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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 790 by mmeineke, Mon Sep 29 21:16:11 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(){
27    excludes = NULL;
28    n_constraints = 0;
29 +  nZconstraints = 0;
30    n_oriented = 0;
31    n_dipoles = 0;
32 +  ndf = 0;
33 +  ndfRaw = 0;
34 +  nZconstraints = 0;
35    the_integrator = NULL;
36    setTemp = 0;
37    thermalTime = 0.0;
38 +  currentTime = 0.0;
39    rCut = 0.0;
40 +  origRcut = -1.0;
41 +  ecr = 0.0;
42 +  origEcr = -1.0;
43 +  est = 0.0;
44 +  oldEcr = 0.0;
45 +  oldRcut = 0.0;
46  
47 +  haveOrigRcut = 0;
48 +  haveOrigEcr = 0;
49 +  boxIsInit = 0;
50 +  
51 +  resetTime = 1e99;
52 +  
53 +
54    usePBC = 0;
55    useLJ = 0;
56    useSticky = 0;
# Line 29 | Line 59 | SimInfo::SimInfo(){
59    useGB = 0;
60    useEAM = 0;
61  
62 +  myConfiguration = new SimState();
63  
33 –
64    wrapMeSimInfo( this );
65   }
66  
67 +
68 + SimInfo::~SimInfo(){
69 +
70 +  delete myConfiguration;
71 +
72 +  map<string, GenericData*>::iterator i;
73 +  
74 +  for(i = properties.begin(); i != properties.end(); i++)
75 +    delete (*i).second;
76 +    
77 + }
78 +
79 + void SimInfo::setBox(double newBox[3]) {
80 +  
81 +  int i, j;
82 +  double tempMat[3][3];
83 +
84 +  for(i=0; i<3; i++)
85 +    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
86 +
87 +  tempMat[0][0] = newBox[0];
88 +  tempMat[1][1] = newBox[1];
89 +  tempMat[2][2] = newBox[2];
90 +
91 +  setBoxM( tempMat );
92 +
93 + }
94 +
95 + void SimInfo::setBoxM( double theBox[3][3] ){
96 +  
97 +  int i, j;
98 +  double FortranHmat[9]; // to preserve compatibility with Fortran the
99 +                         // ordering in the array is as follows:
100 +                         // [ 0 3 6 ]
101 +                         // [ 1 4 7 ]
102 +                         // [ 2 5 8 ]
103 +  double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
104 +
105 +  
106 +  if( !boxIsInit ) boxIsInit = 1;
107 +
108 +  for(i=0; i < 3; i++)
109 +    for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
110 +  
111 +  calcBoxL();
112 +  calcHmatInv();
113 +
114 +  for(i=0; i < 3; i++) {
115 +    for (j=0; j < 3; j++) {
116 +      FortranHmat[3*j + i] = Hmat[i][j];
117 +      FortranHmatInv[3*j + i] = HmatInv[i][j];
118 +    }
119 +  }
120 +
121 +  setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
122 +
123 + }
124 +
125 +
126 + void SimInfo::getBoxM (double theBox[3][3]) {
127 +
128 +  int i, j;
129 +  for(i=0; i<3; i++)
130 +    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
131 + }
132 +
133 +
134 + void SimInfo::scaleBox(double scale) {
135 +  double theBox[3][3];
136 +  int i, j;
137 +
138 +  // cerr << "Scaling box by " << scale << "\n";
139 +
140 +  for(i=0; i<3; i++)
141 +    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
142 +
143 +  setBoxM(theBox);
144 +
145 + }
146 +
147 + void SimInfo::calcHmatInv( void ) {
148 +  
149 +  int i,j;
150 +  double smallDiag;
151 +  double tol;
152 +  double sanity[3][3];
153 +
154 +  invertMat3( Hmat, HmatInv );
155 +
156 +  // Check the inverse to make sure it is sane:
157 +
158 +  matMul3( Hmat, HmatInv, sanity );
159 +    
160 +  // check to see if Hmat is orthorhombic
161 +  
162 +  smallDiag = Hmat[0][0];
163 +  if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1];
164 +  if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2];
165 +  tol = smallDiag * 1E-6;
166 +
167 +  orthoRhombic = 1;
168 +  
169 +  for (i = 0; i < 3; i++ ) {
170 +    for (j = 0 ; j < 3; j++) {
171 +      if (i != j) {
172 +        if (orthoRhombic) {
173 +          if (Hmat[i][j] >= tol) orthoRhombic = 0;
174 +        }        
175 +      }
176 +    }
177 +  }
178 + }
179 +
180 + double SimInfo::matDet3(double a[3][3]) {
181 +  int i, j, k;
182 +  double determinant;
183 +
184 +  determinant = 0.0;
185 +
186 +  for(i = 0; i < 3; i++) {
187 +    j = (i+1)%3;
188 +    k = (i+2)%3;
189 +
190 +    determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]);
191 +  }
192 +
193 +  return determinant;
194 + }
195 +
196 + void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
197 +  
198 +  int  i, j, k, l, m, n;
199 +  double determinant;
200 +
201 +  determinant = matDet3( a );
202 +
203 +  if (determinant == 0.0) {
204 +    sprintf( painCave.errMsg,
205 +             "Can't invert a matrix with a zero determinant!\n");
206 +    painCave.isFatal = 1;
207 +    simError();
208 +  }
209 +
210 +  for (i=0; i < 3; i++) {
211 +    j = (i+1)%3;
212 +    k = (i+2)%3;
213 +    for(l = 0; l < 3; l++) {
214 +      m = (l+1)%3;
215 +      n = (l+2)%3;
216 +      
217 +      b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant;
218 +    }
219 +  }
220 + }
221 +
222 + void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
223 +  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
224 +
225 +  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
226 +  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
227 +  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
228 +  
229 +  r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0];
230 +  r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1];
231 +  r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2];
232 +  
233 +  r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0];
234 +  r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1];
235 +  r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2];
236 +  
237 +  c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
238 +  c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
239 +  c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
240 + }
241 +
242 + void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
243 +  double a0, a1, a2;
244 +
245 +  a0 = inVec[0];  a1 = inVec[1];  a2 = inVec[2];
246 +
247 +  outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2;
248 +  outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
249 +  outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
250 + }
251 +
252 + void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
253 +  double temp[3][3];
254 +  int i, j;
255 +
256 +  for (i = 0; i < 3; i++) {
257 +    for (j = 0; j < 3; j++) {
258 +      temp[j][i] = in[i][j];
259 +    }
260 +  }
261 +  for (i = 0; i < 3; i++) {
262 +    for (j = 0; j < 3; j++) {
263 +      out[i][j] = temp[i][j];
264 +    }
265 +  }
266 + }
267 +  
268 + void SimInfo::printMat3(double A[3][3] ){
269 +
270 +  std::cerr
271 +            << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
