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Comparing trunk/OOPSE-2.0/src/brains/SimInfo.cpp (file contents):
Revision 1617 by chuckv, Wed Oct 20 20:46:20 2004 UTC vs.
Revision 2404 by chrisfen, Tue Nov 1 19:14:27 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;
60	<	useLJ = 0;
61	<	useSticky = 0;
62	<	useCharges = 0;
63	<	useDipoles = 0;
64	<	useReactionField = 0;
65	<	useGB = 0;
66	<	useEAM = 0;
67	<	useSolidThermInt = 0;
68	<	useLiquidThermInt = 0;
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;
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	>	nGlobalMols_ = molStampIds_.size();
144
145	<	}
145	>	#ifdef IS_MPI
146	>	molToProcMap_.resize(nGlobalMols_);
147	>	#endif
148
149	+	}
150
151	<	SimInfo::~SimInfo(){
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	<	delete myConfiguration;
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	<	map<string, GenericData*>::iterator i;
176	<
90	<	for(i = properties.begin(); i != properties.end(); i++)
91	<	delete (*i).second;
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::setBox(double newBox[3]) {
182	<
183	<	int i, j;
184	<	double tempMat[3][3];
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	<	for(i=0; i<3; i++)
193	<	for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
194	<
195	<	tempMat[0][0] = newBox[0];
196	<	tempMat[1][1] = newBox[1];
105	<	tempMat[2][2] = newBox[2];
106	<
107	<	setBoxM( tempMat );
108	<
109	<	}
110	<
111	<	void SimInfo::setBoxM( double theBox[3][3] ){
112	<
113	<	int i, j;
114	<	double FortranHmat[9]; // to preserve compatibility with Fortran the
115	<	// ordering in the array is as follows:
116	<	// [ 0 3 6 ]
117	<	// [ 1 4 7 ]
118	<	// [ 2 5 8 ]
119	<	double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
120	<
121	<	if( !boxIsInit ) boxIsInit = 1;
122	<
123	<	for(i=0; i < 3; i++)
124	<	for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
125	<
126	<	calcBoxL();
127	<	calcHmatInv();
128	<
129	<	for(i=0; i < 3; i++) {
130	<	for (j=0; j < 3; j++) {
131	<	FortranHmat[3*j + i] = Hmat[i][j];
132	<	FortranHmatInv[3*j + i] = HmatInv[i][j];
192	>	addExcludePairs(mol);
193	>
194	>	return true;
195	>	} else {
196	>	return false;
197		}
198		}
199
200	<	setFortranBox(FortranHmat, FortranHmatInv, &orthoRhombic);
201	<
202	<	}
139	<
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
153	–	// cerr << "Scaling box by " << scale << "\n";
227
228	<	for(i=0; i<3; i++)
156	<	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
162	–	void SimInfo::calcHmatInv( void ) {
163	–
164	–	int oldOrtho;
165	–	int i,j;
166	–	double smallDiag;
167	–	double tol;
168	–	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]);
177	<	if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
178	<	if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
179	<	tol = smallDiag * orthoTolerance;
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	<	}
191	<	}
192	<
193	<	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,
197	<	"OOPSE is switching from the default Non-Orthorhombic\n"
198	<	"\tto the faster Orthorhombic periodic boundary computations.\n"
199	<	"\tThis is usually a good thing, but if you wan't the\n"
200	<	"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
201	<	"\tvariable ( currently set to %G ) smaller.\n",
202	<	orthoTolerance);
203	<	painCave.severity = OOPSE_INFO;
204	<	simError();
205	<	}
206	<	else {
207	<	sprintf( painCave.errMsg,
208	<	"OOPSE is switching from the faster Orthorhombic to the more\n"
209	<	"\tflexible Non-Orthorhombic periodic boundary computations.\n"
210	<	"\tThis is usually because the box has deformed under\n"
211	<	"\tNPTf integration. If you wan't to live on the edge with\n"
212	<	"\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
213	<	"\tvariable ( currently set to %G ) larger.\n",
214	<	orthoTolerance);
215	<	painCave.severity = OOPSE_WARNING;
216	<	simError();
217	<	}
218	<	}
219	<	}
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;
233	<	boxL[0] = sqrt( dsq );
234	<	//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();
253	<
254	<	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 ){
297	<	// calc the scaled coordinates.
298	<
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	<
307	<	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	<
313	<	for(i=0; i<3; i++)
314	<	scaled[i] = thePos[i]*HmatInv[i][i];
315	<
316	<	// wrap the scaled coordinates
317	<
318	<	for(i=0; i<3; i++)
319	<	scaled[i] -= roundMe(scaled[i]);
320	<
321	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
322	<
323	<	for(i=0; i<3; i++)
324	<	thePos[i] = scaled[i]*Hmat[i][i];
325	<	}
326	<
327	<	}
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())
339	<	ndf_local += 2;
340	<	else
341	<	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
345	–	// 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);
351	<	#else
352	<	ndf = ndf_local;
353	<	#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;
361	<	}
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
367	<	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
380	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
381	<	#else
382	<	ndfRaw = ndfRaw_local;
383	<	#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	>	int useDW;
532	>	std::string myMethod;
533
534	<	int SimInfo::getTotIntegrableObjects() {
535	<	int nObjs_local;
536	<	int nObjs;
534	>	// set the useRF logical
535	>	useRF = 0;
536	>	useDW = 0;
537
409	–	nObjs_local =  integrableObjects.size();
538
539	+	if (simParams_->haveElectrostaticSummationMethod()) {
540	+	std::string myMethod = simParams_->getElectrostaticSummationMethod();
541	+	toUpper(myMethod);
542	+	if (myMethod == "REACTION_FIELD") {
543	+	useRF=1;
544	+	} else {
545	+	if (myMethod == "DAMPED_WOLF") {
546	+	useDW = 1;
547	+	}
548	+	}
549	+	}
550
551	<	#ifdef IS_MPI
552	<	MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
553	<	#else
554	<	nObjs = nObjs_local;
555	<	#endif
551	>	//loop over all of the atom types
552	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
553	>	useLennardJones |= (*i)->isLennardJones();
554	>	useElectrostatic |= (*i)->isElectrostatic();
555	>	useEAM |= (*i)->isEAM();
556	>	useCharge |= (*i)->isCharge();
557	>	useDirectional |= (*i)->isDirectional();
558	>	useDipole |= (*i)->isDipole();
559	>	useGayBerne |= (*i)->isGayBerne();
560	>	useSticky |= (*i)->isSticky();
561	>	useStickyPower |= (*i)->isStickyPower();
562	>	useShape |= (*i)->isShape();
563	>	}
564
565	+	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
566	+	useDirectionalAtom = 1;
567	+	}
568
569	<	return nObjs;
570	<	}
569	>	if (useCharge || useDipole) {
570	>	useElectrostatics = 1;
571	>	}
572
573	<	void SimInfo::refreshSim(){
573	>	#ifdef IS_MPI
574	>	int temp;
575
576	<	simtype fInfo;
577	<	int isError;
426	<	int n_global;
427	<	int* excl;
576	>	temp = usePBC;
577	>	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
578
579	<	fInfo.dielect = 0.0;
579	>	temp = useDirectionalAtom;
580	>	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
581
582	<	if( useDipoles ){
583	<	if( useReactionField )fInfo.dielect = dielectric;
584	<	}
582	>	temp = useLennardJones;
583	>	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
584	>
585	>	temp = useElectrostatics;
586	>	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
587	>
588	>	temp = useCharge;
589	>	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
590
591	<	fInfo.SIM_uses_PBC = usePBC;
592	<	//fInfo.SIM_uses_LJ = 0;
437	<	fInfo.SIM_uses_LJ = useLJ;
438	<	fInfo.SIM_uses_sticky = useSticky;
439	<	//fInfo.SIM_uses_sticky = 0;
440	<	fInfo.SIM_uses_charges = useCharges;
