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write_atoms test
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‎asimtools/utils.py‎

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Original file line numberDiff line numberDiff line change
@@ -204,6 +204,14 @@ def write_atoms(
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if len(atoms.constraints) > 0:
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columns.append('move_mask')
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if 'initial_magmoms' in columns:
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for atoms in images:
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atoms.arrays['initial_magmoms'] = np.where(
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np.isnan(atoms.arrays['initial_magmoms']),
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0,
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atoms.arrays['initial_magmoms'],
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)
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write(
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image_file,
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images,

‎tests/data/structures/adslab.xyz‎

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55
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Lattice="10.989862374024527 0.0 6.729349889709534e-16 -3.6632874580081776 10.361341611972845 6.729349889709536e-16 0.0 0.0 29.910616844190965" Properties=species:S:1:pos:R:3:initial_magmoms:R:1:surface_properties:S:1:bulk_wyckoff:S:1:bulk_equivalent:S:1:move_mask:L:1 pbc="T T T"
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Na 0.00000000 0.00000000 4.48659253 nan subsurface a 0 F
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Na -1.22109582 3.45378054 4.48659253 nan subsurface a 0 F
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Na -2.44219164 6.90756107 4.48659253 nan subsurface a 0 F
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Na 3.66328746 0.00000000 4.48659253 nan subsurface a 0 F
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Na 2.44219164 3.45378054 4.48659253 nan subsurface a 0 F
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Na 1.22109582 6.90756107 4.48659253 nan subsurface a 0 F
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Na 7.32657492 0.00000000 4.48659253 nan subsurface a 0 F
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Na 6.10547910 3.45378054 4.48659253 nan subsurface a 0 F
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Na 4.88438328 6.90756107 4.48659253 nan subsurface a 0 F
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Na 1.22109582 1.72689027 1.49553084 nan subsurface a 0 F
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Na -0.00000000 5.18067081 1.49553084 nan subsurface a 0 F
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Na -1.22109582 8.63445134 1.49553084 nan subsurface a 0 F
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Na 4.88438328 1.72689027 1.49553084 nan subsurface a 0 F
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Na 3.66328746 5.18067081 1.49553084 nan subsurface a 0 F
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Na 2.44219164 8.63445134 1.49553084 nan subsurface a 0 F
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Na 8.54767074 1.72689027 1.49553084 nan subsurface a 0 F
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Na 7.32657492 5.18067081 1.49553084 nan subsurface a 0 F
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Na 6.10547910 8.63445134 1.49553084 nan subsurface a 0 F
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Na 0.05040356 0.07128126 10.61153565 nan subsurface a 0 T
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Na -1.22088381 3.45363060 10.47942977 nan subsurface a 0 T
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Na -2.43700358 6.91641549 10.46332553 nan subsurface a 0 T
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Na 3.66307537 0.00014975 10.47942998 nan subsurface a 0 T
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Na 2.39178795 3.38249920 10.61153531 nan subsurface a 0 T
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Na 1.21590808 6.89870710 10.46332525 nan subsurface a 0 T
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Na 7.33319379 0.00784251 10.46332545 nan subsurface a 0 T
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Na 6.09886082 3.44593812 10.46332545 nan subsurface a 0 T
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Na 4.88438293 6.90756134 10.52503220 nan subsurface a 0 T
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Na 1.22109579 1.72689044 7.49352623 nan subsurface a 0 T
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Na 0.00009148 5.17841763 7.48202082 nan subsurface a 0 T
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Na -1.22118690 8.63670456 7.48202064 nan subsurface a 0 T
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Na 4.88222840 1.72622555 7.48202032 nan subsurface a 0 T
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Na 3.66029354 5.17643697 7.50198302 nan subsurface a 0 T
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Na 2.44173987 8.63477030 7.48098737 nan subsurface a 0 T
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Na 8.54982542 1.72755533 7.48202044 nan subsurface a 0 T
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Na 7.32702677 5.18035170 7.48098729 nan subsurface a 0 T
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Na 6.10847301 8.63868512 7.50198293 nan subsurface a 0 T
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Na -0.05716541 -0.08084452 16.64749813 nan surface a 0 T
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Na -0.66173064 3.05824944 16.35385328 nan surface a 0 T
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Na -2.36879258 6.61089299 16.32311991 nan surface a 0 T
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Na 3.10392211 0.39553082 16.35385370 nan surface a 0 T
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Na 2.49935741 3.53462570 16.64749940 nan surface a 0 T
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Na 1.14769723 7.20422919 16.32311967 nan surface a 0 T
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Na 7.02240734 -0.02968818 16.32312005 nan surface a 0 T
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Na 6.40964675 3.48346858 16.32312000 nan surface a 0 T
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Na 4.88438260 6.90756112 16.41278280 nan surface a 0 T
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Na 1.22109540 1.72689040 13.93937426 nan subsurface a 0 T
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Na -0.06036830 5.24521596 13.41401878 nan subsurface a 0 T
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Na -1.16072730 8.56990626 13.41401807 nan subsurface a 0 T
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Na 4.96535977 1.69148936 13.41401871 nan subsurface a 0 T
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Na 3.64865650 5.15997986 13.52384317 nan subsurface a 0 T
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Na 2.48037426 8.60745143 13.39723386 nan subsurface a 0 T
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Na 8.46669414 1.76229130 13.41401834 nan subsurface a 0 T
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Na 7.28839235 5.20767012 13.39723382 nan subsurface a 0 T
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Na 6.12011011 8.65514262 13.52384285 nan subsurface a 0 T
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O 1.22109586 1.72688973 16.17505098 2.00000000 adsorbate None None T

‎tests/unit/test_utils.py‎

Lines changed: 13 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -4,6 +4,7 @@
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from pathlib import Path
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import os
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import pytest
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import numpy as np
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from ase.io import read
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from pymatgen.core import Structure, Molecule, IStructure, IMolecule
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from asimtools.utils import (
@@ -60,7 +61,7 @@ def test_join_names(test_input, expected):
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ase.build.fcc111('Al', size=(2,2,3))),
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({'image_file': STRUCT_DIR / 'Ar.xyz'},
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ase.build.bulk('Ar')),
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({'image_file': STRUCT_DIR / 'Ar', 'format': 'cfg'},
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({'image_file': STRUCT_DIR / 'Ar.xyz'},
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ase.build.bulk('Ar')),
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({'atoms': ase.build.bulk('Ar')}, ase.build.bulk('Ar')),
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({
@@ -126,6 +127,7 @@ def test_join_names(test_input, expected):
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coords=[[0, 0, 0], [1.5, 1.5, 1.5], [1.5, -1.5, -1.5]],
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spin_multiplicity=1,
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)),
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])
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def test_get_atoms(test_input, expected):
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''' Test getting atoms from different inputs '''
@@ -173,6 +175,16 @@ def test_get_images(test_input, expected):
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for image in input_images:
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assert image in expected
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def test_write_atoms(tmp_path):
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''' Test write_atoms.
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Also test that when magmoms are provided by ASE which makes them nans
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and kills jobs using VASP etc., we change them to zero '''
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slab_ = read(STRUCT_DIR / 'adslab.xyz')
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write_atoms(tmp_path / 'slab.xyz', slab_)
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slab = read(tmp_path / 'slab.xyz')
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assert not np.any(np.isnan(slab.arrays['initial_magmoms']))
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assert 'surface_properties' in slab.arrays
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@pytest.mark.parametrize("test_input, expected",[
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(['l1', 'l2', 'l3'], {'l1': {'l2': {'l3': 'new_value'}}}),
178190
(['l1', 'l2'], {'l1': {'l2': 'new_value'}}),

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