Bundle commit of all recent changes on pygmx.

pygmx/enxio.pyx

@@ -0,0 +1,99 @@
+
+from cpython.array cimport array
+from array import array
+
+cimport numpy as np
+import numpy as np
+
+from utility cimport *
+from mdtypes cimport *
+
+cdef extern from "gromacs/fileio/enxio.h":
+    ctypedef struct gmx_enxnm_t:
+        char *name
+        char *unit
+
+    ctypedef struct ener_file_t:
+        pass
+
+    ctypedef struct t_enxblock:
+        pass
+
+    ctypedef struct t_enxframe:
+        double          t            # Timestamp of this frame	                     */
+        gmx_int64_t     step         # MD step	                             */
+        gmx_int64_t     nsteps       # The number of steps between frames            */
+        double          dt           # The MD time step                              */
+        int             nsum         # The number of terms for the sums in ener      */
+        int             nre          # Number of energies			     */
+        int             e_size       # Size (in bytes) of energies		     */
+        int             e_alloc      # Allocated size (in elements) of ener          */
+        t_energy       *ener         # The energies                                  */
+        int             nblock       # Number of following energy blocks             */
+        t_enxblock     *block        # The blocks                                    */
+        int             nblock_alloc # The number of blocks allocated                */
+
+    ener_file_t open_enx(const char *fn, const char *mode)
+    void close_enx(ener_file_t ef)
+
+    void do_enxnms(ener_file_t ef, int *nre, gmx_enxnm_t **enms)
+
+    gmx_bool do_enx(ener_file_t ef, t_enxframe *fr)
+
+
+
+cdef class EDRFile:
+
+    cdef:
+        ener_file_t efile
+        gmx_enxnm_t *etypes
+        int n_etypes
+        t_enxframe *frames
+
+    @property
+    def types(self):
+        types = []
+        for i in range(self.n_etypes):
+            types.append(
+
+            )
+    def read(self):
+        cdef t_enxframe *frame
+        cdef np.ndarray[float, ndim=2] energies = np.empty((1,self.n_etypes), np.float32)
+
+        snew(frame, 1)
+
+        while do_enx(self.efile, frame):
+            energies = np.resize(energies, (len(energies)+1, self.n_etypes))
+            for i in range(frame.nre):
+                energies[-1, i] = frame.ener[i].e
+        return energies
+
+
+    def __init__(self, filename):
+        filename = cstr(filename)
+
+        self.efile = open_enx(filename, b'r')
+
+        self.etypes = NULL
+        do_enxnms(self.efile, &self.n_etypes, &self.etypes)
+        print(self.n_etypes)
+
+        #do_enx(self.efile, self.frames)
+
+
+    def __getitem__(self, item):
+        cdef:
+            int f = 0
+            t_enxframe frame = self.frames[f]
+
+        cdef array values = array('d')
+
+        while frame.nblock > 0:
+            if item < frame.nre:
+                values.append(frame.ener[item].e)
+            i += 1
+            frame = self.frames[i]
+            print(i, frame.t, frame.nblock)
+
+        return values