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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 670 by mmeineke, Thu Aug 7 21:47:18 2003 UTC vs.
Revision 965 by gezelter, Mon Jan 19 21:17:39 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  
29   SimInfo::SimInfo(){
30    excludes = NULL;
31    n_constraints = 0;
32 +  nZconstraints = 0;
33    n_oriented = 0;
34    n_dipoles = 0;
35    ndf = 0;
36    ndfRaw = 0;
37 +  nZconstraints = 0;
38    the_integrator = NULL;
39    setTemp = 0;
40    thermalTime = 0.0;
# Line 37 | Line 42 | SimInfo::SimInfo(){
42    rCut = 0.0;
43    ecr = 0.0;
44    est = 0.0;
40 –  oldEcr = 0.0;
41 –  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;
# Line 89 | Line 96 | void SimInfo::setBoxM( double theBox[3][3] ){
96  
97   void SimInfo::setBoxM( double theBox[3][3] ){
98    
99 <  int i, j, status;
93 <  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 98 | Line 104 | void SimInfo::setBoxM( double theBox[3][3] ){
104                           // [ 2 5 8 ]
105    double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
106  
101 –  
107    if( !boxIsInit ) boxIsInit = 1;
108  
109    for(i=0; i < 3; i++)
# Line 142 | Line 147 | void SimInfo::calcHmatInv( void ) {
147  
148   void SimInfo::calcHmatInv( void ) {
149    
150 +  int oldOrtho;
151    int i,j;
152    double smallDiag;
153    double tol;
# Line 149 | Line 155 | void SimInfo::calcHmatInv( void ) {
155  
156    invertMat3( Hmat, HmatInv );
157  
152 –  // Check the inverse to make sure it is sane:
153 –
154 –  matMul3( Hmat, HmatInv, sanity );
155 –    
158    // check to see if Hmat is orthorhombic
159    
160 <  smallDiag = Hmat[0][0];
159 <  if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1];
160 <  if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2];
161 <  tol = smallDiag * 1E-6;
160 >  oldOrtho = orthoRhombic;
161  
162 +  smallDiag = fabs(Hmat[0][0]);
163 +  if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
164 +  if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
165 +  tol = smallDiag * orthoTolerance;
166 +
167    orthoRhombic = 1;
168    
169    for (i = 0; i < 3; i++ ) {
170      for (j = 0 ; j < 3; j++) {
171        if (i != j) {
172          if (orthoRhombic) {
173 <          if (Hmat[i][j] >= tol) orthoRhombic = 0;
173 >          if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
174          }        
175        }
176      }
177    }
178 +
179 +  if( oldOrtho != orthoRhombic ){
180 +    
181 +    if( orthoRhombic ){
182 +      sprintf( painCave.errMsg,
183 +               "Hmat is switching from Non-Orthorhombic to Orthorhombic Box.\n"
184 +               "\tIf this is a bad thing, change the orthoBoxTolerance\n"
185 +               "\tvariable ( currently set to %G ).\n",
186 +               orthoTolerance);
187 +      simError();
188 +    }
189 +    else {
190 +      sprintf( painCave.errMsg,
191 +               "Hmat is switching from Orthorhombic to Non-Orthorhombic Box.\n"
192 +               "\tIf this is a bad thing, change the orthoBoxTolerance\n"
193 +               "\tvariable ( currently set to %G ).\n",
194 +               orthoTolerance);
195 +      simError();
196 +    }
197 +  }
198   }
199  
200   double SimInfo::matDet3(double a[3][3]) {
# Line 275 | Line 299 | void SimInfo::printMat9(double A[9] ){
299              << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
300              << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
301              << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
302 + }
303 +
304 +
305 + void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){
306 +
307 +      out[0] = a[1] * b[2] - a[2] * b[1];
308 +      out[1] = a[2] * b[0] - a[0] * b[2] ;
309 +      out[2] = a[0] * b[1] - a[1] * b[0];
310 +      
311 + }
312 +
313 + double SimInfo::dotProduct3(double a[3], double b[3]){
314 +  return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2];
315   }
316  
317 + double SimInfo::length3(double a[3]){
318 +  return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]);
319 + }
320 +
321   void SimInfo::calcBoxL( void ){
322  
323    double dx, dy, dz, dsq;
283 –  int i;
324  
325    // boxVol = Determinant of Hmat
326  
# Line 291 | Line 331 | void SimInfo::calcBoxL( void ){
331    dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
332    dsq = dx*dx + dy*dy + dz*dz;
333    boxL[0] = sqrt( dsq );
334 <  maxCutoff = 0.5 * boxL[0];
334 >  //maxCutoff = 0.5 * boxL[0];
335  
336    // boxLy
337    
338    dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
339    dsq = dx*dx + dy*dy + dz*dz;
340    boxL[1] = sqrt( dsq );
341 <  if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
341 >  //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
342  
343 +
344    // boxLz
345    
346    dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
347    dsq = dx*dx + dy*dy + dz*dz;
348    boxL[2] = sqrt( dsq );
349 <  if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
349 >  //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
350 >
351 >  //calculate the max cutoff
352 >  maxCutoff =  calcMaxCutOff();
353    
354    checkCutOffs();
355  
356   }
357  
358  
359 + double SimInfo::calcMaxCutOff(){
360 +
361 +  double ri[3], rj[3], rk[3];
362 +  double rij[3], rjk[3], rki[3];
363 +  double minDist;
364 +
365 +  ri[0] = Hmat[0][0];
366 +  ri[1] = Hmat[1][0];
367 +  ri[2] = Hmat[2][0];
368 +
369 +  rj[0] = Hmat[0][1];
370 +  rj[1] = Hmat[1][1];
371 +  rj[2] = Hmat[2][1];
372 +
373 +  rk[0] = Hmat[0][2];
374 +  rk[1] = Hmat[1][2];
375 +  rk[2] = Hmat[2][2];
376 +  
377 +  crossProduct3(ri,rj, rij);
378 +  distXY = dotProduct3(rk,rij) / length3(rij);
379 +
380 +  crossProduct3(rj,rk, rjk);
381 +  distYZ = dotProduct3(ri,rjk) / length3(rjk);
382 +
383 +  crossProduct3(rk,ri, rki);
384 +  distZX = dotProduct3(rj,rki) / length3(rki);
385 +
386 +  minDist = min(min(distXY, distYZ), distZX);
387 +  return minDist/2;
388 +  
389 + }
390 +
391   void SimInfo::wrapVector( double thePos[3] ){
392  
393 <  int i, j, k;
393 >  int i;
394    double scaled[3];
395  
396    if( !orthoRhombic ){
# Line 352 | Line 428 | int SimInfo::getNDF(){
428  
429  
430   int SimInfo::getNDF(){
431 <  int ndf_local, ndf;
431 >  int ndf_local;
432    
433    ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
434  
# Line 362 | Line 438 | int SimInfo::getNDF(){
438    ndf = ndf_local;
439   #endif
440  
441 <  ndf = ndf - 3;
441 >  ndf = ndf - 3 - nZconstraints;
442  
443    return ndf;
444   }
445  
446   int SimInfo::getNDFraw() {
447 <  int ndfRaw_local, ndfRaw;
447 >  int ndfRaw_local;
448  
449    // Raw degrees of freedom that we have to set
450    ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
# Line 381 | Line 457 | int SimInfo::getNDFraw() {
457  
458    return ndfRaw;
459   }
460 <
460 >
461 > int SimInfo::getNDFtranslational() {
462 >  int ndfTrans_local;
463 >
464 >  ndfTrans_local = 3 * n_atoms - n_constraints;
465 >
466 > #ifdef IS_MPI
467 >  MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
468 > #else
469 >  ndfTrans = ndfTrans_local;
470 > #endif
471 >
472 >  ndfTrans = ndfTrans - 3 - nZconstraints;
473 >
474 >  return ndfTrans;
475 > }
476 >
477   void SimInfo::refreshSim(){
478  
479    simtype fInfo;
# Line 391 | Line 483 | void SimInfo::refreshSim(){
483  
484    fInfo.dielect = 0.0;
485  
486 <  if( useDipole ){
486 >  if( useDipoles ){
487      if( useReactionField )fInfo.dielect = dielectric;
488    }
489  
# Line 400 | Line 492 | void SimInfo::refreshSim(){
492    fInfo.SIM_uses_LJ = useLJ;
493    fInfo.SIM_uses_sticky = useSticky;
494    //fInfo.SIM_uses_sticky = 0;
495 <  fInfo.SIM_uses_dipoles = useDipole;
495 >  fInfo.SIM_uses_charges = useCharges;
496 >  fInfo.SIM_uses_dipoles = useDipoles;
497    //fInfo.SIM_uses_dipoles = 0;
498    //fInfo.SIM_uses_RF = useReactionField;
499    fInfo.SIM_uses_RF = 0;
# Line 437 | Line 530 | void SimInfo::refreshSim(){
530  
531    this->ndf = this->getNDF();
532    this->ndfRaw = this->getNDFraw();
533 <
533 >  this->ndfTrans = this->getNDFtranslational();
534   }
535  
536 + void SimInfo::setDefaultRcut( double theRcut ){
537  
538 < void SimInfo::setRcut( double theRcut ){
538 >  haveRcut = 1;
539 >  rCut = theRcut;
540  
541 <  if( !haveOrigRcut ){
447 <    haveOrigRcut = 1;
448 <    origRcut = theRcut;
449 <  }
541 >  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
542  
543 <  rCut = theRcut;
452 <  checkCutOffs();
543 >  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
544   }
545  
546 < void SimInfo::setEcr( double theEcr ){
546 > void SimInfo::setDefaultEcr( double theEcr ){
547  
548 <  if( !haveOrigEcr ){
458 <    haveOrigEcr = 1;
459 <    origEcr = theEcr;
460 <  }
461 <
