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ENH: added flexible command option to lammps input writer

Jon Quinlivan requested to merge (removed):lammpswriter_command into master

Currently it's not possible to concatenate commands with the lammps writer as it uses a dictionary for the command. I have added a general commands option to the end of the script which allows for the creation of more complex commands for LAMMPS. For example concatenating:

 run 100
 minimize 0 0.1 1000 10000
 run 100

It works by providing the lammps parameters as

parameters = {
    "commands":["run 100",
               "minimize 0 0.1 1000 10000",
               "run 100"]
}

It's called after all of the other parameters have been fixed, but before adding the final run 0 command.

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