fix the get_all_positions function and add the new_struc_wo_energy fu…

…nction

pyxtal/db.py

@@ -301,6 +301,53 @@ def compute(self, row, work_dir, skf_dir):
             self.db.update(row.id, data=data)
             print('updated the data for', row.csd_code)
 
+class database_topology():
+    """
+    This is a database class to process atomic crystal data
+
+    Args:
+        db_name: *.db format from ase database
+    """
+
+    def __init__(self, db_name):
+        self.db_name = db_name
+        #if not os.path.exists(db_name):
+        #    raise ValueError(db_name, 'doesnot exist')
+
+        self.db = connect(db_name)
+        self.keys = ['space_group', 'spg_num',
+                     'topology', 'ff_energy',
+                     'similarity',
+                    ]
+
+    def vacuum(self):
+        self.db.vacuum()
+
+
+    def get_pyxtal(self, id):
+        from pyxtal import pyxtal
+        from pyxtal.util import ase2pymatgen
+
+        atom = self.db.get_atoms(id=id)
+        pmg = ase2pymatgen(atom)
+        xtal = pyxtal()
+        try:
+            xtal.from_seed(pmg)
+            return xtal
+        except:
+            print('Cannot load the structure')
+
+
+    def get_all_xtals(self):
+        xtals = []
+        for row in self.db.select():
+            xtal = self.get_pyxtal(id=row.id)
+            if xtal is not None and xtal.valid:
+                xtal.ff_energy = row.ff_energy
+                xtal.similarity = row.similarity
+                xtal.topology = row.topology
+                xtals.append(xtal)
+        return xtals
 
 if __name__ == "__main__":
     # open

pyxtal/symmetry.py

@@ -1951,7 +1951,7 @@ def get_all_positions(self, pos):
                [0.5, 0.5, 0.5]])
         """
 
-        pos0, _, _ = self.merge(pos, np.eye(3), 0.01)
+        pos0 = self.search_generator(pos)
         res = self.apply_ops(pos0)
         res -= np.floor(res)
         return res
@@ -2165,6 +2165,7 @@ def merge(self, pt, lattice, tol, orientations=None, group=None):
                 if y[0] == 0 and y[1] == 0:
                     pass
                 else:
+                    #print(dm); print(y)
                     passed_distance_check = False
                     break
 

pyxtal/util.py

@@ -595,6 +595,38 @@ def new_struc(xtal, xtals):
                         return False
         return True
 
+def new_struc_wo_energy(xtal, xtals):
+    """
+    check if this is a new structure
+
+    Args:
+        xtal: input structure
+        xtals: list of reference structures
+
+    Return:
+        `None` or the id of matched structure
+    """
+    import pymatgen.analysis.structure_matcher as sm
+
+    if xtal is None:
+        return False
+    else:
+        pmg_s1 = xtal.to_pymatgen()
+        pmg_s1.remove_species("H")
+        vol1 = pmg_s1.lattice.volume
+
+        for xtal2 in xtals:
+            #print(rep); print(rep2)
+            pmg_s2 = xtal2.to_pymatgen()
+            vol2 = pmg_s2.lattice.volume
+            if abs(vol1-vol2)/vol1<5e-2:
+                pmg_s2.remove_species("H")
+                if sm.StructureMatcher().fit(pmg_s1, pmg_s2):
+                    #print(pmg_s2); import sys; sys.exit()
+                    return False
+        return True
+
+
 
 if __name__ == "__main__":
     from argparse import ArgumentParser