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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 2220 by chrisfen, Thu May 5 14:47:35 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"
12	<	#include "UseTheForce/DarkSide/simulation_interface.h"
53	>	#include "math/Vector3.hpp"
54	>	#include "primitives/Molecule.hpp"
55	>	#include "UseTheForce/doForces_interface.h"
56		#include "UseTheForce/notifyCutoffs_interface.h"
57	+	#include "utils/MemoryUtils.hpp"
58	+	#include "utils/simError.h"
59	+	#include "selection/SelectionManager.hpp"
60
15	–	//#include "UseTheForce/fortranWrappers.hpp"
16	–
17	–	#include "math/MatVec3.h"
18	–
61		#ifdef IS_MPI
62	<	#include "brains/mpiSimulation.hpp"
63	<	#endif
62	>	#include "UseTheForce/mpiComponentPlan.h"
63	>	#include "UseTheForce/DarkSide/simParallel_interface.h"
64	>	#endif
65
66	<	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	<	}
66	>	namespace oopse {
67
68	<	SimInfo* currentInfo;
68	>	SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
69	>	ForceField* ff, Globals* simParams) :
70	>	stamps_(stamps), forceField_(ff), simParams_(simParams),
71	>	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
72	>	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
73	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
74	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
75	>	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
76	>	sman_(NULL), fortranInitialized_(false) {
77
78	<	SimInfo::SimInfo(){
78	>
79	>	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
80	>	MoleculeStamp* molStamp;
81	>	int nMolWithSameStamp;
82	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
83	>	int nGroups = 0;          //total cutoff groups defined in meta-data file
84	>	CutoffGroupStamp* cgStamp;
85	>	RigidBodyStamp* rbStamp;
86	>	int nRigidAtoms = 0;
87	>
88	>	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
89	>	molStamp = i->first;
90	>	nMolWithSameStamp = i->second;
91	>
92	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
93
94	<	n_constraints = 0;
95	<	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;
94	>	//calculate atoms in molecules
95	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
96
49	–	haveRcut = 0;
50	–	haveRsw = 0;
51	–	boxIsInit = 0;
52	–
53	–	resetTime = 1e99;
97
98	<	orthoRhombic = 0;
99	<	orthoTolerance = 1E-6;
100	<	useInitXSstate = true;
98	>	//calculate atoms in cutoff groups
99	>	int nAtomsInGroups = 0;
100	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
101	>
102	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
103	>	cgStamp = molStamp->getCutoffGroup(j);
104	>	nAtomsInGroups += cgStamp->getNMembers();
105	>	}
106
107	<	usePBC = 0;
108	<	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;
107	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
108	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
109
110	<	haveCutoffGroups = false;
110	>	//calculate atoms in rigid bodies
111	>	int nAtomsInRigidBodies = 0;
112	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
113	>
114	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
115	>	rbStamp = molStamp->getRigidBody(j);
116	>	nAtomsInRigidBodies += rbStamp->getNMembers();
117	>	}
118
119	<	excludes = Exclude::Instance();
119	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
120	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
121	>
122	>	}
123
124	<	myConfiguration = new SimState();
124	>	//every free atom (atom does not belong to cutoff groups) is a cutoff group
125	>	//therefore the total number of cutoff groups in the system is equal to
126	>	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
127	>	//file plus the number of cutoff groups defined in meta-data file
128	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
129
130	<	has_minimizer = false;
131	<	the_minimizer =NULL;
130	>	//every free atom (atom does not belong to rigid bodies) is an integrable object
131	>	//therefore the total number of  integrable objects in the system is equal to
132	>	//the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
133	>	//file plus the number of  rigid bodies defined in meta-data file
134	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
135
136	<	ngroup = 0;
136	>	nGlobalMols_ = molStampIds_.size();
137
138	<	}
138	>	#ifdef IS_MPI
139	>	molToProcMap_.resize(nGlobalMols_);
140	>	#endif
141
142	+	}
143
144	<	SimInfo::~SimInfo(){
144	>	SimInfo::~SimInfo() {
145	>	std::map<int, Molecule*>::iterator i;
146	>	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
147	>	delete i->second;
148	>	}
149	>	molecules_.clear();
150	>
151	>	delete stamps_;
152	>	delete sman_;
153	>	delete simParams_;
154	>	delete forceField_;
155	>	}
156
157	<	delete myConfiguration;
157	>	int SimInfo::getNGlobalConstraints() {
158	>	int nGlobalConstraints;
159	>	#ifdef IS_MPI
160	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
161	>	MPI_COMM_WORLD);
162	>	#else
163	>	nGlobalConstraints =  nConstraints_;
164	>	#endif
165	>	return nGlobalConstraints;
166	>	}
167
168	<	map<string, GenericData*>::iterator i;
169	<
90	<	for(i = properties.begin(); i != properties.end(); i++)
91	<	delete (*i).second;
168	>	bool SimInfo::addMolecule(Molecule* mol) {
169	>	MoleculeIterator i;
170
171	<	}
171	>	i = molecules_.find(mol->getGlobalIndex());
172	>	if (i == molecules_.end() ) {
173
174	<	void SimInfo::setBox(double newBox[3]) {
175	<
176	<	int i, j;
177	<	double tempMat[3][3];
174	>	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
175	>
176	>	nAtoms_ += mol->getNAtoms();
177	>	nBonds_ += mol->getNBonds();
178	>	nBends_ += mol->getNBends();
179	>	nTorsions_ += mol->getNTorsions();
180	>	nRigidBodies_ += mol->getNRigidBodies();
181	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
182	>	nCutoffGroups_ += mol->getNCutoffGroups();
183	>	nConstraints_ += mol->getNConstraintPairs();
184
185	<	for(i=0; i<3; i++)
186	<	for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
185	>	addExcludePairs(mol);
186	>
187	>	return true;
188	>	} else {
189	>	return false;
190	>	}
191	>	}
192
193	<	tempMat[0][0] = newBox[0];
194	<	tempMat[1][1] = newBox[1];
195	<	tempMat[2][2] = newBox[2];
193	>	bool SimInfo::removeMolecule(Molecule* mol) {
194	>	MoleculeIterator i;
195	>	i = molecules_.find(mol->getGlobalIndex());
196
197	<	setBoxM( tempMat );
197	>	if (i != molecules_.end() ) {
198
199	<	}
199	>	assert(mol == i->second);
200	>
201	>	nAtoms_ -= mol->getNAtoms();
202	>	nBonds_ -= mol->getNBonds();
203	>	nBends_ -= mol->getNBends();
204	>	nTorsions_ -= mol->getNTorsions();
205	>	nRigidBodies_ -= mol->getNRigidBodies();
206	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
207	>	nCutoffGroups_ -= mol->getNCutoffGroups();
208	>	nConstraints_ -= mol->getNConstraintPairs();
209
210	<	void SimInfo::setBoxM( double theBox[3][3] ){
211	<
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);
210	>	removeExcludePairs(mol);
211	>	molecules_.erase(mol->getGlobalIndex());
212
213	<	if( !boxIsInit ) boxIsInit = 1;
214	<
215	<	for(i=0; i < 3; i++)
216	<	for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
217	<
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];
213	>	delete mol;
214	>
215	>	return true;
216	>	} else {
217	>	return false;
218		}
134	–	}
219
136	–	setFortranBox(FortranHmat, FortranHmatInv, &orthoRhombic);
137	–
138	–	}
139	–
220
221	<	void SimInfo::getBoxM (double theBox[3][3]) {
221	>	}
222
223	<	int i, j;
224	<	for(i=0; i<3; i++)
225	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
226	<	}
223	>
224	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
225	>	i = molecules_.begin();
226	>	return i == molecules_.end() ? NULL : i->second;
227	>	}
228
229	+	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
230	+	++i;
231	+	return i == molecules_.end() ? NULL : i->second;
232	+	}
233
149	–	void SimInfo::scaleBox(double scale) {
150	–	double theBox[3][3];
151	–	int i, j;
234
235	<	// cerr << "Scaling box by " << scale << "\n";
235	>	void SimInfo::calcNdf() {
236	>	int ndf_local;
237	>	MoleculeIterator i;
238	>	std::vector<StuntDouble*>::iterator j;
239	>	Molecule* mol;
240	>	StuntDouble* integrableObject;
241
242	<	for(i=0; i<3; i++)
243	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
242	>	ndf_local = 0;
243	>
244	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
245	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
246	>	integrableObject = mol->nextIntegrableObject(j)) {
247
248	<	setBoxM(theBox);
248	>	ndf_local += 3;
249
250	<	}
250	>	if (integrableObject->isDirectional()) {
251	>	if (integrableObject->isLinear()) {
252	>	ndf_local += 2;
253	>	} else {
254	>	ndf_local += 3;
255	>	}
256	>	}
257	>
258	>	}//end for (integrableObject)
259	>	}// end for (mol)
260	>
