pyGDM2 1.0.3

A python full-field electrodynamical solver, based on the Green dyadic method (volume integral technique in frequency domain).

pyGDM2 is available on pypi and gitlab.

Detailed documentation with many examples is avaiable at the pyGDM2 documentation website. See also the documentation paper on arXiv (1802.04071)

Requirements

Python

• python (2.7, python)

• numpy (numpy)

• python 2 headers (under linux, install the package python-dev or python-devel)

Fortran

• fortran compiler (tested with gfortran. gcc)

• openmp (openmp)

• f2py (comes with numpy. link)

Optional Python packages

• scipy (Strongly recommended. Used for standard solver LU decomposition and several tools. scipy)

• matplotlib (Strongly recommended. For all 2D visualization tools. matplotlib)

• mpi4py (for MPI parallelized calculation of spectra. mpi4py)

• mayavi (for all 3D visualization. mayavi)

• PIL (image processing. PIL)

• PaGMO / PyGMO (version 2.4+. Required for the EO submodule. pagmo)

(all available via pip)

Installation under linux

Via pip

Install from pypi repository via

$ pip install pygdm2

Via setup script

The easiest possibility to compile (and install) pyGDM is via the setup-script, which uses the extended distutils from numpy.

To install pyGDM, run in the source directory:

$ python setup.py install

To install to a user-defined location, use the prefix option:

$ python setup.py install --prefix=/some/specific/location

To only compile without installation, use

$ python setup.py build

Manual compilation

1. clone git:

   $ git clone https://gitlab.com/wiechapeter/pyGDM2.git

2. compile fortran parts:

   $ cd fortranBase
   $ make

3. optional, for system-wide usage add to path and pythonpath, e.g. add following lines to file “/home/USER/.profile”, where “path_of_pyGDM_folder” is the pyGDM installation directory:

   PATH="path_of_pyGDM_folder:$PATH"
   export PATH
   
   PYTHONPATH="path_of_pyGDM_folder:$PYTHONPATH"
   export PYTHONPATH

Installation under Mac OS X

The default compiler on OSX uses a clang which does not support OpenMP. Hence compilation might fail. We therefore suggest using Anaconda and install gcc from the conda repository in a virtualenv:

$ conda create -n python2 python=2.7 anaconda

“anaconda” at the end will copy the whole anaconda distribution to the virtial env. You can omit this option and create a “blank” virtual environment to install only selected packages.

Next activate the virtualenv and install the required software:

$ source activate python2
$ conda install pip
$ conda install gcc
$ pip install pygdm2

Alternatively, you can download the latest version and compile it manually without OpenMP support, which should work with the default OSX compiler:

$ python setup.py install --no-openmp

Installation under windows

Via pip

There is a binary for 64bit windows on the pypi repository (tested on Win10). Install via

$ pip install pygdm2

Authors

Python code

• P. R. Wiecha

Fortran code

• C. Girard

• A. Arbouet

• R. Marty

• P. R. Wiecha