From b28ecd44c25d7059d20c9b4317ca438c5ffc1934 Mon Sep 17 00:00:00 2001
From: Steve Plimpton <sjplimp@sandia.gov>
Date: Thu, 18 May 2017 13:14:47 -0600
Subject: [PATCH] update docs before patch release
---
doc/src/Section_commands.txt | 2 +
doc/src/Section_python.txt | 39 ++++++---
doc/src/fix_reax_bonds.txt | 15 +++-
doc/src/pair_edip.txt | 9 +-
doc/src/pair_gw.txt | 4 +-
doc/src/pair_python.txt | 94 +++++++++++----------
doc/src/pair_tersoff.txt | 2 +-
src/{USER-MISC => MANYBODY}/pair_gw.cpp | 0
src/{USER-MISC => MANYBODY}/pair_gw.h | 0
src/{USER-MISC => MANYBODY}/pair_gw_zbl.cpp | 0
src/{USER-MISC => MANYBODY}/pair_gw_zbl.h | 0
src/USER-MISC/README | 2 -
12 files changed, 100 insertions(+), 67 deletions(-)
rename src/{USER-MISC => MANYBODY}/pair_gw.cpp (100%)
rename src/{USER-MISC => MANYBODY}/pair_gw.h (100%)
rename src/{USER-MISC => MANYBODY}/pair_gw_zbl.cpp (100%)
rename src/{USER-MISC => MANYBODY}/pair_gw_zbl.h (100%)
diff --git a/doc/src/Section_commands.txt b/doc/src/Section_commands.txt
index ae13c87cb8..dc7ddebe58 100644
--- a/doc/src/Section_commands.txt
+++ b/doc/src/Section_commands.txt
@@ -618,6 +618,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
"press/berendsen"_fix_press_berendsen.html,
"print"_fix_print.html,
"property/atom"_fix_property_atom.html,
+"python"_fix_python.html,
"qeq/comb (o)"_fix_qeq_comb.html,
"qeq/dynamic"_fix_qeq.html,
"qeq/fire"_fix_qeq.html,
@@ -984,6 +985,7 @@ KOKKOS, o = USER-OMP, t = OPT.
"peri/pmb (o)"_pair_peri.html,
"peri/ves"_pair_peri.html,
"polymorphic"_pair_polymorphic.html,
+"python"_pair_python.html,
"reax"_pair_reax.html,
"rebo (o)"_pair_airebo.html,
"resquared (go)"_pair_resquared.html,
diff --git a/doc/src/Section_python.txt b/doc/src/Section_python.txt
index 7b62f7e948..718e9e229c 100644
--- a/doc/src/Section_python.txt
+++ b/doc/src/Section_python.txt
@@ -118,13 +118,21 @@ check which version of Python you have installed, by simply typing
11.2 Overview of using Python from a LAMMPS script :link(py_2),h4
-LAMMPS has a "python"_python.html command which can be used in an
-input script to define and execute a Python function that you write
-the code for. The Python function can also be assigned to a LAMMPS
-python-style variable via the "variable"_variable.html command. Each
-time the variable is evaluated, either in the LAMMPS input script
-itself, or by another LAMMPS command that uses the variable, this will
-trigger the Python function to be invoked.
+LAMMPS has several commands which can be used to invoke Python
+code directly from an input script:
+
+"python"_python.html
+"variable python"_variable.html
+"fix python"_fix_python.html
+"pair_style python"_pair_python.html :ul
+
+The "python"_python.html command which can be used to define and
+execute a Python function that you write the code for. The Python
+function can also be assigned to a LAMMPS python-style variable via
+the "variable"_variable.html command. Each time the variable is
+evaluated, either in the LAMMPS input script itself, or by another
+LAMMPS command that uses the variable, this will trigger the Python
+function to be invoked.
The Python code for the function can be included directly in the input
script or in an auxiliary file. The function can have arguments which
@@ -155,13 +163,18 @@ commands.
See the "python"_python.html doc page and the "variable"_variable.html
doc page for its python-style variables for more info, including
examples of Python code you can write for both pure Python operations
-and callbacks to LAMMPS. See "fix python"_fix_python.html to learn about
-possibilities to execute Python code during each time step.
-Through the "python pair style"_pair_python.html it is also possible
-to define potential functions as python code.
+and callbacks to LAMMPS.
-To run pure Python code from LAMMPS, you only need to build LAMMPS
-with the PYTHON package installed:
+The "fix python"_fix_python.html command can execute
+Python code at selected timesteps during a simulation run.
+
+The "pair_style python"_pair_python command allows you to define
+pairwise potentials as python code which encodes a single pairwise
+interaction. This is useful for rapid-developement and debugging of a
+new potential.
+
+To use any of these commands, you only need to build LAMMPS with the
+PYTHON package installed:
make yes-python
make machine :pre
diff --git a/doc/src/fix_reax_bonds.txt b/doc/src/fix_reax_bonds.txt
index a874fa3d16..aadb0a9cbc 100644
--- a/doc/src/fix_reax_bonds.txt
+++ b/doc/src/fix_reax_bonds.txt
@@ -34,7 +34,20 @@ written to {filename} on timesteps that are multiples of {Nevery},
including timestep 0. For time-averaged chemical species analysis,
please see the "fix reaxc/c/species"_fix_reaxc_species.html command.
-The format of the output file should be self-explanatory.
+The format of the output file should be reasonably self-explanatory.
+The meaning of the column header abbreviations is as follows:
+
+id = atom id
+type = atom type
+nb = number of bonds
+id_1 = atom id of first bond
+id_nb = atom id of Nth bond
+mol = molecule id
+bo_1 = bond order of first bond
+bo_nb = bond order of Nth bond
+abo = atom bond order (sum of all bonds)
+nlp = number of lone pairs
+q = atomic charge :ul
If the filename ends with ".gz", the output file is written in gzipped
format. A gzipped dump file will be about 3x smaller than the text
diff --git a/doc/src/pair_edip.txt b/doc/src/pair_edip.txt
index d0c90d76dd..86453859d3 100644
--- a/doc/src/pair_edip.txt
+++ b/doc/src/pair_edip.txt
@@ -7,12 +7,13 @@
:line
pair_style edip command :h3
+pair_style edip/multi command :h3
[Syntax:]
-pair_style edip :pre
-pair_style edip/omp :pre
-pair_style edip/multi :pre
+pair_style style :pre
+
+style = {edip} or {edip/multi} :ul
[Examples:]
@@ -168,4 +169,4 @@ appropriate units if your simulation doesn't use "metal" units.
:line
:link(EDIP)
-[(EDIP)] J. F. Justo et al., Phys. Rev. B 58, 2539 (1998).
+[(EDIP)] J F Justo et al, Phys Rev B 58, 2539 (1998).
diff --git a/doc/src/pair_gw.txt b/doc/src/pair_gw.txt
index 2240dca6f7..fcf63b1bc4 100644
--- a/doc/src/pair_gw.txt
+++ b/doc/src/pair_gw.txt
@@ -11,7 +11,9 @@ pair_style gw/zbl command :h3
[Syntax:]
-pair_style gw :pre
+pair_style style :pre
+
+style = {gw} or {gw/zbl} :ul
[Examples:]
diff --git a/doc/src/pair_python.txt b/doc/src/pair_python.txt
index 84927e52d9..af6d08cb56 100644
--- a/doc/src/pair_python.txt
+++ b/doc/src/pair_python.txt
@@ -40,34 +40,34 @@ Only a single pair_coeff command is used with the {python} pair style
which specifies a python class inside a python module or file that
LAMMPS will look up in the current directory, the folder pointed to by
the LAMMPS_POTENTIALS environment variable or somewhere in your python
-path. A single python module can hold multiple python pair class
-definitions. The class definitions itself have to follow specific rules
-that are explained below.
+path. A single python module can hold multiple python pair class
+definitions. The class definitions itself have to follow specific
+rules that are explained below.
-Atom types in the python class are specified through symbolic constants,
-typically strings. These are mapped to LAMMPS atom types by specifying
-N additional arguments after the class name in the pair_coeff command,
-where N must be the number of currently defined atom types:
+Atom types in the python class are specified through symbolic
+constants, typically strings. These are mapped to LAMMPS atom types by
+specifying N additional arguments after the class name in the
+pair_coeff command, where N must be the number of currently defined
+atom types:
As an example, imagine a file {py_pot.py} has a python potential class
names {LJCutMelt} with parameters and potential functions for a two
Lennard-Jones atom types labeled as 'LJ1' and 'LJ2'. In your LAMMPS
input and you would have defined 3 atom types, out of which the first
-two are supposed to be using the 'LJ1' parameters and the third
-the 'LJ2' parameters, then you would use the following pair_coeff
-command:
+two are supposed to be using the 'LJ1' parameters and the third the
+'LJ2' parameters, then you would use the following pair_coeff command:
pair_coeff * * py_pot.LJCutMelt LJ1 LJ1 LJ2 :pre
-The first two arguments [must] be * * so as to span all LAMMPS atom types.
-The first two LJ1 arguments map LAMMPS atom types 1 and 2 to the LJ1
-atom type in the LJCutMelt class of the py_pot.py file. The final LJ2
-argument maps LAMMPS atom type 3 to the LJ2 atom type the python file.
-If a mapping value is specified as NULL, the mapping is not performed,
-any pair interaction with this atom type will be skipped. This can be
-used when a {python} potential is used as part of the {hybrid} or
-{hybrid/overlay} pair style. The NULL values are then placeholders for
-atom types that will be used with other potentials.
+The first two arguments [must] be * * so as to span all LAMMPS atom
+types. The first two LJ1 arguments map LAMMPS atom types 1 and 2 to
+the LJ1 atom type in the LJCutMelt class of the py_pot.py file. The
+final LJ2 argument maps LAMMPS atom type 3 to the LJ2 atom type the
+python file. If a mapping value is specified as NULL, the mapping is
+not performed, any pair interaction with this atom type will be
+skipped. This can be used when a {python} potential is used as part of
+the {hybrid} or {hybrid/overlay} pair style. The NULL values are then
+placeholders for atom types that will be used with other potentials.
:line
@@ -88,14 +88,18 @@ class LAMMPSPairPotential(object):
Any classes with definitions of specific potentials have to be derived
from this class and should be initialize in a similar fashion to the
-example given below. NOTE: The class constructor has to set up a data
-structure containing the potential parameters supported by this class.
-It should also define a variable {self.units} containing a string
-matching one of the options of LAMMPS' "units"_units.html command, which
-is used to verify, that the potential definition in the python class and
-in the LAMMPS input match. Example for a single type Lennard-Jones
-potential class {LJCutMelt} in reducted units, which defines an atom
-type {lj} for which the parameters epsilon and sigma are both 1.0:
+example given below.
+
+NOTE: The class constructor has to set up a data structure containing
+the potential parameters supported by this class. It should also
+define a variable {self.units} containing a string matching one of the
+options of LAMMPS' "units"_units.html command, which is used to
+verify, that the potential definition in the python class and in the
+LAMMPS input match.
+
+Here is an example for a single type Lennard-Jones potential class
+{LJCutMelt} in reducted units, which defines an atom type {lj} for
+which the parameters epsilon and sigma are both 1.0:
class LJCutMelt(LAMMPSPairPotential):
def __init__(self):
@@ -136,32 +140,32 @@ the {LJCutMelt} example, here are the two functions:
lj4 = coeff\[3\]
return (r6inv * (lj3*r6inv - lj4)) :pre
-IMPORTANT NOTE: for consistency with the C++ pair styles in LAMMPS,
-the {compute_force} function follows the conventions of the Pair::single()
+NOTE: for consistency with the C++ pair styles in LAMMPS, the
+{compute_force} function follows the conventions of the Pair::single()
methods and does not return the full force, but the force scaled by
the distance between the two atoms, so this value only needs to be
-multiplied by delta x, delta y, and delta z to conveniently obtain
-the three components of the force vector between these two atoms.
+multiplied by delta x, delta y, and delta z to conveniently obtain the
+three components of the force vector between these two atoms.
