findtde 1.0.3__tar.gz

findtde-1.0.3/LICENSE

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+MIT License
+
+Copyright (c) 2023 Alexander Hauck
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

findtde-1.0.3/PKG-INFO

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+Metadata-Version: 2.1
+Name: findtde
+Version: 1.0.3
+Summary: Set of scripts to facilitate easy calculations of threshold displacement energies for materials in VASP/LAMMPS using ab initio/classical molecular dynamics.
+Author-email: Alexander Hauck <ash5615@psu.edu>
+License: MIT License
+        
+        Copyright (c) 2023 Alexander Hauck
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+        SOFTWARE.
+        
+Project-URL: Homepage, https://findTDE.readthedocs.io/en/latest/
+Project-URL: Repository, https://github.com/hauck-as/findTDE
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.6
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: requests
+Requires-Dist: importlib-metadata; python_version < "3.12"
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: matplotlib
+Requires-Dist: plotly
+Requires-Dist: pymatgen
+Requires-Dist: fortranformat
+
+# findTDE
+`findTDE` comprises a set of scripts to facilitate easy, high-throughput calculations of threshold displacement energies (TDEs) for materials using ab initio/classical molecular dynamics in `VASP`/`LAMMPS`. The threshold displacement energy is the minimum kinetic energy transfer from incident radiation to a lattice atom that produces a permanent defect. This property is useful for understanding the radiation hardness of a material, and it is a required parameter for binary collision approximation calculations (e.g., SRIM/TRIM).
+
+## Installation
+Currently, there is no automatic installation method available. The files may be either downloaded manually or using `git clone`.
+
+## Usage
+The find_tde script may be called directly from the command line with several options. The usage may be displayed using the help (-h) option. The convergence mode (-c) determines how subsequent kinetic energy values are chosen for the displacement event, either "standard" (adjust by 5 eV until opposite defect generation is found, then adjust by 1 eV until the TDE is found) or "midpoint" (adjust by 8 eV until opposite defect generation is found, then adjust by half the distance from the current energy to the nearest energy of opposite defect generation). The program selection (-p) chooses whether `VASP` or `LAMMPS` is used for the calculations. If `LAMMPS` is used, the force field file may be chosen (-f).
+
+```bash
+find_tde [-h] [-c <standard|midpoint>] [-p <vasp|lammps>] [-f <lmp_ff.type>]
+```
+
+The script is currently written to execute via `Slurm` workload manager. This can be adjusted temporarily to execute the appropriate program. 
+
+The script relies on a directory structure. Only the base directory (e.g., "project," can be named anything), main input file ("latt_dirs_to_calc.csv"), inputs directory ("inp"), and perfect supercell directory ("perfect") are required to be made and named as described. `findTDE` should be executed in the "project" directory. Each "displacement" directory, associated "energy" directories, and relevant .csv/.txt files are created by the program.
+
+```
+project
+│   latt_dirs_to_calc.csv   
+│
+└───displacement1
+│   │   displacement1_data.csv
+│   │   displacement1_out.txt
+│   │   KE_calcs_list.txt
+│   │
+│   └───energyA
+│   |   │   program_inputs
+│   |   │   program_outputs
+│   |   │   ...
+│   │
+│   └───energyB
+│   |   │   program_inputs
+│   |   │   program_outputs
+│   |   │   ...
+│   │
+│   └───...
+│
+└───...
+│   
+└───inp
+│   │   INCAR_cgm
+│   │   INCAR_md
+│   │   KPOINTS
+│   │   POSCAR
+│   │   POTCAR
+│   │   lmp_ff.type
+│   │   ...
+│   
+└───perfect
+|   │   OUTCAR
+```
+
+The input file "latt_dirs_to_calc.csv" is required to specify the displacement event. This can either be created manually, or by using the `multi_tde.py` accessory script. The heading of this file may be used to describe the file format. The bottom row of the file is read when `findTDE` is executed, and that info is used for that TDE calculation. The first value is a "pseudo" to correspond to the displacement direction, given as an integer number (changes with each unique direction) and either "L" or "S" (describes whether the direction is given as a lattice direction \[u v w\] or spherical direction (rho, phi, theta)). The "atom_type" and "atom_number" detail which atom in the supercell is given the velocity vector to simulate the displacement event (e.g., atom_type: ga and atom_number: 34 corresponds to the 34th Ga atom, as listed in the POSCAR file, being displaced). The initial kinetic energy "ke_i" and cutoff kinetic energy "ke_cut" (stops the program if a defect is not found below this kinetic energy) are then defined. The direction is then defined, either using lattice direction integer notation or spherical coordinate notation (may be floats).
+
+```
+########################################
+# format of text file
+# nL    atom_type    atom_number    ke_i    ke_cut    u    v    w
+# n+1S    atom_type    atom_number    ke_i    ke_cut    r    p    t
+########################################
+```
+
+## Acknowledgements
+The findTDE code was developed by Alexander Hauck, Dr. Mia Jin, and Dr. Blair Tuttle at The Pennsylvania State University.

