catbench

CatBench

CatBench: Benchmark Framework for Graph Neural Networks in Adsorption Energy Predictions

Installation

pip install catbench

Overview

CatBench is a comprehensive benchmarking framework designed to evaluate Graph Neural Networks (GNNs) for adsorption energy predictions. It provides tools for data processing, model evaluation, and result analysis.

Usage Workflow

1. Data Processing

CatBench supports two types of data sources:

A. Direct from Catalysis-Hub

# Import the catbench package
import catbench

# Process data from Catalysis-Hub
catbench.cathub_preprocess("Catalysis-Hub_Dataset_tag")

Example:

# Process specific dataset from Catalysis-Hub
# Using AraComputational2022 as an example
catbench.cathub_preprocess("AraComputational2022")

B. User Dataset

For custom datasets, prepare your data structure as follows:

The data structure should include:

• Gas references (gas/) containing VASP output files for gas phase molecules
• Surface structures (surface1/, surface2/, etc.) containing:
  • Clean slab calculations (slab/)
  • Adsorbate-surface systems (H/, OH/, etc.)

Note: Each directory must contain CONTCAR and OSZICAR files. Other VASP output files can be present as well - the process_output function will automatically clean up (delete) all files except CONTCAR and OSZICAR.

data/
├── gas/
│   ├── H2gas/
│   │   ├── CONTCAR
│   │   └── OSZICAR
│   └── H2Ogas/
│       ├── CONTCAR
│       └── OSZICAR
├── surface1/
│   ├── slab/
│   │   ├── CONTCAR
│   │   └── OSZICAR
│   ├── H/
│   │   ├── CONTCAR
│   │   └── OSZICAR
│   └── OH/
│       ├── CONTCAR
│       └── OSZICAR
└── surface2/
    ├── slab/
    │   ├── CONTCAR
    │   └── OSZICAR
    ├── H/
    │   ├── CONTCAR
    │   └── OSZICAR
    └── OH/
        ├── CONTCAR
        └── OSZICAR

Then process using:

import catbench

# Define coefficients for calculating adsorption energies
# For each adsorbate, specify coefficients based on the reaction equation:
# Example for H*: 
#   E_ads(H*) = E(H*) - E(slab) - 1/2 E(H2_gas)
# Example for OH*:
#   E_ads(OH*) = E(OH*) - E(slab) + 1/2 E(H2_gas) - E(H2O_gas)

coeff_setting = {
    "H": {
        "slab": -1,      # Coefficient for clean surface
        "adslab": 1,     # Coefficient for adsorbate-surface system
        "H2gas": -1/2,   # Coefficient for H2 gas reference
    },
    "OH": {
        "slab": -1,      # Coefficient for clean surface
        "adslab": 1,     # Coefficient for adsorbate-surface system
        "H2gas": +1/2,   # Coefficient for H2 gas reference
        "H2Ogas": -1,    # Coefficient for H2O gas reference
    },
}

# This will clean up directories and keep only CONTCAR and OSZICAR files
catbench.process_output("data", coeff_setting)
catbench.userdata_preprocess("data")

2. Execute Benchmark

A. General Benchmark

This is a general benchmark setup. The range() value determines the number of repetitions for reproducibility testing. If reproducibility testing is not needed, it can be set to 1.

import catbench
from your_calculator import Calculator

# Prepare calculator list
# range(5): Run 5 times for reproducibility testing
# range(1): Single run when reproducibility testing is not needed
calculators = [Calculator() for _ in range(5)]

config = {}
catbench.execute_benchmark(calculators, **config)

After execution, the following files and directories will be created:

1. A result directory is created to store all calculation outputs.
2. Inside the result directory, subdirectories are created for each GNN.
3. Each GNN's subdirectory contains:
   • gases/: Gas reference molecules for adsorption energy calculations
   • log/: Slab and adslab calculation logs
   • traj/: Slab and adslab trajectory files
   • {GNN_name}_gases.json: Gas molecules energies
   • {GNN_name}_outlier.json: Outlier detection status for each adsorption data
   • {GNN_name}_result.json: Raw data (energies, calculation times, outlier detection, slab displacements, etc.)

B. Single-point Calculation Benchmark

import catbench
from your_calculator import Calculator

calculator = Calculator()

config = {}
catbench.execute_benchmark_single(calculator, **config)

3. Analysis

import catbench

config = {}
catbench.analysis_GNNs(**config)

The analysis function processes the calculation data stored in the result directory and generates:

1. A plot/ directory:

   • Parity plots for each GNN model
   • Combined parity plots for comparison
   • Performance visualization plots

2. An Excel file {dataset_name}_Benchmarking_Analysis.xlsx:

   • Comprehensive performance metrics for all GNN models
   • Statistical analysis of predictions
   • Model-specific details and parameters

Single-point Calculation Analysis

import catbench

config = {}
catbench.analysis_GNNs_single(**config)

Outputs

1. Adsorption Energy Parity Plot (mono_version & multi_version)

You can plot adsorption energy parity plots for each adsorbate across all GNNs, either simply or by adsorbate.

2. Comprehensive Performance Table

View various metrics for all GNNs.

3. Outlier Analysis

See how outliers are detected for all GNNs.

4. Analysis by Adsorbate

Observe how each GNN predicts for each adsorbate.

Configuration Options

execute_benchmark

Option	Description	Default
GNN_name	Name of your GNN	Required
benchmark	Name of benchmark dataset	Required
F_CRIT_RELAX	Force convergence criterion	0.05
N_CRIT_RELAX	Maximum number of steps	999
rate	Fix ratio for surface atoms (0: use original constraints, >0: fix atoms from bottom up to specified ratio)	0.5
disp_thrs_slab	Displacement threshold for slab	1.0
disp_thrs_ads	Displacement threshold for adsorbate	1.5
again_seed	Seed variation threshold	0.2
damping	Damping factor for optimization	1.0
gas_distance	Cell size for gas molecules	10
optimizer	Optimization algorithm	"LBFGS"

execute_benchmark_single

Option	Description	Default
GNN_name	Name of your GNN	Required
benchmark	Name of benchmark dataset	Required
gas_distance	Cell size for gas molecules	10

analysis_GNNs

Option	Description	Default
Benchmarking_name	Name for output files	Current directory name
calculating_path	Path to result directory	"./result"
GNN_list	List of GNNs to analyze	All GNNs in result directory
target_adsorbates	Target adsorbates to analyze	All adsorbates
specific_color	Color for plots	"black"
min	Plot y-axis minimum	Auto-calculated
max	Plot y-axis maximum	Auto-calculated
figsize	Figure size	(9, 8)
mark_size	Marker size	100
linewidths	Line width	1.5
dpi	Plot resolution	300
legend_off	Toggle legend	False
error_bar_display	Toggle error bars	False

License

This project is licensed under the MIT License - see the LICENSE file for details.

Citation

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