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Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 143 by chrisfen, Fri Oct 22 22:54:01 2004 UTC vs.
Revision 435 by tim, Fri Mar 11 15:55:17 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(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	<	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	<	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;
107	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
108	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
109
110	<	useSolidThermInt = 0;
111	<	useLiquidThermInt = 0;
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	<	haveCutoffGroups = false;
119	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
120	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
121	>
122	>	}
123
124	<	excludes = Exclude::Instance();
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	<	myConfiguration = new SimState();
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	<	has_minimizer = false;
81	<	the_minimizer =NULL;
136	>	nGlobalMols_ = molStampIds_.size();
137
138	<	ngroup = 0;
138	>	#ifdef IS_MPI
139	>	molToProcMap_.resize(nGlobalMols_);
140	>	#endif
141
142		}
143
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	<	SimInfo::~SimInfo(){
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	<	delete myConfiguration;
169	>	bool SimInfo::addMolecule(Molecule* mol) {
170	>	MoleculeIterator i;
171
172	<	map<string, GenericData*>::iterator i;
173	<
94	<	for(i = properties.begin(); i != properties.end(); i++)
95	<	delete (*i).second;
172	>	i = molecules_.find(mol->getGlobalIndex());
173	>	if (i == molecules_.end() ) {
174
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;
102	<	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++)
105	<	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
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);
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];
136	<	FortranHmatInv[3*j + i] = HmatInv[i][j];
137	<	}
138	<	}
139	<
140	<	setFortranBox(FortranHmat, FortranHmatInv, &orthoRhombic);
141	<
230	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
231	>	++i;
232	>	return i == molecules_.end() ? NULL : i->second;
233		}
143	–
234
145	–	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) {
154	<	double theBox[3][3];
155	<	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	<
168	<	int oldOrtho;
169	<	int i,j;
170	<	double smallDiag;
171	<	double tol;
172	<	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]);
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;
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		}
195	–	}
196	–
197	–	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"
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	<	}
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
229	–	// 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];
236	<	dsq = dx*dx + dy*dy + dz*dz;
237	<	boxL[0] = sqrt( dsq );
238	<	//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;
252	<	boxL[2] = sqrt( dsq );
253	<	//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	+	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		}
384
385	+	void SimInfo::removeExcludePairs(Molecule* mol) {
386	+	std::vector<Bond*>::iterator bondIter;
387	+	std::vector<Bend*>::iterator bendIter;
388	+	std::vector<Torsion*>::iterator torsionIter;
389	+	Bond* bond;
390	+	Bend* bend;
391	+	Torsion* torsion;
392	+	int a;
393	+	int b;
394	+	int c;
395	+	int d;
396	+
397	+	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
398	+	a = bond->getAtomA()->getGlobalIndex();
399	+	b = bond->getAtomB()->getGlobalIndex();
400	+	exclude_.removePair(a, b);
401	+	}
402
403	<	double SimInfo::calcMaxCutOff(){
403	>	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
404	>	a = bend->getAtomA()->getGlobalIndex();
405	>	b = bend->getAtomB()->getGlobalIndex();
406	>	c = bend->getAtomC()->getGlobalIndex();
407
408	<	double ri[3], rj[3], rk[3];
409	<	double rij[3], rjk[3], rki[3];
410	<	double minDist;
408	>	exclude_.removePair(a, b);
409	>	exclude_.removePair(a, c);
410	>	exclude_.removePair(b, c);
411	>	}
412
413	<	ri[0] = Hmat[0][0];
414	<	ri[1] = Hmat[1][0];
415	<	ri[2] = Hmat[2][0];
413	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
414	>	a = torsion->getAtomA()->getGlobalIndex();
415	>	b = torsion->getAtomB()->getGlobalIndex();
416	>	c = torsion->getAtomC()->getGlobalIndex();
417	>	d = torsion->getAtomD()->getGlobalIndex();
418
419	<	rj[0] = Hmat[0][1];
420	<	rj[1] = Hmat[1][1];
421	<	rj[2] = Hmat[2][1];
419	>	exclude_.removePair(a, b);
420	>	exclude_.removePair(a, c);
421	>	exclude_.removePair(a, d);
422	>	exclude_.removePair(b, c);
423	>	exclude_.removePair(b, d);
424	>	exclude_.removePair(c, d);
425	>	}
426
427	<	rk[0] = Hmat[0][2];
428	<	rk[1] = Hmat[1][2];
429	<	rk[2] = Hmat[2][2];
430	<
431	<	crossProduct3(ri, rj, rij);
432	<	distXY = dotProduct3(rk,rij) / norm3(rij);
427	>	Molecule::RigidBodyIterator rbIter;
428	>	RigidBody* rb;
429	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
430	>	std::vector<Atom*> atoms = rb->getAtoms();
431	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
432	>	for (int j = i + 1; j < atoms.size(); ++j) {
433	>	a = atoms[i]->getGlobalIndex();
434	>	b = atoms[j]->getGlobalIndex();
435	>	exclude_.removePair(a, b);
436	>	}
437	>	}
438	>	}
439
440	<	crossProduct3(rj,rk, rjk);
285	<	distYZ = dotProduct3(ri,rjk) / norm3(rjk);
440	>	}
441
287	–	crossProduct3(rk,ri, rki);
288	–	distZX = dotProduct3(rj,rki) / norm3(rki);
442
443	<	minDist = min(min(distXY, distYZ), distZX);
444	<	return minDist/2;
445	<
443	>	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
444	>	int curStampId;
445	>
446	>	//index from 0
447	>	curStampId = moleculeStamps_.size();
448	>
449	>	moleculeStamps_.push_back(molStamp);
450	>	molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
451		}
452
453	<	void SimInfo::wrapVector( double thePos[3] ){
453	>	void SimInfo::update() {
454
455	<	int i;
298	<	double scaled[3];
455	>	setupSimType();
456
457	<	if( !orthoRhombic ){
458	<	// calc the scaled coordinates.
459	<
457	>	#ifdef IS_MPI
458	>	setupFortranParallel();
459	>	#endif
460
461	<	matVecMul3(HmatInv, thePos, scaled);
305	<
306	<	for(i=0; i<3; i++)
307	<	scaled[i] -= roundMe(scaled[i]);
308	<
309	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
310	<
311	<	matVecMul3(Hmat, scaled, thePos);
461	>	setupFortranSim();
462
463	<	}
464	<	else{
465	<	// calc the scaled coordinates.
463	>	//setup fortran force field
464	>	/** @deprecate */
465	>	int isError = 0;
466	>	initFortranFF( &fInfo_.SIM_uses_RF , &isError );
467	>	if(isError){
468	>	sprintf( painCave.errMsg,
469	>	"ForceField error: There was an error initializing the forceField in fortran.\n" );
470	>	painCave.isFatal = 1;
471	>	simError();
472	>	}
473	>
474
475	<	for(i=0; i<3; i++)
476	<	scaled[i] = thePos[i]*HmatInv[i][i];
477	<
478	<	// wrap the scaled coordinates
479	<
480	<	for(i=0; i<3; i++)
481	<	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	<
475	>	setupCutoff();
476	>
477	>	calcNdf();
478	>	calcNdfRaw();
479	>	calcNdfTrans();
480	>
481	>	fortranInitialized_ = true;
482		}
483
484	+	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
485	+	SimInfo::MoleculeIterator mi;
486	+	Molecule* mol;
487	+	Molecule::AtomIterator ai;
488	+	Atom* atom;
489	+	std::set<AtomType*> atomTypes;
490
491	<	int SimInfo::getNDF(){
335	<	int ndf_local;
491	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
492
493	<	ndf_local = 0;
494	<
495	<	for(int i = 0; i < integrableObjects.size(); i++){
496	<	ndf_local += 3;
341	<	if (integrableObjects[i]->isDirectional()) {
342	<	if (integrableObjects[i]->isLinear())
343	<	ndf_local += 2;
344	<	else
345	<	ndf_local += 3;
493	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
494	>	atomTypes.insert(atom->getAtomType());
495	>	}
496	>
497		}
347	–	}
498
499	<	// n_constraints is local, so subtract them on each processor:
499	>	return atomTypes;
500	>	}
501
502	<	ndf_local -= n_constraints;
502	>	void SimInfo::setupSimType() {
503	>	std::set<AtomType*>::iterator i;
504	>	std::set<AtomType*> atomTypes;
505	>	atomTypes = getUniqueAtomTypes();
506	>
507	>	int useLennardJones = 0;
508	>	int useElectrostatic = 0;
509	>	int useEAM = 0;
510	>	int useCharge = 0;
511	>	int useDirectional = 0;
512	>	int useDipole = 0;
513	>	int useGayBerne = 0;
514	>	int useSticky = 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	>	useShape |= (*i)->isShape();
534	>	}
535
536	<	// nZconstraints is global, as are the 3 COM translations for the
537	<	// entire system:
536	>	if (useSticky || useDipole || useGayBerne || useShape) {
537	>	useDirectionalAtom = 1;
538	>	}
539
540	<	ndf = ndf - 3 - nZconstraints;
540	>	if (useCharge || useDipole) {
541	>	useElectrostatics = 1;
542	>	}
543
544	<	return ndf;
545	<	}
544	>	#ifdef IS_MPI
545	>	int temp;
546
547	<	int SimInfo::getNDFraw() {
548	<	int ndfRaw_local;
547	>	temp = usePBC;
548	>	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
549
550	<	// Raw degrees of freedom that we have to set
551	<	ndfRaw_local = 0;
550	>	temp = useDirectionalAtom;
551	>	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
552
553	<	for(int i = 0; i < integrableObjects.size(); i++){
554	<	ndfRaw_local += 3;
555	<	if (integrableObjects[i]->isDirectional()) {
556	<	if (integrableObjects[i]->isLinear())
557	<	ndfRaw_local += 2;
558	<	else
559	<	ndfRaw_local += 3;
560	<	}
561	<	}
553	>	temp = useLennardJones;
554	>	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
555	>
556	>	temp = useElectrostatics;
557	>	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
558	>
559	>	temp = useCharge;
560	>	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
561	>
562	>	temp = useDipole;
563	>	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
564	>
565	>	temp = useSticky;
566	>	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
567	>
568	>	temp = useGayBerne;
569	>	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
570	>
571	>	temp = useEAM;
572	>	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
573	>
574	>	temp = useShape;
575	>	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
576	>
577	>	temp = useFLARB;
578	>	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
579	>
580	>	temp = useRF;
581	>	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
582
383	–	#ifdef IS_MPI
384	–	MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
385	–	#else
386	–	ndfRaw = ndfRaw_local;
583		#endif
584
585	<	return ndfRaw;
585	>	fInfo_.SIM_uses_PBC = usePBC;
