remove obsolete files
This commit is contained in:
Axel Kohlmeyer
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Commands_all.html)
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:line
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kim_query command :h3
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[Syntax:]
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kim_query variable query_function web_query_flags :pre
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variable = name of a (string style) variable where the result of the query is stored
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query_function = name of the OpenKIM web API query function to be used
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web_query_flags = a series of keyword=value pairs that represent the web query; supported keywords depend on query function :ul
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[Examples:]
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kim_query latconst get_test_result test=TE_156715955670 model=MO_800509458712 &
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prop=structure-cubic-crystal-npt species=\["Al"\] keys=\["a"\] units=\["angstrom"\] :pre
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[Description:]
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The kim_query command allows to retrieve properties from the OpenKIM
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through a web query. The result is stored in a string style
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"variable"_variable.html, the name of which must be given as the first
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argument of the kim_query command. The second required argument is the
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name of the actual query function (e.g. {get_test_result}). All following
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arguments are parameters handed over to the web query in the format
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{keyword=value}. The list of supported keywords and the type of how
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the value has to be encoded depends on the query function used. This
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mirrors the functionality available on the OpenKIM webpage at
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"https://query.openkim.org"_https://query.openkim.org/
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[Restrictions:]
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This command is part of the KIM package. It is only enabled if
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LAMMPS was built with that package. Furthermore, its correct
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functioning depends on compiling LAMMPS with libcurl support.
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See the "Build package"_Build_package.html doc page for more info.
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[Related commands:]
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"pair_style kim"_pair_kim.html, "kim_style"_kim_style.html,
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"variable"_variable.html
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@ -1,107 +0,0 @@
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Commands_all.html)
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:line
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kim_style command :h3
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[Syntax:]
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kim_style mode args :pre
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mode = {init model} or {define typeargs} or no mode chosen
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model = name of the KIM model (KIM potential or KIM simulator model)
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typeargs = atom type to species mapping (one entry per atom type)
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args = {unit_variables unit_style} or {unit_from unit_style} (optional):ul
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[Examples:]
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kim_style init ex_sim_model_Si_mod_tersoff unit_variables metal
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kim_style define Si Si
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kim_style unit_variables real
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kim_style init LennardJones_Ar unit_variables metal
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kim_style unit_variables real unit_from metal
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kim_style define Ar :pre
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[Description:]
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The kim_style command is a high-level wrapper around the
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"Knowledge Base for Interatomic Models (OpenKIM)"_https://openkim.org
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repository of interatomic potentials, so that they can be used by
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LAMMPS scripts. It does not implement any computations directly, but
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rather will generate LAMMPS input commands based on the information
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retrieved from the OpenKIM repository. It is able to realize so-called
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"KIM Simulator Models", which are OpenKIM repository entries of models
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using native features of the simulation engine in use, i.e. LAMMPS
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in this case, but it also supports realizing conventional KIM models
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implicitly via generating a "pair_style kim"_pair_kim.html command
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followed by a suitable "pair_coeff"_pair_coeff.html command.
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The kim_style command has two modes, {init} and {define}, indicated by
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the first argument to the kim_style command. An {init} mode command
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must be issued [before] the simulation box is created, while the {define}
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mode version may only be used [after] the simulation box exists. Both
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are required. The {init} mode version sets the model name and may issue
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additional commands changing LAMMPS default settings that are required
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for using a selected simulator model. If needed, those settings can be
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overridden. The second argument to the {kim_style init} command is the
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KIM model ID.
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In both modes, the keywords {unit_variables} and {unit_from} may be
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added. They control the values of a set of
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"internal style variables"_variable.html that can be used to convert
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between different unit styles in LAMMPS. The argument to
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each keyword is a LAMMPS unit style or NULL, which means to look up
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the unit style from what was set with the "units"_units.html command.
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Please note, that KIM simulator models will set their preferred unit style.
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By default all conversion variables are set to 1.0. Converting to or
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from the "lj" unit style is not supported. The following variables are defined:
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_u_length
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_u_mass
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_u_time :ul
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The {kim_style define} command will issue commands that will realize
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the selected model (through generating pair_style and pair_coeff commands,
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but also other commands, as required). It has to be issued [after] the
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the simulation box is defined. The {kim_style define} command allows a
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varying number of additional arguments. Those are used to map the atom
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types in LAMMPS to the available species in the KIM model. This is
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equivalent to the arguments following "pair_coeff * *" in a
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"kim"_pair_kim.html pair style. Thus the commands:
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kim_style init LennardJones_Ar
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kim_style define Ar :pre
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will generate the LAMMPS input commands:
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pair_style kim LennardJones_Ar
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pair_coeff * * Ar :pre
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For simulator models, the generated input commands may be more complex
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and require that LAMMPS is built with the required packages included.
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The commands generated by the kim_style command, can be copied to the
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screen or log file, through the "echo"_echo.html command.
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The kim_style command will also validate, that a selected simulator
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model was generated for the LAMMPS MD code and not some other software.
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In addition, the version strings for LAMMPS version used for defining
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the simulator model and the LAMMPS version being currently run are
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printed, so that it can be tracked down, if there are any incompatible
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changes to input script or command syntax between the two LAMMPS versions.
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[Restrictions:]
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This command is part of the KIM package. It is only enabled if
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LAMMPS was built with that package. Furthermore, its correct
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functioning depends on compiling LAMMPS with all required packages
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installed that are required by the commands embedded in any KIM
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simulator models used.
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See the "Build package"_Build_package.html doc page for more info.
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[Related commands:]
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"pair_style kim"_pair_kim.html, "kim_query"_kim_query.html
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