From e66fe26a9039b38b6961fc146bfb24deae043b44 Mon Sep 17 00:00:00 2001
From: Sarath <sarathmenon@mailbox.org>
Date: Thu, 15 Aug 2024 16:10:15 +0200
Subject: [PATCH 1/2] fix pyiron gb strcuture

---
 atomrdf/workflow/pyiron/pyiron.py | 28 ++++++++++++++++++++++++----
 1 file changed, 24 insertions(+), 4 deletions(-)

diff --git a/atomrdf/workflow/pyiron/pyiron.py b/atomrdf/workflow/pyiron/pyiron.py
index 1f7eb41..18a17e6 100644
--- a/atomrdf/workflow/pyiron/pyiron.py
+++ b/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()

From f335ad7d3e90f69e822ff2f698e10809850cd902 Mon Sep 17 00:00:00 2001
From: Sarath <sarathmenon@mailbox.org>
Date: Thu, 15 Aug 2024 16:11:19 +0200
Subject: [PATCH 2/2] =?UTF-8?q?Bump=20version:=200.9.13=20=E2=86=92=200.9.?=
 =?UTF-8?q?14?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 .bumpversion.cfg | 2 +-
 CITATION.cff     | 2 +-
 setup.py         | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.bumpversion.cfg b/.bumpversion.cfg
index 3a7e77d..c1d3d02 100644
--- a/.bumpversion.cfg
+++ b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.9.13
+current_version = 0.9.14
 commit = True
 tag = False
 
diff --git a/CITATION.cff b/CITATION.cff
index 60f9fbb..c6b841d 100644
--- a/CITATION.cff
+++ b/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
diff --git a/setup.py b/setup.py
index 55921c7..d66cfde 100644
--- a/setup.py
+++ b/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',