From e1627caf04eb20d6fcf2282964f025c866b3aad9 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 27 Sep 2018 07:20:03 -0400
Subject: [PATCH] integrate compute ptm/atom and USER-PTM into the docs
---
doc/src/Commands_compute.txt | 1 +
doc/src/Packages_details.txt | 20 ++++++++++++++++++++
doc/src/Packages_user.txt | 1 +
doc/src/compute_ptm_atom.txt | 6 +++++-
doc/src/computes.txt | 1 +
doc/src/lammps.book | 1 +
6 files changed, 29 insertions(+), 1 deletion(-)
diff --git a/doc/src/Commands_compute.txt b/doc/src/Commands_compute.txt
index 028e274c9b..a89f3adf5d 100644
--- a/doc/src/Commands_compute.txt
+++ b/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,
diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt
index 494f393a16..73345a2940 100644
--- a/doc/src/Packages_details.txt
+++ b/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:]
diff --git a/doc/src/Packages_user.txt b/doc/src/Packages_user.txt
index 70ac6022b6..6d3a8f754a 100644
--- a/doc/src/Packages_user.txt
+++ b/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
diff --git a/doc/src/compute_ptm_atom.txt b/doc/src/compute_ptm_atom.txt
index c668eb7726..6fe4d012f5 100644
--- a/doc/src/compute_ptm_atom.txt
+++ b/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:]
diff --git a/doc/src/computes.txt b/doc/src/computes.txt
index 46dd30f757..aa6cf5bb64 100644
--- a/doc/src/computes.txt
+++ b/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
diff --git a/doc/src/lammps.book b/doc/src/lammps.book
index 828863ae67..ae58e66efd 100644
--- a/doc/src/lammps.book
+++ b/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
--
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