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VarCheatSheet.txt
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VarCheatSheet.txt
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%%%%%%%%%%%% vary_run_*.m %%%%%%%%%%%%%%%%%%%%%%%%%%
Description: Initializes parameters and runs main body of code, diffusion_model
%key parameters and constants
slide_barr_height=0; %barrier height to sliding, in kT
bind_energy=-20; %binding energy of tracers to obstacles, in kT
ffrac_obst=0.1; %filling fraction of obstacles
ffrac_tracer=0.1; %filling fraction of tracers
const.n_gridpoints=100; %number of grid points, same in x and y
const.ntimesteps=1e1; %number of timesteps NOte 1e5 gives errors on my laptop.
%other constants and model options
const.size_obst=1; %obstacle linear dimension, MUST BE odd integer
const.size_tracer=1; %tracer linear dimension, MUST BE odd integer
const.nequil=0; %number of timesteps for initial equilibration
modelopt.obst_excl=1; %1 if obstacles sterically exclude each other, 0 if not
modelopt.tracer_excl=0; %MUST BE 0 so tracers don't interact (ghosts)
modelopt.obst_trace_excl=0; %1 if obstacles and tracers mutually exclude
modelopt.dimension=2; %system dimension, currently must be 2
modelopt.animate=0; %1 to show animation, 0 for no animation
modelopt.tpause=0.0; %pause time in animation, 0.1 s is fast, 1 s is slow
modelopt.movie=0; %1 to record movie
pvec=[ffrac_obst ffrac_tracer slide_barr_height bind_energy]; %parameter vector
%%%%%%%%%%%% diffusion_model_old %%%%%%%%%%%%%%%%%%%
function [tracer,obst] = diffusion_model_old(pvec,const,modelopt,filename)
Description: Main body of the cody. Evolves particles in time
obst_curv=0.2; %curvature for animations
tracer_curv=1; %curvature for animations
lattice.moves=[1 0; -1 0; 0 1; 0 -1]; %possible steps a particle can take
tracer.pmove=exp(-slide_barr); %probability to move
tracer.cen_nomod %center, no periodic wrapping
tracer.center %center with periodic wrapping
%%%%%%%%%%%%%%% place_objects %%%%%%%%%%%%%%%%
function obj=place_objects(n_obj,len_obj,ngridpoints,modelopt, ...
exclude_flag,existing_fig,obj_color, obj_curv, placed_obj)
Description: Places the particles on the grid. Place the obstacles first then
then tracers.
%center x,y positions of each object
obj.center=[x' y'];
%list of lattice index positions for all points inside objects
obj.allpts = zeros(1,len_obj^dim);
%counter for objects that have been placed
obj_counter = n_obj+1;%+n.tracer