def check_pwscf_input(tmpdir, filename, pwscf):
from pylada.espresso import Pwscf
actual = Pwscf()
actual.read(tmpdir.join(filename))
assert abs(actual.system.ecutwfc - pwscf.system.ecutwfc) < 1e-8
assert actual.kpoints.subtitle == pwscf.kpoints.subtitle
assert actual.kpoints.value.rstrip().lstrip() == pwscf.kpoints.value.rstrip().lstrip()
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 check_pwscf_input(tmpdir, pwscf):
from pylada.espresso import Pwscf
actual = Pwscf()
actual.read(tmpdir.join("pwscf.in"))
assert abs(actual.system.ecutwfc - pwscf.system.ecutwfc) < 1e-8
assert actual.kpoints.subtitle == pwscf.kpoints.subtitle
assert (actual.kpoints.value.rstrip().lstrip() ==
pwscf.kpoints.value.rstrip().lstrip())
def diamond_pwscf():
from pylada.espresso import Pwscf
pwscf = Pwscf()
pwscf.system.ecutwfc = 12.0
pwscf.kpoints.subtitle = None
pwscf.kpoints.value = "2\n" "0.25 0.25 0.75 3.0\n" "0.25 0.25 0.25 1.0\n"
pwscf.add_specie("Si", "Si.pz-vbc.UPF")
return pwscf
def diamond_pwscf():
from pylada.espresso import Pwscf
pwscf = Pwscf()
pwscf.system.ecutwfc = 12.0
pwscf.kpoints.subtitle = None
pwscf.kpoints.value = "2\n"\
"0.25 0.25 0.75 3.0\n"\
"0.25 0.25 0.25 1.0\n"
pwscf.add_specie('Si', 'Si.pz-vbc.UPF')
return pwscf
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 pwscf():
from pylada.espresso import Pwscf
from quantities import Ry
pwscf = Pwscf()
pwscf.system.ecutwfc = 12.0 * Ry
pwscf.kpoints.subtitle = None
pwscf.kpoints.value = "2\n"\
"0.25 0.25 0.75 3.0\n"\
"0.25 0.25 0.25 1.0\n"
pwscf.add_specie('Al', 'Al.pz-vbc.UPF')
return pwscf
def aluminum_pwscf():
from pylada.espresso import Pwscf
pwscf = Pwscf()
pwscf.system.ecutwfc = 12.0
pwscf.system.occupations = 'smearing'
pwscf.system.smearing = 'marzari-vanderbilt'
pwscf.system.degauss = 0.06
pwscf.kpoints.subtitle = 'automatic'
pwscf.kpoints.value = '6 6 6 1 1 1'
pwscf.add_specie('Al', 'Al.pz-vbc.UPF')
return pwscf
def pwscf():
from pylada.espresso import Pwscf
from quantities import Ry
pwscf = Pwscf()
pwscf.system.ecutwfc = 12.0*Ry
pwscf.kpoints.subtitle = None
pwscf.kpoints.value = "2\n"\
"0.25 0.25 0.75 3.0\n"\
"0.25 0.25 0.25 1.0\n"
pwscf.add_specie('Al', 'Al.pz-vbc.UPF')
return pwscf
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 aluminum_pwscf():
from pylada.espresso import Pwscf
pwscf = Pwscf()
pwscf.system.ecutwfc = 12.0
pwscf.system.occupations = "smearing"
pwscf.system.smearing = "marzari-vanderbilt"
pwscf.system.degauss = 0.06
pwscf.kpoints.subtitle = "automatic"
pwscf.kpoints.value = "6 6 6 1 1 1"
pwscf.add_specie("Al", "Al.pz-vbc.UPF")
return pwscf
def pwscf():
from pylada.espresso import Pwscf
from quantities import Ry
pwscf = Pwscf()
pwscf.system.ecutwfc = 12.0*Ry
pwscf.kpoints.subtitle = None
pwscf.kpoints.value = "2\n"\
"0.25 0.25 0.75 3.0\n"\
"0.25 0.25 0.25 1.0\n"
pwscf.control.calculation = 'vc-relax'
pwscf.cell.factor = 2.0
pwscf.add_specie('Si', 'Si.pz-vbc.UPF')
return pwscf
def pwscf():
from pylada.espresso import Pwscf
from quantities import Ry
pwscf = Pwscf()
pwscf.system.ecutwfc = 12.0 * Ry
pwscf.kpoints.subtitle = None
pwscf.kpoints.value = "2\n"\
"0.25 0.25 0.75 3.0\n"\
"0.25 0.25 0.25 1.0\n"
pwscf.control.calculation = 'vc-relax'
pwscf.cell.factor = 2.0
pwscf.add_specie('Si', 'Si.pz-vbc.UPF')
return pwscf
def test_ecutwfc_required():
from py.test import raises
from pylada.espresso import Pwscf
from pylada import error
pwscf = Pwscf()
pwscf.system.ecutwfc = 12
pwscf.system.namelist()
pwscf.system.ecutwfc = None
with raises(error.ValueError):
pwscf.system.namelist()
