Diffusion¶
simfs_dif produces a single molecule diffusion trajectory inside a
cylindrical box. In addition to the random walk coordinates, it outputs a
timetag stream containing timetags for every collision with the simulation box.
Parameters¶
-
diffusion.json¶ Parameters of simfs_dif
Object Properties: - coordinate_output (string) – Output filename for coordinates
- collision_output (string) – Output filename for collision times
- experiment_time (float) – Experiment time in seconds
- increment (float) – Time increment per diffusion step in seconds
- diffusion_coefficient (float) – Diffusion \(D\) in \(\rm{m \cdot s}^{-2}\)
- half_height (float) – Half height of diffusion cylinder in meter
- radius (float) – Radius of cylinder in meter
- seed (int) – Random seed
Example:
{
"collision_output": "__collisions__",
"coordinate_output": "__coordinates__",
"diffusion_coefficient": 1e-10,
"experiment_time": 1.0,
"half_height": 1e-06,
"increment": 1e-07,
"radius": 1e-06,
"seed": 1865456046
}
Data streams¶
| Type | Name | Datatype | Size | Layout | Description |
|---|---|---|---|---|---|
| out | coordinate_output | Coordinate | 4 x 8 byte | (x, y, z, time) | Molecular trajectory |
| out | collision_output | Timetag | 1 x 8 byte | (time) | Collision events |
Notes¶
The simulation cylinder is defined by a radius and a half height. The initial position is chosen at random somewhere within the box and moved incrementally for every time increment in x, y and z. The stepsize in all dimension follows the same normal distrubution. Each step is recorded as an (x, y, z, t) record in the coordinate output.
When a coordinate is outside the box (i.e. the molecule would hit the wall of the box), a collision event is written to the collision output and the coordinate is discarded. A new attempt to generate a valid coordinate is calculated until a valid step is acquired. However, when a second collision follows the first immediatly, no collision event is outputted. The event times in the collision output are thereby guaranteed to be unique.
The diffusion coefficient will be converted to the standard deviation of the internal normal distribution according to \(\sigma^2 = 2\cdot D \Delta t\) with \(\Delta t\) being the increment of the diffusion step.