Merge pull request #449 from rbberger/python_refactoring

11.2 Overview of using Python from a LAMMPS script :link(py_2),h4

NOTE: It is not currently possible to use the "python"_python.html

command described in this section with Python 3, only with Python 2.

The C API changed from Python 2 to 3 and the LAMMPS code is not

compatible with both.

LAMMPS has a "python"_python.html command which can be used in an

input script to define and execute a Python function that you write

the code for.  The Python function can also be assigned to a LAMMPS

  return n * factorial(n-1)

 """ :pre

python loop input 1 SELF return v_value format -f here """

python loop input 1 SELF return v_value format pf here """

def loop(lmpptr,N,cut0):

  from lammps import lammps

  lmp = lammps(ptr=lmpptr) :pre

[Description:]

NOTE: It is not currently possible to use the "python"_python.html

command described in this section with Python 3, only with Python 2.

The C API changed from Python 2 to 3 and the LAMMPS code is not

compatible with both.

Define a Python function or execute a previously defined function.

Arguments, including LAMMPS variables, can be passed to the function

from the LAMMPS input script and a value returned by the Python

to work.  If the two have been built at different times using

different source files, problems may occur. 

As described above, you can use the python command to invoke a Python

function which calls back to LAMMPS through its Python-wrapped library

interface.  However you cannot do the opposite.  I.e. you cannot call

LAMMPS from Python and invoke the python command to "callback" to

Python and execute a Python function.  LAMMPS will generate an error

if you try to do that.  Note that we think there actually should be a

way to do that, but haven't yet been able to figure out how to do it

successfully.

[Related commands:]

"shell"_shell.html, "variable"_variable.html

cd $LAMMPS_DIR/src :pre

# generate custom Makefile

python2 Make.py -jpg -png -s ffmpeg exceptions -m mpi -a file :pre

python Make.py -jpg -png -s ffmpeg exceptions -m mpi -a file :pre

# add packages if necessary

make yes-MOLECULE :pre

# Python function that implements a loop of short runs

# calls back to LAMMPS via "lmp" instance

# lammps() must be called with ptr=lmpptr for this to work

from __future__ import print_function

def loop(N,cut0,thresh,lmpptr):

  print "LOOP ARGS",N,cut0,thresh,lmpptr

  print("LOOP ARGS",N,cut0,thresh,lmpptr)

  from lammps import lammps

  lmp = lammps(ptr=lmpptr)

  natoms = lmp.get_natoms()

    cut = cut0 + i*0.1

    lmp.set_variable("cut",cut)                 # set a variable in LAMMPS

    lmp.command("pair_style lj/cut ${cut}")     # LAMMPS command

    #lmp.command("pair_style lj/cut %d" % cut)  # LAMMPS command option

    lmp.command("pair_coeff * * 1.0 1.0")       # ditto

    lmp.command("run 10")                       # ditto

    pe = lmp.extract_compute("thermo_pe",0,0)   # extract total PE from LAMMPS

    print "PE",pe/natoms,thresh

    print("PE",pe/natoms,thresh)

    if pe/natoms < thresh: return

# example of catching a syntax error

python          simple here """

from __future__ import print_function

def simple():

  import exceptions

  print "Inside simple function"

  print("Inside simple function")

  try:

    foo += 1

  except Exception, e:

    print "FOO error:",e

  except Exception as e:

    print("FOO error:", e)

"""

python          simple invoke