Installation#
The atomistics package is a pure python code, which can be installed either via the Python Package Index (pypi) or via
the conda package manager. Still the atomistics package only contains interfaces to the corresponding simulation
codes, not the simulation codes itself. Consequently, an installation via the conda package manager is recommended as
it allows to install many opensource simulation codes in the same environment as the atomistics package without the
need to compile the simulation code manually. The conda packages for these simulation codes are maintained by the
developers of the atomistics package in collaboration with the developers of the corresponding simulation codes.
conda-based Installation#
For the conda-based installation both the atomistics package as well as the corresponding simulation codes are
distributed via the conda-forge community channel. By specifying the option -c conda-forge
the conda package manager installs the dependencies from the conda-forge community channel.
conda install -c conda-forge atomistics
As the atomistics package depends on the Atomic Simulation Environment the effective
medium theory potential simulation code EMT is automatically
installed with the basic installation of the atomistics package. In the following the simulation codes are sorted in
alphabetical order:
Abinit#
Abinit - Plane wave density functional theory:
conda install -c conda-forge abinit
GPAW#
GPAW - Density functional theory Python code based on the projector-augmented wave method:
conda install -c conda-forge gpaw
LAMMPS#
LAMMPS - Molecular Dynamics:
conda install -c conda-forge lammps pylammpsmpi jinja2 pandas iprpy-data
In addition to the conda package for the LAMMPS simulation code the interface in the
atomistics package uses the pylammpsmpi, jinja2
templates, the pandas DataFrames to represent interatomic potentials, and finally it can
leverage the NIST database for interatomic potentials via the iprpy-data
package, which includes a wide range of interatomic potentials. The iprpy-data package is optional.
Quantum Espresso#
Quantum Espresso - Integrated suite of Open-Source computer codes for electronic-structure calculations:
conda install -c conda-forge qe
To support the structure optimization inside quantum espresso the pwtools are required as output parser:
conda install -c conda-forge pwtools
Finally, the Standard solid-state pseudopotentials (SSSP) can also be installed via conda-forge using:
conda install -c conda-forge sssp
To use these inside quantum espresso, the ESPRESSO_PSEUDO environment variable has to be set to:
export ESPRESSO_PSEUDO=${PREFIX}/share/sssp
Siesta#
Siesta - Electronic structure calculations and ab initio molecular dynamics:
conda install -c conda-forge siesta
Phonopy#
Phonopy - open source package for phonon calculations at harmonic and quasi-harmonic levels:
conda install -c phonopy seekpath structuretoolkit
pypi-based Installation#
While the conda-based installation is recommended, it is also possible to install the atomistics package via the
Python Package Index:
pip install atomistics
As the atomistics package depends on the Atomic Simulation Environment the effective
medium theory potential simulation code EMT is automatically
installed with the basic installation of the atomistics package.
Beyond the basic installation of the atomistics package it is also possible to install the extra requirements for
specific simulation codes directly from the Python Package Index. It is important to mention that apart from the
GPAW simulation code, the simulation codes are not distributed via the Python Package
Index, so they have to be installed separately.
GPAW#
GPAW - Density functional theory Python code based on the projector-augmented wave method
pip install atomistics[gpaw]
LAMMPS#
LAMMPS - Molecular Dynamics:
pip install atomistics[lammps]
Phonopy#
Phonopy - open source package for phonon calculations at harmonic and quasi-harmonic levels:
pip install atomistics[phonopy]