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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 874 by mmeineke, Fri Nov 21 20:10:02 2003 UTC vs.
Revision 1163 by gezelter, Wed May 12 14:30:12 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 40 | Line 42 | SimInfo::SimInfo(){
42    thermalTime = 0.0;
43    currentTime = 0.0;
44    rCut = 0.0;
45 <  ecr = 0.0;
44 <  est = 0.0;
45 >  rSw = 0.0;
46  
47    haveRcut = 0;
48 <  haveEcr = 0;
48 >  haveRsw = 0;
49    boxIsInit = 0;
50    
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 74 | 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 179 | Line 191 | void SimInfo::calcHmatInv( void ) {
191      
192      if( orthoRhombic ){
193        sprintf( painCave.errMsg,
194 <               "Hmat is switching from Non-Orthorhombic to OrthoRhombic\n"
195 <               "       If this is a bad thing, change the orthoBoxTolerance( currently %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\n"
205 <               "       If this is a bad thing, change the orthoBoxTolerance( currently %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  
197 – double SimInfo::matDet3(double a[3][3]) {
198 –  int i, j, k;
199 –  double determinant;
200 –
201 –  determinant = 0.0;
202 –
203 –  for(i = 0; i < 3; i++) {
204 –    j = (i+1)%3;
205 –    k = (i+2)%3;
206 –
207 –    determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]);
208 –  }
209 –
210 –  return determinant;
211 – }
212 –
213 – void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
214 –  
215 –  int  i, j, k, l, m, n;
216 –  double determinant;
217 –
218 –  determinant = matDet3( a );
219 –
220 –  if (determinant == 0.0) {
221 –    sprintf( painCave.errMsg,
222 –             "Can't invert a matrix with a zero determinant!\n");
223 –    painCave.isFatal = 1;
224 –    simError();
225 –  }
226 –
227 –  for (i=0; i < 3; i++) {
228 –    j = (i+1)%3;
229 –    k = (i+2)%3;
230 –    for(l = 0; l < 3; l++) {
231 –      m = (l+1)%3;
232 –      n = (l+2)%3;
233 –      
234 –      b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant;
235 –    }
236 –  }
237 – }
238 –
239 – void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
240 –  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
241 –
242 –  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
243 –  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
244 –  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
245 –  
246 –  r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0];
247 –  r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1];
248 –  r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2];
249 –  
250 –  r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0];
251 –  r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1];
252 –  r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2];
253 –  
254 –  c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
255 –  c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
256 –  c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
257 – }
258 –
259 – void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
260 –  double a0, a1, a2;
261 –
262 –  a0 = inVec[0];  a1 = inVec[1];  a2 = inVec[2];
263 –
264 –  outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2;
265 –  outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
266 –  outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
267 – }
268 –
269 – void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
270 –  double temp[3][3];
271 –  int i, j;
272 –
273 –  for (i = 0; i < 3; i++) {
274 –    for (j = 0; j < 3; j++) {
275 –      temp[j][i] = in[i][j];
276 –    }
277 –  }
278 –  for (i = 0; i < 3; i++) {
279 –    for (j = 0; j < 3; j++) {
280 –      out[i][j] = temp[i][j];
281 –    }
282 –  }
283 – }
284 –  
285 – void SimInfo::printMat3(double A[3][3] ){
286 –
287 –  std::cerr
288 –            << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
289 –            << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
290 –            << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
291 – }
292 –
293 – void SimInfo::printMat9(double A[9] ){
294 –
295 –  std::cerr
296 –            << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
297 –            << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
298 –            << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
299 – }
300 –
301 –
302 – void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){
303 –
304 –      out[0] = a[1] * b[2] - a[2] * b[1];
305 –      out[1] = a[2] * b[0] - a[0] * b[2] ;
306 –      out[2] = a[0] * b[1] - a[1] * b[0];
307 –      
308 – }
309 –
310 – double SimInfo::dotProduct3(double a[3], double b[3]){
311 –  return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2];
312 – }
313 –
314 – double SimInfo::length3(double a[3]){
315 –  return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]);
316 – }
317 –
216   void SimInfo::calcBoxL( void ){
217  
218    double dx, dy, dz, dsq;
# Line 370 | 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 426 | 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 444 | 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 458 | 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 471 | Line 397 | int SimInfo::getNDFtranslational() {
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 480 | 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 489 | 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   void SimInfo::setDefaultRcut( double theRcut ){
482 <
482 >  
483    haveRcut = 1;
484    rCut = theRcut;
485 <
537 <  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
538 <
539 <  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
540 < }
541 <
542 < void SimInfo::setDefaultEcr( double theEcr ){
543 <
544 <  haveEcr = 1;
545 <  ecr = theEcr;
485 >  rList = rCut + 1.0;
486    
487 <  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
548 <
549 <  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
487 >  notifyFortranCutOffs( &rCut, &rSw, &rList );
488   }
489  
490 < void SimInfo::setDefaultEcr( double theEcr, double theEst ){
490 > void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
491  
492 <  est = theEst;
493 <  setDefaultEcr( theEcr );
492 >  rSw = theRsw;
493 >  setDefaultRcut( theRcut );
494   }
495  
496  
# Line 564 | Line 502 | void SimInfo::checkCutOffs( void ){
502      
503      if( rCut > maxCutoff ){
504        sprintf( painCave.errMsg,
505 <               "Box size is too small for the long range cutoff radius, "
506 <               "%G, at time %G\n"
507 <               "  [ %G %G %G ]\n"
508 <               "  [ %G %G %G ]\n"
509 <               "  [ %G %G %G ]\n",
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 <    }
579 <    
580 <    if( haveEcr ){
581 <      if( ecr > maxCutoff ){
582 <        sprintf( painCave.errMsg,
583 <                 "Box size is too small for the electrostatic cutoff radius, "
584 <                 "%G, at time %G\n"
585 <                 "  [ %G %G %G ]\n"
586 <                 "  [ %G %G %G ]\n"
587 <                 "  [ %G %G %G ]\n",
588 <                 ecr, currentTime,
589 <                 Hmat[0][0], Hmat[0][1], Hmat[0][2],
590 <                 Hmat[1][0], Hmat[1][1], Hmat[1][2],
591 <                 Hmat[2][0], Hmat[2][1], Hmat[2][2]);
592 <        painCave.isFatal = 1;
593 <        simError();
594 <      }
595 <    }
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 639 | Line 564 | GenericData* SimInfo::getProperty(const string& propNa
564      return NULL;  
565   }
566  
642 – 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 >  double totalMass;
583    
584 <  for(i = properties.begin(); i != properties.end(); i++)
585 <    result.push_back((*i).second);
584 >  mfact.clear();
585 >  groupList.clear();
586 >  groupStart.clear();
587 >  
588 >  //Be careful, fortran array begin at 1
589 >  curIndex = 1;
590 >
591 >  myMols = info->molecules;
592 >  numMol = info->n_mol;
593 >  for(int i  = 0; i < numMol; i++){
594 >    numAtom = myMols[i].getNAtoms();
595 >    myAtoms = myMols[i].getMyAtoms();
596 >
597      
598 <  return result;
651 < }
598 >    for(int j = 0; j < numAtom; j++){
599  
600 < double SimInfo::matTrace3(double m[3][3]){
601 <  double trace;
602 <  trace = m[0][0] + m[1][1] + m[2][2];
600 >    
601 > #ifdef IS_MPI      
602 >      atomIndex = myAtoms[j]->getGlobalIndex();
603 > #else
604 >      atomIndex = myAtoms[j]->getIndex();
605 > #endif
606  
607 <  return trace;
607 >      if(myMols[i].belongToCutoffGroup(atomIndex))
608 >        continue;
609 >      else{
610 >        // this is a fraction of the cutoff group's mass, not the mass itself!
611 >        mfact.push_back(1.0);
612 >        groupList.push_back(myAtoms[j]->getIndex() + 1);
613 >        groupStart.push_back(curIndex++);  
614 >      }
615 >    }
616 >      
617 >    numCutoffGroups = myMols[i].getNCutoffGroups();
618 >    for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff); myCutoffGroup != NULL;
619 >                                                  myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
620 >
621 >      totalMass = myCutoffGroup->getMass();
622 >      
623 >      for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom); cutoffAtom != NULL;
624 >                                           cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
625 >        mfact.push_back(cutoffAtom->getMass()/totalMass);
626 >        groupList.push_back(cutoffAtom->getIndex() + 1);
627 >      }  
628 >                              
629 >      groupStart.push_back(curIndex);
630 >      curIndex += myCutoffGroup->getNumAtom();
631 >
632 >    }//end for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff))
633 >
634 >  }//end for(int i  = 0; i < numMol; i++)
635 >  
636 >  ngroup = groupStart.size();
637   }

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