from netpyne import sim
from netpyne import specs
specs.SimConfig()
file_name = 'SimpleNet.net.nml'
simConfig = specs.SimConfig() # dictionary to store simConfig
# Simulation parameters
simConfig.duration = 1000 # Duration of the simulation, in ms
simConfig.dt = 0.025 # Internal integration timestep to use
simConfig.verbose = True
simConfig.recordCells = ['all'] # which cells to record from
simConfig.recordTraces = {'Vsoma':{'sec':'soma','loc':0.5,'var':'v'}}
simConfig.filename = 'SimpleNet' # Set file output name
simConfig.saveDat = True # save traces
simConfig.plotRaster = True # Whether or not to plot a raster
simConfig.plotCells = ['all'] # plot recorded traces for this list of cells
sim.importNeuroML2SimulateAnalyze(file_name,simConfig)
simConfig.plotWeightChanges = False # whether to plot weight changes (shown in conn matrix)
#simConfig.plot3dArch = True # plot 3d architecture
# Saving
simConfig.filename = 'TestL23.txt' # Set file output name
simConfig.saveFileStep = simConfig.dt # step size in ms to save data to disk
# simConfig.saveDat = True # save to dat file
###############################################################################
# IMPORT & RUN
###############################################################################
print("Running a NetPyNE based simulation for %sms (dt: %sms) at %s degC" %
(simConfig.duration, simConfig.dt, h.celsius))
gids = sim.importNeuroML2SimulateAnalyze(nml2_file_name, simConfig)
print("Finished simulation")
###############################################################################
# Saving data (this ensures the data gets saved in the format/files
# as specified in the LEMS <Simulation> element)
###############################################################################
if sim.rank == 0:
print(
"Saving to file: Sim_TestL23.CG3D_L23PyrRS.v.dat (ref: Volts_file__CG3D_L23PyrRS)"
)
# Column: t
col_Volts_file__CG3D_L23PyrRS_t = [
simConfig.plotWeightChanges = False # whether to plot weight changes (shown in conn matrix)
#simConfig.plot3dArch = True # plot 3d architecture
# Saving
simConfig.filename = 'TestL23.txt' # Set file output name
simConfig.saveFileStep = simConfig.dt # step size in ms to save data to disk
# simConfig.saveDat = True # save to dat file
###############################################################################
# IMPORT & RUN
###############################################################################
print("Running a NetPyNE based simulation for %sms (dt: %sms) at %s degC"%(simConfig.duration, simConfig.dt, h.celsius))
gids = sim.importNeuroML2SimulateAnalyze(nml2_file_name,simConfig)
print("Finished simulation")
###############################################################################
# Saving data (this ensures the data gets saved in the format/files
# as specified in the LEMS <Simulation> element)
###############################################################################
if sim.rank==0:
print("Saving to file: Sim_TestL23.CG3D_L23PyrRS.v.dat (ref: Volts_file__CG3D_L23PyrRS)")
# Column: t