Switched to Headers fo the Gromacs-2016 branch.

README.md

@@ -17,6 +17,14 @@ Pygmx needs mainly two python packages to be installed, which are available in a
 
 Pygmx requires the shared library and header files of Gromacs 5.1 or higher to be installed.
 
+Note that pygmx also supports the Gromacs-2016 version.
+Checkout the followng git branch if this version of Gromacs is desired:
+
+    git checkout gromacs-2016
+
+Note that Gromacs is backwards compatible, i. e. files produced by the 5.1 version will also work in the 2016 version.
+But Gromacs-2016 is required to load files of the 2016 version.
+
 #### Using a module
 
 If gromacs is installed as a module in your system, run

pygmx/mdtypes.pxd

@@ -2,14 +2,14 @@
 from utility cimport *
 from math cimport *
 
-cdef extern from "gromacs/legacyheaders/types/energy.h":
+cdef extern from "gromacs/trajectory/energy.h":
     ctypedef struct t_energy:
         real    e
         double  eav
         double  esum
 
 
-cdef extern from "gromacs/legacyheaders/types/inputrec.h":
+cdef extern from "gromacs/mdtypes/inputrec.h":
     ctypedef struct t_simtemp:
         pass
     ctypedef struct t_lambda:

pygmx/topology.pxd

@@ -43,6 +43,10 @@ cdef extern from "gromacs/topology/atoms.h":
     ctypedef struct t_atomtypes:
         pass
 
+    ctypedef struct t_grps:
+        int   nr;                   # Number of different groups           */
+        int  *nm_ind;               # Index in the group names             */
+
 #ctypedef t_atoms *t_atoms_ptr
 
 cdef extern from "gromacs/topology/symtab.h":
@@ -81,6 +85,11 @@ cdef extern from "gromacs/topology/topology.h":
 
     ctypedef struct gmx_groups_t:
         pass
+#        t_grps            grps[0]   # Groups of things                     */
+#        int               ngrpname      # Number of groupnames                 */
+#        char           ***grpname       # Names of the groups                  */
+#        int               ngrpnr[0]
+#        unsigned char    *grpnr[0]  # Group numbers or NULL                */
 
     ctypedef struct gmx_mtop_t:
         char           **name       # Name of the topology                 */

pygmx/tpxio.pyx

@@ -34,7 +34,7 @@ cdef extern from "gromacs/fileio/tpxio.h":
                  int *natoms,
                  rvec *x,
                  rvec *v,
-                 rvec *f,
+                 # rvec *f,
                  gmx_mtop_t *mtop)
 
 
@@ -83,12 +83,17 @@ cdef atom_mass(t_atom atom):
     return atom.m
 
 
+cdef index_groups_from_topology(gmx_mtop_t *topology):
+    # retrieve the index groups from the topology->groups ?
+    pass
+
+
 cdef open_tpx(const char* filename, t_inputrec *ir, matrix box, int *natoms, gmx_mtop_t *top):
     #cdef stdio.FILE *old_stderr = stdio.stderr
     #stdio.stderr = stdio.freopen('tmp', 'w', stdio.stderr)
     cdef char buffer[stdio.BUFSIZ]
     stdio.setbuf(stdio.stderr, buffer)
-    return_code = read_tpx(filename, ir, box, natoms, NULL, NULL, NULL, top)
+    return_code = read_tpx(filename, ir, box, natoms, NULL, NULL, top)
 
     for i in range(stdio.BUFSIZ):
         buffer[i] = 0

pygmx/utility.pxd

@@ -1,7 +1,10 @@
 # C-API in gromacs/utility
 
+from libc.stdint cimport int64_t
+
 #cdef extern from "inttypes.h":
 ctypedef unsigned long __int64
+ctypedef int64_t gmx_int64_t
 
 cdef extern from "gromacs/utility/basedefinitions.h":
     ctypedef int gmx_bool

pygmx/xtcio.pyx

@@ -21,11 +21,11 @@ cdef extern from "gromacs/fileio/xtcio.h":
     void close_xtc(t_fileio *fio)
 
     int read_first_xtc(t_fileio *fio,
-                       int *natoms, int *step, real *time,
+                       int *natoms, gmx_int64_t *step, real *time,
                        matrix box, rvec **x, real *prec, gmx_bool *_bOK)
 
     int read_next_xtc(t_fileio *fio,
-                      int natoms, int *step, real *time,
+                      int natoms, gmx_int64_t *step, real *time,
                       matrix box, rvec *x, real *prec, gmx_bool *_bOK)
 
 
@@ -53,7 +53,8 @@ else:
 cdef array get_xtc_index(t_fileio *fio):
     cdef:
         gmx_bool _bOK
-        int natoms, step, frame, state = 1
+        int natoms, frame, state = 1
+        gmx_int64_t step
         real time, prec
         matrix box
         rvec *x
@@ -156,7 +157,7 @@ cdef class XTCReader:
             self.filename = filename.decode()
 
         cdef:
-            int step
+            gmx_int64_t step
             matrix box
             gmx_bool _bOK
             real time, prec
@@ -193,7 +194,7 @@ cdef class XTCReader:
         cdef np.ndarray[real, ndim=2] coords = np.empty((self.natoms, 3), dtype=np_real)
         if frame < len(self):
             self.seek(frame)
-            read_next_xtc(self.fio, self.natoms, &self.cur_step, &time, box,
+            read_next_xtc(self.fio, self.natoms, <gmx_int64_t *>self.cur_step, &time, box,
                 <rvec *>coords.data, &self.prec, &_bOK)
             if _bOK:
                 frame = XTCFrame()