Merge pull request #164 from pyscal/fix_pyiron_gb

Fix pyiron gb

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.9.13
+current_version = 0.9.14
 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: 0.9.13
+version: 0.9.14

atomrdf/workflow/pyiron/pyiron.py

@@ -6,7 +6,7 @@
 from functools import partial, update_wrapper
 from pyscal3.core import structure_dict, element_dict
 
-from atomrdf.structure import _make_crystal
+from atomrdf.structure import _make_crystal, _make_grain_boundary
 import atomrdf.workflow.pyiron.lammps as lammps
 import atomrdf.workflow.pyiron.vasp as vasp
 import atomrdf.workflow.pyiron.murnaghan as murnaghan
@@ -100,29 +100,49 @@ def bulk(
 
  def grain_boundary(
  self,
- element,
  axis,
  sigma,
  gb_plane,
- repetitions=(1, 1, 1),
  crystalstructure=None,
+ element=None,
  a=1,
+ covera=1.633,
+ repetitions=(1, 1, 1),
  overlap=0.0,
+ gap=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' 
  ):
 
- struct = self._graph._annotated_make_grain_boundary(
+ struct = _make_grain_boundary(
  axis,
  sigma,
  gb_plane,
  structure=crystalstructure,
  element=element,
  lattice_constant=a,
+ ca_ratio=covera,
  repetitions=repetitions,
  overlap=overlap,
+ gap=gap,
+ vacuum=vacuum,
+ delete_layer=delete_layer,
+ tolerance=tolerance,
+ primitive=primitive,
+ uc_a=uc_a,
+ uc_b=uc_b,
  graph=self._graph,
+ names=names,
  label=label,
+ backend=backend 
  )
 
  ase_structure = struct.write.ase()

setup.py

@@ -6,7 +6,7 @@
 
 setup(
  name='atomrdf',
- version='0.9.13',
+ version='0.9.14',
  author='Abril Azocar Guzman, Sarath Menon',
  author_email='sarath.menon@pyscal.org',
  description='Ontology based structural manipulation and quering',