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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 574 by gezelter, Tue Jul 8 20:56:10 2003 UTC vs.
Revision 617 by gezelter, Tue Jul 15 19:56:08 2003 UTC

# Line 47 | Line 47 | void SimInfo::setBox(double newBox[3]) {
47   }
48  
49   void SimInfo::setBox(double newBox[3]) {
50 +  
51 +  int i, j;
52 +  double tempMat[3][3];
53  
54 <  double smallestBoxL, maxCutoff;
55 <  int status;
53 <  int i;
54 >  for(i=0; i<3; i++)
55 >    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
56  
57 <  for(i=0; i<9; i++) Hmat[i] = 0.0;;
57 >  tempMat[0][0] = newBox[0];
58 >  tempMat[1][1] = newBox[1];
59 >  tempMat[2][2] = newBox[2];
60  
61 <  Hmat[0] = newBox[0];
58 <  Hmat[4] = newBox[1];
59 <  Hmat[8] = newBox[2];
61 >  setBoxM( tempMat );
62  
63 <  calcHmatI();
62 <  calcBoxL();
63 > }
64  
65 <  setFortranBoxSize(Hmat, HmatI, &orthoRhombic);
65 > void SimInfo::setBoxM( double theBox[3][3] ){
66 >  
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  
66 –  smallestBoxL = boxLx;
67 –  if (boxLy < smallestBoxL) smallestBoxL = boxLy;
68 –  if (boxLz < smallestBoxL) smallestBoxL = boxLz;
76  
77 <  maxCutoff = smallestBoxL / 2.0;
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][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  
86 <  if (rList > maxCutoff) {
87 <    sprintf( painCave.errMsg,
74 <             "New Box size is forcing neighborlist radius down to %lf\n",
75 <             maxCutoff );
76 <    painCave.isFatal = 0;
77 <    simError();
86 >  calcBoxL();
87 >  calcHmatInv();
88  
89 <    rList = maxCutoff;
90 <
91 <    sprintf( painCave.errMsg,
92 <             "New Box size is forcing cutoff radius down to %lf\n",
83 <             maxCutoff - 1.0 );
84 <    painCave.isFatal = 0;
85 <    simError();
86 <
87 <    rCut = rList - 1.0;
88 <
89 <    // list radius changed so we have to refresh the simulation structure.
90 <    refreshSim();
91 <  }
92 <
93 <  if (rCut > maxCutoff) {
94 <    sprintf( painCave.errMsg,
95 <             "New Box size is forcing cutoff radius down to %lf\n",
96 <             maxCutoff );
97 <    painCave.isFatal = 0;
98 <    simError();
99 <
100 <    status = 0;
101 <    LJ_new_rcut(&rCut, &status);
102 <    if (status != 0) {
103 <      sprintf( painCave.errMsg,
104 <               "Error in recomputing LJ shifts based on new rcut\n");
105 <      painCave.isFatal = 1;
106 <      simError();
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    }
109 – }
95  
96 < void SimInfo::setBoxM( double theBox[9] ){
112 <  
113 <  int i, status;
114 <  double smallestBoxL, maxCutoff;
115 <
116 <  for(i=0; i<9; i++) Hmat[i] = theBox[i];
117 <  calcHmatI();
118 <  calcBoxL();
119 <
120 <  setFortranBoxSize(Hmat, HmatI, &orthoRhombic);
96 >  setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
97  
98    smallestBoxL = boxLx;
99    if (boxLy < smallestBoxL) smallestBoxL = boxLy;
# Line 165 | Line 141 | void SimInfo::setBoxM( 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 <  for(i=0; i<9; i++) theBox[i] = Hmat[i]*scale;
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;
160 +
161    setBoxM(theBox);
162  
163   }
164  
165 < void SimInfo::calcHmatI( void ) {
166 <
167 <  double C[3][3];
188 <  double detHmat;
189 <  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]);
197 <  C[1][0] = -( Hmat[1]*Hmat[8]) + (Hmat[7]*Hmat[2]);
198 <  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]);
203 <
204 <  C[0][2] =  ( Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]);
205 <  C[1][2] = -( Hmat[0]*Hmat[7]) + (Hmat[6]*Hmat[1]);
206 <  C[2][2] =  ( Hmat[0]*Hmat[4]) - (Hmat[3]*Hmat[1]);
207 <
208 <  // 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;
221 <      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++){
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 >  return determinant;
