Intoduction to cellular simulations example error

Question

This is the tutorial  video example from "Intoduction to cellular simulations", I got the error: 

  File "run.py", line 127, in run

    '--imp={}'.format(args.imp)]

AttributeError: 'Namespace' object has no attribute 'imp'

Here is part of that code, can any one help to answer? thanks!

def parser():

parser = tools.standard_parser()

group = parser.add_argument_group('experiment specific options')

group.add_argument('--ionic_model', default='TT2',

choices=['TT2', 'Courtemanche', 'HH'],

help='pick ionic model')

group.add_argument('--duration',

type=float, default=1000.,

help='Duration of simulation (ms)')

group.add_argument('--stim-strength',

type=float, default=60.,

help='pick transmembrane current stimulus strength')

group.add_argument('--stim-dur',

type=float, default=2.,

help='pick transmembrane current stimulus duration')

return parser

 

def jobID(args):

"""

Generate name of top level output directory.

"""

today = date.today()

return '{}_basic_{}'.format(today.isoformat(), args.duration)

 

@tools.carpexample(parser, jobID)

def run(args, job):

# define & config EP model

cmd = [settings.execs.BENCH,

'--imp={}'.format(args.imp)]

if args.imp_par is not '':

cmd += ['--imp-par', args.imp_par]

 

if args.plug_in is not '':

cmd += ['--plug-in', args.plug_in]

 

if args.plug_par is not '':

cmd += ['--plug-par', args.plug_par]

 

# setup stimulus

cmd += ['--stim-curr', args.stim_strength,

'--numstim', int(float(args.duration)/float(args.bcl)+1),

'--bcl', args.bcl,

'--stim-assign', 'on',

'--stim-species', 'K_i']

# run bench with available ionic models

cmd += ['--duration', args.duration]

 

# executing bench

job.mpi(cmd, 'Running {}'.format(args.imp))

 

if args.visualize:

visualization(args. job.ID)

 

if __name__ == '__main__':

run()

Answer 1

It's hard to see from your screenshot but my guess would be that you have a line break between

cmd = [settings.execs.BECH,

and

'--imp={}'.forma(args.imp)]

these should be in one line. In the video tutorial this is likely a line wrap rather than a line break.

If this is not the issue, please share a minimum example to reproduce.

Another thing to be aware of: the names of the ionic have changed since openCARP v9.0. You'll need to use the new names to make your example work: https://git.opencarp.org/openCARP/openCARP/-/blob/master/physics/limpet/models/README.md