3.1.1.5. Generating simulated CBED patterns of a sample of MoS₂ on amorphous C

In this example, we perform the “action” of simulating some convergent beam electron diffraction (CBED) experiments, where the sample is a 5-layer \(\text{MoS}_2\) thin film with a \(0.5 \ \text{nm}\) thick layer of amorphous carbon (C).

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/MoS2_amorphous_C/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_cbed_pattern_sets, 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 multiple SLURM jobs. 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 multiple SLURM jobs, 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.

The action described at the beginning of the current page takes automatically as input data output data generated by the actions described in the pages Generating the atomic coordinates of a model of MoS2 and Generating the potential slices of a model of MoS2 on amorphous C, hence one must execute the two actions described in those two pages prior to the action described at the beginning of the current page. The action described at the beginning of the current page simulates 3 CBED experiments using prismatique, with the only CBED system model parameters not fixed between simulations being the semi-convergence angle, and the defocus, resulting in different CBED disk sizes for each simulation. For each simulation, chromatic aberrations, spherical aberrations, and thermal effects are included. Furthermore, for each simulation, the only optional output that is saved is the final CBED intensity pattern, that has dimensions of \(1024 \times 1024\), in units of pixels. The first, second, and third simulation yield the smallest, second smallest, and largest CBED disks respectively. Accordingly, let <disk_size> be equal to small, medium, and large, for the first, second, and third simulation respectively. For each simulation, upon successful completion, all output will be saved to the directory <root>/examples/modelling/cbed/simulations/MoS2_amorphous_C/data/cbed_pattern_generator_output/patterns_with_<disk_size>_disks.

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/MoS2_on_amorphous_C/scripts/execute_action.py <root>/examples/modelling/cbed/simulations/MoS2_on_amorphous_C/scripts/generate_cbed_pattern_sets/execute_all_action_steps.py <root>/examples/modelling/cbed/simulations/MoS2_on_amorphous_C/scripts/generate_cbed_pattern_set/execute_all_action_steps.py <root>/examples/modelling/cbed/simulations/MoS2_on_amorphous_C/scripts/generate_cbed_pattern_set/prepare_and_submit_slurm_job.sh <root>/examples/modelling/cbed/simulations/MoS2_on_amorphous_C/scripts/generate_cbed_pattern_set/execute_main_action_steps.py

Otherwise, if <use_slurm> equals no, then the fourth 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 multiple SLURM jobs, 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.