docs: start with howto section
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@ -44,7 +44,7 @@ For large numbers of independent simulations, you can use
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:doc:`variables <variable>` and the :doc:`next <next>` and
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:doc:`jump <jump>` commands to loop over the same input script
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multiple times with different settings. For example, this
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script, named in.polymer
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script, named ``in.polymer``
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.. code-block:: LAMMPS
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@ -57,7 +57,7 @@ script, named in.polymer
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next d
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jump in.polymer
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would run 8 simulations in different directories, using a data.polymer
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would run 8 simulations in different directories, using a ``data.polymer``
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file in each directory. The same concept could be used to run the
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same system at 8 different temperatures, using a temperature variable
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and storing the output in different log and dump files, for example
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@ -83,10 +83,10 @@ partition of processors. LAMMPS can be run on multiple partitions via
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the :doc:`-partition command-line switch <Run_options>`.
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In the last 2 examples, if LAMMPS were run on 3 partitions, the same
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scripts could be used if the "index" and "loop" variables were
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scripts could be used if the ``index`` and ``loop`` variables were
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replaced with *universe*\ -style variables, as described in the
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:doc:`variable <variable>` command. Also, the "next t" and "next a"
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commands would need to be replaced with a single "next a t" command.
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:doc:`variable <variable>` command. Also, the :lammps:`next t` and :lammps:`next a`
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commands would need to be replaced with a single :lammps:`next a t` command.
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With these modifications, the 8 simulations of each script would run
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on the 3 partitions one after the other until all were finished.
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Initially, 3 simulations would be started simultaneously, one on each
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