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Merge branch 'develop' into quick-regression

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This commit is contained in:
Axel Kohlmeyer
2024-08-31 23:16:27 -04:00
parent 6fb50cbdc1 05e836f50e
commit 591d20b00d
143 changed files with 2578 additions and 1607 deletions
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18
.github/CODEOWNERS vendored
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@ -66,6 +66,9 @@ src/MANYBODY/pair_vashishta_table.* @andeplane
src/MANYBODY/pair_atm.* @sergeylishchuk
src/MANYBODY/pair_nb3b_screened.* @flodesani
src/REPLICA/*_grem.* @dstelter92
src/EXTRA-COMMAND/geturl.* @akohlmey
src/EXTRA-COMMAND/group_ndx.* @akohlmey
src/EXTRA-COMMAND/ndx_group.* @akohlmey
src/EXTRA-COMPUTE/compute_stress_mop*.* @RomainVermorel
src/EXTRA-COMPUTE/compute_born_matrix.* @Bibobu @athomps
src/EXTRA-FIX/fix_deform_pressure.* @jtclemm
@ -96,9 +99,10 @@ src/fix.* @sjplimp
src/force.* @sjplimp
src/group.* @sjplimp
src/improper.* @sjplimp
src/info.* @akohlmey
src/kspace.* @sjplimp
src/lmptyp.h @sjplimp
src/library.* @sjplimp
src/library.* @sjplimp @akohlmey
src/main.cpp @sjplimp
src/min_*.* @sjplimp
src/memory.* @sjplimp
@ -106,12 +110,12 @@ src/modify.* @sjplimp @stanmoore1
src/molecule.* @sjplimp
src/my_page.h @sjplimp
src/my_pool_chunk.h @sjplimp
src/npair*.* @sjplimp
src/ntopo*.* @sjplimp
src/nstencil*.* @sjplimp
src/neighbor.* @sjplimp
src/nbin*.* @sjplimp
src/neigh_*.* @sjplimp
src/npair*.* @sjplimp @jtclemm
src/ntopo*.* @sjplimp @jtclemm
src/nstencil*.* @sjplimp @jtclemm
src/neighbor.* @sjplimp @jtclemm
src/nbin*.* @sjplimp @jtclemm
src/neigh_*.* @sjplimp @jtclemm
src/output.* @sjplimp
src/pair.* @sjplimp
src/rcb.* @sjplimp

5
cmake/CMakeLists.txt
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@ -12,6 +12,11 @@ endif()
if(POLICY CMP0075)
cmake_policy(SET CMP0075 NEW)
endif()
# set policy to silence warnings about requiring execute permission for find_program
# we use OLD because the python-config script for the Fedora MinGW cross-compiler requires it currently
if(POLICY CMP0109)
cmake_policy(SET CMP0109 OLD)
endif()
# set policy to silence warnings about timestamps of downloaded files. review occasionally if it may be set to NEW
if(POLICY CMP0135)
cmake_policy(SET CMP0135 OLD)

8
cmake/Modules/Packages/ML-PACE.cmake
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@ -1,5 +1,11 @@
set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2023.11.25.fix.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
# PACE library support for ML-PACE package
# set policy to silence warnings about timestamps of downloaded files. review occasionally if it may be set to NEW
if(POLICY CMP0135)
cmake_policy(SET CMP0135 OLD)
endif()
set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2023.11.25.fix.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
set(PACELIB_MD5 "b45de9a633f42ed65422567e3ce56f9f" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
mark_as_advanced(PACELIB_URL)
mark_as_advanced(PACELIB_MD5)

15
cmake/Modules/Packages/PLUMED.cmake
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@ -1,5 +1,10 @@
# Plumed2 support for PLUMED package
# set policy to silence warnings about timestamps of downloaded files. review occasionally if it may be set to NEW
if(POLICY CMP0135)
cmake_policy(SET CMP0135 OLD)
endif()
# for supporting multiple concurrent plumed2 installations for debugging and testing
set(PLUMED_SUFFIX "" CACHE STRING "Suffix for Plumed2 library")
mark_as_advanced(PLUMED_SUFFIX)
@ -81,6 +86,9 @@ if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND (CMAKE_CROSSCOMPILING))
DEPENDS plumed_build
COMMENT "Copying Plumed files"
)
if(CMAKE_PROJECT_NAME STREQUAL "lammps")
target_link_libraries(lammps INTERFACE LAMMPS::PLUMED)
endif()
else()
@ -155,6 +163,9 @@ else()
endif()
set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_INCLUDE_DIRECTORIES ${INSTALL_DIR}/include)
file(MAKE_DIRECTORY ${INSTALL_DIR}/include)
if(CMAKE_PROJECT_NAME STREQUAL "lammps")
target_link_libraries(lammps PRIVATE LAMMPS::PLUMED)
endif()
else()
find_package(PkgConfig REQUIRED)
pkg_check_modules(PLUMED REQUIRED plumed${PLUMED_SUFFIX})
@ -169,7 +180,9 @@ else()
endif()
set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_LINK_LIBRARIES "${PLUMED_LOAD}")
set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_INCLUDE_DIRECTORIES "${PLUMED_INCLUDE_DIRS}")
if(CMAKE_PROJECT_NAME STREQUAL "lammps")
target_link_libraries(lammps PUBLIC LAMMPS::PLUMED)
endif()
endif()
endif()
target_link_libraries(lammps PRIVATE LAMMPS::PLUMED)

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cmake/packaging/LAMMPS_DMG_Background.xcf Normal file
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4
cmake/presets/clang.cmake
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@ -1,10 +1,10 @@
# preset that will enable clang/clang++ with support for MPI and OpenMP (on Linux boxes)
# prefer flang over gfortran, if available
find_program(CLANG_FORTRAN NAMES flang gfortran f95)
find_program(CLANG_FORTRAN NAMES flang-new flang gfortran f95)
set(ENV{OMPI_FC} ${CLANG_FORTRAN})
get_filename_component(_tmp_fc ${CLANG_FORTRAN} NAME)
if (_tmp_fc STREQUAL "flang")
if ((_tmp_fc STREQUAL "flang") OR (_tmp_fc STREQUAL "flang-new"))
set(FC_STD_VERSION "-std=f2018")
set(BUILD_MPI OFF)
else()

4
doc/lammps.1
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@ -1,7 +1,7 @@
.TH LAMMPS "1" "27 June 2024" "2024-06-27"
.TH LAMMPS "1" "29 August 2024" "2024-08-29"
.SH NAME
.B LAMMPS
\- Molecular Dynamics Simulator. Version 27 June 2024
\- Molecular Dynamics Simulator. Version 29 August 2024
.SH SYNOPSIS
.B lmp

10
doc/src/Build_extras.rst
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@ -1517,6 +1517,11 @@ in lib/pace or somewhere else, which must be done before building
LAMMPS with this package. The code for the library can be found
at: `https://github.com/ICAMS/lammps-user-pace/ <https://github.com/ICAMS/lammps-user-pace/>`_
Instead of including the ML-PACE package directly into LAMMPS, it
is also possible to skip this step and build the ML-PACE package as
a plugin using the CMake script files in the ``examples/PACKAGE/pace/plugin``
folder and then load this plugin at runtime with the :doc:`plugin command <plugin>`.
.. tabs::
.. tab:: CMake build
@ -1701,6 +1706,11 @@ try a different one, switch to a different build system, consider a
global PLUMED installation or consider downloading PLUMED during the
LAMMPS build.
Instead of including the PLUMED package directly into LAMMPS, it
is also possible to skip this step and build the PLUMED package as
a plugin using the CMake script files in the ``examples/PACKAGE/plumed/plugin``
folder and then load this plugin at runtime with the :doc:`plugin command <plugin>`.
.. tabs::
.. tab:: CMake build

2
doc/src/Build_settings.rst
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@ -492,7 +492,7 @@ during a run.
Support for downloading files
-----------------------------
.. versionadded:: TBD
.. versionadded:: 29Aug2024
The :doc:`geturl command <geturl>` command uses the `the libcurl library
<https://curl.se/libcurl/>`_ to download files. This requires that

2
doc/src/Commands_removed.rst
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@ -171,7 +171,7 @@ instructions to install i-PI from PyPI via pip are provided.
LAMMPS shell
------------
.. versionchanged:: TBD
.. versionchanged:: 29Aug2024
The LAMMPS shell has been removed from the LAMMPS distribution. Users
are encouraged to use the :ref:`LAMMPS-GUI <lammps_gui>` tool instead.

2
doc/src/Developer_plugins.rst
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@ -283,7 +283,7 @@ in the ``examples/kim/plugin`` folder. No changes to the sources of the
KIM package themselves are needed; only the plugin interface and loader
code needs to be added. This example only supports building with CMake,
but is probably a more typical example. To compile you need to run CMake
with -DLAMMPS_SOURCE_DIR=<path/to/lammps/src/folder>. Other
with ``-DLAMMPS_SOURCE_DIR=<path/to/lammps/src/folder>``. Other
configuration setting are identical to those for compiling LAMMPS.
A second example for a plugin from a package is in the

337
doc/src/Howto_lammps_gui.rst
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@ -19,9 +19,9 @@ to the online LAMMPS documentation for known LAMMPS commands and styles.
Pre-compiled, ready-to-use LAMMPS-GUI executables for Linux x86\_64
(Ubuntu 20.04LTS or later and compatible), macOS (version 11 aka Big
Sur or later), and Windows (version 10 or later) :ref:`are available
<lammps_gui_install>` for download. None-MPI LAMMPS executables for
running LAMMPS from the command line and :doc:`some LAMMPS tools <Tools>`
are also included.
<lammps_gui_install>` for download. Non-MPI LAMMPS executables (as
``lmp``) for running LAMMPS from the command line and :doc:`some
LAMMPS tools <Tools>` compiled executables are also included.
The source code for LAMMPS-GUI is included in the LAMMPS source code
distribution and can be found in the ``tools/lammps-gui`` folder. It
@ -29,40 +29,50 @@ to the online LAMMPS documentation for known LAMMPS commands and styles.
<Build_cmake>`.
LAMMPS-GUI tries to provide an experience similar to what people
traditionally would have running LAMMPS using a command line window
and the console LAMMPS executable but just rolled into a single executable:
traditionally would have running LAMMPS using a command line window and
the console LAMMPS executable but just rolled into a single executable:
- writing & editing LAMMPS input files with a text editor
- run LAMMPS on those input file with selected command line flags
- use or extract data from the created files and visualize it with
either a molecular visualization program or a plotting program
- extract data from the created files and visualize it with and
external software
That procedure is quite effective for people proficient in using the
command line, as that allows them to use tools for the individual steps
that they are most comfortable with. It is often *required* to adopt
this workflow when running LAMMPS simulations on high-performance
that they are most comfortable with. In fact, it is often *required* to
adopt this workflow when running LAMMPS simulations on high-performance
computing facilities.
The main benefit of using LAMMPS-GUI is that many basic tasks can be
done directly from the GUI without switching to a text console window or
using external programs, let alone writing scripts to extract data from
the generated output. It also integrates well with graphical desktop
environments where the `.lmp` filename extension can be registered with
LAMMPS-GUI as the executable to launch when double clicking on such
files. Also, LAMMPS-GUI has support for drag-n-drop, i.e. an input
file can be selected and then moved and dropped on the LAMMPS-GUI
executable, and LAMMPS-GUI will launch and read the file into its
buffer.
done directly from the GUI **without** switching to a text console
window or using external programs, let alone writing scripts to extract
data from the generated output. It also integrates well with graphical
desktop environments where the `.lmp` filename extension can be
registered with LAMMPS-GUI as the executable to launch when double
clicking on such files. Also, LAMMPS-GUI has support for drag-n-drop,
i.e. an input file can be selected and then moved and dropped on the
LAMMPS-GUI executable, and LAMMPS-GUI will launch and read the file into
its buffer. In many cases LAMMPS-GUI will be integrated into the
graphical desktop environment and can be launched like other
applications.
LAMMPS-GUI thus makes it easier for beginners to get started running
simple LAMMPS simulations. It is very suitable for tutorials on LAMMPS
since you only need to learn how to use a single program for most tasks
and thus time can be saved and people can focus on learning LAMMPS.
The tutorials at https://lammpstutorials.github.io/ were specifically
The tutorials at https://lammpstutorials.github.io/ are specifically
updated for use with LAMMPS-GUI.
Another design goal is to keep the barrier low when replacing part of
the functionality of LAMMPS-GUI with external tools.
the functionality of LAMMPS-GUI with external tools. That said, LAMMPS-GUI
has some unique functionality that is not found elsewhere:
- auto-adapting to features available in the integrated LAMMPS library
- interactive visualization using the :doc:`dump image <dump_image>`
command with the option to copy-paste the resulting settings
- automatic slide show generation from dump image out at runtime
- automatic plotting of thermodynamics data at runtime
- inspection of binary restart files
The following text provides a detailed tour of the features and
functionality of LAMMPS-GUI. Suggestions for new features and
@ -134,9 +144,13 @@ When LAMMPS-GUI starts, it shows the main window, labeled *Editor*, with
either an empty buffer or the contents of the file used as argument. In
the latter case it may look like the following:
.. image:: JPG/lammps-gui-main.png
:align: center
:scale: 50%
.. |gui-main1| image:: JPG/lammps-gui-main.png
:width: 48%
.. |gui-main2| image:: JPG/lammps-gui-dark.png
:width: 48%
|gui-main1| |gui-main2|
There is the typical menu bar at the top, then the main editor buffer,
and a status bar at the bottom. The input file contents are shown
@ -156,7 +170,7 @@ and then starts with an empty buffer in the *Editor* window. If arguments
are given LAMMPS will use first command line argument as the file name for
the *Editor* buffer and reads its contents into the buffer, if the file
exists. All further arguments are ignored. Files can also be opened via
the ``File`` menu, the `Ctrl-O` (`Command-O` on macOS) keyboard shortcut
the *File* menu, the `Ctrl-O` (`Command-O` on macOS) keyboard shortcut
or by drag-and-drop of a file from a graphical file manager into the editor
window. If a file extension (e.g. ``.lmp``) has been registered with the
graphical environment to launch LAMMPS-GUI, an existing input file can
@ -174,7 +188,7 @@ Running LAMMPS
^^^^^^^^^^^^^^
From within the LAMMPS-GUI main window LAMMPS can be started either from
the ``Run`` menu using the ``Run LAMMPS from Editor Buffer`` entry, by
the *Run* menu using the *Run LAMMPS from Editor Buffer* entry, by
the keyboard shortcut `Ctrl-Enter` (`Command-Enter` on macOS), or by
clicking on the green "Run" button in the status bar. All of these
operations causes LAMMPS to process the entire input script in the
@ -189,7 +203,7 @@ using the contents of the input buffer for the run (via the
interface), and **not** the original file it was read from. Thus, if
there are unsaved changes in the buffer, they *will* be used. As an
alternative, it is also possible to run LAMMPS by reading the contents
of a file from the ``Run LAMMPS from File`` menu entry or with
of a file from the *Run LAMMPS from File* menu entry or with
`Ctrl-Shift-Enter`. This option may be required in some rare cases
where the input uses some functionality that is not compatible with
running LAMMPS from a string buffer. For consistency, any unsaved
@ -203,7 +217,7 @@ before LAMMPS can be run from a file.
While LAMMPS is running, the contents of the status bar change. On
the left side there is a text indicating that LAMMPS is running, which
also indicates the number of active threads, when thread-parallel
acceleration was selected in the ``Preferences`` dialog. On the right
acceleration was selected in the *Preferences* dialog. On the right
side, a progress bar is shown that displays the estimated progress for
the current :doc:`run <run>` or :doc:`minimize <minimize>` command.
@ -230,8 +244,8 @@ Up to three additional windows may open during a run:
More information on those windows and how to adjust their behavior and
contents is given below.
An active LAMMPS run can be stopped cleanly by using either the ``Stop
LAMMPS`` entry in the ``Run`` menu, the keyboard shortcut `Ctrl-/`
An active LAMMPS run can be stopped cleanly by using either the *Stop
LAMMPS* entry in the *Run* menu, the keyboard shortcut `Ctrl-/`
(`Command-/` on macOS), or by clicking on the red button in the status
bar. This will cause the running LAMMPS process to complete the current
timestep (or iteration for energy minimization) and then complete the
@ -261,7 +275,7 @@ The runs are counted and the run number for the current run is displayed
in the window title. It is possible to change the behavior of
LAMMPS-GUI in the preferences dialog to create a *new* *Output* window
for every run or to not show the current *Output* window. It is also
possible to show or hide the *current* *Output* window from the ``View``
possible to show or hide the *current* *Output* window from the *View*
menu.
The text in the *Output* window is read-only and cannot be modified, but
@ -276,8 +290,6 @@ right mouse button into the *Output* window text area.
:align: center
:scale: 50%
.. versionadded:: 1.6
Should the *Output* window contain embedded YAML format text (see above for a
demonstration), for example from using :doc:`thermo_style yaml
<thermo_style>` or :doc:`thermo_modify line yaml <thermo_modify>`, the
@ -298,18 +310,32 @@ plot of thermodynamic output of the LAMMPS calculation as shown below.
The drop down menu on the top right allows selection of different
properties that are computed and written to thermo output. Only one
property can be shown at a time. The plots are updated with new data as
the run progresses, so they can be used to visually monitor the
evolution of available properties. The window title shows the current
run number that this chart window corresponds to. Same as for the
*Output* window, the chart window is replaced on each new run, but the
behavior can be changed in the preferences dialog.
property can be shown at a time. The plots are updated regularly with
new data as the run progresses, so they can be used to visually monitor
the evolution of available properties. The update interval can be set
in the *Preferences* dialog. By default, the raw data for the selected
property is plotted as a blue graph. As soon as there are a sufficient
number of data points, there will be a second graph shown in red with a
smoothed version of the data. From the drop down menu on the top left,
you can select whether to plot only the raw data, only the smoothed
data or both. The smoothing uses a `Savitzky-Golay convolution filter
<https://en.wikipedia.org/wiki/Savitzky%E2%80%93Golay_filter>`_ The
window width (left) and order (right) parameters can be set in the boxes
next to the drop down menu. Default settings are 10 and 4 which means
that the smoothing window includes 10 points each to the left and the
right of the current data point and a fourth order polynomial is fit to
the data in the window.
.. versionadded:: 1.6
You can use the mouse to zoom into the graph (hold the left button and
drag to mark an area) or zoom out (right click) and you can reset the
view with a click to the "lens" button next to the data drop down menu.
Support for YAML export added
The window title shows the current run number that this chart window
corresponds to. Same as for the *Output* window, the chart window is
replaced on each new run, but the behavior can be changed in the
*Preferences* dialog.
From the ``File`` menu on the top left, it is possible to save an image
From the *File* menu on the top left, it is possible to save an image
of the currently displayed plot or export the data in either plain text
columns (for use by plotting tools like `gnuplot
<http://www.gnuplot.info/>`_ or `grace
@ -349,8 +375,6 @@ zoom in or zoom out of the displayed images. The button on the very
left triggers an export of the slide show animation to a movie file,
provided the `FFmpeg program <https://ffmpeg.org/>`_ is installed.
.. versionadded:: 1.6
When clicking on the "garbage can" icon, all image files of the slide
show will be deleted. Since their number can be large for long
simulations, this option enables to safely and quickly clean up the
@ -362,20 +386,20 @@ Variable Info
During a run, it may be of interest to monitor the value of input script
variables, for example to monitor the progress of loops. This can be
done by enabling the "Variables Window" in the ``View`` menu or by using
done by enabling the "Variables Window" in the *View* menu or by using
the `Ctrl-Shift-W` keyboard shortcut. This shows info similar to the
:doc:`info variables <info>` command in a separate window as shown
below.
.. image:: JPG/lammps-gui-variable-info.png
:align: center
:scale: 75%
:scale: 50%
Like for the *Output* and *Charts* windows, its content is continuously
updated during a run. It will show "(none)" if there are no variables
defined. Note that it is also possible to *set* :doc:`index style
variables <variable>`, that would normally be set via command line
flags, via the "Set Variables..." dialog from the ``Run`` menu.
flags, via the "Set Variables..." dialog from the *Run* menu.
LAMMPS-GUI automatically defines the variable "gui_run" to the current
value of the run counter. That way it is possible to automatically
record a separate log for each run attempt by using the command
@ -392,7 +416,7 @@ at the beginning of an input file. That would record logs to files
Snapshot Image Viewer
---------------------
By selecting the ``Create Image`` entry in the ``Run`` menu, or by
By selecting the *Create Image* entry in the *Run* menu, or by
hitting the `Ctrl-I` (`Command-I` on macOS) keyboard shortcut, or by
clicking on the "palette" button in the status bar of the *Editor*
window, LAMMPS-GUI sends a custom :doc:`write_dump image <dump_image>`
@ -413,23 +437,24 @@ instance when using reduced (= 'lj') :doc:`units <units>`, then
LAMMPS-GUI will check the current pair style and if it is a
Lennard-Jones type potential, it will extract the *sigma* parameter
for each atom type and assign atom diameters from those numbers.
For cases where atom diameters are not auto-detected, the *Atom size* field
can be edited and a suitable value set manually. The default value
is inferred from the x-direction lattice spacing.
Otherwise the default sequence of colors of the :doc:`dump image
<dump_image>` command is assigned to the different atom types and the
diameters are all the same.
If elements cannot be detected the default sequence of colors of the
:doc:`dump image <dump_image>` command is assigned to the different atom
types.
.. figure:: JPG/lammps-gui-image.png
:align: center
:scale: 50%
.. |gui-image1| image:: JPG/lammps-gui-image.png
:width: 48%
Visualization of LAMMPS "peptide" example
.. |gui-image2| image:: JPG/lammps-gui-funnel.png
:width: 48%
.. versionchanged:: 1.6
Buttons for toggling shininess and re-centering were added.
|gui-image1| |gui-image2|
The default image size, some default image quality settings, the view
style and some colors can be changed in the ``Preferences`` dialog
style and some colors can be changed in the *Preferences* dialog
window. From the image viewer window further adjustments can be made:
actual image size, high-quality (SSAO) rendering, anti-aliasing, view
style, display of box or axes, zoom factor. The view of the system can
@ -441,14 +466,12 @@ display updated. The small palette icon on the top left is colored
while LAMMPS is running to render the new image; it is grayed out when
LAMMPS is finished. When there are many atoms to render and high
quality images with anti-aliasing are requested, re-rendering may take
several seconds. From the ``File`` menu of the image window, the
several seconds. From the *File* menu of the image window, the
current image can be saved to a file (keyboard shortcut `Ctrl-S`) or
copied to the clipboard (keyboard shortcut `Ctrl-C`) for pasting the
image into another application.
.. versionadded:: 1.6
From the ``File`` menu it is also possible to copy the current
From the *File* menu it is also possible to copy the current
:doc:`dump image <dump_image>` and :doc:`dump_modify <dump_image>`
commands to the clipboard so they can be pasted into a LAMMPS input file
so that the visualization settings of the snapshot image can be repeated
@ -466,10 +489,8 @@ Paste (`Ctrl-V`), Undo (`Ctrl-Z`), Redo (`Ctrl-Shift-Z`), Select All
dialog will pop up asking whether to cancel the exit operation, or to
save or not save the buffer contents to a file.
.. versionadded:: 1.6
The editor has an auto-save mode that can be enabled or disabled in the
``Preferences`` dialog. In auto-save mode, the editor buffer is
*Preferences* dialog. In auto-save mode, the editor buffer is
automatically saved before running LAMMPS or before exiting LAMMPS-GUI.
Context Specific Word Completion
@ -486,7 +507,7 @@ a word have been typed.
The word can then be completed through selecting an entry by scrolling
up and down with the cursor keys and selecting with the 'Enter' key or
by clicking on the entry with the mouse. The automatic completion
pop-up can be disabled in the ``Preferences`` dialog, but the completion
pop-up can be disabled in the *Preferences* dialog, but the completion
can still be requested manually by either hitting the 'Shift-TAB' key or
by right-clicking with the mouse and selecting the option from the
context menu. Most of the completion information is retrieved from the
@ -504,7 +525,7 @@ whitespace padding to commands, type specifiers, IDs and names. This
reformatting is performed manually by hitting the 'Tab' key. It is
also possible to have this done automatically when hitting the 'Enter'
key to start a new line. This feature can be turned on or off in the
``Preferences`` dialog for ``Editor Settings`` with the
*Preferences* dialog for *Editor Settings* with the
"Reformat with 'Enter'" checkbox. The amount of padding for multiple
categories can be adjusted in the same dialog.
@ -531,8 +552,6 @@ context menu that open the corresponding documentation page in the
online LAMMPS documentation in a web browser window. When using the
keyboard, the first of those entries is chosen.
.. versionadded:: 1.6
If the word under the cursor is a file, then additionally the context
menu has an entry to open the file in a read-only text viewer window.
If the file is a LAMMPS restart file, instead the menu entry offers to
@ -550,8 +569,6 @@ will contain a corresponding message.
Inspecting a Restart file
^^^^^^^^^^^^^^^^^^^^^^^^^
.. versionadded:: 1.6
When LAMMPS-GUI is asked to "Inspect a Restart", it will read the
restart file into a LAMMPS instance and then open three different
windows. The first window is a text viewer with the output of an
@ -566,56 +583,56 @@ for confirmation before continuing, since large restart files
may require large amounts of RAM since the entire system must
be read into RAM. Thus restart file for large simulations that
have been run on an HPC cluster may overload a laptop or local
workstation. The ``Show Details...`` button will display a rough
workstation. The *Show Details...* button will display a rough
estimate of the additional memory required.
Menu
----
The menu bar has entries ``File``, ``Edit``, ``Run``, ``View``, and
``About``. Instead of using the mouse to click on them, the individual
The menu bar has entries *File*, *Edit*, *Run*, *View*, and
*About*. Instead of using the mouse to click on them, the individual
menus can also be activated by hitting the `Alt` key together with the
corresponding underlined letter, that is `Alt-F` activates the
``File`` menu. For the corresponding activated sub-menus, the key
*File* menu. For the corresponding activated sub-menus, the key
corresponding the underlined letters can be used to select entries
instead of using the mouse.
File
^^^^
The ``File`` menu offers the usual options:
The *File* menu offers the usual options:
- ``New`` clears the current buffer and resets the file name to ``*unknown*``
- ``Open`` opens a dialog to select a new file for editing in the *Editor*
- ``View`` opens a dialog to select a file for viewing in a *separate* window (read-only) with support for on-the-fly decompression as explained above.
- ``Inspect restart`` opens a dialog to select a file. If that file is a :doc:`LAMMPS restart <write_restart>` three windows with :ref:`information about the file are opened <inspect_restart>`.
- ``Save`` saves the current file; if the file name is ``*unknown*``
- *New* clears the current buffer and resets the file name to ``*unknown*``
- *Open* opens a dialog to select a new file for editing in the *Editor*
- *View* opens a dialog to select a file for viewing in a *separate* window (read-only) with support for on-the-fly decompression as explained above.
- *Inspect restart* opens a dialog to select a file. If that file is a :doc:`LAMMPS restart <write_restart>` three windows with :ref:`information about the file are opened <inspect_restart>`.
- *Save* saves the current file; if the file name is ``*unknown*``
a dialog will open to select a new file name
- ``Save As`` opens a dialog to select and new file name (and folder, if
- *Save As* opens a dialog to select and new file name (and folder, if
desired) and saves the buffer to it. Writing the buffer to a
different folder will also switch the current working directory to
that folder.
- ``Quit`` exits LAMMPS-GUI. If there are unsaved changes, a dialog will
- *Quit* exits LAMMPS-GUI. If there are unsaved changes, a dialog will
appear to either cancel the operation, or to save, or to not save the
modified buffer.
In addition, up to 5 recent file names will be listed after the ``Open``
In addition, up to 5 recent file names will be listed after the *Open*
entry that allows re-opening recently opened files. This list is stored
when quitting and recovered when starting again.
Edit
^^^^
The ``Edit`` menu offers the usual editor functions like ``Undo``,
``Redo``, ``Cut``, ``Copy``, ``Paste``. It can also open a
``Preferences`` dialog (keyboard shortcut `Ctrl-P`) and allows deletion
of all stored preferences and settings, so they are reset to their
default values.
The *Edit* menu offers the usual editor functions like *Undo*, *Redo*,
*Cut*, *Copy*, *Paste*, and a *Find and Replace* dialog (keyboard
shortcut `Ctrl-F`). It can also open a *Preferences* dialog (keyboard
shortcut `Ctrl-P`) and allows deleting all stored preferences and
settings, so they are reset to their default values.
Run
^^^
The ``Run`` menu has options to start and stop a LAMMPS process. Rather
The *Run* menu has options to start and stop a LAMMPS process. Rather
than calling the LAMMPS executable as a separate executable, the
LAMMPS-GUI is linked to the LAMMPS library and thus can run LAMMPS
internally through the :ref:`LAMMPS C-library interface <lammps_c_api>`
@ -635,36 +652,36 @@ from a string buffer.
The LAMMPS calculations are run in a concurrent thread so that the GUI
can stay responsive and be updated during the run. The GUI can retrieve
data from the running LAMMPS instance and tell it to stop at the next
timestep. The ``Stop LAMMPS`` entry will do this by calling the
timestep. The *Stop LAMMPS* entry will do this by calling the
:cpp:func:`lammps_force_timeout` library function, which is equivalent
to a :doc:`timer timeout 0 <timer>` command.
The ``Set Variables...`` entry opens a dialog box where
The *Set Variables...* entry opens a dialog box where
:doc:`index style variables <variable>` can be set. Those variables
are passed to the LAMMPS instance when it is created and are thus
set *before* a run is started.
.. image:: JPG/lammps-gui-variables.png
:align: center
:scale: 75%
:scale: 50%
The ``Set Variables`` dialog will be pre-populated with entries that
The *Set Variables* dialog will be pre-populated with entries that
are set as index variables in the input and any variables that are
used but not defined, if the built-in parser can detect them. New
rows for additional variables can be added through the ``Add Row``
button and existing rows can be deleted by clicking on the ``X`` icons
rows for additional variables can be added through the *Add Row*
button and existing rows can be deleted by clicking on the *X* icons
on the right.
The ``Create Image`` entry will send a :doc:`dump image <dump_image>`
The *Create Image* entry will send a :doc:`dump image <dump_image>`
command to the LAMMPS instance, read the resulting file, and show it
in an ``Image Viewer`` window.
in an *Image Viewer* window.
The ``View in OVITO`` entry will launch `OVITO <https://ovito.org>`_
The *View in OVITO* entry will launch `OVITO <https://ovito.org>`_
with a :doc:`data file <write_data>` containing the current state of
the system. This option is only available if LAMMPS-GUI can find
the OVITO executable in the system path.
The ``View in VMD`` entry will launch VMD with a :doc:`data file
The *View in VMD* entry will launch VMD with a :doc:`data file
<write_data>` containing the current state of the system. This option
is only available if LAMMPS-GUI can find the VMD executable in the
system path.
@ -672,33 +689,70 @@ system path.
View
^^^^
The ``View`` menu offers to show or hide additional windows with log
The *View* menu offers to show or hide additional windows with log
output, charts, slide show, variables, or snapshot images. The
default settings for their visibility can be changed in the
``Preferences dialog``.
*Preferences* dialog.
About
^^^^^
The ``About`` menu finally offers a couple of dialog windows and an
The *About* menu finally offers a couple of dialog windows and an
option to launch the LAMMPS online documentation in a web browser. The
``About LAMMPS-GUI`` entry displays a dialog with a summary of the
*About LAMMPS-GUI* entry displays a dialog with a summary of the
configuration settings of the LAMMPS library in use and the version
number of LAMMPS-GUI itself. The ``Quick Help`` displays a dialog with
a minimal description of LAMMPS-GUI. The ``LAMMPS-GUI Howto`` entry
number of LAMMPS-GUI itself. The *Quick Help* displays a dialog with
a minimal description of LAMMPS-GUI. The *LAMMPS-GUI Howto* entry
will open this documentation page from the online documentation in a web
browser window. The ``LAMMPS Manual`` entry will open the main page of
browser window. The *LAMMPS Manual* entry will open the main page of
the LAMMPS online documentation in a web browser window.
The ``LAMMPS Tutorial`` entry will open the main page of the set of
The *LAMMPS Tutorial* entry will open the main page of the set of
LAMMPS tutorials authored and maintained by Simon Gravelle at
https://lammpstutorials.github.io/ in a web browser window.
-----
Find and Replace
----------------
.. image:: JPG/lammps-gui-find.png
:align: center
:scale: 33%
The *Find and Replace* dialog allows searching for and replacing
text in the *Editor* window.
The dialog can be opened either from the *Edit* menu or with the
keyboard shortcut `Ctrl-F`. You can enter the text to search for.
Through three check-boxes the search behavior can be adjusted:
- If checked, "Match case" does a case sensitive search; otherwise
the search is case insensitive.
- If checked, "Wrap around" starts searching from the start of the
document, if there is no match found from the current cursor position
until the end of the document; otherwise the search will stop.
- If checked, the "Whole word" setting only finds full word matches
(white space and special characters are word boundaries).
Clicking on the *Next* button will search for the next occurrence of the
search text and select / highlight it. Clicking on the *Replace* button
will replace an already highlighted search text and find the next one.
If no text is selected, or the selected text does not match the
selection string, then the first click on the *Replace* button will
only search and highlight the next occurrence of the search string.
Clicking on the *Replace All* button will replace all occurrences from
the cursor position to the end of the file; if the *Wrap around* box is
checked, then it will replace **all** occurrences in the **entire**
document. Clicking on the *Done* button will dismiss the dialog.
------
Preferences
-----------
The ``Preferences`` dialog allows customization of the behavior and
The *Preferences* dialog allows customization of the behavior and
look of LAMMPS-GUI. The settings are grouped and each group is
displayed within a tab.
@ -745,7 +799,7 @@ General Settings:
otherwise each command will create a new image window.
- *Path to LAMMPS Shared Library File:* this option is only visible
when LAMMPS-GUI was compiled to load the LAMMPS library at run time
instead of being linked to it directly. With the ``Browse..`` button
instead of being linked to it directly. With the *Browse..* button
or by changing the text, a different shared library file with a
different compilation of LAMMPS with different settings or from a
different version can be loaded. After this setting was changed,
@ -755,16 +809,19 @@ General Settings:
log) of the application can be set.
- *Select Text Font:* Opens a font selection dialog where the type and
size for the text editor and log font of the application can be set.
- *GUI update interval:* Allows to set the time interval between GUI and
data updates during a LAMMPS run in milliseconds. The default is to
update the GUI every 10 milliseconds. This is good for many cases.
Set this to 100 milliseconds or more if LAMMPS-GUI consumes too many
resources during a run. For LAMMPS runs that run *very* fast (for
example in tutorial examples), however, data may be missed and through
lowering this interval, this can be corrected. However, this will
make the GUI use more resources, which may be a problem on some
computers with slower CPUs and a small number of CPU cores. This
- *Data update interval:* Allows to set the time interval between data
updates during a LAMMPS run in milliseconds. The default is to update
the data (for charts and output window) every 10 milliseconds. This
is good for many cases. Set this to 100 milliseconds or more if
LAMMPS-GUI consumes too many resources during a run. For LAMMPS runs
that run *very* fast (for example in tutorial examples), however, data
may be missed and through lowering this interval, this can be
corrected. However, this will make the GUI use more resources. This
setting may be changed to a value between 1 and 1000 milliseconds.
- *Charts update interval:* Allows to set the time interval between redrawing
the plots in the *Charts* window in milliseconds. The default is to
redraw the plots every 500 milliseconds. This is just for the drawing,
data collection is managed with the previous setting.
Accelerators:
^^^^^^^^^^^^^
@ -780,7 +837,7 @@ Snapshot Image:
^^^^^^^^^^^^^^^
This tab allows setting defaults for the snapshot images displayed in
the ``Image Viewer`` window, such as its dimensions and the zoom factor
the *Image Viewer* window, such as its dimensions and the zoom factor
applied. The *Antialias* switch will render images with twice the
number of pixels for width and height and then smoothly scale the image
back to the requested size. This produces higher quality images with
@ -824,7 +881,7 @@ available (On macOS use the Command key instead of Ctrl/Control).
.. list-table::
:header-rows: 1
:widths: auto
:widths: 16 19 13 16 13 22
* - Shortcut
- Function
@ -866,32 +923,32 @@ available (On macOS use the Command key instead of Ctrl/Control).
- Quit Application
- Ctrl+A
- Select All
- Ctrl+P
- Preferences
- Ctrl+F
- Find and Replace
* - Ctrl+W
- Close Window
- Ctrl+Shift+H
- Quick Help
- Ctrl+Shift+G
- LAMMPS-GUI Howto
* - Ctrl+Shift+A
- About LAMMPS
- Ctrl+?
- Context Help
- Ctrl+Shift+W
- Show Variables
* - Ctrl+Shift+M
- LAMMPS Manual
- TAB
- Reformat line
- Shift+TAB
- Show Completions
* - Ctrl+Shift+T
- LAMMPS Tutorial
- Ctrl+Shift+Enter
* - Ctrl+Shift+Enter
- Run File
-
-
- Ctrl+Shift+W
- Show Variables
- Ctrl+P
- Preferences
* - Ctrl+Shift+A
- About LAMMPS
- Ctrl+Shift+H
- Quick Help
- Ctrl+Shift+G
- LAMMPS-GUI Howto
* - Ctrl+Shift+M
- LAMMPS Manual
- Ctrl+?
- Context Help
- Ctrl+Shift+T
- LAMMPS Tutorial
Further editing keybindings `are documented with the Qt documentation
<https://doc.qt.io/qt-5/qplaintextedit.html#editing-key-bindings>`_. In

4
doc/src/Intro_authors.rst
View File

@ -51,7 +51,7 @@ lammps.org". General questions about LAMMPS should be posted in the
* - `Jacob R. Gissinger <jg_>`_
- Stevens Institute of Technology
- jgissing at stevens.edu
- reactive molecular dynamics, macromolecular systems, type labels
- reactive molecular dynamics, macro-molecular systems, type labels
* - James Goff
- SNL
- jmgoff at sandia.gov
@ -59,7 +59,7 @@ lammps.org". General questions about LAMMPS should be posted in the
* - Megan McCarthy
- SNL
- megmcca at sandia.gov
- alloys, microstucture, machine learned potentials
- alloys, micro-structure, machine learned potentials
* - Stan Moore
- SNL
- stamoor at sandia.gov

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9
doc/src/Packages_details.rst
View File

@ -1823,7 +1823,8 @@ Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1.
**Install:**
This package has :ref:`specific installation instructions <ml-pace>` on the
:doc:`Build extras <Build_extras>` page.
:doc:`Build extras <Build_extras>` page. This package may also be compiled
as a plugin to avoid licensing conflicts when distributing binaries.
**Supporting info:**
@ -2344,7 +2345,9 @@ and Gareth Tribello.
**Install:**
This package has :ref:`specific installation instructions <plumed>` on the :doc:`Build extras <Build_extras>` page.
This package has :ref:`specific installation instructions <plumed>` on the
:doc:`Build extras <Build_extras>` page. This package may also be compiled
as a plugin to avoid licensing conflicts when distributing binaries.
**Supporting info:**
@ -2642,7 +2645,7 @@ This package has :ref:`specific installation instructions <rheo>` on the :doc:`B
**Authors:** Joel T. Clemmer (Sandia National Labs),
Thomas C. O'Connor (Carnegie Mellon University)
.. versionadded:: TBD
.. versionadded:: 29Aug2024
**Supporting info:**

2
doc/src/Run_options.rst
View File

@ -508,7 +508,7 @@ e.g. the *nfile* and *fileper* keywords. See the
**-restart2info restartfile keyword ...**
.. versionadded:: TBD
.. versionadded:: 29Aug2024
Write out some info about the restart file and and immediately exit.
This is the same operation as if the following 2-line input script were

30
doc/src/Tools.rst
View File

@ -590,20 +590,31 @@ and the LAMMPS library, via ``-D LAMMPS_SOURCE_DIR=/path/to/lammps/src``.
CMake will try to guess a build folder with the LAMMPS library from that
path, but it can also be set with ``-D LAMMPS_LIB_DIR=/path/to/lammps/lib``.
Plugin version
""""""""""""""
Rather than linking to the LAMMPS library during compilation, it is also
possible to compile the GUI with a plugin loader that will load
the LAMMPS library dynamically at runtime during the start of the GUI
from a shared library; e.g. ``liblammps.so`` or ``liblammps.dylib`` or
possible to compile the GUI with a plugin loader that will load the
LAMMPS library dynamically at runtime during the start of the GUI from a
shared library; e.g. ``liblammps.so`` or ``liblammps.dylib`` or
``liblammps.dll`` (depending on the operating system). This has the
advantage that the LAMMPS library can be built from updated or modified
LAMMPS source without having to recompile the GUI. The ABI of the
LAMMPS C-library interface is very stable and generally backward
compatible. This feature is enabled by setting
``-D LAMMPS_GUI_USE_PLUGIN=on`` and then ``-D
compatible. This feature is enabled by setting ``-D
LAMMPS_GUI_USE_PLUGIN=on`` and then ``-D
LAMMPS_PLUGINLIB_DIR=/path/to/lammps/plugin/loader``. Typically, this
would be the ``examples/COUPLE/plugin`` folder of the LAMMPS
distribution.
When compiling LAMMPS-GUI with plugin support, there is an additional
command line flag (``-p <path>`` or ``--pluginpath <path>``) which
allows to override the path to LAMMPS shared library used by the GUI.
This is usually auto-detected on the first run and can be changed in the
LAMMPS-GUI *Preferences* dialog. The command line flag allows to reset
this path to a valid value in case the original setting has become
invalid. An empty path ("") as argument restores the default setting.
Platform notes
^^^^^^^^^^^^^^
@ -671,6 +682,15 @@ folder> --target tgz`` or ``make tgz`` to build a
``LAMMPS-Linux-amd64.tar.gz`` file with the executables and their
support libraries.
It is also possible to build a `flatpak bundle
<https://docs.flatpak.org/en/latest/single-file-bundles.html>`_ which is
a way to distribute applications in a way that is compatible with most
Linux distributions. Use the "flatpak" target to trigger a compile
(``cmake --build <build folder> --target flatpak`` or ``make flatpak``).
Please note that this will not build from the local sources but from the
repository and branch listed in the ``org.lammps.lammps-gui.yml``
LAMMPS-GUI source folder.
----------
.. _arc:

2
doc/src/bond_rheo_shell.rst
View File

@ -38,7 +38,7 @@ Examples
Description
"""""""""""
.. versionadded:: TBD
.. versionadded:: 29Aug2024
The *rheo/shell* bond style is designed to work with
:doc:`fix rheo/oxidation <fix_rheo_oxidation>` which creates candidate

51
doc/src/compute_pressure.rst
View File

@ -59,11 +59,12 @@ may also contribute to the virial term.
A symmetric pressure tensor, stored as a 6-element vector, is also
calculated by this compute. The six components of the vector are
ordered :math:`xx,` :math:`yy,` :math:`zz,` :math:`xy,` :math:`xz,` :math:`yz.`
The equation for the :math:`(I,J)` components (where :math:`I` and :math:`J`
are :math:`x`, :math:`y`, or :math:`z`) is similar to the above formula,
except that the first term uses components of the kinetic energy tensor and the
second term uses components of the virial tensor:
ordered :math:`xx,` :math:`yy,` :math:`zz,` :math:`xy,` :math:`xz,`
:math:`yz.` The equation for the :math:`(I,J)` components (where
:math:`I` and :math:`J` are :math:`x`, :math:`y`, or :math:`z`) is
similar to the above formula, except that the first term uses
components related to the kinetic energy tensor and the second term
uses components of the virial tensor:
.. math::
@ -75,8 +76,8 @@ calculated. This includes a kinetic energy (temperature) term and the
virial as the sum of pair, bond, angle, dihedral, improper, kspace
(long-range), and fix contributions to the force on each atom. If any
extra keywords are listed, then only those components are summed to
compute temperature or ke and/or the virial. The *virial* keyword
means include all terms except the kinetic energy *ke*\ .
compute temperature or ke and/or the virial. The *virial* keyword means
include all terms except the kinetic energy *ke*\ .
The *pair/hybrid* keyword means to only include contribution
from a sub-style in a *hybrid* or *hybrid/overlay* pair style.
@ -86,26 +87,31 @@ system, including for many-body potentials and accounting for the
effects of periodic boundary conditions are discussed in
:ref:`(Thompson) <Thompson1>`.
The temperature and kinetic energy tensor is not calculated by this
The temperature and kinetic energy tensor are not calculated by this
compute, but rather by the temperature compute specified with the
command. If the kinetic energy is not included in the pressure, than
the temperature compute is not used and can be specified as NULL.
Normally the temperature compute used by compute pressure should
calculate the temperature of all atoms for consistency with the virial
term, but any compute style that calculates temperature can be used
(e.g., one that excludes frozen atoms or other degrees of freedom).
command. See the doc pages for individual compute temp variants for an
explanation of how they calculate temperature and a symmetric tensor
(6-element vector) whose components are twice that of the traditional KE
tensor. That tensor is what appears in the pressure tensor formula
above.
If the kinetic energy is not included in the pressure, than the
temperature compute is not used and can be specified as NULL. Normally
the temperature compute used by compute pressure should calculate the
temperature of all atoms for consistency with the virial term, but any
compute style that calculates temperature can be used (e.g., one that
excludes frozen atoms or other degrees of freedom).
Note that if desired the specified temperature compute can be one that
subtracts off a bias to calculate a temperature using only the thermal
velocity of the atoms (e.g., by subtracting a background streaming
velocity).
See the doc pages for individual :doc:`compute commands <compute>` to determine
which ones include a bias.
velocity). See the doc pages for individual :doc:`compute commands
<compute>` to determine which ones include a bias.
Also note that the :math:`N` in the first formula above is really
degrees-of-freedom divided by :math:`d` = dimensionality, where the DOF value
is calculated by the temperature compute.
See the various :doc:`compute temperature <compute>` styles for details.
degrees-of-freedom divided by :math:`d` = dimensionality, where the
DOF value is calculated by the temperature compute. See the various
:doc:`compute temperature <compute>` styles for details.
A compute of this style with the ID of thermo_press is created when
LAMMPS starts up, as if this command were in the input script:
@ -136,9 +142,8 @@ The ordering of values in the symmetric pressure tensor is as follows:
:math:`p_{xx},` :math:`p_{yy},` :math:`p_{zz},` :math:`p_{xy},`
:math:`p_{xz},` :math:`p_{yz}.`
The scalar and vector values calculated by this compute are
"intensive". The scalar and vector values will be in pressure
:doc:`units <units>`.
The scalar and vector values calculated by this compute are "intensive".
The scalar and vector values will be in pressure :doc:`units <units>`.
Restrictions
""""""""""""

2
doc/src/compute_rheo_property_atom.rst
View File

@ -55,7 +55,7 @@ Examples
Description
"""""""""""
.. versionadded:: TBD
.. versionadded:: 29Aug2024
Define a computation that stores atom attributes specific to the RHEO
package for each atom in the group. This is useful so that the values

31
doc/src/compute_temp.rst
View File

@ -48,13 +48,17 @@ the group, :math:`N_\mathrm{fix DOFs}` is the number of degrees of
freedom removed by fix commands (see below), :math:`k_B` is the
Boltzmann constant, and :math:`T` is the resulting computed temperature.
A kinetic energy tensor, stored as a six-element vector, is also
calculated by this compute for use in the computation of a pressure
tensor. The formula for the components of the tensor is the same as the
above expression for :math:`E_\mathrm{kin}`, except that :math:`v_i^2` is
replaced by :math:`v_{i,x} v_{i,y}` for the :math:`xy` component, and so on.
The six components of the vector are ordered :math:`xx`, :math:`yy`,
:math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`.
A symmetric tensor, stored as a six-element vector, is also calculated
by this compute for use in the computation of a pressure tensor by the
:doc:`compute pressue <compute_pressure>` command. The formula for
the components of the tensor is the same as the above expression for
:math:`E_\mathrm{kin}`, except that the 1/2 factor is NOT included and
the :math:`v_i^2` is replaced by :math:`v_{i,x} v_{i,y}` for the
:math:`xy` component, and so on. Note that because it lacks the 1/2
factor, these tensor components are twice those of the traditional
kinetic energy tensor. The six components of the vector are ordered
:math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`,
:math:`yz`.
The number of atoms contributing to the temperature is assumed to be
constant for the duration of the run; use the *dynamic* option of the
@ -94,16 +98,17 @@ Output info
"""""""""""
This compute calculates a global scalar (the temperature) and a global
vector of length six (KE tensor), which can be accessed by indices
1--6. These values can be used by any command that uses global scalar
or vector values from a compute as input. See the :doc:`Howto output
<Howto_output>` page for an overview of LAMMPS output options.
vector of length six (symmetric tensor), which can be accessed by
indices 1--6. These values can be used by any command that uses
global scalar or vector values from a compute as input. See the
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS
output options.
The scalar value calculated by this compute is "intensive". The
vector values are "extensive".
The scalar value will be in temperature :doc:`units <units>`. The
vector values will be in energy :doc:`units <units>`.
The scalar value is in temperature :doc:`units <units>`. The vector
values are in energy :doc:`units <units>`.
Restrictions
""""""""""""

63
doc/src/compute_temp_asphere.rst
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@ -41,8 +41,8 @@ translational and rotational kinetic energy. This differs from the
usual :doc:`compute temp <compute_temp>` command, which assumes point
particles with only translational kinetic energy.
Only finite-size particles (aspherical or spherical) can be included
in the group. For 3d finite-size particles, each has six degrees of
Only finite-size particles (aspherical or spherical) can be included in
the group. For 3d finite-size particles, each has six degrees of
freedom (three translational, three rotational). For 2d finite-size
particles, each has three degrees of freedom (two translational, one
rotational).
@ -70,25 +70,39 @@ axis. It will also be the case for biaxial ellipsoids when exactly two
of the semiaxes have the same length and the corresponding relative well
depths are equal.
The translational kinetic energy is computed the same as is described
by the :doc:`compute temp <compute_temp>` command. The rotational
kinetic energy is computed as :math:`\frac12 I \omega^2`, where :math:`I` is
the inertia tensor for the aspherical particle and :math:`\omega` is its
The translational kinetic energy is computed the same as is described by
the :doc:`compute temp <compute_temp>` command. The rotational kinetic
energy is computed as :math:`\frac12 I \omega^2`, where :math:`I` is the
inertia tensor for the aspherical particle and :math:`\omega` is its
angular velocity, which is computed from its angular momentum.
.. note::
For :doc:`2d models <dimension>`, particles are treated as
ellipsoids, not ellipses, meaning their moments of inertia will be the
same as in 3d.
ellipsoids, not ellipses, meaning their moments of inertia will be
the same as in 3d.
A kinetic energy tensor, stored as a six-element vector, is also
calculated by this compute. The formula for the components of the
tensor is the same as the above formula, except that :math:`v^2` and
:math:`\omega^2` are replaced by :math:`v_x v_y` and :math:`\omega_x \omega_y`
for the :math:`xy` component, and the appropriate elements of the moment of
inertia tensor are used. The six components of the vector are ordered
:math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`.
:math:`\omega^2` are replaced by :math:`v_x v_y` and :math:`\omega_x
\omega_y` for the :math:`xy` component, and the appropriate elements of
the moment of inertia tensor are used. The six components of the vector
are ordered :math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`,
:math:`yz`.
A symmetric tensor, stored as a six-element vector, is also calculated
by this compute for use in the computation of a pressure tensor by the
:doc:`compute pressue <compute_pressure>` command. The formula for the
components of the tensor is the same as the above expression for
:math:`E_\mathrm{kin}`, except that the 1/2 factor is NOT included and
the :math:`v_i^2` and :math:`\omega^2` are replaced by :math:`v_x v_y`
and :math:`\omega_x \omega_y` for the :math:`xy` component, and so on.
And the appropriate elements of the moment of inertia tensor are used.
Note that because it lacks the 1/2 factor, these tensor components are
twice those of the traditional kinetic energy tensor. The six
components of the vector are ordered :math:`xx`, :math:`yy`, :math:`zz`,
:math:`xy`, :math:`xz`, :math:`yz`.
The number of atoms contributing to the temperature is assumed to be
constant for the duration of the run; use the *dynamic/dof* option of
@ -131,27 +145,26 @@ Output info
"""""""""""
This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1--6.
These values can be used by any command that uses global scalar or
vector values from a compute as input.
See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS
output options.
vector of length 6 (symmetric tensor), which can be accessed by indices
1--6. These values can be used by any command that uses global scalar
or vector values from a compute as input. See the :doc:`Howto output
<Howto_output>` page for an overview of LAMMPS output options.
The scalar value calculated by this compute is "intensive". The
vector values are "extensive".
The scalar value calculated by this compute is "intensive". The vector
values are "extensive".
The scalar value will be in temperature :doc:`units <units>`. The
vector values will be in energy :doc:`units <units>`.
The scalar value is in temperature :doc:`units <units>`. The vector
values are in energy :doc:`units <units>`.
Restrictions
""""""""""""
This compute is part of the ASPHERE package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
This compute requires that atoms store angular momentum and a
quaternion as defined by the :doc:`atom_style ellipsoid <atom_style>`
command.
This compute requires that atoms store angular momentum and a quaternion
as defined by the :doc:`atom_style ellipsoid <atom_style>` command.
All particles in the group must be finite-size. They cannot be point
particles, but they can be aspherical or spherical as defined by their

29
doc/src/compute_temp_body.rst
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@ -62,12 +62,17 @@ kinetic energy is computed as :math:`\frac12 I \omega^2`, where :math:`I`
is the moment of inertia tensor for the aspherical particle and :math:`\omega`
is its angular velocity, which is computed from its angular momentum.
A kinetic energy tensor, stored as a 6-element vector, is also calculated by
this compute. The formula for the components of the tensor is the same as the
above formula, except that :math:`v^2` and :math:`\omega^2` are
replaced by :math:`v_x v_y` and :math:`\omega_x \omega_y` for the
math:`xy` component, and the appropriate elements of the inertia tensor are
used. The six components of the vector are ordered :math:`xx`, :math:`yy`,
A symmetric tensor, stored as a six-element vector, is also calculated
by this compute for use in the computation of a pressure tensor by the
:doc:`compute pressue <compute_pressure>` command. The formula for
the components of the tensor is the same as the above expression for
:math:`E_\mathrm{kin}`, except that the 1/2 factor is NOT included and
the :math:`v_i^2` and :math:`\omega^2` are replaced by :math:`v_x v_y`
and :math:`\omega_x \omega_y` for the :math:`xy` component, and so on.
And the appropriate elements of the moment of inertia tensor are used.
Note that because it lacks the 1/2 factor, these tensor components are
twice those of the traditional kinetic energy tensor. The six
components of the vector are ordered :math:`xx`, :math:`yy`,
:math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`.
The number of atoms contributing to the temperature is assumed to be
@ -111,17 +116,17 @@ Output info
"""""""""""
This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1--6.
These values can be used by any command that uses global scalar or
vector values from a compute as input.
See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS
vector of length 6 (symmetric tensor), which can be accessed by
indices 1--6. These values can be used by any command that uses
global scalar or vector values from a compute as input. See the
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS
output options.
The scalar value calculated by this compute is "intensive". The
vector values are "extensive".
The scalar value will be in temperature :doc:`units <units>`.
The vector values will be in energy :doc:`units <units>`.
The scalar value is in temperature :doc:`units <units>`. The vector
values are in energy :doc:`units <units>`.
Restrictions
""""""""""""

28
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View File

@ -85,12 +85,14 @@ By default, *adof* = 2 or 3 = dimensionality of system, as set via the
:doc:`dimension <dimension>` command, and *cdof* = 0.0.
This gives the usual formula for temperature.
A kinetic energy tensor, stored as a six-element vector, is also
calculated by this compute for use in the computation of a pressure
tensor. The formula for the components of the tensor is the same as
the above formula, except that :math:`v^2` is replaced by
:math:`v_x v_y` for the :math:`xy` component, and so on.
The six components of the vector are ordered :math:`xx`, :math:`yy`,
A symmetric tensor, stored as a six-element vector, is also calculated
by this compute. The formula for the components of the tensor is the
same as the above expression for :math:`E_\mathrm{kin}`, except that
the 1/2 factor is NOT included and the :math:`v_i^2` is replaced by
:math:`v_{i,x} v_{i,y}` for the :math:`xy` component, and so on. Note
that because it lacks the 1/2 factor, these tensor components are
twice those of the traditional kinetic energy tensor. The six
components of the vector are ordered :math:`xx`, :math:`yy`,
:math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`.
Note that the number of atoms contributing to the temperature is
@ -227,10 +229,10 @@ Output info
"""""""""""
This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1--6.
These values can be used by any command that uses global scalar or
vector values from a compute as input.
See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS
vector of length 6 (symmetric tensor), which can be accessed by
indices 1--6. These values can be used by any command that uses
global scalar or vector values from a compute as input. See the
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS
output options.
This compute also optionally calculates a global array, if one or more
@ -245,9 +247,9 @@ page for an overview of LAMMPS output options.
The scalar value calculated by this compute is "intensive". The
vector values are "extensive". The array values are "intensive".
The scalar value will be in temperature :doc:`units <units>`. The
vector values will be in energy :doc:`units <units>`. The array values
will be in temperature :doc:`units <units>` for the *temp* value, and in
The scalar value is in temperature :doc:`units <units>`. The vector
values are in energy :doc:`units <units>`. The array values will be
in temperature :doc:`units <units>` for the *temp* value, and in
energy :doc:`units <units>` for the *kecom* and *internal* values.
Restrictions

31
doc/src/compute_temp_com.rst
View File

@ -44,12 +44,17 @@ where KE is the total kinetic energy of the group of atoms (sum of
simulation, :math:`N` is number of atoms in the group, :math:`k_B` is
the Boltzmann constant, and :math:`T` is the absolute temperature.
A kinetic energy tensor, stored as a six-element vector, is also
calculated by this compute for use in the computation of a pressure
tensor. The formula for the components of the tensor is the same as
the above formula, except that :math:`v^2` is replaced by :math:`v_x v_y`
for the :math:`xy` component, and so on. The six components of the vector are
ordered :math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`.
A symmetric tensor, stored as a six-element vector, is also calculated
by this compute for use in the computation of a pressure tensor by the
:doc:`compute pressue <compute_pressure>` command. The formula for
the components of the tensor is the same as the above expression for
:math:`E_\mathrm{kin}`, except that the 1/2 factor is NOT included and
the :math:`v_i^2` is replaced by :math:`v_{i,x} v_{i,y}` for the
:math:`xy` component, and so on. Note that because it lacks the 1/2
factor, these tensor components are twice those of the traditional
kinetic energy tensor. The six components of the vector are ordered
:math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`,
:math:`yz`.
The number of atoms contributing to the temperature is assumed to be
constant for the duration of the run; use the *dynamic* option of the
@ -81,17 +86,17 @@ Output info
"""""""""""
This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1--6.
These values can be used by any command that uses global scalar or
vector values from a compute as input. See the
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
options.
vector of length 6 (symmetric tensor), which can be accessed by
indices 1--6. These values can be used by any command that uses
global scalar or vector values from a compute as input. See the
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS
output options.
The scalar value calculated by this compute is "intensive". The
vector values are "extensive".
The scalar value will be in temperature :doc:`units <units>`.
The vector values will be in energy :doc:`units <units>`.
The scalar value is in temperature :doc:`units <units>`. The vector
values is in energy :doc:`units <units>`.
Restrictions
""""""""""""

108
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@ -31,27 +31,27 @@ on the center-of-mass velocity of atom pairs that are bonded to each
other. This compute is designed to be used with the adiabatic
core/shell model of :ref:`(Mitchell and Fincham) <MitchellFincham1>`.
See the :doc:`Howto coreshell <Howto_coreshell>` page for an overview of
the model as implemented in LAMMPS. Specifically, this compute
enables correct temperature calculation and thermostatting of
core/shell pairs where it is desirable for the internal degrees of
freedom of the core/shell pairs to not be influenced by a thermostat.
A compute of this style can be used by any command that computes a
temperature via :doc:`fix_modify <fix_modify>`
(e.g., :doc:`fix temp/rescale <fix_temp_rescale>`, :doc:`fix npt <fix_nh>`).
the model as implemented in LAMMPS. Specifically, this compute enables
correct temperature calculation and thermostatting of core/shell pairs
where it is desirable for the internal degrees of freedom of the
core/shell pairs to not be influenced by a thermostat. A compute of
this style can be used by any command that computes a temperature via
:doc:`fix_modify <fix_modify>` (e.g., :doc:`fix temp/rescale
<fix_temp_rescale>`, :doc:`fix npt <fix_nh>`).
Note that this compute does not require all ions to be polarized,
hence defined as core/shell pairs. One can mix core/shell pairs and
ions without a satellite particle if desired. The compute will
consider the non-polarized ions according to the physical system.
Note that this compute does not require all ions to be polarized, hence
defined as core/shell pairs. One can mix core/shell pairs and ions
without a satellite particle if desired. The compute will consider the
non-polarized ions according to the physical system.
For this compute, core and shell particles are specified by two
respective group IDs, which can be defined using the
:doc:`group <group>` command. The number of atoms in the two groups
must be the same and there should be one bond defined between a pair
of atoms in the two groups. Non-polarized ions which might also be
included in the treated system should not be included into either of
these groups, they are taken into account by the *group-ID* (second
argument) of the compute.
respective group IDs, which can be defined using the :doc:`group
<group>` command. The number of atoms in the two groups must be the
same and there should be one bond defined between a pair of atoms in the
two groups. Non-polarized ions which might also be included in the
treated system should not be included into either of these groups, they
are taken into account by the *group-ID* (second argument) of the
compute.
The temperature is calculated by the formula
@ -60,52 +60,56 @@ The temperature is calculated by the formula
\text{KE} = \frac{\text{dim}}{2} N k_B T,
where KE is the total kinetic energy of the group of atoms (sum of
:math:`\frac12 m v^2`), dim = 2 or 3 is the dimensionality of the simulation,
:math:`N` is the number of atoms in the group, :math:`k_B` is the Boltzmann
constant, and :math:`T` is the absolute temperature. Note that
the velocity of each core or shell atom used in the KE calculation is
the velocity of the center-of-mass (COM) of the core/shell pair the
atom is part of.
:math:`\frac12 m v^2`), dim = 2 or 3 is the dimensionality of the
simulation, :math:`N` is the number of atoms in the group, :math:`k_B`
is the Boltzmann constant, and :math:`T` is the absolute temperature.
Note that the velocity of each core or shell atom used in the KE
calculation is the velocity of the center-of-mass (COM) of the
core/shell pair the atom is part of.
A kinetic energy tensor, stored as a six-element vector, is also calculated by
this compute for use in the computation of a pressure tensor. The formula for
the components of the tensor is the same as the above formula, except that
:math:`v^2` is replaced by :math:`v_x v_y` for the :math:`xy` component, and so
on. The six components of the vector are ordered :math:`xx`, :math:`yy`,
:math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`. In contrast to the temperature,
the velocity of each core or shell atom is taken individually.
A symmetric tensor, stored as a six-element vector, is also calculated
by this compute for use in the computation of a pressure tensor by the
:doc:`compute pressue <compute_pressure>` command. The formula for the
components of the tensor is the same as the above expression for
:math:`E_\mathrm{kin}`, except that the 1/2 factor is NOT included and
the :math:`v_i^2` is replaced by :math:`v_{i,x} v_{i,y}` for the
:math:`xy` component, and so on. Note that because it lacks the 1/2
factor, these tensor components are twice those of the traditional
kinetic energy tensor. The six components of the vector are ordered
:math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`.
The change this fix makes to core/shell atom velocities is essentially
computing the temperature after a "bias" has been removed from the velocity of
the atoms. This "bias" is the velocity of the atom relative to the
center-of-mass velocity of the core/shell pair. If this compute is used with a
fix command that performs thermostatting then this bias will be subtracted from
each atom, thermostatting of the remaining center-of-mass velocity will be
performed, and the bias will be added back in. This means the thermostatting
will effectively be performed on the core/shell pairs, instead of on the
individual core and shell atoms. Thermostatting fixes that work in this way
include :doc:`fix nvt <fix_nh>`, :doc:`fix temp/rescale <fix_temp_rescale>`,
:doc:`fix temp/berendsen <fix_temp_berendsen>`, and
:doc:`fix langevin <fix_langevin>`.
computing the temperature after a "bias" has been removed from the
velocity of the atoms. This "bias" is the velocity of the atom relative
to the center-of-mass velocity of the core/shell pair. If this compute
is used with a fix command that performs thermostatting then this bias
will be subtracted from each atom, thermostatting of the remaining
center-of-mass velocity will be performed, and the bias will be added
back in. This means the thermostatting will effectively be performed on
the core/shell pairs, instead of on the individual core and shell atoms.
Thermostatting fixes that work in this way include :doc:`fix nvt
<fix_nh>`, :doc:`fix temp/rescale <fix_temp_rescale>`, :doc:`fix
temp/berendsen <fix_temp_berendsen>`, and :doc:`fix langevin
<fix_langevin>`.
The internal energy of core/shell pairs can be calculated by the
:doc:`compute temp/chunk <compute_temp_chunk>` command, if chunks are defined
as core/shell pairs. See the :doc:`Howto coreshell <Howto_coreshell>` doc
page for more discussion on how to do this.
:doc:`compute temp/chunk <compute_temp_chunk>` command, if chunks are
defined as core/shell pairs. See the :doc:`Howto coreshell
<Howto_coreshell>` doc page for more discussion on how to do this.
Output info
"""""""""""
This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1--6.
These values can be used by any command that uses global scalar or
vector values from a compute as input.
vector of length 6 (symmetric tensor), which can be accessed by indices
1--6. These values can be used by any command that uses global scalar
or vector values from a compute as input.
The scalar value calculated by this compute is "intensive". The
vector values are "extensive".
The scalar value calculated by this compute is "intensive". The vector
values are "extensive".
The scalar value will be in temperature :doc:`units <units>`. The
vector values will be in energy :doc:`units <units>`.
The scalar value is in temperature :doc:`units <units>`. The vector
values are in energy :doc:`units <units>`.
Restrictions
""""""""""""

30
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@ -73,12 +73,16 @@ simulation, :math:`N` is the number of atoms in the group, :math:`k_B`
is the Boltzmann constant, and :math:`T` is the temperature. Note that
:math:`v` in the kinetic energy formula is the atom's velocity.
A kinetic energy tensor, stored as a six-element vector, is also
calculated by this compute for use in the computation of a pressure
tensor. The formula for the components of the tensor is the same as
the above formula, except that :math:`v^2` is replaced by :math:`v_x v_y` for
the :math:`xy` component, and so on. The six components of the vector are
ordered :math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`,
A symmetric tensor, stored as a six-element vector, is also calculated
by this compute for use in the computation of a pressure tensor by the
:doc:`compute pressue <compute_pressure>` command. The formula for
the components of the tensor is the same as the above expression for
:math:`E_\mathrm{kin}`, except that the 1/2 factor is NOT included and
the :math:`v_i^2` is replaced by :math:`v_{i,x} v_{i,y}` for the
:math:`xy` component, and so on. Note that because it lacks the 1/2
factor, these tensor components are twice those of the traditional
kinetic energy tensor. The six components of the vector are ordered
:math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`,
:math:`yz`.
The number of atoms contributing to the temperature is assumed to be
@ -128,17 +132,17 @@ Output info
"""""""""""
This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1--6.
These values can be used by any command that uses global scalar or
vector values from a compute as input. See the
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
options.
vector of length 6 (symmetric tensor), which can be accessed by
indices 1--6. These values can be used by any command that uses
global scalar or vector values from a compute as input. See the
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS
output options.
The scalar value calculated by this compute is "intensive". The
vector values are "extensive".
The scalar value will be in temperature :doc:`units <units>`.
The vector values will be in energy :doc:`units <units>`.
The scalar value is in temperature :doc:`units <units>`. The vector
values are in energy :doc:`units <units>`.
Restrictions
""""""""""""

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@ -29,17 +29,20 @@ model, after subtracting out a streaming velocity induced by the
simulation box changing size and/or shape, for example in a
non-equilibrium MD (NEMD) simulation. The size/shape change is
induced by use of the :doc:`fix deform <fix_deform>` command. A
compute of this style is created by the
:doc:`fix nvt/sllod/eff <fix_nvt_sllod_eff>` command to compute the thermal
temperature of atoms for thermostatting purposes. A compute of this
style can also be used by any command that computes a temperature
(e.g., :doc:`thermo_modify <thermo_modify>`, :doc:`fix npt/eff <fix_nh_eff>`).
compute of this style is created by the :doc:`fix nvt/sllod/eff
<fix_nvt_sllod_eff>` command to compute the thermal temperature of
atoms for thermostatting purposes. A compute of this style can also
be used by any command that computes a temperature (e.g.,
:doc:`thermo_modify <thermo_modify>`, :doc:`fix npt/eff
<fix_nh_eff>`).
The calculation performed by this compute is exactly like that
described by the :doc:`compute temp/deform <compute_temp_deform>`
command, except that the formula for the temperature includes the
radial electron velocity contributions, as discussed by the :doc:`compute temp/eff <compute_temp_eff>` command. Note that only the
translational degrees of freedom for each nuclei or electron are
command, except that the formulas for the temperature (scalar) and
diagonal components of the symmetric tensor (vector) include the
radial electron velocity contributions, as discussed by the
:doc:`compute temp/eff <compute_temp_eff>` command. Note that only
the translational degrees of freedom for each nuclei or electron are
affected by the streaming velocity adjustment. The radial velocity
component of the electrons is not affected.
@ -47,17 +50,17 @@ Output info
"""""""""""
This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1--6.
These values can be used by any command that uses global scalar or
vector values from a compute as input. See the
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
options.
vector of length 6 (symmetric tensor), which can be accessed by
indices 1--6. These values can be used by any command that uses
global scalar or vector values from a compute as input. See the
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS
output options.
The scalar value calculated by this compute is "intensive". The
vector values are "extensive".
The scalar value will be in temperature :doc:`units <units>`. The
vector values will be in energy :doc:`units <units>`.
The scalar value is in temperature :doc:`units <units>`. The vector
values are in energy :doc:`units <units>`.
Restrictions
""""""""""""

28
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View File

@ -44,12 +44,16 @@ constant, and :math:`T` = temperature. The calculation of KE excludes the
is 0. The dim parameter is adjusted to give the correct number of
degrees of freedom.
A kinetic energy tensor, stored as a six-element vector, is also
calculated by this compute for use in the calculation of a pressure
tensor. The formula for the components of the tensor is the same as
the above formula, except that :math:`v^2` is replaced by :math:`v_x v_y` for
the :math:`xy` component, and so on. The six components of the vector are
ordered :math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`,
A symmetric tensor, stored as a six-element vector, is also calculated
by this compute for use in the computation of a pressure tensor by the
:doc:`compute pressue <compute_pressure>` command. The formula for
the components of the tensor is the same as the above expression for
:math:`E_\mathrm{kin}`, except that the 1/2 factor is NOT included and
the :math:`v_i^2` is replaced by :math:`v_{i,x} v_{i,y}` for the
:math:`xy` component, and so on. Note that because it lacks the 1/2
factor, these tensor components are twice those of the traditional
kinetic energy tensor. The six components of the vector are ordered
:math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`,
:math:`yz`.
The number of atoms contributing to the temperature is assumed to be
@ -88,17 +92,17 @@ Output info
"""""""""""
This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1--6.
These values can be used by any command that uses global scalar or
vector values from a compute as input.
See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS
vector of length 6 (symmetric tensor), which can be accessed by
indices 1--6. These values can be used by any command that uses
global scalar or vector values from a compute as input. See the
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS
output options.
The scalar value calculated by this compute is "intensive". The
vector values are "extensive".
The scalar value will be in temperature :doc:`units <units>`. The
vector values will be in energy :doc:`units <units>`.
The scalar value is in temperature :doc:`units <units>`. The vector
values are in energy :doc:`units <units>`.
Restrictions
""""""""""""

64
doc/src/compute_temp_profile.rst
View File

@ -97,21 +97,27 @@ center-of-mass velocity across the group in directions where streaming velocity
is *not* subtracted. This can be altered using the *extra* option of the
:doc:`compute_modify <compute_modify>` command.
If the *out* keyword is used with a *tensor* value, which is the default,
a kinetic energy tensor, stored as a six-element vector, is also calculated by
this compute for use in the computation of a pressure tensor. The formula for
the components of the tensor is the same as the above formula, except that
:math:`v^2` is replaced by :math:`v_x v_y` for the :math:`xy` component, and
so on. The six components of the vector are ordered :math:`xx`, :math:`yy`,
If the *out* keyword is used with a *tensor* value, which is the
default, then a symmetric tensor, stored as a six-element vector, is
also calculated by this compute for use in the computation of a
pressure tensor by the :doc:`compute pressue <compute_pressure>`
command. The formula for the components of the tensor is the same as
the above expression for :math:`E_\mathrm{kin}`, except that the 1/2
factor is NOT included and the :math:`v_i^2` is replaced by
:math:`v_{i,x} v_{i,y}` for the :math:`xy` component, and so on. Note
that because it lacks the 1/2 factor, these tensor components are
twice those of the traditional kinetic energy tensor. The six
components of the vector are ordered :math:`xx`, :math:`yy`,
:math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`.
If the *out* keyword is used with a *bin* value, the count of atoms and
computed temperature for each bin are stored for output, as an array of values,
as described below. The temperature of each bin is calculated as described
above, where the bias velocity is subtracted and only the remaining thermal
velocity of atoms in the bin contributes to the temperature. See the note
below for how the temperature is normalized by the degrees-of-freedom of atoms
in the bin.
If the *out* keyword is used with a *bin* value, the count of atoms
and computed temperature for each bin are stored for output, as an
array of values, as described below. The temperature of each bin is
calculated as described above, where the bias velocity is subtracted
and only the remaining thermal velocity of atoms in the bin
contributes to the temperature. See the note below for how the
temperature is normalized by the degrees-of-freedom of atoms in the
bin.
The number of atoms contributing to the temperature is assumed to be
constant for the duration of the run; use the *dynamic* option of the
@ -166,16 +172,17 @@ Output info
This compute calculates a global scalar (the temperature). Depending
on the setting of the *out* keyword, it also calculates a global
vector or array. For *out* = *tensor*, it calculates a vector of
length 6 (KE tensor), which can be accessed by indices 1--6. For *out*
= *bin* it calculates a global array which has 2 columns and :math:`N` rows,
where :math:`N` is the number of bins. The first column contains the number
of atoms in that bin. The second contains the temperature of that
bin, calculated as described above. The ordering of rows in the array
is as follows. Bins in :math:`x` vary fastest, then :math:`y`, then
:math:`z`. Thus for a :math:`10\times 10\times 10` 3d array of bins, there
will be 1000 rows. The bin with indices :math:`(i_x,i_y,i_z) = (2,3,4)` would
map to row :math:`M = 10^2(i_z-1) + 10(i_y-1) + i_x = 322`, where the rows are
numbered from 1 to 1000 and the bin indices are numbered from 1 to 10 in each
length 6 (symmetric tensor), which can be accessed by indices 1--6.
For *out* = *bin* it calculates a global array which has 2 columns and
:math:`N` rows, where :math:`N` is the number of bins. The first
column contains the number of atoms in that bin. The second contains
the temperature of that bin, calculated as described above. The
ordering of rows in the array is as follows. Bins in :math:`x` vary
fastest, then :math:`y`, then :math:`z`. Thus for a :math:`10\times
10\times 10` 3d array of bins, there will be 1000 rows. The bin with
indices :math:`(i_x,i_y,i_z) = (2,3,4)` would map to row :math:`M =
10^2(i_z-1) + 10(i_y-1) + i_x = 322`, where the rows are numbered from
1 to 1000 and the bin indices are numbered from 1 to 10 in each
dimension.
These values can be used by any command that uses global scalar or
@ -186,9 +193,9 @@ options.
The scalar value calculated by this compute is "intensive". The
vector values are "extensive". The array values are "intensive".
The scalar value will be in temperature :doc:`units <units>`. The
vector values will be in energy :doc:`units <units>`. The first column
of array values are counts; the values in the second column will be in
The scalar value us in temperature :doc:`units <units>`. The vector
values are in energy :doc:`units <units>`. The first column of array
values are counts; the values in the second column will be in
temperature :doc:`units <units>`.
Restrictions
@ -203,7 +210,10 @@ will be for most thermostats.
Related commands
""""""""""""""""
:doc:`compute temp <compute_temp>`, :doc:`compute temp/ramp <compute_temp_ramp>`, :doc:`compute temp/deform <compute_temp_deform>`, :doc:`compute pressure <compute_pressure>`
:doc:`compute temp <compute_temp>`,
:doc:`compute temp/ramp <compute_temp_ramp>`,
:doc:`compute temp/deform <compute_temp_deform>`,
:doc:`compute pressure <compute_pressure>`
Default
"""""""

36
doc/src/compute_temp_ramp.rst
View File

@ -63,12 +63,17 @@ command (e.g., :math:`\AA` for units = real or metal). A
velocity in lattice spacings per unit time). The :doc:`lattice <lattice>`
command must have been previously used to define the lattice spacing.
A kinetic energy tensor, stored as a six-element vector, is also calculated by
this compute for use in the computation of a pressure tensor. The formula for
the components of the tensor is the same as the above formula, except that
:math:`v^2` is replaced by :math:`v_x v_y` for the :math:`xy` component, and
so on. The six components of the vector are ordered :math:`xx`, :math:`yy`,
:math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`.
A symmetric tensor, stored as a six-element vector, is also calculated
by this compute for use in the computation of a pressure tensor by the
:doc:`compute pressue <compute_pressure>` command. The formula for
the components of the tensor is the same as the above expression for
:math:`E_\mathrm{kin}`, except that the 1/2 factor is NOT included and
the :math:`v_i^2` is replaced by :math:`v_{i,x} v_{i,y}` for the
:math:`xy` component, and so on. Note that because it lacks the 1/2
factor, these tensor components are twice those of the traditional
kinetic energy tensor. The six components of the vector are ordered
:math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`,
:math:`yz`.
The number of atoms contributing to the temperature is assumed to be constant
for the duration of the run; use the *dynamic* option of the
@ -100,17 +105,17 @@ Output info
"""""""""""
This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1--6.
These values can be used by any command that uses global scalar or
vector values from a compute as input. See the
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
options.
vector of length 6 (symmetric tensor), which can be accessed by
indices 1--6. These values can be used by any command that uses
global scalar or vector values from a compute as input. See the
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS
output options.
The scalar value calculated by this compute is "intensive". The
vector values are "extensive".
The scalar value will be in temperature :doc:`units <units>`. The
vector values will be in energy :doc:`units <units>`.
The scalar value is in temperature :doc:`units <units>`. The vector
values are in energy :doc:`units <units>`.
Restrictions
""""""""""""
@ -119,7 +124,10 @@ Restrictions
Related commands
""""""""""""""""
:doc:`compute temp <compute_temp>`, :doc:`compute temp/profie <compute_temp_profile>`, :doc:`compute temp/deform <compute_temp_deform>`, :doc:`compute pressure <compute_pressure>`
:doc:`compute temp <compute_temp>`,
:doc:`compute temp/profile <compute_temp_profile>`,
:doc:`compute temp/deform <compute_temp_deform>`,
:doc:`compute pressure <compute_pressure>`
Default
"""""""

44
doc/src/compute_temp_region.rst
View File

@ -49,12 +49,17 @@ where KE = is the total kinetic energy of the group of atoms (sum of
:math:`N` is the number of atoms in both the group and region, :math:`k_B` is
the Boltzmann constant, and :math:`T` temperature.
A kinetic energy tensor, stored as a six-element vector, is also
calculated by this compute for use in the computation of a pressure
tensor. The formula for the components of the tensor is the same as
the above formula, except that :math:`v^2` is replaced by :math:`v_x v_y`
for the :math:`xy` component, and so on. The six components of the vector are
ordered :math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`.
A symmetric tensor, stored as a six-element vector, is also calculated
by this compute for use in the computation of a pressure tensor by the
:doc:`compute pressue <compute_pressure>` command. The formula for
the components of the tensor is the same as the above expression for
:math:`E_\mathrm{kin}`, except that the 1/2 factor is NOT included and
the :math:`v_i^2` is replaced by :math:`v_{i,x} v_{i,y}` for the
:math:`xy` component, and so on. Note that because it lacks the 1/2
factor, these tensor components are twice those of the traditional
kinetic energy tensor. The six components of the vector are ordered
:math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`,
:math:`yz`.
The number of atoms contributing to the temperature is calculated each
time the temperature is evaluated since it is assumed atoms can
@ -78,12 +83,13 @@ will operate only on atoms that are currently in the geometric region.
Unlike other compute styles that calculate temperature, this compute
does not subtract out degrees-of-freedom due to fixes that constrain
motion, such as :doc:`fix shake <fix_shake>` and :doc:`fix rigid <fix_rigid>`. This is because those degrees of freedom
(e.g., a constrained bond) could apply to sets of atoms that straddle
the region boundary, and hence the concept is somewhat ill-defined.
If needed the number of subtracted degrees of freedom can be set
explicitly using the *extra* option of the
:doc:`compute_modify <compute_modify>` command.
motion, such as :doc:`fix shake <fix_shake>` and :doc:`fix rigid
<fix_rigid>`. This is because those degrees of freedom (e.g., a
constrained bond) could apply to sets of atoms that straddle the
region boundary, and hence the concept is somewhat ill-defined. If
needed the number of subtracted degrees of freedom can be set
explicitly using the *extra* option of the :doc:`compute_modify
<compute_modify>` command.
See the :doc:`Howto thermostat <Howto_thermostat>` page for a
discussion of different ways to compute temperature and perform
@ -93,17 +99,17 @@ Output info
"""""""""""
This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1--6.
These values can be used by any command that uses global scalar or
vector values from a compute as input. See the
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
options.
vector of length 6 (symmetric tensor), which can be accessed by
indices 1--6. These values can be used by any command that uses
global scalar or vector values from a compute as input. See the
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS
output options.
The scalar value calculated by this compute is "intensive". The
vector values are "extensive".
The scalar value will be in temperature :doc:`units <units>`.
The vector values will be in energy :doc:`units <units>`.
The scalar value is in temperature :doc:`units <units>`. The vector
values are in energy :doc:`units <units>`.
Restrictions
""""""""""""

27
doc/src/compute_temp_region_eff.rst
View File

@ -32,32 +32,33 @@ temperature (e.g., :doc:`thermo_modify <thermo_modify>`).
The operation of this compute is exactly like that described by the
:doc:`compute temp/region <compute_temp_region>` command, except that
the formula for the temperature itself includes the radial electron
velocity contributions, as discussed by the
:doc:`compute temp/eff <compute_temp_eff>` command.
the formulas for the temperature (scalar) and diagonal components of
the symmetric tensor (vector) include the radial electron velocity
contributions, as discussed by the :doc:`compute temp/eff
<compute_temp_eff>` command.
Output info
"""""""""""
This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1--6.
These values can be used by any command that uses global scalar or
vector values from a compute as input. See the
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
options.
vector of length 6 (symmetric tensor), which can be accessed by
indices 1--6. These values can be used by any command that uses
global scalar or vector values from a compute as input. See the
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS
output options.
The scalar value calculated by this compute is "intensive". The
vector values are "extensive".
The scalar value will be in temperature :doc:`units <units>`. The
vector values will be in energy :doc:`units <units>`.
The scalar value is in temperature :doc:`units <units>`. The vector
values are in energy :doc:`units <units>`.
Restrictions
""""""""""""
This compute is part of the EFF package. It is only enabled if
LAMMPS was built with that package.
See the :doc:`Build package <Build_package>` page for more info.
This compute is part of the EFF 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
""""""""""""""""

30
doc/src/compute_temp_rotate.rst
View File

@ -43,12 +43,17 @@ where KE is the total kinetic energy of the group of atoms (sum of
:math:`N` is the number of atoms in the group, :math:`k_B` is the Boltzmann
constant, and :math:`T` is the absolute temperature.
A kinetic energy tensor, stored as a six-element vector, is also calculated by
this compute for use in the computation of a pressure tensor. The formula for
the components of the tensor is the same as the above formula, except that
:math:`v^2` is replaced by :math:`v_x v_y` for the :math:`xy` component, and
so on. The six components of the vector are ordered :math:`xx`, :math:`yy`,
:math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`.
A symmetric tensor, stored as a six-element vector, is also calculated
by this compute for use in the computation of a pressure tensor by the
:doc:`compute pressue <compute_pressure>` command. The formula for
the components of the tensor is the same as the above expression for
:math:`E_\mathrm{kin}`, except that the 1/2 factor is NOT included and
the :math:`v_i^2` is replaced by :math:`v_{i,x} v_{i,y}` for the
:math:`xy` component, and so on. Note that because it lacks the 1/2
factor, these tensor components are twice those of the traditional
kinetic energy tensor. The six components of the vector are ordered
:math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`,
:math:`yz`.
The number of atoms contributing to the temperature is assumed to be
constant for the duration of the run; use the *dynamic* option of the
@ -80,17 +85,16 @@ Output info
"""""""""""
This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1-6.
These values can be used by any command that uses global scalar or
vector values from a compute as input. See the
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
options.
vector of length 6 (symmetric tensor), which can be accessed by
indices 1-6. These values can be used by any command that uses global
scalar or vector values from a compute as input. See the :doc:`Howto
output <Howto_output>` page for an overview of LAMMPS output options.
The scalar value calculated by this compute is "intensive". The
vector values are "extensive".
The scalar value will be in temperature :doc:`units <units>`. The
vector values will be in energy :doc:`units <units>`.
The scalar value is in temperature :doc:`units <units>`. The vector
values are in energy :doc:`units <units>`.
Restrictions
""""""""""""

24
doc/src/compute_temp_sphere.rst
View File

@ -77,6 +77,18 @@ tensor is the same as the above formulas, except that :math:`v^2` and
vector are ordered :math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`,
:math:`xz`, :math:`yz`.
A symmetric tensor, stored as a six-element vector, is also calculated
by this compute for use in the computation of a pressure tensor by the
:doc:`compute pressue <compute_pressure>` command. The formula for
the components of the tensor is the same as the above expression for
:math:`E_\mathrm{kin}`, except that the 1/2 factor is NOT included and
the :math:`v_i^2` and :math:`\omega^2` are replaced by :math:`v_x v_y`
and :math:`\omega_x \omega_y` for the :math:`xy` component, and so on.
Note that because it lacks the 1/2 factor, these tensor components are
twice those of the traditional kinetic energy tensor. The six
components of the vector are ordered :math:`xx`, :math:`yy`,
:math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`.
The number of atoms contributing to the temperature is assumed to be
constant for the duration of the run; use the *dynamic* option of the
:doc:`compute_modify <compute_modify>` command if this is not the case.
@ -117,17 +129,17 @@ Output info
"""""""""""
This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1--6.
These values can be used by any command that uses global scalar or
vector values from a compute as input.
See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS
vector of length 6 (symmetric tensor), which can be accessed by
indices 1--6. These values can be used by any command that uses
global scalar or vector values from a compute as input. See the
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS
output options.
The scalar value calculated by this compute is "intensive". The
vector values are "extensive".
The scalar value will be in temperature :doc:`units <units>`. The
vector values will be in energy :doc:`units <units>`.
The scalar value is in temperature :doc:`units <units>`. The vector
values are in energy :doc:`units <units>`.
Restrictions
""""""""""""

37
doc/src/compute_viscosity_cos.rst
View File

@ -86,12 +86,17 @@ where KE is the total kinetic energy of the group of atoms (sum of
:math:`N` is the number of atoms in the group, :math:`k_B` is the Boltzmann
constant, and :math:`T` is the absolute temperature.
A kinetic energy tensor, stored as a six-element vector, is also
calculated by this compute for use in the computation of a pressure
tensor. The formula for the components of the tensor is the same as
the above formula, except that :math:`v^2` is replaced by :math:`v_x v_y` for
the :math:`xy` component, and so on. The six components of the vector are
ordered :math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`.
A symmetric tensor, stored as a six-element vector, is also calculated
by this compute for use in the computation of a pressure tensor by the
:doc:`compute pressue <compute_pressure>` command. The formula for
the components of the tensor is the same as the above expression for
:math:`E_\mathrm{kin}`, except that the 1/2 factor is NOT included and
the :math:`v_i^2` is replaced by :math:`v_{i,x} v_{i,y}` for the
:math:`xy` component, and so on. Note that because it lacks the 1/2
factor, these tensor components are twice those of the traditional
kinetic energy tensor. The six components of the vector are ordered
:math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`,
:math:`yz`.
The number of atoms contributing to the temperature is assumed to be
constant for the duration of the run; use the *dynamic* option of the
@ -126,21 +131,21 @@ Output info
"""""""""""
This compute calculates a global scalar (the temperature) and a global
vector of length 7, which can be accessed by indices 1--7.
The first six elements of the vector are the KE tensor,
and the seventh is the cosine-shaped velocity amplitude :math:`V`,
which can be used to calculate the reciprocal viscosity, as shown in the example.
These values can be used by any command that uses global scalar or
vector values from a compute as input.
See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output options.
vector of length 7, which can be accessed by indices 1--7. The first
six elements of the vector are those of the symmetric tensor discussed
above. The seventh is the cosine-shaped velocity amplitude :math:`V`,
which can be used to calculate the reciprocal viscosity, as shown in
the example. These values can be used by any command that uses global
scalar or vector values from a compute as input. See the :doc:`Howto
output <Howto_output>` page for an overview of LAMMPS output options.
The scalar value calculated by this compute is "intensive". The
first six elements of vector values are "extensive",
and the seventh element of vector values is "intensive".
The scalar value will be in temperature :doc:`units <units>`.
The first six elements of vector values will be in energy :doc:`units <units>`.
The seventh element of vector value will be in velocity :doc:`units <units>`.
The scalar value is in temperature :doc:`units <units>`. The first
six elements of vector values are in energy :doc:`units <units>`. The
seventh element of vector value us in velocity :doc:`units <units>`.
Restrictions
""""""""""""

4
doc/src/fix_bond_react.rst
View File

@ -785,3 +785,7 @@ reset_mol_ids = yes, custom_charges = no, molecule = off, modify_create = *fit a
.. _Gissinger2020:
**(Gissinger2020)** Gissinger, Jensen and Wise, Macromolecules, 53, 22, 9953-9961 (2020).
.. _Gissinger2024:
**(Gissinger2024)** Gissinger, Jensen and Wise, Computer Physics Communications, 304, 109287 (2024).

2
doc/src/fix_meso_move.rst
View File

@ -247,7 +247,7 @@ defined by the :doc:`atom_style sph <atom_style>` command.
All particles in the group must be mesoscopic SPH/SDPD particles.
.. versionchanged:: TBD
.. versionchanged:: 29Aug2024
This fix is incompatible with deformation controls that remap velocity,
for instance the *remap v* option of :doc:`fix deform <fix_deform>`.

2
doc/src/fix_mvv_dpd.rst
View File

@ -97,7 +97,7 @@ These fixes are part of the DPD-MESO package. They are only enabled if
LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
.. versionchanged:: TBD
.. versionchanged:: 29Aug2024
This fix is incompatible with deformation controls that remap velocity,
for instance the *remap v* option of :doc:`fix deform <fix_deform>`.

2
doc/src/fix_rheo.rst
View File

@ -44,7 +44,7 @@ Examples
Description
"""""""""""
.. versionadded:: TBD
.. versionadded:: 29Aug2024
Perform time integration for RHEO particles, updating positions, velocities,
and densities. For an overview of other features available in the RHEO package,

2
doc/src/fix_rheo_oxidation.rst
View File

@ -27,7 +27,7 @@ Examples
Description
"""""""""""
.. versionadded:: TBD
.. versionadded:: 29Aug2024
This fix dynamically creates bonds on the surface of fluids to
represent physical processes such as oxidation. It is intended

2
doc/src/fix_rheo_pressure.rst
View File

@ -33,7 +33,7 @@ Examples
Description
"""""""""""
.. versionadded:: TBD
.. versionadded:: 29Aug2024
This fix defines a pressure equation of state for RHEO particles. One can
define different equations of state for different atom types. An equation

2
doc/src/fix_rheo_thermal.rst
View File

@ -48,7 +48,7 @@ Examples
Description
"""""""""""
.. versionadded:: TBD
.. versionadded:: 29Aug2024
This fix performs time integration of temperature for atom style rheo/thermal.
In addition, it defines multiple thermal properties of particles and handles

2
doc/src/fix_rheo_viscosity.rst
View File

@ -38,7 +38,7 @@ Examples
Description
"""""""""""
.. versionadded:: TBD
.. versionadded:: 29Aug2024
This fix defines a viscosity for RHEO particles. One can define different
viscosities for different atom types, but a viscosity must be specified for

2
doc/src/fix_rigid_meso.rst
View File

@ -353,7 +353,7 @@ defined by the :doc:`atom_style sph <atom_style>` command.
All particles in the group must be mesoscopic SPH/SDPD particles.
.. versionchanged:: TBD
.. versionchanged:: 29Aug2024
This fix is incompatible with deformation controls that remap velocity,
for instance the *remap v* option of :doc:`fix deform <fix_deform>`.

2
doc/src/fix_shake.rst
View File

@ -137,7 +137,7 @@ constrained (within a fudge factor of MASSDELTA specified in
both bonds in the angle are constrained then the angle will also be
constrained if its type is in the list.
.. versionchanged:: TBD
.. versionchanged:: 29Aug2024
The types may be given as type labels *only* if there is no atom, bond,
or angle type label named *b*, *a*, *t*, or *m* defined in the

2
doc/src/fix_smd_integrate_tlsph.rst
View File

@ -53,7 +53,7 @@ Restrictions
This fix is part of the MACHDYN package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
.. versionchanged:: TBD
.. versionchanged:: 29Aug2024
This fix is incompatible with deformation controls that remap velocity,
for instance the *remap v* option of :doc:`fix deform <fix_deform>`.

2
doc/src/fix_smd_integrate_ulsph.rst
View File

@ -61,7 +61,7 @@ Restrictions
This fix is part of the MACHDYN package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
.. versionchanged:: TBD
.. versionchanged:: 29Aug2024
This fix is incompatible with deformation controls that remap velocity,
for instance the *remap v* option of :doc:`fix deform <fix_deform>`.

2
doc/src/geturl.rst
View File

@ -32,7 +32,7 @@ Examples
Description
"""""""""""
.. versionadded:: TBD
.. versionadded:: 29Aug2024
Download a file from an URL to the local disk. This is implemented with
the `libcurl library <https:://curl.se/libcurl/>`_ which supports a

2
doc/src/neigh_modify.rst
View File

@ -159,7 +159,7 @@ sample scenarios where this is useful:
* When one or more rigid bodies are specified, interactions within each
body can be turned off to save needless computation. See the :doc:`fix rigid <fix_rigid>` command for more details.
.. versionchanged:: TBD
.. versionchanged:: 29Aug2024
Support for type labels was added.

2
doc/src/pair_rheo.rst
View File

@ -31,7 +31,7 @@ Examples
Description
"""""""""""
.. versionadded:: TBD
.. versionadded:: 29Aug2024
Pair style *rheo* computes pressure and viscous forces between particles
in the :doc:`rheo package <Howto_rheo>`. If thermal evolution is turned

2
doc/src/pair_rheo_solid.rst
View File

@ -21,7 +21,7 @@ Examples
Description
"""""""""""
.. versionadded:: TBD
.. versionadded:: 29Aug2024
Style *rheo/solid* is effectively a copy of pair style
:doc:`bpm/spring <pair_bpm_spring>` except it only applies forces

2
doc/src/variable.rst
View File

@ -1042,7 +1042,7 @@ label2type(), but returns 1 if the type label has been assigned,
otherwise it returns 0. This function can be used to check if a
particular type label already exists in the simulation.
.. versionadded:: TBD
.. versionadded:: 29Aug2024
The is_timeout() function returns 1 when the :doc:`timer timeout
<timer>` has expired otherwise it returns 0. This function can be used

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2
doc/utils/sphinx-config/conf.py.in
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@ -416,7 +416,7 @@ latex_documents = [
# The name of an image file (relative to this directory) to place at the top of
# the title page.
latex_logo = "_static/lammps-logo-large.jpg"
latex_logo = "_static/lammps-logo-large.png"
latex_toplevel_sectioning = 'part'

6
doc/utils/sphinx-config/false_positives.txt
View File

@ -407,6 +407,7 @@ Bybee
bz
Cadarache
cadetblue
Caen
Cagin
calc
calibrationfunctions
@ -1705,6 +1706,7 @@ jec
Jeffers
jewett
Jewett
jgissing
ji
Jiang
Jiao
@ -3550,6 +3552,7 @@ Steinhauser
Stepaniants
stepwise
Stesmans
stevens
stiffnesses
Stillinger
stk
@ -4127,6 +4130,7 @@ Xiaowang
Xie
xk
xlat
xlattice
xlo
xmax
Xmax
@ -4178,6 +4182,7 @@ yflag
yhi
yi
ylat
ylattice
ylo
ylz
ymax
@ -4226,6 +4231,7 @@ Ziegenhain
zincblende
zj
Zj
zlattice
zlim
zlo
Zm

4
examples/COUPLE/plugin/liblammpsplugin.c
View File

@ -41,7 +41,6 @@
#include <stdlib.h>
liblammpsplugin_t *liblammpsplugin_load(const char *lib)
{
liblammpsplugin_t *lmp;
@ -191,6 +190,9 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
ADDSYM(is_running);
ADDSYM(force_timeout);
// symbol not present
if (!lmp->config_has_exceptions) return NULL;
lmp->has_exceptions = lmp->config_has_exceptions();
if (lmp->has_exceptions) {
ADDSYM(has_error);

2
examples/PACKAGES/pace/plugin/paceplugin.nsis
View File

@ -39,7 +39,7 @@ InstallDir "$LOCALAPPDATA\${PACEPLUGIN}"
ShowInstDetails show
ShowUninstDetails show
SetCompressor lzma
SetCompressor zlib
!define MUI_ABORTWARNING

59
examples/PACKAGES/plumed/plugin/CMakeLists.txt Normal file
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@ -0,0 +1,59 @@
# -*- CMake -*- build system for plugin examples.
# The is meant to be used as a template for plugins that are
# distributed independent from the LAMMPS package.
##########################################
cmake_minimum_required(VERSION 3.16)
project(plumedplugin VERSION 1.0 LANGUAGES CXX)
set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR})
include(CheckIncludeFileCXX)
include(LAMMPSInterfacePlugin)
include(PLUMED)
##########################
# building the plugins
add_library(plumedplugin MODULE plumedplugin.cpp ${LAMMPS_SOURCE_DIR}/PLUMED/fix_plumed.cpp)
target_link_libraries(plumedplugin PRIVATE LAMMPS::PLUMED)
target_link_libraries(plumedplugin PRIVATE lammps)
target_include_directories(plumedplugin PRIVATE ${LAMMPS_SOURCE_DIR}/PLUMED)
set_target_properties(plumedplugin PROPERTIES PREFIX "" SUFFIX ".so")
# MacOS seems to need this
if(CMAKE_SYSTEM_NAME STREQUAL Darwin)
set_target_properties(plumedplugin PROPERTIES LINK_FLAGS "-Wl,-undefined,dynamic_lookup")
elseif(CMAKE_SYSTEM_NAME STREQUAL "Windows")
# tell CMake to export all symbols to a .dll on Windows with special case for MinGW cross-compilers
set_target_properties(plumedplugin PROPERTIES WINDOWS_EXPORT_ALL_SYMBOLS TRUE)
if(CMAKE_CROSSCOMPILING)
set_target_properties(plumedplugin PROPERTIES LINK_FLAGS "-Wl,--export-all-symbols")
endif()
get_lammps_version(${LAMMPS_SOURCE_DIR}/version.h LAMMPS_VERSION)
find_program(MAKENSIS_PATH makensis)
if(MAKENSIS_PATH)
execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different ${CMAKE_SOURCE_DIR}/lammps.ico
${CMAKE_SOURCE_DIR}/lammps-text-logo-wide.bmp ${CMAKE_SOURCE_DIR}/plumedplugin.nsis
${CMAKE_BINARY_DIR})
if(BUILD_MPI)
if(USE_MSMPI)
add_custom_target(package ${MAKENSIS_PATH} -V1 -DVERSION=${LAMMPS_VERSION}-MSMPI plumedplugin.nsis
DEPENDS plumedplugin plumed_copy lammps.ico lammps-text-logo-wide.bmp plumedplugin.nsis
BYPRODUCTS LAMMPS-PLUMED-plugin-${LAMMPS_VERSION}-MSMPI.exe)
else()
add_custom_target(package ${MAKENSIS_PATH} -V1 -DVERSION=${LAMMPS_VERSION}-MPI plumedplugin.nsis
DEPENDS plumedplugin plumed_copy lammps.ico lammps-text-logo-wide.bmp plumedplugin.nsis
BYPRODUCTS LAMMPS-PLUMED-plugin-${LAMMPS_VERSION}-MPI.exe)
endif()
else()
add_custom_target(package ${MAKENSIS_PATH} -V1 -DVERSION=${LAMMPS_VERSION} plumedplugin.nsis
COMMAND ${CMAKE_COMMAND} -E echo ${PWD}
DEPENDS plumedplugin plumed_copy lammps.ico lammps-text-logo-wide.bmp plumedplugin.nsis
BYPRODUCTS LAMMPS-PLUMED-plugin-${LAMMPS_VERSION}.exe)
endif()
endif()
else()
set_target_properties(plumedplugin PROPERTIES LINK_FLAGS "-rdynamic")
endif()

1
examples/PACKAGES/plumed/plugin/LAMMPSInterfacePlugin.cmake Symbolic link
View File

@ -0,0 +1 @@
../../../../cmake/Modules/LAMMPSInterfacePlugin.cmake

1
examples/PACKAGES/plumed/plugin/PLUMED.cmake Symbolic link
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@ -0,0 +1 @@
../../../../cmake/Modules/Packages/PLUMED.cmake

2
examples/PACKAGES/plumed/plugin/README.txt Normal file
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@ -0,0 +1,2 @@
This folder contains a loader and support files to build the PLUMED package as plugin.
For more information please see: https://docs.lammps.org/Developer_plugins.html

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28
examples/PACKAGES/plumed/plugin/plumedplugin.cpp Normal file
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@ -0,0 +1,28 @@
#include "lammpsplugin.h"
#include "version.h"
#include "fix_plumed.h"
using namespace LAMMPS_NS;
static Fix *fix_plumed_creator(LAMMPS *lmp, int argc, char **argv)
{
return new FixPlumed(lmp, argc, argv);
}
extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc)
{
lammpsplugin_t plugin;
lammpsplugin_regfunc register_plugin = (lammpsplugin_regfunc) regfunc;
// register plumed fix style
plugin.version = LAMMPS_VERSION;
plugin.style = "fix";
plugin.name = "plumed";
plugin.info = "Plumed2 plugin fix style v1.0";
plugin.author = "Axel Kohlmeyer (akohlmey@gmail.com)";
plugin.creator.v1 = (lammpsplugin_factory1 *) &fix_plumed_creator;
plugin.handle = handle;
(*register_plugin)(&plugin, lmp);
}

172
examples/PACKAGES/plumed/plugin/plumedplugin.nsis Normal file
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@ -0,0 +1,172 @@
#!Nsis Installer Command Script
#
# The following external defines are recognized:
# ${VERSION} = YYYYMMDD
!include "MUI2.nsh"
!include "FileFunc.nsh"
!define MUI_ICON "lammps.ico"
!define MUI_UNICON "lammps.ico"
!define MUI_HEADERIMAGE
!define MUI_HEADERIMAGE_BITMAP "lammps-text-logo-wide.bmp"
!define MUI_HEADERIMAGE_RIGHT
Unicode true
XPStyle on
!include "LogicLib.nsh"
!addplugindir "envvar/Plugins/x86-unicode"
!include "x64.nsh"
RequestExecutionLevel user
!macro VerifyUserIsAdmin
UserInfo::GetAccountType
pop $0
${If} $0 != "admin"
messageBox mb_iconstop "Administrator rights required!"
setErrorLevel 740 ;ERROR_ELEVATION_REQUIRED
quit
${EndIf}
!macroend
!define PLUMEDPLUGIN "LAMMPS PLUMED Plugin ${VERSION}"
OutFile "LAMMPS-PLUMED-plugin-${VERSION}.exe"
Name "${PLUMEDPLUGIN}"
InstallDir "$LOCALAPPDATA\${PLUMEDPLUGIN}"
ShowInstDetails show
ShowUninstDetails show
SetCompressor zlib
!define MUI_ABORTWARNING
!insertmacro MUI_PAGE_DIRECTORY
!insertmacro MUI_PAGE_INSTFILES
!insertmacro MUI_UNPAGE_CONFIRM
!insertmacro MUI_UNPAGE_INSTFILES
!insertmacro MUI_LANGUAGE "English"
function .onInit
# Determine if LAMMPS was already installed and check whether it was in 32-bit
# or 64-bit. Then look up path to uninstaller and offer to uninstall or quit
SetRegView 32
ReadRegDWORD $0 HKCU "Software\LAMMPS-PLUMED" "Bits"
SetRegView LastUsed
${If} $0 == "32"
SetRegView 32
${ElseIf} $0 == "64"
SetRegView 64
${Else}
SetRegView 64
${EndIf}
ClearErrors
ReadRegStr $R0 HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-PLUMED" "UninstallString"
SetRegView LastUsed
${If} ${Errors}
DetailPrint "LAMMPS PLUMED plugin not (yet) installed"
${Else}
MessageBox MB_YESNO "LAMMPS PLUMED plugin ($0 bit) is already installed. Uninstall existing version?" /SD IDYES IDNO Quit
Pop $R1
StrCmp $R1 2 Quit +1
Exec $R0
Quit:
Quit
${EndIf}
setShellVarContext all
functionEnd
Section "${PLUMEDPLUGIN}" SecPlumedplugin
SectionIn RO
# Write LAMMPS installation bitness marker. Always use 32-bit registry view
SetRegView 32
IntFmt $0 "0x%08X" 64
WriteRegDWORD HKCU "Software\LAMMPS-PLUMED" "Bits" $0
# Switch to "native" registry view
SetRegView 64
SetShellVarContext current
SetOutPath "$INSTDIR"
CreateDirectory "$INSTDIR\patches"
CreateDirectory "$INSTDIR\bin"
File lammps.ico
File plumedplugin.so
SetOutPath "$INSTDIR\bin"
File plumed.exe
# Register Application and its uninstaller
WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-PLUMED" \
"DisplayName" "${PLUMEDPLUGIN}"
WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-PLUMED" \
"Publisher" "The LAMMPS and PLUMED Developers"
WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-PLUMED" \
"URLInfoAbout" "lammps.org"
WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-PLUMED" \
"DisplayIcon" "$INSTDIR\lammps.ico"
WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-PLUMED" \
"DisplayVersion" "${VERSION}"
WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-PLUMED" \
"InstallLocation" "$INSTDIR"
WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-PLUMED" \
"UninstallString" "$\"$INSTDIR\uninstall.exe$\""
WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-PLUMED" \
"QuietUninstallString" "$\"$INSTDIR\uninstall.exe$\" /S"
${GetSize} "$INSTDIR" "/S=0K" $0 $1 $2
IntFmt $0 "0x%08X" $0
WriteRegDWORD HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-PLUMED" \
"EstimatedSize" "$0"
# update path variables
EnVar::SetHKCU
# add plumed executable path
EnVar::AddValue "PATH" "$INSTDIR\bin"
# add to LAMMPS plugin search path
EnVar::AddValue "LAMMPS_PLUGIN_PATH" "$INSTDIR"
# add plumed2 patch files
EnVar::AddValue "PLUMED_ROOT" "$INSTDIR"
WriteUninstaller "$INSTDIR\Uninstall.exe"
SectionEnd
function un.onInit
SetShellVarContext current
functionEnd
Section "Uninstall"
# remove LAMMPS bitness/installation indicator always in 32-bit registry view
SetRegView 32
DeleteRegKey HKCU "Software\LAMMPS-PLUMED"
# unregister extension, and uninstall info
SetRegView 64
SetShellVarContext current
# unregister installation
DeleteRegKey HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-PLUMED"
# update path variables
EnVar::SetHKCU
# remove plumed executable path
EnVar::DeleteValue "PATH" "$INSTDIR\bin"
# remove entry from LAMMPS plugin search path
EnVar::DeleteValue "LAMMPS_PLUGIN_PATH" "$INSTDIR"
# remove plumed patch environment
EnVar::Delete "PLUMED_ROOT"
RMDir /r /REBOOTOK "$INSTDIR\patches"
RMDir /r /REBOOTOK "$INSTDIR\bin"
Delete /REBOOTOK "$INSTDIR\plumedplugin.so"
Delete /REBOOTOK "$INSTDIR\Uninstall.exe"
Delete /REBOOTOK "$INSTDIR\lammps.ico"
RMDir /REBOOTOK "$INSTDIR"
SectionEnd
# Local Variables:
# mode: sh
# End:

1
examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized
View File

@ -44,6 +44,7 @@ thermo 50
fix myrxns all bond/react stabilization yes statted_grp .03 &
react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map &
react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map rescale_charges yes
fix 1 statted_grp_REACT nvt temp 300 300 100

2
examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized_variable_probability
View File

@ -47,7 +47,7 @@ thermo 50
fix myrxns all bond/react stabilization yes statted_grp .03 &
react rxn1 all 1 0.0 5.0 mol1 mol2 rxn1_stp1_map prob v_prob1 1234 &
react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map prob v_prob2 1234
react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map prob v_prob2 1234 rescale_charges yes
fix 1 statted_grp_REACT nvt temp 300 300 100

2
examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.unstabilized
View File

@ -44,7 +44,7 @@ thermo 50
fix myrxns all bond/react stabilization no &
react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map &
react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map rescale_charges yes
fix 1 all nve/limit .03

21
examples/PACKAGES/reaction/tiny_nylon/rxn1_stp1_reacted.molecule_template
View File

@ -48,27 +48,6 @@ Types
17 hc
18 hc
Charges
1 -0.300000
2 0.000000
3 0.000000
4 0.000000
5 0.000000
6 0.000000
7 0.000000
8 0.000000
9 0.000000
10 0.300000
11 0.000000
12 0.000000
13 0.000000
14 0.000000
15 0.000000
16 0.000000
17 0.000000
18 0.000000
Molecules
1 1

30
examples/PACKAGES/reaction/tiny_nylon/rxn1_stp2_reacted.molecule_template
View File

@ -44,21 +44,21 @@ Types
Charges
1 -0.300000
2 0.000000
3 0.000000
4 0.410000
5 0.000000
6 0.000000
7 0.000000
8 0.000000
9 0.000000
10 0.300000
11 0.000000
12 -0.820000
13 0.000000
14 0.000000
15 0.410000
1 -0.60533
2 -0.01149
3 -0.76306
4 0.38
5 0.29346
6 0.18360
7 0.15396
8 -0.72636
9 -0.27437
10 0.40603
11 -0.65530
12 -0.76
13 0.21423
14 0.18949
15 0.38
Molecules

1263
examples/PACKAGES/reaction/tiny_nylon/tiny_nylon.data
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File diff suppressed because it is too large Load Diff

4
python/lammps/core.py
View File

@ -941,7 +941,7 @@ class lammps(object):
def extract_pair_dimension(self, name):
"""Retrieve pair style property dimensionality from LAMMPS
.. versionadded:: TBD
.. versionadded:: 29Aug2024
This is a wrapper around the :cpp:func:`lammps_extract_pair_dimension`
function of the C-library interface. The list of supported keywords
@ -970,7 +970,7 @@ class lammps(object):
def extract_pair(self, name):
"""Extract pair style data from LAMMPS.
.. versionadded:: TBD
.. versionadded:: 29Aug2024
This is a wrapper around the :cpp:func:`lammps_extract_pair` function
of the C-library interface. Since there are no pointers in Python, this

10
src/CLASS2/angle_class2.cpp
View File

@ -18,17 +18,17 @@
#include "angle_class2.h"
#include <cmath>
#include <cstring>
#include "atom.h"
#include "neighbor.h"
#include "domain.h"
#include "comm.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
#include "neighbor.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
using namespace MathConst;

4
src/INTEL/intel_intrinsics.h
View File

@ -123,7 +123,9 @@ struct vector_ops<double, KNC> {
static fvec recip(const fvec &a) { return _mm512_recip_pd(a); }
template<int scale>
static void gather_prefetch_t0(const ivec &idx, bvec mask, const void *base) {
#ifdef __AVX512PF__
_mm512_mask_prefetch_i32gather_ps(idx, mask, base, scale, _MM_HINT_T0);
#endif
}
template<int scale>
static fvec gather(const fvec &from, bvec mask, const ivec &idx, const void *base) {
@ -262,7 +264,9 @@ struct vector_ops<float, KNC> {
static fvec recip(const fvec &a) { return _mm512_recip_ps(a); }
template<int scale>
static void gather_prefetch_t0(const ivec &idx, bvec mask, const void *base) {
#ifdef __AVX512PF__
_mm512_mask_prefetch_i32gather_ps(idx, mask, base, scale, _MM_HINT_T0);
#endif
}
template<int scale>
static fvec gather(const fvec &from, bvec mask, const ivec &idx, const void *base) {

4
src/INTEL/intel_intrinsics_airebo.h
View File

@ -639,8 +639,10 @@ public:
AVEC_BINOP(-, sub)
VEC_INLINE static void gather_prefetch0(const IVEC_NAME &a, void * mem) {
#ifdef __AVX512PF__
_mm512_mask_prefetch_i32gather_ps(a.val_, BVEC_NAME::full().val_, mem,
sizeof(FVEC_SCAL_T), _MM_HINT_T0);
#endif
}
};
@ -697,8 +699,10 @@ public:
AVEC2_BINOP(-, sub)
VEC_INLINE static void gather_prefetch0(const IVEC_NAME &a, void * mem) {
#ifdef __AVX512PF__
_mm512_mask_prefetch_i32gather_ps(a.val_, BVEC_NAME::full().val_, mem,
sizeof(double), _MM_HINT_T0);
#endif
}
};
#endif

3
src/KOKKOS/fft3d_kokkos.cpp
View File

@ -43,7 +43,6 @@ FFT3dKokkos<DeviceType>::FFT3dKokkos(LAMMPS *lmp, MPI_Comm comm, int nfast, int
#if defined(LMP_KOKKOS_GPU)
int ngpus = lmp->kokkos->ngpus;
ExecutionSpace execution_space = ExecutionSpaceFromDevice<DeviceType>::space;
#endif
#if defined(FFT_KOKKOS_MKL)
if (ngpus > 0 && execution_space == Device)
@ -69,6 +68,8 @@ FFT3dKokkos<DeviceType>::FFT3dKokkos(LAMMPS *lmp, MPI_Comm comm, int nfast, int
if (stack_size < 2048)
cudaDeviceSetLimit(cudaLimitStackSize,2048);
#endif
#endif
#endif
plan = fft_3d_create_plan_kokkos(comm,nfast,nmid,nslow,

9
src/KOKKOS/fix_qeq_reaxff_kokkos.cpp
View File

@ -301,7 +301,7 @@ void FixQEqReaxFFKokkos<DeviceType>::pre_force(int /*vflag*/)
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void FixQEqReaxFFKokkos<DeviceType>::num_neigh_item(int ii, int &maxneigh) const
void FixQEqReaxFFKokkos<DeviceType>::num_neigh_item(int ii, bigint &maxneigh) const
{
const int i = d_ilist[ii];
maxneigh += d_numneigh[i];
@ -316,13 +316,16 @@ void FixQEqReaxFFKokkos<DeviceType>::allocate_matrix()
// determine the total space for the H matrix
m_cap = 0;
bigint m_cap_big = 0;
// limit scope of functor to allow deallocation of views
{
FixQEqReaxFFKokkosNumNeighFunctor<DeviceType> neigh_functor(this);
Kokkos::parallel_reduce(nn,neigh_functor,m_cap);
Kokkos::parallel_reduce(nn,neigh_functor,m_cap_big);
}
if (m_cap_big > MAXSMALLINT)
error->one(FLERR,"Too many neighbors in fix qeq/reaxff");
m_cap = m_cap_big;
// deallocate first to reduce memory overhead

6
src/KOKKOS/fix_qeq_reaxff_kokkos.h
View File

@ -70,7 +70,7 @@ class FixQEqReaxFFKokkos : public FixQEqReaxFF, public KokkosBase {
void pre_force(int) override;
KOKKOS_INLINE_FUNCTION
void num_neigh_item(int, int&) const;
void num_neigh_item(int, bigint&) const;
KOKKOS_INLINE_FUNCTION
void operator()(TagQEqZero, const int&) const;
@ -290,13 +290,13 @@ class FixQEqReaxFFKokkos : public FixQEqReaxFF, public KokkosBase {
template <class DeviceType>
struct FixQEqReaxFFKokkosNumNeighFunctor {
typedef DeviceType device_type;
typedef int value_type;
typedef bigint value_type;
FixQEqReaxFFKokkos<DeviceType> c;
FixQEqReaxFFKokkosNumNeighFunctor(FixQEqReaxFFKokkos<DeviceType>* c_ptr):c(*c_ptr) {
c.cleanup_copy();
};
KOKKOS_INLINE_FUNCTION
void operator()(const int ii, int &maxneigh) const {
void operator()(const int ii, bigint &maxneigh) const {
c.num_neigh_item(ii, maxneigh);
}
};

4
src/KOKKOS/kokkos.cpp
View File

@ -638,10 +638,10 @@ void KokkosLMP::accelerator(int narg, char **arg)
called by Finish
------------------------------------------------------------------------- */
int KokkosLMP::neigh_count(int m)
bigint KokkosLMP::neigh_count(int m)
{
int inum = 0;
int nneigh = 0;
bigint nneigh = 0;
ArrayTypes<LMPHostType>::t_int_1d h_ilist;
ArrayTypes<LMPHostType>::t_int_1d h_numneigh;

2
src/KOKKOS/kokkos.h
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@ -64,7 +64,7 @@ class KokkosLMP : protected Pointers {
static void initialize(const Kokkos::InitializationSettings&, Error *);
static void finalize();
void accelerator(int, char **);
int neigh_count(int);
bigint neigh_count(int);
template<class DeviceType>
int need_dup(int qeq_flag = 0)

8
src/KOKKOS/pair_reaxff_kokkos.cpp
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@ -1504,10 +1504,18 @@ void PairReaxFFKokkos<DeviceType>::allocate_array()
if (cut_hbsq > 0.0) {
MemKK::realloc_kokkos(d_hb_first,"reaxff/kk:hb_first",nmax);
MemKK::realloc_kokkos(d_hb_num,"reaxff/kk:hb_num",nmax);
if (((bigint) nmax*maxhb) > MAXSMALLINT)
error->one(FLERR,"Too many hydrogen bonds in pair reaxff");
MemKK::realloc_kokkos(d_hb_list,"reaxff/kk:hb_list",nmax*maxhb);
}
MemKK::realloc_kokkos(d_bo_first,"reaxff/kk:bo_first",nmax);
MemKK::realloc_kokkos(d_bo_num,"reaxff/kk:bo_num",nmax);
if (((bigint) nmax*maxbo) > MAXSMALLINT)
error->one(FLERR,"Too many bonds in pair reaxff");
MemKK::realloc_kokkos(d_bo_list,"reaxff/kk:bo_list",nmax*maxbo);
MemKK::realloc_kokkos(d_BO,"reaxff/kk:BO",nmax,maxbo);

2
src/KOKKOS/pair_uf3_kokkos.cpp
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@ -1655,7 +1655,7 @@ double PairUF3Kokkos<DeviceType>::single(int /*i*/, int /*j*/, int itype, int jt
namespace LAMMPS_NS {
template class PairUF3Kokkos<LMPDeviceType>;
#ifdef KOKKOS_ENABLE_GPU
#ifdef LMP_KOKKOS_GPU
template class PairUF3Kokkos<LMPHostType>;
#endif
} // namespace LAMMPS_NS

2
src/LATBOLTZ/fix_lb_fluid.cpp
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@ -2416,7 +2416,6 @@ void FixLbFluid::dump(const bigint step)
// Transpose local arrays to fortran-order for paraview output
std::vector<double> density_2_fort(size2);
std::vector<double> velocity_2_fort(size2 * 3);
int indexc = 0;
for (int i = 0; i < subNbx + 3; i++)
for (int j = 0; j < subNby + 3; j++)
for (int k = 0; k < subNbz + 3; k++) {
@ -2424,7 +2423,6 @@ void FixLbFluid::dump(const bigint step)
velocity_2_fort[0 + 3 * (i + (subNbx + 3) * (j + (subNby + 3) * k))] = u_lb[i][j][k][0];
velocity_2_fort[1 + 3 * (i + (subNbx + 3) * (j + (subNby + 3) * k))] = u_lb[i][j][k][1];
velocity_2_fort[2 + 3 * (i + (subNbx + 3) * (j + (subNby + 3) * k))] = u_lb[i][j][k][2];
indexc++;
}
MPI_File_write_all(dump_file_handle_raw, &density_2_fort[0], 1, fluid_density_2_mpitype,

2
src/MDI/fix_mdi_qm.cpp
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@ -1114,7 +1114,7 @@ void FixMDIQM::unit_conversions()
int compare_IDs(const int i, const int j, void *ptr)
{
tagint *ids = (int *) ptr;
tagint *ids = (tagint *) ptr;
if (ids[i] < ids[j]) return -1;
if (ids[i] > ids[j]) return 1;
return 0;

2
src/MDI/fix_mdi_qmmm.cpp
View File

@ -1962,7 +1962,7 @@ void FixMDIQMMM::unit_conversions()
int compare_IDs(const int i, const int j, void *ptr)
{
tagint *ids = (int *) ptr;
tagint *ids = (tagint *) ptr;
if (ids[i] < ids[j]) return -1;
if (ids[i] > ids[j]) return 1;
return 0;

2
src/OPENMP/pair_lj_cut_tip4p_cut_omp.cpp
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@ -120,7 +120,7 @@ void PairLJCutTIP4PCutOMP::eval(int iifrom, int iito, ThrData * const thr)
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul;
double r,rsq,r2inv,r6inv,forcecoul,forcelj,cforce;
double factor_coul,factor_lj;
double v[6];
double v[6] = {0.0, 0.0, 0.0, 0.0, 0.0, 0.0};
double fdx,fdy,fdz,fOx,fOy,fOz,fHx,fHy,fHz;
dbl3_t x1,x2,xH1,xH2;

2
src/OPENMP/pair_lj_cut_tip4p_long_omp.cpp
View File

@ -139,7 +139,7 @@ void PairLJCutTIP4PLongOMP::eval(int iifrom, int iito, ThrData * const thr)
double r,rsq,r2inv,r6inv,forcecoul,forcelj,cforce;
double factor_coul,factor_lj;
double grij,expm2,prefactor,t,erfc;
double v[6];
double v[6] = {0.0, 0.0, 0.0, 0.0, 0.0, 0.0};
double fdx,fdy,fdz,fOx,fOy,fOz,fHx,fHy,fHz;
dbl3_t x1,x2,xH1,xH2;

2
src/OPENMP/pair_lj_cut_tip4p_long_soft_omp.cpp
View File

@ -127,7 +127,7 @@ void PairLJCutTIP4PLongSoftOMP::eval(int iifrom, int iito, ThrData * const thr)
double factor_coul,factor_lj;
double grij,expm2,prefactor,t,erfc;
double denc, denlj, r4sig6;
double v[6];
double v[6] = {0.0, 0.0, 0.0, 0.0, 0.0, 0.0};
double fdx,fdy,fdz,fOx,fOy,fOz,fHx,fHy,fHz;
dbl3_t x1,x2,xH1,xH2;

2
src/OPENMP/pair_lj_long_tip4p_long_omp.cpp
View File

@ -1614,7 +1614,7 @@ void PairLJLongTIP4PLongOMP::eval_outer(int iifrom, int iito, ThrData * const th
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz;
double r2inv,forcecoul,forcelj,cforce, respa_coul, respa_lj, frespa;
double fdx,fdy,fdz,fOx,fOy,fOz,fHx,fHy,fHz;
double v[6];
double v[6] = {0.0, 0.0, 0.0, 0.0, 0.0, 0.0};
dbl3_t x1,x2,xH1,xH2;
const auto * _noalias const x = (dbl3_t *) atom->x[0];

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