Merge branch release-2020 into merge-2020-into-2021

Resolved Conflicts:
	cmake/gmxVersionInfo.cmake
	src/gromacs/gmxpreprocess/readir.cpp

diff --git a/docs/release-notes/2020/2020.6.rst b/docs/release-notes/2020/2020.6.rst
index 7a00bf163a6986b277f46f9e01ac03d30aceb760..e4c2377079efd39ee1bd8c88f7f9e76dd4020a14 100644 (file)
--- a/docs/release-notes/2020/2020.6.rst
+++ b/docs/release-notes/2020/2020.6.rst
@@ -1,7 +1,7 @@
 GROMACS 2020.6 release notes
 ----------------------------
 
-This version was released on TODO, 2021. These release notes
+This version was released on March 4th, 2021. These release notes
 document the changes that have taken place in GROMACS since the
 previous 2020.5 version, to fix known issues.
 
@@ -14,9 +14,30 @@ previous 2020.5 version, to fix known issues.
 Fixes where mdrun could behave incorrectly
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
+Cosine acceleration failed to abort if it could not be run
+""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+Cosine acceleration is only compatible with the leap-frog
+integrator (:mdp:`integrator = md`). |Gromacs| did, however,
+accept input files requesting cosine acceleration for other
+integration algorithms, and did report viscosity-related
+quantities from these simulations. Since the cosine acceleration
+was never applied in these cases, any results obtained from
+simulations with enabled cosine acceleration and integrators
+other than ``md`` should be regarded as invalid.
+
+:issue:`3903`
+
 Fixes for ``gmx`` tools
 ^^^^^^^^^^^^^^^^^^^^^^^
 
+Fix range checking bug in ``gmx covar``
+"""""""""""""""""""""""""""""""""""""""
+
+A check was inverted causing range checking to be applied wrong.
+
+:issue:`3902`
+
 Fixes that affect portability
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 

diff --git a/src/gromacs/gmxpreprocess/readir.cpp b/src/gromacs/gmxpreprocess/readir.cpp
index f7cb14caecc42010d5d40e86f288caa5fbd33207..9f4d2fa678f25f47a043ff983b4740fc5e6012b8 100644 (file)
--- a/src/gromacs/gmxpreprocess/readir.cpp
+++ b/src/gromacs/gmxpreprocess/readir.cpp
@@ -1506,6 +1506,12 @@ void check_ir(const char*                   mdparin,
     {
         gmx_fatal(FARGS, "AdResS simulations are no longer supported");
     }
+
+    // cosine acceleration is only supported in leap-frog
+    if (ir->cos_accel != 0.0 && ir->eI != eiMD)
+    {
+        warning_error(wi, "cos-acceleration is only supported by integrator = md");
+    }
 }
 
 /* interpret a number of doubles from a string and put them in an array,

diff --git a/src/gromacs/mdrun/runner.cpp b/src/gromacs/mdrun/runner.cpp
index 513d7733eeb026d62b1fb2ce94416af52c9685ae..f5ebb604bbea6d155c4d89377f14734862a5edb4 100644 (file)
--- a/src/gromacs/mdrun/runner.cpp
+++ b/src/gromacs/mdrun/runner.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2011-2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2011-2019,2020,2021, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -1662,6 +1662,11 @@ int Mdrunner::mdrunner()
         gmx_enerdata_t enerd(mtop.groups.groups[SimulationAtomGroupType::EnergyOutput].size(),
                              inputrec->fepvals->n_lambda);
 
+        // cos acceleration is only supported by md, but older tpr
+        // files might still combine it with other integrators
+        GMX_RELEASE_ASSERT(inputrec->cos_accel == 0.0 || inputrec->eI == eiMD,
+                           "cos_acceleration is only supported by integrator=md");
+
         /* Kinetic energy data */
         gmx_ekindata_t ekind;
         init_ekindata(fplog, &mtop, &(inputrec->opts), &ekind, inputrec->cos_accel);