Commit a11e9ab5 authored by Lauri Himanen's avatar Lauri Himanen
Browse files

Removed duplicate phonon parser example.

parent 1677ffcb
......@@ -46,7 +46,7 @@ class EncyclopediaNormalizer(Normalizer):
orig_volume = repr_system.get_volume() * (1e-10)**3
calculation.atomic_density = float(orig_n_atoms / orig_volume)
# NOTE: Enc specific visualization
# NOTE: Does not exist?
def get_atomistic_structure(self) -> None:
pass
......
# control file used to get the finite displacements in the phonon calculations
xc pw-lda
relativistic atomic_zora scalar
k_grid 12 12 12
# Slightly overconverged kp, would need 10.05
sc_accuracy_rho 1E-6
sc_accuracy_eev 1E-4
sc_accuracy_etot 1E-6
sc_accuracy_forces 1E-4
sc_iter_limit 100
occupation_type gaussian 0.01
mixer pulay
n_max_pulay 10
charge_mix_param 0.4
phonon displacement 0.01
phonon supercell -1 1 1 1 -1 1 1 1 -1
phonon frequency_units cm^-1
# phonon cv 0 800 801 200
phonon dos 0 800 800 1 50
phonon free_energy 0 1200 1200 50
phonon band 0 0 0 0.00 0.25 0.25 100 Gamma Delta
phonon band 0.00 0.25 0.25 0 0.5 0.5 100 Delta X
phonon band 0 0.5 0.5 0.25 0.50 0.75 100 X W
phonon band 0.25 0.50 0.75 0.375 0.375 0.75 100 W K
phonon band 0.375 0.375 0.75 0 0 0 100 K Gamma
phonon band 0 0 0 0.25 0.25 0.25 100 Gamma Lambda
phonon band 0.25 0.25 0.25 0.5 0.5 0.5 100 Lambda L
################################################################################
#
# FHI-aims code project
# VB, Fritz-Haber Institut, 2009
#
# Suggested "light" defaults for Ge atom (to be pasted into control.in file)
# Be sure to double-check any results obtained with these settings for post-processing,
# e.g., with the "tight" defaults and larger basis sets.
#
################################################################################
species Ge
# global species definitions
nucleus 32
mass 72.64
#
l_hartree 4
#
cut_pot 3.5 1.5 1.0
basis_dep_cutoff 1e-4
#
radial_base 54 5.0
radial_multiplier 1
angular_grids specified
division 0.0947 110
division 0.1314 194
division 0.7746 302
# division 0.8710 434
# division 0.9770 590
# division 1.1356 770
# division 2.6430 974
# outer_grid 974
outer_grid 302
################################################################################
#
# Definition of "minimal" basis
#
################################################################################
# valence basis states
valence 4 s 2.
valence 4 p 2.
valence 3 d 10.
# ion occupancy
ion_occ 4 s 1.
ion_occ 4 p 1.
ion_occ 3 d 10.
################################################################################
#
# Suggested additional basis functions. For production calculations,
# uncomment them one after another (the most important basis functions are
# listed first).
#
# Constructed for dimers: 1.80 A, 2.00 A, 2.35 A, 3.00 A, 4.00 A
#
################################################################################
# "First tier" - improvements: -329.04 meV to -37.61 meV
hydro 2 p 1.4
hydro 3 d 4.3
# hydro 4 f 7.4
hydro 3 s 3.4
# "Second tier" - improvements: -13.91 meV to -1.23 meV
# hydro 5 g 10.8
# hydro 3 d 2.5
# hydro 3 p 3.3
# hydro 4 f 12
# hydro 6 h 15.6
# hydro 3 s 7.2
# "Third tier" - improvements: -1.47 meV to -0.40 meV
# hydro 3 d 5.8
# hydro 4 f 4.3
# hydro 5 g 11.6
# hydro 5 s 14.8
# hydro 4 p 3.9
# "Fourth tier" -improvements: -0.39 meV to -0.11 meV
# hydro 4 f 23.2
# hydro 2 s 6.2
# hydro 5 d 9.8
# hydro 5 p 6
# hydro 6 h 14.8
# Further functions - -0.13 meV and below
# hydro 5 f 9.6
lattice_vector 0 2.82000 2.82000
lattice_vector 2.82000 0 2.82000
lattice_vector 2.82000 2.82000 0
atom 0 0 0 Ge
atom 1.4100000000 1.4100000000 1.4100000000 Ge
# control file used to get the finite displacements in the phonon calculations
xc pw-lda
relativistic atomic_zora scalar
k_grid 12 12 12
# Slightly overconverged kp, would need 10.05
sc_accuracy_rho 1E-6
sc_accuracy_eev 1E-4
sc_accuracy_etot 1E-6
sc_accuracy_forces 1E-4
sc_iter_limit 100
occupation_type gaussian 0.01
mixer pulay
n_max_pulay 10
charge_mix_param 0.4
phonon displacement 0.01
phonon supercell -1 1 1 1 -1 1 1 1 -1
phonon frequency_units cm^-1
# phonon cv 0 800 801 200
phonon dos 0 800 800 1 50
phonon free_energy 0 1200 1200 50
phonon band 0 0 0 0.00 0.25 0.25 100 Gamma Delta
phonon band 0.00 0.25 0.25 0 0.5 0.5 100 Delta X
phonon band 0 0.5 0.5 0.25 0.50 0.75 100 X W
phonon band 0.25 0.50 0.75 0.375 0.375 0.75 100 W K
phonon band 0.375 0.375 0.75 0 0 0 100 K Gamma
phonon band 0 0 0 0.25 0.25 0.25 100 Gamma Lambda
phonon band 0.25 0.25 0.25 0.5 0.5 0.5 100 Lambda L
################################################################################
#
# FHI-aims code project
# VB, Fritz-Haber Institut, 2009
#
# Suggested "light" defaults for Ge atom (to be pasted into control.in file)
# Be sure to double-check any results obtained with these settings for post-processing,
# e.g., with the "tight" defaults and larger basis sets.
#
################################################################################
species Ge
# global species definitions
nucleus 32
mass 72.64
#
l_hartree 4
#
cut_pot 3.5 1.5 1.0
basis_dep_cutoff 1e-4
#
radial_base 54 5.0
radial_multiplier 1
angular_grids specified
division 0.0947 110
division 0.1314 194
division 0.7746 302
# division 0.8710 434
# division 0.9770 590
# division 1.1356 770
# division 2.6430 974
# outer_grid 974
outer_grid 302
################################################################################
#
# Definition of "minimal" basis
#
################################################################################
# valence basis states
valence 4 s 2.
valence 4 p 2.
valence 3 d 10.
# ion occupancy
ion_occ 4 s 1.
ion_occ 4 p 1.
ion_occ 3 d 10.
################################################################################
#
# Suggested additional basis functions. For production calculations,
# uncomment them one after another (the most important basis functions are
# listed first).
#
# Constructed for dimers: 1.80 A, 2.00 A, 2.35 A, 3.00 A, 4.00 A
#
################################################################################
# "First tier" - improvements: -329.04 meV to -37.61 meV
hydro 2 p 1.4
hydro 3 d 4.3
# hydro 4 f 7.4
hydro 3 s 3.4
# "Second tier" - improvements: -13.91 meV to -1.23 meV
# hydro 5 g 10.8
# hydro 3 d 2.5
# hydro 3 p 3.3
# hydro 4 f 12
# hydro 6 h 15.6
# hydro 3 s 7.2
# "Third tier" - improvements: -1.47 meV to -0.40 meV
# hydro 3 d 5.8
# hydro 4 f 4.3
# hydro 5 g 11.6
# hydro 5 s 14.8
# hydro 4 p 3.9
# "Fourth tier" -improvements: -0.39 meV to -0.11 meV
# hydro 4 f 23.2
# hydro 2 s 6.2
# hydro 5 d 9.8
# hydro 5 p 6
# hydro 6 h 14.8
# Further functions - -0.13 meV and below
# hydro 5 f 9.6
# geometry.in for FHI-aims
# | generated by phonopy.FHIaims.write_aims()
lattice_vector 5.6399999999999988 0.0000000000000000 0.0000000000000000
lattice_vector 0.0000000000000000 5.6399999999999988 0.0000000000000000
lattice_vector 0.0000000000000000 0.0000000000000000 5.6399999999999988
atom 0.0100000000000000 0.0000000000000000 0.0000000000000000 Ge
atom 5.6399999999999988 2.8199999999999994 2.8199999999999994 Ge
atom 2.8199999999999994 0.0000000000000000 2.8199999999999994 Ge
atom 2.8199999999999990 2.8199999999999994 0.0000000000000000 Ge
atom 1.4099999999999995 1.4099999999999997 1.4099999999999997 Ge
atom 1.4099999999999993 4.2299999999999986 4.2299999999999986 Ge
atom 4.2299999999999986 1.4099999999999997 4.2299999999999986 Ge
atom 4.2299999999999986 4.2299999999999986 1.4099999999999997 Ge
......@@ -73,7 +73,7 @@ def molecular_dynamics() -> Encyclopedia:
@pytest.fixture
def phonon() -> Encyclopedia:
parser_name = "parsers/phonopy"
filepath = "tests/data/normalizers/encyclopedia/phonopy_bulk_phonon/phonopy-FHI-aims-displacement-01/control.in"
filepath = "tests/data/parsers/phonopy/phonopy-FHI-aims-displacement-01/control.in"
backend = parse_file((parser_name, filepath))
backend = run_normalize(backend)
enc = backend.get_mi2_section(Encyclopedia.m_def)
......
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