{"action":"created","comment":{"url":"https://api.github.com/repos/MDAnalysis/mdanalysis/pulls/comments/45385182","id":45385182,"diff_hunk":"@@ -170,59 +217,34 @@ def read_DATA_timestep(self, n_atoms, TS_class, TS_kwargs):\n \n         .. versionadded:: 0.9.0\n         \"\"\"\n-        read_coords = False\n-        read_velocities = False\n-        velocities = None\n-\n-        with openany(self.filename, 'r') as datafile:\n-            nitems, ntypes, box = self._parse_header(datafile)\n-\n-            # lammps box: xlo, xhi, ylo, yhi, zlo, zhi\n-            lx = box[1] - box[0]\n-            ly = box[3] - box[2]\n-            lz = box[5] - box[4]\n-            # mda unitcell: A alpha B beta gamma C\n-            unitcell = np.zeros(6, dtype=np.float32)\n-            unitcell[[0, 1, 2]] = lx, ly, lz\n-            unitcell[[3, 4, 5]] = 90.0\n+        header, sects = self.grab_datafile()\n \n-            while not (read_coords & read_velocities):\n-                try:\n-                    section = datafile.next().strip().split()[0]\n-                except IndexError:  # blank lines don't split\n-                    section = ''\n-                except StopIteration:\n-                    break\n-\n-                if section == 'Atoms':\n-                    positions = np.zeros((n_atoms, 3),\n-                                         dtype=np.float32, order='F')\n-                    self._parse_pos(datafile, positions)\n-                    read_coords = True\n-                elif section == 'Velocities':\n-                    velocities = np.zeros((n_atoms, 3),\n-                                          dtype=np.float32, order='F')\n-                    self._parse_vel(datafile, velocities)\n-                    read_velocities = True\n-                elif len(section) > 0:\n-                    self._skip_section(datafile)\n-                else:\n-                    continue\n+        unitcell = self._parse_box(header)\n \n-        if not read_coords:  # Reaches here if StopIteration hit\n+        positions = np.zeros((n_atoms, 3),\n+                             dtype=np.float32, order='F')","path":"package/MDAnalysis/topology/LAMMPSParser.py","position":282,"original_position":282,"commit_id":"af372016f08134ea66d42cdfa3f931174bac5e74","original_commit_id":"af372016f08134ea66d42cdfa3f931174bac5e74","user":{"login":"hainm","id":4451957,"avatar_url":"https://avatars.githubusercontent.com/u/4451957?v=3","gravatar_id":"","url":"https://api.github.com/users/hainm","html_url":"https://github.com/hainm","followers_url":"https://api.github.com/users/hainm/followers","following_url":"https://api.github.com/users/hainm/following{/other_user}","gists_url":"https://api.github.com/users/hainm/gists{/gist_id}","starred_url":"https://api.github.com/users/hainm/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hainm/subscriptions","organizations_url":"https://api.github.com/users/hainm/orgs","repos_url":"https://api.github.com/users/hainm/repos","events_url":"https://api.github.com/users/hainm/events{/privacy}","received_events_url":"https://api.github.com/users/hainm/received_events","type":"User","site_admin":false},"body":"@richardjgowers copying data is very expensive. Can mda avoid it?","created_at":"2015-11-19T19:08:37Z","updated_at":"2015-11-19T19:08:37Z","html_url":"https://github.com/MDAnalysis/mdanalysis/pull/547#discussion_r45385182","pull_request_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/pulls/547","_links":{"self":{"href":"https://api.github.com/repos/MDAnalysis/mdanalysis/pulls/comments/45385182"},"html":{"href":"https://github.com/MDAnalysis/mdanalysis/pull/547#discussion_r45385182"},"pull_request":{"href":"https://api.github.com/repos/MDAnalysis/mdanalysis/pulls/547"}}},"pull_request":{"url":"https://api.github.com/repos/MDAnalysis/mdanalysis/pulls/547","id":51144146,"html_url":"https://github.com/MDAnalysis/mdanalysis/pull/547","diff_url":"https://github.com/MDAnalysis/mdanalysis/pull/547.diff","patch_url":"https://github.com/MDAnalysis/mdanalysis/pull/547.patch","issue_url":"https://api.github.com/repos/MDAnalysis/mdanalysis/issues/547","number":547,"state":"closed","locked":false,"title":"Feature betterdata","user":{"login":"richardjgowers","id":9249543,"avatar_url":"https://avatars.githubusercontent.com/u/9249543?v=3","gravatar_id":"","url":"https://api.github.com/users/richardjgowers","html_url":"https://github.com/richardjgowers","followers_url":"https://api.github.com/users/richardjgowers/followers","following_url":"https://api.github.com/users/richardjgowers/following{/other_user}","gists_url":"https://api.github.com/users/richardjgowers/gists{/gist_id}","starred_url":"https://api.github.com/users/richardjgowers/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/richardjgowers/subscriptions","organizations_url":"https://api.github.com/users/richardjgowers/orgs","repos_url":"https://api.github.com/users/richardjgowers/repos","events_url":"https://api.github.com/users/richardjgowers/events{/privacy}","received_events_url":"https://api.github.com/users/richardjgowers/received_events","type":"User","site_admin":false},"body":"The current lammps data parser is based on the fortran version of lammps, the (newer) C++ seems to have a much looser style.  This fixes the data parser so it can handle 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