Commit b9770766 authored by Axel Kohlmeyer's avatar Axel Kohlmeyer
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add adatom and vacancy examples for AGNI pair style

parent 9cc0c8ba
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+1019 −0

File added.

Preview size limit exceeded, changes collapsed.

+197 −0
Original line number Diff line number Diff line
Data File created from VASP POSCAR

181 atoms
1 atom types

0 17.121440767 xlo xhi
0 14.8276026536 ylo yhi
0 39.3197318979 zlo zhi

Masses

1 26.982

Atoms

1 1 0.0 1.64751140595 15.0
2 1 2.85357346116 1.64751140595 15.0
3 1 5.70714692232 1.64751140595 15.0
4 1 8.56072038348 1.64751140595 15.0
5 1 11.4142938446 1.64751140595 15.0
6 1 14.2678673058 1.64751140595 15.0
7 1 1.42678673058 4.11877851488 15.0
8 1 4.28036019174 4.11877851488 15.0
9 1 7.1339336529 4.11877851488 15.0
10 1 9.98750711406 4.11877851488 15.0
11 1 12.8410805752 4.11877851488 15.0
12 1 15.6946540364 4.11877851488 15.0
13 1 0.0 6.59004562381 15.0
14 1 2.85357346116 6.59004562381 15.0
15 1 5.70714692232 6.59004562381 15.0
16 1 8.56072038348 6.59004562381 15.0
17 1 11.4142938446 6.59004562381 15.0
18 1 14.2678673058 6.59004562381 15.0
19 1 1.42678673058 9.06131273274 15.0
20 1 4.28036019174 9.06131273274 15.0
21 1 7.1339336529 9.06131273274 15.0
22 1 9.98750711406 9.06131273274 15.0
23 1 12.8410805752 9.06131273274 15.0
24 1 15.6946540364 9.06131273274 15.0
25 1 0.0 11.5325798417 15.0
26 1 2.85357346116 11.5325798417 15.0
27 1 5.70714692232 11.5325798417 15.0
28 1 8.56072038348 11.5325798417 15.0
29 1 11.4142938446 11.5325798417 15.0
30 1 14.2678673058 11.5325798417 15.0
31 1 1.42678673058 14.0038469506 15.0
32 1 4.28036019174 14.0038469506 15.0
33 1 7.1339336529 14.0038469506 15.0
34 1 9.98750711406 14.0038469506 15.0
35 1 12.8410805752 14.0038469506 15.0
36 1 15.6946540364 14.0038469506 15.0
37 1 0.0 0.0 17.3299329745
38 1 2.85357346116 0.0 17.3299329745
39 1 5.70714692232 0.0 17.3299329745
40 1 8.56072038348 0.0 17.3299329745
41 1 11.4142938446 0.0 17.3299329745
42 1 14.2678673058 0.0 17.3299329745
43 1 1.42678673058 2.47126710893 17.3299329745
44 1 4.28036019174 2.47126710893 17.3299329745
45 1 7.1339336529 2.47126710893 17.3299329745
46 1 9.98750711406 2.47126710893 17.3299329745
47 1 12.8410805752 2.47126710893 17.3299329745
48 1 15.6946540364 2.47126710893 17.3299329745
49 1 0.0 4.94253421786 17.3299329745
50 1 2.85357346116 4.94253421786 17.3299329745
51 1 5.70714692232 4.94253421786 17.3299329745
52 1 8.56072038348 4.94253421786 17.3299329745
53 1 11.4142938446 4.94253421786 17.3299329745
54 1 14.2678673058 4.94253421786 17.3299329745
55 1 1.42678673058 7.41380132679 17.3299329745
56 1 4.28036019174 7.41380132679 17.3299329745
57 1 7.1339336529 7.41380132679 17.3299329745
58 1 9.98750711406 7.41380132679 17.3299329745
59 1 12.8410805752 7.41380132679 17.3299329745
60 1 15.6946540364 7.41380132679 17.3299329745
61 1 0.0 9.88506843572 17.3299329745
62 1 2.85357346116 9.88506843572 17.3299329745
63 1 5.70714692232 9.88506843572 17.3299329745
64 1 8.56072038348 9.88506843572 17.3299329745
65 1 11.4142938446 9.88506843572 17.3299329745
66 1 14.2678673058 9.88506843572 17.3299329745
67 1 1.42678673058 12.3563355446 17.3299329745
68 1 4.28036019174 12.3563355446 17.3299329745
69 1 7.1339336529 12.3563355446 17.3299329745
70 1 9.98750711406 12.3563355446 17.3299329745
71 1 12.8410805752 12.3563355446 17.3299329745
72 1 15.6946540364 12.3563355446 17.3299329745
73 1 1.42678673058 0.823755702976 19.6598659489
74 1 4.28036019174 0.823755702976 19.6598659489
75 1 7.1339336529 0.823755702976 19.6598659489
76 1 9.98750711406 0.823755702976 19.6598659489
77 1 12.8410805752 0.823755702976 19.6598659489
78 1 15.6946540364 0.823755702976 19.6598659489
79 1 0.0 3.29502281191 19.6598659489
80 1 2.85357346116 3.29502281191 19.6598659489
81 1 5.70714692232 3.29502281191 19.6598659489
82 1 8.56072038348 3.29502281191 19.6598659489
83 1 11.4142938446 3.29502281191 19.6598659489
84 1 14.2678673058 3.29502281191 19.6598659489
85 1 1.42678673058 5.76628992084 19.6598659489
86 1 4.28036019174 5.76628992084 19.6598659489
87 1 7.1339336529 5.76628992084 19.6598659489
88 1 9.98750711406 5.76628992084 19.6598659489
89 1 12.8410805752 5.76628992084 19.6598659489
90 1 15.6946540364 5.76628992084 19.6598659489
