ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

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

Comparing trunk/OOPSE-2.0/src/brains/SimInfo.cpp (file contents):
Revision 1617 by chuckv, Wed Oct 20 20:46:20 2004 UTC vs.
Revision 2285 by gezelter, Wed Sep 7 20:46:46 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"
56	<	#include "UseTheForce/DarkSide/simulation_interface.h"
53	>	#include "math/Vector3.hpp"
54	>	#include "primitives/Molecule.hpp"
55	>	#include "UseTheForce/fCutoffPolicy.h"
56	>	#include "UseTheForce/doForces_interface.h"
57		#include "UseTheForce/notifyCutoffs_interface.h"
58	+	#include "utils/MemoryUtils.hpp"
59	+	#include "utils/simError.h"
60	+	#include "selection/SelectionManager.hpp"
61
15	–	//#include "UseTheForce/fortranWrappers.hpp"
16	–
17	–	#include "math/MatVec3.h"
18	–
62		#ifdef IS_MPI
63	<	#include "brains/mpiSimulation.hpp"
64	<	#endif
63	>	#include "UseTheForce/mpiComponentPlan.h"
64	>	#include "UseTheForce/DarkSide/simParallel_interface.h"
65	>	#endif
66
67	<	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	<	}
67	>	namespace oopse {
68
69	<	SimInfo* currentInfo;
69	>	SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
70	>	ForceField* ff, Globals* simParams) :
71	>	stamps_(stamps), forceField_(ff), simParams_(simParams),
72	>	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
73	>	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
74	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
75	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
76	>	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
77	>	sman_(NULL), fortranInitialized_(false) {
78
79	<	SimInfo::SimInfo(){
79	>
80	>	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
81	>	MoleculeStamp* molStamp;
82	>	int nMolWithSameStamp;
83	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
84	>	int nGroups = 0;          //total cutoff groups defined in meta-data file
85	>	CutoffGroupStamp* cgStamp;
86	>	RigidBodyStamp* rbStamp;
87	>	int nRigidAtoms = 0;
88	>
89	>	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
90	>	molStamp = i->first;
91	>	nMolWithSameStamp = i->second;
92	>
93	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
94
95	<	n_constraints = 0;
96	<	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;
95	>	//calculate atoms in molecules
96	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
97
49	–	haveRcut = 0;
50	–	haveRsw = 0;
51	–	boxIsInit = 0;
52	–
53	–	resetTime = 1e99;
98
99	<	orthoRhombic = 0;
100	<	orthoTolerance = 1E-6;
101	<	useInitXSstate = true;
99	>	//calculate atoms in cutoff groups
100	>	int nAtomsInGroups = 0;
101	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
102	>
103	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
104	>	cgStamp = molStamp->getCutoffGroup(j);
105	>	nAtomsInGroups += cgStamp->getNMembers();
106	>	}
107
108	<	usePBC = 0;
109	<	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;
108	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
109	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
110
111	<	haveCutoffGroups = false;
111	>	//calculate atoms in rigid bodies
112	>	int nAtomsInRigidBodies = 0;
113	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
114	>
115	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
116	>	rbStamp = molStamp->getRigidBody(j);
117	>	nAtomsInRigidBodies += rbStamp->getNMembers();
118	>	}
119
120	<	excludes = Exclude::Instance();
120	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
121	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
122	>
123	>	}
124
125	<	myConfiguration = new SimState();
125	>	//every free atom (atom does not belong to cutoff groups) is a cutoff group
126	>	//therefore the total number of cutoff groups in the system is equal to
127	>	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
128	>	//file plus the number of cutoff groups defined in meta-data file
129	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
130
131	<	has_minimizer = false;
132	<	the_minimizer =NULL;
131	>	//every free atom (atom does not belong to rigid bodies) is an integrable object
132	>	//therefore the total number of  integrable objects in the system is equal to
133	>	//the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
134	>	//file plus the number of  rigid bodies defined in meta-data file
135	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
136
137	<	ngroup = 0;
137	>	nGlobalMols_ = molStampIds_.size();
138
139	<	}
139	>	#ifdef IS_MPI
140	>	molToProcMap_.resize(nGlobalMols_);
141	>	#endif
142
143	+	}
144
145	<	SimInfo::~SimInfo(){
145	>	SimInfo::~SimInfo() {
146	>	std::map<int, Molecule*>::iterator i;
147	>	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
148	>	delete i->second;
149	>	}
150	>	molecules_.clear();
151	>
152	>	delete stamps_;
153	>	delete sman_;
154	>	delete simParams_;
155	>	delete forceField_;
156	>	}
157
158	<	delete myConfiguration;
158	>	int SimInfo::getNGlobalConstraints() {
159	>	int nGlobalConstraints;
160	>	#ifdef IS_MPI
161	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
162	>	MPI_COMM_WORLD);
163	>	#else
164	>	nGlobalConstraints =  nConstraints_;
165	>	#endif
166	>	return nGlobalConstraints;
167	>	}
168
169	<	map<string, GenericData*>::iterator i;
170	<
90	<	for(i = properties.begin(); i != properties.end(); i++)
91	<	delete (*i).second;
169	>	bool SimInfo::addMolecule(Molecule* mol) {
170	>	MoleculeIterator i;
171
172	<	}
172	>	i = molecules_.find(mol->getGlobalIndex());
173	>	if (i == molecules_.end() ) {
174
175	<	void SimInfo::setBox(double newBox[3]) {
176	<
177	<	int i, j;
178	<	double tempMat[3][3];
179	<
180	<	for(i=0; i<3; i++)
181	<	for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
182	<
183	<	tempMat[0][0] = newBox[0];
184	<	tempMat[1][1] = newBox[1];
105	<	tempMat[2][2] = newBox[2];
175	>	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
176	>
177	>	nAtoms_ += mol->getNAtoms();
178	>	nBonds_ += mol->getNBonds();
179	>	nBends_ += mol->getNBends();
180	>	nTorsions_ += mol->getNTorsions();
181	>	nRigidBodies_ += mol->getNRigidBodies();
182	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
183	>	nCutoffGroups_ += mol->getNCutoffGroups();
184	>	nConstraints_ += mol->getNConstraintPairs();
185
186	<	setBoxM( tempMat );
186	>	addExcludePairs(mol);
187	>
188	>	return true;
189	>	} else {
190	>	return false;
191	>	}
192	>	}
193
194	<	}
194	>	bool SimInfo::removeMolecule(Molecule* mol) {
195	>	MoleculeIterator i;
196	>	i = molecules_.find(mol->getGlobalIndex());
197
198	<	void SimInfo::setBoxM( double theBox[3][3] ){
112	<
113	<	int i, j;
114	<	double FortranHmat[9]; // to preserve compatibility with Fortran the
115	<	// ordering in the array is as follows:
116	<	// [ 0 3 6 ]
117	<	// [ 1 4 7 ]
118	<	// [ 2 5 8 ]
119	<	double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
198	>	if (i != molecules_.end() ) {
199
200	<	if( !boxIsInit ) boxIsInit = 1;
200	>	assert(mol == i->second);
201	>
202	>	nAtoms_ -= mol->getNAtoms();
203	>	nBonds_ -= mol->getNBonds();
204	>	nBends_ -= mol->getNBends();
205	>	nTorsions_ -= mol->getNTorsions();
206	>	nRigidBodies_ -= mol->getNRigidBodies();
207	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
208	>	nCutoffGroups_ -= mol->getNCutoffGroups();
209	>	nConstraints_ -= mol->getNConstraintPairs();
210
211	<	for(i=0; i < 3; i++)
212	<	for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
125	<
126	<	calcBoxL();
127	<	calcHmatInv();
211	>	removeExcludePairs(mol);
212	>	molecules_.erase(mol->getGlobalIndex());
213
214	<	for(i=0; i < 3; i++) {
215	<	for (j=0; j < 3; j++) {
216	<	FortranHmat[3*j + i] = Hmat[i][j];
217	<	FortranHmatInv[3*j + i] = HmatInv[i][j];
214	>	delete mol;
215	>
216	>	return true;
217	>	} else {
218	>	return false;
219		}
134	–	}
220
136	–	setFortranBox(FortranHmat, FortranHmatInv, &orthoRhombic);
137	–
138	–	}
139	–
221
222	<	void SimInfo::getBoxM (double theBox[3][3]) {
222	>	}
223
224	<	int i, j;
225	<	for(i=0; i<3; i++)
226	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
227	<	}
224	>
225	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
226	>	i = molecules_.begin();
227	>	return i == molecules_.end() ? NULL : i->second;
228	>	}
229
230	+	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
231	+	++i;
232	+	return i == molecules_.end() ? NULL : i->second;
233	+	}
234
149	–	void SimInfo::scaleBox(double scale) {
150	–	double theBox[3][3];
151	–	int i, j;
235
236	<	// cerr << "Scaling box by " << scale << "\n";
236	>	void SimInfo::calcNdf() {
237	>	int ndf_local;
238	>	MoleculeIterator i;
239	>	std::vector<StuntDouble*>::iterator j;
240	>	Molecule* mol;
241	>	StuntDouble* integrableObject;
242
243	<	for(i=0; i<3; i++)
244	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
243	>	ndf_local = 0;
244	>
245	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
246	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
247	>	integrableObject = mol->nextIntegrableObject(j)) {
248
249	<	setBoxM(theBox);
249	>	ndf_local += 3;
250
251	<	}
251	>	if (integrableObject->isDirectional()) {
252	>	if (integrableObject->isLinear()) {
253	>	ndf_local += 2;
254	>	} else {
255	>	ndf_local += 3;
256	>	}
257	>	}
258	>
259	>	}//end for (integrableObject)
260	>	}// end for (mol)
261	>
262	>	// n_constraints is local, so subtract them on each processor
263	>	ndf_local -= nConstraints_;
264
265	<	void SimInfo::calcHmatInv( void ) {
266	<
267	<	int oldOrtho;
268	<	int i,j;
269	<	double smallDiag;
167	<	double tol;
168	<	double sanity[3][3];
265	>	#ifdef IS_MPI
266	>	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
267	>	#else
268	>	ndf_ = ndf_local;
269	>	#endif
270
271	<	invertMat3( Hmat, HmatInv );
271	>	// nZconstraints_ is global, as are the 3 COM translations for the
272	>	// entire system:
273	>	ndf_ = ndf_ - 3 - nZconstraint_;
274
275	<	// check to see if Hmat is orthorhombic
173	<
174	<	oldOrtho = orthoRhombic;
275	>	}
276
277	<	smallDiag = fabs(Hmat[0][0]);
278	<	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;
277	>	void SimInfo::calcNdfRaw() {
278	>	int ndfRaw_local;
279
280	<	orthoRhombic = 1;
281	<
282	<	for (i = 0; i < 3; i++ ) {
283	<	for (j = 0 ; j < 3; j++) {
185	<	if (i != j) {
186	<	if (orthoRhombic) {
187	<	if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
188	<	}
189	<	}
190	<	}
191	<	}
280	>	MoleculeIterator i;
281	>	std::vector<StuntDouble*>::iterator j;
282	>	Molecule* mol;
283	>	StuntDouble* integrableObject;
284
285	<	if( oldOrtho != orthoRhombic ){
285	>	// Raw degrees of freedom that we have to set
286	>	ndfRaw_local = 0;
287
288	<	if( orthoRhombic ) {
289	<	sprintf( painCave.errMsg,
290	<	"OOPSE is switching from the default Non-Orthorhombic\n"
291	<	"\tto the faster Orthorhombic periodic boundary computations.\n"
292	<	"\tThis is usually a good thing, but if you wan't the\n"
293	<	"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
294	<	"\tvariable ( currently set to %G ) smaller.\n",
295	<	orthoTolerance);
296	<	painCave.severity = OOPSE_INFO;
297	<	simError();
288	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
289	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
290	>	integrableObject = mol->nextIntegrableObject(j)) {
291	>
292	>	ndfRaw_local += 3;
293	>
294	>	if (integrableObject->isDirectional()) {
