Tons of small fixes to documentation.

[alexxy/gromacs.git] / src / tools / gmx_wham.c

diff --git a/src/tools/gmx_wham.c b/src/tools/gmx_wham.c
index a9b9ba079ded6fdf8780e8648bb0db12fdff9909..0538bdc388759cfd5f3337964dcb34b9b9411602 100644 (file)
--- a/src/tools/gmx_wham.c
+++ b/src/tools/gmx_wham.c
@@ -2549,13 +2549,13 @@ int gmx_wham(int argc,char *argv[])
         "which may be useful for, e.g. membranes.[PAR]",
         "AUTOCORRELATIONS[BR]----------------[BR]",
         "With [TT]-ac[tt], [TT]g_wham[tt] estimates the integrated autocorrelation ",
-        "time (IACT) tau for each umbrella window and weights the respective ",
-        "window with 1/[1+2*tau/dt]. The IACTs are written ",
+        "time (IACT) [GRK]tau[grk] for each umbrella window and weights the respective ",
+        "window with 1/[1+2*[GRK]tau[grk]/dt]. The IACTs are written ",
         "to the file defined with [TT]-oiact[tt]. In verbose mode, all ",
         "autocorrelation functions (ACFs) are written to [TT]hist_autocorr.xvg[tt]. ",
         "Because the IACTs can be severely underestimated in case of limited ",
         "sampling, option [TT]-acsig[tt] allows to smooth the IACTs along the ",
-        "reaction coordinate with a Gaussian (sigma provided with [TT]-acsig[tt], ",
+        "reaction coordinate with a Gaussian ([GRK]sigma[grk] provided with [TT]-acsig[tt], ",
         "see output in [TT]iact.xvg[tt]). Note that the IACTs are estimated by simple ",
         "integration of the ACFs while the ACFs are larger 0.05.",
         "If you prefer to compute the IACTs by a more sophisticated (but possibly ",
@@ -2616,7 +2616,7 @@ int gmx_wham(int argc,char *argv[])
         { "-max", FALSE, etREAL, {&opt.max},
           "Maximum coordinate in profile"},
         { "-auto", FALSE, etBOOL, {&opt.bAuto},
-          "determine min and max automatically"},
+          "Determine min and max automatically"},
         { "-bins",FALSE, etINT, {&opt.bins},
           "Number of bins in profile"},
         { "-temp", FALSE, etREAL, {&opt.Temperature},
@@ -2624,11 +2624,11 @@ int gmx_wham(int argc,char *argv[])
         { "-tol", FALSE, etREAL, {&opt.Tolerance},
           "Tolerance"},
         { "-v", FALSE, etBOOL, {&opt.verbose},
-          "verbose mode"},
+          "Verbose mode"},
         { "-b", FALSE, etREAL, {&opt.tmin}, 
-          "first time to analyse (ps)"},
+          "First time to analyse (ps)"},
         { "-e", FALSE, etREAL, {&opt.tmax}, 
-          "last time to analyse (ps)"},
+          "Last time to analyse (ps)"},
         { "-dt", FALSE, etREAL, {&opt.dt},
           "Analyse only every dt ps"},
         { "-histonly", FALSE, etBOOL, {&opt.bHistOnly},
@@ -2638,19 +2638,19 @@ int gmx_wham(int argc,char *argv[])
         { "-log", FALSE, etBOOL, {&opt.bLog},
           "Calculate the log of the profile before printing"},
         { "-unit", FALSE,  etENUM, {en_unit},
-          "energy unit in case of log output" },
+          "Energy unit in case of log output" },
         { "-zprof0", FALSE, etREAL, {&opt.zProf0},
           "Define profile to 0.0 at this position (with [TT]-log[tt])"},
         { "-cycl", FALSE, etBOOL, {&opt.bCycl},
           "Create cyclic/periodic profile. Assumes min and max are the same point."},
         { "-sym", FALSE, etBOOL, {&opt.bSym},
-          "symmetrize profile around z=0"},   
+          "Symmetrize profile around z=0"},   
         { "-hist-eq", FALSE, etBOOL, {&opt.bHistEq},
           "HIDDENEnforce equal weight for all histograms. (Non-Weighed-HAM)"},
         { "-ac", FALSE, etBOOL, {&opt.bCalcTauInt},
-          "calculate integrated autocorrelation times and use in wham"},
+          "Calculate integrated autocorrelation times and use in wham"},
         { "-acsig", FALSE, etREAL, {&opt.sigSmoothIact},
-          "Smooth autocorrelation times along reaction coordinate with Gaussian of this sigma"},
+          "Smooth autocorrelation times along reaction coordinate with Gaussian of this [GRK]sigma[grk]"},
         { "-ac-trestart", FALSE, etREAL, {&opt.acTrestart},
           "When computing autocorrelation functions, restart computing every .. (ps)"},
         { "-acred", FALSE, etBOOL, {&opt.bAllowReduceIact},
@@ -2659,15 +2659,15 @@ int gmx_wham(int argc,char *argv[])
         { "-nBootstrap", FALSE,  etINT, {&opt.nBootStrap},
           "nr of bootstraps to estimate statistical uncertainty (e.g., 200)" },
         { "-bs-method", FALSE,  etENUM, {en_bsMethod},
-          "bootstrap method" },
+          "Bootstrap method" },
         { "-bs-tau", FALSE, etREAL, {&opt.tauBootStrap},
           "Autocorrelation time (ACT) assumed for all histograms. Use option [TT]-ac[tt] if ACT is unknown."},
         { "-bs-seed", FALSE, etINT, {&opt.bsSeed},
-          "seed for bootstrapping. (-1 = use time)"},
+          "Seed for bootstrapping. (-1 = use time)"},
         { "-histbs-block", FALSE, etINT, {&opt.histBootStrapBlockLength},
-          "when mixing histograms only mix within blocks of [TT]-histbs-block[tt]."},
+          "When mixing histograms only mix within blocks of [TT]-histbs-block[tt]."},
         { "-vbs", FALSE, etBOOL, {&opt.bs_verbose},
-          "verbose bootstrapping. Print the CDFs and a histogram file for each bootstrap."},
+          "Verbose bootstrapping. Print the CDFs and a histogram file for each bootstrap."},
         { "-stepout", FALSE, etINT, {&opt.stepchange},
           "HIDDENWrite maximum change every ... (set to 1 with [TT]-v[tt])"},
         { "-updateContr", FALSE, etINT, {&opt.stepUpdateContrib},