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Adds a CREST TS search adapter for finding transition state conformers, leveraging heuristics-generated guesses and CREST's conformer search capabilities. This allows ARC to explore TS geometries using CREST. Adds method source to TS guesses from CREST Ensures CREST is recorded as a method source when a TS guess from CREST is deemed unique and considered as a possible TS guess. This change ensures proper provenance tracking for TS guesses. Improves error logging in CREST adapter Enhances error messages in the CREST adapter to provide more context when failing to determine H abstraction atoms. The error message now includes the reaction label and crest seed iteration number, which aids in debugging. Improves CREST TS search robustness Addresses potential errors in CREST TS searches by: - Preventing crashes due to missing digits in atom labels by raising a ValueError if `extract_digits` fails to find digits. - Handling cases where no H-abstraction atoms can be determined from the distance matrix, preventing related errors and skipping the corresponding seed. - Removes unused local_path argument from h_abstraction function
Adds a script to install CREST using a dedicated conda environment. Integrates CREST into the `install_all.sh` script and the help message. Also adds a `--no-rmg` flag in `install_all.sh` to optionally skip RMG-Py installation, and ensures PyRDL is installed only when ARC is installed. Corrects a problem with the AutoTST activation/deactivation hooks and ensures that RMG-Py's path is correctly removed from the PATH and PYTHONPATH. Also ensures TS-GCN can be correctly installed into its environment. Sanitizes paths for AutoTST hook activation Ensures that paths containing special characters are properly escaped when writing the AutoTST activation hook. This prevents issues with the hook failing to activate correctly when the AutoTST repository or current working directory contain characters that are interpreted specially by the shell.
Adds the CREST adapter as an option for transition state (TS) guess generation, particularly for H_Abstraction reactions, improving the exploration of potential TS geometries. Includes CREST in the default list of in-core adapters and allows it to be used in heuristics. The heuristic adapter now passes the local path of the files to the h_abstraction method so the geometries are saved to the appropriate folders. Saves the method used to generate the TS guesses in the file name so the geometries generated with CREST are clearly labeled as such. Refactors TS guess method source handling Updates TS guess generation to correctly handle multiple method sources. Specifically, it normalizes the method sources for TS guesses by aggregating method labels. Also, removes the unused `path` argument from the `h_abstraction` function, streamlining the H_Abstraction TS guess generation.
Adds a function to reorder XYZ strings between atom-first and coordinate-first formats, with optional unit conversion. Also introduces a backward compatible wrapper with a deprecation warning. Uses constants for unit conversion factors Replaces hardcoded unit conversion factors with values from the `constants` module. Also, determines atom ordering more robustly by inspecting only the first line. Corrects angstrom to bohr conversion factor The conversion factor between angstrom and bohr was inverted, which led to incorrect geometry conversions. This commit corrects the conversion factor to ensure proper unit conversion when dealing with xyz coordinates.
Removes input files and submit script related to a specific server time limit test case. The `err.txt` file is renamed to `wall_exceeded.txt` and moved to the `trsh` folder.
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Enables the usage of CREST as a TS adapter. The implementation includes: - Adding 'crest' to the list of available TS adapters. - Implementing a function to automatically detect the CREST executable in various locations (standalone builds, conda environments, PATH). - Providing instructions for activating the CREST environment, if necessary. This allows ARC to leverage CREST for enhanced transition state search capabilities. Improves crest executable search logic Refactors the crest executable search to more reliably locate the correct version by normalizing path joining. Updates the documentation for clarity. Makes crest standalone directory configurable Allows users to configure the directory where standalone crest builds are located. This enables greater flexibility in managing crest installations, especially in environments where the default location (/Local/ce_dana) is not suitable. Exports all settings variables Makes all settings variables available for import in other modules, which is needed by the CREST adapter.
Adds a `method_sources` attribute to the `TSGuess` class to track all methods/sources that generated a particular transition state guess, allowing for more comprehensive provenance information. This improves the clustering of similar TS guesses. Normalizes method sources to a unique, ordered, lowercase list.
Adds the angstrom to bohr conversion factor. This conversion factor is required for the CREST adapter.
Introduces a function to generate unique project names for parallel test execution using xdist. This prevents collisions when cleaning up project directories, ensuring reliable test execution.
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Addition of CREST Adapter that complements the heuristic adapter.
This pull request adds support for the CREST conformer and transition state (TS) search method to the ARC project, along with several related improvements and code cleanups. The most important changes include integrating CREST as a TS search adapter, updating configuration and constants, and enhancing the heuristics TS search logic for better provenance tracking and code clarity.
CREST Integration:
JobEnum(arc/job/adapter.py), included CREST in the list of adapters and RMG family mapping, and registered it as a default incore adapter (arc/job/adapters/common.py,arc/job/adapters/ts/__init__.py). [1] [2] [3] [4]arc/job/adapters/ts/crest_test.py).Makefile). [1] [2]Constants and Configuration:
angstrom_to_bohrconversion constant to both Cython and Python constants modules (arc/constants.pxd,arc/constants.py). [1] [2] [3]Heuristics TS Search Enhancements and Refactoring:
arc/job/adapters/ts/heuristics.py). [1] [2] [3] [4]arc/job/adapters/ts/heuristics.py). [1] [2] [3] [4] [5] [6] [7].