Spacegroup Trouble

exciting
1

Hi everyone,

I’m trying to create an input.xml file for bulk MoS2 in the 2H crystal phase however I’m having trouble with creating the unit cell for a calculation. I think I’m using the spacegroup command wrong. I tried using spacegroup to create the input.xml file with the following spacegroup.xml file:

<?xml version="1.0" encoding="UTF-8" ?> 
    <symmetries HermannMauguinSymbol="P63/mmc">
    <title>2HMoS2</title>
        <lattice a="5.9733279640198" b="5.9733279640198" c="23.23406024415133" ab="90"
            ac="90" bc="120" ncell="1 1 1" />
        <WyckoffPositions>
            <wspecies speciesfile="Mo.xml">
                <wpos coord="0.3333    0.6666    0.25 " />
            </wspecies>
            <wspecies speciesfile="S.xml">
                <wpos coord=" 0.3333    0.6666    0.6275" />
            </wspecies>
         </WyckoffPositions>
    </symmetries>

I then use the command spacegroup spacegroup.xml, however I do not get a geometry.xml file to use as input.xml. If I just type in spacegroup then I am asked for the different lattice parameters and atoms etc, however the amount of atoms that I need to write down does not match the actual amount of atoms found in the unit cell of MoS2.

Any help would be highly appreciated and thanks in advance,
Louis

2

Hi Louis,

If you want to just convert some cell parameters into an input.xml, you can use excitingtools (packaged in tools/):

from excitingtools.input.ground_state import ExcitingGroundStateInput
from excitingtools.input.structure import ExcitingStructure
from excitingtools.input.input_xml import exciting_input_xml_str

gs_input = ExcitingGroundStateInput(rgkmax=8.0)
cubic_lattice = [[1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]]
arbitrary_atoms = [{'species': 'H', 'position': [0, 0, 0]},
                              {'species': 'H', 'position': [1, 0, 0]},
                              {'species': 'He', 'position': [2, 0, 0]}]
structure = ExcitingStructure(arbitrary_atoms, cubic_lattice, species_path='./')
input_str = exciting_input_xml_str(structure, gs_input)
print(input_str)

If you need to generate your cell from lattice constants, I suggest you look at ASE and SPGLib. ExcitingStructure() will also accept ASE’s Atoms object.

I doubt anyone in the group has experience with the Spacegroup program.

Cheers,
Alex