Open hongyi-zhao opened 2 weeks ago
esoteric-ephemera
commented
5 days ago To update the MAGMOMs via user_incar_settings, you have to specify it as a dict (doesn't make the most sense I know). The dict should be {species: magmom}, like {"Zn2+": 0.5}
The alternative is to add the magmoms to the site properties of a structure, and atomate2 will automatically read those in as MAGMOM:
structure.add_site_property("magmom", incar_settings.pop("magmom") )
hongyi-zhao
commented
4 days ago In general, it should be used this way:
def apply_magmoms_from_incar(structure, incar_settings):
"""
Apply magnetic moments from INCAR settings to structure, handling multiple species.
Args:
structure: pymatgen Structure object
incar_settings: dict containing INCAR settings including MAGMOM
"""
if "MAGMOM" not in incar_settings:
print("No MAGMOM settings found in INCAR")
return structure
magmoms = incar_settings.pop("MAGMOM")
# Check if number of MAGMOMs matches number of sites
if len(magmoms) == len(structure):
# Direct 1:1 mapping case
structure.add_site_property("magmom", magmoms)
else:
# Need to expand magmoms based on unique species
# Get unique species and their counts
species_counts = structure.composition.as_dict()
# Create expanded magmom list matching structure sites
site_magmoms = []
magmom_idx = 0
# Iterate through sites and assign magmoms
for site in structure:
site_magmoms.append(magmoms[magmom_idx])
# Check if we need to move to next magmom value
next_species_sites = structure.indices_from_symbol(site.species_string)
if len(site_magmoms) == max(next_species_sites) + 1:
magmom_idx += 1
structure.add_site_property("magmom", site_magmoms)
return structure
# 使用示例:
structure = apply_magmoms_from_incar(structure, incar_settings)
# 验证结果
print("Site properties:", structure.site_properties)
print("\nDetailed site information:")
for i, site in enumerate(structure):
print(f"Site {i}: {site.species_string} at {site.frac_coords}, "
f"magmom = {site.properties.get('magmom')}")The output:
No MAGMOM settings found in INCAR
Site properties: {'magmom': [-0.002, -0.002, -0.002, -0.002]}
Detailed site information:
Site 0: Pt at [0. 0. 0.], magmom = -0.002
Site 1: Pt at [0. 0.5 0.5], magmom = -0.002
Site 2: Pt at [0.5 0. 0.5], magmom = -0.002
Site 3: Pt at [0.5 0.5 0. ], magmom = -0.002The updated result of structure.site_properties:
In [24]: structure.site_properties
Out[24]: {'magmom': [-0.002, -0.002, -0.002, -0.002]}
The testing code below is adapted from my example here:
But the above code will trigger the following error:
Is there a proper way to handle
MAGMOMsettings when copying from MP calculations without requiring further user adjustment, say, the one done by the code snippetConvert MAGMOM list to dictionary formatshown above?Regards, Zhao