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root/group/branches/new_design/OOPSE-2.0/src/brains/SimInfo.cpp
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trunk/OOPSE-2.0/src/brains/SimInfo.cpp (file contents), Revision 1492 by tim, Fri Sep 24 16:27:58 2004 UTC vs.
branches/new_design/OOPSE-2.0/src/brains/SimInfo.cpp (file contents), Revision 1901 by tim, Tue Jan 4 22:18:36 2005 UTC

# Line 1 | Line 1
1 < #include <stdlib.h>
2 < #include <string.h>
3 < #include <math.h>
1 > /*
2 > * Copyright (C) 2000-2004  Object Oriented Parallel Simulation Engine (OOPSE) project
3 > *
4 > * Contact: oopse@oopse.org
5 > *
6 > * This program is free software; you can redistribute it and/or
7 > * modify it under the terms of the GNU Lesser General Public License
8 > * as published by the Free Software Foundation; either version 2.1
9 > * of the License, or (at your option) any later version.
10 > * All we ask is that proper credit is given for our work, which includes
11 > * - but is not limited to - adding the above copyright notice to the beginning
12 > * of your source code files, and to any copyright notice that you may distribute
13 > * with programs based on this work.
14 > *
15 > * This program is distributed in the hope that it will be useful,
16 > * but WITHOUT ANY WARRANTY; without even the implied warranty of
17 > * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
18 > * GNU Lesser General Public License for more details.
19 > *
20 > * You should have received a copy of the GNU Lesser General Public License
21 > * along with this program; if not, write to the Free Software
22 > * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
23 > *
24 > */
25  
26 < #include <iostream>
27 < using namespace std;
26 > /**
27 > * @file SimInfo.cpp
28 > * @author    tlin
29 > * @date  11/02/2004
30 > * @version 1.0
31 > */
32  
33 + #include <algorithm>
34 + #include <set>
35 +
36   #include "brains/SimInfo.hpp"
37 < #define __C
38 < #include "brains/fSimulation.h"
37 > #include "math/Vector3.hpp"
38 > #include "primitives/Molecule.hpp"
39 > #include "UseTheForce/doForces_interface.h"
40 > #include "UseTheForce/notifyCutoffs_interface.h"
41 > #include "utils/MemoryUtils.hpp"
42   #include "utils/simError.h"
43  
13 – #include "UseTheForce/fortranWrappers.hpp"
14 –
15 – #include "math/MatVec3.h"
16 –
44   #ifdef IS_MPI
45 < #include "brains/mpiSimulation.hpp"
46 < #endif
45 > #include "UseTheForce/mpiComponentPlan.h"
46 > #include "UseTheForce/DarkSide/simParallel_interface.h"
47 > #endif
48  
49 < 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 < }
49 > namespace oopse {
50  
51 < SimInfo* currentInfo;
51 > SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
52 >                                ForceField* ff, Globals* simParams) :
53 >                                forceField_(ff), simParams_(simParams),
54 >                                ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
55 >                                nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
56 >                                nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
57 >                                nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
58 >                                nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
59 >                                sman_(NULL), fortranInitialized_(false) {
60  
61 < SimInfo::SimInfo(){
61 >            
62 >    std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
63 >    MoleculeStamp* molStamp;
64 >    int nMolWithSameStamp;
65 >    int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
66 >    int nGroups = 0;          //total cutoff groups defined in meta-data file
67 >    CutoffGroupStamp* cgStamp;    
68 >    RigidBodyStamp* rbStamp;
69 >    int nRigidAtoms = 0;
70 >    
71 >    for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
72 >        molStamp = i->first;
73 >        nMolWithSameStamp = i->second;
74 >        
75 >        addMoleculeStamp(molStamp, nMolWithSameStamp);
76  
77 <  n_constraints = 0;
78 <  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;
77 >        //calculate atoms in molecules
78 >        nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;  
79  
47 –  haveRcut = 0;
48 –  haveRsw = 0;
49 –  boxIsInit = 0;
50 –  
51 –  resetTime = 1e99;
80  
81 <  orthoRhombic = 0;
82 <  orthoTolerance = 1E-6;
83 <  useInitXSstate = true;
81 >        //calculate atoms in cutoff groups
82 >        int nAtomsInGroups = 0;
83 >        int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
84 >        
85 >        for (int j=0; j < nCutoffGroupsInStamp; j++) {
86 >            cgStamp = molStamp->getCutoffGroup(j);
87 >            nAtomsInGroups += cgStamp->getNMembers();
88 >        }
89  
90 <  usePBC = 0;
91 <  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;
90 >        nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
91 >        nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;            
92  
93 <  haveCutoffGroups = false;
93 >        //calculate atoms in rigid bodies
94 >        int nAtomsInRigidBodies = 0;
95 >        int nRigidBodiesInStamp = molStamp->getNCutoffGroups();
96 >        
97 >        for (int j=0; j < nRigidBodiesInStamp; j++) {
98 >            rbStamp = molStamp->getRigidBody(j);
99 >            nAtomsInRigidBodies += rbStamp->getNMembers();
100 >        }
101  
102 <  excludes = Exclude::Instance();
102 >        nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
103 >        nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;            
104 >        
105 >    }
106  
107 <  myConfiguration = new SimState();
107 >    //every free atom (atom does not belong to cutoff groups) is a cutoff group
108 >    //therefore the total number of cutoff groups in the system is equal to
109 >    //the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
110 >    //file plus the number of cutoff groups defined in meta-data file
111 >    nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
112  
113 <  has_minimizer = false;
114 <  the_minimizer =NULL;
113 >    //every free atom (atom does not belong to rigid bodies) is an integrable object
114 >    //therefore the total number of  integrable objects in the system is equal to
115 >    //the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
116 >    //file plus the number of  rigid bodies defined in meta-data file
117 >    nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
118  
119 <  ngroup = 0;
119 >    nGlobalMols_ = molStampIds_.size();
120  
121 <  wrapMeSimInfo( this );
121 > #ifdef IS_MPI    
122 >    molToProcMap_.resize(nGlobalMols_);
123 > #endif
124 >    
125   }
126  
127 + SimInfo::~SimInfo() {
128 +    //MemoryUtils::deleteVectorOfPointer(molecules_);
129  
130 < SimInfo::~SimInfo(){
130 >    MemoryUtils::deleteVectorOfPointer(moleculeStamps_);
131 >    
132 >    delete sman_;
133 >    delete simParams_;
134 >    delete forceField_;
135  
85 –  delete myConfiguration;
86 –
87 –  map<string, GenericData*>::iterator i;
88 –  
89 –  for(i = properties.begin(); i != properties.end(); i++)
90 –    delete (*i).second;
91 –
136   }
137  
94 – void SimInfo::setBox(double newBox[3]) {
95 –  
96 –  int i, j;
97 –  double tempMat[3][3];
138  
139 <  for(i=0; i<3; i++)
140 <    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
139 > bool SimInfo::addMolecule(Molecule* mol) {
140 >    MoleculeIterator i;
141  
142 <  tempMat[0][0] = newBox[0];
143 <  tempMat[1][1] = newBox[1];
104 <  tempMat[2][2] = newBox[2];
142 >    i = molecules_.find(mol->getGlobalIndex());
143 >    if (i == molecules_.end() ) {
144  
145 <  setBoxM( tempMat );
145 >        molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
146 >        
147 >        nAtoms_ += mol->getNAtoms();
148 >        nBonds_ += mol->getNBonds();
149 >        nBends_ += mol->getNBends();
150 >        nTorsions_ += mol->getNTorsions();
151 >        nRigidBodies_ += mol->getNRigidBodies();
152 >        nIntegrableObjects_ += mol->getNIntegrableObjects();
153 >        nCutoffGroups_ += mol->getNCutoffGroups();
154 >        nConstraints_ += mol->getNConstraintPairs();
155  
156 +        addExcludePairs(mol);
157 +        
158 +        return true;
159 +    } else {
160 +        return false;
161 +    }
162   }
163  
164 < void SimInfo::setBoxM( double theBox[3][3] ){
165 <  
166 <  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);
164 > bool SimInfo::removeMolecule(Molecule* mol) {
165 >    MoleculeIterator i;
166 >    i = molecules_.find(mol->getGlobalIndex());
167  
168 <  if( !boxIsInit ) boxIsInit = 1;
168 >    if (i != molecules_.end() ) {
169  
170 <  for(i=0; i < 3; i++)
171 <    for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
172 <  
173 <  calcBoxL();
174 <  calcHmatInv();
170 >        assert(mol == i->second);
171 >        
172 >        nAtoms_ -= mol->getNAtoms();
173 >        nBonds_ -= mol->getNBonds();
174 >        nBends_ -= mol->getNBends();
175 >        nTorsions_ -= mol->getNTorsions();
176 >        nRigidBodies_ -= mol->getNRigidBodies();
177 >        nIntegrableObjects_ -= mol->getNIntegrableObjects();
178 >        nCutoffGroups_ -= mol->getNCutoffGroups();
179 >        nConstraints_ -= mol->getNConstraintPairs();
180  
181 <  for(i=0; i < 3; i++) {
182 <    for (j=0; j < 3; j++) {
183 <      FortranHmat[3*j + i] = Hmat[i][j];
184 <      FortranHmatInv[3*j + i] = HmatInv[i][j];
181 >        removeExcludePairs(mol);
182 >        molecules_.erase(mol->getGlobalIndex());
183 >
184 >        delete mol;
185 >        
186 >        return true;
187 >    } else {
188 >        return false;
189      }
133 –  }
190  
135 –  setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
136 –
137 – }
138 –
191  
192 < void SimInfo::getBoxM (double theBox[3][3]) {
192 > }    
193  
194 <  int i, j;
195 <  for(i=0; i<3; i++)
196 <    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
194 >        
195 > Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
196 >    i = molecules_.begin();
197 >    return i == molecules_.end() ? NULL : i->second;
198 > }    
199 >
200 > Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
201 >    ++i;
202 >    return i == molecules_.end() ? NULL : i->second;    
203   }
204  
205  
206 < void SimInfo::scaleBox(double scale) {
207 <  double theBox[3][3];
208 <  int i, j;
206 > void SimInfo::calcNdf() {
207 >    int ndf_local;
208 >    MoleculeIterator i;
209 >    std::vector<StuntDouble*>::iterator j;
210 >    Molecule* mol;
211 >    StuntDouble* integrableObject;
212  
213 <  // cerr << "Scaling box by " << scale << "\n";
213 >    ndf_local = 0;
214 >    
215 >    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
216 >        for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
217 >               integrableObject = mol->nextIntegrableObject(j)) {
218  
219 <  for(i=0; i<3; i++)
155 <    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
219 >            ndf_local += 3;
220  
221 <  setBoxM(theBox);
221 >            if (integrableObject->isDirectional()) {
222 >                if (integrableObject->isLinear()) {
223 >                    ndf_local += 2;
224 >                } else {
225 >                    ndf_local += 3;
226 >                }
227 >            }
228 >            
229 >        }//end for (integrableObject)
230 >    }// end for (mol)
231 >    
232 >    // n_constraints is local, so subtract them on each processor
233 >    ndf_local -= nConstraints_;
234  
235 < }
235 > #ifdef IS_MPI
236 >    MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
237 > #else
238 >    ndf_ = ndf_local;
239 > #endif
240  
241 < void SimInfo::calcHmatInv( void ) {
242 <  
243 <  int oldOrtho;
164 <  int i,j;
165 <  double smallDiag;
166 <  double tol;
167 <  double sanity[3][3];
241 >    // nZconstraints_ is global, as are the 3 COM translations for the
242 >    // entire system:
243 >    ndf_ = ndf_ - 3 - nZconstraint_;
244  
245 <  invertMat3( Hmat, HmatInv );
245 > }
246  
247 <  // check to see if Hmat is orthorhombic
248 <  
173 <  oldOrtho = orthoRhombic;
247 > void SimInfo::calcNdfRaw() {
248 >    int ndfRaw_local;
249  
250 <  smallDiag = fabs(Hmat[0][0]);
251 <  if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
252 <  if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
253 <  tol = smallDiag * orthoTolerance;
250 >    MoleculeIterator i;
251 >    std::vector<StuntDouble*>::iterator j;
252 >    Molecule* mol;
253 >    StuntDouble* integrableObject;
254  
255 <  orthoRhombic = 1;
256 <  
257 <  for (i = 0; i < 3; i++ ) {
258 <    for (j = 0 ; j < 3; j++) {
259 <      if (i != j) {
260 <        if (orthoRhombic) {
186 <          if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
187 <        }        
188 <      }
189 <    }
190 <  }
255 >    // Raw degrees of freedom that we have to set
256 >    ndfRaw_local = 0;
257 >    
258 >    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
259 >        for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
260 >               integrableObject = mol->nextIntegrableObject(j)) {
261  
262 <  if( oldOrtho != orthoRhombic ){
263 <    
264 <    if( orthoRhombic ) {
265 <      sprintf( painCave.errMsg,
266 <               "OOPSE is switching from the default Non-Orthorhombic\n"
267 <               "\tto the faster Orthorhombic periodic boundary computations.\n"
268 <               "\tThis is usually a good thing, but if you wan't the\n"
269 <               "\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
270 <               "\tvariable ( currently set to %G ) smaller.\n",
271 <               orthoTolerance);
272 <      painCave.severity = OOPSE_INFO;
203 <      simError();
262 >            ndfRaw_local += 3;
263 >
264 >            if (integrableObject->isDirectional()) {
265 >                if (integrableObject->isLinear()) {
266 >                    ndfRaw_local += 2;
267 >                } else {
268 >                    ndfRaw_local += 3;
269 >                }
270 >            }
271 >            
272 >        }
273      }
274 <    else {
275 <      sprintf( painCave.errMsg,
276 <               "OOPSE is switching from the faster Orthorhombic to the more\n"
277 <               "\tflexible Non-Orthorhombic periodic boundary computations.\n"
278 <               "\tThis is usually because the box has deformed under\n"
279 <               "\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 <  }
274 >    
275 > #ifdef IS_MPI
276 >    MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
277 > #else
278 >    ndfRaw_ = ndfRaw_local;
279 > #endif
280   }
281  
282 < void SimInfo::calcBoxL( void ){
282 > void SimInfo::calcNdfTrans() {
283 >    int ndfTrans_local;
284  
285 <  double dx, dy, dz, dsq;
285 >    ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
286  
224 –  // boxVol = Determinant of Hmat
287  
288 <  boxVol = matDet3( Hmat );
288 > #ifdef IS_MPI
289 >    MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
290 > #else
291 >    ndfTrans_ = ndfTrans_local;
292 > #endif
293  
294 <  // boxLx
295 <  
296 <  dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
231 <  dsq = dx*dx + dy*dy + dz*dz;
232 <  boxL[0] = sqrt( dsq );
233 <  //maxCutoff = 0.5 * boxL[0];
294 >    ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
295 >
296 > }
297  
298 <  // boxLy
299 <  
300 <  dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
301 <  dsq = dx*dx + dy*dy + dz*dz;
302 <  boxL[1] = sqrt( dsq );
