Running Simulations

Program for simulating one line of the penta array. In this new version, only one set of parameters is specified (Nonetheless, for old version one has to use file main.old instead of main.cpp) In new version it is now possible to specify parameters by command line

input file should be as data_example file attached; output_dir and observation dir are setted equal inside the rpogram, but might be better to set also the same value into the data file in order to avoid missunderstandings

run the program with

./TestMitchellSchaeffer1D -f data_file

If you want to modify also some parameters, e.g. conductivity:

./TestMitchellSchaeffer1D -f data_file --conductivity <conductivity value>

up to now, parameters which can be passed are:

  --conductivity
  --tau_in
  --tau_out
  --tau_open
  --tau_close
  --APDmax
  -param_set

where are also abbreviated forms; look at main.cpp.

for readdressing the output (with also eventually the errors) in the file output_file:

./TestMitchellSchaeffer1D -f data_file >output_file$1 2>&1

If you want to use openmp (for example with 6 threads, i.e. 6 procs):

OMP_NUM_THREADS=6 ./TestMitchellSchaeffer1D -f data_file

for output, same syntax as before.

Stimulus type

In data file you can chose astandard stimulus or a balanced one. These options are specified in the data file. The default is the standard stimulus standard stimulus: is an applied currend between lead 1 and 2 non standard: without ground: an input current with intensity specified within the data file applied on 1 lead and the same current with the opposite sign on the 2 lead with ground: groundPotential is the extracellular potential used for stimulus applied at lead 1, whereas at lead 2 a 0 extracellular potential is applied. The modulus of the applied current in this case does not have sense