From bc16a24254b7072ddc476a7fa65ead4ffb007a9b Mon Sep 17 00:00:00 2001
From: Berk Hess <hess@kth.se>
Date: Fri, 9 Dec 2016 09:40:13 +0100
Subject: [PATCH] Make grompp -r obligatory with posres

With position restraints it would often occur that users accidentally
used equilibrated coordinates instead of the original coordinates
for position restraint coordinates due to grompp -r defaulting to -c.
Now -r always need to be supplied with position restraints, but using
the same file name as with -c will reproduce the old behavior.

Change-Id: Ie4d931897e155114d1162b329c9336627af39a45
---
 src/gromacs/gmxpreprocess/grompp.cpp    | 52 +++++++++++++++------------------
 src/programs/mdrun/tests/moduletest.cpp |  1 +
 2 files changed, 24 insertions(+), 29 deletions(-)

diff --git a/src/gromacs/gmxpreprocess/grompp.cpp b/src/gromacs/gmxpreprocess/grompp.cpp
index e8724a7482..6c37eb71f1 100644
--- a/src/gromacs/gmxpreprocess/grompp.cpp
+++ b/src/gromacs/gmxpreprocess/grompp.cpp
@@ -829,7 +829,7 @@ static void cont_status(const char *slog, const char *ener,
 }
 
 static void read_posres(gmx_mtop_t *mtop, t_molinfo *molinfo, gmx_bool bTopB,
-                        char *fn,
+                        const char *fn,
                         int rc_scaling, int ePBC,
                         rvec com,
                         warninp_t wi)
@@ -1011,7 +1011,7 @@ static void read_posres(gmx_mtop_t *mtop, t_molinfo *molinfo, gmx_bool bTopB,
 }
 
 static void gen_posres(gmx_mtop_t *mtop, t_molinfo *mi,
-                       char *fnA, char *fnB,
+                       const char *fnA, const char *fnB,
                        int rc_scaling, int ePBC,
                        rvec com, rvec comB,
                        warninp_t wi)
@@ -1715,12 +1715,11 @@ int gmx_grompp(int argc, char *argv[])
         "Specifying the [TT]-pp[tt] flag will get the pre-processed",
         "topology file written out so that you can verify its contents.[PAR]",
 
-        "When using position restraints a file with restraint coordinates",
-        "can be supplied with [TT]-r[tt], otherwise restraining will be done",
-        "with respect to the conformation from the [TT]-c[tt] option.",
-        "For free energy calculation the the coordinates for the B topology",
-        "can be supplied with [TT]-rb[tt], otherwise they will be equal to",
-        "those of the A topology.[PAR]",
+        "When using position restraints, a file with restraint coordinates",
+        "must be supplied with [TT]-r[tt] (can be the same file as supplied",
+        "for [TT]-c[tt]). For free energy calculations, separate reference",
+        "coordinates for the B topology can be supplied with [TT]-rb[tt],",
+        "otherwise they will be equal to those of the A topology.[PAR]",
 
         "Starting coordinates can be read from trajectory with [TT]-t[tt].",
         "The last frame with coordinates and velocities will be read,",
@@ -1777,7 +1776,6 @@ int gmx_grompp(int argc, char *argv[])
     matrix             box;
     real               fudgeQQ;
     double             reppow;
-    char               fn[STRLEN], fnB[STRLEN];
     const char        *mdparin;
     int                ntype;
     gmx_bool           bNeedVel, bGenVel;
@@ -1791,8 +1789,8 @@ int gmx_grompp(int argc, char *argv[])
         { efMDP, nullptr,  nullptr,        ffREAD  },
         { efMDP, "-po", "mdout",     ffWRITE },
         { efSTX, "-c",  nullptr,        ffREAD  },
-        { efSTX, "-r",  nullptr,        ffOPTRD },
-        { efSTX, "-rb", nullptr,        ffOPTRD },
+        { efSTX, "-r",  "restraint", ffOPTRD },
+        { efSTX, "-rb", "restraint", ffOPTRD },
         { efNDX, nullptr,  nullptr,        ffOPTRD },
         { efTOP, nullptr,  nullptr,        ffREAD  },
         { efTOP, "-pp", "processed", ffOPTWR },
@@ -1889,7 +1887,7 @@ int gmx_grompp(int argc, char *argv[])
         pr_symtab(debug, 0, "Just opened", &sys->symtab);
     }
 
-    strcpy(fn, ftp2fn(efTOP, NFILE, fnm));
+    const char *fn = ftp2fn(efTOP, NFILE, fnm);
     if (!gmx_fexist(fn))
     {
         gmx_fatal(FARGS, "%s does not exist", fn);
@@ -1978,25 +1976,21 @@ int gmx_grompp(int argc, char *argv[])
      */
     check_warning_error(wi, FARGS);
 
-    if (opt2bSet("-r", NFILE, fnm))
+    if (nint_ftype(sys, mi, F_POSRES) > 0 ||
+        nint_ftype(sys, mi, F_FBPOSRES) > 0)
     {
-        sprintf(fn, "%s", opt2fn("-r", NFILE, fnm));
-    }
-    else
-    {
-        sprintf(fn, "%s", opt2fn("-c", NFILE, fnm));
-    }
-    if (opt2bSet("-rb", NFILE, fnm))
-    {
-        sprintf(fnB, "%s", opt2fn("-rb", NFILE, fnm));
-    }
-    else
-    {
-        strcpy(fnB, fn);
-    }
+        const char *fn = opt2fn("-r", NFILE, fnm);
+        const char *fnB;
+
+        if (opt2bSet("-rb", NFILE, fnm))
+        {
+            fnB = opt2fn("-rb", NFILE, fnm);
+        }
+        else
+        {
+            fnB = fn;
+        }
 
-    if (nint_ftype(sys, mi, F_POSRES) > 0 || nint_ftype(sys, mi, F_FBPOSRES) > 0)
-    {
         if (bVerbose)
         {
             fprintf(stderr, "Reading position restraint coords from %s", fn);
diff --git a/src/programs/mdrun/tests/moduletest.cpp b/src/programs/mdrun/tests/moduletest.cpp
index b0c9cef4e9..b3e46c1874 100644
--- a/src/programs/mdrun/tests/moduletest.cpp
+++ b/src/programs/mdrun/tests/moduletest.cpp
@@ -165,6 +165,7 @@ SimulationRunner::callGromppOnThisRank(const CommandLine &callerRef)
     caller.addOption("-n", ndxFileName_);
     caller.addOption("-p", topFileName_);
     caller.addOption("-c", groFileName_);
+    caller.addOption("-r", groFileName_);
 
     caller.addOption("-po", mdpOutputFileName_);
     caller.addOption("-o", tprFileName_);
-- 
2.11.4.GIT