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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 690 by mmeineke, Tue Aug 12 21:44:06 2003 UTC vs.
Revision 1221 by chrisfen, Wed Jun 2 14:56:18 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;
# Line 36 | Line 42 | SimInfo::SimInfo(){
42    thermalTime = 0.0;
43    currentTime = 0.0;
44    rCut = 0.0;
45 <  origRcut = -1.0;
40 <  ecr = 0.0;
41 <  origEcr = -1.0;
42 <  est = 0.0;
43 <  oldEcr = 0.0;
44 <  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  
# Line 71 | Line 88 | SimInfo::~SimInfo(){
88    
89    for(i = properties.begin(); i != properties.end(); i++)
90      delete (*i).second;
91 <    
91 >  
92   }
93  
94   void SimInfo::setBox(double newBox[3]) {
# Line 92 | Line 109 | void SimInfo::setBoxM( double theBox[3][3] ){
109  
110   void SimInfo::setBoxM( double theBox[3][3] ){
111    
112 <  int i, j, status;
96 <  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 101 | Line 117 | void SimInfo::setBoxM( double theBox[3][3] ){
117                           // [ 2 5 8 ]
118    double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
119  
104 –  
120    if( !boxIsInit ) boxIsInit = 1;
121  
122    for(i=0; i < 3; i++)
# Line 145 | 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 152 | Line 168 | void SimInfo::calcHmatInv( void ) {
168  
169    invertMat3( Hmat, HmatInv );
170  
155 –  // Check the inverse to make sure it is sane:
156 –
157 –  matMul3( Hmat, HmatInv, sanity );
158 –    
171    // check to see if Hmat is orthorhombic
172    
173 <  smallDiag = Hmat[0][0];
162 <  if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1];
163 <  if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2];
164 <  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    }
177 – }
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]);
203 <  }
191 <
192 <  return determinant;
193 < }
194 <
195 < void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
196 <  
197 <  int  i, j, k, l, m, n;
198 <  double determinant;
199 <
200 <  determinant = matDet3( a );
201 <
202 <  if (determinant == 0.0) {
203 <    sprintf( painCave.errMsg,
204 <             "Can't invert a matrix with a zero determinant!\n");
205 <    painCave.isFatal = 1;
206 <    simError();
207 <  }
208 <
209 <  for (i=0; i < 3; i++) {
210 <    j = (i+1)%3;
211 <    k = (i+2)%3;
212 <    for(l = 0; l < 3; l++) {
213 <      m = (l+1)%3;
214 <      n = (l+2)%3;
215 <      
216 <      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 >      painCave.severity = OOPSE_INFO;
203 >      simError();
204      }
205 <  }
206 < }
207 <
208 < void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
209 <  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
210 <
211 <  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
212 <  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
213 <  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
214 <  
215 <  r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0];
229 <  r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1];
230 <  r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2];
231 <  
232 <  r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0];
233 <  r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1];
234 <  r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2];
235 <  
236 <  c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
237 <  c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
238 <  c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
239 < }
240 <
241 < void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
242 <  double a0, a1, a2;
243 <
244 <  a0 = inVec[0];  a1 = inVec[1];  a2 = inVec[2];
245 <
246 <  outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2;
247 <  outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
248 <  outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
249 < }
250 <
251 < void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
252 <  double temp[3][3];
