Preliminary step to move types out of legacyheader.
Renamed parameter called "matrix" because cppcheck gets
confused if a parameter is called the same as a type.
Part of #1415
Change-Id: I9207a7b8de7f092bab890da128abbb48a8d97b79
#ifndef GMX_FFT_PARALLEL_3DFFT_H
#define GMX_FFT_PARALLEL_3DFFT_H
-#include "../legacyheaders/types/nrnb.h"
#include "../math/gmxcomplex.h"
+#include "../timing/wallcycle.h"
#include "../utility/basedefinitions.h"
#include "../utility/gmxmpi.h"
#include "../utility/real.h"
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team,
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, 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.
#ifndef GMX_FILEIO_CONFIO_H
#define GMX_FILEIO_CONFIO_H
+#include <stdio.h>
-#include "../legacyheaders/typedefs.h"
+#include "../legacyheaders/types/atoms.h"
+#include "../legacyheaders/types/simple.h"
+#include "../legacyheaders/types/topology.h"
+
+#include "trx.h"
/* For reading coordinate files it is assumed that enough memory
* has been allocated beforehand.
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team,
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, 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.
#ifndef GMX_FILEIO_ENXIO_H
#define GMX_FILEIO_ENXIO_H
-#include "../legacyheaders/typedefs.h"
#include "../legacyheaders/pbc.h"
+#include "../legacyheaders/types/energy.h"
+#include "../legacyheaders/types/topology.h"
#include "gmxfio.h"
#include "xdr_datatype.h"
#ifndef GMX_FILEIO_FILENM_H
#define GMX_FILEIO_FILENM_H
-#include "../legacyheaders/typedefs.h"
+#include "../legacyheaders/types/commrec_fwd.h"
+#include "../utility/basedefinitions.h"
#ifdef __cplusplus
extern "C" {
#include <stdio.h>
-#include "../legacyheaders/typedefs.h"
#include "../utility/cstringutil.h"
#include "../utility/futil.h"
+#include "../utility/real.h"
+#include "../math/vectypes.h"
#ifdef __cplusplus
extern "C" {
sfree(line_buf);
}
-int read_xpm_matrix(const char *fnm, t_matrix **matrix)
+int read_xpm_matrix(const char *fnm, t_matrix **mat)
{
FILE *in;
char *line = NULL;
{
if (strstr(line, "/* XPM */"))
{
- srenew(*matrix, nmat+1);
- read_xpm_entry(in, &(*matrix)[nmat]);
+ srenew(*mat, nmat+1);
+ read_xpm_entry(in, &(*mat)[nmat]);
nmat++;
}
}
return nmat;
}
-real **matrix2real(t_matrix *matrix, real **mat)
+real **matrix2real(t_matrix *in, real **out)
{
t_mapping *map;
double tmp;
real *rmap;
int i, j, nmap;
- nmap = matrix->nmap;
- map = matrix->map;
+ nmap = in->nmap;
+ map = in->map;
snew(rmap, nmap);
for (i = 0; i < nmap; i++)
rmap[i] = tmp;
}
- if (mat == NULL)
+ if (out == NULL)
{
- snew(mat, matrix->nx);
- for (i = 0; i < matrix->nx; i++)
+ snew(out, in->nx);
+ for (i = 0; i < in->nx; i++)
{
- snew(mat[i], matrix->ny);
+ snew(out[i], in->ny);
}
}
- for (i = 0; i < matrix->nx; i++)
+ for (i = 0; i < in->nx; i++)
{
- for (j = 0; j < matrix->ny; j++)
+ for (j = 0; j < in->ny; j++)
{
- mat[i][j] = rmap[matrix->matrix[i][j]];
+ out[i][j] = rmap[in->matrix[i][j]];
}
}
sfree(rmap);
fprintf(stderr, "Converted a %dx%d matrix with %d levels to reals\n",
- matrix->nx, matrix->ny, nmap);
+ in->nx, in->ny, nmap);
- return mat;
+ return out;
}
void write_xpm_header(FILE *out,
}
}
-void write_xpm_data(FILE *out, int n_x, int n_y, real **matrix,
+void write_xpm_data(FILE *out, int n_x, int n_y, real **mat,
real lo, real hi, int nlevels)
{
int i, j, c;
fprintf(out, "\"");
for (i = 0; (i < n_x); i++)
{
- c = gmx_nint((matrix[i][j]-lo)*invlevel);
+ c = gmx_nint((mat[i][j]-lo)*invlevel);
if (c < 0)
{
c = 0;
}
}
-void write_xpm_data3(FILE *out, int n_x, int n_y, real **matrix,
+void write_xpm_data3(FILE *out, int n_x, int n_y, real **mat,
real lo, real mid, real hi, int nlevels)
{
int i, j, c = 0, nmid;
fprintf(out, "\"");
for (i = 0; (i < n_x); i++)
{
- if (matrix[i][j] >= mid)
+ if (mat[i][j] >= mid)
{
- c = nmid+gmx_nint((matrix[i][j]-mid)*invlev_hi);
+ c = nmid+gmx_nint((mat[i][j]-mid)*invlev_hi);
}
- else if (matrix[i][j] >= lo)
+ else if (mat[i][j] >= lo)
{
- c = gmx_nint((matrix[i][j]-lo)*invlev_lo);
+ c = gmx_nint((mat[i][j]-lo)*invlev_lo);
}
else
{
}
}
-void write_xpm_data_split(FILE *out, int n_x, int n_y, real **matrix,
+void write_xpm_data_split(FILE *out, int n_x, int n_y, real **mat,
real lo_top, real hi_top, int nlevel_top,
real lo_bot, real hi_bot, int nlevel_bot)
{
{
if (i < j)
{
- c = nlevel_bot+round((matrix[i][j]-lo_top)*invlev_top);
+ c = nlevel_bot+round((mat[i][j]-lo_top)*invlev_top);
if ((c < nlevel_bot) || (c >= nlevel_bot+nlevel_top))
{
- gmx_fatal(FARGS, "Range checking i = %d, j = %d, c = %d, bot = %d, top = %d matrix[i,j] = %f", i, j, c, nlevel_bot, nlevel_top, matrix[i][j]);
+ gmx_fatal(FARGS, "Range checking i = %d, j = %d, c = %d, bot = %d, top = %d matrix[i,j] = %f", i, j, c, nlevel_bot, nlevel_top, mat[i][j]);
}
}
else if (i > j)
{
- c = round((matrix[i][j]-lo_bot)*invlev_bot);
+ c = round((mat[i][j]-lo_bot)*invlev_bot);
if ((c < 0) || (c >= nlevel_bot+nlevel_bot))
{
- gmx_fatal(FARGS, "Range checking i = %d, j = %d, c = %d, bot = %d, top = %d matrix[i,j] = %f", i, j, c, nlevel_bot, nlevel_top, matrix[i][j]);
+ gmx_fatal(FARGS, "Range checking i = %d, j = %d, c = %d, bot = %d, top = %d matrix[i,j] = %f", i, j, c, nlevel_bot, nlevel_top, mat[i][j]);
}
}
else
const char *title, const char *legend,
const char *label_x, const char *label_y,
int n_x, int n_y, real axis_x[], real axis_y[],
- real *matrix[], real lo, real mid, real hi,
+ real *mat[], real lo, real mid, real hi,
t_rgb rlo, t_rgb rmid, t_rgb rhi, int *nlevels)
{
/* See write_xpm.
write_xpm_map3(out, n_x, n_y, nlevels, lo, mid, hi, rlo, rmid, rhi);
write_xpm_axis(out, "x", flags & MAT_SPATIAL_X, n_x, axis_x);
write_xpm_axis(out, "y", flags & MAT_SPATIAL_Y, n_y, axis_y);
- write_xpm_data3(out, n_x, n_y, matrix, lo, mid, hi, *nlevels);
+ write_xpm_data3(out, n_x, n_y, mat, lo, mid, hi, *nlevels);
}
void write_xpm_split(FILE *out, unsigned int flags,
const char *title, const char *legend,
const char *label_x, const char *label_y,
int n_x, int n_y, real axis_x[], real axis_y[],
- real *matrix[],
+ real *mat[],
real lo_top, real hi_top, int *nlevel_top,
t_rgb rlo_top, t_rgb rhi_top,
real lo_bot, real hi_bot, int *nlevel_bot,
bDiscreteColor, nlevel_bot, lo_bot, hi_bot, rlo_bot, rhi_bot);
write_xpm_axis(out, "x", flags & MAT_SPATIAL_X, n_x, axis_x);
write_xpm_axis(out, "y", flags & MAT_SPATIAL_Y, n_y, axis_y);
- write_xpm_data_split(out, n_x, n_y, matrix, lo_top, hi_top, *nlevel_top,
+ write_xpm_data_split(out, n_x, n_y, mat, lo_top, hi_top, *nlevel_top,
lo_bot, hi_bot, *nlevel_bot);
}
const char *title, const char *legend,
const char *label_x, const char *label_y,
int n_x, int n_y, real axis_x[], real axis_y[],
- real *matrix[], real lo, real hi,
+ real *mat[], real lo, real hi,
t_rgb rlo, t_rgb rhi, int *nlevels)
{
/* out xpm file
write_xpm_map(out, n_x, n_y, nlevels, lo, hi, rlo, rhi);
write_xpm_axis(out, "x", flags & MAT_SPATIAL_X, n_x, axis_x);
write_xpm_axis(out, "y", flags & MAT_SPATIAL_Y, n_y, axis_y);
- write_xpm_data(out, n_x, n_y, matrix, lo, hi, *nlevels);
+ write_xpm_data(out, n_x, n_y, mat, lo, hi, *nlevels);
}
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team,
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, 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.
#ifndef GMX_FILEIO_MATIO_H
#define GMX_FILEIO_MATIO_H
-#include "../legacyheaders/typedefs.h"
+#include <stdio.h>
+
+#include "../legacyheaders/types/matrix.h"
#ifdef __cplusplus
extern "C" {
void writecmap(const char *fn, int n, t_mapping map[]);
/* print mapping table to fn */
-int read_xpm_matrix(const char *fnm, t_matrix **matrix);
+int read_xpm_matrix(const char *fnm, t_matrix **mat);
/* Reads a number of matrices from .xpm file fnm and returns this number */
-real **matrix2real(t_matrix *matrix, real **mat);
+real **matrix2real(t_matrix *in, real **out);
/* Converts an matrix in a t_matrix struct to a matrix of reals
* When mat==NULL memory will be allocated
* Returns NULL when something went wrong
const char *title, const char *legend,
const char *label_x, const char *label_y,
int n_x, int n_y, real axis_x[], real axis_y[],
- real *matrix[], real lo, real mid, real hi,
+ real *mat[], real lo, real mid, real hi,
t_rgb rlo, t_rgb rmid, t_rgb rhi, int *nlevels);
/* See write_xpm.
* Writes a colormap varying as rlo -> rmid -> rhi.
const char *title, const char *legend,
const char *label_x, const char *label_y,
int n_x, int n_y, real axis_x[], real axis_y[],
- real *matrix[],
+ real *mat[],
real lo_top, real hi_top, int *nlevel_top,
t_rgb rlo_top, t_rgb rhi_top,
real lo_bot, real hi_bot, int *nlevel_bot,
const char *title, const char *legend,
const char *label_x, const char *label_y,
int n_x, int n_y, real t_x[], real t_y[],
- real *matrix[], real lo, real hi,
+ real *mat[], real lo, real hi,
t_rgb rlo, t_rgb rhi, int *nlevels);
/* out xpm file
* flags flags, defined types/matrix.h
* n_x, n_y size of the matrix
* axis_x[] the x-ticklabels (n_x or n_x+1)
* axis_y[] the y-ticklables (n_y or n_y+1)
- * *matrix[] element x,y is matrix[x][y]
+ * *mat[] element x,y is mat[x][y]
* lo output lower than lo is set to lo
* hi output higher than hi is set to hi
* rlo rgb value for level lo
#include <stdio.h>
-#include "../legacyheaders/typedefs.h"
-#include "../legacyheaders/symtab.h"
#include "../legacyheaders/atomprop.h"
+#include "../legacyheaders/symtab.h"
+#include "../legacyheaders/types/topology.h"
#ifdef __cplusplus
extern "C" {
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team,
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, 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.
* can also be used with the routines in gmxfio.h
*
**************************************************************/
-#include "../legacyheaders/typedefs.h"
+#include "../legacyheaders/types/inputrec.h"
+#include "../legacyheaders/types/state.h"
+#include "../legacyheaders/types/topology.h"
#include "gmxfio.h"
#ifdef __cplusplus
#include "trajectory_writing.h"
#include "mdoutf.h"
+#include "gromacs/legacyheaders/types/commrec.h"
#include "gromacs/timing/wallcycle.h"
void
#define GMX_FILEIO_TRAJECTORY_WRITING_H
#include <stdio.h>
+
+#include "../legacyheaders/types/commrec_fwd.h"
+#include "../legacyheaders/mdebin.h"
+#include "../timing/wallcycle.h"
+
#include "filenm.h"
#include "mdoutf.h"
-#include "../legacyheaders/typedefs.h"
-#include "../legacyheaders/mdebin.h"
/*! \brief Wrapper routine for writing trajectories during mdrun
*
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team,
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, 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.
