Diffusion lammps addd87c0f7a4

new Section package and start doc pages and build scripts
addd87c0f7a4
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Authored by Steve Plimpton <sjplimp@sandia.gov> on May 4 2017, 19:22.

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new Section package and start doc pages and build scripts

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Committed

Steve Plimpton <sjplimp@sandia.gov>

May 4 2017, 19:22

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Oct 19 2017, 09:53

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rLAMMPSf5cf1f1314b0: Merge pull request #464 from akohlmey/rename-cg-cmm-to-cgsdk

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Steve Plimpton <sjplimp@sandia.gov> committed rLAMMPSaddd87c0f7a4: new Section package and start doc pages and build scripts (authored by Steve Plimpton <sjplimp@sandia.gov>).May 4 2017, 19:22

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				Path
	M			doc/src/Manual.txt
	M			doc/src/Section_commands.txt
	M			doc/src/Section_intro.txt
	M			doc/src/Section_packages.txt
	M			doc/src/Section_start.txt
	M			doc/src/compute_sna_atom.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_cmap.txt
	M			doc/src/fix_gcmc.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/lammps.book
	M			doc/src/pair_hybrid.txt
	M			doc/src/pair_reax.txt
	V			doc/src/{pair_reax_c.txt → pair_reaxc.txt}
	V			doc/src/{pair_reaxc.txt ← pair_reax_c.txt}
	M			doc/src/pairs.txt
	V		(dir)	examples/USER/{flow_gauss/ → misc/flow_gauss}
	V			examples/USER/{ → misc}/flow_gauss/README
	V			examples/USER/{ → misc}/flow_gauss/in.GD
	V		(dir)	examples/USER/{misc/flow_gauss/ ← flow_gauss}
	V			examples/USER/{misc ← }/flow_gauss/README
	V			examples/USER/{misc ← }/flow_gauss/in.GD
	A			examples/mscg/log.31Mar17.g++.1
	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/README
	A			lib/h5md/Install.py
	V			lib/h5md/{Makefile → Makefile.h5cc}
	V			lib/h5md/{Makefile.h5cc ← Makefile}
	M			lib/h5md/README
	A			lib/linalg/Install.py
	M			lib/linalg/README
	A			lib/meam/Install.py
	M			lib/meam/README
	A			lib/mscg/Install.py
	M			lib/mscg/Makefile.lammps
	M			lib/mscg/README
	M			lib/netcdf/README
	A			lib/poems/Install.py
	M			lib/poems/README
	A			lib/qmmm/Install.py
	M			lib/qmmm/README
	A			lib/reax/Install.py
	M			lib/reax/README
	A			lib/smd/Install.py
	M			lib/smd/README
	M			lib/voronoi/Install.py
	M			lib/voronoi/README
	M			lib/vtk/Makefile.lammps
	M			lib/vtk/README
	M			src/KOKKOS/pair_reax_c_kokkos.cpp
	M			src/KSPACE/pair_lj_charmmfsw_coul_long.cpp
	M			src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp
	M			src/Makefile
	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
	D			src/USER-NC-DUMP
	V			src/{USER-NC-DUMP → USER-NETCDF}/Install.sh
	V			src/{USER-NC-DUMP → USER-NETCDF}/README
	V			src/{USER-NC-DUMP/dump_nc.cpp → USER-NETCDF/dump_netcdf.cpp}
	V			src/{USER-NC-DUMP/dump_nc.h → USER-NETCDF/dump_netcdf.h}
	V			src/{USER-NC-DUMP/dump_nc_mpiio.cpp → USER-NETCDF/dump_netcdf_mpiio.cpp}
	V			src/{USER-NC-DUMP/dump_nc_mpiio.h → USER-NETCDF/dump_netcdf_mpiio.h}
	A		(dir)	src/USER-NETCDF/
	V			src/{USER-NETCDF ← USER-NC-DUMP}/Install.sh
	V			src/{USER-NETCDF ← USER-NC-DUMP}/README
	V			src/{USER-NETCDF/dump_netcdf.cpp ← USER-NC-DUMP/dump_nc.cpp}
	V			src/{USER-NETCDF/dump_netcdf.h ← USER-NC-DUMP/dump_nc.h}
	V			src/{USER-NETCDF/dump_netcdf_mpiio.cpp ← USER-NC-DUMP/dump_nc_mpiio.cpp}
	V			src/{USER-NETCDF/dump_netcdf_mpiio.h ← USER-NC-DUMP/dump_nc_mpiio.h}
	M			src/USER-REAXC/compute_spec_atom.cpp
	M			src/USER-REAXC/fix_qeq_reax.cpp
	V			src/USER-REAXC/{fix_reax_c.cpp → fix_reaxc.cpp}
	V			src/USER-REAXC/{fix_reax_c.h → fix_reaxc.h}
	V			src/USER-REAXC/{fix_reaxc.cpp ← fix_reax_c.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
	V			src/USER-REAXC/{pair_reax_c.cpp → pair_reaxc.cpp}
	V			src/USER-REAXC/{pair_reax_c.h → pair_reaxc.h}
	V			src/USER-REAXC/{pair_reaxc.cpp ← pair_reax_c.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-VTK/README
	V			src/USER-VTK/{dump_custom_vtk.cpp → dump_vtk.cpp}
	V			src/USER-VTK/{dump_custom_vtk.h → dump_vtk.h}
	V			src/USER-VTK/{dump_vtk.cpp ← dump_custom_vtk.cpp}
	V			src/USER-VTK/{dump_vtk.h ← dump_custom_vtk.h}
	M			src/compute_dipole_chunk.cpp
	M			src/domain.cpp
	M			src/domain.h
	M			src/neighbor.cpp

