def OnPhbandsDos(self, event):
"""Open Frame for the computation of the DOS."""
if not self.phdos:
awx.showErrorMessage(self, message="PHDOS data should be loaded using the menu Phband->Add phdos data")
else:
plotter = PhononDosPlotter()
try:
label = os.path.relpath(self.active_phdos_file.filepath)
plotter.add_phdos(label, self.phdos)
except:
awx.showErrorMessage(self)
plotter.plot()
def OnComparePhdos(self, event):
"""Plot multiple phonon DOSes"""
plotter = PhononDosPlotter()
for path, phdos in zip(self.phdos_filepaths, self.phdos_list):
try:
label = os.path.relpath(path)
plotter.add_phdos(label, phdos)
except:
awx.showErrorMessage(self)
plotter.plot()
def OnComparePhdos(self, event):
"""Plot multiple phonon DOSes"""
plotter = PhononDosPlotter()
for path, phdos in zip(self.phdos_filepaths, self.phdos_list):
try:
label = os.path.relpath(path)
plotter.add_phdos(label, phdos)
except:
awx.showErrorMessage(self)
plotter.plot()
def OnPhbandsDos(self, event):
"""Open Frame for the computation of the DOS."""
if not self.phdos:
awx.showErrorMessage(self, message="PHDOS data should be loaded using the menu Phband->Add phdos data")
else:
plotter = PhononDosPlotter()
try:
label = os.path.relpath(self.active_phdos_file.filepath)
plotter.add_phdos(label, self.phdos)
except:
awx.showErrorMessage(self)
plotter.plot()
def test_phdos_plotter(self):
"""Testing PhononDosPlotter."""
phdos_paths = 2 * [abidata.ref_file("trf2_5.out_PHDOS.nc")]
plotter = PhononDosPlotter()
plotter.add_phdos("AlAs", phdos_paths[0])
plotter.add_phdos("Same-AlAs", phdos_paths[1])
repr(plotter); str(plotter)
assert len(plotter.phdos_list) == 2
if self.has_matplotlib():
assert plotter.combiplot(show=True)
assert plotter.gridplot(show=True)
assert plotter.plot_harmonic_thermo()
if self.has_ipywidgets():
assert plotter.ipw_select_plot() is not None
assert plotter.ipw_harmonic_thermo() is not None
if self.has_nbformat():
plotter.write_notebook(nbpath=self.get_tmpname(text=True))
def test_phdos_plotter(self):
"""Testing PhononDosPlotter."""
phdos_paths = 2 * [abidata.ref_file("trf2_5.out_PHDOS.nc")]
plotter = PhononDosPlotter()
plotter.add_phdos("AlAs", phdos_paths[0])
plotter.add_phdos("Same-AlAs", phdos_paths[1])
repr(plotter); str(plotter)
assert len(plotter.phdos_list) == 2
if self.has_matplotlib():
assert plotter.combiplot(show=True)
assert plotter.gridplot(show=True)
assert plotter.plot_harmonic_thermo()
if self.has_ipywidgets():
assert plotter.ipw_select_plot() is not None
assert plotter.ipw_harmonic_thermo() is not None
if self.has_nbformat():
plotter.write_notebook(nbpath=self.get_tmpname(text=True))
def anacompare_phdos(self, nqsmalls, asr=2, chneut=1, dipdip=1, dos_method="tetra", ngqpt=None,
num_cpus=None, stream=sys.stdout):
"""
Args:
nqsmalls: List of integers defining the q-mesh for the DOS. Each integer gives
the number of divisions to be used to sample the smallest reciprocal lattice vector.
asr, chneut, dipdp: Anaddb input variable. See official documentation.
dos_method: Technique for DOS computation in Possible choices: "tetra", "gaussian" or "gaussian:0.001 eV".
In the later case, the value 0.001 eV is used as gaussian broadening
ngqpt: Number of divisions for the q-mesh in the DDB file. Auto-detected if None (default)
num_cpus: Number of CPUs (threads) used to parallellize the calculation of the DOSes. Autodetected if None.
stream: File-like object used for printing.
Return:
`namedtuple` with the following attributes:
phdoses: List of :class:`PhononDos` objects
plotter: :class:`PhononDosPlotter` object. Use plotter.plot() to visualize the results.
"""
num_cpus = get_ncpus() if num_cpus is None else num_cpus
if num_cpus <= 0: num_cpus = 1
num_cpus = min(num_cpus, len(nqsmalls))
# TODO: anaget_phdos
def do_work(nqsmall):
_, phdos_file = self.anaget_phbst_and_phdos_files(
nqsmall=nqsmall, ndivsm=1, asr=asr, chneut=chneut, dipdip=dipdip, dos_method=dos_method, ngqpt=ngqpt)
return phdos_file.phdos
if num_cpus == 1:
# Sequential version
phdoses = [do_work(nqs) for nqs in nqsmalls]
else:
# Threads
print("Computing %d phonon DOS with %d threads" % (len(nqsmalls), num_cpus) )
phdoses = [None] * len(nqsmalls)
def worker():
while True:
nqsm, phdos_index = q.get()
phdos = do_work(nqsm)
phdoses[phdos_index] = phdos
q.task_done()
from threading import Thread
try:
from Queue import Queue # py2k
except ImportError:
from queue import Queue # py3k
q = Queue()
for i in range(num_cpus):
t = Thread(target=worker)
t.daemon = True
t.start()
for i, nqsmall in enumerate(nqsmalls):
q.put((nqsmall, i))
# block until all tasks are done
q.join()
# Compute relative difference wrt last phonon DOS. Be careful because the DOSes may be defined
# on different frequency meshes ==> spline on the mesh of the last DOS.
last_mesh, converged = phdoses[-1].mesh, False
for i, phdos in enumerate(phdoses[:-1]):
splined_dos = phdos.spline_on_mesh(last_mesh)
abs_diff = (splined_dos - phdoses[-1]).abs()
print(" Delta(Phdos[%d] - Phdos[%d]) / Phdos[%d]: %f" %
(i, len(phdoses)-1, len(phdoses)-1, abs_diff.integral().values[-1]), file=stream)
# Fill the plotter.
plotter = PhononDosPlotter()
for nqsmall, phdos in zip(nqsmalls, phdoses):
plotter.add_phdos(label="nqsmall %d" % nqsmall, phdos=phdos)
return dict2namedtuple(phdoses=phdoses, plotter=plotter)