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Comparing trunk/OOPSE-2.0/src/brains/SimInfo.cpp (file contents):
Revision 1490 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
Revision 2419 by chrisfen, Tue Nov 8 13:32:06 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/DarkSide/fElectrostaticScreeningMethod.h"
58	>	#include "UseTheForce/doForces_interface.h"
59	>	#include "UseTheForce/DarkSide/electrostatic_interface.h"
60	>	#include "UseTheForce/notifyCutoffs_interface.h"
61	>	#include "utils/MemoryUtils.hpp"
62	>	#include "utils/simError.h"
63	>	#include "selection/SelectionManager.hpp"
64
13	–	#include "fortranWrappers.hpp"
14	–
15	–	#include "MatVec3.h"
16	–
65		#ifdef IS_MPI
66	<	#include "mpiSimulation.hpp"
67	<	#endif
66	>	#include "UseTheForce/mpiComponentPlan.h"
67	>	#include "UseTheForce/DarkSide/simParallel_interface.h"
68	>	#endif
69
70	<	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	<	}
70	>	namespace oopse {
71
72	<	SimInfo* currentInfo;
72	>	SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
73	>	ForceField* ff, Globals* simParams) :
74	>	stamps_(stamps), forceField_(ff), simParams_(simParams),
75	>	ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
76	>	nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
77	>	nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
78	>	nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
79	>	nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
80	>	sman_(NULL), fortranInitialized_(false) {
81
82	<	SimInfo::SimInfo(){
82	>
83	>	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
84	>	MoleculeStamp* molStamp;
85	>	int nMolWithSameStamp;
86	>	int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
87	>	int nGroups = 0;      //total cutoff groups defined in meta-data file
88	>	CutoffGroupStamp* cgStamp;
89	>	RigidBodyStamp* rbStamp;
90	>	int nRigidAtoms = 0;
91	>
92	>	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
93	>	molStamp = i->first;
94	>	nMolWithSameStamp = i->second;
95	>
96	>	addMoleculeStamp(molStamp, nMolWithSameStamp);
97
98	<	n_constraints = 0;
99	<	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;
98	>	//calculate atoms in molecules
99	>	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
100
47	–	haveRcut = 0;
48	–	haveRsw = 0;
49	–	boxIsInit = 0;
50	–
51	–	resetTime = 1e99;
101
102	<	orthoRhombic = 0;
103	<	orthoTolerance = 1E-6;
104	<	useInitXSstate = true;
102	>	//calculate atoms in cutoff groups
103	>	int nAtomsInGroups = 0;
104	>	int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
105	>
106	>	for (int j=0; j < nCutoffGroupsInStamp; j++) {
107	>	cgStamp = molStamp->getCutoffGroup(j);
108	>	nAtomsInGroups += cgStamp->getNMembers();
109	>	}
110
111	<	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;
111	>	nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
112
113	<	haveCutoffGroups = false;
113	>	nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;
114
115	<	excludes = Exclude::Instance();
115	>	//calculate atoms in rigid bodies
116	>	int nAtomsInRigidBodies = 0;
117	>	int nRigidBodiesInStamp = molStamp->getNRigidBodies();
118	>
119	>	for (int j=0; j < nRigidBodiesInStamp; j++) {
120	>	rbStamp = molStamp->getRigidBody(j);
121	>	nAtomsInRigidBodies += rbStamp->getNMembers();
122	>	}
123
124	<	myConfiguration = new SimState();
124	>	nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
125	>	nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;
126	>
127	>	}
128
129	<	has_minimizer = false;
130	<	the_minimizer =NULL;
129	>	//every free atom (atom does not belong to cutoff groups) is a cutoff
130	>	//group therefore the total number of cutoff groups in the system is
131	>	//equal to the total number of atoms minus number of atoms belong to
132	>	//cutoff group defined in meta-data file plus the number of cutoff
133	>	//groups defined in meta-data file
134	>	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
135
136	<	ngroup = 0;
136	>	//every free atom (atom does not belong to rigid bodies) is an
137	>	//integrable object therefore the total number of integrable objects
138	>	//in the system is equal to the total number of atoms minus number of
139	>	//atoms belong to rigid body defined in meta-data file plus the number
140	>	//of rigid bodies defined in meta-data file
141	>	nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms
142	>	+ nGlobalRigidBodies_;
143	>
144	>	nGlobalMols_ = molStampIds_.size();
145
146	<	wrapMeSimInfo( this );
147	<	}
146	>	#ifdef IS_MPI
147	>	molToProcMap_.resize(nGlobalMols_);
148	>	#endif
149
150	+	}
151
152	<	SimInfo::~SimInfo(){
152	>	SimInfo::~SimInfo() {
153	>	std::map<int, Molecule*>::iterator i;
154	>	for (i = molecules_.begin(); i != molecules_.end(); ++i) {
155	>	delete i->second;
156	>	}
157	>	molecules_.clear();
158	>
159	>	delete stamps_;
160	>	delete sman_;
161	>	delete simParams_;
162	>	delete forceField_;
163	>	}
164
165	<	delete myConfiguration;
165	>	int SimInfo::getNGlobalConstraints() {
166	>	int nGlobalConstraints;
167	>	#ifdef IS_MPI
168	>	MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
169	>	MPI_COMM_WORLD);
170	>	#else
171	>	nGlobalConstraints =  nConstraints_;
172	>	#endif
173	>	return nGlobalConstraints;
