python command — LAMMPS 15 May 2015 version documentation

# python command

## Syntax

    python func keyword args ...

- func = name of Python function
- one or more keyword/args pairs must be appended

    keyword = invoke or input or return or format or file or here or exists
      invoke arg = none = invoke the previously defined Python function
      input 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
      return arg = varReturn
        varReturn = v_name  = LAMMPS variable name which return value of function will be assigned to
      format 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
      file arg = filename
        filename = file of Python code, which defines func
      here arg = inline
        inline = one or more lines of Python code which defines func
                 must be a single argument, typically enclosed between triple quotes
      exists arg = none = Python code has been loaded by previous python command

## Examples

    python pForce input 2 v_x 20.0 return v_f format fff file force.py
    python pForce invoke

    python factorial input 1 myN return v_fac format ii here """
    def factorial(n):
      if n == 1: return n
      return n * factorial(n-1)
     """

    python loop input 1 SELF return v_value format -f here """
    def loop(lmpptr,N,cut0):
      from lammps import lammps
      lmp = lammps(ptr=lmpptr)

    # loop N times, increasing cutoff each time

     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")
    """

## Description

Warning

It is not currently possible to use the python 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.

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.

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.

There are two ways to invoke a Python function once it has been defined. One is using the invoke keyword. The other is to assign the function to a python-style variable 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.

A broader overview of how Python can be used with LAMMPS is given in Section python. There is an examples/python directory which illustrates use of the python command.

The func setting specifies the name of the Python function. The code for the function is defined using the file or here keywords as explained below.

If the invoke 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.

The input keyword defines how many arguments N the Python function expects. If it takes no arguments, then the input 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 format 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 variable command. Each time the Python function is invoked, the LAMMPS variable is evaluated and its value is passed to the Python function.

The return keyword is only needed if the Python function returns a value. The specified varReturn must be of the form v_name, where “name” is the name of a python-style LAMMPS variable, defined by the variable command. The Python function can return a numeric or string value, as specified by the format keyword.

As explained on the variable doc page, the definition of a python-style variable associates a Python function name with the variable. This must match the func setting for this command. For exampe these two commands would be self-consistent:

    variable foo python myMultiply
    python myMultiply return v_foo format f file funcs.py

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.

The format keyword must be used if the input or return keyword is used. It defines an fstring 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 python-style variable 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 format keyword.

Either the file, here, or exists keyword must be used, but only one of them. These keywords specify what Python code to load into the Python interpreter. The file 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.

The here keyword does the same thing, except that the Python code follows as a single argument to the here 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 Section 3.2, for an explanation of how triple quotes can be used as part of input script syntax.

The exists keyword takes no argument. It means that Python code containing the required Python function defined by the func setting, is assumed to have been previously loaded by another python command.

Note that the Python code that is loaded and run must contain a function with the specified func name. To operate properly when later invoked, the the function code must match the input and return and format keywords specified by the python command. Otherwise Python will generate an error.

This section describes how Python code can be written to work with LAMMPS.

Whether you load Python code from a file or directly from your input script, via the file and here 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.

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 func setting in the python command. This means you can use the file keyword once to load several functions, and the exists keyword thereafter in subsequent python commands to access the other functions previously loaded.

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:

    nsteplast = -1
    nvaluelast = 0

    def expensive(nstep):
      global nsteplast,nvaluelast
      if nstep == nsteplast: return nvaluelast
      nsteplast = nstep
      # perform complicated calculation
      nvalue = ...
      nvaluelast = nvalue
      return nvalue

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.

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.

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.

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.

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.

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.

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:

    def foo(lmpptr,...):
      from lammps import lammps
      lmp = lammps(ptr=lmpptr)
      lmp.command('print "Hello from inside Python"')
      ...

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

    Hello from inside Python

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.

Section 11.7 describes the syntax for how Python wraps the various functions included in the LAMMPS library interface.

A more interesting example is in the examples/python/in.python script which loads and runs the following function from examples/python/funcs.py:

    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()

    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 command
    #lmp.command("pair_style lj/cut %d" % cut)  # LAMMPS command option

    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

with these input script commands:

    python          loop input 4 10 1.0 -4.0 SELF format iffp file funcs.py
    python          loop invoke

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 jump and if commands.

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.

Warning

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.

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. fix setforce), 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.

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:

    Could not process Python file
    Could not process Python string

When the Python function is invoked, if it does not return properly, you will typically get this generic error from LAMMPS:

    Python function evaluation failed

Here are three suggestions for debugging your Python code while running it under LAMMPS.

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.

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.

Third, use Python exception handling. For example, say this statement in your Python function is failing, because you have not initialized the variable foo:

    foo += 1

If you put one (or more) statements inside a “try” statement, like this:

    import exceptions
    print "Inside simple function"
    try:
      foo += 1      # one or more statements here
    except Exception, e:
      print "FOO error:",e

then you will get this message printed to the screen:

    FOO error: local variable 'foo' referenced before assignment

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).

## Restrictions

This command is part of the PYTHON package. It is only enabled if LAMMPS was built with that package. See the Making LAMMPS section for more info.

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.

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 `Section python`. 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.

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.

## Related commands

shell, variable

Default: none