Merge pull request #11 from lammps/master (00b92cd9) · Commits · 郑智淋 / lammps

.github/CODEOWNERS

+30 −6

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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 −5

Original line number	Diff line number	Diff line
		@@ -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
		@@ -128,10 +128,6 @@ pkg_depends(USER-LB MPI)
		pkg_depends(USER-MISC MANYBODY)
		pkg_depends(USER-PHONON KSPACE)

		if(ENABLE_BODY AND ENABLE_POEMS)
		message(FATAL_ERROR "BODY and POEMS cannot be enabled at the same time")
		endif()

		######################################################
		# packages with special compiler needs or external libs
		######################################################

doc/src/PDF/USER-CGDNA-overview.pdf→doc/src/PDF/USER-CGDNA.pdf

+783 KiB (4.03 MiB)

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doc/src/Section_packages.txt

+38 −0

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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:]

doc/src/bond_oxdna.txt

+8 −3

Original line number	Diff line number	Diff line
		@@ -51,9 +51,11 @@ The coefficients in the above example have to be kept fixed and cannot be change
		Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/.
		A simple python setup tool which creates single straight or helical DNA strands,
		DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/.
		A technical report with more information on the model, the structure of the input file,
		the setup tool and the performance of the LAMMPS-implementation of oxDNA
		can be found "here"_PDF/USER-CGDNA-overview.pdf.

		Please cite "(Henrich)"_#Henrich2 and the relevant oxDNA articles in any publication that uses this implementation.
		The article contains more information on the model, the structure of the input file, the setup tool
		and the performance of the LAMMPS-implementation of oxDNA.
		The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf.

		:line

		@@ -72,6 +74,9 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.

		:line

		:link(Henrich2)
		[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).

		:link(oxdna_fene)
		[(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).

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