Some (personal) addons to AiiDA to help my research. Mainly focusing using VASP through aiida-vasp
and also some workflows for CASTEP are also included.
For phonon calculation the
aiida-phonopy
package needs to be at commit d410a9a309ff45d4c25a9b24bcaf06b65f0c4f1a.
https://github.com/aiida-phonopy/aiida-phonopy/commit/d410a9a309ff45d4c25a9b24bcaf06b65f0c4f1a
for magnetic material, a patched versions might be needed: https://github.com/zhubonan/aiida-phonopy/commit/7cfe9d357348606ea4914e935beb282e573f2e22
For aiida-core>2.0.1
is needed.
The aiida-vasp
should be at the development version.
A recent version aiida-castep
is needed.
vasp-dryrun
is a tool to dryrun VASP calculations. It can obtain key information such as the number of kpoints and bands for working out the best parallelisation strategy.
Usage: vasp-dryrun [OPTIONS]
A simple tool to dryrun a VASP calculation. The calculation will be run
for up to <timeout> seconds. The underlying VASP process will be
terminated once it enters the main loop, which is signalled by the
appearance of a `INWAV` keyword in the OUTCAR.
Options:
--input-dir DIRECTORY Where the VASP input is, default to the current
working directory. [default: .]
--vasp-exe TEXT Executable for VASP [default: vasp_std]
--timeout INTEGER Timeout in seconds to terminate VASP [default: 10]
--work-dir TEXT Working directory for running
--keep Wether to the dryrun files [default: False]
--help Show this message and exit.
This package acts as a plugin for aiida-core
and provides workflows and other functionalities.
The command line interface is integrated with verdi
, additional commands are available under verdi data addons
:
Usage: verdi data addons [OPTIONS] COMMAND [ARGS]...
Entry point for commands under aiida-user-addons
Options:
-h, --help Show this message and exit.
Commands:
check-nelm Perform a sweep to check if any VaspCalculation have...
export_relax Export a VASP relaxation workflow
export_vasp Export a VASP calculation, works for both `VaspCalculation`...
remotecat Print the content of a remote file to STDOUT This command...
remotepull Pull a calculation folder from the remote This command for...
remotetail Follow a file on the remote computer This command will...
The main entry point has the vaspu
prefix:
vaspu.relax
:VaspRelaxWorkChain
with additional check and bug fixes.vaspu.converge
: A simpler convergence testing workchain that runs tests in parallel.vaspu.vasp
: Almost as the original one, used by other workchains.vaspu.bands
: Includes pre-relaxation of the input structure with more functionalities such as dealing with AFM spin arrangement. Based oncastep.bands
.vaspu.hybrid_bands
: Run band structure calculations normal calculations with zero-weighted kpoints. Useful if hybrid functional is used.vaspu.phonopy
: Fully automated Phonon workflow from initial relaxation to final bandstructure/thermal properties.vaspu.magnetic
: Magnetic enumeration workflow for finding lowest energy magnetic states.vaspu.delithiate
: Workchain for delithiate structures and performing relaxation.vaspu.voltage_curve
: Workchain for constructing voltage curve upon delithiation of certain lithiated structure.
This package also provide some convenient routine for the following packages:
- pymatgen: Routines for acquiring structures from Materials Project.
- sumo: Used for plotting band structures and density of states.
- hiphive: Minimum wrapper for generating MC rattled structures.
- clease: For depositing/extracting structures stored in its database.
- phonopy: Used for phonon calculations (vasp). Existing phonon workchains can be exported as files.
sgenodetail
: SGE scheduler plugin that omits thedetailed_job_info
retrieval which can be slow on high-throughput cluster due to the large size of the accoutring file.
Recommend to install in the editable mode to allow any changes to be applied immediately (after daemon restart, of course):
pip install -e .
Development version of aiida-vasp
should be used.
Custom workflows are registered as entry points, so WorkflowFactory('vaspu.relax')
will load the relaxation workflow.
Check the outputs of verdi plugin list aiida.workflows
to see the workflows available.
Example notebooks can be found in the example_notebooks
folder.