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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 393 by mmeineke, Mon Mar 24 18:33:51 2003 UTC vs.
Revision 670 by mmeineke, Thu Aug 7 21:47:18 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 28 | Line 54 | SimInfo::SimInfo(){
54    useGB = 0;
55    useEAM = 0;
56  
57 +  myConfiguration = new SimState();
58  
32 –
59    wrapMeSimInfo( this );
60 + }
61 +
62 +
63 + SimInfo::~SimInfo(){
64 +
65 +  delete myConfiguration;
66 +
67 +  map<string, GenericData*>::iterator i;
68 +  
69 +  for(i = properties.begin(); i != properties.end(); i++)
70 +    delete (*i).second;
71 +    
72 + }
73 +
74 + void SimInfo::setBox(double newBox[3]) {
75 +  
76 +  int i, j;
77 +  double tempMat[3][3];
78 +
79 +  for(i=0; i<3; i++)
80 +    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
81 +
82 +  tempMat[0][0] = newBox[0];
83 +  tempMat[1][1] = newBox[1];
84 +  tempMat[2][2] = newBox[2];
85 +
86 +  setBoxM( tempMat );
87 +
88 + }
89 +
90 + void SimInfo::setBoxM( double theBox[3][3] ){
91 +  
92 +  int i, j, status;
93 +  double smallestBoxL, maxCutoff;
94 +  double FortranHmat[9]; // to preserve compatibility with Fortran the
95 +                         // ordering in the array is as follows:
96 +                         // [ 0 3 6 ]
97 +                         // [ 1 4 7 ]
98 +                         // [ 2 5 8 ]
99 +  double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
100 +
101 +  
102 +  if( !boxIsInit ) boxIsInit = 1;
103 +
104 +  for(i=0; i < 3; i++)
105 +    for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
106 +  
107 +  calcBoxL();
108 +  calcHmatInv();
109 +
110 +  for(i=0; i < 3; i++) {
111 +    for (j=0; j < 3; j++) {
112 +      FortranHmat[3*j + i] = Hmat[i][j];
113 +      FortranHmatInv[3*j + i] = HmatInv[i][j];
114 +    }
115 +  }
116 +
117 +  setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
118 +
119 + }
120 +
121 +
122 + void SimInfo::getBoxM (double theBox[3][3]) {
123 +
124 +  int i, j;
125 +  for(i=0; i<3; i++)
126 +    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
127 + }
128 +
129 +
130 + void SimInfo::scaleBox(double scale) {
131 +  double theBox[3][3];
132 +  int i, j;
133 +
134 +  // cerr << "Scaling box by " << scale << "\n";
135 +
136 +  for(i=0; i<3; i++)
137 +    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
138 +
139 +  setBoxM(theBox);
140 +
141 + }
142 +
143 + void SimInfo::calcHmatInv( void ) {
144 +  
145 +  int i,j;
146 +  double smallDiag;
147 +  double tol;
148 +  double sanity[3][3];
149 +
150 +  invertMat3( Hmat, HmatInv );
151 +
152 +  // Check the inverse to make sure it is sane:
153 +
154 +  matMul3( Hmat, HmatInv, sanity );
155 +    
156 +  // check to see if Hmat is orthorhombic
157 +  
158 +  smallDiag = Hmat[0][0];
159 +  if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1];
160 +  if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2];
161 +  tol = smallDiag * 1E-6;
162 +
163 +  orthoRhombic = 1;
164 +  
165 +  for (i = 0; i < 3; i++ ) {
166 +    for (j = 0 ; j < 3; j++) {
167 +      if (i != j) {
168 +        if (orthoRhombic) {
169 +          if (Hmat[i][j] >= tol) orthoRhombic = 0;
170 +        }        
171 +      }
172 +    }
173 +  }
174 + }
175 +
176 + double SimInfo::matDet3(double a[3][3]) {
177 +  int i, j, k;
178 +  double determinant;
179 +
180 +  determinant = 0.0;
181 +
182 +  for(i = 0; i < 3; i++) {
183 +    j = (i+1)%3;
184 +    k = (i+2)%3;
185 +
186 +    determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]);
187 +  }
188 +
189 +  return determinant;
190 + }
191 +
192 + void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
193 +  
194 +  int  i, j, k, l, m, n;
195 +  double determinant;
196 +
197 +  determinant = matDet3( a );
198 +
199 +  if (determinant == 0.0) {
200 +    sprintf( painCave.errMsg,
201 +             "Can't invert a matrix with a zero determinant!\n");
202 +    painCave.isFatal = 1;
203 +    simError();
204 +  }
205 +
206 +  for (i=0; i < 3; i++) {
207 +    j = (i+1)%3;
208 +    k = (i+2)%3;
209 +    for(l = 0; l < 3; l++) {
210 +      m = (l+1)%3;
211 +      n = (l+2)%3;
212 +      
213 +      b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant;
214 +    }
215 +  }
216 + }
217 +
218 + void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
219 +  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
220 +
221 +  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
222 +  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
223 +  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
224 +  
225 +  r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0];
226 +  r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1];
227 +  r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2];
228 +  
229 +  r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0];
230 +  r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1];
231 +  r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2];
232 +  
233 +  c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
234 +  c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
235 +  c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
236 + }
237 +
238 + void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
239 +  double a0, a1, a2;
240 +
241 +  a0 = inVec[0];  a1 = inVec[1];  a2 = inVec[2];
242 +
243 +  outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2;
244 +  outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
245 +  outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
246 + }
247 +
248 + void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
249 +  double temp[3][3];
250 +  int i, j;
251 +
252 +  for (i = 0; i < 3; i++) {
253 +    for (j = 0; j < 3; j++) {
254 +      temp[j][i] = in[i][j];
255 +    }
256 +  }
257 +  for (i = 0; i < 3; i++) {
258 +    for (j = 0; j < 3; j++) {
259 +      out[i][j] = temp[i][j];
260 +    }
261 +  }
262 + }
263 +  
264 + void SimInfo::printMat3(double A[3][3] ){
265 +
266 +  std::cerr
267 +            << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
268 +            << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
269 +            << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
270 + }
271 +
272 + void SimInfo::printMat9(double A[9] ){
273 +
274 +  std::cerr
275 +            << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
276 +            << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
277 +            << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
278 + }
279 +
280 + void SimInfo::calcBoxL( void ){
281 +
282 +  double dx, dy, dz, dsq;
283 +  int i;
284 +
285 +  // boxVol = Determinant of Hmat
286 +
287 +  boxVol = matDet3( Hmat );
288 +
289 +  // boxLx
290 +  
291 +  dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
292 +  dsq = dx*dx + dy*dy + dz*dz;
293 +  boxL[0] = sqrt( dsq );
294 +  maxCutoff = 0.5 * boxL[0];
295 +
296 +  // boxLy
297 +  
298 +  dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
299 +  dsq = dx*dx + dy*dy + dz*dz;
300 +  boxL[1] = sqrt( dsq );
301 +  if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
302 +
303 +  // boxLz
304 +  
305 +  dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
306 +  dsq = dx*dx + dy*dy + dz*dz;
307 +  boxL[2] = sqrt( dsq );
308 +  if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
309 +  
310 +  checkCutOffs();
311 +
312   }
313  
314 +
315 + void SimInfo::wrapVector( double thePos[3] ){
316 +
317 +  int i, j, k;
318 +  double scaled[3];
319 +
320 +  if( !orthoRhombic ){
321 +    // calc the scaled coordinates.
322 +  
323 +
324 +    matVecMul3(HmatInv, thePos, scaled);
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 +    matVecMul3(Hmat, scaled, thePos);
332 +
333 +  }
334 +  else{
335 +    // calc the scaled coordinates.
