Build graph

Python script

You may want to build a topology graph without atomic energy, forces, stress, and cell. You can achieve this by setting topology_only=True when instantiating the CrystalGraph object:

import os
from agat.data import CrystalGraph
from agat.data import load_graph_build_scheme

graph_build_method = load_graph_build_method(os.path.join('dataset', 'graph_build_scheme.json'))
cg = CrystalGraph(**{**graph_build_method, **{'topology_only': True}})
graph, prop = cg.get_graph('POSCAR')
print(graph.ndata)
print('==========')
print(graph.edata)

You can further save the graph as a binary file to the disk:

from dgl import save_graphs
save_graphs("graph.bin", [graph], prop)