ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
(Generate patch)

Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 660 by tim, Thu Jul 31 19:59:34 2003 UTC vs.
Revision 855 by mmeineke, Thu Nov 6 22:01:37 2003 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 26 | Line 26 | SimInfo::SimInfo(){
26   SimInfo::SimInfo(){
27    excludes = NULL;
28    n_constraints = 0;
29 +  nZconstraints = 0;
30    n_oriented = 0;
31    n_dipoles = 0;
32    ndf = 0;
33    ndfRaw = 0;
34 +  nZconstraints = 0;
35    the_integrator = NULL;
36    setTemp = 0;
37    thermalTime = 0.0;
38    currentTime = 0.0;
39    rCut = 0.0;
40 +  origRcut = -1.0;
41    ecr = 0.0;
42 +  origEcr = -1.0;
43    est = 0.0;
44    oldEcr = 0.0;
45    oldRcut = 0.0;
# Line 44 | Line 48 | SimInfo::SimInfo(){
48    haveOrigEcr = 0;
49    boxIsInit = 0;
50    
51 <  
51 >  resetTime = 1e99;
52  
53 +  orthoTolerance = 1E-6;
54 +  useInitXSstate = true;
55 +
56    usePBC = 0;
57    useLJ = 0;
58    useSticky = 0;
# Line 54 | Line 61 | SimInfo::SimInfo(){
61    useGB = 0;
62    useEAM = 0;
63  
64 +  myConfiguration = new SimState();
65 +
66    wrapMeSimInfo( this );
67   }
68  
69 +
70   SimInfo::~SimInfo(){
71  
72 +  delete myConfiguration;
73 +
74    map<string, GenericData*>::iterator i;
75    
76    for(i = properties.begin(); i != properties.end(); i++)
77      delete (*i).second;
78 <
67 <  
78 >    
79   }
80  
81   void SimInfo::setBox(double newBox[3]) {
# Line 85 | Line 96 | void SimInfo::setBoxM( double theBox[3][3] ){
96  
97   void SimInfo::setBoxM( double theBox[3][3] ){
98    
99 <  int i, j, status;
89 <  double smallestBoxL, maxCutoff;
99 >  int i, j;
100    double FortranHmat[9]; // to preserve compatibility with Fortran the
101                           // ordering in the array is as follows:
102                           // [ 0 3 6 ]
# Line 138 | Line 148 | void SimInfo::calcHmatInv( void ) {
148  
149   void SimInfo::calcHmatInv( void ) {
150    
151 +  int oldOrtho;
152    int i,j;
153    double smallDiag;
154    double tol;
# Line 145 | Line 156 | void SimInfo::calcHmatInv( void ) {
156  
157    invertMat3( Hmat, HmatInv );
158  
148 –  // Check the inverse to make sure it is sane:
149 –
150 –  matMul3( Hmat, HmatInv, sanity );
151 –    
159    // check to see if Hmat is orthorhombic
160    
161 <  smallDiag = Hmat[0][0];
155 <  if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1];
156 <  if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2];
157 <  tol = smallDiag * 1E-6;
161 >  oldOrtho = orthoRhombic;
162  
163 +  smallDiag = fabs(Hmat[0][0]);
164 +  if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
165 +  if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
166 +  tol = smallDiag * orthoTolerance;
167 +
168    orthoRhombic = 1;
169    
170    for (i = 0; i < 3; i++ ) {
171      for (j = 0 ; j < 3; j++) {
172        if (i != j) {
173          if (orthoRhombic) {
174 <          if (Hmat[i][j] >= tol) orthoRhombic = 0;
174 >          if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
175          }        
176        }
177      }
178    }
179 +
180 +  if( oldOrtho != orthoRhombic ){
181 +    
182 +    if( orthoRhombic ){
183 +      sprintf( painCave.errMsg,
184 +               "Hmat is switching from Non-Orthorhombic to OrthoRhombic\n"
185 +               "       If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n",
186 +               orthoTolerance);
187 +      simError();
188 +    }
189 +    else {
190 +      sprintf( painCave.errMsg,
191 +               "Hmat is switching from Orthorhombic to Non-OrthoRhombic\n"
192 +               "       If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n",
193 +               orthoTolerance);
194 +      simError();
195 +    }
196 +  }
197   }
198  
199   double SimInfo::matDet3(double a[3][3]) {
# Line 273 | Line 300 | void SimInfo::calcBoxL( void ){
300              << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
301   }
302  
303 +
304 + void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){
305 +
306 +      out[0] = a[1] * b[2] - a[2] * b[1];
307 +      out[1] = a[2] * b[0] - a[0] * b[2] ;
308 +      out[2] = a[0] * b[1] - a[1] * b[0];
309 +      
310 + }
311 +
312 + double SimInfo::dotProduct3(double a[3], double b[3]){
313 +  return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2];
314 + }
315 +
316 + double SimInfo::length3(double a[3]){
317 +  return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]);
318 + }
319 +
320   void SimInfo::calcBoxL( void ){
321  
322    double dx, dy, dz, dsq;
279 –  int i;
323  
324    // boxVol = Determinant of Hmat
325  
# Line 287 | Line 330 | void SimInfo::calcBoxL( void ){
330    dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
331    dsq = dx*dx + dy*dy + dz*dz;
332    boxL[0] = sqrt( dsq );
333 <  maxCutoff = 0.5 * boxL[0];
333 >  //maxCutoff = 0.5 * boxL[0];
334  
335    // boxLy
336    
337    dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
338    dsq = dx*dx + dy*dy + dz*dz;
339    boxL[1] = sqrt( dsq );
340 <  if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
340 >  //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
341  
342 +
343    // boxLz
344    
345    dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
346    dsq = dx*dx + dy*dy + dz*dz;
347    boxL[2] = sqrt( dsq );
348 <  if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
348 >  //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
349  
350 +  //calculate the max cutoff
351 +  maxCutoff =  calcMaxCutOff();
352 +  
353 +  checkCutOffs();
354 +
355   }
356  
357  
358 + double SimInfo::calcMaxCutOff(){
359 +
360 +  double ri[3], rj[3], rk[3];
361 +  double rij[3], rjk[3], rki[3];
362 +  double minDist;
363 +
364 +  ri[0] = Hmat[0][0];
365 +  ri[1] = Hmat[1][0];
366 +  ri[2] = Hmat[2][0];
367 +
368 +  rj[0] = Hmat[0][1];
369 +  rj[1] = Hmat[1][1];
370 +  rj[2] = Hmat[2][1];
371 +
372 +  rk[0] = Hmat[0][2];
373 +  rk[1] = Hmat[1][2];
374 +  rk[2] = Hmat[2][2];
375 +  
376 +  crossProduct3(ri,rj, rij);
377 +  distXY = dotProduct3(rk,rij) / length3(rij);
378 +
379 +  crossProduct3(rj,rk, rjk);
380 +  distYZ = dotProduct3(ri,rjk) / length3(rjk);
381 +
382 +  crossProduct3(rk,ri, rki);
383 +  distZX = dotProduct3(rj,rki) / length3(rki);
384 +
385 +  minDist = min(min(distXY, distYZ), distZX);
386 +  return minDist/2;
387 +  
388 + }
389 +
390   void SimInfo::wrapVector( double thePos[3] ){
391  
392 <  int i, j, k;
392 >  int i;
393    double scaled[3];
394  
395    if( !orthoRhombic ){
# Line 346 | Line 427 | int SimInfo::getNDF(){
427  
428  
429   int SimInfo::getNDF(){
430 <  int ndf_local, ndf;
430 >  int ndf_local;
431    
432    ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
433  
# Line 356 | Line 437 | int SimInfo::getNDF(){
437    ndf = ndf_local;
438   #endif
439  
440 <  ndf = ndf - 3;
440 >  ndf = ndf - 3 - nZconstraints;
441  
442    return ndf;
443   }
444  
445   int SimInfo::getNDFraw() {
446 <  int ndfRaw_local, ndfRaw;
446 >  int ndfRaw_local;
447  
448    // Raw degrees of freedom that we have to set
449    ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
# Line 375 | Line 456 | int SimInfo::getNDFraw() {
456  
457    return ndfRaw;
458   }
459 <
459 >
460 > int SimInfo::getNDFtranslational() {
461 >  int ndfTrans_local;
462 >
463 >  ndfTrans_local = 3 * n_atoms - n_constraints;
464 >
465 > #ifdef IS_MPI
466 >  MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
467 > #else
468 >  ndfTrans = ndfTrans_local;
469 > #endif
470 >
471 >  ndfTrans = ndfTrans - 3 - nZconstraints;
472 >
473 >  return ndfTrans;
474 > }
475 >
476   void SimInfo::refreshSim(){
477  
478    simtype fInfo;
# Line 431 | Line 528 | void SimInfo::refreshSim(){
528  
529    this->ndf = this->getNDF();
530    this->ndfRaw = this->getNDFraw();
531 <
531 >  this->ndfTrans = this->getNDFtranslational();
532   }
533  
534  
535   void SimInfo::setRcut( double theRcut ){
536  
440 –  if( !haveOrigRcut ){
441 –    haveOrigRcut = 1;
442 –    origRcut = theRcut;
443 –  }
444 –
537    rCut = theRcut;
538    checkCutOffs();
539   }
540  
541 < void SimInfo::setEcr( double theEcr ){
541 > void SimInfo::setDefaultRcut( double theRcut ){
542  
543 <  if( !haveOrigEcr ){
544 <    haveOrigEcr = 1;
545 <    origEcr = theEcr;
454 <  }
543 >  haveOrigRcut = 1;
544 >  origRcut = theRcut;
545 >  rCut = theRcut;
546  
547 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
548 +
549 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
550 + }
551 +
552 + void SimInfo::setEcr( double theEcr ){
553 +
554    ecr = theEcr;
555    checkCutOffs();
556   }
557  
558 + void SimInfo::setDefaultEcr( double theEcr ){
559 +
560 +  haveOrigEcr = 1;
561 +  origEcr = theEcr;
562 +  
563 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
564 +
565 +  ecr = theEcr;
566 +
567 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
568 + }
569 +
570   void SimInfo::setEcr( double theEcr, double theEst ){
571  
572    est = theEst;
573    setEcr( theEcr );
574   }
575  
576 + void SimInfo::setDefaultEcr( double theEcr, double theEst ){
577  
578 +  est = theEst;
579 +  setDefaultEcr( theEcr );
580 + }
581 +
582 +
583   void SimInfo::checkCutOffs( void ){
584  
585    int cutChanged = 0;
586 <
586 >  
587    if( boxIsInit ){
588      
589      //we need to check cutOffs against the box
590 <    
591 <    if( maxCutoff > rCut ){
590 >
591 >    //detect the change of rCut
592 >    if(( maxCutoff > rCut )&&(usePBC)){
593        if( rCut < origRcut ){
594 <        rCut = origRcut;
595 <        if (rCut > maxCutoff) rCut = maxCutoff;
596 <        
597 <        sprintf( painCave.errMsg,
598 <                 "New Box size is setting the long range cutoff radius "
599 <                 "to %lf\n",
600 <                 rCut );
601 <        painCave.isFatal = 0;
602 <        simError();
594 >        rCut = origRcut;
595 >        
596 >        if (rCut > maxCutoff)
597 >          rCut = maxCutoff;
598 >  
599 >          sprintf( painCave.errMsg,
600 >                    "New Box size is setting the long range cutoff radius "
601 >                    "to %lf at time %lf\n",
602 >                    rCut, currentTime );
603 >          painCave.isFatal = 0;
604 >          simError();
605        }
606      }
607 <
489 <    if( maxCutoff > ecr ){
490 <      if( ecr < origEcr ){
491 <        rCut = origEcr;
492 <        if (ecr > maxCutoff) ecr = maxCutoff;
493 <        
494 <        sprintf( painCave.errMsg,
495 <                 "New Box size is setting the electrostaticCutoffRadius "
496 <                 "to %lf\n",
497 <                 ecr );
498 <        painCave.isFatal = 0;
499 <        simError();
500 <      }
501 <    }
502 <
503 <
504 <    if (rCut > maxCutoff) {
607 >    else if ((rCut > maxCutoff)&&(usePBC)) {
608        sprintf( painCave.errMsg,
609                 "New Box size is setting the long range cutoff radius "
610 <               "to %lf\n",
611 <               maxCutoff );
610 >               "to %lf at time %lf\n",
611 >               maxCutoff, currentTime );
612        painCave.isFatal = 0;
613        simError();
614        rCut = maxCutoff;
615      }
616  
617 <    if( ecr > maxCutoff){
617 >
618 >    //detect the change of ecr
619 >    if( maxCutoff > ecr ){
620 >      if( ecr < origEcr ){
621 >        ecr = origEcr;
622 >        if (ecr > maxCutoff) ecr = maxCutoff;
623 >  
624 >          sprintf( painCave.errMsg,
625 >                    "New Box size is setting the electrostaticCutoffRadius "
626 >                    "to %lf at time %lf\n",
627 >                    ecr, currentTime );
628 >            painCave.isFatal = 0;
629 >            simError();
630 >      }
631 >    }
632 >    else if( ecr > maxCutoff){
633        sprintf( painCave.errMsg,
634                 "New Box size is setting the electrostaticCutoffRadius "
635 <               "to %lf\n",
636 <               maxCutoff  );
635 >               "to %lf at time %lf\n",
636 >               maxCutoff, currentTime  );
637        painCave.isFatal = 0;
638        simError();      
639        ecr = maxCutoff;
640      }
641  
642 +    if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
643      
644 <  }
526 <  
527 <
528 <  if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
529 <
530 <  // rlist is the 1.0 plus max( rcut, ecr )
531 <  
532 <  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
533 <
534 <  if( cutChanged ){
644 >    // rlist is the 1.0 plus max( rcut, ecr )
645      
646 <    notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
646 >    ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
647 >    
648 >    if( cutChanged ){
649 >      notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
650 >    }
651 >    
652 >    oldEcr = ecr;
653 >    oldRcut = rCut;
654 >    
655 >  } else {
656 >    // initialize this stuff before using it, OK?
657 >    sprintf( painCave.errMsg,
658 >             "Trying to check cutoffs without a box. Be smarter.\n" );
659 >    painCave.isFatal = 1;
660 >    simError();      
661    }
662 <
539 <  oldEcr = ecr;
540 <  oldRcut = rCut;
662 >  
663   }
664  
665   void SimInfo::addProperty(GenericData* prop){
# Line 587 | Line 709 | vector<GenericData*> SimInfo::getProperties(){
709    return result;
710   }
711  
712 + double SimInfo::matTrace3(double m[3][3]){
713 +  double trace;
714 +  trace = m[0][0] + m[1][1] + m[2][2];
715  
716 +  return trace;
717 + }

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines