Homec4science
Diffusion lammps (lammm-master) Browse

lammps/doc/doc2/Section_python.html
bfb019efa901lammm-master

Last Change
Raw File

Section_python.html
View Options

<HTML>
<CENTER><A HREF = "Section_modify.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> - <A HREF = "Section_errors.html">Next Section</A>
</CENTER>
<HR>
<H3>11. Python interface to LAMMPS
</H3>
<P>LAMMPS can work together with Python in two ways. First, Python can
wrap LAMMPS through the <A HREF = "Section_howto.html#howto_19">LAMMPS library
interface</A>, so that a Python script can
create one or more instances of LAMMPS and launch one or more
simulations. In Python lingo, this is "extending" Python with LAMMPS.
</P>
<P>Second, LAMMPS can use the Python interpreter, so that a LAMMPS input
script can invoke Python code, and pass information back-and-forth
between the input script and Python functions you write. The Python
code can also callback to LAMMPS to query or change its attributes.
In Python lingo, this is "embedding" Python in LAMMPS.
</P>
<P>This section describes how to do both.
</P>
<UL><LI>11.1 <A HREF = "#py_1">Overview of running LAMMPS from Python</A>
<LI>11.2 <A HREF = "#py_2">Overview of using Python from a LAMMPS script</A>
<LI>11.3 <A HREF = "#py_3">Building LAMMPS as a shared library</A>
<LI>11.4 <A HREF = "#py_4">Installing the Python wrapper into Python</A>
<LI>11.5 <A HREF = "#py_5">Extending Python with MPI to run in parallel</A>
<LI>11.6 <A HREF = "#py_6">Testing the Python-LAMMPS interface</A>
<LI>11.7 <A HREF = "#py_7">Using LAMMPS from Python</A>
<LI>11.8 <A HREF = "#py_8">Example Python scripts that use LAMMPS</A>
</UL>
<P>If you are not familiar with it, <A HREF = "http://www.python.org">Python</A> is a
powerful scripting and programming language which can essentially do
anything that faster, lower-level languages like C or C++ can do, but
typically with much fewer lines of code. When used in embedded mode,
Python can perform operations that the simplistic LAMMPS input script
syntax cannot. Python can be also be used as a "glue" language to
drive a program through its library interface, or to hook multiple
pieces of software together, such as a simulation package plus a
visualization package, or to run a coupled multiscale or multiphysics
model.
</P>
<P>See <A HREF = "Section_howto.html#howto_10">Section_howto 10</A> of the manual and
the couple directory of the distribution for more ideas about coupling
LAMMPS to other codes. See <A HREF = "Section_howto.html#howto_19">Section_howto
19</A> for a description of the LAMMPS
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 is exposed to Python either when calling LAMMPS from Python or
when calling Python from a LAMMPS input script and then calling back
to LAMMPS from Python code. The library interface is designed to be
easy to add functions to. Thus the Python interface to LAMMPS is also
easy to extend as well.
</P>
<P>If you create interesting Python scripts that run LAMMPS or
interesting Python functions that can be called from a LAMMPS input
script, that you think would be useful to other users, please <A HREF = "http://lammps.sandia.gov/authors.html">email
them to the developers</A>. We can
include them in the LAMMPS distribution.
</P>
<HR>
<HR>
<A NAME = "py_1"></A><H4>11.1 Overview of running LAMMPS from Python
</H4>
<P>The LAMMPS distribution includes a python directory with all you need
to run LAMMPS from Python. The python/lammps.py file wraps the LAMMPS
library interface, with one wrapper function per LAMMPS library
function. This file makes it is possible to do the following either
from a Python script, or interactively from a Python prompt: create
one or more instances of LAMMPS, invoke LAMMPS commands or give it an
input script, run LAMMPS incrementally, extract LAMMPS results, an
modify internal LAMMPS variables. From a Python script you can do
this in serial or parallel. Running Python interactively in parallel
does not generally work, unless you have a version of Python that
extends standard Python to enable multiple instances of Python to read
what you type.
</P>
<P>To do all of this, you must first build LAMMPS as a shared library,
then insure that your Python can find the python/lammps.py file and
the shared library. These steps are explained in subsequent sections
11.3 and 11.4. Sections 11.5 and 11.6 discuss using MPI from a
parallel Python program and how to test that you are ready to use
LAMMPS from Python. Section 11.7 lists all the functions in the
current LAMMPS library interface and how to call them from Python.
</P>
<P>Section 11.8 gives some examples of coupling LAMMPS to other tools via
Python. For example, LAMMPS can easily be coupled to a GUI or other
visualization tools that display graphs or animations in real time as
LAMMPS runs. Examples of such scripts are inlcluded in the python
directory.
</P>
<P>Two advantages of using Python to run LAMMPS are how concise the
language is, and that it can be run interactively, enabling rapid
development and debugging of programs. If you use it to mostly invoke
costly operations within LAMMPS, such as running a simulation for a
reasonable number of timesteps, then the overhead cost of invoking
LAMMPS thru Python will be negligible.
</P>
<P>The Python wrapper for LAMMPS uses the amazing and magical (to me)
"ctypes" package in Python, which auto-generates the interface code
needed between Python and a set of C interface routines for a library.
Ctypes is part of standard Python for versions 2.5 and later. You can
check which version of Python you have installed, by simply typing
"python" at a shell prompt.
</P>
<HR>
<A NAME = "py_2"></A><H4>11.2 Overview of using Python from a LAMMPS script
</H4>
<P>IMPORTANT NOTE: It is not currently possible to use the
<A HREF = "python.html">python</A> command described in this section with Python 3,
only with Python 2. The C API changed from Python 2 to 3 and the
LAMMPS code is not compatible with both.
</P>
<P>LAMMPS has a <A HREF = "python.html">python</A> 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 <A HREF = "variable.html">variable</A> 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.
</P>
<P>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
are mapped to LAMMPS variables (also defined in the input script) and
it can return a value to a LAMMPS variable. This is thus a mechanism
for your input script to pass information to a piece of Python code,
ask Python to execute the code, and return information to your input
script.
</P>
<P>Note that a Python function can be arbitrarily complex. It can import
other Python modules, instantiate Python classes, call other Python
functions, etc. The Python code that you provide can contain more
code than the single function. It can contain other functions or
Python classes, as well as global variables or other mechanisms for
storing state between calls from LAMMPS to the function.
</P>
<P>The Python function you provide can consist of "pure" Python code that
only performs operations provided by standard Python. However, the
Python function can also "call back" to LAMMPS through its
Python-wrapped library interface, in the manner described in the
previous section 11.1. This means it can issue LAMMPS input script
commands or query and set internal LAMMPS state. As an example, this
can be useful in an input script to create a more complex loop with
branching logic, than can be created using the simple looping and
brancing logic enabled by the <A HREF = "next.html">next</A> and <A HREF = "if.html">if</A>
commands.
</P>
<P>See the <A HREF = "python.html">python</A> doc page and the <A HREF = "variable.html">variable</A>
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.
</P>
<P>To run pure Python code from LAMMPS, you only need to build LAMMPS
with the PYTHON package installed:
</P>
<P>make yes-python
make machine
</P>
<P>Note that this will link LAMMPS with the Python library on your
system, which typically requires several auxiliary system libraries to
also be linked. The list of these libraries and the paths to find
them are specified in the lib/python/Makefile.lammps file. You need
to insure that file contains the correct information for your version
of Python and your machine to successfully build LAMMPS. See the
lib/python/README file for more info.
</P>
<P>If you want to write Python code with callbacks to LAMMPS, then you
must also follow the steps overviewed in the preceeding section (11.1)
for running LAMMPS from Python. I.e. you must build LAMMPS as a
shared library and insure that Python can find the python/lammps.py
file and the shared library.
</P>
<HR>
<A NAME = "py_3"></A><H4>11.3 Building LAMMPS as a shared library
</H4>
<P>Instructions on how to build LAMMPS as a shared library are given in
<A HREF = "Section_start.html#start_5">Section_start 5</A>. A shared library is one
that is dynamically loadable, which is what Python requires to wrap
LAMMPS. On Linux this is a library file that ends in ".so", not ".a".
</P>
<P>>From the src directory, type
</P>
<PRE>make foo mode=shlib
</PRE>
<P>where foo is the machine target name, such as linux or g++ or serial.
This should create the file liblammps_foo.so in the src directory, as
well as a soft link liblammps.so, which is what the Python wrapper will
load by default. Note that if you are building multiple machine
versions of the shared library, the soft link is always set to the
most recently built version.
</P>
<P>If this fails, see <A HREF = "Section_start.html#start_5">Section_start 5</A> for
more details, especially if your LAMMPS build uses auxiliary libraries
like MPI or FFTW which may not be built as shared libraries on your
system.
</P>
<HR>
<A NAME = "py_4"></A><H4>11.4 Installing the Python wrapper into Python
</H4>
<P>For Python to invoke LAMMPS, there are 2 files it needs to know about:
</P>
<UL><LI>python/lammps.py
<LI>src/liblammps.so
</UL>
<P>Lammps.py is the Python wrapper on the LAMMPS library interface.
Liblammps.so is the shared LAMMPS library that Python loads, as
described above.
</P>
<P>You can insure Python can find these files in one of two ways:
</P>
<UL><LI>set two environment variables
<LI>run the python/install.py script
</UL>
<P>If you set the paths to these files as environment variables, you only
have to do it once. For the csh or tcsh shells, add something like
this to your ~/.cshrc file, one line for each of the two files:
</P>
<PRE>setenv PYTHONPATH ${PYTHONPATH}:/home/sjplimp/lammps/python
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/src
</PRE>
<P>If you use the python/install.py script, you need to invoke it every
time you rebuild LAMMPS (as a shared library) or make changes to the
python/lammps.py file.
</P>
<P>You can invoke install.py from the python directory as
</P>
<PRE>% python install.py [libdir] [pydir]
</PRE>
<P>The optional libdir is where to copy the LAMMPS shared library to; the
default is /usr/local/lib. The optional pydir is where to copy the
lammps.py file to; the default is the site-packages directory of the
version of Python that is running the install script.
</P>
<P>Note that libdir must be a location that is in your default
LD_LIBRARY_PATH, like /usr/local/lib or /usr/lib. And pydir must be a
location that Python looks in by default for imported modules, like
its site-packages dir. If you want to copy these files to
non-standard locations, such as within your own user space, you will
need to set your PYTHONPATH and LD_LIBRARY_PATH environment variables
accordingly, as above.
</P>
<P>If the install.py script does not allow you to copy files into system
directories, prefix the python command with "sudo". If you do this,
make sure that the Python that root runs is the same as the Python you
run. E.g. you may need to do something like
</P>
<PRE>% sudo /usr/local/bin/python install.py [libdir] [pydir]
</PRE>
<P>You can also invoke install.py from the make command in the src
directory as
</P>
<PRE>% make install-python
</PRE>
<P>In this mode you cannot append optional arguments. Again, you may
need to prefix this with "sudo". In this mode you cannot control
which Python is invoked by root.
</P>
<P>Note that if you want Python to be able to load different versions of
the LAMMPS shared library (see <A HREF = "#py_5">this section</A> below), you will
need to manually copy files like liblammps_g++.so into the appropriate
system directory. This is not needed if you set the LD_LIBRARY_PATH
environment variable as described above.
</P>
<HR>
<A NAME = "py_5"></A><H4>11.5 Extending Python with MPI to run in parallel
</H4>
<P>If you wish to run LAMMPS in parallel from Python, you need to extend
your Python with an interface to MPI. This also allows you to
make MPI calls directly from Python in your script, if you desire.
</P>
<P>There are several Python packages available that purport to wrap MPI
as a library and allow MPI functions to be called from Python.
</P>
<P>These include
</P>
<UL><LI><A HREF = "http://pympi.sourceforge.net/">pyMPI</A>
<LI><A HREF = "http://code.google.com/p/maroonmpi/">maroonmpi</A>
<LI><A HREF = "http://code.google.com/p/mpi4py/">mpi4py</A>
<LI><A HREF = "http://nbcr.sdsc.edu/forum/viewtopic.php?t=89&sid=c997fefc3933bd66204875b436940f16">myMPI</A>
<LI><A HREF = "http://code.google.com/p/pypar">Pypar</A>
</UL>
<P>All of these except pyMPI work by wrapping the MPI library and
exposing (some portion of) its interface to your Python script. This
means Python cannot be used interactively in parallel, since they do
not address the issue of interactive input to multiple instances of
Python running on different processors. The one exception is pyMPI,
which alters the Python interpreter to address this issue, and (I
believe) creates a new alternate executable (in place of "python"
itself) as a result.
</P>
<P>In principle any of these Python/MPI packages should work to invoke
LAMMPS in parallel and to make MPI calls themselves from a Python
script which is itself running in parallel. However, when I
downloaded and looked at a few of them, their documentation was
incomplete and I had trouble with their installation. It's not clear
if some of the packages are still being actively developed and
supported.
</P>
<P>The one I recommend, since I have successfully used it with LAMMPS, is
Pypar. Pypar requires the ubiquitous <A HREF = "http://numpy.scipy.org">Numpy
package</A> be installed in your Python. After
launching python, type
</P>
<PRE>import numpy
</PRE>
<P>to see if it is installed. If not, here is how to install it (version
1.3.0b1 as of April 2009). Unpack the numpy tarball and from its
top-level directory, type
</P>
<PRE>python setup.py build
sudo python setup.py install
</PRE>
<P>The "sudo" is only needed if required to copy Numpy files into your
Python distribution's site-packages directory.
</P>
<P>To install Pypar (version pypar-2.1.4_94 as of Aug 2012), unpack it
and from its "source" directory, type
</P>
<PRE>python setup.py build
sudo python setup.py install
</PRE>
<P>Again, the "sudo" is only needed if required to copy Pypar files into
your Python distribution's site-packages directory.
</P>
<P>If you have successully installed Pypar, you should be able to run
Python and type
</P>
<PRE>import pypar
</PRE>
<P>without error. You should also be able to run python in parallel
on a simple test script
</P>
<PRE>% mpirun -np 4 python test.py
</PRE>
<P>where test.py contains the lines
</P>
<PRE>import pypar
print "Proc %d out of %d procs" % (pypar.rank(),pypar.size())
</PRE>
<P>and see one line of output for each processor you run on.
</P>
<P>IMPORTANT NOTE: To use Pypar and LAMMPS in parallel from Python, you
must insure both are using the same version of MPI. If you only have
one MPI installed on your system, this is not an issue, but it can be
if you have multiple MPIs. Your LAMMPS build is explicit about which
MPI it is using, since you specify the details in your lo-level
src/MAKE/Makefile.foo file. Pypar uses the "mpicc" command to find
information about the MPI it uses to build against. And it tries to
load "libmpi.so" from the LD_LIBRARY_PATH. This may or may not find
the MPI library that LAMMPS is using. If you have problems running
both Pypar and LAMMPS together, this is an issue you may need to
address, e.g. by moving other MPI installations so that Pypar finds
the right one.
</P>
<HR>
<A NAME = "py_6"></A><H4>11.6 Testing the Python-LAMMPS interface
</H4>
<P>To test if LAMMPS is callable from Python, launch Python interactively
and type:
</P>
<PRE>>>> from lammps import lammps
>>> lmp = lammps()
</PRE>
<P>If you get no errors, you're ready to use LAMMPS from Python. If the
2nd command fails, the most common error to see is
</P>
<PRE>OSError: Could not load LAMMPS dynamic library
</PRE>
<P>which means Python was unable to load the LAMMPS shared library. This
typically occurs if the system can't find the LAMMPS shared library or
one of the auxiliary shared libraries it depends on, or if something
about the library is incompatible with your Python. The error message
should give you an indication of what went wrong.
