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Resolving merge conflicts

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This commit is contained in:
Joel Thomas Clemmer
2022-03-23 14:28:27 -06:00
parent 9417e41676 3e7de83e6e
commit 92a968a8a9
1211 changed files with 219865 additions and 402506 deletions
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6
.gitattributes vendored
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@ -3,3 +3,9 @@
.github export-ignore
.lgtm.yml export-ignore
SECURITY.md export-ignore
* text=auto
*.jpg -text
*.pdf -text
*.gz -text
*.png -text
*.ps -text

1
.gitignore vendored
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@ -12,6 +12,7 @@
*.sif
*.dll
*.pyc
*.whl
a.out
__pycache__

12
cmake/CMakeLists.txt
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@ -16,6 +16,7 @@ endif()
project(lammps CXX)
set(SOVERSION 0)
get_property(BUILD_IS_MULTI_CONFIG GLOBAL PROPERTY GENERATOR_IS_MULTI_CONFIG)
get_filename_component(LAMMPS_DIR ${CMAKE_CURRENT_SOURCE_DIR}/.. ABSOLUTE)
get_filename_component(LAMMPS_LIB_BINARY_DIR ${CMAKE_BINARY_DIR}/lib ABSOLUTE)
@ -749,13 +750,15 @@ if(BUILD_SHARED_LIBS)
else()
find_package(Python COMPONENTS Interpreter)
endif()
if(BUILD_IS_MULTI_CONFIG)
set(LIBLAMMPS_SHARED_BINARY ${CMAKE_BINARY_DIR}/$<CONFIG>/liblammps${LAMMPS_MACHINE}${CMAKE_SHARED_LIBRARY_SUFFIX})
else()
set(LIBLAMMPS_SHARED_BINARY ${CMAKE_BINARY_DIR}/liblammps${LAMMPS_MACHINE}${CMAKE_SHARED_LIBRARY_SUFFIX})
endif()
if(Python_EXECUTABLE)
add_custom_target(
install-python ${CMAKE_COMMAND} -E remove_directory build
COMMAND ${Python_EXECUTABLE} install.py -v ${LAMMPS_SOURCE_DIR}/version.h
-p ${LAMMPS_PYTHON_DIR}/lammps
-l ${CMAKE_BINARY_DIR}/liblammps${LAMMPS_MACHINE}${CMAKE_SHARED_LIBRARY_SUFFIX}
WORKING_DIRECTORY ${LAMMPS_PYTHON_DIR}
COMMAND ${Python_EXECUTABLE} ${LAMMPS_PYTHON_DIR}/install.py -p ${LAMMPS_PYTHON_DIR}/lammps -l ${LIBLAMMPS_SHARED_BINARY}
COMMENT "Installing LAMMPS Python module")
else()
add_custom_target(
@ -800,7 +803,6 @@ if(ClangFormat_FOUND)
endif()
get_target_property(DEFINES lammps COMPILE_DEFINITIONS)
get_property(BUILD_IS_MULTI_CONFIG GLOBAL PROPERTY GENERATOR_IS_MULTI_CONFIG)
if(BUILD_IS_MULTI_CONFIG)
set(LAMMPS_BUILD_TYPE "Multi-Config")
else()

58
cmake/CMakeSettings.json
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@ -82,7 +82,7 @@
"configurationType": "Debug",
"buildRoot": "${workspaceRoot}\\build\\${name}",
"installRoot": "${workspaceRoot}\\install\\${name}",
"cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows.cmake",
"cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows.cmake -DCMAKE_C_COMPILER=clang-cl.exe -DCMAKE_CXX_COMPILER=clang-cl.exe",
"buildCommandArgs": "",
"ctestCommandArgs": "",
"inheritEnvironments": [ "clang_cl_x64" ],
@ -115,15 +115,15 @@
]
},
{
"name": "x64-Debug-OneAPI",
"name": "x64-Release-Clang",
"generator": "Ninja",
"configurationType": "Debug",
"configurationType": "Release",
"buildRoot": "${workspaceRoot}\\build\\${name}",
"installRoot": "${workspaceRoot}\\install\\${name}",
"cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows.cmake -DCMAKE_CXX_COMPILER=icx -DCMAKE_C_COMPILER=icx",
"cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows.cmake -DCMAKE_C_COMPILER=clang-cl.exe -DCMAKE_CXX_COMPILER=clang-cl.exe",
"buildCommandArgs": "",
"ctestCommandArgs": "",
"inheritEnvironments": [ "msvc_x64_x64" ],
"inheritEnvironments": [ "clang_cl_x64" ],
"variables": [
{
"name": "BUILD_SHARED_LIBS",
@ -149,54 +149,6 @@
"name": "ENABLE_TESTING",
"value": "True",
"type": "BOOL"
},
{
"name": "BUILD_MPI",
"value": "False",
"type": "BOOL"
}
]
},
{
"name": "x64-Debug-Intel",
"generator": "Ninja",
"configurationType": "Debug",
"buildRoot": "${workspaceRoot}\\build\\${name}",
"installRoot": "${workspaceRoot}\\install\\${name}",
"cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows.cmake -DCMAKE_CXX_COMPILER=icl -DCMAKE_C_COMPILER=icl -DCMAKE_Fortran_COMPILER=ifort",
"buildCommandArgs": "",
"ctestCommandArgs": "",
"inheritEnvironments": [ "msvc_x64_x64" ],
"variables": [
{
"name": "BUILD_SHARED_LIBS",
"value": "True",
"type": "BOOL"
},
{
"name": "BUILD_TOOLS",
"value": "True",
"type": "BOOL"
},
{
"name": "LAMMPS_EXCEPTIONS",
"value": "True",
"type": "BOOL"
},
{
"name": "PKG_PYTHON",
"value": "True",
"type": "BOOL"
},
{
"name": "ENABLE_TESTING",
"value": "False",
"type": "BOOL"
},
{
"name": "BUILD_MPI",
"value": "False",
"type": "BOOL"
}
]
}

8
cmake/Modules/Packages/GPU.cmake
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@ -30,7 +30,15 @@ file(GLOB GPU_LIB_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cpp)
file(MAKE_DIRECTORY ${LAMMPS_LIB_BINARY_DIR}/gpu)
if(GPU_API STREQUAL "CUDA")
find_package(CUDA QUIET)
# augment search path for CUDA toolkit libraries to include the stub versions. Needed to find libcuda.so on machines without a CUDA driver installation
if(CUDA_FOUND)
set(CMAKE_LIBRARY_PATH "${CUDA_TOOLKIT_ROOT_DIR}/lib64/stubs;${CUDA_TOOLKIT_ROOT_DIR}/lib/stubs;${CUDA_TOOLKIT_ROOT_DIR}/lib64;${CUDA_TOOLKIT_ROOT_DIR}/lib;${CMAKE_LIBRARY_PATH}")
find_package(CUDA REQUIRED)
else()
message(FATAL_ERROR "CUDA Toolkit not found")
endif()
find_program(BIN2C bin2c)
if(NOT BIN2C)
message(FATAL_ERROR "Could not find bin2c, use -DBIN2C=/path/to/bin2c to help cmake finding it.")

1
cmake/Modules/Packages/ML-QUIP.cmake
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@ -51,6 +51,7 @@ if(DOWNLOAD_QUIP)
GIT_TAG origin/public
GIT_SHALLOW YES
GIT_PROGRESS YES
GIT_SUBMODULES "src/fox;src/GAP"
PATCH_COMMAND ${CMAKE_COMMAND} -E copy_if_different ${CMAKE_BINARY_DIR}/quip.config <SOURCE_DIR>/arch/Makefile.lammps
CONFIGURE_COMMAND env QUIP_ARCH=lammps make config
BUILD_COMMAND env QUIP_ARCH=lammps make libquip

4
cmake/Modules/Packages/PLUMED.cmake
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@ -54,8 +54,8 @@ if(DOWNLOAD_PLUMED)
set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/libplumedWrapper.a")
endif()
set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.7.3/plumed-src-2.7.3.tgz" CACHE STRING "URL for PLUMED tarball")
set(PLUMED_MD5 "f00cc82edfefe6bb3df934911dbe32fb" CACHE STRING "MD5 checksum of PLUMED tarball")
set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.7.4/plumed-src-2.7.4.tgz" CACHE STRING "URL for PLUMED tarball")
set(PLUMED_MD5 "858e0b6aed173748fc85b6bc8a9dcb3e" CACHE STRING "MD5 checksum of PLUMED tarball")
mark_as_advanced(PLUMED_URL)
mark_as_advanced(PLUMED_MD5)

18
doc/src/Build_settings.rst
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@ -4,15 +4,15 @@ Optional build settings
LAMMPS can be built with several optional settings. Each sub-section
explain how to do this for building both with CMake and make.
* :ref:`C++11 standard compliance <cxx11>` when building all of LAMMPS
* :ref:`FFT library <fft>` for use with the :doc:`kspace_style pppm <kspace_style>` command
* :ref:`Size of LAMMPS integer types <size>`
* :ref:`Read or write compressed files <gzip>`
* :ref:`Output of JPG and PNG files <graphics>` via the :doc:`dump image <dump_image>` command
* :ref:`Output of movie files <graphics>` via the :doc:`dump_movie <dump_image>` command
* :ref:`Memory allocation alignment <align>`
* :ref:`Workaround for long long integers <longlong>`
* :ref:`Error handling exceptions <exceptions>` when using LAMMPS as a library
* `C++11 standard compliance`_ when building all of LAMMPS
* `FFT library`_ for use with the :doc:`kspace_style pppm <kspace_style>` command
* `Size of LAMMPS integer types and size limits`_
* `Read or write compressed files`_
* `Output of JPG, PNG, and move files` via the :doc:`dump image <dump_image>` or :doc:`dump movie <dump_image>` commands
* `Memory allocation alignment`_
* `Workaround for long long integers`_
* `Exception handling when using LAMMPS as a library`_ to capture errors
* `Trigger selected floating-point exceptions`_
----------

86
doc/src/Build_windows.rst
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@ -16,44 +16,52 @@ General remarks
LAMMPS is developed and tested primarily on Linux machines. The vast
majority of HPC clusters and supercomputers today run on Linux as well.
While portability to other platforms is desired, it is not always achieved.
The LAMMPS developers are dependent on LAMMPS users giving feedback and
providing assistance in resolving portability issues. This is particularly
true for compiling LAMMPS on Windows, since this platform has significant
differences in some low-level functionality.
While portability to other platforms is desired, it is not always
achieved. That is sometimes due to non-portable code in LAMMPS itself,
but more often due to portability limitations of external libraries and
tools required to build a specific feature or package. The LAMMPS
developers are dependent on LAMMPS users giving feedback and providing
assistance in resolving portability issues. This is particularly true
for compiling LAMMPS on Windows, since this platform has significant
differences in some low-level functionality. As of LAMMPS version 14
December 2021, large parts of LAMMPS can be compiled natively with the
Microsoft Visual C++ Compilers. This is largely facilitated by using
the :doc:`Developer_platform` in the ``platform`` namespace.
Before trying to build LAMMPS on Windows yourself, please consider the
`pre-compiled Windows installer packages <https://packages.lammps.org/windows.html>`_
and see if they are sufficient for your needs.
.. _linux:
Running Linux on Windows
^^^^^^^^^^^^^^^^^^^^^^^^
Before trying to build LAMMPS on Windows, please consider if the
pre-compiled Windows binary packages are sufficient for your needs. If
it is necessary for you to compile LAMMPS on a Windows machine
If it is necessary for you to compile LAMMPS on a Windows machine
(e.g. because it is your main desktop), please also consider using a
virtual machine software and compile and run LAMMPS in a Linux virtual
machine, or - if you have a sufficiently up-to-date Windows 10 or
Windows 11 installation - consider using the Windows subsystem for
Linux. This optional Windows feature allows you to run the bash shell
from Ubuntu from within Windows and from there on, you can pretty much
use that shell like you are running on an Ubuntu Linux machine
(e.g. installing software via apt-get and more). For more details on
that, please see :doc:`this tutorial <Howto_wsl>`.
of a Linux system (Ubuntu by default) from within Windows and from there
on, you can pretty much use that shell like you are running on a regular
Ubuntu Linux machine (e.g. installing software via apt-get and more).
For more details on that, please see :doc:`this tutorial <Howto_wsl>`.
.. _gnu:
Using a GNU GCC ported to Windows
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
One option for compiling LAMMPS on Windows natively that has been known
to work in the past is to install a bash shell, unix shell utilities,
perl, GNU make, and a GNU compiler ported to Windows. The Cygwin
package provides a unix/linux interface to low-level Windows functions,
so LAMMPS can be compiled on Windows. The necessary (minor)
modifications to LAMMPS are included, but may not always up-to-date for
recently added functionality and the corresponding new code. A machine
makefile for using cygwin for the old build system is provided. Using
CMake for this mode of compilation is untested and not likely to work.
One option for compiling LAMMPS on Windows natively is to install a Bash
shell, Unix shell utilities, Perl, Python, GNU make, and a GNU compiler
ported to Windows. The Cygwin package provides a unix/linux interface
to low-level Windows functions, so LAMMPS can be compiled on Windows.
The necessary (minor) modifications to LAMMPS are included, but may not
always up-to-date for recently added functionality and the corresponding
new code. A machine makefile for using cygwin for the old build system
is provided. Using CMake for this mode of compilation is untested and
not likely to work.
When compiling for Windows do **not** set the ``-DLAMMPS_MEMALIGN``
define in the LMP_INC makefile variable and add ``-lwsock32 -lpsapi`` to
@ -75,19 +83,27 @@ Using Microsoft Visual Studio
Following the integration of the :doc:`platform namespace
<Developer_platform>` into the LAMMPS code base, portability of LAMMPS
to be compiled on Windows using Visual Studio has been significantly
improved. This has been tested with Visual Studio 2019 (aka version
16). Not all features and packages in LAMMPS are currently supported
out of the box, but a preset ``cmake/presets/windows.cmake`` is provided
that contains the packages that have been compiled successfully. You
must use the CMake based build procedure, and either use the integrated
CMake support of Visual Studio or use an external CMake installation to
create build files for the Visual Studio build system. Please note that
on launching Visual Studio it will scan the directory tree and likely
miss the correct master ``CMakeLists.txt``. Try to open the
``cmake/CMakeSettings.json`` and use those CMake configurations as a
starting point. It is also possible to configure and compile LAMMPS
from the command line with a CMake binary from `cmake.org <https://cmake.org>`_.
for native compilation on Windows using Visual Studio has been
significantly improved. This has been tested with Visual Studio 2019
(aka version 16) and Visual Studio 2022 (aka version 17). We strongly
recommend using Visual Studio 2022 version 17.1 or later. Not all
features and packages in LAMMPS are currently supported out of the box,
but a preset ``cmake/presets/windows.cmake`` is provided that contains
the packages that have been compiled successfully so far. You **must**
use the CMake based build procedure, since there is no support for GNU
make or the Unix shell utilities required for the GNU make build
procedure.
It is possible to use both the integrated CMake support of the Visual
Studio IDE or use an external CMake installation (e.g. downloaded from
cmake.org) to create build files and compile LAMMPS from the command line.
.. note::
Versions of Visual Studio before version 17.1 may scan the entire
LAMMPS source tree and likely miss the correct master
``CMakeLists.txt`` and get confused since there are multiple files
of that name in different folders but none in top level folder.
Please note, that for either approach CMake will create a so-called
:ref:`"multi-configuration" build environment <cmake_multiconfig>`, and
@ -98,6 +114,8 @@ To support running in parallel you can compile with OpenMP enabled using
the OPENMP package or install Microsoft MPI (including the SDK) and compile
LAMMPS with MPI enabled.
.. note::
This is work in progress and you should contact the LAMMPS developers
via GitHub, the forum, or the mailing list, if you have questions or
LAMMPS specific problems.

4
doc/src/Commands_compute.rst
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@ -101,7 +101,6 @@ KOKKOS, o = OPENMP, t = OPT.
* :doc:`pe/tally <compute_tally>`
* :doc:`plasticity/atom <compute_plasticity_atom>`
* :doc:`pressure <compute_pressure>`
* :doc:`pressure/cylinder <compute_pressure_cylinder>`
* :doc:`pressure/uef <compute_pressure_uef>`
* :doc:`property/atom <compute_property_atom>`
* :doc:`property/chunk <compute_property_chunk>`
@ -144,8 +143,11 @@ KOKKOS, o = OPENMP, t = OPT.
* :doc:`sph/t/atom <compute_sph_t_atom>`
* :doc:`spin <compute_spin>`
* :doc:`stress/atom <compute_stress_atom>`
* :doc:`stress/cartesian <compute_stress_profile>`
* :doc:`stress/cylinder <compute_stress_profile>`
* :doc:`stress/mop <compute_stress_mop>`
* :doc:`stress/mop/profile <compute_stress_mop>`
* :doc:`stress/spherical <compute_stress_profile>`
* :doc:`stress/tally <compute_tally>`
* :doc:`tdpd/cc/atom <compute_tdpd_cc_atom>`
* :doc:`temp (k) <compute_temp>`

2
doc/src/Commands_fix.rst
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@ -97,8 +97,6 @@ OPT.
* :doc:`latte <fix_latte>`
* :doc:`lb/fluid <fix_lb_fluid>`
* :doc:`lb/momentum <fix_lb_momentum>`
* :doc:`lb/pc <fix_lb_pc>`
* :doc:`lb/rigid/pc/sphere <fix_lb_rigid_pc_sphere>`
* :doc:`lb/viscous <fix_lb_viscous>`
* :doc:`lineforce <fix_lineforce>`
* :doc:`manifoldforce <fix_manifoldforce>`

3
doc/src/Developer.rst
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@ -11,8 +11,9 @@ of time and requests from the LAMMPS user community.
:maxdepth: 1
Developer_org
Developer_cxx_vs_c_style
Developer_code_design
Developer_parallel
Developer_comm_ops
Developer_flow
Developer_write
Developer_notes

433
doc/src/Developer_code_design.rst Normal file
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@ -0,0 +1,433 @@
Code design
-----------
This section explains some of the code design choices in LAMMPS with
the goal of helping developers write new code similar to the existing
code. Please see the section on :doc:`Requirements for contributed
code <Modify_style>` for more specific recommendations and guidelines.
While that section is organized more in the form of a checklist for
code contributors, the focus here is on overall code design strategy,
choices made between possible alternatives, and discussing some
relevant C++ programming language constructs.
Historically, the basic design philosophy of the LAMMPS C++ code was a
"C with classes" style. The motivation was to make it easy to modify
LAMMPS for people without significant training in C++ programming.
Data structures and code constructs were used that resemble the
previous implementation(s) in Fortran. A contributing factor to this
choice also was that at the time, C++ compilers were often not mature
and some of the advanced features contained bugs or did not function
as the standard required. There were also disagreements between
compiler vendors as to how to interpret the C++ standard documents.
However, C++ compilers have now advanced significantly. In 2020 we
decided to to require the C++11 standard as the minimum C++ language
standard for LAMMPS. Since then we have begun to also replace some of
the C-style constructs with equivalent C++ functionality, either from
the C++ standard library or as custom classes or functions, in order
to improve readability of the code and to increase code reuse through
abstraction of commonly used functionality.
.. note::
Please note that as of spring 2022 there is still a sizable chunk
of legacy code in LAMMPS that has not yet been refactored to
reflect these style conventions in full. LAMMPS has a large code
base and many different contributors and there also is a hierarchy
of precedence in which the code is adapted. Highest priority has
been the code in the ``src`` folder, followed by code in packages
in order of their popularity and complexity (simpler code is
adapted sooner), followed by code in the ``lib`` folder. Source
code that is downloaded from external packages or libraries during
compilation is not subject to the conventions discussed here.
Object oriented code
^^^^^^^^^^^^^^^^^^^^
LAMMPS is designed to be an object oriented code. Each simulation is
represented by an instance of the LAMMPS class. When running in
parallel each MPI process creates such an instance. This can be seen
in the ``main.cpp`` file where the core steps of running a LAMMPS
simulation are the following 3 lines of code:
.. code-block:: C++
LAMMPS *lammps = new LAMMPS(argc, argv, lammps_comm);
lammps->input->file();
delete lammps;
The first line creates a LAMMPS class instance and passes the command
line arguments and the global communicator to its constructor. The
second line triggers the LAMMPS instance to process the input (either
from standard input or a provided input file) until the simulation
ends. The third line deletes the LAMMPS instance. The remainder of
the main.cpp file has code for error handling, MPI configuration, and
other special features.
The basic LAMMPS class hierarchy which is created by the LAMMPS class
constructor is shown in :ref:`class-topology`. When input commands
are processed, additional class instances are created, or deleted, or
replaced. Likewise specific member functions of specific classes are
called to trigger actions such creating atoms, computing forces,
computing properties, time-propagating the system, or writing output.
Compositing and Inheritance
===========================
LAMMPS makes extensive use of the object oriented programming (OOP)
principles of *compositing* and *inheritance*. Classes like the
``LAMMPS`` class are a **composite** containing pointers to instances
of other classes like ``Atom``, ``Comm``, ``Force``, ``Neighbor``,
``Modify``, and so on. Each of these classes implement certain
functionality by storing and manipulating data related to the
simulation and providing member functions that trigger certain
actions. Some of those classes like ``Force`` are themselves
composites, containing instances of classes describing different force
interactions. Similarly the ``Modify`` class contains a list of
``Fix`` and ``Compute`` classes. If the input commands that
correspond to these classes include the word *style*, then LAMMPS
stores only a single instance of that class. E.g. *atom_style*,
*comm_style*, *pair_style*, *bond_style*. It the input command does
not include the word *style*, there can be many instances of that
class defined. E.g. *region*, *fix*, *compute*, *dump*.
**Inheritance** enables creation of *derived* classes that can share
common functionality in their base class while providing a consistent
interface. The derived classes replace (dummy or pure) functions in
the base class. The higher level classes can then call those methods
of the instantiated classes without having to know which specific
derived class variant was instantiated. In LAMMPS these derived
classes are often referred to as "styles", e.g. pair styles, fix
styles, atom styles and so on.
This is the origin of the flexibility of LAMMPS. For example pair
styles implement a variety of different non-bonded interatomic
potentials functions. All details for the implementation of a
potential are stored and executed in a single class.
As mentioned above, there can be multiple instances of classes derived
from the ``Fix`` or ``Compute`` base classes. They represent a
different facet of LAMMPS flexibility as they provide methods which
can be called at different points in time within a timestep, as
explained in `Developer_flow`. This allows the input script to tailor
how a specific simulation is run, what diagnostic computations are
performed, and how the output of those computations is further
processed or output.
Additional code sharing is possible by creating derived classes from the
derived classes (e.g., to implement an accelerated version of a pair
style) where only a subset of the derived class methods are replaced
with accelerated versions.
Polymorphism
============
Polymorphism and dynamic dispatch are another OOP feature that play an
important role in how LAMMPS selects what code to execute. In a
nutshell, this is a mechanism where the decision of which member
function to call from a class is determined at runtime and not when
the code is compiled. To enable it, the function has to be declared
as ``virtual`` and all corresponding functions in derived classes
should use the ``override`` property. Below is a brief example.
.. code-block:: c++
class Base {
public:
virtual ~Base() = default;
void call();
void normal();
virtual void poly();
};
void Base::call() {
normal();
poly();
}
class Derived : public Base {
public:
~Derived() override = default;
void normal();
void poly() override;
};
// [....]
Base *base1 = new Base();
Base *base2 = new Derived();
base1->call();
base2->call();
The difference in behavior of the ``normal()`` and the ``poly()`` member
functions is which of the two member functions is called when executing
`base1->call()` versus `base2->call()`. Without polymorphism, a
function within the base class can only call member functions within the
same scope, that is ``Base::call()`` will always call
``Base::normal()``. But for the `base2->call()` case the call of the
virtual member function will be dispatched to ``Derived::poly()``
instead. This mechanism means that functions are called within the
scope of the class type that was used to *create* the class instance are
invoked; even if they are assigned to a pointer using the type of a base
class. This is the desired behavior and this way LAMMPS can even use
styles that are loaded at runtime from a shared object file with the
:doc:`plugin command <plugin>`.
A special case of virtual functions are so-called pure functions. These
are virtual functions that are initialized to 0 in the class declaration
(see example below).
.. code-block:: c++
class Base {
public:
virtual void pure() = 0;
};
This has the effect that an instance of the base class cannot be
created and that derived classes **must** implement these functions.
Many of the functions listed with the various class styles in the
section :doc:`Modify` are pure functions. The motivation for this is
to define the interface or API of the functions but defer their
implementation to the derived classes.
However, there are downsides to this. For example, calls to virtual
functions from within a constructor, will not be in the scope of the
derived class and thus it is good practice to either avoid calling them
or to provide an explicit scope such as ``Base::poly()`` or
``Derived::poly()``. Furthermore, any destructors in classes containing
virtual functions should be declared virtual too, so they will be
processed in the expected order before types are removed from dynamic
dispatch.
.. admonition:: Important Notes
In order to be able to detect incompatibilities at compile time and
to avoid unexpected behavior, it is crucial that all member functions
that are intended to replace a virtual or pure function use the
``override`` property keyword. For the same reason, the use of
overloads or default arguments for virtual functions should be
avoided as they lead to confusion over which function is supposed to
override which and which arguments need to be declared.
Style Factories
===============
In order to create class instances for different styles, LAMMPS often
uses a programming pattern called `Factory`. Those are functions that
create an instance of a specific derived class, say ``PairLJCut`` and
return a pointer to the type of the common base class of that style,
``Pair`` in this case. To associate the factory function with the
style keyword, an ``std::map`` class is used with function pointers
indexed by their keyword (for example "lj/cut" for ``PairLJCut`` and
"morse" for ``PairMorse``). A couple of typedefs help keep the code
readable and a template function is used to implement the actual
factory functions for the individual classes. Below is an example
of such a factory function from the ``Force`` class as declared in
``force.h`` and implemented in ``force.cpp``. The file ``style_pair.h``
is generated during compilation and includes all main header files
(i.e. those starting with ``pair_``) of pair styles and then the
macro ``PairStyle()`` will associate the style name "lj/cut"
with a factory function creating an instance of the ``PairLJCut``
class.
.. code-block:: C++
// from force.h
typedef Pair *(*PairCreator)(LAMMPS *);
typedef std::map<std::string, PairCreator> PairCreatorMap;
PairCreatorMap *pair_map;
// from force.cpp
template <typename S, typename T> static S *style_creator(LAMMPS *lmp)
{
return new T(lmp);
}
// [...]
pair_map = new PairCreatorMap();
#define PAIR_CLASS
#define PairStyle(key, Class) (*pair_map)[#key] = &style_creator<Pair, Class>;
#include "style_pair.h"
#undef PairStyle
#undef PAIR_CLASS
// from pair_lj_cut.h
#ifdef PAIR_CLASS
PairStyle(lj/cut,PairLJCut);
#else
// [...]
Similar code constructs are present in other files like ``modify.cpp`` and
``modify.h`` or ``neighbor.cpp`` and ``neighbor.h``. Those contain
similar macros and include ``style_*.h`` files for creating class instances
of styles they manage.
I/O and output formatting
^^^^^^^^^^^^^^^^^^^^^^^^^
C-style stdio versus C++ style iostreams
========================================
LAMMPS uses the "stdio" library of the standard C library for reading
from and writing to files and console instead of C++ "iostreams".
This is mainly motivated by better performance, better control over
formatting, and less effort to achieve specific formatting.
Since mixing "stdio" and "iostreams" can lead to unexpected
behavior. use of the latter is strongly discouraged. Also output to
the screen should not use the predefined ``stdout`` FILE pointer, but
rather the ``screen`` and ``logfile`` FILE pointers managed by the
LAMMPS class. Furthermore, output should generally only be done by
MPI rank 0 (``comm->me == 0``). Output that is sent to both
``screen`` and ``logfile`` should use the :cpp:func:`utils::logmesg()
convenience function <LAMMPS_NS::utils::logmesg>`.
We also discourage the use of stringstreams because the bundled {fmt}
library and the customized tokenizer classes can provide the same
functionality in a cleaner way with better performance. This also
helps maintain a consistent programming syntax with code from many
different contributors.
Formatting with the {fmt} library
===================================
The LAMMPS source code includes a copy of the `{fmt} library
<https://fmt.dev>`_ which is preferred over formatting with the
"printf()" family of functions. The primary reason is that it allows
a typesafe default format for any type of supported data. This is
particularly useful for formatting integers of a given size (32-bit or
64-bit) which may require different format strings depending on
compile time settings or compilers/operating systems. Furthermore,
{fmt} gives better performance, has more functionality, a familiar
formatting syntax that has similarities to ``format()`` in Python, and
provides a facility that can be used to integrate format strings and a
variable number of arguments into custom functions in a much simpler
way than the varargs mechanism of the C library. Finally, {fmt} has
been included into the C++20 language standard, so changes to adopt it
are future-proof.
Formatted strings are frequently created by calling the
``fmt::format()`` function which will return a string as a
``std::string`` class instance. In contrast to the ``%`` placeholder
in ``printf()``, the {fmt} library uses ``{}`` to embed format
descriptors. In the simplest case, no additional characters are
needed as {fmt} will choose the default format based on the data type
of the argument. Otherwise the ``fmt::print()`` function may be
used instead of ``printf()`` or ``fprintf()``. In addition, several
LAMMPS output functions, that originally accepted a single string as
argument have been overloaded to accept a format string with optional
arguments as well (e.g., ``Error::all()``, ``Error::one()``,
``utils::logmesg()``).
Summary of the {fmt} format syntax
==================================
The syntax of the format string is "{[<argument id>][:<format spec>]}",
where either the argument id or the format spec (separated by a colon
':') is optional. The argument id is usually a number starting from 0
that is the index to the arguments following the format string. By
default these are assigned in order (i.e. 0, 1, 2, 3, 4 etc.). The most
common case for using argument id would be to use the same argument in
multiple places in the format string without having to provide it as an
argument multiple times. In LAMMPS the argument id is rarely used.
More common is the use of a format specifier, which starts with a colon.
This may optionally be followed by a fill character (default is ' '). If
provided, the fill character **must** be followed by an alignment
character ('<', '^', '>' for left, centered, or right alignment
(default)). The alignment character may be used without a fill
character. The next important format parameter would be the minimum
width, which may be followed by a dot '.' and a precision for floating
point numbers. The final character in the format string would be an
indicator for the "presentation", i.e. 'd' for decimal presentation of
integers, 'x' for hexadecimal, 'o' for octal, 'c' for character etc.
This mostly follows the "printf()" scheme but without requiring an
additional length parameter to distinguish between different integer
widths. The {fmt} library will detect those and adapt the formatting
accordingly. For floating point numbers there are correspondingly, 'g'
for generic presentation, 'e' for exponential presentation, and 'f' for
fixed point presentation.
Thus "{:8}" would represent *any* type argument using at least 8
characters; "{:<8}" would do this as left aligned, "{:^8}" as centered,
"{:>8}" as right aligned. If a specific presentation is selected, the
argument type must be compatible or else the {fmt} formatting code will
throw an exception. Some format string examples are given below:
.. code-block:: C
auto mesg = fmt::format(" CPU time: {:4d}:{:02d}:{:02d}\n", cpuh, cpum, cpus);
mesg = fmt::format("{:<8s}| {:<10.5g} | {:<10.5g} | {:<10.5g} |{:6.1f} |{:6.2f}\n",
label, time_min, time, time_max, time_sq, tmp);
utils::logmesg(lmp,"{:>6} = max # of 1-2 neighbors\n",maxall);
utils::logmesg(lmp,"Lattice spacing in x,y,z = {:.8} {:.8} {:.8}\n",
xlattice,ylattice,zlattice);
which will create the following output lines:
.. parsed-literal::
CPU time: 0:02:16
Pair | 2.0133 | 2.0133 | 2.0133 | 0.0 | 84.21
4 = max # of 1-2 neighbors
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
Finally, a special feature of the {fmt} library is that format
parameters like the width or the precision may be also provided as
arguments. In that case a nested format is used where a pair of curly
braces (with an optional argument id) "{}" are used instead of the
value, for example "{:{}d}" will consume two integer arguments, the
first will be the value shown and the second the minimum width.
For more details and examples, please consult the `{fmt} syntax
documentation <https://fmt.dev/latest/syntax.html>`_ website.
Memory management
^^^^^^^^^^^^^^^^^
Dynamical allocation of small data and objects can be done with the
the C++ commands "new" and "delete/delete[]. Large data should use
the member functions of the ``Memory`` class, most commonly,
``Memory::create()``, ``Memory::grow()``, and ``Memory::destroy()``,
which provide variants for vectors, 2d arrays, 3d arrays, etc.
These can also be used for small data.
The use of ``malloc()``, ``calloc()``, ``realloc()`` and ``free()``
directly is strongly discouraged. To simplify adapting legacy code
into the LAMMPS code base the member functions ``Memory::smalloc()``,
``Memory::srealloc()``, and ``Memory::sfree()`` are available, which
perform additional error checks for safety.
Use of these custom memory allocation functions is motivated by the
following considerations:
- memory allocation failures on *any* MPI rank during a parallel run
will trigger an immediate abort of the entire parallel calculation
instead of stalling it
- a failing "new" will trigger an exception which is also captured by
LAMMPS and triggers a global abort
- allocation of multi-dimensional arrays will be done in a C compatible
fashion but so that the storage of the actual data is stored in one
large contiguous block. Thus when MPI communication is needed,
the data can be communicated directly (similar to Fortran arrays).
- the "destroy()" and "sfree()" functions may safely be called on NULL
pointers
- the "destroy()" functions will nullify the pointer variables making
"use after free" errors easy to detect
- it is possible to use a larger than default memory alignment (not on
all operating systems, since the allocated storage pointers must be
compatible with ``free()`` for technical reasons)
In the practical implementation of code this means that any pointer
variables that are class members should be initialized to a
``nullptr`` value in their respective constructors. That way it is
safe to call ``Memory::destroy()`` or ``delete[]`` on them before
*any* allocation outside the constructor. This helps prevent memory
leaks.

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Communication patterns
----------------------
This page describes various inter-processor communication operations
provided by LAMMPS, mostly in the core *Comm* class. These are operations
for common tasks implemented using MPI library calls. They are used by
other classes to perform communication of different kinds. These
operations are useful to know about when writing new code for LAMMPS
that needs to communicate data between processors.
Owned and ghost atoms
^^^^^^^^^^^^^^^^^^^^^
As described on the :doc:`parallel partitioning algorithms
<Developer_par_part>` page, LAMMPS spatially decomposes the simulation
domain, either in a *brick* or *tiled* manner. Each processor (MPI
task) owns atoms within its sub-domain and additionally stores ghost
atoms within a cutoff distance of its sub-domain.
Forward and reverse communication
=================================
As described on the :doc:`parallel communication algorithms
<Developer_par_comm>` page, the most common communication operations are
first, *forward communication* which sends owned atom information from
each processor to nearby processors to store with their ghost atoms.
The need to do this communication arises when data from the owned atoms
is updated (e.g. their positions) and this updated information needs to
be **copied** to the corresponding ghost atoms.
And second, *reverse communication* which sends ghost atom information
from each processor to the owning processor to **accumulate** (sum)
the values with the corresponding owned atoms. The need for this
arises when data is computed and also stored with ghost atoms
(e.g. forces when using a "half" neighbor list) and thus those terms
need to be added to their corresponding atoms on the process where
they are "owned" atoms. Please note, that with the :doc:`newton off
<newton>` setting this does not happen and the neighbor lists are
constructed so that these interactions are computed on both MPI
processes containing one of the atoms and only the data pertaining to
the local atom is stored.
The time-integration classes in LAMMPS invoke these operations each
timestep via the *forward_comm()* and *reverse_comm()* methods in the
*Comm* class. Which per-atom data is communicated depends on the
currently used :doc:`atom style <atom_style>` and whether
:doc:`comm_modify vel <comm_modify>` setting is "no" (default) or
"yes".
Similarly, *Pair* style classes can invoke the *forward_comm(this)*
and *reverse_comm(this)* methods in the *Comm* class to perform the
same operations on per-atom data that is generated and stored within
the pair style class. Note that this function requires passing the
``this`` pointer as the first argument to enable the *Comm* class to
call the "pack" and "unpack" functions discussed below. An example of
the use of these functions are many-body pair styles like the
embedded-atom method (EAM) which compute intermediate values in the
first part of the compute() function that need to be stored by both
owned and ghost atoms for the second part of the force computation.
The *Comm* class methods perform the MPI communication for buffers of
per-atom data. They "call back" to the *Pair* class so it can *pack*
or *unpack* the buffer with data the *Pair* class owns. There are 4
such methods that the *Pair* class must define, assuming it uses both
forward and reverse communication:
* pack_forward_comm()
* unpack_forward_comm()
* pack_reverse_comm()
* unpack_reverse_comm()
The arguments to these methods include the buffer and a list of atoms
to pack or unpack. The *Pair* class also must set the *comm_forward*
and *comm_reverse* variables which store the number of values stored
in the communication buffers for each operation. This means, if
desired, it can choose to store multiple per-atom values in the
buffer, and they will be communicated together to minimize
communication overhead. The communication buffers are defined vectors
containing ``double`` values. To correctly store integers that may be
64-bit (bigint, tagint, imageint) in the buffer, you need to use the
`ubuf union <Communication buffer coding with ubuf>`_ construct.
The *Fix*, *Compute*, and *Dump* classes can also invoke the same kind
of forward and reverse communication operations using the same *Comm*
class methods. Likewise the same pack/unpack methods and
comm_forward/comm_reverse variables must be defined by the calling
*Fix*, *Compute*, or *Dump* class.
For *Fix* classes there is an optional second argument to the
*forward_comm()* and *reverse_comm()* call which can be used when the
fix performs multiple modes of communication, with different numbers
of values per atom. The fix should set the *comm_forward* and
*comm_reverse* variables to the maximum value, but can invoke the
communication for a particular mode with a smaller value. For this
to work, the *pack_forward_comm()*, etc methods typically use a class
member variable to choose which values to pack/unpack into/from the
buffer.
Finally, for reverse communications in *Fix* classes there is also the
*reverse_comm_variable()* method that allows the communication to have
a different amount of data per-atom. It invokes these corresponding
callback methods:
* pack_reverse_comm_size()
* unpack_reverse_comm_size()
which have extra arguments to specify the amount of data stored
in the buffer for each atom.
Higher level communication
^^^^^^^^^^^^^^^^^^^^^^^^^^
There are also several higher-level communication operations provided
in LAMMPS which work for either *brick* or *tiled* decompositions.
They may be useful for a new class to invoke if it requires more
sophisticated communication than the *forward* and *reverse* methods
provide. The 3 communication operations described here are
* ring
* irregular
* rendezvous
You can invoke these *grep* command in the LAMMPS src directory, to
see a list of classes that invoke the 3 operations.
* ``grep "\->ring" *.cpp */*.cpp``
* ``grep "irregular\->" *.cpp``
* ``grep "\->rendezvous" *.cpp */*.cpp``
Ring operation
==============
The *ring* operation is invoked via the *ring()* method in the *Comm*
class.
Each processor first creates a buffer with a list of values, typically
associated with a subset of the atoms it owns. Now think of the *P*
processors as connected to each other in a *ring*. Each processor *M*
sends data to the next *M+1* processor. It receives data from the
preceding *M-1* processor. The ring is periodic so that the last
processor sends to the first processor, and the first processor
receives from the last processor.
Invoking the *ring()* method passes each processor's buffer in *P*
steps around the ring. At each step a *callback* method, provided as
an argument to ring(), in the caller is invoked. This allows each
processor to examine the data buffer provided by every other
processor. It may extract values needed by its atoms from the
buffers, or it may alter placeholder values in the buffer. In the
latter case, when the *ring* operation is complete, each processor can
examine its original buffer to extract modified values.
Note that the *ring* operation is similar to an MPI_Alltoall()
operation where every processor effectively sends and receives data to
every other processor. The difference is that the *ring* operation
does it one step at a time, so the total volume of data does not need
to be stored by every processor. However, the *ring* operation is
also less efficient than MPI_Alltoall() because of the *P* stages
required. So it is typically only suitable for small data buffers and
occasional operations that are not time-critical.
Irregular operation
===================
The *irregular* operation is provided by the *Irregular* class. What
LAMMPS terms irregular communication is when each processor knows what
data it needs to send to what processor, but does not know what
processors are sending it data. An example is when load-balancing is
performed and each processor needs to send some of its atoms to new
processors.
The *Irregular* class provides 5 high-level methods useful in this
context:
* create_data()
* exchange_data()
* create_atom()
* exchange_atom()
* migrate_atoms()
For the *create_data()* method, each processor specifies a list of *N*
datums to send, each to a specified processor. Internally, the method
creates efficient data structures for performing the communication.
The *exchange_data()* method triggers the communication to be
performed. Each processor provides the vector of *N* datums to send,
and the size of each datum. All datums must be the same size.
The *create_atom()* and *exchange_atom()* methods are similar except
that the size of each datum can be different. Typically this is used
to communicate atoms, each with a variable amount of per-atom data, to
other processors.
The *migrate_atoms()* method is a convenience wrapper on the
*create_atom()* and *exchange_atom()* methods to simplify
communication of all the per-atom data associated with an atom so that
the atom can effectively migrate to a new owning processor. It is
similar to the *exchange()* method in the *Comm* class invoked when
atoms move to neighboring processors (in the regular or tiled
decomposition) during timestepping, except that it allows atoms to
have moved arbitrarily long distances and still be properly
communicated to a new owning processor.
Rendezvous operation
====================
Finally, the *rendezvous* operation is invoked via the *rendezvous()*
method in the *Comm* class. Depending on how much communication is
needed and how many processors a LAMMPS simulation is running on, it
can be a much more efficient choice than the *ring()* method. It uses
the *irregular* operation internally once or twice to do its
communication. The rendezvous algorithm is described in detail in
:ref:`(Plimpton) <Plimpton>`, including some LAMMPS use cases.
For the *rendezvous()* method, each processor specifies a list of *N*
datums to send and which processor to send each of them to.
Internally, this communication is performed as an irregular operation.
The received datums are returned to the caller via invocation of
*callback* function, provided as an argument to *rendezvous()*. The
caller can then process the received datums and (optionally) assemble
a new list of datums to communicate to a new list of specific
processors. When the callback function exits, the *rendezvous()*
method performs a second irregular communication on the new list of
datums.
Examples in LAMMPS of use of the *rendezvous* operation are the
:doc:`fix rigid/small <fix_rigid>` and :doc:`fix shake
<fix_shake>` commands (for one-time identification of the rigid body
atom clusters) and the identification of special_bond 1-2, 1-3 and 1-4
neighbors within molecules. See the :doc:`special_bonds <special_bonds>`
command for context.
----------
.. _Plimpton:
**(Plimpton)** Plimpton and Knight, JPDC, 147, 184-195 (2021).

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Code design
-----------
This section discusses some of the code design choices in LAMMPS and
overall strategy in order to assist developers to write new code that
will fit well with the remaining code. Please see the section on
:doc:`Requirements for contributed code <Modify_style>` for more
specific recommendations and guidelines. While that section is
organized more in the form of a checklist for code contributors, the
focus here is on overall code design strategy, choices made between
possible alternatives, and to discuss of some relevant C++ programming
language constructs.
Historically, the basic design philosophy of the LAMMPS C++ code was
that of a "C with classes" style. The was motivated by the desire to
make it easier to modify LAMMPS for people without significant training
in C++ programming and by trying to use data structures and code constructs
that somewhat resemble the previous implementation(s) in Fortran.
A contributing factor for this choice also was that at the time the
implementation of C++ compilers was not always very mature and some of
the advanced features contained bugs or were not functioning exactly
as the standard required; plus there was some disagreement between
compiler vendors about how to interpret the C++ standard documents.
However, C++ compilers have advanced a lot since then and with the
transition to requiring the C++11 standard in 2020 as the minimum C++ language
standard for LAMMPS, the decision was made to also replace some of the
C-style constructs with equivalent C++ functionality, either from the
C++ standard library or as custom classes or function, in order to
improve readability of the code and to increase code reuse through
abstraction of commonly used functionality.
.. note::
Please note that as of spring 2022 there is still a sizable chunk of
legacy code in LAMMPS that has not yet been refactored to reflect these
style conventions in full. LAMMPS has a large code base and many
different contributors and there also is a hierarchy of precedence
in which the code is adapted. Highest priority has the code in the
``src`` folder, followed by code in packages in order of their popularity
and complexity (simpler code is adapted sooner), followed by code
in the ``lib`` folder. Source code that is downloaded during compilation
is not subject to the conventions discussed here.
Object oriented code
^^^^^^^^^^^^^^^^^^^^
LAMMPS is designed to be an object oriented code, that is each
simulation is represented by an instance of the LAMMPS class. When
running in parallel, of course, each MPI process will create such an
instance. This can be seen in the ``main.cpp`` file where the core
steps of running a LAMMPS simulation are the following 3 lines of code:
.. code-block:: C++
LAMMPS *lammps = new LAMMPS(argc, argv, lammps_comm);
lammps->input->file();
delete lammps;
The first line creates a LAMMPS class instance and passes the command
line arguments and the global communicator to its constructor. The
second line tells the LAMMPS instance to process the input (either from
standard input or the provided input file) until the end. And the third
line deletes that instance again. The remainder of the main.cpp file
are for error handling, MPI configuration and other special features.
In the constructor of the LAMMPS class instance the basic LAMMPS class hierarchy
is created as shown in :ref:`class-topology`. While processing the input further
class instances are created, or deleted, or replaced and specific member functions
of specific classes are called to trigger actions like creating atoms, computing
forces, computing properties, propagating the system, or writing output.
Compositing and Inheritance
===========================
LAMMPS makes extensive use of the object oriented programming (OOP)
principles of *compositing* and *inheritance*. Classes like the
``LAMMPS`` class are a **composite** containing pointers to instances of
other classes like ``Atom``, ``Comm``, ``Force``, ``Neighbor``,
``Modify``, and so on. Each of these classes implement certain
functionality by storing and manipulating data related to the simulation
and providing member functions that trigger certain actions. Some of
those classes like ``Force`` are a composite again containing instances
of classes describing the force interactions or ``Modify`` containing
and calling fixes and computes. In most cases (e.g. ``AtomVec``, ``Comm``,
``Pair``, or ``Bond``) there is only one instance of those member classes
allowed, but in a few cases (e.g. ``Region``, ``Fix``, ``Compute``, or
``Dump``) there can be multiple instances and the parent class is
maintaining a list of the pointers of instantiated classes instead
of a single pointer.
Changing behavior or adjusting how LAMMPS handles a simulation is
implemented via **inheritance** where different variants of the
functionality are realized by creating *derived* classes that can share
common functionality in their base class and provide a consistent
interface where the derived classes replace (dummy or pure) functions in
the base class. The higher level classes can then call those methods of
the instantiated classes without having to know which specific derived
class variant was instantiated. In the LAMMPS documentation those
derived classes are usually referred to a "styles", e.g. pair styles,
fix styles, atom styles and so on.
This is the origin of the flexibility of LAMMPS and facilitates for
example to compute forces for very different non-bonded potential
functions by having different pair styles (implemented as different
classes derived from the ``Pair`` class) where the evaluation of the
potential function is confined to the implementation of the individual
classes. Whenever a new :doc:`pair_style` or :doc:`bond_style` or
:doc:`comm_style` or similar command is processed in the LAMMPS input
any existing class instance is deleted and a new instance created in
it place.
Classes derived from ``Fix`` or ``Compute`` represent a different facet
of LAMMPS' flexibility as there can be multiple instances of them an
their member functions will be called at different phases of the time
integration process (as explained in `Developer_flow`). This way
multiple manipulations of the entire or parts of the system can be
programmed (with fix styles) or different computations can be performed
and accessed and further processed or output through a common interface
(with compute styles).
Further code sharing is possible by creating derived classes from the
derived classes (for instance to implement an accelerated version of a
pair style) where then only a subset of the methods are replaced with
the accelerated versions.
Polymorphism
============
Polymorphism and dynamic dispatch are another OOP feature that play an
important part of how LAMMPS selects which code to execute. In a nutshell,
this is a mechanism where the decision of which member function to call
from a class is determined at runtime and not when the code is compiled.
To enable it, the function has to be declared as ``virtual`` and all
corresponding functions in derived classes should be using the ``override``
property. Below is a brief example.
.. code-block:: c++
class Base {
public:
virtual ~Base() = default;
void call();
void normal();
virtual void poly();
};
void Base::call() {
normal();
poly();
}
class Derived : public Base {
public:
~Derived() override = default;
void normal();
void poly() override;
};
// [....]
Base *base1 = new Base();
Base *base2 = new Derived();
base1->call();
base2->call();
The difference in behavior of the ``normal()`` and the ``poly()`` member
functions is in which of the two member functions is called when
executing `base1->call()` and `base2->call()`. Without polymorphism, a
function within the base class will call only member functions within
the same scope, that is ``Base::call()`` will always call
``Base::normal()``. But for the `base2->call()` the call for the
virtual member function will be dispatched to ``Derived::poly()``
instead. This mechanism allows to always call functions within the
scope of the class type that was used to create the class instance, even
if they are assigned to a pointer using the type of a base class. This
is the desired behavior, and thanks to dynamic dispatch, LAMMPS can even
use styles that are loaded at runtime from a shared object file with the
:doc:`plugin command <plugin>`.
A special case of virtual functions are so-called pure functions. These
are virtual functions that are initialized to 0 in the class declaration
(see example below).
.. code-block:: c++
class Base {
public:
virtual void pure() = 0;
};
This has the effect that it will no longer be possible to create an
instance of the base class and that derived classes **must** implement
these functions. Many of the functions listed with the various class
styles in the section :doc:`Modify` are such pure functions. The
motivation for this is to define the interface or API of the functions
but defer the implementation to the derived classes.
However, there are downsides to this. For example, calls to virtual
functions from within a constructor, will not be in the scope of the
derived class and thus it is good practice to either avoid calling them
or to provide an explicit scope like in ``Base::poly()``. Furthermore,
any destructors in classes containing virtual functions should be
declared virtual, too, so they are processed in the expected order
before types are removed from dynamic dispatch.
.. admonition:: Important Notes
In order to be able to detect incompatibilities and to avoid unexpected
behavior already at compile time, it is crucial that all member functions
that are intended to replace a virtual or pure function use the ``override``
property keyword. For the same reason it should be avoided to use overloads
or default arguments for virtual functions as they lead to confusion over
which function is supposed to override which and which arguments need to be
declared.
Style Factories
===============
In order to create class instances of the different styles, LAMMPS often
uses a programming pattern called `Factory`. Those are functions that create
an instance of a specific derived class, say ``PairLJCut`` and return a pointer
to the type of the common base class of that style, ``Pair`` in this case.
To associate the factory function with the style keyword, an ``std::map``
class is used in which function pointers are indexed by their keyword
(for example "lj/cut" for ``PairLJCut`` and "morse" ``PairMorse``).
A couple of typedefs help to keep the code readable and a template function
is used to implement the actual factory functions for the individual classes.
I/O and output formatting
^^^^^^^^^^^^^^^^^^^^^^^^^
C-style stdio versus C++ style iostreams
========================================
LAMMPS chooses to use the "stdio" library of the standard C library for
reading from and writing to files and console instead of C++
"iostreams". This is mainly motivated by the better performance, better
control over formatting, and less effort to achieve specific formatting.
Since mixing "stdio" and "iostreams" can lead to unexpected behavior using
the latter is strongly discouraged. Also output to the screen should not
use the predefined ``stdout`` FILE pointer, but rather the ``screen`` and
``logfile`` FILE pointers managed by the LAMMPS class. Furthermore, output
should only be done by MPI rank 0 (``comm->me == 0``) and output that is
send to both ``screen`` and ``logfile`` should use the
:cpp:func:`utils::logmesg() convenience function <LAMMPS_NS::utils::logmesg>`.
We also discourage the use for stringstreams as the bundled {fmt} library
and the customized tokenizer classes can provide the same functionality
in a cleaner way with better performance. This will also help to retain
a consistent programming style despite the many different contributors.
Formatting with the {fmt} library
===================================
The LAMMPS source code includes a copy of the `{fmt} library
<https://fmt.dev>`_ which is preferred over formatting with the
"printf()" family of functions. The primary reason is that it allows a
typesafe default format for any type of supported data. This is
particularly useful for formatting integers of a given size (32-bit or
64-bit) which may require different format strings depending on compile
time settings or compilers/operating systems. Furthermore, {fmt} gives
better performance, has more functionality, a familiar formatting syntax
that has similarities to ``format()`` in Python, and provides a facility
that can be used to integrate format strings and a variable number of
arguments into custom functions in a much simpler way that the varargs
mechanism of the C library. Finally, {fmt} has been included into the
C++20 language standard, so changes to adopt it are future proof.
Formatted strings are frequently created by calling the
``fmt::format()`` function which will return a string as ``std::string``
class instance. In contrast to the ``%`` placeholder in ``printf()``,
the {fmt} library uses ``{}`` to embed format descriptors. In the
simplest case, no additional characters are needed as {fmt} will choose
the default format based on the data type of the argument. Alternatively
The ``fmt::print()`` function may be used instead of ``printf()`` or
``fprintf()``. In addition, several LAMMPS output functions, that
originally accepted a single string as arguments have been overloaded to
accept a format string with optional arguments as well (e.g.
``Error::all()``, ``Error::one()``, ``utils::logmesg()``).
Summary of the {fmt} format syntax
==================================
The syntax of the format string is "{[<argument id>][:<format spec>]}",
where either the argument id or the format spec (separated by a colon
':') is optional. The argument id is usually a number starting from 0
that is the index to the arguments following the format string. By
default these are assigned in order (i.e. 0, 1, 2, 3, 4 etc.). The most
common case for using argument id would be to use the same argument in
multiple places in the format string without having to provide it as an
argument multiple times. In LAMMPS the argument id is rarely used.
More common is the use of the format specifier, which starts with a
colon. This may optionally be followed by a fill character (default is
' '). If provided, the fill character **must** be followed by an
alignment character ('<', '^', '>' for left, centered, or right
alignment (default)). The alignment character may be used without a fill
character. The next important format parameter would be the minimum
width, which may be followed by a dot '.' and a precision for floating
point numbers. The final character in the format string would be an
indicator for the "presentation", i.e. 'd' for decimal presentation of
integers, 'x' for hexadecimal, 'o' for octal, 'c' for character
etc. This mostly follows the "printf()" scheme but without requiring an
additional length parameter to distinguish between different integer
widths. The {fmt} library will detect those and adapt the formatting
accordingly. For floating point numbers there are correspondingly, 'g'
for generic presentation, 'e' for exponential presentation, and 'f' for
fixed point presentation.
Thus "{:8}" would represent *any* type argument using at least 8
characters; "{:<8}" would do this as left aligned, "{:^8}" as centered,
"{:>8}" as right aligned. If a specific presentation is selected, the
argument type must be compatible or else the {fmt} formatting code will
throw an exception. Some format string examples are given below:
.. code-block:: C
auto mesg = fmt::format(" CPU time: {:4d}:{:02d}:{:02d}\n", cpuh, cpum, cpus);
mesg = fmt::format("{:<8s}| {:<10.5g} | {:<10.5g} | {:<10.5g} |{:6.1f} |{:6.2f}\n",
label, time_min, time, time_max, time_sq, tmp);
utils::logmesg(lmp,"{:>6} = max # of 1-2 neighbors\n",maxall);
utils::logmesg(lmp,"Lattice spacing in x,y,z = {:.8} {:.8} {:.8}\n",
xlattice,ylattice,zlattice);
which will create the following output lines:
.. parsed-literal::
CPU time: 0:02:16
Pair | 2.0133 | 2.0133 | 2.0133 | 0.0 | 84.21
4 = max # of 1-2 neighbors
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
A special feature of the {fmt} library is that format parameters like
the width or the precision may be also provided as arguments. In that
case a nested format is used where a pair of curly braces (with an
optional argument id) "{}" are used instead of the value, for example
"{:{}d}" will consume two integer arguments, the first will be the value
shown and the second the minimum width.
For more details and examples, please consult the `{fmt} syntax
documentation <https://fmt.dev/latest/syntax.html>`_ website.
Memory management
^^^^^^^^^^^^^^^^^
Dynamical allocation of data and objects should be done with either the
C++ commands "new" and "delete/delete[]" or using member functions of
the ``Memory`` class, most commonly, ``Memory::create()``,
``Memory::grow()``, and ``Memory::destroy()``. The use of ``malloc()``,
``calloc()``, ``realloc()`` and ``free()`` directly is strongly
discouraged. To simplify adapting legacy code into the LAMMPS code base
the member functions ``Memory::smalloc()``, ``Memory::srealloc()``, and
``Memory::sfree()`` are available.
Using those custom memory allocation functions is motivated by the
following considerations:
- memory allocation failures on *any* MPI rank during a parallel run
will trigger an immediate abort of the entire parallel calculation
instead of stalling it
- a failing "new" will trigger an exception which is also captured by
LAMMPS and triggers a global abort
- allocation of multi-dimensional arrays will be done in a C compatible
fashion but so that the storage of the actual data is stored in one
large consecutive block and thus when MPI communication is needed,
only this storage needs to be communicated (similar to Fortran arrays)
- the "destroy()" and "sfree()" functions may safely be called on NULL
pointers
- the "destroy()" functions will nullify the pointer variables making
"use after free" errors easy to detect
- it is possible to use a larger than default memory alignment (not on
all operating systems, since the allocated storage pointers must be
compatible with ``free()`` for technical reasons)
In the practical implementation of code this means that any pointer variables
that are class members should be initialized to a ``nullptr`` value in their
respective constructors. That way it would be safe to call ``Memory::destroy()``
or ``delete[]`` on them before *any* allocation outside the constructor.
This helps to prevent memory leaks.

198
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@ -7,13 +7,22 @@ typically document what a variable stores, what a small section of
code does, or what a function does and its input/outputs. The topics
on this page are intended to document code functionality at a higher level.
Available topics are:
- `Reading and parsing of text and text files`_
- `Requesting and accessing neighbor lists`_
- `Fix contributions to instantaneous energy, virial, and cumulative energy`_
- `KSpace PPPM FFT grids`_
----
Reading and parsing of text and text files
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
It is frequently required for a class in LAMMPS to read in additional
data from a file, most commonly potential parameters from a potential
file for manybody potentials. LAMMPS provides several custom classes
and convenience functions to simplify the process. This offers the
data from a file, e.g. potential parameters from a potential file for
manybody potentials. LAMMPS provides several custom classes and
convenience functions to simplify the process. They offer the
following benefits:
- better code reuse and fewer lines of code needed to implement reading
@ -23,7 +32,7 @@ following benefits:
text to a number or returning a 0 on unrecognized text and thus reading incorrect values
- re-entrant code through avoiding global static variables (as used by ``strtok()``)
- transparent support for translating unsupported UTF-8 characters to their ASCII equivalents
(the text to value conversion functions **only** accept ASCII characters)
(the text-to-value conversion functions **only** accept ASCII characters)
In most cases (e.g. potential files) the same data is needed on all MPI
ranks. Then it is best to do the reading and parsing only on MPI rank
@ -31,16 +40,17 @@ ranks. Then it is best to do the reading and parsing only on MPI rank
calls. For reading generic text and potential parameter files the
custom classes :cpp:class:`TextFileReader <LAMMPS_NS::TextFileReader>`
and :cpp:class:`PotentialFileReader <LAMMPS_NS::PotentialFileReader>`
are available. Those classes allow to read the file as individual lines
for which they can return a tokenizer class (see below) for parsing the
line, or they can return blocks of numbers as a vector directly. The
documentation on `File reader classes <file-reader-classes>`_ contains
an example for a typical case.
are available. They allow reading the file as individual lines for which
they can return a tokenizer class (see below) for parsing the line. Or
they can return blocks of numbers as a vector directly. The
documentation on :ref:`File reader classes <file-reader-classes>`
contains an example for a typical case.
When reading per-atom data, the data in the file usually needs include
an atom ID so it can be associated with a particular atom. In that case
the data can be read in multi-line chunks and broadcast to all MPI ranks
with :cpp:func:`utils::read_lines_from_file()
When reading per-atom data, the data on each line of the file usually
needs to include an atom ID so it can be associated with a particular
atom. In that case the data can be read in multi-line chunks and
broadcast to all MPI ranks with
:cpp:func:`utils::read_lines_from_file()
<LAMMPS_NS::utils::read_lines_from_file>`. Those chunks are then
split into lines, parsed, and applied only to atoms the MPI rank
"owns".
@ -49,19 +59,163 @@ For splitting a string (incrementally) into words and optionally
converting those to numbers, the :cpp:class:`Tokenizer
<LAMMPS_NS::Tokenizer>` and :cpp:class:`ValueTokenizer
<LAMMPS_NS::ValueTokenizer>` can be used. Those provide a superset of
the functionality of ``strtok()`` from the C-library and the latter also
includes conversion to different types. Any errors while processing the
string in those classes will result in an exception, which can be caught
and the error processed as needed. Unlike the C-library functions
``atoi()``, ``atof()``, ``strtol()``, or ``strtod()`` the conversion
will check if the converted text is a valid integer of floating point
number and will not silently return an unexpected or incorrect value.
For example, ``atoi()`` will return 12 when converting "12.5" while the
ValueTokenizer class will throw an :cpp:class:`InvalidIntegerException
the functionality of ``strtok()`` from the C-library and the latter
also includes conversion to different types. Any errors while
processing the string in those classes will result in an exception,
which can be caught and the error processed as needed. Unlike the
C-library functions ``atoi()``, ``atof()``, ``strtol()``, or
``strtod()`` the conversion will check if the converted text is a
valid integer or floating point number and will not silently return an
unexpected or incorrect value. For example, ``atoi()`` will return 12
when converting "12.5", while the ValueTokenizer class will throw an
:cpp:class:`InvalidIntegerException
<LAMMPS_NS::InvalidIntegerException>` if
:cpp:func:`ValueTokenizer::next_int()
<LAMMPS_NS::ValueTokenizer::next_int>` is called on the same string.
Requesting and accessing neighbor lists
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
LAMMPS uses Verlet-style neighbor lists to avoid having to loop over
*all* pairs of *all* atoms when computing pairwise properties with a
cutoff (e.g. pairwise forces or radial distribution functions). There
are three main algorithms that can be selected by the :doc:`neighbor
command <neighbor>`: `bin` (the default, uses binning to achieve linear
scaling with system size), `nsq` (without binning, quadratic scaling),
`multi` (with binning, optimized for varying cutoffs or polydisperse
granular particles). In addition to how the neighbor lists are
constructed a number of different variants of neighbor lists need to be
created (e.g. "full" or "half") for different purposes and styles and
those may be required in every time step ("perpetual") or on some steps
("occasional").
The neighbor list creation is managed by the ``Neighbor`` class.
Individual classes can obtain a neighbor list by creating an instance of
a ``NeighRequest`` class which is stored in a list inside the
``Neighbor`` class. The ``Neighbor`` class will then analyze the
various requests and apply optimizations where neighbor lists that have
the same settings will be created only once and then copied, or a list
may be constructed by processing a neighbor list from a different
request that is a superset of the requested list. The neighbor list
build is then :doc:`processed in parallel <Developer_par_neigh>`.
The most commonly required neighbor list is a so-called "half" neighbor
list, where each pair of atoms is listed only once (except when the
:doc:`newton command setting <newton>` for pair is off; in that case
pairs straddling sub-domains or periodic boundaries will be listed twice).
Thus these are the default settings when a neighbor list request is created in:
.. code-block:: C++
void Pair::init_style()
{
neighbor->add_request(this);
}
void Pair::init_list(int /*id*/, NeighList *ptr)
{
list = ptr;
}
The ``this`` pointer argument is required so the neighbor list code can
access the requesting class instance to store the assembled neighbor
list with that instance by calling its ``init_list()`` member function.
The optional second argument (omitted here) contains a bitmask of flags
that determines the kind of neighbor list requested. The default value
used here asks for a perpetual "half" neighbor list.
Non-default values of the second argument need to be used to adjust a
neighbor list request to the specific needs of a style an additional
request flag is needed. The :doc:`tersoff <pair_tersoff>` pair style,
for example, needs a "full" neighbor list:
.. code-block:: C++
void PairTersoff::init_style()
{
// [...]
neighbor->add_request(this, NeighConst::REQ_FULL);
}
When a pair style supports r-RESPA time integration with different cutoff regions,
the request flag may depend on the corresponding r-RESPA settings. Here an example
from pair style lj/cut:
.. code-block:: C++
void PairLJCut::init_style()
{
int list_style = NeighConst::REQ_DEFAULT;
if (update->whichflag == 1 && utils::strmatch(update->integrate_style, "^respa")) {
auto respa = (Respa *) update->integrate;
if (respa->level_inner >= 0) list_style = NeighConst::REQ_RESPA_INOUT;
if (respa->level_middle >= 0) list_style = NeighConst::REQ_RESPA_ALL;
}
neighbor->add_request(this, list_style);
// [...]
}
Granular pair styles need neighbor lists based on particle sizes and not cutoff
and also may require to have the list of previous neighbors available ("history").
For example with:
.. code-block:: C++
if (use_history) neighbor->add_request(this, NeighConst::REQ_SIZE | NeighConst::REQ_HISTORY);
else neighbor->add_request(this, NeighConst::REQ_SIZE);
In case a class would need to make multiple neighbor list requests with different
settings each request can set an id which is then used in the corresponding
``init_list()`` function to assign it to the suitable pointer variable. This is
done for example by the :doc:`pair style meam <pair_meam>`:
.. code-block:: C++
void PairMEAM::init_style()
{
// [...]
neighbor->add_request(this, NeighConst::REQ_FULL)->set_id(1);
neighbor->add_request(this)->set_id(2);
}
void PairMEAM::init_list(int id, NeighList *ptr)
{
if (id == 1) listfull = ptr;
else if (id == 2) listhalf = ptr;
}
Fixes may require a neighbor list that is only build occasionally (or
just once) and this can also be indicated by a flag. As an example here
is the request from the ``FixPeriNeigh`` class which is created
internally by :doc:`Peridynamics pair styles <pair_peri>`:
.. code-block:: C++
neighbor->add_request(this, NeighConst::REQ_FULL | NeighConst::REQ_OCCASIONAL);
It is also possible to request a neighbor list that uses a different cutoff
than what is usually inferred from the pair style settings (largest cutoff of
all pair styles plus neighbor list skin). The following is used in the
:doc:`compute rdf <compute_rdf>` command implementation:
.. code-block:: C++
if (cutflag)
neighbor->add_request(this, NeighConst::REQ_OCCASIONAL)->set_cutoff(mycutneigh);
else
neighbor->add_request(this, NeighConst::REQ_OCCASIONAL);
The neighbor list request function has a slightly different set of arguments
when created by a command style. In this case the neighbor list is
*always* an occasional neighbor list, so that flag is not needed. However
for printing the neighbor list summary the name of the requesting command
should be set. Below is the request from the :doc:`delete atoms <delete_atoms>`
command:
.. code-block:: C++
neighbor->add_request(this, "delete_atoms", NeighConst::REQ_FULL);
Fix contributions to instantaneous energy, virial, and cumulative energy
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

6
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@ -252,12 +252,6 @@ follows:
- The Timer class logs timing information, output at the end
of a run.
.. TODO section on "Spatial decomposition and parallel operations"
.. diagram of 3d processor grid, brick vs. tiled. local vs. ghost
.. atoms, 6-way communication with pack/unpack functions,
.. PBC as part of the communication, forward and reverse communication
.. rendezvous communication, ring communication.
.. TODO section on "Fixes, Computes, and Variables"
.. how and when data is computed and provided and how it is
.. referenced. flags in Fix/Compute/Variable classes tell

49
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@ -8,11 +8,20 @@ without recompiling LAMMPS. The functionality for this and the
Plugins use the operating system's capability to load dynamic shared
object (DSO) files in a way similar shared libraries and then reference
specific functions in those DSOs. Any DSO file with plugins has to include
an initialization function with a specific name, "lammpsplugin_init", that
has to follow specific rules described below. When loading the DSO with
the "plugin" command, this function is looked up and called and will then
register the contained plugin(s) with LAMMPS.
specific functions in those DSOs. Any DSO file with plugins has to
include an initialization function with a specific name,
"lammpsplugin_init", that has to follow specific rules described below.
When loading the DSO with the "plugin" command, this function is looked
up and called and will then register the contained plugin(s) with
LAMMPS.
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`` (e.g. ``helloplugin.so``) and will
try to load the contained plugins automatically at start-up. For
plugins that are loaded this way, the behavior of LAMMPS should be
identical to a binary where the corresponding code was compiled in
statically as a package.
From the programmer perspective this can work because of the object
oriented design of LAMMPS where all pair style commands are derived from
@ -65,19 +74,18 @@ Members of ``lammpsplugin_t``
* - handle
- Pointer to the open DSO file handle
Only one of the three alternate creator entries can be used at a time
and which of those is determined by the style of plugin. The
"creator.v1" element is for factory functions of supported styles
computing forces (i.e. command, pair, bond, angle, dihedral, or
improper styles) and the function takes as single argument the pointer
to the LAMMPS instance. The factory function is cast to the
``lammpsplugin_factory1`` type before assignment. The "creator.v2"
element is for factory functions creating an instance of a fix, compute,
or region style and takes three arguments: a pointer to the LAMMPS
instance, an integer with the length of the argument list and a ``char
**`` pointer to the list of arguments. The factory function pointer
needs to be cast to the ``lammpsplugin_factory2`` type before
assignment.
Only one of the two alternate creator entries can be used at a time and
which of those is determined by the style of plugin. The "creator.v1"
element is for factory functions of supported styles computing forces
(i.e. pair, bond, angle, dihedral, or improper styles) or command styles
and the function takes as single argument the pointer to the LAMMPS
instance. The factory function is cast to the ``lammpsplugin_factory1``
type before assignment. The "creator.v2" element is for factory
functions creating an instance of a fix, compute, or region style and
takes three arguments: a pointer to the LAMMPS instance, an integer with
the length of the argument list and a ``char **`` pointer to the list of
arguments. The factory function pointer needs to be cast to the
``lammpsplugin_factory2`` type before assignment.
Pair style example
^^^^^^^^^^^^^^^^^^
@ -249,3 +257,8 @@ by ``#ifdef PAIR_CLASS`` is not needed, since the mapping of the class
name to the style name is done by the plugin registration function with
the information from the ``lammpsplugin_t`` struct. It may be included
in case the new code is intended to be later included in LAMMPS directly.
A plugin may be registered under an existing style name. In that case
the plugin will override the existing code. This can be used to modify
the behavior of existing styles or to debug new versions of them without
having to re-compile or re-install all of LAMMPS.

2
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@ -396,7 +396,7 @@ A typical code segment would look like this:
----------
.. file-reader-classes:
.. _file-reader-classes:
File reader classes
-------------------

55
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@ -21,7 +21,8 @@ YAML
print """---
timestep: $(step)
pe: $(pe)
ke: $(ke)""" file current_state.yaml screen no
ke: $(ke)
...""" file current_state.yaml screen no
.. code-block:: yaml
:caption: current_state.yaml
@ -51,6 +52,58 @@ JSON
"ke": 2.4962152903997174569
}
YAML format thermo_style output
===============================
.. versionadded:: 24Mar2022
LAMMPS supports the thermo style "yaml" and for "custom" style
thermodynamic output the format can be changed to YAML with
:doc:`thermo_modify line yaml <thermo_modify>`. This will produce a
block of output in a compact YAML format - one "document" per run - of
the following style:
.. code-block:: yaml
---
keywords: [Step, Temp, E_pair, E_mol, TotEng, Press, ]
data:
- [100, 0.757453103239935, -5.7585054860159, 0, -4.62236133677021, 0.207261053624721, ]
- [110, 0.759322359337036, -5.7614668389562, 0, -4.62251889318624, 0.194314975399602, ]
- [120, 0.759372342462676, -5.76149365656489, 0, -4.62247073844943, 0.191600048851267, ]
- [130, 0.756833027516501, -5.75777334823494, 0, -4.62255928350835, 0.208792327853067, ]
...
This data can be extracted and parsed from a log file using python with:
.. code-block:: python
import re, yaml
docs = ""
with open("log.lammps") as f:
for line in f:
m = re.search(r"^(keywords:.*$|data:$|---$|\.\.\.$| - \[.*\]$)", line)
if m: docs += m.group(0) + '\n'
thermo = list(yaml.load_all(docs, Loader=yaml.SafeLoader))
print("Number of runs: ", len(thermo))
print(thermo[1]['keywords'][4], ' = ', thermo[1]['data'][2][4])
After loading the YAML data, `thermo` is a list containing a dictionary
for each "run" where the tag "keywords" maps to the list of thermo
header strings and the tag "data" has a list of lists where the outer
list represents the lines of output and the inner list the values of the
columns matching the header keywords for that step. The second print()
command for example will print the header string for the fifth keyword
of the second run and the corresponding value for the third output line
of that run:
.. parsed-literal::
Number of runs: 2
TotEng = -4.62140097780047
Writing continuous data during a simulation
===========================================

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@ -165,5 +165,4 @@ changed. How to do this depends on the build system you are using.
URL "git@github.com:lammps/lammps.git".
The LAMMPS GitHub project is currently managed by Axel Kohlmeyer
(Temple U, akohlmey at gmail.com) and Richard Berger (Temple U,
richard.berger at temple.edu).
(Temple U, akohlmey at gmail.com).

17
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@ -1,16 +1,17 @@
Modifying & extending LAMMPS
****************************
LAMMPS is designed in a modular fashion so as to be easy to modify and
LAMMPS is designed in a modular fashion and to be easy to modify or
extend with new functionality. In fact, about 95% of its source code
is add-on files. These doc pages give basic instructions on how to do
this.
are optional. The following pages give basic instructions on what
is required when adding new styles of different kinds to LAMMPS.
If you add a new feature to LAMMPS and think it will be of interest to
general users, we encourage you to submit it for inclusion in LAMMPS
as a pull request on our `GitHub site <https://github.com/lammps/lammps>`_,
after reading about :doc:`how to prepare your code for submission <Modify_contribute>`
and :doc:`the style requirements and recommendations <Modify_style>`.
If you add a new feature to LAMMPS and think it will be of general
interest to other users, we encourage you to submit it for inclusion in
LAMMPS as a pull request on our `GitHub site
<https://github.com/lammps/lammps>`_, after reading about :doc:`how to
prepare your code for submission <Modify_contribute>` and :doc:`the
style requirements and recommendations <Modify_style>`.
.. toctree::
:maxdepth: 1

15
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@ -1,13 +1,14 @@
Overview
========
The best way to add a new feature to LAMMPS is to find a similar
feature and look at the corresponding source and header files to figure
out what it does. You will need some knowledge of C++ to be able to
understand the high-level structure of LAMMPS and its class
organization, but functions (class methods) that do actual
computations are written in vanilla C-style code and operate on simple
C-style data structures (vectors and arrays).
The best way to add a new feature to LAMMPS is to find a similar feature
and look at the corresponding source and header files to figure out what
it does. You will need some knowledge of C++ to be able to understand
the high-level structure of LAMMPS and its class organization, but
functions (class methods) that do actual computations are mostly written
in C-style code and operate on simple C-style data structures (vectors
and arrays). A high-level overview of the programming style choices in
LAMMPS is :doc:`given elsewhere <Developer_code_design>`.
Most of the new features described on the :doc:`Modify <Modify>` doc
page require you to write a new C++ derived class (except for exceptions

17
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@ -250,9 +250,11 @@ keep the code readable to programmers that have limited C++ programming
experience. C++ constructs are acceptable when they help improving the
readability and reliability of the code, e.g. when using the
`std::string` class instead of manipulating pointers and calling the
string functions of the C library. In addition and number of convenient
:doc:`utility functions and classes <Developer_utils>` for recurring
tasks are provided.
string functions of the C library. In addition a collection of
convenient :doc:`utility functions and classes <Developer_utils>` for
recurring tasks and a collection of
:doc:`platform neutral functions <Developer_platform>` for improved
portability are provided.
Included Fortran code has to be compatible with the Fortran 2003
standard. Python code must be compatible with Python 3.5. Large parts
@ -261,10 +263,11 @@ compatible with Python 2.7. Compatibility with Python 2.7 is
desirable, but compatibility with Python 3.5 is **required**.
Compatibility with these older programming language standards is very
important to maintain portability, especially with HPC cluster
environments, which tend to be running older software stacks and LAMMPS
users may be required to use those older tools or not have the option to
install newer compilers.
important to maintain portability and availability of LAMMPS on many
platforms. This applies especially to HPC cluster environments, which
tend to be running older software stacks and LAMMPS users may be
required to use those older tools for access to advanced hardware
features or not have the option to install newer compilers or libraries.
Programming conventions (varied)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

67
doc/src/Modify_thermo.rst
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@ -1,27 +1,54 @@
Thermodynamic output options
============================
There is one class that computes and prints thermodynamic information
to the screen and log file; see the file thermo.cpp.
The ``Thermo`` class computes and prints thermodynamic information to
the screen and log file; see the files ``thermo.cpp`` and ``thermo.h``.
There are two styles defined in thermo.cpp: "one" and "multi". There
is also a flexible "custom" style which allows the user to explicitly
list keywords for quantities to print when thermodynamic info is
output. See the :doc:`thermo_style <thermo_style>` command for a list
of defined quantities.
There are four styles defined in ``thermo.cpp``: "one", "multi", "yaml",
and "custom". The "custom" style allows the user to explicitly list
keywords for individual quantities to print when thermodynamic output is
generated. The others have a fixed list of keywords. See the
:doc:`thermo_style <thermo_style>` command for a list of available
quantities. The formatting of the "custom" style defaults to the "one"
style, but can be adapted using :doc:`thermo_modify line <thermo_modify>`.
The thermo styles (one, multi, etc) are simply lists of keywords.
Adding a new style thus only requires defining a new list of keywords.
Search for the word "customize" with references to "thermo style" in
thermo.cpp to see the two locations where code will need to be added.
The thermo styles (one, multi, etc) are defined by lists of keywords
with associated formats for integer and floating point numbers and
identified but an enumerator constant. Adding a new style thus mostly
requires defining a new list of keywords and the associated formats and
then inserting the required output processing where the enumerators are
identified. Search for the word "CUSTOMIZATION" with references to
"thermo style" in the ``thermo.cpp`` file to see the locations where
code will need to be added. The member function ``Thermo::header()``
prints output at the very beginning of a thermodynamic output block and
can be used to print column headers or other front matter. The member
function ``Thermo::footer()`` prints output at the end of a
thermodynamic output block. The formatting of the output is done by
assembling a "line" (which may span multiple lines if the style inserts
newline characters ("\n" as in the "multi" style).
New keywords can also be added to thermo.cpp to compute new quantities
for output. Search for the word "customize" with references to
"keyword" in thermo.cpp to see the several locations where code will
need to be added.
New thermodynamic keywords can also be added to ``thermo.cpp`` to
compute new quantities for output. Search for the word "CUSTOMIZATION"
with references to "keyword" in ``thermo.cpp`` to see the several
locations where code will need to be added. Effectively, you need to
define a member function that computes the property, add an if statement
in ``Thermo::parse_fields()`` where the corresponding header string for
the keyword and the function pointer is registered by calling the
``Thermo::addfield()`` method, and add an if statement in
``Thermo::evaluate_keyword()`` which is called from the ``Variable``
class when a thermo keyword is encountered.
Note that the :doc:`thermo_style custom <thermo_style>` command already allows
for thermo output of quantities calculated by :doc:`fixes <fix>`,
:doc:`computes <compute>`, and :doc:`variables <variable>`. Thus, it may
be simpler to compute what you wish via one of those constructs, than
by adding a new keyword to the thermo command.
.. note::
The third argument to ``Thermo::addfield()`` is a flag indicating
whether the function for the keyword computes a floating point
(FLOAT), regular integer (INT), or big integer (BIGINT) value. This
information is used for formatting the thermodynamic output. Inside
the function the result must then be stored either in the ``dvalue``,
``ivalue`` or ``bivalue`` member variable, respectively.
Since the :doc:`thermo_style custom <thermo_style>` command allows to
use output of quantities calculated by :doc:`fixes <fix>`,
:doc:`computes <compute>`, and :doc:`variables <variable>`, it may often
be simpler to compute what you wish via one of those constructs, rather
than by adding a new keyword to the thermo_style command.

19
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@ -1,8 +1,8 @@
Variable options
================
There is one class that computes and stores :doc:`variable <variable>`
information in LAMMPS; see the file variable.cpp. The value
The ``Variable`` class computes and stores :doc:`variable <variable>`
information in LAMMPS; see the file ``variable.cpp``. The value
associated with a variable can be periodically printed to the screen
via the :doc:`print <print>`, :doc:`fix print <fix_print>`, or
:doc:`thermo_style custom <thermo_style>` commands. Variables of style
@ -19,21 +19,22 @@ of arguments:
compute values = c_mytemp[0], c_thermo_press[3], ...
Adding keywords for the :doc:`thermo_style custom <thermo_style>`
command (which can then be accessed by variables) is discussed on the
:doc:`Modify thermo <Modify_thermo>` doc page.
command (which can then be accessed by variables) is discussed in the
:doc:`Modify thermo <Modify_thermo>` documentation.
Adding a new math function of one or two arguments can be done by
editing one section of the Variable::evaluate() method. Search for
editing one section of the ``Variable::evaluate()`` method. Search for
the word "customize" to find the appropriate location.
Adding a new group function can be done by editing one section of the
Variable::evaluate() method. Search for the word "customize" to find
the appropriate location. You may need to add a new method to the
Group class as well (see the group.cpp file).
``Variable::evaluate()`` method. Search for the word "customize" to
find the appropriate location. You may need to add a new method to the
Group class as well (see the ``group.cpp`` file).
Accessing a new atom-based vector can be done by editing one section
of the Variable::evaluate() method. Search for the word "customize"
to find the appropriate location.
Adding new :doc:`compute styles <compute>` (whose calculated values can
then be accessed by variables) is discussed on the :doc:`Modify compute <Modify_compute>` doc page.
then be accessed by variables) is discussed in the :doc:`Modify compute
<Modify_compute>` documentation.

7
doc/src/Packages_details.rst
View File

@ -9,7 +9,7 @@ gives links to documentation, example scripts, and pictures/movies (if
available) that illustrate use of the package.
The majority of packages can be included in a LAMMPS build with a
single setting (``-D PGK_<NAME>=on`` for CMake) or command
single setting (``-D PKG_<NAME>=on`` for CMake) or command
(``make yes-<name>`` for make). See the :doc:`Build package <Build_package>`
page for more info. A few packages may require additional steps;
this is indicated in the descriptions below. The :doc:`Build extras <Build_extras>`
@ -2181,6 +2181,11 @@ A :doc:`plugin <plugin>` command that can load and unload several
kind of styles in LAMMPS from shared object files at runtime without
having to recompile and relink LAMMPS.
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`` (e.g. ``helloplugin.so``) and will
try to load the contained plugins automatically at start-up.
**Authors:** Axel Kohlmeyer (Temple U)
**Supporting info:**

102
doc/src/Python_install.rst
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@ -25,11 +25,10 @@ Installing the LAMMPS Python Module and Shared Library
======================================================
Making LAMMPS usable within Python and vice versa requires putting the
LAMMPS Python package (``lammps``) into a location where the
Python interpreter can find it and installing the LAMMPS shared library
into a folder that the dynamic loader searches or inside of the installed
``lammps`` package folder. There are multiple ways to achieve
this.
LAMMPS Python package (``lammps``) into a location where the Python
interpreter can find it and installing the LAMMPS shared library into a
folder that the dynamic loader searches or inside of the installed
``lammps`` package folder. There are multiple ways to achieve this.
#. Do a full LAMMPS installation of libraries, executables, selected
headers, documentation (if enabled), and supporting files (only
@ -159,38 +158,52 @@ this.
make install-python
This will try to install (only) the shared library and the Python
package into a system folder and if that fails (due to missing
write permissions) will instead do the installation to a user
folder under ``$HOME/.local``. For a system-wide installation you
This will try to build a so-called (binary) 'wheel', a compressed
binary python package and then install it with the python package
manager 'pip'. Installation will be attempted into a system-wide
``site-packages`` folder and if that fails into the corresponding
folder in the user's home directory. For a system-wide installation you
would have to gain superuser privilege, e.g. though ``sudo``
+------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
+------------------------+----------------------------------------------------------+-------------------------------------------------------------+
| File | Location | Notes |
+========================+=================================================================+=============================================================+
| LAMMPS Python package | * ``$HOME/.local/lib/pythonX.Y/site-packages/lammps`` (32bit) | ``X.Y`` depends on the installed Python version |
| | * ``$HOME/.local/lib64/pythonX.Y/site-packages/lammps`` (64bit) | |
+------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
| LAMMPS shared library | * ``$HOME/.local/lib/pythonX.Y/site-packages/lammps`` (32bit) | ``X.Y`` depends on the installed Python version |
| | * ``$HOME/.local/lib64/pythonX.Y/site-packages/lammps`` (64bit) | |
+------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
+========================+==========================================================+=============================================================+
| LAMMPS Python package | * ``$HOME/.local/lib/pythonX.Y/site-packages/lammps`` | ``X.Y`` depends on the installed Python version |
+------------------------+----------------------------------------------------------+-------------------------------------------------------------+
| LAMMPS shared library | * ``$HOME/.local/lib/pythonX.Y/site-packages/lammps`` | ``X.Y`` depends on the installed Python version |
+------------------------+----------------------------------------------------------+-------------------------------------------------------------+
For a system-wide installation those folders would then become.
+------------------------+---------------------------------------------------------+-------------------------------------------------------------+
+------------------------+-------------------------------------------------+-------------------------------------------------------------+
| File | Location | Notes |
+========================+=========================================================+=============================================================+
| LAMMPS Python package | * ``/usr/lib/pythonX.Y/site-packages/lammps`` (32bit) | ``X.Y`` depends on the installed Python version |
| | * ``/usr/lib64/pythonX.Y/site-packages/lammps`` (64bit) | |
+------------------------+---------------------------------------------------------+-------------------------------------------------------------+
| LAMMPS shared library | * ``/usr/lib/pythonX.Y/site-packages/lammps`` (32bit) | ``X.Y`` depends on the installed Python version |
| | * ``/usr/lib64/pythonX.Y/site-packages/lammps`` (64bit) | |
+------------------------+---------------------------------------------------------+-------------------------------------------------------------+
+========================+=================================================+=============================================================+
| LAMMPS Python package | * ``/usr/lib/pythonX.Y/site-packages/lammps`` | ``X.Y`` depends on the installed Python version |
+------------------------+-------------------------------------------------+-------------------------------------------------------------+
| LAMMPS shared library | * ``/usr/lib/pythonX.Y/site-packages/lammps`` | ``X.Y`` depends on the installed Python version |
+------------------------+-------------------------------------------------+-------------------------------------------------------------+
No environment variables need to be set for those, as those
folders are searched by default by Python or the LAMMPS Python
package.
.. versionchanged:: 24Mar2022
.. note::
If there is an existing installation of the LAMMPS python
module, ``make install-python`` will try to update it.
However, that will fail if the older version of the module
was installed by LAMMPS versions until 17Feb2022. Those
were using the distutils package, which does not create a
"manifest" that allows a clean uninstall. The ``make
install-python`` command will always produce a
lammps-<version>-<python>-<abi>-<os>-<arch>.whl file (the
'wheel'). And this file can be later installed directly with
``python -m pip install <wheel file>.whl`` without having to
type ``make install-python`` again and repeating the build
step, too.
For the traditional make process you can override the python
version to version x.y when calling ``make`` with
``PYTHON=pythonX.Y``. For a CMake based compilation this choice
@ -201,16 +214,12 @@ this.
.. code-block:: bash
$ python install.py -p <python package> -l <shared library> -v <version.h file> [-d <pydir>]
$ python install.py -p <python package> -l <shared library> [-n]
* The ``-p`` flag points to the ``lammps`` Python package folder to be installed,
* the ``-l`` flag points to the LAMMPS shared library file to be installed,
* the ``-v`` flag points to the ``version.h`` file in the LAMMPS source
* and the optional ``-d`` flag to a custom (legacy) installation folder
If you use a legacy installation folder, you will need to set your
``PYTHONPATH`` and ``LD_LIBRARY_PATH`` (and/or ``DYLD_LIBRARY_PATH``) environment
variables accordingly as explained in the description for "In place use".
* and the optional ``-n`` instructs the script to only build a wheel file
but not attempt to install it.
.. tab:: Virtual environment
@ -257,32 +266,29 @@ this.
package and the shared library file are installed into the
following locations:
+------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
+------------------------+--------------------------------------------------------+-------------------------------------------------------------+
| File | Location | Notes |
+========================+=================================================================+=============================================================+
| LAMMPS Python Module | * ``$VIRTUAL_ENV/lib/pythonX.Y/site-packages/lammps`` (32bit) | ``X.Y`` depends on the installed Python version |
| | * ``$VIRTUAL_ENV/lib64/pythonX.Y/site-packages/lammps`` (64bit) | |
+------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
| LAMMPS shared library | * ``$VIRTUAL_ENV/lib/pythonX.Y/site-packages/lammps`` (32bit) | ``X.Y`` depends on the installed Python version |
| | * ``$VIRTUAL_ENV/lib64/pythonX.Y/site-packages/lammps`` (64bit) | |
+------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
+========================+========================================================+=============================================================+
| LAMMPS Python Module | * ``$VIRTUAL_ENV/lib/pythonX.Y/site-packages/lammps`` | ``X.Y`` depends on the installed Python version |
+------------------------+--------------------------------------------------------+-------------------------------------------------------------+
| LAMMPS shared library | * ``$VIRTUAL_ENV/lib/pythonX.Y/site-packages/lammps`` | ``X.Y`` depends on the installed Python version |
+------------------------+--------------------------------------------------------+-------------------------------------------------------------+
If you do a full installation (CMake only) with "install", this
leads to the following installation locations:
+------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
+------------------------+--------------------------------------------------------+-------------------------------------------------------------+
| File | Location | Notes |
+========================+=================================================================+=============================================================+
| LAMMPS Python Module | * ``$VIRTUAL_ENV/lib/pythonX.Y/site-packages/lammps`` (32bit) | ``X.Y`` depends on the installed Python version |
| | * ``$VIRTUAL_ENV/lib64/pythonX.Y/site-packages/lammps`` (64bit) | |
+------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
+========================+========================================================+=============================================================+
| LAMMPS Python Module | * ``$VIRTUAL_ENV/lib/pythonX.Y/site-packages/lammps`` | ``X.Y`` depends on the installed Python version |
+------------------------+--------------------------------------------------------+-------------------------------------------------------------+
| LAMMPS shared library | * ``$VIRTUAL_ENV/lib/`` (32bit) | Set shared loader environment variable to this path |
| | * ``$VIRTUAL_ENV/lib64/`` (64bit) | (see below for more info on this) |
+------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
+------------------------+--------------------------------------------------------+-------------------------------------------------------------+
| LAMMPS executable | * ``$VIRTUAL_ENV/bin/`` | |
+------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
+------------------------+--------------------------------------------------------+-------------------------------------------------------------+
| LAMMPS potential files | * ``$VIRTUAL_ENV/share/lammps/potentials/`` | Set ``LAMMPS_POTENTIALS`` environment variable to this path |
+------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
+------------------------+--------------------------------------------------------+-------------------------------------------------------------+
In that case you need to modify the ``$HOME/myenv/bin/activate``
script in a similar fashion you need to update your

4
doc/src/compute.rst
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@ -247,7 +247,6 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
* :doc:`pe/tally <compute_tally>` - potential energy between two groups of atoms via the tally callback mechanism
* :doc:`plasticity/atom <compute_plasticity_atom>` - Peridynamic plasticity for each atom
* :doc:`pressure <compute_pressure>` - total pressure and pressure tensor
* :doc:`pressure/cylinder <compute_pressure_cylinder>` - pressure tensor in cylindrical coordinates
* :doc:`pressure/uef <compute_pressure_uef>` - pressure tensor in the reference frame of an applied flow field
* :doc:`property/atom <compute_property_atom>` - convert atom attributes to per-atom vectors/arrays
* :doc:`property/chunk <compute_property_chunk>` - extract various per-chunk attributes
@ -290,8 +289,11 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
* :doc:`sph/t/atom <compute_sph_t_atom>` - per-atom internal temperature of Smooth-Particle Hydrodynamics atoms
* :doc:`spin <compute_spin>` - magnetic quantities for a system of atoms having spins
* :doc:`stress/atom <compute_stress_atom>` - stress tensor for each atom
* :doc:`stress/cartesian <compute_stress_profile>` - stress tensor in cartesian coordinates
* :doc:`stress/cylinder <compute_stress_profile>` - stress tensor in cylindrical coordinates
* :doc:`stress/mop <compute_stress_mop>` - normal components of the local stress tensor using the method of planes
* :doc:`stress/mop/profile <compute_stress_mop>` - profile of the normal components of the local stress tensor using the method of planes
* :doc:`stress/spherical <compute_stress_profile>` - stress tensor in spherical coordinates
* :doc:`stress/tally <compute_tally>` - stress between two groups of atoms via the tally callback mechanism
* :doc:`tdpd/cc/atom <compute_tdpd_cc_atom>` - per-atom chemical concentration of a specified species for each tDPD particle
* :doc:`temp <compute_temp>` - temperature of group of atoms

9
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View File

@ -23,11 +23,10 @@ Examples
Description
"""""""""""
Define a computation that calculates the translational momentum
of a group of particles.
The momentum of each particles is computed as m v, where m and v are
the mass and velocity of the particle.
Define a computation that calculates the translational momentum *p*
of a group of particles. It is computed as the sum :math:`\vec{p} = \sum_i m_i \cdot \vec{v}_i`
over all particles in the compute group, where *m* and *v* are
the mass and velocity vector of the particle, respectively.
Output info
"""""""""""

88
doc/src/compute_pressure_cylinder.rst
View File

@ -1,88 +0,0 @@
.. index:: compute pressure/cylinder
compute pressure/cylinder command
=================================
Syntax
""""""
.. parsed-literal::
compute ID group-ID pressure/cylinder zlo zhi Rmax bin_width
* ID, group-ID are documented in :doc:`compute <compute>` command
* pressure/cylinder = style name of this compute command
* zlo = minimum z-boundary for cylinder
* zhi = maximum z-boundary for cylinder
* Rmax = maximum radius to perform calculation to
* bin_width = width of radial bins to use for calculation
Examples
""""""""
.. code-block:: LAMMPS
compute 1 all pressure/cylinder -10.0 10.0 15.0 0.25
Description
"""""""""""
Define a computation that calculates the pressure tensor of a system in
cylindrical coordinates, as discussed in :ref:`(Addington) <Addington1>`.
This is useful for systems with a single axis of rotational symmetry,
such as cylindrical micelles or carbon nanotubes. The compute splits the
system into radial, cylindrical-shell-type bins of width bin_width,
centered at x=0,y=0, and calculates the radial (P_rhorho), azimuthal
(P_phiphi), and axial (P_zz) components of the configurational pressure
tensor. The local density is also calculated for each bin, so that the
true pressure can be recovered as P_kin+P_conf=density\*k\*T+P_conf. The
output is a global array with 5 columns; one each for bin radius, local
number density, P_rhorho, P_phiphi, and P_zz. The number of rows is
governed by the values of Rmax and bin_width. Pressure tensor values are
output in pressure units.
Output info
"""""""""""
This compute calculates a global array with 5 columns and Rmax/bin_width
rows. The output columns are: R (distance units), number density (inverse
volume units), configurational radial pressure (pressure units),
configurational azimuthal pressure (pressure units), and configurational
axial pressure (pressure units).
The values calculated by this compute are
"intensive". The pressure values will be in pressure
:doc:`units <units>`. The number density values will be in
inverse volume :doc:`units <units>`.
Restrictions
""""""""""""
This compute currently calculates the pressure tensor contributions
for pair styles only (i.e. no bond, angle, dihedral, etc. contributions
and in the presence of bonded interactions, the result will be incorrect
due to exclusions for special bonds) and requires pairwise force
calculations not available for most many-body pair styles. K-space
calculations are also excluded. Note that this pressure compute outputs
the configurational terms only; the kinetic contribution is not included
and may be calculated from the number density output by P_kin=density\*k\*T.
This compute is part of the EXTRA-COMPUTE package. It is only enabled
if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
Related commands
""""""""""""""""
:doc:`compute temp <compute_temp>`, :doc:`compute stress/atom <compute_stress_atom>`,
:doc:`thermo_style <thermo_style>`,
Default
"""""""
none
----------
.. _Addington1:
**(Addington)** Addington, Long, Gubbins, J Chem Phys, 149, 084109 (2018).

38
doc/src/compute_sna_atom.rst
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@ -33,7 +33,7 @@ Syntax
* R_1, R_2,... = list of cutoff radii, one for each type (distance units)
* w_1, w_2,... = list of neighbor weights, one for each type
* zero or more keyword/value pairs may be appended
* keyword = *rmin0* or *switchflag* or *bzeroflag* or *quadraticflag* or *chem* or *bnormflag* or *wselfallflag*
* keyword = *rmin0* or *switchflag* or *bzeroflag* or *quadraticflag* or *chem* or *bnormflag* or *wselfallflag* or *bikflag* or *switchinnerflag*
.. parsed-literal::
@ -56,6 +56,12 @@ Syntax
*wselfallflag* value = *0* or *1*
*0* = self-contribution only for element of central atom
*1* = self-contribution for all elements
*bikflag* value = *0* or *1* (only implemented for compute snap)
*0* = per-atom bispectrum descriptors are summed over atoms
*1* = per-atom bispectrum descriptors are not summed over atoms
*switchinnerflag* values = *rinnerlist* *drinnerlist*
*rinnerlist* = *ntypes* values of rinner (distance units)
*drinnerlist* = *ntypes* values of drinner (distance units)
Examples
""""""""
@ -67,6 +73,7 @@ Examples
compute vb all sna/atom 1.4 0.95 6 2.0 1.0
compute snap all snap 1.4 0.95 6 2.0 1.0
compute snap all snap 1.0 0.99363 6 3.81 3.83 1.0 0.93 chem 2 0 1
compute snap all snap 1.0 0.99363 6 3.81 3.83 1.0 0.93 switchinnerflag 1.1 1.3 0.5 0.6
Description
"""""""""""
@ -296,6 +303,35 @@ This option is typically used in conjunction with the *chem* keyword,
and LAMMPS will generate a warning if both *chem* and *bnormflag*
are not both set or not both unset.
The keyword *bikflag* determines whether or not to expand the bispectrum
rows of the global array returned by compute snap. If *bikflag* is set
to *1* then the bispectrum row, which is typically the per-atom bispectrum
descriptors :math:`B_{i,k}` summed over all atoms *i* to produce
:math:`B_k`, becomes bispectrum rows equal to the number of atoms. Thus,
the resulting bispectrum rows are :math:`B_{i,k}` instead of just
:math:`B_k`. In this case, the entries in the final column for these rows
are set to zero.
The keyword *switchinnerflag* activates an additional radial switching
function similar to :math:`f_c(r)` above, but acting to switch off
smoothly contributions from neighbor atoms at short separation distances.
This is useful when SNAP is used in combination with a simple
repulsive potential. The keyword is followed by the *ntypes*
values for :math:`r_{inner}` and the *ntypes*
values for :math:`\Delta r_{inner}`. For a neighbor atom at
distance :math:`r`, its contribution is scaled by a multiplicative
factor :math:`f_{inner}(r)` defined as follows:
.. math::
= & 0, r \leq r_{inner} \\
f_{inner}(r) = & \frac{1}{2}(1 - \cos(\pi \frac{r-r_{inner}}{\Delta r_{inner}})), r_{inner} < r \leq r_{inner} + \Delta r_{inner} \\
= & 1, r > r_{inner} + \Delta r_{inner}
The values of :math:`r_{inner}` and :math:`\Delta r_{inner}` are
the arithmetic means of the values for the central atom of type I
and the neighbor atom of type J.
.. note::
If you have a bonded system, then the settings of :doc:`special_bonds

25
doc/src/compute_stress_mop.rst
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@ -68,7 +68,19 @@ configurational stress (conf), and/or total stress (total).
NOTE 1: The configurational stress is computed considering all pairs of atoms where at least one atom belongs to group group-ID.
NOTE 2: The local stress does not include any Lennard-Jones tail
corrections to the pressure added by the :doc:`pair_modify tail yes <pair_modify>` command, since those are contributions to the global system pressure.
corrections to the stress added by the :doc:`pair_modify tail yes <pair_modify>`
command, since those are contributions to the global system pressure.
NOTE 3: The local stress profile generated by compute *stress/mop/profile*
is similar to that obtained by compute
:doc:`stress/cartesian <compute_stress_profile>`.
A key difference
is that compute *stress/mop/profile* considers particles
crossing a set of planes,
while compute *stress/cartesian* computes averages for a set of
small volumes. More information
on the similarities and differences can be found in
:ref:`(Ikeshoji)<Ikeshoji2>`.
Output info
"""""""""""
@ -87,7 +99,10 @@ and stress_dir,z.
The values are in pressure :doc:`units <units>`.
The values produced by this compute can be accessed by various :doc:`output commands <Howto_output>`. For instance, the results can be written to a file using the :doc:`fix ave/time <fix_ave_time>` command. Please see the example in the examples/PACKAGES/mop folder.
The values produced by this compute can be accessed by various :doc:`output commands <Howto_output>`.
For instance, the results can be written to a file using the
:doc:`fix ave/time <fix_ave_time>` command. Please see the example
in the examples/PACKAGES/mop folder.
Restrictions
""""""""""""
@ -107,7 +122,7 @@ intra-molecular interactions, and long range (kspace) interactions.
Related commands
""""""""""""""""
:doc:`compute stress/atom <compute_stress_atom>`
:doc:`compute stress/atom <compute_stress_atom>`, :doc:`compute pressure <compute_pressure>`, :doc:`compute stress/cartesian <compute_stress_profile>`, :doc:`compute stress/cylinder <compute_stress_profile>`, :doc:`compute stress/spherical <compute_stress_profile>`
Default
"""""""
@ -120,3 +135,7 @@ none
**(Todd)** B. D. Todd, Denis J. Evans, and Peter J. Daivis: "Pressure tensor for inhomogeneous fluids",
Phys. Rev. E 52, 1627 (1995).
.. _Ikeshoji3:
**(Ikeshoji)** Ikeshoji, Hafskjold, Furuholt, Mol Sim, 29, 101-109, (2003).

165
doc/src/compute_stress_profile.rst Normal file
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@ -0,0 +1,165 @@
.. index:: compute stress/cartesian
.. index:: compute stress/cylinder
.. index:: compute stress/spherical
compute stress/cartesian command
==================================
compute stress/cylinder command
=================================
compute stress/spherical command
==================================
Syntax
""""""
.. parsed-literal::
compute ID group-ID style args
* ID, group-ID are documented in :doc:`compute <compute>` command
* style = stress/cartesian or stress/spherical or stress/cylinder
* args = argument specific to the compute style
.. parsed-literal::
*stress/cartesian* args = dim bin_width
dim = x, y, or z. One or two dim/bin_width pairs may be appended
bin_width = width of the bin
*stress/cylinder* args = zlo zh Rmax bin_width keyword
zlo = minimum z-boundary for cylinder
zhi = maximum z-boundary for cylinder
Rmax = maximum radius to perform calculation to
bin_width = width of radial bins to use for calculation
keyword = ke (zero or one can be specified)
ke = yes or no
*stress/spherical*
x0, y0, z0 = origin of the spherical coordinate system
bin_width = width of spherical shells
Rmax = maximum radius of spherical shells
Examples
""""""""
.. code-block:: LAMMPS
compute 1 all stress/cartesian x 0.1
compute 1 all stress/cartesian y 0.25 z 0.1
compute 1 all stress/cylinder -10.0 10.0 15.0 0.25
compute 1 all stress/cylinder -10.0 10.0 15.0 0.25 ke no
compute 1 all stress/spherical 0 0 0 0.1 10
Description
"""""""""""
Compute *stress/cartesian*, compute *stress/cylinder*, and compute
*stress/spherical* define computations that calculate profiles of the
diagonal components of the local stress tensor in the specified
coordinate system. The stress tensor is split into a kinetic
contribution :math:`P^k` and a virial contribution :math:`P^v`. The sum
gives the total stress tensor :math:`P = P^k+P^v`. These computes can
for example be used to calculate the diagonal components of the local
stress tensor of interfaces with flat, cylindrical, or spherical
symmetry. These computes obeys momentum balance through fluid
interfaces. They use the Irving-Kirkwood contour, which is the straight
line between particle pairs.
The *stress/cartesian* computes the stress profile along one or two
Cartesian coordinates, as described in :ref:`(Ikeshoji)<Ikeshoji2>`. The
compute *stress/cylinder* computes the stress profile along the
radial direction in cylindrical coordinates, as described in
:ref:`(Addington)<Addington1>`. The compute *stress/spherical*
computes the stress profile along the radial direction in spherical
coordinates, as described in :ref:`(Ikeshoji)<Ikeshoji2>`.
Output info
"""""""""""
The output columns for *stress/cartesian* are the position of the
center of the local volume in the first and second dimensions, number
density, :math:`P^k_{xx}`, :math:`P^k_{yy}`, :math:`P^k_{zz}`,
:math:`P^v_{xx}`, :math:`P^v_{yy}`, and :math:`P^v_{zz}`. There are 8
columns when one dimension is specified and 9 columns when two
dimensions are specified. The number of bins/rows are
(L1/bin_width1)*(L2/bin_width2), L1 and L2 are the sizes of the
simulation box in the specified dimensions, and bin_width1 and
bin_width2 are the specified bin widths. When only one dimension is
specified the number of bins/rows are L1/bin_width.
The default output columns for *stress/cylinder* are the radius to the
center of the cylindrical shell, number density, :math:`P^k_{rr}`,
:math:`P^k_{\phi\phi}`, :math:`P^k_{zz}`, :math:`P^v_{rr}`,
:math:`P^v_{\phi\phi}`, and :math:`P^v_{zz}`. When the keyword *ke* is
set to no, the kinetic contributions are not calculated, and
consequently there are only 5 columns the radius to the center of the
cylindrical shell, number density, :math:`P^v_{rr}`,
:math:`P^v_{\phi\phi}`, :math:`P^v_{zz}`. The number of bins/rows are
Rmax/bin_width.
The output columns for *stress/spherical* are the radius to the center
of the spherical shell, number density, :math:`P^k_{rr}`,
:math:`P^k_{\theta\theta}`, :math:`P^k_{\phi\phi}`, :math:`P^v_{rr}`,
:math:`P^v_{\theta\theta}`, and :math:`P^v_{\phi\phi}`. There are 8
columns and the number of bins/rows are Rmax/bin_width.
This array can be output with :doc:`fix ave/time <fix_ave_time>`,
.. code-block:: LAMMPS
compute p all stress/cartesian x 0.1
fix 2 all ave/time 100 1 100 c_p[*] file dump_p.out mode vector
The values calculated by this compute are "intensive". The stress
values will be in pressure :doc:`units <units>`. The number density
values are in inverse volume :doc:`units <units>`.
NOTE 1: The local stress does not include any Lennard-Jones tail
corrections to the stress added by the :doc:`pair_modify tail yes <pair_modify>`
command, since those are contributions to the global system pressure.
NOTE 2: The local stress profiles generated by these computes are
similar to those obtained by the
:doc:`method-of-planes (MOP) <compute_stress_mop>`.
A key difference
is that compute `stress/mop/profile <compute_stress_mop>`
considers particles crossing a set of planes, while
*stress/cartesian* computes averages for a set of small volumes.
More information on the similarities and differences can be found in
:ref:`(Ikeshoji)<Ikeshoji2>`.
Restrictions
""""""""""""
These computes calculate the stress tensor contributions for pair
styles only (i.e. no bond, angle, dihedral, etc. contributions, and in
the presence of bonded interactions, the result will be incorrect due to
exclusions for special bonds) and requires pairwise force calculations
not available for most many-body pair styles. K-space calculations are
also excluded.
These computes are part of the EXTRA-COMPUTE package. They are only
enabled if LAMMPS was built with that package. See the :doc:`Build
package <Build_package>` doc page for more info.
Related commands
""""""""""""""""
:doc:`compute stress/atom <compute_stress_atom>`, :doc:`compute pressure <compute_pressure>`, :doc:`compute stress/mop/profile <compute_stress_mop>`
Default
"""""""
The keyword default for ke in style *stress/cylinder* is yes.
----------
.. _Ikeshoji2:
**(Ikeshoji)** Ikeshoji, Hafskjold, Furuholt, Mol Sim, 29, 101-109, (2003).
.. _Addington1:
**(Addington)** Addington, Long, Gubbins, J Chem Phys, 149, 084109 (2018).

30
doc/src/compute_tally.rst
View File

@ -31,7 +31,7 @@ Syntax
compute ID group-ID style group2-ID
* ID, group-ID are documented in :doc:`compute <compute>` command
* style = *force/tally* or *heat/flux/tally* or *heat/flux/virial/tally* or * or *pe/tally* or *pe/mol/tally* or *stress/tally*
* style = *force/tally* or *heat/flux/tally* or *heat/flux/virial/tally* or *pe/tally* or *pe/mol/tally* or *stress/tally*
* group2-ID = group ID of second (or same) group
Examples
@ -61,7 +61,7 @@ mechanism. Compute *pe/mol/tally* is one such style, that can
- through using this mechanism - separately tally intermolecular
and intramolecular energies. Something that would otherwise be
impossible without integrating this as a core functionality into
the based classes of LAMMPS.
the base classes of LAMMPS.
----------
@ -148,27 +148,35 @@ pairwise property computations.
Output info
"""""""""""
Compute *pe/tally* calculates a global scalar (the energy) and a per
- Compute *pe/tally* calculates a global scalar (the energy) and a per
atom scalar (the contributions of the single atom to the global
scalar). Compute *pe/mol/tally* calculates a global 4-element vector
containing (in this order): *evdwl* and *ecoul* for intramolecular pairs
and *evdwl* and *ecoul* for intermolecular pairs. Since molecules are
scalar).
- Compute *pe/mol/tally* calculates a global 4-element vector containing
(in this order): *evdwl* and *ecoul* for intramolecular pairs and
*evdwl* and *ecoul* for intermolecular pairs. Since molecules are
identified by their molecule IDs, the partitioning does not have to be
related to molecules, but the energies are tallied into the respective
slots depending on whether the molecule IDs of a pair are the same or
different. Compute *force/tally* calculates a global scalar (the force
magnitude) and a per atom 3-element vector (force contribution from
each atom). Compute *stress/tally* calculates a global scalar
different.
- Compute *force/tally* calculates a global scalar (the force magnitude)
and a per atom 3-element vector (force contribution from each atom).
- Compute *stress/tally* calculates a global scalar
(average of the diagonal elements of the stress tensor) and a per atom
vector (the 6 elements of stress tensor contributions from the
individual atom). As in :doc:`compute heat/flux <compute_heat_flux>`,
individual atom).
- As in :doc:`compute heat/flux <compute_heat_flux>`,
compute *heat/flux/tally* calculates a global vector of length 6,
where the first 3 components are the :math:`x`, :math:`y`, :math:`z`
components of the full heat flow vector,
and the next 3 components are the corresponding components
of just the convective portion of the flow, i.e. the
first term in the equation for :math:`\mathbf{Q}`.
Compute *heat/flux/virial/tally* calculates a global scalar (heat flow)
- Compute *heat/flux/virial/tally* calculates a global scalar (heat flow)
and a per atom 3-element vector
(contribution to the force acting over atoms in the first group
from individual atoms in both groups).

2
doc/src/fix.rst
View File

@ -240,8 +240,6 @@ accelerated styles exist.
* :doc:`latte <fix_latte>` - wrapper on LATTE density-functional tight-binding code
* :doc:`lb/fluid <fix_lb_fluid>` -
* :doc:`lb/momentum <fix_lb_momentum>` -
* :doc:`lb/pc <fix_lb_pc>` -
* :doc:`lb/rigid/pc/sphere <fix_lb_rigid_pc_sphere>` -
* :doc:`lb/viscous <fix_lb_viscous>` -
* :doc:`lineforce <fix_lineforce>` - constrain atoms to move in a line
* :doc:`manifoldforce <fix_manifoldforce>` - restrain atoms to a manifold during minimization

9
doc/src/fix_gcmc.rst
View File

@ -444,8 +444,15 @@ doc page for more info.
Do not set "neigh_modify once yes" or else this fix will never be
called. Reneighboring is required.
Only usable for 3D simulations.
Can be run in parallel, but aspects of the GCMC part will not scale
well in parallel. Only usable for 3D simulations.
well in parallel. Currently, molecule translations and rotations
are not supported with more than one MPI process.
It is still possible to do parallel molecule exchange without
translation and rotation moves by setting MC moves to zero
and/or by using the *mcmoves* keyword with *Pmoltrans* = *Pmolrotate* = 0 .
When using fix gcmc in combination with fix shake or fix rigid,
only GCMC exchange moves are supported, so the argument

451
doc/src/fix_lb_fluid.rst
View File

@ -12,55 +12,65 @@ Syntax
* ID, group-ID are documented in :doc:`fix <fix>` command
* lb/fluid = style name of this fix command
* nevery = update the lattice-Boltzmann fluid every this many timesteps
* LBtype = 1 to use the standard finite difference LB integrator,
2 to use the LB integrator of :ref:`Ollila et al. <Ollila>`
* nevery = update the lattice-Boltzmann fluid every this many timesteps (should normally be 1)
* viscosity = the fluid viscosity (units of mass/(time\*length)).
* density = the fluid density.
* zero or more keyword/value pairs may be appended
* keyword = *setArea* or *setGamma* or *scaleGamma* or *dx* or *dm* or *a0* or *noise* or *calcforce* or *trilinear* or *D3Q19* or *read_restart* or *write_restart* or *zwall_velocity* or *bodyforce* or *printfluid*
* keyword = *dx* or *dm* or *noise* or *stencil* or *read_restart* or *write_restart* or *zwall_velocity* or *pressurebcx* or *bodyforce* or *D3Q19* or *dumpxdmf* or *dof* or *scaleGamma* or *a0* or *npits* or *wp* or *sw*
.. parsed-literal::
*setArea* values = type node_area
type = atom type (1-N)
node_area = portion of the surface area of the composite object associated with the particular atom type (used when the force coupling constant is set by default).
*setGamma* values = gamma
gamma = user set value for the force coupling constant.
*scaleGamma* values = type gammaFactor
type = atom type (1-N)
gammaFactor = factor to scale the *setGamma* gamma value by, for the specified atom type.
*dx* values = dx_LB = the lattice spacing.
*dm* values = dm_LB = the lattice-Boltzmann mass unit.
*a0* values = a_0_real = the square of the speed of sound in the fluid.
*noise* values = Temperature seed
Temperature = fluid temperature.
seed = random number generator seed (positive integer)
*calcforce* values = N forcegroup-ID
N = output the force and torque every N timesteps
forcegroup-ID = ID of the particle group to calculate the force and torque of
*trilinear* values = none (used to switch from the default Peskin interpolation stencil to the trilinear stencil).
*D3Q19* values = none (used to switch from the default D3Q15, 15 velocity lattice, to the D3Q19, 19 velocity lattice).
*stencil* values = 2 (trilinear stencil, the default), 3 (3-point immersed boundary stencil), or 4 (4-point Keys' interpolation stencil)
*read_restart* values = restart file = name of the restart file to use to restart a fluid run.
*write_restart* values = N = write a restart file every N MD timesteps.
*zwall_velocity* values = velocity_bottom velocity_top = velocities along the y-direction of the bottom and top walls (located at z=zmin and z=zmax).
*pressurebcx* values = pgradav = imposes a pressure jump at the (periodic) x-boundary of pgradav*Lx*1000.
*bodyforce* values = bodyforcex bodyforcey bodyforcez = the x,y and z components of a constant body force added to the fluid.
*printfluid* values = N = print the fluid density and velocity at each grid point every N timesteps.
*D3Q19* values = none (used to switch from the default D3Q15, 15 velocity lattice, to the D3Q19, 19 velocity lattice).
*dumpxdmf* values = N file timeI
N = output the force and torque every N timesteps
file = output file name
timeI = 1 (use simulation time to index xdmf file), 0 (use output frame number to index xdmf file)
*dof* values = dof = specify the number of degrees of freedom for temperature calculation
*scaleGamma* values = type gammaFactor
type = atom type (1-N)
gammaFactor = factor to scale the *setGamma* gamma value by, for the specified atom type.
*a0* values = a_0_real = the square of the speed of sound in the fluid.
*npits* values = npits h_p l_p l_pp l_e
npits = number of pit regions
h_p = z-height of pit regions (floor to bottom of slit)
l_p = x-length of pit regions
l_pp = x-length of slit regions between consecutive pits
l_e = x-length of slit regions at ends
*wp* values = w_p = y-width of slit regions (defaults to full width if not present or if sw active)
*sw* values = none (turns on y-sidewalls (in xz plane) if npits option active)
Examples
""""""""
.. code-block:: LAMMPS
fix 1 all lb/fluid 1 2 1.0 1.0 setGamma 13.0 dx 4.0 dm 10.0 calcforce sphere1
fix 1 all lb/fluid 1 1 1.0 0.0009982071 setArea 1 1.144592082 dx 2.0 dm 0.3 trilinear noise 300.0 8979873
fix 1 all lb/fluid 1 1.0 0.0009982071 dx 1.2 dm 0.001
fix 1 all lb/fluid 1 1.0 0.0009982071 dx 1.2 dm 0.001 noise 300.0 2761
fix 1 all lb/fluid 1 1.0 1.0 dx 4.0 dm 10.0 dumpxdmf 500 fflow 0 pressurebcx 0.01 npits 2 20 40 5 0 wp 30
Description
"""""""""""
Implement a lattice-Boltzmann fluid on a uniform mesh covering the LAMMPS
simulation domain. The MD particles described by *group-ID* apply a velocity
dependent force to the fluid.
.. versionchanged:: 24Mar2022
Implement a lattice-Boltzmann fluid on a uniform mesh covering the
LAMMPS simulation domain. Note that this fix was updated in 2022 and is
not backward compatible with the previous version. If you need the
previous version, please download an older version of LAMMPS. The MD
particles described by *group-ID* apply a velocity dependent force to
the fluid.
The lattice-Boltzmann algorithm solves for the fluid motion governed by
the Navier Stokes equations,
@ -86,28 +96,23 @@ respectively. Here, we have implemented
\sigma_{\alpha \beta} = -P_{\alpha \beta} = -\rho a_0 \delta_{\alpha \beta}
with :math:`a_0` set to :math:`\frac{1}{3} \frac{dx}{dt}^2` by default.
You should not normally need to change this default.
The algorithm involves tracking the time evolution of a set of partial
distribution functions which evolve according to a velocity
discretized version of the Boltzmann equation,
distribution functions which evolve according to a velocity discretized
version of the Boltzmann equation,
.. math::
\left(\partial_t + e_{i\alpha}\partial_{\alpha}\right)f_i = -\frac{1}{\tau}\left(f_i - f_i^{eq}\right) + W_i
where the first term on the right hand side represents a single time
relaxation towards the equilibrium distribution function, and :math:`\tau` is a
parameter physically related to the viscosity. On a technical note,
we have implemented a 15 velocity model (D3Q15) as default; however,
the user can switch to a 19 velocity model (D3Q19) through the use of
the *D3Q19* keyword. This fix provides the user with the choice of
two algorithms to solve this equation, through the specification of
the keyword *LBtype*\ . If *LBtype* is set equal to 1, the standard
finite difference LB integrator is used. If *LBtype* is set equal to
2, the algorithm of :ref:`Ollila et al. <Ollila>` is used.
Physical variables are then defined in terms of moments of the distribution
functions,
relaxation towards the equilibrium distribution function, and
:math:`\tau` is a parameter physically related to the viscosity. On a
technical note, we have implemented a 15 velocity model (D3Q15) as
default; however, the user can switch to a 19 velocity model (D3Q19)
through the use of the *D3Q19* keyword. Physical variables are then
defined in terms of moments of the distribution functions,
.. math::
@ -115,7 +120,7 @@ functions,
\rho u_{\alpha} = & \displaystyle\sum\limits_{i} f_i e_{i\alpha}
Full details of the lattice-Boltzmann algorithm used can be found in
:ref:`Mackay et al. <fluid-Mackay>`.
:ref:`Denniston et al. <fluid-Denniston>`.
The fluid is coupled to the MD particles described by *group-ID* through
a velocity dependent force. The contribution to the fluid force on a
@ -127,90 +132,64 @@ calculated as:
{\bf F}_{j \alpha} = \gamma \left({\bf v}_n - {\bf u}_f \right) \zeta_{j\alpha}
where :math:`\mathbf{v}_n` is the velocity of the MD particle,
:math:`\mathbf{u}_f` is the fluid
velocity interpolated to the particle location, and :math:`\gamma` is the force
coupling constant. :math:`\zeta` is a weight assigned to the grid point,
obtained by distributing the particle to the nearest lattice sites.
For this, the user has the choice between a trilinear stencil, which
provides a support of 8 lattice sites, or the immersed boundary method
Peskin stencil, which provides a support of 64 lattice sites. While
the Peskin stencil is seen to provide more stable results, the
trilinear stencil may be better suited for simulation of objects close
to walls, due to its smaller support. Therefore, by default, the
Peskin stencil is used; however the user may switch to the trilinear
stencil by specifying the keyword, *trilinear*\ .
:math:`\mathbf{u}_f` is the fluid velocity interpolated to the particle
location, and :math:`\gamma` is the force coupling constant. This
force, as with most forces in LAMMPS, and hence the velocities, are
calculated at the half-time step. :math:`\zeta` is a weight assigned to
the grid point, obtained by distributing the particle to the nearest
lattice sites.
By default, the force coupling constant, :math:`\gamma`, is calculated
The force coupling constant, :math:`\gamma`, is calculated
according to
.. math::
\gamma = \frac{2m_um_v}{m_u+m_v}\left(\frac{1}{\Delta t_{collision}}\right)
\gamma = \frac{2m_um_v}{m_u+m_v}\left(\frac{1}{\Delta t}\right)
Here, :math:`m_v` is the mass of the MD particle, :math:`m_u` is a
representative fluid mass at the particle location, and :math:`\Delta
t_{collision}` is a collision time, chosen such that
:math:`\frac{\tau}{\Delta t_{collision}} = 1` (see :ref:`Mackay and
Denniston <Mackay2>` for full details). In order to calculate :math:`m_u`,
the fluid density is interpolated to the MD particle location, and
multiplied by a volume, node_area * :math:`dx_{LB}`, where node_area
represents the portion of the surface area of the composite object
associated with a given MD particle. By default, node_area is set
equal to :math:`dx_{LB}^2`; however specific values for given atom types
can be set using the *setArea* keyword.
The user also has the option of specifying their own value for the
force coupling constant, for all the MD particles associated with the
fix, through the use of the *setGamma* keyword. This may be useful
when modelling porous particles. See :ref:`Mackay et al. <fluid-Mackay>` for a
detailed description of the method by which the user can choose an
appropriate :math:`\gamma` value.
representative fluid mass at the particle location, and :math:`\Delta t`
is the time step. The fluid mass :math:`m_u` that the MD particle
interacts with is calculated internally. This coupling is chosen to
constrain the particle and associated fluid velocity to match at the end
of the time step. As with other constraints, such as :doc:`shake
<fix_shake>`, this constraint can remove degrees of freedom from the
simulation which are accounted for internally in the algorithm.
.. note::
while this fix applies the force of the particles on the fluid,
it does not apply the force of the fluid to the particles. When the
force coupling constant is set using the default method, there is only
one option to include this hydrodynamic force on the particles, and
that is through the use of the :doc:`lb/viscous <fix_lb_viscous>` fix.
This fix adds the hydrodynamic force to the total force acting on the
particles, after which any of the built-in LAMMPS integrators can be
used to integrate the particle motion. However, if the user specifies
their own value for the force coupling constant, as mentioned in
:ref:`Mackay et al. <fluid-Mackay>`, the built-in LAMMPS integrators may prove to
be unstable. Therefore, we have included our own integrators
:doc:`fix lb/rigid/pc/sphere <fix_lb_rigid_pc_sphere>`, and
:doc:`fix lb/pc <fix_lb_pc>`, to solve for the particle motion in these
cases. These integrators should not be used with the
:doc:`lb/viscous <fix_lb_viscous>` fix, as they add hydrodynamic forces
to the particles directly. In addition, they can not be used if the
force coupling constant has been set the default way.
.. note::
if the force coupling constant is set using the default method,
and the :doc:`lb/viscous <fix_lb_viscous>` fix is NOT used to add the
While this fix applies the force of the particles on the fluid, it
does not apply the force of the fluid to the particles. There is
only one option to include this hydrodynamic force on the particles,
and that is through the use of the :doc:`lb/viscous <fix_lb_viscous>`
fix. This fix adds the hydrodynamic force to the total force acting
on the particles, after which any of the built-in LAMMPS integrators
can be used to integrate the particle motion. If the
:doc:`lb/viscous <fix_lb_viscous>` fix is NOT used to add the
hydrodynamic force to the total force acting on the particles, this
physically corresponds to a situation in which an infinitely massive
particle is moving through the fluid (since collisions between the
particle and the fluid do not act to change the particle's velocity).
Therefore, the user should set the mass of the particle to be
significantly larger than the mass of the fluid at the particle
location, in order to approximate an infinitely massive particle (see
the dragforce test run for an example).
In this case, setting *scaleGamma* to -1 for the corresponding
particle type will explicitly take this limit (of infinite particle
mass) in computing the force coupling for the fluid force.
----------
Inside the fix, parameters are scaled by the lattice-Boltzmann
Physical parameters describing the fluid are specified through
*viscosity* and *density*. These parameters should all be given in
terms of the mass, distance, and time units chosen for the main LAMMPS
run, as they are scaled by the LB timestep, lattice spacing, and mass
unit, inside the fix.
The *dx* keyword allows the user to specify a value for the LB grid
spacing and the *dm* keyword allows the user to specify the LB mass
unit. Inside the fix, parameters are scaled by the lattice-Boltzmann
timestep, :math:`dt_{LB}`, grid spacing, :math:`dx_{LB}`, and mass unit,
:math:`dm_{LB}`. :math:`dt_{LB}` is set equal to
:math:`\mathrm{nevery}\cdot dt_{MD}`, where :math:`dt_{MD}` is the MD timestep.
By default,
:math:`dm_{LB}` is set equal to 1.0, and :math:`dx_{LB}` is chosen so that
:math:`\frac{\tau}{dt} = \frac{3\eta dt}{\rho dx^2}` is approximately equal to 1.
However, the user has the option of specifying their own values for
:math:`dm_{LB}`, and :math:`dx_{LB}`, by using
the optional keywords *dm*, and *dx* respectively.
:math:`\mathrm{nevery}\cdot dt_{MD}`, where :math:`dt_{MD}` is the MD
timestep. By default, :math:`dm_{LB}` is set equal to 1.0, and
:math:`dx_{LB}` is chosen so that :math:`\frac{\tau}{dt} = \frac{3\eta
dt}{\rho dx^2}` is approximately equal to 1.
.. note::
@ -223,74 +202,27 @@ the optional keywords *dm*, and *dx* respectively.
with equal lengths in all dimensions, and the default value for
:math:`dx_{LB}` is used, this will automatically be satisfied.
Physical parameters describing the fluid are specified through
*viscosity*, *density*, and *a0*\ . If the force coupling constant is
set the default way, the surface area associated with the MD particles
is specified using the *setArea* keyword. If the user chooses to
specify a value for the force coupling constant, this is set using the
*setGamma* keyword. These parameters should all be given in terms of
the mass, distance, and time units chosen for the main LAMMPS run, as
they are scaled by the LB timestep, lattice spacing, and mass unit,
inside the fix.
----------
The *setArea* keyword allows the user to associate a surface area with
a given atom type. For example if a spherical composite object of
radius R is represented as a spherical shell of N evenly distributed
MD particles, all of the same type, the surface area per particle
associated with that atom type should be set equal to :math:`\frac{4\pi R^2}{N}`.
This keyword should only be used if the force coupling constant,
:math:`\gamma`, is set the default way.
The *setGamma* keyword allows the user to specify their own value for
the force coupling constant, :math:`\gamma`, instead of using the default
value.
The *scaleGamma* keyword should be used in conjunction with the
*setGamma* keyword, when the user wishes to specify different :math:`\gamma`
values for different atom types. This keyword allows the user to
scale the *setGamma* :math:`\gamma` value by a factor, gammaFactor,
for a given atom type.
The *dx* keyword allows the user to specify a value for the LB grid
spacing.
The *dm* keyword allows the user to specify the LB mass unit.
If the *a0* keyword is used, the value specified is used for the
square of the speed of sound in the fluid. If this keyword is not
present, the speed of sound squared is set equal to
:math:`\frac{1}{3}\left(\frac{dx_{LB}}{dt_{LB}}\right)^2`.
Setting :math:`a0 > (\frac{dx_{LB}}{dt_{LB}})^2` is not allowed,
as this may lead to instabilities.
If the *noise* keyword is used, followed by a positive temperature
value, and a positive integer random number seed, a thermal
lattice-Boltzmann algorithm is used. If *LBtype* is set equal to 1
(i.e. the standard LB integrator is chosen), the thermal LB algorithm
of :ref:`Adhikari et al. <Adhikari>` is used; however if *LBtype* is set
equal to 2 both the LB integrator, and thermal LB algorithm described
in :ref:`Ollila et al. <Ollila>` are used.
value, and a positive integer random number seed, the thermal LB algorithm
of :ref:`Adhikari et al. <Adhikari>` is used.
If the *calcforce* keyword is used, both the fluid force and torque
acting on the specified particle group are printed to the screen every
N timesteps.
If the keyword *stencil* is used, the value sets the number of
interpolation points used in each direction. For this, the user has the
choice between a trilinear stencil (*stencil* 2), which provides a
support of 8 lattice sites, or the 3-point immersed boundary method
stencil (*stencil* 3), which provides a support of 27 lattice sites, or
the 4-point Keys' interpolation stencil (stencil 4), which provides a
support of 64 lattice sites. The trilinear stencil is the default as it
is better suited for simulation of objects close to walls or other
objects, due to its smaller support. The 3-point stencil provides
smoother motion of the lattice and is suitable for particles not likely
to be to close to walls or other objects.
If the keyword *trilinear* is used, the trilinear stencil is used to
interpolate the particle nodes onto the fluid mesh. By default, the
immersed boundary method, Peskin stencil is used. Both of these
interpolation methods are described in :ref:`Mackay et al. <fluid-Mackay>`.
If the keyword *D3Q19* is used, the 19 velocity (D3Q19) lattice is
used by the lattice-Boltzmann algorithm. By default, the 15 velocity
(D3Q15) lattice is used.
If the keyword *write_restart* is used, followed by a positive
integer, N, a binary restart file is printed every N LB timesteps.
This restart file only contains information about the fluid.
Therefore, a LAMMPS restart file should also be written in order to
print out full details of the simulation.
If the keyword *write_restart* is used, followed by a positive integer,
N, a binary restart file is printed every N LB timesteps. This restart
file only contains information about the fluid. Therefore, a LAMMPS
restart file should also be written in order to print out full details
of the simulation.
.. note::
@ -308,19 +240,100 @@ conditions in the z-direction. If fixed boundary conditions are
present in the z-direction, and this keyword is not used, the walls
are assumed to be stationary.
If the *pressurebcx* keyword is used, a pressure jump (implemented by a
step jump in density) is imposed at the (periodic) x-boundary. The
value set specifies what would be the resulting equilibrium average
pressure gradient in the x-direction if the system had a constant
cross-section (i.e. resistance to flow). It is converted to a pressure
jump by multiplication by the system size in the x-direction. As this
value should normally be quite small, it is also assumed to be scaled
by 1000.
If the *bodyforce* keyword is used, a constant body force is added to
the fluid, defined by it's x, y and z components.
If the *printfluid* keyword is used, followed by a positive integer, N,
the fluid densities and velocities at each lattice site are printed to the
screen every N timesteps.
If the keyword *D3Q19* is used, the 19 velocity (D3Q19) lattice is
used by the lattice-Boltzmann algorithm. By default, the 15 velocity
(D3Q15) lattice is used.
If the *dumpxdmf* keyword is used, followed by a positive integer, N,
and a file name, the fluid densities and velocities at each lattice site
are output to an xdmf file every N timesteps. This is a binary file
format that can be read by visualization packages such as `Paraview
<https://www.paraview.org/>`_ . The xdmf file format contains a time
index for each frame dump and the value timeI = 1 uses simulation time
while 0 uses the output frame number to index xdmf file. The later can
be useful if the :doc:`dump vtk <dump_vtk>` command is used to output
the particle positions at the same timesteps and you want to visualize
both the fluid and particle data together in `Paraview
<https://www.paraview.org/>`_ .
The *scaleGamma* keyword allows the user to scale the :math:`\gamma`
value by a factor, gammaFactor, for a given atom type. Setting
*scaleGamma* to -1 for the corresponding particle type will explicitly
take the limit of infinite particle mass in computing the force coupling
for the fluid force (see note above).
If the *a0* keyword is used, the value specified is used for the square
of the speed of sound in the fluid. If this keyword is not present, the
speed of sound squared is set equal to
:math:`\frac{1}{3}\left(\frac{dx_{LB}}{dt_{LB}}\right)^2`. Setting
:math:`a0 > (\frac{dx_{LB}}{dt_{LB}})^2` is not allowed, as this may
lead to instabilities. As the speed of sound should usually be much
larger than any fluid velocity of interest, its value does not normally
have a significant impact on the results. As such, it is usually best
to use the default for this option.
The *npits* keyword (followed by integer arguments: npits, h_p, l_p,
l_pp, l_e) sets the fluid domain to the pits geometry. These arguments
should only be used if you actually want something more complex than a
rectangular/cubic geometry. The npits value sets the number of pits
regions (arranged along x). The remaining arguments are sizes measured
in multiples of dx_lb: h_p is the z-height of the pit regions, l_p is
the x-length of the pit regions, l_pp is the length of the region
between consecutive pits (referred to as a "slit" region), and l_e is
the x-length of the slit regions at each end of the channel. The pit
geometry must fill the system in the x-direction but can be longer, in
which case it is truncated (which enables asymmetric entrance/exit end
sections). The additional *wp* keyword allows the width (in
y-direction) of the pit to be specified (the default is full width) and
the *sw* keyword indicates that there should be sidewalls in the
y-direction (default is periodic in y-direction). These parameters are
illustrated below::
Sideview (in xz plane) of pit geometry:
______________________________________________________________________
slit slit slit ^
|
<---le---><---------lp-------><---lpp---><-------lp--------><---le---> hs = (Nbz-1) - hp
|
__________ __________ __________ v
| | | | ^ z
| | | | | |
| pit | | pit | hp +-x
| | | | |
|__________________| |__________________| v
Endview (in yz plane) of pit geometry (no sw so wp is active):
_____________________
^
|
hs
|
_____________________ v
| | ^
| | | z
|<---wp--->| hp |
| | | +-y
|__________| v
----------
For further details, as well as descriptions and results of several
test runs, see :ref:`Mackay et al. <fluid-Mackay>`. Please include a citation to
this paper if the lb_fluid fix is used in work contributing to
published research.
For further details, as well as descriptions and results of several test
runs, see :ref:`Denniston et al. <fluid-Denniston>`. Please include a
citation to this paper if the lb_fluid fix is used in work contributing
to published research.
----------
@ -333,68 +346,77 @@ binary restart files, if requested, independent of the main LAMMPS
is written to the main LAMMPS :doc:`binary restart files <restart>`.
None of the :doc:`fix_modify <fix_modify>` options are relevant to this
fix. No global or per-atom quantities are stored by this fix for
access by various :doc:`output commands <Howto_output>`. No parameter
of this fix can be used with the *start/stop* keywords of the
:doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`.
fix.
The fix computes a global scalar which can be accessed by various
:doc:`output commands <Howto_output>`. The scalar is the current
temperature of the group of particles described by *group-ID* along with
the fluid constrained to move with them. The temperature is computed via
the kinetic energy of the group and fluid constrained to move with them
and the total number of degrees of freedom (calculated internally). If
the particles are not integrated independently (such as via :doc:`fix
NVE <fix_nve>`) but have additional constraints imposed on them (such as
via integration using :doc:`fix rigid <fix_rigid>`) the degrees of
freedom removed from these additional constraints will not be properly
accounted for. In this case, the user can specify the total degrees of
freedom independently using the *dof* keyword.
The fix also computes a global array of values which can be accessed by
various :doc:`output commands <Howto_output>`. There are 5 entries in
the array. The first entry is the temperature of the fluid, the second
entry is the total mass of the fluid plus particles, the third through
fifth entries give the x, y, and z total momentum of the fluid plus
particles.
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command. This fix is not invoked during
:doc:`energy minimization <minimize>`.
Restrictions
""""""""""""
This fix is part of the LATBOLTZ package. It is only enabled if LAMMPS
was built with that package. See the :doc:`Build package <Build_package>` page for more info.
was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
This fix can only be used with an orthogonal simulation domain.
Walls have only been implemented in the z-direction. Therefore, the
boundary conditions, as specified via the main LAMMPS boundary command
must be periodic for x and y, and either fixed or periodic for z.
Shrink-wrapped boundary conditions are not permitted with this fix.
The boundary conditions for the fluid are specified independently to the
particles. However, these should normally be specified consistently via
the main LAMMPS :doc:`boundary <boundary>` command (p p p, p p f, and p
f f are the only consistent possibilities). Shrink-wrapped boundary
conditions are not permitted with this fix.
This fix must be used before any of :doc:`fix lb/viscous <fix_lb_viscous>`, :doc:`fix lb/momentum <fix_lb_momentum>`, :doc:`fix lb/rigid/pc/sphere <fix_lb_rigid_pc_sphere>`, and/ or :doc:`fix lb/pc <fix_lb_pc>` , as the fluid needs to be initialized before
any of these routines try to access its properties. In addition, in
order for the hydrodynamic forces to be added to the particles, this
fix must be used in conjunction with the
:doc:`lb/viscous <fix_lb_viscous>` fix if the force coupling constant is
set by default, or either the :doc:`lb/viscous <fix_lb_viscous>` fix or
one of the :doc:`lb/rigid/pc/sphere <fix_lb_rigid_pc_sphere>` or
:doc:`lb/pc <fix_lb_pc>` integrators, if the user chooses to specify
their own value for the force coupling constant.
This fix must be used before any of :doc:`fix lb/viscous
<fix_lb_viscous>` and :doc:`fix lb/momentum <fix_lb_momentum>` as the
fluid needs to be initialized before any of these routines try to access
its properties. In addition, in order for the hydrodynamic forces to be
added to the particles, this fix must be used in conjunction with the
:doc:`lb/viscous <fix_lb_viscous>` fix.
This fix needs to be used in conjunction with a standard LAMMPS
integrator such as :doc:`fix NVE <fix_nve>` or :doc:`fix rigid
<fix_rigid>`.
Related commands
""""""""""""""""
:doc:`fix lb/viscous <fix_lb_viscous>`, :doc:`fix lb/momentum <fix_lb_momentum>`, :doc:`fix lb/rigid/pc/sphere <fix_lb_rigid_pc_sphere>`, :doc:`fix lb/pc <fix_lb_pc>`
:doc:`fix lb/viscous <fix_lb_viscous>`, :doc:`fix lb/momentum <fix_lb_momentum>`
Default
"""""""
By default, the force coupling constant is set according to
.. math::
\gamma = \frac{2m_um_v}{m_u+m_v}\left(\frac{1}{\Delta t_{collision}}\right)
and an area of :math:`dx_{LB}^2` per node, used to calculate the fluid mass at
the particle node location, is assumed.
*dx* is chosen such that :math:`\frac{\tau}{dt_{LB}} =
\frac{3\eta dt_{LB}}{\rho dx_{LB}^2}` is approximately equal to 1.
*dx* is chosen such that :math:`\frac{\tau}{dt_{LB}} = \frac{3\eta dt_{LB}}{\rho dx_{LB}^2}` is approximately equal to 1.
*dm* is set equal to 1.0.
*a0* is set equal to :math:`\frac{1}{3}\left(\frac{dx_{LB}}{dt_{LB}}\right)^2`.
The Peskin stencil is used as the default interpolation method.
The trilinear stencil is used as the default interpolation method.
The D3Q15 lattice is used for the lattice-Boltzmann algorithm.
If walls are present, they are assumed to be stationary.
----------
.. _Ollila:
.. _fluid-Denniston:
**(Ollila et al.)** Ollila, S.T.T., Denniston, C., Karttunen, M., and Ala-Nissila, T., Fluctuating lattice-Boltzmann model for complex fluids, J. Chem. Phys. 134 (2011) 064902.
.. _fluid-Mackay:
**(Mackay et al.)** Mackay, F. E., Ollila, S.T.T., and Denniston, C., Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid, Computer Physics Communications 184 (2013) 2021-2031.
**(Denniston et al.)** Denniston, C., Afrasiabian, N., Cole-Andre, M.G., Mackay, F. E., Ollila, S.T.T., and Whitehead, T., LAMMPS lb/fluid fix version 2: Improved Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid, Computer Physics Communications 275 (2022) `108318 <https://doi.org/10.1016/j.cpc.2022.108318>`_ .
.. _Mackay2:
@ -403,3 +425,4 @@ If walls are present, they are assumed to be stationary.
.. _Adhikari:
**(Adhikari et al.)** Adhikari, R., Stratford, K., Cates, M. E., and Wagner, A. J., Fluctuating lattice Boltzmann, Europhys. Lett. 71 (2005) 473-479.

2
doc/src/fix_lb_momentum.rst
View File

@ -38,7 +38,7 @@ lattice-Boltzmann fluid is present.
Zero the total linear momentum of the system, including both the atoms
specified by group-ID and the lattice-Boltzmann fluid every nevery
timesteps. This is accomplished by adjusting the particle velocities
timesteps. If there are no atoms specified by group-ID only the fluid momentum is affected. This is accomplished by adjusting the particle velocities
and the fluid velocities at each lattice site.
.. note::

65
doc/src/fix_lb_pc.rst
View File

@ -1,65 +0,0 @@
.. index:: fix lb/pc
fix lb/pc command
=================
Syntax
""""""
.. parsed-literal::
fix ID group-ID lb/pc
* ID, group-ID are documented in the :doc:`fix <fix>` command
* lb/pc = style name of this fix command
Examples
""""""""
.. code-block:: LAMMPS
fix 1 all lb/pc
Description
"""""""""""
Update the positions and velocities of the individual particles
described by *group-ID*, experiencing velocity-dependent hydrodynamic
forces, using the integration algorithm described in :ref:`Mackay et al. <Mackay1>`. This integration algorithm should only be used if a
user-specified value for the force-coupling constant used in :doc:`fix lb/fluid <fix_lb_fluid>` has been set; do not use this integration
algorithm if the force coupling constant has been set by default.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files <restart>`. None of the :doc:`fix_modify <fix_modify>` options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various :doc:`output commands <Howto_output>`.
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`.
Restrictions
""""""""""""
This fix is part of the LATBOLTZ package. It is only enabled if LAMMPS
was built with that package. See the :doc:`Build package <Build_package>` page for more info.
Can only be used if a lattice-Boltzmann fluid has been created via the
:doc:`fix lb/fluid <fix_lb_fluid>` command, and must come after this
command.
Related commands
""""""""""""""""
:doc:`fix lb/fluid <fix_lb_fluid>` :doc:`fix lb/rigid/pc/sphere <fix_lb_rigid_pc_sphere>`
Default
"""""""
none.
----------
.. _Mackay1:
**(Mackay et al.)** Mackay, F. E., Ollila, S.T.T., and Denniston, C., Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid, Computer Physics Communications 184 (2013) 2021-2031.

167
doc/src/fix_lb_rigid_pc_sphere.rst
View File

@ -1,167 +0,0 @@
.. index:: fix lb/rigid/pc/sphere
fix lb/rigid/pc/sphere command
==============================
Syntax
""""""
.. parsed-literal::
fix ID group-ID lb/rigid/pc/sphere bodystyle args keyword values ...
* ID, group-ID are documented in :doc:`fix <fix>` command
* lb/rigid/pc/sphere = style name of this fix command
* bodystyle = *single* or *molecule* or *group*
.. parsed-literal::
*single* args = none
*molecule* args = none
*group* args = N groupID1 groupID2 ...
N = # of groups
* zero or more keyword/value pairs may be appended
* keyword = *force* or *torque* or *innerNodes*
.. parsed-literal::
*force* values = M xflag yflag zflag
M = which rigid body from 1-Nbody (see asterisk form below)
xflag,yflag,zflag = off/on if component of center-of-mass force is active
*torque* values = M xflag yflag zflag
M = which rigid body from 1-Nbody (see asterisk form below)
xflag,yflag,zflag = off/on if component of center-of-mass torque is active
*innerNodes* values = innergroup-ID
innergroup-ID = ID of the atom group which does not experience a hydrodynamic force from the lattice-Boltzmann fluid
Examples
""""""""
.. code-block:: LAMMPS
fix 1 spheres lb/rigid/pc/sphere
fix 1 all lb/rigid/pc/sphere force 1 0 0 innerNodes ForceAtoms
Description
"""""""""""
This fix is based on the :doc:`fix rigid <fix_rigid>` command, and was
created to be used in place of that fix, to integrate the equations of
motion of spherical rigid bodies when a lattice-Boltzmann fluid is
present with a user-specified value of the force-coupling constant.
The fix uses the integration algorithm described in :ref:`Mackay et
al. <Mackay>` to update the positions, velocities, and orientations of
a set of spherical rigid bodies experiencing velocity dependent
hydrodynamic forces. The spherical bodies are assumed to rotate as
solid, uniform density spheres, with moments of inertia calculated
using the combined sum of the masses of all the constituent particles
(which are assumed to be point particles).
----------
By default, all of the atoms that this fix acts on experience a
hydrodynamic force due to the presence of the lattice-Boltzmann fluid.
However, the *innerNodes* keyword allows the user to specify atoms
belonging to a rigid object which do not interact with the
lattice-Boltzmann fluid (i.e. these atoms do not feel a hydrodynamic
force from the lattice-Boltzmann fluid). This can be used to
distinguish between atoms on the surface of a non-porous object, and
those on the inside.
This feature can be used, for example, when implementing a hard sphere
interaction between two spherical objects. Instead of interactions
occurring between the particles on the surfaces of the two spheres, it
is desirable simply to place an atom at the center of each sphere,
which does not contribute to the hydrodynamic force, and have these
central atoms interact with one another.
----------
Apart from the features described above, this fix is very similar to
the rigid fix (although it includes fewer optional arguments, and
assumes the constituent atoms are point particles); see
:doc:`fix rigid <fix_rigid>` for a complete documentation.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about the *rigid* and *rigid/nve* fixes are written to
:doc:`binary restart files <restart>`.
The :doc:`fix_modify <fix_modify>` *virial* option is supported by
this fix to add the contribution due to the added forces on atoms to
both the global pressure and per-atom stress of the system via the
:doc:`compute pressure <compute_pressure>` and :doc:`compute
stress/atom <compute_stress_atom>` commands. The former can be
accessed by :doc:`thermodynamic output <thermo_style>`. The default
setting for this fix is :doc:`fix_modify virial yes <fix_modify>`.
Similar to the :doc:`fix rigid <fix_rigid>` command: The rigid fix
computes a global scalar which can be accessed by various :doc:`output
commands <Howto_output>`. The scalar value calculated by these fixes
is "intensive". The scalar is the current temperature of the
collection of rigid bodies. This is averaged over all rigid bodies
and their translational and rotational degrees of freedom. The
translational energy of a rigid body is 1/2 m v\^2, where m = total
mass of the body and v = the velocity of its center of mass. The
rotational energy of a rigid body is 1/2 I w\^2, where I = the moment
of inertia tensor of the body and w = its angular velocity. Degrees
of freedom constrained by the *force* and *torque* keywords are
removed from this calculation.
All of these fixes compute a global array of values which can be
accessed by various :doc:`output commands <Howto_output>`. The number
of rows in the array is equal to the number of rigid bodies. The
number of columns is 15. Thus for each rigid body, 15 values are
stored: the xyz coords of the center of mass (COM), the xyz components
of the COM velocity, the xyz components of the force acting on the
COM, the xyz components of the torque acting on the COM, and the xyz
image flags of the COM, which have the same meaning as image flags for
atom positions (see the "dump" command). The force and torque values
in the array are not affected by the *force* and *torque* keywords in
the fix rigid command; they reflect values before any changes are made
by those keywords.
The ordering of the rigid bodies (by row in the array) is as follows.
For the *single* keyword there is just one rigid body. For the
*molecule* keyword, the bodies are ordered by ascending molecule ID.
For the *group* keyword, the list of group IDs determines the ordering
of bodies.
The array values calculated by these fixes are "intensive", meaning
they are independent of the number of atoms in the simulation.
No parameter of these fixes can be used with the *start/stop* keywords
of the :doc:`run <run>` command. These fixes are not invoked during
:doc:`energy minimization <minimize>`.
Restrictions
""""""""""""
This fix is part of the LATBOLTZ package. It is only enabled if LAMMPS
was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
Can only be used if a lattice-Boltzmann fluid has been created via the
:doc:`fix lb/fluid <fix_lb_fluid>` command, and must come after this
command. Should only be used if the force coupling constant used in
:doc:`fix lb/fluid <fix_lb_fluid>` has been set by the user; this
integration fix cannot be used if the force coupling constant is set
by default.
Related commands
""""""""""""""""
:doc:`fix lb/fluid <fix_lb_fluid>`, :doc:`fix lb/pc <fix_lb_pc>`
Default
"""""""
The defaults are force \* on on on, and torque \* on on on.
----------
.. _Mackay:
**(Mackay et al.)** Mackay, F. E., Ollila, S.T.T., and Denniston, C., Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid, Computer Physics Communications 184 (2013) 2021-2031.

30
doc/src/fix_lb_viscous.rst
View File

@ -25,27 +25,14 @@ Description
This fix is similar to the :doc:`fix viscous <fix_viscous>` command, and
is to be used in place of that command when a lattice-Boltzmann fluid
is present, and the user wishes to integrate the particle motion using
one of the built in LAMMPS integrators.
is present using the :doc:`fix lb/fluid <fix_lb_fluid>`. This should be used in conjunction with one of the built-in LAMMPS integrators, such as :doc:`fix NVE <fix_nve>` or :doc:`fix rigid <fix_rigid>`.
This fix adds a force, F = - Gamma\*(velocity-fluid_velocity), to each
atom, where Gamma is the force coupling constant described in the :doc:`fix lb/fluid <fix_lb_fluid>` command (which applies an equal and
opposite force to the fluid).
.. note::
This fix should only be used in conjunction with one of the
built in LAMMPS integrators; it should not be used with the :doc:`fix lb/pc <fix_lb_pc>` or :doc:`fix lb/rigid/pc/sphere <fix_lb_rigid_pc_sphere>` integrators, which
already include the hydrodynamic forces. These latter fixes should
only be used if the force coupling constant has been set by the user
(instead of using the default value); if the default force coupling
value is used, then this fix provides the only method for adding the
hydrodynamic forces to the particles.
This fix adds a viscous force to each atom to cause it move with the same velocity as the fluid (an equal and opposite force is applied to the fluid via :doc:`fix lb/fluid <fix_lb_fluid>`). When :doc:`fix lb/fluid <fix_lb_fluid>` is called with the noise option, the atoms will also experience random forces which will thermalize them to the same temperature as the fluid. In this way, the combination of this fix with :doc:`fix lb/fluid <fix_lb_fluid>` and a LAMMPS integrator like :doc:`fix NVE <fix_nve>` is analogous to :doc:`fix langevin <fix_langevin>` except here the fluid is explicit. The temperature of the particles can be monitored via the scalar output of :doc:`fix lb/fluid <fix_lb_fluid>`.
----------
For further details, as well as descriptions and results of several
test runs, see :ref:`Mackay et al. <Mackay3>`. Please include a citation to
For details of this fix, as well as descriptions and results of several
test runs, see :ref:`Denniston et al. <fluid-Denniston2>`. Please include a citation to
this paper if this fix is used in work contributing to published
research.
@ -78,14 +65,11 @@ Can only be used if a lattice-Boltzmann fluid has been created via the
:doc:`fix lb/fluid <fix_lb_fluid>` command, and must come after this
command.
This fix should not be used if either the :doc:`fix lb/pc <fix_lb_pc>`
or :doc:`fix lb/rigid/pc/sphere <fix_lb_rigid_pc_sphere>` integrator is
used.
Related commands
""""""""""""""""
:doc:`fix lb/fluid <fix_lb_fluid>`, :doc:`fix lb/pc <fix_lb_pc>`, :doc:`fix lb/rigid/pc/sphere <fix_lb_rigid_pc_sphere>`
:doc:`fix lb/fluid <fix_lb_fluid>`
Default
"""""""
@ -94,6 +78,6 @@ none
----------
.. _Mackay3:
.. _fluid-Denniston2:
**(Mackay et al.)** Mackay, F. E., Ollila, S.T.T., and Denniston, C., Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid, Computer Physics Communications 184 (2013) 2021-2031.
**(Denniston et al.)** Denniston, C., Afrasiabian, N., Cole-Andre, M.G., Mackay, F. E., Ollila, S.T.T., and Whitehead, T., LAMMPS lb/fluid fix version 2: Improved Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid, Computer Physics Communications 275 (2022) `108318 <https://doi.org/10.1016/j.cpc.2022.108318>`_ .

81
doc/src/fix_polarize.rst
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@ -21,7 +21,7 @@ Syntax
* ID, group-ID are documented in :doc:`fix <fix>` command
* style = *polarize/bem/gmres* or *polarize/bem/icc* or *polarize/functional*
* Nevery = this fixed is invoked every this many timesteps
* tolerance = the tolerance for the iterative solver to stop
* tolerance = the relative tolerance for the iterative solver to stop
Examples
@ -45,10 +45,45 @@ Description
"""""""""""
These fixes compute induced charges at the interface between two
impermeable media with different dielectric constants.
impermeable media with different dielectric constants. The interfaces
need to be discretized into vertices, each representing a boundary element.
The vertices are treated as if they were regular atoms or particles.
:doc:`atom_style dielectric <atom_style>` should be used since it defines
the additional properties of each interface particle such as
interface normal vectors, element areas, and local dielectric mismatch.
These fixes also require the use of :doc:`pair_style <pair_style>` and
:doc:`kspace_style <kspace_style>` with the *dielectric* suffix.
At every time step, given a configuration of the physical charges in the system
(such as atoms and charged particles) these fixes compute and update
the charge of the interface particles. The interfaces are allowed to move
during the simulation with appropriate time integrators (for example,
with :doc:`fix_rigid <fix_rigid>`).
There are some example scripts for using this fix
with LAMMPS in the examples/PACKAGES/dielectric directory.
Consider an interface between two media: one with dielectric constant
of 78 (water), the other of 4 (silica). The interface is discretized
into 2000 boundary elements, each represented by an interface particle. Suppose that
each interface particle has a normal unit vector pointing from the silica medium to water.
The dielectric difference along the normal vector is then 78 - 4 = 74,
the mean dielectric value is (78 + 4) / 2 = 41. Each boundary element
also has its area and the local mean curvature (which is used by these fixes
for computing a correction term in the local electric field).
To model charged interfaces, the interface particle will have a non-zero charge value,
coming from its area and surface charge density.
For non-interface particles such as atoms and charged particles,
the interface normal vectors, element area, and dielectric mismatch are
irrelevant. Their local dielectric value is used to rescale their actual charge
when computing the Coulombic interactions. For instance, for a cation carrying
a charge of +2 (in charge unit) in an implicit solvent with dielectric constant of 40
would have actual charge of +2, and a local dielectric constant value of 40.
It is assumed that the particles cannot pass through the interface during the simulation
so that its local dielectric constant value does not change.
There are some example scripts for using these fixes
with LAMMPS in the ``examples/PACKAGES/dielectric directory``. The README file
therein contains specific details on the system setup. Note that the example data files
show the additional fields (columns) needed for :doc:`atom_style dielectric <atom_style>`
beyond the conventional fields *id*, *mol*, *type*, *q*, *x*, *y*, and *z*.
----------
@ -75,12 +110,41 @@ as described in :ref:`(Barros) <Barros>` to solve :math:`\sigma_b`.
Fix *polarize/bem/icc* employs the successive over-relaxation algorithm
as described in :ref:`(Tyagi) <Tyagi>` to solve :math:`\sigma_b`.
Fix *polarize/functional* ...
The iterative solvers would terminate either when the maximum relative change
in the induced charges in consecutive iterations is below the set tolerance,
or when the number of iterations reaches *iter_max* (see below).
Fix *polarize/functional* employs the energy functional variation approach
as described in :ref:`(Jadhao) <Jadhao>` to solve :math:`\sigma_b`.
More details on the implementation of these fixes and their recommended use
are described in :ref:`(NguyenTD) <NguyenTD>`.
Restart, fix_modify, output, run start/stop, minimize info
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
...
No information about this fix is written to :doc:`binary restart files <restart>`.
The :doc:`fix_modify <fix_modify>` command provides certain options to
control the induced charge solver and the initial values of the interface elements:
.. parsed-literal::
*itr_max* arg
arg = maximum number of iterations for convergence
*dielectrics* ediff emean epsilon area charge
ediff = dielectric difference
emean = dielectric mean
epsilon = local dielectric value
aree = element area
charge = real interface charge
*polarize/bem/gmres* or *polarize/bem/icc* compute a global 2-element vector
which can be accessed by various :doc:`output commands <Howto_output>`.
The first element is the number of iterations when the solver terminates
(of which the upper bound is set by *iter_max*). The second element is the RMS error.
Restrictions
""""""""""""
@ -94,12 +158,15 @@ KSPACE package is installed. See the :doc:`Build package
Related commands
""""""""""""""""
:doc:`pair_coeff <pair_coeff>`, :doc:`fix polarize <fix_polarize>`, :doc:`read_data <read_data>`,
:doc:`pair_style lj/cut/coul/long/dielectric <pair_dielectric>`,
:doc:`kspace_style pppm/dielectric <kspace_style>`,
:doc:`compute efield/atom <compute_efield_atom>`
Default
"""""""
None.
*iter_max* = 20
----------

8
doc/src/fix_qeq.rst
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@ -201,9 +201,11 @@ larger sizes, and *qeq/fire* is faster than *qeq/dynamic*\ .
.. note::
To avoid the evaluation of the derivative of charge with respect
to position, which is typically ill-defined, the system should have a
zero net charge.
In order to solve the self-consistent equations for electronegativity
equalization, LAMMPS imposes the additional constraint that all the
charges in the fix group must add up to zero. The initial charge
assignments should also satisfy this constraint. LAMMPS will print a
warning if that is not the case.
.. note::

8
doc/src/fix_qeq_comb.rst
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@ -63,6 +63,14 @@ performing charge equilibration (more iterations) and accuracy.
If the *file* keyword is used, then information about each
equilibration calculation is written to the specified file.
.. note::
In order to solve the self-consistent equations for electronegativity
equalization, LAMMPS imposes the additional constraint that all the
charges in the fix group must add up to zero. The initial charge
assignments should also satisfy this constraint. LAMMPS will print a
warning if that is not the case.
----------
.. include:: accel_styles.rst

10
doc/src/fix_qeq_reaxff.rst
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@ -77,6 +77,8 @@ of this fix are hard-coded to be A, eV, and electronic charge.
The optional *dual* keyword allows to perform the optimization
of the S and T matrices in parallel. This is only supported for
the *qeq/reaxff/omp* style. Otherwise they are processed separately.
The *qeq/reaxff/kk* style always solves the S and T matrices in
parallel.
The optional *maxiter* keyword allows changing the max number
of iterations in the linear solver. The default value is 200.
@ -88,6 +90,14 @@ same fixed number of QEq iterations is desired, which can be achieved
by using a very small tolerance and setting *maxiter* to the desired
number of iterations.
.. note::
In order to solve the self-consistent equations for electronegativity
equalization, LAMMPS imposes the additional constraint that all the
charges in the fix group must add up to zero. The initial charge
assignments should also satisfy this constraint. LAMMPS will print a
warning if that is not the case.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

4
doc/src/pair_harmonic_cut.rst
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@ -20,7 +20,7 @@ Examples
.. code-block:: LAMMPS
pair_style harmonic/cut 2.5
pair_style harmonic/cut
pair_coeff * * 0.2 2.0
pair_coeff 1 1 0.5 2.5
@ -58,7 +58,7 @@ coefficients can be mixed. The default mix value is *geometric*.
See the "pair_modify" command for details.
Since the potential is zero at and beyond the cutoff parameter by
construction, there is no need to support support the :doc:`pair_modify
construction, there is no need to support the :doc:`pair_modify
<pair_modify>` shift or tail options for the energy and pressure of the
pair interaction.

4
doc/src/pair_mesocnt.rst
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@ -94,10 +94,6 @@ boron nitride nanotubes.
Atoms belonging to different CNTs need to be assigned
different molecule IDs.
A full summary of the method and LAMMPS implementation details
is expected to soon become available in Computer Physics
Communications.
----------
Mixing, shift, table, tail correction, restart, rRESPA info

82
doc/src/pair_python.rst
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@ -20,6 +20,9 @@ Examples
pair_style python 2.5
pair_coeff * * py_pot.LJCutMelt lj
pair_style python 10.0
pair_coeff * * py_pot.HarmonicCut A B
pair_style hybrid/overlay coul/long 12.0 python 12.0
pair_coeff * * coul/long
pair_coeff * * python py_pot.LJCutSPCE OW NULL
@ -159,23 +162,82 @@ Following the *LJCutMelt* example, here are the two functions:
to be multiplied by delta x, delta y, and delta z to conveniently obtain
the three components of the force vector between these two atoms.
Below is a more complex example using *real* units and defines an interaction
equivalent to:
.. code-block:: LAMMPS
units real
pair_style harmonic/cut
pair_coeff 1 1 0.2 9.0
pair_coeff 2 2 0.4 9.0
This uses the default geometric mixing. The equivalent input with pair
style *python* is:
.. code-block:: LAMMPS
units real
pair_style python 10.0
pair_coeff * * py_pot.Harmonic A B
Note that while for pair style *harmonic/cut* the cutoff is implicitly
set to the minimum of the harmonic potential, for pair style python a
global cutoff must be set and it must be equal or larger to the implicit
cutoff of the potential in python, which has to explicitly return zero
force and energy beyond the cutoff. Also, the mixed parameters have to
be explicitly provided. The corresponding python code is:
.. code-block:: python
class Harmonic(LAMMPSPairPotential):
def __init__(self):
super(Harmonic,self).__init__()
self.units = 'real'
# set coeffs: K, r0
self.coeff = {'A' : {'A' : (0.2,9.0),
'B' : (math.sqrt(0.2*0.4),9.0)},
'B' : {'A' : (math.sqrt(0.2*0.4),9.0),
'B' : (0.4,9.0)}}
def compute_force(self,rsq,itype,jtype):
coeff = self.coeff[self.pmap[itype]][self.pmap[jtype]]
r = math.sqrt(rsq)
delta = coeff[1]-r
if (r < coeff[1]):
return 2.0*delta*coeff[0]/r
else:
return 0.0
def compute_energy(self,rsq,itype,jtype):
coeff = self.coeff[self.pmap[itype]][self.pmap[jtype]]
r = math.sqrt(rsq)
delta = coeff[1]-r
if (r < coeff[1]):
return delta*delta*coeff[0]
else:
return 0.0
----------
.. note::
.. admonition:: Performance Impact
:class: note
The evaluation of scripted python code will slow down the
computation pairwise interactions quite significantly. However, this
can be largely worked around through using the python pair style not
for the actual simulation, but to generate tabulated potentials on the
fly using the :doc:`pair_write <pair_write>` command. Please see below
for an example LAMMPS input of how to build a table file:
The evaluation of scripted python code will slow down the computation
of pairwise interactions quite significantly. However, this performance
penalty can be worked around through using the python pair style not
for the actual simulation, but to generate tabulated potentials using
the :doc:`pair_write <pair_write>` command. This will also enable
GPU or multi-thread acceleration through the GPU, KOKKOS, or OPENMP
package versions of the *table* pair style. Please see below for a
LAMMPS input example demonstrating how to build a table file:
.. code-block:: LAMMPS
pair_style python 2.5
pair_coeff * * py_pot.LJCutMelt lj
shell rm -f melt.table
pair_write 1 1 2000 rsq 0.01 2.5 lj1_lj2.table lj
shell rm -f lj.table
pair_write 1 1 2000 rsq 0.01 2.5 lj.table lj
Note that it is strongly recommended to try to **delete** the potential
table file before generating it. Since the *pair_write* command will
@ -190,7 +252,7 @@ to be assigned to the LAMMPS atom types like this:
.. code-block:: LAMMPS
pair_style table linear 2000
pair_coeff 1 1 melt.table lj
pair_coeff 1 1 lj.table lj
This can also be done for more complex systems. Please see the
*examples/python* folders for a few more examples.

24
doc/src/pair_reaxff.rst
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@ -19,13 +19,15 @@ Syntax
.. parsed-literal::
keyword = *checkqeq* or *lgvdw* or *safezone* or *mincap* or *minhbonds*
keyword = *checkqeq* or *lgvdw* or *safezone* or *mincap* or *minhbonds* or *tabulate* or *list/blocking*
*checkqeq* value = *yes* or *no* = whether or not to require qeq/reaxff or acks2/reaxff fix
*enobonds* value = *yes* or *no* = whether or not to tally energy of atoms with no bonds
*lgvdw* value = *yes* or *no* = whether or not to use a low gradient vdW correction
*safezone* = factor used for array allocation
*mincap* = minimum size for array allocation
*minhbonds* = minimum size use for storing hydrogen bonds
*tabulate* value = size of interpolation table for Lennard-Jones and Coulomb interactions
*list/blocking* value = *yes* or *no* = whether or not to use "blocking" scheme for bond list build
Examples
""""""""
@ -158,6 +160,21 @@ the Kokkos version, which instead uses a more robust memory allocation
scheme that checks if the sizes of the arrays have been exceeded and
automatically allocates more memory.
The keyword *tabulate* controls the size of interpolation table for
Lennard-Jones and Coulomb interactions. Tabulation may also be set in the
control file (see below). If tabulation is set in both the input script and the
control file, the value in the control file will be ignored. A size of 10000 is
typically used for the interpolation table. A value of 0 means no tabulation
will be used.
The keyword *list/blocking* is only supported by the Kokkos version of
ReaxFF and ignored otherwise. Setting the value to *yes* enables the
"blocking" scheme (dynamically building interaction lists) for the
ReaxFF bond neighbor list. This reduces the number of empty
interactions and can improve performance in some cases (e.g. large
number of atoms/GPU on AMD hardware). It is also enabled by default
when running the CPU with Kokkos.
The thermo variable *evdwl* stores the sum of all the ReaxFF potential
energy contributions, with the exception of the Coulombic and charge
equilibration contributions which are stored in the thermo variable
@ -360,8 +377,9 @@ Related commands
Default
"""""""
The keyword defaults are checkqeq = yes, enobonds = yes, lgvdw = no,
safezone = 1.2, mincap = 50, minhbonds = 25.
The keyword defaults are checkqeq = yes, enobonds = yes, lgvdw = no, safezone =
1.2, mincap = 50, minhbonds = 25, tabulate = 0, list/blocking = yes on CPU, no
on GPU.
----------

14
doc/src/pair_snap.rst
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@ -135,7 +135,8 @@ with #) anywhere. Each non-blank non-comment line must contain one
keyword/value pair. The required keywords are *rcutfac* and
*twojmax*\ . Optional keywords are *rfac0*, *rmin0*,
*switchflag*, *bzeroflag*, *quadraticflag*, *chemflag*,
*bnormflag*, *wselfallflag*, *chunksize*, and *parallelthresh*\ .
*bnormflag*, *wselfallflag*, *switchinnerflag*,
*rinner*, *drinner*, *chunksize*, and *parallelthresh*\ .
The default values for these keywords are
@ -147,6 +148,7 @@ The default values for these keywords are
* *chemflag* = 0
* *bnormflag* = 0
* *wselfallflag* = 0
* *switchinnerflag* = 0
* *chunksize* = 32768
* *parallelthresh* = 8192
@ -189,6 +191,16 @@ corresponding *K*-vector of linear coefficients for element
which must equal the number of unique elements appearing in the LAMMPS
pair_coeff command, to avoid ambiguity in the number of coefficients.
The keyword *switchinnerflag* activates an additional switching function
that smoothly turns off contributions to the SNAP potential from neighbor
atoms at short separations. If *switchinnerflag* is set to 1 then
the additional keywords *rinner* and *drinner* must also be provided.
Each of these is followed by *nelements* values, where *nelements*
is the number of unique elements appearing in appearing in the LAMMPS
pair_coeff command. The element order should correspond to the order
in which elements first appear in the pair_coeff command reading from
left to right.
The keywords *chunksize* and *parallelthresh* are only applicable when
using the pair style *snap* with the KOKKOS package on GPUs and are
ignored otherwise. The *chunksize* keyword controls the number of atoms

34
doc/src/pair_style.rst
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@ -67,20 +67,34 @@ If the pair_style command has a cutoff argument, it sets global
cutoffs for all pairs of atom types. The distance(s) can be smaller
or larger than the dimensions of the simulation box.
Typically, the global cutoff value can be overridden for a specific
pair of atom types by the :doc:`pair_coeff <pair_coeff>` command. The
pair style settings (including global cutoffs) can be changed by a
subsequent pair_style command using the same style. This will reset
the cutoffs for all atom type pairs, including those previously set
explicitly by a :doc:`pair_coeff <pair_coeff>` command. The exceptions
to this are that pair_style *table* and *hybrid* settings cannot be
reset. A new pair_style command for these styles will wipe out all
previously specified pair_coeff values.
In many cases, the global cutoff value can be overridden for a
specific pair of atom types by the :doc:`pair_coeff <pair_coeff>`
command.
If a new pair_style command is specified with a new style, all
previous :doc:`pair_coeff <pair_coeff>` and :doc:`pair_modify
<pair_modify>` command settings are erased; those commands must be
re-specified if necessary.
If a new pair_style command is specified with the same style, then
only the global settings in that command are reset. Any previous
doc:`pair_coeff <pair_coeff>` and :doc:`pair_modify <pair_modify>`
command settings are preserved. The only exception is that if the
global cutoff in the pair_style command is changed, it will override
the corresponding cutoff in any of the previous doc:`pair_modify
<pair_coeff>` commands.
Two pair styles which do not follow this rule are the pair_style
*table* and *hybrid* commands. A new pair_style command for these
styles will wipe out all previously specified doc:`pair_coeff
<pair_coeff>` and :doc:`pair_modify <pair_modify>` settings, including
for the sub-styles of the *hybrid* command.
----------
Here is an alphabetic list of pair styles defined in LAMMPS. They are
also listed in more compact form on the :doc:`Commands pair <Commands_pair>` doc page.
also listed in more compact form on the :doc:`Commands pair
<Commands_pair>` doc page.
Click on the style to display the formula it computes, any additional
arguments specified in the pair_style command, and coefficients

9
doc/src/plugin.rst
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@ -56,6 +56,15 @@ styles and names.
The *clear* command will unload all currently loaded plugins.
.. admonition:: Automatic loading of plugins
:class: note
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``
(e.g. ``helloplugin.so``) and will try to load the contained plugins
automatically at start-up.
Restrictions
""""""""""""

58
doc/src/shell.rst
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@ -20,8 +20,9 @@ Syntax
dir1,dir2 = one or more directories to create
*mv* args = old new
old = old filename
new = new filename
*rm* args = file1 file2 ...
new = new filename or destination folder
*rm* args = [-f] file1 file2 ...
-f = turn off warnings (optional)
file1,file2 = one or more filenames to delete
*rmdir* args = dir1 dir2 ...
dir1,dir2 = one or more directories to delete
@ -36,8 +37,8 @@ Examples
shell cd sub1
shell cd ..
shell mkdir tmp1 tmp2 tmp3
shell rmdir tmp1
shell mkdir tmp1 tmp2/tmp3
shell rmdir tmp1 tmp2
shell mv log.lammps hold/log.1
shell rm TMP/file1 TMP/file2
shell putenv LAMMPS_POTENTIALS=../../potentials
@ -50,34 +51,39 @@ Description
Execute a shell command. A few simple file-based shell commands are
supported directly, in Unix-style syntax. Any command not listed
above is passed as-is to the C-library system() call, which invokes
the command in a shell.
the command in a shell. To use the external executable instead of
the built-in version one needs to use a full path, for example
*/bin/rm* instead of *rm*. The built-in commands will also work
on operating systems, that do not - by default - provide the
corresponding external executables (like *mkdir* on Windows).
This is means to invoke other commands from your input script. For
example, you can move files around in preparation for the next section
of the input script. Or you can run a program that pre-processes data
for input into LAMMPS. Or you can run a program that post-processes
LAMMPS output data.
This command provides a ways to invoke custom commands or executables
from your input script. For example, you can move files around in
preparation for the next section of the input script. Or you can run a
program that pre-processes data for input into LAMMPS. Or you can run a
program that post-processes LAMMPS output data.
With the exception of *cd*, all commands, including ones invoked via a
system() call, are executed by only a single processor, so that
files/directories are not being manipulated by multiple processors.
files/directories are not being manipulated by multiple processors
concurrently which may result in unexpected errors or corrupted files.
The *cd* command executes the Unix "cd" command to change the working
directory. All subsequent LAMMPS commands that read/write files will
use the new directory. All processors execute this command.
The *cd* command changes the current working directory similar to
the ``cd`` command. All subsequent LAMMPS commands that read/write files
will use the new directory. All processors execute this command.
The *mkdir* command executes the Unix "mkdir" command to create one or
more directories.
The *mkdir* command creates directories similar to the Unix ``mkdir -p``
command. That is, it will attempt to create the entire path of
sub-directories if they do not exist yet.
The *mv* command executes the Unix "mv" command to rename a file and/or
move it to a new directory.
The *mv* command renames a file and/or moves it to a new directory.
It cannot rename files across filesystem boundaries or between drives.
The *rm* command executes the Unix "rm" command to remove one or more
files.
The *rm* command deletes file similar to the Unix ``rm`` command.
The *rmdir* command executes the Unix "rmdir" command to remove one or
more directories. A directory must be empty to be successfully
removed.
The *rmdir* command deletes directories similar to Unix ``rmdir`` command.
If a directory is not empty, its contents are also removed recursively
similar to the Unix ``rm -r`` command.
The *putenv* command defines or updates an environment variable directly.
Since this command does not pass through the shell, no shell variable
@ -107,9 +113,9 @@ with 3 arguments: file1 10 file2.
Restrictions
""""""""""""
LAMMPS does not detect errors or print warnings when any of these
commands execute. E.g. if the specified directory does not exist,
executing the *cd* command will silently do nothing.
LAMMPS will do a best effort to detect errors and print suitable
warnings, but due to the nature of delegating commands to the C-library
system() call, this is not always reliable.
Related commands
""""""""""""""""

22
doc/src/thermo.rst
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@ -32,18 +32,20 @@ The content and format of what is printed is controlled by the
:doc:`thermo_style <thermo_style>` and
:doc:`thermo_modify <thermo_modify>` commands.
Instead of a numeric value, N can be specified as an :doc:`equal-style variable <variable>`, which should be specified as v_name, where
name is the variable name. In this case, the variable is evaluated at
the beginning of a run to determine the next timestep at which
thermodynamic info will be written out. On that timestep, the
variable will be evaluated again to determine the next timestep, etc.
Thus the variable should return timestep values. See the stagger()
and logfreq() and stride() math functions for :doc:`equal-style variables <variable>`, as examples of useful functions to use in
this context. Other similar math functions could easily be added as
options for :doc:`equal-style variables <variable>`.
Instead of a numeric value, N can be specified as an :doc:`equal-style
variable <variable>`, which should be specified as v_name, where name is
the variable name. In this case, the variable is evaluated at the
beginning of a run to determine the next timestep at which thermodynamic
info will be written out. On that timestep, the variable will be
evaluated again to determine the next timestep, etc. Thus the variable
should return timestep values. See the stagger() and logfreq() and
stride() math functions for :doc:`equal-style variables <variable>`, as
examples of useful functions to use in this context. Other similar math
functions could easily be added as options for :doc:`equal-style
variables <variable>`.
For example, the following commands will output thermodynamic info at
timesteps 0,10,20,30,100,200,300,1000,2000,etc:
timesteps 0, 10, 20, 30, 100, 200, 300, 1000, 2000, *etc*:
.. code-block:: LAMMPS

179
doc/src/thermo_modify.rst
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@ -20,7 +20,7 @@ Syntax
*warn* value = *ignore* or *reset* or *default* or a number
*norm* value = *yes* or *no*
*flush* value = *yes* or *no*
*line* value = *one* or *multi*
*line* value = *one* or *multi* or *yaml*
*format* values = *line* string, *int* string, *float* string, M string, or *none*
string = C-style format string
M = integer from 1 to N, where N = # of quantities being output
@ -36,35 +36,35 @@ Examples
thermo_modify temp myTemp format 3 %15.8g
thermo_modify temp myTemp format line "%ld %g %g %15.8g"
thermo_modify line multi format float %g
themos_modify line yaml format none
Description
"""""""""""
Set options for how thermodynamic information is computed and printed
by LAMMPS.
Set options for how thermodynamic information is computed and printed by
LAMMPS.
.. note::
These options apply to the currently defined thermo style. When
These options apply to the *currently defined* thermo style. When
you specify a :doc:`thermo_style <thermo_style>` command, all
thermodynamic settings are restored to their default values, including
those previously reset by a thermo_modify command. Thus if your input
script specifies a thermo_style command, you should use the
thermo_modify command after it.
thermodynamic settings are restored to their default values,
including those previously reset by a thermo_modify command. Thus if
your input script specifies a thermo_style command, you should use
the thermo_modify command **after** it.
The *lost* keyword determines whether LAMMPS checks for lost atoms
each time it computes thermodynamics and what it does if atoms are
lost. An atom can be "lost" if it moves across a non-periodic
simulation box :doc:`boundary <boundary>` or if it moves more than a box
length outside the simulation domain (or more than a processor
sub-domain length) before reneighboring occurs. The latter case is
typically due to bad dynamics, e.g. too large a timestep or huge
forces and velocities. If the value is *ignore*, LAMMPS does not
check for lost atoms. If the value is *error* or *warn*, LAMMPS
checks and either issues an error or warning. The code will exit with
an error and continue with a warning. A warning will only be issued
once, the first time an atom is lost. This can be a useful debugging
option.
The *lost* keyword determines whether LAMMPS checks for lost atoms each
time it computes thermodynamics and what it does if atoms are lost. An
atom can be "lost" if it moves across a non-periodic simulation box
:doc:`boundary <boundary>` or if it moves more than a box length outside
the simulation domain (or more than a processor sub-domain length)
before reneighboring occurs. The latter case is typically due to bad
dynamics, e.g. too large a timestep or huge forces and velocities. If
the value is *ignore*, LAMMPS does not check for lost atoms. If the
value is *error* or *warn*, LAMMPS checks and either issues an error or
warning. The code will exit with an error and continue with a warning.
A warning will only be issued once, the first time an atom is lost.
This can be a useful debugging option.
The *lost/bond* keyword determines whether LAMMPS throws an error or
not if an atom in a bonded interaction (bond, angle, etc) cannot be
@ -109,55 +109,55 @@ will be reset to zero, and with the value *default*, the counter is
reset and the limit set to 100. An example usage of either *reset* or
*default* would be to re-enable warnings that were disabled or have
reached the limit during equilibration, where the warnings would be
acceptable while the system is still adjusting, but then change
to all warnings for the production run, where they would indicate
problems that would require a closer look at what is causing them.
acceptable while the system is still adjusting, but then change to all
warnings for the production run, where they would indicate problems that
would require a closer look at what is causing them.
The *norm* keyword determines whether various thermodynamic output
values are normalized by the number of atoms or not, depending on
whether it is set to *yes* or *no*\ . Different unit styles have
different defaults for this setting (see below). Even if *norm* is
set to *yes*, a value is only normalized if it is an "extensive"
quantity, meaning that it scales with the number of atoms in the
system. For the thermo keywords described by the page for the
:doc:`thermo_style <thermo_style>` command, all energy-related keywords
are extensive, such as *pe* or *ebond* or *enthalpy*\ . Other keywords
such as *temp* or *press* are "intensive" meaning their value is
independent (in a statistical sense) of the number of atoms in the
system and thus are never normalized. For thermodynamic output values
extracted from fixes and computes in a :doc:`thermo_style custom <thermo_style>` command, the page for the individual
:doc:`fix <fix>` or :doc:`compute <compute>` lists whether the value is
"extensive" or "intensive" and thus whether it is normalized.
Thermodynamic output values calculated by a variable formula are
assumed to be "intensive" and thus are never normalized. You can
always include a divide by the number of atoms in the variable formula
if this is not the case.
different defaults for this setting (see below). Even if *norm* is set
to *yes*, a value is only normalized if it is an "extensive" quantity,
meaning that it scales with the number of atoms in the system. For the
thermo keywords described by the page for the :doc:`thermo_style
<thermo_style>` command, all energy-related keywords are extensive, such
as *pe* or *ebond* or *enthalpy*\ . Other keywords such as *temp* or
*press* are "intensive" meaning their value is independent (in a
statistical sense) of the number of atoms in the system and thus are
never normalized. For thermodynamic output values extracted from fixes
and computes in a :doc:`thermo_style custom <thermo_style>` command, the
page for the individual :doc:`fix <fix>` or :doc:`compute <compute>`
lists whether the value is "extensive" or "intensive" and thus whether
it is normalized. Thermodynamic output values calculated by a variable
formula are assumed to be "intensive" and thus are never normalized.
You can always include a divide by the number of atoms in the variable
formula if this is not the case.
The *flush* keyword invokes a flush operation after thermodynamic info
is written to the screen and log file. This insures the output is
updated and not buffered (by the application) even if LAMMPS halts
before the simulation completes. Please note that this does not
affect buffering by the OS or devices, so you may still lose data
in case the simulation stops due to a hardware failure.
before the simulation completes. Please note that this does not affect
buffering by the OS or devices, so you may still lose data in case the
simulation stops due to a hardware failure.
The *line* keyword determines whether thermodynamics will be output as
a series of numeric values on one line or in a multi-line format with
3 quantities with text strings per line and a dashed-line header
containing the timestep and CPU time. This modify option overrides
the *one* and *multi* thermo_style settings.
The *line* keyword determines whether thermodynamics will be output as a
series of numeric values on one line ("one"), in a multi-line format
with 3 quantities with text strings per line and a dashed-line header
containing the timestep and CPU time ("multi"), or in a YAML format
block ("yaml"). This modify option overrides the *one*, *multi*, or
*yaml* thermo_style settings.
The *format* keyword can be used to change the default numeric format
of any of quantities the :doc:`thermo_style <thermo_style>` command
outputs. All the specified format strings are C-style formats,
e.g. as used by the C/C++ printf() command. The *line* keyword takes
a single argument which is the format string for the entire line of
thermo output, with N fields, which you must enclose in quotes if it
is more than one field. The *int* and *float* keywords take a single
format argument and are applied to all integer or floating-point
quantities output. The setting for *M string* also takes a single
format argument which is used for the Mth value output in each line,
e.g. the fifth column is output in high precision for "format 5
%20.15g".
The *format* keyword can be used to change the default numeric format of
any of quantities the :doc:`thermo_style <thermo_style>` command
outputs. All the specified format strings are C-style formats, e.g. as
used by the C/C++ printf() command. The *line* keyword takes a single
argument which is the format string for the entire line of thermo
output, with N fields, which you must enclose in quotes if it is more
than one field. The *int* and *float* keywords take a single format
argument and are applied to all integer or floating-point quantities
output. The setting for *M string* also takes a single format argument
which is used for the Mth value output in each line, e.g. the fifth
column is output in high precision for "format 5 %20.15g".
The *format* keyword can be used multiple times. The precedence is
that for each value in a line of output, the *M* format (if specified)
@ -168,46 +168,46 @@ settings, reverting all values to their default format.
.. note::
The thermo output values *step* and *atoms* are stored
internally as 8-byte signed integers, rather than the usual 4-byte
signed integers. When specifying the *format int* option you can use
a "%d"-style format identifier in the format string and LAMMPS will
convert this to the corresponding 8-byte form when it is applied to
those keywords. However, when specifying the *line* option or *format
M string* option for *step* and *natoms*, you should specify a format
The thermo output values *step* and *atoms* are stored internally as
8-byte signed integers, rather than the usual 4-byte signed integers.
When specifying the *format int* option you can use a "%d"-style
format identifier in the format string and LAMMPS will convert this
to the corresponding 8-byte form when it is applied to those
keywords. However, when specifying the *line* option or *format M
string* option for *step* and *natoms*, you should specify a format
string appropriate for an 8-byte signed integer, e.g. one with "%ld".
The *temp* keyword is used to determine how thermodynamic temperature
is calculated, which is used by all thermo quantities that require a
The *temp* keyword is used to determine how thermodynamic temperature is
calculated, which is used by all thermo quantities that require a
temperature ("temp", "press", "ke", "etotal", "enthalpy", "pxx", etc).
The specified compute ID must have been previously defined by the user
via the :doc:`compute <compute>` command and it must be a style of
compute that calculates a temperature. As described in the
:doc:`thermo_style <thermo_style>` command, thermo output uses a default
compute for temperature with ID = *thermo_temp*. This option allows
the user to override the default.
compute for temperature with ID = *thermo_temp*. This option allows the
user to override the default.
The *press* keyword is used to determine how thermodynamic pressure is
calculated, which is used by all thermo quantities that require a
pressure ("press", "enthalpy", "pxx", etc). The specified compute ID
must have been previously defined by the user via the
:doc:`compute <compute>` command and it must be a style of compute that
calculates a pressure. As described in the
:doc:`thermo_style <thermo_style>` command, thermo output uses a default
compute for pressure with ID = *thermo_press*. This option allows the
user to override the default.
must have been previously defined by the user via the :doc:`compute
<compute>` command and it must be a style of compute that calculates a
pressure. As described in the :doc:`thermo_style <thermo_style>`
command, thermo output uses a default compute for pressure with ID =
*thermo_press*. This option allows the user to override the default.
.. note::
If both the *temp* and *press* keywords are used in a single
thermo_modify command (or in two separate commands), then the order in
which the keywords are specified is important. Note that a :doc:`pressure compute <compute_pressure>` defines its own temperature compute as
an argument when it is specified. The *temp* keyword will override
this (for the pressure compute being used by thermodynamics), but only
if the *temp* keyword comes after the *press* keyword. If the *temp*
keyword comes before the *press* keyword, then the new pressure
compute specified by the *press* keyword will be unaffected by the
*temp* setting.
thermo_modify command (or in two separate commands), then the order
in which the keywords are specified is important. Note that a
:doc:`pressure compute <compute_pressure>` defines its own
temperature compute as an argument when it is specified. The *temp*
keyword will override this (for the pressure compute being used by
thermodynamics), but only if the *temp* keyword comes after the
*press* keyword. If the *temp* keyword comes before the *press*
keyword, then the new pressure compute specified by the *press*
keyword will be unaffected by the *temp* setting.
Restrictions
""""""""""""
@ -225,7 +225,8 @@ The option defaults are lost = error, warn = 100, norm = yes for unit
style of *lj*, norm = no for unit style of *real* and *metal*,
flush = no, and temp/press = compute IDs defined by thermo_style.
The defaults for the line and format options depend on the thermo
style. For styles "one" and "custom", the line and format defaults
are "one", "%8d", and "%12.8g". For style "multi", the line and
format defaults are "multi", "%8d", and "%14.4f".
The defaults for the line and format options depend on the thermo style.
For styles "one" and "custom", the line and format defaults are "one",
"%10d", and "%12.8g". For style "multi", the line and format defaults
are "multi", "%14d", and "%14.4f". For style "yaml", the line and format
defaults are "%d" and "%.15g".

32
doc/src/thermo_style.rst
View File

@ -10,13 +10,14 @@ Syntax
thermo_style style args
* style = *one* or *multi* or *custom*
* style = *one* or *multi* *yaml* or *custom*
* args = list of arguments for a particular style
.. parsed-literal::
*one* args = none
*multi* args = none
*yaml* args = none
*custom* args = list of keywords
possible keywords = step, elapsed, elaplong, dt, time,
cpu, tpcpu, spcpu, cpuremain, part, timeremain,
@ -92,6 +93,8 @@ Examples
.. code-block:: LAMMPS
thermo_style multi
thermo_style yaml
thermo_style one
thermo_style custom step temp pe etotal press vol
thermo_style custom step temp etotal c_myTemp v_abc
thermo_style custom step temp etotal c_myTemp[*] v_abc
@ -99,18 +102,35 @@ Examples
Description
"""""""""""
Set the style and content for printing thermodynamic data to the
screen and log file.
Set the style and content for printing thermodynamic data to the screen
and log files.
Style *one* prints a one-line summary of thermodynamic info that is
the equivalent of "thermo_style custom step temp epair emol etotal
press". The line contains only numeric values.
Style *one* prints a single line of thermodynamic info that is the
equivalent of "thermo_style custom step temp epair emol etotal press".
The line contains only numeric values.
Style *multi* prints a multiple-line listing of thermodynamic info
that is the equivalent of "thermo_style custom etotal ke temp pe ebond
eangle edihed eimp evdwl ecoul elong press". The listing contains
numeric values and a string ID for each quantity.
.. versionadded:: 24Mar2022
Style *yaml* is similar to style *one* but prints the output in `YAML
<https://yaml.org/>`_ format which can be easily read by a variety of
script languages and data handling packages. Since LAMMPS may print
other output before, after, or in between thermodynamic output, the
YAML format content needs to be separated from the rest. All YAML
format thermodynamic output can be matched with a regular expression
and can thus be extracted with commands like ``egrep`` as follows:
.. code-block:: sh
egrep '^(keywords:|data:$|---$|\.\.\.$| - \[)' log.lammps > log.yaml
Information about processing such YAML files is in the :doc:`structured
data output howto <Howto_structured_data>`.
Style *custom* is the most general setting and allows you to specify
which of the keywords listed above you want printed on each
thermodynamic timestep. Note that the keywords c_ID, f_ID, v_name are

7
doc/utils/check-styles.py
View File

@ -256,12 +256,13 @@ print("Total number of style index entries:", total_index)
skip_fix = ('python', 'NEIGH_HISTORY/omp','acks2/reax','qeq/reax','reax/c/bonds','reax/c/species')
skip_pair = ('meam/c','lj/sf','reax/c')
skip_compute = ('pressure/cylinder')
counter = 0
counter += check_style('Commands_all.rst', doc_dir, ":doc:`(.+) <.+>`",command,'Command',suffix=True)
counter += check_style('Commands_compute.rst', doc_dir, ":doc:`(.+) <compute.+>`",compute,'Compute',suffix=True)
counter += check_style('compute.rst', doc_dir, ":doc:`(.+) <compute.+>` -",compute,'Compute',suffix=False)
counter += check_style('Commands_compute.rst', doc_dir, ":doc:`(.+) <compute.+>`",compute,'Compute',skip=skip_compute,suffix=True)
counter += check_style('compute.rst', doc_dir, ":doc:`(.+) <compute.+>` -",compute,'Compute',skip=skip_compute,suffix=False)
counter += check_style('Commands_fix.rst', doc_dir, ":doc:`(.+) <fix.+>`",fix,'Fix',skip=skip_fix,suffix=True)
counter += check_style('fix.rst', doc_dir, ":doc:`(.+) <fix.+>` -",fix,'Fix',skip=skip_fix,suffix=False)
counter += check_style('Commands_pair.rst', doc_dir, ":doc:`(.+) <pair.+>`",pair,'Pair',skip=skip_pair,suffix=True)
@ -281,7 +282,7 @@ if counter:
counter = 0
counter += check_style_index("compute", compute, index["compute"])
counter += check_style_index("compute", compute, index["compute"], skip=['pressure/cylinder'])
counter += check_style_index("fix", fix, index["fix"], skip=['python','acks2/reax','qeq/reax','reax/c/bonds','reax/c/species'])
counter += check_style_index("angle_style", angle, index["angle_style"])
counter += check_style_index("bond_style", bond, index["bond_style"])

41
doc/utils/sphinx-config/_themes/lammps_theme/__init__.py
View File

@ -5,13 +5,18 @@ From https://github.com/ryan-roemer/sphinx-bootstrap-theme.
"""
from os import path
from sys import version_info as python_version
import sphinx
from sphinx import version_info as sphinx_version
from sphinx.locale import _
from sphinx.util.logging import getLogger
__version__ = '0.5.0'
__version__ = '1.0.0'
__version_full__ = __version__
logger = getLogger(__name__)
def get_html_theme_path():
"""Return list of HTML theme paths."""
@ -19,16 +24,40 @@ def get_html_theme_path():
return cur_dir
def config_initiated(app, config):
theme_options = config.html_theme_options or {}
if theme_options.get('canonical_url'):
logger.warning(
_('The canonical_url option is deprecated, use the html_baseurl option from Sphinx instead.')
)
# See http://www.sphinx-doc.org/en/stable/theming.html#distribute-your-theme-as-a-python-package
def setup(app):
if sphinx.version_info >= (1, 6, 0):
# Register the theme that can be referenced without adding a theme path
app.add_html_theme('sphinx_rtd_theme', path.abspath(path.dirname(__file__)))
if python_version[0] < 3:
logger.warning("Python 2 is deprecated with sphinx_rtd_theme, update to Python 3")
app.require_sphinx('1.6')
if sphinx_version <= (2, 0, 0):
logger.warning("Sphinx 1.x is deprecated with sphinx_rtd_theme, update to Sphinx 2.x or greater")
if not app.config.html_experimental_html5_writer:
logger.warning("'html4_writer' is deprecated with sphinx_rtd_theme")
else:
if app.config.html4_writer:
logger.warning("'html4_writer' is deprecated with sphinx_rtd_theme")
if sphinx.version_info >= (1, 8, 0):
# Register the theme that can be referenced without adding a theme path
app.add_html_theme('lammps_theme', path.abspath(path.dirname(__file__)))
if sphinx_version >= (1, 8, 0):
# Add Sphinx message catalog for newer versions of Sphinx
# See http://www.sphinx-doc.org/en/master/extdev/appapi.html#sphinx.application.Sphinx.add_message_catalog
rtd_locale_path = path.join(path.abspath(path.dirname(__file__)), 'locale')
app.add_message_catalog('sphinx', rtd_locale_path)
app.connect('config-inited', config_initiated)
# sphinx emits the permalink icon for headers, so choose one more in keeping with our theme
if sphinx_version >= (3, 5, 0):
app.config.html_permalinks_icon = "\uf0c1"
else:
app.config.html_add_permalinks = "\uf0c1"
return {'parallel_read_safe': True, 'parallel_write_safe': True}

115
doc/utils/sphinx-config/_themes/lammps_theme/breadcrumbs.html
View File

@ -1,86 +1,79 @@
{# Support for Sphinx 1.3+ page_source_suffix, but don't break old builds. #}
{%- if meta is defined and meta is not none %}
{%- set check_meta = True %}
{%- else %}
{%- set check_meta = False %}
{%- endif %}
{% if page_source_suffix %}
{% set suffix = page_source_suffix %}
{% else %}
{% set suffix = source_suffix %}
{% endif %}
{%- if check_meta and 'github_url' in meta %}
{%- set display_github = True %}
{%- endif %}
{% if meta is defined and meta is not none %}
{% set check_meta = True %}
{% else %}
{% set check_meta = False %}
{% endif %}
{%- if check_meta and 'bitbucket_url' in meta %}
{%- set display_bitbucket = True %}
{%- endif %}
{% if check_meta and 'github_url' in meta %}
{% set display_github = True %}
{% endif %}
{%- if check_meta and 'gitlab_url' in meta %}
{%- set display_gitlab = True %}
{%- endif %}
{% if check_meta and 'bitbucket_url' in meta %}
{% set display_bitbucket = True %}
{% endif %}
{% if check_meta and 'gitlab_url' in meta %}
{% set display_gitlab = True %}
{% endif %}
{% set display_vcs_links = display_vcs_links if display_vcs_links is defined else True %}
<div role="navigation" aria-label="breadcrumbs navigation">
{%- set display_vcs_links = display_vcs_links if display_vcs_links is defined else True %}
{#- Translators: This is an ARIA section label for page links, including previous/next page link and links to GitHub/GitLab/etc. -#}
<div role="navigation" aria-label="{{ _('Page navigation') }}">
<ul class="wy-breadcrumbs">
{% block breadcrumbs %}
{%- block breadcrumbs %}
<li><a href="{{ pathto(master_doc) }}" class="icon icon-home"></a> &raquo;</li>
{% for doc in parents %}
{%- for doc in parents %}
<li><a href="{{ doc.link|e }}">{{ doc.title }}</a> &raquo;</li>
{% endfor %}
{%- endfor %}
<li>{{ title }}</li>
{% endblock %}
{% block breadcrumbs_aside %}
{%- endblock %}
{%- block breadcrumbs_aside %}
<li class="wy-breadcrumbs-aside">
{% if hasdoc(pagename) and display_vcs_links %}
{% if display_github %}
{% if check_meta and 'github_url' in meta %}
{%- if hasdoc(pagename) and display_vcs_links %}
{%- if display_github %}
{%- if check_meta and 'github_url' in meta %}
<!-- User defined GitHub URL -->
<a href="{{ meta['github_url'] }}" class="fa fa-github"> {{ _('Edit on GitHub') }}</a>
{% else %}
<a href="https://{{ github_host|default("github.com") }}/{{ github_user }}/{{ github_repo }}/{{ theme_vcs_pageview_mode|default("blob") }}/{{ github_version }}{{ conf_py_path }}{{ pagename }}{{ suffix }}" class="fa fa-github"> {{ _('Edit on GitHub') }}</a>
{% endif %}
{% elif display_bitbucket %}
{% if check_meta and 'bitbucket_url' in meta %}
{%- else %}
<a href="https://{{ github_host|default("github.com") }}/{{ github_user }}/{{ github_repo }}/{{ theme_vcs_pageview_mode or "blob" }}/{{ github_version }}{{ conf_py_path }}{{ pagename }}{{ page_source_suffix }}" class="fa fa-github"> {{ _('Edit on GitHub') }}</a>
{%- endif %}
{%- elif display_bitbucket %}
{%- if check_meta and 'bitbucket_url' in meta %}
<!-- User defined Bitbucket URL -->
<a href="{{ meta['bitbucket_url'] }}" class="fa fa-bitbucket"> {{ _('Edit on Bitbucket') }}</a>
{% else %}
<a href="https://bitbucket.org/{{ bitbucket_user }}/{{ bitbucket_repo }}/src/{{ bitbucket_version}}{{ conf_py_path }}{{ pagename }}{{ suffix }}?mode={{ theme_vcs_pageview_mode|default("view") }}" class="fa fa-bitbucket"> {{ _('Edit on Bitbucket') }}</a>
{% endif %}
{% elif display_gitlab %}
{% if check_meta and 'gitlab_url' in meta %}
{%- else %}
<a href="https://bitbucket.org/{{ bitbucket_user }}/{{ bitbucket_repo }}/src/{{ bitbucket_version}}{{ conf_py_path }}{{ pagename }}{{ page_source_suffix }}?mode={{ theme_vcs_pageview_mode or "view" }}" class="fa fa-bitbucket"> {{ _('Edit on Bitbucket') }}</a>
{%- endif %}
{%- elif display_gitlab %}
{%- if check_meta and 'gitlab_url' in meta %}
<!-- User defined GitLab URL -->
<a href="{{ meta['gitlab_url'] }}" class="fa fa-gitlab"> {{ _('Edit on GitLab') }}</a>
{% else %}
<a href="https://{{ gitlab_host|default("gitlab.com") }}/{{ gitlab_user }}/{{ gitlab_repo }}/{{ theme_vcs_pageview_mode|default("blob") }}/{{ gitlab_version }}{{ conf_py_path }}{{ pagename }}{{ suffix }}" class="fa fa-gitlab"> {{ _('Edit on GitLab') }}</a>
{% endif %}
{% elif show_source and source_url_prefix %}
<a href="{{ source_url_prefix }}{{ pagename }}{{ suffix }}">{{ _('View page source') }}</a>
{% elif show_source and has_source and sourcename %}
{%- else %}
<a href="https://{{ gitlab_host|default("gitlab.com") }}/{{ gitlab_user }}/{{ gitlab_repo }}/{{ theme_vcs_pageview_mode or "blob" }}/{{ gitlab_version }}{{ conf_py_path }}{{ pagename }}{{ page_source_suffix }}" class="fa fa-gitlab"> {{ _('Edit on GitLab') }}</a>
{%- endif %}
{%- elif show_source and source_url_prefix %}
<a href="{{ source_url_prefix }}{{ pagename }}{{ page_source_suffix }}">{{ _('View page source') }}</a>
{%- elif show_source and has_source and sourcename %}
<a href="{{ pathto('_sources/' + sourcename, true)|e }}" rel="nofollow"> {{ _('View page source') }}</a>
{% endif %}
{%- endif %}
<a href="https://www.lammps.org">Website</a>
<a href="Commands_all.html">Commands</a>
{% endif %}
{%- endif %}
</li>
{% endblock %}
{%- endblock %}
</ul>
{% if (theme_prev_next_buttons_location == 'top' or theme_prev_next_buttons_location == 'both') and (next or prev) %}
<div class="rst-breadcrumbs-buttons" role="navigation" aria-label="breadcrumb navigation">
{% if next %}
<a href="{{ next.link|e }}" class="btn btn-neutral float-right" title="{{ next.title|striptags|e }}" accesskey="n">{{ _('Next') }} <span class="fa fa-arrow-circle-right"></span></a>
{% endif %}
{% if prev %}
<a href="{{ prev.link|e }}" class="btn btn-neutral float-left" title="{{ prev.title|striptags|e }}" accesskey="p"><span class="fa fa-arrow-circle-left"></span> {{ _('Previous') }}</a>
{% endif %}
{%- if (theme_prev_next_buttons_location == 'top' or theme_prev_next_buttons_location == 'both') and (next or prev) %}
{#- Translators: This is an ARIA section label for sequential page links, such as previous and next page links. -#}
<div class="rst-breadcrumbs-buttons" role="navigation" aria-label="{{ _('Sequential page navigation') }}">
{%- if prev %}
<a href="{{ prev.link|e }}" class="btn btn-neutral float-left" title="{{ prev.title|striptags|e }}" accesskey="p"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> {{ _('Previous') }}</a>
{%- endif %}
{%- if next %}
<a href="{{ next.link|e }}" class="btn btn-neutral float-right" title="{{ next.title|striptags|e }}" accesskey="n">{{ _('Next') }} <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
{%- endif %}
</div>
{% endif %}
{%- endif %}
<hr/>
</div>

61
doc/utils/sphinx-config/_themes/lammps_theme/footer.html
View File

@ -1,60 +1,61 @@
<footer>
{% if (theme_prev_next_buttons_location == 'bottom' or theme_prev_next_buttons_location == 'both') and (next or prev) %}
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
{% if next %}
<a href="{{ next.link|e }}" class="btn btn-neutral float-right" title="{{ next.title|striptags|e }}" accesskey="n" rel="next">{{ _('Next') }} <span class="fa fa-arrow-circle-right"></span></a>
{% endif %}
{% if prev %}
<a href="{{ prev.link|e }}" class="btn btn-neutral float-left" title="{{ prev.title|striptags|e }}" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> {{ _('Previous') }}</a>
{% endif %}
{%- if (theme_prev_next_buttons_location == 'bottom' or theme_prev_next_buttons_location == 'both') and (next or prev) %}
{#- Translators: This is an ARIA section label for the footer section of the page. -#}
<div class="rst-footer-buttons" role="navigation" aria-label="{{ _('Footer') }}">
{%- if prev %}
<a href="{{ prev.link|e }}" class="btn btn-neutral float-left" title="{{ prev.title|striptags|e }}" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> {{ _('Previous') }}</a>
{%- endif %}
{%- if next %}
<a href="{{ next.link|e }}" class="btn btn-neutral float-right" title="{{ next.title|striptags|e }}" accesskey="n" rel="next">{{ _('Next') }} <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
{%- endif %}
</div>
{% endif %}
{%- endif %}
<hr/>
<div role="contentinfo">
{%- block contentinfo %}
<p>
{%- if show_copyright %}
{%- if hasdoc('copyright') %}
{% set path = pathto('copyright') %}
{% set copyright = copyright|e %}
&copy; <a href="{{ path }}">{% trans %}Copyright{% endtrans %}</a> {{ copyright }}
{%- trans path=pathto('copyright'), copyright=copyright|e %}&#169; <a href="{{ path }}">Copyright</a> {{ copyright }}.{% endtrans %}
{%- else %}
{% set copyright = copyright|e %}
&copy; {% trans %}Copyright{% endtrans %} {{ copyright }}
{%- trans copyright=copyright|e %}&#169; Copyright {{ copyright }}.{% endtrans %}
{%- endif %}
{%- endif %}
{%- if build_id and build_url %}
<span class="build">
{# Translators: Build is a noun, not a verb #}
{% trans %}Build{% endtrans %}
{#- Translators: Build is a noun, not a verb -#}
{%- trans %}Build{% endtrans -%}
<a href="{{ build_url }}">{{ build_id }}</a>.
</span>
{%- elif commit %}
<span class="commit">
{# Translators: the phrase "revision" comes from Git, referring to a commit #}
{% trans %}Revision{% endtrans %} <code>{{ commit }}</code>.
</span>
{%- elif last_updated %}
<span class="lastupdated">
{% trans last_updated=last_updated|e %}Last updated on {{ last_updated }}.{% endtrans %}
{#- Translators: the phrase "revision" comes from Git, referring to a commit #}
{%- trans %}Revision{% endtrans %} <code>{{ commit }}</code>.
</span>
{%- endif %}
{%- if last_updated %}
<span class="lastupdated">
{%- trans last_updated=last_updated|e %}Last updated on {{ last_updated }}.{% endtrans %}
</span>
{%- endif -%}
</p>
{%- endblock %}
</div>
{%- if show_sphinx %}
{% set sphinx_web = '<a href="https://www.sphinx-doc.org/">Sphinx</a>' %}
{% set readthedocs_web = '<a href="https://readthedocs.org">Read the Docs</a>' %}
{# Translators: the variable "sphinx_web" is a link to the Sphinx project documentation with the text "Sphinx" #}
{% trans sphinx_web=sphinx_web, readthedocs_web=readthedocs_web %}Built with {{ sphinx_web }} using a{% endtrans %}
{# Translators: "theme" refers to a theme for Sphinx, which alters the appearance of the generated documenation #}
{% if show_sphinx %}
{%- set sphinx_web = '<a href="https://www.sphinx-doc.org/">Sphinx</a>' %}
{%- set readthedocs_web = '<a href="https://readthedocs.org">Read the Docs</a>' %}
{#- Translators: the variable "sphinx_web" is a link to the Sphinx project documentation with the text "Sphinx" #}
{%- trans sphinx_web=sphinx_web, readthedocs_web=readthedocs_web %}Built with {{ sphinx_web }} using a{% endtrans %}
{#- Translators: "theme" refers to a theme for Sphinx, which alters the appearance of the generated documenation #}
<a href="https://github.com/readthedocs/sphinx_rtd_theme">{% trans %}theme{% endtrans %}</a>
{# Translators: this is always used as "provided by Read the Docs", and should not imply Read the Docs is an author of the generated documentation. #}
{#- Translators: this is always used as "provided by Read the Docs", and should not imply Read the Docs is an author of the generated documentation. #}
{% trans %}provided by {{ readthedocs_web }}{% endtrans %}.
{%- endif %}
{% endif %}
{%- block extrafooter %} {% endblock %}

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@ -7,21 +7,27 @@
{%- set titlesuffix = "" %}
{%- endif %}
{%- set lang_attr = 'en' if language == None else (language | replace('_', '-')) %}
{%- set sphinx_writer = 'writer-html5' if html5_doctype else 'writer-html4' %}
{%- set sphinx_writer = 'writer-html5' if html5_doctype else 'writer-html4' -%}
{# Build sphinx_version_info tuple from sphinx_version string in pure Jinja #}
{%- set (_ver_major, _ver_minor, _ver_bugfix) = sphinx_version.split('.') | map('int') -%}
{%- set sphinx_version_info = (_ver_major, _ver_minor, _ver_bugfix) -%}
<!DOCTYPE html>
<html class="{{ sphinx_writer }}" lang="{{ lang_attr }}" >
<head>
<meta charset="utf-8">
{{ metatags }}
<meta name="viewport" content="width=device-width, initial-scale=1.0">
{% block htmltitle %}
<meta charset="utf-8" />
{{- metatags }}
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
{%- block htmltitle %}
<title>{{ title|striptags|e }}{{ titlesuffix }}</title>
{% endblock %}
{%- endblock -%}
{# CSS #}
{#- CSS #}
{%- if sphinx_version_info < (4, 0) -%}
<link rel="stylesheet" href="{{ pathto('_static/' + style, 1) }}" type="text/css" />
<link rel="stylesheet" href="{{ pathto('_static/pygments.css', 1) }}" type="text/css" />
{%- endif %}
{%- for css in css_files %}
{%- if css|attr("rel") %}
<link rel="{{ css.rel }}" href="{{ pathto(css.filename, 1) }}" type="text/css"{% if css.title is not none %} title="{{ css.title }}"{% endif %} />
@ -32,19 +38,28 @@
{%- for cssfile in extra_css_files %}
<link rel="stylesheet" href="{{ pathto(cssfile, 1) }}" type="text/css" />
{%- endfor %}
{%- endfor -%}
{# FAVICON #}
{% if favicon %}
{#- FAVICON #}
{%- if favicon %}
{%- if sphinx_version_info < (4, 0) -%}
<link rel="shortcut icon" href="{{ pathto('_static/' + favicon, 1) }}"/>
{% endif %}
{%- else %}
<link rel="shortcut icon" href="{{ favicon_url }}"/>
{%- endif %}
{%- endif -%}
{#- CANONICAL URL (deprecated) #}
{%- if theme_canonical_url and not pageurl %}
<link rel="canonical" href="{{ theme_canonical_url }}{{ pagename }}.html"/>
{%- endif -%}
{#- CANONICAL URL #}
{%- if pageurl %}
<link rel="canonical" href="{{ pageurl|e }}" />
{%- endif -%}
{# JAVASCRIPTS #}
{#- JAVASCRIPTS #}
{%- block scripts %}
<!--[if lt IE 9]>
<script src="{{ pathto('_static/js/html5shiv.min.js', 1) }}"></script>
@ -55,13 +70,15 @@
{%- if not embedded %}
{# XXX Sphinx 1.8.0 made this an external js-file, quick fix until we refactor the template to inherert more blocks directly from sphinx #}
{% if sphinx_version >= "1.8.0" %}
<script type="text/javascript" id="documentation_options" data-url_root="{{ pathto('', 1) }}" src="{{ pathto('_static/documentation_options.js', 1) }}"></script>
{%- if sphinx_version_info >= (1, 8) -%}
{%- if sphinx_version_info < (4, 0) -%}
<script id="documentation_options" data-url_root="{{ url_root }}" src="{{ pathto('_static/documentation_options.js', 1) }}"></script>
{%- endif -%}
{%- for scriptfile in script_files %}
{{ js_tag(scriptfile) }}
{%- endfor %}
{% else %}
<script type="text/javascript">
{%- else %}
<script>
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'{{ url_root }}',
VERSION:'{{ release|e }}',
@ -73,12 +90,12 @@
};
</script>
{%- for scriptfile in script_files %}
<script type="text/javascript" src="{{ pathto(scriptfile, 1) }}"></script>
<script src="{{ pathto(scriptfile, 1) }}"></script>
{%- endfor %}
{% endif %}
<script type="text/javascript" src="{{ pathto('_static/js/theme.js', 1) }}"></script>
{%- endif %}
<script src="{{ pathto('_static/js/theme.js', 1) }}"></script>
{# OPENSEARCH #}
{#- OPENSEARCH #}
{%- if use_opensearch %}
<link rel="search" type="application/opensearchdescription+xml"
title="{% trans docstitle=docstitle|e %}Search within {{ docstitle }}{% endtrans %}"
@ -112,126 +129,124 @@
<body class="wy-body-for-nav">
{% block extrabody %} {% endblock %}
{%- block extrabody %} {% endblock %}
<div class="wy-grid-for-nav">
{# SIDE NAV, TOGGLES ON MOBILE #}
{#- SIDE NAV, TOGGLES ON MOBILE #}
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
<div class="wy-side-scroll">
<div class="wy-side-nav-search" {% if theme_style_nav_header_background %} style="background: {{theme_style_nav_header_background}}" {% endif %}>
{% block sidebartitle %}
{%- block sidebartitle %}
{% if logo and theme_logo_only %}
{%- if logo and theme_logo_only %}
<a href="{{ pathto(master_doc) }}">
{% else %}
{%- else %}
<a href="{{ pathto(master_doc) }}" class="icon icon-home"> {{ project }}
{% endif %}
{%- endif %}
{% if logo %}
{# Not strictly valid HTML, but it's the only way to display/scale
{%- if logo %}
{#- Not strictly valid HTML, but it's the only way to display/scale
it properly, without weird scripting or heaps of work
#}
{%- if sphinx_version_info < (4, 0) -%}
<img src="{{ pathto('_static/' + logo, 1) }}" class="logo" alt="{{ _('Logo') }}"/>
{% endif %}
{%- else %}
<img src="{{ logo_url }}" class="logo" alt="{{ _('Logo') }}"/>
{%- endif %}
{%- endif %}
</a>
{% if theme_display_version %}
{%- if theme_display_version %}
<div class="lammps_version">Version: <b>{{ current_version }}</b></div>
<div class="lammps_release">git info: {{ release }}</div>
{% endif %}
{%- endif %}
{% include "searchbox.html" %}
{%- include "searchbox.html" %}
{% endblock %}
{%- endblock %}
</div>
{% block navigation %}
<div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
{% block menu %}
{#
The singlehtml builder doesn't handle this toctree call when the
toctree is empty. Skip building this for now.
#}
{% if 'singlehtml' not in builder %}
{% set global_toc = toctree(maxdepth=theme_navigation_depth|int,
{%- block navigation %}
{#- Translators: This is an ARIA section label for the main navigation menu -#}
<div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="{{ _('Navigation menu') }}">
{%- block menu %}
{%- set toctree = toctree(maxdepth=theme_navigation_depth|int,
collapse=theme_collapse_navigation|tobool,
includehidden=theme_includehidden|tobool,
titles_only=theme_titles_only|tobool) %}
{% endif %}
{% if global_toc %}
{{ global_toc }}
{% else %}
{%- if toctree %}
{{ toctree }}
{%- else %}
<!-- Local TOC -->
<div class="local-toc">{{ toc }}</div>
{% endif %}
{% endblock %}
{%- endif %}
{%- endblock %}
</div>
{% endblock %}
{%- endblock %}
</div>
</nav>
<section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">
{# MOBILE NAV, TRIGGLES SIDE NAV ON TOGGLE #}
<nav class="wy-nav-top" aria-label="top navigation">
{% block mobile_nav %}
{#- MOBILE NAV, TRIGGLES SIDE NAV ON TOGGLE #}
{#- Translators: This is an ARIA section label for the navigation menu that is visible when viewing the page on mobile devices -#}
<nav class="wy-nav-top" aria-label="{{ _('Mobile navigation menu') }}" {% if theme_style_nav_header_background %} style="background: {{theme_style_nav_header_background}}" {% endif %}>
{%- block mobile_nav %}
<i data-toggle="wy-nav-top" class="fa fa-bars"></i>
<a href="{{ pathto(master_doc) }}">{{ project }}</a>
{% endblock %}
{%- endblock %}
</nav>
<div class="wy-nav-content">
{%- block content %}
{% if theme_style_external_links|tobool %}
{%- if theme_style_external_links|tobool %}
<div class="rst-content style-external-links">
{% else %}
{%- else %}
<div class="rst-content">
{% endif %}
{%- endif %}
{% include "breadcrumbs.html" %}
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
{%- block document %}
<div itemprop="articleBody">
{% block body %}{% endblock %}
</div>
{% if self.comments()|trim %}
{%- if self.comments()|trim %}
<div class="articleComments">
{% block comments %}{% endblock %}
{%- block comments %}{% endblock %}
</div>
{% endif%}
{%- endif%}
</div>
{%- endblock %}
{% include "footer.html" %}
</div>
{%- endblock %}
</div>
</section>
</div>
{% include "versions.html" %}
{% include "versions.html" -%}
<script type="text/javascript">
<script>
jQuery(function () {
SphinxRtdTheme.Navigation.enable({{ 'true' if theme_sticky_navigation|tobool else 'false' }});
});
</script>
{# Do not conflict with RTD insertion of analytics script #}
{% if not READTHEDOCS %}
{% if theme_analytics_id %}
{#- Do not conflict with RTD insertion of analytics script #}
{%- if not READTHEDOCS %}
{%- if theme_analytics_id %}
<!-- Theme Analytics -->
<script async src="https://www.googletagmanager.com/gtag/js?id={{ theme_analytics_id }}"></script>
<script>
(function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
(i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
})(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
window.dataLayer = window.dataLayer || [];
function gtag(){dataLayer.push(arguments);}
gtag('js', new Date());
ga('create', '{{ theme_analytics_id }}', 'auto');
ga('send', 'pageview');
gtag('config', '{{ theme_analytics_id }}', {
'anonymize_ip': {{ 'true' if theme_analytics_anonymize_ip|tobool else 'false' }},
});
</script>
{% endif %}
{% endif %}
{%- endif %}
{%- endif %}
{%- block footer %} {% endblock %}

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@ -11,7 +11,7 @@ msgid ""
msgstr ""
"Project-Id-Version: sphinx_rtd_theme 0.4.3.dev0\n"
"Report-Msgid-Bugs-To: EMAIL@ADDRESS\n"
"POT-Creation-Date: 2020-05-06 13:38-0600\n"
"POT-Creation-Date: 2021-09-13 13:35-0600\n"
"PO-Revision-Date: 2019-07-16 21:44+0000\n"
"Last-Translator: Tom Kunze <transifex.com@tomabrafix.de>, 2019\n"
"Language-Team: German (https://www.transifex.com/readthedocs/teams/101354/de/)\n"
@ -22,37 +22,32 @@ msgstr ""
"Language: de\n"
"Plural-Forms: nplurals=2; plural=(n != 1);\n"
#: sphinx_rtd_theme/breadcrumbs.html:43 sphinx_rtd_theme/breadcrumbs.html:45
#: sphinx_rtd_theme/breadcrumbs.html:37 sphinx_rtd_theme/breadcrumbs.html:39
msgid "Edit on GitHub"
msgstr "Auf GitHub bearbeiten"
#: sphinx_rtd_theme/breadcrumbs.html:50 sphinx_rtd_theme/breadcrumbs.html:52
#: sphinx_rtd_theme/breadcrumbs.html:44 sphinx_rtd_theme/breadcrumbs.html:46
msgid "Edit on Bitbucket"
msgstr "Auf Bitbucket bearbeiten"
#: sphinx_rtd_theme/breadcrumbs.html:57 sphinx_rtd_theme/breadcrumbs.html:59
#: sphinx_rtd_theme/breadcrumbs.html:51 sphinx_rtd_theme/breadcrumbs.html:53
msgid "Edit on GitLab"
msgstr "Auf GitLab bearbeiten"
#: sphinx_rtd_theme/breadcrumbs.html:62 sphinx_rtd_theme/breadcrumbs.html:64
#: sphinx_rtd_theme/breadcrumbs.html:56 sphinx_rtd_theme/breadcrumbs.html:58
msgid "View page source"
msgstr "Quelltext anzeigen"
#: sphinx_rtd_theme/breadcrumbs.html:74 sphinx_rtd_theme/footer.html:5
msgid "Next"
msgstr "Weiter"
#: sphinx_rtd_theme/breadcrumbs.html:77 sphinx_rtd_theme/footer.html:8
#: sphinx_rtd_theme/breadcrumbs.html:69 sphinx_rtd_theme/footer.html:6
msgid "Previous"
msgstr "Zurück"
#: sphinx_rtd_theme/footer.html:21 sphinx_rtd_theme/footer.html:24
#: sphinx_rtd_theme/layout.html:96
msgid "Copyright"
msgstr "Copyright"
#: sphinx_rtd_theme/breadcrumbs.html:72 sphinx_rtd_theme/footer.html:9
msgid "Next"
msgstr "Weiter"
#. Build is a noun, not a verb
#: sphinx_rtd_theme/footer.html:31
#: sphinx_rtd_theme/footer.html:30
msgid "Build"
msgstr "Build"
@ -64,49 +59,53 @@ msgstr "Zuletzt aktualisiert am %(last_updated)s."
#. the variable "sphinx_web" is a link to the Sphinx project documentation
#. with
#. the text "Sphinx"
#: sphinx_rtd_theme/footer.html:52
#: sphinx_rtd_theme/footer.html:53
#, python-format
msgid "Built with %(sphinx_web)s using a"
msgstr "Erstellt mit %(sphinx_web)s mit einem"
#. this is always used as "provided by Read the Docs", and should not imply
#. Read the Docs is an author of the generated documentation.
#: sphinx_rtd_theme/footer.html:56
#: sphinx_rtd_theme/footer.html:57
#, python-format
msgid "provided by %(readthedocs_web)s"
msgstr "bereitgestellt von %(readthedocs_web)s"
#: sphinx_rtd_theme/layout.html:79
#: sphinx_rtd_theme/layout.html:97
#, python-format
msgid "Search within %(docstitle)s"
msgstr "%(docstitle)s durchsuchen"
#: sphinx_rtd_theme/layout.html:87
#: sphinx_rtd_theme/layout.html:105
msgid "About these documents"
msgstr "Über diese Dokumentation"
#: sphinx_rtd_theme/layout.html:90
#: sphinx_rtd_theme/layout.html:108
msgid "Index"
msgstr "Index"
#: sphinx_rtd_theme/layout.html:93 sphinx_rtd_theme/search.html:11
#: sphinx_rtd_theme/layout.html:111 sphinx_rtd_theme/search.html:11
msgid "Search"
msgstr "Suche"
#: sphinx_rtd_theme/layout.html:128
#: sphinx_rtd_theme/layout.html:114
msgid "Copyright"
msgstr "Copyright"
#: sphinx_rtd_theme/layout.html:147 sphinx_rtd_theme/layout.html:149
msgid "Logo"
msgstr "Logo"
#: sphinx_rtd_theme/search.html:29
#: sphinx_rtd_theme/search.html:31
msgid "Please activate JavaScript to enable the search functionality."
msgstr "Bitte aktiviere JavaScript, um die Suchfunktion zu nutzen."
#. Search is a noun, not a verb
#: sphinx_rtd_theme/search.html:37
#: sphinx_rtd_theme/search.html:39
msgid "Search Results"
msgstr "Suchergebnisse"
#: sphinx_rtd_theme/search.html:39
#: sphinx_rtd_theme/search.html:41
msgid ""
"Your search did not match any documents. Please make sure that all words are"
" spelled correctly and that you've selected enough categories."
@ -119,7 +118,7 @@ msgstr ""
msgid "Search docs"
msgstr "Dokumentation durchsuchen"
#: sphinx_rtd_theme/versions.html:11
#: sphinx_rtd_theme/versions.html:3 sphinx_rtd_theme/versions.html:11
msgid "Versions"
msgstr "Versionen"
@ -135,9 +134,3 @@ msgstr "Projektübersicht"
#: sphinx_rtd_theme/versions.html:29
msgid "Builds"
msgstr "Builds"
#~ msgid "Docs"
#~ msgstr "Dokumentation"
#~ msgid "Free document hosting provided by"
#~ msgstr "Kostenloses Dokumentationen-Hosting zur Verfügung gestellt von"

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@ -8,7 +8,7 @@ msgid ""
msgstr ""
"Project-Id-Version: sphinx_rtd_theme 0.4.3.dev0\n"
"Report-Msgid-Bugs-To: EMAIL@ADDRESS\n"
"POT-Creation-Date: 2020-05-06 13:38-0600\n"
"POT-Creation-Date: 2021-09-13 13:35-0600\n"
"PO-Revision-Date: 2019-07-16 15:43-0600\n"
"Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
"Language: en\n"
@ -19,42 +19,64 @@ msgstr ""
"Content-Transfer-Encoding: 8bit\n"
"Generated-By: Babel 2.8.0\n"
#: sphinx_rtd_theme/breadcrumbs.html:43 sphinx_rtd_theme/breadcrumbs.html:45
#. This is an ARIA section label for page links, including previous/next page
#. link and links to GitHub/GitLab/etc.
#: sphinx_rtd_theme/breadcrumbs.html:22
msgid "Page navigation"
msgstr ""
#: sphinx_rtd_theme/breadcrumbs.html:37 sphinx_rtd_theme/breadcrumbs.html:39
msgid "Edit on GitHub"
msgstr ""
#: sphinx_rtd_theme/breadcrumbs.html:50 sphinx_rtd_theme/breadcrumbs.html:52
#: sphinx_rtd_theme/breadcrumbs.html:44 sphinx_rtd_theme/breadcrumbs.html:46
msgid "Edit on Bitbucket"
msgstr ""
#: sphinx_rtd_theme/breadcrumbs.html:57 sphinx_rtd_theme/breadcrumbs.html:59
#: sphinx_rtd_theme/breadcrumbs.html:51 sphinx_rtd_theme/breadcrumbs.html:53
msgid "Edit on GitLab"
msgstr ""
#: sphinx_rtd_theme/breadcrumbs.html:62 sphinx_rtd_theme/breadcrumbs.html:64
#: sphinx_rtd_theme/breadcrumbs.html:56 sphinx_rtd_theme/breadcrumbs.html:58
msgid "View page source"
msgstr ""
#: sphinx_rtd_theme/breadcrumbs.html:74 sphinx_rtd_theme/footer.html:5
msgid "Next"
#. This is an ARIA section label for sequential page links, such as previous
#. and next page links.
#: sphinx_rtd_theme/breadcrumbs.html:67
msgid "Sequential page navigation"
msgstr ""
#: sphinx_rtd_theme/breadcrumbs.html:77 sphinx_rtd_theme/footer.html:8
#: sphinx_rtd_theme/breadcrumbs.html:69 sphinx_rtd_theme/footer.html:6
msgid "Previous"
msgstr ""
#: sphinx_rtd_theme/footer.html:21 sphinx_rtd_theme/footer.html:24
#: sphinx_rtd_theme/layout.html:96
msgid "Copyright"
#: sphinx_rtd_theme/breadcrumbs.html:72 sphinx_rtd_theme/footer.html:9
msgid "Next"
msgstr ""
#. This is an ARIA section label for the footer section of the page.
#: sphinx_rtd_theme/footer.html:4
msgid "Footer"
msgstr ""
#: sphinx_rtd_theme/footer.html:21
#, python-format
msgid "&#169; <a href=\"%(path)s\">Copyright</a> %(copyright)s."
msgstr ""
#: sphinx_rtd_theme/footer.html:23
#, python-format
msgid "&#169; Copyright %(copyright)s."
msgstr ""
#. Build is a noun, not a verb
#: sphinx_rtd_theme/footer.html:31
#: sphinx_rtd_theme/footer.html:30
msgid "Build"
msgstr ""
#. the phrase "revision" comes from Git, referring to a commit
#: sphinx_rtd_theme/footer.html:37
#: sphinx_rtd_theme/footer.html:36
msgid "Revision"
msgstr ""
@ -65,59 +87,70 @@ msgstr ""
#. the variable "sphinx_web" is a link to the Sphinx project documentation with
#. the text "Sphinx"
#: sphinx_rtd_theme/footer.html:52
#: sphinx_rtd_theme/footer.html:53
#, python-format
msgid "Built with %(sphinx_web)s using a"
msgstr ""
#. "theme" refers to a theme for Sphinx, which alters the appearance of the
#. generated documenation
#: sphinx_rtd_theme/footer.html:54
#: sphinx_rtd_theme/footer.html:55
msgid "theme"
msgstr ""
#. this is always used as "provided by Read the Docs", and should not imply
#. Read the Docs is an author of the generated documentation.
#: sphinx_rtd_theme/footer.html:56
#: sphinx_rtd_theme/footer.html:57
#, python-format
msgid "provided by %(readthedocs_web)s"
msgstr ""
#: sphinx_rtd_theme/layout.html:79
#: sphinx_rtd_theme/layout.html:97
#, python-format
msgid "Search within %(docstitle)s"
msgstr ""
#: sphinx_rtd_theme/layout.html:87
#: sphinx_rtd_theme/layout.html:105
msgid "About these documents"
msgstr ""
#: sphinx_rtd_theme/layout.html:90
#: sphinx_rtd_theme/layout.html:108
msgid "Index"
msgstr ""
#: sphinx_rtd_theme/layout.html:93 sphinx_rtd_theme/search.html:11
#: sphinx_rtd_theme/layout.html:111 sphinx_rtd_theme/search.html:11
msgid "Search"
msgstr ""
#: sphinx_rtd_theme/layout.html:121
msgid "Documentation Home"
#: sphinx_rtd_theme/layout.html:114
msgid "Copyright"
msgstr ""
#: sphinx_rtd_theme/layout.html:128
#: sphinx_rtd_theme/layout.html:147 sphinx_rtd_theme/layout.html:149
msgid "Logo"
msgstr ""
#: sphinx_rtd_theme/search.html:29
#. This is an ARIA section label for the main navigation menu
#: sphinx_rtd_theme/layout.html:173
msgid "Navigation menu"
msgstr ""
#. This is an ARIA section label for the navigation menu that is visible when
#. viewing the page on mobile devices
#: sphinx_rtd_theme/layout.html:195
msgid "Mobile navigation menu"
msgstr ""
#: sphinx_rtd_theme/search.html:31
msgid "Please activate JavaScript to enable the search functionality."
msgstr ""
#. Search is a noun, not a verb
#: sphinx_rtd_theme/search.html:37
#: sphinx_rtd_theme/search.html:39
msgid "Search Results"
msgstr ""
#: sphinx_rtd_theme/search.html:39
#: sphinx_rtd_theme/search.html:41
msgid ""
"Your search did not match any documents. Please make sure that all words "
"are spelled correctly and that you've selected enough categories."
@ -127,7 +160,7 @@ msgstr ""
msgid "Search docs"
msgstr ""
#: sphinx_rtd_theme/versions.html:11
#: sphinx_rtd_theme/versions.html:3 sphinx_rtd_theme/versions.html:11
msgid "Versions"
msgstr ""
@ -154,3 +187,15 @@ msgstr ""
#~ msgid "Free document hosting provided by"
#~ msgstr ""
#~ msgid "Documentation Home"
#~ msgstr ""
#~ msgid "Breadcrumbs"
#~ msgstr ""
#~ msgid "Main"
#~ msgstr ""
#~ msgid "Top"
#~ msgstr ""

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@ -6,15 +6,15 @@
#
# Translators:
# Anthony <aj@ohess.org>, 2019
# Leonardo J. Caballero G. <leonardocaballero@gmail.com>, 2020
# Radina Matic <radina.matic@gmail.com>, 2021
#
msgid ""
msgstr ""
"Project-Id-Version: sphinx_rtd_theme 0.4.3.dev0\n"
"Report-Msgid-Bugs-To: EMAIL@ADDRESS\n"
"POT-Creation-Date: 2020-05-06 13:38-0600\n"
"POT-Creation-Date: 2021-09-13 13:35-0600\n"
"PO-Revision-Date: 2019-07-16 21:44+0000\n"
"Last-Translator: Leonardo J. Caballero G. <leonardocaballero@gmail.com>, 2020\n"
"Last-Translator: Radina Matic <radina.matic@gmail.com>, 2021\n"
"Language-Team: Spanish (https://www.transifex.com/readthedocs/teams/101354/es/)\n"
"MIME-Version: 1.0\n"
"Content-Type: text/plain; charset=UTF-8\n"
@ -23,107 +23,117 @@ msgstr ""
"Language: es\n"
"Plural-Forms: nplurals=2; plural=(n != 1);\n"
#: sphinx_rtd_theme/breadcrumbs.html:43 sphinx_rtd_theme/breadcrumbs.html:45
#: sphinx_rtd_theme/breadcrumbs.html:37 sphinx_rtd_theme/breadcrumbs.html:39
msgid "Edit on GitHub"
msgstr "Editar en GitHub"
#: sphinx_rtd_theme/breadcrumbs.html:50 sphinx_rtd_theme/breadcrumbs.html:52
#: sphinx_rtd_theme/breadcrumbs.html:44 sphinx_rtd_theme/breadcrumbs.html:46
msgid "Edit on Bitbucket"
msgstr "Editar en Bitbucket"
#: sphinx_rtd_theme/breadcrumbs.html:57 sphinx_rtd_theme/breadcrumbs.html:59
#: sphinx_rtd_theme/breadcrumbs.html:51 sphinx_rtd_theme/breadcrumbs.html:53
msgid "Edit on GitLab"
msgstr "Editar en GitLab"
#: sphinx_rtd_theme/breadcrumbs.html:62 sphinx_rtd_theme/breadcrumbs.html:64
#: sphinx_rtd_theme/breadcrumbs.html:56 sphinx_rtd_theme/breadcrumbs.html:58
msgid "View page source"
msgstr "Ver código fuente de la página"
#: sphinx_rtd_theme/breadcrumbs.html:74 sphinx_rtd_theme/footer.html:5
msgid "Next"
msgstr "Siguiente"
#: sphinx_rtd_theme/breadcrumbs.html:77 sphinx_rtd_theme/footer.html:8
#: sphinx_rtd_theme/breadcrumbs.html:69 sphinx_rtd_theme/footer.html:6
msgid "Previous"
msgstr "Anterior"
#: sphinx_rtd_theme/footer.html:21 sphinx_rtd_theme/footer.html:24
#: sphinx_rtd_theme/layout.html:96
msgid "Copyright"
msgstr "Derechos de autor"
#: sphinx_rtd_theme/breadcrumbs.html:72 sphinx_rtd_theme/footer.html:9
msgid "Next"
msgstr "Siguiente"
#. This is an ARIA section label for the footer section of the page.
#: sphinx_rtd_theme/footer.html:4
msgid "Footer"
msgstr "Pie de página"
#: sphinx_rtd_theme/footer.html:21
#, python-format
msgid "&#169; <a href=\"%(path)s\">Copyright</a> %(copyright)s."
msgstr "&#169; <a href=\"%(path)s\">Derechos de autor</a> %(copyright)s."
#: sphinx_rtd_theme/footer.html:23
#, python-format
msgid "&#169; Copyright %(copyright)s."
msgstr "&#169; Derechos de autor %(copyright)s."
#. Build is a noun, not a verb
#: sphinx_rtd_theme/footer.html:31
#: sphinx_rtd_theme/footer.html:30
msgid "Build"
msgstr "Construido"
msgstr "Compilación"
#. the phrase "revision" comes from Git, referring to a commit
#: sphinx_rtd_theme/footer.html:37
#: sphinx_rtd_theme/footer.html:36
msgid "Revision"
msgstr "Revisión"
#: sphinx_rtd_theme/footer.html:41
#, python-format
msgid "Last updated on %(last_updated)s."
msgstr "Actualizado por última vez en %(last_updated)s."
msgstr "Actualizado por última vez el %(last_updated)s."
#. the variable "sphinx_web" is a link to the Sphinx project documentation
#. with
#. the text "Sphinx"
#: sphinx_rtd_theme/footer.html:52
#: sphinx_rtd_theme/footer.html:53
#, python-format
msgid "Built with %(sphinx_web)s using a"
msgstr "Construido con %(sphinx_web)s usando un"
msgstr "Compilado con %(sphinx_web)s usando un"
#. "theme" refers to a theme for Sphinx, which alters the appearance of the
#. generated documenation
#: sphinx_rtd_theme/footer.html:54
#: sphinx_rtd_theme/footer.html:55
msgid "theme"
msgstr "tema"
#. this is always used as "provided by Read the Docs", and should not imply
#. Read the Docs is an author of the generated documentation.
#: sphinx_rtd_theme/footer.html:56
#: sphinx_rtd_theme/footer.html:57
#, python-format
msgid "provided by %(readthedocs_web)s"
msgstr "proporcionado por %(readthedocs_web)s"
#: sphinx_rtd_theme/layout.html:79
#: sphinx_rtd_theme/layout.html:97
#, python-format
msgid "Search within %(docstitle)s"
msgstr "Buscar en %(docstitle)s"
#: sphinx_rtd_theme/layout.html:87
#: sphinx_rtd_theme/layout.html:105
msgid "About these documents"
msgstr "Sobre esta documentación"
#: sphinx_rtd_theme/layout.html:90
#: sphinx_rtd_theme/layout.html:108
msgid "Index"
msgstr "Índice"
#: sphinx_rtd_theme/layout.html:93 sphinx_rtd_theme/search.html:11
#: sphinx_rtd_theme/layout.html:111 sphinx_rtd_theme/search.html:11
msgid "Search"
msgstr "Búsqueda"
#: sphinx_rtd_theme/layout.html:121
msgid "Documentation Home"
msgstr "Inicio de Documentación"
#: sphinx_rtd_theme/layout.html:114
msgid "Copyright"
msgstr "Derechos de autor"
#: sphinx_rtd_theme/layout.html:128
#: sphinx_rtd_theme/layout.html:147 sphinx_rtd_theme/layout.html:149
msgid "Logo"
msgstr "Logotipo"
#: sphinx_rtd_theme/search.html:29
#: sphinx_rtd_theme/search.html:31
msgid "Please activate JavaScript to enable the search functionality."
msgstr ""
"Por favor, active JavaScript para habilitar la funcionalidad de búsqueda."
#. Search is a noun, not a verb
#: sphinx_rtd_theme/search.html:37
#: sphinx_rtd_theme/search.html:39
msgid "Search Results"
msgstr "Resultados de la búsqueda"
#: sphinx_rtd_theme/search.html:39
#: sphinx_rtd_theme/search.html:41
msgid ""
"Your search did not match any documents. Please make sure that all words are"
" spelled correctly and that you've selected enough categories."
@ -136,7 +146,7 @@ msgstr ""
msgid "Search docs"
msgstr "Buscar documentos"
#: sphinx_rtd_theme/versions.html:11
#: sphinx_rtd_theme/versions.html:3 sphinx_rtd_theme/versions.html:11
msgid "Versions"
msgstr "Versiones"
@ -155,10 +165,4 @@ msgstr "Página de Proyecto"
#: sphinx_rtd_theme/versions.html:29
msgid "Builds"
msgstr "Construcciones"
#~ msgid "Docs"
#~ msgstr "Documentos"
#~ msgid "Free document hosting provided by"
#~ msgstr "Alojamiento gratuito de documentos proporcionado por"
msgstr "Compilaciones"

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@ -6,15 +6,15 @@
#
# Translators:
# Anthony <aj@ohess.org>, 2020
# Ivar Smolin <okul@linux.ee>, 2020
# Ivar Smolin <okul@linux.ee>, 2021
#
msgid ""
msgstr ""
"Project-Id-Version: sphinx_rtd_theme 0.4.3.dev0\n"
"Report-Msgid-Bugs-To: EMAIL@ADDRESS\n"
"POT-Creation-Date: 2020-05-06 13:38-0600\n"
"POT-Creation-Date: 2021-09-13 13:35-0600\n"
"PO-Revision-Date: 2019-07-16 21:44+0000\n"
"Last-Translator: Ivar Smolin <okul@linux.ee>, 2020\n"
"Last-Translator: Ivar Smolin <okul@linux.ee>, 2021\n"
"Language-Team: Estonian (https://www.transifex.com/readthedocs/teams/101354/et/)\n"
"MIME-Version: 1.0\n"
"Content-Type: text/plain; charset=UTF-8\n"
@ -23,42 +23,52 @@ msgstr ""
"Language: et\n"
"Plural-Forms: nplurals=2; plural=(n != 1);\n"
#: sphinx_rtd_theme/breadcrumbs.html:43 sphinx_rtd_theme/breadcrumbs.html:45
#: sphinx_rtd_theme/breadcrumbs.html:37 sphinx_rtd_theme/breadcrumbs.html:39
msgid "Edit on GitHub"
msgstr "Muuda GitHubis"
#: sphinx_rtd_theme/breadcrumbs.html:50 sphinx_rtd_theme/breadcrumbs.html:52
#: sphinx_rtd_theme/breadcrumbs.html:44 sphinx_rtd_theme/breadcrumbs.html:46
msgid "Edit on Bitbucket"
msgstr "Muuda Bitbucketis"
#: sphinx_rtd_theme/breadcrumbs.html:57 sphinx_rtd_theme/breadcrumbs.html:59
#: sphinx_rtd_theme/breadcrumbs.html:51 sphinx_rtd_theme/breadcrumbs.html:53
msgid "Edit on GitLab"
msgstr "Muuda GitLabis"
#: sphinx_rtd_theme/breadcrumbs.html:62 sphinx_rtd_theme/breadcrumbs.html:64
#: sphinx_rtd_theme/breadcrumbs.html:56 sphinx_rtd_theme/breadcrumbs.html:58
msgid "View page source"
msgstr "Vaata lehe lähtekoodi"
#: sphinx_rtd_theme/breadcrumbs.html:74 sphinx_rtd_theme/footer.html:5
msgid "Next"
msgstr "Järgmine"
#: sphinx_rtd_theme/breadcrumbs.html:77 sphinx_rtd_theme/footer.html:8
#: sphinx_rtd_theme/breadcrumbs.html:69 sphinx_rtd_theme/footer.html:6
msgid "Previous"
msgstr "Eelmine"
#: sphinx_rtd_theme/footer.html:21 sphinx_rtd_theme/footer.html:24
#: sphinx_rtd_theme/layout.html:96
msgid "Copyright"
msgstr "Autoriõigus"
#: sphinx_rtd_theme/breadcrumbs.html:72 sphinx_rtd_theme/footer.html:9
msgid "Next"
msgstr "Järgmine"
#. This is an ARIA section label for the footer section of the page.
#: sphinx_rtd_theme/footer.html:4
msgid "Footer"
msgstr "Jalus"
#: sphinx_rtd_theme/footer.html:21
#, python-format
msgid "&#169; <a href=\"%(path)s\">Copyright</a> %(copyright)s."
msgstr "&#169; <a href=\"%(path)s\">Autoriõigus</a> %(copyright)s."
#: sphinx_rtd_theme/footer.html:23
#, python-format
msgid "&#169; Copyright %(copyright)s."
msgstr "&#169; Autoriõigus %(copyright)s."
#. Build is a noun, not a verb
#: sphinx_rtd_theme/footer.html:31
#: sphinx_rtd_theme/footer.html:30
msgid "Build"
msgstr "Ehitus"
#. the phrase "revision" comes from Git, referring to a commit
#: sphinx_rtd_theme/footer.html:37
#: sphinx_rtd_theme/footer.html:36
msgid "Revision"
msgstr "Redaktsioon"
@ -70,52 +80,59 @@ msgstr "Viimati uuendatud %(last_updated)s."
#. the variable "sphinx_web" is a link to the Sphinx project documentation
#. with
#. the text "Sphinx"
#: sphinx_rtd_theme/footer.html:52
#: sphinx_rtd_theme/footer.html:53
#, python-format
msgid "Built with %(sphinx_web)s using a"
msgstr "Ehitatud %(sphinx_web)s'iga,"
#. "theme" refers to a theme for Sphinx, which alters the appearance of the
#. generated documenation
#: sphinx_rtd_theme/footer.html:54
#: sphinx_rtd_theme/footer.html:55
msgid "theme"
msgstr "kujundusteema"
#: sphinx_rtd_theme/layout.html:79
#. this is always used as "provided by Read the Docs", and should not imply
#. Read the Docs is an author of the generated documentation.
#: sphinx_rtd_theme/footer.html:57
#, python-format
msgid "provided by %(readthedocs_web)s"
msgstr "on loonud %(readthedocs_web)s"
#: sphinx_rtd_theme/layout.html:97
#, python-format
msgid "Search within %(docstitle)s"
msgstr "Otsi dokumendist %(docstitle)s"
#: sphinx_rtd_theme/layout.html:87
#: sphinx_rtd_theme/layout.html:105
msgid "About these documents"
msgstr "Nende dokumentide kirjeldused"
#: sphinx_rtd_theme/layout.html:90
#: sphinx_rtd_theme/layout.html:108
msgid "Index"
msgstr "Indeks"
#: sphinx_rtd_theme/layout.html:93 sphinx_rtd_theme/search.html:11
#: sphinx_rtd_theme/layout.html:111 sphinx_rtd_theme/search.html:11
msgid "Search"
msgstr "Otsing"
#: sphinx_rtd_theme/layout.html:121
msgid "Documentation Home"
msgstr "Dokumentatsiooni kodu"
#: sphinx_rtd_theme/layout.html:114
msgid "Copyright"
msgstr "Autoriõigus"
#: sphinx_rtd_theme/layout.html:128
#: sphinx_rtd_theme/layout.html:147 sphinx_rtd_theme/layout.html:149
msgid "Logo"
msgstr "Logo"
#: sphinx_rtd_theme/search.html:29
#: sphinx_rtd_theme/search.html:31
msgid "Please activate JavaScript to enable the search functionality."
msgstr "Otsimisfunktsiooni lubamiseks aktiveeri palun JavaScript"
#. Search is a noun, not a verb
#: sphinx_rtd_theme/search.html:37
#: sphinx_rtd_theme/search.html:39
msgid "Search Results"
msgstr "Otsingu tulemused"
#: sphinx_rtd_theme/search.html:39
#: sphinx_rtd_theme/search.html:41
msgid ""
"Your search did not match any documents. Please make sure that all words are"
" spelled correctly and that you've selected enough categories."
@ -127,7 +144,7 @@ msgstr ""
msgid "Search docs"
msgstr "Otsi dokumente"
#: sphinx_rtd_theme/versions.html:11
#: sphinx_rtd_theme/versions.html:3 sphinx_rtd_theme/versions.html:11
msgid "Versions"
msgstr "Versioonid"
@ -147,9 +164,3 @@ msgstr "Projekti kodu"
#: sphinx_rtd_theme/versions.html:29
msgid "Builds"
msgstr "Ehitused"
#~ msgid "Docs"
#~ msgstr "Dokumendid"
#~ msgid "Free document hosting provided by"
#~ msgstr "Dokumentatsiooni majutab tasuta"

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@ -0,0 +1,160 @@
# English translations for sphinx_rtd_theme.
# Copyright (C) 2019 ORGANIZATION
# This file is distributed under the same license as the sphinx_rtd_theme
# project.
# FIRST AUTHOR <EMAIL@ADDRESS>, 2019.
#
# Translators:
# Anthony <aj@ohess.org>, 2021
#
msgid ""
msgstr ""
"Project-Id-Version: sphinx_rtd_theme 0.4.3.dev0\n"
"Report-Msgid-Bugs-To: EMAIL@ADDRESS\n"
"POT-Creation-Date: 2021-09-13 13:35-0600\n"
"PO-Revision-Date: 2019-07-16 21:44+0000\n"
"Last-Translator: Anthony <aj@ohess.org>, 2021\n"
"Language-Team: Persian (Iran) (https://www.transifex.com/readthedocs/teams/101354/fa_IR/)\n"
"MIME-Version: 1.0\n"
"Content-Type: text/plain; charset=UTF-8\n"
"Content-Transfer-Encoding: 8bit\n"
"Generated-By: Babel 2.8.0\n"
"Language: fa_IR\n"
"Plural-Forms: nplurals=2; plural=(n > 1);\n"
#: sphinx_rtd_theme/breadcrumbs.html:37 sphinx_rtd_theme/breadcrumbs.html:39
msgid "Edit on GitHub"
msgstr "ویرایش در GitHub"
#: sphinx_rtd_theme/breadcrumbs.html:44 sphinx_rtd_theme/breadcrumbs.html:46
msgid "Edit on Bitbucket"
msgstr "ویرایش در Bitbucket"
#: sphinx_rtd_theme/breadcrumbs.html:51 sphinx_rtd_theme/breadcrumbs.html:53
msgid "Edit on GitLab"
msgstr "ویرایش در GitLab"
#: sphinx_rtd_theme/breadcrumbs.html:56 sphinx_rtd_theme/breadcrumbs.html:58
msgid "View page source"
msgstr "نمایش متن منبع صفحه"
#: sphinx_rtd_theme/breadcrumbs.html:69 sphinx_rtd_theme/footer.html:6
msgid "Previous"
msgstr "پیشین"
#: sphinx_rtd_theme/breadcrumbs.html:72 sphinx_rtd_theme/footer.html:9
msgid "Next"
msgstr "بعدی"
#: sphinx_rtd_theme/footer.html:21
#, python-format
msgid "&#169; <a href=\"%(path)s\">Copyright</a> %(copyright)s."
msgstr "&#169; <a href=\"%(path)s\">حق انتشار</a> %(copyright)s."
#: sphinx_rtd_theme/footer.html:23
#, python-format
msgid "&#169; Copyright %(copyright)s."
msgstr "&#169; حق انتشار%(copyright)s."
#. Build is a noun, not a verb
#: sphinx_rtd_theme/footer.html:30
msgid "Build"
msgstr "ساخت"
#. the phrase "revision" comes from Git, referring to a commit
#: sphinx_rtd_theme/footer.html:36
msgid "Revision"
msgstr "بازبینی"
#: sphinx_rtd_theme/footer.html:41
#, python-format
msgid "Last updated on %(last_updated)s."
msgstr "آخرین بروز رسانی در %(last_updated)s ."
#. the variable "sphinx_web" is a link to the Sphinx project documentation
#. with
#. the text "Sphinx"
#: sphinx_rtd_theme/footer.html:53
#, python-format
msgid "Built with %(sphinx_web)s using a"
msgstr "ساخته شده با %(sphinx_web)s"
#. "theme" refers to a theme for Sphinx, which alters the appearance of the
#. generated documenation
#: sphinx_rtd_theme/footer.html:55
msgid "theme"
msgstr "پوسته"
#. this is always used as "provided by Read the Docs", and should not imply
#. Read the Docs is an author of the generated documentation.
#: sphinx_rtd_theme/footer.html:57
#, python-format
msgid "provided by %(readthedocs_web)s"
msgstr "تهیّه شده با %(readthedocs_web)s"
#: sphinx_rtd_theme/layout.html:97
#, python-format
msgid "Search within %(docstitle)s"
msgstr "جستجو در %(docstitle)s"
#: sphinx_rtd_theme/layout.html:105
msgid "About these documents"
msgstr "درباره این مستندات"
#: sphinx_rtd_theme/layout.html:108
msgid "Index"
msgstr "فهرست"
#: sphinx_rtd_theme/layout.html:111 sphinx_rtd_theme/search.html:11
msgid "Search"
msgstr "جستجوی"
#: sphinx_rtd_theme/layout.html:114
msgid "Copyright"
msgstr "کپی رایت"
#: sphinx_rtd_theme/layout.html:147 sphinx_rtd_theme/layout.html:149
msgid "Logo"
msgstr "آرم"
#: sphinx_rtd_theme/search.html:31
msgid "Please activate JavaScript to enable the search functionality."
msgstr "لطفاً جاوا اسکریپت را فعّال کنید تا قابلیّت جستجو فعّال شود."
#. Search is a noun, not a verb
#: sphinx_rtd_theme/search.html:39
msgid "Search Results"
msgstr "نتایج جستجو"
#: sphinx_rtd_theme/search.html:41
msgid ""
"Your search did not match any documents. Please make sure that all words are"
" spelled correctly and that you've selected enough categories."
msgstr ""
"جستجوی شما با هیچ سندی مطابقت نداشت. لطفاً از درستی املای واژگان مطمئن شوید."
" هم‌چنین بررسی کنید آیا به اندازه کافی دسته بندی انتخاب کرده‌اید."
#: sphinx_rtd_theme/searchbox.html:4
msgid "Search docs"
msgstr "جستجوی مستندات"
#: sphinx_rtd_theme/versions.html:3 sphinx_rtd_theme/versions.html:11
msgid "Versions"
msgstr "نگارش‌ها"
#: sphinx_rtd_theme/versions.html:17
msgid "Downloads"
msgstr "بارگیری‌ها"
#. The phrase "Read the Docs" is not translated
#: sphinx_rtd_theme/versions.html:24
msgid "On Read the Docs"
msgstr "درباره‌ی خواندن مستندات"
#: sphinx_rtd_theme/versions.html:26
msgid "Project Home"
msgstr "صفحه خانگی پروژه"
#: sphinx_rtd_theme/versions.html:29
msgid "Builds"
msgstr "ساخت‌ها"

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@ -5,16 +5,16 @@
# FIRST AUTHOR <EMAIL@ADDRESS>, 2019.
#
# Translators:
# Radina Matic <radina.matic@gmail.com>, 2020
# Anthony <aj@ohess.org>, 2020
# Radina Matic <radina.matic@gmail.com>, 2021
#
msgid ""
msgstr ""
"Project-Id-Version: sphinx_rtd_theme 0.4.3.dev0\n"
"Report-Msgid-Bugs-To: EMAIL@ADDRESS\n"
"POT-Creation-Date: 2020-05-06 13:38-0600\n"
"POT-Creation-Date: 2021-09-13 13:35-0600\n"
"PO-Revision-Date: 2019-07-16 21:44+0000\n"
"Last-Translator: Anthony <aj@ohess.org>, 2020\n"
"Last-Translator: Radina Matic <radina.matic@gmail.com>, 2021\n"
"Language-Team: French (https://www.transifex.com/readthedocs/teams/101354/fr/)\n"
"MIME-Version: 1.0\n"
"Content-Type: text/plain; charset=UTF-8\n"
@ -23,42 +23,52 @@ msgstr ""
"Language: fr\n"
"Plural-Forms: nplurals=2; plural=(n > 1);\n"
#: sphinx_rtd_theme/breadcrumbs.html:43 sphinx_rtd_theme/breadcrumbs.html:45
#: sphinx_rtd_theme/breadcrumbs.html:37 sphinx_rtd_theme/breadcrumbs.html:39
msgid "Edit on GitHub"
msgstr "Éditer sur GitHub"
#: sphinx_rtd_theme/breadcrumbs.html:50 sphinx_rtd_theme/breadcrumbs.html:52
#: sphinx_rtd_theme/breadcrumbs.html:44 sphinx_rtd_theme/breadcrumbs.html:46
msgid "Edit on Bitbucket"
msgstr "Éditer sur Bitbucket"
#: sphinx_rtd_theme/breadcrumbs.html:57 sphinx_rtd_theme/breadcrumbs.html:59
#: sphinx_rtd_theme/breadcrumbs.html:51 sphinx_rtd_theme/breadcrumbs.html:53
msgid "Edit on GitLab"
msgstr "Éditer sur GitLab"
#: sphinx_rtd_theme/breadcrumbs.html:62 sphinx_rtd_theme/breadcrumbs.html:64
#: sphinx_rtd_theme/breadcrumbs.html:56 sphinx_rtd_theme/breadcrumbs.html:58
msgid "View page source"
msgstr "Afficher la source de la page"
#: sphinx_rtd_theme/breadcrumbs.html:74 sphinx_rtd_theme/footer.html:5
msgid "Next"
msgstr "Suivant"
#: sphinx_rtd_theme/breadcrumbs.html:77 sphinx_rtd_theme/footer.html:8
#: sphinx_rtd_theme/breadcrumbs.html:69 sphinx_rtd_theme/footer.html:6
msgid "Previous"
msgstr "Précédent"
#: sphinx_rtd_theme/footer.html:21 sphinx_rtd_theme/footer.html:24
#: sphinx_rtd_theme/layout.html:96
msgid "Copyright"
msgstr "Droits d'auteur"
#: sphinx_rtd_theme/breadcrumbs.html:72 sphinx_rtd_theme/footer.html:9
msgid "Next"
msgstr "Suivant"
#. This is an ARIA section label for the footer section of the page.
#: sphinx_rtd_theme/footer.html:4
msgid "Footer"
msgstr "Pied de page"
#: sphinx_rtd_theme/footer.html:21
#, python-format
msgid "&#169; <a href=\"%(path)s\">Copyright</a> %(copyright)s."
msgstr "&#169; <a href=\"%(path)s\">Droits d'auteur</a> %(copyright)s."
#: sphinx_rtd_theme/footer.html:23
#, python-format
msgid "&#169; Copyright %(copyright)s."
msgstr "&#169; Droits d'auteur %(copyright)s."
#. Build is a noun, not a verb
#: sphinx_rtd_theme/footer.html:31
#: sphinx_rtd_theme/footer.html:30
msgid "Build"
msgstr "Compilation"
#. the phrase "revision" comes from Git, referring to a commit
#: sphinx_rtd_theme/footer.html:37
#: sphinx_rtd_theme/footer.html:36
msgid "Revision"
msgstr "Révision"
@ -70,55 +80,59 @@ msgstr "Dernière mise à jour le %(last_updated)s."
#. the variable "sphinx_web" is a link to the Sphinx project documentation
#. with
#. the text "Sphinx"
#: sphinx_rtd_theme/footer.html:52
#: sphinx_rtd_theme/footer.html:53
#, python-format
msgid "Built with %(sphinx_web)s using a"
msgstr "Compilé avec %(sphinx_web)s en utilisant un"
#. "theme" refers to a theme for Sphinx, which alters the appearance of the
#. generated documenation
#: sphinx_rtd_theme/footer.html:54
#: sphinx_rtd_theme/footer.html:55
msgid "theme"
msgstr "thème"
#. this is always used as "provided by Read the Docs", and should not imply
#. Read the Docs is an author of the generated documentation.
#: sphinx_rtd_theme/footer.html:56
#: sphinx_rtd_theme/footer.html:57
#, python-format
msgid "provided by %(readthedocs_web)s"
msgstr "fourni par %(readthedocs_web)s"
#: sphinx_rtd_theme/layout.html:79
#: sphinx_rtd_theme/layout.html:97
#, python-format
msgid "Search within %(docstitle)s"
msgstr "Rechercher dans %(docstitle)s"
#: sphinx_rtd_theme/layout.html:87
#: sphinx_rtd_theme/layout.html:105
msgid "About these documents"
msgstr "À propos de cette documentation"
#: sphinx_rtd_theme/layout.html:90
#: sphinx_rtd_theme/layout.html:108
msgid "Index"
msgstr "Index"
#: sphinx_rtd_theme/layout.html:93 sphinx_rtd_theme/search.html:11
#: sphinx_rtd_theme/layout.html:111 sphinx_rtd_theme/search.html:11
msgid "Search"
msgstr "Rechercher"
#: sphinx_rtd_theme/layout.html:128
#: sphinx_rtd_theme/layout.html:114
msgid "Copyright"
msgstr "Droits d'auteur"
#: sphinx_rtd_theme/layout.html:147 sphinx_rtd_theme/layout.html:149
msgid "Logo"
msgstr "Logo"
#: sphinx_rtd_theme/search.html:29
#: sphinx_rtd_theme/search.html:31
msgid "Please activate JavaScript to enable the search functionality."
msgstr "Activez JavaScript pour accéder à la fonction de recherche."
#. Search is a noun, not a verb
#: sphinx_rtd_theme/search.html:37
#: sphinx_rtd_theme/search.html:39
msgid "Search Results"
msgstr "Résultats de la recherche"
#: sphinx_rtd_theme/search.html:39
#: sphinx_rtd_theme/search.html:41
msgid ""
"Your search did not match any documents. Please make sure that all words are"
" spelled correctly and that you've selected enough categories."
@ -131,7 +145,7 @@ msgstr ""
msgid "Search docs"
msgstr "Rechercher docs"
#: sphinx_rtd_theme/versions.html:11
#: sphinx_rtd_theme/versions.html:3 sphinx_rtd_theme/versions.html:11
msgid "Versions"
msgstr "Versions"
@ -139,6 +153,11 @@ msgstr "Versions"
msgid "Downloads"
msgstr "Téléchargements"
#. The phrase "Read the Docs" is not translated
#: sphinx_rtd_theme/versions.html:24
msgid "On Read the Docs"
msgstr "À propos de Read the Docs"
#: sphinx_rtd_theme/versions.html:26
msgid "Project Home"
msgstr "Accueil du projet"
@ -146,9 +165,3 @@ msgstr "Accueil du projet"
#: sphinx_rtd_theme/versions.html:29
msgid "Builds"
msgstr "Compilations"
#~ msgid "Docs"
#~ msgstr "Docs"
#~ msgid "Free document hosting provided by"
#~ msgstr "Hébergement gratuit de documents fourni par"

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@ -0,0 +1,190 @@
# English translations for sphinx_rtd_theme.
# Copyright (C) 2019 ORGANIZATION
# This file is distributed under the same license as the sphinx_rtd_theme
# project.
# FIRST AUTHOR <EMAIL@ADDRESS>, 2019.
#
# Translators:
# Anthony <aj@ohess.org>, 2021
# Maurizio Paglia <mpaglia0@gmail.com>, 2021
#
msgid ""
msgstr ""
"Project-Id-Version: sphinx_rtd_theme 0.4.3.dev0\n"
"Report-Msgid-Bugs-To: EMAIL@ADDRESS\n"
"POT-Creation-Date: 2021-09-13 13:35-0600\n"
"PO-Revision-Date: 2019-07-16 21:44+0000\n"
"Last-Translator: Maurizio Paglia <mpaglia0@gmail.com>, 2021\n"
"Language-Team: Italian (https://www.transifex.com/readthedocs/teams/101354/it/)\n"
"MIME-Version: 1.0\n"
"Content-Type: text/plain; charset=UTF-8\n"
"Content-Transfer-Encoding: 8bit\n"
"Generated-By: Babel 2.8.0\n"
"Language: it\n"
"Plural-Forms: nplurals=2; plural=(n != 1);\n"
#. This is an ARIA section label for page links, including previous/next page
#. link and links to GitHub/GitLab/etc.
#: sphinx_rtd_theme/breadcrumbs.html:22
msgid "Page navigation"
msgstr "Naviga tra le pagine"
#: sphinx_rtd_theme/breadcrumbs.html:37 sphinx_rtd_theme/breadcrumbs.html:39
msgid "Edit on GitHub"
msgstr "Modifica su GitHub"
#: sphinx_rtd_theme/breadcrumbs.html:44 sphinx_rtd_theme/breadcrumbs.html:46
msgid "Edit on Bitbucket"
msgstr "Modifica su Bitbucket"
#: sphinx_rtd_theme/breadcrumbs.html:51 sphinx_rtd_theme/breadcrumbs.html:53
msgid "Edit on GitLab"
msgstr "Modifica su GitLab"
#: sphinx_rtd_theme/breadcrumbs.html:56 sphinx_rtd_theme/breadcrumbs.html:58
msgid "View page source"
msgstr "Visualizza sorgente pagina"
#. This is an ARIA section label for sequential page links, such as previous
#. and next page links.
#: sphinx_rtd_theme/breadcrumbs.html:67
msgid "Sequential page navigation"
msgstr "Naviga sequenzialmente tra le pagine"
#: sphinx_rtd_theme/breadcrumbs.html:69 sphinx_rtd_theme/footer.html:6
msgid "Previous"
msgstr "Precedente"
#: sphinx_rtd_theme/breadcrumbs.html:72 sphinx_rtd_theme/footer.html:9
msgid "Next"
msgstr "Prossimo"
#. This is an ARIA section label for the footer section of the page.
#: sphinx_rtd_theme/footer.html:4
msgid "Footer"
msgstr "Piè di pagina"
#: sphinx_rtd_theme/footer.html:21
#, python-format
msgid "&#169; <a href=\"%(path)s\">Copyright</a> %(copyright)s."
msgstr "&#169; <a href=\"%(path)s\">Copyright</a> %(copyright)s."
#: sphinx_rtd_theme/footer.html:23
#, python-format
msgid "&#169; Copyright %(copyright)s."
msgstr "&#169; Copyright %(copyright)s."
#. Build is a noun, not a verb
#: sphinx_rtd_theme/footer.html:30
msgid "Build"
msgstr "Rev."
#. the phrase "revision" comes from Git, referring to a commit
#: sphinx_rtd_theme/footer.html:36
msgid "Revision"
msgstr "Revisione"
#: sphinx_rtd_theme/footer.html:41
#, python-format
msgid "Last updated on %(last_updated)s."
msgstr "Ultimo aggiornamento il %(last_updated)s."
#. the variable "sphinx_web" is a link to the Sphinx project documentation
#. with
#. the text "Sphinx"
#: sphinx_rtd_theme/footer.html:53
#, python-format
msgid "Built with %(sphinx_web)s using a"
msgstr "Realizzato con %(sphinx_web)s e il tema"
#. "theme" refers to a theme for Sphinx, which alters the appearance of the
#. generated documenation
#: sphinx_rtd_theme/footer.html:55
msgid "theme"
msgstr "tema"
#. this is always used as "provided by Read the Docs", and should not imply
#. Read the Docs is an author of the generated documentation.
#: sphinx_rtd_theme/footer.html:57
#, python-format
msgid "provided by %(readthedocs_web)s"
msgstr "fornito da %(readthedocs_web)s"
#: sphinx_rtd_theme/layout.html:97
#, python-format
msgid "Search within %(docstitle)s"
msgstr "Cerca in %(docstitle)s"
#: sphinx_rtd_theme/layout.html:105
msgid "About these documents"
msgstr "Nota sulla documentazione"
#: sphinx_rtd_theme/layout.html:108
msgid "Index"
msgstr "Indice"
#: sphinx_rtd_theme/layout.html:111 sphinx_rtd_theme/search.html:11
msgid "Search"
msgstr "Ricerca"
#: sphinx_rtd_theme/layout.html:114
msgid "Copyright"
msgstr "Copyright"
#: sphinx_rtd_theme/layout.html:147 sphinx_rtd_theme/layout.html:149
msgid "Logo"
msgstr "Logo"
#. This is an ARIA section label for the main navigation menu
#: sphinx_rtd_theme/layout.html:173
msgid "Navigation menu"
msgstr "Menu di navigazione"
#. This is an ARIA section label for the navigation menu that is visible when
#. viewing the page on mobile devices
#: sphinx_rtd_theme/layout.html:195
msgid "Mobile navigation menu"
msgstr "Menu navigazione dispositivi mobili"
#: sphinx_rtd_theme/search.html:31
msgid "Please activate JavaScript to enable the search functionality."
msgstr "Devi attivare JavaScript per attivare la funzione di ricerca."
#. Search is a noun, not a verb
#: sphinx_rtd_theme/search.html:39
msgid "Search Results"
msgstr "Risultati della ricerca"
#: sphinx_rtd_theme/search.html:41
msgid ""
"Your search did not match any documents. Please make sure that all words are"
" spelled correctly and that you've selected enough categories."
msgstr ""
"La tua ricerca non ha prodotto nessun risultato. Assicurati di aver scritto "
"correttamente tutti i termini cercati e di aver selezionato sufficienti "
"categorie."
#: sphinx_rtd_theme/searchbox.html:4
msgid "Search docs"
msgstr "Cerca documenti"
#: sphinx_rtd_theme/versions.html:3 sphinx_rtd_theme/versions.html:11
msgid "Versions"
msgstr "Versioni"
#: sphinx_rtd_theme/versions.html:17
msgid "Downloads"
msgstr "Downloads"
#. The phrase "Read the Docs" is not translated
#: sphinx_rtd_theme/versions.html:24
msgid "On Read the Docs"
msgstr "Riguardo Read the Docs"
#: sphinx_rtd_theme/versions.html:26
msgid "Project Home"
msgstr "Home progetto"
#: sphinx_rtd_theme/versions.html:29
msgid "Builds"
msgstr "Rev."

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@ -0,0 +1,188 @@
# English translations for sphinx_rtd_theme.
# Copyright (C) 2019 ORGANIZATION
# This file is distributed under the same license as the sphinx_rtd_theme
# project.
# FIRST AUTHOR <EMAIL@ADDRESS>, 2019.
#
# Translators:
# Tomas Straupis, 2021
#
msgid ""
msgstr ""
"Project-Id-Version: sphinx_rtd_theme 0.4.3.dev0\n"
"Report-Msgid-Bugs-To: EMAIL@ADDRESS\n"
"POT-Creation-Date: 2021-09-13 13:35-0600\n"
"PO-Revision-Date: 2019-07-16 21:44+0000\n"
"Last-Translator: Tomas Straupis, 2021\n"
"Language-Team: Lithuanian (https://www.transifex.com/readthedocs/teams/101354/lt/)\n"
"MIME-Version: 1.0\n"
"Content-Type: text/plain; charset=UTF-8\n"
"Content-Transfer-Encoding: 8bit\n"
"Generated-By: Babel 2.8.0\n"
"Language: lt\n"
"Plural-Forms: nplurals=4; plural=(n % 10 == 1 && (n % 100 > 19 || n % 100 < 11) ? 0 : (n % 10 >= 2 && n % 10 <=9) && (n % 100 > 19 || n % 100 < 11) ? 1 : n % 1 != 0 ? 2: 3);\n"
#. This is an ARIA section label for page links, including previous/next page
#. link and links to GitHub/GitLab/etc.
#: sphinx_rtd_theme/breadcrumbs.html:22
msgid "Page navigation"
msgstr "Puslapių navigacija"
#: sphinx_rtd_theme/breadcrumbs.html:37 sphinx_rtd_theme/breadcrumbs.html:39
msgid "Edit on GitHub"
msgstr "Keisti GitHub'e"
#: sphinx_rtd_theme/breadcrumbs.html:44 sphinx_rtd_theme/breadcrumbs.html:46
msgid "Edit on Bitbucket"
msgstr "Keisti Bitbucket'e"
#: sphinx_rtd_theme/breadcrumbs.html:51 sphinx_rtd_theme/breadcrumbs.html:53
msgid "Edit on GitLab"
msgstr "Keisti GitLab'e"
#: sphinx_rtd_theme/breadcrumbs.html:56 sphinx_rtd_theme/breadcrumbs.html:58
msgid "View page source"
msgstr "Žiūrėti puslapio šaltinį"
#. This is an ARIA section label for sequential page links, such as previous
#. and next page links.
#: sphinx_rtd_theme/breadcrumbs.html:67
msgid "Sequential page navigation"
msgstr "Puslapių navigacija iš eilės"
#: sphinx_rtd_theme/breadcrumbs.html:69 sphinx_rtd_theme/footer.html:6
msgid "Previous"
msgstr "Ankstesnis"
#: sphinx_rtd_theme/breadcrumbs.html:72 sphinx_rtd_theme/footer.html:9
msgid "Next"
msgstr "Kitas"
#. This is an ARIA section label for the footer section of the page.
#: sphinx_rtd_theme/footer.html:4
msgid "Footer"
msgstr "Poraštė"
#: sphinx_rtd_theme/footer.html:21
#, python-format
msgid "&#169; <a href=\"%(path)s\">Copyright</a> %(copyright)s."
msgstr "&#169; <a href=\"%(path)s\">Copyright</a> %(copyright)s."
#: sphinx_rtd_theme/footer.html:23
#, python-format
msgid "&#169; Copyright %(copyright)s."
msgstr "&#169; Copyright %(copyright)s."
#. Build is a noun, not a verb
#: sphinx_rtd_theme/footer.html:30
msgid "Build"
msgstr "Surinkimas"
#. the phrase "revision" comes from Git, referring to a commit
#: sphinx_rtd_theme/footer.html:36
msgid "Revision"
msgstr "Versija"
#: sphinx_rtd_theme/footer.html:41
#, python-format
msgid "Last updated on %(last_updated)s."
msgstr "Atnaujinta %(last_updated)s."
#. the variable "sphinx_web" is a link to the Sphinx project documentation
#. with
#. the text "Sphinx"
#: sphinx_rtd_theme/footer.html:53
#, python-format
msgid "Built with %(sphinx_web)s using a"
msgstr "Surinkta su %(sphinx_web)s naudojant"
#. "theme" refers to a theme for Sphinx, which alters the appearance of the
#. generated documenation
#: sphinx_rtd_theme/footer.html:55
msgid "theme"
msgstr "temą"
#. this is always used as "provided by Read the Docs", and should not imply
#. Read the Docs is an author of the generated documentation.
#: sphinx_rtd_theme/footer.html:57
#, python-format
msgid "provided by %(readthedocs_web)s"
msgstr "pateiktą %(readthedocs_web)s"
#: sphinx_rtd_theme/layout.html:97
#, python-format
msgid "Search within %(docstitle)s"
msgstr "Ieškoti %(docstitle)s"
#: sphinx_rtd_theme/layout.html:105
msgid "About these documents"
msgstr "Apie šiuos dokumentus"
#: sphinx_rtd_theme/layout.html:108
msgid "Index"
msgstr "Indeksas"
#: sphinx_rtd_theme/layout.html:111 sphinx_rtd_theme/search.html:11
msgid "Search"
msgstr "Paieška"
#: sphinx_rtd_theme/layout.html:114
msgid "Copyright"
msgstr "Autorių teisės"
#: sphinx_rtd_theme/layout.html:147 sphinx_rtd_theme/layout.html:149
msgid "Logo"
msgstr "Logo"
#. This is an ARIA section label for the main navigation menu
#: sphinx_rtd_theme/layout.html:173
msgid "Navigation menu"
msgstr "Navigacijos meniu"
#. This is an ARIA section label for the navigation menu that is visible when
#. viewing the page on mobile devices
#: sphinx_rtd_theme/layout.html:195
msgid "Mobile navigation menu"
msgstr "Mobilios navigacijos meniu"
#: sphinx_rtd_theme/search.html:31
msgid "Please activate JavaScript to enable the search functionality."
msgstr "Prašome įjungti JavaScript, kad veiktų paieškos funkcionalumas."
#. Search is a noun, not a verb
#: sphinx_rtd_theme/search.html:39
msgid "Search Results"
msgstr "Paieškos rezultatai"
#: sphinx_rtd_theme/search.html:41
msgid ""
"Your search did not match any documents. Please make sure that all words are"
" spelled correctly and that you've selected enough categories."
msgstr ""
"Jūsų paieškai neatitiko nei vienas dokumentas. Prašome įsitikinti, kad visi "
"žodžiai parašyti teisingai ir kad parinkote pakankamai kategorijų."
#: sphinx_rtd_theme/searchbox.html:4
msgid "Search docs"
msgstr "Ieškoti dokumentuose"
#: sphinx_rtd_theme/versions.html:3 sphinx_rtd_theme/versions.html:11
msgid "Versions"
msgstr "Versijos"
#: sphinx_rtd_theme/versions.html:17
msgid "Downloads"
msgstr "Atsisiuntimai"
#. The phrase "Read the Docs" is not translated
#: sphinx_rtd_theme/versions.html:24
msgid "On Read the Docs"
msgstr "Apie Read the Docs"
#: sphinx_rtd_theme/versions.html:26
msgid "Project Home"
msgstr "Projekto namai"
#: sphinx_rtd_theme/versions.html:29
msgid "Builds"
msgstr "Surinkimai"

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@ -5,15 +5,15 @@
# FIRST AUTHOR <EMAIL@ADDRESS>, 2019.
#
# Translators:
# Jesse Tan, 2019
# Jesse Tan, 2021
#
msgid ""
msgstr ""
"Project-Id-Version: sphinx_rtd_theme 0.4.3.dev0\n"
"Report-Msgid-Bugs-To: EMAIL@ADDRESS\n"
"POT-Creation-Date: 2020-05-06 13:38-0600\n"
"POT-Creation-Date: 2021-09-13 13:35-0600\n"
"PO-Revision-Date: 2019-07-16 21:44+0000\n"
"Last-Translator: Jesse Tan, 2019\n"
"Last-Translator: Jesse Tan, 2021\n"
"Language-Team: Dutch (https://www.transifex.com/readthedocs/teams/101354/nl/)\n"
"MIME-Version: 1.0\n"
"Content-Type: text/plain; charset=UTF-8\n"
@ -22,42 +22,64 @@ msgstr ""
"Language: nl\n"
"Plural-Forms: nplurals=2; plural=(n != 1);\n"
#: sphinx_rtd_theme/breadcrumbs.html:43 sphinx_rtd_theme/breadcrumbs.html:45
#. This is an ARIA section label for page links, including previous/next page
#. link and links to GitHub/GitLab/etc.
#: sphinx_rtd_theme/breadcrumbs.html:22
msgid "Page navigation"
msgstr "Paginanavigatie"
#: sphinx_rtd_theme/breadcrumbs.html:37 sphinx_rtd_theme/breadcrumbs.html:39
msgid "Edit on GitHub"
msgstr "Bewerk op GitHub"
#: sphinx_rtd_theme/breadcrumbs.html:50 sphinx_rtd_theme/breadcrumbs.html:52
#: sphinx_rtd_theme/breadcrumbs.html:44 sphinx_rtd_theme/breadcrumbs.html:46
msgid "Edit on Bitbucket"
msgstr "Bewerk op BitBucket"
#: sphinx_rtd_theme/breadcrumbs.html:57 sphinx_rtd_theme/breadcrumbs.html:59
#: sphinx_rtd_theme/breadcrumbs.html:51 sphinx_rtd_theme/breadcrumbs.html:53
msgid "Edit on GitLab"
msgstr "Bewerk op GitLab"
#: sphinx_rtd_theme/breadcrumbs.html:62 sphinx_rtd_theme/breadcrumbs.html:64
#: sphinx_rtd_theme/breadcrumbs.html:56 sphinx_rtd_theme/breadcrumbs.html:58
msgid "View page source"
msgstr "Bekijk paginabron"
#: sphinx_rtd_theme/breadcrumbs.html:74 sphinx_rtd_theme/footer.html:5
msgid "Next"
msgstr "Volgende"
#. This is an ARIA section label for sequential page links, such as previous
#. and next page links.
#: sphinx_rtd_theme/breadcrumbs.html:67
msgid "Sequential page navigation"
msgstr "Navigatie voor gerelateerde pagina's"
#: sphinx_rtd_theme/breadcrumbs.html:77 sphinx_rtd_theme/footer.html:8
#: sphinx_rtd_theme/breadcrumbs.html:69 sphinx_rtd_theme/footer.html:6
msgid "Previous"
msgstr "Vorige"
#: sphinx_rtd_theme/footer.html:21 sphinx_rtd_theme/footer.html:24
#: sphinx_rtd_theme/layout.html:96
msgid "Copyright"
msgstr "Copyright"
#: sphinx_rtd_theme/breadcrumbs.html:72 sphinx_rtd_theme/footer.html:9
msgid "Next"
msgstr "Volgende"
#. This is an ARIA section label for the footer section of the page.
#: sphinx_rtd_theme/footer.html:4
msgid "Footer"
msgstr "Voettekst"
#: sphinx_rtd_theme/footer.html:21
#, python-format
msgid "&#169; <a href=\"%(path)s\">Copyright</a> %(copyright)s."
msgstr "&#169; <a href=\"%(path)s\">Copyright</a> %(copyright)s."
#: sphinx_rtd_theme/footer.html:23
#, python-format
msgid "&#169; Copyright %(copyright)s."
msgstr "&#169; Copyright %(copyright)s."
#. Build is a noun, not a verb
#: sphinx_rtd_theme/footer.html:31
#: sphinx_rtd_theme/footer.html:30
msgid "Build"
msgstr "Bouwresultaat"
#. the phrase "revision" comes from Git, referring to a commit
#: sphinx_rtd_theme/footer.html:37
#: sphinx_rtd_theme/footer.html:36
msgid "Revision"
msgstr "Revisie"
@ -69,55 +91,70 @@ msgstr "Laatste update op %(last_updated)s."
#. the variable "sphinx_web" is a link to the Sphinx project documentation
#. with
#. the text "Sphinx"
#: sphinx_rtd_theme/footer.html:52
#: sphinx_rtd_theme/footer.html:53
#, python-format
msgid "Built with %(sphinx_web)s using a"
msgstr "Gebouwd met %(sphinx_web)s met een"
#. "theme" refers to a theme for Sphinx, which alters the appearance of the
#. generated documenation
#: sphinx_rtd_theme/footer.html:54
#: sphinx_rtd_theme/footer.html:55
msgid "theme"
msgstr "thema"
#. this is always used as "provided by Read the Docs", and should not imply
#. Read the Docs is an author of the generated documentation.
#: sphinx_rtd_theme/footer.html:56
#: sphinx_rtd_theme/footer.html:57
#, python-format
msgid "provided by %(readthedocs_web)s"
msgstr "geleverd door %(readthedocs_web)s"
#: sphinx_rtd_theme/layout.html:79
#: sphinx_rtd_theme/layout.html:97
#, python-format
msgid "Search within %(docstitle)s"
msgstr "Zoek binnen %(docstitle)s"
#: sphinx_rtd_theme/layout.html:87
#: sphinx_rtd_theme/layout.html:105
msgid "About these documents"
msgstr "Over deze documenten"
#: sphinx_rtd_theme/layout.html:90
#: sphinx_rtd_theme/layout.html:108
msgid "Index"
msgstr "Index"
#: sphinx_rtd_theme/layout.html:93 sphinx_rtd_theme/search.html:11
#: sphinx_rtd_theme/layout.html:111 sphinx_rtd_theme/search.html:11
msgid "Search"
msgstr "Zoek"
#: sphinx_rtd_theme/layout.html:128
#: sphinx_rtd_theme/layout.html:114
msgid "Copyright"
msgstr "Copyright"
#: sphinx_rtd_theme/layout.html:147 sphinx_rtd_theme/layout.html:149
msgid "Logo"
msgstr "Logo"
#: sphinx_rtd_theme/search.html:29
#. This is an ARIA section label for the main navigation menu
#: sphinx_rtd_theme/layout.html:173
msgid "Navigation menu"
msgstr "Navigatiemenu"
#. This is an ARIA section label for the navigation menu that is visible when
#. viewing the page on mobile devices
#: sphinx_rtd_theme/layout.html:195
msgid "Mobile navigation menu"
msgstr "Navigatiemenu voor mobiel"
#: sphinx_rtd_theme/search.html:31
msgid "Please activate JavaScript to enable the search functionality."
msgstr "Zet JavaScript aan om de zoekfunctie mogelijk te maken."
#. Search is a noun, not a verb
#: sphinx_rtd_theme/search.html:37
#: sphinx_rtd_theme/search.html:39
msgid "Search Results"
msgstr "Zoekresultaten"
#: sphinx_rtd_theme/search.html:39
#: sphinx_rtd_theme/search.html:41
msgid ""
"Your search did not match any documents. Please make sure that all words are"
" spelled correctly and that you've selected enough categories."
@ -129,7 +166,7 @@ msgstr ""
msgid "Search docs"
msgstr "Zoek in documentatie"
#: sphinx_rtd_theme/versions.html:11
#: sphinx_rtd_theme/versions.html:3 sphinx_rtd_theme/versions.html:11
msgid "Versions"
msgstr "Versies"
@ -149,9 +186,3 @@ msgstr "Project Home"
#: sphinx_rtd_theme/versions.html:29
msgid "Builds"
msgstr "Bouwresultaten"
#~ msgid "Docs"
#~ msgstr "Documentatie"
#~ msgid "Free document hosting provided by"
#~ msgstr "Gratis hosting voor documentatie verzorgd door"

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@ -0,0 +1,137 @@
# English translations for sphinx_rtd_theme.
# Copyright (C) 2019 ORGANIZATION
# This file is distributed under the same license as the sphinx_rtd_theme
# project.
# FIRST AUTHOR <EMAIL@ADDRESS>, 2019.
#
# Translators:
# Michal Sniatala, 2021
#
msgid ""
msgstr ""
"Project-Id-Version: sphinx_rtd_theme 0.4.3.dev0\n"
"Report-Msgid-Bugs-To: EMAIL@ADDRESS\n"
"POT-Creation-Date: 2021-09-13 13:35-0600\n"
"PO-Revision-Date: 2019-07-16 21:44+0000\n"
"Last-Translator: Michal Sniatala, 2021\n"
"Language-Team: Polish (https://www.transifex.com/readthedocs/teams/101354/pl/)\n"
"MIME-Version: 1.0\n"
"Content-Type: text/plain; charset=UTF-8\n"
"Content-Transfer-Encoding: 8bit\n"
"Generated-By: Babel 2.8.0\n"
"Language: pl\n"
"Plural-Forms: nplurals=4; plural=(n==1 ? 0 : (n%10>=2 && n%10<=4) && (n%100<12 || n%100>14) ? 1 : n!=1 && (n%10>=0 && n%10<=1) || (n%10>=5 && n%10<=9) || (n%100>=12 && n%100<=14) ? 2 : 3);\n"
#: sphinx_rtd_theme/breadcrumbs.html:37 sphinx_rtd_theme/breadcrumbs.html:39
msgid "Edit on GitHub"
msgstr "Edytuj na GitHub"
#: sphinx_rtd_theme/breadcrumbs.html:44 sphinx_rtd_theme/breadcrumbs.html:46
msgid "Edit on Bitbucket"
msgstr "Edytuj na Bitbucket"
#: sphinx_rtd_theme/breadcrumbs.html:51 sphinx_rtd_theme/breadcrumbs.html:53
msgid "Edit on GitLab"
msgstr "Edytuj na GitLab"
#: sphinx_rtd_theme/breadcrumbs.html:56 sphinx_rtd_theme/breadcrumbs.html:58
msgid "View page source"
msgstr "Zobacz źródło strony"
#: sphinx_rtd_theme/breadcrumbs.html:69 sphinx_rtd_theme/footer.html:6
msgid "Previous"
msgstr "Poprzedni"
#: sphinx_rtd_theme/breadcrumbs.html:72 sphinx_rtd_theme/footer.html:9
msgid "Next"
msgstr "Następny"
#: sphinx_rtd_theme/footer.html:21
#, python-format
msgid "&#169; <a href=\"%(path)s\">Copyright</a> %(copyright)s."
msgstr "&#169; <a href=\"%(path)s\">Prawa zastrzeżone</a> %(copyright)s."
#: sphinx_rtd_theme/footer.html:23
#, python-format
msgid "&#169; Copyright %(copyright)s."
msgstr "&#169; Prawa zastrzeżone %(copyright)s."
#: sphinx_rtd_theme/footer.html:41
#, python-format
msgid "Last updated on %(last_updated)s."
msgstr "Ostatnia aktualizacja %(last_updated)s."
#. the variable "sphinx_web" is a link to the Sphinx project documentation
#. with
#. the text "Sphinx"
#: sphinx_rtd_theme/footer.html:53
#, python-format
msgid "Built with %(sphinx_web)s using a"
msgstr "Zbudowano w %(sphinx_web)s używając"
#. this is always used as "provided by Read the Docs", and should not imply
#. Read the Docs is an author of the generated documentation.
#: sphinx_rtd_theme/footer.html:57
#, python-format
msgid "provided by %(readthedocs_web)s"
msgstr "dostarczone przez %(readthedocs_web)s"
#: sphinx_rtd_theme/layout.html:97
#, python-format
msgid "Search within %(docstitle)s"
msgstr "Szukaj w %(docstitle)s"
#: sphinx_rtd_theme/layout.html:105
msgid "About these documents"
msgstr "O tych dokumentach"
#: sphinx_rtd_theme/layout.html:108
msgid "Index"
msgstr "Indeks"
#: sphinx_rtd_theme/layout.html:111 sphinx_rtd_theme/search.html:11
msgid "Search"
msgstr "Szukaj"
#: sphinx_rtd_theme/layout.html:114
msgid "Copyright"
msgstr "Prawa zastrzeżone"
#: sphinx_rtd_theme/search.html:31
msgid "Please activate JavaScript to enable the search functionality."
msgstr ""
"Proszę aktywować obsługę JavaScript, aby włączyć funkcję wyszukiwania."
#. Search is a noun, not a verb
#: sphinx_rtd_theme/search.html:39
msgid "Search Results"
msgstr "Wyniki wyszukiwania"
#: sphinx_rtd_theme/search.html:41
msgid ""
"Your search did not match any documents. Please make sure that all words are"
" spelled correctly and that you've selected enough categories."
msgstr ""
"Nie znaleziono szukanej frazy. Upewnij się, że wszystkie słowa są napisane "
"poprawnie i że wybrałeś wystarczającą liczbę kategorii."
#: sphinx_rtd_theme/searchbox.html:4
msgid "Search docs"
msgstr "Szukaj"
#: sphinx_rtd_theme/versions.html:3 sphinx_rtd_theme/versions.html:11
msgid "Versions"
msgstr "Wersje"
#: sphinx_rtd_theme/versions.html:17
msgid "Downloads"
msgstr "Pobrania"
#. The phrase "Read the Docs" is not translated
#: sphinx_rtd_theme/versions.html:24
msgid "On Read the Docs"
msgstr "Na Read the Docs"
#: sphinx_rtd_theme/versions.html:26
msgid "Project Home"
msgstr "Strona projektu"

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@ -0,0 +1,161 @@
# English translations for sphinx_rtd_theme.
# Copyright (C) 2019 ORGANIZATION
# This file is distributed under the same license as the sphinx_rtd_theme
# project.
# FIRST AUTHOR <EMAIL@ADDRESS>, 2019.
#
# Translators:
# Ana Costa <anacosta.xl@gmail.com>, 2021
#
msgid ""
msgstr ""
"Project-Id-Version: sphinx_rtd_theme 0.4.3.dev0\n"
"Report-Msgid-Bugs-To: EMAIL@ADDRESS\n"
"POT-Creation-Date: 2021-09-13 13:35-0600\n"
"PO-Revision-Date: 2019-07-16 21:44+0000\n"
"Last-Translator: Ana Costa <anacosta.xl@gmail.com>, 2021\n"
"Language-Team: Portuguese (https://www.transifex.com/readthedocs/teams/101354/pt/)\n"
"MIME-Version: 1.0\n"
"Content-Type: text/plain; charset=UTF-8\n"
"Content-Transfer-Encoding: 8bit\n"
"Generated-By: Babel 2.8.0\n"
"Language: pt\n"
"Plural-Forms: nplurals=2; plural=(n != 1);\n"
#. This is an ARIA section label for page links, including previous/next page
#. link and links to GitHub/GitLab/etc.
#: sphinx_rtd_theme/breadcrumbs.html:22
msgid "Page navigation"
msgstr "Navegação da página"
#: sphinx_rtd_theme/breadcrumbs.html:37 sphinx_rtd_theme/breadcrumbs.html:39
msgid "Edit on GitHub"
msgstr "Editar no GitHub"
#: sphinx_rtd_theme/breadcrumbs.html:44 sphinx_rtd_theme/breadcrumbs.html:46
msgid "Edit on Bitbucket"
msgstr "Editar no Bitbucket"
#: sphinx_rtd_theme/breadcrumbs.html:51 sphinx_rtd_theme/breadcrumbs.html:53
msgid "Edit on GitLab"
msgstr "Editar no GitLab"
#: sphinx_rtd_theme/breadcrumbs.html:56 sphinx_rtd_theme/breadcrumbs.html:58
msgid "View page source"
msgstr "Ver código-fonte da página"
#. This is an ARIA section label for sequential page links, such as previous
#. and next page links.
#: sphinx_rtd_theme/breadcrumbs.html:67
msgid "Sequential page navigation"
msgstr "Navegação sequencial da página"
#: sphinx_rtd_theme/breadcrumbs.html:69 sphinx_rtd_theme/footer.html:6
msgid "Previous"
msgstr "Anterior"
#: sphinx_rtd_theme/breadcrumbs.html:72 sphinx_rtd_theme/footer.html:9
msgid "Next"
msgstr "Seguinte"
#. This is an ARIA section label for the footer section of the page.
#: sphinx_rtd_theme/footer.html:4
msgid "Footer"
msgstr "Rodapé"
#. the phrase "revision" comes from Git, referring to a commit
#: sphinx_rtd_theme/footer.html:36
msgid "Revision"
msgstr "Revisão"
#: sphinx_rtd_theme/footer.html:41
#, python-format
msgid "Last updated on %(last_updated)s."
msgstr "Última actualização em %(last_updated)s."
#. the variable "sphinx_web" is a link to the Sphinx project documentation
#. with
#. the text "Sphinx"
#: sphinx_rtd_theme/footer.html:53
#, python-format
msgid "Built with %(sphinx_web)s using a"
msgstr "Compilado com %(sphinx_web)s usando um"
#. "theme" refers to a theme for Sphinx, which alters the appearance of the
#. generated documenation
#: sphinx_rtd_theme/footer.html:55
msgid "theme"
msgstr "tema"
#. this is always used as "provided by Read the Docs", and should not imply
#. Read the Docs is an author of the generated documentation.
#: sphinx_rtd_theme/footer.html:57
#, python-format
msgid "provided by %(readthedocs_web)s"
msgstr "fornecido por %(readthedocs_web)s"
#: sphinx_rtd_theme/layout.html:97
#, python-format
msgid "Search within %(docstitle)s"
msgstr "Procurar em %(docstitle)s"
#: sphinx_rtd_theme/layout.html:105
msgid "About these documents"
msgstr "Sobre estes documentos"
#: sphinx_rtd_theme/layout.html:108
msgid "Index"
msgstr "Índice"
#: sphinx_rtd_theme/layout.html:111 sphinx_rtd_theme/search.html:11
msgid "Search"
msgstr "Pesquisar"
#: sphinx_rtd_theme/layout.html:147 sphinx_rtd_theme/layout.html:149
msgid "Logo"
msgstr "Logo"
#. This is an ARIA section label for the main navigation menu
#: sphinx_rtd_theme/layout.html:173
msgid "Navigation menu"
msgstr "Menu de navegação"
#. This is an ARIA section label for the navigation menu that is visible when
#. viewing the page on mobile devices
#: sphinx_rtd_theme/layout.html:195
msgid "Mobile navigation menu"
msgstr "Menu de navegação móvel"
#: sphinx_rtd_theme/search.html:31
msgid "Please activate JavaScript to enable the search functionality."
msgstr "Por favor, active o JavaScript para permitir a função de pesquisa."
#. Search is a noun, not a verb
#: sphinx_rtd_theme/search.html:39
msgid "Search Results"
msgstr "Resultados de Pesquisa"
#: sphinx_rtd_theme/search.html:41
msgid ""
"Your search did not match any documents. Please make sure that all words are"
" spelled correctly and that you've selected enough categories."
msgstr ""
"A sua pesquisa não encontrou nenhum documento. Por favor confirme que todas "
"as palavras estão bem escritas e que selecionou categorias suficientes."
#: sphinx_rtd_theme/searchbox.html:4
msgid "Search docs"
msgstr "Pesquisar docs"
#: sphinx_rtd_theme/versions.html:3 sphinx_rtd_theme/versions.html:11
msgid "Versions"
msgstr "Versões"
#: sphinx_rtd_theme/versions.html:17
msgid "Downloads"
msgstr "Transferências"
#. The phrase "Read the Docs" is not translated
#: sphinx_rtd_theme/versions.html:24
msgid "On Read the Docs"
msgstr "No Read the Docs"

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@ -5,15 +5,16 @@
# FIRST AUTHOR <EMAIL@ADDRESS>, 2019.
#
# Translators:
# Rafael Fontenelle <rffontenelle@gmail.com>, 2020
# Rafael Fontenelle <rffontenelle@gmail.com>, 2021
# Wellington Uemura <wellingtonuemura@gmail.com>, 2021
#
msgid ""
msgstr ""
"Project-Id-Version: sphinx_rtd_theme 0.4.3.dev0\n"
"Report-Msgid-Bugs-To: EMAIL@ADDRESS\n"
"POT-Creation-Date: 2020-05-06 13:38-0600\n"
"POT-Creation-Date: 2021-09-13 13:35-0600\n"
"PO-Revision-Date: 2019-07-16 21:44+0000\n"
"Last-Translator: Rafael Fontenelle <rffontenelle@gmail.com>, 2020\n"
"Last-Translator: Wellington Uemura <wellingtonuemura@gmail.com>, 2021\n"
"Language-Team: Portuguese (Brazil) (https://www.transifex.com/readthedocs/teams/101354/pt_BR/)\n"
"MIME-Version: 1.0\n"
"Content-Type: text/plain; charset=UTF-8\n"
@ -22,42 +23,64 @@ msgstr ""
"Language: pt_BR\n"
"Plural-Forms: nplurals=2; plural=(n > 1);\n"
#: sphinx_rtd_theme/breadcrumbs.html:43 sphinx_rtd_theme/breadcrumbs.html:45
#. This is an ARIA section label for page links, including previous/next page
#. link and links to GitHub/GitLab/etc.
#: sphinx_rtd_theme/breadcrumbs.html:22
msgid "Page navigation"
msgstr "Navegação da página"
#: sphinx_rtd_theme/breadcrumbs.html:37 sphinx_rtd_theme/breadcrumbs.html:39
msgid "Edit on GitHub"
msgstr "Editar no GitHub"
#: sphinx_rtd_theme/breadcrumbs.html:50 sphinx_rtd_theme/breadcrumbs.html:52
#: sphinx_rtd_theme/breadcrumbs.html:44 sphinx_rtd_theme/breadcrumbs.html:46
msgid "Edit on Bitbucket"
msgstr "Editar no Bitbucket"
#: sphinx_rtd_theme/breadcrumbs.html:57 sphinx_rtd_theme/breadcrumbs.html:59
#: sphinx_rtd_theme/breadcrumbs.html:51 sphinx_rtd_theme/breadcrumbs.html:53
msgid "Edit on GitLab"
msgstr "Editar no GitLab"
#: sphinx_rtd_theme/breadcrumbs.html:62 sphinx_rtd_theme/breadcrumbs.html:64
#: sphinx_rtd_theme/breadcrumbs.html:56 sphinx_rtd_theme/breadcrumbs.html:58
msgid "View page source"
msgstr "Ver código-fonte da página"
#: sphinx_rtd_theme/breadcrumbs.html:74 sphinx_rtd_theme/footer.html:5
msgid "Next"
msgstr "Próximo"
#. This is an ARIA section label for sequential page links, such as previous
#. and next page links.
#: sphinx_rtd_theme/breadcrumbs.html:67
msgid "Sequential page navigation"
msgstr "Navegação sequencial da página"
#: sphinx_rtd_theme/breadcrumbs.html:77 sphinx_rtd_theme/footer.html:8
#: sphinx_rtd_theme/breadcrumbs.html:69 sphinx_rtd_theme/footer.html:6
msgid "Previous"
msgstr "Anterior"
#: sphinx_rtd_theme/footer.html:21 sphinx_rtd_theme/footer.html:24
#: sphinx_rtd_theme/layout.html:96
msgid "Copyright"
msgstr "Copyright"
#: sphinx_rtd_theme/breadcrumbs.html:72 sphinx_rtd_theme/footer.html:9
msgid "Next"
msgstr "Próximo"
#. This is an ARIA section label for the footer section of the page.
#: sphinx_rtd_theme/footer.html:4
msgid "Footer"
msgstr "Rodapé"
#: sphinx_rtd_theme/footer.html:21
#, python-format
msgid "&#169; <a href=\"%(path)s\">Copyright</a> %(copyright)s."
msgstr "&#169; <a href=\"%(path)s\">Direitos autorais</a> %(copyright)s."
#: sphinx_rtd_theme/footer.html:23
#, python-format
msgid "&#169; Copyright %(copyright)s."
msgstr "&#169; Direitos autorais %(copyright)s."
#. Build is a noun, not a verb
#: sphinx_rtd_theme/footer.html:31
#: sphinx_rtd_theme/footer.html:30
msgid "Build"
msgstr "Compilação"
#. the phrase "revision" comes from Git, referring to a commit
#: sphinx_rtd_theme/footer.html:37
#: sphinx_rtd_theme/footer.html:36
msgid "Revision"
msgstr "Revisão"
@ -69,56 +92,71 @@ msgstr "Última atualização em %(last_updated)s."
#. the variable "sphinx_web" is a link to the Sphinx project documentation
#. with
#. the text "Sphinx"
#: sphinx_rtd_theme/footer.html:52
#: sphinx_rtd_theme/footer.html:53
#, python-format
msgid "Built with %(sphinx_web)s using a"
msgstr "Compilado com %(sphinx_web)s usando um"
#. "theme" refers to a theme for Sphinx, which alters the appearance of the
#. generated documenation
#: sphinx_rtd_theme/footer.html:54
#: sphinx_rtd_theme/footer.html:55
msgid "theme"
msgstr "tema"
#. this is always used as "provided by Read the Docs", and should not imply
#. Read the Docs is an author of the generated documentation.
#: sphinx_rtd_theme/footer.html:56
#: sphinx_rtd_theme/footer.html:57
#, python-format
msgid "provided by %(readthedocs_web)s"
msgstr "fornecido por %(readthedocs_web)s"
#: sphinx_rtd_theme/layout.html:79
#: sphinx_rtd_theme/layout.html:97
#, python-format
msgid "Search within %(docstitle)s"
msgstr "Pesquisar em %(docstitle)s"
#: sphinx_rtd_theme/layout.html:87
#: sphinx_rtd_theme/layout.html:105
msgid "About these documents"
msgstr "Sobre esses documentos"
#: sphinx_rtd_theme/layout.html:90
#: sphinx_rtd_theme/layout.html:108
msgid "Index"
msgstr "Índice"
#: sphinx_rtd_theme/layout.html:93 sphinx_rtd_theme/search.html:11
#: sphinx_rtd_theme/layout.html:111 sphinx_rtd_theme/search.html:11
msgid "Search"
msgstr "Pesquisar"
#: sphinx_rtd_theme/layout.html:128
#: sphinx_rtd_theme/layout.html:114
msgid "Copyright"
msgstr "Copyright"
#: sphinx_rtd_theme/layout.html:147 sphinx_rtd_theme/layout.html:149
msgid "Logo"
msgstr "Logo"
#: sphinx_rtd_theme/search.html:29
#. This is an ARIA section label for the main navigation menu
#: sphinx_rtd_theme/layout.html:173
msgid "Navigation menu"
msgstr "Menu de navegação"
#. This is an ARIA section label for the navigation menu that is visible when
#. viewing the page on mobile devices
#: sphinx_rtd_theme/layout.html:195
msgid "Mobile navigation menu"
msgstr "Menu de navegação móvel"
#: sphinx_rtd_theme/search.html:31
msgid "Please activate JavaScript to enable the search functionality."
msgstr ""
"Por favor, ative JavaScript para habilitar a funcionalidade de pesquisa."
#. Search is a noun, not a verb
#: sphinx_rtd_theme/search.html:37
#: sphinx_rtd_theme/search.html:39
msgid "Search Results"
msgstr "Resultados da pesquisa"
#: sphinx_rtd_theme/search.html:39
#: sphinx_rtd_theme/search.html:41
msgid ""
"Your search did not match any documents. Please make sure that all words are"
" spelled correctly and that you've selected enough categories."
@ -131,7 +169,7 @@ msgstr ""
msgid "Search docs"
msgstr "Pesquisar documentos"
#: sphinx_rtd_theme/versions.html:11
#: sphinx_rtd_theme/versions.html:3 sphinx_rtd_theme/versions.html:11
msgid "Versions"
msgstr "Versões"
@ -151,9 +189,3 @@ msgstr "Página inicial"
#: sphinx_rtd_theme/versions.html:29
msgid "Builds"
msgstr "Compilações"
#~ msgid "Docs"
#~ msgstr "Docs"
#~ msgid "Free document hosting provided by"
#~ msgstr "Hospedagem de documentos livres fornecida por"

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@ -5,16 +5,16 @@
# FIRST AUTHOR <EMAIL@ADDRESS>, 2019.
#
# Translators:
# Dmitry Shachnev <mitya57@gmail.com>, 2019
# lvv83 <vlozhkin83@gmail.com>, 2019
# Dmitry Shachnev <mitya57@gmail.com>, 2021
#
msgid ""
msgstr ""
"Project-Id-Version: sphinx_rtd_theme 0.4.3.dev0\n"
"Report-Msgid-Bugs-To: EMAIL@ADDRESS\n"
"POT-Creation-Date: 2020-05-06 13:38-0600\n"
"POT-Creation-Date: 2021-09-13 13:35-0600\n"
"PO-Revision-Date: 2019-07-16 21:44+0000\n"
"Last-Translator: lvv83 <vlozhkin83@gmail.com>, 2019\n"
"Last-Translator: Dmitry Shachnev <mitya57@gmail.com>, 2021\n"
"Language-Team: Russian (https://www.transifex.com/readthedocs/teams/101354/ru/)\n"
"MIME-Version: 1.0\n"
"Content-Type: text/plain; charset=UTF-8\n"
@ -23,42 +23,64 @@ msgstr ""
"Language: ru\n"
"Plural-Forms: nplurals=4; plural=(n%10==1 && n%100!=11 ? 0 : n%10>=2 && n%10<=4 && (n%100<12 || n%100>14) ? 1 : n%10==0 || (n%10>=5 && n%10<=9) || (n%100>=11 && n%100<=14)? 2 : 3);\n"
#: sphinx_rtd_theme/breadcrumbs.html:43 sphinx_rtd_theme/breadcrumbs.html:45
#. This is an ARIA section label for page links, including previous/next page
#. link and links to GitHub/GitLab/etc.
#: sphinx_rtd_theme/breadcrumbs.html:22
msgid "Page navigation"
msgstr "Навигация по страницам"
#: sphinx_rtd_theme/breadcrumbs.html:37 sphinx_rtd_theme/breadcrumbs.html:39
msgid "Edit on GitHub"
msgstr "Редактировать на GitHub"
#: sphinx_rtd_theme/breadcrumbs.html:50 sphinx_rtd_theme/breadcrumbs.html:52
#: sphinx_rtd_theme/breadcrumbs.html:44 sphinx_rtd_theme/breadcrumbs.html:46
msgid "Edit on Bitbucket"
msgstr "Редактировать на BitBucket"
#: sphinx_rtd_theme/breadcrumbs.html:57 sphinx_rtd_theme/breadcrumbs.html:59
#: sphinx_rtd_theme/breadcrumbs.html:51 sphinx_rtd_theme/breadcrumbs.html:53
msgid "Edit on GitLab"
msgstr "Редактировать на GitLab"
#: sphinx_rtd_theme/breadcrumbs.html:62 sphinx_rtd_theme/breadcrumbs.html:64
#: sphinx_rtd_theme/breadcrumbs.html:56 sphinx_rtd_theme/breadcrumbs.html:58
msgid "View page source"
msgstr "Просмотреть исходный код страницы"
#: sphinx_rtd_theme/breadcrumbs.html:74 sphinx_rtd_theme/footer.html:5
msgid "Next"
msgstr "Следующая"
#. This is an ARIA section label for sequential page links, such as previous
#. and next page links.
#: sphinx_rtd_theme/breadcrumbs.html:67
msgid "Sequential page navigation"
msgstr "Навигация по соседним страницам"
#: sphinx_rtd_theme/breadcrumbs.html:77 sphinx_rtd_theme/footer.html:8
#: sphinx_rtd_theme/breadcrumbs.html:69 sphinx_rtd_theme/footer.html:6
msgid "Previous"
msgstr "Предыдущая"
#: sphinx_rtd_theme/footer.html:21 sphinx_rtd_theme/footer.html:24
#: sphinx_rtd_theme/layout.html:96
msgid "Copyright"
msgstr "Авторские права"
#: sphinx_rtd_theme/breadcrumbs.html:72 sphinx_rtd_theme/footer.html:9
msgid "Next"
msgstr "Следующая"
#. This is an ARIA section label for the footer section of the page.
#: sphinx_rtd_theme/footer.html:4
msgid "Footer"
msgstr "Нижняя область"
#: sphinx_rtd_theme/footer.html:21
#, python-format
msgid "&#169; <a href=\"%(path)s\">Copyright</a> %(copyright)s."
msgstr "&#169; <a href=\"%(path)s\">Авторские права</a> %(copyright)s. "
#: sphinx_rtd_theme/footer.html:23
#, python-format
msgid "&#169; Copyright %(copyright)s."
msgstr "&#169; Авторские права %(copyright)s. "
#. Build is a noun, not a verb
#: sphinx_rtd_theme/footer.html:31
#: sphinx_rtd_theme/footer.html:30
msgid "Build"
msgstr "Сборка"
#. the phrase "revision" comes from Git, referring to a commit
#: sphinx_rtd_theme/footer.html:37
#: sphinx_rtd_theme/footer.html:36
msgid "Revision"
msgstr "Ревизия"
@ -70,55 +92,70 @@ msgstr "Последний раз обновлено %(last_updated)s."
#. the variable "sphinx_web" is a link to the Sphinx project documentation
#. with
#. the text "Sphinx"
#: sphinx_rtd_theme/footer.html:52
#: sphinx_rtd_theme/footer.html:53
#, python-format
msgid "Built with %(sphinx_web)s using a"
msgstr "Собрано при помощи %(sphinx_web)s с использованием"
#. "theme" refers to a theme for Sphinx, which alters the appearance of the
#. generated documenation
#: sphinx_rtd_theme/footer.html:54
#: sphinx_rtd_theme/footer.html:55
msgid "theme"
msgstr "темы,"
#. this is always used as "provided by Read the Docs", and should not imply
#. Read the Docs is an author of the generated documentation.
#: sphinx_rtd_theme/footer.html:56
#: sphinx_rtd_theme/footer.html:57
#, python-format
msgid "provided by %(readthedocs_web)s"
msgstr "предоставленной %(readthedocs_web)s"
#: sphinx_rtd_theme/layout.html:79
#: sphinx_rtd_theme/layout.html:97
#, python-format
msgid "Search within %(docstitle)s"
msgstr "Поиск в %(docstitle)s"
#: sphinx_rtd_theme/layout.html:87
#: sphinx_rtd_theme/layout.html:105
msgid "About these documents"
msgstr "Об этих документах"
#: sphinx_rtd_theme/layout.html:90
#: sphinx_rtd_theme/layout.html:108
msgid "Index"
msgstr "Алфавитный указатель"
#: sphinx_rtd_theme/layout.html:93 sphinx_rtd_theme/search.html:11
#: sphinx_rtd_theme/layout.html:111 sphinx_rtd_theme/search.html:11
msgid "Search"
msgstr "Поиск"
#: sphinx_rtd_theme/layout.html:128
#: sphinx_rtd_theme/layout.html:114
msgid "Copyright"
msgstr "Авторские права"
#: sphinx_rtd_theme/layout.html:147 sphinx_rtd_theme/layout.html:149
msgid "Logo"
msgstr "Логотип"
#: sphinx_rtd_theme/search.html:29
#. This is an ARIA section label for the main navigation menu
#: sphinx_rtd_theme/layout.html:173
msgid "Navigation menu"
msgstr "Меню навигации"
#. This is an ARIA section label for the navigation menu that is visible when
#. viewing the page on mobile devices
#: sphinx_rtd_theme/layout.html:195
msgid "Mobile navigation menu"
msgstr "Меню навигации для мобильных устройств"
#: sphinx_rtd_theme/search.html:31
msgid "Please activate JavaScript to enable the search functionality."
msgstr "Активируйте JavaScript, чтобы использовать функционал поиска."
#. Search is a noun, not a verb
#: sphinx_rtd_theme/search.html:37
#: sphinx_rtd_theme/search.html:39
msgid "Search Results"
msgstr "Результаты поиска"
#: sphinx_rtd_theme/search.html:39
#: sphinx_rtd_theme/search.html:41
msgid ""
"Your search did not match any documents. Please make sure that all words are"
" spelled correctly and that you've selected enough categories."
@ -130,7 +167,7 @@ msgstr ""
msgid "Search docs"
msgstr "Поиск в документации"
#: sphinx_rtd_theme/versions.html:11
#: sphinx_rtd_theme/versions.html:3 sphinx_rtd_theme/versions.html:11
msgid "Versions"
msgstr "Версии"
@ -150,9 +187,3 @@ msgstr "Домашняя страница проекта"
#: sphinx_rtd_theme/versions.html:29
msgid "Builds"
msgstr "Сборки"
#~ msgid "Docs"
#~ msgstr "Документация"
#~ msgid "Free document hosting provided by"
#~ msgstr "Бесплатный хостинг документов, предоставленный"

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@ -1,15 +1,15 @@
# Translations template for sphinx_rtd_theme.
# Copyright (C) 2020 ORGANIZATION
# Copyright (C) 2021 ORGANIZATION
# This file is distributed under the same license as the sphinx_rtd_theme
# project.
# FIRST AUTHOR <EMAIL@ADDRESS>, 2020.
# FIRST AUTHOR <EMAIL@ADDRESS>, 2021.
#
#, fuzzy
msgid ""
msgstr ""
"Project-Id-Version: sphinx_rtd_theme 0.4.3.dev0\n"
"Project-Id-Version: sphinx_rtd_theme 1.0.0\n"
"Report-Msgid-Bugs-To: EMAIL@ADDRESS\n"
"POT-Creation-Date: 2020-05-06 13:38-0600\n"
"POT-Creation-Date: 2021-09-13 13:35-0600\n"
"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
"Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
"Language-Team: LANGUAGE <LL@li.org>\n"
@ -18,42 +18,64 @@ msgstr ""
"Content-Transfer-Encoding: 8bit\n"
"Generated-By: Babel 2.8.0\n"
#: sphinx_rtd_theme/breadcrumbs.html:43 sphinx_rtd_theme/breadcrumbs.html:45
#. This is an ARIA section label for page links, including previous/next page
#. link and links to GitHub/GitLab/etc.
#: sphinx_rtd_theme/breadcrumbs.html:22
msgid "Page navigation"
msgstr ""
#: sphinx_rtd_theme/breadcrumbs.html:37 sphinx_rtd_theme/breadcrumbs.html:39
msgid "Edit on GitHub"
msgstr ""
#: sphinx_rtd_theme/breadcrumbs.html:50 sphinx_rtd_theme/breadcrumbs.html:52
#: sphinx_rtd_theme/breadcrumbs.html:44 sphinx_rtd_theme/breadcrumbs.html:46
msgid "Edit on Bitbucket"
msgstr ""
#: sphinx_rtd_theme/breadcrumbs.html:57 sphinx_rtd_theme/breadcrumbs.html:59
#: sphinx_rtd_theme/breadcrumbs.html:51 sphinx_rtd_theme/breadcrumbs.html:53
msgid "Edit on GitLab"
msgstr ""
#: sphinx_rtd_theme/breadcrumbs.html:62 sphinx_rtd_theme/breadcrumbs.html:64
#: sphinx_rtd_theme/breadcrumbs.html:56 sphinx_rtd_theme/breadcrumbs.html:58
msgid "View page source"
msgstr ""
#: sphinx_rtd_theme/breadcrumbs.html:74 sphinx_rtd_theme/footer.html:5
msgid "Next"
#. This is an ARIA section label for sequential page links, such as previous
#. and next page links.
#: sphinx_rtd_theme/breadcrumbs.html:67
msgid "Sequential page navigation"
msgstr ""
#: sphinx_rtd_theme/breadcrumbs.html:77 sphinx_rtd_theme/footer.html:8
#: sphinx_rtd_theme/breadcrumbs.html:69 sphinx_rtd_theme/footer.html:6
msgid "Previous"
msgstr ""
#: sphinx_rtd_theme/footer.html:21 sphinx_rtd_theme/footer.html:24
#: sphinx_rtd_theme/layout.html:96
msgid "Copyright"
#: sphinx_rtd_theme/breadcrumbs.html:72 sphinx_rtd_theme/footer.html:9
msgid "Next"
msgstr ""
#. This is an ARIA section label for the footer section of the page.
#: sphinx_rtd_theme/footer.html:4
msgid "Footer"
msgstr ""
#: sphinx_rtd_theme/footer.html:21
#, python-format
msgid "&#169; <a href=\"%(path)s\">Copyright</a> %(copyright)s."
msgstr ""
#: sphinx_rtd_theme/footer.html:23
#, python-format
msgid "&#169; Copyright %(copyright)s."
msgstr ""
#. Build is a noun, not a verb
#: sphinx_rtd_theme/footer.html:31
#: sphinx_rtd_theme/footer.html:30
msgid "Build"
msgstr ""
#. the phrase "revision" comes from Git, referring to a commit
#: sphinx_rtd_theme/footer.html:37
#: sphinx_rtd_theme/footer.html:36
msgid "Revision"
msgstr ""
@ -64,59 +86,70 @@ msgstr ""
#. the variable "sphinx_web" is a link to the Sphinx project documentation with
#. the text "Sphinx"
#: sphinx_rtd_theme/footer.html:52
#: sphinx_rtd_theme/footer.html:53
#, python-format
msgid "Built with %(sphinx_web)s using a"
msgstr ""
#. "theme" refers to a theme for Sphinx, which alters the appearance of the
#. generated documenation
#: sphinx_rtd_theme/footer.html:54
#: sphinx_rtd_theme/footer.html:55
msgid "theme"
msgstr ""
#. this is always used as "provided by Read the Docs", and should not imply
#. Read the Docs is an author of the generated documentation.
#: sphinx_rtd_theme/footer.html:56
#: sphinx_rtd_theme/footer.html:57
#, python-format
msgid "provided by %(readthedocs_web)s"
msgstr ""
#: sphinx_rtd_theme/layout.html:79
#: sphinx_rtd_theme/layout.html:97
#, python-format
msgid "Search within %(docstitle)s"
msgstr ""
#: sphinx_rtd_theme/layout.html:87
#: sphinx_rtd_theme/layout.html:105
msgid "About these documents"
msgstr ""
#: sphinx_rtd_theme/layout.html:90
#: sphinx_rtd_theme/layout.html:108
msgid "Index"
msgstr ""
#: sphinx_rtd_theme/layout.html:93 sphinx_rtd_theme/search.html:11
#: sphinx_rtd_theme/layout.html:111 sphinx_rtd_theme/search.html:11
msgid "Search"
msgstr ""
#: sphinx_rtd_theme/layout.html:121
msgid "Documentation Home"
#: sphinx_rtd_theme/layout.html:114
msgid "Copyright"
msgstr ""
#: sphinx_rtd_theme/layout.html:128
#: sphinx_rtd_theme/layout.html:147 sphinx_rtd_theme/layout.html:149
msgid "Logo"
msgstr ""
#: sphinx_rtd_theme/search.html:29
#. This is an ARIA section label for the main navigation menu
#: sphinx_rtd_theme/layout.html:173
msgid "Navigation menu"
msgstr ""
#. This is an ARIA section label for the navigation menu that is visible when
#. viewing the page on mobile devices
#: sphinx_rtd_theme/layout.html:195
msgid "Mobile navigation menu"
msgstr ""
#: sphinx_rtd_theme/search.html:31
msgid "Please activate JavaScript to enable the search functionality."
msgstr ""
#. Search is a noun, not a verb
#: sphinx_rtd_theme/search.html:37
#: sphinx_rtd_theme/search.html:39
msgid "Search Results"
msgstr ""
#: sphinx_rtd_theme/search.html:39
#: sphinx_rtd_theme/search.html:41
msgid ""
"Your search did not match any documents. Please make sure that all words "
"are spelled correctly and that you've selected enough categories."
@ -126,7 +159,7 @@ msgstr ""
msgid "Search docs"
msgstr ""
#: sphinx_rtd_theme/versions.html:11
#: sphinx_rtd_theme/versions.html:3 sphinx_rtd_theme/versions.html:11
msgid "Versions"
msgstr ""

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@ -11,7 +11,7 @@ msgid ""
msgstr ""
"Project-Id-Version: sphinx_rtd_theme 0.4.3.dev0\n"
"Report-Msgid-Bugs-To: EMAIL@ADDRESS\n"
"POT-Creation-Date: 2020-05-06 13:38-0600\n"
"POT-Creation-Date: 2021-09-13 13:35-0600\n"
"PO-Revision-Date: 2019-07-16 21:44+0000\n"
"Last-Translator: Daniel Holmberg <daniel.holmberg97@gmail.com>, 2020\n"
"Language-Team: Swedish (https://www.transifex.com/readthedocs/teams/101354/sv/)\n"
@ -22,42 +22,37 @@ msgstr ""
"Language: sv\n"
"Plural-Forms: nplurals=2; plural=(n != 1);\n"
#: sphinx_rtd_theme/breadcrumbs.html:43 sphinx_rtd_theme/breadcrumbs.html:45
#: sphinx_rtd_theme/breadcrumbs.html:37 sphinx_rtd_theme/breadcrumbs.html:39
msgid "Edit on GitHub"
msgstr "Editera på GitHub"
#: sphinx_rtd_theme/breadcrumbs.html:50 sphinx_rtd_theme/breadcrumbs.html:52
#: sphinx_rtd_theme/breadcrumbs.html:44 sphinx_rtd_theme/breadcrumbs.html:46
msgid "Edit on Bitbucket"
msgstr "Editera på Bitbucket"
#: sphinx_rtd_theme/breadcrumbs.html:57 sphinx_rtd_theme/breadcrumbs.html:59
#: sphinx_rtd_theme/breadcrumbs.html:51 sphinx_rtd_theme/breadcrumbs.html:53
msgid "Edit on GitLab"
msgstr "Editera på GitLab"
#: sphinx_rtd_theme/breadcrumbs.html:62 sphinx_rtd_theme/breadcrumbs.html:64
#: sphinx_rtd_theme/breadcrumbs.html:56 sphinx_rtd_theme/breadcrumbs.html:58
msgid "View page source"
msgstr "Visa sidkälla"
#: sphinx_rtd_theme/breadcrumbs.html:74 sphinx_rtd_theme/footer.html:5
msgid "Next"
msgstr "Nästa"
#: sphinx_rtd_theme/breadcrumbs.html:77 sphinx_rtd_theme/footer.html:8
#: sphinx_rtd_theme/breadcrumbs.html:69 sphinx_rtd_theme/footer.html:6
msgid "Previous"
msgstr "Tillbaka"
#: sphinx_rtd_theme/footer.html:21 sphinx_rtd_theme/footer.html:24
#: sphinx_rtd_theme/layout.html:96
msgid "Copyright"
msgstr "Upphovsrätt"
#: sphinx_rtd_theme/breadcrumbs.html:72 sphinx_rtd_theme/footer.html:9
msgid "Next"
msgstr "Nästa"
#. Build is a noun, not a verb
#: sphinx_rtd_theme/footer.html:31
#: sphinx_rtd_theme/footer.html:30
msgid "Build"
msgstr "Bygg"
#. the phrase "revision" comes from Git, referring to a commit
#: sphinx_rtd_theme/footer.html:37
#: sphinx_rtd_theme/footer.html:36
msgid "Revision"
msgstr "Ändra"
@ -69,60 +64,60 @@ msgstr "Senast uppdaterad %(last_updated)s."
#. the variable "sphinx_web" is a link to the Sphinx project documentation
#. with
#. the text "Sphinx"
#: sphinx_rtd_theme/footer.html:52
#: sphinx_rtd_theme/footer.html:53
#, python-format
msgid "Built with %(sphinx_web)s using a"
msgstr "Gjord med %(sphinx_web)s med hjälp av"
#. "theme" refers to a theme for Sphinx, which alters the appearance of the
#. generated documenation
#: sphinx_rtd_theme/footer.html:54
#: sphinx_rtd_theme/footer.html:55
msgid "theme"
msgstr "tema"
#. this is always used as "provided by Read the Docs", and should not imply
#. Read the Docs is an author of the generated documentation.
#: sphinx_rtd_theme/footer.html:56
#: sphinx_rtd_theme/footer.html:57
#, python-format
msgid "provided by %(readthedocs_web)s"
msgstr "erhållet av %(readthedocs_web)s"
#: sphinx_rtd_theme/layout.html:79
#: sphinx_rtd_theme/layout.html:97
#, python-format
msgid "Search within %(docstitle)s"
msgstr "Sök i %(docstitle)s"
#: sphinx_rtd_theme/layout.html:87
#: sphinx_rtd_theme/layout.html:105
msgid "About these documents"
msgstr "Om dessa dokument"
#: sphinx_rtd_theme/layout.html:90
#: sphinx_rtd_theme/layout.html:108
msgid "Index"
msgstr "Index"
#: sphinx_rtd_theme/layout.html:93 sphinx_rtd_theme/search.html:11
#: sphinx_rtd_theme/layout.html:111 sphinx_rtd_theme/search.html:11
msgid "Search"
msgstr "Sök"
#: sphinx_rtd_theme/layout.html:121
msgid "Documentation Home"
msgstr "Dokumentation Hem"
#: sphinx_rtd_theme/layout.html:114
msgid "Copyright"
msgstr "Upphovsrätt"
#: sphinx_rtd_theme/layout.html:128
#: sphinx_rtd_theme/layout.html:147 sphinx_rtd_theme/layout.html:149
msgid "Logo"
msgstr "Logo"
#: sphinx_rtd_theme/search.html:29
#: sphinx_rtd_theme/search.html:31
msgid "Please activate JavaScript to enable the search functionality."
msgstr ""
"Var vänlig och aktivera JavaScript för att möjliggöra sökfunktionaliteten."
#. Search is a noun, not a verb
#: sphinx_rtd_theme/search.html:37
#: sphinx_rtd_theme/search.html:39
msgid "Search Results"
msgstr "Sökresultat"
#: sphinx_rtd_theme/search.html:39
#: sphinx_rtd_theme/search.html:41
msgid ""
"Your search did not match any documents. Please make sure that all words are"
" spelled correctly and that you've selected enough categories."
@ -134,7 +129,7 @@ msgstr ""
msgid "Search docs"
msgstr "Sök i dokumentationen"
#: sphinx_rtd_theme/versions.html:11
#: sphinx_rtd_theme/versions.html:3 sphinx_rtd_theme/versions.html:11
msgid "Versions"
msgstr "Versioner"
@ -151,8 +146,6 @@ msgstr "På Read the Docs"
msgid "Project Home"
msgstr "Projekt Hem"
#~ msgid "Docs"
#~ msgstr "Dokumentation"
#~ msgid "Free document hosting provided by"
#~ msgstr "Gratis dokumentations hysning erhållen av"
#: sphinx_rtd_theme/versions.html:29
msgid "Builds"
msgstr "Versioner"

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@ -11,7 +11,7 @@ msgid ""
msgstr ""
"Project-Id-Version: sphinx_rtd_theme 0.4.3.dev0\n"
"Report-Msgid-Bugs-To: EMAIL@ADDRESS\n"
"POT-Creation-Date: 2020-05-06 13:38-0600\n"
"POT-Creation-Date: 2021-09-13 13:35-0600\n"
"PO-Revision-Date: 2019-07-16 21:44+0000\n"
"Last-Translator: BouRock, 2020\n"
"Language-Team: Turkish (https://www.transifex.com/readthedocs/teams/101354/tr/)\n"
@ -22,42 +22,37 @@ msgstr ""
"Language: tr\n"
"Plural-Forms: nplurals=2; plural=(n > 1);\n"
#: sphinx_rtd_theme/breadcrumbs.html:43 sphinx_rtd_theme/breadcrumbs.html:45
#: sphinx_rtd_theme/breadcrumbs.html:37 sphinx_rtd_theme/breadcrumbs.html:39
msgid "Edit on GitHub"
msgstr "GitHub'da Düzenle"
#: sphinx_rtd_theme/breadcrumbs.html:50 sphinx_rtd_theme/breadcrumbs.html:52
#: sphinx_rtd_theme/breadcrumbs.html:44 sphinx_rtd_theme/breadcrumbs.html:46
msgid "Edit on Bitbucket"
msgstr "Bitbucket'ta Düzenle"
#: sphinx_rtd_theme/breadcrumbs.html:57 sphinx_rtd_theme/breadcrumbs.html:59
#: sphinx_rtd_theme/breadcrumbs.html:51 sphinx_rtd_theme/breadcrumbs.html:53
msgid "Edit on GitLab"
msgstr "GitLab'ta Düzenle"
#: sphinx_rtd_theme/breadcrumbs.html:62 sphinx_rtd_theme/breadcrumbs.html:64
#: sphinx_rtd_theme/breadcrumbs.html:56 sphinx_rtd_theme/breadcrumbs.html:58
msgid "View page source"
msgstr "Sayfa kaynağını görüntüle"
#: sphinx_rtd_theme/breadcrumbs.html:74 sphinx_rtd_theme/footer.html:5
msgid "Next"
msgstr "Sonraki"
#: sphinx_rtd_theme/breadcrumbs.html:77 sphinx_rtd_theme/footer.html:8
#: sphinx_rtd_theme/breadcrumbs.html:69 sphinx_rtd_theme/footer.html:6
msgid "Previous"
msgstr "Önceki"
#: sphinx_rtd_theme/footer.html:21 sphinx_rtd_theme/footer.html:24
#: sphinx_rtd_theme/layout.html:96
msgid "Copyright"
msgstr "Telif hakkı"
#: sphinx_rtd_theme/breadcrumbs.html:72 sphinx_rtd_theme/footer.html:9
msgid "Next"
msgstr "Sonraki"
#. Build is a noun, not a verb
#: sphinx_rtd_theme/footer.html:31
#: sphinx_rtd_theme/footer.html:30
msgid "Build"
msgstr "Oluşturma"
#. the phrase "revision" comes from Git, referring to a commit
#: sphinx_rtd_theme/footer.html:37
#: sphinx_rtd_theme/footer.html:36
msgid "Revision"
msgstr "Gözden geçirme"
@ -68,49 +63,53 @@ msgstr "Son olarak %(last_updated)s tarihinde güncellendi."
#. "theme" refers to a theme for Sphinx, which alters the appearance of the
#. generated documenation
#: sphinx_rtd_theme/footer.html:54
#: sphinx_rtd_theme/footer.html:55
msgid "theme"
msgstr "tema"
#. this is always used as "provided by Read the Docs", and should not imply
#. Read the Docs is an author of the generated documentation.
#: sphinx_rtd_theme/footer.html:56
#: sphinx_rtd_theme/footer.html:57
#, python-format
msgid "provided by %(readthedocs_web)s"
msgstr "kullanılarak %(readthedocs_web)s tarafından sağlanmasıyla oluşturuldu"
#: sphinx_rtd_theme/layout.html:79
#: sphinx_rtd_theme/layout.html:97
#, python-format
msgid "Search within %(docstitle)s"
msgstr "%(docstitle)s içinde ara"
#: sphinx_rtd_theme/layout.html:87
#: sphinx_rtd_theme/layout.html:105
msgid "About these documents"
msgstr "Bu belgeler hakkında"
#: sphinx_rtd_theme/layout.html:90
#: sphinx_rtd_theme/layout.html:108
msgid "Index"
msgstr "Dizin"
#: sphinx_rtd_theme/layout.html:93 sphinx_rtd_theme/search.html:11
#: sphinx_rtd_theme/layout.html:111 sphinx_rtd_theme/search.html:11
msgid "Search"
msgstr "Arama"
#: sphinx_rtd_theme/layout.html:128
#: sphinx_rtd_theme/layout.html:114
msgid "Copyright"
msgstr "Telif hakkı"
#: sphinx_rtd_theme/layout.html:147 sphinx_rtd_theme/layout.html:149
msgid "Logo"
msgstr "Logo"
#: sphinx_rtd_theme/search.html:29
#: sphinx_rtd_theme/search.html:31
msgid "Please activate JavaScript to enable the search functionality."
msgstr ""
"Arama işlevselliğini etkinleştirmek için lütfen JavaScript'i etkinleştirin."
#. Search is a noun, not a verb
#: sphinx_rtd_theme/search.html:37
#: sphinx_rtd_theme/search.html:39
msgid "Search Results"
msgstr "Arama Sonuçları"
#: sphinx_rtd_theme/search.html:39
#: sphinx_rtd_theme/search.html:41
msgid ""
"Your search did not match any documents. Please make sure that all words are"
" spelled correctly and that you've selected enough categories."
@ -122,7 +121,7 @@ msgstr ""
msgid "Search docs"
msgstr "Belgeleri arayın"
#: sphinx_rtd_theme/versions.html:11
#: sphinx_rtd_theme/versions.html:3 sphinx_rtd_theme/versions.html:11
msgid "Versions"
msgstr "Sürümler"
@ -142,6 +141,3 @@ msgstr "Proje Ana Sayfa"
#: sphinx_rtd_theme/versions.html:29
msgid "Builds"
msgstr "Oluşturmalar"
#~ msgid "Free document hosting provided by"
#~ msgstr "Ücretsiz belge barındırmayı sağlayan"

BIN
doc/utils/sphinx-config/_themes/lammps_theme/locale/zh_CN/LC_MESSAGES/sphinx.mo
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64
doc/utils/sphinx-config/_themes/lammps_theme/locale/zh_CN/LC_MESSAGES/sphinx.po
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@ -12,7 +12,7 @@ msgid ""
msgstr ""
"Project-Id-Version: sphinx_rtd_theme 0.4.3.dev0\n"
"Report-Msgid-Bugs-To: EMAIL@ADDRESS\n"
"POT-Creation-Date: 2020-05-06 13:38-0600\n"
"POT-Creation-Date: 2021-09-13 13:35-0600\n"
"PO-Revision-Date: 2019-07-16 21:44+0000\n"
"Last-Translator: Anthony <aj@ohess.org>, 2020\n"
"Language-Team: Chinese (China) (https://www.transifex.com/readthedocs/teams/101354/zh_CN/)\n"
@ -23,40 +23,40 @@ msgstr ""
"Language: zh_CN\n"
"Plural-Forms: nplurals=1; plural=0;\n"
#: sphinx_rtd_theme/breadcrumbs.html:43 sphinx_rtd_theme/breadcrumbs.html:45
#: sphinx_rtd_theme/breadcrumbs.html:37 sphinx_rtd_theme/breadcrumbs.html:39
msgid "Edit on GitHub"
msgstr "在 GitHub 上修改"
#: sphinx_rtd_theme/breadcrumbs.html:50 sphinx_rtd_theme/breadcrumbs.html:52
#: sphinx_rtd_theme/breadcrumbs.html:44 sphinx_rtd_theme/breadcrumbs.html:46
msgid "Edit on Bitbucket"
msgstr "在 Bitbucket 上修改"
#: sphinx_rtd_theme/breadcrumbs.html:57 sphinx_rtd_theme/breadcrumbs.html:59
#: sphinx_rtd_theme/breadcrumbs.html:51 sphinx_rtd_theme/breadcrumbs.html:53
msgid "Edit on GitLab"
msgstr "在 GitLab 上修改"
#: sphinx_rtd_theme/breadcrumbs.html:62 sphinx_rtd_theme/breadcrumbs.html:64
#: sphinx_rtd_theme/breadcrumbs.html:56 sphinx_rtd_theme/breadcrumbs.html:58
msgid "View page source"
msgstr "查看页面源码"
#: sphinx_rtd_theme/breadcrumbs.html:74 sphinx_rtd_theme/footer.html:5
msgid "Next"
msgstr "下一页"
#: sphinx_rtd_theme/breadcrumbs.html:77 sphinx_rtd_theme/footer.html:8
#: sphinx_rtd_theme/breadcrumbs.html:69 sphinx_rtd_theme/footer.html:6
msgid "Previous"
msgstr "上一页"
#: sphinx_rtd_theme/footer.html:21 sphinx_rtd_theme/footer.html:24
#: sphinx_rtd_theme/layout.html:96
msgid "Copyright"
msgstr "版权所有"
#: sphinx_rtd_theme/breadcrumbs.html:72 sphinx_rtd_theme/footer.html:9
msgid "Next"
msgstr "下一页"
#. Build is a noun, not a verb
#: sphinx_rtd_theme/footer.html:31
#: sphinx_rtd_theme/footer.html:30
msgid "Build"
msgstr "构建"
#. the phrase "revision" comes from Git, referring to a commit
#: sphinx_rtd_theme/footer.html:36
msgid "Revision"
msgstr "修订"
#: sphinx_rtd_theme/footer.html:41
#, python-format
msgid "Last updated on %(last_updated)s."
@ -65,55 +65,59 @@ msgstr "最后更新时间 %(last_updated)s。"
#. the variable "sphinx_web" is a link to the Sphinx project documentation
#. with
#. the text "Sphinx"
#: sphinx_rtd_theme/footer.html:52
#: sphinx_rtd_theme/footer.html:53
#, python-format
msgid "Built with %(sphinx_web)s using a"
msgstr "利用 %(sphinx_web)s 构建，使用了 "
#. "theme" refers to a theme for Sphinx, which alters the appearance of the
#. generated documenation
#: sphinx_rtd_theme/footer.html:54
#: sphinx_rtd_theme/footer.html:55
msgid "theme"
msgstr "主题"
#. this is always used as "provided by Read the Docs", and should not imply
#. Read the Docs is an author of the generated documentation.
#: sphinx_rtd_theme/footer.html:56
#: sphinx_rtd_theme/footer.html:57
#, python-format
msgid "provided by %(readthedocs_web)s"
msgstr "由 %(readthedocs_web)s开发"
#: sphinx_rtd_theme/layout.html:79
#: sphinx_rtd_theme/layout.html:97
#, python-format
msgid "Search within %(docstitle)s"
msgstr "在 %(docstitle)s中搜索"
#: sphinx_rtd_theme/layout.html:87
#: sphinx_rtd_theme/layout.html:105
msgid "About these documents"
msgstr "关于此文档"
#: sphinx_rtd_theme/layout.html:90
#: sphinx_rtd_theme/layout.html:108
msgid "Index"
msgstr "索引"
#: sphinx_rtd_theme/layout.html:93 sphinx_rtd_theme/search.html:11
#: sphinx_rtd_theme/layout.html:111 sphinx_rtd_theme/search.html:11
msgid "Search"
msgstr "搜索"
#: sphinx_rtd_theme/layout.html:128
#: sphinx_rtd_theme/layout.html:114
msgid "Copyright"
msgstr "版权所有"
#: sphinx_rtd_theme/layout.html:147 sphinx_rtd_theme/layout.html:149
msgid "Logo"
msgstr "Logo"
#: sphinx_rtd_theme/search.html:29
#: sphinx_rtd_theme/search.html:31
msgid "Please activate JavaScript to enable the search functionality."
msgstr "请启用 JavaScript 以便使用搜索功能"
#. Search is a noun, not a verb
#: sphinx_rtd_theme/search.html:37
#: sphinx_rtd_theme/search.html:39
msgid "Search Results"
msgstr "搜索结果"
#: sphinx_rtd_theme/search.html:39
#: sphinx_rtd_theme/search.html:41
msgid ""
"Your search did not match any documents. Please make sure that all words are"
" spelled correctly and that you've selected enough categories."
@ -123,7 +127,7 @@ msgstr "您的搜索没有匹配到任何文档。请确保所有单词拼写正
msgid "Search docs"
msgstr "在文档中搜索"
#: sphinx_rtd_theme/versions.html:11
#: sphinx_rtd_theme/versions.html:3 sphinx_rtd_theme/versions.html:11
msgid "Versions"
msgstr "版本列表"
@ -143,9 +147,3 @@ msgstr "项目首页"
#: sphinx_rtd_theme/versions.html:29
msgid "Builds"
msgstr "构建"
#~ msgid "Docs"
#~ msgstr "文档"
#~ msgid "Free document hosting provided by"
#~ msgstr "此文档免费托管于"

4
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2
doc/utils/sphinx-config/_themes/lammps_theme/theme.conf
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@ -5,6 +5,7 @@ pygments_style = default
[options]
analytics_id =
analytics_anonymize_ip = False
collapse_navigation = False
sticky_navigation = False
navigation_depth = 4
@ -15,3 +16,4 @@ display_version = True
prev_next_buttons_location = both
style_external_links = True
style_nav_header_background =
vcs_pageview_mode =

12
doc/utils/sphinx-config/false_positives.txt
View File

@ -3,6 +3,7 @@ aat
abc
abf
ABI
abi
abo
Abramyan
absTol
@ -41,6 +42,7 @@ advect
advection
advects
affine
Afrasiabian
Afshar
agilio
Agilio
@ -1111,6 +1113,7 @@ funcs
functionalities
functionals
funroll
Furuholt
fx
fy
fz
@ -1593,6 +1596,7 @@ Ki
Kikugawa
kim
kinetostats
Kirkwood
kJ
kk
Klahn
@ -1923,7 +1927,9 @@ Mayoral
mbt
MBytes
mc
mcmoves
McLachlan
mcmoves
md
mdf
mdi
@ -2224,6 +2230,7 @@ Nelement
Nelements
nelems
nemd
netapp
netcdf
netstat
Nettleton
@ -2288,6 +2295,7 @@ Nmin
Nmols
nn
nnodes
npits
nO
Nocedal
nocite
@ -2450,6 +2458,7 @@ ortho
orthonormal
orthorhombic
Ortner
os
oso
Otype
Ouadfel
@ -3315,6 +3324,7 @@ THz
Tigran
Tij
Tildesley
timeI
timespan
timestamp
timestamps
@ -3616,6 +3626,7 @@ wget
Whelan
whitesmoke
whitespace
whl
Wi
Wicaksono
widom
@ -3653,6 +3664,7 @@ xcm
Xcm
Xcode
xCORE
xdmf
Xeon
xflag
xhi

31
examples/PACKAGES/latboltz/confined_colloid/in.confined_colloids
View File

@ -6,10 +6,10 @@
# 280 x 280 x 101 lattice-Boltzmann grid sites. #
# #
# This simulation is used to illustrate the simulation time of a realistic #
# implementation of the lb_fluid fix. #
# implementation of the lb/fluid fix. #
# The data file "confinedcolloids.dat" is quite large and so is not #
# included here. It can be obtained from: #
# http://www.apmaths.uwo.ca/~cdennist/confinedcolloids.dat.gz #
# http://publish.uwo.ca/~cdennist/confinedcolloids.dat.gz #
# #
# Sample output from this run can be found in the file: #
# results64.out #
@ -19,7 +19,10 @@ units micro
dimension 3
boundary p p f
atom_style molecular
read_data confinedcolloids.dat
# try to download
shell test -f confinedcolloids.dat.gz || curl -L -o confinedcolloids.dat.gz http://publish.uwo.ca/~cdennist/confinedcolloids.dat.gz
read_data confinedcolloids.dat.gz
mass * 0.00010287
@ -62,23 +65,18 @@ pair_coeff * * 0.0 0.0 1.572
pair_coeff 1 1 10.0 1.400492785 1.572
pair_modify shift yes
timestep 0.0006
timestep 0.001
#---------------------------------------------------------------------------
# Create a lattice-Boltzmann fluid covering the simulation domain.
# This fluid feels a force due to the particles specified through FluidAtoms
# (however, this fix does not explicitly apply a force back on to these
# particles...this is accomplished through the use of the viscous_lb fix).
# Use the standard LB integration scheme, a fluid density = 1.0,
# fluid viscosity = 1.0, lattice spacing dx=0.06, and mass unit, dm=0.00003.
# Use the default method to calculate the interaction force between the
# particles and the fluid. This calculation makes use of the surface area
# of the composite object represented by each particle node. Since this is
# not equal to dx*dx, it is input through the setArea keyword (i.e.
# particles of type 2 correspond to a surface area of 0.0018337299).
# Implement walls moving at speeds of 20.0 in opposite directions.
# particles...this is accomplished through the use of the lb/viscous fix).
# Use a fluid density = 1.0, fluid viscosity = 1.0, (water at STP) and a
# lattice spacing dx=0.06.
# Implement top/bottomw walls moving at speeds of 20.0 in opposite directions
#----------------------------------------------------------------------------
fix 1 FluidAtoms lb/fluid 1 1 1.0 1.0 dx 0.06 dm 0.00003 setArea 2 0.0018337299 zwall_velocity -20.0 20.0
fix 1 FluidAtoms lb/fluid 1 1.0 1.0 dx 0.06 zwall_velocity -20.0 20.0
#----------------------------------------------------------------------------
# Apply the force due to the fluid onto the FluidAtoms particles (again,
@ -105,4 +103,7 @@ fix walllo ForceAtoms wall/lj126 zlo 0.0 20.0 0.8071542386 0.906 units box
#dump ParticleTracking ForceAtoms custom 50 test.track id mol x y z vx vy vz
run 400
thermo 50
#run 400
run 100

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