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Merge pull request #2699 from yury-lysogorskiy/feature/user-pace

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USER-PACE pair_style integration into LAMMPS
This commit is contained in:
Axel Kohlmeyer
2021-04-12 17:05:40 -04:00
committed by GitHub
parent 869fe5a2e1 f1e5d11151
commit 0ca9f2e8a0
31 changed files with 10775 additions and 20 deletions
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41
doc/src/Build_extras.rst
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@ -52,6 +52,7 @@ This is the list of packages that may require additional steps.
* :ref:`USER-MESONT <user-mesont>`
* :ref:`USER-MOLFILE <user-molfile>`
* :ref:`USER-NETCDF <user-netcdf>`
* :ref:`USER-PACE <user-pace>`
* :ref:`USER-PLUMED <user-plumed>`
* :ref:`USER-OMP <user-omp>`
* :ref:`USER-QMMM <user-qmmm>`
@ -1247,6 +1248,46 @@ be built for the most part with all major versions of the C++ language.
----------
.. _user-pace:
USER-PACE package
-----------------------------
This package requires a library that can be downloaded and built
in lib/pace or somewhere else, which must be done before building
LAMMPS with this package. The code for the library can be found
at: `https://github.com/ICAMS/lammps-user-pace/ <https://github.com/ICAMS/lammps-user-pace/>`_
.. tabs::
.. tab:: CMake build
By default the library will be downloaded from the git repository
and built automatically when the USER-PACE package is enabled with
``-D PKG_USER-PACE=yes``. The location for the sources may be
customized by setting the variable ``PACELIB_URL`` when
configuring with CMake (e.g. to use a local archive on machines
without internet access). Since CMake checks the validity of the
archive with ``md5sum`` you may also need to set ``PACELIB_MD5``
if you provide a different library version than what is downloaded
automatically.
.. tab:: Traditional make
You can download and build the USER-PACE library
in one step from the ``lammps/src`` dir, using these commands,
which invoke the ``lib/pace/Install.py`` script.
.. code-block:: bash
$ make lib-pace # print help message
$ make lib-pace args="-b" # download and build the default version in lib/pace
You should not need to edit the ``lib/pace/Makefile.lammps`` file.
----------
.. _user-plumed:
USER-PLUMED package

22
doc/src/Build_package.rst
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@ -30,17 +30,17 @@ steps, as explained on the :doc:`Build extras <Build_extras>` page.
These links take you to the extra instructions for those select
packages:
+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
| :ref:`COMPRESS <compress>` | :ref:`GPU <gpu>` | :ref:`KIM <kim>` | :ref:`KOKKOS <kokkos>` | :ref:`LATTE <latte>` | :ref:`MESSAGE <message>` |
+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
| :ref:`MSCG <mscg>` | :ref:`OPT <opt>` | :ref:`POEMS <poems>` | :ref:`PYTHON <python>` | :ref:`VORONOI <voronoi>` | :ref:`USER-ADIOS <user-adios>` |
+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
| :ref:`USER-ATC <user-atc>` | :ref:`USER-AWPMD <user-awpmd>` | :ref:`USER-COLVARS <user-colvars>` | :ref:`USER-H5MD <user-h5md>` | :ref:`USER-INTEL <user-intel>` | :ref:`USER-MOLFILE <user-molfile>` |
+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
| :ref:`USER-NETCDF <user-netcdf>` | :ref:`USER-PLUMED <user-plumed>` | :ref:`USER-OMP <user-omp>` | :ref:`USER-QMMM <user-qmmm>` | :ref:`USER-QUIP <user-quip>` | :ref:`USER-SCAFACOS <user-scafacos>` |
+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
| :ref:`USER-SMD <user-smd>` | :ref:`USER-VTK <user-vtk>` | | | | |
+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
+--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
| :ref:`COMPRESS <compress>` | :ref:`GPU <gpu>` | :ref:`KIM <kim>` | :ref:`KOKKOS <kokkos>` | :ref:`LATTE <latte>` | :ref:`MESSAGE <message>` |
+--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
| :ref:`MSCG <mscg>` | :ref:`OPT <opt>` | :ref:`POEMS <poems>` | :ref:`PYTHON <python>` | :ref:`VORONOI <voronoi>` | :ref:`USER-ADIOS <user-adios>` |
+--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
| :ref:`USER-ATC <user-atc>` | :ref:`USER-AWPMD <user-awpmd>` | :ref:`USER-COLVARS <user-colvars>` | :ref:`USER-H5MD <user-h5md>` | :ref:`USER-INTEL <user-intel>` | :ref:`USER-MOLFILE <user-molfile>` |
+--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
| :ref:`USER-NETCDF <user-netcdf>` | :ref:`USER-PACE <user-pace>` | :ref:`USER-PLUMED <user-plumed>` | :ref:`USER-OMP <user-omp>` | :ref:`USER-QMMM <user-qmmm>` | :ref:`USER-QUIP <user-quip>` |
+--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
| :ref:`USER-SCAFACOS <user-scafacos>` | :ref:`USER-SMD <user-smd>` | :ref:`USER-VTK <user-vtk>` | | | |
+--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
The mechanism for including packages is simple but different for CMake
versus make.

1
doc/src/Commands_pair.rst
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@ -216,6 +216,7 @@ OPT.
* :doc:`oxrna2/stk <pair_oxrna2>`
* :doc:`oxrna2/xstk <pair_oxrna2>`
* :doc:`oxrna2/coaxstk <pair_oxrna2>`
* :doc:`pace <pair_pace>`
* :doc:`peri/eps <pair_peri>`
* :doc:`peri/lps (o) <pair_peri>`
* :doc:`peri/pmb (o) <pair_peri>`

41
doc/src/Packages_details.rst
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@ -90,6 +90,7 @@ page gives those details.
* :ref:`USER-MOLFILE <PKG-USER-MOLFILE>`
* :ref:`USER-NETCDF <PKG-USER-NETCDF>`
* :ref:`USER-OMP <PKG-USER-OMP>`
* :ref:`USER-PACE <PKG-USER-PACE>`
* :ref:`USER-PHONON <PKG-USER-PHONON>`
* :ref:`USER-PLUMED <PKG-USER-PLUMED>`
* :ref:`USER-PTM <PKG-USER-PTM>`
@ -1349,6 +1350,46 @@ This package has :ref:`specific installation instructions <user-colvars>` on the
----------
.. _PKG-USER-PACE:
USER-PACE package
-------------------
**Contents:**
A pair style for the Atomic Cluster Expansion potential (ACE).
ACE is a methodology for deriving a highly accurate classical potential
fit to a large archive of quantum mechanical (DFT) data. The USER-PACE
package provides an efficient implementation for running simulations
with ACE potentials.
**Authors:**
This package was written by Yury Lysogorskiy^1,
Cas van der Oord^2, Anton Bochkarev^1,
Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1,
Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1.
^1: Ruhr-University Bochum, Bochum, Germany
^2: University of Cambridge, Cambridge, United Kingdom
^3: Sandia National Laboratories, Albuquerque, New Mexico, USA
^4: University of British Columbia, Vancouver, BC, Canada
**Install:**
This package has :ref:`specific installation instructions <user-pace>` on the :doc:`Build extras <Build_extras>` page.
**Supporting info:**
* src/USER-PACE: filenames -> commands
* :doc:`pair_style pace <pair_pace>`
* examples/USER/pace
----------
.. _PKG-USER-PLUMED:
USER-PLUMED package

2
doc/src/Packages_user.rst
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@ -81,6 +81,8 @@ package:
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-OMP <PKG-USER-OMP>` | OpenMP-enabled styles | :doc:`Speed omp <Speed_omp>` | `Benchmarks <https://lammps.sandia.gov/bench.html>`_ | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-PACE <PKG-USER-PACE>` | Fast implementation of Atomic Cluster Expansion (ACE) potential | :doc:`pair pace <pair_pace>` | USER/pace | ext |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-PHONON <PKG-USER-PHONON>` | phonon dynamical matrix | :doc:`fix phonon <fix_phonon>` | USER/phonon | no |
+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
| :ref:`USER-PLUMED <PKG-USER-PLUMED>` | :ref:`PLUMED <PLUMED>` free energy library | :doc:`fix plumed <fix_plumed>` | USER/plumed | ext |

114
doc/src/pair_pace.rst Normal file
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@ -0,0 +1,114 @@
.. index:: pair_style pace
pair_style pace command
========================
Syntax
""""""
.. code-block:: LAMMPS
pair_style pace ... keyword values ...
* an optional keyword may be appended
* keyword = *product* or *recursive*
.. parsed-literal::
*product* = use product algorithm for basis functions
*recursive* = use recursive algorithm for basis functions
Examples
""""""""
.. code-block:: LAMMPS
pair_style pace
pair_style pace product
pair_coeff * * Cu-PBE-core-rep.ace Cu
Description
"""""""""""
Pair style *pace* computes interactions using the Atomic Cluster
Expansion (ACE), which is a general expansion of the atomic energy in
multi-body basis functions. :ref:`(Drautz) <Drautz20191>`.
The *pace* pair style
provides an efficient implementation that
is described in this paper :ref:`(Lysogorskiy) <Lysogorskiy20211>`.
In ACE, the total energy is decomposed into a sum over
atomic energies. The energy of atom *i* is expressed as a
linear or non-linear function of one or more density functions.
By projecting the
density onto a local atomic base, the lowest order contributions
to the energy can be expressed as a set of scalar polynomials in
basis function contributions summed over neighbor atoms.
Only a single pair_coeff command is used with the *pace* style which
specifies an ACE coefficient file followed by N additional arguments
specifying the mapping of ACE elements to LAMMPS atom types,
where N is the number of LAMMPS atom types:
* ACE coefficient file
* N element names = mapping of ACE elements to atom types
Only a single pair_coeff command is used with the *pace* style which
specifies an ACE file that fully defines the potential.
Note that unlike for other potentials, cutoffs are
not set in the pair_style or pair_coeff command; they are specified in
the ACE file.
The pair_style *pace* command may be followed by an optional keyword
*product* or *recursive*, which determines which of two algorithms
is used for the calculation of basis functions and derivatives.
The default is *recursive*.
See the :doc:`pair_coeff <pair_coeff>` doc page for alternate ways
to specify the path for the ACE coefficient file.
Mixing, shift, table, tail correction, restart, rRESPA info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
For atom type pairs I,J and I != J, where types I and J correspond to
two different element types, mixing is performed by LAMMPS with
user-specifiable parameters as described above. You never need to
specify a pair_coeff command with I != J arguments for this style.
This pair style does not support the :doc:`pair_modify <pair_modify>`
shift, table, and tail options.
This pair style does not write its information to :doc:`binary restart files <restart>`, since it is stored in potential files. Thus, you
need to re-specify the pair_style and pair_coeff commands in an input
script that reads a restart file.
This pair style can only be used via the *pair* keyword of the
:doc:`run_style respa <run_style>` command. It does not support the
*inner*\ , *middle*\ , *outer* keywords.
----------
Restrictions
""""""""""""
This pair style is part of the USER-PACE package. It is only enabled if LAMMPS
was built with that package.
See the :doc:`Build package <Build_package>` doc page for more info.
Related commands
""""""""""""""""
:doc:`pair_style snap <pair_snap>`
Default
"""""""
recursive
.. _Drautz20191:
**(Drautz)** Drautz, Phys Rev B, 99, 014104 (2019).
.. _Lysogorskiy20211:
**(Lysogorskiy)** Lysogorskiy, van der Oord, Bochkarev, Menon, Rinaldi, Hammerschmidt, Mrovec, Thompson, Csanyi, Ortner, Drautz, TBD (2021).

5
doc/src/pair_style.rst
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@ -99,7 +99,7 @@ accelerated styles exist.
* :doc:`zero <pair_zero>` - neighbor list but no interactions
* :doc:`adp <pair_adp>` - angular dependent potential (ADP) of Mishin
* :doc:`agni <pair_agni>` - machine learned potential mapping atomic environment to forces
* :doc:`agni <pair_agni>` - AGNI machine-learning potential
* :doc:`airebo <pair_airebo>` - AIREBO potential of Stuart
* :doc:`airebo/morse <pair_airebo>` - AIREBO with Morse instead of LJ
* :doc:`atm <pair_atm>` - Axilrod-Teller-Muto potential
@ -280,6 +280,7 @@ accelerated styles exist.
* :doc:`oxrna2/hbond <pair_oxrna2>` -
* :doc:`oxrna2/stk <pair_oxrna2>` -
* :doc:`oxrna2/xstk <pair_oxrna2>` -
* :doc:`pace <pair_pace>` - Atomic Cluster Expansion (ACE) machine-learning potential
* :doc:`peri/eps <pair_peri>` - peridynamic EPS potential
* :doc:`peri/lps <pair_peri>` - peridynamic LPS potential
* :doc:`peri/pmb <pair_peri>` - peridynamic PMB potential
@ -297,7 +298,7 @@ accelerated styles exist.
* :doc:`smd/ulsph <pair_smd_ulsph>` -
* :doc:`smtbq <pair_smtbq>` -
* :doc:`mliap <pair_mliap>` - Multiple styles of machine-learning potential
* :doc:`snap <pair_snap>` - SNAP quantum-accurate potential
* :doc:`snap <pair_snap>` - SNAP machine-learning potential
* :doc:`soft <pair_soft>` - Soft (cosine) potential
* :doc:`sph/heatconduction <pair_sph_heatconduction>` -
* :doc:`sph/idealgas <pair_sph_idealgas>` -