Merge branch 'master' into lammps-icms
Resolved Conflicts: lib/meam/Makefile.gfortran lib/poems/Makefile.g++ lib/reax/Makefile.gfortran python/lammps.py src/USER-CUDA/cuda.cpp
This commit is contained in:
Axel Kohlmeyer
@ -3,41 +3,29 @@ 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 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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shared library, for use with Python, are given in
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doc/Section_python.html and in doc/Section_start.html#start_5.
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Basically you need to follow these 3 steps:
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Basically you need to follow these steps in the src directory:
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a) Add paths to environment variables in your shell script
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% make makeshlib # creates Makefile.shlib
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% make -f Makefile.shlib g++ # or whatever machine target you wish
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% make install-python # may need to do this via sudo
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For example, for csh or tcsh, add something like this to ~/.cshrc:
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You can replace the last step with running the python/install.py
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script directly to give you more control over where two relevant files
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are installed, or by setting environment variables in your shell
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script. See doc/Section_python.html for details.
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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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You can then launch Python and instantiate an instance of LAMMPS:
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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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Python. See doc/Section_python.html#py_5 for tests you can then use
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to run LAMMPS both in serial or parallel thru Python.
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-------------------------------------------------------------------
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@ -18,6 +18,7 @@ if len(argv) != 2:
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infile = sys.argv[1]
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me = 0
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# uncomment if running in parallel via Pypar
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#import pypar
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#me = pypar.rank()
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@ -38,12 +39,11 @@ for line in lines: lmp.command(line)
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# run a single step with changed coords
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lmp.command("run 10")
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x = lmp.get_coords()
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x = lmp.gather_atoms("x",1,3)
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epsilon = 0.1
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x[0] += epsilon
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lmp.put_coords(x)
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lmp.scatter_atoms("x",1,3,x)
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lmp.command("run 1");
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lmp.command("run 1")
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# uncomment if running in parallel via Pypar
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#print "Proc %d out of %d procs has" % (me,nprocs), lmp
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35
python/install.py
Normal file
35
python/install.py
Normal file
@ -0,0 +1,35 @@
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#!/usr/local/bin/python
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# copy LAMMPS shared library src/liblammps.so and lammps.py to system dirs
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# Syntax: python install.py [libdir] [pydir]
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# libdir = target dir for src/liblammps.so, default = /usr/local/lib
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# pydir = target dir for lammps.py, default = Python site-packages dir
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import sys,commands
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if len(sys.argv) > 3:
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print "Syntax: python install.py [libdir] [pydir]"
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sys.exit()
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if len(sys.argv) >= 2: libdir = sys.argv[1]
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else: libdir = "/usr/local/lib"
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if len(sys.argv) == 3: pydir = sys.argv[2]
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else:
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paths = sys.path
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for i,path in enumerate(paths):
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index = path.rfind("site-packages")
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if index < 0: continue
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if index == len(path) - len("site-packages"): break
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pydir = paths[i]
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str = "cp ../src/liblammps.so %s" % libdir
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print str
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outstr = commands.getoutput(str)
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if len(outstr.strip()): print outstr
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str = "cp ../python/lammps.py %s" % pydir
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print str
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outstr = commands.getoutput(str)
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if len(outstr.strip()): print outstr
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@ -17,23 +17,15 @@ import types
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from ctypes import *
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import os.path
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LMPINT = 0
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LMPDOUBLE = 1
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LMPIPTR = 2
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LMPDPTR = 3
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LMPDPTRPTR = 4
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LOCATION = os.path.dirname(__file__)
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class lammps:
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def __init__(self,name="",cmdlineargs=None):
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def __init__(self,name="",cmdargs=None):
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# load liblmp.so by default
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# if name = "g++", load liblmp_g++.so
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# load liblammps.so by default
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# if name = "g++", load liblammps_g++.so
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try:
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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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if not name: self.lib = CDLL("liblammps.so")
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else: self.lib = CDLL("liblammps_%s.so" % name)
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except:
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raise OSError,"Could not load LAMMPS dynamic library"
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@ -42,10 +34,10 @@ class lammps:
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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 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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if cmdargs:
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cmdargs.insert(0,"lammps.py")
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narg = len(cmdargs)
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cargs = (c_char_p*narg)(*cmdargs)
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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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@ -68,30 +60,26 @@ class lammps:
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self.lib.lammps_command(self.lmp,cmd)
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def extract_global(self,name,type):
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if type == LMPDOUBLE:
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self.lib.lammps_extract_global.restype = POINTER(c_double)
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ptr = self.lib.lammps_extract_global(self.lmp,name)
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return ptr[0]
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if type == LMPINT:
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if type == 0:
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self.lib.lammps_extract_global.restype = POINTER(c_int)
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ptr = self.lib.lammps_extract_global(self.lmp,name)
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return ptr[0]
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return None
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elif type == 1:
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self.lib.lammps_extract_global.restype = POINTER(c_double)
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else: return None
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ptr = self.lib.lammps_extract_global(self.lmp,name)
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return ptr[0]
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def extract_atom(self,name,type):
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if type == LMPDPTRPTR:
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self.lib.lammps_extract_atom.restype = POINTER(POINTER(c_double))
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ptr = self.lib.lammps_extract_atom(self.lmp,name)
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return ptr
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if type == LMPDPTR:
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self.lib.lammps_extract_atom.restype = POINTER(c_double)
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ptr = self.lib.lammps_extract_atom(self.lmp,name)
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return ptr
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if type == LMPIPTR:
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if type == 0:
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self.lib.lammps_extract_atom.restype = POINTER(c_int)
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ptr = self.lib.lammps_extract_atom(self.lmp,name)
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return ptr
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return None
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elif type == 1:
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self.lib.lammps_extract_atom.restype = POINTER(POINTER(c_int))
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elif type == 2:
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self.lib.lammps_extract_atom.restype = POINTER(c_double)
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elif type == 3:
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self.lib.lammps_extract_atom.restype = POINTER(POINTER(c_double))
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else: return None
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ptr = self.lib.lammps_extract_atom(self.lmp,name)
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return ptr
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def extract_compute(self,id,style,type):
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if type == 0:
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@ -153,18 +141,26 @@ class lammps:
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return result
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return None
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# return total number of atoms in system
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def get_natoms(self):
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return self.lib.lammps_get_natoms(self.lmp)
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def get_coords(self):
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nlen = 3 * self.lib.lammps_get_natoms(self.lmp)
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coords = (c_double*nlen)()
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self.lib.lammps_get_coords(self.lmp,coords)
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return coords
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# return vector of atom properties gathered across procs, ordered by atom ID
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# assume coords is an array of c_double, as created by get_coords()
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# could check if it is some other Python object and create c_double array?
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# constructor for c_double array can take an arg to use to fill it?
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def put_coords(self,coords):
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self.lib.lammps_put_coords(self.lmp,coords)
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def gather_atoms(self,name,type,count):
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natoms = self.lib.lammps_get_natoms(self.lmp)
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if type == 0:
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data = ((count*natoms)*c_double)()
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self.lib.lammps_gather_atoms(self.lmp,name,type,count,data)
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elif type == 1:
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data = ((count*natoms)*c_double)()
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self.lib.lammps_gather_atoms(self.lmp,name,type,count,data)
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else: return None
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return data
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# scatter vector of atom properties across procs, ordered by atom ID
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# assume vector is of correct type and length, as created by gather_atoms()
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def scatter_atoms(self,name,type,count,data):
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self.lib.lammps_scatter_atoms(self.lmp,name,type,count,data)
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