update db function with gulp calculation

pyxtal/db.py

@@ -848,7 +848,8 @@ def select_xtals(self, ids, overwrite=False, attribute=None, use_relaxed=None):
  def update_row_ff_energy(self, ff='reaxff', ids=(None, None), ncpu=1,
  calc_folder='gulp_calc',
  criteria=None,
- overwrite=False):
+ overwrite=False,
+ write_freq=10):
  """
  Update row ff_energy with GULP calculator
 
@@ -858,6 +859,7 @@ def update_row_ff_energy(self, ff='reaxff', ids=(None, None), ncpu=1,
  ncpu (int): number of parallel processes
  calc_folder (str): temporary folder for GULP calculations
  overwrite (bool): remove the existing attributes
+ write_freq (int): frequency to write results to db for ncpu=1
  """
 
  os.makedirs(calc_folder, exist_ok=True)
@@ -870,7 +872,11 @@ def update_row_ff_energy(self, ff='reaxff', ids=(None, None), ncpu=1,
  for id, xtal in zip(ids, xtals):
  res = gulp_opt_single(id, xtal, ff, calc_folder, criteria)
  (xtal, eng, status) = res
- if status: gulp_results.append((id, xtal, eng))
+ if status:
+ gulp_results.append((id, xtal, eng))
+ if len(gulp_results) >= write_freq:
+ self._update_db_gulp(gulp_results)
+ gulp_results = []
  else:
  if len(ids) < ncpu: ncpu = len(ids)
  N_cycle = int(np.ceil(len(ids)/ncpu))
@@ -886,7 +892,12 @@ def update_row_ff_energy(self, ff='reaxff', ids=(None, None), ncpu=1,
  results = [executor.submit(gulp_opt_par, *p) for p in args_list]
  for result in results:
  gulp_results.extend(result.result())
+ self._update_db_gulp(gulp_results)
 
+ def _update_db_gulp(self, gulp_results):
+ """
+ Update db with the gulp_results
+ """
  print("Wrap up the final results and update db", len(gulp_results))
  for gulp_result in gulp_results:
  (id, xtal, eng) = gulp_result