def setup(timestep=0.1, min_delay=0.1, max_delay=10.0, **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.
returns: MPI rank
"""
common.setup(timestep, min_delay, max_delay, **extra_params)
simulator.initializer.clear()
simulator.state.clear()
simulator.reset()
simulator.state.dt = timestep
simulator.state.min_delay = min_delay
simulator.state.max_delay = max_delay
if extra_params.has_key('use_cvode'):
simulator.state.cvode.active(int(extra_params['use_cvode']))
if extra_params.has_key('rtol'):
simulator.state.cvode.rtol(float(extra_params['rtol']))
if extra_params.has_key('atol'):
simulator.state.cvode.atol(float(extra_params['atol']))
if extra_params.has_key('default_maxstep'):
simulator.state.default_maxstep = float(
extra_params['default_maxstep'])
return rank()
def test_reset():
simulator.state.running = True
simulator.state.t = 17
simulator.state.tstop = 123
init = simulator.initializer
orig_initialize = init._initialize
init._initialize = Mock()
simulator.reset()
assert_equal(simulator.state.running, False)
assert_equal(simulator.state.t, 0.0)
assert_equal(simulator.state.tstop, 0.0)
init._initialize.assert_called()
init._initialize = orig_initialize
def setup(timestep=0.1, min_delay=0.1, max_delay=10.0, **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, max_delay, **extra_params)
simulator.initializer.clear()
simulator.state.clear()
simulator.reset()
simulator.state.dt = timestep
simulator.state.min_delay = min_delay
simulator.state.max_delay = max_delay
if extra_params.has_key('use_cvode'):
simulator.state.cvode.active(int(extra_params['use_cvode']))
if extra_params.has_key('rtol'):
simulator.state.cvode.rtol(float(extra_params['rtol']))
if extra_params.has_key('atol'):
simulator.state.cvode.atol(float(extra_params['atol']))
if extra_params.has_key('native_rng_baseseed'):
simulator.state.native_rng_baseseed = int(
extra_params['native_rng_baseseed'])
else:
simulator.state.native_rng_baseseed = 0
if extra_params.has_key('default_maxstep'):
simulator.state.default_maxstep = float(
extra_params['default_maxstep'])
return rank()
def setup(timestep=0.1, min_delay=0.1, max_delay=10.0, **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, max_delay, **extra_params)
simulator.initializer.clear()
simulator.state.clear()
simulator.reset()
simulator.state.dt = timestep
simulator.state.min_delay = min_delay
simulator.state.max_delay = max_delay
if extra_params.has_key('use_cvode'):
simulator.state.cvode.active(int(extra_params['use_cvode']))
if extra_params.has_key('rtol'):
simulator.state.cvode.rtol(float(extra_params['rtol']))
if extra_params.has_key('atol'):
simulator.state.cvode.atol(float(extra_params['atol']))
if extra_params.has_key('native_rng_baseseed'):
simulator.state.native_rng_baseseed=int(extra_params['native_rng_baseseed'])
else:
simulator.state.native_rng_baseseed=0
if extra_params.has_key('default_maxstep'):
simulator.state.default_maxstep=float(extra_params['default_maxstep'])
return rank()
def test_run():
simulator.reset()
simulator.run(12.3)
assert_almost_equal(h.t, 12.3, places=11)
simulator.run(7.7)
assert_almost_equal(h.t, 20.0, places=11)