295	>	if (integrableObject->isLinear()) {
296	>	ndfRaw_local += 2;
297	>	} else {
298	>	ndfRaw_local += 3;
299	>	}
300	>	}
301	>
302	>	}
303		}
304	<	else {
305	<	sprintf( painCave.errMsg,
306	<	"OOPSE is switching from the faster Orthorhombic to the more\n"
307	<	"\tflexible Non-Orthorhombic periodic boundary computations.\n"
308	<	"\tThis is usually because the box has deformed under\n"
309	<	"\tNPTf integration. If you wan't to live on the edge with\n"
310	<	"\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	<	}
304	>
305	>	#ifdef IS_MPI
306	>	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
307	>	#else
308	>	ndfRaw_ = ndfRaw_local;
309	>	#endif
310	>	}
311
312	<	void SimInfo::calcBoxL( void ){
312	>	void SimInfo::calcNdfTrans() {
313	>	int ndfTrans_local;
314
315	<	double dx, dy, dz, dsq;
315	>	ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
316
225	–	// boxVol = Determinant of Hmat
317
318	<	boxVol = matDet3( Hmat );
318	>	#ifdef IS_MPI
319	>	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
320	>	#else
321	>	ndfTrans_ = ndfTrans_local;
322	>	#endif
323
324	<	// boxLx
325	<
326	<	dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
232	<	dsq = dx*dx + dy*dy + dz*dz;
233	<	boxL[0] = sqrt( dsq );
234	<	//maxCutoff = 0.5 * boxL[0];
324	>	ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
325	>
326	>	}
327
328	<	// boxLy
329	<
330	<	dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
331	<	dsq = dx*dx + dy*dy + dz*dz;
332	<	boxL[1] = sqrt( dsq );
333	<	//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
328	>	void SimInfo::addExcludePairs(Molecule* mol) {
329	>	std::vector<Bond*>::iterator bondIter;
330	>	std::vector<Bend*>::iterator bendIter;
331	>	std::vector<Torsion*>::iterator torsionIter;
332	>	Bond* bond;
333	>	Bend* bend;
334	>	Torsion* torsion;
335	>	int a;
336	>	int b;
337	>	int c;
338	>	int d;
339	>
340	>	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
341	>	a = bond->getAtomA()->getGlobalIndex();
342	>	b = bond->getAtomB()->getGlobalIndex();
343	>	exclude_.addPair(a, b);
344	>	}
345
346	+	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
347	+	a = bend->getAtomA()->getGlobalIndex();
348	+	b = bend->getAtomB()->getGlobalIndex();
349	+	c = bend->getAtomC()->getGlobalIndex();
350
351	<	// boxLz
352	<
353	<	dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
354	<	dsq = dx*dx + dy*dy + dz*dz;
248	<	boxL[2] = sqrt( dsq );
249	<	//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
351	>	exclude_.addPair(a, b);
352	>	exclude_.addPair(a, c);
353	>	exclude_.addPair(b, c);
354	>	}
355
356	<	//calculate the max cutoff
357	<	maxCutoff =  calcMaxCutOff();
358	<
359	<	checkCutOffs();
356	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
357	>	a = torsion->getAtomA()->getGlobalIndex();
358	>	b = torsion->getAtomB()->getGlobalIndex();
359	>	c = torsion->getAtomC()->getGlobalIndex();
360	>	d = torsion->getAtomD()->getGlobalIndex();
361
362	<	}
362	>	exclude_.addPair(a, b);
363	>	exclude_.addPair(a, c);
364	>	exclude_.addPair(a, d);
365	>	exclude_.addPair(b, c);
366	>	exclude_.addPair(b, d);
367	>	exclude_.addPair(c, d);
368	>	}
369
370	+	Molecule::RigidBodyIterator rbIter;
371	+	RigidBody* rb;
372	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
373	+	std::vector<Atom*> atoms = rb->getAtoms();
374	+	for (int i = 0; i < atoms.size() -1 ; ++i) {
375	+	for (int j = i + 1; j < atoms.size(); ++j) {
376	+	a = atoms[i]->getGlobalIndex();
377	+	b = atoms[j]->getGlobalIndex();
378	+	exclude_.addPair(a, b);
379	+	}
380	+	}
381	+	}
382
383	<	double SimInfo::calcMaxCutOff(){
383	>	}
384
385	<	double ri[3], rj[3], rk[3];
386	<	double rij[3], rjk[3], rki[3];
387	<	double minDist;
388	<
389	<	ri[0] = Hmat[0][0];
390	<	ri[1] = Hmat[1][0];
391	<	ri[2] = Hmat[2][0];
392	<
393	<	rj[0] = Hmat[0][1];
394	<	rj[1] = Hmat[1][1];
395	<	rj[2] = Hmat[2][1];
272	<
273	<	rk[0] = Hmat[0][2];
274	<	rk[1] = Hmat[1][2];
275	<	rk[2] = Hmat[2][2];
385	>	void SimInfo::removeExcludePairs(Molecule* mol) {
386	>	std::vector<Bond*>::iterator bondIter;
387	>	std::vector<Bend*>::iterator bendIter;
388	>	std::vector<Torsion*>::iterator torsionIter;
389	>	Bond* bond;
390	>	Bend* bend;
391	>	Torsion* torsion;
392	>	int a;
393	>	int b;
394	>	int c;
395	>	int d;
396
397	<	crossProduct3(ri, rj, rij);
398	<	distXY = dotProduct3(rk,rij) / norm3(rij);
397	>	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
398	>	a = bond->getAtomA()->getGlobalIndex();
399	>	b = bond->getAtomB()->getGlobalIndex();
400	>	exclude_.removePair(a, b);
401	>	}
402
403	<	crossProduct3(rj,rk, rjk);
404	<	distYZ = dotProduct3(ri,rjk) / norm3(rjk);
403	>	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
404	>	a = bend->getAtomA()->getGlobalIndex();
405	>	b = bend->getAtomB()->getGlobalIndex();
406	>	c = bend->getAtomC()->getGlobalIndex();
407
408	<	crossProduct3(rk,ri, rki);
409	<	distZX = dotProduct3(rj,rki) / norm3(rki);
408	>	exclude_.removePair(a, b);
409	>	exclude_.removePair(a, c);
410	>	exclude_.removePair(b, c);
411	>	}
412
413	<	minDist = min(min(distXY, distYZ), distZX);
414	<	return minDist/2;
415	<
416	<	}
413	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
414	>	a = torsion->getAtomA()->getGlobalIndex();
415	>	b = torsion->getAtomB()->getGlobalIndex();
416	>	c = torsion->getAtomC()->getGlobalIndex();
417	>	d = torsion->getAtomD()->getGlobalIndex();
418
419	<	void SimInfo::wrapVector( double thePos[3] ){
419	>	exclude_.removePair(a, b);
420	>	exclude_.removePair(a, c);
421	>	exclude_.removePair(a, d);
422	>	exclude_.removePair(b, c);
423	>	exclude_.removePair(b, d);
424	>	exclude_.removePair(c, d);
425	>	}
426
427	<	int i;
428	<	double scaled[3];
427	>	Molecule::RigidBodyIterator rbIter;
428	>	RigidBody* rb;
429	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
430	>	std::vector<Atom*> atoms = rb->getAtoms();
431	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
432	>	for (int j = i + 1; j < atoms.size(); ++j) {
433	>	a = atoms[i]->getGlobalIndex();
434	>	b = atoms[j]->getGlobalIndex();
435	>	exclude_.removePair(a, b);
436	>	}
437	>	}
438	>	}
439
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	–
440		}
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	–	}
441
442
443	<	int SimInfo::getNDF(){
444	<	int ndf_local;
443	>	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
444	>	int curStampId;
445
446	<	ndf_local = 0;
447	<
448	<	for(int i = 0; i < integrableObjects.size(); i++){
449	<	ndf_local += 3;
450	<	if (integrableObjects[i]->isDirectional()) {
338	<	if (integrableObjects[i]->isLinear())
339	<	ndf_local += 2;
340	<	else
341	<	ndf_local += 3;
342	<	}
446	>	//index from 0
447	>	curStampId = moleculeStamps_.size();
448	>
449	>	moleculeStamps_.push_back(molStamp);
450	>	molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
451		}
452
453	<	// n_constraints is local, so subtract them on each processor:
453	>	void SimInfo::update() {
454
455	<	ndf_local -= n_constraints;
455	>	setupSimType();
456
457		#ifdef IS_MPI
458	<	MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
351	<	#else
352	<	ndf = ndf_local;
458	>	setupFortranParallel();
459		#endif
460
461	<	// nZconstraints is global, as are the 3 COM translations for the
356	<	// entire system:
461	>	setupFortranSim();
462
463	<	ndf = ndf - 3 - nZconstraints;
463	>	//setup fortran force field
464	>	/** @deprecate */
465	>	int isError = 0;
466	>	initFortranFF( &fInfo_.SIM_uses_RF, &fInfo_.SIM_uses_UW,
467	>	&fInfo_.SIM_uses_DW, &isError );
468	>	if(isError){
469	>	sprintf( painCave.errMsg,
470	>	"ForceField error: There was an error initializing the forceField in fortran.\n" );
471	>	painCave.isFatal = 1;
472	>	simError();
473	>	}
474	>
475	>
476	>	setupCutoff();
477
478	<	return ndf;
479	<	}
478	>	calcNdf();
479	>	calcNdfRaw();
480	>	calcNdfTrans();
481
482	<	int SimInfo::getNDFraw() {
483	<	int ndfRaw_local;
482	>	fortranInitialized_ = true;
483	>	}
484
485	<	// Raw degrees of freedom that we have to set
486	<	ndfRaw_local = 0;
485	>	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
486	>	SimInfo::MoleculeIterator mi;
487	>	Molecule* mol;
488	>	Molecule::AtomIterator ai;
489	>	Atom* atom;
490	>	std::set<AtomType*> atomTypes;
491
492	<	for(int i = 0; i < integrableObjects.size(); i++){
493	<	ndfRaw_local += 3;
494	<	if (integrableObjects[i]->isDirectional()) {
495	<	if (integrableObjects[i]->isLinear())
496	<	ndfRaw_local += 2;
497	<	else
375	<	ndfRaw_local += 3;
492	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
493	>
494	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
495	>	atomTypes.insert(atom->getAtomType());
496	>	}
497	>
498		}
499	+
500	+	return atomTypes;
501		}
502	+
503	+	void SimInfo::setupSimType() {
504	+	std::set<AtomType*>::iterator i;
505	+	std::set<AtomType*> atomTypes;
506	+	atomTypes = getUniqueAtomTypes();
507
508	<	#ifdef IS_MPI
509	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
510	<	#else
511	<	ndfRaw = ndfRaw_local;
512	<	#endif
508	>	int useLennardJones = 0;
509	>	int useElectrostatic = 0;
510	>	int useEAM = 0;
511	>	int useCharge = 0;
512	>	int useDirectional = 0;
513	>	int useDipole = 0;
514	>	int useGayBerne = 0;
515	>	int useSticky = 0;
516	>	int useStickyPower = 0;
517	>	int useShape = 0;
518	>	int useFLARB = 0; //it is not in AtomType yet
519	>	int useDirectionalAtom = 0;
520	>	int useElectrostatics = 0;
521	>	//usePBC and useRF are from simParams
522	>	int usePBC = simParams_->getPBC();
523	>	int useRF = simParams_->getUseRF();
524	>	int useUW = simParams_->getUseUndampedWolf();
525	>	int useDW = simParams_->getUseDampedWolf();
526
527	<	return ndfRaw;
528	<	}
527	>	//loop over all of the atom types
528	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
529	>	useLennardJones |= (*i)->isLennardJones();
530	>	useElectrostatic |= (*i)->isElectrostatic();
531	>	useEAM |= (*i)->isEAM();
532	>	useCharge |= (*i)->isCharge();
533	>	useDirectional |= (*i)->isDirectional();
534	>	useDipole |= (*i)->isDipole();
535	>	useGayBerne |= (*i)->isGayBerne();
536	>	useSticky |= (*i)->isSticky();
537	>	useStickyPower |= (*i)->isStickyPower();
538	>	useShape |= (*i)->isShape();
539	>	}
540
541	<	int SimInfo::getNDFtranslational() {
542	<	int ndfTrans_local;
541	>	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
542	>	useDirectionalAtom = 1;
543	>	}
544
545	<	ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
545	>	if (useCharge || useDipole) {
546	>	useElectrostatics = 1;
547	>	}
548
549	+	#ifdef IS_MPI
550	+	int temp;
551
552	<	#ifdef IS_MPI
553	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
396	<	#else
397	<	ndfTrans = ndfTrans_local;
398	<	#endif
552	>	temp = usePBC;
553	>	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
554
555	<	ndfTrans = ndfTrans - 3 - nZconstraints;
555	>	temp = useDirectionalAtom;
556	>	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
557
558	<	return ndfTrans;
559	<	}
558	>	temp = useLennardJones;
559	>	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
560
561	<	int SimInfo::getTotIntegrableObjects() {
562	<	int nObjs_local;
407	<	int nObjs;
561	>	temp = useElectrostatics;
562	>	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
563
564	<	nObjs_local =  integrableObjects.size();
564	>	temp = useCharge;
565	>	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
566
567	+	temp = useDipole;
568	+	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
569
570	<	#ifdef IS_MPI
571	<	MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
414	<	#else
415	<	nObjs = nObjs_local;
416	<	#endif
570	>	temp = useSticky;
571	>	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
572
573	+	temp = useStickyPower;
574	+	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
575	+
576	+	temp = useGayBerne;
577	+	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
578
579	<	return nObjs;
580	<	}
579	>	temp = useEAM;
580	>	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
581
582	<	void SimInfo::refreshSim(){
582	>	temp = useShape;
583	>	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
584
585	<	simtype fInfo;
586	<	int isError;
426	<	int n_global;
427	<	int* excl;
585	>	temp = useFLARB;
586	>	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
587
588	<	fInfo.dielect = 0.0;
588	>	temp = useRF;
589	>	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
590
591	<	if( useDipoles ){
592	<	if( useReactionField )fInfo.dielect = dielectric;
591	>	temp = useUW;
592	>	MPI_Allreduce(&temp, &useUW, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
593	>
594	>	temp = useDW;
595	>	MPI_Allreduce(&temp, &useDW, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
596	>
597	>	#endif
598	>
599	>	fInfo_.SIM_uses_PBC = usePBC;
600	>	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
601	>	fInfo_.SIM_uses_LennardJones = useLennardJones;
602	>	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
603	>	fInfo_.SIM_uses_Charges = useCharge;
604	>	fInfo_.SIM_uses_Dipoles = useDipole;
605	>	fInfo_.SIM_uses_Sticky = useSticky;
606	>	fInfo_.SIM_uses_StickyPower = useStickyPower;
607	>	fInfo_.SIM_uses_GayBerne = useGayBerne;
608	>	fInfo_.SIM_uses_EAM = useEAM;
609	>	fInfo_.SIM_uses_Shapes = useShape;
610	>	fInfo_.SIM_uses_FLARB = useFLARB;
611	>	fInfo_.SIM_uses_RF = useRF;
612	>	fInfo_.SIM_uses_UW = useUW;
613	>	fInfo_.SIM_uses_DW = useDW;
614	>
615	>	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
616	>
617	>	if (simParams_->haveDielectric()) {
618	>	fInfo_.dielect = simParams_->getDielectric();
619	>	} else {
620	>	sprintf(painCave.errMsg,
621	>	"SimSetup Error: No Dielectric constant was set.\n"
622	>	"\tYou are trying to use Reaction Field without"
623	>	"\tsetting a dielectric constant!\n");
624	>	painCave.isFatal = 1;
625	>	simError();
626	>	}
627	>
628	>	} else {
629	>	fInfo_.dielect = 0.0;
630	>	}
631	>
632		}
633
634	<	fInfo.SIM_uses_PBC = usePBC;
635	<	//fInfo.SIM_uses_LJ = 0;
636	<	fInfo.SIM_uses_LJ = useLJ;
637	<	fInfo.SIM_uses_sticky = useSticky;
638	<	//fInfo.SIM_uses_sticky = 0;
639	<	fInfo.SIM_uses_charges = useCharges;
640	<	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;
634	>	void SimInfo::setupFortranSim() {
635	>	int isError;
636	>	int nExclude;
637	>	std::vector<int> fortranGlobalGroupMembership;
638	>
639	>	nExclude = exclude_.getSize();
640	>	isError = 0;
641
642	<	n_exclude = excludes->getSize();
643	<	excl = excludes->getFortranArray();
644	<
645	<	#ifdef IS_MPI
452	<	n_global = mpiSim->getNAtomsGlobal();
453	<	#else
454	<	n_global = n_atoms;
455	<	#endif
456	<
457	<	isError = 0;
458	<
459	<	getFortranGroupArrays(this, FglobalGroupMembership, mfact);
460	<	//it may not be a good idea to pass the address of first element in vector
461	<	//since c++ standard does not require vector to be stored continuously in meomory
462	<	//Most of the compilers will organize the memory of vector continuously
463	<	setFortranSim( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
464	<	&nGlobalExcludes, globalExcludes, molMembershipArray,
465	<	&mfact[0], &ngroup, &FglobalGroupMembership[0], &isError);
642	>	//globalGroupMembership_ is filled by SimCreator
643	>	for (int i = 0; i < nGlobalAtoms_; i++) {
644	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
645	>	}
646
647	<	if( isError ){
647	>	//calculate mass ratio of cutoff group
648	>	std::vector<double> mfact;
649	>	SimInfo::MoleculeIterator mi;
650	>	Molecule* mol;
651	>	Molecule::CutoffGroupIterator ci;
652	>	CutoffGroup* cg;
653	>	Molecule::AtomIterator ai;
654	>	Atom* atom;
655	>	double totalMass;
656	>
657	>	//to avoid memory reallocation, reserve enough space for mfact
658	>	mfact.reserve(getNCutoffGroups());
659
660	<	sprintf( painCave.errMsg,
661	<	"There was an error setting the simulation information in fortran.\n" );
471	<	painCave.isFatal = 1;
472	<	painCave.severity = OOPSE_ERROR;
473	<	simError();
474	<	}
475	<
476	<	#ifdef IS_MPI
477	<	sprintf( checkPointMsg,
478	<	"succesfully sent the simulation information to fortran.\n");
479	<	MPIcheckPoint();
480	<	#endif // is_mpi
481	<
482	<	this->ndf = this->getNDF();
483	<	this->ndfRaw = this->getNDFraw();
484	<	this->ndfTrans = this->getNDFtranslational();
485	<	}
660	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
661	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
662
663	<	void SimInfo::setDefaultRcut( double theRcut ){
664	<
665	<	haveRcut = 1;
666	<	rCut = theRcut;
491	<	rList = rCut + 1.0;
492	<
493	<	notifyFortranCutoffs( &rCut, &rSw, &rList );
494	<	}
663	>	totalMass = cg->getMass();
664	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
665	>	mfact.push_back(atom->getMass()/totalMass);
666	>	}
667
668	<	void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
668	>	}
669	>	}
670
671	<	rSw = theRsw;
672	<	setDefaultRcut( theRcut );
500	<	}
671	>	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
672	>	std::vector<int> identArray;
673
674	+	//to avoid memory reallocation, reserve enough space identArray