441	<	fInfo.SIM_uses_dipoles = useDipoles;
442	<	//fInfo.SIM_uses_dipoles = 0;
443	<	fInfo.SIM_uses_RF = useReactionField;
444	<	//fInfo.SIM_uses_RF = 0;
445	<	fInfo.SIM_uses_GB = useGB;
446	<	fInfo.SIM_uses_EAM = useEAM;
591	>	temp = useDipole;
592	>	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
593
594	<	n_exclude = excludes->getSize();
595	<	excl = excludes->getFortranArray();
450	<
451	<	#ifdef IS_MPI
452	<	n_global = mpiSim->getNAtomsGlobal();
453	<	#else
454	<	n_global = n_atoms;
455	<	#endif
456	<
457	<	isError = 0;
458	<
459	<	getFortranGroupArrays(this, FglobalGroupMembership, mfact);
460	<	//it may not be a good idea to pass the address of first element in vector
461	<	//since c++ standard does not require vector to be stored continuously in meomory
462	<	//Most of the compilers will organize the memory of vector continuously
463	<	setFortranSim( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
464	<	&nGlobalExcludes, globalExcludes, molMembershipArray,
465	<	&mfact[0], &ngroup, &FglobalGroupMembership[0], &isError);
594	>	temp = useSticky;
595	>	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
596
597	<	if( isError ){
597	>	temp = useStickyPower;
598	>	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
599
600	<	sprintf( painCave.errMsg,
601	<	"There was an error setting the simulation information in fortran.\n" );
602	<	painCave.isFatal = 1;
603	<	painCave.severity = OOPSE_ERROR;
604	<	simError();
600	>	temp = useGayBerne;
601	>	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
602	>
603	>	temp = useEAM;
604	>	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
605	>
606	>	temp = useShape;
607	>	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
608	>
609	>	temp = useFLARB;
610	>	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
611	>
612	>	temp = useRF;
613	>	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
614	>
615	>	temp = useDW;
616	>	MPI_Allreduce(&temp, &useDW, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
617	>
618	>	#endif
619	>
620	>	fInfo_.SIM_uses_PBC = usePBC;
621	>	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
622	>	fInfo_.SIM_uses_LennardJones = useLennardJones;
623	>	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
624	>	fInfo_.SIM_uses_Charges = useCharge;
625	>	fInfo_.SIM_uses_Dipoles = useDipole;
626	>	fInfo_.SIM_uses_Sticky = useSticky;
627	>	fInfo_.SIM_uses_StickyPower = useStickyPower;
628	>	fInfo_.SIM_uses_GayBerne = useGayBerne;
629	>	fInfo_.SIM_uses_EAM = useEAM;
630	>	fInfo_.SIM_uses_Shapes = useShape;
631	>	fInfo_.SIM_uses_FLARB = useFLARB;
632	>	fInfo_.SIM_uses_RF = useRF;
633	>	fInfo_.SIM_uses_DampedWolf = useDW;
634	>
635	>	if( myMethod == "REACTION_FIELD") {
636	>
637	>	if (simParams_->haveDielectric()) {
638	>	fInfo_.dielect = simParams_->getDielectric();
639	>	} else {
640	>	sprintf(painCave.errMsg,
641	>	"SimSetup Error: No Dielectric constant was set.\n"
642	>	"\tYou are trying to use Reaction Field without"
643	>	"\tsetting a dielectric constant!\n");
644	>	painCave.isFatal = 1;
645	>	simError();
646	>	}
647	>	}
648	>
649		}
475	–
476	–	#ifdef IS_MPI
477	–	sprintf( checkPointMsg,
478	–	"succesfully sent the simulation information to fortran.\n");
479	–	MPIcheckPoint();
480	–	#endif // is_mpi
481	–
482	–	this->ndf = this->getNDF();
483	–	this->ndfRaw = this->getNDFraw();
484	–	this->ndfTrans = this->getNDFtranslational();
485	–	}
650
651	<	void SimInfo::setDefaultRcut( double theRcut ){
652	<
653	<	haveRcut = 1;
654	<	rCut = theRcut;
655	<	rList = rCut + 1.0;
656	<
657	<	notifyFortranCutoffs( &rCut, &rSw, &rList );
494	<	}
651	>	void SimInfo::setupFortranSim() {
652	>	int isError;
653	>	int nExclude;
654	>	std::vector<int> fortranGlobalGroupMembership;
655	>
656	>	nExclude = exclude_.getSize();
657	>	isError = 0;
658
659	<	void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
659	>	//globalGroupMembership_ is filled by SimCreator
660	>	for (int i = 0; i < nGlobalAtoms_; i++) {
661	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
662	>	}
663
664	<	rSw = theRsw;
665	<	setDefaultRcut( theRcut );
666	<	}
664	>	//calculate mass ratio of cutoff group
665	>	std::vector<double> mfact;
666	>	SimInfo::MoleculeIterator mi;
667	>	Molecule* mol;
668	>	Molecule::CutoffGroupIterator ci;
669	>	CutoffGroup* cg;
670	>	Molecule::AtomIterator ai;
671	>	Atom* atom;
672	>	double totalMass;
673
674	+	//to avoid memory reallocation, reserve enough space for mfact
675	+	mfact.reserve(getNCutoffGroups());
676	+
677	+	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
678	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
679
680	<	void SimInfo::checkCutOffs( void ){
681	<
682	<	if( boxIsInit ){
680	>	totalMass = cg->getMass();
681	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
682	>	// Check for massless groups - set mfact to 1 if true
683	>	if (totalMass != 0)
684	>	mfact.push_back(atom->getMass()/totalMass);
685	>	else
686	>	mfact.push_back( 1.0 );
687	>	}
688	>
689	>	}
690	>	}
691	>
692	>	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
693	>	std::vector<int> identArray;
694	>
695	>	//to avoid memory reallocation, reserve enough space identArray
696	>	identArray.reserve(getNAtoms());
697
698	<	//we need to check cutOffs against the box
698	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
699	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
700	>	identArray.push_back(atom->getIdent());
701	>	}
702	>	}
703	>
704	>	//fill molMembershipArray
705	>	//molMembershipArray is filled by SimCreator
706	>	std::vector<int> molMembershipArray(nGlobalAtoms_);
707	>	for (int i = 0; i < nGlobalAtoms_; i++) {
708	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
709	>	}
710
711	<	if( rCut > maxCutoff ){
711	>	//setup fortran simulation
712	>	int nGlobalExcludes = 0;
713	>	int* globalExcludes = NULL;
714	>	int* excludeList = exclude_.getExcludeList();
715	>	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
716	>	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
717	>	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
718	>
719	>	if( isError ){
720	>
721		sprintf( painCave.errMsg,
722	<	"cutoffRadius is too large for the current periodic box.\n"
512	<	"\tCurrent Value of cutoffRadius = %G at time %G\n "
513	<	"\tThis is larger than half of at least one of the\n"
514	<	"\tperiodic box vectors.  Right now, the Box matrix is:\n"
515	<	"\n"
516	<	"\t[ %G %G %G ]\n"
517	<	"\t[ %G %G %G ]\n"
518	<	"\t[ %G %G %G ]\n",
519	<	rCut, currentTime,
520	<	Hmat[0][0], Hmat[0][1], Hmat[0][2],
521	<	Hmat[1][0], Hmat[1][1], Hmat[1][2],
522	<	Hmat[2][0], Hmat[2][1], Hmat[2][2]);
523	<	painCave.severity = OOPSE_ERROR;
722	>	"There was an error setting the simulation information in fortran.\n" );
723		painCave.isFatal = 1;
724	+	painCave.severity = OOPSE_ERROR;
725		simError();
726	<	}
727	<	} else {
728	<	// initialize this stuff before using it, OK?
729	<	sprintf( painCave.errMsg,
730	<	"Trying to check cutoffs without a box.\n"
731	<	"\tOOPSE should have better programmers than that.\n" );
732	<	painCave.severity = OOPSE_ERROR;
533	<	painCave.isFatal = 1;
534	<	simError();
726	>	}
727	>
728	>	#ifdef IS_MPI
729	>	sprintf( checkPointMsg,
730	>	"succesfully sent the simulation information to fortran.\n");
731	>	MPIcheckPoint();
732	>	#endif // is_mpi
733		}
536	–
537	–	}
734
539	–	void SimInfo::addProperty(GenericData* prop){
735
736	<	map<string, GenericData*>::iterator result;
737	<	result = properties.find(prop->getID());
543	<
544	<	//we can't simply use  properties[prop->getID()] = prop,
545	<	//it will cause memory leak if we already contain a propery which has the same name of prop
546	<
547	<	if(result != properties.end()){
736	>	#ifdef IS_MPI
737	>	void SimInfo::setupFortranParallel() {
738
739	<	delete (*result).second;
740	<	(*result).second = prop;
741	<
742	<	}
743	<	else{
739	>	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
740	>	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
741	>	std::vector<int> localToGlobalCutoffGroupIndex;
742	>	SimInfo::MoleculeIterator mi;
743	>	Molecule::AtomIterator ai;
744	>	Molecule::CutoffGroupIterator ci;
745	>	Molecule* mol;
746	>	Atom* atom;
747	>	CutoffGroup* cg;
748	>	mpiSimData parallelData;
749	>	int isError;
750
751	<	properties[prop->getID()] = prop;
751	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
752
753	+	//local index(index in DataStorge) of atom is important
754	+	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
755	+	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
756	+	}
757	+
758	+	//local index of cutoff group is trivial, it only depends on the order of travesing
759	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
760	+	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
761	+	}
762	+
763	+	}
764	+
765	+	//fill up mpiSimData struct
766	+	parallelData.nMolGlobal = getNGlobalMolecules();
767	+	parallelData.nMolLocal = getNMolecules();
768	+	parallelData.nAtomsGlobal = getNGlobalAtoms();
769	+	parallelData.nAtomsLocal = getNAtoms();
770	+	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
771	+	parallelData.nGroupsLocal = getNCutoffGroups();
772	+	parallelData.myNode = worldRank;
773	+	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
774	+
775	+	//pass mpiSimData struct and index arrays to fortran
776	+	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
777	+	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
778	+	&localToGlobalCutoffGroupIndex[0], &isError);
779	+
780	+	if (isError) {
781	+	sprintf(painCave.errMsg,
782	+	"mpiRefresh errror: fortran didn't like something we gave it.\n");
783	+	painCave.isFatal = 1;
784	+	simError();
785	+	}
786	+
787	+	sprintf(checkPointMsg, " mpiRefresh successful.\n");
788	+	MPIcheckPoint();
789	+
790	+
791		}
558	–
559	–	}
792
793	<	GenericData* SimInfo::getProperty(const string& propName){
562	<
563	<	map<string, GenericData*>::iterator result;
564	<
565	<	//string lowerCaseName = ();
566	<
567	<	result = properties.find(propName);
568	<
569	<	if(result != properties.end())
570	<	return (*result).second;
571	<	else
572	<	return NULL;
573	<	}
793	>	#endif
794
795	+	double SimInfo::calcMaxCutoffRadius() {
796
576	–	void SimInfo::getFortranGroupArrays(SimInfo* info,
577	–	vector<int>& FglobalGroupMembership,
578	–	vector<double>& mfact){
579	–
580	–	Molecule* myMols;
581	–	Atom** myAtoms;
582	–	int numAtom;
583	–	double mtot;
584	–	int numMol;
585	–	int numCutoffGroups;
586	–	CutoffGroup* myCutoffGroup;
587	–	vector<CutoffGroup*>::iterator iterCutoff;
588	–	Atom* cutoffAtom;
589	–	vector<Atom*>::iterator iterAtom;
590	–	int atomIndex;
591	–	double totalMass;
592	–
593	–	mfact.clear();
594	–	FglobalGroupMembership.clear();
595	–
797
798	<	// Fix the silly fortran indexing problem
798	>	std::set<AtomType*> atomTypes;
799	>	std::set<AtomType*>::iterator i;
800	>	std::vector<double> cutoffRadius;
801	>
802	>	//get the unique atom types
803	>	atomTypes = getUniqueAtomTypes();
804	>
805	>	//query the max cutoff radius among these atom types
806	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
807	>	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
808	>	}
809	>
810	>	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
811		#ifdef IS_MPI
812	<	numAtom = mpiSim->getNAtomsGlobal();
600	<	#else
601	<	numAtom = n_atoms;
812	>	//pick the max cutoff radius among the processors
813		#endif
603	–	for (int i = 0; i < numAtom; i++)
604	–	FglobalGroupMembership.push_back(globalGroupMembership[i] + 1);
605	–
814
815	<	myMols = info->molecules;
816	<	numMol = info->n_mol;
609	<	for(int i  = 0; i < numMol; i++){
610	<	numCutoffGroups = myMols[i].getNCutoffGroups();
611	<	for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff);
612	<	myCutoffGroup != NULL;
613	<	myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
815	>	return maxCutoffRadius;
816	>	}
817
818	<	totalMass = myCutoffGroup->getMass();
819	<
820	<	for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom);
821	<	cutoffAtom != NULL;
822	<	cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
823	<	mfact.push_back(cutoffAtom->getMass()/totalMass);
824	<	}
818	>	void SimInfo::getCutoff(double& rcut, double& rsw) {
819	>
820	>	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
821	>
822	>	if (!simParams_->haveCutoffRadius()){
823	>	sprintf(painCave.errMsg,
824	>	"SimCreator Warning: No value was set for the cutoffRadius.\n"
825	>	"\tOOPSE will use a default value of 15.0 angstroms"
826	>	"\tfor the cutoffRadius.\n");
827	>	painCave.isFatal = 0;
828	>	simError();
829	>	rcut = 15.0;
830	>	} else{
831	>	rcut = simParams_->getCutoffRadius();
832	>	}
833	>
834	>	if (!simParams_->haveSwitchingRadius()){
835	>	sprintf(painCave.errMsg,
836	>	"SimCreator Warning: No value was set for switchingRadius.\n"
837	>	"\tOOPSE will use a default value of\n"
838	>	"\t0.85 * cutoffRadius for the switchingRadius\n");
839	>	painCave.isFatal = 0;
840	>	simError();
841	>	rsw = 0.85 * rcut;
842	>	} else{
843	>	rsw = simParams_->getSwitchingRadius();
844	>	}
845	>
846	>	} else {
847	>	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
848	>	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
849	>
850	>	if (simParams_->haveCutoffRadius()) {
851	>	rcut = simParams_->getCutoffRadius();
852	>	} else {
853	>	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
854	>	rcut = calcMaxCutoffRadius();
855	>	}
856	>
857	>	if (simParams_->haveSwitchingRadius()) {
858	>	rsw  = simParams_->getSwitchingRadius();
859	>	} else {
860	>	rsw = rcut;
861	>	}
862	>
863		}
864		}
865
866	<	}
866	>	void SimInfo::setupCutoff() {
867	>	getCutoff(rcut_, rsw_);
868	>	double rnblist = rcut_ + 1; // skin of neighbor list
869	>
870	>	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
871	>
872	>	int cp =  TRADITIONAL_CUTOFF_POLICY;
873	>	if (simParams_->haveCutoffPolicy()) {
874	>	std::string myPolicy = simParams_->getCutoffPolicy();
875	>	toUpper(myPolicy);
876	>	if (myPolicy == "MIX") {
877	>	cp = MIX_CUTOFF_POLICY;
878	>	} else {
879	>	if (myPolicy == "MAX") {
880	>	cp = MAX_CUTOFF_POLICY;
881	>	} else {
882	>	if (myPolicy == "TRADITIONAL") {
883	>	cp = TRADITIONAL_CUTOFF_POLICY;
884	>	} else {
885	>	// throw error
886	>	sprintf( painCave.errMsg,
887	>	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
888	>	painCave.isFatal = 1;
889	>	simError();
890	>	}
891	>	}
892	>	}
893	>	}
894	>
895	>
896	>	if (simParams_->haveSkinThickness()) {
897	>	double skinThickness = simParams_->getSkinThickness();
898	>	}
899	>
900	>	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
901	>	// also send cutoff notification to electrostatics
902	>	setElectrostaticCutoffRadius(&rcut_, &rsw_);
903	>	}
904	>
905	>	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
906	>
907	>	int errorOut;
908	>	int esm =  NONE;
909	>	double alphaVal;
910	>	double dielectric;
911	>
912	>	errorOut = isError;
913	>	alphaVal = simParams_->getDampingAlpha();
914	>	dielectric = simParams_->getDielectric();
915	>
916	>	if (simParams_->haveElectrostaticSummationMethod()) {
917	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
918	>	toUpper(myMethod);
919	>	if (myMethod == "NONE") {
920	>	esm = NONE;
921	>	} else {
922	>	if (myMethod == "UNDAMPED_WOLF") {
923	>	esm = UNDAMPED_WOLF;
924	>	} else {
925	>	if (myMethod == "DAMPED_WOLF") {
926	>	esm = DAMPED_WOLF;
927	>	if (!simParams_->haveDampingAlpha()) {
928	>	//throw error
929	>	sprintf( painCave.errMsg,
930	>	"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);
931	>	painCave.isFatal = 0;
932	>	simError();
933	>	}
934	>	} else {
935	>	if (myMethod == "REACTION_FIELD") {
936	>	esm = REACTION_FIELD;
937	>	} else {
938	>	// throw error
939	>	sprintf( painCave.errMsg,
940	>	"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() );
941	>	painCave.isFatal = 1;
942	>	simError();
943	>	}
944	>	}
945	>	}
946	>	}
947	>	}
948	>	// let's pass some summation method variables to fortran
949	>	setElectrostaticSummationMethod( &esm );
950	>	setDampedWolfAlpha( &alphaVal );
951	>	setReactionFieldDielectric( &dielectric );
952	>	initFortranFF( &esm, &errorOut );
953	>	}
954	>
955	>	void SimInfo::addProperty(GenericData* genData) {
956	>	properties_.addProperty(genData);
957	>	}
958	>
959	>	void SimInfo::removeProperty(const std::string& propName) {
960	>	properties_.removeProperty(propName);
961	>	}
962	>
963	>	void SimInfo::clearProperties() {
964	>	properties_.clearProperties();
965	>	}
966	>
967	>	std::vector<std::string> SimInfo::getPropertyNames() {
968	>	return properties_.getPropertyNames();
969	>	}
970	>
971	>	std::vector<GenericData*> SimInfo::getProperties() {
972	>	return properties_.getProperties();
973	>	}
974	>
975	>	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
976	>	return properties_.getPropertyByName(propName);
977	>	}
978	>
979	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
980	>	if (sman_ == sman) {
981	>	return;
982	>	}
983	>	delete sman_;
984	>	sman_ = sman;
985	>
986	>	Molecule* mol;
987	>	RigidBody* rb;
988	>	Atom* atom;
989	>	SimInfo::MoleculeIterator mi;
990	>	Molecule::RigidBodyIterator rbIter;
991	>	Molecule::AtomIterator atomIter;;
992	>
993	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
994	>
995	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
996	>	atom->setSnapshotManager(sman_);
997	>	}
998	>
999	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1000	>	rb->setSnapshotManager(sman_);
1001	>	}
1002	>	}
1003	>
1004	>	}
1005	>
1006	>	Vector3d SimInfo::getComVel(){
1007	>	SimInfo::MoleculeIterator i;
1008	>	Molecule* mol;
1009	>
1010	>	Vector3d comVel(0.0);
1011	>	double totalMass = 0.0;
1012	>
1013	>
1014	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1015	>	double mass = mol->getMass();
1016	>	totalMass += mass;
1017	>	comVel += mass * mol->getComVel();
1018	>	}
1019	>
1020	>	#ifdef IS_MPI
1021	>	double tmpMass = totalMass;
1022	>	Vector3d tmpComVel(comVel);
1023	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1024	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1025	>	#endif
1026	>
1027	>	comVel /= totalMass;
1028	>
1029	>	return comVel;
1030	>	}
1031	>
1032	>	Vector3d SimInfo::getCom(){
1033	>	SimInfo::MoleculeIterator i;
1034	>	Molecule* mol;
1035	>
1036	>	Vector3d com(0.0);
1037	>	double totalMass = 0.0;
1038	>
1039	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1040	>	double mass = mol->getMass();
1041	>	totalMass += mass;
1042	>	com += mass * mol->getCom();
1043	>	}
1044	>
1045	>	#ifdef IS_MPI
1046	>	double tmpMass = totalMass;
1047	>	Vector3d tmpCom(com);
1048	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1049	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1050	>	#endif
1051	>
1052	>	com /= totalMass;
1053	>
1054	>	return com;
1055	>
1056	>	}
1057	>
1058	>	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1059	>
1060	>	return o;
1061	>	}
1062	>
1063	>
1064	>	/*
1065	>	Returns center of mass and center of mass velocity in one function call.
1066	>	*/
1067	>
1068	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1069	>	SimInfo::MoleculeIterator i;
1070	>	Molecule* mol;
1071	>
1072	>
1073	>	double totalMass = 0.0;
1074	>
1075	>
1076	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1077	>	double mass = mol->getMass();
1078	>	totalMass += mass;
1079	>	com += mass * mol->getCom();
1080	>	comVel += mass * mol->getComVel();
1081	>	}
1082	>
1083	>	#ifdef IS_MPI
1084	>	double tmpMass = totalMass;
1085	>	Vector3d tmpCom(com);
1086	>	Vector3d tmpComVel(comVel);
1087	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1088	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1089	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1090	>	#endif
1091	>
1092	>	com /= totalMass;
1093	>	comVel /= totalMass;
1094	>	}
1095	>
1096	>	/*
1097	>	Return intertia tensor for entire system and angular momentum Vector.
1098	>
1099	>
1100	>	[  Ixx -Ixy  -Ixz ]
1101	>	J =| -Iyx  Iyy  -Iyz |
1102	>	[ -Izx -Iyz   Izz ]
1103	>	*/
1104	>
1105	>	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1106	>
1107	>
1108	>	double xx = 0.0;
1109	>	double yy = 0.0;
1110	>	double zz = 0.0;
1111	>	double xy = 0.0;
1112	>	double xz = 0.0;
1113	>	double yz = 0.0;
1114	>	Vector3d com(0.0);
1115	>	Vector3d comVel(0.0);
1116	>
1117	>	getComAll(com, comVel);
1118	>
1119	>	SimInfo::MoleculeIterator i;
1120	>	Molecule* mol;
1121	>
1122	>	Vector3d thisq(0.0);
1123	>	Vector3d thisv(0.0);
1124	>
1125	>	double thisMass = 0.0;
1126	>
1127	>
1128	>
1129	>
1130	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1131	>
1132	>	thisq = mol->getCom()-com;
1133	>	thisv = mol->getComVel()-comVel;
1134	>	thisMass = mol->getMass();
1135	>	// Compute moment of intertia coefficients.
1136	>	xx += thisq[0]*thisq[0]*thisMass;
1137	>	yy += thisq[1]*thisq[1]*thisMass;
1138	>	zz += thisq[2]*thisq[2]*thisMass;
1139	>
1140	>	// compute products of intertia
1141	>	xy += thisq[0]*thisq[1]*thisMass;
1142	>	xz += thisq[0]*thisq[2]*thisMass;
1143	>	yz += thisq[1]*thisq[2]*thisMass;
1144	>
1145	>	angularMomentum += cross( thisq, thisv ) * thisMass;
1146	>
1147	>	}
1148	>
1149	>
1150	>	inertiaTensor(0,0) = yy + zz;
1151	>	inertiaTensor(0,1) = -xy;
1152	>	inertiaTensor(0,2) = -xz;
1153	>	inertiaTensor(1,0) = -xy;
1154	>	inertiaTensor(1,1) = xx + zz;
1155	>	inertiaTensor(1,2) = -yz;
1156	>	inertiaTensor(2,0) = -xz;
1157	>	inertiaTensor(2,1) = -yz;
1158	>	inertiaTensor(2,2) = xx + yy;
1159	>
1160	>	#ifdef IS_MPI
1161	>	Mat3x3d tmpI(inertiaTensor);
1162	>	Vector3d tmpAngMom;
1163	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1164	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1165	>	#endif
1166	>
1167	>	return;
1168	>	}
1169	>
1170	>	//Returns the angular momentum of the system
1171	>	Vector3d SimInfo::getAngularMomentum(){
1172	>
1173	>	Vector3d com(0.0);
1174	>	Vector3d comVel(0.0);
1175	>	Vector3d angularMomentum(0.0);
1176	>
1177	>	getComAll(com,comVel);
1178	>
1179	>	SimInfo::MoleculeIterator i;
1180	>	Molecule* mol;
1181	>
1182	>	Vector3d thisr(0.0);
1183	>	Vector3d thisp(0.0);
1184	>
1185	>	double thisMass;
1186	>
1187	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1188	>	thisMass = mol->getMass();
1189	>	thisr = mol->getCom()-com;
1190	>	thisp = (mol->getComVel()-comVel)*thisMass;
1191	>
1192	>	angularMomentum += cross( thisr, thisp );
1193	>
1194	>	}
1195	>
1196	>	#ifdef IS_MPI
1197	>	Vector3d tmpAngMom;
1198	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1199	>	#endif
1200	>
1201	>	return angularMomentum;
1202	>	}
1203	>
1204	>
1205	>	}//end namespace oopse
1206	>

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