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doc: fix errors in the reference manual - #995
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- Close an itemize that was opened before the "Histogramming vector variables" subsubsection and closed after it - gatherVectorColvars is a boolean (was documented as a UNIX filename); remove an unmatched parenthesis in its description - Fix the link to the metadynamics section (wrong label sec:colvarbias_metadynamics) and use \hyperref for links to section labels - Add the missing first argument of a \refkey (its link target was ".") - Merge math expressions that were split across several $...$ - Guard references to sec:apath_scripted with \cvvmdornamd, like the section itself (they were dangling in the Tinker-HP manual) - Use straight quotes in comments of example input - Escape & in a BibTeX publisher field [update-doc] Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
giacomofiorin
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Nov 9, 2026
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I stacked this PR with #997 and added a small fix that got overlooked because we have unrelated CI failures |
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Fixes found while building the manual with LaTeXML (#996). All of them also apply to the PDF.
itemizenesting: anitemizewas opened before the "Histogramming vector variables" subsubsection and closed after it.gatherVectorColvars: documented type was "UNIX filename", should be boolean; removed an unmatched)in its description.sec:colvarbias_metadynamics, which doesn't exist (the label issec:colvarbias_meta). Links to section labels now use\hyperref[...]instead of\hyperlink.\refkeymissing an argument (layeri_activation): the following.was used as the link target.$f(\xi_{1}$, $\xi_{2}$, \ldots $)$and similar are now single formulas.sec:apath_scriptedwere guarded by\cvscriptcallbacks, but the section only exists with\cvvmdornamd, so they were dangling. Both now use\cvvmdornamd.``charge''→"charge").colvars-code-refs.bib: escaped&in a publisher field.Tested: the NAMD and Tinker-HP PDFs build with no errors or undefined references.
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