initialisation of tissue using external model

Question

1) hello i was trying to load an external ionic model to the tissue using this in my python script:

    cmd += [ '-num_external_imp', 1,
    
            '-external_imp[0]', IM_MODULE,
            
           '-imp_region[0].im', args.model]

where IM_MODULE= /tutorials/02_EP_tissue/ACFtiss/my_MBRDR.so and

args.model =my_MBRDR

i got this error: 5 : Illegal IM specified: my_MBRDR, so how can i fix it ?

the second warning is:Warning: Legacy stimuli defined. Please consider switching to stimulus definition "stim[]"! is that mean i  should change my -stimulus[0].stimtype  to 3 or 5 to switch the electrode?

2) I would also like to see the vm(t) as a response of my tissue  to the stimuli, but my output file is not vm.dat but vm.igb that i can not open, so i can give an orientation please of how i can do it in opencarp ?

the error message after running:

/usr/local/bin/openCARP \
  -ellip_use_pt 0 \
  -parab_use_pt 0 \
  -parab_options_file /usr/local/lib/python3.6/dist-packages/carputils/resources/petsc_options/ilu_cg_opts \
  -ellip_options_file /usr/local/lib/python3.6/dist-packages/carputils/resources/petsc_options/amg_cg_opts \
  -num_phys_regions 1 \
  -phys_region[0].name "Intracellular domain" \
  -phys_region[0].ptype 0 \
  -phys_region[0].num_IDs 1 \
  -phys_region[0].ID[0] 1 \
  -simID 2021-09-24_simple_1000_petsc_np1 \
  -meshname meshes/2021-09-23_DUynSYKPxA/block \
  -tend 1000 \
  -num_external_imp 1 \
  -external_imp[0] ./my_MBRDR.so \
  -imp_region[0].im my_MBRDR \
  -bidomain 0 \
  -spacedt 1 \
  -timedt 1 \
  -parab_solve 1 \
  -num_gregions 1 \
  -gregion[0].num_IDs 1 \
  -gregion[0].ID 1 \
  -gregion[0].g_el 0.5329 \
  -gregion[0].g_et 0.236 \
  -gregion[0].g_il 0.1483 \
  -gregion[0].g_it 0.019 \
  -gregion[0].g_mult 0.5 \
  -num_LATs 2 \
  -lats[0].ID activation \
  -lats[0].all 0 \
  -lats[0].measurand 0 \
  -lats[0].mode 0 \
  -lats[0].threshold -10 \
  -lats[1].ID REPs \
  -lats[1].all 0 \
  -lats[1].measurand 0 \
  -lats[1].mode 1 \
  -lats[1].threshold -70 \
  -num_stim 1 stimulus[0].name S1 \
  -stimulus[0].stimtype 0 \
  -stimulus[0].strength 500.0 \
  -stimulus[0].duration 1.0 \
  -stimulus[0].npls 1 \
  -stimulus[0].bcl 750 \
  -stimulus[0].start 250 \
  -stimulus[0].x0 500.0 \
  -stimulus[0].xd 100 \
  -stimulus[0].y0 0 \
  -stimulus[0].yd 100

L2 : Output directory exists: 2021-09-24_simple_1000_petsc_np1

L5 : external_imp[0] error: absolute paths must be used for .so file loading ('./my_MBRDR.so')
Traceback (most recent call last):
  File "./run.py", line 411, in <module>
    run()
  File "/usr/local/lib/python3.6/dist-packages/carputils/tools.py", line 524, in wrapped
    ret = run(args, job)
  File "./run.py", line 350, in run

Comments

so how can i fix this error:  L5 : Illegal IM specified: my_MBRDR, i think i respected this -num_external_imp 1 \
  -external_imp[0] /tutorials/02_EP_tissue/ACFtiss/my_MBRDR.so \
  -imp_region[0].im my_MBRDR \

and should work but this the L5 type error i got, i am using opencarp installing using a docker


and  L1 : Warning: Legacy stimuli defined. Please consider switching to stimulus definition "stim[]"! means hat i should change my -stimulus[0].stimtype  to 3 or 5?

Answer 1

Hi,

Your definition of the imp_region is not complete. Here is a code snippet that might help you.

imp = ['-num_external_imp',      1,

      '-external_imp',        '/AbsolutePath/To/DynamicModel/my_MBRDR.so'),

      '-num_imp_regions',      1,

      '-imp_region[0].im',      'my_MBRDR',

      '-imp_region[0].num_IDs',   1]

Best,

Jorge

Comments

Thanks jorge i wrote exactly this but i still have warning abd the simulation is not running.

I got this message :    L5 : Illegal IM specified: my_MBRDR

and I wrote exactly this

  C=['-num_external_imp',      1,

      '-external_imp',        '/tutorials/02_EP_tissue/essai/my_MBRDR.so ',

      '-num_imp_regions',      1,

      '-imp_region[0].im',      'my_MBRDR',

      '-imp_region[0].num_IDs',   1]

---

Hi,

It looks like the path to the model is still not correct. Please try with the absolute path to the dynamic model.
Best,
Jorge

---

again i was running an GPV model that i modified i try to use this  in the tissue i have got this error L5 : Illegal IM specified: GPVm
Can you plklease help to fix this !

num_external_imp = 1
external_imp=  "/usr/local/lib/opencarp/share/tutorials/essai/figshare/GPVm.so"
num_imp_regions = 1
imp_region[0].name = "LA"
imp_region[0].im = GPVm
imp_region[0].im_param = "AF=1,RA=0"
imp_region[0].im_sv_init = "bcl750.sv"
imp_region[0].num_IDs = 1
imp_region[0].ID[0] = 0