findtde-1.0.3/README.md

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+# findTDE
+`findTDE` comprises a set of scripts to facilitate easy, high-throughput calculations of threshold displacement energies (TDEs) for materials using ab initio/classical molecular dynamics in `VASP`/`LAMMPS`. The threshold displacement energy is the minimum kinetic energy transfer from incident radiation to a lattice atom that produces a permanent defect. This property is useful for understanding the radiation hardness of a material, and it is a required parameter for binary collision approximation calculations (e.g., SRIM/TRIM).
+
+## Installation
+Currently, there is no automatic installation method available. The files may be either downloaded manually or using `git clone`.
+
+## Usage
+The find_tde script may be called directly from the command line with several options. The usage may be displayed using the help (-h) option. The convergence mode (-c) determines how subsequent kinetic energy values are chosen for the displacement event, either "standard" (adjust by 5 eV until opposite defect generation is found, then adjust by 1 eV until the TDE is found) or "midpoint" (adjust by 8 eV until opposite defect generation is found, then adjust by half the distance from the current energy to the nearest energy of opposite defect generation). The program selection (-p) chooses whether `VASP` or `LAMMPS` is used for the calculations. If `LAMMPS` is used, the force field file may be chosen (-f).
+
+```bash
+find_tde [-h] [-c <standard|midpoint>] [-p <vasp|lammps>] [-f <lmp_ff.type>]
+```
+
+The script is currently written to execute via `Slurm` workload manager. This can be adjusted temporarily to execute the appropriate program. 
+
+The script relies on a directory structure. Only the base directory (e.g., "project," can be named anything), main input file ("latt_dirs_to_calc.csv"), inputs directory ("inp"), and perfect supercell directory ("perfect") are required to be made and named as described. `findTDE` should be executed in the "project" directory. Each "displacement" directory, associated "energy" directories, and relevant .csv/.txt files are created by the program.
+
+```
+project
+│   latt_dirs_to_calc.csv   
+│
+└───displacement1
+│   │   displacement1_data.csv
+│   │   displacement1_out.txt
+│   │   KE_calcs_list.txt
+│   │
+│   └───energyA
+│   |   │   program_inputs
+│   |   │   program_outputs
+│   |   │   ...
+│   │
+│   └───energyB
+│   |   │   program_inputs
+│   |   │   program_outputs
+│   |   │   ...
+│   │
+│   └───...
+│
+└───...
+│   
+└───inp
+│   │   INCAR_cgm
+│   │   INCAR_md
+│   │   KPOINTS
+│   │   POSCAR
+│   │   POTCAR
+│   │   lmp_ff.type
+│   │   ...
+│   
+└───perfect
+|   │   OUTCAR
+```
+
+The input file "latt_dirs_to_calc.csv" is required to specify the displacement event. This can either be created manually, or by using the `multi_tde.py` accessory script. The heading of this file may be used to describe the file format. The bottom row of the file is read when `findTDE` is executed, and that info is used for that TDE calculation. The first value is a "pseudo" to correspond to the displacement direction, given as an integer number (changes with each unique direction) and either "L" or "S" (describes whether the direction is given as a lattice direction \[u v w\] or spherical direction (rho, phi, theta)). The "atom_type" and "atom_number" detail which atom in the supercell is given the velocity vector to simulate the displacement event (e.g., atom_type: ga and atom_number: 34 corresponds to the 34th Ga atom, as listed in the POSCAR file, being displaced). The initial kinetic energy "ke_i" and cutoff kinetic energy "ke_cut" (stops the program if a defect is not found below this kinetic energy) are then defined. The direction is then defined, either using lattice direction integer notation or spherical coordinate notation (may be floats).
+
+```
+########################################
+# format of text file
+# nL    atom_type    atom_number    ke_i    ke_cut    u    v    w
+# n+1S    atom_type    atom_number    ke_i    ke_cut    r    p    t
+########################################
+```
+
+## Acknowledgements
+The findTDE code was developed by Alexander Hauck, Dr. Mia Jin, and Dr. Blair Tuttle at The Pennsylvania State University.

findtde-1.0.3/docs/conf.py

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+# Configuration file for the Sphinx documentation builder.
+# Templated from both RTD tutorial and doped by SMTG-Bham.
+
+# -- Project information
+
+project = 'findTDE'
+copyright = '2023, Alexander S. Hauck'
+author = 'Alexander S. Hauck'
+
+release = '0.1'
+version = '1.0.3'
+
+# -- General configuration
+
+extensions = [
+    'sphinx.ext.duration',
+    'sphinx.ext.doctest',
+    'sphinx.ext.autodoc',
+    'sphinx.ext.autosummary',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.coverage',
+    'sphinx.ext.napoleon',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.autosectionlabel',
+    'sphinx_book_theme',
+]
+
+intersphinx_mapping = {
+    'python': ('https://docs.python.org/3/', None),
+    'sphinx': ('https://www.sphinx-doc.org/en/master/', None),
+}
+intersphinx_disabled_domains = ['std']
+
+templates_path = ['_templates']
+
+# -- Options for HTML output
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'sphinx_book_theme'
+
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+# html_logo = "findtde-logo.png"
+html_title = "findTDE"
+
+# If true, SmartyPants will be used to convert quotes and dashes to
+# typographically correct entities.
+html_use_smartypants = True
+
+# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
+# html_show_sphinx = True
+
+html_theme_options = {
+    "repository_url": "https://github.com/hauck-as/findTDE",
+    "github_repo": "https://github.com/hauck-as/findTDE",
+    "github_button": True,
+    "github_user": "hauck-as", # Username
+    "description": "Set of scripts to facilitate easy calculations of threshold displacement energies for materials in VASP/LAMMPS using ab initio/classical molecular dynamics.",
+    "repository_branch": "main",
+    "path_to_docs": "docs",
+    "use_repository_button": True,
+    "home_page_in_toc": True,
+    "launch_buttons": {
+        "binderhub_url": "https://mybinder.org",
+        "colab_url": "https://colab.research.google.com",
+    },
+}
+
+# Adding “Edit Source” links on your Sphinx theme
+html_context = {
+    "display_github": True, # Integrate GitHub
+    "github_user": "hauck-as", # Username
+    "github_repo": "findTDE", # Repo name
+    "github_version": "main", # Version
+    "conf_py_path": "/docs/", # Path in the checkout to the docs root
+}
+
+# -- Options for EPUB output
+epub_show_urls = 'footnote'

findtde-1.0.3/findtde/__init__.py

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+# Copyright (c) 2023 Alexander Hauck. Distributed under the terms of the MIT License.
+
+"""
+findTDE comprises a set of scripts to facilitate easy, high-throughput calculations of threshold displacement energies for materials in VASP/LAMMPS using ab initio/classical molecular dynamics.
+"""
+
+__author__ = "Alexander Hauck"
+__copyright__ = "Copyright (C) 2023 Alexander Hauck"
+__license__ = "MIT License"
+__version__ = "1.0.3"

findtde-1.0.3/findtde/cli/__init__.py

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+# Copyright (c) 2024 Alexander Hauck. Distributed under the terms of the MIT License.
+
+"""
+findTDE package containing command line interfaces.
+"""