single_body_thermal.f90 File Reference

Go to the source code of this file.


program single_body_thermal
 Simulate a single colloidal rigid-body particle. More...
subroutine detect_reaction
subroutine read_links (filename, n_links, links, links_d)
double precision function, dimension(3) get_unit_r ()
subroutine compute_cell_wise_max_v

Function/Subroutine Documentation

◆ compute_cell_wise_max_v()

subroutine single_body_thermal::compute_cell_wise_max_v ( )

Definition at line 998 of file single_body_thermal.f90.

◆ detect_reaction()

subroutine single_body_thermal::detect_reaction ( )

Definition at line 855 of file single_body_thermal.f90.

◆ get_unit_r()

double precision function, dimension(3) single_body_thermal::get_unit_r ( )

Definition at line 980 of file single_body_thermal.f90.

◆ read_links()

subroutine single_body_thermal::read_links ( character(len=*), intent(in)  filename,
integer, intent(out)  n_links,
integer, dimension(:,:), intent(out), allocatable  links,
double precision, dimension(:), intent(out), allocatable  links_d 

Definition at line 949 of file single_body_thermal.f90.

◆ single_body_thermal()

program single_body_thermal ( )

Simulate a single colloidal rigid-body particle.

This simulation models a chemically active colloid particle in either a periodic simulation box or with confinement in the y direction.

The coordinates of the colloid particle's beads must be provided in a H5MD file, as a "fixed-in-time" dataset. The body of the particle can operate as a rigid-body (with either RATTLE or quaternion dynamics) or as an elastic network.

Llength of simulation box in the 3 dimensions
rhofluid number density
TTemperature. Used for setting initial velocities and (if enabled) bulk thermostatting.
tauMPCD collision time
alphaangle of collision
probabilityprobability to change A to B upon collision
bulk_raterate of B->A reaction
N_MDnumber MD steps occuring in tau
N_loopnumber of MPCD timesteps
colloid_samplinginterval (in MD steps) of sampling the colloid position and velocity
do_solvent_ioif true (T), a snapshot of the solvent in the final step is dump to the datafile
equilibration_loopsnumber of MPCD steps for equilibration
epsilon_Cinteraction parameter of C sphere with both solvent species (2 elements)
epsilon_Ninteraction parameter of N sphere with both solvent species (2 elements)
data_filenamefilename for input Janus coordinates
data_groupparticles group in the input file
epsilon_colloidinteraction parameter for colloid-colloid interactions
reaction_radiusradius for the reaction around the Janus particle
link_tresholddistance criterion for finding rigid-body links
do_read_linksread link information from a file
links_filefilename for the links data
do_rattleperform RATTLE
do_lennard_jonescompute colloid-colloid Lennard-Jones forces
do_elasticcompute colloid-colloid elastic network forces
elastic_kelastic constant for the elastic network
rattle_pos_toleranceabsolute tolerance for Rattle (position part)
rattle_vel_toleranceabsolute tolerance for Rattle (velocity part)
do_quaternionperform quaternion velocity Verlet
quaternion_tresholdtreshold for the iterative procedure for the quaternion integrator
sigmaradius of the colloidal beads for colloid-solvent interactions
sigma_colloidradius of the colloidal beads for colloid-colloid interactions
polar_r_maxmaximal radius for the polar fields
do_ywalluse a confining potential in the y direction, 9-3 Lennard-Jones
wall_sigmawall LJ sigma
wall_epsilonwall LJ epsilon
wall_shiftwall shift
fluid_wallboundary condition for the fluid
delta_ureaction exothermicity

Definition at line 53 of file single_body_thermal.f90.