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root/group/trunk/OOPSE-2.0/src/brains/SimInfo.cpp

Comparing trunk/OOPSE-2.0/src/brains/SimInfo.cpp (file contents):
Revision 1492 by tim, Fri Sep 24 16:27:58 2004 UTC vs.
Revision 2116 by tim, Fri Mar 11 15:00:20 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"
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
61	<	#include "UseTheForce/fortranWrappers.hpp"
61	>	#ifdef IS_MPI
62	>	#include "UseTheForce/mpiComponentPlan.h"
63	>	#include "UseTheForce/DarkSide/simParallel_interface.h"
64	>	#endif
65
66	<	#include "math/MatVec3.h"
66	>	namespace oopse {
67
68	<	#ifdef IS_MPI
69	<	#include "brains/mpiSimulation.hpp"
70	<	#endif
68	>	SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
69	>	ForceField* ff, Globals* simParams) :
70	>	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	<	inline double roundMe( double x ){
79	<	return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
80	<	}
81	<
82	<	inline double min( double a, double b ){
83	<	return (a < b ) ? a : b;
84	<	}
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	<	SimInfo* currentInfo;
94	>	//calculate atoms in molecules
95	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
96
31	–	SimInfo::SimInfo(){
97
98	<	n_constraints = 0;
99	<	nZconstraints = 0;
100	<	n_oriented = 0;
101	<	n_dipoles = 0;
102	<	ndf = 0;
103	<	ndfRaw = 0;
104	<	nZconstraints = 0;
105	<	the_integrator = NULL;
41	<	setTemp = 0;
42	<	thermalTime = 0.0;
43	<	currentTime = 0.0;
44	<	rCut = 0.0;
45	<	rSw = 0.0;
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	<	haveRcut = 0;
108	<	haveRsw = 0;
49	<	boxIsInit = 0;
50	<
51	<	resetTime = 1e99;
107	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
108	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
109
110	<	orthoRhombic = 0;
111	<	orthoTolerance = 1E-6;
112	<	useInitXSstate = true;
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	<	usePBC = 0;
120	<	useLJ = 0;
121	<	useSticky = 0;
122	<	useCharges = 0;
61	<	useDipoles = 0;
62	<	useReactionField = 0;
63	<	useGB = 0;
64	<	useEAM = 0;
65	<	useSolidThermInt = 0;
66	<	useLiquidThermInt = 0;
119	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
120	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
121	>
122	>	}
123
124	<	haveCutoffGroups = false;
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	<	excludes = Exclude::Instance();
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	<	myConfiguration = new SimState();
136	>	nGlobalMols_ = molStampIds_.size();
137
138	<	has_minimizer = false;
139	<	the_minimizer =NULL;
138	>	#ifdef IS_MPI
139	>	molToProcMap_.resize(nGlobalMols_);
140	>	#endif
141
142	<	ngroup = 0;
142	>	}
143
144	<	wrapMeSimInfo( this );
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	>	MemoryUtils::deletePointers(moleculeStamps_);
152	>
153	>	delete sman_;
154	>	delete simParams_;
155	>	delete forceField_;
156		}
157
158	+	int SimInfo::getNGlobalConstraints() {
159	+	int nGlobalConstraints;
160	+	#ifdef IS_MPI
161	+	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
162	+	MPI_COMM_WORLD);
163	+	#else
164	+	nGlobalConstraints =  nConstraints_;
165	+	#endif
166	+	return nGlobalConstraints;
167	+	}
168
169	<	SimInfo::~SimInfo(){
169	>	bool SimInfo::addMolecule(Molecule* mol) {
170	>	MoleculeIterator i;
171
172	<	delete myConfiguration;
172	>	i = molecules_.find(mol->getGlobalIndex());
173	>	if (i == molecules_.end() ) {
174
175	<	map<string, GenericData*>::iterator i;
176	<
177	<	for(i = properties.begin(); i != properties.end(); i++)
178	<	delete (*i).second;
175	>	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
176	>
177	>	nAtoms_ += mol->getNAtoms();
178	>	nBonds_ += mol->getNBonds();
179	>	nBends_ += mol->getNBends();
180	>	nTorsions_ += mol->getNTorsions();
181	>	nRigidBodies_ += mol->getNRigidBodies();
182	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
183	>	nCutoffGroups_ += mol->getNCutoffGroups();
184	>	nConstraints_ += mol->getNConstraintPairs();
185
186	+	addExcludePairs(mol);
187	+
188	+	return true;
189	+	} else {
190	+	return false;
191	+	}
192		}
193
194	<	void SimInfo::setBox(double newBox[3]) {
195	<
196	<	int i, j;
97	<	double tempMat[3][3];
194	>	bool SimInfo::removeMolecule(Molecule* mol) {
195	>	MoleculeIterator i;
196	>	i = molecules_.find(mol->getGlobalIndex());
197
198	<	for(i=0; i<3; i++)
100	<	for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
198	>	if (i != molecules_.end() ) {
199
200	<	tempMat[0][0] = newBox[0];
201	<	tempMat[1][1] = newBox[1];
202	<	tempMat[2][2] = newBox[2];
200	>	assert(mol == i->second);
201	>
202	>	nAtoms_ -= mol->getNAtoms();
203	>	nBonds_ -= mol->getNBonds();
204	>	nBends_ -= mol->getNBends();
205	>	nTorsions_ -= mol->getNTorsions();
206	>	nRigidBodies_ -= mol->getNRigidBodies();
207	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
