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add example for Python with vector-style variable

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This commit is contained in:
Steve Plimpton
2025-05-20 13:33:36 -06:00
parent 2351418c94
commit 37a344a2ad
6 changed files with 596 additions and 77 deletions
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17
doc/src/python.rst
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@ -593,7 +593,7 @@ variable which invokes the same Python "truncate" function:
compute ke all temp compute ke all temp
variable ke vector c_ke variable ke vector c_ke
variable ketrunc vector py_foo(v_ke) variable ketrunc vector py_foo(v_ke)
thermo_style custom step temp epair v_ketrunc[*] thermo_style custom step temp epair v_ketrunc[*6]
The vector-style variable "ketrunc" invokes the Python "truncate" The vector-style variable "ketrunc" invokes the Python "truncate"
function on each of the 6 components of the global kinetic energy function on each of the 6 components of the global kinetic energy
@ -601,8 +601,9 @@ tensor calculated by the :doc:`compute ke <compute_ke>` command. The
6 truncated values will be printed with thermo output to the screen 6 truncated values will be printed with thermo output to the screen
and log file. and log file.
Alternatively, the last 2 lines can be replaced by these to define Or the last 2 lines of the equal-style variable example can be
atom-style variables which invoke the same Python "truncate" function: replaced by these to define atom-style variables which invoke the same
Python "truncate" function:
.. code-block:: LAMMPS .. code-block:: LAMMPS
@ -625,13 +626,13 @@ example, consider these (made up) commands:
.. code-block:: LAMMPS .. code-block:: LAMMPS
variable foo python mixedargs variable foo python mixedargs
python mixedargs return v_foo input 6 7.5 v_myValue iv_arg1 iv_argy iv_argz v_flags & python mixedargs return v_foo input 6 7.5 v_myValue iv_arg1 iv_argy iv_argz v_flag &
format fffffsf here """ format fffffsf here """
def mixedargs(a,b,x,y,z,flags): def mixedargs(a,b,x,y,z,flag):
... ...
return result return result
""" """
variable flags string optionABC variable flag string optionABC
variable myValue equal "2.0*temp*c_pe" variable myValue equal "2.0*temp*c_pe"
compute pe all pe compute pe all pe
compute peatom all pe/atom compute peatom all pe/atom
@ -644,13 +645,13 @@ In this example, these arguments are themselves small formulas
containing the x,y,z coordinates of each atom as well as a per-atom containing the x,y,z coordinates of each atom as well as a per-atom
compute (c_peratom) and thermodynamic keyword (zlo). compute (c_peratom) and thermodynamic keyword (zlo).
The other three arguements (7.5,v_myValue,v_flags) are defined by the The other three arguements (7.5,v_myValue,v_flag) are defined by the
*python* command. The first and last are constant values (7.5 and the *python* command. The first and last are constant values (7.5 and the
optionABC string). The second argument (myValue) is the result of an optionABC string). The second argument (myValue) is the result of an
equal-style variable formula which accesses the system temperature and equal-style variable formula which accesses the system temperature and
potential energy. potential energy.
The "result" returned by teach invocation of the Python "mixedargs" The "result" returned by each invocation of the Python "mixedargs"
function becomes the per-atom value in the atom-style "field" function becomes the per-atom value in the atom-style "field"
variable, which could be output to a dump file or used elsewhere in variable, which could be output to a dump file or used elsewhere in
the input script. the input script.

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@ -0,0 +1,234 @@
ITEM: TIMESTEP
0
ITEM: NUMBER OF ATOMS
108
ITEM: BOX BOUNDS pp pp pp
0.0000000000000000e+00 5.0387885741475218e+00
0.0000000000000000e+00 5.0387885741475218e+00
0.0000000000000000e+00 5.0387885741475218e+00
ITEM: ATOMS id x y z v_xtrunc v_ytrunc v_ztrunc
1 0 0 0 0 0 0
2 0.839798 0.839798 0 0 0 0
3 0.839798 0 0.839798 0 0 0
4 0 0.839798 0.839798 0 0 0
5 1.6796 0 0 1 0 0
6 2.51939 0.839798 0 2 0 0
7 2.51939 0 0.839798 2 0 0
8 1.6796 0.839798 0.839798 1 0 0
9 3.35919 0 0 3 0 0
10 4.19899 0.839798 0 4 0 0
11 4.19899 0 0.839798 4 0 0
12 3.35919 0.839798 0.839798 3 0 0
13 0 1.6796 0 0 1 0
14 0.839798 2.51939 0 0 2 0
15 0.839798 1.6796 0.839798 0 1 0
16 0 2.51939 0.839798 0 2 0
17 1.6796 1.6796 0 1 1 0
18 2.51939 2.51939 0 2 2 0
19 2.51939 1.6796 0.839798 2 1 0
20 1.6796 2.51939 0.839798 1 2 0
21 3.35919 1.6796 0 3 1 0
22 4.19899 2.51939 0 4 2 0
23 4.19899 1.6796 0.839798 4 1 0
24 3.35919 2.51939 0.839798 3 2 0
25 0 3.35919 0 0 3 0
26 0.839798 4.19899 0 0 4 0
27 0.839798 3.35919 0.839798 0 3 0
28 0 4.19899 0.839798 0 4 0
29 1.6796 3.35919 0 1 3 0
30 2.51939 4.19899 0 2 4 0
31 2.51939 3.35919 0.839798 2 3 0
32 1.6796 4.19899 0.839798 1 4 0
33 3.35919 3.35919 0 3 3 0
34 4.19899 4.19899 0 4 4 0
35 4.19899 3.35919 0.839798 4 3 0
36 3.35919 4.19899 0.839798 3 4 0
37 0 0 1.6796 0 0 1
38 0.839798 0.839798 1.6796 0 0 1
39 0.839798 0 2.51939 0 0 2
40 0 0.839798 2.51939 0 0 2
41 1.6796 0 1.6796 1 0 1
42 2.51939 0.839798 1.6796 2 0 1
43 2.51939 0 2.51939 2 0 2
44 1.6796 0.839798 2.51939 1 0 2
45 3.35919 0 1.6796 3 0 1
46 4.19899 0.839798 1.6796 4 0 1
47 4.19899 0 2.51939 4 0 2
48 3.35919 0.839798 2.51939 3 0 2
49 0 1.6796 1.6796 0 1 1
50 0.839798 2.51939 1.6796 0 2 1
51 0.839798 1.6796 2.51939 0 1 2
52 0 2.51939 2.51939 0 2 2
53 1.6796 1.6796 1.6796 1 1 1
54 2.51939 2.51939 1.6796 2 2 1
55 2.51939 1.6796 2.51939 2 1 2
56 1.6796 2.51939 2.51939 1 2 2
57 3.35919 1.6796 1.6796 3 1 1
58 4.19899 2.51939 1.6796 4 2 1
59 4.19899 1.6796 2.51939 4 1 2
60 3.35919 2.51939 2.51939 3 2 2
61 0 3.35919 1.6796 0 3 1
62 0.839798 4.19899 1.6796 0 4 1
63 0.839798 3.35919 2.51939 0 3 2
64 0 4.19899 2.51939 0 4 2
65 1.6796 3.35919 1.6796 1 3 1
66 2.51939 4.19899 1.6796 2 4 1
67 2.51939 3.35919 2.51939 2 3 2
68 1.6796 4.19899 2.51939 1 4 2
69 3.35919 3.35919 1.6796 3 3 1
70 4.19899 4.19899 1.6796 4 4 1
71 4.19899 3.35919 2.51939 4 3 2
72 3.35919 4.19899 2.51939 3 4 2
73 0 0 3.35919 0 0 3
74 0.839798 0.839798 3.35919 0 0 3
75 0.839798 0 4.19899 0 0 4
76 0 0.839798 4.19899 0 0 4
77 1.6796 0 3.35919 1 0 3
78 2.51939 0.839798 3.35919 2 0 3
79 2.51939 0 4.19899 2 0 4
80 1.6796 0.839798 4.19899 1 0 4
81 3.35919 0 3.35919 3 0 3
82 4.19899 0.839798 3.35919 4 0 3
83 4.19899 0 4.19899 4 0 4
84 3.35919 0.839798 4.19899 3 0 4
85 0 1.6796 3.35919 0 1 3
86 0.839798 2.51939 3.35919 0 2 3
87 0.839798 1.6796 4.19899 0 1 4
88 0 2.51939 4.19899 0 2 4
89 1.6796 1.6796 3.35919 1 1 3
90 2.51939 2.51939 3.35919 2 2 3
91 2.51939 1.6796 4.19899 2 1 4
92 1.6796 2.51939 4.19899 1 2 4
93 3.35919 1.6796 3.35919 3 1 3
94 4.19899 2.51939 3.35919 4 2 3
95 4.19899 1.6796 4.19899 4 1 4
96 3.35919 2.51939 4.19899 3 2 4
97 0 3.35919 3.35919 0 3 3
98 0.839798 4.19899 3.35919 0 4 3
99 0.839798 3.35919 4.19899 0 3 4
100 0 4.19899 4.19899 0 4 4
101 1.6796 3.35919 3.35919 1 3 3
102 2.51939 4.19899 3.35919 2 4 3
103 2.51939 3.35919 4.19899 2 3 4
104 1.6796 4.19899 4.19899 1 4 4
105 3.35919 3.35919 3.35919 3 3 3
106 4.19899 4.19899 3.35919 4 4 3
107 4.19899 3.35919 4.19899 4 3 4
108 3.35919 4.19899 4.19899 3 4 4
ITEM: TIMESTEP
100
ITEM: NUMBER OF ATOMS
108
ITEM: BOX BOUNDS pp pp pp
0.0000000000000000e+00 5.0387885741475218e+00
0.0000000000000000e+00 5.0387885741475218e+00
0.0000000000000000e+00 5.0387885741475218e+00
ITEM: ATOMS id x y z v_xtrunc v_ytrunc v_ztrunc
1 4.97801 0.0605812 4.88474 4 0 4
2 0.800305 0.813213 0.0576603 0 0 0
3 0.6485 5.00484 0.836947 0 5 0
4 5.01236 0.786108 0.77507 5 0 0
5 1.50261 4.9277 4.9755 1 4 4
6 2.46756 0.653742 5.0003 2 0 5
7 2.55699 4.96491 0.926671 2 4 0
8 1.62464 0.676882 0.777822 1 0 0
9 3.57018 0.00324557 4.76943 3 0 4
10 4.24909 0.985667 5.01613 4 0 5
11 4.13124 0.178555 0.700886 4 0 0
12 3.22537 0.963341 0.639686 3 0 0
13 4.90815 1.75715 0.0826318 4 1 0
14 1.00239 2.45421 0.0111309 1 2 0
15 0.88902 1.62097 0.874547 0 1 0
16 0.269512 2.41383 0.844638 0 2 0
17 1.54513 1.51174 0.0869798 1 1 0
18 2.0637 2.5991 0.0826392 2 2 0
19 2.44634 1.71869 0.918144 2 1 0
20 1.57997 2.52559 1.04361 1 2 1
21 3.26063 2.10027 0.0160498 3 2 0
22 4.21774 2.61172 0.0367453 4 2 0
23 4.32215 1.8333 0.925663 4 1 0
24 3.38151 2.6788 0.906258 3 2 0
25 0.275459 3.26838 0.21932 0 3 0
26 0.675354 4.14887 4.94054 0 4 4
27 0.867201 3.35405 1.17655 0 3 1
28 4.78788 4.34273 0.478103 4 4 0
29 1.42014 3.50181 0.191388 1 3 0
30 2.39935 4.14279 0.0726977 2 4 0
31 2.68157 3.57418 0.921633 2 3 0
32 1.77965 4.13041 0.925765 1 4 0
33 3.10555 3.22911 5.00703 3 3 5
34 4.24908 3.67507 4.83053 4 3 4
35 4.2444 3.59428 0.837193 4 3 0
36 3.52155 4.21032 0.423884 3 4 0
37 0.00881412 4.90616 1.74242 0 4 1
38 0.800033 0.812556 1.72553 0 0 1
39 0.929754 0.0251285 2.53734 0 0 2
40 0.0189933 0.897729 2.4272 0 0 2
41 1.77025 0.0864618 1.69637 1 0 1
42 2.6077 0.984882 1.7897 2 0 1
43 2.55819 4.95626 2.45373 2 4 2
44 1.77963 0.875522 2.5056 1 0 2
45 3.50499 0.0189748 1.5186 3 0 1
46 4.47856 0.849521 1.59138 4 0 1
47 3.99 0.309367 2.42507 3 0 2
48 3.06373 0.748905 2.87477 3 0 2
49 0.149175 1.72252 1.81302 0 1 1
50 0.963279 2.42412 1.76899 0 2 1
51 0.879984 1.74899 2.55389 0 1 2
52 0.211736 2.57456 2.48446 0 2 2
53 1.75238 1.7433 1.79028 1 1 1
54 2.61023 2.6802 1.55816 2 2 1
55 2.55259 1.72904 2.60295 2 1 2
56 1.7903 2.56204 2.41895 1 2 2
57 3.43857 1.71819 1.54054 3 1 1
58 4.20455 2.5331 1.87607 4 2 1
59 4.12961 1.48438 2.40107 4 1 2
60 3.36606 2.52455 2.67203 3 2 2
61 0.0138563 3.23504 1.76147 0 3 1
62 0.968224 4.42746 1.67526 0 4 1
63 0.965745 3.43479 2.52674 0 3 2
64 0.144542 4.27264 2.61793 0 4 2
65 1.7741 3.32184 1.66819 1 3 1
66 2.4878 4.29352 1.69069 2 4 1
67 2.56992 3.44579 2.4534 2 3 2
68 1.72356 4.2344 2.49376 1 4 2
69 3.43363 3.36417 1.87451 3 3 1
70 4.32623 4.1046 1.69102 4 4 1
71 4.22927 3.23505 2.64208 4 3 2
72 3.41086 4.28362 2.42553 3 4 2
73 4.85349 0.0953155 3.14546 4 0 3
74 0.833593 0.840282 3.27238 0 0 3
75 0.578712 4.99093 3.85234 0 4 3
76 0.119704 1.00404 4.09942 0 1 4
77 1.78347 4.95586 3.31184 1 4 3
78 2.34318 0.736887 3.54475 2 0 3
79 2.34858 4.82316 4.28272 2 4 4
80 1.55893 0.765128 4.31112 1 0 4
81 3.13128 0.0257347 3.70936 3 0 3
82 4.10851 0.877375 3.36388 4 0 3
83 4.30691 4.69041 4.14081 4 4 4
84 3.48471 1.07347 4.35888 3 1 4
85 0.0668209 1.77975 3.29313 0 1 3
86 0.894798 2.5043 3.34172 0 2 3
87 0.743432 1.71961 4.3483 0 1 4
88 0.135168 2.69084 4.12098 0 2 4
89 1.73749 1.5259 3.46692 1 1 3
90 2.47391 2.57508 3.27574 2 2 3
91 2.4825 1.46064 4.38907 2 1 4
92 1.67786 2.47309 4.03082 1 2 4
93 3.34694 1.70248 3.44784 3 1 3
94 4.20676 2.29697 3.23228 4 2 3
95 4.31748 1.76411 4.20898 4 1 4
96 3.1135 2.59262 4.08996 3 2 4
97 0.0727406 3.44797 3.30247 0 3 3
98 1.0752 4.05296 3.38036 1 4 3
99 1.0085 3.35058 4.3598 1 3 4
100 0.054939 4.00087 4.11831 0 4 4
101 1.72259 3.24691 3.19685 1 3 3
102 2.54324 4.21582 3.29642 2 4 3
103 2.33008 3.38603 4.27885 2 3 4
104 1.65617 4.10852 4.3491 1 4 4
105 3.14646 3.43756 3.28105 3 3 3
106 4.09781 4.10691 3.24439 4 4 3
107 4.1529 3.22538 3.79605 4 3 3
108 3.16394 3.96553 4.31023 3 3 4

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@ -0,0 +1,234 @@
ITEM: TIMESTEP
0
ITEM: NUMBER OF ATOMS
108
ITEM: BOX BOUNDS pp pp pp
0.0000000000000000e+00 5.0387885741475218e+00
0.0000000000000000e+00 5.0387885741475218e+00
0.0000000000000000e+00 5.0387885741475218e+00
ITEM: ATOMS id x y z v_xtrunc v_ytrunc v_ztrunc
1 0 0 0 0 0 0
2 0.839798 0.839798 0 0 0 0
3 0.839798 0 0.839798 0 0 0
