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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 586 by mmeineke, Wed Jul 9 22:14:06 2003 UTC vs.
Revision 590 by mmeineke, Thu Jul 10 22:15:53 2003 UTC

# Line 48 | Line 48 | void SimInfo::setBox(double newBox[3]) {
48  
49   void SimInfo::setBox(double newBox[3]) {
50    
51 <  int i;
52 <  double tempMat[9];
51 >  int i, j;
52 >  double tempMat[3][3];
53  
54 <  for(i=0; i<9; i++) tempMat[i] = 0.0;;
54 >  for(i=0; i<3; i++)
55 >    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
56  
57 <  tempMat[0] = newBox[0];
58 <  tempMat[4] = newBox[1];
59 <  tempMat[8] = newBox[2];
57 >  tempMat[0][0] = newBox[0];
58 >  tempMat[1][1] = newBox[1];
59 >  tempMat[2][2] = newBox[2];
60  
61    setBoxM( tempMat );
62  
63   }
64  
65 < void SimInfo::setBoxM( double theBox[9] ){
65 > void SimInfo::setBoxM( double theBox[3][3] ){
66    
67 <  int i, status;
67 >  int i, j, status;
68    double smallestBoxL, maxCutoff;
69 +  double FortranHmat[9]; // to preserve compatibility with Fortran the
70 +                         // ordering in the array is as follows:
71 +                         // [ 0 3 6 ]
72 +                         // [ 1 4 7 ]
73 +                         // [ 2 5 8 ]
74 +  double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
75  
69 –  for(i=0; i<9; i++) Hmat[i] = theBox[i];
76  
77 +  for(i=0; i < 3; i++)
78 +    for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
79 +  
80    cerr
81      << "setting Hmat ->\n"
82 <    << "[ " << Hmat[0] << ", " << Hmat[3] << ", " << Hmat[6] << " ]\n"
83 <    << "[ " << Hmat[1] << ", " << Hmat[4] << ", " << Hmat[7] << " ]\n"
84 <    << "[ " << Hmat[2] << ", " << Hmat[5] << ", " << Hmat[8] << " ]\n";
82 >    << "[ " << Hmat[0][0] << ", " << Hmat[0][1] << ", " << Hmat[0][2] << " ]\n"
83 >    << "[ " << Hmat[1][0] << ", " << Hmat[1][1] << ", " << Hmat[1][2] << " ]\n"
84 >    << "[ " << Hmat[2][0] << ", " << Hmat[2][1] << ", " << Hmat[2][2] << " ]\n";
85  
77 –  calcHmatI();
86    calcBoxL();
87 +  calcHmatInv();
88  
89 +  for(i=0; i < 3; i++) {
90 +    for (j=0; j < 3; j++) {
91 +      FortranHmat[3*j + i] = Hmat[i][j];
92 +      FortranHmatInv[3*j + i] = HmatInv[i][j];
93 +    }
94 +  }
95  
96 <
82 <  setFortranBoxSize(Hmat, HmatI, &orthoRhombic);
96 >  setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
97  
98    smallestBoxL = boxLx;
99    if (boxLy < smallestBoxL) smallestBoxL = boxLy;
# Line 127 | Line 141 | void SimInfo::getBoxM (double theBox[9]) {
141   }
142  
143  
144 < void SimInfo::getBoxM (double theBox[9]) {
144 > void SimInfo::getBoxM (double theBox[3][3]) {
145  
146 <  int i;
147 <  for(i=0; i<9; i++) theBox[i] = Hmat[i];
146 >  int i, j;
147 >  for(i=0; i<3; i++)
148 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
149   }
150  
151  
152   void SimInfo::scaleBox(double scale) {
153 <  double theBox[9];
154 <  int i;
153 >  double theBox[3][3];
154 >  int i, j;
155  
156    cerr << "Scaling box by " << scale << "\n";
157  
158 <  for(i=0; i<9; i++) theBox[i] = Hmat[i]*scale;
158 >  for(i=0; i<3; i++)
159 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
160  
161    setBoxM(theBox);
162  
163   }
164  
165 < void SimInfo::calcHmatI( void ) {
166 <
167 <  double C[3][3];
152 <  double detHmat;
153 <  int i, j, k;
165 > void SimInfo::calcHmatInv( void ) {
166 >  
167 >  int i,j;
168    double smallDiag;
169    double tol;
170    double sanity[3][3];
171  
172 <  // calculate the adjunct of Hmat;
172 >  invertMat3( Hmat, HmatInv );
173  
