This will stay distinct from nonequilibrium-gilsonlabucsd
, which should remain
as the "publicly" available version of the code.
nonequilibrium-master
on local.Inside nonequilibrium-master/
create...
manuscript
for files from nonequilibrium-manuscript
. These are similar to -- but not exactly the same as -- the files in nonequilibrium-gilsonlabucsd
. They contain additional explorations that did not make it into the final manuscript. Now this is in code/
, copied there using rsync -au
literature
for files from nonequilibrium-literature-review
. These are
Markdown files with associated build CI build scripts modeled after
deep-review
.
explorations
for files from nonequilibrium/nonequilibrium-explorations
.
These contain notebooks for PDB searching and achiral to chiral transitions.
md-data
for the raw simulation data (excluding trajectories, which are stored in large-file-storage
on Kirkwood and GPFS).
code
filled with nonequilibrium/code/SG-model-v2
, nonequilibrium/code/torsion-individual
, and nonequilibrium/code/torque-scans
copied with rsync -au
.
Now, there needs to be a good way to store the code. There is code from the manuscript, and code from just before making the manuscript, and then much older code.
There are still several side projects that could be merged:
torsion-individual
that...torsion-scan
that ...shiny
web app