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Steve Plimpton
2025-06-09 16:38:42 -06:00
parent 2567a3d802
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247
doc/src/python.rst
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@ -17,9 +17,9 @@ Syntax
.. parsed-literal::
keyword = *here* or name of a *Python file*
*here* arg = one or more lines of Python code
must be a single argument, typically enclosed between triple quotes
the in-lined Python code will be executed immediately
*here* arg = inline
inline = one or more lines of Python code which will be executed immediately
must be a single argument, typically enclosed between triple quotes
*Python file* = name of a file with Python code which will be executed immediately
* if *mode* is *name* of a Python function:
@ -28,8 +28,9 @@ Syntax
one or more keywords with/without arguments must be appended
keyword = *invoke* or *input* or *return* or *format* or *length* or *file* or *here* or *exists*
*invoke* arg = invoke the previously-defined Python function
logreturn = log return value of the invoked python function, if defined (optional)
*invoke* arg = logreturn (optional)
invoke the previously-defined Python function
if logreturn is specified, print the return value of the invoked function to the screen and logfile
*input* args = N i1 i2 ... iN
N = # of inputs to function
i1,...,iN = value, SELF, or LAMMPS variable name
@ -96,31 +97,49 @@ interpreter. This can be done immediately, by using *mode* = *source*.
Or execution can be deferred, by registering a Python function for later
execution, by using *mode* = *name* of a Python function.
Later execution can be triggered in one of two ways. One is to use the
python command again with its *invoke* keyword. The other is to trigger
the evaluation of a python-style, equal-style, vector-style, or
atom-style variable. A python-style variable invokes its associated
Python function; its return value becomes the value of the python-style
variable. Equal-, vector-, and atom-style variables can use a Python
function wrapper in their formulas which encodes the Python function
name, and specifies arguments to pass to the function.
Later execution can be triggered in one of two ways. One is to use
the python command again with its *invoke* keyword. The other is to
trigger the evaluation of a python-style, equal-style, vector-style,
or atom-style variable. A python-style variable invokes its
associated Python function; its return value becomes the value of the
python-style variable. Equal-, vector-, and atom-style variables can
use a Python function wrapper in their formulas which encodes the
python-style variable name, and specifies arguments (which themselves
can be numeric formulas) to pass to the Python function associated
with the python-style variable.
As explained on the :doc:`variable <variable>` doc page, the
definition of a python-style va riable associates a Python function
name with the variable. Its specification must match the *mode*
argument of the *python* command for the Python function name. For
example these two commands would be consistent:
.. code-block:: LAMMPS
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.
Note that python-style, equal-style, vector-style, and atom-style
variables can be used in many different ways within LAMMPS. They can be
evaluated directly in an input script, effectively replacing the
variables can be used in many different ways within LAMMPS. They can
be evaluated directly in an input script, effectively replacing the
variable with its value. Or they can be passed to various commands as
arguments, so that the variable is evaluated multiple times during a
simulation run. See the :doc:`variable <variable>` command doc page for
more details on variable styles which enable Python function evaluation.
simulation run. See the :doc:`variable <variable>` command doc page
for more details on variable styles which enable Python function
evaluation.
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.
The Python code for a Python 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
@ -133,50 +152,90 @@ illustrates use of the python command.
----------
The first argument is the *mode* setting, which is either *source* or
the *name* of a Python function.
The first argument to the *python* command is the *mode* setting,
which is either *source* or the *name* of a Python function.
.. versionchanged:: 22Dec2022
If *source* is used, it is followed by either the *here* keyword or a
file name containing Python code. The *here* keyword is followed by a
string containing python commands, either on a single line enclosed in
quotes, or as multiple lines enclosed in triple quotes. In either
case, the in-line code or file contents are passed to the python
interpreter and executed immediately. The code will be loaded into
and run in the "main" module of the Python interpreter. This allows
running arbitrary Python code at any time while processing the SPARTA
input file. This can be used to pre-load Python modules, initialize
global variables, define functions or classes, or perform operations
using the Python programming language. The Python code will be
executed in parallel on all the MPI processes being used to run
LAMMPS. Note that no arguments can be passed to the executed Python
code.
single *inline* argument which is a string containing one or more
python commands. The string can either be on the same line as the
*python* command, enclosed in quotes, or it can be multiple lines
enclosed in triple quotes.
In either case, the in-line code or the file contents are passed to
the python interpreter and executed immediately. The code will be
loaded into and run in the "main" module of the Python interpreter.
This allows running arbitrary Python code at any time while processing
the LAMMPS input file. This can be used to pre-load Python modules,
initialize global variables, define functions or classes, or perform
operations using the Python programming language. The Python code
will be executed in parallel on all the MPI processes being used to
run LAMMPS. Note that no arguments can be passed to the executed
Python code.
If the *mode* setting is the *name* of a Python function, then it will
be registered with SPARTA for future execution (or already be defined,
see the *exists* keyword). One or more keywords must follow the
*mode* function name. One of the keywords must be *invoke*, *file*,
*here*, or *exists*.
be registered with LAMMPS for future execution (or can already be
defined, see the *exists* keyword). One or more keywords must follow
the *mode* function name. One of the keywords must be *invoke*,
*file*, *here*, or *exists*, which specifies what Python code to load
into the Python interpreter. Note that only one of those 4 keywords
is allowed since their operations are mutually exclusive.
In all other cases, the first argument is the name of a Python function
that will be registered with LAMMPS for future execution. The function
may already be defined (see *exists* keyword) or must be defined using
the *file* or *here* keywords as explained below.
----------
If the *invoke* keyword is used, only the optional *logreturn* keyword
can be used. A previous *python* command must have registered the
Python function referenced by this command. The command invokes the
Python function with the previously defined arguments. A return value
of the Python function will be ignored unless the Python function is
linked to a :doc:`python style variable <variable>` with the *return*
If the *invoke* keyword is used, no other keywords can be used. A
previous *python* command must have registered the Python function
referenced by this command. The *invoke* keyword invokes the Python
function with the previously defined arguments. A return value of the
Python function will be ignored unless the Python function is linked
to a :doc:`python style variable <variable>` with the *return*
keyword. This return value can be logged to the screen and logfile by
adding the *logreturn* keyword to the *invoke* command. In that case a
message with the name of the python command and the return value is
printed. Return values of python functions are otherwise only
accessible when the function is invoked indirectly by expanding a
:doc:`python style variable <variable>`. You can invoke a registered
function as many times as you wish in your input script.
adding the optional *logreturn* argument to the *invoke* keyword. In
that case a message with the name of the python command and the return
value is printed. Note that return values of python functions are
otherwise *only* accessible when the function is invoked indirectly by
expanding a :doc:`python style variable <variable>`, as described
below. A registered function can be invoked as many times as you wish
in your input script.
The *file* keyword gives the name of a file containing Python code,
which should end with a ".py" suffix. The code will be immediately
loaded into and run in the "main" module of the Python interpreter.
The Python code will be executed in parallel on all MPI processes.
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 and below.
This allows Python code to be listed verbatim in your input script,
with proper indentation, blank lines, and comments, as desired. See
the :doc:`Commands parse <Commands_parse>` doc page, for an
explanation of how triple quotes can be used as part of input script
syntax.
The *exists* keyword takes no argument. It simply means that Python
code containing the needed Python function has already been loaded
into the LAMMPS Python interpreter, for example by previous *python
source* command or in a file that was loaded previously with the
*file* keyword. This allows use of a single file of Python code which
contains multiple functions, any of which can be used in the same (or
different) input scripts (see below).
Note that the Python code that is loaded and run by the *file* or
*here* keyword must contain a function with the specified function
*name*. To operate properly when the function is later invoked, the
code for the function must match the *input* and *return* and *format*
keywords specified by the python command. Otherwise Python will
generate an error.
----------
The other keywords which can be used with the *python* command are
*input*, *return*, *format*, and *length*.
The *input* keyword defines how many arguments *N* the Python function
expects. If it takes no arguments, then the *input* keyword should
@ -248,23 +307,6 @@ This return value is *only* accessible when expanding the python-style
variable. When the *invoke* keyword is used, the return value of
the python function is ignored.
----------
As explained on the :doc:`variable <variable>` doc page, the
definition of a python-style variable associates a Python function
name with the variable. Its specification must match the *mode*
argument of the *python* command for the Python function name. For
example these two commands would be consistent:
.. code-block:: LAMMPS
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* keywords
are used. It defines an *fstring* with M characters, where M = sum of
number of inputs and outputs. The order of characters corresponds to
@ -290,41 +332,6 @@ truncated.
----------
As noted above, either the *invoke*, *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 containing Python code, which should
end with a ".py" suffix. The code will be immediately loaded into and
run in the "main" module of the Python interpreter. The Python code
will be executed in parallel on all MPI processes. 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 the
:doc:`Commands parse <Commands_parse>` doc page, 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 with the given name has
already been executed, for example by a *python source* command or in
the same file that was used previously with the *file* keyword. This
allows use of a single file of Python code which contains multiple
functions, any of which can be used in the same (or different) input
scripts (see below).
Note that the Python code that is loaded and run by the *file* or
*here* keyword must contain a function with the specified function
name. To operate properly when later invoked, 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.
@ -537,8 +544,9 @@ the value into the LAMMPS command string.
----------
A Python function can also be invoked during a run, whenever
an associated python-style variable it is assigned to is evaluated.
As noted above, a Python function can be invoked during a run,
whenever an associated python-style variable it is assigned to is
evaluated.
If the variable is an input argument to another LAMMPS command
(e.g. :doc:`fix setforce <fix_setforce>`), then the Python function
@ -557,12 +565,13 @@ simulation run at each time step using the :doc:`fix python/invoke
----------
A Python function can also be invoked within the formula for an
equal-style, vector-style, or atom-style variable. This means the
Python function will be invoked whenever the variable is invoked. In
the case of a vector-style variable, the Python function can be invoked
once per element of the global vector. In the case of an atom-style
variable, the Python function can be invoked once per atom.
As noted above, a Python function can also be invoked within the
formula for an equal-style, vector-style, or atom-style variable.
This means the Python function will be invoked whenever that variable
is invoked. In the case of a vector-style variable, the Python
function can be invoked once per element of the global vector. In the
case of an atom-style variable, the Python function can be invoked
once per atom.
Here are three simple examples using equal-, vector-, and atom-style
variables to trigger execution of a Python function:

10
doc/src/variable.rst
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@ -1223,7 +1223,7 @@ input script:
.. code-block:: LAMMPS
variable foo python truncate
python truncate return v_foo input 1 v_arg format fi here """
python truncate return v_foo input 1 iv_arg format fi here """
def truncate(x):
return int(x)
"""
@ -1252,10 +1252,10 @@ the atoms it owns.
When invoked for the Ith atom, the value of the *arg* internal-style
variable, defined by the *python* command, is set to the x-coord of
the Ith atom. The call via python-style variable *foo* to the Python
*truncate()* function passes the value of the *arg* variable as its
first (and only) argument. Likewise, the return value of the Python
function becomes is stored by the python-style variable *foo* and used
in the *xtrunc* atom-style variable formula for the Ith atom.
*truncate()* function passes the value of the *arg* variable as the
function's first (and only) argument. Likewise, the return value of
the Python function is stored by the python-style variable *foo* and
used in the *xtrunc* atom-style variable formula for the Ith atom.
The resulting per-atom vector for *xtrunc* will thus contain the
truncated x-coord of every atom in the system. The dump command