Sort all includes in src/gromacs

[alexxy/gromacs.git] / src / gromacs / mdlib / nbnxn_internal.h

diff --git a/src/gromacs/mdlib/nbnxn_internal.h b/src/gromacs/mdlib/nbnxn_internal.h
index 8c366ee8cb65faf256490f1cc3437f41fca980f0..909a4b07bb99b5d373df13ea613ba1bfee404f6e 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_internal.h
+++ b/src/gromacs/mdlib/nbnxn_internal.h
@@ -36,9 +36,10 @@
 #ifndef _nbnxn_internal_h
 #define _nbnxn_internal_h
 
-#include "typedefs.h"
-#include "nbnxn_simd.h"
-#include "domdec.h"
+#include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/mdlib/nbnxn_pairlist.h"
+#include "gromacs/mdlib/nbnxn_simd.h"
 #include "gromacs/timing/cyclecounter.h"
 
 
@@ -95,46 +96,47 @@ typedef struct {
 
 /* A pair-search grid struct for one domain decomposition zone */
 typedef struct {
-    rvec        c0;               /* The lower corner of the (local) grid        */
-    rvec        c1;               /* The upper corner of the (local) grid        */
-    real        atom_density;     /* The atom number density for the local grid  */
-
-    gmx_bool    bSimple;          /* Is this grid simple or super/sub            */
-    int         na_c;             /* Number of atoms per cluster                 */
-    int         na_cj;            /* Number of atoms for list j-clusters         */
-    int         na_sc;            /* Number of atoms per super-cluster           */
-    int         na_c_2log;        /* 2log of na_c                                */
-
-    int         ncx;              /* Number of (super-)cells along x             */
-    int         ncy;              /* Number of (super-)cells along y             */
-    int         nc;               /* Total number of (super-)cells               */
-
-    real        sx;               /* x-size of a (super-)cell                    */
-    real        sy;               /* y-size of a (super-)cell                    */
-    real        inv_sx;           /* 1/sx                                        */
-    real        inv_sy;           /* 1/sy                                        */
-
-    int         cell0;            /* Index in nbs->cell corresponding to cell 0  */
-
-    int        *cxy_na;           /* The number of atoms for each column in x,y  */
-    int        *cxy_ind;          /* Grid (super)cell index, offset from cell0   */
-    int         cxy_nalloc;       /* Allocation size for cxy_na and cxy_ind      */
-
-    int        *nsubc;            /* The number of sub cells for each super cell */
-    float      *bbcz;             /* Bounding boxes in z for the super cells     */
-    nbnxn_bb_t *bb;               /* 3D bounding boxes for the sub cells         */
-    nbnxn_bb_t *bbj;              /* 3D j-bounding boxes for the case where      *
-                                   * the i- and j-cluster sizes are different    */
-    float      *pbb;              /* 3D b. boxes in xxxx format per super cell   */
-    int        *flags;            /* Flag for the super cells                    */
-    int         nc_nalloc;        /* Allocation size for the pointers above      */
-
-    float      *bbcz_simple;      /* bbcz for simple grid converted from super   */
-    nbnxn_bb_t *bb_simple;        /* bb for simple grid converted from super     */
-    int        *flags_simple;     /* flags for simple grid converted from super  */
-    int         nc_nalloc_simple; /* Allocation size for the pointers above   */
-
-    int         nsubc_tot;        /* Total number of subcell, used for printing  */
+    rvec          c0;               /* The lower corner of the (local) grid        */
+    rvec          c1;               /* The upper corner of the (local) grid        */
+    real          atom_density;     /* The atom number density for the local grid  */
+
+    gmx_bool      bSimple;          /* Is this grid simple or super/sub            */
+    int           na_c;             /* Number of atoms per cluster                 */
+    int           na_cj;            /* Number of atoms for list j-clusters         */
+    int           na_sc;            /* Number of atoms per super-cluster           */
+    int           na_c_2log;        /* 2log of na_c                                */
+
+    int           ncx;              /* Number of (super-)cells along x             */
+    int           ncy;              /* Number of (super-)cells along y             */
+    int           nc;               /* Total number of (super-)cells               */
+
+    real          sx;               /* x-size of a (super-)cell                    */
+    real          sy;               /* y-size of a (super-)cell                    */
+    real          inv_sx;           /* 1/sx                                        */
+    real          inv_sy;           /* 1/sy                                        */
+
+    int           cell0;            /* Index in nbs->cell corresponding to cell 0  */
+
+    int          *cxy_na;           /* The number of atoms for each column in x,y  */
+    int          *cxy_ind;          /* Grid (super)cell index, offset from cell0   */
+    int           cxy_nalloc;       /* Allocation size for cxy_na and cxy_ind      */
+
+    int          *nsubc;            /* The number of sub cells for each super cell */
+    float        *bbcz;             /* Bounding boxes in z for the super cells     */
+    nbnxn_bb_t   *bb;               /* 3D bounding boxes for the sub cells         */
+    nbnxn_bb_t   *bbj;              /* 3D j-bounding boxes for the case where      *
+                                     * the i- and j-cluster sizes are different    */
+    float        *pbb;              /* 3D b. boxes in xxxx format per super cell   */
+    int          *flags;            /* Flag for the super cells                    */
+    unsigned int *fep;              /* FEP signal bits for sub cells               */
+    int           nc_nalloc;        /* Allocation size for the pointers above      */
+
+    float        *bbcz_simple;      /* bbcz for simple grid converted from super   */
+    nbnxn_bb_t   *bb_simple;        /* bb for simple grid converted from super     */
+    int          *flags_simple;     /* flags for simple grid converted from super  */
+    int           nc_nalloc_simple; /* Allocation size for the pointers above   */
+
+    int           nsubc_tot;        /* Total number of subcell, used for printing  */
 } nbnxn_grid_t;
 
 #ifdef GMX_NBNXN_SIMD
@@ -230,6 +232,8 @@ typedef struct {
 
     int                  ndistc;       /* Number of distance checks for flop counting */
 
+    t_nblist            *nbl_fep;      /* Temporary FEP list for load balancing */
+
     nbnxn_cycle_t        cc[enbsCCnr];
 
     gmx_cache_protect_t  cp1;
@@ -237,6 +241,7 @@ typedef struct {
 
 /* Main pair-search struct, contains the grid(s), not the pair-list(s) */
 typedef struct nbnxn_search {
+    gmx_bool            bFEP;            /* Do we have perturbed atoms? */
     int                 ePBC;            /* PBC type enum                              */
     matrix              box;             /* The periodic unit-cell                     */