Minor changes to mdrun -h descriptions

[alexxy/gromacs.git] / src / programs / mdrun / mdrun.cpp

diff --git a/src/programs/mdrun/mdrun.cpp b/src/programs/mdrun/mdrun.cpp
index e2bc90d50d2506f2c135d938a0cd900cde438f49..52d866fdf89a4809163d10bd0823b04a061a8ee7 100644 (file)
--- a/src/programs/mdrun/mdrun.cpp
+++ b/src/programs/mdrun/mdrun.cpp
@@ -36,13 +36,13 @@
  */
 #include "gmxpre.h"
 
-#include "mdrun_main.h"
-
 #include "config.h"
 
 #include <stdio.h>
 #include <string.h>
 
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/filenm.h"
 #include "gromacs/legacyheaders/checkpoint.h"
 #include "gromacs/legacyheaders/copyrite.h"
 #include "gromacs/legacyheaders/macros.h"
@@ -52,11 +52,10 @@
 #include "gromacs/legacyheaders/readinp.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/commrec.h"
-
-#include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/filenm.h"
 #include "gromacs/utility/fatalerror.h"
 
+#include "mdrun_main.h"
+
 static bool is_multisim_option_set(int argc, const char *const argv[])
 {
     for (int i = 0; i < argc; ++i)
@@ -410,7 +409,7 @@ int gmx_mdrun(int argc, char *argv[])
     };
     t_commrec    *cr;
     t_filenm      fnm[] = {
-        { efTPX, NULL,      NULL,       ffREAD },
+        { efTPR, NULL,      NULL,       ffREAD },
         { efTRN, "-o",      NULL,       ffWRITE },
         { efCOMPRESSED, "-x", NULL,     ffOPTWR },
         { efCPT, "-cpi",    NULL,       ffOPTRD },
@@ -518,9 +517,9 @@ int gmx_mdrun(int argc, char *argv[])
         { "-ntomp_pme", FALSE, etINT, {&hw_opt.nthreads_omp_pme},
           "Number of OpenMP threads per MPI rank to start (0 is -ntomp)" },
         { "-pin",     FALSE, etENUM, {thread_aff_opt},
-          "Set thread affinities" },
+          "Whether mdrun should try to set thread affinities" },
         { "-pinoffset", FALSE, etINT, {&hw_opt.core_pinning_offset},
-          "The starting logical core number for pinning to cores; used to avoid pinning threads from different mdrun instances to the same core" },
+          "The lowest logical core number to which mdrun should pin the first thread" },
         { "-pinstride", FALSE, etINT, {&hw_opt.core_pinning_stride},
           "Pinning distance in logical cores for threads, use 0 to minimize the number of threads per physical core" },
         { "-gpu_id",  FALSE, etSTR, {&hw_opt.gpu_opt.gpu_id},