30 Aug
2023
30 Aug
'23
8:51 a.m.
Dear Jochen,
Thanks a lot, a giant step forward!
I now get another error:
Variable 'g_ex' not defined!
Ode equation lhs-variable 'g_ex$' not defined in state block!
Ode equation lhs-variable 'g_in$' not defined in state block!
Ode equation lhs-variable 'g_NMDA$' not defined in state block!
...
AttributeError: 'NoneType' object has no attribute 'is_state'
While my state block contains:
state:
r integer = 0 # counts number of tick during the
refractory period
V_m mV = E_L # membrane potential
# inputs from the inhibitory conductance
g_in real = 0
g_in$ real = g_I_const * (1 / tau_rise_GABA_A - 1 /
tau_decay_GABA_A)
# inputs from the excitatory conductance
g_ex real = 0
g_ex$ real = g_E_const * (1 / tau_rise_AMPA - 1 / tau_decay_AMPA)
# inputs from the excitatory NMDA conductance
g_NMDA real = 0
g_NMDA$ real = g_NMDA_const * (1 / tau_rise_NMDA - 1 /
tau_decay_NMDA)
Any suggestions?
Thanks,
Hedyeh
On Wed, Aug 30, 2023 at 9:47 AM Jochen Martin Eppler <j.eppler(a)fz-juelich.de>
wrote:
Dear Hedyeh,
the end keyword has recently been removed from NESTML. You indicate
blocks now solely by indentation as in Python.
Cheers,
Jochen!
On 30.08.23 08:42, Hedyeh Rezaei wrote:
Dear all,
I have installed nestml via conda and developed a code describing an LIF
neuron with bi-exponential synaptic currents including NMDA, while the
charge mediated by AMPA and NMDA receptors are not independent. When I try
to compile the .nestml file, it gives me an error as:
from pynestml.frontend.pynestml_frontend import generate_nest_target
WARNING:root:PyGSL is not available. The stiffness test will be skipped.
WARNING:root:Error when importing: No module named 'pygsl'
In [2]:
generate_nest_target(input_path="/home/hrezaei/neuron_model_NMDA.nestml",
...: target_path="/tmp/nestml-component",
...: logging_level="ERROR")
line 61:4 extraneous input 'end' expecting {DEDENT, 'function',
'state',
'parameters', 'internals', 'update', 'equations',
'input', 'output'}
line 63:4 extraneous input 'equations' expecting {<EOF>, NEWLINE,
'neuron', 'synapse'}
line 64:8 extraneous input ' ' expecting {<EOF>, NEWLINE,
'neuron',
'synapse'}
line 67:8 extraneous input 'kernel' expecting {<EOF>, NEWLINE,
'neuron',
'synapse'}
line 70:8 extraneous input 'kernel' expecting {<EOF>, NEWLINE,
'neuron',
'synapse'}
...
r"""Generate and build code for NEST Simulator.
Parameters
A dictionary containing additional options for the target code generator.
"""
I was wondering what the reason could be. I would appreciate it if you
could help.
Thanks in advance.
Best,
Hedyeh
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--
Dr. Jochen Martin Eppler (he/him)
Simulation and Data Lab Neuroscience
Jülich Supercomputing Centre
Institute for Advanced Simulation
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