git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4647 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
@ -1,3 +0,0 @@
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Valence electron ionization in adamantane, adamantane_ionized has one less electron.
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The full adamantane molecule is also included.
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Finite system.
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@ -1,119 +0,0 @@
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Created by AJB
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102 atoms
|
||||
3 atom types
|
||||
|
||||
-500.0 500.0 xlo xhi
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||||
-500.0 500.0 ylo yhi
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||||
-500.0 500.0 zlo zhi
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||||
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||||
Masses
|
||||
|
||||
1 12.01070 # C nuclei
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||||
2 1.000794 # H nuclei
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3 1.000000 # electron
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||||
Atoms
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||||
|
||||
1 1 0.223271 2.836177 0.99547 6.00 0 0.00
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||||
2 1 -0.611326 1.278041 3.303884 6.00 0 0.00
|
||||
3 1 -0.645795 -1.544681 2.608294 6.00 0 0.00
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||||
4 1 -2.509122 -1.980433 0.419368 6.00 0 0.00
|
||||
5 1 -1.674732 -0.422977 -1.889518 6.00 0 0.00
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||||
6 1 -1.640226 2.39965 -1.193097 6.00 0 0.00
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||||
7 1 2.018681 -2.373515 1.79163 6.00 0 0.00
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||||
8 1 2.887596 2.006776 0.178976 6.00 0 0.00
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||||
9 1 0.98999 -1.251962 -2.705445 6.00 0 0.00
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||||
10 1 2.853997 -0.815965 -0.517029 6.00 0 0.00
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||||
11 2 -3.029741 -0.739677 -3.479893 1.00 0 0.00
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||||
12 2 -4.456466 -1.425024 1.003463 1.00 0 0.00
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||||
13 2 -2.581253 -4.027951 -0.074795 1.00 0 0.00
|
||||
14 2 -1.252983 -2.67657 4.28622 1.00 0 0.00
|
||||
15 2 -2.524731 1.891635 3.93955 1.00 0 0.00
|
||||
16 2 0.703394 1.61118 4.917143 1.00 0 0.00
|
||||
17 2 0.247516 4.887701 1.501501 1.00 0 0.00
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||||
18 2 2.027034 -4.428006 1.321731 1.00 0 0.00
|
||||
19 2 3.379737 -2.105382 3.378244 1.00 0 0.00
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||||
20 2 4.790758 -1.418428 -1.109855 1.00 0 0.00
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||||
21 2 -1.077541 3.552194 -2.865467 1.00 0 0.00
|
||||
22 2 -3.572149 3.033181 -0.63782 1.00 0 0.00
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||||
23 2 1.599389 -0.164293 -4.40463 1.00 0 0.00
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||||
24 2 0.980069 -3.286423 -3.255167 1.00 0 0.00
|
||||
25 2 4.264224 2.353276 1.736734 1.00 0 0.00
|
||||
26 2 3.530575 3.152347 -1.469016 1.00 0 0.00
|
||||
27 3 0.223271 2.836177 0.99547 0.00 1 0.332948
|
||||
28 3 0.223271 2.836177 0.99547 0.00 -1 0.332948
|
||||
29 3 -0.611326 1.278041 3.303884 0.00 1 0.332948
|
||||
30 3 -0.611326 1.278041 3.303884 0.00 -1 0.332948
|
||||
31 3 -0.645795 -1.544681 2.608294 0.00 1 0.332948
|
||||
32 3 -0.645795 -1.544681 2.608294 0.00 -1 0.332948
|
||||
33 3 -2.509122 -1.980433 0.419368 0.00 1 0.332948
|
||||
34 3 -2.509122 -1.980433 0.419368 0.00 -1 0.332948
|
||||
35 3 -1.674732 -0.422977 -1.889518 0.00 1 0.332948
|
||||
36 3 -1.674732 -0.422977 -1.889518 0.00 -1 0.332948
|
||||
37 3 -1.640226 2.39965 -1.193097 0.00 1 0.332948
|
||||
38 3 -1.640226 2.39965 -1.193097 0.00 -1 0.332948
|
||||
39 3 2.018681 -2.373515 1.79163 0.00 1 0.332948
|
||||
40 3 2.018681 -2.373515 1.79163 0.00 -1 0.332948
|
||||
41 3 2.887596 2.006776 0.178976 0.00 1 0.332948
|
||||
42 3 2.887596 2.006776 0.178976 0.00 -1 0.332948
|
||||
43 3 0.98999 -1.251962 -2.705445 0.00 1 0.332948
|
||||
44 3 0.98999 -1.251962 -2.705445 0.00 -1 0.332948
|
||||
45 3 2.853997 -0.815965 -0.517029 0.00 1 0.332948
|
||||
46 3 2.853997 -0.815965 -0.517029 0.00 -1 0.332948
|
||||
47 3 -0.194028 2.057109 2.149677 0.00 1 1.258
|
||||
48 3 -0.194028 2.057109 2.149677 0.00 -1 1.258
|
||||
49 3 -0.628561 -0.13332 2.956089 0.00 1 1.258
|
||||
50 3 -0.628561 -0.13332 2.956089 0.00 -1 1.258
|
||||
51 3 -1.577458 -1.762557 1.513831 0.00 1 1.258
|
||||
52 3 -1.577458 -1.762557 1.513831 0.00 -1 1.258
|
||||
53 3 -2.091927 -1.201705 -0.735075 0.00 1 1.258
|
||||
54 3 -2.091927 -1.201705 -0.735075 0.00 -1 1.258
|
||||
55 3 -0.708477 2.617913 -0.098814 0.00 1 1.258
|
||||
56 3 -0.708477 2.617913 -0.098814 0.00 -1 1.258
|
||||
57 3 -1.657479 0.988336 -1.541308 0.00 1 1.258
|
||||
58 3 -1.657479 0.988336 -1.541308 0.00 -1 1.258
|
||||
59 3 0.686443 -1.959098 2.199962 0.00 1 1.258
|
||||
60 3 0.686443 -1.959098 2.199962 0.00 -1 1.258
|
||||
61 3 1.555434 2.421476 0.587223 0.00 1 1.258
|
||||
62 3 1.555434 2.421476 0.587223 0.00 -1 1.258
|
||||
63 3 -0.342371 -0.83747 -2.297482 0.00 1 1.258
|
||||
64 3 -0.342371 -0.83747 -2.297482 0.00 -1 1.258
|
||||
65 3 2.436339 -1.59474 0.637301 0.00 1 1.258
|
||||
66 3 2.436339 -1.59474 0.637301 0.00 -1 1.258
|
||||
67 3 2.870796 0.595405 -0.169027 0.00 1 1.258
|
||||
68 3 2.870796 0.595405 -0.169027 0.00 -1 1.258
|
||||
69 3 1.921993 -1.033964 -1.611237 0.00 1 1.258
|
||||
70 3 1.921993 -1.033964 -1.611237 0.00 -1 1.258
|
||||
71 3 -2.632724 -0.646884 -3.013913 0.00 1 1.543
|
||||
72 3 -2.632724 -0.646884 -3.013913 0.00 -1 1.543
|
||||
73 3 -3.885894 -1.587759 0.832324 0.00 1 1.543
|
||||
74 3 -3.885894 -1.587759 0.832324 0.00 -1 1.543
|
||||
75 3 -2.560118 -3.428028 0.069995 0.00 1 1.543
|
||||
76 3 -2.560118 -3.428028 0.069995 0.00 -1 1.543
|
||||
77 3 -1.075077 -2.344927 3.794588 0.00 1 1.543
|
||||
78 3 -1.075077 -2.344927 3.794588 0.00 -1 1.543
|
||||
79 3 -1.964103 1.711852 3.7533 0.00 1 1.543
|
||||
80 3 -1.964103 1.711852 3.7533 0.00 -1 1.543
|
||||
81 3 0.318181 1.513571 4.444458 0.00 1 1.543
|
||||
82 3 0.318181 1.513571 4.444458 0.00 -1 1.543
|
||||
83 3 0.240412 4.286604 1.353234 0.00 1 1.543
|
||||
84 3 0.240412 4.286604 1.353234 0.00 -1 1.543
|
||||
85 3 2.024586 -3.82604 1.459412 0.00 1 1.543
|
||||
86 3 2.024586 -3.82604 1.459412 0.00 -1 1.543
|
||||
87 3 2.980948 -2.183945 2.913367 0.00 1 1.543
|
||||
88 3 2.980948 -2.183945 2.913367 0.00 -1 1.543
|
||||
89 3 4.223287 -1.241907 -0.936157 0.00 1 1.543
|
||||
90 3 4.223287 -1.241907 -0.936157 0.00 -1 1.543
|
||||
91 3 -1.242407 3.214498 -2.375463 0.00 1 1.543
|
||||
92 3 -1.242407 3.214498 -2.375463 0.00 -1 1.543
|
||||
93 3 -3.006096 2.847556 -0.800517 0.00 1 1.543
|
||||
94 3 -3.006096 2.847556 -0.800517 0.00 -1 1.543
|
||||
95 3 1.420835 -0.48298 -3.906769 0.00 1 1.543
|
||||
96 3 1.420835 -0.48298 -3.906769 0.00 -1 1.543
|
||||
97 3 0.982976 -2.690326 -3.094098 0.00 1 1.543
|
||||
98 3 0.982976 -2.690326 -3.094098 0.00 -1 1.543
|
||||
99 3 3.860872 2.251751 1.280311 0.00 1 1.543
|
||||
100 3 3.860872 2.251751 1.280311 0.00 -1 1.543
|
||||
101 3 3.342182 2.816694 -0.986155 0.00 1 1.543
|
||||
102 3 3.342182 2.816694 -0.986155 0.00 -1 1.543
|
||||
@ -1,118 +0,0 @@
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||||
Created by AJB
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||||
101 atoms
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||||
3 atom types
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||||
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||||
-50.0 50.0 xlo xhi
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||||
-50.0 50.0 ylo yhi
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||||
-50.0 50.0 zlo zhi
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||||
|
||||
Masses
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||||
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1 12.01070 # C nuclei
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2 1.000794 # H nuclei
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3 1.000000 # electron
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Atoms
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||||
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||||
1 1 0.22423 2.918607 1.015812 6 0 0.00
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2 1 -0.63445 1.31446 3.390303 6 0 0.00
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||||
3 1 -0.670162 -1.590173 2.675707 6 0 0.00
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||||
4 1 -2.586695 -2.037708 0.422846 6 0 0.00
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||||
5 1 -1.729127 -0.435706 -1.953488 6 0 0.00
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||||
6 1 -1.692867 2.468206 -1.236 6 0 0.00
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||||
7 1 2.071281 -2.442011 1.834504 6 0 0.00
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||||
8 1 2.965108 2.063979 0.175607 6 0 0.00
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||||
9 1 1.013015 -1.288254 -2.791737 6 0 0.00
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||||
10 1 2.931847 -0.84022 -0.540904 6 0 0.00
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||||
11 2 -3.23707 -0.788493 -3.724286 1 0 0.00
|
||||
12 2 -4.691469 -1.429253 1.05608 1 0 0.00
|
||||
13 2 -2.657034 -4.253233 -0.113602 1 0 0.00
|
||||
14 2 -1.345725 -2.850372 4.543752 1 0 0.00
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||||
15 2 -2.707861 1.976434 4.071194 1 0 0.00
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||||
