You must have successfully installed a release of MESA.
Latest version of the MESA code on which this implementation has been tested: 10398.
Once MESA has been installed:
- copy the
mesa_hdf5_*.incfiles located in the
srcfolder into the
srcfolder in your work directory.
- copy the
hdf5_profile_columns.listfile located in the
testfolder into the MESA working directory and update the
- 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
rho. The other profiles (
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.
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.
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 = 100in your inlist controls and add use in
src/mesa_hdf5_params.incthe same value for
integer, parameter :: hdf5_num_mod_output = 100
Copyright (c) 2014 - 2018, Jean-Claude Passy, NuGrid Collaboration. All rights reserved.
BSD-3-Clause "New" or "Revised" License (see LICENSE.md)