def test_actual_vasp_files(test_data_files: Path):
vasprun_file = str(test_data_files / "MgO_dos_vasprun.xml")
vasprun = Vasprun(vasprun_file)
dos_data = DosDataFromVasp(vasprun, base_energy=1,
vertical_lines=[0.0]).make_dos_data()
plot_data = dos_data.dos_plot_data({"Mg": [0], "O": [1]})
plotter = DosPlotter(plot_data)
plotter.construct_plot()
plotter.plt.show()
def mock_plt_list(mocker):
mock_plt = mocker.patch("vise.analyzer.plot_dos.plt", auto_spec=True)
mock_1st_ax = mocker.MagicMock()
mock_2nd_ax = mocker.MagicMock()
other_axs_len = dos_data_len - 2
mock_axs = [mock_1st_ax, mock_2nd_ax] + [mocker.MagicMock()] * other_axs_len
mock_plt.subplots.return_value = (None, mock_axs)
plotter = DosPlotter(dos_plot_data=dos_plot_data)
plotter.construct_plot()
return mock_plt, mock_1st_ax, mock_2nd_ax
def test_axs_is_list_when_single_dos_passed():
single_dos = [[DosBySpinEnergy("", [total_up, total_down])]]
dos_info = DosPlotData(relative_energies=relative_energies,
doses=single_dos, names=["total"], energy_range=xlim,
dos_ranges=ylim_set, energy_lines=[0.0, 1.0])
plotter = DosPlotter(dos_plot_data=dos_info)
assert isinstance(plotter._axs, list)
assert len(plotter._axs) == 1
def test_dos_data_pdos_single(pdos_list, dos_data_list):
_, dos_plot_data_w_lim, _ = dos_data_list
pdos_sum = pdos_list[1] + pdos_list[2]
assert dos_plot_data_w_lim.names == ["total", "H", "He"]
assert dos_plot_data_w_lim.doses[1][0].name == "s"
assert dos_plot_data_w_lim.doses[1][1].name == "p"
assert dos_plot_data_w_lim.doses[2][0].name == "s"
assert_array_equal(dos_plot_data_w_lim.doses[1][0].dos, pdos_list[0].s)
assert_array_equal(dos_plot_data_w_lim.doses[1][1].dos, pdos_list[0].p)
assert_array_equal(dos_plot_data_w_lim.doses[2][0].dos, pdos_sum.s)
plotter = DosPlotter(dos_plot_data_w_lim)
plotter.construct_plot()
plotter.plt.show()
def test_actual_plot():
plotter = DosPlotter(dos_plot_data)
plotter.construct_plot()
plotter.plt.show()
# def test_plotly_actual_plot():
# pploter = PlotlyDosPlotter(dos_plot_data)
# pploter.show()
# # 1. imports of your dash app
# import dash
# import dash_html_components as html
# # 2. give each testcase a tcid, and pass the fixture
# # as a function argument, less boilerplate
# def test_bsly001_falsy_child(dash_duo):
# # 3. define your app inside the test function
# app = dash.Dash(__name__)
# app.layout = html.Div(id="nully-wrapper", children=0)
# # 4. host the app locally in a thread, all dash server configs could be
# # passed after the first app argument
# dash_duo.start_server(app)
# # 5. use wait_for_* if your target element is the result of a callback,
# # keep in mind even the initial rendering can trigger callbacks
# dash_duo.wait_for_text_to_equal("#nully-wrapper", "0", timeout=4)
# # 6. use this form if its present is expected at the action point
# assert dash_duo.find_element("#nully-wrapper").text == "0"
# # 7. to make the checkpoint more readable, you can describe the
# # acceptance criterion as an assert message after the comma.
# assert dash_duo.get_logs() == [], "browser console should contain no error"
# # 8. visual testing with percy snapshot
# dash_duo.percy_snapshot("bsly001-layout")
def plot_dos(args: Namespace):
vasprun = Vasprun(args.vasprun)
outcar = Outcar(args.outcar)
band_edge = VaspBandEdgeProperties(vasprun, outcar)
if band_edge.band_gap:
vertical_lines = [band_edge.vbm_info.energy, band_edge.cbm_info.energy]
else:
vertical_lines = [vasprun.efermi]
if args.base_energy is None:
base = vertical_lines[0]
else:
base = args.base_energy
dos_data_from_vasp = \
DosDataFromVasp(vasprun, vertical_lines, base, args.crop_first_value)
dos_data = dos_data_from_vasp.make_dos_data()
ylim_set = None
if args.y_max_ranges:
if dos_data.spin:
ylim_set = [[-y_max, y_max] for y_max in args.y_max_ranges]
else:
ylim_set = [[0, y_max] for y_max in args.y_max_ranges]
structure = vasprun.final_structure
grouped_atom_indices = args.type.grouped_atom_indices(
structure, args.target)
logger.info(f"Grouped atom indices: {grouped_atom_indices}")
plot_data = dos_data.dos_plot_data(grouped_atom_indices,
xlim=args.x_range,
ylim_set=ylim_set)
plot_data.to_json_file()
plotter = DosPlotter(plot_data, args.legend)
plotter.construct_plot()
plotter.plt.savefig(args.filename, format="pdf")