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	<CENTER><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>
	</CENTER>






	<HR>

	<H3>python command
	</H3>
	<P><B>Syntax:</B>
	</P>
	<PRE>python func keyword args ...
	</PRE>
	<UL><LI>func = name of Python function

	<LI>one or more keyword/args pairs must be appended

	<PRE>keyword = <I>invoke</I> or <I>input</I> or <I>return</I> or <I>format</I> or <I>file</I> or <I>here</I> or <I>exists</I>
	<I>invoke</I> arg = none = invoke the previously defined Python function
	<I>input</I> args = N i1 i2 ... iN
	N = # of inputs to function
	i1,...,iN = value, SELF, or LAMMPS variable name
	value = integer number, floating point number, or string
	SELF = reference to LAMMPS itself which can be accessed by Python function
	variable = v_name, where name = name of LAMMPS variable, e.g. v_abc
	<I>return</I> arg = varReturn
	varReturn = v_name = LAMMPS variable name which return value of function will be assigned to
	<I>format</I> arg = fstring with M characters
	M = N if no return value, where N = # of inputs
	M = N+1 if there is a return value
	fstring = each character (i,f,s,p) corresponds in order to an input or return value
	'i' = integer, 'f' = floating point, 's' = string, 'p' = SELF
	<I>file</I> arg = filename
	filename = file of Python code, which defines func
	<I>here</I> arg = inline
	inline = one or more lines of Python code which defines func
	must be a single argument, typically enclosed between triple quotes
	<I>exists</I> arg = none = Python code has been loaded by previous python command
	</PRE>

	</UL>
	<P><B>Examples:</B>
	</P>
	<PRE>python pForce input 2 v_x 20.0 return v_f format fff file force.py
	python pForce invoke
	</PRE>
	<PRE>python factorial input 1 myN return v_fac format ii here """
	def factorial(n):
	if n == 1: return n
	return n * factorial(n-1)
	"""
	</PRE>
	<PRE>python loop input 1 SELF return v_value format -f here """
	def loop(lmpptr,N,cut0):
	from lammps import lammps
	lmp = lammps(ptr=lmpptr)
	</PRE>
	<PRE> # loop N times, increasing cutoff each time
	</PRE>
	<PRE> for i in range(N):
	cut = cut0 + i*0.1
	lmp.set_variable("cut",cut) # set a variable in LAMMPS
	lmp.command("pair_style lj/cut ${cut}") # LAMMPS commands
	lmp.command("pair_coeff * * 1.0 1.0")
	lmp.command("run 100")
	"""
	</PRE>
	<P><B>Description:</B>
	</P>
	<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>Define a Python function or execute a previously defined function.
	Arguments, including LAMMPS variables, can be passed to the function
	from the LAMMPS input script and a value returned by the Python
	function to a LAMMPS variable. The Python code for the function can
	be included directly in the input script or in a separate Python file.
	The function can be standard Python code or it can make "callbacks" to
	LAMMPS through its library interface to query or set internal values
	within LAMMPS. This is a powerful mechanism for performing complex
	operations in a LAMMPS input script that are not possible with the
	simple input script and variable syntax which LAMMPS defines. Thus
	your input script can operate more like a true programming language.
	</P>
	<P>Use of this command requires building LAMMPS with the PYTHON package
	which links to the Python library so that the Python interpreter is
	embedded in LAMMPS. More details about this process are given below.
	</P>
	<P>There are two ways to invoke a Python function once it has been
	defined. One is using the <I>invoke</I> keyword. The other is to assign
	the function to a <A HREF = "variable.html">python-style variable</A> defined in
	your input script. Whenever the variable is evaluated, it will
	execute the Python function to assign a value to the variable. Note
	that variables can be evaluated in many different ways within LAMMPS.
	They can be substituted for directly in an input script. Or they can
	be passed to various commands as arguments, so that the variable is
	evaluated during a simulation run.
	</P>
	<P>A broader overview of how Python can be used with LAMMPS is
	given in <A HREF = "Section_python.html">Section python</A>. There is an
	examples/python directory which illustrates use of the python
	command.
	</P>
	<HR>

