materialsvirtuallab/matcalc

A python library for calculating materials properties from the PES

MatCalc

Docs

materialsvirtuallab.github.io/matcalc

Introduction

MatCalc is a Python library for calculating material properties from the potential energy surface (PES). The PES can come from DFT or, more commonly, from machine learning interatomic potentials (MLIPs).

Calculating material properties often requires involved setups of various simulation codes. The goal of MatCalc is to provide a simplified, consistent interface to access these properties with any parameterization of the PES.

Outline

The main base class in MatCalc is PropCalc (property calculator). All PropCalc subclasses should implement a calc(pymatgen.Structure) -> dict method that returns a dictionary of properties.

In general, PropCalc should be initialized with an ML model or ASE calculator, which is then used by either ASE, LAMMPS or some other simulation code to perform calculations of properties.

Cite matcalc

If you use matcalc in your research, see citation.cff or the GitHub sidebar for a BibTeX and APA citation.

matcalc's Issues

`ElasticityCalc` `norm_strains` and `shear_strains` should default to lists

matcalc/matcalc/elasticity.py

Line 24 in 3d90071

norm_strains: float = 0.01,

Shouldn't you be able to input a list of normal/shear strain magnitudes? This is standard in elastic constant calculations, and it is also the default in the pymatgen class used to generate the deformations (see https://github.com/materialsproject/pymatgen/blob/bc5edc5960506f28530739f268fdf31752de2bea/pymatgen/analysis/elasticity/strain.py#L117C20-L117C20)

[Bug]: using mace with dispersion results in crash

What happened?

Using "mace" as calculator with dispersion=True results in

)
  cell: Optional[Tensor] = torch.tensor(
Traceback (most recent call last):
  File "/work4/scd/scarf562/ml/LiFePO4/./LiFePO4-NEB.py", line 89, in <module>
    NEBcalc = NEBCalc.from_end_images(
              ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/work4/scd/scarf562/micromamba/micromamba/envs/mace/lib/python3.11/site-packages/matcalc/neb.py", line 110, in from_end_images
    return cls(images=images, calculator=calculator, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/work4/scd/scarf562/micromamba/micromamba/envs/mace/lib/python3.11/site-packages/matcalc/neb.py", line 65, in __init__
    atoms.calc = get_universal_calculator(self.calculator)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/work4/scd/scarf562/micromamba/micromamba/envs/mace/lib/python3.11/site-packages/matcalc/util.py", line 40, in get_universal_calculator
    if name.lower().startswith("m3gnet"):
       ^^^^^^^^^^
AttributeError: 'SumCalculator' object has no attribute 'lower'

Code snippet

calculator_mace = get_universal_calculator("mace", model="large", default_dtype="float64", dispersion=True)

Log output

Traceback (most recent call last):
  File "/work4/scd/scarf562/ml/LiFePO4/./LiFePO4-NEB.py", line 89, in <module>
    NEBcalc = NEBCalc.from_end_images(
              ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/work4/scd/scarf562/micromamba/micromamba/envs/mace/lib/python3.11/site-packages/matcalc/neb.py", line 110, in from_end_images
    return cls(images=images, calculator=calculator, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/work4/scd/scarf562/micromamba/micromamba/envs/mace/lib/python3.11/site-packages/matcalc/neb.py", line 65, in __init__
    atoms.calc = get_universal_calculator(self.calculator)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/work4/scd/scarf562/micromamba/micromamba/envs/mace/lib/python3.11/site-packages/matcalc/util.py", line 40, in get_universal_calculator
    if name.lower().startswith("m3gnet"):
       ^^^^^^^^^^
AttributeError: 'SumCalculator' object has no attribute 'lower'

Elastic properties

To implement calculators for elastic properties in matcalc. Ideally, we need the following:

1. Bulk modulus (from EOS)
2. Full elastic tensor
3. Bulk modulus from elastic tensor
4. Shear modulus from elastic tensor
5. Young's modulus

Phonon properties

To implement phonon properties in matcalc.