1] = Hmat[1][0];
267	<	ri[2] = Hmat[2][0];
324	>	ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
325
269	–	rj[0] = Hmat[0][1];
270	–	rj[1] = Hmat[1][1];
271	–	rj[2] = Hmat[2][1];
326
327	<	rk[0] = Hmat[0][2];
328	<	rk[1] = Hmat[1][2];
329	<	rk[2] = Hmat[2][2];
330	<
331	<	crossProduct3(ri, rj, rij);
278	<	distXY = dotProduct3(rk,rij) / norm3(rij);
327	>	#ifdef IS_MPI
328	>	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
329	>	#else
330	>	ndfTrans_ = ndfTrans_local;
331	>	#endif
332
333	<	crossProduct3(rj,rk, rjk);
334	<	distYZ = dotProduct3(ri,rjk) / norm3(rjk);
333	>	ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
334	>
335	>	}
336
337	<	crossProduct3(rk,ri, rki);
338	<	distZX = dotProduct3(rj,rki) / norm3(rki);
337	>	void SimInfo::addExcludePairs(Molecule* mol) {
338	>	std::vector<Bond*>::iterator bondIter;
339	>	std::vector<Bend*>::iterator bendIter;
340	>	std::vector<Torsion*>::iterator torsionIter;
341	>	Bond* bond;
342	>	Bend* bend;
343	>	Torsion* torsion;
344	>	int a;
345	>	int b;
346	>	int c;
347	>	int d;
348	>
349	>	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
350	>	a = bond->getAtomA()->getGlobalIndex();
351	>	b = bond->getAtomB()->getGlobalIndex();
352	>	exclude_.addPair(a, b);
353	>	}
354
355	<	minDist = min(min(distXY, distYZ), distZX);
356	<	return minDist/2;
357	<
358	<	}
355	>	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
356	>	a = bend->getAtomA()->getGlobalIndex();
357	>	b = bend->getAtomB()->getGlobalIndex();
358	>	c = bend->getAtomC()->getGlobalIndex();
359
360	<	void SimInfo::wrapVector( double thePos[3] ){
360	>	exclude_.addPair(a, b);
361	>	exclude_.addPair(a, c);
362	>	exclude_.addPair(b, c);
363	>	}
364
365	<	int i;
366	<	double scaled[3];
365	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
366	>	a = torsion->getAtomA()->getGlobalIndex();
367	>	b = torsion->getAtomB()->getGlobalIndex();
368	>	c = torsion->getAtomC()->getGlobalIndex();
369	>	d = torsion->getAtomD()->getGlobalIndex();
370
371	<	if( !orthoRhombic ){
372	<	// calc the scaled coordinates.
373	<
371	>	exclude_.addPair(a, b);
372	>	exclude_.addPair(a, c);
373	>	exclude_.addPair(a, d);
374	>	exclude_.addPair(b, c);
375	>	exclude_.addPair(b, d);
376	>	exclude_.addPair(c, d);
377	>	}
378
379	<	matVecMul3(HmatInv, thePos, scaled);
380	<
381	<	for(i=0; i<3; i++)
382	<	scaled[i] -= roundMe(scaled[i]);
383	<
384	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
385	<
386	<	matVecMul3(Hmat, scaled, thePos);
379	>	Molecule::RigidBodyIterator rbIter;
380	>	RigidBody* rb;
381	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
382	>	std::vector<Atom*> atoms = rb->getAtoms();
383	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
384	>	for (int j = i + 1; j < atoms.size(); ++j) {
385	>	a = atoms[i]->getGlobalIndex();
386	>	b = atoms[j]->getGlobalIndex();
387	>	exclude_.addPair(a, b);
388	>	}
389	>	}
390	>	}
391
392		}
393	<	else{
394	<	// calc the scaled coordinates.
393	>
394	>	void SimInfo::removeExcludePairs(Molecule* mol) {
395	>	std::vector<Bond*>::iterator bondIter;
396	>	std::vector<Bend*>::iterator bendIter;
397	>	std::vector<Torsion*>::iterator torsionIter;
398	>	Bond* bond;
399	>	Bend* bend;
400	>	Torsion* torsion;
401	>	int a;
402	>	int b;
403	>	int c;
404	>	int d;
405
406	<	for(i=0; i<3; i++)
407	<	scaled[i] = thePos[i]*HmatInv[i][i];
408	<
409	<	// wrap the scaled coordinates
410	<
318	<	for(i=0; i<3; i++)
319	<	scaled[i] -= roundMe(scaled[i]);
320	<
321	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
322	<
323	<	for(i=0; i<3; i++)
324	<	thePos[i] = scaled[i]*Hmat[i][i];
325	<	}
326	<
327	<	}
406	>	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
407	>	a = bond->getAtomA()->getGlobalIndex();
408	>	b = bond->getAtomB()->getGlobalIndex();
409	>	exclude_.removePair(a, b);
410	>	}
411
412	+	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
413	+	a = bend->getAtomA()->getGlobalIndex();
414	+	b = bend->getAtomB()->getGlobalIndex();
415	+	c = bend->getAtomC()->getGlobalIndex();
416
417	<	int SimInfo::getNDF(){
418	<	int ndf_local;
417	>	exclude_.removePair(a, b);
418	>	exclude_.removePair(a, c);
419	>	exclude_.removePair(b, c);
420	>	}
421
422	<	ndf_local = 0;
423	<
424	<	for(int i = 0; i < integrableObjects.size(); i++){
425	<	ndf_local += 3;
426	<	if (integrableObjects[i]->isDirectional()) {
427	<	if (integrableObjects[i]->isLinear())
428	<	ndf_local += 2;
429	<	else
430	<	ndf_local += 3;
422	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
423	>	a = torsion->getAtomA()->getGlobalIndex();
424	>	b = torsion->getAtomB()->getGlobalIndex();
425	>	c = torsion->getAtomC()->getGlobalIndex();
426	>	d = torsion->getAtomD()->getGlobalIndex();
427	>
428	>	exclude_.removePair(a, b);
429	>	exclude_.removePair(a, c);
430	>	exclude_.removePair(a, d);
431	>	exclude_.removePair(b, c);
432	>	exclude_.removePair(b, d);
433	>	exclude_.removePair(c, d);
434		}
435	+
436	+	Molecule::RigidBodyIterator rbIter;
437	+	RigidBody* rb;
438	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
439	+	std::vector<Atom*> atoms = rb->getAtoms();
440	+	for (int i = 0; i < atoms.size() -1 ; ++i) {
441	+	for (int j = i + 1; j < atoms.size(); ++j) {
442	+	a = atoms[i]->getGlobalIndex();
443	+	b = atoms[j]->getGlobalIndex();
444	+	exclude_.removePair(a, b);
445	+	}
446	+	}
447	+	}
448	+
449		}
450
345	–	// n_constraints is local, so subtract them on each processor:
451
452	<	ndf_local -= n_constraints;
452	>	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
453	>	int curStampId;
454
455	+	//index from 0
456	+	curStampId = moleculeStamps_.size();
457	+
458	+	moleculeStamps_.push_back(molStamp);
459	+	molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
460	+	}
461	+
462	+	void SimInfo::update() {
463	+
464	+	setupSimType();
465	+
466		#ifdef IS_MPI
467	<	MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
351	<	#else
352	<	ndf = ndf_local;
467	>	setupFortranParallel();
468		#endif
469
470	<	// nZconstraints is global, as are the 3 COM translations for the
356	<	// entire system:
470	>	setupFortranSim();
471
472	<	ndf = ndf - 3 - nZconstraints;
472	>	//setup fortran force field
473	>	/** @deprecate */
474	>	int isError = 0;
475	>
476	>	setupElectrostaticSummationMethod( isError );
477	>	setupSwitchingFunction();
478
479	<	return ndf;
480	<	}
479	>	if(isError){
480	>	sprintf( painCave.errMsg,
481	>	"ForceField error: There was an error initializing the forceField in fortran.\n" );
482	>	painCave.isFatal = 1;
483	>	simError();
484	>	}
485	>
486	>
487	>	setupCutoff();
488
489	<	int SimInfo::getNDFraw() {
490	<	int ndfRaw_local;
489	>	calcNdf();
490	>	calcNdfRaw();
491	>	calcNdfTrans();
492
493	<	// Raw degrees of freedom that we have to set
494	<	ndfRaw_local = 0;
493	>	fortranInitialized_ = true;
494	>	}
495
496	<	for(int i = 0; i < integrableObjects.size(); i++){
497	<	ndfRaw_local += 3;
498	<	if (integrableObjects[i]->isDirectional()) {
499	<	if (integrableObjects[i]->isLinear())
500	<	ndfRaw_local += 2;
501	<	else
502	<	ndfRaw_local += 3;
496	>	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
497	>	SimInfo::MoleculeIterator mi;
498	>	Molecule* mol;
499	>	Molecule::AtomIterator ai;
500	>	Atom* atom;
501	>	std::set<AtomType*> atomTypes;
502	>
503	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
504	>
505	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
506	>	atomTypes.insert(atom->getAtomType());
507	>	}
508	>
509		}
510	+
511	+	return atomTypes;
512		}
513	+
514	+	void SimInfo::setupSimType() {
515	+	std::set<AtomType*>::iterator i;
516	+	std::set<AtomType*> atomTypes;
517	+	atomTypes = getUniqueAtomTypes();
518
519	<	#ifdef IS_MPI
520	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
521	<	#else
522	<	ndfRaw = ndfRaw_local;
523	<	#endif
519	>	int useLennardJones = 0;
520	>	int useElectrostatic = 0;
521	>	int useEAM = 0;
522	>	int useCharge = 0;
523	>	int useDirectional = 0;
524	>	int useDipole = 0;
