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root/group/branches/new-templateless/OOPSE/libmdtools/SimInfo.cpp
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Comparing:
trunk/OOPSE/libmdtools/SimInfo.cpp (file contents), Revision 588 by gezelter, Thu Jul 10 17:10:56 2003 UTC vs.
branches/new-templateless/OOPSE/libmdtools/SimInfo.cpp (file contents), Revision 852 by mmeineke, Thu Nov 6 18:20:47 2003 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 26 | Line 26 | SimInfo::SimInfo(){
26   SimInfo::SimInfo(){
27    excludes = NULL;
28    n_constraints = 0;
29 +  nZconstraints = 0;
30    n_oriented = 0;
31    n_dipoles = 0;
32    ndf = 0;
33    ndfRaw = 0;
34 +  nZconstraints = 0;
35    the_integrator = NULL;
36    setTemp = 0;
37    thermalTime = 0.0;
38 +  currentTime = 0.0;
39    rCut = 0.0;
40 +  origRcut = -1.0;
41 +  ecr = 0.0;
42 +  origEcr = -1.0;
43 +  est = 0.0;
44 +  oldEcr = 0.0;
45 +  oldRcut = 0.0;
46  
47 +  haveOrigRcut = 0;
48 +  haveOrigEcr = 0;
49 +  boxIsInit = 0;
50 +  
51 +  resetTime = 1e99;
52 +  
53 +
54    usePBC = 0;
55    useLJ = 0;
56    useSticky = 0;
# Line 43 | Line 59 | SimInfo::SimInfo(){
59    useGB = 0;
60    useEAM = 0;
61  
62 +  myConfiguration = new SimState();
63 +
64 +  properties = new GenericData();
65 +
66    wrapMeSimInfo( this );
67   }
68  
69 +
70 + SimInfo::~SimInfo(){
71 +
72 +  delete myConfiguration;
73 +  delete properties;    
74 + }
75 +
76   void SimInfo::setBox(double newBox[3]) {
77    
78    int i, j;
# Line 64 | Line 91 | void SimInfo::setBoxM( double theBox[3][3] ){
91  
92   void SimInfo::setBoxM( double theBox[3][3] ){
93    
94 <  int i, j, status;
68 <  double smallestBoxL, maxCutoff;
94 >  int i, j;
95    double FortranHmat[9]; // to preserve compatibility with Fortran the
96                           // ordering in the array is as follows:
97                           // [ 0 3 6 ]
# Line 73 | Line 99 | void SimInfo::setBoxM( double theBox[3][3] ){
99                           // [ 2 5 8 ]
100    double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
101  
102 +  
103 +  if( !boxIsInit ) boxIsInit = 1;
104  
105    for(i=0; i < 3; i++)
106      for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
107    
80 –  cerr
81 –    << "setting Hmat ->\n"
82 –    << "[ " << Hmat[0][0] << ", " << Hmat[0][1] << ", " << Hmat[0][2] << " ]\n"
83 –    << "[ " << Hmat[1][0] << ", " << Hmat[1][1] << ", " << Hmat[1][2] << " ]\n"
84 –    << "[ " << Hmat[2][0] << ", " << Hmat[2][1] << ", " << Hmat[2][2] << " ]\n";
85 –
108    calcBoxL();
109    calcHmatInv();
110  
# Line 93 | Line 115 | void SimInfo::setBoxM( double theBox[3][3] ){
115      }
116    }
117  
118 <  setFortranBoxSize(FortranHmat, FortranHmatI, &orthoRhombic);
118 >  setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
119  
98 –  smallestBoxL = boxLx;
99 –  if (boxLy < smallestBoxL) smallestBoxL = boxLy;
100 –  if (boxLz < smallestBoxL) smallestBoxL = boxLz;
101 –
102 –  maxCutoff = smallestBoxL / 2.0;
103 –
104 –  if (rList > maxCutoff) {
105 –    sprintf( painCave.errMsg,
106 –             "New Box size is forcing neighborlist radius down to %lf\n",
107 –             maxCutoff );
108 –    painCave.isFatal = 0;
109 –    simError();
110 –
111 –    rList = maxCutoff;
112 –
113 –    sprintf( painCave.errMsg,
114 –             "New Box size is forcing cutoff radius down to %lf\n",
115 –             maxCutoff - 1.0 );
116 –    painCave.isFatal = 0;
117 –    simError();
118 –
119 –    rCut = rList - 1.0;
120 –
121 –    // list radius changed so we have to refresh the simulation structure.
122 –    refreshSim();
123 –  }
124 –
125 –  if (rCut > maxCutoff) {
126 –    sprintf( painCave.errMsg,
127 –             "New Box size is forcing cutoff radius down to %lf\n",
128 –             maxCutoff );
129 –    painCave.isFatal = 0;
130 –    simError();
131 –
132 –    status = 0;
133 –    LJ_new_rcut(&rCut, &status);
134 –    if (status != 0) {
135 –      sprintf( painCave.errMsg,
136 –               "Error in recomputing LJ shifts based on new rcut\n");
137 –      painCave.isFatal = 1;
138 –      simError();
139 –    }
140 –  }
120   }
121  
122  
# Line 153 | Line 132 | void SimInfo::scaleBox(double scale) {
132    double theBox[3][3];
133    int i, j;
134  
135 <  cerr << "Scaling box by " << scale << "\n";
135 >  // cerr << "Scaling box by " << scale << "\n";
136  
137    for(i=0; i<3; i++)
138      for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
# Line 164 | Line 143 | void SimInfo::calcHmatInv( void ) {
143  
144   void SimInfo::calcHmatInv( void ) {
145  
146 +  int oldOrtho;
147 +  int i,j;
148    double smallDiag;
149    double tol;
150    double sanity[3][3];
# Line 172 | Line 153 | void SimInfo::calcHmatInv( void ) {
153  
154    // Check the inverse to make sure it is sane:
155  
156 <  matMul3( Hmat, HmatInv, sanity );
176 <
177 <  cerr << "sanity => \n"
178 <       << sanity[0][0] << "\t" << sanity[0][1] << "\t" << sanity [0][2] << "\n"
179 <       << sanity[1][0] << "\t" << sanity[1][1] << "\t" << sanity [1][2] << "\n"
180 <       << sanity[2][0] << "\t" << sanity[2][1] << "\t" << sanity [2][2]
181 <       << "\n";
156 >  // matMul3( Hmat, HmatInv, sanity );
157      
158    // check to see if Hmat is orthorhombic
159 +
160    
161 <  smallDiag = Hmat[0][0];
162 <  if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1];
163 <  if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2];
161 >  oldOrtho = orthoRhombic;
162 >
163 >  smallDiag = fabs(Hmat[0][0]);
164 >  if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
165 >  if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
166    tol = smallDiag * 1E-6;
167  
168    orthoRhombic = 1;
# Line 193 | Line 171 | void SimInfo::calcHmatInv( void ) {
171      for (j = 0 ; j < 3; j++) {
172        if (i != j) {
173          if (orthoRhombic) {
174 <          if (Hmat[i][j] >= tol) orthoRhombic = 0;
174 >          if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
175          }        
176        }
177      }
178    }
179 +  
180 +  if( oldOrtho != orthoRhombic ){
181 +    
182 +    if( orthoRhombic ){
183 +      sprintf( painCave.errMsg,
184 +               "Hmat is switching from Non-Orthorhombic to OrthoRhombic\n"
185 +               "       If this is a bad thing change the ortho tolerance in SimInfo.\n" );
186 +      simError();
187 +    }
188 +    else {
189 +      sprintf( painCave.errMsg,
190 +               "Hmat is switching from Orthorhombic to Non-OrthoRhombic\n"
191 +               "       If this is a bad thing change the ortho tolerance in SimInfo.\n" );
192 +      simError();
193 +    }
194 +  }
195   }
196  
197   double SimInfo::matDet3(double a[3][3]) {
# Line 271 | Line 265 | void SimInfo::matVecMul3(double m[3][3], double inVec[
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 +
318   void SimInfo::calcBoxL( void ){
319  
320    double dx, dy, dz, dsq;
278 –  int i;
321  
322    // boxVol = Determinant of Hmat
323  
# Line 285 | Line 327 | void SimInfo::calcBoxL( void ){
327    
328    dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
329    dsq = dx*dx + dy*dy + dz*dz;
330 <  boxLx = sqrt( dsq );
330 >  boxL[0] = sqrt( dsq );
331 >  //maxCutoff = 0.5 * boxL[0];
332  
333    // boxLy
334    
335    dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
336    dsq = dx*dx + dy*dy + dz*dz;
337 <  boxLy = sqrt( dsq );
337 >  boxL[1] = sqrt( dsq );
338 >  //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
339  
340 +
341    // boxLz
342    
343    dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
344    dsq = dx*dx + dy*dy + dz*dz;
345 <  boxLz = sqrt( dsq );
345 >  boxL[2] = sqrt( dsq );
346 >  //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
347 >
348 >  //calculate the max cutoff
349 >  maxCutoff =  calcMaxCutOff();
350    
351 +  checkCutOffs();
352 +
353   }
354 +
355 +
356 + double SimInfo::calcMaxCutOff(){
357 +
358 +  double ri[3], rj[3], rk[3];
359 +  double rij[3], rjk[3], rki[3];
360 +  double minDist;
361 +
362 +  ri[0] = Hmat[0][0];
363 +  ri[1] = Hmat[1][0];
364 +  ri[2] = Hmat[2][0];
365  
366 +  rj[0] = Hmat[0][1];
367 +  rj[1] = Hmat[1][1];
368 +  rj[2] = Hmat[2][1];
369  
370 +  rk[0] = Hmat[0][2];
371 +  rk[1] = Hmat[1][2];
372 +  rk[2] = Hmat[2][2];
373 +  
374 +  crossProduct3(ri,rj, rij);
375 +  distXY = dotProduct3(rk,rij) / length3(rij);
376 +
377 +  crossProduct3(rj,rk, rjk);
378 +  distYZ = dotProduct3(ri,rjk) / length3(rjk);
379 +
380 +  crossProduct3(rk,ri, rki);
381 +  distZX = dotProduct3(rj,rki) / length3(rki);
382 +
383 +  minDist = min(min(distXY, distYZ), distZX);
384 +  return minDist/2;
385 +  
386 + }
387 +
388   void SimInfo::wrapVector( double thePos[3] ){
389  
390 <  int i, j, k;
390 >  int i;
391    double scaled[3];
392  
393    if( !orthoRhombic ){
# Line 342 | Line 425 | int SimInfo::getNDF(){
425  
426  
427   int SimInfo::getNDF(){
428 <  int ndf_local, ndf;
428 >  int ndf_local;
429    
430    ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
431  
# Line 352 | Line 435 | int SimInfo::getNDF(){
435    ndf = ndf_local;
436   #endif
437  
438 <  ndf = ndf - 3;
438 >  ndf = ndf - 3 - nZconstraints;
439  
440    return ndf;
441   }
442  
443   int SimInfo::getNDFraw() {
444 <  int ndfRaw_local, ndfRaw;
444 >  int ndfRaw_local;
445  
446    // Raw degrees of freedom that we have to set
447    ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
# Line 371 | Line 454 | int SimInfo::getNDFraw() {
454  
455    return ndfRaw;
456   }
457 <
457 >
458 > int SimInfo::getNDFtranslational() {
459 >  int ndfTrans_local;
460 >
461 >  ndfTrans_local = 3 * n_atoms - n_constraints;
462 >
463 > #ifdef IS_MPI
464 >  MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
465 > #else
466 >  ndfTrans = ndfTrans_local;
467 > #endif
468 >
469 >  ndfTrans = ndfTrans - 3 - nZconstraints;
470 >
471 >  return ndfTrans;
472 > }
473 >
474   void SimInfo::refreshSim(){
475  
476    simtype fInfo;
477    int isError;
478    int n_global;
479    int* excl;
480 <  
382 <  fInfo.rrf = 0.0;
383 <  fInfo.rt = 0.0;
480 >
481    fInfo.dielect = 0.0;
482  
386 –  fInfo.rlist = rList;
387 –  fInfo.rcut = rCut;
388 –
483    if( useDipole ){
390 –    fInfo.rrf = ecr;
391 –    fInfo.rt = ecr - est;
484      if( useReactionField )fInfo.dielect = dielectric;
485    }
486  
# Line 434 | Line 526 | void SimInfo::refreshSim(){
526  
527    this->ndf = this->getNDF();
528    this->ndfRaw = this->getNDFraw();
529 +  this->ndfTrans = this->getNDFtranslational();
530 + }
531  
532 +
533 + void SimInfo::setRcut( double theRcut ){
534 +
535 +  rCut = theRcut;
536 +  checkCutOffs();
537   }
538  
539 + void SimInfo::setDefaultRcut( double theRcut ){
540 +
541 +  haveOrigRcut = 1;
542 +  origRcut = theRcut;
543 +  rCut = theRcut;
544 +
545 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
546 +
547 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
548 + }
549 +
550 + void SimInfo::setEcr( double theEcr ){
551 +
552 +  ecr = theEcr;
553 +  checkCutOffs();
554 + }
555 +
556 + void SimInfo::setDefaultEcr( double theEcr ){
557 +
558 +  haveOrigEcr = 1;
559 +  origEcr = theEcr;
560 +  
561 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
562 +
563 +  ecr = theEcr;
564 +
565 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
566 + }
567 +
568 + void SimInfo::setEcr( double theEcr, double theEst ){
569 +
570 +  est = theEst;
571 +  setEcr( theEcr );
572 + }
573 +
574 + void SimInfo::setDefaultEcr( double theEcr, double theEst ){
575 +
576 +  est = theEst;
577 +  setDefaultEcr( theEcr );
578 + }
579 +
580 +
581 + void SimInfo::checkCutOffs( void ){
582 +
583 +  int cutChanged = 0;
584 +  
585 +  if( boxIsInit ){
586 +    
587 +    //we need to check cutOffs against the box
588 +
589 +    //detect the change of rCut
590 +    if(( maxCutoff > rCut )&&(usePBC)){
591 +      if( rCut < origRcut ){
592 +        rCut = origRcut;
593 +        
594 +        if (rCut > maxCutoff)
595 +          rCut = maxCutoff;
596 +  
597 +          sprintf( painCave.errMsg,
598 +                    "New Box size is setting the long range cutoff radius "
599 +                    "to %lf at time %lf\n",
600 +                    rCut, currentTime );
601 +          painCave.isFatal = 0;
602 +          simError();
603 +      }
604 +    }
605 +    else if ((rCut > maxCutoff)&&(usePBC)) {
606 +      sprintf( painCave.errMsg,
607 +               "New Box size is setting the long range cutoff radius "
608 +               "to %lf at time %lf\n",
609 +               maxCutoff, currentTime );
610 +      painCave.isFatal = 0;
611 +      simError();
612 +      rCut = maxCutoff;
613 +    }
614 +
615 +
616 +    //detect the change of ecr
617 +    if( maxCutoff > ecr ){
618 +      if( ecr < origEcr ){
619 +        ecr = origEcr;
620 +        if (ecr > maxCutoff) ecr = maxCutoff;
621 +  
622 +          sprintf( painCave.errMsg,
623 +                    "New Box size is setting the electrostaticCutoffRadius "
624 +                    "to %lf at time %lf\n",
625 +                    ecr, currentTime );
626 +            painCave.isFatal = 0;
627 +            simError();
628 +      }
629 +    }
630 +    else if( ecr > maxCutoff){
631 +      sprintf( painCave.errMsg,
632 +               "New Box size is setting the electrostaticCutoffRadius "
633 +               "to %lf at time %lf\n",
634 +               maxCutoff, currentTime  );
635 +      painCave.isFatal = 0;
636 +      simError();      
637 +      ecr = maxCutoff;
638 +    }
639 +
640 +    if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
641 +    
642 +    // rlist is the 1.0 plus max( rcut, ecr )
643 +    
644 +    ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
645 +    
646 +    if( cutChanged ){
647 +      notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
648 +    }
649 +    
650 +    oldEcr = ecr;
651 +    oldRcut = rCut;
652 +    
653 +  } else {
654 +    // initialize this stuff before using it, OK?
655 +    sprintf( painCave.errMsg,
656 +             "Trying to check cutoffs without a box. Be smarter.\n" );
657 +    painCave.isFatal = 1;
658 +    simError();      
659 +  }
660 +  
661 + }
662 +
663 + GenericData* SimInfo::getProperty(char* propName){
664 +
665 +  return properties->find( propName );
666 + }
667 +
668 + double SimInfo::matTrace3(double m[3][3]){
669 +  double trace;
670 +  trace = m[0][0] + m[1][1] + m[2][2];
671 +
672 +  return trace;
673 + }

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