add adatom and vacancy examples for AGNI pair style
This commit is contained in:
Axel Kohlmeyer
1019
examples/USER/misc/agni/Al_prb.agni
Normal file
1019
examples/USER/misc/agni/Al_prb.agni
Normal file
File diff suppressed because it is too large
Load Diff
197
examples/USER/misc/agni/adatom.data
Normal file
197
examples/USER/misc/agni/adatom.data
Normal file
@ -0,0 +1,197 @@
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Data File created from VASP POSCAR
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181 atoms
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1 atom types
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0 17.121440767 xlo xhi
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0 14.8276026536 ylo yhi
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0 39.3197318979 zlo zhi
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Masses
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1 26.982
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Atoms
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1 1 0.0 1.64751140595 15.0
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2 1 2.85357346116 1.64751140595 15.0
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3 1 5.70714692232 1.64751140595 15.0
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4 1 8.56072038348 1.64751140595 15.0
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5 1 11.4142938446 1.64751140595 15.0
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6 1 14.2678673058 1.64751140595 15.0
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7 1 1.42678673058 4.11877851488 15.0
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8 1 4.28036019174 4.11877851488 15.0
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9 1 7.1339336529 4.11877851488 15.0
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10 1 9.98750711406 4.11877851488 15.0
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||||
11 1 12.8410805752 4.11877851488 15.0
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12 1 15.6946540364 4.11877851488 15.0
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||||
13 1 0.0 6.59004562381 15.0
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14 1 2.85357346116 6.59004562381 15.0
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15 1 5.70714692232 6.59004562381 15.0
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16 1 8.56072038348 6.59004562381 15.0
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17 1 11.4142938446 6.59004562381 15.0
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18 1 14.2678673058 6.59004562381 15.0
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19 1 1.42678673058 9.06131273274 15.0
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20 1 4.28036019174 9.06131273274 15.0
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21 1 7.1339336529 9.06131273274 15.0
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22 1 9.98750711406 9.06131273274 15.0
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23 1 12.8410805752 9.06131273274 15.0
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24 1 15.6946540364 9.06131273274 15.0
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||||
25 1 0.0 11.5325798417 15.0
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||||
26 1 2.85357346116 11.5325798417 15.0
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27 1 5.70714692232 11.5325798417 15.0
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28 1 8.56072038348 11.5325798417 15.0
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29 1 11.4142938446 11.5325798417 15.0
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30 1 14.2678673058 11.5325798417 15.0
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31 1 1.42678673058 14.0038469506 15.0
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32 1 4.28036019174 14.0038469506 15.0
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33 1 7.1339336529 14.0038469506 15.0
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34 1 9.98750711406 14.0038469506 15.0
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35 1 12.8410805752 14.0038469506 15.0
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36 1 15.6946540364 14.0038469506 15.0
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||||
37 1 0.0 0.0 17.3299329745
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||||
38 1 2.85357346116 0.0 17.3299329745
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||||
39 1 5.70714692232 0.0 17.3299329745
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40 1 8.56072038348 0.0 17.3299329745
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41 1 11.4142938446 0.0 17.3299329745
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42 1 14.2678673058 0.0 17.3299329745
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43 1 1.42678673058 2.47126710893 17.3299329745
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44 1 4.28036019174 2.47126710893 17.3299329745
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45 1 7.1339336529 2.47126710893 17.3299329745
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46 1 9.98750711406 2.47126710893 17.3299329745
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47 1 12.8410805752 2.47126710893 17.3299329745
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48 1 15.6946540364 2.47126710893 17.3299329745
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49 1 0.0 4.94253421786 17.3299329745
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||||
50 1 2.85357346116 4.94253421786 17.3299329745
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51 1 5.70714692232 4.94253421786 17.3299329745
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52 1 8.56072038348 4.94253421786 17.3299329745
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53 1 11.4142938446 4.94253421786 17.3299329745
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54 1 14.2678673058 4.94253421786 17.3299329745
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55 1 1.42678673058 7.41380132679 17.3299329745
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56 1 4.28036019174 7.41380132679 17.3299329745
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57 1 7.1339336529 7.41380132679 17.3299329745
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58 1 9.98750711406 7.41380132679 17.3299329745
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59 1 12.8410805752 7.41380132679 17.3299329745
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60 1 15.6946540364 7.41380132679 17.3299329745
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61 1 0.0 9.88506843572 17.3299329745
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62 1 2.85357346116 9.88506843572 17.3299329745
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63 1 5.70714692232 9.88506843572 17.3299329745
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64 1 8.56072038348 9.88506843572 17.3299329745
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65 1 11.4142938446 9.88506843572 17.3299329745
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66 1 14.2678673058 9.88506843572 17.3299329745
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67 1 1.42678673058 12.3563355446 17.3299329745
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68 1 4.28036019174 12.3563355446 17.3299329745
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69 1 7.1339336529 12.3563355446 17.3299329745
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70 1 9.98750711406 12.3563355446 17.3299329745
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71 1 12.8410805752 12.3563355446 17.3299329745
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72 1 15.6946540364 12.3563355446 17.3299329745
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73 1 1.42678673058 0.823755702976 19.6598659489
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74 1 4.28036019174 0.823755702976 19.6598659489
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75 1 7.1339336529 0.823755702976 19.6598659489
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76 1 9.98750711406 0.823755702976 19.6598659489
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77 1 12.8410805752 0.823755702976 19.6598659489
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78 1 15.6946540364 0.823755702976 19.6598659489
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79 1 0.0 3.29502281191 19.6598659489
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80 1 2.85357346116 3.29502281191 19.6598659489
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81 1 5.70714692232 3.29502281191 19.6598659489
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82 1 8.56072038348 3.29502281191 19.6598659489
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83 1 11.4142938446 3.29502281191 19.6598659489
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84 1 14.2678673058 3.29502281191 19.6598659489
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85 1 1.42678673058 5.76628992084 19.6598659489
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86 1 4.28036019174 5.76628992084 19.6598659489
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87 1 7.1339336529 5.76628992084 19.6598659489
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88 1 9.98750711406 5.76628992084 19.6598659489
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89 1 12.8410805752 5.76628992084 19.6598659489
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90 1 15.6946540364 5.76628992084 19.6598659489
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91 1 0.0 8.23755702976 19.6598659489
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92 1 2.85357346116 8.23755702976 19.6598659489
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93 1 5.70714692232 8.23755702976 19.6598659489
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94 1 8.56072038348 8.23755702976 19.6598659489
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95 1 11.4142938446 8.23755702976 19.6598659489
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96 1 14.2678673058 8.23755702976 19.6598659489
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97 1 1.42678673058 10.7088241387 19.6598659489
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98 1 4.28036019174 10.7088241387 19.6598659489
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99 1 7.1339336529 10.7088241387 19.6598659489
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100 1 9.98750711406 10.7088241387 19.6598659489
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101 1 12.8410805752 10.7088241387 19.6598659489
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||||
102 1 15.6946540364 10.7088241387 19.6598659489
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||||
103 1 0.0 13.1800912476 19.6598659489
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104 1 2.85357346116 13.1800912476 19.6598659489
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105 1 5.70714692232 13.1800912476 19.6598659489
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||||
106 1 8.56072038348 13.1800912476 19.6598659489
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107 1 11.4142938446 13.1800912476 19.6598659489
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108 1 14.2678673058 13.1800912476 19.6598659489
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||||
109 1 0.0 1.64751140595 21.9897989234
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||||
110 1 2.85357346116 1.64751140595 21.9897989234
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||||
111 1 5.70714692232 1.64751140595 21.9897989234
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||||
112 1 8.56072038348 1.64751140595 21.9897989234
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||||
113 1 11.4142938446 1.64751140595 21.9897989234
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||||
114 1 14.2678673058 1.64751140595 21.9897989234
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115 1 1.42678673058 4.11877851488 21.9897989234
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||||
116 1 4.28036019174 4.11877851488 21.9897989234
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||||
117 1 7.1339336529 4.11877851488 21.9897989234
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||||
118 1 9.98750711406 4.11877851488 21.9897989234
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||||
119 1 12.8410805752 4.11877851488 21.9897989234
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||||
120 1 15.6946540364 4.11877851488 21.9897989234
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||||
121 1 0.0 6.59004562381 21.9897989234
|
||||
122 1 2.85357346116 6.59004562381 21.9897989234
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||||
123 1 5.70714692232 6.59004562381 21.9897989234
|
||||
124 1 8.56072038348 6.59004562381 21.9897989234
|
||||
125 1 11.4142938446 6.59004562381 21.9897989234
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||||
126 1 14.2678673058 6.59004562381 21.9897989234
|
||||
127 1 1.42678673058 9.06131273274 21.9897989234
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||||
128 1 4.28036019174 9.06131273274 21.9897989234
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||||
129 1 7.1339336529 9.06131273274 21.9897989234
|
||||
130 1 9.98750711406 9.06131273274 21.9897989234
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||||
131 1 12.8410805752 9.06131273274 21.9897989234
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||||
132 1 15.6946540364 9.06131273274 21.9897989234
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||||
133 1 0.0 11.5325798417 21.9897989234
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||||
134 1 2.85357346116 11.5325798417 21.9897989234
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||||
135 1 5.70714692232 11.5325798417 21.9897989234
|
||||
136 1 8.56072038348 11.5325798417 21.9897989234
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||||
137 1 11.4142938446 11.5325798417 21.9897989234
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||||
138 1 14.2678673058 11.5325798417 21.9897989234
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||||
139 1 1.42678673058 14.0038469506 21.9897989234
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||||
140 1 4.28036019174 14.0038469506 21.9897989234
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||||
141 1 7.1339336529 14.0038469506 21.9897989234
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||||
142 1 9.98750711406 14.0038469506 21.9897989234
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||||
143 1 12.8410805752 14.0038469506 21.9897989234
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||||
144 1 15.6946540364 14.0038469506 21.9897989234
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||||
145 1 0.0 0.0 24.3197318979
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||||
146 1 2.85357346116 0.0 24.3197318979
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||||
147 1 5.70714692232 0.0 24.3197318979
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||||
148 1 8.56072038348 0.0 24.3197318979
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||||
149 1 11.4142938446 0.0 24.3197318979
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||||
150 1 14.2678673058 0.0 24.3197318979
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||||
151 1 1.42678673058 2.47126710893 24.3197318979
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||||
152 1 4.28036019174 2.47126710893 24.3197318979
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||||
153 1 7.1339336529 2.47126710893 24.3197318979
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||||
154 1 9.98750711406 2.47126710893 24.3197318979
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||||
155 1 12.8410805752 2.47126710893 24.3197318979
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||||
156 1 15.6946540364 2.47126710893 24.3197318979
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||||
157 1 0.0 4.94253421786 24.3197318979
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||||
158 1 2.85357346116 4.94253421786 24.3197318979
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159 1 5.70714692232 4.94253421786 24.3197318979
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160 1 8.56072038348 4.94253421786 24.3197318979
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161 1 11.4142938446 4.94253421786 24.3197318979
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162 1 14.2678673058 4.94253421786 24.3197318979
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163 1 1.42678673058 7.41380132679 24.3197318979
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164 1 4.28036019174 7.41380132679 24.3197318979
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165 1 7.1339336529 7.41380132679 24.3197318979
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166 1 9.98750711406 7.41380132679 24.3197318979
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167 1 12.8410805752 7.41380132679 24.3197318979
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168 1 15.6946540364 7.41380132679 24.3197318979
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169 1 0.0 9.88506843572 24.3197318979
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170 1 2.85357346116 9.88506843572 24.3197318979
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171 1 5.70714692232 9.88506843572 24.3197318979
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172 1 8.56072038348 9.88506843572 24.3197318979
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173 1 11.4142938446 9.88506843572 24.3197318979
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174 1 14.2678673058 9.88506843572 24.3197318979
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175 1 1.42678673058 12.3563355446 24.3197318979
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176 1 4.28036019174 12.3563355446 24.3197318979
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177 1 7.1339336529 12.3563355446 24.3197318979
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178 1 9.98750711406 12.3563355446 24.3197318979
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179 1 12.8410805752 12.3563355446 24.3197318979
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180 1 15.6946540364 12.3563355446 24.3197318979
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181 1 7.1339336529 4.11877851488 26.7197318979
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23
examples/USER/misc/agni/in.adatom
Normal file
23
examples/USER/misc/agni/in.adatom
Normal file
@ -0,0 +1,23 @@
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processors * * 1
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units metal
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boundary p p f
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read_data adatom.data
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pair_style agni
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pair_coeff * * Al_prb.agni Al
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neighbor 0.3 bin
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neigh_modify delay 2 check yes
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timestep 0.0005
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velocity all create 500 12345
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fix 1 all nvt temp 250 250 0.2
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fix 5 all momentum 1 linear 1 1 1
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thermo 100
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thermo_style custom step ke temp
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# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz
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run 1000
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23
examples/USER/misc/agni/in.vacancy
Normal file
23
examples/USER/misc/agni/in.vacancy
Normal file
@ -0,0 +1,23 @@
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units metal
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boundary p p p
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read_data vacancy.data
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pair_style agni
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pair_coeff * * Al_prb.agni Al
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neighbor 0.3 bin
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neigh_modify delay 2 check yes
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timestep 0.0005
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velocity all create 1000 12345
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fix 1 all nvt temp 900 900 200
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fix 5 all momentum 1 linear 1 1 1
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thermo 100
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thermo_style custom step ke etotal temp
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# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz
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run 1000
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82
examples/USER/misc/agni/log.9Nov16.adatom.g++.1
Normal file
82
examples/USER/misc/agni/log.9Nov16.adatom.g++.1
Normal file
@ -0,0 +1,82 @@
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LAMMPS (9 Nov 2016)
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using 1 OpenMP thread(s) per MPI task
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processors * * 1
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units metal
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boundary p p f
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read_data adatom.data
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orthogonal box = (0 0 0) to (17.1214 14.8276 39.3197)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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181 atoms
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pair_style agni
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pair_coeff * * Al_prb.agni Al
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Reading potential file Al_prb.agni with DATE: 2016-11-11
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||||
|
||||
neighbor 0.3 bin
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||||
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
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||||
|
||||
run 1000
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||||
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
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||||
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
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||||
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
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||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 20.79 | 20.79 | 20.79 | 0.0 | 99.82
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||||
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
|
||||
82
examples/USER/misc/agni/log.9Nov16.adatom.g++.4
Normal file
82
examples/USER/misc/agni/log.9Nov16.adatom.g++.4
Normal file
@ -0,0 +1,82 @@
|
||||
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)
|
||||
2 by 2 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 = 2.48695 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 265.52451
|
||||
700 6.3749266 273.9921
|
||||
800 6.0701481 260.89283
|
||||
900 6.4582394 277.57286
|
||||
1000 6.4047444 275.27366
|
||||
Loop time of 5.96868 on 4 procs for 1000 steps with 181 atoms
|
||||
|
||||
Performance: 7.238 ns/day, 3.316 hours/ns, 167.541 timesteps/s
|
||||
99.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 5.4176 | 5.4602 | 5.5505 | 2.3 | 91.48
|
||||
Neigh | 0.0056074 | 0.0060464 | 0.0062635 | 0.3 | 0.10
|
||||
Comm | 0.39544 | 0.48696 | 0.53111 | 7.9 | 8.16
|
||||
Output | 0.0001545 | 0.00015736 | 0.0001595 | 0.0 | 0.00
|
||||
Modify | 0.010492 | 0.011565 | 0.012588 | 0.9 | 0.19
|
||||
Other | | 0.003794 | | | 0.06
|
||||
|
||||
Nlocal: 45.25 ave 47 max 42 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 2 1
|
||||
Nghost: 374.75 ave 380 max 373 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 4702.5 ave 4868 max 4389 min
|
||||
Histogram: 1 0 0 0 0 0 0 1 1 1
|
||||
|
||||
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: 0:00:05
|
||||
82
examples/USER/misc/agni/log.9Nov16.vacancy.g++.1
Normal file
82
examples/USER/misc/agni/log.9Nov16.vacancy.g++.1
Normal file
@ -0,0 +1,82 @@
|
||||
LAMMPS (9 Nov 2016)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
units metal
|
||||
boundary p p p
|
||||
read_data vac.data
|
||||
orthogonal box = (0 0 0) to (8.07113 8.07113 8.07113)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
31 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 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 ...
|
||||
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 = 2 2 2
|
||||
Memory usage per processor = 2.40842 Mbytes
|
||||
Step KinEng TotEng Temp
|
||||
0 3.8778043 3.8778043 1000
|
||||
100 2.8126642 2.8126642 725.32391
|
||||
200 3.7110413 3.7110413 956.9955
|
||||
300 3.2361084 3.2361084 834.52081
|
||||
400 3.4625769 3.4625769 892.92201
|
||||
500 3.4563307 3.4563307 891.31126
|
||||
600 2.8486344 2.8486344 734.59982
|
||||
700 3.1183057 3.1183057 804.14208
|
||||
800 2.9164818 2.9164818 752.09618
|
||||
900 3.464416 3.464416 893.39629
|
||||
1000 3.5954546 3.5954546 927.18825
|
||||
Loop time of 3.86777 on 1 procs for 1000 steps with 31 atoms
|
||||
|
||||
Performance: 11.169 ns/day, 2.149 hours/ns, 258.547 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 3.8463 | 3.8463 | 3.8463 | 0.0 | 99.44
|
||||
Neigh | 0.011294 | 0.011294 | 0.011294 | 0.0 | 0.29
|
||||
Comm | 0.0057271 | 0.0057271 | 0.0057271 | 0.0 | 0.15
|
||||
Output | 0.00014257 | 0.00014257 | 0.00014257 | 0.0 | 0.00
|
||||
Modify | 0.0029459 | 0.0029459 | 0.0029459 | 0.0 | 0.08
|
||||
Other | | 0.001395 | | | 0.04
|
||||
|
||||
Nlocal: 31 ave 31 max 31 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 878 ave 878 max 878 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: 4334 ave 4334 max 4334 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 4334
|
||||
Ave neighs/atom = 139.806
|
||||
Neighbor list builds = 51
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:03
|
||||
82
examples/USER/misc/agni/log.9Nov16.vacancy.g++.4
Normal file
82
examples/USER/misc/agni/log.9Nov16.vacancy.g++.4
Normal file
@ -0,0 +1,82 @@
|
||||
LAMMPS (9 Nov 2016)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
units metal
|
||||
boundary p p p
|
||||
read_data vac.data
|
||||
orthogonal box = (0 0 0) to (8.07113 8.07113 8.07113)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
31 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 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 ...
|
||||
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 = 2 2 2
|
||||
Memory usage per processor = 2.3974 Mbytes
|
||||
Step KinEng TotEng Temp
|
||||
0 3.8778044 3.8778044 1000
|
||||
100 2.8126642 2.8126642 725.32391
|
||||
200 3.7110413 3.7110413 956.99549
|
||||
300 3.2361084 3.2361084 834.52081
|
||||
400 3.4625769 3.4625769 892.92201
|
||||
500 3.4563307 3.4563307 891.31126
|
||||
600 2.8486343 2.8486343 734.59981
|
||||
700 3.1183057 3.1183057 804.14208
|
||||
800 2.9164819 2.9164819 752.09618
|
||||
900 3.4644161 3.4644161 893.39631
|
||||
1000 3.5954546 3.5954546 927.18824
|
||||
Loop time of 1.11007 on 4 procs for 1000 steps with 31 atoms
|
||||
|
||||
Performance: 38.916 ns/day, 0.617 hours/ns, 900.843 timesteps/s
|
||||
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.906 | 0.99469 | 1.0291 | 5.1 | 89.61
|
||||
Neigh | 0.0026186 | 0.0027665 | 0.0028622 | 0.2 | 0.25
|
||||
Comm | 0.066125 | 0.10079 | 0.1896 | 16.2 | 9.08
|
||||
Output | 0.00012875 | 0.00014615 | 0.00018787 | 0.2 | 0.01
|
||||
Modify | 0.0080338 | 0.0083079 | 0.00861 | 0.2 | 0.75
|
||||
Other | | 0.003372 | | | 0.30
|
||||
|
||||
Nlocal: 7.75 ave 8 max 7 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||
Nghost: 623.5 ave 630 max 616 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 1083.5 ave 1131 max 988 min
|
||||
Histogram: 1 0 0 0 0 0 0 1 1 1
|
||||
|
||||
Total # of neighbors = 4334
|
||||
Ave neighs/atom = 139.806
|
||||
Neighbor list builds = 51
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:01
|
||||
46
examples/USER/misc/agni/vacancy.data
Normal file
46
examples/USER/misc/agni/vacancy.data
Normal file
@ -0,0 +1,46 @@
|
||||
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
|
||||
Reference in New Issue
Block a user