Prepare master for 2020

Change-Id: I0169887a8842a30baf425b0dcf8ddcf9bba6c28b

diff --git a/cmake/gmxVersionInfo.cmake b/cmake/gmxVersionInfo.cmake
index 99ae30fbda0c6abe16d7705be0a991a4e623ae2a..e9b9a1536b7c54393eb094fd274a7aefe32930f0 100644 (file)
--- a/cmake/gmxVersionInfo.cmake
+++ b/cmake/gmxVersionInfo.cmake
@@ -57,6 +57,7 @@
 #         GROMACS     2016   2
 #         GROMACS     2018   3
 #         GROMACS     2019   4
+#         GROMACS     2020   5
 #   LIBRARY_SOVERSION_MINOR so minor version for the built libraries.
 #       Should be increased for each release that changes only the implementation.
 #       In GROMACS, the typical policy is to increase it for each patch version
@@ -195,13 +196,13 @@
 
 # The GROMACS convention is that these are the version number of the next
 # release that is going to be made from this branch.
-set(GMX_VERSION_MAJOR 2019)
+set(GMX_VERSION_MAJOR 2020)
 set(GMX_VERSION_PATCH 0)
 # The suffix, on the other hand, is used mainly for betas and release
 # candidates, where it signifies the most recent such release from
 # this branch; it will be empty before the first such release, as well
 # as after the final release is out.
-set(GMX_VERSION_SUFFIX "-beta1")
+set(GMX_VERSION_SUFFIX "")
 
 # Conventionally with libtool, any ABI change must change the major
 # version number, the minor version number should change if it's just
@@ -212,7 +213,7 @@ set(GMX_VERSION_SUFFIX "-beta1")
 # here. The important thing is to minimize the chance of third-party
 # code being able to dynamically link with a version of libgromacs
 # that might not work.
-set(LIBRARY_SOVERSION_MAJOR 4)
+set(LIBRARY_SOVERSION_MAJOR 5)
 set(LIBRARY_SOVERSION_MINOR 0)
 set(LIBRARY_VERSION ${LIBRARY_SOVERSION_MAJOR}.${LIBRARY_SOVERSION_MINOR}.0)
 

diff --git a/docs/CMakeLists.txt b/docs/CMakeLists.txt
index a31440bb280944b6d93413e7e6ba961d64f1eae1..a883f991cf125b7436b016932bd51b1a3734f679 100644 (file)
--- a/docs/CMakeLists.txt
+++ b/docs/CMakeLists.txt
@@ -318,6 +318,15 @@ if (SPHINX_FOUND)
         how-to/visualize.rst
         install-guide/index.rst
         release-notes/index.rst
+        release-notes/highlights.rst
+        release-notes/features.rst
+        release-notes/performance.rst
+        release-notes/tools.rst
+        release-notes/bugs-fixed.rst
+        release-notes/removed-functionality.rst
+        release-notes/deprecated-functionality.rst
+        release-notes/portability.rst
+        release-notes/miscellaneous.rst
         release-notes/2019/major/highlights.rst
         release-notes/2019/major/features.rst
         release-notes/2019/major/performance.rst

diff --git a/docs/release-notes/2019/major/deprecated-functionality.rst b/docs/release-notes/2019/major/deprecated-functionality.rst
index d9bbea7a00072fbf4fd762131b56096e8cbb8e2b..c2f6ec0fab90719e3882c036b976466742000f8d 100644 (file)
--- a/docs/release-notes/2019/major/deprecated-functionality.rst
+++ b/docs/release-notes/2019/major/deprecated-functionality.rst
@@ -1,5 +1,3 @@
-.. _anticipated-changes:
-
 Changes anticipated to GROMACS 2019 functionality
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 

diff --git a/docs/release-notes/bugs-fixed.rst b/docs/release-notes/bugs-fixed.rst
new file mode 100644 (file)
index 0000000..81b559a
--- /dev/null
+++ b/docs/release-notes/bugs-fixed.rst
@@ -0,0 +1,2 @@
+Bugs fixed
+^^^^^^^^^^

diff --git a/docs/release-notes/deprecated-functionality.rst b/docs/release-notes/deprecated-functionality.rst
new file mode 100644 (file)
index 0000000..90218f4
--- /dev/null
+++ b/docs/release-notes/deprecated-functionality.rst
@@ -0,0 +1,52 @@
+.. _anticipated-changes:
+
+Changes anticipated to |Gromacs| NEXT functionality
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Functionality deprecated in |Gromacs| NEXT
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Functionality deprecated in |Gromacs| 2019
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Generation of virtual sites to replace aromatic rings in standard residues
+""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+These are thought to produce artefacts under some circumstances
+(unpublished results), were never well tested, are not widely used,
+and we need to simplify pdb2gmx.
+
+``gmx mdrun -gcom``
+""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+This feature sometimes overrides the effects of various .mdp settings
+in a way that is difficult to understand and report. A user who wants
+to do communication between PP ranks less often should choose their
+``nst*`` mdp options accordingly.
+
+Benchmarking options only available with ``gmx benchmark``
+""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+Options such as ``-confout``, ``-resethway``, ``-resetstep`` are not
+intended for use by regular mdrun users, so making them only available
+with a dedicated tool is more clear. Also, this permits us to customize
+defaults for e.g. writing files at the end of a simulation part in ways
+that suit the respective mdrun and benchmark use cases, so ``-confout``
+will no longer be required.
+
+``gmx mdrun -nsteps``
+""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+The number of simulation steps described by the .tpr file can be
+changed with ``gmx convert-tpr``, or altered in .mdp file before the
+call to ``gmx grompp``. The convenience of this mdrun option was
+outweighted by the doubtful quality of its implementation, no clear
+record in the log file, and lack of maintenance.
+
+Functionality deprecated before |Gromacs| 2019
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+This functionality has been declared as deprecated in previous versions
+of |Gromacs|, but has not yet been removed.
+
+The group cutoff scheme
+""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+All remaining aspects of the group cutoff scheme will be removed, once
+a few remaining features (e.g. tabulated interactions, energy-group
+exclusions, and vacuum simulations) are available with the Verlet
+scheme. Deprecated in GROMACS 5.1

diff --git a/docs/release-notes/features.rst b/docs/release-notes/features.rst
new file mode 100644 (file)
index 0000000..5aa11eb
--- /dev/null
+++ b/docs/release-notes/features.rst
@@ -0,0 +1,2 @@
+New and improved features
+^^^^^^^^^^^^^^^^^^^^^^^^^

diff --git a/docs/release-notes/highlights.rst b/docs/release-notes/highlights.rst
new file mode 100644 (file)
index 0000000..7026520
--- /dev/null
+++ b/docs/release-notes/highlights.rst
@@ -0,0 +1,14 @@
+Highlights
+^^^^^^^^^^
+
+|Gromacs| NEXT was released on INSERT DATE HERE. Patch releases may
+have been made since then, please use the updated versions!  Here are
+some highlights of what you can expect, along with more detail in the
+links below!
+
+As always, we've got several useful performance improvements, with or
+without GPUs, all enabled and automated by default. We are extremely
+interested in your feedback on how well this worked on your
+simulations and hardware. They are:
+
+* Cool quotes autogenerator 

diff --git a/docs/release-notes/index.rst b/docs/release-notes/index.rst
index 266d26f5562a7141a573de1c630ac62a9b0bd0d6..5c9a98322b003e87ae7211df49e1161234b02f69 100644 (file)
--- a/docs/release-notes/index.rst
+++ b/docs/release-notes/index.rst
@@ -8,18 +8,35 @@ releases of |Gromacs|. Major releases contain changes to the
 functionality supported, whereas patch releases contain only fixes for
 issues identified in the corresponding major releases.
 
-Two versions of |Gromacs| are under active maintenance, the 2019
-series and the 2018 series. In the latter, only highly conservative
+Two versions of |Gromacs| are under active maintenance, the NEXT
+series and the 2019 series. In the latter, only highly conservative
 fixes will be made, and only to address issues that affect scientific
 correctness. Naturally, some of those releases will be made after the
-year 2018 ends, but we keep 2018 in the name so users understand how
+year 2019 ends, but we keep 2018 in the name so users understand how
 up to date their version is. Such fixes will also be incorporated into
-the 2019 release series, as appropriate. Around the time the 2020
-release is made, the 2018 series will no longer be maintained.
+the NEXT release series, as appropriate. Around the time the NEXT+1
+release is made, the 2019 series will no longer be maintained.
 
 Where issue numbers are reported in these release notes, more details
 can be found at https://redmine.gromacs.org at that issue number.
 
+|Gromacs| NEXT series
+---------------------
+
+.. toctree::
+   :maxdepth: 1
+
+   highlights
+   features
+   performance
+   tools
+   bugs-fixed
+   deprecated-functionality
+   removed-functionality
+   portability
+   miscellaneous
+
+
 |Gromacs| 2019 series
 ---------------------
 

diff --git a/docs/release-notes/miscellaneous.rst b/docs/release-notes/miscellaneous.rst
new file mode 100644 (file)
index 0000000..27789e4
--- /dev/null
+++ b/docs/release-notes/miscellaneous.rst
@@ -0,0 +1,2 @@
+Miscellaneous
+^^^^^^^^^^^^^

diff --git a/docs/release-notes/performance.rst b/docs/release-notes/performance.rst
new file mode 100644 (file)
index 0000000..c9d7e7c
--- /dev/null
+++ b/docs/release-notes/performance.rst
@@ -0,0 +1,2 @@
+Performance improvements
+^^^^^^^^^^^^^^^^^^^^^^^^

diff --git a/docs/release-notes/portability.rst b/docs/release-notes/portability.rst
new file mode 100644 (file)
index 0000000..bc64842
--- /dev/null
+++ b/docs/release-notes/portability.rst
@@ -0,0 +1,2 @@
+Portability
+^^^^^^^^^^^

diff --git a/docs/release-notes/removed-functionality.rst b/docs/release-notes/removed-functionality.rst
new file mode 100644 (file)
index 0000000..8d99815
--- /dev/null
+++ b/docs/release-notes/removed-functionality.rst
@@ -0,0 +1,2 @@
+Removed functionality
+^^^^^^^^^^^^^^^^^^^^^

diff --git a/docs/release-notes/tools.rst b/docs/release-notes/tools.rst
new file mode 100644 (file)
index 0000000..fb2512b
--- /dev/null
+++ b/docs/release-notes/tools.rst
@@ -0,0 +1,2 @@
+Improvements to |Gromacs| tools
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^