Merge remote-tracking branch 'origin/master' into refactor-reading
This commit is contained in:
Richard Berger
3
.gitattributes
vendored
Normal file
3
.gitattributes
vendored
Normal file
@ -0,0 +1,3 @@
|
||||
.gitattributes export-ignore
|
||||
.gitignore export-ignore
|
||||
.github export-ignore
|
||||
@ -72,7 +72,7 @@ endif()
|
||||
# we require C++11 without extensions
|
||||
set(CMAKE_CXX_STANDARD 11)
|
||||
set(CMAKE_CXX_STANDARD_REQUIRED ON)
|
||||
set(CMAKE_CXX_EXTENSIONS OFF)
|
||||
set(CMAKE_CXX_EXTENSIONS OFF CACHE BOOL "Use compiler extensions")
|
||||
|
||||
########################################################################
|
||||
# User input options #
|
||||
@ -747,6 +747,12 @@ if (${_index} GREATER -1)
|
||||
endif()
|
||||
message(STATUS "<<< Linker flags: >>>")
|
||||
message(STATUS "Executable name: ${LAMMPS_BINARY}")
|
||||
if(CMAKE_VERSION VERSION_GREATER_EQUAL 3.13)
|
||||
get_target_property(OPTIONS lammps LINK_OPTIONS)
|
||||
if(OPTIONS)
|
||||
message(STATUS "Linker options: ${OPTIONS}")
|
||||
endif()
|
||||
endif()
|
||||
if(CMAKE_EXE_LINKER_FLAGS)
|
||||
message(STATUS "Executable linker flags: ${CMAKE_EXE_LINKER_FLAGS}")
|
||||
endif()
|
||||
|
||||
@ -52,26 +52,26 @@ add_library(GTest::GTest UNKNOWN IMPORTED)
|
||||
set_target_properties(GTest::GTest PROPERTIES
|
||||
IMPORTED_LOCATION ${GTEST_LIBRARY_PATH}
|
||||
INTERFACE_INCLUDE_DIRECTORIES ${GTEST_INCLUDE_DIR}
|
||||
IMPORTED_LINK_INTERFACE_LIBRARIES ${CMAKE_THREAD_LIBS_INIT})
|
||||
INTERFACE_LINK_LIBRARIES "${CMAKE_THREAD_LIBS_INIT}")
|
||||
add_dependencies(GTest::GTest googletest)
|
||||
|
||||
add_library(GTest::GMock UNKNOWN IMPORTED)
|
||||
set_target_properties(GTest::GMock PROPERTIES
|
||||
IMPORTED_LOCATION ${GMOCK_LIBRARY_PATH}
|
||||
INTERFACE_INCLUDE_DIRECTORIES ${GMOCK_INCLUDE_DIR}
|
||||
IMPORTED_LINK_INTERFACE_LIBRARIES ${CMAKE_THREAD_LIBS_INIT})
|
||||
INTERFACE_LINK_LIBRARIES "${CMAKE_THREAD_LIBS_INIT}")
|
||||
add_dependencies(GTest::GMock googletest)
|
||||
|
||||
add_library(GTest::GTestMain UNKNOWN IMPORTED)
|
||||
set_target_properties(GTest::GTestMain PROPERTIES
|
||||
IMPORTED_LOCATION ${GTEST_MAIN_LIBRARY_PATH}
|
||||
INTERFACE_INCLUDE_DIRECTORIES ${GTEST_INCLUDE_DIR}
|
||||
IMPORTED_LINK_INTERFACE_LIBRARIES ${CMAKE_THREAD_LIBS_INIT})
|
||||
INTERFACE_LINK_LIBRARIES "${CMAKE_THREAD_LIBS_INIT}")
|
||||
add_dependencies(GTest::GTestMain googletest)
|
||||
|
||||
add_library(GTest::GMockMain UNKNOWN IMPORTED)
|
||||
set_target_properties(GTest::GMockMain PROPERTIES
|
||||
IMPORTED_LOCATION ${GMOCK_MAIN_LIBRARY_PATH}
|
||||
INTERFACE_INCLUDE_DIRECTORIES ${GMOCK_INCLUDE_DIR}
|
||||
IMPORTED_LINK_INTERFACE_LIBRARIES ${CMAKE_THREAD_LIBS_INIT})
|
||||
INTERFACE_LINK_LIBRARIES "${CMAKE_THREAD_LIBS_INIT}")
|
||||
add_dependencies(GTest::GMockMain googletest)
|
||||
|
||||
@ -16,6 +16,33 @@ if(ENABLE_TESTING)
|
||||
set(MEMORYCHECK_COMMAND "${VALGRIND_BINARY}" CACHE FILEPATH "Memory Check Command")
|
||||
set(MEMORYCHECK_COMMAND_OPTIONS "${VALGRIND_DEFAULT_OPTIONS}" CACHE STRING "Memory Check Command Options")
|
||||
|
||||
# check if a faster linker is available.
|
||||
# only verified with GNU and Clang compilers and new CMake
|
||||
if(CMAKE_VERSION VERSION_GREATER_EQUAL 3.13)
|
||||
if((${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
|
||||
OR (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang"))
|
||||
include(CheckCXXCompilerFlag)
|
||||
set(CMAKE_CUSTOM_LINKER_DEFAULT default)
|
||||
check_cxx_compiler_flag(-fuse-ld=lld HAVE_LLD_LINKER)
|
||||
check_cxx_compiler_flag(-fuse-ld=gold HAVE_GOLD_LINKER)
|
||||
check_cxx_compiler_flag(-fuse-ld=bfd HAVE_BFD_LINKER)
|
||||
if(HAVE_LLD_LINKER)
|
||||
set(CMAKE_CUSTOM_LINKER_DEFAULT lld)
|
||||
elseif(HAVE_GOLD_LINKER)
|
||||
set(CMAKE_CUSTOM_LINKER_DEFAULT gold)
|
||||
elseif(HAVE_BFD_LINKER)
|
||||
set(CMAKE_CUSTOM_LINKER_DEFAULT bfd)
|
||||
endif()
|
||||
set(CMAKE_CUSTOM_LINKER_VALUES lld gold bfd default)
|
||||
set(CMAKE_CUSTOM_LINKER ${CMAKE_CUSTOM_LINKER_DEFAULT} CACHE STRING "Choose a custom linker for faster linking (lld, gold, bfd, default)")
|
||||
validate_option(CMAKE_CUSTOM_LINKER CMAKE_CUSTOM_LINKER_VALUES)
|
||||
mark_as_advanced(CMAKE_CUSTOM_LINKER)
|
||||
if(NOT "${CMAKE_CUSTOM_LINKER}" STREQUAL "default")
|
||||
target_link_options(lammps PUBLIC -fuse-ld=${CMAKE_CUSTOM_LINKER})
|
||||
endif()
|
||||
endif()
|
||||
endif()
|
||||
|
||||
include(CTest)
|
||||
|
||||
enable_testing()
|
||||
|
||||
@ -83,7 +83,7 @@ html: $(ANCHORCHECK) $(MATHJAX)
|
||||
@rm -rf html/JPG
|
||||
@cp -r src/PDF html/PDF
|
||||
@mkdir -p html/JPG
|
||||
@cp `grep -A2 '\.\. .*\(image\|figure\)::' src/*.rst | grep ':target:' | sed -e 's,.*:target: JPG/,src/JPG/,' | sort | uniq` html/JPG/
|
||||
@cp `grep -A2 '\.\. .*\(image\|figure\)::' src/*.rst | grep ':target: JPG' | sed -e 's,.*:target: JPG/,src/JPG/,' | sort | uniq` html/JPG/
|
||||
@rm -rf html/PDF/.[sg]*
|
||||
@mkdir -p html/_static/mathjax
|
||||
@cp -r $(MATHJAX)/es5 html/_static/mathjax/
|
||||
@ -194,9 +194,7 @@ $(VENV):
|
||||
$(VIRTUALENV) -p $(PYTHON) $(VENV); \
|
||||
. $(VENV)/bin/activate; \
|
||||
pip install --upgrade pip; \
|
||||
pip install Sphinx; \
|
||||
pip install sphinxcontrib-spelling ;\
|
||||
pip install breathe; \
|
||||
pip install -r requirements.txt; \
|
||||
deactivate;\
|
||||
)
|
||||
|
||||
|
||||
@ -1,4 +1,4 @@
|
||||
.TH LAMMPS "30 June 2020" "2020-06-30"
|
||||
.TH LAMMPS "21 July 2020" "2020-07-21"
|
||||
.SH NAME
|
||||
.B LAMMPS
|
||||
\- Molecular Dynamics Simulator.
|
||||
|
||||
4
doc/requirements.txt
Normal file
4
doc/requirements.txt
Normal file
@ -0,0 +1,4 @@
|
||||
Sphinx
|
||||
sphinxcontrib-spelling
|
||||
breathe
|
||||
Pygments
|
||||
@ -259,6 +259,23 @@ and working.
|
||||
of mis-compiled code (or an undesired large loss of precision due
|
||||
to significant reordering of operations and thus less error cancellation).
|
||||
|
||||
Use custom linker for faster link times when ENABLE_TESTING is active
|
||||
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
||||
|
||||
When compiling LAMMPS with enabled tests, most test executables will
|
||||
need to be linked against the LAMMPS library. Since this can be a
|
||||
large with many C++ objects when many packages are enabled, link times
|
||||
can become very long on machines that use the GNU BFD linker (e.g.
|
||||
Linux systems). Alternatives like the ``lld`` linker of the LLVM project
|
||||
or the ``gold`` linker available with GNU binutils can speed up this step
|
||||
substantially. CMake will by default test if any of the two can be
|
||||
enabled and use it when ``ENABLE_TESTING`` is active. It can also be
|
||||
selected manually through the ``CMAKE_CUSTOM_LINKER`` CMake variable.
|
||||
Allowed values are ``lld``, ``gold``, ``bfd``, or ``default``. The
|
||||
``default`` option will use the system default linker otherwise, the
|
||||
linker is chosen explicitly. This option is only available for the
|
||||
GNU or Clang C++ compiler.
|
||||
|
||||
Tests for other components and utility functions
|
||||
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
||||
|
||||
|
||||
@ -38,7 +38,7 @@ optional Windows feature allows you to run the bash shell from Ubuntu
|
||||
from within Windows and from there on, you can pretty much use that
|
||||
shell like you are running on an Ubuntu Linux machine (e.g. installing
|
||||
software via apt-get and more). For more details on that, please
|
||||
see :doc:`this tutorial <Howto_bash>`
|
||||
see :doc:`this tutorial <Howto_wsl>`
|
||||
|
||||
.. _gnu:
|
||||
|
||||
|
||||
@ -244,3 +244,4 @@ OPT.
|
||||
* :doc:`wall/region <fix_wall_region>`
|
||||
* :doc:`wall/region/ees <fix_wall_ees>`
|
||||
* :doc:`wall/srd <fix_wall_srd>`
|
||||
* :doc:`widom <fix_widom>`
|
||||
|
||||
@ -19,7 +19,7 @@ Tutorials howto
|
||||
Howto_cmake
|
||||
Howto_github
|
||||
Howto_pylammps
|
||||
Howto_bash
|
||||
Howto_wsl
|
||||
|
||||
General howto
|
||||
=============
|
||||
|
||||
@ -1,264 +0,0 @@
|
||||
Using LAMMPS with Bash on Windows
|
||||
=================================
|
||||
|
||||
**written by Richard Berger**
|
||||
|
||||
----------
|
||||
|
||||
Starting with Windows 10 you can install Linux tools directly in Windows. This
|
||||
allows you to compile LAMMPS following the same procedure as on a real Ubuntu
|
||||
Linux installation. Software can be easily installed using the package manager
|
||||
via apt-get and all files are accessible in both the Windows Explorer and your
|
||||
Linux shell (bash). This avoids switching to a different operating system or
|
||||
installing a virtual machine. Everything runs on Windows.
|
||||
|
||||
.. seealso::
|
||||
|
||||
You can find more detailed information at the `Windows Subsystem for Linux Installation Guide for Windows 10 <https://docs.microsoft.com/en-us/windows/wsl/install-win10>`_.
|
||||
|
||||
Installing Bash on Windows
|
||||
--------------------------
|
||||
|
||||
Prerequisites
|
||||
^^^^^^^^^^^^^
|
||||
|
||||
* Windows 10 (64bit only)
|
||||
* Latest updates installed
|
||||
|
||||
Enable developer mode
|
||||
^^^^^^^^^^^^^^^^^^^^^
|
||||
|
||||
You enable this feature by first opening Windows Settings and enabling
|
||||
Developer mode. Go to the Windows settings and search for "developer". This
|
||||
will allow you to install software which comes from outside of the Windows
|
||||
Store. You might be prompted to reboot your compute. Please do so.
|
||||
|
||||
.. image:: JPG/bow_tutorial_01_small.png
|
||||
:target: JPG/bow_tutorial_01.png
|
||||
|
||||
.. image:: JPG/bow_tutorial_02_small.png
|
||||
:target: JPG/bow_tutorial_02.png
|
||||
|
||||
.. image:: JPG/bow_tutorial_03_small.png
|
||||
:target: JPG/bow_tutorial_03.png
|
||||
|
||||
Install Windows Subsystem for Linux
|
||||
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
||||
|
||||
Next you must ensure that the Window Subsystem for Linux is installed. Again,
|
||||
search for "enable windows features" in the Settings dialog. This opens a
|
||||
dialog with a list of features you can install. Add a checkmark to Windows
|
||||
Subsystem for Linux (Beta) and press OK.
|
||||
|
||||
.. image:: JPG/bow_tutorial_04_small.png
|
||||
:target: JPG/bow_tutorial_04.png
|
||||
|
||||
.. image:: JPG/bow_tutorial_05.png
|
||||
:target: JPG/bow_tutorial_05.png
|
||||
|
||||
Install Bash for Windows
|
||||
^^^^^^^^^^^^^^^^^^^^^^^^
|
||||
|
||||
After installation completes, type "bash" in the Windows Start menu search.
|
||||
Select the first found option. This will launch a command-line window which
|
||||
will prompt you about installing Ubuntu on Windows. Confirm with "y" and press
|
||||
enter. This will then download Ubuntu for Windows.
|
||||
|
||||
.. image:: JPG/bow_tutorial_06.png
|
||||
|
||||
.. image:: JPG/bow_tutorial_07.png
|
||||
|
||||
During installation, you will be asked for a new password. This will be used
|
||||
for installing new software and running commands with sudo.
|
||||
|
||||
.. image:: JPG/bow_tutorial_08.png
|
||||
|
||||
Type exit to close the command-line window.
|
||||
|
||||
Go to the Start menu and type "bash" again. This time you will see a "Bash on
|
||||
Ubuntu on Windows" Icon. Start this program.
|
||||
|
||||
.. image:: JPG/bow_tutorial_09.png
|
||||
|
||||
Congratulations, you have installed **Bash on Ubuntu on Windows**\ .
|
||||
|
||||
.. image:: JPG/bow_tutorial_10.png
|
||||
|
||||
----------
|
||||
|
||||
Compiling LAMMPS in Bash on Windows
|
||||
-----------------------------------
|
||||
|
||||
The installation of LAMMPS in this environment is identical to working inside
|
||||
of a real Ubuntu Linux installation. At the time writing, it uses Ubuntu 16.04.
|
||||
|
||||
Installing prerequisite packages
|
||||
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
||||
|
||||
First upgrade all existing packages using
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
sudo apt update
|
||||
sudo apt upgrade -y
|
||||
|
||||
Next install the following packages, which include compilers and libraries
|
||||
needed for various LAMMPS features:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
sudo apt install -y build-essential ccache gfortran openmpi-bin libopenmpi-dev libfftw3-dev libjpeg-dev libpng-dev python-dev python-virtualenv libblas-dev liblapack-dev libhdf5-serial-dev hdf5-tools
|
||||
|
||||
Files in Ubuntu on Windows
|
||||
^^^^^^^^^^^^^^^^^^^^^^^^^^
|
||||
|
||||
When you launch "Bash on Ubuntu on Windows" you will start out in your Linux
|
||||
user home directory /home/[username]\ . You can access your Windows user directory
|
||||
using the /mnt/c/Users/[username] folder.
|
||||
|
||||
Download LAMMPS
|
||||
^^^^^^^^^^^^^^^
|
||||
|
||||
Obtain a copy of the LAMMPS code and go into it using "cd"
|
||||
|
||||
Option 1: Downloading LAMMPS tarball using wget
|
||||
"""""""""""""""""""""""""""""""""""""""""""""""
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
wget https://lammps.sandia.gov/tars/lammps-stable.tar.gz
|
||||
tar xvzf lammps-stable.tar.gz
|
||||
cd lammps-31Mar17
|
||||
|
||||
Option 2: Obtaining LAMMPS code from GitHub
|
||||
"""""""""""""""""""""""""""""""""""""""""""
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
git clone https://github.com/lammps/lammps.git
|
||||
cd lammps
|
||||
|
||||
Compiling LAMMPS
|
||||
^^^^^^^^^^^^^^^^
|
||||
|
||||
At this point you can compile LAMMPS like on Ubuntu Linux.
|
||||
|
||||
Compiling serial version
|
||||
""""""""""""""""""""""""
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
cd src/
|
||||
make -j 4 serial
|
||||
|
||||
This will create an executable called lmp_serial in the src/ directory
|
||||
|
||||
Compiling MPI version
|
||||
"""""""""""""""""""""
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
cd src/
|
||||
make -j 4 mpi
|
||||
|
||||
This will create an executable called lmp_mpi in the src/ directory
|
||||
|
||||
----------
|
||||
|
||||
Finally, please note the absolute path of your src folder. You can get this using
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
pwd
|
||||
|
||||
or
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
echo $PWD
|
||||
|
||||
To run any examples you need the location of the executable. For now, let us
|
||||
save this location in a temporary variable
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
LAMMPS_DIR=$PWD
|
||||
|
||||
----------
|
||||
|
||||
Running an example script
|
||||
^^^^^^^^^^^^^^^^^^^^^^^^^
|
||||
|
||||
Once compiled you can execute some of the LAMMPS examples. Switch into the
|
||||
examples/melt folder
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
cd ../examples/melt
|
||||
|
||||
The full path of the serial executable is $LAMMPS_DIR/lmp_serial, while the mpi
|
||||
version is $LAMMPS_DIR/lmp_mpi. You can run the melt example with either
|
||||
version as follows:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
$LAMMPS_DIR/lmp_serial -in in.melt
|
||||
|
||||
or
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
mpirun -np 4 $LAMMPS_DIR/lmp_mpi -in in.melt
|
||||
|
||||
Note the use of our variable $LAMMPS_DIR, which expands into the full path of
|
||||
the LAMMPS src folder we saved earlier.
|
||||
|
||||
Adding your executable directory to your PATH
|
||||
"""""""""""""""""""""""""""""""""""""""""""""
|
||||
|
||||
You can avoid having to type the full path of your LAMMPS binary by adding its
|
||||
parent folder to the PATH environment variable as follows:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
export PATH=$LAMMPS_DIR:$PATH
|
||||
|
||||
Input scripts can then be run like this:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
lmp_serial -in in.melt
|
||||
|
||||
or
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
mpirun -np 4 lmp_mpi -in in.melt
|
||||
|
||||
However, this PATH variable will not persist if you close your bash window.
|
||||
To persist this setting edit the $HOME/.bashrc file using your favorite editor
|
||||
and add this line
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
export PATH=/full/path/to/your/lammps/src:$PATH
|
||||
|
||||
**Example:**
|
||||
|
||||
For an executable lmp_serial with a full path
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
/home/richard/lammps/src/lmp_serial
|
||||
|
||||
the PATH variable should be
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
export PATH=/home/richard/lammps/src:$PATH
|
||||
|
||||
.. note::
|
||||
|
||||
This should give you a jump start when trying to run LAMMPS on Windows.
|
||||
To become effective in this environment I encourage you to look into Linux
|
||||
tutorials explaining Bash and Basic Unix commands (e.g., `Linux Journey <https://linuxjourney.com>`_)
|
||||
@ -47,7 +47,7 @@ using a shell like Bash.
|
||||
|
||||
- Linux: any Terminal window will work
|
||||
- MacOS X: launch the Terminal application.
|
||||
- Windows 10: install and run the :doc:`Windows subsystem for Linux <Howto_bash>`
|
||||
- Windows 10: install and run the :doc:`Windows Subsystem for Linux <Howto_wsl>`
|
||||
|
||||
We also assume that you have downloaded and unpacked a recent LAMMPS source code package
|
||||
or used Git to create a clone of the LAMMPS sources on your compilation machine.
|
||||
|
||||
359
doc/src/Howto_wsl.rst
Normal file
359
doc/src/Howto_wsl.rst
Normal file
@ -0,0 +1,359 @@
|
||||
Using LAMMPS on Windows 10 with WSL
|
||||
###################################
|
||||
|
||||
**written by Richard Berger**
|
||||
|
||||
----------
|
||||
|
||||
It's always been tricky for us to have LAMMPS users and developers work on
|
||||
Windows. We primarily develop LAMMPS to run on Linux clusters. To teach
|
||||
LAMMPS in workshop settings, we had to redirect Windows users to
|
||||
Linux Virtual Machines such as VirtualBox or Unix-like compilation with
|
||||
Cygwin.
|
||||
|
||||
With the latest updates in Windows 10 (Version 2004, Build 19041 or higher),
|
||||
Microsoft has added a new way to work on Linux-based code. The Windows
|
||||
Subsystem for Linux (WSL). With WSL Version 2, you now get a Linux Virtual
|
||||
Machine that transparently integrates into Windows. All you need is to ensure
|
||||
you have the latest Windows updates installed and enable this new feature.
|
||||
Linux VMs are then easily installed using the Microsoft Store.
|
||||
|
||||
In this tutorial, I'll show you how to set up and compile LAMMPS for both serial
|
||||
and MPI usage in WSL2.
|
||||
|
||||
Installation
|
||||
============
|
||||
|
||||
Upgrade to the latest Windows 10
|
||||
--------------------------------
|
||||
|
||||
Type "Updates" in Windows Start and select "Check for Updates".
|
||||
|
||||
.. image:: img/wsl_tutorial/updates.png
|
||||
:scale: 50%
|
||||
|
||||
Install all pending updates and reboot your system as many times as
|
||||
necessary. Continue until your Windows installation is updated.
|
||||
|
||||
.. image:: img/wsl_tutorial/windows_update.png
|
||||
:scale: 50%
|
||||
|
||||
Verify your system has at least **version 2004 and build 19041 or later**. You
|
||||
can find this information by clicking on "OS build info".
|
||||
|
||||
.. image:: img/wsl_tutorial/osinfo.png
|
||||
:scale: 50%
|
||||
|
||||
Enable WSL
|
||||
----------
|
||||
Next, we must install two additional Windows features to enable WSL support.
|
||||
Open a PowerShell window as an administrator. Type "PowerShell" in Windows
|
||||
Start and select "Run as Administrator".
|
||||
|
||||
.. image:: img/wsl_tutorial/powershell.png
|
||||
:scale: 50%
|
||||
|
||||
Windows will ask you for administrator access. After you accept a new command
|
||||
line window will appear. Type in the following command to install WSL:
|
||||
|
||||
.. code-block::
|
||||
|
||||
dism.exe /online /enable-feature /featurename:Microsoft-Windows-Subsystem-Linux /all /norestart
|
||||
|
||||
.. image:: img/wsl_tutorial/wsl_install1.png
|
||||
|
||||
Next, enable the VirtualMachinePlatform feature using the following command:
|
||||
|
||||
.. code-block::
|
||||
|
||||
dism.exe /online /enable-feature /featurename:VirtualMachinePlatform /all /norestart
|
||||
|
||||
.. image:: img/wsl_tutorial/wsl_install2.png
|
||||
|
||||
Finally, reboot your system.
|
||||
|
||||
Update WSL kernel component
|
||||
---------------------------
|
||||
|
||||
Download and install the :download:`WSL Kernel Component Update <https://wslstorestorage.blob.core.windows.net/wslblob/wsl_update_x64.msi>`.
|
||||
Afterwards, reboot your system.
|
||||
|
||||
Set WSL2 as default
|
||||
-------------------
|
||||
|
||||
Again, open PowerShell as administrator and run the following command:
|
||||
|
||||
.. code-block:: powershell
|
||||
|
||||
wsl --set-default-version 2
|
||||
|
||||
This command ensures that all future Linux installations will use WSL version 2.
|
||||
|
||||
.. image:: img/wsl_tutorial/wsl_install3.png
|
||||
|
||||
Install a Linux Distribution
|
||||
----------------------------
|
||||
Next, we need to install a Linux distribution via the Microsoft Store.
|
||||
Install `Ubuntu 20.04 LTS <ms-windows-store://pdp/?ProductId=9n6svws3rx71>`_.
|
||||
Once installed, you can launch it like any other application from the Start
|
||||
Menu.
|
||||
|
||||
.. image:: img/wsl_tutorial/ubuntu_in_store.png
|
||||
:scale: 50%
|
||||
|
||||
Initial Setup
|
||||
^^^^^^^^^^^^^
|
||||
The first time you launch the Ubuntu Linux console, it will prompt you for a
|
||||
UNIX username and password. You will need this password to perform :code:`sudo`
|
||||
commands later. Once completed, your Linux shell is ready for use. All your
|
||||
actions and commands will run as the Linux user you specified.
|
||||
|
||||
.. image:: img/wsl_tutorial/first_login.png
|
||||
:scale: 50%
|
||||
|
||||
Windows Explorer / WSL integration
|
||||
==================================
|
||||
|
||||
Your Linux installation will have its own Linux filesystem, which contains
|
||||
the Ubuntu files. Your Linux user will have a regular Linux home directory in
|
||||
:code:`/home/<USERNAME>`. This directory is different from your Windows User
|
||||
directory. Windows and Linux filesystems are connected through WSL.
|
||||
|
||||
All hard drives in Windows are accessible in the :code:`/mnt` directory in Linux.
|
||||
E.g., WSL maps the :code:`C` hard drive to the :code:`/mnt/c` directory. That means you
|
||||
can access your Windows User directory in :code:`/mnt/c/Users/<WINDOWS_USERNAME>`.
|
||||
|
||||
The Windows Explorer can also access the Linux filesystem. To illustrate this
|
||||
integration, open an Ubuntu console and navigate to a directory of your
|
||||
choice. To view this location in Windows Explorer, use the :code:`explorer.exe .`
|
||||
command (do not forget the final dot!).
|
||||
|
||||
.. image:: img/wsl_tutorial/wsl_integration.png
|
||||
:scale: 50%
|
||||
|
||||
--------
|
||||
|
||||
Compiling LAMMPS
|
||||
================
|
||||
|
||||
You now have a fully functioning Ubuntu installation and can follow most
|
||||
guides to install LAMMPS on a Linux system. Here are some of the essential
|
||||
steps to follow:
|
||||
|
||||
Install prerequisite packages
|
||||
-----------------------------
|
||||
|
||||
Before we can begin, we need to download the necessary compiler toolchain and
|
||||
libraries to compile LAMMPS. In our Ubuntu-based Linux installation, we will
|
||||
use the :code:`apt` package manager to install additional packages.
|
||||
|
||||
First, upgrade all existing packages using :code:`apt update` and :code:`apt upgrade`.
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
sudo apt update
|
||||
sudo apt upgrade -y
|
||||
|
||||
Next, install the following packages with :code:`apt install`:
|
||||
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
sudo apt install -y cmake build-essential ccache gfortran openmpi-bin libopenmpi-dev \
|
||||
libfftw3-dev libjpeg-dev libpng-dev python3-dev python3-pip \
|
||||
python3-virtualenv libblas-dev liblapack-dev libhdf5-serial-dev \
|
||||
hdf5-tools
|
||||
|
||||
Download LAMMPS
|
||||
---------------
|
||||
|
||||
Obtain a copy of the LAMMPS source code and go into it using the :code:`cd` command.
|
||||
|
||||
Option 1: Download a LAMMPS tarball using wget
|
||||
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
wget https://github.com/lammps/lammps/archive/stable_3Mar2020.tar.gz
|
||||
tar xvzf stable_3Mar2020.tar.gz
|
||||
cd lammps
|
||||
|
||||
Option 2: Download a LAMMPS development version from GitHub
|
||||
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
git clone --depth=1 https://github.com/lammps/lammps.git
|
||||
cd lammps
|
||||
|
||||
|
||||
Configure and Compile LAMMPS with CMake
|
||||
---------------------------------------
|
||||
|
||||
A beginner-friendly way to compile LAMMPS is to use CMake. Create a :code:`build`
|
||||
directory to compile LAMMPS and move into it. This directory will store the
|
||||
build configuration and any binaries generated during compilation.
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
mkdir build
|
||||
cd build
|
||||
|
||||
There are countless ways to compile LAMMPS. It is beyond the scope of this
|
||||
tutorial. If you want to find out more about what can be enabled, please
|
||||
consult the extensive `documentation <https://lammps.sandia.gov/doc/Build_cmake.html>`_.
|
||||
|
||||
To compile a minimal version of LAMMPS, we're going to use a preset.
|
||||
Presets are a way to specify a collection of CMake options using a file.
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
cmake ../cmake/presets/minimal.cmake ../cmake
|
||||
|
||||
This command configures the build and generates the necessary Makefiles. To compile the binary, run the make command.
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
make -j 4
|
||||
|
||||
The :code:`-j` option specifies how many parallel processes will perform the
|
||||
compilation. This option can significantly speed up compilation times. Use a
|
||||
number that corresponds to the number of processors in your system.
|
||||
|
||||
After the compilation completes successfully, you will have an executable
|
||||
called :code:`lmp` in the :code:`build` directory.
|
||||
|
||||
.. image:: img/wsl_tutorial/compilation_result.png
|
||||
:scale: 50%
|
||||
|
||||
Please take note of the absolute path of your :code:`build` directory. You will
|
||||
need to know the location to execute the LAMMPS binary later.
|
||||
|
||||
One way of getting the absolute path of the current directory is through the
|
||||
:code:`$PWD` variable:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
# prints out the current value of the PWD variable
|
||||
echo $PWD
|
||||
|
||||
Let us save this value in a temporary variable :code:`LAMMPS_BUILD_DIR` for future use:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
LAMMPS_BUILD_DIR=$PWD
|
||||
|
||||
The full path of the LAMMPS binary then is :code:`$LAMMPS_BUILD_DIR/lmp`.
|
||||
|
||||
------------
|
||||
|
||||
Running an example script
|
||||
=========================
|
||||
|
||||
Now that we have a LAMMPS binary, we will run a script from the examples folder.
|
||||
|
||||
Switch into the :code:`examples/melt` folder:
|
||||
|
||||
.. code-block::
|
||||
|
||||
cd ../examples/melt
|
||||
|
||||
To run this example in serial, use the following command line:
|
||||
|
||||
.. code-block::
|
||||
|
||||
$LAMMPS_BUILD_DIR/lmp -in in.melt
|
||||
|
||||
To run the same script in parallel using MPI with 4 processes, do the following:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
mpirun -np 4 $LAMMPS_BUILD_DIR/lmp -in in.melt
|
||||
|
||||
If you run LAMMPS for the first time, the Windows Firewall might prompt you
|
||||
to confirm access. LAMMPS is accessing the network stack to enable parallel
|
||||
computation. Allow the access.
|
||||
|
||||
.. image:: img/wsl_tutorial/windows_firewall.png
|
||||
:scale: 75%
|
||||
|
||||
In either serial or MPI case, LAMMPS executes and will output something similar to this:
|
||||
|
||||
.. code-block::
|
||||
|
||||
LAMMPS (30 Jun 2020)
|
||||
...
|
||||
...
|
||||
...
|
||||
Total # of neighbors = 151513
|
||||
Ave neighs/atom = 37.878250
|
||||
Neighbor list builds = 12
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:00
|
||||
|
||||
**Congratulations! You've successfully compiled and executed LAMMPS on WSL!**
|
||||
|
||||
Final steps
|
||||
===========
|
||||
|
||||
It is cumbersome to always specify the path of your LAMMPS binary. You can
|
||||
avoid this by adding the absolute path of your :code:`build` directory to your PATH
|
||||
environment variable.
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
export PATH=$LAMMPS_BUILD_DIR:$PATH
|
||||
|
||||
You can then run LAMMPS input scripts like this:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
lmp -in in.melt
|
||||
|
||||
or
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
mpirun -np 4 lmp -in in.melt
|
||||
|
||||
.. note::
|
||||
|
||||
The value of this :code:`PATH` variable will disappear once you close your
|
||||
console window. To persist this setting edit the :code:`$HOME/.bashrc` file using your
|
||||
favorite text editor and add this line:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
export PATH=/full/path/to/your/lammps/build:$PATH
|
||||
|
||||
**Example:**
|
||||
If the LAMMPS executable `lmp` has the following absolute path:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
/home/<USERNAME>/lammps/build/lmp
|
||||
|
||||
the :code:`PATH` variable should be:
|
||||
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
export PATH=/home/<USERNAME>/lammps/build:$PATH
|
||||
|
||||
Once set up, all your Ubuntu consoles will always have access to your :code:`lmp`
|
||||
binary without having to specify its location.
|
||||
|
||||
Conclusion
|
||||
==========
|
||||
I hope this gives you good overview on how to start compiling and running LAMMPS on
|
||||
Windows. WSL makes preparing and running scripts on Windows a much better
|
||||
experience.
|
||||
|
||||
If you are completely new to Linux, I highly recommend investing some time in
|
||||
studying Linux online tutorials. E.g., tutorials about Bash Shell and Basic
|
||||
Unix commands (e.g., `Linux Journey <https://linuxjourney.com/>`_). Acquiring
|
||||
these skills will make you much more productive in this environment.
|
||||
|
||||
.. seealso::
|
||||
|
||||
* `Windows Subsystem for Linux Documentation <https://docs.microsoft.com/en-us/windows/wsl/>`_
|
||||
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@ -80,16 +80,23 @@ See the python/README file for instructions on how to run them and the
|
||||
source code for individual scripts for comments about what they do.
|
||||
|
||||
Here are screenshots of the vizplotgui_tool.py script in action for
|
||||
different visualization package options. Click to see larger images:
|
||||
different visualization package options:
|
||||
|
||||
.. image:: JPG/screenshot_gl_small.jpg
|
||||
:target: JPG/screenshot_gl.jpg
|
||||
.. |pyex1| image:: img/screenshot_gl.jpg
|
||||
:width: 24%
|
||||
|
||||
.. image:: JPG/screenshot_atomeye_small.jpg
|
||||
:target: JPG/screenshot_atomeye.jpg
|
||||
.. |pyex2| image:: img/screenshot_atomeye.jpg
|
||||
:width: 24%
|
||||
|
||||
.. image:: JPG/screenshot_pymol_small.jpg
|
||||
:target: JPG/screenshot_pymol.jpg
|
||||
.. |pyex3| image:: img/screenshot_pymol.jpg
|
||||
:width: 24%
|
||||
|
||||
.. |pyex4| image:: img/screenshot_vmd.jpg
|
||||
:width: 24%
|
||||
|
||||
|pyex1| |pyex2| |pyex3| |pyex4|
|
||||
|
||||
.. raw:: html
|
||||
|
||||
Click to see larger versions of the images.
|
||||
|
||||
.. image:: JPG/screenshot_vmd_small.jpg
|
||||
:target: JPG/screenshot_vmd.jpg
|
||||
|
||||
@ -78,7 +78,7 @@ above, create a test.py file containing these lines:
|
||||
pypar.finalize()
|
||||
|
||||
To run LAMMPS in parallel, assuming you have installed the
|
||||
`mpi4py <https://bitbucket.org/mpi4py/mpi4py>`_ package as discussed
|
||||
`mpi4py <https://mpi4py.readthedocs.io>`_ package as discussed
|
||||
above, create a test.py file containing these lines:
|
||||
|
||||
.. code-block:: python
|
||||
|
||||
17
doc/src/accel_styles.rst
Normal file
17
doc/src/accel_styles.rst
Normal file
@ -0,0 +1,17 @@
|
||||
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
|
||||
:doc:`suffix <suffix>` command in your input script.
|
||||
|
||||
See the :doc:`Speed packages <Speed_packages>` doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
@ -95,23 +95,7 @@ since it is the same value from the :math:`E_a` formula.
|
||||
|
||||
----------
|
||||
|
||||
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
|
||||
:doc:`suffix <suffix>` command in your input script.
|
||||
|
||||
See the :doc:`Speed packages <Speed_packages>` doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
----------
|
||||
|
||||
|
||||
@ -44,23 +44,7 @@ or :doc:`read_restart <read_restart>` commands:
|
||||
|
||||
----------
|
||||
|
||||
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
|
||||
:doc:`suffix <suffix>` command in your input script.
|
||||
|
||||
See the :doc:`Speed packages <Speed_packages>` doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
----------
|
||||
|
||||
|
||||
@ -46,23 +46,7 @@ internally.
|
||||
|
||||
----------
|
||||
|
||||
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
|
||||
:doc:`suffix <suffix>` command in your input script.
|
||||
|
||||
See the :doc:`Speed packages <Speed_packages>` doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
----------
|
||||
|
||||
|
||||
@ -54,23 +54,7 @@ geometry.
|
||||
|
||||
----------
|
||||
|
||||
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
|
||||
:doc:`suffix <suffix>` command in your input script.
|
||||
|
||||
See the :doc:`Speed packages <Speed_packages>` doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
----------
|
||||
|
||||
|
||||
@ -45,23 +45,7 @@ or :doc:`read_restart <read_restart>` commands:
|
||||
|
||||
----------
|
||||
|
||||
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
|
||||
:doc:`suffix <suffix>` command in your input script.
|
||||
|
||||
See the :doc:`Speed packages <Speed_packages>` doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
----------
|
||||
|
||||
|
||||
@ -56,23 +56,7 @@ or :doc:`read_restart <read_restart>` commands:
|
||||
|
||||
----------
|
||||
|
||||
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
|
||||
:doc:`suffix <suffix>` command in your input script.
|
||||
|
||||
See the :doc:`Speed packages <Speed_packages>` doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
----------
|
||||
|
||||
|
||||
@ -46,23 +46,7 @@ internally.
|
||||
|
||||
----------
|
||||
|
||||
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
|
||||
:doc:`suffix <suffix>` command in your input script.
|
||||
|
||||
See the :doc:`Speed packages <Speed_packages>` doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
----------
|
||||
|
||||
|
||||
@ -82,23 +82,7 @@ or :doc:`read_restart <read_restart>` commands:
|
||||
|
||||
----------
|
||||
|
||||
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
|
||||
:doc:`suffix <suffix>` command in your input script.
|
||||
|
||||
See the :doc:`Speed packages <Speed_packages>` doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
@ -42,23 +42,7 @@ or :doc:`read_restart <read_restart>` commands:
|
||||
|
||||
----------
|
||||
|
||||
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
|
||||
:doc:`suffix <suffix>` command in your input script.
|
||||
|
||||
See the :doc:`Speed packages <Speed_packages>` doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
----------
|
||||
|
||||
|
||||
@ -41,23 +41,7 @@ or :doc:`read_restart <read_restart>` commands:
|
||||
|
||||
----------
|
||||
|
||||
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
|
||||
:doc:`suffix <suffix>` command in your input script.
|
||||
|
||||
See the :doc:`Speed packages <Speed_packages>` doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
----------
|
||||
|
||||
|
||||
@ -53,25 +53,7 @@ radian\^2.
|
||||
|
||||
----------
|
||||
|
||||
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the :doc:`Build package
|
||||
<Build_package>` doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the :doc:`-suffix
|
||||
command-line switch <Run_options>` when you invoke LAMMPS, or you can
|
||||
use the :doc:`suffix <suffix>` command in your input script.
|
||||
|
||||
See the :doc:`Speed packages <Speed_packages>` doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
----------
|
||||
|
||||
|
||||
@ -49,23 +49,7 @@ per radian\^2 or radian\^3 or radian\^4.
|
||||
|
||||
----------
|
||||
|
||||
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
|
||||
:doc:`suffix <suffix>` command in your input script.
|
||||
|
||||
See the :doc:`Speed packages <Speed_packages>` doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
----------
|
||||
|
||||
|
||||
@ -56,24 +56,7 @@ pair_style.
|
||||
|
||||
----------
|
||||
|
||||
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the :doc:`Build package
|
||||
<Build_package>` doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
|
||||
:doc:`suffix <suffix>` command in your input script.
|
||||
|
||||
See the :doc:`Speed packages <Speed_packages>` doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
----------
|
||||
|
||||
|
||||
@ -126,23 +126,7 @@ one that matches the specified keyword.
|
||||
|
||||
----------
|
||||
|
||||
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
|
||||
:doc:`suffix <suffix>` command in your input script.
|
||||
|
||||
See the :doc:`Speed packages <Speed_packages>` doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
----------
|
||||
|
||||
|
||||
@ -177,16 +177,16 @@ volume (area in 2d) assigned to each processor, as in the following 2d
|
||||
diagram where processor sub-domains are shown and particles are
|
||||
colored by the processor that owns them.
|
||||
|
||||
.. list-table::
|
||||
.. |balance1| image:: img/balance_uniform.jpg
|
||||
:width: 32%
|
||||
|
||||
* - .. figure:: JPG/balance_uniform_small.jpg
|
||||
:target: JPG/balance_uniform.jpg
|
||||
.. |balance2| image:: img/balance_nonuniform.jpg
|
||||
:width: 32%
|
||||
|
||||
- .. figure:: JPG/balance_nonuniform_small.jpg
|
||||
:target: JPG/balance_nonuniform.jpg
|
||||
.. |balance3| image:: img/balance_rcb.jpg
|
||||
:width: 32%
|
||||
|
||||
- .. figure:: JPG/balance_rcb_small.jpg
|
||||
:target: JPG/balance_rcb.jpg
|
||||
|balance1| |balance2| |balance3|
|
||||
|
||||
The leftmost diagram is the default partitioning of the simulation box
|
||||
across processors (one sub-box for each of 16 processors); the middle
|
||||
|
||||
@ -49,23 +49,7 @@ or :doc:`read_restart <read_restart>` commands:
|
||||
|
||||
----------
|
||||
|
||||
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
|
||||
:doc:`suffix <suffix>` command in your input script.
|
||||
|
||||
See the :doc:`Speed packages <Speed_packages>` doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
----------
|
||||
|
||||
|
||||
@ -54,23 +54,7 @@ or :doc:`read_restart <read_restart>` commands:
|
||||
|
||||
----------
|
||||
|
||||
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
|
||||
:doc:`suffix <suffix>` command in your input script.
|
||||
|
||||
See the :doc:`Speed packages <Speed_packages>` doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
----------
|
||||
|
||||
|
||||
@ -52,23 +52,7 @@ or :doc:`read_restart <read_restart>` commands:
|
||||
|
||||
----------
|
||||
|
||||
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
|
||||
:doc:`suffix <suffix>` command in your input script.
|
||||
|
||||
See the :doc:`Speed packages <Speed_packages>` doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
----------
|
||||
|
||||
|
||||
@ -43,23 +43,7 @@ or :doc:`read_restart <read_restart>` commands:
|
||||
|
||||
----------
|
||||
|
||||
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
|
||||
:doc:`suffix <suffix>` command in your input script.
|
||||
|
||||
See the :doc:`Speed packages <Speed_packages>` doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
----------
|
||||
|
||||
|
||||
@ -49,23 +49,7 @@ or :doc:`read_restart <read_restart>` commands:
|
||||
|
||||
----------
|
||||
|
||||
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
|
||||
:doc:`suffix <suffix>` command in your input script.
|
||||
|
||||
See the :doc:`Speed packages <Speed_packages>` doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
----------
|
||||
|
||||
|
||||
@ -48,23 +48,7 @@ or :doc:`read_restart <read_restart>` commands:
|
||||
|
||||
----------
|
||||
|
||||
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
|
||||
:doc:`suffix <suffix>` command in your input script.
|
||||
|
||||
See the :doc:`Speed packages <Speed_packages>` doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
----------
|
||||
|
||||
|
||||
@ -46,23 +46,7 @@ or :doc:`read_restart <read_restart>` commands:
|
||||
|
||||
----------
|
||||
|
||||
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
|
||||
:doc:`suffix <suffix>` command in your input script.
|
||||
|
||||
See the :doc:`Speed packages <Speed_packages>` doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
----------
|
||||
|
||||
|
||||
@ -44,23 +44,7 @@ or :doc:`read_restart <read_restart>` commands:
|
||||
|
||||
----------
|
||||
|
||||
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
|
||||
:doc:`suffix <suffix>` command in your input script.
|
||||
|
||||
See the :doc:`Speed packages <Speed_packages>` doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
----------
|
||||
|
||||
|
||||
@ -44,23 +44,7 @@ or :doc:`read_restart <read_restart>` commands:
|
||||
|
||||
----------
|
||||
|
||||
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
|
||||
:doc:`suffix <suffix>` command in your input script.
|
||||
|
||||
See the :doc:`Speed packages <Speed_packages>` doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
----------
|
||||
|
||||
|
||||
@ -88,23 +88,7 @@ status of broken bonds or permanently delete them, e.g.:
|
||||
|
||||
----------
|
||||
|
||||
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
|
||||
:doc:`suffix <suffix>` command in your input script.
|
||||
|
||||
See the :doc:`Speed packages <Speed_packages>` doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
----------
|
||||
|
||||
|
||||
@ -124,23 +124,7 @@ one that matches the specified keyword.
|
||||
|
||||
----------
|
||||
|
||||
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
|
||||
:doc:`suffix <suffix>` command in your input script.
|
||||
|
||||
See the :doc:`Speed packages <Speed_packages>` doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
----------
|
||||
|
||||
|
||||
@ -55,8 +55,7 @@ commands. The decomposition can be changed via the
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
Communication style *tiled* cannot be used with *triclinic* simulation
|
||||
cells.
|
||||
None
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
@ -115,23 +115,7 @@ too frequently.
|
||||
----------
|
||||
|
||||
|
||||
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
|
||||
:doc:`suffix <suffix>` command in your input script.
|
||||
|
||||
See the :doc:`Speed packages <Speed_packages>` doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
|
||||
----------
|
||||
|
||||
@ -146,23 +146,7 @@ too frequently.
|
||||
----------
|
||||
|
||||
|
||||
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
|
||||
:doc:`suffix <suffix>` command in your input script.
|
||||
|
||||
See the :doc:`Speed packages <Speed_packages>` doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
|
||||
----------
|
||||
|
||||
@ -112,23 +112,7 @@ where "thermo_temp" is the ID of a similarly defined compute of style
|
||||
|
||||
----------
|
||||
|
||||
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
|
||||
:doc:`suffix <suffix>` command in your input script.
|
||||
|
||||
See the :doc:`Speed packages <Speed_packages>` doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
----------
|
||||
|
||||
|
||||
@ -68,8 +68,8 @@ reciprocal lattice nodes. The mesh spacing is defined either (a) by
|
||||
the entire simulation domain or (b) manually using selected values as
|
||||
shown in the 2D diagram below.
|
||||
|
||||
.. image:: JPG/saed_mesh_small.jpg
|
||||
:target: JPG/saed_mesh.jpg
|
||||
.. image:: img/saed_mesh.jpg
|
||||
:scale: 75%
|
||||
:align: center
|
||||
|
||||
For a mesh defined by the simulation domain, a rectilinear grid is
|
||||
@ -103,8 +103,8 @@ mesh and a *dR_Ewald* thick surface of the Ewald sphere. See the
|
||||
example 3D intensity data and the intersection of a [010] zone axis
|
||||
in the below image.
|
||||
|
||||
.. image:: JPG/saed_ewald_intersect_small.jpg
|
||||
:target: JPG/saed_ewald_intersect.jpg
|
||||
.. image:: img/saed_ewald_intersect.jpg
|
||||
:scale: 75%
|
||||
:align: center
|
||||
|
||||
The atomic scattering factors, fj, accounts for the reduction in
|
||||
|
||||
@ -69,23 +69,7 @@ thermostatting.
|
||||
|
||||
----------
|
||||
|
||||
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
|
||||
:doc:`suffix <suffix>` command in your input script.
|
||||
|
||||
See the :doc:`Speed packages <Speed_packages>` doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
----------
|
||||
|
||||
|
||||
@ -69,23 +69,7 @@ thermostatting.
|
||||
|
||||
----------
|
||||
|
||||
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
|
||||
:doc:`suffix <suffix>` command in your input script.
|
||||
|
||||
See the :doc:`Speed packages <Speed_packages>` doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
----------
|
||||
|
||||
|
||||
@ -71,8 +71,8 @@ reciprocal lattice nodes. The mesh spacing is defined either (a)
|
||||
by the entire simulation domain or (b) manually using selected values as
|
||||
shown in the 2D diagram below.
|
||||
|
||||
.. image:: JPG/xrd_mesh_small.jpg
|
||||
:target: JPG/xrd_mesh.jpg
|
||||
.. image:: img/xrd_mesh.jpg
|
||||
:scale: 75%
|
||||
:align: center
|
||||
|
||||
For a mesh defined by the simulation domain, a rectilinear grid is
|
||||
|
||||
@ -257,8 +257,7 @@ individual lattice points being "above" or "below" the mathematical
|
||||
expression for the sinusoidal curve. If a finer lattice were used,
|
||||
the sinusoid would appear to be "smoother". Also note the use of the
|
||||
"xlat" and "ylat" :doc:`thermo_style <thermo_style>` keywords which
|
||||
converts lattice spacings to distance. Click on the image for a
|
||||
larger version.
|
||||
converts lattice spacings to distance.
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
@ -275,10 +274,14 @@ larger version.
|
||||
create_atoms 1 box var v set x xx set y yy
|
||||
write_dump all atom sinusoid.lammpstrj
|
||||
|
||||
.. image:: JPG/sinusoid_small.jpg
|
||||
:target: JPG/sinusoid.jpg
|
||||
.. image:: img/sinusoid.jpg
|
||||
:scale: 50%
|
||||
:align: center
|
||||
|
||||
.. raw:: html
|
||||
|
||||
Click on the image for a larger version.
|
||||
|
||||
The *rotate* keyword allows specification of the orientation
|
||||
at which molecules are inserted. The axis of rotation is
|
||||
determined by the rotation vector (Rx,Ry,Rz) that goes through the
|
||||
|
||||
@ -125,23 +125,7 @@ computed.
|
||||
|
||||
----------
|
||||
|
||||
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
|
||||
:doc:`suffix <suffix>` command in your input script.
|
||||
|
||||
See the :doc:`Speed packages <Speed_packages>` doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
----------
|
||||
|
||||
|
||||
@ -154,23 +154,7 @@ listed under a *BondBond13 Coeffs* heading and you must leave out the
|
||||
|
||||
----------
|
||||
|
||||
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
|
||||
:doc:`suffix <suffix>` command in your input script.
|
||||
|
||||
See the :doc:`Speed packages <Speed_packages>` doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
----------
|
||||
|
||||
|
||||
@ -56,23 +56,7 @@ commands:
|
||||
|
||||
----------
|
||||
|
||||
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
|
||||
:doc:`suffix <suffix>` command in your input script.
|
||||
|
||||
See the :doc:`Speed packages <Speed_packages>` doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
----------
|
||||
|
||||
|
||||
@ -49,23 +49,7 @@ or :doc:`read_restart <read_restart>` commands:
|
||||
|
||||
----------
|
||||
|
||||
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
|
||||
:doc:`suffix <suffix>` command in your input script.
|
||||
|
||||
See the :doc:`Speed packages <Speed_packages>` doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
----------
|
||||
|
||||
|
||||
@ -60,23 +60,7 @@ or :doc:`read_restart <read_restart>` commands:
|
||||
|
||||
----------
|
||||
|
||||
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
|
||||
:doc:`suffix <suffix>` command in your input script.
|
||||
|
||||
See the :doc:`Speed packages <Speed_packages>` doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
----------
|
||||
|
||||
|
||||
@ -51,23 +51,7 @@ or :doc:`read_restart <read_restart>` commands:
|
||||
|
||||
----------
|
||||
|
||||
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
|
||||
:doc:`suffix <suffix>` command in your input script.
|
||||
|
||||
See the :doc:`Speed packages <Speed_packages>` doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
----------
|
||||
|
||||
|
||||
@ -43,23 +43,7 @@ or :doc:`read_restart <read_restart>` commands:
|
||||
|
||||
----------
|
||||
|
||||
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
|
||||
:doc:`suffix <suffix>` command in your input script.
|
||||
|
||||
See the :doc:`Speed packages <Speed_packages>` doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
----------
|
||||
|
||||
|
||||
@ -43,23 +43,7 @@ or :doc:`read_restart <read_restart>` commands:
|
||||
|
||||
----------
|
||||
|
||||
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
|
||||
:doc:`suffix <suffix>` command in your input script.
|
||||
|
||||
See the :doc:`Speed packages <Speed_packages>` doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
----------
|
||||
|
||||
|
||||
@ -56,23 +56,7 @@ or :doc:`read_restart <read_restart>` commands:
|
||||
|
||||
----------
|
||||
|
||||
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
|
||||
:doc:`suffix <suffix>` command in your input script.
|
||||
|
||||
See the :doc:`Speed packages <Speed_packages>` doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
----------
|
||||
|
||||
|
||||
@ -48,23 +48,7 @@ radian\^2.
|
||||
|
||||
----------
|
||||
|
||||
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
|
||||
:doc:`suffix <suffix>` command in your input script.
|
||||
|
||||
See the :doc:`Speed packages <Speed_packages>` doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
----------
|
||||
|
||||
|
||||
@ -177,23 +177,7 @@ that matches the specified keyword.
|
||||
|
||||
----------
|
||||
|
||||
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
|
||||
:doc:`suffix <suffix>` command in your input script.
|
||||
|
||||
See the :doc:`Speed packages <Speed_packages>` doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
**Restart info:**
|
||||
|
||||
|
||||
@ -116,19 +116,17 @@ script to generate the images/movie.
|
||||
|
||||
Here are two sample images, rendered as 1024x1024 JPEG files.
|
||||
|
||||
.. raw:: html
|
||||
|
||||
Click to see the full-size images:
|
||||
|
||||
.. |dump1| image:: JPG/dump1_small.jpg
|
||||
:target: JPG/dump1.jpg
|
||||
.. |dump1| image:: img/dump1.jpg
|
||||
:width: 48%
|
||||
.. |dump2| image:: JPG/dump2_small.jpg
|
||||
:target: JPG/dump2.jpg
|
||||
.. |dump2| image:: img/dump2.jpg
|
||||
:width: 48%
|
||||
|
||||
|dump1| |dump2|
|
||||
|
||||
.. raw:: html
|
||||
|
||||
Click to see the full-size images:
|
||||
|
||||
Only atoms in the specified group are rendered in the image. The
|
||||
:doc:`dump_modify region and thresh <dump_modify>` commands can also
|
||||
alter what atoms are included in the image.
|
||||
|
||||
@ -387,6 +387,7 @@ accelerated styles exist.
|
||||
* :doc:`wall/region <fix_wall_region>` - use region surface as wall
|
||||
* :doc:`wall/region/ees <fix_wall_ees>` - use region surface as wall for ellipsoidal particles
|
||||
* :doc:`wall/srd <fix_wall_srd>` - slip/no-slip wall for SRD particles
|
||||
* :doc:`widom <fix_widom>` - Widom insertions of atoms or molecules
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
@ -111,23 +111,7 @@ converge properly.
|
||||
|
||||
----------
|
||||
|
||||
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
|
||||
:doc:`suffix <suffix>` command in your input script.
|
||||
|
||||
See the :doc:`Speed packages <Speed_packages>` doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
----------
|
||||
|
||||
|
||||
@ -71,23 +71,7 @@ to it.
|
||||
|
||||
----------
|
||||
|
||||
Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
|
||||
:doc:`suffix <suffix>` command in your input script.
|
||||
|
||||
See the :doc:`Speed packages <Speed_packages>` doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
----------
|
||||
|
||||
|
||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user