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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 572 by mmeineke, Wed Jul 2 21:26:55 2003 UTC vs.
Revision 588 by gezelter, Thu Jul 10 17:10:56 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, FortranHmatI, &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   }
173 –
150  
175 – void SimInfo::calcHmatI( void ) {
151  
152 <  double C[3][3];
153 <  double detHmat;
154 <  int i, j, k;
180 <  double smallDiag;
181 <  double tol;
182 <  double sanity[3][3];
152 > void SimInfo::scaleBox(double scale) {
153 >  double theBox[3][3];
154 >  int i, j;
155  
156 <  // calculate the adjunct of Hmat;
156 >  cerr << "Scaling box by " << scale << "\n";
157  
158 <  C[0][0] =  ( Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]);
159 <  C[1][0] = -( Hmat[1]*Hmat[8]) + (Hmat[7]*Hmat[2]);
188 <  C[2][0] =  ( Hmat[1]*Hmat[5]) - (Hmat[4]*Hmat[2]);
158 >  for(i=0; i<3; i++)
159 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
160  
161 <  C[0][1] = -( Hmat[3]*Hmat[8]) + (Hmat[6]*Hmat[5]);
191 <  C[1][1] =  ( Hmat[0]*Hmat[8]) - (Hmat[6]*Hmat[2]);
192 <  C[2][1] = -( Hmat[0]*Hmat[5]) + (Hmat[3]*Hmat[2]);
161 >  setBoxM(theBox);
162  
163 <  C[0][2] =  ( Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]);
195 <  C[1][2] = -( Hmat[0]*Hmat[7]) + (Hmat[6]*Hmat[1]);
196 <  C[2][2] =  ( Hmat[0]*Hmat[4]) - (Hmat[3]*Hmat[1]);
163 > }
164  
165 <  // calcutlate the determinant of Hmat
199 <  
200 <  detHmat = 0.0;
201 <  for(i=0; i<3; i++) detHmat += Hmat[i] * C[i][0];
165 > void SimInfo::calcHmatInv( void ) {
166  
167 <  
168 <  // H^-1 = C^T / det(H)
169 <  
206 <  i=0;
207 <  for(j=0; j<3; j++){
208 <    for(k=0; k<3; k++){
167 >  double smallDiag;
168 >  double tol;
169 >  double sanity[3][3];
170  
171 <      HmatI[i] = C[j][k] / detHmat;
211 <      i++;
212 <    }
213 <  }
171 >  invertMat3( Hmat, HmatInv );
172  
173 <  // sanity check
173 >  // Check the inverse to make sure it is sane:
174  
175 <  for(i=0; i<3; i++){
218 <    for(j=0; j<3; j++){
219 <      
220 <      sanity[i][j] = 0.0;
221 <      for(k=0; k<3; k++){
222 <        sanity[i][j] += Hmat[3*k+i] * HmatI[3*j+k];
223 <      }
224 <    }
225 <  }
175 >  matMul3( Hmat, HmatInv, sanity );
176  
177    cerr << "sanity => \n"
178         << sanity[0][0] << "\t" << sanity[0][1] << "\t" << sanity [0][2] << "\n"
# Line 230 | Line 180 | void SimInfo::calcHmatI( void ) {
180         << sanity[2][0] << "\t" << sanity[2][1] << "\t" << sanity [2][2]
181         << "\n";
182      
233 –
183    // check to see if Hmat is orthorhombic
184    
185 <  smallDiag = Hmat[0];
186 <  if(smallDiag > Hmat[4]) smallDiag = Hmat[4];
187 <  if(smallDiag > Hmat[8]) smallDiag = Hmat[8];
185 >  smallDiag = Hmat[0][0];
186 >  if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1];
187 >  if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2];
188    tol = smallDiag * 1E-6;
189  
190    orthoRhombic = 1;
191 <  for(i=0; (i<9) && orthoRhombic; i++){
192 <    
193 <    if( (i%4) ){ // ignore the diagonals (0, 4, and 8)
194 <      orthoRhombic = (Hmat[i] <= tol);
191 >  
192 >  for (i = 0; i < 3; i++ ) {
193 >    for (j = 0 ; j < 3; j++) {
194 >      if (i != j) {
195 >        if (orthoRhombic) {
196 >          if (Hmat[i][j] >= tol) orthoRhombic = 0;
197 >        }        
198 >      }
199      }
200    }
248 –    
201   }
202  
203 + double SimInfo::matDet3(double a[3][3]) {
204 +  int i, j, k;
205 +  double determinant;
206 +
207 +  determinant = 0.0;
208 +
209 +  for(i = 0; i < 3; i++) {
210 +    j = (i+1)%3;
211 +    k = (i+2)%3;
212 +
213 +    determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]);
214 +  }
215 +
216 +  return determinant;
217 + }
218 +
219 + void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
220 +  
221 +  int  i, j, k, l, m, n;
222 +  double determinant;
223 +
224 +  determinant = matDet3( a );
225 +
226 +  if (determinant == 0.0) {
227 +    sprintf( painCave.errMsg,
228 +             "Can't invert a matrix with a zero determinant!\n");
229 +    painCave.isFatal = 1;
230 +    simError();
231 +  }
232 +
233 +  for (i=0; i < 3; i++) {
234 +    j = (i+1)%3;
235 +    k = (i+2)%3;
236 +    for(l = 0; l < 3; l++) {
237 +      m = (l+1)%3;
238 +      n = (l+2)%3;
239 +      
240 +      b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant;
241 +    }
242 +  }
243 + }
244 +
245 + void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
246 +  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
247 +
248 +  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
249 +  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
250 +  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
251 +  
252 +  r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0];
253 +  r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1];
254 +  r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2];
255 +  
256 +  r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0];
257 +  r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1];
258 +  r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2];
259 +  
260 +  c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
261 +  c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
262 +  c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
263 + }
264 +
265 + void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
266 +  double a0, a1, a2;
267 +
268 +  a0 = inVec[0];  a1 = inVec[1];  a2 = inVec[2];
269 +
270 +  outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2;
271 +  outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
272 +  outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
273 + }
274 +  
275   void SimInfo::calcBoxL( void ){
276  
277    double dx, dy, dz, dsq;
278    int i;
279  
280 <  // boxVol = h1 (dot) h2 (cross) h3
280 >  // boxVol = Determinant of Hmat
281  
282 <  boxVol = Hmat[0] * ( (Hmat[4]*Hmat[8]) - (Hmat[7]*Hmat[5]) )
259 <         + Hmat[1] * ( (Hmat[5]*Hmat[6]) - (Hmat[8]*Hmat[3]) )
260 <         + Hmat[2] * ( (Hmat[3]*Hmat[7]) - (Hmat[6]*Hmat[4]) );
282 >  boxVol = matDet3( Hmat );
283  
262 –
284    // boxLx
285    
286 <  dx = Hmat[0]; dy = Hmat[1]; dz = Hmat[2];
286 >  dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
287    dsq = dx*dx + dy*dy + dz*dz;
288    boxLx = sqrt( dsq );
289  
290    // boxLy
291    
292 <  dx = Hmat[3]; dy = Hmat[4]; dz = Hmat[5];
292 >  dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
293    dsq = dx*dx + dy*dy + dz*dz;
294    boxLy = sqrt( dsq );
295  
296    // boxLz
297    
298 <  dx = Hmat[6]; dy = Hmat[7]; dz = Hmat[8];
298 >  dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
299    dsq = dx*dx + dy*dy + dz*dz;
300    boxLz = sqrt( dsq );
301    
# Line 288 | Line 309 | void SimInfo::wrapVector( double thePos[3] ){
309  
310    if( !orthoRhombic ){
311      // calc the scaled coordinates.
312 +  
313 +
314 +    matVecMul3(HmatInv, thePos, scaled);
315      
316      for(i=0; i<3; i++)
293 –      scaled[i] =
294 –        thePos[0]*HmatI[i] + thePos[1]*HmatI[i+3] + thePos[3]*HmatI[i+6];
295 –    
296 –    // wrap the scaled coordinates
297 –    
298 –    for(i=0; i<3; i++)
317        scaled[i] -= roundMe(scaled[i]);
318      
319      // calc the wrapped real coordinates from the wrapped scaled coordinates
320      
321 <    for(i=0; i<3; i++)
322 <      thePos[i] =
305 <        scaled[0]*Hmat[i] + scaled[1]*Hmat[i+3] + scaled[2]*Hmat[i+6];
321 >    matVecMul3(Hmat, scaled, thePos);
322 >
323    }
324    else{
325      // calc the scaled coordinates.
326      
327      for(i=0; i<3; i++)
328 <      scaled[i] = thePos[i]*HmatI[i*4];
328 >      scaled[i] = thePos[i]*HmatInv[i][i];
329      
330      // wrap the scaled coordinates
331      
# Line 318 | Line 335 | void SimInfo::wrapVector( double thePos[3] ){
335      // calc the wrapped real coordinates from the wrapped scaled coordinates
336      
337      for(i=0; i<3; i++)
338 <      thePos[i] = scaled[i]*Hmat[i*4];
338 >      thePos[i] = scaled[i]*Hmat[i][i];
339    }
340      
324 –    
341   }
342  
343  

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