def visualize_qpoint_nu(self, qpoint, nu, spin=0, appname="vesta"):
iq, qpoint = self._find_iqpt_qpoint(qpoint)
# Fortran array nctkarr_t("v1_qnu", "dp", "two, nfft, nspden, natom3, nqlist")])
v1_qnu = self.reader.read_variable("v1_qnu")[iq, nu, spin]
v1_qnu = v1_qnu[:, 0] + 1j * v1_qnu[:, 1]
#wqnu = self.reader.read_variable["phfreqs"][nu]
#v1_qnu /= np.sqrt(2 * wqnu)
datar = np.reshape(np.abs(v1_qnu), self.ngfft)
visu = Visualizer.from_name(appname)
ext = "xsf"
if ext not in visu.supported_extensions():
raise ValueError("Visualizer %s does not support XSF files" % visu)
from abipy.core.globals import abinb_mkstemp
_, filename = abinb_mkstemp(suffix="." + ext, text=True)
with open(filename, mode="wt") as fh:
if ext == "xsf":
xsf.xsf_write_structure(fh, self.structure)
xsf.xsf_write_data(fh, self.structure, datar, add_replicas=True)
else:
raise NotImplementedError("extension %s is not supported." % ext)
return visu(filename)
def vesta_open(self, temp=300): # pragma: no cover
"""
Visualize termal displacement ellipsoids at temperature `temp` (Kelvin) with Vesta_ application.
"""
filepath = self.write_cif_file(filepath=None, temp=temp)
cprint("Writing structure + Debye-Waller tensor in CIF format for T = %s (K) to file: %s" % (temp, filepath), "green")
cprint("In the Vesta GUI, select: Properties -> Atoms -> Show as displament ellipsoids.", "green")
from abipy.iotools import Visualizer
visu = Visualizer.from_name("vesta")
return visu(filepath)()
def visualize_ur2(self, spin, kpoint, band, visu_name):
"""
Visualize :math:`|u(r)|^2` with visualizer.
See :class:`Visualizer` for the list of applications and formats supported.
"""
visu = Visualizer.from_name(visu_name)
for ext in visu.supported_extensions():
ext = "." + ext
try:
return self.export_ur2(ext, spin, kpoint, band, visu=visu)
except visu.Error:
pass
else:
raise visu.Error("Don't know how to export data for visualizer %s" % visu_name)
def visualize_ur2(self, spin, kpoint, band, visu_name):
"""
Visualize :math:`|u(r)|^2` with visualizer.
See :class:`Visualizer` for the list of applications and formats supported.
"""
visu = Visualizer.from_name(visu_name)
for ext in visu.supported_extensions():
ext = "." + ext
try:
return self.export_ur2(ext, spin, kpoint, band, visu=visu)
except visu.Error:
pass
else:
raise visu.Error(
"Don't know how to export data for visualizer %s" % visu_name)
def visualize(self, appname="ovito"): # pragma: no cover
"""
Visualize the crystalline structure with visualizer.
See :class:`Visualizer` for the list of applications and formats supported.
"""
if appname == "mayavi": return self.mayaview()
# Get the Visualizer subclass from the string.
from abipy.iotools import Visualizer
visu = Visualizer.from_name(appname)
if visu.name != "ovito":
raise NotImplementedError("visualizer: %s" % visu.name)
filepath = self.write_xdatcar(filepath=None, groupby_type=True)
return visu(filepath)()
def visualize(self, appname="ovito"): # pragma: no cover
"""
Visualize the crystalline structure with visualizer.
See :class:`Visualizer` for the list of applications and formats supported.
"""
if appname == "mayavi": return self.mayaview()
# Get the Visualizer subclass from the string.
from abipy.iotools import Visualizer
visu = Visualizer.from_name(appname)
if visu.name != "ovito":
raise NotImplementedError("visualizer: %s" % visu.name)
filepath = self.write_xdatcar(filepath=None, groupby_type=True)
return visu(filepath)()
def visualize(self, appname):
"""
Visualize data with visualizer.
See :class:`Visualizer` for the list of applications and formats supported.
"""
visu = Visualizer.from_name(appname)
# Try to export data to one of the formats supported by the visualizer
# Use a temporary file (note "." + ext)
for ext in visu.supported_extensions():
ext = "." + ext
try:
return self.export(ext, visu=visu)()
except visu.Error:
pass
else:
raise visu.Error("Don't know how to export data for visualizer %s" % appname)
def visualize(self, visu_name):
"""
Visualize the crystalline structure with visualizer.
See :class:`Visualizer` for the list of applications and formats supported.
"""
# Get the Visualizer subclass from the string.
visu = Visualizer.from_name(visu_name)
# Try to export data to one of the formats supported by the visualizer
# Use a temporary file (note "." + ext)
for ext in visu.supported_extensions():
ext = "." + ext
try:
return self.export(ext, visu=visu)()
except visu.Error:
pass
else:
raise visu.Error("Don't know how to export data for %s" % visu_name)
def visualize(self, visu_name):
"""
Visualize data with visualizer.
See :class:`Visualizer` for the list of applications and formats supported.
"""
visu = Visualizer.from_name(visu_name)
# Try to export data to one of the formats supported by the visualizer
# Use a temporary file (note "." + ext)
for ext in visu.supported_extensions():
ext = "." + ext
try:
return self.export(ext, visu=visu)
except visu.Error:
pass
else:
raise visu.Error("Don't know how to export data for visualizer %s" % visu_name)
def visualize_ur2(self, structure, visu_name):
"""
Visualize u(r)**2 visualizer.
See :class:`Visualizer` for the list of applications and formats supported.
"""
# Get the Visualizer subclass from the string.
visu = Visualizer.from_name(visu_name)
# Try to export data to one of the formats supported by the visualizer
# Use a temporary file (note "." + ext)
for ext in visu.supported_extensions():
ext = "." + ext
try:
return self.export_ur2(ext, structure, visu=visu)
except visu.Error:
pass
else:
raise visu.Error("Don't know how to export data for %s" % visu_name)
def visualize_ur2(self, appname="vesta"):
"""
Visualize :math:`|u(r)|^2|`.
See :class:`Visualizer` for the list of applications and formats supported.
"""
# Get the Visualizer subclass from the string.
visu = Visualizer.from_name(appname)
# Try to export data to one of the formats supported by the visualizer
# Use a temporary file (note "." + ext)
for ext in visu.supported_extensions():
ext = "." + ext
try:
return self.export_ur2(ext, visu=visu)
except visu.Error:
pass
else:
raise visu.Error("Don't know how to export data for %s" % str(appname))
