Commit f71f5a83 authored by Johannes Blaschke's avatar Johannes Blaschke
Browse files

fiddle with the way we initialize things

parent 4ade1ef6
[simulation]
nx = 60
ny = 60
nz = 60
particles_per_cell = 10
dt = 0.01
periods_y = 1 ; periodic boundary for cartesian CPU grid
periods_z = 1
boundaries_x = 0 ; 0: bulk 1: Quasi 2D
boundaries_y = 0
boundaries_z = 0
angular_momentum_conservation = 1
compute_explicit_pressure_field = 0
pressure_nhist = 100
pressure_k = 0.01
ntimesteps = 3000000
naverage = 100
[debug]
debug = 0
without_collision = 0
without_particle_stream = 0
without_squirmer_stream = 1
use_serial_md = 0
[externalforce]
pflow = 0
nslices = 30
nsteps = 10 ; number of timesteps for averaging
ax = 0.0
ay = 0.0
az = 0.001
gx = 0 ; constant force on squirmers in x-direction
gy = 0
gz = 0
[activeparticles]
squirmer = 0 ; 0: no squirmers 1: squirmers 2:janus-pusher 3:janus-puller
alpha = 1 ; cutoff angle for janus-particles
nsquirmers = 1 ; doesnt play a role if squirmerposition = 3
nlines = 1
ncolumns = 1
squirmerposition = 2 ; 0: random positions, 1: in the middle of the simulation box, 2: at the walls, 3: hexagonal packed in the middle of the box
fixed_in_plane = 0 ; squirmers are fixed in the yz plane at x=N_x/2 -> e_x=0 v_x=0 at all times
colloid_velocity = 0 ; 0: zero start velocity, 1: random velocities, 2: in x direction, 3: in y direction, 4: in z direction, else: zero start velocity
sradius = 3.0 ; radius of the squirmers
B1 = 0.0 ; surface velocity mode
beta = 0.0 ; B2 / B1
[trypanosome]
trypanosome = 1
trypanosome_head_initpos_x = 30
trypanosome_head_initpos_y = 30
trypanosome_head_initpos_z = 5
network_kspring = 3000000.0; Sujin: 10000000; in Davod's papers it's : 3000000.0
network_kbend = 4500.0; Sujin: 180000; in Davod's paper it's : 4500.0
network_kxlink = 000.0
network_n_slice = 26
network_n_loop = 10
flagellum_kdriving = 500.0; Sujin: 10000; in Davod's paper it's : 500.0
flagellum_lambda = 13; 13
flagellum_period = 1280
flagellum_nplanar = 23
flagellum_bn_avg = 1
flagellum_n_additional_nodes = 0
flagellum_mass_addition_nodes = 1
n_slice_flagellum_start = 2
n_loop_flagellum_start = 0
n_slice_flagellum_bend_start = 2
length_flagellum_helix = 5
flagellum_alpha_amplitude = 1.0
[potentials]
use_potentials = 1
which_potential = 0 ; 0: WCA ; 1: Hertz
n_md_steps = 20
epsilon = 100000.0
[continuesimulation]
continuedsimulation = 1
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