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

Project description

Overview / Installation

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) <>`_


- **python** (2.7 or 3.5+, `python <>`_)
- **numpy** (`numpy <>`_)
- **python headers** (under ubuntu, install the package *python-dev* or *python-devel*)

- *fortran* compiler (tested with **gfortran**. `gcc <>`_)
- **openmp** (usually comes with fortran. `openmp <>`_)
- **f2py** (comes with **numpy**. `link <>`_)

Optional Python packages
- **scipy** >= v0.17.0, lower versions supported with restrictions (*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 <>`_)
- **pathos** (for multi-threaded generalized propagator operations. `pathos <>`_)
- **pytables** (v3.x recommended. For hdf5 saving/loading of simulations. `pytables <>`_)
- **PaGMO / PyGMO** (version 2.4+. *Required* for the **EO** submodule. `pagmo <>`_)
- **pycuda** (tested with version 2018.1, for GPU-based matrix inversion. `pyCUDA <>`_)
- **scikit-cuda** (tested with version 0.5, for GPU-based matrix inversion. `scikit-cuda <>`_)

(all available via `pip <>`_)

Installation under linux

Via pip

Install from pypi repository via

.. code-block:: bash

$ 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:

.. code-block:: bash

$ python install

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

.. code-block:: bash

$ python install --prefix=/some/specific/location

To only compile without installation, use

.. code-block:: bash

$ python build

Manual compilation

1. clone git:

.. code-block:: bash

$ git clone

2. compile fortran parts:

.. code-block:: bash

$ 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:

.. code-block:: bash

export PATH


Installation under windows

For windows, we also recommend `Anaconda <>`_ in which pyGDM can be installed easily via pip. See also the MacOS X instructions, but you can skip all steps for installing the gcc compilers, since the windows version of pyGDM comes as pre-compiled binary package.

Via pip

We provide a 64bit windows binary on the pypi repository (tested on Win7 and Win10). Install via

.. code-block:: bash

$ pip install pygdm2

Compile using the Anaconda distribution (tested with anaconda3)

1. get the repo (e.g. download from gitlab)

2. install gcc compiler:

.. code-block:: bash

$ conda install m2w64-toolchain libpython

3. compile fortran parts:

.. code-block:: bash

$ python build

4. install:

.. code-block:: bash

$ python install

Installation under Mac OS X

Using the Anaconda distribution

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 (Here the example of python2. python3 was not tested on OSX so far):

.. code-block:: bash

$ 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:

.. code-block:: bash

$ source activate python2
$ xcode-select --install
$ conda install pip
$ conda install gcc
$ pip install pygdm2

Also make sure you have the latest versions of numpy and scipy:

.. code-block:: bash

$ pip install numpy scipy --upgrade

Without Anaconda

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

.. code-block:: bash

$ python install --no-openmp


Python code
- P\. R. Wiecha

Fortran code
- C\. Girard
- A\. Arbouet
- R\. Marty
- P\. R. Wiecha

Project details

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