add the discrete option in opt_reps

pyxtal/__init__.py

@@ -1638,7 +1638,6 @@ def build(self, group, species, numIons, lattice, sites, tol=1e-2, dim=3, use_ha
         #    msg = 'The input lattice needs to be a pyxtal.lattice.Lattice class'
         #    raise ValueError(msg, lattice)
         self.lattice = lattice
-
         self.dim = dim
         self.factor = 1.0
         self.PBC = self.group.PBC
@@ -1667,12 +1666,14 @@ def build(self, group, species, numIons, lattice, sites, tol=1e-2, dim=3, use_ha
                 elif len(wp) == 4:  # tuple:
                     (key, x, y, z) = wp
                     _wp = choose_wyckoff(self.group, site=key, dim=dim)
+                    # print(key, x, y, z, _wp.get_label())
                     if _wp is not False:
                         if _wp.get_dof() == 0:  # fixed pos
                             pt = [0.0, 0.0, 0.0]
                         else:
                             ans = _wp.get_all_positions([x, y, z])
                             pt = ans[0] if ans is not None else None
+                            # print('debug', ans)
                         if pt is not None:
                             _sites.append(atom_site(_wp, pt, sp))
                     else:
@@ -3853,12 +3854,15 @@ def from_tabular_representation(
                         # ; print(x, y, z, label, xyz[0], xyz[1], xyz[2])
                         sites.append((label, xyz[0], xyz[1], xyz[2]))
                         numIons += wp.multiplicity
+                        if verbose:
+                            print('add wp', label, xyz)
                     else:
                         if verbose:
-                            print("Cannot find generator from", x, y, z)
-                            print(wp)
+                            print("Cannot get wp in", x, y, z, wp.get_label())
+
             if len(sites) > 0:
                 try:
+                    # print(sites)
                     self.build(group, ["C"], [numIons], lattice, [sites])
                 except:
                     print("Invalid Build", number, lattice, numIons, sites)

pyxtal/database/HM_Full.csv

@@ -50,7 +50,7 @@ Hall,Spg_num,Spg_full,Symbol,P,P^-1,Permutation
 49,9,9:-c2,A 1 1 n,"-a-c,a,-b","b,-c,-a-b",1
 50,9,9:-c3,I 1 1 a,"c,-a-c,-b","-a-b,-c,a",1
 51,9,9:a1,B b 1 1,"b,c,a","c,a,b",1
-52,9,9:a2,C n 1 1,"-b,a,c","b,-a,c",1
+52,9,9:a2,C n 1 1,"b,a,-a-c","b,a,-b-c",1
 53,9,9:a3,I c 1 1,"b,-a-c,c","-b-c,a,c",1
 54,9,9:-a1,C c 1 1,"-b,a,c","b,-a,c",1
 55,9,9:-a2,B n 1 1,"-b,-a-c,a","c,-a,-b-c",1

pyxtal/lego/builder.py

@@ -208,7 +208,7 @@ def minimize_from_x(x, dim, spg, wps, elements, calculator, ref_environments,
         except:
             return None
 
-    x0 = x.copy()
+    x0 = np.array(x.copy())
     # Extract variables, call from Pyxtal
     [N_abc, N_ang] = Lattice.get_dofs(xtal.lattice.ltype)
     rep = xtal.get_1D_representation()
@@ -799,7 +799,7 @@ def optimize_reps(self, reps, ncpu=1, opt_type='local',
                       T=0.2, niter=20, early_quit=0.02,
                       add_db=True, symmetrize=False,
                       minimizers=[('Nelder-Mead', 100), ('L-BFGS-B', 100)],
-                       ):
+                      discrete=False):
         """
         Perform optimization for each structure
 
@@ -809,12 +809,12 @@ def optimize_reps(self, reps, ncpu=1, opt_type='local',
         """
         args = (opt_type, T, niter, early_quit, add_db, symmetrize, minimizers)
         if ncpu > 1:
-            valid_xtals = self.optimize_reps_mproc(reps, ncpu, args)
+            valid_xtals = self.optimize_reps_mproc(reps, ncpu, args, discrete)
             return valid_xtals
         else:
             raise NotImplementedError("optimize_reps works in parallel mode")
 
-    def optimize_reps_mproc(self, reps, ncpu, args):
+    def optimize_reps_mproc(self, reps, ncpu, args, discrete):
         """
         Optimization in multiprocess mode.
 
@@ -847,7 +847,9 @@ def generate_args():
                     for id in _ids:
                         rep = reps[id]
                         xtal = pyxtal()
-                        xtal.from_tabular_representation(rep, normalize=False)
+                        xtal.from_tabular_representation(rep,
+                                                         normalize=False,
+                                                         discrete=discrete)
                         x = xtal.get_1d_rep_x()
                         spg, wps, _ = self.get_input_from_ref_xtal(xtal)
                         wp_libs.append((x, spg, wps))
@@ -1295,13 +1297,8 @@ def process_xtal(self, xtal, sim, count=0, xs=None, energy=None,
             'similarity': sim[1],
         }
         if xs is not None:
-            try:
-                kvp['x_init'] = np.array2string(xs[0])
-                kvp['x_opt'] = np.array2string(xs[1])
-            except:
-                print("Error in xs", xs)
-                kvp['x_init'] = 'N/A'
-                kvp['x_opt'] = 'N/A'
+            kvp['x_init'] = np.array2string(xs[0])
+            kvp['x_opt'] = np.array2string(xs[1])
         if energy is not None:
             kvp['ff_energy'] = energy
         if topology is not None: