# Simulation of diffusion in which half of the system is crowded and half is uncrowded.
# This file addresses the left (crowded) side only.
# Units are nanometers and microseconds
# Model HalfCrowdLeft.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 Rb 5
define Rp 2
define PHI 0.5
define VOLHALF 100*100

#random_seed 1

graphics opengl_good

dim 2

boundaries x -100 0 p
boundaries y 0 100 p

time_start 0
time_stop 1100
time_step 0.01

species ball probe

difc ball 1
difc probe 10

display_size ball Rb
display_size probe Rp
color ball gray
color probe red


reaction rxnbb ball + ball -> ball + ball
reaction rxnbp ball + probe -> ball + probe
binding_radius rxnbb Rb+Rb
binding_radius rxnbp Rb
product_placement rxnbb bounce -1
product_placement rxnbp bounce -1

mol PHI*VOLHALF/(3.14*Rb^2) ball -100-0 u
mol 200 probe u u

output_files HalfCrowdLeftout.txt stdout
cmd i 10 1100 1 meansqrdisp probe all HalfCrowdLeftout.txt
cmd i 10 1100 1 meansqrdisp probe all stdout

end_file