include/md_support.h

   1 /*
   2  *
   3  *                This source code is part of
   4  *
   5  *                 G   R   O   M   A   C   S
   6  *
   7  *          GROningen MAchine for Chemical Simulations
   8  *
   9  *                        VERSION 3.2.0
  10  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  11  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  12  * Copyright (c) 2001-2004, The GROMACS development team,
  13  * check out http://www.gromacs.org for more information.
  14
  15  * This program is free software; you can redistribute it and/or
  16  * modify it under the terms of the GNU General Public License
  17  * as published by the Free Software Foundation; either version 2
  18  * of the License, or (at your option) any later version.
  19  *
  20  * If you want to redistribute modifications, please consider that
  21  * scientific software is very special. Version control is crucial -
  22  * bugs must be traceable. We will be happy to consider code for
  23  * inclusion in the official distribution, but derived work must not
  24  * be called official GROMACS. Details are found in the README & COPYING
  25  * files - if they are missing, get the official version at www.gromacs.org.
  26  *
  27  * To help us fund GROMACS development, we humbly ask that you cite
  28  * the papers on the package - you can find them in the top README file.
  29  *
  30  * For more info, check our website at http://www.gromacs.org
  31  *
  32  * And Hey:
  33  * Gromacs Runs On Most of All Computer Systems
  34  */
  35
  36 #ifndef _md_support_h
  37 #define _md_support_h
  38
  39 #include "typedefs.h"
  40 #include "types/globsig.h"
  41 #include "sim_util.h"
  42 #include "vcm.h"
  43
  44 #ifdef __cplusplus
  45 extern "C" {
  46 #endif
  47
  48 /* Define a number of flags to better control the information
  49  * passed to compute_globals in md.c and global_stat.
  50  */
  51
  52 /* We are rerunning the simulation */
  53 #define CGLO_RERUNMD        (1<<1)
  54 /* we are computing the kinetic energy from average velocities */
  55 #define CGLO_EKINAVEVEL     (1<<2)
  56 /* we are removing the center of mass momenta */
  57 #define CGLO_STOPCM         (1<<3)
  58 /* bGStat is defined in do_md */
  59 #define CGLO_GSTAT          (1<<4)
  60 /* Sum the energy terms in global computation */
  61 #define CGLO_ENERGY         (1<<6)
  62 /* Sum the kinetic energy terms in global computation */
  63 #define CGLO_TEMPERATURE    (1<<7)
  64 /* Sum the kinetic energy terms in global computation */
  65 #define CGLO_PRESSURE       (1<<8)
  66 /* Sum the constraint term in global computation */
  67 #define CGLO_CONSTRAINT     (1<<9)
  68 /* we are using an integrator that requires iteration over some steps - currently not used*/
  69 #define CGLO_ITERATE        (1<<10)
  70 /* it is the first time we are iterating (or, only once through is required */
  71 #define CGLO_FIRSTITERATE   (1<<11)
  72 /* Reading ekin from the trajectory */
  73 #define CGLO_READEKIN       (1<<12)
  74 /* we need to reset the ekin rescaling factor here */
  75 #define CGLO_SCALEEKIN      (1<<13)
  76
  77
  78 /* return the number of steps between global communcations */
  79 int check_nstglobalcomm(FILE *fplog,t_commrec *cr,
  80                         int nstglobalcomm,t_inputrec *ir);
  81
  82 /* check whether an 'nst'-style parameter p is a multiple of nst, and
  83    set it to be one if not, with a warning. */
  84 void check_nst_param(FILE *fplog,t_commrec *cr,
  85                      const char *desc_nst,int nst,
  86                      const char *desc_p,int *p);
  87
  88 /* check which of the multisim simulations has the shortest number of
  89    steps and return that number of nsteps */
  90 gmx_large_int_t get_multisim_nsteps(const t_commrec *cr,
  91                                     gmx_large_int_t nsteps);
  92
  93 void rerun_parallel_comm(t_commrec *cr,t_trxframe *fr,
  94                          gmx_bool *bNotLastFrame);
  95
  96 /* get the conserved energy associated with the ensemble type*/
  97 real compute_conserved_from_auxiliary(t_inputrec *ir, t_state *state,
  98                                       t_extmass *MassQ);
  99
 100 /* set the lambda values at each step of mdrun when they change */
 101 void set_current_lambdas(gmx_large_int_t step, t_lambda *fepvals, gmx_bool bRerunMD,
 102                          t_trxframe *rerun_fr, t_state *state_global, t_state *state, double lam0[]);
 103
 104 int multisim_min(const gmx_multisim_t *ms,int nmin,int n);
 105 /* Set an appropriate value for n across the whole multi-simulation */
 106
 107 int multisim_nstsimsync(const t_commrec *cr,
 108                         const t_inputrec *ir,int repl_ex_nst);
 109 /* Determine the interval for inter-simulation communication */
 110
 111 void init_global_signals(globsig_t *gs,const t_commrec *cr,
 112                          const t_inputrec *ir,int repl_ex_nst);
 113 /* Constructor for globsig_t */
 114
 115 void copy_coupling_state(t_state *statea,t_state *stateb,
 116                          gmx_ekindata_t *ekinda,gmx_ekindata_t *ekindb, t_grpopts* opts);
 117 /* Copy stuff from state A to state B */
 118
 119 void compute_globals(FILE *fplog, gmx_global_stat_t gstat, t_commrec *cr, t_inputrec *ir,
 120                      t_forcerec *fr, gmx_ekindata_t *ekind,
 121                      t_state *state, t_state *state_global, t_mdatoms *mdatoms,
 122                      t_nrnb *nrnb, t_vcm *vcm, gmx_wallcycle_t wcycle,
 123                      gmx_enerdata_t *enerd,tensor force_vir, tensor shake_vir, tensor total_vir,
 124                      tensor pres, rvec mu_tot, gmx_constr_t constr,
 125                      globsig_t *gs,gmx_bool bInterSimGS,
 126                      matrix box, gmx_mtop_t *top_global, real *pcurr,
 127                      int natoms, gmx_bool *bSumEkinhOld, int flags);
 128 /* Compute global variables during integration */
 129
 130 void md_print_info(const t_commrec *cr, FILE *fplog,
 131                    const char *fmt, ...);
 132 /* Print an general information message to stderr on the master node
 133  * and to fplog if fplog!=NULL.
 134  * fmt is a standard printf formatting string which should end in \n,
 135  * the arguments after that contain the values to be printed, as in printf.
 136  */
 137
 138 void md_print_warn(const t_commrec *cr, FILE *fplog,
 139                    const char *fmt, ...);
 140 /* As md_print_info above, but for important notices or warnings.
 141  * The only difference with md_print_info is that a newline is printed
 142  * before and after the message such that it stands out.
 143  */
 144
 145 #ifdef __cplusplus
 146 }
 147 #endif
 148
 149 #endif  /* _md_support_h */