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@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


_______________________________________________
NEST Users mailing list -- users@nest-simulator.org
To unsubscribe send an email to users-leave@nest-simulator.org


-- 
Dr. Jochen Martin Eppler (he/him)
Simulation and Data Lab Neuroscience
Jülich Supercomputing Centre
Institute for Advanced Simulation
---------------------------------------------------------------------
Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens,
Prof. Dr. Astrid Lambrecht, Prof. Dr. Frauke Melchior
---------------------------------------------------------------------
_______________________________________________
NEST Users mailing list -- users@nest-simulator.org
To unsubscribe send an email to users-leave@nest-simulator.org