Merge branch release-2016

[alexxy/gromacs.git] / src / gromacs / imd / imd.cpp

diff --git a/src/gromacs/imd/imd.cpp b/src/gromacs/imd/imd.cpp
index 17a3273211297ece5f0fd715cd3ed1e22f7ff52d..9bd65ae71cfc4ea0a1cca047e62a5d32fe8e9cfc 100644 (file)
--- a/src/gromacs/imd/imd.cpp
+++ b/src/gromacs/imd/imd.cpp
@@ -70,12 +70,14 @@
 #include "gromacs/imd/imdsocket.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/mdlib/broadcaststructs.h"
 #include "gromacs/mdlib/groupcoord.h"
 #include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdlib/sighandler.h"
 #include "gromacs/mdlib/sim_util.h"
 #include "gromacs/mdtypes/inputrec.h"
 #include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/mdtypes/state.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/timing/wallcycle.h"
 #include "gromacs/topology/mtop_util.h"
@@ -94,12 +96,6 @@
 /*! \brief IMD Protocol Version. */
 #define IMDVERSION 2
 
-/*! \brief Broadcast d to all nodes */
-#define  block_bc(cr, d) gmx_bcast(sizeof(d), &(d), (cr))
-
-/*! \brief Broadcast nr elements of d to all nodes */
-#define  nblock_bc(cr, nr, d) gmx_bcast((nr)*sizeof((d)[0]), (d), (cr))
-
 
 /*! \internal
  * \brief
@@ -239,7 +235,7 @@ const char *eIMDType_names[IMD_NR + 1] = {
     "IMD_PAUSE",
     "IMD_TRATE",
     "IMD_IOERROR",
-    NULL
+    nullptr
 };
 
 
@@ -415,7 +411,7 @@ void write_IMDgroup_to_file(gmx_bool bIMD, t_inputrec *ir, t_state *state,
     {
         IMDatoms = gmx_mtop_global_atoms(sys);
         write_sto_conf_indexed(opt2fn("-imd", nfile, fnm), "IMDgroup", &IMDatoms,
-                               state->x, state->v, ir->ePBC, state->box, ir->imd->nat, ir->imd->ind);
+                               as_rvec_array(state->x.data()), as_rvec_array(state->v.data()), ir->ePBC, state->box, ir->imd->nat, ir->imd->ind);
     }
 }
 
@@ -470,7 +466,7 @@ static int imd_send_rvecs(IMDSocket *socket, int nat, rvec *x, char *buffer)
 /*! \brief Initializes the IMD private data. */
 static t_gmx_IMD_setup* imd_create(int imdatoms, int nstimddef, int imdport)
 {
-    t_gmx_IMD_setup *IMDsetup = NULL;
+    t_gmx_IMD_setup *IMDsetup = nullptr;
 
 
     snew(IMDsetup, 1);
@@ -560,7 +556,7 @@ static void imd_disconnect(t_gmx_IMD_setup *IMDsetup)
 
     /* then we reset the IMD step to its default, and reset the connection boolean */
     IMDsetup->nstimd_new   = IMDsetup->nstimd_def;
-    IMDsetup->clientsocket = NULL;
+    IMDsetup->clientsocket = nullptr;
     IMDsetup->bConnected   = FALSE;
 }
 
@@ -1029,7 +1025,7 @@ static FILE *open_imd_out(const char             *fn,
     fprintf(stdout, "%s For a log of the IMD pull forces explicitly specify '-if' on the command line.\n"
             "%s (Not possible with energy minimization.)\n", IMDstr, IMDstr);
 
-    return NULL;
+    return nullptr;
 }
 #endif
 
@@ -1484,7 +1480,7 @@ gmx_bool do_IMD(gmx_bool        bIMD,
                 rvec            x[],
                 t_inputrec     *ir,
                 double          t,
-                gmx_wallcycle_t wcycle)
+                gmx_wallcycle  *wcycle)
 {
     gmx_bool         imdstep = FALSE;
     t_gmx_IMD_setup *IMDsetup;
@@ -1632,7 +1628,7 @@ void IMD_send_positions(t_IMD *imd)
 void IMD_prep_energies_send_positions(gmx_bool bIMD, gmx_bool bIMDstep,
                                       t_IMD *imd, gmx_enerdata_t *enerd,
                                       gmx_int64_t step, gmx_bool bHaveNewEnergies,
-                                      gmx_wallcycle_t wcycle)
+                                      gmx_wallcycle *wcycle)
 {
     if (bIMD)
     {
@@ -1660,8 +1656,9 @@ int IMD_get_step(t_gmx_IMD *IMDsetup)
     return IMDsetup->nstimd;
 }
 
+
 void IMD_apply_forces(gmx_bool bIMD, t_IMD *imd, t_commrec *cr, rvec *f,
-                      gmx_wallcycle_t wcycle)
+                      gmx_wallcycle *wcycle)
 {
     int              i, j;
     int              locndx;