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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 853 by mmeineke, Thu Nov 6 19:11:38 2003 UTC vs.
Revision 1127 by tim, Tue Apr 20 16:56:40 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 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;
40 –  origRcut = -1.0;
45    ecr = 0.0;
42 –  origEcr = -1.0;
46    est = 0.0;
44 –  oldEcr = 0.0;
45 –  oldRcut = 0.0;
47  
48 <  haveOrigRcut = 0;
49 <  haveOrigEcr = 0;
48 >  haveRcut = 0;
49 >  haveEcr = 0;
50    boxIsInit = 0;
51    
52    resetTime = 1e99;
52 –  
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  
67 +  excludes = Exclude::Instance();
68 +
69    myConfiguration = new SimState();
70  
71 +  has_minimizer = false;
72 +  the_minimizer =NULL;
73 +
74    wrapMeSimInfo( this );
75   }
76  
# Line 102 | Line 112 | void SimInfo::setBoxM( double theBox[3][3] ){
112                           // [ 2 5 8 ]
113    double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
114  
105 –  
115    if( !boxIsInit ) boxIsInit = 1;
116  
117    for(i=0; i < 3; i++)
# Line 161 | Line 170 | void SimInfo::calcHmatInv( void ) {
170    smallDiag = fabs(Hmat[0][0]);
171    if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
172    if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
173 <  tol = smallDiag * 1E-6;
173 >  tol = smallDiag * orthoTolerance;
174  
175    orthoRhombic = 1;
176    
# Line 179 | Line 188 | void SimInfo::calcHmatInv( void ) {
188      
189      if( orthoRhombic ){
190        sprintf( painCave.errMsg,
191 <               "Hmat is switching from Non-Orthorhombic to OrthoRhombic\n"
192 <               "       If this is a bad thing change the ortho tolerance in SimInfo.\n" );
191 >               "OOPSE is switching from the default Non-Orthorhombic\n"
192 >               "\tto the faster Orthorhombic periodic boundary computations.\n"
193 >               "\tThis is usually a good thing, but if you wan't the\n"
194 >               "\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
195 >               "\tvariable ( currently set to %G ) smaller.\n",
196 >               orthoTolerance);
197        simError();
198      }
199      else {
200        sprintf( painCave.errMsg,
201 <               "Hmat is switching from Orthorhombic to Non-OrthoRhombic\n"
202 <               "       If this is a bad thing change the ortho tolerance in SimInfo.\n" );
201 >               "OOPSE is switching from the faster Orthorhombic to the more\n"
202 >               "\tflexible Non-Orthorhombic periodic boundary computations.\n"
203 >               "\tThis is usually because the box has deformed under\n"
204 >               "\tNPTf integration. If you wan't to live on the edge with\n"
205 >               "\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
206 >               "\tvariable ( currently set to %G ) larger.\n",
207 >               orthoTolerance);
208        simError();
191 –    }
192 –  }
193 – }
194 –
195 – double SimInfo::matDet3(double a[3][3]) {
196 –  int i, j, k;
197 –  double determinant;
198 –
199 –  determinant = 0.0;
200 –
201 –  for(i = 0; i < 3; i++) {
202 –    j = (i+1)%3;
203 –    k = (i+2)%3;
204 –
205 –    determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]);
206 –  }
207 –
208 –  return determinant;
209 – }
210 –
211 – void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
212 –  
213 –  int  i, j, k, l, m, n;
214 –  double determinant;
215 –
216 –  determinant = matDet3( a );
217 –
218 –  if (determinant == 0.0) {
219 –    sprintf( painCave.errMsg,
220 –             "Can't invert a matrix with a zero determinant!\n");
221 –    painCave.isFatal = 1;
222 –    simError();
223 –  }
224 –
225 –  for (i=0; i < 3; i++) {
226 –    j = (i+1)%3;
227 –    k = (i+2)%3;
228 –    for(l = 0; l < 3; l++) {
229 –      m = (l+1)%3;
230 –      n = (l+2)%3;
231 –      
232 –      b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant;
233 –    }
234 –  }
235 – }
236 –
237 – void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
238 –  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
239 –
240 –  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
241 –  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
242 –  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
243 –  
244 –  r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0];
245 –  r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1];
246 –  r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2];
247 –  
248 –  r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0];
249 –  r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1];
250 –  r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2];
251 –  
252 –  c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
253 –  c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
254 –  c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
255 – }
256 –
257 – void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
258 –  double a0, a1, a2;
259 –
260 –  a0 = inVec[0];  a1 = inVec[1];  a2 = inVec[2];
261 –
262 –  outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2;
263 –  outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
264 –  outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
265 – }
266 –
267 – void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
268 –  double temp[3][3];
269 –  int i, j;
270 –
271 –  for (i = 0; i < 3; i++) {
272 –    for (j = 0; j < 3; j++) {
273 –      temp[j][i] = in[i][j];
209      }
210    }
276 –  for (i = 0; i < 3; i++) {
277 –    for (j = 0; j < 3; j++) {
278 –      out[i][j] = temp[i][j];
279 –    }
280 –  }
211   }
282 –  
283 – void SimInfo::printMat3(double A[3][3] ){
212  
285 –  std::cerr
286 –            << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
287 –            << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
288 –            << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
289 – }
290 –
291 – void SimInfo::printMat9(double A[9] ){
292 –
293 –  std::cerr
294 –            << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
295 –            << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
296 –            << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
297 – }
298 –
299 –
300 – void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){
301 –
302 –      out[0] = a[1] * b[2] - a[2] * b[1];
303 –      out[1] = a[2] * b[0] - a[0] * b[2] ;
304 –      out[2] = a[0] * b[1] - a[1] * b[0];
305 –      
306 – }
307 –
308 – double SimInfo::dotProduct3(double a[3], double b[3]){
309 –  return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2];
310 – }
311 –
312 – double SimInfo::length3(double a[3]){
313 –  return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]);
314 – }
315 –
213   void SimInfo::calcBoxL( void ){
214  
215    double dx, dy, dz, dsq;
# Line 368 | Line 265 | double SimInfo::calcMaxCutOff(){
265    rk[0] = Hmat[0][2];
266    rk[1] = Hmat[1][2];
267    rk[2] = Hmat[2][2];
268 <  
269 <  crossProduct3(ri,rj, rij);
270 <  distXY = dotProduct3(rk,rij) / length3(rij);
268 >    
269 >  crossProduct3(ri, rj, rij);
270 >  distXY = dotProduct3(rk,rij) / norm3(rij);
271  
272    crossProduct3(rj,rk, rjk);
273 <  distYZ = dotProduct3(ri,rjk) / length3(rjk);
273 >  distYZ = dotProduct3(ri,rjk) / norm3(rjk);
274  
275    crossProduct3(rk,ri, rki);
276 <  distZX = dotProduct3(rj,rki) / length3(rki);
276 >  distZX = dotProduct3(rj,rki) / norm3(rki);
277  
278    minDist = min(min(distXY, distYZ), distZX);
279    return minDist/2;
# Line 424 | Line 321 | int SimInfo::getNDF(){
321  
322   int SimInfo::getNDF(){
323    int ndf_local;
324 +
325 +  ndf_local = 0;
326    
327 <  ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
327 >  for(int i = 0; i < integrableObjects.size(); i++){
328 >    ndf_local += 3;
329 >    if (integrableObjects[i]->isDirectional()) {
330 >      if (integrableObjects[i]->isLinear())
331 >        ndf_local += 2;
332 >      else
333 >        ndf_local += 3;
334 >    }
335 >  }
336  
337 +  // n_constraints is local, so subtract them on each processor:
338 +
339 +  ndf_local -= n_constraints;
340 +
341   #ifdef IS_MPI
342    MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
343   #else
344    ndf = ndf_local;
345   #endif
346 +
347 +  // nZconstraints is global, as are the 3 COM translations for the
348 +  // entire system:
349  
350    ndf = ndf - 3 - nZconstraints;
351  
# Line 442 | Line 356 | int SimInfo::getNDFraw() {
356    int ndfRaw_local;
357  
358    // Raw degrees of freedom that we have to set
359 <  ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
360 <  
359 >  ndfRaw_local = 0;
360 >
361 >  for(int i = 0; i < integrableObjects.size(); i++){
362 >    ndfRaw_local += 3;
363 >    if (integrableObjects[i]->isDirectional()) {
364 >       if (integrableObjects[i]->isLinear())
365 >        ndfRaw_local += 2;
366 >      else
367 >        ndfRaw_local += 3;
368 >    }
369 >  }
370 >    
371   #ifdef IS_MPI
372    MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
373   #else
# Line 456 | Line 380 | int SimInfo::getNDFtranslational() {
380   int SimInfo::getNDFtranslational() {
381    int ndfTrans_local;
382  
383 <  ndfTrans_local = 3 * n_atoms - n_constraints;
383 >  ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
384  
385 +
386   #ifdef IS_MPI
387    MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
388   #else
# Line 469 | Line 394 | void SimInfo::refreshSim(){
394    return ndfTrans;
395   }
396  
397 + int SimInfo::getTotIntegrableObjects() {
398 +  int nObjs_local;
399 +  int nObjs;
400 +
401 +  nObjs_local =  integrableObjects.size();
402 +
403 +
404 + #ifdef IS_MPI
405 +  MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
406 + #else
407 +  nObjs = nObjs_local;
408 + #endif
409 +
410 +
411 +  return nObjs;
412 + }
413 +
414   void SimInfo::refreshSim(){
415  
416    simtype fInfo;
# Line 478 | Line 420 | void SimInfo::refreshSim(){
420  
421    fInfo.dielect = 0.0;
422  
423 <  if( useDipole ){
423 >  if( useDipoles ){
424      if( useReactionField )fInfo.dielect = dielectric;
425    }
426  
# Line 487 | Line 429 | void SimInfo::refreshSim(){
429    fInfo.SIM_uses_LJ = useLJ;
430    fInfo.SIM_uses_sticky = useSticky;
431    //fInfo.SIM_uses_sticky = 0;
432 <  fInfo.SIM_uses_dipoles = useDipole;
432 >  fInfo.SIM_uses_charges = useCharges;
433 >  fInfo.SIM_uses_dipoles = useDipoles;
434    //fInfo.SIM_uses_dipoles = 0;
435 <  //fInfo.SIM_uses_RF = useReactionField;
436 <  fInfo.SIM_uses_RF = 0;
435 >  fInfo.SIM_uses_RF = useReactionField;
436 >  //fInfo.SIM_uses_RF = 0;
437    fInfo.SIM_uses_GB = useGB;
438    fInfo.SIM_uses_EAM = useEAM;
439  
440 <  excl = Exclude::getArray();
440 >  n_exclude = excludes->getSize();
441 >  excl = excludes->getFortranArray();
442  
443   #ifdef IS_MPI
444    n_global = mpiSim->getTotAtoms();
# Line 527 | Line 471 | void SimInfo::refreshSim(){
471    this->ndfTrans = this->getNDFtranslational();
472   }
473  
530 –
531 – void SimInfo::setRcut( double theRcut ){
532 –
533 –  rCut = theRcut;
534 –  checkCutOffs();
535 – }
536 –
474   void SimInfo::setDefaultRcut( double theRcut ){
475  
476 <  haveOrigRcut = 1;
540 <  origRcut = theRcut;
476 >  haveRcut = 1;
477    rCut = theRcut;
478  
479    ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
# Line 545 | Line 481 | void SimInfo::setEcr( double theEcr ){
481    notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
482   }
483  
548 – void SimInfo::setEcr( double theEcr ){
549 –
550 –  ecr = theEcr;
551 –  checkCutOffs();
552 – }
553 –
484   void SimInfo::setDefaultEcr( double theEcr ){
485  
486 <  haveOrigEcr = 1;
487 <  origEcr = theEcr;
486 >  haveEcr = 1;
487 >  ecr = theEcr;
488    
489    ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
490  
561 –  ecr = theEcr;
562 –
491    notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
492   }
493  
566 – void SimInfo::setEcr( double theEcr, double theEst ){
567 –
568 –  est = theEst;
569 –  setEcr( theEcr );
570 – }
571 –
494   void SimInfo::setDefaultEcr( double theEcr, double theEst ){
495  
496    est = theEst;
# Line 577 | Line 499 | void SimInfo::checkCutOffs( void ){
499  
500  
501   void SimInfo::checkCutOffs( void ){
580 –
581 –  int cutChanged = 0;
502    
503    if( boxIsInit ){
504      
505      //we need to check cutOffs against the box
506 <
507 <    //detect the change of rCut
588 <    if(( maxCutoff > rCut )&&(usePBC)){
589 <      if( rCut < origRcut ){
590 <        rCut = origRcut;
591 <        
592 <        if (rCut > maxCutoff)
593 <          rCut = maxCutoff;
594 <  
595 <          sprintf( painCave.errMsg,
596 <                    "New Box size is setting the long range cutoff radius "
597 <                    "to %lf at time %lf\n",
598 <                    rCut, currentTime );
599 <          painCave.isFatal = 0;
600 <          simError();
601 <      }
602 <    }
603 <    else if ((rCut > maxCutoff)&&(usePBC)) {
506 >    
507 >    if( rCut > maxCutoff ){
508        sprintf( painCave.errMsg,
509 <               "New Box size is setting the long range cutoff radius "
510 <               "to %lf at time %lf\n",
511 <               maxCutoff, currentTime );
512 <      painCave.isFatal = 0;
509 >               "LJrcut is too large for the current periodic box.\n"
510 >               "\tCurrent Value of LJrcut = %G at time %G\n "
511 >               "\tThis is larger than half of at least one of the\n"
512 >               "\tperiodic box vectors.  Right now, the Box matrix is:\n"
513 >               "\n, %G"
514 >               "\t[ %G %G %G ]\n"
515 >               "\t[ %G %G %G ]\n"
516 >               "\t[ %G %G %G ]\n",
517 >               rCut, currentTime, maxCutoff,
518 >               Hmat[0][0], Hmat[0][1], Hmat[0][2],
519 >               Hmat[1][0], Hmat[1][1], Hmat[1][2],
520 >               Hmat[2][0], Hmat[2][1], Hmat[2][2]);
521 >      painCave.isFatal = 1;
522        simError();
610 –      rCut = maxCutoff;
523      }
524 <
525 <
526 <    //detect the change of ecr
527 <    if( maxCutoff > ecr ){
528 <      if( ecr < origEcr ){
529 <        ecr = origEcr;
530 <        if (ecr > maxCutoff) ecr = maxCutoff;
531 <  
532 <          sprintf( painCave.errMsg,
533 <                    "New Box size is setting the electrostaticCutoffRadius "
534 <                    "to %lf at time %lf\n",
535 <                    ecr, currentTime );
536 <            painCave.isFatal = 0;
537 <            simError();
524 >    
525 >    if( haveEcr ){
526 >      if( ecr > maxCutoff ){
527 >        sprintf( painCave.errMsg,
528 >                 "electrostaticCutoffRadius is too large for the current\n"
529 >                 "\tperiodic box.\n\n"
530 >                 "\tCurrent Value of ECR = %G at time %G\n "
531 >                 "\tThis is larger than half of at least one of the\n"
532 >                 "\tperiodic box vectors.  Right now, the Box matrix is:\n"
533 >                 "\n"
534 >                 "\t[ %G %G %G ]\n"
535 >                 "\t[ %G %G %G ]\n"
536 >                 "\t[ %G %G %G ]\n",
537 >                 ecr, currentTime,
538 >                 Hmat[0][0], Hmat[0][1], Hmat[0][2],
539 >                 Hmat[1][0], Hmat[1][1], Hmat[1][2],
540 >                 Hmat[2][0], Hmat[2][1], Hmat[2][2]);
541 >        painCave.isFatal = 1;
542 >        simError();
543        }
544      }
628 –    else if( ecr > maxCutoff){
629 –      sprintf( painCave.errMsg,
630 –               "New Box size is setting the electrostaticCutoffRadius "
631 –               "to %lf at time %lf\n",
632 –               maxCutoff, currentTime  );
633 –      painCave.isFatal = 0;
634 –      simError();      
635 –      ecr = maxCutoff;
636 –    }
637 –
638 –    if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
639 –    
640 –    // rlist is the 1.0 plus max( rcut, ecr )
641 –    
642 –    ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
643 –    
644 –    if( cutChanged ){
645 –      notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
646 –    }
647 –    
648 –    oldEcr = ecr;
649 –    oldRcut = rCut;
650 –    
545    } else {
546      // initialize this stuff before using it, OK?
547      sprintf( painCave.errMsg,
548 <             "Trying to check cutoffs without a box. Be smarter.\n" );
548 >             "Trying to check cutoffs without a box.\n"
549 >             "\tOOPSE should have better programmers than that.\n" );
550      painCave.isFatal = 1;
551      simError();      
552    }
# Line 694 | Line 589 | vector<GenericData*> SimInfo::getProperties(){
589      return NULL;  
590   }
591  
697 – vector<GenericData*> SimInfo::getProperties(){
698 –
699 –  vector<GenericData*> result;
700 –  map<string, GenericData*>::iterator i;
701 –  
702 –  for(i = properties.begin(); i != properties.end(); i++)
703 –    result.push_back((*i).second);
704 –    
705 –  return result;
706 – }
707 –
708 – double SimInfo::matTrace3(double m[3][3]){
709 –  double trace;
710 –  trace = m[0][0] + m[1][1] + m[2][2];
711 –
712 –  return trace;
713 – }

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