clang-tidy: misc-misplaced-const

Manual fixes

Change-Id: If4174e56c6974c0188af2f1da496f9aa719b23a3

diff --git a/src/gromacs/CMakeLists.txt b/src/gromacs/CMakeLists.txt
index 6aa75f20410d8c029da410793f568560166b58cd..5a68a4eb74662c1b0c06e878506750c4be3a27b5 100644 (file)
--- a/src/gromacs/CMakeLists.txt
+++ b/src/gromacs/CMakeLists.txt
@@ -281,7 +281,6 @@ if (GMX_CLANG_TIDY)
        "-clang-analyzer-security.insecureAPI.strcpy"
        "bugprone-*" "misc-*" "readability-*" "performance-*" "mpi-*"
        "-misc-misplaced-widening-cast"
-       "-misc-misplaced-const"
        "-misc-incorrect-roundings" #TODO: #2562
        "-readability-else-after-return"
        "-readability-inconsistent-declaration-parameter-name"

diff --git a/src/gromacs/fileio/enxio.cpp b/src/gromacs/fileio/enxio.cpp
index 1b3d358ef810912b3dd4c6c9da0e9dd5842d5f5d..984591a63eba84b66cd50a5574edbaffc3ddcf19 100644 (file)
--- a/src/gromacs/fileio/enxio.cpp
+++ b/src/gromacs/fileio/enxio.cpp
@@ -871,7 +871,7 @@ ener_file_t open_enx(const char *fn, const char *mode)
     return ef;
 }
 
-t_fileio *enx_file_pointer(const ener_file_t ef)
+t_fileio *enx_file_pointer(const ener_file* ef)
 {
     return ef->fio;
 }

diff --git a/src/gromacs/fileio/enxio.h b/src/gromacs/fileio/enxio.h
index 86e1a08798e7f45aba71e3a74a63c59aa7a79b65..a4b174344686e9c80103d490ee446ae88b5c87eb 100644 (file)
--- a/src/gromacs/fileio/enxio.h
+++ b/src/gromacs/fileio/enxio.h
@@ -159,7 +159,7 @@ void free_enxframe(t_enxframe *ef);
 
 ener_file_t open_enx(const char *fn, const char *mode);
 
-struct t_fileio *enx_file_pointer(const ener_file_t ef);
+struct t_fileio *enx_file_pointer(const ener_file* ef);
 
 /* Free the contents of ef */
 void close_enx(ener_file_t ef);

diff --git a/src/gromacs/gmxpreprocess/gpp_atomtype.cpp b/src/gromacs/gmxpreprocess/gpp_atomtype.cpp
index f27615c981d9761f81977a565267e787bea3af7e..39ad33601cb8f4d8da135d8129da682176f1007e 100644 (file)
--- a/src/gromacs/gmxpreprocess/gpp_atomtype.cpp
+++ b/src/gromacs/gmxpreprocess/gpp_atomtype.cpp
@@ -143,7 +143,7 @@ int get_atomtype_ptype(int nt, gpp_atomtype_t ga)
     return ga->atom[nt].ptype;
 }
 
-int get_atomtype_batype(int nt, gpp_atomtype_t ga)
+int get_atomtype_batype(int nt, const gpp_atomtype* ga)
 {
     if ((nt < 0) || (nt >= ga->nr))
     {

diff --git a/src/gromacs/gmxpreprocess/gpp_atomtype.h b/src/gromacs/gmxpreprocess/gpp_atomtype.h
index 66edce1ee2059f86a47130a878bcaea2ab2f832e..3578004cc0112d4395a990c69cadc3e946ed5502 100644 (file)
--- a/src/gromacs/gmxpreprocess/gpp_atomtype.h
+++ b/src/gromacs/gmxpreprocess/gpp_atomtype.h
@@ -61,7 +61,7 @@ real get_atomtype_massB(int nt, gpp_atomtype_t at);
 real get_atomtype_qA(int nt, gpp_atomtype_t at);
 real get_atomtype_qB(int nt, gpp_atomtype_t at);
 int get_atomtype_ptype(int nt, gpp_atomtype_t at);
-int get_atomtype_batype(int nt, gpp_atomtype_t at);
+int get_atomtype_batype(int nt, const gpp_atomtype* at);
 int get_atomtype_atomnumber(int nt, gpp_atomtype_t at);
 
 /* Return the above variable for atomtype nt, or NOTSET if not found */

diff --git a/src/gromacs/gmxpreprocess/toppush.cpp b/src/gromacs/gmxpreprocess/toppush.cpp
index d3f065f42a56c58404134c0c029f27698fbd4222..4635e25c138f0e765ecbf41045bf25c96fbd77ed 100644 (file)
--- a/src/gromacs/gmxpreprocess/toppush.cpp
+++ b/src/gromacs/gmxpreprocess/toppush.cpp
@@ -1586,7 +1586,7 @@ static gmx_bool default_cmap_params(t_params bondtype[],
  */
 static int natom_match(t_param *pi,
                        int type_i, int type_j, int type_k, int type_l,
-                       const gpp_atomtype_t atype)
+                       const gpp_atomtype* atype)
 {
     if ((pi->ai() == -1 || get_atomtype_batype(type_i, atype) == pi->ai()) &&
         (pi->aj() == -1 || get_atomtype_batype(type_j, atype) == pi->aj()) &&

diff --git a/src/gromacs/hardware/hardwaretopology.cpp b/src/gromacs/hardware/hardwaretopology.cpp
index 106825d585484def95d22ccc4a21a95964b2a04c..2051990888622b752c30022d3b545dd9bef6dab8 100644 (file)
--- a/src/gromacs/hardware/hardwaretopology.cpp
+++ b/src/gromacs/hardware/hardwaretopology.cpp
@@ -174,7 +174,7 @@ parseCpuInfo(HardwareTopology::Machine *        machine,
  *          were found, the vector will be empty.
  */
 const std::vector<hwloc_obj_t>
-getHwLocDescendantsByType(const hwloc_obj_t obj, const hwloc_obj_type_t type)
+getHwLocDescendantsByType(const hwloc_obj* obj, const hwloc_obj_type_t type)
 {
     GMX_RELEASE_ASSERT(obj, "NULL hwloc object provided to getHwLocDescendantsByType()");
 
@@ -208,10 +208,10 @@ getHwLocDescendantsByType(const hwloc_obj_t obj, const hwloc_obj_type_t type)
  *  \return If all the data is found the return value is 0, otherwise non-zero.
  */
 int
-parseHwLocSocketsCoresThreads(const hwloc_topology_t             topo,
+parseHwLocSocketsCoresThreads(hwloc_topology_t                   topo,
                               HardwareTopology::Machine *        machine)
 {
-    const hwloc_obj_t              root         = hwloc_get_root_obj(topo);
+    const hwloc_obj *const         root         = hwloc_get_root_obj(topo);
     std::vector<hwloc_obj_t>       hwlocSockets = getHwLocDescendantsByType(root, HWLOC_OBJ_PACKAGE);
 
     machine->logicalProcessorCount = hwloc_get_nbobjs_by_type(topo, HWLOC_OBJ_PU);
@@ -289,7 +289,7 @@ parseHwLocSocketsCoresThreads(const hwloc_topology_t             topo,
  *  \return If any cache data is found the return value is 0, otherwise non-zero.
  */
 int
-parseHwLocCache(const hwloc_topology_t             topo,
+parseHwLocCache(hwloc_topology_t                   topo,
                 HardwareTopology::Machine *        machine)
 {
     // Parse caches up to L5
@@ -337,10 +337,10 @@ parseHwLocCache(const hwloc_topology_t             topo,
  *          entire machine) the return value is 0, otherwise non-zero.
  */
 int
-parseHwLocNuma(const hwloc_topology_t             topo,
+parseHwLocNuma(hwloc_topology_t                   topo,
                HardwareTopology::Machine *        machine)
 {
-    const hwloc_obj_t        root           = hwloc_get_root_obj(topo);
+    const hwloc_obj *const   root           = hwloc_get_root_obj(topo);
     std::vector<hwloc_obj_t> hwlocNumaNodes = getHwLocDescendantsByType(root, HWLOC_OBJ_NUMANODE);
     bool                     topologyOk     = true;
 
@@ -398,7 +398,7 @@ parseHwLocNuma(const hwloc_topology_t             topo,
     else
     {
         // No numa nodes found. Use the entire machine as a numa node.
-        const hwloc_obj_t hwlocMachine = hwloc_get_next_obj_by_type(topo, HWLOC_OBJ_MACHINE, nullptr);
+        const hwloc_obj*const hwlocMachine = hwloc_get_next_obj_by_type(topo, HWLOC_OBJ_MACHINE, nullptr);
 
         if (hwlocMachine != nullptr)
         {
@@ -452,16 +452,16 @@ parseHwLocNuma(const hwloc_topology_t             topo,
  *  \return If any devices were found the return value is 0, otherwise non-zero.
  */
 int
-parseHwLocDevices(const hwloc_topology_t             topo,
+parseHwLocDevices(hwloc_topology_t                   topo,
                   HardwareTopology::Machine *        machine)
 {
-    const hwloc_obj_t        root    = hwloc_get_root_obj(topo);
+    const hwloc_obj *const   root    = hwloc_get_root_obj(topo);
     std::vector<hwloc_obj_t> pcidevs = getHwLocDescendantsByType(root, HWLOC_OBJ_PCI_DEVICE);
 
     for (auto &p : pcidevs)
     {
-        const hwloc_obj_t ancestor = hwloc_get_ancestor_obj_by_type(topo, HWLOC_OBJ_NUMANODE, p);
-        int               numaId;
+        const hwloc_obj *const ancestor = hwloc_get_ancestor_obj_by_type(topo, HWLOC_OBJ_NUMANODE, p);
+        int                    numaId;
         if (ancestor != nullptr)
         {
             numaId = ancestor->logical_index;

diff --git a/src/gromacs/mdlib/nbnxn_atomdata.cpp b/src/gromacs/mdlib/nbnxn_atomdata.cpp
index 6cb43f27446532eb5fd941b4c6cbd52b2f91514a..0f3d4e5a5f2b1ecfeab156aa0d24cd21890d21f7 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_atomdata.cpp
+++ b/src/gromacs/mdlib/nbnxn_atomdata.cpp
@@ -792,7 +792,7 @@ static void copy_lj_to_nbat_lj_comb(const real *ljparam_type,
 
 /* Sets the atom type in nbnxn_atomdata_t */
 static void nbnxn_atomdata_set_atomtypes(nbnxn_atomdata_t    *nbat,
-                                         const nbnxn_search_t nbs,
+                                         const nbnxn_search  *nbs,
                                          const int           *type)
 {
     for (const nbnxn_grid_t &grid : nbs->grid)
@@ -811,7 +811,7 @@ static void nbnxn_atomdata_set_atomtypes(nbnxn_atomdata_t    *nbat,
 
 /* Sets the LJ combination rule parameters in nbnxn_atomdata_t */
 static void nbnxn_atomdata_set_ljcombparams(nbnxn_atomdata_t    *nbat,
-                                            const nbnxn_search_t nbs)
+                                            const nbnxn_search  *nbs)
 {
     if (nbat->comb_rule != ljcrNONE)
     {
@@ -851,7 +851,7 @@ static void nbnxn_atomdata_set_ljcombparams(nbnxn_atomdata_t    *nbat,
 
 /* Sets the charges in nbnxn_atomdata_t *nbat */
 static void nbnxn_atomdata_set_charges(nbnxn_atomdata_t    *nbat,
-                                       const nbnxn_search_t nbs,
+                                       const nbnxn_search  *nbs,
                                        const real          *charge)
 {
     for (const nbnxn_grid_t &grid : nbs->grid)
@@ -906,7 +906,7 @@ static void nbnxn_atomdata_set_charges(nbnxn_atomdata_t    *nbat,
  * using the original charge and LJ data, not nbnxn_atomdata_t.
  */
 static void nbnxn_atomdata_mask_fep(nbnxn_atomdata_t    *nbat,
-                                    const nbnxn_search_t nbs)
+                                    const nbnxn_search  *nbs)
 {
     real               *q;
     int                 stride_q, nsubc;
@@ -989,7 +989,7 @@ static void copy_egp_to_nbat_egps(const int *a, int na, int na_round,
 
 /* Set the energy group indices for atoms in nbnxn_atomdata_t */
 static void nbnxn_atomdata_set_energygroups(nbnxn_atomdata_t    *nbat,
-                                            const nbnxn_search_t nbs,
+                                            const nbnxn_search  *nbs,
                                             const int           *atinfo)
 {
     if (nbat->nenergrp == 1)
@@ -1014,7 +1014,7 @@ static void nbnxn_atomdata_set_energygroups(nbnxn_atomdata_t    *nbat,
 
 /* Sets all required atom parameter data in nbnxn_atomdata_t */
 void nbnxn_atomdata_set(nbnxn_atomdata_t    *nbat,
-                        const nbnxn_search_t nbs,
+                        const nbnxn_search  *nbs,
                         const t_mdatoms     *mdatoms,
                         const int           *atinfo)
 {
@@ -1048,7 +1048,7 @@ void nbnxn_atomdata_copy_shiftvec(gmx_bool          bDynamicBox,
 }
 
 /* Copies (and reorders) the coordinates to nbnxn_atomdata_t */
-void nbnxn_atomdata_copy_x_to_nbat_x(const nbnxn_search_t nbs,
+void nbnxn_atomdata_copy_x_to_nbat_x(const nbnxn_search  *nbs,
                                      int                  locality,
                                      gmx_bool             FillLocal,
                                      rvec                *x,
@@ -1215,7 +1215,7 @@ nbnxn_atomdata_reduce_reals_simd(real gmx_unused * gmx_restrict dest,
 
 /* Add part of the force array(s) from nbnxn_atomdata_t to f */
 static void
-nbnxn_atomdata_add_nbat_f_to_f_part(const nbnxn_search_t nbs,
+nbnxn_atomdata_add_nbat_f_to_f_part(const nbnxn_search *nbs,
                                     const nbnxn_atomdata_t *nbat,
                                     nbnxn_atomdata_output_t *out,
                                     int nfa,
@@ -1508,7 +1508,7 @@ static void nbnxn_atomdata_add_nbat_f_to_f_stdreduce(const nbnxn_atomdata_t *nba
 }
 
 /* Add the force array(s) from nbnxn_atomdata_t to f */
-void nbnxn_atomdata_add_nbat_f_to_f(const nbnxn_search_t    nbs,
+void nbnxn_atomdata_add_nbat_f_to_f(nbnxn_search           *nbs,
                                     int                     locality,
                                     const nbnxn_atomdata_t *nbat,
                                     rvec                   *f,

diff --git a/src/gromacs/mdlib/nbnxn_atomdata.h b/src/gromacs/mdlib/nbnxn_atomdata.h
index d6c7eaf017b9e904afb72917589b8b81fd7719c9..d336d4b54616aa5baef590d78ff07619a92a86cb 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_atomdata.h
+++ b/src/gromacs/mdlib/nbnxn_atomdata.h
@@ -97,7 +97,7 @@ void nbnxn_atomdata_init(const gmx::MDLogger &mdlog,
 
 /* Copy the atom data to the non-bonded atom data structure */
 void nbnxn_atomdata_set(nbnxn_atomdata_t    *nbat,
-                        const nbnxn_search_t nbs,
+                        const nbnxn_search  *nbs,
                         const t_mdatoms     *mdatoms,
                         const int           *atinfo);
 
@@ -109,7 +109,7 @@ void nbnxn_atomdata_copy_shiftvec(gmx_bool          dynamic_box,
 /* Copy x to nbat->x.
  * FillLocal tells if the local filler particle coordinates should be zeroed.
  */
-void nbnxn_atomdata_copy_x_to_nbat_x(const nbnxn_search_t nbs,
+void nbnxn_atomdata_copy_x_to_nbat_x(const nbnxn_search  *nbs,
                                      int                  locality,
                                      gmx_bool             FillLocal,
                                      rvec                *x,
@@ -117,7 +117,7 @@ void nbnxn_atomdata_copy_x_to_nbat_x(const nbnxn_search_t nbs,
                                      gmx_wallcycle       *wcycle);
 
 /* Add the forces stored in nbat to f, zeros the forces in nbat */
-void nbnxn_atomdata_add_nbat_f_to_f(const nbnxn_search_t    nbs,
+void nbnxn_atomdata_add_nbat_f_to_f(nbnxn_search           *nbs,
                                     int                     locality,
                                     const nbnxn_atomdata_t *nbat,
                                     rvec                   *f,

diff --git a/src/gromacs/mdlib/nbnxn_grid.cpp b/src/gromacs/mdlib/nbnxn_grid.cpp
index ce996f93681d197bb3ef6f260c626795722dd357..f9b4d5afe0a18efb94f40bb7f428358a56d19c21 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_grid.cpp
+++ b/src/gromacs/mdlib/nbnxn_grid.cpp
@@ -78,7 +78,7 @@ static real grid_atom_density(int        numAtoms,
     return numAtoms/(size[XX]*size[YY]*size[ZZ]);
 }
 
-static void set_grid_size_xy(const nbnxn_search_t  nbs,
+static void set_grid_size_xy(const nbnxn_search   *nbs,
                              nbnxn_grid_t         *grid,
                              int                   ddZone,
                              int                   numAtoms,
@@ -794,7 +794,7 @@ static void sort_cluster_on_flag(int                 numAtomsInCluster,
 /* Fill a pair search cell with atoms.
  * Potentially sorts atoms and sets the interaction flags.
  */
-static void fill_cell(const nbnxn_search_t   nbs,
+static void fill_cell(nbnxn_search          *nbs,
                       nbnxn_grid_t          *grid,
                       nbnxn_atomdata_t      *nbat,
                       int                    atomStart,
@@ -923,7 +923,7 @@ static void fill_cell(const nbnxn_search_t   nbs,
 }
 
 /* Spatially sort the atoms within one grid column */
-static void sort_columns_simple(const nbnxn_search_t nbs,
+static void sort_columns_simple(nbnxn_search *nbs,
                                 int dd_zone,
                                 nbnxn_grid_t *grid,
                                 int atomStart, int atomEnd,
@@ -987,7 +987,7 @@ static void sort_columns_simple(const nbnxn_search_t nbs,
 }
 
 /* Spatially sort the atoms within one grid column */
-static void sort_columns_supersub(const nbnxn_search_t nbs,
+static void sort_columns_supersub(nbnxn_search *nbs,
                                   int dd_zone,
                                   nbnxn_grid_t *grid,
                                   int atomStart, int atomEnd,
@@ -1221,7 +1221,7 @@ static void resizeForNumberOfCells(const nbnxn_grid_t &grid,
 }
 
 /* Determine in which grid cells the atoms should go */
-static void calc_cell_indices(const nbnxn_search_t  nbs,
+static void calc_cell_indices(nbnxn_search         *nbs,
                               int                   ddZone,
                               nbnxn_grid_t         *grid,
                               int                   atomStart,
@@ -1524,7 +1524,7 @@ void nbnxn_get_ncells(nbnxn_search_t nbs, int *ncx, int *ncy)
     *ncy = nbs->grid[0].numCells[YY];
 }
 
-gmx::ArrayRef<const int> nbnxn_get_atomorder(const nbnxn_search_t nbs)
+gmx::ArrayRef<const int> nbnxn_get_atomorder(const nbnxn_search *nbs)
 {
     /* Return the atom order for the home cell (index 0) */
     const nbnxn_grid_t &grid       = nbs->grid[0];

diff --git a/src/gromacs/mdlib/nbnxn_grid.h b/src/gromacs/mdlib/nbnxn_grid.h
index ee8662966ce45fc373403071eb584f55faa27a69..9282e3a5e698a4715398ffbdf2ec8bd4f99564c4 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_grid.h
+++ b/src/gromacs/mdlib/nbnxn_grid.h
@@ -84,7 +84,7 @@ void nbnxn_put_on_grid_nonlocal(nbnxn_search_t                   nbs,
 void nbnxn_get_ncells(nbnxn_search_t nbs, int *ncx, int *ncy);
 
 /* Return the order indices of the atoms on the pairlist search grid */
-gmx::ArrayRef<const int> nbnxn_get_atomorder(const nbnxn_search_t nbs);
+gmx::ArrayRef<const int> nbnxn_get_atomorder(const nbnxn_search* nbs);
 
 /* Renumber the atom indices on the grid to consecutive order */
 void nbnxn_set_atomorder(nbnxn_search_t nbs);

diff --git a/src/gromacs/mdlib/nbnxn_internal.h b/src/gromacs/mdlib/nbnxn_internal.h
index f63d96e04c8c89e26306a6c7cc4d13ac28f74e61..c8815f8091ab8a20e8d4d3d2ef7fffd3dfad28a5 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_internal.h
+++ b/src/gromacs/mdlib/nbnxn_internal.h
@@ -306,7 +306,7 @@ struct nbnxn_search
     gmx_icell_set_x_t   *icell_set_x; /* Function for setting i-coords    */
 
     /* Thread-local work data */
-    std::vector<nbnxn_search_work_t> work;      /* Work array, one entry for each thread */
+    mutable std::vector<nbnxn_search_work_t> work; /* Work array, one entry for each thread */
 };
 
 

diff --git a/src/gromacs/mdlib/nbnxn_search.cpp b/src/gromacs/mdlib/nbnxn_search.cpp
index 5cd0a9bafa6a71eaa7aa8fab07bf53c8537f9d6c..e8f5e4ad470b84b849e829f865aff8d74a66c040 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_search.cpp
+++ b/src/gromacs/mdlib/nbnxn_search.cpp
@@ -96,7 +96,7 @@ static double Mcyc_av(const nbnxn_cycle_t *cc)
     return (double)cc->c*1e-6/cc->count;
 }
 
-static void nbs_cycle_print(FILE *fp, const nbnxn_search_t nbs)
+static void nbs_cycle_print(FILE *fp, const nbnxn_search *nbs)
 {
     fprintf(fp, "\n");
     fprintf(fp, "ns %4d grid %4.1f search %4.1f red.f %5.3f",
@@ -963,7 +963,7 @@ void nbnxn_init_pairlist_set(nbnxn_pairlist_set_t *nbl_list,
 
 /* Print statistics of a pair list, used for debug output */
 static void print_nblist_statistics_simple(FILE *fp, const nbnxn_pairlist_t *nbl,
-                                           const nbnxn_search_t nbs, real rl)
+                                           const nbnxn_search *nbs, real rl)
 {
     const nbnxn_grid_t *grid;
     int                 cs[SHIFTS];
@@ -1012,7 +1012,7 @@ static void print_nblist_statistics_simple(FILE *fp, const nbnxn_pairlist_t *nbl
 
 /* Print statistics of a pair lists, used for debug output */
 static void print_nblist_statistics_supersub(FILE *fp, const nbnxn_pairlist_t *nbl,
-                                             const nbnxn_search_t nbs, real rl)
+                                             const nbnxn_search *nbs, real rl)
 {
     const nbnxn_grid_t *grid;
     int                 b;
@@ -1587,7 +1587,7 @@ static inline int findJClusterInJList(int                jCluster,
  * as masks in the pair-list for simple list entry iEntry.
  */
 static void
-setExclusionsForSimpleIentry(const nbnxn_search_t  nbs,
+setExclusionsForSimpleIentry(const nbnxn_search   *nbs,
                              nbnxn_pairlist_t     *nbl,
                              gmx_bool              diagRemoved,
                              int                   na_cj_2log,
@@ -1687,7 +1687,7 @@ const int max_nrj_fep = 40;
  * LJ parameters have been zeroed in the nbnxn data structure.
  * Simultaneously make a group pair list for the perturbed pairs.
  */
-static void make_fep_list(const nbnxn_search_t    nbs,
+static void make_fep_list(const nbnxn_search     *nbs,
                           const nbnxn_atomdata_t *nbat,
                           nbnxn_pairlist_t       *nbl,
                           gmx_bool                bDiagRemoved,
@@ -1889,7 +1889,7 @@ static inline int a_mod_wj(int a)
 }
 
 /* As make_fep_list above, but for super/sub lists. */
-static void make_fep_list_supersub(const nbnxn_search_t    nbs,
+static void make_fep_list_supersub(const nbnxn_search     *nbs,
                                    const nbnxn_atomdata_t *nbat,
                                    nbnxn_pairlist_t       *nbl,
                                    gmx_bool                bDiagRemoved,
@@ -2068,7 +2068,7 @@ static void make_fep_list_supersub(const nbnxn_search_t    nbs,
  * as masks in the pair-list for i-super-cluster list entry iEntry.
  */
 static void
-setExclusionsForGpuIentry(const nbnxn_search_t  nbs,
+setExclusionsForGpuIentry(const nbnxn_search   *nbs,
                           nbnxn_pairlist_t     *nbl,
                           gmx_bool              diagRemoved,
                           const nbnxn_sci_t    &iEntry,
@@ -2679,7 +2679,7 @@ static real nonlocal_vol2(const struct gmx_domdec_zones_t *zones, const rvec ls,
 }
 
