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RMPCDMD
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Go to the source code of this file.
Functions/Subroutines | |
| 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 |
| subroutine single_body_thermal::compute_cell_wise_max_v | ( | ) |
Definition at line 998 of file single_body_thermal.f90.
| subroutine single_body_thermal::detect_reaction | ( | ) |
Definition at line 855 of file single_body_thermal.f90.
| double precision function, dimension(3) single_body_thermal::get_unit_r | ( | ) |
Definition at line 980 of file single_body_thermal.f90.
| 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.
| 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.
| L | length of simulation box in the 3 dimensions |
| rho | fluid number density |
| T | Temperature. Used for setting initial velocities and (if enabled) bulk thermostatting. |
| tau | MPCD collision time |
| alpha | angle of collision |
| probability | probability to change A to B upon collision |
| bulk_rate | rate of B->A reaction |
| N_MD | number MD steps occuring in tau |
| N_loop | number of MPCD timesteps |
| colloid_sampling | interval (in MD steps) of sampling the colloid position and velocity |
| do_solvent_io | if true (T), a snapshot of the solvent in the final step is dump to the datafile |
| equilibration_loops | number of MPCD steps for equilibration |
| epsilon_C | interaction parameter of C sphere with both solvent species (2 elements) |
| epsilon_N | interaction parameter of N sphere with both solvent species (2 elements) |
| data_filename | filename for input Janus coordinates |
| data_group | particles group in the input file |
| epsilon_colloid | interaction parameter for colloid-colloid interactions |
| reaction_radius | radius for the reaction around the Janus particle |
| link_treshold | distance criterion for finding rigid-body links |
| do_read_links | read link information from a file |
| links_file | filename for the links data |
| do_rattle | perform RATTLE |
| do_lennard_jones | compute colloid-colloid Lennard-Jones forces |
| do_elastic | compute colloid-colloid elastic network forces |
| elastic_k | elastic constant for the elastic network |
| rattle_pos_tolerance | absolute tolerance for Rattle (position part) |
| rattle_vel_tolerance | absolute tolerance for Rattle (velocity part) |
| do_quaternion | perform quaternion velocity Verlet |
| quaternion_treshold | treshold for the iterative procedure for the quaternion integrator |
| sigma | radius of the colloidal beads for colloid-solvent interactions |
| sigma_colloid | radius of the colloidal beads for colloid-colloid interactions |
| polar_r_max | maximal radius for the polar fields |
| do_ywall | use a confining potential in the y direction, 9-3 Lennard-Jones |
| wall_sigma | wall LJ sigma |
| wall_epsilon | wall LJ epsilon |
| wall_shift | wall shift |
| fluid_wall | boundary condition for the fluid |
| delta_u | reaction exothermicity |
Definition at line 53 of file single_body_thermal.f90.
1.8.13