586	>	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
587	>	fInfo_.SIM_uses_LennardJones = useLennardJones;
588	>	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
589	>	fInfo_.SIM_uses_Charges = useCharge;
590	>	fInfo_.SIM_uses_Dipoles = useDipole;
591	>	fInfo_.SIM_uses_Sticky = useSticky;
592	>	fInfo_.SIM_uses_GayBerne = useGayBerne;
593	>	fInfo_.SIM_uses_EAM = useEAM;
594	>	fInfo_.SIM_uses_Shapes = useShape;
595	>	fInfo_.SIM_uses_FLARB = useFLARB;
596	>	fInfo_.SIM_uses_RF = useRF;
597	>
598	>	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
599	>
600	>	if (simParams_->haveDielectric()) {
601	>	fInfo_.dielect = simParams_->getDielectric();
602	>	} else {
603	>	sprintf(painCave.errMsg,
604	>	"SimSetup Error: No Dielectric constant was set.\n"
605	>	"\tYou are trying to use Reaction Field without"
606	>	"\tsetting a dielectric constant!\n");
607	>	painCave.isFatal = 1;
608	>	simError();
609	>	}
610	>
611	>	} else {
612	>	fInfo_.dielect = 0.0;
613	>	}
614	>
615		}
616
617	<	int SimInfo::getNDFtranslational() {
618	<	int ndfTrans_local;
617	>	void SimInfo::setupFortranSim() {
618	>	int isError;
619	>	int nExclude;
620	>	std::vector<int> fortranGlobalGroupMembership;
621	>
622	>	nExclude = exclude_.getSize();
623	>	isError = 0;
624
625	<	ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
625	>	//globalGroupMembership_ is filled by SimCreator
626	>	for (int i = 0; i < nGlobalAtoms_; i++) {
627	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
628	>	}
629
630	+	//calculate mass ratio of cutoff group
631	+	std::vector<double> mfact;
632	+	SimInfo::MoleculeIterator mi;
633	+	Molecule* mol;
634	+	Molecule::CutoffGroupIterator ci;
635	+	CutoffGroup* cg;
636	+	Molecule::AtomIterator ai;
637	+	Atom* atom;
638	+	double totalMass;
639
640	<	#ifdef IS_MPI
641	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
642	<	#else
643	<	ndfTrans = ndfTrans_local;
644	<	#endif
640	>	//to avoid memory reallocation, reserve enough space for mfact
641	>	mfact.reserve(getNCutoffGroups());
642	>
643	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
644	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
645
646	<	ndfTrans = ndfTrans - 3 - nZconstraints;
646	>	totalMass = cg->getMass();
647	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
648	>	mfact.push_back(atom->getMass()/totalMass);
649	>	}
650
651	<	return ndfTrans;
652	<	}
651	>	}
652	>	}
653
654	<	int SimInfo::getTotIntegrableObjects() {
655	<	int nObjs_local;
411	<	int nObjs;
654	>	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
655	>	std::vector<int> identArray;
656
657	<	nObjs_local =  integrableObjects.size();
657	>	//to avoid memory reallocation, reserve enough space identArray
658	>	identArray.reserve(getNAtoms());
659	>
660	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
661	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
662	>	identArray.push_back(atom->getIdent());
663	>	}
664	>	}
665
666	+	//fill molMembershipArray
667	+	//molMembershipArray is filled by SimCreator
668	+	std::vector<int> molMembershipArray(nGlobalAtoms_);
669	+	for (int i = 0; i < nGlobalAtoms_; i++) {
670	+	molMembershipArray[i] = globalMolMembership_[i] + 1;
671	+	}
672	+
673	+	//setup fortran simulation
674	+	int nGlobalExcludes = 0;
675	+	int* globalExcludes = NULL;
676	+	int* excludeList = exclude_.getExcludeList();
677	+	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
678	+	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
679	+	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
680
681	<	#ifdef IS_MPI
417	<	MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
418	<	#else
419	<	nObjs = nObjs_local;
420	<	#endif
681	>	if( isError ){
682
683	+	sprintf( painCave.errMsg,
684	+	"There was an error setting the simulation information in fortran.\n" );
685	+	painCave.isFatal = 1;
686	+	painCave.severity = OOPSE_ERROR;
687	+	simError();
688	+	}
689
690	<	return nObjs;
690	>	#ifdef IS_MPI
691	>	sprintf( checkPointMsg,
692	>	"succesfully sent the simulation information to fortran.\n");
693	>	MPIcheckPoint();
694	>	#endif // is_mpi
695		}
696
426	–	void SimInfo::refreshSim(){
697
698	<	simtype fInfo;
699	<	int isError;
700	<	int n_global;
701	<	int* excl;
698	>	#ifdef IS_MPI
699	>	void SimInfo::setupFortranParallel() {
700	>
701	>	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
702	>	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
703	>	std::vector<int> localToGlobalCutoffGroupIndex;
704	>	SimInfo::MoleculeIterator mi;
705	>	Molecule::AtomIterator ai;
706	>	Molecule::CutoffGroupIterator ci;
707	>	Molecule* mol;
708	>	Atom* atom;
709	>	CutoffGroup* cg;
710	>	mpiSimData parallelData;
711	>	int isError;
712
713	<	fInfo.dielect = 0.0;
713	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
714
715	<	if( useDipoles ){
716	<	if( useReactionField )fInfo.dielect = dielectric;
717	<	}
715	>	//local index(index in DataStorge) of atom is important
716	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
717	>	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
718	>	}
719
720	<	fInfo.SIM_uses_PBC = usePBC;
720	>	//local index of cutoff group is trivial, it only depends on the order of travesing
721	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
722	>	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
723	>	}
724	>
725	>	}
726
727	<	if (useSticky || useDipoles || useGayBerne || useShapes) {
728	<	useDirectionalAtoms = 1;
729	<	fInfo.SIM_uses_DirectionalAtoms = useDirectionalAtoms;
730	<	}
727	>	//fill up mpiSimData struct
728	>	parallelData.nMolGlobal = getNGlobalMolecules();
729	>	parallelData.nMolLocal = getNMolecules();
730	>	parallelData.nAtomsGlobal = getNGlobalAtoms();
731	>	parallelData.nAtomsLocal = getNAtoms();
732	>	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
733	>	parallelData.nGroupsLocal = getNCutoffGroups();
734	>	parallelData.myNode = worldRank;
735	>	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
736
737	<	fInfo.SIM_uses_LennardJones = useLennardJones;
737	>	//pass mpiSimData struct and index arrays to fortran
738	>	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
739	>	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
740	>	&localToGlobalCutoffGroupIndex[0], &isError);
741
742	<	if (useCharges || useDipoles) {
743	<	useElectrostatics = 1;
744	<	fInfo.SIM_uses_Electrostatics = useElectrostatics;
745	<	}
742	>	if (isError) {
743	>	sprintf(painCave.errMsg,
744	>	"mpiRefresh errror: fortran didn't like something we gave it.\n");
745	>	painCave.isFatal = 1;
746	>	simError();
747	>	}
748
749	<	fInfo.SIM_uses_Charges = useCharges;
750	<	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;
749	>	sprintf(checkPointMsg, " mpiRefresh successful.\n");
750	>	MPIcheckPoint();
751
752	<	n_exclude = excludes->getSize();
753	<	excl = excludes->getFortranArray();
754	<
465	<	#ifdef IS_MPI
466	<	n_global = mpiSim->getNAtomsGlobal();
467	<	#else
468	<	n_global = n_atoms;
752	>
753	>	}
754	>
755		#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);
756
757	<	if( isError ){
758	<
759	<	sprintf( painCave.errMsg,
760	<	"There was an error setting the simulation information in fortran.\n" );
761	<	painCave.isFatal = 1;
762	<	painCave.severity = OOPSE_ERROR;
763	<	simError();
764	<	}
765	<
757	>	double SimInfo::calcMaxCutoffRadius() {
758	>
759	>
760	>	std::set<AtomType*> atomTypes;
761	>	std::set<AtomType*>::iterator i;
762	>	std::vector<double> cutoffRadius;
763	>
764	>	//get the unique atom types
765	>	atomTypes = getUniqueAtomTypes();
766	>
767	>	//query the max cutoff radius among these atom types
768	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
769	>	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
770	>	}
771	>
772	>	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
773		#ifdef IS_MPI
774	<	sprintf( checkPointMsg,
775	<	"succesfully sent the simulation information to fortran.\n");
776	<	MPIcheckPoint();
777	<	#endif // is_mpi
495	<
496	<	this->ndf = this->getNDF();
497	<	this->ndfRaw = this->getNDFraw();
498	<	this->ndfTrans = this->getNDFtranslational();
774	>	//pick the max cutoff radius among the processors
775	>	#endif
776	>
777	>	return maxCutoffRadius;
778		}
779
780	<	void SimInfo::setDefaultRcut( double theRcut ){
781	<
782	<	haveRcut = 1;
783	<	rCut = theRcut;
784	<	rList = rCut + 1.0;
785	<
786	<	notifyFortranCutoffs( &rCut, &rSw, &rList );
780	>	void SimInfo::getCutoff(double& rcut, double& rsw) {
781	>
782	>	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
783	>
784	>	if (!simParams_->haveRcut()){
785	>	sprintf(painCave.errMsg,
786	>	"SimCreator Warning: No value was set for the cutoffRadius.\n"
787	>	"\tOOPSE will use a default value of 15.0 angstroms"
788	>	"\tfor the cutoffRadius.\n");
789	>	painCave.isFatal = 0;
790	>	simError();
791	>	rcut = 15.0;
792	>	} else{
793	>	rcut = simParams_->getRcut();
794	>	}
795	>
796	>	if (!simParams_->haveRsw()){
797	>	sprintf(painCave.errMsg,
798	>	"SimCreator Warning: No value was set for switchingRadius.\n"
799	>	"\tOOPSE will use a default value of\n"
800	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
801	>	painCave.isFatal = 0;
802	>	simError();
803	>	rsw = 0.95 * rcut;
804	>	} else{
805	>	rsw = simParams_->getRsw();
806	>	}
807	>
808	>	} else {
809	>	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
810	>	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
811	>
812	>	if (simParams_->haveRcut()) {
813	>	rcut = simParams_->getRcut();
814	>	} else {
815	>	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
816	>	rcut = calcMaxCutoffRadius();
817	>	}
818	>
819	>	if (simParams_->haveRsw()) {
820	>	rsw  = simParams_->getRsw();
821	>	} else {
822	>	rsw = rcut;
823	>	}
824	>
825	>	}
826		}
827
828	<	void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
828	>	void SimInfo::setupCutoff() {
829	>	getCutoff(rcut_, rsw_);
830	>	double rnblist = rcut_ + 1; // skin of neighbor list
831
832	<	rSw = theRsw;
833	<	setDefaultRcut( theRcut );
832	>	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
833	>	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist);
834		}
835
836	+	void SimInfo::addProperty(GenericData* genData) {
837	+	properties_.addProperty(genData);
838	+	}
839
840	<	void SimInfo::checkCutOffs( void ){
841	<
519	<	if( boxIsInit ){
520	<
521	<	//we need to check cutOffs against the box
522	<
523	<	if( rCut > maxCutoff ){
524	<	sprintf( painCave.errMsg,
525	<	"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;
538	<	painCave.isFatal = 1;
539	<	simError();
540	<	}
541	<	} else {
542	<	// initialize this stuff before using it, OK?
543	<	sprintf( painCave.errMsg,
544	<	"Trying to check cutoffs without a box.\n"
545	<	"\tOOPSE should have better programmers than that.\n" );
546	<	painCave.severity = OOPSE_ERROR;
547	<	painCave.isFatal = 1;
548	<	simError();
549	<	}
550	<
840	>	void SimInfo::removeProperty(const std::string& propName) {
841	>	properties_.removeProperty(propName);
842		}
843
844	<	void SimInfo::addProperty(GenericData* prop){
844	>	void SimInfo::clearProperties() {
845	>	properties_.clearProperties();
846	>	}
847
848	<	map<string, GenericData*>::iterator result;
849	<	result = properties.find(prop->getID());
850	<
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()){
562	<
563	<	delete (*result).second;
564	<	(*result).second = prop;
848	>	std::vector<std::string> SimInfo::getPropertyNames() {
849	>	return properties_.getPropertyNames();
850	>	}
851
852	<	}
853	<	else{
852	>	std::vector<GenericData*> SimInfo::getProperties() {
853	>	return properties_.getProperties();
854	>	}
855
856	<	properties[prop->getID()] = prop;
856	>	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
857	>	return properties_.getPropertyByName(propName);
858	>	}
859
860	<	}
860	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
861	>	if (sman_ == sman) {
862	>	return;
863	>	}
864	>	delete sman_;
865	>	sman_ = sman;
866	>
867	>	Molecule* mol;
868	>	RigidBody* rb;
869	>	Atom* atom;
870	>	SimInfo::MoleculeIterator mi;
871	>	Molecule::RigidBodyIterator rbIter;
872	>	Molecule::AtomIterator atomIter;;
873	>
874	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
875	>
876	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
877	>	atom->setSnapshotManager(sman_);
878	>	}
879	>
880	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
881	>	rb->setSnapshotManager(sman_);
882	>	}
883	>	}
884
885		}
886
887	<	GenericData* SimInfo::getProperty(const string& propName){
887	>	Vector3d SimInfo::getComVel(){
888	>	SimInfo::MoleculeIterator i;
889	>	Molecule* mol;
890	>
891	>	Vector3d comVel(0.0);
892	>	double totalMass = 0.0;
893	>
894
895	<	map<string, GenericData*>::iterator result;
896	<
897	<	//string lowerCaseName = ();
898	<
899	<	result = properties.find(propName);
900	<
901	<	if(result != properties.end())
902	<	return (*result).second;
903	<	else
904	<	return NULL;
895	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
896	>	double mass = mol->getMass();
897	>	totalMass += mass;
898	>	comVel += mass * mol->getComVel();
899	>	}
900	>
901	>	#ifdef IS_MPI
902	>	double tmpMass = totalMass;
903	>	Vector3d tmpComVel(comVel);
904	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
905	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
906	>	#endif
907	>
908	>	comVel /= totalMass;
909	>
910	>	return comVel;
911		}
912
913	+	Vector3d SimInfo::getCom(){
914	+	SimInfo::MoleculeIterator i;
915	+	Molecule* mol;
916
917	<	void SimInfo::getFortranGroupArrays(SimInfo* info,
918	<	vector<int>& FglobalGroupMembership,
919	<	vector<double>& mfact){
920	<
921	<	Molecule* myMols;
922	<	Atom** myAtoms;
923	<	int numAtom;
924	<	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	<
917	>	Vector3d com(0.0);
918	>	double totalMass = 0.0;
919	>
920	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
921	>	double mass = mol->getMass();
922	>	totalMass += mass;
923	>	com += mass * mol->getCom();
924	>	}
925
611	–	// Fix the silly fortran indexing problem
926		#ifdef IS_MPI
927	<	numAtom = mpiSim->getNAtomsGlobal();
928	<	#else
929	<	numAtom = n_atoms;
927	>	double tmpMass = totalMass;
928	>	Vector3d tmpCom(com);
929	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
930	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
931		#endif
617	–	for (int i = 0; i < numAtom; i++)
618	–	FglobalGroupMembership.push_back(globalGroupMembership[i] + 1);
619	–
932
933	<	myMols = info->molecules;
622	<	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)){
933	>	com /= totalMass;
934
935	<	totalMass = myCutoffGroup->getMass();
630	<
631	<	for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom);
632	<	cutoffAtom != NULL;
633	<	cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
634	<	mfact.push_back(cutoffAtom->getMass()/totalMass);
635	<	}
636	<	}
637	<	}
935	>	return com;
936
937	+	}
938	+
939	+	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
940	+
941	+	return o;
942		}
943	+
944	+	}//end namespace oopse
945	+

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