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

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 2 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
Revision 701 by chrisfen, Wed Oct 26 23:32:25 2005 UTC

#	Line 1 | Line 1
1	<	#include <stdlib.h>
2	<	#include <string.h>
3	<	#include <math.h>
1	>	/*
2	>	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	>	*
4	>	* The University of Notre Dame grants you ("Licensee") a
5	>	* non-exclusive, royalty free, license to use, modify and
6	>	* redistribute this software in source and binary code form, provided
7	>	* that the following conditions are met:
8	>	*
9	>	* 1. Acknowledgement of the program authors must be made in any
10	>	*    publication of scientific results based in part on use of the
11	>	*    program.  An acceptable form of acknowledgement is citation of
12	>	*    the article in which the program was described (Matthew
13	>	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	>	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	>	*    Parallel Simulation Engine for Molecular Dynamics,"
16	>	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	>	*
18	>	* 2. Redistributions of source code must retain the above copyright
19	>	*    notice, this list of conditions and the following disclaimer.
20	>	*
21	>	* 3. Redistributions in binary form must reproduce the above copyright
22	>	*    notice, this list of conditions and the following disclaimer in the
23	>	*    documentation and/or other materials provided with the
24	>	*    distribution.
25	>	*
26	>	* This software is provided "AS IS," without a warranty of any
27	>	* kind. All express or implied conditions, representations and
28	>	* warranties, including any implied warranty of merchantability,
29	>	* fitness for a particular purpose or non-infringement, are hereby
30	>	* excluded.  The University of Notre Dame and its licensors shall not
31	>	* be liable for any damages suffered by licensee as a result of
32	>	* using, modifying or distributing the software or its
33	>	* derivatives. In no event will the University of Notre Dame or its
34	>	* licensors be liable for any lost revenue, profit or data, or for
35	>	* direct, indirect, special, consequential, incidental or punitive
36	>	* damages, however caused and regardless of the theory of liability,
37	>	* arising out of the use of or inability to use software, even if the
38	>	* University of Notre Dame has been advised of the possibility of
39	>	* such damages.
40	>	*/
41	>
42	>	/**
43	>	* @file SimInfo.cpp
44	>	* @author    tlin
45	>	* @date  11/02/2004
46	>	* @version 1.0
47	>	*/
48
49	<	#include <iostream>
50	<	using namespace std;
49	>	#include <algorithm>
50	>	#include <set>
51
52	<	#include "SimInfo.hpp"
53	<	#define __C
54	<	#include "fSimulation.h"
55	<	#include "simError.h"
52	>	#include "brains/SimInfo.hpp"
53	>	#include "math/Vector3.hpp"
54	>	#include "primitives/Molecule.hpp"
55	>	#include "UseTheForce/fCutoffPolicy.h"
56	>	#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
57	>	#include "UseTheForce/doForces_interface.h"
58	>	#include "UseTheForce/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
13	–	#include "fortranWrappers.hpp"
14	–
15	–	#include "MatVec3.h"
16	–
64		#ifdef IS_MPI
65	<	#include "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 ){
22	<	return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
23	<	}
24	<
25	<	inline double min( double a, double b ){
26	<	return (a < b ) ? a : b;
27	<	}
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;
35	<	n_oriented = 0;
36	<	n_dipoles = 0;
37	<	ndf = 0;
38	<	ndfRaw = 0;
39	<	nZconstraints = 0;
40	<	the_integrator = NULL;
41	<	setTemp = 0;
42	<	thermalTime = 0.0;
43	<	currentTime = 0.0;
44	<	rCut = 0.0;
45	<	rSw = 0.0;
97	>	//calculate atoms in molecules
98	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
99
47	–	haveRcut = 0;
48	–	haveRsw = 0;
49	–	boxIsInit = 0;
50	–
51	–	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;
58	<	useLJ = 0;
59	<	useSticky = 0;
60	<	useCharges = 0;
61	<	useDipoles = 0;
62	<	useReactionField = 0;
63	<	useGB = 0;
64	<	useEAM = 0;
65	<	useSolidThermInt = 0;
66	<	useLiquidThermInt = 0;
110	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
111
112	<	haveCutoffGroups = false;
112	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
113
114	<	excludes = Exclude::Instance();
114	>	//calculate atoms in rigid bodies
115	>	int nAtomsInRigidBodies = 0;
116	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
117	>
118	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
119	>	rbStamp = molStamp->getRigidBody(j);
120	>	nAtomsInRigidBodies += rbStamp->getNMembers();
121	>	}
122
123	<	myConfiguration = new SimState();
123	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
124	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
125	>
126	>	}
127
128	<	has_minimizer = false;
129	<	the_minimizer =NULL;
128	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
129	>	//group therefore the total number of cutoff groups in the system is
130	>	//equal to the total number of atoms minus number of atoms belong to
131	>	//cutoff group defined in meta-data file plus the number of cutoff
132	>	//groups defined in meta-data file
133	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
134
135	<	ngroup = 0;
136	<
137	<	wrapMeSimInfo( this );
138	<	}
139	<
140	<
141	<	SimInfo::~SimInfo(){
84	<
85	<	delete myConfiguration;
86	<
87	<	map<string, GenericData*>::iterator i;
135	>	//every free atom (atom does not belong to rigid bodies) is an
136	>	//integrable object therefore the total number of integrable objects
137	>	//in the system is equal to the total number of atoms minus number of
138	>	//atoms belong to rigid body defined in meta-data file plus the number
139	>	//of rigid bodies defined in meta-data file
140	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
141	>	+ nGlobalRigidBodies_;
142
143	<	for(i = properties.begin(); i != properties.end(); i++)
90	<	delete (*i).second;
143	>	nGlobalMols_ = molStampIds_.size();
