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by (250 points)

Hello,

For multiple biatria regions I run single_cell_initialization with different region specific variations of Courtemanche model and I saved them to init_values_XX.sv

Later when I run biatria simulations I am trying to load these .sv files to initialize imp_regions. My parameters.par has these settings:

num_imp_regions                         = 10
imp_region[0].im_sv_init                = /Experiments/single_cell_pacing/init_values_RAA.sv
imp_region[1].im_sv_init                = 
/Experiments/single_cell_pacing/init_values_RA.sv
imp_region[2].im_sv_init                = 
/Experiments/single_cell_pacing/init_values_SAN.sv
imp_region[3].im_sv_init                = 
/Experiments/single_cell_pacing/init_values_CT.sv
imp_region[4].im_sv_init                = 
/Experiments/single_cell_pacing/init_values_PM.sv
imp_region[5].im_sv_init                =
/Experiments/single_cell_pacing/init_values_BB.sv
imp_region[6].im_sv_init                = 
/Experiments/single_cell_pacing/init_values_LA.sv
imp_region[7].im_sv_init                = 
/Experiments/single_cell_pacing/init_values_LAA.sv
imp_region[8].im_sv_init                =
/Experiments/single_cell_pacing/init_values_CS.sv
imp_region[9].im_sv_init                = 
/Experiments/single_cell_pacing/init_values_Septum.sv

As you see, I don't initialize other imp_region settings like im = Courtemanche or im_param etc, so there is only this what you see above. When I run the simulation I am getting these logs:

*** Initializing physics ***
Initializing Electrics ..
Setting up ionic models and plugins
-----------------------------------
Assigning IMPS to tagged regions:
    Ionic model: LuoRudy91 to tag region(s) [0] (implicitely)
    Ionic model: LuoRudy91 to tag region(s) [0] (implicitely)
    Ionic model: LuoRudy91 to tag region(s) [0] (implicitely)
    Ionic model: LuoRudy91 to tag region(s) [0] (implicitely)
    Ionic model: LuoRudy91 to tag region(s) [0] (implicitely)
    Ionic model: LuoRudy91 to tag region(s) [0] (implicitely)
    Ionic model: LuoRudy91 to tag region(s) [0] (implicitely)
    Ionic model: LuoRudy91 to tag region(s) [0] (implicitely)
    Ionic model: LuoRudy91 to tag region(s) [0] (implicitely)
    Ionic model: LuoRudy91 to tag region(s) [0] (implicitely)

read_sv(): Initialization using file: /home/jg23/Experiments/LAvRA/KCL_torso1_l/af/single_cell_pacing_af_bcl_200_2024-08-08_18-47-33/init_values_RAA.sv
L5 : IMPs do not match region (Courtemanche vs LuoRudy91)
read_sv(): Initialization using file: 
/Experiments/single_cell_pacing/init_values_RA.sv
read_sv(): Initialization using file: 
/Experiments/single_cell_pacing/init_values_SAN.sv
read_sv(): Initialization using file: 
/Experiments/single_cell_pacing/init_values_CT.sv
read_sv(): Initialization using file: 
/Experiments/single_cell_pacing/init_values_PM.sv
read_sv(): Initialization using file: 
/Experiments/single_cell_pacing/init_values_BB.sv
read_sv(): Initialization using file: 
/Experiments/single_cell_pacing/init_values_LA.sv
read_sv(): Initialization using file: 
/Experiments/single_cell_pacing/init_values_LAA.sv
read_sv(): Initialization using file: 
/Experiments/single_cell_pacing/init_values_CS.sv
read_sv(): Initialization using file: 
/Experiments/single_cell_pacing
/init_values_Septum.sv

My question is... if my init_values.sv files have Courtemanche models saved in them, would they replace initialized by default LuoRudy91? Or do I need to initialize other imp_region settings like im, im_param etc despite loading .sv files?

Thanks Jakub

1 Answer

0 votes
by (19.1k points)
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Best answer
The statefile does not get loaded when the IMP does not match. We made the output message more elaborate in the latest commit. You should always set the model to the right one for each imp_region

Another caveat I see is that your initialization only considers the current values of the state variables but does not transfer any potential changes to model parameters (e.g. different GKr in different regions).
by (250 points)
Perfect, thank you Axel. Yes, I was just playing around with some settings and experimenting, so I did not modify the models.
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