This question is related to "vm.igb.gz not generated in tutorials/02_EP_tissue/01_basic_usage"
Please refer to that question since it is the same background and error at the same "job.carp(cmd)" line. Here's the specific error message for this code:
*** Unrecognized keyword -stimulus[0].p0[0]
*** Error reading parameters
Error: 2024-11-07_stim_extra_I_mono_petsc_np1/phie.igb does not exist!
And here's the entire output:
/home/bndr32/PycharmProjects/Example01_openCARP/tutorials/02_EP_tissue/02_stimulation/./run.py:3: SyntaxWarning: invalid escape sequence '\p'
"""
=======================================
SETTINGS SUMMARY
=======================================
Executables
---------------------------------------------------------------------------------------------
CARP: /usr/local/bin/openCARP
MESHER: /usr/local/bin/mesher
BENCH: /usr/local/bin/bench
IGBHEAD: /usr/local/bin/igbhead
IGBOPS: /usr/local/bin/igbops
IGBEXTRACT: /usr/local/bin/igbextract
IGBAPD: /usr/local/bin/igbapd
IGBDFT: /usr/local/bin/igbdft
MESHALYZER: /home/bndr32/.local/share/applications/squashfs-root/meshalyzer
SV2H5B: /home/bndr32/PycharmProjects/Example01_openCARP/.venv/lib/python3.12/site-packages/bin/bin2h5.py
SV2H5T: /home/bndr32/PycharmProjects/Example01_openCARP/.venv/lib/python3.12/site-packages/bin/txt2h5.py
CLOSEST_HC: /home/bndr32/PycharmProjects/Example01_openCARP/.venv/lib/python3.12/site-packages/bin/closest_hc
APDRESTITUTION: /home/bndr32/PycharmProjects/Example01_openCARP/.venv/lib/python3.12/site-packages/bin/APDrestitution
TUNECV: /home/bndr32/PycharmProjects/Example01_openCARP/.venv/lib/python3.12/site-packages/bin/tuneCV
RESTITUTECV: /home/bndr32/PycharmProjects/Example01_openCARP/.venv/lib/python3.12/site-packages/bin/restituteCV
GENERATEMETADATA: /home/bndr32/PycharmProjects/Example01_openCARP/.venv/lib/python3.12/site-packages/bin/generateMetadata
MESHTOOL: /usr/local/bin/meshtool
LIMPETFE: /usr/local/bin/limpet_fe.py
MAKEDYNAMICMODEL: /usr/local/bin/make_dynamic_model.sh
----------------------------------------------------------------------------------------
Command Line Options
----------------------------------------------------------------------------------------
NP: 1
BUILD: CPU
FLAVOR: petsc
DRY: False
VISUALIZE: True
-------------------------------------------------------------------------------------
Solver Option Files
-------------------------------------------------------------------------------------
Parabolic: /home/bndr32/PycharmProjects/Example01_openCARP/.venv/lib/python3.12/site-packages/carputils/resources/petsc_options/ilu_cg_opts
Elliptic: /home/bndr32/PycharmProjects/Example01_openCARP/.venv/lib/python3.12/site-packages/carputils/resources/petsc_options/gamg_cg_opts
-----------------------------------------------------------------------------------
Paths
-----------------------------------------------------------------------------------
OPENCARP_SRC: /usr/local/lib
MPIEXEC: /usr/local/lib/opencarp/lib/petsc/bin/mpiexec
----------------------------------------------------------------------------------
System Info
-----------------------------------------------------------------------------------
Python: 3.12.3
OS: Ubuntu 24.04.1 LTS
SETTINGS: /home/bndr32/.config/carputils/settings.yaml
ORCID: 0000-0000-0000-0000
=======================================
Requested mesh already exists, skipping generation.
----------------------------------------------
stimulus[0]
p0[0]: -5050.0 p1[0]: -4950.0
p0[1]: -100.0 p1[1]: 100.0
p0[2]: -100.0 p1[2]: 100.0
----------------------------------------------
----------------------------------------------
stimulus[1]
p0[0]: 4950.0 p1[0]: 5050.0
p0[1]: -100.0 p1[1]: 100.0
p0[2]: -100.0 p1[2]: 100.0
----------------------------------------------
mkdir -p /home/bndr32/PycharmProjects/Example01_openCARP/tutorials/02_EP_tissue/02_stimulation/2024-11-07_stim_extra_I_mono_petsc_np1
#------------------------------------------------------------------------------------------------------------------
#Launching openCARP Simulation 2024-11-07_stim_extra_I_mono_petsc_np1
#-----------------------------------------------------------------------------------------------------------------
/usr/local/bin/openCARP \
+F /home/bndr32/PycharmProjects/Example01_openCARP/tutorials/02_EP_tissue/02_stimulation/./stimtest.par \
-ellip_use_pt 0 \
-parab_use_pt 0 \
-parab_options_file /home/bndr32/PycharmProjects/Example01_openCARP/.venv/lib/python3.12/site-packages/carputils/resources/petsc_options/ilu_cg_opts \
-ellip_options_file /home/bndr32/PycharmProjects/Example01_openCARP/.venv/lib/python3.12/site-packages/carputils/resources/petsc_options/gamg_cg_opts \
-meshname meshes/2024-10-31_qOPJeEyYAO/block \
-simID 2024-11-07_stim_extra_I_mono_petsc_np1 \
-num_phys_regions 2 \
-phys_region[0].name "Intracellular domain" \
-phys_region[0].ptype 0 \
-phys_region[0].num_IDs 1 \
-phys_region[0].ID[0] 1 \
-phys_region[1].name "Extracellular domain" \
-phys_region[1].ptype 1 \
-phys_region[1].num_IDs 1 \
-phys_region[1].ID[0] 1 \
-stimulus[0].p0[0] -5050.0 \
-stimulus[0].p1[0] -4950.0 \
-stimulus[0].p0[1] -100.0 \
-stimulus[0].p1[1] 100.0 \
-stimulus[0].p0[2] -100.0 \
-stimulus[0].p1[2] 100.0 \
-stimulus[0].stimtype 1 \
-stimulus[0].strength 3.1e6 \
-stimulus[1].p0[0] 4950.0 \
-stimulus[1].p1[0] 5050.0 \
-stimulus[1].p0[1] -100.0 \
-stimulus[1].p1[1] 100.0 \
-stimulus[1].p0[2] -100.0 \
-stimulus[1].p1[2] 100.0 \
-stimulus[1].stimtype 1 \
-stimulus[1].balance 0 \
-stimulus[2].stimtype 3 \
-gridout_i 3 \
-gridout_e 3
*** Unrecognized keyword -stimulus[0].p0[0]
*** Error reading parameters
Error: 2024-11-07_stim_extra_I_mono_petsc_np1/phie.igb does not exist!
#------------------------------------------------------------------------------------------
# Launching Meshalyzer
#------------------------------------------------------------------------------------------
/home/bndr32/.local/share/applications/squashfs-root/meshalyzer \
2024-11-07_stim_extra_I_mono_petsc_np1/block_i \
2024-11-07_stim_extra_I_mono_petsc_np1/phie.igb \
/home/bndr32/PycharmProjects/Example01_openCARP/tutorials/02_EP_tissue/02_stimulation/./stimulation.mshz
/home/bndr32/.local/share/applications/squashfs-root/meshalyzer failed with error code -11
Thanks!
