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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 872 by chrisfen, Fri Nov 21 19:31:05 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 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;
# Line 94 | Line 95 | void SimInfo::setBoxM( double theBox[3][3] ){
95  
96   void SimInfo::setBoxM( double theBox[3][3] ){
97    
98 <  int i, j, status;
98 <  double smallestBoxL, maxCutoff;
98 >  int i, j;
99    double FortranHmat[9]; // to preserve compatibility with Fortran the
100                           // ordering in the array is as follows:
101                           // [ 0 3 6 ]
# Line 103 | Line 103 | void SimInfo::setBoxM( double theBox[3][3] ){
103                           // [ 2 5 8 ]
104    double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
105  
106 –  
106    if( !boxIsInit ) boxIsInit = 1;
107  
108    for(i=0; i < 3; i++)
# Line 147 | Line 146 | void SimInfo::calcHmatInv( void ) {
146  
147   void SimInfo::calcHmatInv( void ) {
148    
149 +  int oldOrtho;
150    int i,j;
151    double smallDiag;
152    double tol;
# Line 154 | Line 154 | void SimInfo::calcHmatInv( void ) {
154  
155    invertMat3( Hmat, HmatInv );
156  
157 –  // Check the inverse to make sure it is sane:
158 –
159 –  matMul3( Hmat, HmatInv, sanity );
160 –    
157    // check to see if Hmat is orthorhombic
158    
159 <  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;
159 >  oldOrtho = orthoRhombic;
160  
161 +  smallDiag = fabs(Hmat[0][0]);
162 +  if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
163 +  if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
164 +  tol = smallDiag * orthoTolerance;
165 +
166    orthoRhombic = 1;
167    
168    for (i = 0; i < 3; i++ ) {
169      for (j = 0 ; j < 3; j++) {
170        if (i != j) {
171          if (orthoRhombic) {
172 <          if (Hmat[i][j] >= tol) orthoRhombic = 0;
172 >          if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
173          }        
174        }
175      }
176    }
177 +
178 +  if( oldOrtho != orthoRhombic ){
179 +    
180 +    if( orthoRhombic ){
181 +      sprintf( painCave.errMsg,
182 +               "Hmat is switching from Non-Orthorhombic to OrthoRhombic\n"
183 +               "       If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n",
184 +               orthoTolerance);
185 +      simError();
186 +    }
187 +    else {
188 +      sprintf( painCave.errMsg,
189 +               "Hmat is switching from Orthorhombic to Non-OrthoRhombic\n"
190 +               "       If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n",
191 +               orthoTolerance);
192 +      simError();
193 +    }
194 +  }
195   }
196  
197   double SimInfo::matDet3(double a[3][3]) {
# Line 302 | Line 318 | void SimInfo::calcBoxL( void ){
318   void SimInfo::calcBoxL( void ){
319  
320    double dx, dy, dz, dsq;
305 –  int i;
321  
322    // boxVol = Determinant of Hmat
323  
# Line 372 | Line 387 | void SimInfo::wrapVector( double thePos[3] ){
387  
388   void SimInfo::wrapVector( double thePos[3] ){
389  
390 <  int i, j, k;
390 >  int i;
391    double scaled[3];
392  
393    if( !orthoRhombic ){
# Line 410 | Line 425 | int SimInfo::getNDF(){
425  
426  
427   int SimInfo::getNDF(){
428 <  int ndf_local, ndf;
428 >  int ndf_local;
429    
430    ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
431  
# Line 426 | Line 441 | int SimInfo::getNDFraw() {
441   }
442  
443   int SimInfo::getNDFraw() {
444 <  int ndfRaw_local, ndfRaw;
444 >  int ndfRaw_local;
445  
446    // Raw degrees of freedom that we have to set
447    ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
# Line 441 | Line 456 | int SimInfo::getNDFtranslational() {
456   }
457  
458   int SimInfo::getNDFtranslational() {
459 <  int ndfTrans_local, ndfTrans;
459 >  int ndfTrans_local;
460  
461    ndfTrans_local = 3 * n_atoms - n_constraints;
462  
# Line 514 | Line 529 | void SimInfo::refreshSim(){
529    this->ndfTrans = this->getNDFtranslational();
530   }
531  
532 + void SimInfo::setDefaultRcut( double theRcut ){
533  
534 < void SimInfo::setRcut( double theRcut ){
534 >  haveRcut = 1;
535 >  rCut = theRcut;
536  
537 <  if( !haveOrigRcut ){
521 <    haveOrigRcut = 1;
522 <    origRcut = theRcut;
523 <  }
537 >  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
538  
539 <  rCut = theRcut;
526 <  checkCutOffs();
539 >  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
540   }
541  
542 < void SimInfo::setEcr( double theEcr ){
542 > void SimInfo::setDefaultEcr( double theEcr ){
543  
544 <  if( !haveOrigEcr ){
532 <    haveOrigEcr = 1;
533 <    origEcr = theEcr;
534 <  }
535 <
544 >  haveEcr = 1;
545    ecr = theEcr;
546 <  checkCutOffs();
546 >  
547 >  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
548 >
549 >  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
550   }
551  
552 < void SimInfo::setEcr( double theEcr, double theEst ){
552 > void SimInfo::setDefaultEcr( double theEcr, double theEst ){
553  
554    est = theEst;
555 <  setEcr( theEcr );
555 >  setDefaultEcr( theEcr );
556   }
557  
558  
559   void SimInfo::checkCutOffs( void ){
548 –
549 –  int cutChanged = 0;
560    
561    if( boxIsInit ){
562      
563      //we need to check cutOffs against the box
564 <
565 <    //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)) {
564 >    
565 >    if( rCut > maxCutoff ){
566        sprintf( painCave.errMsg,
567 <               "New Box size is setting the long range cutoff radius "
568 <               "to %lf at time %lf\n",
569 <               maxCutoff, currentTime );
570 <      painCave.isFatal = 0;
567 >               "Box size is too small for the long range cutoff radius, "
568 >               "%lf, at time %lf\n",
569 >               rCut, currentTime );
570 >      painCave.isFatal = 1;
571        simError();
578 –      rCut = maxCutoff;
572      }
573 <
574 <
575 <    //detect the change of ecr
576 <    if( maxCutoff > ecr ){
577 <      if( ecr < origEcr ){
578 <        ecr = origEcr;
579 <        if (ecr > maxCutoff) ecr = maxCutoff;
580 <  
581 <          sprintf( painCave.errMsg,
589 <                    "New Box size is setting the electrostaticCutoffRadius "
590 <                    "to %lf at time %lf\n",
591 <                    ecr, currentTime );
592 <            painCave.isFatal = 0;
593 <            simError();
573 >    
574 >    if( haveEcr ){
575 >      if( ecr > maxCutoff ){
576 >        sprintf( painCave.errMsg,
577 >                 "Box size is too small for the electrostatic cutoff radius, "
578 >                 "%lf, at time %lf\n",
579 >                 ecr, currentTime );
580 >        painCave.isFatal = 1;
581 >        simError();
582        }
583      }
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 –    
584    } else {
585      // initialize this stuff before using it, OK?
586      sprintf( painCave.errMsg,

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