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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 781 by tim, Mon Sep 22 23:07:57 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    resetTime = 1e99;
52 –  
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 94 | Line 99 | void SimInfo::setBoxM( double theBox[3][3] ){
99  
100   void SimInfo::setBoxM( double theBox[3][3] ){
101    
102 <  int i, j, status;
98 <  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 103 | Line 107 | void SimInfo::setBoxM( double theBox[3][3] ){
107                           // [ 2 5 8 ]
108    double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
109  
106 –  
110    if( !boxIsInit ) boxIsInit = 1;
111  
112    for(i=0; i < 3; i++)
# Line 147 | 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 154 | Line 158 | void SimInfo::calcHmatInv( void ) {
158  
159    invertMat3( Hmat, HmatInv );
160  
157 –  // Check the inverse to make sure it is sane:
158 –
159 –  matMul3( Hmat, HmatInv, sanity );
160 –    
161    // check to see if Hmat is orthorhombic
162    
163 <  smallDiag = Hmat[0][0];
164 <  if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1];
165 <  if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2];
166 <  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 302 | Line 324 | void SimInfo::calcBoxL( void ){
324   void SimInfo::calcBoxL( void ){
325  
326    double dx, dy, dz, dsq;
305 –  int i;
327  
328    // boxVol = Determinant of Hmat
329  
# Line 372 | Line 393 | void SimInfo::wrapVector( double thePos[3] ){
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 410 | 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 426 | 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 441 | Line 462 | int SimInfo::getNDFtranslational() {
462   }
463  
464   int SimInfo::getNDFtranslational() {
465 <  int ndfTrans_local, ndfTrans;
465 >  int ndfTrans_local;
466  
467    ndfTrans_local = 3 * n_atoms - n_constraints;
468  
# Line 465 | 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 474 | 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 514 | Line 536 | void SimInfo::refreshSim(){
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 ){
521 <    haveOrigRcut = 1;
522 <    origRcut = theRcut;
523 <  }
544 >  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
545  
546 <  rCut = theRcut;
526 <  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 ){
532 <    haveOrigEcr = 1;
533 <    origEcr = theEcr;
534 <  }
535 <
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 ){
548 –
549 –  int cutChanged = 0;
567    
568    if( boxIsInit ){
569      
570      //we need to check cutOffs against the box
571 <
572 <    //detect the change of rCut
556 <    if(( maxCutoff > rCut )&&(usePBC)){
557 <      if( rCut < origRcut ){
558 <        rCut = origRcut;
559 <        
560 <        if (rCut > maxCutoff)
561 <          rCut = maxCutoff;
562 <  
563 <          sprintf( painCave.errMsg,
564 <                    "New Box size is setting the long range cutoff radius "
565 <                    "to %lf at time %lf\n",
566 <                    rCut, currentTime );
567 <          painCave.isFatal = 0;
568 <          simError();
569 <      }
570 <    }
571 <    else if ((rCut > maxCutoff)&&(usePBC)) {
571 >    
572 >    if( rCut > maxCutoff ){
573        sprintf( painCave.errMsg,
574 <               "New Box size is setting the long range cutoff radius "
575 <               "to %lf at time %lf\n",
576 <               maxCutoff, currentTime );
577 <      painCave.isFatal = 0;
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();
578 –      rCut = maxCutoff;
585      }
586 <
587 <
588 <    //detect the change of ecr
589 <    if( maxCutoff > ecr ){
590 <      if( ecr < origEcr ){
591 <        ecr = origEcr;
592 <        if (ecr > maxCutoff) ecr = maxCutoff;
593 <  
594 <          sprintf( painCave.errMsg,
595 <                    "New Box size is setting the electrostaticCutoffRadius "
596 <                    "to %lf at time %lf\n",
597 <                    ecr, currentTime );
598 <            painCave.isFatal = 0;
599 <            simError();
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      }
596 –    else if( ecr > maxCutoff){
597 –      sprintf( painCave.errMsg,
598 –               "New Box size is setting the electrostaticCutoffRadius "
599 –               "to %lf at time %lf\n",
600 –               maxCutoff, currentTime  );
601 –      painCave.isFatal = 0;
602 –      simError();      
603 –      ecr = maxCutoff;
604 –    }
605 –
606 –    if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
607 –    
608 –    // rlist is the 1.0 plus max( rcut, ecr )
609 –    
610 –    ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
611 –    
612 –    if( cutChanged ){
613 –      
614 –      notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
615 –    }
616 –    
617 –    oldEcr = ecr;
618 –    oldRcut = rCut;
619 –    
603    } else {
604      // initialize this stuff before using it, OK?
605      sprintf( painCave.errMsg,
606 <             "Trying to check cutoffs without a box. Be smarter.\n" );
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    }

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