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Comparing trunk/OOPSE-2.0/src/brains/SimInfo.cpp (file contents):
Revision 1617 by chuckv, Wed Oct 20 20:46:20 2004 UTC vs.
Revision 2097 by tim, Wed Mar 9 17:30:29 2005 UTC

# Line 1 | Line 1
1 < #include <stdlib.h>
2 < #include <string.h>
3 < #include <math.h>
1 > /*
2 > * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3 > *
4 > * The University of Notre Dame grants you ("Licensee") a
5 > * non-exclusive, royalty free, license to use, modify and
6 > * redistribute this software in source and binary code form, provided
7 > * that the following conditions are met:
8 > *
9 > * 1. Acknowledgement of the program authors must be made in any
10 > *    publication of scientific results based in part on use of the
11 > *    program.  An acceptable form of acknowledgement is citation of
12 > *    the article in which the program was described (Matthew
13 > *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14 > *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15 > *    Parallel Simulation Engine for Molecular Dynamics,"
16 > *    J. Comput. Chem. 26, pp. 252-271 (2005))
17 > *
18 > * 2. Redistributions of source code must retain the above copyright
19 > *    notice, this list of conditions and the following disclaimer.
20 > *
21 > * 3. Redistributions in binary form must reproduce the above copyright
22 > *    notice, this list of conditions and the following disclaimer in the
23 > *    documentation and/or other materials provided with the
24 > *    distribution.
25 > *
26 > * This software is provided "AS IS," without a warranty of any
27 > * kind. All express or implied conditions, representations and
28 > * warranties, including any implied warranty of merchantability,
29 > * fitness for a particular purpose or non-infringement, are hereby
30 > * excluded.  The University of Notre Dame and its licensors shall not
31 > * be liable for any damages suffered by licensee as a result of
32 > * using, modifying or distributing the software or its
33 > * derivatives. In no event will the University of Notre Dame or its
34 > * licensors be liable for any lost revenue, profit or data, or for
35 > * direct, indirect, special, consequential, incidental or punitive
36 > * damages, however caused and regardless of the theory of liability,
37 > * arising out of the use of or inability to use software, even if the
38 > * University of Notre Dame has been advised of the possibility of
39 > * such damages.
40 > */
41 >
42 > /**
43 > * @file SimInfo.cpp
44 > * @author    tlin
45 > * @date  11/02/2004
46 > * @version 1.0
47 > */
48  
49 < #include <iostream>
50 < using namespace std;
49 > #include <algorithm>
50 > #include <set>
51  
52   #include "brains/SimInfo.hpp"
53 < #define __C
54 < #include "brains/fSimulation.h"
55 < #include "utils/simError.h"
12 < #include "UseTheForce/DarkSide/simulation_interface.h"
53 > #include "math/Vector3.hpp"
54 > #include "primitives/Molecule.hpp"
55 > #include "UseTheForce/doForces_interface.h"
56   #include "UseTheForce/notifyCutoffs_interface.h"
57 + #include "utils/MemoryUtils.hpp"
58 + #include "utils/simError.h"
59 + #include "selection/SelectionManager.hpp"
60  
61 < //#include "UseTheForce/fortranWrappers.hpp"
61 > #ifdef IS_MPI
62 > #include "UseTheForce/mpiComponentPlan.h"
63 > #include "UseTheForce/DarkSide/simParallel_interface.h"
64 > #endif
65  
66 < #include "math/MatVec3.h"
66 > namespace oopse {
67  
68 < #ifdef IS_MPI
69 < #include "brains/mpiSimulation.hpp"
70 < #endif
68 > SimInfo::SimInfo(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
69 >                                ForceField* ff, Globals* simParams) :
70 >                                forceField_(ff), simParams_(simParams),
71 >                                ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
72 >                                nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
73 >                                nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
74 >                                nAtoms_(0), nBonds_(0),  nBends_(0), nTorsions_(0), nRigidBodies_(0),
75 >                                nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
76 >                                sman_(NULL), fortranInitialized_(false) {
77  
78 < inline double roundMe( double x ){
79 <  return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
80 < }
81 <          
82 < inline double min( double a, double b ){
83 <  return (a < b ) ? a : b;
84 < }
78 >            
79 >    std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
80 >    MoleculeStamp* molStamp;
81 >    int nMolWithSameStamp;
82 >    int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
83 >    int nGroups = 0;          //total cutoff groups defined in meta-data file
84 >    CutoffGroupStamp* cgStamp;    
85 >    RigidBodyStamp* rbStamp;
86 >    int nRigidAtoms = 0;
87 >    
88 >    for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
89 >        molStamp = i->first;
90 >        nMolWithSameStamp = i->second;
91 >        
92 >        addMoleculeStamp(molStamp, nMolWithSameStamp);
93  
94 < SimInfo* currentInfo;
94 >        //calculate atoms in molecules
95 >        nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;  
96  
33 – SimInfo::SimInfo(){
97  
98 <  n_constraints = 0;
99 <  nZconstraints = 0;
100 <  n_oriented = 0;
101 <  n_dipoles = 0;
102 <  ndf = 0;
103 <  ndfRaw = 0;
104 <  nZconstraints = 0;
105 <  the_integrator = NULL;
43 <  setTemp = 0;
44 <  thermalTime = 0.0;
45 <  currentTime = 0.0;
46 <  rCut = 0.0;
47 <  rSw = 0.0;
98 >        //calculate atoms in cutoff groups
99 >        int nAtomsInGroups = 0;
100 >        int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
101 >        
102 >        for (int j=0; j < nCutoffGroupsInStamp; j++) {
