add vacancy input script

mlip_arena/tasks/vacancy_migration/input.py

@@ -0,0 +1,192 @@
+from mp_api.client import MPRester
+
+from ase import Atom
+from ase.data import covalent_radii
+from ase.spacegroup import crystal
+
+fcc_elements = [
+    "Ac",
+    "Ag",
+    "Al",
+    "Ar",
+    "Au",
+    "Ba",
+    "Be",
+    "Ca",
+    "Cd",
+    "Ce",
+    "Co",
+    "Cs",
+    "Cu",
+    "Dy",
+    "Er",
+    "Fe",
+    "Ga",
+    "Ge",
+    "He",
+    "Hf",
+    "Ho",
+    "In",
+    "Ir",
+    "K",
+    "Kr",
+    "La",
+    "Li",
+    "Mg",
+    "Mn",
+    "Na",
+    "Ni",
+    "Os",
+    "Pa",
+    "Pb",
+    "Pd",
+    "Pr",
+    "Pt",
+    "Rb",
+    "Re",
+    "Rh",
+    "Ru",
+    "Sc",
+    "Sn",
+    "Sr",
+    "Ta",
+    "Tb",
+    "Tc",
+    "Th",
+    "Ti",
+    "Tl",
+    "W",
+    "Xe",
+    "Y",
+    "Zr"
+]
+
+def get_fcc_pristine(mp_api_key = None):
+    for element in fcc_elements:
+        with MPRester(mp_api_key) as mpr:
+            docs = mpr.materials.summary.search(
+                formula=element, spacegroup_number=225, fields=["structure", "energy_above_hull"]
+            )
+
+            docs = sorted(docs, key=lambda x: x.energy_above_hull)
+
+            if len(docs) != 0:
+                pristine = docs[0].structure.to_conventional().to_ase_atoms(msonable=False) * (3, 3, 3)
+            
+                if len(pristine) != 108:
+                    v = pristine.get_volume() / len(pristine)
+                    r = v**(1/3)
+                    a = 2*(2**0.5)*r
+
+                    pristine = crystal(
+                        symbols=[element]*4,
+                        basis=[(0, 0, 0), (0.5, 0.5, 0), (0.5, 0, 0.5), (0, 0.5, 0.5)],
+                        spacegroup=225,
+                        cellpar=[a, a, a, 90, 90, 90],
+                    ) * (3, 3, 3)
+            else:
+                r = covalent_radii[Atom(element).number] or 4
+                a = 2*(2**0.5)*r
+                pristine = crystal(
+                    symbols=[element]*4,
+                    basis=[(0, 0, 0), (0.5, 0.5, 0), (0.5, 0, 0.5), (0, 0.5, 0.5)],
+                    spacegroup=225,
+                    cellpar=[a, a, a, 90, 90, 90],
+                ) * (3, 3, 3)
+        yield pristine
+
+hcp_elements = [
+    "Ag",
+    "Al",
+    "Ar",
+    "Au",
+    "Ba",
+    "Be",
+    "Ca",
+    "Cd",
+    "Ce",
+    "Co",
+    "Cr",
+    "Cs",
+    "Cu",
+    "Fe",
+    "Ga",
+    "Ge",
+    "He",
+    "Hf",
+    "Ho",
+    "In",
+    "Ir",
+    "K",
+    "Kr",
+    "La",
+    "Li",
+    "Mg",
+    "Mn",
+    "Mo",
+    "Nb",
+    "Ne",
+    "Ni",
+    "Os",
+    "P",
+    "Pb",
+    "Pd",
+    "Pt",
+    "Rb",
+    "Re",
+    "Rh",
+    "Ru",
+    "Sc",
+    "Si",
+    "Sn",
+    "Sr",
+    "Ta",
+    "Tc",
+    "Te",
+    "Th",
+    "Ti",
+    "Tl",
+    "V",
+    "W",
+    "Xe",
+    "Y",
+    "Zn",
+    "Zr"
+]
+
+def get_hcp_pristine(mp_api_key = None):
+    for element in hcp_elements:
+        with MPRester(mp_api_key) as mpr:
+            docs = mpr.materials.summary.search(
+                formula=element, spacegroup_number=194, fields=["structure", "energy_above_hull"]
+            )
+
+            docs = sorted(docs, key=lambda x: x.energy_above_hull)
+
+            if len(docs) != 0:
+                pristine = docs[0].structure.to_conventional().to_ase_atoms(msonable=False) * (3, 3, 1)
+            
+                if len(pristine) != 36:
+                    v = pristine.get_volume() / len(pristine)
+                    r = v**(1/3)
+                    a = 2*r
+                    c = 4 * ((2/3) ** 0.5) * r
+
+                    pristine = crystal(
+                        [element],
+                        [(1.0 / 3.0, 2.0 / 3.0, 3.0 / 4.0)],
+                        spacegroup=194,
+                        cellpar=[a, a, c, 90, 90, 120],
+                    ) * (3, 3, 2)
+            else:
+                r = covalent_radii[Atom(element).number] or 4
+                a = 2*r
+                c = 4 * ((2/3) ** 0.5) * r
+
+                pristine = crystal(
+                    [element],
+                    [(1.0 / 3.0, 2.0 / 3.0, 3.0 / 4.0)],
+                    spacegroup=194,
+                    cellpar=[a, a, c, 90, 90, 120],
+                ) * (3, 3, 2)
+        yield pristine