272 +            << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
273 +            << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
274 + }
275 +
276 + void SimInfo::printMat9(double A[9] ){
277 +
278 +  std::cerr
279 +            << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
280 +            << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
281 +            << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
282 + }
283 +
284 +
285 + void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){
286 +
287 +      out[0] = a[1] * b[2] - a[2] * b[1];
288 +      out[1] = a[2] * b[0] - a[0] * b[2] ;
289 +      out[2] = a[0] * b[1] - a[1] * b[0];
290 +      
291 + }
292 +
293 + double SimInfo::dotProduct3(double a[3], double b[3]){
294 +  return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2];
295 + }
296 +
297 + double SimInfo::length3(double a[3]){
298 +  return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]);
299 + }
300 +
301 + void SimInfo::calcBoxL( void ){
302 +
303 +  double dx, dy, dz, dsq;
304 +
305 +  // boxVol = Determinant of Hmat
306 +
307 +  boxVol = matDet3( Hmat );
308 +
309 +  // boxLx
310 +  
311 +  dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
312 +  dsq = dx*dx + dy*dy + dz*dz;
313 +  boxL[0] = sqrt( dsq );
314 +  //maxCutoff = 0.5 * boxL[0];
315 +
316 +  // boxLy
317 +  
318 +  dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
319 +  dsq = dx*dx + dy*dy + dz*dz;
320 +  boxL[1] = sqrt( dsq );
321 +  //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
322 +
323 +
324 +  // boxLz
325 +  
326 +  dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
327 +  dsq = dx*dx + dy*dy + dz*dz;
328 +  boxL[2] = sqrt( dsq );
329 +  //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
330 +
331 +  //calculate the max cutoff
332 +  maxCutoff =  calcMaxCutOff();
333 +  
334 +  checkCutOffs();
335 +
336 + }
337 +
338 +
339 + double SimInfo::calcMaxCutOff(){
340 +
341 +  double ri[3], rj[3], rk[3];
342 +  double rij[3], rjk[3], rki[3];
343 +  double minDist;
344 +
345 +  ri[0] = Hmat[0][0];
346 +  ri[1] = Hmat[1][0];
347 +  ri[2] = Hmat[2][0];
348 +
349 +  rj[0] = Hmat[0][1];
350 +  rj[1] = Hmat[1][1];
351 +  rj[2] = Hmat[2][1];
352 +
353 +  rk[0] = Hmat[0][2];
354 +  rk[1] = Hmat[1][2];
355 +  rk[2] = Hmat[2][2];
356 +  
357 +  crossProduct3(ri,rj, rij);
358 +  distXY = dotProduct3(rk,rij) / length3(rij);
359 +
360 +  crossProduct3(rj,rk, rjk);
361 +  distYZ = dotProduct3(ri,rjk) / length3(rjk);
362 +
363 +  crossProduct3(rk,ri, rki);
364 +  distZX = dotProduct3(rj,rki) / length3(rki);
365 +
366 +  minDist = min(min(distXY, distYZ), distZX);
367 +  return minDist/2;
368 +  
369 + }
370 +
371 + void SimInfo::wrapVector( double thePos[3] ){
372 +
373 +  int i;
374 +  double scaled[3];
375 +
376 +  if( !orthoRhombic ){
377 +    // calc the scaled coordinates.
378 +  
379 +
380 +    matVecMul3(HmatInv, thePos, scaled);
381 +    
382 +    for(i=0; i<3; i++)
383 +      scaled[i] -= roundMe(scaled[i]);
384 +    
385 +    // calc the wrapped real coordinates from the wrapped scaled coordinates
386 +    
387 +    matVecMul3(Hmat, scaled, thePos);
388 +
389 +  }
390 +  else{
391 +    // calc the scaled coordinates.
392 +    
393 +    for(i=0; i<3; i++)
394 +      scaled[i] = thePos[i]*HmatInv[i][i];
395 +    
396 +    // wrap the scaled coordinates
397 +    
398 +    for(i=0; i<3; i++)
399 +      scaled[i] -= roundMe(scaled[i]);
400 +    
401 +    // calc the wrapped real coordinates from the wrapped scaled coordinates
402 +    
403 +    for(i=0; i<3; i++)
404 +      thePos[i] = scaled[i]*Hmat[i][i];
405 +  }
406 +    
407 + }
408 +
409 +
410 + int SimInfo::getNDF(){
411 +  int ndf_local;
412 +  
413 +  ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
414 +
415 + #ifdef IS_MPI
416 +  MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
417 + #else
418 +  ndf = ndf_local;
419 + #endif
420 +
421 +  ndf = ndf - 3 - nZconstraints;
422 +
423 +  return ndf;
424 + }
425 +
426 + int SimInfo::getNDFraw() {
427 +  int ndfRaw_local;
428 +
429 +  // Raw degrees of freedom that we have to set
430 +  ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
431 +  
432 + #ifdef IS_MPI
433 +  MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
434 + #else
435 +  ndfRaw = ndfRaw_local;
436 + #endif
437 +
438 +  return ndfRaw;
439 + }
440 +
441 + int SimInfo::getNDFtranslational() {
442 +  int ndfTrans_local;
443 +
444 +  ndfTrans_local = 3 * n_atoms - n_constraints;
445 +
446 + #ifdef IS_MPI
447 +  MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
448 + #else
449 +  ndfTrans = ndfTrans_local;
450 + #endif
451 +
452 +  ndfTrans = ndfTrans - 3 - nZconstraints;
453 +
454 +  return ndfTrans;
455 + }
456 +
457   void SimInfo::refreshSim(){
458  
459    simtype fInfo;
460    int isError;
461 +  int n_global;
462    int* excl;
463  
464 <  fInfo.box[0] = box_x;
44 <  fInfo.box[1] = box_y;
45 <  fInfo.box[2] = box_z;
464 >  fInfo.dielect = 0.0;
465  
466 <  fInfo.rlist = rList;
467 <  fInfo.rcut = rCut;
468 <  fInfo.rrf = ecr;
50 <  fInfo.rt = ecr - est;
51 <  fInfo.dielect = dielectric;
466 >  if( useDipole ){
467 >    if( useReactionField )fInfo.dielect = dielectric;
468 >  }
469  
470    fInfo.SIM_uses_PBC = usePBC;
471    //fInfo.SIM_uses_LJ = 0;
# Line 64 | Line 481 | void SimInfo::refreshSim(){
481  
482    excl = Exclude::getArray();
483  
484 + #ifdef IS_MPI
485 +  n_global = mpiSim->getTotAtoms();
486 + #else
487 +  n_global = n_atoms;
488 + #endif
489 +
490    isError = 0;
491  
492 < //   fInfo;
493 < //   n_atoms;
494 < //   identArray;
72 < //   n_exclude;
73 < //   excludes;
74 < //   nGlobalExcludes;
75 < //   globalExcludes;
76 < //   isError;
492 >  setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
493 >                  &nGlobalExcludes, globalExcludes, molMembershipArray,
494 >                  &isError );
495  
78 –  setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excl,
79 –                  &nGlobalExcludes, globalExcludes, &isError );
80 –
496    if( isError ){
497  
498      sprintf( painCave.errMsg,
# Line 91 | Line 506 | void SimInfo::refreshSim(){
506             "succesfully sent the simulation information to fortran.\n");
507    MPIcheckPoint();
508   #endif // is_mpi
509 +
510 +  this->ndf = this->getNDF();
511 +  this->ndfRaw = this->getNDFraw();
512 +  this->ndfTrans = this->getNDFtranslational();
513   }
514  
515 +
516 + void SimInfo::setRcut( double theRcut ){
517 +
518 +  if( !haveOrigRcut ){
519 +    haveOrigRcut = 1;
520 +    origRcut = theRcut;
521 +  }
522 +
523 +  rCut = theRcut;
524 +  checkCutOffs();
525 + }
526 +
527 + void SimInfo::setEcr( double theEcr ){
528 +
529 +  if( !haveOrigEcr ){
530 +    haveOrigEcr = 1;
531 +    origEcr = theEcr;
532 +  }
533 +
534 +  ecr = theEcr;
535 +  checkCutOffs();
536 + }
537 +
538 + void SimInfo::setEcr( double theEcr, double theEst ){
539 +
540 +  est = theEst;
541 +  setEcr( theEcr );
542 + }
543 +
544 +
545 + void SimInfo::checkCutOffs( void ){
546 +
547 +  int cutChanged = 0;
548 +  
549 +  if( boxIsInit ){
550 +    