144
145	<	}
145	>	#ifdef IS_MPI
146	>	molToProcMap_.resize(nGlobalMols_);
147	>	#endif
148
149	<	void SimInfo::setBox(double newBox[3]) {
95	<
96	<	int i, j;
97	<	double tempMat[3][3];
149	>	}
150
151	<	for(i=0; i<3; i++)
152	<	for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
151	>	SimInfo::~SimInfo() {
152	>	std::map<int, Molecule*>::iterator i;
153	>	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
154	>	delete i->second;
155	>	}
156	>	molecules_.clear();
157	>
158	>	delete stamps_;
159	>	delete sman_;
160	>	delete simParams_;
161	>	delete forceField_;
162	>	}
163
164	<	tempMat[0][0] = newBox[0];
165	<	tempMat[1][1] = newBox[1];
166	<	tempMat[2][2] = newBox[2];
164	>	int SimInfo::getNGlobalConstraints() {
165	>	int nGlobalConstraints;
166	>	#ifdef IS_MPI
167	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
168	>	MPI_COMM_WORLD);
169	>	#else
170	>	nGlobalConstraints =  nConstraints_;
171	>	#endif
172	>	return nGlobalConstraints;
173	>	}
174
175	<	setBoxM( tempMat );
175	>	bool SimInfo::addMolecule(Molecule* mol) {
176	>	MoleculeIterator i;
177
178	<	}
178	>	i = molecules_.find(mol->getGlobalIndex());
179	>	if (i == molecules_.end() ) {
180
181	<	void SimInfo::setBoxM( double theBox[3][3] ){
182	<
183	<	int i, j;
184	<	double FortranHmat[9]; // to preserve compatibility with Fortran the
185	<	// ordering in the array is as follows:
186	<	// [ 0 3 6 ]
187	<	// [ 1 4 7 ]
188	<	// [ 2 5 8 ]
189	<	double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
181	>	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
182	>
183	>	nAtoms_ += mol->getNAtoms();
184	>	nBonds_ += mol->getNBonds();
185	>	nBends_ += mol->getNBends();
186	>	nTorsions_ += mol->getNTorsions();
187	>	nRigidBodies_ += mol->getNRigidBodies();
188	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
189	>	nCutoffGroups_ += mol->getNCutoffGroups();
190	>	nConstraints_ += mol->getNConstraintPairs();
191
192	<	if( !boxIsInit ) boxIsInit = 1;
193	<
194	<	for(i=0; i < 3; i++)
195	<	for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
196	<
125	<	calcBoxL();
126	<	calcHmatInv();
127	<
128	<	for(i=0; i < 3; i++) {
129	<	for (j=0; j < 3; j++) {
130	<	FortranHmat[3*j + i] = Hmat[i][j];
131	<	FortranHmatInv[3*j + i] = HmatInv[i][j];
192	>	addExcludePairs(mol);
193	>
194	>	return true;
195	>	} else {
196	>	return false;
197		}
198		}
199
200	<	setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
201	<
202	<	}
138	<
200	>	bool SimInfo::removeMolecule(Molecule* mol) {
201	>	MoleculeIterator i;
202	>	i = molecules_.find(mol->getGlobalIndex());
203
204	<	void SimInfo::getBoxM (double theBox[3][3]) {
204	>	if (i != molecules_.end() ) {
205
206	<	int i, j;
207	<	for(i=0; i<3; i++)
208	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
209	<	}
206	>	assert(mol == i->second);
207	>
208	>	nAtoms_ -= mol->getNAtoms();
209	>	nBonds_ -= mol->getNBonds();
210	>	nBends_ -= mol->getNBends();
211	>	nTorsions_ -= mol->getNTorsions();
212	>	nRigidBodies_ -= mol->getNRigidBodies();
213	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
214	>	nCutoffGroups_ -= mol->getNCutoffGroups();
215	>	nConstraints_ -= mol->getNConstraintPairs();
216
217	+	removeExcludePairs(mol);
218	+	molecules_.erase(mol->getGlobalIndex());
219
220	<	void SimInfo::scaleBox(double scale) {
221	<	double theBox[3][3];
222	<	int i, j;
220	>	delete mol;
221	>
222	>	return true;
223	>	} else {
224	>	return false;
225	>	}
226
152	–	// cerr << "Scaling box by " << scale << "\n";
227
228	<	for(i=0; i<3; i++)
155	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
228	>	}
229
230	<	setBoxM(theBox);
230	>
231	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
232	>	i = molecules_.begin();
233	>	return i == molecules_.end() ? NULL : i->second;
234	>	}
235
236	<	}
236	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
237	>	++i;
238	>	return i == molecules_.end() ? NULL : i->second;
239	>	}
240
161	–	void SimInfo::calcHmatInv( void ) {
162	–
163	–	int oldOrtho;
164	–	int i,j;
165	–	double smallDiag;
166	–	double tol;
167	–	double sanity[3][3];
241
242	<	invertMat3( Hmat, HmatInv );
242	>	void SimInfo::calcNdf() {
243	>	int ndf_local;
244	>	MoleculeIterator i;
245	>	std::vector<StuntDouble*>::iterator j;
246	>	Molecule* mol;
247	>	StuntDouble* integrableObject;
248
249	<	// check to see if Hmat is orthorhombic
250	<
251	<	oldOrtho = orthoRhombic;
249	>	ndf_local = 0;
250	>
251	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
252	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
253	>	integrableObject = mol->nextIntegrableObject(j)) {
254
255	<	smallDiag = fabs(Hmat[0][0]);
176	<	if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
177	<	if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
178	<	tol = smallDiag * orthoTolerance;
255	>	ndf_local += 3;
256
257	<	orthoRhombic = 1;
258	<
259	<	for (i = 0; i < 3; i++ ) {
260	<	for (j = 0 ; j < 3; j++) {
261	<	if (i != j) {
262	<	if (orthoRhombic) {
263	<	if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
264	<	}
265	<	}
266	<	}
190	<	}
191	<
192	<	if( oldOrtho != orthoRhombic ){
257	>	if (integrableObject->isDirectional()) {
258	>	if (integrableObject->isLinear()) {
259	>	ndf_local += 2;
260	>	} else {
261	>	ndf_local += 3;
262	>	}
263	>	}
264	>
265	>	}//end for (integrableObject)
266	>	}// end for (mol)
267
268	<	if( orthoRhombic ) {
269	<	sprintf( painCave.errMsg,
196	<	"OOPSE is switching from the default Non-Orthorhombic\n"
197	<	"\tto the faster Orthorhombic periodic boundary computations.\n"
198	<	"\tThis is usually a good thing, but if you wan't the\n"
199	<	"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
200	<	"\tvariable ( currently set to %G ) smaller.\n",
201	<	orthoTolerance);
202	<	painCave.severity = OOPSE_INFO;
203	<	simError();
204	<	}
205	<	else {
206	<	sprintf( painCave.errMsg,
207	<	"OOPSE is switching from the faster Orthorhombic to the more\n"
208	<	"\tflexible Non-Orthorhombic periodic boundary computations.\n"
209	<	"\tThis is usually because the box has deformed under\n"
210	<	"\tNPTf integration. If you wan't to live on the edge with\n"
211	<	"\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
212	<	"\tvariable ( currently set to %G ) larger.\n",
213	<	orthoTolerance);
214	<	painCave.severity = OOPSE_WARNING;
215	<	simError();
216	<	}
217	<	}
218	<	}
268	>	// n_constraints is local, so subtract them on each processor
269	>	ndf_local -= nConstraints_;
270
271	<	void SimInfo::calcBoxL( void ){
271	>	#ifdef IS_MPI
272	>	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
273	>	#else
274	>	ndf_ = ndf_local;
275	>	#endif
276
277	<	double dx, dy, dz, dsq;
277	>	// nZconstraints_ is global, as are the 3 COM translations for the
278	>	// entire system:
279	>	ndf_ = ndf_ - 3 - nZconstraint_;
280
281	<	// boxVol = Determinant of Hmat
281	>	}
282
283	<	boxVol = matDet3( Hmat );
283	>	void SimInfo::calcNdfRaw() {
284	>	int ndfRaw_local;
285
286	<	// boxLx
287	<
288	<	dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
289	<	dsq = dx*dx + dy*dy + dz*dz;
232	<	boxL[0] = sqrt( dsq );
233	<	//maxCutoff = 0.5 * boxL[0];
286	>	MoleculeIterator i;
287	>	std::vector<StuntDouble*>::iterator j;
288	>	Molecule* mol;
289	>	StuntDouble* integrableObject;
290
291	<	// boxLy
292	<
293	<	dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
294	<	dsq = dx*dx + dy*dy + dz*dz;
295	<	boxL[1] = sqrt( dsq );
296	<	//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
291	>	// Raw degrees of freedom that we have to set
292	>	ndfRaw_local = 0;
293	>
294	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
295	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
296	>	integrableObject = mol->nextIntegrableObject(j)) {
297
298	+	ndfRaw_local += 3;
299
300	<	// boxLz
301	<
302	<	dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
303	<	dsq = dx*dx + dy*dy + dz*dz;
304	<	boxL[2] = sqrt( dsq );
305	<	//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
300	>	if (integrableObject->isDirectional()) {
301	>	if (integrableObject->isLinear()) {
302	>	ndfRaw_local += 2;
303	>	} else {
304	>	ndfRaw_local += 3;
305	>	}
306	>	}
307	>
308	>	}
309	>	}
310	>
311	>	#ifdef IS_MPI
312	>	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
313	>	#else
314	>	ndfRaw_ = ndfRaw_local;
315	>	#endif
316	>	}
317
318	<	//calculate the max cutoff
319	<	maxCutoff =  calcMaxCutOff();
252	<
253	<	checkCutOffs();
318	>	void SimInfo::calcNdfTrans() {
319	>	int ndfTrans_local;
320
321	<	}
321	>	ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
322
323
324	<	double SimInfo::calcMaxCutOff(){
324	>	#ifdef IS_MPI
325	>	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
326	>	#else
327	>	ndfTrans_ = ndfTrans_local;
328	>	#endif
329
330	<	double ri[3], rj[3], rk[3];
331	<	double rij[3], rjk[3], rki[3];
332	<	double minDist;
330	>	ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
331	>
332	>	}
333
334	<	ri[0] = Hmat[0][0];
335	<	ri[1] = Hmat[1][0];
336	<	ri[2] = Hmat[2][0];
337	<
338	<	rj[0] = Hmat[0][1];
339	<	rj[1] = Hmat[1][1];
340	<	rj[2] = Hmat[2][1];
341	<
342	<	rk[0] = Hmat[0][2];
343	<	rk[1] = Hmat[1][2];
344	<	rk[2] = Hmat[2][2];
334	>	void SimInfo::addExcludePairs(Molecule* mol) {
335	>	std::vector<Bond*>::iterator bondIter;
336	>	std::vector<Bend*>::iterator bendIter;
337	>	std::vector<Torsion*>::iterator torsionIter;
338	>	Bond* bond;
339	>	Bend* bend;
340	>	Torsion* torsion;
341	>	int a;
342	>	int b;
343	>	int c;
344	>	int d;
345
346	<	crossProduct3(ri, rj, rij);
347	<	distXY = dotProduct3(rk,rij) / norm3(rij);
346	>	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
347	>	a = bond->getAtomA()->getGlobalIndex();
348	>	b = bond->getAtomB()->getGlobalIndex();
349	>	exclude_.addPair(a, b);
350	>	}
351
352	<	crossProduct3(rj,rk, rjk);
353	<	distYZ = dotProduct3(ri,rjk) / norm3(rjk);
352	>	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
353	>	a = bend->getAtomA()->getGlobalIndex();
354	>	b = bend->getAtomB()->getGlobalIndex();
355	>	c = bend->getAtomC()->getGlobalIndex();
356
357	<	crossProduct3(rk,ri, rki);
358	<	distZX = dotProduct3(rj,rki) / norm3(rki);
357	>	exclude_.addPair(a, b);
358	>	exclude_.addPair(a, c);
359	>	exclude_.addPair(b, c);
360	>	}
361
362	<	minDist = min(min(distXY, distYZ), distZX);
363	<	return minDist/2;
364	<
365	<	}
362	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
363	>	a = torsion->getAtomA()->getGlobalIndex();
364	>	b = torsion->getAtomB()->getGlobalIndex();
365	>	c = torsion->getAtomC()->getGlobalIndex();
366	>	d = torsion->getAtomD()->getGlobalIndex();
367
368	<	void SimInfo::wrapVector( double thePos[3] ){
368	>	exclude_.addPair(a, b);
369	>	exclude_.addPair(a, c);
370	>	exclude_.addPair(a, d);
371	>	exclude_.addPair(b, c);
372	>	exclude_.addPair(b, d);
373	>	exclude_.addPair(c, d);
374	>	}
375
376	<	int i;
377	<	double scaled[3];
376	>	Molecule::RigidBodyIterator rbIter;
377	>	RigidBody* rb;
378	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
379	>	std::vector<Atom*> atoms = rb->getAtoms();
380	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
381	>	for (int j = i + 1; j < atoms.size(); ++j) {
382	>	a = atoms[i]->getGlobalIndex();
383	>	b = atoms[j]->getGlobalIndex();
384	>	exclude_.addPair(a, b);
385	>	}
386	>	}
387	>	}
388
389	<	if( !orthoRhombic ){
296	<	// calc the scaled coordinates.
297	<
389	>	}
390
391	<	matVecMul3(HmatInv, thePos, scaled);
391	>	void SimInfo::removeExcludePairs(Molecule* mol) {
392	>	std::vector<Bond*>::iterator bondIter;
393	>	std::vector<Bend*>::iterator bendIter;
394	>	std::vector<Torsion*>::iterator torsionIter;
395	>	Bond* bond;
396	>	Bend* bend;
397	>	Torsion* torsion;
398	>	int a;
399	>	int b;
400	>	int c;
401	>	int d;
402
403	<	for(i=0; i<3; i++)
404	<	scaled[i] -= roundMe(scaled[i]);
405	<
406	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
407	<
306	<	matVecMul3(Hmat, scaled, thePos);
403	>	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
404	>	a = bond->getAtomA()->getGlobalIndex();
405	>	b = bond->getAtomB()->getGlobalIndex();
406	>	exclude_.removePair(a, b);
407	>	}
408
409	<	}
410	<	else{
411	<	// calc the scaled coordinates.
412	<
312	<	for(i=0; i<3; i++)
313	<	scaled[i] = thePos[i]*HmatInv[i][i];
314	<
315	<	// wrap the scaled coordinates
316	<
317	<	for(i=0; i<3; i++)
318	<	scaled[i] -= roundMe(scaled[i]);
319	<
320	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
321	<
322	<	for(i=0; i<3; i++)
323	<	thePos[i] = scaled[i]*Hmat[i][i];
324	<	}
325	<
326	<	}
409	>	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
410	>	a = bend->getAtomA()->getGlobalIndex();
411	>	b = bend->getAtomB()->getGlobalIndex();
412	>	c = bend->getAtomC()->getGlobalIndex();
413
414	+	exclude_.removePair(a, b);
415	+	exclude_.removePair(a, c);
416	+	exclude_.removePair(b, c);
417	+	}
418
419	<	int SimInfo::getNDF(){
420	<	int ndf_local;
419	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
420	>	a = torsion->getAtomA()->getGlobalIndex();
421	>	b = torsion->getAtomB()->getGlobalIndex();
422	>	c = torsion->getAtomC()->getGlobalIndex();
423	>	d = torsion->getAtomD()->getGlobalIndex();
424
425	<	ndf_local = 0;
426	<
427	<	for(int i = 0; i < integrableObjects.size(); i++){
428	<	ndf_local += 3;
429	<	if (integrableObjects[i]->isDirectional()) {
430	<	if (integrableObjects[i]->isLinear())
338	<	ndf_local += 2;
339	<	else
340	<	ndf_local += 3;
425	>	exclude_.removePair(a, b);
426	>	exclude_.removePair(a, c);
427	>	exclude_.removePair(a, d);
428	>	exclude_.removePair(b, c);
429	>	exclude_.removePair(b, d);
430	>	exclude_.removePair(c, d);
431		}
432	+
433	+	Molecule::RigidBodyIterator rbIter;
434	+	RigidBody* rb;
435	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
436	+	std::vector<Atom*> atoms = rb->getAtoms();
437	+	for (int i = 0; i < atoms.size() -1 ; ++i) {
438	+	for (int j = i + 1; j < atoms.size(); ++j) {
439	+	a = atoms[i]->getGlobalIndex();
440	+	b = atoms[j]->getGlobalIndex();
441	+	exclude_.removePair(a, b);
442	+	}
443	+	}
444	+	}
445	+
446		}
447
344	–	// n_constraints is local, so subtract them on each processor:
448
449	<	ndf_local -= n_constraints;
449	>	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
450	>	int curStampId;
451
452	<	#ifdef IS_MPI
453	<	MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
350	<	#else
351	<	ndf = ndf_local;
352	<	#endif
452	>	//index from 0
453	>	curStampId = moleculeStamps_.size();
454
455	<	// nZconstraints is global, as are the 3 COM translations for the
456	<	// entire system:
455	>	moleculeStamps_.push_back(molStamp);
456	>	molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
457	>	}
458
459	<	ndf = ndf - 3 - nZconstraints;
459	>	void SimInfo::update() {
460
461	<	return ndf;
360	<	}
461	>	setupSimType();
462
463	<	int SimInfo::getNDFraw() {
464	<	int ndfRaw_local;
463	>	#ifdef IS_MPI
464	>	setupFortranParallel();
465	>	#endif
466
467	<	// Raw degrees of freedom that we have to set
366	<	ndfRaw_local = 0;
467	>	setupFortranSim();
468
469	<	for(int i = 0; i < integrableObjects.size(); i++){
470	<	ndfRaw_local += 3;
471	<	if (integrableObjects[i]->isDirectional()) {
472	<	if (integrableObjects[i]->isLinear())
473	<	ndfRaw_local += 2;
474	<	else
475	<	ndfRaw_local += 3;
469	>	//setup fortran force field
470	>	/** @deprecate */
471	>	int isError = 0;
472	>
473	>	setupElectrostaticSummationMethod( isError );
474	>
475	>	if(isError){
476	>	sprintf( painCave.errMsg,
477	>	"ForceField error: There was an error initializing the forceField in fortran.\n" );
478	>	painCave.isFatal = 1;
479	>	simError();
480		}
481	<	}
481	>
482
483	<	#ifdef IS_MPI
379	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
380	<	#else
381	<	ndfRaw = ndfRaw_local;
382	<	#endif
483	>	setupCutoff();
484
485	<	return ndfRaw;
486	<	}
485	>	calcNdf();
486	>	calcNdfRaw();
487	>	calcNdfTrans();
488
489	<	int SimInfo::getNDFtranslational() {
490	<	int ndfTrans_local;
489	>	fortranInitialized_ = true;
490	>	}
491
492	<	ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
492	>	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
493	>	SimInfo::MoleculeIterator mi;
494	>	Molecule* mol;
495	>	Molecule::AtomIterator ai;
496	>	Atom* atom;
497	>	std::set<AtomType*> atomTypes;
498
499	+	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
500
501	<	#ifdef IS_MPI
502	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
503	<	#else
504	<	ndfTrans = ndfTrans_local;
505	<	#endif
501	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
502	>	atomTypes.insert(atom->getAtomType());
503	>	}
504	>
505	>	}
506
507	<	ndfTrans = ndfTrans - 3 - nZconstraints;
507	>	return atomTypes;
508	>	}
509
510	<	return ndfTrans;
511	<	}
510	>	void SimInfo::setupSimType() {
511	>	std::set<AtomType*>::iterator i;
512	>	std::set<AtomType*> atomTypes;
513	>	atomTypes = getUniqueAtomTypes();
514	>
515	>	int useLennardJones = 0;
516	>	int useElectrostatic = 0;
517	>	int useEAM = 0;
518	>	int useCharge = 0;
519	>	int useDirectional = 0;
520	>	int useDipole = 0;
521	>	int useGayBerne = 0;
522	>	int useSticky = 0;
523	>	int useStickyPower = 0;
524	>	int useShape = 0;
525	>	int useFLARB = 0; //it is not in AtomType yet
526	>	int useDirectionalAtom = 0;
527	>	int useElectrostatics = 0;
528	>	//usePBC and useRF are from simParams
529	>	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
530	>	int useRF;
531	>	std::string myMethod;
532
533	<	int SimInfo::getTotIntegrableObjects() {
534	<	int nObjs_local;
406	<	int nObjs;
533	>	// set the useRF logical
534	>	useRF = 0;
535
408	–	nObjs_local =  integrableObjects.size();
536
537	+	if (simParams_->haveElectrostaticSummationMethod()) {
538	+	std::string myMethod = simParams_->getElectrostaticSummationMethod();
539	+	toUpper(myMethod);
540	+	if (myMethod == "REACTION_FIELD") {
541	+	useRF=1;
542	+	}
543	+	}
544
545	<	#ifdef IS_MPI
546	<	MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
547	<	#else
548	<	nObjs = nObjs_local;
549	<	#endif
545	>	//loop over all of the atom types
546	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
547	>	useLennardJones |= (*i)->isLennardJones();
548	>	useElectrostatic |= (*i)->isElectrostatic();
549	>	useEAM |= (*i)->isEAM();
550	>	useCharge |= (*i)->isCharge();
551	>	useDirectional |= (*i)->isDirectional();
552	>	useDipole |= (*i)->isDipole();
553	>	useGayBerne |= (*i)->isGayBerne();
554	>	useSticky |= (*i)->isSticky();
555	>	useStickyPower |= (*i)->isStickyPower();
556	>	useShape |= (*i)->isShape();
557	>	}
558
559	+	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
560	+	useDirectionalAtom = 1;
561	+	}
562
563	<	return nObjs;
564	<	}
563	>	if (useCharge || useDipole) {
564	>	useElectrostatics = 1;
565	>	}
566
567	<	void SimInfo::refreshSim(){
567	>	#ifdef IS_MPI
568	>	int temp;
569
570	<	simtype fInfo;
571	<	int isError;
425	<	int n_global;
426	<	int* excl;
570	>	temp = usePBC;
571	>	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
572
573	<	fInfo.dielect = 0.0;
573	>	temp = useDirectionalAtom;
574	>	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
575	>
576	>	temp = useLennardJones;
577	>	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
578	>
579	>	temp = useElectrostatics;
580	>	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
581
582	<	if( useDipoles ){
583	<	if( useReactionField )fInfo.dielect = dielectric;
432	<	}
582	>	temp = useCharge;
583	>	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
584
585	<	fInfo.SIM_uses_PBC = usePBC;
586	<	//fInfo.SIM_uses_LJ = 0;
436	<	fInfo.SIM_uses_LJ = useLJ;
437	<	fInfo.SIM_uses_sticky = useSticky;
438	<	//fInfo.SIM_uses_sticky = 0;
439	<	fInfo.SIM_uses_charges = useCharges;
440	<	fInfo.SIM_uses_dipoles = useDipoles;
441	<	//fInfo.SIM_uses_dipoles = 0;
442	<	fInfo.SIM_uses_RF = useReactionField;
443	<	//fInfo.SIM_uses_RF = 0;
444	<	fInfo.SIM_uses_GB = useGB;
445	<	fInfo.SIM_uses_EAM = useEAM;
585	>	temp = useDipole;
586	>	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
587
588	<	n_exclude = excludes->getSize();
589	<	excl = excludes->getFortranArray();
449	<
450	<	#ifdef IS_MPI
451	<	n_global = mpiSim->getNAtomsGlobal();
452	<	#else
453	<	n_global = n_atoms;
454	<	#endif
455	<
456	<	isError = 0;
457	<
458	<	getFortranGroupArrays(this, FglobalGroupMembership, mfact);
459	<	//it may not be a good idea to pass the address of first element in vector
460	<	//since c++ standard does not require vector to be stored continuously in meomory
461	<	//Most of the compilers will organize the memory of vector continuously
462	<	setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
463	<	&nGlobalExcludes, globalExcludes, molMembershipArray,
464	<	&mfact[0], &ngroup, &FglobalGroupMembership[0], &isError);
588	>	temp = useSticky;
589	>	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
590
591	<	if( isError ){
591	>	temp = useStickyPower;
592	>	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
593
594	<	sprintf( painCave.errMsg,
595	<	"There was an error setting the simulation information in fortran.\n" );
596	<	painCave.isFatal = 1;
597	<	painCave.severity = OOPSE_ERROR;
598	<	simError();
594	>	temp = useGayBerne;
595	>	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
596	>
597	>	temp = useEAM;
598	>	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
599	>
600	>	temp = useShape;
601	>	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
602	>
603	>	temp = useFLARB;
604	>	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
605	>
606	>	temp = useRF;
607	>	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
608	>
609	>	#endif
610	>
611	>	fInfo_.SIM_uses_PBC = usePBC;
612	>	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
613	>	fInfo_.SIM_uses_LennardJones = useLennardJones;
614	>	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
615	>	fInfo_.SIM_uses_Charges = useCharge;
616	>	fInfo_.SIM_uses_Dipoles = useDipole;
617	>	fInfo_.SIM_uses_Sticky = useSticky;
618	>	fInfo_.SIM_uses_StickyPower = useStickyPower;
619	>	fInfo_.SIM_uses_GayBerne = useGayBerne;
620	>	fInfo_.SIM_uses_EAM = useEAM;
621	>	fInfo_.SIM_uses_Shapes = useShape;
622	>	fInfo_.SIM_uses_FLARB = useFLARB;
623	>	fInfo_.SIM_uses_RF = useRF;
624	>
625	>	if( myMethod == "REACTION_FIELD") {
626	>
627	>	if (simParams_->haveDielectric()) {
628	>	fInfo_.dielect = simParams_->getDielectric();
629	>	} else {
630	>	sprintf(painCave.errMsg,
631	>	"SimSetup Error: No Dielectric constant was set.\n"
632	>	"\tYou are trying to use Reaction Field without"
633	>	"\tsetting a dielectric constant!\n");
634	>	painCave.isFatal = 1;
635	>	simError();
636	>	}
637	>	}
638		}
474	–
475	–	#ifdef IS_MPI
476	–	sprintf( checkPointMsg,
477	–	"succesfully sent the simulation information to fortran.\n");
478	–	MPIcheckPoint();
479	–	#endif // is_mpi
480	–
481	–	this->ndf = this->getNDF();
482	–	this->ndfRaw = this->getNDFraw();
483	–	this->ndfTrans = this->getNDFtranslational();
484	–	}
639
640	<	void SimInfo::setDefaultRcut( double theRcut ){
641	<
642	<	haveRcut = 1;
643	<	rCut = theRcut;
644	<	rList = rCut + 1.0;
645	<
646	<	notifyFortranCutOffs( &rCut, &rSw, &rList );
493	<	}
640	>	void SimInfo::setupFortranSim() {
641	>	int isError;
642	>	int nExclude;
643	>	std::vector<int> fortranGlobalGroupMembership;
644	>
645	>	nExclude = exclude_.getSize();
646	>	isError = 0;
647
648	<	void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
648	>	//globalGroupMembership_ is filled by SimCreator
649	>	for (int i = 0; i < nGlobalAtoms_; i++) {
650	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
651	>	}
652
653	<	rSw = theRsw;
654	<	setDefaultRcut( theRcut );
655	<	}
653	>	//calculate mass ratio of cutoff group
654	>	std::vector<double> mfact;
655	>	SimInfo::MoleculeIterator mi;
656	>	Molecule* mol;
657	>	Molecule::CutoffGroupIterator ci;
658	>	CutoffGroup* cg;
659	>	Molecule::AtomIterator ai;
660	>	Atom* atom;
661	>	double totalMass;
662
663	+	//to avoid memory reallocation, reserve enough space for mfact
664	+	mfact.reserve(getNCutoffGroups());
665	+
666	+	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
667	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
668
669	<	void SimInfo::checkCutOffs( void ){
670	<
671	<	if( boxIsInit ){
669	>	totalMass = cg->getMass();
670	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
671	>	// Check for massless groups - set mfact to 1 if true
672	>	if (totalMass != 0)
673	>	mfact.push_back(atom->getMass()/totalMass);
674	>	else
675	>	mfact.push_back( 1.0 );
676	>	}
677	>
678	>	}
679	>	}
680	>
681	>	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
682	>	std::vector<int> identArray;
683	>
684	>	//to avoid memory reallocation, reserve enough space identArray
685	>	identArray.reserve(getNAtoms());
686
687	<	//we need to check cutOffs against the box
687	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
688	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
689	>	identArray.push_back(atom->getIdent());
690	>	}
691	>	}
692	>
693	>	//fill molMembershipArray
694	>	//molMembershipArray is filled by SimCreator
695	>	std::vector<int> molMembershipArray(nGlobalAtoms_);
696	>	for (int i = 0; i < nGlobalAtoms_; i++) {
697	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
698	>	}
699
700	<	if( rCut > maxCutoff ){
700	>	//setup fortran simulation
701	>	int nGlobalExcludes = 0;
702	>	int* globalExcludes = NULL;
703	>	int* excludeList = exclude_.getExcludeList();
704	>	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
705	>	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
706	>	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
707	>
708	>	if( isError ){
709	>
710		sprintf( painCave.errMsg,
711	<	"cutoffRadius is too large for the current periodic box.\n"
511	<	"\tCurrent Value of cutoffRadius = %G at time %G\n "
512	<	"\tThis is larger than half of at least one of the\n"
513	<	"\tperiodic box vectors.  Right now, the Box matrix is:\n"
514	<	"\n"
515	<	"\t[ %G %G %G ]\n"
516	<	"\t[ %G %G %G ]\n"
517	<	"\t[ %G %G %G ]\n",
518	<	rCut, currentTime,
519	<	Hmat[0][0], Hmat[0][1], Hmat[0][2],
520	<	Hmat[1][0], Hmat[1][1], Hmat[1][2],
521	<	Hmat[2][0], Hmat[2][1], Hmat[2][2]);
522	<	painCave.severity = OOPSE_ERROR;
711	>	"There was an error setting the simulation information in fortran.\n" );
712		painCave.isFatal = 1;
713	+	painCave.severity = OOPSE_ERROR;
714		simError();
715	<	}
716	<	} else {
717	<	// initialize this stuff before using it, OK?
718	<	sprintf( painCave.errMsg,
719	<	"Trying to check cutoffs without a box.\n"
720	<	"\tOOPSE should have better programmers than that.\n" );
721	<	painCave.severity = OOPSE_ERROR;
532	<	painCave.isFatal = 1;
533	<	simError();
715	>	}
716	>
717	>	#ifdef IS_MPI
718	>	sprintf( checkPointMsg,
719	>	"succesfully sent the simulation information to fortran.\n");
720	>	MPIcheckPoint();
721	>	#endif // is_mpi
722		}
535	–
536	–	}
723
538	–	void SimInfo::addProperty(GenericData* prop){
724
725	<	map<string, GenericData*>::iterator result;
726	<	result = properties.find(prop->getID());
542	<
543	<	//we can't simply use  properties[prop->getID()] = prop,
544	<	//it will cause memory leak if we already contain a propery which has the same name of prop
545	<
546	<	if(result != properties.end()){
725	>	#ifdef IS_MPI
726	>	void SimInfo::setupFortranParallel() {
727
728	<	delete (*result).second;
729	<	(*result).second = prop;
730	<
731	<	}
732	<	else{
728	>	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
729	>	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
730	>	std::vector<int> localToGlobalCutoffGroupIndex;
731	>	SimInfo::MoleculeIterator mi;
732	>	Molecule::AtomIterator ai;
733	>	Molecule::CutoffGroupIterator ci;
734	>	Molecule* mol;
735	>	Atom* atom;
736	>	CutoffGroup* cg;
737	>	mpiSimData parallelData;
738	>	int isError;
739
740	<	properties[prop->getID()] = prop;
740	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
741
742	+	//local index(index in DataStorge) of atom is important
743	+	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
744	+	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
745	+	}
746	+
747	+	//local index of cutoff group is trivial, it only depends on the order of travesing
748	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
749	+	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
750	+	}
751	+
752	+	}
753	+
754	+	//fill up mpiSimData struct
755	+	parallelData.nMolGlobal = getNGlobalMolecules();
756	+	parallelData.nMolLocal = getNMolecules();
757	+	parallelData.nAtomsGlobal = getNGlobalAtoms();
758	+	parallelData.nAtomsLocal = getNAtoms();
759	+	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
760	+	parallelData.nGroupsLocal = getNCutoffGroups();
761	+	parallelData.myNode = worldRank;
762	+	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
763	+
764	+	//pass mpiSimData struct and index arrays to fortran
765	+	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
766	+	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
767	+	&localToGlobalCutoffGroupIndex[0], &isError);
768	+
769	+	if (isError) {
770	+	sprintf(painCave.errMsg,
771	+	"mpiRefresh errror: fortran didn't like something we gave it.\n");
772	+	painCave.isFatal = 1;
773	+	simError();
774	+	}
775	+
776	+	sprintf(checkPointMsg, " mpiRefresh successful.\n");
777	+	MPIcheckPoint();
778	+
779	+
780		}
557	–
558	–	}
781
782	<	GenericData* SimInfo::getProperty(const string& propName){
561	<
562	<	map<string, GenericData*>::iterator result;
563	<
564	<	//string lowerCaseName = ();
565	<
566	<	result = properties.find(propName);
567	<
568	<	if(result != properties.end())
569	<	return (*result).second;
570	<	else
571	<	return NULL;
572	<	}
782	>	#endif
783
784	+	double SimInfo::calcMaxCutoffRadius() {
785
575	–	void SimInfo::getFortranGroupArrays(SimInfo* info,
576	–	vector<int>& FglobalGroupMembership,
577	–	vector<double>& mfact){
578	–
579	–	Molecule* myMols;
580	–	Atom** myAtoms;
581	–	int numAtom;
582	–	double mtot;
583	–	int numMol;
584	–	int numCutoffGroups;
585	–	CutoffGroup* myCutoffGroup;
586	–	vector<CutoffGroup*>::iterator iterCutoff;
587	–	Atom* cutoffAtom;
588	–	vector<Atom*>::iterator iterAtom;
589	–	int atomIndex;
590	–	double totalMass;
591	–
592	–	mfact.clear();
593	–	FglobalGroupMembership.clear();
594	–
786
787	<	// Fix the silly fortran indexing problem
787	>	std::set<AtomType*> atomTypes;
788	>	std::set<AtomType*>::iterator i;
789	>	std::vector<double> cutoffRadius;
790	>
791	>	//get the unique atom types
792	>	atomTypes = getUniqueAtomTypes();
793	>
794	>	//query the max cutoff radius among these atom types
795	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
796	>	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
797	>	}
798	>
799	>	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
800		#ifdef IS_MPI
801	<	numAtom = mpiSim->getNAtomsGlobal();
599	<	#else
600	<	numAtom = n_atoms;
801	>	//pick the max cutoff radius among the processors
802		#endif
602	–	for (int i = 0; i < numAtom; i++)
603	–	FglobalGroupMembership.push_back(globalGroupMembership[i] + 1);
604	–
803
804	<	myMols = info->molecules;
805	<	numMol = info->n_mol;
608	<	for(int i  = 0; i < numMol; i++){
609	<	numCutoffGroups = myMols[i].getNCutoffGroups();
610	<	for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff);
611	<	myCutoffGroup != NULL;
612	<	myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
804	>	return maxCutoffRadius;
805	>	}
806
807	<	totalMass = myCutoffGroup->getMass();
808	<
809	<	for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom);
810	<	cutoffAtom != NULL;
811	<	cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
812	<	mfact.push_back(cutoffAtom->getMass()/totalMass);
813	<	}
807	>	void SimInfo::getCutoff(double& rcut, double& rsw) {
808	>
809	>	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
810	>
811	>	if (!simParams_->haveCutoffRadius()){
812	>	sprintf(painCave.errMsg,
813	>	"SimCreator Warning: No value was set for the cutoffRadius.\n"
814	>	"\tOOPSE will use a default value of 15.0 angstroms"
815	>	"\tfor the cutoffRadius.\n");
816	>	painCave.isFatal = 0;
817	>	simError();
818	>	rcut = 15.0;
819	>	} else{
820	>	rcut = simParams_->getCutoffRadius();
821	>	}
822	>
823	>	if (!simParams_->haveSwitchingRadius()){
824	>	sprintf(painCave.errMsg,
825	>	"SimCreator Warning: No value was set for switchingRadius.\n"
826	>	"\tOOPSE will use a default value of\n"
827	>	"\t0.85 * cutoffRadius for the switchingRadius\n");
828	>	painCave.isFatal = 0;
829	>	simError();
830	>	rsw = 0.85 * rcut;
831	>	} else{
832	>	rsw = simParams_->getSwitchingRadius();
833	>	}
834	>
835	>	} else {
836	>	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
837	>	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
838	>
839	>	if (simParams_->haveCutoffRadius()) {
840	>	rcut = simParams_->getCutoffRadius();
841	>	} else {
842	>	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
843	>	rcut = calcMaxCutoffRadius();
844	>	}
845	>
846	>	if (simParams_->haveSwitchingRadius()) {
847	>	rsw  = simParams_->getSwitchingRadius();
848	>	} else {
849	>	rsw = rcut;
850	>	}
851	>
852		}
853		}
854
855	<	}
855	>	void SimInfo::setupCutoff() {
856	>	getCutoff(rcut_, rsw_);
857	>	double rnblist = rcut_ + 1; // skin of neighbor list
858	>
859	>	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
860	>
861	>	int cp =  TRADITIONAL_CUTOFF_POLICY;
862	>	if (simParams_->haveCutoffPolicy()) {
863	>	std::string myPolicy = simParams_->getCutoffPolicy();
864	>	toUpper(myPolicy);
865	>	if (myPolicy == "MIX") {
866	>	cp = MIX_CUTOFF_POLICY;
867	>	} else {
868	>	if (myPolicy == "MAX") {
869	>	cp = MAX_CUTOFF_POLICY;
870	>	} else {
871	>	if (myPolicy == "TRADITIONAL") {
872	>	cp = TRADITIONAL_CUTOFF_POLICY;
873	>	} else {
874	>	// throw error
875	>	sprintf( painCave.errMsg,
876	>	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
877	>	painCave.isFatal = 1;
878	>	simError();
879	>	}
880	>	}
881	>	}
882	>	}
883	>
884	>
885	>	if (simParams_->haveSkinThickness()) {
886	>	double skinThickness = simParams_->getSkinThickness();
887	>	}
888	>
889	>	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
890	>	// also send cutoff notification to electrostatics
891	>	setElectrostaticCutoffRadius(&rcut_, &rsw_);
892	>	}
893	>
894	>	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
895	>
896	>	int errorOut;
897	>	int esm =  NONE;
898	>	double alphaVal;
899	>	double dielectric;
900	>
901	>	errorOut = isError;
902	>	alphaVal = simParams_->getDampingAlpha();
903	>	dielectric = simParams_->getDielectric();
904	>
905	>	if (simParams_->haveElectrostaticSummationMethod()) {
906	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
907	>	toUpper(myMethod);
908	>	if (myMethod == "NONE") {
909	>	esm = NONE;
910	>	} else {
911	>	if (myMethod == "UNDAMPED_WOLF") {
912	>	esm = UNDAMPED_WOLF;
913	>	} else {
914	>	if (myMethod == "DAMPED_WOLF") {
915	>	esm = DAMPED_WOLF;
916	>	if (!simParams_->haveDampingAlpha()) {
917	>	//throw error
918	>	sprintf( painCave.errMsg,
919	>	"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);
920	>	painCave.isFatal = 0;
921	>	simError();
922	>	}
923	>	} else {
924	>	if (myMethod == "REACTION_FIELD") {
925	>	esm = REACTION_FIELD;
926	>	} else {
927	>	// throw error
928	>	sprintf( painCave.errMsg,
929	>	"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() );
930	>	painCave.isFatal = 1;
931	>	simError();
932	>	}
933	>	}
934	>	}
935	>	}
936	>	}
937	>	// let's pass some summation method variables to fortran
938	>	setElectrostaticSummationMethod( &esm );
939	>	setDampedWolfAlpha( &alphaVal );
940	>	setReactionFieldDielectric( &dielectric );
941	>	initFortranFF( &esm, &errorOut );
942	>	}
943	>
944	>	void SimInfo::addProperty(GenericData* genData) {
945	>	properties_.addProperty(genData);
946	>	}
947	>
948	>	void SimInfo::removeProperty(const std::string& propName) {
949	>	properties_.removeProperty(propName);
950	>	}
951	>
952	>	void SimInfo::clearProperties() {
953	>	properties_.clearProperties();
954	>	}
955	>
956	>	std::vector<std::string> SimInfo::getPropertyNames() {
957	>	return properties_.getPropertyNames();
958	>	}
959	>
960	>	std::vector<GenericData*> SimInfo::getProperties() {