16 2 0.79423 1.672161 5.131751 1 0 0.00
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||||
17 2 0.251667 5.202465 1.579125 1 0 0.00
|
||||
18 2 2.074796 -4.663951 1.320307 1 0 0.00
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||||
19 2 3.542471 -2.144066 3.551451 1 0 0.00
|
||||
20 2 5.087753 -1.51102 -1.201338 1 0 0.00
|
||||
21 2 -1.077021 3.711707 -3.045901 1 0 0.00
|
||||
22 2 -3.783389 3.148492 -0.629227 1 0 0.00
|
||||
23 2 1.671766 -0.104421 -4.626344 1 0 0.00
|
||||
24 2 0.999815 -3.49189 -3.379184 1 0 0.00
|
||||
25 2 4.450647 2.434018 1.865941 1 0 0.00
|
||||
26 2 3.65466 3.300997 -1.612081 1 0 0.00
|
||||
27 3 -0.634804 1.31502 3.391634 0 -1 0.328405
|
||||
28 3 -0.670512 -1.590826 2.676675 0 -1 0.328107
|
||||
29 3 -2.587889 -2.038591 0.422899 0 -1 0.328405
|
||||
30 3 -1.729909 -0.435889 -1.954405 0 -1 0.328107
|
||||
31 3 -1.693676 2.469262 -1.236661 0 -1 0.328405
|
||||
32 3 2.072091 -2.443067 1.835165 0 -1 0.328405
|
||||
33 3 2.966303 2.064861 0.175553 0 -1 0.328405
|
||||
34 3 1.01337 -1.288814 -2.793067 0 -1 0.328405
|
||||
35 3 2.932965 -0.840567 -0.541247 0 -1 0.328108
|
||||
36 3 -0.210743 2.123398 2.223462 0 -1 1.326096
|
||||
37 3 -0.657351 -0.127988 3.052304 0 -1 1.326096
|
||||
38 3 -1.646634 -1.826737 1.548546 0 -1 1.326093
|
||||
39 3 -2.175416 -1.25026 -0.762988 0 -1 1.326095
|
||||
40 3 -0.747076 2.708081 -0.120938 0 -1 1.326093
|
||||
41 3 -1.722464 1.033139 -1.603613 0 -1 1.326095
|
||||
42 3 0.713852 -2.031645 2.263933 0 -1 1.326092
|
||||
43 3 1.613424 2.503259 0.59442 0 -1 1.326092
|
||||
44 3 -0.351222 -0.870483 -2.392027 0 -1 1.326098
|
||||
45 3 2.512477 -1.657113 0.657756 0 -1 1.3261
|
||||
46 3 2.965428 0.626295 -0.182887 0 -1 1.326099
|
||||
47 3 1.976186 -1.072464 -1.68666 0 -1 1.326101
|
||||
48 3 -2.952851 -0.722 -3.390526 0 -1 1.603792
|
||||
49 3 -4.265445 -1.534526 0.932369 0 -1 1.558563
|
||||
50 3 -2.625986 -3.810249 -0.010226 0 -1 1.558562
|
||||
51 3 -1.218394 -2.612849 4.191661 0 -1 1.603792
|
||||
52 3 -2.300135 1.839753 3.919625 0 -1 1.558507
|
||||
53 3 0.522041 1.594565 4.77431 0 -1 1.55862
|
||||
54 3 0.246496 4.772002 1.472951 0 -1 1.603792
|
||||
55 3 2.062319 -4.217199 1.410516 0 -1 1.558582
|
||||
56 3 3.245048 -2.186529 3.208486 0 -1 1.558537
|
||||
57 3 4.681408 -1.384588 -1.07686 0 -1 1.603791
|
||||
58 3 -1.184793 3.454906 -2.684898 0 -1 1.558565
|
||||
59 3 -3.365733 3.001032 -0.737405 0 -1 1.558559
|
||||
60 3 1.538708 -0.326106 -4.250794 0 -1 1.558551
|
||||
61 3 0.997214 -3.055912 -3.245768 0 -1 1.558563
|
||||
62 3 4.144833 2.349324 1.538532 0 -1 1.558524
|
||||
63 3 3.503398 3.047996 -1.264247 0 -1 1.558594
|
||||
64 3 0.224244 2.91979 1.016104 0 1 0.328107
|
||||
65 3 -0.634804 1.31502 3.391634 0 1 0.328405
|
||||
66 3 -0.670512 -1.590826 2.676675 0 1 0.328107
|
||||
67 3 -2.587889 -2.038591 0.422899 0 1 0.328405
|
||||
68 3 -1.729909 -0.435889 -1.954405 0 1 0.328107
|
||||
69 3 -1.693676 2.469262 -1.236661 0 1 0.328405
|
||||
70 3 2.072091 -2.443067 1.835165 0 1 0.328405
|
||||
71 3 2.966303 2.064861 0.175553 0 1 0.328405
|
||||
72 3 1.01337 -1.288814 -2.793067 0 1 0.328405
|
||||
73 3 2.932965 -0.840567 -0.541247 0 1 0.328108
|
||||
74 3 -0.210743 2.123398 2.223462 0 1 1.326096
|
||||
75 3 -0.657351 -0.127988 3.052304 0 1 1.326096
|
||||
76 3 -1.646634 -1.826737 1.548546 0 1 1.326093
|
||||
77 3 -2.175416 -1.250259 -0.762988 0 1 1.326094
|
||||
78 3 -0.747076 2.708081 -0.120938 0 1 1.326094
|
||||
79 3 -1.722464 1.033139 -1.603613 0 1 1.326096
|
||||
80 3 0.713852 -2.031645 2.263933 0 1 1.326092
|
||||
81 3 1.613424 2.503259 0.59442 0 1 1.326092
|
||||
82 3 -0.351222 -0.870483 -2.392027 0 1 1.326098
|
||||
83 3 2.512477 -1.657113 0.657756 0 1 1.3261
|
||||
84 3 2.965428 0.626295 -0.182887 0 1 1.326099
|
||||
85 3 1.976186 -1.072464 -1.68666 0 1 1.326101
|
||||
86 3 -2.952851 -0.722 -3.390526 0 1 1.603792
|
||||
87 3 -4.265445 -1.534526 0.932369 0 1 1.558563
|
||||
88 3 -2.625986 -3.810249 -0.010226 0 1 1.558562
|
||||
89 3 -1.218394 -2.612849 4.191661 0 1 1.603792
|
||||
90 3 -2.300135 1.839753 3.919625 0 1 1.558507
|
||||
91 3 0.522041 1.594565 4.77431 0 1 1.55862
|
||||
92 3 0.246496 4.772002 1.472951 0 1 1.603792
|
||||
93 3 2.062319 -4.217199 1.410516 0 1 1.558582
|
||||
94 3 3.245048 -2.186529 3.208486 0 1 1.558537
|
||||
95 3 4.681408 -1.384588 -1.07686 0 1 1.603791
|
||||
96 3 -1.184793 3.454906 -2.684898 0 1 1.558565
|
||||
97 3 -3.365733 3.001032 -0.737405 0 1 1.558559
|
||||
98 3 1.538708 -0.326106 -4.250794 0 1 1.558551
|
||||
99 3 0.997214 -3.055912 -3.245768 0 1 1.558563
|
||||
100 3 4.144833 2.349324 1.538532 0 1 1.558524
|
||||
101 3 3.503398 3.047996 -1.264247 0 1 1.558594
|
||||
@ -1,29 +0,0 @@
|
||||
variable sname index adamantane
|
||||
log ${sname}.min.log
|
||||
|
||||
units electron
|
||||
newton on
|
||||
#boundary p p p
|
||||
boundary f f f
|
||||
|
||||
atom_style hybrid charge electron
|
||||
|
||||
read_data data.${sname}
|
||||
|
||||
pair_style eff/cut 500.0
|
||||
pair_coeff * *
|
||||
|
||||
communicate single vel yes
|
||||
|
||||
thermo 1
|
||||
thermo_style multi
|
||||
|
||||
dump 1 all xyz 1 ${sname}.min.xyz
|
||||
dump 2 all custom 1 ${sname}.min.lammpstrj id type x y z radius fx fy fz rf
|
||||
|
||||
min_style cg
|
||||
#min_modify line quadratic
|
||||
minimize 0 1.0e-5 10000 100000
|
||||
|
||||
undump 1
|
||||
undump 2
|
||||
@ -1,40 +0,0 @@
|
||||
variable sname index adamantane
|
||||
|
||||
units electron
|
||||
newton on
|
||||
boundary f f f
|
||||
|
||||
atom_style hybrid charge electron
|
||||
|
||||
read_data data.${sname}
|
||||
|
||||
pair_style eff/cut 500.0
|
||||
pair_coeff * *
|
||||
|
||||
log ${sname}.min.log
|
||||
|
||||
communicate single vel yes
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step etotal pe ke press vol temp
|
||||
|
||||
min_style cg
|
||||
min_modify line quadratic
|
||||
minimize 0 1.0e-5 10000 100000
|
||||
|
||||
velocity all create 300.0 4928459 rot yes dist gaussian
|
||||
|
||||
reset_timestep 0
|
||||
log ${sname}.nvt.log
|
||||
|
||||
timestep 0.001
|
||||
fix 1 all nvt/eff 300.0 300.0 1.0 chain yes
|
||||
compute eff_temp all temp/eff
|
||||
thermo_style custom step etotal pe ke press vol temp c_eff_temp
|
||||
dump 1 all custom 100 ${sname}.nvt.lammpstrj id type x y z spin radius vx vy vz vr
|
||||
|
||||
run 1000000
|
||||
|
||||
unfix 1
|
||||
undump 1
|
||||
|
||||
@ -1,20 +0,0 @@
|
||||
variable sname index adamantane
|
||||
log ${sname}.spe.log
|
||||
|
||||
units electron
|
||||
newton on
|
||||
boundary f f f
|
||||
|
||||
atom_style hybrid charge electron
|
||||
|
||||
read_data data.${sname}
|
||||
|
||||
pair_style eff/cut 500.0
|
||||
pair_coeff * *
|
||||
|
||||
communicate single vel yes
|
||||
|
||||
thermo 1
|
||||
thermo_style multi
|
||||
|
||||
run 0
|
||||
@ -1,49 +0,0 @@
|
||||
variable sname index adamantane_ionized
|
||||
log ${sname}.nve.log
|
||||
|
||||
units electron
|
||||
newton on
|
||||
boundary f f f
|
||||
|
||||
atom_style hybrid charge electron
|
||||
|
||||
read_data data.${sname}
|
||||
|
||||
pair_style eff/cut 100.0
|
||||
pair_coeff * *
|
||||
|
||||
communicate single vel yes
|
||||
|
||||
thermo 1000
|
||||
thermo_style custom step pe temp press
|
||||
|
||||
# Minimization
|
||||
|
||||
#min_style cg
|
||||
#dump 1 all xyz 500 ${sname}.min.xyz
|
||||
#dump 2 all custom 500 ${sname}.min.lammpstrj id type x y z spin radius fx fy fz rf
|
||||
#min_modify line quadratic
|
||||
#minimize 0.0 1.0e-5 10000 100000
|
||||
|
||||
#undump 1
|
||||
#undump 2
|
||||
|
||||
#restart timestep
|
||||
|
||||
# set velocities for nve
|
||||
#velocity all create 300.0 4928459 dist uniform
|
||||
|
||||
# NVE
|
||||
timestep 0.001
|
||||
|
||||
fix 1 all nve/eff
|
||||
dump 1 all xyz 1000 ${sname}.nve.xyz
|
||||
dump 2 all custom 1000 ${sname}.nve.lammpstrj id type x y z spin radius fx fy fz rf
|
||||
#restart 1000 ${sname}.nve.restart1 ${sname}.nve.restart2
|
||||
|
||||
run 200000
|
||||
|
||||
unfix 1
|
||||
undump 1
|
||||
undump 2
|
||||
|
||||
@ -1,50 +0,0 @@
|
||||
variable sname index adamantane_ionized
|
||||
log ${sname}.nvt.log
|
||||
|
||||
units electron
|
||||
newton on
|
||||
boundary f f f
|
||||
|
||||
atom_style hybrid charge electron
|
||||
|
||||
read_data data.${sname}
|
||||
|
||||
pair_style eff/cut 100.0 limit no
|
||||
pair_coeff * *
|
||||
|
||||
communicate single vel yes
|
||||
|
||||
thermo 1000
|
||||
thermo_style custom step pe temp press
|
||||
|
||||
# Minimization
|
||||
|
||||
#min_style cg
|
||||
#dump 1 all xyz 100 ${sname}.min.xyz
|
||||
#dump 2 all custom 100 ${sname}.min.lammpstrj id type x y z spin radius
|
||||
#min_modify line quadratic
|
||||
#minimize 0.0 1.0e-5 4000 10000
|
||||
|
||||
#undump 1
|
||||
#undump 2
|
||||
|
||||
restart timestep
|
||||
|
||||
# set velocities for nvt
|
||||
velocity all create 300.0 4928459 dist uniform
|
||||
|
||||
# NVE
|
||||
reset_timestep 0
|
||||
timestep 0.001
|
||||
|
||||
fix 1 all nvt/eff 300.0 300.0 0.1 drag 0.2
|
||||
#dump 1 all xyz 1000 ${sname}.nvt.xyz
|
||||
dump 2 all custom 1000 ${sname}.nvt.lammpstrj id type x y z spin radius
|
||||
restart 1000 ${sname}.nvt.restart1 ${sname}.nvt.restart2
|
||||
|
||||
run 200000
|
||||
|
||||
unfix 1
|
||||
#undump 1
|
||||
undump 2
|
||||
|
||||
@ -1,2 +0,0 @@
|
||||
Be-solid.spe: beryllium bulk single point energy
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
@ -1,20 +0,0 @@
|
||||
variable sname index Be-solid
|
||||
log ${sname}.spe.log
|
||||
|
||||
units electron
|
||||
newton on
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid charge electron
|
||||
|
||||
read_data data.${sname}
|
||||
|
||||
pair_style eff/cut 31.6125 limit yes
|
||||
pair_coeff * *
|
||||
|
||||
neigh_modify one 10000 page 100000
|
||||
|
||||
dump 1 all custom 1 ${sname}.spe.lammpstrj id type x y z spin radius
|
||||
|
||||
run 0
|
||||
|
||||
@ -1,2 +0,0 @@
|
||||
Methane, core electron ionization and normal molecule (spe, min, dynamics).
