def export_ur2(self, filename, structure):
"""
Export the wavefunction on file filename.
Format is defined by the extension in filename.
"""
if "." not in filename:
raise ValueError("Cannot detect file extension in: %s" % filename)
tokens = filename.strip().split(".")
ext = tokens[-1]
if not tokens[0]: # fname == ".ext" ==> Create temporary file.
filename = tempfile.mkstemp(suffix="." + ext, text=True)[1]
print("Creating temporary file: %s" % filename)
# Compute |u(r)|2 and write data according to ext.
ur2 = np.reshape(self.ur2, (1,) + self.ur2.shape)
with open(filename, mode="w") as fh:
if ext == "xsf":
# xcrysden
xsf_write_structure(fh, structures=[structure])
xsf_write_data(fh, structure, ur2, add_replicas=True)
else:
raise NotImplementedError("extension %s is not supported." % ext)
return Visualizer.from_file(filename)
def export(self, filename):
"""
Export the real space data on file filename.
Format is defined by the extension in filename.
See :class:`Visualizer` for the list of applications and formats supported.
"""
if "." not in filename:
raise ValueError(" Cannot detect file extension in filename: %s " % filename)
tokens = filename.strip().split(".")
ext = tokens[-1]
if not tokens[0]: # filename == ".ext" ==> Create temporary file.
import tempfile
filename = tempfile.mkstemp(suffix="."+ext, text=True)[1]
with open(filename, mode="w") as fh:
if ext == "xsf":
# xcrysden
xsf.xsf_write_structure(fh, self.structure)
xsf.xsf_write_data(fh, self.structure, self.datar, add_replicas=True)
else:
raise NotImplementedError("extension %s is not supported." % ext)
return Visualizer.from_file(filename)
def export(self, filename):
"""
Export the crystalline structure on file filename.
Returns:
Instance of :class:`Visualizer`
The format is defined by the extension in filename:
See :class:`Visualizer` for the list of applications and formats supported.
#. "prefix.xsf" for XcrysDen files.
An *empty* prefix, e.g. ".xsf" makes the code use a temporary file.
"""
if "." not in filename:
raise ValueError("Cannot detect extension in filename %s: " % filename)
tokens = filename.strip().split(".")
ext = tokens[-1]
if not tokens[0]:
# filename == ".ext" ==> Create temporary file.
import tempfile
filename = tempfile.mkstemp(suffix="."+ext, text=True)[1]
with open(filename, mode="w") as fh:
if ext == "xsf": # xcrysden
xsf.xsf_write_structure(fh, structures=[self])
else:
raise Visualizer.Error("extension %s is not supported." % ext)
return Visualizer.from_file(filename)
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 export(self, filename, visu=None):
"""
Export the crystalline structure on file filename.
Args:
filename: String specifying the file path and the file format.
The format is defined by the file extension. filename="prefix.xsf", for example,
will produce a file in XSF format. An *empty* prefix, e.g. ".xsf" makes the code use a temporary file.
visu: `Visualizer` subclass. By default, this method returns the first available
visualizer that supports the given file format. If visu is not None, an
instance of visu is returned. See :class:`Visualizer` for the list of applications and formats supported.
Returns: Instance of :class:`Visualizer`
"""
if "." not in filename:
raise ValueError("Cannot detect extension in filename %s: " %
filename)
tokens = filename.strip().split(".")
ext = tokens[-1]
if not tokens[0]:
# filename == ".ext" ==> Create temporary file.
import tempfile
filename = tempfile.mkstemp(suffix="." + ext, text=True)[1]
with open(filename, mode="w") as fh:
if ext == "xsf":
# xcrysden
xsf.xsf_write_structure(fh, structures=[self])
else:
raise Visualizer.Error("extension %s is not supported." % ext)
if visu is None:
return Visualizer.from_file(filename)
else:
return visu(filename)
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_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, visualizer):
"""
Visualize data with visualizer.
See :class:`Visualizer` for the list of applications and formats supported.
"""
extensions = Visualizer.exts_from_appname(visualizer)
for ext in extensions:
ext = "." + ext
try:
return self.export(ext)
except Visualizer.Error:
pass
else:
raise Visualizer.Error("Don't know how to export data for visualizer %s" % visualizer)
def export(self, filename, visu=None, verbose=1):
"""
Export the real space data to file filename.
Args:
filename: String specifying the file path and the file format.
The format is defined by the file extension. filename="prefix.xsf", for example,
will produce a file in XSF format (xcrysden_).
An *empty* prefix, e.g. ".xsf" makes the code use a temporary file.
visu:
:class:`Visualizer` subclass. By default, this method returns the first available
visualizer that supports the given file format. If visu is not None, an
instance of visu is returned. See :class:`Visualizer` for the list of
applications and formats supported.
verbose: Verbosity level
Returns:
Instance of :class:`Visualizer`
"""
if "." not in filename:
raise ValueError("Cannot detect file extension in filename: %s " % filename)
tokens = filename.strip().split(".")
ext = tokens[-1]
if verbose:
print("tokens", tokens, "ext", ext)
if not tokens[0]:
# filename == ".ext" ==> Create temporary file.
# dir = os.getcwd() is needed when we invoke the method from a notebook.
# nbworkdir in cwd is needed when we invoke the method from a notebook.
from abipy.core.globals import abinb_mkstemp
_, filename = abinb_mkstemp(suffix="." + ext, text=True)
with open(filename, mode="wt") as fh:
if ext == "xsf":
# xcrysden
xsf.xsf_write_structure(fh, self.structure)
xsf.xsf_write_data(fh, self.structure, self.datar, add_replicas=True)
#elif ext == "POSCAR":
else:
raise NotImplementedError("extension %s is not supported." % ext)
if visu is None:
return Visualizer.from_file(filename)
else:
return visu(filename)
def export_ur2(self, filename, structure, visu=None):
"""
Export u(r)**2 on file filename.
