Where can i find other variables of my tissue simulation

Question

Hello i  made a tissue simulation  and i would like to see changes in time  of   all my outputs variables, but the probleme is after running the simulation in my output folder i can only find information  about vm  ( vm.igb), i did not find the  information about others variables as ca_i (ca_i.igb), gate variables and so on, please can some one help me with some orientation!

Another thing is I would like to trace a calcium restitution curve, i was wondering if it is possible to use igb.apd with Ca_i.igb to detect changes in calcium duration at different bcl to trace the curve, please i need your help

Answer 1

Hi,

You can use gvecs to obtain a file with the variable information that you need. For more information please look at openCARP parameters

Best,

Jorge

Comments

Thanks a  lot Jorge, but i still have trouble i can not understand what should i change i wrote this


    I= [ 'num_gvecs ', 1 ,
        '-gvec[0].bogus', 0.,
       '-gvec[0].imp',  'GPVatria',
       '-gvec[0].units', 'uA/cm^2',
       'gvec[0].name', 'INa_m'
       'gvec[0].ID[0]',  'm']

and i got this error: *** Index #1 (0) in -gvec[0].bogus is out of bounds [0--1]

---

Hi,
It looks like your syntax is not correct. You are missing the hyphen before the parameter; for example, in 'num_gvecs', it has to be '-num_gvecs'.
Best,
Jorge

---

/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] 0 \
  -simID 2021-10-14_simple_10_petsc_np1 \
  -meshname meshes/2021-09-23_DUynSYKPxA/block \
  -num_imp_regions 1 \
  -imp_region[0].im GPVatria \
  -imp_region[0].num_IDs 1 imp_region[0].ID[0] 0 bidomain 0 spacedt 1 timedt 1 parab_solve 1  mass_lumping 0 \
  -num_gregions 1 \
  -gregion[0].name m \
  -gregion[0].num_IDs 1 \
  -gregion[0].ID 0 \
  -gregion[0].g_el 0.5533 \
  -gregion[0].g_et 0.236 \
  -gregion[0].g_en 0.236 \
  -gregion[0].g_il 0.154 \
  -gregion[0].g_it 0.019 \
  -gregion[0].g_in 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 \
  -simID 2021-10-14_simple_10_petsc_np1/2batements \
  -num_stim 1 stimulus[0].name S1 \
  -stimulus[0].stimtype 0 \
  -stimulus[0].strength 500.0 \
  -stimulus[0].duration 1.0 \
  -stimulus[0].npls 10 \
  -stimulus[0].bcl 500 \
  -stimulus[0].start 0 \
  -stimulus[0].x0 500.0 \
  -stimulus[0].xd 100 \
  -stimulus[0].y0 -50 \
  -stimulus[0].yd 100 \
  -tend 5000.1 \
  -imp_region[0].im_sv_init GPVatria_bcl_750_beats_20_CI_300.sv \
  -num_gvecs  1 \
  -gvec[0].bogus 0.0 \
  -gvec[0].imp GPVatria \
  -gvec[0].units uA/cm^2 \
  -gvec[0].name INa-gvec[0].ID[0] m


*** Unrecognized keyword -num_gvecs


*** Error reading parameters



this is all the output, if i put num_gvec the simulator does not recognize it, and when i remouve it i got this error  *** Index #1 (0) in -gvec[0].ID[0] is out of bounds [0--1]


*** Error reading parameters

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Hi,

It looks like the file is not correctly define, please check this line in your code

-imp_region[0].num_IDs 1 imp_region[0].ID[0] 0 bidomain 0 spacedt 1 timedt 1 parab_solve 1  mass_lumping 0 \

Cheers,

Jorge