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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 626 by mmeineke, Wed Jul 16 21:30:56 2003 UTC vs.
Revision 1118 by tim, Mon Apr 19 03:52:27 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;
46    est = 0.0;
39 –  oldEcr = 0.0;
40 –  oldRcut = 0.0;
47  
48 <  haveOrigRcut = 0;
49 <  haveOrigEcr = 0;
48 >  haveRcut = 0;
49 >  haveEcr = 0;
50    boxIsInit = 0;
51    
52 <  
52 >  resetTime = 1e99;
53  
54 +  orthoRhombic = 0;
55 +  orthoTolerance = 1E-6;
56 +  useInitXSstate = true;
57 +
58    usePBC = 0;
59    useLJ = 0;
60    useSticky = 0;
61 <  useDipole = 0;
61 >  useCharges = 0;
62 >  useDipoles = 0;
63    useReactionField = 0;
64    useGB = 0;
65    useEAM = 0;
66  
67 +  excludes = Exclude::Instance();
68 +
69 +  myConfiguration = new SimState();
70 +
71 +  has_minimizer = false;
72 +  the_minimizer =NULL;
73 +
74    wrapMeSimInfo( this );
75   }
76  
77 +
78 + SimInfo::~SimInfo(){
79 +
80 +  delete myConfiguration;
81 +
82 +  map<string, GenericData*>::iterator i;
83 +  
84 +  for(i = properties.begin(); i != properties.end(); i++)
85 +    delete (*i).second;
86 +    
87 + }
88 +
89   void SimInfo::setBox(double newBox[3]) {
90    
91    int i, j;
# Line 74 | Line 104 | void SimInfo::setBoxM( double theBox[3][3] ){
104  
105   void SimInfo::setBoxM( double theBox[3][3] ){
106    
107 <  int i, j, status;
78 <  double smallestBoxL, maxCutoff;
107 >  int i, j;
108    double FortranHmat[9]; // to preserve compatibility with Fortran the
109                           // ordering in the array is as follows:
110                           // [ 0 3 6 ]
# Line 83 | Line 112 | void SimInfo::setBoxM( double theBox[3][3] ){
112                           // [ 2 5 8 ]
113    double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
114  
86 –  
115    if( !boxIsInit ) boxIsInit = 1;
116  
117    for(i=0; i < 3; i++)
# Line 127 | Line 155 | void SimInfo::calcHmatInv( void ) {
155  
156   void SimInfo::calcHmatInv( void ) {
157    
158 +  int oldOrtho;
159    int i,j;
160    double smallDiag;
161    double tol;
# Line 134 | Line 163 | void SimInfo::calcHmatInv( void ) {
163  
164    invertMat3( Hmat, HmatInv );
165  
137 –  // Check the inverse to make sure it is sane:
138 –
139 –  matMul3( Hmat, HmatInv, sanity );
140 –    
166    // check to see if Hmat is orthorhombic
167    
168 <  smallDiag = Hmat[0][0];
144 <  if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1];
145 <  if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2];
146 <  tol = smallDiag * 1E-6;
168 >  oldOrtho = orthoRhombic;
169  
170 +  smallDiag = fabs(Hmat[0][0]);
171 +  if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
172 +  if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
173 +  tol = smallDiag * orthoTolerance;
174 +
175    orthoRhombic = 1;
176    
177    for (i = 0; i < 3; i++ ) {
178      for (j = 0 ; j < 3; j++) {
179        if (i != j) {
180          if (orthoRhombic) {
181 <          if (Hmat[i][j] >= tol) orthoRhombic = 0;
181 >          if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
182          }        
183        }
184      }
185    }
159 – }
186  
187 < double SimInfo::matDet3(double a[3][3]) {
188 <  int i, j, k;
189 <  double determinant;
190 <
191 <  determinant = 0.0;
192 <
193 <  for(i = 0; i < 3; i++) {
194 <    j = (i+1)%3;
195 <    k = (i+2)%3;
196 <
197 <    determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]);
172 <  }
173 <
174 <  return determinant;
175 < }
176 <
177 < void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
178 <  
179 <  int  i, j, k, l, m, n;
180 <  double determinant;
181 <
182 <  determinant = matDet3( a );
183 <
184 <  if (determinant == 0.0) {
185 <    sprintf( painCave.errMsg,
186 <             "Can't invert a matrix with a zero determinant!\n");
187 <    painCave.isFatal = 1;
188 <    simError();
189 <  }
190 <
191 <  for (i=0; i < 3; i++) {
192 <    j = (i+1)%3;
193 <    k = (i+2)%3;
194 <    for(l = 0; l < 3; l++) {
195 <      m = (l+1)%3;
196 <      n = (l+2)%3;
197 <      
198 <      b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant;
187 >  if( oldOrtho != orthoRhombic ){
188 >    
189 >    if( orthoRhombic ){
190 >      sprintf( painCave.errMsg,
191 >               "OOPSE is switching from the default Non-Orthorhombic\n"
192 >               "\tto the faster Orthorhombic periodic boundary computations.\n"
193 >               "\tThis is usually a good thing, but if you wan't the\n"
194 >               "\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
195 >               "\tvariable ( currently set to %G ) smaller.\n",
196 >               orthoTolerance);
197 >      simError();
198      }
199 <  }
200 < }
201 <
202 < void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
203 <  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
204 <
205 <  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
206 <  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
207 <  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
208 <  
210 <  r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0];
211 <  r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1];
212 <  r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2];
213 <  
214 <  r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0];
215 <  r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1];
216 <  r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2];
217 <  
218 <  c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
219 <  c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
220 <  c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
221 < }
222 <
223 < void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
224 <  double a0, a1, a2;
225 <
226 <  a0 = inVec[0];  a1 = inVec[1];  a2 = inVec[2];
227 <
228 <  outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2;
229 <  outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
230 <  outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
231 < }
232 <
233 < void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
234 <  double temp[3][3];
235 <  int i, j;
236 <
237 <  for (i = 0; i < 3; i++) {
238 <    for (j = 0; j < 3; j++) {
239 <      temp[j][i] = in[i][j];
199 >    else {
200 >      sprintf( painCave.errMsg,
201 >               "OOPSE is switching from the faster Orthorhombic to the more\n"
202 >               "\tflexible Non-Orthorhombic periodic boundary computations.\n"
203 >               "\tThis is usually because the box has deformed under\n"
204 >               "\tNPTf integration. If you wan't to live on the edge with\n"
205 >               "\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
206 >               "\tvariable ( currently set to %G ) larger.\n",
207 >               orthoTolerance);
208 >      simError();
209      }
210    }
242 –  for (i = 0; i < 3; i++) {
243 –    for (j = 0; j < 3; j++) {
244 –      out[i][j] = temp[i][j];
245 –    }
246 –  }
211   }
248 –  
249 – void SimInfo::printMat3(double A[3][3] ){
212  
251 –  std::cerr
252 –            << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
253 –            << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
254 –            << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
255 – }
256 –
257 – void SimInfo::printMat9(double A[9] ){
258 –
259 –  std::cerr
260 –            << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
261 –            << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
262 –            << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
263 – }
264 –
213   void SimInfo::calcBoxL( void ){
214  
215    double dx, dy, dz, dsq;
268 –  int i;
216  
217    // boxVol = Determinant of Hmat
218  
# Line 276 | Line 223 | void SimInfo::calcBoxL( void ){
223    dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
224    dsq = dx*dx + dy*dy + dz*dz;
225    boxL[0] = sqrt( dsq );
226 <  maxCutoff = 0.5 * boxL[0];
226 >  //maxCutoff = 0.5 * boxL[0];
227  
228    // boxLy
229    
230    dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
231    dsq = dx*dx + dy*dy + dz*dz;
232    boxL[1] = sqrt( dsq );
233 <  if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
233 >  //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
234  
235 +
236    // boxLz
237    
238    dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
239    dsq = dx*dx + dy*dy + dz*dz;
240    boxL[2] = sqrt( dsq );
241 <  if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
241 >  //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
242  
243 +  //calculate the max cutoff
244 +  maxCutoff =  calcMaxCutOff();
245 +  
246 +  checkCutOffs();
247 +
248   }
249  
250  
251 + double SimInfo::calcMaxCutOff(){
252 +
253 +  double ri[3], rj[3], rk[3];
254 +  double rij[3], rjk[3], rki[3];
255 +  double minDist;
256 +
257 +  ri[0] = Hmat[0][0];
258 +  ri[1] = Hmat[1][0];
259 +  ri[2] = Hmat[2][0];
260 +
261 +  rj[0] = Hmat[0][1];
262 +  rj[1] = Hmat[1][1];
263 +  rj[2] = Hmat[2][1];
264 +
265 +  rk[0] = Hmat[0][2];
266 +  rk[1] = Hmat[1][2];
267 +  rk[2] = Hmat[2][2];
268 +    
269 +  crossProduct3(ri, rj, rij);
270 +  distXY = dotProduct3(rk,rij) / norm3(rij);
271 +
272 +  crossProduct3(rj,rk, rjk);
273 +  distYZ = dotProduct3(ri,rjk) / norm3(rjk);
274 +
275 +  crossProduct3(rk,ri, rki);
276 +  distZX = dotProduct3(rj,rki) / norm3(rki);
277 +
278 +  minDist = min(min(distXY, distYZ), distZX);
279 +  return minDist/2;
280 +  
281 + }
282 +
283   void SimInfo::wrapVector( double thePos[3] ){
284  
285 <  int i, j, k;
285 >  int i;
286    double scaled[3];
287  
288    if( !orthoRhombic ){
# Line 335 | Line 320 | int SimInfo::getNDF(){
320  
321  
322   int SimInfo::getNDF(){
323 <  int ndf_local, ndf;
323 >  int ndf_local;
324 >
325 >  ndf_local = 0;
326    
327 <  ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
327 >  for(int i = 0; i < integrableObjects.size(); i++){
328 >    ndf_local += 3;
329 >    if (integrableObjects[i]->isDirectional()) {
330 >      if (integrableObjects[i]->isLinear())
331 >        ndf_local += 2;
332 >      else
333 >        ndf_local += 3;
334 >    }
335 >  }
336  
337 +  // n_constraints is local, so subtract them on each processor:
338 +
339 +  ndf_local -= n_constraints;
340 +
341   #ifdef IS_MPI
342    MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
343   #else
344    ndf = ndf_local;
345   #endif
346  
347 <  ndf = ndf - 3;
347 >  // nZconstraints is global, as are the 3 COM translations for the
348 >  // entire system:
349  
350 +  ndf = ndf - 3 - nZconstraints;
351 +
352    return ndf;
353   }
354  
355   int SimInfo::getNDFraw() {
356 <  int ndfRaw_local, ndfRaw;
356 >  int ndfRaw_local;
357  
358    // Raw degrees of freedom that we have to set
359 <  ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
360 <  
359 >  ndfRaw_local = 0;
360 >
361 >  for(int i = 0; i < integrableObjects.size(); i++){
362 >    ndfRaw_local += 3;
363 >    if (integrableObjects[i]->isDirectional()) {
364 >       if (integrableObjects[i]->isLinear())
365 >        ndfRaw_local += 2;
366 >      else
367 >        ndfRaw_local += 3;
368 >    }
369 >  }
370 >    
371   #ifdef IS_MPI
372    MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
373   #else
# Line 364 | Line 376 | int SimInfo::getNDFraw() {
376  
377    return ndfRaw;
378   }
379 <
379 >
380 > int SimInfo::getNDFtranslational() {
381 >  int ndfTrans_local;
382 >
383 >  ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
384 >
385 >
386 > #ifdef IS_MPI
387 >  MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
388 > #else
389 >  ndfTrans = ndfTrans_local;
390 > #endif
391 >
392 >  ndfTrans = ndfTrans - 3 - nZconstraints;
393 >
394 >  return ndfTrans;
395 > }
396 >
397 > int SimInfo::getTotIntegrableObjects() {
398 >  int nObjs_local;
399 >  int nObjs;
400 >
401 >  nObjs_local =  integrableObjects.size();
402 >
403 >
404 > #ifdef IS_MPI
405 >  MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
406 > #else
407 >  nObjs = nObjs_local;
408 > #endif
409 >
410 >
411 >  return nObjs;
412 > }
413 >
414   void SimInfo::refreshSim(){
415  
416    simtype fInfo;
# Line 374 | Line 420 | void SimInfo::refreshSim(){
420  
421    fInfo.dielect = 0.0;
422  
423 <  if( useDipole ){
423 >  if( useDipoles ){
424      if( useReactionField )fInfo.dielect = dielectric;
425    }
426  
# Line 383 | Line 429 | void SimInfo::refreshSim(){
429    fInfo.SIM_uses_LJ = useLJ;
430    fInfo.SIM_uses_sticky = useSticky;
431    //fInfo.SIM_uses_sticky = 0;
432 <  fInfo.SIM_uses_dipoles = useDipole;
432 >  fInfo.SIM_uses_charges = useCharges;
433 >  fInfo.SIM_uses_dipoles = useDipoles;
434    //fInfo.SIM_uses_dipoles = 0;
435 <  //fInfo.SIM_uses_RF = useReactionField;
436 <  fInfo.SIM_uses_RF = 0;
435 >  fInfo.SIM_uses_RF = useReactionField;
436 >  //fInfo.SIM_uses_RF = 0;
437    fInfo.SIM_uses_GB = useGB;
438    fInfo.SIM_uses_EAM = useEAM;
439  
440 <  excl = Exclude::getArray();
440 >  n_exclude = excludes->getSize();
441 >  excl = excludes->getFortranArray();
442  
443   #ifdef IS_MPI
444    n_global = mpiSim->getTotAtoms();
# Line 420 | Line 468 | void SimInfo::refreshSim(){
468  
469    this->ndf = this->getNDF();
470    this->ndfRaw = this->getNDFraw();
471 <
471 >  this->ndfTrans = this->getNDFtranslational();
472   }
473  
474 + void SimInfo::setDefaultRcut( double theRcut ){
475  
476 < void SimInfo::setRcut( double theRcut ){
476 >  haveRcut = 1;
477 >  rCut = theRcut;
478  
479 <  if( !haveOrigRcut ){
430 <    haveOrigRcut = 1;
431 <    origRcut = theRcut;
432 <  }
479 >  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
480  
481 <  rCut = theRcut;
435 <  checkCutOffs();
481 >  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
482   }
483  
484 < void SimInfo::setEcr( double theEcr ){
484 > void SimInfo::setDefaultEcr( double theEcr ){
485  
486 <  if( !haveOrigEcr ){
441 <    haveOrigEcr = 1;
442 <    origEcr = theEcr;
443 <  }
444 <
486 >  haveEcr = 1;
487    ecr = theEcr;
488 <  checkCutOffs();
488 >  
489 >  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
490 >
491 >  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
492   }
493  
494 < void SimInfo::setEcr( double theEcr, double theEst ){
494 > void SimInfo::setDefaultEcr( double theEcr, double theEst ){
495  
496    est = theEst;
497 <  setEcr( theEcr );
497 >  setDefaultEcr( theEcr );
498   }
499  
500  
501   void SimInfo::checkCutOffs( void ){
502 <
458 <  int cutChanged = 0;
459 <
502 >  
503    if( boxIsInit ){
504      
505      //we need to check cutOffs against the box
506      
507 <    if( maxCutoff > rCut ){
508 <      if( rCut < origRcut ){
509 <        rCut = origRcut;
510 <        if (rCut > maxCutoff) rCut = maxCutoff;
511 <        
512 <        sprintf( painCave.errMsg,
513 <                 "New Box size is setting the long range cutoff radius "
514 <                 "to %lf\n",
515 <                 rCut );
516 <        painCave.isFatal = 0;
517 <        simError();
518 <      }
507 >    if( rCut > maxCutoff ){
508 >      sprintf( painCave.errMsg,
509 >               "LJrcut is too large for the current periodic box.\n"
510 >               "\tCurrent Value of LJrcut = %G at time %G\n "
511 >               "\tThis is larger than half of at least one of the\n"
512 >               "\tperiodic box vectors.  Right now, the Box matrix is:\n"
513 >               "\n, %G"
514 >               "\t[ %G %G %G ]\n"
515 >               "\t[ %G %G %G ]\n"
516 >               "\t[ %G %G %G ]\n",
517 >               rCut, currentTime, maxCutoff,
518 >               Hmat[0][0], Hmat[0][1], Hmat[0][2],
519 >               Hmat[1][0], Hmat[1][1], Hmat[1][2],
520 >               Hmat[2][0], Hmat[2][1], Hmat[2][2]);
521 >      painCave.isFatal = 1;
522 >      simError();
523      }
524 <
525 <    if( maxCutoff > ecr ){
526 <      if( ecr < origEcr ){
480 <        rCut = origEcr;
481 <        if (ecr > maxCutoff) ecr = maxCutoff;
482 <        
524 >    
525 >    if( haveEcr ){
526 >      if( ecr > maxCutoff ){
527          sprintf( painCave.errMsg,
528 <                 "New Box size is setting the electrostaticCutoffRadius "
529 <                 "to %lf\n",
530 <                 ecr );
531 <        painCave.isFatal = 0;
528 >                 "electrostaticCutoffRadius is too large for the current\n"
529 >                 "\tperiodic box.\n\n"
530 >                 "\tCurrent Value of ECR = %G at time %G\n "
531 >                 "\tThis is larger than half of at least one of the\n"
532 >                 "\tperiodic box vectors.  Right now, the Box matrix is:\n"
533 >                 "\n"
534 >                 "\t[ %G %G %G ]\n"
535 >                 "\t[ %G %G %G ]\n"
536 >                 "\t[ %G %G %G ]\n",
537 >                 ecr, currentTime,
538 >                 Hmat[0][0], Hmat[0][1], Hmat[0][2],
539 >                 Hmat[1][0], Hmat[1][1], Hmat[1][2],
540 >                 Hmat[2][0], Hmat[2][1], Hmat[2][2]);
541 >        painCave.isFatal = 1;
542          simError();
543        }
544      }
545 +  } else {
546 +    // initialize this stuff before using it, OK?
547 +    sprintf( painCave.errMsg,
548 +             "Trying to check cutoffs without a box.\n"
549 +             "\tOOPSE should have better programmers than that.\n" );
550 +    painCave.isFatal = 1;
551 +    simError();      
552 +  }
553 +  
554 + }
555  
556 + void SimInfo::addProperty(GenericData* prop){
557  
558 <    if (rCut > maxCutoff) {
559 <      sprintf( painCave.errMsg,
560 <               "New Box size is setting the long range cutoff radius "
561 <               "to %lf\n",
562 <               maxCutoff );
563 <      painCave.isFatal = 0;
564 <      simError();
500 <      rCut = maxCutoff;
501 <    }
502 <
503 <    if( ecr > maxCutoff){
504 <      sprintf( painCave.errMsg,
505 <               "New Box size is setting the electrostaticCutoffRadius "
506 <               "to %lf\n",
507 <               maxCutoff  );
508 <      painCave.isFatal = 0;
509 <      simError();      
510 <      ecr = maxCutoff;
511 <    }
512 <
558 >  map<string, GenericData*>::iterator result;
559 >  result = properties.find(prop->getID());
560 >  
561 >  //we can't simply use  properties[prop->getID()] = prop,
562 >  //it will cause memory leak if we already contain a propery which has the same name of prop
563 >  
564 >  if(result != properties.end()){
565      
566 +    delete (*result).second;
567 +    (*result).second = prop;
568 +      
569    }
570 <  
570 >  else{
571  
572 <  if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
572 >    properties[prop->getID()] = prop;
573  
519 –  // rlist is the 1.0 plus max( rcut, ecr )
520 –  
521 –  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
522 –
523 –  if( cutChanged ){
524 –    
525 –    notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
574    }
575 +    
576 + }
577  
578 <  oldEcr = ecr;
579 <  oldRcut = rCut;
578 > GenericData* SimInfo::getProperty(const string& propName){
579 >
580 >  map<string, GenericData*>::iterator result;
581 >  
582 >  //string lowerCaseName = ();
583 >  
584 >  result = properties.find(propName);
585 >  
586 >  if(result != properties.end())
587 >    return (*result).second;  
588 >  else  
589 >    return NULL;  
590   }
591 +

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