336 +    
337 +    for(i=0; i<3; i++)
338 +      scaled[i] = thePos[i]*HmatInv[i][i];
339 +    
340 +    // wrap the scaled coordinates
341 +    
342 +    for(i=0; i<3; i++)
343 +      scaled[i] -= roundMe(scaled[i]);
344 +    
345 +    // calc the wrapped real coordinates from the wrapped scaled coordinates
346 +    
347 +    for(i=0; i<3; i++)
348 +      thePos[i] = scaled[i]*Hmat[i][i];
349 +  }
350 +    
351 + }
352 +
353 +
354 + int SimInfo::getNDF(){
355 +  int ndf_local, ndf;
356 +  
357 +  ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
358 +
359 + #ifdef IS_MPI
360 +  MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
361 + #else
362 +  ndf = ndf_local;
363 + #endif
364 +
365 +  ndf = ndf - 3;
366 +
367 +  return ndf;
368 + }
369 +
370 + int SimInfo::getNDFraw() {
371 +  int ndfRaw_local, ndfRaw;
372 +
373 +  // Raw degrees of freedom that we have to set
374 +  ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
375 +  
376 + #ifdef IS_MPI
377 +  MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
378 + #else
379 +  ndfRaw = ndfRaw_local;
380 + #endif
381 +
382 +  return ndfRaw;
383 + }
384 +
385   void SimInfo::refreshSim(){
386  
387    simtype fInfo;
388    int isError;
389 +  int n_global;
390 +  int* excl;
391  
392 <  fInfo.box[0] = box_x;
42 <  fInfo.box[1] = box_y;
43 <  fInfo.box[2] = box_z;
392 >  fInfo.dielect = 0.0;
393  
394 <  fInfo.rlist = rList;
395 <  fInfo.rcut = rCut;
396 <  fInfo.rrf = rRF;
48 <  fInfo.rt = 0.95 * rRF;
49 <  fInfo.dielect = dielectric;
50 <
394 >  if( useDipole ){
395 >    if( useReactionField )fInfo.dielect = dielectric;
396 >  }
397  
398    fInfo.SIM_uses_PBC = usePBC;
399 +  //fInfo.SIM_uses_LJ = 0;
400    fInfo.SIM_uses_LJ = useLJ;
401    fInfo.SIM_uses_sticky = useSticky;
402 <  fInfo.SIM_uses_dipoles = 0;
403 <  //  fInfo.SIM_uses_dipoles = useDipole;
402 >  //fInfo.SIM_uses_sticky = 0;
403 >  fInfo.SIM_uses_dipoles = useDipole;
404 >  //fInfo.SIM_uses_dipoles = 0;
405 >  //fInfo.SIM_uses_RF = useReactionField;
406    fInfo.SIM_uses_RF = 0;
58 –  //  fInfo.SIM_uses_RF = useReactionField;
407    fInfo.SIM_uses_GB = useGB;
408    fInfo.SIM_uses_EAM = useEAM;
409  
410 +  excl = Exclude::getArray();
411  
412 + #ifdef IS_MPI
413 +  n_global = mpiSim->getTotAtoms();
414 + #else
415 +  n_global = n_atoms;
416 + #endif
417 +
418    isError = 0;
419  
420 <  fInfo;
421 <  n_atoms;
422 <  identArray;
68 <  n_exclude;
69 <  excludes;
70 <  nGlobalExcludes;
71 <  globalExcludes;
72 <  isError;
420 >  setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
421 >                  &nGlobalExcludes, globalExcludes, molMembershipArray,
422 >                  &isError );
423  
74 –  setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excludes, &nGlobalExcludes, globalExcludes, &isError );
75 –
424    if( isError ){
425  
426      sprintf( painCave.errMsg,
# Line 86 | Line 434 | void SimInfo::refreshSim(){
434             "succesfully sent the simulation information to fortran.\n");
435    MPIcheckPoint();
436   #endif // is_mpi
437 +
438 +  this->ndf = this->getNDF();
439 +  this->ndfRaw = this->getNDFraw();
440 +
441   }
442  
443 +
444 + void SimInfo::setRcut( double theRcut ){
445 +
446 +  if( !haveOrigRcut ){
447 +    haveOrigRcut = 1;
448 +    origRcut = theRcut;
449 +  }
450 +
451 +  rCut = theRcut;
452 +  checkCutOffs();
453 + }
454 +
455 + void SimInfo::setEcr( double theEcr ){
456 +
457 +  if( !haveOrigEcr ){
458 +    haveOrigEcr = 1;
459 +    origEcr = theEcr;
460 +  }
461 +
462 +  ecr = theEcr;
463 +  checkCutOffs();