103 >            cgStamp = molStamp->getCutoffGroup(j);
104 >            nAtomsInGroups += cgStamp->getNMembers();
105 >        }
106  
107 <  haveRcut = 0;
108 <  haveRsw = 0;
51 <  boxIsInit = 0;
52 <  
53 <  resetTime = 1e99;
107 >        nGroups += nCutoffGroupsInStamp * nMolWithSameStamp;
108 >        nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp;            
109  
110 <  orthoRhombic = 0;
111 <  orthoTolerance = 1E-6;
112 <  useInitXSstate = true;
110 >        //calculate atoms in rigid bodies
111 >        int nAtomsInRigidBodies = 0;
112 >        int nRigidBodiesInStamp = molStamp->getNRigidBodies();
113 >        
114 >        for (int j=0; j < nRigidBodiesInStamp; j++) {
115 >            rbStamp = molStamp->getRigidBody(j);
116 >            nAtomsInRigidBodies += rbStamp->getNMembers();
117 >        }
118  
119 <  usePBC = 0;
120 <  useLJ = 0;
121 <  useSticky = 0;
122 <  useCharges = 0;
63 <  useDipoles = 0;
64 <  useReactionField = 0;
65 <  useGB = 0;
66 <  useEAM = 0;
67 <  useSolidThermInt = 0;
68 <  useLiquidThermInt = 0;
119 >        nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp;
120 >        nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp;            
121 >        
122 >    }
123  
124 <  haveCutoffGroups = false;
124 >    //every free atom (atom does not belong to cutoff groups) is a cutoff group
125 >    //therefore the total number of cutoff groups in the system is equal to
126 >    //the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
127 >    //file plus the number of cutoff groups defined in meta-data file
128 >    nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups;
129  
130 <  excludes = Exclude::Instance();
130 >    //every free atom (atom does not belong to rigid bodies) is an integrable object
131 >    //therefore the total number of  integrable objects in the system is equal to
132 >    //the total number of atoms minus number of atoms belong to  rigid body defined in meta-data
133 >    //file plus the number of  rigid bodies defined in meta-data file
134 >    nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_;
135  
136 <  myConfiguration = new SimState();
136 >    nGlobalMols_ = molStampIds_.size();
137  
138 <  has_minimizer = false;
139 <  the_minimizer =NULL;
138 > #ifdef IS_MPI    
139 >    molToProcMap_.resize(nGlobalMols_);
140 > #endif
141  
142 <  ngroup = 0;
142 > }
143  
144 + SimInfo::~SimInfo() {
145 +    std::map<int, Molecule*>::iterator i;
146 +    for (i = molecules_.begin(); i != molecules_.end(); ++i) {
147 +        delete i->second;
148 +    }
149 +    molecules_.clear();
150 +    
151 +    MemoryUtils::deletePointers(moleculeStamps_);
152 +    
153 +    delete sman_;
154 +    delete simParams_;
155 +    delete forceField_;
156   }
157  
158 + int SimInfo::getNGlobalConstraints() {
159 +    int nGlobalConstraints;
160 + #ifdef IS_MPI
161 +    MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM,
162 +                  MPI_COMM_WORLD);    
163 + #else
164 +    nGlobalConstraints =  nConstraints_;
165 + #endif
166 +    return nGlobalConstraints;
167 + }
168  
169 < SimInfo::~SimInfo(){
169 > bool SimInfo::addMolecule(Molecule* mol) {
170 >    MoleculeIterator i;
171  
172 <  delete myConfiguration;
172 >    i = molecules_.find(mol->getGlobalIndex());
173 >    if (i == molecules_.end() ) {
174  
175 <  map<string, GenericData*>::iterator i;
176 <  
177 <  for(i = properties.begin(); i != properties.end(); i++)
178 <    delete (*i).second;
175 >        molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol));
176 >        
177 >        nAtoms_ += mol->getNAtoms();
178 >        nBonds_ += mol->getNBonds();
179 >        nBends_ += mol->getNBends();
180 >        nTorsions_ += mol->getNTorsions();
181 >        nRigidBodies_ += mol->getNRigidBodies();
182 >        nIntegrableObjects_ += mol->getNIntegrableObjects();
183 >        nCutoffGroups_ += mol->getNCutoffGroups();
184 >        nConstraints_ += mol->getNConstraintPairs();
185  
186 +        addExcludePairs(mol);
187 +        
188 +        return true;
189 +    } else {
190 +        return false;
191 +    }
192   }
193  
194 < void SimInfo::setBox(double newBox[3]) {
195 <  
196 <  int i, j;
98 <  double tempMat[3][3];
194 > bool SimInfo::removeMolecule(Molecule* mol) {
195 >    MoleculeIterator i;
196 >    i = molecules_.find(mol->getGlobalIndex());
197  
198 <  for(i=0; i<3; i++)
101 <    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
198 >    if (i != molecules_.end() ) {
199  
200 <  tempMat[0][0] = newBox[0];
201 <  tempMat[1][1] = newBox[1];
202 <  tempMat[2][2] = newBox[2];
200 >        assert(mol == i->second);
201 >        
202 >        nAtoms_ -= mol->getNAtoms();
203 >        nBonds_ -= mol->getNBonds();
204 >        nBends_ -= mol->getNBends();
205 >        nTorsions_ -= mol->getNTorsions();
206 >        nRigidBodies_ -= mol->getNRigidBodies();
207 >        nIntegrableObjects_ -= mol->getNIntegrableObjects();
208 >        nCutoffGroups_ -= mol->getNCutoffGroups();
209 >        nConstraints_ -= mol->getNConstraintPairs();
210  
211 <  setBoxM( tempMat );
211 >        removeExcludePairs(mol);
212 >        molecules_.erase(mol->getGlobalIndex());
213  
214 < }
214 >        delete mol;
215 >        
216 >        return true;
217 >    } else {
218 >        return false;
219 >    }
220  
111 – void SimInfo::setBoxM( double theBox[3][3] ){
112 –  
113 –  int i, j;
114 –  double FortranHmat[9]; // to preserve compatibility with Fortran the
115 –                         // ordering in the array is as follows:
116 –                         // [ 0 3 6 ]
117 –                         // [ 1 4 7 ]
118 –                         // [ 2 5 8 ]
119 –  double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
221  
222 <  if( !boxIsInit ) boxIsInit = 1;
222 > }    
223  
224 <  for(i=0; i < 3; i++)
225 <    for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
226 <  
227 <  calcBoxL();
228 <  calcHmatInv();
224 >        
225 > Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
226 >    i = molecules_.begin();
227 >    return i == molecules_.end() ? NULL : i->second;
228 > }    
229  
230 <  for(i=0; i < 3; i++) {
231 <    for (j=0; j < 3; j++) {
232 <      FortranHmat[3*j + i] = Hmat[i][j];
132 <      FortranHmatInv[3*j + i] = HmatInv[i][j];
133 <    }
134 <  }
135 <
136 <  setFortranBox(FortranHmat, FortranHmatInv, &orthoRhombic);
137 <
230 > Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
231 >    ++i;
232 >    return i == molecules_.end() ? NULL : i->second;    
233   }
139 –
234  
141 – void SimInfo::getBoxM (double theBox[3][3]) {
235  
236 <  int i, j;
237 <  for(i=0; i<3; i++)
238 <    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
239 < }
236 > void SimInfo::calcNdf() {
237 >    int ndf_local;
238 >    MoleculeIterator i;
239 >    std::vector<StuntDouble*>::iterator j;
240 >    Molecule* mol;
241 >    StuntDouble* integrableObject;
242  
243 +    ndf_local = 0;
244 +    
245 +    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
246 +        for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
247 +               integrableObject = mol->nextIntegrableObject(j)) {
248  
249 < void SimInfo::scaleBox(double scale) {
150 <  double theBox[3][3];
151 <  int i, j;
249 >            ndf_local += 3;
250  
251 <  // cerr << "Scaling box by " << scale << "\n";
251 >            if (integrableObject->isDirectional()) {
252 >                if (integrableObject->isLinear()) {
253 >                    ndf_local += 2;
254 >                } else {
255 >                    ndf_local += 3;
256 >                }
257 >            }
258 >            
259 >        }//end for (integrableObject)
260 >    }// end for (mol)
261 >    
262 >    // n_constraints is local, so subtract them on each processor
263 >    ndf_local -= nConstraints_;
264  
265 <  for(i=0; i<3; i++)
266 <    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
265 > #ifdef IS_MPI
266 >    MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
267 > #else
268 >    ndf_ = ndf_local;
269 > #endif
270  
271 <  setBoxM(theBox);
271 >    // nZconstraints_ is global, as are the 3 COM translations for the
272 >    // entire system:
273 >    ndf_ = ndf_ - 3 - nZconstraint_;
274  
275   }
276  
277 < void SimInfo::calcHmatInv( void ) {
278 <  
164 <  int oldOrtho;
165 <  int i,j;
166 <  double smallDiag;
167 <  double tol;
168 <  double sanity[3][3];
277 > void SimInfo::calcNdfRaw() {
278 >    int ndfRaw_local;
279  
280 <  invertMat3( Hmat, HmatInv );
281 <
282 <  // check to see if Hmat is orthorhombic
283 <  
174 <  oldOrtho = orthoRhombic;
280 >    MoleculeIterator i;
281 >    std::vector<StuntDouble*>::iterator j;
282 >    Molecule* mol;
283 >    StuntDouble* integrableObject;
284  
285 <  smallDiag = fabs(Hmat[0][0]);
286 <  if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
287 <  if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
288 <  tol = smallDiag * orthoTolerance;
285 >    // Raw degrees of freedom that we have to set
286 >    ndfRaw_local = 0;
287 >    
288 >    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
289 >        for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
290 >               integrableObject = mol->nextIntegrableObject(j)) {
291  
292 <  orthoRhombic = 1;
182 <  
183 <  for (i = 0; i < 3; i++ ) {
184 <    for (j = 0 ; j < 3; j++) {
185 <      if (i != j) {
186 <        if (orthoRhombic) {
187 <          if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
188 <        }        
189 <      }
190 <    }
191 <  }
292 >            ndfRaw_local += 3;
293  
294 <  if( oldOrtho != orthoRhombic ){
295 <    
296 <    if( orthoRhombic ) {
297 <      sprintf( painCave.errMsg,
298 <               "OOPSE is switching from the default Non-Orthorhombic\n"
299 <               "\tto the faster Orthorhombic periodic boundary computations.\n"
300 <               "\tThis is usually a good thing, but if you wan't the\n"
301 <               "\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
302 <               "\tvariable ( currently set to %G ) smaller.\n",
202 <               orthoTolerance);
203 <      painCave.severity = OOPSE_INFO;
204 <      simError();
294 >            if (integrableObject->isDirectional()) {
295 >                if (integrableObject->isLinear()) {
296 >                    ndfRaw_local += 2;
297 >                } else {
298 >                    ndfRaw_local += 3;
299 >                }
300 >            }
301 >            
302 >        }
303      }
304 <    else {
305 <      sprintf( painCave.errMsg,
306 <               "OOPSE is switching from the faster Orthorhombic to the more\n"
307 <               "\tflexible Non-Orthorhombic periodic boundary computations.\n"
308 <               "\tThis is usually because the box has deformed under\n"
309 <               "\tNPTf integration. If you wan't to live on the edge with\n"
212 <               "\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
213 <               "\tvariable ( currently set to %G ) larger.\n",
214 <               orthoTolerance);
215 <      painCave.severity = OOPSE_WARNING;
216 <      simError();
217 <    }
218 <  }
304 >    
305 > #ifdef IS_MPI
306 >    MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
307 > #else
308 >    ndfRaw_ = ndfRaw_local;
309 > #endif
310   }
311  
312 < void SimInfo::calcBoxL( void ){
312 > void SimInfo::calcNdfTrans() {
313 >    int ndfTrans_local;
314  
315 <  double dx, dy, dz, dsq;
315 >    ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
316  
225 –  // boxVol = Determinant of Hmat
317  
318 <  boxVol = matDet3( Hmat );
318 > #ifdef IS_MPI
319 >    MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
320 > #else
321 >    ndfTrans_ = ndfTrans_local;
322 > #endif
323  
324 <  // boxLx
325 <  
326 <  dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
232 <  dsq = dx*dx + dy*dy + dz*dz;
233 <  boxL[0] = sqrt( dsq );
234 <  //maxCutoff = 0.5 * boxL[0];
324 >    ndfTrans_ = ndfTrans_ - 3 - nZconstraint_;
325 >
326 > }
327  
328 <  // boxLy
329 <  
330 <  dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
331 <  dsq = dx*dx + dy*dy + dz*dz;
332 <  boxL[1] = sqrt( dsq );
333 <  //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
328 > void SimInfo::addExcludePairs(Molecule* mol) {
329 >    std::vector<Bond*>::iterator bondIter;
330 >    std::vector<Bend*>::iterator bendIter;
331 >    std::vector<Torsion*>::iterator torsionIter;
332 >    Bond* bond;
333 >    Bend* bend;
334 >    Torsion* torsion;
335 >    int a;
336 >    int b;
337 >    int c;
338 >    int d;
339 >    
340 >    for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
341 >        a = bond->getAtomA()->getGlobalIndex();
342 >        b = bond->getAtomB()->getGlobalIndex();        
343 >        exclude_.addPair(a, b);
344 >    }
345  
346 +    for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
347 +        a = bend->getAtomA()->getGlobalIndex();
348 +        b = bend->getAtomB()->getGlobalIndex();        
349 +        c = bend->getAtomC()->getGlobalIndex();
350  
351 <  // boxLz
352 <  
353 <  dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
354 <  dsq = dx*dx + dy*dy + dz*dz;
248 <  boxL[2] = sqrt( dsq );
249 <  //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
351 >        exclude_.addPair(a, b);
352 >        exclude_.addPair(a, c);
353 >        exclude_.addPair(b, c);        
354 >    }
355  
356 <  //calculate the max cutoff
357 <  maxCutoff =  calcMaxCutOff();
358 <  
359 <  checkCutOffs();
356 >    for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
357 >        a = torsion->getAtomA()->getGlobalIndex();
358 >        b = torsion->getAtomB()->getGlobalIndex();        
359 >        c = torsion->getAtomC()->getGlobalIndex();        
360 >        d = torsion->getAtomD()->getGlobalIndex();        
361  
362 +        exclude_.addPair(a, b);
363 +        exclude_.addPair(a, c);
364 +        exclude_.addPair(a, d);
365 +        exclude_.addPair(b, c);
366 +        exclude_.addPair(b, d);
367 +        exclude_.addPair(c, d);        
368 +    }
369 +
370 +    
371   }
372  
373 + void SimInfo::removeExcludePairs(Molecule* mol) {
374 +    std::vector<Bond*>::iterator bondIter;
375 +    std::vector<Bend*>::iterator bendIter;
376 +    std::vector<Torsion*>::iterator torsionIter;
377 +    Bond* bond;
378 +    Bend* bend;
379 +    Torsion* torsion;
380 +    int a;
381 +    int b;
382 +    int c;
383 +    int d;
384 +    
385 +    for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
386 +        a = bond->getAtomA()->getGlobalIndex();
387 +        b = bond->getAtomB()->getGlobalIndex();        
388 +        exclude_.removePair(a, b);
389 +    }
390  
391 < double SimInfo::calcMaxCutOff(){
391 >    for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
392 >        a = bend->getAtomA()->getGlobalIndex();
393 >        b = bend->getAtomB()->getGlobalIndex();        
394 >        c = bend->getAtomC()->getGlobalIndex();
395  
396 <  double ri[3], rj[3], rk[3];
397 <  double rij[3], rjk[3], rki[3];
398 <  double minDist;
396 >        exclude_.removePair(a, b);
397 >        exclude_.removePair(a, c);
398 >        exclude_.removePair(b, c);        
399 >    }
400  
401 <  ri[0] = Hmat[0][0];
402 <  ri[1] = Hmat[1][0];
403 <  ri[2] = Hmat[2][0];
401 >    for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
402 >        a = torsion->getAtomA()->getGlobalIndex();
403 >        b = torsion->getAtomB()->getGlobalIndex();        
404 >        c = torsion->getAtomC()->getGlobalIndex();        
405 >        d = torsion->getAtomD()->getGlobalIndex();        
406  
407 <  rj[0] = Hmat[0][1];
408 <  rj[1] = Hmat[1][1];
409 <  rj[2] = Hmat[2][1];
407 >        exclude_.removePair(a, b);
408 >        exclude_.removePair(a, c);
409 >        exclude_.removePair(a, d);
410 >        exclude_.removePair(b, c);
411 >        exclude_.removePair(b, d);
412 >        exclude_.removePair(c, d);        
413 >    }
414  
415 <  rk[0] = Hmat[0][2];
274 <  rk[1] = Hmat[1][2];
275 <  rk[2] = Hmat[2][2];
276 <    
277 <  crossProduct3(ri, rj, rij);
278 <  distXY = dotProduct3(rk,rij) / norm3(rij);
415 > }
416  
280 –  crossProduct3(rj,rk, rjk);
281 –  distYZ = dotProduct3(ri,rjk) / norm3(rjk);
417  
418 <  crossProduct3(rk,ri, rki);
419 <  distZX = dotProduct3(rj,rki) / norm3(rki);
418 > void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
419 >    int curStampId;
420  
421 <  minDist = min(min(distXY, distYZ), distZX);
422 <  return minDist/2;
423 <  
421 >    //index from 0
422 >    curStampId = moleculeStamps_.size();
423 >
424 >    moleculeStamps_.push_back(molStamp);
425 >    molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
426   }
427  
428 < void SimInfo::wrapVector( double thePos[3] ){
428 > void SimInfo::update() {
429  
430 <  int i;
294 <  double scaled[3];
430 >    setupSimType();
431  
432 <  if( !orthoRhombic ){
433 <    // calc the scaled coordinates.
434 <  
432 > #ifdef IS_MPI
433 >    setupFortranParallel();
434 > #endif
435  
436 <    matVecMul3(HmatInv, thePos, scaled);
301 <    
302 <    for(i=0; i<3; i++)
303 <      scaled[i] -= roundMe(scaled[i]);
304 <    
305 <    // calc the wrapped real coordinates from the wrapped scaled coordinates
306 <    
307 <    matVecMul3(Hmat, scaled, thePos);
436 >    setupFortranSim();
437  
438 <  }
439 <  else{
440 <    // calc the scaled coordinates.
438 >    //setup fortran force field
439 >    /** @deprecate */    
440 >    int isError = 0;
441 >    initFortranFF( &fInfo_.SIM_uses_RF , &isError );
442 >    if(isError){
443 >        sprintf( painCave.errMsg,
444 >         "ForceField error: There was an error initializing the forceField in fortran.\n" );
445 >        painCave.isFatal = 1;
446 >        simError();
447 >    }
448 >  
449      
450 <    for(i=0; i<3; i++)
451 <      scaled[i] = thePos[i]*HmatInv[i][i];
452 <    
453 <    // wrap the scaled coordinates
454 <    
455 <    for(i=0; i<3; i++)
456 <      scaled[i] -= roundMe(scaled[i]);
320 <    
321 <    // calc the wrapped real coordinates from the wrapped scaled coordinates
322 <    
323 <    for(i=0; i<3; i++)
324 <      thePos[i] = scaled[i]*Hmat[i][i];
325 <  }
326 <    
450 >    setupCutoff();
451 >
452 >    calcNdf();
453 >    calcNdfRaw();
454 >    calcNdfTrans();
455 >
456 >    fortranInitialized_ = true;
457   }
458  
459 + std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
460 +    SimInfo::MoleculeIterator mi;
461 +    Molecule* mol;
462 +    Molecule::AtomIterator ai;
463 +    Atom* atom;
464 +    std::set<AtomType*> atomTypes;
465  
466 < int SimInfo::getNDF(){
331 <  int ndf_local;
466 >    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
467  
468 <  ndf_local = 0;
469 <  
470 <  for(int i = 0; i < integrableObjects.size(); i++){
471 <    ndf_local += 3;
337 <    if (integrableObjects[i]->isDirectional()) {
338 <      if (integrableObjects[i]->isLinear())
339 <        ndf_local += 2;
340 <      else
341 <        ndf_local += 3;
468 >        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
469 >            atomTypes.insert(atom->getAtomType());
470 >        }
471 >        
472      }
343 –  }
473  
474 <  // n_constraints is local, so subtract them on each processor:
474 >    return atomTypes;        
475 > }
476  
477 <  ndf_local -= n_constraints;
477 > void SimInfo::setupSimType() {
478 >    std::set<AtomType*>::iterator i;
479 >    std::set<AtomType*> atomTypes;
480 >    atomTypes = getUniqueAtomTypes();
481 >    
482 >    int useLennardJones = 0;
483 >    int useElectrostatic = 0;
484 >    int useEAM = 0;
485 >    int useCharge = 0;
486 >    int useDirectional = 0;
487 >    int useDipole = 0;
488 >    int useGayBerne = 0;
489 >    int useSticky = 0;
490 >    int useShape = 0;
491 >    int useFLARB = 0; //it is not in AtomType yet
492 >    int useDirectionalAtom = 0;    
493 >    int useElectrostatics = 0;
494 >    //usePBC and useRF are from simParams
495 >    int usePBC = simParams_->getPBC();
496 >    int useRF = simParams_->getUseRF();
497  
498 < #ifdef IS_MPI
499 <  MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
500 < #else
501 <  ndf = ndf_local;
498 >    //loop over all of the atom types
499 >    for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
500 >        useLennardJones |= (*i)->isLennardJones();
501 >        useElectrostatic |= (*i)->isElectrostatic();
502 >        useEAM |= (*i)->isEAM();
503 >        useCharge |= (*i)->isCharge();
504 >        useDirectional |= (*i)->isDirectional();
505 >        useDipole |= (*i)->isDipole();
506 >        useGayBerne |= (*i)->isGayBerne();
507 >        useSticky |= (*i)->isSticky();
508 >        useShape |= (*i)->isShape();
509 >    }
510 >
511 >    if (useSticky || useDipole || useGayBerne || useShape) {
512 >        useDirectionalAtom = 1;
513 >    }
514 >
515 >    if (useCharge || useDipole) {
516 >        useElectrostatics = 1;
517 >    }
518 >
519 > #ifdef IS_MPI    
520 >    int temp;
521 >
522 >    temp = usePBC;
523 >    MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
524 >
525 >    temp = useDirectionalAtom;
526 >    MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
527 >
528 >    temp = useLennardJones;
529 >    MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
530 >
531 >    temp = useElectrostatics;
532 >    MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
533 >
534 >    temp = useCharge;
535 >    MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
536 >
537 >    temp = useDipole;
538 >    MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
539 >
540 >    temp = useSticky;
541 >    MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
542 >
543 >    temp = useGayBerne;
544 >    MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
545 >
546 >    temp = useEAM;
547 >    MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
548 >
549 >    temp = useShape;
550 >    MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);  
551 >
552 >    temp = useFLARB;
553 >    MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
554 >
555 >    temp = useRF;
556 >    MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
557 >    
558   #endif
559  
560 <  // nZconstraints is global, as are the 3 COM translations for the
561 <  // entire system:
560 >    fInfo_.SIM_uses_PBC = usePBC;    
561 >    fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
562 >    fInfo_.SIM_uses_LennardJones = useLennardJones;
563 >    fInfo_.SIM_uses_Electrostatics = useElectrostatics;    
564 >    fInfo_.SIM_uses_Charges = useCharge;
565 >    fInfo_.SIM_uses_Dipoles = useDipole;
566 >    fInfo_.SIM_uses_Sticky = useSticky;
567 >    fInfo_.SIM_uses_GayBerne = useGayBerne;
568 >    fInfo_.SIM_uses_EAM = useEAM;
569 >    fInfo_.SIM_uses_Shapes = useShape;
570 >    fInfo_.SIM_uses_FLARB = useFLARB;
571 >    fInfo_.SIM_uses_RF = useRF;
572  
573 <  ndf = ndf - 3 - nZconstraints;
573 >    if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
574  
575 <  return ndf;
575 >        if (simParams_->haveDielectric()) {
576 >            fInfo_.dielect = simParams_->getDielectric();
577 >        } else {
578 >            sprintf(painCave.errMsg,
579 >                    "SimSetup Error: No Dielectric constant was set.\n"
580 >                    "\tYou are trying to use Reaction Field without"
581 >                    "\tsetting a dielectric constant!\n");
582 >            painCave.isFatal = 1;
583 >            simError();
584 >        }
585 >        
586 >    } else {
587 >        fInfo_.dielect = 0.0;
588 >    }
589 >
590   }
591  
592 < int SimInfo::getNDFraw() {
593 <  int ndfRaw_local;
592 > void SimInfo::setupFortranSim() {
593 >    int isError;
594 >    int nExclude;
595 >    std::vector<int> fortranGlobalGroupMembership;
596 >    
597 >    nExclude = exclude_.getSize();
598 >    isError = 0;
599  
600 <  // Raw degrees of freedom that we have to set
601 <  ndfRaw_local = 0;
600 >    //globalGroupMembership_ is filled by SimCreator    
601 >    for (int i = 0; i < nGlobalAtoms_; i++) {
602 >        fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
603 >    }
604  
605 <  for(int i = 0; i < integrableObjects.size(); i++){
606 <    ndfRaw_local += 3;
607 <    if (integrableObjects[i]->isDirectional()) {
608 <       if (integrableObjects[i]->isLinear())
609 <        ndfRaw_local += 2;
610 <      else
611 <        ndfRaw_local += 3;
605 >    //calculate mass ratio of cutoff group
606 >    std::vector<double> mfact;
607 >    SimInfo::MoleculeIterator mi;
608 >    Molecule* mol;
609 >    Molecule::CutoffGroupIterator ci;
610 >    CutoffGroup* cg;
611 >    Molecule::AtomIterator ai;
612 >    Atom* atom;
613 >    double totalMass;
614 >
615 >    //to avoid memory reallocation, reserve enough space for mfact
616 >    mfact.reserve(getNCutoffGroups());
617 >    
618 >    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
619 >        for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
620 >
621 >            totalMass = cg->getMass();
622 >            for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
623 >                        mfact.push_back(atom->getMass()/totalMass);
624 >            }
625 >
626 >        }      
627      }
628 <  }
628 >
629 >    //fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
630 >    std::vector<int> identArray;
631 >
632 >    //to avoid memory reallocation, reserve enough space identArray
633 >    identArray.reserve(getNAtoms());
634      
635 < #ifdef IS_MPI
636 <  MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
637 < #else
638 <  ndfRaw = ndfRaw_local;
639 < #endif
635 >    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
636 >        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
637 >            identArray.push_back(atom->getIdent());
638 >        }
639 >    }    
640  
641 <  return ndfRaw;
642 < }
641 >    //fill molMembershipArray
642 >    //molMembershipArray is filled by SimCreator    
643 >    std::vector<int> molMembershipArray(nGlobalAtoms_);
644 >    for (int i = 0; i < nGlobalAtoms_; i++) {
645 >        molMembershipArray[i] = globalMolMembership_[i] + 1;
646 >    }
647 >    
648 >    //setup fortran simulation
649 >    //gloalExcludes and molMembershipArray should go away (They are never used)
650 >    //why the hell fortran need to know molecule?
651 >    //OOPSE = Object-Obfuscated Parallel Simulation Engine
652 >    int nGlobalExcludes = 0;
653 >    int* globalExcludes = NULL;
654 >    int* excludeList = exclude_.getExcludeList();
655 >    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList ,
656 >                  &nGlobalExcludes, globalExcludes, &molMembershipArray[0],
657 >                  &mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
658  
659 < int SimInfo::getNDFtranslational() {
389 <  int ndfTrans_local;
659 >    if( isError ){
660  
661 <  ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
661 >        sprintf( painCave.errMsg,
662 >                 "There was an error setting the simulation information in fortran.\n" );
663 >        painCave.isFatal = 1;
664 >        painCave.severity = OOPSE_ERROR;
665 >        simError();
666 >    }
667  
668 + #ifdef IS_MPI
669 +    sprintf( checkPointMsg,
670 +       "succesfully sent the simulation information to fortran.\n");
671 +    MPIcheckPoint();
672 + #endif // is_mpi
673 + }
674  
675 +
676   #ifdef IS_MPI
677 <  MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
678 < #else
679 <  ndfTrans = ndfTrans_local;
680 < #endif
677 > void SimInfo::setupFortranParallel() {
678 >    
679 >    //SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
680 >    std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
681 >    std::vector<int> localToGlobalCutoffGroupIndex;
682 >    SimInfo::MoleculeIterator mi;
683 >    Molecule::AtomIterator ai;
684 >    Molecule::CutoffGroupIterator ci;
685 >    Molecule* mol;
686 >    Atom* atom;
687 >    CutoffGroup* cg;
688 >    mpiSimData parallelData;
689 >    int isError;
690  
691 <  ndfTrans = ndfTrans - 3 - nZconstraints;
691 >    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
692  
693 <  return ndfTrans;
694 < }
693 >        //local index(index in DataStorge) of atom is important
694 >        for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
695 >            localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
696 >        }
697  
698 < int SimInfo::getTotIntegrableObjects() {
699 <  int nObjs_local;
700 <  int nObjs;
698 >        //local index of cutoff group is trivial, it only depends on the order of travesing
699 >        for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
700 >            localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
701 >        }        
702 >        
703 >    }
704  
705 <  nObjs_local =  integrableObjects.size();
705 >    //fill up mpiSimData struct
706 >    parallelData.nMolGlobal = getNGlobalMolecules();
707 >    parallelData.nMolLocal = getNMolecules();
708 >    parallelData.nAtomsGlobal = getNGlobalAtoms();
709 >    parallelData.nAtomsLocal = getNAtoms();
710 >    parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
711 >    parallelData.nGroupsLocal = getNCutoffGroups();
712 >    parallelData.myNode = worldRank;
713 >    MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors));
714  
715 +    //pass mpiSimData struct and index arrays to fortran
716 +    setFsimParallel(&parallelData, &(parallelData.nAtomsLocal),
717 +                    &localToGlobalAtomIndex[0],  &(parallelData.nGroupsLocal),
718 +                    &localToGlobalCutoffGroupIndex[0], &isError);
719  
720 < #ifdef IS_MPI
721 <  MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
722 < #else
723 <  nObjs = nObjs_local;
724 < #endif
720 >    if (isError) {
721 >        sprintf(painCave.errMsg,
722 >                "mpiRefresh errror: fortran didn't like something we gave it.\n");
723 >        painCave.isFatal = 1;
724 >        simError();
725 >    }
726  
727 +    sprintf(checkPointMsg, " mpiRefresh successful.\n");
728 +    MPIcheckPoint();
729  
730 <  return nObjs;
730 >
731   }
732  
733 < void SimInfo::refreshSim(){
733 > #endif
734  
735 <  simtype fInfo;
425 <  int isError;
426 <  int n_global;
427 <  int* excl;
735 > double SimInfo::calcMaxCutoffRadius() {
736  
429 –  fInfo.dielect = 0.0;
737  
738 <  if( useDipoles ){
739 <    if( useReactionField )fInfo.dielect = dielectric;
740 <  }
738 >    std::set<AtomType*> atomTypes;
739 >    std::set<AtomType*>::iterator i;
740 >    std::vector<double> cutoffRadius;
741  
742 <  fInfo.SIM_uses_PBC = usePBC;
743 <  //fInfo.SIM_uses_LJ = 0;
437 <  fInfo.SIM_uses_LJ = useLJ;
438 <  fInfo.SIM_uses_sticky = useSticky;
439 <  //fInfo.SIM_uses_sticky = 0;
440 <  fInfo.SIM_uses_charges = useCharges;
441 <  fInfo.SIM_uses_dipoles = useDipoles;
442 <  //fInfo.SIM_uses_dipoles = 0;
443 <  fInfo.SIM_uses_RF = useReactionField;
444 <  //fInfo.SIM_uses_RF = 0;
445 <  fInfo.SIM_uses_GB = useGB;
446 <  fInfo.SIM_uses_EAM = useEAM;
742 >    //get the unique atom types
743 >    atomTypes = getUniqueAtomTypes();
744  
745 <  n_exclude = excludes->getSize();
746 <  excl = excludes->getFortranArray();
747 <  
745 >    //query the max cutoff radius among these atom types
746 >    for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
747 >        cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
748 >    }
749 >
750 >    double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
751   #ifdef IS_MPI
752 <  n_global = mpiSim->getNAtomsGlobal();
453 < #else
454 <  n_global = n_atoms;
752 >    //pick the max cutoff radius among the processors
753   #endif
754 <  
755 <  isError = 0;
756 <  
459 <  getFortranGroupArrays(this, FglobalGroupMembership, mfact);
460 <  //it may not be a good idea to pass the address of first element in vector
461 <  //since c++ standard does not require vector to be stored continuously in meomory
462 <  //Most of the compilers will organize the memory of vector continuously
463 <  setFortranSim( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
464 <                  &nGlobalExcludes, globalExcludes, molMembershipArray,
465 <                  &mfact[0], &ngroup, &FglobalGroupMembership[0], &isError);
754 >
755 >    return maxCutoffRadius;
756 > }
757  
758 <  if( isError ){
758 > void SimInfo::getCutoff(double& rcut, double& rsw) {
759      
760 <    sprintf( painCave.errMsg,
761 <             "There was an error setting the simulation information in fortran.\n" );
762 <    painCave.isFatal = 1;
763 <    painCave.severity = OOPSE_ERROR;
764 <    simError();
765 <  }
766 <  
767 < #ifdef IS_MPI
768 <  sprintf( checkPointMsg,
769 <           "succesfully sent the simulation information to fortran.\n");
770 <  MPIcheckPoint();
771 < #endif // is_mpi
772 <  
482 <  this->ndf = this->getNDF();
483 <  this->ndfRaw = this->getNDFraw();
484 <  this->ndfTrans = this->getNDFtranslational();
485 < }
760 >    if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
761 >        
762 >        if (!simParams_->haveRcut()){
763 >            sprintf(painCave.errMsg,
764 >                "SimCreator Warning: No value was set for the cutoffRadius.\n"
765 >                "\tOOPSE will use a default value of 15.0 angstroms"
766 >                "\tfor the cutoffRadius.\n");
767 >            painCave.isFatal = 0;
768 >            simError();
769 >            rcut = 15.0;
770 >        } else{
771 >            rcut = simParams_->getRcut();
772 >        }
773  
774 < void SimInfo::setDefaultRcut( double theRcut ){
775 <  
776 <  haveRcut = 1;
777 <  rCut = theRcut;
778 <  rList = rCut + 1.0;
779 <  
780 <  notifyFortranCutoffs( &rCut, &rSw, &rList );
774 >        if (!simParams_->haveRsw()){
775 >            sprintf(painCave.errMsg,
776 >                "SimCreator Warning: No value was set for switchingRadius.\n"
777 >                "\tOOPSE will use a default value of\n"
778 >                "\t0.95 * cutoffRadius for the switchingRadius\n");
779 >            painCave.isFatal = 0;
780 >            simError();
781 >            rsw = 0.95 * rcut;
782 >        } else{
783 >            rsw = simParams_->getRsw();
784 >        }
785 >
786 >    } else {
787 >        // if charge, dipole or reaction field is not used and the cutofff radius is not specified in
788 >        //meta-data file, the maximum cutoff radius calculated from forcefiled will be used
789 >        
790 >        if (simParams_->haveRcut()) {
791 >            rcut = simParams_->getRcut();
792 >        } else {
793 >            //set cutoff radius to the maximum cutoff radius based on atom types in the whole system
794 >            rcut = calcMaxCutoffRadius();
795 >        }
796 >
797 >        if (simParams_->haveRsw()) {
798 >            rsw  = simParams_->getRsw();
799 >        } else {
800 >            rsw = rcut;
801 >        }
802 >    
803 >    }
804   }
805  
806 < void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
806 > void SimInfo::setupCutoff() {
807 >    getCutoff(rcut_, rsw_);    
808 >    double rnblist = rcut_ + 1; // skin of neighbor list
809  
810 <  rSw = theRsw;
811 <  setDefaultRcut( theRcut );
810 >    //Pass these cutoff radius etc. to fortran. This function should be called once and only once
811 >    notifyFortranCutoffs(&rcut_, &rsw_, &rnblist);
812   }
813  
814 + void SimInfo::addProperty(GenericData* genData) {
815 +    properties_.addProperty(genData);  
816 + }
817  
818 < void SimInfo::checkCutOffs( void ){
819 <  
505 <  if( boxIsInit ){
506 <    
507 <    //we need to check cutOffs against the box
508 <    
509 <    if( rCut > maxCutoff ){
510 <      sprintf( painCave.errMsg,
511 <               "cutoffRadius is too large for the current periodic box.\n"
512 <               "\tCurrent Value of cutoffRadius = %G at time %G\n "
513 <               "\tThis is larger than half of at least one of the\n"
514 <               "\tperiodic box vectors.  Right now, the Box matrix is:\n"
515 <               "\n"
516 <               "\t[ %G %G %G ]\n"
517 <               "\t[ %G %G %G ]\n"
518 <               "\t[ %G %G %G ]\n",
519 <               rCut, currentTime,
520 <               Hmat[0][0], Hmat[0][1], Hmat[0][2],
521 <               Hmat[1][0], Hmat[1][1], Hmat[1][2],
522 <               Hmat[2][0], Hmat[2][1], Hmat[2][2]);
523 <      painCave.severity = OOPSE_ERROR;
524 <      painCave.isFatal = 1;
525 <      simError();
526 <    }    
527 <  } else {
528 <    // initialize this stuff before using it, OK?
529 <    sprintf( painCave.errMsg,
530 <             "Trying to check cutoffs without a box.\n"
531 <             "\tOOPSE should have better programmers than that.\n" );
532 <    painCave.severity = OOPSE_ERROR;
533 <    painCave.isFatal = 1;
534 <    simError();      
535 <  }
536 <  
818 > void SimInfo::removeProperty(const std::string& propName) {
819 >    properties_.removeProperty(propName);  
820   }
821  
822 < void SimInfo::addProperty(GenericData* prop){
822 > void SimInfo::clearProperties() {
823 >    properties_.clearProperties();
824 > }
825  
826 <  map<string, GenericData*>::iterator result;
827 <  result = properties.find(prop->getID());
828 <  
544 <  //we can't simply use  properties[prop->getID()] = prop,
545 <  //it will cause memory leak if we already contain a propery which has the same name of prop
546 <  
547 <  if(result != properties.end()){
548 <    
549 <    delete (*result).second;
550 <    (*result).second = prop;
826 > std::vector<std::string> SimInfo::getPropertyNames() {
827 >    return properties_.getPropertyNames();  
828 > }
829        
830 <  }
831 <  else{
830 > std::vector<GenericData*> SimInfo::getProperties() {
831 >    return properties_.getProperties();
832 > }
833  
834 <    properties[prop->getID()] = prop;
834 > GenericData* SimInfo::getPropertyByName(const std::string& propName) {
835 >    return properties_.getPropertyByName(propName);
836 > }
837  
838 <  }
838 > void SimInfo::setSnapshotManager(SnapshotManager* sman) {
839 >    //if (sman_ == sman_) {
840 >    //    return;
841 >    //}
842      
843 +    //delete sman_;
844 +    sman_ = sman;
845 +
846 +    Molecule* mol;
847 +    RigidBody* rb;
848 +    Atom* atom;
849 +    SimInfo::MoleculeIterator mi;
850 +    Molecule::RigidBodyIterator rbIter;
851 +    Molecule::AtomIterator atomIter;;
852 +
853 +    for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
854 +        
855 +        for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) {
856 +            atom->setSnapshotManager(sman_);
857 +        }
858 +        
859 +        for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
860 +            rb->setSnapshotManager(sman_);
861 +        }
862 +    }    
863 +    
864   }
865  
866 < GenericData* SimInfo::getProperty(const string& propName){
866 > Vector3d SimInfo::getComVel(){
867 >    SimInfo::MoleculeIterator i;
868 >    Molecule* mol;
869 >
870 >    Vector3d comVel(0.0);
871 >    double totalMass = 0.0;
872 >    
873  
874 <  map<string, GenericData*>::iterator result;
875 <  
876 <  //string lowerCaseName = ();
877 <  
878 <  result = properties.find(propName);
879 <  
880 <  if(result != properties.end())
881 <    return (*result).second;  
882 <  else  
883 <    return NULL;  
874 >    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
875 >        double mass = mol->getMass();
876 >        totalMass += mass;
877 >        comVel += mass * mol->getComVel();
878 >    }  
879 >
880 > #ifdef IS_MPI
881 >    double tmpMass = totalMass;
882 >    Vector3d tmpComVel(comVel);    
883 >    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
884 >    MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
885 > #endif
886 >
887 >    comVel /= totalMass;
888 >
889 >    return comVel;
890   }
891  
892 + Vector3d SimInfo::getCom(){
893 +    SimInfo::MoleculeIterator i;
894 +    Molecule* mol;
895  
896 < void SimInfo::getFortranGroupArrays(SimInfo* info,
897 <                                    vector<int>& FglobalGroupMembership,
898 <                                    vector<double>& mfact){
899 <  
900 <  Molecule* myMols;
901 <  Atom** myAtoms;
902 <  int numAtom;
903 <  double mtot;
584 <  int numMol;
585 <  int numCutoffGroups;
586 <  CutoffGroup* myCutoffGroup;
587 <  vector<CutoffGroup*>::iterator iterCutoff;
588 <  Atom* cutoffAtom;
589 <  vector<Atom*>::iterator iterAtom;
590 <  int atomIndex;
591 <  double totalMass;
592 <  
593 <  mfact.clear();
594 <  FglobalGroupMembership.clear();
595 <  
896 >    Vector3d com(0.0);
897 >    double totalMass = 0.0;
898 >    
899 >    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
900 >        double mass = mol->getMass();
901 >        totalMass += mass;
902 >        com += mass * mol->getCom();
903 >    }  
904  
597 –  // Fix the silly fortran indexing problem
905   #ifdef IS_MPI
906 <  numAtom = mpiSim->getNAtomsGlobal();
907 < #else
908 <  numAtom = n_atoms;
906 >    double tmpMass = totalMass;
907 >    Vector3d tmpCom(com);    
908 >    MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
909 >    MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
910   #endif
603 –  for (int i = 0; i < numAtom; i++)
604 –    FglobalGroupMembership.push_back(globalGroupMembership[i] + 1);
605 –  
911  
912 <  myMols = info->molecules;
608 <  numMol = info->n_mol;
609 <  for(int i  = 0; i < numMol; i++){
610 <    numCutoffGroups = myMols[i].getNCutoffGroups();
611 <    for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff);
612 <        myCutoffGroup != NULL;
613 <        myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
912 >    com /= totalMass;
913  
914 <      totalMass = myCutoffGroup->getMass();
616 <      
617 <      for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom);
618 <          cutoffAtom != NULL;
619 <          cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
620 <        mfact.push_back(cutoffAtom->getMass()/totalMass);
621 <      }  
622 <    }
623 <  }
914 >    return com;
915  
916 + }        
917 +
918 + std::ostream& operator <<(std::ostream& o, SimInfo& info) {
919 +
920 +    return o;
921   }
922 +
923 + }//end namespace oopse
924 +

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