/usr/include/gromacs/legacyheaders/mdrun.h

/*
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 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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#ifndef _mdrun_h
#define _mdrun_h

#include <stdio.h>
#include <time.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/membedt.h"
#include "gromacs/timing/wallcycle.h"

#ifdef __cplusplus
extern "C" {
#endif

#define MD_POLARISE       (1<<2)
#define MD_RERUN          (1<<4)
#define MD_RERUN_VSITE    (1<<5)
#define MD_DDBONDCHECK    (1<<10)
#define MD_DDBONDCOMM     (1<<11)
#define MD_CONFOUT        (1<<12)
#define MD_REPRODUCIBLE   (1<<13)
#define MD_APPENDFILES    (1<<15)
#define MD_APPENDFILESSET (1<<21)
#define MD_KEEPANDNUMCPT  (1<<16)
#define MD_READ_EKIN      (1<<17)
#define MD_STARTFROMCPT   (1<<18)
#define MD_RESETCOUNTERSHALFWAY (1<<19)
#define MD_TUNEPME        (1<<20)
#define MD_NTOMPSET       (1<<21)
#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
};

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_bool bCompact, int nstglobalcomm,
                                 gmx_vsite_t *vsite, gmx_constr_t constr,
                                 int stepout,
                                 t_inputrec *inputrec,
                                 gmx_mtop_t *mtop, t_fcdata *fcd,
                                 t_state *state,
                                 t_mdatoms *mdatoms,
                                 t_nrnb *nrnb, gmx_wallcycle_t wcycle,
                                 gmx_edsam_t ed,
                                 t_forcerec *fr,
                                 int repl_ex_nst, int repl_ex_nex, int repl_ex_seed,
                                 gmx_membed_t membed,
                                 real cpt_period, real max_hours,
                                 int imdport,
                                 unsigned long Flags,
                                 gmx_walltime_accounting_t walltime_accounting);

/* ROUTINES from md.c */

gmx_integrator_t do_md;


/* ROUTINES from minimize.c */

gmx_integrator_t do_steep;
/* Do steepest descents EM */

gmx_integrator_t do_cg;
/* Do conjugate gradient EM */

gmx_integrator_t do_lbfgs;
/* Do conjugate gradient L-BFGS */

gmx_integrator_t do_nm;
/* Do normal mode analysis */

/* ROUTINES from tpi.c */

gmx_integrator_t do_tpi;
/* Do test particle insertion */

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, 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 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);

/* 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,
             FILE *fplog, t_commrec *cr, int nfile,
             const t_filenm fnm[], const output_env_t oenv, gmx_bool bVerbose,
             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, 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,
             int imdport, unsigned long Flags);
/* Driver routine, that calls the different methods */

void bcast_state(const struct t_commrec *cr, t_state *state);
/* Broadcasts state from the master to all nodes in cr->mpi_comm_mygroup.
 */

#ifdef __cplusplus
}
#endif

#endif  /* _mdrun_h */
libgromacs-dev 5.1.2-1ubuntu1 / usr / include / gromacs / legacyheaders / mdrun.h
