ajustador

ajustador.basic_simulation

Run a single simulation from the command-line

This module takes a set of parameters which override the defaults provides by the moose_nerp module and runs the simulation and saves the results. In particular, this is useful when running multiple simulation in parallel, where each one should be run out-of-process:

$ python3 -m ajustador.basic_simulation \
    --baseline=-0.07639880161359705 \
    --RA=9.273975490852102 \
    --RM=0.11241922550664576 \
    --CM=0.0298401595465488 \
    --Cond-Kir=6.441375022294002 \
    --Kir-offset=6.529897906031442e-07 \
    --morph-file=MScell-tertDendlongRE.p \
    --simtime=0.9 \
    -i=-5.0000000000000034e-11 \
    --save=ivdata--5.0000000000000034e-11.npy

This module is not automatically imported as a child of ajustador. An explicit import is needed: >>> import ajustador.basic_simulation

ajustador.basic_simulation.cond_setting(s)[source]

Splits ‘NaF,0=123.4’ → (‘NaF’, 0, 123.4)

usage: basic_simulation [-h] [--simtime SIMTIME] [--simdt SIMDT]
                        [--plotdt PLOTDT] [--hsolve [HSOLVE]]
                        [--injection-current CURRENT] [--injection-delay TIME]
                        [--injection-width TIME] [--stimtimes TIMEPOINTS]
                        [--syncomp SYNCOMP] [--plot-vm [PLOT_VM]]
                        [--plot-current [PLOT_CURRENT]]
                        [--plot-calcium [PLOT_CALCIUM]]
                        [--plot-current-message NAME]
                        [--plot-current-label LABEL] [--plot-synapse [BOOL]]
                        [--plot-synapse-message NAME]
                        [--plot-synapse-label LABEL] [--plot-channels [BOOL]]
                        [--plot-activation [BOOL]] [--plot-network [BOOL]]
                        [--plot-netvm [BOOL]] [--morph-file MORPH_FILE]
                        [--baseline BASELINE] --model MODEL --neuron-type
                        NEURON_TYPE [--RA RA] [--RM RM] [--CM CM]
                        [--Erest EREST] [--Eleak ELEAK]
                        [--Kir-offset KIR_OFFSET] [--cond COND [COND ...]]
                        [--save SAVE]
Options:
--simtime=0.9, -t=0.9
 Simulation time
--simdt=1e-05 Simulation step
--plotdt=0.0002
 Plot point distance
--hsolve=True Use the HSOLVE solver
--injection-current=[-1.5e-10, 1.5e-10, 3.5e-10], -i=[-1.5e-10, 1.5e-10, 3.5e-10]
 One or more injection currents (V)
--injection-delay=0.2
 Start current injection at this time
--injection-width=0.4
 Inject current for this much time
--stimtimes=[0.04, 0.19, 0.46]
 Undocumented
--syncomp=4 Synapse compartment number
--plot-vm Whether to plot membrane potential Vm
--plot-current Whether to plot the current
--plot-calcium Whether to plot calcium
--plot-current-message=getGk
 The moose message to use
--plot-current-label=Cond, S
 Current plot label
--plot-synapse Undocumented
--plot-synapse-message=getGk
 Undocumented
--plot-synapse-label=Cond, nS
 Undocumented
--plot-channels
 Undocumented
--plot-activation
 Undocumented
--plot-network Undocumented
--plot-netvm Undocumented
--morph-file Undocumented
--baseline Undocumented
--model Undocumented
--neuron-type Undocumented
--RA Undocumented
--RM Undocumented
--CM Undocumented
--Erest Undocumented
--Eleak Undocumented
--Kir-offset Undocumented
--cond=[] Undocumented
--save Undocumented
ref:ajustador.utilities

Indices and tables