[aalhossary]

Description

KENREF needs whole molecules: it fits all GUIDE_ATOMS at once, and the pair distances have no cutoff. KEnRef (≥ 2.0.0) already does the setup work. It builds a spanning tree over the reference structure and defines makeRequestedAtomsWhole(), which moves each requested atom to the periodic image nearest its tree parent. Nothing called it, though. getGuideAtomsX() and fillSubAtomsX() read getPositions() directly, so on a molecule split across the box, KEnRef's split check stopped the run.

This PR makes three small changes to src/kenref/KEnRefBias.cpp:

• getLocalModelX() calls makeRequestedAtomsWhole() first;
• getGuideAtomsX() and fillSubAtomsX() read the repaired positions.

It also adds a paragraph to the KENREF documentation and a note in module.md. For builds of master made before this change, the note shows the MOLINFO ... WHOLE + WHOLEMOLECULES workaround.

Effect:

• Coordinates that are already whole are left unchanged, bit for bit.
• A reference that is itself split is refused. The tree then has an edge at least half the smallest box width, and KEnRef stops with an error naming the reference.

The declarations come from KEnRef's KEnRefBias.h, so this needs KEnRef ≥ 2.0.0. That is already the floor in configure.ac (KENREF_MIN_VERSION). v2.0.0 has both functions, and so do v2.0.1 and KEnRef master, the default for KENREF_GIT_TAG.

A second commit moves CI from KEnRef v2.0.0 to v2.0.1 (.ci/install.kenref), its newest release. The changes since v2.0.0 are all in KEnRef's GROMACS interface. The workflow resolves the tag to its commit for the cache key, so the cached v2.0.0 prefix is not reused.

New regtest rt-kenref-sigma-torn. It uses the GB3 fragment of rt-kenref-sigma, with residue 3 moved by −b and residue 5 by +a. The torn frame must give the same colvar and forces as the whole one, within 1e-6; the measured difference is ≤ 1e-11. The frames are .xyz rather than .pdb, because --mf_pdb stores single-precision coordinates. Without this change, the test fails (KEnRef refuses the split structure).

Checked locally against KEnRef v2.0.0 (1dccb2d):

case	without this PR	with it
torn GB3 frame (KEnRef's rt_validate_plumed.sh), no MOLINFO/WHOLEMOLECULES	refused by the split check	E0 = 3.65155e-05, the GROMACS value; same as MOLINFO WHOLE + WHOLEMOLECULES (forces within 1e-10)
whole ubiquitin	7.18869e-08	7.18869e-08, forces byte-identical to without
split reference	refused by the split check	refused by the reference check (longest edge 31.49 Å, half box 30.61 Å)
--debug-dd on 2 and 4 ranks, GB3 and ubiquitin		forces byte-identical to serial
--multi 2, 2 ranks per replica vs 1		forces byte-identical
regtest/kenref (4 tests)		pass

Prepared with the help of Claude.

Target release

I would like my code to appear in release 2.11 (master). v2.10 does not have the kenref module.

Type of contribution

• changes to code or doc authored by PLUMED developers, or additions of code in the core or within the default modules
• changes to a module not authored by you
• new module contribution or edit of a module authored by you

Copyright

• the module I added or modified contains a COPYRIGHT file with the correct license information. Code should be released under an open source license. I also used the command cd src && ./header.sh mymodulename in order to make sure the headers of the module are correct.

Tests

• I added a new regtest or modified an existing regtest to validate my changes.
• I verified that all regtests are passed successfully on GitHub Actions.