# 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