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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 658 by tim, Thu Jul 31 15:35:07 2003 UTC

# Line 33 | Line 33 | SimInfo::SimInfo(){
33    the_integrator = NULL;
34    setTemp = 0;
35    thermalTime = 0.0;
36 +  currentTime = 0.0;
37    rCut = 0.0;
38 +  ecr = 0.0;
39 +  est = 0.0;
40 +  oldEcr = 0.0;
41 +  oldRcut = 0.0;
42  
43 +  haveOrigRcut = 0;
44 +  haveOrigEcr = 0;
45 +  boxIsInit = 0;
46 +  
47 +  
48 +
49    usePBC = 0;
50    useLJ = 0;
51    useSticky = 0;
# Line 48 | Line 59 | void SimInfo::setBox(double newBox[3]) {
59  
60   void SimInfo::setBox(double newBox[3]) {
61    
62 <  int i;
63 <  double tempMat[9];
62 >  int i, j;
63 >  double tempMat[3][3];
64  
65 <  for(i=0; i<9; i++) tempMat[i] = 0.0;;
65 >  for(i=0; i<3; i++)
66 >    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
67  
68 <  tempMat[0] = newBox[0];
69 <  tempMat[4] = newBox[1];
70 <  tempMat[8] = newBox[2];
68 >  tempMat[0][0] = newBox[0];
69 >  tempMat[1][1] = newBox[1];
70 >  tempMat[2][2] = newBox[2];
71  
72    setBoxM( tempMat );
73  
74   }
75  
76 < void SimInfo::setBoxM( double theBox[9] ){
76 > void SimInfo::setBoxM( double theBox[3][3] ){
77    
78 <  int i, status;
78 >  int i, j, status;
79    double smallestBoxL, maxCutoff;
80 +  double FortranHmat[9]; // to preserve compatibility with Fortran the
81 +                         // ordering in the array is as follows:
82 +                         // [ 0 3 6 ]
83 +                         // [ 1 4 7 ]
84 +                         // [ 2 5 8 ]
85 +  double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
86  
87 <  for(i=0; i<9; i++) Hmat[i] = theBox[i];
87 >  
88 >  if( !boxIsInit ) boxIsInit = 1;
89  
90 <  cerr
91 <    << "setting Hmat ->\n"
92 <    << "[ " << Hmat[0] << ", " << Hmat[3] << ", " << Hmat[6] << " ]\n"
74 <    << "[ " << Hmat[1] << ", " << Hmat[4] << ", " << Hmat[7] << " ]\n"
75 <    << "[ " << Hmat[2] << ", " << Hmat[5] << ", " << Hmat[8] << " ]\n";
76 <
77 <  calcHmatI();
90 >  for(i=0; i < 3; i++)
91 >    for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
92 >  
93    calcBoxL();
94 +  calcHmatInv();
95  
96 <
97 <
98 <  setFortranBoxSize(Hmat, HmatI, &orthoRhombic);
99 <
84 <  smallestBoxL = boxLx;
85 <  if (boxLy < smallestBoxL) smallestBoxL = boxLy;
86 <  if (boxLz < smallestBoxL) smallestBoxL = boxLz;
87 <
88 <  maxCutoff = smallestBoxL / 2.0;
89 <
90 <  if (rList > maxCutoff) {
91 <    sprintf( painCave.errMsg,
92 <             "New Box size is forcing neighborlist radius down to %lf\n",
93 <             maxCutoff );
94 <    painCave.isFatal = 0;
95 <    simError();
96 <
97 <    rList = maxCutoff;
98 <
99 <    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) {
121 <      sprintf( painCave.errMsg,
122 <               "Error in recomputing LJ shifts based on new rcut\n");
123 <      painCave.isFatal = 1;
124 <      simError();
96 >  for(i=0; i < 3; i++) {
97 >    for (j=0; j < 3; j++) {
98 >      FortranHmat[3*j + i] = Hmat[i][j];
99 >      FortranHmatInv[3*j + i] = HmatInv[i][j];
100      }
101    }
102 +
103 +  setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
104 +
105   }
106  
107  
108 < void SimInfo::getBoxM (double theBox[9]) {
108 > void SimInfo::getBoxM (double theBox[3][3]) {
109  
110 <  int i;
111 <  for(i=0; i<9; i++) theBox[i] = Hmat[i];
110 >  int i, j;
111 >  for(i=0; i<3; i++)
112 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
113   }
114  
115  
116   void SimInfo::scaleBox(double scale) {
117 <  double theBox[9];
118 <  int i;
117 >  double theBox[3][3];
118 >  int i, j;
119  
120 <  cerr << "Scaling box by " << scale << "\n";
120 >  // cerr << "Scaling box by " << scale << "\n";
121  
122 <  for(i=0; i<9; i++) theBox[i] = Hmat[i]*scale;
122 >  for(i=0; i<3; i++)
123 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
124  
125    setBoxM(theBox);
126  
127   }
128  
129 < void SimInfo::calcHmatI( void ) {
130 <
131 <  double C[3][3];
152 <  double detHmat;
153 <  int i, j, k;
129 > void SimInfo::calcHmatInv( void ) {
130 >  
131 >  int i,j;
132    double smallDiag;
133    double tol;
134    double sanity[3][3];
135  
136 <  // calculate the adjunct of Hmat;
136 >  invertMat3( Hmat, HmatInv );
137  
138 <  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]);
138 >  // Check the inverse to make sure it is sane:
139  
140 <  C[0][1] = -( Hmat[3]*Hmat[8]) + (Hmat[6]*Hmat[5]);
141 <  C[1][1] =  ( Hmat[0]*Hmat[8]) - (Hmat[6]*Hmat[2]);
142 <  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
140 >  matMul3( Hmat, HmatInv, sanity );
141 >    
142 >  // check to see if Hmat is orthorhombic
143    
144 <  detHmat = 0.0;
145 <  for(i=0; i<3; i++) detHmat += Hmat[i] * C[i][0];
144 >  smallDiag = Hmat[0][0];
145 >  if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1];
146 >  if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2];
147 >  tol = smallDiag * 1E-6;
148  
149 +  orthoRhombic = 1;
150    
151 <  // H^-1 = C^T / det(H)
152 <  
153 <  i=0;
154 <  for(j=0; j<3; j++){
155 <    for(k=0; k<3; k++){
156 <
157 <      HmatI[i] = C[j][k] / detHmat;
185 <      i++;
151 >  for (i = 0; i < 3; i++ ) {
152 >    for (j = 0 ; j < 3; j++) {
153 >      if (i != j) {
154 >        if (orthoRhombic) {
155 >          if (Hmat[i][j] >= tol) orthoRhombic = 0;
156 >        }        
157 >      }
158      }
159    }
160 + }
161  
162 <  // sanity check
162 > double SimInfo::matDet3(double a[3][3]) {
163 >  int i, j, k;
164 >  double determinant;
165  
166 <  for(i=0; i<3; i++){
167 <    for(j=0; j<3; j++){
166 >  determinant = 0.0;
167 >
168 >  for(i = 0; i < 3; i++) {
169 >    j = (i+1)%3;
170 >    k = (i+2)%3;
171 >
172 >    determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]);
173 >  }
174 >
175 >  return determinant;
176 > }
177 >
178 > void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
179 >  
180 >  int  i, j, k, l, m, n;
181 >  double determinant;
182 >
183 >  determinant = matDet3( a );
184 >
185 >  if (determinant == 0.0) {
186 >    sprintf( painCave.errMsg,
187 >             "Can't invert a matrix with a zero determinant!\n");
188 >    painCave.isFatal = 1;
189 >    simError();
190 >  }
191 >
192 >  for (i=0; i < 3; i++) {
193 >    j = (i+1)%3;
194 >    k = (i+2)%3;
195 >    for(l = 0; l < 3; l++) {
196 >      m = (l+1)%3;
197 >      n = (l+2)%3;
198        
199 <      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 <      }
199 >      b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant;
200      }
201    }
202 + }
203  
204 <  cerr << "sanity => \n"
205 <       << 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 <    
204 > void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
205 >  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
206  
207 <  // check to see if Hmat is orthorhombic
207 >  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
208 >  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
209 >  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
210    
211 <  smallDiag = Hmat[0];
212 <  if(smallDiag > Hmat[4]) smallDiag = Hmat[4];
213 <  if(smallDiag > Hmat[8]) smallDiag = Hmat[8];
214 <  tol = smallDiag * 1E-6;
211 >  r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0];
212 >  r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1];
213 >  r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2];
214 >  
215 >  r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0];
216 >  r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1];
217 >  r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2];
218 >  
219 >  c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
220 >  c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
221 >  c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
222 > }
223  
224 <  orthoRhombic = 1;
225 <  for(i=0; (i<9) && orthoRhombic; i++){
226 <    
227 <    if( (i%4) ){ // ignore the diagonals (0, 4, and 8)
228 <      orthoRhombic = (Hmat[i] <= tol);
224 > void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
225 >  double a0, a1, a2;
226 >
227 >  a0 = inVec[0];  a1 = inVec[1];  a2 = inVec[2];
228 >
229 >  outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2;
230 >  outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
231 >  outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
232 > }
233 >
234 > void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
235 >  double temp[3][3];
236 >  int i, j;
237 >
238 >  for (i = 0; i < 3; i++) {
239 >    for (j = 0; j < 3; j++) {
240 >      temp[j][i] = in[i][j];
241      }
242    }
243 <    
243 >  for (i = 0; i < 3; i++) {
244 >    for (j = 0; j < 3; j++) {
245 >      out[i][j] = temp[i][j];
246 >    }
247 >  }
248   }
249 +  
250 + void SimInfo::printMat3(double A[3][3] ){
251  
252 +  std::cerr
253 +            << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
254 +            << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
255 +            << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
256 + }
257 +
258 + void SimInfo::printMat9(double A[9] ){
259 +
260 +  std::cerr
261 +            << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
262 +            << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
263 +            << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
264 + }
265 +
266   void SimInfo::calcBoxL( void ){
267  
268    double dx, dy, dz, dsq;
269    int i;
270  
271 <  // boxVol = h1 (dot) h2 (cross) h3
271 >  // boxVol = Determinant of Hmat
272  
273 <  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]) );
273 >  boxVol = matDet3( Hmat );
274  
236 –
275    // boxLx
276    
277 <  dx = Hmat[0]; dy = Hmat[1]; dz = Hmat[2];
277 >  dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
278    dsq = dx*dx + dy*dy + dz*dz;
279 <  boxLx = sqrt( dsq );
279 >  boxL[0] = sqrt( dsq );
280 >  maxCutoff = 0.5 * boxL[0];
281  
282    // boxLy
283    
284 <  dx = Hmat[3]; dy = Hmat[4]; dz = Hmat[5];
284 >  dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
285    dsq = dx*dx + dy*dy + dz*dz;
286 <  boxLy = sqrt( dsq );
286 >  boxL[1] = sqrt( dsq );
287 >  if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
288  
289    // boxLz
290    
291 <  dx = Hmat[6]; dy = Hmat[7]; dz = Hmat[8];
291 >  dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
292    dsq = dx*dx + dy*dy + dz*dz;
293 <  boxLz = sqrt( dsq );
294 <  
293 >  boxL[2] = sqrt( dsq );
294 >  if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
295 >
296   }
297  
298  
# Line 262 | Line 303 | void SimInfo::wrapVector( double thePos[3] ){
303  
304    if( !orthoRhombic ){
305      // calc the scaled coordinates.
306 +  
307 +
308 +    matVecMul3(HmatInv, thePos, scaled);
309      
310      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++)
311        scaled[i] -= roundMe(scaled[i]);
312      
313      // calc the wrapped real coordinates from the wrapped scaled coordinates
314      
315 <    for(i=0; i<3; i++)
316 <      thePos[i] =
279 <        scaled[0]*Hmat[i] + scaled[1]*Hmat[i+3] + scaled[2]*Hmat[i+6];
315 >    matVecMul3(Hmat, scaled, thePos);
316 >
317    }
318    else{
319      // calc the scaled coordinates.
320      
321      for(i=0; i<3; i++)
322 <      scaled[i] = thePos[i]*HmatI[i*4];
322 >      scaled[i] = thePos[i]*HmatInv[i][i];
323      
324      // wrap the scaled coordinates
325      
# Line 292 | Line 329 | void SimInfo::wrapVector( double thePos[3] ){
329      // calc the wrapped real coordinates from the wrapped scaled coordinates
330      
331      for(i=0; i<3; i++)
332 <      thePos[i] = scaled[i]*Hmat[i*4];
332 >      thePos[i] = scaled[i]*Hmat[i][i];
333    }
334      
298 –    
335   }
336  
337  
# Line 336 | Line 372 | void SimInfo::refreshSim(){
372    int isError;
373    int n_global;
374    int* excl;
375 <  
340 <  fInfo.rrf = 0.0;
341 <  fInfo.rt = 0.0;
375 >
376    fInfo.dielect = 0.0;
377  
344 –  fInfo.rlist = rList;
345 –  fInfo.rcut = rCut;
346 –
378    if( useDipole ){
348 –    fInfo.rrf = ecr;
349 –    fInfo.rt = ecr - est;
379      if( useReactionField )fInfo.dielect = dielectric;
380    }
381  
# Line 395 | Line 424 | void SimInfo::refreshSim(){
424  
425   }
426  
427 +
428 + void SimInfo::setRcut( double theRcut ){
429 +
430 +  if( !haveOrigRcut ){
431 +    haveOrigRcut = 1;
432 +    origRcut = theRcut;
433 +  }
434 +
435 +  rCut = theRcut;
436 +  checkCutOffs();
437 + }
438 +
439 + void SimInfo::setEcr( double theEcr ){
440 +
441 +  if( !haveOrigEcr ){
442 +    haveOrigEcr = 1;
443 +    origEcr = theEcr;
444 +  }
445 +
446 +  ecr = theEcr;
447 +  checkCutOffs();
448 + }
449 +
450 + void SimInfo::setEcr( double theEcr, double theEst ){
451 +
452 +  est = theEst;
453 +  setEcr( theEcr );
454 + }
455 +
456 +
457 + void SimInfo::checkCutOffs( void ){
458 +
459 +  int cutChanged = 0;
460 +
461 +  if( boxIsInit ){
462 +    
463 +    //we need to check cutOffs against the box
464 +    
465 +    if( maxCutoff > rCut ){
466 +      if( rCut < origRcut ){
467 +        rCut = origRcut;
468 +        if (rCut > maxCutoff) rCut = maxCutoff;
469 +        
470 +        sprintf( painCave.errMsg,
471 +                 "New Box size is setting the long range cutoff radius "
472 +                 "to %lf\n",
473 +                 rCut );
474 +        painCave.isFatal = 0;
475 +        simError();
476 +      }
477 +    }
478 +
479 +    if( maxCutoff > ecr ){
480 +      if( ecr < origEcr ){
481 +        rCut = origEcr;
482 +        if (ecr > maxCutoff) ecr = maxCutoff;
483 +        
484 +        sprintf( painCave.errMsg,
485 +                 "New Box size is setting the electrostaticCutoffRadius "
486 +                 "to %lf\n",
487 +                 ecr );
488 +        painCave.isFatal = 0;
489 +        simError();
490 +      }
491 +    }
492 +
493 +
494 +    if (rCut > maxCutoff) {
495 +      sprintf( painCave.errMsg,
496 +               "New Box size is setting the long range cutoff radius "
497 +               "to %lf\n",
498 +               maxCutoff );
499 +      painCave.isFatal = 0;
500 +      simError();
501 +      rCut = maxCutoff;
502 +    }
503 +
504 +    if( ecr > maxCutoff){
505 +      sprintf( painCave.errMsg,
506 +               "New Box size is setting the electrostaticCutoffRadius "
507 +               "to %lf\n",
508 +               maxCutoff  );
509 +      painCave.isFatal = 0;
510 +      simError();      
511 +      ecr = maxCutoff;
512 +    }
513 +
514 +    
515 +  }
516 +  
517 +
518 +  if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
519 +
520 +  // rlist is the 1.0 plus max( rcut, ecr )
521 +  
522 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
523 +
524 +  if( cutChanged ){
525 +    
526 +    notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
527 +  }
528 +
529 +  oldEcr = ecr;
530 +  oldRcut = rCut;
531 + }
532 +
533 + void SimInfo::addProperty(GenericData* prop){
534 +
535 +  map<string, GenericData*>::iterator result;
536 +  result = properties.find(prop->getID());
537 +  
538 +  //we can't simply use  properties[prop->getID()] = prop,
539 +  //it will cause memory leak if we already contain a propery which has the same name of prop
540 +  
541 +  if(result != properties.end()){
542 +    
543 +    delete (*result).second;
544 +    (*result).second = prop;
545 +      
546 +  }
547 +  else{
548 +
549 +    properties[prop->getID()] = prop;
550 +
551 +  }
552 +    
553 + }
554 +
555 + GenericData* SimInfo::getProperty(const string& propName){
556 +
557 +  map<string, GenericData*>::iterator result;
558 +  
559 +  //string lowerCaseName = ();
560 +  
561 +  result = properties.find(propName);
562 +  
563 +  if(result != properties.end())
564 +    return (*result).second;  
565 +  else  
566 +    return NULL;  
567 + }
568 +
569 + vector<GenericData*> SimInfo::getProperties(){
570 +
571 +  vector<GenericData*> result;
572 +  map<string, GenericData*>::iterator i;
573 +  
574 +  for(i = properties.begin(); i != properties.end(); i++)
575 +    result.push_back((*i).second);
576 +    
577 +  return result;
578 + }
579 +
580 +

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