Clean up mdrun help description

Details about how unix signals are implemented can go in the user
guide.

The nice level does not actually change with whether mpirun is used,
so we should not say so.

Mentions of "experimental" features that have been in the code for a
decade don't belong here.

Fixed a repeated word.

Preparation for #2877

Change-Id: Ib68ab15717e52a9155be869581c18ba21513f067

diff --git a/docs/user-guide/mdrun-features.rst b/docs/user-guide/mdrun-features.rst
index da5137f6455e2d5a20313b56bb25d92b80ee2958..5444f97ade920afe6ea3781895ae846de9c9682f 100644 (file)
--- a/docs/user-guide/mdrun-features.rst
+++ b/docs/user-guide/mdrun-features.rst
@@ -45,6 +45,23 @@ different hardware, or with a different compiler, etc. will not be
 reproducible. This should normally only be used when investigating
 possible problems.
 
+Halting running simulations
+---------------------------
+
+When :ref:`gmx mdrun` receives a TERM or INT signal (e.g. when ctrl+C is
+pressed), it will stop at the next neighbor search step or at the
+second global communication step, whichever happens later.
+When :ref:`gmx mdrun` receives a second TERM or INT signal and
+reproducibility is not requested, it will stop at the first global
+communication step.
+In both cases all the usual output will be written to file and
+a checkpoint file is written at the last step.
+When :ref:`gmx mdrun` receives an ABRT signal or the third TERM or INT signal,
+it will abort directly without writing a new checkpoint file.
+When running with MPI, a signal to one of the :ref:`gmx mdrun` ranks
+is sufficient, this signal should not be sent to mpirun or
+the :ref:`gmx mdrun` process that is the parent of the others.
+
 Running multi-simulations
 -------------------------
 There are numerous situations where running a related set of

diff --git a/src/programs/mdrun/mdrun.cpp b/src/programs/mdrun/mdrun.cpp
index 32be1b5ef95d3d8bf438eadde377b20dd457cae3..c8015149612cb417b914a50c6b85da97e6b750f2 100644 (file)
--- a/src/programs/mdrun/mdrun.cpp
+++ b/src/programs/mdrun/mdrun.cpp
@@ -99,7 +99,7 @@ int gmx_mdrun(int argc, char *argv[])
         "([TT]-x[tt]).[PAR]",
         "The option [TT]-dhdl[tt] is only used when free energy calculation is",
         "turned on.[PAR]",
-        "Running mdrun efficiently in parallel is a complex topic topic,",
+        "Running mdrun efficiently in parallel is a complex topic,",
         "many aspects of which are covered in the online User Guide. You",
         "should look there for practical advice on using many of the options",
         "available in mdrun.[PAR]",
@@ -129,10 +129,7 @@ int gmx_mdrun(int argc, char *argv[])
         "these options are deprecated, and in future will be available via grompp.[PAR]",
         "The options [TT]-px[tt] and [TT]-pf[tt] are used for writing pull COM",
         "coordinates and forces when pulling is selected",
-        "in the [REF].mdp[ref] file.[PAR]",
-        "Finally some experimental algorithms can be tested when the",
-        "appropriate options have been given. Currently under",
-        "investigation are: polarizability.",
+        "in the [REF].mdp[ref] file.",
         "[PAR]",
         "The option [TT]-membed[tt] does what used to be g_membed, i.e. embed",
         "a protein into a membrane. This module requires a number of settings",
@@ -195,20 +192,6 @@ int gmx_mdrun(int argc, char *argv[])
         "terminated only when the time limit set by [TT]-maxh[tt] is reached (if any)",
         "or upon receiving a signal.",
         "[PAR]",
-        "When [TT]mdrun[tt] receives a TERM or INT signal (e.g. when ctrl+C is",
-        "pressed), it will stop at the next neighbor search step or at the",
-        "second global communication step, whichever happens later.",
-        "When [TT]mdrun[tt] receives a second TERM or INT signal and",
-        "reproducibility is not requested, it will stop at the first global",
-        "communication step.",
-        "In both cases all the usual output will be written to file and",
-        "a checkpoint file is written at the last step.",
-        "When [TT]mdrun[tt] receives an ABRT signal or the third TERM or INT signal,",
-        "it will abort directly without writing a new checkpoint file.",
-        "When running with MPI, a signal to one of the [TT]mdrun[tt] ranks",
-        "is sufficient, this signal should not be sent to mpirun or",
-        "the [TT]mdrun[tt] process that is the parent of the others.",
-        "[PAR]",
         "Interactive molecular dynamics (IMD) can be activated by using at least one",
         "of the three IMD switches: The [TT]-imdterm[tt] switch allows one to terminate",
         "the simulation from the molecular viewer (e.g. VMD). With [TT]-imdwait[tt],",
@@ -216,9 +199,7 @@ int gmx_mdrun(int argc, char *argv[])
         "IMD remote can be turned on by [TT]-imdpull[tt].",
         "The port [TT]mdrun[tt] listens to can be altered by [TT]-imdport[tt].The",
         "file pointed to by [TT]-if[tt] contains atom indices and forces if IMD",
-        "pulling is used.",
-        "[PAR]",
-        "When [TT]mdrun[tt] is started with MPI, it does not run niced by default."
+        "pulling is used."
     };
 
     LegacyMdrunOptions       options;