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Comparing trunk/OOPSE-2.0/src/brains/SimInfo.cpp (file contents):
Revision 1636 by chrisfen, Fri Oct 22 22:54:01 2004 UTC vs.
Revision 2309 by chrisfen, Sun Sep 18 20:45:38 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/DarkSide/fElectrostaticSummationMethod.h"
57	>	#include "UseTheForce/doForces_interface.h"
58	>	#include "UseTheForce/DarkSide/electrostatic_interface.h"
59		#include "UseTheForce/notifyCutoffs_interface.h"
60	+	#include "utils/MemoryUtils.hpp"
61	+	#include "utils/simError.h"
62	+	#include "selection/SelectionManager.hpp"
63
15	–	//#include "UseTheForce/fortranWrappers.hpp"
16	–
17	–	#include "math/MatVec3.h"
18	–
64		#ifdef IS_MPI
65	<	#include "brains/mpiSimulation.hpp"
66	<	#endif
65	>	#include "UseTheForce/mpiComponentPlan.h"
66	>	#include "UseTheForce/DarkSide/simParallel_interface.h"
67	>	#endif
68
69	<	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	<	}
69	>	namespace oopse {
70
71	<	SimInfo* currentInfo;
71	>	SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
72	>	ForceField* ff, Globals* simParams) :
73	>	stamps_(stamps), forceField_(ff), simParams_(simParams),
74	>	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
75	>	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
76	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
77	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
78	>	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
79	>	sman_(NULL), fortranInitialized_(false) {
80
81	<	SimInfo::SimInfo(){
81	>
82	>	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
83	>	MoleculeStamp* molStamp;
84	>	int nMolWithSameStamp;
85	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
86	>	int nGroups = 0;          //total cutoff groups defined in meta-data file
87	>	CutoffGroupStamp* cgStamp;
88	>	RigidBodyStamp* rbStamp;
89	>	int nRigidAtoms = 0;
90	>
91	>	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
92	>	molStamp = i->first;
93	>	nMolWithSameStamp = i->second;
94	>
95	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
96
97	<	n_constraints = 0;
98	<	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;
97	>	//calculate atoms in molecules
98	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
99
49	–	haveRcut = 0;
50	–	haveRsw = 0;
51	–	boxIsInit = 0;
52	–
53	–	resetTime = 1e99;
100
101	<	orthoRhombic = 0;
102	<	orthoTolerance = 1E-6;
103	<	useInitXSstate = true;
101	>	//calculate atoms in cutoff groups
102	>	int nAtomsInGroups = 0;
103	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
104	>
105	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
106	>	cgStamp = molStamp->getCutoffGroup(j);
107	>	nAtomsInGroups += cgStamp->getNMembers();
108	>	}
109
110	<	usePBC = 0;
111	<	useDirectionalAtoms = 0;
61	<	useLennardJones = 0;
62	<	useElectrostatics = 0;
63	<	useCharges = 0;
64	<	useDipoles = 0;
65	<	useSticky = 0;
66	<	useGayBerne = 0;
67	<	useEAM = 0;
68	<	useShapes = 0;
69	<	useFLARB = 0;
110	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
111	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
112
113	<	useSolidThermInt = 0;
114	<	useLiquidThermInt = 0;
113	>	//calculate atoms in rigid bodies
114	>	int nAtomsInRigidBodies = 0;
115	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
116	>
117	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
118	>	rbStamp = molStamp->getRigidBody(j);
119	>	nAtomsInRigidBodies += rbStamp->getNMembers();
120	>	}
121
122	<	haveCutoffGroups = false;
122	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
123	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
124	>
125	>	}
126
127	<	excludes = Exclude::Instance();
127	>	//every free atom (atom does not belong to cutoff groups) is a cutoff group
128	>	//therefore the total number of cutoff groups in the system is equal to
129	>	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
130	>	//file plus the number of cutoff groups defined in meta-data file
131	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
132
133	<	myConfiguration = new SimState();
133	>	//every free atom (atom does not belong to rigid bodies) is an integrable object
134	>	//therefore the total number of  integrable objects in the system is equal to
135	>	//the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
136	>	//file plus the number of  rigid bodies defined in meta-data file
137	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
138
139	<	has_minimizer = false;
81	<	the_minimizer =NULL;
139	>	nGlobalMols_ = molStampIds_.size();
140
141	<	ngroup = 0;
141	>	#ifdef IS_MPI
142	>	molToProcMap_.resize(nGlobalMols_);
143	>	#endif
144
145	<	}
145	>	}
146
147	+	SimInfo::~SimInfo() {
148	+	std::map<int, Molecule*>::iterator i;
149	+	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
150	+	delete i->second;
151	+	}
152	+	molecules_.clear();
153	+
154	+	delete stamps_;
155	+	delete sman_;
156	+	delete simParams_;
157	+	delete forceField_;
158	+	}
159
160	<	SimInfo::~SimInfo(){
160	>	int SimInfo::getNGlobalConstraints() {
161	>	int nGlobalConstraints;
162	>	#ifdef IS_MPI
163	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
164	>	MPI_COMM_WORLD);
165	>	#else
166	>	nGlobalConstraints =  nConstraints_;
167	>	#endif
168	>	return nGlobalConstraints;
169	>	}
170
171	<	delete myConfiguration;
171	>	bool SimInfo::addMolecule(Molecule* mol) {
172	>	MoleculeIterator i;
173
174	<	map<string, GenericData*>::iterator i;
175	<
94	<	for(i = properties.begin(); i != properties.end(); i++)
95	<	delete (*i).second;
174	>	i = molecules_.find(mol->getGlobalIndex());
175	>	if (i == molecules_.end() ) {
176
177	<	}
178	<
179	<	void SimInfo::setBox(double newBox[3]) {
180	<
181	<	int i, j;
182	<	double tempMat[3][3];
183	<
184	<	for(i=0; i<3; i++)
185	<	for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
186	<
107	<	tempMat[0][0] = newBox[0];
108	<	tempMat[1][1] = newBox[1];
109	<	tempMat[2][2] = newBox[2];
110	<
111	<	setBoxM( tempMat );
177	>	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
178	>
179	>	nAtoms_ += mol->getNAtoms();
180	>	nBonds_ += mol->getNBonds();
181	>	nBends_ += mol->getNBends();
182	>	nTorsions_ += mol->getNTorsions();
183	>	nRigidBodies_ += mol->getNRigidBodies();
184	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
185	>	nCutoffGroups_ += mol->getNCutoffGroups();
186	>	nConstraints_ += mol->getNConstraintPairs();
187
188	<	}
189	<
190	<	void SimInfo::setBoxM( double theBox[3][3] ){
191	<
192	<	int i, j;
118	<	double FortranHmat[9]; // to preserve compatibility with Fortran the
119	<	// ordering in the array is as follows:
120	<	// [ 0 3 6 ]
121	<	// [ 1 4 7 ]
122	<	// [ 2 5 8 ]
123	<	double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
124	<
125	<	if( !boxIsInit ) boxIsInit = 1;
126	<
127	<	for(i=0; i < 3; i++)
128	<	for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
129	<
130	<	calcBoxL();
131	<	calcHmatInv();
132	<
133	<	for(i=0; i < 3; i++) {
134	<	for (j=0; j < 3; j++) {
135	<	FortranHmat[3*j + i] = Hmat[i][j];
136	<	FortranHmatInv[3*j + i] = HmatInv[i][j];
188	>	addExcludePairs(mol);
189	>
190	>	return true;
191	>	} else {
192	>	return false;
193		}
194		}
195
196	<	setFortranBox(FortranHmat, FortranHmatInv, &orthoRhombic);
197	<
198	<	}
143	<
196	>	bool SimInfo::removeMolecule(Molecule* mol) {
197	>	MoleculeIterator i;
198	>	i = molecules_.find(mol->getGlobalIndex());
199
200	<	void SimInfo::getBoxM (double theBox[3][3]) {
200	>	if (i != molecules_.end() ) {
201
202	<	int i, j;
203	<	for(i=0; i<3; i++)
204	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
205	<	}
202	>	assert(mol == i->second);
203	>
204	>	nAtoms_ -= mol->getNAtoms();
205	>	nBonds_ -= mol->getNBonds();
206	>	nBends_ -= mol->getNBends();
207	>	nTorsions_ -= mol->getNTorsions();
208	>	nRigidBodies_ -= mol->getNRigidBodies();
209	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
210	>	nCutoffGroups_ -= mol->getNCutoffGroups();
211	>	nConstraints_ -= mol->getNConstraintPairs();
212
213	+	removeExcludePairs(mol);
214	+	molecules_.erase(mol->getGlobalIndex());
215
216	<	void SimInfo::scaleBox(double scale) {
217	<	double theBox[3][3];
218	<	int i, j;
216	>	delete mol;
217	>
218	>	return true;
219	>	} else {
220	>	return false;
221	>	}
222
157	–	// cerr << "Scaling box by " << scale << "\n";
223
224	<	for(i=0; i<3; i++)
160	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
224	>	}
225
226	<	setBoxM(theBox);
226	>
227	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
228	>	i = molecules_.begin();
229	>	return i == molecules_.end() ? NULL : i->second;
230	>	}
231
232	<	}
232	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
233	>	++i;
234	>	return i == molecules_.end() ? NULL : i->second;
235	>	}
236
166	–	void SimInfo::calcHmatInv( void ) {
167	–
168	–	int oldOrtho;
169	–	int i,j;
170	–	double smallDiag;
171	–	double tol;
172	–	double sanity[3][3];
237
238	<	invertMat3( Hmat, HmatInv );
238	>	void SimInfo::calcNdf() {
239	>	int ndf_local;
240	>	MoleculeIterator i;
241	>	std::vector<StuntDouble*>::iterator j;
242	>	Molecule* mol;
243	>	StuntDouble* integrableObject;
244
245	<	// check to see if Hmat is orthorhombic
246	<
247	<	oldOrtho = orthoRhombic;
245	>	ndf_local = 0;
246	>
247	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
248	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
249	>	integrableObject = mol->nextIntegrableObject(j)) {
250
251	<	smallDiag = fabs(Hmat[0][0]);
181	<	if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
182	<	if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
183	<	tol = smallDiag * orthoTolerance;
251	>	ndf_local += 3;
252
253	<	orthoRhombic = 1;
254	<
255	<	for (i = 0; i < 3; i++ ) {
256	<	for (j = 0 ; j < 3; j++) {
257	<	if (i != j) {
258	<	if (orthoRhombic) {
259	<	if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
260	<	}
261	<	}
262	<	}
195	<	}
196	<
197	<	if( oldOrtho != orthoRhombic ){
253	>	if (integrableObject->isDirectional()) {
254	>	if (integrableObject->isLinear()) {
255	>	ndf_local += 2;
256	>	} else {
257	>	ndf_local += 3;
258	>	}
259	>	}
260	>
261	>	}//end for (integrableObject)
262	>	}// end for (mol)
263
264	<	if( orthoRhombic ) {
265	<	sprintf( painCave.errMsg,
201	<	"OOPSE is switching from the default Non-Orthorhombic\n"
202	<	"\tto the faster Orthorhombic periodic boundary computations.\n"
203	<	"\tThis is usually a good thing, but if you wan't the\n"
204	<	"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
205	<	"\tvariable ( currently set to %G ) smaller.\n",
206	<	orthoTolerance);
207	<	painCave.severity = OOPSE_INFO;
208	<	simError();
209	<	}
210	<	else {
211	<	sprintf( painCave.errMsg,
212	<	"OOPSE is switching from the faster Orthorhombic to the more\n"
213	<	"\tflexible Non-Orthorhombic periodic boundary computations.\n"
214	<	"\tThis is usually because the box has deformed under\n"
215	<	"\tNPTf integration. If you wan't to live on the edge with\n"
216	<	"\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
217	<	"\tvariable ( currently set to %G ) larger.\n",
218	<	orthoTolerance);
219	<	painCave.severity = OOPSE_WARNING;
220	<	simError();
221	<	}
222	<	}
223	<	}
264	>	// n_constraints is local, so subtract them on each processor
265	>	ndf_local -= nConstraints_;
266
267	<	void SimInfo::calcBoxL( void ){