551 +    //we need to check cutOffs against the box
552 +
553 +    //detect the change of rCut
554 +    if(( maxCutoff > rCut )&&(usePBC)){
555 +      if( rCut < origRcut ){
556 +        rCut = origRcut;
557 +        
558 +        if (rCut > maxCutoff)
559 +          rCut = maxCutoff;
560 +  
561 +          sprintf( painCave.errMsg,
562 +                    "New Box size is setting the long range cutoff radius "
563 +                    "to %lf at time %lf\n",
564 +                    rCut, currentTime );
565 +          painCave.isFatal = 0;
566 +          simError();
567 +      }
568 +    }
569 +    else if ((rCut > maxCutoff)&&(usePBC)) {
570 +      sprintf( painCave.errMsg,
571 +               "New Box size is setting the long range cutoff radius "
572 +               "to %lf at time %lf\n",
573 +               maxCutoff, currentTime );
574 +      painCave.isFatal = 0;
575 +      simError();
576 +      rCut = maxCutoff;
577 +    }
578 +
579 +
580 +    //detect the change of ecr
581 +    if( maxCutoff > ecr ){
582 +      if( ecr < origEcr ){
583 +        ecr = origEcr;
584 +        if (ecr > maxCutoff) ecr = maxCutoff;
585 +  
586 +          sprintf( painCave.errMsg,
587 +                    "New Box size is setting the electrostaticCutoffRadius "
588 +                    "to %lf at time %lf\n",
589 +                    ecr, currentTime );
590 +            painCave.isFatal = 0;
591 +            simError();
592 +      }
593 +    }
594 +    else if( ecr > maxCutoff){
595 +      sprintf( painCave.errMsg,
596 +               "New Box size is setting the electrostaticCutoffRadius "
597 +               "to %lf at time %lf\n",
598 +               maxCutoff, currentTime  );
599 +      painCave.isFatal = 0;
600 +      simError();      
601 +      ecr = maxCutoff;
602 +    }
603 +
604 +    if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
605 +    
606 +    // rlist is the 1.0 plus max( rcut, ecr )
607 +    
608 +    ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
609 +    
610 +    if( cutChanged ){
611 +      
612 +      notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
613 +    }
614 +    
615 +    oldEcr = ecr;
616 +    oldRcut = rCut;
617 +    
618 +  } else {
619 +    // initialize this stuff before using it, OK?
620 +    sprintf( painCave.errMsg,
621 +             "Trying to check cutoffs without a box. Be smarter.\n" );
622 +    painCave.isFatal = 1;
623 +    simError();      
624 +  }
625 +  
626 + }
627 +
628 + void SimInfo::addProperty(GenericData* prop){
629 +
630 +  map<string, GenericData*>::iterator result;
631 +  result = properties.find(prop->getID());
632 +  
633 +  //we can't simply use  properties[prop->getID()] = prop,
634 +  //it will cause memory leak if we already contain a propery which has the same name of prop
635 +  
636 +  if(result != properties.end()){
637 +    
638 +    delete (*result).second;
639 +    (*result).second = prop;
640 +      
641 +  }
642 +  else{
643 +
644 +    properties[prop->getID()] = prop;
645 +
646 +  }
647 +    
648 + }
649 +
650 + GenericData* SimInfo::getProperty(const string& propName){
651 +
652 +  map<string, GenericData*>::iterator result;
653 +  
654 +  //string lowerCaseName = ();
655 +  
656 +  result = properties.find(propName);
657 +  
658 +  if(result != properties.end())
659 +    return (*result).second;  
660 +  else  
661 +    return NULL;  
662 + }
663 +
664 + vector<GenericData*> SimInfo::getProperties(){
665 +
666 +  vector<GenericData*> result;
667 +  map<string, GenericData*>::iterator i;
668 +  
669 +  for(i = properties.begin(); i != properties.end(); i++)
670 +    result.push_back((*i).second);
671 +    
672 +  return result;
673 + }
674 +
675 + double SimInfo::matTrace3(double m[3][3]){
676 +  double trace;
677 +  trace = m[0][0] + m[1][1] + m[2][2];
678 +
679 +  return trace;
680 + }

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