"""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)