 /* Estimates the average size of a full j-list for super/sub setup */
-static void get_nsubpair_target(const nbnxn_search_t  nbs,
+static void get_nsubpair_target(const nbnxn_search   *nbs,
                                 int                   iloc,
                                 real                  rlist,
                                 int                   min_ci_balanced,
@@ -2944,7 +2944,7 @@ static void combine_nblists(int nnbl, nbnxn_pairlist_t **nbl,
     }
 }
 
-static void balance_fep_lists(const nbnxn_search_t  nbs,
+static void balance_fep_lists(const nbnxn_search   *nbs,
                               nbnxn_pairlist_set_t *nbl_lists)
 {
     int       nnbl;
@@ -3200,7 +3200,7 @@ static int getBufferFlagShift(int numAtomsPerCluster)
 }
 
 /* Generates the part of pair-list nbl assigned to our thread */
-static void nbnxn_make_pairlist_part(const nbnxn_search_t nbs,
+static void nbnxn_make_pairlist_part(const nbnxn_search *nbs,
                                      const nbnxn_grid_t *gridi,
                                      const nbnxn_grid_t *gridj,
                                      nbnxn_search_work_t *work,
@@ -3812,7 +3812,7 @@ static void nbnxn_make_pairlist_part(const nbnxn_search_t nbs,
     }
 }
 
-static void reduce_buffer_flags(const nbnxn_search_t        nbs,
+static void reduce_buffer_flags(const nbnxn_search         *nbs,
                                 int                         nsrc,
                                 const nbnxn_buffer_flags_t *dest)
 {
@@ -4118,7 +4118,7 @@ static void sort_sci(nbnxn_pairlist_t *nbl)
 }
 
 /* Make a local or non-local pair-list, depending on iloc */
-void nbnxn_make_pairlist(const nbnxn_search_t  nbs,
+void nbnxn_make_pairlist(nbnxn_search         *nbs,
                          nbnxn_atomdata_t     *nbat,
                          const t_blocka       *excl,
                          real                  rlist,

diff --git a/src/gromacs/timing/walltime_accounting.cpp b/src/gromacs/timing/walltime_accounting.cpp
index 0e50d7d41a21c12c2ccef8e8d5418e6daa2b5b12..874f28ef6c7fe00fccdb5de7660adba8588ddd83 100644 (file)
--- a/src/gromacs/timing/walltime_accounting.cpp
+++ b/src/gromacs/timing/walltime_accounting.cpp
@@ -237,7 +237,7 @@ walltime_accounting_set_valid_finish(gmx_walltime_accounting_t walltime_accounti
 
 //! Return whether the simulation finished in a way valid for reporting walltime.
 bool
-walltime_accounting_get_valid_finish(const gmx_walltime_accounting_t walltime_accounting)
+walltime_accounting_get_valid_finish(const gmx_walltime_accounting* walltime_accounting)
 {
     return walltime_accounting->isValidFinish;
 }

diff --git a/src/gromacs/timing/walltime_accounting.h b/src/gromacs/timing/walltime_accounting.h
index 41f4df888aa3d4157f331dcbee9ddaf3ad4d0792..196ba3fd98a84a1977fe164ec7b101585588234f 100644 (file)
--- a/src/gromacs/timing/walltime_accounting.h
+++ b/src/gromacs/timing/walltime_accounting.h
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2017,2018, 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.
@@ -108,7 +108,7 @@ walltime_accounting_set_valid_finish(gmx_walltime_accounting_t walltime_accounti
 
 //! Return whether the simulation finished in a way valid for reporting walltime.
 bool
-walltime_accounting_get_valid_finish(const gmx_walltime_accounting_t walltime_accounting);
+walltime_accounting_get_valid_finish(const gmx_walltime_accounting* walltime_accounting);
 
 /*! \brief
  * Calls system timing routines (e.g. clock_gettime) to get the (fractional)