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root/OpenMD/trunk/src/brains/SimInfo.cpp

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 124 by chuckv, Wed Oct 20 20:46:20 2004 UTC vs.
Revision 580 by chrisfen, Tue Aug 30 18:23:50 2005 UTC

#	Line 1 | Line 1
1	<	#include <stdlib.h>
2	<	#include <string.h>
3	<	#include <math.h>
1	>	/*
2	>	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	>	*
4	>	* The University of Notre Dame grants you ("Licensee") a
5	>	* non-exclusive, royalty free, license to use, modify and
6	>	* redistribute this software in source and binary code form, provided
7	>	* that the following conditions are met:
8	>	*
9	>	* 1. Acknowledgement of the program authors must be made in any
10	>	*    publication of scientific results based in part on use of the
11	>	*    program.  An acceptable form of acknowledgement is citation of
12	>	*    the article in which the program was described (Matthew
13	>	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	>	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	>	*    Parallel Simulation Engine for Molecular Dynamics,"
16	>	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	>	*
18	>	* 2. Redistributions of source code must retain the above copyright
19	>	*    notice, this list of conditions and the following disclaimer.
20	>	*
21	>	* 3. Redistributions in binary form must reproduce the above copyright
22	>	*    notice, this list of conditions and the following disclaimer in the
23	>	*    documentation and/or other materials provided with the
24	>	*    distribution.
25	>	*
26	>	* This software is provided "AS IS," without a warranty of any
27	>	* kind. All express or implied conditions, representations and
28	>	* warranties, including any implied warranty of merchantability,
29	>	* fitness for a particular purpose or non-infringement, are hereby
30	>	* excluded.  The University of Notre Dame and its licensors shall not
31	>	* be liable for any damages suffered by licensee as a result of
32	>	* using, modifying or distributing the software or its
33	>	* derivatives. In no event will the University of Notre Dame or its
34	>	* licensors be liable for any lost revenue, profit or data, or for
35	>	* direct, indirect, special, consequential, incidental or punitive
36	>	* damages, however caused and regardless of the theory of liability,
37	>	* arising out of the use of or inability to use software, even if the
38	>	* University of Notre Dame has been advised of the possibility of
39	>	* such damages.
40	>	*/
41	>
42	>	/**
43	>	* @file SimInfo.cpp
44	>	* @author    tlin
45	>	* @date  11/02/2004
46	>	* @version 1.0
47	>	*/
48
49	<	#include <iostream>
50	<	using namespace std;
49	>	#include <algorithm>
50	>	#include <set>
51
52		#include "brains/SimInfo.hpp"
53	<	#define __C
54	<	#include "brains/fSimulation.h"
55	<	#include "utils/simError.h"
12	<	#include "UseTheForce/DarkSide/simulation_interface.h"
53	>	#include "math/Vector3.hpp"
54	>	#include "primitives/Molecule.hpp"
55	>	#include "UseTheForce/doForces_interface.h"
56		#include "UseTheForce/notifyCutoffs_interface.h"
57	+	#include "utils/MemoryUtils.hpp"
58	+	#include "utils/simError.h"
59	+	#include "selection/SelectionManager.hpp"
60
15	–	//#include "UseTheForce/fortranWrappers.hpp"
16	–
17	–	#include "math/MatVec3.h"
18	–
61		#ifdef IS_MPI
62	<	#include "brains/mpiSimulation.hpp"
63	<	#endif
62	>	#include "UseTheForce/mpiComponentPlan.h"
63	>	#include "UseTheForce/DarkSide/simParallel_interface.h"
64	>	#endif
65
66	<	inline double roundMe( double x ){
24	<	return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
25	<	}
26	<
27	<	inline double min( double a, double b ){
28	<	return (a < b ) ? a : b;
29	<	}
66	>	namespace oopse {
67
68	<	SimInfo* currentInfo;
68	>	SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
69	>	ForceField* ff, Globals* simParams) :
70	>	stamps_(stamps), forceField_(ff), simParams_(simParams),
71	>	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
72	>	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
73	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
74	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
75	>	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
76	>	sman_(NULL), fortranInitialized_(false) {
77
78	<	SimInfo::SimInfo(){
78	>
79	>	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
80	>	MoleculeStamp* molStamp;
81	>	int nMolWithSameStamp;
82	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
83	>	int nGroups = 0;          //total cutoff groups defined in meta-data file
84	>	CutoffGroupStamp* cgStamp;
85	>	RigidBodyStamp* rbStamp;
86	>	int nRigidAtoms = 0;
87	>
88	>	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
89	>	molStamp = i->first;
90	>	nMolWithSameStamp = i->second;
91	>
92	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
93
94	<	n_constraints = 0;
95	<	nZconstraints = 0;
37	<	n_oriented = 0;
38	<	n_dipoles = 0;
39	<	ndf = 0;
40	<	ndfRaw = 0;
41	<	nZconstraints = 0;
42	<	the_integrator = NULL;
43	<	setTemp = 0;
44	<	thermalTime = 0.0;
45	<	currentTime = 0.0;
46	<	rCut = 0.0;
47	<	rSw = 0.0;
94	>	//calculate atoms in molecules
95	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
96
49	–	haveRcut = 0;
50	–	haveRsw = 0;
51	–	boxIsInit = 0;
52	–
53	–	resetTime = 1e99;
97
98	<	orthoRhombic = 0;
99	<	orthoTolerance = 1E-6;
100	<	useInitXSstate = true;
98	>	//calculate atoms in cutoff groups
99	>	int nAtomsInGroups = 0;
100	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
101	>
102	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
103	>	cgStamp = molStamp->getCutoffGroup(j);
104	>	nAtomsInGroups += cgStamp->getNMembers();
105	>	}
106
107	<	usePBC = 0;
108	<	useLJ = 0;
61	<	useSticky = 0;
62	<	useCharges = 0;
63	<	useDipoles = 0;
64	<	useReactionField = 0;
65	<	useGB = 0;
66	<	useEAM = 0;
67	<	useSolidThermInt = 0;
68	<	useLiquidThermInt = 0;
107	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
108	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
109
110	<	haveCutoffGroups = false;
110	>	//calculate atoms in rigid bodies
111	>	int nAtomsInRigidBodies = 0;
112	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
113	>
114	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
115	>	rbStamp = molStamp->getRigidBody(j);
116	>	nAtomsInRigidBodies += rbStamp->getNMembers();
117	>	}
118
119	<	excludes = Exclude::Instance();
119	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
120	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
121	>
122	>	}
123
124	<	myConfiguration = new SimState();
124	>	//every free atom (atom does not belong to cutoff groups) is a cutoff group
125	>	//therefore the total number of cutoff groups in the system is equal to
126	>	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
127	>	//file plus the number of cutoff groups defined in meta-data file
128	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
129
130	<	has_minimizer = false;
131	<	the_minimizer =NULL;
130	>	//every free atom (atom does not belong to rigid bodies) is an integrable object
131	>	//therefore the total number of  integrable objects in the system is equal to
132	>	//the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
133	>	//file plus the number of  rigid bodies defined in meta-data file
134	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
135
136	<	ngroup = 0;
136	>	nGlobalMols_ = molStampIds_.size();
137
138	<	}
138	>	#ifdef IS_MPI
139	>	molToProcMap_.resize(nGlobalMols_);
140	>	#endif
141
142	+	}
143
144	<	SimInfo::~SimInfo(){
144	>	SimInfo::~SimInfo() {
145	>	std::map<int, Molecule*>::iterator i;
146	>	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
147	>	delete i->second;
148	>	}
149	>	molecules_.clear();
150	>
151	>	delete stamps_;
152	>	delete sman_;
153	>	delete simParams_;
154	>	delete forceField_;
155	>	}
156
157	<	delete myConfiguration;
157	>	int SimInfo::getNGlobalConstraints() {
158	>	int nGlobalConstraints;
159	>	#ifdef IS_MPI
160	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
161	>	MPI_COMM_WORLD);
162	>	#else
163	>	nGlobalConstraints =  nConstraints_;
164	>	#endif
165	>	return nGlobalConstraints;
166	>	}
167
168	<	map<string, GenericData*>::iterator i;
169	<
90	<	for(i = properties.begin(); i != properties.end(); i++)
91	<	delete (*i).second;
168	>	bool SimInfo::addMolecule(Molecule* mol) {
169	>	MoleculeIterator i;
170
171	<	}
171	>	i = molecules_.find(mol->getGlobalIndex());
172	>	if (i == molecules_.end() ) {
173
174	<	void SimInfo::setBox(double newBox[3]) {
175	<
176	<	int i, j;
177	<	double tempMat[3][3];
178	<
179	<	for(i=0; i<3; i++)
180	<	for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
174	>	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
175	>
176	>	nAtoms_ += mol->getNAtoms();
177	>	nBonds_ += mol->getNBonds();
178	>	nBends_ += mol->getNBends();
179	>	nTorsions_ += mol->getNTorsions();
180	>	nRigidBodies_ += mol->getNRigidBodies();
181	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
182	>	nCutoffGroups_ += mol->getNCutoffGroups();
183	>	nConstraints_ += mol->getNConstraintPairs();
184
185	<	tempMat[0][0] = newBox[0];
186	<	tempMat[1][1] = newBox[1];
187	<	tempMat[2][2] = newBox[2];
185	>	addExcludePairs(mol);
186	>
187	>	return true;
188	>	} else {
189	>	return false;
190	>	}
191	>	}
192
193	<	setBoxM( tempMat );
193	>	bool SimInfo::removeMolecule(Molecule* mol) {
194	>	MoleculeIterator i;
195	>	i = molecules_.find(mol->getGlobalIndex());
196
197	<	}
197	>	if (i != molecules_.end() ) {
198
199	<	void SimInfo::setBoxM( double theBox[3][3] ){
200	<
201	<	int i, j;
202	<	double FortranHmat[9]; // to preserve compatibility with Fortran the
203	<	// ordering in the array is as follows:
204	<	// [ 0 3 6 ]
205	<	// [ 1 4 7 ]
206	<	// [ 2 5 8 ]
207	<	double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
199	>	assert(mol == i->second);
200	>
201	>	nAtoms_ -= mol->getNAtoms();
202	>	nBonds_ -= mol->getNBonds();
203	>	nBends_ -= mol->getNBends();
204	>	nTorsions_ -= mol->getNTorsions();
205	>	nRigidBodies_ -= mol->getNRigidBodies();
206	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
207	>	nCutoffGroups_ -= mol->getNCutoffGroups();
208	>	nConstraints_ -= mol->getNConstraintPairs();
209
210	<	if( !boxIsInit ) boxIsInit = 1;
210	>	removeExcludePairs(mol);
211	>	molecules_.erase(mol->getGlobalIndex());
212
213	<	for(i=0; i < 3; i++)
214	<	for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
215	<
216	<	calcBoxL();
217	<	calcHmatInv();
128	<
129	<	for(i=0; i < 3; i++) {
130	<	for (j=0; j < 3; j++) {
131	<	FortranHmat[3*j + i] = Hmat[i][j];
132	<	FortranHmatInv[3*j + i] = HmatInv[i][j];
213	>	delete mol;
214	>
215	>	return true;
216	>	} else {
217	>	return false;
218		}
134	–	}
219
136	–	setFortranBox(FortranHmat, FortranHmatInv, &orthoRhombic);
137	–
138	–	}
139	–
220
221	<	void SimInfo::getBoxM (double theBox[3][3]) {
221	>	}
222
223	<	int i, j;
224	<	for(i=0; i<3; i++)
225	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
226	<	}
223	>
224	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
225	>	i = molecules_.begin();
226	>	return i == molecules_.end() ? NULL : i->second;
227	>	}
228
229	+	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
230	+	++i;
231	+	return i == molecules_.end() ? NULL : i->second;
232	+	}
233
149	–	void SimInfo::scaleBox(double scale) {
150	–	double theBox[3][3];
151	–	int i, j;
234
235	<	// cerr << "Scaling box by " << scale << "\n";
235	>	void SimInfo::calcNdf() {
236	>	int ndf_local;
237	>	MoleculeIterator i;
238	>	std::vector<StuntDouble*>::iterator j;
239	>	Molecule* mol;
240	>	StuntDouble* integrableObject;
241
242	<	for(i=0; i<3; i++)
243	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
242	>	ndf_local = 0;
243	>
244	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
245	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
246	>	integrableObject = mol->nextIntegrableObject(j)) {
247
248	<	setBoxM(theBox);
248	>	ndf_local += 3;
249
250	<	}
250	>	if (integrableObject->isDirectional()) {
251	>	if (integrableObject->isLinear()) {
252	>	ndf_local += 2;
253	>	} else {
254	>	ndf_local += 3;
255	>	}
256	>	}
257	>
258	>	}//end for (integrableObject)
259	>	}// end for (mol)
260	>
261	>	// n_constraints is local, so subtract them on each processor
262	>	ndf_local -= nConstraints_;
263
264	<	void SimInfo::calcHmatInv( void ) {
265	<
266	<	int oldOrtho;
267	<	int i,j;
268	<	double smallDiag;
167	<	double tol;
168	<	double sanity[3][3];
264	>	#ifdef IS_MPI
265	>	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
266	>	#else
267	>	ndf_ = ndf_local;
268	>	#endif
269
270	<	invertMat3( Hmat, HmatInv );
270	>	// nZconstraints_ is global, as are the 3 COM translations for the
271	>	// entire system:
272	>	ndf_ = ndf_ - 3 - nZconstraint_;
273
274	<	// check to see if Hmat is orthorhombic
173	<
174	<	oldOrtho = orthoRhombic;
274	>	}
275
276	<	smallDiag = fabs(Hmat[0][0]);
277	<	if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
178	<	if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
179	<	tol = smallDiag * orthoTolerance;
276	>	void SimInfo::calcNdfRaw() {
277	>	int ndfRaw_local;
278
279	<	orthoRhombic = 1;
280	<
281	<	for (i = 0; i < 3; i++ ) {
282	<	for (j = 0 ; j < 3; j++) {
283	<	if (i != j) {
284	<	if (orthoRhombic) {
285	<	if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
286	<	}
279	>	MoleculeIterator i;
280	>	std::vector<StuntDouble*>::iterator j;
281	>	Molecule* mol;
282	>	StuntDouble* integrableObject;
283	>
284	>	// Raw degrees of freedom that we have to set
285	>	ndfRaw_local = 0;
286	>
287	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
288	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
289	>	integrableObject = mol->nextIntegrableObject(j)) {
290	>
291	>	ndfRaw_local += 3;
292	>
293	>	if (integrableObject->isDirectional()) {
294	>	if (integrableObject->isLinear()) {
295	>	ndfRaw_local += 2;
296	>	} else {
297	>	ndfRaw_local += 3;
298	>	}
299	>	}
300	>
301		}
302		}
303	+
304	+	#ifdef IS_MPI
305	+	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
306	+	#else
307	+	ndfRaw_ = ndfRaw_local;
308	+	#endif
309		}
310
311	<	if( oldOrtho != orthoRhombic ){
312	<
195	<	if( orthoRhombic ) {
196	<	sprintf( painCave.errMsg,
197	<	"OOPSE is switching from the default Non-Orthorhombic\n"
198	<	"\tto the faster Orthorhombic periodic boundary computations.\n"
199	<	"\tThis is usually a good thing, but if you wan't the\n"
200	<	"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
201	<	"\tvariable ( currently set to %G ) smaller.\n",
202	<	orthoTolerance);
203	<	painCave.severity = OOPSE_INFO;
204	<	simError();
205	<	}
206	<	else {
207	<	sprintf( painCave.errMsg,
208	<	"OOPSE is switching from the faster Orthorhombic to the more\n"
209	<	"\tflexible Non-Orthorhombic periodic boundary computations.\n"
210	<	"\tThis is usually because the box has deformed under\n"
211	<	"\tNPTf integration. If you wan't to live on the edge with\n"
212	<	"\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
213	<	"\tvariable ( currently set to %G ) larger.\n",
214	<	orthoTolerance);
215	<	painCave.severity = OOPSE_WARNING;
216	<	simError();
217	<	}
218	<	}
219	<	}
311	>	void SimInfo::calcNdfTrans() {
312	>	int ndfTrans_local;
313
314	<	void SimInfo::calcBoxL( void ){
314	>	ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
315
223	–	double dx, dy, dz, dsq;
316
317	<	// boxVol = Determinant of Hmat
317	>	#ifdef IS_MPI
318	>	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
319	>	#else
320	>	ndfTrans_ = ndfTrans_local;
321	>	#endif
322
323	<	boxVol = matDet3( Hmat );
323	>	ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
324	>
325	>	}
326
327	<	// boxLx
328	<
329	<	dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
330	<	dsq = dx*dx + dy*dy + dz*dz;
331	<	boxL[0] = sqrt( dsq );
332	<	//maxCutoff = 0.5 * boxL[0];
327	>	void SimInfo::addExcludePairs(Molecule* mol) {
328	>	std::vector<Bond*>::iterator bondIter;
329	>	std::vector<Bend*>::iterator bendIter;
330	>	std::vector<Torsion*>::iterator torsionIter;
331	>	Bond* bond;
332	>	Bend* bend;
333	>	Torsion* torsion;
334	>	int a;
335	>	int b;
336	>	int c;
337	>	int d;
338	>
339	>	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
340	>	a = bond->getAtomA()->getGlobalIndex();
341	>	b = bond->getAtomB()->getGlobalIndex();
342	>	exclude_.addPair(a, b);
343	>	}
344
345	<	// boxLy
346	<
347	<	dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
348	<	dsq = dx*dx + dy*dy + dz*dz;
240	<	boxL[1] = sqrt( dsq );
241	<	//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
345	>	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
346	>	a = bend->getAtomA()->getGlobalIndex();
347	>	b = bend->getAtomB()->getGlobalIndex();
348	>	c = bend->getAtomC()->getGlobalIndex();
349
350	+	exclude_.addPair(a, b);
351	+	exclude_.addPair(a, c);
352	+	exclude_.addPair(b, c);
353	+	}
354
355	<	// boxLz
356	<
357	<	dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
358	<	dsq = dx*dx + dy*dy + dz*dz;
359	<	boxL[2] = sqrt( dsq );
249	<	//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
355	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
356	>	a = torsion->getAtomA()->getGlobalIndex();
357	>	b = torsion->getAtomB()->getGlobalIndex();
358	>	c = torsion->getAtomC()->getGlobalIndex();
359	>	d = torsion->getAtomD()->getGlobalIndex();
360
361	<	//calculate the max cutoff
362	<	maxCutoff =  calcMaxCutOff();
363	<
364	<	checkCutOffs();
361	>	exclude_.addPair(a, b);
362	>	exclude_.addPair(a, c);
363	>	exclude_.addPair(a, d);
364	>	exclude_.addPair(b, c);
365	>	exclude_.addPair(b, d);
366	>	exclude_.addPair(c, d);
367	>	}
368
369	<	}
369	>	Molecule::RigidBodyIterator rbIter;
370	>	RigidBody* rb;
371	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
372	>	std::vector<Atom*> atoms = rb->getAtoms();
373	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
374	>	for (int j = i + 1; j < atoms.size(); ++j) {
375	>	a = atoms[i]->getGlobalIndex();
376	>	b = atoms[j]->getGlobalIndex();
377	>	exclude_.addPair(a, b);
378	>	}
379	>	}
380	>	}
381
382	+	}
383
384	<	double SimInfo::calcMaxCutOff(){
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];
270	<	rj[1] = Hmat[1][1];
271	<	rj[2] = Hmat[2][1];
272	<
273	<	rk[0] = Hmat[0][2];
274	<	rk[1] = Hmat[1][2];
275	<	rk[2] = Hmat[2][2];
384	>	void SimInfo::removeExcludePairs(Molecule* mol) {
385	>	std::vector<Bond*>::iterator bondIter;
386	>	std::vector<Bend*>::iterator bendIter;
387	>	std::vector<Torsion*>::iterator torsionIter;
388	>	Bond* bond;
389	>	Bend* bend;
390	>	Torsion* torsion;
391	>	int a;
392	>	int b;
393	>	int c;
394	>	int d;
395
396	<	crossProduct3(ri, rj, rij);
397	<	distXY = dotProduct3(rk,rij) / norm3(rij);
396	>	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
397	>	a = bond->getAtomA()->getGlobalIndex();
398	>	b = bond->getAtomB()->getGlobalIndex();
399	>	exclude_.removePair(a, b);
400	>	}
401
402	<	crossProduct3(rj,rk, rjk);
403	<	distYZ = dotProduct3(ri,rjk) / norm3(rjk);
402	>	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
403	>	a = bend->getAtomA()->getGlobalIndex();
404	>	b = bend->getAtomB()->getGlobalIndex();
405	>	c = bend->getAtomC()->getGlobalIndex();
406
407	<	crossProduct3(rk,ri, rki);
408	<	distZX = dotProduct3(rj,rki) / norm3(rki);
407	>	exclude_.removePair(a, b);
408	>	exclude_.removePair(a, c);
409	>	exclude_.removePair(b, c);
410	>	}
411
412	<	minDist = min(min(distXY, distYZ), distZX);
413	<	return minDist/2;
414	<
415	<	}
412	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
413	>	a = torsion->getAtomA()->getGlobalIndex();
414	>	b = torsion->getAtomB()->getGlobalIndex();
415	>	c = torsion->getAtomC()->getGlobalIndex();
416	>	d = torsion->getAtomD()->getGlobalIndex();
417
418	<	void SimInfo::wrapVector( double thePos[3] ){
418	>	exclude_.removePair(a, b);
419	>	exclude_.removePair(a, c);
420	>	exclude_.removePair(a, d);
421	>	exclude_.removePair(b, c);
422	>	exclude_.removePair(b, d);
423	>	exclude_.removePair(c, d);
424	>	}
425
426	<	int i;
427	<	double scaled[3];
426	>	Molecule::RigidBodyIterator rbIter;
427	>	RigidBody* rb;
428	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
429	>	std::vector<Atom*> atoms = rb->getAtoms();
430	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
431	>	for (int j = i + 1; j < atoms.size(); ++j) {
432	>	a = atoms[i]->getGlobalIndex();
433	>	b = atoms[j]->getGlobalIndex();
434	>	exclude_.removePair(a, b);
435	>	}
436	>	}
437	>	}
438
296	–	if( !orthoRhombic ){
297	–	// calc the scaled coordinates.
298	–
299	–
300	–	matVecMul3(HmatInv, thePos, scaled);
301	–
302	–	for(i=0; i<3; i++)
303	–	scaled[i] -= roundMe(scaled[i]);
304	–
305	–	// calc the wrapped real coordinates from the wrapped scaled coordinates
306	–
307	–	matVecMul3(Hmat, scaled, thePos);
308	–
439		}
310	–	else{
311	–	// calc the scaled coordinates.
312	–
313	–	for(i=0; i<3; i++)
314	–	scaled[i] = thePos[i]*HmatInv[i][i];
315	–
316	–	// wrap the scaled coordinates
317	–
318	–	for(i=0; i<3; i++)
319	–	scaled[i] -= roundMe(scaled[i]);
320	–
321	–	// calc the wrapped real coordinates from the wrapped scaled coordinates
322	–
323	–	for(i=0; i<3; i++)
324	–	thePos[i] = scaled[i]*Hmat[i][i];
325	–	}
326	–
327	–	}
440
441
442	<	int SimInfo::getNDF(){
443	<	int ndf_local;
442	>	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
443	>	int curStampId;
444
445	<	ndf_local = 0;
446	<
447	<	for(int i = 0; i < integrableObjects.size(); i++){
448	<	ndf_local += 3;
449	<	if (integrableObjects[i]->isDirectional()) {
338	<	if (integrableObjects[i]->isLinear())
339	<	ndf_local += 2;
340	<	else
341	<	ndf_local += 3;
342	<	}
445	>	//index from 0
446	>	curStampId = moleculeStamps_.size();
447	>
448	>	moleculeStamps_.push_back(molStamp);
449	>	molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
450		}
451
452	<	// n_constraints is local, so subtract them on each processor:
452	>	void SimInfo::update() {
453
454	<	ndf_local -= n_constraints;
454	>	setupSimType();
455
456		#ifdef IS_MPI
457	<	MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
351	<	#else
352	<	ndf = ndf_local;
457	>	setupFortranParallel();
458		#endif
459
460	<	// nZconstraints is global, as are the 3 COM translations for the
356	<	// entire system:
460	>	setupFortranSim();
461
462	<	ndf = ndf - 3 - nZconstraints;
462	>	//setup fortran force field
463	>	/** @deprecate */
464	>	int isError = 0;
465	>	initFortranFF( &fInfo_.SIM_uses_RF, &fInfo_.SIM_uses_UW,
466	>	&fInfo_.SIM_uses_DW, &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	>	setupCutoff();
476
477	<	return ndf;
478	<	}
477	>	calcNdf();
478	>	calcNdfRaw();
479	>	calcNdfTrans();
480
481	<	int SimInfo::getNDFraw() {
482	<	int ndfRaw_local;
481	>	fortranInitialized_ = true;
482	>	}
483
484	<	// Raw degrees of freedom that we have to set
485	<	ndfRaw_local = 0;
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	<	for(int i = 0; i < integrableObjects.size(); i++){
492	<	ndfRaw_local += 3;
493	<	if (integrableObjects[i]->isDirectional()) {
494	<	if (integrableObjects[i]->isLinear())
495	<	ndfRaw_local += 2;
496	<	else
375	<	ndfRaw_local += 3;
491	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
492	>
493	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
494	>	atomTypes.insert(atom->getAtomType());
495	>	}
496	>
497		}
498	+
499	+	return atomTypes;
500		}
501	+
502	+	void SimInfo::setupSimType() {
503	+	std::set<AtomType*>::iterator i;
504	+	std::set<AtomType*> atomTypes;
505	+	atomTypes = getUniqueAtomTypes();
506
507	<	#ifdef IS_MPI
508	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
509	<	#else
510	<	ndfRaw = ndfRaw_local;
511	<	#endif
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 useStickyPower = 0;
516	>	int useShape = 0;
517	>	int useFLARB = 0; //it is not in AtomType yet
518	>	int useDirectionalAtom = 0;
519	>	int useElectrostatics = 0;
520	>	//usePBC and useRF are from simParams
521	>	int usePBC = simParams_->getPBC();
522	>	int useRF = simParams_->getUseRF();
523	>	int useUW = simParams_->getUseUndampedWolf();
524	>	int useDW = simParams_->getUseDampedWolf();
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);
396	<	#else
397	<	ndfTrans = ndfTrans_local;
398	<	#endif
551	>	temp = usePBC;
552	>	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
553
554	<	ndfTrans = ndfTrans - 3 - nZconstraints;
555	<
402	<	return ndfTrans;
403	<	}
554	>	temp = useDirectionalAtom;
555	>	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
556
557	<	int SimInfo::getTotIntegrableObjects() {
558	<	int nObjs_local;
407	<	int nObjs;
557	>	temp = useLennardJones;
558	>	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
559
560	<	nObjs_local =  integrableObjects.size();
560	>	temp = useElectrostatics;
561	>	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
562
563	+	temp = useCharge;
564	+	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
565
566	<	#ifdef IS_MPI
567	<	MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
414	<	#else
415	<	nObjs = nObjs_local;
416	<	#endif
566	>	temp = useDipole;
567	>	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
568
569	+	temp = useSticky;
570	+	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
571
572	<	return nObjs;
573	<	}
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	<	void SimInfo::refreshSim(){
578	>	temp = useEAM;
579	>	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
580
581	<	simtype fInfo;
582	<	int isError;
426	<	int n_global;
427	<	int* excl;
581	>	temp = useShape;
582	>	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
583
584	<	fInfo.dielect = 0.0;
584	>	temp = useFLARB;
585	>	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
586
587	<	if( useDipoles ){
588	<	if( useReactionField )fInfo.dielect = dielectric;
433	<	}
587	>	temp = useRF;
588	>	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
589
590	<	fInfo.SIM_uses_PBC = usePBC;
591	<	//fInfo.SIM_uses_LJ = 0;
437	<	fInfo.SIM_uses_LJ = useLJ;
438	<	fInfo.SIM_uses_sticky = useSticky;
439	<	//fInfo.SIM_uses_sticky = 0;
440	<	fInfo.SIM_uses_charges = useCharges;
441	<	fInfo.SIM_uses_dipoles = useDipoles;
442	<	//fInfo.SIM_uses_dipoles = 0;
443	<	fInfo.SIM_uses_RF = useReactionField;
444	<	//fInfo.SIM_uses_RF = 0;
445	<	fInfo.SIM_uses_GB = useGB;
446	<	fInfo.SIM_uses_EAM = useEAM;
590	>	temp = useUW;
591	>	MPI_Allreduce(&temp, &useUW, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
592
593	<	n_exclude = excludes->getSize();
594	<	excl = excludes->getFortranArray();
595	<
451	<	#ifdef IS_MPI
452	<	n_global = mpiSim->getNAtomsGlobal();
453	<	#else
454	<	n_global = n_atoms;
593	>	temp = useDW;
594	>	MPI_Allreduce(&temp, &useDW, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
595	>
596		#endif
456	–
457	–	isError = 0;
458	–
459	–	getFortranGroupArrays(this, FglobalGroupMembership, mfact);
460	–	//it may not be a good idea to pass the address of first element in vector
461	–	//since c++ standard does not require vector to be stored continuously in meomory
462	–	//Most of the compilers will organize the memory of vector continuously
463	–	setFortranSim( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
464	–	&nGlobalExcludes, globalExcludes, molMembershipArray,
465	–	&mfact[0], &ngroup, &FglobalGroupMembership[0], &isError);
597
598	<	if( isError ){
599	<
600	<	sprintf( painCave.errMsg,
601	<	"There was an error setting the simulation information in fortran.\n" );
602	<	painCave.isFatal = 1;
603	<	painCave.severity = OOPSE_ERROR;
604	<	simError();
598	>	fInfo_.SIM_uses_PBC = usePBC;
599	>	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
600	>	fInfo_.SIM_uses_LennardJones = useLennardJones;
601	>	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
602	>	fInfo_.SIM_uses_Charges = useCharge;
603	>	fInfo_.SIM_uses_Dipoles = useDipole;
604	>	fInfo_.SIM_uses_Sticky = useSticky;
605	>	fInfo_.SIM_uses_StickyPower = useStickyPower;
606	>	fInfo_.SIM_uses_GayBerne = useGayBerne;
607	>	fInfo_.SIM_uses_EAM = useEAM;
608	>	fInfo_.SIM_uses_Shapes = useShape;
609	>	fInfo_.SIM_uses_FLARB = useFLARB;
610	>	fInfo_.SIM_uses_RF = useRF;
611	>	fInfo_.SIM_uses_UW = useUW;
612	>	fInfo_.SIM_uses_DW = useDW;
613	>
614	>	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
615	>
616	>	if (simParams_->haveDielectric()) {
617	>	fInfo_.dielect = simParams_->getDielectric();
618	>	} else {
619	>	sprintf(painCave.errMsg,
620	>	"SimSetup Error: No Dielectric constant was set.\n"
621	>	"\tYou are trying to use Reaction Field without"
622	>	"\tsetting a dielectric constant!\n");
623	>	painCave.isFatal = 1;
624	>	simError();
625	>	}
626	>
627	>	} else {
628	>	fInfo_.dielect = 0.0;
629	>	}
630	>
631		}
475	–
476	–	#ifdef IS_MPI
477	–	sprintf( checkPointMsg,
478	–	"succesfully sent the simulation information to fortran.\n");
479	–	MPIcheckPoint();
480	–	#endif // is_mpi
481	–
482	–	this->ndf = this->getNDF();
483	–	this->ndfRaw = this->getNDFraw();
484	–	this->ndfTrans = this->getNDFtranslational();
485	–	}
632
633	<	void SimInfo::setDefaultRcut( double theRcut ){
634	<
635	<	haveRcut = 1;
636	<	rCut = theRcut;
637	<	rList = rCut + 1.0;
638	<
639	<	notifyFortranCutoffs( &rCut, &rSw, &rList );
494	<	}
633	>	void SimInfo::setupFortranSim() {
634	>	int isError;
635	>	int nExclude;
636	>	std::vector<int> fortranGlobalGroupMembership;
637	>
638	>	nExclude = exclude_.getSize();
639	>	isError = 0;
640
641	<	void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
641	>	//globalGroupMembership_ is filled by SimCreator
642	>	for (int i = 0; i < nGlobalAtoms_; i++) {
643	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
644	>	}
645
646	<	rSw = theRsw;
647	<	setDefaultRcut( theRcut );
648	<	}
646	>	//calculate mass ratio of cutoff group
647	>	std::vector<double> mfact;
648	>	SimInfo::MoleculeIterator mi;
649	>	Molecule* mol;
650	>	Molecule::CutoffGroupIterator ci;
651	>	CutoffGroup* cg;
652	>	Molecule::AtomIterator ai;
653	>	Atom* atom;
654	>	double totalMass;
655
656	+	//to avoid memory reallocation, reserve enough space for mfact
657	+	mfact.reserve(getNCutoffGroups());
658	+
659	+	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
660	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
661
662	<	void SimInfo::checkCutOffs( void ){
663	<
664	<	if( boxIsInit ){
662	>	totalMass = cg->getMass();
663	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
664	>	mfact.push_back(atom->getMass()/totalMass);
665	>	}
666	>
667	>	}
668	>	}
669	>
670	>	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
671	>	std::vector<int> identArray;
672	>
673	>	//to avoid memory reallocation, reserve enough space identArray
674	>	identArray.reserve(getNAtoms());
675
676	<	//we need to check cutOffs against the box
676	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
677	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
678	>	identArray.push_back(atom->getIdent());
679	>	}
680	>	}
681	>
682	>	//fill molMembershipArray
683	>	//molMembershipArray is filled by SimCreator
684	>	std::vector<int> molMembershipArray(nGlobalAtoms_);
685	>	for (int i = 0; i < nGlobalAtoms_; i++) {
686	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
687	>	}
688
689	<	if( rCut > maxCutoff ){
689	>	//setup fortran simulation
690	>	int nGlobalExcludes = 0;
691	>	int* globalExcludes = NULL;
692	>	int* excludeList = exclude_.getExcludeList();
693	>	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
694	>	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
695	>	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
696	>
697	>	if( isError ){
698	>
699		sprintf( painCave.errMsg,
700	<	"cutoffRadius is too large for the current periodic box.\n"
512	<	"\tCurrent Value of cutoffRadius = %G at time %G\n "
513	<	"\tThis is larger than half of at least one of the\n"
514	<	"\tperiodic box vectors.  Right now, the Box matrix is:\n"
515	<	"\n"
516	<	"\t[ %G %G %G ]\n"
517	<	"\t[ %G %G %G ]\n"
518	<	"\t[ %G %G %G ]\n",
519	<	rCut, currentTime,
520	<	Hmat[0][0], Hmat[0][1], Hmat[0][2],
521	<	Hmat[1][0], Hmat[1][1], Hmat[1][2],
522	<	Hmat[2][0], Hmat[2][1], Hmat[2][2]);
523	<	painCave.severity = OOPSE_ERROR;
700	>	"There was an error setting the simulation information in fortran.\n" );
701		painCave.isFatal = 1;
702	+	painCave.severity = OOPSE_ERROR;
703		simError();
704	<	}
527	<	} else {
528	<	// initialize this stuff before using it, OK?
529	<	sprintf( painCave.errMsg,
530	<	"Trying to check cutoffs without a box.\n"
531	<	"\tOOPSE should have better programmers than that.\n" );
532	<	painCave.severity = OOPSE_ERROR;
533	<	painCave.isFatal = 1;
534	<	simError();
535	<	}
536	<
537	<	}
704	>	}
705
706	<	void SimInfo::addProperty(GenericData* prop){
707	<
708	<	map<string, GenericData*>::iterator result;
709	<	result = properties.find(prop->getID());
710	<
544	<	//we can't simply use  properties[prop->getID()] = prop,
545	<	//it will cause memory leak if we already contain a propery which has the same name of prop
546	<
547	<	if(result != properties.end()){
548	<
549	<	delete (*result).second;
550	<	(*result).second = prop;
551	<
706	>	#ifdef IS_MPI
707	>	sprintf( checkPointMsg,
708	>	"succesfully sent the simulation information to fortran.\n");
709	>	MPIcheckPoint();
710	>	#endif // is_mpi
711		}
553	–	else{
712
555	–	properties[prop->getID()] = prop;
713
714	<	}
714	>	#ifdef IS_MPI
715	>	void SimInfo::setupFortranParallel() {
716
717	<	}
717	>	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
718	>	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
719	>	std::vector<int> localToGlobalCutoffGroupIndex;
720	>	SimInfo::MoleculeIterator mi;
721	>	Molecule::AtomIterator ai;
722	>	Molecule::CutoffGroupIterator ci;
723	>	Molecule* mol;
724	>	Atom* atom;
725	>	CutoffGroup* cg;
726	>	mpiSimData parallelData;
727	>	int isError;
728
729	<	GenericData* SimInfo::getProperty(const string& propName){
562	<
563	<	map<string, GenericData*>::iterator result;
564	<
565	<	//string lowerCaseName = ();
566	<
567	<	result = properties.find(propName);
568	<
569	<	if(result != properties.end())
570	<	return (*result).second;
571	<	else
572	<	return NULL;
573	<	}
729	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
730
731	+	//local index(index in DataStorge) of atom is important
732	+	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
733	+	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
734	+	}
735
736	<	void SimInfo::getFortranGroupArrays(SimInfo* info,
737	<	vector<int>& FglobalGroupMembership,
738	<	vector<double>& mfact){
739	<
740	<	Molecule* myMols;
741	<	Atom** myAtoms;
582	<	int numAtom;
583	<	double mtot;
584	<	int numMol;
585	<	int numCutoffGroups;
586	<	CutoffGroup* myCutoffGroup;
587	<	vector<CutoffGroup*>::iterator iterCutoff;
588	<	Atom* cutoffAtom;
589	<	vector<Atom*>::iterator iterAtom;
590	<	int atomIndex;
591	<	double totalMass;
592	<
593	<	mfact.clear();
594	<	FglobalGroupMembership.clear();
595	<
736	>	//local index of cutoff group is trivial, it only depends on the order of travesing
737	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
738	>	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
739	>	}
740	>
741	>	}
742
743	<	// Fix the silly fortran indexing problem
744	<	#ifdef IS_MPI
745	<	numAtom = mpiSim->getNAtomsGlobal();
746	<	#else
747	<	numAtom = n_atoms;
748	<	#endif
749	<	for (int i = 0; i < numAtom; i++)
750	<	FglobalGroupMembership.push_back(globalGroupMembership[i] + 1);
751	<
743	>	//fill up mpiSimData struct
744	>	parallelData.nMolGlobal = getNGlobalMolecules();
745	>	parallelData.nMolLocal = getNMolecules();
746	>	parallelData.nAtomsGlobal = getNGlobalAtoms();
747	>	parallelData.nAtomsLocal = getNAtoms();
748	>	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
749	>	parallelData.nGroupsLocal = getNCutoffGroups();
750	>	parallelData.myNode = worldRank;
751	>	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
752
753	<	myMols = info->molecules;
754	<	numMol = info->n_mol;
755	<	for(int i  = 0; i < numMol; i++){
756	<	numCutoffGroups = myMols[i].getNCutoffGroups();
757	<	for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff);
758	<	myCutoffGroup != NULL;
759	<	myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
760	<
761	<	totalMass = myCutoffGroup->getMass();
762	<
617	<	for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom);
618	<	cutoffAtom != NULL;
619	<	cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
620	<	mfact.push_back(cutoffAtom->getMass()/totalMass);
621	<	}
753	>	//pass mpiSimData struct and index arrays to fortran
754	>	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
755	>	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
756	>	&localToGlobalCutoffGroupIndex[0], &isError);
757	>
758	>	if (isError) {
759	>	sprintf(painCave.errMsg,
760	>	"mpiRefresh errror: fortran didn't like something we gave it.\n");
761	>	painCave.isFatal = 1;
762	>	simError();
763		}
764	+
765	+	sprintf(checkPointMsg, " mpiRefresh successful.\n");
766	+	MPIcheckPoint();
767	+
768	+
769		}
770
771	<	}
771	>	#endif
772	>
773	>	double SimInfo::calcMaxCutoffRadius() {
774	>
775	>
776	>	std::set<AtomType*> atomTypes;
777	>	std::set<AtomType*>::iterator i;
778	>	std::vector<double> cutoffRadius;
779	>
780	>	//get the unique atom types
781	>	atomTypes = getUniqueAtomTypes();
782	>
783	>	//query the max cutoff radius among these atom types
784	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
785	>	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
786	>	}
787	>
788	>	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
789	>	#ifdef IS_MPI
790	>	//pick the max cutoff radius among the processors
791	>	#endif
792	>
793	>	return maxCutoffRadius;
794	>	}
795	>
796	>	void SimInfo::getCutoff(double& rcut, double& rsw) {
797	>
798	>	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
799	>
800	>	if (!simParams_->haveRcut()){
801	>	sprintf(painCave.errMsg,
802	>	"SimCreator Warning: No value was set for the cutoffRadius.\n"
803	>	"\tOOPSE will use a default value of 15.0 angstroms"
804	>	"\tfor the cutoffRadius.\n");
805	>	painCave.isFatal = 0;
806	>	simError();
807	>	rcut = 15.0;
808	>	} else{
809	>	rcut = simParams_->getRcut();
810	>	}
811	>
812	>	if (!simParams_->haveRsw()){
813	>	sprintf(painCave.errMsg,
814	>	"SimCreator Warning: No value was set for switchingRadius.\n"
815	>	"\tOOPSE will use a default value of\n"
816	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
817	>	painCave.isFatal = 0;
818	>	simError();
819	>	rsw = 0.95 * rcut;
820	>	} else{
821	>	rsw = simParams_->getRsw();
822	>	}
823	>
824	>	} else {
825	>	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
826	>	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
827	>
828	>	if (simParams_->haveRcut()) {
829	>	rcut = simParams_->getRcut();
830	>	} else {
831	>	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
832	>	rcut = calcMaxCutoffRadius();
833	>	}
834	>
835	>	if (simParams_->haveRsw()) {
836	>	rsw  = simParams_->getRsw();
837	>	} else {
838	>	rsw = rcut;
839	>	}
840	>
841	>	}
842	>	}
843	>
844	>	void SimInfo::setupCutoff() {
845	>	getCutoff(rcut_, rsw_);
846	>	double rnblist = rcut_ + 1; // skin of neighbor list
847	>
848	>	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
849	>	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist);
850	>	}
851	>
852	>	void SimInfo::addProperty(GenericData* genData) {
853	>	properties_.addProperty(genData);
854	>	}
855	>
856	>	void SimInfo::removeProperty(const std::string& propName) {
857	>	properties_.removeProperty(propName);
858	>	}
859	>
860	>	void SimInfo::clearProperties() {
861	>	properties_.clearProperties();
862	>	}
863	>
864	>	std::vector<std::string> SimInfo::getPropertyNames() {
865	>	return properties_.getPropertyNames();
866	>	}
867	>
868	>	std::vector<GenericData*> SimInfo::getProperties() {
869	>	return properties_.getProperties();
870	>	}
871	>
872	>	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
873	>	return properties_.getPropertyByName(propName);
874	>	}
875	>
876	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
877	>	if (sman_ == sman) {
878	>	return;
879	>	}
880	>	delete sman_;
881	>	sman_ = sman;
882	>
883	>	Molecule* mol;
884	>	RigidBody* rb;
885	>	Atom* atom;
886	>	SimInfo::MoleculeIterator mi;
887	>	Molecule::RigidBodyIterator rbIter;
888	>	Molecule::AtomIterator atomIter;;
889	>
890	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
891	>
892	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
893	>	atom->setSnapshotManager(sman_);
894	>	}
895	>
896	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
897	>	rb->setSnapshotManager(sman_);
898	>	}
899	>	}
900	>
901	>	}
902	>
903	>	Vector3d SimInfo::getComVel(){
904	>	SimInfo::MoleculeIterator i;
905	>	Molecule* mol;
906	>
907	>	Vector3d comVel(0.0);
908	>	double totalMass = 0.0;
909	>
910	>
911	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
912	>	double mass = mol->getMass();
913	>	totalMass += mass;
914	>	comVel += mass * mol->getComVel();
915	>	}
916	>
917	>	#ifdef IS_MPI
918	>	double tmpMass = totalMass;
919	>	Vector3d tmpComVel(comVel);
920	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
921	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
922	>	#endif
923	>
924	>	comVel /= totalMass;
925	>
926	>	return comVel;
927	>	}
928	>
929	>	Vector3d SimInfo::getCom(){
930	>	SimInfo::MoleculeIterator i;
931	>	Molecule* mol;
932	>
933	>	Vector3d com(0.0);
934	>	double totalMass = 0.0;
935	>
936	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
937	>	double mass = mol->getMass();
938	>	totalMass += mass;
939	>	com += mass * mol->getCom();
940	>	}
941	>
942	>	#ifdef IS_MPI
943	>	double tmpMass = totalMass;
944	>	Vector3d tmpCom(com);
945	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
946	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
947	>	#endif
948	>
949	>	com /= totalMass;
950	>
951	>	return com;
952	>
953	>	}
954	>
955	>	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
956	>
957	>	return o;
958	>	}
959	>
960	>
961	>	/*
962	>	Returns center of mass and center of mass velocity in one function call.
963	>	*/
964	>
965	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
966	>	SimInfo::MoleculeIterator i;
967	>	Molecule* mol;
968	>
969	>
970	>	double totalMass = 0.0;
971	>
972	>
973	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
974	>	double mass = mol->getMass();
975	>	totalMass += mass;
976	>	com += mass * mol->getCom();
977	>	comVel += mass * mol->getComVel();
978	>	}
979	>
980	>	#ifdef IS_MPI
981	>	double tmpMass = totalMass;
982	>	Vector3d tmpCom(com);
983	>	Vector3d tmpComVel(comVel);
984	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
985	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
986	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
987	>	#endif
988	>
989	>	com /= totalMass;
990	>	comVel /= totalMass;
991	>	}
992	>
993	>	/*
994	>	Return intertia tensor for entire system and angular momentum Vector.
995	>
996	>
997	>	[  Ixx -Ixy  -Ixz ]
998	>	J =| -Iyx  Iyy  -Iyz |
999	>	[ -Izx -Iyz   Izz ]
1000	>	*/
1001	>
1002	>	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1003	>
1004	>
1005	>	double xx = 0.0;
1006	>	double yy = 0.0;
1007	>	double zz = 0.0;
1008	>	double xy = 0.0;
1009	>	double xz = 0.0;
1010	>	double yz = 0.0;
1011	>	Vector3d com(0.0);
1012	>	Vector3d comVel(0.0);
1013	>
1014	>	getComAll(com, comVel);
1015	>
1016	>	SimInfo::MoleculeIterator i;
1017	>	Molecule* mol;
1018	>
1019	>	Vector3d thisq(0.0);
1020	>	Vector3d thisv(0.0);
1021	>
1022	>	double thisMass = 0.0;
1023	>
1024	>
1025	>
1026	>
1027	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1028	>
1029	>	thisq = mol->getCom()-com;
1030	>	thisv = mol->getComVel()-comVel;
1031	>	thisMass = mol->getMass();
1032	>	// Compute moment of intertia coefficients.
1033	>	xx += thisq[0]*thisq[0]*thisMass;
1034	>	yy += thisq[1]*thisq[1]*thisMass;
1035	>	zz += thisq[2]*thisq[2]*thisMass;
1036	>
1037	>	// compute products of intertia
1038	>	xy += thisq[0]*thisq[1]*thisMass;
1039	>	xz += thisq[0]*thisq[2]*thisMass;
1040	>	yz += thisq[1]*thisq[2]*thisMass;
1041	>
1042	>	angularMomentum += cross( thisq, thisv ) * thisMass;
1043	>
1044	>	}
1045	>
1046	>
1047	>	inertiaTensor(0,0) = yy + zz;
1048	>	inertiaTensor(0,1) = -xy;
1049	>	inertiaTensor(0,2) = -xz;
1050	>	inertiaTensor(1,0) = -xy;
1051	>	inertiaTensor(1,1) = xx + zz;
1052	>	inertiaTensor(1,2) = -yz;
1053	>	inertiaTensor(2,0) = -xz;
1054	>	inertiaTensor(2,1) = -yz;
1055	>	inertiaTensor(2,2) = xx + yy;
1056	>
1057	>	#ifdef IS_MPI
1058	>	Mat3x3d tmpI(inertiaTensor);
1059	>	Vector3d tmpAngMom;
1060	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1061	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1062	>	#endif
1063	>
1064	>	return;
1065	>	}
1066	>
1067	>	//Returns the angular momentum of the system
1068	>	Vector3d SimInfo::getAngularMomentum(){
1069	>
1070	>	Vector3d com(0.0);
1071	>	Vector3d comVel(0.0);
1072	>	Vector3d angularMomentum(0.0);
1073	>
1074	>	getComAll(com,comVel);
1075	>
1076	>	SimInfo::MoleculeIterator i;
1077	>	Molecule* mol;
1078	>
1079	>	Vector3d thisr(0.0);
1080	>	Vector3d thisp(0.0);
1081	>
1082	>	double thisMass;
1083	>
1084	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1085	>	thisMass = mol->getMass();
1086	>	thisr = mol->getCom()-com;
1087	>	thisp = (mol->getComVel()-comVel)*thisMass;
1088	>
1089	>	angularMomentum += cross( thisr, thisp );
1090	>
1091	>	}
1092	>
1093	>	#ifdef IS_MPI
1094	>	Vector3d tmpAngMom;
1095	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1096	>	#endif
1097	>
1098	>	return angularMomentum;
1099	>	}
1100	>
1101	>
1102	>	}//end namespace oopse
1103	>

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