Updating from master to 19May17
2cf83d9fca6e
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Authored by Stan Moore <stamoor@sandia.gov> on May 25 2017, 19:21.

Description

Updating from master to 19May17

Details

Committed

Stan Moore <stamoor@sandia.gov>

May 25 2017, 19:21

Pushed

junge

Oct 19 2017, 09:53

Parents

rLAMMPSbceaa5761426: Merge branch 'master' into USER-DPD_kokkos as of patch 31Mar17
rLAMMPS2225fce94eee: patch 19May17

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Stan Moore <stamoor@sandia.gov> committed rLAMMPS2cf83d9fca6e: Updating from master to 19May17 (authored by Stan Moore <stamoor@sandia.gov>).May 25 2017, 19:21

Merged Changes

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

Commit	Author	Details	Committed
2225fce94eee	Steve Plimpton	patch 19May17	May 19 2017
941b7373192a	sjplimp/GitHub	Merge pull request #493 from akohlmey/doc-and-example-fixes	May 19 2017
654e09e999b8	Axel Kohlmeyer	correct input examples affected by the Pair::settings() bugfix	May 19 2017
8751850ecaa8	Axel Kohlmeyer	a few formatting fixes for pair style python	May 19 2017
0f8834891790	sjplimp/GitHub	Merge pull request #492 from lammps/pre-patch	May 18 2017
b28ecd44c25d	Steve Plimpton	update docs before patch release	May 18 2017
9db9fc9de3f8	sjplimp/GitHub	Merge pull request #491 from akohlmey/fix-bigint-thermo-in-variables-bug	May 18 2017
6ac9b7a1b070	sjplimp/GitHub	Merge pull request #482 from akohlmey/add-pair-python	May 18 2017
34dbf6b225ac	Axel Kohlmeyer	do not compute properties twice	May 18 2017
26d71b66e413	Axel Kohlmeyer	convert bigint values for bonds/angles/dihedrals/impropers to doubles when…	May 18 2017
65eacb6b9060	Richard Berger	Fix compilation warnings in fix_python	May 18 2017
cb3344a33715	sjplimp/GitHub	Merge pull request #489 from akohlmey/thread-safe-biasing	May 18 2017
5d38cbbce9c6	sjplimp/GitHub	Merge pull request #487 from akohlmey/pair_edip_multi_element	May 18 2017
30babd81570f	sjplimp/GitHub	Merge pull request #485 from akohlmey/pair_settings_cut_bugfix	May 18 2017
aa09f45b7e1e	sjplimp/GitHub	Merge pull request #484 from akohlmey/add-gao-weber-styles	May 18 2017
4b61cf6f52f3	sjplimp/GitHub	Merge pull request #483 from akohlmey/airebo-spline-bugfix-refactor	May 18 2017
683f3d9d2ac3	sjplimp/GitHub	Merge pull request #481 from akohlmey/collected-small-changes	May 18 2017
ce18524251fe	sjplimp/GitHub	Merge pull request #480 from akohlmey/pair_morse_smooth_linear_bugfix	May 18 2017
95dae9737b74	sjplimp/GitHub	Merge pull request #488 from lammps/neigh_occasional_bugfix	May 18 2017
4b1914aa1f29	Axel Kohlmeyer	update citations for multi-element edip potential	May 18 2017
bd11479a1688	Axel Kohlmeyer	lock the sphinx command to version 1.5.6, since version 1.6.x seems to break…	May 18 2017
0208fe9996be	Axel Kohlmeyer	update example outputs	May 18 2017
24654ad28f37	Axel Kohlmeyer	small formatting corrections to pair python style	May 18 2017
8d46aa605606	Axel Kohlmeyer	add readme file to discuss various python pair style usage examples	May 18 2017
09f3b687f7d7	Axel Kohlmeyer	new long-rance example with using hybrid/overlay and table only for lj part	May 18 2017
436d3fd76188	Axel Kohlmeyer	make hybrid example use half the atoms with python, half with lj/cut	May 18 2017
9833f38499a0	Axel Kohlmeyer	change coulomb example to use cutoff coulomb	May 18 2017
9725708b90b9	Axel Kohlmeyer	update pair style python docs	May 18 2017
67962b15fc07	Axel Kohlmeyer	a bunch refactoring changes in the python pair style and the examples	May 18 2017
1d48f287f00a	Axel Kohlmeyer	add partial documentation for pair style python	May 18 2017
43efe9e417ee	Axel Kohlmeyer	adding Pair::single() support to python pair style and examples	May 17 2017
278b9f7fba47	Axel Kohlmeyer	move pair gw and gw/zbl to USER-MISC package	May 17 2017
085f3afdfb08	Axel Kohlmeyer	fix typo in docs	May 17 2017
45becfb235d7	Axel Kohlmeyer	correct author attributions	May 17 2017
a34c935e207b	Axel Kohlmeyer	update log files in python pair style example	May 17 2017
13e16dc3f14a	Axel Kohlmeyer	update log files for pair style python examples	May 17 2017
96f0a82aa5ad	Axel Kohlmeyer	simplify class names in pair style python examples. add SPC/E water example	May 17 2017
7caf6cf459d3	Richard Berger	Change how a Python pair style is loaded	May 17 2017
8936b99e9f89	Axel Kohlmeyer	add contributed SiC.edip potential file	May 17 2017
d2810f9f8372	Axel Kohlmeyer	port thread-safe temperature biasing from LAMMPS-ICMS	May 17 2017
597f95fb1b29	Axel Kohlmeyer	fix duplicate reference	May 16 2017
7f9a331c7355	Steve Plimpton	bugfix for 2 recenty reported neighbor issues, also a ReaxFF fix species issue	May 16 2017
35e92733e9da	Axel Kohlmeyer	import multi-element compatible pair style edip as edip/multi	May 16 2017
c11e87618bc8	Axel Kohlmeyer	implement second bugfix suggestion from @CF17 on issue #59	May 16 2017
ca87e571294f	Axel Kohlmeyer	improved version of AIREBO splines based on a suggestion by markus hoehnerbach	May 16 2017
66084ad1f41a	Axel Kohlmeyer	fix typo in rerun docs. closes #486	May 16 2017
d807ba1974d5	Axel Kohlmeyer	whitespace cleanup	May 16 2017
51fc386e7224	Axel Kohlmeyer	correct the inner loop range for resetting cutoffs when redefining a pair style	May 16 2017
a6f0d700f101	Richard Berger	Merge branch 'add-pair-python' of github.com:akohlmey/lammps into add-pair…	May 16 2017
14f3deed6b83	Richard Berger	Minor coefficient lookup improvement	May 16 2017

Changes (927)
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Very Large Commit

This commit is very large. Load each file individually.

