ORB Examples¶

Overview¶

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

Example Commands¶

The orb_test.sh script demonstrates four different types of ORB calculations:

Molecular Dynamics (MD)¶

Runs an MD simulation using the orb_v3_conservative_inf foundation model with omat modal:

amaceing_orb --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': 'orb_v3_conservative_inf', 'modal': 'omat', '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'}"

Multi-Configuration MD (MULTI_MD)¶

Runs multiple MD simulations with different ORB models for comparison:

amaceing_orb --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': '['orb_v2' 'orb_v3_conservative_inf']', 'dispersion_via_simenv': '['n' 'n']', 'modal': '['' 'omat']', 'temperature': '300', 'pressure': '1.0', 'thermostat': 'Langevin', 'nsteps': 10, 'write_interval': 10, 'timestep': 0.5, 'log_interval': 10, 'print_ext_traj': 'y'}"

Fine-tuning (FINETUNE)¶

Fine-tunes an ORB foundation model with custom training data:

amaceing_orb --run_type="FINETUNE" --config="{'project_name': '4koh_92h2o_ft', 'train_file': '../../data/train_file_7net.xyz', 'foundation_model': 'orb_v2', 'epochs': 2, 'batch_size': 4, 'seed': 1, 'lr': 0.0003, 'force_loss_ratio': 1.0}"

Energy Recalculation (RECALC)¶

Recomputes energies for structures using an ORB model:

amaceing_orb --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': 'orb_v3_conservative_inf', 'modal': 'omat', 'dispersion_via_simenv': 'n'}"

Running the Examples¶

You can run all ORB examples with:

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

Alternatively, you can use the interactive Q&A interface by running amaceing_orb 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_orb.py             # Python script for molecular dynamics
│   ├── runscript.sh          # HPC runscript
│   └── orb_input.log         # Log of choices

Multi-Configuration MD¶

sevennet/
├── MULTI_MD/
│   ├── 4koh_92h2o_md_run-1/  # Directory for first configuration (orb_v2)
│   │   ├── md_orb.py
│   │   └── runscript.sh
│   ├── 4koh_92h2o_md_run-2/  # Directory for second configuration (orb_v3_conservative_inf)
│   │   ├── md_orb.py
│   │   └── runscript.sh
│   └── orb_input.log         # Log of choices

Fine-tuning¶

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

Energy Recalculation¶

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

Technical Details¶

The simulation cell is cubic with dimensions 14.2067 × 14.2067 × 14.2067 Å³
Both orb_v2 and orb_v3_conservative_inf foundation models 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
The omat modal is used with the orb_v3_conservative_inf foundation model

API Usage Example¶

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

from amaceing_toolkit.workflow import orb_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': 'orb_v3_conservative_inf',
    'modal': 'omat',
    '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'
}

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

# Fine-tuning
ft_config = {
    'project_name': '4koh_92h2o_ft',
    'train_file': 'train_file_7net.xyz',
    'foundation_model': 'orb_v2',
    'epochs': 2,
    'batch_size': 4,
    'seed': 1,
    'lr': 0.0003,
    'force_loss_ratio': 1.0
}

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