Docs: Add example of LammpsCalculation with script input

examples/launch_lammps_base_script.py

@@ -0,0 +1,106 @@
+"""Run a LAMMPS calculation from a pre-defined complete input script.
+
+The example input script is taken from https://www.lammps.org/inputs/in.lj.txt and is the first example script for the
+official benchmarks of LAMMPS. It is a simple NVE simulation of a Lennard-Jones liquid. When passing a complete input
+script for the ``script`` input of the ``LammpsBaseCalculation``, other inputs, such as ``structure`` and ``potential``
+no longer have to be specified.
+"""
+import io
+import textwrap
+
+from aiida import orm
+from aiida.engine import run_get_node
+from aiida.plugins import CalculationFactory
+import numpy as np
+
+from aiida_lammps.data.potential import LammpsPotentialData
+
+
+def main(
+    script: orm.SinglefileData,
+    options: AttributeDict,
+    code: orm.Code,
+) -> orm.Node:
+    """Submission of the calculation.
+
+    :param script: complete input script to be used in the calculation
+    :type script: orm.SinglefileData
+    :param options: options to control the submission parameters
+    :type options: AttributeDict
+    :param code: code describing the ``LAMMPS`` calculation
+    :type code: orm.Code
+    :return: node containing the ``LAMMPS`` calculation
+    :rtype: orm.Node
+    """
+    calculation = CalculationFactory("lammps.base")
+
+    builder = calculation.get_builder()
+    builder.code = code
+    builder.script = script
+    builder.metadata.options = options
+
+    _, node = run_get_node(calculation, **builder)
+
+    return node
+
+
+if __name__ == "__main__":
+
+    # Get the lammps code defined in AiiDA database
+    CODE = orm.load_code("lammps-23.06.2022@localhost")
+    # Define the parameters for the resources requested for the calculation
+    OPTIONS = AttributeDict()
+    OPTIONS.resources = AttributeDict()
+    # Total number of machines used
+    OPTIONS.resources.num_machines = 1
+    # Total number of mpi processes
+    OPTIONS.resources.tot_num_mpiprocs = 2
+
+    # Define the complete input script that should be run
+    SCRIPT = orm.SinglefileData(
+        io.StringIO(
+            textwrap.dedent(
+                """
+                # 3d Lennard-Jones melt
+
+                variable      x index 1
+                variable      y index 1
+                variable      z index 1
+
+                variable      xx equal 20*$x
+                variable      yy equal 20*$y
+                variable      zz equal 20*$z
+
+                units         lj
+                atom_style    atomic
+
+                lattice       fcc 0.8442
+                region        box block 0 ${xx} 0 ${yy} 0 ${zz}
+                create_box    1 box
+                create_atoms  1 box
+                mass          1 1.0
+
+                velocity      all create 1.44 87287 loop geom
+
+                pair_style    lj/cut 2.5
+                pair_coeff    1 1 1.0 1.0 2.5
+
+                neighbor      0.3 bin
+                neigh_modify  delay 0 every 20 check no
+
+                fix           1 all nve
+
+                run           100
+                """
+            )
+        )
+    )
+
+    # Run the aiida-lammps calculation
+    submission_node = main(
+        script=SCRIPT,
+        options=OPTIONS,
+        code=CODE,
+    )
+
+    print(f"Calculation node: {submission_node}")