ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
(Generate patch)

Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 588 by gezelter, Thu Jul 10 17:10:56 2003 UTC vs.
Revision 941 by gezelter, Tue Jan 13 23:01:43 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 20 | Line 20 | inline double roundMe( double x ){
20    return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
21   }
22            
23 + inline double min( double a, double b ){
24 +  return (a < b ) ? a : b;
25 + }
26  
27   SimInfo* currentInfo;
28  
29   SimInfo::SimInfo(){
30    excludes = NULL;
31    n_constraints = 0;
32 +  nZconstraints = 0;
33    n_oriented = 0;
34    n_dipoles = 0;
35    ndf = 0;
36    ndfRaw = 0;
37 +  nZconstraints = 0;
38    the_integrator = NULL;
39    setTemp = 0;
40    thermalTime = 0.0;
41 +  currentTime = 0.0;
42    rCut = 0.0;
43 +  ecr = 0.0;
44 +  est = 0.0;
45  
46 +  haveRcut = 0;
47 +  haveEcr = 0;
48 +  boxIsInit = 0;
49 +  
50 +  resetTime = 1e99;
51 +
52 +  orthoTolerance = 1E-6;
53 +  useInitXSstate = true;
54 +
55    usePBC = 0;
56    useLJ = 0;
57    useSticky = 0;
58 <  useDipole = 0;
58 >  useCharges = 0;
59 >  useDipoles = 0;
60    useReactionField = 0;
61    useGB = 0;
62    useEAM = 0;
63  
64 +  myConfiguration = new SimState();
65 +
66    wrapMeSimInfo( this );
67   }
68  
69 +
70 + SimInfo::~SimInfo(){
71 +
72 +  delete myConfiguration;
73 +
74 +  map<string, GenericData*>::iterator i;
75 +  
76 +  for(i = properties.begin(); i != properties.end(); i++)
77 +    delete (*i).second;
78 +    
79 + }
80 +
81   void SimInfo::setBox(double newBox[3]) {
82    
83    int i, j;
# Line 64 | Line 96 | void SimInfo::setBoxM( double theBox[3][3] ){
96  
97   void SimInfo::setBoxM( double theBox[3][3] ){
98    
99 <  int i, j, status;
68 <  double smallestBoxL, maxCutoff;
99 >  int i, j;
100    double FortranHmat[9]; // to preserve compatibility with Fortran the
101                           // ordering in the array is as follows:
102                           // [ 0 3 6 ]
# Line 73 | Line 104 | void SimInfo::setBoxM( double theBox[3][3] ){
104                           // [ 2 5 8 ]
105    double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
106  
107 +  if( !boxIsInit ) boxIsInit = 1;
108  
109    for(i=0; i < 3; i++)
110      for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
111    
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 –
112    calcBoxL();
113    calcHmatInv();
114  
# Line 93 | Line 119 | void SimInfo::setBoxM( double theBox[3][3] ){
119      }
120    }
121  
122 <  setFortranBoxSize(FortranHmat, FortranHmatI, &orthoRhombic);
122 >  setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
123  
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 –  }
124   }
125  
126  
# Line 153 | Line 136 | void SimInfo::scaleBox(double scale) {
136    double theBox[3][3];
137    int i, j;
138  
139 <  cerr << "Scaling box by " << scale << "\n";
139 >  // cerr << "Scaling box by " << scale << "\n";
140  
141    for(i=0; i<3; i++)
142      for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
# Line 163 | Line 146 | void SimInfo::calcHmatInv( void ) {
146   }
147  
148   void SimInfo::calcHmatInv( void ) {
149 <
149 >  
150 >  int oldOrtho;
151 >  int i,j;
152    double smallDiag;
153    double tol;
154    double sanity[3][3];
155  
156    invertMat3( Hmat, HmatInv );
157  
173 –  // Check the inverse to make sure it is sane:
174 –
175 –  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";
182 –    
158    // check to see if Hmat is orthorhombic
159    
160 <  smallDiag = Hmat[0][0];
186 <  if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1];
187 <  if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2];
188 <  tol = smallDiag * 1E-6;
160 >  oldOrtho = orthoRhombic;
161  
162 +  smallDiag = fabs(Hmat[0][0]);
163 +  if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
164 +  if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
165 +  tol = smallDiag * orthoTolerance;
166 +
167    orthoRhombic = 1;
168    
169    for (i = 0; i < 3; i++ ) {
170      for (j = 0 ; j < 3; j++) {
171        if (i != j) {
172          if (orthoRhombic) {
173 <          if (Hmat[i][j] >= tol) orthoRhombic = 0;
173 >          if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
174          }        
175        }
176      }
177    }
178 +
179 +  if( oldOrtho != orthoRhombic ){
180 +    
181 +    if( orthoRhombic ){
182 +      sprintf( painCave.errMsg,
183 +               "Hmat is switching from Non-Orthorhombic to OrthoRhombic\n"
184 +               "       If this is a bad thing, change the orthoBoxTolerance( currently %G ).\n",
185 +               orthoTolerance);
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 orthoBoxTolerance( currently %G ).\n",
192 +               orthoTolerance);
193 +      simError();
194 +    }
195 +  }
196   }
197  
198   double SimInfo::matDet3(double a[3][3]) {
# Line 271 | Line 266 | void SimInfo::matVecMul3(double m[3][3], double inVec[
266    outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
267    outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
268   }
269 +
270 + void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
271 +  double temp[3][3];
272 +  int i, j;
273 +
274 +  for (i = 0; i < 3; i++) {
275 +    for (j = 0; j < 3; j++) {
276 +      temp[j][i] = in[i][j];
277 +    }
278 +  }
279 +  for (i = 0; i < 3; i++) {
280 +    for (j = 0; j < 3; j++) {
281 +      out[i][j] = temp[i][j];
282 +    }
283 +  }
284 + }
285    
286 + void SimInfo::printMat3(double A[3][3] ){
287 +
288 +  std::cerr
289 +            << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
290 +            << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
291 +            << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
292 + }
293 +
294 + void SimInfo::printMat9(double A[9] ){
295 +
296 +  std::cerr
297 +            << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
298 +            << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
299 +            << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
300 + }
301 +
302 +
303 + void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){
304 +
305 +      out[0] = a[1] * b[2] - a[2] * b[1];
306 +      out[1] = a[2] * b[0] - a[0] * b[2] ;
307 +      out[2] = a[0] * b[1] - a[1] * b[0];
308 +      
309 + }
310 +
311 + double SimInfo::dotProduct3(double a[3], double b[3]){
312 +  return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2];
313 + }
314 +
315 + double SimInfo::length3(double a[3]){
316 +  return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]);
317 + }
318 +
319   void SimInfo::calcBoxL( void ){
320  
321    double dx, dy, dz, dsq;
278 –  int i;
322  
323    // boxVol = Determinant of Hmat
324  
# Line 285 | Line 328 | void SimInfo::calcBoxL( void ){
328    
329    dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
330    dsq = dx*dx + dy*dy + dz*dz;
331 <  boxLx = sqrt( dsq );
331 >  boxL[0] = sqrt( dsq );
332 >  //maxCutoff = 0.5 * boxL[0];
333  
334    // boxLy
335    
336    dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
337    dsq = dx*dx + dy*dy + dz*dz;
338 <  boxLy = sqrt( dsq );
338 >  boxL[1] = sqrt( dsq );
339 >  //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
340  
341 +
342    // boxLz
343    
344    dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
345    dsq = dx*dx + dy*dy + dz*dz;
346 <  boxLz = sqrt( dsq );
346 >  boxL[2] = sqrt( dsq );
347 >  //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
348 >
349 >  //calculate the max cutoff
350 >  maxCutoff =  calcMaxCutOff();
351    
352 +  checkCutOffs();
353 +
354   }
355  
356  
357 + double SimInfo::calcMaxCutOff(){
358 +
359 +  double ri[3], rj[3], rk[3];
360 +  double rij[3], rjk[3], rki[3];
361 +  double minDist;
362 +
363 +  ri[0] = Hmat[0][0];
364 +  ri[1] = Hmat[1][0];
365 +  ri[2] = Hmat[2][0];
366 +
367 +  rj[0] = Hmat[0][1];
368 +  rj[1] = Hmat[1][1];
369 +  rj[2] = Hmat[2][1];
370 +
371 +  rk[0] = Hmat[0][2];
372 +  rk[1] = Hmat[1][2];
373 +  rk[2] = Hmat[2][2];
374 +  
375 +  crossProduct3(ri,rj, rij);
376 +  distXY = dotProduct3(rk,rij) / length3(rij);
377 +
378 +  crossProduct3(rj,rk, rjk);
379 +  distYZ = dotProduct3(ri,rjk) / length3(rjk);
380 +
381 +  crossProduct3(rk,ri, rki);
382 +  distZX = dotProduct3(rj,rki) / length3(rki);
383 +
384 +  minDist = min(min(distXY, distYZ), distZX);
385 +  return minDist/2;
386 +  
387 + }
388 +
389   void SimInfo::wrapVector( double thePos[3] ){
390  
391 <  int i, j, k;
391 >  int i;
392    double scaled[3];
393  
394    if( !orthoRhombic ){
# Line 342 | Line 426 | int SimInfo::getNDF(){
426  
427  
428   int SimInfo::getNDF(){
429 <  int ndf_local, ndf;
429 >  int ndf_local;
430    
431    ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
432  
# Line 352 | Line 436 | int SimInfo::getNDF(){
436    ndf = ndf_local;
437   #endif
438  
439 <  ndf = ndf - 3;
439 >  ndf = ndf - 3 - nZconstraints;
440  
441    return ndf;
442   }
443  
444   int SimInfo::getNDFraw() {
445 <  int ndfRaw_local, ndfRaw;
445 >  int ndfRaw_local;
446  
447    // Raw degrees of freedom that we have to set
448    ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
# Line 371 | Line 455 | int SimInfo::getNDFraw() {
455  
456    return ndfRaw;
457   }
458 <
458 >
459 > int SimInfo::getNDFtranslational() {
460 >  int ndfTrans_local;
461 >
462 >  ndfTrans_local = 3 * n_atoms - n_constraints;
463 >
464 > #ifdef IS_MPI
465 >  MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
466 > #else
467 >  ndfTrans = ndfTrans_local;
468 > #endif
469 >
470 >  ndfTrans = ndfTrans - 3 - nZconstraints;
471 >
472 >  return ndfTrans;
473 > }
474 >
475   void SimInfo::refreshSim(){
476  
477    simtype fInfo;
478    int isError;
479    int n_global;
480    int* excl;
481 <  
382 <  fInfo.rrf = 0.0;
383 <  fInfo.rt = 0.0;
481 >
482    fInfo.dielect = 0.0;
483  
484 <  fInfo.rlist = rList;
387 <  fInfo.rcut = rCut;
388 <
389 <  if( useDipole ){
390 <    fInfo.rrf = ecr;
391 <    fInfo.rt = ecr - est;
484 >  if( useDipoles ){
485      if( useReactionField )fInfo.dielect = dielectric;
486    }
487  
# Line 397 | Line 490 | void SimInfo::refreshSim(){
490    fInfo.SIM_uses_LJ = useLJ;
491    fInfo.SIM_uses_sticky = useSticky;
492    //fInfo.SIM_uses_sticky = 0;
493 <  fInfo.SIM_uses_dipoles = useDipole;
493 >  fInfo.SIM_uses_charges = useCharges;
494 >  fInfo.SIM_uses_dipoles = useDipoles;
495    //fInfo.SIM_uses_dipoles = 0;
496    //fInfo.SIM_uses_RF = useReactionField;
497    fInfo.SIM_uses_RF = 0;
# Line 434 | Line 528 | void SimInfo::refreshSim(){
528  
529    this->ndf = this->getNDF();
530    this->ndfRaw = this->getNDFraw();
531 +  this->ndfTrans = this->getNDFtranslational();
532 + }
533  
534 + void SimInfo::setDefaultRcut( double theRcut ){
535 +
536 +  haveRcut = 1;
537 +  rCut = theRcut;
538 +
539 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
540 +
541 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
542   }
543  
544 + void SimInfo::setDefaultEcr( double theEcr ){
545 +
546 +  haveEcr = 1;
547 +  ecr = theEcr;
548 +  
549 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
550 +
551 +  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
552 + }
553 +
554 + void SimInfo::setDefaultEcr( double theEcr, double theEst ){
555 +
556 +  est = theEst;
557 +  setDefaultEcr( theEcr );
558 + }
559 +
560 +
561 + void SimInfo::checkCutOffs( void ){
562 +  
563 +  if( boxIsInit ){
564 +    
565 +    //we need to check cutOffs against the box
566 +    
567 +    if( rCut > maxCutoff ){
568 +      sprintf( painCave.errMsg,
569 +               "Box size is too small for the long range cutoff radius, "
570 +               "%G, at time %G\n"
571 +               "  [ %G %G %G ]\n"
572 +               "  [ %G %G %G ]\n"
573 +               "  [ %G %G %G ]\n",
574 +               rCut, currentTime,
575 +               Hmat[0][0], Hmat[0][1], Hmat[0][2],
576 +               Hmat[1][0], Hmat[1][1], Hmat[1][2],
577 +               Hmat[2][0], Hmat[2][1], Hmat[2][2]);
578 +      painCave.isFatal = 1;
579 +      simError();
580 +    }
581 +    
582 +    if( haveEcr ){
583 +      if( ecr > maxCutoff ){
584 +        sprintf( painCave.errMsg,
585 +                 "Box size is too small for the electrostatic cutoff radius, "
586 +                 "%G, at time %G\n"
587 +                 "  [ %G %G %G ]\n"
588 +                 "  [ %G %G %G ]\n"
589 +                 "  [ %G %G %G ]\n",
590 +                 ecr, currentTime,
591 +                 Hmat[0][0], Hmat[0][1], Hmat[0][2],
592 +                 Hmat[1][0], Hmat[1][1], Hmat[1][2],
593 +                 Hmat[2][0], Hmat[2][1], Hmat[2][2]);
594 +        painCave.isFatal = 1;
595 +        simError();
596 +      }
597 +    }
598 +  } else {
599 +    // initialize this stuff before using it, OK?
600 +    sprintf( painCave.errMsg,
601 +             "Trying to check cutoffs without a box. Be smarter.\n" );
602 +    painCave.isFatal = 1;
603 +    simError();      
604 +  }
605 +  
606 + }
607 +
608 + void SimInfo::addProperty(GenericData* prop){
609 +
610 +  map<string, GenericData*>::iterator result;
611 +  result = properties.find(prop->getID());
612 +  
613 +  //we can't simply use  properties[prop->getID()] = prop,
614 +  //it will cause memory leak if we already contain a propery which has the same name of prop
615 +  
616 +  if(result != properties.end()){
617 +    
618 +    delete (*result).second;
619 +    (*result).second = prop;
620 +      
621 +  }
622 +  else{
623 +
624 +    properties[prop->getID()] = prop;
625 +
626 +  }
627 +    
628 + }
629 +
630 + GenericData* SimInfo::getProperty(const string& propName){
631 +
632 +  map<string, GenericData*>::iterator result;
633 +  
634 +  //string lowerCaseName = ();
635 +  
636 +  result = properties.find(propName);
637 +  
638 +  if(result != properties.end())
639 +    return (*result).second;  
640 +  else  
641 +    return NULL;  
642 + }
643 +
644 + vector<GenericData*> SimInfo::getProperties(){
645 +
646 +  vector<GenericData*> result;
647 +  map<string, GenericData*>::iterator i;
648 +  
649 +  for(i = properties.begin(); i != properties.end(); i++)
650 +    result.push_back((*i).second);
651 +    
652 +  return result;
653 + }
654 +
655 + double SimInfo::matTrace3(double m[3][3]){
656 +  double trace;
657 +  trace = m[0][0] + m[1][1] + m[2][2];
658 +
659 +  return trace;
660 + }

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines