From 64b88f2e138533d2fb700331d787cd5cec5d8f18 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 25 Sep 2022 03:20:29 -0400 Subject: [PATCH] add versionadded/versionchanged markers for features from 15Sep2022 and 3Aug2022 --- doc/src/compute_sna_atom.rst | 24 +++++++++++++----------- doc/src/fix_latte.rst | 2 ++ doc/src/fix_shake.rst | 11 +++++++---- doc/src/pair_modify.rst | 2 ++ doc/src/pair_srp.rst | 2 ++ doc/src/pair_sw.rst | 2 ++ doc/src/read_dump.rst | 2 ++ 7 files changed, 30 insertions(+), 15 deletions(-) diff --git a/doc/src/compute_sna_atom.rst b/doc/src/compute_sna_atom.rst index 1b6b200685..ac55aebd08 100644 --- a/doc/src/compute_sna_atom.rst +++ b/doc/src/compute_sna_atom.rst @@ -228,18 +228,20 @@ command: See section below on output for a detailed explanation of the data layout in the global array. +.. versionadded:: 3Aug2022 + The compute *sna/grid* and *sna/grid/local* commands calculate -bispectrum components for a regular grid of points. -These are calculated from the local density of nearby atoms *i'* -around each grid point, as if there was a central atom *i* -at the grid point. This is useful for characterizing fine-scale -structure in a configuration of atoms, and it is used -in the `MALA package `_ -to build machine-learning surrogates for finite-temperature Kohn-Sham -density functional theory (:ref:`Ellis et al. `) -Neighbor atoms not in the group do not contribute to the -bispectrum components of the grid points. The distance cutoff :math:`R_{ii'}` -assumes that *i* has the same type as the neighbor atom *i'*. +bispectrum components for a regular grid of points. These are +calculated from the local density of nearby atoms *i'* around each grid +point, as if there was a central atom *i* at the grid point. This is +useful for characterizing fine-scale structure in a configuration of +atoms, and it is used in the `MALA package +`_ to build machine-learning surrogates +for finite-temperature Kohn-Sham density functional theory (:ref:`Ellis +et al. `) Neighbor atoms not in the group do not contribute +to the bispectrum components of the grid points. The distance cutoff +:math:`R_{ii'}` assumes that *i* has the same type as the neighbor atom +*i'*. Compute *sna/grid* calculates a global array containing bispectrum components for a regular grid of points. diff --git a/doc/src/fix_latte.rst b/doc/src/fix_latte.rst index 202f8cf374..de3ac5adde 100644 --- a/doc/src/fix_latte.rst +++ b/doc/src/fix_latte.rst @@ -81,6 +81,8 @@ The *coulomb* argument is not yet supported by fix latte (as of Sept Coulomb potential as an alternative to LATTE performing the calculation. +.. versionadded:: 15Sep2022 + The *exclude* argument allows this fix to work in tandem with another fix which may decide to delete one or more atoms of molecules. The specified fixID is the ID of the other fix. diff --git a/doc/src/fix_shake.rst b/doc/src/fix_shake.rst index f5742b8f9f..e6fbad7fdc 100644 --- a/doc/src/fix_shake.rst +++ b/doc/src/fix_shake.rst @@ -58,10 +58,13 @@ Description Apply bond and angle constraints to specified bonds and angles in the simulation by either the SHAKE or RATTLE algorithms. This typically -enables a longer timestep. The SHAKE or RATTLE algorithms, however, can -*only* be applied during molecular dynamics runs. When this fix is used -during a minimization, the constraints are *approximated* by strong -harmonic restraints. +enables a longer timestep. The SHAKE or RATTLE constraint algorithms, +however, can *only* be applied during molecular dynamics runs. + +.. versionchanged:: 15Sep2022 + +These fixes may still be used during minimization. In that case the +constraints are *approximated* by strong harmonic restraints. **SHAKE vs RATTLE:** diff --git a/doc/src/pair_modify.rst b/doc/src/pair_modify.rst index 6d4171fbc9..f08fb7a82f 100644 --- a/doc/src/pair_modify.rst +++ b/doc/src/pair_modify.rst @@ -284,6 +284,8 @@ the *pair* keyword. Use *no* to disable, or *yes* to enable. The "pair_modify pair compute/tally" command must be issued **before** the corresponding compute style is defined. +.. versionadded:: 3Aug2022 + The *neigh/trim* keyword controls whether an explicit cutoff is set for each neighbor list request issued by individual pair sub-styles when using :doc:`pair hybrid/overlay `. When this keyword is diff --git a/doc/src/pair_srp.rst b/doc/src/pair_srp.rst index 6c9a128447..7122c40c1e 100644 --- a/doc/src/pair_srp.rst +++ b/doc/src/pair_srp.rst @@ -132,6 +132,8 @@ at the cutoff distance :math:`r_c`. ---------- +.. versionadded:: 3Aug2022 + Pair style *srp/react* interfaces the pair style *srp* with the bond breaking and formation mechanisms provided by fix *bond/break* and fix *bond/create*, respectively. When using this pair style, whenever a diff --git a/doc/src/pair_sw.rst b/doc/src/pair_sw.rst index 438eabc711..579e4c6f3f 100644 --- a/doc/src/pair_sw.rst +++ b/doc/src/pair_sw.rst @@ -130,6 +130,8 @@ terms. so the inconsistency between potential and force can be neglected in actual simulations. +.. versionadded:: 3Aug2022 + The *threebody* keyword is optional and determines whether or not the three-body term of the potential is calculated. The default value is "on" and it is only available for the plain *sw* pair style variants, diff --git a/doc/src/read_dump.rst b/doc/src/read_dump.rst index 311727f2c6..bee4629dfd 100644 --- a/doc/src/read_dump.rst +++ b/doc/src/read_dump.rst @@ -266,6 +266,8 @@ replace properties of the current system. There are various options for how this is done, determined by the specified fields and optional keywords. +.. versionchanged:: 3Aug2022 + The timestep of the snapshot becomes the current timestep for the simulation unless the *timestep* keyword is specified with a *no* value (default setting is *yes*). See the :doc:`reset_timestep `