def test_read_aluminum(tmpdir, aluminum_file):
from pylada.espresso import read_structure
espresso = Pwscf()
espresso.read(aluminum_file)
structure = read_structure(aluminum_file)
check_aluminum_functional(tmpdir, espresso)
check_aluminum_structure(structure)
def test_read_aluminum(tmpdir, aluminum_file):
from pylada.espresso import read_structure
espresso = Pwscf()
espresso.read(aluminum_file)
structure = read_structure(aluminum_file)
check_aluminum_functional(tmpdir, espresso)
check_aluminum_structure(structure)
def structure_is_passed_on(tmpdir, extract):
from numpy import allclose
from pylada.espresso import read_structure
actual = read_structure(str(tmpdir.join("second", "pwscf.in")))
assert len(actual) == len(extract.structure)
assert allclose(actual.cell, extract.structure.cell)
for a, b in zip(actual, extract.structure):
assert a.type == b.type
assert allclose(a.pos, b.pos)
def structure_is_passed_on(tmpdir, extract):
from numpy import allclose
from pylada.espresso import read_structure
actual = read_structure(str(tmpdir.join("second", "pwscf.in")))
assert len(actual) == len(extract.structure)
assert allclose(actual.cell, extract.structure.cell)
for a, b in zip(actual, extract.structure):
assert a.type == b.type
assert allclose(a.pos, b.pos)
def test_read_write_loop(aluminum_file, tmpdir, espresso):
from pylada.espresso import read_structure
espresso.read(aluminum_file)
espresso.control.pseudo_dir = str(tmpdir.join('pseudos'))
tmpdir.join('pseudos', 'Al.vbc.UPF').ensure(file=True)
structure = read_structure(aluminum_file)
espresso.write(str(tmpdir.join('al2.scf')), structure=structure)
espresso = Pwscf()
espresso.read(str(tmpdir.join('al2.scf')))
check_aluminum_functional(tmpdir, espresso)
def test_read_write_loop(aluminum_file, tmpdir, espresso):
from pylada.espresso import read_structure
espresso.read(aluminum_file)
espresso.control.pseudo_dir = str(tmpdir.join("pseudos"))
tmpdir.join("pseudos", "Al.vbc.UPF").ensure(file=True)
structure = read_structure(aluminum_file)
espresso.write(str(tmpdir.join("al2.scf")), structure=structure)
espresso = Pwscf()
espresso.read(str(tmpdir.join("al2.scf")))
check_aluminum_functional(tmpdir, espresso)
def test_iteration(tmpdir, aluminum_file, espresso):
""" Checks iterations goes through the expected steps """
from sys import executable as python
from os.path import dirname, join
from pylada.espresso import read_structure
from pylada.espresso.tests.extract import Extract
structure = read_structure(aluminum_file)
espresso.read(aluminum_file)
espresso.program = python + " " + join(dirname(__file__), 'dummy_pwscf.py')
espresso.Extract = Extract
tmpdir.join('pseudos', 'Al.vbc.UPF').ensure(file=True)
iterator = espresso.iter(outdir=str(tmpdir), overwrite=True, structure=structure)
program_process = next(iterator)
assert hasattr(program_process, 'start')
assert hasattr(program_process, 'wait')
program_process.start()
program_process.wait()
assert tmpdir.join("%s.out" % espresso.control.prefix).check()
extract = next(iterator)
assert isinstance(extract, Extract)
assert extract.success
def test_iteration(tmpdir, aluminum_file, espresso):
""" Checks iterations goes through the expected steps """
from sys import executable as python
from os.path import dirname, join
from pylada.espresso import read_structure
from pylada.espresso.tests.extract import Extract
structure = read_structure(aluminum_file)
espresso.read(aluminum_file)
espresso.program = python + " " + join(dirname(__file__), "dummy_pwscf.py")
espresso.Extract = Extract
tmpdir.join("pseudos", "Al.vbc.UPF").ensure(file=True)
iterator = espresso.iter(outdir=str(tmpdir), overwrite=True, structure=structure)
program_process = next(iterator)
assert hasattr(program_process, "start")
assert hasattr(program_process, "wait")
program_process.start()
program_process.wait()
assert tmpdir.join("%s.out" % espresso.control.prefix).check()
extract = next(iterator)
assert isinstance(extract, Extract)
assert extract.success
#
# PyLaDa is free software: you can redistribute it and/or modify it under the terms of the GNU
# General Public License as published by the Free Software Foundation, either version 3 of the
# License, or (at your option) any later version.
#
# PyLaDa is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even
# the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
# Public License for more details.
#
# You should have received a copy of the GNU General Public License along with PyLaDa. If not, see
# <http://www.gnu.org/licenses/>.
###############################
# -*- coding: utf-8 -*-
from pylada.espresso import Pwscf
from tempfile import NamedTemporaryFile
from pylada.espresso.tests.fixtures import check_aluminum_functional, check_aluminum_structure
from pylada.espresso import read_structure
from py.path import local
from sys import stdin
pwscf = Pwscf()
with NamedTemporaryFile(mode="w") as file:
file.write(stdin.read())
file.flush()
pwscf.read(file.name)
structure = read_structure(file.name)
check_aluminum_functional(local(), pwscf)
check_aluminum_structure(structure)
pwscf.pseudos_do_exist(structure)
print("JOB IS DONE!")