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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 660 by tim, Thu Jul 31 19:59:34 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 + SimInfo::~SimInfo(){
61  
62 <  wrapMeSimInfo( this );
62 >  map<string, GenericData*>::iterator i;
63 >  
64 >  for(i = properties.begin(); i != properties.end(); i++)
65 >    delete (*i).second;
66 >
67 >  
68 > }
69 >
70 > void SimInfo::setBox(double newBox[3]) {
71 >  
72 >  int i, j;
73 >  double tempMat[3][3];
74 >
75 >  for(i=0; i<3; i++)
76 >    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
77 >
78 >  tempMat[0][0] = newBox[0];
79 >  tempMat[1][1] = newBox[1];
80 >  tempMat[2][2] = newBox[2];
81 >
82 >  setBoxM( tempMat );
83 >
84 > }
85 >
86 > void SimInfo::setBoxM( double theBox[3][3] ){
87 >  
88 >  int i, j, status;
89 >  double smallestBoxL, maxCutoff;
90 >  double FortranHmat[9]; // to preserve compatibility with Fortran the
91 >                         // ordering in the array is as follows:
92 >                         // [ 0 3 6 ]
93 >                         // [ 1 4 7 ]
94 >                         // [ 2 5 8 ]
95 >  double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
96 >
97 >  
98 >  if( !boxIsInit ) boxIsInit = 1;
99 >
100 >  for(i=0; i < 3; i++)
101 >    for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
102 >  
103 >  calcBoxL();
104 >  calcHmatInv();
105 >
106 >  for(i=0; i < 3; i++) {
107 >    for (j=0; j < 3; j++) {
108 >      FortranHmat[3*j + i] = Hmat[i][j];
109 >      FortranHmatInv[3*j + i] = HmatInv[i][j];
110 >    }
111 >  }
112 >
113 >  setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
114 >
115 > }
116 >
117 >
118 > void SimInfo::getBoxM (double theBox[3][3]) {
119 >
120 >  int i, j;
121 >  for(i=0; i<3; i++)
122 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
123 > }
124 >
125 >
126 > void SimInfo::scaleBox(double scale) {
127 >  double theBox[3][3];
128 >  int i, j;
129 >
130 >  // cerr << "Scaling box by " << scale << "\n";
131 >
132 >  for(i=0; i<3; i++)
133 >    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
134 >
135 >  setBoxM(theBox);
136 >
137 > }
138 >
139 > void SimInfo::calcHmatInv( void ) {
140 >  
141 >  int i,j;
142 >  double smallDiag;
143 >  double tol;
144 >  double sanity[3][3];
145 >
146 >  invertMat3( Hmat, HmatInv );
147 >
148 >  // Check the inverse to make sure it is sane:
149 >
150 >  matMul3( Hmat, HmatInv, sanity );
151 >    
152 >  // check to see if Hmat is orthorhombic
153 >  
154 >  smallDiag = Hmat[0][0];
155 >  if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1];
156 >  if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2];
157 >  tol = smallDiag * 1E-6;
158 >
159 >  orthoRhombic = 1;
160 >  
161 >  for (i = 0; i < 3; i++ ) {
162 >    for (j = 0 ; j < 3; j++) {
163 >      if (i != j) {
164 >        if (orthoRhombic) {
165 >          if (Hmat[i][j] >= tol) orthoRhombic = 0;
166 >        }        
167 >      }
168 >    }
169 >  }
170 > }
171 >
172 > double SimInfo::matDet3(double a[3][3]) {
173 >  int i, j, k;
174 >  double determinant;
175 >
176 >  determinant = 0.0;
177 >
178 >  for(i = 0; i < 3; i++) {
179 >    j = (i+1)%3;
180 >    k = (i+2)%3;
181 >
182 >    determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]);
183 >  }
184 >
185 >  return determinant;
186 > }
187 >
188 > void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
189 >  
190 >  int  i, j, k, l, m, n;
191 >  double determinant;
192 >
193 >  determinant = matDet3( a );
194 >
195 >  if (determinant == 0.0) {
196 >    sprintf( painCave.errMsg,
197 >             "Can't invert a matrix with a zero determinant!\n");
198 >    painCave.isFatal = 1;
199 >    simError();
200 >  }
201 >
202 >  for (i=0; i < 3; i++) {
203 >    j = (i+1)%3;
204 >    k = (i+2)%3;
205 >    for(l = 0; l < 3; l++) {
206 >      m = (l+1)%3;
207 >      n = (l+2)%3;
208 >      
209 >      b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant;
210 >    }
211 >  }
212 > }
213 >
214 > void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
215 >  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
216 >
217 >  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
218 >  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
219 >  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
220 >  
221 >  r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0];
222 >  r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1];
223 >  r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2];
224 >  
225 >  r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0];
226 >  r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1];
227 >  r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2];
228 >  
229 >  c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
230 >  c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
231 >  c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
232 > }
233 >
234 > void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
235 >  double a0, a1, a2;
236 >
237 >  a0 = inVec[0];  a1 = inVec[1];  a2 = inVec[2];
238 >
239 >  outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2;
240 >  outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
241 >  outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
242 > }
243 >
244 > void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
245 >  double temp[3][3];
246 >  int i, j;
247 >
248 >  for (i = 0; i < 3; i++) {
249 >    for (j = 0; j < 3; j++) {
250 >      temp[j][i] = in[i][j];
251 >    }
252 >  }
253 >  for (i = 0; i < 3; i++) {
254 >    for (j = 0; j < 3; j++) {
255 >      out[i][j] = temp[i][j];
256 >    }
257 >  }
258 > }
259 >  
260 > void SimInfo::printMat3(double A[3][3] ){
261 >
262 >  std::cerr
263 >            << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
264 >            << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
265 >            << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
266 > }
267 >
268 > void SimInfo::printMat9(double A[9] ){
269 >
270 >  std::cerr
271 >            << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
272 >            << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
273 >            << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
274 > }
275 >
276 > void SimInfo::calcBoxL( void ){
277 >
278 >  double dx, dy, dz, dsq;
279 >  int i;
280 >
281 >  // boxVol = Determinant of Hmat
282 >
283 >  boxVol = matDet3( Hmat );
284 >
285 >  // boxLx
286 >  
287 >  dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
288 >  dsq = dx*dx + dy*dy + dz*dz;
289 >  boxL[0] = sqrt( dsq );
290 >  maxCutoff = 0.5 * boxL[0];
291 >
292 >  // boxLy
293 >  
294 >  dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
295 >  dsq = dx*dx + dy*dy + dz*dz;
296 >  boxL[1] = sqrt( dsq );
297 >  if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
298 >
299 >  // boxLz
300 >  
301 >  dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
302 >  dsq = dx*dx + dy*dy + dz*dz;
303 >  boxL[2] = sqrt( dsq );
304 >  if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
305 >
306 > }
307 >
308 >
309 > void SimInfo::wrapVector( double thePos[3] ){
310 >
311 >  int i, j, k;
312 >  double scaled[3];
313 >
314 >  if( !orthoRhombic ){
315 >    // calc the scaled coordinates.
316 >  
317 >
318 >    matVecMul3(HmatInv, thePos, scaled);
319 >    
320 >    for(i=0; i<3; i++)
321 >      scaled[i] -= roundMe(scaled[i]);
322 >    
323 >    // calc the wrapped real coordinates from the wrapped scaled coordinates
324 >    
325 >    matVecMul3(Hmat, scaled, thePos);
326 >
327 >  }
328 >  else{
329 >    // calc the scaled coordinates.
330 >    
331 >    for(i=0; i<3; i++)
332 >      scaled[i] = thePos[i]*HmatInv[i][i];
333 >    
334 >    // wrap the scaled coordinates
335 >    
336 >    for(i=0; i<3; i++)
337 >      scaled[i] -= roundMe(scaled[i]);
338 >    
339 >    // calc the wrapped real coordinates from the wrapped scaled coordinates
340 >    
341 >    for(i=0; i<3; i++)
342 >      thePos[i] = scaled[i]*Hmat[i][i];
343 >  }
344 >    
345   }
346  
347 +
348 + int SimInfo::getNDF(){
349 +  int ndf_local, ndf;
350 +  
351 +  ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
352 +
353 + #ifdef IS_MPI
354 +  MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
355 + #else
356 +  ndf = ndf_local;
357 + #endif
358 +
359 +  ndf = ndf - 3;
360 +
361 +  return ndf;
362 + }
363 +
364 + int SimInfo::getNDFraw() {
365 +  int ndfRaw_local, ndfRaw;
366 +
367 +  // Raw degrees of freedom that we have to set
368 +  ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
369 +  
370 + #ifdef IS_MPI
371 +  MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
372 + #else
373 +  ndfRaw = ndfRaw_local;
374 + #endif
375 +
376 +  return ndfRaw;
377 + }
378 +
379   void SimInfo::refreshSim(){
380  
381    simtype fInfo;
382    int isError;
383 +  int n_global;
384 +  int* excl;
385  
386 <  fInfo.box[0] = box_x;
42 <  fInfo.box[1] = box_y;
43 <  fInfo.box[2] = box_z;
386 >  fInfo.dielect = 0.0;
387  
388 <  fInfo.rlist = rList;
389 <  fInfo.rcut = rCut;
390 <  fInfo.rrf = ecr;
48 <  fInfo.rt = ecr - est;
49 <  fInfo.dielect = dielectric;
388 >  if( useDipole ){
389 >    if( useReactionField )fInfo.dielect = dielectric;
390 >  }
391  
392    fInfo.SIM_uses_PBC = usePBC;
393 +  //fInfo.SIM_uses_LJ = 0;
394    fInfo.SIM_uses_LJ = useLJ;
395 <  //fInfo.SIM_uses_sticky = useSticky;
396 <  fInfo.SIM_uses_sticky = 0;
395 >  fInfo.SIM_uses_sticky = useSticky;
396 >  //fInfo.SIM_uses_sticky = 0;
397    fInfo.SIM_uses_dipoles = useDipole;
398 <  fInfo.SIM_uses_RF = useReactionField;
398 >  //fInfo.SIM_uses_dipoles = 0;
399 >  //fInfo.SIM_uses_RF = useReactionField;
400 >  fInfo.SIM_uses_RF = 0;
401    fInfo.SIM_uses_GB = useGB;
402    fInfo.SIM_uses_EAM = useEAM;
403  
404 +  excl = Exclude::getArray();
405  
406 + #ifdef IS_MPI
407 +  n_global = mpiSim->getTotAtoms();
408 + #else
409 +  n_global = n_atoms;
410 + #endif
411 +
412    isError = 0;
413  
414 <  fInfo;
415 <  n_atoms;
416 <  identArray;
66 <  n_exclude;
67 <  excludes;
68 <  nGlobalExcludes;
69 <  globalExcludes;
70 <  isError;
414 >  setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
415 >                  &nGlobalExcludes, globalExcludes, molMembershipArray,
416 >                  &isError );
417  
72 –  setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excludes, &nGlobalExcludes, globalExcludes, &isError );
73 –
418    if( isError ){
419  
420      sprintf( painCave.errMsg,
# Line 84 | Line 428 | void SimInfo::refreshSim(){
428             "succesfully sent the simulation information to fortran.\n");
429    MPIcheckPoint();
430   #endif // is_mpi
431 +
432 +  this->ndf = this->getNDF();
433 +  this->ndfRaw = this->getNDFraw();
434 +
435   }
436  
437 +
438 + void SimInfo::setRcut( double theRcut ){
439 +
440 +  if( !haveOrigRcut ){
441 +    haveOrigRcut = 1;
442 +    origRcut = theRcut;
443 +  }
444 +
445 +  rCut = theRcut;
446 +  checkCutOffs();
447 + }
448 +
449 + void SimInfo::setEcr( double theEcr ){
450 +
451 +  if( !haveOrigEcr ){
452 +    haveOrigEcr = 1;
453 +    origEcr = theEcr;
454 +  }
455 +
456 +  ecr = theEcr;
457 +  checkCutOffs();
458 + }
459 +
460 + void SimInfo::setEcr( double theEcr, double theEst ){
461 +
462 +  est = theEst;
463 +  setEcr( theEcr );
464 + }
465 +
466 +
467 + void SimInfo::checkCutOffs( void ){
468 +
469 +  int cutChanged = 0;
470 +
471 +  if( boxIsInit ){
472 +    
473 +    //we need to check cutOffs against the box
474 +    
475 +    if( maxCutoff > rCut ){
476 +      if( rCut < origRcut ){
477 +        rCut = origRcut;
478 +        if (rCut > maxCutoff) rCut = maxCutoff;
479 +        
480 +        sprintf( painCave.errMsg,
481 +                 "New Box size is setting the long range cutoff radius "
482 +                 "to %lf\n",
483 +                 rCut );
484 +        painCave.isFatal = 0;
485 +        simError();
486 +      }
487 +    }
488 +
489 +    if( maxCutoff > ecr ){
490 +      if( ecr < origEcr ){
491 +        rCut = origEcr;
492 +        if (ecr > maxCutoff) ecr = maxCutoff;
493 +        
494 +        sprintf( painCave.errMsg,
495 +                 "New Box size is setting the electrostaticCutoffRadius "
496 +                 "to %lf\n",
497 +                 ecr );
498 +        painCave.isFatal = 0;
499 +        simError();
500 +      }
501 +    }
502 +
503 +
504 +    if (rCut > maxCutoff) {
505 +      sprintf( painCave.errMsg,
506 +               "New Box size is setting the long range cutoff radius "
507 +               "to %lf\n",
508 +               maxCutoff );
509 +      painCave.isFatal = 0;
510 +      simError();
511 +      rCut = maxCutoff;
512 +    }
513 +
514 +    if( ecr > maxCutoff){
515 +      sprintf( painCave.errMsg,
516 +               "New Box size is setting the electrostaticCutoffRadius "
517 +               "to %lf\n",
518 +               maxCutoff  );
519 +      painCave.isFatal = 0;
520 +      simError();      
521 +      ecr = maxCutoff;
522 +    }
523 +
524 +    
525 +  }
526 +  
527 +
528 +  if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
529 +
530 +  // rlist is the 1.0 plus max( rcut, ecr )
531 +  
532 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
533 +
534 +  if( cutChanged ){
535 +    
536 +    notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
537 +  }
538 +
539 +  oldEcr = ecr;
540 +  oldRcut = rCut;
541 + }
542 +
543 + void SimInfo::addProperty(GenericData* prop){
544 +
545 +  map<string, GenericData*>::iterator result;
546 +  result = properties.find(prop->getID());
547 +  
548 +  //we can't simply use  properties[prop->getID()] = prop,
549 +  //it will cause memory leak if we already contain a propery which has the same name of prop
550 +  
551 +  if(result != properties.end()){
552 +    
553 +    delete (*result).second;
554 +    (*result).second = prop;
555 +      
556 +  }
557 +  else{
558 +
559 +    properties[prop->getID()] = prop;
560 +
561 +  }
562 +    
563 + }
564 +
565 + GenericData* SimInfo::getProperty(const string& propName){
566 +
567 +  map<string, GenericData*>::iterator result;
568 +  
569 +  //string lowerCaseName = ();
570 +  
571 +  result = properties.find(propName);
572 +  
573 +  if(result != properties.end())
574 +    return (*result).second;  
575 +  else  
576 +    return NULL;  
577 + }
578 +
579 + vector<GenericData*> SimInfo::getProperties(){
580 +
581 +  vector<GenericData*> result;
582 +  map<string, GenericData*>::iterator i;
583 +  
584 +  for(i = properties.begin(); i != properties.end(); i++)
585 +    result.push_back((*i).second);
586 +    
587 +  return result;
588 + }
589 +
590 +

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