1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
|
/*
*
* 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 _mdebin_h
#define _mdebin_h
#include "typedefs.h"
#include "sysstuff.h"
#include "ebin.h"
#include "enxio.h"
#include "types/state.h"
#ifdef __cplusplus
extern "C" {
#endif
/* The functions & data structures here determine the content for outputting
the .edr file; the file format and actual writing is done with functions
defined in enxio.h */
/* forward declaration */
typedef struct t_mde_delta_h_coll t_mde_delta_h_coll;
/* This is the collection of energy averages collected during mdrun, and to
be written out to the .edr file. */
typedef struct {
double delta_t;
t_ebin *ebin;
int ie,iconrmsd,ib,ivol,idens,ipv,ienthalpy;
int isvir,ifvir,ipres,ivir,isurft,ipc,itemp,itc,itcb,iu,imu;
int ivcos,ivisc;
int nE,nEg,nEc,nTC,nTCP,nU,nNHC;
int *igrp;
char **grpnms;
int mde_n,mdeb_n;
real *tmp_r;
rvec *tmp_v;
gmx_bool bConstr;
gmx_bool bConstrVir;
gmx_bool bTricl;
gmx_bool bDynBox;
gmx_bool bNHC_trotter;
gmx_bool bMTTK;
gmx_bool bDiagPres;
int f_nre;
int epc;
real ref_p;
int etc;
int nCrmsd;
gmx_bool bEner[F_NRE];
gmx_bool bEInd[egNR];
char **print_grpnms;
FILE *fp_dhdl; /* the dhdl.xvg output file */
gmx_bool dhdl_derivatives; /* whether to write the derivatives to dhdl.xvg */
t_mde_delta_h_coll *dhc; /* the BAR delta U (raw data + histogram) */
} t_mdebin;
t_mdebin *init_mdebin(ener_file_t fp_ene,
const gmx_mtop_t *mtop,
const t_inputrec *ir,
FILE *fp_dhdl);
/* Initiate MD energy bin and write header to energy file. */
FILE *open_dhdl(const char *filename,const t_inputrec *ir,
const output_env_t oenv);
/* Open the dhdl file for output */
/* update the averaging structures. Called every time
the energies are evaluated. */
void upd_mdebin(t_mdebin *md,
gmx_bool write_dhdl,
gmx_bool bSum,
double time,
real tmass,
gmx_enerdata_t *enerd,
t_state *state,
matrix lastbox,
tensor svir,
tensor fvir,
tensor vir,
tensor pres,
gmx_ekindata_t *ekind,
rvec mu_tot,
gmx_constr_t constr);
void upd_mdebin_step(t_mdebin *md);
/* Updates only the step count in md */
void print_ebin_header(FILE *log,gmx_large_int_t steps,double time,real lamb);
void print_ebin(ener_file_t fp_ene,gmx_bool bEne,gmx_bool bDR,gmx_bool bOR,
FILE *log,
gmx_large_int_t step,double time,
int mode,gmx_bool bCompact,
t_mdebin *md,t_fcdata *fcd,
gmx_groups_t *groups,t_grpopts *opts);
/* Between .edr writes, the averages are history dependent,
and that history needs to be retained in checkpoints.
These functions set/read the energyhistory_t structure
that is written to checkpoints in checkpoint.c */
/* Set the energyhistory_t data structure from a mdebin structure */
void update_energyhistory(energyhistory_t * enerhist,t_mdebin * mdebin);
/* Read the energyhistory_t data structure to a mdebin structure*/
void restore_energyhistory_from_state(t_mdebin * mdebin,
energyhistory_t * enerhist);
#ifdef __cplusplus
}
#endif
#endif /* _mdebin_h */
|