174	>	}
175
176	<	map<string, GenericData*>::iterator i;
177	<
89	<	for(i = properties.begin(); i != properties.end(); i++)
90	<	delete (*i).second;
176	>	bool SimInfo::addMolecule(Molecule* mol) {
177	>	MoleculeIterator i;
178
179	<	}
179	>	i = molecules_.find(mol->getGlobalIndex());
180	>	if (i == molecules_.end() ) {
181
182	<	void SimInfo::setBox(double newBox[3]) {
183	<
184	<	int i, j;
185	<	double tempMat[3][3];
182	>	molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
183	>
184	>	nAtoms_ += mol->getNAtoms();
185	>	nBonds_ += mol->getNBonds();
186	>	nBends_ += mol->getNBends();
187	>	nTorsions_ += mol->getNTorsions();
188	>	nRigidBodies_ += mol->getNRigidBodies();
189	>	nIntegrableObjects_ += mol->getNIntegrableObjects();
190	>	nCutoffGroups_ += mol->getNCutoffGroups();
191	>	nConstraints_ += mol->getNConstraintPairs();
192
193	<	for(i=0; i<3; i++)
194	<	for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
195	<
196	<	tempMat[0][0] = newBox[0];
197	<	tempMat[1][1] = newBox[1];
104	<	tempMat[2][2] = newBox[2];
105	<
106	<	setBoxM( tempMat );
107	<
108	<	}
109	<
110	<	void SimInfo::setBoxM( double theBox[3][3] ){
111	<
112	<	int i, j;
113	<	double FortranHmat[9]; // to preserve compatibility with Fortran the
114	<	// ordering in the array is as follows:
115	<	// [ 0 3 6 ]
116	<	// [ 1 4 7 ]
117	<	// [ 2 5 8 ]
118	<	double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
119	<
120	<	if( !boxIsInit ) boxIsInit = 1;
121	<
122	<	for(i=0; i < 3; i++)
123	<	for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
124	<
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];
193	>	addExcludePairs(mol);
194	>
195	>	return true;
196	>	} else {
197	>	return false;
198		}
199		}
200
201	<	setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
202	<
203	<	}
138	<
201	>	bool SimInfo::removeMolecule(Molecule* mol) {
202	>	MoleculeIterator i;
203	>	i = molecules_.find(mol->getGlobalIndex());
204
205	<	void SimInfo::getBoxM (double theBox[3][3]) {
205	>	if (i != molecules_.end() ) {
206
207	<	int i, j;
208	<	for(i=0; i<3; i++)
209	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
210	<	}
207	>	assert(mol == i->second);
208	>
209	>	nAtoms_ -= mol->getNAtoms();
210	>	nBonds_ -= mol->getNBonds();
211	>	nBends_ -= mol->getNBends();
212	>	nTorsions_ -= mol->getNTorsions();
213	>	nRigidBodies_ -= mol->getNRigidBodies();
214	>	nIntegrableObjects_ -= mol->getNIntegrableObjects();
215	>	nCutoffGroups_ -= mol->getNCutoffGroups();
216	>	nConstraints_ -= mol->getNConstraintPairs();
217
218	+	removeExcludePairs(mol);
219	+	molecules_.erase(mol->getGlobalIndex());
220
221	<	void SimInfo::scaleBox(double scale) {
222	<	double theBox[3][3];
223	<	int i, j;
221	>	delete mol;
222	>
223	>	return true;
224	>	} else {
225	>	return false;
226	>	}
227
152	–	// cerr << "Scaling box by " << scale << "\n";
228
229	<	for(i=0; i<3; i++)
155	<	for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
229	>	}
230
231	<	setBoxM(theBox);
231	>
232	>	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
233	>	i = molecules_.begin();
234	>	return i == molecules_.end() ? NULL : i->second;
235	>	}
236
237	<	}
237	>	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
238	>	++i;
239	>	return i == molecules_.end() ? NULL : i->second;
240	>	}
241
161	–	void SimInfo::calcHmatInv( void ) {
162	–
163	–	int oldOrtho;
164	–	int i,j;
165	–	double smallDiag;
166	–	double tol;
167	–	double sanity[3][3];
242
243	<	invertMat3( Hmat, HmatInv );
243	>	void SimInfo::calcNdf() {
244	>	int ndf_local;
245	>	MoleculeIterator i;
246	>	std::vector<StuntDouble*>::iterator j;
247	>	Molecule* mol;
248	>	StuntDouble* integrableObject;
249
250	<	// check to see if Hmat is orthorhombic
251	<
252	<	oldOrtho = orthoRhombic;
250	>	ndf_local = 0;
251	>
252	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
253	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
254	>	integrableObject = mol->nextIntegrableObject(j)) {
255
256	<	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;
256	>	ndf_local += 3;
257
258	<	orthoRhombic = 1;
259	<
260	<	for (i = 0; i < 3; i++ ) {
261	<	for (j = 0 ; j < 3; j++) {
262	<	if (i != j) {
263	<	if (orthoRhombic) {
264	<	if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
265	<	}
266	<	}
267	<	}
190	<	}
191	<
192	<	if( oldOrtho != orthoRhombic ){
258	>	if (integrableObject->isDirectional()) {
259	>	if (integrableObject->isLinear()) {
260	>	ndf_local += 2;
261	>	} else {
262	>	ndf_local += 3;
263	>	}
264	>	}
265	>
266	>	}//end for (integrableObject)
267	>	}// end for (mol)
268
269	<	if( orthoRhombic ) {
270	<	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	<	}
269	>	// n_constraints is local, so subtract them on each processor
270	>	ndf_local -= nConstraints_;
271
272	<	void SimInfo::calcBoxL( void ){
272	>	#ifdef IS_MPI
273	>	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
274	>	#else
275	>	ndf_ = ndf_local;
276	>	#endif
277
278	<	double dx, dy, dz, dsq;
278	>	// nZconstraints_ is global, as are the 3 COM translations for the
279	>	// entire system:
280	>	ndf_ = ndf_ - 3 - nZconstraint_;
281
282	<	// boxVol = Determinant of Hmat
282	>	}
283
284	<	boxVol = matDet3( Hmat );
284	>	void SimInfo::calcNdfRaw() {
