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"Previous Section"_Section_modify.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_errors.html :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
11. Python interface to LAMMPS :h3
LAMMPS can work together with Python in three ways. First, Python can
wrap LAMMPS through the "LAMMPS library
interface"_Section_howto.html#howto_19, 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.
Second, the low-level Python interface can be used indirectly through the
PyLammps and IPyLammps wrapper classes in Python. These wrappers try to
simplify the usage of LAMMPS in Python by providing an object-based interface
to common LAMMPS functionality. It also reduces the amount of code necessary to
parameterize LAMMPS scripts through Python and makes variables and computes
directly accessible. See "PyLammps interface"_#py_9 for more details.
Third, 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.
This section describes how to use these three approaches.
11.1 "Overview of running LAMMPS from Python"_#py_1
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
11.6 "Testing the Python-LAMMPS interface"_#py_6
11.7 "Using LAMMPS from Python"_#py_7
11.8 "Example Python scripts that use LAMMPS"_#py_8
11.9 "PyLammps interface"_#py_9 :ul
If you are not familiar with it, "Python"_http://www.python.org 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.
See "Section 6.10"_Section_howto.html#howto_10 of the manual and
the couple directory of the distribution for more ideas about coupling
LAMMPS to other codes. See "Section
6.19"_Section_howto.html#howto_19 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.
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 "email
them to the developers"_http://lammps.sandia.gov/authors.html. We can
include them in the LAMMPS distribution.
:line
:line
11.1 Overview of running LAMMPS from Python :link(py_1),h4
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.
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.
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 included in the python
directory.
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.
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.
:line
11.2 Overview of using Python from a LAMMPS script :link(py_2),h4
NOTE: It is not currently possible to use the "python"_python.html
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.
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.
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.
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.
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
branching logic enabled by the "next"_next.html and "if"_if.html
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.
To run pure Python code from LAMMPS, you only need to build LAMMPS
with the PYTHON package installed:
make yes-python
make machine :pre
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.
If you want to write Python code with callbacks to LAMMPS, then you
must also follow the steps overviewed in the preceding 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.
:line
11.3 Building LAMMPS as a shared library :link(py_3),h4
Instructions on how to build LAMMPS as a shared library are given in
"Section 2.5"_Section_start.html#start_5. 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".
From the src directory, type
make foo mode=shlib :pre
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.
NOTE: If you are building LAMMPS with an MPI or FFT library or other
auxiliary libraries (used by various packages), then all of these
extra libraries must also be shared libraries. If the LAMMPS
shared-library build fails with an error complaining about this, see
"Section 2.5"_Section_start.html#start_5 for more details.
:line
11.4 Installing the Python wrapper into Python :link(py_4),h4
For Python to invoke LAMMPS, there are 2 files it needs to know about:
python/lammps.py
src/liblammps.so :ul
Lammps.py is the Python wrapper on the LAMMPS library interface.
Liblammps.so is the shared LAMMPS library that Python loads, as
described above.
You can insure Python can find these files in one of two ways:
set two environment variables
run the python/install.py script :ul
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:
setenv PYTHONPATH $\{PYTHONPATH\}:/home/sjplimp/lammps/python
setenv LD_LIBRARY_PATH $\{LD_LIBRARY_PATH\}:/home/sjplimp/lammps/src :pre
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.
You can invoke install.py from the python directory as
% python install.py \[libdir\] \[pydir\] :pre
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.
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.
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
% sudo /usr/local/bin/python install.py \[libdir\] \[pydir\] :pre
You can also invoke install.py from the make command in the src
directory as
% make install-python :pre
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.
Note that if you want Python to be able to load different versions of
the LAMMPS shared library (see "this section"_#py_5 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.
:line
11.5 Extending Python with MPI to run in parallel :link(py_5),h4
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.
There are several Python packages available that purport to wrap MPI
as a library and allow MPI functions to be called from Python. However,
development on most of them seems to be halted except on:
"mpi4py"_https://bitbucket.org/mpi4py/mpi4py
"PyPar"_https://github.com/daleroberts/pypar :ul
Both packages, PyPar and mpi4py have been successfully tested with
LAMMPS. PyPar is simpler and easy to set up and use, but supports
only a subset of MPI. Mpi4py is more MPI-feature complete, but also a
bit more complex to use. As of version 2.0.0, mpi4py is the only
python MPI wrapper that allows passing a custom MPI communicator to
the LAMMPS constructor, which means one can easily run one or more
LAMMPS instances on subsets of the total MPI ranks.
:line
PyPar requires the ubiquitous "Numpy package"_http://numpy.scipy.org
be installed in your Python. After launching Python, type
import numpy :pre
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
python setup.py build
sudo python setup.py install :pre
The "sudo" is only needed if required to copy Numpy files into your
Python distribution's site-packages directory.
To install PyPar (version pypar-2.1.4_94 as of Aug 2012), unpack it
and from its "source" directory, type
python setup.py build
sudo python setup.py install :pre
Again, the "sudo" is only needed if required to copy PyPar files into
your Python distribution's site-packages directory.
If you have successfully installed PyPar, you should be able to run
Python and type
import pypar :pre
without error. You should also be able to run python in parallel
on a simple test script
% mpirun -np 4 python test.py :pre
where test.py contains the lines
import pypar
print "Proc %d out of %d procs" % (pypar.rank(),pypar.size()) :pre
and see one line of output for each processor you run on.
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.
:line
To install mpi4py (version mpi4py-2.0.0 as of Oct 2015), unpack it
and from its main directory, type
python setup.py build
sudo python setup.py install :pre
Again, the "sudo" is only needed if required to copy mpi4py files into
your Python distribution's site-packages directory. To install with
user privilege into the user local directory type
python setup.py install --user :pre
If you have successfully installed mpi4py, you should be able to run
Python and type
from mpi4py import MPI :pre
without error. You should also be able to run python in parallel
on a simple test script
% mpirun -np 4 python test.py :pre
where test.py contains the lines
from mpi4py import MPI
comm = MPI.COMM_WORLD
print "Proc %d out of %d procs" % (comm.Get_rank(),comm.Get_size()) :pre
and see one line of output for each processor you run on.
NOTE: To use mpi4py 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. Mpi4py 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 mpi4py and LAMMPS together, this is an issue you may need to
address, e.g. by moving other MPI installations so that mpi4py finds
the right one.
:line
11.6 Testing the Python-LAMMPS interface :link(py_6),h4
To test if LAMMPS is callable from Python, launch Python interactively
and type:
>>> from lammps import lammps
>>> lmp = lammps() :pre
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
OSError: Could not load LAMMPS dynamic library :pre
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.
You can also test the load directly in Python as follows, without
first importing from the lammps.py file:
>>> from ctypes import CDLL
>>> CDLL("liblammps.so") :pre
If an error occurs, carefully go thru the steps in "Section
2.5"_Section_start.html#start_5 and above about building a shared
library and about insuring Python can find the necessary two files
it needs.
[Test LAMMPS and Python in serial:] :h5
To run a LAMMPS test in serial, type these lines into Python
interactively from the bench directory:
>>> from lammps import lammps
>>> lmp = lammps()
>>> lmp.file("in.lj") :pre
Or put the same lines in the file test.py and run it as
% python test.py :pre
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:
lmp_g++ -in in.lj :pre
[Test LAMMPS and Python in parallel:] :h5
To run LAMMPS in parallel, assuming you have installed the
"PyPar"_https://github.com/daleroberts/pypar package as discussed
above, create a test.py file containing these lines:
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
To run LAMMPS in parallel, assuming you have installed the
"mpi4py"_https://bitbucket.org/mpi4py/mpi4py package as discussed
above, create a test.py file containing these lines:
from mpi4py import MPI
from lammps import lammps
lmp = lammps()
lmp.file("in.lj")
me = MPI.COMM_WORLD.Get_rank()
nprocs = MPI.COMM_WORLD.Get_size()
print "Proc %d out of %d procs has" % (me,nprocs),lmp
MPI.Finalize() :pre
You can either script in parallel as:
% mpirun -np 4 python test.py :pre
and you should see the same output as if you had typed
% mpirun -np 4 lmp_g++ -in in.lj :pre
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.
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.
[Running Python scripts:] :h5
Note that any Python script (not just for LAMMPS) can be invoked in
one of several ways:
% python foo.script
% python -i foo.script
% foo.script :pre
The last command requires that the first line of the script be
something like this:
#!/usr/local/bin/python
#!/usr/local/bin/python -i :pre
where the path points to where you have Python installed, and that you
have made the script file executable:
% chmod +x foo.script :pre
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.
:line
:line
11.7 Using LAMMPS from Python :link(py_7),h4
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:
from lammps import lammps :pre
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, and which are described in
"Section 6.19"_Section_howto.html#howto_19 of the manual.
lmp = lammps() # create a LAMMPS object using the default liblammps.so library
# 4 optional args are allowed: name, cmdargs, ptr, comm
lmp = lammps(ptr=lmpptr) # use lmpptr as previously created LAMMPS object
lmp = lammps(comm=split) # create a LAMMPS object with a custom communicator, requires mpi4py 2.0.0 or later
lmp = lammps(name="g++") # create a LAMMPS object using the liblammps_g++.so library
lmp = lammps(name="g++",cmdargs=list) # add LAMMPS command-line args, e.g. list = \["-echo","screen"\] :pre
lmp.close() # destroy a LAMMPS object :pre
version = lmp.version() # return the numerical version id, e.g. LAMMPS 2 Sep 2015 -> 20150902
lmp.file(file) # run an entire input script, file = "in.lj"
lmp.command(cmd) # invoke a single LAMMPS command, cmd = "run 100" :pre
lmp.commands_list(cmdlist) # invoke commands in cmdlist = ["run 10", "run 20"]
lmp.commands_string(multicmd) # invoke commands in multicmd = "run 10\nrun 20"
xlo = lmp.extract_global(name,type) # extract a global quantity
# name = "boxxlo", "nlocal", etc
# type = 0 = int
# 1 = double :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
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
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
flag = lmp.set_variable(name,value) # set existing named string-style variable to value, flag = 0 if successful
value = lmp.get_thermo(name) # return current value of a thermo keyword
natoms = lmp.get_natoms() # total # of atoms as int
data = lmp.gather_atoms(name,type,count) # return per-atom property 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 per-atom property to all atoms from data, ordered by atom ID
# name = "x", "charge", "type", etc
# count = # of per-atom values, 1 or 3, etc :pre
:line
The lines
from lammps import lammps
lmp = lammps() :pre
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 subsequent calls to the LAMMPS library.
Additional arguments to lammps() 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.
If the ptr argument is set like this:
lmp = lammps(ptr=lmpptr) :pre
then lmpptr must be an argument passed to Python via the LAMMPS
"python"_python.html 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 "python"_python.html command doc page for examples
using this syntax.
Note that you can create multiple LAMMPS objects in your Python
script, and coordinate and run multiple simulations, e.g.
from lammps import lammps
lmp1 = lammps()
lmp2 = lammps()
lmp1.file("in.file1")
lmp2.file("in.file2") :pre
The file(), command(), commands_list(), commands_string() methods
allow an input script, a single command, or multiple commands to be
invoked.
The extract_global(), extract_atom(), extract_compute(),
extract_fix(), and extract_variable() methods return values or
pointers to data structures internal to LAMMPS.
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.
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 if the property you want is not
listed. 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.
For extract_compute() and extract_fix(), the global, per-atom, or
local data calculated 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 "Section 6.15"_Section_howto.html#howto_15 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
"computes"_compute.html and "fixes"_fix.html for a description of what
they calculate and store.
For extract_variable(), an "equal-style or atom-style
variable"_variable.html is evaluated and its result returned.
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.
The get_natoms() method returns the total number of atoms in the
simulation, as an int.
The gather_atoms() method allows any per-atom property (coordinates,
velocities, etc) to be extracted from LAMMPS. It returns a ctypes
vector of ints or doubles as specified by type, of length
count*natoms, for the named property for all atoms in the simulation.
The data is ordered by count and then by atom ID. See the extract()
method in the src/atom.cpp file for a list of valid names. Again, new
names could easily be added if the property you want is missing. 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. A special treatment is applied for image flags
stored in the "image" property. All three image flags are stored in
a packed format in a single integer, so count would be 1 to retrieve
that integer, however also a count value of 3 can be used and then
the image flags will be unpacked into 3 individual integers, ordered
in a similar fashion as coordinates.
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.
The scatter_atoms() method allows any per-atom property (coordinates,
velocities, etc) to be inserted into LAMMPS, overwriting the current
property. It takes a vector of ints or doubles as specified by type,
of length count*natoms, for the named property for all atoms in the
simulation. The data should be ordered by count and then by atom ID.
See the extract() method in the src/atom.cpp file for a list of valid
names. Again, new names could easily be added if the property you
want is missing. 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
"atom_modify"_atom_modify.html command for details. If it is not, or
if atom IDs are not consecutively ordered, no coordinates are reset.
Similar as for gather_atoms() a special treatment is applied for image
flags, which can be provided in packed (count = 1) or unpacked (count = 3)
format and in the latter case, they will be packed before applied to
atoms.
The array of coordinates passed to scatter_atoms() must be a ctypes
vector of ints or doubles, allocated and initialized something like
this:
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_atoms("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
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:
Add a new interface function to src/library.cpp and
src/library.h. :ulb,l
Rebuild LAMMPS as a shared library. :l
Add a wrapper method to python/lammps.py for this interface
function. :l
You should now be able to invoke the new interface function from a
Python script. Isn't ctypes amazing? :l
:ule
:line
:line
11.8 Example Python scripts that use LAMMPS :link(py_8),h4
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.
trivial.py, read/run a LAMMPS input script thru Python,
demo.py, invoke various LAMMPS library interface routines,
simple.py, run in parallel, similar to examples/COUPLE/simple/simple.cpp,
split.py, same as simple.py but running in parallel on a subset of procs,
gui.py, GUI go/stop/temperature-slider to control LAMMPS,
plot.py, real-time temperature plot with GnuPlot via Pizza.py,
viz_tool.py, real-time viz via some viz package,
vizplotgui_tool.py, combination of viz_tool.py and plot.py and gui.py :tb(c=2)
:line
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.
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
pages"_pizza for more info:
:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html)
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 "here"_atomeye or "here"_atomeye3 for more details:
http://mt.seas.upenn.edu/Archive/Graphics/A
http://mt.seas.upenn.edu/Archive/Graphics/A3/A3.html :pre
:link(atomeye,http://mt.seas.upenn.edu/Archive/Graphics/A)
:link(atomeye3,http://mt.seas.upenn.edu/Archive/Graphics/A3/A3.html)
The latter link is to AtomEye 3 which has the scriping
capability needed by these Python scripts.
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 "here"_pymolhome or
"here"_pymolopen for more details:
http://www.pymol.org
http://sourceforge.net/scm/?type=svn&group_id=4546 :pre
:link(pymolhome,http://www.pymol.org)
:link(pymolopen,http://sourceforge.net/scm/?type=svn&group_id=4546)
The latter link is to the open-source version.
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.
:line
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.
Here are screenshots of the vizplotgui_tool.py script in action for
different visualization package options. Click to see larger images:
:image(JPG/screenshot_gl_small.jpg,JPG/screenshot_gl.jpg)
:image(JPG/screenshot_atomeye_small.jpg,JPG/screenshot_atomeye.jpg)
:image(JPG/screenshot_pymol_small.jpg,JPG/screenshot_pymol.jpg)
:image(JPG/screenshot_vmd_small.jpg,JPG/screenshot_vmd.jpg)
11.9 PyLammps interface :link(py_9),h4
Please see the "PyLammps Tutorial"_tutorial_pylammps.html.
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