# File to test molecule sticking rate
# Figures 6A and 6B of adsorb paper
# units micons, seconds

define XLO -2
define XHI 2
define YLO 0
define YHI 1
define ZLO 0
define ZHI 1
define XSIZE 4
define YSIZE 1
define ZSIZE 1

graphics opengl
graphic_iter 10

dim 3
names A B C A2 B2 C2
max_mol 122000

difc all(solution) 5
# in 10 s, with D=5, diff. dist. is 10 microns

color A(all) 1 0 0
color A2(all) 1 0 0
color B(all) 0 1 0
color B2(all) 0 1 0
color C(all) 0 0 1
color C2(all) 0 0 1
display_size all 2

time_start 0
time_stop 0.1
time_step 0.001
# with D=5 and Ęt=0.001, rms step length is 0.1 micron

boundaries 0 XLO XHI
boundaries 1 YLO YHI
boundaries 2 ZLO ZHI

max_surface 2

start_surface
name walls
action both all reflect
color both 0 0 0
polygon both edge
max_panels rect 6
panel rect +0 XLO YLO ZLO YSIZE ZSIZE
panel rect -0 XHI YLO ZLO YSIZE ZSIZE
panel rect +1 XLO YLO ZLO XSIZE ZSIZE
panel rect -1 XLO YHI ZLO XSIZE ZSIZE
panel rect +2 XLO YLO ZLO XSIZE YSIZE
panel rect -2 XLO YLO ZHI XSIZE YSIZE
end_surface

start_surface
name stick
rate_internal A fsoln front 1
rate B fsoln front 85.8559
rate B front fsoln 276
rate_internal C fsoln bsoln 1
rate_internal C bsoln fsoln 1
#rate_internal A2 fsoln front 0.1
rate_internal A2 fsoln front 0.105993
#rate B2 fsoln front 4.22852
rate_internal B2 fsoln front 0.105993
#rate B2 front fsoln 28
rate_internal B2 front fsoln 0.027612
#rate_internal C2 fsoln bsoln 0.1
#rate_internal C2 bsoln fsoln 0.1
rate_internal C2 fsoln bsoln 0.10938
rate_internal C2 bsoln fsoln 0.10938
color both 0.5 0.5 0.5
max_panels rect 1
panel rect +0 0 YLO ZLO YSIZE ZSIZE
end_surface

mol 20000 A 0-XHI u u
mol 20000 B 0-XHI u u
mol 20000 C 0-XHI u u
mol 20000 A2 0-XHI u u
mol 20000 B2 0-XHI u u
mol 20000 C2 0-XHI u u
# 20000 molecules in 2x1x1 micron^3 is 10000 per cubic micron

output_files FILEROOT1out.txt FILEROOT2out.txt FILEROOT3out.txt
cmd B molcountheader FILEROOT1out.txt
cmd B molcountheader FILEROOT2out.txt
cmd E molcountonsurf stick FILEROOT1out.txt
cmd E molcountinbox XLO 0 YLO YHI ZLO ZHI FILEROOT2out.txt

cmd i 0 0.1 0.0099 molcountspace A(fsoln) 0 0 1 20 YLO YHI ZLO ZHI 0 FILEROOT3out.txt
cmd @ 0.0009 molcountspace A(fsoln) 0 0 1 20 YLO YHI ZLO ZHI 0 FILEROOT3out.txt

end_file