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lundborgmagnusal42and
lundborgmagnus
authored and
al42and
committed
Fix tool names (e.g., g_energy to gmx energy) in some commands
Fixes #5074
1 parent 2de89cf commit 922e31f

20 files changed

+37
-27
lines changed

‎docs/reference-manual/file-formats.rst

+1-1
Original file line numberDiff line numberDiff line change
@@ -877,7 +877,7 @@ The C-comment delimiters and the colon in the extra fields are optional.
877877
::
878878

879879
/* XPM */
880-
/* This matrix is generated by g_rms. */
880+
/* This matrix is generated by gmx rms. */
881881
/* title: "Backbone RMSD matrix" */
882882
/* legend: "RMSD (nm)" */
883883
/* x-label: "Time (ps)" */

‎docs/release-notes/2023/2023.5.rst

+8
Original file line numberDiff line numberDiff line change
@@ -110,6 +110,14 @@ the output group names had empty prefix).
110110

111111
:issue:`5050`
112112

113+
Fixed references to old tool names in some commands
114+
"""""""""""""""""""""""""""""""""""""""""""""""""""
115+
116+
There were references to old tool names, e.g., g_energy and g_bar in some
117+
commands.
118+
119+
:issue:`5074`
120+
113121
Fixes that affect portability
114122
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
115123

‎src/gromacs/gmxana/gmx_anaeig.cpp

+3-2
Original file line numberDiff line numberDiff line change
@@ -1317,10 +1317,11 @@ int gmx_anaeig(int argc, char* argv[])
13171317
if (xref1 == nullptr)
13181318
{
13191319
printf("\nNote: the structure in %s should be the same\n"
1320-
" as the one used for the fit in g_covar\n",
1320+
" as the one used for the fit in gmx covar\n",
13211321
topfile);
13221322
}
1323-
printf("\nSelect the index group that was used for the least squares fit in g_covar\n");
1323+
printf("\nSelect the index group that was used for the least squares fit in gmx "
1324+
"covar\n");
13241325
get_index(atoms, indexfile, 1, &nfit, &ifit, &grpname);
13251326

13261327
snew(w_rls, atoms->nr);

‎src/gromacs/gmxana/gmx_bar.cpp

+1-1
Original file line numberDiff line numberDiff line change
@@ -1150,7 +1150,7 @@ static barres_t* barres_list_create(sim_data_t* sd, int* nres, gmx_bool use_dhdl
11501150
gmx_fatal(FARGS,
11511151
"There is no path between the states X & Y below that is covered by foreign "
11521152
"lambdas:\ncannot proceed with BAR.\nUse thermodynamic integration of dH/dl "
1153-
"by calculating the averages of dH/dl\nwith g_analyze and integrating "
1153+
"by calculating the averages of dH/dl\nwith gmx analyze and integrating "
11541154
"them.\nAlternatively, use the -extp option if (and only if) the "
11551155
"Hamiltonian\ndepends linearly on lambda, which is NOT normally the "
11561156
"case.\n\n%s\n%s\n",

‎src/gromacs/gmxana/gmx_chi.cpp

+2-2
Original file line numberDiff line numberDiff line change
@@ -1179,7 +1179,7 @@ static void order_params(FILE* log,
11791179
}
11801180

11811181
fp = gmx_ffopen(pdbfn, "w");
1182-
fprintf(fp, "REMARK generated by g_chi\n");
1182+
fprintf(fp, "REMARK generated by gmx chi\n");
11831183
fprintf(fp,
11841184
"REMARK "
11851185
"B-factor field contains negative of dihedral order parameters\n");
@@ -1430,7 +1430,7 @@ int gmx_chi(int argc, char* argv[])
14301430
{ efXVG, "-jc", "Jcoupling", ffWRITE },
14311431
{ efXVG, "-corr", "dihcorr", ffOPTWR },
14321432
{ efLOG, "-g", "chi", ffWRITE },
1433-
/* add two more arguments copying from g_angle */
1433+
/* add two more arguments copying from gmx angle */
14341434
{ efXVG, "-ot", "dihtrans", ffOPTWR },
14351435
{ efXVG, "-oh", "trhisto", ffOPTWR },
14361436
{ efXVG, "-rt", "restrans", ffOPTWR },

‎src/gromacs/gmxana/gmx_density.cpp

+1-1
Original file line numberDiff line numberDiff line change
@@ -667,7 +667,7 @@ int gmx_density(int argc, char* argv[])
667667
int** index; /* indices for all groups */
668668

669669
t_filenm fnm[] = {
670-
/* files for g_density */
670+
/* files for gmx density */
671671
{ efTRX, "-f", nullptr, ffREAD },
672672
{ efNDX, nullptr, nullptr, ffOPTRD },
673673
{ efTPR, nullptr, nullptr, ffREAD },

‎src/gromacs/gmxana/gmx_energy.cpp

+3-3
Original file line numberDiff line numberDiff line change
@@ -821,10 +821,10 @@ if (tt != NOTSET)
821821
fprintf(fp, "\nTemperature dependent fluctuation properties at T = %g.\n", tt);
822822
fprintf(fp, "\nHeat capacities obtained from fluctuations do *not* include\n");
823823
fprintf(fp, "quantum corrections. If you want to get a more accurate estimate\n");
824-
fprintf(fp, "please use the g_dos program.\n\n");
824+
fprintf(fp, "please use the gmx dos program.\n\n");
825825
fprintf(fp,
826826
"WARNING: Please verify that your simulations are converged and perform\n"
827-
"a block-averaging error analysis (not implemented in g_energy yet)\n");
827+
"a block-averaging error analysis (not implemented in gmx energy yet)\n");
828828

829829
if (debug != nullptr)
830830
{
@@ -1502,7 +1502,7 @@ static void do_dhdl(t_enxframe* fr,
15021502
call open_dhdl to open the file */
15031503
/* TODO this is an ugly hack that needs to be fixed: this will only
15041504
work if the order of data is always the same and if we're
1505-
only using the g_energy compiled with the mdrun that produced
1505+
only using the gmx energy compiled with the mdrun that produced
15061506
the ener.edr. */
15071507
*fp_dhdl = open_dhdl(filename, ir, oenv);
15081508
}

‎src/gromacs/gmxana/gmx_h2order.cpp

+1-1
Original file line numberDiff line numberDiff line change
@@ -313,7 +313,7 @@ int gmx_h2order(int argc, char* argv[])
313313
*micelle = nullptr;
314314
gmx_bool bMicel = FALSE; /* think we're a micel */
315315
t_filenm fnm[] = {
316-
/* files for g_order */
316+
/* files for gmx order */
317317
{ efTRX, "-f", nullptr, ffREAD }, /* trajectory file */
318318
{ efNDX, nullptr, nullptr, ffREAD }, /* index file */
319319
{ efNDX, "-nm", nullptr, ffOPTRD }, /* index with micelle atoms */

‎src/gromacs/gmxana/gmx_hbond.cpp

+1-1
Original file line numberDiff line numberDiff line change
@@ -414,7 +414,7 @@ static int donor_index_function(t_donors* d, int grp, int i, const char* file, i
414414

415415
static gmx_bool isInterchangable(HydrogenBondData* hb, int d, int a, int grpa, int grpd)
416416
{
417-
/* g_hbond doesn't allow overlapping groups */
417+
/* gmx hbond doesn't allow overlapping groups */
418418
if (grpa != grpd)
419419
{
420420
return FALSE;

‎src/gromacs/gmxana/gmx_hydorder.cpp

+1-1
Original file line numberDiff line numberDiff line change
@@ -627,7 +627,7 @@ int gmx_hydorder(int argc, char* argv[])
627627
};
628628

629629
t_filenm fnm[] = {
630-
/* files for g_order */
630+
/* files for gmx order */
631631
{ efTRX, "-f", nullptr, ffREAD }, /* trajectory file */
632632
{ efNDX, "-n", nullptr, ffREAD }, /* index file */
633633
{ efTPR, "-s", nullptr, ffREAD }, /* topology file */

‎src/gromacs/gmxana/gmx_make_edi.cpp

+5-4
Original file line numberDiff line numberDiff line change
@@ -1029,15 +1029,16 @@ int gmx_make_edi(int argc, char* argv[])
10291029
{
10301030
if (bFit1)
10311031
{
1032-
/* if g_covar used different coordinate groups to fit and to do the PCA */
1032+
/* if gmx covar used different coordinate groups to fit and to do the PCA */
10331033
printf("\nNote: the structure in %s should be the same\n"
1034-
" as the one used for the fit in g_covar\n",
1034+
" as the one used for the fit in gmx covar\n",
10351035
ftp2fn(efTPS, NFILE, fnm));
1036-
printf("\nSelect the index group that was used for the least squares fit in g_covar\n");
1036+
printf("\nSelect the index group that was used for the least squares fit in gmx "
1037+
"covar\n");
10371038
}
10381039
else
10391040
{
1040-
printf("\nNote: Apparently no fitting was done in g_covar.\n"
1041+
printf("\nNote: Apparently no fitting was done in gmx covar.\n"
10411042
" However, you need to select a reference group for fitting in mdrun\n");
10421043
}
10431044
get_index(atoms, indexfile, 1, &nfit, &ifit, &grpname);

‎src/gromacs/gmxana/gmx_mindist.cpp

+1-1
Original file line numberDiff line numberDiff line change
@@ -83,7 +83,7 @@ periodic_dist(PbcType pbcType, matrix box, rvec x[], int n, const int index[], r
8383
}
8484
else
8585
{
86-
gmx_fatal(FARGS, "pbc = %s is not supported by g_mindist", c_pbcTypeNames[pbcType].c_str());
86+
gmx_fatal(FARGS, "pbc = %s is not supported by gmx mindist", c_pbcTypeNames[pbcType].c_str());
8787
}
8888

