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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 588 by gezelter, Thu Jul 10 17:10:56 2003 UTC vs.
Revision 618 by mmeineke, Tue Jul 15 21:34:56 2003 UTC

# Line 34 | Line 34 | SimInfo::SimInfo(){
34    setTemp = 0;
35    thermalTime = 0.0;
36    rCut = 0.0;
37 +  ecr = 0.0;
38  
39    usePBC = 0;
40    useLJ = 0;
# Line 77 | Line 78 | void SimInfo::setBoxM( double theBox[3][3] ){
78    for(i=0; i < 3; i++)
79      for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
80    
81 <  cerr
82 <    << "setting Hmat ->\n"
83 <    << "[ " << Hmat[0][0] << ", " << Hmat[0][1] << ", " << Hmat[0][2] << " ]\n"
84 <    << "[ " << Hmat[1][0] << ", " << Hmat[1][1] << ", " << Hmat[1][2] << " ]\n"
85 <    << "[ " << Hmat[2][0] << ", " << Hmat[2][1] << ", " << Hmat[2][2] << " ]\n";
81 >  //  cerr
82 >  // << "setting Hmat ->\n"
83 >  // << "[ " << Hmat[0][0] << ", " << Hmat[0][1] << ", " << Hmat[0][2] << " ]\n"
84 >  // << "[ " << Hmat[1][0] << ", " << Hmat[1][1] << ", " << Hmat[1][2] << " ]\n"
85 >  // << "[ " << Hmat[2][0] << ", " << Hmat[2][1] << ", " << Hmat[2][2] << " ]\n";
86  
87    calcBoxL();
88    calcHmatInv();
# Line 93 | Line 94 | void SimInfo::setBoxM( double theBox[3][3] ){
94      }
95    }
96  
97 <  setFortranBoxSize(FortranHmat, FortranHmatI, &orthoRhombic);
97 >  setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
98  
99    smallestBoxL = boxLx;
100    if (boxLy < smallestBoxL) smallestBoxL = boxLy;
# Line 122 | Line 123 | void SimInfo::setBoxM( double theBox[3][3] ){
123      refreshSim();
124    }
125  
126 <  if (rCut > maxCutoff) {
126 >  if( ecr > maxCutoff ){
127 >
128      sprintf( painCave.errMsg,
129 <             "New Box size is forcing cutoff radius down to %lf\n",
129 >             "New Box size is forcing electrostatic cutoff radius "
130 >             "down to %lf\n",
131               maxCutoff );
132      painCave.isFatal = 0;
133      simError();
134  
135 <    status = 0;
136 <    LJ_new_rcut(&rCut, &status);
137 <    if (status != 0) {
138 <      sprintf( painCave.errMsg,
136 <               "Error in recomputing LJ shifts based on new rcut\n");
137 <      painCave.isFatal = 1;
138 <      simError();
139 <    }
135 >    ecr = maxCutoff;
136 >    est = 0.05 * ecr;
137 >
138 >    refreshSim();
139    }
140 +    
141   }
142  
143  
# Line 153 | Line 153 | void SimInfo::scaleBox(double scale) {
153    double theBox[3][3];
154    int i, j;
155  
156 <  cerr << "Scaling box by " << scale << "\n";
156 >  // cerr << "Scaling box by " << scale << "\n";
157  
158    for(i=0; i<3; i++)
159      for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
# Line 163 | Line 163 | void SimInfo::calcHmatInv( void ) {
163   }
164  
165   void SimInfo::calcHmatInv( void ) {
166 <
166 >  
167 >  int i,j;
168    double smallDiag;
169    double tol;
170    double sanity[3][3];
# Line 173 | Line 174 | void SimInfo::calcHmatInv( void ) {
174    // Check the inverse to make sure it is sane:
175  
176    matMul3( Hmat, HmatInv, sanity );
176 –
177 –  cerr << "sanity => \n"
178 –       << sanity[0][0] << "\t" << sanity[0][1] << "\t" << sanity [0][2] << "\n"
179 –       << sanity[1][0] << "\t" << sanity[1][1] << "\t" << sanity [1][2] << "\n"
180 –       << sanity[2][0] << "\t" << sanity[2][1] << "\t" << sanity [2][2]
181 –       << "\n";
177      
178    // check to see if Hmat is orthorhombic
179    
# Line 271 | Line 266 | void SimInfo::matVecMul3(double m[3][3], double inVec[
266    outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
267    outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
268   }
269 +
270 + void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
271 +  double temp[3][3];
272 +  int i, j;
273 +
274 +  for (i = 0; i < 3; i++) {
275 +    for (j = 0; j < 3; j++) {
276 +      temp[j][i] = in[i][j];
277 +    }
278 +  }
279 +  for (i = 0; i < 3; i++) {
280 +    for (j = 0; j < 3; j++) {
281 +      out[i][j] = temp[i][j];
282 +    }
283 +  }
284 + }
285    
286 + void SimInfo::printMat3(double A[3][3] ){
287 +
288 +  std::cerr
289 +            << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
290 +            << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
291 +            << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
292 + }
293 +
294 + void SimInfo::printMat9(double A[9] ){
295 +
296 +  std::cerr
297 +            << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
298 +            << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
299 +            << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
300 + }
301 +
302   void SimInfo::calcBoxL( void ){
303  
304    double dx, dy, dz, dsq;

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