rename SNAP package to ML-SNAP and fix up some remaining MLIAP to ML-IAP issues

cmake/CMakeLists.txt

@@ -139,8 +139,8 @@ install(TARGETS lmp EXPORT LAMMPS_Targets DESTINATION ${CMAKE_INSTALL_BINDIR})
 option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF)
 
 set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE
-  GRANULAR KSPACE LATTE MANYBODY MC MESSAGE MISC MLIAP MOLECULE PERI POEMS
+  GRANULAR KSPACE LATTE MANYBODY MC MESSAGE MISC ML-IAP MOLECULE PERI POEMS
-  PLUGIN QEQ REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI
+  PLUGIN QEQ REPLICA RIGID SHOCK SPIN ML-SNAP SRD KIM PYTHON MSCG MPIIO VORONOI
   USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESODPD USER-CGSDK
   USER-COLVARS USER-DIELECTRIC USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP
   USER-H5MD USER-HDNNP USER-LB USER-MANIFOLD USER-MDI USER-MEAMC USER-MESONT USER-MGPT
@@ -229,7 +229,7 @@ endif()
 
 # "hard" dependencies between packages resulting
 # in an error instead of skipping over files
-pkg_depends(MLIAP SNAP)
+pkg_depends(ML-IAP ML-SNAP)
 pkg_depends(MPIIO MPI)
 pkg_depends(USER-ATC MANYBODY)
 pkg_depends(USER-LB MPI)
@@ -350,7 +350,7 @@ else()
   set(CUDA_REQUEST_PIC)
 endif()
 
-foreach(PKG_WITH_INCL KSPACE PYTHON MLIAP VORONOI USER-COLVARS USER-HDNNP USER-MDI USER-MOLFILE USER-NETCDF
+foreach(PKG_WITH_INCL KSPACE PYTHON ML-IAP VORONOI USER-COLVARS USER-HDNNP USER-MDI USER-MOLFILE USER-NETCDF
         USER-PLUMED USER-QMMM USER-QUIP USER-SCAFACOS USER-SMD USER-VTK KIM LATTE MESSAGE MSCG COMPRESS USER-PACE)
   if(PKG_${PKG_WITH_INCL})
     include(Packages/${PKG_WITH_INCL})

cmake/Modules/Packages/ML-IAP.cmake

@@ -1,4 +1,4 @@
-# if PYTHON package is included we may also include Python support in MLIAP
+# if PYTHON package is included we may also include Python support in ML-IAP
 set(MLIAP_ENABLE_PYTHON_DEFAULT OFF)
 if(PKG_PYTHON)
   find_package(Cythonize QUIET)
@@ -7,20 +7,20 @@ if(PKG_PYTHON)
   endif()
 endif()
 
-option(MLIAP_ENABLE_PYTHON "Build MLIAP package with Python support" ${MLIAP_ENABLE_PYTHON_DEFAULT})
+option(MLIAP_ENABLE_PYTHON "Build ML-IAP package with Python support" ${MLIAP_ENABLE_PYTHON_DEFAULT})
 
 if(MLIAP_ENABLE_PYTHON)
   find_package(Cythonize REQUIRED)
   if(NOT PKG_PYTHON)
-    message(FATAL_ERROR "Must enable PYTHON package for including Python support in MLIAP")
+    message(FATAL_ERROR "Must enable PYTHON package for including Python support in ML-IAP")
   endif()
   if(CMAKE_VERSION VERSION_LESS 3.12)
     if(PYTHONLIBS_VERSION_STRING VERSION_LESS 3.6)
-      message(FATAL_ERROR "Python support in MLIAP requires Python 3.6 or later")
+      message(FATAL_ERROR "Python support in ML-IAP requires Python 3.6 or later")
     endif()
   else()
     if(Python_VERSION VERSION_LESS 3.6)
-      message(FATAL_ERROR "Python support in MLIAP requires Python 3.6 or later")
+      message(FATAL_ERROR "Python support in ML-IAP requires Python 3.6 or later")
     endif()
   endif()
 

cmake/presets/all_off.cmake

@@ -2,8 +2,8 @@
 # an existing package selection without losing any other settings
 
 set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
-  GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MESSAGE MISC MLIAP MOLECULE
+  GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MESSAGE MISC ML-IAP MOLECULE
-  MPIIO MSCG OPT PERI PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN
+  MPIIO MSCG OPT PERI PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK ML-SNAP SPIN
   SRD VORONOI
   USER-ADIOS USER-ATC USER-AWPMD USER-BROWNIAN USER-BOCS USER-CGDNA USER-CGSDK
   USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD

cmake/presets/all_on.cmake

@@ -4,8 +4,8 @@
 # with just a working C++ compiler and an MPI library.
 
 set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
-  GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MESSAGE MISC MLIAP MOLECULE
+  GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MESSAGE MISC ML-IAP MOLECULE
-  MPIIO MSCG OPT PERI PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN
+  MPIIO MSCG OPT PERI PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK ML-SNAP SPIN
   SRD VORONOI
   USER-ADIOS USER-ATC USER-AWPMD USER-BROWNIAN USER-BOCS USER-CGDNA USER-CGSDK
   USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD

cmake/presets/mingw-cross.cmake

@@ -1,6 +1,6 @@
 set(WIN_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
-                 GRANULAR KSPACE LATTE MANYBODY MC MISC MLIAP MOLECULE OPT
+                 GRANULAR KSPACE LATTE MANYBODY MC MISC ML-IAP MOLECULE OPT
-                 PERI POEMS QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI
+                 PERI POEMS QEQ REPLICA RIGID SHOCK ML-SNAP SPIN SRD VORONOI
                  USER-ATC USER-AWPMD USER-BOCS USER-BROWNIAN USER-CGDNA USER-CGSDK
                  USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP
                  USER-HDNNP USER-INTEL USER-MANIFOLD USER-MDI USER-MEAMC USER-MESODPD

cmake/presets/most.cmake

@@ -3,8 +3,8 @@
 # are removed. The resulting binary should be able to run most inputs.
 
 set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE
-        GRANULAR KSPACE MANYBODY MC MISC MLIAP MOLECULE OPT PERI
+        GRANULAR KSPACE MANYBODY MC MISC ML-IAP MOLECULE OPT PERI
-        PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI
+        PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK ML-SNAP SPIN SRD VORONOI
         USER-BROWNIAN USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS
         USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-MEAMC
         USER-MESODPD USER-MISC USER-MOFFF USER-OMP USER-PHONON USER-REACTION

doc/src/Build_basics.rst

@@ -130,7 +130,7 @@ package can be compiled to include OpenMP threading.
 
 In addition, there are a few commands in LAMMPS that have native OpenMP
 support included as well.  These are commands in the ``MPIIO``,
-``SNAP``, ``USER-DIFFRACTION``, and ``USER-DPD`` packages.  In addition
+``ML-SNAP``, ``USER-DIFFRACTION``, and ``USER-DPD`` packages.  In addition
 some packages support OpenMP threading indirectly through the libraries
 they interface to: e.g. ``LATTE``, ``KSPACE``, and ``USER-COLVARS``.
 See the :doc:`Packages details <Packages_details>` page for more

doc/src/Build_extras.rst

@@ -814,8 +814,8 @@ be installed on your system.
 ML-IAP package
 ---------------------------
 
-Building the ML-IAP package requires including the :ref:`SNAP
+Building the ML-IAP package requires including the :ref:`ML-SNAP
-<PKG-SNAP>` package.  There will be an error message if this requirement
+<PKG-ML-SNAP>` package.  There will be an error message if this requirement
 is not satisfied.  Using the *mliappy* model also requires enabling
 Python support, which in turn requires to include the :ref:`PYTHON
 <PKG-PYTHON>` package **and** requires to have the `cython

doc/src/Packages_details.rst

@@ -57,7 +57,7 @@ page gives those details.
    * :ref:`REPLICA <PKG-REPLICA>`
    * :ref:`RIGID <PKG-RIGID>`
    * :ref:`SHOCK <PKG-SHOCK>`
-   * :ref:`SNAP <PKG-SNAP>`
+   * :ref:`ML-SNAP <PKG-ML-SNAP>`
    * :ref:`SPIN <PKG-SPIN>`
    * :ref:`SRD <PKG-SRD>`
    * :ref:`VORONOI <PKG-VORONOI>`
@@ -671,7 +671,7 @@ listing, "ls src/MISC", to see the list of commands.
 .. _PKG-ML-IAP:
 
 ML-IAP package
--------------
+--------------
 
 **Contents:**
 
@@ -679,7 +679,7 @@ A general interface for machine-learning interatomic potentials, including PyTor
 
 **Install:**
 
-To use this package, also the :ref:`SNAP package <PKG-SNAP>` package needs
+To use this package, also the :ref:`ML-SNAP package <PKG-ML-SNAP>` package needs
 to be installed.  To make the *mliappy* model available, also the
 :ref:`PYTHON package <PKG-PYTHON>` package needs to be installed, the version
 of Python must be 3.6 or later, and the `cython <https://cython.org/>`_ software
@@ -1038,10 +1038,10 @@ a material.
 
 ----------
 
-.. _PKG-SNAP:
+.. _PKG-ML-SNAP:
 
-SNAP package
+ML-SNAP package
-------------
+---------------
 
 **Contents:**
 
@@ -1054,7 +1054,7 @@ computes which analyze attributes of the potential.
 
 **Supporting info:**
 
-* src/SNAP: filenames -> commands
+* src/ML-SNAP: filenames -> commands
 * :doc:`pair_style snap <pair_snap>`
 * :doc:`compute sna/atom <compute_sna_atom>`
 * :doc:`compute snad/atom <compute_sna_atom>`

doc/src/Packages_standard.rst

@@ -85,7 +85,7 @@ package:
 +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
 | :ref:`SHOCK <PKG-SHOCK>`         | shock loading methods                | :doc:`fix msst <fix_msst>`                         | n/a                                                  | no      |
 +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
-| :ref:`SNAP <PKG-SNAP>`           | quantum-fitted potential             | :doc:`pair_style snap <pair_snap>`                 | snap                                                 | no      |
+| :ref:`ML-SNAP <PKG-ML-SNAP>`     | quantum-fitted potential             | :doc:`pair_style snap <pair_snap>`                 | snap                                                 | no      |
 +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
 | :ref:`SPIN <PKG-SPIN>`           | magnetic atomic spin dynamics        | :doc:`Howto spins <Howto_spins>`                   | SPIN                                                 | no      |
 +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+

doc/src/compute_mliap.rst

@@ -167,9 +167,10 @@ Restrictions
 
 This compute is part of the ML-IAP package.  It is only enabled if
 LAMMPS was built with that package. In addition, building LAMMPS with
-the ML-IAP package requires building LAMMPS with the SNAP package.  The
+the ML-IAP package requires building LAMMPS with the ML-SNAP package.
-*mliappy* model also requires building LAMMPS with the PYTHON package.
+The *mliappy* model also requires building LAMMPS with the PYTHON
-See the :doc:`Build package <Build_package>` doc page for more info.
+package.  See the :doc:`Build package <Build_package>` doc page for more
+info.
 
 Related commands
 """"""""""""""""

doc/src/compute_sna_atom.rst

@@ -72,64 +72,66 @@ Description
 """""""""""
 
 Define a computation that calculates a set of quantities related to the
-bispectrum components of the atoms in a group. These computes are
+bispectrum components of the atoms in a group. These computes are used
-used primarily for calculating the dependence of energy, force, and
+primarily for calculating the dependence of energy, force, and stress
-stress components on the linear coefficients in the
+components on the linear coefficients in the :doc:`snap pair_style
-:doc:`snap pair_style <pair_snap>`, which is useful when training a
+<pair_snap>`, which is useful when training a SNAP potential to match
-SNAP potential to match target data.
+target data.
 
-Bispectrum components of an atom are order parameters characterizing
+Bispectrum components of an atom are order parameters characterizing the
-the radial and angular distribution of neighbor atoms. The detailed
+radial and angular distribution of neighbor atoms. The detailed
 mathematical definition is given in the paper by Thompson et
 al. :ref:`(Thompson) <Thompson20141>`
 
-The position of a neighbor atom *i'* relative to a central atom *i* is
+The position of a neighbor atom *i'* relative to a central atom *i* is a
-a point within the 3D ball of radius :math:`R_{ii'}` = *rcutfac* :math:`(R_i + R_i')`
+point within the 3D ball of radius :math:`R_{ii'}` = *rcutfac*
+:math:`(R_i + R_i')`
 
-Bartok et al. :ref:`(Bartok) <Bartok20101>`, proposed mapping this 3D ball
+Bartok et al. :ref:`(Bartok) <Bartok20101>`, proposed mapping this 3D
-onto the 3-sphere, the surface of the unit ball in a four-dimensional
+ball onto the 3-sphere, the surface of the unit ball in a
-space.  The radial distance *r*  within *R_ii'* is mapped on to a third
+four-dimensional space.  The radial distance *r* within *R_ii'* is
-polar angle :math:`\theta_0` defined by,
+mapped on to a third polar angle :math:`\theta_0` defined by,
 
 .. math::
 
   \theta_0 = {\sf rfac0} \frac{r-r_{min0}}{R_{ii'}-r_{min0}} \pi
 
 In this way, all possible neighbor positions are mapped on to a subset
-of the 3-sphere.  Points south of the latitude :math:`\theta_0` = *rfac0* :math:`\pi`
+of the 3-sphere.  Points south of the latitude :math:`\theta_0` =
-are excluded.
+*rfac0* :math:`\pi` are excluded.
 
 The natural basis for functions on the 3-sphere is formed by the
-representatives of *SU(2)*, the matrices :math:`U^j_{m,m'}(\theta, \phi, \theta_0)`.
+representatives of *SU(2)*, the matrices :math:`U^j_{m,m'}(\theta, \phi,
-These functions are better known as :math:`D^j_{m,m'}`, the elements of the Wigner
+\theta_0)`.  These functions are better known as :math:`D^j_{m,m'}`, the
-*D*\ -matrices :ref:`(Meremianin <Meremianin2006>`,
+elements of the Wigner *D*\ -matrices :ref:`(Meremianin
-:ref:`Varshalovich <Varshalovich1987>`, :ref:`Mason) <Mason2009>`
+<Meremianin2006>`, :ref:`Varshalovich <Varshalovich1987>`, :ref:`Mason)
-The density of neighbors on the 3-sphere can be written as a sum of
+<Mason2009>` The density of neighbors on the 3-sphere can be written as
-Dirac-delta functions, one for each neighbor, weighted by species and
+a sum of Dirac-delta functions, one for each neighbor, weighted by
-radial distance. Expanding this density function as a generalized
+species and radial distance. Expanding this density function as a
-Fourier series in the basis functions, we can write each Fourier
+generalized Fourier series in the basis functions, we can write each
-coefficient as
+Fourier coefficient as
 
 .. math::
 
   u^j_{m,m'} = U^j_{m,m'}(0,0,0) + \sum_{r_{ii'} < R_{ii'}}{f_c(r_{ii'}) w_{\mu_{i'}} U^j_{m,m'}(\theta_0,\theta,\phi)}
 
-The :math:`w_{\mu_{i'}}` neighbor weights are dimensionless numbers that depend on
+The :math:`w_{\mu_{i'}}` neighbor weights are dimensionless numbers that
-:math:`\mu_{i'}`, the SNAP element of atom *i'*, while the central atom is
+depend on :math:`\mu_{i'}`, the SNAP element of atom *i'*, while the
-arbitrarily assigned a unit weight.  The function :math:`f_c(r)` ensures that
+central atom is arbitrarily assigned a unit weight.  The function
-the contribution of each neighbor atom goes smoothly to zero at
+:math:`f_c(r)` ensures that the contribution of each neighbor atom goes
-:math:`R_{ii'}`:
+smoothly to zero at :math:`R_{ii'}`:
 
 .. math::
 
   f_c(r)   = & \frac{1}{2}(\cos(\pi \frac{r-r_{min0}}{R_{ii'}-r_{min0}}) + 1), r \leq R_{ii'} \\
            = & 0,  r > R_{ii'}
 
-The expansion coefficients :math:`u^j_{m,m'}` are complex-valued and they are
+The expansion coefficients :math:`u^j_{m,m'}` are complex-valued and
-not directly useful as descriptors, because they are not invariant
+they are not directly useful as descriptors, because they are not
-under rotation of the polar coordinate frame. However, the following
+invariant under rotation of the polar coordinate frame. However, the
-scalar triple products of expansion coefficients can be shown to be
+following scalar triple products of expansion coefficients can be shown
-real-valued and invariant under rotation :ref:`(Bartok) <Bartok20101>`.
+to be real-valued and invariant under rotation :ref:`(Bartok)
+<Bartok20101>`.
 
 .. math::
 
@@ -140,21 +142,20 @@ real-valued and invariant under rotation :ref:`(Bartok) <Bartok20101>`.
         {j_2} {m_2} {m'_2} \end{array}}
         u^{j_1}_{m_1,m'_1} u^{j_2}_{m_2,m'_2}
 
-The constants :math:`H^{jmm'}_{j_1 m_1 m_{1'},j_2 m_ 2m_{2'}}`
+The constants :math:`H^{jmm'}_{j_1 m_1 m_{1'},j_2 m_ 2m_{2'}}` are
-are coupling coefficients,
+coupling coefficients, analogous to Clebsch-Gordan coefficients for
-analogous to Clebsch-Gordan coefficients for rotations on the
+rotations on the 2-sphere. These invariants are the components of the
-2-sphere. These invariants are the components of the bispectrum and
+bispectrum and these are the quantities calculated by the compute
-these are the quantities calculated by the compute *sna/atom*\ . They
+*sna/atom*\ . They characterize the strength of density correlations at
-characterize the strength of density correlations at three points on
+three points on the 3-sphere. The j2=0 subset form the power spectrum,
-the 3-sphere. The j2=0 subset form the power spectrum, which
+which characterizes the correlations of two points. The lowest-order
-characterizes the correlations of two points. The lowest-order
+components describe the coarsest features of the density function, while
-components describe the coarsest features of the density function,
+higher-order components reflect finer detail. Each bispectrum component
-while higher-order components reflect finer detail. Each bispectrum
+contains terms that depend on the positions of up to 4 atoms (3
-component contains terms that depend on the positions of up to 4
+neighbors and the central atom).
-atoms (3 neighbors and the central atom).
 
