Sort all includes in src/gromacs

[alexxy/gromacs.git] / src / gromacs / fileio / mdoutf.c

diff --git a/src/gromacs/fileio/mdoutf.c b/src/gromacs/fileio/mdoutf.c
index d140e1dc6a80b232aa4a7e3469d074e5b6047dfb..844c84602e5eec689f081782194c2f331d6e5701 100644 (file)
--- a/src/gromacs/fileio/mdoutf.c
+++ b/src/gromacs/fileio/mdoutf.c
@@ -32,20 +32,25 @@
  * To help us fund GROMACS development, we humbly ask that you cite
  * the research papers on the package. Check out http://www.gromacs.org.
  */
+#include "gmxpre.h"
+
 #include "mdoutf.h"
 
-#include "gromacs/legacyheaders/xvgr.h"
+#include "gromacs/fileio/tngio.h"
+#include "gromacs/fileio/trajectory_writing.h"
+#include "gromacs/fileio/trnio.h"
+#include "gromacs/fileio/xtcio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/checkpoint.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/domdec.h"
 #include "gromacs/legacyheaders/mdrun.h"
-#include "gromacs/legacyheaders/smalloc.h"
-#include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/legacyheaders/mvdata.h"
-#include "gromacs/legacyheaders/domdec.h"
-#include "trnio.h"
-#include "xtcio.h"
-#include "tngio.h"
-#include "trajectory_writing.h"
-#include "checkpoint.h"
-#include "copyrite.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/timing/wallcycle.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 struct gmx_mdoutf {
     t_fileio         *fp_trn;
@@ -65,13 +70,14 @@ struct gmx_mdoutf {
     int               natoms_global;
     int               natoms_x_compressed;
     gmx_groups_t     *groups; /* for compressed position writing */
+    gmx_wallcycle_t   wcycle;
 };
 
 
 gmx_mdoutf_t init_mdoutf(FILE *fplog, int nfile, const t_filenm fnm[],
                          int mdrun_flags, const t_commrec *cr,
                          const t_inputrec *ir, gmx_mtop_t *top_global,
-                         const output_env_t oenv)
+                         const output_env_t oenv, gmx_wallcycle_t wcycle)
 {
     gmx_mdoutf_t  of;
     char          filemode[3];
@@ -93,6 +99,7 @@ gmx_mdoutf_t init_mdoutf(FILE *fplog, int nfile, const t_filenm fnm[],
     of->elamstats               = ir->expandedvals->elamstats;
     of->simulation_part         = ir->simulation_part;
     of->x_compression_precision = ir->x_compression_precision;
+    of->wcycle                  = wcycle;
 
     if (MASTER(cr))
     {
@@ -229,6 +236,11 @@ FILE *mdoutf_get_fp_dhdl(gmx_mdoutf_t of)
     return of->fp_dhdl;
 }
 
+gmx_wallcycle_t mdoutf_get_wcycle(gmx_mdoutf_t of)
+{
+    return of->wcycle;
+}
+
 void mdoutf_write_to_trajectory_files(FILE *fplog, t_commrec *cr,
                                       gmx_mdoutf_t of,
                                       int mdof_flags,
@@ -339,7 +351,7 @@ void mdoutf_write_to_trajectory_files(FILE *fplog, t_commrec *cr,
                 int i, j;
 
                 snew(xxtc, of->natoms_x_compressed);
-                for (i = 0, j = 0; (i < of->natoms_x_compressed); i++)
+                for (i = 0, j = 0; (i < of->natoms_global); i++)
                 {
                     if (ggrpnr(of->groups, egcCompressedX, i) == 0)
                     {
@@ -370,6 +382,17 @@ void mdoutf_write_to_trajectory_files(FILE *fplog, t_commrec *cr,
     }
 }
 
+void mdoutf_tng_close(gmx_mdoutf_t of)
+{
+    if (of->tng || of->tng_low_prec)
+    {
+        wallcycle_start(of->wcycle, ewcTRAJ);
+        gmx_tng_close(&of->tng);
+        gmx_tng_close(&of->tng_low_prec);
+        wallcycle_stop(of->wcycle, ewcTRAJ);
+    }
+}
+
 void done_mdoutf(gmx_mdoutf_t of)
 {
     if (of->fp_ene != NULL)
@@ -392,6 +415,7 @@ void done_mdoutf(gmx_mdoutf_t of)
     {
         gmx_fio_fclose(of->fp_field);
     }
+
     gmx_tng_close(&of->tng);
     gmx_tng_close(&of->tng_low_prec);