hello i am new on opencarp and i use it to make an experiment on a tissue with stimulation at different bcl, for the initialisation i use a stable state of a cell at 750ms, i was expecting that the APD of the tissue i mesured will decrise when i decrease bcl but my result gave me every time an increase of apd when i use de GPVatria cell model, but the result was ok for MDRBD model, please if some one can help me to find the issu ?
here is my script
Pace GPVatria to limit cycle at basic cycle length bcl=750
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Computing state files for chosen CIs
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Perform APD restitution experiments
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#-----------------------------------------------------------------------------------------------------------------------
# Launching openCARP Simulation 2021-12-16_simple_20_petsc_np1
#-----------------------------------------------------------------------------------------------------------------------
/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 2021-12-16_simple_20_petsc_np1 \
-meshname meshes/2021-12-08_MBxYYskUvP/block \
-num_imp_regions 1 \
-imp_region[0].im GPVatria \
-imp_region[0].num_IDs 1 \
-bidomain 0 \
-spacedt 1 \
-timedt 1 \
-parab_solve 1 \
-cg_tol_parab 0.01 \
-num_gregions 1 \
-gregion[0].name m \
-gregion[0].num_IDs 1 \
-gregion[0].ID 1 \
-gregion[0].g_el 0.5329 \
-gregion[0].g_et 0.1155 \
-gregion[0].g_en 0.1155 \
-gregion[0].g_il 0.1483 \
-gregion[0].g_it 0.0322 \
-gregion[0].g_in 0.0322 \
-num_LATs 2 \
-lats[0].ID activation \
-lats[0].all 0 \
-lats[0].measurand 0 \
-lats[0].mode 0 \
-lats[0].threshold -20 \
-lats[1].ID REPs \
-lats[1].all 0 \
-lats[1].measurand 0 \
-lats[1].mode 1 \
-lats[1].threshold -70 \
-imp_region[0].im_sv_init GPVatria_bcl_750_beats_20_limitcycle.sv \
-num_gvecs 1 \
-gvec[0].name cai \
-gvec[0].ID[0] Ca_i \
-num_stim 1 stimulus[0].name S1 \
-stimulus[0].stimtype 0 \
-stimulus[0].strength 60.0 \
-stimulus[0].duration 1.0 \
-stimulus[0].npls 20 \
-stimulus[0].bcl 350 \
-stimulus[0].start 0 \
-stimulus[0].x0 -4950 \
-stimulus[0].xd 100 \
-stimulus[0].y0 -150 \
-stimulus[0].yd 300 \
-tend 7000
for the APD calculation i use this in the script:
igbdir1 = simID + '/vm.igb'
igbdir2 = simID + '/cai.igb'
#igbout = '--output-file=' + simID + '/data.dat'
apdmode ='all'
apdt0 = 0
cmd2 = [ settings.execs.igbapd,
'-t', apdt0,
'--repol=90',
'--vup=-10',
'--peak-value=plateau',
'-M', apdmode,
'-m', 10.0,
# igbout,
igbdir1 ]
job.bash(cmd2)
# #Now compute tcd cdhe APD at register '{}_limitcycle.sv'.format(lcyc)
hh=list(xrange(numbeats-2,0,-1))
for o in range(len(hh)):
h=hh[o]
apdfile = './' + '{}_apd.dat'.format(h)
print(apdfile)
file = open(apdfile, 'r')
lines=file.readlines()
LAPD = float(lines[295])
file.close()
#Now compute the CV between electrodes
actfile = './' + simID + '/init_acts_REPs-thresh.dat'
#print(actfile)
file = open(actfile, 'r')
lines=file.readlines()
LCV1 = float(lines[295])
LCV2 = float(lines[285])
LCV = (1/(LCV2-LCV1))*1000.0
LWL = LAPD*LCV*0.001
file.close()
apdm.append(LAPD)
APDF.append(apdm)
print(APDF)
with open('apdrestitutionCI.dat', 'a') as fp:
fp.write('{:>6s} {:>10.4f}\n'.format('CI=', CI))
for j in range(len(apdm)):
val=round(apdm[j])
fp.write('{:>6.1f}\n'.format(val))
apdm=[]
print(APDF)
