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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 855 by mmeineke, Thu Nov 6 22:01:37 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 49 | Line 49 | SimInfo::SimInfo(){
49    boxIsInit = 0;
50    
51    resetTime = 1e99;
52 –  
52  
53 +  orthoTolerance = 1E-6;
54 +  useInitXSstate = true;
55 +
56    usePBC = 0;
57    useLJ = 0;
58    useSticky = 0;
# Line 94 | Line 96 | void SimInfo::setBoxM( double theBox[3][3] ){
96  
97   void SimInfo::setBoxM( double theBox[3][3] ){
98    
99 <  int i, j, status;
98 <  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 147 | Line 148 | void SimInfo::calcHmatInv( void ) {
148  
149   void SimInfo::calcHmatInv( void ) {
150    
151 +  int oldOrtho;
152    int i,j;
153    double smallDiag;
154    double tol;
# Line 154 | Line 156 | void SimInfo::calcHmatInv( void ) {
156  
157    invertMat3( Hmat, HmatInv );
158  
157 –  // Check the inverse to make sure it is sane:
158 –
159 –  matMul3( Hmat, HmatInv, sanity );
160 –    
159    // check to see if Hmat is orthorhombic
160    
161 <  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;
161 >  oldOrtho = orthoRhombic;
162  
163 +  smallDiag = fabs(Hmat[0][0]);
164 +  if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
165 +  if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
166 +  tol = smallDiag * orthoTolerance;
167 +
168    orthoRhombic = 1;
169    
170    for (i = 0; i < 3; i++ ) {
171      for (j = 0 ; j < 3; j++) {
172        if (i != j) {
173          if (orthoRhombic) {
174 <          if (Hmat[i][j] >= tol) orthoRhombic = 0;
174 >          if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
175          }        
176        }
177 +    }
178 +  }
179 +
180 +  if( oldOrtho != orthoRhombic ){
181 +    
182 +    if( orthoRhombic ){
183 +      sprintf( painCave.errMsg,
184 +               "Hmat is switching from Non-Orthorhombic to OrthoRhombic\n"
185 +               "       If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n",
186 +               orthoTolerance);
187 +      simError();
188      }
189 +    else {
190 +      sprintf( painCave.errMsg,
191 +               "Hmat is switching from Orthorhombic to Non-OrthoRhombic\n"
192 +               "       If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n",
193 +               orthoTolerance);
194 +      simError();
195 +    }
196    }
197   }
198  
# Line 302 | Line 320 | void SimInfo::calcBoxL( void ){
320   void SimInfo::calcBoxL( void ){
321  
322    double dx, dy, dz, dsq;
305 –  int i;
323  
324    // boxVol = Determinant of Hmat
325  
# Line 372 | Line 389 | void SimInfo::wrapVector( double thePos[3] ){
389  
390   void SimInfo::wrapVector( double thePos[3] ){
391  
392 <  int i, j, k;
392 >  int i;
393    double scaled[3];
394  
395    if( !orthoRhombic ){
# Line 410 | Line 427 | int SimInfo::getNDF(){
427  
428  
429   int SimInfo::getNDF(){
430 <  int ndf_local, ndf;
430 >  int ndf_local;
431    
432    ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
433  
# Line 426 | Line 443 | int SimInfo::getNDFraw() {
443   }
444  
445   int SimInfo::getNDFraw() {
446 <  int ndfRaw_local, ndfRaw;
446 >  int ndfRaw_local;
447  
448    // Raw degrees of freedom that we have to set
449    ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
# Line 441 | Line 458 | int SimInfo::getNDFtranslational() {
458   }
459  
460   int SimInfo::getNDFtranslational() {
461 <  int ndfTrans_local, ndfTrans;
461 >  int ndfTrans_local;
462  
463    ndfTrans_local = 3 * n_atoms - n_constraints;
464  
# Line 517 | Line 534 | void SimInfo::setRcut( double theRcut ){
534  
535   void SimInfo::setRcut( double theRcut ){
536  
520 –  if( !haveOrigRcut ){
521 –    haveOrigRcut = 1;
522 –    origRcut = theRcut;
523 –  }
524 –
537    rCut = theRcut;
538    checkCutOffs();
539   }
540  
541 < void SimInfo::setEcr( double theEcr ){
541 > void SimInfo::setDefaultRcut( double theRcut ){
542  
543 <  if( !haveOrigEcr ){
544 <    haveOrigEcr = 1;
545 <    origEcr = theEcr;
534 <  }
543 >  haveOrigRcut = 1;
544 >  origRcut = theRcut;
545 >  rCut = theRcut;
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 ){
553 +
554    ecr = theEcr;
555    checkCutOffs();
556   }
557  
558 + void SimInfo::setDefaultEcr( double theEcr ){
559 +
560 +  haveOrigEcr = 1;
561 +  origEcr = theEcr;
562 +  
563 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
564 +
565 +  ecr = theEcr;
566 +
567 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
568 + }
569 +
570   void SimInfo::setEcr( double theEcr, double theEst ){
571  
572    est = theEst;
573    setEcr( theEcr );
574   }
575  
576 + void SimInfo::setDefaultEcr( double theEcr, double theEst ){
577  
578 +  est = theEst;
579 +  setDefaultEcr( theEcr );
580 + }
581 +
582 +
583   void SimInfo::checkCutOffs( void ){
584  
585    int cutChanged = 0;
# Line 610 | Line 646 | void SimInfo::checkCutOffs( void ){
646      ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
647      
648      if( cutChanged ){
613 –      
649        notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
650      }
651      

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