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 767 by tim, Tue Sep 16 20:02:11 2003 UTC vs.
Revision 829 by gezelter, Tue Oct 28 16:03:37 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 48 | Line 48 | SimInfo::SimInfo(){
48    haveOrigEcr = 0;
49    boxIsInit = 0;
50    
51 +  resetTime = 1e99;
52    
53  
54    usePBC = 0;
# Line 93 | Line 94 | void SimInfo::setBoxM( double theBox[3][3] ){
94  
95   void SimInfo::setBoxM( double theBox[3][3] ){
96    
97 <  int i, j, status;
97 <  double smallestBoxL, maxCutoff;
97 >  int i, j;
98    double FortranHmat[9]; // to preserve compatibility with Fortran the
99                           // ordering in the array is as follows:
100                           // [ 0 3 6 ]
# Line 281 | Line 281 | void SimInfo::printMat9(double A[9] ){
281              << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
282   }
283  
284 +
285 + void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){
286 +
287 +      out[0] = a[1] * b[2] - a[2] * b[1];
288 +      out[1] = a[2] * b[0] - a[0] * b[2] ;
289 +      out[2] = a[0] * b[1] - a[1] * b[0];
290 +      
291 + }
292 +
293 + double SimInfo::dotProduct3(double a[3], double b[3]){
294 +  return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2];
295 + }
296 +
297 + double SimInfo::length3(double a[3]){
298 +  return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]);
299 + }
300 +
301   void SimInfo::calcBoxL( void ){
302  
303    double dx, dy, dz, dsq;
287 –  int i;
304  
305    // boxVol = Determinant of Hmat
306  
# Line 295 | Line 311 | void SimInfo::calcBoxL( void ){
311    dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
312    dsq = dx*dx + dy*dy + dz*dz;
313    boxL[0] = sqrt( dsq );
314 <  maxCutoff = 0.5 * boxL[0];
314 >  //maxCutoff = 0.5 * boxL[0];
315  
316    // boxLy
317    
318    dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
319    dsq = dx*dx + dy*dy + dz*dz;
320    boxL[1] = sqrt( dsq );
321 <  if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
321 >  //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
322  
323 +
324    // boxLz
325    
326    dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
327    dsq = dx*dx + dy*dy + dz*dz;
328    boxL[2] = sqrt( dsq );
329 <  if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
329 >  //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
330 >
331 >  //calculate the max cutoff
332 >  maxCutoff =  calcMaxCutOff();
333    
334    checkCutOffs();
335  
336   }
337  
338  
339 + double SimInfo::calcMaxCutOff(){
340 +
341 +  double ri[3], rj[3], rk[3];
342 +  double rij[3], rjk[3], rki[3];
343 +  double minDist;
344 +
345 +  ri[0] = Hmat[0][0];
346 +  ri[1] = Hmat[1][0];
347 +  ri[2] = Hmat[2][0];
348 +
349 +  rj[0] = Hmat[0][1];
350 +  rj[1] = Hmat[1][1];
351 +  rj[2] = Hmat[2][1];
352 +
353 +  rk[0] = Hmat[0][2];
354 +  rk[1] = Hmat[1][2];
355 +  rk[2] = Hmat[2][2];
356 +  
357 +  crossProduct3(ri,rj, rij);
358 +  distXY = dotProduct3(rk,rij) / length3(rij);
359 +
360 +  crossProduct3(rj,rk, rjk);
361 +  distYZ = dotProduct3(ri,rjk) / length3(rjk);
362 +
363 +  crossProduct3(rk,ri, rki);
364 +  distZX = dotProduct3(rj,rki) / length3(rki);
365 +
366 +  minDist = min(min(distXY, distYZ), distZX);
367 +  return minDist/2;
368 +  
369 + }
370 +
371   void SimInfo::wrapVector( double thePos[3] ){
372  
373 <  int i, j, k;
373 >  int i;
374    double scaled[3];
375  
376    if( !orthoRhombic ){
# Line 356 | Line 408 | int SimInfo::getNDF(){
408  
409  
410   int SimInfo::getNDF(){
411 <  int ndf_local, ndf;
411 >  int ndf_local;
412    
413    ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
414  
# Line 372 | Line 424 | int SimInfo::getNDFraw() {
424   }
425  
426   int SimInfo::getNDFraw() {
427 <  int ndfRaw_local, ndfRaw;
427 >  int ndfRaw_local;
428  
429    // Raw degrees of freedom that we have to set
430    ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
# Line 387 | Line 439 | int SimInfo::getNDFtranslational() {
439   }
440  
441   int SimInfo::getNDFtranslational() {
442 <  int ndfTrans_local, ndfTrans;
442 >  int ndfTrans_local;
443  
444    ndfTrans_local = 3 * n_atoms - n_constraints;
445  
# Line 493 | Line 545 | void SimInfo::checkCutOffs( void ){
545   void SimInfo::checkCutOffs( void ){
546  
547    int cutChanged = 0;
548 <
497 <
498 <
548 >  
549    if( boxIsInit ){
550      
551      //we need to check cutOffs against the box
552 <  
552 >
553 >    //detect the change of rCut
554      if(( maxCutoff > rCut )&&(usePBC)){
555        if( rCut < origRcut ){
556 <        rCut = origRcut;
557 <        if (rCut > maxCutoff) rCut = maxCutoff;
558 <        
559 <        sprintf( painCave.errMsg,
560 <                 "New Box size is setting the long range cutoff radius "
561 <                 "to %lf\n",
562 <                 rCut );
563 <        painCave.isFatal = 0;
564 <        simError();
556 >        rCut = origRcut;
557 >        
558 >        if (rCut > maxCutoff)
559 >          rCut = maxCutoff;
560 >  
561 >          sprintf( painCave.errMsg,
562 >                    "New Box size is setting the long range cutoff radius "
563 >                    "to %lf at time %lf\n",
564 >                    rCut, currentTime );
565 >          painCave.isFatal = 0;
566 >          simError();
567        }
568      }
569 <
517 <    if( maxCutoff > ecr ){
518 <      if( ecr < origEcr ){
519 <        ecr = origEcr;
520 <        if (ecr > maxCutoff) ecr = maxCutoff;
521 <        
522 <        sprintf( painCave.errMsg,
523 <                 "New Box size is setting the electrostaticCutoffRadius "
524 <                 "to %lf\n",
525 <                 ecr );
526 <        painCave.isFatal = 0;
527 <        simError();
528 <      }
529 <    }
530 <
531 <
532 <    if ((rCut > maxCutoff)&&(usePBC)) {
569 >    else if ((rCut > maxCutoff)&&(usePBC)) {
570        sprintf( painCave.errMsg,
571                 "New Box size is setting the long range cutoff radius "
572 <               "to %lf\n",
573 <               maxCutoff );
572 >               "to %lf at time %lf\n",
573 >               maxCutoff, currentTime );
574        painCave.isFatal = 0;
575        simError();
576        rCut = maxCutoff;
577      }
578  
579 <    if( ecr > maxCutoff){
579 >
580 >    //detect the change of ecr
581 >    if( maxCutoff > ecr ){
582 >      if( ecr < origEcr ){
583 >        ecr = origEcr;
584 >        if (ecr > maxCutoff) ecr = maxCutoff;
585 >  
586 >          sprintf( painCave.errMsg,
587 >                    "New Box size is setting the electrostaticCutoffRadius "
588 >                    "to %lf at time %lf\n",
589 >                    ecr, currentTime );
590 >            painCave.isFatal = 0;
591 >            simError();
592 >      }
593 >    }
594 >    else if( ecr > maxCutoff){
595        sprintf( painCave.errMsg,
596                 "New Box size is setting the electrostaticCutoffRadius "
597 <               "to %lf\n",
598 <               maxCutoff  );
597 >               "to %lf at time %lf\n",
598 >               maxCutoff, currentTime  );
599        painCave.isFatal = 0;
600        simError();      
601        ecr = maxCutoff;
602      }
603  
552 –
604      if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
605 <
605 >    
606      // rlist is the 1.0 plus max( rcut, ecr )
607      
608      ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
# Line 563 | Line 614 | void SimInfo::checkCutOffs( void ){
614      
615      oldEcr = ecr;
616      oldRcut = rCut;
617 <
617 >    
618    } else {
619      // initialize this stuff before using it, OK?
620 <      sprintf( painCave.errMsg,
621 <               "Trying to check cutoffs without a box. Be smarter.\n" );
622 <      painCave.isFatal = 1;
623 <      simError();      
620 >    sprintf( painCave.errMsg,
621 >             "Trying to check cutoffs without a box. Be smarter.\n" );
622 >    painCave.isFatal = 1;
623 >    simError();      
624    }
625 <
625 >  
626   }
627  
628   void SimInfo::addProperty(GenericData* prop){

Diff Legend

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