From 111644b87b2e3366a52828f9e516f61bc7cc7705 Mon Sep 17 00:00:00 2001 From: Mark Abraham Date: Sat, 18 Jan 2014 22:31:47 +0100 Subject: [PATCH] Rename 'gmx tpbconv' to 'gmx convert-tpr' This should help people find the tool they are looking for, rather than one that is named for a file format that hasn't been written in over 5 years. Updated comments and documentation accordingly. Uncrustified, added copyright headers. Change-Id: I5c29c30af54b90081cfb44f5b24764c8280c49fa --- share/html/online/files.html | 2 +- share/html/online/mdp_opt.html | 2 +- src/gromacs/gmxlib/mshift.c | 4 ++-- src/gromacs/legacyheaders/types/inputrec.h | 4 ++-- src/gromacs/tools/{tpbconv.c => convert_tpr.c} | 8 ++++---- src/gromacs/tools/{tpbconv.h => convert_tpr.h} | 8 ++++---- src/programs/gmx/grompp.c | 4 ++-- src/programs/gmx/legacymodules.cpp | 6 +++--- 8 files changed, 19 insertions(+), 19 deletions(-) rename src/gromacs/tools/{tpbconv.c => convert_tpr.c} (98%) rename src/gromacs/tools/{tpbconv.h => convert_tpr.h} (92%) diff --git a/share/html/online/files.html b/share/html/online/files.html index 9be08f4729..dc84d82fe8 100644 --- a/share/html/online/files.html +++ b/share/html/online/files.html @@ -5,7 +5,7 @@ mdp
run parameters, input for gmx grompp and -gmx tpbconv +gmx convert-tpr
m2p
input for gmx xpm2ps diff --git a/share/html/online/mdp_opt.html b/share/html/online/mdp_opt.html index e63311dd48..a759d4df72 100644 --- a/share/html/online/mdp_opt.html +++ b/share/html/online/mdp_opt.html @@ -233,7 +233,7 @@ The free-energy lambda is calculated as: lambda = init-lambda + del Also non-equilibrium MD parameters can depend on the step number. Thus for exact restarts or redoing part of a run it might be necessary to set init-step to the step number of the restart frame. -tpbconv does this automatically. +gmx convert-tpr does this automatically.
comm-mode:
diff --git a/src/gromacs/gmxlib/mshift.c b/src/gromacs/gmxlib/mshift.c index ec0bc79c2e..0b688298b2 100644 --- a/src/gromacs/gmxlib/mshift.c +++ b/src/gromacs/gmxlib/mshift.c @@ -3,7 +3,7 @@ * * Copyright (c) 1991-2000, University of Groningen, The Netherlands. * Copyright (c) 2001-2004, The GROMACS development team. - * Copyright (c) 2013, by the GROMACS development team, led by + * Copyright (c) 2013,2014, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. @@ -110,7 +110,7 @@ static void mk_igraph(t_graph *g, int ftype, t_ilist *il, "above natoms (%d).\n" "You are probably trying to use a trajectory which does " "not match the first %d atoms of the run input file.\n" - "You can make a matching run input file with tpbconv.", + "You can make a matching run input file with gmx convert-tpr.", at_end, at_end); } if (ftype == F_SETTLE) diff --git a/src/gromacs/legacyheaders/types/inputrec.h b/src/gromacs/legacyheaders/types/inputrec.h index b3746da2ca..2e8d678cff 100644 --- a/src/gromacs/legacyheaders/types/inputrec.h +++ b/src/gromacs/legacyheaders/types/inputrec.h @@ -3,7 +3,7 @@ * * Copyright (c) 1991-2000, University of Groningen, The Netherlands. * Copyright (c) 2001-2004, The GROMACS development team. - * Copyright (c) 2013, by the GROMACS development team, led by + * Copyright (c) 2013,2014, by the GROMACS development team, led by * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, * and including many others, as listed in the AUTHORS file in the * top-level source directory and at http://www.gromacs.org. @@ -295,7 +295,7 @@ typedef struct { int eI; /* Integration method */ gmx_int64_t nsteps; /* number of steps to be taken */ int simulation_part; /* Used in checkpointing to separate chunks */ - gmx_int64_t init_step; /* start at a stepcount >0 (used w. tpbconv) */ + gmx_int64_t init_step; /* start at a stepcount >0 (used w. convert-tpr) */ int nstcalcenergy; /* frequency of energy calc. and T/P coupl. upd. */ int cutoff_scheme; /* group or verlet cutoffs */ int ns_type; /* which ns method should we use? */ diff --git a/src/gromacs/tools/tpbconv.c b/src/gromacs/tools/convert_tpr.c similarity index 98% rename from src/gromacs/tools/tpbconv.c rename to src/gromacs/tools/convert_tpr.c index ff39619810..e1cf09dcd1 100644 --- a/src/gromacs/tools/tpbconv.c +++ b/src/gromacs/tools/convert_tpr.c @@ -321,7 +321,7 @@ static void zeroq(atom_id index[], gmx_mtop_t *mtop) } } -int gmx_tpbconv(int argc, char *argv[]) +int gmx_convert_tpr(int argc, char *argv[]) { const char *desc[] = { "[THISMODULE] can edit run input files in four ways.