LAMMPS can be run interactively using iPython easily. This tutorial shows how to set this up.
$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 $LAMMPS_DIR/python
(testing) python install.py
(testing) cd # move to your working directoryInstall jupyter and ipython in the virtualenv
(testing) pip install ipython jupyter
Run jupyter notebook
(testing) jupyter notebook
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from lammps import IPyLammps
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L = IPyLammps()
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# 3d Lennard-Jones melt
L.units("lj")
L.atom_style("atomic")
L.atom_modify("map array")
L.lattice("fcc", 0.8442)
L.region("box block", 0, 4, 0, 4, 0, 4)
L.create_box(1, "box")
L.create_atoms(1, "box")
L.mass(1, 1.0)
L.velocity("all create", 1.44, 87287, "loop geom")
L.pair_style("lj/cut", 2.5)
L.pair_coeff(1, 1, 1.0, 1.0, 2.5)
L.neighbor(0.3, "bin")
L.neigh_modify("delay 0 every 20 check no")
L.fix("1 all nve")
L.variable("fx atom fx")
L.run(10)
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L.image(zoom=1)
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L.system
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L.system.natoms
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L.communication
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L.fixes
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L.computes
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L.dumps
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L.groups
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L.variable("a index 2")
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L.variables
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L.variable("t equal temp")
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L.variables
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import sys
if sys.version_info < (3, 0):
# In Python 2 'print' is a restricted keyword, which is why you have to use the lmp_print function instead.
x = float(L.lmp_print('"${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")
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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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L.variables['fx'].value
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L.runs
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L.runs[0]
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L.runs[0].thermo
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L.runs[0].thermo
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L.write_script("in.output")
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dir(L.runs[0].thermo)
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