3.1.1.2. Generating the atomic coordinates of a model of amorphous C superblock

In this example, we perform the “action” of generating the atomic coordinates of a model of a \(25 \times 25 \times 1 \ \text{nm}^3\) large superblock of amorphous carbon (C), that is subsequently truncated to the same lateral dimensions of a model of \(\text{MoS}_2\) generated in another script, and to \(0.5 \ \text{nm}\) along the \(z\)-axis. The superblock, prior to truncation, is generating by tiling various transformations of a model of a \(5 \times 5 \times 1 \ \text{nm}^3\) large block of amorphous C. The atomic coordinates of the \(5 \times 5 \times 1 \ \text{nm}^3\) large block of amorphous C were taken from Ref. [Ricolleau1].

NOTE: Users are advised to read the remainder of the current page in its entirety before trying to execute this action.

To execute the action, first we need to change into the directory <root>/examples/modelling/cbed/simulations/amorphous_C_superblock/scripts, where <root> is the root of the emicroml repository. Then, we need to run the Python script ./execute_action.py via the terminal command:

python execute_action.py --action=<action> --use_slurm=<use_slurm>

where <action> must be equal to generate_atomic_coords, and <use_slurm> is either yes or no. If <use_slurm> equals yes and a SLURM workload manager is available on the server from which you intend to run the script, then the action will be performed as a SLURM job. If <use_slurm> is equal to no, then the action will be performed locally without using a SLURM workload manager.

If the action is to be performed locally without using a SLURM workload manager, then prior to executing the above Python script, a set of Python libraries need to be installed in the Python environment within which said Python script is to be executed. See this page for instructions on how to do so. If the action is being performed as a SLURM job, then prior to executing any Python commands that do not belong to Python’s standard library, a customizable sequence of commands are executed that are expected to try to either activate an existing Python virtual environment, or create then activate one, in which the Python libraries needed to complete the action successfully are installed. See this page for instructions how to customize the sequence of commands.

We assume that the C atoms are subject to room temperature, and that their root-mean-square \(x\)-displacement is 0.141 Å. This value was taken from Ref. [Boothroyd1].

The action described at the beginning of the current page takes automatically as input data output data generated by the action described in the page Generating the atomic coordinates of a model of MoS2, hence one must execute the latter action first, prior to the former. Upon successful completion of the former action, the atomic coordinates of the model of the truncated superblock of amorphous C are stored in the file at the file path <root>/examples/modelling/cbed/simulations/amorphous_C_superblock/data/atomic_coords.xyz. The atomic coordinates file will be formatted as an atomic coordinates file that is accepted by prismatique: see the description of the parameter atomic_coords_filename of the class prismatique.sample.ModelParams for a discussion on the correct formatting of such an atomic coordinates file.

In executing the action described at the beginning of the current page, multiple scripts are executed. The particular scripts that are executed depend on the command line arguments of the parent Python script introduced at the beginning of this page. If <use_slurm> equals yes, then the following scripts are executed in the order that they appear directly below:

<root>/examples/modelling/cbed/simulations/amorphous_C_superblock/scripts/execute_action.py <root>/examples/modelling/cbed/simulations/amorphous_C_superblock/scripts/generate_atomic_coords/execute_all_action_steps.py <root>/examples/modelling/cbed/simulations/amorphous_C_superblock/scripts/generate_atomic_coords/prepare_and_submit_slurm_job.sh <root>/examples/modelling/cbed/simulations/amorphous_C_superblock/scripts/generate_atomic_coords/execute_main_action_steps.py

Otherwise, if <use_slurm> equals no, then the third script, i.e. the one with the basename prepare_and_submit_slurm_job.sh is not executed. See the contents of the scripts listed above for implementation details. Lastly, if the action is being performed as a SLURM job, then the default sbatch options, which are specified in the file with the basename prepare_and_submit_slurm_job.sh, can be overridden by following the instructions in this page.