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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 443 by mmeineke, Wed Apr 2 22:19:03 2003 UTC vs.
Revision 658 by tim, Thu Jul 31 15:35:07 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 +  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 29 | Line 54 | SimInfo::SimInfo(){
54    useGB = 0;
55    useEAM = 0;
56  
57 +  wrapMeSimInfo( this );
58 + }
59  
60 + void SimInfo::setBox(double newBox[3]) {
61 +  
62 +  int i, j;
63 +  double tempMat[3][3];
64  
65 <  wrapMeSimInfo( this );
65 >  for(i=0; i<3; i++)
66 >    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
67 >
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[3][3] ){
77 +  
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 +  
88 +  if( !boxIsInit ) boxIsInit = 1;
89 +
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 +  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[3][3]) {
109 +
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[3][3];
118 +  int i, j;
119 +
120 +  // cerr << "Scaling box by " << scale << "\n";
121 +
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::calcHmatInv( void ) {
130 +  
131 +  int i,j;
132 +  double smallDiag;
133 +  double tol;
134 +  double sanity[3][3];
135 +
136 +  invertMat3( Hmat, HmatInv );
137 +
138 +  // Check the inverse to make sure it is sane:
139 +
140 +  matMul3( Hmat, HmatInv, sanity );
141 +    
142 +  // check to see if Hmat is orthorhombic
143 +  
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 +  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 + double SimInfo::matDet3(double a[3][3]) {
163 +  int i, j, k;
164 +  double determinant;
165 +
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 +      b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant;
200 +    }
201 +  }
202 + }
203 +
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 +  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 +  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 + 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 +  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 = Determinant of Hmat
272 +
273 +  boxVol = matDet3( Hmat );
274 +
275 +  // boxLx
276 +  
277 +  dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
278 +  dsq = dx*dx + dy*dy + dz*dz;
279 +  boxL[0] = sqrt( dsq );
280 +  maxCutoff = 0.5 * boxL[0];
281 +
282 +  // boxLy
283 +  
284 +  dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
285 +  dsq = dx*dx + dy*dy + dz*dz;
286 +  boxL[1] = sqrt( dsq );
287 +  if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
288 +
289 +  // boxLz
290 +  
291 +  dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
292 +  dsq = dx*dx + dy*dy + dz*dz;
293 +  boxL[2] = sqrt( dsq );
294 +  if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
295 +
296 + }
297 +
298 +
299 + void SimInfo::wrapVector( double thePos[3] ){
300 +
301 +  int i, j, k;
302 +  double scaled[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++)
311 +      scaled[i] -= roundMe(scaled[i]);
312 +    
313 +    // calc the wrapped real coordinates from the wrapped scaled coordinates
314 +    
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]*HmatInv[i][i];
323 +    
324 +    // wrap the scaled coordinates
325 +    
326 +    for(i=0; i<3; i++)
327 +      scaled[i] -= roundMe(scaled[i]);
328 +    
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][i];
333 +  }
334 +    
335 + }
336 +
337 +
338 + int SimInfo::getNDF(){
339 +  int ndf_local, ndf;
340 +  
341 +  ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
342 +
343 + #ifdef IS_MPI
344 +  MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
345 + #else
346 +  ndf = ndf_local;
347 + #endif
348 +
349 +  ndf = ndf - 3;
350 +
351 +  return ndf;
352 + }
353 +
354 + int SimInfo::getNDFraw() {
355 +  int ndfRaw_local, ndfRaw;
356 +
357 +  // Raw degrees of freedom that we have to set
358 +  ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
359 +  
360 + #ifdef IS_MPI
361 +  MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
362 + #else
363 +  ndfRaw = ndfRaw_local;
364 + #endif
365 +
366 +  return ndfRaw;
367 + }
368 +
369   void SimInfo::refreshSim(){
370  
371    simtype fInfo;
372    int isError;
373 +  int n_global;
374    int* excl;
375  
376 <  fInfo.box[0] = box_x;
44 <  fInfo.box[1] = box_y;
45 <  fInfo.box[2] = box_z;
376 >  fInfo.dielect = 0.0;
377  
378 <  fInfo.rlist = rList;
379 <  fInfo.rcut = rCut;
380 <  fInfo.rrf = ecr;
50 <  fInfo.rt = ecr - est;
51 <  fInfo.dielect = dielectric;
378 >  if( useDipole ){
379 >    if( useReactionField )fInfo.dielect = dielectric;
380 >  }
381  
382    fInfo.SIM_uses_PBC = usePBC;
383    //fInfo.SIM_uses_LJ = 0;
# Line 64 | Line 393 | void SimInfo::refreshSim(){
393  
394    excl = Exclude::getArray();
395  
396 + #ifdef IS_MPI
397 +  n_global = mpiSim->getTotAtoms();
398 + #else
399 +  n_global = n_atoms;
400 + #endif
401 +
402    isError = 0;
403  
404 < //   fInfo;
405 < //   n_atoms;
406 < //   identArray;
72 < //   n_exclude;
73 < //   excludes;
74 < //   nGlobalExcludes;
75 < //   globalExcludes;
76 < //   isError;
404 >  setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
405 >                  &nGlobalExcludes, globalExcludes, molMembershipArray,
406 >                  &isError );
407  
78 –  setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excl,
79 –                  &nGlobalExcludes, globalExcludes, &isError );
80 –
408    if( isError ){
409  
410      sprintf( painCave.errMsg,
# Line 91 | Line 418 | void SimInfo::refreshSim(){
418             "succesfully sent the simulation information to fortran.\n");
419    MPIcheckPoint();
420   #endif // is_mpi
421 +
422 +  this->ndf = this->getNDF();
423 +  this->ndfRaw = this->getNDFraw();
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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