267	>	#ifdef IS_MPI
268	>	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
269	>	#else
270	>	ndf_ = ndf_local;
271	>	#endif
272
273	<	double dx, dy, dz, dsq;
273	>	// nZconstraints_ is global, as are the 3 COM translations for the
274	>	// entire system:
275	>	ndf_ = ndf_ - 3 - nZconstraint_;
276
277	<	// boxVol = Determinant of Hmat
277	>	}
278
279	<	boxVol = matDet3( Hmat );
279	>	void SimInfo::calcNdfRaw() {
280	>	int ndfRaw_local;
281
282	<	// boxLx
283	<
284	<	dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
285	<	dsq = dx*dx + dy*dy + dz*dz;
237	<	boxL[0] = sqrt( dsq );
238	<	//maxCutoff = 0.5 * boxL[0];
282	>	MoleculeIterator i;
283	>	std::vector<StuntDouble*>::iterator j;
284	>	Molecule* mol;
285	>	StuntDouble* integrableObject;
286
287	<	// boxLy
288	<
289	<	dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
290	<	dsq = dx*dx + dy*dy + dz*dz;
291	<	boxL[1] = sqrt( dsq );
292	<	//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
287	>	// Raw degrees of freedom that we have to set
288	>	ndfRaw_local = 0;
289	>
290	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
291	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
292	>	integrableObject = mol->nextIntegrableObject(j)) {
293
294	+	ndfRaw_local += 3;
295
296	<	// boxLz
297	<
298	<	dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
299	<	dsq = dx*dx + dy*dy + dz*dz;
300	<	boxL[2] = sqrt( dsq );
301	<	//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
296	>	if (integrableObject->isDirectional()) {
297	>	if (integrableObject->isLinear()) {
298	>	ndfRaw_local += 2;
299	>	} else {
300	>	ndfRaw_local += 3;
301	>	}
302	>	}
303	>
304	>	}
305	>	}
306	>
307	>	#ifdef IS_MPI
308	>	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
309	>	#else
310	>	ndfRaw_ = ndfRaw_local;
311	>	#endif
312	>	}
313
314	<	//calculate the max cutoff
315	<	maxCutoff =  calcMaxCutOff();
257	<
258	<	checkCutOffs();
314	>	void SimInfo::calcNdfTrans() {
315	>	int ndfTrans_local;
316
317	<	}
317	>	ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
318
319
320	<	double SimInfo::calcMaxCutOff(){
320	>	#ifdef IS_MPI
321	>	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
322	>	#else
323	>	ndfTrans_ = ndfTrans_local;
324	>	#endif
325
326	<	double ri[3], rj[3], rk[3];
327	<	double rij[3], rjk[3], rki[3];
328	<	double minDist;
326	>	ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
327	>
328	>	}
329
330	<	ri[0] = Hmat[0][0];
331	<	ri[1] = Hmat[1][0];
332	<	ri[2] = Hmat[2][0];
333	<
334	<	rj[0] = Hmat[0][1];
335	<	rj[1] = Hmat[1][1];
336	<	rj[2] = Hmat[2][1];
337	<
338	<	rk[0] = Hmat[0][2];
339	<	rk[1] = Hmat[1][2];
340	<	rk[2] = Hmat[2][2];
330	>	void SimInfo::addExcludePairs(Molecule* mol) {
331	>	std::vector<Bond*>::iterator bondIter;
332	>	std::vector<Bend*>::iterator bendIter;
333	>	std::vector<Torsion*>::iterator torsionIter;
334	>	Bond* bond;
335	>	Bend* bend;
336	>	Torsion* torsion;
337	>	int a;
338	>	int b;
339	>	int c;
340	>	int d;
341
342	<	crossProduct3(ri, rj, rij);
343	<	distXY = dotProduct3(rk,rij) / norm3(rij);
342	>	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
343	>	a = bond->getAtomA()->getGlobalIndex();
344	>	b = bond->getAtomB()->getGlobalIndex();
345	>	exclude_.addPair(a, b);
346	>	}
347
348	<	crossProduct3(rj,rk, rjk);
349	<	distYZ = dotProduct3(ri,rjk) / norm3(rjk);
348	>	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
349	>	a = bend->getAtomA()->getGlobalIndex();
350	>	b = bend->getAtomB()->getGlobalIndex();
351	>	c = bend->getAtomC()->getGlobalIndex();
352
353	<	crossProduct3(rk,ri, rki);
354	<	distZX = dotProduct3(rj,rki) / norm3(rki);
353	>	exclude_.addPair(a, b);
354	>	exclude_.addPair(a, c);
355	>	exclude_.addPair(b, c);
356	>	}
357
358	<	minDist = min(min(distXY, distYZ), distZX);
359	<	return minDist/2;
360	<
361	<	}
358	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
359	>	a = torsion->getAtomA()->getGlobalIndex();
360	>	b = torsion->getAtomB()->getGlobalIndex();
361	>	c = torsion->getAtomC()->getGlobalIndex();
362	>	d = torsion->getAtomD()->getGlobalIndex();
363
364	<	void SimInfo::wrapVector( double thePos[3] ){
364	>	exclude_.addPair(a, b);
365	>	exclude_.addPair(a, c);
366	>	exclude_.addPair(a, d);
367	>	exclude_.addPair(b, c);
368	>	exclude_.addPair(b, d);
369	>	exclude_.addPair(c, d);
370	>	}
371
372	<	int i;
373	<	double scaled[3];
372	>	Molecule::RigidBodyIterator rbIter;
373	>	RigidBody* rb;
374	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
375	>	std::vector<Atom*> atoms = rb->getAtoms();
376	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
377	>	for (int j = i + 1; j < atoms.size(); ++j) {
378	>	a = atoms[i]->getGlobalIndex();
379	>	b = atoms[j]->getGlobalIndex();
380	>	exclude_.addPair(a, b);
381	>	}
382	>	}
383	>	}
384
385	<	if( !orthoRhombic ){
301	<	// calc the scaled coordinates.
302	<
385	>	}
386
387	<	matVecMul3(HmatInv, thePos, scaled);
387	>	void SimInfo::removeExcludePairs(Molecule* mol) {
388	>	std::vector<Bond*>::iterator bondIter;
389	>	std::vector<Bend*>::iterator bendIter;
390	>	std::vector<Torsion*>::iterator torsionIter;
391	>	Bond* bond;
392	>	Bend* bend;
393	>	Torsion* torsion;
394	>	int a;
395	>	int b;
396	>	int c;
397	>	int d;
398
399	<	for(i=0; i<3; i++)
400	<	scaled[i] -= roundMe(scaled[i]);
401	<
402	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
403	<
311	<	matVecMul3(Hmat, scaled, thePos);
399	>	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
400	>	a = bond->getAtomA()->getGlobalIndex();
401	>	b = bond->getAtomB()->getGlobalIndex();
402	>	exclude_.removePair(a, b);
403	>	}
404
405	<	}
406	<	else{
407	<	// calc the scaled coordinates.
408	<
317	<	for(i=0; i<3; i++)
318	<	scaled[i] = thePos[i]*HmatInv[i][i];
319	<
320	<	// wrap the scaled coordinates
321	<
322	<	for(i=0; i<3; i++)
323	<	scaled[i] -= roundMe(scaled[i]);
324	<
325	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
326	<
327	<	for(i=0; i<3; i++)
328	<	thePos[i] = scaled[i]*Hmat[i][i];
329	<	}
330	<
331	<	}
405	>	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
406	>	a = bend->getAtomA()->getGlobalIndex();
407	>	b = bend->getAtomB()->getGlobalIndex();
408	>	c = bend->getAtomC()->getGlobalIndex();
409
410	+	exclude_.removePair(a, b);
411	+	exclude_.removePair(a, c);
412	+	exclude_.removePair(b, c);
413	+	}
414
415	<	int SimInfo::getNDF(){
416	<	int ndf_local;
415	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
416	>	a = torsion->getAtomA()->getGlobalIndex();
417	>	b = torsion->getAtomB()->getGlobalIndex();
418	>	c = torsion->getAtomC()->getGlobalIndex();
419	>	d = torsion->getAtomD()->getGlobalIndex();
420
421	<	ndf_local = 0;
422	<
423	<	for(int i = 0; i < integrableObjects.size(); i++){
424	<	ndf_local += 3;
425	<	if (integrableObjects[i]->isDirectional()) {
426	<	if (integrableObjects[i]->isLinear())
343	<	ndf_local += 2;
344	<	else
345	<	ndf_local += 3;
421	>	exclude_.removePair(a, b);
422	>	exclude_.removePair(a, c);
423	>	exclude_.removePair(a, d);
424	>	exclude_.removePair(b, c);
425	>	exclude_.removePair(b, d);
426	>	exclude_.removePair(c, d);
427		}
428	+
429	+	Molecule::RigidBodyIterator rbIter;
430	+	RigidBody* rb;
431	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
432	+	std::vector<Atom*> atoms = rb->getAtoms();
433	+	for (int i = 0; i < atoms.size() -1 ; ++i) {
434	+	for (int j = i + 1; j < atoms.size(); ++j) {
435	+	a = atoms[i]->getGlobalIndex();
436	+	b = atoms[j]->getGlobalIndex();
437	+	exclude_.removePair(a, b);
438	+	}
439	+	}
440	+	}
441	+
442		}
443
349	–	// n_constraints is local, so subtract them on each processor:
444
445	<	ndf_local -= n_constraints;
445	>	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
446	>	int curStampId;
447
448	<	#ifdef IS_MPI
449	<	MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
355	<	#else
356	<	ndf = ndf_local;
357	<	#endif
448	>	//index from 0
449	>	curStampId = moleculeStamps_.size();
450
451	<	// nZconstraints is global, as are the 3 COM translations for the
452	<	// entire system:
451	>	moleculeStamps_.push_back(molStamp);
452	>	molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
453	>	}
454
455	<	ndf = ndf - 3 - nZconstraints;
455	>	void SimInfo::update() {
456
457	<	return ndf;
365	<	}
457	>	setupSimType();
458
459	<	int SimInfo::getNDFraw() {
460	<	int ndfRaw_local;
459	>	#ifdef IS_MPI
460	>	setupFortranParallel();
461	>	#endif
462
463	<	// Raw degrees of freedom that we have to set
371	<	ndfRaw_local = 0;
463	>	setupFortranSim();
464
465	<	for(int i = 0; i < integrableObjects.size(); i++){
466	<	ndfRaw_local += 3;
467	<	if (integrableObjects[i]->isDirectional()) {
468	<	if (integrableObjects[i]->isLinear())
469	<	ndfRaw_local += 2;
470	<	else
471	<	ndfRaw_local += 3;
465	>	//setup fortran force field
466	>	/** @deprecate */
467	>	int isError = 0;
468	>
469	>	setupElectrostaticSummationMethod( isError );
470	>
471	>	if(isError){
472	>	sprintf( painCave.errMsg,
473	>	"ForceField error: There was an error initializing the forceField in fortran.\n" );
474	>	painCave.isFatal = 1;
475	>	simError();
476		}
477	<	}
477	>
478
479	<	#ifdef IS_MPI
384	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
385	<	#else
386	<	ndfRaw = ndfRaw_local;
387	<	#endif
479	>	setupCutoff();
480
481	<	return ndfRaw;
482	<	}
481	>	calcNdf();
482	>	calcNdfRaw();
483	>	calcNdfTrans();
484
485	<	int SimInfo::getNDFtranslational() {
486	<	int ndfTrans_local;
485	>	fortranInitialized_ = true;
486	>	}
487
488	<	ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
488	>	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
489	>	SimInfo::MoleculeIterator mi;
490	>	Molecule* mol;
491	>	Molecule::AtomIterator ai;
492	>	Atom* atom;
493	>	std::set<AtomType*> atomTypes;
494
495	+	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
496
497	<	#ifdef IS_MPI
498	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
499	<	#else
500	<	ndfTrans = ndfTrans_local;
501	<	#endif
497	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
498	>	atomTypes.insert(atom->getAtomType());
499	>	}
500	>
501	>	}
502
503	<	ndfTrans = ndfTrans - 3 - nZconstraints;
503	>	return atomTypes;
504	>	}
505
506	<	return ndfTrans;
507	<	}
506	>	void SimInfo::setupSimType() {
507	>	std::set<AtomType*>::iterator i;
508	>	std::set<AtomType*> atomTypes;
509	>	atomTypes = getUniqueAtomTypes();
510	>
511	>	int useLennardJones = 0;
512	>	int useElectrostatic = 0;
513	>	int useEAM = 0;
514	>	int useCharge = 0;
515	>	int useDirectional = 0;
516	>	int useDipole = 0;
517	>	int useGayBerne = 0;
518	>	int useSticky = 0;
519	>	int useStickyPower = 0;
520	>	int useShape = 0;
521	>	int useFLARB = 0; //it is not in AtomType yet
522	>	int useDirectionalAtom = 0;
523	>	int useElectrostatics = 0;
524	>	//usePBC and useRF are from simParams
525	>	int usePBC = simParams_->getPBC();
526
527	<	int SimInfo::getTotIntegrableObjects() {
528	<	int nObjs_local;
529	<	int nObjs;
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	<	nObjs_local =  integrableObjects.size();
541	>	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
542	>	useDirectionalAtom = 1;
543	>	}
544
545	+	if (useCharge || useDipole) {
546	+	useElectrostatics = 1;
547	+	}
548
549	<	#ifdef IS_MPI
550	<	MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
418	<	#else
419	<	nObjs = nObjs_local;
420	<	#endif
549	>	#ifdef IS_MPI
550	>	int temp;
551
552	+	temp = usePBC;
553	+	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
554
555	<	return nObjs;
556	<	}
555	>	temp = useDirectionalAtom;
556	>	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
557
558	<	void SimInfo::refreshSim(){
558	>	temp = useLennardJones;
559	>	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
560
561	<	simtype fInfo;
562	<	int isError;
430	<	int n_global;
431	<	int* excl;
561	>	temp = useElectrostatics;
562	>	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
563
564	<	fInfo.dielect = 0.0;
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	>	temp = useSticky;
571	>	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
572
573	<	if( useDipoles ){
574	<	if( useReactionField )fInfo.dielect = dielectric;
575	<	}
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	<	fInfo.SIM_uses_PBC = usePBC;
579	>	temp = useEAM;
580	>	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
581
582	<	if (useSticky || useDipoles || useGayBerne || useShapes) {
583	<	useDirectionalAtoms = 1;
443	<	fInfo.SIM_uses_DirectionalAtoms = useDirectionalAtoms;
444	<	}
582	>	temp = useShape;
583	>	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
584
585	<	fInfo.SIM_uses_LennardJones = useLennardJones;
585	>	temp = useFLARB;
586	>	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
587
588	<	if (useCharges || useDipoles) {
589	<	useElectrostatics = 1;
590	<	fInfo.SIM_uses_Electrostatics = useElectrostatics;
588	>	#endif
589	>
590	>	fInfo_.SIM_uses_PBC = usePBC;
591	>	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
592	>	fInfo_.SIM_uses_LennardJones = useLennardJones;
593	>	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
594	>	fInfo_.SIM_uses_Charges = useCharge;
595	>	fInfo_.SIM_uses_Dipoles = useDipole;
596	>	fInfo_.SIM_uses_Sticky = useSticky;
597	>	fInfo_.SIM_uses_StickyPower = useStickyPower;
598	>	fInfo_.SIM_uses_GayBerne = useGayBerne;
599	>	fInfo_.SIM_uses_EAM = useEAM;
600	>	fInfo_.SIM_uses_Shapes = useShape;
601	>	fInfo_.SIM_uses_FLARB = useFLARB;
602	>
603	>	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
604	>
605	>	if (simParams_->haveDielectric()) {
606	>	fInfo_.dielect = simParams_->getDielectric();
607	>	} else {
608	>	sprintf(painCave.errMsg,
609	>	"SimSetup Error: No Dielectric constant was set.\n"
610	>	"\tYou are trying to use Reaction Field without"
611	>	"\tsetting a dielectric constant!\n");
612	>	painCave.isFatal = 1;
613	>	simError();
614	>	}
615	>
616	>	} else {
617	>	fInfo_.dielect = 0.0;
618	>	}
619	>
620		}
621
622	<	fInfo.SIM_uses_Charges = useCharges;
623	<	fInfo.SIM_uses_Dipoles = useDipoles;
624	<	fInfo.SIM_uses_Sticky = useSticky;
625	<	fInfo.SIM_uses_GayBerne = useGayBerne;
626	<	fInfo.SIM_uses_EAM = useEAM;
627	<	fInfo.SIM_uses_Shapes = useShapes;
628	<	fInfo.SIM_uses_FLARB = useFLARB;
460	<	fInfo.SIM_uses_RF = useReactionField;
622	>	void SimInfo::setupFortranSim() {
623	>	int isError;
624	>	int nExclude;
625	>	std::vector<int> fortranGlobalGroupMembership;
626	>
627	>	nExclude = exclude_.getSize();
628	>	isError = 0;
629
630	<	n_exclude = excludes->getSize();
631	<	excl = excludes->getFortranArray();
632	<
633	<	#ifdef IS_MPI
466	<	n_global = mpiSim->getNAtomsGlobal();
467	<	#else
468	<	n_global = n_atoms;
469	<	#endif
470	<
471	<	isError = 0;
472	<
473	<	getFortranGroupArrays(this, FglobalGroupMembership, mfact);
474	<	//it may not be a good idea to pass the address of first element in vector
475	<	//since c++ standard does not require vector to be stored continuously in meomory
476	<	//Most of the compilers will organize the memory of vector continuously
477	<	setFortranSim( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
478	<	&nGlobalExcludes, globalExcludes, molMembershipArray,
479	<	&mfact[0], &ngroup, &FglobalGroupMembership[0], &isError);
630	>	//globalGroupMembership_ is filled by SimCreator
631	>	for (int i = 0; i < nGlobalAtoms_; i++) {
632	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
633	>	}
634
635	<	if( isError ){
635	>	//calculate mass ratio of cutoff group
636	>	std::vector<double> mfact;
637	>	SimInfo::MoleculeIterator mi;
638	>	Molecule* mol;
639	>	Molecule::CutoffGroupIterator ci;
640	>	CutoffGroup* cg;
641	>	Molecule::AtomIterator ai;
642	>	Atom* atom;
643	>	double totalMass;
644	>
645	>	//to avoid memory reallocation, reserve enough space for mfact
646	>	mfact.reserve(getNCutoffGroups());
647
648	<	sprintf( painCave.errMsg,
649	<	"There was an error setting the simulation information in fortran.\n" );
485	<	painCave.isFatal = 1;
486	<	painCave.severity = OOPSE_ERROR;
487	<	simError();
488	<	}
489	<
490	<	#ifdef IS_MPI
491	<	sprintf( checkPointMsg,
492	<	"succesfully sent the simulation information to fortran.\n");
493	<	MPIcheckPoint();
494	<	#endif // is_mpi
495	<
496	<	this->ndf = this->getNDF();
497	<	this->ndfRaw = this->getNDFraw();
498	<	this->ndfTrans = this->getNDFtranslational();
499	<	}
648	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
649	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
650
651	<	void SimInfo::setDefaultRcut( double theRcut ){
652	<
653	<	haveRcut = 1;
654	<	rCut = theRcut;
505	<	rList = rCut + 1.0;
506	<
507	<	notifyFortranCutoffs( &rCut, &rSw, &rList );
508	<	}
651	>	totalMass = cg->getMass();
652	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
653	>	mfact.push_back(atom->getMass()/totalMass);
654	>	}
655
656	<	void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
656	>	}
657	>	}
658
659	<	rSw = theRsw;
660	<	setDefaultRcut( theRcut );
514	<	}
659	>	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
660	>	std::vector<int> identArray;
661
662	+	//to avoid memory reallocation, reserve enough space identArray
663	+	identArray.reserve(getNAtoms());
664	+
665	+	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
666	+	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
667	+	identArray.push_back(atom->getIdent());
668	+	}
669	+	}
670
671	<	void SimInfo::checkCutOffs( void ){
672	<
673	<	if( boxIsInit ){
671	>	//fill molMembershipArray
672	>	//molMembershipArray is filled by SimCreator
673	>	std::vector<int> molMembershipArray(nGlobalAtoms_);
674	>	for (int i = 0; i < nGlobalAtoms_; i++) {
675	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
676	>	}
677
678	<	//we need to check cutOffs against the box
679	<
680	<	if( rCut > maxCutoff ){
678	>	//setup fortran simulation
679	>	int nGlobalExcludes = 0;
680	>	int* globalExcludes = NULL;
681	>	int* excludeList = exclude_.getExcludeList();
682	>	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
683	>	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
684	>	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
685	>
686	>	if( isError ){
687	>
688		sprintf( painCave.errMsg,
689	<	"cutoffRadius is too large for the current periodic box.\n"
526	<	"\tCurrent Value of cutoffRadius = %G at time %G\n "
527	<	"\tThis is larger than half of at least one of the\n"
528	<	"\tperiodic box vectors.  Right now, the Box matrix is:\n"
529	<	"\n"
530	<	"\t[ %G %G %G ]\n"
531	<	"\t[ %G %G %G ]\n"
532	<	"\t[ %G %G %G ]\n",
533	<	rCut, currentTime,
534	<	Hmat[0][0], Hmat[0][1], Hmat[0][2],
535	<	Hmat[1][0], Hmat[1][1], Hmat[1][2],
536	<	Hmat[2][0], Hmat[2][1], Hmat[2][2]);
537	<	painCave.severity = OOPSE_ERROR;
689	>	"There was an error setting the simulation information in fortran.\n" );
690		painCave.isFatal = 1;
691	+	painCave.severity = OOPSE_ERROR;
692		simError();
693	<	}
694	<	} else {
695	<	// initialize this stuff before using it, OK?
696	<	sprintf( painCave.errMsg,
697	<	"Trying to check cutoffs without a box.\n"
698	<	"\tOOPSE should have better programmers than that.\n" );
699	<	painCave.severity = OOPSE_ERROR;
547	<	painCave.isFatal = 1;
548	<	simError();
693	>	}
694	>
695	>	#ifdef IS_MPI
696	>	sprintf( checkPointMsg,
697	>	"succesfully sent the simulation information to fortran.\n");
698	>	MPIcheckPoint();
699	>	#endif // is_mpi
700		}
550	–
551	–	}
701
553	–	void SimInfo::addProperty(GenericData* prop){
702
703	<	map<string, GenericData*>::iterator result;
704	<	result = properties.find(prop->getID());
557	<
558	<	//we can't simply use  properties[prop->getID()] = prop,
559	<	//it will cause memory leak if we already contain a propery which has the same name of prop
560	<
561	<	if(result != properties.end()){
703	>	#ifdef IS_MPI
704	>	void SimInfo::setupFortranParallel() {
705
706	<	delete (*result).second;
707	<	(*result).second = prop;
708	<
709	<	}
710	<	else{
706	>	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
707	>	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
708	>	std::vector<int> localToGlobalCutoffGroupIndex;
709	>	SimInfo::MoleculeIterator mi;
710	>	Molecule::AtomIterator ai;
711	>	Molecule::CutoffGroupIterator ci;
712	>	Molecule* mol;
713	>	Atom* atom;
714	>	CutoffGroup* cg;
715	>	mpiSimData parallelData;
716	>	int isError;
717
718	<	properties[prop->getID()] = prop;
718	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
719
720	+	//local index(index in DataStorge) of atom is important
721	+	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
722	+	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
723	+	}
724	+
725	+	//local index of cutoff group is trivial, it only depends on the order of travesing
726	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
727	+	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
728	+	}
729	+
730	+	}
731	+
732	+	//fill up mpiSimData struct
733	+	parallelData.nMolGlobal = getNGlobalMolecules();
734	+	parallelData.nMolLocal = getNMolecules();
735	+	parallelData.nAtomsGlobal = getNGlobalAtoms();
736	+	parallelData.nAtomsLocal = getNAtoms();
737	+	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
738	+	parallelData.nGroupsLocal = getNCutoffGroups();
739	+	parallelData.myNode = worldRank;
740	+	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
741	+
742	+	//pass mpiSimData struct and index arrays to fortran
743	+	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
744	+	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
745	+	&localToGlobalCutoffGroupIndex[0], &isError);
746	+
747	+	if (isError) {
748	+	sprintf(painCave.errMsg,
749	+	"mpiRefresh errror: fortran didn't like something we gave it.\n");
750	+	painCave.isFatal = 1;
751	+	simError();
752	+	}
753	+
754	+	sprintf(checkPointMsg, " mpiRefresh successful.\n");
755	+	MPIcheckPoint();
756	+
757	+
758		}
572	–
573	–	}
759
760	<	GenericData* SimInfo::getProperty(const string& propName){
576	<
577	<	map<string, GenericData*>::iterator result;
578	<
579	<	//string lowerCaseName = ();
580	<
581	<	result = properties.find(propName);
582	<
583	<	if(result != properties.end())
584	<	return (*result).second;
585	<	else
586	<	return NULL;
587	<	}
760	>	#endif
761
762	+	double SimInfo::calcMaxCutoffRadius() {
763
590	–	void SimInfo::getFortranGroupArrays(SimInfo* info,
591	–	vector<int>& FglobalGroupMembership,
592	–	vector<double>& mfact){
593	–
594	–	Molecule* myMols;
595	–	Atom** myAtoms;
596	–	int numAtom;
597	–	double mtot;
598	–	int numMol;
599	–	int numCutoffGroups;
600	–	CutoffGroup* myCutoffGroup;
601	–	vector<CutoffGroup*>::iterator iterCutoff;
602	–	Atom* cutoffAtom;
603	–	vector<Atom*>::iterator iterAtom;
604	–	int atomIndex;
605	–	double totalMass;
606	–
607	–	mfact.clear();
608	–	FglobalGroupMembership.clear();
609	–
764
765	<	// Fix the silly fortran indexing problem
765	>	std::set<AtomType*> atomTypes;
766	>	std::set<AtomType*>::iterator i;
767	>	std::vector<double> cutoffRadius;
768	>
769	>	//get the unique atom types
770	>	atomTypes = getUniqueAtomTypes();
771	>
772	>	//query the max cutoff radius among these atom types
773	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
774	>	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
775	>	}
776	>
777	>	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
778		#ifdef IS_MPI
779	<	numAtom = mpiSim->getNAtomsGlobal();
614	<	#else
615	<	numAtom = n_atoms;
779	>	//pick the max cutoff radius among the processors
780		#endif
617	–	for (int i = 0; i < numAtom; i++)
618	–	FglobalGroupMembership.push_back(globalGroupMembership[i] + 1);
619	–
781
782	<	myMols = info->molecules;
783	<	numMol = info->n_mol;
623	<	for(int i  = 0; i < numMol; i++){
624	<	numCutoffGroups = myMols[i].getNCutoffGroups();
625	<	for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff);
626	<	myCutoffGroup != NULL;
627	<	myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
782	>	return maxCutoffRadius;
783	>	}
784
785	<	totalMass = myCutoffGroup->getMass();
786	<
787	<	for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom);
788	<	cutoffAtom != NULL;
789	<	cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
790	<	mfact.push_back(cutoffAtom->getMass()/totalMass);
791	<	}
785	>	void SimInfo::getCutoff(double& rcut, double& rsw) {
786	>
787	>	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
788	>
789	>	if (!simParams_->haveRcut()){
790	>	sprintf(painCave.errMsg,
791	>	"SimCreator Warning: No value was set for the cutoffRadius.\n"
792	>	"\tOOPSE will use a default value of 15.0 angstroms"
793	>	"\tfor the cutoffRadius.\n");
794	>	painCave.isFatal = 0;
795	>	simError();
796	>	rcut = 15.0;
797	>	} else{
798	>	rcut = simParams_->getRcut();
799	>	}
800	>
801	>	if (!simParams_->haveRsw()){
802	>	sprintf(painCave.errMsg,
803	>	"SimCreator Warning: No value was set for switchingRadius.\n"
804	>	"\tOOPSE will use a default value of\n"
805	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
806	>	painCave.isFatal = 0;
807	>	simError();
808	>	rsw = 0.95 * rcut;
809	>	} else{
810	>	rsw = simParams_->getRsw();
811	>	}
812	>
813	>	} else {
814	>	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
815	>	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
816	>
817	>	if (simParams_->haveRcut()) {
818	>	rcut = simParams_->getRcut();
819	>	} else {
820	>	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
821	>	rcut = calcMaxCutoffRadius();
822	>	}
823	>
824	>	if (simParams_->haveRsw()) {
825	>	rsw  = simParams_->getRsw();
826	>	} else {
827	>	rsw = rcut;
828	>	}
829	>
830		}
831		}
832
833	<	}
833	>	void SimInfo::setupCutoff() {
834	>	getCutoff(rcut_, rsw_);
835	>	double rnblist = rcut_ + 1; // skin of neighbor list
836	>
837	>	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
838	>
839	>	int cp =  TRADITIONAL_CUTOFF_POLICY;
840	>	if (simParams_->haveCutoffPolicy()) {
841	>	std::string myPolicy = simParams_->getCutoffPolicy();
842	>	if (myPolicy == "MIX") {
843	>	cp = MIX_CUTOFF_POLICY;
844	>	} else {
845	>	if (myPolicy == "MAX") {
846	>	cp = MAX_CUTOFF_POLICY;
847	>	} else {
848	>	if (myPolicy == "TRADITIONAL") {
849	>	cp = TRADITIONAL_CUTOFF_POLICY;
850	>	} else {
851	>	// throw error
852	>	sprintf( painCave.errMsg,
853	>	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
854	>	painCave.isFatal = 1;
855	>	simError();
856	>	}
857	>	}
858	>	}
859	>	}
860	>	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
861	>	// also send cutoff notification to electrostatics
862	>	setElectrostaticCutoffRadius(&rcut_);
863	>	}
864	>
865	>	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
866	>
867	>	int errorOut;
868	>	int esm =  NONE;
869	>	double alphaVal;
870	>	double dielectric;
871	>
872	>	errorOut = isError;
873	>	alphaVal = simParams_->getDampingAlpha();
874	>	dielectric = simParams_->getDielectric();
875	>
876	>	if (simParams_->haveElectrostaticSummationMethod()) {
877	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
878	>	if (myMethod == "NONE") {
879	>	esm = NONE;
880	>	} else {
881	>	if (myMethod == "UNDAMPED_WOLF") {
882	>	esm = UNDAMPED_WOLF;
883	>	} else {
884	>	if (myMethod == "DAMPED_WOLF") {
885	>	esm = DAMPED_WOLF;
886	>	if (!simParams_->haveDampingAlpha()) {
887	>	//throw error
888	>	sprintf( painCave.errMsg,
889	>	"SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used for the Damped Wolf Method.", alphaVal);
890	>	painCave.isFatal = 0;
891	>	simError();
892	>	}
893	>	} else {
894	>	if (myMethod == "REACTION_FIELD") {
895	>	esm = REACTION_FIELD;
896	>	} else {
897	>	// throw error
898	>	sprintf( painCave.errMsg,
899	>	"SimInfo error: Unknown electrostaticSummationMethod. (Input file specified %s .)\n\telectrostaticSummationMethod must be one of: \"none\", \"undamped_wolf\", \"damped_wolf\", or \"reaction_field\".", myMethod.c_str() );
900	>	painCave.isFatal = 1;
901	>	simError();
902	>	}
903	>	}
904	>	}
905	>	}
906	>	}
907	>	// let's pass some summation method variables to fortran
908	>	setElectrostaticSummationMethod( &esm );
909	>	setDampedWolfAlpha( &alphaVal );
910	>	setReactionFieldDielectric( &dielectric );
911	>	initFortranFF( &esm, &errorOut );
912	>	}
913	>
914	>	void SimInfo::addProperty(GenericData* genData) {
915	>	properties_.addProperty(genData);
916	>	}
917	>
918	>	void SimInfo::removeProperty(const std::string& propName) {
919	>	properties_.removeProperty(propName);
920	>	}
921	>
922	>	void SimInfo::clearProperties() {
923	>	properties_.clearProperties();
924	>	}
925	>
926	>	std::vector<std::string> SimInfo::getPropertyNames() {
927	>	return properties_.getPropertyNames();
928	>	}
929	>
930	>	std::vector<GenericData*> SimInfo::getProperties() {
931	>	return properties_.getProperties();
932	>	}
933	>
934	>	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
935	>	return properties_.getPropertyByName(propName);
936	>	}
937	>
938	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
939	>	if (sman_ == sman) {
940	>	return;
941	>	}
942	>	delete sman_;
943	>	sman_ = sman;
944	>
945	>	Molecule* mol;
946	>	RigidBody* rb;
947	>	Atom* atom;
948	>	SimInfo::MoleculeIterator mi;
949	>	Molecule::RigidBodyIterator rbIter;
950	>	Molecule::AtomIterator atomIter;;
951	>
952	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
953	>
954	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
955	>	atom->setSnapshotManager(sman_);
956	>	}
957	>
958	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
959	>	rb->setSnapshotManager(sman_);
960	>	}
961	>	}
962	>
963	>	}
964	>
965	>	Vector3d SimInfo::getComVel(){
966	>	SimInfo::MoleculeIterator i;
967	>	Molecule* mol;
968	>
969	>	Vector3d comVel(0.0);
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	>	comVel += mass * mol->getComVel();
977	>	}
978	>
979	>	#ifdef IS_MPI
980	>	double tmpMass = totalMass;
981	>	Vector3d tmpComVel(comVel);
982	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
983	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
984	>	#endif
985	>
986	>	comVel /= totalMass;
987	>
988	>	return comVel;
989	>	}
990	>
991	>	Vector3d SimInfo::getCom(){
992	>	SimInfo::MoleculeIterator i;
993	>	Molecule* mol;
994	>
995	>	Vector3d com(0.0);
996	>	double totalMass = 0.0;
997	>
998	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
999	>	double mass = mol->getMass();
1000	>	totalMass += mass;
1001	>	com += mass * mol->getCom();
1002	>	}
1003	>
1004	>	#ifdef IS_MPI
1005	>	double tmpMass = totalMass;
1006	>	Vector3d tmpCom(com);
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	>	#endif
1010	>
1011	>	com /= totalMass;
1012	>
1013	>	return com;
1014	>
1015	>	}
1016	>
1017	>	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1018	>
1019	>	return o;
1020	>	}
1021	>
1022	>
1023	>	/*
1024	>	Returns center of mass and center of mass velocity in one function call.
1025	>	*/
1026	>
1027	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1028	>	SimInfo::MoleculeIterator i;
1029	>	Molecule* mol;
1030	>
1031	>
1032	>	double totalMass = 0.0;
1033	>
1034	>
1035	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1036	>	double mass = mol->getMass();
1037	>	totalMass += mass;
1038	>	com += mass * mol->getCom();
1039	>	comVel += mass * mol->getComVel();
1040	>	}
1041	>
1042	>	#ifdef IS_MPI
1043	>	double tmpMass = totalMass;
1044	>	Vector3d tmpCom(com);
1045	>	Vector3d tmpComVel(comVel);
1046	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1047	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1048	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1049	>	#endif
1050	>
1051	>	com /= totalMass;
1052	>	comVel /= totalMass;
1053	>	}
1054	>
1055	>	/*
1056	>	Return intertia tensor for entire system and angular momentum Vector.
1057	>
1058	>
1059	>	[  Ixx -Ixy  -Ixz ]
1060	>	J =| -Iyx  Iyy  -Iyz |
1061	>	[ -Izx -Iyz   Izz ]
1062	>	*/
1063	>
1064	>	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1065	>
1066	>
1067	>	double xx = 0.0;
1068	>	double yy = 0.0;
1069	>	double zz = 0.0;
1070	>	double xy = 0.0;
1071	>	double xz = 0.0;
1072	>	double yz = 0.0;
1073	>	Vector3d com(0.0);
1074	>	Vector3d comVel(0.0);
1075	>
1076	>	getComAll(com, comVel);
1077	>
1078	>	SimInfo::MoleculeIterator i;
1079	>	Molecule* mol;
1080	>
1081	>	Vector3d thisq(0.0);
1082	>	Vector3d thisv(0.0);
1083	>
1084	>	double thisMass = 0.0;
1085	>
1086	>
1087	>
1088	>
1089	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1090	>
1091	>	thisq = mol->getCom()-com;
1092	>	thisv = mol->getComVel()-comVel;
1093	>	thisMass = mol->getMass();
1094	>	// Compute moment of intertia coefficients.
1095	>	xx += thisq[0]*thisq[0]*thisMass;
1096	>	yy += thisq[1]*thisq[1]*thisMass;
1097	>	zz += thisq[2]*thisq[2]*thisMass;
1098	>
1099	>	// compute products of intertia
1100	>	xy += thisq[0]*thisq[1]*thisMass;
1101	>	xz += thisq[0]*thisq[2]*thisMass;
1102	>	yz += thisq[1]*thisq[2]*thisMass;
1103	>
1104	>	angularMomentum += cross( thisq, thisv ) * thisMass;
1105	>
1106	>	}
1107	>
1108	>
1109	>	inertiaTensor(0,0) = yy + zz;
1110	>	inertiaTensor(0,1) = -xy;
1111	>	inertiaTensor(0,2) = -xz;
1112	>	inertiaTensor(1,0) = -xy;
1113	>	inertiaTensor(1,1) = xx + zz;
1114	>	inertiaTensor(1,2) = -yz;
1115	>	inertiaTensor(2,0) = -xz;
1116	>	inertiaTensor(2,1) = -yz;
1117	>	inertiaTensor(2,2) = xx + yy;
1118	>
1119	>	#ifdef IS_MPI
1120	>	Mat3x3d tmpI(inertiaTensor);
1121	>	Vector3d tmpAngMom;
1122	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1123	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1124	>	#endif
1125	>
1126	>	return;
1127	>	}
1128	>
1129	>	//Returns the angular momentum of the system
1130	>	Vector3d SimInfo::getAngularMomentum(){
1131	>
1132	>	Vector3d com(0.0);
1133	>	Vector3d comVel(0.0);
1134	>	Vector3d angularMomentum(0.0);
1135	>
1136	>	getComAll(com,comVel);
1137	>
1138	>	SimInfo::MoleculeIterator i;
1139	>	Molecule* mol;
1140	>
1141	>	Vector3d thisr(0.0);
1142	>	Vector3d thisp(0.0);
1143	>
1144	>	double thisMass;
1145	>
1146	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1147	>	thisMass = mol->getMass();
1148	>	thisr = mol->getCom()-com;
1149	>	thisp = (mol->getComVel()-comVel)*thisMass;
1150	>
1151	>	angularMomentum += cross( thisr, thisp );
1152	>
1153	>	}
1154	>
1155	>	#ifdef IS_MPI
1156	>	Vector3d tmpAngMom;
1157	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1158	>	#endif
1159	>
1160	>	return angularMomentum;
1161	>	}
1162	>
1163	>
1164	>	}//end namespace oopse
1165	>

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