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Given the following text description, write Python code to implement the functionality described below step by step
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Description:
 Example 2
Step1:  Visualize the initial state
Step2:  Queries about LAMMPS simulation
Step3:  Working with LAMMPS Variables
Step4:  Accessing Atom data
Step5:  Accessing thermo data
Step6:  Saving session to as LAMMPS input file
PyLammps can keep track of all LAMMPS commands that are executed. This allows you to prototype a script and then later on save it as a regular input script
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Python Code:
from lammps import IPyLammps
L = IPyLammps()
# 3d Lennard-Jones melt
L.units("lj")
L.atom_style("atomic")
L.atom_modify("map array")
L.lattice("fcc", 0.8442)
L.region("box block", 0, 4, 0, 4, 0, 4)
L.create_box(1, "box")
L.create_atoms(1, "box")
L.mass(1, 1.0)
L.velocity("all create", 1.44, 87287, "loop geom")
L.pair_style("lj/cut", 2.5)
L.pair_coeff(1, 1, 1.0, 1.0, 2.5)
L.neighbor(0.3, "bin")
L.neigh_modify("delay 0 every 20 check no")
L.fix("1 all nve")
L.variable("fx atom fx")
L.run(10)
Explanation: Example 2: Using the PyLammps interface
Prerequisites
Before running this example, make sure your Python environment can find the LAMMPS shared library (liblammps.so) and the LAMMPS Python package is installed. If you followed the README in this folder, this should already be the case. You can also find more information about how to compile LAMMPS and install the LAMMPS Python package in the LAMMPS manual. There is also a dedicated PyLammps HowTo.
Setup system
End of explanation
L.image(zoom=1)
Explanation: Visualize the initial state
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L.system
L.system.natoms
L.communication
L.fixes
L.computes
L.dumps
L.groups
Explanation: Queries about LAMMPS simulation
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L.variable("a index 2")
L.variables
L.variable("t equal temp")
L.variables
import sys
if sys.version_info < (3, 0):
    # In Python 2 'print' is a restricted keyword, which is why you have to use the lmp_print function instead.
    x = float(L.lmp_print('"${a}"'))
else:
    # In Python 3 the print function can be redefined.
    # x = float(L.print('"${a}"')")
    
    # To avoid a syntax error in Python 2 executions of this notebook, this line is packed into an eval statement
    x = float(eval("L.print('\"${a}\"')"))
x
L.variables['t'].value
L.eval("v_t/2.0")
L.variable("b index a b c")
L.variables['b'].value
L.eval("v_b")
L.variables['b'].definition
L.lmp.command('variable i loop 10')
L.variable("i loop 10")
L.variables['i'].value
L.next("i")
L.variables['i'].value
L.eval("ke")
Explanation: Working with LAMMPS Variables
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L.atoms[0]
dir(L.atoms[0])
L.atoms[0].position
L.atoms[0].id
L.atoms[0].velocity
L.atoms[0].force
L.atoms[0].type
L.variables['fx'].value
Explanation: Accessing Atom data
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L.runs
L.runs[0]
L.runs[0].thermo
L.runs[0].thermo
dir(L.runs[0].thermo)
Explanation: Accessing thermo data
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L = IPyLammps()
# enable command history
L.enable_cmd_history = True
# 3d Lennard-Jones melt
L.units("lj")
L.atom_style("atomic")
L.atom_modify("map array")
L.lattice("fcc", 0.8442)
L.region("box block", 0, 4, 0, 4, 0, 4)
L.create_box(1, "box")
L.create_atoms(1, "box")
L.mass(1, 1.0)
L.velocity("all create", 1.44, 87287, "loop geom")
L.pair_style("lj/cut", 2.5)
L.pair_coeff(1, 1, 1.0, 1.0, 2.5)
L.neighbor(0.3, "bin")
L.neigh_modify("delay 0 every 20 check no")
L.fix("1 all nve")
L.run(10)
# write LAMMPS input script with all commands executed so far (including implicit ones)
L.write_script("in.output")
!cat in.output
Explanation: Saving session to as LAMMPS input file
PyLammps can keep track of all LAMMPS commands that are executed. This allows you to prototype a script and then later on save it as a regular input script:
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