Jérôme Hénin

Smaller variant of multicol files for 3D grids (and beyond)

10

Multicol files in their current states are great in 1D and 2D because they are read seamlessly by many plotting programs. In 3D they can get quite bulky, and plotting...

Offer some way for parser to deal with spaces in file paths

2

This is particularly relevant in Windows, where user directories often have spaces in them (maybe OSX as well?). Right now, a path with spaces (say in refPositionsFile) will be detected...

This would allow for more compact files, increased performance, and no need to store zgrad files separately. Takes advantage of more flexible restart reading added recently.

Cannot create object with empty config block on single line

3

E.g. a CVC without parameters (yes that is possible now) cannot be defined as: `functionType {}` because the parser tries to interpret "}" as a keyword. So the block has...

Should we convert most parse_silent options to parse_echo ?

4

Most often those are advanced options that were silent to make them less verbose, but now that parse_echo is available it seems appropriate in a lot of places. Notable exception...

I think this happens when the last line is something else than a closing brace. Example : ``` cv config "colvarsTrajfrequency 12 \n smp off" cv getconfig ``` Gives: ```...

Lambda-ABF implementation for the NAMD interface

7

As fully documented in the [Lagardère et al. paper](https://pubs.acs.org/doi/10.1021/acs.jctc.3c01249) complements the Tinker-HP implementation, which is maintained on the [Tinker-HP repo](https://github.com/TinkerTools/tinker-hp). TODO - [x] Regression tests - [x] Document current limitations...

Protein-specific coordinates based on index groups

2

The goal is to make the alpha_angles CVC (and dihedralPC) available on all back-ends. TODO: - [x] allow for series of groups to describe non-contiguous alpha segments - [x] extend...

Will become relevant when https://gitlab.com/gromacs/gromacs/-/merge_requests/3955 is merged.

CTest coverage reporting

1

I am trying to get CTest coverage reporting to work for our unit/functional tests, but no success so far. I've had to add `include(CTest)` to the make CMakeLists.txt. Then enabling...