# create the Structure object
structure = Structure(Lattice.cubic(4.2), ["Na", "K"],
[[0, 0, 0], [0.5, 0.5, 0.5]])
from pymatgen import MPRester
# create an input structure as an example
structure_component = ctc.StructureMoleculeComponent(
MPRester().get_structure_by_material_id("mp-804"), id="structure_in")
# and a way to view the transformed structure
structure_component_transformed = ctc.StructureMoleculeComponent(
MPRester().get_structure_by_material_id("mp-804"), id="structure_out")
# and the transformation component itself
transformation_component = ctc.AllTransformationsComponent(
input_structure_component=structure_component, )
# example layout to demonstrate capabilities of component
my_layout = html.Div([
html.H1("TransformationComponent Example"),
html.H2("Standard Layout"),
transformation_component.layout(),
html.H3("Example Input Structure"),
structure_component.layout(size="500px"),
html.H3("Example Transformed Structure"),
structure_component_transformed.layout(size="500px"),
html.H3("JSON View of Transformations"),
JsonView(id="json"),
])
# tell crystal toolkit about your app and layout
# struct_component.attach_from(transformation_component, origin_store_name="out")
# TODO: change to link to struct_or_mol instead of graph ?
# download_component = ctc.DownloadPanelComponent(links={"default": struct_component.id()})
search_component = ctc.SearchComponent()
upload_component = ctc.StructureMoleculeUploadComponent()
transformation_component = ctc.AllTransformationsComponent(
transformations=[
"SupercellTransformationComponent",
"AutoOxiStateDecorationTransformationComponent",
"CubicSupercellTransformationComponent",
"GrainBoundaryTransformationComponent",
"MonteCarloRattleTransformationComponent",
"SlabTransformationComponent",
"SubstitutionTransformationComponent",
]
)
struct_component = ctc.StructureMoleculeComponent(
links={"default": transformation_component.id()}
)
robocrys_panel = ctc.RobocrysComponent(links={"default": transformation_component.id()})
xrd_panel = ctc.XRayDiffractionPanelComponent(
links={"default": transformation_component.id()}
)
# pbx_component = ctc.PourbaixDiagramPanelComponent(origin_component=struct_component)
logger = logging.getLogger(app.title)
# endregion
################################################################################
# region INSTANTIATE CORE COMPONENTS
################################################################################
supercell = ctc.SupercellTransformationComponent()
# grain_boundary = ctc.GrainBoundaryTransformationComponent()
# oxi_state = ctc.AutoOxiStateDecorationTransformationComponent()
# slab = ctc.SlabTransformationComponent()
# substitution = ctc.SubstitutionTransformationComponent()
transformation_component = ctc.AllTransformationsComponent(
transformations=[supercell
] # , slab, grain_boundary, oxi_state, substitution],
)
struct_component = ctc.StructureMoleculeComponent(
links={"default": transformation_component.id("out")})
# struct_component.attach_from(transformation_component, origin_store_name="out")
# TODO: change to link to struct_or_mol instead of graph ?
# download_component = ctc.DownloadPanelComponent(links={"default": struct_component.id()})
search_component = ctc.SearchComponent()
upload_component = ctc.StructureMoleculeUploadComponent()
# robocrys_component = ctc.RobocrysComponent(origin_component=struct_component)
# magnetism_component = ctc.MagnetismComponent(origin_component=struct_component)
# xrd_component = ctc.XRayDiffractionPanelComponent(origin_component=struct_component)
from pymatgen.ext.matproj import MPRester
# create an input structure as an example
structure = MPRester().get_structure_by_material_id("mp-804")
structure_in = dcc.Store(id="structure_in", data=structure.as_dict())
# patch, this should be a JSON component ...
structure_in.id = lambda: "structure_in"
# and the transformation component itself
transformation_component = ctc.AllTransformationsComponent(
transformations=[
"AutoOxiStateDecorationTransformationComponent",
"SupercellTransformationComponent",
# "SlabTransformationComponent",
# "SubstitutionTransformationComponent",
"CubicSupercellTransformationComponent",
# "GrainBoundaryTransformationComponent"
],
input_structure=structure_in,
)
# example layout to demonstrate capabilities of component
my_layout = html.Div([
html.H1("TransformationComponent Example"),
html.H2("Standard Layout"),
transformation_component.layout(),
html.H3("Example Input Structure"),
JsonView(src=structure.as_dict()),
html.H3("Example Transformed Structure"),
JsonView(src={}, id="structure_out"),
# region INSTANTIATE CORE COMPONENTS
################################################################################
# struct_component.attach_from(transformation_component, origin_store_name="out")
# TODO: change to link to struct_or_mol instead of graph ?
# download_component = ctc.DownloadPanelComponent(links={"default": struct_component.id()})
search_component = ctc.SearchComponent()
upload_component = ctc.StructureMoleculeUploadComponent()
transformation_component = ctc.AllTransformationsComponent(
transformations=[
"SupercellTransformationComponent",
"AutoOxiStateDecorationTransformationComponent",
"CubicSupercellTransformationComponent",
]
)
struct_component = ctc.StructureMoleculeComponent(
links={"default": transformation_component.id()}
)
# robocrys_component = ctc.RobocrysComponent(origin_component=struct_component)
# magnetism_component = ctc.MagnetismComponent(origin_component=struct_component)
# xrd_component = ctc.XRayDiffractionPanelComponent(origin_component=struct_component)
# pbx_component = ctc.PourbaixDiagramPanelComponent(origin_component=struct_component)
#
# symmetry_component = ctc.SymmetryComponent(origin_component=struct_component)
# localenv_component = ctc.LocalEnvironmentPanel()
