Phonons with WFQ files (q-mesh denser than k-mesh)¶
This example shows how to use WFQ files to compute phonons on a q-mesh
that is not necessarily commensurate with the k-mesh used for electrons.
Symmetries are taken into account: only q-points in the IBZ are generated.
Moreover WFQ files are computed only if k + q does not belong to the initial mesh and,
for each q-point, only the independent atomic perturbations are computed.
The final results (out_DDB, out_DVDB) will be produced automatically at the end of the run
and saved in the
outdata/ of the work.
import sys import os import abipy.abilab as abilab import abipy.data as abidata from abipy import flowtk def make_scf_input(paral_kgb=0): """ This function constructs the input file for the GS calculation: """ # Crystalline AlAs: computation of the second derivative of the total energy structure = abidata.structure_from_ucell("AlAs") pseudos = abidata.pseudos("13al.981214.fhi", "33as.pspnc") gs_inp = abilab.AbinitInput(structure, pseudos=pseudos) gs_inp.set_vars( nband=4, ecut=2.0, ngkpt=[2, 2, 2], nshiftk=1, shiftk=[0, 0, 0], #nshiftk=4, #shiftk=[0.0, 0.0, 0.5, # This gives the usual fcc Monkhorst-Pack grid # 0.0, 0.5, 0.0, # 0.5, 0.0, 0.0, # 0.5, 0.5, 0.5], paral_kgb=paral_kgb, tolvrs=1.0e-10, diemac=9.0, ) return gs_inp def build_flow(options): """ Create a `Flow` for phonon calculations. The flow has two works. """ # Working directory (default is the name of the script with '.py' removed and "run_" replaced by "flow_") if not options.workdir: options.workdir = os.path.basename(sys.argv).replace(".py", "").replace("run_", "flow_") flow = flowtk.Flow(workdir=options.workdir) # Build input for GS calculation and create first work with 1 ScfTask. scf_input = make_scf_input() work = flow.register_scf_task(scf_input) scf_task = work # Create work for phonon calculation with WFQ files with a [4, 4, 4] q-mesh. # Electric field and Born effective charges are also computed. wfkq_work = flowtk.PhononWfkqWork.from_scf_task(scf_task, ngqpt=[4, 4, 4], with_becs=True) flow.register_work(wfkq_work) return flow # This block generates the thumbnails in the AbiPy gallery. # You can safely REMOVE this part if you are using this script for production runs. if os.getenv("READTHEDOCS", False): __name__ = None import tempfile options = flowtk.build_flow_main_parser().parse_args(["-w", tempfile.mkdtemp()]) build_flow(options).graphviz_imshow() @flowtk.flow_main def main(options): """ This is our main function that will be invoked by the script. flow_main is a decorator implementing the command line interface. Command line args are stored in `options`. """ return build_flow(options) if __name__ == "__main__": sys.exit(main())
Run the script with:
abirun.py flow_phonons_wkq history
to get the list of actions perfomed by AbiPy to complete the flow.
Note how the
PhononWfkqWork has merged all the partial DDB/DVDB files
and removed the WFQ files at runtime to optimize the disk space.
========================================================================================================================= ============================= <PhononWfkqWork, node_id=360036, workdir=flow_phonons_wkq/w1> ============================= ========================================================================================================================= [Tue Sep 18 00:04:18 2018] Removing WFQ: flow_phonons_wkq/w1/t5/outdata/out_WFQ [Tue Sep 18 00:04:54 2018] Removing WFQ: flow_phonons_wkq/w1/t14/outdata/out_WFQ
Now open the final DDB file with:
and invoke anaddb to compute the phonon band structure and the phonon DOS with:
In : phbst_file, phdos_file = abifile.anaget_phbst_and_phdos_files() In : %matplotlib In : phbst_file.plot_phbands()
Total running time of the script: ( 0 minutes 1.770 seconds)