feature/SOF 7599 categorization new #341
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VsevolodX
commented
May 20, 2025
VsevolodX
commented
- wip: categorization yaml
- wip: add combinations
- wip: add pristine structures
- update: add primitive schemas
- update: add categorization file
- update: clenaup
- update: clenaup 2
| crystal_site: | ||
| # created by reference to some crystal, can be populated with atom, vacancy, void, can be merged with a crystal of the same lattice | ||
| - reference_crystal | ||
| - crystal_coordinate |
VsevolodX
commented
May 20, 2025
| - direction = "z" | ||
| - number_of_layers = 3 | ||
| - terminations = [termination_1, termination_3] | ||
|
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# You provide material
material: SrTiO3
# You specify the layering configuration (Miller indices)
layers_configuration:
- crystal = material
- miller_indices = [ 0, 1, 1 ]
# Function gets all possible layers and their terminations:
layers: get_layers(layers_configuration) => [ layer_1, layer_2, layer_3 ]
terminations: get_terminations(layers) => [ "SrO", "Ti", "TiO" ]
# or layers: generate_layers(layers_configuration) => [ {layer_1, termination_1}, {layer_2, termination_2}, {layer_3, termination_3} ]
# You use those layers object and top and bottom terminations to specify a slab configuration
slab_configuration:
- stack_components = [ layers, vacuum(10) ]
- direction = "z"
- number_of_layers = 7
- terminations = ["SrO", "SrO" ]
# You can generate the slab, with terminations and vacuum added
slab: generate_slab(slab_configuration)
| - is_isometric = bool | ||
| combinations: | ||
| stack_component: | ||
| - structure = (material | vacuum) |
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It doesn't have the structure key it's just material or vacuum
| crystal_lattice_planes: | ||
| - crystal = material | ||
| - miller_indices = [ h, k, l ] | ||
| (termination): # not a configuration, but a data-model |
| (termination): # not a configuration, but a data-model | ||
| - stoichiometry # e.g. SrO, TiO, etc. | ||
| - symmetry #P6/mmm, P3m1, etc. | ||
| unique_atomic_layers: |
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maybe atomic_layers_unique atomic_layers_unique_repeated and atomic_layers
| - direction = (x | y){1} | ||
| wire_section: | ||
| # we created a supercell, cut the shape | ||
| - supercell = ref:/.../supercell |
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The actual wire length, width should be first, not supercell
| zero-dimensional: | ||
| nanoparticle: | ||
| # we created a supercell, cut the shape and added vacuum on all sides | ||
| - supercell = ref:/.../supercell |
| - crystal = ref:/primitive/base/crystal | ||
| # In the code properties below can be supplied externally or generated based on the above with a wizard | ||
| - stacking_order? = ("natural" | "AB" | "ABC" | ...){1} # Natural by default, can be described as a ABC... configurations based on the symmetry | ||
| heterostack: |
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we can just call it stack
| - stack_components = [ slab, vacuum, slab, vacuum ] | ||
| - direction = "z" | ||
| interface_slab_monolayer: | ||
| - stack_components = [ slab, vacuum, monolayer ] |
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This should not have vacuum
| - stack_components = [ slab, vacuum, monolayer ] | ||
| - direction = "z" | ||
| interface_slab_monolayer_vacuum: | ||
| - stack_components = [ slab, vacuum, monolayer, vacuum ] |
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should be only one vacuum
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