Args:
filename:
String specifying the file path and the file format.
The format is defined by the file extension. filename="prefix.xsf", for example,
will produce a file in XSF format. An *empty* prefix, e.g. ".xsf" makes the code use a temporary file.
structure:
Structure object.
visu:
`Visualizer` subclass. By default, this method returns the first available
visualizer that supports the given file format. If visu is not None, an
instance of visu is returned. See :class:`Visualizer` for the list of
applications and formats supported.
Returns:
Instance of :class:`Visualizer`
"""
if "." not in filename:
raise ValueError("Cannot detect file extension in: %s" % filename)
tokens = filename.strip().split(".")
ext = tokens[-1]
if not tokens[0]: # fname == ".ext" ==> Create temporary file.
filename = tempfile.mkstemp(suffix="." + ext, text=True)[1]
print("Creating temporary file: %s" % filename)
# Compute |u(r)|2 and write data according to ext.
ur2 = np.reshape(self.ur2, (1,) + self.ur2.shape)
with open(filename, mode="w") as fh:
if ext == "xsf":
# xcrysden
xsf_write_structure(fh, structures=[structure])
xsf_write_data(fh, structure, ur2, add_replicas=True)
else:
raise NotImplementedError("extension %s is not supported." % ext)
if visu is None:
return Visualizer.from_file(filename)
else:
return visu(filename)
def export_ur2(self, filename, visu=None):
"""
Export :math:`|u(r)|^2` to file ``filename``.
Args:
filename: String specifying the file path and the file format.
The format is defined by the file extension. filename="prefix.xsf", for example,
will produce a file in XSF format. An *empty* prefix, e.g. ".xsf" makes the code use a temporary file.
visu: :class:`Visualizer` subclass. By default, this method returns the first available
visualizer that supports the given file format. If visu is not None, an
instance of visu is returned. See :class:`Visualizer` for the list of
applications and formats supported.
Returns:
Instance of :class:`Visualizer`
"""
if "." not in filename:
raise ValueError("Cannot detect file extension in: %s" % filename)
tokens = filename.strip().split(".")
ext = tokens[-1]
if not tokens[0]:
# fname == ".ext" ==> Create temporary file.
# dir = os.getcwd() is needed when we invoke the method from a notebook.
from abipy.core.globals import abinb_mkstemp
_, filename = abinb_mkstemp(suffix="." + ext, text=True)
print("Creating temporary file: %s" % filename)
# Compute |u(r)|2 and write data according to ext.
ur2 = np.reshape(self.ur2, (1, ) + self.ur2.shape)
with open(filename, mode="wt") as fh:
if ext == "xsf":
# xcrysden
xsf_write_structure(fh, structures=self.structure)
xsf_write_data(fh, self.structure, ur2, add_replicas=True)
else:
raise NotImplementedError("extension %s is not supported." %
ext)
if visu is None:
return Visualizer.from_file(filename)
else:
return visu(filename)
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, 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))
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 ipw_visualize_widget(self): # pragma: no cover
"""
Return an ipython widget with controllers to visualize the wavefunctions.
.. warning::
It seems there's a bug with Vesta on MacOs if the user tries to open multiple wavefunctions
as the tab in vesta is not updated!
"""
def wfk_visualize(spin, kpoint, band, appname):
kpoint = int(kpoint.split()[0])
self.visualize_ur2(spin, kpoint, band, appname=appname)
import ipywidgets as ipw
return ipw.interact_manual(
wfk_visualize,
spin=list(range(self.nsppol)),
kpoint=["%d %s" % (i, repr(kpt)) for i, kpt in enumerate(self.kpoints)],
band=list(range(self.nband)),
appname=[v.name for v in Visualizer.get_available()],
)
def export(self, filename, visu=None):
"""
Export the crystalline structure on file filename.
Args:
filename:
String specifying the file path and the file format.
The format is defined by the file extension. filename="prefix.xsf", for example,
will produce a file in XSF format. An *empty* prefix, e.g. ".xsf" makes the code use a temporary file.
visu:
`Visualizer` subclass. By default, this method returns the first available
visualizer that supports the given file format. If visu is not None, an
instance of visu is returned. See :class:`Visualizer` for the list of
applications and formats supported.
Returns:
Instance of :class:`Visualizer`
"""
if "." not in filename:
raise ValueError("Cannot detect extension in filename %s: " % filename)
tokens = filename.strip().split(".")
ext = tokens[-1]
if not tokens[0]:
# filename == ".ext" ==> Create temporary file.
import tempfile
filename = tempfile.mkstemp(suffix="." + ext, text=True)[1]
with open(filename, mode="w") as fh:
if ext == "xsf":
# xcrysden
xsf.xsf_write_structure(fh, structures=[self])
else:
raise Visualizer.Error("extension %s is not supported." % ext)
if visu is None:
return Visualizer.from_file(filename)
else:
return visu(filename)
