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 420 by mmeineke, Thu Mar 27 17:32:03 2003 UTC vs.
Revision 626 by mmeineke, Wed Jul 16 21:30:56 2003 UTC

# Line 1 | Line 1
1   #include <cstdlib>
2   #include <cstring>
3 + #include <cmath>
4  
5 + #include <iostream>
6 + using namespace std;
7  
8   #include "SimInfo.hpp"
9   #define __C
# Line 9 | Line 12 | SimInfo* currentInfo;
12  
13   #include "fortranWrappers.hpp"
14  
15 + #ifdef IS_MPI
16 + #include "mpiSimulation.hpp"
17 + #endif
18 +
19 + inline double roundMe( double x ){
20 +  return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
21 + }
22 +          
23 +
24   SimInfo* currentInfo;
25  
26   SimInfo::SimInfo(){
# Line 16 | Line 28 | SimInfo::SimInfo(){
28    n_constraints = 0;
29    n_oriented = 0;
30    n_dipoles = 0;
31 +  ndf = 0;
32 +  ndfRaw = 0;
33    the_integrator = NULL;
34    setTemp = 0;
35    thermalTime = 0.0;
36    rCut = 0.0;
37 +  ecr = 0.0;
38 +  est = 0.0;
39 +  oldEcr = 0.0;
40 +  oldRcut = 0.0;
41  
42 +  haveOrigRcut = 0;
43 +  haveOrigEcr = 0;
44 +  boxIsInit = 0;
45 +  
46 +  
47 +
48    usePBC = 0;
49    useLJ = 0;
50    useSticky = 0;
# Line 29 | Line 53 | SimInfo::SimInfo(){
53    useGB = 0;
54    useEAM = 0;
55  
56 +  wrapMeSimInfo( this );
57 + }
58  
59 + void SimInfo::setBox(double newBox[3]) {
60 +  
61 +  int i, j;
62 +  double tempMat[3][3];
63  
64 <  wrapMeSimInfo( this );
64 >  for(i=0; i<3; i++)
65 >    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
66 >
67 >  tempMat[0][0] = newBox[0];
68 >  tempMat[1][1] = newBox[1];
69 >  tempMat[2][2] = newBox[2];
70 >
71 >  setBoxM( tempMat );
72 >
73 > }
74 >
75 > void SimInfo::setBoxM( double theBox[3][3] ){
76 >  
77 >  int i, j, status;
78 >  double smallestBoxL, maxCutoff;
79 >  double FortranHmat[9]; // to preserve compatibility with Fortran the
80 >                         // ordering in the array is as follows:
81 >                         // [ 0 3 6 ]
82 >                         // [ 1 4 7 ]
83 >                         // [ 2 5 8 ]
84 >  double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
85 >
86 >  
87 >  if( !boxIsInit ) boxIsInit = 1;
88 >
89 >  for(i=0; i < 3; i++)
90 >    for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
91 >  
92 >  calcBoxL();
93 >  calcHmatInv();
94 >
95 >  for(i=0; i < 3; i++) {
96 >    for (j=0; j < 3; j++) {
97 >      FortranHmat[3*j + i] = Hmat[i][j];
98 >      FortranHmatInv[3*j + i] = HmatInv[i][j];
99 >    }
100 >  }
101 >
102 >  setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
103 >
104 > }
105 >
106 >
107 > void SimInfo::getBoxM (double theBox[3][3]) {
108 >
109 >  int i, j;
110 >  for(i=0; i<3; i++)
111 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
112 > }
113 >
114 >
115 > void SimInfo::scaleBox(double scale) {
116 >  double theBox[3][3];
117 >  int i, j;
118 >
119 >  // cerr << "Scaling box by " << scale << "\n";
120 >
121 >  for(i=0; i<3; i++)
122 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
123 >
124 >  setBoxM(theBox);
125 >
126 > }
127 >
128 > void SimInfo::calcHmatInv( void ) {
129 >  
130 >  int i,j;
131 >  double smallDiag;
132 >  double tol;
133 >  double sanity[3][3];
134 >
135 >  invertMat3( Hmat, HmatInv );
136 >
137 >  // Check the inverse to make sure it is sane:
138 >
139 >  matMul3( Hmat, HmatInv, sanity );
140 >    
141 >  // check to see if Hmat is orthorhombic
142 >  
143 >  smallDiag = Hmat[0][0];
144 >  if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1];
145 >  if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2];
146 >  tol = smallDiag * 1E-6;
147 >
148 >  orthoRhombic = 1;
149 >  
150 >  for (i = 0; i < 3; i++ ) {
151 >    for (j = 0 ; j < 3; j++) {
152 >      if (i != j) {
153 >        if (orthoRhombic) {
154 >          if (Hmat[i][j] >= tol) orthoRhombic = 0;
155 >        }        
156 >      }
157 >    }
158 >  }
159 > }
160 >
161 > double SimInfo::matDet3(double a[3][3]) {
162 >  int i, j, k;
163 >  double determinant;
164 >
165 >  determinant = 0.0;
166 >
167 >  for(i = 0; i < 3; i++) {
168 >    j = (i+1)%3;
169 >    k = (i+2)%3;
170 >
171 >    determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]);
172 >  }
173 >
174 >  return determinant;
175 > }
176 >
177 > void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
178 >  
179 >  int  i, j, k, l, m, n;
180 >  double determinant;
181 >
182 >  determinant = matDet3( a );
183 >
184 >  if (determinant == 0.0) {
185 >    sprintf( painCave.errMsg,
186 >             "Can't invert a matrix with a zero determinant!\n");
187 >    painCave.isFatal = 1;
188 >    simError();
189 >  }
190 >
191 >  for (i=0; i < 3; i++) {
192 >    j = (i+1)%3;
193 >    k = (i+2)%3;
194 >    for(l = 0; l < 3; l++) {
195 >      m = (l+1)%3;
196 >      n = (l+2)%3;
197 >      
198 >      b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant;
199 >    }
200 >  }
201 > }
202 >
203 > void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
204 >  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
205 >
206 >  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
207 >  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
208 >  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
209 >  
210 >  r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0];
211 >  r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1];
212 >  r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2];
213 >  
214 >  r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0];
215 >  r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1];
216 >  r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2];
217 >  
218 >  c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
219 >  c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
220 >  c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
221 > }
222 >
223 > void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
224 >  double a0, a1, a2;
225 >
226 >  a0 = inVec[0];  a1 = inVec[1];  a2 = inVec[2];
227 >
228 >  outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2;
229 >  outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
230 >  outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
231 > }
232 >
233 > void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
234 >  double temp[3][3];
235 >  int i, j;
236 >
237 >  for (i = 0; i < 3; i++) {
238 >    for (j = 0; j < 3; j++) {
239 >      temp[j][i] = in[i][j];
240 >    }
241 >  }
242 >  for (i = 0; i < 3; i++) {
243 >    for (j = 0; j < 3; j++) {
244 >      out[i][j] = temp[i][j];
245 >    }
246 >  }
247 > }
248 >  
249 > void SimInfo::printMat3(double A[3][3] ){
250 >
251 >  std::cerr
252 >            << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
253 >            << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
254 >            << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
255 > }
256 >
257 > void SimInfo::printMat9(double A[9] ){
258 >
259 >  std::cerr
260 >            << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
261 >            << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
262 >            << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
263 > }
264 >
265 > void SimInfo::calcBoxL( void ){
266 >
267 >  double dx, dy, dz, dsq;
268 >  int i;
269 >
270 >  // boxVol = Determinant of Hmat
271 >
272 >  boxVol = matDet3( Hmat );
273 >
274 >  // boxLx
275 >  
276 >  dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
277 >  dsq = dx*dx + dy*dy + dz*dz;
278 >  boxL[0] = sqrt( dsq );
279 >  maxCutoff = 0.5 * boxL[0];
280 >
281 >  // boxLy
282 >  
283 >  dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
284 >  dsq = dx*dx + dy*dy + dz*dz;
285 >  boxL[1] = sqrt( dsq );
286 >  if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
287 >
288 >  // boxLz
289 >  
290 >  dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
291 >  dsq = dx*dx + dy*dy + dz*dz;
292 >  boxL[2] = sqrt( dsq );
293 >  if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
294 >
295   }
296  
297 +
298 + void SimInfo::wrapVector( double thePos[3] ){
299 +
300 +  int i, j, k;
301 +  double scaled[3];
302 +
303 +  if( !orthoRhombic ){
304 +    // calc the scaled coordinates.
305 +  
306 +
307 +    matVecMul3(HmatInv, thePos, scaled);
308 +    
309 +    for(i=0; i<3; i++)
310 +      scaled[i] -= roundMe(scaled[i]);
311 +    
312 +    // calc the wrapped real coordinates from the wrapped scaled coordinates
313 +    
314 +    matVecMul3(Hmat, scaled, thePos);
315 +
316 +  }
317 +  else{
318 +    // calc the scaled coordinates.
319 +    
320 +    for(i=0; i<3; i++)
321 +      scaled[i] = thePos[i]*HmatInv[i][i];
322 +    
323 +    // wrap the scaled coordinates
324 +    
325 +    for(i=0; i<3; i++)
326 +      scaled[i] -= roundMe(scaled[i]);
327 +    
328 +    // calc the wrapped real coordinates from the wrapped scaled coordinates
329 +    
330 +    for(i=0; i<3; i++)
331 +      thePos[i] = scaled[i]*Hmat[i][i];
332 +  }
333 +    
334 + }
335 +
336 +
337 + int SimInfo::getNDF(){
338 +  int ndf_local, ndf;
339 +  
340 +  ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
341 +
342 + #ifdef IS_MPI
343 +  MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
344 + #else
345 +  ndf = ndf_local;
346 + #endif
347 +
348 +  ndf = ndf - 3;
349 +
350 +  return ndf;
351 + }
352 +
353 + int SimInfo::getNDFraw() {
354 +  int ndfRaw_local, ndfRaw;
355 +
356 +  // Raw degrees of freedom that we have to set
357 +  ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
358 +  
359 + #ifdef IS_MPI
360 +  MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
361 + #else
362 +  ndfRaw = ndfRaw_local;
363 + #endif
364 +
365 +  return ndfRaw;
366 + }
367 +
368   void SimInfo::refreshSim(){
369  
370    simtype fInfo;
371    int isError;
372 +  int n_global;
373 +  int* excl;
374  
375 <  fInfo.box[0] = box_x;
43 <  fInfo.box[1] = box_y;
44 <  fInfo.box[2] = box_z;
375 >  fInfo.dielect = 0.0;
376  
377 <  fInfo.rlist = rList;
378 <  fInfo.rcut = rCut;
379 <  fInfo.rrf = ecr;
49 <  fInfo.rt = ecr - est;
50 <  fInfo.dielect = dielectric;
377 >  if( useDipole ){
378 >    if( useReactionField )fInfo.dielect = dielectric;
379 >  }
380  
381    fInfo.SIM_uses_PBC = usePBC;
382 +  //fInfo.SIM_uses_LJ = 0;
383    fInfo.SIM_uses_LJ = useLJ;
384 <  //fInfo.SIM_uses_sticky = useSticky;
385 <  fInfo.SIM_uses_sticky = 0;
384 >  fInfo.SIM_uses_sticky = useSticky;
385 >  //fInfo.SIM_uses_sticky = 0;
386    fInfo.SIM_uses_dipoles = useDipole;
387    //fInfo.SIM_uses_dipoles = 0;
388 <  fInfo.SIM_uses_RF = useReactionField;
388 >  //fInfo.SIM_uses_RF = useReactionField;
389 >  fInfo.SIM_uses_RF = 0;
390    fInfo.SIM_uses_GB = useGB;
391    fInfo.SIM_uses_EAM = useEAM;
392  
393 +  excl = Exclude::getArray();
394  
395 + #ifdef IS_MPI
396 +  n_global = mpiSim->getTotAtoms();
397 + #else
398 +  n_global = n_atoms;
399 + #endif
400 +
401    isError = 0;
402  
403 <  fInfo;
404 <  n_atoms;
405 <  identArray;
68 <  n_exclude;
69 <  excludes;
70 <  nGlobalExcludes;
71 <  globalExcludes;
72 <  isError;
403 >  setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
404 >                  &nGlobalExcludes, globalExcludes, molMembershipArray,
405 >                  &isError );
406  
74 –  setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excludes, &nGlobalExcludes, globalExcludes, &isError );
75 –
407    if( isError ){
408  
409      sprintf( painCave.errMsg,
# Line 86 | Line 417 | void SimInfo::refreshSim(){
417             "succesfully sent the simulation information to fortran.\n");
418    MPIcheckPoint();
419   #endif // is_mpi
420 +
421 +  this->ndf = this->getNDF();
422 +  this->ndfRaw = this->getNDFraw();
423 +
424   }
425  
426 +
427 + void SimInfo::setRcut( double theRcut ){
428 +
429 +  if( !haveOrigRcut ){
430 +    haveOrigRcut = 1;
431 +    origRcut = theRcut;
432 +  }
433 +
434 +  rCut = theRcut;
435 +  checkCutOffs();
436 + }
437 +
438 + void SimInfo::setEcr( double theEcr ){
439 +
440 +  if( !haveOrigEcr ){
441 +    haveOrigEcr = 1;
442 +    origEcr = theEcr;
443 +  }
444 +
445 +  ecr = theEcr;
446 +  checkCutOffs();
447 + }
448 +
449 + void SimInfo::setEcr( double theEcr, double theEst ){
450 +
451 +  est = theEst;
452 +  setEcr( theEcr );
453 + }
454 +
455 +
456 + void SimInfo::checkCutOffs( void ){
457 +
458 +  int cutChanged = 0;
459 +
460 +  if( boxIsInit ){
461 +    
462 +    //we need to check cutOffs against the box
463 +    
464 +    if( maxCutoff > rCut ){
465 +      if( rCut < origRcut ){
466 +        rCut = origRcut;
467 +        if (rCut > maxCutoff) rCut = maxCutoff;
468 +        
469 +        sprintf( painCave.errMsg,
470 +                 "New Box size is setting the long range cutoff radius "
471 +                 "to %lf\n",
472 +                 rCut );
473 +        painCave.isFatal = 0;
474 +        simError();
475 +      }
476 +    }
477 +
478 +    if( maxCutoff > ecr ){
479 +      if( ecr < origEcr ){
480 +        rCut = origEcr;
481 +        if (ecr > maxCutoff) ecr = maxCutoff;
482 +        
483 +        sprintf( painCave.errMsg,
484 +                 "New Box size is setting the electrostaticCutoffRadius "
485 +                 "to %lf\n",
486 +                 ecr );
487 +        painCave.isFatal = 0;
488 +        simError();
489 +      }
490 +    }
491 +
492 +
493 +    if (rCut > maxCutoff) {
494 +      sprintf( painCave.errMsg,
495 +               "New Box size is setting the long range cutoff radius "
496 +               "to %lf\n",
497 +               maxCutoff );
498 +      painCave.isFatal = 0;
499 +      simError();
500 +      rCut = maxCutoff;
501 +    }
502 +
503 +    if( ecr > maxCutoff){
504 +      sprintf( painCave.errMsg,
505 +               "New Box size is setting the electrostaticCutoffRadius "
506 +               "to %lf\n",
507 +               maxCutoff  );
508 +      painCave.isFatal = 0;
509 +      simError();      
510 +      ecr = maxCutoff;
511 +    }
512 +
513 +    
514 +  }
515 +  
516 +
517 +  if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
518 +
519 +  // rlist is the 1.0 plus max( rcut, ecr )
520 +  
521 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
522 +
523 +  if( cutChanged ){
524 +    
525 +    notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
526 +  }
527 +
528 +  oldEcr = ecr;
529 +  oldRcut = rCut;
530 + }

Diff Legend

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