Source code for pyNN.neuron.control

NEURON implementation of functions for simulation set-up and control

:copyright: Copyright 2006-2024 by the PyNN team, see AUTHORS.
:license: CeCILL, see LICENSE for details.

import logging
from .. import common
from ..recording import get_io
from . import simulator

logger = logging.getLogger("PyNN")

# ==============================================================================
#   Functions for simulation set-up and control
# ==============================================================================

[docs] def setup(timestep=DEFAULT_TIMESTEP, min_delay=DEFAULT_MIN_DELAY, **extra_params): """ Should be called at the very beginning of a script. `extra_params` contains any keyword arguments that are required by a given simulator but not by others. NEURON specific extra_params: use_cvode - use the NEURON cvode solver. Defaults to False. Optional cvode Parameters: -> rtol - specify relative error tolerance -> atol - specify absolute error tolerance native_rng_baseseed - added to MPI.rank to form seed for SpikeSourcePoisson, etc. default_maxstep - TODO returns: MPI rank """ common.setup(timestep, min_delay, **extra_params) simulator.initializer.clear() simulator.state.clear() simulator.state.dt = timestep simulator.state.min_delay = min_delay simulator.state.max_delay = extra_params.get('max_delay', DEFAULT_MAX_DELAY) if 'use_cvode' in extra_params: simulator.state.record_sample_times = extra_params['use_cvode']['use_cvode'])) if 'rtol' in extra_params: simulator.state.cvode.rtol(float(extra_params['rtol'])) if 'atol' in extra_params: simulator.state.cvode.atol(float(extra_params['atol'])) if 'native_rng_baseseed' in extra_params: simulator.state.native_rng_baseseed = int(extra_params['native_rng_baseseed']) if 'default_maxstep' in extra_params: simulator.state.default_maxstep = float(extra_params['default_maxstep']) return rank()
[docs] def end(compatible_output=True): """Do any necessary cleaning up before exiting.""" for (population, variables, filename) in simulator.state.write_on_end: io = get_io(filename) population.write_data(io, variables) simulator.state.write_on_end = []
# simulator.state.finalize() run, run_until = common.build_run(simulator) run_for = run reset = common.build_reset(simulator) initialize = common.initialize # ============================================================================== # Functions returning information about the simulation state # ============================================================================== get_current_time, get_time_step, get_min_delay, get_max_delay, \ num_processes, rank = common.build_state_queries(simulator)