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[alexxy/gromacs.git] / src / gromacs / gmxana / gmx_tune_pme.c

diff --git a/src/gromacs/gmxana/gmx_tune_pme.c b/src/gromacs/gmxana/gmx_tune_pme.c
index 31413b2551f964699628fbbc709be92242db99da..e2c3dcc09cfedfa1e97f4f76ace856bee0afc665 100644 (file)
--- a/src/gromacs/gmxana/gmx_tune_pme.c
+++ b/src/gromacs/gmxana/gmx_tune_pme.c
@@ -2133,7 +2133,7 @@ int gmx_tune_pme(int argc, char *argv[])
         "which setting is fastest. It will also test whether performance can",
         "be enhanced by shifting load from the reciprocal to the real space",
         "part of the Ewald sum. ",
-        "Simply pass your [TT].tpr[tt] file to [THISMODULE] together with other options",
+        "Simply pass your [REF].tpr[ref] file to [THISMODULE] together with other options",
         "for [gmx-mdrun] as needed.[PAR]",
         "Which executables are used can be set in the environment variables",
         "MPIRUN and MDRUN. If these are not present, 'mpirun' and 'mdrun'",
@@ -2149,16 +2149,16 @@ int gmx_tune_pme(int argc, char *argv[])
         "tests on, or [TT]-ntmpi[tt] for the number of threads. You can also add [TT]-r[tt]",
         "to repeat each test several times to get better statistics. [PAR]",
         "[THISMODULE] can test various real space / reciprocal space workloads",
-        "for you. With [TT]-ntpr[tt] you control how many extra [TT].tpr[tt] files will be",
+        "for you. With [TT]-ntpr[tt] you control how many extra [REF].tpr[ref] files will be",
         "written with enlarged cutoffs and smaller Fourier grids respectively.",
         "Typically, the first test (number 0) will be with the settings from the input",
-        "[TT].tpr[tt] file; the last test (number [TT]ntpr[tt]) will have the Coulomb cutoff",
+        "[REF].tpr[ref] file; the last test (number [TT]ntpr[tt]) will have the Coulomb cutoff",
         "specified by [TT]-rmax[tt] with a somewhat smaller PME grid at the same time. ",
         "In this last test, the Fourier spacing is multiplied with [TT]rmax[tt]/rcoulomb. ",
-        "The remaining [TT].tpr[tt] files will have equally-spaced Coulomb radii (and Fourier "
+        "The remaining [REF].tpr[ref] files will have equally-spaced Coulomb radii (and Fourier "
         "spacings) between these extremes. [BB]Note[bb] that you can set [TT]-ntpr[tt] to 1",
         "if you just seek the optimal number of PME-only ranks; in that case",
-        "your input [TT].tpr[tt] file will remain unchanged.[PAR]",
+        "your input [REF].tpr[ref] file will remain unchanged.[PAR]",
         "For the benchmark runs, the default of 1000 time steps should suffice for most",
         "MD systems. The dynamic load balancing needs about 100 time steps",
         "to adapt to local load imbalances, therefore the time step counters",
@@ -2334,18 +2334,18 @@ int gmx_tune_pme(int argc, char *argv[])
         { "-scalevdw",  FALSE, etBOOL, {&bScaleRvdw},
           "Scale rvdw along with rcoulomb"},
         { "-ntpr",     FALSE, etINT,  {&ntprs},
-          "Number of [TT].tpr[tt] files to benchmark. Create this many files with different rcoulomb scaling factors depending on -rmin and -rmax. "
-          "If < 1, automatically choose the number of [TT].tpr[tt] files to test" },
+          "Number of [REF].tpr[ref] files to benchmark. Create this many files with different rcoulomb scaling factors depending on -rmin and -rmax. "
+          "If < 1, automatically choose the number of [REF].tpr[ref] files to test" },
         { "-steps",    FALSE, etINT64, {&bench_nsteps},
           "Take timings for this many steps in the benchmark runs" },
         { "-resetstep", FALSE, etINT,  {&presteps},
           "Let dlb equilibrate this many steps before timings are taken (reset cycle counters after this many steps)" },
         { "-nsteps",   FALSE, etINT64, {&new_sim_nsteps},
-          "If non-negative, perform this many steps in the real run (overwrites nsteps from [TT].tpr[tt], add [TT].cpt[tt] steps)" },
+          "If non-negative, perform this many steps in the real run (overwrites nsteps from [REF].tpr[ref], add [REF].cpt[ref] steps)" },
         { "-launch",   FALSE, etBOOL, {&bLaunch},
           "Launch the real simulation after optimization" },
         { "-bench",    FALSE, etBOOL, {&bBenchmark},
-          "Run the benchmarks or just create the input [TT].tpr[tt] files?" },
+          "Run the benchmarks or just create the input [REF].tpr[ref] files?" },
         { "-check",    FALSE, etBOOL, {&bCheck},
           "Before the benchmark runs, check whether mdrun works in parallel" },
         { "-gpu_id",   FALSE, etSTR,  {&eligible_gpu_ids},