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root/OpenMD/branches/development/src/brains/SimInfo.cpp

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 2 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
Revision 606 by chrisfen, Fri Sep 16 19:35:14 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 "SimInfo.hpp"
53	<	#define __C
54	<	#include "fSimulation.h"
55	<	#include "simError.h"
52	>	#include "brains/SimInfo.hpp"
53	>	#include "math/Vector3.hpp"
54	>	#include "primitives/Molecule.hpp"
55	>	#include "UseTheForce/fCutoffPolicy.h"
56	>	#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
57	>	#include "UseTheForce/doForces_interface.h"
58	>	#include "UseTheForce/notifyCutoffs_interface.h"
59	>	#include "utils/MemoryUtils.hpp"
60	>	#include "utils/simError.h"
61	>	#include "selection/SelectionManager.hpp"
62
13	–	#include "fortranWrappers.hpp"
14	–
15	–	#include "MatVec3.h"
16	–
63		#ifdef IS_MPI
64	<	#include "mpiSimulation.hpp"
65	<	#endif
64	>	#include "UseTheForce/mpiComponentPlan.h"
65	>	#include "UseTheForce/DarkSide/simParallel_interface.h"
66	>	#endif
67
68	<	inline double roundMe( double x ){
22	<	return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
23	<	}
24	<
25	<	inline double min( double a, double b ){
26	<	return (a < b ) ? a : b;
27	<	}
68	>	namespace oopse {
69
70	<	SimInfo* currentInfo;
70	>	SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
71	>	ForceField* ff, Globals* simParams) :
72	>	stamps_(stamps), forceField_(ff), simParams_(simParams),
73	>	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
74	>	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
75	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
76	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
77	>	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
78	>	sman_(NULL), fortranInitialized_(false) {
79
80	<	SimInfo::SimInfo(){
80	>
81	>	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
82	>	MoleculeStamp* molStamp;
83	>	int nMolWithSameStamp;
84	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
85	>	int nGroups = 0;          //total cutoff groups defined in meta-data file
86	>	CutoffGroupStamp* cgStamp;
87	>	RigidBodyStamp* rbStamp;
88	>	int nRigidAtoms = 0;
89	>
90	>	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
91	>	molStamp = i->first;
92	>	nMolWithSameStamp = i->second;
93	>
94	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
95
96	<	n_constraints = 0;
97	<	nZconstraints = 0;
35	<	n_oriented = 0;
36	<	n_dipoles = 0;
37	<	ndf = 0;
38	<	ndfRaw = 0;
39	<	nZconstraints = 0;
40	<	the_integrator = NULL;
41	<	setTemp = 0;
42	<	thermalTime = 0.0;
43	<	currentTime = 0.0;
44	<	rCut = 0.0;
45	<	rSw = 0.0;
96	>	//calculate atoms in molecules
97	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
98
47	–	haveRcut = 0;
48	–	haveRsw = 0;
49	–	boxIsInit = 0;
50	–
51	–	resetTime = 1e99;
99
100	<	orthoRhombic = 0;
101	<	orthoTolerance = 1E-6;
102	<	useInitXSstate = true;
100	>	//calculate atoms in cutoff groups
101	>	int nAtomsInGroups = 0;
102	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
103	>
104	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
105	>	cgStamp = molStamp->getCutoffGroup(j);
106	>	nAtomsInGroups += cgStamp->getNMembers();
107	>	}
108
109	<	usePBC = 0;
110	<	useLJ = 0;
59	<	useSticky = 0;
60	<	useCharges = 0;
61	<	useDipoles = 0;
62	<	useReactionField = 0;
63	<	useGB = 0;
64	<	useEAM = 0;
65	<	useSolidThermInt = 0;
66	<	useLiquidThermInt = 0;
109	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
110	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
111
112	<	haveCutoffGroups = false;
112	>	//calculate atoms in rigid bodies
113	>	int nAtomsInRigidBodies = 0;
114	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
115	>
116	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
117	>	rbStamp = molStamp->getRigidBody(j);
118	>	nAtomsInRigidBodies += rbStamp->getNMembers();
119	>	}
120
121	<	excludes = Exclude::Instance();
121	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
122	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
123	>
124	>	}
125
126	<	myConfiguration = new SimState();
126	>	//every free atom (atom does not belong to cutoff groups) is a cutoff group
127	>	//therefore the total number of cutoff groups in the system is equal to
128	>	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
129	>	//file plus the number of cutoff groups defined in meta-data file
130	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
131
132	<	has_minimizer = false;
133	<	the_minimizer =NULL;
132	>	//every free atom (atom does not belong to rigid bodies) is an integrable object
133	>	//therefore the total number of  integrable objects in the system is equal to
134	>	//the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
135	>	//file plus the number of  rigid bodies defined in meta-data file
136	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
137
138	<	ngroup = 0;
138	>	nGlobalMols_ = molStampIds_.size();
139
140	<	wrapMeSimInfo( this );
141	<	}
140	>	#ifdef IS_MPI
141	>	molToProcMap_.resize(nGlobalMols_);
142	>	#endif
143
144	+	}
145
146	<	SimInfo::~SimInfo(){
146	>	SimInfo::~SimInfo() {
147	>	std::map<int, Molecule*>::iterator i;
148	>	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
149	>	delete i->second;
150	>	}
151	>	molecules_.clear();
152	>
153	>	delete stamps_;
154	>	delete sman_;
155	>	delete simParams_;
156	>	delete forceField_;
157	>	}
158
159	<	delete myConfiguration;
159	>	int SimInfo::getNGlobalConstraints() {
160	>	int nGlobalConstraints;
161	>	#ifdef IS_MPI
162	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
163	>	MPI_COMM_WORLD);
164	>	#else
165	>	nGlobalConstraints =  nConstraints_;
166	>	#endif
167	>	return nGlobalConstraints;
168	>	}
169
170	<	map<string, GenericData*>::iterator i;
171	<
89	<	for(i = properties.begin(); i != properties.end(); i++)
90	<	delete (*i).second;
170	>	bool SimInfo::addMolecule(Molecule* mol) {
171	>	MoleculeIterator i;
172
173	<	}
173	>	i = molecules_.find(mol->getGlobalIndex());
174	>	if (i == molecules_.end() ) {
175
176	<	void SimInfo::setBox(double newBox[3]) {
177	<
178	<	int i, j;
179	<	double tempMat[3][3];
180	<
181	<	for(i=0; i<3; i++)
182	<	for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
183	<
184	<	tempMat[0][0] = newBox[0];
185	<	tempMat[1][1] = newBox[1];
104	<	tempMat[2][2] = newBox[2];
105	<
106	<	setBoxM( tempMat );
176	>	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
177	>
178	>	nAtoms_ += mol->getNAtoms();
179	>	nBonds_ += mol->getNBonds();
180	>	nBends_ += mol->getNBends();
181	>	nTorsions_ += mol->getNTorsions();
182	>	nRigidBodies_ += mol->getNRigidBodies();
183	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
184	>	nCutoffGroups_ += mol->getNCutoffGroups();
185	>	nConstraints_ += mol->getNConstraintPairs();
186
187	<	}
187	>	addExcludePairs(mol);
188	>
189	>	return true;
190	>	} else {
191	>	return false;
192	>	}
193	>	}
194
195	<	void SimInfo::setBoxM( double theBox[3][3] ){
196	<
197	<	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);
195	>	bool SimInfo::removeMolecule(Molecule* mol) {
196	>	MoleculeIterator i;
197	>	i = molecules_.find(mol->getGlobalIndex());
198
199	<	if( !boxIsInit ) boxIsInit = 1;
199	>	if (i != molecules_.end() ) {
200
201	<	for(i=0; i < 3; i++)
202	<	for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
203	<
204	<	calcBoxL();
205	<	calcHmatInv();
201	>	assert(mol == i->second);
202	>
203	>	nAtoms_ -= mol->getNAtoms();
204	>	nBonds_ -= mol->getNBonds();
205	>	nBends_ -= mol->getNBends();
206	>	nTorsions_ -= mol->getNTorsions();
207	>	nRigidBodies_ -= mol->getNRigidBodies();
208	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
209	>	nCutoffGroups_ -= mol->getNCutoffGroups();
210	>	nConstraints_ -= mol->getNConstraintPairs();
211
212	<	for(i=0; i < 3; i++) {
213	<	for (j=0; j < 3; j++) {
214	<	FortranHmat[3*j + i] = Hmat[i][j];
215	<	FortranHmatInv[3*j + i] = HmatInv[i][j];
212	>	removeExcludePairs(mol);
213	>	molecules_.erase(mol->getGlobalIndex());
214	>
215	>	delete mol;
216	>
217	>	return true;
218	>	} else {
219	>	return false;
220		}
133	–	}
221
135	–	setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
136	–
137	–	}
138	–
222
223	<	void SimInfo::getBoxM (double theBox[3][3]) {
223	>	}
224
225	<	int i, j;
226	<	for(i=0; i<3; i++)
227	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
228	<	}
225	>
226	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
227	>	i = molecules_.begin();
228	>	return i == molecules_.end() ? NULL : i->second;
229	>	}
230
231	+	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
232	+	++i;
233	+	return i == molecules_.end() ? NULL : i->second;
234	+	}
235
148	–	void SimInfo::scaleBox(double scale) {
149	–	double theBox[3][3];
150	–	int i, j;
236
237	<	// cerr << "Scaling box by " << scale << "\n";
237	>	void SimInfo::calcNdf() {
238	>	int ndf_local;
239	>	MoleculeIterator i;
240	>	std::vector<StuntDouble*>::iterator j;
241	>	Molecule* mol;
242	>	StuntDouble* integrableObject;
243
244	<	for(i=0; i<3; i++)
245	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
244	>	ndf_local = 0;
245	>
246	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
247	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
248	>	integrableObject = mol->nextIntegrableObject(j)) {
249
250	<	setBoxM(theBox);
250	>	ndf_local += 3;
251
252	<	}
252	>	if (integrableObject->isDirectional()) {
253	>	if (integrableObject->isLinear()) {
254	>	ndf_local += 2;
255	>	} else {
256	>	ndf_local += 3;
257	>	}
258	>	}
259	>
260	>	}//end for (integrableObject)
261	>	}// end for (mol)
262	>
263	>	// n_constraints is local, so subtract them on each processor
264	>	ndf_local -= nConstraints_;
265
266	<	void SimInfo::calcHmatInv( void ) {
267	<
268	<	int oldOrtho;
269	<	int i,j;
270	<	double smallDiag;
166	<	double tol;
167	<	double sanity[3][3];
266	>	#ifdef IS_MPI
267	>	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
268	>	#else
269	>	ndf_ = ndf_local;
270	>	#endif
271
272	<	invertMat3( Hmat, HmatInv );
272	>	// nZconstraints_ is global, as are the 3 COM translations for the
273	>	// entire system:
274	>	ndf_ = ndf_ - 3 - nZconstraint_;
275
276	<	// check to see if Hmat is orthorhombic
172	<
173	<	oldOrtho = orthoRhombic;
276	>	}
277
278	<	smallDiag = fabs(Hmat[0][0]);
279	<	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;
278	>	void SimInfo::calcNdfRaw() {
279	>	int ndfRaw_local;
280
281	<	orthoRhombic = 1;
282	<
283	<	for (i = 0; i < 3; i++ ) {
284	<	for (j = 0 ; j < 3; j++) {
184	<	if (i != j) {
185	<	if (orthoRhombic) {
186	<	if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
187	<	}
188	<	}
189	<	}
190	<	}
281	>	MoleculeIterator i;
282	>	std::vector<StuntDouble*>::iterator j;
283	>	Molecule* mol;
284	>	StuntDouble* integrableObject;
285
286	<	if( oldOrtho != orthoRhombic ){
286	>	// Raw degrees of freedom that we have to set
287	>	ndfRaw_local = 0;
288
289	<	if( orthoRhombic ) {
290	<	sprintf( painCave.errMsg,
291	<	"OOPSE is switching from the default Non-Orthorhombic\n"
292	<	"\tto the faster Orthorhombic periodic boundary computations.\n"
293	<	"\tThis is usually a good thing, but if you wan't the\n"
294	<	"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
295	<	"\tvariable ( currently set to %G ) smaller.\n",
296	<	orthoTolerance);
297	<	painCave.severity = OOPSE_INFO;
298	<	simError();
289	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
290	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
291	>	integrableObject = mol->nextIntegrableObject(j)) {
292	>
293	>	ndfRaw_local += 3;
294	>
295	>	if (integrableObject->isDirectional()) {
296	>	if (integrableObject->isLinear()) {
297	>	ndfRaw_local += 2;
298	>	} else {
299	>	ndfRaw_local += 3;
300	>	}
301	>	}
302	>
303	>	}
304		}
305	<	else {
306	<	sprintf( painCave.errMsg,
307	<	"OOPSE is switching from the faster Orthorhombic to the more\n"
308	<	"\tflexible Non-Orthorhombic periodic boundary computations.\n"
309	<	"\tThis is usually because the box has deformed under\n"
310	<	"\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	<	}
305	>
306	>	#ifdef IS_MPI
307	>	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
308	>	#else
309	>	ndfRaw_ = ndfRaw_local;
310	>	#endif
311		}
218	–	}
312
313	<	void SimInfo::calcBoxL( void ){
313	>	void SimInfo::calcNdfTrans() {
314	>	int ndfTrans_local;
315
316	<	double dx, dy, dz, dsq;
316	>	ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
317
224	–	// boxVol = Determinant of Hmat
318
319	<	boxVol = matDet3( Hmat );
319	>	#ifdef IS_MPI
320	>	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
321	>	#else
322	>	ndfTrans_ = ndfTrans_local;
323	>	#endif
324
325	<	// boxLx
326	<
327	<	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];
325	>	ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
326	>
327	>	}
328
329	<	// boxLy
330	<
331	<	dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
332	<	dsq = dx*dx + dy*dy + dz*dz;
333	<	boxL[1] = sqrt( dsq );
334	<	//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
329	>	void SimInfo::addExcludePairs(Molecule* mol) {
330	>	std::vector<Bond*>::iterator bondIter;
331	>	std::vector<Bend*>::iterator bendIter;
332	>	std::vector<Torsion*>::iterator torsionIter;
333	>	Bond* bond;
334	>	Bend* bend;
335	>	Torsion* torsion;
336	>	int a;
337	>	int b;
338	>	int c;
339	>	int d;
340	>
341	>	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
342	>	a = bond->getAtomA()->getGlobalIndex();
343	>	b = bond->getAtomB()->getGlobalIndex();
344	>	exclude_.addPair(a, b);
345	>	}
346
347	+	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
348	+	a = bend->getAtomA()->getGlobalIndex();
349	+	b = bend->getAtomB()->getGlobalIndex();
350	+	c = bend->getAtomC()->getGlobalIndex();
351
352	<	// boxLz
353	<
354	<	dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
355	<	dsq = dx*dx + dy*dy + dz*dz;
247	<	boxL[2] = sqrt( dsq );
248	<	//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
352	>	exclude_.addPair(a, b);
353	>	exclude_.addPair(a, c);
354	>	exclude_.addPair(b, c);
355	>	}
356
357	<	//calculate the max cutoff
358	<	maxCutoff =  calcMaxCutOff();
359	<
360	<	checkCutOffs();
357	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
358	>	a = torsion->getAtomA()->getGlobalIndex();
359	>	b = torsion->getAtomB()->getGlobalIndex();
360	>	c = torsion->getAtomC()->getGlobalIndex();
361	>	d = torsion->getAtomD()->getGlobalIndex();
362
363	<	}
363	>	exclude_.addPair(a, b);
364	>	exclude_.addPair(a, c);
365	>	exclude_.addPair(a, d);
366	>	exclude_.addPair(b, c);
367	>	exclude_.addPair(b, d);
368	>	exclude_.addPair(c, d);
369	>	}
370
371	+	Molecule::RigidBodyIterator rbIter;
372	+	RigidBody* rb;
373	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
374	+	std::vector<Atom*> atoms = rb->getAtoms();
375	+	for (int i = 0; i < atoms.size() -1 ; ++i) {
376	+	for (int j = i + 1; j < atoms.size(); ++j) {
377	+	a = atoms[i]->getGlobalIndex();
378	+	b = atoms[j]->getGlobalIndex();
379	+	exclude_.addPair(a, b);
380	+	}
381	+	}
382	+	}
383
384	<	double SimInfo::calcMaxCutOff(){
384	>	}
385
386	<	double ri[3], rj[3], rk[3];
387	<	double rij[3], rjk[3], rki[3];
388	<	double minDist;
389	<
390	<	ri[0] = Hmat[0][0];
391	<	ri[1] = Hmat[1][0];
392	<	ri[2] = Hmat[2][0];
393	<
394	<	rj[0] = Hmat[0][1];
395	<	rj[1] = Hmat[1][1];
396	<	rj[2] = Hmat[2][1];
271	<
272	<	rk[0] = Hmat[0][2];
273	<	rk[1] = Hmat[1][2];
274	<	rk[2] = Hmat[2][2];
386	>	void SimInfo::removeExcludePairs(Molecule* mol) {
387	>	std::vector<Bond*>::iterator bondIter;
388	>	std::vector<Bend*>::iterator bendIter;
389	>	std::vector<Torsion*>::iterator torsionIter;
390	>	Bond* bond;
391	>	Bend* bend;
392	>	Torsion* torsion;
393	>	int a;
394	>	int b;
395	>	int c;
396	>	int d;
397
398	<	crossProduct3(ri, rj, rij);
399	<	distXY = dotProduct3(rk,rij) / norm3(rij);
398	>	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
399	>	a = bond->getAtomA()->getGlobalIndex();
400	>	b = bond->getAtomB()->getGlobalIndex();
401	>	exclude_.removePair(a, b);
402	>	}
403
404	<	crossProduct3(rj,rk, rjk);
405	<	distYZ = dotProduct3(ri,rjk) / norm3(rjk);
404	>	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
405	>	a = bend->getAtomA()->getGlobalIndex();
406	>	b = bend->getAtomB()->getGlobalIndex();
407	>	c = bend->getAtomC()->getGlobalIndex();
408
409	<	crossProduct3(rk,ri, rki);
410	<	distZX = dotProduct3(rj,rki) / norm3(rki);
409	>	exclude_.removePair(a, b);
410	>	exclude_.removePair(a, c);
411	>	exclude_.removePair(b, c);
412	>	}
413
414	<	minDist = min(min(distXY, distYZ), distZX);
415	<	return minDist/2;
416	<
417	<	}
414	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
415	>	a = torsion->getAtomA()->getGlobalIndex();
416	>	b = torsion->getAtomB()->getGlobalIndex();
417	>	c = torsion->getAtomC()->getGlobalIndex();
418	>	d = torsion->getAtomD()->getGlobalIndex();
419
420	<	void SimInfo::wrapVector( double thePos[3] ){
420	>	exclude_.removePair(a, b);
421	>	exclude_.removePair(a, c);
422	>	exclude_.removePair(a, d);
423	>	exclude_.removePair(b, c);
424	>	exclude_.removePair(b, d);
425	>	exclude_.removePair(c, d);
426	>	}
427
428	<	int i;
429	<	double scaled[3];
428	>	Molecule::RigidBodyIterator rbIter;
429	>	RigidBody* rb;
430	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
431	>	std::vector<Atom*> atoms = rb->getAtoms();
432	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
433	>	for (int j = i + 1; j < atoms.size(); ++j) {
434	>	a = atoms[i]->getGlobalIndex();
435	>	b = atoms[j]->getGlobalIndex();
436	>	exclude_.removePair(a, b);
437	>	}
438	>	}
439	>	}
440
295	–	if( !orthoRhombic ){
296	–	// calc the scaled coordinates.
297	–
298	–
299	–	matVecMul3(HmatInv, thePos, scaled);
300	–
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);
307	–
441		}
309	–	else{
310	–	// calc the scaled coordinates.
311	–
312	–	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	–
326	–	}
442
443
444	<	int SimInfo::getNDF(){
445	<	int ndf_local;
444	>	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
445	>	int curStampId;
446
447	<	ndf_local = 0;
448	<
449	<	for(int i = 0; i < integrableObjects.size(); i++){
450	<	ndf_local += 3;
451	<	if (integrableObjects[i]->isDirectional()) {
337	<	if (integrableObjects[i]->isLinear())
338	<	ndf_local += 2;
339	<	else
340	<	ndf_local += 3;
341	<	}
447	>	//index from 0
448	>	curStampId = moleculeStamps_.size();
449	>
450	>	moleculeStamps_.push_back(molStamp);
451	>	molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
452		}
453
454	<	// n_constraints is local, so subtract them on each processor:
454	>	void SimInfo::update() {
455
456	<	ndf_local -= n_constraints;
456	>	setupSimType();
457
458		#ifdef IS_MPI
459	<	MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
350	<	#else
351	<	ndf = ndf_local;
459	>	setupFortranParallel();
460		#endif
461
462	<	// nZconstraints is global, as are the 3 COM translations for the
355	<	// entire system:
462	>	setupFortranSim();
463
464	<	ndf = ndf - 3 - nZconstraints;
464	>	//setup fortran force field
465	>	/** @deprecate */
466	>	int isError = 0;
467	>
468	>	setupElectrostaticSummationMethod( isError );
469
470	<	return ndf;
471	<	}
470	>	if(isError){
471	>	sprintf( painCave.errMsg,
472	>	"ForceField error: There was an error initializing the forceField in fortran.\n" );
473	>	painCave.isFatal = 1;
474	>	simError();
475	>	}
476	>
477	>
478	>	setupCutoff();
479
480	<	int SimInfo::getNDFraw() {
481	<	int ndfRaw_local;
480	>	calcNdf();
481	>	calcNdfRaw();
482	>	calcNdfTrans();
483
484	<	// Raw degrees of freedom that we have to set
485	<	ndfRaw_local = 0;
484	>	fortranInitialized_ = true;
485	>	}
486
487	<	for(int i = 0; i < integrableObjects.size(); i++){
488	<	ndfRaw_local += 3;
489	<	if (integrableObjects[i]->isDirectional()) {
490	<	if (integrableObjects[i]->isLinear())
491	<	ndfRaw_local += 2;
492	<	else
493	<	ndfRaw_local += 3;
487	>	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
488	>	SimInfo::MoleculeIterator mi;
489	>	Molecule* mol;
490	>	Molecule::AtomIterator ai;
491	>	Atom* atom;
492	>	std::set<AtomType*> atomTypes;
493	>
494	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
495	>
496	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
497	>	atomTypes.insert(atom->getAtomType());
498	>	}
499	>
500		}
501	+
502	+	return atomTypes;
503		}
504	+
505	+	void SimInfo::setupSimType() {
506	+	std::set<AtomType*>::iterator i;
507	+	std::set<AtomType*> atomTypes;
508	+	atomTypes = getUniqueAtomTypes();
509
510	<	#ifdef IS_MPI
511	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
512	<	#else
513	<	ndfRaw = ndfRaw_local;
514	<	#endif
510	>	int useLennardJones = 0;
511	>	int useElectrostatic = 0;
512	>	int useEAM = 0;
513	>	int useCharge = 0;
514	>	int useDirectional = 0;
515	>	int useDipole = 0;
516	>	int useGayBerne = 0;
517	>	int useSticky = 0;
518	>	int useStickyPower = 0;
519	>	int useShape = 0;
520	>	int useFLARB = 0; //it is not in AtomType yet
521	>	int useDirectionalAtom = 0;
522	>	int useElectrostatics = 0;
523	>	//usePBC and useRF are from simParams
524	>	int usePBC = simParams_->getPBC();
525
526	<	return ndfRaw;
527	<	}
526	>	//loop over all of the atom types
527	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
528	>	useLennardJones |= (*i)->isLennardJones();
529	>	useElectrostatic |= (*i)->isElectrostatic();
530	>	useEAM |= (*i)->isEAM();
531	>	useCharge |= (*i)->isCharge();
532	>	useDirectional |= (*i)->isDirectional();
533	>	useDipole |= (*i)->isDipole();
534	>	useGayBerne |= (*i)->isGayBerne();
535	>	useSticky |= (*i)->isSticky();
536	>	useStickyPower |= (*i)->isStickyPower();
537	>	useShape |= (*i)->isShape();
538	>	}
539
540	<	int SimInfo::getNDFtranslational() {
541	<	int ndfTrans_local;
540	>	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
541	>	useDirectionalAtom = 1;
542	>	}
543
544	<	ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
544	>	if (useCharge || useDipole) {
545	>	useElectrostatics = 1;
546	>	}
547
548	+	#ifdef IS_MPI
549	+	int temp;
550
551	<	#ifdef IS_MPI
552	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
395	<	#else
396	<	ndfTrans = ndfTrans_local;
397	<	#endif
551	>	temp = usePBC;
552	>	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
553
554	<	ndfTrans = ndfTrans - 3 - nZconstraints;
554	>	temp = useDirectionalAtom;
555	>	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
556
557	<	return ndfTrans;
558	<	}
557	>	temp = useLennardJones;
558	>	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
559
560	<	int SimInfo::getTotIntegrableObjects() {
561	<	int nObjs_local;
406	<	int nObjs;
560	>	temp = useElectrostatics;
561	>	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
562
563	<	nObjs_local =  integrableObjects.size();
563	>	temp = useCharge;
564	>	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
565
566	+	temp = useDipole;
567	+	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
568
569	<	#ifdef IS_MPI
570	<	MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
571	<	#else
572	<	nObjs = nObjs_local;
573	<	#endif
569	>	temp = useSticky;
570	>	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
571	>
572	>	temp = useStickyPower;
573	>	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
574	>
575	>	temp = useGayBerne;
576	>	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
577
578	+	temp = useEAM;
579	+	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
580
581	<	return nObjs;
582	<	}
581	>	temp = useShape;
582	>	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
583
584	<	void SimInfo::refreshSim(){
584	>	temp = useFLARB;
585	>	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
586
587	<	simtype fInfo;
424	<	int isError;
425	<	int n_global;
426	<	int* excl;
587	>	#endif
588
589	<	fInfo.dielect = 0.0;
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
602	<	if( useDipoles ){
603	<	if( useReactionField )fInfo.dielect = dielectric;
602	>	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
603	>
604	>	if (simParams_->haveDielectric()) {
605	>	fInfo_.dielect = simParams_->getDielectric();
606	>	} else {
607	>	sprintf(painCave.errMsg,
608	>	"SimSetup Error: No Dielectric constant was set.\n"
609	>	"\tYou are trying to use Reaction Field without"
610	>	"\tsetting a dielectric constant!\n");
611	>	painCave.isFatal = 1;
612	>	simError();
613	>	}
614	>
615	>	} else {
616	>	fInfo_.dielect = 0.0;
617	>	}
618	>
619		}
620
621	<	fInfo.SIM_uses_PBC = usePBC;
622	<	//fInfo.SIM_uses_LJ = 0;
623	<	fInfo.SIM_uses_LJ = useLJ;
624	<	fInfo.SIM_uses_sticky = useSticky;
625	<	//fInfo.SIM_uses_sticky = 0;
626	<	fInfo.SIM_uses_charges = useCharges;
627	<	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;
621	>	void SimInfo::setupFortranSim() {
622	>	int isError;
623	>	int nExclude;
624	>	std::vector<int> fortranGlobalGroupMembership;
625	>
626	>	nExclude = exclude_.getSize();
627	>	isError = 0;
628
629	<	n_exclude = excludes->getSize();
630	<	excl = excludes->getFortranArray();
631	<
632	<	#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);
629	>	//globalGroupMembership_ is filled by SimCreator
630	>	for (int i = 0; i < nGlobalAtoms_; i++) {
631	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
632	>	}
633
634	<	if( isError ){
634	>	//calculate mass ratio of cutoff group
635	>	std::vector<double> mfact;
636	>	SimInfo::MoleculeIterator mi;
637	>	Molecule* mol;
638	>	Molecule::CutoffGroupIterator ci;
639	>	CutoffGroup* cg;
640	>	Molecule::AtomIterator ai;
641	>	Atom* atom;
642	>	double totalMass;
643	>
644	>	//to avoid memory reallocation, reserve enough space for mfact
645	>	mfact.reserve(getNCutoffGroups());
646
647	<	sprintf( painCave.errMsg,
648	<	"There was an error setting the simulation information in fortran.\n" );
470	<	painCave.isFatal = 1;
471	<	painCave.severity = OOPSE_ERROR;
472	<	simError();
473	<	}
474	<
475	<	#ifdef IS_MPI
476	<	sprintf( checkPointMsg,
477	<	"succesfully sent the simulation information to fortran.\n");
478	<	MPIcheckPoint();
479	<	#endif // is_mpi
480	<
481	<	this->ndf = this->getNDF();
482	<	this->ndfRaw = this->getNDFraw();
483	<	this->ndfTrans = this->getNDFtranslational();
484	<	}
647	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
648	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
649
650	<	void SimInfo::setDefaultRcut( double theRcut ){
651	<
652	<	haveRcut = 1;
653	<	rCut = theRcut;
490	<	rList = rCut + 1.0;
491	<
492	<	notifyFortranCutOffs( &rCut, &rSw, &rList );
493	<	}
650	>	totalMass = cg->getMass();
651	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
652	>	mfact.push_back(atom->getMass()/totalMass);
653	>	}
654
655	<	void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
655	>	}
656	>	}
657
658	<	rSw = theRsw;
659	<	setDefaultRcut( theRcut );
499	<	}
658	>	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
659	>	std::vector<int> identArray;
660
661	+	//to avoid memory reallocation, reserve enough space identArray
662	+	identArray.reserve(getNAtoms());
663	+
664	+	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
665	+	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
666	+	identArray.push_back(atom->getIdent());
667	+	}
668	+	}
669
670	<	void SimInfo::checkCutOffs( void ){
671	<
672	<	if( boxIsInit ){
670	>	//fill molMembershipArray
671	>	//molMembershipArray is filled by SimCreator
672	>	std::vector<int> molMembershipArray(nGlobalAtoms_);
673	>	for (int i = 0; i < nGlobalAtoms_; i++) {
674	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
675	>	}
676
677	<	//we need to check cutOffs against the box
678	<
679	<	if( rCut > maxCutoff ){
677	>	//setup fortran simulation
678	>	int nGlobalExcludes = 0;
679	>	int* globalExcludes = NULL;
680	>	int* excludeList = exclude_.getExcludeList();
681	>	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
682	>	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
683	>	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
684	>
685	>	if( isError ){
686	>
687		sprintf( painCave.errMsg,
688	<	"cutoffRadius is too large for the current periodic box.\n"
511	<	"\tCurrent Value of cutoffRadius = %G at time %G\n "
512	<	"\tThis is larger than half of at least one of the\n"
513	<	"\tperiodic box vectors.  Right now, the Box matrix is:\n"
514	<	"\n"
515	<	"\t[ %G %G %G ]\n"
516	<	"\t[ %G %G %G ]\n"
517	<	"\t[ %G %G %G ]\n",
518	<	rCut, currentTime,
519	<	Hmat[0][0], Hmat[0][1], Hmat[0][2],
520	<	Hmat[1][0], Hmat[1][1], Hmat[1][2],
521	<	Hmat[2][0], Hmat[2][1], Hmat[2][2]);
522	<	painCave.severity = OOPSE_ERROR;
688	>	"There was an error setting the simulation information in fortran.\n" );
689		painCave.isFatal = 1;
690	+	painCave.severity = OOPSE_ERROR;
691		simError();
692	<	}
693	<	} else {
694	<	// initialize this stuff before using it, OK?
