Computational Medicine Laboratory

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Jan 16

New CellML-based Cardiac EP Model

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Edited: Jan 16

New Cardiac EP model (2D/3D)

/scratch4/marcell/CellML2D3DSimulator/bin/CEPCellML

 

New Cardiac EP model (Single cell)

/scratch4/marcell/CellMLSimulator/bin/cell

 

Available ionmodel ID

tn2006endo

tn2006epi

tn2006epi18

crn1998

priebe1998

 

Example of .sh file

 

#PBS -N kimoo_2d_Test

#PBS -l nodes=1:ppn=12

#PBS -l walltime=20000:00:00

#PBS -e stderr.log

#PBS -o stdout.log

# Specific the shell types

#PBS -S /bin/bash

# Specific the queue type

#PBS -q dque

 

cd $PBS_O_WORKDIR

 

ulimit -s unlimited

 

NPROCS=`wc -l < $PBS_NODEFILE`

 

echo This job has allocated $NPROCS nodes

 

cd $PBS_O_WORKDIR

 

rm -rf *.vtk *.plt output.* logfile_square *.log

 

/opt/Lib/openmpi-2.1.3/bin/mpirun -v -machinefile $PBS_NODEFILE -np $NPROCS /scratch4/marcell/CellML2D3DSimulator/bin/CEPCellML \

-tmax 5000.0 \

-twrite 0.0 \

-ionmodel tn2006epi18\

-ic /scratch4/maincode/elecphy/cellc/init/tn2006/init_ori.dat \

-meshtype square \

-celltype 3 \

-dt 0.05 \

-irepeat 2 \

-ibclb 1000 \

-stimdur 5.0 \

-iopt 0 \

-Dscale 0.6 \

-femesh_dir /scratch4/maincode/file_transform/make2Dmesh \

-heart 15_15_0.05_0.05.inp \

-pace1 15_15_0.05_0.05_left.dat \

-pace2 15_15_0.05_0.05_bottom_half.dat \

-vtkout_states V,Ca_i \

-vtkout_algebraic i_NaK \

-dtw 10.0 -on_error_abort >& logfile_square

 

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