91 1 0.0 8.23755702976 19.6598659489
92 1 2.85357346116 8.23755702976 19.6598659489
93 1 5.70714692232 8.23755702976 19.6598659489
94 1 8.56072038348 8.23755702976 19.6598659489
95 1 11.4142938446 8.23755702976 19.6598659489
96 1 14.2678673058 8.23755702976 19.6598659489
97 1 1.42678673058 10.7088241387 19.6598659489
98 1 4.28036019174 10.7088241387 19.6598659489
99 1 7.1339336529 10.7088241387 19.6598659489
100 1 9.98750711406 10.7088241387 19.6598659489
101 1 12.8410805752 10.7088241387 19.6598659489
102 1 15.6946540364 10.7088241387 19.6598659489
103 1 0.0 13.1800912476 19.6598659489
104 1 2.85357346116 13.1800912476 19.6598659489
105 1 5.70714692232 13.1800912476 19.6598659489
106 1 8.56072038348 13.1800912476 19.6598659489
107 1 11.4142938446 13.1800912476 19.6598659489
108 1 14.2678673058 13.1800912476 19.6598659489
109 1 0.0 1.64751140595 21.9897989234
110 1 2.85357346116 1.64751140595 21.9897989234
111 1 5.70714692232 1.64751140595 21.9897989234
112 1 8.56072038348 1.64751140595 21.9897989234
113 1 11.4142938446 1.64751140595 21.9897989234
114 1 14.2678673058 1.64751140595 21.9897989234
115 1 1.42678673058 4.11877851488 21.9897989234
116 1 4.28036019174 4.11877851488 21.9897989234
117 1 7.1339336529 4.11877851488 21.9897989234
118 1 9.98750711406 4.11877851488 21.9897989234
119 1 12.8410805752 4.11877851488 21.9897989234
120 1 15.6946540364 4.11877851488 21.9897989234
121 1 0.0 6.59004562381 21.9897989234
122 1 2.85357346116 6.59004562381 21.9897989234
123 1 5.70714692232 6.59004562381 21.9897989234
124 1 8.56072038348 6.59004562381 21.9897989234
125 1 11.4142938446 6.59004562381 21.9897989234
126 1 14.2678673058 6.59004562381 21.9897989234
127 1 1.42678673058 9.06131273274 21.9897989234
128 1 4.28036019174 9.06131273274 21.9897989234
129 1 7.1339336529 9.06131273274 21.9897989234
130 1 9.98750711406 9.06131273274 21.9897989234
131 1 12.8410805752 9.06131273274 21.9897989234
132 1 15.6946540364 9.06131273274 21.9897989234
133 1 0.0 11.5325798417 21.9897989234
134 1 2.85357346116 11.5325798417 21.9897989234
135 1 5.70714692232 11.5325798417 21.9897989234
136 1 8.56072038348 11.5325798417 21.9897989234
137 1 11.4142938446 11.5325798417 21.9897989234
138 1 14.2678673058 11.5325798417 21.9897989234
139 1 1.42678673058 14.0038469506 21.9897989234
140 1 4.28036019174 14.0038469506 21.9897989234
141 1 7.1339336529 14.0038469506 21.9897989234
142 1 9.98750711406 14.0038469506 21.9897989234
143 1 12.8410805752 14.0038469506 21.9897989234
144 1 15.6946540364 14.0038469506 21.9897989234
145 1 0.0 0.0 24.3197318979
146 1 2.85357346116 0.0 24.3197318979
147 1 5.70714692232 0.0 24.3197318979
148 1 8.56072038348 0.0 24.3197318979
149 1 11.4142938446 0.0 24.3197318979
150 1 14.2678673058 0.0 24.3197318979
151 1 1.42678673058 2.47126710893 24.3197318979
152 1 4.28036019174 2.47126710893 24.3197318979
153 1 7.1339336529 2.47126710893 24.3197318979
154 1 9.98750711406 2.47126710893 24.3197318979
155 1 12.8410805752 2.47126710893 24.3197318979
156 1 15.6946540364 2.47126710893 24.3197318979
157 1 0.0 4.94253421786 24.3197318979
158 1 2.85357346116 4.94253421786 24.3197318979
159 1 5.70714692232 4.94253421786 24.3197318979
160 1 8.56072038348 4.94253421786 24.3197318979
161 1 11.4142938446 4.94253421786 24.3197318979
162 1 14.2678673058 4.94253421786 24.3197318979
163 1 1.42678673058 7.41380132679 24.3197318979
164 1 4.28036019174 7.41380132679 24.3197318979
165 1 7.1339336529 7.41380132679 24.3197318979
166 1 9.98750711406 7.41380132679 24.3197318979
167 1 12.8410805752 7.41380132679 24.3197318979
168 1 15.6946540364 7.41380132679 24.3197318979
169 1 0.0 9.88506843572 24.3197318979
170 1 2.85357346116 9.88506843572 24.3197318979
171 1 5.70714692232 9.88506843572 24.3197318979
172 1 8.56072038348 9.88506843572 24.3197318979
173 1 11.4142938446 9.88506843572 24.3197318979
174 1 14.2678673058 9.88506843572 24.3197318979
175 1 1.42678673058 12.3563355446 24.3197318979
176 1 4.28036019174 12.3563355446 24.3197318979
177 1 7.1339336529 12.3563355446 24.3197318979
178 1 9.98750711406 12.3563355446 24.3197318979
179 1 12.8410805752 12.3563355446 24.3197318979
180 1 15.6946540364 12.3563355446 24.3197318979
181 1 7.1339336529 4.11877851488 26.7197318979
+23 −0
Original line number Diff line number Diff line

processors * * 1
units metal
boundary p p f
read_data adatom.data

pair_style agni
pair_coeff * * Al_prb.agni Al

neighbor 0.3 bin 
neigh_modify delay 2 check yes 

timestep 0.0005
velocity all create 500 12345
fix 1 all nvt temp 250 250 0.2 
fix 5 all momentum 1 linear 1 1 1

thermo 100
thermo_style custom step ke temp

# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz

run 1000
+23 −0
Original line number Diff line number Diff line

units metal
boundary p p p
read_data vacancy.data

pair_style agni
pair_coeff * * Al_prb.agni Al
neighbor 0.3 bin 
neigh_modify delay 2 check yes 


timestep 0.0005
velocity all create 1000 12345
fix 1 all nvt temp 900 900 200
fix 5 all momentum 1 linear 1 1 1


thermo 100
thermo_style custom step ke etotal temp

# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz

run 1000
+82 −0
Original line number Diff line number Diff line
LAMMPS (9 Nov 2016)
  using 1 OpenMP thread(s) per MPI task

processors * * 1
units metal
boundary p p f
read_data adatom.data
  orthogonal box = (0 0 0) to (17.1214 14.8276 39.3197)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  181 atoms

pair_style agni
pair_coeff * * Al_prb.agni Al
Reading potential file Al_prb.agni with DATE: 2016-11-11

neighbor 0.3 bin
neigh_modify delay 2 check yes

timestep 0.0005
velocity all create 500 12345
fix 1 all nvt temp 250 250 0.2
fix 5 all momentum 1 linear 1 1 1

thermo 100
thermo_style custom step ke temp

# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz

run 1000
Neighbor list info ...
  1 neighbor list requests
  update every 1 steps, delay 2 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 8.3
  ghost atom cutoff = 8.3
  binsize = 4.15 -> bins = 5 4 10
Memory usage per processor = 2.37049 Mbytes
Step KinEng Temp 
       0    11.633413          500 
     100     4.049974    174.06646 
     200    5.8983472    253.50889 
     300    5.3667309    230.66021 
     400    4.9343935     212.0785 
     500    5.4054496    232.32432 
     600    6.1779127    265.52452 
     700    6.3749266     273.9921 
     800    6.0701481    260.89283 
     900    6.4582394    277.57286 
    1000    6.4047444    275.27366 
Loop time of 20.8273 on 1 procs for 1000 steps with 181 atoms

Performance: 2.074 ns/day, 11.571 hours/ns, 48.014 timesteps/s
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 20.79      | 20.79      | 20.79      |   0.0 | 99.82
Neigh   | 0.022742   | 0.022742   | 0.022742   |   0.0 |  0.11
Comm    | 0.0040836  | 0.0040836  | 0.0040836  |   0.0 |  0.02
Output  | 0.00011086 | 0.00011086 | 0.00011086 |   0.0 |  0.00
Modify  | 0.0089345  | 0.0089345  | 0.0089345  |   0.0 |  0.04
Other   |            | 0.001819   |            |       |  0.01

Nlocal:    181 ave 181 max 181 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    562 ave 562 max 562 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:  18810 ave 18810 max 18810 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 18810
Ave neighs/atom = 103.923
Neighbor list builds = 33
Dangerous builds = 0

Please see the log.cite file for references relevant to this simulation

Total wall time: 0:00:20
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