/*
- *
- * 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.
+ * This file is part of the GROMACS molecular simulation package.
+ *
* 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.
+ *
+ * GROMACS is free software; you can redistribute it and/or
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* of the License, or (at your option) any later version.
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+ *
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+ *
* To help us fund GROMACS development, we humbly ask that you cite
- * the papers on the package - you can find them in the top README file.
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+ * the research papers on the package. Check out http://www.gromacs.org.
*/
#ifndef _mdrun_h
#include <stdio.h>
#include <time.h>
-#include "typedefs.h"
-#include "network.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"
-
-#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_READ_EKIN (1<<17)
#define MD_STARTFROMCPT (1<<18)
#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)
-/* Define a number of flags to better control the information
- * passed to compute_globals in md.c and global_stat.
- */
-
-/* We are rerunning the simulation */
-#define CGLO_RERUNMD (1<<1)
-/* we are computing the kinetic energy from average velocities */
-#define CGLO_EKINAVEVEL (1<<2)
-/* we are removing the center of mass momenta */
-#define CGLO_STOPCM (1<<3)
-/* bGStat is defined in do_md */
-#define CGLO_GSTAT (1<<4)
-/* Sum the energy terms in global computation */
-#define CGLO_ENERGY (1<<6)
-/* Sum the kinetic energy terms in global computation */
-#define CGLO_TEMPERATURE (1<<7)
-/* Sum the kinetic energy terms in global computation */
-#define CGLO_PRESSURE (1<<8)
-/* Sum the constraint term in global computation */
-#define CGLO_CONSTRAINT (1<<9)
-/* we are using an integrator that requires iteration over some steps - currently not used*/
-#define CGLO_ITERATE (1<<10)
-/* it is the first time we are iterating (or, only once through is required */
-#define CGLO_FIRSTITERATE (1<<11)
-/* Reading ekin from the trajectory */
-#define CGLO_READEKIN (1<<12)
-/* we need to reset the ekin rescaling factor here */
-#define CGLO_SCALEEKIN (1<<13)
-
+/* The options for the domain decomposition MPI task ordering */
enum {
- ddnoSEL, ddnoINTERLEAVE, ddnoPP_PME, ddnoCARTESIAN, ddnoNR
+ ddnoSEL, ddnoINTERLEAVE, ddnoPP_PME, ddnoCARTESIAN, ddnoNR
};
-typedef struct {
- double real;
-#ifdef GMX_CRAY_XT3
- double proc;
-#else
- clock_t proc;
-#endif
- double realtime;
- double proctime;
- double time_per_step;
- double last;
- gmx_large_int_t nsteps_done;
-} gmx_runtime_t;
-
-typedef struct {
- t_fileio *fp_trn;
- t_fileio *fp_xtc;
- int xtc_prec;
- ener_file_t fp_ene;
- const char *fn_cpt;
- gmx_bool bKeepAndNumCPT;
- int eIntegrator;
- gmx_bool bExpanded;
- int elamstats;
- int simulation_part;
- FILE *fp_dhdl;
- FILE *fp_field;
-} gmx_mdoutf_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 thread. With fewer atoms than this,
- * the number of threads will get lowered.
- */
-#define MIN_ATOMS_PER_THREAD 90
-#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_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,
- const char *deviceOptions,
- unsigned long Flags,
- gmx_runtime_t *runtime);
-
-typedef struct gmx_global_stat *gmx_global_stat_t;
+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,
+ const char *deviceOptions,
+ int imdport,
+ unsigned long Flags,
+ gmx_walltime_accounting_t walltime_accounting);
/* ROUTINES from md.c */
gmx_integrator_t do_md;
-gmx_integrator_t do_md_openmm;
-
-
/* ROUTINES from minimize.c */
gmx_integrator_t do_tpi;
/* Do test particle insertion */
-
-/* ROUTINES from md_support.c */
-
-/* return the number of steps between global communcations */
-int check_nstglobalcomm(FILE *fplog,t_commrec *cr,
- int nstglobalcomm,t_inputrec *ir);
-
-/* check whether an 'nst'-style parameter p is a multiple of nst, and
- set it to be one if not, with a warning. */
-void check_nst_param(FILE *fplog,t_commrec *cr,
- const char *desc_nst,int nst,
- const char *desc_p,int *p);
-
-/* check which of the multisim simulations has the shortest number of
- steps and return that number of nsteps */
-gmx_large_int_t get_multisim_nsteps(const t_commrec *cr,
- gmx_large_int_t nsteps);
-
-void rerun_parallel_comm(t_commrec *cr,t_trxframe *fr,
- gmx_bool *bNotLastFrame);
-
-/* get the conserved energy associated with the ensemble type*/
-real compute_conserved_from_auxiliary(t_inputrec *ir, t_state *state,
- t_extmass *MassQ);
-
-/* set the lambda values at each step of mdrun when they change */
-void set_current_lambdas(gmx_large_int_t step, t_lambda *fepvals, gmx_bool bRerunMD,
- t_trxframe *rerun_fr, t_state *state_global, t_state *state, double lam0[]);
-
-/* reset all cycle and time counters. */
-void reset_all_counters(FILE *fplog,t_commrec *cr,
- gmx_large_int_t step,
- gmx_large_int_t *step_rel,t_inputrec *ir,
- gmx_wallcycle_t wcycle,t_nrnb *nrnb,
- gmx_runtime_t *runtime);
-
-
-
-/* ROUTINES from sim_util.c */
-void do_pbc_first(FILE *log,matrix box,t_forcerec *fr,
- t_graph *graph,rvec x[]);
-
-void do_pbc_first_mtop(FILE *fplog,int ePBC,matrix box,
- gmx_mtop_t *mtop,rvec x[]);
-
-void do_pbc_mtop(FILE *fplog,int ePBC,matrix box,
- gmx_mtop_t *mtop,rvec x[]);
-
-
-
-/* ROUTINES from stat.c */
-gmx_global_stat_t global_stat_init(t_inputrec *ir);
-
-void global_stat_destroy(gmx_global_stat_t gs);
-
-void global_stat(FILE *log,gmx_global_stat_t gs,
- t_commrec *cr,gmx_enerdata_t *enerd,
- tensor fvir,tensor svir,rvec mu_tot,
- t_inputrec *inputrec,
- gmx_ekindata_t *ekind,
- gmx_constr_t constr,t_vcm *vcm,
- int nsig,real *sig,
- gmx_mtop_t *top_global, t_state *state_local,
- gmx_bool bSumEkinhOld, int flags);
-/* Communicate statistics over cr->mpi_comm_mysim */
-
-gmx_mdoutf_t *init_mdoutf(int nfile,const t_filenm fnm[],
- int mdrun_flags,
- const t_commrec *cr,const t_inputrec *ir,
- const output_env_t oenv);
-/* Returns a pointer to a data structure with all output file pointers
- * and names required by mdrun.
- */
-
-void done_mdoutf(gmx_mdoutf_t *of);
-/* Close all open output files and free the of pointer */
-
-#define MDOF_X (1<<0)
-#define MDOF_V (1<<1)
-#define MDOF_F (1<<2)
-#define MDOF_XTC (1<<3)
-#define MDOF_CPT (1<<4)
-
-void write_traj(FILE *fplog,t_commrec *cr,
- gmx_mdoutf_t *of,
- int mdof_flags,
- gmx_mtop_t *top_global,
- gmx_large_int_t step,double t,
- t_state *state_local,t_state *state_global,
- rvec *f_local,rvec *f_global,
- int *n_xtc,rvec **x_xtc);
-/* Routine that writes frames to trn, xtc and/or checkpoint.
- * What is written is determined by the mdof_flags defined above.
- * Data is collected to the master node only when necessary.
- */
-
-int do_per_step(gmx_large_int_t step,gmx_large_int_t nstep);
-/* Return TRUE if io should be done */
-
-int do_any_io(int step, t_inputrec *ir);
-
-/* ROUTINES from sim_util.c */
-
-double gmx_gettime();
-
-void print_time(FILE *out, gmx_runtime_t *runtime,
- gmx_large_int_t step,t_inputrec *ir, t_commrec *cr);
-
-void runtime_start(gmx_runtime_t *runtime);
-
-void runtime_end(gmx_runtime_t *runtime);
-
-void runtime_upd_proc(gmx_runtime_t *runtime);
-/* The processor time should be updated every once in a while,
- * since on 32-bit manchines it loops after 72 minutes.
- */
-
-void print_date_and_time(FILE *log,int pid,const char *title,
- const gmx_runtime_t *runtime);
-
-void nstop_cm(FILE *log,t_commrec *cr,
- int start,int nr_atoms,real mass[],rvec x[],rvec v[]);
-
-void finish_run(FILE *log,t_commrec *cr,const char *confout,
- t_inputrec *inputrec,
- t_nrnb nrnb[],gmx_wallcycle_t wcycle,
- gmx_runtime_t *runtime,
- gmx_bool bWriteStat);
-
-void calc_enervirdiff(FILE *fplog,int eDispCorr,t_forcerec *fr);
-
-void calc_dispcorr(FILE *fplog,t_inputrec *ir,t_forcerec *fr,
- gmx_large_int_t step, int natoms,
- matrix box,real lambda,tensor pres,tensor virial,
- real *prescorr, real *enercorr, real *dvdlcorr);
-
-void initialize_lambdas(FILE *fplog,t_inputrec *ir,int *fep_state,real *lambda,double *lam0);
-
void init_npt_masses(t_inputrec *ir, t_state *state, t_extmass *MassQ, gmx_bool bInit);
-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,
+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 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);
-
-
-typedef enum
-{
- LIST_SCALARS =0001,
- LIST_INPUTREC =0002,
- LIST_TOP =0004,
- LIST_X =0010,
- LIST_V =0020,
- LIST_F =0040,
- LIST_LOAD =0100
-} t_listitem;
-
-void check_nnodes_top(char *fn,t_topology *top);
-/* Reset the tpr file to work with one node if necessary */
-
+ 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);
+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,
- gmx_mtop_t *mtop);
+/* Broadcast the data for a simulation, and allocate node-specific settings */
+void init_parallel(t_commrec *cr, t_inputrec *inputrec,
+ gmx_mtop_t *mtop);
-
-void do_constrain_first(FILE *log,gmx_constr_t constr,
- t_inputrec *inputrec,t_mdatoms *md,
- t_state *state,rvec *f,
- t_graph *graph,t_commrec *cr,t_nrnb *nrnb,
- t_forcerec *fr, gmx_localtop_t *top, tensor shake_vir);
-
-void dynamic_load_balancing(gmx_bool bVerbose,t_commrec *cr,real capacity[],
- int dimension,t_mdatoms *md,t_topology *top,
- rvec x[],rvec v[],matrix box);
-/* Perform load balancing, i.e. split the particles over processors
- * based on their coordinates in the "dimension" direction.
- */
-
-int multisim_min(const gmx_multisim_t *ms,int nmin,int n);
-/* Set an appropriate value for n across the whole multi-simulation */
-
-int multisim_nstsimsync(const t_commrec *cr,
- const t_inputrec *ir,int repl_ex_nst);
-/* Determine the interval for inter-simulation communication */
-
-void init_global_signals(globsig_t *gs,const t_commrec *cr,
- const t_inputrec *ir,int repl_ex_nst);
-/* Constructor for globsig_t */
-
-void copy_coupling_state(t_state *statea,t_state *stateb,
- gmx_ekindata_t *ekinda,gmx_ekindata_t *ekindb, t_grpopts* opts);
-/* Copy stuff from state A to state B */
-
-void compute_globals(FILE *fplog, gmx_global_stat_t gstat, t_commrec *cr, t_inputrec *ir,
- t_forcerec *fr, gmx_ekindata_t *ekind,
- t_state *state, t_state *state_global, t_mdatoms *mdatoms,
- t_nrnb *nrnb, t_vcm *vcm, gmx_wallcycle_t wcycle,
- gmx_enerdata_t *enerd,tensor force_vir, tensor shake_vir, tensor total_vir,
- tensor pres, rvec mu_tot, gmx_constr_t constr,
- globsig_t *gs,gmx_bool bInterSimGS,
- matrix box, gmx_mtop_t *top_global, real *pcurr,
- int natoms, gmx_bool *bSumEkinhOld, int flags);
-/* Compute global variables during integration */
-
-int mdrunner(int nthreads_requested, FILE *fplog,t_commrec *cr,int nfile,
+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,
- 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);
+ 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,
+ const char *deviceOptions, int imdport, unsigned long Flags);
/* Driver routine, that calls the different methods */
-void md_print_warning(const t_commrec *cr,FILE *fplog,const char *buf);
-/* Print a warning message to stderr on the master node
- * and to fplog if fplog!=NULL.
- */
-
-void init_md(FILE *fplog,
- t_commrec *cr,t_inputrec *ir, const output_env_t oenv,
- double *t,double *t0,
- real *lambda,int *fep_state, double *lam0,
- t_nrnb *nrnb,gmx_mtop_t *mtop,
- gmx_update_t *upd,
- int nfile,const t_filenm fnm[],
- gmx_mdoutf_t **outf,t_mdebin **mdebin,
- tensor force_vir,tensor shake_vir,
- rvec mu_tot,
- gmx_bool *bSimAnn,t_vcm **vcm,
- t_state *state, unsigned long Flags);
- /* Routine in sim_util.c */
-
#ifdef __cplusplus
}
#endif
-#endif /* _mdrun_h */
+#endif /* _mdrun_h */
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff