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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 619 by mmeineke, Tue Jul 15 22:22:41 2003 UTC

# Line 34 | Line 34 | SimInfo::SimInfo(){
34    setTemp = 0;
35    thermalTime = 0.0;
36    rCut = 0.0;
37 +  ecr = 0.0;
38 +  est = 0.0;
39  
40    usePBC = 0;
41    useLJ = 0;
# Line 48 | Line 50 | void SimInfo::setBox(double newBox[3]) {
50  
51   void SimInfo::setBox(double newBox[3]) {
52    
53 <  int i;
54 <  double tempMat[9];
53 >  int i, j;
54 >  double tempMat[3][3];
55  
56 <  for(i=0; i<9; i++) tempMat[i] = 0.0;;
56 >  for(i=0; i<3; i++)
57 >    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
58  
59 <  tempMat[0] = newBox[0];
60 <  tempMat[4] = newBox[1];
61 <  tempMat[8] = newBox[2];
59 >  tempMat[0][0] = newBox[0];
60 >  tempMat[1][1] = newBox[1];
61 >  tempMat[2][2] = newBox[2];
62  
63    setBoxM( tempMat );
64  
65   }
66  
67 < void SimInfo::setBoxM( double theBox[9] ){
67 > void SimInfo::setBoxM( double theBox[3][3] ){
68    
69 <  int i, status;
69 >  int i, j, status;
70    double smallestBoxL, maxCutoff;
71 +  double FortranHmat[9]; // to preserve compatibility with Fortran the
72 +                         // ordering in the array is as follows:
73 +                         // [ 0 3 6 ]
74 +                         // [ 1 4 7 ]
75 +                         // [ 2 5 8 ]
76 +  double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
77  
69 –  for(i=0; i<9; i++) Hmat[i] = theBox[i];
78  
79 <  cerr
80 <    << "setting Hmat ->\n"
81 <    << "[ " << Hmat[0] << ", " << Hmat[3] << ", " << Hmat[6] << " ]\n"
82 <    << "[ " << Hmat[1] << ", " << Hmat[4] << ", " << Hmat[7] << " ]\n"
83 <    << "[ " << Hmat[2] << ", " << Hmat[5] << ", " << Hmat[8] << " ]\n";
79 >  for(i=0; i < 3; i++)
80 >    for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
81 >  
82 >  //  cerr
83 >  // << "setting Hmat ->\n"
84 >  // << "[ " << Hmat[0][0] << ", " << Hmat[0][1] << ", " << Hmat[0][2] << " ]\n"
85 >  // << "[ " << Hmat[1][0] << ", " << Hmat[1][1] << ", " << Hmat[1][2] << " ]\n"
86 >  // << "[ " << Hmat[2][0] << ", " << Hmat[2][1] << ", " << Hmat[2][2] << " ]\n";
87  
77 –  calcHmatI();
88    calcBoxL();
89 +  calcHmatInv();
90  
91 +  for(i=0; i < 3; i++) {
92 +    for (j=0; j < 3; j++) {
93 +      FortranHmat[3*j + i] = Hmat[i][j];
94 +      FortranHmatInv[3*j + i] = HmatInv[i][j];
95 +    }
96 +  }
97  
98 <
82 <  setFortranBoxSize(Hmat, HmatI, &orthoRhombic);
98 >  setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
99  
100    smallestBoxL = boxLx;
101    if (boxLy < smallestBoxL) smallestBoxL = boxLy;
# Line 108 | Line 124 | void SimInfo::setBoxM( double theBox[9] ){
124      refreshSim();
125    }
126  
127 <  if (rCut > maxCutoff) {
127 >  if( ecr > maxCutoff ){
128 >
129      sprintf( painCave.errMsg,
130 <             "New Box size is forcing cutoff radius down to %lf\n",
130 >             "New Box size is forcing electrostatic cutoff radius "
131 >             "down to %lf\n",
132               maxCutoff );
133      painCave.isFatal = 0;
134      simError();
135  
136 <    status = 0;
137 <    LJ_new_rcut(&rCut, &status);
138 <    if (status != 0) {
139 <      sprintf( painCave.errMsg,
122 <               "Error in recomputing LJ shifts based on new rcut\n");
123 <      painCave.isFatal = 1;
124 <      simError();
125 <    }
136 >    ecr = maxCutoff;
137 >    est = 0.05 * ecr;
138 >
139 >    refreshSim();
140    }
141 +    
142   }
143  
144  
145 < void SimInfo::getBoxM (double theBox[9]) {
145 > void SimInfo::getBoxM (double theBox[3][3]) {
146  
147 <  int i;
148 <  for(i=0; i<9; i++) theBox[i] = Hmat[i];
147 >  int i, j;
148 >  for(i=0; i<3; i++)
149 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
150   }
151  
152  
153   void SimInfo::scaleBox(double scale) {
154 <  double theBox[9];
155 <  int i;
154 >  double theBox[3][3];
155 >  int i, j;
156  
157 <  cerr << "Scaling box by " << scale << "\n";
157 >  // cerr << "Scaling box by " << scale << "\n";
158  
159 <  for(i=0; i<9; i++) theBox[i] = Hmat[i]*scale;
159 >  for(i=0; i<3; i++)
160 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
161  
162    setBoxM(theBox);
163  
164   }
165  
166 < void SimInfo::calcHmatI( void ) {
167 <
168 <  double C[3][3];
152 <  double detHmat;
153 <  int i, j, k;
166 > void SimInfo::calcHmatInv( void ) {
167 >  
168 >  int i,j;
169    double smallDiag;
170    double tol;
171    double sanity[3][3];
172  
173 <  // calculate the adjunct of Hmat;
173 >  invertMat3( Hmat, HmatInv );
174  
175 <  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]);
175 >  // Check the inverse to make sure it is sane:
176  
177 <  C[0][1] = -( Hmat[3]*Hmat[8]) + (Hmat[6]*Hmat[5]);
178 <  C[1][1] =  ( Hmat[0]*Hmat[8]) - (Hmat[6]*Hmat[2]);
179 <  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
177 >  matMul3( Hmat, HmatInv, sanity );
178 >    
179 >  // check to see if Hmat is orthorhombic
180    
181 <  detHmat = 0.0;
182 <  for(i=0; i<3; i++) detHmat += Hmat[i] * C[i][0];
181 >  smallDiag = Hmat[0][0];
182 >  if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1];
183 >  if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2];
184 >  tol = smallDiag * 1E-6;
185  
186 +  orthoRhombic = 1;
187    
188 <  // H^-1 = C^T / det(H)
189 <  
190 <  i=0;
191 <  for(j=0; j<3; j++){
192 <    for(k=0; k<3; k++){
193 <
194 <      HmatI[i] = C[j][k] / detHmat;
185 <      i++;
188 >  for (i = 0; i < 3; i++ ) {
189 >    for (j = 0 ; j < 3; j++) {
190 >      if (i != j) {
191 >        if (orthoRhombic) {
192 >          if (Hmat[i][j] >= tol) orthoRhombic = 0;
193 >        }        
194 >      }
195      }
196    }
197 + }
198  
199 <  // sanity check
199 > double SimInfo::matDet3(double a[3][3]) {
200 >  int i, j, k;
201 >  double determinant;
202  
203 <  for(i=0; i<3; i++){
204 <    for(j=0; j<3; j++){
203 >  determinant = 0.0;
204 >
205 >  for(i = 0; i < 3; i++) {
206 >    j = (i+1)%3;
207 >    k = (i+2)%3;
208 >
209 >    determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]);
210 >  }
211 >
212 >  return determinant;
213 > }
214 >
215 > void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
216 >  
217 >  int  i, j, k, l, m, n;
218 >  double determinant;
219 >
220 >  determinant = matDet3( a );
221 >
222 >  if (determinant == 0.0) {
223 >    sprintf( painCave.errMsg,
224 >             "Can't invert a matrix with a zero determinant!\n");
225 >    painCave.isFatal = 1;
226 >    simError();
227 >  }
228 >
229 >  for (i=0; i < 3; i++) {
230 >    j = (i+1)%3;
231 >    k = (i+2)%3;
232 >    for(l = 0; l < 3; l++) {
233 >      m = (l+1)%3;
234 >      n = (l+2)%3;
235        
236 <      sanity[i][j] = 0.0;
195 <      for(k=0; k<3; k++){
196 <        sanity[i][j] += Hmat[3*k+i] * HmatI[3*j+k];
197 <      }
236 >      b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant;
237      }
238    }
239 + }
240  
241 <  cerr << "sanity => \n"
242 <       << 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 <    
241 > void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
242 >  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
243  
244 <  // check to see if Hmat is orthorhombic
244 >  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
245 >  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
246 >  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
247    
248 <  smallDiag = Hmat[0];
249 <  if(smallDiag > Hmat[4]) smallDiag = Hmat[4];
250 <  if(smallDiag > Hmat[8]) smallDiag = Hmat[8];
251 <  tol = smallDiag * 1E-6;
248 >  r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0];
249 >  r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1];
250 >  r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2];
251 >  
252 >  r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0];
253 >  r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1];
