Remove unnecessary config.h includes

[alexxy/gromacs.git] / src / gromacs / gmxana / gmx_dyndom.c

diff --git a/src/gromacs/gmxana/gmx_dyndom.c b/src/gromacs/gmxana/gmx_dyndom.c
index 57bb3fc39e64942ccee9d123041bd72ab54b0a41..7b2ac8e4993c2884e3ffdba910bdd161c5451ae1 100644 (file)
--- a/src/gromacs/gmxana/gmx_dyndom.c
+++ b/src/gromacs/gmxana/gmx_dyndom.c
@@ -34,23 +34,21 @@
  * To help us fund GROMACS development, we humbly ask that you cite
  * the research papers on the package. Check out http://www.gromacs.org.
  */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
 
-#include "gromacs/math/3dview.h"
-#include "gromacs/commandline/pargs.h"
-#include "smalloc.h"
-#include "index.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/fileio/confio.h"
-#include "gmx_fatal.h"
-#include "vec.h"
-#include "physics.h"
-#include "random.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, int isize, atom_id index[],
@@ -113,31 +111,34 @@ static void rot_conf(t_atoms *atoms, rvec x[], rvec v[], real trans, real angle,
 
     /* 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]);
     }
 }