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 PNG support

cd $LAMMPS_DIR/src
python2 Make.py -m mpi -png -a file
make mode=shlib auto

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



In [1]:

    
from lammps import IPyLammps



In [2]:

    
L = IPyLammps()









    



LAMMPS output is captured by PyLammps wrapper



In [3]:

    
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)









    Out[3]:





['Neighbor list info ...',
 '  1 neighbor list requests',
 '  update every 20 steps, delay 0 steps, check no',
 '  max neighbors/atom: 2000, page size: 100000',
 '  master list distance cutoff = 2.8',
 '  ghost atom cutoff = 2.8',
 '  binsize = 1.4, bins = 5 5 5',
 'Setting up Verlet run ...',
 '  Unit style    : lj',
 '  Current step  : 0',
 '  Time step     : 0.005',
 'Memory usage per processor = 2.04486 Mbytes',
 'Step Temp E_pair E_mol TotEng Press ',
 '       0         1.44   -6.7733681            0   -4.6218056   -5.0244179 ',
 '      10    1.1298532   -6.3095502            0   -4.6213906   -2.6058175 ',
 'Loop time of 0.001143 on 1 procs for 10 steps with 256 atoms',
 '',
 'Performance: 3779527.555 tau/day, 8748.906 timesteps/s',
 '291.6% CPU use with 1 MPI tasks x no OpenMP threads',
 '',
 'MPI task timing breakdown:',
 'Section |  min time  |  avg time  |  max time  |%varavg| %total',
 '---------------------------------------------------------------',
 'Pair    | 0.001048   | 0.001048   | 0.001048   |   0.0 | 91.69',
 'Neigh   | 0          | 0          | 0          |   0.0 |  0.00',
 'Comm    | 5.3e-05    | 5.3e-05    | 5.3e-05    |   0.0 |  4.64',
 'Output  | 6e-06      | 6e-06      | 6e-06      |   0.0 |  0.52',
 'Modify  | 2.1e-05    | 2.1e-05    | 2.1e-05    |   0.0 |  1.84',
 'Other   |            | 1.5e-05    |            |       |  1.31',
 '',
 'Nlocal:    256 ave 256 max 256 min',
 'Histogram: 1 0 0 0 0 0 0 0 0 0',
 'Nghost:    1431 ave 1431 max 1431 min',
 'Histogram: 1 0 0 0 0 0 0 0 0 0',
 'Neighs:    9984 ave 9984 max 9984 min',
 'Histogram: 1 0 0 0 0 0 0 0 0 0',
 '',
 'Total # of neighbors = 9984',
 'Ave neighs/atom = 39',
 'Neighbor list builds = 0',
 'Dangerous builds not checked']



In [4]:

    
L.image(zoom=1.0)









    Out[4]: