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Using MCFOST with Phantom

The MCFOST documentation is at http://ipag-old.osug.fr/~pintec/mcfost/docs/html/overview.html.

Acquiring and setting up mcfost

Email Christophe to ask for permission, and a link to download the tar ball with MCFOST.

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Reading and writing Phantom output files in HDF5 format

From Wikipedia:

Hierarchical Data Format (HDF) is a set of file formats (HDF4, HDF5) designed to store and organize large amounts of data. Originally developed at the National Center for Supercomputing Applications, it is supported by The HDF Group, a non-profit corporation whose mission is to ensure continued development of HDF5 technologies and the continued accessibility of data stored in HDF.

HDF5 has the following nice features.

• It is widely available.

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Fortran issues with renaming subroutines when using from modules

There are issues with naming a subroutine the same as a subroutine that is used from another module but is renamed. See the code for details.

Instructions

Download all files in this gist.

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! ---------------------------------------------------------------------------- !
!
! MODULE: hdf5_utils
!
! DESCRIPTION: Utilities for reading and writing HDF5 files in Fortran.
!
! AUTHORS: Daniel Mentiplay, David Liptai, Conrad Chan
!
! YEAR: 2019
!

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Phantom dump size comparison

Phantom dump size comparison between pb, ie. Price-Bate Fortran binary format, and HDF5, both with and without compression. The compression is gzip with the highest level of compression (level 9).

Gas only

Gas disc.

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ADS & BibDesk

Install BibDesk from https://bibdesk.sourceforge.io/.

Alternatively, via the Homebrew Cask.

brew cask install bibdesk

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#!/bin/bash
#
# Takes a .tex file and finds citations of the form:
#
#   \cite{mentiplay:2018}
#   \citet{mentiplay:2018}
#   \citep{mentiplay:2018}
#   \cite{mentiplay:2018a}
#   \citet{mentiplay:2018b}
#   \citep{mentiplay:2018c}

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#!/usr/bin/env python
"""
Generate bibtex from citations in tex using a master bibtex.

It uses the following regex to find citations in the tex file:

    regex = re.compile(r'\\|no|cite[a-z]*\*?{(.*?)}')

This regex matches citations like \cite{}, \citet{}, \citep{},
\citeauthor{}, \citet*{}, and so on, and returns the captured citekey.

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#
# Make notebook, html, slides from markdown

.PHONY:
help:
	@echo "Usage:"
	@echo "  make <target>"
	@echo
	@echo "  notebook         Make .ipynb notebook"
	@echo "  html             Make .html notebook"

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#!/usr/bin/env python
"""
Fix file links in bibtex file used with BibDesk using bibtexparser.

To use, run the script then open the resulting bibtex file in BibDesk
and save it. This should fix all file links.

Daniel Mentiplay, 2019.
"""