From af3da50bda9aeb897f3a1a163acffbe41bca9e9d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 25 Sep 2022 09:36:27 -0400 Subject: [PATCH] add some more versionadded tags, now mostly complete for 2022 --- doc/src/Packages_details.rst | 24 ++++++++++++++++++++++++ doc/src/compute_ave_sphere_atom.rst | 2 ++ doc/src/compute_fep_ta.rst | 2 ++ doc/src/create_atoms.rst | 4 ++++ doc/src/delete_atoms.rst | 2 ++ doc/src/fix_adapt.rst | 2 ++ doc/src/fix_mdi_qm.rst | 2 ++ doc/src/fix_numdiff_virial.rst | 2 ++ doc/src/pair_harmonic_cut.rst | 2 ++ doc/src/pair_ilp_tmd.rst | 2 ++ doc/src/pair_mliap.rst | 2 ++ doc/src/pair_saip_metal.rst | 2 ++ doc/src/plugin.rst | 2 ++ doc/src/region.rst | 2 ++ 14 files changed, 52 insertions(+) diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index dea49034a3..85857a4e1d 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -134,6 +134,8 @@ commands to write and read data using the ADIOS library. **Authors:** Norbert Podhorszki (ORNL) from the ADIOS developer team. +.. versionadded:: 28Feb2019 + **Install:** This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. @@ -364,6 +366,8 @@ and also support self-propelled particles. **Authors:** Sam Cameron (University of Bristol), Stefan Paquay (while at Brandeis University) (initial version of fix propel/self) +.. versionadded:: 14May2021 + Example inputs are in the examples/PACKAGES/brownian folder. ---------- @@ -592,6 +596,8 @@ To use this package, also the :ref:`KSPACE ` and **Author:** Trung Nguyen and Monica Olvera de la Cruz (Northwestern U) +.. versionadded:: 2Jul2021 + **Supporting info:** * src/DIELECTRIC: filenames -> commands @@ -1512,6 +1518,8 @@ workflows via the `MolSSI Driver Interface **Author:** Taylor Barnes - MolSSI, taylor.a.barnes at gmail.com +.. versionadded:: 14May2021 + **Install:** This package has :ref:`specific installation instructions ` on @@ -1596,6 +1604,8 @@ of Alabama), Leonid V. Zhigilei (University of Virginia) **Author of the *mesocnt* styles:** Philipp Kloza (U Cambridge) +.. versionadded:: 15Jun2020 + **Supporting info:** * src/MESONT: filenames -> commands @@ -1688,6 +1698,8 @@ compiled on your system. **Author:** Andreas Singraber +.. versionadded:: 27May2021 + **Install:** This package has :ref:`specific installation instructions ` on the @@ -1722,6 +1734,10 @@ must be installed. **Author:** Aidan Thompson (Sandia), Nicholas Lubbers (LANL). +.. versionadded:: 30Jun2020 + + .. versionadded:: 30Jun2020 + **Supporting info:** * src/ML-IAP: filenames -> commands @@ -1766,6 +1782,8 @@ Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1. ^4: University of British Columbia, Vancouver, BC, Canada +.. versionadded:: 14May2021 + **Install:** This package has :ref:`specific installation instructions ` on the @@ -1829,6 +1847,8 @@ of a neural network. This package was written by Christopher Barrett with contributions by Doyl Dickel, Mississippi State University. +.. versionadded:: 27May2021 + **Supporting info:** * src/ML-RANN: filenames -> commands @@ -2264,6 +2284,8 @@ try to load the contained plugins automatically at start-up. **Authors:** Axel Kohlmeyer (Temple U) +.. versionadded:: 8Apr2021 + **Supporting info:** * src/PLUGIN: filenames -> commands @@ -2907,6 +2929,8 @@ which discuss the `QuickFF `_ methodology. **Author:** Steven Vandenbrande. +.. versionadded:: 1Feb2019 + **Supporting info:** * src/YAFF/README diff --git a/doc/src/compute_ave_sphere_atom.rst b/doc/src/compute_ave_sphere_atom.rst index e5ed7e1437..ecb67ae7b5 100644 --- a/doc/src/compute_ave_sphere_atom.rst +++ b/doc/src/compute_ave_sphere_atom.rst @@ -35,6 +35,8 @@ Examples Description """"""""""" +.. versionadded:: 7Jan2022 + Define a computation that calculates the local mass density and temperature for each atom based on its neighbors inside a spherical cutoff. If an atom has :math:`M` neighbors, then its local mass density is diff --git a/doc/src/compute_fep_ta.rst b/doc/src/compute_fep_ta.rst index 1fe89194ca..5b08d08718 100644 --- a/doc/src/compute_fep_ta.rst +++ b/doc/src/compute_fep_ta.rst @@ -34,6 +34,8 @@ Examples Description """"""""""" +.. versionadded:: 4May2022 + Define a computation that calculates the change in the free energy due to a test-area (TA) perturbation :ref:`(Gloor) `. The test-area approach can be used to determine the interfacial tension of the system diff --git a/doc/src/create_atoms.rst b/doc/src/create_atoms.rst index c8f94f7d5e..17df11a5bf 100644 --- a/doc/src/create_atoms.rst +++ b/doc/src/create_atoms.rst @@ -189,6 +189,10 @@ to the area of that triangle. beneficial to exclude computing interactions between the created particles using :doc:`neigh_modify exclude `. +.. versionchanged:: 2Jun2022 + +The *porosity* style has been renamed to *random* with added functionality. + For the *random* style, *N* particles are added to the system at randomly generated coordinates, which can be useful for generating an amorphous system. The particles are created one by one using the diff --git a/doc/src/delete_atoms.rst b/doc/src/delete_atoms.rst index 749fc298b9..2fdd152196 100644 --- a/doc/src/delete_atoms.rst +++ b/doc/src/delete_atoms.rst @@ -116,6 +116,8 @@ must be in both the specified group and region. If *group-ID* = all, there is effectively no group criterion. If *region-ID* is specified as NULL, no region criterion is imposed. +.. versionadded:: 4May2022 + For style *variable*, all atoms for which the atom-style variable with the given name evaluates to non-zero will be deleted. Additional atoms can be deleted if they are in a molecule for which one or more atoms diff --git a/doc/src/fix_adapt.rst b/doc/src/fix_adapt.rst index a0c9c5edea..18caa3d54f 100644 --- a/doc/src/fix_adapt.rst +++ b/doc/src/fix_adapt.rst @@ -319,6 +319,8 @@ with fix_adapt are ---------- +.. versionadded:: 4May2022 + The *angle* keyword uses the specified variable to change the value of an angle coefficient over time, very similar to how the *pair* keyword operates. The only difference is that now an angle coefficient for a diff --git a/doc/src/fix_mdi_qm.rst b/doc/src/fix_mdi_qm.rst index fd0c6f13af..667dea710a 100644 --- a/doc/src/fix_mdi_qm.rst +++ b/doc/src/fix_mdi_qm.rst @@ -43,6 +43,8 @@ Examples Description """"""""""" +.. versionadded:: 3Aug2022 + This command enables LAMMPS to act as a client with another server code that will compute the total energy, per-atom forces, and total virial for atom conformations and simulation box size/shapes that diff --git a/doc/src/fix_numdiff_virial.rst b/doc/src/fix_numdiff_virial.rst index 647a0e592a..f909d41111 100644 --- a/doc/src/fix_numdiff_virial.rst +++ b/doc/src/fix_numdiff_virial.rst @@ -25,6 +25,8 @@ Examples Description """"""""""" +.. versionadded:: 17Feb2022 + Calculate the virial stress tensor through a finite difference calculation of energy versus strain. These values can be compared to the analytic virial tensor computed by pair styles, bond styles, etc. This can be useful for diff --git a/doc/src/pair_harmonic_cut.rst b/doc/src/pair_harmonic_cut.rst index 6b28db5fda..d91c3cf550 100644 --- a/doc/src/pair_harmonic_cut.rst +++ b/doc/src/pair_harmonic_cut.rst @@ -27,6 +27,8 @@ Examples Description """"""""""" +.. versionadded:: 17Feb2022 + Style *harmonic/cut* computes pairwise repulsive-only harmonic interactions with the formula .. math:: diff --git a/doc/src/pair_ilp_tmd.rst b/doc/src/pair_ilp_tmd.rst index a509b10cc3..77fa8bbfd5 100644 --- a/doc/src/pair_ilp_tmd.rst +++ b/doc/src/pair_ilp_tmd.rst @@ -32,6 +32,8 @@ Examples Description """"""""""" +.. versionadded:: 17Feb2022 + The *ilp/tmd* style computes the registry-dependent interlayer potential (ILP) potential for transition metal dichalcogenides (TMD) as described in :ref:`(Ouyang7) `. diff --git a/doc/src/pair_mliap.rst b/doc/src/pair_mliap.rst index 900a2c2e6a..32737eaf50 100644 --- a/doc/src/pair_mliap.rst +++ b/doc/src/pair_mliap.rst @@ -55,6 +55,8 @@ useful to know the gradient or derivative of energy, force, and stress w.r.t. model parameters. This information can be accessed using the related :doc:`compute mliap ` command. +.. versionadded:: 2Jun2022 + The descriptor style *so3* is a descriptor that is derived from the the smooth SO(3) power spectrum with the explicit inclusion of a radial basis :ref:`(Bartok) ` and :ref:`(Zagaceta) `. diff --git a/doc/src/pair_saip_metal.rst b/doc/src/pair_saip_metal.rst index 0acf519a0e..21bfeb0aa9 100644 --- a/doc/src/pair_saip_metal.rst +++ b/doc/src/pair_saip_metal.rst @@ -32,6 +32,8 @@ Examples Description """"""""""" +.. versionadded:: 17Feb2022 + The *saip/metal* style computes the registry-dependent interlayer potential (ILP) potential for hetero-junctions formed with hexagonal 2D materials and metal surfaces, as described in :ref:`(Ouyang6) `. diff --git a/doc/src/plugin.rst b/doc/src/plugin.rst index 1a10ab84ad..41e2621fef 100644 --- a/doc/src/plugin.rst +++ b/doc/src/plugin.rst @@ -59,6 +59,8 @@ The *clear* command will unload all currently loaded plugins. .. admonition:: Automatic loading of plugins :class: note + .. versionadded:: 4May2022 + When the environment variable ``LAMMPS_PLUGIN_PATH`` is set, then LAMMPS will search the directory (or directories) listed in this path for files with names that end in ``plugin.so`` diff --git a/doc/src/region.rst b/doc/src/region.rst index db09bcfd42..4ebd731073 100644 --- a/doc/src/region.rst +++ b/doc/src/region.rst @@ -162,6 +162,8 @@ Thus the third example above specifies a cylinder with its axis in the y-direction located at x = 2.0 and z = 3.0, with a radius of 5.0, and extending in the y-direction from -5.0 to the upper box boundary. +.. versionadded:: 4May2022 + For style *ellipsoid*, an axis-aligned ellipsoid is defined. The ellipsoid has its center at (x,y,z) and is defined by 3 axis-aligned vectors given by A = (a,0,0); B = (0,b,0); C = (0,0,c). Note that