From 90ad1d6026d3c4b557970d6cc7626e85195ca4dc Mon Sep 17 00:00:00 2001 From: Marnik Bercx Date: Sun, 4 Jun 2023 09:20:15 +0200 Subject: [PATCH] Docs: Small improvements to "Installation" page Several small improvments to the Get started, installation page: 1. Improved use of MyST substitutions. 2. Fix instructions for `localhost` computer setup by adding the `workdir` option. Although using `AIIDA_PATH` in the `workdir` was considered, in the end `~/aiida_work_dir` was chosen since this should always work and is straightforward to use and find. 3. The filepath executable for the `pw.x` code is simply set to `pw.x`, as an absolute path is no longer necessary since `aiida-core==2.3`. A note is added for users that want to specify a different binary. --- docs/source/installation/index.md | 40 ++++++++++++++++++------------- 1 file changed, 24 insertions(+), 16 deletions(-) diff --git a/docs/source/installation/index.md b/docs/source/installation/index.md index 3fd244f51..0efba8ad6 100644 --- a/docs/source/installation/index.md +++ b/docs/source/installation/index.md @@ -3,7 +3,8 @@ myst: substitutions: SSSP: Standard Solid-State Pseudopotentials (SSSP) aiida-pseudo: '`aiida-pseudo`' - pip: '`pip`' + pip: '[`pip`](https://pip.pypa.io/en/stable/index.html)' + PyPI: '[PyPI](https://pypi.org/)' --- # Get started @@ -23,22 +24,22 @@ Please refer to the [documentation](https://aiida.readthedocs.io/projects/aiida- ## Installation -The Python package can be installed from the Python Package index [PyPI](https://pypi.org/) or directly from the source: +The Python package can be installed from the Python Package index {{ PyPI }} or directly from the source: ::::{tab-set} :::{tab-item} PyPI -The recommended method of installation is to use the Python package manager `pip`: +The recommended method of installation is to use the Python package manager {{ pip }}: ```console $ pip install aiida-quantumespresso ``` -This will install the latest stable version that was released to PyPI. +This will install the latest stable version that was released to {{ PyPI }}. ::: :::{tab-item} Source -To install the package from source, first clone the repository and then install using `pip`: +To install the package from source, first clone the repository and then install using {{ pip }}: ```console $ git clone https://github.com/aiidateam/aiida-quantumespresso @@ -108,10 +109,10 @@ In this example, we will set up the `localhost`, the computer where AiiDA itself To set up a computer, use the ``verdi`` CLI of ``aiida-core``. ```console -$ verdi computer setup -n -L localhost -H localhost -T core.local -S core.direct +$ verdi computer setup -n -L localhost -H localhost -T core.local -S core.direct -w ~/aiida_work_dir ``` -After creating the localhost computer, configure it using: +After creating the localhost computer, configure the `core.local` transport using: ```console $ verdi computer configure core.local localhost -n --safe-interval 0 @@ -126,17 +127,18 @@ $ verdi computer test localhost :::{tab-item} API -To setup a computer using the Python API, run the following code in a Python script or interactive shell: +To setup a computer using the Python API, run the following code in a Python script with `verdi run` or in the `verdi` shell: ```python - from aiida.orm import Computer +from pathlib import Path computer = Computer( label='localhost', hostname='localhost', transport_type='core.local', - scheduler_type='core.direct' + scheduler_type='core.direct', + workdir=Path('~/aiida_work_dir').resolve() ).store() computer.configure() ``` @@ -160,23 +162,22 @@ In this example, we will setup the `pw.x` code that is installed on the computer To setup a particular Quantum ESPRESSO code, use the ``verdi`` CLI of ``aiida-core``. ```console -$ verdi code create core.code.installed -n --computer localhost --label pw --default-calc-job-plugin quantumespresso.pw --filepath-executable /path/to/pw.x +$ verdi code create core.code.installed -n --computer localhost --label pw --default-calc-job-plugin quantumespresso.pw --filepath-executable pw.x ``` ::: :::{tab-item} API -To setup particular Quantum ESPRESSO code using the Python API, run the following code in a Python script or interactive shell: +To setup particular Quantum ESPRESSO code using the Python API, run the following code in a Python script with `verdi run` or in the `verdi` shell: ```python - from aiida.orm import InstalledCode computer = load_computer('localhost') code = InstalledCode( label='pw', computer=computer, -filepath_executable='/path/to/pw.x', +filepath_executable='pw.x', default_calc_job_plugin='quantumespresso.pw', ).store() ``` @@ -185,14 +186,21 @@ default_calc_job_plugin='quantumespresso.pw', :::: :::{important} -Make sure to replace `/path/to/pw.x` with the actual absolute path to the `pw.x` binary. +Using the commands above, you will set up a code that uses the first `pw.x` binary your `PATH`. +You can find out the absolute path to this binary using the `which` command: + +```console +which pw.x +``` + +If this is not the Quantum ESPRESSO version you want to run, pass the correct absolute path as the filepath executable. ::: For more detailed information, please refer to the documentation [on setting up codes](https://aiida.readthedocs.io/projects/aiida-core/en/latest/howto/run_codes.html#how-to-setup-a-code). (installation-setup-pseudopotentials)= -### Pseudopotentials +### Pseudo potentials Many Quantum ESPRESSO codes require pseudo potentials. The simplest way of installing these is through the `aiida-pseudo` plugin package.