Symgo

Symgo#

Symgo is a Python-based geometry optimization code under constraint of crystal symmetry. Currently pypolymlp and mattersim interfaces are provided.

Algorithm#

Crystal symmetry is used to determine the degrees of freedom for atomic positions and the basis vectors of the crystal structure. The crystal geometry optimization is performed with respect to these degrees of freedom; that is, structural changes are represented as linear combinations of the basis vectors spanning these degrees of freedom.

Usage#

Note

The usage can change in the future.

The GeometryOptimization class is the core of this code. The first and second arguments are the crystal structure and crystal structure is represented by a SymfcAtoms class instance, and the latter should have energy, force, and stress attributes as well as an eval method that takes a SymfcAtoms instance and stores the energy, force, and stress in it. The following is an example using pypolymlp as the force calculator.

from symfc.utils.utils import SymfcAtoms
from symgo.interface.pypolymlp import PypolymlpPropertyCalculator
from symgo.optimization import GeometryOptimization

def relax(
    cell: SymfcAtoms, mlp: PypolymlpPropertyCalculator
) -> SymfcAtoms:
    try:
        go = GeometryOptimization(cell, mlp, verbose=True)
        go.run()
    except ValueError as e:
        if "Geometry optimization failed" in str(e):
            print("Geometry optimization by BFGS failed. Try TNC.")
            go = GeometryOptimization(cell, mlp, verbose=True)
            go.run(method="TNC", xtol=1e-10, ftol=1e-10)
        else:
            raise ValueError(e)

    if not go.relaxed:
        print(
            "Geometry optimization was not performed because of no degree of freedoms."
        )
    return go.structure

History#

The initial code was forked from optimization.py in pypolymlp (see Jan-20-2026: Version 0.1.0).

License#

BSD-3-Clause.

Contributors#

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