Get started#
Requirements#
To work with aiida-phonopy
, you should have:
installed
aiida-core
.configured an AiiDA profile.
Please refer to the
documentation
of aiida-core
for detailed instructions.
Installation#
The Python package can be installed from the Python Package Index (PyPI) or directly from the source:
The recommended method of installation is to use the Python package manager pip
:
$ pip install aiida-phonopy
This will install the latest stable version that was released to the PyPI.
To install the package from source, first clone the repository and then install using pip
:
$ git clone https://github.com/aiida-phonopy/aiida-phonopy
$ pip install -e aiida-phonopy
The -e
flag will install the package in editable mode, meaning that changes to the source code will be automatically picked up.
Setup#
Computer#
To run Phonopy calculations on a compute resource, the computer should first be set up in AiiDA.
This can be done from the command line interface (CLI) or the Python application programming interface (API).
In this example, we will set up the localhost
, the computer where AiiDA itself is running:
To set up a computer, use the verdi
CLI of aiida-core
.
$ verdi computer setup -n -L localhost -H localhost -T core.local -S core.direct -w $AIIDA_PATH/workdir
After creating the localhost computer, configure the core.local
transport using:
$ verdi computer configure core.local localhost -n --safe-interval 0
Verify that the computer was properly setup by running:
$ verdi computer test localhost
To setup a computer using the Python API, run the following code in a Python script with verdi run
or in the verdi
shell:
from aiida.orm import Computer
from pathlib import Path
computer = Computer(
label='localhost',
hostname='localhost',
transport_type='core.local',
scheduler_type='core.direct',
workdir=Path('$AIIDA_PATH/workdir').absolute().as_posix()
).store()
computer.configure()
For more detailed information, please refer to the documentation on setting up compute resources.
Note
The computer workdir
is where AiiDA will run the calculations for codes set up for this computer.
The commands above will set the workdir
of the localhost
computer in $AIIDA_PATH/workdir
.
Code#
To run a Phonopy code, it should first be setup in AiiDA.
This can be done from the command line interface (CLI) or the Python application programming interface (API).
In this example, we will setup the phonopy
code that is installed on the computer where AiiDA is running:
To setup a particular Phonopy code, use the verdi
CLI of aiida-core
.
$ verdi code create core.code.installed -n --computer localhost --label phonopy --default-calc-job-plugin phonopy.phonopy --filepath-executable $(which phonopy)
To set up the Phonopy code using the Python API, run the following code in a Python script with verdi run
or in the verdi
shell:
from aiida.orm import InstalledCode
import shutil
computer = load_computer('localhost')
code = InstalledCode(
label='phonopy',
computer=computer,
filepath_executable=shutil.which('phonopy'),
default_calc_job_plugin='phonopy.phonopy',
).store()
Important
The CLI command and Python script above will automatically find the first phonopy
binary in your PATH
directories using the which
command:
which phonopy
If you have installed phonopy
in a different python environment, make sure to pass the correct filepath to the executable and activate the environment correctly.
The latter can be done by adding the required commands to the preprend_text
of the code.
For more detailed information, please refer to the documentation on setting up codes.