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 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)
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))