Note
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FOO BAR
Flow to compute with finite differences.
Finite electric field calculation of AlP at clamped atomic positions
Here the polarization of the cell is computed as a function of increasing external homogeneous electric field.
berryopt 4 is used to trigger the finite field calculation, while the efield variable sets the strength (in atomic units) and direction of the field
Based on tutorespfn/Input/tpolarization_6.abi
Downloading repository from: https://github.com/PseudoDojo/ONCVPSP-PBE-PDv0.4/archive/refs/heads/master.zip ...
Installing ONCVPSP-PBE-SR-PDv0.4 in: /home/runner/.abinit/pseudos/ONCVPSP-PBE-SR-PDv0.4
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Validating md5 checksums of ONCVPSP-PBE-SR-PDv0.4...
Checksum test: OK
Installation completed successfully in 16.10 [s]
import sys
import os
import abipy.flowtk as flowtk
from abipy.core.structure import Structure
from abipy.abio.inputs import AbinitInput
from abipy.flowtk.works import PhononWork
from abipy.flowtk.dfpt_works import ElasticWork
from abipy.flowtk.finitediff import FiniteEfieldWork, FiniteDisplWork, FiniteStrainWork, FiniteHfieldWork
def build_flow(options):
# Set 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[0]).replace(".py", "").replace("run_", "flow_")
structure = Structure.from_abistring("""
# Definition of the unit cell
acell 3*7.2728565836E+00
rprim
0.0000000000E+00 7.0710678119E-01 7.0710678119E-01
7.0710678119E-01 0.0000000000E+00 7.0710678119E-01
7.0710678119E-01 7.0710678119E-01 0.0000000000E+00
natom 2 # two atoms in the cell
typat 1 2 # type 1 is Phosphorous, type 2 is Aluminum (order defined by znucl above and pseudos list)
# Definition of the atom types and pseudopotentials
ntypat 2 # two types of atoms
znucl 15 13 # the atom types are Phosphorous and Aluminum
#atomic positions, given in units of the cell vectors. Thus as the cell vectors
#change due to strain the atoms will move as well.
xred
1/4 1/4 1/4
0 0 0
""")
# Get NC pseudos from pseudodojo.
from abipy.flowtk.psrepos import get_oncvpsp_pseudos
pseudos = get_oncvpsp_pseudos(xc_name="PBE", version="0.4",
relativity_type="SR", accuracy="standard")
#nband 4
# nband is restricted here to the number of filled bands only, no empty bands. The theory of
# the Berrys phase polarization formula assumes filled bands only. Our pseudopotential choice
# includes 5 valence electrons on P, 3 on Al, for 8 total in the primitive unit cell, hence
# 4 filled bands.
scf_input = AbinitInput(structure, pseudos)
num_ele = scf_input.num_valence_electrons
scf_input.set_vars(
ecut=5,
nband=4,
tolvrs=1.0e-8,
nstep=100, # Maximal number of SCF cycles
ecutsm=0.5,
dilatmx=1.05,
paral_kgb=0,
)
shiftk = [0.5, 0.5, 0.5,
0.5, 0.0, 0.0,
0.0, 0.5, 0.0,
0.0, 0.0, 0.5,
]
scf_input.set_kmesh(ngkpt=[6, 6, 6], shiftk=shiftk)
#scf_input.set_kmesh(ngkpt=[1, 1, 1], shiftk=[0, 0, 0])
# Initialize the flow.
flow = flowtk.Flow(workdir=options.workdir, manager=options.manager)
fd_accuracy = 2 # 3 points
#fd_accuracy = 4 # 5 points
relax_ions = True
relax_ions_opts = None
flow.register_work(FiniteEfieldWork.from_scf_input(
scf_input,
fd_accuracy=fd_accuracy,
step_au=0.0001,
relax_ions=relax_ions,
relax_ions_opts=relax_ions_opts,
))
#flow.register_work(FiniteDisplWork.from_scf_input(
# scf_input,
# fd_accuracy=fd_accuracy,
# step_au=0.01,
# extra_abivars=dict(berryopt=-1), # This to compute the polarization at E = 0
#))
flow.register_work(FiniteStrainWork.from_scf_input(
scf_input,
fd_accuracy=fd_accuracy,
norm_step=0.005,
shear_step=0.03,
extra_abivars=dict(berryopt=-1), # This to compute the polarization at E = 0
relax_ions=relax_ions,
relax_ions_opts=relax_ions_opts,
))
#flow.register_work(FiniteHfieldWork.from_scf_input(
# scf_input,
# fd_accuracy=fd_accuracy,
# step_au=0.01,
# relax_ions=relax_ions,
# relax_ions_opts=relax_ions_opts,
#))
#flow.register_work(PhononWork.from_scf_input(scf_input,
# qpoints=[0, 0, 0],
# is_ngqpt=False,
# with_becs=True,
# with_quad=False,
# with_flexoe=False,
# with_dvdb=False,
# tolerance=None,
# ddk_tolerance=None
#))
flow.register_work(ElasticWork.from_scf_input(scf_input,
with_relaxed_ion=True,
with_piezo=True,
with_dde=False,
tolerances=None
))
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())
Total running time of the script: (0 minutes 18.288 seconds)