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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 621 by gezelter, Wed Jul 16 02:11:02 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  
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;
41 +  currentTime = 0.0;
42    rCut = 0.0;
43    ecr = 0.0;
44    est = 0.0;
45  
46 +  haveRcut = 0;
47 +  haveEcr = 0;
48 +  boxIsInit = 0;
49 +  
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  
72 +
73 + SimInfo::~SimInfo(){
74 +
75 +  delete myConfiguration;
76 +
77 +  map<string, GenericData*>::iterator i;
78 +  
79 +  for(i = properties.begin(); i != properties.end(); i++)
80 +    delete (*i).second;
81 +    
82 + }
83 +
84   void SimInfo::setBox(double newBox[3]) {
85    
86    int i, j;
# Line 66 | Line 99 | void SimInfo::setBoxM( double theBox[3][3] ){
99  
100   void SimInfo::setBoxM( double theBox[3][3] ){
101    
102 <  int i, j, status;
70 <  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 75 | Line 107 | void SimInfo::setBoxM( double theBox[3][3] ){
107                           // [ 2 5 8 ]
108    double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
109  
110 +  if( !boxIsInit ) boxIsInit = 1;
111  
112    for(i=0; i < 3; i++)
113      for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
114    
82 –  //  cerr
83 –  // << "setting Hmat ->\n"
84 –  // << "[ " << Hmat[0][0] << ", " << Hmat[0][1] << ", " << Hmat[0][2] << " ]\n"
85 –  // << "[ " << Hmat[1][0] << ", " << Hmat[1][1] << ", " << Hmat[1][2] << " ]\n"
86 –  // << "[ " << Hmat[2][0] << ", " << Hmat[2][1] << ", " << Hmat[2][2] << " ]\n";
87 –
115    calcBoxL();
116    calcHmatInv();
117  
# Line 97 | Line 124 | void SimInfo::setBoxM( double theBox[3][3] ){
124  
125    setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
126  
100 –  smallestBoxL = boxL[0];
101 –  if (boxL[1] < smallestBoxL) smallestBoxL = boxL[1];
102 –  if (boxL[2] > smallestBoxL) smallestBoxL = boxL[2];
103 –
104 –  maxCutoff = smallestBoxL / 2.0;
105 –
106 –  if (rList > maxCutoff) {
107 –    sprintf( painCave.errMsg,
108 –             "New Box size is forcing neighborlist radius down to %lf\n",
109 –             maxCutoff );
110 –    painCave.isFatal = 0;
111 –    simError();
112 –    rList = maxCutoff;
113 –
114 –    if (rCut > (rList - 1.0)) {
115 –      sprintf( painCave.errMsg,
116 –               "New Box size is forcing LJ cutoff radius down to %lf\n",
117 –               rList - 1.0 );
118 –      painCave.isFatal = 0;
119 –      simError();
120 –      rCut = rList - 1.0;
121 –    }
122 –
123 –    if( ecr > (rList - 1.0) ){
124 –      sprintf( painCave.errMsg,
125 –               "New Box size is forcing electrostaticCutoffRadius "
126 –               "down to %lf\n"
127 –               "electrostaticSkinThickness is now %lf\n",
128 –               rList - 1.0, 0.05*(rList-1.0) );
129 –      painCave.isFatal = 0;
130 –      simError();      
131 –      ecr = maxCutoff;
132 –      est = 0.05 * ecr;
133 –    }
134 –
135 –    // At least one of the radii changed, so we need a refresh:
136 –    refreshSim();
137 –  }    
127   }
128  
129  
# Line 161 | 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 168 | Line 158 | void SimInfo::calcHmatInv( void ) {
158  
159    invertMat3( Hmat, HmatInv );
160  
171 –  // Check the inverse to make sure it is sane:
172 –
173 –  matMul3( Hmat, HmatInv, sanity );
174 –    
161    // check to see if Hmat is orthorhombic
162    
163 <  smallDiag = Hmat[0][0];
178 <  if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1];
179 <  if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2];
180 <  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 296 | Line 304 | void SimInfo::calcBoxL( void ){
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;
302 –  int i;
327  
328    // boxVol = Determinant of Hmat
329  
# Line 310 | 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];
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];
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];
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 366 | 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 376 | Line 441 | int SimInfo::getNDF(){
441    ndf = ndf_local;
442   #endif
443  
444 <  ndf = ndf - 3;
444 >  ndf = ndf - 3 - nZconstraints;
445  
446    return ndf;
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 395 | 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;
483    int isError;
484    int n_global;
485    int* excl;
486 <  
406 <  fInfo.rrf = 0.0;
407 <  fInfo.rt = 0.0;
486 >
487    fInfo.dielect = 0.0;
488  
489 <  fInfo.rlist = rList;
411 <  fInfo.rcut = rCut;
412 <
413 <  if( useDipole ){
414 <    fInfo.rrf = ecr;
415 <    fInfo.rt = ecr - est;
489 >  if( useDipoles ){
490      if( useReactionField )fInfo.dielect = dielectric;
491    }
492  
# Line 421 | 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 458 | Line 533 | void SimInfo::refreshSim(){
533  
534    this->ndf = this->getNDF();
535    this->ndfRaw = this->getNDFraw();
536 +  this->ndfTrans = this->getNDFtranslational();
537 + }
538  
539 + void SimInfo::setDefaultRcut( double theRcut ){
540 +
541 +  haveRcut = 1;
542 +  rCut = theRcut;
543 +
544 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
545 +
546 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
547   }
548  
549 + void SimInfo::setDefaultEcr( double theEcr ){
550 +
551 +  haveEcr = 1;
552 +  ecr = theEcr;
553 +  
554 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
555 +
556 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
557 + }
558 +
559 + void SimInfo::setDefaultEcr( double theEcr, double theEst ){
560 +
561 +  est = theEst;
562 +  setDefaultEcr( theEcr );
563 + }
564 +
565 +
566 + void SimInfo::checkCutOffs( void ){
567 +  
568 +  if( boxIsInit ){
569 +    
570 +    //we need to check cutOffs against the box
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( haveEcr ){
588 +      if( ecr > maxCutoff ){
589 +        sprintf( painCave.errMsg,
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 +  } 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 +  }
611 +  
612 + }
613 +
614 + void SimInfo::addProperty(GenericData* prop){
615 +
616 +  map<string, GenericData*>::iterator result;
617 +  result = properties.find(prop->getID());
618 +  
619 +  //we can't simply use  properties[prop->getID()] = prop,
620 +  //it will cause memory leak if we already contain a propery which has the same name of prop
621 +  
622 +  if(result != properties.end()){
623 +    
624 +    delete (*result).second;
625 +    (*result).second = prop;
626 +      
627 +  }
628 +  else{
629 +
630 +    properties[prop->getID()] = prop;
631 +
632 +  }
633 +    
634 + }
635 +
636 + GenericData* SimInfo::getProperty(const string& propName){
637 +
638 +  map<string, GenericData*>::iterator result;
639 +  
640 +  //string lowerCaseName = ();
641 +  
642 +  result = properties.find(propName);
643 +  
644 +  if(result != properties.end())
645 +    return (*result).second;  
646 +  else  
647 +    return NULL;  
648 + }
649 +
650 + vector<GenericData*> SimInfo::getProperties(){
651 +
652 +  vector<GenericData*> result;
653 +  map<string, GenericData*>::iterator i;
654 +  
655 +  for(i = properties.begin(); i != properties.end(); i++)
656 +    result.push_back((*i).second);
657 +    
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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