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Commits on Jun 23, 2015
  1. Moved the resetting of the restart variable until after doing the

    the check for it in connection with generating the first output.
    This was a bug introduced by checking for the restart variable when
    calling output.
Commits on May 19, 2015
  1. Stopped the program from writing an initial output if the code is

    Garrelt Mellema authored
    doing a restart. This behaviour let to overwriting of the original
    results, not necessarily with the correct values (e.g. IonRates files).
  2. Merge branch 'master' of

    Garrelt Mellema authored
    No change, just a local conflict on laptop.
Commits on Mar 24, 2015
  1. Changes related to position dependent LLS configuration.

    These changes may be out of date compared to changes made on sfinx.
Commits on Mar 16, 2015
  1. Minor bug fixes on the position dependent LLS part. This was triggered

    in a bug in make_LLS so I am not sure the code has changed fundamentally
    but this version has been tested and validated.
Commits on Mar 13, 2015
  1. Setting average column density of LLS per cell to zero if mfp limit

    is not reached. Useful for the reporting to the log file, making it
    consistent with the behaviour for homogeneous LLS case.
  2. Introduced the mean free path limit also for the position dependent

    case of LLS. If the mean free path is less than a certain value,
    LLS opacity is not applied.
  3. Revision of the LLS subroutines in view of simulations with

    position dependent LLSs. Previous versions of position dependent
    LLS were never tested or used and were wrong.
Commits on Feb 5, 2015
  1. More efficient version for isothermal 10^4 K case.

    Do not use for other cases!!!!
  2. Made evolve use the clocks routines instead of direct call to system_…

    Possible improvement to consider: make timestep_wallclock function return time
    in specified units (seconds, minutes, hours, etc..)
Commits on Dec 1, 2014
  1. Probably no major changes

Commits on Aug 14, 2014
  1. Changed all 1pe10.3 (old fashioned Fortran) to es10.3. This should

    cause no change in the output being produced by the code
  2. changed old fashioned 1pe10.3 to es10.3 format.

    Will do so for more format statements.
  3. The variables volfrac and massfrac which are meant to hold the volume

    and mass weighted mean ionization fractions for writing to PhotonCounts2.dat
    (unit 95) were wrongly defined as arrays running from 0 to 2. This
    mistake was due to synchronization with the Helium version of the code
    (where both the HeII and HeIII fractions are calculated and stored
    in these arrays).
    volfrac and massfrac are now scalars again.
Commits on Aug 13, 2014
  1. Moved the compressed versions of the material, evolve, sourceprops,

    photonstatistics and output modules to a separate directory, called compressed.
    The modules use a compressed version of the ionized/neutral fractions
    but have not been kept up to date. They are to retained for future
    use but are for now moved out of the way to create a cleaner source
Commits on Aug 1, 2014
  1. Added a check for rank=0 to the write_stream2 routine. This check

    was missing, leading to all nodes writing out the data!!!!
  2. Added flushing to the PhotonCounts output streams.

    Added more comments to the  write_photonstatistics subroutine
    Increased the length of various filename variables to 512.
Commits on Jul 22, 2014
Commits on Jul 21, 2014
  1. Introduced a flag start up error to track start up errors. For now

    it just checks that the intermediate redshift is indeed intermediate
    between the current and the next redshift (intermediate redshift
    when restarting).
  2. Extended the storage space for file names to 512 characters in order

    to accommodate full path names in file_admin.f90. Likewise in file_admin.f90
    to 400 characters
Commits on May 30, 2014
  1. Fixed bug in handling restarts from iteration dumps. On Aug 16, 2013

    the mpi_bcast of the phih_grid array was erroneously removed. This
    has now been restored.
    Additionally the two quantities used in checking convergence of the
    global ionization fractions (prev_sum_xh1_int, prev_sum_xh0_int)
    are being mpi_bcast.
Commits on May 14, 2014
  1. The quantity sum_xh0_int was not being calculated correctly for the n…

    …on ALLFRAC
    case. It should not be 1.0 - sum_xh1_int, but real(mesh(1)*mesh(2)*mesh(3)) - sum_xh1_int.
    The global average fractions are not normalized during this calculation hence
    this factor instead of 1.0
    This is now fixed.
Commits on Apr 22, 2014
  1. Removed the use of the variable temper from the output routines.

    This module now uses the new temperature structures.
  2. Fixed the use of temperature in photon statistics, subroutine total_r…

    The code was still using the temper variable which has become undefined.
    This can lead to divbyzero errors.
    SHould use get_temperature_point. This has now been added to this
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