Merge pull request #48 from pyscal/update_pyscal3_backend

Update pyscal3 backend
pyscal · Nov 7, 2023 · 388dc53 · 388dc53
2 parents 91986aa + af58585
commit 388dc53
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diff --git a/environment.yml b/environment.yml
@@ -3,7 +3,7 @@ channels:
  - conda-forge
 dependencies:
  - python >3.8
- - pyscal3 =3.1.0
+ - pyscal3 =3.1.1
  - rdflib
  - pyyaml
  - jupyterlab

diff --git a/pyscal_rdf/properties.py b/pyscal_rdf/properties.py
@@ -26,18 +26,12 @@ def get_angle(vec1, vec2):
  return np.round(np.arccos(np.dot(vec1, vec2)/(np.linalg.norm(vec1)*np.linalg.norm(vec2)))*180/np.pi, decimals=2)
 
 def get_coordination(sys):
- sys.find_neighbors(method="cutoff")
+ sys.find.neighbors(method="cutoff")
  coordination = [len(x) for x in sys.atoms.neighbors.index]
  return coordination
 
 def get_lattice_vector(sys, cartesian=False):
- box = [[sys._structure_dict['scaling_factors'][0], 0, 0], 
- [0, sys._structure_dict['scaling_factors'][1], 0], 
- [0, 0, sys._structure_dict['scaling_factors'][2]]]
- if cartesian:
- box[0][0] = box[0][0]*sys.atoms._lattice_constant 
- box[1][1] = box[1][1]*sys.atoms._lattice_constant 
- box[2][2] = box[2][2]*sys.atoms._lattice_constant
+ box = sys.box
  return box
 
 def get_bravais_lattice(sys):