rhd_dq is a library for reading CO5BOLD UIO files. It includes a python wrapper, pybold, and some additional tools. Only the python wrapper is documented hereafter.

Copyright (C) 2019 Flavio Calvo flavio.calvo@irsol.ch.

This program is free software: you can redistribute it and/or modify it under the terms of the MIT license as published by the Open Source Initiative.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the MIT license for more details.

You should have received a copy of the MIT license along with this program. If not, see https://opensource.org/licenses/MIT.

Whatever work you do and distribute based on the present code IS HEAVILY ENCOURAGED to be licensed with a free and open-source software license.

The files under the 3dparty directory are external 3rd-party software and are not covered by the present copyright, as well as the files that explicitly provide copyright information and license. All files outside of the 3dparty folder and with no explicit copyright notice are part of the present project and are threfore covered by the present copyright.

The pybold python module was tested with both Python 2.7 and Python 3, and with NumPy 1.11.0 and above. f2py is required at compile time, and many distributions provide it as a side package numpy-develop.

The sources of the CO5BOLD code are also required.

First identify the path to the CO5BOLD source files on your computer and check the configuration in <CO5BOLD_SRC>/hd/rhd/<YOUR_MACHINE>/.configurerc. The CO5BOLD code must compile with no errors on your machine, and the F90_POSTFLAGS variable in the configuration file must contain the compilation flag "-Drhd_box_arrays01=0".

You can find additional information about CO5BOLD configuration and compilation in <CO5BOLD_SRC>/README.

Compile the pybold module with

./configure ARCH=<YOUR_MACHINE> F90_BASEPATH=<CO5BOLD_SRC> COBOLD_3DPARTY=no
make pybold

Compilation went successful if the last output line is

...
rm -rf "rhd_dq_module.a"

and if _pybold.so was created. Make sure that both pybold.py and _pybols.so are in a place where Python can find them.

In Python, start importing the pybold module and creating a model structure. You can easily get help on the model structure:

import pybold
model = pybold.uio_struct()
help(model)

The contents of an UIO file can be loaded into the model structure and displayed with

model.load('myfile.uio')
model

For instance, you could load a parameter file and display its contents with

model.load('myfile.uio')
model

Note however that if the UIO file contains several atmosphere snapshots, only the last one is loaded. If you need to process all the snapshots of an UIO file, say a MEAN file rhd.mean, you might prefer to use

model.open('rhd.mean')
model.header        # load the header
model.next          # load the first snapshot
# ...do your processing...
model.next
# ...do your processing...
# ...
model.close

Assuming you have a parameter file rhd.par with the corresponding files for the equation of state and for opacities, and you are interested in the second snapshot of the FULL file rhd.full, you can load it into the model structure using

model.load('rhd.full', 'rhd.par', 2)

You will find a new substructure dq with all derived quantities:

model.dq
model.dq.T          # compute temperature

Derived quantities are computed (and corresponding memory allocated) on an on-request basis.

It is also possible to use the open statement with parameter files:

model.open('rhd.full', 'rhd.par')
model.header        # load the header into the model structure
model.next          # load the first snapshot
model.next          # load the second snapshot
model.close         # close `rhd.full'