aiida-user-addons (probably should be rename to something else)

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.

Requirements

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.

Command line tools

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...

Additional VASP workflows

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 on castep.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.

Related codes

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.

Additional Scheduler plugins

sgenodetail: SGE scheduler plugin that omits the detailed_job_info retrieval which can be slow on high-throughput cluster due to the large size of the accoutring file.

Installation

Recommend to install in the editable mode to allow any changes to be applied immediately (after daemon restart, of course):

pip install -e .

Required package version

Development version of aiida-vasp should be used.

Usage

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.

leslie-zheng/aiida-user-addons