464 + }
465 +
466 + void SimInfo::setEcr( double theEcr, double theEst ){
467 +
468 +  est = theEst;
469 +  setEcr( theEcr );
470 + }
471 +
472 +
473 + void SimInfo::checkCutOffs( void ){
474 +
475 +  int cutChanged = 0;
476 +
477 +
478 +
479 +  if( boxIsInit ){
480 +    
481 +    //we need to check cutOffs against the box
482 +  
483 +    if(( maxCutoff > rCut )&&(usePBC)){
484 +      if( rCut < origRcut ){
485 +        rCut = origRcut;
486 +        if (rCut > maxCutoff) rCut = maxCutoff;
487 +        
488 +        sprintf( painCave.errMsg,
489 +                 "New Box size is setting the long range cutoff radius "
490 +                 "to %lf\n",
491 +                 rCut );
492 +        painCave.isFatal = 0;
493 +        simError();
494 +      }
495 +    }
496 +
497 +    if( maxCutoff > ecr ){
498 +      if( ecr < origEcr ){
499 +        rCut = origEcr;
500 +        if (ecr > maxCutoff) ecr = maxCutoff;
501 +        
502 +        sprintf( painCave.errMsg,
503 +                 "New Box size is setting the electrostaticCutoffRadius "
504 +                 "to %lf\n",
505 +                 ecr );
506 +        painCave.isFatal = 0;
507 +        simError();
508 +      }
509 +    }
510 +
511 +
512 +    if ((rCut > maxCutoff)&&(usePBC)) {
513 +      sprintf( painCave.errMsg,
514 +               "New Box size is setting the long range cutoff radius "
515 +               "to %lf\n",
516 +               maxCutoff );
517 +      painCave.isFatal = 0;
518 +      simError();
519 +      rCut = maxCutoff;
520 +    }
521 +
522 +    if( ecr > maxCutoff){
523 +      sprintf( painCave.errMsg,
524 +               "New Box size is setting the electrostaticCutoffRadius "
525 +               "to %lf\n",
526 +               maxCutoff  );
527 +      painCave.isFatal = 0;
528 +      simError();      
529 +      ecr = maxCutoff;
530 +    }
531 +
532 +    
533 +  }
534 +  
535 +
536 +  if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
537 +
538 +  // rlist is the 1.0 plus max( rcut, ecr )
539 +  
540 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
541 +
542 +  if( cutChanged ){
543 +    
544 +    notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
545 +  }
546 +
547 +  oldEcr = ecr;
548 +  oldRcut = rCut;
549 + }
550 +
551 + void SimInfo::addProperty(GenericData* prop){
552 +
553 +  map<string, GenericData*>::iterator result;
554 +  result = properties.find(prop->getID());
555 +  
556 +  //we can't simply use  properties[prop->getID()] = prop,
557 +  //it will cause memory leak if we already contain a propery which has the same name of prop
558 +  
559 +  if(result != properties.end()){
560 +    
561 +    delete (*result).second;
562 +    (*result).second = prop;
563 +      
564 +  }
565 +  else{
566 +
567 +    properties[prop->getID()] = prop;
568 +
569 +  }
570 +    
571 + }
572 +
573 + GenericData* SimInfo::getProperty(const string& propName){
574 +
575 +  map<string, GenericData*>::iterator result;
576 +  
577 +  //string lowerCaseName = ();
578 +  
579 +  result = properties.find(propName);
580 +  
581 +  if(result != properties.end())
582 +    return (*result).second;  
583 +  else  
584 +    return NULL;  
585 + }
586 +
587 + vector<GenericData*> SimInfo::getProperties(){
588 +
589 +  vector<GenericData*> result;
590 +  map<string, GenericData*>::iterator i;
591 +  
592 +  for(i = properties.begin(); i != properties.end(); i++)
593 +    result.push_back((*i).second);
594 +    
595 +  return result;
596 + }
597 +
598 +

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