2F. Output requests

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--(*) All the commands listed here can be freely modified if system exportation from a previous simulation is done

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The KMC algorithm within KIMERA makes the dissolution events happen one by one. In each simulation step, the program evaluates to print the information of the simulation in the output files according to what has been specified by the user. Each command enables the printing of a type of output file. The number in the command indicates the steps that are going to be printed uniformely, in time or in steps, depending on the ending clause (see next section).

The available output files are the following:

DATA_ANALYSIS                       (int)

It constains information of the quantity and fraction of the dissolved atoms of each type with time, as well as the derivative. Moreover, if we are studying a particle (with no PBC in any direction), it also reports information about the gyradius, but we need to specify the mass of each type of atom (see 2G. Other parameters section). This file is essential to study the time evolution of the dissolution rate.

MEAN_DISSOLVED_ANALYSIS             (int)

This file constains information of the avarage quantity of neighbours an atom has when it dissolves. This file is essential to obtain the ΔG and ΔG^* relation.

LAYER_ANALYSIS                      (optional)A   (optional)B  (optional)C  (int)

This command prints a maximun of three different files, one for each system direction. They contain information of the time evolution of the quantity of atoms that each system layer has. Each system layer has a tickness of one unit cell.

BOX_FRAMES                          (int)

This command prints the file with snapshots of the whole system with time, in LAMMPS format. As this file contains several times all the system positions, the size of the file may be too big. It is readable by visualization tools as OVITO.

SURFACE_FRAMES                      (int)

This command allows to obtain a similar file to the previous one but it only contains the positions of the reactive surface, thus it is much smaller. Same as before, the output file has LAMMPS format and can be viewed by OVITO program.

INITIAL_KIMERA_STATE
FINAL_KIMERA_STATE          

If these commands are used, the initial and the final states of the system are printed respectively. They have their own KIMERA format, as seen in 3. KIMERA format section. These output files can be used in subsequent simulations to save time, although the use of the commands are limited (see 2. Input structure section). In the case that FINAL_KIMERA_STATE has been used and KIMERA encounters an error during the simulation, it still prints the final state just before the error.

At this point, the only step remaining is to indicate when we want our simulation to finish. This, and other side commands like the name we give to the simulation or the number of cores we want to use to to run it are explained in the next 2G. Other parameters section.