Fix tool names (e.g., g_energy to gmx energy) in some commands

Fixes #5074

docs/reference-manual/file-formats.rst

@@ -877,7 +877,7 @@ The C-comment delimiters and the colon in the extra fields are optional.
 ::
 
     /* XPM */
-    /* This matrix is generated by g_rms. */
+    /* This matrix is generated by gmx rms. */
     /* title:   "Backbone RMSD matrix" */
     /* legend:  "RMSD (nm)" */
     /* x-label: "Time (ps)" */

docs/release-notes/2023/2023.5.rst

@@ -110,6 +110,14 @@ the output group names had empty prefix).
 
 :issue:`5050`
 
+Fixed references to old tool names in some commands
+"""""""""""""""""""""""""""""""""""""""""""""""""""
+
+There were references to old tool names, e.g., g_energy and g_bar in some
+commands.
+
+:issue:`5074`
+
 Fixes that affect portability
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 

src/gromacs/gmxana/gmx_anaeig.cpp

@@ -1317,10 +1317,11 @@ int gmx_anaeig(int argc, char* argv[])
             if (xref1 == nullptr)
             {
                 printf("\nNote: the structure in %s should be the same\n"
-                       "      as the one used for the fit in g_covar\n",
+                       "      as the one used for the fit in gmx covar\n",
                        topfile);
             }
-            printf("\nSelect the index group that was used for the least squares fit in g_covar\n");
+            printf("\nSelect the index group that was used for the least squares fit in gmx "
+                   "covar\n");
             get_index(atoms, indexfile, 1, &nfit, &ifit, &grpname);
 
             snew(w_rls, atoms->nr);

src/gromacs/gmxana/gmx_bar.cpp

@@ -1150,7 +1150,7 @@ static barres_t* barres_list_create(sim_data_t* sd, int* nres, gmx_bool use_dhdl
             gmx_fatal(FARGS,
                       "There is no path between the states X & Y below that is covered by foreign "
                       "lambdas:\ncannot proceed with BAR.\nUse thermodynamic integration of dH/dl "
-                      "by calculating the averages of dH/dl\nwith g_analyze and integrating "
+                      "by calculating the averages of dH/dl\nwith gmx analyze and integrating "
                       "them.\nAlternatively, use the -extp option if (and only if) the "
                       "Hamiltonian\ndepends linearly on lambda, which is NOT normally the "
                       "case.\n\n%s\n%s\n",

src/gromacs/gmxana/gmx_chi.cpp

@@ -1179,7 +1179,7 @@ static void order_params(FILE*                        log,
         }
 
         fp = gmx_ffopen(pdbfn, "w");
-        fprintf(fp, "REMARK generated by g_chi\n");
+        fprintf(fp, "REMARK generated by gmx chi\n");
         fprintf(fp,
                 "REMARK "
                 "B-factor field contains negative of dihedral order parameters\n");
@@ -1430,7 +1430,7 @@ int gmx_chi(int argc, char* argv[])
                        { efXVG, "-jc", "Jcoupling", ffWRITE },
                        { efXVG, "-corr", "dihcorr", ffOPTWR },
                        { efLOG, "-g", "chi", ffWRITE },
-                       /* add two more arguments copying from g_angle */
+                       /* add two more arguments copying from gmx angle */
                        { efXVG, "-ot", "dihtrans", ffOPTWR },
                        { efXVG, "-oh", "trhisto", ffOPTWR },
                        { efXVG, "-rt", "restrans", ffOPTWR },

src/gromacs/gmxana/gmx_density.cpp

@@ -667,7 +667,7 @@ int gmx_density(int argc, char* argv[])
     int**       index;        /* indices for all groups     */
 
     t_filenm fnm[] = {
-        /* files for g_density       */
+        /* files for gmx density       */
         { efTRX, "-f", nullptr, ffREAD },
         { efNDX, nullptr, nullptr, ffOPTRD },
         { efTPR, nullptr, nullptr, ffREAD },

src/gromacs/gmxana/gmx_energy.cpp

@@ -821,10 +821,10 @@ if (tt != NOTSET)
     fprintf(fp, "\nTemperature dependent fluctuation properties at T = %g.\n", tt);
     fprintf(fp, "\nHeat capacities obtained from fluctuations do *not* include\n");
     fprintf(fp, "quantum corrections. If you want to get a more accurate estimate\n");
-    fprintf(fp, "please use the g_dos program.\n\n");
+    fprintf(fp, "please use the gmx dos program.\n\n");
     fprintf(fp,
             "WARNING: Please verify that your simulations are converged and perform\n"
-            "a block-averaging error analysis (not implemented in g_energy yet)\n");
+            "a block-averaging error analysis (not implemented in gmx energy yet)\n");
 
     if (debug != nullptr)
     {
@@ -1502,7 +1502,7 @@ static void do_dhdl(t_enxframe*             fr,
                call open_dhdl to open the file */
             /* TODO this is an ugly hack that needs to be fixed: this will only
                work if the order of data is always the same and if we're
-               only using the g_energy compiled with the mdrun that produced
+               only using the gmx energy compiled with the mdrun that produced
                the ener.edr. */
             *fp_dhdl = open_dhdl(filename, ir, oenv);
         }

src/gromacs/gmxana/gmx_h2order.cpp

@@ -313,7 +313,7 @@ int gmx_h2order(int argc, char* argv[])
             *micelle = nullptr;
     gmx_bool bMicel  = FALSE; /* think we're a micel        */
     t_filenm fnm[]   = {
-        /* files for g_order      */
+        /* files for gmx order      */
         { efTRX, "-f", nullptr, ffREAD },    /* trajectory file            */
         { efNDX, nullptr, nullptr, ffREAD }, /* index file         */
         { efNDX, "-nm", nullptr, ffOPTRD },  /* index with micelle atoms   */

src/gromacs/gmxana/gmx_hbond.cpp

@@ -414,7 +414,7 @@ static int donor_index_function(t_donors* d, int grp, int i, const char* file, i
 
 static gmx_bool isInterchangable(HydrogenBondData* hb, int d, int a, int grpa, int grpd)
 {
-    /* g_hbond doesn't allow overlapping groups */
+    /* gmx hbond doesn't allow overlapping groups */
     if (grpa != grpd)
     {
         return FALSE;

src/gromacs/gmxana/gmx_hydorder.cpp

@@ -627,7 +627,7 @@ int gmx_hydorder(int argc, char* argv[])
     };
 
     t_filenm fnm[] = {
-        /* files for g_order    */
+        /* files for gmx order    */
         { efTRX, "-f", nullptr, ffREAD },              /* trajectory file              */
         { efNDX, "-n", nullptr, ffREAD },              /* index file           */
         { efTPR, "-s", nullptr, ffREAD },              /* topology file                */

src/gromacs/gmxana/gmx_make_edi.cpp

@@ -1029,15 +1029,16 @@ int gmx_make_edi(int argc, char* argv[])
     {
         if (bFit1)
         {
-            /* if g_covar used different coordinate groups to fit and to do the PCA */
+            /* if gmx covar used different coordinate groups to fit and to do the PCA */
             printf("\nNote: the structure in %s should be the same\n"
-                   "      as the one used for the fit in g_covar\n",
+                   "      as the one used for the fit in gmx covar\n",
                    ftp2fn(efTPS, NFILE, fnm));
-            printf("\nSelect the index group that was used for the least squares fit in g_covar\n");
+            printf("\nSelect the index group that was used for the least squares fit in gmx "
+                   "covar\n");
         }
         else
         {
-            printf("\nNote: Apparently no fitting was done in g_covar.\n"
+            printf("\nNote: Apparently no fitting was done in gmx covar.\n"
                    "      However, you need to select a reference group for fitting in mdrun\n");
         }
         get_index(atoms, indexfile, 1, &nfit, &ifit, &grpname);

src/gromacs/gmxana/gmx_mindist.cpp

@@ -83,7 +83,7 @@ periodic_dist(PbcType pbcType, matrix box, rvec x[], int n, const int index[], r
     }
     else
     {
-        gmx_fatal(FARGS, "pbc = %s is not supported by g_mindist", c_pbcTypeNames[pbcType].c_str());
+        gmx_fatal(FARGS, "pbc = %s is not supported by gmx mindist", c_pbcTypeNames[pbcType].c_str());
     }
 
     nshift = 0;

src/gromacs/gmxana/gmx_order.cpp

@@ -994,7 +994,7 @@ int gmx_order(int argc, char* argv[])
     PbcType     pbcType;       /* type of periodic boundary conditions */
 
     t_filenm fnm[] = {
-        /* files for g_order    */
+        /* files for gmx order    */
         { efTRX, "-f", nullptr, ffREAD },     /* trajectory file              */
         { efNDX, "-n", nullptr, ffREAD },     /* index file           */
         { efNDX, "-nr", nullptr, ffOPTRD },   /* index for radial axis calculation */

src/gromacs/gmxana/gmx_potential.cpp

@@ -604,7 +604,7 @@ int gmx_potential(int argc, char* argv[])
     int         ncenter;      /* size of centering group    */
     int**       index;        /* indices for all groups     */
     t_filenm    fnm[] = {
-        /* files for g_order       */
+        /* files for gmx order       */
         { efTRX, "-f", nullptr, ffREAD },      /* trajectory file             */
         { efNDX, nullptr, nullptr, ffREAD },   /* index file          */
         { efTPR, nullptr, nullptr, ffREAD },   /* topology file               */

src/gromacs/gmxana/gmx_wham.cpp

@@ -1081,7 +1081,7 @@ static void create_synthetic_histo(t_UmbrellaWindow*  synthWindow,
                 "autocorrelation times (ACTs) are required. Otherwise the statistical error\n"
                 "cannot be predicted. You have 3 options:\n"
                 "1) Make gmx wham estimate the ACTs (options -ac and -acsig).\n"
-                "2) Calculate the ACTs by yourself (e.g. with g_analyze) and provide them\n");
+                "2) Calculate the ACTs by yourself (e.g. with gmx analyze) and provide them\n");
         std::strcat(errstr,
                     "   with option -iiact for all umbrella windows.\n"
                     "3) If all ACTs are identical and know, you can define them with -bs-tau.\n"

src/gromacs/gmxana/gmx_xpm2ps.cpp

@@ -1203,7 +1203,7 @@ static void write_combined_matrix(int                     ecombine,
         {
             gmx_fatal(FARGS,
                       "Could not extract real data from %s xpm matrices. Note that, e.g.,\n"
-                      "g_rms and g_mdmat provide such data.\n",
+                      "gmx rms and gmx mdmat provide such data.\n",
                       (nullptr == rmat1 && nullptr == rmat2) ? "both" : "one of the");
         }
         rlo = 1e38;

src/gromacs/mdlib/energyoutput.cpp

@@ -785,7 +785,7 @@ FILE* open_dhdl(const char* filename, const t_inputrec* ir, const gmx_output_env
 
     if (fep->n_lambda > 0)
     {
-        /* g_bar has to determine the lambda values used in this simulation
+        /* gmx bar has to determine the lambda values used in this simulation
          * from this xvg legend.
          */
 

src/gromacs/mdlib/mdebin_bar.cpp

@@ -482,7 +482,7 @@ t_mde_delta_h_coll::t_mde_delta_h_coll(const t_inputrec& inputrec)
 
         /* now initialize them */
         /* the order, for now, must match that of the dhdl.xvg file because of
-           how g_energy -odh is implemented */
+           how gmx energy -odh is implemented */
         n = 0;
         if (bExpanded)
         {

src/gromacs/mdlib/mdebin_bar.h

@@ -43,7 +43,7 @@
 #include "gromacs/utility/real.h"
 
 /* The functions & data structures here describe writing
-   energy differences (or their histogram )for use with g_bar */
+   energy differences (or their histogram )for use with gmx bar */
 
 class delta_h_history_t;
 struct t_enxframe;

src/gromacs/tools/eneconv.cpp

@@ -745,8 +745,8 @@ int gmx_eneconv(int argc, char* argv[])
                                                "want.\n"
                                                "         Use the -rmdh option to throw all delta H "
                                                "samples away.\n"
-                                               "         Use g_energy -odh option to extract these "
-                                               "samples.\n",
+                                               "         Use gmx energy -odh option to extract "
+                                               "these samples.\n",
                                                files[f].c_str(),
                                                size);
                                         warned_about_dh = TRUE;