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‎crystal_toolkit/components/pourbaix.py‎

Lines changed: 4 additions & 323 deletions
Original file line numberDiff line numberDiff line change
@@ -127,173 +127,6 @@ class PourbaixDiagramComponent(MPComponent):
127127
}
128128
)
129129

130-
# @staticmethod
131-
# def get_figure_with_shapes(
132-
# pourbaix_diagram, heatmap_entry=None, heatmap_as_contour=True, show_labels=True
133-
# ):
134-
# """
135-
# Deprecated. This method returns a figure with Pourbaix domains as "shapes" and labels
136-
# as "annotations." The new figure method instead returns a Pourbaix diagram with
137-
# domains and labels as independent traces, so that they can be interacted with and
138-
# placed on a legend.
139-
#
140-
# Static method for getting plotly figure from a Pourbaix diagram.
141-
#
142-
# Args:
143-
# pourbaix_diagram (PourbaixDiagram): Pourbaix diagram to plot
144-
# heatmap_entry (PourbaixEntry): id for the heatmap generation
145-
# heatmap_as_contour (bool): if True, display contours, if False heatmap as grid
146-
#
147-
# Returns:
148-
# (dict) figure layout
149-
#
150-
# """
151-
# # TODO: fix mpid problem. Can't attach from mpid without it being a structure.
152-
# data = []
153-
#
154-
# # Get data for heatmap
155-
# if heatmap_entry is not None:
156-
# ph_range = np.arange(-2, 16.001, 0.1)
157-
# v_range = np.arange(-2, 4.001, 0.1)
158-
# ph_mesh, v_mesh = np.meshgrid(ph_range, v_range)
159-
# decomposition_e = pourbaix_diagram.get_decomposition_energy(
160-
# heatmap_entry, ph_mesh, v_mesh
161-
# )
162-
#
163-
# # Generate hoverinfo
164-
# hovertexts = []
165-
# for ph_val, v_val, de_val in zip(
166-
# ph_mesh.ravel(), v_mesh.ravel(), decomposition_e.ravel()
167-
# ):
168-
# hovertext = [
169-
# f"∆G<sub>pbx</sub>={de_val:.2f}",
170-
# f"ph={ph_val:.2f}",
171-
# f"V={v_val:.2f}",
172-
# ]
173-
# hovertext = "<br>".join(hovertext)
174-
# hovertexts.append(hovertext)
175-
# hovertexts = np.reshape(hovertexts, list(decomposition_e.shape))
176-
#
177-
# # Enforce decomposition limit energy
178-
# decomposition_e = np.min(
179-
# [decomposition_e, np.ones(decomposition_e.shape)], axis=0
180-
# )
181-
#
182-
# if not heatmap_as_contour:
183-
# # Plotly needs a list here for validation
184-
# h_map = go.Heatmap(
185-
# x=list(ph_range),
186-
# y=list(v_range),
187-
# z=decomposition_e,
188-
# text=hovertexts,
189-
# hoverinfo="text",
190-
# colorbar={
191-
# "title": "∆G<sub>pbx</sub> (eV/atom)",
192-
# "titleside": "right",
193-
# },
194-
# colorscale=PourbaixDiagramComponent.colorscale,
195-
# zmin=0,
196-
# zmax=1,
197-
# )
198-
# data.append(h_map)
199-
#
200-
# else:
201-
#
202-
# h_map = go.Contour(
203-
# z=decomposition_e,
204-
# x=list(ph_range),
205-
# y=list(v_range),
206-
# colorscale=PourbaixDiagramComponent.colorscale, # or magma
207-
# zmin=0,
208-
# zmax=1,
209-
# connectgaps=True,
210-
# line_smoothing=0,
211-
# line_width=0,
212-
# contours_coloring="heatmap",
213-
# text=hovertexts,
214-
# )
215-
# data.insert(0, h_map)
216-
#
217-
# shapes = []
218-
# xy_data = []
219-
# labels = []
220-
#
221-
# for entry, vertices in pourbaix_diagram._stable_domain_vertices.items():
222-
# formula = entry.name
223-
# clean_formula = PourbaixDiagramComponent.clean_formula(formula)
224-
#
225-
# # Generate annotation
226-
# xy_data.append(np.average(vertices, axis=0))
227-
# labels.append(clean_formula)
228-
#
229-
# # Info on SVG paths: https://developer.mozilla.org/en-US/docs/Web/SVG/Tutorial/Paths
230-
# # Move to first point
231-
# path = "M {},{}".format(*vertices[0])
232-
# # Draw lines to each other point
233-
# path += "".join("L {},{}".format(*vertex) for vertex in vertices[1:])
234-
# # Close path
235-
# path += "Z"
236-
#
237-
# # Note that the lines and fills are added separately
238-
# # so that the lines but not the fills will show up on heatmap.
239-
# # This may be condensable in the future if plotly adds a more
240-
# # general z-ordering of objects
241-
#
242-
# # Fill with turquoise if solution
243-
# if heatmap_entry is None:
244-
# fillcolor = "White" if "Ion" in entry.phase_type else "PaleTurquoise"
245-
# shape = go.layout.Shape(
246-
# type="path",
247-
# path=path,
248-
# fillcolor=fillcolor,
249-
# layer="below",
250-
# )
251-
# shapes.append(shape)
252-
#
253-
# # Add lines separately so they show up on heatmap
254-
# shape = go.layout.Shape(
255-
# type="path",
256-
# path=path,
257-
# fillcolor="rgba(0,0,0,0)",
258-
# line={"color": "Black", "width": 1},
259-
# )
260-
# shapes.append(shape)
261-
#
262-
# layout = {**PourbaixDiagramComponent.default_plot_style}
263-
# layout.update({"shapes": shapes})
264-
#
265-
# if show_labels:
266-
# if len(pourbaix_diagram.pbx_elts) == 1:
267-
# # Add annotations to layout
268-
# annotations = [
269-
# {
270-
# "align": "center",
271-
# "font": {"color": "#000000", "size": 15.0},
272-
# "opacity": 1,
273-
# "showarrow": False,
274-
# "text": label,
275-
# "x": x,
276-
# "xanchor": "center",
277-
# "yanchor": "auto",
278-
# # "xshift": -10,
279-
# # "yshift": -10,
280-
# "xref": "x",
281-
# "y": y,
282-
# "yref": "y",
283-
# }
284-
# for (x, y), label in zip(xy_data, labels)
285-
# ]
286-
# layout.update({"annotations": annotations})
287-
# else:
288-
# x, y = zip(*xy_data)
289-
# data.append(
290-
# go.Scatter(x=x, y=y, text=labels, hoverinfo="text", mode="markers")
291-
# )
292-
#
293-
# figure = go.Figure(data=data, layout=layout)
294-
#
295-
# return figure
296-
297130
@staticmethod
298131
def get_figure(
299132
pourbaix_diagram: PourbaixDiagram, heatmap_entry=None, show_water_lines=True
@@ -820,23 +653,8 @@ def update_element_specific_sliders(
820653

821654
comp_inputs = []
822655
conc_inputs = []
823-
for element in sorted(elements):
824-
if len(elements) > 1:
825-
"""
826-
comp_input = html.Div(
827-
[
828-
self.get_slider_input(
829-
f"comp-{element}",
830-
default=comp_defaults[element],
831-
label=f"Composition of {element}",
832-
domain=[0, 1],
833-
step=0.01,
834-
)
835-
]
836-
)
837-
comp_inputs.append(comp_input)
838-
"""
839656

657+
for element in sorted(elements):
840658
conc_input = html.Div(
841659
[
842660
self.get_numerical_input(
@@ -853,11 +671,6 @@ def update_element_specific_sliders(
853671
conc_inputs.append(conc_input)
854672

855673
comp_conc_controls = []
856-
# comp_conc_controls.append(
857-
# ctl.Block(html.Div(id=self.id("display-composition")))
858-
# )
859-
# if comp_inputs and (not show_heatmap) and (not heatmap_entry):
860-
# comp_conc_controls += comp_inputs
861674
comp_conc_controls += comp_inputs
862675

863676
ion_label = (
@@ -870,7 +683,9 @@ def update_element_specific_sliders(
870683
comp_conc_controls += conc_inputs
871684

872685
#
873-
comp_panel_style = {"display": "block"}
686+
comp_panel_style = {"display": "none"}
687+
if len(elements) > 1:
688+
comp_panel_style = {"display": "block"}
874689

875690
#
876691
elements = [element.symbol for element in elements]
@@ -889,120 +704,6 @@ def update_element_specific_sliders(
889704
title,
890705
)
891706

892-
"""
893-
@app.callback(
894-
Output(self.id("element_specific_controls"), "children"),
895-
Output(self.id("ext-link"), "hidden"),
896-
Output(self.id("ext-link"), "href"),
897-
Input(self.id(), "data"),
898-
Input(self.get_kwarg_id("heatmap_choice"), "value"),
899-
State(self.get_kwarg_id("show_heatmap"), "value"),
900-
prevent_initial_call=True,
901-
)
902-
def update_element_specific_sliders(entries, heatmap_choice, show_heatmap):
903-
if (not entries) or (not heatmap_choice[0]):
904-
raise PreventUpdate
905-
906-
elements = set()
907-
908-
kwargs = self.reconstruct_kwargs_from_state()
909-
heatmap_choice = kwargs.get("heatmap_choice")
910-
show_heatmap = kwargs.get("show_heatmap")
911-
heatmap_entry = None
912-
913-
for entry in entries:
914-
if entry["entry_id"].startswith("mp"):
915-
composition = Composition(entry["entry"]["composition"])
916-
elements.update(composition.elements)
917-
if entry["entry_id"] == heatmap_choice:
918-
heatmap_entry = entry
919-
920-
# exclude O and H
921-
elements = elements - ELEMENTS_HO
922-
923-
comp_defaults = {element: 1 / len(elements) for element in elements}
924-
925-
comp_inputs = []
926-
conc_inputs = []
927-
for element in sorted(elements):
928-
if len(elements) > 1:
929-
comp_input = html.Div(
930-
[
931-
self.get_slider_input(
932-
f"comp-{element}",
933-
default=comp_defaults[element],
934-
label=f"Composition of {element}",
935-
domain=[0, 1],
936-
step=0.01,
937-
)
938-
]
939-
)
940-
comp_inputs.append(comp_input)
941-
942-
conc_input = html.Div(
943-
[
944-
self.get_numerical_input(
945-
f"conc-{element}",
946-
default=1e-6,
947-
label=f"Concentration of {element} ion",
948-
style={"width": "10rem"},
949-
)
950-
]
951-
)
952-
953-
conc_inputs.append(conc_input)
954-
955-
comp_conc_controls = []
956-
if comp_inputs and (not show_heatmap) and (not heatmap_entry):
957-
comp_conc_controls += comp_inputs
958-
comp_conc_controls.append(
959-
ctl.Block(html.Div(id=self.id("display-composition")))
960-
)
961-
if len(elements) > 1:
962-
comp_conc_controls.append(ctl.Label("Set Ion Concentrations"))
963-
else:
964-
comp_conc_controls.append(ctl.Label("Set Ion Concentration"))
965-
comp_conc_controls += conc_inputs
966-
967-
# external link to detail page
968-
mpid_wo_function = "mp-" + heatmap_choice.split("-")[1]
969-
external_link = (
970-
f"https://next-gen.materialsproject.org/materials/{mpid_wo_function}"
971-
)
972-
return html.Div(comp_conc_controls), False, external_link
973-
974-
975-
@app.callback(
976-
Output(self.id("display-composition"), "children"),
977-
Input(self.id("element_specific_controls"), "children"),
978-
prevent_initial_call=True,
979-
# Input(self.get_all_kwargs_id(), "value"),
980-
)
981-
def update_displayed_composition(dependency): # **kwargs):
982-
kwargs = self.reconstruct_kwargs_from_state()
983-
984-
comp_dict = {}
985-
for key, val in kwargs.items():
986-
if "comp" in key: # keys are encoded like "comp-Ag"
987-
el = key.split("-")[1]
988-
comp_dict[el] = val
989-
comp_dict = comp_dict or None
990-
if not comp_dict:
991-
return ""
992-
993-
try:
994-
comp = Composition(comp_dict)
995-
formula = Composition(
996-
comp.get_integer_formula_and_factor()[0]
997-
).reduced_formula
998-
except Exception:
999-
return html.Small(
1000-
"Invalid composition selected.", style={"color": "red"}
1001-
)
1002-
1003-
return html.Small(f"Pourbaix composition set to {unicodeify(formula)}.")
1004-
"""
1005-
1006707
@cache.memoize(timeout=5 * 60)
1007708
def get_pourbaix_diagram(pourbaix_entries, **kwargs):
1008709
return PourbaixDiagram(pourbaix_entries, **kwargs)
@@ -1030,8 +731,6 @@ def make_figure(
1030731
comp_text,
1031732
dependency2,
1032733
) -> go.Figure:
1033-
# show_heatmap, heatmap_choice, filter_solids
1034-
1035734
if pourbaix_entries is None:
1036735
raise PreventUpdate
1037736

@@ -1077,21 +776,7 @@ def make_figure(
1077776
for element, coeff in heatmap_entry.composition.items()
1078777
if element not in ELEMENTS_HO
1079778
}
1080-
"""
1081-
else:
1082-
heatmap_entry = None
1083-
1084-
# otherwise, user sets comp_dict
1085-
comp_dict = {}
1086-
# e.g. kwargs contains {"comp-Ag": 0.5, "comp-Fe": 0.5},
1087-
# essentially {slider_name: slider_value}
1088-
1089-
comp_dict = {}
1090-
for comp_val, element in zip(comp_list, elements):
1091-
comp_dict[element] = comp_val
1092779

1093-
comp_dict = comp_dict or None
1094-
"""
1095780
conc_dict = {}
1096781
# e.g. kwargs contains {"conc-Ag": 1e-6, "conc-Fe": 1e-4},
1097782
# essentially {slider_name: slider_value}
@@ -1129,7 +814,3 @@ def make_figure(
1129814
False,
1130815
html.Small(f"Pourbaix composition set to {unicodeify(formula)}."),
1131816
)
1132-
1133-
# TODO
1134-
# def graph_layout(self):
1135-
# return self._sub_layouts["graph"]

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