Merge release-4-6 into master

[alexxy/gromacs.git] / src / programs / mdrun / runner.c

diff --git a/src/programs/mdrun/runner.c b/src/programs/mdrun/runner.c
index fb3cecf874f1b13ea60f089ac389acb4d49a57c6..8ff74dbdd5af48281df4335180d9078b0553a7f7 100644 (file)
--- a/src/programs/mdrun/runner.c
+++ b/src/programs/mdrun/runner.c
@@ -128,7 +128,7 @@ struct mdrunner_arglist
     const char     *ddcsy;
     const char     *ddcsz;
     const char     *nbpu_opt;
-    int             nsteps_cmdline;
+    gmx_large_int_t nsteps_cmdline;
     int             nstepout;
     int             resetstep;
     int             nmultisim;
@@ -190,7 +190,8 @@ static t_commrec *mdrunner_start_threads(gmx_hw_opt_t *hw_opt,
                                          const char *dddlb_opt, real dlb_scale,
                                          const char *ddcsx, const char *ddcsy, const char *ddcsz,
                                          const char *nbpu_opt,
-                                         int nsteps_cmdline, int nstepout, int resetstep,
+                                         gmx_large_int_t nsteps_cmdline,
+                                         int nstepout, int resetstep,
                                          int nmultisim, int repl_ex_nst, int repl_ex_nex, int repl_ex_seed,
                                          real pforce, real cpt_period, real max_hours,
                                          const char *deviceOptions, unsigned long Flags)
@@ -862,10 +863,12 @@ static void check_and_update_hw_opt(gmx_hw_opt_t *hw_opt,
 
 /* Override the value in inputrec with value passed on the command line (if any) */
 static void override_nsteps_cmdline(FILE            *fplog,
-                                    int              nsteps_cmdline,
+                                    gmx_large_int_t  nsteps_cmdline,
                                     t_inputrec      *ir,
                                     const t_commrec *cr)
 {
+    char sbuf[STEPSTRSIZE];
+
     assert(ir);
     assert(cr);
 
@@ -877,13 +880,14 @@ static void override_nsteps_cmdline(FILE            *fplog,
         ir->nsteps = nsteps_cmdline;
         if (EI_DYNAMICS(ir->eI))
         {
-            sprintf(stmp, "Overriding nsteps with value passed on the command line: %d steps, %.3f ps",
-                    nsteps_cmdline, nsteps_cmdline*ir->delta_t);
+            sprintf(stmp, "Overriding nsteps with value passed on the command line: %s steps, %.3f ps",
+                    gmx_step_str(nsteps_cmdline, sbuf),
+                    nsteps_cmdline*ir->delta_t);
         }
         else
         {
-            sprintf(stmp, "Overriding nsteps with value passed on the command line: %d steps",
-                    nsteps_cmdline);
+            sprintf(stmp, "Overriding nsteps with value passed on the command line: %s steps",
+                    gmx_step_str(nsteps_cmdline, sbuf));
         }
 
         md_print_warn(cr, fplog, "%s\n", stmp);
@@ -906,7 +910,7 @@ int mdrunner(gmx_hw_opt_t *hw_opt,
              const char *dddlb_opt, real dlb_scale,
              const char *ddcsx, const char *ddcsy, const char *ddcsz,
              const char *nbpu_opt,
-             int nsteps_cmdline, int nstepout, int resetstep,
+             gmx_large_int_t nsteps_cmdline, int nstepout, int resetstep,
              int nmultisim, int repl_ex_nst, int repl_ex_nex,
              int repl_ex_seed, real pforce, real cpt_period, real max_hours,
              const char *deviceOptions, unsigned long Flags)
@@ -1444,6 +1448,11 @@ int mdrunner(gmx_hw_opt_t *hw_opt,
          */
         mdatoms = init_mdatoms(fplog, mtop, inputrec->efep != efepNO);
 
+        if (mdatoms->nPerturbed > 0 && inputrec->cutoff_scheme == ecutsVERLET)
+        {
+            gmx_fatal(FARGS, "The Verlet cut-off scheme does not (yet) support free-energy calculations with perturbed atoms, only perturbed interactions. This will be implemented soon. Use the group scheme for now.");
+        }
+
         /* Initialize the virtual site communication */
         vsite = init_vsite(mtop, cr, FALSE);