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 scipy.optimize import curve_fit from mlip_arena.models import REGISTRY DATA_DIR = Path("mlip_arena/tasks/stability") st.markdown(""" # High Pressure Stability Stable and accurate molecular dynamics (MD) simulations are important for understanding the properties of matters. However, many MLIPs have unphysical potential energy surface (PES) at the short-range interatomic distances or under many-body effect. These are often manifested as softened repulsion and hole in the PES and can lead to incorrect and sampling of the phase space. Here, we analyze the stability of the MD simulations under high pressure conditions by gradually increasing the pressure from 0 to 1000 GPa at 300K until the system crashes or completes 100 ps trajectory. This benchmark also explores faster the far-from-equilibrium dynamics of the system and the "durability" of the MLIPs under extreme conditions. """) st.markdown("### Methods") container = st.container(border=True) valid_models = [model for model, metadata in REGISTRY.items() if Path(__file__).stem in metadata.get("gpu-tasks", [])] models = container.multiselect("MLIPs", valid_models, ["MACE-MP(M)", "CHGNet", "ORB", "SevenNet"]) 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() @st.cache_data def get_data(models): 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"]) return df df = get_data(models) method_color_mapping = { method: color_sequence[i % len(color_sequence)] for i, method in enumerate(df["method"].unique()) } ### # Determine the bin edges for the entire dataset to keep them consistent across groups # bins = np.histogram_bin_edges(df['total_steps'], bins=10) max_steps = df["total_steps"].max() max_target_steps = df["target_steps"].max() bins = np.append(np.arange(0, max_steps + 1, max_steps // 10), max_target_steps) bin_labels = [f"{bins[i]}-{bins[i+1]}" for i in range(len(bins)-1)] num_bins = len(bin_labels) colormap = px.colors.sequential.Darkmint_r indices = np.linspace(0, len(colormap) - 1, num_bins, dtype=int) bin_colors = [colormap[i] for i in indices] # bin_colors[-1] = px.colors.sequential.Greens[-1] # Initialize a dictionary to hold the counts for each method and bin range # counts_per_method = {method: [0] * len(bin_labels) for method in df["method"].unique()} counts_per_method = {method: [0] * len(bin_labels) for method in df["method"].unique()} # Populate the dictionary with counts for method, group in df.groupby("method"): counts, _ = np.histogram(group["total_steps"], bins=bins) counts_per_method[method] = counts # Sort the dictionary by the percentage of the last bin counts_per_method = {k: v for k, v in sorted(counts_per_method.items(), key=lambda item: item[1][-1]/sum(item[1]))} count_or_percetange = st.toggle("show counts", False) @st.experimental_fragment() def plot_md_steps(counts_per_method, count_or_percetange): # Create a figure fig = go.Figure() # Add a bar for each bin range across all methods for i, bin_label in enumerate(bin_labels): for method, counts in counts_per_method.items(): fig.add_trace(go.Bar( # name=method, # This will be the legend entry x=[counts[i]/counts.sum()*100] if not count_or_percetange else [counts[i]], y=[method], # Method as the y-axis category # name=bin_label, orientation="h", # Horizontal bars marker=dict( color=bin_colors[i], line=dict(color="rgb(248, 248, 249)", width=1) ), text=f"{bin_label}: {counts[i]/counts.sum()*100:.0f}%", width=0.5 )) # Update the layout to stack the bars fig.update_layout( barmode="stack", # Stack the bars title="Total MD steps (before crash or completion)", xaxis_title="Percentage (%)" if not count_or_percetange else "Count", yaxis_title="Method", showlegend=False ) # bins = np.linspace(0, 0.9, 10) # for method, data in df.groupby("method"): # # print(method, data) # counts, bins = np.histogram(data['total_steps']) # bin_labels = [f"{int(bins[i])}-{int(bins[i+1])}" for i in range(len(bins)-1)] # # Create a horizontal bar chart # fig = go.Figure(go.Bar( # x=[counts[i]], # Count for this bin # y=[method], # Method as the y-axis category # # x=counts, # Bar lengths # # y=bin_labels, # Bin labels as y-tick labels # orientation='h' # Horizontal bars # )) # # Update layout for clarity # fig.update_layout( # title="Histogram of Total Steps", # xaxis_title="Count", # yaxis_title="Total Steps Range" # ) st.plotly_chart(fig) plot_md_steps(counts_per_method, count_or_percetange) ### # st.markdown(""" # ## Runtime Analysis # """) def func(x, a, n): return a * x ** (-n) @st.experimental_fragment() def plot_speed(df, method_color_mapping): fig = px.scatter( df, x="natoms", y="steps_per_second", color="method", size="total_steps", hover_data=["material_id", "formula"], color_discrete_map=method_color_mapping, # trendline="ols", # trendline_options=dict(log_x=True), log_x=True, # log_y=True, # range_y=[1, 1e2], range_x=[df["natoms"].min()*0.9, df["natoms"].max()*1.1], # range_x=[1e3, 1e2], title="Inference speed (on single A100 GPU)", labels={"steps_per_second": "Steps per second", "natoms": "Number of atoms"}, ) x = np.linspace(df["natoms"].min(), df["natoms"].max(), 100) for method, data in df.groupby("method"): data.dropna(subset=["steps_per_second"], inplace=True) popt, pcov = curve_fit(func, data["natoms"], data["steps_per_second"]) fig.add_trace(go.Scatter( x=x, y=func(x, *popt), mode="lines", # name='Fit', line=dict(color=method_color_mapping[method], width=3), showlegend=False, name=f"{popt[0]:.2f}N^{-popt[1]:.2f}", hovertext=f"{popt[0]:.2f}N^{-popt[1]:.2f}", )) st.plotly_chart(fig) plot_speed(df, method_color_mapping)