Self Diffusivity
Description
This function calculates the self-diffusion coefficient (D) of a specific molecule type, specified by its component name in the input. The value of D is obtained from the mean squared displacement (MSD) curve using a linear fit. The MSD for each molecule of the selected component is calculated independently. At each time step, the MSD values are averaged across the molecules, and the diffusivity is then determined by fitting the resulting averaged curve.
Latest version
Allowed number of parents: 1
| Parameter | Description | Value type | Value restrictions | Default value | Units |
|---|---|---|---|---|---|
Component names |
Indicate the component names for the self diffusitivy calculation |
selector_component |
component names |
N/A |
N/A |
Include H atoms? |
Whether to include the hydrogen atoms in the calculation |
bool |
True, False |
false |
N/A |
Beginning time |
The staring simulation time to consider for the calculation of the diffusivity. -1 means the beginning of the simulation. |
float |
-1, >0 |
-1 |
ps |
End time |
The final simulation time to consider for the calculation of the diffusivity. -1 means the end of the simulation. |
float |
-1, >0 |
-1 |
ps |