Using LAMMPS with iPython and Jupyter

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

Installation

Download the latest version of LAMMPS into a folder (we will calls this $LAMMPS_DIR from now on)

Compile LAMMPS as a shared library and enable exceptions and PNG support

cd $LAMMPS_DIR/src
make mpi mode=shlib LMP_INC="-DLAMMPS_PNG -DLAMMPS_EXCEPTIONS" JPG_LIB="-lpng"

Create a python virtualenv

virtualenv testing
source testing/bin/activate

Inside the virtualenv install the lammps package

(testing) cd $LAMMPS_DIR/python
(testing) python install.py
(testing) cd   # move to your working directory

Install jupyter and ipython in the virtualenv
```
(testing) pip install ipython jupyter
```
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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import math

# 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.info("all")

L.run(10)



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L.image(zoom=1.0)