diff --git a/doc/sphinx/io.rst b/doc/sphinx/io.rst index c7faa9dd8ab..4570a750621 100644 --- a/doc/sphinx/io.rst +++ b/doc/sphinx/io.rst @@ -327,7 +327,7 @@ a whole simulation in a single file. For more details on the format, refer to the VTF homepage (https://github.com/olenz/vtfplugin/wiki). Creating files in these formats from within is supported by the commands :meth:`espressomd.io.writer.vtf.writevsf` -and :meth:`espressomd.io.writer.vtf.writevcf`, that write a structure and coordinate block (respectively ) to the +and :meth:`espressomd.io.writer.vtf.writevcf`, that write a structure and coordinate block (respectively) to the given file. To create a standalone VTF file, first use ``writevsf`` at the beginning of the simulation to write the particle definitions as a header, and then ``writevcf`` to generate a timeframe of the simulation state. For example: @@ -344,7 +344,7 @@ A standalone VTF file can simply be # ... add particles here # write structure block as header - vtf.writevtf(system, fp) + vtf.writevsf(system, fp) # write initial positions as coordinate block vtf.writevcf(system, fp) @@ -359,7 +359,7 @@ can easily add further structure lines to the VTF/VSF file after a structure block has been written to specify further particle properties for visualization. -Note that the ``ids`` of the particles in and VMD may differ. VMD requires +Note that the ``ids`` of the particles in |es| and VMD may differ. VMD requires the particle ids to be enumerated continuously without any holes, while this is not required in |es|. When using ``writevsf`` and ``writevcf``, the particle ids are @@ -380,8 +380,7 @@ timesteps. This is a restriction of VMD itself, not of the format. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :meth:`espressomd.io.writer.vtf.writevsf` -Writes a structure block describing the system's structure to the given channel. -for example +Writes a structure block describing the system's structure to the given channel, for example: .. code:: python