Sort all includes in src/gromacs

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

diff --git a/src/gromacs/legacyheaders/mdrun.h b/src/gromacs/legacyheaders/mdrun.h
index 013a266beee56d393967adfc45d1fa27928d8150..754a3796c3c1b7aed409c92f62fae2acb3f66710 100644 (file)
--- a/src/gromacs/legacyheaders/mdrun.h
+++ b/src/gromacs/legacyheaders/mdrun.h
@@ -40,20 +40,19 @@
 
 #include <stdio.h>
 #include <time.h>
-#include "typedefs.h"
-#include "network.h"
-#include "sim_util.h"
-#include "tgroup.h"
-#include "../fileio/filenm.h"
-#include "mshift.h"
-#include "mdebin.h"
-#include "vcm.h"
-#include "vsite.h"
-#include "update.h"
-#include "types/membedt.h"
-#include "types/globsig.h"
-
-#include "thread_mpi/threads.h"
+
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/legacyheaders/mdebin.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/sim_util.h"
+#include "gromacs/legacyheaders/tgroup.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/update.h"
+#include "gromacs/legacyheaders/vcm.h"
+#include "gromacs/legacyheaders/vsite.h"
+#include "gromacs/legacyheaders/types/globsig.h"
+#include "gromacs/legacyheaders/types/membedt.h"
+#include "gromacs/timing/wallcycle.h"
 
 #ifdef __cplusplus
 extern "C" {
@@ -62,13 +61,10 @@ extern "C" {
 #define MD_POLARISE       (1<<2)
 #define MD_RERUN          (1<<4)
 #define MD_RERUN_VSITE    (1<<5)
-#define MD_SEPPOT         (1<<7)
-#define MD_PARTDEC        (1<<9)
 #define MD_DDBONDCHECK    (1<<10)
 #define MD_DDBONDCOMM     (1<<11)
 #define MD_CONFOUT        (1<<12)
 #define MD_REPRODUCIBLE   (1<<13)
-#define MD_READ_RNG       (1<<14)
 #define MD_APPENDFILES    (1<<15)
 #define MD_APPENDFILESSET (1<<21)
 #define MD_KEEPANDNUMCPT  (1<<16)
@@ -77,29 +73,15 @@ extern "C" {
 #define MD_RESETCOUNTERSHALFWAY (1<<19)
 #define MD_TUNEPME        (1<<20)
 #define MD_TESTVERLET     (1<<22)
+#define MD_IMDWAIT        (1<<23)
+#define MD_IMDTERM        (1<<24)
+#define MD_IMDPULL        (1<<25)
 
 /* The options for the domain decomposition MPI task ordering */
 enum {
     ddnoSEL, ddnoINTERLEAVE, ddnoPP_PME, ddnoCARTESIAN, ddnoNR
 };
 
-/* Variables for temporary use with the deform option,
- * used in runner.c and md.c.
- * (These variables should be stored in the tpx file.)
- */
-extern gmx_int64_t         deform_init_init_step_tpx;
-extern matrix              deform_init_box_tpx;
-extern tMPI_Thread_mutex_t deform_init_box_mutex;
-
-#ifdef GMX_THREAD_MPI
-/* The minimum number of atoms per tMPI thread. With fewer atoms than this,
- * the number of threads will get lowered.
- */
-#define MIN_ATOMS_PER_MPI_THREAD    90
-#define MIN_ATOMS_PER_GPU           900
-#endif
-
-
 typedef double gmx_integrator_t (FILE *log, t_commrec *cr,
                                  int nfile, const t_filenm fnm[],
                                  const output_env_t oenv, gmx_bool bVerbose,
@@ -117,6 +99,7 @@ typedef double gmx_integrator_t (FILE *log, t_commrec *cr,
                                  gmx_membed_t membed,
                                  real cpt_period, real max_hours,
                                  const char *deviceOptions,
+                                 int imdport,
                                  unsigned long Flags,
                                  gmx_walltime_accounting_t walltime_accounting);
 
@@ -146,29 +129,24 @@ gmx_integrator_t do_tpi;
 
 void init_npt_masses(t_inputrec *ir, t_state *state, t_extmass *MassQ, gmx_bool bInit);
 
-void init_expanded_ensemble(gmx_bool bStateFromCP, t_inputrec *ir, gmx_rng_t *mcrng, df_history_t *dfhist);
+void init_expanded_ensemble(gmx_bool bStateFromCP, t_inputrec *ir, df_history_t *dfhist);
 
 int ExpandedEnsembleDynamics(FILE *log, t_inputrec *ir, gmx_enerdata_t *enerd,
                              t_state *state, t_extmass *MassQ, int fep_state, df_history_t *dfhist,
-                             gmx_int64_t step, gmx_rng_t mcrng,
+                             gmx_int64_t step,
                              rvec *v, t_mdatoms *mdatoms);
 
 void PrintFreeEnergyInfoToFile(FILE *outfile, t_lambda *fep, t_expanded *expand, t_simtemp *simtemp, df_history_t *dfhist,
                                int fep_state, int frequency, gmx_int64_t step);
 
-void get_mc_state(gmx_rng_t rng, t_state *state);
-
-void set_mc_state(gmx_rng_t rng, t_state *state);
-
 /* check the version */
 void check_ir_old_tpx_versions(t_commrec *cr, FILE *fplog,
                                t_inputrec *ir, gmx_mtop_t *mtop);
 
 /* Allocate and initialize node-local state entries. */
-void set_state_entries(t_state *state, const t_inputrec *ir, int nnodes);
+void set_state_entries(t_state *state, const t_inputrec *ir);
 
-/* Broadcast the data for a simulation, and allocate node-specific settings
-   such as rng generators. */
+/* Broadcast the data for a simulation, and allocate node-specific settings */
 void init_parallel(t_commrec *cr, t_inputrec *inputrec,
                    gmx_mtop_t *mtop);
 
@@ -182,7 +160,7 @@ int mdrunner(gmx_hw_opt_t *hw_opt,
              gmx_int64_t nsteps_cmdline, int nstepout, int resetstep,
              int nmultisim, int repl_ex_nst, int repl_ex_nex,
              int repl_ex_seed, real pforce, real cpt_period, real max_hours,
-             const char *deviceOptions, unsigned long Flags);
+             const char *deviceOptions, int imdport, unsigned long Flags);
 /* Driver routine, that calls the different methods */
 
 #ifdef __cplusplus