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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 845 by gezelter, Thu Oct 30 18:59:20 2003 UTC vs.
Revision 1139 by gezelter, Wed Apr 28 22:06:29 2004 UTC

# Line 12 | Line 12 | using namespace std;
12  
13   #include "fortranWrappers.hpp"
14  
15 + #include "MatVec3.h"
16 +
17   #ifdef IS_MPI
18   #include "mpiSimulation.hpp"
19   #endif
# Line 20 | Line 22 | inline double roundMe( double x ){
22    return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
23   }
24            
25 + inline double min( double a, double b ){
26 +  return (a < b ) ? a : b;
27 + }
28  
29   SimInfo* currentInfo;
30  
31   SimInfo::SimInfo(){
32 <  excludes = NULL;
32 >
33    n_constraints = 0;
34    nZconstraints = 0;
35    n_oriented = 0;
# Line 37 | Line 42 | SimInfo::SimInfo(){
42    thermalTime = 0.0;
43    currentTime = 0.0;
44    rCut = 0.0;
40 –  origRcut = -1.0;
45    ecr = 0.0;
42 –  origEcr = -1.0;
46    est = 0.0;
44 –  oldEcr = 0.0;
45 –  oldRcut = 0.0;
47  
48 <  haveOrigRcut = 0;
49 <  haveOrigEcr = 0;
48 >  haveRcut = 0;
49 >  haveEcr = 0;
50    boxIsInit = 0;
51    
52    resetTime = 1e99;
52 –  
53  
54 +  orthoRhombic = 0;
55 +  orthoTolerance = 1E-6;
56 +  useInitXSstate = true;
57 +
58    usePBC = 0;
59    useLJ = 0;
60    useSticky = 0;
61 <  useDipole = 0;
61 >  useCharges = 0;
62 >  useDipoles = 0;
63    useReactionField = 0;
64    useGB = 0;
65    useEAM = 0;
66 +  useMolecularCutoffs = 0;
67  
68 +  excludes = Exclude::Instance();
69 +
70    myConfiguration = new SimState();
71  
72 +  has_minimizer = false;
73 +  the_minimizer =NULL;
74 +
75    wrapMeSimInfo( this );
76   }
77  
# Line 102 | Line 113 | void SimInfo::setBoxM( double theBox[3][3] ){
113                           // [ 2 5 8 ]
114    double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
115  
105 –  
116    if( !boxIsInit ) boxIsInit = 1;
117  
118    for(i=0; i < 3; i++)
# Line 146 | Line 156 | void SimInfo::calcHmatInv( void ) {
156  
157   void SimInfo::calcHmatInv( void ) {
158    
159 +  int oldOrtho;
160    int i,j;
161    double smallDiag;
162    double tol;
# Line 153 | Line 164 | void SimInfo::calcHmatInv( void ) {
164  
165    invertMat3( Hmat, HmatInv );
166  
156 –  // Check the inverse to make sure it is sane:
157 –
158 –  matMul3( Hmat, HmatInv, sanity );
159 –    
167    // check to see if Hmat is orthorhombic
168    
169 <  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;
169 >  oldOrtho = orthoRhombic;
170  
171 +  smallDiag = fabs(Hmat[0][0]);
172 +  if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
173 +  if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
174 +  tol = smallDiag * orthoTolerance;
175 +
176    orthoRhombic = 1;
177    
178    for (i = 0; i < 3; i++ ) {
179      for (j = 0 ; j < 3; j++) {
180        if (i != j) {
181          if (orthoRhombic) {
182 <          if (Hmat[i][j] >= tol) orthoRhombic = 0;
182 >          if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
183          }        
184        }
185      }
186    }
178 – }
187  
188 < double SimInfo::matDet3(double a[3][3]) {
189 <  int i, j, k;
190 <  double determinant;
191 <
192 <  determinant = 0.0;
193 <
194 <  for(i = 0; i < 3; i++) {
195 <    j = (i+1)%3;
196 <    k = (i+2)%3;
197 <
198 <    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;
188 >  if( oldOrtho != orthoRhombic ){
189 >    
190 >    if( orthoRhombic ){
191 >      sprintf( painCave.errMsg,
192 >               "OOPSE is switching from the default Non-Orthorhombic\n"
193 >               "\tto the faster Orthorhombic periodic boundary computations.\n"
194 >               "\tThis is usually a good thing, but if you wan't the\n"
195 >               "\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
196 >               "\tvariable ( currently set to %G ) smaller.\n",
197 >               orthoTolerance);
198 >      simError();
199      }
200 <  }
201 < }
202 <
203 < void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
204 <  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
205 <
206 <  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
207 <  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
208 <  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
209 <  
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];
200 >    else {
201 >      sprintf( painCave.errMsg,
202 >               "OOPSE is switching from the faster Orthorhombic to the more\n"
203 >               "\tflexible Non-Orthorhombic periodic boundary computations.\n"
204 >               "\tThis is usually because the box has deformed under\n"
205 >               "\tNPTf integration. If you wan't to live on the edge with\n"
206 >               "\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
207 >               "\tvariable ( currently set to %G ) larger.\n",
208 >               orthoTolerance);
209 >      simError();
210      }
211    }
261 –  for (i = 0; i < 3; i++) {
262 –    for (j = 0; j < 3; j++) {
263 –      out[i][j] = temp[i][j];
264 –    }
265 –  }
212   }
267 –  
268 – void SimInfo::printMat3(double A[3][3] ){
213  
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 –
214   void SimInfo::calcBoxL( void ){
215  
216    double dx, dy, dz, dsq;
# Line 353 | Line 266 | double SimInfo::calcMaxCutOff(){
266    rk[0] = Hmat[0][2];
267    rk[1] = Hmat[1][2];
268    rk[2] = Hmat[2][2];
269 <  
270 <  crossProduct3(ri,rj, rij);
271 <  distXY = dotProduct3(rk,rij) / length3(rij);
269 >    
270 >  crossProduct3(ri, rj, rij);
271 >  distXY = dotProduct3(rk,rij) / norm3(rij);
272  
273    crossProduct3(rj,rk, rjk);
274 <  distYZ = dotProduct3(ri,rjk) / length3(rjk);
274 >  distYZ = dotProduct3(ri,rjk) / norm3(rjk);
275  
276    crossProduct3(rk,ri, rki);
277 <  distZX = dotProduct3(rj,rki) / length3(rki);
277 >  distZX = dotProduct3(rj,rki) / norm3(rki);
278  
279    minDist = min(min(distXY, distYZ), distZX);
280    return minDist/2;
# Line 409 | Line 322 | int SimInfo::getNDF(){
322  
323   int SimInfo::getNDF(){
324    int ndf_local;
325 +
326 +  ndf_local = 0;
327    
328 <  ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
328 >  for(int i = 0; i < integrableObjects.size(); i++){
329 >    ndf_local += 3;
330 >    if (integrableObjects[i]->isDirectional()) {
331 >      if (integrableObjects[i]->isLinear())
332 >        ndf_local += 2;
333 >      else
334 >        ndf_local += 3;
335 >    }
336 >  }
337  
338 +  // n_constraints is local, so subtract them on each processor:
339 +
340 +  ndf_local -= n_constraints;
341 +
342   #ifdef IS_MPI
343    MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
344   #else
345    ndf = ndf_local;
346   #endif
347  
348 +  // nZconstraints is global, as are the 3 COM translations for the
349 +  // entire system:
350 +
351    ndf = ndf - 3 - nZconstraints;
352  
353    return ndf;
# Line 427 | Line 357 | int SimInfo::getNDFraw() {
357    int ndfRaw_local;
358  
359    // Raw degrees of freedom that we have to set
360 <  ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
361 <  
360 >  ndfRaw_local = 0;
361 >
362 >  for(int i = 0; i < integrableObjects.size(); i++){
363 >    ndfRaw_local += 3;
364 >    if (integrableObjects[i]->isDirectional()) {
365 >       if (integrableObjects[i]->isLinear())
366 >        ndfRaw_local += 2;
367 >      else
368 >        ndfRaw_local += 3;
369 >    }
370 >  }
371 >    
372   #ifdef IS_MPI
373    MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
374   #else
# Line 441 | Line 381 | int SimInfo::getNDFtranslational() {
381   int SimInfo::getNDFtranslational() {
382    int ndfTrans_local;
383  
384 <  ndfTrans_local = 3 * n_atoms - n_constraints;
384 >  ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
385  
386 +
387   #ifdef IS_MPI
388    MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
389   #else
# Line 454 | Line 395 | int SimInfo::getNDFtranslational() {
395    return ndfTrans;
396   }
397  
398 + int SimInfo::getTotIntegrableObjects() {
399 +  int nObjs_local;
400 +  int nObjs;
401 +
402 +  nObjs_local =  integrableObjects.size();
403 +
404 +
405 + #ifdef IS_MPI
406 +  MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
407 + #else
408 +  nObjs = nObjs_local;
409 + #endif
410 +
411 +
412 +  return nObjs;
413 + }
414 +
415   void SimInfo::refreshSim(){
416  
417    simtype fInfo;
# Line 463 | Line 421 | void SimInfo::refreshSim(){
421  
422    fInfo.dielect = 0.0;
423  
424 <  if( useDipole ){
424 >  if( useDipoles ){
425      if( useReactionField )fInfo.dielect = dielectric;
426    }
427  
# Line 472 | Line 430 | void SimInfo::refreshSim(){
430    fInfo.SIM_uses_LJ = useLJ;
431    fInfo.SIM_uses_sticky = useSticky;
432    //fInfo.SIM_uses_sticky = 0;
433 <  fInfo.SIM_uses_dipoles = useDipole;
433 >  fInfo.SIM_uses_charges = useCharges;
434 >  fInfo.SIM_uses_dipoles = useDipoles;
435    //fInfo.SIM_uses_dipoles = 0;
436 <  //fInfo.SIM_uses_RF = useReactionField;
437 <  fInfo.SIM_uses_RF = 0;
436 >  fInfo.SIM_uses_RF = useReactionField;
437 >  //fInfo.SIM_uses_RF = 0;
438    fInfo.SIM_uses_GB = useGB;
439    fInfo.SIM_uses_EAM = useEAM;
440 +  fInfo.SIM_uses_molecular_cutoffs = useMolecularCutoffs;
441  
442 <  excl = Exclude::getArray();
442 >  n_exclude = excludes->getSize();
443 >  excl = excludes->getFortranArray();
444  
445   #ifdef IS_MPI
446    n_global = mpiSim->getTotAtoms();
# Line 512 | Line 473 | void SimInfo::refreshSim(){
473    this->ndfTrans = this->getNDFtranslational();
474   }
475  
515 –
516 – void SimInfo::setRcut( double theRcut ){
517 –
518 –  rCut = theRcut;
519 –  checkCutOffs();
520 – }
521 –
476   void SimInfo::setDefaultRcut( double theRcut ){
477  
478 <  haveOrigRcut = 1;
525 <  origRcut = theRcut;
478 >  haveRcut = 1;
479    rCut = theRcut;
480  
481    ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
# Line 530 | Line 483 | void SimInfo::setDefaultRcut( double theRcut ){
483    notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
484   }
485  
533 – void SimInfo::setEcr( double theEcr ){
534 –
535 –  ecr = theEcr;
536 –  checkCutOffs();
537 – }
538 –
486   void SimInfo::setDefaultEcr( double theEcr ){
487  
488 <  haveOrigEcr = 1;
489 <  origEcr = theEcr;
488 >  haveEcr = 1;
489 >  ecr = theEcr;
490    
491    ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
492  
546 –  ecr = theEcr;
547 –
493    notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
494   }
495  
551 – void SimInfo::setEcr( double theEcr, double theEst ){
552 –
553 –  est = theEst;
554 –  setEcr( theEcr );
555 – }
556 –
496   void SimInfo::setDefaultEcr( double theEcr, double theEst ){
497  
498    est = theEst;
# Line 562 | Line 501 | void SimInfo::checkCutOffs( void ){
501  
502  
503   void SimInfo::checkCutOffs( void ){
565 –
566 –  int cutChanged = 0;
504    
505    if( boxIsInit ){
506      
507      //we need to check cutOffs against the box
508 <
509 <    //detect the change of rCut
573 <    if(( maxCutoff > rCut )&&(usePBC)){
574 <      if( rCut < origRcut ){
575 <        rCut = origRcut;
576 <        
577 <        if (rCut > maxCutoff)
578 <          rCut = maxCutoff;
579 <  
580 <          sprintf( painCave.errMsg,
581 <                    "New Box size is setting the long range cutoff radius "
582 <                    "to %lf at time %lf\n",
583 <                    rCut, currentTime );
584 <          painCave.isFatal = 0;
585 <          simError();
586 <      }
587 <    }
588 <    else if ((rCut > maxCutoff)&&(usePBC)) {
508 >    
509 >    if( rCut > maxCutoff ){
510        sprintf( painCave.errMsg,
511 <               "New Box size is setting the long range cutoff radius "
512 <               "to %lf at time %lf\n",
513 <               maxCutoff, currentTime );
514 <      painCave.isFatal = 0;
511 >               "LJrcut is too large for the current periodic box.\n"
512 >               "\tCurrent Value of LJrcut = %G at time %G\n "
513 >               "\tThis is larger than half of at least one of the\n"
514 >               "\tperiodic box vectors.  Right now, the Box matrix is:\n"
515 >               "\n"
516 >               "\t[ %G %G %G ]\n"
517 >               "\t[ %G %G %G ]\n"
518 >               "\t[ %G %G %G ]\n",
519 >               rCut, currentTime,
520 >               Hmat[0][0], Hmat[0][1], Hmat[0][2],
521 >               Hmat[1][0], Hmat[1][1], Hmat[1][2],
522 >               Hmat[2][0], Hmat[2][1], Hmat[2][2]);
523 >      painCave.isFatal = 1;
524        simError();
595 –      rCut = maxCutoff;
525      }
526 <
527 <
528 <    //detect the change of ecr
529 <    if( maxCutoff > ecr ){
530 <      if( ecr < origEcr ){
531 <        ecr = origEcr;
532 <        if (ecr > maxCutoff) ecr = maxCutoff;
533 <  
534 <          sprintf( painCave.errMsg,
535 <                    "New Box size is setting the electrostaticCutoffRadius "
536 <                    "to %lf at time %lf\n",
537 <                    ecr, currentTime );
538 <            painCave.isFatal = 0;
539 <            simError();
526 >    
527 >    if( haveEcr ){
528 >      if( ecr > maxCutoff ){
529 >        sprintf( painCave.errMsg,
530 >                 "electrostaticCutoffRadius is too large for the current\n"
531 >                 "\tperiodic box.\n\n"
532 >                 "\tCurrent Value of ECR = %G at time %G\n "
533 >                 "\tThis is larger than half of at least one of the\n"
534 >                 "\tperiodic box vectors.  Right now, the Box matrix is:\n"
535 >                 "\n"
536 >                 "\t[ %G %G %G ]\n"
537 >                 "\t[ %G %G %G ]\n"
538 >                 "\t[ %G %G %G ]\n",
539 >                 ecr, currentTime,
540 >                 Hmat[0][0], Hmat[0][1], Hmat[0][2],
541 >                 Hmat[1][0], Hmat[1][1], Hmat[1][2],
542 >                 Hmat[2][0], Hmat[2][1], Hmat[2][2]);
543 >        painCave.isFatal = 1;
544 >        simError();
545        }
546      }
613 –    else if( ecr > maxCutoff){
614 –      sprintf( painCave.errMsg,
615 –               "New Box size is setting the electrostaticCutoffRadius "
616 –               "to %lf at time %lf\n",
617 –               maxCutoff, currentTime  );
618 –      painCave.isFatal = 0;
619 –      simError();      
620 –      ecr = maxCutoff;
621 –    }
622 –
623 –    if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
624 –    
625 –    // rlist is the 1.0 plus max( rcut, ecr )
626 –    
627 –    ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
628 –    
629 –    if( cutChanged ){
630 –      notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
631 –    }
632 –    
633 –    oldEcr = ecr;
634 –    oldRcut = rCut;
635 –    
547    } else {
548      // initialize this stuff before using it, OK?
549      sprintf( painCave.errMsg,
550 <             "Trying to check cutoffs without a box. Be smarter.\n" );
550 >             "Trying to check cutoffs without a box.\n"
551 >             "\tOOPSE should have better programmers than that.\n" );
552      painCave.isFatal = 1;
553      simError();      
554    }
# Line 679 | Line 591 | GenericData* SimInfo::getProperty(const string& propNa
591      return NULL;  
592   }
593  
682 – vector<GenericData*> SimInfo::getProperties(){
683 –
684 –  vector<GenericData*> result;
685 –  map<string, GenericData*>::iterator i;
686 –  
687 –  for(i = properties.begin(); i != properties.end(); i++)
688 –    result.push_back((*i).second);
689 –    
690 –  return result;
691 – }
692 –
693 – double SimInfo::matTrace3(double m[3][3]){
694 –  double trace;
695 –  trace = m[0][0] + m[1][1] + m[2][2];
696 –
697 –  return trace;
698 – }

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