camr.cc 16.7 KB
Newer Older
jclamber's avatar
jclamber committed
1
// ============================================================================
2
// Copyright Jean-Charles LAMBERT - 2007-2016
jclamber's avatar
jclamber committed
3 4 5
//           Centre de donneeS Astrophysiques de Marseille (CeSAM)              
// e-mail:   Jean-Charles.Lambert@lam.fr                                      
// address:  Aix Marseille Universite, CNRS, LAM 
jclamber's avatar
jclamber committed
6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
//           Laboratoire d'Astrophysique de Marseille                          
//           Pole de l'Etoile, site de Chateau-Gombert                         
//           38, rue Frederic Joliot-Curie                                     
//           13388 Marseille cedex 13 France                                   
//           CNRS U.M.R 7326                                                   
// ============================================================================

#include <cstdlib>
#include <cstring>
#include <sstream>
#include <iomanip>
#include <cmath>
#include "camr.h"
#include "cfortio.h"
#include "snapshotramses.h"
21

jclamber's avatar
jclamber committed
22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45
namespace ramses {
const double CAmr::XH = 0.76;
const double CAmr::mH = 1.6600000e-24;
const double CAmr::kB = 1.3806200e-16;

// ============================================================================
//
CAmr::CAmr(const std::string _indir, const bool _v)
{
  nbody=0;
  //pos = mass = vel = NULL;
  verbose=_v;
  indir = _indir;
  infile="";
  
  // keep filename untill last /
  int found=indir.find_last_of("/");
  if (found != (int) std::string::npos && (int) indir.rfind("output_")<found) {
    indir.erase(found,indir.length()-found);
  }
  if (verbose)
    std::cerr << "indir =[" << indir <<"]\n";
  
  found=(int) indir.rfind("output_"); 
46
  if (found!=(int) std::string::npos) {
jclamber's avatar
jclamber committed
47 48 49 50 51 52
    s_run_index= indir.substr(found+7,indir.length()-1); // output_ = 7 characters
    
    while ((found=s_run_index.find_last_of("/"))>0) { // remove trailing "/"
      s_run_index.erase(found,found);
    }
    infile = indir + "/amr_" + s_run_index + ".out00001";
53
    testhydrofile = indir + "/hydro_" + s_run_index + ".out00001";
jclamber's avatar
jclamber committed
54 55 56
    if (verbose)
      std::cerr << "Run index = " << s_run_index <<  "  infile=[" << infile << "]\n";
  }
57 58 59 60 61 62
  // readHeader
  if (amr.open(infile)) {
    readHeader();
    amr.close();
  }

jclamber's avatar
jclamber committed
63 64 65 66 67 68 69
  //computeNbody();
  //loadData();
}
// ============================================================================
//
CAmr::~CAmr()
{
70 71
   amr.close();
   hydro.close();
LAMBERT Jean-charles's avatar
LAMBERT Jean-charles committed
72
   grav.close();
jclamber's avatar
jclamber committed
73 74 75 76 77
}
// ----------------------------------------------------------------------------
//
bool CAmr::isValid()
{    
78
  if (amr.open(infile) && hydro.open(testhydrofile)) {
jclamber's avatar
jclamber committed
79
    valid=true;
80
    //readHeader();
jclamber's avatar
jclamber committed
81
    amr.close();
82
    hydro.close();
jclamber's avatar
jclamber committed
83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121
    if (verbose)
      std::cerr << "ncpu="<<ncpu<<"  ndim="<<ndim<< "\n";// "npart=" << npart << "\n";
    xbound[0] = nx/2;
    xbound[1] = ny/2;
    xbound[2] = nz/2;
    twotondim = pow(2,ndim);  
    ordering = "hilbert";
    scale_nH =  XH/mH * 0.276090728884102e-29;
  }
  else
    valid=false;
  amr.close();
  return valid;
}
// ============================================================================
// readHeader
int CAmr::readHeader()
{
  int len1,len2;
  amr.readDataBlock((char *) &ncpu);

  amr.readDataBlock((char *) &ndim);

  len1=amr.readFRecord();
  amr.readData((char *) &nx,sizeof(int),1);
  amr.readData((char *) &ny,sizeof(int),1);
  amr.readData((char *) &nz,sizeof(int),1);
  len2=amr.readFRecord();
  assert(amr.good() && len1==len2);

  amr.readDataBlock((char *) &nlevelmax);
  if (verbose)
    std::cerr << "AMR Nlevel max="<<nlevelmax<<"\n";
  amr.readDataBlock((char *) &ngridmax);

  amr.readDataBlock((char *) &nboundary);
  
  amr.readDataBlock((char *) &ngrid_current);
  
122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152
  amr.readDataBlock((char *) &header.boxlen);
  std::cerr << "BOX LEN ="<<header.boxlen<<"\n";
  amr.skipBlock(3); // noutput,iout,ifout
                    // tout
                    // aout
  amr.readDataBlock((char *) &header.time);
  std::cerr << "TIME  ="<<header.time<<"\n";
  amr.skipBlock(4); // dtold
                    // dtnew
                    // nstep,nstep_coarse
                    // const,mass_tot_0,rho_tot
  len1=amr.readFRecord();
  amr.readData((char *) &header.omega_m   ,sizeof(double),1);
  amr.readData((char *) &header.omega_l   ,sizeof(double),1);
  amr.readData((char *) &header.omega_k   ,sizeof(double),1);
  amr.readData((char *) &header.omega_b   ,sizeof(double),1);
  amr.readData((char *) &header.h0        ,sizeof(double),1);
  amr.readData((char *) &header.aexp_ini  ,sizeof(double),1);
  amr.readData((char *) &header.boxlen_ini,sizeof(double),1);
  len2=amr.readFRecord();
  assert(amr.good() && len1==len2);

  len1=amr.readFRecord();
  amr.readData((char *) &header.aexp,sizeof(double),1);
  amr.readData((char *) &header.hexp,sizeof(double),1);
  amr.readData((char *) &header.aexp_old,sizeof(double),1);
  amr.readData((char *) &header.epot_tot_int,sizeof(double),1);
  amr.readData((char *) &header.epot_tot_old,sizeof(double),1);
  len2=amr.readFRecord();
  assert(amr.good() && len1==len2);

153
  if (len2==len1) ; // remove warning....
jclamber's avatar
jclamber committed
154 155 156 157
  return 1;
}
// ============================================================================
// loadData
158 159 160 161 162
template int CAmr::loadData<float> (uns::CParticles<float> * particles,
                   const unsigned int req_bits);
template int CAmr::loadData<double> (uns::CParticles<double> * particles,
                   const unsigned int req_bits);
template <class T> int CAmr::loadData(uns::CParticles<T> * particles,
jclamber's avatar
jclamber committed
163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212
                   const unsigned int req_bits)
{
  int ngridfile  [nlevelmax][ncpu+nboundary];
  int ngridlevel [nlevelmax][ncpu          ];
  int ngridbound [nlevelmax][     nboundary];
  double xc[3][8];
  int ngrida;
  std::string infile;
  
  nbody = 0;
  bool count_only=false;
  //if (index==NULL)  count_only=true;

  // loop on all cpus/files
  for (int icpu=0; icpu<ncpu; icpu++) {
    std::ostringstream osf;
    osf << std::fixed << std::setw(5) << std::setfill('0') <<icpu+1;
    infile = indir + "/amr_" + s_run_index + ".out" + osf.str();
    if (verbose) std::cerr << "CAmr::loadData infile-> ["<<infile << "]\n";
    amr.open(infile);
    amr.skipBlock(21);
    
    amr.readDataBlock((char *) &ngridlevel);
    memcpy(ngridfile,ngridlevel,sizeof(int)*nlevelmax*ncpu);
    
    amr.skipBlock();    
    
    if (nboundary>0) {
      amr.skipBlock(2);
      
      amr.readDataBlock((char *) &ngridbound);
      // must convert the following line
      //ngridfile(ncpu+1:ncpu+nboundary,1:nlevelmax)=ngridbound
      for (int i=0;i<nlevelmax;i++) {
        // copy grid level
        memcpy(&ngridfile [i][0],
               &ngridlevel[i][0],sizeof(int)*ncpu);
        // copy gridbound
        memcpy(&ngridfile [i][ncpu],
               &ngridbound[i][0],sizeof(int)*nboundary);
      }
    }
    amr.skipBlock();    
    // ROM: comment the single following line for old stuff
    amr.skipBlock();    
    if (ordering=="bisection") 
      amr.skipBlock(5);
    else 
      amr.skipBlock();
    amr.skipBlock(3);
LAMBERT Jean-charles's avatar
LAMBERT Jean-charles committed
213
    // --------------
jclamber's avatar
jclamber committed
214 215 216 217
    // Open HYDRO file and skip header
    std::string hydrofile = indir + "/hydro_" + s_run_index + ".out" + osf.str();
    //if (verbose) std::cerr << "CAmr::loadData hydrofile-> ["<<hydrofile << "]\n";
    hydro.open(hydrofile,count_only);
LAMBERT Jean-charles's avatar
LAMBERT Jean-charles committed
218
    hydro.skipBlock(); // ncpu
jclamber's avatar
jclamber committed
219 220
    hydro.readDataBlock((char *) &nvarh);
    //std::cerr << "nvarh = " << nvarh << "\n" ;
LAMBERT Jean-charles's avatar
LAMBERT Jean-charles committed
221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238
    hydro.skipBlock(4); // ndim,levelmax,nboundary,gamma

    // --------------
    // Open GRAV file and skip header
    if (req_bits&POT_BIT || req_bits&ACC_BIT) {
      std::string gravfile = indir + "/grav_" + s_run_index + ".out" + osf.str();
      //if (verbose) std::cerr << "CAmr::loadData hydrofile-> ["<<hydrofile << "]\n";
      grav.open(gravfile,count_only);
      grav.skipBlock(); // ncpu
      grav.readDataBlock((char *) &nvarg); // buggy in new RAMSES version
      //nvarg=ndim+1; // this is MUST be the real value
                    // ndim = 3; nvarg =4, phi,ax,ay,az
                    // ndim = 2; nvarg =3, phi,ax,ay
      if (verbose) {
        std::cerr << "\nWARNING\nWe assume that you are using ramses data files produces with new RAMSES released\n";
      }
      grav.skipBlock(2); //  levelmax,nboundary
    }
jclamber's avatar
jclamber committed
239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255
    // loop over levels
    for (int ilevel=0; ilevel<lmax; ilevel++) {
      
      // Geometry
      double dx=pow(0.5,ilevel+1);
      double dx2=0.5*dx;
      for (int ind=0; ind<twotondim; ind++) {
        int iz=ind/4;
        int iy=(ind-4*iz)/2;
        int ix=(ind-2*iy-4*iz);
        xc[0][ind]=(ix-0.5)*dx;
        xc[1][ind]=(iy-0.5)*dx;
        xc[2][ind]=(iz-0.5)*dx;
      }
      // allocate work arrays
      ngrida=ngridfile[ilevel][icpu];
      
LAMBERT Jean-charles's avatar
LAMBERT Jean-charles committed
256
      double * xg=NULL, *var=NULL, *varg=NULL;
jclamber's avatar
jclamber committed
257 258 259 260
      int * son=NULL;
      if (ngrida>0) {
        xg = new double[ngrida*ndim];
        son= new int   [ngrida*twotondim];
LAMBERT Jean-charles's avatar
LAMBERT Jean-charles committed
261
        if (!count_only) {
jclamber's avatar
jclamber committed
262
          var= new double[ngrida*twotondim*nvarh];
LAMBERT Jean-charles's avatar
LAMBERT Jean-charles committed
263 264 265 266
          if (req_bits&POT_BIT || req_bits&ACC_BIT) {
            varg= new double[ngrida*twotondim*nvarg];
          }
        }
jclamber's avatar
jclamber committed
267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311
      }
      // Loop over domains
      for (int j=0; j<(nboundary+ncpu); j++) {
        if (ngridfile[ilevel][j]>0) {
          amr.skipBlock(); // Skip grid index
          amr.skipBlock(); // Skip next index
          amr.skipBlock(); // Skip prev index
          //
          // Read grid center
          //
          for (int idim=0;idim<ndim;idim++) {
            if (j==icpu) {
              amr.readDataBlock((char *) &xg[idim*ngrida]);
            } 
            else amr.skipBlock();
          }
          amr.skipBlock();       // Skip father index
          amr.skipBlock(2*ndim); // Skip nbor index
          //
          // Read son index
          //
          for (int ind=0;ind<twotondim;ind++) {
            if (j==icpu) {
              amr.readDataBlock((char *) &son[ind*ngrida]);
            }
            else amr.skipBlock();
          }          
          amr.skipBlock(twotondim); // Skip cpu map          
          amr.skipBlock(twotondim); // Skip refinement map
        }
        //
        // Read HYDRO data
        //
        hydro.skipBlock(2);
        if (!count_only && ngridfile[ilevel][j]>0) {
          // Read hydro variables
          for (int ind=0;ind<twotondim;ind++) {
            for (int ivar=0; ivar<nvarh; ivar++) {
              if (j==icpu) {
                hydro.readDataBlock((char *) &var[ivar*ngrida*twotondim+ind*ngrida]);
              }
              else hydro.skipBlock();
            }
          }
        }
LAMBERT Jean-charles's avatar
LAMBERT Jean-charles committed
312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329
        //
        // Read GRAV data
        //
        if (req_bits&POT_BIT || req_bits&ACC_BIT) {
          grav.skipBlock(2);
          if (!count_only && ngridfile[ilevel][j]>0) {
            // Read grav variables
            for (int ind=0;ind<twotondim;ind++) {
              for (int ivar=0; ivar<nvarg; ivar++) {
                if (j==icpu) {
                  grav.readDataBlock((char *) &varg[ivar*ngrida*twotondim+ind*ngrida]);
                }
                else grav.skipBlock();
              }
            }
          }
        }

jclamber's avatar
jclamber committed
330 331 332 333 334 335 336 337 338
      }      
      if (ngrida>0) {
        //  Loop over cells
        for (int ind=0;ind<twotondim;ind++) {
          // Store data cube
          for (int i=0;i<ngrida;i++) {
            // compute cell center
            double px=xg[0*ngrida+i]+xc[0][ind]-xbound[0]; // x
            double py=xg[1*ngrida+i]+xc[1][ind]-xbound[1]; // y
339 340 341 342
            double pz=0.0;
            if (ndim > 2) {
              pz=xg[2*ngrida+i]+xc[2][ind]-xbound[2]; // z
            }
jclamber's avatar
jclamber committed
343 344 345 346 347
            bool ok_cell =       (
                !(son[ind*ngrida+i]>0 && ilevel<lmax) && // cells is NOT refined
                (ilevel>=lmin)                        &&
                ((px+dx2)>=xmin)                      &&
                ((py+dx2)>=ymin)                      &&
jclamber's avatar
jclamber committed
348
                ((ndim<3) || ((pz+dx2)>=zmin))        &&
jclamber's avatar
jclamber committed
349 350
                ((px-dx2)<=xmax)                      &&
                ((py-dx2)<=ymax)                      &&
jclamber's avatar
jclamber committed
351
                ((ndim<3) || ((pz-dx2)<=zmax)));
jclamber's avatar
jclamber committed
352 353 354 355
            if (ok_cell) {
              if (!count_only) {
                bool take=false;
                if (req_bits&POS_BIT) {
356 357
                  particles->pos.push_back(px*header.boxlen);  // x
                  particles->pos.push_back(py*header.boxlen);  // y
jclamber's avatar
jclamber committed
358 359 360 361
                  if (ndim>2)
                    particles->pos.push_back(pz*header.boxlen);  // z
                  else
                    particles->pos.push_back(0.0);  // z
jclamber's avatar
jclamber committed
362 363 364 365
                  particles->load_bits |= POS_BIT;
                  take=true;
                }
                if (req_bits&VEL_BIT) {
366 367
                  particles->vel.push_back(var[1*ngrida*twotondim+ind*ngrida+i]); // vx
                  particles->vel.push_back(var[2*ngrida*twotondim+ind*ngrida+i]); // vy
jclamber's avatar
jclamber committed
368 369 370 371
                  if (ndim>2)
                    particles->vel.push_back(var[3*ngrida*twotondim+ind*ngrida+i]); // vz
                  else
                    particles->vel.push_back(0.0); // vz
jclamber's avatar
jclamber committed
372 373 374
                  particles->load_bits |= VEL_BIT;
                  take=true;
                }
375
                // gas density
376
                double rho = var[0*ngrida*twotondim+ind*ngrida+i];
377
                if (req_bits&MASS_BIT) {                
jclamber's avatar
jclamber committed
378
                  particles->mass.push_back(rho*dx*header.boxlen*dx*header.boxlen*dx*header.boxlen);
jclamber's avatar
jclamber committed
379 380 381 382
                  particles->load_bits |= MASS_BIT;
                  take=true;
                }
                if (req_bits&HSML_BIT) {
jclamber's avatar
jclamber committed
383
                  particles->hsml.push_back(dx*header.boxlen); // hsml
jclamber's avatar
jclamber committed
384 385 386 387 388 389
                  particles->load_bits |= HSML_BIT;
                }
                if (req_bits&RHO_BIT) {                  
                  particles->rho.push_back(rho); // rho var(i,ind,1) * scale_nH
                  particles->load_bits |= RHO_BIT;
                }
LAMBERT Jean-charles's avatar
LAMBERT Jean-charles committed
390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413
                //
                // Get gavitationnal data
                //
                if (req_bits&POT_BIT && (nvarg==ndim+1)) {
                  particles->phi.push_back(varg[0*ngrida*twotondim+ind*ngrida+i]);
                  particles->load_bits |= POT_BIT;
                }
                if (req_bits&ACC_BIT && nvarg>=ndim ) {
                  int offset=0;
                  if (nvarg==ndim+1) { // there is pot/ax/ay/az
                    offset=1;          //  shift to ax
                  }
                  for (int k=0; k<nvarg; k++) {
                    particles->acc.push_back(varg[(offset+k)*ngrida*twotondim+ind*ngrida+i]);
                  }
                  if (ndim<3) { // ndim = 2 , set az=0.0
                    particles->acc.push_back(0.0);
                  }
                  particles->load_bits |= ACC_BIT;
                }
                //
                // Get hydrodinamic data
                //
                // with 2D simulations, hydro variables from var[] array are shifted to the left
jclamber's avatar
jclamber committed
414 415 416 417
                int offset_2d=-1;
                if (ndim>2) offset_2d=0;

                if (req_bits&TEMP_BIT && nvarh>(4+offset_2d)) {
418
                  double temp=0.0;
419
                  if (rho!=0.0) {
jclamber's avatar
jclamber committed
420
                    temp=std::max(0.0,var[(4+offset_2d)*ngrida*twotondim+ind*ngrida+i]/rho);
421
                  }
jclamber's avatar
jclamber committed
422 423 424
                  particles->temp.push_back(temp);
                  particles->load_bits |= TEMP_BIT;
                }
jclamber's avatar
jclamber committed
425
                if (req_bits&METAL_BIT && nvarh>(5+offset_2d)) {
426
                  double metal= var[(5+offset_2d)*ngrida*twotondim+ind*ngrida+i];
jclamber's avatar
jclamber committed
427 428 429
                  particles->metal.push_back(metal);
                  particles->load_bits |= METAL_BIT;
                }
jclamber's avatar
jclamber committed
430
                if (req_bits&METAL_BIT && nvarh<=5) {
431
                  double metal= -1.0; // we put -1.0 when no metellicity
jclamber's avatar
jclamber committed
432 433 434
                  particles->metal.push_back(metal);
                  particles->load_bits |= METAL_BIT;
                }
jclamber's avatar
jclamber committed
435 436 437 438
                if (req_bits&ID_BIT) {
                  particles->id.push_back(-1.); // no id for gas, use "-1"
                  particles->load_bits |= ID_BIT;
                }
jclamber's avatar
jclamber committed
439
                if (take|| !req_bits) { // !req_bits for uns_info and siplay=f
jclamber's avatar
jclamber committed
440 441
                  particles->indexes.push_back(0); // GAS particles
                  particles->ngas++; // One more gas particles
jclamber's avatar
jclamber committed
442

jclamber's avatar
jclamber committed
443
                }
jclamber's avatar
jclamber committed
444 445
                particles->ntot++; // one more total particles
                                   // this variable count all particles
jclamber's avatar
jclamber committed
446 447 448
              }
              nbody++;
            }
449 450 451 452 453 454 455
            else {
//              if (ilevel>=lmin) {
//              std::cerr << "Not ok lmin="<<lmin<<" ilevel="<<ilevel<<" xmin="<<xmin<<" xmax="<<xmax
//                           <<" ymin="<<ymin<<" ymax="<<ymax
//                          <<" zmin="<<zmin<<" zmax="<<zmax<<"\n";
//              }
            }
jclamber's avatar
jclamber committed
456 457 458 459 460 461 462 463 464 465 466
          }
        }
        // garbage collecting
        delete [] xg;
        //delete [] x;
        delete [] son;
        if (!count_only) 
          delete [] var;
      }
    } // ilevel
    amr.close();    
LAMBERT Jean-charles's avatar
LAMBERT Jean-charles committed
467 468
    hydro.close();
    grav.close();
jclamber's avatar
jclamber committed
469 470 471 472
  } //for (int icpu=0 .... 
  return nbody;
}
} // end of namespace ramses