Using LAMMPS with iPython and Jupyter

LAMMPS can be run interactively using iPython easily. This tutorial shows how to set this up.

Installation

  1. Download the latest version of LAMMPS into a folder (we will calls this $LAMMPS_DIR from now on)
  2. Compile LAMMPS as a shared library and enable exceptions and PNG support

    cd $LAMMPS_DIR/src
    make yes-molecule
    python Make.py -m mpi -png -s exceptions -a file
    make mode=shlib auto
    
  3. Create a python virtualenv

    virtualenv testing
    source testing/bin/activate
    
  4. Inside the virtualenv install the lammps package

    (testing) cd $LAMMPS_DIR/python
    (testing) python install.py
    (testing) cd   # move to your working directory
  5. Install jupyter and ipython in the virtualenv

    (testing) pip install ipython jupyter
    
  6. Run jupyter notebook

    (testing) jupyter notebook
    

Example


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from lammps import IPyLammps

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L = IPyLammps()

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# 2d circle of particles inside a box with LJ walls
import math

b = 0
x = 50
y = 20
d = 20

# careful not to slam into wall too hard

v = 0.3
w = 0.08
                
L.units("lj")
L.dimension(2)
L.atom_style("bond")
L.boundary("f f p")

L.lattice("hex", 0.85)
L.region("box", "block", 0, x, 0, y, -0.5, 0.5)
L.create_box(1, "box", "bond/types", 1, "extra/bond/per/atom", 6)
L.region("circle", "sphere", d/2.0+1.0, d/2.0/math.sqrt(3.0)+1, 0.0, d/2.0)
L.create_atoms(1, "region", "circle")
L.mass(1, 1.0)

L.velocity("all create 0.5 87287 loop geom")
L.velocity("all set", v, w, 0, "sum yes")

L.pair_style("lj/cut", 2.5)
L.pair_coeff(1, 1, 10.0, 1.0, 2.5)

L.bond_style("harmonic")
L.bond_coeff(1, 10.0, 1.2)

L.create_bonds("all", "all", 1, 1.0, 1.5)

L.neighbor(0.3, "bin")
L.neigh_modify("delay", 0, "every", 1, "check yes")

L.fix(1, "all", "nve")

L.fix(2, "all wall/lj93 xlo 0.0 1 1 2.5 xhi", x, "1 1 2.5")
L.fix(3, "all wall/lj93 ylo 0.0 1 1 2.5 yhi", y, "1 1 2.5")

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L.image(zoom=1.8)

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L.thermo_style("custom step temp epair press")
L.thermo(100)
output = L.run(40000)
L.image(zoom=1.8)

Queries about LAMMPS simulation


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L.system

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L.system.natoms

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L.system.nbonds

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L.system.nbondtypes

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L.communication

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L.fixes

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L.computes

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L.dumps

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L.groups

Working with LAMMPS Variables


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L.variable("a index 2")

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L.variables

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L.variable("t equal temp")

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L.variables

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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

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L.variables['t'].value

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L.eval("v_t/2.0")

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L.variable("b index a b c")

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L.variables['b'].value

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L.eval("v_b")

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L.variables['b'].definition

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L.variable("i loop 10")

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L.variables['i'].value

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L.next("i")
L.variables['i'].value

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L.eval("ke")

Accessing Atom data


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L.atoms[0]

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[x for x in dir(L.atoms[0]) if not x.startswith('__')]

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L.atoms[0].position

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L.atoms[0].id

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L.atoms[0].velocity

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L.atoms[0].force

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L.atoms[0].type

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