Small patches in various packages

[jtclemm]

Summary

Patches various little bugs in various packages. Still hoping to add a few more before merging.

Related Issue(s)

Closes #4727 and closes #4730 and closes #4752

Author(s)

Dan Bolintineanu & Joel Clemmer (SNL) & Axel Kohlmeyer(Temple U)

Licensing

By submitting this pull request, I agree, that my contribution will be included in LAMMPS and redistributed under either the GNU General Public License version 2 (GPL v2) or the GNU Lesser General Public License version 2.1 (LGPL v2.1).

[akohlmey]

@jtclemm Just adding this comment as a reminder that we should backport the fixes in this pull request to the maintenance branch.

[akohlmey]

@jtclemm since this has been sitting for a while, it may be better to check and merge this right away and - if needed - start another PR. I've been following this strategy with my own collections so they won't pick up too many changes, since after going from draft to reviewable there is the delay of actually getting a review these days.

P.S.: also, I am eager to backport the bugfixes to the maintenance branch before it gets too convoluted and complex. ;-)

[jtclemm]

@jtclemm since this has been sitting for a while, it may be better to check and merge this right away and - if needed - start another PR. I've been following this strategy with my own collections so they won't pick up too many changes, since after going from draft to reviewable there is the delay of actually getting a review these days.

P.S.: also, I am eager to backport the bugfixes to the maintenance branch before it gets too convoluted and complex. ;-)

Makes sense, I just pushed a final patch and it should be good now.

[Copilot]

Pull Request Overview

This PR applies bug fixes and corrections across multiple LAMMPS packages (RHEO, GRANULAR, EXTRA-FIX) and their documentation. The changes address thermal conductivity calculations, neighbor list cutoff computations, array memory allocation, and documentation errors.

Key changes:

• Fixed thermal conductivity formulation in RHEO package to use thermal diffusivity instead of conductivity directly
• Corrected neighbor list cutoff calculation in granular pair style to account for frozen particle radii
• Fixed array memory allocation bug in fix_nonaffine_displacement

Reviewed Changes

Copilot reviewed 15 out of 15 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
src/RHEO/pair_rheo.h	Adds fix_thermal pointer for thermal property access
src/RHEO/pair_rheo.cpp	Refactors thermal evolution to use thermal diffusivity; fixes volume factor errors in force calculations
src/RHEO/fix_rheo_thermal.cpp	Corrects error message to reference correct fix name
src/RHEO/fix_rheo_pressure.cpp	Fixes argument index in error message
src/GRANULAR/pair_granular.cpp	Adds missing frozen particle radius terms to cutoff calculation
src/EXTRA-FIX/fix_nonaffine_displacement.cpp	Fixes array allocation size and adds zero initialization for inactive mode
src/EXTRA-FIX/fix_deform_pressure.cpp	Removes redundant NONE check from strain_flag logic
examples/rheo/ice-cubes/*	Updates example log files and input parameters
doc/src/pair_granular.rst	Corrects typo "normal normals" to "normal models"
doc/src/fix_rheo_thermal.rst	Corrects conductivity units documentation
doc/src/fix_rheo_pressure.rst	Removes trailing period from equation
doc/src/fix_nonaffine_displacement.rst	Adds missing "nevery" parameter to syntax
doc/src/bond_bpm_spring_plastic.rst	Adds subscript formatting to equilibrium length notation