a preliminary support on partial information cconstraints

Author: qzhu2017

pyxtal/crystal.py

@@ -139,9 +139,14 @@ def set_sites(self, sites):
         # Symmetry sites
         self.sites = {}
         for i, specie in enumerate(self.species):
-            if sites is not None and sites[i] is not None:
+            if sites is not None and sites[i] is not None and len(sites[i])>0:
                 self._check_consistency(sites[i], self.numIons[i])
-                self.sites[specie] = sites[i]
+                if type(sites[i][0]) is dict:
+                    self.sites[specie] = []
+                    for item in sites[i][0].items():
+                        self.sites[specie].append({item[0]: item[1]})
+                else:
+                    self.sites[specie] = sites[i]
             else:
                 self.sites[specie] = None
 
@@ -292,7 +297,6 @@ def _set_ion_wyckoffs(self, numIon, specie, cell, wyks):
         """
         numIon_added = 0
         tol = self.tol_matrix.get_tol(specie, specie)
-        tol_matrix = self.tol_matrix
         wyckoff_sites_tmp = []
 
         # Now we start to add the specie to the wyckoff position
@@ -312,51 +316,66 @@ def _set_ion_wyckoffs(self, numIon, specie, cell, wyks):
             else: # Selecting the merging
                 site = None
 
-            wp = choose_wyckoff(self.group, numIon - numIon_added, site, self.dim)
-            if wp is not False:
-                # Generate a list of coords from ops
-                mult = wp.multiplicity # remember the original multiplicity
-                pt = self.lattice.generate_point()
-                # Merge coordinates if the atoms are close
-                pt, wp, _ = wp.merge(pt, cell, tol)
-                # For pure planar structure
-                if self.dim == 2 and self.thickness is not None and self.thickness < 0.1:
-                    pt[-1] = 0.5
-
-                # If site the pre-assigned, do not accept merge
+            new_site = None
+            if type(site) is dict: #site with coordinates
+                key = list(site.keys())[0]
+                wp = choose_wyckoff(self.group, numIon-numIon_added, key, self.dim)
+                new_site = atom_site(wp, site[key], specie)
+            else:
+                wp = choose_wyckoff(self.group, numIon-numIon_added, site, self.dim)
                 if wp is not False:
-                    if site is not None and mult != wp.multiplicity:
-                        cycle += 1
-                        continue
-                    # Use a Wyckoff_site object for the current site
-                    new_site = atom_site(wp, pt, specie)
-
-                    # Check current WP against existing WP's
-                    passed_wp_check = True
-                    for ws in wyckoff_sites_tmp + wyks:
-                        if not new_site.check_with_ws2(ws, cell, tol_matrix):
-                            passed_wp_check = False
-
-                    if passed_wp_check:
-                        if sites_list is not None:
-                            sites_list.pop(0)
-                        wyckoff_sites_tmp.append(new_site)
-                        numIon_added += new_site.multiplicity
-
-                        # Check if enough atoms have been added
-                        if numIon_added == numIon:
-                            return wyckoff_sites_tmp
+                    # Generate a list of coords from ops
+                    mult = wp.multiplicity # remember the original multiplicity
+                    pt = self.lattice.generate_point()
+                    # Merge coordinates if the atoms are close
+                    pt, wp, _ = wp.merge(pt, cell, tol)
+                    # For pure planar structure
+                    if self.dim == 2 and self.thickness is not None and self.thickness < 0.1:
+                        pt[-1] = 0.5
+
+                    # If site the pre-assigned, do not accept merge
+                    if wp is not False:
+                        if site is not None and mult != wp.multiplicity:
+                            cycle += 1
+                            continue
+                        # Use a Wyckoff_site object for the current site
+                        new_site = atom_site(wp, pt, specie)
+
+            # Check current WP against existing WP's
+            if self.check_wp(wyckoff_sites_tmp, wyks, cell, new_site):
+                if sites_list is not None:
+                    sites_list.pop(0)
+                wyckoff_sites_tmp.append(new_site)
+                numIon_added += new_site.multiplicity
+
+                # Check if enough atoms have been added
+                if numIon_added == numIon:
+                    return wyckoff_sites_tmp
 
             cycle += 1
             self.numattempts += 1
 
         return None
 
+    def check_wp(self, wyckoff_sites_tmp, wyks, cell, new_site):
+        # Check current WP against existing WP's
+        if new_site is None:
+            return False
+
+        for ws in wyckoff_sites_tmp + wyks:
+            if not new_site.check_with_ws2(ws, cell, self.tol_matrix):
+                return False
+        return True
+
 
     def _check_consistency(self, site, numIon):
         num = 0
         for s in site:
-            num += int(s[:-1])
+            if type(s) is dict:
+                for key in s.keys():
+                    num += int(key[:-1])
+            else:
+                num += int(s[:-1])
         if numIon == num:
             return True
         else:

pyxtal/database/cifs/Al2SiO5_mp-4753_symmetrized.cif

@@ -0,0 +1,40 @@
+# generated using pymatgen
+data_Al2SiO5
+_symmetry_space_group_name_H-M   Pnnm
+_cell_length_a   7.87578500
+_cell_length_b   7.97942000
+_cell_length_c   5.61389800
+_cell_angle_alpha   90.00000000
+_cell_angle_beta   90.00000000
+_cell_angle_gamma   90.00000000
+_symmetry_Int_Tables_number   58
+_chemical_formula_structural   Al2SiO5
+_chemical_formula_sum   'Al8 Si4 O20'
+_cell_volume   352.80090817
+_cell_formula_units_Z   4
+loop_
+ _symmetry_equiv_pos_site_id
+ _symmetry_equiv_pos_as_xyz
+  1  'x, y, z'
+  2  '-x, -y, -z'
+  3  '-x, -y, z'
+  4  'x, y, -z'
+  5  'x+1/2, -y+1/2, -z+1/2'
+  6  '-x+1/2, y+1/2, z+1/2'
+  7  '-x+1/2, y+1/2, -z+1/2'
+  8  'x+1/2, -y+1/2, z+1/2'
+loop_
+ _atom_site_type_symbol
+ _atom_site_label
+ _atom_site_symmetry_multiplicity
+ _atom_site_fract_x
+ _atom_site_fract_y
+ _atom_site_fract_z
+ _atom_site_occupancy
+  Al  Al0  4  0.00000000  0.00000000  0.24176400  1
+  Al  Al1  4  0.12942900  0.63918100  0.00000000  1
+  Si  Si2  4  0.24575200  0.25224100  0.00000000  1
+  O  O3  8  0.23075400  0.13422900  0.23971600  1
+  O  O4  4  0.07587800  0.86359200  0.50000000  1
+  O  O5  4  0.07596900  0.86286100  0.00000000  1
+  O  O6  4  0.10253200  0.40066200  0.00000000  1

pyxtal/test_all.py

@@ -927,6 +927,23 @@ def test_molecular(self):
         pmg_s2 = s2.to_pymatgen()
         self.assertTrue(sm.StructureMatcher().fit(pmg_s1, pmg_s2))
 
+class TestPartial(unittest.TestCase):
+    def test_Al2SiO5(self):
+        cell = Lattice.from_para(7.8758, 7.9794, 5.6139, 90, 90, 90)
+        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]}],
+                 [], #empty for oxygen
+                ]
+
+        s = pyxtal()
+        s.from_random(3, spg, elements, composition, lattice=cell, sites=sites)
+        self.assertTrue(s.valid)
+
 class Test_operations(unittest.TestCase):
     def test_inverse(self):
         coord0 = [0.35, 0.1, 0.4]