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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 853 by mmeineke, Thu Nov 6 19:11:38 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 94 | Line 94 | void SimInfo::setBoxM( double theBox[3][3] ){
94  
95   void SimInfo::setBoxM( double theBox[3][3] ){
96    
97 <  int i, j, status;
98 <  double smallestBoxL, maxCutoff;
97 >  int i, j;
98    double FortranHmat[9]; // to preserve compatibility with Fortran the
99                           // ordering in the array is as follows:
100                           // [ 0 3 6 ]
# 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];
160 <  if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1];
161 <  if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2];
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 * 1E-6;
165  
166    orthoRhombic = 1;
# Line 171 | Line 169 | void SimInfo::calcHmatInv( void ) {
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 ortho tolerance in SimInfo.\n" );
184 +      simError();
185 +    }
186 +    else {
187 +      sprintf( painCave.errMsg,
188 +               "Hmat is switching from Orthorhombic to Non-OrthoRhombic\n"
189 +               "       If this is a bad thing change the ortho tolerance in SimInfo.\n" );
190 +      simError();
191 +    }
192 +  }
193   }
194  
195   double SimInfo::matDet3(double a[3][3]) {
# Line 302 | Line 316 | void SimInfo::calcBoxL( void ){
316   void SimInfo::calcBoxL( void ){
317  
318    double dx, dy, dz, dsq;
305 –  int i;
319  
320    // boxVol = Determinant of Hmat
321  
# Line 372 | Line 385 | void SimInfo::wrapVector( double thePos[3] ){
385  
386   void SimInfo::wrapVector( double thePos[3] ){
387  
388 <  int i, j, k;
388 >  int i;
389    double scaled[3];
390  
391    if( !orthoRhombic ){
# Line 410 | Line 423 | int SimInfo::getNDF(){
423  
424  
425   int SimInfo::getNDF(){
426 <  int ndf_local, ndf;
426 >  int ndf_local;
427    
428    ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
429  
# Line 426 | Line 439 | int SimInfo::getNDFraw() {
439   }
440  
441   int SimInfo::getNDFraw() {
442 <  int ndfRaw_local, ndfRaw;
442 >  int ndfRaw_local;
443  
444    // Raw degrees of freedom that we have to set
445    ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
# Line 441 | Line 454 | int SimInfo::getNDFtranslational() {
454   }
455  
456   int SimInfo::getNDFtranslational() {
457 <  int ndfTrans_local, ndfTrans;
457 >  int ndfTrans_local;
458  
459    ndfTrans_local = 3 * n_atoms - n_constraints;
460  
# Line 517 | Line 530 | void SimInfo::setRcut( double theRcut ){
530  
531   void SimInfo::setRcut( double theRcut ){
532  
520 –  if( !haveOrigRcut ){
521 –    haveOrigRcut = 1;
522 –    origRcut = theRcut;
523 –  }
524 –
533    rCut = theRcut;
534    checkCutOffs();
535   }
536  
537 < void SimInfo::setEcr( double theEcr ){
537 > void SimInfo::setDefaultRcut( double theRcut ){
538  
539 <  if( !haveOrigEcr ){
540 <    haveOrigEcr = 1;
541 <    origEcr = theEcr;
534 <  }
539 >  haveOrigRcut = 1;
540 >  origRcut = theRcut;
541 >  rCut = theRcut;
542  
543 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
544 +
545 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
546 + }
547 +
548 + void SimInfo::setEcr( double theEcr ){
549 +
550    ecr = theEcr;
551    checkCutOffs();
552   }
553  
554 + void SimInfo::setDefaultEcr( double theEcr ){
555 +
556 +  haveOrigEcr = 1;
557 +  origEcr = theEcr;
558 +  
559 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
560 +
561 +  ecr = theEcr;
562 +
563 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
564 + }
565 +
566   void SimInfo::setEcr( double theEcr, double theEst ){
567  
568    est = theEst;
569    setEcr( theEcr );
570   }
571  
572 + void SimInfo::setDefaultEcr( double theEcr, double theEst ){
573  
574 +  est = theEst;
575 +  setDefaultEcr( theEcr );
576 + }
577 +
578 +
579   void SimInfo::checkCutOffs( void ){
580  
581    int cutChanged = 0;
# Line 610 | Line 642 | void SimInfo::checkCutOffs( void ){
642      ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
643      
644      if( cutChanged ){
613 –      
645        notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
646      }
647      

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