Sort all includes in src/gromacs

[alexxy/gromacs.git] / src / gromacs / legacyheaders / typedefs.h

diff --git a/src/gromacs/legacyheaders/typedefs.h b/src/gromacs/legacyheaders/typedefs.h
index 520f7730feb1bc95b8f8995928a050bf5f62d122..ad79e254bdc3ddcdbf1f9f2d7d84ccbc180cc382 100644 (file)
--- a/src/gromacs/legacyheaders/typedefs.h
+++ b/src/gromacs/legacyheaders/typedefs.h
@@ -44,61 +44,30 @@
 
 #include <sys/types.h>
 
-#include "types/simple.h"
-#include "types/enums.h"
-#include "types/idef.h"
-#include "../fileio/trx.h"
-#include "types/topology.h"
-#include "types/energy.h"
-#include "types/inputrec.h"
-#include "types/nrnb.h"
-#include "types/nblist.h"
-#include "types/nbnxn_pairlist.h"
-#include "types/nsgrid.h"
-#include "types/forcerec.h"
-#include "types/fcdata.h"
-#include "types/mdatom.h"
-#include "types/ifunc.h"
-#include "types/group.h"
-#include "types/state.h"
-#include "types/shellfc.h"
-#include "types/constr.h"
-#include "types/oenv.h"
-#include "types/commrec_fwd.h"
+#include "gromacs/fileio/trx.h"
+#include "gromacs/legacyheaders/types/commrec_fwd.h"
+#include "gromacs/legacyheaders/types/constr.h"
+#include "gromacs/legacyheaders/types/energy.h"
+#include "gromacs/legacyheaders/types/enums.h"
+#include "gromacs/legacyheaders/types/fcdata.h"
+#include "gromacs/legacyheaders/types/forcerec.h"
+#include "gromacs/legacyheaders/types/group.h"
+#include "gromacs/legacyheaders/types/ifunc.h"
+#include "gromacs/legacyheaders/types/inputrec.h"
+#include "gromacs/legacyheaders/types/mdatom.h"
+#include "gromacs/legacyheaders/types/nblist.h"
+#include "gromacs/legacyheaders/types/nrnb.h"
+#include "gromacs/legacyheaders/types/nsgrid.h"
+#include "gromacs/legacyheaders/types/oenv.h"
+#include "gromacs/legacyheaders/types/shellfc.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/legacyheaders/types/state.h"
+#include "gromacs/topology/topology.h"
 
 #ifdef __cplusplus
 extern "C" {
 #endif
 
-/*
- * Memory (re)allocation can be VERY slow, especially with some
- * MPI libraries that replace the standard malloc and realloc calls.
- * To avoid slow memory allocation we use over_alloc to set the memory
- * allocation size for large data blocks. Since this scales the size
- * with a factor, we use log(n) realloc calls instead of n.
- * This can reduce allocation times from minutes to seconds.
- */
-/* This factor leads to 4 realloc calls to double the array size */
-#define OVER_ALLOC_FAC 1.19
-
-void set_over_alloc_dd(gmx_bool set);
-/* Turns over allocation for variable size atoms/cg/top arrays on or off,
- * default is off.
- */
-
-int over_alloc_dd(int n);
-/* Returns n when domain decomposition over allocation is off.
- * Returns OVER_ALLOC_FAC*n + 100 when over allocation in on.
- * This is to avoid frequent reallocation
- * during domain decomposition in mdrun.
- */
-
-/* Over allocation for small data types: int, real etc. */
-#define over_alloc_small(n) (int)(OVER_ALLOC_FAC*(n) + 8000)
-
-/* Over allocation for large data types: complex structs */
-#define over_alloc_large(n) (int)(OVER_ALLOC_FAC*(n) + 1000)
-
 int gmx_int64_to_int(gmx_int64_t step, const char *warn);
 /* Convert a gmx_int64_t value to int.
  * If warn!=NULL a warning message will be written
@@ -107,20 +76,9 @@ int gmx_int64_to_int(gmx_int64_t step, const char *warn);
  * "WARNING during %s:", where warn is printed in %s.
  */
 
-#define STEPSTRSIZE 22
-
-char *gmx_step_str(gmx_int64_t i, char *buf);
-/* Prints a gmx_int64_t value in buf and returns the pointer to buf.
- * buf should be large enough to contain i: STEPSTRSIZE (22) chars.
- * When multiple gmx_int64_t values are printed in the same printf call,
- * be sure to call gmx_step_str with different buffers.
- */
-
 /* Functions to initiate and delete structures *
  * These functions are defined in gmxlib/typedefs.c
  */
-void init_mtop(gmx_mtop_t *mtop);
-void init_top(t_topology *top);
 void init_inputrec(t_inputrec *ir);
 void init_energyhistory(energyhistory_t * enerhist);
 void done_energyhistory(energyhistory_t * enerhist);
@@ -130,10 +88,6 @@ t_state *serial_init_local_state(t_state *state_global);
 void init_df_history(df_history_t *dfhist, int nlambda);
 void done_df_history(df_history_t *dfhist);
 void copy_df_history(df_history_t * df_dest, df_history_t *df_source);
-void done_moltype(gmx_moltype_t *molt);
-void done_molblock(gmx_molblock_t *molb);
-void done_mtop(gmx_mtop_t *mtop, gmx_bool bDoneSymtab);
-void done_top(t_topology *top);
 void done_inputrec(t_inputrec *ir);
 void done_state(t_state *state);
 
@@ -143,9 +97,6 @@ void set_box_rel(t_inputrec *ir, t_state *state);
 void preserve_box_shape(t_inputrec *ir, matrix box_rel, matrix b);
 /* Preserve the box shape, b can be box or boxv */
 
-t_atoms *mtop2atoms(gmx_mtop_t *mtop);
-/* generate a t_atoms struct for the system from gmx_mtop_t */
-
 real max_cutoff(real cutoff1, real cutoff2);
 /* Returns the maximum of the cut-off's, taking into account that 0=inf. */