*
**************************************************************/
-#include "../legacyheaders/typedefs.h"
#include "gmxfio.h"
#ifdef __cplusplus
#ifndef GMX_FILEIO_TRXIO_H
#define GMX_FILEIO_TRXIO_H
-#include "../legacyheaders/typedefs.h"
-#include "filenm.h"
+#include "../legacyheaders/types/topology.h"
#include "../legacyheaders/readinp.h"
-#include "pdbio.h"
#include "../legacyheaders/oenv.h"
+
+#include "filenm.h"
#include "gmxfio.h"
+#include "pdbio.h"
#ifdef __cplusplus
extern "C" {
#include "gromacs/legacyheaders/copyrite.h"
#include "gromacs/legacyheaders/oenv.h"
+#include "gromacs/legacyheaders/typedefs.h"
#include "gromacs/fileio/gmxfio.h"
#include "gromacs/math/vec.h"
#include <config.h>
#endif
+#include "gromacs/legacyheaders/symtab.h"
+#include "gromacs/legacyheaders/typedefs.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/fatalerror.h"
-#include "symtab.h"
void replace_atom(t_topology *top, int inr, char *anm, char *resnm,
real q, real m, int type)
#ifndef _nsfactor_h
#define _nsfactor_h
-#include "index.h"
-#include "types/simple.h"
-#include "oenv.h"
+#include "gromacs/legacyheaders/index.h"
+#include "gromacs/legacyheaders/oenv.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/legacyheaders/types/topology.h"
#ifdef __cplusplus
extern "C" {
#include <ctype.h>
#include <string.h>
-#include "gromacs/utility/smalloc.h"
+#include "gromacs/fileio/strdb.h"
+#include "gromacs/legacyheaders/atomprop.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/index.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/utilities.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/fatalerror.h"
-#include "atomprop.h"
-#include "macros.h"
-#include "index.h"
-#include "copyrite.h"
-
#include "gromacs/utility/futil.h"
-#include "gromacs/fileio/strdb.h"
-#include "gromacs/math/utilities.h"
+#include "gromacs/utility/smalloc.h"
typedef struct {
gmx_bool bSet;
*/
#include "read-conformation.h"
-#include "atomprop.h"
-#include "types/simple.h"
-#include "types/atoms.h"
-
#include "gromacs/fileio/confio.h"
+#include "gromacs/legacyheaders/atomprop.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/legacyheaders/types/atoms.h"
+#include "gromacs/legacyheaders/typedefs.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/smalloc.h"
#include "typedefs.h"
#include "../fileio/filenm.h"
+#include "../timing/wallcycle.h"
#ifdef GMX_NATIVE_WINDOWS
#include <Windows.h>
#include "vsite.h"
#include "genborn.h"
+#include "../timing/wallcycle.h"
+
#ifdef __cplusplus
extern "C" {
#endif
#include "vsite.h"
#include "genborn.h"
+#include "../timing/wallcycle.h"
#ifdef __cplusplus
extern "C" {
#ifndef _index_h
#define _index_h
-#include "typedefs.h"
+#include <stdio.h>
+
+#include "types/atoms.h"
+#include "types/block.h"
#ifdef __cplusplus
extern "C" {
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, 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.
#include "sim_util.h"
#include "vcm.h"
+#include "../timing/wallcycle.h"
+
#ifdef __cplusplus
extern "C" {
#endif
#include "network.h"
#include "sim_util.h"
#include "tgroup.h"
-#include "../fileio/filenm.h"
#include "mshift.h"
#include "mdebin.h"
#include "vcm.h"
#include "types/membedt.h"
#include "types/globsig.h"
+#include "../fileio/filenm.h"
+#include "../timing/wallcycle.h"
+
#ifdef __cplusplus
extern "C" {
#endif
#include <stdio.h>
#include "typedefs.h"
#include "../math/gmxcomplex.h"
+#include "../timing/wallcycle.h"
#include "../timing/walltime_accounting.h"
#include "../legacyheaders/network.h"
* the research papers on the package. Check out http://www.gromacs.org.
*/
+#include "../timing/wallcycle.h"
+
#include "typedefs.h"
#include "vsite.h"
#include "vcm.h"
#include "../fileio/enxio.h"
#include "../fileio/mdoutf.h"
+#include "../timing/wallcycle.h"
#include "../timing/walltime_accounting.h"
#ifdef __cplusplus
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014, 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.
#define _symtab_h
#include <stdio.h>
-#include "typedefs.h"
+#include "types/symtab.h"
#ifdef __cplusplus
extern "C" {
#include "types/constr.h"
#include "types/matrix.h"
#include "types/oenv.h"
+#include "types/commrec_fwd.h"
#ifdef __cplusplus
extern "C" {
real max_cutoff(real cutoff1, real cutoff2);
/* Returns the maximum of the cut-off's, taking into account that 0=inf. */
-/* Following are forward declarations for structures in commrec.h */
-typedef struct t_commrec t_commrec;
-typedef struct gmx_domdec_t gmx_domdec_t;
-typedef struct gmx_multisim_t gmx_multisim_t;
-typedef struct gmx_domdec_zones_t gmx_domdec_zones_t;
-typedef struct gmx_ddbox_t gmx_ddbox_t;
-
#ifdef __cplusplus
}
#endif
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 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.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, 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 http://www.gromacs.org.
+ *
+ * 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_TYPES_COMMREC_FWD_H
+#define GMX_TYPES_COMMREC_FWD_H
+
+typedef struct t_commrec t_commrec;
+typedef struct gmx_domdec_t gmx_domdec_t;
+typedef struct gmx_multisim_t gmx_multisim_t;
+typedef struct gmx_domdec_zones_t gmx_domdec_zones_t;
+typedef struct gmx_ddbox_t gmx_ddbox_t;
+
+#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014, 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.
* the research papers on the package. Check out http://www.gromacs.org.
*/
+#ifndef GMX_TYPES_ENERGY_H
+#define GMX_TYPES_ENERGY_H
+
#include "simple.h"
#ifdef __cplusplus
#ifdef __cplusplus
}
#endif
+
+#endif
extern "C" {
#endif
-#include "simple.h"
+#include "../../utility/basedefinitions.h"
+#include "../../utility/real.h"
typedef struct {
real r, g, b;
t_nrnb;
-typedef struct gmx_wallcycle *gmx_wallcycle_t;
-
#ifdef __cplusplus
}
#endif
#include "tgroup.h"
#include "network.h"
+#include "../timing/wallcycle.h"
+
#ifdef __cplusplus
extern "C" {
#endif
#include "qmmm.h"
#include "gmx_omp_nthreads.h"
+#include "gromacs/legacyheaders/types/commrec.h"
#include "gromacs/math/vec.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/utility/fatalerror.h"
#include "md_logging.h"
#include "md_support.h"
+#include "gromacs/legacyheaders/types/commrec.h"
#include "gromacs/math/vec.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/trajectory_writing.h"
+#include "gromacs/legacyheaders/types/commrec.h"
#include "gromacs/linearalgebra/mtxio.h"
#include "gromacs/linearalgebra/sparsematrix.h"
#include "gromacs/timing/wallcycle.h"
#include "nrnb.h"
#include "macros.h"
+#include "gromacs/legacyheaders/types/commrec.h"
#include "gromacs/fft/parallel_3dfft.h"
#include "gromacs/utility/futil.h"
#include "gromacs/fileio/pdbio.h"
#include "../gmxlib/nonbonded/nb_kernel.h"
#include "../gmxlib/nonbonded/nb_free_energy.h"
+#include "gromacs/legacyheaders/types/commrec.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/timing/walltime_accounting.h"
#include "gromacs/utility/gmxmpi.h"
#include "pme.h"
#include "gromacs/gmxlib/conformation-utilities.h"
+#include "gromacs/legacyheaders/types/commrec.h"
#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/gmxfio.h"
#include "gromacs/fileio/trxio.h"
set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${TIMING_SOURCES} PARENT_SCOPE)
set(TIMING_PUBLIC_HEADERS
+ wallcycle.h
walltime_accounting.h)
+
gmx_install_headers(timing ${TIMING_PUBLIC_HEADERS})
if (BUILD_TESTING)
#include <stdlib.h>
#include <string.h>
-#include "md_logging.h"
-
-#include "gromacs/timing/cyclecounter.h"
+#include "gromacs/legacyheaders/md_logging.h"
+#include "gromacs/legacyheaders/types/commrec.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxmpi.h"
#include "gromacs/utility/smalloc.h"
+#include "cyclecounter.h"
+
/* DEBUG_WCYCLE adds consistency checking for the counters.
* It checks if you stop a counter different from the last
* one that was opened and if you do nest too deep.
#define GMX_TIMING_WALLCYCLE_H
#include <stdio.h>
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/types/commrec.h"
+
+#include "../legacyheaders/types/commrec_fwd.h"
+#include "../legacyheaders/types/nbnxn_cuda_types_ext.h"
+#include "../utility/basedefinitions.h"
#ifdef __cplusplus
extern "C" {
#endif
+typedef struct gmx_wallcycle *gmx_wallcycle_t;
+
enum {
ewcRUN, ewcSTEP, ewcPPDURINGPME, ewcDOMDEC, ewcDDCOMMLOAD,
ewcDDCOMMBOUND, ewcVSITECONSTR, ewcPP_PMESENDX, ewcNS, ewcLAUNCH_GPU_NB,
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff