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Comparing trunk/OOPSE-2.0/src/brains/SimInfo.cpp (file contents):
Revision 1636 by chrisfen, Fri Oct 22 22:54:01 2004 UTC vs.
Revision 2297 by chrisfen, Thu Sep 15 00:14:35 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/fCoulombicCorrection.h"
57	>	#include "UseTheForce/doForces_interface.h"
58		#include "UseTheForce/notifyCutoffs_interface.h"
59	+	#include "utils/MemoryUtils.hpp"
60	+	#include "utils/simError.h"
61	+	#include "selection/SelectionManager.hpp"
62
15	–	//#include "UseTheForce/fortranWrappers.hpp"
16	–
17	–	#include "math/MatVec3.h"
18	–
63		#ifdef IS_MPI
64	<	#include "brains/mpiSimulation.hpp"
65	<	#endif
64	>	#include "UseTheForce/mpiComponentPlan.h"
65	>	#include "UseTheForce/DarkSide/simParallel_interface.h"
66	>	#endif
67
68	<	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	<	}
68	>	namespace oopse {
69
70	<	SimInfo* currentInfo;
70	>	SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
71	>	ForceField* ff, Globals* simParams) :
72	>	stamps_(stamps), forceField_(ff), simParams_(simParams),
73	>	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
74	>	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
75	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
76	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
77	>	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
78	>	sman_(NULL), fortranInitialized_(false) {
79
80	<	SimInfo::SimInfo(){
80	>
81	>	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
82	>	MoleculeStamp* molStamp;
83	>	int nMolWithSameStamp;
84	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
85	>	int nGroups = 0;          //total cutoff groups defined in meta-data file
86	>	CutoffGroupStamp* cgStamp;
87	>	RigidBodyStamp* rbStamp;
88	>	int nRigidAtoms = 0;
89	>
90	>	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
91	>	molStamp = i->first;
92	>	nMolWithSameStamp = i->second;
93	>
94	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
95
96	<	n_constraints = 0;
97	<	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;
96	>	//calculate atoms in molecules
97	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
98
49	–	haveRcut = 0;
50	–	haveRsw = 0;
51	–	boxIsInit = 0;
52	–
53	–	resetTime = 1e99;
99
100	<	orthoRhombic = 0;
101	<	orthoTolerance = 1E-6;
102	<	useInitXSstate = true;
100	>	//calculate atoms in cutoff groups
101	>	int nAtomsInGroups = 0;
102	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
103	>
104	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
105	>	cgStamp = molStamp->getCutoffGroup(j);
106	>	nAtomsInGroups += cgStamp->getNMembers();
107	>	}
108
109	<	usePBC = 0;
110	<	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;
109	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
110	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
111
112	<	useSolidThermInt = 0;
113	<	useLiquidThermInt = 0;
112	>	//calculate atoms in rigid bodies
113	>	int nAtomsInRigidBodies = 0;
114	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
115	>
116	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
117	>	rbStamp = molStamp->getRigidBody(j);
118	>	nAtomsInRigidBodies += rbStamp->getNMembers();
119	>	}
120
121	<	haveCutoffGroups = false;
121	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
122	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
123	>
124	>	}
125
126	<	excludes = Exclude::Instance();
126	>	//every free atom (atom does not belong to cutoff groups) is a cutoff group
127	>	//therefore the total number of cutoff groups in the system is equal to
128	>	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
129	>	//file plus the number of cutoff groups defined in meta-data file
130	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
131
132	<	myConfiguration = new SimState();
132	>	//every free atom (atom does not belong to rigid bodies) is an integrable object
133	>	//therefore the total number of  integrable objects in the system is equal to
134	>	//the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
135	>	//file plus the number of  rigid bodies defined in meta-data file
136	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
137
138	<	has_minimizer = false;
81	<	the_minimizer =NULL;
138	>	nGlobalMols_ = molStampIds_.size();
139
140	<	ngroup = 0;
140	>	#ifdef IS_MPI
141	>	molToProcMap_.resize(nGlobalMols_);
142	>	#endif
143
144	<	}
144	>	}
145
146	+	SimInfo::~SimInfo() {
147	+	std::map<int, Molecule*>::iterator i;
148	+	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
149	+	delete i->second;
150	+	}
151	+	molecules_.clear();
152	+
153	+	delete stamps_;
154	+	delete sman_;
155	+	delete simParams_;
156	+	delete forceField_;
157	+	}
158
159	<	SimInfo::~SimInfo(){
159	>	int SimInfo::getNGlobalConstraints() {
160	>	int nGlobalConstraints;
161	>	#ifdef IS_MPI
162	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
163	>	MPI_COMM_WORLD);
164	>	#else
165	>	nGlobalConstraints =  nConstraints_;
166	>	#endif
167	>	return nGlobalConstraints;
168	>	}
169
170	<	delete myConfiguration;
170	>	bool SimInfo::addMolecule(Molecule* mol) {
171	>	MoleculeIterator i;
172
173	<	map<string, GenericData*>::iterator i;
174	<
94	<	for(i = properties.begin(); i != properties.end(); i++)
95	<	delete (*i).second;
173	>	i = molecules_.find(mol->getGlobalIndex());
174	>	if (i == molecules_.end() ) {
175
176	<	}
176	>	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
177	>
178	>	nAtoms_ += mol->getNAtoms();
179	>	nBonds_ += mol->getNBonds();
180	>	nBends_ += mol->getNBends();
181	>	nTorsions_ += mol->getNTorsions();
182	>	nRigidBodies_ += mol->getNRigidBodies();
183	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
184	>	nCutoffGroups_ += mol->getNCutoffGroups();
185	>	nConstraints_ += mol->getNConstraintPairs();
186
187	<	void SimInfo::setBox(double newBox[3]) {
188	<
189	<	int i, j;
190	<	double tempMat[3][3];
191	<
104	<	for(i=0; i<3; i++)
105	<	for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
106	<
107	<	tempMat[0][0] = newBox[0];
108	<	tempMat[1][1] = newBox[1];
109	<	tempMat[2][2] = newBox[2];
110	<
111	<	setBoxM( tempMat );
112	<
113	<	}
114	<
115	<	void SimInfo::setBoxM( double theBox[3][3] ){
116	<
117	<	int i, j;
118	<	double FortranHmat[9]; // to preserve compatibility with Fortran the
119	<	// 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];
187	>	addExcludePairs(mol);
188	>
189	>	return true;
190	>	} else {
191	>	return false;
192		}
193		}
194
195	<	setFortranBox(FortranHmat, FortranHmatInv, &orthoRhombic);
196	<
197	<	}
143	<
195	>	bool SimInfo::removeMolecule(Molecule* mol) {
196	>	MoleculeIterator i;
197	>	i = molecules_.find(mol->getGlobalIndex());
198
199	<	void SimInfo::getBoxM (double theBox[3][3]) {
199	>	if (i != molecules_.end() ) {
200
201	<	int i, j;
202	<	for(i=0; i<3; i++)
203	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
204	<	}
201	>	assert(mol == i->second);
202	>
203	>	nAtoms_ -= mol->getNAtoms();
204	>	nBonds_ -= mol->getNBonds();
205	>	nBends_ -= mol->getNBends();
206	>	nTorsions_ -= mol->getNTorsions();
207	>	nRigidBodies_ -= mol->getNRigidBodies();
208	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
209	>	nCutoffGroups_ -= mol->getNCutoffGroups();
210	>	nConstraints_ -= mol->getNConstraintPairs();
211
212	+	removeExcludePairs(mol);
213	+	molecules_.erase(mol->getGlobalIndex());
214
215	<	void SimInfo::scaleBox(double scale) {
216	<	double theBox[3][3];
217	<	int i, j;
215	>	delete mol;
216	>
217	>	return true;
218	>	} else {
219	>	return false;
220	>	}
221
157	–	// cerr << "Scaling box by " << scale << "\n";
222
223	<	for(i=0; i<3; i++)
160	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
223	>	}
224
225	<	setBoxM(theBox);
225	>
226	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
227	>	i = molecules_.begin();
228	>	return i == molecules_.end() ? NULL : i->second;
229	>	}
230
231	<	}
231	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
232	>	++i;
233	>	return i == molecules_.end() ? NULL : i->second;
234	>	}
235
166	–	void SimInfo::calcHmatInv( void ) {
167	–
168	–	int oldOrtho;
169	–	int i,j;
170	–	double smallDiag;
171	–	double tol;
172	–	double sanity[3][3];
236
237	<	invertMat3( Hmat, HmatInv );
237	>	void SimInfo::calcNdf() {
238	>	int ndf_local;
239	>	MoleculeIterator i;
240	>	std::vector<StuntDouble*>::iterator j;
241	>	Molecule* mol;
242	>	StuntDouble* integrableObject;
243
244	<	// check to see if Hmat is orthorhombic
245	<
246	<	oldOrtho = orthoRhombic;
244	>	ndf_local = 0;
245	>
246	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
247	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
248	>	integrableObject = mol->nextIntegrableObject(j)) {
249
250	<	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;
250	>	ndf_local += 3;
251
252	<	orthoRhombic = 1;
253	<
254	<	for (i = 0; i < 3; i++ ) {
255	<	for (j = 0 ; j < 3; j++) {
256	<	if (i != j) {
257	<	if (orthoRhombic) {
258	<	if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
259	<	}
260	<	}
261	<	}
195	<	}
196	<
197	<	if( oldOrtho != orthoRhombic ){
252	>	if (integrableObject->isDirectional()) {
253	>	if (integrableObject->isLinear()) {
254	>	ndf_local += 2;
255	>	} else {
256	>	ndf_local += 3;
257	>	}
258	>	}
259	>
260	>	}//end for (integrableObject)
261	>	}// end for (mol)
262
263	<	if( orthoRhombic ) {
264	<	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	<	}
263	>	// n_constraints is local, so subtract them on each processor
264	>	ndf_local -= nConstraints_;
265
266	<	void SimInfo::calcBoxL( void ){
266	>	#ifdef IS_MPI
267	>	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
268	>	#else
269	>	ndf_ = ndf_local;
270	>	#endif
271
272	<	double dx, dy, dz, dsq;
272	>	// nZconstraints_ is global, as are the 3 COM translations for the
273	>	// entire system:
274	>	ndf_ = ndf_ - 3 - nZconstraint_;
275
276	<	// boxVol = Determinant of Hmat
276	>	}
277
278	<	boxVol = matDet3( Hmat );
278	>	void SimInfo::calcNdfRaw() {
279	>	int ndfRaw_local;
280
281	<	// boxLx
282	<
283	<	dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
284	<	dsq = dx*dx + dy*dy + dz*dz;
237	<	boxL[0] = sqrt( dsq );
238	<	//maxCutoff = 0.5 * boxL[0];
281	>	MoleculeIterator i;
282	>	std::vector<StuntDouble*>::iterator j;
283	>	Molecule* mol;
284	>	StuntDouble* integrableObject;
285
286	<	// boxLy
287	<
288	<	dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
289	<	dsq = dx*dx + dy*dy + dz*dz;
290	<	boxL[1] = sqrt( dsq );
291	<	//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
286	>	// Raw degrees of freedom that we have to set
287	>	ndfRaw_local = 0;
288	>
289	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
290	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
291	>	integrableObject = mol->nextIntegrableObject(j)) {
292
293	+	ndfRaw_local += 3;
294
295	<	// boxLz
296	<
297	<	dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
298	<	dsq = dx*dx + dy*dy + dz*dz;
299	<	boxL[2] = sqrt( dsq );
300	<	//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
295	>	if (integrableObject->isDirectional()) {
296	>	if (integrableObject->isLinear()) {
297	>	ndfRaw_local += 2;
298	>	} else {
299	>	ndfRaw_local += 3;
300	>	}
301	>	}
302	>
303	>	}
304	>	}
305	>
306	>	#ifdef IS_MPI
307	>	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
308	>	#else
309	>	ndfRaw_ = ndfRaw_local;
310	>	#endif
311	>	}
312
313	<	//calculate the max cutoff
314	<	maxCutoff =  calcMaxCutOff();
257	<
258	<	checkCutOffs();
313	>	void SimInfo::calcNdfTrans() {
314	>	int ndfTrans_local;
315
316	<	}
316	>	ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
317
318
319	<	double SimInfo::calcMaxCutOff(){
319	>	#ifdef IS_MPI
320	>	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
321	>	#else
322	>	ndfTrans_ = ndfTrans_local;
323	>	#endif
324
325	<	double ri[3], rj[3], rk[3];
326	<	double rij[3], rjk[3], rki[3];
327	<	double minDist;
325	>	ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
326	>
327	>	}
328
329	<	ri[0] = Hmat[0][0];
330	<	ri[1] = Hmat[1][0];
331	<	ri[2] = Hmat[2][0];
332	<
333	<	rj[0] = Hmat[0][1];
334	<	rj[1] = Hmat[1][1];
335	<	rj[2] = Hmat[2][1];
336	<
337	<	rk[0] = Hmat[0][2];
338	<	rk[1] = Hmat[1][2];
339	<	rk[2] = Hmat[2][2];
329	>	void SimInfo::addExcludePairs(Molecule* mol) {
330	>	std::vector<Bond*>::iterator bondIter;
331	>	std::vector<Bend*>::iterator bendIter;
332	>	std::vector<Torsion*>::iterator torsionIter;
333	>	Bond* bond;
334	>	Bend* bend;
335	>	Torsion* torsion;
336	>	int a;
337	>	int b;
338	>	int c;
339	>	int d;
340
341	<	crossProduct3(ri, rj, rij);
342	<	distXY = dotProduct3(rk,rij) / norm3(rij);
341	>	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
342	>	a = bond->getAtomA()->getGlobalIndex();
343	>	b = bond->getAtomB()->getGlobalIndex();
344	>	exclude_.addPair(a, b);
345	>	}
346
347	<	crossProduct3(rj,rk, rjk);
348	<	distYZ = dotProduct3(ri,rjk) / norm3(rjk);
347	>	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
348	>	a = bend->getAtomA()->getGlobalIndex();
349	>	b = bend->getAtomB()->getGlobalIndex();
350	>	c = bend->getAtomC()->getGlobalIndex();
351
352	<	crossProduct3(rk,ri, rki);
353	<	distZX = dotProduct3(rj,rki) / norm3(rki);
352	>	exclude_.addPair(a, b);
353	>	exclude_.addPair(a, c);
354	>	exclude_.addPair(b, c);
355	>	}
356
357	<	minDist = min(min(distXY, distYZ), distZX);
358	<	return minDist/2;
359	<
360	<	}
357	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
358	>	a = torsion->getAtomA()->getGlobalIndex();
359	>	b = torsion->getAtomB()->getGlobalIndex();
360	>	c = torsion->getAtomC()->getGlobalIndex();
361	>	d = torsion->getAtomD()->getGlobalIndex();
362
363	<	void SimInfo::wrapVector( double thePos[3] ){
363	>	exclude_.addPair(a, b);
364	>	exclude_.addPair(a, c);
365	>	exclude_.addPair(a, d);
366	>	exclude_.addPair(b, c);
367	>	exclude_.addPair(b, d);
368	>	exclude_.addPair(c, d);
369	>	}
370
371	<	int i;
372	<	double scaled[3];
371	>	Molecule::RigidBodyIterator rbIter;
372	>	RigidBody* rb;
373	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
374	>	std::vector<Atom*> atoms = rb->getAtoms();
375	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
376	>	for (int j = i + 1; j < atoms.size(); ++j) {
377	>	a = atoms[i]->getGlobalIndex();
378	>	b = atoms[j]->getGlobalIndex();
379	>	exclude_.addPair(a, b);
380	>	}
381	>	}
382	>	}
383
384	<	if( !orthoRhombic ){
301	<	// calc the scaled coordinates.
302	<
384	>	}
385
386	<	matVecMul3(HmatInv, thePos, scaled);
386	>	void SimInfo::removeExcludePairs(Molecule* mol) {
387	>	std::vector<Bond*>::iterator bondIter;
388	>	std::vector<Bend*>::iterator bendIter;
389	>	std::vector<Torsion*>::iterator torsionIter;
390	>	Bond* bond;
391	>	Bend* bend;
392	>	Torsion* torsion;
393	>	int a;
394	>	int b;
395	>	int c;
396	>	int d;
397
398	<	for(i=0; i<3; i++)
399	<	scaled[i] -= roundMe(scaled[i]);
400	<
401	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
402	<
311	<	matVecMul3(Hmat, scaled, thePos);
398	>	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
399	>	a = bond->getAtomA()->getGlobalIndex();
400	>	b = bond->getAtomB()->getGlobalIndex();
401	>	exclude_.removePair(a, b);
402	>	}
403
404	<	}
405	<	else{
406	<	// calc the scaled coordinates.
407	<
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	<	}
404	>	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
405	>	a = bend->getAtomA()->getGlobalIndex();
406	>	b = bend->getAtomB()->getGlobalIndex();
407	>	c = bend->getAtomC()->getGlobalIndex();
408
409	+	exclude_.removePair(a, b);
410	+	exclude_.removePair(a, c);
411	+	exclude_.removePair(b, c);
412	+	}
413
414	<	int SimInfo::getNDF(){
415	<	int ndf_local;
414	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
415	>	a = torsion->getAtomA()->getGlobalIndex();
416	>	b = torsion->getAtomB()->getGlobalIndex();
417	>	c = torsion->getAtomC()->getGlobalIndex();
418	>	d = torsion->getAtomD()->getGlobalIndex();
419
420	<	ndf_local = 0;
421	<
422	<	for(int i = 0; i < integrableObjects.size(); i++){
423	<	ndf_local += 3;
424	<	if (integrableObjects[i]->isDirectional()) {
425	<	if (integrableObjects[i]->isLinear())
343	<	ndf_local += 2;
344	<	else
345	<	ndf_local += 3;
420	>	exclude_.removePair(a, b);
421	>	exclude_.removePair(a, c);
422	>	exclude_.removePair(a, d);
423	>	exclude_.removePair(b, c);
424	>	exclude_.removePair(b, d);
425	>	exclude_.removePair(c, d);
426		}
427	+
428	+	Molecule::RigidBodyIterator rbIter;
429	+	RigidBody* rb;
430	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
431	+	std::vector<Atom*> atoms = rb->getAtoms();
432	+	for (int i = 0; i < atoms.size() -1 ; ++i) {
433	+	for (int j = i + 1; j < atoms.size(); ++j) {
434	+	a = atoms[i]->getGlobalIndex();
435	+	b = atoms[j]->getGlobalIndex();
436	+	exclude_.removePair(a, b);
437	+	}
438	+	}
439	+	}
440	+
441		}
442
349	–	// n_constraints is local, so subtract them on each processor:
443
444	<	ndf_local -= n_constraints;
444	>	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
445	>	int curStampId;
446
447	<	#ifdef IS_MPI
448	<	MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
355	<	#else
356	<	ndf = ndf_local;
357	<	#endif
447	>	//index from 0
448	>	curStampId = moleculeStamps_.size();
449
450	<	// nZconstraints is global, as are the 3 COM translations for the
451	<	// entire system:
450	>	moleculeStamps_.push_back(molStamp);
451	>	molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
452	>	}
453
454	<	ndf = ndf - 3 - nZconstraints;
454	>	void SimInfo::update() {
455
456	<	return ndf;
365	<	}
456	>	setupSimType();
457
458	<	int SimInfo::getNDFraw() {
459	<	int ndfRaw_local;
458	>	#ifdef IS_MPI
459	>	setupFortranParallel();
460	>	#endif
461
462	<	// Raw degrees of freedom that we have to set
371	<	ndfRaw_local = 0;
462	>	setupFortranSim();
463
464	<	for(int i = 0; i < integrableObjects.size(); i++){
465	<	ndfRaw_local += 3;
466	<	if (integrableObjects[i]->isDirectional()) {
467	<	if (integrableObjects[i]->isLinear())
468	<	ndfRaw_local += 2;
469	<	else
470	<	ndfRaw_local += 3;
464	>	//setup fortran force field
465	>	/** @deprecate */
466	>	int isError = 0;
467	>
468	>	setupCoulombicCorrection( isError );
469	>
470	>	if(isError){
471	>	sprintf( painCave.errMsg,
472	>	"ForceField error: There was an error initializing the forceField in fortran.\n" );
473	>	painCave.isFatal = 1;
474	>	simError();
475		}
476	<	}
476	>
477
478	<	#ifdef IS_MPI
384	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
385	<	#else
386	<	ndfRaw = ndfRaw_local;
387	<	#endif
478	>	setupCutoff();
479
480	<	return ndfRaw;
481	<	}
480	>	calcNdf();
481	>	calcNdfRaw();
482	>	calcNdfTrans();
483
484	<	int SimInfo::getNDFtranslational() {
485	<	int ndfTrans_local;
484	>	fortranInitialized_ = true;
485	>	}
486
487	<	ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
487	>	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
488	>	SimInfo::MoleculeIterator mi;
489	>	Molecule* mol;
490	>	Molecule::AtomIterator ai;
491	>	Atom* atom;
492	>	std::set<AtomType*> atomTypes;
493
494	+	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
495
496	<	#ifdef IS_MPI
497	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
498	<	#else
499	<	ndfTrans = ndfTrans_local;
500	<	#endif
496	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
497	>	atomTypes.insert(atom->getAtomType());
498	>	}
499	>
500	>	}
501
502	<	ndfTrans = ndfTrans - 3 - nZconstraints;
502	>	return atomTypes;
503	>	}
504
505	<	return ndfTrans;
506	<	}
505	>	void SimInfo::setupSimType() {
506	>	std::set<AtomType*>::iterator i;
507	>	std::set<AtomType*> atomTypes;
508	>	atomTypes = getUniqueAtomTypes();
509	>
510	>	int useLennardJones = 0;
511	>	int useElectrostatic = 0;
512	>	int useEAM = 0;
513	>	int useCharge = 0;
514	>	int useDirectional = 0;
515	>	int useDipole = 0;
516	>	int useGayBerne = 0;
517	>	int useSticky = 0;
518	>	int useStickyPower = 0;
519	>	int useShape = 0;
520	>	int useFLARB = 0; //it is not in AtomType yet
521	>	int useDirectionalAtom = 0;
522	>	int useElectrostatics = 0;
523	>	//usePBC and useRF are from simParams
524	>	int usePBC = simParams_->getPBC();
525	>	int useRF = simParams_->getUseRF();
526
527	<	int SimInfo::getTotIntegrableObjects() {
528	<	int nObjs_local;
529	<	int nObjs;
527	>	//loop over all of the atom types
528	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
529	>	useLennardJones |= (*i)->isLennardJones();
530	>	useElectrostatic |= (*i)->isElectrostatic();
531	>	useEAM |= (*i)->isEAM();
532	>	useCharge |= (*i)->isCharge();
533	>	useDirectional |= (*i)->isDirectional();
534	>	useDipole |= (*i)->isDipole();
535	>	useGayBerne |= (*i)->isGayBerne();
536	>	useSticky |= (*i)->isSticky();
537	>	useStickyPower |= (*i)->isStickyPower();
538	>	useShape |= (*i)->isShape();
539	>	}
540
541	<	nObjs_local =  integrableObjects.size();
541	>	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
542	>	useDirectionalAtom = 1;
543	>	}
544
545	+	if (useCharge || useDipole) {
546	+	useElectrostatics = 1;
547	+	}
548
549	<	#ifdef IS_MPI
550	<	MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
418	<	#else
419	<	nObjs = nObjs_local;
420	<	#endif
549	>	#ifdef IS_MPI
550	>	int temp;
551
552	+	temp = usePBC;
553	+	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
554
555	<	return nObjs;
556	<	}
555	>	temp = useDirectionalAtom;
556	>	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
557
558	<	void SimInfo::refreshSim(){
558	>	temp = useLennardJones;
559	>	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
560
561	<	simtype fInfo;
562	<	int isError;
430	<	int n_global;
431	<	int* excl;
561	>	temp = useElectrostatics;
562	>	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
563
564	<	fInfo.dielect = 0.0;
564	>	temp = useCharge;
565	>	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
566	>
567	>	temp = useDipole;
568	>	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
569	>
570	>	temp = useSticky;
571	>	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
572
573	<	if( useDipoles ){
574	<	if( useReactionField )fInfo.dielect = dielectric;
575	<	}
573	>	temp = useStickyPower;
574	>	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
575	>
576	>	temp = useGayBerne;
577	>	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
578
579	<	fInfo.SIM_uses_PBC = usePBC;
579	>	temp = useEAM;
580	>	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
581
582	<	if (useSticky || useDipoles || useGayBerne || useShapes) {
583	<	useDirectionalAtoms = 1;
443	<	fInfo.SIM_uses_DirectionalAtoms = useDirectionalAtoms;
444	<	}
582	>	temp = useShape;
583	>	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
584
585	<	fInfo.SIM_uses_LennardJones = useLennardJones;
585	>	temp = useFLARB;
586	>	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
587
588	<	if (useCharges || useDipoles) {
589	<	useElectrostatics = 1;
450	<	fInfo.SIM_uses_Electrostatics = useElectrostatics;
451	<	}
588	>	temp = useRF;
589	>	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
590
591	<	fInfo.SIM_uses_Charges = useCharges;
592	<	fInfo.SIM_uses_Dipoles = useDipoles;
455	<	fInfo.SIM_uses_Sticky = useSticky;
456	<	fInfo.SIM_uses_GayBerne = useGayBerne;
457	<	fInfo.SIM_uses_EAM = useEAM;
458	<	fInfo.SIM_uses_Shapes = useShapes;
459	<	fInfo.SIM_uses_FLARB = useFLARB;
460	<	fInfo.SIM_uses_RF = useReactionField;
591	>	temp = useUW;
592	>	MPI_Allreduce(&temp, &useUW, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
593
594	<	n_exclude = excludes->getSize();
595	<	excl = excludes->getFortranArray();
596	<
465	<	#ifdef IS_MPI
466	<	n_global = mpiSim->getNAtomsGlobal();
467	<	#else
468	<	n_global = n_atoms;
594	>	temp = useDW;
595	>	MPI_Allreduce(&temp, &useDW, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
596	>
597		#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);
598
599	<	if( isError ){
600	<
601	<	sprintf( painCave.errMsg,
602	<	"There was an error setting the simulation information in fortran.\n" );
603	<	painCave.isFatal = 1;
604	<	painCave.severity = OOPSE_ERROR;
605	<	simError();
599	>	fInfo_.SIM_uses_PBC = usePBC;
600	>	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
601	>	fInfo_.SIM_uses_LennardJones = useLennardJones;
602	>	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
603	>	fInfo_.SIM_uses_Charges = useCharge;
604	>	fInfo_.SIM_uses_Dipoles = useDipole;
605	>	fInfo_.SIM_uses_Sticky = useSticky;
606	>	fInfo_.SIM_uses_StickyPower = useStickyPower;
607	>	fInfo_.SIM_uses_GayBerne = useGayBerne;
608	>	fInfo_.SIM_uses_EAM = useEAM;
609	>	fInfo_.SIM_uses_Shapes = useShape;
610	>	fInfo_.SIM_uses_FLARB = useFLARB;
611	>	fInfo_.SIM_uses_RF = useRF;
612	>
613	>	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
614	>
615	>	if (simParams_->haveDielectric()) {
616	>	fInfo_.dielect = simParams_->getDielectric();
617	>	} else {
618	>	sprintf(painCave.errMsg,
619	>	"SimSetup Error: No Dielectric constant was set.\n"
620	>	"\tYou are trying to use Reaction Field without"
621	>	"\tsetting a dielectric constant!\n");
622	>	painCave.isFatal = 1;
623	>	simError();
624	>	}
625	>
626	>	} else {
627	>	fInfo_.dielect = 0.0;
628	>	}
629	>
630		}
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	–	}
631
632	<	void SimInfo::setDefaultRcut( double theRcut ){
633	<
634	<	haveRcut = 1;
635	<	rCut = theRcut;
636	<	rList = rCut + 1.0;
637	<
638	<	notifyFortranCutoffs( &rCut, &rSw, &rList );
508	<	}
632	>	void SimInfo::setupFortranSim() {
633	>	int isError;
634	>	int nExclude;
635	>	std::vector<int> fortranGlobalGroupMembership;
636	>
637	>	nExclude = exclude_.getSize();
638	>	isError = 0;
639
640	<	void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
640	>	//globalGroupMembership_ is filled by SimCreator
641	>	for (int i = 0; i < nGlobalAtoms_; i++) {
642	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
643	>	}
644
645	<	rSw = theRsw;
646	<	setDefaultRcut( theRcut );
647	<	}
645	>	//calculate mass ratio of cutoff group
646	>	std::vector<double> mfact;
647	>	SimInfo::MoleculeIterator mi;
648	>	Molecule* mol;
649	>	Molecule::CutoffGroupIterator ci;
650	>	CutoffGroup* cg;
651	>	Molecule::AtomIterator ai;
652	>	Atom* atom;
653	>	double totalMass;
654
655	+	//to avoid memory reallocation, reserve enough space for mfact
656	+	mfact.reserve(getNCutoffGroups());
657	+
658	+	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
659	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
660
661	<	void SimInfo::checkCutOffs( void ){
662	<
663	<	if( boxIsInit ){
661	>	totalMass = cg->getMass();
662	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
663	>	mfact.push_back(atom->getMass()/totalMass);
664	>	}
665	>
666	>	}
667	>	}
668	>
669	>	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
670	>	std::vector<int> identArray;
671	>
672	>	//to avoid memory reallocation, reserve enough space identArray
673	>	identArray.reserve(getNAtoms());
674
675	<	//we need to check cutOffs against the box
675	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
676	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
677	>	identArray.push_back(atom->getIdent());
678	>	}
679	>	}
680	>
681	>	//fill molMembershipArray
682	>	//molMembershipArray is filled by SimCreator
683	>	std::vector<int> molMembershipArray(nGlobalAtoms_);
684	>	for (int i = 0; i < nGlobalAtoms_; i++) {
685	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
686	>	}
687
688	<	if( rCut > maxCutoff ){
688	>	//setup fortran simulation
689	>	int nGlobalExcludes = 0;
690	>	int* globalExcludes = NULL;
691	>	int* excludeList = exclude_.getExcludeList();
692	>	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
693	>	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
694	>	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
695	>
696	>	if( isError ){
697	>
698		sprintf( painCave.errMsg,
699	<	"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;
699	>	"There was an error setting the simulation information in fortran.\n" );
700		painCave.isFatal = 1;
701	+	painCave.severity = OOPSE_ERROR;
702		simError();
703	<	}
704	<	} else {
705	<	// initialize this stuff before using it, OK?
706	<	sprintf( painCave.errMsg,
707	<	"Trying to check cutoffs without a box.\n"
708	<	"\tOOPSE should have better programmers than that.\n" );
709	<	painCave.severity = OOPSE_ERROR;
547	<	painCave.isFatal = 1;
548	<	simError();
703	>	}
704	>
705	>	#ifdef IS_MPI
706	>	sprintf( checkPointMsg,
707	>	"succesfully sent the simulation information to fortran.\n");
708	>	MPIcheckPoint();
709	>	#endif // is_mpi
710		}
550	–
551	–	}
711
553	–	void SimInfo::addProperty(GenericData* prop){
712
713	<	map<string, GenericData*>::iterator result;
714	<	result = properties.find(prop->getID());
557	<
558	<	//we can't simply use  properties[prop->getID()] = prop,
559	<	//it will cause memory leak if we already contain a propery which has the same name of prop
560	<
561	<	if(result != properties.end()){
713	>	#ifdef IS_MPI
714	>	void SimInfo::setupFortranParallel() {
715
716	<	delete (*result).second;
717	<	(*result).second = prop;
718	<
719	<	}
720	<	else{
716	>	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
717	>	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
718	>	std::vector<int> localToGlobalCutoffGroupIndex;
719	>	SimInfo::MoleculeIterator mi;
720	>	Molecule::AtomIterator ai;
721	>	Molecule::CutoffGroupIterator ci;
722	>	Molecule* mol;
723	>	Atom* atom;
724	>	CutoffGroup* cg;
725	>	mpiSimData parallelData;
726	>	int isError;
727
728	<	properties[prop->getID()] = prop;
728	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
729
730	+	//local index(index in DataStorge) of atom is important
731	+	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
732	+	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
733	+	}
734	+
735	+	//local index of cutoff group is trivial, it only depends on the order of travesing
736	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
737	+	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
738	+	}
739	+
740	+	}
741	+
742	+	//fill up mpiSimData struct
743	+	parallelData.nMolGlobal = getNGlobalMolecules();
744	+	parallelData.nMolLocal = getNMolecules();
745	+	parallelData.nAtomsGlobal = getNGlobalAtoms();
746	+	parallelData.nAtomsLocal = getNAtoms();
747	+	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
748	+	parallelData.nGroupsLocal = getNCutoffGroups();
749	+	parallelData.myNode = worldRank;
750	+	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
751	+
752	+	//pass mpiSimData struct and index arrays to fortran
753	+	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
754	+	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
755	+	&localToGlobalCutoffGroupIndex[0], &isError);
756	+
757	+	if (isError) {
758	+	sprintf(painCave.errMsg,
759	+	"mpiRefresh errror: fortran didn't like something we gave it.\n");
760	+	painCave.isFatal = 1;
761	+	simError();
762	+	}
763	+
764	+	sprintf(checkPointMsg, " mpiRefresh successful.\n");
765	+	MPIcheckPoint();
766	+
767	+
768		}
572	–
573	–	}
769
770	<	GenericData* SimInfo::getProperty(const string& propName){
576	<
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	<	}
770	>	#endif
771
772	+	double SimInfo::calcMaxCutoffRadius() {
773
590	–	void SimInfo::getFortranGroupArrays(SimInfo* info,
591	–	vector<int>& FglobalGroupMembership,
592	–	vector<double>& mfact){
593	–
594	–	Molecule* myMols;
595	–	Atom** myAtoms;
596	–	int numAtom;
597	–	double mtot;
598	–	int numMol;
599	–	int numCutoffGroups;
600	–	CutoffGroup* myCutoffGroup;
601	–	vector<CutoffGroup*>::iterator iterCutoff;
602	–	Atom* cutoffAtom;
603	–	vector<Atom*>::iterator iterAtom;
604	–	int atomIndex;
605	–	double totalMass;
606	–
607	–	mfact.clear();
608	–	FglobalGroupMembership.clear();
609	–
774
775	<	// Fix the silly fortran indexing problem
775	>	std::set<AtomType*> atomTypes;
776	>	std::set<AtomType*>::iterator i;
777	>	std::vector<double> cutoffRadius;
778	>
779	>	//get the unique atom types
780	>	atomTypes = getUniqueAtomTypes();
781	>
782	>	//query the max cutoff radius among these atom types
783	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
784	>	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
785	>	}
786	>
787	>	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
788		#ifdef IS_MPI
789	<	numAtom = mpiSim->getNAtomsGlobal();
614	<	#else
615	<	numAtom = n_atoms;
789	>	//pick the max cutoff radius among the processors
790		#endif
617	–	for (int i = 0; i < numAtom; i++)
618	–	FglobalGroupMembership.push_back(globalGroupMembership[i] + 1);
619	–
791
792	<	myMols = info->molecules;
793	<	numMol = info->n_mol;
623	<	for(int i  = 0; i < numMol; i++){
624	<	numCutoffGroups = myMols[i].getNCutoffGroups();
625	<	for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff);
626	<	myCutoffGroup != NULL;
627	<	myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
792	>	return maxCutoffRadius;
793	>	}
794
795	<	totalMass = myCutoffGroup->getMass();
796	<
797	<	for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom);
798	<	cutoffAtom != NULL;
799	<	cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
800	<	mfact.push_back(cutoffAtom->getMass()/totalMass);
801	<	}
795	>	void SimInfo::getCutoff(double& rcut, double& rsw) {
796	>
797	>	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
798	>
799	>	if (!simParams_->haveRcut()){
800	>	sprintf(painCave.errMsg,
801	>	"SimCreator Warning: No value was set for the cutoffRadius.\n"
802	>	"\tOOPSE will use a default value of 15.0 angstroms"
803	>	"\tfor the cutoffRadius.\n");
804	>	painCave.isFatal = 0;
805	>	simError();
806	>	rcut = 15.0;
807	>	} else{
808	>	rcut = simParams_->getRcut();
809	>	}
810	>
811	>	if (!simParams_->haveRsw()){
812	>	sprintf(painCave.errMsg,
813	>	"SimCreator Warning: No value was set for switchingRadius.\n"
814	>	"\tOOPSE will use a default value of\n"
815	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
816	>	painCave.isFatal = 0;
817	>	simError();
818	>	rsw = 0.95 * rcut;
819	>	} else{
820	>	rsw = simParams_->getRsw();
821	>	}
822	>
823	>	} else {
824	>	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
825	>	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
826	>
827	>	if (simParams_->haveRcut()) {
828	>	rcut = simParams_->getRcut();
829	>	} else {
830	>	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
831	>	rcut = calcMaxCutoffRadius();
832	>	}
833	>
834	>	if (simParams_->haveRsw()) {
835	>	rsw  = simParams_->getRsw();
836	>	} else {
837	>	rsw = rcut;
838	>	}
839	>
840		}
841		}
842
843	<	}
843	>	void SimInfo::setupCutoff() {
844	>	getCutoff(rcut_, rsw_);
845	>	double rnblist = rcut_ + 1; // skin of neighbor list
846	>
847	>	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
848	>
849	>	int cp =  TRADITIONAL_CUTOFF_POLICY;
850	>	if (simParams_->haveCutoffPolicy()) {
851	>	std::string myPolicy = simParams_->getCutoffPolicy();
852	>	if (myPolicy == "MIX") {
853	>	cp = MIX_CUTOFF_POLICY;
854	>	} else {
855	>	if (myPolicy == "MAX") {
856	>	cp = MAX_CUTOFF_POLICY;
857	>	} else {
858	>	if (myPolicy == "TRADITIONAL") {
859	>	cp = TRADITIONAL_CUTOFF_POLICY;
860	>	} else {
861	>	// throw error
862	>	sprintf( painCave.errMsg,
863	>	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
864	>	painCave.isFatal = 1;
865	>	simError();
866	>	}
867	>	}
868	>	}
869	>	}
870	>	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
871	>	}
872	>
873	>	void SimInfo::setupCoulombicCorrection( int isError ) {
874	>
875	>	int errorOut;
876	>	int cc =  NONE;
877	>	double alphaVal;
878	>
879	>	errorOut = isError;
880	>
881	>	if (simParams_->haveCoulombicCorrection()) {
882	>	std::string myCorrection = simParams_->getCoulombicCorrection();
883	>	if (myCorrection == "NONE") {
884	>	cc = NONE;
885	>	} else {
886	>	if (myCorrection == "UNDAMPED_WOLF") {
887	>	cc = UNDAMPED_WOLF;
888	>	} else {
889	>	if (myCorrection == "WOLF") {
890	>	cc = WOLF;
891	>	if (!simParams_->haveDampingAlpha()) {
892	>	//throw error
893	>	sprintf( painCave.errMsg,
894	>	"SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used for the Wolf Coulombic Correction.", simParams_->getDampingAlpha());
895	>	painCave.isFatal = 0;
896	>	simError();
897	>	}
898	>	alphaVal = simParams_->getDampingAlpha();
899	>	} else {
900	>	if (myCorrection == "REACTION_FIELD") {
901	>	cc = REACTION_FIELD;
902	>	} else {
903	>	// throw error
904	>	sprintf( painCave.errMsg,
905	>	"SimInfo error: Unknown coulombicCorrection. (Input file specified %s .)\n\tcoulombicCorrection must be one of: \"none\", \"undamped_wolf\", \"wolf\", or \"reaction_field\".", myCorrection.c_str() );
906	>	painCave.isFatal = 1;
907	>	simError();
908	>	}
909	>	}
910	>	}
911	>	}
912	>	}
913	>	initFortranFF( &fInfo_.SIM_uses_RF, &cc, &alphaVal, &errorOut );
914	>	}
915	>
916	>	void SimInfo::addProperty(GenericData* genData) {
917	>	properties_.addProperty(genData);
918	>	}
919	>
920	>	void SimInfo::removeProperty(const std::string& propName) {
921	>	properties_.removeProperty(propName);
922	>	}
923	>
924	>	void SimInfo::clearProperties() {
925	>	properties_.clearProperties();
926	>	}
927	>
928	>	std::vector<std::string> SimInfo::getPropertyNames() {
929	>	return properties_.getPropertyNames();
930	>	}
931	>
932	>	std::vector<GenericData*> SimInfo::getProperties() {
933	>	return properties_.getProperties();
934	>	}
935	>
936	>	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
937	>	return properties_.getPropertyByName(propName);
938	>	}
939	>
940	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
941	>	if (sman_ == sman) {
942	>	return;
943	>	}
944	>	delete sman_;
945	>	sman_ = sman;
946	>
947	>	Molecule* mol;
948	>	RigidBody* rb;
949	>	Atom* atom;
950	>	SimInfo::MoleculeIterator mi;
951	>	Molecule::RigidBodyIterator rbIter;
952	>	Molecule::AtomIterator atomIter;;
953	>
954	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
955	>
956	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
957	>	atom->setSnapshotManager(sman_);
958	>	}
959	>
960	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
961	>	rb->setSnapshotManager(sman_);
962	>	}
963	>	}
964	>
965	>	}
966	>
967	>	Vector3d SimInfo::getComVel(){
968	>	SimInfo::MoleculeIterator i;
969	>	Molecule* mol;
970	>
971	>	Vector3d comVel(0.0);
972	>	double totalMass = 0.0;
973	>
974	>
975	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
976	>	double mass = mol->getMass();
977	>	totalMass += mass;
978	>	comVel += mass * mol->getComVel();
979	>	}
980	>
981	>	#ifdef IS_MPI
982	>	double tmpMass = totalMass;
983	>	Vector3d tmpComVel(comVel);
984	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
985	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
986	>	#endif
987	>
988	>	comVel /= totalMass;
989	>
990	>	return comVel;
991	>	}
992	>
993	>	Vector3d SimInfo::getCom(){
994	>	SimInfo::MoleculeIterator i;
995	>	Molecule* mol;
996	>
997	>	Vector3d com(0.0);
998	>	double totalMass = 0.0;
999	>
1000	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1001	>	double mass = mol->getMass();
1002	>	totalMass += mass;
1003	>	com += mass * mol->getCom();
1004	>	}
1005	>
1006	>	#ifdef IS_MPI
1007	>	double tmpMass = totalMass;
1008	>	Vector3d tmpCom(com);
1009	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1010	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1011	>	#endif
1012	>
1013	>	com /= totalMass;
1014	>
1015	>	return com;
1016	>
1017	>	}
1018	>
1019	>	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1020	>
1021	>	return o;
1022	>	}
1023	>
1024	>
1025	>	/*
1026	>	Returns center of mass and center of mass velocity in one function call.
1027	>	*/
1028	>
1029	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1030	>	SimInfo::MoleculeIterator i;
1031	>	Molecule* mol;
1032	>
1033	>
1034	>	double totalMass = 0.0;
1035	>
1036	>
1037	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1038	>	double mass = mol->getMass();
1039	>	totalMass += mass;
1040	>	com += mass * mol->getCom();
1041	>	comVel += mass * mol->getComVel();
1042	>	}
1043	>
1044	>	#ifdef IS_MPI
1045	>	double tmpMass = totalMass;
1046	>	Vector3d tmpCom(com);
1047	>	Vector3d tmpComVel(comVel);
1048	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1049	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1050	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1051	>	#endif
1052	>
1053	>	com /= totalMass;
1054	>	comVel /= totalMass;
1055	>	}
1056	>
1057	>	/*
1058	>	Return intertia tensor for entire system and angular momentum Vector.
1059	>
1060	>
1061	>	[  Ixx -Ixy  -Ixz ]
1062	>	J =| -Iyx  Iyy  -Iyz |
1063	>	[ -Izx -Iyz   Izz ]
1064	>	*/
1065	>
1066	>	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1067	>
1068	>
1069	>	double xx = 0.0;
1070	>	double yy = 0.0;
1071	>	double zz = 0.0;
1072	>	double xy = 0.0;
1073	>	double xz = 0.0;
1074	>	double yz = 0.0;
1075	>	Vector3d com(0.0);
1076	>	Vector3d comVel(0.0);
1077	>
1078	>	getComAll(com, comVel);
1079	>
1080	>	SimInfo::MoleculeIterator i;
1081	>	Molecule* mol;
1082	>
1083	>	Vector3d thisq(0.0);
1084	>	Vector3d thisv(0.0);
1085	>
1086	>	double thisMass = 0.0;
1087	>
1088	>
1089	>
1090	>
1091	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1092	>
1093	>	thisq = mol->getCom()-com;
1094	>	thisv = mol->getComVel()-comVel;
1095	>	thisMass = mol->getMass();
1096	>	// Compute moment of intertia coefficients.
1097	>	xx += thisq[0]*thisq[0]*thisMass;
1098	>	yy += thisq[1]*thisq[1]*thisMass;
1099	>	zz += thisq[2]*thisq[2]*thisMass;
1100	>
1101	>	// compute products of intertia
1102	>	xy += thisq[0]*thisq[1]*thisMass;
1103	>	xz += thisq[0]*thisq[2]*thisMass;
1104	>	yz += thisq[1]*thisq[2]*thisMass;
1105	>
1106	>	angularMomentum += cross( thisq, thisv ) * thisMass;
1107	>
1108	>	}
1109	>
1110	>
1111	>	inertiaTensor(0,0) = yy + zz;
1112	>	inertiaTensor(0,1) = -xy;
1113	>	inertiaTensor(0,2) = -xz;
1114	>	inertiaTensor(1,0) = -xy;
1115	>	inertiaTensor(1,1) = xx + zz;
1116	>	inertiaTensor(1,2) = -yz;
1117	>	inertiaTensor(2,0) = -xz;
1118	>	inertiaTensor(2,1) = -yz;
1119	>	inertiaTensor(2,2) = xx + yy;
1120	>
1121	>	#ifdef IS_MPI
1122	>	Mat3x3d tmpI(inertiaTensor);
1123	>	Vector3d tmpAngMom;
1124	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1125	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1126	>	#endif
1127	>
1128	>	return;
1129	>	}
1130	>
1131	>	//Returns the angular momentum of the system
1132	>	Vector3d SimInfo::getAngularMomentum(){
1133	>
1134	>	Vector3d com(0.0);
1135	>	Vector3d comVel(0.0);
1136	>	Vector3d angularMomentum(0.0);
1137	>
1138	>	getComAll(com,comVel);
1139	>
1140	>	SimInfo::MoleculeIterator i;
1141	>	Molecule* mol;
1142	>
1143	>	Vector3d thisr(0.0);
1144	>	Vector3d thisp(0.0);
1145	>
1146	>	double thisMass;
1147	>
1148	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1149	>	thisMass = mol->getMass();
1150	>	thisr = mol->getCom()-com;
1151	>	thisp = (mol->getComVel()-comVel)*thisMass;
1152	>
1153	>	angularMomentum += cross( thisr, thisp );
1154	>
1155	>	}
1156	>
1157	>	#ifdef IS_MPI
1158	>	Vector3d tmpAngMom;
1159	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1160	>	#endif
1161	>
1162	>	return angularMomentum;
1163	>	}
1164	>
1165	>
1166	>	}//end namespace oopse
1167	>

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