add the support for Si-based molecular crystals

MaterSim · Dec 18, 2023 · a99cd5d · a99cd5d
1 parent 675ab83
commit a99cd5d
Show file tree

Hide file tree

Showing 3 changed files with 7 additions and 4 deletions.
diff --git a/pyxtal/__init__.py b/pyxtal/__init__.py
@@ -2847,7 +2847,7 @@ def from_CSD(self, csd_code):
             for ele in pmg.composition.elements:
                 if ele.symbol == 'D':
                     pmg.replace_species({ele: Element("H")})
-                elif ele.value not in ["C", "H", "O", "N", "S", "F", "Cl", "Br", "I", "P"]:
+                elif ele.value not in ["C", "Si", "H", "O", "N", "S", "F", "Cl", "Br", "I", "P"]:
                     organic = False
                     break
 
@@ -2856,6 +2856,7 @@ def from_CSD(self, csd_code):
                 msg += entry.formula
                 raise CSDError(msg)
             else:
+                #print(smiles); self.from_seed(pmg, smiles)
                 try:
                     #print(smiles)#; import sys; sys.exit()
                     self.from_seed(pmg, smiles)

diff --git a/pyxtal/io.py b/pyxtal/io.py
@@ -390,9 +390,9 @@ def resort(self, molecules):
                 if id not in ids_done:
                     msg = "This molecule cannot be matched to the reference\n"
                     msg += 'Molecules extracted from the structure\n'
-                    msg += molecules[id].to('xyz') + '\n'
+                    msg += molecules[id].to(fmt='xyz') + '\n'
                     msg += "Reference molecule from smiles or xyz\n"
-                    msg += mol2.mol.to('xyz')
+                    msg += mol2.mol.to(fmt='xyz')
                     raise ReadSeedError(msg)
 
     def add_Hydrogens(self, smile, xyz):

diff --git a/pyxtal/molecule.py b/pyxtal/molecule.py
@@ -193,6 +193,7 @@ def __init__(self,
         mo = None
         self.smile = None
         self.torsionlist = None
+        self.reflect = False
         if seed is None: seed = 0xf00d
         self.seed = seed
 
@@ -244,7 +245,8 @@ def __init__(self,
         self.tols_matrix = self.get_tols_matrix()
         xyz = self.mol.cart_coords
         self.reset_positions(xyz-self.get_center(xyz))
-
+        if self.smile is not None: ori, _, self.reflect = self.get_orientation(xyz)
+
     def __str__(self):
         return '[' + self.name + ']'