Installation

The installation on a Linux system is split into four simple parts:

Download and extract the source file

Download the newest release TheoDORE_v.s.tgz from the github releases page.

Extract the source file

tar -xf TheoDORE_v.s.tgz

Setup the path specification

To use TheoDORE the PATH and PYTHONPATH variables have to be adjusted. For this purpose you can use the provided bash script setpaths.bash

#!/bin/bash
export THEODIR=/yourpath/TheoDORE/TheoDORE_v.s
export PATH=$THEODIR/bin:$PATH
export PYTHONPATH=$THEODIR:$PYTHONPATH

Note: PYTHONPATH no longer points to the lib directory starting in TheoDORE_2.0.

Copy the above lines into your .bashrc file or run:

source setpaths.bash

Alternatively, a csh script setpaths.csh is provided.

Python3

TheoDORE 3 is compatible with python3 (ideally >3.7). No compatibility to python2 is maintained.

The older release, TheoDORE 2.4, is still compatible with python v2.7.14.

External packages

The following external packages are used by TheoDORE and require a separate installation:

python3-numpy - for basic numerical manipulations

python3-matplotlib (optional) - for plotting of graphs

python3-openbabel (optional) - for extended file-parsing capabilities of molecular structure files

ORBKIT (optional) - For creating cube files of densities

The first three are usually readily available with the standard installation tools, e.g. apt-get, yum etc. Alternatively, they may be downloaded from the URLs specified. If no integrated installation is performed, then it is necessary to add these libraries to the PYTHONPATH (see above). For ORBKIT, you can try

cd $THEODIR/external/orbkit
python3 setup.py build_ext --inplace

Otherwise, please follow the ORBKIT installation instructions.

The following external packages are provided along with the TheoDORE distribution and do not require installation.

cclib - for file parsing work

periodictable - information about periodic table (needed by cclib)

colt - user interface

Using anaconda

A straightforward and universal way of installing most of the required packages is through the use of Anaconda.

First download the anaconda distribution and do the installation. Then run the commands:

conda install numpy matplotlib
conda install -c openbabel openbabel

Testing

The tests are invoked with pytest-3. In the EXAMPLES directory run (depending on the packages you want to test)

pytest-3 UTILS STANDARD CCLIB
pytest-3 EXTRA

The first three tests should always work. For all tests in EXTRA to pass openbabel, ADF and ORBKIT need to be installed.

The tests are distributed within the standard TheoDORE distribution. They are maintained via the theodore-test repository.