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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 642 by mmeineke, Mon Jul 21 16:23:57 2003 UTC vs.
Revision 1154 by gezelter, Tue May 11 16:00:22 2004 UTC

# Line 1 | Line 1
1 < #include <cstdlib>
2 < #include <cstring>
3 < #include <cmath>
1 > #include <stdlib.h>
2 > #include <string.h>
3 > #include <math.h>
4  
5   #include <iostream>
6   using namespace std;
# Line 12 | Line 12 | using namespace std;
12  
13   #include "fortranWrappers.hpp"
14  
15 + #include "MatVec3.h"
16 +
17   #ifdef IS_MPI
18   #include "mpiSimulation.hpp"
19   #endif
# Line 20 | Line 22 | 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 + }
28  
29   SimInfo* currentInfo;
30  
31   SimInfo::SimInfo(){
32 <  excludes = NULL;
32 >
33    n_constraints = 0;
34 +  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 <  ecr = 0.0;
39 <  est = 0.0;
40 <  oldEcr = 0.0;
41 <  oldRcut = 0.0;
45 >  rSw = 0.0;
46  
47 <  haveOrigRcut = 0;
48 <  haveOrigEcr = 0;
47 >  haveRcut = 0;
48 >  haveRsw = 0;
49    boxIsInit = 0;
50    
51 <  
51 >  resetTime = 1e99;
52  
53 +  orthoRhombic = 0;
54 +  orthoTolerance = 1E-6;
55 +  useInitXSstate = true;
56 +
57    usePBC = 0;
58    useLJ = 0;
59    useSticky = 0;
60 <  useDipole = 0;
60 >  useCharges = 0;
61 >  useDipoles = 0;
62    useReactionField = 0;
63    useGB = 0;
64    useEAM = 0;
65  
66 +  excludes = Exclude::Instance();
67 +
68 +  myConfiguration = new SimState();
69 +
70 +  has_minimizer = false;
71 +  the_minimizer =NULL;
72 +
73 +  ngroup = 0;
74 +
75    wrapMeSimInfo( this );
76   }
77  
78 +
79 + SimInfo::~SimInfo(){
80 +
81 +  delete myConfiguration;
82 +
83 +  map<string, GenericData*>::iterator i;
84 +  
85 +  for(i = properties.begin(); i != properties.end(); i++)
86 +    delete (*i).second;
87 +  
88 + }
89 +
90   void SimInfo::setBox(double newBox[3]) {
91    
92    int i, j;
# Line 75 | Line 105 | void SimInfo::setBoxM( double theBox[3][3] ){
105  
106   void SimInfo::setBoxM( double theBox[3][3] ){
107    
108 <  int i, j, status;
79 <  double smallestBoxL, maxCutoff;
108 >  int i, j;
109    double FortranHmat[9]; // to preserve compatibility with Fortran the
110                           // ordering in the array is as follows:
111                           // [ 0 3 6 ]
# Line 84 | Line 113 | void SimInfo::setBoxM( double theBox[3][3] ){
113                           // [ 2 5 8 ]
114    double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
115  
87 –  
116    if( !boxIsInit ) boxIsInit = 1;
117  
118    for(i=0; i < 3; i++)
# Line 128 | Line 156 | void SimInfo::calcHmatInv( void ) {
156  
157   void SimInfo::calcHmatInv( void ) {
158    
159 +  int oldOrtho;
160    int i,j;
161    double smallDiag;
162    double tol;
# Line 135 | Line 164 | void SimInfo::calcHmatInv( void ) {
164  
165    invertMat3( Hmat, HmatInv );
166  
138 –  // Check the inverse to make sure it is sane:
139 –
140 –  matMul3( Hmat, HmatInv, sanity );
141 –    
167    // check to see if Hmat is orthorhombic
168    
169 <  smallDiag = Hmat[0][0];
145 <  if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1];
146 <  if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2];
147 <  tol = smallDiag * 1E-6;
169 >  oldOrtho = orthoRhombic;
170  
171 +  smallDiag = fabs(Hmat[0][0]);
172 +  if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
173 +  if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
174 +  tol = smallDiag * orthoTolerance;
175 +
176    orthoRhombic = 1;
177    
178    for (i = 0; i < 3; i++ ) {
179      for (j = 0 ; j < 3; j++) {
180        if (i != j) {
181          if (orthoRhombic) {
182 <          if (Hmat[i][j] >= tol) orthoRhombic = 0;
182 >          if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
183          }        
184        }
185      }
186    }
160 – }
187  
188 < double SimInfo::matDet3(double a[3][3]) {
189 <  int i, j, k;
190 <  double determinant;
191 <
192 <  determinant = 0.0;
193 <
194 <  for(i = 0; i < 3; i++) {
195 <    j = (i+1)%3;
196 <    k = (i+2)%3;
197 <
198 <    determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]);
173 <  }
174 <
175 <  return determinant;
176 < }
177 <
178 < void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
179 <  
180 <  int  i, j, k, l, m, n;
181 <  double determinant;
182 <
183 <  determinant = matDet3( a );
184 <
185 <  if (determinant == 0.0) {
186 <    sprintf( painCave.errMsg,
187 <             "Can't invert a matrix with a zero determinant!\n");
188 <    painCave.isFatal = 1;
189 <    simError();
190 <  }
191 <
192 <  for (i=0; i < 3; i++) {
193 <    j = (i+1)%3;
194 <    k = (i+2)%3;
195 <    for(l = 0; l < 3; l++) {
196 <      m = (l+1)%3;
197 <      n = (l+2)%3;
198 <      
199 <      b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant;
188 >  if( oldOrtho != orthoRhombic ){
189 >    
190 >    if( orthoRhombic ){
191 >      sprintf( painCave.errMsg,
192 >               "OOPSE is switching from the default Non-Orthorhombic\n"
193 >               "\tto the faster Orthorhombic periodic boundary computations.\n"
194 >               "\tThis is usually a good thing, but if you wan't the\n"
195 >               "\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
196 >               "\tvariable ( currently set to %G ) smaller.\n",
197 >               orthoTolerance);
198 >      simError();
199      }
200 <  }
201 < }
202 <
203 < void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
204 <  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
205 <
206 <  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
207 <  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
208 <  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
209 <  
211 <  r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0];
212 <  r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1];
213 <  r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2];
214 <  
215 <  r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0];
216 <  r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1];
217 <  r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2];
218 <  
219 <  c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
220 <  c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
221 <  c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
222 < }
223 <
224 < void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
225 <  double a0, a1, a2;
226 <
227 <  a0 = inVec[0];  a1 = inVec[1];  a2 = inVec[2];
228 <
229 <  outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2;
230 <  outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
231 <  outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
232 < }
233 <
234 < void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
235 <  double temp[3][3];
236 <  int i, j;
237 <
238 <  for (i = 0; i < 3; i++) {
239 <    for (j = 0; j < 3; j++) {
240 <      temp[j][i] = in[i][j];
200 >    else {
201 >      sprintf( painCave.errMsg,
202 >               "OOPSE is switching from the faster Orthorhombic to the more\n"
203 >               "\tflexible Non-Orthorhombic periodic boundary computations.\n"
204 >               "\tThis is usually because the box has deformed under\n"
205 >               "\tNPTf integration. If you wan't to live on the edge with\n"
206 >               "\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
207 >               "\tvariable ( currently set to %G ) larger.\n",
208 >               orthoTolerance);
209 >      simError();
210      }
211    }
243 –  for (i = 0; i < 3; i++) {
244 –    for (j = 0; j < 3; j++) {
245 –      out[i][j] = temp[i][j];
246 –    }
247 –  }
212   }
249 –  
250 – void SimInfo::printMat3(double A[3][3] ){
213  
252 –  std::cerr
253 –            << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
254 –            << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
255 –            << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
256 – }
257 –
258 – void SimInfo::printMat9(double A[9] ){
259 –
260 –  std::cerr
261 –            << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
262 –            << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
263 –            << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
264 – }
265 –
214   void SimInfo::calcBoxL( void ){
215  
216    double dx, dy, dz, dsq;
269 –  int i;
217  
218    // boxVol = Determinant of Hmat
219  
# Line 277 | Line 224 | void SimInfo::calcBoxL( void ){
224    dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
225    dsq = dx*dx + dy*dy + dz*dz;
226    boxL[0] = sqrt( dsq );
227 <  maxCutoff = 0.5 * boxL[0];
227 >  //maxCutoff = 0.5 * boxL[0];
228  
229    // boxLy
230    
231    dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
232    dsq = dx*dx + dy*dy + dz*dz;
233    boxL[1] = sqrt( dsq );
234 <  if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
234 >  //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
235  
236 +
237    // boxLz
238    
239    dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
240    dsq = dx*dx + dy*dy + dz*dz;
241    boxL[2] = sqrt( dsq );
242 <  if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
242 >  //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
243  
244 +  //calculate the max cutoff
245 +  maxCutoff =  calcMaxCutOff();
246 +  
247 +  checkCutOffs();
248 +
249   }
250  
251  
252 + double SimInfo::calcMaxCutOff(){
253 +
254 +  double ri[3], rj[3], rk[3];
255 +  double rij[3], rjk[3], rki[3];
256 +  double minDist;
257 +
258 +  ri[0] = Hmat[0][0];
259 +  ri[1] = Hmat[1][0];
260 +  ri[2] = Hmat[2][0];
261 +
262 +  rj[0] = Hmat[0][1];
263 +  rj[1] = Hmat[1][1];
264 +  rj[2] = Hmat[2][1];
265 +
266 +  rk[0] = Hmat[0][2];
267 +  rk[1] = Hmat[1][2];
268 +  rk[2] = Hmat[2][2];
269 +    
270 +  crossProduct3(ri, rj, rij);
271 +  distXY = dotProduct3(rk,rij) / norm3(rij);
272 +
273 +  crossProduct3(rj,rk, rjk);
274 +  distYZ = dotProduct3(ri,rjk) / norm3(rjk);
275 +
276 +  crossProduct3(rk,ri, rki);
277 +  distZX = dotProduct3(rj,rki) / norm3(rki);
278 +
279 +  minDist = min(min(distXY, distYZ), distZX);
280 +  return minDist/2;
281 +  
282 + }
283 +
284   void SimInfo::wrapVector( double thePos[3] ){
285  
286 <  int i, j, k;
286 >  int i;
287    double scaled[3];
288  
289    if( !orthoRhombic ){
# Line 336 | Line 321 | int SimInfo::getNDF(){
321  
322  
323   int SimInfo::getNDF(){
324 <  int ndf_local, ndf;
324 >  int ndf_local;
325 >
326 >  ndf_local = 0;
327    
328 <  ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
328 >  for(int i = 0; i < integrableObjects.size(); i++){
329 >    ndf_local += 3;
330 >    if (integrableObjects[i]->isDirectional()) {
331 >      if (integrableObjects[i]->isLinear())
332 >        ndf_local += 2;
333 >      else
334 >        ndf_local += 3;
335 >    }
336 >  }
337  
338 +  // n_constraints is local, so subtract them on each processor:
339 +
340 +  ndf_local -= n_constraints;
341 +
342   #ifdef IS_MPI
343    MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
344   #else
345    ndf = ndf_local;
346   #endif
347  
348 <  ndf = ndf - 3;
348 >  // nZconstraints is global, as are the 3 COM translations for the
349 >  // entire system:
350  
351 +  ndf = ndf - 3 - nZconstraints;
352 +
353    return ndf;
354   }
355  
356   int SimInfo::getNDFraw() {
357 <  int ndfRaw_local, ndfRaw;
357 >  int ndfRaw_local;
358  
359    // Raw degrees of freedom that we have to set
360 <  ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
361 <  
360 >  ndfRaw_local = 0;
361 >
362 >  for(int i = 0; i < integrableObjects.size(); i++){
363 >    ndfRaw_local += 3;
364 >    if (integrableObjects[i]->isDirectional()) {
365 >       if (integrableObjects[i]->isLinear())
366 >        ndfRaw_local += 2;
367 >      else
368 >        ndfRaw_local += 3;
369 >    }
370 >  }
371 >    
372   #ifdef IS_MPI
373    MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
374   #else
# Line 365 | Line 377 | int SimInfo::getNDFraw() {
377  
378    return ndfRaw;
379   }
380 <
380 >
381 > int SimInfo::getNDFtranslational() {
382 >  int ndfTrans_local;
383 >
384 >  ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
385 >
386 >
387 > #ifdef IS_MPI
388 >  MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
389 > #else
390 >  ndfTrans = ndfTrans_local;
391 > #endif
392 >
393 >  ndfTrans = ndfTrans - 3 - nZconstraints;
394 >
395 >  return ndfTrans;
396 > }
397 >
398 > int SimInfo::getTotIntegrableObjects() {
399 >  int nObjs_local;
400 >  int nObjs;
401 >
402 >  nObjs_local =  integrableObjects.size();
403 >
404 >
405 > #ifdef IS_MPI
406 >  MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
407 > #else
408 >  nObjs = nObjs_local;
409 > #endif
410 >
411 >
412 >  return nObjs;
413 > }
414 >
415   void SimInfo::refreshSim(){
416  
417    simtype fInfo;
# Line 375 | Line 421 | void SimInfo::refreshSim(){
421  
422    fInfo.dielect = 0.0;
423  
424 <  if( useDipole ){
424 >  if( useDipoles ){
425      if( useReactionField )fInfo.dielect = dielectric;
426    }
427  
# Line 384 | Line 430 | void SimInfo::refreshSim(){
430    fInfo.SIM_uses_LJ = useLJ;
431    fInfo.SIM_uses_sticky = useSticky;
432    //fInfo.SIM_uses_sticky = 0;
433 <  fInfo.SIM_uses_dipoles = useDipole;
433 >  fInfo.SIM_uses_charges = useCharges;
434 >  fInfo.SIM_uses_dipoles = useDipoles;
435    //fInfo.SIM_uses_dipoles = 0;
436 <  //fInfo.SIM_uses_RF = useReactionField;
437 <  fInfo.SIM_uses_RF = 0;
436 >  fInfo.SIM_uses_RF = useReactionField;
437 >  //fInfo.SIM_uses_RF = 0;
438    fInfo.SIM_uses_GB = useGB;
439    fInfo.SIM_uses_EAM = useEAM;
440  
441 <  excl = Exclude::getArray();
442 <
441 >  n_exclude = excludes->getSize();
442 >  excl = excludes->getFortranArray();
443 >  
444   #ifdef IS_MPI
445    n_global = mpiSim->getTotAtoms();
446   #else
447    n_global = n_atoms;
448   #endif
449 <
449 >  
450    isError = 0;
451 <
451 >  
452 >  getFortranGroupArray(this, mfact, ngroup, groupList, groupStart);
453 >  
454    setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
455 <                  &nGlobalExcludes, globalExcludes, molMembershipArray,
456 <                  &isError );
457 <
455 >                  &nGlobalExcludes, globalExcludes, molMembershipArray,
456 >                  &mfact[0], &ngroup, &groupList[0], &groupStart[0], &isError);
457 >  
458    if( isError ){
459 <
459 >    
460      sprintf( painCave.errMsg,
461 <             "There was an error setting the simulation information in fortran.\n" );
461 >             "There was an error setting the simulation information in fortran.\n" );
462      painCave.isFatal = 1;
463      simError();
464    }
465 <
465 >  
466   #ifdef IS_MPI
467    sprintf( checkPointMsg,
468             "succesfully sent the simulation information to fortran.\n");
469    MPIcheckPoint();
470   #endif // is_mpi
471 <
471 >  
472    this->ndf = this->getNDF();
473    this->ndfRaw = this->getNDFraw();
474 <
474 >  this->ndfTrans = this->getNDFtranslational();
475   }
476  
477 <
478 < void SimInfo::setRcut( double theRcut ){
479 <
430 <  if( !haveOrigRcut ){
431 <    haveOrigRcut = 1;
432 <    origRcut = theRcut;
433 <  }
434 <
477 > void SimInfo::setDefaultRcut( double theRcut ){
478 >  
479 >  haveRcut = 1;
480    rCut = theRcut;
481 <  checkCutOffs();
481 >  rList = rCut + 1.0;
482 >  
483 >  notifyFortranCutOffs( &rCut, &rSw, &rList );
484   }
485  
486 < void SimInfo::setEcr( double theEcr ){
486 > void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
487  
488 <  if( !haveOrigEcr ){
489 <    haveOrigEcr = 1;
443 <    origEcr = theEcr;
444 <  }
445 <
446 <  ecr = theEcr;
447 <  checkCutOffs();
488 >  rSw = theRsw;
489 >  setDefaultRcut( theRcut );
490   }
491  
450 – void SimInfo::setEcr( double theEcr, double theEst ){
492  
452 –  est = theEst;
453 –  setEcr( theEcr );
454 – }
455 –
456 –
493   void SimInfo::checkCutOffs( void ){
494 <
459 <  int cutChanged = 0;
460 <
494 >  
495    if( boxIsInit ){
496      
497      //we need to check cutOffs against the box
498      
499 <    if( maxCutoff > rCut ){
466 <      if( rCut < origRcut ){
467 <        rCut = origRcut;
468 <        if (rCut > maxCutoff) rCut = maxCutoff;
469 <        
470 <        sprintf( painCave.errMsg,
471 <                 "New Box size is setting the long range cutoff radius "
472 <                 "to %lf\n",
473 <                 rCut );
474 <        painCave.isFatal = 0;
475 <        simError();
476 <      }
477 <    }
478 <
479 <    if( maxCutoff > ecr ){
480 <      if( ecr < origEcr ){
481 <        rCut = origEcr;
482 <        if (ecr > maxCutoff) ecr = maxCutoff;
483 <        
484 <        sprintf( painCave.errMsg,
485 <                 "New Box size is setting the electrostaticCutoffRadius "
486 <                 "to %lf\n",
487 <                 ecr );
488 <        painCave.isFatal = 0;
489 <        simError();
490 <      }
491 <    }
492 <
493 <
494 <    if (rCut > maxCutoff) {
499 >    if( rCut > maxCutoff ){
500        sprintf( painCave.errMsg,
501 <               "New Box size is setting the long range cutoff radius "
502 <               "to %lf\n",
503 <               maxCutoff );
504 <      painCave.isFatal = 0;
501 >               "cutoffRadius is too large for the current periodic box.\n"
502 >               "\tCurrent Value of cutoffRadius = %G at time %G\n "
503 >               "\tThis is larger than half of at least one of the\n"
504 >               "\tperiodic box vectors.  Right now, the Box matrix is:\n"
505 >               "\n"
506 >               "\t[ %G %G %G ]\n"
507 >               "\t[ %G %G %G ]\n"
508 >               "\t[ %G %G %G ]\n",
509 >               rCut, currentTime,
510 >               Hmat[0][0], Hmat[0][1], Hmat[0][2],
511 >               Hmat[1][0], Hmat[1][1], Hmat[1][2],
512 >               Hmat[2][0], Hmat[2][1], Hmat[2][2]);
513 >      painCave.isFatal = 1;
514        simError();
515 <      rCut = maxCutoff;
516 <    }
515 >    }    
516 >  } else {
517 >    // initialize this stuff before using it, OK?
518 >    sprintf( painCave.errMsg,
519 >             "Trying to check cutoffs without a box.\n"
520 >             "\tOOPSE should have better programmers than that.\n" );
521 >    painCave.isFatal = 1;
522 >    simError();      
523 >  }
524 >  
525 > }
526  
527 <    if( ecr > maxCutoff){
505 <      sprintf( painCave.errMsg,
506 <               "New Box size is setting the electrostaticCutoffRadius "
507 <               "to %lf\n",
508 <               maxCutoff  );
509 <      painCave.isFatal = 0;
510 <      simError();      
511 <      ecr = maxCutoff;
512 <    }
527 > void SimInfo::addProperty(GenericData* prop){
528  
529 +  map<string, GenericData*>::iterator result;
530 +  result = properties.find(prop->getID());
531 +  
532 +  //we can't simply use  properties[prop->getID()] = prop,
533 +  //it will cause memory leak if we already contain a propery which has the same name of prop
534 +  
535 +  if(result != properties.end()){
536      
537 +    delete (*result).second;
538 +    (*result).second = prop;
539 +      
540    }
541 <  
541 >  else{
542  
543 <  if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
543 >    properties[prop->getID()] = prop;
544  
545 <  // rlist is the 1.0 plus max( rcut, ecr )
545 >  }
546 >    
547 > }
548 >
549 > GenericData* SimInfo::getProperty(const string& propName){
550 >
551 >  map<string, GenericData*>::iterator result;
552    
553 <  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
553 >  //string lowerCaseName = ();
554 >  
555 >  result = properties.find(propName);
556 >  
557 >  if(result != properties.end())
558 >    return (*result).second;  
559 >  else  
560 >    return NULL;  
561 > }
562  
563 <  if( cutChanged ){
563 >
564 > void getFortranGroupArray(SimInfo* info, vector<double>& mfact, int& ngroup,
565 >                          vector<int>& groupList, vector<int>& groupStart){
566 >  Molecule* mol;
567 >  Atom** myAtoms;
568 >  int numAtom;
569 >  int curIndex;
570 >  double mtot;
571 >
572 >  mfact.clear();
573 >  groupList.clear();
574 >  groupStart.clear();
575 >  
576 >  //Be careful, fortran array begin at 1
577 >  curIndex = 1;
578 >  
579 >  if(info->useMolecularCutoffs){
580      
581 <    notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
582 <  }
581 > #ifdef IS_MPI
582 >    ngroup = mpiSim->getMyNMol();
583 > #else
584 >    ngroup = info->n_mol;
585 > #endif
586 >    
587 >    for(int i = 0; i < ngroup; i ++){
588 >      mol = &(info->molecules[i]);
589 >      numAtom = mol->getNAtoms();
590 >      myAtoms = mol->getMyAtoms();
591 >      mtot = 0.0;
592  
593 <  oldEcr = ecr;
594 <  oldRcut = rCut;
593 >      for(int j=0; j < numAtom; j++)
594 >        mtot += myAtoms[j]->getMass();                
595 >      
596 >      for(int j=0; j < numAtom; j++){
597 >              
598 >        // We want the local Index:
599 >        groupList.push_back(myAtoms[j]->getIndex() + 1);
600 >        mfact.push_back(myAtoms[j]->getMass() / mtot);
601 >
602 >      }
603 >      
604 >      groupStart.push_back(curIndex);
605 >      curIndex += numAtom;
606 >      
607 >    } //end for(int i =0 ; i < ngroup; i++)    
608 >  }
609 >  else{
610 >    //using atomic cutoff, every single atom is just a group
611 >    
612 > #ifdef IS_MPI
613 >    ngroup = mpiSim->getMyNlocal();
614 > #else
615 >    ngroup = info->n_atoms;
616 > #endif
617 >    
618 >    for(int i =0 ; i < ngroup; i++){
619 >      groupStart.push_back(curIndex++);      
620 >      groupList.push_back((info->atoms[i])->getIndex() + 1);
621 >      mfact.push_back(1.0);
622 >      
623 >    }//end for(int i =0 ; i < ngroup; i++)
624 >    
625 >  }//end if (info->useMolecularCutoffs)
626 >  
627   }

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