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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 790 by mmeineke, Mon Sep 29 21:16:11 2003 UTC vs.
Revision 1108 by tim, Wed Apr 14 15:37:41 2004 UTC

# Line 1 | Line 1
1 < #include <cstdlib>
2 < #include <cstring>
3 < #include <cmath>
1 > #include <stdlib.h>
2 > #include <string.h>
3 > #include <math.h>
4  
5   #include <iostream>
6   using namespace std;
# 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;
324 <  
325 <  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 454 | Line 383 | void SimInfo::refreshSim(){
383    return ndfTrans;
384   }
385  
386 + int SimInfo::getTotIntegrableObjects() {
387 +  int nObjs_local;
388 +  int nObjs;
389 +
390 +  nObjs_local =  integrableObjects.size();
391 +
392 +
393 + #ifdef IS_MPI
394 +  MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
395 + #else
396 +  nObjs = nObjs_local;
397 + #endif
398 +
399 +
400 +  return nObjs;
401 + }
402 +
403   void SimInfo::refreshSim(){
404  
405    simtype fInfo;
# Line 463 | Line 409 | void SimInfo::refreshSim(){
409  
410    fInfo.dielect = 0.0;
411  
412 <  if( useDipole ){
412 >  if( useDipoles ){
413      if( useReactionField )fInfo.dielect = dielectric;
414    }
415  
# Line 472 | Line 418 | void SimInfo::refreshSim(){
418    fInfo.SIM_uses_LJ = useLJ;
419    fInfo.SIM_uses_sticky = useSticky;
420    //fInfo.SIM_uses_sticky = 0;
421 <  fInfo.SIM_uses_dipoles = useDipole;
421 >  fInfo.SIM_uses_charges = useCharges;
422 >  fInfo.SIM_uses_dipoles = useDipoles;
423    //fInfo.SIM_uses_dipoles = 0;
424 <  //fInfo.SIM_uses_RF = useReactionField;
425 <  fInfo.SIM_uses_RF = 0;
424 >  fInfo.SIM_uses_RF = useReactionField;
425 >  //fInfo.SIM_uses_RF = 0;
426    fInfo.SIM_uses_GB = useGB;
427    fInfo.SIM_uses_EAM = useEAM;
428  
429 <  excl = Exclude::getArray();
429 >  n_exclude = excludes->getSize();
430 >  excl = excludes->getFortranArray();
431  
432   #ifdef IS_MPI
433    n_global = mpiSim->getTotAtoms();
# Line 512 | Line 460 | void SimInfo::refreshSim(){
460    this->ndfTrans = this->getNDFtranslational();
461   }
462  
463 + void SimInfo::setDefaultRcut( double theRcut ){
464  
465 < void SimInfo::setRcut( double theRcut ){
465 >  haveRcut = 1;
466 >  rCut = theRcut;
467  
468 <  if( !haveOrigRcut ){
519 <    haveOrigRcut = 1;
520 <    origRcut = theRcut;
521 <  }
468 >  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
469  
470 <  rCut = theRcut;
524 <  checkCutOffs();
470 >  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
471   }
472  
473 < void SimInfo::setEcr( double theEcr ){
473 > void SimInfo::setDefaultEcr( double theEcr ){
474  
475 <  if( !haveOrigEcr ){
530 <    haveOrigEcr = 1;
531 <    origEcr = theEcr;
532 <  }
533 <
475 >  haveEcr = 1;
476    ecr = theEcr;
477 <  checkCutOffs();
477 >  
478 >  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
479 >
480 >  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
481   }
482  
483 < void SimInfo::setEcr( double theEcr, double theEst ){
483 > void SimInfo::setDefaultEcr( double theEcr, double theEst ){
484  
485    est = theEst;
486 <  setEcr( theEcr );
486 >  setDefaultEcr( theEcr );
487   }
488  
489  
490   void SimInfo::checkCutOffs( void ){
546 –
547 –  int cutChanged = 0;
491    
492    if( boxIsInit ){
493      
494      //we need to check cutOffs against the box
495 <
496 <    //detect the change of rCut
554 <    if(( maxCutoff > rCut )&&(usePBC)){
555 <      if( rCut < origRcut ){
556 <        rCut = origRcut;
557 <        
558 <        if (rCut > maxCutoff)
559 <          rCut = maxCutoff;
560 <  
561 <          sprintf( painCave.errMsg,
562 <                    "New Box size is setting the long range cutoff radius "
563 <                    "to %lf at time %lf\n",
564 <                    rCut, currentTime );
565 <          painCave.isFatal = 0;
566 <          simError();
567 <      }
568 <    }
569 <    else if ((rCut > maxCutoff)&&(usePBC)) {
495 >    
496 >    if( rCut > maxCutoff ){
497        sprintf( painCave.errMsg,
498 <               "New Box size is setting the long range cutoff radius "
499 <               "to %lf at time %lf\n",
500 <               maxCutoff, currentTime );
501 <      painCave.isFatal = 0;
498 >               "LJrcut is too large for the current periodic box.\n"
499 >               "\tCurrent Value of LJrcut = %G at time %G\n "
500 >               "\tThis is larger than half of at least one of the\n"
501 >               "\tperiodic box vectors.  Right now, the Box matrix is:\n"
502 >               "\n, %G"
503 >               "\t[ %G %G %G ]\n"
504 >               "\t[ %G %G %G ]\n"
505 >               "\t[ %G %G %G ]\n",
506 >               rCut, currentTime, maxCutoff,
507 >               Hmat[0][0], Hmat[0][1], Hmat[0][2],
508 >               Hmat[1][0], Hmat[1][1], Hmat[1][2],
509 >               Hmat[2][0], Hmat[2][1], Hmat[2][2]);
510 >      painCave.isFatal = 1;
511        simError();
576 –      rCut = maxCutoff;
512      }
513 <
514 <
515 <    //detect the change of ecr
516 <    if( maxCutoff > ecr ){
517 <      if( ecr < origEcr ){
518 <        ecr = origEcr;
519 <        if (ecr > maxCutoff) ecr = maxCutoff;
520 <  
521 <          sprintf( painCave.errMsg,
522 <                    "New Box size is setting the electrostaticCutoffRadius "
523 <                    "to %lf at time %lf\n",
524 <                    ecr, currentTime );
525 <            painCave.isFatal = 0;
526 <            simError();
513 >    
514 >    if( haveEcr ){
515 >      if( ecr > maxCutoff ){
516 >        sprintf( painCave.errMsg,
517 >                 "electrostaticCutoffRadius is too large for the current\n"
518 >                 "\tperiodic box.\n\n"
519 >                 "\tCurrent Value of ECR = %G at time %G\n "
520 >                 "\tThis is larger than half of at least one of the\n"
521 >                 "\tperiodic box vectors.  Right now, the Box matrix is:\n"
522 >                 "\n"
523 >                 "\t[ %G %G %G ]\n"
524 >                 "\t[ %G %G %G ]\n"
525 >                 "\t[ %G %G %G ]\n",
526 >                 ecr, currentTime,
527 >                 Hmat[0][0], Hmat[0][1], Hmat[0][2],
528 >                 Hmat[1][0], Hmat[1][1], Hmat[1][2],
529 >                 Hmat[2][0], Hmat[2][1], Hmat[2][2]);
530 >        painCave.isFatal = 1;
531 >        simError();
532        }
533      }
594 –    else if( ecr > maxCutoff){
595 –      sprintf( painCave.errMsg,
596 –               "New Box size is setting the electrostaticCutoffRadius "
597 –               "to %lf at time %lf\n",
598 –               maxCutoff, currentTime  );
599 –      painCave.isFatal = 0;
600 –      simError();      
601 –      ecr = maxCutoff;
602 –    }
603 –
604 –    if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
605 –    
606 –    // rlist is the 1.0 plus max( rcut, ecr )
607 –    
608 –    ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
609 –    
610 –    if( cutChanged ){
611 –      
612 –      notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
613 –    }
614 –    
615 –    oldEcr = ecr;
616 –    oldRcut = rCut;
617 –    
534    } else {
535      // initialize this stuff before using it, OK?
536      sprintf( painCave.errMsg,
537 <             "Trying to check cutoffs without a box. Be smarter.\n" );
537 >             "Trying to check cutoffs without a box.\n"
538 >             "\tOOPSE should have better programmers than that.\n" );
539      painCave.isFatal = 1;
540      simError();      
541    }
# Line 671 | Line 588 | vector<GenericData*> SimInfo::getProperties(){
588      
589    return result;
590   }
674 –
675 – double SimInfo::matTrace3(double m[3][3]){
676 –  double trace;
677 –  trace = m[0][0] + m[1][1] + m[2][2];
678 –
679 –  return trace;
680 – }

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