*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
double **v;
} t_oriresdata;
+typedef struct {
+ int n; /* n+1 is the number of points */
+ real scale; /* distance between two points */
+ real *data; /* the actual table data, per point there are 4 numbers */
+} bondedtable_t;
+
/*
* Data struct used in the force calculation routines
* for storing the tables for bonded interactions and
#include <stdio.h>
#include "gromacs/legacyheaders/types/simple.h"
-#include "gromacs/legacyheaders/types/idef.h"
#include "gromacs/math/vectypes.h"
#include "gromacs/utility/basedefinitions.h"
extern "C" {
#endif
+struct t_idef;
+struct t_ilist;
+
typedef enum {
egcolWhite, egcolGrey, egcolBlack, egcolNR
} egCol;
#define SHIFT_IVEC(g, i) ((g)->ishift[i])
t_graph *mk_graph(FILE *fplog,
- t_idef *idef, int at_start, int at_end,
+ struct t_idef *idef, int at_start, int at_end,
gmx_bool bShakeOnly, gmx_bool bSettle);
/* Build a graph from an idef description. The graph can be used
* to generate mol-shift indices.
*/
void mk_graph_ilist(FILE *fplog,
- t_ilist *ilist, int at_start, int at_end,
+ struct t_ilist *ilist, int at_start, int at_end,
gmx_bool bShakeOnly, gmx_bool bSettle,
t_graph *g);
/* As mk_graph, but takes t_ilist iso t_idef and does not allocate g */
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+#ifndef GMX_TOPOLOGY_IDEF_H
+#define GMX_TOPOLOGY_IDEF_H
-
-#ifndef _idef_h
-#define _idef_h
-
-#include "simple.h"
+#include "../legacyheaders/types/simple.h"
#ifdef __cplusplus
extern "C" {
F_DVDL_BONDED,
F_DVDL_RESTRAINT,
F_DVDL_TEMPERATURE, /* not calculated for now, but should just be the energy (NVT) or enthalpy (NPT), or 0 (NVE) */
- F_NRE /* This number is for the total number of energies */
+ F_NRE /* This number is for the total number of energies */
};
#define IS_RESTRAINT_TYPE(ifunc) (((ifunc == F_POSRES) || (ifunc == F_FBPOSRES) || (ifunc == F_DISRES) || (ifunc == F_RESTRBONDS) || (ifunc == F_DISRESVIOL) || (ifunc == F_ORIRES) || (ifunc == F_ORIRESDEV) || (ifunc == F_ANGRES) || (ifunc == F_ANGRESZ) || (ifunc == F_DIHRES)))
*/
#define IS_LISTED_LJ_C(ftype) ((ftype) >= F_LJ14 && (ftype) <= F_LJC_PAIRS_NB)
-typedef union
+typedef union t_iparams
{
/* Some parameters have A and B values for free energy calculations.
* The B values are not used for regular simulations of course.
* the remaining ones from nr_nonperturbed..(nr-1) are perturbed bonded
* interactions.
*/
-typedef struct
+typedef struct t_ilist
{
int nr;
int nr_nonperturbed;
* The struct t_ilist defines a list of atoms with their interactions.
* General field description:
* int nr
- * the size (nr elements) of the interactions array (iatoms[]).
+ * the size (nr elements) of the interactions array (iatoms[]).
* t_iatom *iatoms
* specifies which atoms are involved in an interaction of a certain
* type. The layout of this array is as follows:
*
- * +-----+---+---+---+-----+---+---+-----+---+---+---+-----+---+---+...
- * |type1|at1|at2|at3|type2|at1|at2|type1|at1|at2|at3|type3|at1|at2|
- * +-----+---+---+---+-----+---+---+-----+---+---+---+-----+---+---+...
+ * +-----+---+---+---+-----+---+---+-----+---+---+---+-----+---+---+...
+ * |type1|at1|at2|at3|type2|at1|at2|type1|at1|at2|at3|type3|at1|at2|
+ * +-----+---+---+---+-----+---+---+-----+---+---+---+-----+---+---+...
*
* So for interaction type type1 3 atoms are needed, and for type2 and
* type3 only 2. The type identifier is used to select the function to
- * calculate the interaction and its actual parameters. This type
- * identifier is an index in a params[] and functype[] array.
+ * calculate the interaction and its actual parameters. This type
+ * identifier is an index in a params[] and functype[] array.
*/
typedef struct
{
real *cmap; /* Has length 4*grid_spacing*grid_spacing, */
/* there are 4 entries for each cmap type (V,dVdx,dVdy,d2dVdxdy) */
-} cmapdata_t;
+} gmx_cmapdata_t;
-typedef struct
+typedef struct gmx_cmap_t
{
- int ngrid; /* Number of allocated cmap (cmapdata_t ) grids */
- int grid_spacing; /* Grid spacing */
- cmapdata_t *cmapdata; /* Pointer to grid with actual, pre-interpolated data */
+ int ngrid; /* Number of allocated cmap (cmapdata_t ) grids */
+ int grid_spacing; /* Grid spacing */
+ gmx_cmapdata_t *cmapdata; /* Pointer to grid with actual, pre-interpolated data */
} gmx_cmap_t;
-typedef struct
+typedef struct gmx_ffparams_t
{
int ntypes;
int atnr;
ilsortUNKNOWN, ilsortNO_FE, ilsortFE_UNSORTED, ilsortFE_SORTED
};
-typedef struct
+typedef struct t_idef
{
int ntypes;
int atnr;
* version of the program can use it as easy as the single node version.
* General field description:
* int ntypes
- * defines the number of elements in functype[] and param[].
+ * defines the number of elements in functype[] and param[].
* int nodeid
* the node id (if parallel machines)
* int atnr
* the number of atomtypes
* t_functype *functype
- * array of length ntypes, defines for every force type what type of
+ * array of length ntypes, defines for every force type what type of
* function to use. Every "bond" with the same function but different
- * force parameters is a different force type. The type identifier in the
- * forceatoms[] array is an index in this array.
+ * force parameters is a different force type. The type identifier in the
+ * forceatoms[] array is an index in this array.
* t_iparams *iparams
- * array of length ntypes, defines the parameters for every interaction
+ * array of length ntypes, defines the parameters for every interaction
* type. The type identifier in the actual interaction list
* (ilist[ftype].iatoms[]) is an index in this array.
* gmx_cmap_t cmap_grid
* the grid for the dihedral pair correction maps.
* t_iparams *iparams_posres, *iparams_fbposres
- * defines the parameters for position restraints only.
+ * defines the parameters for position restraints only.
* Position restraints are the only interactions that have different
* parameters (reference positions) for different molecules
* of the same type. ilist[F_POSRES].iatoms[] is an index in this array.
* should be at least F_NRE*(nthreads+1).
*/
-typedef struct {
- int n; /* n+1 is the number of points */
- real scale; /* distance between two points */
- real *data; /* the actual table data, per point there are 4 numbers */
-} bondedtable_t;
-
#ifdef __cplusplus
}
#endif
-
#endif
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff