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/*
* $Id: mdrun.h,v 1.71.2.1 2006/04/06 08:43:28 spoel Exp $
*
* 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
* of the License, or (at your option) any later version.
*
* If you want to redistribute modifications, please consider that
* scientific software is very special. Version control is crucial -
* bugs must be traceable. We will be happy to consider code for
* inclusion in the official distribution, but derived work must not
* be called official GROMACS. Details are found in the README & COPYING
* files - if they are missing, get the official version at www.gromacs.org.
*
* 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.
*
* For more info, check our website at http://www.gromacs.org
*
* And Hey:
* Gromacs Runs On Most of All Computer Systems
*/
#ifndef _mdrun_h
#define _mdrun_h
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#include <stdio.h>
#include "typedefs.h"
#include "network.h"
#include "tgroup.h"
#include "filenm.h"
#include "nsb.h"
#include "mshift.h"
#include "force.h"
#include "time.h"
#include "edsam.h"
#include "mdebin.h"
#include "vcm.h"
#include "vsite.h"
#include "pull.h"
#define MD_MULTISIM (1<<0)
#define MD_GLAS (1<<1)
#define MD_POLARISE (1<<2)
#define MD_IONIZE (1<<3)
#define MD_RERUN (1<<4)
#define MD_FFSCAN (1<<6)
#define MD_SEPDVDL (1<<7)
/* ROUTINES from md.c */
extern time_t do_md(FILE *log,t_commrec *cr,t_commrec *mcr,
int nfile,t_filenm fnm[],
bool bVerbose,bool bCompact,bool bVsites,
t_comm_vsites *vsitecomm,int stepout,
t_inputrec *inputrec,t_groups *grps,
t_topology *top,real ener[],t_fcdata *fcd,
t_state *state,rvec vold[],rvec vt[],rvec f[],
rvec buf[],t_mdatoms *mdatoms,
t_nsborder *nsb,t_nrnb nrnb[],
t_graph *graph,t_edsamyn *edyn,
t_forcerec *fr,
int repl_ex_nst,int repl_ex_seed,
unsigned long Flags);
/* ROUTINES from minimize.c */
extern time_t do_steep(FILE *log,int nfile,t_filenm fnm[],
t_inputrec *inputrec,t_topology *top,
t_groups *grps,t_nsborder *nsb,
t_state *state,rvec grad[],rvec buf[],t_mdatoms *mdatoms,
real ener[],t_fcdata *fcd,t_nrnb nrnb[],
bool bVerbose,bool bVsites,t_comm_vsites *vsitecomm,
t_commrec *cr,t_commrec *mcr,
t_graph *graph,t_forcerec *fr);
/* Do steepest descents EM or something like that! */
extern time_t do_cg(FILE *log,int nfile,t_filenm fnm[],
t_inputrec *inputrec,t_topology *top,
t_groups *grps,t_nsborder *nsb,
t_state *state,rvec grad[],rvec buf[],t_mdatoms *mdatoms,
real ener[],t_fcdata *fcd,t_nrnb nrnb[],
bool bVerbose,bool bVsites,t_comm_vsites *vsitecomm,
t_commrec *cr,t_commrec *mcr,
t_graph *graph,t_forcerec *fr);
/* Do conjugate gradients EM! */
extern time_t do_lbfgs(FILE *log,int nfile,t_filenm fnm[],
t_inputrec *inputrec,t_topology *top,
t_groups *grps,t_nsborder *nsb, t_state *state,
rvec grad[],rvec buf[],t_mdatoms *mdatoms,
real ener[],t_fcdata *fcd,t_nrnb nrnb[],
bool bVerbose,bool bVsites,t_comm_vsites *vsitecomm,
t_commrec *cr,t_commrec *mcr,
t_graph *graph,t_forcerec *fr);
/* Do conjugate gradients EM! */
extern time_t do_nm(FILE *log,t_commrec *cr,int nfile,t_filenm fnm[],
bool bVerbose,bool bCompact,int stepout,
t_inputrec *inputrec,t_groups *grps,
t_topology *top,real ener[],t_fcdata *fcd,
t_state *state,rvec vold[],rvec vt[],rvec f[],
rvec buf[],t_mdatoms *mdatoms,
t_nsborder *nsb,t_nrnb nrnb[],
t_graph *graph,t_edsamyn *edyn,
t_forcerec *fr);
/* Do normal mode analysis */
extern time_t do_tpi(FILE *log,int nfile,t_filenm fnm[],
t_inputrec *inputrec,t_topology *top,
t_groups *grps,t_nsborder *nsb,
t_state *state,rvec f[],rvec buf[],t_mdatoms *mdatoms,
real ener[],t_fcdata *fcd,t_nrnb nrnb[],
bool bVerbose,
t_commrec *cr,t_commrec *mcr,t_graph *graph,
t_forcerec *fr);
/* Do test particle insertion */
/* ROUTINES from runner.c */
extern bool optRerunMDset (int nfile, t_filenm fnm[]);
extern void do_pbc_first(FILE *log,matrix box,t_forcerec *fr,
t_graph *graph,rvec x[]);
/* ROUTINES from stat.c */
extern void global_stat(FILE *log,
t_commrec *cr,real ener[],
tensor fvir,tensor svir,
t_grpopts *opts,t_groups *grps,
t_nrnb *mynrnb,t_nrnb nrnb[],
t_vcm *vcm,real *terminate);
/* Communicate statistics around the ring */
extern int write_traj(FILE *log,t_commrec *cr,char *traj,t_nsborder *nsb,
int step,real t,real lambda,t_nrnb nr_nb[],
int natoms,rvec *xx,rvec *vv,rvec *ff,matrix box,
t_topology *top);
/* Routine to output statusfiles during a run, as specified in
* in inputrec->ir. If any of the pointers xx,vv,ff or ener is not NULL
* it is written to the trajectory file.
* Also write the energies etc. to the log file.
* Returns the file handle (to be closed with close_trn).
*/
extern int do_per_step(int step,int nstep);
/* Return TRUE if io should be done */
extern int do_any_io(int step, t_inputrec *ir);
extern void write_xtc_traj(FILE *log,t_commrec *cr,
char *xtc_traj,t_nsborder *nsb,t_mdatoms *md,
int step,real t,rvec *xx,
matrix box,real prec);
extern void close_xtc_traj(void);
/* ROUTINES from sim_util.c */
extern void update_mdatoms(t_mdatoms *md,real lambda, bool bFirst);
/* Compute fields from mdatoms struct (invmass etc.) which may change
* due to lambda dependent FEP calculations.
* If bFirst all values are set, this is necessary once in the
* first step.
* You only have to call this routine again if lambda changes.
*/
extern void print_time(FILE *out,time_t start,int step,t_inputrec *ir);
extern time_t print_date_and_time(FILE *log,int pid,char *title);
extern void do_force(FILE *log,t_commrec *cr,t_commrec *mcr,
t_inputrec *inputrec,t_nsborder *nsb,
int step,t_nrnb *nrnb,t_topology *top,t_groups *grps,
matrix box,rvec x[],rvec f[],rvec buf[],
t_mdatoms *mdatoms,real ener[],t_fcdata *fcd,
bool bVerbose,real lambda,t_graph *graph,
bool bStateChanged,bool bNS,bool bNBFonly,bool bDoForces,
t_forcerec *fr, rvec mu_tot,
bool bGatherOnly,real t,FILE *field,t_edsamyn *edyn);
extern void sum_lrforces(rvec f[],t_forcerec *fr,int start,int homenr);
extern void calc_virial(FILE *log,int start,int homenr,rvec x[],rvec f[],
tensor vir_part,tensor vir_el_recip,
t_graph *graph,matrix box,
t_nrnb *nrnb,const t_forcerec *fr);
extern void nstop_cm(FILE *log,t_commrec *cr,
int start,int nr_atoms,real mass[],rvec x[],rvec v[]);
extern void finish_run(FILE *log,t_commrec *cr,char *confout, t_nsborder *nsb,
t_topology *top, t_inputrec *inputrec,t_nrnb nrnb[],
double nodetime,double realtime,int step,
bool bWriteStat);
extern void calc_dispcorr(FILE *fplog,t_inputrec *ir,t_forcerec *fr,int step,
int natoms,matrix box,real lambda,
tensor pres,tensor virial,real ener[]);
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;
extern void check_nnodes_top(char *fn,t_topology *top,int nnodes);
/* Verify whether this tpr file is for nnodes nodes, and quit if not */
extern void init_single(FILE *log,
t_inputrec *inputrec, char *tpbfile, t_topology *top,
t_state *state,t_mdatoms **mdatoms,
t_nsborder *nsb);
/*
* Allocates space for the topology (top), the coordinates x, the
* velocities v, masses mass. Reads the parameters, topology,
* coordinates and velocities from the file specified in tpbfile
*/
extern void distribute_parts(int left,int right,int pid,int nprocs,
t_inputrec *inputrec,char *tpbfile,int nstDlb);
/*
* Reads the parameters, topology, coordinates and velocities for the
* multi processor version of the program from the file specified in
* inputrec->files[STATUS_NM]. This file should also contain a so called
* split descriptor which describes how to distribute particles over
* the system. It then selects for all subsystems the appropriate data
* and sends this to the processor using the left and right channels.
* At last it sends its own subsystem down the ring where it is buffered.
* Its own buffers for reading the data from the file are freed, and it
* is now possible to reload this processor from the ring by using the
* init_parts() routine.
* The routine also creates a renum array which can be used for writing
* out the x,v and f for analysis purpose.
*/
extern void init_parts(FILE *log,t_commrec *cr,
t_inputrec *inputrec,t_topology *top,
t_state *state,t_mdatoms **mdatoms,
t_nsborder *nsb,int list,
bool *bParallelVsites,
t_comm_vsites *vsitecomm);
/*
* Loads the data for a simulation from the ring. Parameters, topology
* coordinates, velocities, and masses are initialised equal to using
* init_single() in the single processor version. The extra argument
* f_add is allocated to use for the update of the forces, the load
* array specifies in which part of the x and f array the subsystems
* of the other processors are located. Homenr0, homenr1, nparts0 and
* nparts1 are necessary to calculate the non bonded interaction using
* the symmetry and thus calculating every force only once. List is a facility
* for logging (and debugging). One can decide to print none or a set of
* selected parameters to the file specified by log. Parameters are
* printed by or-ing the corresponding items from t_listitem. A 0 (zero)
* specifies that nothing is to be printed on the file. The function
* returns the number of shifts over the ring to perform to calculate
* all interactions.
*/
extern void start_time(void);
/* Start timing routines */
extern void update_time(void);
/* Update the timer.This must be done at least every INT_MAX microseconds,
* or 2400 s, in order to give reliable answers.
*/
extern double node_time(void);
/* Return the node time so far in seconds. */
extern void do_shakefirst(FILE *log,real ener[],
t_inputrec *inputrec,t_nsborder *nsb,t_mdatoms *md,
t_state *state,rvec vold[],rvec buf[],rvec f[],
t_graph *graph,t_commrec *cr,t_nrnb *nrnb,
t_groups *grps,t_forcerec *fr,t_topology *top,
t_edsamyn *edyn,t_pull *pulldata);
extern void dynamic_load_balancing(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.
*/
extern void mdrunner(t_commrec *cr,t_commrec *mcr,int nfile,t_filenm fnm[],
bool bVerbose,bool bCompact,
int nDlb,int nstepout,
t_edsamyn *edyn,int repl_ex_nst,int repl_ex_seed,
unsigned long Flags);
/* Driver routine, that calls the different methods */
extern void init_md(t_commrec *cr,t_inputrec *ir,real *t,real *t0,
real *lambda,real *lam0,
t_nrnb *mynrnb,t_topology *top,
int nfile,t_filenm fnm[],char **traj,
char **xtc_traj,int *fp_ene,
FILE **fp_dgdl,FILE **fp_field,
t_mdebin **mdebin,t_groups *grps,
tensor force_vir,tensor shake_vir,
t_mdatoms *mdatoms,rvec mu_tot,
bool *bNEMD,bool *bSimAnn,t_vcm **vcm,t_nsborder *nsb);
/* Routine in sim_util.c */
extern void init_em(FILE *log,const char *title,t_inputrec *inputrec,
real *lambda,t_nrnb *mynrnb,rvec mu_tot,
matrix box,
t_forcerec *fr,t_mdatoms *mdatoms,t_topology *top,
t_nsborder *nsb,
t_commrec *cr,t_vcm **vcm,int *start,int *end);
/* Routine in minimize.c */
#endif /* _mdrun_h */
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