/*
+ * This file is part of the GROMACS molecular simulation package.
*
- * This source code is part of
- *
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- * GROningen MAchine for Chemical Simulations
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- * VERSION 3.2.0
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* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
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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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*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include "3dview.h"
-#include "statutil.h"
-#include "smalloc.h"
-#include "copyrite.h"
-#include "index.h"
-#include "confio.h"
-#include "gmx_fatal.h"
-#include "vec.h"
-#include "physics.h"
-#include "random.h"
+#include "gmxpre.h"
+
+#include "gromacs/topology/index.h"
+#include "gromacs/fileio/confio.h"
+#include "gromacs/math/units.h"
#include "gmx_ana.h"
-#include "macros.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/math/3dtransforms.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/atoms.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
static void rot_conf(t_atoms *atoms, rvec x[], rvec v[], real trans, real angle,
- rvec head, rvec tail, matrix box, int isize, atom_id index[],
+ rvec head, rvec tail, int isize, atom_id index[],
rvec xout[], rvec vout[])
{
- rvec arrow, center, xcm;
+ rvec arrow, xcm;
real theta, phi, arrow_len;
- mat4 Rx, Ry, Rz, Rinvy, Rinvz, Mtot, Tcm, Tinvcm, Tx;
- mat4 temp1, temp2, temp3, temp4, temp21, temp43;
+ mat4 Rx, Ry, Rz, Rinvy, Rinvz, Mtot;
+ mat4 temp1, temp2, temp3;
vec4 xv;
int i, j, ai;
/* Now the total rotation matrix: */
/* Rotate a couple of times */
- rotate(ZZ, -phi, Rz);
- rotate(YY, M_PI/2-theta, Ry);
- rotate(XX, angle*DEG2RAD, Rx);
+ gmx_mat4_init_rotation(ZZ, -phi, Rz);
+ gmx_mat4_init_rotation(YY, M_PI/2-theta, Ry);
+ gmx_mat4_init_rotation(XX, angle*DEG2RAD, Rx);
Rx[WW][XX] = trans;
- rotate(YY, theta-M_PI/2, Rinvy);
- rotate(ZZ, phi, Rinvz);
+ gmx_mat4_init_rotation(YY, theta-M_PI/2, Rinvy);
+ gmx_mat4_init_rotation(ZZ, phi, Rinvz);
- mult_matrix(temp1, Ry, Rz);
- mult_matrix(temp2, Rinvy, Rx);
- mult_matrix(temp3, temp2, temp1);
- mult_matrix(Mtot, Rinvz, temp3);
+ gmx_mat4_mmul(temp1, Ry, Rz);
+ gmx_mat4_mmul(temp2, Rinvy, Rx);
+ gmx_mat4_mmul(temp3, temp2, temp1);
+ gmx_mat4_mmul(Mtot, Rinvz, temp3);
- print_m4(debug, "Rz", Rz);
- print_m4(debug, "Ry", Ry);
- print_m4(debug, "Rx", Rx);
- print_m4(debug, "Rinvy", Rinvy);
- print_m4(debug, "Rinvz", Rinvz);
- print_m4(debug, "Mtot", Mtot);
+ if (debug)
+ {
+ gmx_mat4_print(debug, "Rz", Rz);
+ gmx_mat4_print(debug, "Ry", Ry);
+ gmx_mat4_print(debug, "Rx", Rx);
+ gmx_mat4_print(debug, "Rinvy", Rinvy);
+ gmx_mat4_print(debug, "Rinvz", Rinvz);
+ gmx_mat4_print(debug, "Mtot", Mtot);
+ }
for (i = 0; (i < isize); i++)
{
ai = index[i];
- m4_op(Mtot, xout[ai], xv);
+ gmx_mat4_transform_point(Mtot, xout[ai], xv);
rvec_add(xv, xcm, xout[ai]);
- m4_op(Mtot, v[ai], xv);
+ gmx_mat4_transform_point(Mtot, v[ai], xv);
copy_rvec(xv, vout[ai]);
}
}
int gmx_dyndom(int argc, char *argv[])
{
const char *desc[] = {
- "[TT]g_dyndom[tt] reads a [TT].pdb[tt] file output from DynDom",
+ "[THISMODULE] reads a [TT].pdb[tt] file output from DynDom",
"(http://www.cmp.uea.ac.uk/dyndom/).",
"It reads the coordinates, the coordinates of the rotation axis,",
"and an index file containing the domains.",
"determined by DynDom is given, one should be able to recover the",
"second structure used for generating the DynDom output.",
"Because of limited numerical accuracy this should be verified by",
- "computing an all-atom RMSD (using [TT]g_confrms[tt]) rather than by file",
+ "computing an all-atom RMSD (using [gmx-confrms]) rather than by file",
"comparison (using diff).[PAR]",
"The purpose of this program is to interpolate and extrapolate the",
"rotation as found by DynDom. As a result unphysical structures with",
};
#define NFILE asize(fnm)
- parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
- asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
+ asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
get_stx_coordnum (opt2fn("-f", NFILE, fnm), &natoms);
init_t_atoms(&atoms, natoms, TRUE);
trans = trans0*0.1*angle/maxangle;
printf("Frame: %2d (label %c), angle: %8.3f deg., trans: %8.3f nm\n",
i, label, angle, trans);
- rot_conf(&atoms, x, v, trans, angle, head, tail, box, isize, index, xout, vout);
+ rot_conf(&atoms, x, v, trans, angle, head, tail, isize, index, xout, vout);
if (label > 'Z')
{
}
close_trx(status);
- thanx(stderr);
-
return 0;
}