Jérôme Hénin

Reorganize Colvars repo tree

1

The root level contains a large number of directories that play different roles. Some directories, like python and C_fortran contain only experimental features. One of the goals would be making...

Replaces the Tcl script. Generalizes to all supported MD engines.

cv save changes prefix for future output

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From the name and the documentation, I expect "cv save" to save files to the given prefix when called, with no further side effects. In practice, it changes the file...

Create abf::setup_output() for consistency

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Partial response to #683

- save replica-local ABF data to restart file - simplify CZAR data sharing by not taking deltas (useless) and summing complete data from each replica instead Fixes #685

The new scheme that tracks per-replica data does not treat local vs. global data correctly, leading to the wrong state upon restart.

Add Colvars logo

1

Right now, just the source files. We might want to include it in the doc itself eventually.

Mix of shared and raw pointers caused double deallocation upon exit. This only affected the poisson_integrator standalone tool.

Now that Colvars has access to the multisim communicator in GROMACS, mwABF is possible in principle, however it had not been tested with the current code base. I disabled an...

Ability to define custom grid in ABF biases

3

This creates a new keyword, `gridParameters`, which mimics `histogramGrid` within a histogram bias. In the process, unify both keywords under the new name and deprecate `histogramGrid`. See Issue #476 TODO:...