Giacomo Fiorin

Use map of output streams, and return references to its elements

1

As mentioned in the conversation for #481, update the registry of output files to use a `std::map` rather than two paired lists, which are no longer worth using any more.

Discuss Jacobian term in the doc

3

See #367 #407 and some messages in the [NAMD](https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2020-2021/0223.html) and [LAMMPS](https://matsci.org/t/re-lammps-users-jacobian-terms-in-the-colvar-package/41288) forums. Nothing too verbose or extensive is needed: users just ought to be aware that the term is present...

Finally remove support for appending to files?

6

@HanatoK Appending to files that already exist on disk is useful in some cases, but also rather fragile (for examples, when jobs crash and are restarted). @jhenin had already removed...

Implement fit gradients for non-scalar components (see also #61)

16

These would be easily calculated if the atomic gradients were stored in the atom group. Solving issue #61 would allow to solve this easily, too. Meanwhile, a `f_cvc_fit_gradients` feature could...

Make corrFunc and runAve restartable biases

2

Currently, these are features of a `colvar`, which limits to defining only one instance of either function, and is not continued between runs, leading to not using a few frames...

Extend support for fix_modify to remaining script API commands

5

This PR extends the interface introduced in #216 while taking advantage of the scripting API enhancements from #316. The LAMMPS command `fix_modify` is used as the main command, which behaves...

Allowing custom grid definition for each bias instance

1

See #468 and links therein. The following is a list of classes that use grids, and which could be optionally be allowed to define custom grids: - [ ] `colvarbias_abf`...

Move cvm::atom member data to synchronized vectors within cvm::atom_group

11

This issue can be broken up in multiple steps: - [ ] Transform the `atom_group` class into a container for vectors of shape `xxxx...`, `yyyy...` and `zzzz...` for positions, velocities...

Clarify purpose of functions that only handle PDB files anyway

2

Coordinate loading functions are renamed to reflect that they are specific to the PDB format. Fixes #667

Better error message when trying to load coordinates from missing files

3

When loading a file that isn't XYZ the first branch of the conditional below fails, falling back to the PDB reader: https://github.com/Colvars/colvars/blob/8eb35e75c43d6f7e16d8e634e827639097d16368/src/colvarmodule.cpp#L2159-L2171 In GROMACS the resulting error message can be...