|
||||
Note: electron mass set to 1
|
||||
@ -1,32 +0,0 @@
|
||||
Created by AJB
|
||||
|
||||
15 atoms
|
||||
3 atom types
|
||||
|
||||
-500.0 500.0 xlo xhi
|
||||
-500.0 500.0 ylo yhi
|
||||
-500.0 500.0 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 12.01070 # C nuclei mass
|
||||
2 1.000794 # H nuclei mass
|
||||
3 1.000000 # electron mass
|
||||
|
||||
Atoms
|
||||
#tag|type|x|y|z|q|spin|r
|
||||
1 1 0.0 0.0 0.0 6.0 0 0.0
|
||||
2 2 1.0 1.0 1.0 1.0 0 0.0
|
||||
3 2 -1.0 -1.0 1.0 1.0 0 0.0
|
||||
4 2 1.0 -1.0 -1.0 1.0 0 0.0
|
||||
5 2 -1.0 1.0 -1.0 1.0 0 0.0
|
||||
6 3 0.0 0.0 0.0 0.0 -1 0.5
|
||||
7 3 1.0 1.0 1.0 0.0 -1 1.0
|
||||
8 3 -1.0 -1.0 1.0 0.0 -1 1.0
|
||||
9 3 1.0 -1.0 -1.0 0.0 -1 1.0
|
||||
10 3 -1.0 1.0 -1.0 0.0 -1 1.0
|
||||
11 3 0.0 0.0 0.0 0.0 1 0.5
|
||||
12 3 1.0 1.0 1.0 0.0 1 1.0
|
||||
13 3 -1.0 -1.0 1.0 0.0 1 1.0
|
||||
14 3 1.0 -1.0 -1.0 0.0 1 1.0
|
||||
15 3 -1.0 1.0 -1.0 0.0 1 1.0
|
||||
@ -1,32 +0,0 @@
|
||||
Created by AJB
|
||||
|
||||
14 atoms
|
||||
3 atom types
|
||||
|
||||
-5000.0 5000.0 xlo xhi
|
||||
-5000.0 5000.0 ylo yhi
|
||||
-5000.0 5000.0 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 12.01070 # C nuclei mass
|
||||
2 1.000794 # H nuclei mass
|
||||
3 1.000000 # electron mass
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 0.000000 -0.000000 0.000000 6.000000 0 0.0
|
||||
2 2 1.247211 1.247211 1.247211 1.000000 0 0.0
|
||||
3 2 -1.247211 -1.247211 1.247211 1.000000 0 0.0
|
||||
4 2 1.247211 -1.247211 -1.247211 1.000000 0 0.0
|
||||
5 2 -1.247211 1.247211 -1.247211 1.000000 0 0.0
|
||||
6 3 -0.000000 0.000000 -0.000000 0.000000 -1 0.329128
|
||||
7 3 0.979221 0.979221 0.979221 0.000000 -1 1.486181
|
||||
8 3 -0.979221 -0.979221 0.979221 0.000000 -1 1.486181
|
||||
9 3 0.979221 -0.979221 -0.979221 0.000000 -1 1.486181
|
||||
10 3 -0.979221 0.979221 -0.979221 0.000000 -1 1.486181
|
||||
11 3 -0.000000 0.000000 0.000000 0.000000 1 0.329128
|
||||
12 3 -0.979221 -0.979221 0.979221 0.000000 1 1.486181
|
||||
13 3 0.979221 -0.979221 -0.979221 0.000000 1 1.486181
|
||||
14 3 -0.979221 0.979221 -0.979221 0.000000 1 1.486181
|
||||
|
||||
@ -1,29 +0,0 @@
|
||||
variable sname index ch4
|
||||
log ${sname}.min.log
|
||||
|
||||
units electron
|
||||
newton on
|
||||
boundary f f f
|
||||
|
||||
atom_style hybrid charge electron
|
||||
|
||||
read_data data.${sname}
|
||||
|
||||
pair_style eff/cut 100.0
|
||||
pair_coeff * *
|
||||
|
||||
communicate single vel yes
|
||||
|
||||
thermo 1
|
||||
thermo_style custom step pe temp press
|
||||
|
||||
# Minimize
|
||||
min_style cg
|
||||
dump 1 all custom 1 ${sname}.min.lammpstrj id type x y z spin radius
|
||||
dump 2 all xyz 1 ${sname}.min.xyz
|
||||
min_modify line quadratic dmax 0.1
|
||||
minimize 1.0e-6 1.0e-6 1000 10000
|
||||
|
||||
undump 1
|
||||
undump 2
|
||||
|
||||
@ -1,29 +0,0 @@
|
||||
variable sname index ch4
|
||||
log ${sname}.nve.log
|
||||
|
||||
units electron
|
||||
newton on
|
||||
boundary f f f
|
||||
|
||||
atom_style hybrid charge electron
|
||||
|
||||
read_data data.${sname}
|
||||
|
||||
pair_style eff/cut 100.0
|
||||
pair_coeff * *
|
||||
|
||||
communicate single vel yes
|
||||
|
||||
thermo 1000
|
||||
thermo_style custom step pe temp press
|
||||
|
||||
#velocity all create 300.0 4928459 dist gaussian rot yes mom yes
|
||||
|
||||
timestep 0.005
|
||||
fix 1 all nve/eff
|
||||
|
||||
# the custom dump includes the radii
|
||||
dump 1 all custom 1000 ${sname}.nve.lammpstrj id type x y z radius
|
||||
dump 2 all xyz 1000 ${sname}.nve.xyz
|
||||
|
||||
run 100000
|
||||
@ -1,27 +0,0 @@
|
||||
variable sname index ch4
|
||||
log ${sname}.nvt.log
|
||||
|
||||
units electron
|
||||
newton on
|
||||
boundary f f f
|
||||
|
||||
atom_style hybrid charge electron
|
||||
|
||||
read_data data.${sname}
|
||||
|
||||
pair_style eff/cut 10000.0
|
||||
pair_coeff * *
|
||||
|
||||
communicate single vel yes
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step pe temp press
|
||||
|
||||
timestep 0.001
|
||||
fix 1 all nvt/eff 300.0 300.0 0.1 drag 0.5
|
||||
|
||||
# the custom dump includes the radii
|
||||
dump 1 all custom 1000 ${sname}.nvt.lammpstrj id type x y z spin radius
|
||||
dump 2 all xyz 1000 ${sname}.nvt.xyz
|
||||
|
||||
run 100000
|
||||
@ -1,20 +0,0 @@
|
||||
variable sname index ch4
|
||||
log ${sname}.spe.log
|
||||
|
||||
units electron
|
||||
newton on
|
||||
boundary f f f
|
||||
|
||||
atom_style hybrid charge electron
|
||||
|
||||
read_data data.${sname}
|
||||
|
||||
pair_style eff/cut 10000.0
|
||||
pair_coeff * *
|
||||
|
||||
communicate single vel yes
|
||||
|
||||
thermo 1
|
||||
thermo_style multi
|
||||
|
||||
run 0
|
||||
@ -1,26 +0,0 @@
|
||||
variable sname index ch4_ionized
|
||||
log ${sname}.min.log
|
||||
|
||||
units electron
|
||||
newton on
|
||||
boundary f f f
|
||||
|
||||
atom_style hybrid charge electron
|
||||
|
||||
read_data data.${sname}
|
||||
|
||||
pair_style eff/cut 100.0
|
||||
pair_coeff * *
|
||||
|
||||
communicate single vel yes
|
||||
|
||||
thermo 1
|
||||
thermo_style multi
|
||||
|
||||
dump 1 all custom 1 ${sname}.min.lammpstrj id type x y z spin radius
|
||||
dump 2 all xyz 1 ${sname}.min.xyz
|
||||
|
||||
min_style cg
|
||||
min_modify line quadratic
|
||||
minimize 0 1.0e-6 10000 100000
|
||||
|
||||
@ -1,30 +0,0 @@
|
||||
variable sname index ch4_ionized
|
||||
log ${sname}.nve.log
|
||||
|
||||
units electron
|
||||
newton on
|
||||
boundary f f f
|
||||
|
||||
atom_style hybrid charge electron
|
||||
|
||||
read_data data.${sname}
|
||||