525	>	int useGayBerne = 0;
526	>	int useSticky = 0;
527	>	int useStickyPower = 0;
528	>	int useShape = 0;
529	>	int useFLARB = 0; //it is not in AtomType yet
530	>	int useDirectionalAtom = 0;
531	>	int useElectrostatics = 0;
532	>	//usePBC and useRF are from simParams
533	>	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
534	>	int useRF;
535	>	int useSF;
536	>	std::string myMethod;
537
538	<	return ndfRaw;
539	<	}
538	>	// set the useRF logical
539	>	useRF = 0;
540	>	useSF = 0;
541
388	–	int SimInfo::getNDFtranslational() {
389	–	int ndfTrans_local;
542
543	<	ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
543	>	if (simParams_->haveElectrostaticSummationMethod()) {
544	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
545	>	toUpper(myMethod);
546	>	if (myMethod == "REACTION_FIELD") {
547	>	useRF=1;
548	>	} else {
549	>	if (myMethod == "SHIFTED_FORCE") {
550	>	useSF = 1;
551	>	}
552	>	}
553	>	}
554
555	+	//loop over all of the atom types
556	+	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
557	+	useLennardJones |= (*i)->isLennardJones();
558	+	useElectrostatic |= (*i)->isElectrostatic();
559	+	useEAM |= (*i)->isEAM();
560	+	useCharge |= (*i)->isCharge();
561	+	useDirectional |= (*i)->isDirectional();
562	+	useDipole |= (*i)->isDipole();
563	+	useGayBerne |= (*i)->isGayBerne();
564	+	useSticky |= (*i)->isSticky();
565	+	useStickyPower |= (*i)->isStickyPower();
566	+	useShape |= (*i)->isShape();
567	+	}
568
569	<	#ifdef IS_MPI
570	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
571	<	#else
397	<	ndfTrans = ndfTrans_local;
398	<	#endif
569	>	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
570	>	useDirectionalAtom = 1;
571	>	}
572
573	<	ndfTrans = ndfTrans - 3 - nZconstraints;
573	>	if (useCharge || useDipole) {
574	>	useElectrostatics = 1;
575	>	}
576
577	<	return ndfTrans;
578	<	}
577	>	#ifdef IS_MPI
578	>	int temp;
579
580	<	int SimInfo::getTotIntegrableObjects() {
581	<	int nObjs_local;
407	<	int nObjs;
580	>	temp = usePBC;
581	>	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
582
583	<	nObjs_local =  integrableObjects.size();
583	>	temp = useDirectionalAtom;
584	>	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
585
586	+	temp = useLennardJones;
587	+	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
588
589	<	#ifdef IS_MPI
590	<	MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
414	<	#else
415	<	nObjs = nObjs_local;
416	<	#endif
589	>	temp = useElectrostatics;
590	>	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
591
592	+	temp = useCharge;
593	+	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
594
595	<	return nObjs;
596	<	}
595	>	temp = useDipole;
596	>	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
597
598	<	void SimInfo::refreshSim(){
598	>	temp = useSticky;
599	>	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
600
601	<	simtype fInfo;
602	<	int isError;
603	<	int n_global;
604	<	int* excl;
601	>	temp = useStickyPower;
602	>	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
603	>
604	>	temp = useGayBerne;
605	>	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
606
607	<	fInfo.dielect = 0.0;
607	>	temp = useEAM;
608	>	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
609	>
610	>	temp = useShape;
611	>	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
612	>
613	>	temp = useFLARB;
614	>	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
615	>
616	>	temp = useRF;
617	>	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
618	>
619	>	temp = useSF;
620	>	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
621
622	<	if( useDipoles ){
623	<	if( useReactionField )fInfo.dielect = dielectric;
622	>	#endif
623	>
624	>	fInfo_.SIM_uses_PBC = usePBC;
625	>	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
626	>	fInfo_.SIM_uses_LennardJones = useLennardJones;
627	>	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
628	>	fInfo_.SIM_uses_Charges = useCharge;
629	>	fInfo_.SIM_uses_Dipoles = useDipole;
630	>	fInfo_.SIM_uses_Sticky = useSticky;
631	>	fInfo_.SIM_uses_StickyPower = useStickyPower;
632	>	fInfo_.SIM_uses_GayBerne = useGayBerne;
633	>	fInfo_.SIM_uses_EAM = useEAM;
634	>	fInfo_.SIM_uses_Shapes = useShape;
635	>	fInfo_.SIM_uses_FLARB = useFLARB;
636	>	fInfo_.SIM_uses_RF = useRF;
637	>	fInfo_.SIM_uses_SF = useSF;
638	>
639	>	if( myMethod == "REACTION_FIELD") {
640	>
641	>	if (simParams_->haveDielectric()) {
642	>	fInfo_.dielect = simParams_->getDielectric();
643	>	} else {
644	>	sprintf(painCave.errMsg,
645	>	"SimSetup Error: No Dielectric constant was set.\n"
646	>	"\tYou are trying to use Reaction Field without"
647	>	"\tsetting a dielectric constant!\n");
648	>	painCave.isFatal = 1;
649	>	simError();
650	>	}
651	>	}
652	>
653		}
654
655	<	fInfo.SIM_uses_PBC = usePBC;
656	<	//fInfo.SIM_uses_LJ = 0;
657	<	fInfo.SIM_uses_LJ = useLJ;
658	<	fInfo.SIM_uses_sticky = useSticky;
659	<	//fInfo.SIM_uses_sticky = 0;
660	<	fInfo.SIM_uses_charges = useCharges;
661	<	fInfo.SIM_uses_dipoles = useDipoles;
442	<	//fInfo.SIM_uses_dipoles = 0;
443	<	fInfo.SIM_uses_RF = useReactionField;
444	<	//fInfo.SIM_uses_RF = 0;
445	<	fInfo.SIM_uses_GB = useGB;
446	<	fInfo.SIM_uses_EAM = useEAM;
655	>	void SimInfo::setupFortranSim() {
656	>	int isError;
657	>	int nExclude;
658	>	std::vector<int> fortranGlobalGroupMembership;
659	>
660	>	nExclude = exclude_.getSize();
661	>	isError = 0;
662
663	<	n_exclude = excludes->getSize();
664	<	excl = excludes->getFortranArray();
665	<
666	<	#ifdef IS_MPI
452	<	n_global = mpiSim->getNAtomsGlobal();
453	<	#else
454	<	n_global = n_atoms;
455	<	#endif
456	<
457	<	isError = 0;
458	<
459	<	getFortranGroupArrays(this, FglobalGroupMembership, mfact);
460	<	//it may not be a good idea to pass the address of first element in vector
461	<	//since c++ standard does not require vector to be stored continuously in meomory
462	<	//Most of the compilers will organize the memory of vector continuously
463	<	setFortranSim( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
464	<	&nGlobalExcludes, globalExcludes, molMembershipArray,
465	<	&mfact[0], &ngroup, &FglobalGroupMembership[0], &isError);
663	>	//globalGroupMembership_ is filled by SimCreator
664	>	for (int i = 0; i < nGlobalAtoms_; i++) {
665	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
666	>	}
667
668	<	if( isError ){
668	>	//calculate mass ratio of cutoff group
669	>	std::vector<double> mfact;
670	>	SimInfo::MoleculeIterator mi;
671	>	Molecule* mol;
672	>	Molecule::CutoffGroupIterator ci;
673	>	CutoffGroup* cg;
674	>	Molecule::AtomIterator ai;
675	>	Atom* atom;
676	>	double totalMass;
677	>
678	>	//to avoid memory reallocation, reserve enough space for mfact
679	>	mfact.reserve(getNCutoffGroups());
680
681	<	sprintf( painCave.errMsg,
682	<	"There was an error setting the simulation information in fortran.\n" );
471	<	painCave.isFatal = 1;
472	<	painCave.severity = OOPSE_ERROR;
473	<	simError();
474	<	}
475	<
476	<	#ifdef IS_MPI
477	<	sprintf( checkPointMsg,
478	<	"succesfully sent the simulation information to fortran.\n");
479	<	MPIcheckPoint();
480	<	#endif // is_mpi
481	<
482	<	this->ndf = this->getNDF();
483	<	this->ndfRaw = this->getNDFraw();
484	<	this->ndfTrans = this->getNDFtranslational();
485	<	}
681	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
682	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
683
684	<	void SimInfo::setDefaultRcut( double theRcut ){
685	<
686	<	haveRcut = 1;
687	<	rCut = theRcut;
688	<	rList = rCut + 1.0;
689	<
690	<	notifyFortranCutoffs( &rCut, &rSw, &rList );
691	<	}
684	>	totalMass = cg->getMass();
685	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
686	>	// Check for massless groups - set mfact to 1 if true
687	>	if (totalMass != 0)
688	>	mfact.push_back(atom->getMass()/totalMass);
689	>	else
690	>	mfact.push_back( 1.0 );
691	>	}
692
693	<	void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
693	>	}
694	>	}
695
696	<	rSw = theRsw;
697	<	setDefaultRcut( theRcut );
500	<	}
696	>	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
697	>	std::vector<int> identArray;
698
699	+	//to avoid memory reallocation, reserve enough space identArray
700	+	identArray.reserve(getNAtoms());
701	+
702	+	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
703	+	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
704	+	identArray.push_back(atom->getIdent());
705	+	}
706	+	}
707
708	<	void SimInfo::checkCutOffs( void ){
709	<
710	<	if( boxIsInit ){
708	>	//fill molMembershipArray
709	>	//molMembershipArray is filled by SimCreator
710	>	std::vector<int> molMembershipArray(nGlobalAtoms_);
711	>	for (int i = 0; i < nGlobalAtoms_; i++) {
712	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
713	>	}
714
715	<	//we need to check cutOffs against the box
716	<
717	<	if( rCut > maxCutoff ){
715	>	//setup fortran simulation
716	>	int nGlobalExcludes = 0;
717	>	int* globalExcludes = NULL;
718	>	int* excludeList = exclude_.getExcludeList();
719	>	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
720	>	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
721	>	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
722	>
723	>	if( isError ){
724	>
725		sprintf( painCave.errMsg,
726	<	"cutoffRadius is too large for the current periodic box.\n"
512	<	"\tCurrent Value of cutoffRadius = %G at time %G\n "
513	<	"\tThis is larger than half of at least one of the\n"
514	<	"\tperiodic box vectors.  Right now, the Box matrix is:\n"
515	<	"\n"
516	<	"\t[ %G %G %G ]\n"
517	<	"\t[ %G %G %G ]\n"
518	<	"\t[ %G %G %G ]\n",
519	<	rCut, currentTime,
520	<	Hmat[0][0], Hmat[0][1], Hmat[0][2],
521	<	Hmat[1][0], Hmat[1][1], Hmat[1][2],
522	<	Hmat[2][0], Hmat[2][1], Hmat[2][2]);
523	<	painCave.severity = OOPSE_ERROR;
726	>	"There was an error setting the simulation information in fortran.\n" );
727		painCave.isFatal = 1;
728	+	painCave.severity = OOPSE_ERROR;
729		simError();
730	<	}
731	<	} else {
732	<	// initialize this stuff before using it, OK?
