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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 674 by mmeineke, Mon Aug 11 18:29:46 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 +  nZconstraints = 0;
34    the_integrator = NULL;
35    setTemp = 0;
36    thermalTime = 0.0;
37 +  currentTime = 0.0;
38 +  rCut = 0.0;
39 +  ecr = 0.0;
40 +  est = 0.0;
41 +  oldEcr = 0.0;
42 +  oldRcut = 0.0;
43  
44 +  haveOrigRcut = 0;
45 +  haveOrigEcr = 0;
46 +  boxIsInit = 0;
47 +  
48 +  
49 +
50    usePBC = 0;
51    useLJ = 0;
52    useSticky = 0;
# Line 28 | Line 55 | SimInfo::SimInfo(){
55    useGB = 0;
56    useEAM = 0;
57  
58 +  myConfiguration = new SimState();
59  
32 –
60    wrapMeSimInfo( this );
61   }
62  
63 +
64 + SimInfo::~SimInfo(){
65 +
66 +  delete myConfiguration;
67 +
68 +  map<string, GenericData*>::iterator i;
69 +  
70 +  for(i = properties.begin(); i != properties.end(); i++)
71 +    delete (*i).second;
72 +    
73 + }
74 +
75 + void SimInfo::setBox(double newBox[3]) {
76 +  
77 +  int i, j;
78 +  double tempMat[3][3];
79 +
80 +  for(i=0; i<3; i++)
81 +    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
82 +
83 +  tempMat[0][0] = newBox[0];
84 +  tempMat[1][1] = newBox[1];
85 +  tempMat[2][2] = newBox[2];
86 +
87 +  setBoxM( tempMat );
88 +
89 + }
90 +
91 + void SimInfo::setBoxM( double theBox[3][3] ){
92 +  
93 +  int i, j, status;
94 +  double smallestBoxL, maxCutoff;
95 +  double FortranHmat[9]; // to preserve compatibility with Fortran the
96 +                         // ordering in the array is as follows:
97 +                         // [ 0 3 6 ]
98 +                         // [ 1 4 7 ]
99 +                         // [ 2 5 8 ]
100 +  double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
101 +
102 +  
103 +  if( !boxIsInit ) boxIsInit = 1;
104 +
105 +  for(i=0; i < 3; i++)
106 +    for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
107 +  
108 +  calcBoxL();
109 +  calcHmatInv();
110 +
111 +  for(i=0; i < 3; i++) {
112 +    for (j=0; j < 3; j++) {
113 +      FortranHmat[3*j + i] = Hmat[i][j];
114 +      FortranHmatInv[3*j + i] = HmatInv[i][j];
115 +    }
116 +  }
117 +
118 +  setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
119 +
120 + }
121 +
122 +
123 + void SimInfo::getBoxM (double theBox[3][3]) {
124 +
125 +  int i, j;
126 +  for(i=0; i<3; i++)
127 +    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
128 + }
129 +
130 +
131 + void SimInfo::scaleBox(double scale) {
132 +  double theBox[3][3];
133 +  int i, j;
134 +
135 +  // cerr << "Scaling box by " << scale << "\n";
136 +
137 +  for(i=0; i<3; i++)
138 +    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
139 +
140 +  setBoxM(theBox);
141 +
142 + }
143 +
144 + void SimInfo::calcHmatInv( void ) {
145 +  
146 +  int i,j;
147 +  double smallDiag;
148 +  double tol;
149 +  double sanity[3][3];
150 +
151 +  invertMat3( Hmat, HmatInv );
152 +
153 +  // Check the inverse to make sure it is sane:
154 +
155 +  matMul3( Hmat, HmatInv, sanity );
156 +    
157 +  // check to see if Hmat is orthorhombic
158 +  
159 +  smallDiag = Hmat[0][0];
160 +  if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1];
161 +  if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2];
162 +  tol = smallDiag * 1E-6;
163 +
164 +  orthoRhombic = 1;
165 +  
166 +  for (i = 0; i < 3; i++ ) {
167 +    for (j = 0 ; j < 3; j++) {
168 +      if (i != j) {
169 +        if (orthoRhombic) {
170 +          if (Hmat[i][j] >= tol) orthoRhombic = 0;
171 +        }        
172 +      }
173 +    }
174 +  }
175 + }
176 +
177 + double SimInfo::matDet3(double a[3][3]) {
178 +  int i, j, k;
179 +  double determinant;
180 +
181 +  determinant = 0.0;
182 +
183 +  for(i = 0; i < 3; i++) {
184 +    j = (i+1)%3;
185 +    k = (i+2)%3;
186 +
187 +    determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]);
188 +  }
189 +
190 +  return determinant;
191 + }
192 +
193 + void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
194 +  
195 +  int  i, j, k, l, m, n;
196 +  double determinant;
197 +
198 +  determinant = matDet3( a );
199 +
200 +  if (determinant == 0.0) {
201 +    sprintf( painCave.errMsg,
202 +             "Can't invert a matrix with a zero determinant!\n");
203 +    painCave.isFatal = 1;
204 +    simError();
205 +  }
206 +
207 +  for (i=0; i < 3; i++) {
208 +    j = (i+1)%3;
209 +    k = (i+2)%3;
210 +    for(l = 0; l < 3; l++) {
211 +      m = (l+1)%3;
212 +      n = (l+2)%3;
213 +      
214 +      b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant;
215 +    }
216 +  }
217 + }
218 +
219 + void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
220 +  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
221 +
222 +  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
223 +  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
224 +  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
225 +  
226 +  r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0];
227 +  r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1];
228 +  r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2];
229 +  
230 +  r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0];
231 +  r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1];
232 +  r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2];
233 +  
234 +  c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
235 +  c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
236 +  c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
237 + }
238 +
239 + void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
240 +  double a0, a1, a2;
241 +
242 +  a0 = inVec[0];  a1 = inVec[1];  a2 = inVec[2];
243 +
244 +  outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2;
245 +  outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
246 +  outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
247 + }
248 +
249 + void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
250 +  double temp[3][3];
251 +  int i, j;
252 +
253 +  for (i = 0; i < 3; i++) {
254 +    for (j = 0; j < 3; j++) {
255 +      temp[j][i] = in[i][j];
256 +    }
257 +  }
258 +  for (i = 0; i < 3; i++) {
259 +    for (j = 0; j < 3; j++) {
260 +      out[i][j] = temp[i][j];
261 +    }
262 +  }
263 + }
264 +  
265 + void SimInfo::printMat3(double A[3][3] ){
266 +
267 +  std::cerr
268 +            << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
269 +            << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
270 +            << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
271 + }
272 +
273 + void SimInfo::printMat9(double A[9] ){
274 +
275 +  std::cerr
276 +            << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
277 +            << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
278 +            << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
279 + }
280 +
281 + void SimInfo::calcBoxL( void ){
282 +
283 +  double dx, dy, dz, dsq;
284 +  int i;
285 +
286 +  // boxVol = Determinant of Hmat
287 +
288 +  boxVol = matDet3( Hmat );
289 +
290 +  // boxLx
291 +  
292 +  dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
293 +  dsq = dx*dx + dy*dy + dz*dz;
294 +  boxL[0] = sqrt( dsq );
295 +  maxCutoff = 0.5 * boxL[0];
296 +
297 +  // boxLy
298 +  
299 +  dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
300 +  dsq = dx*dx + dy*dy + dz*dz;
301 +  boxL[1] = sqrt( dsq );
302 +  if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
303 +
304 +  // boxLz
305 +  
306 +  dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
307 +  dsq = dx*dx + dy*dy + dz*dz;
308 +  boxL[2] = sqrt( dsq );
309 +  if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
310 +  
311 +  checkCutOffs();
312 +
313 + }
314 +
315 +
316 + void SimInfo::wrapVector( double thePos[3] ){
317 +
318 +  int i, j, k;
319 +  double scaled[3];
320 +
321 +  if( !orthoRhombic ){
322 +    // calc the scaled coordinates.
323 +  
324 +
325 +    matVecMul3(HmatInv, thePos, scaled);
326 +    
327 +    for(i=0; i<3; i++)
328 +      scaled[i] -= roundMe(scaled[i]);
329 +    
330 +    // calc the wrapped real coordinates from the wrapped scaled coordinates
331 +    
332 +    matVecMul3(Hmat, scaled, thePos);
333 +
334 +  }
335 +  else{
336 +    // calc the scaled coordinates.
337 +    
338 +    for(i=0; i<3; i++)
339 +      scaled[i] = thePos[i]*HmatInv[i][i];
340 +    
341 +    // wrap the scaled coordinates
342 +    
343 +    for(i=0; i<3; i++)
344 +      scaled[i] -= roundMe(scaled[i]);
345 +    
346 +    // calc the wrapped real coordinates from the wrapped scaled coordinates
347 +    
348 +    for(i=0; i<3; i++)
349 +      thePos[i] = scaled[i]*Hmat[i][i];
350 +  }
351 +    
352 + }
353 +
354 +
355 + int SimInfo::getNDF(){
356 +  int ndf_local, ndf;
357 +  
358 +  ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
359 +
360 + #ifdef IS_MPI
361 +  MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
362 + #else
363 +  ndf = ndf_local;
364 + #endif
365 +
366 +  ndf = ndf - 3 - nZconstraints;
367 +
368 +  return ndf;
369 + }
370 +
371 + int SimInfo::getNDFraw() {
372 +  int ndfRaw_local, ndfRaw;
373 +
374 +  // Raw degrees of freedom that we have to set
375 +  ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
376 +  
377 + #ifdef IS_MPI
378 +  MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
379 + #else
380 +  ndfRaw = ndfRaw_local;
381 + #endif
382 +
383 +  return ndfRaw;
384 + }
385 +
386   void SimInfo::refreshSim(){
387  
388    simtype fInfo;
389    int isError;
390 +  int n_global;
391 +  int* excl;
392  
393 <  fInfo.box[0] = box_x;
42 <  fInfo.box[1] = box_y;
43 <  fInfo.box[2] = box_z;
393 >  fInfo.dielect = 0.0;
394  
395 <  fInfo.rlist = rList;
396 <  fInfo.rcut = rCut;
397 <  fInfo.rrf = rRF;
48 <  fInfo.rt = 0.95 * rRF;
49 <  fInfo.dielect = dielectric;
50 <
395 >  if( useDipole ){
396 >    if( useReactionField )fInfo.dielect = dielectric;
397 >  }
398  
399    fInfo.SIM_uses_PBC = usePBC;
400 +  //fInfo.SIM_uses_LJ = 0;
401    fInfo.SIM_uses_LJ = useLJ;
402    fInfo.SIM_uses_sticky = useSticky;
403 <  fInfo.SIM_uses_dipoles = 0;
404 <  //  fInfo.SIM_uses_dipoles = useDipole;
403 >  //fInfo.SIM_uses_sticky = 0;
404 >  fInfo.SIM_uses_dipoles = useDipole;
405 >  //fInfo.SIM_uses_dipoles = 0;
406 >  //fInfo.SIM_uses_RF = useReactionField;
407    fInfo.SIM_uses_RF = 0;
58 –  //  fInfo.SIM_uses_RF = useReactionField;
408    fInfo.SIM_uses_GB = useGB;
409    fInfo.SIM_uses_EAM = useEAM;
410  
411 +  excl = Exclude::getArray();
412  
413 + #ifdef IS_MPI
414 +  n_global = mpiSim->getTotAtoms();
415 + #else
416 +  n_global = n_atoms;
417 + #endif
418 +
419    isError = 0;
420  
421 <  fInfo;
422 <  n_atoms;
423 <  identArray;
68 <  n_exclude;
69 <  excludes;
70 <  nGlobalExcludes;
71 <  globalExcludes;
72 <  isError;
421 >  setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
422 >                  &nGlobalExcludes, globalExcludes, molMembershipArray,
423 >                  &isError );
424  
74 –  setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excludes, &nGlobalExcludes, globalExcludes, &isError );
75 –
425    if( isError ){
426  
427      sprintf( painCave.errMsg,
# Line 86 | Line 435 | void SimInfo::refreshSim(){
435             "succesfully sent the simulation information to fortran.\n");
436    MPIcheckPoint();
437   #endif // is_mpi
438 +
439 +  this->ndf = this->getNDF();
440 +  this->ndfRaw = this->getNDFraw();
441 +
442   }
443  
444 +
445 + void SimInfo::setRcut( double theRcut ){
446 +
447 +  if( !haveOrigRcut ){
448 +    haveOrigRcut = 1;
449 +    origRcut = theRcut;
450 +  }
451 +
452 +  rCut = theRcut;
453 +  checkCutOffs();
454 + }
455 +
456 + void SimInfo::setEcr( double theEcr ){
457 +
458 +  if( !haveOrigEcr ){
459 +    haveOrigEcr = 1;
460 +    origEcr = theEcr;
461 +  }
462 +
463 +  ecr = theEcr;
464 +  checkCutOffs();
465 + }
466 +
467 + void SimInfo::setEcr( double theEcr, double theEst ){
468 +
469 +  est = theEst;
470 +  setEcr( theEcr );
471 + }
472 +
473 +
474 + void SimInfo::checkCutOffs( void ){
475 +
476 +  int cutChanged = 0;
477 +
478 +
479 +
480 +  if( boxIsInit ){
481 +    
482 +    //we need to check cutOffs against the box
483 +  
484 +    if(( maxCutoff > rCut )&&(usePBC)){
485 +      if( rCut < origRcut ){
486 +        rCut = origRcut;
487 +        if (rCut > maxCutoff) rCut = maxCutoff;
488 +        
489 +        sprintf( painCave.errMsg,
490 +                 "New Box size is setting the long range cutoff radius "
491 +                 "to %lf\n",
492 +                 rCut );
493 +        painCave.isFatal = 0;
494 +        simError();
495 +      }
496 +    }
497 +
498 +    if( maxCutoff > ecr ){
499 +      if( ecr < origEcr ){
500 +        rCut = origEcr;
501 +        if (ecr > maxCutoff) ecr = maxCutoff;
502 +        
503 +        sprintf( painCave.errMsg,
504 +                 "New Box size is setting the electrostaticCutoffRadius "
505 +                 "to %lf\n",
506 +                 ecr );
507 +        painCave.isFatal = 0;
508 +        simError();
509 +      }
510 +    }
511 +
512 +
513 +    if ((rCut > maxCutoff)&&(usePBC)) {
514 +      sprintf( painCave.errMsg,
515 +               "New Box size is setting the long range cutoff radius "
516 +               "to %lf\n",
517 +               maxCutoff );
518 +      painCave.isFatal = 0;
519 +      simError();
520 +      rCut = maxCutoff;
521 +    }
522 +
523 +    if( ecr > maxCutoff){
524 +      sprintf( painCave.errMsg,
525 +               "New Box size is setting the electrostaticCutoffRadius "
526 +               "to %lf\n",
527 +               maxCutoff  );
528 +      painCave.isFatal = 0;
529 +      simError();      
530 +      ecr = maxCutoff;
531 +    }
532 +
533 +    
534 +  }
535 +  
536 +
537 +  if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
538 +
539 +  // rlist is the 1.0 plus max( rcut, ecr )
540 +  
541 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
542 +
543 +  if( cutChanged ){
544 +    
545 +    notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
546 +  }
547 +
548 +  oldEcr = ecr;
549 +  oldRcut = rCut;
550 + }
551 +
552 + void SimInfo::addProperty(GenericData* prop){
553 +
554 +  map<string, GenericData*>::iterator result;
555 +  result = properties.find(prop->getID());
556 +  
557 +  //we can't simply use  properties[prop->getID()] = prop,
558 +  //it will cause memory leak if we already contain a propery which has the same name of prop
559 +  
560 +  if(result != properties.end()){
561 +    
562 +    delete (*result).second;
563 +    (*result).second = prop;
564 +      
565 +  }
566 +  else{
567 +
568 +    properties[prop->getID()] = prop;
569 +
570 +  }
571 +    
572 + }
573 +
574 + GenericData* SimInfo::getProperty(const string& propName){
575 +
576 +  map<string, GenericData*>::iterator result;
577 +  
578 +  //string lowerCaseName = ();
579 +  
580 +  result = properties.find(propName);
581 +  
582 +  if(result != properties.end())
583 +    return (*result).second;  
584 +  else  
585 +    return NULL;  
586 + }
587 +
588 + vector<GenericData*> SimInfo::getProperties(){
589 +
590 +  vector<GenericData*> result;
591 +  map<string, GenericData*>::iterator i;
592 +  
593 +  for(i = properties.begin(); i != properties.end(); i++)
594 +    result.push_back((*i).second);
595 +    
596 +  return result;
597 + }
598 +
599 +

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