Sort all includes in src/gromacs

[alexxy/gromacs.git] / src / gromacs / gmxpreprocess / genconf.c

diff --git a/src/gromacs/gmxpreprocess/genconf.c b/src/gromacs/gmxpreprocess/genconf.c
index 52b7b048b38769c14b51ec8ac8fc23c327918f4b..9f9a57ce8cda8b3f08e81d47b2aa7b9273ffca21 100644 (file)
--- a/src/gromacs/gmxpreprocess/genconf.c
+++ b/src/gromacs/gmxpreprocess/genconf.c
@@ -34,24 +34,24 @@
  * To help us fund GROMACS development, we humbly ask that you cite
  * the research papers on the package. Check out http://www.gromacs.org.
  */
+#include "gmxpre.h"
+
 #include "genconf.h"
 
-#include "gromacs/math/utilities.h"
-#include "macros.h"
-#include "gromacs/utility/smalloc.h"
-#include "sysstuff.h"
-#include "gromacs/fileio/confio.h"
 #include "gromacs/commandline/pargs.h"
-#include "vec.h"
-#include "gromacs/random/random.h"
-#include "gromacs/math/3dview.h"
-#include "txtdump.h"
-#include "readinp.h"
-#include "names.h"
-#include "sortwater.h"
+#include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/trxio.h"
-
-#include "gmx_fatal.h"
+#include "gromacs/gmxpreprocess/sortwater.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/readinp.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/math/3dtransforms.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/random/random.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 
 static void rand_rot(int natoms, rvec x[], rvec v[], vec4 xrot[], vec4 vrot[],
                      gmx_rng_t rng, rvec max_rot)
@@ -71,27 +71,28 @@ static void rand_rot(int natoms, rvec x[], rvec v[], vec4 xrot[], vec4 vrot[],
     }
     fprintf(stderr, "center of geometry: %f, %f, %f\n", xcm[0], xcm[1], xcm[2]);
 
-    translate(-xcm[XX], -xcm[YY], -xcm[ZZ], mt1); /* move c.o.ma to origin */
+    /* move c.o.ma to origin */
+    gmx_mat4_init_translation(-xcm[XX], -xcm[YY], -xcm[ZZ], mt1);
     for (m = 0; (m < DIM); m++)
     {
         phi = M_PI*max_rot[m]*(2*gmx_rng_uniform_real(rng) - 1)/180;
-        rotate(m, phi, mr[m]);
+        gmx_mat4_init_rotation(m, phi, mr[m]);
     }
-    translate(xcm[XX], xcm[YY], xcm[ZZ], mt2);
+    gmx_mat4_init_translation(xcm[XX], xcm[YY], xcm[ZZ], mt2);
 
-    /* For mult_matrix we need to multiply in the opposite order
+    /* For gmx_mat4_mmul() we need to multiply in the opposite order
      * compared to normal mathematical notation.
      */
-    mult_matrix(mtemp1, mt1, mr[XX]);
-    mult_matrix(mtemp2, mr[YY], mr[ZZ]);
-    mult_matrix(mtemp3, mtemp1, mtemp2);
-    mult_matrix(mxtot, mtemp3, mt2);
-    mult_matrix(mvtot, mr[XX], mtemp2);
+    gmx_mat4_mmul(mtemp1, mt1, mr[XX]);
+    gmx_mat4_mmul(mtemp2, mr[YY], mr[ZZ]);
+    gmx_mat4_mmul(mtemp3, mtemp1, mtemp2);
+    gmx_mat4_mmul(mxtot, mtemp3, mt2);
+    gmx_mat4_mmul(mvtot, mr[XX], mtemp2);
 
     for (i = 0; (i < natoms); i++)
     {
-        m4_op(mxtot, x[i], xrot[i]);
-        m4_op(mvtot, v[i], vrot[i]);
+        gmx_mat4_transform_point(mxtot, x[i], xrot[i]);
+        gmx_mat4_transform_point(mvtot, v[i], vrot[i]);
     }
 }