diff --git a/doc/src/Commands_compute.txt b/doc/src/Commands_compute.txt index 028e274c9be4a80555dfcab5a417d738b763bfda..a89f3adf5d8d24d14203e5c21ac24dbfc9484cdb 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 494f393a16906b4f4436d133d45210fb144505f7..73345a2940873bc8ed82521d2a1be4df32c6ed1b 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 70ac6022b6cb9bfc86eebbe3df45ece1d6ca28e8..6d3a8f754a8f8de6e72dd3fa67a83ca950c7d948 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 c668eb772614f237f54516fab6be48b89c86285b..6fe4d012f5a1679f61ef7bb2e81de3790b9ca9ce 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 46dd30f7570f7a87d9874367f67f1d4af85a2fca..aa6cf5bb6482b3b0ac0581a541cc9efb1d38867a 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 828863ae67d0afa794ce315b05d69b77587ada5e..ae58e66efd81a9ea83447f2fa5e520577de5a870 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