rLAMMPSaddd87c0f7a4

doc/src/Manual.txt

doc/src/Section_commands.txt

doc/src/Section_intro.txt

doc/src/Section_packages.txt

doc/src/Section_start.txt

doc/src/compute_sna_atom.txt

doc/src/dump.txt

doc/src/dump_custom_vtk.txt

doc/src/dump_h5md.txt

doc/src/dump_nc.txt

doc/src/dump_netcdf.txt

doc/src/dump_vtk.txt

doc/src/fix_cmap.txt

doc/src/fix_gcmc.txt

doc/src/fix_qeq.txt

doc/src/fix_qeq_reax.txt

doc/src/fix_reax_bonds.txt

doc/src/fix_reaxc_species.txt

doc/src/lammps.book

doc/src/pair_hybrid.txt

doc/src/pair_reax.txt

doc/src/pair_reax_c.txt

doc/src/pair_reaxc.txt

doc/src/pairs.txt

examples/USER/flow_gauss/README

examples/USER/flow_gauss/in.GD

examples/USER/misc/flow_gauss/README

examples/USER/misc/flow_gauss/in.GD

examples/mscg/log.31Mar17.g++.1

lib/Install.py

lib/README

lib/atc/Install.py

lib/atc/README

lib/awpmd/Install.py

lib/awpmd/README

lib/colvars/Install.py

lib/colvars/README

lib/gpu/Install.py

lib/gpu/README

lib/h5md/Install.py

lib/h5md/Makefile

lib/h5md/Makefile.h5cc

lib/h5md/README

lib/linalg/Install.py

lib/linalg/README

lib/meam/Install.py

lib/meam/README

lib/mscg/Install.py

lib/mscg/Makefile.lammps

lib/mscg/README

lib/netcdf/README

lib/poems/Install.py

lib/poems/README

lib/qmmm/Install.py

lib/qmmm/README

lib/reax/Install.py

lib/reax/README

lib/smd/Install.py

lib/smd/README

lib/voronoi/Install.py

lib/voronoi/README

lib/vtk/Makefile.lammps

lib/vtk/README

src/KOKKOS/pair_reax_c_kokkos.cpp

src/KSPACE/pair_lj_charmmfsw_coul_long.cpp

src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp

src/Makefile

src/RIGID/fix_shake.cpp

src/SNAP/compute_sna_atom.cpp

src/SNAP/compute_sna_atom.h

src/SNAP/compute_snad_atom.cpp

src/SNAP/compute_snad_atom.h

src/SNAP/compute_snav_atom.cpp

src/SNAP/compute_snav_atom.h

src/SNAP/pair_snap.cpp

src/USER-NC-DUMP

src/USER-NC-DUMP/Install.sh

src/USER-NC-DUMP/README

src/USER-NC-DUMP/dump_nc.cpp

src/USER-NC-DUMP/dump_nc.h

src/USER-NC-DUMP/dump_nc_mpiio.cpp

src/USER-NC-DUMP/dump_nc_mpiio.h

src/USER-NETCDF/Install.sh

src/USER-NETCDF/README

src/USER-NETCDF/dump_netcdf.cpp

src/USER-NETCDF/dump_netcdf.h

src/USER-NETCDF/dump_netcdf_mpiio.cpp

src/USER-NETCDF/dump_netcdf_mpiio.h

src/USER-REAXC/compute_spec_atom.cpp

src/USER-REAXC/fix_qeq_reax.cpp

src/USER-REAXC/fix_reax_c.cpp

src/USER-REAXC/fix_reax_c.h

src/USER-REAXC/fix_reaxc.cpp

src/USER-REAXC/fix_reaxc.h

src/USER-REAXC/fix_reaxc_bonds.cpp

src/USER-REAXC/fix_reaxc_species.cpp

src/USER-REAXC/fix_reaxc_species.h

src/USER-REAXC/pair_reax_c.cpp

src/USER-REAXC/pair_reax_c.h

src/USER-REAXC/pair_reaxc.cpp

src/USER-REAXC/pair_reaxc.h

src/USER-REAXC/reaxc_allocate.cpp

src/USER-REAXC/reaxc_bond_orders.cpp

src/USER-REAXC/reaxc_bonds.cpp

src/USER-REAXC/reaxc_control.cpp

src/USER-REAXC/reaxc_defs.h

src/USER-REAXC/reaxc_ffield.cpp

src/USER-REAXC/reaxc_forces.cpp

src/USER-REAXC/reaxc_hydrogen_bonds.cpp

src/USER-REAXC/reaxc_init_md.cpp

src/USER-REAXC/reaxc_io_tools.cpp

src/USER-REAXC/reaxc_list.cpp

src/USER-REAXC/reaxc_lookup.cpp

src/USER-REAXC/reaxc_multi_body.cpp

src/USER-REAXC/reaxc_nonbonded.cpp

src/USER-REAXC/reaxc_reset_tools.cpp

src/USER-REAXC/reaxc_system_props.cpp

src/USER-REAXC/reaxc_tool_box.cpp

src/USER-REAXC/reaxc_torsion_angles.cpp

src/USER-REAXC/reaxc_traj.cpp

src/USER-REAXC/reaxc_types.h

src/USER-REAXC/reaxc_valence_angles.cpp

src/USER-REAXC/reaxc_vector.cpp

src/USER-VTK/README

src/USER-VTK/dump_custom_vtk.cpp

src/USER-VTK/dump_custom_vtk.h

src/USER-VTK/dump_vtk.cpp

src/USER-VTK/dump_vtk.h

src/compute_dipole_chunk.cpp

src/domain.cpp

src/domain.h

src/neighbor.cpp