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
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96

# Neighbor list access

Access to neighbor lists is handled through a couple of wrapper classes
that allows to treat it like either a python list or a NumPy array. The
access procedure is similar to that of the C-library interface: use one
of the \"find\" functions to look up the index of the neighbor list in
the global table of neighbor lists and then get access to the neighbor
list data. The code sample below demonstrates reading the neighbor list
data using the NumPy access method.

``` python
from lammps import lammps
import numpy as np

lmp = lammps()
lmp.commands_string("""
region box block -2 2 -2 2 -2 2
lattice fcc 1.0
create_box 1 box
create_atoms 1 box
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0
run 0 post no""")

# look up the neighbor list
nlidx = lmp.find_pair_neighlist('lj/cut')
nl = lmp.numpy.get_neighlist(nlidx)
tags = lmp.extract_atom('id')
print("half neighbor list with {} entries".format(nl.size))
# print neighbor list contents
for i in range(0,nl.size):
    idx, nlist  = nl.get(i)
    print("\natom {} with ID {} has {} neighbors:".format(idx,tags[idx],nlist.size))
    if nlist.size > 0:
        for n in np.nditer(nlist):
            print("  atom {} with ID {}".format(n,tags[n]))
```

Another example for extracting a full neighbor list without evaluating a
potential is shown below.

``` python
from lammps import lammps
import numpy as np

lmp = lammps()
lmp.commands_string("""
newton off
region box block -2 2 -2 2 -2 2
lattice fcc 1.0
create_box 1 box
create_atoms 1 box
mass 1 1.0
pair_style zero 1.0 full
pair_coeff * *
run 0 post no""")

# look up the neighbor list
nlidx = lmp.find_pair_neighlist('zero')
nl = lmp.numpy.get_neighlist(nlidx)
tags = lmp.extract_atom('id')
print("full neighbor list with {} entries".format(nl.size))
# print neighbor list contents
for i in range(0,nl.size):
    idx, nlist  = nl.get(i)
    print("\natom {} with ID {} has {} neighbors:".format(idx,tags[idx],nlist.size))
    if nlist.size > 0:
        for n in np.nditer(nlist):
            pass
            print("  atom {} with ID {}".format(n,tags[n]))
```

**Methods:**

-   `lammps.get_neighlist() <lammps.lammps.get_neighlist()>`{.interpreted-text
    role="py:meth"}\_\_: Get neighbor list for given index
-   `lammps.get_neighlist_size()`{.interpreted-text role="py:meth"}: Get
    number of elements in neighbor list
-   `lammps.get_neighlist_element_neighbors()`{.interpreted-text
    role="py:meth"}: Get element in neighbor list and its neighbors
-   `lammps.find_pair_neighlist() <lammps.lammps.find_pair_neighlist()>`{.interpreted-text
    role="py:meth"}\_\_: Find neighbor list of pair style
-   `lammps.find_fix_neighlist() <lammps.lammps.find_pair_neighlist()>`{.interpreted-text
    role="py:meth"}\_\_: Find neighbor list of pair style
-   `lammps.find_compute_neighlist() <lammps.lammps.find_pair_neighlist()>`{.interpreted-text
    role="py:meth"}\_\_: Find neighbor list of pair style

**NumPy Methods:**

-   `lammps.numpy.get_neighlist() <lammps.numpy_wrapper.numpy_wrapper.get_neighlist()>`{.interpreted-text
    role="py:meth"}\_\_: Get neighbor list for given index, which uses
    NumPy arrays for its element neighbor arrays
-   `lammps.numpy.get_neighlist_element_neighbors() <lammps.numpy_wrapper.numpy_wrapper.get_neighlist_element_neighbors()>`{.interpreted-text
    role="py:meth"}\_\_: Get element in neighbor list and its neighbors
    (as numpy array)