Merge branch 'master' into USER-DPD_kokkos_testing
bc446bb8b01b
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Authored by Stan Moore <stamoor@sandia.gov> on Jul 25 2017, 20:12.

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Merge branch 'master' into USER-DPD_kokkos_testing

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Committed

Stan Moore <stamoor@sandia.gov>

Jul 25 2017, 20:12

Pushed

junge

Oct 19 2017, 09:53

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rLAMMPSea4d11fc5eff: Merge branch 'master' into USER-DPD_kokkos_testing
rLAMMPSa59b7e4d5647: patch 24Jul17

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Stan Moore <stamoor@sandia.gov> committed rLAMMPSbc446bb8b01b: Merge branch 'master' into USER-DPD_kokkos_testing (authored by Stan Moore <stamoor@sandia.gov>).Jul 25 2017, 20:12

Merged Changes

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

Commit	Author	Details	Committed
a59b7e4d5647	Steve Plimpton	patch 24Jul17	Jul 24 2017
2eaea2d274e5	sjplimp/GitHub	Merge pull request #594 from junghans/license	Jul 24 2017
1ddace4dba51	sjplimp/GitHub	Merge pull request #595 from libAtoms/idces2quip	Jul 24 2017
af3d0ca381dd	sjplimp/GitHub	Merge pull request #593 from akohlmey/collected-bug-fixes-and-small-updates	Jul 24 2017
c24e316baaa6	Axel Kohlmeyer	avoid floating point overflows in iterative solvers of fix shake	Jul 23 2017
2c6e177d5c55	Axel Kohlmeyer	avoid reporting negative memory allocation when memory_usage() is called before…	Jul 23 2017
7b2182833fea	Axel Kohlmeyer	disallow binary output with dump style local. fixes #596	Jul 22 2017
1afab981b022	Max Veit	Clarified some points in in.molecular example	Jul 22 2017
1af937e99d71	Axel Kohlmeyer/GitHub	Update in.molecular	Jul 22 2017
4e0a249e2779	Max Veit	Add a (contrived) molecular example for USER-QUIP	Jul 22 2017
edc756a65f76	Christoph Junghans	LICENSE: update address of Free Software Foundation	Jul 22 2017
a477f26477fa	Axel Kohlmeyer	add support for trapping floating point exception as an optional compile time…	Jul 21 2017
b1b399d5c3dd	Axel Kohlmeyer	update readme for examples	Jul 21 2017
00474ab09dcd	Axel Kohlmeyer	handle one more case where allowing shifted potential with cutoff 0.0 would…	Jul 21 2017
733ea61bf107	Axel Kohlmeyer	correct typo in USER-REAXC code	Jul 21 2017
5c13b087e4a1	sjplimp/GitHub	Merge pull request #592 from akohlmey/reaxc-bugfix	Jul 21 2017
ec23aef20b22	Axel Kohlmeyer	fix reaxc division by zero bug also for USER-OMP variant	Jul 21 2017
61b1487cbd93	Axel Kohlmeyer	avoid division by zero in reaxff bond interaction computations in very rare…	Jul 21 2017
e53583d9c652	sjplimp/GitHub	Merge pull request #590 from lammps/fortran-dftb	Jul 20 2017
551001f172a3	Axel Kohlmeyer	revert change, that is part of the kim-install branch and changeset	Jul 20 2017
5dbe2df85455	Axel Kohlmeyer	revert change that accidentally undoes part of PRs #583 and #588	Jul 20 2017
3f83396837ea	sjplimp/GitHub	Merge pull request #588 from akohlmey/colvars-quickfix	Jul 20 2017
59db5f6a1782	Steve Plimpton	update of Fortran-DFTB interface to be compatible with fix msst	Jul 20 2017
1b704bab18ba	Axel Kohlmeyer	Merge branch 'colvars-safer-makefiles' of https://github.	Jul 20 2017
c98f6140e755	Giacomo Fiorin	Change order of targets in Makefiles for Colvars	Jul 20 2017
5031f5b8079c	Giacomo Fiorin	Comment out use by Colvars of Makefile.lammps from other packages	Jul 20 2017
9d0d90c03860	Axel Kohlmeyer	README clarification from giacomo	Jul 20 2017
66154e8a8b31	Axel Kohlmeyer	avoid makefile failure, if LAMMPS has not been configured yet	Jul 20 2017
3cd597e948fa	sjplimp/GitHub	Merge pull request #585 from akohlmey/make-py-manual-cleanup	Jul 20 2017
eca61226c267	sjplimp/GitHub	Merge pull request #583 from giacomofiorin/colvars-update-2017-07-19	Jul 20 2017
fac3e3daa237	sjplimp/GitHub	Merge pull request #581 from libAtoms/idces2quip	Jul 20 2017
72e5f537c8d0	sjplimp/GitHub	Merge pull request #576 from akohlmey/sanitizer-changes	Jul 20 2017
bdd2f3a6b2c7	Axel Kohlmeyer	remove references to Make.py and USER-CUDA	Jul 20 2017
a351977c5904	Axel Kohlmeyer	update manual links that got broken when removing and renumbering a section	Jul 20 2017
8499e72cdc91	Axel Kohlmeyer	updates to USER-REAXC code in USER-OMP from Chris Knight. addresses issues with…	Jul 20 2017
ef9fb944c727	Giacomo Fiorin	Detect number of processors for make	Jul 20 2017
187a80be7738	Giacomo Fiorin	Add forgotten decode() in Install.py	Jul 20 2017
ee6cac826e65	Giacomo Fiorin	Update Colvars to version 2017-07-15 and support automated builds for it	Jul 19 2017
52a1c54d500e	Axel Kohlmeyer	support QUIP wrapper API version query, relax hybrid restriction to allow…	Jul 19 2017
fcf9607a6666	Max Veit	Update USER_QUIP docs to clarify use of "special_bonds"	Jul 19 2017
148364949e21	Axel Kohlmeyer	fix memory corruption issue in fix reax/c/species	Jul 18 2017
17aff29fe2e7	Axel Kohlmeyer	fix off-by-one bug when copying strings	Jul 18 2017
f96b9e0dcf55	Axel Kohlmeyer	add various checks and improvements to identify incompatible uses and warn or…	Jul 18 2017
02572a4099a6	Axel Kohlmeyer	add workaround that allows pair style quip to work with -DLAMMPS_BIGBIG…	Jul 18 2017
085cbee1163d	Axel Kohlmeyer	protect LAMMPS from calling incompatible QUIP library with -DLAMMPS_BIGBIG	Jul 18 2017
4ad952899922	Axel Kohlmeyer	safer handling of memory management for lists in reax/c	Jul 18 2017
358915d16ee7	Axel Kohlmeyer	avoid division by zero in peri pair styles	Jul 18 2017
d9186c8fde6d	Axel Kohlmeyer	Revert "use neighbor list exclusions instead of a zero cutoff"	Jul 18 2017
bc5186bc30e1	Axel Kohlmeyer	fix unitialized pointer issue in USER-OMP with pppm/disp	Jul 18 2017
c083d5d6f3f8	Axel Kohlmeyer	fix memory leak in list of neighbor list requests	Jul 18 2017

Changes (496)
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This commit is very large. Load each file individually.