		Path
M		doc/Makefile
M		doc/src/Eqs/pair_meam_spline.jpg
M		doc/src/Eqs/pair_meam_spline.tex
A		doc/src/Eqs/pair_meam_spline_multicomponent.jpg
A		doc/src/Eqs/pair_meam_spline_multicomponent.tex
M		doc/src/Manual.txt
M		doc/src/Section_commands.txt
M		doc/src/Section_errors.txt
M		doc/src/Section_howto.txt
M		doc/src/Section_intro.txt
M		doc/src/Section_packages.txt
M		doc/src/Section_python.txt
M		doc/src/Section_start.txt
M		doc/src/Section_tools.txt
M		doc/src/accelerate_intel.txt
M		doc/src/accelerate_kokkos.txt
M		doc/src/angle_sdk.txt
M		doc/src/bond_oxdna.txt
M		doc/src/bonds.txt
M		doc/src/commands.txt
M		doc/src/compute_sna_atom.txt
M		doc/src/dihedral_charmm.txt
M		doc/src/dihedral_spherical.txt
M		doc/src/dump.txt
D		doc/src/dump_custom_vtk.txt
M		doc/src/dump_h5md.txt
D		doc/src/dump_nc.txt
A		doc/src/dump_netcdf.txt
A		doc/src/dump_vtk.txt
M		doc/src/fix_adapt.txt
M		doc/src/fix_box_relax.txt
M		doc/src/fix_cmap.txt
M		doc/src/fix_gcmc.txt
M		doc/src/fix_gle.txt
A		doc/src/fix_python.txt
M		doc/src/fix_qeq.txt
M		doc/src/fix_qeq_reax.txt
M		doc/src/fix_reax_bonds.txt
M		doc/src/fix_reaxc_species.txt
M		doc/src/fixes.txt
M		doc/src/improper_cossq.txt
M		doc/src/improper_ring.txt
M		doc/src/kspace_modify.txt
M		doc/src/lammps.book
M		doc/src/pair_buck.txt
M		doc/src/pair_charmm.txt
M		doc/src/pair_edip.txt
M		doc/src/pair_gauss.txt
A		doc/src/pair_gw.txt
M		doc/src/pair_hybrid.txt
M		doc/src/pair_meam_spline.txt
M		doc/src/pair_modify.txt
A		doc/src/pair_python.txt
M		doc/src/pair_reax.txt
D		doc/src/pair_reax_c.txt
A		doc/src/pair_reaxc.txt
M		doc/src/pair_sdk.txt
M		doc/src/pair_srp.txt
M		doc/src/pair_tersoff.txt
M		doc/src/pair_yukawa_colloid.txt
M		doc/src/pairs.txt
M		doc/src/python.txt
M		doc/src/rerun.txt
M		doc/src/tutorial_pylammps.txt
M		doc/src/velocity.txt
M		examples/ASPHERE/poly/in.poly
M		examples/ASPHERE/poly/in.poly.mp
D		examples/USER/cg-cmm
D		examples/USER/cg-cmm/README
V	(dir)	examples/USER/{cg-cmm/peg-verlet/ → cgsdk/peg-verlet}
V		examples/USER/{cg-cmm → cgsdk}/peg-verlet/data.pegc12e8.gz
V		examples/USER/{cg-cmm → cgsdk}/peg-verlet/in.pegc12e8
V		examples/USER/{cg-cmm → cgsdk}/peg-verlet/in.pegc12e8-angle
V		examples/USER/{cg-cmm → cgsdk}/peg-verlet/log.pegc12e8
V		examples/USER/{cg-cmm → cgsdk}/peg-verlet/log.pegc12e8-angle
V	(dir)	examples/USER/{cg-cmm/sds-monolayer/ → cgsdk/sds-monolayer}
V		examples/USER/{cg-cmm → cgsdk}/sds-monolayer/data.sds.gz
V		examples/USER/{cg-cmm → cgsdk}/sds-monolayer/in.sds-hybrid
V		examples/USER/{cg-cmm → cgsdk}/sds-monolayer/in.sds-regular
V		examples/USER/{cg-cmm → cgsdk}/sds-monolayer/log.sds-hybrid
V		examples/USER/{cg-cmm → cgsdk}/sds-monolayer/log.sds-regular
A	(dir)	examples/USER/cgsdk/
A		examples/USER/cgsdk/README
V	(dir)	examples/USER/{cgsdk/peg-verlet/ ← cg-cmm/peg-verlet}
V		examples/USER/{cgsdk ← cg-cmm}/peg-verlet/data.pegc12e8.gz
V		examples/USER/{cgsdk ← cg-cmm}/peg-verlet/in.pegc12e8
V		examples/USER/{cgsdk ← cg-cmm}/peg-verlet/in.pegc12e8-angle
V		examples/USER/{cgsdk ← cg-cmm}/peg-verlet/log.pegc12e8
V		examples/USER/{cgsdk ← cg-cmm}/peg-verlet/log.pegc12e8-angle
V	(dir)	examples/USER/{cgsdk/sds-monolayer/ ← cg-cmm/sds-monolayer}
V		examples/USER/{cgsdk ← cg-cmm}/sds-monolayer/data.sds.gz
V		examples/USER/{cgsdk ← cg-cmm}/sds-monolayer/in.sds-hybrid
V		examples/USER/{cgsdk ← cg-cmm}/sds-monolayer/in.sds-regular
V		examples/USER/{cgsdk ← cg-cmm}/sds-monolayer/log.sds-hybrid
V		examples/USER/{cgsdk ← cg-cmm}/sds-monolayer/log.sds-regular
V	(dir)	examples/USER/{flow_gauss/ → misc/flow_gauss}
V		examples/USER/{ → misc}/flow_gauss/README
V		examples/USER/{ → misc}/flow_gauss/in.GD
A	(dir)	examples/USER/misc/edip/
A		examples/USER/misc/edip/Si.edip
A		examples/USER/misc/edip/SiC.edip
A		examples/USER/misc/edip/data.SiC
A		examples/USER/misc/edip/in.edip-Si
A		examples/USER/misc/edip/in.edip-Si-multi
A		examples/USER/misc/edip/in.edip-SiC
A		examples/USER/misc/edip/log.4May2017.g++.edip-Si-multi.1
A		examples/USER/misc/edip/log.4May2017.g++.edip-Si-multi.4
A		examples/USER/misc/edip/log.4May2017.g++.edip-Si.1
A		examples/USER/misc/edip/log.4May2017.g++.edip-Si.4
A		examples/USER/misc/edip/log.4May2017.g++.edip-SiC.1
A		examples/USER/misc/edip/log.4May2017.g++.edip-SiC.4
V	(dir)	examples/USER/misc/{filter-corotate/ → filter_corotate}
V		examples/USER/misc/{filter-corotate → filter_corotate}/data.bpti
V		examples/USER/misc/{filter-corotate → filter_corotate}/data.peptide
V		examples/USER/misc/{filter-corotate → filter_corotate}/in.bpti
V		examples/USER/misc/{filter-corotate → filter_corotate}/in.peptide
V		examples/USER/misc/{filter-corotate → filter_corotate}/log.10Mar2017.bpti.g++.1
V		examples/USER/misc/{filter-corotate → filter_corotate}/log.10Mar2017.bpti.g++.4
V		examples/USER/misc/{filter-corotate → filter_corotate}/log.10Mar2017.peptide.g++.1
V		examples/USER/misc/{filter-corotate → filter_corotate}/log.10Mar2017.peptide.g++.4
V	(dir)	examples/USER/misc/{filter_corotate/ ← filter-corotate}
V		examples/USER/misc/{filter_corotate ← filter-corotate}/data.bpti
V		examples/USER/misc/{filter_corotate ← filter-corotate}/data.peptide
V		examples/USER/misc/{filter_corotate ← filter-corotate}/in.bpti
V		examples/USER/misc/{filter_corotate ← filter-corotate}/in.peptide
V		examples/USER/misc/{filter_corotate ← filter-corotate}/log.10Mar2017.bpti.g++.1
V		examples/USER/misc/{filter_corotate ← filter-corotate}/log.10Mar2017.bpti.g++.4
V		examples/USER/misc/{filter_corotate ← filter-corotate}/log.10Mar2017.peptide.g++.1
V		examples/USER/misc/{filter_corotate ← filter-corotate}/log.10Mar2017.peptide.g++.4
V	(dir)	examples/USER/{misc/flow_gauss/ ← flow_gauss}
V		examples/USER/{misc ← }/flow_gauss/README
V		examples/USER/{misc ← }/flow_gauss/in.GD
V	(dir)	examples/USER/misc/{gauss-diel/ → gauss_diel}
V		examples/USER/misc/{gauss-diel → gauss_diel}/data.gauss-diel
V		examples/USER/misc/{gauss-diel → gauss_diel}/in.gauss-diel
V		examples/USER/misc/{gauss-diel → gauss_diel}/in.gauss-diel-cg
V		examples/USER/misc/{gauss-diel → gauss_diel}/in.gauss-diel-split
V		examples/USER/misc/{gauss-diel → gauss_diel}/log.gauss-diel
V		examples/USER/misc/{gauss-diel → gauss_diel}/log.gauss-diel-cg
V		examples/USER/misc/{gauss-diel → gauss_diel}/log.gauss-diel-split
V	(dir)	examples/USER/misc/{gauss_diel/ ← gauss-diel}
V		examples/USER/misc/{gauss_diel ← gauss-diel}/data.gauss-diel
V		examples/USER/misc/{gauss_diel ← gauss-diel}/in.gauss-diel
V		examples/USER/misc/{gauss_diel ← gauss-diel}/in.gauss-diel-cg
V		examples/USER/misc/{gauss_diel ← gauss-diel}/in.gauss-diel-split
V		examples/USER/misc/{gauss_diel ← gauss-diel}/log.gauss-diel
V		examples/USER/misc/{gauss_diel ← gauss-diel}/log.gauss-diel-cg
V		examples/USER/misc/{gauss_diel ← gauss-diel}/log.gauss-diel-split
V	(dir)	examples/USER/misc/{i-pi/ → ipi}
V		examples/USER/misc/{i-pi → ipi}/C.opt.tersoff
V		examples/USER/misc/{i-pi → ipi}/README
V		examples/USER/misc/{i-pi → ipi}/data.graphene
V		examples/USER/misc/{i-pi → ipi}/i-pi_input.xml
V		examples/USER/misc/{i-pi → ipi}/i-pi_positions.xyz
V		examples/USER/misc/{i-pi → ipi}/in.graphene
V	(dir)	examples/USER/misc/{ipi/ ← i-pi}
V		examples/USER/misc/{ipi ← i-pi}/C.opt.tersoff
V		examples/USER/misc/{ipi ← i-pi}/README
V		examples/USER/misc/{ipi ← i-pi}/data.graphene
V		examples/USER/misc/{ipi ← i-pi}/i-pi_input.xml
V		examples/USER/misc/{ipi ← i-pi}/i-pi_positions.xyz
V		examples/USER/misc/{ipi ← i-pi}/in.graphene
V	(dir)	examples/USER/misc/{kolmogorov-crespi/ → kolmogorov_crespi}
V		examples/USER/misc/{kolmogorov-crespi → kolmogorov_crespi}/data.bilayer-graphene
V		examples/USER/misc/{kolmogorov-crespi → kolmogorov_crespi}/data.graphene-adsorbant
V		examples/USER/misc/{kolmogorov-crespi → kolmogorov_crespi}/in.atom-diffusion
V		examples/USER/misc/{kolmogorov-crespi → kolmogorov_crespi}/in.bilayer-graphene
V		examples/USER/misc/{kolmogorov-crespi → kolmogorov_crespi}/log.atom-diffusion
V		examples/USER/misc/{kolmogorov-crespi → kolmogorov_crespi}/log.bilayer-graphene
V	(dir)	examples/USER/misc/{kolmogorov_crespi/ ← kolmogorov-crespi}
V		examples/USER/misc/{kolmogorov_crespi ← kolmogorov-crespi}/data.bilayer-graphene
V		examples/USER/misc/{kolmogorov_crespi ← kolmogorov-crespi}/data.graphene-adsorbant
V		examples/USER/misc/{kolmogorov_crespi ← kolmogorov-crespi}/in.atom-diffusion
V		examples/USER/misc/{kolmogorov_crespi ← kolmogorov-crespi}/in.bilayer-graphene
V		examples/USER/misc/{kolmogorov_crespi ← kolmogorov-crespi}/log.atom-diffusion
V		examples/USER/misc/{kolmogorov_crespi ← kolmogorov-crespi}/log.bilayer-graphene
A	(dir)	examples/USER/misc/meam_spline/
A		examples/USER/misc/meam_spline/Si_1.meam.spline
A		examples/USER/misc/meam_spline/TiO.meam.spline
A		examples/USER/misc/meam_spline/in.meam-spline.Si
A		examples/USER/misc/meam_spline/in.meam-spline.TiO2
A		examples/USER/misc/meam_spline/log.4May2017.meam-spline.Si.g++.1
A		examples/USER/misc/meam_spline/log.4May2017.meam-spline.Si.g++.4
A		examples/USER/misc/meam_spline/log.4May2017.meam-spline.TiO2.g++.1
A		examples/USER/misc/meam_spline/log.4May2017.meam-spline.TiO2.g++.4
A	(dir)	examples/USER/vtk/
A		examples/USER/vtk/.gitignore
A		examples/USER/vtk/in.vtk
A		examples/USER/vtk/in.vtp
M		examples/cmap/in.cmap
A		examples/cmap/log.11Apr17.cmap.g++.1
A		examples/cmap/log.11Apr17.cmap.g++.4
D		examples/cmap/log.5Oct16.cmap.g++.1
D		examples/cmap/log.5Oct16.cmap.g++.4
A		examples/mscg/log.31Mar17.g++.1
A		examples/python/README.pair_python
A		examples/python/data.spce
M		examples/python/funcs.py
A		examples/python/in.fix_python
A		examples/python/in.pair_python_coulomb
A		examples/python/in.pair_python_hybrid
A		examples/python/in.pair_python_long
A		examples/python/in.pair_python_melt
A		examples/python/in.pair_python_spce
A		examples/python/in.pair_python_table
M		examples/python/in.python
A		examples/python/log.4May17.pair_python_coulomb.1
A		examples/python/log.4May17.pair_python_coulomb.g++.1
A		examples/python/log.4May17.pair_python_coulomb.g++.4
A		examples/python/log.4May17.pair_python_hybrid.g++.1
A		examples/python/log.4May17.pair_python_hybrid.g++.4
A		examples/python/log.4May17.pair_python_long.g++.1
A		examples/python/log.4May17.pair_python_long.g++.4
A		examples/python/log.4May17.pair_python_melt.g++.1
A		examples/python/log.4May17.pair_python_melt.g++.4
A		examples/python/log.4May17.pair_python_spce.g++.1
A		examples/python/log.4May17.pair_python_spce.g++.4
A		examples/python/log.4May17.pair_python_table.g++.1
A		examples/python/log.4May17.pair_python_table.g++.4
A		examples/python/py_pot.py
A		lib/Install.py
M		lib/README
A		lib/atc/Install.py
M		lib/atc/README
A		lib/awpmd/Install.py
M		lib/awpmd/README
A		lib/colvars/Install.py
M		lib/colvars/README
A		lib/gpu/Install.py
M		lib/gpu/Nvidia.makefile
M		lib/gpu/Opencl.makefile
M		lib/gpu/README
D		lib/gpu/lal_cg_cmm.cpp
D		lib/gpu/lal_cg_cmm.cu
D		lib/gpu/lal_cg_cmm.h
D		lib/gpu/lal_cg_cmm_ext.cpp
D		lib/gpu/lal_cg_cmm_long.cpp
D		lib/gpu/lal_cg_cmm_long.cu
D		lib/gpu/lal_cg_cmm_long.h
D		lib/gpu/lal_cg_cmm_long_ext.cpp
A		lib/gpu/lal_lj_sdk.cpp
A		lib/gpu/lal_lj_sdk.cu
A		lib/gpu/lal_lj_sdk.h
A		lib/gpu/lal_lj_sdk_ext.cpp
A		lib/gpu/lal_lj_sdk_long.cpp
A		lib/gpu/lal_lj_sdk_long.cu
A		lib/gpu/lal_lj_sdk_long.h
A		lib/gpu/lal_lj_sdk_long_ext.cpp
A		lib/h5md/Install.py
D		lib/h5md/Makefile
A		lib/h5md/Makefile.h5cc
M		lib/h5md/README
M		lib/kokkos/CHANGELOG.md
M		lib/kokkos/CMakeLists.txt
M		lib/kokkos/Makefile.kokkos
M		lib/kokkos/Makefile.targets
M		lib/kokkos/README
M		lib/kokkos/algorithms/cmake/Dependencies.cmake
M		lib/kokkos/algorithms/src/Kokkos_Random.hpp
M		lib/kokkos/algorithms/src/Kokkos_Sort.hpp
M		lib/kokkos/algorithms/unit_tests/TestSort.hpp
M		lib/kokkos/bin/nvcc_wrapper
D		lib/kokkos/cmake/deps/QTHREAD.cmake
A		lib/kokkos/cmake/deps/QTHREADS.cmake
D		lib/kokkos/cmake/tpls/FindTPLQTHREAD.cmake
A		lib/kokkos/cmake/tpls/FindTPLQTHREADS.cmake
M		lib/kokkos/config/kokkos_dev/config-core-all.sh
M		lib/kokkos/config/master_history.txt
M		lib/kokkos/config/test_all_sandia
M		lib/kokkos/containers/src/Kokkos_DynamicView.hpp
M		lib/kokkos/containers/src/Kokkos_UnorderedMap.hpp
M		lib/kokkos/containers/unit_tests/CMakeLists.txt
M		lib/kokkos/containers/unit_tests/TestDynamicView.hpp
M		lib/kokkos/core/cmake/Dependencies.cmake
M		lib/kokkos/core/cmake/KokkosCore_config.h.in
M		lib/kokkos/core/perf_test/Makefile
M		lib/kokkos/core/perf_test/PerfTestCuda.cpp
M		lib/kokkos/core/perf_test/PerfTestDriver.hpp
M		lib/kokkos/core/perf_test/PerfTestHost.cpp
A		lib/kokkos/core/perf_test/PerfTestMDRange.hpp
M		lib/kokkos/core/src/CMakeLists.txt
A		lib/kokkos/core/src/Cuda/KokkosExp_Cuda_IterateTile.hpp
M		lib/kokkos/core/src/Cuda/Kokkos_CudaExec.hpp
M		lib/kokkos/core/src/Cuda/Kokkos_CudaSpace.cpp
M		lib/kokkos/core/src/Cuda/Kokkos_Cuda_Impl.cpp
M		lib/kokkos/core/src/Cuda/Kokkos_Cuda_Parallel.hpp
M		lib/kokkos/core/src/Cuda/Kokkos_Cuda_ReduceScan.hpp
M		lib/kokkos/core/src/Cuda/Kokkos_Cuda_Task.cpp
M		lib/kokkos/core/src/Cuda/Kokkos_Cuda_Task.hpp
M		lib/kokkos/core/src/KokkosExp_MDRangePolicy.hpp
M		lib/kokkos/core/src/Kokkos_Array.hpp
M		lib/kokkos/core/src/Kokkos_Concepts.hpp
M		lib/kokkos/core/src/Kokkos_Core.hpp
M		lib/kokkos/core/src/Kokkos_Core_fwd.hpp
M		lib/kokkos/core/src/Kokkos_Cuda.hpp
M		lib/kokkos/core/src/Kokkos_HBWSpace.hpp
M		lib/kokkos/core/src/Kokkos_HostSpace.hpp
M		lib/kokkos/core/src/Kokkos_Macros.hpp
M		lib/kokkos/core/src/Kokkos_MemoryPool.hpp
M		lib/kokkos/core/src/Kokkos_OpenMP.hpp
M		lib/kokkos/core/src/Kokkos_Pair.hpp
M		lib/kokkos/core/src/Kokkos_Parallel.hpp
M		lib/kokkos/core/src/Kokkos_Parallel_Reduce.hpp
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M		lib/kokkos/core/src/Kokkos_TaskScheduler.hpp
M		lib/kokkos/core/src/Kokkos_Threads.hpp
M		lib/kokkos/core/src/Makefile
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M		lib/kokkos/core/src/OpenMP/Kokkos_OpenMP_Task.hpp
M		lib/kokkos/core/src/OpenMP/Kokkos_OpenMPexec.cpp
M		lib/kokkos/core/src/OpenMP/Kokkos_OpenMPexec.hpp
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D		lib/kokkos/core/src/Qthread/Kokkos_QthreadExec.hpp
D		lib/kokkos/core/src/Qthread/Kokkos_Qthread_Parallel.hpp
D		lib/kokkos/core/src/Qthread/Kokkos_Qthread_TaskPolicy.cpp
D		lib/kokkos/core/src/Qthread/Kokkos_Qthread_TaskPolicy.hpp
D		lib/kokkos/core/src/Qthread/README
A	(dir)	lib/kokkos/core/src/Qthreads/
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A		lib/kokkos/core/src/Qthreads/Kokkos_QthreadsExec.hpp
A		lib/kokkos/core/src/Qthreads/Kokkos_Qthreads_Parallel.hpp
A		lib/kokkos/core/src/Qthreads/Kokkos_Qthreads_Task.cpp
A		lib/kokkos/core/src/Qthreads/Kokkos_Qthreads_Task.hpp
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A		lib/kokkos/core/src/Qthreads/Kokkos_Qthreads_TaskPolicy.hpp.old
A		lib/kokkos/core/src/Qthreads/Kokkos_Qthreads_TaskQueue.hpp
A		lib/kokkos/core/src/Qthreads/Kokkos_Qthreads_TaskQueue_impl.hpp
A		lib/kokkos/core/src/Qthreads/README
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M		lib/kokkos/core/src/Threads/Kokkos_ThreadsTeam.hpp
A		lib/kokkos/core/src/impl/KokkosExp_Host_IterateTile.hpp
M		lib/kokkos/core/src/impl/Kokkos_BitOps.hpp
M		lib/kokkos/core/src/impl/Kokkos_Core.cpp
A		lib/kokkos/core/src/impl/Kokkos_FunctorAnalysis.hpp
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M		lib/kokkos/core/src/impl/Kokkos_HostSpace.cpp
A		lib/kokkos/core/src/impl/Kokkos_HostThreadTeam.cpp
A		lib/kokkos/core/src/impl/Kokkos_HostThreadTeam.hpp
M		lib/kokkos/core/src/impl/Kokkos_Memory_Fence.hpp
M		lib/kokkos/core/src/impl/Kokkos_OldMacros.hpp
M		lib/kokkos/core/src/impl/Kokkos_Profiling_Interface.cpp
M		lib/kokkos/core/src/impl/Kokkos_Profiling_Interface.hpp
A		lib/kokkos/core/src/impl/Kokkos_Reducer.hpp
M		lib/kokkos/core/src/impl/Kokkos_Serial.cpp
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M		lib/kokkos/core/src/impl/Kokkos_Serial_Task.hpp
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D		lib/kokkos/core/src/impl/Kokkos_Synchronic_n3998.hpp
M		lib/kokkos/core/src/impl/Kokkos_TaskQueue.hpp
M		lib/kokkos/core/src/impl/Kokkos_TaskQueue_impl.hpp
M		lib/kokkos/core/src/impl/Kokkos_Utilities.hpp
M		lib/kokkos/core/src/impl/Kokkos_spinwait.cpp
M		lib/kokkos/core/src/impl/Kokkos_spinwait.hpp
M		lib/kokkos/core/unit_test/CMakeLists.txt
M		lib/kokkos/core/unit_test/Makefile
M		lib/kokkos/core/unit_test/TestAggregate.hpp
M		lib/kokkos/core/unit_test/TestAtomic.hpp
M		lib/kokkos/core/unit_test/TestAtomicOperations.hpp
M		lib/kokkos/core/unit_test/TestAtomicViews.hpp
M		lib/kokkos/core/unit_test/TestCXX11.hpp
M		lib/kokkos/core/unit_test/TestCXX11Deduction.hpp
M		lib/kokkos/core/unit_test/TestCompilerMacros.hpp
M		lib/kokkos/core/unit_test/TestDefaultDeviceType.cpp
M		lib/kokkos/core/unit_test/TestDefaultDeviceTypeInit.hpp
M		lib/kokkos/core/unit_test/TestDefaultDeviceType_a.cpp
M		lib/kokkos/core/unit_test/TestDefaultDeviceType_b.cpp
M		lib/kokkos/core/unit_test/TestDefaultDeviceType_c.cpp
M		lib/kokkos/core/unit_test/TestDefaultDeviceType_d.cpp
M		lib/kokkos/core/unit_test/TestHWLOC.cpp
M		lib/kokkos/core/unit_test/TestMDRange.hpp
M		lib/kokkos/core/unit_test/TestMemoryPool.hpp
M		lib/kokkos/core/unit_test/TestPolicyConstruction.hpp
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M		lib/kokkos/core/unit_test/TestRange.hpp
M		lib/kokkos/core/unit_test/TestReduce.hpp
M		lib/kokkos/core/unit_test/TestScan.hpp
M		lib/kokkos/core/unit_test/TestSharedAlloc.hpp
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M		lib/kokkos/core/unit_test/TestTaskScheduler.hpp
M		lib/kokkos/core/unit_test/TestTeam.hpp
M		lib/kokkos/core/unit_test/TestTeamVector.hpp
M		lib/kokkos/core/unit_test/TestTemplateMetaFunctions.hpp
M		lib/kokkos/core/unit_test/TestTile.hpp
M		lib/kokkos/core/unit_test/TestUtilities.hpp
M		lib/kokkos/core/unit_test/TestViewAPI.hpp
M		lib/kokkos/core/unit_test/TestViewMapping.hpp
M		lib/kokkos/core/unit_test/TestViewOfClass.hpp
M		lib/kokkos/core/unit_test/TestViewSpaceAssign.hpp
M		lib/kokkos/core/unit_test/TestViewSubview.hpp
M		lib/kokkos/core/unit_test/UnitTestMain.cpp
M		lib/kokkos/core/unit_test/cuda/TestCuda.hpp
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M		lib/kokkos/core/unit_test/cuda/TestCuda_Other.cpp
M		lib/kokkos/core/unit_test/cuda/TestCuda_Reductions_a.cpp
M		lib/kokkos/core/unit_test/cuda/TestCuda_Reductions_b.cpp
M		lib/kokkos/core/unit_test/cuda/TestCuda_Spaces.cpp
M		lib/kokkos/core/unit_test/cuda/TestCuda_SubView_a.cpp
M		lib/kokkos/core/unit_test/cuda/TestCuda_SubView_b.cpp
M		lib/kokkos/core/unit_test/cuda/TestCuda_SubView_c01.cpp
M		lib/kokkos/core/unit_test/cuda/TestCuda_SubView_c02.cpp
M		lib/kokkos/core/unit_test/cuda/TestCuda_SubView_c03.cpp
M		lib/kokkos/core/unit_test/cuda/TestCuda_SubView_c04.cpp
M		lib/kokkos/core/unit_test/cuda/TestCuda_SubView_c05.cpp
M		lib/kokkos/core/unit_test/cuda/TestCuda_SubView_c06.cpp
M		lib/kokkos/core/unit_test/cuda/TestCuda_SubView_c07.cpp
M		lib/kokkos/core/unit_test/cuda/TestCuda_SubView_c08.cpp
M		lib/kokkos/core/unit_test/cuda/TestCuda_SubView_c09.cpp
M		lib/kokkos/core/unit_test/cuda/TestCuda_SubView_c10.cpp
M		lib/kokkos/core/unit_test/cuda/TestCuda_SubView_c11.cpp
M		lib/kokkos/core/unit_test/cuda/TestCuda_SubView_c12.cpp
M		lib/kokkos/core/unit_test/cuda/TestCuda_SubView_c_all.cpp
M		lib/kokkos/core/unit_test/cuda/TestCuda_Team.cpp
M		lib/kokkos/core/unit_test/cuda/TestCuda_ViewAPI_a.cpp
M		lib/kokkos/core/unit_test/cuda/TestCuda_ViewAPI_b.cpp
M		lib/kokkos/core/unit_test/cuda/TestCuda_ViewAPI_c.cpp
M		lib/kokkos/core/unit_test/cuda/TestCuda_ViewAPI_d.cpp
M		lib/kokkos/core/unit_test/cuda/TestCuda_ViewAPI_e.cpp
M		lib/kokkos/core/unit_test/cuda/TestCuda_ViewAPI_f.cpp
M		lib/kokkos/core/unit_test/cuda/TestCuda_ViewAPI_g.cpp
M		lib/kokkos/core/unit_test/cuda/TestCuda_ViewAPI_h.cpp
M		lib/kokkos/core/unit_test/cuda/TestCuda_ViewAPI_s.cpp
M		lib/kokkos/core/unit_test/openmp/TestOpenMP.hpp
M		lib/kokkos/core/unit_test/openmp/TestOpenMP_Atomics.cpp
M		lib/kokkos/core/unit_test/openmp/TestOpenMP_Other.cpp
M		lib/kokkos/core/unit_test/openmp/TestOpenMP_Reductions.cpp
M		lib/kokkos/core/unit_test/openmp/TestOpenMP_SubView_a.cpp
M		lib/kokkos/core/unit_test/openmp/TestOpenMP_SubView_b.cpp
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M		lib/kokkos/core/unit_test/openmp/TestOpenMP_SubView_c02.cpp
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M		lib/kokkos/core/unit_test/openmp/TestOpenMP_SubView_c04.cpp
M		lib/kokkos/core/unit_test/openmp/TestOpenMP_SubView_c05.cpp
M		lib/kokkos/core/unit_test/openmp/TestOpenMP_SubView_c06.cpp
M		lib/kokkos/core/unit_test/openmp/TestOpenMP_SubView_c07.cpp
M		lib/kokkos/core/unit_test/openmp/TestOpenMP_SubView_c08.cpp
M		lib/kokkos/core/unit_test/openmp/TestOpenMP_SubView_c09.cpp
M		lib/kokkos/core/unit_test/openmp/TestOpenMP_SubView_c10.cpp
M		lib/kokkos/core/unit_test/openmp/TestOpenMP_SubView_c11.cpp
M		lib/kokkos/core/unit_test/openmp/TestOpenMP_SubView_c12.cpp
M		lib/kokkos/core/unit_test/openmp/TestOpenMP_SubView_c_all.cpp
M		lib/kokkos/core/unit_test/openmp/TestOpenMP_Team.cpp
M		lib/kokkos/core/unit_test/openmp/TestOpenMP_ViewAPI_a.cpp
M		lib/kokkos/core/unit_test/openmp/TestOpenMP_ViewAPI_b.cpp
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A		lib/kokkos/core/unit_test/qthreads/TestQthreads_Atomics.cpp
A		lib/kokkos/core/unit_test/qthreads/TestQthreads_Other.cpp
A		lib/kokkos/core/unit_test/qthreads/TestQthreads_Reductions.cpp
A		lib/kokkos/core/unit_test/qthreads/TestQthreads_SubView_a.cpp
A		lib/kokkos/core/unit_test/qthreads/TestQthreads_SubView_b.cpp
A		lib/kokkos/core/unit_test/qthreads/TestQthreads_SubView_c01.cpp
A		lib/kokkos/core/unit_test/qthreads/TestQthreads_SubView_c02.cpp
A		lib/kokkos/core/unit_test/qthreads/TestQthreads_SubView_c03.cpp
A		lib/kokkos/core/unit_test/qthreads/TestQthreads_SubView_c04.cpp
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A		lib/kokkos/core/unit_test/qthreads/TestQthreads_SubView_c07.cpp
A		lib/kokkos/core/unit_test/qthreads/TestQthreads_SubView_c08.cpp
A		lib/kokkos/core/unit_test/qthreads/TestQthreads_SubView_c09.cpp
A		lib/kokkos/core/unit_test/qthreads/TestQthreads_SubView_c10.cpp
A		lib/kokkos/core/unit_test/qthreads/TestQthreads_SubView_c11.cpp
A		lib/kokkos/core/unit_test/qthreads/TestQthreads_SubView_c12.cpp
A		lib/kokkos/core/unit_test/qthreads/TestQthreads_SubView_c_all.cpp
A		lib/kokkos/core/unit_test/qthreads/TestQthreads_Team.cpp
A		lib/kokkos/core/unit_test/qthreads/TestQthreads_ViewAPI_a.cpp
A		lib/kokkos/core/unit_test/qthreads/TestQthreads_ViewAPI_b.cpp
M		lib/kokkos/core/unit_test/serial/TestSerial.hpp
M		lib/kokkos/core/unit_test/serial/TestSerial_Atomics.cpp
M		lib/kokkos/core/unit_test/serial/TestSerial_Other.cpp
M		lib/kokkos/core/unit_test/serial/TestSerial_Reductions.cpp
M		lib/kokkos/core/unit_test/serial/TestSerial_SubView_a.cpp
M		lib/kokkos/core/unit_test/serial/TestSerial_SubView_b.cpp
M		lib/kokkos/core/unit_test/serial/TestSerial_SubView_c01.cpp
M		lib/kokkos/core/unit_test/serial/TestSerial_SubView_c02.cpp
M		lib/kokkos/core/unit_test/serial/TestSerial_SubView_c03.cpp
M		lib/kokkos/core/unit_test/serial/TestSerial_SubView_c04.cpp
M		lib/kokkos/core/unit_test/serial/TestSerial_SubView_c05.cpp
M		lib/kokkos/core/unit_test/serial/TestSerial_SubView_c06.cpp
M		lib/kokkos/core/unit_test/serial/TestSerial_SubView_c07.cpp
M		lib/kokkos/core/unit_test/serial/TestSerial_SubView_c08.cpp
M		lib/kokkos/core/unit_test/serial/TestSerial_SubView_c09.cpp
M		lib/kokkos/core/unit_test/serial/TestSerial_SubView_c10.cpp
M		lib/kokkos/core/unit_test/serial/TestSerial_SubView_c11.cpp
M		lib/kokkos/core/unit_test/serial/TestSerial_SubView_c12.cpp
M		lib/kokkos/core/unit_test/serial/TestSerial_SubView_c_all.cpp
M		lib/kokkos/core/unit_test/serial/TestSerial_Team.cpp
M		lib/kokkos/core/unit_test/serial/TestSerial_ViewAPI_a.cpp
M		lib/kokkos/core/unit_test/serial/TestSerial_ViewAPI_b.cpp
M		lib/kokkos/core/unit_test/threads/TestThreads.hpp
M		lib/kokkos/core/unit_test/threads/TestThreads_Atomics.cpp
M		lib/kokkos/core/unit_test/threads/TestThreads_Other.cpp
M		lib/kokkos/core/unit_test/threads/TestThreads_Reductions.cpp
M		lib/kokkos/core/unit_test/threads/TestThreads_SubView_a.cpp
M		lib/kokkos/core/unit_test/threads/TestThreads_SubView_b.cpp
M		lib/kokkos/core/unit_test/threads/TestThreads_SubView_c01.cpp
M		lib/kokkos/core/unit_test/threads/TestThreads_SubView_c02.cpp
M		lib/kokkos/core/unit_test/threads/TestThreads_SubView_c03.cpp
M		lib/kokkos/core/unit_test/threads/TestThreads_SubView_c04.cpp
M		lib/kokkos/core/unit_test/threads/TestThreads_SubView_c05.cpp
M		lib/kokkos/core/unit_test/threads/TestThreads_SubView_c06.cpp
M		lib/kokkos/core/unit_test/threads/TestThreads_SubView_c07.cpp
M		lib/kokkos/core/unit_test/threads/TestThreads_SubView_c08.cpp
M		lib/kokkos/core/unit_test/threads/TestThreads_SubView_c09.cpp
M		lib/kokkos/core/unit_test/threads/TestThreads_SubView_c10.cpp
M		lib/kokkos/core/unit_test/threads/TestThreads_SubView_c11.cpp
M		lib/kokkos/core/unit_test/threads/TestThreads_SubView_c12.cpp
M		lib/kokkos/core/unit_test/threads/TestThreads_Team.cpp
M		lib/kokkos/core/unit_test/threads/TestThreads_ViewAPI_a.cpp
M		lib/kokkos/core/unit_test/threads/TestThreads_ViewAPI_b.cpp
M		lib/kokkos/doc/design_notes_space_instances.md
M		lib/kokkos/example/md_skeleton/types.h
M		lib/kokkos/example/tutorial/01_hello_world_lambda/hello_world_lambda.cpp
M		lib/kokkos/example/tutorial/02_simple_reduce_lambda/simple_reduce_lambda.cpp
M		lib/kokkos/example/tutorial/03_simple_view_lambda/simple_view_lambda.cpp
M		lib/kokkos/example/tutorial/Hierarchical_Parallelism/01_thread_teams_lambda/thread_teams_lambda.cpp
M		lib/kokkos/generate_makefile.bash
A		lib/linalg/Install.py
M		lib/linalg/README
A		lib/meam/Install.py
M		lib/meam/README
M		lib/molfile/Makefile.lammps
M		lib/molfile/README
A		lib/molfile/molfile_plugin.h
A		lib/molfile/vmdplugin.h
A		lib/mscg/Install.py
M		lib/mscg/Makefile.lammps
M		lib/mscg/README
M		lib/netcdf/README
A		lib/poems/Install.py
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M		lib/python/Makefile.lammps.python2.7
A		lib/python/Makefile.lammps.python3
M		lib/python/README
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M		lib/qmmm/README
A		lib/reax/Install.py
M		lib/reax/README
A		lib/smd/Install.py
M		lib/smd/README
A		lib/voronoi/Install.py
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D		lib/voronoi/install.py
M		lib/vtk/Makefile.lammps
M		lib/vtk/README
A		potentials/SiC.edip
A		potentials/SiC.gw
A		potentials/SiC.gw.zbl
A		potentials/TiO.meam.spline
M		python/lammps.py
M		src/.gitignore
M		src/ASPHERE/compute_temp_asphere.cpp
M		src/ASPHERE/compute_temp_asphere.h
M		src/ASPHERE/pair_gayberne.cpp
M		src/ASPHERE/pair_line_lj.cpp
M		src/ASPHERE/pair_resquared.cpp
M		src/ASPHERE/pair_tri_lj.cpp
M		src/BODY/pair_body.cpp
M		src/CLASS2/pair_lj_class2.cpp
M		src/CLASS2/pair_lj_class2_coul_cut.cpp
M		src/CLASS2/pair_lj_class2_coul_long.cpp
M		src/COLLOID/pair_brownian.cpp
M		src/COLLOID/pair_colloid.cpp
M		src/COLLOID/pair_lubricate.cpp
M		src/COLLOID/pair_lubricateU.cpp
M		src/COLLOID/pair_lubricateU_poly.cpp
M		src/COMPRESS/Install.sh
M		src/DIPOLE/pair_lj_cut_dipole_cut.cpp
M		src/DIPOLE/pair_lj_cut_dipole_long.cpp
M		src/DIPOLE/pair_lj_long_dipole_long.cpp
M		src/Depend.sh
M		src/GPU/pair_lj_sdk_coul_long_gpu.cpp
M		src/GPU/pair_lj_sdk_coul_long_gpu.h
M		src/GPU/pair_lj_sdk_gpu.cpp
M		src/GPU/pair_lj_sdk_gpu.h
M		src/Install.sh
M		src/KIM/Install.sh
M		src/KOKKOS/Install.sh
M		src/KOKKOS/atom_vec_angle_kokkos.cpp
M		src/KOKKOS/atom_vec_atomic_kokkos.cpp
M		src/KOKKOS/atom_vec_bond_kokkos.cpp
M		src/KOKKOS/atom_vec_charge_kokkos.cpp
M		src/KOKKOS/atom_vec_full_kokkos.cpp
M		src/KOKKOS/atom_vec_kokkos.h
M		src/KOKKOS/atom_vec_molecular_kokkos.cpp
M		src/KOKKOS/fix_qeq_reax_kokkos.cpp
M		src/KOKKOS/fix_reaxc_bonds_kokkos.cpp
M		src/KOKKOS/fix_reaxc_species_kokkos.cpp
M		src/KOKKOS/modify_kokkos.cpp
M		src/KOKKOS/pair_coul_debye_kokkos.cpp
D		src/KOKKOS/pair_reax_c_kokkos.cpp
D		src/KOKKOS/pair_reax_c_kokkos.h
A		src/KOKKOS/pair_reaxc_kokkos.cpp
A		src/KOKKOS/pair_reaxc_kokkos.h
M		src/KOKKOS/verlet_kokkos.cpp
M		src/KOKKOS/verlet_kokkos.h
M		src/KSPACE/ewald_disp.cpp
M		src/KSPACE/pair_born_coul_long.cpp
M		src/KSPACE/pair_buck_coul_long.cpp
M		src/KSPACE/pair_buck_long_coul_long.cpp
M		src/KSPACE/pair_lj_charmmfsw_coul_long.cpp
M		src/KSPACE/pair_lj_cut_coul_long.cpp
M		src/KSPACE/pair_lj_cut_tip4p_long.cpp
M		src/KSPACE/pair_lj_long_coul_long.cpp
M		src/KSPACE/pair_lj_long_tip4p_long.cpp
M		src/KSPACE/pppm_disp.cpp
M		src/MANYBODY/pair_airebo.cpp
A		src/MANYBODY/pair_gw.cpp
A		src/MANYBODY/pair_gw.h
A		src/MANYBODY/pair_gw_zbl.cpp
A		src/MANYBODY/pair_gw_zbl.h
M		src/MC/fix_gcmc.cpp
M		src/MC/fix_gcmc.h
M		src/MC/pair_dsmc.cpp
M		src/MEAM/Install.sh
M		src/MISC/pair_nm_cut.cpp
M		src/MISC/pair_nm_cut_coul_cut.cpp
M		src/MISC/pair_nm_cut_coul_long.cpp
M		src/MOLECULE/bond_harmonic.cpp
M		src/MOLECULE/bond_harmonic.h
D		src/MOLECULE/dihedral_charmmfsh.cpp
D		src/MOLECULE/dihedral_charmmfsh.h
A		src/MOLECULE/dihedral_charmmfsw.cpp
A		src/MOLECULE/dihedral_charmmfsw.h
M		src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp
M		src/MOLECULE/pair_lj_cut_tip4p_cut.cpp
M		src/MPIIO/Install.sh
M		src/MSCG/Install.sh
M		src/Makefile
M		src/POEMS/Install.sh
M		src/PYTHON/Install.sh
A		src/PYTHON/fix_python.cpp
A		src/PYTHON/fix_python.h
A		src/PYTHON/pair_python.cpp
A		src/PYTHON/pair_python.h
D		src/PYTHON/python.cpp
D		src/PYTHON/python.h
A		src/PYTHON/python_compat.h
A		src/PYTHON/python_impl.cpp
A		src/PYTHON/python_impl.h
M		src/Purge.list
M		src/QEQ/fix_qeq.cpp
M		src/QEQ/fix_qeq_point.cpp
M		src/REAX/Install.sh
M		src/REAX/fix_reax_bonds.cpp
M		src/REPLICA/compute_event_displace.cpp
M		src/REPLICA/compute_event_displace.h
M		src/RIGID/fix_shake.cpp
M		src/SNAP/compute_sna_atom.cpp
M		src/SNAP/compute_sna_atom.h
M		src/SNAP/compute_snad_atom.cpp
M		src/SNAP/compute_snad_atom.h
M		src/SNAP/compute_snav_atom.cpp
M		src/SNAP/compute_snav_atom.h
M		src/SNAP/pair_snap.cpp
M		src/USER-ATC/Install.sh
M		src/USER-AWPMD/Install.sh
M		src/USER-AWPMD/pair_awpmd_cut.cpp
D		src/USER-CG-CMM
V		src/{USER-CG-CMM → USER-CGSDK}/Install.sh
D		src/USER-CG-CMM/README
V		src/{USER-CG-CMM → USER-CGSDK}/angle_sdk.cpp
D		src/USER-CG-CMM/angle_sdk.h
V		src/{USER-CG-CMM → USER-CGSDK}/lj_sdk_common.h
D		src/USER-CG-CMM/pair_lj_sdk.cpp
D		src/USER-CG-CMM/pair_lj_sdk.h
D		src/USER-CG-CMM/pair_lj_sdk_coul_long.cpp
D		src/USER-CG-CMM/pair_lj_sdk_coul_long.h
V		src/{USER-CG-CMM → USER-CGSDK}/pair_lj_sdk_coul_msm.cpp
D		src/USER-CG-CMM/pair_lj_sdk_coul_msm.h
A	(dir)	src/USER-CGSDK/
V		src/{USER-CGSDK ← USER-CG-CMM}/Install.sh
A		src/USER-CGSDK/README
V		src/{USER-CGSDK ← USER-CG-CMM}/angle_sdk.cpp
A		src/USER-CGSDK/angle_sdk.h
V		src/{USER-CGSDK ← USER-CG-CMM}/lj_sdk_common.h
A		src/USER-CGSDK/pair_lj_sdk.cpp
A		src/USER-CGSDK/pair_lj_sdk.h
A		src/USER-CGSDK/pair_lj_sdk_coul_long.cpp
A		src/USER-CGSDK/pair_lj_sdk_coul_long.h
V		src/{USER-CGSDK ← USER-CG-CMM}/pair_lj_sdk_coul_msm.cpp
A		src/USER-CGSDK/pair_lj_sdk_coul_msm.h
M		src/USER-COLVARS/Install.sh
M		src/USER-DPD/nbin_ssa.cpp
M		src/USER-DPD/npair_half_bin_newton_ssa.cpp
M		src/USER-DPD/pair_dpd_fdt.cpp
M		src/USER-DPD/pair_dpd_fdt_energy.cpp
M		src/USER-DPD/pair_exp6_rx.cpp
M		src/USER-DRUDE/pair_lj_cut_thole_long.cpp
M		src/USER-DRUDE/pair_thole.cpp
M		src/USER-EFF/pair_eff_cut.cpp
M		src/USER-FEP/pair_coul_cut_soft.cpp
M		src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp
M		src/USER-FEP/pair_lj_cut_coul_long_soft.cpp
M		src/USER-FEP/pair_lj_cut_soft.cpp
M		src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp
M		src/USER-FEP/pair_morse_soft.cpp
M		src/USER-H5MD/Install.sh
M		src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp
M		src/USER-MANIFOLD/fix_nve_manifold_rattle.h
M		src/USER-MISC/Install.sh
M		src/USER-MISC/compute_temp_rotate.cpp
M		src/USER-MISC/compute_temp_rotate.h
M		src/USER-MISC/fix_srp.cpp
M		src/USER-MISC/improper_ring.cpp
M		src/USER-MISC/pair_buck_mdf.cpp
M		src/USER-MISC/pair_coul_diel.cpp
M		src/USER-MISC/pair_edip.cpp
A		src/USER-MISC/pair_edip_multi.cpp
A		src/USER-MISC/pair_edip_multi.h
M		src/USER-MISC/pair_gauss_cut.cpp
M		src/USER-MISC/pair_kolmogorov_crespi_z.cpp
M		src/USER-MISC/pair_lennard_mdf.cpp
M		src/USER-MISC/pair_lj_mdf.cpp
M		src/USER-MISC/pair_lj_sf.cpp
M		src/USER-MISC/pair_lj_sf_dipole_sf.cpp
M		src/USER-MISC/pair_meam_spline.cpp
M		src/USER-MISC/pair_meam_spline.h
M		src/USER-MISC/pair_momb.cpp
M		src/USER-MISC/pair_morse_smooth_linear.cpp
M		src/USER-MISC/pair_srp.cpp
M		src/USER-MOLFILE/Install.sh
M		src/USER-MOLFILE/README
D		src/USER-MOLFILE/molfile_plugin.h
D		src/USER-MOLFILE/vmdplugin.h
D		src/USER-NC-DUMP
D		src/USER-NC-DUMP/Install.sh
D		src/USER-NC-DUMP/README
D		src/USER-NC-DUMP/dump_nc.cpp
D		src/USER-NC-DUMP/dump_nc.h
D		src/USER-NC-DUMP/dump_nc_mpiio.cpp
D		src/USER-NC-DUMP/dump_nc_mpiio.h
A	(dir)	src/USER-NETCDF/
A		src/USER-NETCDF/Install.sh
A		src/USER-NETCDF/README
A		src/USER-NETCDF/dump_netcdf.cpp
A		src/USER-NETCDF/dump_netcdf.h
A		src/USER-NETCDF/dump_netcdf_mpiio.cpp
A		src/USER-NETCDF/dump_netcdf_mpiio.h
M		src/USER-OMP/angle_sdk_omp.h
M		src/USER-OMP/fix_nh_asphere_omp.cpp
M		src/USER-OMP/fix_nh_omp.cpp
M		src/USER-OMP/fix_nh_sphere_omp.cpp
M		src/USER-OMP/fix_nvt_sllod_omp.cpp
M		src/USER-OMP/improper_ring_omp.cpp
M		src/USER-OMP/npair_full_bin_ghost_omp.cpp
M		src/USER-OMP/npair_full_bin_omp.cpp
M		src/USER-OMP/npair_full_multi_omp.cpp
M		src/USER-OMP/npair_half_bin_newtoff_ghost_omp.cpp
M		src/USER-OMP/npair_half_bin_newtoff_omp.cpp
M		src/USER-OMP/npair_half_bin_newton_omp.cpp
M		src/USER-OMP/npair_half_bin_newton_tri_omp.cpp
M		src/USER-OMP/npair_half_multi_newtoff_omp.cpp
M		src/USER-OMP/npair_half_multi_newton_omp.cpp
M		src/USER-OMP/npair_half_multi_newton_tri_omp.cpp
M		src/USER-OMP/npair_half_respa_bin_newtoff_omp.cpp
M		src/USER-OMP/npair_half_respa_bin_newton_omp.cpp
M		src/USER-OMP/npair_half_respa_bin_newton_tri_omp.cpp
M		src/USER-OMP/npair_half_size_bin_newtoff_omp.cpp
M		src/USER-OMP/npair_half_size_bin_newton_omp.cpp
M		src/USER-OMP/npair_half_size_bin_newton_tri_omp.cpp
M		src/USER-OMP/pair_airebo_omp.cpp
M		src/USER-OMP/pair_lj_sdk_coul_long_omp.h
M		src/USER-OMP/pair_lj_sdk_coul_msm_omp.h
M		src/USER-OMP/pair_lj_sdk_omp.h
M		src/USER-OMP/pair_meam_spline_omp.cpp
M		src/USER-QMMM/Install.sh
M		src/USER-QUIP/Install.sh
M		src/USER-REAXC/compute_spec_atom.cpp
M		src/USER-REAXC/fix_qeq_reax.cpp
D		src/USER-REAXC/fix_reax_c.cpp
V		src/USER-REAXC/{fix_reax_c.h → fix_reaxc.h}
A		src/USER-REAXC/fix_reaxc.cpp
V		src/USER-REAXC/{fix_reaxc.h ← fix_reax_c.h}
M		src/USER-REAXC/fix_reaxc_bonds.cpp
M		src/USER-REAXC/fix_reaxc_species.cpp
M		src/USER-REAXC/fix_reaxc_species.h
D		src/USER-REAXC/pair_reax_c.cpp
V		src/USER-REAXC/{pair_reax_c.h → pair_reaxc.h}
A		src/USER-REAXC/pair_reaxc.cpp
V		src/USER-REAXC/{pair_reaxc.h ← pair_reax_c.h}
M		src/USER-REAXC/reaxc_allocate.cpp
M		src/USER-REAXC/reaxc_bond_orders.cpp
M		src/USER-REAXC/reaxc_bonds.cpp
M		src/USER-REAXC/reaxc_control.cpp
M		src/USER-REAXC/reaxc_defs.h
M		src/USER-REAXC/reaxc_ffield.cpp
M		src/USER-REAXC/reaxc_forces.cpp
M		src/USER-REAXC/reaxc_hydrogen_bonds.cpp
M		src/USER-REAXC/reaxc_init_md.cpp
M		src/USER-REAXC/reaxc_io_tools.cpp
M		src/USER-REAXC/reaxc_list.cpp
M		src/USER-REAXC/reaxc_lookup.cpp
M		src/USER-REAXC/reaxc_multi_body.cpp
M		src/USER-REAXC/reaxc_nonbonded.cpp
M		src/USER-REAXC/reaxc_reset_tools.cpp
M		src/USER-REAXC/reaxc_system_props.cpp
M		src/USER-REAXC/reaxc_tool_box.cpp
M		src/USER-REAXC/reaxc_torsion_angles.cpp
M		src/USER-REAXC/reaxc_traj.cpp
M		src/USER-REAXC/reaxc_types.h
M		src/USER-REAXC/reaxc_valence_angles.cpp
M		src/USER-REAXC/reaxc_vector.cpp
M		src/USER-SMD/Install.sh
M		src/USER-TALLY/compute_force_tally.cpp
M		src/USER-TALLY/compute_heat_flux_tally.cpp
M		src/USER-TALLY/compute_pe_mol_tally.cpp
M		src/USER-TALLY/compute_pe_tally.cpp
M		src/USER-TALLY/compute_stress_tally.cpp
M		src/USER-VTK/Install.sh
M		src/USER-VTK/README
D		src/USER-VTK/dump_custom_vtk.cpp
D		src/USER-VTK/dump_custom_vtk.h
A		src/USER-VTK/dump_vtk.cpp
A		src/USER-VTK/dump_vtk.h
M		src/VORONOI/Install.sh
M		src/bond.cpp
M		src/bond.h
M		src/compute.h
M		src/compute_dipole_chunk.cpp
M		src/compute_temp_com.cpp
M		src/compute_temp_com.h
M		src/compute_temp_deform.cpp
M		src/compute_temp_deform.h
M		src/compute_temp_partial.cpp
M		src/compute_temp_partial.h
M		src/compute_temp_profile.cpp
M		src/compute_temp_profile.h
M		src/compute_temp_ramp.cpp
M		src/compute_temp_ramp.h
M		src/compute_temp_region.cpp
M		src/compute_temp_region.h
M		src/compute_temp_sphere.cpp
M		src/compute_temp_sphere.h
M		src/domain.cpp
M		src/domain.h
M		src/dump_custom.cpp
M		src/finish.cpp
M		src/fix_adapt.cpp
M		src/fix_adapt.h
M		src/fix_ave_histo.cpp
M		src/integrate.h
M		src/lammps.cpp
M		src/lammps.h
M		src/min.cpp
M		src/min.h
M		src/nbin.cpp
M		src/nbin.h
M		src/nbin_standard.cpp
M		src/neigh_request.cpp
M		src/neighbor.cpp
M		src/npair.cpp
M		src/npair.h
M		src/npair_full_bin.cpp
M		src/npair_full_bin_atomonly.cpp
M		src/npair_full_bin_ghost.cpp
M		src/npair_full_multi.cpp
M		src/npair_half_bin_atomonly_newton.cpp
M		src/npair_half_bin_newtoff.cpp
M		src/npair_half_bin_newtoff_ghost.cpp
M		src/npair_half_bin_newton.cpp
M		src/npair_half_bin_newton_tri.cpp
M		src/npair_half_multi_newtoff.cpp
M		src/npair_half_multi_newton.cpp
M		src/npair_half_multi_newton_tri.cpp
M		src/npair_half_respa_bin_newtoff.cpp
M		src/npair_half_respa_bin_newton.cpp
M		src/npair_half_respa_bin_newton_tri.cpp
M		src/npair_half_size_bin_newtoff.cpp
M		src/npair_half_size_bin_newton.cpp
M		src/npair_half_size_bin_newton_tri.cpp
M		src/output.cpp
M		src/output.h
M		src/pair.h
M		src/pair_beck.cpp
M		src/pair_born.cpp
M		src/pair_born_coul_dsf.cpp
M		src/pair_born_coul_wolf.cpp
M		src/pair_buck.cpp
M		src/pair_buck_coul_cut.cpp
M		src/pair_coul_cut.cpp
M		src/pair_coul_debye.cpp
M		src/pair_dpd.cpp
M		src/pair_dpd_tstat.cpp
M		src/pair_gauss.cpp
M		src/pair_hybrid.cpp
M		src/pair_hybrid.h
M		src/pair_lj96_cut.cpp
M		src/pair_lj_cubic.cpp
M		src/pair_lj_cut.cpp
M		src/pair_lj_cut_coul_cut.cpp
M		src/pair_lj_cut_coul_dsf.cpp
M		src/pair_lj_expand.cpp
M		src/pair_lj_gromacs.cpp
M		src/pair_lj_smooth.cpp
M		src/pair_lj_smooth_linear.cpp
M		src/pair_mie_cut.cpp
M		src/pair_morse.cpp
M		src/pair_soft.cpp
M		src/pair_yukawa.cpp
M		src/pointers.h
A		src/python.cpp
A		src/python.h
D		src/python_wrapper.h
M		src/respa.cpp
M		src/respa.h
M		src/thermo.cpp
M		src/variable.cpp
M		src/variable.h
M		src/verlet.cpp
M		src/verlet.h
M		src/version.h
M		src/write_restart.cpp
M		tools/msi2lmp/README
M		tools/msi2lmp/src/GetParameters.c
M		tools/msi2lmp/src/InitializeItems.c
M		tools/msi2lmp/src/WriteDataFile.c
M		tools/msi2lmp/src/msi2lmp.c
M		tools/msi2lmp/src/msi2lmp.h

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examples/ASPHERE/poly/in.poly.mp

examples/USER/cg-cmm

examples/USER/cg-cmm/README

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