Closed some .xvg files that were being left open

Closed donor properties file in gmx hbond after removing use of
function static file pointer.

Improved naming and scoping of some file pointers in
analyze_clusters().

Added done_ed() as a place to close the essential dynamics output
file. Later, destructor content for ED should go here (or preferably
RAII).

Removed pr_energy() from gmx_cluster since it was never called.

Change-Id: I4c288e924eb81e9e0f87b8e59ee64dacc0708567

diff --git a/src/gromacs/essentialdynamics/edsam.c b/src/gromacs/essentialdynamics/edsam.c
index 558eb13dad1be2f3acb3a83e655fc5428761b7ff..35855ffde15a2b9103dd24f1f297baa750d112b1 100644 (file)
--- a/src/gromacs/essentialdynamics/edsam.c
+++ b/src/gromacs/essentialdynamics/edsam.c
@@ -3184,3 +3184,16 @@ void do_edsam(t_inputrec     *ir,
 
     ed->bFirst = FALSE;
 }
+
+void done_ed(gmx_edsam_t *ed)
+{
+    if (*ed)
+    {
+        /* ed->edo is opened sometimes with xvgropen, sometimes with
+         * gmx_fio_fopen, so we use the least common denominator for
+         * closing. */
+        gmx_fio_fclose((*ed)->edo);
+    }
+
+    /* TODO deallocate ed and set pointer to NULL */
+}

diff --git a/src/gromacs/essentialdynamics/edsam.h b/src/gromacs/essentialdynamics/edsam.h
index 20cbaf442b0e3e2ed59abf8a06b282466389c6d1..e6ab9810cdc4dbe0c1e63d176d3da5b78e8874e1 100644 (file)
--- a/src/gromacs/essentialdynamics/edsam.h
+++ b/src/gromacs/essentialdynamics/edsam.h
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, 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.
@@ -129,6 +129,11 @@ void dd_make_local_ed_indices(gmx_domdec_t *dd, gmx_edsam_t ed);
 void do_flood(t_commrec *cr, t_inputrec *ir, rvec x[], rvec force[], gmx_edsam_t ed,
               matrix box, gmx_int64_t step, gmx_bool bNS);
 
+/*! \brief Clean up
+ *
+ * \param ed                The essential dynamics data
+ */
+void done_ed(gmx_edsam_t *ed);
 
 #ifdef __cplusplus
 }

diff --git a/src/gromacs/gmxana/gmx_cluster.c b/src/gromacs/gmxana/gmx_cluster.c
index 3d0b0bef8daf84cdf544fa2439f3bd55dd1420d0..034e10a2b05b03580b9ebb4575efdb2c44807c54 100644 (file)
--- a/src/gromacs/gmxana/gmx_cluster.c
+++ b/src/gromacs/gmxana/gmx_cluster.c
@@ -136,11 +136,6 @@ typedef struct {
     int *nb;
 } t_nnb;
 
-void pr_energy(FILE *fp, real e)
-{
-    fprintf(fp, "Energy: %8.4f\n", e);
-}
-
 void cp_index(int nn, int from[], int to[])
 {
     int i;
@@ -1018,7 +1013,7 @@ static void analyze_clusters(int nf, t_clusters *clust, real **rmsd,
                              gmx_bool bFit, FILE *log, t_rgb rlo, t_rgb rhi,
                              const output_env_t oenv)
 {
-    FILE        *fp = NULL;
+    FILE        *size_fp = NULL;
     char         buf[STRLEN], buf1[40], buf2[40], buf3[40], *trxsfn;
     t_trxstatus *trxout  = NULL;
     t_trxstatus *trxsout = NULL;
@@ -1093,7 +1088,7 @@ static void analyze_clusters(int nf, t_clusters *clust, real **rmsd,
 
     if (clustidfn)
     {
-        fp = xvgropen(clustidfn, "Clusters", output_env_get_xvgr_tlabel(oenv), "Cluster #", oenv);
+        FILE *fp = xvgropen(clustidfn, "Clusters", output_env_get_xvgr_tlabel(oenv), "Cluster #", oenv);
         if (output_env_get_print_xvgr_codes(oenv))
         {
             fprintf(fp, "@    s0 symbol 2\n");
@@ -1108,11 +1103,10 @@ static void analyze_clusters(int nf, t_clusters *clust, real **rmsd,
     }
     if (sizefn)
     {
-        /* FIXME: This file is never closed. */
-        fp = xvgropen(sizefn, "Cluster Sizes", "Cluster #", "# Structures", oenv);
+        size_fp = xvgropen(sizefn, "Cluster Sizes", "Cluster #", "# Structures", oenv);
         if (output_env_get_print_xvgr_codes(oenv))
         {
-            fprintf(fp, "@g%d type %s\n", 0, "bar");
+            fprintf(size_fp, "@g%d type %s\n", 0, "bar");
         }
     }
     snew(structure, nf);
@@ -1161,7 +1155,7 @@ static void analyze_clusters(int nf, t_clusters *clust, real **rmsd,
         }
         if (sizefn)
         {
-            fprintf(fp, "%8d %8d\n", cl, nstr);
+            fprintf(size_fp, "%8d %8d\n", cl, nstr);
         }
         clrmsd  = 0;
         midstr  = 0;
@@ -1307,6 +1301,11 @@ static void analyze_clusters(int nf, t_clusters *clust, real **rmsd,
     {
         sfree(trxsfn);
     }
+
+    if (size_fp)
+    {
+        xvgrclose(size_fp);
+    }
 }
 
 static void convert_mat(t_matrix *mat, t_mat *rms)

diff --git a/src/gromacs/gmxana/gmx_hbond.c b/src/gromacs/gmxana/gmx_hbond.c
index 2f9d4578f8d3c17699892fea7936929122c81722..8bf0e44054fbe92cdb36f5ef50e682a4efc4ece5 100644 (file)
--- a/src/gromacs/gmxana/gmx_hbond.c
+++ b/src/gromacs/gmxana/gmx_hbond.c
@@ -3328,22 +3328,31 @@ static void init_hbframe(t_hbdata *hb, int nframes, real t)
     /*set_hb(hb->hbmap[i][j]->h[m],nframes-hb->hbmap[i][j]->n0,HB_NO);*/
 }
 
-static void analyse_donor_props(const char *fn, t_hbdata *hb, int nframes, real t,
-                                const output_env_t oenv)
+static FILE *open_donor_properties_file(const char        *fn,
+                                        t_hbdata          *hb,
+                                        const output_env_t oenv)
 {
-    static FILE *fp    = NULL;
-    const char  *leg[] = { "Nbound", "Nfree" };
-    int          i, j, k, nbound, nb, nhtot;
+    FILE       *fp    = NULL;
+    const char *leg[] = { "Nbound", "Nfree" };
 
-    if (!fn)
+    if (!fn || !hb)
     {
-        return;
+        return NULL;
     }
-    if (!fp)
+
+    fp = xvgropen(fn, "Donor properties", output_env_get_xvgr_tlabel(oenv), "Number", oenv);
+    xvgr_legend(fp, asize(leg), leg, oenv);
+
+    return fp;
+}
+
+static void analyse_donor_properties(FILE *fp, t_hbdata *hb, int nframes, real t)
+{
+    int i, j, k, nbound, nb, nhtot;
+
+    if (!fp || !hb)
     {
-        // TODO: This file is never closed...
-        fp = xvgropen(fn, "Donor properties", output_env_get_xvgr_tlabel(oenv), "Number", oenv);
-        xvgr_legend(fp, asize(leg), leg, oenv);
+        return;
     }
     nbound = 0;
     nhtot  = 0;
@@ -3689,7 +3698,7 @@ int gmx_hbond(int argc, char *argv[])
     int                   grp, nabin, nrbin, bin, resdist, ihb;
     char                **leg;
     t_hbdata             *hb, *hbptr;
-    FILE                 *fp, *fpins = NULL, *fpnhb = NULL;
+    FILE                 *fp, *fpins = NULL, *fpnhb = NULL, *donor_properties = NULL;
     t_gridcell         ***grid;
     t_ncell              *icell, *jcell, *kcell;
     ivec                  ngrid;
@@ -3948,6 +3957,8 @@ int gmx_hbond(int argc, char *argv[])
     /*if (bSelected)
        snew(donors[gr0D], dons[gr0D].nrd);*/
 
+    donor_properties = open_donor_properties_file(opt2fn_null("-don", NFILE, fnm), hb, oenv);
+
     if (bHBmap)
     {
         printf("Making hbmap structure...");
@@ -4376,10 +4387,7 @@ int gmx_hbond(int argc, char *argv[])
 #pragma omp barrier
 #pragma omp single
                 {
-                    if (hb != NULL)
-                    {
-                        analyse_donor_props(opt2fn_null("-don", NFILE, fnm), hb, k, t, oenv);
-                    }
+                    analyse_donor_properties(donor_properties, hb, k, t);
                 }
 
 #pragma omp single
@@ -4449,6 +4457,12 @@ int gmx_hbond(int argc, char *argv[])
     free_grid(ngrid, &grid);
 
     close_trj(status);
+
+    if (donor_properties)
+    {
+        xvgrclose(donor_properties);
+    }
+
     if (fpnhb)
     {
         xvgrclose(fpnhb);

diff --git a/src/programs/mdrun/runner.cpp b/src/programs/mdrun/runner.cpp
index 9093d6c05787392ef6994d98e494034668c432e8..229c25e3e1e14852a4407d6f770d625904654609 100644 (file)
--- a/src/programs/mdrun/runner.cpp
+++ b/src/programs/mdrun/runner.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2011,2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2011,2012,2013,2014,2015, 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.
@@ -1774,6 +1774,8 @@ int mdrunner(gmx_hw_opt_t *hw_opt,
 
     rc = (int)gmx_get_stop_condition();
 
+    done_ed(&ed);
+
 #ifdef GMX_THREAD_MPI
     /* we need to join all threads. The sub-threads join when they
        exit this function, but the master thread needs to be told to