Diffusion lammps de2730522733

lammps into USER-DPD_kokkos
de2730522733
Actions

Authored by Stan Moore <stamoor@sandia.gov> on Mar 7 2017, 19:47.

Description

Merge branch 'master' of https://github.com/lammps/lammps into USER-DPD_kokkos

Details

Committed

Stan Moore <stamoor@sandia.gov>

Mar 7 2017, 19:47

Pushed

junge

Oct 19 2017, 09:53

Parents

rLAMMPS5b3101cb346f: Merge pull request #16 from ibaned/cuda-runtime
rLAMMPS79b005dc3d5f: patch 7Mar17

Branches

Unknown

Tags

Unknown

Event Timeline

Stan Moore <stamoor@sandia.gov> committed rLAMMPSde2730522733: Merge branch 'master' of https://github.com/lammps/lammps into USER-DPD_kokkos (authored by Stan Moore <stamoor@sandia.gov>).Mar 7 2017, 19:47

Merged Changes

Commit	Author	Details	Committed
79b005dc3d5f	Steve Plimpton	patch 7Mar17	Mar 7 2017
a2fa6ef4524c	sjplimp/GitHub	Merge pull request #393 from akohlmey/small-bugfixes	Mar 7 2017
920641bbffbc	sjplimp/GitHub	Merge pull request #399 from rbberger/docs_spelling_fixes	Mar 7 2017
c2aabdec229c	sjplimp/GitHub	Merge pull request #398 from stanmoore1/kokkos_changes	Mar 7 2017
e4aa735a6809	sjplimp/GitHub	Merge pull request #395 from timattox/USER-DPD_bugfix	Mar 7 2017
4af6557568e7	sjplimp/GitHub	Merge pull request #394 from jaapkroe/kolmogorov-crespi	Mar 7 2017
0798885bdb2a	sjplimp/GitHub	Merge pull request #389 from akohlmey/update-agni-potential	Mar 7 2017
020e75e7efff	sjplimp/GitHub	Merge pull request #386 from akohlmey/doc-consistentcy	Mar 7 2017
d6866f1cfdd7	sjplimp/GitHub	Merge pull request #376 from v0i0/airebo-bondorderLJ-fixes	Mar 7 2017
efaa4c67109f	Steve Plimpton	new neigh_modify exclude option, other SNAP changes	Mar 7 2017
08baaa9d8ede	Richard Berger	Fix more typos in tools	Mar 7 2017
359af419a7ab	Richard Berger	Fix typo in python README	Mar 7 2017
21be86c42393	Richard Berger	Fix typos in txt2html	Mar 7 2017
d6800405a518	Richard Berger	Fix more typos in examples	Mar 7 2017
3a054d1a82b2	Richard Berger	Fix more typos in src files	Mar 7 2017
007f3c66a033	Richard Berger	Third batch of spelling fixes in manual	Mar 7 2017
32708860a9fa	Richard Berger	Add remaining false positives	Mar 7 2017
fc9eebb9367c	Richard Berger	Added spellcheck utility to documentation build	Mar 6 2017
dd76ac5010ae	Richard Berger	Fix typos in tools folder	Mar 6 2017
17486a9319f8	Richard Berger	Convert USER/lb/polymer files to UNIX line endings and remove trailing…	Mar 6 2017
778a79b8eef7	Richard Berger	Fix typos in examples folder	Mar 6 2017
7dd60f97377a	Richard Berger	Fix typos in src files	Mar 6 2017
084d831bce01	Richard Berger	Second batch of spelling fixes in manual	Mar 6 2017
e261bef7bba7	Richard Berger	Spelling fixes in source files	Mar 6 2017
fd78486086d9	Richard Berger	First batch of spelling fixes in manual	Mar 6 2017
6382d3c89a2f	Stan Moore	Improving memory access in comm_kokkos	Mar 3 2017
ce1a3f25e193	Axel Kohlmeyer	Merge branch 'pair_write_fix' of https://github.com/andeplane/lammps into small…	Mar 3 2017
eaf7ed770750	Anders Hafreager	Print error if pair_write does not get correct number of arguments	Mar 3 2017
8a0e44db83de	Jaap Kroes	updated documentation and ev_tally	Mar 1 2017
3ac74a1d6995	Axel Kohlmeyer	update lammps.book file for latest doc changes	Feb 28 2017
3605208a45bb	Axel Kohlmeyer	add a few more missing details for integrating pair style kolmogorov/crespi/z	Feb 28 2017
9b01949cacfc	Axel Kohlmeyer	make the introduction of the command-by-category list less confusing	Feb 28 2017
323570c92036	Jaap Kroes	added jpg for kolmogorov-crespi-z equations and fixed hybrid/overlay check in…	Feb 28 2017
df13a7a00382	Jaap Kroes	email added	Feb 28 2017
a1b40b902d3e	Jaap Kroes	Added Kolmogorov-Crespi potential	Feb 28 2017
b921b69f4792	Axel Kohlmeyer	implement bugfix from issue #388	Feb 28 2017
c0cf50bce551	Axel Kohlmeyer	trigger recomputing ichunk between runs unless requested otherwise	Feb 28 2017
2708c8683626	Axel Kohlmeyer	fix typos: moleclue -> molecule	Feb 28 2017
9999f363a1f8	Axel Kohlmeyer	remove outdated log files, too.	Feb 24 2017
a18b4ef4b0cf	Axel Kohlmeyer	update AGNI potential for Al, reference runs and output and citation	Feb 24 2017
20a9ffe69dfd	Axel Kohlmeyer	improve consistency and resolve dead links for USER-CGDNA related doc files	Feb 22 2017
904609a7a3a5	Markus Hoehnerbach	Fixed issue with switching function derivative in PairAIREBO::FLJ	Feb 15 2017
fc3505fac47d	Markus Hoehnerbach	Fixed a number of issues after verifying against the KIM version	Feb 15 2017
a323ca1edd79	Markus Hoehnerbach	Moved variable declarations to front for consistency	Feb 13 2017
de4af6f15d6a	Markus Hoehnerbach	In PairAIREBO::bondorderLJ correct omega sum d/drij.	Feb 13 2017
0e16dc3ead0b	Markus Hoehnerbach	In PairAIREBO::bondorderLJ: p^sigma pi account for d/drij derivatives.	Feb 13 2017
1b3f6e257a88	Markus Hoehnerbach	In PairAIREBO::bondorderLJ only compute torsion term once.	Feb 13 2017

Changes (473)

		Path
M		bench/FERMI/README
M		doc/.gitignore
M		doc/Makefile
M		doc/src/2001/input_commands.html
M		doc/src/99/basics.html
M		doc/src/99/crib.html
M		doc/src/99/input_commands.html
A		doc/src/Eqs/pair_kolmogorov_crespi_z.jpg
A		doc/src/Eqs/pair_kolmogorov_crespi_z.tex
M		doc/src/Manual.txt
M		doc/src/Section_commands.txt
M		doc/src/Section_errors.txt
M		doc/src/Section_history.txt
M		doc/src/Section_howto.txt
M		doc/src/Section_modify.txt
M		doc/src/Section_packages.txt
M		doc/src/Section_perf.txt
M		doc/src/Section_python.txt
M		doc/src/Section_start.txt
M		doc/src/Section_tools.txt
M		doc/src/USER/atc/man_consistent_fe_initialization.html
M		doc/src/accelerate_intel.txt
M		doc/src/accelerate_kokkos.txt
M		doc/src/angle_hybrid.txt
M		doc/src/atom_modify.txt
M		doc/src/atom_style.txt
M		doc/src/balance.txt
M		doc/src/body.txt
M		doc/src/bond_hybrid.txt
V		doc/src/{bond_oxdna.txt ← bond_oxdna_fene.txt}
V		doc/src/{bond_oxdna_fene.txt → bond_oxdna.txt}
M		doc/src/bonds.txt
M		doc/src/change_box.txt
M		doc/src/comm_style.txt
M		doc/src/compute.txt
M		doc/src/compute_angmom_chunk.txt
M		doc/src/compute_centro_atom.txt
M		doc/src/compute_chunk_atom.txt
M		doc/src/compute_cna_atom.txt
M		doc/src/compute_com.txt
M		doc/src/compute_coord_atom.txt
M		doc/src/compute_damage_atom.txt
M		doc/src/compute_dilatation_atom.txt
M		doc/src/compute_displace_atom.txt
M		doc/src/compute_event_displace.txt
M		doc/src/compute_global_atom.txt
M		doc/src/compute_heat_flux.txt
M		doc/src/compute_inertia_chunk.txt
M		doc/src/compute_msd.txt
M		doc/src/compute_msd_chunk.txt
M		doc/src/compute_msd_nongauss.txt
M		doc/src/compute_pair.txt
M		doc/src/compute_pair_local.txt
M		doc/src/compute_pe_atom.txt
M		doc/src/compute_plasticity_atom.txt
M		doc/src/compute_pressure.txt
M		doc/src/compute_property_chunk.txt
M		doc/src/compute_rdf.txt
M		doc/src/compute_rigid_local.txt
M		doc/src/compute_saed.txt
M		doc/src/compute_smd_ulsph_num_neighs.txt
M		doc/src/compute_stress_atom.txt
M		doc/src/compute_temp_asphere.txt
M		doc/src/compute_temp_body.txt
M		doc/src/compute_temp_chunk.txt
M		doc/src/compute_temp_profile.txt
M		doc/src/compute_vacf.txt
M		doc/src/compute_voronoi_atom.txt
M		doc/src/create_atoms.txt
M		doc/src/dihedral_hybrid.txt
M		doc/src/dump.txt
M		doc/src/dump_custom_vtk.txt
M		doc/src/dump_image.txt
M		doc/src/dump_modify.txt
M		doc/src/fix_ave_chunk.txt
M		doc/src/fix_ave_correlate.txt
M		doc/src/fix_ave_time.txt
M		doc/src/fix_balance.txt
M		doc/src/fix_bond_break.txt
M		doc/src/fix_bond_create.txt
M		doc/src/fix_bond_swap.txt
M		doc/src/fix_box_relax.txt
M		doc/src/fix_cmap.txt
M		doc/src/fix_colvars.txt
M		doc/src/fix_controller.txt
M		doc/src/fix_deform.txt
M		doc/src/fix_deposit.txt
M		doc/src/fix_eos_table.txt
M		doc/src/fix_eos_table_rx.txt
M		doc/src/fix_evaporate.txt
M		doc/src/fix_gle.txt
M		doc/src/fix_gravity.txt
M		doc/src/fix_indent.txt
M		doc/src/fix_langevin.txt
M		doc/src/fix_langevin_eff.txt
M		doc/src/fix_lb_fluid.txt
M		doc/src/fix_modify.txt
M		doc/src/fix_move.txt
M		doc/src/fix_mscg.txt
M		doc/src/fix_nph_asphere.txt
M		doc/src/fix_nph_body.txt
M		doc/src/fix_npt_asphere.txt
M		doc/src/fix_npt_body.txt
M		doc/src/fix_nve_asphere.txt
M		doc/src/fix_nve_asphere_noforce.txt
M		doc/src/fix_nve_body.txt
M		doc/src/fix_nve_limit.txt
M		doc/src/fix_nvt_asphere.txt
M		doc/src/fix_nvt_body.txt
M		doc/src/fix_nvt_sllod_eff.txt
M		doc/src/fix_orient.txt
M		doc/src/fix_phonon.txt
M		doc/src/fix_pour.txt
M		doc/src/fix_property_atom.txt
M		doc/src/fix_qeq.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_restrain.txt
M		doc/src/fix_rigid.txt
M		doc/src/fix_rx.txt
M		doc/src/fix_saed_vtk.txt
M		doc/src/fix_shake.txt
M		doc/src/fix_smd_wall_surface.txt
M		doc/src/fix_spring_self.txt
M		doc/src/fix_srd.txt
M		doc/src/fix_temp_berendsen.txt
M		doc/src/fix_temp_csvr.txt
M		doc/src/fix_temp_rescale.txt
M		doc/src/fix_temp_rescale_eff.txt
M		doc/src/fix_tfmc.txt
M		doc/src/fix_thermal_conductivity.txt
M		doc/src/fix_ttm.txt
M		doc/src/fix_vector.txt
M		doc/src/fix_viscosity.txt
M		doc/src/fix_wall.txt
M		doc/src/fix_wall_gran.txt
M		doc/src/fix_wall_gran_region.txt
M		doc/src/fix_wall_piston.txt
M		doc/src/group.txt
M		doc/src/if.txt
M		doc/src/improper_hybrid.txt
M		doc/src/improper_ring.txt
M		doc/src/info.txt
M		doc/src/jump.txt
M		doc/src/kspace_modify.txt
M		doc/src/kspace_style.txt
M		doc/src/lammps.book
M		doc/src/minimize.txt
M		doc/src/molecule.txt
M		doc/src/neb.txt
M		doc/src/neigh_modify.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_body.txt
M		doc/src/pair_bop.txt
M		doc/src/pair_comb.txt
M		doc/src/pair_coul.txt
M		doc/src/pair_coul_diel.txt
M		doc/src/pair_dpd.txt
M		doc/src/pair_eam.txt
M		doc/src/pair_edip.txt
M		doc/src/pair_eff.txt
M		doc/src/pair_eim.txt
M		doc/src/pair_exp6_rx.txt
M		doc/src/pair_gran.txt
M		doc/src/pair_hbond_dreiding.txt
M		doc/src/pair_hybrid.txt
M		doc/src/pair_kim.txt
A		doc/src/pair_kolmogorov_crespi_z.txt
M		doc/src/pair_line_lj.txt
M		doc/src/pair_lj.txt
M		doc/src/pair_lj_long.txt
M		doc/src/pair_lj_smooth.txt
M		doc/src/pair_lj_soft.txt
M		doc/src/pair_lubricate.txt
M		doc/src/pair_meam_spline.txt
M		doc/src/pair_mgpt.txt
M		doc/src/pair_mie.txt
M		doc/src/pair_morse.txt
V		doc/src/{pair_oxdna.txt ← pair_oxdna_excv.txt}
V		doc/src/{pair_oxdna_excv.txt → pair_oxdna.txt}
M		doc/src/pair_peri.txt
M		doc/src/pair_quip.txt
M		doc/src/pair_resquared.txt
M		doc/src/pair_smd_ulsph.txt
M		doc/src/pair_smtbq.txt
M		doc/src/pair_soft.txt
M		doc/src/pair_sph_heatconduction.txt
M		doc/src/pair_sph_idealgas.txt
M		doc/src/pair_sph_lj.txt
M		doc/src/pair_sph_taitwater.txt
M		doc/src/pair_srp.txt
M		doc/src/pair_table.txt
M		doc/src/pair_tri_lj.txt
M		doc/src/pairs.txt
M		doc/src/partition.txt
M		doc/src/prd.txt
M		doc/src/processors.txt
M		doc/src/python.txt
M		doc/src/read_data.txt
M		doc/src/read_dump.txt
M		doc/src/read_restart.txt
M		doc/src/region.txt
M		doc/src/replicate.txt
M		doc/src/rerun.txt
M		doc/src/restart.txt
M		doc/src/run_style.txt
M		doc/src/set.txt
M		doc/src/suffix.txt
M		doc/src/tad.txt
M		doc/src/thermo.txt
M		doc/src/thermo_style.txt
M		doc/src/timer.txt
M		doc/src/tutorial_drude.txt
M		doc/src/tutorial_pylammps.txt
M		doc/src/units.txt
M		doc/src/variable.txt
M		doc/src/write_dump.txt
M		doc/utils/sphinx-config/conf.py
A		doc/utils/sphinx-config/false_positives.txt
M		doc/utils/txt2html/README.html
M		doc/utils/txt2html/txt2html.cpp
M		examples/KAPPA/README
M		examples/README
M		examples/USER/atc/README
M		examples/USER/atc/fluids/in.bar1d_fluids
M		examples/USER/atc/thermal/in.bar1d
M		examples/USER/atc/thermal/in.bar1d_all_atoms
M		examples/USER/atc/thermal/in.bar1d_combined
M		examples/USER/atc/thermal/in.bar1d_flux
M		examples/USER/atc/thermal/in.bar1d_frac_step
M		examples/USER/atc/thermal/in.bar1d_hoover
M		examples/USER/atc/thermal/in.bar1d_interpolate
M		examples/USER/atc/thermal/in.bar1d_lumped
M		examples/USER/lb/confined_colloid/in.confined_colloids
M		examples/USER/lb/microrheology/in.microrheology_default_gamma
M		examples/USER/lb/microrheology/in.microrheology_set_gamma
M		examples/USER/lb/planewall/in.planewall_default_gamma
M		examples/USER/lb/planewall/in.planewall_set_gamma
M		examples/USER/lb/polymer/data.polymer
M		examples/USER/lb/polymer/in.polymer_default_gamma
M		examples/USER/lb/polymer/in.polymer_setgamma
A		examples/USER/misc/agni/Al_jpc.agni
D		examples/USER/misc/agni/Al_prb.agni
M		examples/USER/misc/agni/in.adatom
M		examples/USER/misc/agni/in.vacancy
A		examples/USER/misc/agni/log.21Feb17.adatom.g++.1
A		examples/USER/misc/agni/log.21Feb17.adatom.g++.4
A		examples/USER/misc/agni/log.21Feb17.vacancy.g++.1
A		examples/USER/misc/agni/log.21Feb17.vacancy.g++.4
D		examples/USER/misc/agni/log.9Nov16.adatom.g++.1
D		examples/USER/misc/agni/log.9Nov16.adatom.g++.4
D		examples/USER/misc/agni/log.9Nov16.vacancy.g++.1
D		examples/USER/misc/agni/log.9Nov16.vacancy.g++.4
M		examples/USER/misc/gauss-diel/in.gauss-diel
M		examples/USER/misc/gauss-diel/in.gauss-diel-cg
M		examples/USER/misc/gauss-diel/in.gauss-diel-split
A	(dir)	examples/USER/misc/kolmogorov-crespi/
A		examples/USER/misc/kolmogorov-crespi/data.bilayer-graphene
A		examples/USER/misc/kolmogorov-crespi/data.graphene-adsorbant
A		examples/USER/misc/kolmogorov-crespi/in.atom-diffusion
A		examples/USER/misc/kolmogorov-crespi/in.bilayer-graphene
A		examples/USER/misc/kolmogorov-crespi/log.atom-diffusion
A		examples/USER/misc/kolmogorov-crespi/log.bilayer-graphene
M		examples/USER/misc/srp/in.srp
M		examples/USER/phonon/3-3D-FCC-Cu-EAM/README
M		examples/USER/phonon/4-Graphene/README
M		examples/USER/tally/README
M		examples/VISCOSITY/README
M		examples/accelerate/README
M		examples/rigid/in.rigid.tnr
P		examples/snap/Ta06A.snap Copied from potentials/Ta06A_pot.snap
D		examples/snap/Ta06A_pot.snap
V		examples/snap/{W.SNAP_HePair.pot → W_2940_2017_2_He_JW2013.snap}
V		examples/snap/{W_2940_2017_2.pot.snap → W_2940_2017_2.snap}
V		examples/snap/{W_2940_2017_2.snap ← W_2940_2017_2.pot.snap}