253 <  int i, j;
254 <
255 <  for (i = 0; i < 3; i++) {
256 <    for (j = 0; j < 3; j++) {
257 <      temp[j][i] = in[i][j];
205 >    else {
206 >      sprintf( painCave.errMsg,
207 >               "OOPSE is switching from the faster Orthorhombic to the more\n"
208 >               "\tflexible Non-Orthorhombic periodic boundary computations.\n"
209 >               "\tThis is usually because the box has deformed under\n"
210 >               "\tNPTf integration. If you wan't to live on the edge with\n"
211 >               "\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
212 >               "\tvariable ( currently set to %G ) larger.\n",
213 >               orthoTolerance);
214 >      painCave.severity = OOPSE_WARNING;
215 >      simError();
216      }
217    }
260 –  for (i = 0; i < 3; i++) {
261 –    for (j = 0; j < 3; j++) {
262 –      out[i][j] = temp[i][j];
263 –    }
264 –  }
218   }
266 –  
267 – void SimInfo::printMat3(double A[3][3] ){
219  
269 –  std::cerr
270 –            << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
271 –            << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
272 –            << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
273 – }
274 –
275 – void SimInfo::printMat9(double A[9] ){
276 –
277 –  std::cerr
278 –            << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
279 –            << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
280 –            << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
281 – }
282 –
220   void SimInfo::calcBoxL( void ){
221  
222    double dx, dy, dz, dsq;
286 –  int i;
223  
224    // boxVol = Determinant of Hmat
225  
# Line 294 | Line 230 | void SimInfo::calcBoxL( void ){
230    dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
231    dsq = dx*dx + dy*dy + dz*dz;
232    boxL[0] = sqrt( dsq );
233 <  maxCutoff = 0.5 * boxL[0];
233 >  //maxCutoff = 0.5 * boxL[0];
234  
235    // boxLy
236    
237    dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
238    dsq = dx*dx + dy*dy + dz*dz;
239    boxL[1] = sqrt( dsq );
240 <  if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
240 >  //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
241  
242 +
243    // boxLz
244    
245    dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
246    dsq = dx*dx + dy*dy + dz*dz;
247    boxL[2] = sqrt( dsq );
248 <  if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
248 >  //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
249 >
250 >  //calculate the max cutoff
251 >  maxCutoff =  calcMaxCutOff();
252    
253    checkCutOffs();
254  
255   }
256  
257  
258 + double SimInfo::calcMaxCutOff(){
259 +
260 +  double ri[3], rj[3], rk[3];
261 +  double rij[3], rjk[3], rki[3];
262 +  double minDist;
263 +
264 +  ri[0] = Hmat[0][0];
265 +  ri[1] = Hmat[1][0];
266 +  ri[2] = Hmat[2][0];
267 +
268 +  rj[0] = Hmat[0][1];
269 +  rj[1] = Hmat[1][1];
270 +  rj[2] = Hmat[2][1];
271 +
272 +  rk[0] = Hmat[0][2];
273 +  rk[1] = Hmat[1][2];
274 +  rk[2] = Hmat[2][2];
275 +    
276 +  crossProduct3(ri, rj, rij);
277 +  distXY = dotProduct3(rk,rij) / norm3(rij);
278 +
279 +  crossProduct3(rj,rk, rjk);
280 +  distYZ = dotProduct3(ri,rjk) / norm3(rjk);
281 +
282 +  crossProduct3(rk,ri, rki);
283 +  distZX = dotProduct3(rj,rki) / norm3(rki);
284 +
285 +  minDist = min(min(distXY, distYZ), distZX);
286 +  return minDist/2;
287 +  
288 + }
289 +
290   void SimInfo::wrapVector( double thePos[3] ){
291  
292 <  int i, j, k;
292 >  int i;
293    double scaled[3];
294  
295    if( !orthoRhombic ){
# Line 355 | Line 327 | int SimInfo::getNDF(){
327  
328  
329   int SimInfo::getNDF(){
330 <  int ndf_local, ndf;
330 >  int ndf_local;
331 >
332 >  ndf_local = 0;
333    
334 <  ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
334 >  for(int i = 0; i < integrableObjects.size(); i++){
335 >    ndf_local += 3;
336 >    if (integrableObjects[i]->isDirectional()) {
337 >      if (integrableObjects[i]->isLinear())
338 >        ndf_local += 2;
339 >      else
340 >        ndf_local += 3;
341 >    }
342 >  }
343  
344 +  // n_constraints is local, so subtract them on each processor:
345 +
346 +  ndf_local -= n_constraints;
347 +
348   #ifdef IS_MPI
349    MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
350   #else
351    ndf = ndf_local;
352   #endif
353  
354 +  // nZconstraints is global, as are the 3 COM translations for the
355 +  // entire system:
356 +
357    ndf = ndf - 3 - nZconstraints;
358  
359    return ndf;
360   }
361  
362   int SimInfo::getNDFraw() {
363 <  int ndfRaw_local, ndfRaw;
363 >  int ndfRaw_local;
364  
365    // Raw degrees of freedom that we have to set
366 <  ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
367 <  
366 >  ndfRaw_local = 0;
367 >
368 >  for(int i = 0; i < integrableObjects.size(); i++){
369 >    ndfRaw_local += 3;
370 >    if (integrableObjects[i]->isDirectional()) {
371 >       if (integrableObjects[i]->isLinear())
372 >        ndfRaw_local += 2;
373 >      else
374 >        ndfRaw_local += 3;
375 >    }
376 >  }
377 >    
378   #ifdef IS_MPI
379    MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
380   #else
# Line 384 | Line 383 | int SimInfo::getNDFraw() {
383  
384    return ndfRaw;
385   }
386 <
386 >
387 > int SimInfo::getNDFtranslational() {
388 >  int ndfTrans_local;
389 >
390 >  ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
391 >
392 >
393 > #ifdef IS_MPI
394 >  MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
395 > #else
396 >  ndfTrans = ndfTrans_local;
397 > #endif
398 >
399 >  ndfTrans = ndfTrans - 3 - nZconstraints;
400 >
401 >  return ndfTrans;
402 > }
403 >
404 > int SimInfo::getTotIntegrableObjects() {
405 >  int nObjs_local;
406 >  int nObjs;
407 >
408 >  nObjs_local =  integrableObjects.size();
409 >
410 >
411 > #ifdef IS_MPI
412 >  MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
413 > #else
414 >  nObjs = nObjs_local;
415 > #endif
416 >
417 >
418 >  return nObjs;
419 > }
420 >
421   void SimInfo::refreshSim(){
422  
423    simtype fInfo;
# Line 394 | Line 427 | void SimInfo::refreshSim(){
427  
428    fInfo.dielect = 0.0;
429  
430 <  if( useDipole ){
430 >  if( useDipoles ){
431      if( useReactionField )fInfo.dielect = dielectric;
432    }
433  
# Line 403 | Line 436 | void SimInfo::refreshSim(){
436    fInfo.SIM_uses_LJ = useLJ;
437    fInfo.SIM_uses_sticky = useSticky;
438    //fInfo.SIM_uses_sticky = 0;
439 <  fInfo.SIM_uses_dipoles = useDipole;
439 >  fInfo.SIM_uses_charges = useCharges;
440 >  fInfo.SIM_uses_dipoles = useDipoles;
441    //fInfo.SIM_uses_dipoles = 0;
442 <  //fInfo.SIM_uses_RF = useReactionField;
443 <  fInfo.SIM_uses_RF = 0;
442 >  fInfo.SIM_uses_RF = useReactionField;
443 >  //fInfo.SIM_uses_RF = 0;
444    fInfo.SIM_uses_GB = useGB;
445    fInfo.SIM_uses_EAM = useEAM;
446  
447 <  excl = Exclude::getArray();
448 <
447 >  n_exclude = excludes->getSize();
448 >  excl = excludes->getFortranArray();
449 >  
450   #ifdef IS_MPI
451 <  n_global = mpiSim->getTotAtoms();
451 >  n_global = mpiSim->getNAtomsGlobal();
452   #else
453    n_global = n_atoms;
454   #endif
455 <
455 >  
456    isError = 0;
457 <
457 >  
458 >  getFortranGroupArrays(this, FglobalGroupMembership, mfact);
459 >  //it may not be a good idea to pass the address of first element in vector
460 >  //since c++ standard does not require vector to be stored continuously in meomory
461 >  //Most of the compilers will organize the memory of vector continuously
462    setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
463 <                  &nGlobalExcludes, globalExcludes, molMembershipArray,
464 <                  &isError );
463 >                  &nGlobalExcludes, globalExcludes, molMembershipArray,
464 >                  &mfact[0], &ngroup, &FglobalGroupMembership[0], &isError);
465  
466    if( isError ){
467 <
467 >    
468      sprintf( painCave.errMsg,
469 <             "There was an error setting the simulation information in fortran.\n" );
469 >             "There was an error setting the simulation information in fortran.\n" );
470      painCave.isFatal = 1;
471 +    painCave.severity = OOPSE_ERROR;
472      simError();
473    }
474 <
474 >  
475   #ifdef IS_MPI
476    sprintf( checkPointMsg,
477             "succesfully sent the simulation information to fortran.\n");
478    MPIcheckPoint();
479   #endif // is_mpi
480 <
480 >  
481    this->ndf = this->getNDF();
482    this->ndfRaw = this->getNDFraw();
483 <
483 >  this->ndfTrans = this->getNDFtranslational();
484   }
485  
486 <
487 < void SimInfo::setRcut( double theRcut ){
488 <
449 <  if( !haveOrigRcut ){
450 <    haveOrigRcut = 1;
451 <    origRcut = theRcut;
452 <  }
453 <
486 > void SimInfo::setDefaultRcut( double theRcut ){
487 >  
488 >  haveRcut = 1;
489    rCut = theRcut;
490 <  checkCutOffs();
490 >  rList = rCut + 1.0;
491 >  
492 >  notifyFortranCutOffs( &rCut, &rSw, &rList );
493   }
494  
495 < void SimInfo::setEcr( double theEcr ){
495 > void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
496  
497 <  if( !haveOrigEcr ){
498 <    haveOrigEcr = 1;
462 <    origEcr = theEcr;
463 <  }
464 <
465 <  ecr = theEcr;
466 <  checkCutOffs();
497 >  rSw = theRsw;
498 >  setDefaultRcut( theRcut );
499   }
500  
469 – void SimInfo::setEcr( double theEcr, double theEst ){
501  
471 –  est = theEst;
472 –  setEcr( theEcr );
473 – }
474 –
475 –
502   void SimInfo::checkCutOffs( void ){
503 <
478 <  int cutChanged = 0;
479 <
480 <
481 <
503 >  
504    if( boxIsInit ){
505      
506      //we need to check cutOffs against the box
507 <  
508 <    if(( maxCutoff > rCut )&&(usePBC)){
487 <      if( rCut < origRcut ){
488 <        rCut = origRcut;
489 <        if (rCut > maxCutoff) rCut = maxCutoff;
490 <        
491 <        sprintf( painCave.errMsg,
492 <                 "New Box size is setting the long range cutoff radius "
493 <                 "to %lf\n",
494 <                 rCut );
495 <        painCave.isFatal = 0;
496 <        simError();
497 <      }
498 <    }
499 <
500 <    if( maxCutoff > ecr ){
501 <      if( ecr < origEcr ){
502 <        rCut = origEcr;
503 <        if (ecr > maxCutoff) ecr = maxCutoff;
504 <        
505 <        sprintf( painCave.errMsg,
506 <                 "New Box size is setting the electrostaticCutoffRadius "
507 <                 "to %lf\n",
508 <                 ecr );
509 <        painCave.isFatal = 0;
510 <        simError();
511 <      }
512 <    }
513 <
514 <
515 <    if ((rCut > maxCutoff)&&(usePBC)) {
507 >    
508 >    if( rCut > maxCutoff ){
509        sprintf( painCave.errMsg,
510 <               "New Box size is setting the long range cutoff radius "
511 <               "to %lf\n",
512 <               maxCutoff );
513 <      painCave.isFatal = 0;
510 >               "cutoffRadius is too large for the current periodic box.\n"
511 >               "\tCurrent Value of cutoffRadius = %G at time %G\n "
512 >               "\tThis is larger than half of at least one of the\n"
513 >               "\tperiodic box vectors.  Right now, the Box matrix is:\n"
514 >               "\n"
515 >               "\t[ %G %G %G ]\n"
516 >               "\t[ %G %G %G ]\n"
517 >               "\t[ %G %G %G ]\n",
518 >               rCut, currentTime,
519 >               Hmat[0][0], Hmat[0][1], Hmat[0][2],
520 >               Hmat[1][0], Hmat[1][1], Hmat[1][2],
521 >               Hmat[2][0], Hmat[2][1], Hmat[2][2]);
522 >      painCave.severity = OOPSE_ERROR;
523 >      painCave.isFatal = 1;
524        simError();
525 <      rCut = maxCutoff;
526 <    }
527 <
528 <    if( ecr > maxCutoff){
529 <      sprintf( painCave.errMsg,
530 <               "New Box size is setting the electrostaticCutoffRadius "
531 <               "to %lf\n",
532 <               maxCutoff  );
533 <      painCave.isFatal = 0;
531 <      simError();      
532 <      ecr = maxCutoff;
533 <    }
534 <
535 <    
525 >    }    
526 >  } else {
527 >    // initialize this stuff before using it, OK?
528 >    sprintf( painCave.errMsg,
529 >             "Trying to check cutoffs without a box.\n"
530 >             "\tOOPSE should have better programmers than that.\n" );
531 >    painCave.severity = OOPSE_ERROR;
532 >    painCave.isFatal = 1;
533 >    simError();      
534    }
537 –  
538 –
539 –  if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
540 –
541 –  // rlist is the 1.0 plus max( rcut, ecr )
535    
543 –  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
544 –
545 –  if( cutChanged ){
546 –    
547 –    notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
548 –  }
549 –
550 –  oldEcr = ecr;
551 –  oldRcut = rCut;
536   }
537  
538   void SimInfo::addProperty(GenericData* prop){
# Line 587 | Line 571 | GenericData* SimInfo::getProperty(const string& propNa
571      return NULL;  
572   }
573  
590 – vector<GenericData*> SimInfo::getProperties(){
574  
575 <  vector<GenericData*> result;
576 <  map<string, GenericData*>::iterator i;
575 > void SimInfo::getFortranGroupArrays(SimInfo* info,
576 >                                    vector<int>& FglobalGroupMembership,
577 >                                    vector<double>& mfact){
578    
579 <  for(i = properties.begin(); i != properties.end(); i++)
580 <    result.push_back((*i).second);
581 <    
582 <  return result;
583 < }
579 >  Molecule* myMols;
580 >  Atom** myAtoms;
581 >  int numAtom;
582 >  double mtot;
583 >  int numMol;
584 >  int numCutoffGroups;
585 >  CutoffGroup* myCutoffGroup;
586 >  vector<CutoffGroup*>::iterator iterCutoff;
587 >  Atom* cutoffAtom;
588 >  vector<Atom*>::iterator iterAtom;
589 >  int atomIndex;
590 >  double totalMass;
591 >  
592 >  mfact.clear();
593 >  FglobalGroupMembership.clear();
594 >  
595  
596 +  // Fix the silly fortran indexing problem
597 + #ifdef IS_MPI
598 +  numAtom = mpiSim->getNAtomsGlobal();
599 + #else
600 +  numAtom = n_atoms;
601 + #endif
602 +  for (int i = 0; i < numAtom; i++)
603 +    FglobalGroupMembership.push_back(globalGroupMembership[i] + 1);
604 +  
605  
606 +  myMols = info->molecules;
607 +  numMol = info->n_mol;
608 +  for(int i  = 0; i < numMol; i++){
609 +    numCutoffGroups = myMols[i].getNCutoffGroups();
610 +    for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff);
611 +        myCutoffGroup != NULL;
612 +        myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
613 +
614 +      totalMass = myCutoffGroup->getMass();
615 +      
616 +      for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom);
617 +          cutoffAtom != NULL;
618 +          cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
619 +        mfact.push_back(cutoffAtom->getMass()/totalMass);
620 +      }  
621 +    }
622 +  }
623 +
624 + }

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