lammps-analyser 0.1.0-pre-release-3

A CLI tool and language server for LAMMPS simulation input scripts.
Documentation 
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78

# fix python/invoke command

## Syntax

    fix ID group-ID python/invoke N callback function_name

-   ID, group-ID are ignored by this fix

-   python/invoke = style name of this fix command

-   N = execute every N steps

-   callback = *post_force* or *end_of_step*

        *post_force* = callback after force computations on atoms every N time steps
        *end_of_step* = callback after every N time steps

## Examples

``` LAMMPS
python post_force_callback here """
from lammps import lammps

def post_force_callback(lammps_ptr, vflag):
    lmp = lammps(ptr=lammps_ptr)
    # access LAMMPS state using Python interface
"""

python end_of_step_callback here """
def end_of_step_callback(lammps_ptr):
    lmp = lammps(ptr=lammps_ptr)
    # access LAMMPS state using Python interface
"""

fix pf  all python/invoke 50 post_force post_force_callback
fix eos all python/invoke 50 end_of_step end_of_step_callback
```

## Description

This fix allows you to call a Python function during a simulation run.
The callback is either executed after forces have been applied to atoms
or at the end of every N time steps.

Callback functions must be declared in the global scope of the active
Python interpreter. This can either be done by defining it inline using
the python command or by importing functions from other Python modules.
If LAMMPS is driven using the library interface from Python, functions
defined in the driving Python interpreter can also be executed.

Each callback is given a pointer object as first argument. This can be
used to initialize an instance of the lammps Python interface, which
gives access to the LAMMPS state from Python.

:::: warning
::: title
Warning
:::

While you can access the state of LAMMPS via library functions from
these callbacks, trying to execute input script commands will in the
best case not work or in the worst case result in undefined behavior.
::::

## Restrictions

This fix is part of the PYTHON package. It is only enabled if LAMMPS was
built with that package. See the [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
lib/python/Makefile.lammps file. See the lib/python/README file for
information on those settings.

## Related commands

[python command](python)