|
||||
pair_style eff/cut 1000.0
|
||||
pair_coeff * *
|
||||
|
||||
communicate single vel yes
|
||||
|
||||
thermo 200
|
||||
thermo_style custom step pe temp press
|
||||
|
||||
# NVE
|
||||
timestep 0.005
|
||||
fix 1 all nve/eff
|
||||
dump 1 all custom 200 ${sname}.nve.lammpstrj id type x y z spin radius
|
||||
dump 2 all xyz 200 ${sname}.nve.xyz
|
||||
|
||||
run 100000
|
||||
|
||||
unfix 1
|
||||
undump 1
|
||||
undump 2
|
||||
@ -1,32 +0,0 @@
|
||||
variable sname index ch4_ionized
|
||||
log ${sname}.nvt.log
|
||||
|
||||
units electron
|
||||
newton on
|
||||
boundary f f f
|
||||
|
||||
atom_style hybrid charge electron
|
||||
|
||||
read_data data.${sname}
|
||||
|
||||
pair_style eff/cut 10000.0
|
||||
pair_coeff * *
|
||||
|
||||
communicate single vel yes
|
||||
|
||||
thermo 100
|
||||
thermo_style multi
|
||||
|
||||
thermo_style custom step etotal pe ke temp press
|
||||
compute t all temp/eff
|
||||
compute ke all ke/eff/atom
|
||||
thermo_style custom etotal pe ke c_ke temp c_t
|
||||
|
||||
timestep 0.005
|
||||
fix 1 all nvt/eff 300.0 300.0 10.0
|
||||
|
||||
# the custom dump includes the radii
|
||||
dump 1 all custom 100 ${sname}.nvt.lammpstrj id type x y z radius
|
||||
dump 2 all xyz 100 ${sname}.nvt.xyz
|
||||
|
||||
run 1000000
|
||||
@ -1,211 +0,0 @@
|
||||
# radii.vmd --
|
||||
# Script to read and change electron radii in vmd dynamics traj
|
||||
#
|
||||
|
||||
# openFile --
|
||||
# Open the file and start looking for data
|
||||
#
|
||||
# Arguments:
|
||||
# filename Name of the file to read
|
||||
#
|
||||
# Result:
|
||||
# infile Handle to the opened file
|
||||
#
|
||||
# Side effects:
|
||||
# A file in question is opened. Lines containing a * or# as
|
||||
# the first non-blank character are considered comments. The
|
||||
# first line without this is considered to be a line with the
|
||||
# names of the columns.
|
||||
#
|
||||
proc openFile {filename} {
|
||||
set infile [open $filename "r"]
|
||||
return $infile
|
||||
}
|
||||
|
||||
# readNames --
|
||||
# Read the names of the columns
|
||||
#
|
||||
# Arguments:
|
||||
# infile Handle to the file
|
||||
#
|
||||
# Result:
|
||||
# names List of names, the number indicates the number of
|
||||
# the snapshot frame
|
||||
#
|
||||
proc readNames {infile} {
|
||||
#
|
||||
# Skip the header - if any
|
||||
#
|
||||
set pos 0
|
||||
while { [gets $infile line] >= 0 } {
|
||||
if { [regexp {[ \t]*[*#]} $line] } {
|
||||
incr pos
|
||||
} else {
|
||||
break
|
||||
}
|
||||
}
|
||||
seek $infile 0 start
|
||||
while { $pos > 0 } {
|
||||
gets $infile line
|
||||
incr pos -1
|
||||
}
|
||||
|
||||
#
|
||||
# Read the line with the column names
|
||||
#
|
||||
gets $infile line
|
||||
|
||||
# Force the line to be interpreted as a list
|
||||
set nocols [llength $line]
|
||||
|
||||
return $line
|
||||
}
|
||||
|
||||
# readData --
|
||||
# Read the data per line
|
||||
#
|
||||
# Arguments:
|
||||
# infile Handle to the file
|
||||
#
|
||||
# Result:
|
||||
# values List of values, representing each column.
|
||||
# A list of length zero indicates the end of file
|
||||
#
|
||||
proc readData {infile} {
|
||||
while { [gets $infile values] == 0 } { ;# Just go on - skip empty lines }
|
||||
|
||||
set nocols [llength $values]
|
||||
|
||||
return $values
|
||||
}
|
||||
|
||||
# readFile --
|
||||
# Read the file and store the data in a (global) array
|
||||
#
|
||||
# Arguments:
|
||||
# filename Name of the file
|
||||
#
|
||||
# Result:
|
||||
# None
|
||||
#
|
||||
# Side effects:
|
||||
# Filled array, ready for display
|
||||
#
|
||||
proc readFile {filename} {
|
||||
global data_array
|
||||
|
||||
set infile [openFile $filename]
|
||||
|
||||
set data_array(names) [readNames $infile]
|
||||
set i 0
|
||||
foreach name $data_array(names) {
|
||||
set data_array($i) {}
|
||||
incr i
|
||||
}
|
||||
|
||||
while 1 {
|
||||
set values [readData $infile]
|
||||
if { [llength $values] > 0 } {
|
||||
set i 0
|
||||
foreach value $values {
|
||||
lappend data_array($i) $value
|
||||
incr i
|
||||
}
|
||||
} else {
|
||||
break
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
# makeXYData --
|
||||
# Make a list useable by frame-electron
|
||||
#
|
||||
# Arguments:
|
||||
# xindex Index of frame data
|
||||
# yindex Index of electron data
|
||||
#
|
||||
# Result:
|
||||
# None
|
||||
#
|
||||
# Side effects:
|
||||
# A dataset for changing the electron radii, per trajectory frame
|
||||
#
|
||||
proc makeXYData {xindex yindex} {
|
||||
global data_array
|
||||
|
||||
set xydata {}
|
||||
foreach x $data_array($xindex) y $data_array($yindex) {
|
||||
lappend xydata $x $y
|
||||
}
|
||||
return $xydata
|
||||
}
|
||||
|
||||
proc returnXYPair {x y} {
|
||||
global data_array
|
||||
|
||||
return [list $data_array($x) $data_array($y)]
|
||||
}
|
||||
|
||||
# do_radii --
|
||||
# Changes the radii of electrons per trajectory frame
|
||||
#
|
||||
# Arguments:
|
||||
# xindex Index of frame data
|
||||
# yindex Index of electron data
|
||||
#
|
||||
# Result:
|
||||
# prints the frame:atomID:radius
|
||||
#
|
||||
proc do_radii {args} {
|
||||
global molid data_array
|
||||
|
||||
#set n [molinfo $molid get numatoms]
|
||||
set f [molinfo $molid get frame]
|
||||
|
||||
set fr [expr {$f+1}]
|
||||
|
||||
foreach elec $data_array(0) r $data_array($fr) {
|
||||
set s [atomselect $molid "index [expr {$elec -1}]"]
|
||||
#set nr [expr {exp($r)}]
|
||||
set nr $r
|
||||
$s set radius $nr
|
||||
$s delete
|
||||
#puts stderr "$fr $elec $nr"
|
||||
}
|
||||
}
|
||||
|
||||
# main --
|
||||
# Main control flow
|
||||
#
|
||||
|
||||
# Check input arguments
|
||||
#for {set i 0} {$i<[llength $argv]} {incr i}
|
||||
# puts " - $i: [lindex $argv $i]"
|
||||
|
||||
global data_array molid
|
||||
|
||||
# Set input files manually
|
||||
set xyz ch4.nvt.sorted.xyz
|
||||
set data ch4.nvt.sorted.lammpstrj.out
|
||||
|
||||
# switch default rep to VDW.
|
||||
mol default style VDW
|
||||
|
||||
# load nuclear and electron xyz trajectory
|
||||
#set xyz [lindex $::argv 0]
|
||||
|
||||
# load electron radii information for trajectory
|
||||
#set datafile [lindex $::argv 1]
|
||||
|
||||
set molid [mol new $xyz waitfor all]
|
||||
mol modstyle 0 [molinfo top] VDW 1.0 32.0
|
||||
|
||||
puts "Starting ..."
|
||||
readFile $data
|
||||
puts "Read datafile and created array of radii ..."
|
||||
|
||||
puts "Visualize trajectory"
|
||||
trace variable vmd_frame($molid) w do_radii
|
||||
animate goto start
|
||||
do_radii
|
||||
|
||||
@ -1 +0,0 @@
|
||||
Simple Hydrogen atom example (finite)
|
||||
@ -1,19 +0,0 @@
|
||||
Created by AJB
|
||||
|
||||
2 atoms
|
||||
2 atom types
|
||||
|
||||
-10.0 10.0 xlo xhi
|
||||
-10.0 10.0 ylo yhi
|
||||
-10.0 10.0 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 1.000794 # H nuclei mass
|
||||
2 1.000000 # electron mass
|
||||
|
||||
Atoms
|
||||
#id|type|x|y|z|q|spin|r
|
||||
1 1 0.0 0.0 0.0 1.0 0 0.0
|
||||
2 2 0.0 0.0 0.0 0.0 1 1.0
|
||||
|
||||
@ -1,27 +0,0 @@
|
||||
variable sname index h_atom
|
||||
log ${sname}.min.log
|
||||
|
||||
units electron
|
||||
newton on
|
||||
boundary f f f
|
||||
|
||||
atom_style hybrid charge electron
|
||||
|
||||
read_data data.${sname}
|
||||
|
||||
pair_style eff/cut 10.0
|
||||
pair_coeff * *
|
||||
|
||||
communicate single vel yes
|
||||
|
||||
thermo 1
|
||||
thermo_style multi
|
||||
|
||||
dump 1 all xyz 1 ${sname}.min.xyz
|
||||
dump 2 all custom 1 ${sname}.min.lammpstrj id type x y z radius
|
||||
dump 3 all custom 1 ${sname}.min.forces id type fx fy fz rf
|
||||
|
||||
min_style cg
|
||||
min_modify line quadratic dmax 2.0
|
||||
minimize 1.0e-4 1.0e-4 1000 100000
|
||||
|
||||
@ -1,21 +0,0 @@
|
||||
variable sname index h_atom
|
||||
log ${sname}.spe.log
|
||||
|
||||
units electron
|
||||
newton on
|
||||
#boundary p p p
|
||||
boundary f f f
|
||||
|
||||
atom_style hybrid charge electron
|
||||
|
||||
read_data data.${sname}
|
||||
|
||||
pair_style eff/cut 500.0
|
||||
pair_coeff * *
|
||||
|
||||
communicate single vel yes
|
||||
|
||||
thermo 1
|
||||
thermo_style multi
|
||||
|
||||
run 0
|
||||
@ -1,2 +0,0 @@
|
||||
Example of a hydrogen plasma, using pre-set velocities for a temperature of 20000K (nve), setting the velocities to 50000K (nvt), and an isobaric-isothermic case (npt) to show volume and density convergence at specified temperature (20000K) and pressure (1GPa).
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
@ -1,31 +0,0 @@
|
||||
variable sname index h2bulk
|
||||
log ${sname}.min.log
|
||||
|
||||
units electron
|
||||
newton on
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid charge electron
|
||||
|
||||
read_data data.${sname}
|
||||
|
||||
pair_style eff/cut 30.627847 limit yes
|
||||
pair_coeff * *
|
||||
|
||||
neigh_modify one 8000 page 80000
|
||||
|
||||
communicate single vel yes
|
||||
|
||||
thermo 1
|
||||
thermo_style multi
|
||||
|
||||
# structure minimization
|
||||
dump 1 all custom 1 ${sname}.min.lammpstrj id type x y z spin radius
|
||||
#dump 2 all custom 1 ${sname}.min.forces id type fx fy fz rf
|
||||
|
||||
min_style cg
|
||||
min_modify line quadratic dmax 0.1
|
||||
minimize 0 1.0e-6 1000 10000
|
||||
|
||||
undump 1
|
||||
#undump 2
|
||||
@ -1,39 +0,0 @@
|
||||
variable sname index large_plasma
|
||||
log ${sname}.npt.log
|
||||
|
||||
units electron
|
||||
newton on
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid charge electron
|
||||
|
||||
read_data data.${sname}
|
||||
|
||||
pair_style eff/cut 30.627847 limit yes
|
||||
pair_coeff * *
|
||||
|
||||
neigh_modify one 20000 page 200000
|
||||
#communicate single vel yes
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step pe temp press vol
|
||||
|
||||
# structure minimization
|
||||
dump 1 all xyz 1 ${sname}.min.xyz
|
||||
min_style cg
|
||||
minimize 0 1.0e-4 1000 10000
|
||||
undump 1
|
||||
|
||||
# npt
|
||||
fix 1 all npt/eff 20000.0 20000.0 1.0 xyz 1e9 1e9 1.0
|
||||
variable density equal 11.2058851*mass(all)
|
||||
thermo_style custom step pe temp press vol v_density
|
||||
|
||||
dump 2 all xyz 10000 ${sname}.npt.xyz
|
||||
dump 3 all custom 10000 ${sname}.npt.lammpstrj id type x y z spin radius
|
||||
|
||||
run 10000000
|
||||
|
||||
unfix 1
|
||||
undump 2
|
||||
undump 3
|
||||
@ -1,45 +0,0 @@
|
||||
variable sname index h2bulk
|
||||
log ${sname}.nve.log
|
||||
|
||||
units electron
|
||||
newton on
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid charge electron
|
||||
|
||||
read_data data.${sname}
|
||||
|
||||
pair_style eff/cut 30.627847 limit yes
|
||||
pair_coeff * *
|
||||
|
||||
neigh_modify one 10000 page 100000
|
||||
|
||||
communicate single vel yes
|
||||
|
||||
thermo 1000
|
||||
thermo_style custom step pe temp press
|
||||
|
||||
# structure minimization
|
||||
min_style cg
|
||||
minimize 0 1.0e-4 1000 10000
|
||||
|
||||
timestep 0.001
|
||||
|
||||
velocity all create 20000.0 4928459 rot yes mom yes dist gaussian
|
||||
|
||||
# nve
|
||||
fix 1 all nve/eff
|
||||
#fix 2 all imd 8888 trate 1 unwrap on nowait on
|
||||
|
||||
compute peatom all pe/atom
|
||||
compute keatom all ke/atom/eff
|
||||
|
||||
dump 2 all xyz 1000 ${sname}.nve.xyz
|
||||
dump 3 all custom 1000 ${sname}.nve.lammpstrj id type x y z spin radius c_peatom c_keatom
|
||||
|
||||
run 100000
|
||||
|
||||
unfix 1
|
||||
#unfix 2
|
||||
undump 2
|
||||
undump 3
|
||||
@ -1,38 +0,0 @@
|
||||
variable sname index h2bulk
|
||||
log ${sname}.nvt.log
|
||||
|
||||
units electron
|
||||
newton on
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid charge electron
|
||||
|
||||
read_data data.${sname}
|
||||
|
||||
pair_style eff/cut 30.627847 limit yes
|
||||
pair_coeff * *
|
||||
|
||||
communicate single vel yes
|
||||
|
||||
thermo 10000
|
||||
thermo_style custom step pe temp press
|
||||
|
||||
# structure minimization
|
||||
dump 1 all xyz 1000 ${sname}.min.xyz
|
||||
min_style cg
|
||||
minimize 0 1.0e-4 1000 10000
|
||||
undump 1
|
||||
|
||||
timestep 0.005
|
||||
|
||||
# nvt
|
||||
fix 1 all nvt/eff 50000.0 50000.0 0.1
|
||||
|
||||
dump 2 all xyz 1000 ${sname}.nvt.xyz
|
||||
dump 3 all custom 1000 ${sname}.nvt.lammpstrj id type x y z spin radius
|
||||
|
||||
run 5000000
|
||||
|
||||
unfix 1
|
||||
undump 2
|
||||
undump 3
|
||||
@ -1,2 +0,0 @@
|
||||
Shows the formation of lithium dendrites during the minimization of a volume expanded lithium cell with particle positions remaped to fit the cell.
|
||||
This depicts the process of electrode replating in lithium batteries, which leads to failure (short-circuit).
|
||||
File diff suppressed because it is too large
Load Diff
@ -1,26 +0,0 @@
|
||||
variable sname index Li-dendritic
|
||||
log ${sname}.min.log
|
||||
|
||||
units electron
|
||||
newton on
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid charge electron
|
||||
|
||||
read_data data.${sname}
|
||||
|
||||
pair_style eff/cut 50.112
|
||||
pair_coeff * *
|
||||
|
||||
communicate single vel yes
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step etotal press
|
||||
|
||||
dump 1 all custom 10 ${sname}.min.lammpstrj id type x y z q spin radius
|
||||
dump 2 all xyz 10 ${sname}.min.xyz
|
||||
|
||||
min_style cg
|
||||
min_modify line quadratic dmax 2.0
|
||||
minimize 0.0 1.0e-5 10000 100000
|
||||
|
||||
@ -1,52 +0,0 @@
|
||||
variable sname index Li-dendritic
|
||||
log ${sname}.min.log
|
||||
|
||||
units electron
|
||||
newton on
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid charge electron
|
||||
|
||||
#read_data data.${sname}
|
||||
read_restart ${sname}.min.restart
|
||||
|
||||
pair_style eff/cut 50.112
|
||||
pair_coeff * *
|
||||
|
||||
communicate single vel yes
|
||||
|
||||
|
||||
communicate single vel yes
|
||||
|
||||
thermo 100
|
||||
communicate single vel yes
|
||||
|
||||
thermo_style custom step pe temp press
|
||||
|
||||
print "Starting minimizer"
|
||||
min_style cg
|
||||
#dump 1 all custom 100 ${sname}.min.lammpstrj id type x y z q spin radius
|
||||
#dump 2 all xyz 100 ${sname}.min.xyz
|
||||
min_modify line quadratic
|
||||
minimize 1.0e-10 1.0e-10 1 2
|
||||
|
||||
#write_restart ${sname}.min.restart
|
||||
|
||||
#undump 1
|
||||
#undump 2
|
||||
|
||||
# NVT
|
||||
reset_timestep 0
|
||||
timestep 0.005
|
||||
print "Starting nvt"
|
||||
#fix 1 all nve/eff
|
||||
fix 1 all nvt/eff 300.0 300.0 0.1
|
||||
dump 1 all custom 100 ${sname}.nvt.lammpstrj id type x y z spin radius
|
||||
dump 2 all xyz 100 ${sname}.nvt.xyz
|
||||
restart 100 ${sname}.nvt.restart1 ${sname}.nvt.restart2
|
||||
|
||||
run 10000
|
||||
|
||||
undump 1
|
||||
undump 2
|
||||
|
||||
@ -1,2 +0,0 @@
|
||||
This example is just for illustration purposes, and should not be used to determine the proper dynamics of this system because the cell size is too small (you will not get the correct energies). Note, the impact velocities are introduced in the data file, but the user may choose to override these with the velocity command in LAMMPS.
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
@ -1,32 +0,0 @@
|
||||
variable sname index lishock
|
||||
|
||||
units electron
|
||||
newton on
|
||||
boundary s p p
|
||||
|
||||
atom_style hybrid charge electron
|
||||
|
||||
read_data data.${sname}
|
||||
#read_restart ${sname}.nve.restart1
|
||||
|
||||
pair_style eff/cut 12.528
|
||||
pair_coeff * *
|
||||
|
||||
communicate single vel yes
|
||||
|
||||
timestep 0.005
|
||||
|
||||
fix 1 all nve/eff
|
||||
|
||||
thermo 1000
|
||||
thermo_style custom step etotal temp press
|
||||
|
||||
restart 1000 ${sname}.nve.restart1 ${sname}.nve.restart2
|
||||
compute peatom all pe/atom
|
||||
compute keatom all ke/atom/eff
|
||||
dump 1 all custom 1000 ${sname}.nve.lammpstrj id type x y z spin radius vx vy vz vr c_keatom c_peatom
|
||||
|
||||
run 1500000
|
||||
|
||||
unfix 1
|
||||
undump 1
|
||||
@ -1,7 +0,0 @@
|
||||
NOTE: most of these examples are provided to demonstrate the
|
||||
functionality of pEFF, i.e. as illustrative examples, and should not
|
||||
be used w/out including the proper equilibration procedures, or data
|
||||
files with unit cell sizes appropriate for minimum image calculations.
|
||||
For more details, please contact the author at
|
||||
ajaramil@wag.caltech.edu.
|
||||
|
||||
Reference in New Issue
Block a user