254 >  r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2];
255 >  
256 >  c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
257 >  c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
258 >  c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
259 > }
260  
261 <  orthoRhombic = 1;
262 <  for(i=0; (i<9) && orthoRhombic; i++){
263 <    
264 <    if( (i%4) ){ // ignore the diagonals (0, 4, and 8)
265 <      orthoRhombic = (Hmat[i] <= tol);
261 > void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
262 >  double a0, a1, a2;
263 >
264 >  a0 = inVec[0];  a1 = inVec[1];  a2 = inVec[2];
265 >
266 >  outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2;
267 >  outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
268 >  outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
269 > }
270 >
271 > void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
272 >  double temp[3][3];
273 >  int i, j;
274 >
275 >  for (i = 0; i < 3; i++) {
276 >    for (j = 0; j < 3; j++) {
277 >      temp[j][i] = in[i][j];
278      }
279    }
280 <    
280 >  for (i = 0; i < 3; i++) {
281 >    for (j = 0; j < 3; j++) {
282 >      out[i][j] = temp[i][j];
283 >    }
284 >  }
285   }
286 +  
287 + void SimInfo::printMat3(double A[3][3] ){
288  
289 +  std::cerr
290 +            << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
291 +            << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
292 +            << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
293 + }
294 +
295 + void SimInfo::printMat9(double A[9] ){
296 +
297 +  std::cerr
298 +            << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
299 +            << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
300 +            << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
301 + }
302 +
303   void SimInfo::calcBoxL( void ){
304  
305    double dx, dy, dz, dsq;
306    int i;
307  
308 <  // boxVol = h1 (dot) h2 (cross) h3
308 >  // boxVol = Determinant of Hmat
309  
310 <  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]) );
310 >  boxVol = matDet3( Hmat );
311  
236 –
312    // boxLx
313    
314 <  dx = Hmat[0]; dy = Hmat[1]; dz = Hmat[2];
314 >  dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
315    dsq = dx*dx + dy*dy + dz*dz;
316    boxLx = sqrt( dsq );
317  
318    // boxLy
319    
320 <  dx = Hmat[3]; dy = Hmat[4]; dz = Hmat[5];
320 >  dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
321    dsq = dx*dx + dy*dy + dz*dz;
322    boxLy = sqrt( dsq );
323  
324    // boxLz
325    
326 <  dx = Hmat[6]; dy = Hmat[7]; dz = Hmat[8];
326 >  dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
327    dsq = dx*dx + dy*dy + dz*dz;
328    boxLz = sqrt( dsq );
329    
# Line 262 | Line 337 | void SimInfo::wrapVector( double thePos[3] ){
337  
338    if( !orthoRhombic ){
339      // calc the scaled coordinates.
340 +  
341 +
342 +    matVecMul3(HmatInv, thePos, scaled);
343      
344      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++)
345        scaled[i] -= roundMe(scaled[i]);
346      
347      // calc the wrapped real coordinates from the wrapped scaled coordinates
348      
349 <    for(i=0; i<3; i++)
350 <      thePos[i] =
279 <        scaled[0]*Hmat[i] + scaled[1]*Hmat[i+3] + scaled[2]*Hmat[i+6];
349 >    matVecMul3(Hmat, scaled, thePos);
350 >
351    }
352    else{
353      // calc the scaled coordinates.
354      
355      for(i=0; i<3; i++)
356 <      scaled[i] = thePos[i]*HmatI[i*4];
356 >      scaled[i] = thePos[i]*HmatInv[i][i];
357      
358      // wrap the scaled coordinates
359      
# Line 292 | Line 363 | void SimInfo::wrapVector( double thePos[3] ){
363      // calc the wrapped real coordinates from the wrapped scaled coordinates
364      
365      for(i=0; i<3; i++)
366 <      thePos[i] = scaled[i]*Hmat[i*4];
366 >      thePos[i] = scaled[i]*Hmat[i][i];
367    }
368      
298 –    
369   }
370  
371  

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