:line
-IMPORTANT NOTE: The evaluation of scripted python code will slow down
-the computation pair-wise interactions quite significantly. However,
-this can be largely worked around through using the python pair style
-not for the actual simulation, but to generate tabulated potentials
-on the fly using the "pair_write"_pair_write.html command. Please
-see below for an example LAMMPS input of how to build a table file:
+NOTE: The evaluation of scripted python code will slow down the
+computation pair-wise interactions quite significantly. However, this
+can be largely worked around through using the python pair style not
+for the actual simulation, but to generate tabulated potentials on the
+fly using the "pair_write"_pair_write.html command. Please see below
+for an example LAMMPS input of how to build a table file:
pair_style python 2.5
pair_coeff * * py_pot.LJCutMelt lj
shell rm -f melt.table
pair_write 1 1 2000 rsq 0.01 2.5 lj1_lj2.table lj :pre
-Note, that it is strong recommended to try to [delete] the potential
+Note that it is strongly recommended to try to [delete] the potential
table file before generating it. Since the {pair_write} command will
-always append to a table file, which pair style table will use the first
-match. Thus when changing the potential function in the python class,
-the table pair style will still read the old variant.
+always append to a table file, which pair style table will use the
+first match. Thus when changing the potential function in the python
+class, the table pair style will still read the old variant.
After switching the pair style to {table}, the potential tables need
to be assigned to the LAMMPS atom types like this:
@@ -169,7 +173,7 @@ to be assigned to the LAMMPS atom types like this:
pair_style table linear 2000
pair_coeff 1 1 melt.table lj :pre
-This can also be done for more complex systems. Please see the
+This can also be done for more complex systems. Please see the
{examples/python} folders for a few more examples.
:line
@@ -198,9 +202,9 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
-This pair style is part of the PYTHON package. It is only enabled
-if LAMMPS was built with that package. See
-the "Making LAMMPS"_Section_start.html#start_3 section for more info.
+This pair style is part of the PYTHON package. It is only enabled if
+LAMMPS was built with that package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]
diff --git a/doc/src/pair_tersoff.txt b/doc/src/pair_tersoff.txt
index eb4a8993cf..23a20ad0fd 100644
--- a/doc/src/pair_tersoff.txt
+++ b/doc/src/pair_tersoff.txt
@@ -18,7 +18,7 @@ pair_style tersoff/table/omp command :h3
pair_style style :pre
-style = {tersoff} or {tersoff/table} or {tersoff/gpu} or {tersoff/omp} or {tersoff/table/omp}
+style = {tersoff} or {tersoff/table} or {tersoff/gpu} or {tersoff/omp} or {tersoff/table/omp} :ul
[Examples:]
diff --git a/src/USER-MISC/pair_gw.cpp b/src/MANYBODY/pair_gw.cpp
similarity index 100%
rename from src/USER-MISC/pair_gw.cpp
rename to src/MANYBODY/pair_gw.cpp
diff --git a/src/USER-MISC/pair_gw.h b/src/MANYBODY/pair_gw.h
similarity index 100%
rename from src/USER-MISC/pair_gw.h
rename to src/MANYBODY/pair_gw.h
diff --git a/src/USER-MISC/pair_gw_zbl.cpp b/src/MANYBODY/pair_gw_zbl.cpp
similarity index 100%
rename from src/USER-MISC/pair_gw_zbl.cpp
rename to src/MANYBODY/pair_gw_zbl.cpp
diff --git a/src/USER-MISC/pair_gw_zbl.h b/src/MANYBODY/pair_gw_zbl.h
similarity index 100%
rename from src/USER-MISC/pair_gw_zbl.h
rename to src/MANYBODY/pair_gw_zbl.h
diff --git a/src/USER-MISC/README b/src/USER-MISC/README
index 1e927fdfab..cacee41e0c 100644
--- a/src/USER-MISC/README
+++ b/src/USER-MISC/README
@@ -60,8 +60,6 @@ pair_style dipole/sf, Mario Orsi, orsimario at gmail.com, 8 Aug 11
pair_style edip, Luca Ferraro, luca.ferraro at caspur.it, 15 Sep 11
pair_style eam/cd, Alexander Stukowski, stukowski at mm.tu-darmstadt.de, 7 Nov 09
pair_style gauss/cut, Axel Kohlmeyer, akohlmey at gmail.com, 1 Dec 11
-pair_style gw, German Samolyuk, samolyuk at gmail.com, 17 May 17
-pair_style gw/zbl, German Samolyuk, samolyuk at gmail.com, 17 May 17
pair_style lennard/mdf, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15
pair_style list, Axel Kohlmeyer (Temple U), akohlmey at gmail.com, 1 Jun 13
pair_style lj/mdf, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15
--
GitLab