diff --git a/doc/src/Commands_all.rst b/doc/src/Commands_all.rst index a263d6c8a2..f9d4a5aa36 100644 --- a/doc/src/Commands_all.rst +++ b/doc/src/Commands_all.rst @@ -127,7 +127,7 @@ additional letter in parenthesis: k = KOKKOS. * :doc:`group2ndx ` * :doc:`hyper ` * :doc:`kim ` - * :doc:`fitpod ` + * :doc:`fitpod ` * :doc:`mdi ` * :doc:`ndx2group ` * :doc:`neb ` diff --git a/doc/src/Commands_pair.rst b/doc/src/Commands_pair.rst index 192c822b80..3f5deef24a 100644 --- a/doc/src/Commands_pair.rst +++ b/doc/src/Commands_pair.rst @@ -237,7 +237,7 @@ OPT. * :doc:`oxrna2/coaxstk ` * :doc:`pace (k) ` * :doc:`pace/extrapolation ` - * :doc:`mlpod ` + * :doc:`pod ` * :doc:`peri/eps ` * :doc:`peri/lps (o) ` * :doc:`peri/pmb (o) ` diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index b1ecd200a6..39b6ec776b 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -1829,9 +1829,9 @@ Go to the `lammps` directory and build with the POD package:: **Supporting info:** * src/ML-POD: filenames -> commands -* :doc:`pair_style mlpod ` -* :doc:`command_style fitpod ` -* examples/mlpod +* :doc:`pair_style pod ` +* :doc:`command_style fitpod ` +* examples/pod ---------- diff --git a/doc/src/Packages_list.rst b/doc/src/Packages_list.rst index 5f0a26822a..439a066737 100644 --- a/doc/src/Packages_list.rst +++ b/doc/src/Packages_list.rst @@ -300,8 +300,8 @@ whether an extra library is needed to build and use the package: - ext * - :ref:`ML-POD ` - Proper orthogonal decomposition potentials - - :doc:`pair mlpod ` - - mlpod + - :doc:`pair pod ` + - pod - ext * - :ref:`ML-QUIP ` - QUIP/libatoms interface diff --git a/doc/src/commands_list.rst b/doc/src/commands_list.rst index f01ed6860d..62f2fc5107 100644 --- a/doc/src/commands_list.rst +++ b/doc/src/commands_list.rst @@ -43,7 +43,7 @@ Commands echo fix fix_modify - fitpod_command + fitpod group group2ndx hyper diff --git a/doc/src/fitpod_command.rst b/doc/src/fitpod.rst similarity index 99% rename from doc/src/fitpod_command.rst rename to doc/src/fitpod.rst index 9ef28a691d..5bcce615e7 100644 --- a/doc/src/fitpod_command.rst +++ b/doc/src/fitpod.rst @@ -69,7 +69,7 @@ On successful training, it produces a number of output files: * coefficents.txt contains the coeffcients of the POD potential After training the POD potential, pod.txt and coefficents.txt are two files needed to use the -POD potential in LAMMPS. See :doc:`pair_style mlpod ` for using the POD potential. Examples about training and using POD potentials are found in the directory lammps/examples/mlpod. +POD potential in LAMMPS. See :doc:`pair_style pod ` for using the POD potential. Examples about training and using POD potentials are found in the directory lammps/examples/PACKAGES/pod. Parametrized Potential Energy Surface """"""""""""""""""""""""""""""""""""" @@ -573,7 +573,7 @@ if LAMMPS was built with that package by setting -D PKG_ML-POD=on. See the :doc: Related commands """""""""""""""" -:doc:`pair_style mlpod ` +:doc:`pair_style pod ` Default """"""" diff --git a/doc/src/pair_mlpod.rst b/doc/src/pair_pod.rst similarity index 74% rename from doc/src/pair_mlpod.rst rename to doc/src/pair_pod.rst index 11a123b673..e05b8b000f 100644 --- a/doc/src/pair_mlpod.rst +++ b/doc/src/pair_pod.rst @@ -1,6 +1,6 @@ -.. index:: pair_style mlpod +.. index:: pair_style pod -pair_style mlpod command +pair_style pod command ======================== Syntax @@ -8,25 +8,25 @@ Syntax .. code-block:: LAMMPS - pair_style mlpod + pair_style pod Examples """""""" .. code-block:: LAMMPS - pair_style mlpod + pair_style pod pair_coeff * * pod.txt coefficient.txt Description """"""""""" -Pair style *mlpod* defines the proper orthogonal descriptor (POD) potential +Pair style *pod* defines the proper orthogonal descriptor (POD) potential :ref:`(Nguyen) `. The mathematical definition of the POD potential -is described from :doc:`fitpod `, which is used to fit the POD +is described from :doc:`fitpod `, which is used to fit the POD potential to *ab initio* energy and force data. -Only a single pair_coeff command is used with the *mlpod* style which +Only a single pair_coeff command is used with the *pod* style which specifies a POD parameter file followed by a coefficient file. The coefficient file (coefficient.txt) contains coefficients for the POD potential. The top of the coefficient @@ -36,13 +36,15 @@ strict format after that. The first non-blank non-comment line must contain: * POD_coefficients: *ncoeff* This is followed by *ncoeff* coefficients, one per line. The coefficient file -is generated after training the POD potential using :doc:`fitpod `. +is generated after training the POD potential using :doc:`fitpod `. The POD parameter file (pod.txt) can contain blank and comment lines (start with #) anywhere. Each non-blank non-comment line must contain one -keyword/value pair. See :doc:`fitpod ` for the description +keyword/value pair. See :doc:`fitpod ` for the description of all the keywords that can be assigned in the parameter file. +Examples about training and using POD potentials are found in the directory lammps/examples/PACKAGES/pod. + ---------- Restrictions @@ -57,7 +59,7 @@ This pair style does not compute per-atom energies and per-atom stresses. Related commands """""""""""""""" -:doc:`fitpod `, +:doc:`fitpod `, Default """"""" diff --git a/doc/src/pair_style.rst b/doc/src/pair_style.rst index 5477f89925..48daf34f17 100644 --- a/doc/src/pair_style.rst +++ b/doc/src/pair_style.rst @@ -314,7 +314,7 @@ accelerated styles exist. * :doc:`oxrna2/xstk ` - * :doc:`pace ` - Atomic Cluster Expansion (ACE) machine-learning potential * :doc:`pace/extrapolation ` - Atomic Cluster Expansion (ACE) machine-learning potential with extrapolation grades -* :doc:`mlpod ` - Proper orthogonal decomposition (POD) machine-learning potential +* :doc:`pod ` - Proper orthogonal decomposition (POD) machine-learning potential * :doc:`peri/eps ` - peridynamic EPS potential * :doc:`peri/lps ` - peridynamic LPS potential * :doc:`peri/pmb ` - peridynamic PMB potential