208	>	nCutoffGroups_ -= mol->getNCutoffGroups();
209	>	nConstraints_ -= mol->getNConstraintPairs();
210
211	<	setBoxM( tempMat );
211	>	removeExcludePairs(mol);
212	>	molecules_.erase(mol->getGlobalIndex());
213
214	<	}
214	>	delete mol;
215	>
216	>	return true;
217	>	} else {
218	>	return false;
219	>	}
220
110	–	void SimInfo::setBoxM( double theBox[3][3] ){
111	–
112	–	int i, j;
113	–	double FortranHmat[9]; // to preserve compatibility with Fortran the
114	–	// ordering in the array is as follows:
115	–	// [ 0 3 6 ]
116	–	// [ 1 4 7 ]
117	–	// [ 2 5 8 ]
118	–	double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
221
222	<	if( !boxIsInit ) boxIsInit = 1;
222	>	}
223
224	<	for(i=0; i < 3; i++)
225	<	for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
226	<
227	<	calcBoxL();
228	<	calcHmatInv();
224	>
225	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
226	>	i = molecules_.begin();
227	>	return i == molecules_.end() ? NULL : i->second;
228	>	}
229
230	<	for(i=0; i < 3; i++) {
231	<	for (j=0; j < 3; j++) {
232	<	FortranHmat[3*j + i] = Hmat[i][j];
131	<	FortranHmatInv[3*j + i] = HmatInv[i][j];
132	<	}
133	<	}
134	<
135	<	setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
136	<
230	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
231	>	++i;
232	>	return i == molecules_.end() ? NULL : i->second;
233		}
138	–
234
140	–	void SimInfo::getBoxM (double theBox[3][3]) {
235
236	<	int i, j;
237	<	for(i=0; i<3; i++)
238	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
239	<	}
236	>	void SimInfo::calcNdf() {
237	>	int ndf_local;
238	>	MoleculeIterator i;
239	>	std::vector<StuntDouble*>::iterator j;
240	>	Molecule* mol;
241	>	StuntDouble* integrableObject;
242
243	+	ndf_local = 0;
244	+
245	+	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
246	+	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
247	+	integrableObject = mol->nextIntegrableObject(j)) {
248
249	<	void SimInfo::scaleBox(double scale) {
149	<	double theBox[3][3];
150	<	int i, j;
249	>	ndf_local += 3;
250
251	<	// cerr << "Scaling box by " << scale << "\n";
251	>	if (integrableObject->isDirectional()) {
252	>	if (integrableObject->isLinear()) {
253	>	ndf_local += 2;
254	>	} else {
255	>	ndf_local += 3;
256	>	}
257	>	}
258	>
259	>	}//end for (integrableObject)
260	>	}// end for (mol)
261	>
262	>	// n_constraints is local, so subtract them on each processor
263	>	ndf_local -= nConstraints_;
264
265	<	for(i=0; i<3; i++)
266	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
265	>	#ifdef IS_MPI
266	>	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
267	>	#else
268	>	ndf_ = ndf_local;
269	>	#endif
270
271	<	setBoxM(theBox);
271	>	// nZconstraints_ is global, as are the 3 COM translations for the
272	>	// entire system:
273	>	ndf_ = ndf_ - 3 - nZconstraint_;
274
275		}
276
277	<	void SimInfo::calcHmatInv( void ) {
278	<
163	<	int oldOrtho;
164	<	int i,j;
165	<	double smallDiag;
166	<	double tol;
167	<	double sanity[3][3];
277	>	void SimInfo::calcNdfRaw() {
278	>	int ndfRaw_local;
279
280	<	invertMat3( Hmat, HmatInv );
280	>	MoleculeIterator i;
281	>	std::vector<StuntDouble*>::iterator j;
282	>	Molecule* mol;
283	>	StuntDouble* integrableObject;
284
285	<	// check to see if Hmat is orthorhombic
286	<
287	<	oldOrtho = orthoRhombic;
285	>	// Raw degrees of freedom that we have to set
286	>	ndfRaw_local = 0;
287	>
288	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
289	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
290	>	integrableObject = mol->nextIntegrableObject(j)) {
291
292	<	smallDiag = fabs(Hmat[0][0]);
176	<	if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
177	<	if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
178	<	tol = smallDiag * orthoTolerance;
292	>	ndfRaw_local += 3;
293
294	<	orthoRhombic = 1;
295	<
296	<	for (i = 0; i < 3; i++ ) {
297	<	for (j = 0 ; j < 3; j++) {
298	<	if (i != j) {
299	<	if (orthoRhombic) {
300	<	if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
301	<	}
302	<	}
294	>	if (integrableObject->isDirectional()) {
295	>	if (integrableObject->isLinear()) {
296	>	ndfRaw_local += 2;
297	>	} else {
298	>	ndfRaw_local += 3;
299	>	}
300	>	}
301	>
302	>	}
303		}
190	–	}
191	–
192	–	if( oldOrtho != orthoRhombic ){
304
305	<	if( orthoRhombic ) {
306	<	sprintf( painCave.errMsg,
307	<	"OOPSE is switching from the default Non-Orthorhombic\n"
308	<	"\tto the faster Orthorhombic periodic boundary computations.\n"
309	<	"\tThis is usually a good thing, but if you wan't the\n"
199	<	"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
200	<	"\tvariable ( currently set to %G ) smaller.\n",
201	<	orthoTolerance);
202	<	painCave.severity = OOPSE_INFO;
203	<	simError();
204	<	}
205	<	else {
206	<	sprintf( painCave.errMsg,
207	<	"OOPSE is switching from the faster Orthorhombic to the more\n"
