setPhases()
Description
setPhases() is a function used to assign manually the states of the molecules from the system.
The function can take as input either the name of the phase, or an array of names of dimension (# Frames, # Molecules); it will both update the input system
and output an array of all the states.
Alternatively, the method .setPhases() from the System class can be used for the exact same purpose.
Argument, keywords and outputs
Input(s) / Argument(s)
| Name | Flag | Type | Description |
|---|---|---|---|
| System | class System | Instance of the system classes containing all the informations on the system as well as the positions and configurations. | |
| Phases | str or np.ndarray | Phases to assign manually to the molecules. |
Output(s)
| Name | Type | Description |
|---|---|---|
| Phases | np.ndarray | Array of all the molecule phases predicted in the system. Dimension(s) are in (N frames, N molecules). |
Examples
Assigning a single phase
The following example will assign the phase name fluid to all molecules of system_A, an instance of the System class. The output will be stored in a variable named phase_array in addition to the attributes of the instance.
import mllpa
phase_array = mllpa.setPhases(system_A, "fluid")
Assigning a phase array
The following example will assign the array of phases phase_array to system_A, an instance of the System class. The output will only be stored in the instance of the System class.
mllpa.setPhases(system_A, phase_array)
Using the method instead of the function
The following example will assign the phase name fluid to all molecules of system_A, an instance of the System class, but will call the method of the instance instead of the function. The output will be stored directly in the instance of the System class.
system_A.setPhases("fluid")
Related tutorials
The following tutorial(s) detail further the use of the setPhases() function through the .setPhases() method of the system class: