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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 699 by tim, Fri Aug 15 19:24:13 2003 UTC vs.
Revision 1031 by tim, Fri Feb 6 18:58:06 2004 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 20 | Line 20 | inline double roundMe( double x ){
20    return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
21   }
22            
23 + inline double min( double a, double b ){
24 +  return (a < b ) ? a : b;
25 + }
26  
27   SimInfo* currentInfo;
28  
# Line 37 | Line 40 | SimInfo::SimInfo(){
40    thermalTime = 0.0;
41    currentTime = 0.0;
42    rCut = 0.0;
40 –  origRcut = -1.0;
43    ecr = 0.0;
42 –  origEcr = -1.0;
44    est = 0.0;
44 –  oldEcr = 0.0;
45 –  oldRcut = 0.0;
45  
46 <  haveOrigRcut = 0;
47 <  haveOrigEcr = 0;
46 >  haveRcut = 0;
47 >  haveEcr = 0;
48    boxIsInit = 0;
49    
50 <  
50 >  resetTime = 1e99;
51  
52 +  orthoTolerance = 1E-6;
53 +  useInitXSstate = true;
54 +
55    usePBC = 0;
56    useLJ = 0;
57    useSticky = 0;
58 <  useDipole = 0;
58 >  useCharges = 0;
59 >  useDipoles = 0;
60    useReactionField = 0;
61    useGB = 0;
62    useEAM = 0;
63  
64    myConfiguration = new SimState();
65  
66 +  has_minimizer = false;
67 +  the_minimizer =NULL;
68 +
69    wrapMeSimInfo( this );
70   }
71  
# Line 93 | Line 99 | void SimInfo::setBoxM( double theBox[3][3] ){
99  
100   void SimInfo::setBoxM( double theBox[3][3] ){
101    
102 <  int i, j, status;
97 <  double smallestBoxL, maxCutoff;
102 >  int i, j;
103    double FortranHmat[9]; // to preserve compatibility with Fortran the
104                           // ordering in the array is as follows:
105                           // [ 0 3 6 ]
# Line 102 | Line 107 | void SimInfo::setBoxM( double theBox[3][3] ){
107                           // [ 2 5 8 ]
108    double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
109  
105 –  
110    if( !boxIsInit ) boxIsInit = 1;
111  
112    for(i=0; i < 3; i++)
# Line 146 | Line 150 | void SimInfo::calcHmatInv( void ) {
150  
151   void SimInfo::calcHmatInv( void ) {
152    
153 +  int oldOrtho;
154    int i,j;
155    double smallDiag;
156    double tol;
# Line 153 | Line 158 | void SimInfo::calcHmatInv( void ) {
158  
159    invertMat3( Hmat, HmatInv );
160  
156 –  // Check the inverse to make sure it is sane:
157 –
158 –  matMul3( Hmat, HmatInv, sanity );
159 –    
161    // check to see if Hmat is orthorhombic
162    
163 <  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;
163 >  oldOrtho = orthoRhombic;
164  
165 +  smallDiag = fabs(Hmat[0][0]);
166 +  if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
167 +  if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
168 +  tol = smallDiag * orthoTolerance;
169 +
170    orthoRhombic = 1;
171    
172    for (i = 0; i < 3; i++ ) {
173      for (j = 0 ; j < 3; j++) {
174        if (i != j) {
175          if (orthoRhombic) {
176 <          if (Hmat[i][j] >= tol) orthoRhombic = 0;
176 >          if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
177          }        
178        }
179      }
180    }
181 +
182 +  if( oldOrtho != orthoRhombic ){
183 +    
184 +    if( orthoRhombic ){
185 +      sprintf( painCave.errMsg,
186 +               "Hmat is switching from Non-Orthorhombic to Orthorhombic Box.\n"
187 +               "\tIf this is a bad thing, change the orthoBoxTolerance\n"
188 +               "\tvariable ( currently set to %G ).\n",
