integrate compute ptm/atom and USER-PTM into the docs

doc/src/Commands_compute.txt

@@ -95,6 +95,7 @@ KOKKOS, o = USER-OMP, t = OPT.
 "property/atom"_compute_property_atom.html,
 "property/chunk"_compute_property_chunk.html,
 "property/local"_compute_property_local.html,
+"ptm/atom"_compute_ptm_atom.html
 "rdf"_compute_rdf.html,
 "reduce"_compute_reduce.html,
 "reduce/region"_compute_reduce.html,

doc/src/Packages_details.txt

@@ -89,6 +89,7 @@ as contained in the file name.
 "USER-NETCDF"_#PKG-USER-NETCDF,
 "USER-OMP"_#PKG-USER-OMP,
 "USER-PHONON"_#PKG-USER-PHONON,
+"USER-PTM"_#PKG-USER-PTM,
 "USER-QMMM"_#PKG-USER-QMMM,
 "USER-QTB"_#PKG-USER-QTB,
 "USER-QUIP"_#PKG-USER-QUIP,
@@ -1744,6 +1745,25 @@ examples/USER/phonon :ul
 
 :line
 
+USER-PTM package :link(PKG-USER-PTM),h4
+
+[Contents:]
+
+A "compute ptm/atom"_compute_ptm.html command that calculates
+local structure characterization using the Polyhedral Template
+Matching methodology.
+
+[Author:] Peter Mahler Larsen (MIT).
+
+[Supporting info:]
+
+src/USER-PHONON: filenames -> commands
+src/USER-PHONON/README
+"fix phonon"_fix_phonon.html
+examples/USER/phonon :ul
+
+:line
+
 USER-QMMM package :link(PKG-USER-QMMM),h4
 
 [Contents:]

doc/src/Packages_user.txt

@@ -62,6 +62,7 @@ Package, Description, Doc page, Example, Library
 "USER-NETCDF"_Packages_details.html#PKG-USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, n/a, ext
 "USER-OMP"_Packages_details.html#PKG-USER-OMP, OpenMP-enabled styles,"Speed omp"_Speed_omp.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, no
 "USER-PHONON"_Packages_details.html#PKG-USER-PHONON, phonon dynamical matrix,"fix phonon"_fix_phonon.html, USER/phonon, no
+"USER-PTM"_Packages_details.html#PKG-USER-PTM, Polyhedral Template Matching,"compute ptm/atom"_compute_ptm.html, n/a, no
 "USER-QMMM"_Packages_details.html#PKG-USER-QMMM, QM/MM coupling,"fix qmmm"_fix_qmmm.html, USER/qmmm, ext
 "USER-QTB"_Packages_details.html#PKG-USER-QTB, quantum nuclear effects,"fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, no
 "USER-QUIP"_Packages_details.html#PKG-USER-QUIP, QUIP/libatoms interface,"pair_style quip"_pair_quip.html, USER/quip, ext

doc/src/compute_ptm_atom.txt

@@ -101,7 +101,11 @@ The (qw,qx,qy,qz) parameters represent the orientation of the local structure
 in quaternion form.  The reference coordinates for each template (from which the
 orientation is determined) can be found in the {ptm_constants.h} file in the PTM source directory.
 
-[Restrictions:] none
+[Restrictions:]
+
+This fix is part of the USER-PTM package.  It is only enabled if
+LAMMPS was built with that package.  See the "Build
+package"_Build_package.html doc page for more info.
 
 [Related commands:]
 

doc/src/computes.txt

@@ -70,6 +70,7 @@ Computes :h1
    compute_property_atom
    compute_property_chunk
    compute_property_local
+   compute_ptm_atom
    compute_rdf
    compute_reduce
    compute_rigid_local

doc/src/lammps.book

@@ -467,6 +467,7 @@ compute_pressure_uef.html
 compute_property_atom.html
 compute_property_chunk.html
 compute_property_local.html
+compute_ptm_atom.html
 compute_rdf.html
 compute_reduce.html
 compute_rigid_local.html