303 <  //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
298 > void SimInfo::addExcludePairs(Molecule* mol) {
299 >    std::vector<Bond*>::iterator bondIter;
300 >    std::vector<Bend*>::iterator bendIter;
301 >    std::vector<Torsion*>::iterator torsionIter;
302 >    Bond* bond;
303 >    Bend* bend;
304 >    Torsion* torsion;
305 >    int a;
306 >    int b;
307 >    int c;
308 >    int d;
309 >    
310 >    for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
311 >        a = bond->getAtomA()->getGlobalIndex();
312 >        b = bond->getAtomB()->getGlobalIndex();        
313 >        exclude_.addPair(a, b);
314 >    }
315  
316 +    for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
317 +        a = bend->getAtomA()->getGlobalIndex();
318 +        b = bend->getAtomB()->getGlobalIndex();        
319 +        c = bend->getAtomC()->getGlobalIndex();
320  
321 <  // boxLz
322 <  
323 <  dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
324 <  dsq = dx*dx + dy*dy + dz*dz;
247 <  boxL[2] = sqrt( dsq );
248 <  //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
321 >        exclude_.addPair(a, b);
322 >        exclude_.addPair(a, c);
323 >        exclude_.addPair(b, c);        
324 >    }
325  
326 <  //calculate the max cutoff
327 <  maxCutoff =  calcMaxCutOff();
328 <  
329 <  checkCutOffs();
326 >    for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
327 >        a = torsion->getAtomA()->getGlobalIndex();
328 >        b = torsion->getAtomB()->getGlobalIndex();        
329 >        c = torsion->getAtomC()->getGlobalIndex();        
330 >        d = torsion->getAtomD()->getGlobalIndex();        
331  
332 +        exclude_.addPair(a, b);
333 +        exclude_.addPair(a, c);
334 +        exclude_.addPair(a, d);
335 +        exclude_.addPair(b, c);
336 +        exclude_.addPair(b, d);
337 +        exclude_.addPair(c, d);        
338 +    }
339 +
340 +    
341   }
342  
343 + void SimInfo::removeExcludePairs(Molecule* mol) {
344 +    std::vector<Bond*>::iterator bondIter;
345 +    std::vector<Bend*>::iterator bendIter;
346 +    std::vector<Torsion*>::iterator torsionIter;
347 +    Bond* bond;
348 +    Bend* bend;
349 +    Torsion* torsion;
350 +    int a;
351 +    int b;
352 +    int c;
353 +    int d;
354 +    
355 +    for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
356 +        a = bond->getAtomA()->getGlobalIndex();
357 +        b = bond->getAtomB()->getGlobalIndex();        
358 +        exclude_.removePair(a, b);
359 +    }
360  
361 < double SimInfo::calcMaxCutOff(){
361 >    for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
362 >        a = bend->getAtomA()->getGlobalIndex();
363 >        b = bend->getAtomB()->getGlobalIndex();        
364 >        c = bend->getAtomC()->getGlobalIndex();
365  
366 <  double ri[3], rj[3], rk[3];
367 <  double rij[3], rjk[3], rki[3];
368 <  double minDist;
366 >        exclude_.removePair(a, b);
367 >        exclude_.removePair(a, c);
368 >        exclude_.removePair(b, c);        
369 >    }
370  
371 <  ri[0] = Hmat[0][0];
372 <  ri[1] = Hmat[1][0];
373 <  ri[2] = Hmat[2][0];
371 >    for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
372 >        a = torsion->getAtomA()->getGlobalIndex();
373 >        b = torsion->getAtomB()->getGlobalIndex();        
374 >        c = torsion->getAtomC()->getGlobalIndex();        
375 >        d = torsion->getAtomD()->getGlobalIndex();        
376  
377 <  rj[0] = Hmat[0][1];
378 <  rj[1] = Hmat[1][1];
379 <  rj[2] = Hmat[2][1];
377 >        exclude_.removePair(a, b);
378 >        exclude_.removePair(a, c);
379 >        exclude_.removePair(a, d);
380 >        exclude_.removePair(b, c);
381 >        exclude_.removePair(b, d);
382 >        exclude_.removePair(c, d);        
383 >    }
384  
385 <  rk[0] = Hmat[0][2];
273 <  rk[1] = Hmat[1][2];
274 <  rk[2] = Hmat[2][2];
275 <    
276 <  crossProduct3(ri, rj, rij);
277 <  distXY = dotProduct3(rk,rij) / norm3(rij);
385 > }
386  
279 –  crossProduct3(rj,rk, rjk);
280 –  distYZ = dotProduct3(ri,rjk) / norm3(rjk);
387  
388 <  crossProduct3(rk,ri, rki);
389 <  distZX = dotProduct3(rj,rki) / norm3(rki);
388 > void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
389 >    int curStampId;
390  
391 <  minDist = min(min(distXY, distYZ), distZX);
392 <  return minDist/2;
393 <  
391 >    //index from 0
392 >    curStampId = moleculeStamps_.size();
393 >
394 >    moleculeStamps_.push_back(molStamp);
395 >    molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
396   }
397  
398 < void SimInfo::wrapVector( double thePos[3] ){
398 > void SimInfo::update() {
399  
400 <  int i;
293 <  double scaled[3];
400 >    setupSimType();
401  
402 <  if( !orthoRhombic ){
403 <    // calc the scaled coordinates.
404 <  
402 > #ifdef IS_MPI
403 >    setupFortranParallel();
404 > #endif
405  
406 <    matVecMul3(HmatInv, thePos, scaled);
300 <    
301 <    for(i=0; i<3; i++)
302 <      scaled[i] -= roundMe(scaled[i]);
303 <    
304 <    // calc the wrapped real coordinates from the wrapped scaled coordinates
305 <    
306 <    matVecMul3(Hmat, scaled, thePos);
406 >    setupFortranSim();
407  
408 <  }
409 <  else{
410 <    // calc the scaled coordinates.