285	>	int ndfRaw_local;
286
287	<	// boxLx
288	<
289	<	dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
290	<	dsq = dx*dx + dy*dy + dz*dz;
232	<	boxL[0] = sqrt( dsq );
233	<	//maxCutoff = 0.5 * boxL[0];
287	>	MoleculeIterator i;
288	>	std::vector<StuntDouble*>::iterator j;
289	>	Molecule* mol;
290	>	StuntDouble* integrableObject;
291
292	<	// boxLy
293	<
294	<	dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
295	<	dsq = dx*dx + dy*dy + dz*dz;
296	<	boxL[1] = sqrt( dsq );
297	<	//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
292	>	// Raw degrees of freedom that we have to set
293	>	ndfRaw_local = 0;
294	>
295	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
296	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
297	>	integrableObject = mol->nextIntegrableObject(j)) {
298
299	<
243	<	// boxLz
244	<
245	<	dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
246	<	dsq = dx*dx + dy*dy + dz*dz;
247	<	boxL[2] = sqrt( dsq );
248	<	//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
299	>	ndfRaw_local += 3;
300
301	<	//calculate the max cutoff
302	<	maxCutoff =  calcMaxCutOff();
303	<
304	<	checkCutOffs();
301	>	if (integrableObject->isDirectional()) {
302	>	if (integrableObject->isLinear()) {
303	>	ndfRaw_local += 2;
304	>	} else {
305	>	ndfRaw_local += 3;
306	>	}
307	>	}
308	>
309	>	}
310	>	}
311	>
312	>	#ifdef IS_MPI
313	>	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
314	>	#else
315	>	ndfRaw_ = ndfRaw_local;
316	>	#endif
317	>	}
318
319	<	}
319	>	void SimInfo::calcNdfTrans() {
320	>	int ndfTrans_local;
321
322	+	ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
323
258	–	double SimInfo::calcMaxCutOff(){
324
325	<	double ri[3], rj[3], rk[3];
326	<	double rij[3], rjk[3], rki[3];
327	<	double minDist;
325	>	#ifdef IS_MPI
326	>	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
327	>	#else
328	>	ndfTrans_ = ndfTrans_local;
329	>	#endif
330
331	<	ri[0] = Hmat[0][0];
332	<	ri[1] = Hmat[1][0];
333	<	ri[2] = Hmat[2][0];
331	>	ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
332	>
333	>	}
334
335	<	rj[0] = Hmat[0][1];
336	<	rj[1] = Hmat[1][1];
337	<	rj[2] = Hmat[2][1];
338	<
339	<	rk[0] = Hmat[0][2];
340	<	rk[1] = Hmat[1][2];
341	<	rk[2] = Hmat[2][2];
335	>	void SimInfo::addExcludePairs(Molecule* mol) {
336	>	std::vector<Bond*>::iterator bondIter;
337	>	std::vector<Bend*>::iterator bendIter;
338	>	std::vector<Torsion*>::iterator torsionIter;
339	>	Bond* bond;
340	>	Bend* bend;
341	>	Torsion* torsion;
342	>	int a;
343	>	int b;
344	>	int c;
345	>	int d;
346
347	<	crossProduct3(ri, rj, rij);
348	<	distXY = dotProduct3(rk,rij) / norm3(rij);
347	>	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
348	>	a = bond->getAtomA()->getGlobalIndex();
349	>	b = bond->getAtomB()->getGlobalIndex();
350	>	exclude_.addPair(a, b);
351	>	}
352
353	<	crossProduct3(rj,rk, rjk);
354	<	distYZ = dotProduct3(ri,rjk) / norm3(rjk);
353	>	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
354	>	a = bend->getAtomA()->getGlobalIndex();
355	>	b = bend->getAtomB()->getGlobalIndex();
356	>	c = bend->getAtomC()->getGlobalIndex();
357
358	<	crossProduct3(rk,ri, rki);
359	<	distZX = dotProduct3(rj,rki) / norm3(rki);
358	>	exclude_.addPair(a, b);
359	>	exclude_.addPair(a, c);
360	>	exclude_.addPair(b, c);
361	>	}
362
363	<	minDist = min(min(distXY, distYZ), distZX);
364	<	return minDist/2;
365	<
366	<	}
363	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
364	>	a = torsion->getAtomA()->getGlobalIndex();
365	>	b = torsion->getAtomB()->getGlobalIndex();
366	>	c = torsion->getAtomC()->getGlobalIndex();
367	>	d = torsion->getAtomD()->getGlobalIndex();
368
369	<	void SimInfo::wrapVector( double thePos[3] ){
369	>	exclude_.addPair(a, b);
370	>	exclude_.addPair(a, c);
371	>	exclude_.addPair(a, d);
372	>	exclude_.addPair(b, c);
373	>	exclude_.addPair(b, d);
374	>	exclude_.addPair(c, d);
375	>	}
376
377	<	int i;
378	<	double scaled[3];
377	>	Molecule::RigidBodyIterator rbIter;
378	>	RigidBody* rb;
379	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
380	>	std::vector<Atom*> atoms = rb->getAtoms();
381	>	for (int i = 0; i < atoms.size() -1 ; ++i) {
382	>	for (int j = i + 1; j < atoms.size(); ++j) {
383	>	a = atoms[i]->getGlobalIndex();
384	>	b = atoms[j]->getGlobalIndex();
385	>	exclude_.addPair(a, b);
386	>	}
387	>	}
388	>	}
389
390	<	if( !orthoRhombic ){
296	<	// calc the scaled coordinates.
297	<
390	>	}
391
392	<	matVecMul3(HmatInv, thePos, scaled);
392	>	void SimInfo::removeExcludePairs(Molecule* mol) {
393	>	std::vector<Bond*>::iterator bondIter;
394	>	std::vector<Bend*>::iterator bendIter;
395	>	std::vector<Torsion*>::iterator torsionIter;
396	>	Bond* bond;
397	>	Bend* bend;
398	>	Torsion* torsion;
399	>	int a;
400	>	int b;
401	>	int c;
402	>	int d;
403
404	<	for(i=0; i<3; i++)
405	<	scaled[i] -= roundMe(scaled[i]);
406	<
407	<	// calc the wrapped real coordinates from the wrapped scaled coordinates
408	<
306	<	matVecMul3(Hmat, scaled, thePos);
404	>	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
405	>	a = bond->getAtomA()->getGlobalIndex();
406	>	b = bond->getAtomB()->getGlobalIndex();
407	>	exclude_.removePair(a, b);
408	>	}
409
410	<	}
411	<	else{
412	<	// calc the scaled coordinates.
413	<
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	<	}
410	>	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
411	>	a = bend->getAtomA()->getGlobalIndex();
412	>	b = bend->getAtomB()->getGlobalIndex();
413	>	c = bend->getAtomC()->getGlobalIndex();
414
415	+	exclude_.removePair(a, b);
416	+	exclude_.removePair(a, c);
417	+	exclude_.removePair(b, c);
418	+	}
419
420	<	int SimInfo::getNDF(){
421	<	int ndf_local;
420	>	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
421	>	a = torsion->getAtomA()->getGlobalIndex();
422	>	b = torsion->getAtomB()->getGlobalIndex();
423	>	c = torsion->getAtomC()->getGlobalIndex();
424	>	d = torsion->getAtomD()->getGlobalIndex();
425
426	<	ndf_local = 0;
427	<
428	<	for(int i = 0; i < integrableObjects.size(); i++){
429	<	ndf_local += 3;
430	<	if (integrableObjects[i]->isDirectional()) {
431	<	if (integrableObjects[i]->isLinear())
338	<	ndf_local += 2;
339	<	else
340	<	ndf_local += 3;
426	>	exclude_.removePair(a, b);
427	>	exclude_.removePair(a, c);
428	>	exclude_.removePair(a, d);
429	>	exclude_.removePair(b, c);
430	>	exclude_.removePair(b, d);
431	>	exclude_.removePair(c, d);
432		}
433	+
434	+	Molecule::RigidBodyIterator rbIter;
435	+	RigidBody* rb;
436	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
437	+	std::vector<Atom*> atoms = rb->getAtoms();
438	+	for (int i = 0; i < atoms.size() -1 ; ++i) {
439	+	for (int j = i + 1; j < atoms.size(); ++j) {
440	+	a = atoms[i]->getGlobalIndex();
441	+	b = atoms[j]->getGlobalIndex();
442	+	exclude_.removePair(a, b);
443	+	}
444	+	}
445	+	}
446	+
447		}
448
344	–	// n_constraints is local, so subtract them on each processor:
449
450	<	ndf_local -= n_constraints;
450	>	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
451	>	int curStampId;
452
453	+	//index from 0
454	+	curStampId = moleculeStamps_.size();
455	+
456	+	moleculeStamps_.push_back(molStamp);
457	+	molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
458	+	}
459	+
460	+	void SimInfo::update() {
461	+
462	+	setupSimType();
463	+
464		#ifdef IS_MPI
465	<	MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
350	<	#else
351	<	ndf = ndf_local;
465	>	setupFortranParallel();
466		#endif
467
468	<	// nZconstraints is global, as are the 3 COM translations for the
355	<	// entire system:
468	>	setupFortranSim();
469
470	<	ndf = ndf - 3 - nZconstraints;
470	>	//setup fortran force field
471	>	/** @deprecate */
472	>	int isError = 0;
473	>
474	>	setupElectrostaticSummationMethod( isError );
475
476	<	return ndf;
477	<	}
476	>	if(isError){
477	>	sprintf( painCave.errMsg,
478	>	"ForceField error: There was an error initializing the forceField in fortran.\n" );
479	>	painCave.isFatal = 1;
480	>	simError();
481	>	}
482	>
483	>
484	>	setupCutoff();
485
486	<	int SimInfo::getNDFraw() {
487	<	int ndfRaw_local;
486	>	calcNdf();
487	>	calcNdfRaw();
488	>	calcNdfTrans();
489
490	<	// Raw degrees of freedom that we have to set
491	<	ndfRaw_local = 0;
490	>	fortranInitialized_ = true;
491	>	}
492
493	<	for(int i = 0; i < integrableObjects.size(); i++){
494	<	ndfRaw_local += 3;
495	<	if (integrableObjects[i]->isDirectional()) {
496	<	if (integrableObjects[i]->isLinear())
497	<	ndfRaw_local += 2;
498	<	else
499	<	ndfRaw_local += 3;
493	>	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
494	>	SimInfo::MoleculeIterator mi;
495	>	Molecule* mol;
496	>	Molecule::AtomIterator ai;
497	>	Atom* atom;
498	>	std::set<AtomType*> atomTypes;
499	>
500	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
501	>
502	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
503	>	atomTypes.insert(atom->getAtomType());
504	>	}
505	>
506		}
507	+
508	+	return atomTypes;
509		}
510	+
511	+	void SimInfo::setupSimType() {
512	+	std::set<AtomType*>::iterator i;
513	+	std::set<AtomType*> atomTypes;
514	+	atomTypes = getUniqueAtomTypes();
515
516	<	#ifdef IS_MPI
517	<	MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
518	<	#else
519	<	ndfRaw = ndfRaw_local;
520	<	#endif
516	>	int useLennardJones = 0;
517	>	int useElectrostatic = 0;
518	>	int useEAM = 0;
519	>	int useCharge = 0;
520	>	int useDirectional = 0;
521	>	int useDipole = 0;
522	>	int useGayBerne = 0;
523	>	int useSticky = 0;
524	>	int useStickyPower = 0;
525	>	int useShape = 0;
526	>	int useFLARB = 0; //it is not in AtomType yet
527	>	int useDirectionalAtom = 0;
528	>	int useElectrostatics = 0;
529	>	//usePBC and useRF are from simParams
530	>	int usePBC = simParams_->getUsePeriodicBoundaryConditions();
531	>	int useRF;
532	>	int useSF;
533	>	std::string myMethod;
534
535	<	return ndfRaw;
536	<	}
535	>	// set the useRF logical
536	>	useRF = 0;
537	>	useSF = 0;
538
387	–	int SimInfo::getNDFtranslational() {
388	–	int ndfTrans_local;
539
540	<	ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
540	>	if (simParams_->haveElectrostaticSummationMethod()) {
541	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
542	>	toUpper(myMethod);
543	>	if (myMethod == "REACTION_FIELD") {
544	>	useRF=1;
545	>	} else {
546	>	if (myMethod == "SHIFTED_FORCE") {
547	>	useSF = 1;
548	>	}
549	>	}
550	>	}
551
552	+	//loop over all of the atom types
553	+	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
554	+	useLennardJones |= (*i)->isLennardJones();
555	+	useElectrostatic |= (*i)->isElectrostatic();
556	+	useEAM |= (*i)->isEAM();
557	+	useCharge |= (*i)->isCharge();
558	+	useDirectional |= (*i)->isDirectional();
559	+	useDipole |= (*i)->isDipole();
560	+	useGayBerne |= (*i)->isGayBerne();
561	+	useSticky |= (*i)->isSticky();
562	+	useStickyPower |= (*i)->isStickyPower();
563	+	useShape |= (*i)->isShape();
564	+	}
565
566	<	#ifdef IS_MPI
567	<	MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
568	<	#else
396	<	ndfTrans = ndfTrans_local;
397	<	#endif
566	>	if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
567	>	useDirectionalAtom = 1;
568	>	}
569
570	<	ndfTrans = ndfTrans - 3 - nZconstraints;
570	>	if (useCharge || useDipole) {
571	>	useElectrostatics = 1;
572	>	}
573
574	<	return ndfTrans;
575	<	}
574	>	#ifdef IS_MPI
575	>	int temp;
576
577	<	int SimInfo::getTotIntegrableObjects() {
578	<	int nObjs_local;
406	<	int nObjs;
577	>	temp = usePBC;
578	>	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
579
580	<	nObjs_local =  integrableObjects.size();
580	>	temp = useDirectionalAtom;
