add the functions to convert between mol and atom

pyxtal/__init__.py

@@ -1455,7 +1455,7 @@ def load_dict(self, dict0):
                 sites.append(atom_site.load_dict(site))
             self.atom_sites = sites
 
-    def build(self, group, species, numIons, lattice, sites, tol=1e-2):
+    def build(self, group, species, numIons, lattice, sites, tol=1e-2, use_hall=False):
         """
         Build a atomic crystal based on the necessary input
 
@@ -1475,7 +1475,7 @@ def build(self, group, species, numIons, lattice, sites, tol=1e-2):
         if type(group) == Group:
             self.group = group
         else:
-            self.group = Group(group)
+            self.group = Group(group, use_hall=use_hall)
 
         self.lattice = lattice
         self.dim = 3
@@ -2924,3 +2924,53 @@ def get_structure_factor(self, hkl, coeffs=None):
         if coeffs is not None:
             F *= coeffs
         return F.sum()
+
+    def to_molecular_xtal(self, molecules, oris=None, reflects=None):
+        """
+        Convert the atomic xtal to molecular xtal
+        the input molecules must have the same length of the self.atom_sites
+        """
+        if not self.molecular:
+            xtal = pyxtal(molecular=True)
+            # updates mol_sites
+            sites = []
+            for i, site in enumerate(self.atom_sites):
+                if oris is None:
+                    ori = [0, 0, 0]
+                else:
+                    ori = oris[i]
+                if reflects is None:
+                    reflect = False
+                else:
+                    reflect = reflects[i]
+                sites.append(site.to_mol_site(self.lattice, molecules[i], ori=ori, reflect=reflect))
+            xtal.lattice = self.lattice
+            xtal.group = self.group
+            xtal.mol_sites = sites
+            xtal.numMols = [sum([wp.multiplicity for wp in self.atom_sites])]
+            xtal._get_formula()
+            xtal.valid = True
+            xtal.source = 'Center'
+
+            return xtal
+        else:
+            raise RuntimeError('The input must be molecular xtal')
+
+    def to_atomic_xtal(self):
+        """
+        Convert the molecular
+        """
+        if self.molecular:
+            xtal = pyxtal()
+            sites = []
+            for i, site in enumerate(self.mol_sites):
+                sites.append(site.to_atom_site(i+1))
+            xtal.lattice = self.lattice
+            xtal.group = self.group
+            xtal.atom_sites = sites
+            xtal._get_formula()
+            xtal.valid = True
+            xtal.source = 'Mol. Center'
+            return xtal
+        else:
+            raise RuntimeError('The input must be molecular xtal')

pyxtal/representation.py

@@ -380,9 +380,10 @@ def to_string(self, time=None, eng=None, tag=None):
         # data for molecule
         strs += "{:d} ".format(len(x)-1)
         for i in range(1, len(x)):
-            for v in x[i][:3]:
+            strs += "{:d} ".format(x[i][0])
+            for v in x[i][1:4]:
                 strs += "{:4.2f} ".format(v)      
-            for v in x[i][3:-1]:
+            for v in x[i][4:-1]:
                 strs += "{:6.1f} ".format(v)      
             strs += "{:d} ".format(int(x[i][-1]))
 

pyxtal/wyckoff_site.py

@@ -84,15 +84,18 @@ def _get_dof(self):
         #self.dof = len(freedom[freedom==True])
         #self.dof = len(freedom[freedom==True])
 
-
     @classmethod
     def load_dict(cls, dicts):
         """
         load the sites from a dictionary
         """
         position = dicts["position"]
         specie = dicts["specie"]
-        wp = Wyckoff_position.load_dict(dicts['wp'])
+        if 'wp' in dicts:
+            wp = Wyckoff_position.load_dict(dicts['wp'])
+        else:
+            hn, index = dicts['hn'], dicts['index']
+            wp = Wyckoff_position.from_group_and_index(hn, index, use_hall=True)
         return cls(wp, position, specie)
 
     def perturbate(self, lattice, magnitude=0.1):
@@ -307,6 +310,26 @@ def substitute_with_linear(self, eles, direction, lattice):
         site2.update(site2.position - shift)
         return site1, site2
 
+    def to_mol_site(self, lattice, molecule, ori=[0, 0, 0], reflect=False, type_id=0):
+        """
+        transform it to the mol_sites, i.e., to build a molecule on 
+        the current WP
+        """
+        dicts = {}
+        dicts['smile'] = molecule.smile
+        dicts['type'] = type_id
+        dicts['dim'] = 3
+        dicts['PBC'] = [1, 1, 1]
+        dicts['hn'] = self.wp.hall_number
+        dicts['index'] = self.wp.index
+        dicts['lattice'] = lattice.matrix
+        dicts['lattice_type'] = lattice.ltype
+        dicts['center'] = self.position
+        if molecule.smile not in ["Cl-"]:
+            dicts['orientation'] = np.array(ori)
+            dicts['rotor'] = molecule.get_torsion_angles()
+            dicts['reflect'] = reflect
+        return mol_site.from_1D_dicts(dicts)
 
 class mol_site:
     """
@@ -482,6 +505,7 @@ def from_1D_dicts(cls, dicts):
         position = dicts["center"] #np.dot(dicts["center"], lattice.inv_matrix)
         position, wp, _ = wp.merge(position, lattice.matrix, 0.01)
 
+
         return cls(mol, position, orientation, wp, lattice)
 
     def show(self, id=None, **kwargs):
@@ -1162,3 +1186,19 @@ def get_ijk_lists(self, value=None):
             self.ijk_lists = ijk_lists
         else:
             self.ijk_lists = value
+
+    def to_atom_site(self, specie=1):
+        """
+        transform it to the mol_sites, i.e., to build a molecule on 
+        the current WP
+        """
+        dicts = {}
+        dicts['specie'] = specie
+        dicts['position'] = self.position
+        dicts['hn'] = self.wp.hall_number
+        dicts['index'] = self.wp.index
+        return atom_site.load_dict(dicts)
+
+
+
+