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clean up doc src

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This commit is contained in:
Steve Plimpton
2016-10-06 13:00:46 -06:00
parent 02bfa898ee
commit 493873fb93
458 changed files with 16897 additions and 11014 deletions
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8
doc/src/Section_python.txt
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@ -23,7 +23,7 @@ In Python lingo, this is "embedding" Python in LAMMPS.
This section describes how to do both.
11.1 "Overview of running LAMMPS from Python"_#py_1
11.2 "Overview of using Python from a LAMMPS script"_#py_2
11.2 "Overview of using Python from a LAMMPS script"_#py_2
11.3 "Building LAMMPS as a shared library"_#py_3
11.4 "Installing the Python wrapper into Python"_#py_4
11.5 "Extending Python with MPI to run in parallel"_#py_5
@ -503,7 +503,7 @@ one of several ways:
The last command requires that the first line of the script be
something like this:
#!/usr/local/bin/python
#!/usr/local/bin/python
#!/usr/local/bin/python -i :pre
where the path points to where you have Python installed, and that you
@ -724,7 +724,7 @@ lmp.scatter_coords("x",1,3,x) :pre
Alternatively, you can just change values in the vector returned by
gather_atoms("x",1,3), since it is a ctypes vector of doubles.
:line
:line
As noted above, these Python class methods correspond one-to-one with
the functions in the LAMMPS library interface in src/library.cpp and
@ -767,7 +767,7 @@ vizplotgui_tool.py, combination of viz_tool.py and plot.py and gui.py :tb(c=2)
For the viz_tool.py and vizplotgui_tool.py commands, replace "tool"
with "gl" or "atomeye" or "pymol" or "vmd", depending on what
visualization package you have installed.
visualization package you have installed.
Note that for GL, you need to be able to run the Pizza.py GL tool,
which is included in the pizza sub-directory. See the "Pizza.py doc