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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 1144 by tim, Sat May 1 18:52:38 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;
39 –  origRcut = -1.0;
45    ecr = 0.0;
41 –  origEcr = -1.0;
46    est = 0.0;
43 –  oldEcr = 0.0;
44 –  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 +  useMolecularCutoffs = 0;
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 71 | 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 92 | Line 107 | void SimInfo::setBoxM( double theBox[3][3] ){
107  
108   void SimInfo::setBoxM( double theBox[3][3] ){
109    
110 <  int i, j, status;
96 <  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 101 | Line 115 | void SimInfo::setBoxM( double theBox[3][3] ){
115                           // [ 2 5 8 ]
116    double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
117  
104 –  
118    if( !boxIsInit ) boxIsInit = 1;
119  
120    for(i=0; i < 3; i++)
# Line 145 | 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 152 | Line 166 | void SimInfo::calcHmatInv( void ) {
166  
167    invertMat3( Hmat, HmatInv );
168  
155 –  // Check the inverse to make sure it is sane:
156 –
157 –  matMul3( Hmat, HmatInv, sanity );
158 –    
169    // check to see if Hmat is orthorhombic
170    
171 <  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;
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    }
177 – }
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]);
190 <  }
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;
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 <  
228 <  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];
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    }
260 –  for (i = 0; i < 3; i++) {
261 –    for (j = 0; j < 3; j++) {
262 –      out[i][j] = temp[i][j];
263 –    }
264 –  }
214   }
266 –  
267 – void SimInfo::printMat3(double A[3][3] ){
215  
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 –
216   void SimInfo::calcBoxL( void ){
217  
218    double dx, dy, dz, dsq;
286 –  int i;
219  
220    // boxVol = Determinant of Hmat
221  
# Line 294 | 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 355 | 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 384 | Line 379 | int SimInfo::getNDFraw() {
379  
380    return ndfRaw;
381   }
382 <
382 >
383 > int SimInfo::getNDFtranslational() {
384 >  int ndfTrans_local;
385 >
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
392 >  ndfTrans = ndfTrans_local;
393 > #endif
394 >
395 >  ndfTrans = ndfTrans - 3 - nZconstraints;
396 >
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 394 | 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 403 | 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
# Line 420 | Line 451 | void SimInfo::refreshSim(){
451  
452    isError = 0;
453  
454 + getFortranGroupArray(this, mfact, ngroup, groupList, groupStart);
455 +
456    setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
457 <                  &nGlobalExcludes, globalExcludes, molMembershipArray,
458 <                  &isError );
457 >                                    &nGlobalExcludes, globalExcludes, molMembershipArray,
458 >                                    &mfact[0], &ngroup, &groupList[0], &groupStart[0], &isError );
459  
460    if( isError ){
461  
# Line 440 | Line 473 | void SimInfo::refreshSim(){
473  
474    this->ndf = this->getNDF();
475    this->ndfRaw = this->getNDFraw();
476 <
476 >  this->ndfTrans = this->getNDFtranslational();
477   }
478  
479 + void SimInfo::setDefaultRcut( double theRcut ){
480  
481 < void SimInfo::setRcut( double theRcut ){
481 >  haveRcut = 1;
482 >  rCut = theRcut;
483  
484 <  if( !haveOrigRcut ){
450 <    haveOrigRcut = 1;
451 <    origRcut = theRcut;
452 <  }
484 >  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
485  
486 <  rCut = theRcut;
455 <  checkCutOffs();
486 >  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
487   }
488  
489 < void SimInfo::setEcr( double theEcr ){
489 > void SimInfo::setDefaultEcr( double theEcr ){
490  
491 <  if( !haveOrigEcr ){
461 <    haveOrigEcr = 1;
462 <    origEcr = theEcr;
463 <  }
464 <
491 >  haveEcr = 1;
492    ecr = theEcr;
493 <  checkCutOffs();
493 >  
494 >  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
495 >
496 >  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
497   }
498  
499 < void SimInfo::setEcr( double theEcr, double theEst ){
499 > void SimInfo::setDefaultEcr( double theEcr, double theEst ){
500  
501    est = theEst;
502 <  setEcr( theEcr );
502 >  setDefaultEcr( theEcr );
503   }
504  
505  
506   void SimInfo::checkCutOffs( void ){
507 <
478 <  int cutChanged = 0;
479 <
480 <
481 <
507 >  
508    if( boxIsInit ){
509      
510      //we need to check cutOffs against the box
511 <  
512 <    if(( maxCutoff > rCut )&&(usePBC)){
513 <      if( rCut < origRcut ){
514 <        rCut = origRcut;
515 <        if (rCut > maxCutoff) rCut = maxCutoff;
516 <        
517 <        sprintf( painCave.errMsg,
518 <                 "New Box size is setting the long range cutoff radius "
519 <                 "to %lf\n",
520 <                 rCut );
521 <        painCave.isFatal = 0;
522 <        simError();
523 <      }
511 >    
512 >    if( rCut > maxCutoff ){
513 >      sprintf( painCave.errMsg,
514 >               "LJrcut is too large for the current periodic box.\n"
515 >               "\tCurrent Value of LJrcut = %G at time %G\n "
516 >               "\tThis is larger than half of at least one of the\n"
517 >               "\tperiodic box vectors.  Right now, the Box matrix is:\n"
518 >               "\n"
519 >               "\t[ %G %G %G ]\n"
520 >               "\t[ %G %G %G ]\n"
521 >               "\t[ %G %G %G ]\n",
522 >               rCut, currentTime,
523 >               Hmat[0][0], Hmat[0][1], Hmat[0][2],
524 >               Hmat[1][0], Hmat[1][1], Hmat[1][2],
525 >               Hmat[2][0], Hmat[2][1], Hmat[2][2]);
526 >      painCave.isFatal = 1;
527 >      simError();
528      }
529 <
530 <    if( maxCutoff > ecr ){
531 <      if( ecr < origEcr ){
502 <        rCut = origEcr;
503 <        if (ecr > maxCutoff) ecr = maxCutoff;
504 <        
529 >    
530 >    if( haveEcr ){
531 >      if( ecr > maxCutoff ){
532          sprintf( painCave.errMsg,
533 <                 "New Box size is setting the electrostaticCutoffRadius "
534 <                 "to %lf\n",
535 <                 ecr );
536 <        painCave.isFatal = 0;
533 >                 "electrostaticCutoffRadius is too large for the current\n"
534 >                 "\tperiodic box.\n\n"
535 >                 "\tCurrent Value of ECR = %G at time %G\n "
536 >                 "\tThis is larger than half of at least one of the\n"
537 >                 "\tperiodic box vectors.  Right now, the Box matrix is:\n"
538 >                 "\n"
539 >                 "\t[ %G %G %G ]\n"
540 >                 "\t[ %G %G %G ]\n"
541 >                 "\t[ %G %G %G ]\n",
542 >                 ecr, currentTime,
543 >                 Hmat[0][0], Hmat[0][1], Hmat[0][2],
544 >                 Hmat[1][0], Hmat[1][1], Hmat[1][2],
545 >                 Hmat[2][0], Hmat[2][1], Hmat[2][2]);
546 >        painCave.isFatal = 1;
547          simError();
548        }
549      }
550 <
551 <
552 <    if ((rCut > maxCutoff)&&(usePBC)) {
553 <      sprintf( painCave.errMsg,
554 <               "New Box size is setting the long range cutoff radius "
555 <               "to %lf\n",
556 <               maxCutoff );
520 <      painCave.isFatal = 0;
521 <      simError();
522 <      rCut = maxCutoff;
523 <    }
524 <
525 <    if( ecr > maxCutoff){
526 <      sprintf( painCave.errMsg,
527 <               "New Box size is setting the electrostaticCutoffRadius "
528 <               "to %lf\n",
529 <               maxCutoff  );
530 <      painCave.isFatal = 0;
531 <      simError();      
532 <      ecr = maxCutoff;
533 <    }
534 <
535 <    
550 >  } else {
551 >    // initialize this stuff before using it, OK?
552 >    sprintf( painCave.errMsg,
553 >             "Trying to check cutoffs without a box.\n"
554 >             "\tOOPSE should have better programmers than that.\n" );
555 >    painCave.isFatal = 1;
556 >    simError();      
557    }
537 –  
538 –
539 –  if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
540 –
541 –  // rlist is the 1.0 plus max( rcut, ecr )
558    
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;
559   }
560  
561   void SimInfo::addProperty(GenericData* prop){
# Line 587 | Line 594 | GenericData* SimInfo::getProperty(const string& propNa
594      return NULL;  
595   }
596  
590 – vector<GenericData*> SimInfo::getProperties(){
597  
598 <  vector<GenericData*> result;
599 <  map<string, GenericData*>::iterator i;
600 <  
601 <  for(i = properties.begin(); i != properties.end(); i++)
602 <    result.push_back((*i).second);
598 > void getFortranGroupArray(SimInfo* info, vector<double>& mfact, int& ngroup,
599 >                                                          vector<int>& groupList, vector<int>& groupStart){
600 >  Molecule* mol;
601 >  int numAtom;
602 >  int curIndex;
603 >
604 >  mfact.clear();
605 >  groupList.clear();
606 >  groupStart.clear();
607 >
608 >  //Be careful, fortran array begin at 1
609 >  curIndex = 1;
610      
611 <  return result;
612 < }
611 >  if(info->useMolecularCutoffs){
612 >    //if using molecular cutoff
613 >    ngroup = info->n_mol;
614  
615 +    for(int i = 0; i < ngroup; i ++){
616 +      mol = &(info->molecules[i]);
617 +      numAtom = mol->getNAtoms();
618 +      
619 +      for(int j=0; j < numAtom; j++){
620 + #ifdef IS_MPI
621 +        groupList.push_back((info->atoms[i])->getGlobalIndex() + 1);
622 + #else
623 +        groupList.push_back((info->atoms[i])->getIndex() + 1);
624 + #endif
625 +      }//for(int j=0; j < numAtom; j++)
626 +            
627 +      groupStart.push_back(curIndex);
628 +      curIndex += numAtom;
629 +      
630 +    }//end for(int i =0 ; i < ngroup; i++)    
631 +  }
632 +  else{
633 +    //using atomic cutoff, every single atom is just a group
634 +    ngroup = info->n_atoms;
635 +    for(int i =0 ; i < ngroup; i++){
636 +      groupStart.push_back(curIndex++);
637  
638 + #ifdef IS_MPI
639 +      groupList.push_back((info->atoms[i])->getGlobalIndex() + 1);
640 + #else
641 +      groupList.push_back((info->atoms[i])->getIndex() + 1);
642 + #endif
643 +
644 +    }//end for(int i =0 ; i < ngroup; i++)
645 +
646 +  }//end if (info->useMolecularCutoffs)
647 +
648 + }

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