add stability data, update page

handle large files

handle large files

.gitattributes

@@ -0,0 +1 @@
+.json filter=lfs diff=lfs merge=lfs -text

.gitignore

@@ -2,8 +2,10 @@ tests/
 *.out
 *.ipynb
 *.extxyz
+*.traj
 mlip_arena/tasks/*/*/*/
 
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

mlip_arena/models/__init__.py

@@ -13,6 +13,7 @@ from torch import nn
 with open(Path(__file__).parent / "registry.yaml") as f:
     REGISTRY = yaml.safe_load(f)
 
+
 class MLIP(
     nn.Module,
     PyTorchModelHubMixin,
@@ -25,6 +26,7 @@ class MLIP(
     def forward(self, x):
         return self.model(x)
 
+
 class MLIPCalculator(MLIP, Calculator):
     name: str
     implemented_properties: list[str] = ["energy", "forces", "stress"]
@@ -39,7 +41,9 @@ class MLIPCalculator(MLIP, Calculator):
         calculator_kwargs: dict = {},
     ):
         MLIP.__init__(self, model=model)  # Initialize MLIP part
-        Calculator.__init__(self, restart=restart, atoms=atoms, directory=directory, **calculator_kwargs)  # Initialize ASE Calculator part
+        Calculator.__init__(
+            self, restart=restart, atoms=atoms, directory=directory, **calculator_kwargs
+        )  # Initialize ASE Calculator part
         # Additional initialization if needed
         # self.name: str = self.__class__.__name__
         # self.device = device or torch.device(
@@ -49,7 +53,10 @@ class MLIPCalculator(MLIP, Calculator):
         # self.implemented_properties = ["energy", "forces", "stress"]
 
     def calculate(
-        self, atoms: Atoms, properties: list[str], system_changes: list = all_changes,
+        self,
+        atoms: Atoms,
+        properties: list[str],
+        system_changes: list = all_changes,
     ):
         """Calculate energies and forces for the given Atoms object"""
         super().calculate(atoms, properties, system_changes)

mlip_arena/models/registry.yaml

@@ -3,7 +3,7 @@
 MACE-MP(M):
   module: externals
   class: MACE_MP_Medium
-  family: mace
+  family: mace-mp
   username: cyrusyc # HF username
   last-update: 2024-03-25T14:30:00
   datetime: 2024-03-25T14:30:00 # TODO: Fake datetime

mlip_arena/tasks/stability/chgnet/chloride-salts.json

@@ -0,0 +1 @@
+[{"material_id":"mp-568540","formula":"Ag135Cl135Hg108P216","method":"CHGNet","natoms":594,"total_time_seconds":878.366427,"total_steps":340,"steps_per_second":0.3870821898,"seconds_per_step":2.5834306676,"seconds_per_step_per_atom":0.0043492099},{"material_id":"mp-28361","formula":"Al72Cd36Cl288","method":"CHGNet","natoms":396,"total_time_seconds":2024.840096,"total_steps":49990,"steps_per_second":24.6883692686,"seconds_per_step":0.0405049029,"seconds_per_step_per_atom":0.0001022851},{"material_id":"mp-566301","formula":"As48Cl16O192Pb80","method":"CHGNet","natoms":336,"total_time_seconds":2443.199102,"total_steps":49990,"steps_per_second":20.4608785093,"seconds_per_step":0.0488737568,"seconds_per_step_per_atom":0.0001454576},{"material_id":"mp-553919","formula":"Ag162Cl27F81Mo54O189","method":"CHGNet","natoms":513,"total_time_seconds":49.747983,"total_steps":210,"steps_per_second":4.2212766696,"seconds_per_step":0.2368951571,"seconds_per_step_per_atom":0.0004617839},{"material_id":"mp-567334","formula":"Ag64B384Cl384","method":"CHGNet","natoms":832,"total_time_seconds":6094.657858,"total_steps":4020,"steps_per_second":0.6595940402,"seconds_per_step":1.5160840443,"seconds_per_step_per_atom":0.0018222164},{"material_id":"mp-637206","formula":"Al64Bi64Cl256Se64","method":"CHGNet","natoms":448,"total_time_seconds":2102.670703,"total_steps":49990,"steps_per_second":23.7745263339,"seconds_per_step":0.0420618264,"seconds_per_step_per_atom":0.000093888},{"material_id":"mp-27346","formula":"Al48Cl192Hg72","method":"CHGNet","natoms":312,"total_time_seconds":620.864262,"total_steps":190,"steps_per_second":0.3060250229,"seconds_per_step":3.2677066421,"seconds_per_step_per_atom":0.0104734187},{"material_id":"mp-680722","formula":"As32Cl64O272Pb224","method":"CHGNet","natoms":592,"total_time_seconds":153.997307,"total_steps":540,"steps_per_second":3.5065548257,"seconds_per_step":0.2851801981,"seconds_per_step_per_atom":0.0004817233},{"material_id":"mp-567734","formula":"Al32As96Cl128Se128","method":"CHGNet","natoms":384,"total_time_seconds":1934.45237,"total_steps":49990,"steps_per_second":25.8419389256,"seconds_per_step":0.0386967868,"seconds_per_step_per_atom":0.0001007729},{"material_id":"mp-672352","formula":"Al48Cl288I144","method":"CHGNet","natoms":480,"total_time_seconds":697.476109,"total_steps":1940,"steps_per_second":2.7814572786,"seconds_per_step":0.3595237675,"seconds_per_step_per_atom":0.0007490078},{"material_id":"mp-27863","formula":"Al100Cl100O100","method":"CHGNet","natoms":300,"total_time_seconds":2977.600956,"total_steps":1181,"steps_per_second":0.3966280296,"seconds_per_step":2.5212539848,"seconds_per_step_per_atom":0.0084041799}]

mlip_arena/tasks/stability/equiformer/chloride-salts.json

@@ -0,0 +1 @@
+[{"material_id":"mp-25469","formula":"Al54Cl162","method":"EquiformerV2(OC22)","natoms":216,"total_time_seconds":1289.686627,"total_steps":49990,"steps_per_second":38.7613540789,"seconds_per_step":0.0257988923,"seconds_per_step_per_atom":0.0001194393},{"material_id":"mp-568540","formula":"Ag135Cl135Hg108P216","method":"EquiformerV2(OC22)","natoms":594,"total_time_seconds":855.203801,"total_steps":340,"steps_per_second":0.3975660534,"seconds_per_step":2.5153052971,"seconds_per_step_per_atom":0.0042345207},{"material_id":"mp-568923","formula":"B96Ba192Cl96N192","method":"EquiformerV2(OC22)","natoms":576,"total_time_seconds":799.132371,"total_steps":11900,"steps_per_second":14.891149992,"seconds_per_step":0.0671539808,"seconds_per_step_per_atom":0.0001165868},{"material_id":"mp-568443","formula":"Al32Cl128V16","method":"EquiformerV2(OC22)","natoms":176,"total_time_seconds":1179.514714,"total_steps":49990,"steps_per_second":42.3818367051,"seconds_per_step":0.0235950133,"seconds_per_step_per_atom":0.0001340626},{"material_id":"mp-28361","formula":"Al72Cd36Cl288","method":"EquiformerV2(OC22)","natoms":396,"total_time_seconds":516.631174,"total_steps":1301,"steps_per_second":2.5182375077,"seconds_per_step":0.3971031314,"seconds_per_step_per_atom":0.0010027857},{"material_id":"mp-1214746","formula":"Ba48Cl168Dy24","method":"EquiformerV2(OC22)","natoms":240,"total_time_seconds":1189.535266,"total_steps":40720,"steps_per_second":34.2318560566,"seconds_per_step":0.0292125556,"seconds_per_step_per_atom":0.000121719},{"material_id":"mp-22993","formula":"Ag64Cl64O256","method":"EquiformerV2(OC22)","natoms":384,"total_time_seconds":2998.510846,"total_steps":49990,"steps_per_second":16.6716088643,"seconds_per_step":0.0599822134,"seconds_per_step_per_atom":0.0001562037},{"material_id":"mp-566301","formula":"As48Cl16O192Pb80","method":"EquiformerV2(OC22)","natoms":336,"total_time_seconds":7681.971428,"total_steps":3123,"steps_per_second":0.4065362686,"seconds_per_step":2.4598051322,"seconds_per_step_per_atom":0.0073208486},{"material_id":"mp-555805","formula":"Al36Cl252S36","method":"EquiformerV2(OC22)","natoms":324,"total_time_seconds":2034.579734,"total_steps":49990,"steps_per_second":24.5701847731,"seconds_per_step":0.0406997346,"seconds_per_step_per_atom":0.0001256165},{"material_id":"mp-1214988","formula":"Ag16Cl208Mo96","method":"EquiformerV2(OC22)","natoms":320,"total_time_seconds":1770.09089,"total_steps":49990,"steps_per_second":28.2414876447,"seconds_per_step":0.0354088996,"seconds_per_step_per_atom":0.0001106528},{"material_id":"mp-567334","formula":"Ag64B384Cl384","method":"EquiformerV2(OC22)","natoms":832,"total_time_seconds":3567.962024,"total_steps":4214,"steps_per_second":1.1810663823,"seconds_per_step":0.8466924594,"seconds_per_step_per_atom":0.0010176592},{"material_id":"mp-638061","formula":"Al48Cl192In48","method":"EquiformerV2(OC22)","natoms":288,"total_time_seconds":1576.40944,"total_steps":49990,"steps_per_second":31.7113046468,"seconds_per_step":0.0315344957,"seconds_per_step_per_atom":0.0001094948},{"material_id":"mp-560833","formula":"B72Cl24O240Pb144","method":"EquiformerV2(OC22)","natoms":480,"total_time_seconds":3217.219664,"total_steps":49990,"steps_per_second":15.5382613626,"seconds_per_step":0.0643572647,"seconds_per_step_per_atom":0.0001340776},{"material_id":"mp-560549","formula":"Au64Cl64O192Se64","method":"EquiformerV2(OC22)","natoms":384,"total_time_seconds":2518.062072,"total_steps":49990,"steps_per_second":19.8525685907,"seconds_per_step":0.0503713157,"seconds_per_step_per_atom":0.0001311753},{"material_id":"mp-637206","formula":"Al64Bi64Cl256Se64","method":"EquiformerV2(OC22)","natoms":448,"total_time_seconds":1762.787761,"total_steps":1895,"steps_per_second":1.0750017909,"seconds_per_step":0.9302310084,"seconds_per_step_per_atom":0.0020764085},{"material_id":"mp-510724","formula":"As72Cl24O216Pb120","method":"EquiformerV2(OC22)","natoms":432,"total_time_seconds":2746.961559,"total_steps":49990,"steps_per_second":18.1982888826,"seconds_per_step":0.0549502212,"seconds_per_step_per_atom":0.0001271996},{"material_id":"mp-551456","formula":"Ba80Cl40Cu40O80","method":"EquiformerV2(OC22)","natoms":240,"total_time_seconds":48569.923768,"total_steps":1294,"steps_per_second":0.0266420019,"seconds_per_step":37.5347169768,"seconds_per_step_per_atom":0.1563946541},{"material_id":"mp-23575","formula":"As32Cl96F192Se96","method":"EquiformerV2(OC22)","natoms":416,"total_time_seconds":7242.212461,"total_steps":3086,"steps_per_second":0.4261128787,"seconds_per_step":2.3467960016,"seconds_per_step_per_atom":0.0056413365},{"material_id":"mp-27346","formula":"Al48Cl192Hg72","method":"EquiformerV2(OC22)","natoms":312,"total_time_seconds":56.74321,"total_steps":320,"steps_per_second":5.6394412653,"seconds_per_step":0.1773225312,"seconds_per_step_per_atom":0.0005683414},{"material_id":"mp-30023","formula":"Al48Ba24Cl192","method":"EquiformerV2(OC22)","natoms":264,"total_time_seconds":1444.744189,"total_step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mlip_arena/tasks/stability/mace-mp/chloride-salts.json

@@ -0,0 +1 @@
+[{"material_id":"mp-567334","formula":"Ag64B384Cl384","method":"MACE-MP(M)","natoms":832,"total_time_seconds":3578.503151,"total_steps":40470,"steps_per_second":11.3091978105,"seconds_per_step":0.0884236015,"seconds_per_step_per_atom":0.0001062784},{"material_id":"mp-30273","formula":"Ac96Cl96O96","method":"MACE-MP(M)","natoms":288,"total_time_seconds":1974.313713,"total_steps":49990,"steps_per_second":25.3201908445,"seconds_per_step":0.0394941731,"seconds_per_step_per_atom":0.0001371325},{"material_id":"mp-573465","formula":"Ag320Cl64Te128","method":"MACE-MP(M)","natoms":512,"total_time_seconds":2296.972442,"total_steps":39000,"steps_per_second":16.9788715297,"seconds_per_step":0.0588967293,"seconds_per_step_per_atom":0.0001150327},{"material_id":"mp-27971","formula":"Ac48Cl144","method":"MACE-MP(M)","natoms":192,"total_time_seconds":1228.139194,"total_steps":49990,"steps_per_second":40.7038552668,"seconds_per_step":0.0245676974,"seconds_per_step_per_atom":0.0001279568},{"material_id":"mp-560328","formula":"Ag60Cl12P16S64","method":"MACE-MP(M)","natoms":152,"total_time_seconds":350.457564,"total_steps":14360,"steps_per_second":40.9750037525,"seconds_per_step":0.0244051228,"seconds_per_step_per_atom":0.00016056}]

mlip_arena/tasks/stability/run.py

@@ -277,6 +277,7 @@ def md(
 
         def _callback(dyn: MolecularDynamics = md_runner) -> None:
             step = last_step + dyn.nsteps
+            dyn.atoms.info["restart"] = last_step
             dyn.atoms.info["datetime"] = datetime.now()
             dyn.atoms.info["step"] = step
             if ensemble == "nve":

pyproject.toml

@@ -44,6 +44,7 @@ app = [
     "streamlit",
     "plotly",
     "bokeh==2.4.3",
+    "statsmodels"
 ]
 
 [project.urls]

serve/tasks/homonuclear-diatomics.py

@@ -40,6 +40,8 @@ palette_name = vis.selectbox(
 color_sequence = color_palettes[palette_name] # type: ignore
 
 DATA_DIR = Path("mlip_arena/tasks/diatomics")
+if not methods:
+    st.stop()
 dfs = [pd.read_json(DATA_DIR / method.lower() /  "homonuclear-diatomics.json") for method in methods]
 df = pd.concat(dfs, ignore_index=True)
 df.drop_duplicates(inplace=True, subset=["name", "method"])

serve/tasks/stability.py

@@ -3,26 +3,66 @@ from pathlib import Path
 import numpy as np
 import pandas as pd
 import plotly.colors as pcolors
+import plotly.express as px
 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
+from mlip_arena.models import REGISTRY
+
+DATA_DIR = Path("mlip_arena/tasks/stability")
+
 
 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"])
+models = container.multiselect("MLIPs", REGISTRY.keys(), ['MACE-MP(M)', "CHGNet", "EquiformerV2(OC22)"])
+
+st.markdown("### Settings")
+vis = st.container(border=True)
+# Get all attributes from pcolors.qualitative
+all_attributes = dir(pcolors.qualitative)
+color_palettes = {attr: getattr(pcolors.qualitative, attr) for attr in all_attributes if isinstance(getattr(pcolors.qualitative, attr), list)}
+color_palettes.pop("__all__", None)
+
+palette_names = list(color_palettes.keys())
+palette_colors = list(color_palettes.values())
+
+palette_name = vis.selectbox(
+    "Color sequence",
+    options=palette_names, index=22
+)
+
+color_sequence = color_palettes[palette_name]
+
+if not models:
+    st.stop()
+
+families = [REGISTRY[str(model)]['family'] for model in models]
+
+dfs = [pd.read_json(DATA_DIR / family.lower() /  "chloride-salts.json") for family in families]
+df = pd.concat(dfs, ignore_index=True)
+df.drop_duplicates(inplace=True, subset=["material_id", "formula", "method"])
+
+method_color_mapping = {method: color_sequence[i % len(color_sequence)] for i, method in enumerate(df["method"].unique())}
 
 
-DATA_DIR = Path("mlip_arena/tasks/stability")
 
+# fig = px.scatter(df, x="natoms", y="seconds_per_step", trendline="ols", trendline_options=dict(log_y=True), log_y=True)
+fig = px.scatter(
+    df, x="natoms", y="steps_per_second", 
+    color="method",
+    color_discrete_map=method_color_mapping,
+    trendline="ols", trendline_options=dict(log_x=True), log_x=True
+)
 
 
+event = st.plotly_chart(
+    fig, 
+    key="stability", 
+    on_select="rerun"
+)
 
+event