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root/group/branches/new-templateless/OOPSE/libmdtools/SimInfo.cpp
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Comparing:
trunk/OOPSE/libmdtools/SimInfo.cpp (file contents), Revision 441 by chuckv, Tue Apr 1 16:50:14 2003 UTC vs.
branches/new-templateless/OOPSE/libmdtools/SimInfo.cpp (file contents), Revision 850 by mmeineke, Mon Nov 3 22:07:17 2003 UTC

# Line 1 | Line 1
1 < #include <cstdlib>
2 < #include <cstring>
1 > #include <stdlib.h>
2 > #include <string.h>
3 > #include <math.h>
4  
5 + #include <iostream>
6 + using namespace std;
7  
8   #include "SimInfo.hpp"
9   #define __C
# Line 9 | Line 12
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  
64 +  properties = new GenericData();
65  
66    wrapMeSimInfo( this );
67   }
68  
69 +
70 + SimInfo::~SimInfo(){
71 +
72 +  delete myConfiguration;
73 +  delete properties;    
74 + }
75 +
76 + void SimInfo::setBox(double newBox[3]) {
77 +  
78 +  int i, j;
79 +  double tempMat[3][3];
80 +
81 +  for(i=0; i<3; i++)
82 +    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
83 +
84 +  tempMat[0][0] = newBox[0];
85 +  tempMat[1][1] = newBox[1];
86 +  tempMat[2][2] = newBox[2];
87 +
88 +  setBoxM( tempMat );
89 +
90 + }
91 +
92 + void SimInfo::setBoxM( double theBox[3][3] ){
93 +  
94 +  int i, j;
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 +
282 + void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){
283 +
284 +      out[0] = a[1] * b[2] - a[2] * b[1];
285 +      out[1] = a[2] * b[0] - a[0] * b[2] ;
286 +      out[2] = a[0] * b[1] - a[1] * b[0];
287 +      
288 + }
289 +
290 + double SimInfo::dotProduct3(double a[3], double b[3]){
291 +  return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2];
292 + }
293 +
294 + double SimInfo::length3(double a[3]){
295 +  return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]);
296 + }
297 +
298 + void SimInfo::calcBoxL( void ){
299 +
300 +  double dx, dy, dz, dsq;
301 +
302 +  // boxVol = Determinant of Hmat
303 +
304 +  boxVol = matDet3( Hmat );
305 +
306 +  // boxLx
307 +  
308 +  dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
309 +  dsq = dx*dx + dy*dy + dz*dz;
310 +  boxL[0] = sqrt( dsq );
311 +  //maxCutoff = 0.5 * boxL[0];
312 +
313 +  // boxLy
314 +  
315 +  dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
316 +  dsq = dx*dx + dy*dy + dz*dz;
317 +  boxL[1] = sqrt( dsq );
318 +  //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
319 +
320 +
321 +  // boxLz
322 +  
323 +  dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
324 +  dsq = dx*dx + dy*dy + dz*dz;
325 +  boxL[2] = sqrt( dsq );
326 +  //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
327 +
328 +  //calculate the max cutoff
329 +  maxCutoff =  calcMaxCutOff();
330 +  
331 +  checkCutOffs();
332 +
333 + }
334 +
335 +
336 + double SimInfo::calcMaxCutOff(){
337 +
338 +  double ri[3], rj[3], rk[3];
339 +  double rij[3], rjk[3], rki[3];
340 +  double minDist;
341 +
342 +  ri[0] = Hmat[0][0];
343 +  ri[1] = Hmat[1][0];
344 +  ri[2] = Hmat[2][0];
345 +
346 +  rj[0] = Hmat[0][1];
347 +  rj[1] = Hmat[1][1];
348 +  rj[2] = Hmat[2][1];
349 +
350 +  rk[0] = Hmat[0][2];
351 +  rk[1] = Hmat[1][2];
352 +  rk[2] = Hmat[2][2];
353 +  
354 +  crossProduct3(ri,rj, rij);
355 +  distXY = dotProduct3(rk,rij) / length3(rij);
356 +
357 +  crossProduct3(rj,rk, rjk);
358 +  distYZ = dotProduct3(ri,rjk) / length3(rjk);
359 +
360 +  crossProduct3(rk,ri, rki);
361 +  distZX = dotProduct3(rj,rki) / length3(rki);
362 +
363 +  minDist = min(min(distXY, distYZ), distZX);
364 +  return minDist/2;
365 +  
366 + }
367 +
368 + void SimInfo::wrapVector( double thePos[3] ){
369 +
370 +  int i;
371 +  double scaled[3];
372 +
373 +  if( !orthoRhombic ){
374 +    // calc the scaled coordinates.
375 +  
376 +
377 +    matVecMul3(HmatInv, thePos, scaled);
378 +    
379 +    for(i=0; i<3; i++)
380 +      scaled[i] -= roundMe(scaled[i]);
381 +    
382 +    // calc the wrapped real coordinates from the wrapped scaled coordinates
383 +    
384 +    matVecMul3(Hmat, scaled, thePos);
385 +
386 +  }
387 +  else{
388 +    // calc the scaled coordinates.
389 +    
390 +    for(i=0; i<3; i++)
391 +      scaled[i] = thePos[i]*HmatInv[i][i];
392 +    
393 +    // wrap the scaled coordinates
394 +    
395 +    for(i=0; i<3; i++)
396 +      scaled[i] -= roundMe(scaled[i]);
397 +    
398 +    // calc the wrapped real coordinates from the wrapped scaled coordinates
399 +    
400 +    for(i=0; i<3; i++)
401 +      thePos[i] = scaled[i]*Hmat[i][i];
402 +  }
403 +    
404 + }
405 +
406 +
407 + int SimInfo::getNDF(){
408 +  int ndf_local;
409 +  
410 +  ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
411 +
412 + #ifdef IS_MPI
413 +  MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
414 + #else
415 +  ndf = ndf_local;
416 + #endif
417 +
418 +  ndf = ndf - 3 - nZconstraints;
419 +
420 +  return ndf;
421 + }
422 +
423 + int SimInfo::getNDFraw() {
424 +  int ndfRaw_local;
425 +
426 +  // Raw degrees of freedom that we have to set
427 +  ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
428 +  
429 + #ifdef IS_MPI
430 +  MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
431 + #else
432 +  ndfRaw = ndfRaw_local;
433 + #endif
434 +
435 +  return ndfRaw;
436 + }
437 +
438 + int SimInfo::getNDFtranslational() {
439 +  int ndfTrans_local;
440 +
441 +  ndfTrans_local = 3 * n_atoms - n_constraints;
442 +
443 + #ifdef IS_MPI
444 +  MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
445 + #else
446 +  ndfTrans = ndfTrans_local;
447 + #endif
448 +
449 +  ndfTrans = ndfTrans - 3 - nZconstraints;
450 +
451 +  return ndfTrans;
452 + }
453 +
454   void SimInfo::refreshSim(){
455  
456    simtype fInfo;
457    int isError;
458 +  int n_global;
459    int* excl;
460  
461 <  fInfo.box[0] = box_x;
44 <  fInfo.box[1] = box_y;
45 <  fInfo.box[2] = box_z;
461 >  fInfo.dielect = 0.0;
462  
463 <  fInfo.rlist = rList;
464 <  fInfo.rcut = rCut;
465 <  fInfo.rrf = ecr;
50 <  fInfo.rt = ecr - est;
51 <  fInfo.dielect = dielectric;
463 >  if( useDipole ){
464 >    if( useReactionField )fInfo.dielect = dielectric;
465 >  }
466  
467    fInfo.SIM_uses_PBC = usePBC;
468 +  //fInfo.SIM_uses_LJ = 0;
469    fInfo.SIM_uses_LJ = useLJ;
470 <
471 <  //fInfo.SIM_uses_sticky = useSticky;
57 <  fInfo.SIM_uses_sticky = 0;
470 >  fInfo.SIM_uses_sticky = useSticky;
471 >  //fInfo.SIM_uses_sticky = 0;
472    fInfo.SIM_uses_dipoles = useDipole;
473    //fInfo.SIM_uses_dipoles = 0;
474 <  fInfo.SIM_uses_RF = useReactionField;
474 >  //fInfo.SIM_uses_RF = useReactionField;
475 >  fInfo.SIM_uses_RF = 0;
476    fInfo.SIM_uses_GB = useGB;
477    fInfo.SIM_uses_EAM = useEAM;
478  
479    excl = Exclude::getArray();
480  
481 + #ifdef IS_MPI
482 +  n_global = mpiSim->getTotAtoms();
483 + #else
484 +  n_global = n_atoms;
485 + #endif
486 +
487    isError = 0;
488  
489 < //   fInfo;
490 < //   n_atoms;
491 < //   identArray;
71 < //   n_exclude;
72 < //   excludes;
73 < //   nGlobalExcludes;
74 < //   globalExcludes;
75 < //   isError;
489 >  setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
490 >                  &nGlobalExcludes, globalExcludes, molMembershipArray,
491 >                  &isError );
492  
77 –  setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excl,
78 –                  &nGlobalExcludes, globalExcludes, &isError );
79 –
493    if( isError ){
494  
495      sprintf( painCave.errMsg,
# Line 90 | Line 503 | void SimInfo::refreshSim(){
503             "succesfully sent the simulation information to fortran.\n");
504    MPIcheckPoint();
505   #endif // is_mpi
506 +
507 +  this->ndf = this->getNDF();
508 +  this->ndfRaw = this->getNDFraw();
509 +  this->ndfTrans = this->getNDFtranslational();
510   }
511  
512 +
513 + void SimInfo::setRcut( double theRcut ){
514 +
515 +  rCut = theRcut;
516 +  checkCutOffs();
517 + }
518 +
519 + void SimInfo::setDefaultRcut( double theRcut ){
520 +
521 +  haveOrigRcut = 1;
522 +  origRcut = theRcut;
523 +  rCut = theRcut;
524 +
525 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
526 +
527 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
528 + }
529 +
530 + void SimInfo::setEcr( double theEcr ){
531 +
532 +  ecr = theEcr;
533 +  checkCutOffs();
534 + }
535 +
536 + void SimInfo::setDefaultEcr( double theEcr ){
537 +
538 +  haveOrigEcr = 1;
539 +  origEcr = theEcr;
540 +  
541 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
542 +
543 +  ecr = theEcr;
544 +
545 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
546 + }
547 +
548 + void SimInfo::setEcr( double theEcr, double theEst ){
549 +
550 +  est = theEst;
551 +  setEcr( theEcr );
552 + }
553 +
554 + void SimInfo::setDefaultEcr( double theEcr, double theEst ){
555 +
556 +  est = theEst;
557 +  setDefaultEcr( theEcr );
558 + }
559 +
560 +
561 + void SimInfo::checkCutOffs( void ){
562 +
563 +  int cutChanged = 0;
564 +  
565 +  if( boxIsInit ){
566 +    
567 +    //we need to check cutOffs against the box
568 +
569 +    //detect the change of rCut
570 +    if(( maxCutoff > rCut )&&(usePBC)){
571 +      if( rCut < origRcut ){
572 +        rCut = origRcut;
573 +        
574 +        if (rCut > maxCutoff)
575 +          rCut = maxCutoff;
576 +  
577 +          sprintf( painCave.errMsg,
578 +                    "New Box size is setting the long range cutoff radius "
579 +                    "to %lf at time %lf\n",
580 +                    rCut, currentTime );
581 +          painCave.isFatal = 0;
582 +          simError();
583 +      }
584 +    }
585 +    else if ((rCut > maxCutoff)&&(usePBC)) {
586 +      sprintf( painCave.errMsg,
587 +               "New Box size is setting the long range cutoff radius "
588 +               "to %lf at time %lf\n",
589 +               maxCutoff, currentTime );
590 +      painCave.isFatal = 0;
591 +      simError();
592 +      rCut = maxCutoff;
593 +    }
594 +
595 +
596 +    //detect the change of ecr
597 +    if( maxCutoff > ecr ){
598 +      if( ecr < origEcr ){
599 +        ecr = origEcr;
600 +        if (ecr > maxCutoff) ecr = maxCutoff;
601 +  
602 +          sprintf( painCave.errMsg,
603 +                    "New Box size is setting the electrostaticCutoffRadius "
604 +                    "to %lf at time %lf\n",
605 +                    ecr, currentTime );
606 +            painCave.isFatal = 0;
607 +            simError();
608 +      }
609 +    }
610 +    else if( ecr > maxCutoff){
611 +      sprintf( painCave.errMsg,
612 +               "New Box size is setting the electrostaticCutoffRadius "
613 +               "to %lf at time %lf\n",
614 +               maxCutoff, currentTime  );
615 +      painCave.isFatal = 0;
616 +      simError();      
617 +      ecr = maxCutoff;
618 +    }
619 +
620 +    if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
621 +    
622 +    // rlist is the 1.0 plus max( rcut, ecr )
623 +    
624 +    ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
625 +    
626 +    if( cutChanged ){
627 +      notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
628 +    }
629 +    
630 +    oldEcr = ecr;
631 +    oldRcut = rCut;
632 +    
633 +  } else {
634 +    // initialize this stuff before using it, OK?
635 +    sprintf( painCave.errMsg,
636 +             "Trying to check cutoffs without a box. Be smarter.\n" );
637 +    painCave.isFatal = 1;
638 +    simError();      
639 +  }
640 +  
641 + }
642 +
643 + GenericData* SimInfo::getProperty(char* propName){
644 +
645 +  return properties->find( propName );
646 + }
647 +
648 + double SimInfo::matTrace3(double m[3][3]){
649 +  double trace;
650 +  trace = m[0][0] + m[1][1] + m[2][2];
651 +
652 +  return trace;
653 + }

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