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@ -20,11 +20,11 @@ either from a Python script or interactively from a Python prompt.
<P><A HREF = "http://www.python.org">Python</A> is a powerful scripting and programming
language which can be used to wrap software like LAMMPS and other
packages. It can be used to glue multiple pieces of software
together, e.g. to run a coupled or multiscale model. See <A HREF = "Section_howto.html#4_10">this
together, e.g. to run a coupled or multiscale model. See <A HREF = "Section_howto.html#howto_10">this
section</A> of the manual and the couple
directory of the distribution for more ideas about coupling LAMMPS to
other codes. See <A HREF = "Section_start.html#start_4">this section</A> about how
to build LAMMPS as a library, and <A HREF = "Section_howto.html#4_19">this
to build LAMMPS as a library, and <A HREF = "Section_howto.html#howto_19">this
section</A> for a description of the library
interface provided in src/library.cpp and src/library.h and how to
extend it for your needs. As described below, that interface is what
@ -89,13 +89,13 @@ setup discussion. The next to last sub-section describes the Python
syntax used to invoke LAMMPS. The last sub-section describes example
Python scripts included in the python directory.
</P>
<UL><LI>11.1 <A HREF = "#11_1">Extending Python with a serial version of LAMMPS</A>
<LI>11.2 <A HREF = "#11_2">Creating a shared MPI library</A>
<LI>11.3 <A HREF = "#11_3">Extending Python with a parallel version of LAMMPS</A>
<LI>11.4 <A HREF = "#11_4">Extending Python with MPI</A>
<LI>11.5 <A HREF = "#11_5">Testing the Python-LAMMPS interface</A>
<LI>11.6 <A HREF = "#11_6">Using LAMMPS from Python</A>
<LI>11.7 <A HREF = "#11_7">Example Python scripts that use LAMMPS</A>
<UL><LI>11.1 <A HREF = "#py_1">Extending Python with a serial version of LAMMPS</A>
<LI>11.2 <A HREF = "#py_2">Creating a shared MPI library</A>
<LI>11.3 <A HREF = "#py_3">Extending Python with a parallel version of LAMMPS</A>
<LI>11.4 <A HREF = "#py_4">Extending Python with MPI</A>
<LI>11.5 <A HREF = "#py_5">Testing the Python-LAMMPS interface</A>
<LI>11.6 <A HREF = "#py_6">Using LAMMPS from Python</A>
<LI>11.7 <A HREF = "#py_7">Example Python scripts that use LAMMPS</A>
</UL>
<P>Before proceeding, there are 2 items to note.
</P>
@ -135,7 +135,7 @@ LAMMPS wrapper.
<HR>
<A NAME = "11_1"></A><H4>11.1 Extending Python with a serial version of LAMMPS
<A NAME = "py_1"></A><H4>11.1 Extending Python with a serial version of LAMMPS
</H4>
<P>From the python directory in the LAMMPS distribution, type
</P>
@ -165,7 +165,7 @@ this, where you should replace "foo" with your directory of choice.
</P>
<HR>
<A NAME = "11_2"></A><H4>11.2 Creating a shared MPI library
<A NAME = "py_2"></A><H4>11.2 Creating a shared MPI library
</H4>
<P>A shared library is one that is dynamically loadable, which is what
Python requires. On Linux this is a library file that ends in ".so",
@ -196,7 +196,7 @@ stand-alone code.
</P>
<HR>
<A NAME = "11_3"></A><H4>11.3 Extending Python with a parallel version of LAMMPS
<A NAME = "py_3"></A><H4>11.3 Extending Python with a parallel version of LAMMPS
</H4>
<P>From the python directory, type
</P>
@ -234,7 +234,7 @@ will be put in the appropriate directory.
</P>
<HR>
<A NAME = "11_4"></A><H4>11.4 Extending Python with MPI
<A NAME = "py_4"></A><H4>11.4 Extending Python with MPI
</H4>
<P>There are several Python packages available that purport to wrap MPI
as a library and allow MPI functions to be called from Python.
@ -309,7 +309,7 @@ print "Proc %d out of %d procs" % (pypar.rank(),pypar.size())
</P>
<HR>
<A NAME = "11_5"></A><H4>11.5 Testing the Python-LAMMPS interface
<A NAME = "py_5"></A><H4>11.5 Testing the Python-LAMMPS interface
</H4>
<P>Before using LAMMPS in a Python program, one more step is needed. The
interface to LAMMPS is via the Python ctypes package, which loads the
@ -403,7 +403,7 @@ Python on a single processor, not in parallel.
<HR>
<A NAME = "11_6"></A><H4>11.6 Using LAMMPS from Python
<A NAME = "py_6"></A><H4>11.6 Using LAMMPS from Python
</H4>
<P>The Python interface to LAMMPS consists of a Python "lammps" module,
the source code for which is in python/lammps.py, which creates a
@ -499,7 +499,7 @@ subscripting. The one exception is that for a fix that calculates a
global vector or array, a single double value from the vector or array
is returned, indexed by I (vector) or I and J (array). I,J are
zero-based indices. The I,J arguments can be left out if not needed.
See <A HREF = "Section_howto.html#4_15">this section</A> of the manual for a
See <A HREF = "Section_howto.html#howto_15">this section</A> of the manual for a
discussion of global, per-atom, and local data, and of scalar, vector,
and array data types. See the doc pages for individual
<A HREF = "compute.html">computes</A> and <A HREF = "fix.html">fixes</A> for a description of what
@ -595,7 +595,7 @@ Python script. Isn't ctypes amazing?
<HR>
<A NAME = "11_7"></A><H4>11.7 Example Python scripts that use LAMMPS
<A NAME = "py_7"></A><H4>11.7 Example Python scripts that use LAMMPS
</H4>
<P>These are the Python scripts included as demos in the python/examples
directory of the LAMMPS distribution, to illustrate the kinds of