695	<	sprintf( painCave.errMsg,
696	<	"Trying to check cutoffs without a box.\n"
697	<	"\tOOPSE should have better programmers than that.\n" );
698	<	painCave.severity = OOPSE_ERROR;
532	<	painCave.isFatal = 1;
533	<	simError();
692	>	}
693	>
694	>	#ifdef IS_MPI
695	>	sprintf( checkPointMsg,
696	>	"succesfully sent the simulation information to fortran.\n");
697	>	MPIcheckPoint();
698	>	#endif // is_mpi
699		}
535	–
536	–	}
700
538	–	void SimInfo::addProperty(GenericData* prop){
701
702	<	map<string, GenericData*>::iterator result;
703	<	result = properties.find(prop->getID());
542	<
543	<	//we can't simply use  properties[prop->getID()] = prop,
544	<	//it will cause memory leak if we already contain a propery which has the same name of prop
545	<
546	<	if(result != properties.end()){
702	>	#ifdef IS_MPI
703	>	void SimInfo::setupFortranParallel() {
704
705	<	delete (*result).second;
706	<	(*result).second = prop;
707	<
708	<	}
709	<	else{
705	>	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
706	>	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
707	>	std::vector<int> localToGlobalCutoffGroupIndex;
708	>	SimInfo::MoleculeIterator mi;
709	>	Molecule::AtomIterator ai;
710	>	Molecule::CutoffGroupIterator ci;
711	>	Molecule* mol;
712	>	Atom* atom;
713	>	CutoffGroup* cg;
714	>	mpiSimData parallelData;
715	>	int isError;
716
717	<	properties[prop->getID()] = prop;
717	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
718
719	+	//local index(index in DataStorge) of atom is important
720	+	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
721	+	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
722	+	}
723	+
724	+	//local index of cutoff group is trivial, it only depends on the order of travesing
725	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
726	+	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
727	+	}
728	+
729	+	}
730	+
731	+	//fill up mpiSimData struct
732	+	parallelData.nMolGlobal = getNGlobalMolecules();
733	+	parallelData.nMolLocal = getNMolecules();
734	+	parallelData.nAtomsGlobal = getNGlobalAtoms();
735	+	parallelData.nAtomsLocal = getNAtoms();
736	+	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
737	+	parallelData.nGroupsLocal = getNCutoffGroups();
738	+	parallelData.myNode = worldRank;
739	+	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
740	+
741	+	//pass mpiSimData struct and index arrays to fortran
742	+	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
743	+	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
744	+	&localToGlobalCutoffGroupIndex[0], &isError);
745	+
746	+	if (isError) {
747	+	sprintf(painCave.errMsg,
748	+	"mpiRefresh errror: fortran didn't like something we gave it.\n");
749	+	painCave.isFatal = 1;
750	+	simError();
751	+	}
752	+
753	+	sprintf(checkPointMsg, " mpiRefresh successful.\n");
754	+	MPIcheckPoint();
755	+
756	+
757		}
557	–
558	–	}
758
759	<	GenericData* SimInfo::getProperty(const string& propName){
561	<
562	<	map<string, GenericData*>::iterator result;
563	<
564	<	//string lowerCaseName = ();
565	<
566	<	result = properties.find(propName);
567	<
568	<	if(result != properties.end())
569	<	return (*result).second;
570	<	else
571	<	return NULL;
572	<	}
759	>	#endif
760
761	+	double SimInfo::calcMaxCutoffRadius() {
762
575	–	void SimInfo::getFortranGroupArrays(SimInfo* info,
576	–	vector<int>& FglobalGroupMembership,
577	–	vector<double>& mfact){
578	–
579	–	Molecule* myMols;
580	–	Atom** myAtoms;
581	–	int numAtom;
582	–	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	–
763
764	<	// Fix the silly fortran indexing problem
764	>	std::set<AtomType*> atomTypes;
765	>	std::set<AtomType*>::iterator i;
766	>	std::vector<double> cutoffRadius;
767	>
768	>	//get the unique atom types
769	>	atomTypes = getUniqueAtomTypes();
770	>
771	>	//query the max cutoff radius among these atom types
772	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
773	>	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
774	>	}
775	>
776	>	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
777		#ifdef IS_MPI
778	<	numAtom = mpiSim->getNAtomsGlobal();
599	<	#else
600	<	numAtom = n_atoms;
778	>	//pick the max cutoff radius among the processors
779		#endif
602	–	for (int i = 0; i < numAtom; i++)
603	–	FglobalGroupMembership.push_back(globalGroupMembership[i] + 1);
604	–
780
781	<	myMols = info->molecules;
782	<	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)){
781	>	return maxCutoffRadius;
782	>	}
783
784	<	totalMass = myCutoffGroup->getMass();
785	<
786	<	for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom);
787	<	cutoffAtom != NULL;
788	<	cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
789	<	mfact.push_back(cutoffAtom->getMass()/totalMass);
790	<	}
784	>	void SimInfo::getCutoff(double& rcut, double& rsw) {
785	>
786	>	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
787	>
788	>	if (!simParams_->haveRcut()){
789	>	sprintf(painCave.errMsg,
790	>	"SimCreator Warning: No value was set for the cutoffRadius.\n"
791	>	"\tOOPSE will use a default value of 15.0 angstroms"
792	>	"\tfor the cutoffRadius.\n");
793	>	painCave.isFatal = 0;
794	>	simError();
795	>	rcut = 15.0;
796	>	} else{
797	>	rcut = simParams_->getRcut();
798	>	}
799	>
800	>	if (!simParams_->haveRsw()){
801	>	sprintf(painCave.errMsg,
802	>	"SimCreator Warning: No value was set for switchingRadius.\n"
803	>	"\tOOPSE will use a default value of\n"
804	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
805	>	painCave.isFatal = 0;
806	>	simError();
807	>	rsw = 0.95 * rcut;
808	>	} else{
809	>	rsw = simParams_->getRsw();
810	>	}
811	>
812	>	} else {
813	>	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
814	>	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
815	>
816	>	if (simParams_->haveRcut()) {
817	>	rcut = simParams_->getRcut();
818	>	} else {
819	>	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
820	>	rcut = calcMaxCutoffRadius();
821	>	}
822	>
823	>	if (simParams_->haveRsw()) {
824	>	rsw  = simParams_->getRsw();
825	>	} else {
826	>	rsw = rcut;
827	>	}
828	>
829		}
830		}
831
832	<	}
832	>	void SimInfo::setupCutoff() {
833	>	getCutoff(rcut_, rsw_);
834	>	double rnblist = rcut_ + 1; // skin of neighbor list
835	>
836	>	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
837	>
838	>	int cp =  TRADITIONAL_CUTOFF_POLICY;
839	>	if (simParams_->haveCutoffPolicy()) {
840	>	std::string myPolicy = simParams_->getCutoffPolicy();
841	>	if (myPolicy == "MIX") {
842	>	cp = MIX_CUTOFF_POLICY;
843	>	} else {
844	>	if (myPolicy == "MAX") {
845	>	cp = MAX_CUTOFF_POLICY;
846	>	} else {
847	>	if (myPolicy == "TRADITIONAL") {
848	>	cp = TRADITIONAL_CUTOFF_POLICY;
849	>	} else {
850	>	// throw error
851	>	sprintf( painCave.errMsg,
852	>	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
853	>	painCave.isFatal = 1;
854	>	simError();
855	>	}
856	>	}
857	>	}
858	>	}
859	>	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
860	>	}
861	>
862	>	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
863	>
864	>	int errorOut;
865	>	int esm =  NONE;
866	>	double alphaVal;
867	>
868	>	errorOut = isError;
869	>
870	>	if (simParams_->haveElectrostaticSummationMethod()) {
871	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
872	>	if (myMethod == "NONE") {
873	>	esm = NONE;
874	>	} else {
875	>	if (myMethod == "UNDAMPED_WOLF") {
876	>	esm = UNDAMPED_WOLF;
877	>	} else {
878	>	if (myMethod == "DAMPED_WOLF") {
879	>	esm = DAMPED_WOLF;
880	>	if (!simParams_->haveDampingAlpha()) {
881	>	//throw error
882	>	sprintf( painCave.errMsg,
883	>	"SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used for the Damped Wolf Method.", simParams_->getDampingAlpha());
884	>	painCave.isFatal = 0;
885	>	simError();
886	>	}
887	>	alphaVal = simParams_->getDampingAlpha();
888	>	} else {
889	>	if (myMethod == "REACTION_FIELD") {
890	>	esm = REACTION_FIELD;
891	>	} else {
892	>	// throw error
893	>	sprintf( painCave.errMsg,
894	>	"SimInfo error: Unknown electrostaticSummationMethod. (Input file specified %s .)\n\telectrostaticSummationMethod must be one of: \"none\", \"undamped_wolf\", \"damped_wolf\", or \"reaction_field\".", myMethod.c_str() );
895	>	painCave.isFatal = 1;
896	>	simError();
897	>	}
898	>	}
899	>	}
900	>	}
901	>	}
902	>	initFortranFF( &fInfo_.SIM_uses_RF, &esm, &alphaVal, &errorOut );
903	>	}
904	>
905	>	void SimInfo::addProperty(GenericData* genData) {
906	>	properties_.addProperty(genData);
907	>	}
908	>
909	>	void SimInfo::removeProperty(const std::string& propName) {
910	>	properties_.removeProperty(propName);
911	>	}
912	>
913	>	void SimInfo::clearProperties() {
914	>	properties_.clearProperties();
915	>	}
916	>
917	>	std::vector<std::string> SimInfo::getPropertyNames() {
918	>	return properties_.getPropertyNames();
919	>	}
920	>
921	>	std::vector<GenericData*> SimInfo::getProperties() {
922	>	return properties_.getProperties();
923	>	}
924	>
925	>	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
926	>	return properties_.getPropertyByName(propName);
927	>	}
928	>
929	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
930	>	if (sman_ == sman) {
931	>	return;
932	>	}
933	>	delete sman_;
934	>	sman_ = sman;
935	>
936	>	Molecule* mol;
937	>	RigidBody* rb;
938	>	Atom* atom;
939	>	SimInfo::MoleculeIterator mi;
940	>	Molecule::RigidBodyIterator rbIter;
941	>	Molecule::AtomIterator atomIter;;
942	>
943	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
944	>
945	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
946	>	atom->setSnapshotManager(sman_);
947	>	}
948	>
949	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
950	>	rb->setSnapshotManager(sman_);
951	>	}
952	>	}
953	>
954	>	}
955	>
956	>	Vector3d SimInfo::getComVel(){
957	>	SimInfo::MoleculeIterator i;
958	>	Molecule* mol;
959	>
960	>	Vector3d comVel(0.0);
961	>	double totalMass = 0.0;
962	>
963	>
964	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
965	>	double mass = mol->getMass();
966	>	totalMass += mass;
967	>	comVel += mass * mol->getComVel();
968	>	}
969	>
970	>	#ifdef IS_MPI
971	>	double tmpMass = totalMass;
972	>	Vector3d tmpComVel(comVel);
973	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
974	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
975	>	#endif
976	>
977	>	comVel /= totalMass;
978	>
979	>	return comVel;
980	>	}
981	>
982	>	Vector3d SimInfo::getCom(){
983	>	SimInfo::MoleculeIterator i;
984	>	Molecule* mol;
985	>
986	>	Vector3d com(0.0);
987	>	double totalMass = 0.0;
988	>
989	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
990	>	double mass = mol->getMass();
991	>	totalMass += mass;
992	>	com += mass * mol->getCom();
993	>	}
994	>
995	>	#ifdef IS_MPI
996	>	double tmpMass = totalMass;
997	>	Vector3d tmpCom(com);
998	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
999	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1000	>	#endif
1001	>
1002	>	com /= totalMass;
1003	>
1004	>	return com;
1005	>
1006	>	}
1007	>
1008	>	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1009	>
1010	>	return o;
1011	>	}
1012	>
1013	>
1014	>	/*
1015	>	Returns center of mass and center of mass velocity in one function call.
1016	>	*/
1017	>
1018	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1019	>	SimInfo::MoleculeIterator i;
1020	>	Molecule* mol;
1021	>
1022	>
1023	>	double totalMass = 0.0;
1024	>
1025	>
1026	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1027	>	double mass = mol->getMass();
1028	>	totalMass += mass;
1029	>	com += mass * mol->getCom();
1030	>	comVel += mass * mol->getComVel();
1031	>	}
1032	>
1033	>	#ifdef IS_MPI
1034	>	double tmpMass = totalMass;
1035	>	Vector3d tmpCom(com);
1036	>	Vector3d tmpComVel(comVel);
1037	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1038	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1039	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1040	>	#endif
1041	>
1042	>	com /= totalMass;
1043	>	comVel /= totalMass;
1044	>	}
1045	>
1046	>	/*
1047	>	Return intertia tensor for entire system and angular momentum Vector.
1048	>
1049	>
1050	>	[  Ixx -Ixy  -Ixz ]
1051	>	J =| -Iyx  Iyy  -Iyz |
1052	>	[ -Izx -Iyz   Izz ]
1053	>	*/
1054	>
1055	>	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1056	>
1057	>
1058	>	double xx = 0.0;
1059	>	double yy = 0.0;
1060	>	double zz = 0.0;
1061	>	double xy = 0.0;
1062	>	double xz = 0.0;
1063	>	double yz = 0.0;
1064	>	Vector3d com(0.0);
1065	>	Vector3d comVel(0.0);
1066	>
1067	>	getComAll(com, comVel);
1068	>
1069	>	SimInfo::MoleculeIterator i;
1070	>	Molecule* mol;
1071	>
1072	>	Vector3d thisq(0.0);
1073	>	Vector3d thisv(0.0);
1074	>
1075	>	double thisMass = 0.0;
1076	>
1077	>
1078	>
1079	>
1080	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1081	>
1082	>	thisq = mol->getCom()-com;
1083	>	thisv = mol->getComVel()-comVel;
1084	>	thisMass = mol->getMass();
1085	>	// Compute moment of intertia coefficients.
1086	>	xx += thisq[0]*thisq[0]*thisMass;
1087	>	yy += thisq[1]*thisq[1]*thisMass;
1088	>	zz += thisq[2]*thisq[2]*thisMass;
1089	>
1090	>	// compute products of intertia
1091	>	xy += thisq[0]*thisq[1]*thisMass;
1092	>	xz += thisq[0]*thisq[2]*thisMass;
1093	>	yz += thisq[1]*thisq[2]*thisMass;
1094	>
1095	>	angularMomentum += cross( thisq, thisv ) * thisMass;
1096	>
1097	>	}
1098	>
1099	>
1100	>	inertiaTensor(0,0) = yy + zz;
1101	>	inertiaTensor(0,1) = -xy;
1102	>	inertiaTensor(0,2) = -xz;
1103	>	inertiaTensor(1,0) = -xy;
1104	>	inertiaTensor(1,1) = xx + zz;
1105	>	inertiaTensor(1,2) = -yz;
1106	>	inertiaTensor(2,0) = -xz;
1107	>	inertiaTensor(2,1) = -yz;
1108	>	inertiaTensor(2,2) = xx + yy;
1109	>
1110	>	#ifdef IS_MPI
1111	>	Mat3x3d tmpI(inertiaTensor);
1112	>	Vector3d tmpAngMom;
1113	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1114	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1115	>	#endif
1116	>
1117	>	return;
1118	>	}
1119	>
1120	>	//Returns the angular momentum of the system
1121	>	Vector3d SimInfo::getAngularMomentum(){
1122	>
1123	>	Vector3d com(0.0);
1124	>	Vector3d comVel(0.0);
1125	>	Vector3d angularMomentum(0.0);
1126	>
1127	>	getComAll(com,comVel);
1128	>
1129	>	SimInfo::MoleculeIterator i;
1130	>	Molecule* mol;
1131	>
1132	>	Vector3d thisr(0.0);
1133	>	Vector3d thisp(0.0);
1134	>
1135	>	double thisMass;
1136	>
1137	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1138	>	thisMass = mol->getMass();
1139	>	thisr = mol->getCom()-com;
1140	>	thisp = (mol->getComVel()-comVel)*thisMass;
1141	>
1142	>	angularMomentum += cross( thisr, thisp );
1143	>
1144	>	}
1145	>
1146	>	#ifdef IS_MPI
1147	>	Vector3d tmpAngMom;
1148	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1149	>	#endif
1150	>
1151	>	return angularMomentum;
1152	>	}
1153	>
1154	>
1155	>	}//end namespace oopse
1156	>

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