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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 874 by mmeineke, Fri Nov 21 20:10:02 2003 UTC vs.
Revision 1125 by gezelter, Mon Apr 19 22:13:01 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 27 | Line 29 | SimInfo::SimInfo(){
29   SimInfo* currentInfo;
30  
31   SimInfo::SimInfo(){
32 <  excludes = NULL;
32 >
33    n_constraints = 0;
34    nZconstraints = 0;
35    n_oriented = 0;
# Line 49 | 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  
67 +  excludes = Exclude::Instance();
68 +
69    myConfiguration = new SimState();
70  
71 +  has_minimizer = false;
72 +  the_minimizer =NULL;
73 +
74    wrapMeSimInfo( this );
75   }
76  
# Line 179 | Line 188 | void SimInfo::calcHmatInv( void ) {
188      
189      if( orthoRhombic ){
190        sprintf( painCave.errMsg,
191 <               "Hmat is switching from Non-Orthorhombic to OrthoRhombic\n"
192 <               "       If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n",
191 >               "OOPSE is switching from the default Non-Orthorhombic\n"
192 >               "\tto the faster Orthorhombic periodic boundary computations.\n"
193 >               "\tThis is usually a good thing, but if you wan't the\n"
194 >               "\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
195 >               "\tvariable ( currently set to %G ) smaller.\n",
196                 orthoTolerance);
197        simError();
198      }
199      else {
200        sprintf( painCave.errMsg,
201 <               "Hmat is switching from Orthorhombic to Non-OrthoRhombic\n"
202 <               "       If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n",
201 >               "OOPSE is switching from the faster Orthorhombic to the more\n"
202 >               "\tflexible Non-Orthorhombic periodic boundary computations.\n"
203 >               "\tThis is usually because the box has deformed under\n"
204 >               "\tNPTf integration. If you wan't to live on the edge with\n"
205 >               "\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
206 >               "\tvariable ( currently set to %G ) larger.\n",
207                 orthoTolerance);
208        simError();
193 –    }
194 –  }
195 – }
196 –
197 – double SimInfo::matDet3(double a[3][3]) {
198 –  int i, j, k;
199 –  double determinant;
200 –
201 –  determinant = 0.0;
202 –
203 –  for(i = 0; i < 3; i++) {
204 –    j = (i+1)%3;
205 –    k = (i+2)%3;
206 –
207 –    determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]);
208 –  }
209 –
210 –  return determinant;
211 – }
212 –
213 – void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
214 –  
215 –  int  i, j, k, l, m, n;
216 –  double determinant;
217 –
218 –  determinant = matDet3( a );
219 –
220 –  if (determinant == 0.0) {
221 –    sprintf( painCave.errMsg,
222 –             "Can't invert a matrix with a zero determinant!\n");
223 –    painCave.isFatal = 1;
224 –    simError();
225 –  }
226 –
227 –  for (i=0; i < 3; i++) {
228 –    j = (i+1)%3;
229 –    k = (i+2)%3;
230 –    for(l = 0; l < 3; l++) {
231 –      m = (l+1)%3;
232 –      n = (l+2)%3;
233 –      
234 –      b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant;
209      }
210    }
211   }
212  
239 – void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
240 –  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
241 –
242 –  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
243 –  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
244 –  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
245 –  
246 –  r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0];
247 –  r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1];
248 –  r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2];
249 –  
250 –  r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0];
251 –  r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1];
252 –  r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2];
253 –  
254 –  c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
255 –  c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
256 –  c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
257 – }
258 –
259 – void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
260 –  double a0, a1, a2;
261 –
262 –  a0 = inVec[0];  a1 = inVec[1];  a2 = inVec[2];
263 –
264 –  outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2;
265 –  outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
266 –  outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
267 – }
268 –
269 – void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
270 –  double temp[3][3];
271 –  int i, j;
272 –
273 –  for (i = 0; i < 3; i++) {
274 –    for (j = 0; j < 3; j++) {
275 –      temp[j][i] = in[i][j];
276 –    }
277 –  }
278 –  for (i = 0; i < 3; i++) {
279 –    for (j = 0; j < 3; j++) {
280 –      out[i][j] = temp[i][j];
281 –    }
282 –  }
283 – }
284 –  
285 – void SimInfo::printMat3(double A[3][3] ){
286 –
287 –  std::cerr
288 –            << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
289 –            << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
290 –            << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
291 – }
292 –
293 – void SimInfo::printMat9(double A[9] ){
294 –
295 –  std::cerr
296 –            << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
297 –            << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
298 –            << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
299 – }
300 –
301 –
302 – void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){
303 –
304 –      out[0] = a[1] * b[2] - a[2] * b[1];
305 –      out[1] = a[2] * b[0] - a[0] * b[2] ;
306 –      out[2] = a[0] * b[1] - a[1] * b[0];
307 –      
308 – }
309 –
310 – double SimInfo::dotProduct3(double a[3], double b[3]){
311 –  return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2];
312 – }
313 –
314 – double SimInfo::length3(double a[3]){
315 –  return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]);
316 – }
317 –
213   void SimInfo::calcBoxL( void ){
214  
215    double dx, dy, dz, dsq;
# Line 370 | Line 265 | double SimInfo::calcMaxCutOff(){
265    rk[0] = Hmat[0][2];
266    rk[1] = Hmat[1][2];
267    rk[2] = Hmat[2][2];
268 <  
269 <  crossProduct3(ri,rj, rij);
270 <  distXY = dotProduct3(rk,rij) / length3(rij);
268 >    
269 >  crossProduct3(ri, rj, rij);
270 >  distXY = dotProduct3(rk,rij) / norm3(rij);
271  
272    crossProduct3(rj,rk, rjk);
273 <  distYZ = dotProduct3(ri,rjk) / length3(rjk);
273 >  distYZ = dotProduct3(ri,rjk) / norm3(rjk);
274  
275    crossProduct3(rk,ri, rki);
276 <  distZX = dotProduct3(rj,rki) / length3(rki);
276 >  distZX = dotProduct3(rj,rki) / norm3(rki);
277  
278    minDist = min(min(distXY, distYZ), distZX);
279    return minDist/2;
# Line 426 | Line 321 | int SimInfo::getNDF(){
321  
322   int SimInfo::getNDF(){
323    int ndf_local;
324 +
325 +  ndf_local = 0;
326    
327 <  ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
327 >  for(int i = 0; i < integrableObjects.size(); i++){
328 >    ndf_local += 3;
329 >    if (integrableObjects[i]->isDirectional()) {
330 >      if (integrableObjects[i]->isLinear())
331 >        ndf_local += 2;
332 >      else
333 >        ndf_local += 3;
334 >    }
335 >  }
336  
337 +  // n_constraints is local, so subtract them on each processor:
338 +
339 +  ndf_local -= n_constraints;
340 +
341   #ifdef IS_MPI
342    MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
343   #else
344    ndf = ndf_local;
345   #endif
346  
347 +  // nZconstraints is global, as are the 3 COM translations for the
348 +  // entire system:
349 +
350    ndf = ndf - 3 - nZconstraints;
351  
352 +  std::cerr << "ndf = " << ndf;
353 +
354    return ndf;
355   }
356  
# Line 444 | Line 358 | int SimInfo::getNDFraw() {
358    int ndfRaw_local;
359  
360    // Raw degrees of freedom that we have to set
361 <  ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
362 <  
361 >  ndfRaw_local = 0;
362 >
363 >  for(int i = 0; i < integrableObjects.size(); i++){
364 >    ndfRaw_local += 3;
365 >    if (integrableObjects[i]->isDirectional()) {
366 >       if (integrableObjects[i]->isLinear())
367 >        ndfRaw_local += 2;
368 >      else
369 >        ndfRaw_local += 3;
370 >    }
371 >  }
372 >    
373   #ifdef IS_MPI
374    MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
375   #else
# Line 458 | Line 382 | int SimInfo::getNDFtranslational() {
382   int SimInfo::getNDFtranslational() {
383    int ndfTrans_local;
384  
385 <  ndfTrans_local = 3 * n_atoms - n_constraints;
385 >  ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
386  
387 +
388   #ifdef IS_MPI
389    MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
390   #else
# Line 469 | Line 394 | int SimInfo::getNDFtranslational() {
394    ndfTrans = ndfTrans - 3 - nZconstraints;
395  
396    return ndfTrans;
397 + }
398 +
399 + int SimInfo::getTotIntegrableObjects() {
400 +  int nObjs_local;
401 +  int nObjs;
402 +
403 +  nObjs_local =  integrableObjects.size();
404 +
405 +
406 + #ifdef IS_MPI
407 +  MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
408 + #else
409 +  nObjs = nObjs_local;
410 + #endif
411 +
412 +
413 +  return nObjs;
414   }
415  
416   void SimInfo::refreshSim(){
# Line 480 | Line 422 | void SimInfo::refreshSim(){
422  
423    fInfo.dielect = 0.0;
424  
425 <  if( useDipole ){
425 >  if( useDipoles ){
426      if( useReactionField )fInfo.dielect = dielectric;
427    }
428  
# Line 489 | Line 431 | void SimInfo::refreshSim(){
431    fInfo.SIM_uses_LJ = useLJ;
432    fInfo.SIM_uses_sticky = useSticky;
433    //fInfo.SIM_uses_sticky = 0;
434 <  fInfo.SIM_uses_dipoles = useDipole;
434 >  fInfo.SIM_uses_charges = useCharges;
435 >  fInfo.SIM_uses_dipoles = useDipoles;
436    //fInfo.SIM_uses_dipoles = 0;
437 <  //fInfo.SIM_uses_RF = useReactionField;
438 <  fInfo.SIM_uses_RF = 0;
437 >  fInfo.SIM_uses_RF = useReactionField;
438 >  //fInfo.SIM_uses_RF = 0;
439    fInfo.SIM_uses_GB = useGB;
440    fInfo.SIM_uses_EAM = useEAM;
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 564 | 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 <               "%G, at time %G\n"
513 <               "  [ %G %G %G ]\n"
514 <               "  [ %G %G %G ]\n"
515 <               "  [ %G %G %G ]\n",
516 <               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, %G"
516 >               "\t[ %G %G %G ]\n"
517 >               "\t[ %G %G %G ]\n"
518 >               "\t[ %G %G %G ]\n",
519 >               rCut, currentTime, maxCutoff,
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]);
# Line 580 | 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 <                 "%G, at time %G\n"
532 <                 "  [ %G %G %G ]\n"
533 <                 "  [ %G %G %G ]\n"
534 <                 "  [ %G %G %G ]\n",
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],
# Line 596 | 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 639 | Line 591 | GenericData* SimInfo::getProperty(const string& propNa
591      return NULL;  
592   }
593  
642 – vector<GenericData*> SimInfo::getProperties(){
643 –
644 –  vector<GenericData*> result;
645 –  map<string, GenericData*>::iterator i;
646 –  
647 –  for(i = properties.begin(); i != properties.end(); i++)
648 –    result.push_back((*i).second);
649 –    
650 –  return result;
651 – }
652 –
653 – double SimInfo::matTrace3(double m[3][3]){
654 –  double trace;
655 –  trace = m[0][0] + m[1][1] + m[2][2];
656 –
657 –  return trace;
658 – }

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