display failures in from_tab function

pyxtal/__init__.py

@@ -200,9 +200,11 @@ def __str__(self):
  symbol = self.group.symbol
  else:
  if self.molecular:
- symbol = self.mol_sites[0].wp.get_hm_symbol()
+ if len(self.mol_sites) > 0:
+ symbol = self.mol_sites[0].wp.get_hm_symbol()
  else:
- symbol = self.atom_sites[0].wp.get_hm_symbol()
+ if len(self.atom_sites) > 0:
+ symbol = self.atom_sites[0].wp.get_hm_symbol()
  s += "\nGroup: {} ({})".format(symbol, self.group.number)
  s += "\n{}".format(self.lattice)
  s += "\nWyckoff sites:"
@@ -3635,7 +3637,8 @@ def get_tabular_representation(self, ids=None, normalize=True, N_wp=6,
  return rep
 
 
- def from_tabular_representation(self, rep, max_abc=50.0, max_angle=180, normalize=True):
+ def from_tabular_representation(self, rep, max_abc=50.0, max_angle=180,
+ normalize=True, verbose=False):
  """
  Reconstruc xtal from 1d tabular_representation
  Currently assuming the elemental composition like carbon
@@ -3644,13 +3647,13 @@ def from_tabular_representation(self, rep, max_abc=50.0, max_angle=180, normaliz
  rep: 1D array
  max_abc (float): maximum a, b, c length (used in normalization)
  max_angle (float): maximum angle in radian (used in normalization)
-
+ normalize (bool): whether normalize or not?
+ verbose (bool): output detailed error
  """
  if normalize:
  number = int(np.round(rep[0] * 230))
  else:
  number = int(rep[0])
-
  if 1 <= number <= 230:
  group = Group(number)
  [a, b, c, alpha, beta, gamma] = rep[1:7]
@@ -3666,6 +3669,8 @@ def from_tabular_representation(self, rep, max_abc=50.0, max_angle=180, normaliz
  numIons = 0
  for site_info in sites_info:
  [id, x, y, z] = site_info
+ # exclude data containing negative values
+ if verbose: print("site_info", site_info)
  if min(site_info) > -0.01:
  if normalize:
  wp_id = int(np.round(len(group)*id))
@@ -3679,11 +3684,23 @@ def from_tabular_representation(self, rep, max_abc=50.0, max_angle=180, normaliz
  label = wp.get_label()
  sites.append((label, xyz[0], xyz[1], xyz[2]))#; print(x, y, z, label, xyz[0], xyz[1], xyz[2])
  numIons += wp.multiplicity
- try:
- self.build(group, ['C'], [numIons], lattice, [sites])
- except:
- print("Invalid Build", number, lattice, numIons, sites)
+ else:
+ if verbose:
+ print("Cannot find generator from the input", x, y, z)
+ print(wp)
+ if len(sites) > 0:
+ try:
+ self.build(group, ['C'], [numIons], lattice, [sites])
+ except:
+ print("Invalid Build", number, lattice, numIons, sites)
+ self.valid = False
+ else:
+ print("Empty sites in tabular_representation", rep)
+ print("parsed sites info", sites_info)
  self.valid = False
+ else:
+ if verbose:
+ print('The input space group is invalid', rep[0])
 
  def get_Pearson_Symbol(self):
  """