with raises(error.ValueError):
pwscf.write()
def test_ecutwfc_required():
from py.test import raises
from pylada.espresso import Pwscf
from pylada import error
pwscf = Pwscf()
pwscf.system.ecutwfc = 12
pwscf.system.namelist()
pwscf.system.ecutwfc = None
with raises(error.ValueError):
pwscf.system.namelist()
with raises(error.ValueError):
pwscf.write()
def test_aliases():
espresso = Pwscf()
espresso.electrons.itermax = 1
ms = espresso.electrons.electron_maxstep
assert ms == 1
espresso.electrons.itermax = 10
assert espresso.electrons.electron_maxstep == 10
espresso.electrons.electron_maxstep = None
assert espresso.electrons.itermax is None
assert 'itermax' not in espresso.electrons.namelist()
assert 'electron_maxstep' not in espresso.electrons.namelist()
def test_ions_and_cells_do_not_appear_unless_relaxing(espresso, tmpdir):
espresso.ions.something = 1
espresso.cell.something = 1
espresso.control.calculation = "scf"
espresso.write(str(tmpdir.join("pwscf.in")))
pwscf = Pwscf()
pwscf.read(str(tmpdir.join("pwscf.in")))
assert not hasattr(pwscf.ions, "something")
assert not hasattr(pwscf.cell, "something")
espresso.control.calculation = "relax"
espresso.write(str(tmpdir.join("pwscf.in")))
pwscf = Pwscf()
pwscf.read(str(tmpdir.join("pwscf.in")))
assert getattr(pwscf.ions, "something", 0) == 1
assert not hasattr(pwscf.cell, "something")
espresso.control.calculation = "vc-relax"
espresso.write(str(tmpdir.join("pwscf.in")))
pwscf = Pwscf()
pwscf.read(str(tmpdir.join("pwscf.in")))
assert getattr(pwscf.ions, "something", 0) == 1
assert getattr(pwscf.cell, "something", 0) == 1
def pwscf(text):
from quantities import Ry
from pylada.espresso import Pwscf
pwscf = Pwscf()
exec(text, globals(), {'pwscf': pwscf, 'Ry': Ry})
return pwscf
def read_pwscf(tmpdir, filename):
from pylada.espresso import Pwscf
assert tmpdir.join(filename).check(file=True)
result = Pwscf()
result.read(tmpdir.join(filename))
return result
def check_start_from_wfcn(tmpdir):
from pylada.espresso import Pwscf
pwscf = Pwscf()
pwscf.read(tmpdir.join("second", "pwscf.in"))
assert pwscf.electrons.startingwfc == 'file'
def empty_pwscf():
from pylada.espresso import Pwscf
return Pwscf()
def check_start_from_wfcn(tmpdir):
from pylada.espresso import Pwscf
pwscf = Pwscf()
pwscf.read(tmpdir.join("second", "pwscf.in"))
assert pwscf.electrons.startingwfc == 'file'
#
# 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!")
def espresso():
pwscf = Pwscf()
# Required for all writing because required by Pwscf
pwscf.system.ecutwfc = 12.0
return pwscf
def test_ions_and_cells_do_not_appear_unless_relaxing(espresso, tmpdir):
espresso.ions.something = 1
espresso.cell.something = 1
espresso.control.calculation = 'scf'
espresso.write(str(tmpdir.join('pwscf.in')))
pwscf = Pwscf()
pwscf.read(str(tmpdir.join('pwscf.in')))
assert not hasattr(pwscf.ions, 'something')
assert not hasattr(pwscf.cell, 'something')
espresso.control.calculation = 'relax'
espresso.write(str(tmpdir.join('pwscf.in')))
pwscf = Pwscf()
pwscf.read(str(tmpdir.join('pwscf.in')))
assert getattr(pwscf.ions, 'something', 0) == 1
assert not hasattr(pwscf.cell, 'something')
espresso.control.calculation = 'vc-relax'
espresso.write(str(tmpdir.join('pwscf.in')))
pwscf = Pwscf()
pwscf.read(str(tmpdir.join('pwscf.in')))
assert getattr(pwscf.ions, 'something', 0) == 1
assert getattr(pwscf.cell, 'something', 0) == 1
def read_pwscf(tmpdir, filename):
from pylada.espresso import Pwscf
assert tmpdir.join(filename).check(file=True)
result = Pwscf()
result.read(tmpdir.join(filename))
return result