resolve #153

MaterSim · Jul 25, 2021 · fb778d2 · fb778d2
1 parent 4bdbec1
commit fb778d2
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Showing 4 changed files with 13 additions and 9 deletions.
diff --git a/pyxtal/__init__.py b/pyxtal/__init__.py
@@ -918,7 +918,7 @@ def get_zprime(self, integer=False):
         mult = len(self.group[0])
         comp = [c/mult for c in self.numMols]
         if integer:
-            comp = [int(c) for c in comp]
+            comp = [int(np.ceil(c)) for c in comp]
         return comp
 
     def get_num_torsions(self):

diff --git a/pyxtal/io.py b/pyxtal/io.py
@@ -281,21 +281,20 @@ def resort(self, molecules):
         self.p_mols = []
         self.wps = []
         ids_done = []
-        for j, mol2 in enumerate(self.ref_mols):
-            if self.add_H:
-                mol2.mol.remove_species("H")
+        for j, mol2_ref in enumerate(self.ref_mols):
+            mol2 = mol2_ref.copy()
+            if self.add_H: mol2.mol.remove_species("H")
 
             for i, id in enumerate(ids):
-                p_mol = mol2.copy() # create p_mol
                 mol1 = molecules[id]
                 if id not in ids_done and len(mol2.mol) == len(mol1):
+                    p_mol = mol2_ref.copy() # create p_mol
                     match, mapping = compare_mol_connectivity(mol2.mol, mol1)
                     if match:
                         self.numMols[j] += mults[i] 
                         if len(mol1) > 1:
                             # rearrange the order
                             order = [mapping[at] for at in range(len(mol1))]
-
                             xyz = mol1.cart_coords[order] 
                             # add hydrogen positions here
                             if self.add_H: xyz = self.add_Hydrogens(mol2.smile, xyz)

diff --git a/pyxtal/representation.py b/pyxtal/representation.py
@@ -71,7 +71,7 @@ def from_string(cls, inputs, smiles, composition=None):
 
         x = [cell]
         n_site = int(inputs[n_cell])
-        if n_site != sum(composition) :
+        if n_site != sum(composition):
             msg = "Composition is inconsistent: {:d}/{:d}\n".format(sum(composition), n_site)
             msg += str(inputs)
             raise ValueError(msg)
@@ -126,6 +126,10 @@ def to_pyxtal(self, smiles=None, composition=None):
             a, b, c, alpha, beta, gamma = v[2], v[3], v[4], 90, 90, 90
         elif ltype == 'tetragonal':
             a, b, c, alpha, beta, gamma = v[2], v[2], v[3], 90, 90, 90
+        elif ltype == 'hexagonal':
+            a, b, c, alpha, beta, gamma = v[2], v[2], v[3], 90, 90, 120
+        else:
+            a, b, c, alpha, beta, gamma = v[2], v[2], v[2], 90, 90, 90
         struc.lattice = Lattice.from_para(a, b, c, alpha, beta, gamma, ltype=ltype)
 
         # sites

diff --git a/pyxtal/wyckoff_site.py b/pyxtal/wyckoff_site.py
@@ -182,8 +182,8 @@ def from_1D_dicts(cls, dicts):
             #print(conf.GetPositions()[:3]); print(dicts["rotor"])
             if dicts['reflect']:
                 mol.set_torsion_angles(conf, dicts["rotor"], False)
-            #    print(mol.set_torsion_angles(conf, dicts["rotor"], True))
-            #    #import sys; sys.exit()
+                #print(mol.set_torsion_angles(conf, dicts["rotor"], True))
+                #import sys; sys.exit()
             xyz = mol.set_torsion_angles(conf, dicts["rotor"], dicts['reflect'])
             mol.reset_positions(xyz)
         g = dicts["number"]
@@ -199,6 +199,7 @@ def from_1D_dicts(cls, dicts):
         diag = dicts["diag"]
         lattice = Lattice.from_matrix(dicts["lattice"], ltype=dicts["lattice_type"])
         position = dicts["center"] #np.dot(dicts["center"], lattice.inv_matrix)
+        position, wp, _ = WP_merge(position, lattice.matrix, wp, 0.01)
 
         return cls(mol, position, orientation, wp, lattice, diag)