4 0 0.839798 0.839798 0 0 0
13 0 1.6796 0 0 1 0
14 0.839798 1.6796 0.839798 0 1 0
19 0 0 1.6796 0 0 1
20 0.839798 0.839798 1.6796 0 0 1
25 0 1.6796 1.6796 0 1 1
5 1.6796 0 0 1 0 0
6 2.51939 0.839798 0 2 0 0
7 2.51939 0 0.839798 2 0 0
8 1.6796 0.839798 0.839798 1 0 0
15 1.6796 1.6796 0 1 1 0
16 2.51939 1.6796 0.839798 2 1 0
21 1.6796 0 1.6796 1 0 1
22 2.51939 0.839798 1.6796 2 0 1
26 1.6796 1.6796 1.6796 1 1 1
9 3.35919 0 0 3 0 0
10 4.19899 0.839798 0 4 0 0
11 4.19899 0 0.839798 4 0 0
12 3.35919 0.839798 0.839798 3 0 0
17 3.35919 1.6796 0 3 1 0
18 4.19899 1.6796 0.839798 4 1 0
23 3.35919 0 1.6796 3 0 1
24 4.19899 0.839798 1.6796 4 0 1
27 3.35919 1.6796 1.6796 3 1 1
28 0.839798 0 2.51939 0 0 2
29 0 0.839798 2.51939 0 0 2
34 0.839798 1.6796 2.51939 0 1 2
37 0 0 3.35919 0 0 3
38 0.839798 0.839798 3.35919 0 0 3
39 0.839798 0 4.19899 0 0 4
40 0 0.839798 4.19899 0 0 4
49 0 1.6796 3.35919 0 1 3
50 0.839798 1.6796 4.19899 0 1 4
30 2.51939 0 2.51939 2 0 2
31 1.6796 0.839798 2.51939 1 0 2
35 2.51939 1.6796 2.51939 2 1 2
41 1.6796 0 3.35919 1 0 3
42 2.51939 0.839798 3.35919 2 0 3
43 2.51939 0 4.19899 2 0 4
44 1.6796 0.839798 4.19899 1 0 4
51 1.6796 1.6796 3.35919 1 1 3
52 2.51939 1.6796 4.19899 2 1 4
32 4.19899 0 2.51939 4 0 2
33 3.35919 0.839798 2.51939 3 0 2
36 4.19899 1.6796 2.51939 4 1 2
45 3.35919 0 3.35919 3 0 3
46 4.19899 0.839798 3.35919 4 0 3
47 4.19899 0 4.19899 4 0 4
48 3.35919 0.839798 4.19899 3 0 4
53 3.35919 1.6796 3.35919 3 1 3
54 4.19899 1.6796 4.19899 4 1 4
55 0.839798 2.51939 0 0 2 0
56 0 2.51939 0.839798 0 2 0
61 0 3.35919 0 0 3 0
62 0.839798 4.19899 0 0 4 0
63 0.839798 3.35919 0.839798 0 3 0
64 0 4.19899 0.839798 0 4 0
73 0.839798 2.51939 1.6796 0 2 1
76 0 3.35919 1.6796 0 3 1
77 0.839798 4.19899 1.6796 0 4 1
57 2.51939 2.51939 0 2 2 0
58 1.6796 2.51939 0.839798 1 2 0
65 1.6796 3.35919 0 1 3 0
66 2.51939 4.19899 0 2 4 0
67 2.51939 3.35919 0.839798 2 3 0
68 1.6796 4.19899 0.839798 1 4 0
74 2.51939 2.51939 1.6796 2 2 1
78 1.6796 3.35919 1.6796 1 3 1
79 2.51939 4.19899 1.6796 2 4 1
59 4.19899 2.51939 0 4 2 0
60 3.35919 2.51939 0.839798 3 2 0
69 3.35919 3.35919 0 3 3 0
70 4.19899 4.19899 0 4 4 0
71 4.19899 3.35919 0.839798 4 3 0
72 3.35919 4.19899 0.839798 3 4 0
75 4.19899 2.51939 1.6796 4 2 1
80 3.35919 3.35919 1.6796 3 3 1
81 4.19899 4.19899 1.6796 4 4 1
82 0 2.51939 2.51939 0 2 2
85 0.839798 3.35919 2.51939 0 3 2
86 0 4.19899 2.51939 0 4 2
91 0.839798 2.51939 3.35919 0 2 3
92 0 2.51939 4.19899 0 2 4
97 0 3.35919 3.35919 0 3 3
98 0.839798 4.19899 3.35919 0 4 3
99 0.839798 3.35919 4.19899 0 3 4
100 0 4.19899 4.19899 0 4 4
83 1.6796 2.51939 2.51939 1 2 2
87 2.51939 3.35919 2.51939 2 3 2
88 1.6796 4.19899 2.51939 1 4 2
93 2.51939 2.51939 3.35919 2 2 3
94 1.6796 2.51939 4.19899 1 2 4
101 1.6796 3.35919 3.35919 1 3 3
102 2.51939 4.19899 3.35919 2 4 3
103 2.51939 3.35919 4.19899 2 3 4
104 1.6796 4.19899 4.19899 1 4 4
84 3.35919 2.51939 2.51939 3 2 2
89 4.19899 3.35919 2.51939 4 3 2
90 3.35919 4.19899 2.51939 3 4 2
95 4.19899 2.51939 3.35919 4 2 3
96 3.35919 2.51939 4.19899 3 2 4
105 3.35919 3.35919 3.35919 3 3 3
106 4.19899 4.19899 3.35919 4 4 3
107 4.19899 3.35919 4.19899 4 3 4
108 3.35919 4.19899 4.19899 3 4 4
ITEM: TIMESTEP
100
ITEM: NUMBER OF ATOMS
108
ITEM: BOX BOUNDS pp pp pp
0.0000000000000000e+00 5.0387885741475218e+00
0.0000000000000000e+00 5.0387885741475218e+00
0.0000000000000000e+00 5.0387885741475218e+00
ITEM: ATOMS id x y z v_xtrunc v_ytrunc v_ztrunc
27 3.43857 1.71819 1.54054 3 1 1
55 1.00239 2.45421 0.0111309 1 2 0
24 4.47856 0.849521 1.59138 4 0 1
4 5.01236 0.786108 0.77507 5 0 0
13 4.90815 1.75715 0.0826318 4 1 0
14 0.88902 1.62097 0.874547 0 1 0
23 3.50499 0.0189748 1.5186 3 0 1
20 0.800033 0.812556 1.72553 0 0 1
25 0.149175 1.72252 1.81302 0 1 1
18 4.32215 1.8333 0.925663 4 1 0
2 0.800305 0.813213 0.0576603 0 0 0
11 4.13124 0.178555 0.700886 4 0 0
8 1.62464 0.676882 0.777822 1 0 0
15 1.54513 1.51174 0.0869798 1 1 0
16 2.44634 1.71869 0.918144 2 1 0
21 1.77025 0.0864618 1.69637 1 0 1
22 2.6077 0.984882 1.7897 2 0 1
26 1.75238 1.7433 1.79028 1 1 1
56 0.269512 2.41383 0.844638 0 2 0
73 0.963279 2.42412 1.76899 0 2 1
12 3.22537 0.963341 0.639686 3 0 0
29 0.0189933 0.897729 2.4272 0 0 2
36 4.12961 1.48438 2.40107 4 1 2
31 1.77963 0.875522 2.5056 1 0 2
17 3.26063 2.10027 0.0160498 3 2 0
32 3.99 0.309367 2.42507 3 0 2
10 4.24909 0.985667 5.01613 4 0 5
9 3.57018 0.00324557 4.76943 3 0 4
34 0.879984 1.74899 2.55389 0 1 2
54 4.31748 1.76411 4.20898 4 1 4
38 0.833593 0.840282 3.27238 0 0 3
53 3.34694 1.70248 3.44784 3 1 3
40 0.119704 1.00404 4.09942 0 1 4
49 0.0668209 1.77975 3.29313 0 1 3
50 0.743432 1.71961 4.3483 0 1 4
1 4.97801 0.0605812 4.88474 4 0 4
28 0.929754 0.0251285 2.53734 0 0 2
94 1.67786 2.47309 4.03082 1 2 4
48 3.48471 1.07347 4.35888 3 1 4
42 2.34318 0.736887 3.54475 2 0 3
46 4.10851 0.877375 3.36388 4 0 3
44 1.55893 0.765128 4.31112 1 0 4
51 1.73749 1.5259 3.46692 1 1 3
52 2.4825 1.46064 4.38907 2 1 4
45 3.13128 0.0257347 3.70936 3 0 3
33 3.06373 0.748905 2.87477 3 0 2
37 4.85349 0.0953155 3.14546 4 0 3
95 4.20676 2.29697 3.23228 4 2 3
91 0.894798 2.5043 3.34172 0 2 3
6 2.46756 0.653742 5.0003 2 0 5
35 2.55259 1.72904 2.60295 2 1 2
75 4.20455 2.5331 1.87607 4 2 1
83 1.7903 2.56204 2.41895 1 2 2
90 3.41086 4.28362 2.42553 3 4 2
7 2.55699 4.96491 0.926671 2 4 0
63 0.867201 3.35405 1.17655 0 3 1
64 4.78788 4.34273 0.478103 4 4 0
81 4.32623 4.1046 1.69102 4 4 1
76 0.0138563 3.23504 1.76147 0 3 1
77 0.968224 4.42746 1.67526 0 4 1
57 2.0637 2.5991 0.0826392 2 2 0
80 3.43363 3.36417 1.87451 3 3 1
65 1.42014 3.50181 0.191388 1 3 0
58 1.57997 2.52559 1.04361 1 2 1
67 2.68157 3.57418 0.921633 2 3 0
68 1.77965 4.13041 0.925765 1 4 0
74 2.61023 2.6802 1.55816 2 2 1
78 1.7741 3.32184 1.66819 1 3 1
79 2.4878 4.29352 1.69069 2 4 1
59 4.21774 2.61172 0.0367453 4 2 0
72 3.52155 4.21032 0.423884 3 4 0
19 0.00881412 4.90616 1.74242 0 4 1
71 4.2444 3.59428 0.837193 4 3 0
60 3.38151 2.6788 0.906258 3 2 0
88 1.72356 4.2344 2.49376 1 4 2
87 2.56992 3.44579 2.4534 2 3 2
61 0.275459 3.26838 0.21932 0 3 0
3 0.6485 5.00484 0.836947 0 5 0
66 2.39935 4.14279 0.0726977 2 4 0
82 0.211736 2.57456 2.48446 0 2 2
30 2.55819 4.95626 2.45373 2 4 2
108 3.16394 3.96553 4.31023 3 3 4
62 0.675354 4.14887 4.94054 0 4 4
47 4.30691 4.69041 4.14081 4 4 4
107 4.1529 3.22538 3.79605 4 3 3
92 0.135168 2.69084 4.12098 0 2 4
97 0.0727406 3.44797 3.30247 0 3 3
98 1.0752 4.05296 3.38036 1 4 3
99 1.0085 3.35058 4.3598 1 3 4
100 0.054939 4.00087 4.11831 0 4 4
106 4.09781 4.10691 3.24439 4 4 3
70 4.24908 3.67507 4.83053 4 3 4
43 2.34858 4.82316 4.28272 2 4 4
105 3.14646 3.43756 3.28105 3 3 3
96 3.1135 2.59262 4.08996 3 2 4
101 1.72259 3.24691 3.19685 1 3 3
102 2.54324 4.21582 3.29642 2 4 3
103 2.33008 3.38603 4.27885 2 3 4
104 1.65617 4.10852 4.3491 1 4 4
84 3.36606 2.52455 2.67203 3 2 2
89 4.22927 3.23505 2.64208 4 3 2
41 1.78347 4.95586 3.31184 1 4 3
93 2.47391 2.57508 3.27574 2 2 3
39 0.578712 4.99093 3.85234 0 4 3
86 0.144542 4.27264 2.61793 0 4 2
5 1.50261 4.9277 4.9755 1 4 4
69 3.10555 3.22911 5.00703 3 3 5
85 0.965745 3.43479 2.52674 0 3 2

26
examples/python/in.python.wrap
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@ -1,9 +1,9 @@
# 3d Lennard-Jones melt with equal- and atom-style variables which # 3d Lennard-Jones melt with equal- and atom-style variables which
# use a Python function wrapper in their formulas # use a Python function wrapper in their formulas
variable x index 5 variable x index 3
variable y index 5 variable y index 3
variable z index 5 variable z index 3
units lj units lj
atom_style atomic atom_style atomic
@ -24,21 +24,37 @@ neigh_modify delay 0 every 20 check no
fix 1 all nve fix 1 all nve
# define Python truncate() function
variable foo python truncate variable foo python truncate
python truncate return v_foo input 1 iv_arg format fi here """ python truncate return v_foo input 1 iv_arg format fi here """
def truncate(x): def truncate(x):
return int(x) return int(x)
""" """
# use in equal-style variable
variable scalar equal py_foo(4.5) variable scalar equal py_foo(4.5)
print "TRUNCATE ${scalar}" print "TRUNCATE ${scalar}"
# use in atom-style variable
# examine dump file to see truncated xyz coords of each atom
variable xtrunc atom py_foo(x) variable xtrunc atom py_foo(x)
variable ytrunc atom py_foo(y) variable ytrunc atom py_foo(y)
variable ztrunc atom py_foo(z) variable ztrunc atom py_foo(z)
# examine dump file to see truncated xyz coords of each atom
dump 1 all custom 100 tmp.dump id x y z v_xtrunc v_ytrunc v_ztrunc dump 1 all custom 100 tmp.dump id x y z v_xtrunc v_ytrunc v_ztrunc
# use in vector-style variable
compute ke all temp
variable ke vector c_ke
variable ketrunc vector py_foo(v_ke)
thermo_style custom step temp epair v_ketrunc[*6]
run 100 run 100
print "KE TENSOR ${ketrunc}"

77
examples/python/log.1May25.python.wrap.g++.1
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@ -1,10 +1,10 @@
LAMMPS (2 Apr 2025 - Development - patch_2Apr2025-266-gebfb94a717-modified) LAMMPS (2 Apr 2025 - Development - patch_2Apr2025-270-g2351418c94-modified)
# 3d Lennard-Jones melt with equal- and atom-style variables which # 3d Lennard-Jones melt with equal- and atom-style variables which
# use a Python function wrapper in their formulas # use a Python function wrapper in their formulas
variable x index 5 variable x index 3
variable y index 5 variable y index 3
variable z index 5 variable z index 3
units lj units lj
atom_style atomic atom_style atomic
@ -12,15 +12,15 @@ atom_style atomic
lattice fcc 0.8442 lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
region box block 0 $x 0 $y 0 $z region box block 0 $x 0 $y 0 $z
region box block 0 5 0 $y 0 $z region box block 0 3 0 $y 0 $z
region box block 0 5 0 5 0 $z region box block 0 3 0 3 0 $z
region box block 0 5 0 5 0 5 region box block 0 3 0 3 0 3
create_box 1 box create_box 1 box
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) Created orthogonal box = (0 0 0) to (5.0387886 5.0387886 5.0387886)
1 by 1 by 1 MPI processor grid 1 by 1 by 1 MPI processor grid
create_atoms 1 box create_atoms 1 box
Created 500 atoms Created 108 atoms
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) using lattice units in orthogonal box = (0 0 0) to (5.0387886 5.0387886 5.0387886)
create_atoms CPU = 0.000 seconds create_atoms CPU = 0.000 seconds
mass 1 1.0 mass 1 1.0
@ -34,24 +34,36 @@ neigh_modify delay 0 every 20 check no
fix 1 all nve fix 1 all nve
# define Python truncate() function
variable foo python truncate variable foo python truncate
python truncate return v_foo input 1 iv_arg format fi here """ python truncate return v_foo input 1 iv_arg format fi here """
def truncate(x): def truncate(x):
return int(x) return int(x)
""" """
# use in equal-style variable
variable scalar equal py_foo(4.5) variable scalar equal py_foo(4.5)
print "TRUNCATE ${scalar}" print "TRUNCATE ${scalar}"
TRUNCATE 4 TRUNCATE 4
# use in atom-style variable
# examine dump file to see truncated xyz coords of each atom
variable xtrunc atom py_foo(x) variable xtrunc atom py_foo(x)
variable ytrunc atom py_foo(y) variable ytrunc atom py_foo(y)
variable ztrunc atom py_foo(z) variable ztrunc atom py_foo(z)
# examine dump file to see truncated xyz coords of each atom
dump 1 all custom 100 tmp.dump id x y z v_xtrunc v_ytrunc v_ztrunc dump 1 all custom 100 tmp.dump id x y z v_xtrunc v_ytrunc v_ztrunc
# use in vector-style variable
compute ke all temp
variable ke vector c_ke
variable ketrunc vector py_foo(v_ke)
thermo_style custom step temp epair v_ketrunc[*6]
run 100 run 100
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ... Neighbor list info ...
@ -59,41 +71,46 @@ Neighbor list info ...
max neighbors/atom: 2000, page size: 100000 max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8 master list distance cutoff = 2.8
ghost atom cutoff = 2.8 ghost atom cutoff = 2.8
binsize = 1.4, bins = 6 6 6 binsize = 1.4, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0 1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual (1) pair lj/cut, perpetual
attributes: half, newton on attributes: half, newton on
pair build: half/bin/atomonly/newton pair build: half/bin/atomonly/newton
stencil: half/bin/3d stencil: half/bin/3d
bin: standard bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.644 | 2.644 | 2.644 Mbytes Per MPI rank memory allocation (min/avg/max) = 2.598 | 2.598 | 2.598 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair v_ketrunc[1] v_ketrunc[2] v_ketrunc[3] v_ketrunc[4] v_ketrunc[5] v_ketrunc[6]
0 1.44 -6.7733681 0 -4.6176881 -5.0221006 0 1.44 -6.7733681 155 152 154 -10 -4 -6
100 0.75627408 -5.7580082 0 -4.6258659 0.21870071 100 0.82217015 -5.8614684 113 65 84 7 -1 -12
Loop time of 0.014627 on 1 procs for 100 steps with 500 atoms Loop time of 0.00278186 on 1 procs for 100 steps with 108 atoms
Performance: 2953445.899 tau/day, 6836.680 timesteps/s, 3.418 Matom-step/s Performance: 15529161.573 tau/day, 35947.133 timesteps/s, 3.882 Matom-step/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads 100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 0.010546 | 0.010546 | 0.010546 | 0.0 | 72.10 Pair | 0.0018161 | 0.0018161 | 0.0018161 | 0.0 | 65.29
Neigh | 0.0027775 | 0.0027775 | 0.0027775 | 0.0 | 18.99 Neigh | 0.00057543 | 0.00057543 | 0.00057543 | 0.0 | 20.68
Comm | 0.00044818 | 0.00044818 | 0.00044818 | 0.0 | 3.06 Comm | 0.00019634 | 0.00019634 | 0.00019634 | 0.0 | 7.06
Output | 0.00060601 | 0.00060601 | 0.00060601 | 0.0 | 4.14 Output | 0.00012056 | 0.00012056 | 0.00012056 | 0.0 | 4.33
Modify | 0.00018516 | 0.00018516 | 0.00018516 | 0.0 | 1.27 Modify | 4.8221e-05 | 4.8221e-05 | 4.8221e-05 | 0.0 | 1.73
Other | | 6.39e-05 | | | 0.44 Other | | 2.516e-05 | | | 0.90
Nlocal: 500 ave 500 max 500 min Nlocal: 108 ave 108 max 108 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1941 ave 1941 max 1941 min Nghost: 980 ave 980 max 980 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 18766 ave 18766 max 18766 min Neighs: 4071 ave 4071 max 4071 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 18766 Total # of neighbors = 4071
Ave neighs/atom = 37.532 Ave neighs/atom = 37.694444
Neighbor list builds = 5 Neighbor list builds = 5
Dangerous builds not checked Dangerous builds not checked
print "KE TENSOR ${ketrunc}"
KE TENSOR [113,65,84,7,-1,-12]
Total wall time: 0:00:00 Total wall time: 0:00:00

85
examples/python/log.1May25.python.wrap.g++.4
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@ -1,10 +1,10 @@
LAMMPS (2 Apr 2025 - Development - patch_2Apr2025-266-gebfb94a717-modified) LAMMPS (2 Apr 2025 - Development - patch_2Apr2025-270-g2351418c94-modified)
# 3d Lennard-Jones melt with equal- and atom-style variables which # 3d Lennard-Jones melt with equal- and atom-style variables which
# use a Python function wrapper in their formulas # use a Python function wrapper in their formulas
variable x index 5 variable x index 3
variable y index 5 variable y index 3
variable z index 5 variable z index 3
units lj units lj
atom_style atomic atom_style atomic
@ -12,15 +12,15 @@ atom_style atomic
lattice fcc 0.8442 lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
region box block 0 $x 0 $y 0 $z region box block 0 $x 0 $y 0 $z
region box block 0 5 0 $y 0 $z region box block 0 3 0 $y 0 $z
region box block 0 5 0 5 0 $z region box block 0 3 0 3 0 $z
region box block 0 5 0 5 0 5 region box block 0 3 0 3 0 3
create_box 1 box create_box 1 box
Created orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) Created orthogonal box = (0 0 0) to (5.0387886 5.0387886 5.0387886)
1 by 2 by 2 MPI processor grid 1 by 2 by 2 MPI processor grid
create_atoms 1 box create_atoms 1 box
Created 500 atoms Created 108 atoms
using lattice units in orthogonal box = (0 0 0) to (8.397981 8.397981 8.397981) using lattice units in orthogonal box = (0 0 0) to (5.0387886 5.0387886 5.0387886)
create_atoms CPU = 0.000 seconds create_atoms CPU = 0.000 seconds
mass 1 1.0 mass 1 1.0
@ -34,24 +34,36 @@ neigh_modify delay 0 every 20 check no
fix 1 all nve fix 1 all nve
# define Python truncate() function
variable foo python truncate variable foo python truncate
python truncate return v_foo input 1 iv_arg format fi here """ python truncate return v_foo input 1 iv_arg format fi here """
def truncate(x): def truncate(x):
return int(x) return int(x)
""" """
# use in equal-style variable
variable scalar equal py_foo(4.5) variable scalar equal py_foo(4.5)
print "TRUNCATE ${scalar}" print "TRUNCATE ${scalar}"
TRUNCATE 4 TRUNCATE 4
# use in atom-style variable
# examine dump file to see truncated xyz coords of each atom
variable xtrunc atom py_foo(x) variable xtrunc atom py_foo(x)
variable ytrunc atom py_foo(y) variable ytrunc atom py_foo(y)
variable ztrunc atom py_foo(z) variable ztrunc atom py_foo(z)
# examine dump file to see truncated xyz coords of each atom
dump 1 all custom 100 tmp.dump id x y z v_xtrunc v_ytrunc v_ztrunc dump 1 all custom 100 tmp.dump id x y z v_xtrunc v_ytrunc v_ztrunc
# use in vector-style variable
compute ke all temp
variable ke vector c_ke
variable ketrunc vector py_foo(v_ke)
thermo_style custom step temp epair v_ketrunc[*6]
run 100 run 100
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ... Neighbor list info ...
@ -59,41 +71,46 @@ Neighbor list info ...
max neighbors/atom: 2000, page size: 100000 max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8 master list distance cutoff = 2.8
ghost atom cutoff = 2.8 ghost atom cutoff = 2.8
binsize = 1.4, bins = 6 6 6 binsize = 1.4, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0 1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual (1) pair lj/cut, perpetual
attributes: half, newton on attributes: half, newton on
pair build: half/bin/atomonly/newton pair build: half/bin/atomonly/newton
stencil: half/bin/3d stencil: half/bin/3d
bin: standard bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.609 | 2.609 | 2.609 Mbytes Per MPI rank memory allocation (min/avg/max) = 2.59 | 2.59 | 2.59 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair v_ketrunc[1] v_ketrunc[2] v_ketrunc[3] v_ketrunc[4] v_ketrunc[5] v_ketrunc[6]
0 1.44 -6.7733681 0 -4.6176881 -5.0221006 0 1.44 -6.7733681 155 152 154 -10 -4 -6
100 0.75627408 -5.7580082 0 -4.6258659 0.21870071 100 0.82217015 -5.8614684 113 65 84 7 -1 -12
Loop time of 0.0062374 on 4 procs for 100 steps with 500 atoms Loop time of 0.00268845 on 4 procs for 100 steps with 108 atoms
Performance: 6925957.189 tau/day, 16032.308 timesteps/s, 8.016 Matom-step/s Performance: 16068745.964 tau/day, 37196.171 timesteps/s, 4.017 Matom-step/s
74.7% CPU use with 4 MPI tasks x no OpenMP threads 66.7% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 0.0027648 | 0.0028431 | 0.0029465 | 0.1 | 45.58 Pair | 0.00043389 | 0.00051695 | 0.00061255 | 0.0 | 19.23
Neigh | 0.00084567 | 0.00086563 | 0.00088168 | 0.0 | 13.88 Neigh | 0.00017121 | 0.00018976 | 0.00019891 | 0.0 | 7.06
Comm | 0.0020822 | 0.0021609 | 0.0022418 | 0.1 | 34.64 Comm | 0.0017423 | 0.0018487 | 0.0019509 | 0.2 | 68.76
Output | 0.00021567 | 0.00022125 | 0.00022624 | 0.0 | 3.55 Output | 6.7449e-05 | 6.9998e-05 | 7.5195e-05 | 0.0 | 2.60
Modify | 6.2567e-05 | 6.4105e-05 | 6.63e-05 | 0.0 | 1.03 Modify | 2.1329e-05 | 2.2855e-05 | 2.4821e-05 | 0.0 | 0.85
Other | | 8.241e-05 | | | 1.32 Other | | 4.018e-05 | | | 1.49
Nlocal: 125 ave 126 max 123 min Nlocal: 27 ave 30 max 25 min
Histogram: 1 0 0 0 0 0 1 0 0 2 Histogram: 1 0 1 0 1 0 0 0 0 1
Nghost: 1085.75 ave 1090 max 1082 min Nghost: 614 ave 616 max 612 min
Histogram: 1 0 1 0 0 0 1 0 0 1 Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs: 4691.5 ave 4969 max 4368 min Neighs: 1017.75 ave 1149 max 894 min
Histogram: 1 0 0 0 1 0 0 1 0 1 Histogram: 1 1 0 0 0 0 0 1 0 1
Total # of neighbors = 18766 Total # of neighbors = 4071
Ave neighs/atom = 37.532 Ave neighs/atom = 37.694444
Neighbor list builds = 5 Neighbor list builds = 5
Dangerous builds not checked Dangerous builds not checked
print "KE TENSOR ${ketrunc}"
KE TENSOR [113,65,84,7,-1,-12]
Total wall time: 0:00:00 Total wall time: 0:00:00