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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 841 by mmeineke, Wed Oct 29 17:55:28 2003 UTC vs.
Revision 1097 by gezelter, Mon Apr 12 20:32:20 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  
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 102 | Line 112 | void SimInfo::setBoxM( double theBox[3][3] ){
112                           // [ 2 5 8 ]
113    double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
114  
105 –  
115    if( !boxIsInit ) boxIsInit = 1;
116  
117    for(i=0; i < 3; i++)
# Line 146 | Line 155 | void SimInfo::calcHmatInv( void ) {
155  
156   void SimInfo::calcHmatInv( void ) {
157    
158 +  int oldOrtho;
159    int i,j;
160    double smallDiag;
161    double tol;
# Line 153 | Line 163 | void SimInfo::calcHmatInv( void ) {
163  
164    invertMat3( Hmat, HmatInv );
165  
156 –  // Check the inverse to make sure it is sane:
157 –
158 –  matMul3( Hmat, HmatInv, sanity );
159 –    
166    // check to see if Hmat is orthorhombic
167    
168 <  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;
168 >  oldOrtho = orthoRhombic;
169  
170 +  smallDiag = fabs(Hmat[0][0]);
171 +  if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
172 +  if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
173 +  tol = smallDiag * orthoTolerance;
174 +
175    orthoRhombic = 1;
176    
177    for (i = 0; i < 3; i++ ) {
178      for (j = 0 ; j < 3; j++) {
179        if (i != j) {
180          if (orthoRhombic) {
181 <          if (Hmat[i][j] >= tol) orthoRhombic = 0;
181 >          if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
182          }        
183        }
184      }
185    }
178 – }
186  
187 < double SimInfo::matDet3(double a[3][3]) {
188 <  int i, j, k;
189 <  double determinant;
190 <
191 <  determinant = 0.0;
192 <
193 <  for(i = 0; i < 3; i++) {
194 <    j = (i+1)%3;
195 <    k = (i+2)%3;
196 <
197 <    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;
187 >  if( oldOrtho != orthoRhombic ){
188 >    
189 >    if( orthoRhombic ){
190 >      sprintf( painCave.errMsg,
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 <  }
200 < }
201 <
202 < void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
203 <  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
204 <
205 <  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
206 <  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
207 <  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
208 <  
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];
199 >    else {
200 >      sprintf( painCave.errMsg,
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();
209      }
210    }
261 –  for (i = 0; i < 3; i++) {
262 –    for (j = 0; j < 3; j++) {
263 –      out[i][j] = temp[i][j];
264 –    }
265 –  }
211   }
267 –  
268 – void SimInfo::printMat3(double A[3][3] ){
212  
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 –
213   void SimInfo::calcBoxL( void ){
214  
215    double dx, dy, dz, dsq;
# Line 353 | 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 409 | Line 321 | int SimInfo::getNDF(){
321  
322   int SimInfo::getNDF(){
323    int ndf_local;
412 –  
413 –  ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
324  
325 +  for(int i = 0; i < integrableObjects.size(); i++){
326 +    ndf_local += 3;
327 +    if (integrableObjects[i]->isDirectional())
328 +      ndf_local += 3;
329 +  }
330 +
331 +  // n_constraints is local, so subtract them on each processor:
332 +
333 +  ndf_local -= n_constraints;
334 +
335   #ifdef IS_MPI
336    MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
337   #else
338    ndf = ndf_local;
339   #endif
340  
341 +  // nZconstraints is global, as are the 3 COM translations for the
342 +  // entire system:
343 +
344    ndf = ndf - 3 - nZconstraints;
345  
346    return ndf;
# Line 427 | Line 350 | int SimInfo::getNDFraw() {
350    int ndfRaw_local;
351  
352    // Raw degrees of freedom that we have to set
353 <  ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
354 <  
353 >
354 >  for(int i = 0; i < integrableObjects.size(); i++){
355 >    ndfRaw_local += 3;
356 >    if (integrableObjects[i]->isDirectional())
357 >      ndfRaw_local += 3;
358 >  }
359 >    
360   #ifdef IS_MPI
361    MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
362   #else
# Line 441 | Line 369 | int SimInfo::getNDFtranslational() {
369   int SimInfo::getNDFtranslational() {
370    int ndfTrans_local;
371  
372 <  ndfTrans_local = 3 * n_atoms - n_constraints;
372 >  ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
373  
374 +
375   #ifdef IS_MPI
376    MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
377   #else
# Line 463 | Line 392 | void SimInfo::refreshSim(){
392  
393    fInfo.dielect = 0.0;
394  
395 <  if( useDipole ){
395 >  if( useDipoles ){
396      if( useReactionField )fInfo.dielect = dielectric;
397    }
398  
# Line 472 | Line 401 | void SimInfo::refreshSim(){
401    fInfo.SIM_uses_LJ = useLJ;
402    fInfo.SIM_uses_sticky = useSticky;
403    //fInfo.SIM_uses_sticky = 0;
404 <  fInfo.SIM_uses_dipoles = useDipole;
404 >  fInfo.SIM_uses_charges = useCharges;
405 >  fInfo.SIM_uses_dipoles = useDipoles;
406    //fInfo.SIM_uses_dipoles = 0;
407 <  //fInfo.SIM_uses_RF = useReactionField;
408 <  fInfo.SIM_uses_RF = 0;
407 >  fInfo.SIM_uses_RF = useReactionField;
408 >  //fInfo.SIM_uses_RF = 0;
409    fInfo.SIM_uses_GB = useGB;
410    fInfo.SIM_uses_EAM = useEAM;
411  
412 <  excl = Exclude::getArray();
412 >  n_exclude = excludes->getSize();
413 >  excl = excludes->getFortranArray();
414  
415   #ifdef IS_MPI
416    n_global = mpiSim->getTotAtoms();
# Line 512 | Line 443 | void SimInfo::refreshSim(){
443    this->ndfTrans = this->getNDFtranslational();
444   }
445  
515 –
516 – void SimInfo::setRcut( double theRcut ){
517 –
518 –  rCut = theRcut;
519 –  checkCutOffs();
520 – }
521 –
446   void SimInfo::setDefaultRcut( double theRcut ){
447  
448 <  haveOrigRcut = 1;
525 <  origRcut = theRcut;
448 >  haveRcut = 1;
449    rCut = theRcut;
527 – }
450  
451 < void SimInfo::setEcr( double theEcr ){
451 >  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
452  
453 <  ecr = theEcr;
532 <  checkCutOffs();
453 >  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
454   }
455  
456   void SimInfo::setDefaultEcr( double theEcr ){
457  
458 <  haveOrigEcr = 1;
538 <  origEcr = theEcr;
539 <  
458 >  haveEcr = 1;
459    ecr = theEcr;
460 < }
460 >  
461 >  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
462  
463 < void SimInfo::setEcr( double theEcr, double theEst ){
544 <
545 <  est = theEst;
546 <  setEcr( theEcr );
463 >  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
464   }
465  
466   void SimInfo::setDefaultEcr( double theEcr, double theEst ){
# Line 554 | Line 471 | void SimInfo::checkCutOffs( void ){
471  
472  
473   void SimInfo::checkCutOffs( void ){
557 –
558 –  int cutChanged = 0;
474    
475    if( boxIsInit ){
476      
477      //we need to check cutOffs against the box
478 <
479 <    //detect the change of rCut
565 <    if(( maxCutoff > rCut )&&(usePBC)){
566 <      if( rCut < origRcut ){
567 <        rCut = origRcut;
568 <        
569 <        if (rCut > maxCutoff)
570 <          rCut = maxCutoff;
571 <  
572 <          sprintf( painCave.errMsg,
573 <                    "New Box size is setting the long range cutoff radius "
574 <                    "to %lf at time %lf\n",
575 <                    rCut, currentTime );
576 <          painCave.isFatal = 0;
577 <          simError();
578 <      }
579 <    }
580 <    else if ((rCut > maxCutoff)&&(usePBC)) {
478 >    
479 >    if( rCut > maxCutoff ){
480        sprintf( painCave.errMsg,
481 <               "New Box size is setting the long range cutoff radius "
482 <               "to %lf at time %lf\n",
483 <               maxCutoff, currentTime );
484 <      painCave.isFatal = 0;
481 >               "LJrcut is too large for the current periodic box.\n"
482 >               "\tCurrent Value of LJrcut = %G at time %G\n "
483 >               "\tThis is larger than half of at least one of the\n"
484 >               "\tperiodic box vectors.  Right now, the Box matrix is:\n"
485 >               "\n, %G"
486 >               "\t[ %G %G %G ]\n"
487 >               "\t[ %G %G %G ]\n"
488 >               "\t[ %G %G %G ]\n",
489 >               rCut, currentTime, maxCutoff,
490 >               Hmat[0][0], Hmat[0][1], Hmat[0][2],
491 >               Hmat[1][0], Hmat[1][1], Hmat[1][2],
492 >               Hmat[2][0], Hmat[2][1], Hmat[2][2]);
493 >      painCave.isFatal = 1;
494        simError();
587 –      rCut = maxCutoff;
495      }
496 <
497 <
498 <    //detect the change of ecr
499 <    if( maxCutoff > ecr ){
500 <      if( ecr < origEcr ){
501 <        ecr = origEcr;
502 <        if (ecr > maxCutoff) ecr = maxCutoff;
503 <  
504 <          sprintf( painCave.errMsg,
505 <                    "New Box size is setting the electrostaticCutoffRadius "
506 <                    "to %lf at time %lf\n",
507 <                    ecr, currentTime );
508 <            painCave.isFatal = 0;
509 <            simError();
496 >    
497 >    if( haveEcr ){
498 >      if( ecr > maxCutoff ){
499 >        sprintf( painCave.errMsg,
500 >                 "electrostaticCutoffRadius is too large for the current\n"
501 >                 "\tperiodic box.\n\n"
502 >                 "\tCurrent Value of ECR = %G at time %G\n "
503 >                 "\tThis is larger than half of at least one of the\n"
504 >                 "\tperiodic box vectors.  Right now, the Box matrix is:\n"
505 >                 "\n"
506 >                 "\t[ %G %G %G ]\n"
507 >                 "\t[ %G %G %G ]\n"
508 >                 "\t[ %G %G %G ]\n",
509 >                 ecr, currentTime,
510 >                 Hmat[0][0], Hmat[0][1], Hmat[0][2],
511 >                 Hmat[1][0], Hmat[1][1], Hmat[1][2],
512 >                 Hmat[2][0], Hmat[2][1], Hmat[2][2]);
513 >        painCave.isFatal = 1;
514 >        simError();
515        }
516      }
605 –    else if( ecr > maxCutoff){
606 –      sprintf( painCave.errMsg,
607 –               "New Box size is setting the electrostaticCutoffRadius "
608 –               "to %lf at time %lf\n",
609 –               maxCutoff, currentTime  );
610 –      painCave.isFatal = 0;
611 –      simError();      
612 –      ecr = maxCutoff;
613 –    }
614 –
615 –    if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
616 –    
617 –    // rlist is the 1.0 plus max( rcut, ecr )
618 –    
619 –    ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
620 –    
621 –    if( cutChanged ){
622 –      
623 –      notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
624 –    }
625 –    
626 –    oldEcr = ecr;
627 –    oldRcut = rCut;
628 –    
517    } else {
518      // initialize this stuff before using it, OK?
519      sprintf( painCave.errMsg,
520 <             "Trying to check cutoffs without a box. Be smarter.\n" );
520 >             "Trying to check cutoffs without a box.\n"
521 >             "\tOOPSE should have better programmers than that.\n" );
522      painCave.isFatal = 1;
523      simError();      
524    }
# Line 682 | Line 571 | vector<GenericData*> SimInfo::getProperties(){
571      
572    return result;
573   }
685 –
686 – double SimInfo::matTrace3(double m[3][3]){
687 –  double trace;
688 –  trace = m[0][0] + m[1][1] + m[2][2];
689 –
690 –  return trace;
691 – }

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