diff --git a/doc/src/Commands_removed.rst b/doc/src/Commands_removed.rst index 777be3bf16..be775f4c19 100644 --- a/doc/src/Commands_removed.rst +++ b/doc/src/Commands_removed.rst @@ -1,6 +1,10 @@ Removed commands and packages ============================= +.. contents:: + +------ + This page lists LAMMPS commands and packages that have been removed from the distribution and provides suggestions for alternatives or replacements. LAMMPS has special dummy styles implemented, that will @@ -8,47 +12,60 @@ stop LAMMPS and print a suitable error message in most cases, when a style/command is used that has been removed or will replace the command with the direct alternative (if available) and print a warning. -restart2data tool ------------------ +LAMMPS shell +------------ -.. versionchanged:: 23Nov2013 +.. versionchanged:: 29Aug2024 -The functionality of the restart2data tool has been folded into the -LAMMPS executable directly instead of having a separate tool. A -combination of the commands :doc:`read_restart ` and -:doc:`write_data ` can be used to the same effect. For -added convenience this conversion can also be triggered by -:doc:`command-line flags ` +The LAMMPS shell has been removed from the LAMMPS distribution. Users +are encouraged to use the :ref:`LAMMPS-GUI ` tool instead. -Fix ave/spatial and fix ave/spatial/sphere ------------------------------------------- +i-PI tool +--------- -.. deprecated:: 11Dec2015 +.. versionchanged:: 27Jun2024 -The fixes ave/spatial and ave/spatial/sphere have been removed from LAMMPS -since they were superseded by the more general and extensible "chunk -infrastructure". Here the system is partitioned in one of many possible -ways through the :doc:`compute chunk/atom ` command -and then averaging is done using :doc:`fix ave/chunk `. -Please refer to the :doc:`chunk HOWTO ` section for an overview. +The i-PI tool has been removed from the LAMMPS distribution. Instead, +instructions to install i-PI from PyPI via pip are provided. -Box command ------------ +USER-REAXC package +------------------ -.. deprecated:: 22Dec2022 +.. deprecated:: 7Feb2024 -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. +The USER-REAXC package has been renamed to :ref:`REAXFF `. +In the process also the pair style and related fixes were renamed to use +the "reaxff" string instead of "reax/c". For a while LAMMPS was maintaining +backward compatibility by providing aliases for the styles. These have +been removed, so using "reaxff" is now *required*. -Reset_ids, reset_atom_ids, reset_mol_ids commands -------------------------------------------------- +MPIIO package +------------- -.. deprecated:: 22Dec2022 +.. deprecated:: 21Nov2023 -The *reset_ids*, *reset_atom_ids*, and *reset_mol_ids* commands have -been folded into the :doc:`reset_atoms ` command. If -present, LAMMPS will replace the commands accordingly and print a -warning. +The MPIIO package has been removed from LAMMPS since it was unmaintained +for many years and thus not updated to incorporate required changes that +had been applied to the corresponding non-MPIIO commands. As a +consequence the MPIIO commands had become unreliable and sometimes +crashing LAMMPS or corrupting data. Similar functionality is available +through the :ref:`ADIOS package ` and the :ref:`NETCDF +package `. Also, the :doc:`dump_modify nfile or dump_modify +fileper ` keywords may be used for an efficient way of +writing out dump files when running on large numbers of processors. +Similarly, the "nfile" and "fileper" keywords exist for restarts: +see :doc:`restart `, :doc:`read_restart `, +:doc:`write_restart `. + +MSCG package +------------ + +.. deprecated:: 21Nov2023 + +The MSCG package has been removed from LAMMPS since it was unmaintained +for many years and instead superseded by the `OpenMSCG software +`_ of the Voth group at the +University of Chicago, which can be used independent from LAMMPS. LATTE package ------------- @@ -64,18 +81,6 @@ packages, including LATTE. See the ``examples/QUANTUM`` dir and the with LATTE as a plugin library (similar to the way fix latte worked), as well as on a different set of MPI processors. -MEAM package ------------- - -The MEAM package in Fortran has been replaced by a C++ implementation. -The code in the :ref:`MEAM package ` is a translation of the -Fortran code of MEAM into C++, which removes several restrictions -(e.g. there can be multiple instances in hybrid pair styles) and allows -for some optimizations leading to better performance. The pair style -:doc:`meam ` has the exact same syntax. For a transition -period the C++ version of MEAM was called USER-MEAMC so it could -coexist with the Fortran version. - Minimize style fire/old ----------------------- @@ -97,38 +102,38 @@ The same functionality is available through :doc:`bond style mesocnt ` and :doc:`angle style mesocnt `. -MPIIO package -------------- +Box command +----------- -.. deprecated:: 21Nov2023 +.. deprecated:: 22Dec2022 -The MPIIO package has been removed from LAMMPS since it was unmaintained -for many years and thus not updated to incorporate required changes that -had been applied to the corresponding non-MPIIO commands. As a -consequence the MPIIO commands had become unreliable and sometimes -crashing LAMMPS or corrupting data. Similar functionality is available -through the :ref:`ADIOS package ` and the :ref:`NETCDF -package `. Also, the :doc:`dump_modify nfile or dump_modify -fileper ` keywords may be used for an efficient way of -writing out dump files when running on large numbers of processors. -Similarly, the "nfile" and "fileper" keywords exist for restarts: -see :doc:`restart `, :doc:`read_restart `, -:doc:`write_restart `. +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. +Reset_ids, reset_atom_ids, reset_mol_ids commands +------------------------------------------------- -MSCG package ------------- +.. deprecated:: 22Dec2022 -.. deprecated:: 21Nov2023 +The *reset_ids*, *reset_atom_ids*, and *reset_mol_ids* commands have +been folded into the :doc:`reset_atoms ` command. If +present, LAMMPS will replace the commands accordingly and print a +warning. -The MSCG package has been removed from LAMMPS since it was unmaintained -for many years and instead superseded by the `OpenMSCG software -`_ of the Voth group at the -University of Chicago, which can be used independent from LAMMPS. +MESSAGE package +--------------- + +.. deprecated:: 4May2022 + +The MESSAGE package has been removed since it was superseded by the +:ref:`MDI package `. MDI implements the same functionality +and in a more general way with direct support for more applications. REAX package ------------ +.. deprecated:: 4Jan2019 + The REAX package has been removed since it was superseded by the :ref:`REAXFF package `. The REAXFF package has been tested to yield equivalent results to the REAX package, offers better @@ -138,20 +143,25 @@ syntax compatible with the removed reax pair style, so input files will have to be adapted. The REAXFF package was originally called USER-REAXC. -USER-REAXC package ------------------- +MEAM package +------------ -.. deprecated:: 7Feb2024 +.. deprecated:: 4Jan2019 -The USER-REAXC package has been renamed to :ref:`REAXFF `. -In the process also the pair style and related fixes were renamed to use -the "reaxff" string instead of "reax/c". For a while LAMMPS was maintaining -backward compatibility by providing aliases for the styles. These have -been removed, so using "reaxff" is now *required*. +The MEAM package in Fortran has been replaced by a C++ implementation. +The code in the :ref:`MEAM package ` is a translation of the +Fortran code of MEAM into C++, which removes several restrictions +(e.g. there can be multiple instances in hybrid pair styles) and allows +for some optimizations leading to better performance. The pair style +:doc:`meam ` has the exact same syntax. For a transition +period the C++ version of MEAM was called USER-MEAMC so it could +coexist with the Fortran version. USER-CUDA package ----------------- +.. deprecated:: 31May2016 + The USER-CUDA package had been removed, since it had been unmaintained for a long time and had known bugs and problems. Significant parts of the design were transferred to the @@ -160,19 +170,27 @@ performance characteristics on NVIDIA GPUs. Both, the KOKKOS and the :ref:`GPU package ` are maintained and allow running LAMMPS with GPU acceleration. -i-PI tool ---------- +Fix ave/spatial and fix ave/spatial/sphere +------------------------------------------ -.. versionchanged:: 27Jun2024 +.. deprecated:: 11Dec2015 -The i-PI tool has been removed from the LAMMPS distribution. Instead, -instructions to install i-PI from PyPI via pip are provided. +The fixes ave/spatial and ave/spatial/sphere have been removed from LAMMPS +since they were superseded by the more general and extensible "chunk +infrastructure". Here the system is partitioned in one of many possible +ways through the :doc:`compute chunk/atom ` command +and then averaging is done using :doc:`fix ave/chunk `. +Please refer to the :doc:`chunk HOWTO ` section for an overview. -LAMMPS shell ------------- +restart2data tool +----------------- -.. versionchanged:: 29Aug2024 +.. deprecated:: 23Nov2013 -The LAMMPS shell has been removed from the LAMMPS distribution. Users -are encouraged to use the :ref:`LAMMPS-GUI ` tool instead. +The functionality of the restart2data tool has been folded into the +LAMMPS executable directly instead of having a separate tool. A +combination of the commands :doc:`read_restart ` and +:doc:`write_data ` can be used to the same effect. For +added convenience this conversion can also be triggered by +:doc:`command-line flags ` diff --git a/doc/src/Library_objects.rst b/doc/src/Library_objects.rst index 89056a5db0..53edfce9e6 100644 --- a/doc/src/Library_objects.rst +++ b/doc/src/Library_objects.rst @@ -1,5 +1,5 @@ -Compute, fixes, variables -========================= +Computes, fixes, variables +========================== This section documents accessing or modifying data stored by computes, fixes, or variables in LAMMPS using the following functions: diff --git a/python/lammps/core.py b/python/lammps/core.py index accf20b5d1..3eb74cb550 100644 --- a/python/lammps/core.py +++ b/python/lammps/core.py @@ -103,7 +103,7 @@ class command_wrapper(object): This method is where the Python 'magic' happens. If a method is not defined by the class command_wrapper, it assumes it is a LAMMPS command. It takes all the arguments, concatinates them to a single string, and executes it using - :py:meth:`lammps.command()`. + :py:meth:`lammps.command`. Starting with Python 3.6 it also supports keyword arguments. key=value is transformed into 'key value'. Note, since these have come last in the diff --git a/python/lammps/ipython/wrapper.py b/python/lammps/ipython/wrapper.py index 729c0d62bf..6f6669f55a 100644 --- a/python/lammps/ipython/wrapper.py +++ b/python/lammps/ipython/wrapper.py @@ -17,7 +17,7 @@ ################################################################################ class wrapper(object): - """lammps API IPython Wrapper + """ lammps API IPython Wrapper This is a wrapper class that provides additional methods on top of an existing :py:class:`lammps` instance. It provides additional methods