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# fmt: off
"""Test file for exciting ASE calculator."""
import xml.etree.ElementTree as ET
import numpy as np
import pytest
import ase
import ase.calculators.exciting.exciting
import ase.calculators.exciting.runner
# Note this is an imitation of an exciting INFO.out output file.
# We've removed many of the lines of text that were originally in this outfile
# that are note usefule for testing purposes to save space in this file.
# We've also modified the file to contain a Ti atom and use an HCP cell to
# make the test more interesting since the HCP cell gives non-symmetric cell
# vectors in a cartesian basis set.
LDA_VWN_AR_INFO_OUT = """
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Starting initialization +
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Lattice vectors (cartesian) :
10.3360193975 10.3426010725 0.0054547264
-10.3461511392 10.3527307290 0.0059928210
10.3354645037 10.3540072605 20.6246241525
Reciprocal lattice vectors (cartesian) :
0.3039381122 0.3039214341 -0.3048853768
-0.3036485697 0.3034554311 -0.0001760382
0.0000078456 -0.0001685540 0.3047255253
Unit cell volume : 4412.7512103067
Brillouin zone volume : 0.0562121456
Species : 1 (Ti)
parameters loaded from : Ti.xml
name : titanium
atomic positions (lattice) :
1 : 0.00000000 0.00000000 0.00000000
Total number of atoms per unit cell : 1
Spin treatment : spin-unpolarised
Number of Bravais lattice symmetries : 48
Number of crystal symmetries : 48
k-point grid : 1 1 1
Total number of k-points : 1
k-point set is reduced with crystal symmetries
R^MT_min * |G+k|_max (rgkmax) : 10.00000000
Species with R^MT_min : 1 (Ti)
Maximum |G+k| for APW functions : 1.66666667
Maximum |G| for potential and density : 7.50000000
Polynomial order for pseudochg. density : 9
G-vector grid sizes : 36 36 36
Total number of G-vectors : 23871
Maximum angular momentum used for
APW functions : 8
computing H and O matrix elements : 4
potential and density : 4
inner part of muffin-tin : 2
Total nuclear charge : -22.00000000
Total electronic charge : 22.00000000
Total core charge : 18.00000000
Total valence charge : 4.00000000
Effective Wigner radius, r_s : 3.55062021
Number of empty states : 5
Total number of valence states : 10
Maximum Hamiltonian size : 263
Maximum number of plane-waves : 251
Total number of local-orbitals : 12
Exchange-correlation type : 100
libxc; exchange: Slater exchange; correlation: Vosko, Wilk & Nusair (VWN5)
Smearing scheme : Gaussian
Smearing width : 0.00100000
Using multisecant Broyden potential mixing
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Ending initialization +
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ SCF iteration number : 1 +
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Total energy : -527.82493279
_______________________________________________________________
Fermi energy : -0.20111449
Kinetic energy : 530.56137212
Coulomb energy : -1029.02167746
Exchange energy : -27.93377198
Correlation energy : -1.43085548
Sum of eigenvalues : -305.07886015
Effective potential energy : -835.64023227
Coulomb potential energy : -796.81322609
xc potential energy : -38.82700618
Hartree energy : 205.65681157
Electron-nuclear energy : -1208.12684923
Nuclear-nuclear energy : -26.55163980
Madelung energy : -630.61506441
Core-electron kinetic energy : 0.00000000
DOS at Fermi energy (states/Ha/cell) : 0.00000000
Electron charges :
core : 10.00000000
core leakage : 0.00000000
valence : 8.00000000
interstitial : 0.00183897
charge in muffin-tin spheres :
atom 1 Ar : 17.99816103
total charge in muffin-tins : 17.99816103
total charge : 18.00000000
Estimated fundamental gap : 0.36071248
valence-band maximum at 1 0.0000 0.0000 0.0000
conduction-band minimum at 1 0.0000 0.0000 0.0000
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
| Convergency criteria checked for the last 2 iterations +
| Convergence targets achieved. Performing final SCF iteration +
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Total energy : -527.81796101
_______________________________________________________________
Fermi energy : -0.20044598
Kinetic energy : 530.57303096
Coulomb energy : -1029.02642037
Exchange energy : -27.93372809
Correlation energy : -1.43084350
Sum of eigenvalues : -305.07413840
Effective potential energy : -835.64716936
Coulomb potential energy : -796.82023455
xc potential energy : -38.82693481
Hartree energy : 205.65454603
Electron-nuclear energy : -1208.12932661
Nuclear-nuclear energy : -26.55163980
Madelung energy : -630.61630310
Core-electron kinetic energy : 0.00000000
DOS at Fermi energy (states/Ha/cell) : 0.00000000
Electron charges :
core : 10.00000000
core leakage : 0.00000000
valence : 8.00000000
interstitial : 0.00184037
charge in muffin-tin spheres :
atom 1 Ar : 17.99815963
total charge in muffin-tins : 17.99815963
total charge : 18.00000000
Estimated fundamental gap : 0.36095838
valence-band maximum at 1 0.0000 0.0000 0.0000
conduction-band minimum at 1 0.0000 0.0000 0.0000
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Self-consistent loop stopped +
| EXCITING NITROGEN-14 stopped =
"""
@pytest.fixture()
def nitrogen_trioxide_atoms():
"""Pytest fixture that creates ASE Atoms cell for other tests."""
return ase.Atoms('NO3',
cell=[[2, 2, 0], [0, 4, 0], [0, 0, 6]],
scaled_positions=[(0, 0, 0), (0.25, 0.25, 0),
(0, 0, 0.75), (0.5, 0.5, 0.5)],
pbc=True)
def test_ground_state_template_init(excitingtools):
"""Test initialization of the ExcitingGroundStateTemplate class."""
gs_template_obj = (
ase.calculators.exciting.exciting.ExcitingGroundStateTemplate())
assert gs_template_obj.name == 'exciting'
assert len(gs_template_obj.implemented_properties) == 2
assert 'energy' in gs_template_obj.implemented_properties
def test_ground_state_template_write_input(
tmp_path, nitrogen_trioxide_atoms, excitingtools):
"""Test the write input method of ExcitingGroundStateTemplate.
We test is by writing a ground state calculation and a bandstructure
calculation after that is run.
Args:
tmp_path: This tells pytest to create a temporary directory
in which we will store the exciting input file.
nitrogen_trioxide_atoms: pytest fixture to create ASE Atoms
unit cell composed of NO3.
"""
from excitingtools.input.bandstructure import (
band_structure_input_from_ase_atoms_obj,
)
expected_path = tmp_path / 'input.xml'
# Expected number of points in the bandstructure.
expected_number_of_special_points = 12
bandstructure_steps = 100
binary_path = tmp_path / 'exciting_binary'
gs_template_obj = (
ase.calculators.exciting.exciting.ExcitingGroundStateTemplate())
exciting_profile = ase.calculators.exciting.exciting.ExcitingProfile(
command=str(binary_path))
gs_template_obj.write_input(
profile=exciting_profile,
directory=tmp_path,
atoms=nitrogen_trioxide_atoms,
parameters={
'title': None,
'species_path': tmp_path,
'ground_state_input': {
'rgkmax': 8.0,
'do': 'fromscratch',
"ngridk": [6, 6, 6],
'xctype': 'GGA_PBE_SOL',
'vkloff': [0, 0, 0]},
'properties_input': {
'bandstructure': band_structure_input_from_ase_atoms_obj(
nitrogen_trioxide_atoms, steps=bandstructure_steps)}})
# Let's assert the file we just wrote exists.
assert expected_path.exists()
# Let's assert it's what we expect.
element_tree = ET.parse(expected_path)
# Ensure the coordinates of the atoms in the unit cell is correct.
# We could test the other parts of the input file related coming from
# the ASE Atoms object like species data but this is tested already in
# test/io/exciting/test_exciting.py.
coords_list = element_tree.findall('./structure/species/atom')
positions = np.array([[float(x)
for x in coords_list[i].get('coord').split()]
for i in range(len(coords_list))])
assert positions == pytest.approx(
nitrogen_trioxide_atoms.get_scaled_positions())
# Ensure that the exciting calculator properites (e.g. functional type have
# been set).
assert element_tree.findall('input') is not None
assert element_tree.getroot().tag == 'input'
assert element_tree.getroot()[2].attrib['xctype'] == 'GGA_PBE_SOL'
assert element_tree.getroot()[2].attrib['rgkmax'] == '8.0'
# Ensure the bandstructure path is correct:
band_path = element_tree.findall(
'./properties/bandstructure/plot1d/path')[0]
assert band_path.tag == 'path'
assert int(band_path.get('steps')) == bandstructure_steps
assert len(list(band_path)) == expected_number_of_special_points
def test_ground_state_template_read_results(tmp_path, excitingtools):
"""Test the read result method of ExcitingGroundStateTemplate."""
# ASE doesn't want us to store any other files for test, so instead
# we copy an example exciting INFO.out file into the global variable
# LDA_VWN_AR_INFO_OUT.
output_file_path = tmp_path / 'info.xml'
with open(output_file_path, "w", encoding="utf8") as xml_file:
xml_file.write(LDA_VWN_AR_INFO_OUT)
gs_template_obj = (
ase.calculators.exciting.exciting.ExcitingGroundStateTemplate())
results = gs_template_obj.read_results(tmp_path)
final_scl_iteration = list(results["scl"].keys())[-1]
assert pytest.approx(float(results["scl"][
final_scl_iteration]["Hartree energy"])) == 205.65454603
def test_get_total_energy_and_bandgap(excitingtools):
"""Test getter methods for energy/bandgap results."""
# Create a fake results dictionary that has two SCL cycles
# and only contains values for the total energy and bandgap.
results_dict = {
'scl': {
'1':
{
'Total energy': '-240.3',
'Estimated fundamental gap': 2.0,
},
'2':
{
'Total energy': '-242.3',
'Estimated fundamental gap': 3.1,
}
}
}
results_obj = ase.calculators.exciting.exciting.ExcitingGroundStateResults(
results_dict)
assert pytest.approx(results_obj.total_energy()) == -242.3
assert pytest.approx(results_obj.band_gap()) == 3.1
def test_ground_state_calculator_init(tmpdir, excitingtools):
"""Test initiliazation of the ExcitingGroundStateCalculator"""
ground_state_input_dict = {
"rgkmax": 8.0,
"do": "fromscratch",
"ngridk": [6, 6, 6],
"xctype": "GGA_PBE_SOL",
"vkloff": [0, 0, 0]}
calc_obj = ase.calculators.exciting.exciting.ExcitingGroundStateCalculator(
runner=ase.calculators.exciting.runner.SimpleBinaryRunner(
"exciting_serial", ['./'], 1, tmpdir, ['']),
ground_state_input=ground_state_input_dict, directory=tmpdir)
assert calc_obj.parameters["ground_state_input"]["rgkmax"] == 8.0
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