3.7. Example of running a HRTEM simulation
3.7.1. Prerequisites for running this example
Prior to running any scripts or Jupyter notebooks in the directory
<root>/examples, where <root> is the root of the prismatique
repository, a set of Python libraries need to be installed in the Python
environment within which any such scripts or Jupyter notebooks are to be
executed. See this page
for instructions on how to do so.
3.7.2. Example description
In this example, we simulate a HRTEM experiment involving the bilayer
\(\text{MoS}_2\) sample that we defined in the
Example of atomic coordinate generation page. See the documentation for the
subpackage prismatique.hrtem for a discussion on the algorithm used to
simulate HRTEM experiments.
3.7.3. Code
Below is the code that performs the aforementioned HRTEM simulation. You can
also find the same code in the file <root>/examples/hrtem_sim/run.py of the
repository, where <root> is the root of the prismatique repository. To
run the script from the terminal, change into the directory containing said
script, and then issue the following command:
python run.py
The output files generated by this script are saved in the directory
<root>/examples/data/hrtem_sim_output, where <root> is the root of the
prismatique repository. To analyze the output, use the Jupyter notebook
<root>/examples/output_data_analysis_notebooks/analyzing_hrtem_sim_output.ipynb.
If you would like to modify this script for your own work, it is recommended that you copy the original script and save it elsewhere outside of the git repository so that the changes made are not tracked by git.
# -*- coding: utf-8 -*-
# Copyright 2024 Matthew Fitzpatrick.
#
# This program is free software: you can redistribute it and/or modify it under
# the terms of the GNU General Public License as published by the Free Software
# Foundation, version 3.
#
# This program is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License along with
# this program. If not, see <https://www.gnu.org/licenses/gpl-3.0.html>.
"""An example of running a HRTEM simulation.
See the link https://mrfitzpa.github.io/prismatique/examples/hrtem-sim/run.html
for a description of the example.
A NOTE BEFORE STARTING
----------------------
To run this script from the terminal as is, i.e. without modifications, change
into the directory containing said script, and then issue the following
command::
python run.py
The output files generated by this script are saved in the directory
``<root>/examples/data/hrtem-sim-output``, where ``<root>`` is the root of the
``prismatique`` repository. To analyze the output, use the Jupyter notebook
``<root>/examples/output-data-analysis-notebooks/analyzing-hrtem-sim-output.ipynb``.
If you would like to modify this script for your own work, it is recommended
that you copy the original script and save it elsewhere outside of the git
repository so that the changes made are not tracked by git.
"""
#####################################
## Load libraries/packages/modules ##
#####################################
# For making directories and creating path objects.
import pathlib
# For spawning shell processes and getting the path to current script.
import os
# For running the HRTEM simulation.
import prismatique
###############################################
## Define classes, functions, and contstants ##
###############################################
###########################
## Define error messages ##
###########################
#########################
## Main body of script ##
#########################
msg = "Setting up the HRTEM simulation for the MoS2 sample..."
print(msg)
print()
# In another example script, we generate all the simulation parameters required
# to generate the potential slices, the S-matrices, and for simulating STEM and
# HRTEM experiments involving the MoS2 sample. Rather than set explicitly again
# all the simulation parameters required for the HRTEM simulation, we can run
# the other script to generate the parameters if they do not already exist, and
# then load these parameters in this current script.
path_to_current_script = pathlib.Path(os.path.realpath(__file__))
path_to_examples_dir = str(path_to_current_script.parent.parent)
path_to_data_dir = path_to_examples_dir + "/data"
path_to_serialized_params = (path_to_data_dir
+ "/sim_param_generator_output"
+ "/hrtem_sim_params.json")
for try_count in range(2):
try:
hrtem_sim_params = \
prismatique.hrtem.sim.Params.load(path_to_serialized_params)
hrtem_system_model_params = \
hrtem_sim_params.core_attrs["hrtem_system_model_params"]
sample_specification = \
hrtem_system_model_params.core_attrs["sample_specification"]
atomic_coords_filename = \
sample_specification.core_attrs["atomic_coords_filename"]
mod_alias = prismatique.sample
mod_alias.check_atomic_coords_file_format(atomic_coords_filename)
break # No exceptions raised, hence we can exit the for-loop early.
except:
msg = ("Need to generate the simulation parameter sets for the various "
"simulated experiments involving the MoS2 sample...")
print(msg)
print()
script_to_execute = (path_to_examples_dir
+ "/sim_param_generator/generate.py")
os.system("python " + script_to_execute)
msg = ("Resuming the setup of the HRTEM simulation for the MoS2 "
"sample...")
print(msg)
print()
sample_model_params = sample_specification
# In another example script, we generate the potential slices for the MoS2
# sample, which can be used in turn as the sample model to perform the HRTEM
# simulation, rather than the sample model parameters we loaded above. Below we
# check whether the potential slices have been generated: if they exists then we
# load and use them in this current script to perform the HRTEM simulation,
# otherwise we use the sample model parameters that we loaded above to perform
# the HRTEM simulation from scratch.
path_to_potential_slices = (path_to_data_dir
+ "/potential_slice_generator_output")
try:
thermal_params = \
sample_model_params.core_attrs["thermal_params"]
num_frozen_phonon_configs_per_subset = \
thermal_params.core_attrs["num_frozen_phonon_configs_per_subset"]
num_subsets = \
thermal_params.core_attrs["num_subsets"]
filenames = tuple((path_to_potential_slices
+ "/potential_slices_of_subset_{}.h5".format(idx))
for idx in range(num_subsets))
# See the documentation for the class
# :class:`prismatique.sample.PotentialSliceSubsetIDs` for a description of
# its construction parameters and how they relate to specifying
# precalculated potential slices.
discretization_params = \
sample_model_params.core_attrs["discretization_params"]
interpolation_factors = \
discretization_params.core_attrs["interpolation_factors"]
kwargs = \
{"filenames": filenames,
"interpolation_factors": interpolation_factors,
"max_num_frozen_phonon_configs_per_subset": \
num_frozen_phonon_configs_per_subset}
sample_specification = \
prismatique.sample.PotentialSliceSubsetIDs(**kwargs)
# Lastly, we use the potential slices and the parameters loaded above to
# perform the HRTEM simulation. See the documentation for the function
# :func:`prismatique.hrtem.sim.run` for a discussion on the input parameters
# of said function.
new_core_attr_subset_candidate = {"sample_specification": \
sample_specification}
hrtem_system_model_params.update(new_core_attr_subset_candidate)
new_core_attr_subset_candidate = {"hrtem_system_model_params": \
hrtem_system_model_params}
hrtem_sim_params.update(new_core_attr_subset_candidate)
msg = "Running the HRTEM simulation for the MoS2 sample..."
print(msg)
print()
prismatique.hrtem.sim.run(sim_params=hrtem_sim_params)
except:
# Could not find valid potential slices to load, hence we perform the HRTEM
# simulation from scratch using the sample model parameters.
new_core_attr_subset_candidate = {"sample_specification": \
sample_model_params}
hrtem_system_model_params.update(new_core_attr_subset_candidate)
new_core_attr_subset_candidate = {"hrtem_system_model_params": \
hrtem_system_model_params}
hrtem_sim_params.update(new_core_attr_subset_candidate)
prismatique.hrtem.sim.run(sim_params=hrtem_sim_params)
output_params = hrtem_sim_params.core_attrs["output_params"]
output_dirname = output_params.core_attrs["output_dirname"]
msg = ("Finished the HRTEM simulation for the MoS2 sample: all output files "
"were saved in the directory {}.".format(output_dirname))
print(msg)
print()