Merge branch 'kim-install' into install-and-docs-reviewed (da7a5f55) · Commits · 郑智淋 / lammps

doc/src/Section_accelerate.txt

+2 −2

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		@@ -233,8 +233,8 @@ set any needed options for the package via "-pk" "command-line switch"_Section_s
		use accelerated styles in your input via "-sf" "command-line switch"_Section_start.html#start_6 or "suffix"_suffix.html command \| lmp_machine -in in.script -sf gpu
		:tb(c=2,s=\|)

		Note that the first 4 steps can be done as a single command, using the
		src/Make.py tool. This tool is discussed in "Section
		Note that the first 4 steps can be done as a single command with
		suitable make command invocations. This is discussed in "Section
		4"_Section_packages.html of the manual, and its use is
		illustrated in the individual accelerator sections. Typically these
		steps only need to be done once, to create an executable that uses one

doc/src/Section_commands.txt

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		@@ -734,8 +734,8 @@ package"_Section_start.html#start_3.
		"smd/wall/surface"_fix_smd_wall_surface.html,
		"temp/rescale/eff"_fix_temp_rescale_eff.html,
		"ti/spring"_fix_ti_spring.html,
		"ttm/mod"_fix_ttm.html
		"wall/ees"_fix_wall_ees.html
		"ttm/mod"_fix_ttm.html,
		"wall/ees"_fix_wall_ees.html,
		"wall/region/ees"_fix_wall_ees.html :tb(c=6,ea=c)

		:line

doc/src/Section_example.txt

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		@@ -49,6 +49,7 @@ Lists of both kinds of directories are given below.
		Lowercase directories :h4

		accelerate: run with various acceleration options (OpenMP, GPU, Phi)
		airebo: polyethylene with AIREBO potential
		balance: dynamic load balancing, 2d system
		body: body particles, 2d system
		cmap: CMAP 5-body contributions to CHARMM force field

doc/src/Section_packages.txt

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		@@ -492,14 +492,38 @@ Minnesota).

		[Install or un-install:]

		Using this package requires the KIM library and its models
		(interatomic potentials) to be downloaded and installed on your
		system. The library can be downloaded and built in lib/kim or
		elsewhere on your system. Details of the download, build, and install
		process for KIM are given in the lib/kim/README file.
		Before building LAMMPS with this package, you must first download and
		build the KIM library and include the KIM models that you want to
		use. You can do this manually if you prefer; follow the instructions
		in lib/kim/README. You can also do it in one step from the lammps/src
		dir, using a command like these, which simply invoke the
		lib/kim/Install.py script with the specified args.

		make lib-kim # print help message
		make lib-kim args="-b . none" # install KIM API lib with only example models
		make lib-kim args="-b . Glue_Ercolessi_Adams_Al__MO_324507536345_001" # ditto plus one model
		make lib-kim args="-b . OpenKIM" # install KIM API lib with all models
		make lib-kim args="-a EAM_Dynamo_Ackland_W__MO_141627196590_002" # add one model or model driver :pre

		Note that in LAMMPS lingo, a KIM model driver is a pair style
		(e.g. EAM or Tersoff). A KIM model is a pair style for a particular
		element or alloy and set of parameters, e.g. EAM for Cu with a
		specific EAM potential file. Also note that installing the KIM API
		library with all its models, may take around 30 min to build. Of
		course you only need to do that once.

		See the list of KIM model drivers here:
		https://openkim.org/kim-items/model-drivers/alphabetical

		Once that process is complete, you can then install/un-install the
		package and build LAMMPS in the usual manner:
		See the list of all KIM models here:
		https://openkim.org/kim-items/models/by-model-drivers

		See the list of example KIM models included by default here:
		https://openkim.org/kim-api
		in the "What is in the KIM API source package?" section

		You can then install/un-install the package and build LAMMPS in the
		usual manner:

		make yes-kim
		make machine :pre
		@@ -1414,7 +1438,7 @@ lib/linalg. In the latter case you also need to build the library
		in lib/linalg with a command like these:

		make lib-linalg # print help message
		make lib-atc args="-m gfortran" # build with GNU Fortran compiler
		make lib-linalg args="-m gfortran" # build with GNU Fortran compiler

		You can then install/un-install the package and build LAMMPS in the
		usual manner:
		@@ -2469,8 +2493,8 @@ step from the lammps/src dir, using a command like these, which simply
		invoke the lib/smd/Install.py script with the specified args:

		make lib-smd # print help message
		make lib-smd args="-g -l" # download in default lib/smd/eigen-eigen-*
		make lib-smd args="-h . eigen -g -l" # download in lib/smd/eigen
		make lib-smd args="-g -l" # download and build in default lib/smd/eigen-eigen-*
		make lib-smd args="-h . eigen -g -l" # download and build in lib/smd/eigen
		make lib-smd args="-h ~ eigen -g -l" # download and build in ~/eigen :pre

		Note that the final -l switch is to create a symbolic (soft) link

doc/src/accelerate_gpu.txt

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		@@ -74,13 +74,8 @@ Run lammps/lib/gpu/nvc_get_devices (after building the GPU library, see below) t
		This requires two steps (a,b): build the GPU library, then build
		LAMMPS with the GPU package.

		You can do both these steps in one line, using the src/Make.py script,
		described in "Section 4"_Section_packages.html of the manual.
		Type "Make.py -h" for help. If run from the src directory, this
		command will create src/lmp_gpu using src/MAKE/Makefile.mpi as the
		starting Makefile.machine:

		Make.py -p gpu -gpu mode=single arch=31 -o gpu -a lib-gpu file mpi :pre
		You can do both these steps in one line as described in
		"Section 4"_Section_packages.html of the manual.

		Or you can follow these two (a,b) steps:

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