agat 7.13

Atomic Graph ATtention networks for predicting atomic energies and forces.

AGAT (Atomic Graph ATtention networks)

Installation

Install with conda environment

• Create a new environment

conda create -n agat python==3.10

• Activate the environment

conda activate agat

• Install package

pip install agat

• Install dgl.
  Please navigate to the Get Started page of dgl. For example:

conda install -c dglteam/label/cu118 dgl

• Change dgl backend to tensorflow.

Using AGAT

The documentation of AGAT API is available.

Quick start

Prepare VASP calculations

Collect paths of VASP calculations

• We provided examples of VASP outputs at VASP_calculations_example.
• Find all directories containing OUTCAR file:

  find . -name OUTCAR > paths.log
  

• Remove the string 'OUTCAR' in paths.log.

  sed -i 's/OUTCAR$//g' paths.log
  

• Specify the absolute paths in paths.log.

  sed -i "s#^.#${PWD}#g" paths.log
  

Build database

from agat.data import AgatDatabase
if __name__ == '__main__':
    ad = AgatDatabase(mode_of_NN='ase_dist', num_of_cores=2)
    ad.build()

Train AGAT model

from agat.model import Train
at = Train()
at.fit_energy_model()
at.fit_force_model()

Model prediction

from agat.app import GatApp
energy_model_save_dir = os.path.join('out_file', 'energy_ckpt')
force_model_save_dir = os.path.join('out_file', 'force_ckpt')
graph_build_scheme_dir = 'dataset'
app = GatApp(energy_model_save_dir, force_model_save_dir, graph_build_scheme_dir)
graph, info = app.get_graph('POSCAR')
energy = app.get_energy(graph)
forces = app.get_forces(graph)

Geometry optimization

from ase.io import read
from ase.optimize import BFGS
from agat.app import GatAseCalculator
from agat.default_parameters import default_hp_config
poscar = read('POSCAR')
calculator=GatAseCalculator(energy_model_save_dir,
                            force_model_save_dir,
                            graph_build_scheme_dir)
poscar = Atoms(poscar, calculator=calculator)
dyn = BFGS(poscar, trajectory='test.traj')
dyn.run(**default_hp_config['opt_config'])

Change log

Please check Change_log.md