581	>	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
582
583	+	temp = useLennardJones;
584	+	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
585
586	<	#ifdef IS_MPI
587	<	MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
413	<	#else
414	<	nObjs = nObjs_local;
415	<	#endif
586	>	temp = useElectrostatics;
587	>	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
588
589	+	temp = useCharge;
590	+	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
591
592	<	return nObjs;
593	<	}
592	>	temp = useDipole;
593	>	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
594
595	<	void SimInfo::refreshSim(){
595	>	temp = useSticky;
596	>	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
597
598	<	simtype fInfo;
599	<	int isError;
600	<	int n_global;
601	<	int* excl;
602	<
428	<	fInfo.dielect = 0.0;
598	>	temp = useStickyPower;
599	>	MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
600	>
601	>	temp = useGayBerne;
602	>	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
603
604	<	if( useDipoles ){
605	<	if( useReactionField )fInfo.dielect = dielectric;
432	<	}
604	>	temp = useEAM;
605	>	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
606
607	<	fInfo.SIM_uses_PBC = usePBC;
608	<	//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;
607	>	temp = useShape;
608	>	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
609
610	<	n_exclude = excludes->getSize();
611	<	excl = excludes->getFortranArray();
612	<
613	<	#ifdef IS_MPI
614	<	n_global = mpiSim->getNAtomsGlobal();
615	<	#else
616	<	n_global = n_atoms;
610	>	temp = useFLARB;
611	>	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
612	>
613	>	temp = useRF;
614	>	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
615	>
616	>	temp = useSF;
617	>	MPI_Allreduce(&temp, &useSF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
618	>
619		#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);
620
621	<	if( isError ){
622	<
623	<	sprintf( painCave.errMsg,
624	<	"There was an error setting the simulation information in fortran.\n" );
625	<	painCave.isFatal = 1;
626	<	painCave.severity = OOPSE_ERROR;
627	<	simError();
621	>	fInfo_.SIM_uses_PBC = usePBC;
622	>	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
623	>	fInfo_.SIM_uses_LennardJones = useLennardJones;
624	>	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
625	>	fInfo_.SIM_uses_Charges = useCharge;
626	>	fInfo_.SIM_uses_Dipoles = useDipole;
627	>	fInfo_.SIM_uses_Sticky = useSticky;
628	>	fInfo_.SIM_uses_StickyPower = useStickyPower;
629	>	fInfo_.SIM_uses_GayBerne = useGayBerne;
630	>	fInfo_.SIM_uses_EAM = useEAM;
631	>	fInfo_.SIM_uses_Shapes = useShape;
632	>	fInfo_.SIM_uses_FLARB = useFLARB;
633	>	fInfo_.SIM_uses_RF = useRF;
634	>	fInfo_.SIM_uses_SF = useSF;
635	>
636	>	if( myMethod == "REACTION_FIELD") {
637	>
638	>	if (simParams_->haveDielectric()) {
639	>	fInfo_.dielect = simParams_->getDielectric();
640	>	} else {
641	>	sprintf(painCave.errMsg,
642	>	"SimSetup Error: No Dielectric constant was set.\n"
643	>	"\tYou are trying to use Reaction Field without"
644	>	"\tsetting a dielectric constant!\n");
645	>	painCave.isFatal = 1;
646	>	simError();
647	>	}
648	>	}
649	>
650		}
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	–	}
651
652	<	void SimInfo::setDefaultRcut( double theRcut ){
653	<
654	<	haveRcut = 1;
655	<	rCut = theRcut;
656	<	rList = rCut + 1.0;
657	<
658	<	notifyFortranCutOffs( &rCut, &rSw, &rList );
493	<	}
652	>	void SimInfo::setupFortranSim() {
653	>	int isError;
654	>	int nExclude;
655	>	std::vector<int> fortranGlobalGroupMembership;
656	>
657	>	nExclude = exclude_.getSize();
658	>	isError = 0;
659
660	<	void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
660	>	//globalGroupMembership_ is filled by SimCreator
661	>	for (int i = 0; i < nGlobalAtoms_; i++) {
662	>	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
663	>	}
664
665	<	rSw = theRsw;
666	<	setDefaultRcut( theRcut );
667	<	}
665	>	//calculate mass ratio of cutoff group
666	>	std::vector<double> mfact;
667	>	SimInfo::MoleculeIterator mi;
668	>	Molecule* mol;
669	>	Molecule::CutoffGroupIterator ci;
670	>	CutoffGroup* cg;
671	>	Molecule::AtomIterator ai;
672	>	Atom* atom;
673	>	double totalMass;
674
675	+	//to avoid memory reallocation, reserve enough space for mfact
676	+	mfact.reserve(getNCutoffGroups());
677	+
678	+	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
679	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
680
681	<	void SimInfo::checkCutOffs( void ){
682	<
683	<	if( boxIsInit ){
681	>	totalMass = cg->getMass();
682	>	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
683	>	// Check for massless groups - set mfact to 1 if true
684	>	if (totalMass != 0)
685	>	mfact.push_back(atom->getMass()/totalMass);
686	>	else
687	>	mfact.push_back( 1.0 );
688	>	}
689	>
690	>	}
691	>	}
692	>
693	>	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
694	>	std::vector<int> identArray;
695	>
696	>	//to avoid memory reallocation, reserve enough space identArray
697	>	identArray.reserve(getNAtoms());
698
699	<	//we need to check cutOffs against the box
699	>	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
700	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
701	>	identArray.push_back(atom->getIdent());
702	>	}
703	>	}
704	>
705	>	//fill molMembershipArray
706	>	//molMembershipArray is filled by SimCreator
707	>	std::vector<int> molMembershipArray(nGlobalAtoms_);
708	>	for (int i = 0; i < nGlobalAtoms_; i++) {
709	>	molMembershipArray[i] = globalMolMembership_[i] + 1;
710	>	}
711
712	<	if( rCut > maxCutoff ){
712	>	//setup fortran simulation
713	>	int nGlobalExcludes = 0;
714	>	int* globalExcludes = NULL;
715	>	int* excludeList = exclude_.getExcludeList();
716	>	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
717	>	&nGlobalExcludes, globalExcludes, &molMembershipArray[0],
718	>	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
719	>
720	>	if( isError ){
721	>
722		sprintf( painCave.errMsg,
723	<	"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;
723	>	"There was an error setting the simulation information in fortran.\n" );
724		painCave.isFatal = 1;
725	+	painCave.severity = OOPSE_ERROR;
726		simError();
727	<	}
728	<	} else {
729	<	// initialize this stuff before using it, OK?
730	<	sprintf( painCave.errMsg,
731	<	"Trying to check cutoffs without a box.\n"
732	<	"\tOOPSE should have better programmers than that.\n" );
733	<	painCave.severity = OOPSE_ERROR;
532	<	painCave.isFatal = 1;
533	<	simError();
727	>	}
728	>
729	>	#ifdef IS_MPI
730	>	sprintf( checkPointMsg,
731	>	"succesfully sent the simulation information to fortran.\n");
732	>	MPIcheckPoint();
733	>	#endif // is_mpi
734		}
535	–
536	–	}
735
538	–	void SimInfo::addProperty(GenericData* prop){
736
737	<	map<string, GenericData*>::iterator result;
738	<	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()){
737	>	#ifdef IS_MPI
738	>	void SimInfo::setupFortranParallel() {
739
740	<	delete (*result).second;
741	<	(*result).second = prop;
742	<
743	<	}
744	<	else{
740	>	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
741	>	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
742	>	std::vector<int> localToGlobalCutoffGroupIndex;
743	>	SimInfo::MoleculeIterator mi;
744	>	Molecule::AtomIterator ai;
745	>	Molecule::CutoffGroupIterator ci;
746	>	Molecule* mol;
747	>	Atom* atom;
748	>	CutoffGroup* cg;
749	>	mpiSimData parallelData;
750	>	int isError;
751
752	<	properties[prop->getID()] = prop;
752	>	for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
753
754	+	//local index(index in DataStorge) of atom is important
755	+	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
756	+	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
757	+	}
758	+
759	+	//local index of cutoff group is trivial, it only depends on the order of travesing
760	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
761	+	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
762	+	}
763	+
764	+	}
765	+
766	+	//fill up mpiSimData struct
767	+	parallelData.nMolGlobal = getNGlobalMolecules();
768	+	parallelData.nMolLocal = getNMolecules();
769	+	parallelData.nAtomsGlobal = getNGlobalAtoms();
770	+	parallelData.nAtomsLocal = getNAtoms();
771	+	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
772	+	parallelData.nGroupsLocal = getNCutoffGroups();
773	+	parallelData.myNode = worldRank;
774	+	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
775	+
776	+	//pass mpiSimData struct and index arrays to fortran
777	+	setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
778	+	&localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
779	+	&localToGlobalCutoffGroupIndex[0], &isError);
780	+
781	+	if (isError) {
782	+	sprintf(painCave.errMsg,
783	+	"mpiRefresh errror: fortran didn't like something we gave it.\n");
784	+	painCave.isFatal = 1;
785	+	simError();
786	+	}
787	+
788	+	sprintf(checkPointMsg, " mpiRefresh successful.\n");
789	+	MPIcheckPoint();
790	+
791	+
792		}
557	–
558	–	}
793
794	<	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	<	}
794	>	#endif
795
796	+	double SimInfo::calcMaxCutoffRadius() {
797
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	–
798
799	<	// Fix the silly fortran indexing problem
799	>	std::set<AtomType*> atomTypes;
800	>	std::set<AtomType*>::iterator i;
801	>	std::vector<double> cutoffRadius;
802	>
803	>	//get the unique atom types
804	>	atomTypes = getUniqueAtomTypes();
805	>
806	>	//query the max cutoff radius among these atom types
807	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
808	>	cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
809	>	}
810	>
811	>	double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
812		#ifdef IS_MPI
813	<	numAtom = mpiSim->getNAtomsGlobal();
599	<	#else
600	<	numAtom = n_atoms;
813	>	//pick the max cutoff radius among the processors
814		#endif
602	–	for (int i = 0; i < numAtom; i++)
603	–	FglobalGroupMembership.push_back(globalGroupMembership[i] + 1);
604	–
815
816	<	myMols = info->molecules;
817	<	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)){
816	>	return maxCutoffRadius;
817	>	}
818
819	<	totalMass = myCutoffGroup->getMass();
820	<
821	<	for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom);
822	<	cutoffAtom != NULL;
823	<	cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
824	<	mfact.push_back(cutoffAtom->getMass()/totalMass);
825	<	}
819	>	void SimInfo::getCutoff(double& rcut, double& rsw) {
820	>
821	>	if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
822	>
823	>	if (!simParams_->haveCutoffRadius()){
824	>	sprintf(painCave.errMsg,
825	>	"SimCreator Warning: No value was set for the cutoffRadius.\n"
826	>	"\tOOPSE will use a default value of 15.0 angstroms"
827	>	"\tfor the cutoffRadius.\n");
828	>	painCave.isFatal = 0;
829	>	simError();
830	>	rcut = 15.0;
831	>	} else{
832	>	rcut = simParams_->getCutoffRadius();
833	>	}
834	>
835	>	if (!simParams_->haveSwitchingRadius()){
836	>	sprintf(painCave.errMsg,
837	>	"SimCreator Warning: No value was set for switchingRadius.\n"
838	>	"\tOOPSE will use a default value of\n"
839	>	"\t0.85 * cutoffRadius for the switchingRadius\n");
840	>	painCave.isFatal = 0;
841	>	simError();
842	>	rsw = 0.85 * rcut;
843	>	} else{
844	>	rsw = simParams_->getSwitchingRadius();
845	>	}
846	>
847	>	} else {
848	>	// if charge, dipole or reaction field is not used and the cutofff radius is not specified in
849	>	//meta-data file, the maximum cutoff radius calculated from forcefiled will be used
850	>
851	>	if (simParams_->haveCutoffRadius()) {
852	>	rcut = simParams_->getCutoffRadius();
853	>	} else {
854	>	//set cutoff radius to the maximum cutoff radius based on atom types in the whole system
855	>	rcut = calcMaxCutoffRadius();
856	>	}
857	>
858	>	if (simParams_->haveSwitchingRadius()) {
859	>	rsw  = simParams_->getSwitchingRadius();
860	>	} else {
861	>	rsw = rcut;
862	>	}
863	>
864		}
865		}
866
867	<	}
867	>	void SimInfo::setupCutoff() {
868	>	getCutoff(rcut_, rsw_);
869	>	double rnblist = rcut_ + 1; // skin of neighbor list
870	>
871	>	//Pass these cutoff radius etc. to fortran. This function should be called once and only once
872	>
873	>	int cp =  TRADITIONAL_CUTOFF_POLICY;
874	>	if (simParams_->haveCutoffPolicy()) {
875	>	std::string myPolicy = simParams_->getCutoffPolicy();
876	>	toUpper(myPolicy);
877	>	if (myPolicy == "MIX") {
878	>	cp = MIX_CUTOFF_POLICY;
879	>	} else {
880	>	if (myPolicy == "MAX") {
881	>	cp = MAX_CUTOFF_POLICY;
882	>	} else {
883	>	if (myPolicy == "TRADITIONAL") {
884	>	cp = TRADITIONAL_CUTOFF_POLICY;
885	>	} else {
886	>	// throw error
887	>	sprintf( painCave.errMsg,
888	>	"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
889	>	painCave.isFatal = 1;
890	>	simError();
891	>	}
892	>	}
893	>	}
894	>	}
895	>
896	>
897	>	if (simParams_->haveSkinThickness()) {
898	>	double skinThickness = simParams_->getSkinThickness();
899	>	}
900	>
901	>	notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
902	>	// also send cutoff notification to electrostatics
903	>	setElectrostaticCutoffRadius(&rcut_, &rsw_);
904	>	}
905	>
906	>	void SimInfo::setupElectrostaticSummationMethod( int isError ) {
907	>
908	>	int errorOut;
909	>	int esm =  NONE;
910	>	int sm = UNDAMPED;
911	>	double alphaVal;
912	>	double dielectric;
913	>
914	>	errorOut = isError;
915	>	alphaVal = simParams_->getDampingAlpha();
916	>	dielectric = simParams_->getDielectric();
917	>
918	>	if (simParams_->haveElectrostaticSummationMethod()) {
919	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
920	>	toUpper(myMethod);
921	>	if (myMethod == "NONE") {
922	>	esm = NONE;
923	>	} else {
924	>	if (myMethod == "SWITCHING_FUNCTION") {
925	>	esm = SWITCHING_FUNCTION;
926	>	} else {
927	>	if (myMethod == "SHIFTED_POTENTIAL") {
928	>	esm = SHIFTED_POTENTIAL;
929	>	} else {
930	>	if (myMethod == "SHIFTED_FORCE") {
931	>	esm = SHIFTED_FORCE;
932	>	} else {
933	>	if (myMethod == "REACTION_FIELD") {
934	>	esm = REACTION_FIELD;
935	>	} else {
936	>	// throw error
937	>	sprintf( painCave.errMsg,
938	>	"SimInfo error: Unknown electrostaticSummationMethod. (Input file specified %s .)\n\telectrostaticSummationMethod must be one of: \"none\", \"shifted_potential\", \"shifted_force\", or \"reaction_field\".", myMethod.c_str() );
939	>	painCave.isFatal = 1;
940	>	simError();
941	>	}
942	>	}
943	>	}
944	>	}
945	>	}
946	>	}
947	>
948	>	if (simParams_->haveElectrostaticScreeningMethod()) {
949	>	std::string myScreen = simParams_->getElectrostaticScreeningMethod();
950	>	toUpper(myScreen);
951	>	if (myScreen == "UNDAMPED") {
952	>	sm = UNDAMPED;
953	>	} else {
954	>	if (myScreen == "DAMPED") {
955	>	sm = DAMPED;
956	>	if (!simParams_->haveDampingAlpha()) {
957	>	//throw error
958	>	sprintf( painCave.errMsg,
959	>	"SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used.", alphaVal);
960	>	painCave.isFatal = 0;
961	>	simError();
962	>	}
963	>	} else {
964	>	// throw error
965	>	sprintf( painCave.errMsg,
966	>	"SimInfo error: Unknown electrostaticScreeningMethod. (Input file specified %s .)\n\telectrostaticScreeningMethod must be one of: \"undamped\" or \"damped\".", myScreen.c_str() );
967	>	painCave.isFatal = 1;
968	>	simError();
969	>	}
970	>	}
971	>	}
972	>
973	>	// let's pass some summation method variables to fortran
974	>	setElectrostaticSummationMethod( &esm );
975	>	setScreeningMethod( &sm );
976	>	setDampingAlpha( &alphaVal );
977	>	setReactionFieldDielectric( &dielectric );
978	>	initFortranFF( &esm, &errorOut );
979	>	}
980	>
981	>	void SimInfo::addProperty(GenericData* genData) {
982	>	properties_.addProperty(genData);
983	>	}
984	>
985	>	void SimInfo::removeProperty(const std::string& propName) {
986	>	properties_.removeProperty(propName);
987	>	}
988	>
989	>	void SimInfo::clearProperties() {
990	>	properties_.clearProperties();
991	>	}
992	>
993	>	std::vector<std::string> SimInfo::getPropertyNames() {
994	>	return properties_.getPropertyNames();
995	>	}
996	>
997	>	std::vector<GenericData*> SimInfo::getProperties() {
998	>	return properties_.getProperties();
999	>	}
1000	>
1001	>	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
1002	>	return properties_.getPropertyByName(propName);
1003	>	}
1004	>
1005	>	void SimInfo::setSnapshotManager(SnapshotManager* sman) {
1006	>	if (sman_ == sman) {
1007	>	return;
1008	>	}
1009	>	delete sman_;
1010	>	sman_ = sman;
1011	>
1012	>	Molecule* mol;
1013	>	RigidBody* rb;
1014	>	Atom* atom;
1015	>	SimInfo::MoleculeIterator mi;
1016	>	Molecule::RigidBodyIterator rbIter;
1017	>	Molecule::AtomIterator atomIter;;
1018	>
1019	>	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
1020	>
1021	>	for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
1022	>	atom->setSnapshotManager(sman_);
1023	>	}
1024	>
1025	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1026	>	rb->setSnapshotManager(sman_);
1027	>	}
1028	>	}
1029	>
1030	>	}
1031	>
1032	>	Vector3d SimInfo::getComVel(){
1033	>	SimInfo::MoleculeIterator i;
1034	>	Molecule* mol;
1035	>
1036	>	Vector3d comVel(0.0);
1037	>	double totalMass = 0.0;
1038	>
1039	>
1040	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1041	>	double mass = mol->getMass();
1042	>	totalMass += mass;
1043	>	comVel += mass * mol->getComVel();
1044	>	}
1045	>
1046	>	#ifdef IS_MPI
1047	>	double tmpMass = totalMass;
1048	>	Vector3d tmpComVel(comVel);
1049	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1050	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1051	>	#endif
1052	>
1053	>	comVel /= totalMass;
1054	>
1055	>	return comVel;
1056	>	}
1057	>
1058	>	Vector3d SimInfo::getCom(){
1059	>	SimInfo::MoleculeIterator i;
1060	>	Molecule* mol;
1061	>
1062	>	Vector3d com(0.0);
1063	>	double totalMass = 0.0;
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	>	}
1070	>
1071	>	#ifdef IS_MPI
1072	>	double tmpMass = totalMass;
1073	>	Vector3d tmpCom(com);
1074	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1075	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1076	>	#endif
1077	>
1078	>	com /= totalMass;
1079	>
1080	>	return com;
1081	>
1082	>	}
1083	>
1084	>	std::ostream& operator <<(std::ostream& o, SimInfo& info) {
1085	>
1086	>	return o;
1087	>	}
1088	>
1089	>
1090	>	/*
1091	>	Returns center of mass and center of mass velocity in one function call.
1092	>	*/
1093	>
1094	>	void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1095	>	SimInfo::MoleculeIterator i;
1096	>	Molecule* mol;
1097	>
1098	>
1099	>	double totalMass = 0.0;
1100	>
1101	>
1102	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1103	>	double mass = mol->getMass();
1104	>	totalMass += mass;
1105	>	com += mass * mol->getCom();
1106	>	comVel += mass * mol->getComVel();
1107	>	}
1108	>
1109	>	#ifdef IS_MPI
1110	>	double tmpMass = totalMass;
1111	>	Vector3d tmpCom(com);
1112	>	Vector3d tmpComVel(comVel);
1113	>	MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1114	>	MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1115	>	MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1116	>	#endif
1117	>
1118	>	com /= totalMass;
1119	>	comVel /= totalMass;
1120	>	}
1121	>
1122	>	/*
1123	>	Return intertia tensor for entire system and angular momentum Vector.
1124	>
1125	>
1126	>	[  Ixx -Ixy  -Ixz ]
1127	>	J =| -Iyx  Iyy  -Iyz |
1128	>	[ -Izx -Iyz   Izz ]
1129	>	*/
1130	>
1131	>	void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1132	>
1133	>
1134	>	double xx = 0.0;
1135	>	double yy = 0.0;
1136	>	double zz = 0.0;
1137	>	double xy = 0.0;
1138	>	double xz = 0.0;
1139	>	double yz = 0.0;
1140	>	Vector3d com(0.0);
1141	>	Vector3d comVel(0.0);
1142	>
1143	>	getComAll(com, comVel);
1144	>
1145	>	SimInfo::MoleculeIterator i;
1146	>	Molecule* mol;
1147	>
1148	>	Vector3d thisq(0.0);
1149	>	Vector3d thisv(0.0);
1150	>
1151	>	double thisMass = 0.0;
1152	>
1153	>
1154	>
1155	>
1156	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1157	>
1158	>	thisq = mol->getCom()-com;
1159	>	thisv = mol->getComVel()-comVel;
1160	>	thisMass = mol->getMass();
1161	>	// Compute moment of intertia coefficients.
1162	>	xx += thisq[0]*thisq[0]*thisMass;
1163	>	yy += thisq[1]*thisq[1]*thisMass;
1164	>	zz += thisq[2]*thisq[2]*thisMass;
1165	>
1166	>	// compute products of intertia
1167	>	xy += thisq[0]*thisq[1]*thisMass;
1168	>	xz += thisq[0]*thisq[2]*thisMass;
1169	>	yz += thisq[1]*thisq[2]*thisMass;
1170	>
1171	>	angularMomentum += cross( thisq, thisv ) * thisMass;
1172	>
1173	>	}
1174	>
1175	>
1176	>	inertiaTensor(0,0) = yy + zz;
1177	>	inertiaTensor(0,1) = -xy;
1178	>	inertiaTensor(0,2) = -xz;
1179	>	inertiaTensor(1,0) = -xy;
1180	>	inertiaTensor(1,1) = xx + zz;
1181	>	inertiaTensor(1,2) = -yz;
1182	>	inertiaTensor(2,0) = -xz;
1183	>	inertiaTensor(2,1) = -yz;
1184	>	inertiaTensor(2,2) = xx + yy;
1185	>
1186	>	#ifdef IS_MPI
1187	>	Mat3x3d tmpI(inertiaTensor);
1188	>	Vector3d tmpAngMom;
1189	>	MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1190	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1191	>	#endif
1192	>
1193	>	return;
1194	>	}
1195	>
1196	>	//Returns the angular momentum of the system
1197	>	Vector3d SimInfo::getAngularMomentum(){
1198	>
1199	>	Vector3d com(0.0);
1200	>	Vector3d comVel(0.0);
1201	>	Vector3d angularMomentum(0.0);
1202	>
1203	>	getComAll(com,comVel);
1204	>
1205	>	SimInfo::MoleculeIterator i;
1206	>	Molecule* mol;
1207	>
1208	>	Vector3d thisr(0.0);
1209	>	Vector3d thisp(0.0);
1210	>
1211	>	double thisMass;
1212	>
1213	>	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1214	>	thisMass = mol->getMass();
1215	>	thisr = mol->getCom()-com;
1216	>	thisp = (mol->getComVel()-comVel)*thisMass;
1217	>
1218	>	angularMomentum += cross( thisr, thisp );
1219	>
1220	>	}
1221	>
1222	>	#ifdef IS_MPI
1223	>	Vector3d tmpAngMom;
1224	>	MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1225	>	#endif
1226	>
1227	>	return angularMomentum;
1228	>	}
1229	>
1230	>
1231	>	}//end namespace oopse
1232	>

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