8989
nshift = 0;

‎src/gromacs/gmxana/gmx_order.cpp

+1-1
Original file line numberDiff line numberDiff line change
@@ -994,7 +994,7 @@ int gmx_order(int argc, char* argv[])
994994
PbcType pbcType; /* type of periodic boundary conditions */
995995

996996
t_filenm fnm[] = {
997-
/* files for g_order */
997+
/* files for gmx order */
998998
{ efTRX, "-f", nullptr, ffREAD }, /* trajectory file */
999999
{ efNDX, "-n", nullptr, ffREAD }, /* index file */
10001000
{ efNDX, "-nr", nullptr, ffOPTRD }, /* index for radial axis calculation */

‎src/gromacs/gmxana/gmx_potential.cpp

+1-1
Original file line numberDiff line numberDiff line change
@@ -604,7 +604,7 @@ int gmx_potential(int argc, char* argv[])
604604
int ncenter; /* size of centering group */
605605
int** index; /* indices for all groups */
606606
t_filenm fnm[] = {
607-
/* files for g_order */
607+
/* files for gmx order */
608608
{ efTRX, "-f", nullptr, ffREAD }, /* trajectory file */
609609
{ efNDX, nullptr, nullptr, ffREAD }, /* index file */
610610
{ efTPR, nullptr, nullptr, ffREAD }, /* topology file */

‎src/gromacs/gmxana/gmx_wham.cpp

+1-1
Original file line numberDiff line numberDiff line change
@@ -1081,7 +1081,7 @@ static void create_synthetic_histo(t_UmbrellaWindow* synthWindow,
10811081
"autocorrelation times (ACTs) are required. Otherwise the statistical error\n"
10821082
"cannot be predicted. You have 3 options:\n"
10831083
"1) Make gmx wham estimate the ACTs (options -ac and -acsig).\n"
1084-
"2) Calculate the ACTs by yourself (e.g. with g_analyze) and provide them\n");
1084+
"2) Calculate the ACTs by yourself (e.g. with gmx analyze) and provide them\n");
10851085
std::strcat(errstr,
10861086
" with option -iiact for all umbrella windows.\n"
10871087
"3) If all ACTs are identical and know, you can define them with -bs-tau.\n"

‎src/gromacs/gmxana/gmx_xpm2ps.cpp

+1-1
Original file line numberDiff line numberDiff line change
@@ -1203,7 +1203,7 @@ static void write_combined_matrix(int ecombine,
12031203
{
12041204
gmx_fatal(FARGS,
12051205
"Could not extract real data from %s xpm matrices. Note that, e.g.,\n"
1206-
"g_rms and g_mdmat provide such data.\n",
1206+
"gmx rms and gmx mdmat provide such data.\n",
12071207
(nullptr == rmat1 && nullptr == rmat2) ? "both" : "one of the");
12081208
}
12091209
rlo = 1e38;

‎src/gromacs/mdlib/energyoutput.cpp

+1-1
Original file line numberDiff line numberDiff line change
@@ -785,7 +785,7 @@ FILE* open_dhdl(const char* filename, const t_inputrec* ir, const gmx_output_env
785785

786786
if (fep->n_lambda > 0)
787787
{
788-
/* g_bar has to determine the lambda values used in this simulation
788+
/* gmx bar has to determine the lambda values used in this simulation
789789
* from this xvg legend.
790790
*/
791791

‎src/gromacs/mdlib/mdebin_bar.cpp

+1-1
Original file line numberDiff line numberDiff line change
@@ -482,7 +482,7 @@ t_mde_delta_h_coll::t_mde_delta_h_coll(const t_inputrec& inputrec)
482482

483483
/* now initialize them */
484484
/* the order, for now, must match that of the dhdl.xvg file because of
485-
how g_energy -odh is implemented */
485+
how gmx energy -odh is implemented */
486486
n = 0;
487487
if (bExpanded)
488488
{

‎src/gromacs/mdlib/mdebin_bar.h

+1-1
Original file line numberDiff line numberDiff line change
@@ -43,7 +43,7 @@
4343
#include "gromacs/utility/real.h"
4444

4545
/* The functions & data structures here describe writing
46-
energy differences (or their histogram )for use with g_bar */
46+
energy differences (or their histogram )for use with gmx bar */
4747

4848
class delta_h_history_t;
4949
struct t_enxframe;

‎src/gromacs/tools/eneconv.cpp

+2-2
Original file line numberDiff line numberDiff line change
@@ -745,8 +745,8 @@ int gmx_eneconv(int argc, char* argv[])
745745
"want.\n"
746746
" Use the -rmdh option to throw all delta H "
747747
"samples away.\n"
748-
" Use g_energy -odh option to extract these "
749-
"samples.\n",
748+
" Use gmx energy -odh option to extract "
749+
"these samples.\n",
750750
files[f].c_str(),
751751
size);
752752
warned_about_dh = TRUE;

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