212 > }
213 >
214 > void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
215 >  
216 >  int  i, j, k, l, m, n;
217 >  double determinant;
218 >
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 <      sanity[i][j] = 0.0;
231 <      for(k=0; k<3; k++){
232 <        sanity[i][j] += Hmat[3*k+i] * HmatI[3*j+k];
233 <      }
235 >      b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant;
236      }
237    }
238 + }
239  
240 <  cerr << "sanity => \n"
241 <       << sanity[0][0] << "\t" << sanity[0][1] << "\t" << sanity [0][2] << "\n"
239 <       << sanity[1][0] << "\t" << sanity[1][1] << "\t" << sanity [1][2] << "\n"
240 <       << sanity[2][0] << "\t" << sanity[2][1] << "\t" << sanity [2][2]
241 <       << "\n";
242 <    
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 <  // check to see if Hmat is orthorhombic
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 <  smallDiag = Hmat[0];
248 <  if(smallDiag > Hmat[4]) smallDiag = Hmat[4];
249 <  if(smallDiag > Hmat[8]) smallDiag = Hmat[8];
250 <  tol = smallDiag * 1E-6;
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 <  orthoRhombic = 1;
261 <  for(i=0; (i<9) && orthoRhombic; i++){
262 <    
263 <    if( (i%4) ){ // ignore the diagonals (0, 4, and 8)
264 <      orthoRhombic = (Hmat[i] <= tol);
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::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 <    
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;
305    int i;
306  
307 <  // boxVol = h1 (dot) h2 (cross) h3
307 >  // boxVol = Determinant of Hmat
308  
309 <  boxVol = Hmat[0] * ( (Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]) )
269 <         + Hmat[1] * ( (Hmat[5]*Hmat[6]) - (Hmat[8]*Hmat[3]) )
270 <         + Hmat[2] * ( (Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]) );
309 >  boxVol = matDet3( Hmat );
310  
272 –
311    // boxLx
312    
313 <  dx = Hmat[0]; dy = Hmat[1]; dz = Hmat[2];
313 >  dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
314    dsq = dx*dx + dy*dy + dz*dz;
315    boxLx = sqrt( dsq );
316  
317    // boxLy
318    
319 <  dx = Hmat[3]; dy = Hmat[4]; dz = Hmat[5];
319 >  dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
320    dsq = dx*dx + dy*dy + dz*dz;
321    boxLy = sqrt( dsq );
322  
323    // boxLz
324    
325 <  dx = Hmat[6]; dy = Hmat[7]; dz = Hmat[8];
325 >  dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
326    dsq = dx*dx + dy*dy + dz*dz;
327    boxLz = sqrt( dsq );
328    
# Line 298 | Line 336 | void SimInfo::wrapVector( double thePos[3] ){
336  
337    if( !orthoRhombic ){
338      // calc the scaled coordinates.
339 +  
340 +
341 +    matVecMul3(HmatInv, thePos, scaled);
342      
343      for(i=0; i<3; i++)
303 –      scaled[i] =
304 –        thePos[0]*HmatI[i] + thePos[1]*HmatI[i+3] + thePos[3]*HmatI[i+6];
305 –    
306 –    // wrap the scaled coordinates
307 –    
308 –    for(i=0; i<3; i++)
344        scaled[i] -= roundMe(scaled[i]);
345      
346      // calc the wrapped real coordinates from the wrapped scaled coordinates
347      
348 <    for(i=0; i<3; i++)
349 <      thePos[i] =
315 <        scaled[0]*Hmat[i] + scaled[1]*Hmat[i+3] + scaled[2]*Hmat[i+6];
348 >    matVecMul3(Hmat, scaled, thePos);
349 >
350    }
351    else{
352      // calc the scaled coordinates.
353      
354      for(i=0; i<3; i++)
355 <      scaled[i] = thePos[i]*HmatI[i*4];
355 >      scaled[i] = thePos[i]*HmatInv[i][i];
356      
357      // wrap the scaled coordinates
358      
# Line 328 | Line 362 | void SimInfo::wrapVector( double thePos[3] ){
362      // calc the wrapped real coordinates from the wrapped scaled coordinates
363      
364      for(i=0; i<3; i++)
365 <      thePos[i] = scaled[i]*Hmat[i*4];
365 >      thePos[i] = scaled[i]*Hmat[i][i];
366    }
367      
334 –    
368   }
369  
370  

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