add partial constriants #191

Author: qzhu2017

doc/Usage.rst

@@ -42,6 +42,61 @@ This would create a crystal structure with 3D structure with space group 225, 12
 
 would create a random BaTiO3 crystal.
 
+Sometimes, it is also convenient to generate the random crystal with partial information
+
+.. code-block:: Python
+
+    my_crystal.from_random(3, 99, ['Ba','Ti','O'], [1,1,3])
+    my_crystal
+    ------Random Crystal------
+    Composition: Ba1 Ti1 O3
+    Dimension: 3
+    Group: P4mm (99)
+    Volume factor: 1.0
+    tetragonal lattice:   5.1029   5.1029   4.3018  90.0000  90.0000  90.0000
+    Wyckoff sites:
+    	Ba @ [0.5000 0.5000 0.3612], Wyckoff letter:  1b, Site symmetry: 4 m m
+    	Ti @ [0.5000 0.5000 0.8701], Wyckoff letter:  1b, Site symmetry: 4 m m
+    	 O @ [0.5000 0.0000 0.0823], Wyckoff letter:  2c, Site symmetry: 2 mm .
+    	 O @ [0.5000 0.5000 0.8177], Wyckoff letter:  1b, Site symmetry: 4 m m
+
+    from pyxtal.lattice import Lattice
+    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]}, #partial information on oxygen sites
+            ]
+    
+    s = pyxtal()
+    s.from_random(3, spg, elements, composition, lattice=cell, sites=sites)
+    print(s)
+
+    ------Crystal from random------
+    Dimension: 3
+    Composition: O20Si4Al8
+    Group: Pnnm (58)
+      7.8758,   7.9794,   5.6139,  90.0000,  90.0000,  90.0000, orthorhombic
+    Wyckoff sites:
+    	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]
+
+
+The above script will create a crystal with constrained unit cell and sites on Si/Al, but random sites on O sites.
+
+
+
+
 If the generation is successful, the value ``my_crystal.valid`` will be set to ``True``; otherwise, it will be ``False``. 
 
 2D Crystals

doc/conf.py

@@ -24,9 +24,9 @@
 author = "Qiang Zhu, Scott Fredericks, Kevin Parrish"
 
 # The short X.Y version
-version = "0.4.4"
+version = "0.4.5"
 # The full version, including alpha/beta/rc tags
-release = "0.4.4"
+release = "0.4.5"
 
 
 # -- General configuration ---------------------------------------------------

doc/index.rst

@@ -23,7 +23,7 @@ PyXtal (pronounced ``pie-crystal``) is an open source Python library for the ab-
 - Structural manipulation via symmetry relation (both subgroup and supergroup)
 - Geometry optimization from built-in and external optimization methods
 
-The current version is ``0.4.4`` at `GitHub <https://github.com/qzhu2017/PyXtal>`_. It is available for use under the MIT license. Expect updates upon request by `Qiang Zhu\'s group <http://www.physics.unlv.edu/~qzhu/index.html>`_ at University of Nevada Las Vegas.
+The current version is ``0.4.5`` at `GitHub <https://github.com/qzhu2017/PyXtal>`_. It is available for use under the MIT license. Expect updates upon request by `Qiang Zhu\'s group <http://www.physics.unlv.edu/~qzhu/index.html>`_ at University of Nevada Las Vegas.
 
 PyXtal is an open source project. You are welcome to contribute it directly via the `GitHub platform <https://github.com/qzhu2017/PyXtal>`_ or send your comments and suggestions to the `developer <http://www.physics.unlv.edu/~qzhu/>`_.
 

pyxtal/crystal.py

@@ -141,9 +141,9 @@ def set_sites(self, sites):
         for i, specie in enumerate(self.species):
             if sites is not None and sites[i] is not None and len(sites[i])>0:
                 self._check_consistency(sites[i], self.numIons[i])
-                if type(sites[i][0]) is dict:
+                if type(sites[i]) is dict:
                     self.sites[specie] = []
-                    for item in sites[i][0].items():
+                    for item in sites[i].items():
                         self.sites[specie].append({item[0]: item[1]})
                 else:
                     self.sites[specie] = sites[i]
@@ -311,7 +311,7 @@ def _set_ion_wyckoffs(self, numIon, specie, cell, wyks):
         cycle = 0
         while cycle < wyckoff_attempts:
             # Choose a random WP for given multiplicity: 2a, 2b
-            if sites_list is not None:
+            if sites_list is not None and len(sites_list)>0:
                 site = sites_list[0]
             else: # Selecting the merging
                 site = None
@@ -343,7 +343,7 @@ def _set_ion_wyckoffs(self, numIon, specie, cell, wyks):
 
             # Check current WP against existing WP's
             if self.check_wp(wyckoff_sites_tmp, wyks, cell, new_site):
-                if sites_list is not None:
+                if sites_list is not None and len(sites_list)>0:
                     sites_list.pop(0)
                 wyckoff_sites_tmp.append(new_site)
                 numIon_added += new_site.multiplicity
@@ -379,8 +379,20 @@ def _check_consistency(self, site, numIon):
         if numIon == num:
             return True
         else:
-            msg = "\nThe requested number of atoms is inconsistent: " + str(site)
-            msg += "\nfrom numIons: {:d}".format(numIon)
-            msg += "\nfrom Wyckoff list: {:d}".format(num)
-            raise ValueError(msg)
+            diff = numIon - num
+            if diff > 0:
+                #check if compatible
+                compat, self.degrees = self.group.check_compatible([diff])
+                if compat:
+                    return True
+                else:
+                    msg += "\nfrom numIons: {:d}".format(numIon)
+                    msg += "\nfrom Wyckoff list: {:d}".format(num)
+                    msg = "\nThe number of atoms is incompatible with composition: " + str(site)
+                raise ValueError(msg)
+            else:
+                msg += "\nfrom numIons: {:d}".format(numIon)
+                msg += "\nfrom Wyckoff list: {:d}".format(num)
+                msg = "\nThe requested number of atoms is greater than composition: " + str(site)
+                raise ValueError(msg)
 

pyxtal/test_all.py

@@ -933,17 +933,28 @@ def test_Al2SiO5(self):
         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]}],
+        sites = [{"4e": [0.0000,  0.0000,  0.2418],
+                  "4g": [0.1294,  0.6392,  0.0000],
+                 },
+                 {"4g": [0.2458,  0.2522,  0.0000]},
                  [], #empty for oxygen
                 ]
 
         s = pyxtal()
         s.from_random(3, spg, elements, composition, lattice=cell, sites=sites)
         self.assertTrue(s.valid)
 
+        sites2 = [{"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]}, #partial info on O
+                 ]
+        
+        s = pyxtal()
+        s.from_random(3, spg, elements, composition, lattice=cell, sites=sites2)
+        self.assertTrue(s.valid)
+
 class Test_operations(unittest.TestCase):
     def test_inverse(self):
         coord0 = [0.35, 0.1, 0.4]