ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
(Generate patch)

Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 586 by mmeineke, Wed Jul 9 22:14:06 2003 UTC vs.
Revision 621 by gezelter, Wed Jul 16 02:11:02 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;
102 <  if (boxLz < smallestBoxL) smallestBoxL = boxLz;
100 >  smallestBoxL = boxL[0];
101 >  if (boxL[1] < smallestBoxL) smallestBoxL = boxL[1];
102 >  if (boxL[2] > smallestBoxL) smallestBoxL = boxL[2];
103  
104    maxCutoff = smallestBoxL / 2.0;
105  
# Line 93 | Line 109 | void SimInfo::setBoxM( double theBox[9] ){
109               maxCutoff );
110      painCave.isFatal = 0;
111      simError();
96 –
112      rList = maxCutoff;
113  
114 <    sprintf( painCave.errMsg,
100 <             "New Box size is forcing cutoff radius down to %lf\n",
101 <             maxCutoff - 1.0 );
102 <    painCave.isFatal = 0;
103 <    simError();
104 <
105 <    rCut = rList - 1.0;
106 <
107 <    // list radius changed so we have to refresh the simulation structure.
108 <    refreshSim();
109 <  }
110 <
111 <  if (rCut > maxCutoff) {
112 <    sprintf( painCave.errMsg,
113 <             "New Box size is forcing cutoff radius down to %lf\n",
114 <             maxCutoff );
115 <    painCave.isFatal = 0;
116 <    simError();
117 <
118 <    status = 0;
119 <    LJ_new_rcut(&rCut, &status);
120 <    if (status != 0) {
114 >    if (rCut > (rList - 1.0)) {
115        sprintf( painCave.errMsg,
116 <               "Error in recomputing LJ shifts based on new rcut\n");
117 <      painCave.isFatal = 1;
116 >               "New Box size is forcing LJ cutoff radius down to %lf\n",
117 >               rList - 1.0 );
118 >      painCave.isFatal = 0;
119        simError();
120 +      rCut = rList - 1.0;
121      }
122 <  }
122 >
123 >    if( ecr > (rList - 1.0) ){
124 >      sprintf( painCave.errMsg,
125 >               "New Box size is forcing electrostaticCutoffRadius "
126 >               "down to %lf\n"
127 >               "electrostaticSkinThickness is now %lf\n",
128 >               rList - 1.0, 0.05*(rList-1.0) );
129 >      painCave.isFatal = 0;
130 >      simError();      
131 >      ecr = maxCutoff;
132 >      est = 0.05 * ecr;
133 >    }
134 >
135 >    // At least one of the radii changed, so we need a refresh:
136 >    refreshSim();
137 >  }    
138   }
139  
140  
141 < void SimInfo::getBoxM (double theBox[9]) {
141 > void SimInfo::getBoxM (double theBox[3][3]) {
142  
143 <  int i;
144 <  for(i=0; i<9; i++) theBox[i] = Hmat[i];
143 >  int i, j;
144 >  for(i=0; i<3; i++)
145 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
146   }
147  
148  
149   void SimInfo::scaleBox(double scale) {
150 <  double theBox[9];
151 <  int i;
150 >  double theBox[3][3];
151 >  int i, j;
152  
153 <  cerr << "Scaling box by " << scale << "\n";
153 >  // cerr << "Scaling box by " << scale << "\n";
154  
155 <  for(i=0; i<9; i++) theBox[i] = Hmat[i]*scale;
155 >  for(i=0; i<3; i++)
156 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
157  
158    setBoxM(theBox);
159  
160   }
161  
162 < void SimInfo::calcHmatI( void ) {
163 <
164 <  double C[3][3];
152 <  double detHmat;
153 <  int i, j, k;
162 > void SimInfo::calcHmatInv( void ) {
163 >  
164 >  int i,j;
165    double smallDiag;
166    double tol;
167    double sanity[3][3];
168  
169 <  // calculate the adjunct of Hmat;
169 >  invertMat3( Hmat, HmatInv );
170  
171 <  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]);
171 >  // Check the inverse to make sure it is sane:
172  
173 <  C[0][1] = -( Hmat[3]*Hmat[8]) + (Hmat[6]*Hmat[5]);
174 <  C[1][1] =  ( Hmat[0]*Hmat[8]) - (Hmat[6]*Hmat[2]);
175 <  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
173 >  matMul3( Hmat, HmatInv, sanity );
174 >    
175 >  // check to see if Hmat is orthorhombic
176    
177 <  detHmat = 0.0;
178 <  for(i=0; i<3; i++) detHmat += Hmat[i] * C[i][0];
177 >  smallDiag = Hmat[0][0];
178 >  if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1];
179 >  if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2];
180 >  tol = smallDiag * 1E-6;
181  
182 +  orthoRhombic = 1;
183    
184 <  // H^-1 = C^T / det(H)
185 <  
186 <  i=0;
187 <  for(j=0; j<3; j++){
188 <    for(k=0; k<3; k++){
189 <
190 <      HmatI[i] = C[j][k] / detHmat;
185 <      i++;
184 >  for (i = 0; i < 3; i++ ) {
185 >    for (j = 0 ; j < 3; j++) {
186 >      if (i != j) {
187 >        if (orthoRhombic) {
188 >          if (Hmat[i][j] >= tol) orthoRhombic = 0;
189 >        }        
190 >      }
191      }
192    }
193 + }
194  
195 <  // sanity check
195 > double SimInfo::matDet3(double a[3][3]) {
196 >  int i, j, k;
197 >  double determinant;
198  
199 <  for(i=0; i<3; i++){
200 <    for(j=0; j<3; j++){
199 >  determinant = 0.0;
200 >
201 >  for(i = 0; i < 3; i++) {
202 >    j = (i+1)%3;
203 >    k = (i+2)%3;
204 >
205 >    determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]);
206 >  }
207 >
208 >  return determinant;
209 > }
210 >
211 > void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
212 >  
213 >  int  i, j, k, l, m, n;
214 >  double determinant;
215 >
216 >  determinant = matDet3( a );
217 >
218 >  if (determinant == 0.0) {
219 >    sprintf( painCave.errMsg,
220 >             "Can't invert a matrix with a zero determinant!\n");
221 >    painCave.isFatal = 1;
222 >    simError();
223 >  }
224 >
225 >  for (i=0; i < 3; i++) {
226 >    j = (i+1)%3;
227 >    k = (i+2)%3;
228 >    for(l = 0; l < 3; l++) {
229 >      m = (l+1)%3;
230 >      n = (l+2)%3;
231        
232 <      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 <      }
232 >      b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant;
233      }
234    }
235 + }
236  
237 <  cerr << "sanity => \n"
238 <       << 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 <    
237 > void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
238 >  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
239  
240 <  // check to see if Hmat is orthorhombic
240 >  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
241 >  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
242 >  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
243    
244 <  smallDiag = Hmat[0];
245 <  if(smallDiag > Hmat[4]) smallDiag = Hmat[4];
246 <  if(smallDiag > Hmat[8]) smallDiag = Hmat[8];
247 <  tol = smallDiag * 1E-6;
244 >  r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0];
245 >  r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1];
246 >  r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2];
247 >  
248 >  r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0];
249 >  r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1];
250 >  r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2];
251 >  
252 >  c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
253 >  c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
254 >  c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
255 > }
256  
257 <  orthoRhombic = 1;
258 <  for(i=0; (i<9) && orthoRhombic; i++){
259 <    
260 <    if( (i%4) ){ // ignore the diagonals (0, 4, and 8)
261 <      orthoRhombic = (Hmat[i] <= tol);
257 > void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
258 >  double a0, a1, a2;
259 >
260 >  a0 = inVec[0];  a1 = inVec[1];  a2 = inVec[2];
261 >
262 >  outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2;
263 >  outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
264 >  outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
265 > }
266 >
267 > void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
268 >  double temp[3][3];
269 >  int i, j;
270 >
271 >  for (i = 0; i < 3; i++) {
272 >    for (j = 0; j < 3; j++) {
273 >      temp[j][i] = in[i][j];
274      }
275    }
276 <    
276 >  for (i = 0; i < 3; i++) {
277 >    for (j = 0; j < 3; j++) {
278 >      out[i][j] = temp[i][j];
279 >    }
280 >  }
281   }
282 +  
283 + void SimInfo::printMat3(double A[3][3] ){
284  
285 +  std::cerr
286 +            << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
287 +            << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
288 +            << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
289 + }
290 +
291 + void SimInfo::printMat9(double A[9] ){
292 +
293 +  std::cerr
294 +            << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
295 +            << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
296 +            << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
297 + }
298 +
299   void SimInfo::calcBoxL( void ){
300  
301    double dx, dy, dz, dsq;
302    int i;
303  
304 <  // boxVol = h1 (dot) h2 (cross) h3
304 >  // boxVol = Determinant of Hmat
305  
306 <  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]) );
306 >  boxVol = matDet3( Hmat );
307  
236 –
308    // boxLx
309    
310 <  dx = Hmat[0]; dy = Hmat[1]; dz = Hmat[2];
310 >  dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
311    dsq = dx*dx + dy*dy + dz*dz;
312 <  boxLx = sqrt( dsq );
312 >  boxL[0] = sqrt( dsq );
313  
314    // boxLy
315    
316 <  dx = Hmat[3]; dy = Hmat[4]; dz = Hmat[5];
316 >  dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
317    dsq = dx*dx + dy*dy + dz*dz;
318 <  boxLy = sqrt( dsq );
318 >  boxL[1] = sqrt( dsq );
319  
320    // boxLz
321    
322 <  dx = Hmat[6]; dy = Hmat[7]; dz = Hmat[8];
322 >  dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
323    dsq = dx*dx + dy*dy + dz*dz;
324 <  boxLz = sqrt( dsq );
324 >  boxL[2] = sqrt( dsq );
325    
326   }
327  
# Line 262 | Line 333 | void SimInfo::wrapVector( double thePos[3] ){
333  
334    if( !orthoRhombic ){
335      // calc the scaled coordinates.
336 +  
337 +
338 +    matVecMul3(HmatInv, thePos, scaled);
339      
340      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++)
341        scaled[i] -= roundMe(scaled[i]);
342      
343      // calc the wrapped real coordinates from the wrapped scaled coordinates
344      
345 <    for(i=0; i<3; i++)
346 <      thePos[i] =
279 <        scaled[0]*Hmat[i] + scaled[1]*Hmat[i+3] + scaled[2]*Hmat[i+6];
345 >    matVecMul3(Hmat, scaled, thePos);
346 >
347    }
348    else{
349      // calc the scaled coordinates.
350      
351      for(i=0; i<3; i++)
352 <      scaled[i] = thePos[i]*HmatI[i*4];
352 >      scaled[i] = thePos[i]*HmatInv[i][i];
353      
354      // wrap the scaled coordinates
355      
# Line 292 | Line 359 | void SimInfo::wrapVector( double thePos[3] ){
359      // calc the wrapped real coordinates from the wrapped scaled coordinates
360      
361      for(i=0; i<3; i++)
362 <      thePos[i] = scaled[i]*Hmat[i*4];
362 >      thePos[i] = scaled[i]*Hmat[i][i];
363    }
364      
298 –    
365   }
366  
367  

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines