def addRxD (self, nthreads=None):
"""
Function for/to <short description of `netpyne.network.netrxd.addRxD`>
Parameters
----------
self : <type>
<Short description of self>
**Default:** *required*
"""
from .. import sim
if len(self.params.rxdParams):
try:
global rxd
from neuron import crxd as rxd
sim.net.rxd = {'species': {}, 'regions': {}} # dictionary for rxd
if nthreads:
rxd.nthread(nthreads)
print('Using %d threads for RxD' % (nthreads))
except:
print('cRxD module not available')
return -1
else:
return -1
# Instantiate network connections based on the connectivity rules defined in params
sim.timing('start', 'rxdTime')
if sim.rank==0:
print('Adding RxD...')
# make copy of Python structure
#if sim.cfg.createPyStruct: -- don't make conditional since need to have Python structure
sim.net.rxd = copy.deepcopy(sim.net.params.rxdParams)
# add NEURON objects
if sim.cfg.createNEURONObj:
rxdParams = sim.net.params.rxdParams
if 'regions' in rxdParams:
self._addRegions(rxdParams['regions'])
if 'extracellular' in rxdParams:
#self._addExtracellular(rxdParams['extracellular'])
self._addExtracellularRegion('extracellular', rxdParams['extracellular'])
if 'species' in rxdParams:
self._addSpecies(rxdParams['species'])
if 'states' in rxdParams:
self._addStates(rxdParams['states'])
if 'reactions' in rxdParams:
self._addReactions(rxdParams['reactions'])
if 'parameters' in rxdParams:
self._addParameters(rxdParams['parameters'])
if 'multicompartmentReactions' in rxdParams:
self._addReactions(rxdParams['multicompartmentReactions'], multicompartment=True)
if 'rates' in rxdParams:
self._addRates(rxdParams['rates'])
sim.pc.barrier()
sim.timing('stop', 'rxdTime')
if sim.rank == 0 and sim.cfg.timing: print((' Done; RxD setup time = %0.2f s.' % sim.timingData['rxdTime']))
return sim.net.rxd
from neuron import gui
'''
Oriens-lacunosum moleculare (OLM) cells are a major subclass of hippocampal interneurons
involved in controlling synaptic plasticity in Shaffer collateral synapses
and electrogenesis in pyramidal cell (PC) dendrites.
see more in here: https://www.frontiersin.org/articles/10.3389/fncel.2015.00201/full
for run : mpiexec -n 1 nrniv -mpi -python OLM_cell.py
'''
pc = h.ParallelContext()
pcid = pc.id()
nhost = pc.nhost()
rxd.nthread()
rxd.options.enable.extracellular = True
h.load_file('stdrun.hoc')
h.celsius = 37
numpy.random.seed(6324555+pcid)
outdir = os.path.abspath('tests/305')
k_na_dir = os.path.abspath(os.path.join(outdir, 'K_NA'))
nmh_dir = os.path.abspath(os.path.join(outdir, 'n_m_h'))
if not os.path.exists(k_na_dir):
diff_constant = 1
h.cvode_active(True)
r = rxd.Region(h.allsec(), dx=0.25)
rxd.set_solve_type([dend1], dimension=3)
ca = rxd.Species(
r,
d=diff_constant,
atolscale=0.1,
initial=lambda node: 1 if (0.8 < node.x and node.segment in dend1) or
(node.x < 0.2 and node.segment in dend2) else 0,
)
bistable_reaction = rxd.Rate(ca, -ca * (1 - ca) * (0.01 - ca))
h.finitialize()
for i in range(2):
h.fadvance()
rxd.nthread(2)
for i in range(2, 4):
h.fadvance()
rxd.nthread(3)
for i in range(4, 6):
h.fadvance()
rxd.nthread(4)
for i in range(6, 8):
h.fadvance()
rxd.nthread(1)
for i in range(8, 11):
h.fadvance()
type=str,
help='a directory to save the figures and data')
args = parser.parse_args()
except:
os._exit(1)
outdir = os.path.abspath(args.dir)
if pcid == 0 and not os.path.exists(outdir):
try:
os.makedirs(outdir)
except:
print("Unable to create the directory %r for the data and figures" %
outdir)
os._exit(1)
rxd.nthread(4) # set the number of rxd threads
rxd.options.enable.extracellular = True # enable extracellular rxd
h.load_file('stdrun.hoc')
h.celsius = 37
numpy.random.seed(6324555 + pcid) # use a difference seed for each process
# simulation parameters
Lx, Ly, Lz = 1000, 1000, 1000 # size of the extracellular space mu m^3
Kceil = 15.0 # threshold used to determine wave speed
Ncell = int(9e4 * (Lx * Ly * Lz * 1e-9)) # number of neurons (90'000 per mm^3)
Nrec = 1000
somaR = 11.0 # soma radius
dendR = 1.4 # dendrite radius