Update tutorial/docs, improve C++ error handling, and fix Kokkos types

[DavidW99]

This pull request introduces several improvements across the documentation, Python, and C++/Kokkos codebases for FLARE. The changes include updating documentation and installation instructions, improving error handling in the LAMMPS plugin C++ code, and correcting data types for Kokkos compatibility. Additionally, there are minor bug fixes and code cleanups.

Documentation and Installation Updates:

• Updated installation instructions to use Python 3.10 and GCC 11, removed the requirement to clone the development branch, and updated example paths to reflect Python 3.10. [1] [2] [3] [4]
• Revised tutorial links and descriptions in colabs.rst, updating the main FLARE tutorial and improving clarity.

LAMMPS Plugin and C++ Improvements:

• Added error handling for file reading in the LAMMPS plugin C++ code, ensuring errors on unexpected end-of-file conditions. [1] [2] [3] [4] [5] [6] [7]

Kokkos Codebase Corrections:

• Updated Kokkos floating-point types including from X_FLOAT/F_FLOAT to KK_FLOAT/KK_ACC_FLOAT throughout the Kokkos pair potential implementation. [1] [2] [3] [4] [5] [6] [7] [8]

Python Code Fixes:

• Fixed handling of model_post and compute commands in flare/md/lammps.py to use lists consistently, preventing string concatenation bugs. Also, corrected the expected type for the velocity parameter for ASE LAMMPS calculator. [1] [2]
• Corrected a typo in a comment from "intialize" to "initialize" in flare/scripts/otf_train.py.

Workflow Simplification:

• Removed a patch step for ASE in the GitHub Actions workflow.

[Copilot]

Pull request overview

This pull request enhances the FLARE codebase with comprehensive improvements across documentation, C++ LAMMPS plugins, Kokkos implementations, and Python code. The changes focus on updating installation requirements, improving error handling in file I/O operations, modernizing Kokkos type definitions, and fixing several bugs in Python code.

Changes:

• Updated installation documentation to use Python 3.10 and GCC 11, and removed the development branch requirement
• Added comprehensive error handling for file reading operations in LAMMPS C++ plugins with NULL checks on fgets() calls
• Migrated Kokkos code from deprecated float types (X_FLOAT, F_FLOAT, E_FLOAT) to modern types (KK_FLOAT, KK_ACC_FLOAT)
• Fixed Python bugs in LAMMPS calculator related to list/string type handling and corrected sscanf pointer usage in C++ code

Reviewed changes

Copilot reviewed 14 out of 14 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
tests/test_mgp.py	Moved pytest skip check from decorator to inside fixture body for better clarity
tests/test_lammps.py	Corrected velocity parameter type from list to string to match ASE LAMMPS API
lammps_plugins/pair_mgp.cpp	Added NULL checks for fgets() calls and fixed sscanf char array pointer usage
lammps_plugins/pair_flare.cpp	Added NULL checks for fgets() calls and fixed sscanf char array pointer usage
lammps_plugins/compute_flare_std_atom.cpp	Added comprehensive error handling for file reading operations
lammps_plugins/kokkos/pair_mgp_kokkos.h	Updated type definitions from F_FLOAT/E_FLOAT to KK_FLOAT/KK_ACC_FLOAT
lammps_plugins/kokkos/pair_mgp_kokkos.cpp	Replaced all deprecated Kokkos float types with modern equivalents
lammps_plugins/kokkos/pair_flare_kokkos.h	Updated Kokkos type definitions and view types
lammps_plugins/kokkos/pair_flare_kokkos.cpp	Migrated to KK_FLOAT and KK_ACC_FLOAT throughout
flare/scripts/otf_train.py	Fixed typo: "intialize" → "initialize"
flare/md/lammps.py	Fixed model_post list append operations and velocity parameter type
docs/source/tutorials/colabs.rst	Updated main tutorial link and description
docs/source/installation/install.rst	Updated Python version examples from 3.8 to 3.10
.github/workflows/flare.yml	Updated to GCC 11 and removed ASE patch step

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