def test_specify_potentials_attribute():
# default specify_potentials = False
pwig = PwxInputGenerator(crystal_structure=feo_struct)
assert not pwig.specify_potentials
pwig = PwxInputGenerator(crystal_structure=feo_struct,
specify_potentials=True)
assert pwig.specify_potentials
def test_scf_base_calculation_settings():
pwig = PwxInputGenerator(crystal_structure=al_fcc_struct)
pwig.calculation_presets = "scf"
cs = pwig.calculation_settings
assert cs["calculation"] == "scf"
assert cs["namelists"] == ["control", "system", "electrons"]
assert cs["kpoints"]["scheme"] == "automatic"
assert cs["kpoints"]["shift"] == [0, 0, 0]
assert cs["pseudo_dir"] == os.path.join("~", "pseudos", "qe", "default")
def test_namelist_to_str():
pwig = PwxInputGenerator(
crystal_structure=al_fcc_struct,
calculation_presets="scf",
custom_sett_dict={"pseudo_dir": pseudo_dir},
)
control = "\n".join(al_fcc_scf_in.splitlines()[:7])
assert pwig._namelist_to_str("control") == control
electrons = "\n".join(al_fcc_scf_in.splitlines()[17:20])
assert pwig._namelist_to_str("electrons") == electrons
def test_get_pseudo_name():
# specified pseudo_dir not found
_pseudo_dir = os.path.expanduser("~/missing_dir/default")
with pytest.raises(PwxInputGeneratorError):
PwxInputGenerator._get_pseudo_name("Fe34", _pseudo_dir)
# pseudo not found for species
pseudo_name = PwxInputGenerator._get_pseudo_name("Cu", pseudo_dir)
assert pseudo_name is None
# normal function
pseudo_name = PwxInputGenerator._get_pseudo_name("Fe-34", pseudo_dir)
assert pseudo_name == "fe_pbe_v1.5.uspp.F.UPF"
def generate_pwx_input_files(args):
"""Write input files for the input crystal structure."""
pwig = PwxInputGenerator(
crystal_structure=args.crystal_structure,
calculation_presets=args.calculation_presets,
custom_sett_file=args.custom_settings_file,
custom_sett_dict=args.custom_settings_dict,
specify_potentials=args.specify_potentials,
write_location=args.write_location,
pwx_input_file=args.pwx_input_file,
)
pwig.write_input_files()
def test_get_atomic_species_card():
# specify_potentials = False, no pseudo_dir: no error
pwig = PwxInputGenerator(crystal_structure=feo_struct)
pwig.specify_potentials = False
ref_line = "O 15.99940000 None"
ac = pwig.atomic_species_card
assert ac.splitlines()[-1] == ref_line
# specify_potentials = True, no pseudo_dir: error
pwig.specify_potentials = True
with pytest.raises(PwxInputGeneratorError):
pwig.atomic_species_card
# normal functionality
pwig.custom_sett_dict.update({"pseudo_dir": pseudo_dir})
ref_line = "O 15.99940000 {}".format(os.path.basename(o_pseudo))
ac = pwig.atomic_species_card
assert ac.splitlines()[-1] == ref_line
def test_pwx_input_as_str():
pwig = PwxInputGenerator(
crystal_structure=feo_struct,
calculation_presets="scf",
custom_sett_dict={"pseudo_dir": pseudo_dir},
specify_potentials=True,
)
assert pwig.pwx_input_as_str == feo_scf_in.rstrip("\n")
def test_all_namelists_as_str():
pwig = PwxInputGenerator(
crystal_structure=al_fcc_struct,
calculation_presets="scf",
custom_sett_dict={"pseudo_dir": pseudo_dir},
)
namelists = "\n".join(al_fcc_scf_in.splitlines()[:20])
assert pwig.all_namelists_as_str == namelists
def test_all_cards_as_str():
pwig = PwxInputGenerator(
crystal_structure=feo_struct,
calculation_presets="scf",
custom_sett_dict={"pseudo_dir": pseudo_dir},
