update db function with max_id

pyxtal/db.py

@@ -819,6 +819,16 @@ def clean_structures_pmg(self, ids=(None, None), min_id=None, dtol=5e-2, criteri
  self.db.delete(to_delete)
 
 
+ def get_max_id(self):
+ """
+ Get the maximum row id
+ """
+ max_id = None
+ for row in self.db.select():
+ if max_id is None or row.id > max_id:
+ max_id = row.id + 1
+ return max_id
+
  def select_xtals(self, ids, overwrite=False, attribute=None, use_relaxed=None):
  """
  Extract xtals based on attribute name.
@@ -832,8 +842,7 @@ def select_xtals(self, ids, overwrite=False, attribute=None, use_relaxed=None):
  """
  (min_id, max_id) = ids
  if min_id is None: min_id = 1
- if max_id is None: max_id = self.db.count() + 10000
-
+ if max_id is None: max_id = self.get_max_id()
  ids, xtals = [], []
  for row in self.db.select():
  if overwrite or attribute is None or not hasattr(row, attribute):
@@ -865,34 +874,37 @@ def update_row_ff_energy(self, ff='reaxff', ids=(None, None), ncpu=1,
  os.makedirs(calc_folder, exist_ok=True)
  ids, xtals = self.select_xtals(ids, overwrite, 'ff_energy')
 
- gulp_results = []
-
- # Serial or Parallel computation
- if 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 len(gulp_results) >= write_freq:
- self._update_db_gulp(gulp_results, ff)
- gulp_results = []
+ if len(ids) > 0:
+ gulp_results = []
+
+ # Serial or Parallel computation
+ if 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 len(gulp_results) >= write_freq:
+ self._update_db_gulp(gulp_results, ff)
+ gulp_results = []
+ else:
+ if len(ids) < ncpu: ncpu = len(ids)
+ N_cycle = int(np.ceil(len(ids)/ncpu))
+ print("\n# Parallel GULP optimizations", ncpu, N_cycle, len(ids))
+ args_list = []
+
+ for i in range(ncpu):
+ id1 = i * N_cycle
+ id2 = min([id1 + N_cycle, len(ids)])
+ args_list.append((ids[id1:id2], xtals[id1:id2], ff, calc_folder, criteria))
+
+ with ProcessPoolExecutor(max_workers=ncpu) as executor:
+ 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, ff)
  else:
- if len(ids) < ncpu: ncpu = len(ids)
- N_cycle = int(np.ceil(len(ids)/ncpu))
- print("\n# Parallel GULP optimizations", ncpu, N_cycle, len(ids))
- args_list = []
-
- for i in range(ncpu):
- id1 = i * N_cycle
- id2 = min([id1 + N_cycle, len(ids)])
- args_list.append((ids[id1:id2], xtals[id1:id2], ff, calc_folder, criteria))
-
- with ProcessPoolExecutor(max_workers=ncpu) as executor:
- 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, ff)
+ print("All structures have the ff_energy already")
 
  def _update_db_gulp(self, gulp_results, ff):
  """