208	<	"\tflexible Non-Orthorhombic periodic boundary computations.\n"
209	<	"\tThis is usually because the box has deformed under\n"
210	<	"\tNPTf integration. If you wan't to live on the edge with\n"
211	<	"\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
212	<	"\tvariable ( currently set to %G ) larger.\n",
213	<	orthoTolerance);
214	<	painCave.severity = OOPSE_WARNING;
215	<	simError();
216	<	}
217	<	}
305	>	#ifdef IS_MPI
306	>	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
307	>	#else
308	>	ndfRaw_ = ndfRaw_local;
309	>	#endif
310		}
311
312	<	void SimInfo::calcBoxL( void ){
312	>	void SimInfo::calcNdfTrans() {
313	>	int ndfTrans_local;
314
315	<	double dx, dy, dz, dsq;
315	>	ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
316
224	–	// boxVol = Determinant of Hmat
317
318	<	boxVol = matDet3( Hmat );
318	>	#ifdef IS_MPI
319	>	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
320	>	#else
321	>	ndfTrans_ = ndfTrans_local;
322	>	#endif
323
324	<	// boxLx
325	<
326	<	dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
231	<	dsq = dx*dx + dy*dy + dz*dz;
232	<	boxL[0] = sqrt( dsq );
233	<	//maxCutoff = 0.5 * boxL[0];
324	>	ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
325	>
326	>	}
327
328	<	// boxLy
329	<
330	<	dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
331	<	dsq = dx*dx + dy*dy + dz*dz;
332	<	boxL[1] = sqrt( dsq );
333	<	//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
328	>	void SimInfo::addExcludePairs(Molecule* mol) {
329	>	std::vector<Bond*>::iterator bondIter;
330	>	std::vector<Bend*>::iterator bendIter;
331	>	std::vector<Torsion*>::iterator torsionIter;
332	>	Bond* bond;
333	>	Bend* bend;
334	>	Torsion* torsion;
335	>	int a;
336	>	int b;
337	>	int c;
338	>	int d;
339	>
340	>	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
341	>	a = bond->getAtomA()->getGlobalIndex();
342	>	b = bond->getAtomB()->getGlobalIndex();
343	>	exclude_.addPair(a, b);
344	>	}
345
346	+	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
347	+	a = bend->getAtomA()->getGlobalIndex();
348	+	b = bend->getAtomB()->getGlobalIndex();
349	+	c = bend->getAtomC()->getGlobalIndex();
350
351	<	// boxLz
352	<
353	<	dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
354	<	dsq = dx*dx + dy*dy + dz*dz;
247	<	boxL[2] = sqrt( dsq );
248	<	//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
351	>	exclude_.addPair(a, b);
352	>	exclude_.addPair(a, c);
353	>	exclude_.addPair(b, c);
354	>	}
355
356	<	//calculate the max cutoff
357	<	maxCutoff =  calcMaxCutOff();
358	<
359	<	checkCutOffs();
356	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
357	>	a = torsion->getAtomA()->getGlobalIndex();
358	>	b = torsion->getAtomB()->getGlobalIndex();
359	>	c = torsion->getAtomC()->getGlobalIndex();
360	>	d = torsion->getAtomD()->getGlobalIndex();
361
362	<	}
362	>	exclude_.addPair(a, b);
363	>	exclude_.addPair(a, c);
364	>	exclude_.addPair(a, d);
365	>	exclude_.addPair(b, c);
366	>	exclude_.addPair(b, d);
367	>	exclude_.addPair(c, d);
368	>	}
369
370	+	Molecule::RigidBodyIterator rbIter;
371	+	RigidBody* rb;
372	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
373	+	std::vector<Atom*> atoms = rb->getAtoms();
374	+	for (int i = 0; i < atoms.size() -1 ; ++i) {
375	+	for (int j = i + 1; j < atoms.size(); ++j) {
376	+	a = atoms[i]->getGlobalIndex();
377	+	b = atoms[j]->getGlobalIndex();
378	+	exclude_.addPair(a, b);
379	+	}
380	+	}
381	+	}
382
383	<	double SimInfo::calcMaxCutOff(){
383	>	Molecule::CutoffGroupIterator cgIter;
384	>	CutoffGroup* cg;
385	>	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
386	>	std::vector<Atom*> atoms = cg->getAtoms();
387	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
388	>	for (int j = i + 1; j < atoms.size(); ++j) {
389	>	a = atoms[i]->getGlobalIndex();
390	>	b = atoms[j]->getGlobalIndex();
391	>	exclude_.addPair(a, b);
392	>	}
393	>	}
394	>	}
395
396	<	double ri[3], rj[3], rk[3];
261	<	double rij[3], rjk[3], rki[3];
262	<	double minDist;
396	>	}
397
398	<	ri[0] = Hmat[0][0];
399	<	ri[1] = Hmat[1][0];
400	<	ri[2] = Hmat[2][0];
398	>	void SimInfo::removeExcludePairs(Molecule* mol) {
399	>	std::vector<Bond*>::iterator bondIter;
400	>	std::vector<Bend*>::iterator bendIter;
401	>	std::vector<Torsion*>::iterator torsionIter;
402	>	Bond* bond;
403	>	Bend* bend;
404	>	Torsion* torsion;
405	>	int a;
406	>	int b;
407	>	int c;
408	>	int d;
409	>
410	>	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
411	>	a = bond->getAtomA()->getGlobalIndex();
412	>	b = bond->getAtomB()->getGlobalIndex();
413	>	exclude_.removePair(a, b);
414	>	}
415
416	<	rj[0] = Hmat[0][1];
417	<	rj[1] = Hmat[1][1];
418	<	rj[2] = Hmat[2][1];
416	>	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
417	>	a = bend->getAtomA()->getGlobalIndex();
418	>	b = bend->getAtomB()->getGlobalIndex();
419	>	c = bend->getAtomC()->getGlobalIndex();
420