M		examples/snap/W_2940_2017_2.snapcoeff
M		examples/snap/W_2940_2017_2.snapparam
V		examples/snap/{W_2940_2017_2_He_JW2013.snap ← W.SNAP_HePair.pot}
M		examples/snap/in.snap.Ta06A
M		examples/snap/in.snap.W.2940
M		examples/snap/in.snap.hybrid.WSNAP.HePair
M		lib/atc/LinearSolver.cpp
A		potentials/Al_jpc.agni
M		potentials/Al_prb.agni
A		potentials/CC.KC
V		potentials/{Ta06A.snap ← Ta06A_pot.snap}
P		potentials/Ta06A_pot.snap Deleted after being copied to multiple locations: examples/snap/Ta06A.snap potentials/Ta06A.snap
V		potentials/{W.SNAP_HePair.pot → W_2940_2017_2_He_JW2013.snap}
V		potentials/{W_2940_2017_2.pot.snap → W_2940_2017_2.snap}
V		potentials/{W_2940_2017_2.snap ← W_2940_2017_2.pot.snap}
M		potentials/W_2940_2017_2.snapcoeff
M		potentials/W_2940_2017_2.snapparam
V		potentials/{W_2940_2017_2_He_JW2013.snap ← W.SNAP_HePair.pot}
M		python/README
M		python/examples/demo.py
M		python/examples/gui.py
M		python/examples/mc.py
M		python/examples/plot.py
M		python/examples/simple.py
M		python/examples/split.py
M		python/examples/trivial.py
M		python/examples/viz_atomeye.py
M		python/examples/viz_gl.py
M		python/examples/viz_pymol.py
M		python/examples/viz_vmd.py
M		python/examples/vizplotgui_atomeye.py
M		python/examples/vizplotgui_gl.py
M		python/examples/vizplotgui_pymol.py
M		python/examples/vizplotgui_vmd.py
M		src/ASPHERE/compute_erotate_asphere.h
M		src/ASPHERE/compute_temp_asphere.h
M		src/COLLOID/pair_lubricateU.cpp
M		src/COLLOID/pair_lubricateU_poly.cpp
M		src/COLLOID/pair_yukawa_colloid.h
M		src/DEPEND/fastdep.c
M		src/GPU/README
M		src/GPU/pair_born_gpu.h
M		src/GPU/pair_zbl_gpu.h
M		src/KIM/README
M		src/KIM/pair_kim.h
M		src/KOKKOS/comm_kokkos.cpp
M		src/KOKKOS/comm_kokkos.h
M		src/KOKKOS/neighbor_kokkos.cpp
M		src/KOKKOS/neighbor_kokkos.h
M		src/KOKKOS/npair_kokkos.cpp
M		src/KOKKOS/npair_kokkos.h
M		src/KOKKOS/pair_reax_c_kokkos.cpp
M		src/KSPACE/pair_buck_long_coul_long.h
M		src/KSPACE/pppm_disp.h
M		src/MAKE/OPTIONS/Makefile.omp
M		src/MANYBODY/pair_airebo.cpp
M		src/MANYBODY/pair_bop.h
M		src/MISC/fix_ttm.h
M		src/PYTHON/python.cpp
M		src/PYTHON/python.h
M		src/REAX/fix_reax_bonds.h
M		src/REPLICA/neb.h
M		src/REPLICA/prd.h
M		src/REPLICA/tad.h
M		src/REPLICA/temper.h
M		src/RIGID/fix_rigid_small.cpp
M		src/RIGID/fix_shake.cpp
M		src/RIGID/fix_shake.h
M		src/SHOCK/fix_append_atoms.h
M		src/SNAP/pair_snap.cpp
M		src/SNAP/sna.cpp
M		src/SRD/fix_srd.cpp
M		src/SRD/fix_srd.h
M		src/USER-AWPMD/atom_vec_wavepacket.h
M		src/USER-DIFFRACTION/fix_saed_vtk.h
M		src/USER-DPD/fix_eos_table_rx.h
M		src/USER-DPD/pair_exp6_rx.cpp
M		src/USER-LB/fix_lb_fluid.cpp
M		src/USER-MANIFOLD/README
M		src/USER-MANIFOLD/fix_manifoldforce.cpp
M		src/USER-MANIFOLD/manifold.h
M		src/USER-MISC/README
M		src/USER-MISC/fix_grem.h
M		src/USER-MISC/fix_imd.cpp
M		src/USER-MISC/improper_ring.cpp
M		src/USER-MISC/pair_agni.cpp
M		src/USER-MISC/pair_edip.cpp
M		src/USER-MISC/pair_edip.h
A		src/USER-MISC/pair_kolmogorov_crespi_z.cpp
A		src/USER-MISC/pair_kolmogorov_crespi_z.h
M		src/USER-MISC/temper_grem.h
M		src/USER-MOLFILE/molfile_interface.cpp
M		src/USER-OMP/pair_buck_long_coul_long_omp.h
M		src/USER-OMP/thr_data.cpp
M		src/USER-QTB/fix_qbmsst.h
M		src/USER-REAXC/README
M		src/USER-REAXC/reaxc_nonbonded.cpp
M		src/USER-SMD/pair_smd_triangulated_surface.cpp
M		src/USER-SMTBQ/pair_smtbq.cpp
M		src/USER-VTK/dump_custom_vtk.h
M		src/angle.h
M		src/atom.cpp
M		src/atom.h
M		src/atom_vec_hybrid.cpp
M		src/atom_vec_tri.h
M		src/balance.cpp
M		src/balance.h
M		src/bond.h
M		src/citeme.h
M		src/compute_angle.h
M		src/compute_bond.h
M		src/compute_chunk_atom.cpp
M		src/compute_chunk_atom.h
M		src/compute_cna_atom.h
M		src/compute_contact_atom.h
M		src/compute_coord_atom.h
M		src/compute_dihedral.h
M		src/compute_group_group.h
M		src/compute_hexorder_atom.h
M		src/compute_improper.h
M		src/compute_orientorder_atom.h
M		src/compute_pair.h
M		src/compute_property_chunk.h
M		src/compute_property_local.h
M		src/create_atoms.cpp
M		src/create_atoms.h
M		src/dihedral.h
M		src/domain.cpp
M		src/dump_custom.h
M		src/dump_local.h
M		src/fix.h
M		src/fix_addforce.h
M		src/fix_ave_chunk.h
M		src/fix_ave_histo_weight.cpp
M		src/fix_ave_time.h
M		src/fix_balance.cpp
M		src/fix_deform.h
M		src/fix_group.h
M		src/fix_langevin.h
M		src/fix_shear_history.cpp
M		src/improper.h
M		src/kspace.h
M		src/library.cpp
M		src/lmptype.h
M		src/molecule.cpp
M		src/molecule.h
M		src/neighbor.cpp
M		src/neighbor.h
M		src/npair.cpp
M		src/npair.h
M		src/output.h
M		src/pair.cpp
M		src/pair_gauss.cpp
M		src/procmap.cpp
M		src/region_block.cpp
M		src/region_cylinder.h
M		src/region_sphere.h
M		src/rerun.cpp
M		src/run.h
M		src/thermo.cpp
M		src/thermo.h
M		src/variable.cpp
M		src/variable.h
M		src/version.h
M		tools/eff/cfg2lammps.py
M		tools/i-pi/drivers/driver.f90
M		tools/i-pi/ipi/engine/atoms.py
M		tools/i-pi/ipi/engine/initializer.py
M		tools/i-pi/ipi/engine/properties.py
M		tools/i-pi/ipi/engine/simulation.py
M		tools/i-pi/ipi/engine/thermostats.py
M		tools/i-pi/ipi/interfaces/sockets.py
M		tools/i-pi/ipi/utils/depend.py
M		tools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/README.TXT
M		tools/moltemplate/src/bonds_by_type.py
M		tools/moltemplate/src/chargepairs_by_type.py
M		tools/moltemplate/src/dump2data.py
M		tools/moltemplate/src/lttree.py
M		tools/moltemplate/src/moltemplate.sh
M		tools/moltemplate/src/moltemplate_force_fields/amber/amberparm2lt.sh
M		tools/moltemplate/src/moltemplate_force_fields/gaff.lt
M		tools/moltemplate/src/moltemplate_force_fields/oplsaa/README.TXT
M		tools/moltemplate/src/moltemplate_scripts_depreciated/oplsaa_moltemplate.py
M		tools/moltemplate/src/nbody_by_type.py
M		tools/moltemplate/src/ttree.py
M		tools/moltemplate/src/ttree_lex.py
M		tools/msi2lmp/frc_files/cvff_aug.frc
M		tools/msi2lmp/frc_files/pcff.frc
M		tools/msi2lmp/src/msi2lmp.h
M		tools/phonon/dynmat.cpp
M		tools/pymol_asphere/src/cartesian.cpp
M		tools/pymol_asphere/src/cartesian.h
M		tools/python/pizza/dump.py