675	+	identArray.reserve(getNAtoms());
676	+
677	+	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
678	+	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
679	+	identArray.push_back(atom->getIdent());
680	+	}
681	+	}
682
683	<	void SimInfo::checkCutOffs( void ){
684	<
685	<	if( boxIsInit ){
683	>	//fill molMembershipArray
684	>	//molMembershipArray is filled by SimCreator
685	>	std::vector<int> molMembershipArray(nGlobalAtoms_);
686	>	for (int i = 0; i < nGlobalAtoms_; i++) {
687	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
688	>	}
689
690	<	//we need to check cutOffs against the box
691	<
692	<	if( rCut > maxCutoff ){
690	>	//setup fortran simulation
691	>	int nGlobalExcludes = 0;
692	>	int* globalExcludes = NULL;
693	>	int* excludeList = exclude_.getExcludeList();
694	>	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
695	>	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
696	>	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
697	>
698	>	if( isError ){
699	>
700		sprintf( painCave.errMsg,
701	<	"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;
701	>	"There was an error setting the simulation information in fortran.\n" );
702		painCave.isFatal = 1;
703	+	painCave.severity = OOPSE_ERROR;
704		simError();
705	<	}
706	<	} else {
707	<	// initialize this stuff before using it, OK?
708	<	sprintf( painCave.errMsg,
709	<	"Trying to check cutoffs without a box.\n"
710	<	"\tOOPSE should have better programmers than that.\n" );
711	<	painCave.severity = OOPSE_ERROR;
533	<	painCave.isFatal = 1;
534	<	simError();
705	>	}
706	>
707	>	#ifdef IS_MPI
708	>	sprintf( checkPointMsg,
709	>	"succesfully sent the simulation information to fortran.\n");
710	>	MPIcheckPoint();
711	>	#endif // is_mpi
712		}
536	–
537	–	}
713
539	–	void SimInfo::addProperty(GenericData* prop){
714
715	<	map<string, GenericData*>::iterator result;
716	<	result = properties.find(prop->getID());
543	<
544	<	//we can't simply use  properties[prop->getID()] = prop,
545	<	//it will cause memory leak if we already contain a propery which has the same name of prop
546	<
547	<	if(result != properties.end()){
715	>	#ifdef IS_MPI
716	>	void SimInfo::setupFortranParallel() {
717
718	<	delete (*result).second;
719	<	(*result).second = prop;
720	<
721	<	}
722	<	else{
718	>	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
719	>	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
720	>	std::vector<int> localToGlobalCutoffGroupIndex;
721	>	SimInfo::MoleculeIterator mi;
722	>	Molecule::AtomIterator ai;
723	>	Molecule::CutoffGroupIterator ci;
724	>	Molecule* mol;
725	>	Atom* atom;
726	>	CutoffGroup* cg;
727	>	mpiSimData parallelData;
728	>	int isError;
729
730	<	properties[prop->getID()] = prop;
730	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
731
732	<	}
733	<
734	<	}
732	>	//local index(index in DataStorge) of atom is important
733	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
734	>	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
735	>	}
736
737	<	GenericData* SimInfo::getProperty(const string& propName){
738	<
739	<	map<string, GenericData*>::iterator result;
740	<
741	<	//string lowerCaseName = ();
742	<
567	<	result = properties.find(propName);
568	<
569	<	if(result != properties.end())
570	<	return (*result).second;
571	<	else
572	<	return NULL;
573	<	}
737	>	//local index of cutoff group is trivial, it only depends on the order of travesing
738	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
739	>	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
740	>	}
741	>
742	>	}
743
744	+	//fill up mpiSimData struct
745	+	parallelData.nMolGlobal = getNGlobalMolecules();
746	+	parallelData.nMolLocal = getNMolecules();
747	+	parallelData.nAtomsGlobal = getNGlobalAtoms();
748	+	parallelData.nAtomsLocal = getNAtoms();
749	+	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
750	+	parallelData.nGroupsLocal = getNCutoffGroups();
751	+	parallelData.myNode = worldRank;
752	+	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
753
754	<	void SimInfo::getFortranGroupArrays(SimInfo* info,
755	<	vector<int>& FglobalGroupMembership,
756	<	vector<double>& mfact){
757	<
580	<	Molecule* myMols;
581	<	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	<
754	>	//pass mpiSimData struct and index arrays to fortran
755	>	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
756	>	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
757	>	&localToGlobalCutoffGroupIndex[0], &isError);
758
759	<	// Fix the silly fortran indexing problem
760	<	#ifdef IS_MPI
761	<	numAtom = mpiSim->getNAtomsGlobal();
762	<	#else
763	<	numAtom = n_atoms;
764	<	#endif
603	<	for (int i = 0; i < numAtom; i++)
604	<	FglobalGroupMembership.push_back(globalGroupMembership[i] + 1);
605	<
759	>	if (isError) {
760	>	sprintf(painCave.errMsg,
761	>	"mpiRefresh errror: fortran didn't like something we gave it.\n");
762	>	painCave.isFatal = 1;
763	>	simError();
764	>	}
765
766	<	myMols = info->molecules;
767	<	numMol = info->n_mol;
609	<	for(int i  = 0; i < numMol; i++){
610	<	numCutoffGroups = myMols[i].getNCutoffGroups();
611	<	for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff);
612	<	myCutoffGroup != NULL;
613	<	myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
766	>	sprintf(checkPointMsg, " mpiRefresh successful.\n");
767	>	MPIcheckPoint();
768
769	<	totalMass = myCutoffGroup->getMass();
770	<
771	<	for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom);
772	<	cutoffAtom != NULL;
773	<	cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
774	<	mfact.push_back(cutoffAtom->getMass()/totalMass);
775	<	}
769	>
770	>	}
771	>
772	>	#endif
773	>
774	>	double SimInfo::calcMaxCutoffRadius() {
775	>
776	>
777	>	std::set<AtomType*> atomTypes;
778	>	std::set<AtomType*>::iterator i;
779	>	std::vector<double> cutoffRadius;
780	>
781	>	//get the unique atom types
782	>	atomTypes = getUniqueAtomTypes();
783	>
784	>	//query the max cutoff radius among these atom types
785	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
786	>	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
787		}
788	+
789	+	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
790	+	#ifdef IS_MPI
791	+	//pick the max cutoff radius among the processors
792	+	#endif
793	+
794	+	return maxCutoffRadius;
795		}
796
797	<	}
797	>	void SimInfo::getCutoff(double& rcut, double& rsw) {
798	>
799	>	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
800	>
801	>	if (!simParams_->haveRcut()){
802	>	sprintf(painCave.errMsg,
803	>	"SimCreator Warning: No value was set for the cutoffRadius.\n"
804	>	"\tOOPSE will use a default value of 15.0 angstroms"
805	>	"\tfor the cutoffRadius.\n");
806	>	painCave.isFatal = 0;
807	>	simError();
808	>	rcut = 15.0;
809	>	} else{
810	>	rcut = simParams_->getRcut();
811	>	}
812	>
813	>	if (!simParams_->haveRsw()){
814	>	sprintf(painCave.errMsg,
815	>	"SimCreator Warning: No value was set for switchingRadius.\n"
816	>	"\tOOPSE will use a default value of\n"
817	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
818	>	painCave.isFatal = 0;
819	>	simError();
820	>	rsw = 0.95 * rcut;
821	>	} else{
822	>	rsw = simParams_->getRsw();
823	>	}
824	>
825	>	} else {
826	>	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
827	>	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
828	>
829	>	if (simParams_->haveRcut()) {
830	>	rcut = simParams_->getRcut();
831	>	} else {
832	>	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
833	>	rcut = calcMaxCutoffRadius();
834	>	}
835	>
836	>	if (simParams_->haveRsw()) {
837	>	rsw  = simParams_->getRsw();
838	>	} else {
839	>	rsw = rcut;
840	>	}
841	>
842	>	}
843	>	}
844	>
845	>	void SimInfo::setupCutoff() {
846	>	getCutoff(rcut_, rsw_);
847	>	double rnblist = rcut_ + 1; // skin of neighbor list
848	>
849	>	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
850	>
851	>	int cp =  TRADITIONAL_CUTOFF_POLICY;
852	>	if (simParams_->haveCutoffPolicy()) {
853	>	std::string myPolicy = simParams_->getCutoffPolicy();
854	>	if (myPolicy == "MIX") {
855	>	cp = MIX_CUTOFF_POLICY;
856	>	} else {
857	>	if (myPolicy == "MAX") {
858	>	cp = MAX_CUTOFF_POLICY;
859	>	} else {
860	>	if (myPolicy == "TRADITIONAL") {
861	>	cp = TRADITIONAL_CUTOFF_POLICY;
862	>	} else {
863	>	// throw error
864	>	sprintf( painCave.errMsg,
865	>	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
866	>	painCave.isFatal = 1;
867	>	simError();
868	>	}
869	>	}
870	>	}
871	>	}
872	>	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
873	>	}
874	>
875	>	void SimInfo::addProperty(GenericData* genData) {
876	>	properties_.addProperty(genData);
877	>	}
878	>
879	>	void SimInfo::removeProperty(const std::string& propName) {
880	>	properties_.removeProperty(propName);
881	>	}
882	>
883	>	void SimInfo::clearProperties() {
884	>	properties_.clearProperties();
885	>	}
886	>
887	>	std::vector<std::string> SimInfo::getPropertyNames() {
888	>	return properties_.getPropertyNames();
889	>	}
890	>
891	>	std::vector<GenericData*> SimInfo::getProperties() {
892	>	return properties_.getProperties();
893	>	}
894	>
895	>	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
896	>	return properties_.getPropertyByName(propName);
897	>	}
898	>
899	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
900	>	if (sman_ == sman) {
901	>	return;
902	>	}
903	>	delete sman_;
904	>	sman_ = sman;
905	>
906	>	Molecule* mol;
907	>	RigidBody* rb;
908	>	Atom* atom;
909	>	SimInfo::MoleculeIterator mi;
910	>	Molecule::RigidBodyIterator rbIter;
911	>	Molecule::AtomIterator atomIter;;
912	>
913	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
914	>
915	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
916	>	atom->setSnapshotManager(sman_);
917	>	}
918	>
919	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
920	>	rb->setSnapshotManager(sman_);
921	>	}
922	>	}
923	>
924	>	}
925	>
926	>	Vector3d SimInfo::getComVel(){
927	>	SimInfo::MoleculeIterator i;
928	>	Molecule* mol;
929	>
930	>	Vector3d comVel(0.0);
931	>	double totalMass = 0.0;
932	>
933	>
934	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
935	>	double mass = mol->getMass();
936	>	totalMass += mass;
937	>	comVel += mass * mol->getComVel();
938	>	}
939	>
940	>	#ifdef IS_MPI
941	>	double tmpMass = totalMass;
942	>	Vector3d tmpComVel(comVel);
943	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
944	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
945	>	#endif
946	>
947	>	comVel /= totalMass;
948	>
949	>	return comVel;
950	>	}
951	>
952	>	Vector3d SimInfo::getCom(){
953	>	SimInfo::MoleculeIterator i;
954	>	Molecule* mol;
955	>
956	>	Vector3d com(0.0);
957	>	double totalMass = 0.0;
958	>
959	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
960	>	double mass = mol->getMass();
961	>	totalMass += mass;
962	>	com += mass * mol->getCom();
963	>	}
964	>
965	>	#ifdef IS_MPI
966	>	double tmpMass = totalMass;
967	>	Vector3d tmpCom(com);
968	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
969	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
970	>	#endif
971	>
972	>	com /= totalMass;
973	>
974	>	return com;
975	>
976	>	}
977	>
978	>	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
979	>
980	>	return o;
981	>	}
982	>
983	>
984	>	/*
985	>	Returns center of mass and center of mass velocity in one function call.
986	>	*/
987	>
988	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
989	>	SimInfo::MoleculeIterator i;
990	>	Molecule* mol;
991	>
992	>
993	>	double totalMass = 0.0;
994	>
995	>
996	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
997	>	double mass = mol->getMass();
998	>	totalMass += mass;
999	>	com += mass * mol->getCom();
1000	>	comVel += mass * mol->getComVel();
1001	>	}
1002	>
1003	>	#ifdef IS_MPI
1004	>	double tmpMass = totalMass;
1005	>	Vector3d tmpCom(com);
1006	>	Vector3d tmpComVel(comVel);
1007	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1008	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1009	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1010	>	#endif
1011	>
1012	>	com /= totalMass;
1013	>	comVel /= totalMass;
1014	>	}
1015	>
1016	>	/*
1017	>	Return intertia tensor for entire system and angular momentum Vector.
1018	>
1019	>
1020	>	[  Ixx -Ixy  -Ixz ]
1021	>	J =| -Iyx  Iyy  -Iyz |
1022	>	[ -Izx -Iyz   Izz ]
1023	>	*/
1024	>
1025	>	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1026	>
1027	>
1028	>	double xx = 0.0;
1029	>	double yy = 0.0;
1030	>	double zz = 0.0;
1031	>	double xy = 0.0;
1032	>	double xz = 0.0;
1033	>	double yz = 0.0;
1034	>	Vector3d com(0.0);
1035	>	Vector3d comVel(0.0);
1036	>
1037	>	getComAll(com, comVel);
1038	>
1039	>	SimInfo::MoleculeIterator i;
1040	>	Molecule* mol;
1041	>
1042	>	Vector3d thisq(0.0);
1043	>	Vector3d thisv(0.0);
1044	>
1045	>	double thisMass = 0.0;
1046	>
1047	>
1048	>
1049	>
1050	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1051	>
1052	>	thisq = mol->getCom()-com;
1053	>	thisv = mol->getComVel()-comVel;
1054	>	thisMass = mol->getMass();
1055	>	// Compute moment of intertia coefficients.
1056	>	xx += thisq[0]*thisq[0]*thisMass;
1057	>	yy += thisq[1]*thisq[1]*thisMass;
1058	>	zz += thisq[2]*thisq[2]*thisMass;
1059	>
1060	>	// compute products of intertia
1061	>	xy += thisq[0]*thisq[1]*thisMass;
1062	>	xz += thisq[0]*thisq[2]*thisMass;
1063	>	yz += thisq[1]*thisq[2]*thisMass;
1064	>
1065	>	angularMomentum += cross( thisq, thisv ) * thisMass;
1066	>
1067	>	}
1068	>
1069	>
1070	>	inertiaTensor(0,0) = yy + zz;
1071	>	inertiaTensor(0,1) = -xy;
1072	>	inertiaTensor(0,2) = -xz;
1073	>	inertiaTensor(1,0) = -xy;
1074	>	inertiaTensor(1,1) = xx + zz;
1075	>	inertiaTensor(1,2) = -yz;
1076	>	inertiaTensor(2,0) = -xz;
1077	>	inertiaTensor(2,1) = -yz;
1078	>	inertiaTensor(2,2) = xx + yy;
1079	>
1080	>	#ifdef IS_MPI
1081	>	Mat3x3d tmpI(inertiaTensor);
1082	>	Vector3d tmpAngMom;
1083	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1084	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1085	>	#endif
1086	>
1087	>	return;
1088	>	}
1089	>
1090	>	//Returns the angular momentum of the system
1091	>	Vector3d SimInfo::getAngularMomentum(){
1092	>
1093	>	Vector3d com(0.0);
1094	>	Vector3d comVel(0.0);
1095	>	Vector3d angularMomentum(0.0);
1096	>
1097	>	getComAll(com,comVel);
1098	>
1099	>	SimInfo::MoleculeIterator i;
1100	>	Molecule* mol;
1101	>
1102	>	Vector3d thisr(0.0);
1103	>	Vector3d thisp(0.0);
1104	>
1105	>	double thisMass;
1106	>
1107	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1108	>	thisMass = mol->getMass();
1109	>	thisr = mol->getCom()-com;
1110	>	thisp = (mol->getComVel()-comVel)*thisMass;
1111	>
1112	>	angularMomentum += cross( thisr, thisp );
1113	>
1114	>	}
1115	>
1116	>	#ifdef IS_MPI
1117	>	Vector3d tmpAngMom;
1118	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1119	>	#endif
1120	>
1121	>	return angularMomentum;
1122	>	}
1123	>
1124	>
1125	>	}//end namespace oopse
1126	>

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines