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Merge branch 'master' of github.com:lammps/lammps into pair-style-nnp

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This commit is contained in:
Andreas Singraber
2021-02-24 23:37:21 +01:00
parent 037441b502 e916c5d852
commit 992d0e13aa
79 changed files with 5000 additions and 2694 deletions
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31
doc/src/Build_extras.rst
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@ -134,6 +134,8 @@ CMake build
# value = yes (default) or no
-D CUDA_MPS_SUPPORT=value # enables some tweaks required to run with active nvidia-cuda-mps daemon
# value = yes or no (default)
-D USE_STATIC_OPENCL_LOADER=value # downloads/includes OpenCL ICD loader library, no local OpenCL headers/libs needed
# value = yes (default) or no
:code:`GPU_ARCH` settings for different GPU hardware is as follows:
@ -160,6 +162,12 @@ When building with CMake, you **must NOT** build the GPU library in ``lib/gpu``
using the traditional build procedure. CMake will detect files generated by that
process and will terminate with an error and a suggestion for how to remove them.
If you are compiling for OpenCL, the default setting is to download, build, and
link with a static OpenCL ICD loader library and standard OpenCL headers. This
way no local OpenCL development headers or library needs to be present and only
OpenCL compatible drivers need to be installed to use OpenCL. If this is not
desired, you can set :code:`USE_STATIC_OPENCL_LOADER` to :code:`no`.
If you are compiling with HIP, note that before running CMake you will have to
set appropriate environment variables. Some variables such as
:code:`HCC_AMDGPU_TARGET` or :code:`CUDA_PATH` are necessary for :code:`hipcc`
@ -257,18 +265,18 @@ To build with this package, the KIM library with API v2 must be downloaded
and built on your system. It must include the KIM models that you want to
use with LAMMPS.
If you would like to use the :doc:`kim_query <kim_commands>`
If you would like to use the :doc:`kim query <kim_commands>`
command, you also need to have libcurl installed with the matching
development headers and the curl-config tool.
If you would like to use the :doc:`kim_property <kim_commands>`
If you would like to use the :doc:`kim property <kim_commands>`
command, you need to build LAMMPS with the PYTHON package installed
and linked to Python 3.6 or later. See the :ref:`PYTHON package build info <python>`
for more details on this. After successfully building LAMMPS with Python, you
also need to install the kim-property Python package, which can be easily done using
*pip* as ``pip install kim-property``, or from the *conda-forge* channel as
``conda install kim-property`` if LAMMPS is built in Conda. More detailed
information is available at:
also need to install the ``kim-property`` Python package, which can be easily
done using *pip* as ``pip install kim-property``, or from the *conda-forge*
channel as ``conda install kim-property`` if LAMMPS is built in Conda. More
detailed information is available at:
`kim-property installation <https://github.com/openkim/kim-property#installing-kim-property>`_.
In addition to installing the KIM API, it is also necessary to install the
@ -308,7 +316,7 @@ minutes to hours) to build. Of course you only need to do that once.)
You can download and build the KIM library manually if you prefer;
follow the instructions in ``lib/kim/README``. You can also do
this in one step from the lammps/src dir, using a command like
this in one step from the lammps/src directory, using a command like
these, which simply invoke the ``lib/kim/Install.py`` script with
the specified args.
@ -328,7 +336,7 @@ minutes to hours) to build. Of course you only need to do that once.)
.. code-block:: make
LMP_INC = -DLMP_NO_SSL_CHECK
LMP_INC = -DLMP_NO_SSL_CHECK
Debugging OpenKIM web queries in LAMMPS
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@ -376,10 +384,11 @@ Enabling the extra unit tests have some requirements,
Conda. More detailed information is available at:
`kim-property installation <https://github.com/openkim/kim-property#installing-kim-property>`_.
* It is also necessary to install
``EAM_Dynamo_Mendelev_2007_Zr__MO_848899341753_000``, and
``EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005`` KIM models.
``EAM_Dynamo_MendelevAckland_2007v3_Zr__MO_004835508849_000``,
``EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005``, and
``LennardJones612_UniversalShifted__MO_959249795837_003`` KIM models.
See `Obtaining KIM Models <http://openkim.org/doc/usage/obtaining-models>`_
to learn how to install a pre-build binary of the OpenKIM Repository of
to learn how to install a pre-built binary of the OpenKIM Repository of
Models or see
`Installing KIM Models <https://openkim.org/doc/usage/obtaining-models/#installing_models>`_
to learn how to install the specific KIM models.

6
doc/src/Commands_all.rst
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@ -60,11 +60,7 @@ An alphabetic list of all general LAMMPS commands.
* :doc:`include <include>`
* :doc:`info <info>`
* :doc:`jump <jump>`
* :doc:`kim_init <kim_commands>`
* :doc:`kim_interactions <kim_commands>`
* :doc:`kim_param <kim_commands>`
* :doc:`kim_property <kim_commands>`
* :doc:`kim_query <kim_commands>`
* :doc:`kim <kim_commands>`
* :doc:`kspace_modify <kspace_modify>`
* :doc:`kspace_style <kspace_style>`
* :doc:`label <label>`

2
doc/src/Intro_features.rst
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@ -85,7 +85,7 @@ commands)
* water potentials: TIP3P, TIP4P, SPC
* implicit solvent potentials: hydrodynamic lubrication, Debye
* force-field compatibility with common CHARMM, AMBER, DREIDING, OPLS, GROMACS, COMPASS options
* access to the `OpenKIM Repository <http://openkim.org>`_ of potentials via :doc:`kim_init, kim_interactions, and kim_query <kim_commands>` commands
* access to the `OpenKIM Repository <http://openkim.org>`_ of potentials via :doc:`kim command <kim_commands>`
* hybrid potentials: multiple pair, bond, angle, dihedral, improper potentials can be used in one simulation
* overlaid potentials: superposition of multiple pair potentials

22
doc/src/Packages_details.rst
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@ -368,17 +368,19 @@ KIM package
**Contents:**
This package contains a set of commands that serve as a wrapper on the
This package contains a command with a set of subcommands that serve as a
wrapper on the
`Open Knowledgebase of Interatomic Models (OpenKIM) <https://openkim.org>`_
repository of interatomic models (IMs) enabling compatible ones to be used in
LAMMPS simulations.
This includes :doc:`kim_init <kim_commands>`, and
:doc:`kim_interactions <kim_commands>` commands to select, initialize and
instantiate the IM, a :doc:`kim_query <kim_commands>` command to perform web
This includes :doc:`kim init <kim_commands>`, and
:doc:`kim interactions <kim_commands>` commands to select, initialize and
instantiate the IM, a :doc:`kim query <kim_commands>` command to perform web
queries for material property predictions of OpenKIM IMs, a
:doc:`kim_param <kim_commands>` command to access KIM Model Parameters from
LAMMPS, and a :doc:`kim_property <kim_commands>` command to write material
:doc:`kim param <kim_commands>` command to access KIM Model Parameters from
LAMMPS, and a :doc:`kim property <kim_commands>` command to write material
properties computed in LAMMPS to standard KIM property instance format.
Support for KIM IMs that conform to the
@ -387,8 +389,8 @@ is provided by the :doc:`pair_style kim <pair_kim>` command.
.. note::
The command *pair_style kim* is called by *kim_interactions* and
is not recommended to be directly used in input scripts.
The command *pair_style kim* is called by *kim interactions* and is not
recommended to be directly used in input scripts.
To use this package you must have the KIM API library available on your
system. The KIM API is available for download on the
@ -405,7 +407,7 @@ and is funded by the `National Science Foundation <https://www.nsf.gov/>`_.
API and the *pair_style kim* command. Yaser Afshar (U Minnesota),
Axel Kohlmeyer (Temple U), Ellad Tadmor (U Minnesota), and
Daniel Karls (U Minnesota) contributed to the
:doc:`kim_commands <kim_commands>` interface in close collaboration with
:doc:`kim command <kim_commands>` interface in close collaboration with
Ryan Elliott.
**Install:**
@ -415,7 +417,7 @@ This package has :ref:`specific installation instructions <kim>` on the
**Supporting info:**
* :doc:`kim_commands <kim_commands>`
* :doc:`kim command <kim_commands>`
* :doc:`pair_style kim <pair_kim>`
* src/KIM: filenames -> commands
* src/KIM/README

2
doc/src/compute_temp_chunk.rst
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@ -153,7 +153,7 @@ temp/chunk calculation to a file is to use the :doc:`fix ave/time <fix_ave_time>
compute cc1 all chunk/atom molecule
compute myChunk all temp/chunk cc1 temp
fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
fix 1 all ave/time 100 1 100 c_myChunk[1] file tmp.out mode vector
----------

1352
doc/src/kim_commands.rst
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2
doc/src/pair_adp.rst
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@ -59,7 +59,7 @@ command to specify them.
* The OpenKIM Project at
`https://openkim.org/browse/models/by-type <https://openkim.org/browse/models/by-type>`_
provides ADP potentials that can be used directly in LAMMPS with the
:doc:`kim_commands <kim_commands>` interface.
:doc:`kim command <kim_commands>` interface.
----------

2
doc/src/pair_eam.rst
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@ -141,7 +141,7 @@ interatomic potentials and file formats.
The OpenKIM Project at
`https://openkim.org/browse/models/by-type <https://openkim.org/browse/models/by-type>`_
provides EAM potentials that can be used directly in LAMMPS with the
:doc:`kim_commands <kim_commands>` interface.
:doc:`kim command <kim_commands>` interface.
----------

21
doc/src/pair_kim.rst
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@ -23,29 +23,30 @@ Examples
Description
"""""""""""
This pair style is a wrapper on the `Open Knowledgebase of Interatomic Models (OpenKIM) <https://openkim.org>`_ repository of interatomic
potentials to enable their use in LAMMPS scripts.
This pair style is a wrapper on the
`Open Knowledgebase of Interatomic Models (OpenKIM) <https://openkim.org>`_
repository of interatomic potentials to enable their use in LAMMPS scripts.
The preferred interface for using interatomic models archived in
OpenKIM is the :doc:`kim_commands interface <kim_commands>`. That
OpenKIM is the :doc:`kim command <kim_commands>` interface. That
interface supports both "KIM Portable Models" (PMs) that conform to the
KIM API Portable Model Interface (PMI) and can be used by any
simulation code that conforms to the KIM API/PMI, and
"KIM Simulator Models" that are natively implemented within a single
"KIM Simulator Models" (SMs) that are natively implemented within a single
simulation code (like LAMMPS) and can only be used with it.
The *pair_style kim* command is limited to KIM PMs. It is
used by the :doc:`kim_commands interface <kim_commands>` as needed.
used by the :doc:`kim command <kim_commands>` interface as needed.
.. note::
Since *pair_style kim* is called by *kim_interactions* as needed,
is not recommended to be directly used in input scripts.
Since *pair_style kim* is called by *kim interactions* as needed,
it is not recommended to be directly used in input scripts.
----------
The argument *model* is the name of the KIM PM.
For potentials archived in OpenKIM
this is the extended KIM ID (see :doc:`kim_commands <kim_commands>`
this is the extended KIM ID (see :doc:`kim command <kim_commands>`
for details). LAMMPS can invoke any KIM PM, however there can
be incompatibilities (for example due to unit matching issues).
In the event of an incompatibility, the code will terminate with
@ -106,7 +107,7 @@ Restrictions
""""""""""""
This pair style is part of the KIM package. See details on
restrictions in :doc:`kim_commands <kim_commands>`.
restrictions in :doc:`kim command <kim_commands>`.
This current version of pair_style kim is compatible with the
kim-api package version 2.0.0 and higher.
@ -114,7 +115,7 @@ kim-api package version 2.0.0 and higher.
Related commands
""""""""""""""""
:doc:`pair_coeff <pair_coeff>`, :doc:`kim_commands <kim_commands>`
:doc:`pair_coeff <pair_coeff>`, :doc:`kim command <kim_commands>`
Default
"""""""