	<P>The <I>func</I> setting specifies the name of the Python function. The
	code for the function is defined using the <I>file</I> or <I>here</I> keywords
	as explained below.
	</P>
	<P>If the <I>invoke</I> keyword is used, no other keywords can be used, and a
	previous python command must have defined the Python function
	referenced by this command. This invokes the Python function with the
	previously defined arguments and return value processed as explained
	below. You can invoke the function as many times as you wish in your
	input script.
	</P>
	<P>The <I>input</I> keyword defines how many arguments <I>N</I> the Python function
	expects. If it takes no arguments, then the <I>input</I> keyword should
	not be used. Each argument can be specified directly as a value,
	e.g. 6 or 3.14159 or abc (a string of characters). The type of each
	argument is specified by the <I>format</I> keyword as explained below, so
	that Python will know how to interpret the value. If the word SELF is
	used for an argument it has a special meaning. A pointer is passed to
	the Python function which it converts into a reference to LAMMPS
	itself. This enables the function to call back to LAMMPS through its
	library interface as explained below. This allows the Python function
	to query or set values internal to LAMMPS which can affect the
	subsequent execution of the input script. A LAMMPS variable can also
	be used as an argument, specified as v_name, where "name" is the name
	of the variable. Any style of LAMMPS variable can be used, as defined
	by the <A HREF = "variable.html">variable</A> command. Each time the Python
	function is invoked, the LAMMPS variable is evaluated and its value is
	passed to the Python function.
	</P>
	<P>The <I>return</I> keyword is only needed if the Python function returns a
	value. The specified <I>varReturn</I> must be of the form v_name, where
	"name" is the name of a python-style LAMMPS variable, defined by the
	<A HREF = "variable.html">variable</A> command. The Python function can return a
	numeric or string value, as specified by the <I>format</I> keyword.
	</P>
	<P>As explained on the <A HREF = "variable.html">variable</A> doc page, the definition
	of a python-style variable associates a Python function name with the
	variable. This must match the <I>func</I> setting for this command. For
	exampe these two commands would be self-consistent:
	</P>
	<PRE>variable foo python myMultiply
	python myMultiply return v_foo format f file funcs.py
	</PRE>
	<P>The two commands can appear in either order in the input script so
	long as both are specified before the Python function is invoked for
	the first time.
	</P>
	<P>The <I>format</I> keyword must be used if the <I>input</I> or <I>return</I> keyword
	is used. It defines an <I>fstring</I> with M characters, where M = sum of
	number of inputs and outputs. The order of characters corresponds to
	the N inputs, followed by the return value (if it exists). Each
	character must be one of the following: "i" for integer, "f" for
	floating point, "s" for string, or "p" for SELF. Each character
	defines the type of the corresponding input or output value of the
	Python function and affects the type conversion that is performed
	internally as data is passed back and forth between LAMMPS and Python.
	Note that it is permissible to use a <A HREF = "variable.html">python-style
	variable</A> in a LAMMPS command that allows for an
	equal-style variable as an argument, but only if the output of the
	Python function is flagged as a numeric value ("i" or "f") via the
	<I>format</I> keyword.
	</P>
	<P>Either the <I>file</I>, <I>here</I>, or <I>exists</I> keyword must be used, but only
	one of them. These keywords specify what Python code to load into the
	Python interpreter. The <I>file</I> keyword gives the name of a file,
	which should end with a ".py" suffix, which contains Python code. The
	code will be immediately loaded into and run in the "main" module of
	the Python interpreter. Note that Python code which contains a
	function definition does not "execute" the function when it is run; it
	simply defines the function so that it can be invoked later.
	</P>
	<P>The <I>here</I> keyword does the same thing, except that the Python code
	follows as a single argument to the <I>here</I> keyword. This can be done
	using triple quotes as delimiters, as in the examples above. This
	allows Python code to be listed verbatim in your input script, with
	proper indentation, blank lines, and comments, as desired. See
	<A HREF = "Section_commands.html#cmd_2">Section 3.2</A>, for an explanation of how
	triple quotes can be used as part of input script syntax.
	</P>
	<P>The <I>exists</I> keyword takes no argument. It means that Python code
	containing the required Python function defined by the <I>func</I> setting,
	is assumed to have been previously loaded by another python command.
	</P>
	<P>Note that the Python code that is loaded and run must contain a
	function with the specified <I>func</I> name. To operate properly when
	later invoked, the the function code must match the <I>input</I> and
	<I>return</I> and <I>format</I> keywords specified by the python command.
	Otherwise Python will generate an error.
	</P>
	<HR>

	<P>This section describes how Python code can be written to work with
	LAMMPS.
	</P>
	<P>Whether you load Python code from a file or directly from your input
	script, via the <I>file</I> and <I>here</I> keywords, the code can be identical.
	It must be indented properly as Python requires. It can contain
	comments or blank lines. If the code is in your input script, it
	cannot however contain triple-quoted Python strings, since that will
	conflict with the triple-quote parsing that the LAMMPS input script
	performs.
	</P>
	<P>All the Python code you specify via one or more python commands is
	loaded into the Python "main" module, i.e. __main__. The code can
	define global variables or statements that are outside of function
	definitions. It can contain multiple functions, only one of which
	matches the <I>func</I> setting in the python command. This means you can
	use the <I>file</I> keyword once to load several functions, and the
	<I>exists</I> keyword thereafter in subsequent python commands to access
	the other functions previously loaded.
	</P>
	<P>A Python function you define (or more generally, the code you load)
	can import other Python modules or classes, it can make calls to other
	system functions or functions you define, and it can access or modify
	global variables (in the "main" module) which will persist between
	successive function calls. The latter can be useful, for example, to
	prevent a function from being invoke multiple times per timestep by
	different commands in a LAMMPS input script that access the returned
	python-style variable associated with the function. For example,
	consider this function loaded with two global variables defined
	outside the function:
	</P>
	<PRE>nsteplast = -1
	nvaluelast = 0
	</PRE>
	<PRE>def expensive(nstep):
	global nsteplast,nvaluelast
	if nstep == nsteplast: return nvaluelast
	nsteplast = nstep
	# perform complicated calculation
	nvalue = ...
	nvaluelast = nvalue
	return nvalue
	</PRE>
	<P>Nsteplast stores the previous timestep the function was invoked
	(passed as an argument to the function). Nvaluelast stores the return
	value computed on the last function invocation. If the function is
	invoked again on the same timestep, the previous value is simply
	returned, without re-computing it. The "global" statement inside the
	Python function allows it to overwrite the global variables.
	</P>
	<P>Note that if you load Python code multiple times (via multiple python
	commands), you can overwrite previously loaded variables and functions
	if you are not careful. E.g. if the code above were loaded twice, the
	global variables would be re-initialized, which might not be what you
	want. Likewise, if a function with the same name exists in two chunks
	of Python code you load, the function loaded second will override the
	function loaded first.
	</P>
	<P>It's important to realize that if you are running LAMMPS in parallel,
	each MPI task will load the Python interpreter and execute a local
	copy of the Python function(s) you define. There is no connection
	between the Python interpreters running on different processors.
	This implies three important things.
	</P>
	<P>First, if you put a print statement in your Python function, you will
	see P copies of the output, when running on P processors. If the
	prints occur at (nearly) the same time, the P copies of the output may
	be mixed together. Welcome to the world of parallel programming and
	debugging.
	</P>
	<P>Second, if your Python code loads modules that are not pre-loaded by
	the Python library, then it will load the module from disk. This may
	be a bottleneck if 1000s of processors try to load a module at the
	same time. On some large supercomputers, loading of modules from disk
	by Python may be disabled. In this case you would need to pre-build a
	Python library that has the required modules pre-loaded and link
	LAMMPS with that library.
	</P>
	<P>Third, if your Python code calls back to LAMMPS (discussed in the
	next section) and causes LAMMPS to perform an MPI operation requires
	global communication (e.g. via MPI_Allreduce), such as computing the
	global temperature of the system, then you must insure all your Python
	functions (running independently on different processors) call back to
	LAMMPS. Otherwise the code may hang.
	</P>
	<HR>

	<P>Your Python function can "call back" to LAMMPS through its
	library interface, if you use the SELF input to pass Python
	a pointer to LAMMPS. The mechanism for doing this in your
	Python function is as follows:
	</P>
	<PRE>def foo(lmpptr,...):
	from lammps import lammps
	lmp = lammps(ptr=lmpptr)
	lmp.command('print "Hello from inside Python"')
	...
	</PRE>
	<P>The function definition must include a variable (lmpptr in this case)
	which corresponds to SELF in the python command. The first line of
	the function imports the Python module lammps.py in the python dir of
	the distribution. The second line creates a Python object "lmp" which
	wraps the instance of LAMMPS that called the function. The
	"ptr=lmpptr" argument is what makes that happen. The thrid line
	invokes the command() function in the LAMMPS library interface. It
	takes a single string argument which is a LAMMPS input script command
	for LAMMPS to execute, the same as if it appeared in your input
	script. In this case, LAMMPS should output
	</P>
	<PRE>Hello from inside Python
	</PRE>
	<P>to the screen and log file. Note that since the LAMMPS print command
	itself takes a string in quotes as its argument, the Python string
	must be delimited with a different style of quotes.
	</P>
	<P><A HREF = "Section_python.html#py_7">Section 11.7</A> describes the syntax for how
	Python wraps the various functions included in the LAMMPS library
	interface.
	</P>
	<P>A more interesting example is in the examples/python/in.python script
	which loads and runs the following function from examples/python/funcs.py:
	</P>
	<PRE>def loop(N,cut0,thresh,lmpptr):
	print "LOOP ARGS",N,cut0,thresh,lmpptr
	from lammps import lammps
	lmp = lammps(ptr=lmpptr)
	natoms = lmp.get_natoms()
	</PRE>
	<PRE> for i in range(N):
	cut = cut0 + i*0.1
	</PRE>
	<PRE> lmp.set_variable("cut",cut) # set a variable in LAMMPS
	lmp.command("pair_style lj/cut ${cut}") # LAMMPS command
	#lmp.command("pair_style lj/cut %d" % cut) # LAMMPS command option
	</PRE>
	<PRE> lmp.command("pair_coeff * * 1.0 1.0") # ditto
	lmp.command("run 10") # ditto
	pe = lmp.extract_compute("thermo_pe",0,0) # extract total PE from LAMMPS
	print "PE",pe/natoms,thresh
	if pe/natoms < thresh: return
	</PRE>
	<P>with these input script commands:
	</P>
	<PRE>python loop input 4 10 1.0 -4.0 SELF format iffp file funcs.py
	python loop invoke
	</PRE>
	<P>This has the effect of looping over a series of 10 short runs (10
	timesteps each) where the pair style cutoff is increased from a value
	of 1.0 in distance units, in increments of 0.1. The looping stops
	when the per-atom potential energy falls below a threshhold of -4.0 in
	energy units. More generally, Python can be used to implement a loop
	with complex logic, much more so than can be created using the LAMMPS
	<A HREF = "jump.html">jump</A> and <A HREF = "if.html">if</A> commands.
	</P>
	<P>Several LAMMPS library functions are called from the loop function.
	Get_natoms() returns the number of atoms in the simulation, so that it
	can be used to normalize the potential energy that is returned by
	extract_compute() for the "thermo_pe" compute that is defined by
	default for LAMMPS thermodynamic output. Set_variable() sets the
	value of a string variable defined in LAMMPS. This library function
	is a useful way for a Python function to return multiple values to
	LAMMPS, more than the single value that can be passed back via a
	return statement. This cutoff value in the "cut" variable is then
	substituted (by LAMMPS) in the pair_style command that is executed
	next. Alternatively, the "LAMMPS command option" line could be used
	in place of the 2 preceeding lines, to have Python insert the value
	into the LAMMPS command string.
	</P>
	<P>IMPORTANT NOTE: When using the callback mechanism just described,
	recognize that there are some operations you should not attempt
	because LAMMPS cannot execute them correctly. If the Python function
	is invoked between runs in the LAMMPS input script, then it should be
	OK to invoke any LAMMPS input script command via the library interface
	command() or file() functions, so long as the command would work if it
	were executed in the LAMMPS input script directly at the same point.
	</P>
	<P>However, a Python function can also be invoked during a run, whenever
	an associated LAMMPS variable it is assigned to is evaluted. If the
	variable is an input argument to another LAMMPS command (e.g. <A HREF = "fix_setforce.html">fix
	setforce</A>), then the Python function will be invoked
	inside the class for that command, in one of its methods that is
	invoked in the middle of a timestep. You cannot execute arbitrary
	input script commands from the Python function (again, via the
	command() or file() functions) at that point in the run and expect it
	to work. Other library functions such as those that invoke computes
	or other variables may have hidden side effects as well. In these
	cases, LAMMPS has no simple way to check that something illogical is
	being attempted.
	</P>
	<HR>

	<P>If you run Python code directly on your workstation, either
	interactively or by using Python to launch a Python script stored in a
	file, and your code has an error, you will typically see informative
	error messages. That is not the case when you run Python code from
	LAMMPS using an embedded Python interpreter. The code will typically
	fail silently. LAMMPS will catch some errors but cannot tell you
	where in the Python code the problem occurred. For example, if the
	Python code cannot be loaded and run because it has syntax or other
	logic errors, you may get an error from Python pointing to the
	offending line, or you may get one of these generic errors from
	LAMMPS:
	</P>
	<PRE>Could not process Python file
	Could not process Python string
	</PRE>
	<P>When the Python function is invoked, if it does not return properly,
	you will typically get this generic error from LAMMPS:
	</P>
	<PRE>Python function evaluation failed
	</PRE>
	<P>Here are three suggestions for debugging your Python code while
	running it under LAMMPS.
	</P>
	<P>First, don't run it under LAMMPS, at least to start with! Debug it
	using plain Python. Load and invoke your function, pass it arguments,
	check return values, etc.
	</P>
	<P>Second, add Python print statements to the function to check how far
	it gets and intermediate values it calculates. See the discussion
	above about printing from Python when running in parallel.
	</P>
	<P>Third, use Python exception handling. For example, say this statement
	in your Python function is failing, because you have not initialized the
	variable foo:
	</P>
	<PRE>foo += 1
	</PRE>
	<P>If you put one (or more) statements inside a "try" statement,
	like this:
	</P>
	<PRE>import exceptions
	print "Inside simple function"
	try:
	foo += 1 # one or more statements here
	except Exception, e:
	print "FOO error:",e
	</PRE>
	<P>then you will get this message printed to the screen:
	</P>
	<PRE>FOO error: local variable 'foo' referenced before assignment
	</PRE>
	<P>If there is no error in the try statements, then nothing is printed.
	Either way the function continues on (unless you put a return or
	sys.exit() in the except clause).
	</P>
	<HR>

	<P><B>Restrictions:</B>
	</P>
	<P>This command is part of the PYTHON package. It is only enabled if
	LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
	LAMMPS</A> section for more info.
	</P>
	<P>Building LAMMPS with the PYTHON package will link LAMMPS with the
	Python library on your system. Settings to enable this are in the
	lib/python/Makefile.lammps file. See the lib/python/README file for
	information on those settings.
	</P>
	<P>If you use Python code which calls back to LAMMPS, via the SELF input
	argument explained above, there is an extra step required when
	building LAMMPS. LAMMPS must also be built as a shared library and
	your Python function must be able to to load the Python module in
	python/lammps.py that wraps the LAMMPS library interface. These are
	the same steps required to use Python by itself to wrap LAMMPS.
	Details on these steps are explained in <A HREF = "Section.python.html">Section
	python</A>. Note that it is important that the
	stand-alone LAMMPS executable and the LAMMPS shared library be
	consistent (built from the same source code files) in order for this
	to work. If the two have been built at different times using
	different source files, problems may occur.
	</P>
	<P>As described above, you can use the python command to invoke a Python
	function which calls back to LAMMPS through its Python-wrapped library
	interface. However you cannot do the opposite. I.e. you cannot call
	LAMMPS from Python and invoke the python command to "callback" to
	Python and execute a Python function. LAMMPS will generate an error
	if you try to do that. Note that we think there actually should be a
	way to do that, but haven't yet been able to figure out how to do it
	successfully.
	</P>
	<P><B>Related commands:</B>
	</P>
	<P><A HREF = "shell.html">shell</A>, <A HREF = "variable.html">variable</A>
	</P>
	<P><B>Default:</B> none
	</P>
	</HTML>

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