189 +               orthoTolerance);
190 +      simError();
191 +    }
192 +    else {
193 +      sprintf( painCave.errMsg,
194 +               "Hmat is switching from Orthorhombic to Non-Orthorhombic Box.\n"
195 +               "\tIf this is a bad thing, change the orthoBoxTolerance\n"
196 +               "\tvariable ( currently set to %G ).\n",
197 +               orthoTolerance);
198 +      simError();
199 +    }
200 +  }
201   }
202  
203   double SimInfo::matDet3(double a[3][3]) {
# Line 279 | Line 302 | void SimInfo::printMat9(double A[9] ){
302              << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
303              << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
304              << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
305 + }
306 +
307 +
308 + void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){
309 +
310 +      out[0] = a[1] * b[2] - a[2] * b[1];
311 +      out[1] = a[2] * b[0] - a[0] * b[2] ;
312 +      out[2] = a[0] * b[1] - a[1] * b[0];
313 +      
314 + }
315 +
316 + double SimInfo::dotProduct3(double a[3], double b[3]){
317 +  return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2];
318   }
319  
320 + double SimInfo::length3(double a[3]){
321 +  return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]);
322 + }
323 +
324   void SimInfo::calcBoxL( void ){
325  
326    double dx, dy, dz, dsq;
287 –  int i;
327  
328    // boxVol = Determinant of Hmat
329  
# Line 295 | Line 334 | void SimInfo::calcBoxL( void ){
334    dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
335    dsq = dx*dx + dy*dy + dz*dz;
336    boxL[0] = sqrt( dsq );
337 <  maxCutoff = 0.5 * boxL[0];
337 >  //maxCutoff = 0.5 * boxL[0];
338  
339    // boxLy
340    
341    dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
342    dsq = dx*dx + dy*dy + dz*dz;
343    boxL[1] = sqrt( dsq );
344 <  if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
344 >  //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
345  
346 +
347    // boxLz
348    
349    dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
350    dsq = dx*dx + dy*dy + dz*dz;
351    boxL[2] = sqrt( dsq );
352 <  if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
352 >  //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
353 >
354 >  //calculate the max cutoff
355 >  maxCutoff =  calcMaxCutOff();
356    
357    checkCutOffs();
358  
359   }
360  
361  
362 + double SimInfo::calcMaxCutOff(){
363 +
364 +  double ri[3], rj[3], rk[3];
365 +  double rij[3], rjk[3], rki[3];
366 +  double minDist;
367 +
368 +  ri[0] = Hmat[0][0];
369 +  ri[1] = Hmat[1][0];
370 +  ri[2] = Hmat[2][0];
371 +
372 +  rj[0] = Hmat[0][1];
373 +  rj[1] = Hmat[1][1];
374 +  rj[2] = Hmat[2][1];
375 +
376 +  rk[0] = Hmat[0][2];
377 +  rk[1] = Hmat[1][2];
378 +  rk[2] = Hmat[2][2];
379 +  
380 +  crossProduct3(ri,rj, rij);
381 +  distXY = dotProduct3(rk,rij) / length3(rij);
382 +
383 +  crossProduct3(rj,rk, rjk);
384 +  distYZ = dotProduct3(ri,rjk) / length3(rjk);
385 +
386 +  crossProduct3(rk,ri, rki);
387 +  distZX = dotProduct3(rj,rki) / length3(rki);
388 +
389 +  minDist = min(min(distXY, distYZ), distZX);
390 +  return minDist/2;
391 +  
392 + }
393 +
394   void SimInfo::wrapVector( double thePos[3] ){
395  
396 <  int i, j, k;
396 >  int i;
397    double scaled[3];
398  
399    if( !orthoRhombic ){
# Line 356 | Line 431 | int SimInfo::getNDF(){
431  
432  
433   int SimInfo::getNDF(){
434 <  int ndf_local, ndf;
434 >  int ndf_local;
435    
436    ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
437  
# Line 372 | Line 447 | int SimInfo::getNDFraw() {
447   }
448  
449   int SimInfo::getNDFraw() {
450 <  int ndfRaw_local, ndfRaw;
450 >  int ndfRaw_local;
451  
452    // Raw degrees of freedom that we have to set
453    ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
# Line 385 | Line 460 | int SimInfo::getNDFraw() {
460  
461    return ndfRaw;
462   }
463 <
463 >
464 > int SimInfo::getNDFtranslational() {
465 >  int ndfTrans_local;
466 >
467 >  ndfTrans_local = 3 * n_atoms - n_constraints;
468 >
469 > #ifdef IS_MPI
470 >  MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
471 > #else
472 >  ndfTrans = ndfTrans_local;
473 > #endif
474 >
475 >  ndfTrans = ndfTrans - 3 - nZconstraints;
476 >
477 >  return ndfTrans;
478 > }
479 >
480   void SimInfo::refreshSim(){
481  
482    simtype fInfo;
# Line 395 | Line 486 | void SimInfo::refreshSim(){
486  
487    fInfo.dielect = 0.0;
488  
489 <  if( useDipole ){
489 >  if( useDipoles ){
490      if( useReactionField )fInfo.dielect = dielectric;
491    }
492  
# Line 404 | Line 495 | void SimInfo::refreshSim(){
495    fInfo.SIM_uses_LJ = useLJ;
496    fInfo.SIM_uses_sticky = useSticky;
497    //fInfo.SIM_uses_sticky = 0;
498 <  fInfo.SIM_uses_dipoles = useDipole;
498 >  fInfo.SIM_uses_charges = useCharges;
499 >  fInfo.SIM_uses_dipoles = useDipoles;
500    //fInfo.SIM_uses_dipoles = 0;
501 <  //fInfo.SIM_uses_RF = useReactionField;
502 <  fInfo.SIM_uses_RF = 0;
501 >  fInfo.SIM_uses_RF = useReactionField;
502 >  //fInfo.SIM_uses_RF = 0;
503    fInfo.SIM_uses_GB = useGB;
504    fInfo.SIM_uses_EAM = useEAM;
505  
# Line 441 | Line 533 | void SimInfo::refreshSim(){
533  
534    this->ndf = this->getNDF();
535    this->ndfRaw = this->getNDFraw();
536 <
536 >  this->ndfTrans = this->getNDFtranslational();
537   }
538  
539 + void SimInfo::setDefaultRcut( double theRcut ){
540  
541 < void SimInfo::setRcut( double theRcut ){
541 >  haveRcut = 1;
542 >  rCut = theRcut;
543  
544 <  if( !haveOrigRcut ){
451 <    haveOrigRcut = 1;
452 <    origRcut = theRcut;
453 <  }
544 >  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
545  
546 <  rCut = theRcut;
456 <  checkCutOffs();
546 >  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
547   }
548  
549 < void SimInfo::setEcr( double theEcr ){
549 > void SimInfo::setDefaultEcr( double theEcr ){
550  
551 <  if( !haveOrigEcr ){
462 <    haveOrigEcr = 1;
463 <    origEcr = theEcr;
464 <  }
465 <
551 >  haveEcr = 1;
552    ecr = theEcr;
553 <  checkCutOffs();
553 >  
554 >  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
555 >
556 >  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
557   }
558  
559 < void SimInfo::setEcr( double theEcr, double theEst ){
559 > void SimInfo::setDefaultEcr( double theEcr, double theEst ){
560  
561    est = theEst;
562 <  setEcr( theEcr );
562 >  setDefaultEcr( theEcr );
563   }
564  
565  
566   void SimInfo::checkCutOffs( void ){
567 <
479 <  int cutChanged = 0;
480 <
481 <
482 <
567 >  
568    if( boxIsInit ){
569      
570      //we need to check cutOffs against the box
571 <  
572 <    if(( maxCutoff > rCut )&&(usePBC)){
573 <      if( rCut < origRcut ){
574 <        rCut = origRcut;
575 <        if (rCut > maxCutoff) rCut = maxCutoff;
576 <        
577 <        sprintf( painCave.errMsg,
578 <                 "New Box size is setting the long range cutoff radius "
579 <                 "to %lf\n",
580 <                 rCut );
581 <        painCave.isFatal = 0;
582 <        simError();
583 <      }
571 >    
572 >    if( rCut > maxCutoff ){
573 >      sprintf( painCave.errMsg,
574 >               "Box size is too small for the long range cutoff radius, "
575 >               "%G, at time %G\n"
576 >               "\t[ %G %G %G ]\n"
577 >               "\t[ %G %G %G ]\n"
578 >               "\t[ %G %G %G ]\n",
579 >               rCut, currentTime,
580 >               Hmat[0][0], Hmat[0][1], Hmat[0][2],
581 >               Hmat[1][0], Hmat[1][1], Hmat[1][2],
582 >               Hmat[2][0], Hmat[2][1], Hmat[2][2]);
583 >      painCave.isFatal = 1;
584 >      simError();
585      }
586 <
587 <    if( maxCutoff > ecr ){
588 <      if( ecr < origEcr ){
503 <        rCut = origEcr;
504 <        if (ecr > maxCutoff) ecr = maxCutoff;
505 <        
586 >    
587 >    if( haveEcr ){
588 >      if( ecr > maxCutoff ){
589          sprintf( painCave.errMsg,
590 <                 "New Box size is setting the electrostaticCutoffRadius "
591 <                 "to %lf\n",
592 <                 ecr );
593 <        painCave.isFatal = 0;
590 >                 "Box size is too small for the electrostatic cutoff radius, "
591 >                 "%G, at time %G\n"
592 >                 "\t[ %G %G %G ]\n"
593 >                 "\t[ %G %G %G ]\n"
594 >                 "\t[ %G %G %G ]\n",
595 >                 ecr, currentTime,
596 >                 Hmat[0][0], Hmat[0][1], Hmat[0][2],
597 >                 Hmat[1][0], Hmat[1][1], Hmat[1][2],
598 >                 Hmat[2][0], Hmat[2][1], Hmat[2][2]);
599 >        painCave.isFatal = 1;
600          simError();
601        }
602      }
603 <
604 <
605 <    if ((rCut > maxCutoff)&&(usePBC)) {
606 <      sprintf( painCave.errMsg,
607 <               "New Box size is setting the long range cutoff radius "
608 <               "to %lf\n",
609 <               maxCutoff );
521 <      painCave.isFatal = 0;
522 <      simError();
523 <      rCut = maxCutoff;
524 <    }
525 <
526 <    if( ecr > maxCutoff){
527 <      sprintf( painCave.errMsg,
528 <               "New Box size is setting the electrostaticCutoffRadius "
529 <               "to %lf\n",
530 <               maxCutoff  );
531 <      painCave.isFatal = 0;
532 <      simError();      
533 <      ecr = maxCutoff;
534 <    }
535 <
536 <    
603 >  } else {
604 >    // initialize this stuff before using it, OK?
605 >    sprintf( painCave.errMsg,
606 >             "Trying to check cutoffs without a box.\n"
607 >             "\tOOPSE should have better programmers than that.\n" );
608 >    painCave.isFatal = 1;
609 >    simError();      
610    }
538 –  
539 –
540 –  if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
541 –
542 –  // rlist is the 1.0 plus max( rcut, ecr )
611    
544 –  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
545 –
546 –  if( cutChanged ){
547 –    
548 –    notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
549 –  }
550 –
551 –  oldEcr = ecr;
552 –  oldRcut = rCut;
612   }
613  
614   void SimInfo::addProperty(GenericData* prop){
# Line 599 | Line 658 | vector<GenericData*> SimInfo::getProperties(){
658    return result;
659   }
660  
661 + double SimInfo::matTrace3(double m[3][3]){
662 +  double trace;
663 +  trace = m[0][0] + m[1][1] + m[2][2];
664  
665 +  return trace;
666 + }

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