def test_write_read_loop(tmpdir, pwscfin):
from numpy import abs, allclose
from f90nml import Namelist as F90Namelist
from pylada.espresso.structure_handling import add_structure, read_structure
from pylada.espresso.misc import write_pwscf_input
structure = read_structure(str(pwscfin))
namelist = F90Namelist()
cards = []
add_structure(structure, namelist, cards)
write_pwscf_input(namelist, cards, str(tmpdir.join('other.in')))
reread = read_structure(str(tmpdir.join('other.in')))
assert allclose(reread.cell, structure.cell)
assert abs(reread.scale - structure.scale) < 1e-12
assert len(reread) == len(structure)
for i in range(len(reread)):
assert allclose(reread[i].pos, structure[i].pos)
assert reread[i].type == structure[i].type
def test_read_structure(pwscfin):
from numpy import allclose, sqrt
from quantities import bohr_radius
from pylada.espresso.structure_handling import read_structure
structure = read_structure(str(pwscfin))
c = 0.5
tx, ty, tz = sqrt((1. - c) / 2.), sqrt((1. - c) / 6.), sqrt(
(1. + 2. * c) / 3.)
assert allclose(structure.cell.transpose(),
[[tx, -ty, tz], [0, 2 * ty, tz], [-tx, -ty, tz]])
assert abs(structure.scale - bohr_radius) < 1e-8
assert len(structure) == 2
assert structure[0].type == 'A'
assert allclose(structure[0].pos, [0, 0, 0.])
assert structure[1].type == 'B'
assert allclose(structure[1].pos, [1, 2, 3.])
def test_read_forces(tmpdir):
from quantities import Ry, bohr_radius as a0
from numpy import allclose
from pylada.espresso.structure_handling import read_structure
string = """
&system
ibrav=5,
celldm = 1.0 0.0 0.0 0.5,
/
ATOMIC_POSITIONS alat
A 0 0 0
B 1 2 3
ATOMIC_FORCES
A 0 0 0
B 1 2 3
"""
tmpdir.join('pos.in').write(string)
structure = read_structure(str(tmpdir.join('pos.in')))
for atom in structure:
assert hasattr(atom, 'force')
assert atom.force.units == (Ry / a0)
assert allclose(structure[0].force.magnitude, [0, 0, 0])
assert allclose(structure[1].force.magnitude, [1, 2, 3])