diff --git a/doc/src/Section_commands.txt b/doc/src/Section_commands.txt index 571c6c4920eb658b20d03c3540e0341fe8e7ddad..80a3ef5c64f6b1ef783c4a96324121fbe6c80f7e 100644 --- a/doc/src/Section_commands.txt +++ b/doc/src/Section_commands.txt @@ -532,7 +532,8 @@ package"_Section_start.html#start_3. "dump vtk"_dump_vtk.html, "group2ndx"_group2ndx.html, "ndx2group"_group2ndx.html, -"temper/grem"_temper_grem.html :tb(c=3,ea=c) +"temper/grem"_temper_grem.html +"temper/npt"_temper_npt.html :tb(c=3,ea=c) :line diff --git a/doc/src/commands.txt b/doc/src/commands.txt index 7889ea5e7a3638ae40d3b057675f30570f5b9bfd..06752f6960af88e82a389977681e81a29ac89ba7 100644 --- a/doc/src/commands.txt +++ b/doc/src/commands.txt @@ -92,6 +92,7 @@ Commands :h1 tad temper temper_grem + temper_npt thermo thermo_modify thermo_style diff --git a/doc/src/lammps.book b/doc/src/lammps.book index 76b67436578d1ffa2969052dd1eab3fb91487d73..d879e05026cf617c8dbaef80296205c35c18bf81 100644 --- a/doc/src/lammps.book +++ b/doc/src/lammps.book @@ -115,6 +115,7 @@ suffix.html tad.html temper.html temper_grem.html +temper_npt.html thermo.html thermo_modify.html thermo_style.html @@ -644,4 +645,3 @@ USER/atc/man_unfix_flux.html USER/atc/man_unfix_nodes.html USER/atc/man_write_atom_weights.html USER/atc/man_write_restart.html - diff --git a/doc/src/temper_npt.txt b/doc/src/temper_npt.txt index e51f582d3dae30a8daa913a6a51b115dc9f8a0d7..4ad49f9e3327ded89da41c2fd405929175990a67 100644 --- a/doc/src/temper_npt.txt +++ b/doc/src/temper_npt.txt @@ -28,9 +28,20 @@ temper/npt 5000000 2000 $t nptfix 0 12523 1 $w :pre [Description:] -Run a parallel tempering or replica exchange simulation using multiple replicas (ensembles) of a system in the isothermal-isobaric (NPT) ensemble. The command temper/npt works like "temper"_temper.html but is designed for the NPT ensemble instead of the canonical (NVT) ensemble and allows for pressure to be set in the ensembles. The multiple ensembles can run in parallel at different temperatures or different pressures. The acceptance criteria for temper/npt is specific to the NPT ensemble and can be found in references "(Okabe)"_#Okabe and "(Mori)"_#Mori. - -Apart from the difference in acceptance criteria and the specification of pressure, this command works much like the "temper"_temper.html command. See the documentation on "temper"_temper.html for information on how the parallel tempering is handled. +Run a parallel tempering or replica exchange simulation using multiple +replicas (ensembles) of a system in the isothermal-isobaric (NPT) +ensemble. The command temper/npt works like "temper"_temper.html but +requires running replicas in the NPT ensemble instead of the canonical +(NVT) ensemble and allows for pressure to be set in the ensembles. +These multiple ensembles can run in parallel at different temperatures +or different pressures. The acceptance criteria for temper/npt is +specific to the NPT ensemble and can be found in references +"(Okabe)"_#Okabe2 and "(Mori)"_#Mori2. + +Apart from the difference in acceptance criteria and the specification +of pressure, this command works much like the "temper"_temper.html +command. See the documentation on "temper"_temper.html for information +on how the parallel tempering is handled in general. :line @@ -40,7 +51,8 @@ This command can only be used if LAMMPS was built with the USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3 section for more info on packages. -This command should be used with a fix that maintains the isothermal-isobaric (NPT) ensemble. +This command should be used with a fix that maintains the +isothermal-isobaric (NPT) ensemble. [Related commands:] diff --git a/examples/USER/temper_npt/data.peptide b/examples/USER/misc/temper_npt/data.peptide similarity index 100% rename from examples/USER/temper_npt/data.peptide rename to examples/USER/misc/temper_npt/data.peptide diff --git a/examples/USER/temper_npt/in.temper_npt b/examples/USER/misc/temper_npt/in.temper_npt similarity index 100% rename from examples/USER/temper_npt/in.temper_npt rename to examples/USER/misc/temper_npt/in.temper_npt