def get_panel(self):
"""Build panel with widgets to interact with the structure either in a notebook or in a bokeh app"""
tabs = pn.Tabs()
app = tabs.append
row = pn.Row(
bkw.PreText(text=self.structure.to_string(verbose=self.verbose),
sizing_mode="scale_both"))
app(("Summary", row))
ws = pn.Column('# Spglib options', self.spglib_symprec,
self.spglib_angtol)
app(("Spglib", pn.Row(ws, self.spglib_summary)))
ws = pn.Column('# K-path options', self.kpath_format,
self.line_density)
app(("Kpath", pn.Row(ws, self.get_kpath)))
app(("Convert",
pn.Row(pn.Column("# Convert structure", self.output_format),
self.convert)))
app(("View",
pn.Row(
pn.Column("# Visualize structure", self.viewer,
self.viewer_btn), self.view)))
ws = pn.Column('# Generate GS input', self.gs_type, self.spin_mode,
self.kppra, self.gs_input_btn)
app(("GS-input", pn.Row(ws, self.on_gs_input_btn)))
app(("MP-match",
pn.Row(pn.Column(self.mp_match_btn), self.on_mp_match_btn)))
return tabs
def on_debug_btn(self):
if self.debug_btn.clicks == 0: return
#TODO https://github.com/ralphbean/ansi2html ?
stream = StringIO()
#flow.debug(status=options.task_status, nids=selected_nids(flow, options))
self.flow.debug(stream=stream)
return pn.Row(bkw.PreText(text=stream.getvalue()))
def on_history_btn(self):
if self.history_btn.clicks == 0: return
stream = StringIO()
#flow.show_history(status=options.task_status, nids=selected_nids(flow, options),
# full_history=options.full_history, metadata=options.metadata)
self.flow.show_history(stream=stream)
return pn.Row(bkw.PreText(text=stream.getvalue()))
def get_panel(self):
"""Return tabs with widgets to interact with the DDB file."""
tabs = pn.Tabs()
app = tabs.append
row = pn.Row(
bkw.PreText(text=self.ddb.to_string(verbose=self.verbose),
sizing_mode="scale_both"))
app(("Summary", row))
app(("Ph-bands",
pn.Row(
pn.Column(
"# PH-bands options", *[
self.param[k]
for k in ("nqsmall", "ndivsm", "asr", "chneut",
"dipdip", "lo_to_splitting", "dos_method")
], self.temp_range, self.plot_phbands_btn),
self.plot_phbands_and_phdos)))
app(("BECs",
pn.Row(
pn.Column(
"# Born effective charges options", *[
self.param[k]
for k in ("asr", "chneut", "dipdip", "gamma_ev")
], self.get_epsinf_btn), self.get_epsinf)))
app(("eps0",
pn.Row(
pn.Column(
"# epsilon_0", *[
self.param[k]
for k in ("asr", "chneut", "dipdip", "gamma_ev")
], self.w_range, self.plot_eps0w_btn), self.plot_eps0w)))
app(("Speed of sound",
pn.Row(
pn.Column(
"# Speed of sound options",
*[self.param[k] for k in ("asr", "chneut", "dipdip")],
self.plot_vsound_btn), self.plot_vsound)))
app(("Check ASR and DIPDIP",
pn.Row(
pn.Column(
"# Options", *[
self.param[k]
for k in ("nqsmall", "ndivsm", "dos_method")
], self.plot_check_asr_dipdip_btn),
self.plot_without_asr_dipdip)))
app(("IFCs",
pn.Row(
pn.Column(
"# Options",
*[self.param[k] for k in ("asr", "dipdip", "chneut")],
self.plot_ifc_btn), self.plot_ifc)))
app(("Global Opts",
pn.Column(
"# Global Options",
*[self.param[k] for k in ("units", "mpi_procs", "verbose")])))
return tabs
def on_handlers_btn(self):
#if self.handlers_btn.clicks == 0: return
stream = StringIO()
#if options.doc:
# flowtk.autodoc_event_handlers()
#else:
#show_events(self, status=None, nids=None, stream=sys.stdout):
self.flow.show_event_handlers(verbose=self.verbose.value,
stream=stream)
return pn.Row(bkw.PreText(text=stream.getvalue()))
def on_plot_ebands_btn(self):
"""Button triggering ebands plot."""
if self.plot_ebands_btn.clicks == 0: return
if self.set_fermie_to_vbm.value:
self.ebands.set_fermie_to_vbm()
fig1 = self.ebands.plot(e0="fermie",
ylims=None,
with_gaps=self.with_gaps.value,
max_phfreq=None,
fontsize=8,
**self.fig_kwargs)
fig2 = self.ebands.kpoints.plot(**self.fig_kwargs)
row = pn.Row(self._mp(fig1),
self._mp(fig2)) #, sizing_mode='scale_width')
text = bkw.PreText(text=self.ebands.to_string(verbose=self.verbose))
return pn.Column(row, text, sizing_mode='scale_width')
def get_panel(self):
"""Return tabs with widgets to interact with the FATBANDS.nc file."""
tabs = pn.Tabs()
app = tabs.append
app(("Summary",
pn.Row(
bkw.PreText(text=self.ncfile.to_string(verbose=self.verbose),
sizing_mode="scale_both"))))
app(("e-Bands",
pn.Row(self.get_plot_ebands_widgets(), self.on_plot_ebands_btn)))
if self.ncfile.ebands.kpoints.is_ibz:
# Add DOS tab only if k-sampling.
app(("e-DOS",
pn.Row(self.get_plot_edos_widgets(), self.on_plot_edos_btn)))
# Plot the L-PJDOS grouped by atomic type.
#self.ncfile.plot_pjdos_typeview(lmax=lmax, **self.fig_kwargs)
# Plot the L-PJDOS grouped by L.
#self.ncfile.plot_pjdos_lview(lmax=lmax, **self.fig_kwargs)
# Fermi surface requires a gamma-centered k-mesh
if self.ncfile.ebands.supports_fermi_surface:
app(("Fermi Surface",
pn.Row(self.get_plot_fermi_surface_widgets(),
self.on_plot_fermi_surface_btn)))
elif self.ncfile.ebands.kpoints.is_path:
# NC files have contributions up to L=4 (g channel)
# but here we are intererested in s,p,d terms only so
# we use the optional argument lmax
lmax = 2
# Plot the electronic fatbands grouped by atomic type.
#self.ncfile.plot_fatbands_typeview(lmax=lmax, **self.fig_kwargs)
# Plot the electronic fatbands grouped by L.
#self.ncfile.plot_fatbands_lview(lmax=lmax, **self.fig_kwargs)
else:
raise ValueError("Neither a IBZ nor k-path!")
return tabs
def get_panel(self):
"""Return tabs with widgets to interact with the Abinit output file."""
tabs = pn.Tabs()
app = tabs.append
app(("Summary",
pn.Row(
bkw.PreText(text=self.outfile.to_string(verbose=self.verbose),
sizing_mode="scale_both"))))
df = self.outfile.get_dims_spginfo_dataframe().transpose()
df.index.name = "Dataset"
app(("Dims", self._df(df)))
# Add tabs with plots for the GS/DFPT SCF cycles.
for what in ("GS", "DFPT"):
box = self._get_gridbox(what)
if box is not None:
app(("%s Cycles" % what, box))
#timer = self.get_timer()
#timer.plot_all(**self.fig_kwargs)
return tabs
def get_panel(self):
"""Return tabs with widgets to interact with the |GsrRobot|."""
tabs = pn.Tabs()
app = tabs.append
app(("Summary",
pn.Row(
bkw.PreText(text=self.robot.to_string(verbose=self.verbose),
sizing_mode="scale_both"))))
app(("e-Bands",
pn.Row(self.get_ebands_plotter_widgets(),
self.on_ebands_plotter_btn)))
# Add e-DOS tab only if all ebands have k-sampling.
if all(abifile.ebands.kpoints.is_ibz
for abifile in self.robot.abifiles):
app(("e-DOS",
pn.Row(self.get_edos_plotter_widgets(),
self.on_edos_plotter_btn)))
app(("GSR-DataFrame",
pn.Row(self.gsr_dataframe_btn, self.on_gsr_dataframe_btn)))
return tabs
def get_panel(self):
"""Return tabs with widgets to interact with the DDB file."""
tabs = pn.Tabs()
app = tabs.append
app(("Summary",
pn.Row(
bkw.PreText(text=self.gsr.to_string(verbose=self.verbose),
sizing_mode="scale_both"))))
app(("e-Bands",
pn.Row(self.get_plot_ebands_widgets(), self.on_plot_ebands_btn)))
# Add DOS tab only if k-sampling.
kpoints = self.gsr.ebands.kpoints
if kpoints.is_ibz:
app(("e-DOS",
pn.Row(self.get_plot_edos_widgets(), self.on_plot_edos_btn)))
if self.gsr.ebands.supports_fermi_surface:
# Fermi surface requires gamma-centered k-mesh
app(("Fermi Surface",
pn.Row(self.get_plot_fermi_surface_widgets(),
self.on_plot_fermi_surface_btn)))
return tabs
def __init__(self, plot, tabs): # pylint: disable=redefined-outer-name
"""Initialize form.
:param plot: IsothermPlot instance for validation of results.
:param tabs: Panel tabs instance for triggering tab switching.
"""
self.plot = plot
self.tabs = tabs
# isotherm metadata
self.inp_doi = pw.TextInput(name='Article DOI',
placeholder='10.1021/jacs.9b01891')
self.inp_doi.param.watch(self.on_change_doi, 'value')
self.inp_temperature = pw.TextInput(name='Temperature',
placeholder='303')
self.inp_adsorbent = pw.AutocompleteInput(
name='Adsorbent Material',
options=QUANTITIES['adsorbents']['names'],
placeholder='Zeolite 5A',
case_sensitive=False,
**restrict_kwargs)
self.inp_isotherm_type = pw.Select(
name='Isotherm type',
options=['Select'] + QUANTITIES['isotherm_type']['names'])
self.inp_measurement_type = pw.Select(
name='Measurement type',
options=['Select'] + QUANTITIES['measurement_type']['names'])
self.inp_pressure_scale = pw.Checkbox(
name='Logarithmic pressure scale')
self.inp_isotherm_data = pw.TextAreaInput(
name='Isotherm Data',
height=200,
placeholder=config.SINGLE_COMPONENT_EXAMPLE)
self.inp_figure_image = pw.FileInput(name='Figure snapshot')
# units metadata
self.inp_pressure_units = pw.Select(
name='Pressure units',
options=['Select'] + QUANTITIES['pressure_units']['names'])
self.inp_pressure_units.param.watch(self.on_change_pressure_units,
'value')
self.inp_saturation_pressure = pw.TextInput(
name='Saturation pressure [bar]', disabled=True)
self.inp_adsorption_units = pw.AutocompleteInput(
name='Adsorption Units',
options=QUANTITIES['adsorption_units']['names'],
placeholder='mmol/g',
case_sensitive=False,
**restrict_kwargs)
# digitizer info
self.inp_source_type = pw.TextInput(name='Source description',
placeholder='Figure 1a')
self.inp_tabular = pw.Checkbox(
name='Tabular Data (i.e., not digitized from a graphical source)')
self.inp_digitizer = pw.TextInput(name='Digitized by',
placeholder='Your full name')
# fill form from JSON upload
self.inp_json = pw.FileInput(name='Upload JSON Isotherm')
# buttons
self.btn_prefill = pn.widgets.Button(
name='Prefill (default or from JSON)', button_type='primary')
self.btn_prefill.on_click(self.on_click_prefill)
self.out_info = bw.PreText(
text='Press "Plot" in order to download json.')
self.inp_adsorbates = Adsorbates(show_controls=False, )
self.btn_plot = pn.widgets.Button(name='Plot', button_type='primary')
self.btn_plot.on_click(self.on_click_plot)
for inp in self.required_inputs:
inp.css_classes = ['required']
# create layout
self.layout = pn.Column(
pn.pane.HTML('<h2>Isotherm Digitizer</h2>'),
self.inp_digitizer,
self.inp_doi,
pn.pane.HTML('<hr>'),
self.inp_source_type,
pn.Row(pn.pane.HTML("""Attach Figure Graphics"""),
self.inp_figure_image),
self.inp_measurement_type,
self.inp_adsorbent,
self.inp_adsorbates.column,
self.inp_temperature,
self.inp_isotherm_type,
pn.Row(self.inp_pressure_units, self.inp_saturation_pressure),
self.inp_pressure_scale,
self.inp_adsorption_units,
pn.pane.HTML("""We recommend the
<b><a href='https://apps.automeris.io/wpd/' target="_blank">WebPlotDigitizer</a></b>
for data extraction."""),
self.inp_isotherm_data,
self.inp_tabular,
pn.Row(self.btn_plot, self.btn_prefill, self.inp_json),
self.out_info,
)
def get_kpath(self):
s = self.structure.get_kpath_input_string(
fmt=self.kpath_format.value, line_density=self.line_density.value)
return pn.Row(bkw.PreText(text=s, sizing_mode='stretch_width'))
def spglib_summary(self):
s = self.structure.spget_summary(
symprec=self.spglib_symprec.value,
angle_tolerance=self.spglib_angtol.value)
return pn.Row(bkw.PreText(text=s, sizing_mode='stretch_width'))
def convert(self):
return pn.Row(bkw.PreText(text=self.structure.convert(
fmt=self.output_format.value)),
sizing_mode='stretch_width')
def on_status_btn(self):
if self.status_btn.clicks == 0: return
stream = StringIO()
self.flow.show_status(stream=stream, verbose=self.verbose.value)
return pn.Row(bkw.PreText(text=stream.getvalue()))
def on_corrections_btn(self):
if self.corrections_btn.clicks == 0: return
stream = StringIO()
self.flow.show_corrections(stream=stream)
#flow.show_corrections(status=options.task_status, nids=selected_nids(flow, options))
return pn.Row(bkw.PreText(text=stream.getvalue()))