integrate compute ptm/atom and USER-PTM into the docs (e1627caf) · Commits · 郑智淋 / lammps

doc/src/Commands_compute.txt

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		@@ -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,

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		@@ -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:]

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		@@ -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

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		@@ -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:]

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