How to use pymatgen.command_line.vampire_caller module.When I use vampire_caller it report an error AttributeError.

[xbunax]

I use vampire to simulate. I want to use pymatgen.command_line.vampire_caller and VampireCaller._create _ucf to generate ucf file.

Structure = structure.Structure.from_file(path)
hmMn=HeisenbergMapper(Structure, [0.5, 0.5],cutoff=1.0)
vc = VampireCaller(ordered_structures=Structure, energies=[0,0,1],hm=hmMn)
vc._create_ucf()

But when I use this structure parameters in class VampireCaller ,it reports error

Traceback (most recent call last):
  File "/opt/anaconda3/lib/python3.9/site-packages/IPython/core/interactiveshell.py", line 3444, in run_code
    exec(code_obj, self.user_global_ns, self.user_ns)
  File "<ipython-input-2-9dee7c724d05>", line 1, in <module>
    runfile('/Users/xbunax/PycharmProjects/pythonProject/test.py', wdir='/Users/xbunax/PycharmProjects/pythonProject')
  File "/Users/xbunax/Library/Application Support/JetBrains/Toolbox/apps/PyCharm-P/ch-0/223.7571.203/PyCharm.app/Contents/plugins/python/helpers/pydev/_pydev_bundle/pydev_umd.py", line 198, in runfile
    pydev_imports.execfile(filename, global_vars, local_vars)  # execute the script
  File "/Users/xbunax/Library/Application Support/JetBrains/Toolbox/apps/PyCharm-P/ch-0/223.7571.203/PyCharm.app/Contents/plugins/python/helpers/pydev/_pydev_imps/_pydev_execfile.py", line 18, in execfile
    exec(compile(contents+"\n", file, 'exec'), glob, loc)
  File "/Users/xbunax/PycharmProjects/pythonProject/test.py", line 21, in <module>
    hmMn=HeisenbergMapper(mn2au.as_dict(), [0.5, 0.5],cutoff=1.0)
  File "/opt/anaconda3/lib/python3.9/site-packages/pymatgen/analysis/magnetism/heisenberg.py", line 78, in __init__
    hs = HeisenbergScreener(ordered_structures, energies, screen=False)
  File "/opt/anaconda3/lib/python3.9/site-packages/pymatgen/analysis/magnetism/heisenberg.py", line 708, in __init__
    structures, energies = self._do_cleanup(structures, energies)
  File "/opt/anaconda3/lib/python3.9/site-packages/pymatgen/analysis/magnetism/heisenberg.py", line 741, in _do_cleanup
    ordered_structures = [
  File "/opt/anaconda3/lib/python3.9/site-packages/pymatgen/analysis/magnetism/heisenberg.py", line 742, in <listcomp>
    CollinearMagneticStructureAnalyzer(
  File "/opt/anaconda3/lib/python3.9/site-packages/pymatgen/analysis/magnetism/analyzer.py", line 150, in __init__
    structure = structure.copy()
AttributeError: 'str' object has no attribute 'copy'

If someone know how to solve this, I will be grateful.

[janosh]

If you look at the HeisenbergMapper doc string, it expects a list of ordered Structures as it's 1st argument:

pymatgen/pymatgen/analysis/magnetism/heisenberg.py

Line 56 in 5c05f30

ordered_structures (list): Structure objects with magmoms.

So try changing:

- hmMn=HeisenbergMapper(Structure, [0.5, 0.5],cutoff=1.0)
+ hmMn=HeisenbergMapper([Structure], [0.5, 0.5],cutoff=1.0)

Also, I'd advise against using the name of a class as variable name. Better to use lower case structure or struct rather than Structure.

[xbunax]

Thank you to give some suggestions. I have change my code to this

from pymatgen.core import struct
from pymatgen.command_line.vampire_caller import VampireCaller
from pymatgen.analysis.magnetism.heisenberg import HeisenbergMapper

path="/Users/xbunax/Downloads/Mn2Au-2.cif"
Mn2Au=struct.Structure.from_file(path)

hmMn=HeisenbergMapper([Mn2Au], [0.5, 0.5, 0.5], cutoff=1.0)


vc = VampireCaller(ordered_structures=[Mn2Au], energies=[0,0,1],hm=hmMn)
vc._create_ucf()

But it still error

ValueError: You need at least one site to construct a <class 'pymatgen.core.structure.Structure'>

I try to output Mn2Au.sites,it exists

[PeriodicSite: Mn (0.0000, 0.0000, 3.7050) [0.0000, 0.0000, 0.3267], PeriodicSite: Mn (0.0000, 0.0000, 7.6367) [0.0000, 0.0000, 0.6733], PeriodicSite: Mn (1.4317, 1.4317, 9.3758) [0.5000, 0.5000, 0.8267], PeriodicSite: Mn (1.4317, 1.4317, 1.9658) [0.5000, 0.5000, 0.1733], PeriodicSite: Au (0.0000, 0.0000, 0.0000) [0.0000, 0.0000, 0.0000], PeriodicSite: Au (1.4317, 1.4317, 5.6708) [0.5000, 0.5000, 0.5000]]

This confuse me😂

[xbunax]

Oh,I solve this issue, my cif file doesn't contain the magmom. But when I add this manually, another issue appear.😂

We need at least 2 unique orderings.

I read the source code ,

 # Check how many commensurate graphs we found
        if len(self.sgraphs) < 2:
            print("We need at least 2 unique orderings.")
            sys.exit(1)

But I don't know how to solve this.