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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 1212 by chrisfen, Tue Jun 1 17:15:43 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 +  useSolidThermInt = 0;
66 +  useLiquidThermInt = 0;
67  
68 +  haveCutoffGroups = false;
69 +
70 +  excludes = Exclude::Instance();
71 +
72 +  myConfiguration = new SimState();
73 +
74 +  has_minimizer = false;
75 +  the_minimizer =NULL;
76 +
77 +  ngroup = 0;
78 +
79    wrapMeSimInfo( this );
80   }
81  
82 +
83 + SimInfo::~SimInfo(){
84 +
85 +  delete myConfiguration;
86 +
87 +  map<string, GenericData*>::iterator i;
88 +  
89 +  for(i = properties.begin(); i != properties.end(); i++)
90 +    delete (*i).second;
91 +  
92 + }
93 +
94   void SimInfo::setBox(double newBox[3]) {
95    
96    int i, j;
# Line 75 | Line 109 | void SimInfo::setBoxM( double theBox[3][3] ){
109  
110   void SimInfo::setBoxM( double theBox[3][3] ){
111    
112 <  int i, j, status;
79 <  double smallestBoxL, maxCutoff;
112 >  int i, j;
113    double FortranHmat[9]; // to preserve compatibility with Fortran the
114                           // ordering in the array is as follows:
115                           // [ 0 3 6 ]
# Line 84 | Line 117 | void SimInfo::setBoxM( double theBox[3][3] ){
117                           // [ 2 5 8 ]
118    double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
119  
87 –  
120    if( !boxIsInit ) boxIsInit = 1;
121  
122    for(i=0; i < 3; i++)
# Line 128 | Line 160 | void SimInfo::calcHmatInv( void ) {
160  
161   void SimInfo::calcHmatInv( void ) {
162    
163 +  int oldOrtho;
164    int i,j;
165    double smallDiag;
166    double tol;
# Line 135 | Line 168 | void SimInfo::calcHmatInv( void ) {
168  
169    invertMat3( Hmat, HmatInv );
170  
138 –  // Check the inverse to make sure it is sane:
139 –
140 –  matMul3( Hmat, HmatInv, sanity );
141 –    
171    // check to see if Hmat is orthorhombic
172    
173 <  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;
173 >  oldOrtho = orthoRhombic;
174  
175 +  smallDiag = fabs(Hmat[0][0]);
176 +  if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
177 +  if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
178 +  tol = smallDiag * orthoTolerance;
179 +
180    orthoRhombic = 1;
181    
182    for (i = 0; i < 3; i++ ) {
183      for (j = 0 ; j < 3; j++) {
184        if (i != j) {
185          if (orthoRhombic) {
186 <          if (Hmat[i][j] >= tol) orthoRhombic = 0;
186 >          if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
187          }        
188        }
189      }
190    }
160 – }
191  
192 < double SimInfo::matDet3(double a[3][3]) {
193 <  int i, j, k;
194 <  double determinant;
195 <
196 <  determinant = 0.0;
197 <
198 <  for(i = 0; i < 3; i++) {
199 <    j = (i+1)%3;
200 <    k = (i+2)%3;
201 <
202 <    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;
192 >  if( oldOrtho != orthoRhombic ){
193 >    
194 >    if( orthoRhombic ){
195 >      sprintf( painCave.errMsg,
196 >               "OOPSE is switching from the default Non-Orthorhombic\n"
197 >               "\tto the faster Orthorhombic periodic boundary computations.\n"
198 >               "\tThis is usually a good thing, but if you wan't the\n"
199 >               "\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
200 >               "\tvariable ( currently set to %G ) smaller.\n",
201 >               orthoTolerance);
202 >      simError();
203      }
204 <  }
205 < }
206 <
207 < void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
208 <  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
209 <
210 <  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
211 <  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
212 <  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
213 <  
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];
204 >    else {
205 >      sprintf( painCave.errMsg,
206 >               "OOPSE is switching from the faster Orthorhombic to the more\n"
207 >               "\tflexible Non-Orthorhombic periodic boundary computations.\n"
208 >               "\tThis is usually because the box has deformed under\n"
209 >               "\tNPTf integration. If you wan't to live on the edge with\n"
210 >               "\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
211 >               "\tvariable ( currently set to %G ) larger.\n",
212 >               orthoTolerance);
213 >      simError();
214      }
215    }
243 –  for (i = 0; i < 3; i++) {
244 –    for (j = 0; j < 3; j++) {
245 –      out[i][j] = temp[i][j];
246 –    }
247 –  }
216   }
249 –  
250 – void SimInfo::printMat3(double A[3][3] ){
217  
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 –
218   void SimInfo::calcBoxL( void ){
219  
220    double dx, dy, dz, dsq;
269 –  int i;
221  
222    // boxVol = Determinant of Hmat
223  
# Line 277 | Line 228 | void SimInfo::calcBoxL( void ){
228    dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
229    dsq = dx*dx + dy*dy + dz*dz;
230    boxL[0] = sqrt( dsq );
231 <  maxCutoff = 0.5 * boxL[0];
231 >  //maxCutoff = 0.5 * boxL[0];
232  
233    // boxLy
234    
235    dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
236    dsq = dx*dx + dy*dy + dz*dz;
237    boxL[1] = sqrt( dsq );
238 <  if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
238 >  //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
239  
240 +
241    // boxLz
242    
243    dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
244    dsq = dx*dx + dy*dy + dz*dz;
245    boxL[2] = sqrt( dsq );
246 <  if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
246 >  //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
247  
248 +  //calculate the max cutoff
249 +  maxCutoff =  calcMaxCutOff();
250 +  
251 +  checkCutOffs();
252 +
253   }
254  
255  
256 + double SimInfo::calcMaxCutOff(){
257 +
258 +  double ri[3], rj[3], rk[3];
259 +  double rij[3], rjk[3], rki[3];
260 +  double minDist;
261 +
262 +  ri[0] = Hmat[0][0];
263 +  ri[1] = Hmat[1][0];
264 +  ri[2] = Hmat[2][0];
265 +
266 +  rj[0] = Hmat[0][1];
267 +  rj[1] = Hmat[1][1];
268 +  rj[2] = Hmat[2][1];
269 +
270 +  rk[0] = Hmat[0][2];
271 +  rk[1] = Hmat[1][2];
272 +  rk[2] = Hmat[2][2];
273 +    
274 +  crossProduct3(ri, rj, rij);
275 +  distXY = dotProduct3(rk,rij) / norm3(rij);
276 +
277 +  crossProduct3(rj,rk, rjk);
278 +  distYZ = dotProduct3(ri,rjk) / norm3(rjk);
279 +
280 +  crossProduct3(rk,ri, rki);
281 +  distZX = dotProduct3(rj,rki) / norm3(rki);
282 +
283 +  minDist = min(min(distXY, distYZ), distZX);
284 +  return minDist/2;
285 +  
286 + }
287 +
288   void SimInfo::wrapVector( double thePos[3] ){
289  
290 <  int i, j, k;
290 >  int i;
291    double scaled[3];
292  
293    if( !orthoRhombic ){
# Line 336 | Line 325 | int SimInfo::getNDF(){
325  
326  
327   int SimInfo::getNDF(){
328 <  int ndf_local, ndf;
328 >  int ndf_local;
329 >
330 >  ndf_local = 0;
331    
332 <  ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
332 >  for(int i = 0; i < integrableObjects.size(); i++){
333 >    ndf_local += 3;
334 >    if (integrableObjects[i]->isDirectional()) {
335 >      if (integrableObjects[i]->isLinear())
336 >        ndf_local += 2;
337 >      else
338 >        ndf_local += 3;
339 >    }
340 >  }
341  
342 +  // n_constraints is local, so subtract them on each processor:
343 +
344 +  ndf_local -= n_constraints;
345 +
346   #ifdef IS_MPI
347    MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
348   #else
349    ndf = ndf_local;
350   #endif
351  
352 <  ndf = ndf - 3;
352 >  // nZconstraints is global, as are the 3 COM translations for the
353 >  // entire system:
354  
355 +  ndf = ndf - 3 - nZconstraints;
356 +
357    return ndf;
358   }
359  
360   int SimInfo::getNDFraw() {
361 <  int ndfRaw_local, ndfRaw;
361 >  int ndfRaw_local;
362  
363    // Raw degrees of freedom that we have to set
364 <  ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
365 <  
364 >  ndfRaw_local = 0;
365 >
366 >  for(int i = 0; i < integrableObjects.size(); i++){
367 >    ndfRaw_local += 3;
368 >    if (integrableObjects[i]->isDirectional()) {
369 >       if (integrableObjects[i]->isLinear())
370 >        ndfRaw_local += 2;
371 >      else
372 >        ndfRaw_local += 3;
373 >    }
374 >  }
375 >    
376   #ifdef IS_MPI
377    MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
378   #else
# Line 365 | Line 381 | int SimInfo::getNDFraw() {
381  
382    return ndfRaw;
383   }
384 <
384 >
385 > int SimInfo::getNDFtranslational() {
386 >  int ndfTrans_local;
387 >
388 >  ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
389 >
390 >
391 > #ifdef IS_MPI
392 >  MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
393 > #else
394 >  ndfTrans = ndfTrans_local;
395 > #endif
396 >
397 >  ndfTrans = ndfTrans - 3 - nZconstraints;
398 >
399 >  return ndfTrans;
400 > }
401 >
402 > int SimInfo::getTotIntegrableObjects() {
403 >  int nObjs_local;
404 >  int nObjs;
405 >
406 >  nObjs_local =  integrableObjects.size();
407 >
408 >
409 > #ifdef IS_MPI
410 >  MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
411 > #else
412 >  nObjs = nObjs_local;
413 > #endif
414 >
415 >
416 >  return nObjs;
417 > }
418 >
419   void SimInfo::refreshSim(){
420  
421    simtype fInfo;
# Line 375 | Line 425 | void SimInfo::refreshSim(){
425  
426    fInfo.dielect = 0.0;
427  
428 <  if( useDipole ){
428 >  if( useDipoles ){
429      if( useReactionField )fInfo.dielect = dielectric;
430    }
431  
# Line 384 | Line 434 | void SimInfo::refreshSim(){
434    fInfo.SIM_uses_LJ = useLJ;
435    fInfo.SIM_uses_sticky = useSticky;
436    //fInfo.SIM_uses_sticky = 0;
437 <  fInfo.SIM_uses_dipoles = useDipole;
437 >  fInfo.SIM_uses_charges = useCharges;
438 >  fInfo.SIM_uses_dipoles = useDipoles;
439    //fInfo.SIM_uses_dipoles = 0;
440 <  //fInfo.SIM_uses_RF = useReactionField;
441 <  fInfo.SIM_uses_RF = 0;
440 >  fInfo.SIM_uses_RF = useReactionField;
441 >  //fInfo.SIM_uses_RF = 0;
442    fInfo.SIM_uses_GB = useGB;
443    fInfo.SIM_uses_EAM = useEAM;
444  
445 <  excl = Exclude::getArray();
446 <
445 >  n_exclude = excludes->getSize();
446 >  excl = excludes->getFortranArray();
447 >  
448   #ifdef IS_MPI
449 <  n_global = mpiSim->getTotAtoms();
449 >  n_global = mpiSim->getNAtomsGlobal();
450   #else
451    n_global = n_atoms;
452   #endif
453 <
453 >  
454    isError = 0;
455 <
455 >  
456 >  getFortranGroupArray(this, mfact, ngroup, groupList, groupStart);
457 >  //it may not be a good idea to pass the address of first element in vector
458 >  //since c++ standard does not require vector to be stored continuously in meomory
459 >  //Most of the compilers will organize the memory of vector continuously
460    setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
461 <                  &nGlobalExcludes, globalExcludes, molMembershipArray,
462 <                  &isError );
463 <
461 >                  &nGlobalExcludes, globalExcludes, molMembershipArray,
462 >                  &mfact[0], &ngroup, &groupList[0], &groupStart[0], &isError);
463 >  
464    if( isError ){
465 <
465 >    
466      sprintf( painCave.errMsg,
467 <             "There was an error setting the simulation information in fortran.\n" );
467 >             "There was an error setting the simulation information in fortran.\n" );
468      painCave.isFatal = 1;
469      simError();
470    }
471 <
471 >  
472   #ifdef IS_MPI
473    sprintf( checkPointMsg,
474             "succesfully sent the simulation information to fortran.\n");
475    MPIcheckPoint();
476   #endif // is_mpi
477 <
477 >  
478    this->ndf = this->getNDF();
479    this->ndfRaw = this->getNDFraw();
480 <
480 >  this->ndfTrans = this->getNDFtranslational();
481   }
482  
483 <
484 < void SimInfo::setRcut( double theRcut ){
485 <
430 <  if( !haveOrigRcut ){
431 <    haveOrigRcut = 1;
432 <    origRcut = theRcut;
433 <  }
434 <
483 > void SimInfo::setDefaultRcut( double theRcut ){
484 >  
485 >  haveRcut = 1;
486    rCut = theRcut;
487 <  checkCutOffs();
487 >  rList = rCut + 1.0;
488 >  
489 >  notifyFortranCutOffs( &rCut, &rSw, &rList );
490   }
491  
492 < void SimInfo::setEcr( double theEcr ){
492 > void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
493  
494 <  if( !haveOrigEcr ){
495 <    haveOrigEcr = 1;
443 <    origEcr = theEcr;
444 <  }
445 <
446 <  ecr = theEcr;
447 <  checkCutOffs();
494 >  rSw = theRsw;
495 >  setDefaultRcut( theRcut );
496   }
497  
450 – void SimInfo::setEcr( double theEcr, double theEst ){
498  
452 –  est = theEst;
453 –  setEcr( theEcr );
454 – }
455 –
456 –
499   void SimInfo::checkCutOffs( void ){
500 <
459 <  int cutChanged = 0;
460 <
500 >  
501    if( boxIsInit ){
502      
503      //we need to check cutOffs against the box
504      
505 <    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) {
505 >    if( rCut > maxCutoff ){
506        sprintf( painCave.errMsg,
507 <               "New Box size is setting the long range cutoff radius "
508 <               "to %lf\n",
509 <               maxCutoff );
510 <      painCave.isFatal = 0;
507 >               "cutoffRadius is too large for the current periodic box.\n"
508 >               "\tCurrent Value of cutoffRadius = %G at time %G\n "
509 >               "\tThis is larger than half of at least one of the\n"
510 >               "\tperiodic box vectors.  Right now, the Box matrix is:\n"
511 >               "\n"
512 >               "\t[ %G %G %G ]\n"
513 >               "\t[ %G %G %G ]\n"
514 >               "\t[ %G %G %G ]\n",
515 >               rCut, currentTime,
516 >               Hmat[0][0], Hmat[0][1], Hmat[0][2],
517 >               Hmat[1][0], Hmat[1][1], Hmat[1][2],
518 >               Hmat[2][0], Hmat[2][1], Hmat[2][2]);
519 >      painCave.isFatal = 1;
520        simError();
521 <      rCut = maxCutoff;
522 <    }
521 >    }    
522 >  } else {
523 >    // initialize this stuff before using it, OK?
524 >    sprintf( painCave.errMsg,
525 >             "Trying to check cutoffs without a box.\n"
526 >             "\tOOPSE should have better programmers than that.\n" );
527 >    painCave.isFatal = 1;
528 >    simError();      
529 >  }
530 >  
531 > }
532  
533 <    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 <    }
533 > void SimInfo::addProperty(GenericData* prop){
534  
535 +  map<string, GenericData*>::iterator result;
536 +  result = properties.find(prop->getID());
537 +  
538 +  //we can't simply use  properties[prop->getID()] = prop,
539 +  //it will cause memory leak if we already contain a propery which has the same name of prop
540 +  
541 +  if(result != properties.end()){
542      
543 +    delete (*result).second;
544 +    (*result).second = prop;
545 +      
546    }
547 <  
547 >  else{
548  
549 <  if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
549 >    properties[prop->getID()] = prop;
550  
551 <  // rlist is the 1.0 plus max( rcut, ecr )
551 >  }
552 >    
553 > }
554 >
555 > GenericData* SimInfo::getProperty(const string& propName){
556 >
557 >  map<string, GenericData*>::iterator result;
558    
559 <  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
559 >  //string lowerCaseName = ();
560 >  
561 >  result = properties.find(propName);
562 >  
563 >  if(result != properties.end())
564 >    return (*result).second;  
565 >  else  
566 >    return NULL;  
567 > }
568  
524 –  if( cutChanged ){
525 –    
526 –    notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
527 –  }
569  
570 <  oldEcr = ecr;
571 <  oldRcut = rCut;
570 > void getFortranGroupArray(SimInfo* info, vector<double>& mfact, int& ngroup,
571 >                          vector<int>& groupList, vector<int>& groupStart){
572 >  Molecule* myMols;
573 >  Atom** myAtoms;
574 >  int numAtom;
575 >  int curIndex;
576 >  double mtot;
577 >  int numMol;
578 >  int numCutoffGroups;
579 >  CutoffGroup* myCutoffGroup;
580 >  vector<CutoffGroup*>::iterator iterCutoff;
581 >  Atom* cutoffAtom;
582 >  vector<Atom*>::iterator iterAtom;
583 >  int atomIndex;
584 >  double totalMass;
585 >  
586 >  mfact.clear();
587 >  groupList.clear();
588 >  groupStart.clear();
589 >  
590 >  //Be careful, fortran array begin at 1
591 >  curIndex = 1;
592 >
593 >  myMols = info->molecules;
594 >  numMol = info->n_mol;
595 >  for(int i  = 0; i < numMol; i++){
596 >    numCutoffGroups = myMols[i].getNCutoffGroups();
597 >    for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff); myCutoffGroup != NULL;
598 >                                                  myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
599 >
600 >      totalMass = myCutoffGroup->getMass();
601 >      
602 >      for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom); cutoffAtom != NULL;
603 >                                           cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
604 >        mfact.push_back(cutoffAtom->getMass()/totalMass);
605 > #ifdef IS_MPI        
606 >        groupList.push_back(cutoffAtom->getGlobalIndex() + 1);
607 > #else
608 >        groupList.push_back(cutoffAtom->getIndex() + 1);
609 > #endif
610 >      }  
611 >                              
612 >      groupStart.push_back(curIndex);
613 >      curIndex += myCutoffGroup->getNumAtom();
614 >
615 >    }//end for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff))
616 >
617 >  }//end for(int i  = 0; i < numMol; i++)
618 >
619 >
620 >  //The last cutoff group need more element to indicate the end of the cutoff
621 >  ngroup = groupStart.size();
622   }

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