Update Colvars to version 2017-07-14 (forceNoPBC, colvars folder, cleaner interface) 90/2790/2
authorGiacomo Fiorin <giacomo.fiorin@gmail.com>
Fri, 14 Jul 2017 13:46:08 +0000 (09:46 -0400)
committerGiacomo Fiorin <giacomo.fiorin@gmail.com>
Fri, 14 Jul 2017 20:29:34 +0000 (16:29 -0400)
commit9fc81a31c3fa26df98bb3e77e1a0391928fe3443
treee18c7cdc8fd9b0c791d2d42dfc139a38857119f4
parentb3379089d8fc5474cfbc2c7ef51c54f56cfb6d29
Update Colvars to version 2017-07-14 (forceNoPBC, colvars folder, cleaner interface)

This is primarily a maintenance update, including several changes:

- All Colvars source files that don't include NAMD headers were moved to the folder "colvars".  This allows an easier update method to NAMD, by reducing the chance of concurrent modifications to files shared by the NAMD and Colvars repositories.

- The header colvarproxy.h is now more readable, thanks to the colvarproxy class being now organized in sub-classes, and many functions being moved to colvarproxy.cpp.

- The last remaining occurrences of std::ofstream were eliminated (all disk output now goes through ofstream_namd).

- The forceNoPBC flag is now available to all variables based on centers of mass.

Below are the relevant commits from https://github.com/colvars/colvars/

9c392e9 2017-07-14 Change installation point for NAMD in separate folder [Giacomo Fiorin]
3a7eb50 2017-06-29 Remove now obsoleted cvm::ofstream typedef aliasing ofstream_namd [Giacomo Fiorin]
0dc615f 2017-06-27 Replace forceNoPBC with f_cvc_pbc_minimum_image feature, update doc [Giacomo Fiorin]
f70fe19 2017-06-26 Merge branch 'master' into proxy-cleanup [Giacomo Fiorin]
37ce1bc 2017-06-26 Add missing preprocessor macros for Lepton [Jérôme Hénin]
a6fa0db 2017-06-26 Move pertinent methods to colvarproxy_system, remove unused functions [Giacomo Fiorin]
43e63d8 2017-06-26 Move all but inline functions from colvarproxy.h to colvarproxy.cpp [Giacomo Fiorin]
e113c6e 2017-06-23 Split up colvarproxy members in multiple classes [Giacomo Fiorin]
31a232a 2017-06-23 Track CVCs that do not calculate explicit gradient [Jérôme Hénin]
4f4ced8 2017-06-22 Solve deps in new children [Jérôme Hénin]
9a39814 2017-06-22 Code and comment cleanup [Jérôme Hénin]
d8e2514 2017-06-22 Proper memory management - lepton [Jérôme Hénin]
3eb7ac7 2017-06-14 Keep init_custom_function() as a stub when Lepton is unavailable [Giacomo Fiorin]
7544936 2017-06-14 Complete the NAMD regtest for custom functions [Jérôme Hénin]

Change-Id: I4d824d4be298bf311633de52d5e5661dfdb01d80
48 files changed:
Make.depends
Makefile
colvars/src/Makefile.namd [new file with mode: 0644]
colvars/src/colvar.cpp [moved from src/colvar.C with 97% similarity]
colvars/src/colvar.h [moved from src/colvar.h with 99% similarity]
colvars/src/colvaratoms.cpp [moved from src/colvaratoms.C with 99% similarity]
colvars/src/colvaratoms.h [moved from src/colvaratoms.h with 100% similarity]
colvars/src/colvarbias.cpp [moved from src/colvarbias.C with 100% similarity]
colvars/src/colvarbias.h [moved from src/colvarbias.h with 100% similarity]
colvars/src/colvarbias_abf.cpp [moved from src/colvarbias_abf.C with 90% similarity]
colvars/src/colvarbias_abf.h [moved from src/colvarbias_abf.h with 100% similarity]
colvars/src/colvarbias_alb.cpp [moved from src/colvarbias_alb.C with 100% similarity]
colvars/src/colvarbias_alb.h [moved from src/colvarbias_alb.h with 100% similarity]
colvars/src/colvarbias_histogram.cpp [moved from src/colvarbias_histogram.C with 90% similarity]
colvars/src/colvarbias_histogram.h [moved from src/colvarbias_histogram.h with 100% similarity]
colvars/src/colvarbias_meta.cpp [moved from src/colvarbias_meta.C with 94% similarity]
colvars/src/colvarbias_meta.h [moved from src/colvarbias_meta.h with 98% similarity]
colvars/src/colvarbias_restraint.cpp [moved from src/colvarbias_restraint.C with 98% similarity]
colvars/src/colvarbias_restraint.h [moved from src/colvarbias_restraint.h with 100% similarity]
colvars/src/colvarcomp.cpp [moved from src/colvarcomp.C with 96% similarity]
colvars/src/colvarcomp.h [moved from src/colvarcomp.h with 99% similarity]
colvars/src/colvarcomp_angles.cpp [moved from src/colvarcomp_angles.C with 93% similarity]
colvars/src/colvarcomp_coordnums.cpp [moved from src/colvarcomp_coordnums.C with 96% similarity]
colvars/src/colvarcomp_distances.cpp [moved from src/colvarcomp_distances.C with 94% similarity]
colvars/src/colvarcomp_protein.cpp [moved from src/colvarcomp_protein.C with 88% similarity]
colvars/src/colvarcomp_rotations.cpp [moved from src/colvarcomp_rotations.C with 99% similarity]
colvars/src/colvardeps.cpp [moved from src/colvardeps.C with 93% similarity]
colvars/src/colvardeps.h [moved from src/colvardeps.h with 96% similarity]
colvars/src/colvargrid.cpp [moved from src/colvargrid.C with 100% similarity]
colvars/src/colvargrid.h [moved from src/colvargrid.h with 100% similarity]
colvars/src/colvarmodule.cpp [moved from src/colvarmodule.C with 97% similarity]
colvars/src/colvarmodule.h [moved from src/colvarmodule.h with 93% similarity]
colvars/src/colvarparse.cpp [moved from src/colvarparse.C with 100% similarity]
colvars/src/colvarparse.h [moved from src/colvarparse.h with 100% similarity]
colvars/src/colvarproxy.cpp [new file with mode: 0644]
colvars/src/colvarproxy.h [moved from src/colvarproxy.h with 53% similarity]
colvars/src/colvars_version.h [moved from src/colvars_version.h with 85% similarity]
colvars/src/colvarscript.cpp [moved from src/colvarscript.C with 99% similarity]
colvars/src/colvarscript.h [moved from src/colvarscript.h with 100% similarity]
colvars/src/colvartypes.cpp [moved from src/colvartypes.C with 100% similarity]
colvars/src/colvartypes.h [moved from src/colvartypes.h with 100% similarity]
colvars/src/colvarvalue.cpp [moved from src/colvarvalue.C with 100% similarity]
colvars/src/colvarvalue.h [moved from src/colvarvalue.h with 100% similarity]
config
src/colvarproxy_namd.C
src/colvarproxy_namd.h
src/colvarproxy_namd_version.h
ug/ug_colvars.tex