408 >    //setup fortran force field
409 >    /** @deprecate */    
410 >    int isError = 0;
411 >    initFortranFF( &fInfo_.SIM_uses_RF , &isError );
412 >    if(isError){
413 >        sprintf( painCave.errMsg,
414 >         "ForceField error: There was an error initializing the forceField in fortran.\n" );
415 >        painCave.isFatal = 1;
416 >        simError();
417 >    }
418 >  
419      
420 <    for(i=0; i<3; i++)
421 <      scaled[i] = thePos[i]*HmatInv[i][i];
422 <    
423 <    // wrap the scaled coordinates
424 <    
425 <    for(i=0; i<3; i++)
426 <      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 <    
420 >    setupCutoff();
421 >
422 >    calcNdf();
423 >    calcNdfRaw();
424 >    calcNdfTrans();
425 >
426 >    fortranInitialized_ = true;
427   }
428  
429 + std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
430 +    SimInfo::MoleculeIterator mi;
431 +    Molecule* mol;
432 +    Molecule::AtomIterator ai;
433 +    Atom* atom;
434 +    std::set<AtomType*> atomTypes;
435  
436 < int SimInfo::getNDF(){
330 <  int ndf_local;
436 >    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
437  
438 <  ndf_local = 0;
439 <  
440 <  for(int i = 0; i < integrableObjects.size(); i++){
441 <    ndf_local += 3;
336 <    if (integrableObjects[i]->isDirectional()) {
337 <      if (integrableObjects[i]->isLinear())
338 <        ndf_local += 2;
339 <      else
340 <        ndf_local += 3;
438 >        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
439 >            atomTypes.insert(atom->getAtomType());
440 >        }
441 >        
442      }
342 –  }
443  
444 <  // n_constraints is local, so subtract them on each processor:
444 >    return atomTypes;        
445 > }
446  
447 <  ndf_local -= n_constraints;
447 > void SimInfo::setupSimType() {
448 >    std::set<AtomType*>::iterator i;
449 >    std::set<AtomType*> atomTypes;
450 >    atomTypes = getUniqueAtomTypes();
451 >    
452 >    int useLennardJones = 0;
453 >    int useElectrostatic = 0;
454 >    int useEAM = 0;
455 >    int useCharge = 0;
456 >    int useDirectional = 0;
457 >    int useDipole = 0;
458 >    int useGayBerne = 0;
459 >    int useSticky = 0;
460 >    int useShape = 0;
461 >    int useFLARB = 0; //it is not in AtomType yet
462 >    int useDirectionalAtom = 0;    
463 >    int useElectrostatics = 0;
464 >    //usePBC and useRF are from simParams
465 >    int usePBC = simParams_->getPBC();
466 >    int useRF = simParams_->getUseRF();
467  
468 < #ifdef IS_MPI
469 <  MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
470 < #else
471 <  ndf = ndf_local;
468 >    //loop over all of the atom types
469 >    for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
470 >        useLennardJones |= (*i)->isLennardJones();
471 >        useElectrostatic |= (*i)->isElectrostatic();
472 >        useEAM |= (*i)->isEAM();
473 >        useCharge |= (*i)->isCharge();
474 >        useDirectional |= (*i)->isDirectional();
475 >        useDipole |= (*i)->isDipole();
476 >        useGayBerne |= (*i)->isGayBerne();
477 >        useSticky |= (*i)->isSticky();
478 >        useShape |= (*i)->isShape();
479 >    }
480 >
481 >    if (useSticky || useDipole || useGayBerne || useShape) {
482 >        useDirectionalAtom = 1;
483 >    }
484 >
485 >    if (useCharge || useDipole) {
486 >        useElectrostatics = 1;
487 >    }
488 >
489 > #ifdef IS_MPI    
490 >    int temp;
491 >
492 >    temp = usePBC;
493 >    MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
494 >
495 >    temp = useDirectionalAtom;
496 >    MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
497 >
498 >    temp = useLennardJones;
499 >    MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
500 >
501 >    temp = useElectrostatics;
502 >    MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
503 >
504 >    temp = useCharge;
505 >    MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
506 >
507 >    temp = useDipole;
508 >    MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
509 >
510 >    temp = useSticky;
511 >    MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
512 >
513 >    temp = useGayBerne;
514 >    MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
515 >
516 >    temp = useEAM;
517 >    MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
518 >
519 >    temp = useShape;
520 >    MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);  
521 >
522 >    temp = useFLARB;
523 >    MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
524 >
525 >    temp = useRF;
526 >    MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
527 >    
528   #endif
529  
530 <  // nZconstraints is global, as are the 3 COM translations for the
531 <  // entire system:
530 >    fInfo_.SIM_uses_PBC = usePBC;    
531 >    fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
532 >    fInfo_.SIM_uses_LennardJones = useLennardJones;
533 >    fInfo_.SIM_uses_Electrostatics = useElectrostatics;    
534 >    fInfo_.SIM_uses_Charges = useCharge;
535 >    fInfo_.SIM_uses_Dipoles = useDipole;
536 >    fInfo_.SIM_uses_Sticky = useSticky;
537 >    fInfo_.SIM_uses_GayBerne = useGayBerne;
538 >    fInfo_.SIM_uses_EAM = useEAM;
539 >    fInfo_.SIM_uses_Shapes = useShape;
540 >    fInfo_.SIM_uses_FLARB = useFLARB;
541 >    fInfo_.SIM_uses_RF = useRF;
542  
543 <  ndf = ndf - 3 - nZconstraints;
543 >    if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
544  
545 <  return ndf;
545 >        if (simParams_->haveDielectric()) {
546 >            fInfo_.dielect = simParams_->getDielectric();
547 >        } else {
548 >            sprintf(painCave.errMsg,
549 >                    "SimSetup Error: No Dielectric constant was set.\n"
550 >                    "\tYou are trying to use Reaction Field without"
551 >                    "\tsetting a dielectric constant!\n");
552 >            painCave.isFatal = 1;
553 >            simError();
554 >        }
555 >        
556 >    } else {
557 >        fInfo_.dielect = 0.0;
558 >    }
559 >
560   }
561  
562 < int SimInfo::getNDFraw() {
563 <  int ndfRaw_local;
562 > void SimInfo::setupFortranSim() {
563 >    int isError;
564 >    int nExclude;
565 >    std::vector<int> fortranGlobalGroupMembership;
566 >    
567 >    nExclude = exclude_.getSize();
568 >    isError = 0;
569  
570 <  // Raw degrees of freedom that we have to set
571 <  ndfRaw_local = 0;
570 >    //globalGroupMembership_ is filled by SimCreator    
571 >    for (int i = 0; i < nGlobalAtoms_; i++) {
572 >        fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
573 >    }
574  
575 <  for(int i = 0; i < integrableObjects.size(); i++){
576 <    ndfRaw_local += 3;
577 <    if (integrableObjects[i]->isDirectional()) {
578 <       if (integrableObjects[i]->isLinear())
579 <        ndfRaw_local += 2;
580 <      else
581 <        ndfRaw_local += 3;
575 >    //calculate mass ratio of cutoff group
576 >    std::vector<double> mfact;
577 >    SimInfo::MoleculeIterator mi;
578 >    Molecule* mol;
579 >    Molecule::CutoffGroupIterator ci;
580 >    CutoffGroup* cg;
581 >    Molecule::AtomIterator ai;
582 >    Atom* atom;
583 >    double totalMass;
584 >
585 >    //to avoid memory reallocation, reserve enough space for mfact
586 >    mfact.reserve(getNCutoffGroups());
587 >    
588 >    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
589 >        for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
590 >
591 >            totalMass = cg->getMass();
592 >            for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
593 >                        mfact.push_back(atom->getMass()/totalMass);
594 >            }
595 >
596 >        }      
597      }
598 <  }
598 >
599 >    //fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
600 >    std::vector<int> identArray;
601 >
602 >    //to avoid memory reallocation, reserve enough space identArray
603 >    identArray.reserve(getNAtoms());
604      
605 < #ifdef IS_MPI
606 <  MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
607 < #else
608 <  ndfRaw = ndfRaw_local;
609 < #endif
605 >    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
606 >        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
607 >            identArray.push_back(atom->getIdent());
608 >        }
609 >    }    
610  
611 <  return ndfRaw;
612 < }
611 >    //fill molMembershipArray
612 >    //molMembershipArray is filled by SimCreator    
613 >    std::vector<int> molMembershipArray(nGlobalAtoms_);
614 >    for (int i = 0; i < nGlobalAtoms_; i++) {
615 >        molMembershipArray[i] = globalMolMembership_[i] + 1;
616 >    }
617 >    
618 >    //setup fortran simulation
619 >    //gloalExcludes and molMembershipArray should go away (They are never used)
620 >    //why the hell fortran need to know molecule?
621 >    //OOPSE = Object-Obfuscated Parallel Simulation Engine
622 >    int nGlobalExcludes = 0;
623 >    int* globalExcludes = NULL;
624 >    int* excludeList = exclude_.getExcludeList();
625 >    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
626 >                  &nGlobalExcludes, globalExcludes, &molMembershipArray[0],
627 >                  &mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
628  
629 < int SimInfo::getNDFtranslational() {
388 <  int ndfTrans_local;
629 >    if( isError ){
630  
631 <  ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
631 >        sprintf( painCave.errMsg,
632 >                 "There was an error setting the simulation information in fortran.\n" );
633 >        painCave.isFatal = 1;
634 >        painCave.severity = OOPSE_ERROR;
635 >        simError();
636 >    }
637  
638 + #ifdef IS_MPI
639 +    sprintf( checkPointMsg,
640 +       "succesfully sent the simulation information to fortran.\n");
641 +    MPIcheckPoint();
642 + #endif // is_mpi
643 + }
644  
645 +
646   #ifdef IS_MPI
647 <  MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
648 < #else
649 <  ndfTrans = ndfTrans_local;
650 < #endif
647 > void SimInfo::setupFortranParallel() {
648 >    
649 >    //SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
650 >    std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
651 >    std::vector<int> localToGlobalCutoffGroupIndex;
652 >    SimInfo::MoleculeIterator mi;
653 >    Molecule::AtomIterator ai;
654 >    Molecule::CutoffGroupIterator ci;
655 >    Molecule* mol;
656 >    Atom* atom;
657 >    CutoffGroup* cg;
658 >    mpiSimData parallelData;
659 >    int isError;
660  
661 <  ndfTrans = ndfTrans - 3 - nZconstraints;
661 >    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
662  
663 <  return ndfTrans;
664 < }
663 >        //local index(index in DataStorge) of atom is important
664 >        for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
665 >            localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
666 >        }
667  
668 < int SimInfo::getTotIntegrableObjects() {
669 <  int nObjs_local;
670 <  int nObjs;
668 >        //local index of cutoff group is trivial, it only depends on the order of travesing
669 >        for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
670 >            localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
671 >        }        
672 >        
673 >    }
674  
675 <  nObjs_local =  integrableObjects.size();
675 >    //fill up mpiSimData struct
676 >    parallelData.nMolGlobal = getNGlobalMolecules();
677 >    parallelData.nMolLocal = getNMolecules();
678 >    parallelData.nAtomsGlobal = getNGlobalAtoms();