174 <  C[0][0] =  ( Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]);
161 <  C[1][0] = -( Hmat[1]*Hmat[8]) + (Hmat[7]*Hmat[2]);
162 <  C[2][0] =  ( Hmat[1]*Hmat[5]) - (Hmat[4]*Hmat[2]);
174 >  // Check the inverse to make sure it is sane:
175  
176 <  C[0][1] = -( Hmat[3]*Hmat[8]) + (Hmat[6]*Hmat[5]);
177 <  C[1][1] =  ( Hmat[0]*Hmat[8]) - (Hmat[6]*Hmat[2]);
178 <  C[2][1] = -( Hmat[0]*Hmat[5]) + (Hmat[3]*Hmat[2]);
167 <
168 <  C[0][2] =  ( Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]);
169 <  C[1][2] = -( Hmat[0]*Hmat[7]) + (Hmat[6]*Hmat[1]);
170 <  C[2][2] =  ( Hmat[0]*Hmat[4]) - (Hmat[3]*Hmat[1]);
171 <
172 <  // calcutlate the determinant of Hmat
176 >  matMul3( Hmat, HmatInv, sanity );
177 >    
178 >  // check to see if Hmat is orthorhombic
179    
180 <  detHmat = 0.0;
181 <  for(i=0; i<3; i++) detHmat += Hmat[i] * C[i][0];
180 >  smallDiag = Hmat[0][0];
181 >  if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1];
182 >  if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2];
183 >  tol = smallDiag * 1E-6;
184  
185 +  orthoRhombic = 1;
186    
187 <  // H^-1 = C^T / det(H)
188 <  
189 <  i=0;
190 <  for(j=0; j<3; j++){
191 <    for(k=0; k<3; k++){
192 <
193 <      HmatI[i] = C[j][k] / detHmat;
185 <      i++;
187 >  for (i = 0; i < 3; i++ ) {
188 >    for (j = 0 ; j < 3; j++) {
189 >      if (i != j) {
190 >        if (orthoRhombic) {
191 >          if (Hmat[i][j] >= tol) orthoRhombic = 0;
192 >        }        
193 >      }
194      }
195    }
196 + }
197  
198 <  // sanity check
198 > double SimInfo::matDet3(double a[3][3]) {
199 >  int i, j, k;
200 >  double determinant;
201  
202 <  for(i=0; i<3; i++){
203 <    for(j=0; j<3; j++){
204 <      
205 <      sanity[i][j] = 0.0;
206 <      for(k=0; k<3; k++){
207 <        sanity[i][j] += Hmat[3*k+i] * HmatI[3*j+k];
208 <      }
198 <    }
202 >  determinant = 0.0;
203 >
204 >  for(i = 0; i < 3; i++) {
205 >    j = (i+1)%3;
206 >    k = (i+2)%3;
207 >
208 >    determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]);
209    }
210  
211 <  cerr << "sanity => \n"
212 <       << sanity[0][0] << "\t" << sanity[0][1] << "\t" << sanity [0][2] << "\n"
203 <       << sanity[1][0] << "\t" << sanity[1][1] << "\t" << sanity [1][2] << "\n"
204 <       << sanity[2][0] << "\t" << sanity[2][1] << "\t" << sanity [2][2]
205 <       << "\n";
206 <    
211 >  return determinant;
212 > }
213  
214 <  // check to see if Hmat is orthorhombic
214 > void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
215    
216 <  smallDiag = Hmat[0];
217 <  if(smallDiag > Hmat[4]) smallDiag = Hmat[4];
212 <  if(smallDiag > Hmat[8]) smallDiag = Hmat[8];
213 <  tol = smallDiag * 1E-6;
216 >  int  i, j, k, l, m, n;
217 >  double determinant;
218  
219 <  orthoRhombic = 1;
220 <  for(i=0; (i<9) && orthoRhombic; i++){
221 <    
222 <    if( (i%4) ){ // ignore the diagonals (0, 4, and 8)
223 <      orthoRhombic = (Hmat[i] <= tol);
219 >  determinant = matDet3( a );
220 >
221 >  if (determinant == 0.0) {
222 >    sprintf( painCave.errMsg,
223 >             "Can't invert a matrix with a zero determinant!\n");
224 >    painCave.isFatal = 1;
225 >    simError();
226 >  }
227 >
228 >  for (i=0; i < 3; i++) {
229 >    j = (i+1)%3;
230 >    k = (i+2)%3;
231 >    for(l = 0; l < 3; l++) {
232 >      m = (l+1)%3;
233 >      n = (l+2)%3;
234 >      
235 >      b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant;
236      }
237    }
222 –    
238   }
239  
240 + void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
241 +  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
242 +
243 +  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
244 +  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
245 +  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
246 +  
247 +  r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0];
248 +  r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1];
249 +  r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2];
250 +  
251 +  r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0];
252 +  r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1];
253 +  r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2];
254 +  
255 +  c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
256 +  c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
257 +  c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
258 + }
259 +
260 + void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
261 +  double a0, a1, a2;
262 +
263 +  a0 = inVec[0];  a1 = inVec[1];  a2 = inVec[2];
264 +
265 +  outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2;
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::calcBoxL( void ){
271  
272    double dx, dy, dz, dsq;
273    int i;
274  
275 <  // boxVol = h1 (dot) h2 (cross) h3
275 >  // boxVol = Determinant of Hmat
276  
277 <  boxVol = Hmat[0] * ( (Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]) )
233 <         + Hmat[1] * ( (Hmat[5]*Hmat[6]) - (Hmat[8]*Hmat[3]) )
234 <         + Hmat[2] * ( (Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]) );
277 >  boxVol = matDet3( Hmat );
278  
236 –
279    // boxLx
280    
281 <  dx = Hmat[0]; dy = Hmat[1]; dz = Hmat[2];
281 >  dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
282    dsq = dx*dx + dy*dy + dz*dz;
283    boxLx = sqrt( dsq );
284  
285    // boxLy
286    
287 <  dx = Hmat[3]; dy = Hmat[4]; dz = Hmat[5];
287 >  dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
288    dsq = dx*dx + dy*dy + dz*dz;
289    boxLy = sqrt( dsq );
290  
291    // boxLz
292    
293 <  dx = Hmat[6]; dy = Hmat[7]; dz = Hmat[8];
293 >  dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
294    dsq = dx*dx + dy*dy + dz*dz;
295    boxLz = sqrt( dsq );
296    
# Line 262 | Line 304 | void SimInfo::wrapVector( double thePos[3] ){
304  
305    if( !orthoRhombic ){
306      // calc the scaled coordinates.
307 +  
308 +
309 +    matVecMul3(HmatInv, thePos, scaled);
310      
311      for(i=0; i<3; i++)
267 –      scaled[i] =
268 –        thePos[0]*HmatI[i] + thePos[1]*HmatI[i+3] + thePos[3]*HmatI[i+6];
269 –    
270 –    // wrap the scaled coordinates
271 –    
272 –    for(i=0; i<3; i++)
312        scaled[i] -= roundMe(scaled[i]);
313      
314      // calc the wrapped real coordinates from the wrapped scaled coordinates
315      
316 <    for(i=0; i<3; i++)
317 <      thePos[i] =
279 <        scaled[0]*Hmat[i] + scaled[1]*Hmat[i+3] + scaled[2]*Hmat[i+6];
316 >    matVecMul3(Hmat, scaled, thePos);
317 >
318    }
319    else{
320      // calc the scaled coordinates.
321      
322      for(i=0; i<3; i++)
323 <      scaled[i] = thePos[i]*HmatI[i*4];
323 >      scaled[i] = thePos[i]*HmatInv[i][i];
324      
325      // wrap the scaled coordinates
326      
# Line 292 | Line 330 | void SimInfo::wrapVector( double thePos[3] ){
330      // calc the wrapped real coordinates from the wrapped scaled coordinates
331      
332      for(i=0; i<3; i++)
333 <      thePos[i] = scaled[i]*Hmat[i*4];
333 >      thePos[i] = scaled[i]*Hmat[i][i];
334    }
335      
298 –    
336   }
337  
338  

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