</P>
<P>You can also test the load directly in Python as follows, without
first importing from the lammps.py file:
</P>
<PRE>>>> from ctypes import CDLL
>>> CDLL("liblammps.so")
</PRE>
<P>If an error occurs, carefully go thru the steps in <A HREF = "Section_start.html#start_5">Section_start
5</A> and above about building a shared
library and about insuring Python can find the necessary two files
it needs.
</P>
<H5><B>Test LAMMPS and Python in serial:</B>
</H5>
<P>To run a LAMMPS test in serial, type these lines into Python
interactively from the bench directory:
</P>
<PRE>>>> from lammps import lammps
>>> lmp = lammps()
>>> lmp.file("in.lj")
</PRE>
<P>Or put the same lines in the file test.py and run it as
</P>
<PRE>% python test.py
</PRE>
<P>Either way, you should see the results of running the in.lj benchmark
on a single processor appear on the screen, the same as if you had
typed something like:
</P>
<PRE>lmp_g++ -in in.lj
</PRE>
<H5><B>Test LAMMPS and Python in parallel:</B>
</H5>
<P>To run LAMMPS in parallel, assuming you have installed the
<A HREF = "http://datamining.anu.edu.au/~ole/pypar">Pypar</A> package as discussed
above, create a test.py file containing these lines:
</P>
<PRE>import pypar
from lammps import lammps
lmp = lammps()
lmp.file("in.lj")
print "Proc %d out of %d procs has" % (pypar.rank(),pypar.size()),lmp
pypar.finalize()
</PRE>
<P>You can then run it in parallel as:
</P>
<PRE>% mpirun -np 4 python test.py
</PRE>
<P>and you should see the same output as if you had typed
</P>
<PRE>% mpirun -np 4 lmp_g++ -in in.lj
</PRE>
<P>Note that if you leave out the 3 lines from test.py that specify Pypar
commands you will instantiate and run LAMMPS independently on each of
the P processors specified in the mpirun command. In this case you
should get 4 sets of output, each showing that a LAMMPS run was made
on a single processor, instead of one set of output showing that
LAMMPS ran on 4 processors. If the 1-processor outputs occur, it
means that Pypar is not working correctly.
</P>
<P>Also note that once you import the PyPar module, Pypar initializes MPI
for you, and you can use MPI calls directly in your Python script, as
described in the Pypar documentation. The last line of your Python
script should be pypar.finalize(), to insure MPI is shut down
correctly.
</P>
<H5><B>Running Python scripts:</B>
</H5>
<P>Note that any Python script (not just for LAMMPS) can be invoked in
one of several ways:
</P>
<PRE>% python foo.script
% python -i foo.script
% foo.script
</PRE>
<P>The last command requires that the first line of the script be
something like this:
</P>
<PRE>#!/usr/local/bin/python
#!/usr/local/bin/python -i
</PRE>
<P>where the path points to where you have Python installed, and that you
have made the script file executable:
</P>
<PRE>% chmod +x foo.script
</PRE>
<P>Without the "-i" flag, Python will exit when the script finishes.
With the "-i" flag, you will be left in the Python interpreter when
the script finishes, so you can type subsequent commands. As
mentioned above, you can only run Python interactively when running
Python on a single processor, not in parallel.
</P>
<HR>
<HR>
<A NAME = "py_7"></A><H4>11.7 Using LAMMPS from Python
</H4>
<P>As described above, the Python interface to LAMMPS consists of a
Python "lammps" module, the source code for which is in
python/lammps.py, which creates a "lammps" object, with a set of
methods that can be invoked on that object. The sample Python code
below assumes you have first imported the "lammps" module in your
Python script, as follows:
</P>
<PRE>from lammps import lammps
</PRE>
<P>These are the methods defined by the lammps module. If you look at
the files src/library.cpp and src/library.h you will see that they
correspond one-to-one with calls you can make to the LAMMPS library
from a C++ or C or Fortran program.
</P>
<PRE>lmp = lammps() # create a LAMMPS object using the default liblammps.so library
lmp = lammps(ptr=lmpptr) # ditto, but use lmpptr as previously created LAMMPS object
lmp = lammps("g++") # create a LAMMPS object using the liblammps_g++.so library
lmp = lammps("",list) # ditto, with command-line args, e.g. list = ["-echo","screen"]
lmp = lammps("g++",list)
</PRE>
<PRE>lmp.close() # destroy a LAMMPS object
</PRE>
<P>version = lmp.version() # return the numerical version id, e.g. LAMMPS 2 Sep 2015 -> 20150902
</P>
<PRE>lmp.file(file) # run an entire input script, file = "in.lj"
lmp.command(cmd) # invoke a single LAMMPS command, cmd = "run 100"
</PRE>
<PRE>xlo = lmp.extract_global(name,type) # extract a global quantity
# name = "boxxlo", "nlocal", etc
# type = 0 = int
# 1 = double
</PRE>
<PRE>coords = lmp.extract_atom(name,type) # extract a per-atom quantity
# name = "x", "type", etc
# type = 0 = vector of ints
# 1 = array of ints
# 2 = vector of doubles
# 3 = array of doubles
</PRE>
<PRE>eng = lmp.extract_compute(id,style,type) # extract value(s) from a compute
v3 = lmp.extract_fix(id,style,type,i,j) # extract value(s) from a fix
# id = ID of compute or fix
# style = 0 = global data
# 1 = per-atom data
# 2 = local data
# type = 0 = scalar
# 1 = vector
# 2 = array
# i,j = indices of value in global vector or array
</PRE>
<PRE>var = lmp.extract_variable(name,group,flag) # extract value(s) from a variable
# name = name of variable
# group = group ID (ignored for equal-style variables)
# flag = 0 = equal-style variable
# 1 = atom-style variable
</PRE>
<PRE>flag = lmp.set_variable(name,value) # set existing named string-style variable to value, flag = 0 if successful
natoms = lmp.get_natoms() # total # of atoms as int
data = lmp.gather_atoms(name,type,count) # return atom attribute of all atoms gathered into data, ordered by atom ID
# name = "x", "charge", "type", etc
# count = # of per-atom values, 1 or 3, etc
lmp.scatter_atoms(name,type,count,data) # scatter atom attribute of all atoms from data, ordered by atom ID
# name = "x", "charge", "type", etc
# count = # of per-atom values, 1 or 3, etc
</PRE>
<HR>
<P>IMPORTANT NOTE: Currently, the creation of a LAMMPS object from within
lammps.py does not take an MPI communicator as an argument. There
should be a way to do this, so that the LAMMPS instance runs on a
subset of processors if desired, but I don't know how to do it from
Pypar. So for now, it runs with MPI_COMM_WORLD, which is all the
processors. If someone figures out how to do this with one or more of
the Python wrappers for MPI, like Pypar, please let us know and we
will amend these doc pages.
</P>
<P>The lines
</P>
<PRE>from lammps import lammps
lmp = lammps()
</PRE>
<P>create an instance of LAMMPS, wrapped in a Python class by the lammps
Python module, and return an instance of the Python class as lmp. It
is used to make all subequent calls to the LAMMPS library.
</P>
<P>Additional arguments can be used to tell Python the name of the shared
library to load or to pass arguments to the LAMMPS instance, the same
as if LAMMPS were launched from a command-line prompt.
</P>
<P>If the ptr argument is set like this:
</P>
<PRE>lmp = lammps(ptr=lmpptr)
</PRE>
<P>then lmpptr must be an argument passed to Python via the LAMMPS
<A HREF = "python.html">python</A> command, when it is used to define a Python
function that is invoked by the LAMMPS input script. This mode of
using Python with LAMMPS is described above in 11.2. The variable
lmpptr refers to the instance of LAMMPS that called the embedded
Python interpreter. Using it as an argument to lammps() allows the
returned Python class instance "lmp" to make calls to that instance of
LAMMPS. See the <A HREF = "python.html">python</A> command doc page for examples
using this syntax.
</P>
<P>Note that you can create multiple LAMMPS objects in your Python
script, and coordinate and run multiple simulations, e.g.
</P>
<PRE>from lammps import lammps
lmp1 = lammps()
lmp2 = lammps()
lmp1.file("in.file1")
lmp2.file("in.file2")
</PRE>
<P>The file() and command() methods allow an input script or single
commands to be invoked.
</P>
<P>The extract_global(), extract_atom(), extract_compute(),
extract_fix(), and extract_variable() methods return values or
pointers to data structures internal to LAMMPS.
</P>
<P>For extract_global() see the src/library.cpp file for the list of
valid names. New names could easily be added. A double or integer is
returned. You need to specify the appropriate data type via the type
argument.
</P>
<P>For extract_atom(), a pointer to internal LAMMPS atom-based data is
returned, which you can use via normal Python subscripting. See the
extract() method in the src/atom.cpp file for a list of valid names.
Again, new names could easily be added. A pointer to a vector of
doubles or integers, or a pointer to an array of doubles (double **)
or integers (int **) is returned. You need to specify the appropriate
data type via the type argument.
</P>
<P>For extract_compute() and extract_fix(), the global, per-atom, or
local data calulated by the compute or fix can be accessed. What is
returned depends on whether the compute or fix calculates a scalar or
vector or array. For a scalar, a single double value is returned. If
the compute or fix calculates a vector or array, a pointer to the
internal LAMMPS data is returned, which you can use via normal Python
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#howto_15">Section_howto 15</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
they calculate and store.
</P>
<P>For extract_variable(), an <A HREF = "variable.html">equal-style or atom-style
variable</A> is evaluated and its result returned.
</P>
<P>For equal-style variables a single double value is returned and the
group argument is ignored. For atom-style variables, a vector of
doubles is returned, one value per atom, which you can use via normal
Python subscripting. The values will be zero for atoms not in the
specified group.
</P>
<P>The get_natoms() method returns the total number of atoms in the
simulation, as an int.
</P>
<P>The gather_atoms() method returns a ctypes vector of ints or doubles
as specified by type, of length count*natoms, for the property of all
the atoms in the simulation specified by name, ordered by count and
then by atom ID. The vector can be used via normal Python
subscripting. If atom IDs are not consecutively ordered within
LAMMPS, a None is returned as indication of an error.
</P>
<P>Note that the data structure gather_atoms("x") returns is different
from the data structure returned by extract_atom("x") in four ways.
(1) Gather_atoms() returns a vector which you index as x[i];
extract_atom() returns an array which you index as x[i][j]. (2)
Gather_atoms() orders the atoms by atom ID while extract_atom() does
not. (3) Gathert_atoms() returns a list of all atoms in the
simulation; extract_atoms() returns just the atoms local to each
processor. (4) Finally, the gather_atoms() data structure is a copy
of the atom coords stored internally in LAMMPS, whereas extract_atom()
returns an array that effectively points directly to the internal
data. This means you can change values inside LAMMPS from Python by
assigning a new values to the extract_atom() array. To do this with
the gather_atoms() vector, you need to change values in the vector,
then invoke the scatter_atoms() method.
</P>
<P>The scatter_atoms() method takes a vector of ints or doubles as
specified by type, of length count*natoms, for the property of all the
atoms in the simulation specified by name, ordered by bount and then
by atom ID. It uses the vector of data to overwrite the corresponding
properties for each atom inside LAMMPS. This requires LAMMPS to have
its "map" option enabled; see the <A HREF = "atom_modify.html">atom_modify</A>
command for details. If it is not, or if atom IDs are not
consecutively ordered, no coordinates are reset.
</P>
<P>The array of coordinates passed to scatter_atoms() must be a ctypes
vector of ints or doubles, allocated and initialized something like
this:
</P>
<PRE>from ctypes import *
natoms = lmp.get_natoms()
n3 = 3*natoms
x = (n3*c_double)()
x[0] = x coord of atom with ID 1
x[1] = y coord of atom with ID 1
x[2] = z coord of atom with ID 1
x[3] = x coord of atom with ID 2
...
x[n3-1] = z coord of atom with ID natoms
lmp.scatter_coords("x",1,3,x)
</PRE>
<P>Alternatively, you can just change values in the vector returned by
gather_atoms("x",1,3), since it is a ctypes vector of doubles.
</P>
<HR>
<P>As noted above, these Python class methods correspond one-to-one with
the functions in the LAMMPS library interface in src/library.cpp and
library.h. This means you can extend the Python wrapper via the
following steps:
</P>
<UL><LI>Add a new interface function to src/library.cpp and
src/library.h.
<LI>Rebuild LAMMPS as a shared library.
<LI>Add a wrapper method to python/lammps.py for this interface
function.
<LI>You should now be able to invoke the new interface function from a
Python script. Isn't ctypes amazing?
</UL>
<HR>
<HR>
<A NAME = "py_8"></A><H4>11.8 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
things that are possible when Python wraps LAMMPS. If you create your
own scripts, send them to us and we can include them in the LAMMPS
distribution.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD >trivial.py</TD><TD > read/run a LAMMPS input script thru Python</TD></TR>
<TR><TD >demo.py</TD><TD > invoke various LAMMPS library interface routines</TD></TR>
<TR><TD >simple.py</TD><TD > mimic operation of couple/simple/simple.cpp in Python</TD></TR>
<TR><TD >gui.py</TD><TD > GUI go/stop/temperature-slider to control LAMMPS</TD></TR>
<TR><TD >plot.py</TD><TD > real-time temeperature plot with GnuPlot via Pizza.py</TD></TR>
<TR><TD >viz_tool.py</TD><TD > real-time viz via some viz package</TD></TR>
<TR><TD >vizplotgui_tool.py</TD><TD > combination of viz_tool.py and plot.py and gui.py
</TD></TR></TABLE></DIV>
<HR>
<P>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.
</P>
<P>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 <A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py doc
pages</A> for more info:
</P>
<P>Note that for AtomEye, you need version 3, and there is a line in the
scripts that specifies the path and name of the executable. See the
AtomEye WWW pages <A HREF = "http://mt.seas.upenn.edu/Archive/Graphics/A">here</A> or <A HREF = "http://mt.seas.upenn.edu/Archive/Graphics/A3/A3.html">here</A> for more details:
</P>
<PRE>http://mt.seas.upenn.edu/Archive/Graphics/A
http://mt.seas.upenn.edu/Archive/Graphics/A3/A3.html
</PRE>
<P>The latter link is to AtomEye 3 which has the scriping
capability needed by these Python scripts.
</P>
<P>Note that for PyMol, you need to have built and installed the
open-source version of PyMol in your Python, so that you can import it
from a Python script. See the PyMol WWW pages <A HREF = "http://www.pymol.org">here</A> or
<A HREF = "http://sourceforge.net/scm/?type=svn&group_id=4546">here</A> for more details:
</P>
<PRE>http://www.pymol.org
http://sourceforge.net/scm/?type=svn&group_id=4546
</PRE>
<P>The latter link is to the open-source version.
</P>
<P>Note that for VMD, you need a fairly current version (1.8.7 works for
me) and there are some lines in the pizza/vmd.py script for 4 PIZZA
variables that have to match the VMD installation on your system.
</P>
<HR>
<P>See the python/README file for instructions on how to run them and the
source code for individual scripts for comments about what they do.
</P>
<P>Here are screenshots of the vizplotgui_tool.py script in action for
different visualization package options. Click to see larger images:
</P>
<A HREF = "JPG/screenshot_gl.jpg"><IMG SRC = "JPG/screenshot_gl_small.jpg"></A>
<A HREF = "JPG/screenshot_atomeye.jpg"><IMG SRC = "JPG/screenshot_atomeye_small.jpg"></A>
<A HREF = "JPG/screenshot_pymol.jpg"><IMG SRC = "JPG/screenshot_pymol_small.jpg"></A>
<A HREF = "JPG/screenshot_vmd.jpg"><IMG SRC = "JPG/screenshot_vmd_small.jpg"></A>
</HTML>
c4science · Help