specify_potentials=True,
)
all_cards = "\n".join(feo_scf_in.splitlines()[20:])
assert pwig.all_cards_as_str == all_cards
def test_write_input_files():
import tempfile
_tmp_file = tempfile.NamedTemporaryFile(mode="w", delete=True)
filename = _tmp_file.name
write_location = os.path.dirname(filename)
pwig = PwxInputGenerator(crystal_structure=feo_struct)
pwig.calculation_presets = "scf"
pwig.specify_potentials = True
pwig.custom_sett_dict["pseudo_dir"] = pseudo_dir
pwig.write_location = write_location
pwig.pwx_input_file = filename
pwig.write_input_files()
with open(filename, "r") as fr:
assert fr.read() == feo_scf_in.rstrip("\n")
def test_pwx_input_file():
# defaults: "pwx.in" if `calculation_presets` is not input
pwig = PwxInputGenerator(crystal_structure=feo_struct)
assert pwig.pwx_input_file == "pwx.in"
# default otherwise: "[calculation_presets].in"
pwig = PwxInputGenerator(crystal_structure=feo_struct,
calculation_presets="vc-relax")
assert pwig.pwx_input_file == "vc-relax.in"
# or use any user-input file name
pwig = PwxInputGenerator(crystal_structure=feo_struct)
pwig.pwx_input_file = "test.in"
assert pwig.pwx_input_file == "test.in"
def test_kpoints_card():
# unknown scheme: error
pwig = PwxInputGenerator(crystal_structure=feo_struct)
pwig.custom_sett_dict = {"kpoints": {"scheme": "monkhorst-pack"}}
with pytest.raises(NotImplementedError):
print(pwig.kpoints_card)
# default scheme from presets
pwig = PwxInputGenerator(crystal_structure=feo_struct)
pwig.calculation_presets = "scf"
assert pwig.kpoints_card == "K_POINTS {automatic}\n9 9 9 0 0 0"
pwig = PwxInputGenerator(
crystal_structure=al_fcc_struct,
custom_sett_dict={"kpoints": {
"scheme": "gamma"
}},
)
assert pwig.kpoints_card == "K_POINTS {gamma}"
def test_bare_base_calculation_settings():
pwig = PwxInputGenerator(crystal_structure=al_fcc_struct)
calc_sett = pwig._get_calculation_settings()
assert calc_sett["nat"] == 4
def test_get_pseudo_names():
# do not setup potentials: no errors
pwig = PwxInputGenerator(crystal_structure=al_fcc_struct)
pseudo_names = pwig._get_pseudo_names()
assert pseudo_names == {"Al": None}
# all `pseudo_names` provided in input: return them
pwig = PwxInputGenerator(crystal_structure=al_fcc_struct)
pwig.specify_potentials = True
pwig.custom_sett_dict = {"pseudo_names": {"Al": al_pseudo}}
assert pwig._get_pseudo_names() == {"Al": al_pseudo}
# missing pseudos but non-existing `pseudo_dir`: error/no-op
pwig = PwxInputGenerator(crystal_structure=feo_struct)
pwig.specify_potentials = True
# 1. no `pseudo_dir`: dir not specified error
with pytest.raises(PwxInputGeneratorError, match="not specified"):
pwig._get_pseudo_names()
# 2. missing/wrong `pseudo_dir`: cannot listdir error
pwig.custom_sett_dict = {"pseudo_dir": "wrong_dir"}
with pytest.raises(PwxInputGeneratorError, match="list contents"):
pwig._get_pseudo_names()
# 3. all ok with correct `pseudo_dir`
pwig.custom_sett_dict = {"pseudo_dir": pseudo_dir}
pseudo_names = pwig._get_pseudo_names()
assert pseudo_names == {
"Fe": os.path.basename(fe_pseudo),
"O": os.path.basename(o_pseudo),
}
# failed to find some pseudos: list of missing potentials error
pwig = PwxInputGenerator(crystal_structure=feo_struct)
pwig.specify_potentials = True
pwig.custom_sett_dict = {"pseudo_dir": os.path.dirname(pseudo_dir)}
with pytest.raises(PwxInputGeneratorError, match="Fe, O"):
pwig._get_pseudo_names()
def test_relax_base_calculation_settings():
pwig = PwxInputGenerator(crystal_structure=al_fcc_struct)
pwig.calculation_presets = "relax"
cs = pwig.calculation_settings
assert cs["calculation"] == "relax"
assert cs["namelists"] == ["control", "system", "electrons", "ions"]
def test_dft_package_name():
pwig = PwxInputGenerator(crystal_structure=feo_struct)
assert pwig.dft_package == "qe"
def test_control_namelist_to_str():
# control namelist without pseudo, settings: error
pwig = PwxInputGenerator(crystal_structure=feo_struct)
pwig.specify_potentials = True
with pytest.raises(PwxInputGeneratorError):
pwig._namelist_to_str("control")
# specify_potentials = False: no error
pwig.specify_potentials = False
nl = pwig._namelist_to_str("control")
assert nl == "&CONTROL\n/"
# with no pseudo, with settings
pwig.custom_sett_dict.update({"calculation": "scf"})
nl = pwig._namelist_to_str("control")
assert nl == '&CONTROL\n calculation = "scf"\n/'
# specify_potentials = True: throw error
pwig.specify_potentials = True
with pytest.raises(PwxInputGeneratorError):
pwig._namelist_to_str("control")
# normal functionality
pwig.custom_sett_dict.update({"pseudo_dir": pseudo_dir})
pwig.calculation_presets = "scf"
control = "\n".join(feo_scf_in.splitlines()[:7])
assert pwig._namelist_to_str("control") == control
def test_parameters_from_structure():
pwig = PwxInputGenerator(crystal_structure=feo_struct)
assert pwig.parameters_from_structure == {"nat": 4, "ntyp": 2}
def test_no_crystal_structure_input_error():
with pytest.raises(TypeError):
PwxInputGenerator()
def test_write_pwx_input():
# no input settings: error
pwig = PwxInputGenerator(crystal_structure=feo_struct)
with pytest.raises(PwxInputGeneratorError, match="input settings"):
pwig.write_pwx_input()
# no `write_location` input: error
pwig.calculation_presets = "scf"
with pytest.raises(PwxInputGeneratorError, match="Location to write"):
pwig.write_pwx_input()
# no input filename: error
with pytest.raises(PwxInputGeneratorError, match="file to write"):
pwig.write_pwx_input(write_location="/path/to/write_location")
# all ok
import tempfile
_tmp_file = tempfile.NamedTemporaryFile(mode="w", delete=True)
filename = _tmp_file.name
write_location = os.path.dirname(filename)
pwig.specify_potentials = True
pwig.custom_sett_dict = {"pseudo_dir": pseudo_dir}
pwig.write_pwx_input(write_location=write_location, filename=filename)
with open(filename, "r") as fr:
assert fr.read() == feo_scf_in.rstrip("\n")
def test_atomic_positions_card():
pwig = PwxInputGenerator(crystal_structure=feo_struct,
calculation_presets="scf")
card = "\n".join(feo_scf_in.splitlines()[23:28])
assert pwig.atomic_positions_card == card
def test_atomic_forces_card():
pwig = PwxInputGenerator(crystal_structure=feo_struct)
with pytest.raises(NotImplementedError):
print(pwig.atomic_forces_card)
def test_occupations_card():
pwig = PwxInputGenerator(crystal_structure=feo_struct)
with pytest.raises(NotImplementedError):
print(pwig.occupations_card)
def test_cell_parameters_card():
pwig = PwxInputGenerator(crystal_structure=feo_struct)
card = "\n".join(feo_scf_in.splitlines()[30:])
assert pwig.cell_parameters_card == card