diff --git a/doc/src/Howto_type_labels.rst b/doc/src/Howto_type_labels.rst index 8f03f45ef9..d7460d50a7 100644 --- a/doc/src/Howto_type_labels.rst +++ b/doc/src/Howto_type_labels.rst @@ -14,16 +14,17 @@ wherever they appear in LAMMPS input or output files. The total number Ntypes for each interaction is "locked in" when the simulation box is created. -A recent addition to LAMMPS is the option to use strings - referred -to as type labels - as an alternative. Using type labels instead of +A recent addition to LAMMPS is the option to use strings - referred to +as type labels - as an alternative. Using type labels instead of numeric types can be advantageous in various scenarios. For example, -type labels can make inputs more readable and generic (i.e. usable through -the :doc:`include command ` for different systems with different -numerical values assigned to types. This generality also applies to -other inputs like data files read by :doc:`read_data ` or -molecule template files read by the :doc:`molecule ` -command. See below for a list of other commands that can use -type labels in different ways. +type labels can make inputs more readable and generic (i.e. usable +through the :doc:`include command ` for different systems with +different numerical values assigned to types. This generality also +applies to other inputs like data files read by :doc:`read_data +` or molecule template files read by the :doc:`molecule +` command. A discussion of the current type label support can +be found in :ref:`(Gissinger) `. See below for a list of +other commands that can use type labels in different ways. LAMMPS will *internally* continue to use numeric types, which means that many previous restrictions still apply. For example, the total @@ -124,3 +125,9 @@ between the files. The creation of simulation-ready reaction templates for :doc:`fix bond/react ` is much simpler when using type labels, and results in templates that can be used without modification in multiple simulations or different systems. + +----------- + +.. _Typelabel24: + +**(Gissinger)** J. Gissinger, I. Nikiforov, Y. Afshar, B. Waters, M. Choi, D. Karls, A. Stukowski, W, Im, H. Heinz, A. Kohlmeyer, and E. Tadmor, J Phys Chem B, 128, 3282-3297 (2024) diff --git a/doc/src/labelmap.rst b/doc/src/labelmap.rst index 9e3d705101..5e0d1e92e9 100644 --- a/doc/src/labelmap.rst +++ b/doc/src/labelmap.rst @@ -43,7 +43,8 @@ The label map can also be defined by the :doc:`read_data ` command when it reads these sections in a data file: Atom Type Labels, Bond Type Labels, etc. See the :doc:`Howto type labels ` doc page for a general discussion of how type -labels can be used. +labels can be used. See :ref:`(Gissinger) ` for a discussion +of the type label implementation in LAMMPS and its uses. Valid type labels can contain any alphanumeric character, but must not start with a number, a '#', or a '*' character. They can contain other @@ -98,3 +99,9 @@ Default """"""" none + +----------- + +.. _Typelabel: + +**(Gissinger)** J. Gissinger, I. Nikiforov, Y. Afshar, B. Waters, M. Choi, D. Karls, A. Stukowski, W, Im, H. Heinz, A. Kohlmeyer, and E. Tadmor, J Phys Chem B, 128, 3282-3297 (2024) diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 88ac0e3140..cf4e48feff 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -476,6 +476,7 @@ ChiralIDs chirality Cho Chodera +Choi ChooseOffset chris Christoph