		Path
A	(dir)	.github/
A		.github/CONTRIBUTING.md
A		.github/ISSUE_TEMPLATE.md
A		.github/PULL_REQUEST_TEMPLATE.md
M		LICENSE
M		bench/FERMI/README
M		bench/README
A		doc/src/Eqs/fix_wall_ees.jpg
A		doc/src/Eqs/fix_wall_ees.tex
A		doc/src/JPG/fix_wall_ees_image.jpg
M		doc/src/Manual.txt
M		doc/src/PDF/colvars-refman-lammps.pdf
M		doc/src/Section_accelerate.txt
M		doc/src/Section_commands.txt
M		doc/src/Section_errors.txt
M		doc/src/Section_howto.txt
M		doc/src/Section_packages.txt
M		doc/src/Section_python.txt
M		doc/src/Section_start.txt
M		doc/src/accelerate_gpu.txt
M		doc/src/accelerate_intel.txt
M		doc/src/accelerate_kokkos.txt
M		doc/src/accelerate_omp.txt
M		doc/src/accelerate_opt.txt
M		doc/src/angle_charmm.txt
M		doc/src/angle_class2.txt
M		doc/src/angle_cosine.txt
M		doc/src/angle_cosine_delta.txt
M		doc/src/angle_cosine_periodic.txt
M		doc/src/angle_cosine_shift.txt
M		doc/src/angle_cosine_shift_exp.txt
M		doc/src/angle_cosine_squared.txt
M		doc/src/angle_fourier.txt
M		doc/src/angle_fourier_simple.txt
M		doc/src/angle_harmonic.txt
M		doc/src/angle_quartic.txt
M		doc/src/angle_table.txt
M		doc/src/balance.txt
M		doc/src/bond_class2.txt
M		doc/src/bond_fene.txt
M		doc/src/bond_fene_expand.txt
M		doc/src/bond_harmonic.txt
M		doc/src/bond_harmonic_shift.txt
M		doc/src/bond_harmonic_shift_cut.txt
M		doc/src/bond_morse.txt
M		doc/src/bond_nonlinear.txt
M		doc/src/bond_quartic.txt
M		doc/src/bond_table.txt
M		doc/src/compute_pressure.txt
M		doc/src/compute_rdf.txt
M		doc/src/compute_temp.txt
M		doc/src/compute_temp_partial.txt
M		doc/src/create_bonds.txt
M		doc/src/dihedral_charmm.txt
M		doc/src/dihedral_class2.txt
M		doc/src/dihedral_cosine_shift_exp.txt
M		doc/src/dihedral_fourier.txt
M		doc/src/dihedral_harmonic.txt
M		doc/src/dihedral_helix.txt
M		doc/src/dihedral_multi_harmonic.txt
M		doc/src/dihedral_nharmonic.txt
M		doc/src/dihedral_opls.txt
M		doc/src/dihedral_quadratic.txt
M		doc/src/echo.txt
M		doc/src/fix_addforce.txt
M		doc/src/fix_aveforce.txt
M		doc/src/fix_deform.txt
M		doc/src/fix_enforce2d.txt
M		doc/src/fix_freeze.txt
M		doc/src/fix_gcmc.txt
M		doc/src/fix_gravity.txt
M		doc/src/fix_langevin.txt
M		doc/src/fix_momentum.txt
M		doc/src/fix_msst.txt
M		doc/src/fix_nh.txt
M		doc/src/fix_nph_asphere.txt
M		doc/src/fix_nph_body.txt
M		doc/src/fix_nph_sphere.txt
M		doc/src/fix_nphug.txt
M		doc/src/fix_npt_asphere.txt
M		doc/src/fix_npt_body.txt
M		doc/src/fix_npt_sphere.txt
M		doc/src/fix_nve.txt
M		doc/src/fix_nve_asphere.txt
M		doc/src/fix_nve_sphere.txt
M		doc/src/fix_nvt_asphere.txt
M		doc/src/fix_nvt_body.txt
M		doc/src/fix_nvt_sllod.txt
M		doc/src/fix_nvt_sphere.txt
M		doc/src/fix_qeq_comb.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/fix_rigid.txt
M		doc/src/fix_setforce.txt
M		doc/src/fix_shake.txt
A		doc/src/fix_wall_ees.txt
M		doc/src/fix_wall_reflect.txt
M		doc/src/fixes.txt
M		doc/src/improper_class2.txt
M		doc/src/improper_cossq.txt
M		doc/src/improper_cvff.txt
M		doc/src/improper_fourier.txt
M		doc/src/improper_harmonic.txt
M		doc/src/improper_ring.txt
M		doc/src/improper_umbrella.txt
M		doc/src/jump.txt
M		doc/src/lammps.book
M		doc/src/log.txt
M		doc/src/neb.txt
M		doc/src/neighbor.txt
M		doc/src/next.txt
M		doc/src/package.txt
M		doc/src/pair_adp.txt
M		doc/src/pair_agni.txt
M		doc/src/pair_airebo.txt
M		doc/src/pair_beck.txt
M		doc/src/pair_born.txt
M		doc/src/pair_brownian.txt
M		doc/src/pair_buck.txt
M		doc/src/pair_buck_long.txt
M		doc/src/pair_charmm.txt
M		doc/src/pair_class2.txt
M		doc/src/pair_colloid.txt
M		doc/src/pair_comb.txt
M		doc/src/pair_coul.txt
M		doc/src/pair_dipole.txt
M		doc/src/pair_dpd.txt
M		doc/src/pair_eam.txt
M		doc/src/pair_edip.txt
M		doc/src/pair_eim.txt
M		doc/src/pair_gayberne.txt
M		doc/src/pair_gran.txt
M		doc/src/pair_gromacs.txt
M		doc/src/pair_hbond_dreiding.txt
M		doc/src/pair_hybrid.txt
M		doc/src/pair_lj.txt
M		doc/src/pair_lj96.txt
M		doc/src/pair_lj_cubic.txt
M		doc/src/pair_lj_expand.txt
M		doc/src/pair_lj_long.txt
M		doc/src/pair_lj_smooth.txt
M		doc/src/pair_lj_smooth_linear.txt
M		doc/src/pair_lj_soft.txt
M		doc/src/pair_lubricate.txt
M		doc/src/pair_meam.txt
M		doc/src/pair_meam_spline.txt
M		doc/src/pair_morse.txt
M		doc/src/pair_nb3b_harmonic.txt
M		doc/src/pair_nm.txt
M		doc/src/pair_peri.txt
M		doc/src/pair_quip.txt
M		doc/src/pair_reaxc.txt
M		doc/src/pair_resquared.txt
M		doc/src/pair_sdk.txt
M		doc/src/pair_soft.txt
M		doc/src/pair_sw.txt
M		doc/src/pair_table.txt
M		doc/src/pair_tersoff.txt
M		doc/src/pair_tersoff_mod.txt
M		doc/src/pair_tersoff_zbl.txt
M		doc/src/pair_thole.txt
M		doc/src/pair_vashishta.txt
M		doc/src/pair_yukawa.txt
M		doc/src/pair_yukawa_colloid.txt
M		doc/src/pair_zbl.txt
M		doc/src/partition.txt
M		doc/src/prd.txt
M		doc/src/processors.txt
M		doc/src/read_data.txt
M		doc/src/read_restart.txt
M		doc/src/region.txt
M		doc/src/restart.txt
M		doc/src/run_style.txt
M		doc/src/suffix.txt
M		doc/src/temper.txt
M		doc/src/thermo_style.txt
M		doc/src/timer.txt
M		doc/src/variable.txt
M		doc/src/write_data.txt
M		doc/src/write_restart.txt
M		examples/COUPLE/README
A	(dir)	examples/COUPLE/fortran_dftb/
A		examples/COUPLE/fortran_dftb/LAMMPS-wrapper.cpp
A		examples/COUPLE/fortran_dftb/LAMMPS-wrapper.h
A		examples/COUPLE/fortran_dftb/LAMMPS-wrapper2.cpp
A		examples/COUPLE/fortran_dftb/LAMMPS-wrapper2.h
A		examples/COUPLE/fortran_dftb/LAMMPS.F90
A		examples/COUPLE/fortran_dftb/README
A		examples/COUPLE/fortran_dftb/data.diamond
A		examples/COUPLE/fortran_dftb/dftb_in.hsd
A		examples/COUPLE/fortran_dftb/dftb_pin.hsd
A		examples/COUPLE/fortran_dftb/in.simple
A		examples/COUPLE/fortran_dftb/log.simple
A		examples/COUPLE/fortran_dftb/makefile
A		examples/COUPLE/fortran_dftb/simple.f90
M		examples/README
A	(dir)	examples/USER/misc/ees/
A		examples/USER/misc/ees/Data_region
A		examples/USER/misc/ees/Data_wall
A		examples/USER/misc/ees/README
A		examples/USER/misc/ees/in.fix_wall
A		examples/USER/misc/ees/in.fix_wall_region
A		examples/USER/misc/ees/log.23Jun17.fix_wall.g++.1
A		examples/USER/misc/ees/log.23Jun17.fix_wall.g++.4
A		examples/USER/misc/ees/log.23Jun17.fix_wall_region.g++.1
A		examples/USER/misc/ees/log.23Jun17.fix_wall_region.g++.4
M		examples/USER/misc/flow_gauss/README
M		examples/USER/misc/flow_gauss/in.GD
A		examples/USER/misc/flow_gauss/log.6Jul17.GD.g++.1
A		examples/USER/misc/flow_gauss/log.6Jul17.GD.g++.4
A	(dir)	examples/USER/misc/flow_gauss/output-files/
A		examples/USER/misc/flow_gauss/output-files/GD.out
A		examples/USER/misc/flow_gauss/output-files/Vy_profile
A		examples/USER/misc/flow_gauss/output-files/x_profiles
A		examples/USER/quip/in.molecular
A		examples/USER/quip/methane-box-8.data
A		examples/USER/quip/out.molecular
M		examples/accelerate/README
A	(dir)	examples/airebo/
A		examples/airebo/data.airebo
A		examples/airebo/in.airebo
A		examples/airebo/in.airebo-m
A		examples/airebo/log.23Jun17.airebo-m.g++.1
A		examples/airebo/log.23Jun17.airebo-m.g++.4
A		examples/airebo/log.23Jun17.airebo.g++.1
A		examples/airebo/log.23Jun17.airebo.g++.4
M		examples/balance/in.balance.bond.fast
M		examples/balance/in.balance.bond.slow
A		examples/gcmc/H2O.txt
P		examples/gcmc/in.gcmc.co2 Copied to examples/gcmc/in.gcmc.h2o
P		examples/gcmc/in.gcmc.h2o Copied from examples/gcmc/in.gcmc.co2
V		examples/gcmc/{log.24Mar17.gcmc.co2.g++.1 → log.6Jul17.gcmc.co2.g++.1}
D		examples/gcmc/log.24Mar17.gcmc.co2.g++.4
V		examples/gcmc/{log.24Mar17.gcmc.lj.g++.1 → log.6Jul17.gcmc.lj.g++.1}
V		examples/gcmc/{log.24Mar17.gcmc.lj.g++.4 → log.6Jul17.gcmc.lj.g++.4}
V		examples/gcmc/{log.6Jul17.gcmc.co2.g++.1 ← log.24Mar17.gcmc.co2.g++.1}
A		examples/gcmc/log.6Jul17.gcmc.co2.g++.4
A		examples/gcmc/log.6Jul17.gcmc.h2o.g++.1
A		examples/gcmc/log.6Jul17.gcmc.h2o.g++.4
V		examples/gcmc/{log.6Jul17.gcmc.lj.g++.1 ← log.24Mar17.gcmc.lj.g++.1}
V		examples/gcmc/{log.6Jul17.gcmc.lj.g++.4 ← log.24Mar17.gcmc.lj.g++.4}
A		examples/meam/in.meamc
A		examples/meam/in.meamc.shear
P		examples/meam/log.19May17.meam.g++.1 Copied from examples/meam/log.5Oct16.meam.icc.1
P		examples/meam/log.19May17.meam.g++.4 Copied from examples/meam/log.5Oct16.meam.icc.4
V		examples/meam/{log.19May17.meam.shear.g++.1 ← log.5Oct16.meam.shear.icc.1}
V		examples/meam/{log.19May17.meam.shear.g++.4 ← log.5Oct16.meam.shear.icc.4}
V		examples/meam/{log.19May17.meamc.g++.1 ← log.5Oct16.meam.icc.1}
V		examples/meam/{log.19May17.meamc.g++.4 ← log.5Oct16.meam.icc.4}
A		examples/meam/log.19May17.meamc.shear.g++.1
A		examples/meam/log.19May17.meamc.shear.g++.4
P		examples/meam/log.5Oct16.meam.icc.1 Deleted after being copied to multiple locations: examples/meam/log.19May17.meam.g++.1 examples/meam/log.19May17.meamc.g++.1
P		examples/meam/log.5Oct16.meam.icc.4 Deleted after being copied to multiple locations: examples/meam/log.19May17.meam.g++.4 examples/meam/log.19May17.meamc.g++.4
V		examples/meam/{log.5Oct16.meam.shear.icc.1 → log.19May17.meam.shear.g++.1}
V		examples/meam/{log.5Oct16.meam.shear.icc.4 → log.19May17.meam.shear.g++.4}
P		examples/peri/in.peri Deleted after being copied to multiple locations: examples/peri/in.peri-pmb examples/peri/in.peri.eps examples/peri/in.peri.lps examples/peri/in.peri.pmb examples/peri/in.peri.ves
P		examples/peri/in.peri-pmb Copied from examples/peri/in.peri
P		examples/peri/in.peri.eps Copied from examples/peri/in.peri
P		examples/peri/in.peri.lps Copied from examples/peri/in.peri
P		examples/peri/in.peri.pmb Copied from examples/peri/in.peri
V		examples/peri/{in.peri.ves ← in.peri}
V		examples/peri/{log.5Oct16.peri.g++.1 → log.6Jul17.peri.pmb.g++.1}
V		examples/peri/{log.5Oct16.peri.g++.4 → log.6Jul17.peri.pmb.g++.4}
A		examples/peri/log.6Jul17.peri.eps.g++.1
A		examples/peri/log.6Jul17.peri.eps.g++.4
A		examples/peri/log.6Jul17.peri.lps.g++.1
A		examples/peri/log.6Jul17.peri.lps.g++.4
V		examples/peri/{log.6Jul17.peri.pmb.g++.1 ← log.5Oct16.peri.g++.1}
V		examples/peri/{log.6Jul17.peri.pmb.g++.4 ← log.5Oct16.peri.g++.4}
A		examples/peri/log.6Jul17.peri.ves.g++.1
A		examples/peri/log.6Jul17.peri.ves.g++.4
M		lib/colvars/Install.py
D		lib/colvars/Makefile.colvars
A		lib/colvars/Makefile.common
A		lib/colvars/Makefile.deps
D		lib/colvars/Makefile.fermi
M		lib/colvars/Makefile.g++
A		lib/colvars/Makefile.g++-debug
P		lib/colvars/Makefile.lammps Copied from lib/colvars/Makefile.lammps.debug
P		lib/colvars/Makefile.lammps.debug Copied to lib/colvars/Makefile.lammps
M		lib/colvars/Makefile.lammps.empty
M		lib/colvars/Makefile.mingw32-cross
M		lib/colvars/Makefile.mingw64-cross
M		lib/colvars/README
M		lib/colvars/colvar.cpp
M		lib/colvars/colvar.h
M		lib/colvars/colvaratoms.cpp
M		lib/colvars/colvaratoms.h
M		lib/colvars/colvarbias.cpp
M		lib/colvars/colvarbias.h
M		lib/colvars/colvarbias_abf.cpp
M		lib/colvars/colvarbias_alb.cpp
M		lib/colvars/colvarbias_histogram.cpp
M		lib/colvars/colvarbias_meta.cpp
M		lib/colvars/colvarbias_meta.h
M		lib/colvars/colvarbias_restraint.cpp
M		lib/colvars/colvarcomp.cpp
M		lib/colvars/colvarcomp.h
M		lib/colvars/colvarcomp_angles.cpp
M		lib/colvars/colvarcomp_coordnums.cpp
M		lib/colvars/colvarcomp_distances.cpp
M		lib/colvars/colvarcomp_protein.cpp
M		lib/colvars/colvarcomp_rotations.cpp
M		lib/colvars/colvardeps.cpp
M		lib/colvars/colvardeps.h
M		lib/colvars/colvargrid.cpp
M		lib/colvars/colvargrid.h
M		lib/colvars/colvarmodule.cpp
M		lib/colvars/colvarmodule.h
M		lib/colvars/colvarparse.cpp
M		lib/colvars/colvarparse.h
A		lib/colvars/colvarproxy.cpp
M		lib/colvars/colvarproxy.h
A		lib/colvars/colvars_version.h
M		lib/colvars/colvarscript.cpp
M		lib/colvars/colvarscript.h
M		lib/colvars/colvartypes.h
M		lib/colvars/colvarvalue.cpp
M		lib/colvars/colvarvalue.h
A		lib/kim/.gitignore
A		lib/kim/Install.py
M		lib/kim/Makefile.lammps
M		lib/kim/README
M		src/.gitignore
M		src/ASPHERE/pair_gayberne.cpp
M		src/ASPHERE/pair_resquared.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_colloid.cpp
M		src/COLLOID/pair_yukawa_colloid.cpp
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/KOKKOS/pair_reaxc_kokkos.cpp
M		src/KOKKOS/pair_vashishta_kokkos.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_cut_coul_long.cpp
M		src/KSPACE/pair_lj_long_coul_long.cpp
M		src/KSPACE/pppm.cpp
M		src/KSPACE/pppm_disp.cpp
M		src/KSPACE/pppm_tip4p.cpp
M		src/KSPACE/pppm_tip4p.h
M		src/MANYBODY/pair_airebo.cpp
M		src/MANYBODY/pair_airebo.h
M		src/MANYBODY/pair_eam.cpp
M		src/MANYBODY/pair_eam_alloy.cpp
M		src/MANYBODY/pair_eam_fs.cpp
M		src/MC/fix_gcmc.cpp
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/pair_lj_cut_tip4p_cut.cpp
D		src/Make.py
M		src/Makefile
M		src/PERI/fix_peri_neigh.cpp
M		src/PERI/pair_peri_eps.cpp
M		src/PERI/pair_peri_lps.cpp
M		src/RIGID/fix_rigid.cpp
M		src/RIGID/fix_rigid_small.cpp
M		src/RIGID/fix_shake.cpp
M		src/SHOCK/fix_msst.cpp
M		src/SHOCK/fix_msst.h
M		src/SNAP/pair_snap.cpp
M		src/USER-CGSDK/pair_lj_sdk.cpp
M		src/USER-CGSDK/pair_lj_sdk_coul_long.cpp
M		src/USER-COLVARS/colvarproxy_lammps.cpp
M		src/USER-COLVARS/colvarproxy_lammps.h
A		src/USER-COLVARS/colvarproxy_lammps_version.h
M		src/USER-DRUDE/pair_lj_cut_thole_long.cpp
M		src/USER-FEP/pair_lj_charmm_coul_long_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-INTEL/fix_intel.cpp
M		src/USER-INTEL/intel_buffers.h
M		src/USER-INTEL/intel_preprocess.h
M		src/USER-INTEL/pppm_disp_intel.cpp
M		src/USER-INTEL/pppm_intel.cpp
M		src/USER-INTEL/pppm_intel.h
M		src/USER-MANIFOLD/manifold_gaussian_bump.cpp
M		src/USER-MANIFOLD/manifold_gaussian_bump.h
A	(dir)	src/USER-MEAMC/
A		src/USER-MEAMC/README
A		src/USER-MEAMC/meam.h
A		src/USER-MEAMC/meam_dens_final.cpp
A		src/USER-MEAMC/meam_dens_init.cpp
A		src/USER-MEAMC/meam_force.cpp
A		src/USER-MEAMC/meam_funcs.cpp
A		src/USER-MEAMC/meam_impl.cpp
A		src/USER-MEAMC/meam_setup_done.cpp
A		src/USER-MEAMC/meam_setup_global.cpp
A		src/USER-MEAMC/meam_setup_param.cpp
A		src/USER-MEAMC/pair_meamc.cpp
A		src/USER-MEAMC/pair_meamc.h
M		src/USER-MISC/README
A		src/USER-MISC/fix_wall_ees.cpp
A		src/USER-MISC/fix_wall_ees.h
A		src/USER-MISC/fix_wall_region_ees.cpp
P		src/USER-MISC/fix_wall_region_ees.h Copied from src/fix_external.h
M		src/USER-MISC/pair_buck_mdf.cpp
M		src/USER-MISC/pair_coul_diel.cpp
M		src/USER-MISC/pair_gauss_cut.cpp
M		src/USER-MISC/pair_kolmogorov_crespi_z.cpp
M		src/USER-MISC/pair_list.cpp
M		src/USER-MISC/pair_morse_smooth_linear.cpp
M		src/USER-OMP/fix_nphug_omp.cpp
M		src/USER-OMP/fix_qeq_comb_omp.cpp
M		src/USER-OMP/fix_qeq_reax_omp.cpp
M		src/USER-OMP/fix_qeq_reax_omp.h
M		src/USER-OMP/pair_agni_omp.cpp
M		src/USER-OMP/pair_airebo_omp.cpp
M		src/USER-OMP/pair_peri_lps_omp.cpp
M		src/USER-OMP/pair_reaxc_omp.cpp
M		src/USER-OMP/pair_reaxc_omp.h
M		src/USER-OMP/pppm_cg_omp.cpp
M		src/USER-OMP/pppm_cg_omp.h
M		src/USER-OMP/pppm_disp_omp.cpp
M		src/USER-OMP/pppm_disp_omp.h
M		src/USER-OMP/pppm_disp_tip4p_omp.cpp
M		src/USER-OMP/pppm_disp_tip4p_omp.h
M		src/USER-OMP/pppm_omp.cpp
M		src/USER-OMP/pppm_omp.h
M		src/USER-OMP/pppm_tip4p_omp.cpp
M		src/USER-OMP/pppm_tip4p_omp.h
M		src/USER-OMP/reaxc_bond_orders_omp.cpp
M		src/USER-OMP/reaxc_bond_orders_omp.h
M		src/USER-OMP/reaxc_bonds_omp.cpp
M		src/USER-OMP/reaxc_bonds_omp.h
M		src/USER-OMP/reaxc_forces_omp.cpp
M		src/USER-OMP/reaxc_forces_omp.h
M		src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp
M		src/USER-OMP/reaxc_hydrogen_bonds_omp.h
M		src/USER-OMP/reaxc_init_md_omp.cpp
M		src/USER-OMP/reaxc_init_md_omp.h
M		src/USER-OMP/reaxc_multi_body_omp.cpp
M		src/USER-OMP/reaxc_multi_body_omp.h
M		src/USER-OMP/reaxc_nonbonded_omp.cpp
M		src/USER-OMP/reaxc_nonbonded_omp.h
M		src/USER-OMP/reaxc_torsion_angles_omp.cpp
M		src/USER-OMP/reaxc_torsion_angles_omp.h
M		src/USER-OMP/reaxc_valence_angles_omp.cpp
M		src/USER-OMP/reaxc_valence_angles_omp.h
M		src/USER-OMP/thr_data.cpp
M		src/USER-QUIP/pair_quip.cpp
M		src/USER-QUIP/pair_quip.h
M		src/USER-REAXC/fix_reaxc_species.cpp
M		src/USER-REAXC/pair_reaxc.cpp
M		src/USER-REAXC/reaxc_allocate.cpp
M		src/USER-REAXC/reaxc_bonds.cpp
M		src/USER-REAXC/reaxc_ffield.cpp
M		src/USER-REAXC/reaxc_list.cpp
M		src/USER-REAXC/reaxc_types.h
M		src/USER-TALLY/compute_force_tally.cpp
M		src/USER-TALLY/compute_heat_flux_tally.cpp
M		src/USER-TALLY/compute_pe_tally.cpp
M		src/USER-TALLY/compute_stress_tally.cpp
M		src/atom.cpp
M		src/comm_brick.cpp
M		src/compute_rdf.cpp
M		src/compute_rdf.h
M		src/create_bonds.cpp
M		src/create_bonds.h
M		src/dump_local.cpp
M		src/fix.cpp
M		src/fix_enforce2d.cpp
M		src/fix_external.cpp
P		src/fix_external.h Copied to src/USER-MISC/fix_wall_region_ees.h
M		src/info.cpp
M		src/main.cpp
M		src/math_special.cpp
M		src/math_special.h
M		src/modify.cpp
M		src/molecule.cpp
M		src/neighbor.cpp
M		src/pair.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_lj96_cut.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_mie_cut.cpp
M		src/pair_table.cpp
M		src/pair_yukawa.cpp
M		src/read_data.cpp
M		src/read_data.h
M		src/version.h
M		tools/Makefile