733	<	sprintf( painCave.errMsg,
734	<	"Trying to check cutoffs without a box.\n"
735	<	"\tOOPSE should have better programmers than that.\n" );
736	<	painCave.severity = OOPSE_ERROR;
533	<	painCave.isFatal = 1;
534	<	simError();
730	>	}
731	>
732	>	#ifdef IS_MPI
733	>	sprintf( checkPointMsg,
734	>	"succesfully sent the simulation information to fortran.\n");
735	>	MPIcheckPoint();
736	>	#endif // is_mpi
737		}
536	–
537	–	}
738
539	–	void SimInfo::addProperty(GenericData* prop){
739
740	<	map<string, GenericData*>::iterator result;
741	<	result = properties.find(prop->getID());
543	<
544	<	//we can't simply use  properties[prop->getID()] = prop,
545	<	//it will cause memory leak if we already contain a propery which has the same name of prop
546	<
547	<	if(result != properties.end()){
740	>	#ifdef IS_MPI
741	>	void SimInfo::setupFortranParallel() {
742
743	<	delete (*result).second;
744	<	(*result).second = prop;
745	<
746	<	}
747	<	else{
743	>	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
744	>	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
745	>	std::vector<int> localToGlobalCutoffGroupIndex;
746	>	SimInfo::MoleculeIterator mi;
747	>	Molecule::AtomIterator ai;
748	>	Molecule::CutoffGroupIterator ci;
749	>	Molecule* mol;
750	>	Atom* atom;
751	>	CutoffGroup* cg;
752	>	mpiSimData parallelData;
753	>	int isError;
754
755	<	properties[prop->getID()] = prop;
755	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
756
757	+	//local index(index in DataStorge) of atom is important
758	+	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
759	+	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
760	+	}
761	+
762	+	//local index of cutoff group is trivial, it only depends on the order of travesing
763	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
764	+	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
765	+	}
766	+
767	+	}
768	+
769	+	//fill up mpiSimData struct
770	+	parallelData.nMolGlobal = getNGlobalMolecules();
771	+	parallelData.nMolLocal = getNMolecules();
772	+	parallelData.nAtomsGlobal = getNGlobalAtoms();
773	+	parallelData.nAtomsLocal = getNAtoms();
774	+	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
775	+	parallelData.nGroupsLocal = getNCutoffGroups();
776	+	parallelData.myNode = worldRank;
777	+	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
778	+
779	+	//pass mpiSimData struct and index arrays to fortran
780	+	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
781	+	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
782	+	&localToGlobalCutoffGroupIndex[0], &isError);
783	+
784	+	if (isError) {
785	+	sprintf(painCave.errMsg,
786	+	"mpiRefresh errror: fortran didn't like something we gave it.\n");
787	+	painCave.isFatal = 1;
788	+	simError();
789	+	}
790	+
791	+	sprintf(checkPointMsg, " mpiRefresh successful.\n");
792	+	MPIcheckPoint();
793	+
794	+
795		}
558	–
559	–	}
796
797	<	GenericData* SimInfo::getProperty(const string& propName){
562	<
563	<	map<string, GenericData*>::iterator result;
564	<
565	<	//string lowerCaseName = ();
566	<
567	<	result = properties.find(propName);
568	<
569	<	if(result != properties.end())
570	<	return (*result).second;
571	<	else
572	<	return NULL;
573	<	}
797	>	#endif
798
799	+	double SimInfo::calcMaxCutoffRadius() {
800
576	–	void SimInfo::getFortranGroupArrays(SimInfo* info,
577	–	vector<int>& FglobalGroupMembership,
578	–	vector<double>& mfact){
579	–
580	–	Molecule* myMols;
581	–	Atom** myAtoms;
582	–	int numAtom;
583	–	double mtot;
584	–	int numMol;
585	–	int numCutoffGroups;
586	–	CutoffGroup* myCutoffGroup;
587	–	vector<CutoffGroup*>::iterator iterCutoff;
588	–	Atom* cutoffAtom;
589	–	vector<Atom*>::iterator iterAtom;
590	–	int atomIndex;
591	–	double totalMass;
592	–
593	–	mfact.clear();
594	–	FglobalGroupMembership.clear();
595	–
801
802	<	// Fix the silly fortran indexing problem
802	>	std::set<AtomType*> atomTypes;
803	>	std::set<AtomType*>::iterator i;
804	>	std::vector<double> cutoffRadius;
805	>
806	>	//get the unique atom types
807	>	atomTypes = getUniqueAtomTypes();
808	>
809	>	//query the max cutoff radius among these atom types
810	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
811	>	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
812	>	}
813	>
814	>	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
815		#ifdef IS_MPI
816	<	numAtom = mpiSim->getNAtomsGlobal();
600	<	#else
601	<	numAtom = n_atoms;
816	>	//pick the max cutoff radius among the processors
817		#endif
603	–	for (int i = 0; i < numAtom; i++)
604	–	FglobalGroupMembership.push_back(globalGroupMembership[i] + 1);
605	–
818
819	<	myMols = info->molecules;
820	<	numMol = info->n_mol;
609	<	for(int i  = 0; i < numMol; i++){
610	<	numCutoffGroups = myMols[i].getNCutoffGroups();
611	<	for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff);
612	<	myCutoffGroup != NULL;
613	<	myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
819	>	return maxCutoffRadius;
820	>	}
821
822	<	totalMass = myCutoffGroup->getMass();
823	<
824	<	for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom);
825	<	cutoffAtom != NULL;
826	<	cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
827	<	mfact.push_back(cutoffAtom->getMass()/totalMass);
828	<	}
822	>	void SimInfo::getCutoff(double& rcut, double& rsw) {
823	>
824	>	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
825	>
826	>	if (!simParams_->haveCutoffRadius()){
827	>	sprintf(painCave.errMsg,
828	>	"SimCreator Warning: No value was set for the cutoffRadius.\n"
829	>	"\tOOPSE will use a default value of 15.0 angstroms"
830	>	"\tfor the cutoffRadius.\n");
831	>	painCave.isFatal = 0;
832	>	simError();
833	>	rcut = 15.0;
834	>	} else{
835	>	rcut = simParams_->getCutoffRadius();
836	>	}
837	>
838	>	if (!simParams_->haveSwitchingRadius()){
839	>	sprintf(painCave.errMsg,
840	>	"SimCreator Warning: No value was set for switchingRadius.\n"
841	>	"\tOOPSE will use a default value of\n"
842	>	"\t0.85 * cutoffRadius for the switchingRadius\n");
843	>	painCave.isFatal = 0;
844	>	simError();
845	>	rsw = 0.85 * rcut;
846	>	} else{
847	>	rsw = simParams_->getSwitchingRadius();
848	>	}
849	>
850	>	} else {
851	>	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
852	>	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
853	>
854	>	if (simParams_->haveCutoffRadius()) {
855	>	rcut = simParams_->getCutoffRadius();
856	>	} else {
857	>	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
858	>	rcut = calcMaxCutoffRadius();
859	>	}
860	>
861	>	if (simParams_->haveSwitchingRadius()) {
862	>	rsw  = simParams_->getSwitchingRadius();
863	>	} else {
864	>	rsw = rcut;
865	>	}
866	>
867		}
868		}
869
870	<	}
870	>	void SimInfo::setupCutoff() {
871	>	getCutoff(rcut_, rsw_);
872	>	double rnblist = rcut_ + 1; // skin of neighbor list
873	>
874	>	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
875	>
876	>	int cp =  TRADITIONAL_CUTOFF_POLICY;
877	>	if (simParams_->haveCutoffPolicy()) {
878	>	std::string myPolicy = simParams_->getCutoffPolicy();
879	>	toUpper(myPolicy);
880	>	if (myPolicy == "MIX") {
881	>	cp = MIX_CUTOFF_POLICY;
882	>	} else {
883	>	if (myPolicy == "MAX") {
884	>	cp = MAX_CUTOFF_POLICY;
885	>	} else {
886	>	if (myPolicy == "TRADITIONAL") {
887	>	cp = TRADITIONAL_CUTOFF_POLICY;
888	>	} else {
889	>	// throw error
890	>	sprintf( painCave.errMsg,
891	>	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
892	>	painCave.isFatal = 1;
893	>	simError();
894	>	}
895	>	}
896	>	}
897	>	}
898	>
899	>
900	>	if (simParams_->haveSkinThickness()) {
901	>	double skinThickness = simParams_->getSkinThickness();
902	>	}
903	>
904	>	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
905	>	// also send cutoff notification to electrostatics
906	>	setElectrostaticCutoffRadius(&rcut_, &rsw_);
907	>	}
908	>
909	>	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
910	>
911	>	int errorOut;
912	>	int esm =  NONE;
913	>	int sm = UNDAMPED;
914	>	double alphaVal;
915	>	double dielectric;
916	>
917	>	errorOut = isError;
918	>	alphaVal = simParams_->getDampingAlpha();
919	>	dielectric = simParams_->getDielectric();
920	>
921	>	if (simParams_->haveElectrostaticSummationMethod()) {
922	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
923	>	toUpper(myMethod);
924	>	if (myMethod == "NONE") {
925	>	esm = NONE;
926	>	} else {
927	>	if (myMethod == "SWITCHING_FUNCTION") {
928	>	esm = SWITCHING_FUNCTION;
929	>	} else {
930	>	if (myMethod == "SHIFTED_POTENTIAL") {
931	>	esm = SHIFTED_POTENTIAL;
932	>	} else {
933	>	if (myMethod == "SHIFTED_FORCE") {
934	>	esm = SHIFTED_FORCE;
935	>	} else {
936	>	if (myMethod == "REACTION_FIELD") {
937	>	esm = REACTION_FIELD;
938	>	} else {
939	>	// throw error
940	>	sprintf( painCave.errMsg,
941	>	"SimInfo error: Unknown electrostaticSummationMethod. (Input file specified %s .)\n\telectrostaticSummationMethod must be one of: \"none\", \"shifted_potential\", \"shifted_force\", or \"reaction_field\".", myMethod.c_str() );
942	>	painCave.isFatal = 1;
943	>	simError();
944	>	}
945	>	}
946	>	}
947	>	}
948	>	}
949	>	}
950	>
951	>	if (simParams_->haveElectrostaticScreeningMethod()) {
952	>	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
953	>	toUpper(myScreen);
954	>	if (myScreen == "UNDAMPED") {
955	>	sm = UNDAMPED;
956	>	} else {
957	>	if (myScreen == "DAMPED") {
958	>	sm = DAMPED;
959	>	if (!simParams_->haveDampingAlpha()) {
960	>	//throw error
961	>	sprintf( painCave.errMsg,
962	>	"SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used.", alphaVal);
963	>	painCave.isFatal = 0;
964	>	simError();
965	>	}
966	>	} else {
967	>	// throw error
968	>	sprintf( painCave.errMsg,
969	>	"SimInfo error: Unknown electrostaticScreeningMethod. (Input file specified %s .)\n\telectrostaticScreeningMethod must be one of: \"undamped\" or \"damped\".", myScreen.c_str() );
970	>	painCave.isFatal = 1;
971	>	simError();
972	>	}
973	>	}
974	>	}
975	>
976	>	// let's pass some summation method variables to fortran
977	>	setElectrostaticSummationMethod( &esm );
978	>	setScreeningMethod( &sm );
979	>	setDampingAlpha( &alphaVal );
980	>	setReactionFieldDielectric( &dielectric );
981	>	initFortranFF( &esm, &errorOut );
982	>	}
983	>
984	>	void SimInfo::setupSwitchingFunction() {
985	>	int ft = CUBIC;
986	>
987	>	if (simParams_->haveSwitchingFunctionType()) {
988	>	std::string funcType = simParams_->getSwitchingFunctionType();
989	>	toUpper(funcType);
990	>	if (funcType == "CUBIC") {
991	>	ft = CUBIC;
992	>	} else {
993	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
994	>	ft = FIFTH_ORDER_POLY;
995	>	} else {
996	>	// throw error
997	>	sprintf( painCave.errMsg,
998	>	"SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
999	>	painCave.isFatal = 1;
1000	>	simError();
1001	>	}
1002	>	}
1003	>	}
1004	>
1005	>	// send switching function notification to switcheroo
1006	>	setFunctionType(&ft);
1007	>
1008	>	}
1009	>
1010	>	void SimInfo::addProperty(GenericData* genData) {
1011	>	properties_.addProperty(genData);
1012	>	}
1013	>
1014	>	void SimInfo::removeProperty(const std::string& propName) {
1015	>	properties_.removeProperty(propName);
1016	>	}
1017	>
1018	>	void SimInfo::clearProperties() {
1019	>	properties_.clearProperties();
1020	>	}
1021	>
1022	>	std::vector<std::string> SimInfo::getPropertyNames() {
1023	>	return properties_.getPropertyNames();
1024	>	}
1025	>
1026	>	std::vector<GenericData*> SimInfo::getProperties() {
1027	>	return properties_.getProperties();
1028	>	}
1029	>
1030	>	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1031	>	return properties_.getPropertyByName(propName);
1032	>	}
1033	>
1034	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1035	>	if (sman_ == sman) {
1036	>	return;
1037	>	}
1038	>	delete sman_;
1039	>	sman_ = sman;
1040	>
1041	>	Molecule* mol;
1042	>	RigidBody* rb;
1043	>	Atom* atom;
1044	>	SimInfo::MoleculeIterator mi;
1045	>	Molecule::RigidBodyIterator rbIter;
1046	>	Molecule::AtomIterator atomIter;;
1047	>
1048	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1049	>
1050	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1051	>	atom->setSnapshotManager(sman_);
1052	>	}
1053	>
1054	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1055	>	rb->setSnapshotManager(sman_);
1056	>	}
1057	>	}
1058	>
1059	>	}
1060	>
1061	>	Vector3d SimInfo::getComVel(){
1062	>	SimInfo::MoleculeIterator i;
1063	>	Molecule* mol;
1064	>
1065	>	Vector3d comVel(0.0);
1066	>	double totalMass = 0.0;
1067	>
1068	>
1069	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1070	>	double mass = mol->getMass();
1071	>	totalMass += mass;
1072	>	comVel += mass * mol->getComVel();
1073	>	}
1074	>
1075	>	#ifdef IS_MPI
1076	>	double tmpMass = totalMass;
1077	>	Vector3d tmpComVel(comVel);
1078	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1079	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1080	>	#endif
1081	>
1082	>	comVel /= totalMass;
1083	>
1084	>	return comVel;
1085	>	}
1086	>
1087	>	Vector3d SimInfo::getCom(){
1088	>	SimInfo::MoleculeIterator i;
1089	>	Molecule* mol;
1090	>
1091	>	Vector3d com(0.0);
1092	>	double totalMass = 0.0;
1093	>
1094	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1095	>	double mass = mol->getMass();
1096	>	totalMass += mass;
1097	>	com += mass * mol->getCom();
1098	>	}
1099	>
1100	>	#ifdef IS_MPI
1101	>	double tmpMass = totalMass;
1102	>	Vector3d tmpCom(com);
1103	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1104	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1105	>	#endif
1106	>
1107	>	com /= totalMass;
1108	>
1109	>	return com;
1110	>
1111	>	}
1112	>
1113	>	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1114	>
1115	>	return o;
1116	>	}
1117	>
1118	>
1119	>	/*
1120	>	Returns center of mass and center of mass velocity in one function call.
1121	>	*/
1122	>
1123	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1124	>	SimInfo::MoleculeIterator i;
1125	>	Molecule* mol;
1126	>
1127	>
1128	>	double totalMass = 0.0;
1129	>
1130	>
1131	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1132	>	double mass = mol->getMass();
1133	>	totalMass += mass;
1134	>	com += mass * mol->getCom();
1135	>	comVel += mass * mol->getComVel();
1136	>	}
1137	>
1138	>	#ifdef IS_MPI
1139	>	double tmpMass = totalMass;
1140	>	Vector3d tmpCom(com);
1141	>	Vector3d tmpComVel(comVel);
1142	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1143	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1144	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1145	>	#endif
1146	>
1147	>	com /= totalMass;
1148	>	comVel /= totalMass;
1149	>	}
1150	>
1151	>	/*
1152	>	Return intertia tensor for entire system and angular momentum Vector.
1153	>
1154	>
1155	>	[  Ixx -Ixy  -Ixz ]
1156	>	J =| -Iyx  Iyy  -Iyz |
1157	>	[ -Izx -Iyz   Izz ]
1158	>	*/
1159	>
1160	>	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1161	>
1162	>
1163	>	double xx = 0.0;
1164	>	double yy = 0.0;
1165	>	double zz = 0.0;
1166	>	double xy = 0.0;
1167	>	double xz = 0.0;
1168	>	double yz = 0.0;
1169	>	Vector3d com(0.0);
1170	>	Vector3d comVel(0.0);
1171	>
1172	>	getComAll(com, comVel);
1173	>
1174	>	SimInfo::MoleculeIterator i;
1175	>	Molecule* mol;
1176	>
1177	>	Vector3d thisq(0.0);
1178	>	Vector3d thisv(0.0);
1179	>
1180	>	double thisMass = 0.0;
1181	>
1182	>
1183	>
1184	>
1185	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1186	>
1187	>	thisq = mol->getCom()-com;
1188	>	thisv = mol->getComVel()-comVel;
1189	>	thisMass = mol->getMass();
1190	>	// Compute moment of intertia coefficients.
1191	>	xx += thisq[0]*thisq[0]*thisMass;
1192	>	yy += thisq[1]*thisq[1]*thisMass;
1193	>	zz += thisq[2]*thisq[2]*thisMass;
1194	>
1195	>	// compute products of intertia
1196	>	xy += thisq[0]*thisq[1]*thisMass;
1197	>	xz += thisq[0]*thisq[2]*thisMass;
1198	>	yz += thisq[1]*thisq[2]*thisMass;
1199	>
1200	>	angularMomentum += cross( thisq, thisv ) * thisMass;
1201	>
1202	>	}
1203	>
1204	>
1205	>	inertiaTensor(0,0) = yy + zz;
1206	>	inertiaTensor(0,1) = -xy;
1207	>	inertiaTensor(0,2) = -xz;
1208	>	inertiaTensor(1,0) = -xy;
1209	>	inertiaTensor(1,1) = xx + zz;
1210	>	inertiaTensor(1,2) = -yz;
1211	>	inertiaTensor(2,0) = -xz;
1212	>	inertiaTensor(2,1) = -yz;
1213	>	inertiaTensor(2,2) = xx + yy;
1214	>
1215	>	#ifdef IS_MPI
1216	>	Mat3x3d tmpI(inertiaTensor);
1217	>	Vector3d tmpAngMom;
1218	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1219	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1220	>	#endif
1221	>
1222	>	return;
1223	>	}
1224	>
1225	>	//Returns the angular momentum of the system
1226	>	Vector3d SimInfo::getAngularMomentum(){
1227	>
1228	>	Vector3d com(0.0);
1229	>	Vector3d comVel(0.0);
1230	>	Vector3d angularMomentum(0.0);
1231	>
1232	>	getComAll(com,comVel);
1233	>
1234	>	SimInfo::MoleculeIterator i;
1235	>	Molecule* mol;
1236	>
1237	>	Vector3d thisr(0.0);
1238	>	Vector3d thisp(0.0);
1239	>
1240	>	double thisMass;
1241	>
1242	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1243	>	thisMass = mol->getMass();
1244	>	thisr = mol->getCom()-com;
1245	>	thisp = (mol->getComVel()-comVel)*thisMass;
1246	>
1247	>	angularMomentum += cross( thisr, thisp );
1248	>
1249	>	}
1250	>
1251	>	#ifdef IS_MPI
1252	>	Vector3d tmpAngMom;
1253	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1254	>	#endif
1255	>
1256	>	return angularMomentum;
1257	>	}
1258	>
1259	>
1260	>	}//end namespace oopse
1261	>

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