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"""Quantum ESPRESSO file parsers.
Implemented:
* Input file (pwi)
* Output file (pwo) with vc-relax
"""
import numpy as np
from ase import io
from ase import build
from pytest import approx
# 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) = 0.32 /
&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
"""
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 = io.read('pw_input.pwi', format='espresso-in')
assert len(pw_input_atoms) == 8
assert (pw_input_atoms.get_initial_magnetic_moments()
== 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"""
from ase.io.espresso import get_atomic_species, read_fortran_namelist
with open('pw_input.pwi', 'w') as pw_input_f:
pw_input_f.write(pw_input_text)
with open('pw_input.pwi', 'r') 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", approx(1.008), "H.pbe-rrkjus_psl.0.1.UPF")
assert species_card[1] == ("Fe", 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 = 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_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 = 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 = 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 = 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 = 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 = 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])
bulk.write('espresso_test.pwi')
readback = io.read('espresso_test.pwi')
assert np.allclose(bulk.positions, readback.positions)
|
