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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 859 by mmeineke, Mon Nov 10 21:50:36 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 46 | Line 51 | SimInfo::SimInfo(){
51    
52    resetTime = 1e99;
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 176 | Line 189 | void SimInfo::calcHmatInv( void ) {
189      
190      if( orthoRhombic ){
191        sprintf( painCave.errMsg,
192 <               "Hmat is switching from Non-Orthorhombic to OrthoRhombic\n"
193 <               "       If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n",
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      else {
201        sprintf( painCave.errMsg,
202 <               "Hmat is switching from Orthorhombic to Non-OrthoRhombic\n"
203 <               "       If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n",
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();
190 –    }
191 –  }
192 – }
193 –
194 – double SimInfo::matDet3(double a[3][3]) {
195 –  int i, j, k;
196 –  double determinant;
197 –
198 –  determinant = 0.0;
199 –
200 –  for(i = 0; i < 3; i++) {
201 –    j = (i+1)%3;
202 –    k = (i+2)%3;
203 –
204 –    determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]);
205 –  }
206 –
207 –  return determinant;
208 – }
209 –
210 – void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
211 –  
212 –  int  i, j, k, l, m, n;
213 –  double determinant;
214 –
215 –  determinant = matDet3( a );
216 –
217 –  if (determinant == 0.0) {
218 –    sprintf( painCave.errMsg,
219 –             "Can't invert a matrix with a zero determinant!\n");
220 –    painCave.isFatal = 1;
221 –    simError();
222 –  }
223 –
224 –  for (i=0; i < 3; i++) {
225 –    j = (i+1)%3;
226 –    k = (i+2)%3;
227 –    for(l = 0; l < 3; l++) {
228 –      m = (l+1)%3;
229 –      n = (l+2)%3;
230 –      
231 –      b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant;
210      }
211    }
212   }
213  
236 – void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
237 –  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
238 –
239 –  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
240 –  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
241 –  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
242 –  
243 –  r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0];
244 –  r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1];
245 –  r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2];
246 –  
247 –  r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0];
248 –  r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1];
249 –  r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2];
250 –  
251 –  c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
252 –  c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
253 –  c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
254 – }
255 –
256 – void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
257 –  double a0, a1, a2;
258 –
259 –  a0 = inVec[0];  a1 = inVec[1];  a2 = inVec[2];
260 –
261 –  outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2;
262 –  outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
263 –  outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
264 – }
265 –
266 – void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
267 –  double temp[3][3];
268 –  int i, j;
269 –
270 –  for (i = 0; i < 3; i++) {
271 –    for (j = 0; j < 3; j++) {
272 –      temp[j][i] = in[i][j];
273 –    }
274 –  }
275 –  for (i = 0; i < 3; i++) {
276 –    for (j = 0; j < 3; j++) {
277 –      out[i][j] = temp[i][j];
278 –    }
279 –  }
280 – }
281 –  
282 – void SimInfo::printMat3(double A[3][3] ){
283 –
284 –  std::cerr
285 –            << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
286 –            << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
287 –            << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
288 – }
289 –
290 – void SimInfo::printMat9(double A[9] ){
291 –
292 –  std::cerr
293 –            << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
294 –            << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
295 –            << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
296 – }
297 –
298 –
299 – void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){
300 –
301 –      out[0] = a[1] * b[2] - a[2] * b[1];
302 –      out[1] = a[2] * b[0] - a[0] * b[2] ;
303 –      out[2] = a[0] * b[1] - a[1] * b[0];
304 –      
305 – }
306 –
307 – double SimInfo::dotProduct3(double a[3], double b[3]){
308 –  return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2];
309 – }
310 –
311 – double SimInfo::length3(double a[3]){
312 –  return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]);
313 – }
314 –
214   void SimInfo::calcBoxL( void ){
215  
216    double dx, dy, dz, dsq;
# Line 367 | 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 423 | 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 441 | 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 455 | 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 466 | Line 393 | int SimInfo::getNDFtranslational() {
393    ndfTrans = ndfTrans - 3 - nZconstraints;
394  
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(){
# Line 477 | 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 486 | 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 539 | Line 486 | void SimInfo::setDefaultEcr( double theEcr ){
486   void SimInfo::setDefaultEcr( double theEcr ){
487  
488    haveEcr = 1;
489 +  ecr = theEcr;
490    
491    ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
492  
545 –  ecr = theEcr;
546 –
493    notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
494   }
495  
# Line 562 | Line 508 | void SimInfo::checkCutOffs( void ){
508      
509      if( rCut > maxCutoff ){
510        sprintf( painCave.errMsg,
511 <               "Box size is too small for the long range cutoff radius, "
512 <               "%lf, at time %lf\n",
513 <               rCut, currentTime );
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();
525      }
# Line 572 | Line 527 | void SimInfo::checkCutOffs( void ){
527      if( haveEcr ){
528        if( ecr > maxCutoff ){
529          sprintf( painCave.errMsg,
530 <                 "Box size is too small for the electrostatic cutoff radius, "
531 <                 "%lf, at time %lf\n",
532 <                 ecr, currentTime );
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        }
# Line 582 | Line 547 | void SimInfo::checkCutOffs( void ){
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 625 | Line 591 | GenericData* SimInfo::getProperty(const string& propNa
591      return NULL;  
592   }
593  
628 – vector<GenericData*> SimInfo::getProperties(){
629 –
630 –  vector<GenericData*> result;
631 –  map<string, GenericData*>::iterator i;
632 –  
633 –  for(i = properties.begin(); i != properties.end(); i++)
634 –    result.push_back((*i).second);
635 –    
636 –  return result;
637 – }
638 –
639 – double SimInfo::matTrace3(double m[3][3]){
640 –  double trace;
641 –  trace = m[0][0] + m[1][1] + m[2][2];
642 –
643 –  return trace;
644 – }

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