mirror of https://github.com/abinit/abipy.git
Add run_gkq
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gmatteo
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386264f889
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name: AbiPy linting
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on: [push, pull_request]
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jobs:
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build:
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runs-on: ubuntu-latest
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strategy:
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max-parallel: 4
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matrix:
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python-version: [3.7]
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steps:
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- uses: actions/checkout@v1
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v1
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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#- name: Lint with pycodestyle
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# run: |
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# pip install pycodestyle
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# pycodestyle abipy
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#- name: Lint with mypy
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# run: |
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# pip install mypy
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# mypy abipy
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- name: Lint with flake8
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run: |
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pip install flake8
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# stop the build if there are Python syntax errors or undefined names
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flake8 --count --show-source --statistics abipy
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# exit-zero treats all errors as warnings.
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flake8 --count --exit-zero --max-complexity=20 --statistics abipy
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- name: Lint with pylint
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run: |
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pip install pylint
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# stop the build if there are Python syntax errors or undefined names
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pylint --exit-zero abipy
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name: AbiPy testing
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on: [push, pull_request]
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jobs:
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build:
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strategy:
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max-parallel: 6
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matrix:
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os: [ubuntu-latest]
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python-version: [3.7]
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runs-on: ${{ matrix.os }}
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steps:
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- uses: actions/checkout@v1
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v1
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install binary dependencies (Linux)
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if: matrix.os == 'ubuntu-latest'
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run: |
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wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh;
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bash miniconda.sh -b -p ${HOME}/miniconda
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export PATH="${HOME}/miniconda/bin:${PATH}"
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hash -r
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conda config --set always_yes yes --set changeps1 yes
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conda update -q conda
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# Useful for debugging any issues with conda
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conda info -a
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# Replace dep1 dep2 ... with your dependencies
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conda create -q -n test-environment python=${{ matrix.python-version }}
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source activate test-environment
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- name: Install Python dependencies
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run: |
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python -m pip install --upgrade pip
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pip install -r requirements.txt
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pip install -r requirements-optional.txt
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- name: Test with pytest
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run: |
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pip install -e .
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pytest abipy
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#!/usr/bin/env python
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r"""
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Flow for computing e-ph matrix elements along a q-path
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======================================================
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This example shows how to compute the phonon band structure of AlAs with AbiPy flows.
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The final results (out_DDB, out_DVDB) will be produced automatically at the end of the run
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and saved in ``flow_phonons/outdata/``.
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"""
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import sys
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import os
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import abipy.abilab as abilab
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import abipy.data as abidata
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from abipy import flowtk
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def make_scf_input(ngkpt):
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"""
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This function constructs the input file for the GS calculation:
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"""
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structure = abidata.structure_from_ucell("AlAs")
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pseudos = abidata.pseudos("13al.981214.fhi", "33as.pspnc")
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gs_inp = abilab.AbinitInput(structure, pseudos=pseudos)
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gs_inp.set_vars(
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nband=6,
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ecut=6.0,
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ngkpt=ngkpt,
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nshiftk=1,
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shiftk=[0, 0, 0],
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tolvrs=1.0e-10,
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)
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return gs_inp
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def build_flow(options):
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"""
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Create a `Flow` for phonon calculations. The flow has two works.
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The first work contains a single GS task that produces the WFK file used in DFPT
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Then we have multiple Works that are generated automatically
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in order to compute the dynamical matrix on a [2, 2, 2] mesh.
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Symmetries are taken into account: only q-points in the IBZ are generated and
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for each q-point only the independent atomic perturbations are computed.
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"""
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# Working directory (default is the name of the script with '.py' removed and "run_" replaced by "flow_")
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if not options.workdir:
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__file__ = os.path.join(os.getcwd(), "run_gkq.py")
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options.workdir = os.path.basename(__file__).replace(".py", "").replace("run_", "flow_")
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# Use 2x2x2 both for k-mesh and q-mesh
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# Build input for GS calculation
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scf_input = make_scf_input(ngkpt=(2, 2, 2))
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# Create flow to compute all the independent atomic perturbations
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# corresponding to a [4, 4, 4] q-mesh.
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# Electric field and Born effective charges are also computed.
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from abipy.flowtk.eph_flows import GkqPathFlow
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ngqpt = (2, 2, 2)
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#qpath_list = [[0.01, 0, 0], [0.02, 0, 0], [0.24, 0, 0], [0.45, 0, 0]]
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qpath_list = [[0.0, 0.0, 0.0], [0.01, 0, 0], [0.1, 0, 0],
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[0.24, 0, 0], [0.3, 0, 0], [0.45, 0, 0], [0.5, 0.0, 0.0]]
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flow = GkqPathFlow.from_scf_input(options.workdir, scf_input,
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ngqpt, qpath_list, ndivsm=0, with_becs=True)
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return flow
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# This block generates the thumbnails in the Abipy gallery.
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# You can safely REMOVE this part if you are using this script for production runs.
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if os.getenv("READTHEDOCS", False):
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__name__ = None
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import tempfile
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options = flowtk.build_flow_main_parser().parse_args(["-w", tempfile.mkdtemp()])
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build_flow(options).graphviz_imshow()
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@flowtk.flow_main
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def main(options):
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"""
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This is our main function that will be invoked by the script.
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flow_main is a decorator implementing the command line interface.
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Command line args are stored in `options`.
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"""
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return build_flow(options)
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if __name__ == "__main__":
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sys.exit(main())
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############################################################################
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#
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# Run the script with:
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#
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# run_phonons.py -s
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#
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# then use:
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#
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# abirun.py flow_phonons history
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#
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# to get the list of actions perfomed by AbiPy to complete the flow.
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# Note how the ``PhononWork`` has merged all the partial DDB files produced by the PhononTasks
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#
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# .. code-block:: bash
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#
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# ===================================================================================================================================
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# ====================================== <PhononWork, node_id=241274, workdir=flow_phonons/w1> ================================
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# ===================================================================================================================================
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# [Thu Dec 7 22:55:02 2017] Finalized set to True
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# [Thu Dec 7 22:55:02 2017] Will call mrgddb to merge [ .... ]
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#
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# Now open the final DDB file with:
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#
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# abiopen.py flow_phonons/outdata/out_DDB
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#
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# and invoke anaddb to compute the phonon band structure and the phonon DOS with:
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#
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# .. code-block:: ipython
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#
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# In [1]: phbst_file, phdos_file = abifile.anaget_phbst_and_phdos_files()
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# In [2]: %matplotlib
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# In [3]: phbst_file.plot_phbands()
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#
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# .. image:: https://github.com/abinit/abipy_assets/blob/master/run_phonons.png?raw=true
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# :alt: Phonon band structure of AlAs.
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#
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