Split genbox into 'solvate' and 'insert-molecules'
authorMark Abraham <mark.j.abraham@gmail.com>
Sun, 2 Feb 2014 20:31:20 +0000 (21:31 +0100)
committerGerrit Code Review <gerrit@gerrit.gromacs.org>
Tue, 11 Feb 2014 21:18:19 +0000 (22:18 +0100)
commitfda91536f4ce962c6b62e647edb4cd58f9b2e2f6
tree45561493b718c10272c7ef59d19e680148b15ede
parentb9a814f8b39edd4206f22a28d7e0e8505d23e0ef
Split genbox into 'solvate' and 'insert-molecules'

All working old functionality is retained in new 'solvate' and
'insert-molecules' programs. Registered genbox as obsolete, so someone
using gmx genbox gets a hint, which is also triggered by the old
symlink. No new symlinks, of course. Updated all mentions of genbox in
the whole repo.

For gmx solvate:
* Cleaned up unused functions
* Cleaned up unused headers
* Cleaned up useless command-line options
* Updated documentation
* Checked that its behaviour for writing velocities is OK (but there's
  no good way to test that)

For gmx insert-molecules:
* Cleaned up unused functions
* Cleaned up unused headers
* Cleaned up useless command-line options
* Updated documentation
* Added tests, worked out that -vdwd and spc216.gro were not required
  for a decent test and updated accordingly
* Renamed -cs to -f for consistency with other tools. It would be nice
  to have a hidden fallback so that -cs does the right thing, but the
  machinery does not exist.
* Added helpful check now that -ci is required (generic file I/O error
  previously)
* Fixed bug with gmx insert-molecules -ci and velocities. Old version
  would dereference v pointer because the insertion function does not
  return velocities for the inserted molecules.

Split the respective test cases into separate compilation
units. Consolidated functions called by both new tools into
read-conformation.[ch]. The naming and use of those functions are
horrendous, and will be fixed in the next patch.

genbox-addconf.[ch] is no longer specific to any tool, so renamed it
back to addconf.[ch].

Change-Id: I7781c3db189f5d95d5731e4e86cc0585f7d677c7
16 files changed:
share/html/online/flow.html
share/html/online/getting_started.html
src/gromacs/gmxana/gmx_genion.c
src/gromacs/gmxpreprocess/addconf.c [moved from src/gromacs/gmxpreprocess/genbox-addconf.c with 99% similarity]
src/gromacs/gmxpreprocess/addconf.h [moved from src/gromacs/gmxpreprocess/genbox-addconf.h with 96% similarity]
src/gromacs/gmxpreprocess/insert-molecules.cpp [new file with mode: 0644]
src/gromacs/gmxpreprocess/insert-molecules.h [new file with mode: 0644]
src/gromacs/gmxpreprocess/read-conformation.cpp [new file with mode: 0644]
src/gromacs/gmxpreprocess/read-conformation.h [new file with mode: 0644]
src/gromacs/gmxpreprocess/solvate.cpp [moved from src/gromacs/gmxpreprocess/genbox.cpp with 65% similarity]
src/gromacs/gmxpreprocess/solvate.h [moved from src/gromacs/gmxpreprocess/genbox.h with 94% similarity]
src/gromacs/gmxpreprocess/tests/CMakeLists.txt
src/gromacs/gmxpreprocess/tests/insert-molecules.cpp [new file with mode: 0644]
src/gromacs/gmxpreprocess/tests/solvate.cpp [moved from src/gromacs/gmxpreprocess/tests/genbox.cpp with 74% similarity]
src/gromacs/gmxpreprocess/tests/spc216.gro [deleted file]
src/programs/legacymodules.cpp