Programs¶
Configuration files¶
The parameters listed for each program are read from text configuration files. The syntax is given by example for the arguments that follow.
T Temperature
L Box size
enable_thermostat Activate the thermostat
T = 1.2
L = 32 32 32
enable_thermostat = F
Boolean values are input as T (True) or F (False). For vectors (such as the box size L),
several components are listed, separated by a space. For more examples, the subdirectories
in experiments/ contain configuration files for some simulations.
single_dimer_pbc¶
Synopsis¶
Source code: single_dimer_pbc
Simulate a single dimer nanomotor
Consider a dimer nanomotor in a periodic simulation cell filled with A particles. After a collision with the catalytic sphere of the dimer, a A particle is converted to B.
Parameters¶
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.
do_thermostat enable MPCD-AT thermostat
do_hydro conserve cell-wise momentum (can be turned off only with thermostat enabled)
probability probability to change A to B upon collision
bulk_rmpcd use bulkd rmpcd reaction for B->A instead of resetting
bulk_rate rate of B->A reaction
dt MD collision time
N_MD number MD steps occuring in tau
N_loop number of MPCD timesteps
collide_every interval for collision. the MPCD time tau is collide_every*n_MD*dt
colloid_sampling interval (in MD steps) of sampling the colloid position and velocity
equilibration_loops number of MPCD steps for equilibration
sigma_C radius of C sphere
sigma_N radius of N sphere
d length of rigid link
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)
epsilon_C_C interaction parameter among C spheres
epsilon_N_C interaction parameter among N and C spheres
epsilon_N_N interaction parameter among N spheres
chemotactic_cell¶
Synopsis¶
Source code: chemotactic_cell
Model a chemotactic experiment in a microfluidic channel
In this simulation, an inlet (x=0) is fed with A and S fluid species in the lower and upper halves in the y direction, respectively. A constant accerelation is applied in the x direction and walls in the z direction confine the flow, leading to a Poiseuille velocity profile.
The colloid is a passive sphere, an active sphere or a dimer nanomotor.
Parameters¶
g magnitude of acceleration
buffer_length length of the inlet buffer
max_speed maximum velocity of profile to initialize the velocities
probability probability of reaction
alpha angle of collision
store_rho_xy store the xy density of solvent particles on a grid
store_rho_xy_z bounds in z for the slice of rho_xy to store (2 elements)
dimer simulate a dimer nanomotor (boolean, else it is a single sphere)
N_type assign N species to the single sphere (boolean, else it is a C sphere)
L length of simulation box in the 3 dimensions
rho fluid number density
T Temperature. Used for setting initial velocities and for wall thermostatting.
d length of rigid link
N_in_front place N sphere in front (higher x), for the dimer nanomotor
tau MPCD collision time
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
steps_fixed number of steps during which the colloid is fixed (only when buffer_length>0)
equilibration_loops number of MPCD steps for equilibration (only when buffer_length=0)
sigma_C radius of C sphere
sigma_N radius of N sphere
track_y_shift shift of the track in the y direction with respect to Ly/2
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)
single_body¶
Synopsis¶
Source code: single_body
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.
Parameters¶
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.
alpha angle of collision
do_hydro set to T for usual MPCD
do_thermostat enable thermostatting. mandatory if do_hydro=F
probability probability to change A to B upon collision
bulk_rate rate of B->A reaction
dt MD collision time
N_MD number MD steps occuring in tau
N_loop number of MPCD timesteps
collide_every interval for collision. the MPCD time tau is collide_every*n_MD*dt
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
planar_size Size of planar field sampling region (length 2)
planar_n number of grid points for the planar field sampling (length 2)
coordinates_sampling outer-loop interval for storing the body’s coordinates
poiseuille_flow¶
Synopsis¶
Source code: poiseuille_flow
Simulate a forced flow between two plates
Consider a pure fluid under a constant acceleration in the x-direction. Confining plates, modeled as Bounce-back boundary conditions are used in the z-direction in addition to ghost cells for the collisions near the walls.
Parameters¶
L length of simulation box in the 3 dimensions
g strength of the constant acceleration in x
rho fluid number density
T Temperature. Used for setting initial velocities, for wall thermostatting and (if enabled) bulk thermostatting.
tau MPCD collision time
alpha MPCD collision angle
thermostat whether to enable bulk thermostatting
do_hydro whether to conserve momentum cell-wise
N_therm number of unsampled thermalization MPCD timesteps
N_loop number of MPCD timesteps
single_sphere_thermo_trap¶
Synopsis¶
Source code: single_sphere_thermo_trap
Simulate a thermal gradient with an embedded colloidal sphere
Consider a pure fluid under a thermal gradient in the z-direction. The confining plates are modeled as bounce-back boundary conditions in the z-direction in addition to ghost cells for the collisions near the walls.
The x-z components of the fluid velocity field is stored at fixed intervals in the center-y layer of cells.
The sphere can be either fixed or held by an harmonic trap.
Parameters¶
L length of simulation box in the 3 dimensions
rho fluid number density
T Temperature. Used for setting initial velocities.
wall_T Temperature at the walls (two values).
k trap stiffness
tau MPCD collision time
alpha MPCD collision angle
N_therm number of unsampled thermalization MPCD timesteps
N_loop number of MPCD timesteps
N_MD number of MD timesteps per tau
vxz_interval interval for storing the xz velocity field
sigma size of spherical colloid
epsilon interaction parameter of sphere with fluid
move enable motion of the sphere (boolean)
n_colloids_pbc¶
Synopsis¶
Source code: n_colloids_pbc
Simulate an ensemble of spherical colloids
The periodic simulation box is filled with a number of spherical colloids, that interact with an attractive Lennard-Jones potential, and with solvent particles. The temperature can be controlled with the MPCD Anderson thermostat.
Parameters¶
L length of simulation box in the 3 dimensions
rho fluid number density
T Temperature. Used for setting initial velocities and for thermostatting.
T_final Target temperature. Used for thermostatting with temperature program from T to T_final.
tau MPCD collision time
do_thermostat enable MPCD-AT thermostat
do_hydro conserve cell-wise momentum (can be turned off only with thermostat enabled)
N_MD number MD steps occuring in tau
colloid_sampling interval (in MD steps) of sampling the colloid position and velocity
N_loop number of MPCD timesteps
N_thermo_loop number of initial thermostatting MPCD timesteps
N_colloids number of colloids
epsilon solvent-colloid epsilon
sigma radius of the colloids
epsilon_colloids colloid-colloid epsilon
three_bead_enzyme¶
Parameters¶
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
N_enzymes Number of enzyme molecules
substrate_fraction initial fraction of non-inert (substrate and product) fluid particles
product_relative_fraction inital relative fraction of product among non-inert fluid particles
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
equilibration_loops number of MPCD steps for equilibration
sigma_E radius of enzymatic_site
sigma_N radius of N sphere
link_d length of rigid link
link_angles angle of the model at rest
elastic_k stiffness of the link
angle_k stiffness of the angular link
epsilon_E interaction parameter of E sphere with solvent species (3 elements)
epsilon_N interaction parameter of N sphere with solvent species (3 elements)
epsilon_colloid interaction parameter among colloids
enzyme_capture_radius capture and release radius for substrate/product
rate_release_s rate of release of substrate from enzyme
rate_release_p rate of release of product from enzyme
proba_s probability of capture of substrate
proba_p probability of capture of product
bulk_rmpcd use bulkd rmpcd reaction for B->A instead of resetting
immediate_chemistry start to process chemical event before sampling
bulk_rate rates for the A->B and B->A bulk reaction