# Simulation of diffusion in which half of the system is implicitly crowded and half is uncrowded.
# This file focuses on time dependence. It uses a slower slow diffusion constant than the other files.
# Units are nanometers and microseconds
# Model HalfSlowTimeDep.txt by Steve Andrews, September 2023.
# Written for "Modeling diffusion between regions with different diffusion coefficients" for submission to IEEE Transactions on Molecular, Biological, and Multi-scale Communications

define Rp 2

#random_seed 1

graphics opengl_good
graphic_iter 50

dim 2

boundaries x -100 100
boundaries y 0 100

time_start 0
time_stop 1100
time_step 0.01

species probes probef

difc probef 10
difc probes 3

display_size probe* Rp
color probef red
color probes red

start_surface walls
color both black
polygon both edge
action both all reflect
panel rect +x -100 0  100
panel rect -x 100 0  100
panel rect +y -100 0  200
panel rect -y -100 100  200
end_surface

start_surface membrane
color both 0 0.5 0.5
action probef back reflect
action probes front reflect
rate probef soln bsoln -1 probes
rate probes bsoln soln -1 probef
panel rect +x 0 0  100
end_surface

mol 10000 probef 99.99 u

output_files HalfSlowTimeDepout.txt
output_format csv
cmd @ 100 molcountspace all x  -100 100  20  0 100  0 HalfSlowTimeDepout.txt
cmd @ 200 molcountspace all x  -100 100  20  0 100  0 HalfSlowTimeDepout.txt
cmd @ 500 molcountspace all x  -100 100  20  0 100  0 HalfSlowTimeDepout.txt
cmd @ 1000 molcountspace all x  -100 100  20  0 100  0 HalfSlowTimeDepout.txt

#cmd B pause

end_file