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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 770 by gezelter, Fri Sep 19 14:55:41 2003 UTC vs.
Revision 1157 by tim, Tue May 11 20:33:41 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;
# Line 37 | Line 42 | SimInfo::SimInfo(){
42    thermalTime = 0.0;
43    currentTime = 0.0;
44    rCut = 0.0;
45 <  origRcut = -1.0;
41 <  ecr = 0.0;
42 <  origEcr = -1.0;
43 <  est = 0.0;
44 <  oldEcr = 0.0;
45 <  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 +  haveCutoffGroups = false;
67  
68 +  excludes = Exclude::Instance();
69 +
70    myConfiguration = new SimState();
71  
72 +  has_minimizer = false;
73 +  the_minimizer =NULL;
74 +
75 +  ngroup = 0;
76 +
77    wrapMeSimInfo( this );
78   }
79  
# Line 72 | Line 86 | SimInfo::~SimInfo(){
86    
87    for(i = properties.begin(); i != properties.end(); i++)
88      delete (*i).second;
89 <    
89 >  
90   }
91  
92   void SimInfo::setBox(double newBox[3]) {
# Line 93 | Line 107 | void SimInfo::setBoxM( double theBox[3][3] ){
107  
108   void SimInfo::setBoxM( double theBox[3][3] ){
109    
110 <  int i, j, status;
97 <  double smallestBoxL, maxCutoff;
110 >  int i, j;
111    double FortranHmat[9]; // to preserve compatibility with Fortran the
112                           // ordering in the array is as follows:
113                           // [ 0 3 6 ]
# Line 102 | Line 115 | void SimInfo::setBoxM( double theBox[3][3] ){
115                           // [ 2 5 8 ]
116    double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
117  
105 –  
118    if( !boxIsInit ) boxIsInit = 1;
119  
120    for(i=0; i < 3; i++)
# Line 146 | Line 158 | void SimInfo::calcHmatInv( void ) {
158  
159   void SimInfo::calcHmatInv( void ) {
160    
161 +  int oldOrtho;
162    int i,j;
163    double smallDiag;
164    double tol;
# Line 153 | Line 166 | void SimInfo::calcHmatInv( void ) {
166  
167    invertMat3( Hmat, HmatInv );
168  
156 –  // Check the inverse to make sure it is sane:
157 –
158 –  matMul3( Hmat, HmatInv, sanity );
159 –    
169    // check to see if Hmat is orthorhombic
170    
171 <  smallDiag = Hmat[0][0];
163 <  if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1];
164 <  if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2];
165 <  tol = smallDiag * 1E-6;
171 >  oldOrtho = orthoRhombic;
172  
173 +  smallDiag = fabs(Hmat[0][0]);
174 +  if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
175 +  if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
176 +  tol = smallDiag * orthoTolerance;
177 +
178    orthoRhombic = 1;
179    
180    for (i = 0; i < 3; i++ ) {
181      for (j = 0 ; j < 3; j++) {
182        if (i != j) {
183          if (orthoRhombic) {
184 <          if (Hmat[i][j] >= tol) orthoRhombic = 0;
184 >          if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
185          }        
186        }
187      }
188    }
178 – }
189  
190 < double SimInfo::matDet3(double a[3][3]) {
191 <  int i, j, k;
192 <  double determinant;
193 <
194 <  determinant = 0.0;
195 <
196 <  for(i = 0; i < 3; i++) {
197 <    j = (i+1)%3;
198 <    k = (i+2)%3;
199 <
200 <    determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]);
191 <  }
192 <
193 <  return determinant;
194 < }
195 <
196 < void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
197 <  
198 <  int  i, j, k, l, m, n;
199 <  double determinant;
200 <
201 <  determinant = matDet3( a );
202 <
203 <  if (determinant == 0.0) {
204 <    sprintf( painCave.errMsg,
205 <             "Can't invert a matrix with a zero determinant!\n");
206 <    painCave.isFatal = 1;
207 <    simError();
208 <  }
209 <
210 <  for (i=0; i < 3; i++) {
211 <    j = (i+1)%3;
212 <    k = (i+2)%3;
213 <    for(l = 0; l < 3; l++) {
214 <      m = (l+1)%3;
215 <      n = (l+2)%3;
216 <      
217 <      b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant;
190 >  if( oldOrtho != orthoRhombic ){
191 >    
192 >    if( orthoRhombic ){
193 >      sprintf( painCave.errMsg,
194 >               "OOPSE is switching from the default Non-Orthorhombic\n"
195 >               "\tto the faster Orthorhombic periodic boundary computations.\n"
196 >               "\tThis is usually a good thing, but if you wan't the\n"
197 >               "\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
198 >               "\tvariable ( currently set to %G ) smaller.\n",
199 >               orthoTolerance);
200 >      simError();
201      }
202 <  }
203 < }
204 <
205 < void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
206 <  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
207 <
208 <  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
209 <  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
210 <  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
211 <  
229 <  r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0];
230 <  r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1];
231 <  r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2];
232 <  
233 <  r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0];
234 <  r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1];
235 <  r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2];
236 <  
237 <  c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
238 <  c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
239 <  c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
240 < }
241 <
242 < void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
243 <  double a0, a1, a2;
244 <
245 <  a0 = inVec[0];  a1 = inVec[1];  a2 = inVec[2];
246 <
247 <  outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2;
248 <  outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
249 <  outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
250 < }
251 <
252 < void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
253 <  double temp[3][3];
254 <  int i, j;
255 <
256 <  for (i = 0; i < 3; i++) {
257 <    for (j = 0; j < 3; j++) {
258 <      temp[j][i] = in[i][j];
202 >    else {
203 >      sprintf( painCave.errMsg,
204 >               "OOPSE is switching from the faster Orthorhombic to the more\n"
205 >               "\tflexible Non-Orthorhombic periodic boundary computations.\n"
206 >               "\tThis is usually because the box has deformed under\n"
207 >               "\tNPTf integration. If you wan't to live on the edge with\n"
208 >               "\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
209 >               "\tvariable ( currently set to %G ) larger.\n",
210 >               orthoTolerance);
211 >      simError();
212      }
213    }
261 –  for (i = 0; i < 3; i++) {
262 –    for (j = 0; j < 3; j++) {
263 –      out[i][j] = temp[i][j];
264 –    }
265 –  }
214   }
267 –  
268 – void SimInfo::printMat3(double A[3][3] ){
215  
270 –  std::cerr
271 –            << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
272 –            << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
273 –            << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
274 – }
275 –
276 – void SimInfo::printMat9(double A[9] ){
277 –
278 –  std::cerr
279 –            << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
280 –            << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
281 –            << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
282 – }
283 –
216   void SimInfo::calcBoxL( void ){
217  
218    double dx, dy, dz, dsq;
287 –  int i;
219  
220    // boxVol = Determinant of Hmat
221  
# Line 295 | Line 226 | void SimInfo::calcBoxL( void ){
226    dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
227    dsq = dx*dx + dy*dy + dz*dz;
228    boxL[0] = sqrt( dsq );
229 <  maxCutoff = 0.5 * boxL[0];
229 >  //maxCutoff = 0.5 * boxL[0];
230  
231    // boxLy
232    
233    dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
234    dsq = dx*dx + dy*dy + dz*dz;
235    boxL[1] = sqrt( dsq );
236 <  if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
236 >  //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
237  
238 +
239    // boxLz
240    
241    dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
242    dsq = dx*dx + dy*dy + dz*dz;
243    boxL[2] = sqrt( dsq );
244 <  if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
244 >  //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
245 >
246 >  //calculate the max cutoff
247 >  maxCutoff =  calcMaxCutOff();
248    
249    checkCutOffs();
250  
251   }
252  
253  
254 + double SimInfo::calcMaxCutOff(){
255 +
256 +  double ri[3], rj[3], rk[3];
257 +  double rij[3], rjk[3], rki[3];
258 +  double minDist;
259 +
260 +  ri[0] = Hmat[0][0];
261 +  ri[1] = Hmat[1][0];
262 +  ri[2] = Hmat[2][0];
263 +
264 +  rj[0] = Hmat[0][1];
265 +  rj[1] = Hmat[1][1];
266 +  rj[2] = Hmat[2][1];
267 +
268 +  rk[0] = Hmat[0][2];
269 +  rk[1] = Hmat[1][2];
270 +  rk[2] = Hmat[2][2];
271 +    
272 +  crossProduct3(ri, rj, rij);
273 +  distXY = dotProduct3(rk,rij) / norm3(rij);
274 +
275 +  crossProduct3(rj,rk, rjk);
276 +  distYZ = dotProduct3(ri,rjk) / norm3(rjk);
277 +
278 +  crossProduct3(rk,ri, rki);
279 +  distZX = dotProduct3(rj,rki) / norm3(rki);
280 +
281 +  minDist = min(min(distXY, distYZ), distZX);
282 +  return minDist/2;
283 +  
284 + }
285 +
286   void SimInfo::wrapVector( double thePos[3] ){
287  
288 <  int i, j, k;
288 >  int i;
289    double scaled[3];
290  
291    if( !orthoRhombic ){
# Line 356 | Line 323 | int SimInfo::getNDF(){
323  
324  
325   int SimInfo::getNDF(){
326 <  int ndf_local, ndf;
326 >  int ndf_local;
327 >
328 >  ndf_local = 0;
329    
330 <  ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
330 >  for(int i = 0; i < integrableObjects.size(); i++){
331 >    ndf_local += 3;
332 >    if (integrableObjects[i]->isDirectional()) {
333 >      if (integrableObjects[i]->isLinear())
334 >        ndf_local += 2;
335 >      else
336 >        ndf_local += 3;
337 >    }
338 >  }
339  
340 +  // n_constraints is local, so subtract them on each processor:
341 +
342 +  ndf_local -= n_constraints;
343 +
344   #ifdef IS_MPI
345    MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
346   #else
347    ndf = ndf_local;
348   #endif
349  
350 +  // nZconstraints is global, as are the 3 COM translations for the
351 +  // entire system:
352 +
353    ndf = ndf - 3 - nZconstraints;
354  
355    return ndf;
356   }
357  
358   int SimInfo::getNDFraw() {
359 <  int ndfRaw_local, ndfRaw;
359 >  int ndfRaw_local;
360  
361    // Raw degrees of freedom that we have to set
362 <  ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
363 <  
362 >  ndfRaw_local = 0;
363 >
364 >  for(int i = 0; i < integrableObjects.size(); i++){
365 >    ndfRaw_local += 3;
366 >    if (integrableObjects[i]->isDirectional()) {
367 >       if (integrableObjects[i]->isLinear())
368 >        ndfRaw_local += 2;
369 >      else
370 >        ndfRaw_local += 3;
371 >    }
372 >  }
373 >    
374   #ifdef IS_MPI
375    MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
376   #else
# Line 387 | Line 381 | int SimInfo::getNDFtranslational() {
381   }
382  
383   int SimInfo::getNDFtranslational() {
384 <  int ndfTrans_local, ndfTrans;
384 >  int ndfTrans_local;
385  
386 <  ndfTrans_local = 3 * n_atoms - n_constraints;
386 >  ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
387  
388 +
389   #ifdef IS_MPI
390    MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
391   #else
# Line 402 | Line 397 | void SimInfo::refreshSim(){
397    return ndfTrans;
398   }
399  
400 + int SimInfo::getTotIntegrableObjects() {
401 +  int nObjs_local;
402 +  int nObjs;
403 +
404 +  nObjs_local =  integrableObjects.size();
405 +
406 +
407 + #ifdef IS_MPI
408 +  MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
409 + #else
410 +  nObjs = nObjs_local;
411 + #endif
412 +
413 +
414 +  return nObjs;
415 + }
416 +
417   void SimInfo::refreshSim(){
418  
419    simtype fInfo;
# Line 411 | Line 423 | void SimInfo::refreshSim(){
423  
424    fInfo.dielect = 0.0;
425  
426 <  if( useDipole ){
426 >  if( useDipoles ){
427      if( useReactionField )fInfo.dielect = dielectric;
428    }
429  
# Line 420 | Line 432 | void SimInfo::refreshSim(){
432    fInfo.SIM_uses_LJ = useLJ;
433    fInfo.SIM_uses_sticky = useSticky;
434    //fInfo.SIM_uses_sticky = 0;
435 <  fInfo.SIM_uses_dipoles = useDipole;
435 >  fInfo.SIM_uses_charges = useCharges;
436 >  fInfo.SIM_uses_dipoles = useDipoles;
437    //fInfo.SIM_uses_dipoles = 0;
438 <  //fInfo.SIM_uses_RF = useReactionField;
439 <  fInfo.SIM_uses_RF = 0;
438 >  fInfo.SIM_uses_RF = useReactionField;
439 >  //fInfo.SIM_uses_RF = 0;
440    fInfo.SIM_uses_GB = useGB;
441    fInfo.SIM_uses_EAM = useEAM;
442  
443 <  excl = Exclude::getArray();
444 <
443 >  n_exclude = excludes->getSize();
444 >  excl = excludes->getFortranArray();
445 >  
446   #ifdef IS_MPI
447    n_global = mpiSim->getTotAtoms();
448   #else
449    n_global = n_atoms;
450   #endif
451 <
451 >  
452    isError = 0;
453 <
453 >  
454 >  getFortranGroupArray(this, mfact, ngroup, groupList, groupStart);
455 >  //it may not be a good idea to pass the address of first element in vector
456 >  //since c++ standard does not require vector to be stored continously in meomory
457 >  //Most of the compilers will organize the memory of vector continously
458    setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
459 <                  &nGlobalExcludes, globalExcludes, molMembershipArray,
460 <                  &isError );
461 <
459 >                  &nGlobalExcludes, globalExcludes, molMembershipArray,
460 >                  &mfact[0], &ngroup, &groupList[0], &groupStart[0], &isError);
461 >  
462    if( isError ){
463 <
463 >    
464      sprintf( painCave.errMsg,
465 <             "There was an error setting the simulation information in fortran.\n" );
465 >             "There was an error setting the simulation information in fortran.\n" );
466      painCave.isFatal = 1;
467      simError();
468    }
469 <
469 >  
470   #ifdef IS_MPI
471    sprintf( checkPointMsg,
472             "succesfully sent the simulation information to fortran.\n");
473    MPIcheckPoint();
474   #endif // is_mpi
475 <
475 >  
476    this->ndf = this->getNDF();
477    this->ndfRaw = this->getNDFraw();
478    this->ndfTrans = this->getNDFtranslational();
479   }
480  
481 <
482 < void SimInfo::setRcut( double theRcut ){
483 <
466 <  if( !haveOrigRcut ){
467 <    haveOrigRcut = 1;
468 <    origRcut = theRcut;
469 <  }
470 <
481 > void SimInfo::setDefaultRcut( double theRcut ){
482 >  
483 >  haveRcut = 1;
484    rCut = theRcut;
485 <  checkCutOffs();
485 >  rList = rCut + 1.0;
486 >  
487 >  notifyFortranCutOffs( &rCut, &rSw, &rList );
488   }
489  
490 < void SimInfo::setEcr( double theEcr ){
490 > void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
491  
492 <  if( !haveOrigEcr ){
493 <    haveOrigEcr = 1;
479 <    origEcr = theEcr;
480 <  }
481 <
482 <  ecr = theEcr;
483 <  checkCutOffs();
492 >  rSw = theRsw;
493 >  setDefaultRcut( theRcut );
494   }
495  
486 – void SimInfo::setEcr( double theEcr, double theEst ){
496  
488 –  est = theEst;
489 –  setEcr( theEcr );
490 – }
491 –
492 –
497   void SimInfo::checkCutOffs( void ){
494 –
495 –  int cutChanged = 0;
498    
499    if( boxIsInit ){
500      
501      //we need to check cutOffs against the box
502      
503 <    if(( maxCutoff > rCut )&&(usePBC)){
502 <      if( rCut < origRcut ){
503 <        rCut = origRcut;
504 <        if (rCut > maxCutoff) rCut = maxCutoff;
505 <        
506 <        sprintf( painCave.errMsg,
507 <                 "New Box size is setting the long range cutoff radius "
508 <                 "to %lf at time %lf\n",
509 <                 rCut, currentTime );
510 <        painCave.isFatal = 0;
511 <        simError();
512 <      }
513 <    }
514 <    
515 <    if( maxCutoff > ecr ){
516 <      if( ecr < origEcr ){
517 <        ecr = origEcr;
518 <        if (ecr > maxCutoff) ecr = maxCutoff;
519 <        
520 <        sprintf( painCave.errMsg,
521 <                 "New Box size is setting the electrostaticCutoffRadius "
522 <                 "to %lf at time %lf\n",
523 <                 ecr, currentTime );
524 <        painCave.isFatal = 0;
525 <        simError();
526 <      }
527 <    }
528 <    
529 <    
530 <    if ((rCut > maxCutoff)&&(usePBC)) {
503 >    if( rCut > maxCutoff ){
504        sprintf( painCave.errMsg,
505 <               "New Box size is setting the long range cutoff radius "
506 <               "to %lf at time %lf\n",
507 <               maxCutoff, currentTime );
508 <      painCave.isFatal = 0;
505 >               "cutoffRadius is too large for the current periodic box.\n"
506 >               "\tCurrent Value of cutoffRadius = %G at time %G\n "
507 >               "\tThis is larger than half of at least one of the\n"
508 >               "\tperiodic box vectors.  Right now, the Box matrix is:\n"
509 >               "\n"
510 >               "\t[ %G %G %G ]\n"
511 >               "\t[ %G %G %G ]\n"
512 >               "\t[ %G %G %G ]\n",
513 >               rCut, currentTime,
514 >               Hmat[0][0], Hmat[0][1], Hmat[0][2],
515 >               Hmat[1][0], Hmat[1][1], Hmat[1][2],
516 >               Hmat[2][0], Hmat[2][1], Hmat[2][2]);
517 >      painCave.isFatal = 1;
518        simError();
519 <      rCut = maxCutoff;
538 <    }
539 <    
540 <    if( ecr > maxCutoff){
541 <      sprintf( painCave.errMsg,
542 <               "New Box size is setting the electrostaticCutoffRadius "
543 <               "to %lf at time %lf\n",
544 <               maxCutoff, currentTime  );
545 <      painCave.isFatal = 0;
546 <      simError();      
547 <      ecr = maxCutoff;
548 <    }
549 <
550 <    if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
551 <    
552 <    // rlist is the 1.0 plus max( rcut, ecr )
553 <    
554 <    ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
555 <    
556 <    if( cutChanged ){
557 <      
558 <      notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
559 <    }
560 <    
561 <    oldEcr = ecr;
562 <    oldRcut = rCut;
563 <    
519 >    }    
520    } else {
521      // initialize this stuff before using it, OK?
522      sprintf( painCave.errMsg,
523 <             "Trying to check cutoffs without a box. Be smarter.\n" );
523 >             "Trying to check cutoffs without a box.\n"
524 >             "\tOOPSE should have better programmers than that.\n" );
525      painCave.isFatal = 1;
526      simError();      
527    }
# Line 607 | Line 564 | vector<GenericData*> SimInfo::getProperties(){
564      return NULL;  
565   }
566  
610 – vector<GenericData*> SimInfo::getProperties(){
567  
568 <  vector<GenericData*> result;
569 <  map<string, GenericData*>::iterator i;
568 > void getFortranGroupArray(SimInfo* info, vector<double>& mfact, int& ngroup,
569 >                          vector<int>& groupList, vector<int>& groupStart){
570 >  Molecule* myMols;
571 >  Atom** myAtoms;
572 >  int numAtom;
573 >  int curIndex;
574 >  double mtot;
575 >  int numMol;
576 >  int numCutoffGroups;
577 >  CutoffGroup* myCutoffGroup;
578 >  vector<CutoffGroup*>::iterator iterCutoff;
579 >  Atom* cutoffAtom;
580 >  vector<Atom*>::iterator iterAtom;
581 >  int atomIndex;
582    
583 <  for(i = properties.begin(); i != properties.end(); i++)
584 <    result.push_back((*i).second);
583 >  mfact.clear();
584 >  groupList.clear();
585 >  groupStart.clear();
586 >  
587 >  //Be careful, fortran array begin at 1
588 >  curIndex = 1;
589 >
590 >  myMols = info->molecules;
591 >  numMol = info->n_mol;
592 >  for(int i  = 0; i < numMol; i++){
593 >    numAtom = myMols[i].getNAtoms();
594 >    myAtoms = myMols[i].getMyAtoms();
595 >
596      
597 <  return result;
619 < }
597 >    for(int j = 0; j < numAtom; j++){
598  
599 < double SimInfo::matTrace3(double m[3][3]){
600 <  double trace;
601 <  trace = m[0][0] + m[1][1] + m[2][2];
599 >    
600 > #ifdef IS_MPI      
601 >      atomIndex = myAtoms[j]->getGlobalIndex();
602 > #else
603 >      atomIndex = myAtoms[j]->getIndex();
604 > #endif
605  
606 <  return trace;
606 >      if(myMols[i].belongToCutoffGroup(atomIndex))
607 >        continue;
608 >      else{
609 >        mfact.push_back(myAtoms[j]->getMass());
610 >        groupList.push_back(myAtoms[j]->getIndex() + 1);
611 >        groupStart.push_back(curIndex++);  
612 >      }
613 >    }
614 >      
615 >    numCutoffGroups = myMols[i].getNCutoffGroups();
616 >    for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff); myCutoffGroup != NULL;
617 >                                                  myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
618 >      
619 >      for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom); cutoffAtom != NULL;
620 >                                           cutoffAtom = myCutoffGroup->beginAtom(iterAtom)){
621 >        groupList.push_back(cutoffAtom->getIndex() + 1);
622 >      }  
623 >                              
624 >      groupStart.push_back(curIndex);
625 >      curIndex += myCutoffGroup->getNumAtom();
626 >    }
627 >    
628 >  }
629 >
630 >  ngroup = groupStart.size();
631   }

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