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refactor handling of the python source command. document it and more limits.

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Axel Kohlmeyer
2022-11-10 16:03:06 -05:00
parent dd8c1df9c2
commit 34a5093229
3 changed files with 141 additions and 117 deletions
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doc/src/python.rst
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@ -8,14 +8,24 @@ Syntax
.. parsed-literal::
python func keyword args ...
python function keyword args ...
* func = name of Python function
* one or more keyword/args pairs must be appended
* function = *source* or name of Python function
if function is *source*:
.. parsed-literal::
keyword = *invoke* or *input* or *return* or *format* or *length* or *file* or *here* or *exists* or *source*
keyword = *inline* or name of a Python file
inline = one or more lines of Python code which will be executed immediately
must be a single argument, typically enclosed in triple quotes
Python file = name of a file with Python code which will be executed immediately
* if function is the name of a Python function, one or more keyword/args pairs must be appended
.. parsed-literal::
keyword = *invoke* or *input* or *return* or *format* or *length* 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
@ -38,10 +48,6 @@ Syntax
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
*source* arg = *filename* or *inline*
filename = file of Python code which will be executed immediately
inline = one or more lines of Python code which will be executed immediately
must be a single argument, typically enclosed between triple quotes
Examples
""""""""
@ -72,78 +78,87 @@ Examples
lmp.command("run 100")
"""
python source funcdef.py
python source inline "from lammps import lammps"
Description
"""""""""""
Define a Python function or execute a previously defined function or
execute some arbitrary python code.
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.
execute some arbitrary python code. 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 :doc:`python-style variable <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.
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 :doc:`python-style variable <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
with their result 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 on
the :doc:`Python <Python_head>` doc page. There is an examples/python
directory which illustrates use of the python command.
A broader overview of how Python can be used with LAMMPS is given in the
:doc:`Use Python with LAMMPS <Python_head>` section of the
documentation. 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. In case of the *source* keyword, the name of
the function is ignored.
The first argument of the *python* command is either the *source*
keyword or the name of a Python function.
If the *source* keyword is used, no other keywords can be used. The
argument either can be a filename or the keyword *inline* followed by a
string with python commands, either on a single line enclosed in quotes,
or as multiple lines enclosed in triple quotes. These python commands
will be passed to the python interpreter and executed immediately
without registering a python function for future execution.
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, no other keywords can be used, and a
previous python command must have defined the Python function
previous python command must have registered 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.
If the *source* keyword is used, no other keywords can be used.
The argument can be a filename or a string with python commands,
either on a single line enclosed in quotes, or as multiple lines
enclosed in triple quotes. These python commands will be passed
to the python interpreter and executed immediately without registering
a python function for future execution.
previously defined arguments and the return value is 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 :doc:`variable <variable>` command. Each time the Python
function is invoked, the LAMMPS variable is evaluated and its value is
passed to 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
:doc:`variable <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
@ -165,19 +180,19 @@ 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
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 :doc:`python-style variable <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.
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 :doc:`python-style variable <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.
If the *return* keyword is used and the *format* keyword specifies the
output as a string, then the default maximum length of that string is
@ -192,12 +207,12 @@ truncated.
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.
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. 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
@ -208,14 +223,15 @@ proper indentation, blank lines, and comments, as desired. See the
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.
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.
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 function code must match the *input* and
*return* and *format* keywords specified by the python command.
Otherwise Python will generate an error.
Note that the Python code that is loaded and run 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.
----------
@ -225,19 +241,18 @@ 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.
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.
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
@ -495,24 +510,35 @@ Restrictions
""""""""""""
This command is part of the PYTHON package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page 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
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
load the :doc:`"lammps" Python module <Python_module>` 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 on the :doc:`Python
<Python_head>` doc page. 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
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 load the :doc:`"lammps" Python module
<Python_module>` 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 on the :doc:`Python <Python_head>` doc page.
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.
Another limitation of calling back to Python from the LAMMPS module
using the *python* command in a LAMMPS input is that both, the Python
interpreter and LAMMPS, must be linked to the same Python runtime as a
shared library. If the Python interpreter is linked to Python
statically (which seems to happen with Conda) then loading the shared
LAMMPS library will create a second python "main" module that hides the
one from the Python interpreter and all previous defined function and
global variables will become invisible.
Related commands
""""""""""""""""

18
src/PYTHON/python_impl.cpp
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@ -130,19 +130,17 @@ void PythonImpl::command(int narg, char **arg)
return;
}
// if source is only keyword, execute the python code
// if source is only keyword, execute the python code in file
if (narg == 3 && strcmp(arg[1], "source") == 0) {
int err;
if ((narg > 1) && (strcmp(arg[0], "source") == 0)) {
int err = -1;
FILE *fp = fopen(arg[2], "r");
if (fp == nullptr)
if ((narg > 2) && (strcmp(arg[1], "inline") == 0)) {
err = execute_string(arg[2]);
else
err = execute_file(arg[2]);
if (fp) fclose(fp);
if (err) error->all(FLERR, "Could not process Python source command");
} else {
if (platform::file_is_readable(arg[1])) err = execute_file(arg[1]);
}
if (err) error->warning(FLERR, "Could not process Python source command. Error code: {}", err);
return;
}

4
unittest/python/test_python_package.cpp
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@ -276,7 +276,7 @@ TEST_F(PythonPackageTest, RunSource)
{
// execute python script from file
auto output = CAPTURE_OUTPUT([&] {
command("python xyz source ${input_dir}/run.py");
command("python source ${input_dir}/run.py");
});
ASSERT_THAT(output, HasSubstr(LOREM_IPSUM));
@ -286,7 +286,7 @@ TEST_F(PythonPackageTest, RunSourceInline)
{
// execute inline python script
auto output = CAPTURE_OUTPUT([&] {
command("python xyz source \"\"\"\n"
command("python source inline \"\"\"\n"
"from __future__ import print_function\n"
"print(2+2)\n"
"\"\"\"");