2.3.5. Executing commands — LAMMPS documentation

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# 2.3.5. Executing commands

Once an instance of the `lammps` class is created, there are multiple ways to “feed” it commands. In a way that is not very different from running a LAMMPS input script, except that Python has many more facilities for structured programming than the LAMMPS input script syntax. Furthermore it is possible to “compute” what the next LAMMPS command should be.

Same as in the equivalent C library functions, commands can be read from a file, a single string, a list of strings and a block of commands in a single multi-line string. They are processed under the same boundary conditions as the C library counterparts. The example below demonstrates the use of `lammps.file()`, `lammps.command()`, `lammps.commands_list()`, and `lammps.commands_string()`:

    from lammps import lammps
    lmp = lammps()

    # read commands from file 'in.melt'
    lmp.file('in.melt')

    # issue a single command
    lmp.command('variable zpos index 1.0')

    # create 10 groups with 10 atoms each
    cmds = [f"group g{i} id {10*i+1}:{10*(i+1)}" for i in range(10)]
    lmp.commands_list(cmds)

    # run commands from a multi-line string
    block = """
    clear
    region  box block 0 2 0 2 0 2
    create_box 1 box
    create_atoms 1 single 1.0 1.0 ${zpos}
    """
    lmp.commands_string(block)

For convenience, the `lammps` class also provides a command wrapper `cmd` that turns any LAMMPS command into a regular function call.

For instance, the following LAMMPS command

    region box block 0 10 0 5 -0.5 0.5

would normally be executed with the following Python code:

    from lammps import lammps

    lmp = lammps()
    lmp.command("region box block 0 10 0 5 -0.5 0.5")

With the `cmd` wrapper, any LAMMPS command can be split up into arbitrary parts. These parts are then passed to a member function with the name of the command. For the region command that means the `region()` method can be called. The arguments of the command can be passed as one string, or individually.

    from lammps import lammps

    L = lammps()

    # pass command parameters as one string
    L.cmd.region("box block 0 10 0 5 -0.5 0.5")

    # OR pass them individually
    L.cmd.region("box block", 0, 10, 0, 5, -0.5, 0.5)

In the latter example, all parameters except the first are Python floating-point literals. The member function takes the entire parameter list and transparently merges it to a single command string.

The benefit of this approach is avoiding redundant command calls and easier parameterization. With command, commands_list, and commands_string the parameterization needed to be done manually by creating formatted command strings.

    lmp.command("region box block %f %f %f %f %f %f" % (xlo, xhi, ylo, yhi, zlo, zhi))

In contrast, methods of the cmd wrapper accept parameters directly and will convert them automatically to a final command string.

    L.cmd.region("box block", xlo, xhi, ylo, yhi, zlo, zhi)

Note

When running in IPython you can use Tab-completion after `L.cmd.` to see all available LAMMPS commands.

Using these facilities, the previous example shown above can be rewritten as follows:

    from lammps import lammps
    L = lammps()

    # read commands from file 'in.melt'
    L.file('in.melt')

    # issue a single command
    L.cmd.variable('zpos', 'index', 1.0)

    # create 10 groups with 10 atoms each
    for i in range(10):
       L.cmd.group(f"g{i}", "id", f"{10*i+1}:{10*(i+1)}")

    L.cmd.clear()
    L.cmd.region("box block", 0, 2, 0, 2, 0, 2)
    L.cmd.create_box(1, "box")
    L.cmd.create_atoms(1, "single", 1.0, 1.0, "${zpos}")