Fixed atoms

In pDynamo3 simulations, as well as in EasyHybrid, it is possible to freeze or fix groups of atoms during the simulation process. To do this, follow these steps:

1. Select the group of atoms you wish to freeze or fix.

2. Access the main menu and click on the "Selections" item.

3. In the "Selections" menu, choose the option "Set as fixed atoms" to assign the selected atoms as fixed.

4. Alternatively, you can right-click (Mouse Button 3) in the GL area while a selection is active.

5. In the GL area context menu, select "Set as fixed atoms."

Once these steps are completed, the selected atoms will be designated as fixed, ensuring that their positions remain unchanged during simulations or other processes. In EasyHybrid, atoms assigned as fixed are displayed in gray by default. This visual cue helps distinguish them from other atoms in the system, clearly indicating that their positions will remain unchanged throughout the simulation (see Figure 1).

The assignments of atoms in the fixed condition in EasyHybrid are additive. This means that if the selection process is performed multiple times, the number of fixed atoms will be the sum of the selected atoms in each process. By repeatedly selecting additional atoms, you can gradually add them to the group of fixed atoms.

To make a group of atoms free (i.e., unfixed), a similar process is followed. The user selects the atoms of interest and then accesses the "Selections" item in the main menu. From there, the user can choose the "Set as Free Atoms" option. Alternatively, the same option can be accessed from the GL area selection menu. This process allows you to remove the fixed assignment from the selected atoms, making them free to move and interact during simulations or other processes.