261	>	// n_constraints is local, so subtract them on each processor
262	>	ndf_local -= nConstraints_;
263
264	<	void SimInfo::calcHmatInv( void ) {
265	<
266	<	int oldOrtho;
267	<	int i,j;
268	<	double smallDiag;
167	<	double tol;
168	<	double sanity[3][3];
264	>	#ifdef IS_MPI
265	>	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
266	>	#else
267	>	ndf_ = ndf_local;
268	>	#endif
269
270	<	invertMat3( Hmat, HmatInv );
270	>	// nZconstraints_ is global, as are the 3 COM translations for the
271	>	// entire system:
272	>	ndf_ = ndf_ - 3 - nZconstraint_;
273
274	<	// check to see if Hmat is orthorhombic
173	<
174	<	oldOrtho = orthoRhombic;
274	>	}
275
276	<	smallDiag = fabs(Hmat[0][0]);
277	<	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;
276	>	void SimInfo::calcNdfRaw() {
277	>	int ndfRaw_local;
278
279	<	orthoRhombic = 1;
280	<
281	<	for (i = 0; i < 3; i++ ) {
282	<	for (j = 0 ; j < 3; j++) {
283	<	if (i != j) {
284	<	if (orthoRhombic) {
285	<	if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
286	<	}
279	>	MoleculeIterator i;
280	>	std::vector<StuntDouble*>::iterator j;
281	>	Molecule* mol;
282	>	StuntDouble* integrableObject;
283	>
284	>	// Raw degrees of freedom that we have to set
285	>	ndfRaw_local = 0;
286	>
287	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
288	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
289	>	integrableObject = mol->nextIntegrableObject(j)) {
290	>
291	>	ndfRaw_local += 3;
292	>
293	>	if (integrableObject->isDirectional()) {
294	>	if (integrableObject->isLinear()) {
295	>	ndfRaw_local += 2;
296	>	} else {
297	>	ndfRaw_local += 3;
298	>	}
299	>	}
300	>
301		}
302		}
303	+
304	+	#ifdef IS_MPI
305	+	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
306	+	#else
307	+	ndfRaw_ = ndfRaw_local;
308	+	#endif
309		}
310
311	<	if( oldOrtho != orthoRhombic ){
311	>	void SimInfo::calcNdfTrans() {
312	>	int ndfTrans_local;
313	>
314	>	ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
315	>
316	>
317	>	#ifdef IS_MPI
318	>	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
319	>	#else
320	>	ndfTrans_ = ndfTrans_local;
321	>	#endif
322	>
323	>	ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
324	>
325	>	}
326	>
327	>	void SimInfo::addExcludePairs(Molecule* mol) {
328	>	std::vector<Bond*>::iterator bondIter;
329	>	std::vector<Bend*>::iterator bendIter;
330	>	std::vector<Torsion*>::iterator torsionIter;
331	>	Bond* bond;
332	>	Bend* bend;
333	>	Torsion* torsion;
334	>	int a;
335	>	int b;
336	>	int c;
337	>	int d;
338
339	<	if( orthoRhombic ) {
340	<	sprintf( painCave.errMsg,
341	<	"OOPSE is switching from the default Non-Orthorhombic\n"
342	<	"\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();
339	>	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
340	>	a = bond->getAtomA()->getGlobalIndex();
341	>	b = bond->getAtomB()->getGlobalIndex();
342	>	exclude_.addPair(a, b);
343		}
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	–	}
344
345	<	void SimInfo::calcBoxL( void ){
345	>	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
346	>	a = bend->getAtomA()->getGlobalIndex();
347	>	b = bend->getAtomB()->getGlobalIndex();
348	>	c = bend->getAtomC()->getGlobalIndex();
349
350	<	double dx, dy, dz, dsq;
350	>	exclude_.addPair(a, b);
351	>	exclude_.addPair(a, c);
352	>	exclude_.addPair(b, c);
353	>	}
354
355	<	// boxVol = Determinant of Hmat
355	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
356	>	a = torsion->getAtomA()->getGlobalIndex();
357	>	b = torsion->getAtomB()->getGlobalIndex();
358	>	c = torsion->getAtomC()->getGlobalIndex();
359	>	d = torsion->getAtomD()->getGlobalIndex();
360
361	<	boxVol = matDet3( Hmat );
361	>	exclude_.addPair(a, b);
362	>	exclude_.addPair(a, c);
363	>	exclude_.addPair(a, d);
364	>	exclude_.addPair(b, c);
365	>	exclude_.addPair(b, d);
366	>	exclude_.addPair(c, d);
367	>	}
368
369	<	// boxLx
370	<
371	<	dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
372	<	dsq = dx*dx + dy*dy + dz*dz;
373	<	boxL[0] = sqrt( dsq );
374	<	//maxCutoff = 0.5 * boxL[0];
369	>	Molecule::RigidBodyIterator rbIter;
370	>	RigidBody* rb;
371	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
372	>	std::vector<Atom*> atoms = rb->getAtoms();
373	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
374	>	for (int j = i + 1; j < atoms.size(); ++j) {
375	>	a = atoms[i]->getGlobalIndex();
376	>	b = atoms[j]->getGlobalIndex();
377	>	exclude_.addPair(a, b);
378	>	}
379	>	}
380	>	}
381
382	<	// boxLy
237	<
238	<	dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
239	<	dsq = dx*dx + dy*dy + dz*dz;
240	<	boxL[1] = sqrt( dsq );
241	<	//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
382	>	}
383
384	+	void SimInfo::removeExcludePairs(Molecule* mol) {
385	+	std::vector<Bond*>::iterator bondIter;
386	+	std::vector<Bend*>::iterator bendIter;
387	+	std::vector<Torsion*>::iterator torsionIter;
388	+	Bond* bond;
389	+	Bend* bend;
390	+	Torsion* torsion;
391	+	int a;
392	+	int b;
393	+	int c;
394	+	int d;
395	+
396	+	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
397	+	a = bond->getAtomA()->getGlobalIndex();
398	+	b = bond->getAtomB()->getGlobalIndex();
399	+	exclude_.removePair(a, b);
400	+	}
401
402	<	// boxLz
403	<
404	<	dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
405	<	dsq = dx*dx + dy*dy + dz*dz;
248	<	boxL[2] = sqrt( dsq );
249	<	//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
402	>	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
403	>	a = bend->getAtomA()->getGlobalIndex();
404	>	b = bend->getAtomB()->getGlobalIndex();
405	>	c = bend->getAtomC()->getGlobalIndex();
406
407	<	//calculate the max cutoff
408	<	maxCutoff =  calcMaxCutOff();
409	<
410	<	checkCutOffs();
407	>	exclude_.removePair(a, b);
408	>	exclude_.removePair(a, c);
409	>	exclude_.removePair(b, c);
410	>	}
411
412	<	}
412	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
413	>	a = torsion->getAtomA()->getGlobalIndex();
414	>	b = torsion->getAtomB()->getGlobalIndex();
415	>	c = torsion->getAtomC()->getGlobalIndex();
416	>	d = torsion->getAtomD()->getGlobalIndex();
417
418	+	exclude_.removePair(a, b);
419	+	exclude_.removePair(a, c);
420	+	exclude_.removePair(a, d);
421	+	exclude_.removePair(b, c);
422	+	exclude_.removePair(b, d);
423	+	exclude_.removePair(c, d);
424	+	}
425
426	<	double SimInfo::calcMaxCutOff(){
426	>	Molecule::RigidBodyIterator rbIter;
427	>	RigidBody* rb;
428	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
429	>	std::vector<Atom*> atoms = rb->getAtoms();
430	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
431	>	for (int j = i + 1; j < atoms.size(); ++j) {
432	>	a = atoms[i]->getGlobalIndex();
433	>	b = atoms[j]->getGlobalIndex();
434	>	exclude_.removePair(a, b);
435	>	}
436	>	}
437	>	}
438
439	<	double ri[3], rj[3], rk[3];
262	<	double rij[3], rjk[3], rki[3];
263	<	double minDist;
439	>	}
440
265	–	ri[0] = Hmat[0][0];
266	–	ri[1] = Hmat[1][0];
267	–	ri[2] = Hmat[2][0];
441
442	<	rj[0] = Hmat[0][1];
443	<	rj[1] = Hmat[1][1];
271	<	rj[2] = Hmat[2][1];
442	>	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
443	>	int curStampId;
444
445	<	rk[0] = Hmat[0][2];
446	<	rk[1] = Hmat[1][2];
275	<	rk[2] = Hmat[2][2];
276	<
277	<	crossProduct3(ri, rj, rij);
278	<	distXY = dotProduct3(rk,rij) / norm3(rij);
445	>	//index from 0
446	>	curStampId = moleculeStamps_.size();
447
448	<	crossProduct3(rj,rk, rjk);
449	<	distYZ = dotProduct3(ri,rjk) / norm3(rjk);
448	>	moleculeStamps_.push_back(molStamp);
449	>	molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
450	>	}
451
452	<	crossProduct3(rk,ri, rki);
284	<	distZX = dotProduct3(rj,rki) / norm3(rki);
452	>	void SimInfo::update() {
453
454	<	minDist = min(min(distXY, distYZ), distZX);
287	<	return minDist/2;
288	<
289	<	}
454	>	setupSimType();
455
456	<	void SimInfo::wrapVector( double thePos[3] ){
456	>	#ifdef IS_MPI
457	>	setupFortranParallel();
458	>	#endif
459
460	<	int i;
294	<	double scaled[3];
460	>	setupFortranSim();
461
462	<	if( !orthoRhombic ){
463	<	// calc the scaled coordinates.
462	>	//setup fortran force field
463	>	/** @deprecate */
464	>	int isError = 0;
465	>	initFortranFF( &fInfo_.SIM_uses_RF , &isError );
466	>	if(isError){
467	>	sprintf( painCave.errMsg,
468	>	"ForceField error: There was an error initializing the forceField in fortran.\n" );
469	>	painCave.isFatal = 1;
470	>	simError();
471	>	}
472
299	–
300	–	matVecMul3(HmatInv, thePos, scaled);
473
474	<	for(i=0; i<3; i++)
303	<	scaled[i] -= roundMe(scaled[i]);
304	<
305	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
306	<
307	<	matVecMul3(Hmat, scaled, thePos);
474	>	setupCutoff();
475
476	+	calcNdf();
477	+	calcNdfRaw();
478	+	calcNdfTrans();
479	+
480	+	fortranInitialized_ = true;
481		}
310	–	else{
311	–	// calc the scaled coordinates.
312	–
313	–	for(i=0; i<3; i++)
314	–	scaled[i] = thePos[i]*HmatInv[i][i];
315	–
316	–	// wrap the scaled coordinates
317	–
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	–	}
482
483	+	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
484	+	SimInfo::MoleculeIterator mi;
485	+	Molecule* mol;
486	+	Molecule::AtomIterator ai;
487	+	Atom* atom;
488	+	std::set<AtomType*> atomTypes;
489
490	<	int SimInfo::getNDF(){
331	<	int ndf_local;
490	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
491
492	<	ndf_local = 0;
493	<
494	<	for(int i = 0; i < integrableObjects.size(); i++){
495	<	ndf_local += 3;
337	<	if (integrableObjects[i]->isDirectional()) {
338	<	if (integrableObjects[i]->isLinear())
339	<	ndf_local += 2;
340	<	else
341	<	ndf_local += 3;
492	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
493	>	atomTypes.insert(atom->getAtomType());
494	>	}
495	>
496		}
497	+
498	+	return atomTypes;
499		}
500
501	<	// n_constraints is local, so subtract them on each processor:
502	<
503	<	ndf_local -= n_constraints;
501	>	void SimInfo::setupSimType() {
502	>	std::set<AtomType*>::iterator i;
503	>	std::set<AtomType*> atomTypes;
504	>	atomTypes = getUniqueAtomTypes();
505	>
506	>	int useLennardJones = 0;
507	>	int useElectrostatic = 0;
508	>	int useEAM = 0;
509	>	int useCharge = 0;
510	>	int useDirectional = 0;
511	>	int useDipole = 0;
512	>	int useGayBerne = 0;
513	>	int useSticky = 0;
514	>	int useStickyPower = 0;
515	>	int useShape = 0;
516	>	int useFLARB = 0; //it is not in AtomType yet
517	>	int useDirectionalAtom = 0;
518	>	int useElectrostatics = 0;
519	>	//usePBC and useRF are from simParams
520	>	int usePBC = simParams_->getPBC();
521	>	int useRF = simParams_->getUseRF();
522
523	<	#ifdef IS_MPI
524	<	MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
525	<	#else
526	<	ndf = ndf_local;
527	<	#endif
523	>	//loop over all of the atom types
524	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
525	>	useLennardJones |= (*i)->isLennardJones();
526	>	useElectrostatic |= (*i)->isElectrostatic();
527	>	useEAM |= (*i)->isEAM();
528	>	useCharge |= (*i)->isCharge();
529	>	useDirectional |= (*i)->isDirectional();
530	>	useDipole |= (*i)->isDipole();
531	>	useGayBerne |= (*i)->isGayBerne();
532	>	useSticky |= (*i)->isSticky();
533	>	useStickyPower |= (*i)->isStickyPower();
534	>	useShape |= (*i)->isShape();
535	>	}
536
537	<	// nZconstraints is global, as are the 3 COM translations for the
538	<	// entire system:
537	>	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
538	>	useDirectionalAtom = 1;
539	>	}
540
541	<	ndf = ndf - 3 - nZconstraints;
541	>	if (useCharge || useDipole) {
542	>	useElectrostatics = 1;
543	>	}
544
545	<	return ndf;
546	<	}
545	>	#ifdef IS_MPI
546	>	int temp;
547
548	<	int SimInfo::getNDFraw() {
549	<	int ndfRaw_local;
548	>	temp = usePBC;
549	>	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
550
551	<	// Raw degrees of freedom that we have to set
552	<	ndfRaw_local = 0;
551	>	temp = useDirectionalAtom;
552	>	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
553
554	<	for(int i = 0; i < integrableObjects.size(); i++){
555	<	ndfRaw_local += 3;
371	<	if (integrableObjects[i]->isDirectional()) {
372	<	if (integrableObjects[i]->isLinear())
373	<	ndfRaw_local += 2;
374	<	else
375	<	ndfRaw_local += 3;
376	<	}
377	<	}
378	<
379	<	#ifdef IS_MPI
380	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
381	<	#else
382	<	ndfRaw = ndfRaw_local;
383	<	#endif
554	>	temp = useLennardJones;
555	>	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
556
557	<	return ndfRaw;
558	<	}
557	>	temp = useElectrostatics;
558	>	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
559
560	<	int SimInfo::getNDFtranslational() {
561	<	int ndfTrans_local;
560	>	temp = useCharge;
561	>	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
562
563	<	ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
563	>	temp = useDipole;
564	>	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
565
566	+	temp = useSticky;
567	+	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
568
569	<	#ifdef IS_MPI
570	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
571	<	#else
572	<	ndfTrans = ndfTrans_local;
573	<	#endif
569	>	temp = useStickyPower;
570	>	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
571	>
572	>	temp = useGayBerne;
573	>	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
574
575	<	ndfTrans = ndfTrans - 3 - nZconstraints;
575	>	temp = useEAM;
576	>	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
577
578	<	return ndfTrans;
579	<	}
578	>	temp = useShape;
579	>	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
580
581	<	int SimInfo::getTotIntegrableObjects() {
582	<	int nObjs_local;
407	<	int nObjs;
581	>	temp = useFLARB;
582	>	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
583
584	<	nObjs_local =  integrableObjects.size();
585	<
586	<
412	<	#ifdef IS_MPI
413	<	MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
414	<	#else
415	<	nObjs = nObjs_local;
584	>	temp = useRF;
585	>	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
586	>
587		#endif
588
589	+	fInfo_.SIM_uses_PBC = usePBC;
590	+	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
591	+	fInfo_.SIM_uses_LennardJones = useLennardJones;
592	+	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
593	+	fInfo_.SIM_uses_Charges = useCharge;
594	+	fInfo_.SIM_uses_Dipoles = useDipole;
595	+	fInfo_.SIM_uses_Sticky = useSticky;
596	+	fInfo_.SIM_uses_StickyPower = useStickyPower;
597	+	fInfo_.SIM_uses_GayBerne = useGayBerne;
598	+	fInfo_.SIM_uses_EAM = useEAM;
599	+	fInfo_.SIM_uses_Shapes = useShape;
600	+	fInfo_.SIM_uses_FLARB = useFLARB;
601	+	fInfo_.SIM_uses_RF = useRF;
602
603	<	return nObjs;
420	<	}
603	>	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
604
605	<	void SimInfo::refreshSim(){
605	>	if (simParams_->haveDielectric()) {
606	>	fInfo_.dielect = simParams_->getDielectric();
607	>	} else {
608	>	sprintf(painCave.errMsg,
609	>	"SimSetup Error: No Dielectric constant was set.\n"
610	>	"\tYou are trying to use Reaction Field without"
611	>	"\tsetting a dielectric constant!\n");
612	>	painCave.isFatal = 1;
613	>	simError();
614	>	}
615	>
616	>	} else {
617	>	fInfo_.dielect = 0.0;
618	>	}
619
424	–	simtype fInfo;
425	–	int isError;
426	–	int n_global;
427	–	int* excl;
428	–
429	–	fInfo.dielect = 0.0;
430	–
431	–	if( useDipoles ){
432	–	if( useReactionField )fInfo.dielect = dielectric;
620		}
621
622	<	fInfo.SIM_uses_PBC = usePBC;
623	<	//fInfo.SIM_uses_LJ = 0;
624	<	fInfo.SIM_uses_LJ = useLJ;
625	<	fInfo.SIM_uses_sticky = useSticky;
626	<	//fInfo.SIM_uses_sticky = 0;
627	<	fInfo.SIM_uses_charges = useCharges;
628	<	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;
622	>	void SimInfo::setupFortranSim() {
623	>	int isError;
624	>	int nExclude;
625	>	std::vector<int> fortranGlobalGroupMembership;
626	>
627	>	nExclude = exclude_.getSize();
628	>	isError = 0;
629
630	<	n_exclude = excludes->getSize();
631	<	excl = excludes->getFortranArray();
632	<
633	<	#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);
630	>	//globalGroupMembership_ is filled by SimCreator
631	>	for (int i = 0; i < nGlobalAtoms_; i++) {
632	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
633	>	}
634
635	<	if( isError ){
635	>	//calculate mass ratio of cutoff group
636	>	std::vector<double> mfact;
637	>	SimInfo::MoleculeIterator mi;
638	>	Molecule* mol;
639	>	Molecule::CutoffGroupIterator ci;
640	>	CutoffGroup* cg;
641	>	Molecule::AtomIterator ai;
642	>	Atom* atom;
643	>	double totalMass;
644	>
645	>	//to avoid memory reallocation, reserve enough space for mfact
646	>	mfact.reserve(getNCutoffGroups());
647
648	<	sprintf( painCave.errMsg,
649	<	"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	<	}
648	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
649	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
650
651	<	void SimInfo::setDefaultRcut( double theRcut ){
652	<
653	<	haveRcut = 1;
654	<	rCut = theRcut;
491	<	rList = rCut + 1.0;
492	<
493	<	notifyFortranCutoffs( &rCut, &rSw, &rList );
494	<	}
651	>	totalMass = cg->getMass();
652	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
653	>	mfact.push_back(atom->getMass()/totalMass);
654	>	}
655
656	<	void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
656	>	}
657	>	}
658
659	<	rSw = theRsw;
660	<	setDefaultRcut( theRcut );
500	<	}
659	>	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
660	>	std::vector<int> identArray;
661
662	+	//to avoid memory reallocation, reserve enough space identArray
663	+	identArray.reserve(getNAtoms());
664	+
665	+	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
666	+	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
667	+	identArray.push_back(atom->getIdent());
668	+	}
669	+	}
670
671	<	void SimInfo::checkCutOffs( void ){
672	<
673	<	if( boxIsInit ){
671	>	//fill molMembershipArray
672	>	//molMembershipArray is filled by SimCreator
673	>	std::vector<int> molMembershipArray(nGlobalAtoms_);
674	>	for (int i = 0; i < nGlobalAtoms_; i++) {
675	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
676	>	}
677
678	<	//we need to check cutOffs against the box
679	<
680	<	if( rCut > maxCutoff ){
678	>	//setup fortran simulation
679	>	int nGlobalExcludes = 0;
680	>	int* globalExcludes = NULL;
681	>	int* excludeList = exclude_.getExcludeList();
682	>	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
683	>	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
684	>	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
685	>
686	>	if( isError ){
687	>
688		sprintf( painCave.errMsg,
689	<	"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;
689	>	"There was an error setting the simulation information in fortran.\n" );
690		painCave.isFatal = 1;
691	+	painCave.severity = OOPSE_ERROR;
692		simError();
693	<	}
694	<	} else {
695	<	// initialize this stuff before using it, OK?
696	<	sprintf( painCave.errMsg,
697	<	"Trying to check cutoffs without a box.\n"
698	<	"\tOOPSE should have better programmers than that.\n" );
699	<	painCave.severity = OOPSE_ERROR;
533	<	painCave.isFatal = 1;
534	<	simError();
693	>	}
694	>
695	>	#ifdef IS_MPI
696	>	sprintf( checkPointMsg,
697	>	"succesfully sent the simulation information to fortran.\n");
698	>	MPIcheckPoint();
699	>	#endif // is_mpi
700		}
536	–
537	–	}
701
539	–	void SimInfo::addProperty(GenericData* prop){
702
703	<	map<string, GenericData*>::iterator result;
704	<	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()){
703	>	#ifdef IS_MPI
704	>	void SimInfo::setupFortranParallel() {
705
706	<	delete (*result).second;
707	<	(*result).second = prop;
708	<
706	>	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
707	>	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
708	>	std::vector<int> localToGlobalCutoffGroupIndex;
709	>	SimInfo::MoleculeIterator mi;
710	>	Molecule::AtomIterator ai;
711	>	Molecule::CutoffGroupIterator ci;
712	>	Molecule* mol;
713	>	Atom* atom;
714	>	CutoffGroup* cg;
715	>	mpiSimData parallelData;
716	>	int isError;
717	>
718	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
719	>
720	>	//local index(index in DataStorge) of atom is important
721	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
722	>	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
723	>	}
724	>
725	>	//local index of cutoff group is trivial, it only depends on the order of travesing
726	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
727	>	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
728	>	}
729	>
730	>	}
731	>
732	>	//fill up mpiSimData struct
733	>	parallelData.nMolGlobal = getNGlobalMolecules();
734	>	parallelData.nMolLocal = getNMolecules();
735	>	parallelData.nAtomsGlobal = getNGlobalAtoms();
736	>	parallelData.nAtomsLocal = getNAtoms();
737	>	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
738	>	parallelData.nGroupsLocal = getNCutoffGroups();
739	>	parallelData.myNode = worldRank;
740	>	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
741	>
742	>	//pass mpiSimData struct and index arrays to fortran
743	>	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
744	>	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
745	>	&localToGlobalCutoffGroupIndex[0], &isError);
746	>
747	>	if (isError) {
748	>	sprintf(painCave.errMsg,
749	>	"mpiRefresh errror: fortran didn't like something we gave it.\n");
750	>	painCave.isFatal = 1;
751	>	simError();
752	>	}
753	>
754	>	sprintf(checkPointMsg, " mpiRefresh successful.\n");
755	>	MPIcheckPoint();
756	>
757	>
758		}
553	–	else{
759
760	<	properties[prop->getID()] = prop;
760	>	#endif
761
762	+	double SimInfo::calcMaxCutoffRadius() {
763	+
764	+
765	+	std::set<AtomType*> atomTypes;
766	+	std::set<AtomType*>::iterator i;
767	+	std::vector<double> cutoffRadius;
768	+
769	+	//get the unique atom types
770	+	atomTypes = getUniqueAtomTypes();
771	+
772	+	//query the max cutoff radius among these atom types
773	+	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
774	+	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
775	+	}
776	+
777	+	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
778	+	#ifdef IS_MPI
779	+	//pick the max cutoff radius among the processors
780	+	#endif
781	+
782	+	return maxCutoffRadius;
783		}
784	+
785	+	void SimInfo::getCutoff(double& rcut, double& rsw) {
786
787	<	}
787	>	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
788	>
789	>	if (!simParams_->haveRcut()){
790	>	sprintf(painCave.errMsg,
791	>	"SimCreator Warning: No value was set for the cutoffRadius.\n"
792	>	"\tOOPSE will use a default value of 15.0 angstroms"
793	>	"\tfor the cutoffRadius.\n");
794	>	painCave.isFatal = 0;
795	>	simError();
796	>	rcut = 15.0;
797	>	} else{
798	>	rcut = simParams_->getRcut();
799	>	}
800
801	<	GenericData* SimInfo::getProperty(const string& propName){
801	>	if (!simParams_->haveRsw()){
802	>	sprintf(painCave.errMsg,
803	>	"SimCreator Warning: No value was set for switchingRadius.\n"
804	>	"\tOOPSE will use a default value of\n"
805	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
806	>	painCave.isFatal = 0;
807	>	simError();
808	>	rsw = 0.95 * rcut;
809	>	} else{
810	>	rsw = simParams_->getRsw();
811	>	}
812	>
813	>	} else {
814	>	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
815	>	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
816	>
817	>	if (simParams_->haveRcut()) {
818	>	rcut = simParams_->getRcut();
819	>	} else {
820	>	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
821	>	rcut = calcMaxCutoffRadius();
822	>	}
823	>
824	>	if (simParams_->haveRsw()) {
825	>	rsw  = simParams_->getRsw();
826	>	} else {
827	>	rsw = rcut;
828	>	}
829	>
830	>	}
831	>	}
832	>
833	>	void SimInfo::setupCutoff() {
834	>	getCutoff(rcut_, rsw_);
835	>	double rnblist = rcut_ + 1; // skin of neighbor list
836	>
837	>	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
838	>	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist);
839	>	}
840	>
841	>	void SimInfo::addProperty(GenericData* genData) {
842	>	properties_.addProperty(genData);
843	>	}
844	>
845	>	void SimInfo::removeProperty(const std::string& propName) {
846	>	properties_.removeProperty(propName);
847	>	}
848	>
849	>	void SimInfo::clearProperties() {
850	>	properties_.clearProperties();
851	>	}
852	>
853	>	std::vector<std::string> SimInfo::getPropertyNames() {
854	>	return properties_.getPropertyNames();
855	>	}
856	>
857	>	std::vector<GenericData*> SimInfo::getProperties() {
858	>	return properties_.getProperties();
859	>	}
860	>
861	>	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
862	>	return properties_.getPropertyByName(propName);
863	>	}
864	>
865	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
866	>	if (sman_ == sman) {
867	>	return;
868	>	}
869	>	delete sman_;
870	>	sman_ = sman;
871	>
872	>	Molecule* mol;
873	>	RigidBody* rb;
874	>	Atom* atom;
875	>	SimInfo::MoleculeIterator mi;
876	>	Molecule::RigidBodyIterator rbIter;
877	>	Molecule::AtomIterator atomIter;;
878
879	<	map<string, GenericData*>::iterator result;
880	<
881	<	//string lowerCaseName = ();
882	<
883	<	result = properties.find(propName);
884	<
885	<	if(result != properties.end())
886	<	return (*result).second;
887	<	else
888	<	return NULL;
889	<	}
879	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
880	>
881	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
882	>	atom->setSnapshotManager(sman_);
883	>	}
884	>
885	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
886	>	rb->setSnapshotManager(sman_);
887	>	}
888	>	}
889	>
890	>	}
891
892	+	Vector3d SimInfo::getComVel(){
893	+	SimInfo::MoleculeIterator i;
894	+	Molecule* mol;
895
896	<	void SimInfo::getFortranGroupArrays(SimInfo* info,
897	<	vector<int>& FglobalGroupMembership,
898	<	vector<double>& mfact){
899	<
900	<	Molecule* myMols;
901	<	Atom** myAtoms;
902	<	int numAtom;
903	<	double mtot;
904	<	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	<
896	>	Vector3d comVel(0.0);
897	>	double totalMass = 0.0;
898	>
899	>
900	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
901	>	double mass = mol->getMass();
902	>	totalMass += mass;
903	>	comVel += mass * mol->getComVel();
904	>	}
905
597	–	// Fix the silly fortran indexing problem
906		#ifdef IS_MPI
907	<	numAtom = mpiSim->getNAtomsGlobal();
908	<	#else
909	<	numAtom = n_atoms;
907	>	double tmpMass = totalMass;
908	>	Vector3d tmpComVel(comVel);
909	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
910	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
911		#endif
603	–	for (int i = 0; i < numAtom; i++)
604	–	FglobalGroupMembership.push_back(globalGroupMembership[i] + 1);
605	–
912
913	<	myMols = info->molecules;
608	<	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)){
913	>	comVel /= totalMass;
914
915	<	totalMass = myCutoffGroup->getMass();
616	<
617	<	for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom);
618	<	cutoffAtom != NULL;
619	<	cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
620	<	mfact.push_back(cutoffAtom->getMass()/totalMass);
621	<	}
622	<	}
915	>	return comVel;
916		}
917
918	<	}
918	>	Vector3d SimInfo::getCom(){
919	>	SimInfo::MoleculeIterator i;
920	>	Molecule* mol;
921	>
922	>	Vector3d com(0.0);
923	>	double totalMass = 0.0;
924	>
925	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
926	>	double mass = mol->getMass();
927	>	totalMass += mass;
928	>	com += mass * mol->getCom();
929	>	}
930	>
931	>	#ifdef IS_MPI
932	>	double tmpMass = totalMass;
933	>	Vector3d tmpCom(com);
934	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
935	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
936	>	#endif
937	>
938	>	com /= totalMass;
939	>
940	>	return com;
941	>
942	>	}
943	>
944	>	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
945	>
946	>	return o;
947	>	}
948	>
949	>	}//end namespace oopse
950	>

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