Merge branch 'master' into kk_dep (624173d2) · Commits · 郑智淋 / lammps

.github/CODEOWNERS

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		@@ -9,13 +9,37 @@ lib/kokkos/* @stanmoore1
		lib/molfile/* @akohlmey
		lib/qmmm/* @akohlmey
		lib/vtk/* @rbberger
		lib/kim/* @ellio167

		# packages
		src/KOKKOS @stanmoore1
		src/USER-CGSDK @akohlmey
		src/USER-COLVARS @giacomofiorin
		src/USER-OMP @akohlmey
		src/USER-QMMM @akohlmey
		# whole packages
		src/COMPRESS/* @akohlmey
		src/GPU/* @ndtrung81
		src/KOKKOS/* @stanmoore1
		src/KIM/* @ellio167
		src/USER-CGDNA/* @ohenrich
		src/USER-CGSDK/* @akohlmey
		src/USER-COLVARS/* @giacomofiorin
		src/USER-DPD/* @timattox
		src/USER-INTEL/* @wmbrownintel
		src/USER-MANIFOLD/* @Pakketeretet2
		src/USER-MEAMC/* @martok
		src/USER-MOFFF/* @hheenen
		src/USER-MOLFILE/* @akohlmey
		src/USER-NETCDF/* @pastewka
		src/USER-PHONON/* @lingtikong
		src/USER-OMP/* @akohlmey
		src/USER-QMMM/* @akohlmey
		src/USER-REAXC/* @hasanmetin
		src/USER-TALLY/* @akohlmey
		src/USER-UEF/* @danicholson
		src/USER-VTK/* @rbberger

		# individual files in packages
		src/GPU/pair_vashishta_gpu.* @andeplane
		src/KOKKOS/pair_vashishta_kokkos.* @andeplane
		src/MANYBODY/pair_vashishta_table.* @andeplane
		src/USER-MISC/fix_bond_react.* @jrgissing
		src/USER-MISC/_grem. @dstelter92

		# tools
		tools/msi2lmp/* @akohlmey

cmake/CMakeLists.txt

+1 −1

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		@@ -101,7 +101,7 @@ set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GRANU
		KSPACE MANYBODY MC MEAM MISC MOLECULE PERI QEQ
		REAX REPLICA RIGID SHOCK SNAP SRD)
		set(OTHER_PACKAGES KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE
		USER-ATC USER-AWPMD USER-CGDNA USER-MESO
		USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESO
		USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF
		USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC
		USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-QTB USER-REAXC USER-SMD

doc/src/PDF/colvars-refman-lammps.pdf

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doc/src/Section_commands.txt

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		@@ -684,6 +684,7 @@ package"_Section_start.html#start_3.
		"addtorque"_fix_addtorque.html,
		"atc"_fix_atc.html,
		"ave/correlate/long"_fix_ave_correlate_long.html,
		"bond/react"_fix_bond_react.html,
		"colvars"_fix_colvars.html,
		"dpd/energy (k)"_fix_dpd_energy.html,
		"drude"_fix_drude.html,

doc/src/Section_packages.txt

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		@@ -122,6 +122,7 @@ Package, Description, Doc page, Example, Library
		Package, Description, Doc page, Example, Library
		"USER-ATC"_#USER-ATC, atom-to-continuum coupling, "fix atc"_fix_atc.html, USER/atc, int
		"USER-AWPMD"_#USER-AWPMD, wave-packet MD, "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, int
		"USER-BOCS"_#USER-BOCS, BOCS bottom up coarse graining, "fix bocs"_fix_bocs.html, USER/bocs, -
		"USER-CGDNA"_#USER-CGDNA, coarse-grained DNA force fields, src/USER-CGDNA/README, USER/cgdna, -
		"USER-CGSDK"_#USER-CGSDK, SDK coarse-graining model, "pair_style lj/sdk"_pair_sdk.html, USER/cgsdk, -
		"USER-COLVARS"_#USER-COLVARS, collective variables library, "fix colvars"_fix_colvars.html, USER/colvars, int
		@@ -1625,6 +1626,43 @@ examples/USER/awpmd :ul

		:line

		USER-BOCS package :link(USER-BOCS),h4

		[Contents:]

		This package provides "fix bocs"_fix_bocs.html, a modified version
		of "fix npt"_fix_nh.html which includes the pressure correction to
		the barostat as outlined in:

		N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that
		accurately describe the structure, pressure, and compressibility of
		molecular liquids," J. Chem. Phys. 143, 243148 (2015).

		[Authors:] Nicholas J. H. Dunn and Michael R. DeLyser (The Pennsylvania State University)

		[Install or un-install:]

		make yes-user-bocs
		make machine :pre

		make no-user-bocs
		make machine :pre

		[Supporting info:]

		The USER-BOCS user package for LAMMPS is part of the BOCS software package:
		"https://github.com/noid-group/BOCS"_https://github.com/noid-group/BOCS

		See the following reference for information about the entire package:

		Dunn, NJH; Lebold, KM; DeLyser, MR; Rudzinski, JF; Noid, WG.
		"BOCS: Bottom-Up Open-Source Coarse-Graining Software."
		J. Phys. Chem. B. 122, 13, 3363-3377 (2018).

		Example inputs are in the examples/USER/bocs folder.

		:line

		USER-CGDNA package :link(USER-CGDNA),h4

		[Contents:]

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