diff --git a/doc/src/Commands_removed.rst b/doc/src/Commands_removed.rst index 6d7e7619bd..942aed12b8 100644 --- a/doc/src/Commands_removed.rst +++ b/doc/src/Commands_removed.rst @@ -23,7 +23,7 @@ Please refer to the :doc:`chunk HOWTO ` section for an overview. Box command ----------- -.. deprecated:: TBD +.. deprecated:: 22Dec2022 The *box* command has been removed and the LAMMPS code changed so it won't be needed. If present, LAMMPS will ignore the command and print a warning. @@ -31,7 +31,7 @@ be needed. If present, LAMMPS will ignore the command and print a warning. Reset_ids, reset_atom_ids, reset_mol_ids commands ------------------------------------------------- -.. deprecated:: TBD +.. deprecated:: 22Dec2022 The *reset_ids*, *reset_atom_ids*, and *reset_mol_ids* commands have been folded into the :doc:`reset_atoms ` command. If diff --git a/doc/src/Developer_grid.rst b/doc/src/Developer_grid.rst index b840ae7251..f60a688c5b 100644 --- a/doc/src/Developer_grid.rst +++ b/doc/src/Developer_grid.rst @@ -1,7 +1,7 @@ Use of distributed grids within style classes --------------------------------------------- -.. versionadded:: TBD +.. versionadded:: 22Dec2022 The LAMMPS source code includes two classes which facilitate the creation and use of distributed grids. These are the Grid2d and diff --git a/doc/src/Fortran.rst b/doc/src/Fortran.rst index 4c450a0c08..98e6194861 100644 --- a/doc/src/Fortran.rst +++ b/doc/src/Fortran.rst @@ -1525,7 +1525,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type Gather the named per-atom, per-atom fix, per-atom compute, or fix property/atom-based entities from all processes, in order by atom ID. - .. versionadded:: TBD + .. versionadded:: 22Dec2022 This subroutine gathers data from all processes and stores them in a one-dimensional allocatable array. The array *data* will be @@ -1567,7 +1567,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type Gather the named per-atom, per-atom fix, per-atom compute, or fix property/atom-based entities from all processes, unordered. - .. versionadded:: TBD + .. versionadded:: 22Dec2022 This subroutine gathers data for all atoms and stores them in a one-dimensional allocatable array. The data will be a @@ -1613,7 +1613,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type Gather the named per-atom, per-atom fix, per-atom compute, or fix property/atom-based entities from all processes for a subset of atoms. - .. versionadded:: TBD + .. versionadded:: 22Dec2022 This subroutine gathers data for the requested atom IDs and stores them in a one-dimensional allocatable array. The data will be ordered by atom ID, but @@ -1661,7 +1661,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type per-atom, per-atom fix, per-atom compute, or fix property/atom-based entity in *data* to all processes. - .. versionadded:: TBD + .. versionadded:: 22Dec2022 This subroutine takes data stored in a one-dimensional array supplied by the user and scatters them to all atoms on all processes. The data must be @@ -1694,7 +1694,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type per-atom, per-atom fix, per-atom compute, or fix property/atom-based entities in *data* from a subset of atoms to all processes. - .. versionadded:: TBD + .. versionadded:: 22Dec2022 This subroutine takes data stored in a one-dimensional array supplied by the user and scatters them to a subset of atoms on all processes. The array @@ -2381,7 +2381,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type Set the callback function for a :doc:`fix external ` instance with the given ID. - .. versionadded:: TBD + .. versionadded:: 22Dec2022 Fix :doc:`external ` allows programs that are running LAMMPS through its library interface to modify certain LAMMPS properties on @@ -2497,7 +2497,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type Get pointer to the force array storage in a fix external instance with the given ID. - .. versionadded:: TBD + .. versionadded:: 22Dec2022 Fix :doc:`external ` allows programs that are running LAMMPS through its library interfaces to add or modify certain LAMMPS properties on @@ -2541,7 +2541,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type Set the global energy contribution for a :doc:`fix external ` instance with the given ID. - .. versionadded:: TBD + .. versionadded:: 22Dec2022 This is a companion function to :f:func:`set_fix_external_callback` and :f:func:`fix_external_get_force` that also sets the contribution to the @@ -2569,7 +2569,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type Set the global virial contribution for a fix external instance with the given ID. - .. versionadded:: TBD + .. versionadded:: 22Dec2022 This is a companion function to :f:subr:`set_fix_external_callback` and :f:func:`fix_external_get_force` to set the contribution to the global @@ -2601,7 +2601,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type Set the per-atom energy contribution for a fix external instance with the given ID. - .. versionadded:: TBD + .. versionadded:: 22Dec2022 This is a companion function to :f:subr:`set_fix_external_callback` to set the per-atom energy contribution due to the fix from the external program as @@ -2636,7 +2636,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type part of the callback function. For this to work, the LAMMPS object must be passed as the *caller* argument when registering the callback function. - .. versionadded:: TBD + .. versionadded:: 22Dec2022 .. note:: @@ -2666,7 +2666,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type Set the vector length for a global vector stored with fix external for analysis. - .. versionadded:: TBD + .. versionadded:: 22Dec2022 This is a companion function to :f:subr:`set_fix_external_callback` and :f:func:`fix_external_get_force` to set the length of a global vector of @@ -2693,7 +2693,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type Store a global vector value for a fix external instance with the given ID. - .. versionadded:: TBD + .. versionadded:: 22Dec2022 This is a companion function to :f:subr:`set_fix_external_callback` and :f:func:`fix_external_get_force` to set the values of a global vector of diff --git a/doc/src/Howto_grid.rst b/doc/src/Howto_grid.rst index bd651628e7..9094afffa0 100644 --- a/doc/src/Howto_grid.rst +++ b/doc/src/Howto_grid.rst @@ -1,7 +1,7 @@ Distributed grids ================= -.. versionadded:: TBD +.. versionadded:: 22Dec2022 LAMMPS has internal capabilities to create uniformly spaced grids which overlay the simulation domain. For 2d and 3d simulations these diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index d90ee68b75..74ddb066c6 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -1816,7 +1816,7 @@ fitting the potentials natively in LAMMPS. Ngoc Cuong Nguyen (MIT), Andrew Rohskopf (Sandia) -.. versionadded:: TBD +.. versionadded:: 22Dec2022 **Install:** diff --git a/doc/src/Tools.rst b/doc/src/Tools.rst index 73ca11e689..145c283fd8 100644 --- a/doc/src/Tools.rst +++ b/doc/src/Tools.rst @@ -1164,7 +1164,7 @@ For illustration purposes below is a part of the Tcl example script. tabulate tool -------------- -.. versionadded:: TBD +.. versionadded:: 22Dec2022 The ``tabulate`` folder contains Python scripts scripts to generate tabulated potential files for LAMMPS. The bulk of the code is in the ``tabulate`` module diff --git a/doc/src/dump.rst b/doc/src/dump.rst index 7a31996581..4b60a9705e 100644 --- a/doc/src/dump.rst +++ b/doc/src/dump.rst @@ -346,7 +346,7 @@ so atom attributes will include effects due to fixes that are applied during the timestep. An explanation of the possible dump custom attributes is given below. -.. versionadded:: TBD +.. versionadded:: 22Dec2022 For style *grid* the extent of the Nx by Ny by Nz grid that overlays the simulation domain is output with each snapshot: @@ -450,7 +450,7 @@ from using the (numerical) atom type to an element name (or some other label). This will help many visualization programs to guess bonds and colors. -.. versionadded:: TBD +.. versionadded:: 22Dec2022 The *grid/vtk* style writes VTK files for grid data on a regular rectilinear grid. Its content is conceptually similar to that of the diff --git a/doc/src/fitpod_command.rst b/doc/src/fitpod_command.rst index 9670bf5dd2..fc21caec70 100644 --- a/doc/src/fitpod_command.rst +++ b/doc/src/fitpod_command.rst @@ -23,7 +23,7 @@ Examples Description """"""""""" -.. versionadded:: TBD +.. versionadded:: 22Dec2022 Fit a machine-learning interatomic potential (ML-IAP) based on proper orthogonal descriptors (POD). Two input files are required for this diff --git a/doc/src/fix_bond_react.rst b/doc/src/fix_bond_react.rst index 4377d9d946..5385bec5b9 100644 --- a/doc/src/fix_bond_react.rst +++ b/doc/src/fix_bond_react.rst @@ -520,7 +520,7 @@ example, the molecule fragment could consist of only the backbone atoms of a polymer chain. This constraint can be used to enforce a specific relative position and orientation between reacting molecules. -.. versionchanged:: TBD +.. versionchanged:: 22Dec2022 The constraint of type "custom" has the following syntax: @@ -637,7 +637,7 @@ eligible reaction only occurs if the random number is less than the fraction. Up to :math:`N` reactions are permitted to occur, as optionally specified by the *max_rxn* keyword. -.. versionadded:: TBD +.. versionadded:: 22Dec2022 The *rate_limit* keyword can enforce an upper limit on the overall rate of the reaction. The number of reaction occurrences is limited to @@ -664,7 +664,7 @@ charges are updated to those specified by the post-reaction template fragment defined in the pre-reaction molecule template. In this case, only the atomic charges of atoms in the molecule fragment are updated. -.. versionadded:: TBD +.. versionadded:: 22Dec2022 The *rescale_charges* keyword can be used to ensure the total charge of the system does not change as reactions occur. When the argument is diff --git a/doc/src/fix_electrode.rst b/doc/src/fix_electrode.rst index 9da8dcbdf9..3d543f08d2 100644 --- a/doc/src/fix_electrode.rst +++ b/doc/src/fix_electrode.rst @@ -125,7 +125,7 @@ usually modelled as a Gaussian distribution to make the charge-charge interaction matrix invertible (:ref:`Gingrich `). The keyword *eta* specifies the distribution's width in units of inverse length. -.. versionadded:: TBD +.. versionadded:: 22Dec2022 Three algorithms are available to minimize the energy, varying in how matrices are pre-calculated before a run to provide computational @@ -234,7 +234,7 @@ issue an error with any other number of electrodes. This keyword requires electroneutrality to be imposed (*symm on*) and will issue an error otherwise. -.. versionchanged:: TBD +.. versionchanged:: 22Dec2022 For all versions of the fix, the keyword-value *etypes on* enables type-based optimized neighbor lists. With this feature enabled, LAMMPS diff --git a/doc/src/fix_sgcmc.rst b/doc/src/fix_sgcmc.rst index 214c461a7c..4a9c4b16e3 100644 --- a/doc/src/fix_sgcmc.rst +++ b/doc/src/fix_sgcmc.rst @@ -44,7 +44,7 @@ Examples Description """"""""""" -.. versionadded:: TBD +.. versionadded:: 22Dec2022 This command allows to carry out parallel hybrid molecular dynamics/Monte Carlo (MD/MC) simulations using the algorithms described diff --git a/doc/src/pair_pod.rst b/doc/src/pair_pod.rst index 0aa6250dab..cb4edcb9e9 100644 --- a/doc/src/pair_pod.rst +++ b/doc/src/pair_pod.rst @@ -21,7 +21,7 @@ Examples Description """"""""""" -.. versionadded:: TBD +.. versionadded:: 22Dec2022 Pair style *pod* defines the proper orthogonal descriptor (POD) potential :ref:`(Nguyen) `. The mathematical definition of diff --git a/doc/src/python.rst b/doc/src/python.rst index 5316fb28a5..19abbf93e2 100644 --- a/doc/src/python.rst +++ b/doc/src/python.rst @@ -129,7 +129,7 @@ The first argument of the *python* command is either the *source* keyword or the name of a Python function. This defines the mode of the python command. -.. versionchanged:: TBD +.. versionchanged:: 22Dec2022 If the *source* keyword is used, it is followed by either a file name or the *here* keyword. No other keywords can be used. The *here* keyword diff --git a/doc/src/reset_atoms.rst b/doc/src/reset_atoms.rst index 8643eaf725..89f9557d7c 100644 --- a/doc/src/reset_atoms.rst +++ b/doc/src/reset_atoms.rst @@ -63,7 +63,7 @@ Examples Description """"""""""" -.. versionadded:: TBD +.. versionadded:: 22Dec2022 The *reset_atoms* command resets the values of a specified atom property. In contrast to the set command, it does this in a