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2.3.5. Executing commands

Once an instance of the lammps, PyLammps, or IPyLammps 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 = ["group g{} id {}:{}".format(i,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)

Unlike the lammps API, the PyLammps/IPyLammps APIs allow running LAMMPS commands by calling equivalent member functions of PyLammps and IPyLammps instances.

For instance, the following LAMMPS command

region box block 0 10 0 5 -0.5 0.5

can be executed using with the lammps API with the following Python code if lmp is an instance of lammps:

from lammps import lammps

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

With the PyLammps interface, 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 PyLammps

L = PyLammps()

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

# OR pass them individually
L.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. In the lammps API 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 PyLammps accept parameters directly and will convert them automatically to a final command string.

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

Using these facilities, the example shown for the lammps API can be rewritten as follows:

from lammps import PyLammps
L = PyLammps()

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

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

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

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