Merge branch 'master' of https://github.com/MaterSim/PyXtal

Author: qzhu2017

flask/requirements.txt

@@ -1,5 +1,5 @@
 click==7.1.2
-Flask==2.3.2
+Flask==3.1.3
 Flask-Bootstrap==3.3.7.1
 Flask-Uploads==0.2.1
 Flask-WTF==0.15.1
@@ -8,5 +8,5 @@ Jinja2==3.1.6
 MarkupSafe==2.0.1
 python-dotenv==0.17.1
 visitor==0.1.3
-Werkzeug==3.1.5
+Werkzeug==3.1.6
 WTForms==2.2.1

pyxtal/XRD.py

@@ -536,7 +536,7 @@ def plotly_pxrd(
             title="PXRD of " + self.name,
         )
 
-        if os.environ["_"].find("jupyter") == -1:
+        if os.environ.get("_", "").find("jupyter") == -1:
             if html is None:
                 return fig.to_html()
             else:

pyxtal/crystal.py

@@ -119,7 +119,7 @@ def __init__(
         compat, self.has_freedom = self.group.check_compatible(self.numIons)
         if not compat:
             self.valid = False
-            msg = "Compoisition " + str(self.numIons)
+            msg = "Composition " + str(self.numIons)
             msg += " not compatible with symmetry "
             msg += str(self.group.number)
             raise Comp_CompatibilityError(msg)

pyxtal/molecular_crystal.py

@@ -125,7 +125,7 @@ def __init__(
             compat, self.has_freedom = self.group.check_compatible(self.numMols) #self.valid_orientations)
 
         if not compat:
-            msg = f"Inincompatible compoisition {self.numMols} with symmetry {self.group.number}"
+            msg = f"Incompatible composition {self.numMols} with symmetry {self.group.number}"
             raise Comp_CompatibilityError(msg)
 
         self.set_volume()

pyxtal/representation.py

@@ -48,7 +48,7 @@ def to_pyxtal(self):
 
         Args:
             smiles: list of smiles
-            compoisition: list of composition
+            composition: list of composition
         """
         from pyxtal import pyxtal
 
@@ -113,7 +113,7 @@ def to_pyxtal(self):
 
     def to_array(self):
         """
-        Export only varibles to a 1d numpy array
+        Export only variables to a 1d numpy array
         """
         cells, xyzs = self.x[0][1:], self.x[1:]
         x = cells
@@ -278,7 +278,7 @@ def to_pyxtal(self, smiles=None, composition=None):
 
         Args:
             smiles: list of smiles
-            compoisition: list of composition
+            composition: list of composition
         """
         from pyxtal import pyxtal
 

pyxtal/symmetry.py

@@ -1232,10 +1232,8 @@ def get_spg_symmetry_object(self):
             elif bravis == "F":
                 ops = ops[: int(len(ops) / 4)]
 
-            return site_symmetry(ops, l_type, bravis, self.number, True)
-            # ss.to_beautiful_matrix_representation()
-        else:
-            raise ValueError("Only supports space group symmetry")
+            return site_symmetry(ops, l_type, bravis, self.number, wp_id=0, parse_trans=True)
+        raise ValueError("Only supports space group symmetry")
 
     def get_wyckoff_position(self, index):
         """