All output is recorded and no extra simulation steps are run

[K20shores]

We seem to not add the last row of data produced. Or, we do get the last row of data, but only because we simulate one more time step than is necessary, from what I can understand

music-box/src/acom_music_box/music_box.py

Lines 504 to 565 in 3de91fb

	while (curr_time <= self.box_model_options.simulation_length):
	# iterates evolving conditions if enough time has elapsed
	while (
	next_conditions is not None and next_conditions_time <= curr_time):
	curr_conditions.update_conditions(next_conditions)
	ordered_rate_constants = self.order_reaction_rates(
	curr_conditions, rate_constant_ordering)
	# iterates next_conditions if there are remaining evolving
	# conditions
	if (len(self.evolving_conditions) > next_conditions_index + 1):
	next_conditions_index += 1
	next_conditions = self.evolving_conditions.conditions[next_conditions_index]
	next_conditions_time = self.evolving_conditions.times[next_conditions_index]
	else:
	next_conditions = None
	# calculate air density from the ideal gas law
	BOLTZMANN_CONSTANT = 1.380649e-23
	AVOGADRO_CONSTANT = 6.02214076e23
	GAS_CONSTANT = BOLTZMANN_CONSTANT * AVOGADRO_CONSTANT
	air_density = curr_conditions.pressure / \
	(GAS_CONSTANT * curr_conditions.temperature)
	# outputs to output_array if enough time has elapsed
	if (next_output_time <= curr_time):
	row = []
	row.append(next_output_time)
	row.append(curr_conditions.temperature)
	row.append(curr_conditions.pressure)
	row.append(air_density)
	for conc in ordered_concentrations:
	row.append(conc)
	output_array.append(row)
	next_output_time += self.box_model_options.output_step_time
	# ensure the time step is not greater than the next update to the
	# evolving conditions or the next output time
	time_step = self.box_model_options.chem_step_time
	if (next_conditions is not None and next_conditions_time > curr_time):
	time_step = min(time_step, next_conditions_time - curr_time)
	if (next_output_time > curr_time):
	time_step = min(time_step, next_output_time - curr_time)
	# solves and updates concentration values in concentration array
	if (not ordered_concentrations):
	logger.info("Warning: ordered_concentrations list is empty.")
	musica.micm_solve(
	self.solver,
	time_step,
	curr_conditions.temperature,
	curr_conditions.pressure,
	air_density,
	ordered_concentrations,
	ordered_rate_constants)
	# increments time
	curr_time += time_step
	df = pd.DataFrame(output_array[1:], columns=output_array[0])

Acceptance criteria

• No rows of output are missed
• No extra time steps are taken

Ideas

• This contains an emission reaction for 1 species. It should run for 100 seconds, but we only output up to 99 seconds
  • config.zip