Diffusion lammps d61136b1d08f

Merge branch 'lammps-icms' into lammps-colvars
d61136b1d08f
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Authored by Axel Kohlmeyer <akohlmey@gmail.com> on Aug 18 2012, 23:19.

Description

Merge branch 'lammps-icms' into lammps-colvars

Details

Committed

Axel Kohlmeyer <akohlmey@gmail.com>

Aug 18 2012, 23:19

Pushed

junge

Oct 6 2016, 16:49

Parents

rLAMMPS788b01cd7186: Merge branch 'master' into lammps-icms
rLAMMPSb898d5d163b4: update colvarmodule code to svn as of aug 8 2012

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Axel Kohlmeyer <akohlmey@gmail.com> committed rLAMMPSd61136b1d08f: Merge branch 'lammps-icms' into lammps-colvars (authored by Axel Kohlmeyer <akohlmey@gmail.com>).Aug 18 2012, 23:19

Merged Changes

This commit merges a very large number of changes. Only the first 50 are shown.

Commit	Author	Details	Committed
788b01cd7186	Axel Kohlmeyer	Merge branch 'master' into lammps-icms	Aug 18 2012
4cb989a2d3a6	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8680 f3b2605a-c512-4ea7…	Aug 17 2012
02b9a79d3850	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8679 f3b2605a-c512-4ea7…	Aug 17 2012
d29dd35c4554	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8678 f3b2605a-c512-4ea7…	Aug 17 2012
53bb7e981d3d	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8677 f3b2605a-c512-4ea7…	Aug 17 2012
d510654bc360	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8676 f3b2605a-c512-4ea7…	Aug 16 2012
d4215d884402	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8675 f3b2605a-c512-4ea7…	Aug 16 2012
0df7e3716903	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8674 f3b2605a-c512-4ea7…	Aug 16 2012
5c58881400ad	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8673 f3b2605a-c512-4ea7…	Aug 16 2012
2e7bd3367f6b	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8672 f3b2605a-c512-4ea7…	Aug 15 2012
8af673c69d5f	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8671 f3b2605a-c512-4ea7…	Aug 15 2012
448637286853	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8670 f3b2605a-c512-4ea7…	Aug 15 2012
127f12e6fafb	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8669 f3b2605a-c512-4ea7…	Aug 15 2012
ffc41c52c5cd	Axel Kohlmeyer	Merge branch 'master' into lammps-icms	Aug 15 2012
e02a64ecc0b3	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8667 f3b2605a-c512-4ea7…	Aug 15 2012
bdbaacd8fb3f	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8665 f3b2605a-c512-4ea7…	Aug 15 2012
6139908a11e2	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8664 f3b2605a-c512-4ea7…	Aug 15 2012
c0f36fd0af9a	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8663 f3b2605a-c512-4ea7…	Aug 15 2012
7487754a4d4a	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8659 f3b2605a-c512-4ea7…	Aug 14 2012
39818495c5c2	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8658 f3b2605a-c512-4ea7…	Aug 14 2012
617a28d8f434	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8657 f3b2605a-c512-4ea7…	Aug 14 2012
7f5e8cb8962c	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8656 f3b2605a-c512-4ea7…	Aug 14 2012
dff995a3234a	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8655 f3b2605a-c512-4ea7…	Aug 14 2012
3994c1335314	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8653 f3b2605a-c512-4ea7…	Aug 14 2012
10d0ca126df8	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8652 f3b2605a-c512-4ea7…	Aug 14 2012
dd51b1a0c86e	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8651 f3b2605a-c512-4ea7…	Aug 14 2012
ee321aabc64c	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8650 f3b2605a-c512-4ea7…	Aug 14 2012
1512b14f9809	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8649 f3b2605a-c512-4ea7…	Aug 14 2012
7365c2cfe623	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8648 f3b2605a-c512-4ea7…	Aug 14 2012
f2bade874d39	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8647 f3b2605a-c512-4ea7…	Aug 14 2012
e19e06952fcc	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8646 f3b2605a-c512-4ea7…	Aug 14 2012
15a86b4bcdbf	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8645 f3b2605a-c512-4ea7…	Aug 14 2012
533db036493e	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8644 f3b2605a-c512-4ea7…	Aug 14 2012
1b8aa27fe555	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8643 f3b2605a-c512-4ea7…	Aug 14 2012
14e3a6e2c9b4	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8642 f3b2605a-c512-4ea7…	Aug 14 2012
77c7d4c7113e	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8641 f3b2605a-c512-4ea7…	Aug 14 2012
01830d476bc0	Axel Kohlmeyer	Merge branch 'master' into lammps-icms	Aug 14 2012
5a306adbf4dd	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8639 f3b2605a-c512-4ea7…	Aug 14 2012
5a74d4f88be2	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8637 f3b2605a-c512-4ea7…	Aug 14 2012
a2f01ca5763e	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8636 f3b2605a-c512-4ea7…	Aug 14 2012
e69d5dacc92c	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8634 f3b2605a-c512-4ea7…	Aug 14 2012
9bb3b04ec4d1	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8633 f3b2605a-c512-4ea7…	Aug 14 2012
bd34e152dfa6	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8632 f3b2605a-c512-4ea7…	Aug 14 2012
8df0f9c2e6e5	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8631 f3b2605a-c512-4ea7…	Aug 14 2012
6f4f134d4db2	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8630 f3b2605a-c512-4ea7…	Aug 14 2012
c98a5d41496a	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8629 f3b2605a-c512-4ea7…	Aug 13 2012
6618a2a19d6f	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8628 f3b2605a-c512-4ea7…	Aug 13 2012
21e03d8e5c06	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8627 f3b2605a-c512-4ea7…	Aug 13 2012
6304a8c9bf8a	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8626 f3b2605a-c512-4ea7…	Aug 13 2012
9b2440a0abe7	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8625 f3b2605a-c512-4ea7…	Aug 13 2012

Changes (275)
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Very Large Commit

This commit is very large. Load each file individually.

		Path
V		{couple → examples/COUPLE}/README
D		couple/fortran
D		couple/fortran/README
V		{couple → examples/COUPLE}/fortran/libfwrapper.c
V	(dir)	{couple/lammps_quest/ → examples/COUPLE/lammps_quest}
V		{couple → examples/COUPLE}/lammps_quest/Makefile.g++
V		{couple → examples/COUPLE}/lammps_quest/README
V		{couple → examples/COUPLE}/lammps_quest/in.lammps
V		{couple → examples/COUPLE}/lammps_quest/lmppath.h
V		{couple → examples/COUPLE}/lammps_quest/lmpqst.cpp
V		{couple → examples/COUPLE}/lammps_quest/log.lammps.1
V		{couple → examples/COUPLE}/lammps_quest/log.lammps.4
V		{couple → examples/COUPLE}/lammps_quest/qstexe.h
V		{couple → examples/COUPLE}/lammps_quest/si_111.in
D		couple/lammps_spparks
V		{couple → examples/COUPLE}/lammps_spparks/Makefile.g++
V		{couple → examples/COUPLE}/lammps_spparks/README
D		couple/lammps_spparks/image.lammps.1.png
D		couple/lammps_spparks/image.lammps.10.png
D		couple/lammps_spparks/image.lammps.20.png
D		couple/lammps_spparks/image.spparks.1.png
D		couple/lammps_spparks/image.spparks.10.png
D		couple/lammps_spparks/image.spparks.20.png
V		{couple → examples/COUPLE}/lammps_spparks/in.spparks
V		{couple → examples/COUPLE}/lammps_spparks/lmppath.h
V		{couple → examples/COUPLE}/lammps_spparks/lmpspk.cpp
V		{couple → examples/COUPLE}/lammps_spparks/log.lammps.1
V		{couple → examples/COUPLE}/lammps_spparks/log.lammps.4
V		{couple → examples/COUPLE}/lammps_spparks/log.spparks.1
V		{couple → examples/COUPLE}/lammps_spparks/log.spparks.4
V		{couple → examples/COUPLE}/lammps_spparks/spkpath.h
V	(dir)	{couple/library/ → examples/COUPLE/library}
V		{couple → examples/COUPLE}/library/Makefile.g++
V		{couple → examples/COUPLE}/library/README
V		{couple → examples/COUPLE}/library/error.cpp
V		{couple → examples/COUPLE}/library/error.h
V		{couple → examples/COUPLE}/library/files.cpp
V		{couple → examples/COUPLE}/library/files.h
V		{couple → examples/COUPLE}/library/irregular.cpp
V		{couple → examples/COUPLE}/library/irregular.h
V		{couple → examples/COUPLE}/library/lammps_data_write.cpp
V		{couple → examples/COUPLE}/library/lammps_data_write.h
V		{couple → examples/COUPLE}/library/many2many.cpp
V		{couple → examples/COUPLE}/library/many2many.h
V		{couple → examples/COUPLE}/library/many2one.cpp
V		{couple → examples/COUPLE}/library/many2one.h
V		{couple → examples/COUPLE}/library/memory.cpp
V		{couple → examples/COUPLE}/library/memory.h
V		{couple → examples/COUPLE}/library/one2many.cpp
V		{couple → examples/COUPLE}/library/one2many.h
V		{couple → examples/COUPLE}/library/send2one.cpp
V		{couple → examples/COUPLE}/library/send2one.h
V		{couple → examples/COUPLE}/simple/README
V		{couple → examples/COUPLE}/simple/in.lj
V		{couple → examples/COUPLE}/simple/log.simple.c++.1
V		{couple → examples/COUPLE}/simple/log.simple.c++.4
V		{couple → examples/COUPLE}/simple/simple.c
V		{couple → examples/COUPLE}/simple/simple.cpp
V		{couple → examples/COUPLE}/simple/simple.f90
M		doc/Section_commands.html
M		doc/Section_commands.txt
M		doc/Section_howto.html
M		doc/Section_howto.txt
M		doc/Section_python.html
M		doc/Section_python.txt
M		doc/Section_start.html
M		doc/Section_start.txt
A		doc/box.html
A		doc/box.txt
M		doc/change_box.html
M		doc/change_box.txt
M		doc/compute.html
M		doc/compute.txt
A		doc/compute_contact_atom.html
A		doc/compute_contact_atom.txt
M		doc/compute_coord_atom.html
M		doc/compute_coord_atom.txt
M		doc/compute_property_local.html
M		doc/compute_property_local.txt
M		doc/fix_box_relax.html
M		doc/fix_box_relax.txt
M		doc/fix_deform.html
M		doc/fix_deform.txt
M		doc/fix_gcmc.html
M		doc/fix_gcmc.txt
M		doc/fix_nh.html
M		doc/fix_nh.txt
M		doc/pair_kim.html
M		doc/pair_kim.txt
M		doc/units.html
M		doc/units.txt
A	(dir)	examples/COUPLE/
V		{examples/COUPLE ← couple}/README
A	(dir)	examples/COUPLE/fortran/
A		examples/COUPLE/fortran/README
V		{examples/COUPLE ← couple}/fortran/libfwrapper.c
A	(dir)	examples/COUPLE/fortran2/
A		examples/COUPLE/fortran2/LAMMPS-wrapper.cpp
A		examples/COUPLE/fortran2/LAMMPS-wrapper.h
A		examples/COUPLE/fortran2/LAMMPS.F90
A		examples/COUPLE/fortran2/README
A		examples/COUPLE/fortran2/in.simple
A		examples/COUPLE/fortran2/makefile
A		examples/COUPLE/fortran2/simple.f90
V	(dir)	{examples/COUPLE/lammps_quest/ ← couple/lammps_quest}
V		{examples/COUPLE ← couple}/lammps_quest/Makefile.g++
V		{examples/COUPLE ← couple}/lammps_quest/README
V		{examples/COUPLE ← couple}/lammps_quest/in.lammps
V		{examples/COUPLE ← couple}/lammps_quest/lmppath.h
V		{examples/COUPLE ← couple}/lammps_quest/lmpqst.cpp
V		{examples/COUPLE ← couple}/lammps_quest/log.lammps.1
V		{examples/COUPLE ← couple}/lammps_quest/log.lammps.4
V		{examples/COUPLE ← couple}/lammps_quest/qstexe.h
V		{examples/COUPLE ← couple}/lammps_quest/si_111.in
A	(dir)	examples/COUPLE/lammps_spparks/
V		{examples/COUPLE ← couple}/lammps_spparks/Makefile.g++
V		{examples/COUPLE ← couple}/lammps_spparks/README
A		examples/COUPLE/lammps_spparks/in.lammps
V		{examples/COUPLE ← couple}/lammps_spparks/in.spparks
V		{examples/COUPLE ← couple}/lammps_spparks/lmppath.h
V		{examples/COUPLE ← couple}/lammps_spparks/lmpspk.cpp
V		{examples/COUPLE ← couple}/lammps_spparks/log.lammps.1
V		{examples/COUPLE ← couple}/lammps_spparks/log.lammps.4
V		{examples/COUPLE ← couple}/lammps_spparks/log.spparks.1
V		{examples/COUPLE ← couple}/lammps_spparks/log.spparks.4
V		{examples/COUPLE ← couple}/lammps_spparks/spkpath.h
V	(dir)	{examples/COUPLE/library/ ← couple/library}
V		{examples/COUPLE ← couple}/library/Makefile.g++
V		{examples/COUPLE ← couple}/library/README
V		{examples/COUPLE ← couple}/library/error.cpp
V		{examples/COUPLE ← couple}/library/error.h
V		{examples/COUPLE ← couple}/library/files.cpp
V		{examples/COUPLE ← couple}/library/files.h
V		{examples/COUPLE ← couple}/library/irregular.cpp
V		{examples/COUPLE ← couple}/library/irregular.h
V		{examples/COUPLE ← couple}/library/lammps_data_write.cpp
V		{examples/COUPLE ← couple}/library/lammps_data_write.h
V		{examples/COUPLE ← couple}/library/many2many.cpp
V		{examples/COUPLE ← couple}/library/many2many.h
V		{examples/COUPLE ← couple}/library/many2one.cpp
V		{examples/COUPLE ← couple}/library/many2one.h
V		{examples/COUPLE ← couple}/library/memory.cpp
V		{examples/COUPLE ← couple}/library/memory.h
V		{examples/COUPLE ← couple}/library/one2many.cpp
V		{examples/COUPLE ← couple}/library/one2many.h
V		{examples/COUPLE ← couple}/library/send2one.cpp
V		{examples/COUPLE ← couple}/library/send2one.h
A	(dir)	examples/COUPLE/simple/
V		{examples/COUPLE ← couple}/simple/README
V		{examples/COUPLE ← couple}/simple/in.lj
V		{examples/COUPLE ← couple}/simple/log.simple.c++.1
V		{examples/COUPLE ← couple}/simple/log.simple.c++.4
V		{examples/COUPLE ← couple}/simple/simple.c
V		{examples/COUPLE ← couple}/simple/simple.cpp
V		{examples/COUPLE ← couple}/simple/simple.f90
M		examples/README
M		examples/kim/in.kim.lj
M		examples/kim/in.kim.lj.lmp
V		examples/kim/{log.kim.lj.12Jul12.mac_mpi.1 ← log.kim.lj.9Jan12.linux.1}
V		examples/kim/{log.kim.lj.12Jul12.mac_mpi.4 ← log.kim.lj.9Jan12.linux.4}
V		examples/kim/{log.kim.lj.9Jan12.linux.1 → log.kim.lj.12Jul12.mac_mpi.1}
V		examples/kim/{log.kim.lj.9Jan12.linux.4 → log.kim.lj.12Jul12.mac_mpi.4}
V		examples/kim/{log.kim.lj.lmp.12Jul12.mac_mpi.1 ← log.kim.lj.lmp.9Jan12.linux.1}
V		examples/kim/{log.kim.lj.lmp.12Jul12.mac_mpi.4 ← log.kim.lj.lmp.9Jan12.linux.4}
V		examples/kim/{log.kim.lj.lmp.9Jan12.linux.1 → log.kim.lj.lmp.12Jul12.mac_mpi.1}
V		examples/kim/{log.kim.lj.lmp.9Jan12.linux.4 → log.kim.lj.lmp.12Jul12.mac_mpi.4}
M		lib/atc/Makefile.g++
M		lib/atc/Makefile.icc
M		lib/atc/Makefile.serial
M		lib/awpmd/Makefile.openmpi
M		lib/colvars/Makefile.g++
M		lib/linalg/Makefile.gfortran
M		lib/meam/Makefile.g95
M		lib/meam/Makefile.gfortran
M		lib/meam/Makefile.ifort
M		lib/meam/Makefile.pgf90
M		lib/meam/Makefile.tbird
M		lib/poems/Makefile.g++
M		lib/poems/Makefile.icc
M		lib/poems/Makefile.storm
M		lib/reax/Makefile.g77
M		lib/reax/Makefile.g95
M		lib/reax/Makefile.gfortran
M		lib/reax/Makefile.ifort
M		lib/reax/Makefile.pgf90
M		lib/reax/Makefile.redsky
M		lib/reax/Makefile.tbird
M		python/README
M		python/examples/simple.py
A		python/install.py
M		python/lammps.py
D		python/setup.py
D		python/setup_serial.py
M		src/GRANULAR/pair_gran_hooke_history.cpp
M		src/KIM/pair_kim.cpp
M		src/KIM/pair_kim.h
M		src/KSPACE/fft3d_wrap.h
M		src/KSPACE/pppm.cpp
M		src/MAKE/Makefile.altix
M		src/MAKE/Makefile.bgl
M		src/MAKE/Makefile.cygwin
M		src/MAKE/Makefile.encanto
M		src/MAKE/Makefile.fink
M		src/MAKE/Makefile.g++
M		src/MAKE/Makefile.g++3
M		src/MAKE/Makefile.glory
M		src/MAKE/Makefile.jaguar
M		src/MAKE/Makefile.lam
M		src/MAKE/Makefile.linux
M		src/MAKE/Makefile.mac
M		src/MAKE/Makefile.mac_mpi
M		src/MAKE/Makefile.mingw
M		src/MAKE/Makefile.mkl
M		src/MAKE/Makefile.odin
M		src/MAKE/Makefile.openmpi
M		src/MAKE/Makefile.pgi
M		src/MAKE/Makefile.power5
M		src/MAKE/Makefile.qed
M		src/MAKE/Makefile.redsky
M		src/MAKE/Makefile.sdsc
M		src/MAKE/Makefile.seaborg
M		src/MAKE/Makefile.serial
M		src/MAKE/Makefile.serial_debug
M		src/MAKE/Makefile.sgi
M		src/MAKE/Makefile.solaris
M		src/MAKE/Makefile.spirit
M		src/MAKE/Makefile.storm
M		src/MAKE/Makefile.tacc
M		src/MAKE/Makefile.tbird
M		src/MAKE/Makefile.tesla
M		src/MAKE/Makefile.tunnison
M		src/MAKE/Makefile.xe6
M		src/MAKE/Makefile.xt3
M		src/MAKE/Makefile.xt5
M		src/MC/fix_gcmc.cpp
M		src/MC/fix_gcmc.h
M		src/Make.sh
M		src/Makefile
M		src/Makefile.lib
M		src/Makefile.list
A		src/Makefile.shlib
M		src/REPLICA/prd.cpp
M		src/REPLICA/prd.h
M		src/REPLICA/tad.h
M		src/STUBS/Makefile
M		src/USER-CUDA/cuda.cpp
M		src/USER-CUDA/neighbor_cuda.cpp
M		src/USER-CUDA/neighbor_cuda.h
M		src/USER-CUDA/pppm_cuda.cpp
M		src/USER-CUDA/verlet_cuda.cpp
M		src/USER-OMP/pair_lj_expand_omp.h
M		src/atom.cpp
P		src/compute_contact_atom.cpp Copied from src/compute_coord_atom.cpp
P		src/compute_contact_atom.h Copied from src/compute_coord_atom.h
P		src/compute_coord_atom.cpp Copied to src/compute_contact_atom.cpp
P		src/compute_coord_atom.h Copied to src/compute_contact_atom.h
M		src/compute_property_local.cpp
M		src/compute_property_local.h
M		src/domain.cpp
M		src/domain.h
M		src/finish.cpp
M		src/fix_deform.cpp
M		src/fix_deform.h
M		src/fix_nh.cpp
M		src/fix_nh.h
M		src/input.cpp
M		src/input.h
M		src/library.cpp
M		src/library.h
M		src/neigh_request.h
M		src/neighbor.cpp
M		src/neighbor.h
M		src/thermo.cpp
M		src/version.h
M		tools/restart2data.cpp