SevenNet Examples

Overview

This example demonstrates using SevenNet with the 4KOH_92H2O system to perform various types of calculations.

Example Commands

The sevennet_test.sh script demonstrates four different types of SevenNet calculations:

Molecular Dynamics (MD)

Runs an MD simulation using the 7net-mf-ompa foundation model with mpa modal:

amaceing_sevennet --run_type="MD" --config="{'project_name': '4koh_92h2o_md', 'coord_file': '../../data/system.xyz', 'pbc_list': '[14.2067 0 0 0 14.2067 0 0 0 14.2067]', 'foundation_model': '7net-mf-ompa', 'modal': 'mpa', 'dispersion_via_simenv': 'n', 'temperature': '300', 'pressure': '1.0', 'thermostat': 'Langevin', 'nsteps': 10, 'write_interval': 10, 'timestep': 0.5, 'log_interval': 10, 'print_ext_traj': 'y', 'simulation_environment': 'ase'}"

Multi-Configuration MD (MULTI_MD)

Runs multiple MD simulations with different SevenNet models for comparison:

amaceing_sevennet --run_type="MULTI_MD" --config="{'project_name': '4koh_92h2o_md', 'coord_file': '../../data/system.xyz', 'pbc_list': '[14.2067 0 0 0 14.2067 0 0 0 14.2067]', 'foundation_model': '['7net-0' '7net-mf-ompa']', 'dispersion_via_simenv': '['n' 'n']', 'modal': '['' 'mpa']', 'temperature': '300', 'pressure': '1.0', 'thermostat': 'Langevin', 'nsteps': 10, 'write_interval': 10, 'timestep': 0.5, 'log_interval': 10, 'print_ext_traj': 'y', 'simulation_environment': 'ase'}"

Fine-tuning (FINETUNE)

Fine-tunes a SevenNet foundation model with custom training data:

amaceing_sevennet --run_type="FINETUNE" --config="{'project_name': '4koh_92h2o_ft', 'device': 'cuda', 'train_file': '../../data/train_file_7net.xyz', 'foundation_model': '7net-0', 'epochs': 2, 'batch_size': 4, 'seed': 1, 'lr': 0.01, 'force_loss_ratio': 1.0}"

Energy Recalculation (RECALC)

Recomputes energies for structures using a SevenNet model:

amaceing_sevennet --run_type="RECALC" --config="{'project_name': '4koh_92h2o_recalc', 'coord_file': '../../data/system.xyz', 'pbc_list': '[14.2067 0 0 0 14.2067 0 0 0 14.2067', 'foundation_model': '7net-mf-ompa', 'modal': 'mpa', 'dispersion_via_simenv': 'n', 'simulation_environment': 'ase'}"

Running the Examples

You can run all SevenNet examples with:

bash /path/to/amaceing_toolkit/examples/4KOH_92H2O_333K/sevennet_test.sh

Alternatively, you can use the interactive Q&A interface by running amaceing_sevennet without command-line parameters and following the prompts.

Output Files

After running these examples, each calculation type will create its own directory with the following files:

Molecular Dynamics

sevennet/
├── MD/
│   ├── md_sevennet.py         # Python script for molecular dynamics
│   ├── runscript.sh           # HPC runscript
│   └── sevennet_input.log     # Log of choices

Multi-Configuration MD

sevennet/
├── MULTI_MD/
│   ├── 4koh_92h2o_md_run-1/   # Directory for first configuration (7net-0)
│   │   ├── md_sevennet.py
│   │   └── runscript.sh
│   ├── 4koh_92h2o_md_run-2/   # Directory for second configuration (7net-mf-ompa)
│   │   ├── md_sevennet.py
│   │   └── runscript.sh
│   └── sevennet_input.log     # Log of choices

Fine-tuning

sevennet/
├── FINETUNE/
│   ├── finetune_sevennet.py   # Python script for fine-tuning
│   ├── runscript.sh           # HPC runscript
│   └── sevennet_input.log     # Log of choices

Energy Recalculation

sevennet/
├── RECALC/
│   ├── recalc_sevennet.py     # Python script for energy recalculation
│   └── sevennet_input.log     # Log of choices

Technical Details

  • The simulation cell is cubic with dimensions 14.2067 × 14.2067 × 14.2067 ų

  • Both 7net-0 (base model) and 7net-mf-ompa (multifidelity model) are demonstrated

  • For molecular dynamics, the timestep is set to 0.5 fs

  • The system temperature is set to 300 K

  • The Langevin thermostat is used for temperature control

  • CUDA is used for GPU acceleration in fine-tuning

  • The mpa modal is used with the 7net-mf-ompa foundation model

API Usage Example

The same functionality can be accessed programmatically through the Python API:

from amaceing_toolkit.workflow import sevennet_api

# Molecular dynamics simulation
md_config = {
    'project_name': '4koh_92h2o_md',
    'coord_file': 'system.xyz',
    'pbc_list': [14.2067, 0, 0, 0, 14.2067, 0, 0, 0, 14.2067],
    'foundation_model': '7net-mf-ompa',
    'modal': 'mpa',
    'dispersion_via_simenv': 'n',
    'temperature': '300',
    'pressure': '1.0',
    'thermostat': 'Langevin',
    'nsteps': 10,
    'write_interval': 10,
    'timestep': 0.5,
    'log_interval': 10,
    'print_ext_traj': 'y',
    'simulation_environment': 'ase'
}

sevennet_api(run_type='MD', config=md_config)

# Fine-tuning
ft_config = {
    'project_name': '4koh_92h2o_ft',
    'device': 'cuda',
    'train_file': 'train_file_7net.xyz',
    'foundation_model': '7net-0',
    'epochs': 2,
    'batch_size': 4,
    'seed': 1,
    'lr': 0.01,
    'force_loss_ratio': 1.0
}

sevennet_api(run_type='FINETUNE', config=ft_config)