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NotImplementedError in ASE NPT-MD (convert_atoms_to_upper)

  • Updated

When calculating NPT-MD in ASE, the lattice vectors (atoms.cell) of a target structure must be in triangular matrix form (upper triangular matrix form for versions prior to ASE 3.24). For example, using ase.build.bulk to create the Cu-FCC structure yields an atoms object with the following lattice vectors.

from ase.build import bulk
Cu_fcc_atoms = bulk(name="Cu", crystalstructure="fcc")
Cu_fcc_atoms = Cu_fcc_atoms * (4, 4, 4)
Cu_fcc_atoms.cell[:]
array([[0.  , 7.22, 7.22],
       [7.22, 0.  , 7.22],
       [7.22, 7.22, 0. ]])

If NPT-MD is performed on such atoms objects without transforming the lattice vectors, the following error (NotImplementedError) will occur and the MD calculation will not proceed.

 

・ For ASE 3.25.0 (Click image to enlarge)

mceclip1.png

 

・ For ASE 3.24.0 (Click image to enlarge)

mceclip3.png

 

convert_atoms_to_upper

By using the function "convert_atoms_to_upper" in matlantis-futures, one can obtain an atoms object in which the lattice vectors have been converted to upper triangular matrix form.

from matlantis_features.utils.atoms_util import convert_atoms_to_upper
Cu_fcc_atoms = convert_atoms_to_upper(Cu_fcc_atoms)
Cu_fcc_atoms.cell[:]
array([[ 8.33693789, 2.94755266,  5.10531096],
       [ 0.        , 8.84265797,  5.10531096],
       [ 0.        , 0.        , 10.21062192]])

By using the atoms object after lattice vector transformation, NPT-MD calculations can be performed in ASE.

 

Tips (Added 8/5/2025)

If you save the file in CIF format, please note that you will need to convert it again after loading.

 

 

Reference

・ NPT_example_ja.ipynb( github, matlantis-contrib)

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