GROMACS

Move essential dynamics / flooding code to separate directory

Part of #1415 Get rid of legacyheaders.

Additional changes:
- provided doxygen-style documentation for functions in edsam.h
(partly copied over from edsam.c and removed there to avoid
duplication)
- uncrustified edsam.c and edsam.h

Change-Id: If4af498470c5200d50ac1d1b5537917c873380b5

Move pull code to separate subdirectory

Another part of #1415 Get rid of legacy headers.

Other changes:
- updated pulling-related include guards to new format
- updated documentation for doxygen
- updated .h includes
- uncrustified pull.h and pull_rotation.h
- updated copyright year for all files touched by this commit

Change-Id: Ief1ed3543b84f651d1bff01f1952b342850f5c22

Move more preprocessing files into the module

This removes the need for the gmx_objlib CMake object library, because
there is no longer random functionality orphaned in src/programs/gmx
(which is there because it was orphaned in src/kernel in release-4-6).

Moved legacyheaders/grompp.h to gmxpreprocess/grompp-impl.h since it
only declared structures that are (now) only used in that module (and
it no longer #includes stdio.h). gmxpreprocess/grompp.h now only
declares gmx_grompp().

Likewise, pdb2gmx, protonate and x2top now have their own
single-function headers.

Removed useless declaration of ncontrol from h_db.h

Removed grompp.h-related useless dependencies, declarations and
definitions from Generalized Born files.

Updated include and added C++ guards for files already within the
module (and new ones). Uncrustified, bumped copyrights

Refs #1415

Change-Id: Ie7967d7d7f61df684d530e3c2d982486a3cd128f

Move smalloc.h to utility/

One common header away from legacyheaders/.
Mostly mechanical replacement for the include paths, but removed a few
instances where the header was included more than once. Also, reordered
the headers a bit, mainly in C++ files.

Part of #1415.

Change-Id: Ic438d501ebf5eccc285655a9e8f2f625eb12f1d1

Move string2.* to utility/cstringutil.*

Another common header away from legacyheaders/.
Some associated #include cleanup.
This reintroduces some unwanted dependencies (like utility -> fileio),
but those need to be fixed separately.

Part of #1415.

Change-Id: Iffb2820019e2b41ef74bcabcd202364917e43d58

Move gmx_fatal.* to utility/fatalerror.*

One more included-by-all header to utility/.
Mainly mechanical replacement of include paths, some reordering in C++
files. Minor clean-up in the moved files.
gmx_fatal_collective.h not moved at this point, as it is unclear whether
it should go here, or somewhere else (utility/ should not depend on
t_commrec...).

Now, it's mainly types/simple.h that prevents removing some module-level
dependencies to legacyheaders/. Finding a good location for that (or
its contents, if it needs to be split), and reorganizing the code a bit
more should now allow really putting utility/ at the bottom of the
dependency stack where it belongs.

Part of #1415.

Change-Id: I6e487566d5bd7c9ec7a1455a2d31bd6d645bada3

Remove sysstuff.h

Replace this with those standard headers that are actually necessary for
the source files. There are likely several transitively covered header
dependencies now, but those can be resolved when they give problems.
One more header off from legacyheaders/.

Part of #1415.

Change-Id: I4cc3f0eec0f546dad929512e532d8efb11da3694

Move xvgr.* to fileio/

Part of #1415

Change-Id: Ib3d78bce62a4c03c4d72001164921edd556657a2

Move vec.h to math/

Most of the changes are scripted replacement of include paths.
Exceptions:
- #includes in the moved file were cleaned up slightly, and include
guards adjusted.
- Places where it was included as "gromacs/legacyheaders/vec.h" were
handled manually and the include order adjusted.
- Removal of unnecessary #include "vec.h" from update.h revealed some
transitive dependencies that were fixed. Some associated include
order cleanup in these files.
- Removed some duplicate includes.
- Remove dependency from linearalgebra/matrix.c to vec.h (only needed
for a single sqr()) to avoid a cyclic math <-> linearalgebra
dependency.

Part of #1415.

Change-Id: I7ece6eafa22139215510148807c5979f8950a885

Move part of macros.h to grompp-impl.h

Part of #1415.

Change-Id: I360ae1f220b6c51e90edbbe136053fd2e1c0ad5b

Move 'real' definition to utility/real.h

- types/simple.h still includes the new header to avoid touching all
code depending on this.
- Go through most files outside gmxlib and mdlib that included
types/simple.h, and checked whether headers from utility/ could
fulfill the needs. Replaced at least in places where this helped
fully remove legacyheaders/ dependencies.
- Some minor changes elsewhere to remove legacyheaders/ dependencies
from modules. Now linearalgebra/ and statistics/ don't depend on
legacyheaders, improving the layout of the dependency graph
significantly.

In the long run, this may be better outside utility/ to better
distinguish code that depends on 'real' from parts that do not.
Currently, it would create a lot of cyclic dependencies everywhere else.

Part of #1415.

Change-Id: I2aa1890357377d0d14c05b3968e1b36e1023458f

Move rvec and friends to math/vectypes.h

Adjust a few more types/simple.h includes to use only its component
parts. Now, math/ has only very few legacyheaders/ dependencies left.

Part of #1415

Change-Id: Iffeafa4fac5c5e0c744cf6deecac4eedaee2caf5

Reduced usage of typdefs.h

Preliminary step to move types out of legacyheader.

Renamed parameter called "matrix" because cppcheck gets
confused if a parameter is called the same as a type.

Part of #1415

Change-Id: I9207a7b8de7f092bab890da128abbb48a8d97b79

Move physics.* to math/units.*

- Remove some unnecessary #includes.
- Remove the dummy tests; easy to rewrite as usable tests using GTest if
someone needs those. They were anyways testing code that no one is
still calling, even though it was introduced several years ago.
Now gmxlib is free of *_test.c files.

Now, only one file using atom_id is keeping math/ dependent on
legacyheaders/.

Part of #1415.

Change-Id: I31312b92cf9f5d5129fbd90f31fcf27be2f7afaf

Removed legacyheaders/types/commrec_fwd.h from typedef.h

Related to #1415
Change-Id: I9a9dd7f1e62cfd040d183370d187f6a23ede78fa

Moved df_history utility routines from typedefs to new file.

Part of #1415.

Change-Id: Ia2b9e6e5342cb3bb5820894fb82ef2908d969bc6

Removed legacyheaders/typedefs.h

More cleaning up in legacyheaders. Mostly this patch involves
shuffling around include files, and adding a couple of forward
declarations. Renames gmxlib/typedefs.* to mdtypes/state.* and
introduces new utility/int64_to_int.cpp with header.
Introduced new directory mdtypes to resolve circular dependencies.
Right now state.* and history files
are the only files living there.

Part of #1415

Change-Id: I5dc59a2ca3bd1f9c5391f4b9deb9f116b30106fc

Moved inputrec.* from gmxlib and legacyheaders to mdtypes.

Part of #1415

Change-Id: Idb00712d1b6ea9648a36d349f670790aaaf2c6d4

Moved copyrite.* to fileio from gmxlib and legacyheaders.

Part of #1415

Change-Id: Id6cfb84cc683f88731fac7d80053aadc9b828806

Moved txtdump.* to fileio.

Some cleanups in edsam.cpp too.

Part of #1415

Change-Id: I6cd58951eff1bac0dad75dbd448a958e57c767e7

Moved genborn.h to mdlib

Part of #1415

Change-Id: Ia2d734be40df97426348a153040cf311a3abf7a3

Merged legacyheaders/types/state.h into mdtypes/state.h

Also merged swap/enum.h into legacyheaders/types/enums.h
to be moved later out of legacyheaders.
Part of #1415, #1854.

Change-Id: Ie53f190d6798b81c531896de80ef25c060836479

Merged legacyheaders/types/inputrec.h into mdtypes/inputrec.h

Part of #1415.

Change-Id: I39885a01474173170bc6a7a7c2e54e7f21d64370

Moved legacyheaders/types/energy.h to mdtypes.

Part of #1415

Change-Id: I65a00cc49110a09edfafc7520a7a480f73b5165c

Moved mdatom.h from legacyheader/types to mdtypes.

Add doxygen comments to the elements of the structure.

Part of #1415.

Change-Id: I811ad4782dd482ac7fe198c85c85b91af6e20b67

Merged legacyheaders/nrnb.h and types/nrnb.h to gmxlib.

Part of #1415

Change-Id: I33922419a6a5a7976bda12fd81e2d752eb0c5c6d

Combine enums.h and names*.

Combined enums.h and names* to mdtypes/md_enums.cpp/h.
Added doxygen comments to md_enums.h
Removed macros in inputrec.h to reduce cyclic dependencies.

Clean up of legacyheaders. By removing some unnecessary includes
from the files names.h and enums.h (now md_enums.h)
a lot of 'freeriders' showed up, therefore had to include
topology.h in many files.

Part of #1415

Change-Id: I12b8ef4f82b7aec806aea2eee7d77604e86dc576

Merged legacyheaders/types/ns.h and nblist.h to mdtypes/nblist.h

Also parts moved out of forcerec.h.
In order to make this work some parts of the forcerec structure
had to be made pointers, and the same for nblist structures.

Part of #1415.

Change-Id: Iaaadd76ccca001a11371b9a0ad1b75a727732f00

Moved legacyheaders/types/group.h to mdtypes.

Part of #1415.

Change-Id: I959941cf586b90e97359e8ec026dc923ff7f8aa5

Merged genborn.h from legacyheaders/types into mdlib/genborn.h

Part of #1415.

Change-Id: I2c9dcb827219649791183d016bf07d056a9ca049

Cleanups in legacyheader/types/commrec.h

Removed superfluous typedefs from above file.

Part of #1415.

Change-Id: If3d99dc24864d21dbbfa2eaf57fd5264f7d3d9ec

Moved domdec structures out of commrec.h.

In order to clean up the legacyheaders directory here the
structures relating to domain decomposition are taken out of
commrec.h and moved to a new file domdec/domdec_struct.h

To not introduce new cyclic dependencies modified the
interface of write_checkpoint and gmx_fatal_collective.

Part of #1415

Change-Id: I485a03eddbb87dcc236b7e2e7d85d03383d86f61

Merge remaining legacyheaders/types/ to mdtypes/

One cyclic dependency suppressed for now.
legacyheaders/ is no more.

Closes #1415 (but this just moves us to the next phase of the clean-up)

Change-Id: Ie80d24d347acb61216002a309cb4118f8dc99b6b

Broke up copyright.*

Split unrelated content into binaryinformation.* and pleasecite.*, and
move them to utility/. This removes functionality from fileio that does
not really belong there, and helps in removing cyclic dependencies.

One new cyclic dependency suppressed for now; it will disappear with
simplification of gmx_invsqrt().

Part of #1415.

Change-Id: I65f07768d46852783d30cf1a28dd22d614dde125