[PAR]", @@ -438,10 +438,10 @@ int gmx_tpbconv(int argc, char *argv[]) if (bTraj) { fprintf(stderr, "\n" - "NOTE: Reading the state from trajectory is an obsolete feature of tpbconv.\n" + "NOTE: Reading the state from trajectory is an obsolete feature of gmx convert-tpr.\n" " Continuation should be done by loading a checkpoint file with mdrun -cpi\n" " This guarantees that all state variables are transferred.\n" - " tpbconv is now only useful for increasing nsteps,\n" + " gmx convert-tpr is now only useful for increasing nsteps,\n" " but even that can often be avoided by using mdrun -maxh\n" "\n"); @@ -460,7 +460,7 @@ int gmx_tpbconv(int argc, char *argv[]) if (ir->epc != epcNO || EI_SD(ir->eI) || ir->eI == eiBD) { fprintf(stderr, "NOTE: The simulation uses pressure coupling and/or stochastic dynamics.\n" - "tpbconv can not provide binary identical continuation.\n" + "gmx convert-tpr can not provide binary identical continuation.\n" "If you want that, supply a checkpoint file to mdrun\n\n"); } diff --git a/src/gromacs/tools/tpbconv.h b/src/gromacs/tools/convert_tpr.h similarity index 92% rename from src/gromacs/tools/tpbconv.h rename to src/gromacs/tools/convert_tpr.h index abc0d1be30..bb7fc46c44 100644 --- a/src/gromacs/tools/tpbconv.h +++ b/src/gromacs/tools/convert_tpr.h @@ -32,8 +32,8 @@ * To help us fund GROMACS development, we humbly ask that you cite * the research papers on the package. Check out http://www.gromacs.org. */ -#ifndef GMX_TOOLS_TPBCONV_H -#define GMX_TOOLS_TPBCONV_H +#ifndef GMX_TOOLS_CONVERT_TPR_H +#define GMX_TOOLS_CONVERT_TPR_H #ifdef __cplusplus extern "C" { @@ -42,12 +42,12 @@ extern "C" { } #endif -/*! \brief Implements gmx tpbconv +/*! \brief Implements gmx convert-tpr * * \param[in] argc argc value passed to main(). * \param[in] argv argv array passed to main(). */ -int gmx_tpbconv(int argc, char *argv[]); +int gmx_convert_tpr(int argc, char *argv[]); #ifdef __cplusplus } diff --git a/src/programs/gmx/grompp.c b/src/programs/gmx/grompp.c index b1e77afdb6..1bc1da737c 100644 --- a/src/programs/gmx/grompp.c +++ b/src/programs/gmx/grompp.c @@ -737,7 +737,7 @@ static void cont_status(const char *slog, const char *ener, /* Set the relative box lengths for preserving the box shape. * Note that this call can lead to differences in the last bit - * with respect to using tpbconv to create a [TT].tpx[tt] file. + * with respect to using gmx convert-tpr to create a [TT].tpx[tt] file. */ set_box_rel(ir, state); @@ -1388,7 +1388,7 @@ int gmx_grompp(int argc, char *argv[]) "[THISMODULE] can be used to restart simulations (preserving", "continuity) by supplying just a checkpoint file with [TT]-t[tt].", "However, for simply changing the number of run steps to extend", - "a run, using [gmx-tpbconv] is more convenient than [THISMODULE].", + "a run, using [gmx-convert-tpr] is more convenient than [THISMODULE].", "You then supply the old checkpoint file directly to [gmx-mdrun]", "with [TT]-cpi[tt]. If you wish to change the ensemble or things", "like output frequency, then supplying the checkpoint file to", diff --git a/src/programs/gmx/legacymodules.cpp b/src/programs/gmx/legacymodules.cpp index 3b22a25894..e763651943 100644 --- a/src/programs/gmx/legacymodules.cpp +++ b/src/programs/gmx/legacymodules.cpp @@ -50,7 +50,7 @@ #include "../mdrun/mdrun_main.h" #include "gromacs/tools/check.h" #include "gromacs/tools/dump.h" -#include "gromacs/tools/tpbconv.h" +#include "gromacs/tools/convert_tpr.h" #include "legacycmainfunctions.h" @@ -146,7 +146,7 @@ void registerLegacyModules(gmx::CommandLineModuleManager *manager) "Make a run input file"); registerModule(manager, &gmx_pdb2gmx, "pdb2gmx", "Convert coordinate files to topology and FF-compliant coordinate files"); - registerModule(manager, &gmx_tpbconv, "tpbconv", + registerModule(manager, &gmx_convert_tpr, "convert-tpr", "Make a modifed run-input file"); registerModule(manager, &gmx_protonate, "protonate", @@ -346,7 +346,7 @@ void registerLegacyModules(gmx::CommandLineModuleManager *manager) manager->addModuleGroup("Running a simulation"); group.addModule("grompp"); group.addModule("mdrun"); - group.addModule("tpbconv"); + group.addModule("convert-tpr"); } { gmx::CommandLineModuleGroup group = -- 2.22.0