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root/group/branches/new-templateless/OOPSE/libmdtools/SimInfo.cpp
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Comparing:
trunk/OOPSE/libmdtools/SimInfo.cpp (file contents), Revision 618 by mmeineke, Tue Jul 15 21:34:56 2003 UTC vs.
branches/new-templateless/OOPSE/libmdtools/SimInfo.cpp (file contents), Revision 850 by mmeineke, Mon Nov 3 22:07:17 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;
46  
47 +  haveOrigRcut = 0;
48 +  haveOrigEcr = 0;
49 +  boxIsInit = 0;
50 +  
51 +  resetTime = 1e99;
52 +  
53 +
54    usePBC = 0;
55    useLJ = 0;
56    useSticky = 0;
# Line 44 | Line 59 | SimInfo::SimInfo(){
59    useGB = 0;
60    useEAM = 0;
61  
62 +  myConfiguration = new SimState();
63 +
64 +  properties = new GenericData();
65 +
66    wrapMeSimInfo( this );
67   }
68  
69 +
70 + SimInfo::~SimInfo(){
71 +
72 +  delete myConfiguration;
73 +  delete properties;    
74 + }
75 +
76   void SimInfo::setBox(double newBox[3]) {
77    
78    int i, j;
# Line 65 | Line 91 | void SimInfo::setBoxM( double theBox[3][3] ){
91  
92   void SimInfo::setBoxM( double theBox[3][3] ){
93    
94 <  int i, j, status;
69 <  double smallestBoxL, maxCutoff;
94 >  int i, j;
95    double FortranHmat[9]; // to preserve compatibility with Fortran the
96                           // ordering in the array is as follows:
97                           // [ 0 3 6 ]
# Line 74 | Line 99 | void SimInfo::setBoxM( double theBox[3][3] ){
99                           // [ 2 5 8 ]
100    double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
101  
102 +  
103 +  if( !boxIsInit ) boxIsInit = 1;
104  
105    for(i=0; i < 3; i++)
106      for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
107    
81 –  //  cerr
82 –  // << "setting Hmat ->\n"
83 –  // << "[ " << Hmat[0][0] << ", " << Hmat[0][1] << ", " << Hmat[0][2] << " ]\n"
84 –  // << "[ " << Hmat[1][0] << ", " << Hmat[1][1] << ", " << Hmat[1][2] << " ]\n"
85 –  // << "[ " << Hmat[2][0] << ", " << Hmat[2][1] << ", " << Hmat[2][2] << " ]\n";
86 –
108    calcBoxL();
109    calcHmatInv();
110  
# Line 96 | Line 117 | void SimInfo::setBoxM( double theBox[3][3] ){
117  
118    setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
119  
99 –  smallestBoxL = boxLx;
100 –  if (boxLy < smallestBoxL) smallestBoxL = boxLy;
101 –  if (boxLz < smallestBoxL) smallestBoxL = boxLz;
102 –
103 –  maxCutoff = smallestBoxL / 2.0;
104 –
105 –  if (rList > maxCutoff) {
106 –    sprintf( painCave.errMsg,
107 –             "New Box size is forcing neighborlist radius down to %lf\n",
108 –             maxCutoff );
109 –    painCave.isFatal = 0;
110 –    simError();
111 –
112 –    rList = maxCutoff;
113 –
114 –    sprintf( painCave.errMsg,
115 –             "New Box size is forcing cutoff radius down to %lf\n",
116 –             maxCutoff - 1.0 );
117 –    painCave.isFatal = 0;
118 –    simError();
119 –
120 –    rCut = rList - 1.0;
121 –
122 –    // list radius changed so we have to refresh the simulation structure.
123 –    refreshSim();
124 –  }
125 –
126 –  if( ecr > maxCutoff ){
127 –
128 –    sprintf( painCave.errMsg,
129 –             "New Box size is forcing electrostatic cutoff radius "
130 –             "down to %lf\n",
131 –             maxCutoff );
132 –    painCave.isFatal = 0;
133 –    simError();
134 –
135 –    ecr = maxCutoff;
136 –    est = 0.05 * ecr;
137 –
138 –    refreshSim();
139 –  }
140 –    
120   }
121  
122  
# Line 299 | Line 278 | void SimInfo::printMat9(double A[9] ){
278              << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
279   }
280  
281 +
282 + void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){
283 +
284 +      out[0] = a[1] * b[2] - a[2] * b[1];
285 +      out[1] = a[2] * b[0] - a[0] * b[2] ;
286 +      out[2] = a[0] * b[1] - a[1] * b[0];
287 +      
288 + }
289 +
290 + double SimInfo::dotProduct3(double a[3], double b[3]){
291 +  return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2];
292 + }
293 +
294 + double SimInfo::length3(double a[3]){
295 +  return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]);
296 + }
297 +
298   void SimInfo::calcBoxL( void ){
299  
300    double dx, dy, dz, dsq;
305 –  int i;
301  
302    // boxVol = Determinant of Hmat
303  
# Line 312 | Line 307 | void SimInfo::calcBoxL( void ){
307    
308    dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
309    dsq = dx*dx + dy*dy + dz*dz;
310 <  boxLx = sqrt( dsq );
310 >  boxL[0] = sqrt( dsq );
311 >  //maxCutoff = 0.5 * boxL[0];
312  
313    // boxLy
314    
315    dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
316    dsq = dx*dx + dy*dy + dz*dz;
317 <  boxLy = sqrt( dsq );
317 >  boxL[1] = sqrt( dsq );
318 >  //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
319  
320 +
321    // boxLz
322    
323    dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
324    dsq = dx*dx + dy*dy + dz*dz;
325 <  boxLz = sqrt( dsq );
325 >  boxL[2] = sqrt( dsq );
326 >  //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
327 >
328 >  //calculate the max cutoff
329 >  maxCutoff =  calcMaxCutOff();
330    
331 +  checkCutOffs();
332 +
333   }
334 +
335 +
336 + double SimInfo::calcMaxCutOff(){
337 +
338 +  double ri[3], rj[3], rk[3];
339 +  double rij[3], rjk[3], rki[3];
340 +  double minDist;
341  
342 +  ri[0] = Hmat[0][0];
343 +  ri[1] = Hmat[1][0];
344 +  ri[2] = Hmat[2][0];
345  
346 +  rj[0] = Hmat[0][1];
347 +  rj[1] = Hmat[1][1];
348 +  rj[2] = Hmat[2][1];
349 +
350 +  rk[0] = Hmat[0][2];
351 +  rk[1] = Hmat[1][2];
352 +  rk[2] = Hmat[2][2];
353 +  
354 +  crossProduct3(ri,rj, rij);
355 +  distXY = dotProduct3(rk,rij) / length3(rij);
356 +
357 +  crossProduct3(rj,rk, rjk);
358 +  distYZ = dotProduct3(ri,rjk) / length3(rjk);
359 +
360 +  crossProduct3(rk,ri, rki);
361 +  distZX = dotProduct3(rj,rki) / length3(rki);
362 +
363 +  minDist = min(min(distXY, distYZ), distZX);
364 +  return minDist/2;
365 +  
366 + }
367 +
368   void SimInfo::wrapVector( double thePos[3] ){
369  
370 <  int i, j, k;
370 >  int i;
371    double scaled[3];
372  
373    if( !orthoRhombic ){
# Line 369 | Line 405 | int SimInfo::getNDF(){
405  
406  
407   int SimInfo::getNDF(){
408 <  int ndf_local, ndf;
408 >  int ndf_local;
409    
410    ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
411  
# Line 379 | Line 415 | int SimInfo::getNDF(){
415    ndf = ndf_local;
416   #endif
417  
418 <  ndf = ndf - 3;
418 >  ndf = ndf - 3 - nZconstraints;
419  
420    return ndf;
421   }
422  
423   int SimInfo::getNDFraw() {
424 <  int ndfRaw_local, ndfRaw;
424 >  int ndfRaw_local;
425  
426    // Raw degrees of freedom that we have to set
427    ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
# Line 398 | Line 434 | int SimInfo::getNDFraw() {
434  
435    return ndfRaw;
436   }
437 <
437 >
438 > int SimInfo::getNDFtranslational() {
439 >  int ndfTrans_local;
440 >
441 >  ndfTrans_local = 3 * n_atoms - n_constraints;
442 >
443 > #ifdef IS_MPI
444 >  MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
445 > #else
446 >  ndfTrans = ndfTrans_local;
447 > #endif
448 >
449 >  ndfTrans = ndfTrans - 3 - nZconstraints;
450 >
451 >  return ndfTrans;
452 > }
453 >
454   void SimInfo::refreshSim(){
455  
456    simtype fInfo;
457    int isError;
458    int n_global;
459    int* excl;
460 <  
409 <  fInfo.rrf = 0.0;
410 <  fInfo.rt = 0.0;
460 >
461    fInfo.dielect = 0.0;
462  
413 –  fInfo.rlist = rList;
414 –  fInfo.rcut = rCut;
415 –
463    if( useDipole ){
417 –    fInfo.rrf = ecr;
418 –    fInfo.rt = ecr - est;
464      if( useReactionField )fInfo.dielect = dielectric;
465    }
466  
# Line 461 | Line 506 | void SimInfo::refreshSim(){
506  
507    this->ndf = this->getNDF();
508    this->ndfRaw = this->getNDFraw();
509 +  this->ndfTrans = this->getNDFtranslational();
510 + }
511  
512 +
513 + void SimInfo::setRcut( double theRcut ){
514 +
515 +  rCut = theRcut;
516 +  checkCutOffs();
517   }
518  
519 + void SimInfo::setDefaultRcut( double theRcut ){
520 +
521 +  haveOrigRcut = 1;
522 +  origRcut = theRcut;
523 +  rCut = theRcut;
524 +
525 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
526 +
527 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
528 + }
529 +
530 + void SimInfo::setEcr( double theEcr ){
531 +
532 +  ecr = theEcr;
533 +  checkCutOffs();
534 + }
535 +
536 + void SimInfo::setDefaultEcr( double theEcr ){
537 +
538 +  haveOrigEcr = 1;
539 +  origEcr = theEcr;
540 +  
541 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
542 +
543 +  ecr = theEcr;
544 +
545 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
546 + }
547 +
548 + void SimInfo::setEcr( double theEcr, double theEst ){
549 +
550 +  est = theEst;
551 +  setEcr( theEcr );
552 + }
553 +
554 + void SimInfo::setDefaultEcr( double theEcr, double theEst ){
555 +
556 +  est = theEst;
557 +  setDefaultEcr( theEcr );
558 + }
559 +
560 +
561 + void SimInfo::checkCutOffs( void ){
562 +
563 +  int cutChanged = 0;
564 +  
565 +  if( boxIsInit ){
566 +    
567 +    //we need to check cutOffs against the box
568 +
569 +    //detect the change of rCut
570 +    if(( maxCutoff > rCut )&&(usePBC)){
571 +      if( rCut < origRcut ){
572 +        rCut = origRcut;
573 +        
574 +        if (rCut > maxCutoff)
575 +          rCut = maxCutoff;
576 +  
577 +          sprintf( painCave.errMsg,
578 +                    "New Box size is setting the long range cutoff radius "
579 +                    "to %lf at time %lf\n",
580 +                    rCut, currentTime );
581 +          painCave.isFatal = 0;
582 +          simError();
583 +      }
584 +    }
585 +    else if ((rCut > maxCutoff)&&(usePBC)) {
586 +      sprintf( painCave.errMsg,
587 +               "New Box size is setting the long range cutoff radius "
588 +               "to %lf at time %lf\n",
589 +               maxCutoff, currentTime );
590 +      painCave.isFatal = 0;
591 +      simError();
592 +      rCut = maxCutoff;
593 +    }
594 +
595 +
596 +    //detect the change of ecr
597 +    if( maxCutoff > ecr ){
598 +      if( ecr < origEcr ){
599 +        ecr = origEcr;
600 +        if (ecr > maxCutoff) ecr = maxCutoff;
601 +  
602 +          sprintf( painCave.errMsg,
603 +                    "New Box size is setting the electrostaticCutoffRadius "
604 +                    "to %lf at time %lf\n",
605 +                    ecr, currentTime );
606 +            painCave.isFatal = 0;
607 +            simError();
608 +      }
609 +    }
610 +    else if( ecr > maxCutoff){
611 +      sprintf( painCave.errMsg,
612 +               "New Box size is setting the electrostaticCutoffRadius "
613 +               "to %lf at time %lf\n",
614 +               maxCutoff, currentTime  );
615 +      painCave.isFatal = 0;
616 +      simError();      
617 +      ecr = maxCutoff;
618 +    }
619 +
620 +    if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
621 +    
622 +    // rlist is the 1.0 plus max( rcut, ecr )
623 +    
624 +    ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
625 +    
626 +    if( cutChanged ){
627 +      notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
628 +    }
629 +    
630 +    oldEcr = ecr;
631 +    oldRcut = rCut;
632 +    
633 +  } else {
634 +    // initialize this stuff before using it, OK?
635 +    sprintf( painCave.errMsg,
636 +             "Trying to check cutoffs without a box. Be smarter.\n" );
637 +    painCave.isFatal = 1;
638 +    simError();      
639 +  }
640 +  
641 + }
642 +
643 + GenericData* SimInfo::getProperty(char* propName){
644 +
645 +  return properties->find( propName );
646 + }
647 +
648 + double SimInfo::matTrace3(double m[3][3]){
649 +  double trace;
650 +  trace = m[0][0] + m[1][1] + m[2][2];
651 +
652 +  return trace;
653 + }

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