rename some examples folders
This commit is contained in:
Axel Kohlmeyer
@ -211,6 +211,8 @@ Uppercase directories
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+------------+--------------------------------------------------------------------------------------------------+
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| UNITS | examples that run the same simulation in lj, real, metal units |
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+------------+--------------------------------------------------------------------------------------------------+
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| USER-MISC | examples for commands in the USER-MISC packages |
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+------------+--------------------------------------------------------------------------------------------------+
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| VISCOSITY | compute viscosity via several methods |
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+------------+--------------------------------------------------------------------------------------------------+
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@ -224,4 +226,7 @@ of the sub-directories have their own README files which give further
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instructions. See the :doc:`Packages_details <Packages_details>` doc
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page for more info on specific packages.
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Similarly the USER-MISC directory has sub-directories for examples
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corresponding to individual commands or styles in the USER-MISC package.
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.. _openkim: https://openkim.org
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@ -1461,7 +1461,7 @@ Brennan (ARL).
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* :doc:`pair_style exp6/rx <pair_exp6_rx>`
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* :doc:`pair_style multi/lucy <pair_multi_lucy>`
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* :doc:`pair_style multi/lucy/rx <pair_multi_lucy_rx>`
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* examples/PACKAGES/dpd
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* examples/PACKAGES/dpd-react
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----------
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@ -1746,7 +1746,7 @@ src/USER-MISC/README file.
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* src/USER-MISC: filenames -> commands
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* src/USER-MISC/README
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* one page per individual command listed in src/USER-MISC/README
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* examples/PACKAGES/USER-MISC
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* examples/USER-MISC
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----------
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@ -2442,7 +2442,7 @@ Sciences, Iran).
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* :doc:`pair_style sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>`
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* :doc:`fix meso/move <fix_meso_move>`
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* :doc:`fix rigid/meso <fix_rigid_meso>`
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* examples/PACKAGES/sdpd
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* examples/PACKAGES/dpd-smooth
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----------
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@ -42,7 +42,7 @@ too frequently or to have multiple compute/dump commands, each of
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which computes this quantity.
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An example input script that uses this compute is provided
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in examples/PACKAGES/USER-MISC/basal.
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in examples/USER-MISC/basal.
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Output info
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"""""""""""
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@ -45,7 +45,7 @@ can be specified by using fix *dpd/energy*\ , fix *nve* and pair_style
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*dpd/fdt/energy*\ . DPD under isoenthalpic conditions can
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be specified by using fix *dpd/energy*\ , fix *nph* and pair_style
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*dpd/fdt/energy*\ . Examples of each DPD variant are provided in the
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examples/PACKAGES/dpd directory.
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examples/PACKAGES/dpd-react directory.
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----------
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@ -153,7 +153,7 @@ atoms moving above some minimum cutoff velocity (i.e., kinetic energy).
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These coefficients can be determined by fitting a quadratic polynomial to
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electronic stopping data predicted by, for example, SRIM or TD-DFT. Multiple
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'Ecut c1 c2' values can be provided for multi-species simulations in the order
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of the atom types. There is an examples/PACKAGES/USER-MISC/electron_stopping/ directory,
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of the atom types. There is an examples/USER-MISC/electron_stopping/ directory,
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which illustrates uses of this command. Details of this implementation are
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further described in :ref:`Stewart2018 <Stewart2018>` and :ref:`Lee2020 <Lee2020>`.
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@ -66,7 +66,7 @@ processors be on the order of the number of desired replicas. A
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100-replica simulation would require at least 100 processors (1 per
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world at minimum). If many replicas are needed on a small number of
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processors, multi-replica runs can be run outside of LAMMPS. An
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example of this can be found in examples/PACKAGES/USER-MISC/grem and has no
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example of this can be found in examples/USER-MISC/grem and has no
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limit on the number of replicas per processor. However, this is very
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inefficient and error prone and should be avoided if possible.
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@ -45,7 +45,7 @@ projection is also calculated, whose time integral can be shown to be equal to
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the true free energy gradient along the minimum free energy path local to the reference pathway.
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A detailed discussion of the projection technique can be found in :ref:`(Swinburne) <Swinburne>`.
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This fix can be used with LAMMPS as demonstrated in examples/PACKAGES/USER-MISC/pafi,
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This fix can be used with LAMMPS as demonstrated in examples/USER-MISC/pafi,
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though it is primarily intended to be coupled with the PAFI C++ code, developed
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at `https://github.com/tomswinburne/pafi <https://github.com/tomswinburne/pafi>`_,
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which distributes multiple LAMMPS workers in parallel to compute and collate
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@ -43,7 +43,7 @@ used to study crystal-liquid interfaces and determine melting
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temperatures :ref:`(Pedersen) <Pedersen>`.
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An example of using the interface pinning method is located in the
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*examples/PACKAGES/USER-MISC/rhok* directory.
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*examples/USER-MISC/rhok* directory.
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Restart, fix_modify, output, run start/stop, minimize info
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"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
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@ -49,7 +49,7 @@ under isobaric conditions can be specified by using fix shardlow, fix
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*nph* and pair_style *dpd/fdt*\ . DPD under isoenthalpic conditions can
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be specified by using fix shardlow, fix *nph* and pair_style
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*dpd/fdt/energy*\ . Examples of each DPD variant are provided in the
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examples/PACKAGES/dpd directory.
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examples/PACKAGES/dpd-react directory.
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----------
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@ -117,7 +117,7 @@ ellipsoidal particles according to the EES potential introduced above.
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Other details of this command are the same as for the :doc:`fix
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wall/region <fix_wall_region>` command. One may also find an example
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of using this fix in the examples/PACKAGES/USER-MISC/ees/ directory.
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of using this fix in the examples/USER-MISC/ees/ directory.
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----------
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@ -63,7 +63,7 @@ to specify the path for the force field file.
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An AGNI force field is fully specified by the filename which contains the
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parameters of the force field, i.e., the reference training environments
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used to construct the machine learning force field. Example force field
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and input files are provided in the examples/PACKAGES/USER-MISC/agni directory.
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and input files are provided in the examples/USER-MISC/agni directory.
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----------
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@ -111,7 +111,7 @@ If the neigh setting is too large, the pair style will use more memory than nece
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This pair style tallies a breakdown of the total E3B potential energy into sub-categories, which can be accessed via the :doc:`compute pair <compute_pair>` command as a vector of values of length 4.
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The 4 values correspond to the terms in the first equation above: the E2 term, the Ea term, the Eb term, and the Ec term.
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See the examples/PACKAGES/USER-MISC/e3b directory for a complete example script.
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See the examples/USER-MISC/e3b directory for a complete example script.
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----------
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@ -94,7 +94,7 @@ potentials.
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systems in the future.
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Example input scripts that use this pair style are provided
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in the examples/PACKAGES/USER-MISC/meam_sw_spline directory.
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in the examples/USER-MISC/meam_sw_spline directory.
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----------
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@ -5,7 +5,8 @@ problems you can run with LAMMPS.
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lower-case directories = simple test problems for LAMMPS and its packages
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upper-case directories = more complex problems
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PACKAGE directory with its own sub-directories = tests for specific packages
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PACKAGES directory with its own sub-directories = tests for specific packages
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USER-MISC directory with its own sub-directories = tests for commands in USER-MISC package
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Each is discussed below.
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@ -170,6 +171,12 @@ The MC directory has an example script for using LAMMPS as an
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energy-evaluation engine in a iterative Monte Carlo energy-relaxation
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loop.
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The PACKAGES directory contains subdirectories of example scripts for
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individual packages. Most of those are contributed by the corresponding
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package developers. See the README files in those directories
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for more info. See the doc/html/Build_package.html file for more info
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about installing and building packages.
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The TIP4P directory has an example for testing forces computed on a
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GPU.
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@ -179,11 +186,11 @@ lj, real, and metal. So that you can see how to scale/unscale input
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and output values read/written by LAMMPS to verify you are performing
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the same simulation in different unit systems.
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The PACKAGES directory contains subdirectories of example scripts for
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individual packages. Most of those are contributed by the corresponding
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package developers. See the README files in those directories
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The USER-MISC directory contains subdirectories of example scripts for
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individual commands in the USER-MISC package. Most of those are contributed
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by the corresponding developers. See the README files in those directories
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for more info. See the doc/html/Build_package.html file for more info
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about installing and building user packages.
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about installing and building packages.
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The VISCOSITY directory has example scripts for computing the
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viscosity of a LJ liquid using 4 different methods. See the
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