Some sphinx fixes and removed private and special members from sphinx…

… documentation.

doc/sphinx/conf.py.in

@@ -300,8 +300,7 @@ texinfo_documents = [
 # http://stackoverflow.com/questions/12206334/sphinx-autosummary-toctree-contains-reference-to-nonexisting-document-warnings
 numpydoc_show_class_members = False
 autodoc_mock_imports = ['featuredefs', ]
-autodoc_default_flags = ['members', 'private-members', 
-                         'special-members',
+autodoc_default_flags = ['members',
                          'show-inheritance', 'undoc-members']
 # Replacements
 rst_epilog = """

doc/sphinx/dg.rst

@@ -236,7 +236,7 @@ Espresso uses two communication models, namely master-slave and synchronous.
   involved in the communication. If this is not done, a deadlock will result.
 
 Adding calls to the master-slave framework
------------------------------------------
+------------------------------------------
 
 Using an instance of MpiCallback
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

doc/sphinx/io.rst

@@ -150,13 +150,15 @@ re-registered when the same checkpoint id is used later.
 Following the example above, the next example loads the last checkpoint,
 restores the state of all checkpointed objects and registers a signal.
 
-.. code:: python
+.. code::
+
     import espressomd from espressomd import checkpointing import signal
 
-    checkpoint = checkpointing.Checkpointing(checkpoint\_id=“mycheckpoint”)
+    checkpoint = checkpointing.Checkpointing(checkpoint_id=“mycheckpoint”)
     checkpoint.load()
 
-    system = espressomd.System() system.cell\_system.skin = skin
+    system = espressomd.System()
+    system.cell_system.skin = skin
     system.actors.add(p3m)
 
     #signal.SIGINT: signal 2, is sent when ctrl+c is pressed
@@ -237,88 +239,6 @@ h5.write()
 After the last write call, you have to call the close() method to remove
 the backup file and to close the datasets etc.
 
-Writing and reading binary files
---------------------------------
-
-Binary files are written using the command
-
-writemd …
-
-This will write out particle data to the Tcl channel for all particles
-in binary format. Apart from the mandatory particle id, only limited
-information can be stored. The coordinates (, and ), velocities (, and )
-and forces (, and ). Other information should be stored in a blockfile
-or reconstructed differently. Note that since both ``blockfile`` and
-``writemd`` are using a Tcl channel, it is actually possible to mix
-them, so that you can write a single checkpoint file. However, the
-``blockfile read auto`` mechanism cannot handle the binary section, thus
-you need to read this section manually. Reading of binary particle data
-happens through
-
-readmd
-
-For the exact format of the written binary sequence, see
-``src/tcl/binary_file_tcl.cpp``.
-
-MPI-IO
-------
-
-When using with MPI, blockfiles and writemd have the disadvantage, that
-the master node does *all* the output. This is done by sequentially
-communicating all particle data to the master node. MPI-IO offers the
-possibility to write out particle data in parallel using binary IO. To
-output variables and other non-array information, use normal blockfiles
-(section [sec:structured-file-format]).
-
-To dump data using MPI-IO, use the following syntax:
-
-mpiio …
-
-This command writes data to several files using as common filename
-prefix. Beware, that must not be a Tcl channel but a string which must
-not contain colons. The data can be positions (), velocities (),
-particle types () and particle bonds () or any combination of these. The
-particle ids are always dumped. For safety reasons, MPI-IO will not
-overwrite existing files, so if the command fails and prints
-``MPI_ERR_IO`` make sure the files are non-existent.
-
-The files produced by this command are (assumed is “1”):
-
-1.head
-    Internal information (Dumped fields, bond partner num); always
-    produced
-
-1.pref
-    Internal information (Exscan results of nlocalparts); always
-    produced
-
-1.ids
-    Particle ids; always produced
-
-1.type
-    Particle types; optional
-
-1.pos
-    Particle positions; optional
-
-1.vel
-    Particle velocities; optional
-
-1.bond
-    Bond information; optional
-
-1.boff
-    Internal bond prefix information; optional, necessary to read 1.bond
-
-Currently, these files have to be read by exactly the same number of MPI
-processes that was used to dump them, otherwise an error is signalled.
-Also, the same type of machine (endianess, byte order) has to be used.
-Otherwise only garbage will be read. The read command replaces the
-particles, i.e. all previous existent particles will be *deleted*.
-
-There is a python script (``tools/mpiio2blockfile.py``) which converts
-MPI-IO snapshots to regular blockfiles.
-
 Writing VTF files
 -----------------
 
@@ -431,122 +351,6 @@ vtfpid
 If is the id of a particle as used in , this command returns the atom id
 used in the VTF, VSF or VCF formats.
 
-``writevtk``: Particle Visualization in paraview
-------------------------------------------------
-
-This feature allows to export the particle positions in a paraview  [3]_
-compatible VTK file. Paraview is a powerful and easy to use open-source
-visualization program for scientific data. Since can export the
-lattice-Boltzmann velocity field [ssec:LBvisualization] in the VTK
-format as well and paraview allows to visualize particles with glyphs
-and vector fields with stream lines, glyphs, contourplots, etc., one can
-use it so completely visualize a coupled lattice-Boltzmann MD
-simulation. It can also create videos without much effort if one exports
-data of individual time steps into separate files with filenames
-including a running index (``data_0.vtk``, ``data_1.vtk``, ...).
-
-writevtk
-
-Name of the file to export the particle positions into.
-
-Specifies a list of particle types which should be exported. The default
-is . Alternatively, a list of type number can be given. Exporting the
-positions of all particles but in separate files might make sense if one
-wants to distinguish the different particle types in the visualization
-(i.e. by color or size). To export a type ``1`` use something along
-``writevtk test.tcl 1``. To export types ``1``, ``5``, ``7``, which are
-not to be distinguished in the visualization, use
-``writevtk test.tcl 7 1 5``. The order in the list is arbitrary, but
-duplicates are *not* ignored!
-
-Reading and Writing PDB/PSF files
----------------------------------
-
-The PDB (Brookhaven Protein DataBase) format is a widely used format for
-describing atomistic configurations. PSF is a format that is used to
-describe the topology of a PDB file.
-
-When visualizing your system with VMD, it is recommended to use the VTF
-format instead (see section [sec:vtf]), as it was specifically designed
-for visualizations with VMD. In contrast to the PDB/PSF formats, in VTF
-files it is possible to specify the VDW radii of the particles, to have
-a varying simulation box size, etc.
-
-: Writing the topology
-~~~~~~~~~~~~~~~~~~~~~~
-
-writepsf
-
-Writes the current topology to the file (here, is not a channel, since
-additional information cannot be written anyway). , and so on are
-parameters describing a system consisting of equally long charged
-polymers, counterions and salt. This information is used to set the
-residue name and can be used to color the atoms in VMD. If you specify ,
-the residue name is taken from the molecule identity of the particle. Of
-course different kinds of topologies can also be handled by modified
-versions of .
-
-: Writing the coordinates
-~~~~~~~~~~~~~~~~~~~~~~~~~
-
-writepdb writepdbfoldchains writepdbfoldtopo
-
-Variant writes the corresponding particle data.
-
-Variant writes folded particle data where the folding is performed on
-chain centers of mass rather than single particles. In order to fold in
-this way the chain topology and box length must be specified. Note that
-this method is outdated. Use variant instead.
-
-Variant writes folded particle data where the folding is performed on
-chain centers of mass rather than single particles. This method uses the
-internal box length and topology information from espresso. If you wish
-to shift particles prior to folding then supply the optional shift
-information. should be a three member tcl list consisting of x, y, and z
-shifts respectively and each number should be a floating point (ie with
-decimal point).
-
-: Reading the coordinates and interactions
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-| readpdb pdb\_file type first\_id
-
-Reads the positions and possibly charges, types and Lennard-Jones
-interactions from the file and a corresponding Gromacs topology file .
-The topology file must contain the ``atoms`` and ``atomtypes`` sections,
-it may be necessary to use the Gromacs preprocessor to obtain a complete
-file from a system configuration and a force field.
-
-Any offset of the particle positions if removed, such that the lower
-left corner bounding box of the particles is in the origin. If
-``fit_to_box`` is given, the box size if increased to hold the particles
-if necessary. If it is not set and the particles do not fit into the
-box, the behavior is undefined.
-
-sets the particle type for the added particles. If there is a topology
-file give that contains a types for the particles, the particles get
-types by the order in the topology file plus . If the corresponding type
-in the topology file has a charge, it is used, otherwise the particle
-charge defaults to zero.
-
-The particles get consecutive id’s in the order of the pdb file,
-starting at . Please be aware that existing particles get overwritten by
-values from the file.
-
-The ``lj_with`` section produces Lennard-Jones interactions between the
-type and the types defined by the topology file. The interaction
-parameters are calculated as :math:`\epsilon_{\text{othertype},j} =
-\sqrt{\epsilon_{\text{othertype}} \epsilon_j}` and
-:math:`\sigma_{\text{othertype},j}
-=\frac{1}{2}\left( \sigma_{\text{othertype}} + \sigma_j \right)`, where
-:math:`j` runs over the atomtypes defined in the topology file. This
-corresponds to the combination rule 2 of Gromacs. There may be multiple
-such sections. The cutoff is determined by as
-:math:`\text{cutoff}\times \sigma_{ij}` in a relative fashion. The
-potential is shifted so that it vanishes at the cutoff. The command
-returns the number of particles that were successfully added.
-
-Reading bonded interactions and dihedrals is currently not supported.
 
 Online-visualisation with Mayavi or OpenGL
 ------------------------------------------