update pod doc

doc/src/Commands_all.rst

@@ -127,6 +127,7 @@ additional letter in parenthesis: k = KOKKOS.
    * :doc:`group2ndx <group2ndx>`
    * :doc:`hyper <hyper>`
    * :doc:`kim <kim_commands>`
+   * :doc:`fitpod <fitpod_command>`
    * :doc:`mdi <mdi>`
    * :doc:`ndx2group <group2ndx>`
    * :doc:`neb <neb>`

doc/src/Commands_compute.rst

@@ -103,7 +103,6 @@ KOKKOS, o = OPENMP, t = OPT.
    * :doc:`pe/mol/tally <compute_tally>`
    * :doc:`pe/tally <compute_tally>`
    * :doc:`plasticity/atom <compute_plasticity_atom>`
-   * :doc:`podfit <compute_podfit>`
    * :doc:`pressure <compute_pressure>`
    * :doc:`pressure/uef <compute_pressure_uef>`
    * :doc:`property/atom <compute_property_atom>`

doc/src/Packages_details.rst

@@ -1804,11 +1804,11 @@ ML-POD package
 
 **Contents:**
 
-A pair style and compute for Proper Orthogonal Descriptors (POD). POD
-is a methodology for deriving descriptors based on the Karhuen-Loeve
-expansion. The ML-POD package provides an efficient implementation for
+A pair style and fitpod style for Proper Orthogonal Descriptors (POD). POD
+is a methodology for deriving descriptors based on the proper orthogonal
+decomposition. The ML-POD package provides an efficient implementation for
 running simulations with POD potentials, along with fitting the potentials
-natively in LAMMPS. If you want to use the fitting functionality in `compute_podfit`,
+natively in LAMMPS. If you want to use the fitting functionality in `fitpod`,
 you must install the LAPACK library on your machine, which will be included in
 your build via `CMakeLists.txt`
 
@@ -1830,7 +1830,7 @@ Go to the `lammps` directory and build with the POD package::
 
 * src/ML-POD: filenames -> commands
 * :doc:`pair_style pod <pair_pod>`
-* :doc:`compute_style podfit <compute_podfit>`
+* :doc:`command_style fitpod <fitpod_command>`
 * examples/pod
 
 ----------

doc/src/commands_list.rst

@@ -43,6 +43,7 @@ Commands
    echo
    fix
    fix_modify
+   fitpod_command
    group
    group2ndx
    hyper

doc/src/compute.rst

@@ -248,7 +248,6 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
 * :doc:`pe/mol/tally <compute_tally>` - potential energy between two groups of atoms separated into intermolecular and intramolecular components via the tally callback mechanism
 * :doc:`pe/tally <compute_tally>` - potential energy between two groups of atoms via the tally callback mechanism
 * :doc:`plasticity/atom <compute_plasticity_atom>` - Peridynamic plasticity for each atom
-* :doc:`podfit <compute_podfit>` - Proper orthogonal descriptor potentials and parameterization
 * :doc:`pressure <compute_pressure>` - total pressure and pressure tensor
 * :doc:`pressure/uef <compute_pressure_uef>` - pressure tensor in the reference frame of an applied flow field
 * :doc:`property/atom <compute_property_atom>` - convert atom attributes to per-atom vectors/arrays

doc/src/fitpod_command.rst

@@ -1,6 +1,6 @@
-.. index:: compute podfit
+.. index:: fitpod
 
-compute podfit command
+fitpod command
 ======================
 
 Syntax
@@ -8,20 +8,18 @@ Syntax
 
 .. parsed-literal::
 
-   compute ID group-ID podfit pod.txt data.txt
+   fitpod pod.txt data.txt
 
-* ID, group-ID are documented in :doc:`compute <compute>` command
-* podfit = style name of this compute command
+* fitpod = style name of this command
 * pod.txt = an input file that describes proper orthogonal descriptors (PODs)
 * data.txt = an input file that specifies DFT data used to fit a POD potential
 
-
 Examples
 """"""""
 
 .. code-block:: LAMMPS
 
-   compute pod all podfit pod.txt data.txt
+   fitpod pod.txt data.txt
 
 Description
 """""""""""
@@ -568,7 +566,7 @@ PODs for constructing the new descriptors.
 Restrictions
 """"""""""""
 
-This compute is part of the ML-POD package.  It is only enabled
+This command is part of the ML-POD package.  It is only enabled
 if LAMMPS was built with that package by setting -D PKG_ML-POD=on. See the :doc:`Build package
 <Build_package>` page for more info.
 

doc/src/pair_pod.rst

@@ -23,7 +23,7 @@ Description
 
 Pair style *pod* defines the proper orthogonal descriptor (POD) potential
 :ref:`(Nguyen) <Nguyen20221>`.  The mathematical definition of the POD potential
-is described from :doc:`compute podfit <compute_podfit>`, which is used to fit the POD
+is described from :doc:`fitpod <fitpod_command>`, 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 *pod* style which
@@ -36,11 +36,11 @@ 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:`compute podfit <compute_podfit>`.
+is generated after training the POD potential using :doc:`fitpod <fitpod_command>`.
 
 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:`compute podfit <compute_podfit>` for the description
+keyword/value pair. See :doc:`fitpod <fitpod_command>` for the description
 of all the keywords that can be assigned in the parameter file.
 
 ----------
@@ -55,7 +55,7 @@ was built with that package by setting -D PKG_ML-POD=on. See the :doc:`Build pac
 Related commands
 """"""""""""""""
 
-:doc:`compute podfit <compute_podfit>`,
+:doc:`fitpod <fitpod_command>`,
 
 Default
 """""""