679 >    parallelData.nAtomsLocal = getNAtoms();
680 >    parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
681 >    parallelData.nGroupsLocal = getNCutoffGroups();
682 >    parallelData.myNode = worldRank;
683 >    MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
684  
685 +    //pass mpiSimData struct and index arrays to fortran
686 +    setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
687 +                    &localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
688 +                    &localToGlobalCutoffGroupIndex[0], &isError);
689  
690 < #ifdef IS_MPI
691 <  MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
692 < #else
693 <  nObjs = nObjs_local;
694 < #endif
690 >    if (isError) {
691 >        sprintf(painCave.errMsg,
692 >                "mpiRefresh errror: fortran didn't like something we gave it.\n");
693 >        painCave.isFatal = 1;
694 >        simError();
695 >    }
696  
697 +    sprintf(checkPointMsg, " mpiRefresh successful.\n");
698 +    MPIcheckPoint();
699  
700 <  return nObjs;
700 >
701   }
702  
703 < void SimInfo::refreshSim(){
703 > #endif
704  
705 <  simtype fInfo;
424 <  int isError;
425 <  int n_global;
426 <  int* excl;
705 > double SimInfo::calcMaxCutoffRadius() {
706  
428 –  fInfo.dielect = 0.0;
707  
708 <  if( useDipoles ){
709 <    if( useReactionField )fInfo.dielect = dielectric;
710 <  }
708 >    std::set<AtomType*> atomTypes;
709 >    std::set<AtomType*>::iterator i;
710 >    std::vector<double> cutoffRadius;
711  
712 <  fInfo.SIM_uses_PBC = usePBC;
713 <  //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;
712 >    //get the unique atom types
713 >    atomTypes = getUniqueAtomTypes();
714  
715 <  n_exclude = excludes->getSize();
716 <  excl = excludes->getFortranArray();
717 <  
715 >    //query the max cutoff radius among these atom types
716 >    for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
717 >        cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
718 >    }
719 >
720 >    double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
721   #ifdef IS_MPI
722 <  n_global = mpiSim->getNAtomsGlobal();
452 < #else
453 <  n_global = n_atoms;
722 >    //pick the max cutoff radius among the processors
723   #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);
724  
725 <  if( isError ){
467 <    
468 <    sprintf( painCave.errMsg,
469 <             "There was an error setting the simulation information in fortran.\n" );
470 <    painCave.isFatal = 1;
471 <    painCave.severity = OOPSE_ERROR;
472 <    simError();
473 <  }
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();
725 >    return maxCutoffRadius;
726   }
727  
728 < void SimInfo::setDefaultRcut( double theRcut ){
729 <  
730 <  haveRcut = 1;
731 <  rCut = theRcut;
732 <  rList = rCut + 1.0;
733 <  
734 <  notifyFortranCutOffs( &rCut, &rSw, &rList );
735 < }
728 > void SimInfo::setupCutoff() {
729 >    double rcut_;  //cutoff radius
730 >    double rsw_; //switching radius
731 >    
732 >    if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
733 >        
734 >        if (!simParams_->haveRcut()){
735 >            sprintf(painCave.errMsg,
736 >                "SimCreator Warning: No value was set for the cutoffRadius.\n"
737 >                "\tOOPSE will use a default value of 15.0 angstroms"
738 >                "\tfor the cutoffRadius.\n");
739 >            painCave.isFatal = 0;
740 >            simError();
741 >            rcut_ = 15.0;
742 >        } else{
743 >            rcut_ = simParams_->getRcut();
744 >        }
745  
746 < void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
746 >        if (!simParams_->haveRsw()){
747 >            sprintf(painCave.errMsg,
748 >                "SimCreator Warning: No value was set for switchingRadius.\n"
749 >                "\tOOPSE will use a default value of\n"
750 >                "\t0.95 * cutoffRadius for the switchingRadius\n");
751 >            painCave.isFatal = 0;
752 >            simError();
753 >            rsw_ = 0.95 * rcut_;
754 >        } else{
755 >            rsw_ = simParams_->getRsw();
756 >        }
757  
758 <  rSw = theRsw;
759 <  setDefaultRcut( theRcut );
758 >    } else {
759 >        // if charge, dipole or reaction field is not used and the cutofff radius is not specified in
760 >        //meta-data file, the maximum cutoff radius calculated from forcefiled will be used
761 >        
762 >        if (simParams_->haveRcut()) {
763 >            rcut_ = simParams_->getRcut();
764 >        } else {
765 >            //set cutoff radius to the maximum cutoff radius based on atom types in the whole system
766 >            rcut_ = calcMaxCutoffRadius();
767 >        }
768 >
769 >        if (simParams_->haveRsw()) {
770 >            rsw_  = simParams_->getRsw();
771 >        } else {
772 >            rsw_ = rcut_;
773 >        }
774 >    
775 >    }
776 >        
777 >    double rnblist = rcut_ + 1; // skin of neighbor list
778 >
779 >    //Pass these cutoff radius etc. to fortran. This function should be called once and only once
780 >    notifyFortranCutoffs(&rcut_, &rsw_, &rnblist);
781   }
782  
783 + void SimInfo::addProperty(GenericData* genData) {
784 +    properties_.addProperty(genData);  
785 + }
786  
787 < void SimInfo::checkCutOffs( void ){
788 <  
504 <  if( boxIsInit ){
505 <    
506 <    //we need to check cutOffs against the box
507 <    
508 <    if( rCut > maxCutoff ){
509 <      sprintf( painCave.errMsg,
510 <               "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;
523 <      painCave.isFatal = 1;
524 <      simError();
525 <    }    
526 <  } else {
527 <    // initialize this stuff before using it, OK?
528 <    sprintf( painCave.errMsg,
529 <             "Trying to check cutoffs without a box.\n"
530 <             "\tOOPSE should have better programmers than that.\n" );
531 <    painCave.severity = OOPSE_ERROR;
532 <    painCave.isFatal = 1;
533 <    simError();      
534 <  }
535 <  
787 > void SimInfo::removeProperty(const std::string& propName) {
788 >    properties_.removeProperty(propName);  
789   }
790  
791 < void SimInfo::addProperty(GenericData* prop){
791 > void SimInfo::clearProperties() {
792 >    properties_.clearProperties();
793 > }
794  
795 <  map<string, GenericData*>::iterator result;
796 <  result = properties.find(prop->getID());
797 <  
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()){
547 <    
548 <    delete (*result).second;
549 <    (*result).second = prop;
795 > std::vector<std::string> SimInfo::getPropertyNames() {
796 >    return properties_.getPropertyNames();  
797 > }
798        
799 <  }
800 <  else{
799 > std::vector<GenericData*> SimInfo::getProperties() {
800 >    return properties_.getProperties();
801 > }
802  
803 <    properties[prop->getID()] = prop;
803 > GenericData* SimInfo::getPropertyByName(const std::string& propName) {
804 >    return properties_.getPropertyByName(propName);
805 > }
806  
807 <  }
807 > void SimInfo::setSnapshotManager(SnapshotManager* sman) {
808 >    sman_ = sman;
809 >
810 >    Molecule* mol;
811 >    RigidBody* rb;
812 >    Atom* atom;
813 >    SimInfo::MoleculeIterator mi;
814 >    Molecule::RigidBodyIterator rbIter;
815 >    Molecule::AtomIterator atomIter;;
816 >
817 >    for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
818 >        
819 >        for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
820 >            atom->setSnapshotManager(sman_);
821 >        }
822 >        
823 >        for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
824 >            rb->setSnapshotManager(sman_);
825 >        }
826 >    }    
827      
828   }
829  
830 < GenericData* SimInfo::getProperty(const string& propName){
830 > Vector3d SimInfo::getComVel(){
831 >    SimInfo::MoleculeIterator i;
832 >    Molecule* mol;
833 >
834 >    Vector3d comVel(0.0);
835 >    double totalMass = 0.0;
836 >    
837  
838 <  map<string, GenericData*>::iterator result;
839 <  
840 <  //string lowerCaseName = ();
841 <  
842 <  result = properties.find(propName);
843 <  
844 <  if(result != properties.end())
845 <    return (*result).second;  
846 <  else  
847 <    return NULL;  
838 >    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
839 >        double mass = mol->getMass();
840 >        totalMass += mass;
841 >        comVel += mass * mol->getComVel();
842 >    }  
843 >
844 > #ifdef IS_MPI
845 >    double tmpMass = totalMass;
846 >    Vector3d tmpComVel(comVel);    
847 >    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
848 >    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
849 > #endif
850 >
851 >    comVel /= totalMass;
852 >
853 >    return comVel;
854   }
855  
856 + Vector3d SimInfo::getCom(){
857 +    SimInfo::MoleculeIterator i;
858 +    Molecule* mol;
859  
860 < void SimInfo::getFortranGroupArrays(SimInfo* info,
861 <                                    vector<int>& FglobalGroupMembership,
862 <                                    vector<double>& mfact){
863 <  
864 <  Molecule* myMols;
865 <  Atom** myAtoms;
866 <  int numAtom;
867 <  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 <  
860 >    Vector3d com(0.0);
861 >    double totalMass = 0.0;
862 >    
863 >    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
864 >        double mass = mol->getMass();
865 >        totalMass += mass;
866 >        com += mass * mol->getCom();
867 >    }  
868  
596 –  // Fix the silly fortran indexing problem
869   #ifdef IS_MPI
870 <  numAtom = mpiSim->getNAtomsGlobal();
871 < #else
872 <  numAtom = n_atoms;
870 >    double tmpMass = totalMass;
871 >    Vector3d tmpCom(com);    
872 >    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
873 >    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
874   #endif
602 –  for (int i = 0; i < numAtom; i++)
603 –    FglobalGroupMembership.push_back(globalGroupMembership[i] + 1);
604 –  
875  
876 <  myMols = info->molecules;
607 <  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)){
876 >    com /= totalMass;
877  
878 <      totalMass = myCutoffGroup->getMass();
615 <      
616 <      for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom);
617 <          cutoffAtom != NULL;
618 <          cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
619 <        mfact.push_back(cutoffAtom->getMass()/totalMass);
620 <      }  
621 <    }
622 <  }
878 >    return com;
879  
880 + }        
881 +
882 + std::ostream& operator <<(std::ostream& o, SimInfo& info) {
883 +
884 +    return o;
885   }
886 +
887 + }//end namespace oopse
888 +

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