update ptable, add statbility, update pyproject.toml

mlip_arena/models/registry.yaml

@@ -3,6 +3,7 @@
 MACE-MP(M):
   module: externals
   class: MACE_MP_Medium
+  family: mace
   username: cyrusyc # HF username
   last-update: 2024-03-25T14:30:00
   datetime: 2024-03-25T14:30:00 # TODO: Fake datetime
@@ -20,6 +21,7 @@ MACE-MP(M):
 CHGNet:
   module: externals
   class: CHGNet
+  family: chgnet
   username: cyrusyc
   last-update: 2024-07-08T00:00:00
   datetime: 2024-07-08T00:00:00
@@ -31,6 +33,7 @@ CHGNet:
 EquiformerV2(OC22):
   module: externals
   class: EquiformerV2
+  family: equiformer
   username: cyrusyc
   last-update: 2024-07-08T00:00:00
   datetime: 2024-07-08T00:00:00
@@ -42,6 +45,7 @@ EquiformerV2(OC22):
 eSCN(OC20):
   module: externals
   class: eSCN
+  family: escn
   username: cyrusyc
   last-update: 2024-07-08T00:00:00
   datetime: 2024-07-08T00:00:00

mlip_arena/tasks/stability/run.py

@@ -119,7 +119,7 @@ def _get_ensemble_defaults(
         ase_md_kwargs.pop("externalstress", None)
     elif ensemble == "npt":
         ase_md_kwargs["temperature_K"] = t_schedule[0]
-        ase_md_kwargs["externalstress"] = p_schedule[0] * 1e3 * units.bar
+        ase_md_kwargs["externalstress"] = p_schedule[0] # * 1e3 * units.bar
 
     if isinstance(dynamics, str) and dynamics.lower() == "langevin":
         ase_md_kwargs["friction"] = ase_md_kwargs.get(

pyproject.toml

@@ -26,12 +26,13 @@ classifiers=[
     "Programming Language :: Python :: 3 :: Only",
 ]
 dependencies=[
-    "torch",
     "ase",
+    "torch",
     "torch_dftd>=0.4.0",
     "huggingface_hub",
     "torch-geometric",
-    "safetensors"
+    "safetensors",
+    "pymatgen"
 ]
 
 [project.optional-dependencies]
@@ -39,6 +40,11 @@ m3gnet = ["matgl", "dgl", "torch<=2.2.1"]
 mace = ["mace-torch"]
 chgnet = ["chgnet"]
 fairchem = ["fairchem"]
+app = [
+    "streamlit",
+    "plotly",
+    "bokeh==2.4.3",
+]
 
 [project.urls]
 Homepage = "https://github.com/atomind-ai/mlip-arena"

serve/app.py

@@ -40,6 +40,8 @@ history = st.Page("tools/history.py", title="History", icon=":material/history:"
 ptable = st.Page("tools/ptable.py", title="Periodic table", icon=":material/gradient:")
 
 diatomics = st.Page("tasks/homonuclear-diatomics.py", title="Homonuclear diatomics", icon=":material/target:", default=True)
+stability = st.Page("tasks/stability.py", title="Stability", icon=":material/target:")
+
 
 # if st.session_state.logged_in:
 pg = st.navigation(
@@ -48,7 +50,7 @@ pg = st.navigation(
         # "Reports": [dashboard, bugs, alerts],
         # "Tools": [search, history, ptable],
         "": [leaderboard],
-        "Tasks": [diatomics],
+        "Tasks": [diatomics, stability],
         "Tools": [ptable],
     }
 )

serve/tasks/homonuclear-diatomics.py

@@ -9,6 +9,8 @@ from ase.data import chemical_symbols
 from plotly.subplots import make_subplots
 from scipy.interpolate import CubicSpline
 
+from mlip_arena.models.utils import MLIPMap
+
 st.markdown("# Homonuclear diatomics")
 
 st.markdown("### Methods")

serve/tasks/stability.py

@@ -0,0 +1,28 @@
+from pathlib import Path
+
+import numpy as np
+import pandas as pd
+import plotly.colors as pcolors
+import plotly.graph_objects as go
+import streamlit as st
+from ase.data import chemical_symbols
+from ase.io import read, write
+from plotly.subplots import make_subplots
+from scipy.interpolate import CubicSpline
+
+from mlip_arena.models.utils import MLIPMap
+
+st.markdown("# Stability")
+
+st.markdown("### Methods")
+container = st.container(border=True)
+methods = container.multiselect("MLIPs", ["MACE-MP", "Equiformer", "CHGNet", "MACE-OFF", "eSCN", "ALIGNN"], ["MACE-MP", "Equiformer", "CHGNet", "eSCN", "ALIGNN"])
+
+
+DATA_DIR = Path("mlip_arena/tasks/stability")
+
+
+
+
+
+

serve/tools/ptable.py

@@ -1,93 +1,78 @@
-import streamlit as st
-from ase.data import chemical_symbols
-from pymatgen.core import Element
-
-elements = [Element.from_Z(z) for z in range(1, 119)]
-
-# Define the number of rows and columns in the periodic table
-rows = 9  # There are 7 rows in the conventional periodic table
-columns = 18
-
-# Define a function to display the periodic table
-def display_periodic_table():
-    # elements = [
-    #     (element, element) for element in chemical_symbols[1:]
-    # ]
-
-    # cols = st.columns(18, gap='small', vertical_alignment='bottom')  # Create 18 columns for the periodic table layout
-
-    row = 0
-    for element in elements:
-        symbol = element.symbol
-        atomic_number = element.Z
-        group = element.group
-
-        if element.row > row:
-            cols = st.columns(columns, gap='small', vertical_alignment='bottom')
-        row = element.row
-
-        if element.block == 'f':
-            continue
-
-        with cols[group - 1]:
-            if st.button(symbol, use_container_width=True):
-                st.session_state.selected_element = symbol
-                st.session_state.selected_name = symbol
-                st.rerun()
-                # st.experimental_rerun()
-    
-    for element in elements:
-        symbol = element.symbol
-        atomic_number = element.Z
-        group = element.group
-
-        if element.row > row:
-            cols = st.columns(columns, gap='small', vertical_alignment='bottom')
-        row = element.row
-
-        if element.block == 'f':
-            noble = Element.from_row_and_group(row-1, 18)
-            row += 2
-            group += atomic_number - noble.Z - 2
-        else:
-            continue
-
-        with cols[group - 1]:
-            if st.button(symbol, use_container_width=True):
-                st.session_state.selected_element = symbol
-                st.session_state.selected_name = symbol
-                st.rerun()
-                # st.experimental_rerun()
-    
-    
-    # for idx, (symbol, name) in enumerate(elements):
-    #     with cols[idx % 18]:  # Place each element in the correct column
-    #         if st.button(symbol, use_container_width=True):
-    #             st.session_state.selected_element = symbol
-    #             st.session_state.selected_name = name
-    #             st.experimental_rerun()
-
-# Define a function to display the details of an element
-def display_element_details():
-    symbol = st.session_state.selected_element
-    name = st.session_state.selected_name
-    st.write(f"### {name} ({symbol})")
-    st.write(f"Details about {name} ({symbol}) will be displayed here.")
-    if st.button("Back to Periodic Table"):
-        st.session_state.selected_element = None
-        st.session_state.selected_name = None
-        st.rerun()
-        # st.experimental_rerun()
-
-
-st.title("Periodic Table")
-
-# st.balloons()
-if 'selected_element' not in st.session_state:
-    st.session_state.selected_element = None
-
-if st.session_state.selected_element:
-    display_element_details()
-else:
-    display_periodic_table()
 
+
+# NOTE: https://stackoverflow.com/questions/77062368/streamlit-bokeh-event-callback-to-get-clicked-values
+# Taptool: https://docs.bokeh.org/en/2.4.2/docs/reference/models/tools.html#taptool
+
+import streamlit as st
+from bokeh.plotting import figure
+from bokeh.plotting import figure, show
+from bokeh.sampledata.periodic_table import elements
+from bokeh.transform import dodge, factor_cmap
+
+periods = ["I", "II", "III", "IV", "V", "VI", "VII"]
+groups = [str(x) for x in range(1, 19)]
+
+df = elements.copy()
+df["atomic mass"] = df["atomic mass"].astype(str)
+df["group"] = df["group"].astype(str)
+df["period"] = [periods[x-1] for x in df.period]
+df = df[df.group != "-"]
+df = df[df.symbol != "Lr"]
+df = df[df.symbol != "Lu"]
+
+cmap = {
+    "alkali metal"         : "#a6cee3",
+    "alkaline earth metal" : "#1f78b4",
+    "metal"                : "#d93b43",
+    "halogen"              : "#999d9a",
+    "metalloid"            : "#e08d49",
+    "noble gas"            : "#eaeaea",
+    "nonmetal"             : "#f1d4Af",
+    "transition metal"     : "#599d7A",
+}
+
+TOOLTIPS = [
+    ("Name", "@name"),
+    ("Atomic number", "@{atomic number}"),
+    ("Atomic mass", "@{atomic mass}"),
+    ("Type", "@metal"),
+    ("CPK color", "$color[hex, swatch]:CPK"),
+    ("Electronic configuration", "@{electronic configuration}"),
+]
+
+p = figure(title="Periodic Table (omitting LA and AC Series)", width=1000, height=450,
+           x_range=groups, y_range=list(reversed(periods)),
+           tools="hover", toolbar_location=None, tooltips=TOOLTIPS)
+
+r = p.rect("group", "period", 0.95, 0.95, source=df, fill_alpha=0.6, legend_field="metal",
+           color=factor_cmap('metal', palette=list(cmap.values()), factors=list(cmap.keys())))
+
+text_props = dict(source=df, text_align="left", text_baseline="middle")
+
+x = dodge("group", -0.4, range=p.x_range)
+
+p.text(x=x, y="period", text="symbol", text_font_style="bold", **text_props)
+
+p.text(x=x, y=dodge("period", 0.3, range=p.y_range), text="atomic number",
+       text_font_size="11px", **text_props)
+
+p.text(x=x, y=dodge("period", -0.35, range=p.y_range), text="name",
+       text_font_size="7px", **text_props)
+
+p.text(x=x, y=dodge("period", -0.2, range=p.y_range), text="atomic mass",
+       text_font_size="7px", **text_props)
+
+p.text(x=["3", "3"], y=["VI", "VII"], text=["LA", "AC"], text_align="center", text_baseline="middle")
+
+p.outline_line_color = None
+p.grid.grid_line_color = None
+p.axis.axis_line_color = None
+p.axis.major_tick_line_color = None
+p.axis.major_label_standoff = 0
+p.legend.orientation = "horizontal"
+p.legend.location ="top_center"
+p.hover.renderers = [r] # only hover element boxes
+
+st.bokeh_chart(p, use_container_width=True)
+
+# show(p)