Merge pull request #144 from pyscal/add_aimsgb

add aimsgb

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.9.5
+current_version = 0.9.6
 commit = True
 tag = False
 

CITATION.cff

@@ -19,4 +19,4 @@ url: 'https://atomrdf.pyscal.org'
 license: "MIT"
 repository-code: https://github.com/pyscal/atomRDF
 type: software
-version: 0.9.5
+version: 0.9.6

atomrdf/structure.py

@@ -382,8 +382,170 @@ def _make_dislocation(
         return output_structure, disc
     return output_structure
 
-
 def _make_grain_boundary(
+    axis,
+    sigma,
+    gb_plane,
+    structure=None,
+    element=None,
+    lattice_constant=1,
+    ca_ratio=1.633,
+    repetitions=(1, 1, 1),
+    overlap=0.0,
+    vacuum=0.0,
+    delete_layer="0b0t0b0t",
+    tolerance=  0.25,
+    primitive=False,
+    uc_a=1,
+    uc_b=1,
+    graph=None,
+    names=False,
+    label=None,
+    backend='aimsgb'         
+):
+    if backend == 'aimsgb':
+        return _make_grain_boundary_aimsgb(
+            axis,
+            sigma,
+            gb_plane,
+            structure=structure,
+            element=element,
+            lattice_constant=lattice_constant,
+            ca_ratio=ca_ratio,
+            repetitions=repetitions,
+            overlap=overlap,
+            vacuum=vacuum,
+            delete_layer=delete_layer,
+            tolerance=  tolerance,
+            primitive=primitive,
+            uc_a=uc_a,
+            uc_b=uc_b,
+            graph=graph,
+            names=names,
+            label=label,             
+        )
+    else:
+        return _make_grain_boundary_inbuilt(
+            axis,
+            sigma,
+            gb_plane,
+            structure=structure,
+            element=element,
+            lattice_constant=lattice_constant,
+            repetitions=repetitions,
+            overlap=overlap,
+            graph=graph,
+            names=names,
+            label=label,
+        )
+
+def _make_grain_boundary_aimsgb(
+    axis,
+    sigma,
+    gb_plane,
+    structure=None,
+    element=None,
+    lattice_constant=1,
+    ca_ratio=1.633,
+    repetitions=(1, 1, 1),
+    overlap=0.0,
+    vacuum=0.0,
+    delete_layer="0b0t0b0t",
+    tolerance=  0.25,
+    primitive=False,
+    uc_a=1,
+    uc_b=1,
+    graph=None,
+    names=False,
+    label=None,  
+):  
+    try:
+        from pymatgen.io.ase import AseAtomsAdaptor
+        from aimsgb import GrainBoundary as AIMSGrainBoundary
+        from aimsgb import Grain as AIMSGrain
+    except ImportError:
+        raise ImportError("This function requires the aimsgb and pymatgen packages to be installed")
+
+
+    if structure is not None:
+        # create a structure with the info
+        init_sys = _make_crystal(
+            structure,
+            lattice_constant=_declass(lattice_constant),
+            repetitions=repetitions,
+            ca_ratio=_declass(ca_ratio),
+            noise=0,
+            element=element,
+            primitive=primitive,
+        )
+    elif element is not None:
+        if element in element_dict.keys():
+            structure = element_dict[element]["structure"]
+            lattice_constant = element_dict[element]["lattice_constant"]
+        else:
+            raise ValueError("Please provide structure")
+        init_sys = _make_crystal(
+            structure,
+            lattice_constant=_declass(lattice_constant),
+            repetitions=repetitions,
+            ca_ratio=_declass(ca_ratio),
+            noise=0,
+            element=element,
+            primitive=primitive,
+        )
+    else:
+        raise ValueError("Provide either structure or element")
+
+    sdict = copy.deepcopy(init_sys._structure_dict)
+
+    asesys = init_sys.write.ase()
+    pmsys = AseAtomsAdaptor().get_structure(atoms=asesys)
+    grain = AIMSGrain(pmsys.lattice, pmsys.species, pmsys.frac_coords)
+    gb = AIMSGrainBoundary(axis=axis, sigma=sigma, 
+                    plane=gb_plane, 
+                    initial_struct=grain, 
+                    uc_a=uc_a, 
+                    uc_b=uc_b)
+    gb_struct = AIMSGrain.stack_grains(
+                grain_a = gb.grain_a,
+                grain_b = gb.grain_b,
+                vacuum = vacuum,
+                gap=overlap,
+                direction = gb.direction,
+                delete_layer=delete_layer,
+                tol=tolerance,
+                to_primitive=primitive,
+            )
+    asestruct = AseAtomsAdaptor().get_atoms(structure=gb_struct)
+    sys = System.read.ase(asestruct, graph=graph, names=names, label=label)
+    sys.atoms._lattice = structure
+    sys.atoms._lattice_constant = _declass(lattice_constant)
+    sys._structure_dict = sdict
+    sys.label = label
+    sys.to_graph()
+    sys.add_property_mappings(lattice_constant, mapping_quantity='lattice_constant')
+    sys.add_property_mappings(ca_ratio, mapping_quantity='lattice_constant')
+
+    try:
+        gb_inb = GrainBoundary()
+        gb_inb.create_grain_boundary(axis=axis, sigma=sigma, gb_plane=gb_plane)
+        gb_type = gb_inb.find_gb_character()
+    except:
+        gb_type = None
+
+    gb_dict = {
+        "GBPlane": " ".join(np.array(gb_plane).astype(str)),
+        "RotationAxis": axis,
+        "MisorientationAngle": gb.theta[0],
+        "GBType": gb_type,
+        "sigma": gb.sigma,
+    }
+    sys.add_gb(gb_dict)
+    return sys
+
+
+
+def _make_grain_boundary_inbuilt(
     axis,
     sigma,
     gb_plane,
@@ -2095,7 +2257,7 @@ def add_gb(self, gb_dict):
             return
 
         if gb_dict["GBType"] is None:
-            plane_defect = self.graph.create_node(f"{self._name}_GrainBoundary")
+            plane_defect = self.graph.create_node(f"{self._name}_GrainBoundary", PLDO.GrainBoundary)
 
         elif gb_dict["GBType"] == "Twist":
             plane_defect = self.graph.create_node(

environment.yml

@@ -18,5 +18,7 @@ dependencies:
   #- atomman
   - mp-api
   - sqlalchemy
+  - aimsgb
+  - pymatgen
   - pip:
     - "git+https://github.com/RDFLib/rdflib-sqlalchemy.git@develop"