Merge a8c6783 into 8a4b1af

catkit/build.py

@@ -38,7 +38,6 @@ def bulk(name, crystalstructure=None, primitive=False, **kwargs):
 def surface(
         elements,
         size,
-        crystal='fcc',
         miller=(1, 1, 1),
         termination=0,
         fixed=0,
@@ -55,8 +54,6 @@ def surface(
         or an atoms object representing the bulk structure to use.
     size : list (3,)
         Number of time to expand the x, y, and z primitive cell.
-    crystal : str
-        The bulk crystal structure to pass to the ase bulk builder.
     miller : list (3,) or (4,)
         The miller index to cleave the surface structure from. If 4 values
         are used, assume Miller-Bravis convention.
@@ -77,7 +74,13 @@ def surface(
     if isinstance(elements, ase.Atoms):
         atoms = elements
     else:
-        atoms = ase.build.bulk(elements, crystal, cubic=True, **kwargs)
+        bkwargs = kwargs.copy()
+        keys = ['crystalstructure', 'a', 'c', 'covera',
+                'u', 'orthorhombic', 'cubic']
+        for key in kwargs:
+            if key not in keys:
+                del bkwargs[key]
+        atoms = ase.build.bulk(elements, **bkwargs)
 
     generator = catkit.gen.surface.SlabGenerator(
         bulk=atoms,

catkit/gen/adsorption.py

@@ -596,10 +596,7 @@ def _single_adsorption(
         atoms.translate(-atoms.positions[bond])
 
         if auto_construct:
-            root = None
-            for i, branch in enumerate(branches):
-                root = catkit.gen.molecules._branch_molecule(
-                    atoms, branch, root, adsorption=True)
+            atoms = catkit.gen.molecules.get_3D_positions(atoms, bond)
 
             # Align with the adsorption vector
             atoms.rotate([0, 0, 1], vector)

catkit/gen/surface.py

@@ -500,12 +500,13 @@ def set_size(self, slab, size):
                 metrics += [[d.sum(), angle, M]]
 
             if metrics:
+                order = [0, 1]
                 if defaults.get('orthogonal'):
-                    matrix = sorted(metrics,
-                                    key=lambda x: (x[1], x[0]))[0][-1]
-                else:
-                    matrix = sorted(metrics,
-                                    key=lambda x: (x[0], x[1]))[0][-1]
+                    order = [1, 0]
+
+                matrix = sorted(metrics,
+                                key=lambda x: (
+                                    x[order[0]], x[order[1]]))[0][-1]
                 supercell = transform_ab(supercell, matrix)
 
         elif isinstance(size, (list, tuple, np.ndarray)):

catkit/hub/__init__.py

@@ -0,0 +1,2 @@
+import warnings
+warnings.warn("The cathub module will be moved from catkit.hub.* to cathub.* in a future release.", DeprecationWarning)

catkit/hub/ase_tools/__init__.py

@@ -37,7 +37,7 @@ def get_chemical_formula(atoms, mode='metal'):
 
 def symbols(atoms):
     formula = get_chemical_formula(atoms)
-    symbols = ase.atoms.string2symbols(formula)
+    symbols = ase.symbols.string2symbols(formula)
     return ''.join(symbols)
 
 

catkit/hub/ase_tools/gas_phase_references.py

@@ -3,6 +3,7 @@
 import numpy as np
 import optparse
 import pprint
+from ase.symbols import string2symbols
 
 
 def molecules2symbols(molecules, add_hydrogen=True):
@@ -11,10 +12,10 @@ def molecules2symbols(molecules, add_hydrogen=True):
     """
     symbols = sorted(
         list(set(
-            ase.atoms.string2symbols(''.join(
+            string2symbols(''.join(
                 map(
                     lambda _x:
-                    ''.join(ase.atoms.string2symbols(_x)), molecules)
+                    ''.join(string2symbols(_x)), molecules)
             ))
         )),
         key=lambda _y: ase.data.atomic_numbers[_y])
@@ -61,7 +62,7 @@ def construct_reference_system(
     for symbol in symbols:
         added_symbols.append(symbol)
         for candidate in candidates:
-            _symbols = ase.atoms.string2symbols(candidate)
+            _symbols = string2symbols(candidate)
 
             # Add partial adsorbate species
             # is subset of reference species
@@ -93,7 +94,7 @@ def construct_reference_system(
     # only adds one one additional species in each step
     while references:
         for i, reference in enumerate(references):
-            if len(set(ase.atoms.string2symbols(reference[1])) -
+            if len(set(string2symbols(reference[1])) -
                     set(x[0] for x in sorted_references)) == 1:
                 sorted_references.append(references.pop(i))
                 break
@@ -116,7 +117,7 @@ def get_atomic_stoichiometry(references):
         species = species.split('_')[0]
 
         key_index[key] = i
-        composition = ase.atoms.string2symbols(species)
+        composition = string2symbols(species)
         for j, symbol in enumerate(composition):
             stoichiometry[i, key_index[symbol]] += 1
     istoichiometry = np.linalg.inv(stoichiometry)
@@ -133,7 +134,7 @@ def get_stoichiometry_factors(adsorbates, references):
     stoichiometry = get_atomic_stoichiometry(references)
     stoichiometry_factors = {}
     for adsorbate in adsorbates:
-        for symbol in ase.atoms.string2symbols(adsorbate):
+        for symbol in string2symbols(adsorbate):
             symbol_index = list(
                 map(lambda _x: _x[0], references)).index(symbol)
 

catkit/hub/cli.py

@@ -6,7 +6,7 @@
 import six
 import collections
 from tabulate import tabulate
-from ase.atoms import string2symbols
+from ase.symbols import string2symbols
 from ase.cli import main
 from . import query
 from . import make_folders_template

catkit/hub/organize.py

@@ -26,6 +26,7 @@
 import ase.utils
 import ase.io
 import numpy as np
+from ase.symbols import string2symbols
 
 
 # local imports
@@ -215,7 +216,7 @@ def fuzzy_match(structures, options):
                     try:
                         subtractions = ''.join(
                             sorted(
-                                ase.atoms.string2symbols(
+                                string2symbols(
                                     subtractions)))
                     except Exception as e:
                         if options.verbose:
@@ -224,7 +225,7 @@ def fuzzy_match(structures, options):
                     try:
                         additions = ''.join(
                             sorted(
-                                    ase.atoms.string2symbols(
+                                    string2symbols(
                                         additions)))
                     except Exception as e:
                         if options.verbose:

requirements.txt

@@ -1,4 +1,5 @@
 git+https://gitlab.com/ase/ase.git@d441dd6a1c71a2e1a925043e6974a9b3ae961854
+cathub>=0.1.0
 numpy>=1.14
 networkx>=2.1
 spglib>=1.10