Change grompp decoupling SD warning to note

The warning that grompp issues when decoupling a molecule
without the use of the SD integrator has been changed to a note,
since there are valid use cases for using normal MD when not
running in the completely decoupled state.

Note that checking for actual decoupled VdW states requires a lot of
code and would still not be 100% correct.

Fixes #2767

Change-Id: I55c84afcbcb7b19bdb8a7a8bc586a65c50f8d0c1

diff --git a/docs/release-notes/2020/major/miscellaneous.rst b/docs/release-notes/2020/major/miscellaneous.rst
index 599f230be27d30226034b932c8d4d7870fc41091..3e71441866fc4ad6193f2513f9fae329e5a838a2 100644 (file)
--- a/docs/release-notes/2020/major/miscellaneous.rst
+++ b/docs/release-notes/2020/major/miscellaneous.rst
@@ -43,3 +43,14 @@ Reproducibility of computed quantities is easiest to achieve if software
 stays up to date with the standards. The values for standard units have thus
 been updated to conform with the data available
 `here <http://www.codata.org/committees-and-groups/fundamental-physical-constants>`_.
+
+Change grompp warning about decoupling without SD to a note
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The warning that grompp issues when decoupling a molecule
+without the use of the SD integrator has been changed to a note,
+since there are valid use cases for using normal MD when not
+running in the completely decoupled state.
+
+:issue:`2767`
+

diff --git a/src/gromacs/gmxpreprocess/readir.cpp b/src/gromacs/gmxpreprocess/readir.cpp
index 35f663a8f40e34f9900fc9c59f36bddd54830749..8ad44f530073e2a3ecd3167c08cff8d0f0a9f9c7 100644 (file)
--- a/src/gromacs/gmxpreprocess/readir.cpp
+++ b/src/gromacs/gmxpreprocess/readir.cpp
@@ -2496,7 +2496,8 @@ void get_ir(const char*     mdparin,
             }
             if (ir->eI == eiMD && (opts->couple_lam0 == ecouplamNONE || opts->couple_lam1 == ecouplamNONE))
             {
-                warning(wi,
+                warning_note(
+                        wi,
                         "For proper sampling of the (nearly) decoupled state, stochastic dynamics "
                         "should be used");
             }