ICODE-ADC/lammps
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new fix halt command, other sundry small bug fixes

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This commit is contained in:
Steve Plimpton
2016-10-18 13:11:40 -06:00
parent 713b2af067
commit 2106dce2b3
41 changed files with 118040 additions and 110939 deletions
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25
python/lammps.py
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@ -14,15 +14,18 @@
# Python wrappers on LAMMPS library via ctypes
# for python3 compatibility
from __future__ import print_function
# imports for simple LAMMPS python wrapper module "lammps"
import sys,traceback,types
from ctypes import *
from os.path import dirname,abspath,join
from inspect import getsourcefile
# imports for advanced LAMMPS python wrapper modules "PyLammps" and "IPyLammps"
from collections import namedtuple
import os
import select
@ -38,6 +41,7 @@ class MPIAbortException(Exception):
class lammps(object):
# detect if Python is using version of mpi4py that can pass a communicator
has_mpi4py_v2 = False
@ -60,23 +64,27 @@ class lammps(object):
modpath = dirname(abspath(getsourcefile(lambda:0)))
self.lib = None
# if a pointer to a LAMMPS object is handed in, all symbols should already be available.
# if a pointer to a LAMMPS object is handed in,
# all symbols should already be available
try:
if ptr: self.lib = CDLL("",RTLD_GLOBAL)
except:
self.lib = None
# load liblammps.so unless name is given.
# e.g. if name = "g++", load liblammps_g++.so
# load liblammps.so unless name is given
# if name = "g++", load liblammps_g++.so
# try loading the LAMMPS shared object from the location
# of lammps.py with an absolute path (so that LD_LIBRARY_PATH
# does not need to be set for regular installations.
# fall back to loading with a relative path, which typically
# requires LD_LIBRARY_PATH to be set appropriately.
# of lammps.py with an absolute path,
# so that LD_LIBRARY_PATH does not need to be set for regular install
# fall back to loading with a relative path,
# typically requires LD_LIBRARY_PATH to be set appropriately
if not self.lib:
try:
if not name: self.lib = CDLL(join(modpath,"liblammps.so"),RTLD_GLOBAL)
else: self.lib = CDLL(join(modpath,"liblammps_%s.so" % name),RTLD_GLOBAL)
else: self.lib = CDLL(join(modpath,"liblammps_%s.so" % name),
RTLD_GLOBAL)
except:
if not name: self.lib = CDLL("liblammps.so",RTLD_GLOBAL)
else: self.lib = CDLL("liblammps_%s.so" % name,RTLD_GLOBAL)
@ -91,6 +99,7 @@ class lammps(object):
# just convert it to ctypes ptr and store in self.lmp
if not ptr:
# with mpi4py v2, can pass MPI communicator to LAMMPS
# need to adjust for type of MPI communicator object
# allow for int (like MPICH) or void* (like OpenMPI)