-Compute *snad/atom* calculates the derivative of the bispectrum components
+Compute *snad/atom* calculates the derivative of the bispectrum
-summed separately for each LAMMPS atom type:
+components summed separately for each LAMMPS atom type:
 
 .. math::
 
@@ -180,16 +181,16 @@ section below on output for a detailed explanation.
 Compute *snap* calculates a global array containing information related
 to all three of the above per-atom computes *sna/atom*\ , *snad/atom*\ ,
 and *snav/atom*\ . The first row of the array contains the summation of
-*sna/atom* over all atoms, but broken out by type. The last six rows
+*sna/atom* over all atoms, but broken out by type. The last six rows of
-of the array contain the summation of *snav/atom* over all atoms, broken
+the array contain the summation of *snav/atom* over all atoms, broken
-out by type. In between these are 3\*\ *N* rows containing the same values
+out by type. In between these are 3\*\ *N* rows containing the same
-computed by *snad/atom* (these are already summed over all atoms and
+values computed by *snad/atom* (these are already summed over all atoms
-broken out by type). The element in the last column of each row contains
+and broken out by type). The element in the last column of each row
-the potential energy, force, or stress, according to the row.
+contains the potential energy, force, or stress, according to the row.
 These quantities correspond to the user-specified reference potential
-that must be subtracted from the target data when fitting SNAP.
+that must be subtracted from the target data when fitting SNAP.  The
-The potential energy calculation uses the built in compute *thermo_pe*.
+potential energy calculation uses the built in compute *thermo_pe*.  The
-The stress calculation uses a compute called *snap_press* that is
+stress calculation uses a compute called *snap_press* that is
 automatically created behind the scenes, according to the following
 command:
 
@@ -225,36 +226,32 @@ The keyword *switchflag* can be used to turn off the switching
 function :math:`f_c(r)`.
 
 The keyword *bzeroflag* determines whether or not *B0*\ , the bispectrum
-components of an atom with no neighbors, are subtracted from
+components of an atom with no neighbors, are subtracted from the
-the calculated bispectrum components. This optional keyword
+calculated bispectrum components. This optional keyword normally only
-normally only affects compute *sna/atom*\ . However, when
+affects compute *sna/atom*\ . However, when *quadraticflag* is on, it
-*quadraticflag* is on, it also affects *snad/atom* and *snav/atom*\ .
+also affects *snad/atom* and *snav/atom*\ .
 
-The keyword *quadraticflag* determines whether or not the
+The keyword *quadraticflag* determines whether or not the quadratic
-quadratic combinations of bispectrum quantities are generated.
+combinations of bispectrum quantities are generated.  These are formed
-These are formed by taking the outer product of the vector
+by taking the outer product of the vector of bispectrum components with
-of bispectrum components with itself.
+itself.  See section below on output for a detailed explanation of the
-See section below on output for a
+number of quadratic terms and the ordered in which they are listed.
-detailed explanation of the number of quadratic terms and the
-ordered in which they are listed.
 
-The keyword *chem* activates the explicit multi-element variant
+The keyword *chem* activates the explicit multi-element variant of the
-of the SNAP bispectrum components. The argument *nelements*
+SNAP bispectrum components. The argument *nelements* specifies the
-specifies the number of SNAP elements that will be handled.
+number of SNAP elements that will be handled.  This is followed by
-This is followed by *elementlist*, a list of integers of
+*elementlist*, a list of integers of length *ntypes*, with values in the
-length *ntypes*, with values in the range [0, *nelements* ),
+range [0, *nelements* ), which maps each LAMMPS type to one of the SNAP
-which maps each LAMMPS type to one of the SNAP elements.
+elements.  Note that multiple LAMMPS types can be mapped to the same
-Note that multiple LAMMPS types can be mapped to the same element,
+element, and some elements may be mapped by no LAMMPS type. However, in
-and some elements may be mapped by no LAMMPS type. However, in typical
+typical use cases (training SNAP potentials) the mapping from LAMMPS
-use cases (training SNAP potentials) the mapping from LAMMPS types
+types to elements is one-to-one.
-to elements is one-to-one.
 
 The explicit multi-element variant invoked by the *chem* keyword
-partitions the density of neighbors into partial densities
+partitions the density of neighbors into partial densities for each
-for each chemical element.  This is described in detail in the
+chemical element.  This is described in detail in the paper by
-paper by :ref:`Cusentino et al. <Cusentino2020>`
+:ref:`Cusentino et al. <Cusentino2020>` The bispectrum components are
-The bispectrum components are indexed on
+indexed on ordered triplets of elements:
-ordered triplets of elements:
 
 .. math::
 
@@ -272,17 +269,19 @@ of element :math:`\mu`
 
   u^{\mu}_{j,m,m'} =  w^{self}_{\mu_{i}\mu} U^{j,m,m'}(0,0,0) + \sum_{r_{ii'} < R_{ii'}}{\delta_{\mu\mu_{i'}}f_c(r_{ii'}) w_{\mu_{i'}} U^{j,m,m'}(\theta_0,\theta,\phi)}
 
-where :math:`w^{self}_{\mu_{i}\mu}` is the self-contribution, which is either 1 or 0
+where :math:`w^{self}_{\mu_{i}\mu}` is the self-contribution, which is
-(see keyword *wselfallflag* below), :math:`\delta_{\mu\mu_{i'}}` indicates
+either 1 or 0 (see keyword *wselfallflag* below),
-that the sum is only over neighbor atoms of element :math:`\mu`,
+:math:`\delta_{\mu\mu_{i'}}` indicates that the sum is only over
-and all other quantities are the same as those appearing in the
+neighbor atoms of element :math:`\mu`, and all other quantities are the
-original equation for :math:`u^j_{m,m'}` given above.
+same as those appearing in the original equation for :math:`u^j_{m,m'}`
+given above.
 
-The keyword *wselfallflag* defines the rule used for the self-contribution.
+The keyword *wselfallflag* defines the rule used for the
-If *wselfallflag* is on, then :math:`w^{self}_{\mu_{i}\mu}` = 1. If it is
+self-contribution.  If *wselfallflag* is on, then
-off then :math:`w^{self}_{\mu_{i}\mu}` = 0, except in the case
+:math:`w^{self}_{\mu_{i}\mu}` = 1. If it is off then
-of :math:`{\mu_{i}=\mu}`, when :math:`w^{self}_{\mu_{i}\mu}` = 1.
+:math:`w^{self}_{\mu_{i}\mu}` = 0, except in the case of
-When the *chem* keyword is not used, this keyword has no effect.
+:math:`{\mu_{i}=\mu}`, when :math:`w^{self}_{\mu_{i}\mu}` = 1.  When the
+*chem* keyword is not used, this keyword has no effect.
 
 The keyword *bnormflag* determines whether or not the bispectrum
 component :math:`B_{j_1,j_2,j}` is divided by a factor of :math:`2j+1`.
@@ -299,16 +298,16 @@ are not both set or not both unset.
 
 .. note::
 
-   If you have a bonded system, then the settings of
+   If you have a bonded system, then the settings of :doc:`special_bonds
-   :doc:`special_bonds <special_bonds>` command can remove pairwise
+   <special_bonds>` command can remove pairwise interactions between
-   interactions between atoms in the same bond, angle, or dihedral.  This
+   atoms in the same bond, angle, or dihedral.  This is the default
-   is the default setting for the :doc:`special_bonds <special_bonds>`
+   setting for the :doc:`special_bonds <special_bonds>` command, and
-   command, and means those pairwise interactions do not appear in the
+   means those pairwise interactions do not appear in the neighbor list.
-   neighbor list.  Because this fix uses the neighbor list, it also means
+   Because this fix uses the neighbor list, it also means those pairs
-   those pairs will not be included in the calculation.  One way to get
+   will not be included in the calculation.  One way to get around this,
-   around this, is to write a dump file, and use the :doc:`rerun <rerun>`
+   is to write a dump file, and use the :doc:`rerun <rerun>` command to
-   command to compute the bispectrum components for snapshots in the dump
+   compute the bispectrum components for snapshots in the dump file.
-   file.  The rerun script can use a :doc:`special_bonds <special_bonds>`
+   The rerun script can use a :doc:`special_bonds <special_bonds>`
    command that includes all pairs in the neighbor list.
 
 ----------
@@ -317,10 +316,10 @@ Output info
 """""""""""
 
 Compute *sna/atom* calculates a per-atom array, each column
-corresponding to a particular bispectrum component.  The total number
+corresponding to a particular bispectrum component.  The total number of
-of columns and the identity of the bispectrum component contained in
+columns and the identity of the bispectrum component contained in each
-each column depend of the value of *twojmax*\ , as
+column depend of the value of *twojmax*\ , as described by the following
-described by the following piece of python code:
+piece of python code:
 
 .. parsed-literal::
 
@@ -338,73 +337,72 @@ For even twojmax = 2(*m*\ -1), :math:`K = m(m+1)(2m+1)/6`, the *m*\ -th pyramida
    since all potentials use the value of 3, corresponding to the
    above set of bispectrum components.
 
-Compute *snad/atom* evaluates a per-atom array. The columns are
+Compute *snad/atom* evaluates a per-atom array. The columns are arranged
-arranged into *ntypes* blocks, listed in order of atom type *I*\ .  Each
+into *ntypes* blocks, listed in order of atom type *I*\ .  Each block
-block contains three sub-blocks corresponding to the *x*\ , *y*\ , and *z*
+contains three sub-blocks corresponding to the *x*\ , *y*\ , and *z*
 components of the atom position.  Each of these sub-blocks contains *K*
-columns for the *K* bispectrum components, the same as for compute *sna/atom*
+columns for the *K* bispectrum components, the same as for compute
+*sna/atom*
 
-Compute *snav/atom* evaluates a per-atom array. The columns are
+Compute *snav/atom* evaluates a per-atom array. The columns are arranged
-arranged into *ntypes* blocks, listed in order of atom type *I*\ .  Each
+into *ntypes* blocks, listed in order of atom type *I*\ .  Each block
-block contains six sub-blocks corresponding to the *xx*\ , *yy*\ , *zz*\ ,
+contains six sub-blocks corresponding to the *xx*\ , *yy*\ , *zz*\ ,
 *yz*\ , *xz*\ , and *xy* components of the virial tensor in Voigt
-notation.  Each of these sub-blocks contains *K*
+notation.  Each of these sub-blocks contains *K* columns for the *K*
-columns for the *K* bispectrum components, the same as for compute *sna/atom*
+bispectrum components, the same as for compute *sna/atom*
 
-Compute *snap* evaluates a global array.
+Compute *snap* evaluates a global array.  The columns are arranged into
-The columns are arranged into
+*ntypes* blocks, listed in order of atom type *I*\ . Each block contains
-*ntypes* blocks, listed in order of atom type *I*\ . Each block
+one column for each bispectrum component, the same as for compute
-contains one column for each bispectrum component, the same as for compute
+*sna/atom*\ . A final column contains the corresponding energy, force
-*sna/atom*\ . A final column contains the corresponding energy, force component
+component on an atom, or virial stress component. The rows of the array
-on an atom, or virial stress component. The rows of the array appear
+appear in the following order:
-in the following order:
 
 * 1 row: *sna/atom* quantities summed for all atoms of type *I*
 * 3\*\ *N* rows: *snad/atom* quantities, with derivatives w.r.t. x, y, and z coordinate of atom *i* appearing in consecutive rows. The atoms are sorted based on atom ID.
 * 6 rows: *snav/atom* quantities summed for all atoms of type *I*
 
-For example, if *K* =30 and ntypes=1, the number of columns in the per-atom
+For example, if *K* =30 and ntypes=1, the number of columns in the
-arrays generated by *sna/atom*\ , *snad/atom*\ , and *snav/atom*
+per-atom arrays generated by *sna/atom*\ , *snad/atom*\ , and
-are 30, 90, and 180, respectively. With *quadratic* value=1,
+*snav/atom* are 30, 90, and 180, respectively. With *quadratic* value=1,
-the numbers of columns are 930, 2790, and 5580, respectively.
+the numbers of columns are 930, 2790, and 5580, respectively.  The
-The number of columns in the global array generated by *snap*
+number of columns in the global array generated by *snap* are 31, and
-are 31, and 931, respectively, while the number of rows is
+931, respectively, while the number of rows is 1+3\*\ *N*\ +6, where *N*
-1+3\*\ *N*\ +6, where *N* is the total number of atoms.
+is the total number of atoms.
 
-If the *quadratic* keyword value is set to 1, then additional
+If the *quadratic* keyword value is set to 1, then additional columns
-columns are generated, corresponding to
+are generated, corresponding to the products of all distinct pairs of
-the products of all distinct pairs of  bispectrum components. If the
+bispectrum components. If the number of bispectrum components is *K*\ ,
-number of bispectrum components is *K*\ , then the number of distinct pairs
+then the number of distinct pairs is *K*\ (\ *K*\ +1)/2.  For compute
-is  *K*\ (\ *K*\ +1)/2.
+*sna/atom* these columns are appended to existing *K* columns.  The
-For compute *sna/atom* these columns are appended to existing *K* columns.
+ordering of quadratic terms is upper-triangular, (1,1),(1,2)...(1,\ *K*\
-The ordering of quadratic terms is upper-triangular,
+),(2,1)...(\ *K*\ -1,\ *K*\ -1),(\ *K*\ -1,\ *K*\ ),(\ *K*\ ,\ *K*\ ).
-(1,1),(1,2)...(1,\ *K*\ ),(2,1)...(\ *K*\ -1,\ *K*\ -1),(\ *K*\ -1,\ *K*\ ),(\ *K*\ ,\ *K*\ ).
 For computes *snad/atom* and *snav/atom* each set of *K*\ (\ *K*\ +1)/2
-additional columns is inserted directly after each of sub-block
+additional columns is inserted directly after each of sub-block of
-of linear terms i.e. linear and quadratic terms are contiguous.
+linear terms i.e. linear and quadratic terms are contiguous.  So the
-So the nesting order from inside to outside is bispectrum component,
+nesting order from inside to outside is bispectrum component, linear
-linear then quadratic, vector/tensor component, type.
+then quadratic, vector/tensor component, type.
 
-If the *chem* keyword is used, then the data is arranged into :math:`N_{elem}^3`
+If the *chem* keyword is used, then the data is arranged into
-sub-blocks, each sub-block corresponding to a particular chemical labeling
+:math:`N_{elem}^3` sub-blocks, each sub-block corresponding to a
-:math:`\kappa\lambda\mu` with the last label changing fastest.
+particular chemical labeling :math:`\kappa\lambda\mu` with the last
-Each sub-block contains *K* bispectrum components. For the purposes
+label changing fastest.  Each sub-block contains *K* bispectrum
-of handling contributions to force, virial, and quadratic combinations,
+components. For the purposes of handling contributions to force, virial,
-these :math:`N_{elem}^3` sub-blocks are treated as a single block
+and quadratic combinations, these :math:`N_{elem}^3` sub-blocks are
-of :math:`K N_{elem}^3` columns.
+treated as a single block of :math:`K N_{elem}^3` columns.
 
 These values can be accessed by any command that uses per-atom values
 from a compute as input.  See the :doc:`Howto output <Howto_output>` doc
 page for an overview of LAMMPS output options. To see how this command
-can be used within a Python workflow to train SNAP potentials,
+can be used within a Python workflow to train SNAP potentials, see the
-see the examples in `FitSNAP <https://github.com/FitSNAP/FitSNAP>`_.
+examples in `FitSNAP <https://github.com/FitSNAP/FitSNAP>`_.
 
 Restrictions
 """"""""""""
 
-These computes are part of the SNAP package.  They are only enabled if
+These computes are part of the ML-SNAP package.  They are only enabled
-LAMMPS was built with that package.  See the :doc:`Build package <Build_package>`
+if LAMMPS was built with that package.  See the :doc:`Build package
-doc page for more info.
+<Build_package>` doc page for more info.
 
 Related commands
 """"""""""""""""

doc/src/pair_mliap.rst

@@ -194,9 +194,9 @@ Restrictions
 
 This pair style is part of the ML-IAP package.  It is only enabled if
 LAMMPS was built with that package. In addition, building LAMMPS with
-the ML-IAP package requires building LAMMPS with the SNAP package.  The
+the ML-IAP package requires building LAMMPS with the ML-SNAP package.
-*mliappy* model requires building LAMMPS with the PYTHON package.  See
+The *mliappy* model requires building LAMMPS with the PYTHON package.
-the :doc:`Build package <Build_package>` doc page for more info.
+See the :doc:`Build package <Build_package>` doc page for more info.
 
 
 Related commands

doc/src/pair_snap.rst

@@ -24,32 +24,28 @@ Examples
 Description
 """""""""""
 
-Pair style *snap* defines the spectral
+Pair style *snap* defines the spectral neighbor analysis potential
-neighbor analysis potential (SNAP), a machine-learning
+(SNAP), a machine-learning interatomic potential :ref:`(Thompson)
-interatomic potential :ref:`(Thompson) <Thompson20142>`.
+<Thompson20142>`.  Like the GAP framework of Bartok et
-Like the GAP framework of Bartok et al. :ref:`(Bartok2010) <Bartok20102>`,
+al. :ref:`(Bartok2010) <Bartok20102>`, SNAP uses bispectrum components
-SNAP uses bispectrum components
+to characterize the local neighborhood of each atom in a very general
-to characterize the local neighborhood of each atom
+way. The mathematical definition of the bispectrum calculation and its
-in a very general way. The mathematical definition of the
+derivatives w.r.t. atom positions is identical to that used by
-bispectrum calculation and its derivatives w.r.t. atom positions
+:doc:`compute snap <compute_sna_atom>`, which is used to fit SNAP
-is identical to that used by :doc:`compute snap <compute_sna_atom>`,
+potentials to *ab initio* energy, force, and stress data.  In SNAP, the
-which is used to fit SNAP potentials to *ab initio* energy, force,
+total energy is decomposed into a sum over atom energies. The energy of
-and stress data.
+atom *i* is expressed as a weighted sum over bispectrum components.
-In SNAP, the total energy is decomposed into a sum over
-atom energies. The energy of atom *i* is
-expressed as a weighted sum over bispectrum components.
 
 .. math::
 
    E^i_{SNAP}(B_1^i,...,B_K^i) = \beta^{\mu_i}_0 + \sum_{k=1}^K \beta_k^{\mu_i} B_k^i
 
 where :math:`B_k^i` is the *k*\ -th bispectrum component of atom *i*\ ,
-and :math:`\beta_k^{\mu_i}` is the corresponding linear coefficient
+and :math:`\beta_k^{\mu_i}` is the corresponding linear coefficient that
-that depends on :math:`\mu_i`, the SNAP element of atom *i*\ . The
+depends on :math:`\mu_i`, the SNAP element of atom *i*\ . The number of
-number of bispectrum components used and their definitions
+bispectrum components used and their definitions depend on the value of
-depend on the value of *twojmax* and other parameters
+*twojmax* and other parameters defined in the SNAP parameter file
-defined in the SNAP parameter file described below.
+described below.  The bispectrum calculation is described in more detail
-The bispectrum calculation is described in more detail
 in :doc:`compute sna/atom <compute_sna_atom>`.
 
 Note that unlike for other potentials, cutoffs for SNAP potentials are
@@ -80,32 +76,28 @@ The two trailing 'In' arguments map LAMMPS atom types 1 and 2 to the
 SNAP 'In' element. The two trailing 'P' arguments map LAMMPS atom types
 3 and 4 to the SNAP 'P' element.
 
-If a SNAP mapping value is
+If a SNAP mapping value is specified as NULL, the mapping is not
-specified as NULL, the mapping is not performed.
+performed.  This can be used when a *snap* potential is used as part of
-This can be used when a *snap* potential is used as part of the
+the *hybrid* pair style.  The NULL values are placeholders for atom
-*hybrid* pair style.  The NULL values are placeholders for atom types
+types that will be used with other potentials.
-that will be used with other potentials.
 
-The name of the SNAP coefficient file usually ends in the
+The name of the SNAP coefficient file usually ends in the ".snapcoeff"
-".snapcoeff" extension. It may contain coefficients
+extension. It may contain coefficients for many SNAP elements. The only
-for many SNAP elements. The only requirement is that
+requirement is that each of the unique element names appearing in the
-each of the unique element names appearing in the
+LAMMPS pair_coeff command appear exactly once in the SNAP coefficient
-LAMMPS pair_coeff command appear exactly once in
+file. It is okay if the SNAP coefficient file contains additional
-the SNAP coefficient file. It is okay if the SNAP coefficient file
+elements not in the pair_coeff command, except when using *chemflag*
-contains additional elements not in the pair_coeff command,
+(see below).  The name of the SNAP parameter file usually ends in the
-except when using *chemflag* (see below).
+".snapparam" extension. It contains a small number of parameters that
-The name of the SNAP parameter file usually ends in the ".snapparam"
+define the overall form of the SNAP potential.  See the :doc:`pair_coeff
-extension. It contains a small number
+<pair_coeff>` doc page for alternate ways to specify the path for these
-of parameters that define the overall form of the SNAP potential.
+files.
-See the :doc:`pair_coeff <pair_coeff>` doc page for alternate ways
-to specify the path for these files.
 
-Quite commonly,
+SNAP potentials are quite commonly combined with one or more other
-SNAP potentials are combined with one or more other LAMMPS pair styles
+LAMMPS pair styles using the *hybrid/overlay* pair style.  As an
-using the *hybrid/overlay* pair style. As an example, the SNAP
+example, the SNAP tantalum potential provided in the LAMMPS potentials
-tantalum potential provided in the LAMMPS potentials directory
+directory combines the *snap* and *zbl* pair styles. It is invoked by
-combines the *snap* and *zbl* pair styles. It is invoked
+the following commands:
-by the following commands:
 
 .. code-block:: LAMMPS
 
@@ -118,13 +110,13 @@ by the following commands:
    pair_coeff 1 1 zbl ${zblz}
    pair_coeff * * snap Ta06A.snapcoeff Ta06A.snapparam Ta
 
-It is convenient to keep these commands in a separate file that can
+It is convenient to keep these commands in a separate file that can be
-be inserted in any LAMMPS input script using the :doc:`include <include>`
+inserted in any LAMMPS input script using the :doc:`include <include>`
 command.
 
-The top of the SNAP coefficient file can contain any number of blank and comment lines (start with #), but follows a strict
+The top of the SNAP coefficient file can contain any number of blank and
-format after that. The first non-blank non-comment
+comment lines (start with #), but follows a strict format after
-line must contain two integers:
+that. The first non-blank non-comment line must contain two integers:
 
 * nelem  = Number of elements
 * ncoeff = Number of coefficients
@@ -157,39 +149,44 @@ The default values for these keywords are
 * *wselfallflag* = 0
 * *chunksize* = 4096
 
-If *quadraticflag* is set to 1, then the SNAP energy expression includes additional quadratic terms
+If *quadraticflag* is set to 1, then the SNAP energy expression includes
-that have been shown to increase the overall accuracy of the potential without much increase
+additional quadratic terms that have been shown to increase the overall
-in computational cost :ref:`(Wood) <Wood20182>`.
+accuracy of the potential without much increase in computational cost
+:ref:`(Wood) <Wood20182>`.
 
 .. math::
 
    E^i_{SNAP}(\mathbf{B}^i) = \beta^{\mu_i}_0 + \boldsymbol{\beta}^{\mu_i} \cdot \mathbf{B}_i + \frac{1}{2}\mathbf{B}^t_i \cdot \boldsymbol{\alpha}^{\mu_i} \cdot \mathbf{B}_i
 
 where :math:`\mathbf{B}_i` is the *K*-vector of bispectrum components,
-:math:`\boldsymbol{\beta}^{\mu_i}` is the *K*-vector of linear coefficients
+:math:`\boldsymbol{\beta}^{\mu_i}` is the *K*-vector of linear
-for element :math:`\mu_i`, and :math:`\boldsymbol{\alpha}^{\mu_i}`
+coefficients for element :math:`\mu_i`, and
-is the symmetric *K* by *K* matrix of quadratic coefficients.
+:math:`\boldsymbol{\alpha}^{\mu_i}` is the symmetric *K* by *K* matrix
-The SNAP coefficient file should contain *K*\ (\ *K*\ +1)/2 additional coefficients
+of quadratic coefficients.  The SNAP coefficient file should contain
-in each element block, the upper-triangular elements of :math:`\boldsymbol{\alpha}^{\mu_i}`.
+*K*\ (\ *K*\ +1)/2 additional coefficients in each element block, the
+upper-triangular elements of :math:`\boldsymbol{\alpha}^{\mu_i}`.
 
-If *chemflag* is set to 1, then the energy expression is written in terms of explicit multi-element bispectrum
+If *chemflag* is set to 1, then the energy expression is written in
-components indexed on ordered triplets of elements, which has been shown to increase the ability of the SNAP
+terms of explicit multi-element bispectrum components indexed on ordered
-potential to capture energy differences in chemically complex systems,
+triplets of elements, which has been shown to increase the ability of
-at the expense of a significant increase in computational cost :ref:`(Cusentino) <Cusentino20202>`.
+the SNAP potential to capture energy differences in chemically complex
+systems, at the expense of a significant increase in computational cost
+:ref:`(Cusentino) <Cusentino20202>`.
 
 .. math::
 
    E^i_{SNAP}(\mathbf{B}^i) = \beta^{\mu_i}_0 + \sum_{\kappa,\lambda,\mu} \boldsymbol{\beta}^{\kappa\lambda\mu}_{\mu_i} \cdot \mathbf{B}^{\kappa\lambda\mu}_i
 
-where :math:`\mathbf{B}^{\kappa\lambda\mu}_i` is the *K*-vector of bispectrum components
+where :math:`\mathbf{B}^{\kappa\lambda\mu}_i` is the *K*-vector of
-for neighbors of elements :math:`\kappa`, :math:`\lambda`, and :math:`\mu` and
+bispectrum components for neighbors of elements :math:`\kappa`,
-:math:`\boldsymbol{\beta}^{\kappa\lambda\mu}_{\mu_i}` is the corresponding *K*-vector
+:math:`\lambda`, and :math:`\mu` and
-of linear coefficients for element :math:`\mu_i`. The SNAP coefficient file should contain
+:math:`\boldsymbol{\beta}^{\kappa\lambda\mu}_{\mu_i}` is the
-a total of :math:`K N_{elem}^3` coefficients in each element block,
+corresponding *K*-vector of linear coefficients for element
-where :math:`N_{elem}` is the number of elements in the SNAP coefficient file,
+:math:`\mu_i`. The SNAP coefficient file should contain a total of
-which must equal the number of unique elements appearing in the
+:math:`K N_{elem}^3` coefficients in each element block, where
-LAMMPS pair_coeff command, to avoid ambiguity in the
+:math:`N_{elem}` is the number of elements in the SNAP coefficient file,
-number of coefficients.
+which must equal the number of unique elements appearing in the LAMMPS
+pair_coeff command, to avoid ambiguity in the number of coefficients.
 
 The keyword *chunksize* is only applicable when using the
 pair style *snap* with the KOKKOS package and is ignored otherwise.
@@ -221,9 +218,10 @@ 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
+This pair style does not write its information to :doc:`binary restart
-need to re-specify the pair_style and pair_coeff commands in an input
+files <restart>`, since it is stored in potential files.  Thus, you need
-script that reads a restart file.
+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
@@ -238,8 +236,9 @@ This pair style can only be used via the *pair* keyword of the
 Restrictions
 """"""""""""
 
-This style is part of the SNAP package.  It is only enabled if LAMMPS
+This style is part of the ML-SNAP package.  It is only enabled if LAMMPS
-was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+was built with that package.  See the :doc:`Build package
+<Build_package>` doc page for more info.
 
 Related commands
 """"""""""""""""

potentials/README

@@ -100,9 +100,9 @@ meam.spline   modified EAM (MEAM) spline potential
 meam.sw.spline modified EAM (MEAM) Stillinger-Weber spline potential
 mesocnt       mesoscopic carbon nanotube (CNT) potential
 mgpt          model generalized pseudopotential theory (MGPT) potential
-mliap         ML-IAP potential
+mliap         MLIAP potential
-mliap.descriptor ML-IAP potential descriptor
+mliap.descriptor MLIAP potential descriptor
-mliap.model   ML-IAP potential model
+mliap.model   MLIAP potential model
 nb3b.harmonic nonbonded 3-body harmonic potential
 poly          polymorphic 3-body potential
 reax          ReaxFF potential (see README.reax for more info)

src/Depend.sh

@@ -116,7 +116,7 @@ if (test $1 = "RIGID") then
   depend USER-SDPD
 fi
 
-if (test $1 = "SNAP") then
+if (test $1 = "ML-SNAP") then
   depend KOKKOS
   depend ML-IAP
 fi

src/Makefile

@@ -49,7 +49,7 @@ endif
 PACKAGE = asphere body class2 colloid compress coreshell dipole gpu \
 	  granular kim kokkos kspace latte manybody mc message misc \
 	  ml-iap molecule mpiio mscg opt peri plugin poems \
-	  python qeq replica rigid shock snap spin srd voronoi
+	  python qeq replica rigid shock ml-snap spin srd voronoi
 
 PACKUSER = user-adios user-atc user-awpmd user-brownian user-bocs user-cgdna \
 	   user-cgsdk user-colvars user-dielectric user-diffraction user-dpd user-drude \