548 >  haveEcr = 1;
549    ecr = theEcr;
550 <  checkCutOffs();
550 >  
551 >  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
552 >
553 >  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
554   }
555  
556 < void SimInfo::setEcr( double theEcr, double theEst ){
556 > void SimInfo::setDefaultEcr( double theEcr, double theEst ){
557  
558    est = theEst;
559 <  setEcr( theEcr );
559 >  setDefaultEcr( theEcr );
560   }
561  
562  
563   void SimInfo::checkCutOffs( void ){
564 <
475 <  int cutChanged = 0;
476 <
477 <
478 <
564 >  
565    if( boxIsInit ){
566      
567      //we need to check cutOffs against the box
568 <  
569 <    if(( maxCutoff > rCut )&&(usePBC)){
570 <      if( rCut < origRcut ){
571 <        rCut = origRcut;
572 <        if (rCut > maxCutoff) rCut = maxCutoff;
573 <        
574 <        sprintf( painCave.errMsg,
575 <                 "New Box size is setting the long range cutoff radius "
576 <                 "to %lf\n",
577 <                 rCut );
578 <        painCave.isFatal = 0;
579 <        simError();
580 <      }
568 >    
569 >    if( rCut > maxCutoff ){
570 >      sprintf( painCave.errMsg,
571 >               "Box size is too small for the long range cutoff radius, "
572 >               "%G, at time %G\n"
573 >               "\t[ %G %G %G ]\n"
574 >               "\t[ %G %G %G ]\n"
575 >               "\t[ %G %G %G ]\n",
576 >               rCut, currentTime,
577 >               Hmat[0][0], Hmat[0][1], Hmat[0][2],
578 >               Hmat[1][0], Hmat[1][1], Hmat[1][2],
579 >               Hmat[2][0], Hmat[2][1], Hmat[2][2]);
580 >      painCave.isFatal = 1;
581 >      simError();
582      }
583 <
584 <    if( maxCutoff > ecr ){
585 <      if( ecr < origEcr ){
499 <        rCut = origEcr;
500 <        if (ecr > maxCutoff) ecr = maxCutoff;
501 <        
583 >    
584 >    if( haveEcr ){
585 >      if( ecr > maxCutoff ){
586          sprintf( painCave.errMsg,
587 <                 "New Box size is setting the electrostaticCutoffRadius "
588 <                 "to %lf\n",
589 <                 ecr );
590 <        painCave.isFatal = 0;
587 >                 "Box size is too small for the electrostatic cutoff radius, "
588 >                 "%G, at time %G\n"
589 >                 "\t[ %G %G %G ]\n"
590 >                 "\t[ %G %G %G ]\n"
591 >                 "\t[ %G %G %G ]\n",
592 >                 ecr, currentTime,
593 >                 Hmat[0][0], Hmat[0][1], Hmat[0][2],
594 >                 Hmat[1][0], Hmat[1][1], Hmat[1][2],
595 >                 Hmat[2][0], Hmat[2][1], Hmat[2][2]);
596 >        painCave.isFatal = 1;
597          simError();
598        }
599      }
600 <
601 <
602 <    if ((rCut > maxCutoff)&&(usePBC)) {
603 <      sprintf( painCave.errMsg,
604 <               "New Box size is setting the long range cutoff radius "
605 <               "to %lf\n",
606 <               maxCutoff );
517 <      painCave.isFatal = 0;
518 <      simError();
519 <      rCut = maxCutoff;
520 <    }
521 <
522 <    if( ecr > maxCutoff){
523 <      sprintf( painCave.errMsg,
524 <               "New Box size is setting the electrostaticCutoffRadius "
525 <               "to %lf\n",
526 <               maxCutoff  );
527 <      painCave.isFatal = 0;
528 <      simError();      
529 <      ecr = maxCutoff;
530 <    }
531 <
532 <    
600 >  } else {
601 >    // initialize this stuff before using it, OK?
602 >    sprintf( painCave.errMsg,
603 >             "Trying to check cutoffs without a box.\n"
604 >             "\tOOPSE should have better programmers than that.\n" );
605 >    painCave.isFatal = 1;
606 >    simError();      
607    }
534 –  
535 –
536 –  if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
537 –
538 –  // rlist is the 1.0 plus max( rcut, ecr )
608    
540 –  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
541 –
542 –  if( cutChanged ){
543 –    
544 –    notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
545 –  }
546 –
547 –  oldEcr = ecr;
548 –  oldRcut = rCut;
609   }
610  
611   void SimInfo::addProperty(GenericData* prop){
# Line 595 | Line 655 | vector<GenericData*> SimInfo::getProperties(){
655    return result;
656   }
657  
658 + double SimInfo::matTrace3(double m[3][3]){
659 +  double trace;
660 +  trace = m[0][0] + m[1][1] + m[2][2];
661  
662 +  return trace;
663 + }

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