def test_ncread_density(self):
"""Read density from NC example data files"""
assert abidata.DEN_NCFILES
for path in abidata.DEN_NCFILES:
print("Reading DEN file %s " % path)
# Read data directly from file.
with ETSF_Reader(path) as r:
nelect_file = r.read_value("number_of_electrons")
# Compute nelect from data.
den = Density.from_file(path)
print(den)
structure = den.structure
rhor_tot = den.total_rhor
rhog_tot = den.total_rhog
nelect_calc = den.get_nelect().sum()
# Diff between nelect computed and the one written on file.
self.assert_almost_equal(nelect_calc, nelect_file)
self.assert_almost_equal(rhog_tot[0,0,0] * structure.volume, nelect_file)
if self.which("xcrysden") is not None:
# Export data in xsf format.
visu = den.export(".xsf")
self.assertTrue(callable(visu))
# Test CUBE files.
_, tmp_cubefile = tempfile.mkstemp(text=True)
den.export_to_cube(tmp_cubefile)
total_den = Density.from_cube(tmp_cubefile)
assert total_den.structure == den.structure
assert abs(total_den.get_nelect().sum() - nelect_file) < 1e-3
def test_ncread_density(self):
"""Read density from NC example data files"""
assert abidata.DEN_NCFILES
for path in abidata.DEN_NCFILES:
print("Reading DEN file %s " % path)
# Read data directly from file.
with ETSF_Reader(path) as r:
nelect_file = r.read_value("number_of_electrons")
# Compute nelect from data.
den = Density.from_file(path)
print(den)
structure = den.structure
rhor_tot = den.total_rhor
rhog_tot = den.total_rhog
nelect_calc = den.get_nelect().sum()
# Diff between nelect computed and the one written on file.
self.assert_almost_equal(nelect_calc, nelect_file)
self.assert_almost_equal(rhog_tot[0,0,0] * structure.volume, nelect_file)
if self.which("xcrysden") is not None:
# Export data in xsf format.
visu = den.export(".xsf")
self.assertTrue(callable(visu))
# Test CUBE files.
_, tmp_cubefile = tempfile.mkstemp(text=True)
den.export_to_cube(tmp_cubefile)
total_den = Density.from_cube(tmp_cubefile)
assert total_den.structure == den.structure
assert abs(total_den.get_nelect().sum() - nelect_file) < 1e-3
def test_ncread_density(self):
"""Read density from NC example data files"""
assert DEN_NCFILES
for filename in DEN_NCFILES:
print("Reading file %s " % filename)
# Read data directly from file.
with ETSF_Reader(filename) as r:
nelect_file = r.read_value("number_of_electrons")
# Compute nelect from data.
den = Density.from_file(filename)
print(den)
den.get_rhor_tot()
den.get_rhog_tot()
nelect_calc = den.get_nelect().sum()
# Diff between nelect computed and the one written on file.
self.assert_almost_equal(nelect_calc, nelect_file)
visu = den.export(".xsf")
def visualize(self, *args, **kwargs):
# TODO Here I have to decide if this method should be defined
# in a subclass of Launcher e.g GSLauncher or in the base class
from .utils import find_file
what_visualize = kwargs.get("what_visualize", "crystal")
visualizer = abipy_env.get_uservar("visualizer", kwargs)
# Find the correct output file
out_files = self.odat_files()
gsfname = find_file(out_files, "GSR")
if gsfname is None:
raise RuntimeError("Cannot find GSR file among " % out_files)
if what_visualize == "crystal":
structure = Structure.from_file(gsfname)
structure.visualize(visualizer)()
elif what_visualize == "density":
raise NotImplementedError("den_fname?")
density = Density.from_file(den_fname)
density.visualize(visualizer)()
elif what_visualize in [
"electrons",
"fermisurface",
]:
from ..electrons import ElectronBands
energies = ElectronBands.from_file(gsfname)
if what_visualize == "electrons": energies.plot()
if what_visualize == "fermisurface":
raise RuntimeError("No hanlder found for fermisurface")
#visu = energies.visualize(self, visualizer, structure)
#visu()
else:
raise RuntimeError("No handler found for %s" % what_visualize)
def visualize(self, *args, **kwargs):
# TODO Here I have to decide if this method should be defined
# in a subclass of Launcher e.g GSLauncher or in the base class
from .utils import find_file
what_visualize = kwargs.get("what_visualize", "crystal")
visualizer = abipy_env.get_uservar("visualizer", kwargs)
# Find the correct output file
out_files = self.odat_files()
gsfname = find_file(out_files, "GSR")
if gsfname is None:
raise RuntimeError("Cannot find GSR file among " % out_files)
if what_visualize == "crystal":
structure = Structure.from_file(gsfname)
structure.visualize(visualizer)()
elif what_visualize == "density":
raise NotImplementedError("den_fname?")
density = Density.from_file(den_fname)
density.visualize(visualizer)()
elif what_visualize in ["electrons", "fermisurface",]:
from ..electrons import ElectronBands
energies = ElectronBands.from_file(gsfname)
if what_visualize == "electrons": energies.plot()
if what_visualize == "fermisurface":
raise RuntimeError("No hanlder found for fermisurface")
#visu = energies.visualize(self, visualizer, structure)
#visu()
else:
raise RuntimeError("No handler found for %s" % what_visualize)
