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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 965 by gezelter, Mon Jan 19 21:17:39 2004 UTC vs.
Revision 1144 by tim, Sat May 1 18:52:38 2004 UTC

# 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 27 | Line 29 | SimInfo::SimInfo(){
29   SimInfo* currentInfo;
30  
31   SimInfo::SimInfo(){
32 <  excludes = NULL;
32 >
33    n_constraints = 0;
34    nZconstraints = 0;
35    n_oriented = 0;
# Line 49 | Line 51 | SimInfo::SimInfo(){
51    
52    resetTime = 1e99;
53  
54 +  orthoRhombic = 0;
55    orthoTolerance = 1E-6;
56    useInitXSstate = true;
57  
# Line 60 | Line 63 | SimInfo::SimInfo(){
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 75 | 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 180 | Line 191 | void SimInfo::calcHmatInv( void ) {
191      
192      if( orthoRhombic ){
193        sprintf( painCave.errMsg,
194 <               "Hmat is switching from Non-Orthorhombic to Orthorhombic Box.\n"
195 <               "\tIf this is a bad thing, change the orthoBoxTolerance\n"
196 <               "\tvariable ( currently set to %G ).\n",
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      else {
203        sprintf( painCave.errMsg,
204 <               "Hmat is switching from Orthorhombic to Non-Orthorhombic Box.\n"
205 <               "\tIf this is a bad thing, change the orthoBoxTolerance\n"
206 <               "\tvariable ( currently set to %G ).\n",
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    }
214   }
215  
200 – double SimInfo::matDet3(double a[3][3]) {
201 –  int i, j, k;
202 –  double determinant;
203 –
204 –  determinant = 0.0;
205 –
206 –  for(i = 0; i < 3; i++) {
207 –    j = (i+1)%3;
208 –    k = (i+2)%3;
209 –
210 –    determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]);
211 –  }
212 –
213 –  return determinant;
214 – }
215 –
216 – void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
217 –  
218 –  int  i, j, k, l, m, n;
219 –  double determinant;
220 –
221 –  determinant = matDet3( a );
222 –
223 –  if (determinant == 0.0) {
224 –    sprintf( painCave.errMsg,
225 –             "Can't invert a matrix with a zero determinant!\n");
226 –    painCave.isFatal = 1;
227 –    simError();
228 –  }
229 –
230 –  for (i=0; i < 3; i++) {
231 –    j = (i+1)%3;
232 –    k = (i+2)%3;
233 –    for(l = 0; l < 3; l++) {
234 –      m = (l+1)%3;
235 –      n = (l+2)%3;
236 –      
237 –      b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant;
238 –    }
239 –  }
240 – }
241 –
242 – void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
243 –  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
244 –
245 –  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
246 –  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
247 –  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
248 –  
249 –  r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0];
250 –  r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1];
251 –  r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2];
252 –  
253 –  r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0];
254 –  r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1];
255 –  r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2];
256 –  
257 –  c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
258 –  c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
259 –  c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
260 – }
261 –
262 – void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
263 –  double a0, a1, a2;
264 –
265 –  a0 = inVec[0];  a1 = inVec[1];  a2 = inVec[2];
266 –
267 –  outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2;
268 –  outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
269 –  outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
270 – }
271 –
272 – void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
273 –  double temp[3][3];
274 –  int i, j;
275 –
276 –  for (i = 0; i < 3; i++) {
277 –    for (j = 0; j < 3; j++) {
278 –      temp[j][i] = in[i][j];
279 –    }
280 –  }
281 –  for (i = 0; i < 3; i++) {
282 –    for (j = 0; j < 3; j++) {
283 –      out[i][j] = temp[i][j];
284 –    }
285 –  }
286 – }
287 –  
288 – void SimInfo::printMat3(double A[3][3] ){
289 –
290 –  std::cerr
291 –            << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
292 –            << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
293 –            << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
294 – }
295 –
296 – void SimInfo::printMat9(double A[9] ){
297 –
298 –  std::cerr
299 –            << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
300 –            << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
301 –            << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
302 – }
303 –
304 –
305 – void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){
306 –
307 –      out[0] = a[1] * b[2] - a[2] * b[1];
308 –      out[1] = a[2] * b[0] - a[0] * b[2] ;
309 –      out[2] = a[0] * b[1] - a[1] * b[0];
310 –      
311 – }
312 –
313 – double SimInfo::dotProduct3(double a[3], double b[3]){
314 –  return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2];
315 – }
316 –
317 – double SimInfo::length3(double a[3]){
318 –  return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]);
319 – }
320 –
216   void SimInfo::calcBoxL( void ){
217  
218    double dx, dy, dz, dsq;
# Line 373 | Line 268 | double SimInfo::calcMaxCutOff(){
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) / length3(rij);
271 >    
272 >  crossProduct3(ri, rj, rij);
273 >  distXY = dotProduct3(rk,rij) / norm3(rij);
274  
275    crossProduct3(rj,rk, rjk);
276 <  distYZ = dotProduct3(ri,rjk) / length3(rjk);
276 >  distYZ = dotProduct3(ri,rjk) / norm3(rjk);
277  
278    crossProduct3(rk,ri, rki);
279 <  distZX = dotProduct3(rj,rki) / length3(rki);
279 >  distZX = dotProduct3(rj,rki) / norm3(rki);
280  
281    minDist = min(min(distXY, distYZ), distZX);
282    return minDist/2;
# Line 429 | Line 324 | int SimInfo::getNDF(){
324  
325   int SimInfo::getNDF(){
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;
# Line 447 | Line 359 | int SimInfo::getNDFraw() {
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 461 | Line 383 | int SimInfo::getNDFtranslational() {
383   int SimInfo::getNDFtranslational() {
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 474 | 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 495 | Line 435 | void SimInfo::refreshSim(){
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 510 | 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 568 | Line 511 | void SimInfo::checkCutOffs( void ){
511      
512      if( rCut > maxCutoff ){
513        sprintf( painCave.errMsg,
514 <               "Box size is too small for the long range cutoff radius, "
515 <               "%G, at time %G\n"
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",
# Line 584 | Line 530 | void SimInfo::checkCutOffs( void ){
530      if( haveEcr ){
531        if( ecr > maxCutoff ){
532          sprintf( painCave.errMsg,
533 <                 "Box size is too small for the electrostatic cutoff radius, "
534 <                 "%G, at time %G\n"
535 <                 "\t[ %G %G %G ]\n"
536 <                 "\t[ %G %G %G ]\n"
537 <                 "\t[ %G %G %G ]\n",
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],
# Line 644 | Line 594 | vector<GenericData*> SimInfo::getProperties(){
594      return NULL;  
595   }
596  
647 – 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 < double SimInfo::matTrace3(double m[3][3]){
616 <  double trace;
617 <  trace = m[0][0] + m[1][1] + m[2][2];
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 <  return trace;
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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