allow mutliple sites with the same label #310

Author: qzhu2017

doc/Usage.rst

@@ -887,7 +887,7 @@ O atoms.
               "4g": [0.1294, 0.6392, 0.0000],
              },
              {"4g": [0.2458, 0.2522, 0.0000]},
-             {"4g": [0.4241, 0.3636, 0.0000]}, #partial information on O sites
+             {"4g": [[0.4241, 0.3636, 0.0000], [0.5538, 0.2648, 0.0000]]}, #partial information on O sites
             ]
 
     s = pyxtal()
@@ -903,10 +903,11 @@ O atoms.
     Al @ [ 0.0000  0.0000  0.2418], WP [4e] Site [..2]
     Al @ [ 0.1294  0.6392  0.0000], WP [4g] Site [..m]
     Si @ [ 0.2458  0.2522  0.0000], WP [4g] Site [..m]
-    O  @ [ 0.4241  0.3636  0.0000], WP [4g] Site [..m]
-    O  @ [ 0.5538  0.2648  0.0000], WP [4g] Site [..m]
-    O  @ [ 0.0000  0.5000  0.6057], WP [4f] Site [..2]
-    O  @ [ 0.8809  0.5970  0.0786], WP [8h] Site [1]
+	 O @ [ 0.4241  0.3636  0.0000], WP [4g] Site [..m]
+	 O @ [ 0.5538  0.2648  0.0000], WP [4g] Site [..m]
+	 O @ [ 0.0000  0.0000  0.5000], WP [2b] Site [..2/m]
+	 O @ [ 0.0000  0.5000  0.0000], WP [2c] Site [..2/m]
+	 O @ [ 0.4348  0.6979  0.2566], WP [8h] Site [1]
 
 
 Similarly, PyXtal allows the user to pre-assign the partial information (e.g.,

pyxtal/crystal.py

@@ -161,7 +161,11 @@ def set_sites(self, sites):
                     for item in sites[i].items():
                         # keep the record of wp index
                         id = self.group.get_index_by_letter(item[0])
-                        self.sites[specie].append((id, item[1]))
+                        if isinstance(item[1][0], list):
+                            for it in range(len(item[1])):
+                                self.sites[specie].append((id, item[1][it]))
+                        else:
+                            self.sites[specie].append((id, item[1]))
                 elif isinstance(sites[i], (list, tuple)):
                     for site in sites[i]:
                         if type(site) is tuple:

tests/test_crystal.py

@@ -33,6 +33,24 @@ def test_atomic(self):
 
 
 class TestAtomic3D(unittest.TestCase):
+
+    def test_partial(self):
+        cell = Lattice.from_para(7.8758, 7.9794, 5.6139, 90, 90, 90, ltype='orthorhombic')
+        spg = 58
+        elements = ['Al', 'Si', 'O']
+        composition = [8, 4, 20]
+
+        sites = [{"4e": [0.0000, 0.0000, 0.2418],
+                  "4g": [0.1294, 0.6392, 0.0000],
+                 },
+                 {"4g": [0.2458, 0.2522, 0.0000]},
+                 {"4g": [[0.4241, 0.3636, 0.0000], [0.5538, 0.2648, 0.0000]]},
+                ]
+
+        s = pyxtal()
+        s.from_random(3, spg, elements, composition, lattice=cell, sites=sites)
+        assert s.valid
+
     def test_single_specie(self):
         struc = pyxtal()
         struc.from_random(3, 225, ["C"], [4], 1.2, conventional=False)