/*
- *
- * This source code is part of
- *
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- * GROningen MAchine for Chemical Simulations
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- * 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.
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+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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*/
#ifndef _mdebin_h
#define _mdebin_h
-#include "typedefs.h"
-#include "sysstuff.h"
-#include "ebin.h"
-#include "enxio.h"
-#include "types/state.h"
+#include <stdio.h>
+
+#include "gromacs/fileio/enxio.h"
+#include "gromacs/legacyheaders/ebin.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/state.h"
#ifdef __cplusplus
extern "C" {
#endif
-/* The functions & data structures here determine the content for outputting
+/* 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
+
+/* 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 bPrintNHChains;
- gmx_bool bMTTK;
- gmx_bool bMu; /* true if dipole is calculated */
- gmx_bool bDiagPres;
- gmx_bool bVir;
- gmx_bool bPress;
- gmx_bool bSurft;
- 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 */
- t_mde_delta_h_coll *dhc; /* the delta U components (raw data + histogram) */
- real *temperatures;
+ 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 bPrintNHChains;
+ gmx_bool bMTTK;
+ gmx_bool bMu; /* true if dipole is calculated */
+ gmx_bool bDiagPres;
+ gmx_bool bVir;
+ gmx_bool bPress;
+ gmx_bool bSurft;
+ 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 */
+ double *dE; /* energy components for dhdl.xvg output */
+ t_mde_delta_h_coll *dhc; /* the delta U components (raw data + histogram) */
+ real *temperatures;
} t_mdebin;
-t_mdebin *init_mdebin(ener_file_t fp_ene,
- const gmx_mtop_t *mtop,
- const t_inputrec *ir,
- FILE *fp_dhdl);
+
+/* delta_h block type enum: the kinds of energies written out. */
+enum
+{
+ dhbtDH = 0, /* delta H BAR energy difference*/
+ dhbtDHDL = 1, /* dH/dlambda derivative */
+ dhbtEN, /* System energy */
+ dhbtPV, /* pV term */
+ dhbtEXPANDED, /* expanded ensemble statistics */
+ dhbtNR
+};
+
+
+
+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);
+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
+/* update the averaging structures. Called every time
the energies are evaluated. */
-void upd_mdebin(t_mdebin *md,
- gmx_bool bDoDHDL,
- gmx_bool bSum,
- double time,
- real tmass,
- gmx_enerdata_t *enerd,
- t_state *state,
- t_lambda *fep,
- t_expanded *expand,
- matrix lastbox,
- tensor svir,
- tensor fvir,
- tensor vir,
- tensor pres,
- gmx_ekindata_t *ekind,
- rvec mu_tot,
- gmx_constr_t constr);
+void upd_mdebin(t_mdebin *md,
+ gmx_bool bDoDHDL,
+ gmx_bool bSum,
+ double time,
+ real tmass,
+ gmx_enerdata_t *enerd,
+ t_state *state,
+ t_lambda *fep,
+ t_expanded *expand,
+ 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);
+void print_ebin_header(FILE *log, gmx_int64_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_int64_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.
+ 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);
+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);
+void restore_energyhistory_from_state(t_mdebin * mdebin,
+ energyhistory_t * enerhist);
#ifdef __cplusplus
}
#endif
-#endif /* _mdebin_h */
-
+#endif /* _mdebin_h */
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff