Initial commit

.gitignore

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+*.pyc
+*.png
+*.dat
+*.pdf
+*.o
+*.mod
+*.exe
+*.out
+.ipynb_checkpoints
+docs/html
+docs/latex
+docs/doxygen.log

LICENSE.txt

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+Copyright © 2014- msleigh
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

README.md

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+fcimc
+=====
+
+A Python implementation of Fleck and Cummings's implicit Monte Carlo (IMC) scheme, as published in Journal of Computational Physics (JCP) in 1971.
+
+<img src="https://img.shields.io/github/v/release/msleigh/fcimc?include_prereleases"> <img src="https://img.shields.io/github/license/msleigh/fcimc"> <img src="https://img.shields.io/tokei/lines/github/msleigh/fcimc"> <img src="https://img.shields.io/github/last-commit/msleigh/fcimc"> <img src="https://img.shields.io/badge/code%20style-black-lightgrey">
+
+## Dependencies
+
+### Python version
+
+- Python 3 (<3.8, see note 1)
+- Numpy
+
+### Fortran version
+
+- GFortran
+
+### Bundled calculations
+
+- Matplotlib (to plot the figures)
+- Jupyter (to open the verification notebook)
+
+### Documentation
+
+- Doxygen
+- Graphviz
+- Doxypypy (requires Python<3.8, see note 1)
+
+### Notes
+
+1. The requirement for Python < 3.8 is due to a bug in Doxypypy; see
+   [https://github.com/Feneric/doxypypy/issues/70]. If documentation is not required
+   then this limit can be ignored.
+
+## Installation
+
+To create a Conda env with the necessary Python packages:
+
+    conda env create -n <env-name> -f environment.yml
+    conda activate <env-name>
+
+To install the non-Python dependencies on macOS:
+
+    brew install gfortran
+    brew install doxygen
+    brew install graphviz
+
+## Usage
+
+### Execution
+
+To build and run everythina from scratch, run the top-level script:
+
+    ./runall
+
+To see the aggregated output:
+
+    jupyter notebook verification.ipynb
+
+To open the documentation:
+
+    open docs/html/index.html
+
+### Cleaning
+
+To clean up intermediiate build files etc.:
+
+    ./runall clean
+
+and to clean out everything (output files, executables, etc.) for a fresh start:
+
+    ./runall clobber
+
+### Fine control
+
+Each part of the project has its own `Makefile` which can be invoked directly:
+
+    ./fortran/src/Makefile
+    ./fortran/calcs/Makefile
+    ./python/calcs/Makefile
+    ./docs/Makefile
+
+to either clean up one part, e.g.:
+
+    make -C fortran/src clean
+    make -C docs clobber
+
+or build/execute, e.g.:
+
+    make -C python/calcs -j 4 all
+    make -C docs html
+
+