sage_lib
Overview
sage_lib is a versatile library designed for advanced scientific computations and visualization. It enables users to process atomic structures, perform thermodynamic analyses, generate band structures, and handle various tasks commonly required in quantum mechanical and molecular dynamics studies. The primary focus of this library is to simplify complex workflows, enabling researchers to conduct simulations, generate graphical representations, and export data in multiple formats with ease.
Features
Atomic Position Export: Converts atomic position files from one format to another, making data compatible with different simulation tools or visualization software.
Plot Generation: Generates plots based on simulation data, such as band structures or molecular arrangements. This includes support for visualizing results from popular tools like VASP.
Thermodynamic Analysis: Provides methods to calculate thermodynamic properties based on ab initio data. This includes phase diagrams, ensemble analysis, and more.
Blender Integration for Rendering: Uses Blender to render atomic structures and molecular arrangements. Supports customization like resolution, camera angles, and the addition of fog effects.
Dynamic Molecular Analysis: Analyzes molecular dynamics data, tracking species counts, evaluating force fields, and computing properties such as diffusion coefficients and bond distances.
Configuration Generation and Editing: Reads atomic structures and configurations, applies specified editing operations, and exports new structures. This includes operations like creating supercells, rattling atomic positions, and applying compressions.
Solvent Environment Generation: Creates a solvent environment around a given molecular or atomic structure, supporting various solvents and configurations to simulate realistic environments.
Dimer Search and Analysis: Facilitates dimer search to analyze interactions between specific pairs of atoms, which is useful for studying catalytic activity and other atomic-scale interactions.
Surface Disassembly: Generates configurations that allow the disassembly of surfaces, which is particularly useful for understanding surface stability and catalysis.
Customizable File Management: Provides functionalities for handling, reading, and exporting files in different formats including VASP, XYZ, and others.
Installation
To install sage_lib, use the following command:
pip install sage_lib
Ensure that you have Python 3.7 or higher.
Usage
sage_lib can be used from the command line or programmatically.
Command Line Usage
The library includes a console command sage which can be used to execute various subcommands:
sage export --path ./data --source VASP --output_path ./converted --output_source PDB
This command will convert atomic position files from VASP format to PDB format, saving the output in the ./converted directory.
Another example for generating a plot:
sage plot --path ./data --plot bands --fermi 5.0 --output_path ./plots
This command generates a band structure plot using the data found in the specified directory.
Programmatic Usage
Below is a Python example that demonstrates how to use sage_lib programmatically:
from sage_lib.partition import Partition
# Initialize a Partition object
PT = Partition(path='./data')
# Read files from a specified location
PT.read_files(file_location='./data', source='VASP', verbose=True)
# Export files in a different format
PT.export_files(file_location='./output', source='PDB', verbose=True)
This example initializes a Partition object, reads files from a directory, and exports them to a different format.
Dependencies
sage_lib requires the following packages:
numpy: for numerical operations
matplotlib: for plotting and visualization
scipy: for scientific computations
imageio: for managing image files
Optional dependencies include:
pytest: for testing
flake8: for code linting
sphinx: for generating documentation
License
sage_lib is licensed under the MIT License. For more details, refer to the LICENSE file.
Contributing
Contributions are welcome! Please feel free to open an issue or a pull request on the GitHub repository to contribute to the project.
Contact
For questions, please contact the author via email: lombardi@fhi-berlin.mpg.de
For bug reports or feature requests, visit the issues page.
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"description": "sage_lib\n\nOverview\n\nsage_lib is a versatile library designed for advanced scientific computations and visualization. It enables users to process atomic structures, perform thermodynamic analyses, generate band structures, and handle various tasks commonly required in quantum mechanical and molecular dynamics studies. The primary focus of this library is to simplify complex workflows, enabling researchers to conduct simulations, generate graphical representations, and export data in multiple formats with ease.\n\nFeatures\n\nAtomic Position Export: Converts atomic position files from one format to another, making data compatible with different simulation tools or visualization software.\n\nPlot Generation: Generates plots based on simulation data, such as band structures or molecular arrangements. This includes support for visualizing results from popular tools like VASP.\n\nThermodynamic Analysis: Provides methods to calculate thermodynamic properties based on ab initio data. This includes phase diagrams, ensemble analysis, and more.\n\nBlender Integration for Rendering: Uses Blender to render atomic structures and molecular arrangements. Supports customization like resolution, camera angles, and the addition of fog effects.\n\nDynamic Molecular Analysis: Analyzes molecular dynamics data, tracking species counts, evaluating force fields, and computing properties such as diffusion coefficients and bond distances.\n\nConfiguration Generation and Editing: Reads atomic structures and configurations, applies specified editing operations, and exports new structures. This includes operations like creating supercells, rattling atomic positions, and applying compressions.\n\nSolvent Environment Generation: Creates a solvent environment around a given molecular or atomic structure, supporting various solvents and configurations to simulate realistic environments.\n\nDimer Search and Analysis: Facilitates dimer search to analyze interactions between specific pairs of atoms, which is useful for studying catalytic activity and other atomic-scale interactions.\n\nSurface Disassembly: Generates configurations that allow the disassembly of surfaces, which is particularly useful for understanding surface stability and catalysis.\n\nCustomizable File Management: Provides functionalities for handling, reading, and exporting files in different formats including VASP, XYZ, and others.\n\nInstallation\n\nTo install sage_lib, use the following command:\n\npip install sage_lib\n\nEnsure that you have Python 3.7 or higher.\n\nUsage\n\nsage_lib can be used from the command line or programmatically.\n\nCommand Line Usage\n\nThe library includes a console command sage which can be used to execute various subcommands:\n\nsage export --path ./data --source VASP --output_path ./converted --output_source PDB\n\nThis command will convert atomic position files from VASP format to PDB format, saving the output in the ./converted directory.\n\nAnother example for generating a plot:\n\nsage plot --path ./data --plot bands --fermi 5.0 --output_path ./plots\n\nThis command generates a band structure plot using the data found in the specified directory.\n\nProgrammatic Usage\n\nBelow is a Python example that demonstrates how to use sage_lib programmatically:\n\nfrom sage_lib.partition import Partition\n\n# Initialize a Partition object\nPT = Partition(path='./data')\n\n# Read files from a specified location\nPT.read_files(file_location='./data', source='VASP', verbose=True)\n\n# Export files in a different format\nPT.export_files(file_location='./output', source='PDB', verbose=True)\n\nThis example initializes a Partition object, reads files from a directory, and exports them to a different format.\n\nDependencies\n\nsage_lib requires the following packages:\n\nnumpy: for numerical operations\n\nmatplotlib: for plotting and visualization\n\nscipy: for scientific computations\n\nimageio: for managing image files\n\nOptional dependencies include:\n\npytest: for testing\n\nflake8: for code linting\n\nsphinx: for generating documentation\n\nLicense\n\nsage_lib is licensed under the MIT License. For more details, refer to the LICENSE file.\n\nContributing\n\nContributions are welcome! Please feel free to open an issue or a pull request on the GitHub repository to contribute to the project.\n\nContact\n\nFor questions, please contact the author via email: lombardi@fhi-berlin.mpg.de\n\nFor bug reports or feature requests, visit the issues page.\n\n",
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