/*
+ * This file is part of the GROMACS molecular simulation package.
*
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * VERSION 3.2.0
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team,
- * check out http://www.gromacs.org for more information.
-
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, 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.
+ *
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*/
#ifndef _mdrun_h
#include <stdio.h>
#include <time.h>
-#include "typedefs.h"
-#include "network.h"
-#include "sim_util.h"
-#include "tgroup.h"
-#include "filenm.h"
-#include "mshift.h"
-#include "force.h"
-#include "edsam.h"
-#include "mdebin.h"
-#include "vcm.h"
-#include "vsite.h"
-#include "pull.h"
-#include "update.h"
-#include "types/membedt.h"
-#include "types/globsig.h"
-
-
-#ifdef GMX_THREAD_MPI
-#include "thread_mpi/threads.h"
-#endif
+
+#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" {
#endif
#define MD_POLARISE (1<<2)
-#define MD_IONIZE (1<<3)
#define MD_RERUN (1<<4)
#define MD_RERUN_VSITE (1<<5)
-#define MD_FFSCAN (1<<6)
-#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)
#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
};
-/* The options for the thread affinity setting, default: auto */
-enum {
- threadaffSEL, threadaffAUTO, threadaffON, threadaffOFF, threadaffNR
-};
-
-typedef struct {
- int nthreads_tot; /* Total number of threads requested (TMPI) */
- int nthreads_tmpi; /* Number of TMPI threads requested */
- int nthreads_omp; /* Number of OpenMP threads requested */
- int nthreads_omp_pme; /* As nthreads_omp, but for PME only nodes */
- int thread_affinity; /* Thread affinity switch, see enum above */
- int core_pinning_stride; /* Logical core pinning stride */
- int core_pinning_offset; /* Logical core pinning offset */
- char *gpu_id; /* GPU id's to use, each specified as chars */
-} gmx_hw_opt_t;
-
-/* 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_large_int_t deform_init_init_step_tpx;
-extern matrix deform_init_box_tpx;
-#ifdef GMX_THREAD_MPI
-extern tMPI_Thread_mutex_t deform_init_box_mutex;
-
-/* 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,
gmx_membed_t membed,
real cpt_period, real max_hours,
const char *deviceOptions,
+ int imdport,
unsigned long Flags,
- gmx_runtime_t *runtime);
+ gmx_walltime_accounting_t walltime_accounting);
/* ROUTINES from md.c */
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, df_history_t *dfhist);
+
int ExpandedEnsembleDynamics(FILE *log, t_inputrec *ir, gmx_enerdata_t *enerd,
- t_state *state, t_extmass *MassQ, df_history_t *dfhist,
- gmx_large_int_t step, gmx_rng_t mcrng,
+ t_state *state, t_extmass *MassQ, int fep_state, df_history_t *dfhist,
+ 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 nlam, int frequency, gmx_large_int_t step);
-
-void get_mc_state(gmx_rng_t rng, t_state *state);
-
-void set_mc_state(gmx_rng_t rng, t_state *state);
+ int fep_state, int frequency, gmx_int64_t step);
/* 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. */
-void init_parallel(FILE *log, t_commrec *cr, t_inputrec *inputrec,
+/* Broadcast the data for a simulation, and allocate node-specific settings */
+void init_parallel(t_commrec *cr, t_inputrec *inputrec,
gmx_mtop_t *mtop);
int mdrunner(gmx_hw_opt_t *hw_opt,
gmx_bool bCompact, int nstglobalcomm, ivec ddxyz, int dd_node_order,
real rdd, real rconstr, const char *dddlb_opt, real dlb_scale,
const char *ddcsx, const char *ddcsy, const char *ddcsz,
- const char *nbpu_opt,
- gmx_large_int_t nsteps_cmdline, int nstepout, int resetstep,
+ const char *nbpu_opt, int nstlist_cmdline,
+ 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
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff