Merge branch 'master' into lammps-icms
Resolved Conflicts: python/lammps.py src/MAKE/Makefile.mingw src/MAKE/Makefile.openmpi src/MAKE/Makefile.serial src/MAKE/Makefile.serial_debug src/USER-CUDA/verlet_cuda.cpp
This commit is contained in:
Axel Kohlmeyer
@ -1,26 +1,48 @@
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This directory contains Python code which wraps LAMMPS as a library
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and allows the library interface to be invoked from a Python, either
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from a script or interactively.
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and allows the LAMMPS library interface to be invoked from Python,
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either from a script or interactively.
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Details on how to build and use this Python interface are given in
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Details on the Python interface to LAMMPS and how to build LAMMPS as a
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shared library for use with Python are given in
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doc/Section_python.html.
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Basically you have to extend the Python on your box to include the
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LAMMPS wrappers:
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Basically you need to follow these 3 steps:
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python setup_serial.py build # for serial LAMMPS and Python
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sudo python setup_serial.py install
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a) Add paths to environment variables in your shell script
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python setup.py build # for parallel LAMMPS and Python
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sudo python setup.py install
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For example, for csh or tcsh, add something like this to ~/.cshrc:
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but there are several issues to be aware of, as discussed in the doc
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pages.
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setenv PYTHONPATH ${PYTHONPATH}:/home/sjplimp/lammps/python
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setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/src
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setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/src/STUBS
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The latter is only necessary if you will use the MPI stubs library
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instead of an MPI installed on your machine.
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b) Build LAMMPS as a dynamic library, including dynamic versions of
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any libraries it includes for the packages you have installed,
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e.g. STUBS, MPI, FFTW, JPEG, package libs.
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From the src directory:
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% make makeshlib
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% make -f Makefile.shlib g++
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If successful, this results in the file src/liblmp_g++.so
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c) Launch Python and import the LAMMPS wrapper
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% python
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>>> from lammps import lammps
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>>> lmp = lammps()
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If that gives no errors, you have succesfully wrapped LAMMPS with
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Python.
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-------------------------------------------------------------------
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Once you have successfully built and tested the wrappers, you can run
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the Python scripts in the examples sub-directory:
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Once you have successfully wrapped LAMMPS, you can run the Python
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scripts in the examples sub-directory:
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trivial.py read/run a LAMMPS input script thru Python
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demo.py invoke various LAMMPS library interface routines
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@ -26,28 +26,26 @@ LMPDPTRPTR = 4
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LOCATION = os.path.dirname(__file__)
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class lammps:
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def __init__(self,args=None):
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def __init__(self,name="",cmdlineargs=None):
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# attempt to load parallel library first, serial library next
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# could provide caller a flag to choose which library to load
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# load liblmp.so by default
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# if name = "g++", load liblmp_g++.so
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try:
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self.lib = CDLL(os.path.join(LOCATION, "_lammps.so"))
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if not name: self.lib = CDLL("liblmp.so")
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else: self.lib = CDLL("liblmp_%s.so" % name)
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except:
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try:
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self.lib = CDLL(os.path.join(LOCATION, "_lammps_serial.so"))
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except:
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raise OSError,"Could not load LAMMPS dynamic library"
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raise OSError,"Could not load LAMMPS dynamic library"
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# create an instance of LAMMPS
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# don't know how to pass an MPI communicator from PyPar
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# no_mpi call lets LAMMPS use MPI_COMM_WORLD
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# cargs = array of C strings from args
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if args:
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args.insert(0,"lammps.py")
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narg = len(args)
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cargs = (c_char_p*narg)(*args)
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if cmdlineargs:
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cmdlineargs.insert(0,"lammps.py")
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narg = len(cmdlineargs)
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cargs = (c_char_p*narg)(*cmdlineargs)
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self.lmp = c_void_p()
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self.lib.lammps_open_no_mpi(narg,cargs,byref(self.lmp))
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else:
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@ -1,39 +0,0 @@
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#!/usr/local/bin/python
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"""
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setup.py file for LAMMPS with system MPICH library
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"""
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from distutils.core import setup, Extension
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import os, glob
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path = os.path.dirname(os.getcwd())
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# list of src files for LAMMPS
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libfiles = glob.glob("%s/src/*.cpp" % path)
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lammps_library = Extension("_lammps",
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sources = libfiles,
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define_macros = [("MPICH_IGNORE_CXX_SEEK",1),
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("LAMMPS_GZIP",1),
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("FFT_NONE",1),],
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# src files for LAMMPS
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include_dirs = ["../src"],
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# additional libs for MPICH on Linux
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libraries = ["mpich","mpl","pthread"],
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# where to find the MPICH lib on Linux
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library_dirs = ["/usr/local/lib"],
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# additional libs for MPI on Mac
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# libraries = ["mpi"],
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)
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setup(name = "lammps",
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version = "28Nov11",
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author = "Steve Plimpton",
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author_email = "sjplimp@sandia.gov",
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url = "http://lammps.sandia.gov",
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description = """LAMMPS molecular dynamics library - parallel""",
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py_modules = ["lammps"],
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ext_modules = [lammps_library]
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)
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@ -1,34 +0,0 @@
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#!/usr/local/bin/python
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"""
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setup_serial.py file for LAMMPS with dummy serial MPI library
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"""
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from distutils.core import setup, Extension
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import os, glob
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path = os.path.dirname(os.getcwd())
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# list of src files for LAMMPS and MPI STUBS
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libfiles = glob.glob("%s/src/*.cpp" % path) + \
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glob.glob("%s/src/STUBS/*.c" % path)
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lammps_library = Extension("_lammps_serial",
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sources = libfiles,
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define_macros = [("MPICH_IGNORE_CXX_SEEK",1),
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("LAMMPS_GZIP",1),
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("FFT_NONE",1),],
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# src files for LAMMPS and MPI STUBS
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include_dirs = ["../src", "../src/STUBS"]
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)
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setup(name = "lammps_serial",
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version = "28Nov11",
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author = "Steve Plimpton",
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author_email = "sjplimp@sandia.gov",
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url = "http://lammps.sandia.gov",
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description = """LAMMPS molecular dynamics library - serial""",
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py_modules = ["lammps"],
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ext_modules = [lammps_library]
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)
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