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Merge branch 'master' into lammps-icms

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Resolved Conflicts:
	doc/Eqs/pair_coul_diel.jpg
	doc/Section_commands.html
	doc/Section_commands.txt
	doc/pair_coul_diel.html
	doc/pair_coul_diel.txt
	doc/processors.html
	doc/processors.txt
	examples/USER/imd/bucky_cnt_imd.vmd
	examples/USER/imd/in.bucky-plus-cnt
	examples/USER/imd/in.deca-ala-solv_imd
	examples/USER/imd/in.deca-ala_imd
	lib/gpu/Makefile.fermi
	lib/gpu/Makefile.lincoln
	lib/gpu/Makefile.longhorn
	lib/gpu/Makefile.serial
	lib/gpu/geryon/VERSION.txt
	lib/gpu/pair_gpu_device.cpp
	src/ASPHERE/atom_vec_ellipsoid.cpp
	src/CLASS2/Install.sh
	src/COLLOID/atom_vec_colloid.cpp
	src/DIPOLE/atom_vec_dipole.cpp
	src/GPU/fix_gpu.cpp
	src/GRANULAR/atom_vec_granular.cpp
	src/GRANULAR/fix_pour.h
	src/KSPACE/Install.sh
	src/KSPACE/fft3d.cpp
	src/KSPACE/fft3d.h
	src/KSPACE/kissfft.h
	src/KSPACE/pppm.cpp
	src/KSPACE/pppm.h
	src/KSPACE/pppm_tip4p.cpp
	src/MAKE/Makefile.openmpi
	src/MAKE/Makefile.serial
	src/MANYBODY/pair_airebo.cpp
	src/MANYBODY/pair_comb.cpp
	src/MANYBODY/pair_eam.cpp
	src/MANYBODY/pair_eim.cpp
	src/MANYBODY/pair_sw.cpp
	src/MANYBODY/pair_tersoff.cpp
	src/MANYBODY/pair_tersoff_zbl.cpp
	src/MOLECULE/atom_vec_angle.cpp
	src/MOLECULE/atom_vec_bond.cpp
	src/MOLECULE/atom_vec_full.cpp
	src/MOLECULE/atom_vec_molecular.cpp
	src/Makefile
	src/Makefile.lib
	src/PERI/atom_vec_peri.cpp
	src/USER-CG-CMM/Install.sh
	src/USER-IMD/README
	src/USER-IMD/fix_imd.cpp
	src/USER-IMD/fix_imd.h
	src/USER-SMD/Install.sh
	src/atom_vec_atomic.cpp
	src/atom_vec_charge.cpp
	src/comm.cpp
	src/finish.cpp
	src/fix_box_relax.cpp
	src/fix_deposit.cpp
	src/fix_spring_self.cpp
	src/fix_store_state.cpp
	src/fix_wall.cpp
	src/fix_wall_reflect.cpp
	src/input.cpp
	src/input.h
	src/memory.cpp
	src/memory.h
	src/pair_lj_cut.cpp
	tools/restart2data.cpp
This commit is contained in:
Axel Kohlmeyer
2011-12-31 19:07:46 -05:00
parent 72c3988b9a adbeb0277b
commit 9259ae8699
2579 changed files with 905870 additions and 99854 deletions
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2
python/README
View File

@ -12,7 +12,7 @@ python setup_serial.py build # for serial LAMMPS and Python
sudo python setup_serial.py install
python setup.py build # for parallel LAMMPS and Python
sudo python setuppy install
sudo python setup.py install
but there are several issues to be aware of, as discussed in the doc
pages.

4
python/lammps.py
View File

@ -33,8 +33,8 @@ class lammps:
except:
try:
self.lib = CDLL("_lammps_serial.so")
except:
raise StandardError,"Could not load LAMMPS dynamic library"
#except:
# raise OSError,"Could not load LAMMPS dynamic library"
# create an instance of LAMMPS
# don't know how to pass an MPI communicator from PyPar

6
python/setup.py
View File

@ -1,7 +1,7 @@
#!/usr/local/bin/python
"""
setup.py file for LAMMPS with system MPI library
setup.py file for LAMMPS with system MPICH library
"""
from distutils.core import setup, Extension
@ -21,7 +21,7 @@ lammps_library = Extension("_lammps",
# src files for LAMMPS
include_dirs = ["../src"],
# additional libs for MPICH on Linux
libraries = ["mpich","rt"],
libraries = ["mpich","mpl","pthread"],
# where to find the MPICH lib on Linux
library_dirs = ["/usr/local/lib"],
# additional libs for MPI on Mac
@ -29,7 +29,7 @@ lammps_library = Extension("_lammps",
)
setup(name = "lammps",
version = "26Oct10",
version = "28Nov11",
author = "Steve Plimpton",
author_email = "sjplimp@sandia.gov",
url = "http://lammps.sandia.gov",

2
python/setup_serial.py
View File

@ -24,7 +24,7 @@ lammps_library = Extension("_lammps_serial",
)
setup(name = "lammps_serial",
version = "26Oct10",
version = "28Nov11",
author = "Steve Plimpton",
author_email = "sjplimp@sandia.gov",
url = "http://lammps.sandia.gov",