3 * This source code is part of
7 * GROningen MAchine for Chemical Simulations
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.
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.
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.
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.
30 * For more info, check our website at http://www.gromacs.org
33 * Gromacs Runs On Most of All Computer Systems
43 #include "types/state.h"
49 /* The functions & data structures here determine the content for outputting
50 the .edr file; the file format and actual writing is done with functions
53 /* forward declaration */
54 typedef struct t_mde_delta_h_coll t_mde_delta_h_coll
;
56 /* This is the collection of energy averages collected during mdrun, and to
57 be written out to the .edr file. */
61 int ie
,iconrmsd
,ib
,ivol
,idens
,ipv
,ienthalpy
;
62 int isvir
,ifvir
,ipres
,ivir
,isurft
,ipc
,itemp
,itc
,itcb
,iu
,imu
;
64 int nE
,nEg
,nEc
,nTC
,nTCP
,nU
,nNHC
;
74 gmx_bool bNHC_trotter
;
82 gmx_bool bEner
[F_NRE
];
86 FILE *fp_dhdl
; /* the dhdl.xvg output file */
87 gmx_bool dhdl_derivatives
; /* whether to write the derivatives to dhdl.xvg */
88 t_mde_delta_h_coll
*dhc
; /* the BAR delta U (raw data + histogram) */
91 t_mdebin
*init_mdebin(ener_file_t fp_ene
,
92 const gmx_mtop_t
*mtop
,
95 /* Initiate MD energy bin and write header to energy file. */
97 FILE *open_dhdl(const char *filename
,const t_inputrec
*ir
,
98 const output_env_t oenv
);
99 /* Open the dhdl file for output */
101 /* update the averaging structures. Called every time
102 the energies are evaluated. */
103 void upd_mdebin(t_mdebin
*md
,
108 gmx_enerdata_t
*enerd
,
115 gmx_ekindata_t
*ekind
,
117 gmx_constr_t constr
);
119 void upd_mdebin_step(t_mdebin
*md
);
120 /* Updates only the step count in md */
122 void print_ebin_header(FILE *log
,gmx_large_int_t steps
,double time
,real lamb
);
124 void print_ebin(ener_file_t fp_ene
,gmx_bool bEne
,gmx_bool bDR
,gmx_bool bOR
,
126 gmx_large_int_t step
,double time
,
127 int mode
,gmx_bool bCompact
,
128 t_mdebin
*md
,t_fcdata
*fcd
,
129 gmx_groups_t
*groups
,t_grpopts
*opts
);
133 /* Between .edr writes, the averages are history dependent,
134 and that history needs to be retained in checkpoints.
135 These functions set/read the energyhistory_t structure
136 that is written to checkpoints in checkpoint.c */
138 /* Set the energyhistory_t data structure from a mdebin structure */
139 void update_energyhistory(energyhistory_t
* enerhist
,t_mdebin
* mdebin
);
141 /* Read the energyhistory_t data structure to a mdebin structure*/
142 void restore_energyhistory_from_state(t_mdebin
* mdebin
,
143 energyhistory_t
* enerhist
);
149 #endif /* _mdebin_h */