Cache chunk_exists results on frame 0.

gsd/hoomd.py

@@ -694,6 +694,9 @@ def __init__(self, file):
  self._file = file
  self._initial_frame = None
 
+ # Used to cache positive results when chunks exist in frame 0.
+ self._chunk_exists_frame_0 = {}
+
  logger.info('opening HOOMDTrajectory: ' + str(self.file))
 
  if self.file.schema != 'hoomd':
@@ -829,8 +832,8 @@ def _should_write(self, path, name, frame):
  data, container._default_value[name]
  )
 
- if matches_default_value and not self.file.chunk_exists(
- frame=0, name=path + '/' + name
+ if matches_default_value and not self._chunk_exists_frame_0.get(
+ path + '/' + name, False
  ):
  logger.debug('skipping data chunk, default value: ' + path + '/' + name)
  return False
@@ -875,6 +878,9 @@ def _read_frame(self, idx):
  if self.file.chunk_exists(frame=idx, name='configuration/step'):
  step_arr = self.file.read_chunk(frame=idx, name='configuration/step')
  frame.configuration.step = step_arr[0]
+
+ if idx == 0:
+ self._chunk_exists_frame_0['configuration/step'] = True
  elif self._initial_frame is not None:
  frame.configuration.step = self._initial_frame.configuration.step
  else:
@@ -885,6 +891,9 @@ def _read_frame(self, idx):
  frame=idx, name='configuration/dimensions'
  )
  frame.configuration.dimensions = dimensions_arr[0]
+
+ if idx == 0:
+ self._chunk_exists_frame_0['configuration/dimensions'] = True
  elif self._initial_frame is not None:
  frame.configuration.dimensions = (
  self._initial_frame.configuration.dimensions
@@ -898,6 +907,9 @@ def _read_frame(self, idx):
  frame.configuration.box = self.file.read_chunk(
  frame=idx, name='configuration/box'
  )
+
+ if idx == 0:
+ self._chunk_exists_frame_0['configuration/box'] = True
  elif self._initial_frame is not None:
  frame.configuration.box = copy.copy(self._initial_frame.configuration.box)
  else:
@@ -923,6 +935,9 @@ def _read_frame(self, idx):
  if self.file.chunk_exists(frame=idx, name=path + '/N'):
  N_arr = self.file.read_chunk(frame=idx, name=path + '/N')
  container.N = N_arr[0]
+
+ if idx == 0:
+ self._chunk_exists_frame_0[path + '/N'] = True
  elif self._initial_frame is not None:
  container.N = initial_frame_container.N
 
@@ -933,6 +948,9 @@ def _read_frame(self, idx):
  tmp = tmp.view(dtype=numpy.dtype((bytes, tmp.shape[1])))
  tmp = tmp.reshape([tmp.shape[0]])
  container.types = list(a.decode('UTF-8') for a in tmp)
+
+ if idx == 0:
+ self._chunk_exists_frame_0[path + '/types'] = True
  elif self._initial_frame is not None:
  container.types = copy.copy(initial_frame_container.types)
  else:
@@ -947,6 +965,9 @@ def _read_frame(self, idx):
  container.type_shapes = list(
  json.loads(json_string.decode('UTF-8')) for json_string in tmp
  )
+
+ if idx == 0:
+ self._chunk_exists_frame_0[path + '/type_shapes'] = True
  elif self._initial_frame is not None:
  container.type_shapes = copy.copy(
  initial_frame_container.type_shapes
@@ -965,6 +986,9 @@ def _read_frame(self, idx):
  container.__dict__[name] = self.file.read_chunk(
  frame=idx, name=path + '/' + name
  )
+
+ if idx == 0:
+ self._chunk_exists_frame_0[path + '/' + name] = True
  else:
  if (
  self._initial_frame is not None
@@ -996,6 +1020,9 @@ def _read_frame(self, idx):
  for log in logged_data_names:
  if self.file.chunk_exists(frame=idx, name=log):
  frame.log[log[4:]] = self.file.read_chunk(frame=idx, name=log)
+
+ if idx == 0:
+ self._chunk_exists_frame_0[log] = True
  elif self._initial_frame is not None:
  frame.log[log[4:]] = self._initial_frame.log[log[4:]]
  frame.log[log[4:]].flags.writeable = False