Density Functional Theory Code for a polymer film + colloids. This modelling code was used to generate the data in "Crowding-induced phase separation of nuclear transport receptors in FG nucleoporin assemblies" that is published in eLife available here https://elifesciences.org/articles/72627.
Any questions please send an email to luke.davis.16@ucl.ac.uk.
Density functional theory (DFT) for polymers + colloids in a film
Usage: ./dftpolymercolloid2 [OPTIONS]
Options:
-h,--help Print this help message and exit
--config TEXT=./config.dft configuration file for dftpolymercolloid
Simulation parameters:
-p,--potential_mode INT REQUIRED
Attractive potential to use for all particles (0 = long ranged gaussian, 1 = short ranged gaussian)
-c,--ctol,--convergence_tolerance FLOAT REQUIRED
Convergence tolerance for DFT simulation.
-t,--dt,--timestep FLOAT REQUIRED
timestep for the numerical algorithm to advance system to equilibrium (for polymers)
--DT,--coltimestep FLOAT REQUIRED
timestep for the numerical algorithm but for colloids
--Nz,--spatial_points INT REQUIRED
Number of spatial points
--polymers_off Switch polymers off
--topwall_off_c1 Switch top wall off for colloid 1
--botwall_off_c1 Switch bottom wall off for colloid 1
--topwall_off_c2 Switch top wall off for colloid 2
--botwall_off_c2 Switch bottom wall off for colloid 2
Output files:
--poly_dens_file TEXT filename for polymer density
--col1_dens_file TEXT filename for colloid density 1
--col2_dens_file TEXT filename for colloid density 2
--meanfield_file TEXT filename for meanfield
--external_pot_file TEXT REQUIRED
filename for external potential
--system_out_file TEXT REQUIRED
filename for system output
Simulation box parameters:
-H,--height FLOAT REQUIRED Height (z) of the simulation box
-A,--area FLOAT REQUIRED area (x-y) of the simulation box
--wall_strength FLOAT REQUIRED
Strength of wall repulsive wall interactions
Particle interactions:
--epp FLOAT Needs: --lambdapp
Polymer - polymer cohesion strength
--epc1 FLOAT Needs: --lambdapc1
Polymer - colloid type 1 cohesion strength
--epc2 FLOAT Needs: --lambdapc2
Polymer - colloid type 2 cohesion strength
--ec1c1 FLOAT Needs: --lambdac1c1
colloid 1 - colloid 1 cohesion strength
--ec2c2 FLOAT Needs: --lambdac2c2
colloid 2 - colloid 2 cohesion strength
--ec1c2 FLOAT Needs: --lambdac1c2
colloid 1 - colloid 2 cohesion strength
--lambdapp FLOAT Needs: --epp
Polymer - polymer cohesion range
--lambdapc1 FLOAT Needs: --epc1
Polymer - colloid type 1 cohesion range
--lambdapc2 FLOAT Needs: --epc2
Polymer - colloid type 2 cohesion range
--lambdac1c1 FLOAT Needs: --ec1c1
colloid 1 - colloid type 1 cohesion range
--lambdac2c2 FLOAT Needs: --ec2c2
colloid 2 - colloid type 2 cohesion range
--lambdac1c2 FLOAT Needs: --ec1c2
colloid 1 - colloid type 2 cohesion range
Polymer parameters:
--poly_bondlength FLOAT Needs: --npolymers --nbeads
Bondlength of beads in a polymer
--poly_diameter FLOAT Needs: --poly_bondlength --npolymers --nbeads
diameter of beads in a polymer
--npolymers INT Number of polymers in system
-N,--nbeads INT Needs: --npolymers
Number of beads in a polymer
--Ns INT Needs: --npolymers --nbeads
Number of points for solving polymer diffusion equation
--tether INT Needs: --npolymers --nbeads
z tethering index for polymer grafting
Colloid 1 parameters:
--chem1 FLOAT Colloid (1) excess chemical potential
--Nc1 INT Colloid (1) number of colloids
--rc1 FLOAT Colloids (1) radius
--col1_init_cut FLOAT Colloids (1) height which below density is zero (to begin with)
Colloid 2 parameters:
--chem2 FLOAT Colloid (2) excess chemical potential
--Nc2 INT Colloid (2) number of colloids
--rc2 FLOAT Colloids (2) radius
--col2_init_cut FLOAT Colloids (2) height which below density is zero (to begin with)
Shield:
This work is licensed under a Creative Commons Attribution 4.0 International License.
