Sort all includes in src/gromacs

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

diff --git a/src/gromacs/fileio/mdoutf.h b/src/gromacs/fileio/mdoutf.h
index fab17b971b642adfba0ff4682fd4ab7f739fe470..8e241f4e3e366425ceba47533ddaa23192802f50 100644 (file)
--- a/src/gromacs/fileio/mdoutf.h
+++ b/src/gromacs/fileio/mdoutf.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * 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.
@@ -36,42 +36,85 @@
 #ifndef GMX_FILEIO_MDOUTF_H
 #define GMX_FILEIO_MDOUTF_H
 
-#include "filenm.h"
 #include <stdio.h>
-#include "../legacyheaders/types/simple.h"
-#include "enxio.h"
-#include "gmxfio.h"
-
-typedef struct {
-    t_fileio   *fp_trn;
-    t_fileio   *fp_xtc;
-    int         xtc_prec;
-    ener_file_t fp_ene;
-    const char *fn_cpt;
-    gmx_bool    bKeepAndNumCPT;
-    int         eIntegrator;
-    gmx_bool    bExpanded;
-    int         elamstats;
-    int         simulation_part;
-    FILE       *fp_dhdl;
-    FILE       *fp_field;
-} gmx_mdoutf_t;
-
-gmx_mdoutf_t *init_mdoutf(int nfile, const t_filenm fnm[],
-                          int mdrun_flags,
-                          const t_commrec *cr, const t_inputrec *ir,
-                          const output_env_t oenv);
-/* Returns a pointer to a data structure with all output file pointers
+
+#include "gromacs/fileio/enxio.h"
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/types/inputrec.h"
+#include "gromacs/legacyheaders/types/oenv.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/timing/wallcycle.h"
+#include "gromacs/utility/basedefinitions.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+struct gmx_mtop_t;
+
+typedef struct gmx_mdoutf *gmx_mdoutf_t;
+
+/*! \brief Allocate and initialize object to manager trajectory writing output
+ *
+ * Returns a pointer to a data structure with all output file pointers
  * and names required by mdrun.
  */
+gmx_mdoutf_t init_mdoutf(FILE              *fplog,
+                         int                nfile,
+                         const t_filenm     fnm[],
+                         int                mdrun_flags,
+                         const t_commrec   *cr,
+                         const t_inputrec  *ir,
+                         struct gmx_mtop_t *mtop,
+                         const output_env_t oenv,
+                         gmx_wallcycle_t    wcycle);
+
+/*! \brief Getter for file pointer */
+FILE *mdoutf_get_fp_field(gmx_mdoutf_t of);
+
+/*! \brief Getter for file pointer */
+ener_file_t mdoutf_get_fp_ene(gmx_mdoutf_t of);
+
+/*! \brief Getter for file pointer */
+FILE *mdoutf_get_fp_dhdl(gmx_mdoutf_t of);
+
+/*! \brief Getter for wallcycle timer */
+gmx_wallcycle_t mdoutf_get_wcycle(gmx_mdoutf_t of);
+
+/*! \brief Close TNG files if they are open.
+ *
+ * This also measures the time it takes to close the TNG
+ * files.
+ */
+void mdoutf_tng_close(gmx_mdoutf_t of);
+
+/*! \brief Close all open output files and free the of pointer */
+void done_mdoutf(gmx_mdoutf_t of);
+
+/*! \brief Routine that writes trajectory-like frames.
+ *
+ * Writes data to trn, xtc and/or checkpoint. What is written is
+ * determined by the mdof_flags defined below. Data is collected to
+ * the master node only when necessary.
+ */
+void mdoutf_write_to_trajectory_files(FILE *fplog, t_commrec *cr,
+                                      gmx_mdoutf_t of,
+                                      int mdof_flags,
+                                      struct gmx_mtop_t *top_global,
+                                      gmx_int64_t step, double t,
+                                      t_state *state_local, t_state *state_global,
+                                      rvec *f_local, rvec *f_global);
 
-void done_mdoutf(gmx_mdoutf_t *of);
-/* Close all open output files and free the of pointer */
+#define MDOF_X            (1<<0)
+#define MDOF_V            (1<<1)
+#define MDOF_F            (1<<2)
+#define MDOF_X_COMPRESSED (1<<3)
+#define MDOF_CPT          (1<<4)
+#define MDOF_IMD          (1<<5)
 
-#define MDOF_X   (1<<0)
-#define MDOF_V   (1<<1)
-#define MDOF_F   (1<<2)
-#define MDOF_XTC (1<<3)
-#define MDOF_CPT (1<<4)
+#ifdef __cplusplus
+}
+#endif
 
 #endif /* GMX_FILEIO_MDOUTF_H */