From f3dda30f8ef3a3a660794de1e2b470c477b1a7ad Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 31 Aug 2017 13:53:40 -0400
Subject: [PATCH] fully integrate temper/npt command into manual
---
doc/src/Section_commands.txt | 3 ++-
doc/src/commands.txt | 1 +
doc/src/lammps.book | 2 +-
doc/src/temper_npt.txt | 20 +++++++++++++++----
.../USER/{ => misc}/temper_npt/data.peptide | 0
.../USER/{ => misc}/temper_npt/in.temper_npt | 0
6 files changed, 20 insertions(+), 6 deletions(-)
rename examples/USER/{ => misc}/temper_npt/data.peptide (100%)
rename examples/USER/{ => misc}/temper_npt/in.temper_npt (100%)
diff --git a/doc/src/Section_commands.txt b/doc/src/Section_commands.txt
index 571c6c4920..80a3ef5c64 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 7889ea5e7a..06752f6960 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 76b6743657..d879e05026 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 e51f582d3d..4ad49f9e33 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
--
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