961	>	return properties_.getProperties();
962	>	}
963	>
964	>	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
965	>	return properties_.getPropertyByName(propName);
966	>	}
967	>
968	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
969	>	if (sman_ == sman) {
970	>	return;
971	>	}
972	>	delete sman_;
973	>	sman_ = sman;
974	>
975	>	Molecule* mol;
976	>	RigidBody* rb;
977	>	Atom* atom;
978	>	SimInfo::MoleculeIterator mi;
979	>	Molecule::RigidBodyIterator rbIter;
980	>	Molecule::AtomIterator atomIter;;
981	>
982	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
983	>
984	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
985	>	atom->setSnapshotManager(sman_);
986	>	}
987	>
988	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
989	>	rb->setSnapshotManager(sman_);
990	>	}
991	>	}
992	>
993	>	}
994	>
995	>	Vector3d SimInfo::getComVel(){
996	>	SimInfo::MoleculeIterator i;
997	>	Molecule* mol;
998	>
999	>	Vector3d comVel(0.0);
1000	>	double totalMass = 0.0;
1001	>
1002	>
1003	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1004	>	double mass = mol->getMass();
1005	>	totalMass += mass;
1006	>	comVel += mass * mol->getComVel();
1007	>	}
1008	>
1009	>	#ifdef IS_MPI
1010	>	double tmpMass = totalMass;
1011	>	Vector3d tmpComVel(comVel);
1012	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1013	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1014	>	#endif
1015	>
1016	>	comVel /= totalMass;
1017	>
1018	>	return comVel;
1019	>	}
1020	>
1021	>	Vector3d SimInfo::getCom(){
1022	>	SimInfo::MoleculeIterator i;
1023	>	Molecule* mol;
1024	>
1025	>	Vector3d com(0.0);
1026	>	double totalMass = 0.0;
1027	>
1028	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1029	>	double mass = mol->getMass();
1030	>	totalMass += mass;
1031	>	com += mass * mol->getCom();
1032	>	}
1033	>
1034	>	#ifdef IS_MPI
1035	>	double tmpMass = totalMass;
1036	>	Vector3d tmpCom(com);
1037	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1038	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1039	>	#endif
1040	>
1041	>	com /= totalMass;
1042	>
1043	>	return com;
1044	>
1045	>	}
1046	>
1047	>	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1048	>
1049	>	return o;
1050	>	}
1051	>
1052	>
1053	>	/*
1054	>	Returns center of mass and center of mass velocity in one function call.
1055	>	*/
1056	>
1057	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1058	>	SimInfo::MoleculeIterator i;
1059	>	Molecule* mol;
1060	>
1061	>
1062	>	double totalMass = 0.0;
1063	>
1064	>
1065	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1066	>	double mass = mol->getMass();
1067	>	totalMass += mass;
1068	>	com += mass * mol->getCom();
1069	>	comVel += mass * mol->getComVel();
1070	>	}
1071	>
1072	>	#ifdef IS_MPI
1073	>	double tmpMass = totalMass;
1074	>	Vector3d tmpCom(com);
1075	>	Vector3d tmpComVel(comVel);
1076	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1077	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1078	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1079	>	#endif
1080	>
1081	>	com /= totalMass;
1082	>	comVel /= totalMass;
1083	>	}
1084	>
1085	>	/*
1086	>	Return intertia tensor for entire system and angular momentum Vector.
1087	>
1088	>
1089	>	[  Ixx -Ixy  -Ixz ]
1090	>	J =| -Iyx  Iyy  -Iyz |
1091	>	[ -Izx -Iyz   Izz ]
1092	>	*/
1093	>
1094	>	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1095	>
1096	>
1097	>	double xx = 0.0;
1098	>	double yy = 0.0;
1099	>	double zz = 0.0;
1100	>	double xy = 0.0;
1101	>	double xz = 0.0;
1102	>	double yz = 0.0;
1103	>	Vector3d com(0.0);
1104	>	Vector3d comVel(0.0);
1105	>
1106	>	getComAll(com, comVel);
1107	>
1108	>	SimInfo::MoleculeIterator i;
1109	>	Molecule* mol;
1110	>
1111	>	Vector3d thisq(0.0);
1112	>	Vector3d thisv(0.0);
1113	>
1114	>	double thisMass = 0.0;
1115	>
1116	>
1117	>
1118	>
1119	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1120	>
1121	>	thisq = mol->getCom()-com;
1122	>	thisv = mol->getComVel()-comVel;
1123	>	thisMass = mol->getMass();
1124	>	// Compute moment of intertia coefficients.
1125	>	xx += thisq[0]*thisq[0]*thisMass;
1126	>	yy += thisq[1]*thisq[1]*thisMass;
1127	>	zz += thisq[2]*thisq[2]*thisMass;
1128	>
1129	>	// compute products of intertia
1130	>	xy += thisq[0]*thisq[1]*thisMass;
1131	>	xz += thisq[0]*thisq[2]*thisMass;
1132	>	yz += thisq[1]*thisq[2]*thisMass;
1133	>
1134	>	angularMomentum += cross( thisq, thisv ) * thisMass;
1135	>
1136	>	}
1137	>
1138	>
1139	>	inertiaTensor(0,0) = yy + zz;
1140	>	inertiaTensor(0,1) = -xy;
1141	>	inertiaTensor(0,2) = -xz;
1142	>	inertiaTensor(1,0) = -xy;
1143	>	inertiaTensor(1,1) = xx + zz;
1144	>	inertiaTensor(1,2) = -yz;
1145	>	inertiaTensor(2,0) = -xz;
1146	>	inertiaTensor(2,1) = -yz;
1147	>	inertiaTensor(2,2) = xx + yy;
1148	>
1149	>	#ifdef IS_MPI
1150	>	Mat3x3d tmpI(inertiaTensor);
1151	>	Vector3d tmpAngMom;
1152	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1153	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1154	>	#endif
1155	>
1156	>	return;
1157	>	}
1158	>
1159	>	//Returns the angular momentum of the system
1160	>	Vector3d SimInfo::getAngularMomentum(){
1161	>
1162	>	Vector3d com(0.0);
1163	>	Vector3d comVel(0.0);
1164	>	Vector3d angularMomentum(0.0);
1165	>
1166	>	getComAll(com,comVel);
1167	>
1168	>	SimInfo::MoleculeIterator i;
1169	>	Molecule* mol;
1170	>
1171	>	Vector3d thisr(0.0);
1172	>	Vector3d thisp(0.0);
1173	>
1174	>	double thisMass;
1175	>
1176	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1177	>	thisMass = mol->getMass();
1178	>	thisr = mol->getCom()-com;
1179	>	thisp = (mol->getComVel()-comVel)*thisMass;
1180	>
1181	>	angularMomentum += cross( thisr, thisp );
1182	>
1183	>	}
1184	>
1185	>	#ifdef IS_MPI
1186	>	Vector3d tmpAngMom;
1187	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1188	>	#endif
1189	>
1190	>	return angularMomentum;
1191	>	}
1192	>
1193	>
1194	>	}//end namespace oopse
1195	>

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