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MESA-H5

This is the new implementation of HDF5 support for MESA based on the former SE format. It is used by the NuGrid collaboration and provides mppnp compatibility.

Requirements

You must have successfully installed a release of MESA.

Latest version of the MESA code on which this implementation has been tested: 10398.

Installation

Once MESA has been installed:

  • copy the run_star_extras.f and mesa_hdf5_*.inc files located in the src folder into the src folder in your work directory.
  • copy the hdf5_profile_columns.list file located in the test folder into the MESA working directory and update the profile_columns.list MESA file.
  • clean, compile, and enjoy!

Profiles in the HDF5 file

The user must specify which MESA profiles should be included in the HDF5. This is done in the file hdf5_profile_columns.list (default name) similar to the profile_columns.list MESA file.

Note that the profiles in the HDF5 file MUST be a subset of the profiles written out in the MESA ASCII files. So whatever contains hdf5_profile_columns.list should also be either in profile_columns.list or is calculated in the extra routines. For example, when the default hdf5_profile_columns.list is used the profile_columns.list needs to include dm, radius, rmid, temperature, log_D_mix, mass and rho. The other profiles (delta_mass and dcoeff) are calculated by the subroutines provided in this package.

Also the MESA profile_columns.list MUST contain time_step if the HDF5 output will be used for post-processing.

Customization

The mesa_hdf5_params.inc file contains the different setup parameters of the HDF5 outputs. You can modify them as you wish, but remember to clean and recompile for your changes to be applied. For example, for productions runs you will most likely set

       integer, parameter :: hdf5_num_mod_output

to a value of 100 or more depending on how long you will expect your run to be. Typically you would have 20-30 files per run. Putting 1000 cycles or time steps into one file is a practical number for longer runs.

Testing

If you would like to run an example, you can use the inlist and columns files located in the test folder. An IPython notebook is also provided as an example for the analysis of the HDF5 data created by this framework.

Known issues and tips

You can use the nugridpy.nugridse module to work with the mesa_h5 hdf5 output files. Here are some notes:

  • if the simulation has been stopped the last file may be corrupted and you may get some error when trying to extract or access data in that file. Just delete that last corrputed file.
  • it is advisable to include photo_interval = 100 in your inlist controls and add use in src/mesa_hdf5_params.inc the same value for integer, parameter :: hdf5_num_mod_output = 100

Authors

Jean-Claude Passy

Falk Herwig

Copyright

Copyright (c) 2014 - 2018, Jean-Claude Passy, NuGrid Collaboration. All rights reserved.

License

BSD-3-Clause "New" or "Revised" License (see LICENSE.md)