From 0b51e9b2ffb8bc4e9b1d697645ce3b74eec451cb Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 7 Dec 2017 16:36:36 -0500
Subject: [PATCH] add documentation for fix move/python
---
doc/src/Section_commands.txt | 1 +
doc/src/fix_python_move.txt | 102 +++++++++++++++++++++++++++++++++++
doc/src/fixes.txt | 1 +
doc/src/lammps.book | 1 +
src/.gitignore | 4 +-
5 files changed, 107 insertions(+), 2 deletions(-)
create mode 100644 doc/src/fix_python_move.txt
diff --git a/doc/src/Section_commands.txt b/doc/src/Section_commands.txt
index 62d3bf3d71..d2b837581a 100644
--- a/doc/src/Section_commands.txt
+++ b/doc/src/Section_commands.txt
@@ -585,6 +585,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
"lineforce"_fix_lineforce.html,
"momentum (k)"_fix_momentum.html,
"move"_fix_move.html,
+"move/python"_fix_move_python.html,
"mscg"_fix_mscg.html,
"msst"_fix_msst.html,
"neb"_fix_neb.html,
diff --git a/doc/src/fix_python_move.txt b/doc/src/fix_python_move.txt
new file mode 100644
index 0000000000..156fde9f49
--- /dev/null
+++ b/doc/src/fix_python_move.txt
@@ -0,0 +1,102 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+fix move/python command :h3
+
+[Syntax:]
+
+fix move/python pymodule.CLASS :pre
+
+pymodule.CLASS = use class [CLASS] in module/file [pymodule] to compute how to move atoms
+
+[Examples:]
+
+fix 1 all move/python py_nve.NVE
+fix 1 all move/python py_nve.NVE_OPT :pre
+
+[Description:]
+
+The {move/python} fix style provides a way to define ways how particles
+are moved during an MD run from python script code, that is loaded from
+a file into LAMMPS and executed at the various steps where other fixes
+can be executed. This python script must contain specific python class
+definitions.
+
+This allows to implement complex position updates and also modified
+time integration methods. Due to python being an interpreted language,
+however, the performance of this fix can be moderately to significantly
+slower than the corresponding C++ code. For specific cases, this
+performance penalty can be limited through effective use of NumPy.
+
+:line
+
+The python module file has to start with the following code:
+
+from __future__ import print_function
+import lammps
+import ctypes
+import traceback
+import numpy as np
+#
+class LAMMPSFix(object):
+ def __init__(self, ptr, group_name="all"):
+ self.lmp = lammps.lammps(ptr=ptr)
+ self.group_name = group_name
+#
+class LAMMPSFixMove(LAMMPSFix):
+ def __init__(self, ptr, group_name="all"):
+ super(LAMMPSFixMove, self).__init__(ptr, group_name)
+#
+ def init(self):
+ pass
+#
+ def initial_integrate(self, vflag):
+ pass
+#
+ def final_integrate(self):
+ pass
+#
+ def initial_integrate_respa(self, vflag, ilevel, iloop):
+ pass
+#
+ def final_integrate_respa(self, ilevel, iloop):
+ pass
+#
+ def reset_dt(self):
+ pass :pre
+
+Any classes implementing new atom motion functionality have to be
+derived from the [LAMMPSFixMove] class, overriding the available
+methods as needed.
+
+Examples for how to do this are in the {examples/python} folder.
+
+:line
+
+[Restart, fix_modify, output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html. None of the "fix_modify"_fix_modify.html options
+are relevant to this fix. No global or per-atom quantities are stored
+by this fix for access by various "output
+commands"_Section_howto.html#howto_15. No parameter of this fix can
+be used with the {start/stop} keywords of the "run"_run.html command.
+This fix is not invoked during "energy minimization"_minimize.html.
+
+[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.
+
+[Related commands:]
+
+"fix nve"_fix_nve.html, "fix python"_fix_python.html
+
+[Default:] none
+
diff --git a/doc/src/fixes.txt b/doc/src/fixes.txt
index ad3e95fa41..4649d6ec12 100644
--- a/doc/src/fixes.txt
+++ b/doc/src/fixes.txt
@@ -71,6 +71,7 @@ Fixes :h1
fix_meso_stationary
fix_momentum
fix_move
+ fix_move_python
fix_mscg
fix_msst
fix_mvv_dpd
diff --git a/doc/src/lammps.book b/doc/src/lammps.book
index 0691f43e9b..b62ec3e5be 100644
--- a/doc/src/lammps.book
+++ b/doc/src/lammps.book
@@ -200,6 +200,7 @@ fix_meso.html
fix_meso_stationary.html
fix_momentum.html
fix_move.html
+fix_move_python.html
fix_mscg.html
fix_msst.html
fix_mvv_dpd.html
diff --git a/src/.gitignore b/src/.gitignore
index 3abd3a549b..dd7082243a 100644
--- a/src/.gitignore
+++ b/src/.gitignore
@@ -908,10 +908,10 @@
/python_impl.cpp
/python_impl.h
/python_compat.h
+/fix_move_python.cpp
+/fix_move_python.h
/fix_python.cpp
/fix_python.h
-/fix_python_move.cpp
-/fix_python_move.h
/pair_python.cpp
/pair_python.h
/reader_molfile.cpp
--
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