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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 394 by gezelter, Mon Mar 24 21:55:34 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 28 | 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;
42 <  fInfo.box[1] = box_y;
43 <  fInfo.box[2] = box_z;
376 >  fInfo.dielect = 0.0;
377  
378 <  fInfo.rlist = rList;
379 <  fInfo.rcut = rCut;
380 <  fInfo.rrf = ecr;
48 <  fInfo.rt = ecr - est;
49 <  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;
384    fInfo.SIM_uses_LJ = useLJ;
385 <  //fInfo.SIM_uses_sticky = useSticky;
386 <  fInfo.SIM_uses_sticky = 0;
385 >  fInfo.SIM_uses_sticky = useSticky;
386 >  //fInfo.SIM_uses_sticky = 0;
387    fInfo.SIM_uses_dipoles = useDipole;
388 <  fInfo.SIM_uses_RF = useReactionField;
388 >  //fInfo.SIM_uses_dipoles = 0;
389 >  //fInfo.SIM_uses_RF = useReactionField;
390 >  fInfo.SIM_uses_RF = 0;
391    fInfo.SIM_uses_GB = useGB;
392    fInfo.SIM_uses_EAM = useEAM;
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;
66 <  n_exclude;
67 <  excludes;
68 <  nGlobalExcludes;
69 <  globalExcludes;
70 <  isError;
404 >  setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
405 >                  &nGlobalExcludes, globalExcludes, molMembershipArray,
406 >                  &isError );
407  
72 –  setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excludes, &nGlobalExcludes, globalExcludes, &isError );
73 –
408    if( isError ){
409  
410      sprintf( painCave.errMsg,
# Line 84 | 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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