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rename some examples folders

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This commit is contained in:
Axel Kohlmeyer
2021-06-29 20:21:53 -04:00
parent 878795e64a
commit 9d208c9ebd
396 changed files with 32 additions and 20 deletions
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3020
examples/USER-MISC/agni/Al_jpc.agni Normal file
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examples/USER-MISC/agni/adatom.data Normal file
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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

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examples/USER-MISC/agni/in.adatom Normal file
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processors * * 1
units metal
boundary p p f
read_data adatom.data
pair_style agni
pair_coeff * * Al_jpc.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

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examples/USER-MISC/agni/in.vacancy Normal file
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units metal
boundary p p p
read_data vacancy.data
pair_style agni
pair_coeff * * Al_jpc.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

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examples/USER-MISC/agni/log.20Jan21.adatom.g++.1 Normal file
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LAMMPS (24 Dec 2020)
using 1 OpenMP thread(s) per MPI task
processors * * 1
units metal
boundary p p f
read_data adatom.data
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (17.121441 14.827603 39.319732)
1 by 1 by 1 MPI processor grid
reading atoms ...
181 atoms
read_data CPU = 0.002 seconds
pair_style agni
pair_coeff * * Al_jpc.agni Al
Reading agni potential file Al_jpc.agni with DATE: 2017-02-24
WARNING: Ignoring unknown tag 'Rs' in AGNI potential file. (src/USER-MISC/pair_agni.cpp:440)
WARNING: Ignoring unknown tag 'neighbors' in AGNI potential file. (src/USER-MISC/pair_agni.cpp:440)
WARNING: Ignoring unknown tag 'lambda' in AGNI potential file. (src/USER-MISC/pair_agni.cpp:440)
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 ...
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
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair agni, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.072 | 3.072 | 3.072 Mbytes
Step KinEng Temp
0 11.633413 500
100 4.6059941 197.96401
200 7.3700156 316.76068
300 6.0443915 259.78582
400 6.163119 264.88869
500 6.2647284 269.25582
600 5.2732533 226.64257
700 5.651448 242.89725
800 6.5572404 281.82788
900 6.0576743 260.35671
1000 6.5622234 282.04205
Loop time of 16.4158 on 1 procs for 1000 steps with 181 atoms
Performance: 2.632 ns/day, 9.120 hours/ns, 60.917 timesteps/s
97.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 16.395 | 16.395 | 16.395 | 0.0 | 99.88
Neigh | 0.013275 | 0.013275 | 0.013275 | 0.0 | 0.08
Comm | 0.0023484 | 0.0023484 | 0.0023484 | 0.0 | 0.01
Output | 0.00014842 | 0.00014842 | 0.00014842 | 0.0 | 0.00
Modify | 0.0035522 | 0.0035522 | 0.0035522 | 0.0 | 0.02
Other | | 0.001173 | | | 0.01
Nlocal: 181.000 ave 181 max 181 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 563.000 ave 563 max 563 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 19484.0 ave 19484 max 19484 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 19484
Ave neighs/atom = 107.64641
Neighbor list builds = 33
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:16

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examples/USER-MISC/agni/log.20Jan21.adatom.g++.4 Normal file
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LAMMPS (24 Dec 2020)
using 1 OpenMP thread(s) per MPI task
processors * * 1
units metal
boundary p p f
read_data adatom.data
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (17.121441 14.827603 39.319732)
2 by 2 by 1 MPI processor grid
reading atoms ...
181 atoms
read_data CPU = 0.001 seconds
pair_style agni
pair_coeff * * Al_jpc.agni Al
Reading agni potential file Al_jpc.agni with DATE: 2017-02-24
WARNING: Ignoring unknown tag 'Rs' in AGNI potential file. (src/USER-MISC/pair_agni.cpp:440)
WARNING: Ignoring unknown tag 'neighbors' in AGNI potential file. (src/USER-MISC/pair_agni.cpp:440)
WARNING: Ignoring unknown tag 'lambda' in AGNI potential file. (src/USER-MISC/pair_agni.cpp:440)
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 ...
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
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair agni, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.063 | 3.063 | 3.063 Mbytes
Step KinEng Temp
0 11.633413 500
100 4.6059939 197.964
200 7.3700154 316.76067
300 6.0443914 259.78582
400 6.1631193 264.8887
500 6.2647281 269.25581
600 5.273254 226.6426
700 5.6514484 242.89726
800 6.5572409 281.82791
900 6.0576737 260.35668
1000 6.5622233 282.04205
Loop time of 4.67437 on 4 procs for 1000 steps with 181 atoms
Performance: 9.242 ns/day, 2.597 hours/ns, 213.933 timesteps/s
98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.0668 | 4.2058 | 4.4078 | 7.1 | 89.98
Neigh | 0.0033048 | 0.0033794 | 0.0034381 | 0.1 | 0.07
Comm | 0.2547 | 0.45656 | 0.59576 | 21.5 | 9.77
Output | 9.8817e-05 | 0.00035464 | 0.001121 | 0.0 | 0.01
Modify | 0.0059429 | 0.0060754 | 0.0061966 | 0.2 | 0.13
Other | | 0.002172 | | | 0.05
Nlocal: 45.2500 ave 52 max 40 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Nghost: 376.500 ave 382 max 366 min
Histogram: 1 0 0 0 0 0 0 0 2 1
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 4871.00 ave 5578 max 4374 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Total # of neighbors = 19484
Ave neighs/atom = 107.64641
Neighbor list builds = 33
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:04

