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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 770 by gezelter, Fri Sep 19 14:55:41 2003 UTC vs.
Revision 859 by mmeineke, Mon Nov 10 21:50:36 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 37 | Line 37 | SimInfo::SimInfo(){
37    thermalTime = 0.0;
38    currentTime = 0.0;
39    rCut = 0.0;
40 –  origRcut = -1.0;
40    ecr = 0.0;
42 –  origEcr = -1.0;
41    est = 0.0;
44 –  oldEcr = 0.0;
45 –  oldRcut = 0.0;
42  
43 <  haveOrigRcut = 0;
44 <  haveOrigEcr = 0;
43 >  haveRcut = 0;
44 >  haveEcr = 0;
45    boxIsInit = 0;
46    
47 <  
47 >  resetTime = 1e99;
48  
49 +  orthoTolerance = 1E-6;
50 +  useInitXSstate = true;
51 +
52    usePBC = 0;
53    useLJ = 0;
54    useSticky = 0;
# Line 93 | Line 92 | void SimInfo::setBoxM( double theBox[3][3] ){
92  
93   void SimInfo::setBoxM( double theBox[3][3] ){
94    
95 <  int i, j, status;
97 <  double smallestBoxL, maxCutoff;
95 >  int i, j;
96    double FortranHmat[9]; // to preserve compatibility with Fortran the
97                           // ordering in the array is as follows:
98                           // [ 0 3 6 ]
# Line 102 | Line 100 | void SimInfo::setBoxM( double theBox[3][3] ){
100                           // [ 2 5 8 ]
101    double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
102  
105 –  
103    if( !boxIsInit ) boxIsInit = 1;
104  
105    for(i=0; i < 3; i++)
# Line 146 | Line 143 | void SimInfo::calcHmatInv( void ) {
143  
144   void SimInfo::calcHmatInv( void ) {
145    
146 +  int oldOrtho;
147    int i,j;
148    double smallDiag;
149    double tol;
# Line 153 | Line 151 | void SimInfo::calcHmatInv( void ) {
151  
152    invertMat3( Hmat, HmatInv );
153  
156 –  // Check the inverse to make sure it is sane:
157 –
158 –  matMul3( Hmat, HmatInv, sanity );
159 –    
154    // check to see if Hmat is orthorhombic
155    
156 <  smallDiag = Hmat[0][0];
163 <  if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1];
164 <  if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2];
165 <  tol = smallDiag * 1E-6;
156 >  oldOrtho = orthoRhombic;
157  
158 +  smallDiag = fabs(Hmat[0][0]);
159 +  if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
160 +  if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
161 +  tol = smallDiag * orthoTolerance;
162 +
163    orthoRhombic = 1;
164    
165    for (i = 0; i < 3; i++ ) {
166      for (j = 0 ; j < 3; j++) {
167        if (i != j) {
168          if (orthoRhombic) {
169 <          if (Hmat[i][j] >= tol) orthoRhombic = 0;
169 >          if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
170          }        
171        }
172      }
173    }
174 +
175 +  if( oldOrtho != orthoRhombic ){
176 +    
177 +    if( orthoRhombic ){
178 +      sprintf( painCave.errMsg,
179 +               "Hmat is switching from Non-Orthorhombic to OrthoRhombic\n"
180 +               "       If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n",
181 +               orthoTolerance);
182 +      simError();
183 +    }
184 +    else {
185 +      sprintf( painCave.errMsg,
186 +               "Hmat is switching from Orthorhombic to Non-OrthoRhombic\n"
187 +               "       If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n",
188 +               orthoTolerance);
189 +      simError();
190 +    }
191 +  }
192   }
193  
194   double SimInfo::matDet3(double a[3][3]) {
# Line 281 | Line 295 | void SimInfo::printMat9(double A[9] ){
295              << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
296   }
297  
298 +
299 + void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){
300 +
301 +      out[0] = a[1] * b[2] - a[2] * b[1];
302 +      out[1] = a[2] * b[0] - a[0] * b[2] ;
303 +      out[2] = a[0] * b[1] - a[1] * b[0];
304 +      
305 + }
306 +
307 + double SimInfo::dotProduct3(double a[3], double b[3]){
308 +  return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2];
309 + }
310 +
311 + double SimInfo::length3(double a[3]){
312 +  return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]);
313 + }
314 +
315   void SimInfo::calcBoxL( void ){
316  
317    double dx, dy, dz, dsq;
287 –  int i;
318  
319    // boxVol = Determinant of Hmat
320  
# Line 295 | Line 325 | void SimInfo::calcBoxL( void ){
325    dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
326    dsq = dx*dx + dy*dy + dz*dz;
327    boxL[0] = sqrt( dsq );
328 <  maxCutoff = 0.5 * boxL[0];
328 >  //maxCutoff = 0.5 * boxL[0];
329  
330    // boxLy
331    
332    dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
333    dsq = dx*dx + dy*dy + dz*dz;
334    boxL[1] = sqrt( dsq );
335 <  if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
335 >  //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
336  
337 +
338    // boxLz
339    
340    dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
341    dsq = dx*dx + dy*dy + dz*dz;
342    boxL[2] = sqrt( dsq );
343 <  if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
343 >  //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
344 >
345 >  //calculate the max cutoff
346 >  maxCutoff =  calcMaxCutOff();
347    
348    checkCutOffs();
349  
350   }
351  
352  
353 + double SimInfo::calcMaxCutOff(){
354 +
355 +  double ri[3], rj[3], rk[3];
356 +  double rij[3], rjk[3], rki[3];
357 +  double minDist;
358 +
359 +  ri[0] = Hmat[0][0];
360 +  ri[1] = Hmat[1][0];
361 +  ri[2] = Hmat[2][0];
362 +
363 +  rj[0] = Hmat[0][1];
364 +  rj[1] = Hmat[1][1];
365 +  rj[2] = Hmat[2][1];
366 +
367 +  rk[0] = Hmat[0][2];
368 +  rk[1] = Hmat[1][2];
369 +  rk[2] = Hmat[2][2];
370 +  
371 +  crossProduct3(ri,rj, rij);
372 +  distXY = dotProduct3(rk,rij) / length3(rij);
373 +
374 +  crossProduct3(rj,rk, rjk);
375 +  distYZ = dotProduct3(ri,rjk) / length3(rjk);
376 +
377 +  crossProduct3(rk,ri, rki);
378 +  distZX = dotProduct3(rj,rki) / length3(rki);
379 +
380 +  minDist = min(min(distXY, distYZ), distZX);
381 +  return minDist/2;
382 +  
383 + }
384 +
385   void SimInfo::wrapVector( double thePos[3] ){
386  
387 <  int i, j, k;
387 >  int i;
388    double scaled[3];
389  
390    if( !orthoRhombic ){
# Line 356 | Line 422 | int SimInfo::getNDF(){
422  
423  
424   int SimInfo::getNDF(){
425 <  int ndf_local, ndf;
425 >  int ndf_local;
426    
427    ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
428  
# Line 372 | Line 438 | int SimInfo::getNDFraw() {
438   }
439  
440   int SimInfo::getNDFraw() {
441 <  int ndfRaw_local, ndfRaw;
441 >  int ndfRaw_local;
442  
443    // Raw degrees of freedom that we have to set
444    ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
# Line 387 | Line 453 | int SimInfo::getNDFtranslational() {
453   }
454  
455   int SimInfo::getNDFtranslational() {
456 <  int ndfTrans_local, ndfTrans;
456 >  int ndfTrans_local;
457  
458    ndfTrans_local = 3 * n_atoms - n_constraints;
459  
# Line 460 | Line 526 | void SimInfo::refreshSim(){
526    this->ndfTrans = this->getNDFtranslational();
527   }
528  
529 + void SimInfo::setDefaultRcut( double theRcut ){
530  
531 < void SimInfo::setRcut( double theRcut ){
531 >  haveRcut = 1;
532 >  rCut = theRcut;
533  
534 <  if( !haveOrigRcut ){
467 <    haveOrigRcut = 1;
468 <    origRcut = theRcut;
469 <  }
534 >  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
535  
536 <  rCut = theRcut;
472 <  checkCutOffs();
536 >  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
537   }
538  
539 < void SimInfo::setEcr( double theEcr ){
539 > void SimInfo::setDefaultEcr( double theEcr ){
540  
541 <  if( !haveOrigEcr ){
542 <    haveOrigEcr = 1;
543 <    origEcr = theEcr;
480 <  }
541 >  haveEcr = 1;
542 >  
543 >  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
544  
545    ecr = theEcr;
546 <  checkCutOffs();
546 >
547 >  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
548   }
549  
550 < void SimInfo::setEcr( double theEcr, double theEst ){
550 > void SimInfo::setDefaultEcr( double theEcr, double theEst ){
551  
552    est = theEst;
553 <  setEcr( theEcr );
553 >  setDefaultEcr( theEcr );
554   }
555  
556  
557   void SimInfo::checkCutOffs( void ){
494 –
495 –  int cutChanged = 0;
558    
559    if( boxIsInit ){
560      
561      //we need to check cutOffs against the box
562      
563 <    if(( maxCutoff > rCut )&&(usePBC)){
564 <      if( rCut < origRcut ){
565 <        rCut = origRcut;
566 <        if (rCut > maxCutoff) rCut = maxCutoff;
567 <        
568 <        sprintf( painCave.errMsg,
569 <                 "New Box size is setting the long range cutoff radius "
508 <                 "to %lf at time %lf\n",
509 <                 rCut, currentTime );
510 <        painCave.isFatal = 0;
511 <        simError();
512 <      }
563 >    if( rCut > maxCutoff ){
564 >      sprintf( painCave.errMsg,
565 >               "Box size is too small for the long range cutoff radius, "
566 >               "%lf, at time %lf\n",
567 >               rCut, currentTime );
568 >      painCave.isFatal = 1;
569 >      simError();
570      }
571      
572 <    if( maxCutoff > ecr ){
573 <      if( ecr < origEcr ){
517 <        ecr = origEcr;
518 <        if (ecr > maxCutoff) ecr = maxCutoff;
519 <        
572 >    if( haveEcr ){
573 >      if( ecr > maxCutoff ){
574          sprintf( painCave.errMsg,
575 <                 "New Box size is setting the electrostaticCutoffRadius "
576 <                 "to %lf at time %lf\n",
575 >                 "Box size is too small for the electrostatic cutoff radius, "
576 >                 "%lf, at time %lf\n",
577                   ecr, currentTime );
578 <        painCave.isFatal = 0;
578 >        painCave.isFatal = 1;
579          simError();
580        }
581      }
528 –    
529 –    
530 –    if ((rCut > maxCutoff)&&(usePBC)) {
531 –      sprintf( painCave.errMsg,
532 –               "New Box size is setting the long range cutoff radius "
533 –               "to %lf at time %lf\n",
534 –               maxCutoff, currentTime );
535 –      painCave.isFatal = 0;
536 –      simError();
537 –      rCut = maxCutoff;
538 –    }
539 –    
540 –    if( ecr > maxCutoff){
541 –      sprintf( painCave.errMsg,
542 –               "New Box size is setting the electrostaticCutoffRadius "
543 –               "to %lf at time %lf\n",
544 –               maxCutoff, currentTime  );
545 –      painCave.isFatal = 0;
546 –      simError();      
547 –      ecr = maxCutoff;
548 –    }
549 –
550 –    if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
551 –    
552 –    // rlist is the 1.0 plus max( rcut, ecr )
553 –    
554 –    ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
555 –    
556 –    if( cutChanged ){
557 –      
558 –      notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
559 –    }
560 –    
561 –    oldEcr = ecr;
562 –    oldRcut = rCut;
563 –    
582    } else {
583      // initialize this stuff before using it, OK?
584      sprintf( painCave.errMsg,

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