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|
# fmt: off
"""Quantum ESPRESSO file parsers.
Implemented:
* Input file (pwi)
* Output file (pwo) with vc-relax
"""
import io
import numpy as np
import pytest
import ase.build
import ase.io
from ase import Atoms
from ase.calculators.calculator import compare_atoms
from ase.constraints import FixAtoms, FixCartesian, FixScaled
from ase.io.espresso import (
get_atomic_species,
parse_position_line,
read_espresso_in,
read_fortran_namelist,
write_espresso_in,
write_fortran_namelist,
)
from ase.units import create_units
# This file is parsed correctly by pw.x, even though things are
# scattered all over the place with some namelist edge cases
pw_input_text = """
&CONTrol
prefix = 'surf_110_H2_md'
calculation = 'md'
restart_mode = 'from_scratch'
pseudo_dir = '.'
outdir = './surf_110_!H2_m=d_sc,ratch/'
verbosity = 'default'
tprnfor = .true.
tstress = .True.
! disk_io = 'low'
wf_collect = .false.
max_seconds = 82800
forc_con!v_thr = 1e-05
etot_conv_thr = 1e-06
dt = 41.3 , /
&SYSTEM ecutwfc = 63, ecutrho = 577, ibrav = 0,
nat = 8, ntyp = 2, occupations = 'smearing',
smearing = 'marzari-vanderbilt',
degauss = 0.01, nspin = 2, ! nosym = .true. ,
starting_magnetization(2) = 5.12 /
&ELECTRONS
electron_maxstep = 300
mixing_beta = 0.1
conv_thr = 1d-07
mixing_mode = 'local-TF'
scf_must_converge = False
/
&IONS
ion_dynamics = 'verlet'
ion_temperature = 'rescaling'
tolp = 50.0
tempw = 500.0
/
ATOMIC_SPECIES
H 1.008 H.pbe-rrkjus_psl.0.1.UPF
Fe 55.845 Fe.pbe-spn-rrkjus_psl.0.2.1.UPF
K_POINTS automatic
2 2 2 1 1 1
CELL_PARAMETERS angstrom
5.6672000000000002 0.0000000000000000 0.0000000000000000
0.0000000000000000 8.0146311006808038 0.0000000000000000
0.0000000000000000 0.0000000000000000 27.0219466510212101
ATOMIC_POSITIONS angstrom
Fe 0.0000000000 0.0000000000 0.0000000000 0 0 0
Fe 1.4168000000 2.0036577752 -0.0000000000 0 0 0
Fe 0.0000000000 2.0036577752 2.0036577752 0 0 0
Fe 1.4168000000 0.0000000000 2.0036577752 0 0 0
Fe 0.0000000000 0.0000000000 4.0073155503
Fe 1.4168000000 2.0036577752 4.0073155503
H 0.0000000000 2.0036577752 6.0109733255
H 1.4168000000 0.0000000000 6.0109733255
"""
# Trimmed to only include lines of relevance
pw_output_text = """
Program PWSCF v.5.3.0 (svn rev. 11974) starts on 19May2016 at 7:48:12
This program is part of the open-source Quantum ESPRESSO suite
for quantum simulation of materials; please cite
"P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
URL http://www.quantum-espresso.org",
in publications or presentations arising from this work. More details at
http://www.quantum-espresso.org/quote
...
bravais-lattice index = 0
lattice parameter (alat) = 5.3555 a.u.
unit-cell volume = 155.1378 (a.u.)^3
number of atoms/cell = 3
number of atomic types = 2
number of electrons = 33.00
number of Kohn-Sham states= 21
kinetic-energy cutoff = 144.0000 Ry
charge density cutoff = 1728.0000 Ry
convergence threshold = 1.0E-10
mixing beta = 0.1000
number of iterations used = 8 plain mixing
Exchange-correlation = PBE ( 1 4 3 4 0 0)
nstep = 50
celldm(1)= 5.355484 celldm(2)= 0.000000 celldm(3)= 0.000000
celldm(4)= 0.000000 celldm(5)= 0.000000 celldm(6)= 0.000000
crystal axes: (cart. coord. in units of alat)
a(1) = ( 1.000000 0.000000 0.000000 )
a(2) = ( 0.000000 1.010000 0.000000 )
a(3) = ( 0.000000 0.000000 1.000000 )
...
Cartesian axes
site n. atom positions (alat units)
1 Fe tau( 1) = ( 0.0000000 0.0000000 0.0000000 )
2 Fe tau( 2) = ( 0.5000000 0.5050000 0.5000000 )
3 H tau( 3) = ( 0.5000000 0.5050000 0.0000000 )
...
Magnetic moment per site:
atom: 1 charge: 10.9188 magn: 1.9476 constr: 0.0000
atom: 2 charge: 10.9402 magn: 1.5782 constr: 0.0000
atom: 3 charge: 0.8835 magn: -0.0005 constr: 0.0000
total cpu time spent up to now is 125.3 secs
End of self-consistent calculation
Number of k-points >= 100: set verbosity='high' to print the bands.
the Fermi energy is 19.3154 ev
! total energy = -509.83425823 Ry
Harris-Foulkes estimate = -509.83425698 Ry
estimated scf accuracy < 8.1E-11 Ry
The total energy is the sum of the following terms:
one-electron contribution = -218.72329117 Ry
hartree contribution = 130.90381466 Ry
xc contribution = -70.71031046 Ry
ewald contribution = -351.30448923 Ry
smearing contrib. (-TS) = 0.00001797 Ry
total magnetization = 4.60 Bohr mag/cell
absolute magnetization = 4.80 Bohr mag/cell
convergence has been achieved in 23 iterations
negative rho (up, down): 0.000E+00 3.221E-05
Forces acting on atoms (Ry/au):
atom 1 type 2 force = 0.00000000 0.00000000 0.00000000
atom 2 type 2 force = 0.00000000 0.00000000 0.00000000
atom 3 type 1 force = 0.00000000 0.00000000 0.00000000
Total force = 0.000000 Total SCF correction = 0.000000
entering subroutine stress ...
negative rho (up, down): 0.000E+00 3.221E-05
total stress (Ry/bohr**3) (kbar) P= 384.59
0.00125485 0.00000000 0.00000000 184.59 0.00 0.00
0.00000000 0.00115848 0.00000000 0.00 170.42 0.00
0.00000000 0.00000000 0.00542982 0.00 0.00 798.75
BFGS Geometry Optimization
number of scf cycles = 1
number of bfgs steps = 0
enthalpy new = -509.8342582307 Ry
new trust radius = 0.0721468508 bohr
new conv_thr = 1.0E-10 Ry
new unit-cell volume = 159.63086 a.u.^3 ( 23.65485 Ang^3 )
CELL_PARAMETERS (angstrom)
2.834000000 0.000000000 0.000000000
0.000000000 2.945239106 0.000000000
0.000000000 0.000000000 2.834000000
ATOMIC_POSITIONS (angstrom)
Fe 0.000000000 0.000000000 0.000000000 0 0 0
Fe 1.417000000 1.472619553 1.417000000
H 1.417000000 1.472619553 0.000000000
...
Magnetic moment per site:
atom: 1 charge: 10.9991 magn: 2.0016 constr: 0.0000
atom: 2 charge: 11.0222 magn: 1.5951 constr: 0.0000
atom: 3 charge: 0.8937 magn: -0.0008 constr: 0.0000
total cpu time spent up to now is 261.2 secs
End of self-consistent calculation
Number of k-points >= 100: set verbosity='high' to print the bands.
the Fermi energy is 18.6627 ev
! total energy = -509.83806077 Ry
Harris-Foulkes estimate = -509.83805972 Ry
estimated scf accuracy < 1.3E-11 Ry
The total energy is the sum of the following terms:
one-electron contribution = -224.15358901 Ry
hartree contribution = 132.85863781 Ry
xc contribution = -70.66684834 Ry
ewald contribution = -347.87622740 Ry
smearing contrib. (-TS) = -0.00003383 Ry
total magnetization = 4.66 Bohr mag/cell
absolute magnetization = 4.86 Bohr mag/cell
convergence has been achieved in 23 iterations
negative rho (up, down): 0.000E+00 3.540E-05
Forces acting on atoms (Ry/au):
atom 1 type 2 force = 0.00000000 0.00000000 0.00000000
atom 2 type 2 force = 0.00000000 0.00000000 0.00000000
atom 3 type 1 force = 0.00000000 0.00000000 0.00000000
Total force = 0.000000 Total SCF correction = 0.000000
entering subroutine stress ...
negative rho (up, down): 0.000E+00 3.540E-05
total stress (Ry/bohr**3) (kbar) P= 311.25
0.00088081 0.00000000 0.00000000 129.57 0.00 0.00
0.00000000 0.00055559 0.00000000 0.00 81.73 0.00
0.00000000 0.00000000 0.00491106 0.00 0.00 722.44
number of scf cycles = 2
number of bfgs steps = 1
...
Begin final coordinates
CELL_PARAMETERS (angstrom)
2.834000000 0.000000000 0.000000000
0.000000000 2.945239106 0.000000000
0.000000000 0.000000000 2.834000000
ATOMIC_POSITIONS (angstrom)
Fe 0.000000000 0.000000000 0.000000000 0 0 0
Fe 1.417000000 1.472619553 1.417000000
H 1.417000000 1.472619553 0.000000000
End final coordinates
"""
pw_output_cell = """
Program PWSCF v.7.4 starts on 30Dec2024 at 16:10:39
bravais-lattice index = 0
lattice parameter (alat) = 7.2558 a.u.
unit-cell volume = 270.1072 (a.u.)^3
number of atoms/cell = 2
number of atomic types = 1
number of electrons = 8.00
number of Kohn-Sham states= 8
kinetic-energy cutoff = 30.0000 Ry
charge density cutoff = 240.0000 Ry
scf convergence threshold = 1.0E-08
mixing beta = 0.3500
number of iterations used = 8 local-TF mixing
energy convergence thresh.= 1.0E+00
force convergence thresh. = 1.0E-03
press convergence thresh. = 1.5E+02
Exchange-correlation= PBE
( 1 4 3 4 0 0 0)
nstep = 50
celldm(1)= 7.255773 celldm(2)= 0.000000 celldm(3)= 0.000000
celldm(4)= 0.000000 celldm(5)= 0.000000 celldm(6)= 0.000000
crystal axes: (cart. coord. in units of alat)
a(1) = ( 0.000000 0.707107 0.707107 )
a(2) = ( 0.707107 0.000000 0.707107 )
a(3) = ( 0.707107 0.707107 0.000000 )
reciprocal axes: (cart. coord. in units 2 pi/alat)
b(1) = ( -0.707107 0.707107 0.707107 )
b(2) = ( 0.707107 -0.707107 0.707107 )
b(3) = ( 0.707107 0.707107 -0.707107 )
Cartesian axes
site n. atom positions (alat units)
1 Si tau( 1) = ( 0.0000000 0.0000000 0.0000000 )
2 Si tau( 2) = ( 0.3535534 0.3535534 0.3535534 )
number of k points= 1 Gaussian smearing, width (Ry)= 0.0010
cart. coord. in units 2pi/alat
k( 1) = ( 0.0000000 0.0000000 0.0000000), wk = 2.0000000
End of self-consistent calculation
k = 0.0000 0.0000 0.0000 ( 375 PWs) bands (ev):
-4.9573 7.1990 7.1990 7.1991 9.4854 9.4854 9.4854 10.6559
the Fermi energy is 8.8063 ev
! total energy = -21.58743321 Ry
estimated scf accuracy < 1.5E-09 Ry
smearing contrib. (-TS) = -0.00000000 Ry
internal energy E=F+TS = -21.58743321 Ry
The total energy is F=E-TS. E is the sum of the following terms:
one-electron contribution = 6.13011013 Ry
hartree contribution = 1.69362248 Ry
xc contribution = -12.61222208 Ry
ewald contribution = -16.79894374 Ry
convergence has been achieved in 11 iterations
Forces acting on atoms (cartesian axes, Ry/au):
atom 1 type 1 force = 0.00000000 0.00000000 0.00000000
atom 2 type 1 force = 0.00000000 0.00000000 0.00000000
Total force = 0.000000 Total SCF correction = 0.000007
Computing stress (Cartesian axis) and pressure
total stress (Ry/bohr**3) (kbar) P= 433
0.00294455 -0.00000000 -0.00000000 433.16 -0.00 -0.00
-0.00000000 0.00294455 -0.00000000 -0.00 433.16 -0.00
-0.00000000 -0.00000000 0.00294455 -0.00 -0.00 433.16
BFGS Geometry Optimization
Energy error = 1.6E-01 Ry
Gradient error = 0.0E+00 Ry/Bohr
Cell gradient error = 4.3E+02 kbar
number of scf cycles = 1
number of bfgs steps = 0
enthalpy new = -21.5874332073 Ry
new trust radius = 0.2419674028 bohr
new conv_thr = 0.0000000100 Ry
new unit-cell volume = 334.25681 a.u.^3 ( 49.53175 Ang^3 )
density = 1.88308 g/cm^3
CELL_PARAMETERS (angstrom)
-0.000000000 2.914861274 2.914861274
2.914861274 -0.000000000 2.914861274
2.914861274 2.914861274 -0.000000000
ATOMIC_POSITIONS (angstrom)
Si 0.0000000000 0.0000000000 0.0000000000
Si 1.4574306371 1.4574306371 1.4574306371
End of self-consistent calculation
k = 0.0000 0.0000 0.0000 ( 375 PWs) bands (ev):
-5.7174 5.0283 5.0283 5.0283 6.2048 7.2660 7.2660 7.2660
the Fermi energy is 5.7451 ev
! total energy = -21.70179088 Ry
estimated scf accuracy < 3.1E-09 Ry
smearing contrib. (-TS) = -0.00000000 Ry
internal energy E=F+TS = -21.70179088 Ry
The total energy is F=E-TS. E is the sum of the following terms:
one-electron contribution = 4.44939949 Ry
hartree contribution = 1.82078558 Ry
xc contribution = -12.32487369 Ry
ewald contribution = -15.64710226 Ry
convergence has been achieved in 7 iterations
Forces acting on atoms (cartesian axes, Ry/au):
atom 1 type 1 force = 0.00000000 0.00000000 -0.00000000
atom 2 type 1 force = 0.00000000 0.00000000 -0.00000000
Total force = 0.000000 Total SCF correction = 0.000001
Computing stress (Cartesian axis) and pressure
total stress (Ry/bohr**3) (kbar) P= 133
0.00090960 0.00000000 0.00000000 133.81 0.00 0.00
-0.00000000 0.00090960 0.00000000 -0.00 133.81 0.00
0.00000000 0.00000000 0.00090960 0.00 0.00 133.81
Energy error = 1.1E-01 Ry
Gradient error = 1.0E-23 Ry/Bohr
Cell gradient error = 1.3E+02 kbar
bfgs converged in 2 scf cycles and 1 bfgs steps
(criteria: energy < 1.0E+00 Ry, force < 1.0E-03 Ry/Bohr, cell < 1.5E+02
End of BFGS Geometry Optimization
Final enthalpy = -21.7017908769 Ry
File XXX/tmp-quacc-2024-12-30-15-09-59-202291-63636/pwscf.bfgs deleted, as
Begin final coordinates
new unit-cell volume = 334.25681 a.u.^3 ( 49.53175 Ang^3 )
density = 1.88308 g/cm^3
CELL_PARAMETERS (angstrom)
-0.000000000 2.914861274 2.914861274
2.914861274 -0.000000000 2.914861274
2.914861274 2.914861274 -0.000000000
ATOMIC_POSITIONS (angstrom)
Si 0.0000000000 0.0000000000 0.0000000000
Si 1.4574306371 1.4574306371 1.4574306371
End final coordinates
bravais-lattice index = 0
lattice parameter (alat) = 7.2558 a.u.
unit-cell volume = 334.2568 (a.u.)^3
number of atoms/cell = 2
number of atomic types = 1
number of electrons = 8.00
number of Kohn-Sham states= 8
kinetic-energy cutoff = 30.0000 Ry
charge density cutoff = 240.0000 Ry
scf convergence threshold = 1.0E-08
mixing beta = 0.3500
number of iterations used = 8 local-TF mixing
press convergence thresh. = 1.5E+02
Exchange-correlation= PBE
( 1 4 3 4 0 0 0)
celldm(1)= 7.255773 celldm(2)= 0.000000 celldm(3)= 0.000000
celldm(4)= 0.000000 celldm(5)= 0.000000 celldm(6)= 0.000000
crystal axes: (cart. coord. in units of alat)
a(1) = ( -0.000000 0.759160 0.759160 )
a(2) = ( 0.759160 -0.000000 0.759160 )
a(3) = ( 0.759160 0.759160 -0.000000 )
reciprocal axes: (cart. coord. in units 2 pi/alat)
b(1) = ( -0.658623 0.658623 0.658623 )
b(2) = ( 0.658623 -0.658623 0.658623 )
b(3) = ( 0.658623 0.658623 -0.658623 )
Cartesian axes
site n. atom positions (alat units)
1 Si tau( 1) = ( 0.0000000 0.0000000 0.0000000 )
2 Si tau( 2) = ( 0.3795798 0.3795798 0.3795798 )
number of k points= 1 Gaussian smearing, width (Ry)= 0.0010
cart. coord. in units 2pi/alat
k( 1) = ( 0.0000000 0.0000000 0.0000000), wk = 2.0000000
End of self-consistent calculation
k = 0.0000 0.0000 0.0000 ( 471 PWs) bands (ev):
-5.7176 5.0274 5.0274 5.0274 6.2042 7.2647 7.2647 7.2647
the Fermi energy is 5.7439 ev
! total energy = -21.70223615 Ry
estimated scf accuracy < 4.9E-10 Ry
smearing contrib. (-TS) = -0.00000000 Ry
internal energy E=F+TS = -21.70223615 Ry
The total energy is F=E-TS. E is the sum of the following terms:
one-electron contribution = 4.44893174 Ry
hartree contribution = 1.82082186 Ry
xc contribution = -12.32488755 Ry
ewald contribution = -15.64710220 Ry
convergence has been achieved in 9 iterations
Forces acting on atoms (cartesian axes, Ry/au):
atom 1 type 1 force = 0.00000000 0.00000000 0.00000000
atom 2 type 1 force = 0.00000000 0.00000000 0.00000000
Total force = 0.000000 Total SCF correction = 0.000002
Computing stress (Cartesian axis) and pressure
total stress (Ry/bohr**3) (kbar) P= 134
0.00091401 -0.00000000 -0.00000000 134.46 -0.00 -0.00
-0.00000000 0.00091401 -0.00000000 -0.00 134.46 -0.00
-0.00000000 -0.00000000 0.00091401 -0.00 -0.00 134.46
"""
def test_pw_input():
"""Read pw input file."""
with open('pw_input.pwi', 'w') as pw_input_f:
pw_input_f.write(pw_input_text)
pw_input_atoms = ase.io.read('pw_input.pwi', format='espresso-in')
assert len(pw_input_atoms) == 8
assert (pw_input_atoms.get_initial_magnetic_moments()
== pytest.approx([5.12, 5.12, 5.12, 5.12, 5.12, 5.12, 0., 0.]))
def test_get_atomic_species():
"""Parser for atomic species section"""
with open('pw_input.pwi', 'w') as pw_input_f:
pw_input_f.write(pw_input_text)
with open('pw_input.pwi') as pw_input_f:
data, card_lines = read_fortran_namelist(pw_input_f)
species_card = get_atomic_species(card_lines,
n_species=data['system']['ntyp'])
assert len(species_card) == 2
assert species_card[0] == (
"H", pytest.approx(1.008), "H.pbe-rrkjus_psl.0.1.UPF")
assert species_card[1] == (
"Fe", pytest.approx(55.845), "Fe.pbe-spn-rrkjus_psl.0.2.1.UPF")
def test_pw_output():
"""Read pw output file."""
with open('pw_output.pwo', 'w') as pw_output_f:
pw_output_f.write(pw_output_text)
pw_output_traj = ase.io.read('pw_output.pwo', index=':')
assert len(pw_output_traj) == 2
assert pw_output_traj[1].get_volume() > pw_output_traj[0].get_volume()
def test_pw_output_cell():
"""Read pw output file with cell optimization."""
with open('pw_output.pwo', 'w') as pw_output_f:
pw_output_f.write(pw_output_cell)
pw_output_traj = ase.io.read('pw_output.pwo', index=':')
assert len(pw_output_traj) == 3
units = create_units('2006')
expected_first_cell = units["Bohr"] * 7.255773 * np.array(
[[0.000000, 0.707107, 0.707107],
[0.707107, 0.000000, 0.707107],
[0.707107, 0.707107, 0.000000]]
)
expected_second_cell = np.array(
[[-0.000000, 2.914861274, 2.914861274],
[2.914861274, -0.000000, 2.914861274],
[2.914861274, 2.914861274, -0.000000]]
)
assert np.allclose(pw_output_traj[0].cell, expected_first_cell)
assert np.allclose(pw_output_traj[1].cell, expected_second_cell)
def test_pw_parse_line():
"""Parse a single position line from a pw.x output file."""
txt = """ 994 Pt tau( 994) = \
( 1.4749849 0.7329881 0.0719387 )
995 Sb tau( 995) = ( 1.4212023 0.7037863 0.1242640 )
996 Sb tau( 996) = ( 1.5430640 0.7699524 0.1700400 )
997 Sb tau( 997) = ( 1.4892815 0.7407506 0.2223653 )
998 Sb tau( 998) = ( 1.6111432 0.8069166 0.2681414 )
999 Sb tau( 999) = ( 1.5573606 0.7777148 0.3204667 )
1000 Sb tau(1000) = ( 1.6792223 0.8438809 0.3662427 )
1001 Sb tau(1001) = ( 1.6254398 0.8146791 0.4185680 )
1002 Sb tau(1002) = ( 1.7473015 0.8808452 0.4643440 )
1003 Sb tau(1003) = ( 1.6935189 0.8516434 0.5166693 )
"""
x_result = [1.4749849, 1.4212023, 1.5430640, 1.4892815, 1.6111432,
1.5573606, 1.6792223, 1.6254398, 1.7473015, 1.6935189]
y_result = [0.7329881, 0.7037863, 0.7699524, 0.7407506, 0.8069166,
0.7777148, 0.8438809, 0.8146791, 0.8808452, 0.8516434]
z_result = [0.0719387, 0.1242640, 0.1700400, 0.2223653, 0.2681414,
0.3204667, 0.3662427, 0.4185680, 0.4643440, 0.5166693]
for i, line in enumerate(txt.splitlines()):
sym, x, y, z = parse_position_line(line)
if i == 0:
assert sym == "Pt"
else:
assert sym == "Sb"
assert abs(x - x_result[i]) < 1e-7
assert abs(y - y_result[i]) < 1e-7
assert abs(z - z_result[i]) < 1e-7
def test_pw_results_required():
"""Check only configurations with results are read unless requested."""
with open('pw_output.pwo', 'w') as pw_output_f:
pw_output_f.write(pw_output_text)
# ignore 'final coordinates' with no results
pw_output_traj = ase.io.read('pw_output.pwo', index=':')
assert 'energy' in pw_output_traj[-1].calc.results
assert len(pw_output_traj) == 2
# include un-calculated final config
pw_output_traj = ase.io.read('pw_output.pwo', index=':',
results_required=False)
assert len(pw_output_traj) == 3
assert 'energy' not in pw_output_traj[-1].calc.results
# get default index=-1 with results
pw_output_config = ase.io.read('pw_output.pwo')
assert 'energy' in pw_output_config.calc.results
# get default index=-1 with no results "final coordinates'
pw_output_config = ase.io.read('pw_output.pwo', results_required=False)
assert 'energy' not in pw_output_config.calc.results
def test_pw_input_write():
"""Write a structure and read it back."""
bulk = ase.build.bulk('NiO', 'rocksalt', 4.813, cubic=True)
bulk.set_initial_magnetic_moments([2.2 if atom.symbol == 'Ni' else 0.0
for atom in bulk])
fh = 'espresso_test.pwi'
pseudos = {'Ni': 'potato', 'O': 'orange'}
write_espresso_in(fh, bulk, pseudopotentials=pseudos)
readback = read_espresso_in('espresso_test.pwi')
assert np.allclose(bulk.positions, readback.positions)
sections = {'system': {
'lda_plus_u': True,
'Hubbard_U(1)': 4.0,
'Hubbard_U(2)': 0.0}}
write_espresso_in(fh, bulk, sections, pseudopotentials=pseudos,
additional_cards=["test1", "test2", "test3"])
readback = read_espresso_in('espresso_test.pwi')
with open('espresso_test.pwi') as f:
_, cards = read_fortran_namelist(f)
assert "K_POINTS gamma" in cards
assert cards[-3] == "test1"
assert cards[-1] == "test3"
assert np.allclose(bulk.positions, readback.positions)
def test_pw_input_write_raw_kpts():
"""Write a structure and read it back."""
bulk = ase.build.bulk('NiO', 'rocksalt', 4.813, cubic=True)
bulk.set_initial_magnetic_moments([2.2 if atom.symbol == 'Ni' else 0.0
for atom in bulk])
fh = 'espresso_test.pwi'
pseudos = {'Ni': 'potato', 'O': 'orange'}
rng = np.random.RandomState(42)
kpts = rng.random((10, 4))
write_espresso_in(fh, bulk, pseudopotentials=pseudos, kpts=kpts)
readback = read_espresso_in('espresso_test.pwi')
assert np.allclose(bulk.positions, readback.positions)
sections = {'system': {
'lda_plus_u': True,
'Hubbard_U(1)': 4.0,
'Hubbard_U(2)': 0.0}}
write_espresso_in(fh, bulk, sections, pseudopotentials=pseudos,
additional_cards=["test1", "test2", "test3"],
kpts=kpts)
readback = read_espresso_in('espresso_test.pwi')
with open('espresso_test.pwi') as f:
_, cards = read_fortran_namelist(f)
assert "K_POINTS crystal" in cards
assert cards[5].startswith(f"{kpts[0, 0]:.12f}"[:10])
assert cards[6].startswith(f"{kpts[1, 0]:.12f}"[:10])
assert cards[-3] == "test1"
assert cards[-1] == "test3"
assert np.allclose(bulk.positions, readback.positions)
def test_pw_input_write_nested_flat():
"""Write a structure and read it back."""
bulk = ase.build.bulk('Fe')
fh = 'espresso_test.pwi'
pseudos = {'Fe': 'carrot'}
input_data = {"control": {"calculation": "scf"},
"unused_keyword1": "unused_value1",
"used_sections": {"used_keyword1": "used_value1"}
}
with pytest.raises(DeprecationWarning):
write_espresso_in(fh, bulk, input_data=input_data,
pseudopotentials=pseudos,
mixing_mode="local-TF")
write_espresso_in(fh, bulk, input_data=input_data,
pseudopotentials=pseudos,
unusedkwarg="unused")
with open(fh) as f:
new_atoms = read_espresso_in(f)
f.seek(0)
readback = read_fortran_namelist(f)
read_string = readback[0].to_string()
assert "&USED_SECTIONS\n" in read_string
assert " used_keyword1 = 'used_value1'\n" in read_string
assert np.allclose(bulk.positions, new_atoms.positions)
def test_write_fortran_namelist_any():
fd = io.StringIO()
input_data = {
"environ": {"environ_type": "vacuum"},
"electrostatic": {"tol": 1e-10, "mix": 0.5},
"boundary": {"solvent_mode": "full"}
}
additional_cards = [
"EXTERNAL_CHARGES (bohr)",
"-0.5 0. 0. 25.697 1.0 2 3",
"-0.5 0. 0. 20.697 1.0 2 3"
]
write_fortran_namelist(fd, input_data, additional_cards=additional_cards)
result = fd.getvalue()
expected = (
"&ENVIRON\n"
" environ_type = 'vacuum'\n"
"/\n"
"&ELECTROSTATIC\n"
" tol = 1e-10\n"
" mix = 0.5\n"
"/\n"
"&BOUNDARY\n"
" solvent_mode = 'full'\n"
"/\n"
"EXTERNAL_CHARGES (bohr)\n"
"-0.5 0. 0. 25.697 1.0 2 3\n"
"-0.5 0. 0. 20.697 1.0 2 3\n"
"EOF"
)
assert result == expected
assert "ENVIRON" in result
assert "ELECTROSTATIC" in result
assert "BOUNDARY" in result
assert result.endswith("EOF")
fd.seek(0)
reread = read_fortran_namelist(fd)
assert reread[1][:-1] == additional_cards
assert reread[0] == input_data
def test_write_fortran_namelist_pw():
fd = io.StringIO()
input_data = {
"calculation": "scf",
"ecutwfc": 30.0,
"ibrav": 0,
"nat": 10,
"nbnd": 8,
"conv_thr": 1e-6,
"random": True}
binary = "pw"
write_fortran_namelist(fd, input_data, binary)
result = fd.getvalue()
assert "scf" in result
assert "ibrav" in result
assert "conv_thr" in result
assert result.endswith("EOF")
fd.seek(0)
reread = read_fortran_namelist(fd)
assert reread != input_data
def test_write_fortran_namelist_fields():
fd = io.StringIO()
input_data = {
"INPUT": {
"amass": 28.0855,
"niter_ph": 50,
"tr2_ph": 1e-6,
"flfrc": "silicon.fc"},
}
binary = "q2r"
write_fortran_namelist(
fd,
input_data,
binary,
additional_cards="test1\ntest2\ntest3\n")
result = fd.getvalue()
expected = ("&INPUT\n"
" flfrc = 'silicon.fc'\n"
" amass = 28.0855\n"
" niter_ph = 50\n"
" tr2_ph = 1e-06\n"
"/\n"
"test1\n"
"test2\n"
"test3\n"
"EOF")
assert result == expected
def test_write_fortran_namelist_list_fields():
fd = io.StringIO()
input_data = {
"PRESS_AI": {
"amass": 28.0855,
"niter_ph": 50,
"tr2_ph": 1e-6,
"flfrc": "silicon.fc"},
}
binary = "cp"
write_fortran_namelist(
fd,
input_data,
binary,
additional_cards=[
"test1",
"test2",
"test3"])
result = fd.getvalue()
expected = ("&CONTROL\n"
"/\n"
"&SYSTEM\n"
"/\n"
"&ELECTRONS\n"
"/\n"
"&IONS\n"
"/\n"
"&CELL\n"
"/\n"
"&PRESS_AI\n"
" amass = 28.0855\n"
" niter_ph = 50\n"
" tr2_ph = 1e-06\n"
" flfrc = 'silicon.fc'\n"
"/\n"
"&WANNIER\n"
"/\n"
"test1\n"
"test2\n"
"test3\n"
"EOF")
assert result == expected
class TestConstraints:
"""Test if the constraint can be recovered when writing and reading.
Notes
-----
Linear constraints in the ATOMIC_POSITIONS block in the quantum ESPRESSO
`.pwi` format apply to Cartesian coordinates, regardless of whether the
atomic positions are written in the "angstrom" or the "crystal" units.
"""
# TODO: test also mask for FixCartesian
@staticmethod
def _make_atoms_ref():
"""water molecule"""
atoms = ase.build.molecule("H2O")
atoms.cell = 10.0 * np.eye(3)
atoms.pbc = True
atoms.set_initial_magnetic_moments(len(atoms) * [0.0])
return atoms
def _apply_write_read(self, constraint) -> Atoms:
atoms_ref = self._make_atoms_ref()
atoms_ref.set_constraint(constraint)
pseudopotentials = {
"H": "h_lda_v1.2.uspp.F.UPF",
"O": "o_lda_v1.2.uspp.F.UPF",
}
buf = io.StringIO()
write_espresso_in(buf, atoms_ref, pseudopotentials=pseudopotentials)
buf.seek(0)
atoms = read_espresso_in(buf)
assert not compare_atoms(atoms_ref, atoms)
print(atoms_ref.constraints, atoms.constraints)
return atoms
def test_fix_atoms(self):
"""Test FixAtoms"""
constraint = FixAtoms(indices=(1, 2))
atoms = self._apply_write_read(constraint)
assert len(atoms.constraints) == 1
assert isinstance(atoms.constraints[0], FixAtoms)
assert all(atoms.constraints[0].index == constraint.index)
def test_fix_cartesian_line(self):
"""Test FixCartesian along line"""
# moved only along the z direction
constraint = FixCartesian(0, mask=(1, 1, 0))
atoms = self._apply_write_read(constraint)
assert len(atoms.constraints) == 1
assert isinstance(atoms.constraints[0], FixCartesian)
assert all(atoms.constraints[0].index == constraint.index)
def test_fix_cartesian_plane(self):
"""Test FixCartesian in plane"""
# moved only in the yz plane
constraint = FixCartesian((1, 2), mask=(1, 0, 0))
atoms = self._apply_write_read(constraint)
assert len(atoms.constraints) == 1
assert isinstance(atoms.constraints[0], FixCartesian)
assert all(atoms.constraints[0].index == constraint.index)
def test_fix_cartesian_multiple(self):
"""Test multiple FixCartesian"""
constraint = [FixCartesian(1), FixCartesian(2)]
atoms = self._apply_write_read(constraint)
assert len(atoms.constraints) == 1
assert isinstance(atoms.constraints[0], FixAtoms)
assert atoms.constraints[0].index.tolist() == [1, 2]
def test_fix_scaled(self):
"""Test FixScaled"""
constraint = FixScaled(0, mask=(1, 1, 0))
with pytest.raises(UserWarning):
self._apply_write_read(constraint)
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