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examples/USER-MISC/agni/log.20Jan21.vacancy.g++.1 Normal file
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LAMMPS (24 Dec 2020)
using 1 OpenMP thread(s) per MPI task
units metal
boundary p p p
read_data vacancy.data
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (8.0711250 8.0711250 8.0711250)
1 by 1 by 1 MPI processor grid
reading atoms ...
31 atoms
read_data CPU = 0.002 seconds
pair_style agni
pair_coeff * * Al_jpc.agni Al
Reading agni potential file Al_jpc.agni with DATE: 2017-02-24
WARNING: Ignoring unknown tag 'Rs' in AGNI potential file. (src/USER-MISC/pair_agni.cpp:440)
WARNING: Ignoring unknown tag 'neighbors' in AGNI potential file. (src/USER-MISC/pair_agni.cpp:440)
WARNING: Ignoring unknown tag 'lambda' in AGNI potential file. (src/USER-MISC/pair_agni.cpp:440)
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
Neighbor list info ...
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 = 2 2 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair agni, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.241 | 4.241 | 4.241 Mbytes
Step KinEng TotEng Temp
0 3.8778043 3.8778043 1000
100 2.9986261 2.9986261 773.27936
200 3.6860313 3.6860313 950.54598
300 3.8133153 3.8133153 983.3697
400 3.7330285 3.7330285 962.6655
500 3.5875467 3.5875467 925.14897
600 3.533152 3.533152 911.12178
700 2.6509457 2.6509457 683.62028
800 3.376349 3.376349 870.68576
900 3.9036736 3.9036736 1006.6711
1000 3.0884833 3.0884833 796.45156
Loop time of 2.92678 on 1 procs for 1000 steps with 31 atoms
Performance: 14.760 ns/day, 1.626 hours/ns, 341.673 timesteps/s
97.5% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.9144 | 2.9144 | 2.9144 | 0.0 | 99.58
Neigh | 0.0068263 | 0.0068263 | 0.0068263 | 0.0 | 0.23
Comm | 0.0029868 | 0.0029868 | 0.0029868 | 0.0 | 0.10
Output | 0.00050202 | 0.00050202 | 0.00050202 | 0.0 | 0.02
Modify | 0.0013382 | 0.0013382 | 0.0013382 | 0.0 | 0.05
Other | | 0.0007672 | | | 0.03
Nlocal: 31.0000 ave 31 max 31 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 869.000 ave 869 max 869 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 4360.00 ave 4360 max 4360 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 4360
Ave neighs/atom = 140.64516
Neighbor list builds = 53
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:02

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examples/USER-MISC/agni/log.20Jan21.vacancy.g++.4 Normal file
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LAMMPS (24 Dec 2020)
using 1 OpenMP thread(s) per MPI task
units metal
boundary p p p
read_data vacancy.data
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (8.0711250 8.0711250 8.0711250)
1 by 2 by 2 MPI processor grid
reading atoms ...
31 atoms
read_data CPU = 0.001 seconds
pair_style agni
pair_coeff * * Al_jpc.agni Al
Reading agni potential file Al_jpc.agni with DATE: 2017-02-24
WARNING: Ignoring unknown tag 'Rs' in AGNI potential file. (src/USER-MISC/pair_agni.cpp:440)
WARNING: Ignoring unknown tag 'neighbors' in AGNI potential file. (src/USER-MISC/pair_agni.cpp:440)
WARNING: Ignoring unknown tag 'lambda' in AGNI potential file. (src/USER-MISC/pair_agni.cpp:440)
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
Neighbor list info ...
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 = 2 2 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair agni, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.227 | 4.227 | 4.227 Mbytes
Step KinEng TotEng Temp
0 3.8778043 3.8778043 1000
100 2.9986264 2.9986264 773.27944
200 3.6860316 3.6860316 950.54606
300 3.8133152 3.8133152 983.36966
400 3.7330288 3.7330288 962.66559
500 3.5875468 3.5875468 925.149
600 3.5331519 3.5331519 911.12176
700 2.6509452 2.6509452 683.62015
800 3.3763492 3.3763492 870.68579
900 3.9036736 3.9036736 1006.6711
1000 3.0884821 3.0884821 796.45125
Loop time of 0.91769 on 4 procs for 1000 steps with 31 atoms
Performance: 47.075 ns/day, 0.510 hours/ns, 1089.693 timesteps/s
95.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.67405 | 0.76047 | 0.81748 | 6.1 | 82.87
Neigh | 0.0015411 | 0.001691 | 0.001774 | 0.2 | 0.18
Comm | 0.091364 | 0.14959 | 0.23513 | 13.8 | 16.30
Output | 0.00027996 | 0.00040391 | 0.00075917 | 0.0 | 0.04
Modify | 0.0028397 | 0.0039247 | 0.0050072 | 1.7 | 0.43
Other | | 0.001611 | | | 0.18
Nlocal: 7.75000 ave 8 max 7 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Nghost: 617.250 ave 621 max 612 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 1090.00 ave 1131 max 993 min
Histogram: 1 0 0 0 0 0 0 0 1 2
Total # of neighbors = 4360
Ave neighs/atom = 140.64516
Neighbor list builds = 53
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00

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Data File created from VASP POSCAR
31 atoms
1 atom types
0 8.071125 xlo xhi
0 8.071125 ylo yhi
0 8.071125 zlo zhi
Masses
1 26.9815
Atoms
1 1 8.05711986217 3.20498589607 7.09652861184
2 1 8.05262255028 3.62006786258 3.16719841667
3 1 2.08891866821 1.38430927213 3.14852514324
4 1 4.25446836692 3.27689661974 3.35678388118
5 1 7.92524269451 7.20500664579 3.03232792051
6 1 6.04056771113 7.24499020906 1.11223380379
7 1 2.32585852889 5.29910389395 7.31500292009
8 1 2.09613190567 1.27658214906 7.44277603054
9 1 3.96852985867 7.2805082905 3.37568009522
10 1 0.0773420461671 1.29964047903 5.27451616984
11 1 7.96501442334 1.24471347504 1.17853896176
12 1 2.13035246804 5.36148411996 3.3817805118
13 1 2.06211525033 7.25482811482 1.52039033766
14 1 3.99735704234 7.4099829467 7.05753768668
15 1 3.84113228596 5.1855444403 1.41642147402
16 1 0.231862769544 5.38528175164 5.51171817022
17 1 0.12718452785 5.35814065671 1.11669573581
18 1 8.05303937039 7.38861123542 7.41398359808
19 1 1.88506066609 3.17578974033 1.20929473631
20 1 4.33739926831 1.37976783613 5.28141762358
21 1 2.23200994743 3.12419127088 5.36881641316
22 1 6.22871004896 1.34968648416 7.24032447626
23 1 6.08380394159 1.16222146146 3.30535465675
24 1 6.16629028099 5.22806528503 3.7675179617
25 1 4.30194966153 1.14526017671 1.45054175732
26 1 6.24221620153 5.05377575942 7.17573714759
27 1 3.92820642281 2.9627641757 7.71515743722
28 1 4.33686872315 4.73096617728 5.57649231331
29 1 6.05033104136 3.51389714904 1.34127903322
30 1 6.27311587476 7.19257797516 5.46814369382
31 1 1.81274009101 7.47392095028 5.35484578074