421	<	rk[0] = Hmat[0][2];
422	<	rk[1] = Hmat[1][2];
423	<	rk[2] = Hmat[2][2];
424	<
276	<	crossProduct3(ri, rj, rij);
277	<	distXY = dotProduct3(rk,rij) / norm3(rij);
421	>	exclude_.removePair(a, b);
422	>	exclude_.removePair(a, c);
423	>	exclude_.removePair(b, c);
424	>	}
425
426	<	crossProduct3(rj,rk, rjk);
427	<	distYZ = dotProduct3(ri,rjk) / norm3(rjk);
426	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
427	>	a = torsion->getAtomA()->getGlobalIndex();
428	>	b = torsion->getAtomB()->getGlobalIndex();
429	>	c = torsion->getAtomC()->getGlobalIndex();
430	>	d = torsion->getAtomD()->getGlobalIndex();
431
432	<	crossProduct3(rk,ri, rki);
433	<	distZX = dotProduct3(rj,rki) / norm3(rki);
432	>	exclude_.removePair(a, b);
433	>	exclude_.removePair(a, c);
434	>	exclude_.removePair(a, d);
435	>	exclude_.removePair(b, c);
436	>	exclude_.removePair(b, d);
437	>	exclude_.removePair(c, d);
438	>	}
439
440	<	minDist = min(min(distXY, distYZ), distZX);
441	<	return minDist/2;
442	<
443	<	}
440	>	Molecule::RigidBodyIterator rbIter;
441	>	RigidBody* rb;
442	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
443	>	std::vector<Atom*> atoms = rb->getAtoms();
444	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
445	>	for (int j = i + 1; j < atoms.size(); ++j) {
446	>	a = atoms[i]->getGlobalIndex();
447	>	b = atoms[j]->getGlobalIndex();
448	>	exclude_.removePair(a, b);
449	>	}
450	>	}
451	>	}
452
453	<	void SimInfo::wrapVector( double thePos[3] ){
453	>	Molecule::CutoffGroupIterator cgIter;
454	>	CutoffGroup* cg;
455	>	for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) {
456	>	std::vector<Atom*> atoms = cg->getAtoms();
457	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
458	>	for (int j = i + 1; j < atoms.size(); ++j) {
459	>	a = atoms[i]->getGlobalIndex();
460	>	b = atoms[j]->getGlobalIndex();
461	>	exclude_.removePair(a, b);
462	>	}
463	>	}
464	>	}
465
466	<	int i;
293	<	double scaled[3];
466	>	}
467
295	–	if( !orthoRhombic ){
296	–	// calc the scaled coordinates.
297	–
468
469	<	matVecMul3(HmatInv, thePos, scaled);
470	<
301	<	for(i=0; i<3; i++)
302	<	scaled[i] -= roundMe(scaled[i]);
303	<
304	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
305	<
306	<	matVecMul3(Hmat, scaled, thePos);
469	>	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
470	>	int curStampId;
471
472	<	}
473	<	else{
474	<	// calc the scaled coordinates.
475	<
476	<	for(i=0; i<3; i++)
313	<	scaled[i] = thePos[i]*HmatInv[i][i];
314	<
315	<	// wrap the scaled coordinates
316	<
317	<	for(i=0; i<3; i++)
318	<	scaled[i] -= roundMe(scaled[i]);
319	<
320	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
321	<
322	<	for(i=0; i<3; i++)
323	<	thePos[i] = scaled[i]*Hmat[i][i];
324	<	}
325	<
472	>	//index from 0
473	>	curStampId = moleculeStamps_.size();
474	>
475	>	moleculeStamps_.push_back(molStamp);
476	>	molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
477		}
478
479	+	void SimInfo::update() {
480
481	<	int SimInfo::getNDF(){
330	<	int ndf_local;
481	>	setupSimType();
482
483	<	ndf_local = 0;
484	<
485	<	for(int i = 0; i < integrableObjects.size(); i++){
486	<	ndf_local += 3;
487	<	if (integrableObjects[i]->isDirectional()) {
488	<	if (integrableObjects[i]->isLinear())
489	<	ndf_local += 2;
490	<	else
491	<	ndf_local += 3;
483	>	#ifdef IS_MPI
484	>	setupFortranParallel();
485	>	#endif
486	>
487	>	setupFortranSim();
488	>
489	>	//setup fortran force field
490	>	/** @deprecate */
491	>	int isError = 0;
492	>	initFortranFF( &fInfo_.SIM_uses_RF , &isError );
493	>	if(isError){
494	>	sprintf( painCave.errMsg,
495	>	"ForceField error: There was an error initializing the forceField in fortran.\n" );
496	>	painCave.isFatal = 1;
497	>	simError();
498		}
499	<	}
499	>
500	>
501	>	setupCutoff();
502
503	<	// n_constraints is local, so subtract them on each processor:
503	>	calcNdf();
504	>	calcNdfRaw();
505	>	calcNdfTrans();
506
507	<	ndf_local -= n_constraints;
507	>	fortranInitialized_ = true;
508	>	}
509
510	<	#ifdef IS_MPI
511	<	MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
512	<	#else
513	<	ndf = ndf_local;
514	<	#endif
510	>	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
511	>	SimInfo::MoleculeIterator mi;
512	>	Molecule* mol;
513	>	Molecule::AtomIterator ai;
514	>	Atom* atom;
515	>	std::set<AtomType*> atomTypes;
516
517	<	// nZconstraints is global, as are the 3 COM translations for the
355	<	// entire system:
517	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
518
519	<	ndf = ndf - 3 - nZconstraints;
519	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
520	>	atomTypes.insert(atom->getAtomType());
521	>	}
522	>
523	>	}
524
525	<	return ndf;
525	>	return atomTypes;
526		}
527
528	<	int SimInfo::getNDFraw() {
529	<	int ndfRaw_local;
528	>	void SimInfo::setupSimType() {
529	>	std::set<AtomType*>::iterator i;
530	>	std::set<AtomType*> atomTypes;
531	>	atomTypes = getUniqueAtomTypes();
532	>
533	>	int useLennardJones = 0;
534	>	int useElectrostatic = 0;
535	>	int useEAM = 0;
536	>	int useCharge = 0;
537	>	int useDirectional = 0;
538	>	int useDipole = 0;
539	>	int useGayBerne = 0;
540	>	int useSticky = 0;
541	>	int useShape = 0;
542	>	int useFLARB = 0; //it is not in AtomType yet
543	>	int useDirectionalAtom = 0;
544	>	int useElectrostatics = 0;
545	>	//usePBC and useRF are from simParams
546	>	int usePBC = simParams_->getPBC();
547	>	int useRF = simParams_->getUseRF();
548
549	<	// Raw degrees of freedom that we have to set
550	<	ndfRaw_local = 0;
549	>	//loop over all of the atom types
550	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
551	>	useLennardJones |= (*i)->isLennardJones();
552	>	useElectrostatic |= (*i)->isElectrostatic();
553	>	useEAM |= (*i)->isEAM();
554	>	useCharge |= (*i)->isCharge();
555	>	useDirectional |= (*i)->isDirectional();
556	>	useDipole |= (*i)->isDipole();
557	>	useGayBerne |= (*i)->isGayBerne();
558	>	useSticky |= (*i)->isSticky();
559	>	useShape |= (*i)->isShape();
560	>	}
561
562	<	for(int i = 0; i < integrableObjects.size(); i++){
563	<	ndfRaw_local += 3;
370	<	if (integrableObjects[i]->isDirectional()) {
371	<	if (integrableObjects[i]->isLinear())
372	<	ndfRaw_local += 2;
373	<	else
374	<	ndfRaw_local += 3;
562	>	if (useSticky || useDipole || useGayBerne || useShape) {
563	>	useDirectionalAtom = 1;
564		}
376	–	}
377	–
378	–	#ifdef IS_MPI
379	–	MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
380	–	#else
381	–	ndfRaw = ndfRaw_local;
382	–	#endif
565
566	<	return ndfRaw;
567	<	}
566	>	if (useCharge || useDipole) {
567	>	useElectrostatics = 1;
568	>	}
569
570	<	int SimInfo::getNDFtranslational() {
571	<	int ndfTrans_local;
570	>	#ifdef IS_MPI
571	>	int temp;
572
573	<	ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
573	>	temp = usePBC;
574	>	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
575
576	+	temp = useDirectionalAtom;
577	+	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
578
579	<	#ifdef IS_MPI
580	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
395	<	#else
396	<	ndfTrans = ndfTrans_local;
397	<	#endif
579	>	temp = useLennardJones;
580	>	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
581
582	<	ndfTrans = ndfTrans - 3 - nZconstraints;
582	>	temp = useElectrostatics;
583	>	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
584
585	<	return ndfTrans;
586	<	}
585	>	temp = useCharge;
586	>	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
587
588	<	int SimInfo::getTotIntegrableObjects() {
589	<	int nObjs_local;
406	<	int nObjs;
588	>	temp = useDipole;
589	>	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
590
591	<	nObjs_local =  integrableObjects.size();
591	>	temp = useSticky;
592	>	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
593
594	+	temp = useGayBerne;
595	+	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
596
597	<	#ifdef IS_MPI
598	<	MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
599	<	#else
600	<	nObjs = nObjs_local;
597	>	temp = useEAM;
598	>	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
599	>
600	>	temp = useShape;
601	>	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
602	>
603	>	temp = useFLARB;
604	>	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
605	>
606	>	temp = useRF;
607	>	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
608	>
609		#endif
610
611	+	fInfo_.SIM_uses_PBC = usePBC;
612	+	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
613	+	fInfo_.SIM_uses_LennardJones = useLennardJones;
614	+	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
615	+	fInfo_.SIM_uses_Charges = useCharge;
616	+	fInfo_.SIM_uses_Dipoles = useDipole;
617	+	fInfo_.SIM_uses_Sticky = useSticky;
618	+	fInfo_.SIM_uses_GayBerne = useGayBerne;
619	+	fInfo_.SIM_uses_EAM = useEAM;
620	+	fInfo_.SIM_uses_Shapes = useShape;
621	+	fInfo_.SIM_uses_FLARB = useFLARB;
622	+	fInfo_.SIM_uses_RF = useRF;
623
624	<	return nObjs;
624	>	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
625	>
626	>	if (simParams_->haveDielectric()) {
627	>	fInfo_.dielect = simParams_->getDielectric();
628	>	} else {
629	>	sprintf(painCave.errMsg,
630	>	"SimSetup Error: No Dielectric constant was set.\n"
631	>	"\tYou are trying to use Reaction Field without"
632	>	"\tsetting a dielectric constant!\n");
633	>	painCave.isFatal = 1;
634	>	simError();
635	>	}
636	>
637	>	} else {
638	>	fInfo_.dielect = 0.0;
639	>	}
640	>
641		}
642
643	<	void SimInfo::refreshSim(){
643	>	void SimInfo::setupFortranSim() {
644	>	int isError;
645	>	int nExclude;
646	>	std::vector<int> fortranGlobalGroupMembership;
647	>
648	>	nExclude = exclude_.getSize();
649	>	isError = 0;
650
651	<	simtype fInfo;
652	<	int isError;
653	<	int n_global;
654	<	int* excl;
651	>	//globalGroupMembership_ is filled by SimCreator
652	>	for (int i = 0; i < nGlobalAtoms_; i++) {
653	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
654	>	}
655
656	<	fInfo.dielect = 0.0;
656	>	//calculate mass ratio of cutoff group
657	>	std::vector<double> mfact;
658	>	SimInfo::MoleculeIterator mi;
659	>	Molecule* mol;
660	>	Molecule::CutoffGroupIterator ci;
661	>	CutoffGroup* cg;
662	>	Molecule::AtomIterator ai;
663	>	Atom* atom;
664	>	double totalMass;
665
666	<	if( useDipoles ){
667	<	if( useReactionField )fInfo.dielect = dielectric;
668	<	}
666	>	//to avoid memory reallocation, reserve enough space for mfact
667	>	mfact.reserve(getNCutoffGroups());
668	>
669	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
670	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
671
672	<	fInfo.SIM_uses_PBC = usePBC;
673	<	//fInfo.SIM_uses_LJ = 0;
674	<	fInfo.SIM_uses_LJ = useLJ;
675	<	fInfo.SIM_uses_sticky = useSticky;
438	<	//fInfo.SIM_uses_sticky = 0;
439	<	fInfo.SIM_uses_charges = useCharges;
440	<	fInfo.SIM_uses_dipoles = useDipoles;
441	<	//fInfo.SIM_uses_dipoles = 0;
442	<	fInfo.SIM_uses_RF = useReactionField;
443	<	//fInfo.SIM_uses_RF = 0;
444	<	fInfo.SIM_uses_GB = useGB;
445	<	fInfo.SIM_uses_EAM = useEAM;
672	>	totalMass = cg->getMass();
673	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
674	>	mfact.push_back(atom->getMass()/totalMass);
675	>	}
676
677	<	n_exclude = excludes->getSize();
678	<	excl = excludes->getFortranArray();
449	<
450	<	#ifdef IS_MPI
451	<	n_global = mpiSim->getNAtomsGlobal();
452	<	#else
453	<	n_global = n_atoms;
454	<	#endif
455	<
456	<	isError = 0;
457	<
458	<	getFortranGroupArrays(this, FglobalGroupMembership, mfact);
459	<	//it may not be a good idea to pass the address of first element in vector
460	<	//since c++ standard does not require vector to be stored continuously in meomory
461	<	//Most of the compilers will organize the memory of vector continuously
462	<	setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
463	<	&nGlobalExcludes, globalExcludes, molMembershipArray,
464	<	&mfact[0], &ngroup, &FglobalGroupMembership[0], &isError);
677	>	}
678	>	}
679
680	<	if( isError ){
680	>	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
681	>	std::vector<int> identArray;
682	>
683	>	//to avoid memory reallocation, reserve enough space identArray
684	>	identArray.reserve(getNAtoms());
685
686	<	sprintf( painCave.errMsg,
687	<	"There was an error setting the simulation information in fortran.\n" );
688	<	painCave.isFatal = 1;
689	<	painCave.severity = OOPSE_ERROR;
690	<	simError();
691	<	}
692	<
686	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
687	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
688	>	identArray.push_back(atom->getIdent());
689	>	}
690	>	}
691	>
692	>	//fill molMembershipArray
693	>	//molMembershipArray is filled by SimCreator
694	>	std::vector<int> molMembershipArray(nGlobalAtoms_);
695	>	for (int i = 0; i < nGlobalAtoms_; i++) {
696	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
697	>	}
698	>
699	>	//setup fortran simulation
700	>	int nGlobalExcludes = 0;
701	>	int* globalExcludes = NULL;
702	>	int* excludeList = exclude_.getExcludeList();
703	>	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
704	>	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
705	>	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
706	>
707	>	if( isError ){
708	>
709	>	sprintf( painCave.errMsg,
710	>	"There was an error setting the simulation information in fortran.\n" );
711	>	painCave.isFatal = 1;
712	>	painCave.severity = OOPSE_ERROR;
713	>	simError();
714	>	}
715	>
716		#ifdef IS_MPI
717	<	sprintf( checkPointMsg,
718	<	"succesfully sent the simulation information to fortran.\n");
719	<	MPIcheckPoint();
717	>	sprintf( checkPointMsg,
718	>	"succesfully sent the simulation information to fortran.\n");
719	>	MPIcheckPoint();
720		#endif // is_mpi
480	–
481	–	this->ndf = this->getNDF();
482	–	this->ndfRaw = this->getNDFraw();
483	–	this->ndfTrans = this->getNDFtranslational();
721		}
722
486	–	void SimInfo::setDefaultRcut( double theRcut ){
487	–
488	–	haveRcut = 1;
489	–	rCut = theRcut;
490	–	rList = rCut + 1.0;
491	–
492	–	notifyFortranCutOffs( &rCut, &rSw, &rList );
493	–	}
723
724	<	void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
724	>	#ifdef IS_MPI
725	>	void SimInfo::setupFortranParallel() {
726	>
727	>	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
728	>	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
729	>	std::vector<int> localToGlobalCutoffGroupIndex;
730	>	SimInfo::MoleculeIterator mi;
731	>	Molecule::AtomIterator ai;
732	>	Molecule::CutoffGroupIterator ci;
733	>	Molecule* mol;
734	>	Atom* atom;
735	>	CutoffGroup* cg;
736	>	mpiSimData parallelData;
737	>	int isError;
738
739	<	rSw = theRsw;
498	<	setDefaultRcut( theRcut );
499	<	}
739	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
740
741	+	//local index(index in DataStorge) of atom is important
742	+	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
743	+	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
744	+	}
745
746	<	void SimInfo::checkCutOffs( void ){
747	<
748	<	if( boxIsInit ){
749	<
750	<	//we need to check cutOffs against the box
751	<
752	<	if( rCut > maxCutoff ){
753	<	sprintf( painCave.errMsg,
754	<	"cutoffRadius is too large for the current periodic box.\n"
755	<	"\tCurrent Value of cutoffRadius = %G at time %G\n "
756	<	"\tThis is larger than half of at least one of the\n"
757	<	"\tperiodic box vectors.  Right now, the Box matrix is:\n"
758	<	"\n"
759	<	"\t[ %G %G %G ]\n"
760	<	"\t[ %G %G %G ]\n"
761	<	"\t[ %G %G %G ]\n",
762	<	rCut, currentTime,
763	<	Hmat[0][0], Hmat[0][1], Hmat[0][2],
764	<	Hmat[1][0], Hmat[1][1], Hmat[1][2],
765	<	Hmat[2][0], Hmat[2][1], Hmat[2][2]);
766	<	painCave.severity = OOPSE_ERROR;
767	<	painCave.isFatal = 1;
768	<	simError();
769	<	}
770	<	} else {
771	<	// initialize this stuff before using it, OK?
772	<	sprintf( painCave.errMsg,
773	<	"Trying to check cutoffs without a box.\n"
774	<	"\tOOPSE should have better programmers than that.\n" );
775	<	painCave.severity = OOPSE_ERROR;
776	<	painCave.isFatal = 1;
777	<	simError();
778	<	}
535	<
746	>	//local index of cutoff group is trivial, it only depends on the order of travesing
747	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
748	>	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
749	>	}
750	>
751	>	}
752	>
753	>	//fill up mpiSimData struct
754	>	parallelData.nMolGlobal = getNGlobalMolecules();
755	>	parallelData.nMolLocal = getNMolecules();
756	>	parallelData.nAtomsGlobal = getNGlobalAtoms();
757	>	parallelData.nAtomsLocal = getNAtoms();
758	>	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
759	>	parallelData.nGroupsLocal = getNCutoffGroups();
760	>	parallelData.myNode = worldRank;
761	>	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
762	>
763	>	//pass mpiSimData struct and index arrays to fortran
764	>	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
765	>	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
766	>	&localToGlobalCutoffGroupIndex[0], &isError);
767	>
768	>	if (isError) {
769	>	sprintf(painCave.errMsg,
770	>	"mpiRefresh errror: fortran didn't like something we gave it.\n");
771	>	painCave.isFatal = 1;
772	>	simError();
773	>	}
774	>
775	>	sprintf(checkPointMsg, " mpiRefresh successful.\n");
776	>	MPIcheckPoint();
777	>
778	>
779		}
780
781	<	void SimInfo::addProperty(GenericData* prop){
781	>	#endif
782
783	<	map<string, GenericData*>::iterator result;
784	<	result = properties.find(prop->getID());
785	<
786	<	//we can't simply use  properties[prop->getID()] = prop,
787	<	//it will cause memory leak if we already contain a propery which has the same name of prop
788	<
789	<	if(result != properties.end()){
783	>	double SimInfo::calcMaxCutoffRadius() {
784	>
785	>
786	>	std::set<AtomType*> atomTypes;
787	>	std::set<AtomType*>::iterator i;
788	>	std::vector<double> cutoffRadius;
789	>
790	>	//get the unique atom types
791	>	atomTypes = getUniqueAtomTypes();
792	>
793	>	//query the max cutoff radius among these atom types
794	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
795	>	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
796	>	}
797	>
798	>	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
799	>	#ifdef IS_MPI
800	>	//pick the max cutoff radius among the processors
801	>	#endif
802	>
803	>	return maxCutoffRadius;
804	>	}
805	>
806	>	void SimInfo::getCutoff(double& rcut, double& rsw) {
807
808	<	delete (*result).second;
809	<	(*result).second = prop;
808	>	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
809	>
810	>	if (!simParams_->haveRcut()){
811	>	sprintf(painCave.errMsg,
812	>	"SimCreator Warning: No value was set for the cutoffRadius.\n"
813	>	"\tOOPSE will use a default value of 15.0 angstroms"
814	>	"\tfor the cutoffRadius.\n");
815	>	painCave.isFatal = 0;
816	>	simError();
817	>	rcut = 15.0;
818	>	} else{
819	>	rcut = simParams_->getRcut();
820	>	}
821	>
822	>	if (!simParams_->haveRsw()){
823	>	sprintf(painCave.errMsg,
824	>	"SimCreator Warning: No value was set for switchingRadius.\n"
825	>	"\tOOPSE will use a default value of\n"
826	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
827	>	painCave.isFatal = 0;
828	>	simError();
829	>	rsw = 0.95 * rcut;
830	>	} else{
831	>	rsw = simParams_->getRsw();
832	>	}
833	>
834	>	} else {
835	>	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
836	>	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
837	>
838	>	if (simParams_->haveRcut()) {
839	>	rcut = simParams_->getRcut();
840	>	} else {
841	>	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
842	>	rcut = calcMaxCutoffRadius();
843	>	}
844	>
845	>	if (simParams_->haveRsw()) {
846	>	rsw  = simParams_->getRsw();
847	>	} else {
848	>	rsw = rcut;
849	>	}
850	>
851	>	}
852	>	}
853	>
854	>	void SimInfo::setupCutoff() {
855	>	getCutoff(rcut_, rsw_);
856	>	double rnblist = rcut_ + 1; // skin of neighbor list
857	>
858	>	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
859	>	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist);
860	>	}
861	>
862	>	void SimInfo::addProperty(GenericData* genData) {
863	>	properties_.addProperty(genData);
864	>	}
865	>
866	>	void SimInfo::removeProperty(const std::string& propName) {
867	>	properties_.removeProperty(propName);
868	>	}
869	>
870	>	void SimInfo::clearProperties() {
871	>	properties_.clearProperties();
872	>	}
873	>
874	>	std::vector<std::string> SimInfo::getPropertyNames() {
875	>	return properties_.getPropertyNames();
876	>	}
877
878	<	}
879	<	else{
878	>	std::vector<GenericData*> SimInfo::getProperties() {
879	>	return properties_.getProperties();
880	>	}
881
882	<	properties[prop->getID()] = prop;
882	>	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
883	>	return properties_.getPropertyByName(propName);
884	>	}
885
886	<	}
886	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
887	>	if (sman_ == sman) {
888	>	return;
889	>	}
890	>	delete sman_;
891	>	sman_ = sman;
892	>
893	>	Molecule* mol;
894	>	RigidBody* rb;
895	>	Atom* atom;
896	>	SimInfo::MoleculeIterator mi;
897	>	Molecule::RigidBodyIterator rbIter;
898	>	Molecule::AtomIterator atomIter;;
899	>
900	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
901	>
902	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
903	>	atom->setSnapshotManager(sman_);
904	>	}
905	>
906	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
907	>	rb->setSnapshotManager(sman_);
908	>	}
909	>	}
910
911		}
912
913	<	GenericData* SimInfo::getProperty(const string& propName){
913	>	Vector3d SimInfo::getComVel(){
914	>	SimInfo::MoleculeIterator i;
915	>	Molecule* mol;
916	>
917	>	Vector3d comVel(0.0);
918	>	double totalMass = 0.0;
919	>
920
921	<	map<string, GenericData*>::iterator result;
922	<
923	<	//string lowerCaseName = ();
924	<
925	<	result = properties.find(propName);
926	<
927	<	if(result != properties.end())
928	<	return (*result).second;
929	<	else
930	<	return NULL;
921	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
922	>	double mass = mol->getMass();
923	>	totalMass += mass;
924	>	comVel += mass * mol->getComVel();
925	>	}
926	>
927	>	#ifdef IS_MPI
928	>	double tmpMass = totalMass;
929	>	Vector3d tmpComVel(comVel);
930	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
931	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
932	>	#endif
933	>
934	>	comVel /= totalMass;
935	>
936	>	return comVel;
937		}
938
939	+	Vector3d SimInfo::getCom(){
940	+	SimInfo::MoleculeIterator i;
941	+	Molecule* mol;
942
943	<	void SimInfo::getFortranGroupArrays(SimInfo* info,
944	<	vector<int>& FglobalGroupMembership,
945	<	vector<double>& mfact){
946	<
947	<	Molecule* myMols;
948	<	Atom** myAtoms;
949	<	int numAtom;
950	<	double mtot;
583	<	int numMol;
584	<	int numCutoffGroups;
585	<	CutoffGroup* myCutoffGroup;
586	<	vector<CutoffGroup*>::iterator iterCutoff;
587	<	Atom* cutoffAtom;
588	<	vector<Atom*>::iterator iterAtom;
589	<	int atomIndex;
590	<	double totalMass;
591	<
592	<	mfact.clear();
593	<	FglobalGroupMembership.clear();
594	<
943	>	Vector3d com(0.0);
944	>	double totalMass = 0.0;
945	>
946	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
947	>	double mass = mol->getMass();
948	>	totalMass += mass;
949	>	com += mass * mol->getCom();
950	>	}
951
596	–	// Fix the silly fortran indexing problem
952		#ifdef IS_MPI
953	<	numAtom = mpiSim->getNAtomsGlobal();
954	<	#else
955	<	numAtom = n_atoms;
953	>	double tmpMass = totalMass;
954	>	Vector3d tmpCom(com);
955	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
956	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
957		#endif
602	–	for (int i = 0; i < numAtom; i++)
603	–	FglobalGroupMembership.push_back(globalGroupMembership[i] + 1);
604	–
958
959	<	myMols = info->molecules;
607	<	numMol = info->n_mol;
608	<	for(int i  = 0; i < numMol; i++){
609	<	numCutoffGroups = myMols[i].getNCutoffGroups();
610	<	for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff);
611	<	myCutoffGroup != NULL;
612	<	myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
959	>	com /= totalMass;
960
961	<	totalMass = myCutoffGroup->getMass();
615	<
616	<	for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom);
617	<	cutoffAtom != NULL;
618	<	cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
619	<	mfact.push_back(cutoffAtom->getMass()/totalMass);
620	<	}
621	<	}
622	<	}
961	>	return com;
962
963	+	}
964	+
965	+	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
966	+
967	+	return o;
968		}
969	+
970	+	}//end namespace oopse
971	+

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